RUN: /usr/share/launchpad-buildd/slavebin/slave-prep ['slave-prep'] Forking launchpad-buildd slave process... Kernel version: Linux z13-015 4.4.0-64-generic #85-Ubuntu SMP Mon Feb 20 11:55:38 UTC 2017 s390x Buildd toolchain package versions: launchpad-buildd_142 python-lpbuildd_142 sbuild_0.67.0-2ubuntu7 dpkg-dev_1.18.4ubuntu1.1 python-debian_0.1.27ubuntu2 qemu-user-static_1:2.5+dfsg-5ubuntu10.9. Syncing the system clock with the buildd NTP service... 9 Apr 01:03:07 ntpdate[22972]: adjust time server 10.211.37.1 offset -0.000624 sec RUN: /usr/share/launchpad-buildd/slavebin/unpack-chroot ['unpack-chroot', 'PACKAGEBUILD-11749295', '/home/buildd/filecache-default/309330829b4f61930f4191d7be733906953ac6c4'] Unpacking chroot for build PACKAGEBUILD-11749295 RUN: /usr/share/launchpad-buildd/slavebin/mount-chroot ['mount-chroot', 'PACKAGEBUILD-11749295'] Mounting chroot for build PACKAGEBUILD-11749295 RUN: /usr/share/launchpad-buildd/slavebin/override-sources-list ['override-sources-list', 'PACKAGEBUILD-11749295', 'deb http://ftpmaster.internal/ubuntu zesty main universe'] Overriding sources.list in build-PACKAGEBUILD-11749295 RUN: /usr/share/launchpad-buildd/slavebin/update-debian-chroot ['update-debian-chroot', 'PACKAGEBUILD-11749295', 's390x'] Updating debian chroot for build PACKAGEBUILD-11749295 Get:1 http://ftpmaster.internal/ubuntu zesty InRelease [243 kB] Get:2 http://ftpmaster.internal/ubuntu zesty/main s390x Packages [1135 kB] Get:3 http://ftpmaster.internal/ubuntu zesty/main Translation-en [576 kB] Get:4 http://ftpmaster.internal/ubuntu zesty/universe s390x Packages [7767 kB] Get:5 http://ftpmaster.internal/ubuntu zesty/universe Translation-en [4679 kB] Fetched 14.4 MB in 14s (970 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: libperl5.22 perl-modules-5.22 Use 'sudo apt autoremove' to remove them. The following NEW packages will be installed: libidn2-0 libldap-common libperl5.24 libpsl5 libunistring0 perl-modules-5.24 The following packages will be upgraded: adduser apt apt-transport-https base-files base-passwd bash binutils bsdutils bzip2 ca-certificates coreutils cpp cpp-6 debianutils diffutils dmsetup e2fslibs e2fsprogs findutils g++ g++-6 gcc gcc-6 gcc-6-base gnupg gnupg-agent gpgv grep init init-system-helpers libapparmor1 libapt-pkg5.0 libasn1-8-heimdal libassuan0 libatomic1 libblkid1 libbz2-1.0 libc-bin libc-dev-bin libc6 libc6-dev libcc1-0 libcomerr2 libcurl3-gnutls libdevmapper1.02.1 libfdisk1 libgcc-6-dev libgcc1 libgcrypt20 libgmp10 libgnutls30 libgomp1 libgpg-error0 libgssapi-krb5-2 libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhogweed4 libhx509-5-heimdal libisl15 libitm1 libk5crypto3 libkrb5-26-heimdal libkrb5-3 libkrb5support0 libksba8 libldap-2.4-2 liblockfile-bin liblockfile1 liblzma5 libmount1 libnettle6 libnpth0 libp11-kit0 libpcre3 libpng16-16 libroken18-heimdal libsasl2-2 libsasl2-modules-db libseccomp2 libselinux1 libsemanage-common libsemanage1 libsepol1 libslang2 libsmartcols1 libsqlite3-0 libss2 libssl1.0.0 libstdc++-6-dev libstdc++6 libsystemd0 libtasn1-6 libudev1 libustr-1.0-1 libuuid1 libwind0-heimdal linux-libc-dev make mount multiarch-support openssl perl perl-base pinentry-curses pkg-create-dbgsym sed systemd systemd-sysv tar tzdata ubuntu-keyring util-linux xz-utils zlib1g 116 upgraded, 6 newly installed, 0 to remove and 0 not upgraded. Need to get 52.2 MB of archives. After this operation, 43.1 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu zesty/main s390x perl-modules-5.24 all 5.24.1-2ubuntu1 [2663 kB] Get:2 http://ftpmaster.internal/ubuntu zesty/main s390x libperl5.24 s390x 5.24.1-2ubuntu1 [3301 kB] Get:3 http://ftpmaster.internal/ubuntu zesty/main s390x perl s390x 5.24.1-2ubuntu1 [218 kB] Get:4 http://ftpmaster.internal/ubuntu zesty/main s390x perl-base s390x 5.24.1-2ubuntu1 [1271 kB] Get:5 http://ftpmaster.internal/ubuntu zesty/main s390x libc6-dev s390x 2.24-9ubuntu2 [2058 kB] Get:6 http://ftpmaster.internal/ubuntu zesty/main s390x libc-dev-bin s390x 2.24-9ubuntu2 [62.4 kB] Get:7 http://ftpmaster.internal/ubuntu zesty/main s390x linux-libc-dev s390x 4.10.0-19.21 [902 kB] Get:8 http://ftpmaster.internal/ubuntu zesty/main s390x libgomp1 s390x 6.3.0-12ubuntu2 [71.1 kB] Get:9 http://ftpmaster.internal/ubuntu zesty/main s390x libitm1 s390x 6.3.0-12ubuntu2 [27.3 kB] Get:10 http://ftpmaster.internal/ubuntu zesty/main s390x gcc-6-base s390x 6.3.0-12ubuntu2 [17.4 kB] Get:11 http://ftpmaster.internal/ubuntu zesty/main s390x libgcc1 s390x 1:6.3.0-12ubuntu2 [24.6 kB] Get:12 http://ftpmaster.internal/ubuntu zesty/main s390x libcc1-0 s390x 6.3.0-12ubuntu2 [31.0 kB] Get:13 http://ftpmaster.internal/ubuntu zesty/main s390x binutils s390x 2.28-3ubuntu1 [1073 kB] Get:14 http://ftpmaster.internal/ubuntu zesty/main s390x libatomic1 s390x 6.3.0-12ubuntu2 [8192 B] Get:15 http://ftpmaster.internal/ubuntu zesty/main s390x g++-6 s390x 6.3.0-12ubuntu2 [5831 kB] Get:16 http://ftpmaster.internal/ubuntu zesty/main s390x libstdc++-6-dev s390x 6.3.0-12ubuntu2 [1421 kB] Get:17 http://ftpmaster.internal/ubuntu zesty/main s390x libgcc-6-dev s390x 6.3.0-12ubuntu2 [269 kB] Get:18 http://ftpmaster.internal/ubuntu zesty/main s390x gcc-6 s390x 6.3.0-12ubuntu2 [5668 kB] Get:19 http://ftpmaster.internal/ubuntu zesty/main s390x cpp-6 s390x 6.3.0-12ubuntu2 [5073 kB] Get:20 http://ftpmaster.internal/ubuntu zesty/main s390x libstdc++6 s390x 6.3.0-12ubuntu2 [404 kB] Get:21 http://ftpmaster.internal/ubuntu zesty/main s390x zlib1g s390x 1:1.2.11.dfsg-0ubuntu1 [51.6 kB] Get:22 http://ftpmaster.internal/ubuntu zesty/main s390x libgmp10 s390x 2:6.1.2+dfsg-1 [227 kB] Get:23 http://ftpmaster.internal/ubuntu zesty/main s390x libisl15 s390x 0.18-1 [510 kB] Get:24 http://ftpmaster.internal/ubuntu zesty/main s390x libc6 s390x 2.24-9ubuntu2 [2309 kB] Get:25 http://ftpmaster.internal/ubuntu zesty/main s390x bzip2 s390x 1.0.6-8.1 [33.1 kB] Get:26 http://ftpmaster.internal/ubuntu zesty/main s390x libbz2-1.0 s390x 1.0.6-8.1 [31.6 kB] Get:27 http://ftpmaster.internal/ubuntu zesty/main s390x init-system-helpers all 1.47 [37.8 kB] Get:28 http://ftpmaster.internal/ubuntu zesty/main s390x base-files s390x 9.6ubuntu12 [59.0 kB] Get:29 http://ftpmaster.internal/ubuntu zesty/main s390x debianutils s390x 4.8.1 [85.8 kB] Get:30 http://ftpmaster.internal/ubuntu zesty/main s390x bash s390x 4.4-2ubuntu1 [595 kB] Get:31 http://ftpmaster.internal/ubuntu zesty/main s390x bsdutils s390x 1:2.29-1ubuntu2 [54.8 kB] Get:32 http://ftpmaster.internal/ubuntu zesty/main s390x coreutils s390x 8.26-3ubuntu3 [1200 kB] Get:33 http://ftpmaster.internal/ubuntu zesty/main s390x diffutils s390x 1:3.5-3 [164 kB] Get:34 http://ftpmaster.internal/ubuntu zesty/main s390x e2fslibs s390x 1.43.4-2 [151 kB] Get:35 http://ftpmaster.internal/ubuntu zesty/main s390x e2fsprogs s390x 1.43.4-2 [473 kB] Get:36 http://ftpmaster.internal/ubuntu zesty/main s390x findutils s390x 4.6.0+git+20161106-2 [277 kB] Get:37 http://ftpmaster.internal/ubuntu zesty/main s390x grep s390x 2.27-2 [148 kB] Get:38 http://ftpmaster.internal/ubuntu zesty/main s390x libuuid1 s390x 2.29-1ubuntu2 [14.9 kB] Get:39 http://ftpmaster.internal/ubuntu zesty/main s390x libblkid1 s390x 2.29-1ubuntu2 [104 kB] Get:40 http://ftpmaster.internal/ubuntu zesty/main s390x libfdisk1 s390x 2.29-1ubuntu2 [134 kB] Get:41 http://ftpmaster.internal/ubuntu zesty/main s390x libpcre3 s390x 2:8.39-3 [154 kB] Get:42 http://ftpmaster.internal/ubuntu zesty/main s390x libselinux1 s390x 2.6-3 [64.5 kB] Get:43 http://ftpmaster.internal/ubuntu zesty/main s390x util-linux s390x 2.29-1ubuntu2 [888 kB] Get:44 http://ftpmaster.internal/ubuntu zesty/main s390x mount s390x 2.29-1ubuntu2 [127 kB] Get:45 http://ftpmaster.internal/ubuntu zesty/main s390x sed s390x 4.4-1 [181 kB] Get:46 http://ftpmaster.internal/ubuntu zesty/main s390x tar s390x 1.29b-1.1 [222 kB] Get:47 http://ftpmaster.internal/ubuntu zesty/main s390x base-passwd s390x 3.5.43 [47.6 kB] Get:48 http://ftpmaster.internal/ubuntu zesty/main s390x libc-bin s390x 2.24-9ubuntu2 [542 kB] Get:49 http://ftpmaster.internal/ubuntu zesty/main s390x liblzma5 s390x 5.2.2-1.2 [90.8 kB] Get:50 http://ftpmaster.internal/ubuntu zesty/main s390x libapt-pkg5.0 s390x 1.4 [730 kB] Get:51 http://ftpmaster.internal/ubuntu zesty/main s390x adduser all 3.113+nmu3ubuntu5 [161 kB] Get:52 http://ftpmaster.internal/ubuntu zesty/main s390x libgpg-error0 s390x 1.26-2 [33.5 kB] Get:53 http://ftpmaster.internal/ubuntu zesty/main s390x libgcrypt20 s390x 1.7.6-1 [338 kB] Get:54 http://ftpmaster.internal/ubuntu zesty/main s390x