RUN: /usr/share/launchpad-buildd/slavebin/slave-prep ['slave-prep'] Forking launchpad-buildd slave process... Kernel version: Linux z13-019 4.4.0-87-generic #110-Ubuntu SMP Tue Jul 18 12:56:43 UTC 2017 s390x Buildd toolchain package versions: launchpad-buildd_147 python-lpbuildd_147 sbuild_0.67.0-2ubuntu7 dpkg-dev_1.18.4ubuntu1.2 python-debian_0.1.27ubuntu2 qemu-user-static_1:2.5+dfsg-5ubuntu10.14. Syncing the system clock with the buildd NTP service... 29 Jul 22:33:34 ntpdate[61789]: adjust time server 10.211.37.1 offset 0.000223 sec RUN: /usr/share/launchpad-buildd/slavebin/unpack-chroot ['unpack-chroot', 'PACKAGEBUILD-12921756', '/home/buildd/filecache-default/6fa5c2199508da5ee864769667103e5baa50a34d'] Unpacking chroot for build PACKAGEBUILD-12921756 RUN: /usr/share/launchpad-buildd/slavebin/mount-chroot ['mount-chroot', 'PACKAGEBUILD-12921756'] Mounting chroot for build PACKAGEBUILD-12921756 RUN: /usr/share/launchpad-buildd/slavebin/override-sources-list ['override-sources-list', 'PACKAGEBUILD-12921756', 'deb http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu artful main', 'deb http://ftpmaster.internal/ubuntu artful main restricted universe multiverse', 'deb http://ftpmaster.internal/ubuntu artful-security main restricted universe multiverse', 'deb http://ftpmaster.internal/ubuntu artful-updates main restricted universe multiverse'] Overriding sources.list in build-PACKAGEBUILD-12921756 RUN: /usr/share/launchpad-buildd/slavebin/add-trusted-keys ['add-trusted-keys', 'PACKAGEBUILD-12921756'] Adding trusted keys to build-PACKAGEBUILD-12921756 Warning: apt-key output should not be parsed (stdout is not a terminal) OK Warning: apt-key output should not be parsed (stdout is not a terminal) /etc/apt/trusted.gpg -------------------- pub rsa1024 2009-10-22 [SC] 60C3 1780 3A41 BA51 845E 371A 1E93 77A2 BA9E F27F uid [ unknown] Launchpad Toolchain builds /etc/apt/trusted.gpg.d/ubuntu-keyring-2012-archive.gpg ------------------------------------------------------ pub rsa4096 2012-05-11 [SC] 790B C727 7767 219C 42C8 6F93 3B4F E6AC C0B2 1F32 uid [ unknown] Ubuntu Archive Automatic Signing Key (2012) /etc/apt/trusted.gpg.d/ubuntu-keyring-2012-cdimage.gpg ------------------------------------------------------ pub rsa4096 2012-05-11 [SC] 8439 38DF 228D 22F7 B374 2BC0 D94A A3F0 EFE2 1092 uid [ unknown] Ubuntu CD Image Automatic Signing Key (2012) RUN: /usr/share/launchpad-buildd/slavebin/update-debian-chroot ['update-debian-chroot', 'PACKAGEBUILD-12921756', 's390x'] Updating debian chroot for build PACKAGEBUILD-12921756 Get:1 http://ftpmaster.internal/ubuntu artful InRelease [237 kB] Get:2 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu artful InRelease [15.4 kB] Get:3 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu artful/main s390x Packages [25.2 kB] Get:4 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu artful/main Translation-en [16.6 kB] Get:5 http://ftpmaster.internal/ubuntu artful-security InRelease [65.5 kB] Get:6 http://ftpmaster.internal/ubuntu artful-updates InRelease [65.5 kB] Get:7 http://ftpmaster.internal/ubuntu artful/main s390x Packages [1082 kB] Get:8 http://ftpmaster.internal/ubuntu artful/main Translation-en [558 kB] Get:9 http://ftpmaster.internal/ubuntu artful/restricted Translation-en [2724 B] Get:10 http://ftpmaster.internal/ubuntu artful/universe s390x Packages [7963 kB] Get:11 http://ftpmaster.internal/ubuntu artful/universe Translation-en [4776 kB] Get:12 http://ftpmaster.internal/ubuntu artful/multiverse s390x Packages [128 kB] Get:13 http://ftpmaster.internal/ubuntu artful/multiverse Translation-en [109 kB] Fetched 15.0 MB in 11s (1347 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following NEW packages will be installed: gcc-7-base The following packages will be upgraded: advancecomp apt apt-transport-https base-files bash binutils bsdutils ca-certificates cpp cpp-6 debconf debianutils dmsetup dpkg dpkg-dev findutils g++ g++-6 gcc gcc-6 gcc-6-base grep libapparmor1 libapt-pkg5.0 libasn1-8-heimdal libatomic1 libaudit-common libaudit1 libblkid1 libc-bin libc-dev-bin libc6 libc6-dev libcap-ng0 libcc1-0 libdb5.3 libdevmapper1.02.1 libdpkg-perl libfdisk1 libgcc-6-dev libgcc1 libgcrypt20 libgnutls30 libgomp1 libgpg-error0 libgssapi-krb5-2 libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhx509-5-heimdal libidn2-0 libip4tc0 libitm1 libk5crypto3 libkmod2 libkrb5-26-heimdal libkrb5-3 libkrb5support0 libldap-2.4-2 libldap-common libmount1 libnpth0 libp11-kit0 libpcre3 libperl5.24 libpng16-16 libpsl5 libroken18-heimdal libselinux1 libsemanage-common libsemanage1 libsmartcols1 libsqlite3-0 libssl1.0.0 libstdc++-6-dev libstdc++6 libsystemd0 libtasn1-6 libudev1 libusb-0.1-4 libuuid1 libwind0-heimdal linux-libc-dev login mount multiarch-support openssl passwd perl perl-base perl-modules-5.24 sensible-utils systemd systemd-sysv tar tzdata util-linux 98 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 50.2 MB of archives. After this operation, 1107 kB disk space will be freed. Get:1 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu artful/main s390x linux-libc-dev s390x 4.11.0-10.15 [917 kB] Get:2 http://ftpmaster.internal/ubuntu artful/main s390x base-files s390x 9.6ubuntu101 [59.1 kB] Get:3 http://ftpmaster.internal/ubuntu artful/main s390x sensible-utils all 0.0.9+nmu1 [10.2 kB] Get:4 http://ftpmaster.internal/ubuntu artful/main s390x debianutils s390x 4.8.1.1 [85.8 kB] Get:5 http://ftpmaster.internal/ubuntu artful/main s390x bash s390x 4.4-5ubuntu1 [594 kB] Get:6 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu artful/main s390x gcc-7-base s390x 7.1.0-9ubuntu1 [18.8 kB] Get:7 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu artful/main s390x libgcc1 s390x 1:7.1.0-9ubuntu1 [25.2 kB] Get:8 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu artful/main s390x libstdc++6 s390x 7.1.0-9ubuntu1 [408 kB] Get:9 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu artful/main s390x binutils s390x 2.28.90.20170704-0ubuntu1 [1105 kB] Get:10 http://ftpmaster.internal/ubuntu artful/main s390x bsdutils s390x 1:2.29.2-2ubuntu1 [55.1 kB] Get:11 http://ftpmaster.internal/ubuntu artful/main s390x tar s390x 1.29b-2 [222 kB] Get:12 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu artful/main s390x libgomp1 s390x 7.1.0-9ubuntu1 [69.9 