RUN: /usr/share/launchpad-buildd/slavebin/slave-prep ['slave-prep'] Forking launchpad-buildd slave process... Kernel version: Linux z13-018 4.4.0-31-generic #50-Ubuntu SMP Wed Jul 13 00:19:48 UTC 2016 s390x Buildd toolchain package versions: launchpad-buildd_140 python-lpbuildd_140 sbuild_0.67.0-2ubuntu7 dpkg-dev_1.18.4ubuntu1.1 python-debian_0.1.27ubuntu2 qemu-user-static_1:2.5+dfsg-5ubuntu10.2. Syncing the system clock with the buildd NTP service... 10 Oct 06:21:32 ntpdate[45951]: adjust time server 10.211.37.1 offset -0.000239 sec RUN: /usr/share/launchpad-buildd/slavebin/unpack-chroot ['unpack-chroot', 'PACKAGEBUILD-10765800', '/home/buildd/filecache-default/4c2dc15a2bd8eb52aaecab56c2b5c3013e453e5b'] Unpacking chroot for build PACKAGEBUILD-10765800 RUN: /usr/share/launchpad-buildd/slavebin/mount-chroot ['mount-chroot', 'PACKAGEBUILD-10765800'] Mounting chroot for build PACKAGEBUILD-10765800 RUN: /usr/share/launchpad-buildd/slavebin/override-sources-list ['override-sources-list', 'PACKAGEBUILD-10765800', 'deb http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu yakkety main', 'deb http://ftpmaster.internal/ubuntu yakkety main restricted universe multiverse', 'deb http://ftpmaster.internal/ubuntu yakkety-security main restricted universe multiverse', 'deb http://ftpmaster.internal/ubuntu yakkety-updates main restricted universe multiverse'] Overriding sources.list in build-PACKAGEBUILD-10765800 RUN: /usr/share/launchpad-buildd/slavebin/update-debian-chroot ['update-debian-chroot', 'PACKAGEBUILD-10765800', 's390x'] Updating debian chroot for build PACKAGEBUILD-10765800 Get:1 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu yakkety InRelease [17.5 kB] Get:2 http://ftpmaster.internal/ubuntu yakkety InRelease [247 kB] Ign:1 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu yakkety InRelease Get:3 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu yakkety/main s390x Packages [15.6 kB] Get:4 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu yakkety/main Translation-en [9916 B] Get:5 http://ftpmaster.internal/ubuntu yakkety-security InRelease [92.2 kB] Get:6 http://ftpmaster.internal/ubuntu yakkety-updates InRelease [92.2 kB] Get:7 http://ftpmaster.internal/ubuntu yakkety/main s390x Packages [1158 kB] Get:8 http://ftpmaster.internal/ubuntu yakkety/main Translation-en [583 kB] Get:9 http://ftpmaster.internal/ubuntu yakkety/restricted Translation-en [2992 B] Get:10 http://ftpmaster.internal/ubuntu yakkety/universe s390x Packages [7434 kB] Get:11 http://ftpmaster.internal/ubuntu yakkety/universe Translation-en [4489 kB] Get:12 http://ftpmaster.internal/ubuntu yakkety/multiverse s390x Packages [121 kB] Get:13 http://ftpmaster.internal/ubuntu yakkety/multiverse Translation-en [107 kB] Get:14 http://ftpmaster.internal/ubuntu yakkety-security/main s390x Packages [64 B] Get:15 http://ftpmaster.internal/ubuntu yakkety-security/main Translation-en [64 B] Get:16 http://ftpmaster.internal/ubuntu yakkety-security/restricted s390x Packages [64 B] Get:17 http://ftpmaster.internal/ubuntu yakkety-security/restricted Translation-en [64 B] Get:18 http://ftpmaster.internal/ubuntu yakkety-security/universe s390x Packages [64 B] Get:19 http://ftpmaster.internal/ubuntu yakkety-security/universe Translation-en [64 B] Get:20 http://ftpmaster.internal/ubuntu yakkety-security/multiverse s390x Packages [64 B] Get:21 http://ftpmaster.internal/ubuntu yakkety-security/multiverse Translation-en [64 B] Get:22 http://ftpmaster.internal/ubuntu yakkety-updates/main s390x Packages [64 B] Get:23 http://ftpmaster.internal/ubuntu yakkety-updates/main Translation-en [64 B] Get:24 http://ftpmaster.internal/ubuntu yakkety-updates/restricted s390x Packages [64 B] Get:25 http://ftpmaster.internal/ubuntu yakkety-updates/restricted Translation-en [64 B] Get:26 http://ftpmaster.internal/ubuntu yakkety-updates/universe s390x Packages [64 B] Get:27 http://ftpmaster.internal/ubuntu yakkety-updates/universe Translation-en [64 B] Get:28 http://ftpmaster.internal/ubuntu yakkety-updates/multiverse s390x Packages [64 B] Get:29 http://ftpmaster.internal/ubuntu yakkety-updates/multiverse Translation-en [64 B] Fetched 14.4 MB in 24s (598 kB/s) Reading package lists... W: GPG error: http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu yakkety InRelease: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY 1E9377A2BA9EF27F W: The repository 'http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu yakkety InRelease' is not signed. W: There is no public key available for the following key IDs: 1E9377A2BA9EF27F Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: libpng12-0 libprocps4 Use 'sudo apt autoremove' to remove them. The following NEW packages will be installed: cpp-6 g++-6 gcc-6 gnupg-agent libassuan0 libcap-ng0 libgcc-6-dev libip4tc0 libksba8 libnpth0 libpng16-16 libprocps6 libreadline7 libstdc++-6-dev pinentry-curses The following packages will be upgraded: apt apt-transport-https base-files base-passwd bash binutils bsdutils bzip2 cpp cpp-5 dash debconf debianutils dmsetup dpkg dpkg-dev e2fslibs e2fsprogs fakeroot findutils g++ g++-5 gcc gcc-5 gcc-5-base gcc-6-base gnupg gpgv grep hostname init init-system-helpers libapparmor1 libapt-pkg5.0 libatomic1 libaudit-common libaudit1 libblkid1 libbz2-1.0 libc-bin libc-dev-bin libc6 libc6-dev libcap2 libcap2-bin libcc1-0 libcomerr2 libcryptsetup4 libcurl3-gnutls libdb5.3 libdebconfclient0 libdevmapper1.02.1 libdpkg-perl libfakeroot libfdisk1 libffi6 libgcc-5-dev libgcc1 libgcrypt20 libgdbm3 libgmp10 libgnutls30 libgomp1 libgpg-error0 libgssapi-krb5-2 libidn11 libisl15 libitm1 libk5crypto3 libkeyutils1 libkmod2 libkrb5-3 libkrb5support0 libldap-2.4-2 liblzma5 libmount1 libmpfr4 libncurses5 libncursesw5 libp11-kit0 libpcre3 libperl5.22 libreadline6 librtmp1 libsasl2-2 libsasl2-modules-db libseccomp2 libselinux1 libsemanage-common libsemanage1 libsepol1 libslang2 libsmartcols1 libsqlite3-0 libss2 libssl1.0.0 libstdc++-5-dev libstdc++6 libsystemd0 libtasn1-6 libtinfo5 libudev1 libusb-0.1-4 libuuid1 linux-libc-dev login lsb-base make mount multiarch-support ncurses-base ncurses-bin openssl optipng passwd perl perl-base perl-modules-5.22 pkgbinarymangler policyrcd-script-zg2 procps readline-common sed systemd systemd-sysv sysvinit-utils tar tzdata ubuntu-keyring util-linux xz-utils zlib1g 132 upgraded, 15 newly installed, 0 to remove and 0 not upgraded. Need to get 143 MB of archives. After this operation, 414 MB of additional disk space will be used. WARNING: The following packages cannot be authenticated! gcc-6-base libgcc1 libstdc++6 cpp-6 libgomp1 libitm1 libatomic1 libcc1-0 libgcc-6-dev gcc-6 libstdc++-6-dev g++-6 Authentication warning overridden. Get:1 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu yakkety/main s390x gcc-6-base s390x 6.2.0-5ubuntu23 [16.8 kB] Get:2 http://ftpmaster.internal/ubuntu yakkety/main s390x base-files s390x 9.6ubuntu5 [55.8 kB] Get:3 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu yakkety/main s390x libgcc1 s390x 1:6.2.0-5ubuntu23 [24.5 kB] Get:4 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu yakkety/main s390x libstdc++6 s390x 6.2.0-5ubuntu23 [403 kB] Get:5 http://ftpmaster.internal/ubuntu yakkety/main s390x debianutils s390x 4.8 [85.9 kB] Get:6 http://ftpmaster.internal/ubuntu yakkety/main s390x bash s390x 4.3-15ubuntu1 [569 kB] Get:7 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu yakkety/main s390x cpp-6 s390x 6.2.0-5ubuntu23 [27.0 MB] Get:8 http://ftpmaster.internal/ubuntu yakkety/main s390x bsdutils s390x 1:2.28.2-1ubuntu1 [53.9 kB] Get:9 http://ftpmaster.internal/ubuntu yakkety/main s390x tar s390x 1.29b-1 [223 kB] Get:10 http://ftpmaster.internal/ubuntu yakkety/main s390x dpkg s390x 1.18.10ubuntu1 [2145 kB] Get:11 http://ftpmaster.internal/ubuntu yakkety/main s390x dash s390x 0.5.8-2.3ubuntu1 [100 kB] Get:12 http://ftpmaster.internal/ubuntu yakkety/main s390x libc6-dev s390x 2.24-3ubuntu1 [2073 kB] Get:13 http://ftpmaster.internal/ubuntu yakkety/main s390x libc-dev-bin s390x 2.24-3ubuntu1 [62.4 kB] Get:14 http://ftpmaster.internal/ubuntu yakkety/main s390x linux-libc-dev s390x 4.8.0-21.23 [844 kB] Get:15 http://ftpmaster.internal/ubuntu yakkety/main s390x libc6 s390x 2.24-3ubuntu1 [2305 kB] Get:16 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu yakkety/main s390x libgomp1 s390x 6.2.0-5ubuntu23 [71.0 kB] Get:17 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu yakkety/main s390x libitm1 s390x 6.2.0-5ubuntu23 [27.2 kB] Get:18 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu yakkety/main s390x libatomic1 s390x 6.2.0-5ubuntu23 [8150 B] Get:19 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu yakkety/main s390x libcc1-0 s390x 6.2.0-5ubuntu23 [31.0 kB] Get:20 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu yakkety/main s390x libgcc-6-dev s390x 6.2.0-5ubuntu23 [268 kB] Get:21 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu yakkety/main s390x gcc-6 s390x 6.2.0-5ubuntu23 [26.7 MB] Get:22 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu yakkety/main s390x libstdc++-6-dev s390x 6.2.0-5ubuntu23 [1410 kB] Get:23 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu yakkety/main s390x g++-6 s390x 6.2.0-5ubuntu23 [29.4 MB] Get:24 http://ftpmaster.internal/ubuntu yakkety/main s390x libc-bin s390x 2.24-3ubuntu1 [554 kB] Get:25 http://ftpmaster.internal/ubuntu yakkety/main s390x e2fslibs s390x 1.43.3-1 [151 kB] Get:26 http://ftpmaster.internal/ubuntu yakkety/main s390x e2fsprogs s390x 1.43.3-1 [471 kB] Get:27 http://ftpmaster.internal/ubuntu yakkety/main s390x findutils s390x 4.6.0+git+20160703-2 [278 kB] Get:28 http://ftpmaster.internal/ubuntu yakkety/main s390x grep s390x 2.25-6 [148 kB] Get:29 http://ftpmaster.internal/ubuntu yakkety/main s390x hostname s390x 3.18 [11.1 kB] Get:30 http://ftpmaster.internal/ubuntu yakkety/main s390x login s390x 1:4.2-3.2ubuntu1 [302 kB] Get:31 http://ftpmaster.internal/ubuntu yakkety/main s390x libsmartcols1 s390x 2.28.2-1ubuntu1 [61.1 kB] Get:32 http://ftpmaster.internal/ubuntu yakkety/main s390x libaudit-common all 1:2.6.6-1ubuntu1 [4628 B] Get:33 http://ftpmaster.internal/ubuntu yakkety/main s390x libcap-ng0 s390x 0.7.7-3 [10.6 kB] Get:34 http://ftpmaster.internal/ubuntu yakkety/main s390x libaudit1 s390x 1:2.6.6-1ubuntu1 [36.2 kB] Get:35 http://ftpmaster.internal/ubuntu yakkety/main s390x libpcre3 s390x 2:8.39-2 [155 kB] Get:36 http://ftpmaster.internal/ubuntu yakkety/main s390x libselinux1 s390x 2.5-3 [62.1 kB] Get:37 http://ftpmaster.internal/ubuntu yakkety/main s390x libsepol1 s390x 2.5-1 [198 kB] Get:38 http://ftpmaster.internal/ubuntu yakkety/main s390x libsemanage-common all 2.5-1 [6800 B] Get:39 http://ftpmaster.internal/ubuntu yakkety/main s390x libsemanage1 s390x 2.5-1 [75.1 kB] Get:40 http://ftpmaster.internal/ubuntu yakkety/main s390x bzip2 s390x 1.0.6-8build1 [33.3 kB] Get:41 http://ftpmaster.internal/ubuntu yakkety/main s390x libbz2-1.0 s390x 1.0.6-8build1 [32.7 kB] Get:42 http://ftpmaster.internal/ubuntu yakkety/main s390x passwd s390x 1:4.2-3.2ubuntu1 [769 kB] Get:43 http://ftpmaster.internal/ubuntu yakkety/main s390x libuuid1 s390x 2.28.2-1ubuntu1 [14.8 kB] Get:44 http://ftpmaster.internal/ubuntu yakkety/main s390x libblkid1 s390x 2.28.2-1ubuntu1 [100 kB] Get:45 http://ftpmaster.internal/ubuntu yakkety/main s390x libfdisk1 s390x 2.28.2-1ubuntu1 [128 kB] Get:46 http://ftpmaster.internal/ubuntu yakkety/main s390x perl-modules-5.22 all 5.22.2-3 [2631 kB] Get:47 http://ftpmaster.internal/ubuntu yakkety/main s390x libperl5.22 s390x 5.22.2-3 [3252 kB] Get:48 http://ftpmaster.internal/ubuntu yakkety/main s390x perl s390x 5.22.2-3 [238 kB] Get:49 http://ftpmaster.internal/ubuntu yakkety/main s390x perl-base s390x 5.22.2-3 [1246 kB] Get:50 http://ftpmaster.internal/ubuntu yakkety/main s390x libdb5.3 s390x 5.3.28-12 [616 kB] Get:51 http://ftpmaster.internal/ubuntu yakkety/main s390x libgdbm3 s390x 1.8.3-14 [16.9 kB] Get:52 http://ftpmaster.internal/ubuntu yakkety/main s390x zlib1g s390x 1:1.2.8.dfsg-2ubuntu5 [51.6 kB] Get:53 http://ftpmaster.internal/ubuntu yakkety/main s390x init-system-helpers all 1.45 [37.6 kB] Get:54 http://ftpmaster.internal/ubuntu yakkety/main s390x util-linux s390x 2.28.2-1ubuntu1 [867 kB] Get:55 http://ftpmaster.internal/ubuntu yakkety/main s390x sysvinit-utils s390x 2.88dsf-59.8git1 [18.6 kB] Get:56 http://ftpmaster.internal/ubuntu yakkety/main s390x mount s390x 2.28.2-1ubuntu1 [121 kB] Get:57 http://ftpmaster.internal/ubuntu yakkety/main s390x ncurses-bin s390x 6.0+20160625-1ubuntu1 [135 kB] Get:58 http://ftpmaster.internal/ubuntu yakkety/main s390x sed s390x 4.2.2-8 [139 kB] Get:59 http://ftpmaster.internal/ubuntu yakkety/main s390x init s390x 1.45 [5218 B] Get:60 http://ftpmaster.internal/ubuntu yakkety/main s390x libdebconfclient0 s390x 0.213ubuntu1 [5988 B] Get:61 http://ftpmaster.internal/ubuntu yakkety/main s390x base-passwd s390x 3.5.40 [47.7 kB] Get:62 http://ftpmaster.internal/ubuntu yakkety/main s390x ncurses-base all 6.0+20160625-1ubuntu1 [16.6 kB] Get:63 http://ftpmaster.internal/ubuntu yakkety/main s390x liblzma5 s390x 5.1.1alpha+20120614-2.1ubuntu1 [81.8 kB] Get:64 http://ftpmaster.internal/ubuntu yakkety/main s390x libapt-pkg5.0 s390x 1.3.1 [712 kB] Get:65 http://ftpmaster.internal/ubuntu yakkety/main s390x libgpg-error0 s390x 1.24-1 [32.7 kB] Get:66 http://ftpmaster.internal/ubuntu yakkety/main s390x libgcrypt20 s390x 1.7.2-2ubuntu1 [337 kB] Get:67 http://ftpmaster.internal/ubuntu yakkety/main s390x gpgv s390x 2.1.15-1ubuntu6 [171 kB] Get:68 http://ftpmaster.internal/ubuntu yakkety/main s390x ubuntu-keyring all 2016.09.19 [17.0 kB] Get:69 http://ftpmaster.internal/ubuntu yakkety/main s390x apt s390x 1.3.1 [1022 kB] Get:70 http://ftpmaster.internal/ubuntu yakkety/main s390x debconf all 1.5.59ubuntu1 [136 kB] Get:71 http://ftpmaster.internal/ubuntu yakkety/main s390x libip4tc0 s390x 1.6.0-3ubuntu2 [19.9 kB] Get:72 http://ftpmaster.internal/ubuntu yakkety/main s390x libapparmor1 s390x 2.10.95-4ubuntu5 [30.5 kB] Get:73 http://ftpmaster.internal/ubuntu yakkety/main s390x libcap2 s390x 1:2.25-1 [13.7 kB] Get:74 http://ftpmaster.internal/ubuntu yakkety/main s390x libudev1 s390x 231-9git1 [53.8 kB] Get:75 http://ftpmaster.internal/ubuntu yakkety/main s390x libdevmapper1.02.1 s390x 2:1.02.130-1ubuntu1 [147 kB] Get:76 http://ftpmaster.internal/ubuntu yakkety/main s390x libcryptsetup4 s390x 2:1.7.2-0ubuntu1 [70.1 kB] Get:77 http://ftpmaster.internal/ubuntu yakkety/main s390x libidn11 s390x 1.33-1 [44.4 kB] Get:78 http://ftpmaster.internal/ubuntu yakkety/main s390x libkmod2 s390x 22-1.1ubuntu1 [36.8 kB] Get:79 http://ftpmaster.internal/ubuntu yakkety/main s390x libmount1 s390x 2.28.2-1ubuntu1 [108 kB] Get:80 http://ftpmaster.internal/ubuntu yakkety/main s390x libseccomp2 s390x 2.3.1-2ubuntu2 [38.5 kB] Get:81 http://ftpmaster.internal/ubuntu yakkety/main s390x libsystemd0 s390x 231-9git1 [192 kB] Get:82 http://ftpmaster.internal/ubuntu yakkety/main s390x systemd s390x 231-9git1 [2172 kB] Get:83 http://ftpmaster.internal/ubuntu yakkety/main s390x systemd-sysv s390x 231-9git1 [14.1 