gpgv s390x 2.1.15-1ubuntu7 [171 kB] Get:55 http://ftpmaster.internal/ubuntu zesty/main s390x ubuntu-keyring all 2016.10.27 [16.6 kB] Get:56 http://ftpmaster.internal/ubuntu zesty/main s390x apt s390x 1.4 [1072 kB] Get:57 http://ftpmaster.internal/ubuntu zesty/main s390x libapparmor1 s390x 2.11.0-2ubuntu3 [30.2 kB] Get:58 http://ftpmaster.internal/ubuntu zesty/main s390x libmount1 s390x 2.29-1ubuntu2 [111 kB] Get:59 http://ftpmaster.internal/ubuntu zesty/main s390x libseccomp2 s390x 2.3.1-2.1ubuntu1 [38.9 kB] Get:60 http://ftpmaster.internal/ubuntu zesty/main s390x systemd s390x 232-21ubuntu2 [2254 kB] Get:61 http://ftpmaster.internal/ubuntu zesty/main s390x libsystemd0 s390x 232-21ubuntu2 [192 kB] Get:62 http://ftpmaster.internal/ubuntu zesty/main s390x init s390x 1.47 [5832 B] Get:63 http://ftpmaster.internal/ubuntu zesty/main s390x systemd-sysv s390x 232-21ubuntu2 [12.6 kB] Get:64 http://ftpmaster.internal/ubuntu zesty/main s390x liblockfile-bin s390x 1.14-1 [11.0 kB] Get:65 http://ftpmaster.internal/ubuntu zesty/main s390x liblockfile1 s390x 1.14-1 [6198 B] Get:66 http://ftpmaster.internal/ubuntu zesty/main s390x libcomerr2 s390x 1.43.4-2 [9328 B] Get:67 http://ftpmaster.internal/ubuntu zesty/main s390x libsepol1 s390x 2.6-2 [200 kB] Get:68 http://ftpmaster.internal/ubuntu zesty/main s390x libustr-1.0-1 s390x 1.0.4-6 [60.0 kB] Get:69 http://ftpmaster.internal/ubuntu zesty/main s390x libsemanage-common all 2.6-2 [6794 B] Get:70 http://ftpmaster.internal/ubuntu zesty/main s390x libsemanage1 s390x 2.6-2 [76.5 kB] Get:71 http://ftpmaster.internal/ubuntu zesty/main s390x libsmartcols1 s390x 2.29-1ubuntu2 [66.0 kB] Get:72 http://ftpmaster.internal/ubuntu zesty/main s390x libss2 s390x 1.43.4-2 [10.8 kB] Get:73 http://ftpmaster.internal/ubuntu zesty/main s390x libudev1 s390x 232-21ubuntu2 [52.4 kB] Get:74 http://ftpmaster.internal/ubuntu zesty/main s390x multiarch-support s390x 2.24-9ubuntu2 [6816 B] Get:75 http://ftpmaster.internal/ubuntu zesty/main s390x libdevmapper1.02.1 s390x 2:1.02.136-1ubuntu5 [123 kB] Get:76 http://ftpmaster.internal/ubuntu zesty/main s390x dmsetup s390x 2:1.02.136-1ubuntu5 [68.8 kB] Get:77 http://ftpmaster.internal/ubuntu zesty/main s390x libassuan0 s390x 2.4.3-2 [32.0 kB] Get:78 http://ftpmaster.internal/ubuntu zesty/main s390x pinentry-curses s390x 1.0.0-2 [32.0 kB] Get:79 http://ftpmaster.internal/ubuntu zesty/main s390x libnpth0 s390x 1.3-1 [7906 B] Get:80 http://ftpmaster.internal/ubuntu zesty/main s390x gnupg s390x 2.1.15-1ubuntu7 [736 kB] Get:81 http://ftpmaster.internal/ubuntu zesty/main s390x gnupg-agent s390x 2.1.15-1ubuntu7 [233 kB] Get:82 http://ftpmaster.internal/ubuntu zesty/main s390x libksba8 s390x 1.3.5-2 [86.3 kB] Get:83 http://ftpmaster.internal/ubuntu zesty/main s390x libsqlite3-0 s390x 3.16.2-3 [457 kB] Get:84 http://ftpmaster.internal/ubuntu zesty/main s390x libroken18-heimdal s390x 7.1.0+dfsg-9ubuntu1 [39.1 kB] Get:85 http://ftpmaster.internal/ubuntu zesty/main s390x libasn1-8-heimdal s390x 7.1.0+dfsg-9ubuntu1 [149 kB] Get:86 http://ftpmaster.internal/ubuntu zesty/main s390x libhogweed4 s390x 3.3-1 [134 kB] Get:87 http://ftpmaster.internal/ubuntu zesty/main s390x libnettle6 s390x 3.3-1 [104 kB] Get:88 http://ftpmaster.internal/ubuntu zesty/main s390x libp11-kit0 s390x 0.23.3-5 [97.8 kB] Get:89 http://ftpmaster.internal/ubuntu zesty/main s390x libtasn1-6 s390x 4.10-1 [33.7 kB] Get:90 http://ftpmaster.internal/ubuntu zesty/main s390x libgnutls30 s390x 3.5.6-4ubuntu4 [543 kB] Get:91 http://ftpmaster.internal/ubuntu zesty/main s390x libheimbase1-heimdal s390x 7.1.0+dfsg-9ubuntu1 [27.6 kB] Get:92 http://ftpmaster.internal/ubuntu zesty/main s390x libhcrypto4-heimdal s390x 7.1.0+dfsg-9ubuntu1 [82.9 kB] Get:93 http://ftpmaster.internal/ubuntu zesty/main s390x libwind0-heimdal s390x 7.1.0+dfsg-9ubuntu1 [47.8 kB] Get:94 http://ftpmaster.internal/ubuntu zesty/main s390x libhx509-5-heimdal s390x 7.1.0+dfsg-9ubuntu1 [98.8 kB] Get:95 http://ftpmaster.internal/ubuntu zesty/main s390x libkrb5-26-heimdal s390x 7.1.0+dfsg-9ubuntu1 [190 kB] Get:96 http://ftpmaster.internal/ubuntu zesty/main s390x libheimntlm0-heimdal s390x 7.1.0+dfsg-9ubuntu1 [14.5 kB] Get:97 http://ftpmaster.internal/ubuntu zesty/main s390x libgssapi3-heimdal s390x 7.1.0+dfsg-9ubuntu1 [87.6 kB] Get:98 http://ftpmaster.internal/ubuntu zesty/main s390x libsasl2-modules-db s390x 2.1.27~101-g0780600+dfsg-2ubuntu1 [13.9 kB] Get:99 http://ftpmaster.internal/ubuntu zesty/main s390x libsasl2-2 s390x 2.1.27~101-g0780600+dfsg-2ubuntu1 [46.7 kB] Get:100 http://ftpmaster.internal/ubuntu zesty/main s390x libldap-common all 2.4.44+dfsg-3ubuntu2 [16.8 kB] Get:101 http://ftpmaster.internal/ubuntu zesty/main s390x libldap-2.4-2 s390x 2.4.44+dfsg-3ubuntu2 [145 kB] Get:102 http://ftpmaster.internal/ubuntu zesty/main s390x libslang2 s390x 2.3.1-5ubuntu1 [413 kB] Get:103 http://ftpmaster.internal/ubuntu zesty/main s390x libssl1.0.0 s390x 1.0.2g-1ubuntu11 [776 kB] Get:104 http://ftpmaster.internal/ubuntu zesty/main s390x tzdata all 2017b-1 [203 kB] Get:105 http://ftpmaster.internal/ubuntu zesty/main s390x xz-utils s390x 5.2.2-1.2 [82.1 kB] Get:106 http://ftpmaster.internal/ubuntu zesty/main s390x libgssapi-krb5-2 s390x 1.15-1 [109 kB] Get:107 http://ftpmaster.internal/ubuntu zesty/main s390x libkrb5-3 s390x 1.15-1 [259 kB] Get:108 http://ftpmaster.internal/ubuntu zesty/main s390x libkrb5support0 s390x 1.15-1 [31.3 kB] Get:109 http://ftpmaster.internal/ubuntu zesty/main s390x libk5crypto3 s390x 1.15-1 [83.8 kB] Get:110 http://ftpmaster.internal/ubuntu zesty/main s390x libunistring0 s390x 0.9.3-5.2ubuntu1 [262 kB] Get:111 http://ftpmaster.internal/ubuntu zesty/main s390x libidn2-0 s390x 0.16-1 [47.8 kB] Get:112 http://ftpmaster.internal/ubuntu zesty/main s390x libpsl5 s390x 0.17.0-4 [39.3 kB] Get:113 http://ftpmaster.internal/ubuntu zesty/main s390x libcurl3-gnutls s390x 7.52.1-3ubuntu1 [178 kB] Get:114 http://ftpmaster.internal/ubuntu zesty/main s390x apt-transport-https s390x 1.4 [36.7 kB] Get:115 http://ftpmaster.internal/ubuntu zesty/main s390x openssl s390x 1.0.2g-1ubuntu11 [477 kB] Get:116 http://ftpmaster.internal/ubuntu zesty/main s390x ca-certificates all 20161130 [193 kB] Get:117 http://ftpmaster.internal/ubuntu zesty/main s390x libpng16-16 s390x 1.6.28-1 [169 kB] Get:118 http://ftpmaster.internal/ubuntu zesty/main s390x cpp s390x 4:6.3.0-2ubuntu1 [27.5 kB] Get:119 http://ftpmaster.internal/ubuntu zesty/main s390x gcc s390x 4:6.3.0-2ubuntu1 [5188 B] Get:120 http://ftpmaster.internal/ubuntu zesty/main s390x g++ s390x 4:6.3.0-2ubuntu1 [1478 B] Get:121 http://ftpmaster.internal/ubuntu zesty/main s390x make s390x 4.1-9.1 [148 kB] Get:122 http://ftpmaster.internal/ubuntu zesty/main s390x pkg-create-dbgsym all 0.73 [8952 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 52.2 MB in 44s (1163 kB/s) (Reading database ... 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Setting up libc6:s390x (2.24-9ubuntu2) ... (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 ... 13874 files and directories currently installed.) Preparing to unpack .../0-bzip2_1.0.6-8.1_s390x.deb ... Unpacking bzip2 (1.0.6-8.1) over (1.0.6-8build1) ... Preparing to unpack .../1-libbz2-1.0_1.0.6-8.1_s390x.deb ... Unpacking libbz2-1.0:s390x (1.0.6-8.1) over (1.0.6-8build1) ... Setting up libbz2-1.0:s390x (1.0.6-8.1) ... (Reading database ... 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Created symlink /etc/systemd/system/timers.target.wants/motd-news.timer -> /lib/systemd/system/motd-news.timer. (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 ... 13878 files and directories currently installed.) Preparing to unpack .../debianutils_4.8.1_s390x.deb ... Unpacking debianutils (4.8.1) over (4.8) ... Setting up debianutils (4.8.1) ... (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 ... 13875 files and directories currently installed.) Preparing to unpack .../libc-bin_2.24-9ubuntu2_s390x.deb ... Unpacking libc-bin (2.24-9ubuntu2) over (2.24-3ubuntu1) ... Setting up libc-bin (2.24-9ubuntu2) ... Updating /etc/nsswitch.conf to current default. (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 ... 13875 files and directories currently installed.) Preparing to unpack .../adduser_3.113+nmu3ubuntu5_all.deb ... Unpacking adduser (3.113+nmu3ubuntu5) over (3.113+nmu3ubuntu4) ... Setting up adduser (3.113+nmu3ubuntu5) ... (Reading database ... 