kB] Get:13 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu artful/main s390x libitm1 s390x 7.1.0-9ubuntu1 [26.9 kB] Get:14 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu artful/main s390x libatomic1 s390x 7.1.0-9ubuntu1 [8198 B] Get:15 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu artful/main s390x g++-6 s390x 6.4.0-1ubuntu2 [5841 kB] Get:16 http://ftpmaster.internal/ubuntu artful/main s390x dpkg s390x 1.18.24ubuntu1 [1121 kB] Get:17 http://ftpmaster.internal/ubuntu artful/main s390x findutils s390x 4.6.0+git+20170606-3 [288 kB] Get:18 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu artful/main s390x libstdc++-6-dev s390x 6.4.0-1ubuntu2 [1403 kB] Get:19 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu artful/main s390x gcc-6 s390x 6.4.0-1ubuntu2 [5692 kB] Get:20 http://ftpmaster.internal/ubuntu artful/main s390x grep s390x 3.1-2 [152 kB] Get:21 http://ftpmaster.internal/ubuntu artful/main s390x login s390x 1:4.2-3.2ubuntu2 [302 kB] Get:22 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu artful/main s390x libgcc-6-dev s390x 6.4.0-1ubuntu2 [269 kB] Get:23 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu artful/main s390x libcc1-0 s390x 7.1.0-9ubuntu1 [37.6 kB] Get:24 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu artful/main s390x cpp-6 s390x 6.4.0-1ubuntu2 [5058 kB] Get:25 http://ftpmaster.internal/ubuntu artful/main s390x util-linux s390x 2.29.2-2ubuntu1 [867 kB] Get:26 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu artful/main s390x gcc-6-base s390x 6.4.0-1ubuntu2 [17.3 kB] Get:27 http://ftpmaster.internal/ubuntu artful/main s390x mount s390x 2.29.2-2ubuntu1 [127 kB] Get:28 http://ftpmaster.internal/ubuntu artful/main s390x libperl5.24 s390x 5.24.1-7ubuntu1 [3311 kB] Get:29 http://ftpmaster.internal/ubuntu artful/main s390x perl s390x 5.24.1-7ubuntu1 [219 kB] Get:30 http://ftpmaster.internal/ubuntu artful/main s390x perl-base s390x 5.24.1-7ubuntu1 [1275 kB] Get:31 http://ftpmaster.internal/ubuntu artful/main s390x perl-modules-5.24 all 5.24.1-7ubuntu1 [2664 kB] Get:32 http://ftpmaster.internal/ubuntu artful/main s390x libc6-dev s390x 2.24-12ubuntu1 [1984 kB] Get:33 http://ftpmaster.internal/ubuntu artful/main s390x libc-dev-bin s390x 2.24-12ubuntu1 [62.4 kB] Get:34 http://ftpmaster.internal/ubuntu artful/main s390x libc6 s390x 2.24-12ubuntu1 [2305 kB] Get:35 http://ftpmaster.internal/ubuntu artful/main s390x libdb5.3 s390x 5.3.28-13 [609 kB] Get:36 http://ftpmaster.internal/ubuntu artful/main s390x libc-bin s390x 2.24-12ubuntu1 [552 kB] Get:37 http://ftpmaster.internal/ubuntu artful/main s390x libapt-pkg5.0 s390x 1.5~beta1 [732 kB] Get:38 http://ftpmaster.internal/ubuntu artful/main s390x apt-transport-https s390x 1.5~beta1 [32.1 kB] Get:39 http://ftpmaster.internal/ubuntu artful/main s390x libp11-kit0 s390x 0.23.7-3 [186 kB] Get:40 http://ftpmaster.internal/ubuntu artful/main s390x libtasn1-6 s390x 4.12-2.1 [33.8 kB] Get:41 http://ftpmaster.internal/ubuntu artful/main s390x libgnutls30 s390x 3.5.8-6ubuntu1 [591 kB] Get:42 http://ftpmaster.internal/ubuntu artful/main s390x apt s390x 1.5~beta1 [1076 kB] Get:43 http://ftpmaster.internal/ubuntu artful/main s390x debconf all 1.5.63 [136 kB] Get:44 http://ftpmaster.internal/ubuntu artful/main s390x libip4tc0 s390x 1.6.1-2ubuntu1 [19.4 kB] Get:45 http://ftpmaster.internal/ubuntu artful/main s390x libapparmor1 s390x 2.11.0-2ubuntu8 [29.0 kB] Get:46 http://ftpmaster.internal/ubuntu artful/main s390x libaudit-common all 1:2.7.7-1ubuntu1 [4118 B] Get:47 http://ftpmaster.internal/ubuntu artful/main s390x libcap-ng0 s390x 0.7.7-3build1 [10.5 kB] Get:48 http://ftpmaster.internal/ubuntu artful/main s390x libaudit1 s390x 1:2.7.7-1ubuntu1 [36.7 kB] Get:49 http://ftpmaster.internal/ubuntu artful/main s390x libuuid1 s390x 2.29.2-2ubuntu1 [14.6 kB] Get:50 http://ftpmaster.internal/ubuntu artful/main s390x libblkid1 s390x 2.29.2-2ubuntu1 [104 kB] Get:51 http://ftpmaster.internal/ubuntu artful/main s390x libgpg-error0 s390x 1.27-3 [35.2 kB] Get:52 http://ftpmaster.internal/ubuntu artful/main s390x libgcrypt20 s390x 1.7.8-2 [338 kB] Get:53 http://ftpmaster.internal/ubuntu artful/main s390x libkmod2 s390x 24-1ubuntu1 [36.7 kB] Get:54 http://ftpmaster.internal/ubuntu artful/main s390x libpcre3 s390x 2:8.39-4 [154 kB] Get:55 http://ftpmaster.internal/ubuntu artful/main s390x libselinux1 s390x 2.6-3build1 [64.3 kB] Get:56 http://ftpmaster.internal/ubuntu artful/main s390x libmount1 s390x 2.29.2-2ubuntu1 [112 kB] Get:57 http://ftpmaster.internal/ubuntu artful/main s390x systemd s390x 233-8ubuntu3 [2336 kB] Get:58 http://ftpmaster.internal/ubuntu artful/main s390x libsystemd0 s390x 233-8ubuntu3 [193 kB] Get:59 http://ftpmaster.internal/ubuntu artful/main s390x systemd-sysv s390x 233-8ubuntu3 [12.3 kB] Get:60 http://ftpmaster.internal/ubuntu artful/main s390x libfdisk1 s390x 2.29.2-2ubuntu1 [135 kB] Get:61 http://ftpmaster.internal/ubuntu artful/main s390x libsemanage-common all 2.6-2build1 [6738 B] Get:62 http://ftpmaster.internal/ubuntu artful/main s390x libsemanage1 s390x 2.6-2build1 [76.5 kB] Get:63 http://ftpmaster.internal/ubuntu artful/main s390x libsmartcols1 s390x 2.29.2-2ubuntu1 [66.4 kB] Get:64 http://ftpmaster.internal/ubuntu artful/main s390x libudev1 s390x 233-8ubuntu3 [53.3 kB] Get:65 http://ftpmaster.internal/ubuntu artful/main s390x passwd s390x 1:4.2-3.2ubuntu2 [770 kB] Get:66 http://ftpmaster.internal/ubuntu artful/main s390x multiarch-support s390x 2.24-12ubuntu1 [6836 B] Get:67 http://ftpmaster.internal/ubuntu artful/main s390x libdevmapper1.02.1 s390x 2:1.02.137-2ubuntu2 [123 kB] Get:68 http://ftpmaster.internal/ubuntu artful/main s390x dmsetup s390x 2:1.02.137-2ubuntu2 [68.8 kB] Get:69 http://ftpmaster.internal/ubuntu artful/main s390x libroken18-heimdal s390x 7.4.0.dfsg.1-2 [39.2 kB] Get:70 http://ftpmaster.internal/ubuntu artful/main s390x libasn1-8-heimdal s390x 7.4.0.dfsg.1-2 [150 kB] Get:71 http://ftpmaster.internal/ubuntu artful/main s390x libheimbase1-heimdal s390x 7.4.0.dfsg.1-2 [27.5 kB] Get:72 http://ftpmaster.internal/ubuntu artful/main s390x libhcrypto4-heimdal s390x 7.4.0.dfsg.1-2 [83.1 kB] Get:73 http://ftpmaster.internal/ubuntu artful/main s390x libwind0-heimdal s390x 7.4.0.dfsg.1-2 [48.1 kB] Get:74 http://ftpmaster.internal/ubuntu artful/main s390x libhx509-5-heimdal s390x 