kB] Get:84 http://ftpmaster.internal/ubuntu yakkety/main s390x libcomerr2 s390x 1.43.3-1 [9872 B] Get:85 http://ftpmaster.internal/ubuntu yakkety/main s390x libncurses5 s390x 6.0+20160625-1ubuntu1 [89.7 kB] Get:86 http://ftpmaster.internal/ubuntu yakkety/main s390x libtinfo5 s390x 6.0+20160625-1ubuntu1 [75.8 kB] Get:87 http://ftpmaster.internal/ubuntu yakkety/main s390x libncursesw5 s390x 6.0+20160625-1ubuntu1 [107 kB] Get:88 http://ftpmaster.internal/ubuntu yakkety/main s390x libss2 s390x 1.43.3-1 [10.8 kB] Get:89 http://ftpmaster.internal/ubuntu yakkety/main s390x lsb-base all 9.20160110ubuntu5 [13.2 kB] Get:90 http://ftpmaster.internal/ubuntu yakkety/main s390x multiarch-support s390x 2.24-3ubuntu1 [6820 B] Get:91 http://ftpmaster.internal/ubuntu yakkety/main s390x libassuan0 s390x 2.4.3-1 [32.1 kB] Get:92 http://ftpmaster.internal/ubuntu yakkety/main s390x pinentry-curses s390x 0.9.7-5 [31.1 kB] Get:93 http://ftpmaster.internal/ubuntu yakkety/main s390x libnpth0 s390x 1.2-3 [7906 B] Get:94 http://ftpmaster.internal/ubuntu yakkety/main s390x readline-common all 7.0-0ubuntu2 [52.8 kB] Get:95 http://ftpmaster.internal/ubuntu yakkety/main s390x libreadline7 s390x 7.0-0ubuntu2 [118 kB] Get:96 http://ftpmaster.internal/ubuntu yakkety/main s390x gnupg-agent s390x 2.1.15-1ubuntu6 [233 kB] Get:97 http://ftpmaster.internal/ubuntu yakkety/main s390x libksba8 s390x 1.3.4-4 [86.3 kB] Get:98 http://ftpmaster.internal/ubuntu yakkety/main s390x libsqlite3-0 s390x 3.14.1-1build1 [451 kB] Get:99 http://ftpmaster.internal/ubuntu yakkety/main s390x gnupg s390x 2.1.15-1ubuntu6 [737 kB] Get:100 http://ftpmaster.internal/ubuntu yakkety/universe s390x libreadline6 s390x 6.3-8ubuntu8 [111 kB] Get:101 http://ftpmaster.internal/ubuntu yakkety/main s390x libusb-0.1-4 s390x 2:0.1.12-30 [16.6 kB] Get:102 http://ftpmaster.internal/ubuntu yakkety/main s390x libprocps6 s390x 2:3.3.12-1ubuntu2 [30.3 kB] Get:103 http://ftpmaster.internal/ubuntu yakkety/main s390x procps s390x 2:3.3.12-1ubuntu2 [218 kB] Get:104 http://ftpmaster.internal/ubuntu yakkety/main s390x tzdata all 2016g-1 [168 kB] Get:105 http://ftpmaster.internal/ubuntu yakkety/main s390x dmsetup s390x 2:1.02.130-1ubuntu1 [72.4 kB] Get:106 http://ftpmaster.internal/ubuntu yakkety/main s390x libcap2-bin s390x 1:2.25-1 [20.4 kB] Get:107 http://ftpmaster.internal/ubuntu yakkety/main s390x libslang2 s390x 2.3.0-2.3ubuntu1 [405 kB] Get:108 http://ftpmaster.internal/ubuntu yakkety/main s390x libssl1.0.0 s390x 1.0.2g-1ubuntu9 [777 kB] Get:109 http://ftpmaster.internal/ubuntu yakkety/main s390x xz-utils s390x 5.1.1alpha+20120614-2.1ubuntu1 [78.6 kB] Get:110 http://ftpmaster.internal/ubuntu yakkety/main s390x libgmp10 s390x 2:6.1.1+dfsg-1 [228 kB] Get:111 http://ftpmaster.internal/ubuntu yakkety/main s390x libffi6 s390x 3.2.1-6 [16.2 kB] Get:112 http://ftpmaster.internal/ubuntu yakkety/main s390x libp11-kit0 s390x 0.23.2-5 [97.2 kB] Get:113 http://ftpmaster.internal/ubuntu yakkety/main s390x libtasn1-6 s390x 4.9-4 [33.6 kB] Get:114 http://ftpmaster.internal/ubuntu yakkety/main s390x libgnutls30 s390x 3.5.3-5ubuntu1 [534 kB] Get:115 http://ftpmaster.internal/ubuntu yakkety/main s390x libgssapi-krb5-2 s390x 1.14.3+dfsg-2 [110 kB] Get:116 http://ftpmaster.internal/ubuntu yakkety/main s390x libkrb5-3 s390x 1.14.3+dfsg-2 [259 kB] Get:117 http://ftpmaster.internal/ubuntu yakkety/main s390x libkrb5support0 s390x 1.14.3+dfsg-2 [31.0 kB] Get:118 http://ftpmaster.internal/ubuntu yakkety/main s390x libk5crypto3 s390x 1.14.3+dfsg-2 [79.6 kB] Get:119 http://ftpmaster.internal/ubuntu yakkety/main s390x libkeyutils1 s390x 1.5.9-9ubuntu1 [9450 B] Get:120 http://ftpmaster.internal/ubuntu yakkety/main s390x libsasl2-modules-db s390x 2.1.26.dfsg1-15 [14.0 kB] Get:121 http://ftpmaster.internal/ubuntu yakkety/main s390x libsasl2-2 s390x 2.1.26.dfsg1-15 [46.8 kB] Get:122 http://ftpmaster.internal/ubuntu yakkety/main s390x libldap-2.4-2 s390x 2.4.42+dfsg-2ubuntu4 [151 kB] Get:123 http://ftpmaster.internal/ubuntu yakkety/main s390x librtmp1 s390x 2.4+20151223.gitfa8646d.1-1 [51.8 kB] Get:124 http://ftpmaster.internal/ubuntu yakkety/main s390x libcurl3-gnutls s390x 7.50.1-1ubuntu1 [175 kB] Get:125 http://ftpmaster.internal/ubuntu yakkety/main s390x apt-transport-https s390x 1.3.1 [31.8 kB] Get:126 http://ftpmaster.internal/ubuntu yakkety/main s390x libpng16-16 s390x 1.6.25-1 [169 kB] Get:127 http://ftpmaster.internal/ubuntu yakkety/main s390x openssl s390x 1.0.2g-1ubuntu9 [478 kB] Get:128 http://ftpmaster.internal/ubuntu yakkety/main s390x binutils s390x 2.27-8ubuntu2 [1057 kB] Get:129 http://ftpmaster.internal/ubuntu yakkety/main s390x libisl15 s390x 0.17.1-1 [505 kB] Get:130 http://ftpmaster.internal/ubuntu yakkety/main s390x libmpfr4 s390x 3.1.5-1 [189 kB] Get:131 http://ftpmaster.internal/ubuntu yakkety/main s390x cpp s390x 4:6.1.1-1ubuntu2 [27.4 kB] Get:132 http://ftpmaster.internal/ubuntu yakkety/main s390x g++-5 s390x 5.4.1-2ubuntu2 [6760 kB] Get:133 http://ftpmaster.internal/ubuntu yakkety/main s390x gcc-5 s390x 5.4.1-2ubuntu2 [6911 kB] Get:134 http://ftpmaster.internal/ubuntu yakkety/main s390x libstdc++-5-dev s390x 5.4.1-2ubuntu2 [1376 kB] Get:135 http://ftpmaster.internal/ubuntu yakkety/main s390x libgcc-5-dev s390x 5.4.1-2ubuntu2 [245 kB] Get:136 http://ftpmaster.internal/ubuntu yakkety/main s390x cpp-5 s390x 5.4.1-2ubuntu2 [6162 kB] Get:137 http://ftpmaster.internal/ubuntu yakkety/main s390x gcc-5-base s390x 5.4.1-2ubuntu2 [17.5 kB] Get:138 http://ftpmaster.internal/ubuntu yakkety/main s390x dpkg-dev all 1.18.10ubuntu1 [651 kB] Get:139 http://ftpmaster.internal/ubuntu yakkety/main s390x libdpkg-perl all 1.18.10ubuntu1 [204 kB] Get:140 http://ftpmaster.internal/ubuntu yakkety/main s390x make s390x 4.1-9 [149 kB] Get:141 http://ftpmaster.internal/ubuntu yakkety/main s390x libfakeroot s390x 1.21-1ubuntu2 [24.9 kB] Get:142 http://ftpmaster.internal/ubuntu yakkety/main s390x fakeroot s390x 1.21-1ubuntu2 [61.1 kB] Get:143 http://ftpmaster.internal/ubuntu yakkety/main s390x gcc s390x 4:6.1.1-1ubuntu2 [5166 B] Get:144 http://ftpmaster.internal/ubuntu yakkety/main s390x g++ s390x 4:6.1.1-1ubuntu2 [1478 B] Get:145 http://ftpmaster.internal/ubuntu yakkety/main s390x optipng s390x 0.7.6-1build1 [81.5 kB] Get:146 http://ftpmaster.internal/ubuntu yakkety/main s390x pkgbinarymangler all 131 [43.7 kB] Get:147 http://ftpmaster.internal/ubuntu yakkety/main s390x policyrcd-script-zg2 all 0.1-3 [5610 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 143 MB in 2min 22s (1007 kB/s) (Reading database ... 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Processing triggers for libc-bin (2.24-3ubuntu1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 11927 files and directories currently installed.) Preparing to unpack .../libgdbm3_1.8.3-14_s390x.deb ... Unpacking libgdbm3:s390x (1.8.3-14) over (1.8.3-13.1) ... Preparing to unpack .../zlib1g_1%3a1.2.8.dfsg-2ubuntu5_s390x.deb ... Unpacking zlib1g:s390x (1:1.2.8.dfsg-2ubuntu5) over (1:1.2.8.dfsg-2ubuntu4) ... Processing triggers for libc-bin (2.24-3ubuntu1) ... Setting up zlib1g:s390x (1:1.2.8.dfsg-2ubuntu5) ... Processing triggers for libc-bin (2.24-3ubuntu1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 11927 files and directories currently installed.) Preparing to unpack .../init-system-helpers_1.45_all.deb ... Unpacking init-system-helpers (1.45) over (1.29ubuntu1) ... Setting up init-system-helpers (1.45) ... (Reading database ... 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Removing obsolete conffile /etc/init/hwclock-save.conf ... Removing obsolete conffile /etc/init/hwclock.conf ... Removing obsolete conffile /etc/init/hwclock.sh.conf ... Processing triggers for systemd (229-4ubuntu4) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 11933 files and directories currently installed.) Preparing to unpack .../mount_2.28.2-1ubuntu1_s390x.deb ... Unpacking mount (2.28.2-1ubuntu1) over (2.27.1-6ubuntu3) ... Setting up mount (2.28.2-1ubuntu1) ... 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(Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 11938 files and directories currently installed.) Preparing to unpack .../debconf_1.5.59ubuntu1_all.deb ... Unpacking debconf (1.5.59ubuntu1) over (1.5.58ubuntu1) ... Setting up debconf (1.5.59ubuntu1) ... Selecting previously unselected package libip4tc0:s390x. (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 11944 files and directories currently installed.) Preparing to unpack .../libdevmapper1.02.1_2%3a1.02.130-1ubuntu1_s390x.deb ... Unpacking libdevmapper1.02.1:s390x (2:1.02.130-1ubuntu1) over (2:1.02.110-1ubuntu10) ... Processing triggers for libc-bin (2.24-3ubuntu1) ... Setting up libdevmapper1.02.1:s390x (2:1.02.130-1ubuntu1) ... Processing triggers for libc-bin (2.24-3ubuntu1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 11944 files and directories currently installed.) Preparing to unpack .../libcryptsetup4_2%3a1.7.2-0ubuntu1_s390x.deb ... Unpacking libcryptsetup4:s390x (2:1.7.2-0ubuntu1) over (2:1.6.6-5ubuntu2) ... Processing triggers for libc-bin (2.24-3ubuntu1) ... Setting up libcryptsetup4:s390x (2:1.7.2-0ubuntu1) ... Processing triggers for libc-bin (2.24-3ubuntu1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 11944 files and directories currently installed.) Preparing to unpack .../libidn11_1.33-1_s390x.deb ... Unpacking libidn11:s390x (1.33-1) over (1.32-3ubuntu1) ... Processing triggers for libc-bin (2.24-3ubuntu1) ... Setting up libidn11:s390x (1.33-1) ... Processing triggers for libc-bin (2.24-3ubuntu1) ... (Reading database ... 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Installing new version of config file /etc/systemd/journald.conf ... Installing new version of config file /etc/systemd/logind.conf ... Installing new version of config file /etc/systemd/resolved.conf ... Installing new version of config file /etc/systemd/system.conf ... Installing new version of config file /etc/systemd/user.conf ... Synchronizing state of ondemand.service with SysV service script with /lib/systemd/systemd-sysv-install. Executing: /lib/systemd/systemd-sysv-install enable ondemand addgroup: The group `systemd-journal' already exists as a system group. Exiting. Removing obsolete conffile /etc/systemd/bootchart.conf ... (Reading database ... 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Setting up libtinfo5:s390x (6.0+20160625-1ubuntu1) ... Processing triggers for libc-bin (2.24-3ubuntu1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 11938 files and directories currently installed.) Preparing to unpack .../libncursesw5_6.0+20160625-1ubuntu1_s390x.deb ... Unpacking libncursesw5:s390x (6.0+20160625-1ubuntu1) over (6.0+20160213-1ubuntu1) ... Processing triggers for libc-bin (2.24-3ubuntu1) ... Setting up libncursesw5:s390x (6.0+20160625-1ubuntu1) ... Processing triggers for libc-bin (2.24-3ubuntu1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 11938 files and directories currently installed.) Preparing to unpack .../libss2_1.43.3-1_s390x.deb ... Unpacking libss2:s390x (1.43.3-1) over (1.42.13-1ubuntu1) ... Processing triggers for libc-bin (2.24-3ubuntu1) ... Setting up libss2:s390x (1.43.3-1) ... Processing triggers for libc-bin (2.24-3ubuntu1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 11938 files and directories currently installed.) Preparing to unpack .../lsb-base_9.20160110ubuntu5_all.deb ... Unpacking lsb-base (9.20160110ubuntu5) over (9.20160110) ... Setting up lsb-base (9.20160110ubuntu5) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 11938 files and directories currently installed.) Preparing to unpack .../multiarch-support_2.24-3ubuntu1_s390x.deb ... Unpacking multiarch-support (2.24-3ubuntu1) over (2.23-0ubuntu3) ... Setting up multiarch-support (2.24-3ubuntu1) ... Selecting previously unselected package libassuan0:s390x. (Reading database ... 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Preparing to unpack .../readline-common_7.0-0ubuntu2_all.deb ... Unpacking readline-common (7.0-0ubuntu2) over (6.3-8ubuntu2) ... Processing triggers for libc-bin (2.24-3ubuntu1) ... Setting up readline-common (7.0-0ubuntu2) ... Selecting previously unselected package libreadline7:s390x. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 11956 files and directories currently installed.) Preparing to unpack .../libreadline7_7.0-0ubuntu2_s390x.deb ... Unpacking libreadline7:s390x (7.0-0ubuntu2) ... Selecting previously unselected package gnupg-agent. Preparing to unpack .../gnupg-agent_2.1.15-1ubuntu6_s390x.deb ... Unpacking gnupg-agent (2.1.15-1ubuntu6) ... Selecting previously unselected package libksba8:s390x. Preparing to unpack .../libksba8_1.3.4-4_s390x.deb ... Unpacking libksba8:s390x (1.3.4-4) ... Preparing to unpack .../libsqlite3-0_3.14.1-1build1_s390x.deb ... Unpacking libsqlite3-0:s390x (3.14.1-1build1) over (3.11.0-1ubuntu1) ... Preparing to unpack .../gnupg_2.1.15-1ubuntu6_s390x.deb ... Unpacking gnupg (2.1.15-1ubuntu6) over (1.4.20-1ubuntu3) ... Processing triggers for libc-bin (2.24-3ubuntu1) ... Setting up libassuan0:s390x (2.4.3-1) ... Setting up pinentry-curses (0.9.7-5) ... Setting up libnpth0:s390x (1.2-3) ... Setting up libreadline7:s390x (7.0-0ubuntu2) ... Setting up gnupg-agent (2.1.15-1ubuntu6) ... Setting up libksba8:s390x (1.3.4-4) ... Setting up libsqlite3-0:s390x (3.14.1-1build1) ... Setting up gnupg (2.1.15-1ubuntu6) ... Processing triggers for libc-bin (2.24-3ubuntu1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12018 files and directories currently installed.) Preparing to unpack .../libreadline6_6.3-8ubuntu8_s390x.deb ... Unpacking libreadline6:s390x (6.3-8ubuntu8) over (6.3-8ubuntu2) ... Processing triggers for libc-bin (2.24-3ubuntu1) ... Setting up libreadline6:s390x (6.3-8ubuntu8) ... Processing triggers for libc-bin (2.24-3ubuntu1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12018 files and directories currently installed.) Preparing to unpack .../libusb-0.1-4_2%3a0.1.12-30_s390x.deb ... Unpacking libusb-0.1-4:s390x (2:0.1.12-30) over (2:0.1.12-28) ... Processing triggers for libc-bin (2.24-3ubuntu1) ... Setting up libusb-0.1-4:s390x (2:0.1.12-30) ... Processing triggers for libc-bin (2.24-3ubuntu1) ... Selecting previously unselected package libprocps6:s390x. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12018 files and directories currently installed.) Preparing to unpack .../libprocps6_2%3a3.3.12-1ubuntu2_s390x.deb ... Unpacking libprocps6:s390x (2:3.3.12-1ubuntu2) ... Preparing to unpack .../procps_2%3a3.3.12-1ubuntu2_s390x.deb ... Running in chroot, ignoring request. invoke-rc.d: policy-rc.d denied execution of stop. Unpacking procps (2:3.3.12-1ubuntu2) over (2:3.3.10-4ubuntu2) ... Preparing to unpack .../tzdata_2016g-1_all.deb ... Unpacking tzdata (2016g-1) over (2016d-0ubuntu0.16.04) ... Preparing to unpack .../dmsetup_2%3a1.02.130-1ubuntu1_s390x.deb ... Unpacking dmsetup (2:1.02.130-1ubuntu1) over (2:1.02.110-1ubuntu10) ... Preparing to unpack .../libcap2-bin_1%3a2.25-1_s390x.deb ... Unpacking libcap2-bin (1:2.25-1) over (1:2.24-12) ... Preparing to unpack .../libslang2_2.3.0-2.3ubuntu1_s390x.deb ... Unpacking libslang2:s390x (2.3.0-2.3ubuntu1) over (2.3.0-2ubuntu1) ... Preparing to unpack .../libssl1.0.0_1.0.2g-1ubuntu9_s390x.deb ... Unpacking libssl1.0.0:s390x (1.0.2g-1ubuntu9) over (1.0.2g-1ubuntu4) ... Preparing to unpack .../xz-utils_5.1.1alpha+20120614-2.1ubuntu1_s390x.deb ... Unpacking xz-utils (5.1.1alpha+20120614-2.1ubuntu1) over (5.1.1alpha+20120614-2ubuntu2) ... Preparing to unpack .../libgmp10_2%3a6.1.1+dfsg-1_s390x.deb ... Unpacking libgmp10:s390x (2:6.1.1+dfsg-1) over (2:6.1.0+dfsg-2) ... Preparing to unpack .../libffi6_3.2.1-6_s390x.deb ... Unpacking libffi6:s390x (3.2.1-6) over (3.2.1-4) ... 