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Setting up libperl5.24:s390x (5.24.1-2ubuntu1) ... Setting up libnettle6:s390x (3.3-1) ... Setting up liblockfile-bin (1.14-1) ... Setting up libcc1-0:s390x (6.3.0-12ubuntu2) ... Setting up make (4.1-9.1) ... Setting up libssl1.0.0:s390x (1.0.2g-1ubuntu11) ... Setting up libpng16-16:s390x (1.6.28-1) ... Setting up libldap-common (2.4.44+dfsg-3ubuntu2) ... Setting up tzdata (2017b-1) ... Current default time zone: 'Etc/UTC' Local time is now: Sun Apr 9 01:04:25 UTC 2017. Universal Time is now: Sun Apr 9 01:04:25 UTC 2017. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up systemd-sysv (232-21ubuntu2) ... Setting up liblockfile1:s390x (1.14-1) ... Setting up libsasl2-modules-db:s390x (2.1.27~101-g0780600+dfsg-2ubuntu1) ... Setting up linux-libc-dev:s390x (4.10.0-19.21) ... Setting up libsasl2-2:s390x (2.1.27~101-g0780600+dfsg-2ubuntu1) ... Setting up libroken18-heimdal:s390x (7.1.0+dfsg-9ubuntu1) ... Setting up libksba8:s390x (1.3.5-2) ... Setting up libdevmapper1.02.1:s390x (2:1.02.136-1ubuntu5) ... Setting up libkrb5support0:s390x (1.15-1) ... Setting up libtasn1-6:s390x (4.10-1) ... Setting up bzip2 (1.0.6-8.1) ... Setting up perl (5.24.1-2ubuntu1) ... Installing new version of config file /etc/perl/sitecustomize.pl ... Setting up libgmp10:s390x (2:6.1.2+dfsg-1) ... Processing triggers for libc-bin (2.24-9ubuntu2) ... Setting up pkg-create-dbgsym (0.73) ... Setting up libunistring0:s390x (0.9.3-5.2ubuntu1) ... Setting up xz-utils (5.2.2-1.2) ... Setting up libheimbase1-heimdal:s390x (7.1.0+dfsg-9ubuntu1) ... Setting up libp11-kit0:s390x (0.23.3-5) ... Setting up openssl (1.0.2g-1ubuntu11) ... Setting up libsqlite3-0:s390x (3.16.2-3) ... Setting up dmsetup (2:1.02.136-1ubuntu5) ... Setting up binutils (2.28-3ubuntu1) ... Setting up libc-dev-bin (2.24-9ubuntu2) ... Setting up ca-certificates (20161130) ... Updating certificates in /etc/ssl/certs... 10 added, 10 removed; done. Setting up libc6-dev:s390x (2.24-9ubuntu2) ... Setting up libslang2:s390x (2.3.1-5ubuntu1) ... Setting up libassuan0:s390x (2.4.3-2) ... Setting up libitm1:s390x (6.3.0-12ubuntu2) ... Setting up libk5crypto3:s390x (1.15-1) ... Setting up libgcc-6-dev:s390x (6.3.0-12ubuntu2) ... Setting up libidn2-0:s390x (0.16-1) ... Setting up libstdc++-6-dev:s390x (6.3.0-12ubuntu2) ... Setting up libwind0-heimdal:s390x (7.1.0+dfsg-9ubuntu1) ... Setting up libpsl5:s390x (0.17.0-4) ... Setting up init (1.47) ... Setting up libasn1-8-heimdal:s390x (7.1.0+dfsg-9ubuntu1) ... Setting up libhcrypto4-heimdal:s390x (7.1.0+dfsg-9ubuntu1) ... Setting up libhx509-5-heimdal:s390x (7.1.0+dfsg-9ubuntu1) ... Setting up libhogweed4:s390x (3.3-1) ... Setting up libisl15:s390x (0.18-1) ... Setting up pinentry-curses (1.0.0-2) ... Setting up libkrb5-3:s390x (1.15-1) ... Setting up cpp-6 (6.3.0-12ubuntu2) ... Setting up libkrb5-26-heimdal:s390x (7.1.0+dfsg-9ubuntu1) ... Setting up gnupg-agent (2.1.15-1ubuntu7) ... Setting up libheimntlm0-heimdal:s390x (7.1.0+dfsg-9ubuntu1) ... Setting up cpp (4:6.3.0-2ubuntu1) ... Setting up gnupg (2.1.15-1ubuntu7) ... Setting up libgnutls30:s390x (3.5.6-4ubuntu4) ... Setting up gcc-6 (6.3.0-12ubuntu2) ... Setting up libgssapi-krb5-2:s390x (1.15-1) ... Setting up g++-6 (6.3.0-12ubuntu2) ... Setting up libgssapi3-heimdal:s390x (7.1.0+dfsg-9ubuntu1) ... Setting up gcc (4:6.3.0-2ubuntu1) ... Setting up libldap-2.4-2:s390x (2.4.44+dfsg-3ubuntu2) ... Setting up g++ (4:6.3.0-2ubuntu1) ... Setting up libcurl3-gnutls:s390x (7.52.1-3ubuntu1) ... Setting up apt-transport-https (1.4) ... Processing triggers for libc-bin (2.24-9ubuntu2) ... Processing triggers for ca-certificates (20161130) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package ['sbuild-package', 'PACKAGEBUILD-11749295', 's390x', 'zesty', '-c', 'chroot:autobuild', '--arch=s390x', '--dist=zesty', '--purge=never', '--nolog', 'bcftools_1.3.1-1.dsc'] Initiating build PACKAGEBUILD-11749295 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.4.0-64-generic #85-Ubuntu SMP Mon Feb 20 11:55:38 UTC 2017 s390x sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on z13-015.buildd +==============================================================================+ | bcftools 1.3.1-1 (s390x) 09 Apr 2017 01:04 | +==============================================================================+ Package: bcftools Version: 1.3.1-1 Source Version: 1.3.1-1 Distribution: zesty Machine Architecture: s390x Host Architecture: s390x Build Architecture: s390x I: NOTICE: Log filtering will replace 'build/bcftools-xQB9zQ/bcftools-1.3.1' with '<>' I: NOTICE: Log filtering will replace 'build/bcftools-xQB9zQ' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-11749295/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-4E_3Jp/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/<>/resolver-4E_3Jp/apt_archive ./ InRelease Get:2 copy:/<>/resolver-4E_3Jp/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-4E_3Jp/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-4E_3Jp/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-4E_3Jp/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: libperl5.22 perl-modules-5.22 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-4E_3Jp/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 ... 13918 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-SK_UKp/apt_archive/sbuild-build-depends-bcftools-dummy.deb'. Ign:1 copy:/<>/resolver-SK_UKp/apt_archive ./ InRelease Get:2 copy:/<>/resolver-SK_UKp/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-SK_UKp/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-SK_UKp/apt_archive ./ Sources [248 B] Get:5 copy:/<>/resolver-SK_UKp/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: libperl5.22 perl-modules-5.22 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 libbsd0 libcroco3 libfile-stripnondeterminism-perl libglib2.0-0 libgsl-dev libgsl2 libhts-dev libhts1 libicu57 libio-pty-perl libmagic-mgc libmagic1 libpipeline1 libsigsegv2 libtimedate-perl libtool 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 m4-doc 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 libbsd0 libcroco3 libfile-stripnondeterminism-perl libglib2.0-0 libgsl-dev libgsl2 libhts-dev libhts1 libicu57 libio-pty-perl libmagic-mgc libmagic1 libpipeline1 libsigsegv2 libtimedate-perl libtool libxml2 m4 man-db po-debconf sbuild-build-depends-bcftools-dummy tabix zlib1g-dev 0 upgraded, 37 newly installed, 0 to remove and 0 not upgraded. Need to get 18.4 MB of archives. After this operation, 75.1 MB of additional disk space will be used. Get:1 copy:/<>/resolver-SK_UKp/apt_archive ./ sbuild-build-depends-bcftools-dummy 0.invalid.0 [812 B] Get:2 http://ftpmaster.internal/ubuntu zesty/main s390x groff-base s390x 1.22.3-9 [1174 kB] Get:3 http://ftpmaster.internal/ubuntu zesty/main s390x libbsd0 s390x 0.8.3-1 [40.6 kB] Get:4 http://ftpmaster.internal/ubuntu zesty/main s390x bsdmainutils s390x 9.0.12ubuntu1 [179 kB] Get:5 http://ftpmaster.internal/ubuntu zesty/main s390x libpipeline1 s390x 1.4.1-2 [24.8 kB] Get:6 http://ftpmaster.internal/ubuntu zesty/main s390x man-db s390x 2.7.6.1-2 [887 kB] Get:7 http://ftpmaster.internal/ubuntu zesty/main s390x libmagic-mgc s390x 1:5.29-3 [182 kB] Get:8 http://ftpmaster.internal/ubuntu zesty/main s390x libmagic1 s390x 1:5.29-3 [66.5 kB] Get:9 http://ftpmaster.internal/ubuntu zesty/main s390x file s390x 1:5.29-3 [21.9 kB] Get:10 http://ftpmaster.internal/ubuntu zesty/main s390x gettext-base s390x 0.19.8.1-1ubuntu2 [47.7 kB] Get:11 http://ftpmaster.internal/ubuntu zesty/main s390x libglib2.0-0 s390x 2.52.0-1 [1063 kB] Get:12 http://ftpmaster.internal/ubuntu zesty/main s390x libicu57 s390x 57.1-5 [7466 kB] Get:13 http://ftpmaster.internal/ubuntu zesty/main s390x libxml2 s390x 2.9.4+dfsg1-2.2 [626 kB] Get:14 http://ftpmaster.internal/ubuntu zesty/main s390x libsigsegv2 s390x 2.10-5 [13.5 kB] Get:15 http://ftpmaster.internal/ubuntu zesty/main s390x m4 s390x 1.4.18-1 [195 kB] Get:16 http://ftpmaster.internal/ubuntu zesty/main s390x autoconf all 2.69-10 [321 kB] Get:17 http://ftpmaster.internal/ubuntu zesty/main s390x autotools-dev all 20161112.1 [39.5 kB] Get:18 http://ftpmaster.internal/ubuntu zesty/main s390x automake all 1:1.15-5ubuntu1 [509 kB] Get:19 http://ftpmaster.internal/ubuntu zesty/main s390x autopoint all 0.19.8.1-1ubuntu2 [412 kB] Get:20 http://ftpmaster.internal/ubuntu zesty/main s390x libtool all 2.4.6-2 [194 kB] Get:21 http://ftpmaster.internal/ubuntu zesty/main s390x dh-autoreconf all 13 [15.6 kB] Get:22 http://ftpmaster.internal/ubuntu zesty/main s390x libarchive-zip-perl all 1.59-1 [84.0 kB] Get:23 http://ftpmaster.internal/ubuntu zesty/main