7.4.0.dfsg.1-2 [99.6 kB] Get:75 http://ftpmaster.internal/ubuntu artful/main s390x libsqlite3-0 s390x 3.19.3-3 [463 kB] Get:76 http://ftpmaster.internal/ubuntu artful/main s390x libkrb5-26-heimdal s390x 7.4.0.dfsg.1-2 [191 kB] Get:77 http://ftpmaster.internal/ubuntu artful/main s390x libheimntlm0-heimdal s390x 7.4.0.dfsg.1-2 [14.5 kB] Get:78 http://ftpmaster.internal/ubuntu artful/main s390x libgssapi3-heimdal s390x 7.4.0.dfsg.1-2 [88.7 kB] Get:79 http://ftpmaster.internal/ubuntu artful/main s390x libldap-2.4-2 s390x 2.4.44+dfsg-8ubuntu1 [144 kB] Get:80 http://ftpmaster.internal/ubuntu artful/main s390x libldap-common all 2.4.44+dfsg-8ubuntu1 [16.4 kB] Get:81 http://ftpmaster.internal/ubuntu artful/main s390x libnpth0 s390x 1.5-2 [7448 B] Get:82 http://ftpmaster.internal/ubuntu artful/main s390x libssl1.0.0 s390x 1.0.2g-1ubuntu13 [773 kB] Get:83 http://ftpmaster.internal/ubuntu artful/main s390x tzdata all 2017b-2 [203 kB] Get:84 http://ftpmaster.internal/ubuntu artful/main s390x openssl s390x 1.0.2g-1ubuntu13 [476 kB] Get:85 http://ftpmaster.internal/ubuntu artful/main s390x ca-certificates all 20161130+nmu1 [186 kB] Get:86 http://ftpmaster.internal/ubuntu artful/main s390x libgssapi-krb5-2 s390x 1.15.1-2 [109 kB] Get:87 http://ftpmaster.internal/ubuntu artful/main s390x libkrb5-3 s390x 1.15.1-2 [261 kB] Get:88 http://ftpmaster.internal/ubuntu artful/main s390x libkrb5support0 s390x 1.15.1-2 [31.5 kB] Get:89 http://ftpmaster.internal/ubuntu artful/main s390x libk5crypto3 s390x 1.15.1-2 [84.0 kB] Get:90 http://ftpmaster.internal/ubuntu artful/main s390x libidn2-0 s390x 2.0.2-1 [89.6 kB] Get:91 http://ftpmaster.internal/ubuntu artful/main s390x libpng16-16 s390x 1.6.30-2 [169 kB] Get:92 http://ftpmaster.internal/ubuntu artful/main s390x libpsl5 s390x 0.17.0-5 [40.4 kB] Get:93 http://ftpmaster.internal/ubuntu artful/main s390x advancecomp s390x 2.0-1 [183 kB] Get:94 http://ftpmaster.internal/ubuntu artful/main s390x cpp s390x 4:6.3.0-2ubuntu2 [27.5 kB] Get:95 http://ftpmaster.internal/ubuntu artful/main s390x dpkg-dev all 1.18.24ubuntu1 [608 kB] Get:96 http://ftpmaster.internal/ubuntu artful/main s390x libdpkg-perl all 1.18.24ubuntu1 [209 kB] Get:97 http://ftpmaster.internal/ubuntu artful/main s390x gcc s390x 4:6.3.0-2ubuntu2 [5252 B] Get:98 http://ftpmaster.internal/ubuntu artful/main s390x g++ s390x 4:6.3.0-2ubuntu2 [1488 B] Get:99 http://ftpmaster.internal/ubuntu artful/main s390x libusb-0.1-4 s390x 2:0.1.12-31 [16.4 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 50.2 MB in 24s (2052 kB/s) (Reading database ... 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Setting up perl-base (5.24.1-7ubuntu1) ... (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 ... 12200 files and directories currently installed.) Preparing to unpack .../perl-modules-5.24_5.24.1-7ubuntu1_all.deb ... Unpacking perl-modules-5.24 (5.24.1-7ubuntu1) over (5.24.1-2ubuntu1) ... Preparing to unpack .../libc6-dev_2.24-12ubuntu1_s390x.deb ... Unpacking libc6-dev:s390x (2.24-12ubuntu1) over (2.24-9ubuntu2) ... Preparing to unpack .../libc-dev-bin_2.24-12ubuntu1_s390x.deb ... 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Unpacking libsystemd0:s390x (233-8ubuntu3) over (232-21ubuntu3) ... Setting up libsystemd0:s390x (233-8ubuntu3) ... Setting up libapparmor1:s390x (2.11.0-2ubuntu8) ... Setting up libip4tc0:s390x (1.6.1-2ubuntu1) ... Setting up libkmod2:s390x (24-1ubuntu1) ... Setting up systemd (233-8ubuntu3) ... Installing new version of config file /etc/systemd/resolved.conf ... addgroup: The group `systemd-journal' already exists as a system group. Exiting. Removing obsolete conffile /etc/dbus-1/system.d/org.freedesktop.hostname1.conf ... Removing obsolete conffile /etc/dbus-1/system.d/org.freedesktop.locale1.conf ... Removing obsolete conffile /etc/dbus-1/system.d/org.freedesktop.login1.conf ... Removing obsolete conffile /etc/dbus-1/system.d/org.freedesktop.network1.conf ... Removing obsolete conffile /etc/dbus-1/system.d/org.freedesktop.resolve1.conf ... Removing obsolete conffile /etc/dbus-1/system.d/org.freedesktop.systemd1.conf ... Removing obsolete conffile /etc/dbus-1/system.d/org.freedesktop.timedate1.conf ... (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 ... 12249 files and directories currently installed.) Preparing to unpack .../systemd-sysv_233-8ubuntu3_s390x.deb ... Unpacking systemd-sysv (233-8ubuntu3) over (232-21ubuntu3) ... Preparing to unpack .../libfdisk1_2.29.2-2ubuntu1_s390x.deb ... Unpacking libfdisk1:s390x (2.29.2-2ubuntu1) over (2.29-1ubuntu2) ... Setting up libfdisk1:s390x (2.29.2-2ubuntu1) ... (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 ... 12249 files and directories currently installed.) Preparing to unpack .../libsemanage-common_2.6-2build1_all.deb ... Unpacking libsemanage-common (2.6-2build1) over (2.6-2) ... Setting up libsemanage-common (2.6-2build1) ... (Reading database ... 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Preparing to unpack .../38-gcc-6-base_6.4.0-1ubuntu2_s390x.deb ... Unpacking gcc-6-base:s390x (6.4.0-1ubuntu2) over (6.3.0-14ubuntu3) ... Preparing to unpack .../39-cpp_4%3a6.3.0-2ubuntu2_s390x.deb ... Unpacking cpp (4:6.3.0-2ubuntu2) over (4:6.3.0-2ubuntu1) ... Preparing to unpack .../40-dpkg-dev_1.18.24ubuntu1_all.deb ... Unpacking dpkg-dev (1.18.24ubuntu1) over (1.18.23ubuntu4) ... Preparing to unpack .../41-libdpkg-perl_1.18.24ubuntu1_all.deb ... Unpacking libdpkg-perl (1.18.24ubuntu1) over (1.18.23ubuntu4) ... Preparing to unpack .../42-gcc_4%3a6.3.0-2ubuntu2_s390x.deb ... Removing old gcc doc directory. Unpacking gcc (4:6.3.0-2ubuntu2) over (4:6.3.0-2ubuntu1) ... Preparing to unpack .../43-g++_4%3a6.3.0-2ubuntu2_s390x.deb ... Unpacking g++ (4:6.3.0-2ubuntu2) over (4:6.3.0-2ubuntu1) ... Preparing to unpack .../44-libusb-0.1-4_2%3a0.1.12-31_s390x.deb ... Unpacking libusb-0.1-4:s390x (2:0.1.12-31) over (2:0.1.12-30) ... Setting up libnpth0:s390x (1.5-2) ... Setting up libgomp1:s390x (7.1.0-9ubuntu1) ... Setting up libatomic1:s390x (7.1.0-9ubuntu1) ... Setting up perl-modules-5.24 (5.24.1-7ubuntu1) ... Setting up libperl5.24:s390x (5.24.1-7ubuntu1) ... Setting up libcc1-0:s390x (7.1.0-9ubuntu1) ... Setting up apt-transport-https (1.5~beta1) ... Setting up libidn2-0:s390x (2.0.2-1) ... Setting up libssl1.0.0:s390x (1.0.2g-1ubuntu13) ... Setting up libpng16-16:s390x (1.6.30-2) ... Setting up libldap-common (2.4.44+dfsg-8ubuntu1) ... Setting up libpsl5:s390x (0.17.0-5) ... Setting up multiarch-support (2.24-12ubuntu1) ... Setting up tzdata (2017b-2) ... Current default time zone: 'Etc/UTC' Local time is now: Sat Jul 29 22:34:26 UTC 2017. Universal Time is now: Sat Jul 29 22:34:26 UTC 2017. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up systemd-sysv (233-8ubuntu3) ... Setting up gcc-6-base:s390x (6.4.0-1ubuntu2) ... Setting up linux-libc-dev:s390x (4.11.0-10.15) ... Setting up advancecomp (2.0-1) ... Setting up libroken18-heimdal:s390x (7.4.0.dfsg.1-2) ... Setting up libdevmapper1.02.1:s390x (2:1.02.137-2ubuntu2) ... Setting up libkrb5support0:s390x (1.15.1-2) ... Setting up perl (5.24.1-7ubuntu1) ... Processing triggers for libc-bin (2.24-12ubuntu1) ... Setting up libheimbase1-heimdal:s390x (7.4.0.dfsg.1-2) ... Setting up openssl (1.0.2g-1ubuntu13) ... Setting up libsqlite3-0:s390x (3.19.3-3) ... Setting up dmsetup (2:1.02.137-2ubuntu2) ... Setting up binutils (2.28.90.20170704-0ubuntu1) ... Setting up cpp-6 (6.4.0-1ubuntu2) ... Setting up libc-dev-bin (2.24-12ubuntu1) ... Setting up ca-certificates (20161130+nmu1) ... Updating certificates in /etc/ssl/certs... 0 added, 7 removed; done. Setting up libc6-dev:s390x (2.24-12ubuntu1) ... Setting up libusb-0.1-4:s390x (2:0.1.12-31) ... Setting up libitm1:s390x (7.1.0-9ubuntu1) ... Setting up cpp (4:6.3.0-2ubuntu2) ... Setting up libk5crypto3:s390x (1.15.1-2) ... Setting up libgcc-6-dev:s390x (6.4.0-1ubuntu2) ... Setting up libstdc++-6-dev:s390x (6.4.0-1ubuntu2) ... Setting up libwind0-heimdal:s390x (7.4.0.dfsg.1-2) ... Setting up libasn1-8-heimdal:s390x (7.4.0.dfsg.1-2) ... Setting up libhcrypto4-heimdal:s390x (7.4.0.dfsg.1-2) ... Setting up libdpkg-perl (1.18.24ubuntu1) ... Setting up libhx509-5-heimdal:s390x (7.4.0.dfsg.1-2) ... Setting up gcc-6 (6.4.0-1ubuntu2) ... Setting up g++-6 (6.4.0-1ubuntu2) ... Setting up dpkg-dev (1.18.24ubuntu1) ... Setting up libkrb5-3:s390x (1.15.1-2) ... Setting up libkrb5-26-heimdal:s390x (7.4.0.dfsg.1-2) ... Setting up libheimntlm0-heimdal:s390x (7.4.0.dfsg.1-2) ... Setting up gcc (4:6.3.0-2ubuntu2) ... Setting up libgssapi-krb5-2:s390x (1.15.1-2) ... Setting up g++ (4:6.3.0-2ubuntu2) ... Setting up libgssapi3-heimdal:s390x (7.4.0.dfsg.1-2) ... Setting up libldap-2.4-2:s390x (2.4.44+dfsg-8ubuntu1) ... Processing triggers for libc-bin (2.24-12ubuntu1) ... Processing triggers for ca-certificates (20161130+nmu1) ... 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-12921756', 's390x', 'artful', '-c', 'chroot:autobuild', '--arch=s390x', '--dist=artful', '--purge=never', '--nolog', 'pbbam_0.7.4+ds-1.dsc'] Initiating build PACKAGEBUILD-12921756 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.4.0-87-generic #110-Ubuntu SMP Tue Jul 18 12:56:43 UTC 2017 s390x sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on z13-019.buildd +==============================================================================+ | pbbam 0.7.4+ds-1 (s390x) 29 Jul 2017 22:34 | +==============================================================================+ Package: pbbam Version: 0.7.4+ds-1 Source Version: 0.7.4+ds-1 Distribution: artful Machine Architecture: s390x Host Architecture: s390x Build Architecture: s390x I: NOTICE: Log filtering will replace 'build/pbbam-oLJ4fv/pbbam-0.7.4+ds' with '<>' I: NOTICE: Log filtering will replace 'build/pbbam-oLJ4fv' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-12921756/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- pbbam_0.7.4+ds-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-7rSI4R/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/<>/resolver-7rSI4R/apt_archive ./ InRelease Get:2 copy:/<>/resolver-7rSI4R/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-7rSI4R/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-7rSI4R/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-7rSI4R/apt_archive ./ Packages [528 B] Fetched 2861 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 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 778 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-7rSI4R/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [778 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 778 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 ... 12242 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 (>= 10), dh-exec, cmake, python, libboost-dev (>= 1.54), zlib1g-dev, libssl-dev, libhts-dev, python-cram, samtools Filtered Build-Depends: debhelper (>= 10), dh-exec, cmake, python, libboost-dev (>= 1.54), zlib1g-dev, libssl-dev, libhts-dev, python-cram, samtools dpkg-deb: building package 'sbuild-build-depends-pbbam-dummy' in '/<>/resolver-Cq6BFU/apt_archive/sbuild-build-depends-pbbam-dummy.deb'. Ign:1 copy:/<>/resolver-Cq6BFU/apt_archive ./ InRelease Get:2 copy:/<>/resolver-Cq6BFU/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-Cq6BFU/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-Cq6BFU/apt_archive ./ Sources [264 B] Get:5 copy:/<>/resolver-Cq6BFU/apt_archive ./ Packages [584 B] Fetched 2967 B in 0s (0 B/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install pbbam build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils cmake cmake-data debhelper dh-autoreconf dh-exec dh-strip-nondeterminism file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libarchive13 libboost-dev libboost1.62-dev libbsd0 libcroco3 libcurl3 libexpat1 libfile-stripnondeterminism-perl libglib2.0-0 libhts-dev libhts2 libicu57 libjsoncpp1 liblzo2-2 libmagic-mgc libmagic1 libpipeline1 libpython-stdlib libpython2.7-minimal libpython2.7-stdlib librhash0 libsigsegv2 libssl-dev libtimedate-perl libtool libuv1 libxml2 m4 man-db mime-support po-debconf python python-cram python-minimal python2.7 python2.7-minimal samtools zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois vacation ninja-build dh-make gettext-doc libasprintf-dev libgettextpo-dev groff lrzip libboost-doc libboost1.62-doc libboost-atomic1.62-dev libboost-chrono1.62-dev libboost-date-time1.62-dev libboost-exception1.62-dev libboost-filesystem1.62-dev libboost-graph1.62-dev libboost-graph-parallel1.62-dev libboost-iostreams1.62-dev libboost-locale1.62-dev libboost-log1.62-dev libboost-math1.62-dev