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Unpacking libkeyutils1:s390x (1.5.9-9ubuntu1) over (1.5.9-8ubuntu1) ... Preparing to unpack .../libsasl2-modules-db_2.1.26.dfsg1-15_s390x.deb ... Unpacking libsasl2-modules-db:s390x (2.1.26.dfsg1-15) over (2.1.26.dfsg1-14build1) ... Preparing to unpack .../libsasl2-2_2.1.26.dfsg1-15_s390x.deb ... Unpacking libsasl2-2:s390x (2.1.26.dfsg1-15) over (2.1.26.dfsg1-14build1) ... Preparing to unpack .../libldap-2.4-2_2.4.42+dfsg-2ubuntu4_s390x.deb ... Unpacking libldap-2.4-2:s390x (2.4.42+dfsg-2ubuntu4) over (2.4.42+dfsg-2ubuntu3) ... Preparing to unpack .../librtmp1_2.4+20151223.gitfa8646d.1-1_s390x.deb ... Unpacking librtmp1:s390x (2.4+20151223.gitfa8646d.1-1) over (2.4+20151223.gitfa8646d-1build1) ... Preparing to unpack .../libcurl3-gnutls_7.50.1-1ubuntu1_s390x.deb ... Unpacking libcurl3-gnutls:s390x (7.50.1-1ubuntu1) over (7.47.0-1ubuntu2) ... Preparing to unpack .../apt-transport-https_1.3.1_s390x.deb ... Unpacking apt-transport-https (1.3.1) over (1.2.10ubuntu1) ... Selecting previously unselected package libpng16-16:s390x. Preparing to unpack .../libpng16-16_1.6.25-1_s390x.deb ... Unpacking libpng16-16:s390x (1.6.25-1) ... Preparing to unpack .../openssl_1.0.2g-1ubuntu9_s390x.deb ... Unpacking openssl (1.0.2g-1ubuntu9) over (1.0.2g-1ubuntu4) ... Preparing to unpack .../binutils_2.27-8ubuntu2_s390x.deb ... Unpacking binutils (2.27-8ubuntu2) over (2.26-8ubuntu2) ... Preparing to unpack .../libisl15_0.17.1-1_s390x.deb ... Unpacking libisl15:s390x (0.17.1-1) over (0.16.1-1) ... Preparing to unpack .../libmpfr4_3.1.5-1_s390x.deb ... Unpacking libmpfr4:s390x (3.1.5-1) over (3.1.4-1) ... Selecting previously unselected package cpp-6. Preparing to unpack .../cpp-6_6.2.0-5ubuntu23_s390x.deb ... Unpacking cpp-6 (6.2.0-5ubuntu23) ... Preparing to unpack .../cpp_4%3a6.1.1-1ubuntu2_s390x.deb ... Unpacking cpp (4:6.1.1-1ubuntu2) over (4:5.3.1-1ubuntu1) ... Preparing to unpack .../libgomp1_6.2.0-5ubuntu23_s390x.deb ... 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Unpacking pkgbinarymangler (131) over (129) ... Preparing to unpack .../policyrcd-script-zg2_0.1-3_all.deb ... Unpacking policyrcd-script-zg2 (0.1-3) over (0.1-2) ... Processing triggers for libc-bin (2.24-3ubuntu1) ... Processing triggers for systemd (231-9git1) ... Setting up libc-dev-bin (2.24-3ubuntu1) ... Setting up linux-libc-dev:s390x (4.8.0-21.23) ... Setting up libc6-dev:s390x (2.24-3ubuntu1) ... Setting up bzip2 (1.0.6-8build1) ... Setting up perl-modules-5.22 (5.22.2-3) ... Setting up libgdbm3:s390x (1.8.3-14) ... Setting up libperl5.22:s390x (5.22.2-3) ... Setting up perl (5.22.2-3) ... Setting up sysvinit-utils (2.88dsf-59.8git1) ... Setting up libncurses5:s390x (6.0+20160625-1ubuntu1) ... Setting up libprocps6:s390x (2:3.3.12-1ubuntu2) ... Setting up procps (2:3.3.12-1ubuntu2) ... Installing new version of config file /etc/init.d/procps ... Installing new version of config file /etc/sysctl.conf ... Setting up tzdata (2016g-1) ... Current default time zone: 'Etc/UTC' Local time is now: Mon Oct 10 06:24:49 UTC 2016. Universal Time is now: Mon Oct 10 06:24:49 UTC 2016. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up dmsetup (2:1.02.130-1ubuntu1) ... Setting up libcap2-bin (1:2.25-1) ... Setting up libslang2:s390x (2.3.0-2.3ubuntu1) ... Setting up libssl1.0.0:s390x (1.0.2g-1ubuntu9) ... Setting up xz-utils (5.1.1alpha+20120614-2.1ubuntu1) ... Setting up libgmp10:s390x (2:6.1.1+dfsg-1) ... Setting up libffi6:s390x (3.2.1-6) ... Setting up libp11-kit0:s390x (0.23.2-5) ... Setting up libtasn1-6:s390x (4.9-4) ... Setting up libgnutls30:s390x (3.5.3-5ubuntu1) ... Setting up libkrb5support0:s390x (1.14.3+dfsg-2) ... Setting up libk5crypto3:s390x (1.14.3+dfsg-2) ... Setting up libkeyutils1:s390x (1.5.9-9ubuntu1) ... Setting up libkrb5-3:s390x (1.14.3+dfsg-2) ... Setting up libgssapi-krb5-2:s390x (1.14.3+dfsg-2) ... Setting up libsasl2-modules-db:s390x (2.1.26.dfsg1-15) ... Setting up libsasl2-2:s390x (2.1.26.dfsg1-15) ... Setting up libldap-2.4-2:s390x (2.4.42+dfsg-2ubuntu4) ... Setting up librtmp1:s390x (2.4+20151223.gitfa8646d.1-1) ... Setting up libcurl3-gnutls:s390x (7.50.1-1ubuntu1) ... Setting up apt-transport-https (1.3.1) ... Setting up libpng16-16:s390x (1.6.25-1) ... Setting up openssl (1.0.2g-1ubuntu9) ... Setting up binutils (2.27-8ubuntu2) ... Setting up libisl15:s390x (0.17.1-1) ... Setting up libmpfr4:s390x (3.1.5-1) ... Setting up cpp-6 (6.2.0-5ubuntu23) ... Setting up cpp (4:6.1.1-1ubuntu2) ... Setting up libgomp1:s390x (6.2.0-5ubuntu23) ... Setting up libitm1:s390x (6.2.0-5ubuntu23) ... Setting up libatomic1:s390x (6.2.0-5ubuntu23) ... Setting up gcc-5-base:s390x (5.4.1-2ubuntu2) ... Setting up cpp-5 (5.4.1-2ubuntu2) ... Setting up libcc1-0:s390x (6.2.0-5ubuntu23) ... Setting up libgcc-5-dev:s390x (5.4.1-2ubuntu2) ... Setting up gcc-5 (5.4.1-2ubuntu2) ... Setting up libstdc++-5-dev:s390x (5.4.1-2ubuntu2) ... Setting up g++-5 (5.4.1-2ubuntu2) ... Setting up libdpkg-perl (1.18.10ubuntu1) ... Setting up make (4.1-9) ... Setting up dpkg-dev (1.18.10ubuntu1) ... Setting up libfakeroot:s390x (1.21-1ubuntu2) ... Setting up fakeroot (1.21-1ubuntu2) ... Setting up libgcc-6-dev:s390x (6.2.0-5ubuntu23) ... Setting up gcc-6 (6.2.0-5ubuntu23) ... Setting up gcc (4:6.1.1-1ubuntu2) ... Setting up libstdc++-6-dev:s390x (6.2.0-5ubuntu23) ... Setting up g++-6 (6.2.0-5ubuntu23) ... Setting up g++ (4:6.1.1-1ubuntu2) ... Setting up optipng (0.7.6-1build1) ... Setting up pkgbinarymangler (131) ... Setting up policyrcd-script-zg2 (0.1-3) ... Processing triggers for libc-bin (2.24-3ubuntu1) ... Processing triggers for systemd (231-9git1) ... RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package ['sbuild-package', 'PACKAGEBUILD-10765800', 's390x', 'yakkety', '-c', 'chroot:autobuild', '--arch=s390x', '--dist=yakkety', '--purge=never', '--nolog', 'bcftools_1.3.1-1.dsc'] Initiating build PACKAGEBUILD-10765800 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.4.0-31-generic #50-Ubuntu SMP Wed Jul 13 00:19:48 UTC 2016 s390x sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on z13-018.buildd +==============================================================================+ | bcftools 1.3.1-1 (s390x) 10 Oct 2016 06:24 | +==============================================================================+ Package: bcftools Version: 1.3.1-1 Source Version: 1.3.1-1 Distribution: yakkety Machine Architecture: s390x Host Architecture: s390x Build Architecture: s390x I: NOTICE: Log filtering will replace 'build/bcftools-iqUIH3/bcftools-1.3.1' with '<>' I: NOTICE: Log filtering will replace 'build/bcftools-iqUIH3' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-10765800/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- bcftools_1.3.1-1.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-KiBkpk/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/<>/resolver-KiBkpk/apt_archive ./ InRelease Get:2 copy:/<>/resolver-KiBkpk/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-KiBkpk/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-KiBkpk/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-KiBkpk/apt_archive ./ Packages [527 B] Fetched 2860 B in 0s (0 B/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install core build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: libpng12-0 libprocps4 Use 'sudo apt autoremove' to remove them. The following NEW packages will be installed: sbuild-build-depends-core-dummy 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 772 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-KiBkpk/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [772 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 772 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12980 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_s390x.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... Merged Build-Depends: debhelper (>= 9), zlib1g-dev, libhts-dev (>= 1.3.1), libgsl-dev, tabix, libio-pty-perl Filtered Build-Depends: debhelper (>= 9), zlib1g-dev, libhts-dev (>= 1.3.1), libgsl-dev, tabix, libio-pty-perl dpkg-deb: building package 'sbuild-build-depends-bcftools-dummy' in '/<>/resolver-0F9y2h/apt_archive/sbuild-build-depends-bcftools-dummy.deb'. Ign:1 copy:/<>/resolver-0F9y2h/apt_archive ./ InRelease Get:2 copy:/<>/resolver-0F9y2h/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-0F9y2h/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-0F9y2h/apt_archive ./ Sources [248 B] Get:5 copy:/<>/resolver-0F9y2h/apt_archive ./ Packages [568 B] Fetched 2935 B in 0s (0 B/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install bcftools build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: libpng12-0 libprocps4 Use 'sudo apt autoremove' to remove them. The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libcroco3 libfile-stripnondeterminism-perl libglib2.0-0 libgsl-dev libgsl2 libhts-dev libhts1 libicu57 libio-pty-perl libmagic1 libpipeline1 libsigsegv2 libtimedate-perl libtool libunistring0 libxml2 m4 man-db po-debconf tabix zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois vacation dh-make gettext-doc libasprintf-dev libgettextpo-dev groff gsl-ref-psdoc | gsl-doc-pdf | gsl-doc-info | gsl-ref-html libtool-doc gfortran | fortran95-compiler gcj-jdk less www-browser libmail-box-perl Recommended packages: curl | wget | lynx-cur libglib2.0-data shared-mime-info xdg-user-dirs libltdl-dev xml-core libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libcroco3 libfile-stripnondeterminism-perl libglib2.0-0 libgsl-dev libgsl2 libhts-dev libhts1 libicu57 libio-pty-perl libmagic1 libpipeline1 libsigsegv2 libtimedate-perl libtool libunistring0 libxml2 m4 man-db po-debconf sbuild-build-depends-bcftools-dummy tabix zlib1g-dev 0 upgraded, 36 newly installed, 0 to remove and 0 not upgraded. Need to get 18.5 MB of archives. After this operation, 76.3 MB of additional disk space will be used. Get:1 copy:/<>/resolver-0F9y2h/apt_archive ./ sbuild-build-depends-bcftools-dummy 0.invalid.0 [814 B] Get:2 http://ftpmaster.internal/ubuntu yakkety/main s390x groff-base s390x 1.22.3-8 [1175 kB] Get:3 http://ftpmaster.internal/ubuntu yakkety/main s390x bsdmainutils s390x 9.0.6ubuntu3 [179 kB] Get:4 http://ftpmaster.internal/ubuntu yakkety/main s390x libpipeline1 s390x 1.4.1-2 [24.8 kB] Get:5 http://ftpmaster.internal/ubuntu yakkety/main s390x man-db s390x 2.7.5-1 [850 kB] Get:6 http://ftpmaster.internal/ubuntu yakkety/main s390x libmagic1 s390x 1:5.28-2ubuntu1 [233 kB] Get:7 http://ftpmaster.internal/ubuntu yakkety/main s390x file s390x 1:5.28-2ubuntu1 [21.9 kB] Get:8 http://ftpmaster.internal/ubuntu yakkety/main s390x gettext-base s390x 0.19.8.1-1ubuntu2 [47.7 kB] Get:9 http://ftpmaster.internal/ubuntu yakkety/main s390x libglib2.0-0 s390x 2.50.0-1 [1058 kB] Get:10 http://ftpmaster.internal/ubuntu yakkety/main s390x libicu57 s390x 57.1-4 [7469 kB] Get:11 http://ftpmaster.internal/ubuntu yakkety/main s390x libxml2 s390x 2.9.4+dfsg1-2 [626 kB] Get:12 http://ftpmaster.internal/ubuntu yakkety/main s390x libsigsegv2 s390x 2.10-5 [13.5 kB] Get:13 http://ftpmaster.internal/ubuntu yakkety/main s390x m4 s390x 1.4.17-5 [192 kB] Get:14 http://ftpmaster.internal/ubuntu yakkety/main s390x autoconf all 2.69-10 [321 kB] Get:15 http://ftpmaster.internal/ubuntu yakkety/main s390x autotools-dev all 20160430.1 [39.6 kB] Get:16 http://ftpmaster.internal/ubuntu yakkety/main s390x automake all 1:1.15-4ubuntu1 [510 kB] Get:17 http://ftpmaster.internal/ubuntu yakkety/main s390x autopoint all 0.19.8.1-1ubuntu2 [412 kB] Get:18 http://ftpmaster.internal/ubuntu yakkety/main s390x libtool all 2.4.6-1 [194 kB] Get:19 http://ftpmaster.internal/ubuntu yakkety/main s390x dh-autoreconf all 12 [15.8 kB] Get:20 http://ftpmaster.internal/ubuntu yakkety/main s390x libarchive-zip-perl all 1.59-1 [84.0 kB] Get:21 http://ftpmaster.internal/ubuntu yakkety/main s390x libfile-stripnondeterminism-perl all 0.028-1 [12.5 kB] Get:22 http://ftpmaster.internal/ubuntu yakkety/main s390x libtimedate-perl all 2.3000-2 [37.5 kB] Get:23 http://ftpmaster.internal/ubuntu yakkety/main s390x dh-strip-nondeterminism all 0.028-1 [4820 B] Get:24 http://ftpmaster.internal/ubuntu yakkety/main s390x libcroco3 s390x 0.6.11-1 [76.5 kB] Get:25 http://ftpmaster.internal/ubuntu yakkety/main s390x libunistring0 s390x 0.9.3-5.2ubuntu1 [262 kB] Get:26 http://ftpmaster.internal/ubuntu yakkety/main s390x gettext s390x 0.19.8.1-1ubuntu2 [1054 kB] Get:27 http://ftpmaster.internal/ubuntu yakkety/main s390x intltool-debian all 0.35.0+20060710.4 [24.9 kB] Get:28 http://ftpmaster.internal/ubuntu yakkety/main s390x po-debconf all 1.0.19 [234 kB] Get:29 http://ftpmaster.internal/ubuntu yakkety/main s390x debhelper all 10ubuntu1 [731 kB] Get:30 http://ftpmaster.internal/ubuntu yakkety/main s390x libgsl2 s390x 2.1+dfsg-2 [747 kB] Get:31 http://ftpmaster.internal/ubuntu yakkety/main s390x libgsl-dev s390x 2.1+dfsg-2 [854 kB] Get:32 http://ftpmaster.internal/ubuntu yakkety/universe s390x libhts1 s390x 1.3.1-3ubuntu1 [234 kB] Get:33 http://ftpmaster.internal/ubuntu yakkety/universe s390x libhts-dev s390x 1.3.1-3ubuntu1 [300 kB] Get:34 http://ftpmaster.internal/ubuntu yakkety/main s390x libio-pty-perl s390x 1:1.08-1.1build1 [29.6 kB] Get:35 http://ftpmaster.internal/ubuntu yakkety/universe s390x tabix s390x 1.3.1-3ubuntu1 [234 kB] Get:36 http://ftpmaster.internal/ubuntu yakkety/main s390x zlib1g-dev s390x 1:1.2.8.dfsg-2ubuntu5 [168 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 18.5 MB in 12s (1514 kB/s) Selecting previously unselected package groff-base. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12980 files and directories currently installed.) Preparing to unpack .../00-groff-base_1.22.3-8_s390x.deb ... Unpacking groff-base (1.22.3-8) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_9.0.6ubuntu3_s390x.deb ... Unpacking bsdmainutils (9.0.6ubuntu3) ... Selecting previously unselected package libpipeline1:s390x. Preparing to unpack .../02-libpipeline1_1.4.1-2_s390x.deb ... Unpacking libpipeline1:s390x (1.4.1-2) ... Selecting previously unselected package man-db. Preparing to unpack .../03-man-db_2.7.5-1_s390x.deb ... Unpacking man-db (2.7.5-1) ... Selecting previously unselected package libmagic1:s390x. Preparing to unpack .../04-libmagic1_1%3a5.28-2ubuntu1_s390x.deb ... Unpacking libmagic1:s390x (1:5.28-2ubuntu1) ... Selecting previously unselected package file. Preparing to unpack .../05-file_1%3a5.28-2ubuntu1_s390x.deb ... Unpacking file (1:5.28-2ubuntu1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../06-gettext-base_0.19.8.1-1ubuntu2_s390x.deb ... Unpacking gettext-base (0.19.8.1-1ubuntu2) ... Selecting previously unselected package libglib2.0-0:s390x. Preparing to unpack .../07-libglib2.0-0_2.50.0-1_s390x.deb ... Unpacking libglib2.0-0:s390x (2.50.0-1) ... Selecting previously unselected package libicu57:s390x. Preparing to unpack .../08-libicu57_57.1-4_s390x.deb ... Unpacking libicu57:s390x (57.1-4) ... Selecting previously unselected package libxml2:s390x. Preparing to unpack .../09-libxml2_2.9.4+dfsg1-2_s390x.deb ... Unpacking libxml2:s390x (2.9.4+dfsg1-2) ... Selecting previously unselected package libsigsegv2:s390x. Preparing to unpack .../10-libsigsegv2_2.10-5_s390x.deb ... Unpacking libsigsegv2:s390x (2.10-5) ... Selecting previously unselected package m4. Preparing to unpack .../11-m4_1.4.17-5_s390x.deb ... Unpacking m4 (1.4.17-5) ... Selecting previously unselected package autoconf. Preparing to unpack .../12-autoconf_2.69-10_all.deb ... Unpacking autoconf (2.69-10) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../13-autotools-dev_20160430.1_all.deb ... Unpacking autotools-dev (20160430.1) ... Selecting previously unselected package automake. Preparing to unpack .../14-automake_1%3a1.15-4ubuntu1_all.deb ... Unpacking automake (1:1.15-4ubuntu1) ... Selecting previously unselected package autopoint. Preparing to unpack .../15-autopoint_0.19.8.1-1ubuntu2_all.deb ... Unpacking autopoint (0.19.8.1-1ubuntu2) ... Selecting previously unselected package libtool. Preparing to unpack .../16-libtool_2.4.6-1_all.deb ... Unpacking libtool (2.4.6-1) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../17-dh-autoreconf_12_all.deb ... Unpacking dh-autoreconf (12) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../18-libarchive-zip-perl_1.59-1_all.deb ... Unpacking libarchive-zip-perl (1.59-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../19-libfile-stripnondeterminism-perl_0.028-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (0.028-1) ... Selecting previously unselected package libtimedate-perl. Preparing to unpack .../20-libtimedate-perl_2.3000-2_all.deb ... Unpacking libtimedate-perl (2.3000-2) ... 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Unpacking libio-pty-perl (1:1.08-1.1build1) ... Selecting previously unselected package tabix. Preparing to unpack .../33-tabix_1.3.1-3ubuntu1_s390x.deb ... Unpacking tabix (1.3.1-3ubuntu1) ... Selecting previously unselected package zlib1g-dev:s390x. Preparing to unpack .../34-zlib1g-dev_1%3a1.2.8.dfsg-2ubuntu5_s390x.deb ... Unpacking zlib1g-dev:s390x (1:1.2.8.dfsg-2ubuntu5) ... Selecting previously unselected package sbuild-build-depends-bcftools-dummy. Preparing to unpack .../35-sbuild-build-depends-bcftools-dummy_0.invalid.0_s390x.deb ... Unpacking sbuild-build-depends-bcftools-dummy (0.invalid.0) ... Setting up libhts1:s390x (1.3.1-3ubuntu1) ... Setting up libarchive-zip-perl (1.59-1) ... Setting up libio-pty-perl (1:1.08-1.1build1) ... Setting up libtimedate-perl (2.3000-2) ... Setting up libsigsegv2:s390x (2.10-5) ... Setting up libhts-dev:s390x (1.3.1-3ubuntu1) ... Setting up groff-base (1.22.3-8) ... Setting up libglib2.0-0:s390x (2.50.0-1) ... No schema files found: doing nothing. Setting up gettext-base (0.19.8.1-1ubuntu2) ... Setting up libpipeline1:s390x (1.4.1-2) ... Setting up libgsl2:s390x (2.1+dfsg-2) ... Setting up m4 (1.4.17-5) ... Setting up libicu57:s390x (57.1-4) ... Setting up libxml2:s390x (2.9.4+dfsg1-2) ... Setting up libmagic1:s390x (1:5.28-2ubuntu1) ... Setting up libcroco3:s390x (0.6.11-1) ... Processing triggers for libc-bin (2.24-3ubuntu1) ... Setting up autotools-dev (20160430.1) ... Setting up libunistring0:s390x (0.9.3-5.2ubuntu1) ... Setting up tabix (1.3.1-3ubuntu1) ... Setting up bsdmainutils (9.0.6ubuntu3) ... 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 autopoint (0.19.8.1-1ubuntu2) ... Setting up zlib1g-dev:s390x (1:1.2.8.dfsg-2ubuntu5) ... Setting up libfile-stripnondeterminism-perl (0.028-1) ... Setting up gettext (0.19.8.1-1ubuntu2) ... Setting up libgsl-dev (2.1+dfsg-2) ... Setting up autoconf (2.69-10) ... Setting up file (1:5.28-2ubuntu1) ... Setting up intltool-debian (0.35.0+20060710.4) ... Setting up automake (1:1.15-4ubuntu1) ... update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode Setting up man-db (2.7.5-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libtool (2.4.6-1) ... Setting up po-debconf (1.0.19) ... Setting up dh-autoreconf (12) ... Setting up dh-strip-nondeterminism (0.028-1) ... Setting up debhelper (10ubuntu1) ... Setting up sbuild-build-depends-bcftools-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.24-3ubuntu1) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.4.0-31-generic s390x (s390x) Toolchain package versions: binutils_2.27-8ubuntu2 dpkg-dev_1.18.10ubuntu1 g++-5_5.4.1-2ubuntu2 g++-6_6.2.0-5ubuntu23 gcc-5_5.4.1-2ubuntu2 gcc-6_6.2.0-5ubuntu23 libc6-dev_2.24-3ubuntu1 libstdc++-5-dev_5.4.1-2ubuntu2 libstdc++-6-dev_6.2.0-5ubuntu23 libstdc++6_6.2.0-5ubuntu23 linux-libc-dev_4.8.0-21.23 Package versions: adduser_3.113+nmu3ubuntu4 advancecomp_1.20-1 apt_1.3.1 apt-transport-https_1.3.1 autoconf_2.69-10 automake_1:1.15-4ubuntu1 autopoint_0.19.8.1-1ubuntu2 autotools-dev_20160430.1 base-files_9.6ubuntu5 base-passwd_3.5.40 bash_4.3-15ubuntu1 binutils_2.27-8ubuntu2 bsdmainutils_9.0.6ubuntu3 bsdutils_1:2.28.2-1ubuntu1 build-essential_12.1ubuntu2 bzip2_1.0.6-8build1 ca-certificates_20160104ubuntu1 coreutils_8.25-2ubuntu2 cpp_4:6.1.1-1ubuntu2 cpp-5_5.4.1-2ubuntu2 cpp-6_6.2.0-5ubuntu23 dash_0.5.8-2.3ubuntu1 debconf_1.5.59ubuntu1 debhelper_10ubuntu1 debianutils_4.8 dh-autoreconf_12 dh-strip-nondeterminism_0.028-1 diffutils_1:3.3-3 dmsetup_2:1.02.130-1ubuntu1 dpkg_1.18.10ubuntu1 dpkg-dev_1.18.10ubuntu1 e2fslibs_1.43.3-1 e2fsprogs_1.43.3-1 fakeroot_1.21-1ubuntu2 file_1:5.28-2ubuntu1 findutils_4.6.0+git+20160703-2 g++_4:6.1.1-1ubuntu2 g++-5_5.4.1-2ubuntu2 g++-6_6.2.0-5ubuntu23 gcc_4:6.1.1-1ubuntu2 gcc-5_5.4.1-2ubuntu2 gcc-5-base_5.4.1-2ubuntu2 gcc-6_6.2.0-5ubuntu23 gcc-6-base_6.2.0-5ubuntu23 gettext_0.19.8.1-1ubuntu2 gettext-base_0.19.8.1-1ubuntu2 gnupg_2.1.15-1ubuntu6 gnupg-agent_2.1.15-1ubuntu6 gpgv_2.1.15-1ubuntu6 grep_2.25-6 groff-base_1.22.3-8 gzip_1.6-4ubuntu1 hostname_3.18 init_1.45 init-system-helpers_1.45 initscripts_2.88dsf-59.3ubuntu2 insserv_1.14.0-5ubuntu3 intltool-debian_0.35.0+20060710.4 libacl1_2.2.52-3 libapparmor1_2.10.95-4ubuntu5 libapt-pkg5.0_1.3.1 libarchive-zip-perl_1.59-1 libasn1-8-heimdal_1.7~git20150920+dfsg-4ubuntu1 libassuan0_2.4.3-1 libatomic1_6.2.0-5ubuntu23 libattr1_1:2.4.47-2 libaudit-common_1:2.6.6-1ubuntu1 libaudit1_1:2.6.6-1ubuntu1 libblkid1_2.28.2-1ubuntu1 libbz2-1.0_1.0.6-8build1 libc-bin_2.24-3ubuntu1 libc-dev-bin_2.24-3ubuntu1 libc6_2.24-3ubuntu1 libc6-dev_2.24-3ubuntu1 libcap-ng0_0.7.7-3 libcap2_1:2.25-1 libcap2-bin_1:2.25-1 libcc1-0_6.2.0-5ubuntu23 libcomerr2_1.43.3-1 libcroco3_0.6.11-1 libcryptsetup4_2:1.7.2-0ubuntu1 libcurl3-gnutls_7.50.1-1ubuntu1 libdb5.3_5.3.28-12 libdebconfclient0_0.213ubuntu1 libdevmapper1.02.1_2:1.02.130-1ubuntu1 libdpkg-perl_1.18.10ubuntu1 libfakeroot_1.21-1ubuntu2 libfdisk1_2.28.2-1ubuntu1 libffi6_3.2.1-6 libfile-stripnondeterminism-perl_0.028-1 libgcc-5-dev_5.4.1-2ubuntu2 libgcc-6-dev_6.2.0-5ubuntu23 libgcc1_1:6.2.0-5ubuntu23 libgcrypt20_1.7.2-2ubuntu1 libgdbm3_1.8.3-14 libglib2.0-0_2.50.0-1 libgmp10_2:6.1.1+dfsg-1 libgnutls30_3.5.3-5ubuntu1 libgomp1_6.2.0-5ubuntu23 libgpg-error0_1.24-1 libgsl-dev_2.1+dfsg-2 libgsl2_2.1+dfsg-2 libgssapi-krb5-2_1.14.3+dfsg-2 libgssapi3-heimdal_1.7~git20150920+dfsg-4ubuntu1 libhcrypto4-heimdal_1.7~git20150920+dfsg-4ubuntu1 libheimbase1-heimdal_1.7~git20150920+dfsg-4ubuntu1 libheimntlm0-heimdal_1.7~git20150920+dfsg-4ubuntu1 libhogweed4_3.2-1 libhts-dev_1.3.1-3ubuntu1 libhts1_1.3.1-3ubuntu1 libhx509-5-heimdal_1.7~git20150920+dfsg-4ubuntu1 libicu57_57.1-4 libidn11_1.33-1 libio-pty-perl_1:1.08-1.1build1 libip4tc0_1.6.0-3ubuntu2 libisl15_0.17.1-1 libitm1_6.2.0-5ubuntu23 libk5crypto3_1.14.3+dfsg-2 libkeyutils1_1.5.9-9ubuntu1 libkmod2_22-1.1ubuntu1 libkrb5-26-heimdal_1.7~git20150920+dfsg-4ubuntu1 libkrb5-3_1.14.3+dfsg-2 libkrb5support0_1.14.3+dfsg-2 libksba8_1.3.4-4 libldap-2.4-2_2.4.42+dfsg-2ubuntu4 liblockfile-bin_1.09-6ubuntu1 liblockfile1_1.09-6ubuntu1 liblz4-1_0.0~r131-2ubuntu2 liblzma5_5.1.1alpha+20120614-2.1ubuntu1 libmagic1_1:5.28-2ubuntu1 libmount1_2.28.2-1ubuntu1 libmpc3_1.0.3-1 libmpfr4_3.1.5-1 libncurses5_6.0+20160625-1ubuntu1 libncursesw5_6.0+20160625-1ubuntu1 libnettle6_3.2-1 libnpth0_1.2-3 libp11-kit0_0.23.2-5 libpam-modules_1.1.8-3.2ubuntu2 libpam-modules-bin_1.1.8-3.2ubuntu2 libpam-runtime_1.1.8-3.2ubuntu2 libpam0g_1.1.8-3.2ubuntu2 libpcre3_2:8.39-2 libperl5.22_5.22.2-3 libpipeline1_1.4.1-2 libpng12-0_1.2.54-1ubuntu1 libpng16-16_1.6.25-1 libprocps4_2:3.3.10-4ubuntu2 libprocps6_2:3.3.12-1ubuntu2 libreadline6_6.3-8ubuntu8 libreadline7_7.0-0ubuntu2 libroken18-heimdal_1.7~git20150920+dfsg-4ubuntu1 librtmp1_2.4+20151223.gitfa8646d.1-1 libsasl2-2_2.1.26.dfsg1-15 libsasl2-modules-db_2.1.26.dfsg1-15 libseccomp2_2.3.1-2ubuntu2 libselinux1_2.5-3 libsemanage-common_2.5-1 libsemanage1_2.5-1 libsepol1_2.5-1 libsigsegv2_2.10-5 libslang2_2.3.0-2.3ubuntu1 libsmartcols1_2.28.2-1ubuntu1 libsqlite3-0_3.14.1-1build1 libss2_1.43.3-1 libssl1.0.0_1.0.2g-1ubuntu9 libstdc++-5-dev_5.4.1-2ubuntu2 libstdc++-6-dev_6.2.0-5ubuntu23 libstdc++6_6.2.0-5ubuntu23 libsystemd0_231-9git1 libtasn1-6_4.9-4 libtimedate-perl_2.3000-2 libtinfo5_6.0+20160625-1ubuntu1 libtool_2.4.6-1 libudev1_231-9git1 libunistring0_0.9.3-5.2ubuntu1 libusb-0.1-4_2:0.1.12-30 libustr-1.0-1_1.0.4-5 libuuid1_2.28.2-1ubuntu1 libwind0-heimdal_1.7~git20150920+dfsg-4ubuntu1 libxml2_2.9.4+dfsg1-2 linux-libc-dev_4.8.0-21.23 lockfile-progs_0.1.17 login_1:4.2-3.2ubuntu1 lsb-base_9.20160110ubuntu5 m4_1.4.17-5 make_4.1-9 man-db_2.7.5-1 mawk_1.3.3-17ubuntu2 mount_2.28.2-1ubuntu1 multiarch-support_2.24-3ubuntu1 ncurses-base_6.0+20160625-1ubuntu1 ncurses-bin_6.0+20160625-1ubuntu1 openssl_1.0.2g-1ubuntu9 optipng_0.7.6-1build1 passwd_1:4.2-3.2ubuntu1 patch_2.7.5-1 perl_5.22.2-3 perl-base_5.22.2-3 perl-modules-5.22_5.22.2-3 pinentry-curses_0.9.7-5 pkg-create-dbgsym_0.72 pkgbinarymangler_131 po-debconf_1.0.19 policyrcd-script-zg2_0.1-3 procps_2:3.3.12-1ubuntu2 readline-common_7.0-0ubuntu2 sbuild-build-depends-bcftools-dummy_0.invalid.0 sbuild-build-depends-core-dummy_0.invalid.0 sed_4.2.2-8 sensible-utils_0.0.9 systemd_231-9git1 systemd-sysv_231-9git1 sysv-rc_2.88dsf-59.3ubuntu2 sysvinit-utils_2.88dsf-59.8git1 tabix_1.3.1-3ubuntu1 tar_1.29b-1 tzdata_2016g-1 ubuntu-keyring_2016.09.19 util-linux_2.28.2-1ubuntu1 xz-utils_5.1.1alpha+20120614-2.1ubuntu1 zlib1g_1:1.2.8.dfsg-2ubuntu5 zlib1g-dev_1:1.2.8.dfsg-2ubuntu5 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Tue Apr 26 05:26:43 2016 UTC gpgv: using RSA key gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./bcftools_1.3.1-1.dsc dpkg-source: info: extracting bcftools in bcftools-1.3.1 dpkg-source: info: unpacking bcftools_1.3.1.orig.tar.gz dpkg-source: info: unpacking bcftools_1.3.1-1.debian.tar.xz dpkg-source: info: applying external-libs.patch dpkg-source: info: applying compiler-flags.patch dpkg-source: info: applying destdir.patch dpkg-source: info: applying tests-pluginpath.patch Check disc space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=4 HOME=/home/buildd LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd MAIL=/var/mail/buildd OLDPWD=/ PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games PWD=/<> SHELL=/bin/sh SUDO_COMMAND=/usr/sbin/chroot /<> su buildd -s /bin/sh -c cd '/<>' && 'env' SUDO_GID=2501 SUDO_UID=2001 SUDO_USER=buildd TERM=unknown USER=buildd USERNAME=root dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package bcftools dpkg-buildpackage: info: source version 1.3.1-1 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build bcftools-1.3.1 dpkg-buildpackage: info: host architecture s390x fakeroot debian/rules clean dh clean --parallel dh_testdir -O--parallel dh_auto_clean -O--parallel make -j4 distclean make[1]: Entering directory '/<>' rm -f test/*.o test/*~ test/test-rbuf rm -f plugins/*.so plugins/*.P rm -rf plugins/*.dSYM rm -f gmon.out *.o *~ bcftools version.h plugins/*.so plugins/*.P rm -rf *.dSYM plugins/*.dSYM test/*.dSYM rm -f TAGS make[1]: Leaving directory '/<>' dh_clean -O--parallel debian/rules build-arch dh build-arch --parallel dh_testdir -a -O--parallel dh_update_autotools_config -a -O--parallel dh_auto_configure -a -O--parallel dh_auto_build -a -O--parallel make -j4 make[1]: Entering directory '/<>' echo '#define BCFTOOLS_VERSION "1.3.1"' > version.h cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/s390x-linux-gnu/bcftools\" -DUSE_GPL -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfindex.o vcfindex.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/s390x-linux-gnu/bcftools\" -DUSE_GPL -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tabix.o tabix.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/s390x-linux-gnu/bcftools\" -DUSE_GPL -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfstats.o vcfstats.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/s390x-linux-gnu/bcftools\" -DUSE_GPL -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfisec.o vcfisec.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/s390x-linux-gnu/bcftools\" -DUSE_GPL -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfmerge.o vcfmerge.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/s390x-linux-gnu/bcftools\" -DUSE_GPL -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfquery.o vcfquery.c vcfmerge.c: In function ‘info_rules_init’: vcfmerge.c:277:9: warning: this ‘while’ clause does not guard... [-Wmisleading-indentation] while ( *ss ) ss++; ss++; ^~~~~ vcfmerge.c:277:29: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the ‘while’ while ( *ss ) ss++; ss++; ^~ vcfmerge.c:303:9: warning: this ‘while’ clause does not guard... [-Wmisleading-indentation] while ( *ss ) ss++; ss++; n++; ^~~~~ vcfmerge.c:303:29: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the ‘while’ while ( *ss ) ss++; ss++; n++; ^~ vcfmerge.c: In function ‘debug_maux’: vcfmerge.c:1661:5: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] for (j=0; jnals; j++) fprintf(stderr,"%s %dx %s", j==0?"":",",maux->cnt[j], maux->als[j]); fprintf(stderr,"\n"); ^~~ vcfmerge.c:1661:105: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the ‘for’ for (j=0; jnals; j++) fprintf(stderr,"%s %dx %s", j==0?"":",",maux->cnt[j], maux->als[j]); fprintf(stderr,"\n"); ^~~~~~~ cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/s390x-linux-gnu/bcftools\" -DUSE_GPL -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcffilter.o vcffilter.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/s390x-linux-gnu/bcftools\" -DUSE_GPL -Wdate-time -D_FORTIFY_SOURCE=2 -c -o filter.o filter.