s390x libfile-stripnondeterminism-perl all 0.032-1 [12.9 kB] Get:24 http://ftpmaster.internal/ubuntu zesty/main s390x libtimedate-perl all 2.3000-2 [37.5 kB] Get:25 http://ftpmaster.internal/ubuntu zesty/main s390x dh-strip-nondeterminism all 0.032-1 [4894 B] Get:26 http://ftpmaster.internal/ubuntu zesty/main s390x libcroco3 s390x 0.6.11-2 [74.6 kB] Get:27 http://ftpmaster.internal/ubuntu zesty/main s390x gettext s390x 0.19.8.1-1ubuntu2 [1054 kB] Get:28 http://ftpmaster.internal/ubuntu zesty/main s390x intltool-debian all 0.35.0+20060710.4 [24.9 kB] Get:29 http://ftpmaster.internal/ubuntu zesty/main s390x po-debconf all 1.0.20 [232 kB] Get:30 http://ftpmaster.internal/ubuntu zesty/main s390x debhelper all 10.2.2ubuntu1 [742 kB] Get:31 http://ftpmaster.internal/ubuntu zesty/main s390x libgsl2 s390x 2.3+dfsg-1 [771 kB] Get:32 http://ftpmaster.internal/ubuntu zesty/main s390x libgsl-dev s390x 2.3+dfsg-1 [882 kB] Get:33 http://ftpmaster.internal/ubuntu zesty/universe s390x libhts1 s390x 1.3.2-2ubuntu1 [234 kB] Get:34 http://ftpmaster.internal/ubuntu zesty/universe s390x libhts-dev s390x 1.3.2-2ubuntu1 [300 kB] Get:35 http://ftpmaster.internal/ubuntu zesty/main s390x libio-pty-perl s390x 1:1.08-1.1build3 [29.4 kB] Get:36 http://ftpmaster.internal/ubuntu zesty/universe s390x tabix s390x 1.3.2-2ubuntu1 [234 kB] Get:37 http://ftpmaster.internal/ubuntu zesty/main s390x zlib1g-dev s390x 1:1.2.11.dfsg-0ubuntu1 [170 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 18.4 MB in 6s (2637 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 ... 13918 files and directories currently installed.) Preparing to unpack .../00-groff-base_1.22.3-9_s390x.deb ... Unpacking groff-base (1.22.3-9) ... Selecting previously unselected package libbsd0:s390x. Preparing to unpack .../01-libbsd0_0.8.3-1_s390x.deb ... Unpacking libbsd0:s390x (0.8.3-1) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../02-bsdmainutils_9.0.12ubuntu1_s390x.deb ... Unpacking bsdmainutils (9.0.12ubuntu1) ... Selecting previously unselected package libpipeline1:s390x. Preparing to unpack .../03-libpipeline1_1.4.1-2_s390x.deb ... Unpacking libpipeline1:s390x (1.4.1-2) ... Selecting previously unselected package man-db. Preparing to unpack .../04-man-db_2.7.6.1-2_s390x.deb ... Unpacking man-db (2.7.6.1-2) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../05-libmagic-mgc_1%3a5.29-3_s390x.deb ... Unpacking libmagic-mgc (1:5.29-3) ... Selecting previously unselected package libmagic1:s390x. Preparing to unpack .../06-libmagic1_1%3a5.29-3_s390x.deb ... Unpacking libmagic1:s390x (1:5.29-3) ... Selecting previously unselected package file. Preparing to unpack .../07-file_1%3a5.29-3_s390x.deb ... Unpacking file (1:5.29-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../08-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 .../09-libglib2.0-0_2.52.0-1_s390x.deb ... Unpacking libglib2.0-0:s390x (2.52.0-1) ... Selecting previously unselected package libicu57:s390x. Preparing to unpack .../10-libicu57_57.1-5_s390x.deb ... Unpacking libicu57:s390x (57.1-5) ... Selecting previously unselected package libxml2:s390x. Preparing to unpack .../11-libxml2_2.9.4+dfsg1-2.2_s390x.deb ... Unpacking libxml2:s390x (2.9.4+dfsg1-2.2) ... Selecting previously unselected package libsigsegv2:s390x. Preparing to unpack .../12-libsigsegv2_2.10-5_s390x.deb ... Unpacking libsigsegv2:s390x (2.10-5) ... Selecting previously unselected package m4. Preparing to unpack .../13-m4_1.4.18-1_s390x.deb ... Unpacking m4 (1.4.18-1) ... Selecting previously unselected package autoconf. Preparing to unpack .../14-autoconf_2.69-10_all.deb ... Unpacking autoconf (2.69-10) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../15-autotools-dev_20161112.1_all.deb ... Unpacking autotools-dev (20161112.1) ... Selecting previously unselected package automake. Preparing to unpack .../16-automake_1%3a1.15-5ubuntu1_all.deb ... Unpacking automake (1:1.15-5ubuntu1) ... Selecting previously unselected package autopoint. Preparing to unpack .../17-autopoint_0.19.8.1-1ubuntu2_all.deb ... Unpacking autopoint (0.19.8.1-1ubuntu2) ... Selecting previously unselected package libtool. Preparing to unpack .../18-libtool_2.4.6-2_all.deb ... Unpacking libtool (2.4.6-2) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../19-dh-autoreconf_13_all.deb ... Unpacking dh-autoreconf (13) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../20-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 .../21-libfile-stripnondeterminism-perl_0.032-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (0.032-1) ... Selecting previously unselected package libtimedate-perl. Preparing to unpack .../22-libtimedate-perl_2.3000-2_all.deb ... Unpacking libtimedate-perl (2.3000-2) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../23-dh-strip-nondeterminism_0.032-1_all.deb ... Unpacking dh-strip-nondeterminism (0.032-1) ... Selecting previously unselected package libcroco3:s390x. Preparing to unpack .../24-libcroco3_0.6.11-2_s390x.deb ... Unpacking libcroco3:s390x (0.6.11-2) ... Selecting previously unselected package gettext. Preparing to unpack .../25-gettext_0.19.8.1-1ubuntu2_s390x.deb ... Unpacking gettext (0.19.8.1-1ubuntu2) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../26-intltool-debian_0.35.0+20060710.4_all.deb ... Unpacking intltool-debian (0.35.0+20060710.4) ... Selecting previously unselected package po-debconf. Preparing to unpack .../27-po-debconf_1.0.20_all.deb ... Unpacking po-debconf (1.0.20) ... Selecting previously unselected package debhelper. Preparing to unpack .../28-debhelper_10.2.2ubuntu1_all.deb ... Unpacking debhelper (10.2.2ubuntu1) ... Selecting previously unselected package libgsl2:s390x. Preparing to unpack .../29-libgsl2_2.3+dfsg-1_s390x.deb ... Unpacking libgsl2:s390x (2.3+dfsg-1) ... Selecting previously unselected package libgsl-dev. Preparing to unpack .../30-libgsl-dev_2.3+dfsg-1_s390x.deb ... Unpacking libgsl-dev (2.3+dfsg-1) ... Selecting previously unselected package libhts1:s390x. Preparing to unpack .../31-libhts1_1.3.2-2ubuntu1_s390x.deb ... Unpacking libhts1:s390x (1.3.2-2ubuntu1) ... Selecting previously unselected package libhts-dev:s390x. Preparing to unpack .../32-libhts-dev_1.3.2-2ubuntu1_s390x.deb ... Unpacking libhts-dev:s390x (1.3.2-2ubuntu1) ... Selecting previously unselected package libio-pty-perl. Preparing to unpack .../33-libio-pty-perl_1%3a1.08-1.1build3_s390x.deb ... Unpacking libio-pty-perl (1:1.08-1.1build3) ... Selecting previously unselected package tabix. Preparing to unpack .../34-tabix_1.3.2-2ubuntu1_s390x.deb ... Unpacking tabix (1.3.2-2ubuntu1) ... Selecting previously unselected package zlib1g-dev:s390x. Preparing to unpack .../35-zlib1g-dev_1%3a1.2.11.dfsg-0ubuntu1_s390x.deb ... Unpacking zlib1g-dev:s390x (1:1.2.11.dfsg-0ubuntu1) ... Selecting previously unselected package sbuild-build-depends-bcftools-dummy. Preparing to unpack .../36-sbuild-build-depends-bcftools-dummy_0.invalid.0_s390x.deb ... Unpacking sbuild-build-depends-bcftools-dummy (0.invalid.0) ... Setting up libhts1:s390x (1.3.2-2ubuntu1) ... Setting up libarchive-zip-perl (1.59-1) ... Setting up libio-pty-perl (1:1.08-1.1build3) ... Setting up libtimedate-perl (2.3000-2) ... Setting up libsigsegv2:s390x (2.10-5) ... Setting up libhts-dev:s390x (1.3.2-2ubuntu1) ... Setting up groff-base (1.22.3-9) ... Setting up libglib2.0-0:s390x (2.52.0-1) ... 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 (2.3+dfsg-1) ... Setting up m4 (1.4.18-1) ... Setting up libicu57:s390x (57.1-5) ... Setting up libbsd0:s390x (0.8.3-1) ... Setting up libxml2:s390x (2.9.4+dfsg1-2.2) ... Setting up libmagic-mgc (1:5.29-3) ... Setting up libmagic1:s390x (1:5.29-3) ... Setting up libcroco3:s390x (0.6.11-2) ... Processing triggers for libc-bin (2.24-9ubuntu2) ... Setting up autotools-dev (20161112.1) ... Setting up tabix (1.3.2-2ubuntu1) ... Setting up bsdmainutils (9.0.12ubuntu1) ... 