libboost-mpi1.62-dev libboost-mpi-python1.62-dev libboost-program-options1.62-dev libboost-python1.62-dev libboost-random1.62-dev libboost-regex1.62-dev libboost-serialization1.62-dev libboost-signals1.62-dev libboost-system1.62-dev libboost-test1.62-dev libboost-thread1.62-dev libboost-timer1.62-dev libboost-type-erasure1.62-dev libboost-wave1.62-dev libboost1.62-tools-dev libmpfrc++-dev libntl-dev libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc less www-browser libmail-box-perl python-doc python-tk python2.7-doc binfmt-support Recommended packages: curl | wget | lynx-cur libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs libssl-doc libltdl-dev xml-core libmail-sendmail-perl The following packages will be REMOVED: pkg-create-dbgsym* The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils cmake cmake-data debhelper dh-autoreconf dh-exec dh-strip-nondeterminism file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libarchive13 libboost-dev libboost1.62-dev libbsd0 libcroco3 libcurl3 libexpat1 libfile-stripnondeterminism-perl libglib2.0-0 libhts-dev libhts2 libicu57 libjsoncpp1 liblzo2-2 libmagic-mgc libmagic1 libpipeline1 libpython-stdlib libpython2.7-minimal libpython2.7-stdlib librhash0 libsigsegv2 libssl-dev libtimedate-perl libtool libuv1 libxml2 m4 man-db mime-support po-debconf python python-cram python-minimal python2.7 python2.7-minimal samtools sbuild-build-depends-pbbam-dummy zlib1g-dev 0 upgraded, 56 newly installed, 1 to remove and 0 not upgraded. Need to get 33.7 MB of archives. After this operation, 234 MB of additional disk space will be used. Get:1 copy:/<>/resolver-Cq6BFU/apt_archive ./ sbuild-build-depends-pbbam-dummy 0.invalid.0 [836 B] Get:2 http://ftpmaster.internal/ubuntu artful/main s390x groff-base s390x 1.22.3-9 [1174 kB] Get:3 http://ftpmaster.internal/ubuntu artful/main s390x libbsd0 s390x 0.8.6-1 [40.7 kB] Get:4 http://ftpmaster.internal/ubuntu artful/main s390x bsdmainutils s390x 9.0.12+nmu1ubuntu1 [179 kB] Get:5 http://ftpmaster.internal/ubuntu artful/main s390x libpipeline1 s390x 1.4.2-1 [24.3 kB] Get:6 http://ftpmaster.internal/ubuntu artful/main s390x man-db s390x 2.7.6.1-2 [887 kB] Get:7 http://ftpmaster.internal/ubuntu artful/main s390x cmake-data all 3.9.0-1 [1277 kB] Get:8 http://ftpmaster.internal/ubuntu artful/main s390x liblzo2-2 s390x 2.08-1.2 [44.6 kB] Get:9 http://ftpmaster.internal/ubuntu artful/main s390x libicu57 s390x 57.1-6 [7484 kB] Get:10 http://ftpmaster.internal/ubuntu artful/main s390x libxml2 s390x 2.9.4+dfsg1-3build1 [584 kB] Get:11 http://ftpmaster.internal/ubuntu artful/main s390x 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s390x m4 s390x 1.4.18-1 [195 kB] Get:33 http://ftpmaster.internal/ubuntu artful/main s390x autoconf all 2.69-10 [321 kB] Get:34 http://ftpmaster.internal/ubuntu artful/main s390x autotools-dev all 20161112.1 [39.5 kB] Get:35 http://ftpmaster.internal/ubuntu artful/main s390x automake all 1:1.15-6ubuntu1 [509 kB] Get:36 http://ftpmaster.internal/ubuntu artful/main s390x autopoint all 0.19.8.1-2ubuntu1 [411 kB] Get:37 http://ftpmaster.internal/ubuntu artful/main s390x libtool all 2.4.6-2 [194 kB] Get:38 http://ftpmaster.internal/ubuntu artful/main s390x dh-autoreconf all 14 [15.5 kB] Get:39 http://ftpmaster.internal/ubuntu artful/main s390x libarchive-zip-perl all 1.59-1 [84.0 kB] Get:40 http://ftpmaster.internal/ubuntu artful/main s390x libfile-stripnondeterminism-perl all 0.038-1 [13.3 kB] Get:41 http://ftpmaster.internal/ubuntu artful/main s390x libtimedate-perl all 2.3000-2 [37.5 kB] Get:42 http://ftpmaster.internal/ubuntu artful/main s390x dh-strip-nondeterminism all 0.038-1 [5026 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http://ftpmaster.internal/ubuntu artful/main s390x libssl-dev s390x 1.0.2g-1ubuntu13 [1054 kB] Get:54 http://ftpmaster.internal/ubuntu artful/universe s390x python-cram all 0.7-1 [16.7 kB] Get:55 http://ftpmaster.internal/ubuntu artful/universe s390x samtools s390x 1.4.1-1build1 [236 kB] Get:56 http://ftpmaster.internal/ubuntu artful/main s390x dh-exec s390x 0.23build1 [24.5 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 33.7 MB in 13s (2410 kB/s) (Reading database ... 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Processing triggers for libc-bin (2.24-12ubuntu1) ... Setting up autotools-dev (20161112.1) ... Setting up libboost-dev:s390x (1.62.0.1) ... Setting up bsdmainutils (9.0.12+nmu1ubuntu1) ... 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 libhts2:s390x (1.4.1-5) ... Setting up libpython2.7-stdlib:s390x (2.7.13-2) ... Setting up autopoint (0.19.8.1-2ubuntu1) ... Setting up liblzo2-2:s390x (2.08-1.2) ... Setting up zlib1g-dev:s390x (1:1.2.11.dfsg-0ubuntu1) ... Setting up libfile-stripnondeterminism-perl (0.038-1) ... Setting up libjsoncpp1:s390x (1.7.4-3) ... Setting up gettext (0.19.8.1-2ubuntu1) ... Setting up libarchive13:s390x (3.2.2-2) ... Setting up libhts-dev:s390x (1.4.1-5) ... Setting up libssl-dev:s390x (1.0.2g-1ubuntu13) ... Setting up python2.7 (2.7.13-2) ... Setting up autoconf (2.69-10) ... Setting up file (1:5.30-1) ... 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Processing triggers for libc-bin (2.24-12ubuntu1) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.4.0-87-generic s390x (s390x) Toolchain package versions: binutils_2.28.90.20170704-0ubuntu1 dpkg-dev_1.18.24ubuntu1 g++-6_6.4.0-1ubuntu2 gcc-6_6.4.0-1ubuntu2 libc6-dev_2.24-12ubuntu1 libstdc++-6-dev_6.4.0-1ubuntu2 libstdc++6_7.1.0-9ubuntu1 linux-libc-dev_4.11.0-10.15 Package versions: adduser_3.113+nmu3ubuntu5 advancecomp_2.0-1 apt_1.5~beta1 apt-transport-https_1.5~beta1 autoconf_2.69-10 automake_1:1.15-6ubuntu1 autopoint_0.19.8.1-2ubuntu1 autotools-dev_20161112.1 base-files_9.6ubuntu101 base-passwd_3.5.43 bash_4.4-5ubuntu1 binutils_2.28.90.20170704-0ubuntu1 bsdmainutils_9.0.12+nmu1ubuntu1 bsdutils_1:2.29.2-2ubuntu1 build-essential_12.1ubuntu2 bzip2_1.0.6-8.1 ca-certificates_20161130+nmu1 cmake_3.9.0-1 cmake-data_3.9.0-1 coreutils_8.26-3ubuntu3 cpp_4:6.3.0-2ubuntu2 cpp-6_6.4.0-1ubuntu2 dash_0.5.8-2.3ubuntu1 debconf_1.5.63 debhelper_10.6.4ubuntu1 debianutils_4.8.1.1 dh-autoreconf_14 dh-exec_0.23build1 dh-strip-nondeterminism_0.038-1 diffutils_1:3.5-3 dmsetup_2:1.02.137-2ubuntu2 dpkg_1.18.24ubuntu1 dpkg-dev_1.18.24ubuntu1 e2fslibs_1.43.4-2 e2fsprogs_1.43.4-2 