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/s390x-linux-gnu/bcftools\" -DUSE_GPL -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfsom.o vcfsom.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/s390x-linux-gnu/bcftools\" -DUSE_GPL -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfnorm.o vcfnorm.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/s390x-linux-gnu/bcftools\" -DUSE_GPL -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfgtcheck.o vcfgtcheck.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/s390x-linux-gnu/bcftools\" -DUSE_GPL -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfview.o vcfview.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/s390x-linux-gnu/bcftools\" -DUSE_GPL -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfannotate.o vcfannotate.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/s390x-linux-gnu/bcftools\" -DUSE_GPL -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfroh.o vcfroh.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/s390x-linux-gnu/bcftools\" -DUSE_GPL -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfconcat.o vcfconcat.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/s390x-linux-gnu/bcftools\" -DUSE_GPL -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfcall.o vcfcall.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/s390x-linux-gnu/bcftools\" -DUSE_GPL -Wdate-time -D_FORTIFY_SOURCE=2 -c -o mcall.o mcall.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/s390x-linux-gnu/bcftools\" -DUSE_GPL -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcmp.o vcmp.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/s390x-linux-gnu/bcftools\" -DUSE_GPL -Wdate-time -D_FORTIFY_SOURCE=2 -c -o gvcf.o gvcf.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/s390x-linux-gnu/bcftools\" -DUSE_GPL -Wdate-time -D_FORTIFY_SOURCE=2 -c -o reheader.o reheader.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/s390x-linux-gnu/bcftools\" -DUSE_GPL -Wdate-time -D_FORTIFY_SOURCE=2 -c -o convert.o convert.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/s390x-linux-gnu/bcftools\" -DUSE_GPL -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfconvert.o vcfconvert.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/s390x-linux-gnu/bcftools\" -DUSE_GPL -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tsv2vcf.o tsv2vcf.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/s390x-linux-gnu/bcftools\" -DUSE_GPL -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfcnv.o vcfcnv.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/s390x-linux-gnu/bcftools\" -DUSE_GPL -Wdate-time -D_FORTIFY_SOURCE=2 -c -o HMM.o HMM.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/s390x-linux-gnu/bcftools\" -DUSE_GPL -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfplugin.o vcfplugin.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/s390x-linux-gnu/bcftools\" -DUSE_GPL -Wdate-time -D_FORTIFY_SOURCE=2 -c -o consensus.o consensus.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/s390x-linux-gnu/bcftools\" -DUSE_GPL -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ploidy.o ploidy.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/s390x-linux-gnu/bcftools\" -DUSE_GPL -Wdate-time -D_FORTIFY_SOURCE=2 -c -o version.o version.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/s390x-linux-gnu/bcftools\" -DUSE_GPL -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ccall.o ccall.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/s390x-linux-gnu/bcftools\" -DUSE_GPL -Wdate-time -D_FORTIFY_SOURCE=2 -c -o em.o em.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/s390x-linux-gnu/bcftools\" -DUSE_GPL -Wdate-time -D_FORTIFY_SOURCE=2 -c -o prob1.o prob1.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/s390x-linux-gnu/bcftools\" -DUSE_GPL -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kmin.o kmin.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/s390x-linux-gnu/bcftools\" -DUSE_GPL -Wdate-time -D_FORTIFY_SOURCE=2 -c -o polysomy.o polysomy.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/s390x-linux-gnu/bcftools\" -DUSE_GPL -Wdate-time -D_FORTIFY_SOURCE=2 -c -o peakfit.o peakfit.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/s390x-linux-gnu/bcftools\" -DUSE_GPL -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-rbuf.o test/test-rbuf.c test/test-rbuf.c: In function ‘debug_print’: test/test-rbuf.c:32:5: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] for (i=-1; rbuf_next(rbuf, &i); ) printf(" %2d", i); printf("\n"); ^~~ test/test-rbuf.c:32:58: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the ‘for’ for (i=-1; rbuf_next(rbuf, &i); ) printf(" %2d", i); printf("\n"); ^~~~~~ test/test-rbuf.c:33:5: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] for (i=-1; rbuf_next(rbuf, &i); ) printf(" %2d", dat[i]); printf("\n"); ^~~ test/test-rbuf.c:33:63: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the ‘for’ for (i=-1; rbuf_next(rbuf, &i); ) printf(" %2d", dat[i]); printf("\n"); ^~~~~~ cc -fPIC -shared -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/s390x-linux-gnu/bcftools\" -DUSE_GPL -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/setGT.so version.c plugins/setGT.c -Wl,-Bsymbolic-functions -Wl,-z,relro -lhts cc -fPIC -shared -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/s390x-linux-gnu/bcftools\" -DUSE_GPL -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/tag2tag.so version.c plugins/tag2tag.c -Wl,-Bsymbolic-functions -Wl,-z,relro -lhts cc -fPIC -shared -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/s390x-linux-gnu/bcftools\" -DUSE_GPL -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/fixploidy.so ploidy.c version.c plugins/fixploidy.c -Wl,-Bsymbolic-functions -Wl,-z,relro -lhts cc -fPIC -shared -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/s390x-linux-gnu/bcftools\" -DUSE_GPL -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/frameshifts.so version.c plugins/frameshifts.c -Wl,-Bsymbolic-functions -Wl,-z,relro -lhts cc -fPIC -shared -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/s390x-linux-gnu/bcftools\" -DUSE_GPL -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/vcf2sex.so ploidy.c version.c plugins/vcf2sex.c -Wl,-Bsymbolic-functions -Wl,-z,relro -lhts cc -fPIC -shared -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/s390x-linux-gnu/bcftools\" -DUSE_GPL -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/fill-tags.so version.c plugins/fill-tags.c -Wl,-Bsymbolic-functions -Wl,-z,relro -lhts cc -fPIC -shared -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/s390x-linux-gnu/bcftools\" -DUSE_GPL -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/counts.so version.c plugins/counts.c -Wl,-Bsymbolic-functions -Wl,-z,relro -lhts cc -fPIC -shared -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/s390x-linux-gnu/bcftools\" -DUSE_GPL -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/color-chrs.so HMM.c version.c plugins/color-chrs.c -Wl,-Bsymbolic-functions -Wl,-z,relro -lhts cc -fPIC -shared -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/s390x-linux-gnu/bcftools\" -DUSE_GPL -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/mendelian.so version.c plugins/mendelian.c -Wl,-Bsymbolic-functions -Wl,-z,relro -lhts plugins/mendelian.c: In function ‘init’: plugins/mendelian.c:149:13: warning: this ‘while’ clause does not guard... [-Wmisleading-indentation] while ( *se && *se!=',' ) se++; if ( *se!=',' ) error("Could not parse %s: %s\n",trio_file, ss); ^~~~~ plugins/mendelian.c:149:45: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the ‘while’ while ( *se && *se!=',' ) se++; if ( *se!=',' ) error("Could not parse %s: %s\n",trio_file, ss); ^~ plugins/mendelian.c:154:13: warning: this ‘while’ clause does not guard... [-Wmisleading-indentation] while ( *se && *se!=',' ) se++; if ( *se!=',' ) error("Could not parse %s\n",trio_file); ^~~~~ plugins/mendelian.c:154:45: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the ‘while’ while ( *se && *se!=',' ) se++; if ( *se!=',' ) error("Could not parse %s\n",trio_file); ^~ plugins/mendelian.c:159:13: warning: this ‘while’ clause does not guard... [-Wmisleading-indentation] while ( *se ) se++; if ( ss==se ) error("Could not parse %s\n",trio_file); ^~~~~ plugins/mendelian.c:159:33: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the ‘while’ while ( *se ) se++; if ( ss==se ) error("Could not parse %s\n",trio_file); ^~ cc -fPIC -shared -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/s390x-linux-gnu/bcftools\" -DUSE_GPL -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/missing2ref.so version.c plugins/missing2ref.c -Wl,-Bsymbolic-functions -Wl,-z,relro -lhts cc -fPIC -shared -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/s390x-linux-gnu/bcftools\" -DUSE_GPL -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/GTisec.so version.c plugins/GTisec.c -Wl,-Bsymbolic-functions -Wl,-z,relro -lhts plugins/vcf2sex.c: In function ‘run’: plugins/vcf2sex.c:415:17: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] if (*tmp) error("Unexpected argument to --nsites: %s\n", optarg); break; ^~ plugins/vcf2sex.c:415:83: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the ‘if’ if (*tmp) error("Unexpected argument to --nsites: %s\n", optarg); break; ^~~~~ cc -fPIC -shared -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/s390x-linux-gnu/bcftools\" -DUSE_GPL -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/dosage.so version.c plugins/dosage.c -Wl,-Bsymbolic-functions -Wl,-z,relro -lhts cc -fPIC -shared -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/s390x-linux-gnu/bcftools\" -DUSE_GPL -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/impute-info.so version.c plugins/impute-info.c -Wl,-Bsymbolic-functions -Wl,-z,relro -lhts cc -fPIC -shared -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/s390x-linux-gnu/bcftools\" -DUSE_GPL -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/fill-AN-AC.so version.c plugins/fill-AN-AC.c -Wl,-Bsymbolic-functions -Wl,-z,relro -lhts cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -I. -I/usr/include -DPLUGINPATH=\"/usr/lib/s390x-linux-gnu/bcftools\" -DUSE_GPL -Wdate-time -D_FORTIFY_SOURCE=2 -c -o main.o main.c cc -Wl,-Bsymbolic-functions -Wl,-z,relro -o test/test-rbuf test/test-rbuf.o -lm -Wl,-Bsymbolic-functions -Wl,-z,relro -lhts cc -rdynamic -Wl,-Bsymbolic-functions -Wl,-z,relro -o bcftools main.o vcfindex.o tabix.o vcfstats.o vcfisec.o vcfmerge.o vcfquery.o vcffilter.o filter.o vcfsom.o vcfnorm.o vcfgtcheck.o vcfview.o vcfannotate.o vcfroh.o vcfconcat.o vcfcall.o mcall.o vcmp.o gvcf.o reheader.o convert.o vcfconvert.o tsv2vcf.o vcfcnv.o HMM.o vcfplugin.o consensus.o ploidy.o version.o ccall.o em.o prob1.o kmin.o polysomy.o peakfit.o -lpthread -lz -lm -ldl -lgsl -lgslcblas -Wl,-Bsymbolic-functions -Wl,-z,relro -lhts make[1]: Leaving directory '/<>' dh_auto_test -a -O--parallel make -j4 test make[1]: Entering directory '/<>' ./test/test.pl --exec bgzip=/usr/bin/bgzip --exec tabix=/usr/bin/tabix test_usage: bcftools .. ok test_usage_subcommand: bcftools index .. ok test_usage_subcommand: bcftools annotate .. ok test_usage_subcommand: bcftools concat .. ok test_usage_subcommand: bcftools convert .. ok test_usage_subcommand: bcftools isec .. ok test_usage_subcommand: bcftools merge .. ok test_usage_subcommand: bcftools norm .. ok test_usage_subcommand: bcftools plugin .. ok test_usage_subcommand: bcftools query .. ok test_usage_subcommand: bcftools reheader .. ok test_usage_subcommand: bcftools view .. ok test_usage_subcommand: bcftools call .. ok test_usage_subcommand: bcftools consensus .. ok test_usage_subcommand: bcftools cnv .. ok test_usage_subcommand: bcftools filter .. ok test_usage_subcommand: bcftools gtcheck .. ok test_usage_subcommand: bcftools polysomy .. ok test_usage_subcommand: bcftools roh .. ok test_usage_subcommand: bcftools stats .. ok test_tabix: /usr/bin/tabix /tmp/bOQqbKDDk5/merge.a.vcf.gz 2:3199812-3199812 .. ok test_tabix: /<>/bcftools view -H /tmp/bOQqbKDDk5/merge.a.bcf 2:3199812-3199812 .. ok test_tabix: /usr/bin/tabix /tmp/bOQqbKDDk5/merge.a.vcf.gz 1:3000151-3000151 .. ok test_tabix: /<>/bcftools view -H /tmp/bOQqbKDDk5/merge.a.bcf 1:3000151-3000151 .. ok test_tabix: /usr/bin/tabix /tmp/bOQqbKDDk5/large_chrom_tbi_limit.vcf.gz chr11:1-536870912 .. ok test_tabix: /<>/bcftools view -H /tmp/bOQqbKDDk5/large_chrom_tbi_limit.bcf chr11:1-536870912 .. ok test_index: /<>/bcftools view -H /tmp/bOQqbKDDk5/large_chrom_csi_limit.vcf.gz chr20:1-2147483647 The outputs differ: /<>/test/large_chrom_csi_limit.20.1.2147483647.out /<>/test/large_chrom_csi_limit.20.1.2147483647.out.new .. failed ... test_index: /<>/bcftools view -H /tmp/bOQqbKDDk5/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /<>/bcftools view -H /tmp/bOQqbKDDk5/large_chrom_csi_limit.vcf.gz chr20 The outputs differ: /<>/test/large_chrom.20.1.2147483647.out /<>/test/large_chrom.20.1.2147483647.out.new .. failed ... test_index: /<>/bcftools view -H /tmp/bOQqbKDDk5/large_chrom_csi_limit.bcf chr20 .. ok test_vcf_idxstats: /<>/bcftools index -s /tmp/bOQqbKDDk5/idx.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -s /tmp/bOQqbKDDk5/idx.vcf.gz The outputs differ: /<>/test/idx.out /<>/test/idx.out.new .. failed ... test_vcf_idxstats: /<>/bcftools index -s /tmp/bOQqbKDDk5/idx.bcf .. ok test_vcf_idxstats: /<>/bcftools index -n /tmp/bOQqbKDDk5/idx.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -n /tmp/bOQqbKDDk5/idx.vcf.gz The outputs differ: /<>/test/idx_count.out /<>/test/idx_count.out.new .. failed ... test_vcf_idxstats: /<>/bcftools index -n /tmp/bOQqbKDDk5/idx.bcf .. ok test_vcf_idxstats: /<>/bcftools index -s /tmp/bOQqbKDDk5/empty.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -s /tmp/bOQqbKDDk5/empty.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -s /tmp/bOQqbKDDk5/empty.bcf .. ok test_vcf_idxstats: /<>/bcftools index -n /tmp/bOQqbKDDk5/empty.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -n /tmp/bOQqbKDDk5/empty.