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 (1:1.2.11.dfsg-0ubuntu1) ... Setting up libfile-stripnondeterminism-perl (0.032-1) ... Setting up gettext (0.19.8.1-1ubuntu2) ... Setting up libgsl-dev (2.3+dfsg-1) ... Setting up autoconf (2.69-10) ... Setting up file (1:5.29-3) ... Setting up intltool-debian (0.35.0+20060710.4) ... Setting up automake (1:1.15-5ubuntu1) ... update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode Setting up man-db (2.7.6.1-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libtool (2.4.6-2) ... Setting up po-debconf (1.0.20) ... Setting up dh-autoreconf (13) ... Setting up dh-strip-nondeterminism (0.032-1) ... Setting up debhelper (10.2.2ubuntu1) ... Setting up sbuild-build-depends-bcftools-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.24-9ubuntu2) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.4.0-64-generic s390x (s390x) Toolchain package versions: binutils_2.28-3ubuntu1 dpkg-dev_1.18.10ubuntu1 g++-6_6.3.0-12ubuntu2 gcc-6_6.3.0-12ubuntu2 libc6-dev_2.24-9ubuntu2 libstdc++-6-dev_6.3.0-12ubuntu2 libstdc++6_6.3.0-12ubuntu2 linux-libc-dev_4.10.0-19.21 Package versions: adduser_3.113+nmu3ubuntu5 advancecomp_1.20-1 apt_1.4 apt-transport-https_1.4 autoconf_2.69-10 automake_1:1.15-5ubuntu1 autopoint_0.19.8.1-1ubuntu2 autotools-dev_20161112.1 base-files_9.6ubuntu12 base-passwd_3.5.43 bash_4.4-2ubuntu1 binutils_2.28-3ubuntu1 bsdmainutils_9.0.12ubuntu1 bsdutils_1:2.29-1ubuntu2 build-essential_12.1ubuntu2 bzip2_1.0.6-8.1 ca-certificates_20161130 coreutils_8.26-3ubuntu3 cpp_4:6.3.0-2ubuntu1 cpp-6_6.3.0-12ubuntu2 dash_0.5.8-2.3ubuntu1 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+------------------------------------------------------------------------------+ | 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 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++; ^~ 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 ‘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); ^~ 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/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 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/FhjXVMUh42/merge.a.vcf.gz 2:3199812-3199812 .. ok test_tabix: /<>/bcftools view -H /tmp/FhjXVMUh42/merge.a.bcf 2:3199812-3199812 .. ok test_tabix: /usr/bin/tabix /tmp/FhjXVMUh42/merge.a.vcf.gz 1:3000151-3000151 .. ok test_tabix: /<>/bcftools view -H /tmp/FhjXVMUh42/merge.a.bcf 1:3000151-3000151 .. ok test_tabix: /usr/bin/tabix /tmp/FhjXVMUh42/large_chrom_tbi_limit.vcf.gz chr11:1-536870912 .. ok test_tabix: /<>/bcftools view -H /tmp/FhjXVMUh42/large_chrom_tbi_limit.bcf chr11:1-536870912 .. ok test_index: /<>/bcftools view -H /tmp/FhjXVMUh42/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/FhjXVMUh42/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /<>/bcftools view -H /tmp/FhjXVMUh42/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/FhjXVMUh42/large_chrom_csi_limit.bcf chr20 .. ok test_vcf_idxstats: /<>/bcftools index -s /tmp/FhjXVMUh42/idx.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -s /tmp/FhjXVMUh42/idx.vcf.gz The outputs differ: /<>/test/idx.out /<>/test/idx.out.new .. failed ... test_vcf_idxstats: /<>/bcftools index -s /tmp/FhjXVMUh42/idx.bcf .. ok test_vcf_idxstats: /<>/bcftools index -n /tmp/FhjXVMUh42/idx.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -n /tmp/FhjXVMUh42/idx.vcf.gz The outputs differ: /<>/test/idx_count.out /<>/test/idx_count.out.new .. failed ... test_vcf_idxstats: /<>/bcftools index -n /tmp/FhjXVMUh42/idx.bcf .. ok test_vcf_idxstats: /<>/bcftools index -s /tmp/FhjXVMUh42/empty.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -s /tmp/FhjXVMUh42/empty.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -s /tmp/FhjXVMUh42/empty.bcf .. ok test_vcf_idxstats: /<>/bcftools index -n /tmp/FhjXVMUh42/empty.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -n /tmp/FhjXVMUh42/empty.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -n /tmp/FhjXVMUh42/empty.bcf .. ok test_vcf_check: /<>/bcftools stats -s - /tmp/FhjXVMUh42/check.vcf.gz | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID ' .. ok test_vcf_check: /<>/bcftools view -Ob /tmp/FhjXVMUh42/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/FhjXVMUh42/check.1.chk /tmp/FhjXVMUh42/check.2.chk /tmp/FhjXVMUh42/check.3.chk /tmp/FhjXVMUh42/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/FhjXVMUh42/stats.a.vcf.gz /tmp/FhjXVMUh42/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_isec: /<>/bcftools isec -n =2 /tmp/FhjXVMUh42/isec.a.vcf.gz /tmp/FhjXVMUh42/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: /<>/bcftools isec -Ob -n =2 /tmp/FhjXVMUh42/isec.a.vcf.gz /tmp/FhjXVMUh42/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: /<>/bcftools isec -n =2 -i"STRLEN(REF)==2" /tmp/FhjXVMUh42/isec.a.vcf.gz /tmp/FhjXVMUh42/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: /<>/bcftools isec -Ob -n =2 -i"STRLEN(REF)==2" /tmp/FhjXVMUh42/isec.a.vcf.gz /tmp/FhjXVMUh42/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: /<>/bcftools isec -n =2 -c both /tmp/FhjXVMUh42/isec.a.vcf.gz /tmp/FhjXVMUh42/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: /<>/bcftools isec -Ob -n =2 -c both /tmp/FhjXVMUh42/isec.a.vcf.gz /tmp/FhjXVMUh42/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: /<>/bcftools isec -n =2 -c any /tmp/FhjXVMUh42/isec.a.vcf.gz /tmp/FhjXVMUh42/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: /<>/bcftools isec -Ob -n =2 -c any /tmp/FhjXVMUh42/isec.a.vcf.gz /tmp/FhjXVMUh42/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: /<>/bcftools isec -C -c any /tmp/FhjXVMUh42/isec.a.vcf.gz /tmp/FhjXVMUh42/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: /<>/bcftools isec -Ob -C -c any /tmp/FhjXVMUh42/isec.a.vcf.gz /tmp/FhjXVMUh42/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec2: /<>/bcftools isec --no-version -T /tmp/FhjXVMUh42/isec.tab.gz /tmp/FhjXVMUh42/isec.a.vcf.gz 2>/dev/null .. ok test_vcf_isec2: /<>/bcftools isec -Ob -T /tmp/FhjXVMUh42/isec.tab.gz /tmp/FhjXVMUh42/isec.a.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples /tmp/FhjXVMUh42/merge.a.vcf.gz /tmp/FhjXVMUh42/merge.b.vcf.gz /tmp/FhjXVMUh42/merge.c.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob --force-samples /tmp/FhjXVMUh42/merge.a.vcf.gz /tmp/FhjXVMUh42/merge.b.vcf.gz /tmp/FhjXVMUh42/merge.c.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples -m none /tmp/FhjXVMUh42/merge.2.a.vcf.gz /tmp/FhjXVMUh42/merge.2.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob --force-samples -m none /tmp/FhjXVMUh42/merge.2.a.vcf.gz /tmp/FhjXVMUh42/merge.2.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples -m both /tmp/FhjXVMUh42/merge.2.a.vcf.gz /tmp/FhjXVMUh42/merge.2.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob --force-samples -m both /tmp/FhjXVMUh42/merge.2.a.vcf.gz /tmp/FhjXVMUh42/merge.2.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples -m all /tmp/FhjXVMUh42/merge.2.a.vcf.gz /tmp/FhjXVMUh42/merge.2.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob --force-samples -m all /tmp/FhjXVMUh42/merge.2.a.vcf.gz /tmp/FhjXVMUh42/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/FhjXVMUh42/merge.3.a.vcf.gz /tmp/FhjXVMUh42/merge.3.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob --force-samples -i TR:sum,TA:sum,TG:sum /tmp/FhjXVMUh42/merge.3.a.vcf.gz /tmp/FhjXVMUh42/merge.3.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples -m id /tmp/FhjXVMUh42/merge.4.a.vcf.gz /tmp/FhjXVMUh42/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/FhjXVMUh42/merge.4.a.vcf.gz /tmp/FhjXVMUh42/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/FhjXVMUh42/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/FhjXVMUh42/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/FhjXVMUh42/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/FhjXVMUh42/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/FhjXVMUh42/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/FhjXVMUh42/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/FhjXVMUh42/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/FhjXVMUh42/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/FhjXVMUh42/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/FhjXVMUh42/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/FhjXVMUh42/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/FhjXVMUh42/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/FhjXVMUh42/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/FhjXVMUh42/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/FhjXVMUh42/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/FhjXVMUh42/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/FhjXVMUh42/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/FhjXVMUh42/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/FhjXVMUh42/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/FhjXVMUh42/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/FhjXVMUh42/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/FhjXVMUh42/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/FhjXVMUh42/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/FhjXVMUh42/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/FhjXVMUh42/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/FhjXVMUh42/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/FhjXVMUh42/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/FhjXVMUh42/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/FhjXVMUh42/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/FhjXVMUh42/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/FhjXVMUh42/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/FhjXVMUh42/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/FhjXVMUh42/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/FhjXVMUh42/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/FhjXVMUh42/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/FhjXVMUh42/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/FhjXVMUh42/view.vectors.