fakeroot_1.21-1ubuntu2 file_1:5.30-1 findutils_4.6.0+git+20170606-3 g++_4:6.3.0-2ubuntu2 g++-6_6.4.0-1ubuntu2 gcc_4:6.3.0-2ubuntu2 gcc-6_6.4.0-1ubuntu2 gcc-6-base_6.4.0-1ubuntu2 gcc-7-base_7.1.0-9ubuntu1 gettext_0.19.8.1-2ubuntu1 gettext-base_0.19.8.1-2ubuntu1 gnupg_2.1.15-1ubuntu7 gnupg-agent_2.1.15-1ubuntu7 gpgv_2.1.15-1ubuntu7 grep_3.1-2 groff-base_1.22.3-9 gzip_1.6-5ubuntu1 hostname_3.18 init_1.47 init-system-helpers_1.47 initscripts_2.88dsf-59.3ubuntu2 insserv_1.14.0-5ubuntu3 intltool-debian_0.35.0+20060710.4 libacl1_2.2.52-3build1 libapparmor1_2.11.0-2ubuntu8 libapt-pkg5.0_1.5~beta1 libarchive-zip-perl_1.59-1 libarchive13_3.2.2-2 libasn1-8-heimdal_7.4.0.dfsg.1-2 libassuan0_2.4.3-2 libatomic1_7.1.0-9ubuntu1 libattr1_1:2.4.47-2build1 libaudit-common_1:2.7.7-1ubuntu1 libaudit1_1:2.7.7-1ubuntu1 libblkid1_2.29.2-2ubuntu1 libboost-dev_1.62.0.1 libboost1.62-dev_1.62.0+dfsg-4build3 libbsd0_0.8.6-1 libbz2-1.0_1.0.6-8.1 libc-bin_2.24-12ubuntu1 libc-dev-bin_2.24-12ubuntu1 libc6_2.24-12ubuntu1 libc6-dev_2.24-12ubuntu1 libcap-ng0_0.7.7-3build1 libcap2_1:2.25-1 libcc1-0_7.1.0-9ubuntu1 libcomerr2_1.43.4-2 libcroco3_0.6.12-1 libcryptsetup4_2:1.7.2-0ubuntu1 libcurl3_7.52.1-5ubuntu1 libcurl3-gnutls_7.52.1-5ubuntu1 libdb5.3_5.3.28-13 libdebconfclient0_0.213ubuntu1 libdevmapper1.02.1_2:1.02.137-2ubuntu2 libdpkg-perl_1.18.24ubuntu1 libexpat1_2.2.2-2 libfakeroot_1.21-1ubuntu2 libfdisk1_2.29.2-2ubuntu1 libffi6_3.2.1-6 libfile-stripnondeterminism-perl_0.038-1 libgcc-6-dev_6.4.0-1ubuntu2 libgcc1_1:7.1.0-9ubuntu1 libgcrypt20_1.7.8-2 libgdbm3_1.8.3-14 libglib2.0-0_2.53.4-1 libgmp10_2:6.1.2+dfsg-1 libgnutls30_3.5.8-6ubuntu1 libgomp1_7.1.0-9ubuntu1 libgpg-error0_1.27-3 libgssapi-krb5-2_1.15.1-2 libgssapi3-heimdal_7.4.0.dfsg.1-2 libhcrypto4-heimdal_7.4.0.dfsg.1-2 libheimbase1-heimdal_7.4.0.dfsg.1-2 libheimntlm0-heimdal_7.4.0.dfsg.1-2 libhogweed4_3.3-1 libhts-dev_1.4.1-5 libhts2_1.4.1-5 libhx509-5-heimdal_7.4.0.dfsg.1-2 libicu57_57.1-6 libidn11_1.33-1 libidn2-0_2.0.2-1 libip4tc0_1.6.1-2ubuntu1 libisl15_0.18-1 libitm1_7.1.0-9ubuntu1 libjsoncpp1_1.7.4-3 libk5crypto3_1.15.1-2 libkeyutils1_1.5.9-9ubuntu1 libkmod2_24-1ubuntu1 libkrb5-26-heimdal_7.4.0.dfsg.1-2 libkrb5-3_1.15.1-2 libkrb5support0_1.15.1-2 libksba8_1.3.5-2 libldap-2.4-2_2.4.44+dfsg-8ubuntu1 libldap-common_2.4.44+dfsg-8ubuntu1 liblockfile-bin_1.14-1 liblockfile1_1.14-1 liblz4-1_0.0~r131-2ubuntu2 liblzma5_5.2.2-1.2 liblzo2-2_2.08-1.2 libmagic-mgc_1:5.30-1 libmagic1_1:5.30-1 libmount1_2.29.2-2ubuntu1 libmpc3_1.0.3-1 libmpfr4_3.1.5-1 libncurses5_6.0+20160625-1ubuntu1 libncursesw5_6.0+20160625-1ubuntu1 libnettle6_3.3-1 libnpth0_1.5-2 libp11-kit0_0.23.7-3 libpam-modules_1.1.8-3.2ubuntu3 libpam-modules-bin_1.1.8-3.2ubuntu3 libpam-runtime_1.1.8-3.2ubuntu3 libpam0g_1.1.8-3.2ubuntu3 libpcre3_2:8.39-4 libperl5.24_5.24.1-7ubuntu1 libpipeline1_1.4.2-1 libpng16-16_1.6.30-2 libprocps6_2:3.3.12-1ubuntu2 libpsl5_0.17.0-5 libpython-stdlib_2.7.13-2 libpython2.7-minimal_2.7.13-2 libpython2.7-stdlib_2.7.13-2 libreadline7_7.0-0ubuntu2 librhash0_1.3.4-2 libroken18-heimdal_7.4.0.dfsg.1-2 librtmp1_2.4+20151223.gitfa8646d.1-1 libsasl2-2_2.1.27~101-g0780600+dfsg-2ubuntu1 libsasl2-modules-db_2.1.27~101-g0780600+dfsg-2ubuntu1 libseccomp2_2.3.1-2.1ubuntu1 libselinux1_2.6-3build1 libsemanage-common_2.6-2build1 libsemanage1_2.6-2build1 libsepol1_2.6-2 libsigsegv2_2.11-1 libslang2_2.3.1-5ubuntu1 libsmartcols1_2.29.2-2ubuntu1 libsqlite3-0_3.19.3-3 libss2_1.43.4-2 libssl-dev_1.0.2g-1ubuntu13 libssl1.0.0_1.0.2g-1ubuntu13 libstdc++-6-dev_6.4.0-1ubuntu2 libstdc++6_7.1.0-9ubuntu1 libsystemd0_233-8ubuntu3 libtasn1-6_4.12-2.1 libtimedate-perl_2.3000-2 libtinfo5_6.0+20160625-1ubuntu1 libtool_2.4.6-2 libudev1_233-8ubuntu3 libunistring0_0.9.3-5.2ubuntu1 libusb-0.1-4_2:0.1.12-31 libustr-1.0-1_1.0.4-6 libuuid1_2.29.2-2ubuntu1 libuv1_1.9.1-3 libwind0-heimdal_7.4.0.dfsg.1-2 libxml2_2.9.4+dfsg1-3build1 linux-libc-dev_4.11.0-10.15 lockfile-progs_0.1.17build1 login_1:4.2-3.2ubuntu2 lsb-base_9.20160110ubuntu5 m4_1.4.18-1 make_4.1-9.1 man-db_2.7.6.1-2 mawk_1.3.3-17ubuntu2 mime-support_3.60ubuntu1 mount_2.29.2-2ubuntu1 multiarch-support_2.24-12ubuntu1 ncurses-base_6.0+20160625-1ubuntu1 ncurses-bin_6.0+20160625-1ubuntu1 openssl_1.0.2g-1ubuntu13 optipng_0.7.6-1build1 passwd_1:4.2-3.2ubuntu2 patch_2.7.5-1build1 perl_5.24.1-7ubuntu1 perl-base_5.24.1-7ubuntu1 perl-modules-5.24_5.24.1-7ubuntu1 pinentry-curses_1.0.0-2 pkgbinarymangler_131 po-debconf_1.0.20 policyrcd-script-zg2_0.1-3 procps_2:3.3.12-1ubuntu2 python_2.7.13-2 python-cram_0.7-1 python-minimal_2.7.13-2 python2.7_2.7.13-2 python2.7-minimal_2.7.13-2 readline-common_7.0-0ubuntu2 samtools_1.4.1-1build1 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-pbbam-dummy_0.invalid.0 sed_4.4-1 sensible-utils_0.0.9+nmu1 systemd_233-8ubuntu3 systemd-sysv_233-8ubuntu3 sysv-rc_2.88dsf-59.3ubuntu2 sysvinit-utils_2.88dsf-59.8git1 tar_1.29b-2 tzdata_2017b-2 ubuntu-keyring_2016.10.27 util-linux_2.29.2-2ubuntu1 xz-utils_5.2.2-1.2 zlib1g_1:1.2.11.dfsg-0ubuntu1 zlib1g-dev_1:1.2.11.dfsg-0ubuntu1 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Sun Jan 22 07:51:30 2017 UTC gpgv: using RSA key gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./pbbam_0.7.4+ds-1.dsc dpkg-source: info: extracting pbbam in pbbam-0.7.4+ds dpkg-source: info: unpacking pbbam_0.7.4+ds.orig.tar.gz dpkg-source: info: unpacking pbbam_0.7.4+ds-1.debian.tar.xz dpkg-source: info: applying ssl-md5.patch dpkg-source: info: applying remove-bam2sam.