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -n /tmp/bOQqbKDDk5/empty.bcf .. ok test_vcf_check: /<>/bcftools stats -s - /tmp/bOQqbKDDk5/check.vcf.gz | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID ' .. ok test_vcf_check: /<>/bcftools view -Ob /tmp/bOQqbKDDk5/check.vcf.gz | /<>/bcftools stats -s - | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID ' .. ok test_vcf_check_merge: /<>/plot-vcfstats -m /tmp/bOQqbKDDk5/check.1.chk /tmp/bOQqbKDDk5/check.2.chk /tmp/bOQqbKDDk5/check.3.chk /tmp/bOQqbKDDk5/check.4.chk 2>/dev/null | grep -v 'plot-vcfstats' | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID ' .. ok test_vcf_stats: /<>/bcftools stats -s - /tmp/bOQqbKDDk5/stats.a.vcf.gz /tmp/bOQqbKDDk5/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_isec: /<>/bcftools isec -n =2 /tmp/bOQqbKDDk5/isec.a.vcf.gz /tmp/bOQqbKDDk5/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: /<>/bcftools isec -Ob -n =2 /tmp/bOQqbKDDk5/isec.a.vcf.gz /tmp/bOQqbKDDk5/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: /<>/bcftools isec -n =2 -i"STRLEN(REF)==2" /tmp/bOQqbKDDk5/isec.a.vcf.gz /tmp/bOQqbKDDk5/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: /<>/bcftools isec -Ob -n =2 -i"STRLEN(REF)==2" /tmp/bOQqbKDDk5/isec.a.vcf.gz /tmp/bOQqbKDDk5/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: /<>/bcftools isec -n =2 -c both /tmp/bOQqbKDDk5/isec.a.vcf.gz /tmp/bOQqbKDDk5/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: /<>/bcftools isec -Ob -n =2 -c both /tmp/bOQqbKDDk5/isec.a.vcf.gz /tmp/bOQqbKDDk5/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: /<>/bcftools isec -n =2 -c any /tmp/bOQqbKDDk5/isec.a.vcf.gz /tmp/bOQqbKDDk5/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: /<>/bcftools isec -Ob -n =2 -c any /tmp/bOQqbKDDk5/isec.a.vcf.gz /tmp/bOQqbKDDk5/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: /<>/bcftools isec -C -c any /tmp/bOQqbKDDk5/isec.a.vcf.gz /tmp/bOQqbKDDk5/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: /<>/bcftools isec -Ob -C -c any /tmp/bOQqbKDDk5/isec.a.vcf.gz /tmp/bOQqbKDDk5/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec2: /<>/bcftools isec --no-version -T /tmp/bOQqbKDDk5/isec.tab.gz /tmp/bOQqbKDDk5/isec.a.vcf.gz 2>/dev/null .. ok test_vcf_isec2: /<>/bcftools isec -Ob -T /tmp/bOQqbKDDk5/isec.tab.gz /tmp/bOQqbKDDk5/isec.a.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples /tmp/bOQqbKDDk5/merge.a.vcf.gz /tmp/bOQqbKDDk5/merge.b.vcf.gz /tmp/bOQqbKDDk5/merge.c.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob --force-samples /tmp/bOQqbKDDk5/merge.a.vcf.gz /tmp/bOQqbKDDk5/merge.b.vcf.gz /tmp/bOQqbKDDk5/merge.c.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples -m none /tmp/bOQqbKDDk5/merge.2.a.vcf.gz /tmp/bOQqbKDDk5/merge.2.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob --force-samples -m none /tmp/bOQqbKDDk5/merge.2.a.vcf.gz /tmp/bOQqbKDDk5/merge.2.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples -m both /tmp/bOQqbKDDk5/merge.2.a.vcf.gz /tmp/bOQqbKDDk5/merge.2.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob --force-samples -m both /tmp/bOQqbKDDk5/merge.2.a.vcf.gz /tmp/bOQqbKDDk5/merge.2.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples -m all /tmp/bOQqbKDDk5/merge.2.a.vcf.gz /tmp/bOQqbKDDk5/merge.2.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob --force-samples -m all /tmp/bOQqbKDDk5/merge.2.a.vcf.gz /tmp/bOQqbKDDk5/merge.2.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples -i TR:sum,TA:sum,TG:sum /tmp/bOQqbKDDk5/merge.3.a.vcf.gz /tmp/bOQqbKDDk5/merge.3.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob --force-samples -i TR:sum,TA:sum,TG:sum /tmp/bOQqbKDDk5/merge.3.a.vcf.gz /tmp/bOQqbKDDk5/merge.3.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples -m id /tmp/bOQqbKDDk5/merge.4.a.vcf.gz /tmp/bOQqbKDDk5/merge.4.b.vcf.gz The outputs differ: /<>/test/merge.4.out /<>/test/merge.4.out.new .. failed ... test_vcf_merge: /<>/bcftools merge -Ob --force-samples -m id /tmp/bOQqbKDDk5/merge.4.a.vcf.gz /tmp/bOQqbKDDk5/merge.4.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ The outputs differ: /<>/test/merge.4.out /<>/test/merge.4.out.new .. failed ... test_vcf_query: /<>/bcftools query -f '%CHROM\t%POS\t%REF\t%ALT\t%DP4\t%AN[\t%GT\t%TGT]\n' /tmp/bOQqbKDDk5/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/bOQqbKDDk5/query.vcf.gz | /<>/bcftools query -f '%CHROM\t%POS\t%REF\t%ALT\t%DP4\t%AN[\t%GT\t%TGT]\n' .. ok test_vcf_query: /<>/bcftools query -f'%XRI\n' -i'XRI[*]>1111' /tmp/bOQqbKDDk5/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/bOQqbKDDk5/view.filter.vcf.gz | /<>/bcftools query -f'%XRI\n' -i'XRI[*]>1111' .. ok test_vcf_query: /<>/bcftools query -f'%XRF\n' -i'XRF[*]=2e6' /tmp/bOQqbKDDk5/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/bOQqbKDDk5/view.filter.vcf.gz | /<>/bcftools query -f'%XRF\n' -i'XRF[*]=2e6' .. ok test_vcf_query: /<>/bcftools query -f'%XGS\n' -i'XGS[5]="PQR"' /tmp/bOQqbKDDk5/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/bOQqbKDDk5/view.filter.vcf.gz | /<>/bcftools query -f'%XGS\n' -i'XGS[5]="PQR"' .. ok test_vcf_query: /<>/bcftools query -f'%XGS\n' -i'XGS[*]="GHI"' /tmp/bOQqbKDDk5/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/bOQqbKDDk5/view.filter.vcf.gz | /<>/bcftools query -f'%XGS\n' -i'XGS[*]="GHI"' .. ok test_vcf_query: /<>/bcftools query -f'%XGS\n' -i'XGS[2]~"H"' /tmp/bOQqbKDDk5/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/bOQqbKDDk5/view.filter.vcf.gz | /<>/bcftools query -f'%XGS\n' -i'XGS[2]~"H"' .. ok test_vcf_query: /<>/bcftools query -f'%XGS\n' -i'XGS[3]!~"H"' /tmp/bOQqbKDDk5/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/bOQqbKDDk5/view.filter.vcf.gz | /<>/bcftools query -f'%XGS\n' -i'XGS[3]!~"H"' .. ok test_vcf_query: /<>/bcftools query -f'%XGS\n' -i'XGS[*]~"H"' /tmp/bOQqbKDDk5/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/bOQqbKDDk5/view.filter.vcf.gz | /<>/bcftools query -f'%XGS\n' -i'XGS[*]~"H"' .. ok test_vcf_query: /<>/bcftools query -f'%XGS\n' -i'XGS[*]~"HI,JK"' /tmp/bOQqbKDDk5/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/bOQqbKDDk5/view.filter.vcf.gz | /<>/bcftools query -f'%XGS\n' -i'XGS[*]~"HI,JK"' .. ok test_vcf_query: /<>/bcftools query -f'%POS %REF %ALT\n' -i'REF~"C" && ALT~"CT"' /tmp/bOQqbKDDk5/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/bOQqbKDDk5/query.vcf.gz | /<>/bcftools query -f'%POS %REF %ALT\n' -i'REF~"C" && ALT~"CT"' .. ok test_vcf_query: /<>/bcftools query -f'%POS %REF %ALT\n' -i'N_ALT=2' /tmp/bOQqbKDDk5/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/bOQqbKDDk5/query.vcf.gz | /<>/bcftools query -f'%POS %REF %ALT\n' -i'N_ALT=2' .. ok test_vcf_query: /<>/bcftools query -f'%POS %AN\n' -i'AN!=2*N_SAMPLES' /tmp/bOQqbKDDk5/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/bOQqbKDDk5/query.vcf.gz | /<>/bcftools query -f'%POS %AN\n' -i'AN!=2*N_SAMPLES' .. ok test_vcf_query: /<>/bcftools query -f'%POS[ %GL]\n' -i'min(abs(GL[0]))=10' /tmp/bOQqbKDDk5/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/bOQqbKDDk5/query.vcf.gz | /<>/bcftools query -f'%POS[ %GL]\n' -i'min(abs(GL[0]))=10' .. ok test_vcf_query: /<>/bcftools query -f'%POS %CIGAR\n' -i'strlen(CIGAR[*])=4' /tmp/bOQqbKDDk5/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/bOQqbKDDk5/view.filter.vcf.gz | /<>/bcftools query -f'%POS %CIGAR\n' -i'strlen(CIGAR[*])=4' .. ok test_vcf_query: /<>/bcftools query -f'%POS[ %GT]\n' -i'AC[0]=3' /tmp/bOQqbKDDk5/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/bOQqbKDDk5/query.vcf.gz | /<>/bcftools query -f'%POS[ %GT]\n' -i'AC[0]=3' .. ok test_vcf_query: /<>/bcftools query -f'%POS[ %GT]\n' -i'AF[0]=3/4' /tmp/bOQqbKDDk5/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/bOQqbKDDk5/query.vcf.gz | /<>/bcftools query -f'%POS[ %GT]\n' -i'AF[0]=3/4' .. ok test_vcf_query: /<>/bcftools query -f'%POS[ %GT]\n' -i'MAC[0]=1' /tmp/bOQqbKDDk5/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/bOQqbKDDk5/query.vcf.gz | /<>/bcftools query -f'%POS[ %GT]\n' -i'MAC[0]=1' .. ok test_vcf_query: /<>/bcftools query -f'%POS[ %GT]\n' -i'MAF[0]=1/4' /tmp/bOQqbKDDk5/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/bOQqbKDDk5/query.vcf.gz | /<>/bcftools query -f'%POS[ %GT]\n' -i'MAF[0]=1/4' .. ok test_vcf_query: /<>/bcftools query -f'I8=%I8 I16=%I16 I32=%I32 IF=%IF IA8=%IA8 IA16=%IA16 IA32=%IA32 IAF=%IAF IA8=%IA8{1} IA16=%IA16{1} IA32=%IA32{1} IAF=%IAF{1} [ %F8:%F16:%F32:%FF]\n' /tmp/bOQqbKDDk5/view.vectors.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/bOQqbKDDk5/view.vectors.vcf.gz | /<>/bcftools query -f'I8=%I8 I16=%I16 I32=%I32 IF=%IF IA8=%IA8 IA16=%IA16 IA32=%IA32 IAF=%IAF IA8=%IA8{1} IA16=%IA16{1} IA32=%IA32{1} IAF=%IAF{1} [ %F8:%F16:%F32:%FF]\n' .. ok test_vcf_query: /<>/bcftools query -f'%POS[ %GT]\n' -i'GT ="1"' /tmp/bOQqbKDDk5/query.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/bOQqbKDDk5/query.filter.vcf.gz | /<>/bcftools query -f'%POS[ %GT]\n' -i'GT ="1"' .. ok test_vcf_query: /<>/bcftools query -f'%POS[ %GT]\n' -i'GT!="1"' /tmp/bOQqbKDDk5/query.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/bOQqbKDDk5/query.filter.vcf.gz | /<>/bcftools query -f'%POS[ %GT]\n' -i'GT!="1"' .. ok test_vcf_query: /<>/bcftools query -f'%POS[ %GT]\n' -e'GT ="1"' /tmp/bOQqbKDDk5/query.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/bOQqbKDDk5/query.filter.vcf.gz | /<>/bcftools query -f'%POS[ %GT]\n' -e'GT ="1"' .. ok test_vcf_query: /<>/bcftools query -f'%POS[ %GT]\n' -e'GT!="1"' /tmp/bOQqbKDDk5/query.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/bOQqbKDDk5/query.filter.vcf.gz | /<>/bcftools query -f'%POS[ %GT]\n' -e'GT!="1"' .. ok test_vcf_query: /<>/bcftools query -f'%XX_A %XX.A %XX.A0 %xx.a0\n' /tmp/bOQqbKDDk5/query.2.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/bOQqbKDDk5/query.2.vcf.gz | /<>/bcftools query -f'%XX_A %XX.A %XX.A0 %xx.a0\n' .. ok test_vcf_query: /<>/bcftools query -i'IINT="."' -f'%POS %IINT\n' /tmp/bOQqbKDDk5/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/bOQqbKDDk5/missing.vcf.gz | /<>/bcftools query -i'IINT="."' -f'%POS %IINT\n' .. ok test_vcf_query: /<>/bcftools query -i'IINT!="."' -f'%POS %IINT\n' /tmp/bOQqbKDDk5/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/bOQqbKDDk5/missing.vcf.gz | /<>/bcftools query -i'IINT!="."' -f'%POS %IINT\n' .. ok test_vcf_query: /<>/bcftools query -e'IINT!="."' -f'%POS %IINT\n' /tmp/bOQqbKDDk5/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/bOQqbKDDk5/missing.vcf.gz | /<>/bcftools query -e'IINT!="."' -f'%POS %IINT\n' .. ok test_vcf_query: /<>/bcftools query -e'IINT="."' -f'%POS %IINT\n' /tmp/bOQqbKDDk5/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/bOQqbKDDk5/missing.vcf.gz | /<>/bcftools query -e'IINT="."' -f'%POS %IINT\n' .. ok test_vcf_query: /<>/bcftools query -i'IFLT="."' -f'%POS %IFLT\n' /tmp/bOQqbKDDk5/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/bOQqbKDDk5/missing.vcf.gz | /<>/bcftools query -i'IFLT="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /<>/bcftools query -i'IFLT!="."' -f'%POS %IFLT\n' /tmp/bOQqbKDDk5/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/bOQqbKDDk5/missing.vcf.gz | /<>/bcftools query -i'IFLT!="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /<>/bcftools query -e'IFLT!="."' -f'%POS %IFLT\n' /tmp/bOQqbKDDk5/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/bOQqbKDDk5/missing.vcf.gz | /<>/bcftools query -e'IFLT!="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /<>/bcftools query -e'IFLT="."' -f'%POS %IFLT\n' /tmp/bOQqbKDDk5/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/bOQqbKDDk5/missing.vcf.gz | /<>/bcftools query -e'IFLT="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /<>/bcftools query -i'ISTR="."' -f'%POS %ISTR\n' /tmp/bOQqbKDDk5/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/bOQqbKDDk5/missing.vcf.gz | /<>/bcftools query -i'ISTR="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /<>/bcftools query -i'ISTR!="."' -f'%POS %ISTR\n' /tmp/bOQqbKDDk5/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/bOQqbKDDk5/missing.vcf.gz | /<>/bcftools query -i'ISTR!="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /<>/bcftools query -e'ISTR="."' -f'%POS %ISTR\n' /tmp/bOQqbKDDk5/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/bOQqbKDDk5/missing.vcf.gz | /<>/bcftools query -e'ISTR="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /<>/bcftools query -e'ISTR!="."' -f'%POS %ISTR\n' /tmp/bOQqbKDDk5/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/bOQqbKDDk5/missing.vcf.gz | /<>/bcftools query -e'ISTR!="."' -f'%POS %ISTR\n' .. ok test_vcf_norm: /<>/bcftools norm --no-version -f /<>/test/norm.fa /tmp/bOQqbKDDk5/norm.vcf.gz 2>/dev/null .. ok test_vcf_norm: /<>/bcftools norm -Ob -f /<>/test/norm.fa /tmp/bOQqbKDDk5/norm.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -m- /tmp/bOQqbKDDk5/norm.split.vcf.gz 2>/dev/null .. ok test_vcf_norm: /<>/bcftools norm -Ob -m- /tmp/bOQqbKDDk5/norm.split.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -m- /tmp/bOQqbKDDk5/norm.split.2.vcf.gz 2>/dev/null .. ok test_vcf_norm: /<>/bcftools norm -Ob -m- /tmp/bOQqbKDDk5/norm.split.2.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -m- -f /<>/test/norm.fa /tmp/bOQqbKDDk5/norm.split.vcf.gz 2>/dev/null .. ok test_vcf_norm: /<>/bcftools norm -Ob -m- -f /<>/test/norm.fa /tmp/bOQqbKDDk5/norm.split.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -m+ /tmp/bOQqbKDDk5/norm.merge.vcf.gz 2>/dev/null .. ok test_vcf_norm: /<>/bcftools norm -Ob -m+ /tmp/bOQqbKDDk5/norm.merge.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -m+ /tmp/bOQqbKDDk5/norm.merge.2.vcf.gz 2>/dev/null .. ok test_vcf_norm: /<>/bcftools norm -Ob -m+ /tmp/bOQqbKDDk5/norm.merge.2.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -m+ /tmp/bOQqbKDDk5/norm.merge.3.vcf.gz 2>/dev/null .. ok test_vcf_norm: /<>/bcftools norm -Ob -m+ /tmp/bOQqbKDDk5/norm.merge.3.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -m+ -s /tmp/bOQqbKDDk5/norm.merge.vcf.gz 2>/dev/null .. ok test_vcf_norm: /<>/bcftools norm -Ob -m+ -s /tmp/bOQqbKDDk5/norm.merge.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -Nc s -f /<>/test/norm.fa /tmp/bOQqbKDDk5/norm.setref.vcf.gz 2>/dev/null .. ok test_vcf_norm: /<>/bcftools norm -Ob -Nc s -f /<>/test/norm.fa /tmp/bOQqbKDDk5/norm.setref.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -f /<>/test/norm.fa /tmp/bOQqbKDDk5/norm.telomere.vcf.gz 2>/dev/null .. ok test_vcf_norm: /<>/bcftools norm -Ob -f /<>/test/norm.fa /tmp/bOQqbKDDk5/norm.telomere.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -aUc1 -C1 -s NA00002 -v snps /tmp/bOQqbKDDk5/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -aUc1 -C1 -s NA00002 -v snps /tmp/bOQqbKDDk5/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -f PASS -Xks NA00003 /tmp/bOQqbKDDk5/view.vcf.gz -r20,Y .. ok test_vcf_view: /<>/bcftools view -Ob -f PASS -Xks NA00003 /tmp/bOQqbKDDk5/view.vcf.gz -r20,Y | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -xs NA00003 /tmp/bOQqbKDDk5/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -xs NA00003 /tmp/bOQqbKDDk5/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -i 'QUAL==999 && (FS<20 || FS>=41.02) && ICF>-0.1 && HWE*2>1.2' /tmp/bOQqbKDDk5/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -i 'QUAL==999 && (FS<20 || FS>=41.02) && ICF>-0.1 && HWE*2>1.2' /tmp/bOQqbKDDk5/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -p /tmp/bOQqbKDDk5/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -p /tmp/bOQqbKDDk5/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -P /tmp/bOQqbKDDk5/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -P /tmp/bOQqbKDDk5/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -hm2 -M2 -q0.3 -Q0.7 /tmp/bOQqbKDDk5/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -hm2 -M2 -q0.3 -Q0.7 /tmp/bOQqbKDDk5/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -Hu /tmp/bOQqbKDDk5/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -GVsnps /tmp/bOQqbKDDk5/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -GVsnps /tmp/bOQqbKDDk5/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -ne 'INDEL=1 || PV4[0]<0.006' /tmp/bOQqbKDDk5/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -ne 'INDEL=1 || PV4[0]<0.006' /tmp/bOQqbKDDk5/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -s ^NA00003 /tmp/bOQqbKDDk5/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -s ^NA00003 /tmp/bOQqbKDDk5/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version /tmp/bOQqbKDDk5/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob /tmp/bOQqbKDDk5/view.omitgenotypes.