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/FhjXVMUh42/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/FhjXVMUh42/query.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/FhjXVMUh42/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/FhjXVMUh42/query.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/FhjXVMUh42/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/FhjXVMUh42/query.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/FhjXVMUh42/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/FhjXVMUh42/query.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/FhjXVMUh42/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/FhjXVMUh42/query.2.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/FhjXVMUh42/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/FhjXVMUh42/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/FhjXVMUh42/missing.vcf.gz | /<>/bcftools query -i'IINT="."' -f'%POS %IINT\n' .. ok test_vcf_query: /<>/bcftools query -i'IINT!="."' -f'%POS %IINT\n' /tmp/FhjXVMUh42/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/FhjXVMUh42/missing.vcf.gz | /<>/bcftools query -i'IINT!="."' -f'%POS %IINT\n' .. ok test_vcf_query: /<>/bcftools query -e'IINT!="."' -f'%POS %IINT\n' /tmp/FhjXVMUh42/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/FhjXVMUh42/missing.vcf.gz | /<>/bcftools query -e'IINT!="."' -f'%POS %IINT\n' .. ok test_vcf_query: /<>/bcftools query -e'IINT="."' -f'%POS %IINT\n' /tmp/FhjXVMUh42/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/FhjXVMUh42/missing.vcf.gz | /<>/bcftools query -e'IINT="."' -f'%POS %IINT\n' .. ok test_vcf_query: /<>/bcftools query -i'IFLT="."' -f'%POS %IFLT\n' /tmp/FhjXVMUh42/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/FhjXVMUh42/missing.vcf.gz | /<>/bcftools query -i'IFLT="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /<>/bcftools query -i'IFLT!="."' -f'%POS %IFLT\n' /tmp/FhjXVMUh42/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/FhjXVMUh42/missing.vcf.gz | /<>/bcftools query -i'IFLT!="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /<>/bcftools query -e'IFLT!="."' -f'%POS %IFLT\n' /tmp/FhjXVMUh42/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/FhjXVMUh42/missing.vcf.gz | /<>/bcftools query -e'IFLT!="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /<>/bcftools query -e'IFLT="."' -f'%POS %IFLT\n' /tmp/FhjXVMUh42/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/FhjXVMUh42/missing.vcf.gz | /<>/bcftools query -e'IFLT="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /<>/bcftools query -i'ISTR="."' -f'%POS %ISTR\n' /tmp/FhjXVMUh42/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/FhjXVMUh42/missing.vcf.gz | /<>/bcftools query -i'ISTR="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /<>/bcftools query -i'ISTR!="."' -f'%POS %ISTR\n' /tmp/FhjXVMUh42/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/FhjXVMUh42/missing.vcf.gz | /<>/bcftools query -i'ISTR!="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /<>/bcftools query -e'ISTR="."' -f'%POS %ISTR\n' /tmp/FhjXVMUh42/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/FhjXVMUh42/missing.vcf.gz | /<>/bcftools query -e'ISTR="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /<>/bcftools query -e'ISTR!="."' -f'%POS %ISTR\n' /tmp/FhjXVMUh42/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/FhjXVMUh42/missing.vcf.gz | /<>/bcftools query -e'ISTR!="."' -f'%POS %ISTR\n' .. ok test_vcf_norm: /<>/bcftools norm --no-version -f /<>/test/norm.fa /tmp/FhjXVMUh42/norm.vcf.gz 2>/dev/null .. ok test_vcf_norm: /<>/bcftools norm -Ob -f /<>/test/norm.fa /tmp/FhjXVMUh42/norm.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -m- /tmp/FhjXVMUh42/norm.split.vcf.gz 2>/dev/null .. ok test_vcf_norm: /<>/bcftools norm -Ob -m- /tmp/FhjXVMUh42/norm.split.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -m- /tmp/FhjXVMUh42/norm.split.2.vcf.gz 2>/dev/null .. ok test_vcf_norm: /<>/bcftools norm -Ob -m- /tmp/FhjXVMUh42/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/FhjXVMUh42/norm.split.vcf.gz 2>/dev/null .. ok test_vcf_norm: /<>/bcftools norm -Ob -m- -f /<>/test/norm.fa /tmp/FhjXVMUh42/norm.split.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -m+ /tmp/FhjXVMUh42/norm.merge.vcf.gz 2>/dev/null .. ok test_vcf_norm: /<>/bcftools norm -Ob -m+ /tmp/FhjXVMUh42/norm.merge.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -m+ /tmp/FhjXVMUh42/norm.merge.2.vcf.gz 2>/dev/null .. ok test_vcf_norm: /<>/bcftools norm -Ob -m+ /tmp/FhjXVMUh42/norm.merge.2.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -m+ /tmp/FhjXVMUh42/norm.merge.3.vcf.gz 2>/dev/null .. ok test_vcf_norm: /<>/bcftools norm -Ob -m+ /tmp/FhjXVMUh42/norm.merge.3.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -m+ -s /tmp/FhjXVMUh42/norm.merge.vcf.gz 2>/dev/null .. ok test_vcf_norm: /<>/bcftools norm -Ob -m+ -s /tmp/FhjXVMUh42/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/FhjXVMUh42/norm.setref.vcf.gz 2>/dev/null .. ok test_vcf_norm: /<>/bcftools norm -Ob -Nc s -f /<>/test/norm.fa /tmp/FhjXVMUh42/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/FhjXVMUh42/norm.telomere.vcf.gz 2>/dev/null .. ok test_vcf_norm: /<>/bcftools norm -Ob -f /<>/test/norm.fa /tmp/FhjXVMUh42/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/FhjXVMUh42/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -aUc1 -C1 -s NA00002 -v snps /tmp/FhjXVMUh42/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -f PASS -Xks NA00003 /tmp/FhjXVMUh42/view.vcf.gz -r20,Y .. ok test_vcf_view: /<>/bcftools view -Ob -f PASS -Xks NA00003 /tmp/FhjXVMUh42/view.vcf.gz -r20,Y | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -xs NA00003 /tmp/FhjXVMUh42/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -xs NA00003 /tmp/FhjXVMUh42/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/FhjXVMUh42/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/FhjXVMUh42/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -p /tmp/FhjXVMUh42/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -p /tmp/FhjXVMUh42/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -P /tmp/FhjXVMUh42/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -P /tmp/FhjXVMUh42/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -hm2 -M2 -q0.3 -Q0.7 /tmp/FhjXVMUh42/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -hm2 -M2 -q0.3 -Q0.7 /tmp/FhjXVMUh42/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -Hu /tmp/FhjXVMUh42/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -GVsnps /tmp/FhjXVMUh42/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -GVsnps /tmp/FhjXVMUh42/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -ne 'INDEL=1 || PV4[0]<0.006' /tmp/FhjXVMUh42/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -ne 'INDEL=1 || PV4[0]<0.006' /tmp/FhjXVMUh42/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -s ^NA00003 /tmp/FhjXVMUh42/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -s ^NA00003 /tmp/FhjXVMUh42/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version /tmp/FhjXVMUh42/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob /tmp/FhjXVMUh42/view.omitgenotypes.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -G /tmp/FhjXVMUh42/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -G /tmp/FhjXVMUh42/view.omitgenotypes.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -HG /tmp/FhjXVMUh42/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -a /tmp/FhjXVMUh42/many.alleles.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -a /tmp/FhjXVMUh42/many.alleles.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -asA /tmp/FhjXVMUh42/view.vectors.