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=/<>/pbbam-0.7.4+ds SHELL=/bin/sh SUDO_COMMAND=/usr/sbin/chroot /<> su buildd -s /bin/sh -c cd '/<>/pbbam-0.7.4+ds' && 'env' SUDO_GID=2501 SUDO_UID=2001 SUDO_USER=buildd TERM=unknown USER=buildd USERNAME=root dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package pbbam dpkg-buildpackage: info: source version 0.7.4+ds-1 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build pbbam-0.7.4+ds dpkg-buildpackage: info: host architecture s390x fakeroot debian/rules clean dh clean dh_testdir debian/rules override_dh_auto_clean make[1]: Entering directory '/<>/pbbam-0.7.4+ds' dh_auto_clean find -name "*.deb.t" -delete rm -f -r /<>/pbbam-0.7.4+ds/gendata make[1]: Leaving directory '/<>/pbbam-0.7.4+ds' dh_autoreconf_clean dh_clean debian/rules build-arch dh build-arch dh_testdir -a dh_update_autotools_config -a dh_autoreconf -a debian/rules override_dh_auto_configure make[1]: Entering directory '/<>/pbbam-0.7.4+ds' dh_auto_configure -- \ -DPacBioBAM_build_shared=ON \ -DPacBioBAM_build_tests=OFF \ -DCMAKE_LIBRARY_PATH=s390x-linux-gnu \ -DCMAKE_SKIP_RPATH=ON \ -DHTSLIB_INCLUDE_DIRS=/usr/include \ -DHTSLIB_LIBRARIES="-lssl -lcrypto -lhts" \ -DCMAKE_SHARED_LINKER_FLAGS="-Wl,-Bsymbolic-functions -Wl,-z,relro" cmake .. -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DPacBioBAM_build_shared=ON -DPacBioBAM_build_tests=OFF -DCMAKE_LIBRARY_PATH=s390x-linux-gnu -DCMAKE_SKIP_RPATH=ON -DHTSLIB_INCLUDE_DIRS=/usr/include "-DHTSLIB_LIBRARIES=-lssl -lcrypto -lhts" "-DCMAKE_SHARED_LINKER_FLAGS=-Wl,-Bsymbolic-functions -Wl,-z,relro" -- The CXX compiler identification is GNU 6.4.0 -- The C compiler identification is GNU 6.4.0 -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- Check for working C compiler: /usr/bin/cc -- Check for working C compiler: /usr/bin/cc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Performing Test HAS_NO_UNUSED_LOCAL_TYPEDEFS -- Performing Test HAS_NO_UNUSED_LOCAL_TYPEDEFS - Success -- Performing Test HAS_NO_SIGN_COMPARE -- Performing Test HAS_NO_SIGN_COMPARE - Success -- Looking for pthread.h -- Looking for pthread.h - found -- Looking for pthread_create -- Looking for pthread_create - not found -- Looking for pthread_create in pthreads -- Looking for pthread_create in pthreads - not found -- Looking for pthread_create in pthread -- Looking for pthread_create in pthread - found -- Found Threads: TRUE -- Boost version: 1.62.0 -- Found ZLIB: /usr/lib/s390x-linux-gnu/libz.so (found version "1.2.11") -- Performing Test HAS_NO_UNUSED_PRIVATE_FIELD -- Performing Test HAS_NO_UNUSED_PRIVATE_FIELD - Success -- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE) -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_SYSCONFDIR -- Build files have been written to: /<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu make[1]: Leaving directory '/<>/pbbam-0.7.4+ds' dh_auto_build -a make -j4 make[1]: Entering directory '/<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu' /usr/bin/cmake -H/<>/pbbam-0.7.4+ds -B/<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu/CMakeFiles /<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu/CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu' make -f src/CMakeFiles/pbbam.dir/build.make src/CMakeFiles/pbbam.dir/depend make[3]: Entering directory '/<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu' cd /<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/pbbam-0.7.4+ds /<>/pbbam-0.7.4+ds/src /<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu /<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu/src /<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu/src/CMakeFiles/pbbam.dir/DependInfo.cmake --color= Scanning dependencies of target pbbam make[3]: Leaving directory '/<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu' make -f src/CMakeFiles/pbbam.dir/build.make src/CMakeFiles/pbbam.dir/build make[3]: Entering directory '/<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu' [ 1%] Building CXX object src/CMakeFiles/pbbam.dir/Accuracy.cpp.o cd /<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/Accuracy.cpp.o -c /<>/pbbam-0.7.4+ds/src/Accuracy.cpp [ 2%] Building CXX object src/CMakeFiles/pbbam.dir/AlignmentPrinter.cpp.o cd /<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/AlignmentPrinter.cpp.o -c /<>/pbbam-0.7.4+ds/src/AlignmentPrinter.cpp [ 3%] Building CXX object src/CMakeFiles/pbbam.dir/BaiIndexedBamReader.cpp.o cd /<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/BaiIndexedBamReader.cpp.o -c /<>/pbbam-0.7.4+ds/src/BaiIndexedBamReader.cpp [ 4%] Building CXX object src/CMakeFiles/pbbam.dir/AssertUtils.cpp.o cd /<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/AssertUtils.cpp.o -c /<>/pbbam-0.7.4+ds/src/AssertUtils.cpp [ 5%] Building CXX object src/CMakeFiles/pbbam.dir/BamFile.cpp.o cd /<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/BamFile.cpp.o -c /<>/pbbam-0.7.4+ds/src/BamFile.cpp [ 6%] Building CXX object src/CMakeFiles/pbbam.dir/BamHeader.cpp.o cd /<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/BamHeader.cpp.o -c /<>/pbbam-0.7.4+ds/src/BamHeader.cpp [ 8%] Building CXX object src/CMakeFiles/pbbam.dir/BamReader.cpp.o cd /<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/BamReader.cpp.o -c /<>/pbbam-0.7.4+ds/src/BamReader.cpp [ 9%] Building CXX object src/CMakeFiles/pbbam.dir/BamRecord.cpp.o cd /<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/BamRecord.cpp.o -c /<>/pbbam-0.7.4+ds/src/BamRecord.cpp [ 10%] Building CXX object src/CMakeFiles/pbbam.dir/BamRecordBuilder.cpp.o cd /<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/BamRecordBuilder.cpp.o -c /<>/pbbam-0.7.4+ds/src/BamRecordBuilder.cpp [ 11%] Building CXX object src/CMakeFiles/pbbam.dir/BamRecordImpl.cpp.o cd /<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/BamRecordImpl.cpp.o -c /<>/pbbam-0.7.4+ds/src/BamRecordImpl.cpp [ 12%] Building CXX object src/CMakeFiles/pbbam.dir/BamRecordTags.cpp.o cd /<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/BamRecordTags.cpp.o -c /<>/pbbam-0.7.4+ds/src/BamRecordTags.cpp [ 13%] Building CXX object src/CMakeFiles/pbbam.dir/BamTagCodec.cpp.o cd /<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/BamTagCodec.cpp.o -c /<>/pbbam-0.7.4+ds/src/BamTagCodec.cpp [ 14%] Building CXX object src/CMakeFiles/pbbam.dir/BamWriter.cpp.o cd /<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/BamWriter.cpp.o -c /<>/pbbam-0.7.4+ds/src/BamWriter.cpp [ 16%] Building CXX object src/CMakeFiles/pbbam.dir/BarcodeQuery.cpp.o cd /<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/BarcodeQuery.cpp.o -c /<>/pbbam-0.7.4+ds/src/BarcodeQuery.cpp /<>/pbbam-0.7.4+ds/src/BamWriter.cpp: In member function ‘void PacBio::BAM::internal::BamWriterPrivate::Write(const PacBio::BAM::BamRecord&, int64_t*)’: /<>/pbbam-0.7.4+ds/src/BamWriter.cpp:143:21: warning: ignoring return value of ‘int bgzf_flush(BGZF*)’, declared with attribute warn_unused_result [-Wunused-result] bgzf_flush(bgzf); ^ /<>/pbbam-0.7.4+ds/src/BamWriter.cpp: In destructor ‘PacBio::BAM::BamWriter::~BamWriter()’: /<>/pbbam-0.7.4+ds/src/BamWriter.cpp:182:41: warning: ignoring return value of ‘int bgzf_flush(BGZF*)’, declared