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -G /tmp/bOQqbKDDk5/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -G /tmp/bOQqbKDDk5/view.omitgenotypes.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -HG /tmp/bOQqbKDDk5/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -a /tmp/bOQqbKDDk5/many.alleles.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -a /tmp/bOQqbKDDk5/many.alleles.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -asA /tmp/bOQqbKDDk5/view.vectors.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -asA /tmp/bOQqbKDDk5/view.vectors.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -asB /tmp/bOQqbKDDk5/view.vectors.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -asB /tmp/bOQqbKDDk5/view.vectors.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -H -i'FMT/FGS[0]="AAAAAA"' /tmp/bOQqbKDDk5/view.filter.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -i'FMT/FGS[2]="C"' /tmp/bOQqbKDDk5/view.filter.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -i'FMT/FGS[4]="EE"' /tmp/bOQqbKDDk5/view.filter.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -i'FMT/FRS[1]="BB"' /tmp/bOQqbKDDk5/view.filter.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -i'TXT0="text"' /tmp/bOQqbKDDk5/view.filter.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -T /<>/test/view.chrs.tab /tmp/bOQqbKDDk5/view.chrs.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -T /<>/test/view.chrs.tab /tmp/bOQqbKDDk5/view.chrs.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -i 'POS>=3062917' /tmp/bOQqbKDDk5/filter.2.vcf.gz 1:3062917-3157410 .. ok test_vcf_view: /<>/bcftools view -Ob -i 'POS>=3062917' /tmp/bOQqbKDDk5/filter.2.vcf.gz 1:3062917-3157410 | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -S. -e'TXT0="text"' /<>/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -Ob -S. -e'TXT0="text"' /<>/test/view.filter.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -S. -e'FMT/FRS[1]="BB"' /<>/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -Ob -S. -e'FMT/FRS[1]="BB"' /<>/test/view.filter.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -S. -e'FMT/FGS[0]="AAAAAA"' /<>/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -Ob -S. -e'FMT/FGS[0]="AAAAAA"' /<>/test/view.filter.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -S. -e'FMT/FGS[1]="BBB"' /<>/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -Ob -S. -e'FMT/FGS[1]="BBB"' /<>/test/view.filter.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -S. -e'FMT/FGS[4]="EE"' /<>/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -Ob -S. -e'FMT/FGS[4]="EE"' /<>/test/view.filter.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -S. -e'FMT/STR="XX"' /<>/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -Ob -S. -e'FMT/STR="XX"' /<>/test/view.filter.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -H -C5:nonmajor /tmp/bOQqbKDDk5/view.minmaxac.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -c6:nonmajor /tmp/bOQqbKDDk5/view.minmaxac.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -q0.3:major /tmp/bOQqbKDDk5/view.minmaxac.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -i 'Gene.refGene=="RAD21L1"' /tmp/bOQqbKDDk5/view.filter.annovar.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -i 'Gene.refGene~"NOD"' /tmp/bOQqbKDDk5/view.filter.annovar.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -i 'LJB2_MutationTaster=="0.291000"' /tmp/bOQqbKDDk5/view.filter.annovar.vcf.gz .. ok test_vcf_call: /<>/bcftools call --no-version -mv /<>/test/mpileup.vcf 2>/dev/null .. ok test_vcf_call: /<>/bcftools call -Ob -mv /<>/test/mpileup.vcf 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /<>/bcftools call --no-version -mg0 /<>/test/mpileup.vcf 2>/dev/null .. ok test_vcf_call: /<>/bcftools call -Ob -mg0 /<>/test/mpileup.vcf 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /<>/bcftools call --no-version -mv --ploidy-file /<>/test/mpileup.ploidy -S /<>/test/mpileup.samples /<>/test/mpileup.X.vcf 2>/dev/null .. ok test_vcf_call: /<>/bcftools call -Ob -mv --ploidy-file /<>/test/mpileup.ploidy -S /<>/test/mpileup.samples /<>/test/mpileup.X.vcf 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /<>/bcftools call --no-version -mv --ploidy-file /<>/test/mpileup.ploidy -S /<>/test/mpileup.ped /<>/test/mpileup.X.vcf 2>/dev/null .. ok test_vcf_call: /<>/bcftools call -Ob -mv --ploidy-file /<>/test/mpileup.ploidy -S /<>/test/mpileup.ped /<>/test/mpileup.X.vcf 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /<>/bcftools call --no-version -mA -C alleles -T /tmp/bOQqbKDDk5/mpileup.tab.gz /<>/test/mpileup.vcf 2>/dev/null .. ok test_vcf_call_cAls: /<>/bcftools call -Ob -mA -C alleles -T /tmp/bOQqbKDDk5/mpileup.tab.gz /<>/test/mpileup.vcf 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /<>/bcftools call --no-version -cv /<>/test/mpileup.c.vcf 2>/dev/null .. ok test_vcf_call: /<>/bcftools call -Ob -cv /<>/test/mpileup.c.vcf 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /<>/bcftools call --no-version -cv --ploidy-file /<>/test/mpileup.ploidy -S /<>/test/mpileup.samples /<>/test/mpileup.c.X.vcf 2>/dev/null .. ok test_vcf_call: /<>/bcftools call -Ob -cv --ploidy-file /<>/test/mpileup.ploidy -S /<>/test/mpileup.samples /<>/test/mpileup.c.X.vcf 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /<>/bcftools call --no-version -cv --ploidy-file /<>/test/mpileup.ploidy -S /<>/test/mpileup.ped /<>/test/mpileup.c.X.vcf 2>/dev/null .. ok test_vcf_call: /<>/bcftools call -Ob -cv --ploidy-file /<>/test/mpileup.ploidy -S /<>/test/mpileup.ped /<>/test/mpileup.c.X.vcf 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -mx -g2 -G2 /<>/test/filter.1.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -Ob -mx -g2 -G2 /<>/test/filter.1.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -e'QUAL==59.2 || (INDEL=0 & (FMT/GQ=25 | FMT/DP=10))' -sModified -S. /<>/test/filter.2.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -Ob -e'QUAL==59.2 || (INDEL=0 & (FMT/GQ=25 | FMT/DP=10))' -sModified -S. /<>/test/filter.2.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -e'DP=19' /<>/test/filter.3.vcf | /<>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -e'DP=19' /<>/test/filter.3.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -e'DP=19' -s XX /<>/test/filter.3.vcf | /<>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -e'DP=19' -s XX /<>/test/filter.3.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -e'DP=19' -s XX -m+ /<>/test/filter.3.vcf | /<>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -e'DP=19' -s XX -m+ /<>/test/filter.3.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -e'DP=19' -s XX -mx /<>/test/filter.3.vcf | /<>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -e'DP=19' -s XX -mx /<>/test/filter.3.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -e'DP=19' -s XX -m+x /<>/test/filter.3.vcf | /<>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -e'DP=19' -s XX -m+x /<>/test/filter.3.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -e'FMT/GT="0/2"' /<>/test/filter.3.vcf | /<>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -e'FMT/GT="0/2"' /<>/test/filter.3.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -e'FMT/GT="0/2"' -s XX /<>/test/filter.3.vcf | /<>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX /<>/test/filter.3.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -e'FMT/GT="0/2"' -s XX -m+ /<>/test/filter.3.vcf | /<>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -m+ /<>/test/filter.3.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -e'FMT/GT="0/2"' -s XX -mx /<>/test/filter.3.vcf | /<>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -mx /<>/test/filter.3.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -e'FMT/GT="0/2"' -s XX -m+x /<>/test/filter.3.vcf | /<>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -m+x /<>/test/filter.3.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -i'FMT/GT="0/0" && AC[*]=2' /<>/test/filter.2.vcf | /<>/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -i'FMT/GT="0/0" && AC[*]=2' /<>/test/filter.2.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -i'AC[*]=2 && FMT/GT="0/0"' /<>/test/filter.2.vcf | /<>/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -i'AC[*]=2 && FMT/GT="0/0"' /<>/test/filter.2.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -i'ALT="."' /<>/test/filter.2.vcf | /<>/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -i'ALT="."' /<>/test/filter.2.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -S . -i 'FORMAT/TEST3<25' /<>/test/filter.4.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -Ob -S . -i 'FORMAT/TEST3<25' /<>/test/filter.4.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -S . -i 'FORMAT/TEST4<25' /<>/test/filter.4.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -Ob -S . -i 'FORMAT/TEST4<25' /<>/test/filter.4.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_regions: /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /<>/test/regions.tab /tmp/bOQqbKDDk5/regions.vcf.gz .. ok test_vcf_regions: /<>/bcftools view -Ob /tmp/bOQqbKDDk5/regions.vcf.gz | /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /<>/test/regions.tab .. ok test_vcf_regions: /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /<>/test/regions.tab /tmp/bOQqbKDDk5/regions.vcf.gz .. ok test_vcf_regions: /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/bOQqbKDDk5/regions.tab.gz /tmp/bOQqbKDDk5/regions.vcf.gz .. ok test_vcf_regions: /<>/bcftools view -Ob /tmp/bOQqbKDDk5/regions.vcf.gz | /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/bOQqbKDDk5/regions.tab.gz .. ok test_vcf_regions: /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/bOQqbKDDk5/regions.tab.gz /tmp/bOQqbKDDk5/regions.vcf.gz .. ok test_vcf_regions: /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/bOQqbKDDk5/regions.bed /tmp/bOQqbKDDk5/regions.vcf.gz .. ok test_vcf_regions: /<>/bcftools view -Ob /tmp/bOQqbKDDk5/regions.vcf.gz | /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/bOQqbKDDk5/regions.bed .. ok test_vcf_regions: /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/bOQqbKDDk5/regions.bed /tmp/bOQqbKDDk5/regions.vcf.gz .. ok test_vcf_regions: /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/bOQqbKDDk5/regions.bed.gz /tmp/bOQqbKDDk5/regions.vcf.gz .. ok test_vcf_regions: /<>/bcftools view -Ob /tmp/bOQqbKDDk5/regions.vcf.gz | /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/bOQqbKDDk5/regions.bed.gz .. ok test_vcf_regions: /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/bOQqbKDDk5/regions.bed.gz /tmp/bOQqbKDDk5/regions.vcf.gz .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/bOQqbKDDk5/annotate.tab.gz -h /<>/test/annotate.hdr -c CHROM,POS,REF,ALT,ID,QUAL,INFO/T_INT,INFO/T_FLOAT,INDEL /<>/test/annotate.vcf 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/bOQqbKDDk5/annotate.tab.gz -h /<>/test/annotate.hdr -c CHROM,POS,REF,ALT,ID,QUAL,INFO/T_INT,INFO/T_FLOAT,INDEL /<>/test/annotate.vcf 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/bOQqbKDDk5/annotate2.tab.gz -h /<>/test/annotate.hdr -c CHROM,FROM,TO,T_STR /<>/test/annotate.vcf 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/bOQqbKDDk5/annotate2.tab.gz -h /<>/test/annotate.hdr -c CHROM,FROM,TO,T_STR /<>/test/annotate.vcf 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/bOQqbKDDk5/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/bOQqbKDDk5/annotate.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/bOQqbKDDk5/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/bOQqbKDDk5/annotate.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/bOQqbKDDk5/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/bOQqbKDDk5/annotate2.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/bOQqbKDDk5/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/bOQqbKDDk5/annotate2.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/bOQqbKDDk5/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/bOQqbKDDk5/annotate2.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/bOQqbKDDk5/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/bOQqbKDDk5/annotate2.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -x ID,QUAL,^FILTER/fltA,FILTER/fltB,^INFO/AA,INFO/BB,^FMT/GT,FMT/PL /<>/test/annotate3.vcf 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -x ID,QUAL,^FILTER/fltA,FILTER/fltB,^INFO/AA,INFO/BB,^FMT/GT,FMT/PL /<>/test/annotate3.vcf 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -x FORMAT /<>/test/annotate3.vcf 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -x FORMAT /<>/test/annotate3.vcf 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/bOQqbKDDk5/annots4.vcf.gz -c +INFO /tmp/bOQqbKDDk5/annotate4.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/bOQqbKDDk5/annots4.vcf.gz -c +INFO /tmp/bOQqbKDDk5/annotate4.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/bOQqbKDDk5/annots4.tab.gz -h /<>/test/annotate4.hdr -c CHROM,POS,REF,ALT,+FA,+FR,+IA,+IR,+SA,+SR /<>/test/annotate4.vcf 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/bOQqbKDDk5/annots4.tab.gz -h /<>/test/annotate4.hdr -c CHROM,POS,REF,ALT,+FA,+FR,+IA,+IR,+SA,+SR /<>/test/annotate4.vcf 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/bOQqbKDDk5/annots10.tab.gz -h /<>/test/annotate10.hdr -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR /<>/test/annotate10.vcf 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/bOQqbKDDk5/annots10.tab.gz -h /<>/test/annotate10.hdr -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR /<>/test/annotate10.vcf 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/bOQqbKDDk5/annots9.tab.gz -c CHROM,POS,REF,ALT,+ID /<>/test/annotate9.vcf 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/bOQqbKDDk5/annots9.tab.gz -c CHROM,POS,REF,ALT,+ID /<>/test/annotate9.vcf 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat --no-version /tmp/bOQqbKDDk5/concat.1.a.vcf.gz /tmp/bOQqbKDDk5/concat.1.b.vcf.gz .. ok test_vcf_concat: /<>/bcftools concat -Ob /tmp/bOQqbKDDk5/concat.1.a.vcf.gz /tmp/bOQqbKDDk5/concat.1.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat --no-version /tmp/bOQqbKDDk5/concat.1.a.bcf /tmp/bOQqbKDDk5/concat.1.b.bcf .. ok test_vcf_concat: /<>/bcftools concat -Ob /tmp/bOQqbKDDk5/concat.1.a.bcf /tmp/bOQqbKDDk5/concat.1.b.bcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat --no-version -a /tmp/bOQqbKDDk5/concat.2.a.vcf.gz /tmp/bOQqbKDDk5/concat.2.b.vcf.gz .. ok test_vcf_concat: /<>/bcftools concat -Ob -a /tmp/bOQqbKDDk5/concat.2.a.vcf.gz /tmp/bOQqbKDDk5/concat.2.