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -asA /tmp/FhjXVMUh42/view.vectors.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -asB /tmp/FhjXVMUh42/view.vectors.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -asB /tmp/FhjXVMUh42/view.vectors.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -H -i'FMT/FGS[0]="AAAAAA"' /tmp/FhjXVMUh42/view.filter.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -i'FMT/FGS[2]="C"' /tmp/FhjXVMUh42/view.filter.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -i'FMT/FGS[4]="EE"' /tmp/FhjXVMUh42/view.filter.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -i'FMT/FRS[1]="BB"' /tmp/FhjXVMUh42/view.filter.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -i'TXT0="text"' /tmp/FhjXVMUh42/view.filter.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -T /<>/test/view.chrs.tab /tmp/FhjXVMUh42/view.chrs.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -T /<>/test/view.chrs.tab /tmp/FhjXVMUh42/view.chrs.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -i 'POS>=3062917' /tmp/FhjXVMUh42/filter.2.vcf.gz 1:3062917-3157410 .. ok test_vcf_view: /<>/bcftools view -Ob -i 'POS>=3062917' /tmp/FhjXVMUh42/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/FhjXVMUh42/view.minmaxac.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -c6:nonmajor /tmp/FhjXVMUh42/view.minmaxac.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -q0.3:major /tmp/FhjXVMUh42/view.minmaxac.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -i 'Gene.refGene=="RAD21L1"' /tmp/FhjXVMUh42/view.filter.annovar.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -i 'Gene.refGene~"NOD"' /tmp/FhjXVMUh42/view.filter.annovar.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -i 'LJB2_MutationTaster=="0.291000"' /tmp/FhjXVMUh42/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/FhjXVMUh42/mpileup.tab.gz /<>/test/mpileup.vcf 2>/dev/null .. ok test_vcf_call_cAls: /<>/bcftools call -Ob -mA -C alleles -T /tmp/FhjXVMUh42/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/FhjXVMUh42/regions.vcf.gz .. ok test_vcf_regions: /<>/bcftools view -Ob /tmp/FhjXVMUh42/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/FhjXVMUh42/regions.vcf.gz .. ok test_vcf_regions: /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/FhjXVMUh42/regions.tab.gz /tmp/FhjXVMUh42/regions.vcf.gz .. ok test_vcf_regions: /<>/bcftools view -Ob /tmp/FhjXVMUh42/regions.vcf.gz | /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/FhjXVMUh42/regions.tab.gz .. ok test_vcf_regions: /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/FhjXVMUh42/regions.tab.gz /tmp/FhjXVMUh42/regions.vcf.gz .. ok test_vcf_regions: /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/FhjXVMUh42/regions.bed /tmp/FhjXVMUh42/regions.vcf.gz .. ok test_vcf_regions: /<>/bcftools view -Ob /tmp/FhjXVMUh42/regions.vcf.gz | /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/FhjXVMUh42/regions.bed .. ok test_vcf_regions: /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/FhjXVMUh42/regions.bed /tmp/FhjXVMUh42/regions.vcf.gz .. ok test_vcf_regions: /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/FhjXVMUh42/regions.bed.gz /tmp/FhjXVMUh42/regions.vcf.gz .. ok test_vcf_regions: /<>/bcftools view -Ob /tmp/FhjXVMUh42/regions.vcf.gz | /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/FhjXVMUh42/regions.bed.gz .. ok test_vcf_regions: /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/FhjXVMUh42/regions.bed.gz /tmp/FhjXVMUh42/regions.vcf.gz .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/FhjXVMUh42/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/FhjXVMUh42/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/FhjXVMUh42/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/FhjXVMUh42/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/FhjXVMUh42/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/FhjXVMUh42/annotate.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/FhjXVMUh42/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/FhjXVMUh42/annotate.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/FhjXVMUh42/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/FhjXVMUh42/annotate2.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/FhjXVMUh42/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/FhjXVMUh42/annotate2.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/FhjXVMUh42/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/FhjXVMUh42/annotate2.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/FhjXVMUh42/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/FhjXVMUh42/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/FhjXVMUh42/annots4.vcf.gz -c +INFO /tmp/FhjXVMUh42/annotate4.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/FhjXVMUh42/annots4.vcf.gz -c +INFO /tmp/FhjXVMUh42/annotate4.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/FhjXVMUh42/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/FhjXVMUh42/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/FhjXVMUh42/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/FhjXVMUh42/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/FhjXVMUh42/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/FhjXVMUh42/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/FhjXVMUh42/concat.1.a.vcf.gz /tmp/FhjXVMUh42/concat.1.b.vcf.gz .. ok test_vcf_concat: /<>/bcftools concat -Ob /tmp/FhjXVMUh42/concat.1.a.vcf.gz /tmp/FhjXVMUh42/concat.1.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat --no-version /tmp/FhjXVMUh42/concat.1.a.bcf /tmp/FhjXVMUh42/concat.1.b.bcf .. ok test_vcf_concat: /<>/bcftools concat -Ob /tmp/FhjXVMUh42/concat.1.a.bcf /tmp/FhjXVMUh42/concat.1.b.bcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat --no-version -a /tmp/FhjXVMUh42/concat.2.a.vcf.gz /tmp/FhjXVMUh42/concat.2.b.vcf.gz .. ok test_vcf_concat: /<>/bcftools concat -Ob -a /tmp/FhjXVMUh42/concat.2.a.vcf.gz /tmp/FhjXVMUh42/concat.2.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat --no-version -a /tmp/FhjXVMUh42/concat.2.a.bcf /tmp/FhjXVMUh42/concat.2.b.bcf .. ok test_vcf_concat: /<>/bcftools concat -Ob -a /tmp/FhjXVMUh42/concat.2.a.bcf /tmp/FhjXVMUh42/concat.2.b.bcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat --no-version -aD /tmp/FhjXVMUh42/concat.2.a.vcf.gz /tmp/FhjXVMUh42/concat.2.b.vcf.gz .. ok test_vcf_concat: /<>/bcftools concat -Ob -aD /tmp/FhjXVMUh42/concat.2.a.vcf.gz /tmp/FhjXVMUh42/concat.2.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat --no-version -aD /tmp/FhjXVMUh42/concat.2.a.bcf /tmp/FhjXVMUh42/concat.2.b.bcf .. ok test_vcf_concat: /<>/bcftools concat -Ob -aD /tmp/FhjXVMUh42/concat.2.a.bcf /tmp/FhjXVMUh42/concat.2.b.bcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat --no-version -l /tmp/FhjXVMUh42/concat.3.a.vcf.gz /tmp/FhjXVMUh42/concat.3.b.vcf.gz /tmp/FhjXVMUh42/concat.3.0.vcf.gz /tmp/FhjXVMUh42/concat.3.c.vcf.gz /tmp/FhjXVMUh42/concat.3.d.vcf.gz /tmp/FhjXVMUh42/concat.3.e.vcf.gz /tmp/FhjXVMUh42/concat.3.f.vcf.gz .. ok test_vcf_concat: /<>/bcftools concat -Ob -l /tmp/FhjXVMUh42/concat.3.a.vcf.gz /tmp/FhjXVMUh42/concat.3.b.vcf.gz /tmp/FhjXVMUh42/concat.3.0.vcf.gz /tmp/FhjXVMUh42/concat.3.c.vcf.gz /tmp/FhjXVMUh42/concat.3.d.vcf.gz /tmp/FhjXVMUh42/concat.3.e.vcf.gz /tmp/FhjXVMUh42/concat.3.f.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat --no-version -l /tmp/FhjXVMUh42/concat.3.a.bcf /tmp/FhjXVMUh42/concat.3.b.bcf /tmp/FhjXVMUh42/concat.3.0.bcf /tmp/FhjXVMUh42/concat.3.c.bcf /tmp/FhjXVMUh42/concat.3.d.bcf /tmp/FhjXVMUh42/concat.3.e.bcf /tmp/FhjXVMUh42/concat.3.f.bcf .. ok test_vcf_concat: /<>/bcftools concat -Ob -l /tmp/FhjXVMUh42/concat.3.a.bcf /tmp/FhjXVMUh42/concat.3.b.bcf /tmp/FhjXVMUh42/concat.3.0.bcf /tmp/FhjXVMUh42/concat.3.c.bcf /tmp/FhjXVMUh42/concat.3.d.bcf /tmp/FhjXVMUh42/concat.3.e.bcf /tmp/FhjXVMUh42/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/FhjXVMUh42/reheader.bcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/FhjXVMUh42/reheader.bcf | /<>/bcftools reheader -h /<>/test/reheader.hdr | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -h /<>/test/reheader.hdr /tmp/FhjXVMUh42/reheader.vcf.gz | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/FhjXVMUh42/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/FhjXVMUh42/reheader.bcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/FhjXVMUh42/reheader.bcf | /<>/bcftools reheader -s /<>/test/reheader.samples | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -s /<>/test/reheader.samples /tmp/FhjXVMUh42/reheader.vcf.gz | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/FhjXVMUh42/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/FhjXVMUh42/reheader.bcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/FhjXVMUh42/reheader.bcf | /<>/bcftools reheader -s /<>/test/reheader.samples2 | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -s /<>/test/reheader.samples2 /tmp/FhjXVMUh42/reheader.vcf.gz | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/FhjXVMUh42/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/FhjXVMUh42/reheader.bcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/FhjXVMUh42/reheader.bcf | /<>/bcftools reheader -s /<>/test/reheader.samples3 | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -s /<>/test/reheader.samples3 /tmp/FhjXVMUh42/reheader.vcf.gz | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/FhjXVMUh42/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/FhjXVMUh42/reheader.bcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/FhjXVMUh42/reheader.bcf | /<>/bcftools reheader -s /<>/test/reheader.samples4 | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -s /<>/test/reheader.samples4 /tmp/FhjXVMUh42/reheader.vcf.gz | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/FhjXVMUh42/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/FhjXVMUh42/empty.bcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/FhjXVMUh42/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/FhjXVMUh42/empty.vcf.gz | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/FhjXVMUh42/empty.vcf.gz | /<>/bcftools reheader -h /<>/test/reheader.empty.hdr | /<>/bcftools view --no-version .. ok test_rename_chrs: /<>/bcftools annotate --rename-chrs /tmp/FhjXVMUh42/rename.map -Ov /tmp/FhjXVMUh42/annotate.bcf | /<>/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: /<>/bcftools annotate --rename-chrs /tmp/FhjXVMUh42/rename.map -Ob /tmp/FhjXVMUh42/annotate.bcf | /<>/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: /<>/bcftools annotate --rename-chrs /tmp/FhjXVMUh42/rename.map -Ov /<>/test/annotate.vcf | /<>/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: /<>/bcftools annotate --rename-chrs /tmp/FhjXVMUh42/rename.map -Ob /<>/test/annotate.vcf | /<>/bcftools query -f'%CHROM\t%POS\n' .. ok test_vcf_convert: /<>/bcftools convert -g -,. /tmp/FhjXVMUh42/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/FhjXVMUh42/convert.vcf.gz | /<>/bcftools convert -g -,. 2>/dev/null .. ok test_vcf_convert: /<>/bcftools convert -g .,- /tmp/FhjXVMUh42/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/FhjXVMUh42/convert.vcf.gz | /<>/bcftools convert -g .,- 2>/dev/null .. ok test_vcf_convert: /<>/bcftools convert -g -,. --tag PL /tmp/FhjXVMUh42/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/FhjXVMUh42/convert.vcf.gz | /<>/bcftools convert -g -,. --tag PL 2>/dev/null .. ok test_vcf_convert: /<>/bcftools convert -g .,- --tag PL /tmp/FhjXVMUh42/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/FhjXVMUh42/convert.vcf.gz | /<>/bcftools convert -g .,- --tag PL 2>/dev/null .. ok test_vcf_convert: /<>/bcftools convert -g -,. --vcf-ids /tmp/FhjXVMUh42/check.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/FhjXVMUh42/check.vcf.gz | /<>/bcftools convert -g -,. --vcf-ids 2>/dev/null .. ok test_vcf_convert: /<>/bcftools convert -g .,- --vcf-ids /tmp/FhjXVMUh42/check.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/FhjXVMUh42/check.vcf.gz | /<>/bcftools convert -g .,- --vcf-ids 2>/dev/null .. ok test_vcf_convert: /<>/bcftools convert -g -,. --chrom /tmp/FhjXVMUh42/check.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/FhjXVMUh42/check.vcf.gz | /<>/bcftools convert -g -,. --chrom 2>/dev/null .. ok test_vcf_convert: /<>/bcftools convert -g .,- --chrom /tmp/FhjXVMUh42/check.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/FhjXVMUh42/check.vcf.gz | /<>/bcftools convert -g .,- --chrom 2>/dev/null .. ok test_vcf_convert: /<>/bcftools convert -g -,. --chrom --vcf-ids /tmp/FhjXVMUh42/check.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/FhjXVMUh42/check.vcf.gz | /<>/bcftools convert -g -,. --chrom --vcf-ids 2>/dev/null .. ok test_vcf_convert: /<>/bcftools convert -g .,- --chrom --vcf-ids /tmp/FhjXVMUh42/check.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/FhjXVMUh42/check.vcf.gz | /<>/bcftools convert -g .,- --chrom --vcf-ids 2>/dev/null .. ok test_vcf_convert: /<>/bcftools convert -h -,.,. /tmp/FhjXVMUh42/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/FhjXVMUh42/convert.vcf.gz | /<>/bcftools convert -h -,.,. 2>/dev/null .. ok test_vcf_convert: /<>/bcftools convert -h .,-,. /tmp/FhjXVMUh42/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/FhjXVMUh42/convert.vcf.gz | /<>/bcftools convert -h .,-,. 2>/dev/null .. ok test_vcf_convert: /<>/bcftools convert -h .,.,- /tmp/FhjXVMUh42/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/FhjXVMUh42/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/FhjXVMUh42/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/FhjXVMUh42/convert.vcf.gz | /<>/bcftools convert --hapsample -,. 2>/dev/null .. ok test_vcf_convert: /<>/bcftools convert --hapsample .,- /tmp/FhjXVMUh42/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/FhjXVMUh42/convert.vcf.gz | /<>/bcftools convert --hapsample .,- 2>/dev/null .. ok test_vcf_convert_gvcf: /<>/bcftools convert --no-version --gvcf2vcf -f /<>/test/gvcf.fa /tmp/FhjXVMUh42/convert.gvcf.vcf.gz 2>/dev/null .. ok test_vcf_convert_gvcf: /<>/bcftools view -Ob /tmp/FhjXVMUh42/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/FhjXVMUh42/consensus.vcf.gz -f /<>/test/consensus.fa -m /<>/test/consensus.tab 2>/dev/null .. ok test_vcf_consensus_chain: /<>/bcftools consensus /tmp/FhjXVMUh42/consensus.vcf.gz -f /<>/test/consensus.fa -m /<>/test/consensus.tab -c /tmp/FhjXVMUh42/consensus.1.chain.new > /dev/null 2>/dev/null; cat /tmp/FhjXVMUh42/consensus.1.chain.new .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/FhjXVMUh42/consensus.vcf.gz -f /<>/test/consensus.fa -H 1 -m /<>/test/consensus.tab 2>/dev/null .. ok test_vcf_consensus_chain: /<>/bcftools consensus /tmp/FhjXVMUh42/consensus.vcf.gz -f /<>/test/consensus.fa -H 1 -m /<>/test/consensus.tab -c /tmp/FhjXVMUh42/consensus.2.chain.new > /dev/null 2>/dev/null; cat /tmp/FhjXVMUh42/consensus.2.chain.new .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/FhjXVMUh42/consensus.vcf.gz -f /<>/test/consensus.fa -i -m /<>/test/consensus.tab 2>/dev/null .. ok test_vcf_consensus_chain: /<>/bcftools consensus /tmp/FhjXVMUh42/consensus.vcf.gz -f /<>/test/consensus.fa -i -m /<>/test/consensus.tab -c /tmp/FhjXVMUh42/consensus.3.chain.new > /dev/null 2>/dev/null; cat /tmp/FhjXVMUh42/consensus.3.chain.new .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/FhjXVMUh42/consensus.vcf.gz -f /<>/test/consensus.fa -H 1 2>/dev/null .. ok test_vcf_consensus_chain: /<>/bcftools consensus /tmp/FhjXVMUh42/consensus.vcf.gz -f /<>/test/consensus.fa -H 1 -c /tmp/FhjXVMUh42/consensus.4.chain.new > /dev/null 2>/dev/null; cat /tmp/FhjXVMUh42/consensus.4.chain.new .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/FhjXVMUh42/consensus2.vcf.gz -f /<>/test/consensus2.fa -H 1 2>/dev/null .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/FhjXVMUh42/consensus2.vcf.gz -f /<>/test/consensus2.fa -H 2 2>/dev/null .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/FhjXVMUh42/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 20170409-0104 Finished -------- E: Build failure (dpkg-buildpackage died) +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Not removing build depends: as requested Keeping session: +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: s390x Build-Space: 14156 Build-Time: 11 Distribution: zesty Fail-Stage: build Host Architecture: s390x Install-Time: 13 Job: bcftools_1.3.1-1.dsc Machine Architecture: s390x Package: bcftools Package-Time: 25 Source-Version: 1.3.1-1 Space: 14156 Status: attempted Version: 1.3.1-1 -------------------------------------------------------------------------------- Finished at 20170409-0104 Build needed 00:00:25, 14156k disc space RUN: /usr/share/launchpad-buildd/slavebin/scan-for-processes ['scan-for-processes', 'PACKAGEBUILD-11749295'] Scanning for processes to kill in build /home/buildd/build-PACKAGEBUILD-11749295/chroot-autobuild... RUN: /usr/share/launchpad-buildd/slavebin/umount-chroot ['umount-chroot', 'PACKAGEBUILD-11749295'] Unmounting chroot for build PACKAGEBUILD-11749295... RUN: /usr/share/launchpad-buildd/slavebin/remove-build ['remove-build', 'PACKAGEBUILD-11749295'] Removing build PACKAGEBUILD-11749295