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat --no-version -a /tmp/bOQqbKDDk5/concat.2.a.bcf /tmp/bOQqbKDDk5/concat.2.b.bcf .. ok test_vcf_concat: /<>/bcftools concat -Ob -a /tmp/bOQqbKDDk5/concat.2.a.bcf /tmp/bOQqbKDDk5/concat.2.b.bcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat --no-version -aD /tmp/bOQqbKDDk5/concat.2.a.vcf.gz /tmp/bOQqbKDDk5/concat.2.b.vcf.gz .. ok test_vcf_concat: /<>/bcftools concat -Ob -aD /tmp/bOQqbKDDk5/concat.2.a.vcf.gz /tmp/bOQqbKDDk5/concat.2.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat --no-version -aD /tmp/bOQqbKDDk5/concat.2.a.bcf /tmp/bOQqbKDDk5/concat.2.b.bcf .. ok test_vcf_concat: /<>/bcftools concat -Ob -aD /tmp/bOQqbKDDk5/concat.2.a.bcf /tmp/bOQqbKDDk5/concat.2.b.bcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat --no-version -l /tmp/bOQqbKDDk5/concat.3.a.vcf.gz /tmp/bOQqbKDDk5/concat.3.b.vcf.gz /tmp/bOQqbKDDk5/concat.3.0.vcf.gz /tmp/bOQqbKDDk5/concat.3.c.vcf.gz /tmp/bOQqbKDDk5/concat.3.d.vcf.gz /tmp/bOQqbKDDk5/concat.3.e.vcf.gz /tmp/bOQqbKDDk5/concat.3.f.vcf.gz .. ok test_vcf_concat: /<>/bcftools concat -Ob -l /tmp/bOQqbKDDk5/concat.3.a.vcf.gz /tmp/bOQqbKDDk5/concat.3.b.vcf.gz /tmp/bOQqbKDDk5/concat.3.0.vcf.gz /tmp/bOQqbKDDk5/concat.3.c.vcf.gz /tmp/bOQqbKDDk5/concat.3.d.vcf.gz /tmp/bOQqbKDDk5/concat.3.e.vcf.gz /tmp/bOQqbKDDk5/concat.3.f.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat --no-version -l /tmp/bOQqbKDDk5/concat.3.a.bcf /tmp/bOQqbKDDk5/concat.3.b.bcf /tmp/bOQqbKDDk5/concat.3.0.bcf /tmp/bOQqbKDDk5/concat.3.c.bcf /tmp/bOQqbKDDk5/concat.3.d.bcf /tmp/bOQqbKDDk5/concat.3.e.bcf /tmp/bOQqbKDDk5/concat.3.f.bcf .. ok test_vcf_concat: /<>/bcftools concat -Ob -l /tmp/bOQqbKDDk5/concat.3.a.bcf /tmp/bOQqbKDDk5/concat.3.b.bcf /tmp/bOQqbKDDk5/concat.3.0.bcf /tmp/bOQqbKDDk5/concat.3.c.bcf /tmp/bOQqbKDDk5/concat.3.d.bcf /tmp/bOQqbKDDk5/concat.3.e.bcf /tmp/bOQqbKDDk5/concat.3.f.bcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_reheader: /<>/bcftools reheader -h /<>/test/reheader.hdr /<>/test/reheader.vcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /<>/test/reheader.vcf | /<>/bcftools reheader -h /<>/test/reheader.hdr | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -h /<>/test/reheader.hdr /tmp/bOQqbKDDk5/reheader.bcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/bOQqbKDDk5/reheader.bcf | /<>/bcftools reheader -h /<>/test/reheader.hdr | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -h /<>/test/reheader.hdr /tmp/bOQqbKDDk5/reheader.vcf.gz | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/bOQqbKDDk5/reheader.vcf.gz | /<>/bcftools reheader -h /<>/test/reheader.hdr | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -s /<>/test/reheader.samples /<>/test/reheader.vcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /<>/test/reheader.vcf | /<>/bcftools reheader -s /<>/test/reheader.samples | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -s /<>/test/reheader.samples /tmp/bOQqbKDDk5/reheader.bcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/bOQqbKDDk5/reheader.bcf | /<>/bcftools reheader -s /<>/test/reheader.samples | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -s /<>/test/reheader.samples /tmp/bOQqbKDDk5/reheader.vcf.gz | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/bOQqbKDDk5/reheader.vcf.gz | /<>/bcftools reheader -s /<>/test/reheader.samples | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -s /<>/test/reheader.samples2 /<>/test/reheader.vcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /<>/test/reheader.vcf | /<>/bcftools reheader -s /<>/test/reheader.samples2 | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -s /<>/test/reheader.samples2 /tmp/bOQqbKDDk5/reheader.bcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/bOQqbKDDk5/reheader.bcf | /<>/bcftools reheader -s /<>/test/reheader.samples2 | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -s /<>/test/reheader.samples2 /tmp/bOQqbKDDk5/reheader.vcf.gz | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/bOQqbKDDk5/reheader.vcf.gz | /<>/bcftools reheader -s /<>/test/reheader.samples2 | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -s /<>/test/reheader.samples3 /<>/test/reheader.vcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /<>/test/reheader.vcf | /<>/bcftools reheader -s /<>/test/reheader.samples3 | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -s /<>/test/reheader.samples3 /tmp/bOQqbKDDk5/reheader.bcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/bOQqbKDDk5/reheader.bcf | /<>/bcftools reheader -s /<>/test/reheader.samples3 | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -s /<>/test/reheader.samples3 /tmp/bOQqbKDDk5/reheader.vcf.gz | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/bOQqbKDDk5/reheader.vcf.gz | /<>/bcftools reheader -s /<>/test/reheader.samples3 | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -s /<>/test/reheader.samples4 /<>/test/reheader.vcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /<>/test/reheader.vcf | /<>/bcftools reheader -s /<>/test/reheader.samples4 | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -s /<>/test/reheader.samples4 /tmp/bOQqbKDDk5/reheader.bcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/bOQqbKDDk5/reheader.bcf | /<>/bcftools reheader -s /<>/test/reheader.samples4 | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -s /<>/test/reheader.samples4 /tmp/bOQqbKDDk5/reheader.vcf.gz | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/bOQqbKDDk5/reheader.vcf.gz | /<>/bcftools reheader -s /<>/test/reheader.samples4 | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -h /<>/test/reheader.empty.hdr /<>/test/empty.vcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /<>/test/empty.vcf | /<>/bcftools reheader -h /<>/test/reheader.empty.hdr | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -h /<>/test/reheader.empty.hdr /tmp/bOQqbKDDk5/empty.bcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/bOQqbKDDk5/empty.bcf | /<>/bcftools reheader -h /<>/test/reheader.empty.hdr | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -h /<>/test/reheader.empty.hdr /tmp/bOQqbKDDk5/empty.vcf.gz | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/bOQqbKDDk5/empty.vcf.gz | /<>/bcftools reheader -h /<>/test/reheader.empty.hdr | /<>/bcftools view --no-version .. ok test_rename_chrs: /<>/bcftools annotate --rename-chrs /tmp/bOQqbKDDk5/rename.map -Ov /tmp/bOQqbKDDk5/annotate.bcf | /<>/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: /<>/bcftools annotate --rename-chrs /tmp/bOQqbKDDk5/rename.map -Ob /tmp/bOQqbKDDk5/annotate.bcf | /<>/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: /<>/bcftools annotate --rename-chrs /tmp/bOQqbKDDk5/rename.map -Ov /<>/test/annotate.vcf | /<>/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: /<>/bcftools annotate --rename-chrs /tmp/bOQqbKDDk5/rename.map -Ob /<>/test/annotate.vcf | /<>/bcftools query -f'%CHROM\t%POS\n' .. ok test_vcf_convert: /<>/bcftools convert -g -,. /tmp/bOQqbKDDk5/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/bOQqbKDDk5/convert.vcf.gz | /<>/bcftools convert -g -,. 2>/dev/null .. ok test_vcf_convert: /<>/bcftools convert -g .,- /tmp/bOQqbKDDk5/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/bOQqbKDDk5/convert.vcf.gz | /<>/bcftools convert -g .,- 2>/dev/null .. ok test_vcf_convert: /<>/bcftools convert -g -,. --tag PL /tmp/bOQqbKDDk5/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/bOQqbKDDk5/convert.vcf.gz | /<>/bcftools convert -g -,. --tag PL 2>/dev/null .. ok test_vcf_convert: /<>/bcftools convert -g .,- --tag PL /tmp/bOQqbKDDk5/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/bOQqbKDDk5/convert.vcf.gz | /<>/bcftools convert -g .,- --tag PL 2>/dev/null .. ok test_vcf_convert: /<>/bcftools convert -g -,. --vcf-ids /tmp/bOQqbKDDk5/check.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/bOQqbKDDk5/check.vcf.gz | /<>/bcftools convert -g -,. --vcf-ids 2>/dev/null .. ok test_vcf_convert: /<>/bcftools convert -g .,- --vcf-ids /tmp/bOQqbKDDk5/check.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/bOQqbKDDk5/check.vcf.gz | /<>/bcftools convert -g .,- --vcf-ids 2>/dev/null .. ok test_vcf_convert: /<>/bcftools convert -g -,. --chrom /tmp/bOQqbKDDk5/check.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/bOQqbKDDk5/check.vcf.gz | /<>/bcftools convert -g -,. --chrom 2>/dev/null .. ok test_vcf_convert: /<>/bcftools convert -g .,- --chrom /tmp/bOQqbKDDk5/check.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/bOQqbKDDk5/check.vcf.gz | /<>/bcftools convert -g .,- --chrom 2>/dev/null .. ok test_vcf_convert: /<>/bcftools convert -g -,. --chrom --vcf-ids /tmp/bOQqbKDDk5/check.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/bOQqbKDDk5/check.vcf.gz | /<>/bcftools convert -g -,. --chrom --vcf-ids 2>/dev/null .. ok test_vcf_convert: /<>/bcftools convert -g .,- --chrom --vcf-ids /tmp/bOQqbKDDk5/check.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/bOQqbKDDk5/check.vcf.gz | /<>/bcftools convert -g .,- --chrom --vcf-ids 2>/dev/null .. ok test_vcf_convert: /<>/bcftools convert -h -,.,. /tmp/bOQqbKDDk5/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/bOQqbKDDk5/convert.vcf.gz | /<>/bcftools convert -h -,.,. 2>/dev/null .. ok test_vcf_convert: /<>/bcftools convert -h .,-,. /tmp/bOQqbKDDk5/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/bOQqbKDDk5/convert.vcf.gz | /<>/bcftools convert -h .,-,. 2>/dev/null .. ok test_vcf_convert: /<>/bcftools convert -h .,.,- /tmp/bOQqbKDDk5/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/bOQqbKDDk5/convert.vcf.gz | /<>/bcftools convert -h .,.,- 2>/dev/null .. ok test_vcf_convert_hls2vcf: /<>/bcftools convert -H /<>/test/convert.hls.gt.hap,/<>/test/convert.hls.gt.legend,/<>/test/convert.hls.gt.samples 2>/dev/null | grep -v ^## The outputs differ: /<>/test/convert.gt.noHead.vcf /<>/test/convert.gt.noHead.vcf.new .. failed ... test_vcf_convert_hls2vcf: /<>/bcftools convert -H /<>/test/convert.hls.gt.hap,/<>/test/convert.hls.gt.legend,/<>/test/convert.hls.gt.samples -Ou 2>/dev/null | /<>/bcftools view | grep -v ^## The outputs differ: /<>/test/convert.gt.noHead.vcf /<>/test/convert.gt.noHead.vcf.new .. failed ... test_vcf_convert_hs2vcf: /<>/bcftools convert --hapsample2vcf /<>/test/convert.hs.gt.hap,/<>/test/convert.hs.gt.samples 2>/dev/null | grep -v ^## The outputs differ: /<>/test/convert.gt.noHead.vcf /<>/test/convert.gt.noHead.vcf.new .. failed ... test_vcf_convert_hs2vcf: /<>/bcftools convert --hapsample2vcf /<>/test/convert.hs.gt.hap,/<>/test/convert.hs.gt.samples -Ou 2>/dev/null | /<>/bcftools view | grep -v ^## The outputs differ: /<>/test/convert.gt.noHead.vcf /<>/test/convert.gt.noHead.vcf.new .. failed ... test_vcf_convert: /<>/bcftools convert --hapsample -,. /tmp/bOQqbKDDk5/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/bOQqbKDDk5/convert.vcf.gz | /<>/bcftools convert --hapsample -,. 2>/dev/null .. ok test_vcf_convert: /<>/bcftools convert --hapsample .,- /tmp/bOQqbKDDk5/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/bOQqbKDDk5/convert.vcf.gz | /<>/bcftools convert --hapsample .,- 2>/dev/null .. ok test_vcf_convert_gvcf: /<>/bcftools convert --no-version --gvcf2vcf -f /<>/test/gvcf.fa /tmp/bOQqbKDDk5/convert.gvcf.vcf.gz 2>/dev/null .. ok test_vcf_convert_gvcf: /<>/bcftools view -Ob /tmp/bOQqbKDDk5/convert.gvcf.vcf.gz | /<>/bcftools convert --gvcf2vcf -f /<>/test/gvcf.fa 2>/dev/null | grep -v ^##bcftools .. ok test_vcf_convert_tsv2vcf: /<>/bcftools convert --no-version -c ID,CHROM,POS,AA -s SAMPLE1 -f /<>/test/23andme.fa --tsv2vcf /<>/test/convert.23andme 2>/dev/null .. ok test_vcf_convert_tsv2vcf: /<>/bcftools convert -Ou -c ID,CHROM,POS,AA -s SAMPLE1 -f /<>/test/23andme.fa --tsv2vcf /<>/test/convert.23andme 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/bOQqbKDDk5/consensus.vcf.gz -f /<>/test/consensus.fa -m /<>/test/consensus.tab 2>/dev/null .. ok test_vcf_consensus_chain: /<>/bcftools consensus /tmp/bOQqbKDDk5/consensus.vcf.gz -f /<>/test/consensus.fa -m /<>/test/consensus.tab -c /tmp/bOQqbKDDk5/consensus.1.chain.new > /dev/null 2>/dev/null; cat /tmp/bOQqbKDDk5/consensus.1.chain.new .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/bOQqbKDDk5/consensus.vcf.gz -f /<>/test/consensus.fa -H 1 -m /<>/test/consensus.tab 2>/dev/null .. ok test_vcf_consensus_chain: /<>/bcftools consensus /tmp/bOQqbKDDk5/consensus.vcf.gz -f /<>/test/consensus.fa -H 1 -m /<>/test/consensus.tab -c /tmp/bOQqbKDDk5/consensus.2.chain.new > /dev/null 2>/dev/null; cat /tmp/bOQqbKDDk5/consensus.2.chain.new .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/bOQqbKDDk5/consensus.vcf.gz -f /<>/test/consensus.fa -i -m /<>/test/consensus.tab 2>/dev/null .. ok test_vcf_consensus_chain: /<>/bcftools consensus /tmp/bOQqbKDDk5/consensus.vcf.gz -f /<>/test/consensus.fa -i -m /<>/test/consensus.tab -c /tmp/bOQqbKDDk5/consensus.3.chain.new > /dev/null 2>/dev/null; cat /tmp/bOQqbKDDk5/consensus.3.chain.new .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/bOQqbKDDk5/consensus.vcf.gz -f /<>/test/consensus.fa -H 1 2>/dev/null .. ok test_vcf_consensus_chain: /<>/bcftools consensus /tmp/bOQqbKDDk5/consensus.vcf.gz -f /<>/test/consensus.fa -H 1 -c /tmp/bOQqbKDDk5/consensus.4.chain.new > /dev/null 2>/dev/null; cat /tmp/bOQqbKDDk5/consensus.4.chain.new .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/bOQqbKDDk5/consensus2.vcf.gz -f /<>/test/consensus2.fa -H 1 2>/dev/null .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/bOQqbKDDk5/consensus2.vcf.gz -f /<>/test/consensus2.fa -H 2 2>/dev/null .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/bOQqbKDDk5/empty.vcf.gz -f /<>/test/consensus.fa 2>/dev/null .. ok Number of tests: total .. 410 passed .. 400 failed .. 10 Makefile:102: recipe for target 'test' failed make[1]: *** [test] Error 1 make[1]: Leaving directory '/<>' dh_auto_test: make -j4 test returned exit code 2 debian/rules:11: recipe for target 'build-arch' failed make: *** [build-arch] Error 2 dpkg-buildpackage: error: debian/rules build-arch gave error exit status 2 -------------------------------------------------------------------------------- Build finished at 20161010-0625 Finished -------- E: Build failure (dpkg-buildpackage died) +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Not removing build depends: as requested Keeping session: +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: s390x Build-Space: 14148 Build-Time: 11 Distribution: yakkety Fail-Stage: build Host Architecture: s390x Install-Time: 19 Job: bcftools_1.3.1-1.dsc Machine Architecture: s390x Package: bcftools Package-Time: 30 Source-Version: 1.3.1-1 Space: 14148 Status: attempted Version: 1.3.1-1 -------------------------------------------------------------------------------- Finished at 20161010-0625 Build needed 00:00:30, 14148k disc space RUN: /usr/share/launchpad-buildd/slavebin/scan-for-processes ['scan-for-processes', 'PACKAGEBUILD-10765800'] Scanning for processes to kill in build /home/buildd/build-PACKAGEBUILD-10765800/chroot-autobuild... RUN: /usr/share/launchpad-buildd/slavebin/umount-chroot ['umount-chroot', 'PACKAGEBUILD-10765800'] Unmounting chroot for build PACKAGEBUILD-10765800... RUN: /usr/share/launchpad-buildd/slavebin/remove-build ['remove-build', 'PACKAGEBUILD-10765800'] Removing build PACKAGEBUILD-10765800