with attribute warn_unused_result [-Wunused-result] bgzf_flush(d_->file_.get()->fp.bgzf); ^ [ 17%] Building CXX object src/CMakeFiles/pbbam.dir/ChemistryTable.cpp.o cd /<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/ChemistryTable.cpp.o -c /<>/pbbam-0.7.4+ds/src/ChemistryTable.cpp [ 18%] Building CXX object src/CMakeFiles/pbbam.dir/Cigar.cpp.o cd /<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/Cigar.cpp.o -c /<>/pbbam-0.7.4+ds/src/Cigar.cpp [ 19%] Building CXX object src/CMakeFiles/pbbam.dir/CigarOperation.cpp.o cd /<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/CigarOperation.cpp.o -c /<>/pbbam-0.7.4+ds/src/CigarOperation.cpp [ 20%] Building CXX object src/CMakeFiles/pbbam.dir/Compare.cpp.o cd /<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/Compare.cpp.o -c /<>/pbbam-0.7.4+ds/src/Compare.cpp [ 21%] Building CXX object src/CMakeFiles/pbbam.dir/Config.cpp.o cd /<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/Config.cpp.o -c /<>/pbbam-0.7.4+ds/src/Config.cpp [ 22%] Building CXX object src/CMakeFiles/pbbam.dir/DataSet.cpp.o cd /<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/DataSet.cpp.o -c /<>/pbbam-0.7.4+ds/src/DataSet.cpp [ 24%] Building CXX object src/CMakeFiles/pbbam.dir/DataSetBaseTypes.cpp.o cd /<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/DataSetBaseTypes.cpp.o -c /<>/pbbam-0.7.4+ds/src/DataSetBaseTypes.cpp [ 25%] Building CXX object src/CMakeFiles/pbbam.dir/DataSetElement.cpp.o cd /<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/DataSetElement.cpp.o -c /<>/pbbam-0.7.4+ds/src/DataSetElement.cpp [ 26%] Building CXX object src/CMakeFiles/pbbam.dir/DataSetIO.cpp.o cd /<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/DataSetIO.cpp.o -c /<>/pbbam-0.7.4+ds/src/DataSetIO.cpp [ 27%] Building CXX object src/CMakeFiles/pbbam.dir/DataSetTypes.cpp.o cd /<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/DataSetTypes.cpp.o -c /<>/pbbam-0.7.4+ds/src/DataSetTypes.cpp [ 28%] Building CXX object src/CMakeFiles/pbbam.dir/DataSetXsd.cpp.o cd /<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/DataSetXsd.cpp.o -c /<>/pbbam-0.7.4+ds/src/DataSetXsd.cpp [ 29%] Building CXX object src/CMakeFiles/pbbam.dir/EntireFileQuery.cpp.o cd /<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/EntireFileQuery.cpp.o -c /<>/pbbam-0.7.4+ds/src/EntireFileQuery.cpp [ 31%] Building CXX object src/CMakeFiles/pbbam.dir/FastaReader.cpp.o cd /<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/FastaReader.cpp.o -c /<>/pbbam-0.7.4+ds/src/FastaReader.cpp [ 32%] Building CXX object src/CMakeFiles/pbbam.dir/FileProducer.cpp.o cd /<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/FileProducer.cpp.o -c /<>/pbbam-0.7.4+ds/src/FileProducer.cpp [ 33%] Building CXX object src/CMakeFiles/pbbam.dir/FileUtils.cpp.o cd /<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/FileUtils.cpp.o -c /<>/pbbam-0.7.4+ds/src/FileUtils.cpp [ 34%] Building CXX object src/CMakeFiles/pbbam.dir/FofnReader.cpp.o cd /<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/FofnReader.cpp.o -c /<>/pbbam-0.7.4+ds/src/FofnReader.cpp [ 35%] Building CXX object src/CMakeFiles/pbbam.dir/Frames.cpp.o cd /<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/Frames.cpp.o -c /<>/pbbam-0.7.4+ds/src/Frames.cpp [ 36%] Building CXX object src/CMakeFiles/pbbam.dir/GenomicInterval.cpp.o cd /<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/GenomicInterval.cpp.o -c /<>/pbbam-0.7.4+ds/src/GenomicInterval.cpp [ 37%] Building CXX object src/CMakeFiles/pbbam.dir/GenomicIntervalQuery.cpp.o cd /<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/GenomicIntervalQuery.cpp.o -c /<>/pbbam-0.7.4+ds/src/GenomicIntervalQuery.cpp [ 39%] Building CXX object src/CMakeFiles/pbbam.dir/IndexedFastaReader.cpp.o cd /<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/IndexedFastaReader.cpp.o -c /<>/pbbam-0.7.4+ds/src/IndexedFastaReader.cpp [ 40%] Building CXX object src/CMakeFiles/pbbam.dir/IRecordWriter.cpp.o cd /<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/IRecordWriter.cpp.o -c /<>/pbbam-0.7.4+ds/src/IRecordWriter.cpp [ 41%] Building CXX object src/CMakeFiles/pbbam.dir/MD5.cpp.o cd /<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/MD5.cpp.o -c /<>/pbbam-0.7.4+ds/src/MD5.cpp [ 42%] Building CXX object src/CMakeFiles/pbbam.dir/MemoryUtils.cpp.o cd /<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/MemoryUtils.cpp.o -c /<>/pbbam-0.7.4+ds/src/MemoryUtils.cpp [ 43%] Building CXX object src/CMakeFiles/pbbam.dir/PbiBuilder.cpp.o cd /<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/PbiBuilder.cpp.o -c /<>/pbbam-0.7.4+ds/src/PbiBuilder.cpp [ 44%] Building CXX object src/CMakeFiles/pbbam.dir/PbiFile.cpp.o cd /<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/PbiFile.cpp.o -c /<>/pbbam-0.7.4+ds/src/PbiFile.cpp [ 45%] Building CXX object src/CMakeFiles/pbbam.dir/PbiFilter.cpp.o cd /<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/PbiFilter.cpp.o -c /<>/pbbam-0.7.4+ds/src/PbiFilter.cpp [ 47%] Building CXX object src/CMakeFiles/pbbam.dir/PbiFilterQuery.cpp.o cd /<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/PbiFilterQuery.cpp.o -c /<>/pbbam-0.7.4+ds/src/PbiFilterQuery.cpp [ 48%] Building CXX object src/CMakeFiles/pbbam.dir/PbiFilterTypes.cpp.o cd /<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/PbiFilterTypes.cpp.o -c /<>/pbbam-0.7.4+ds/src/PbiFilterTypes.cpp [ 49%] Building CXX object src/CMakeFiles/pbbam.dir/PbiIndex.cpp.o cd /<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/PbiIndex.cpp.o -c /<>/pbbam-0.7.4+ds/src/PbiIndex.cpp [ 50%] Building CXX object src/CMakeFiles/pbbam.dir/PbiIndexedBamReader.cpp.o cd /<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/PbiIndexedBamReader.cpp.o -c /<>/pbbam-0.7.4+ds/src/PbiIndexedBamReader.cpp [ 51%] Building CXX object src/CMakeFiles/pbbam.dir/PbiIndexIO.cpp.o cd /<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/PbiIndexIO.cpp.o -c /<>/pbbam-0.7.4+ds/src/PbiIndexIO.cpp [ 52%] Building CXX object src/CMakeFiles/pbbam.dir/PbiRawData.cpp.o cd /<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/PbiRawData.cpp.o -c /<>/pbbam-0.7.4+ds/src/PbiRawData.cpp [ 54%] Building CXX object src/CMakeFiles/pbbam.dir/ProgramInfo.cpp.o cd /<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/ProgramInfo.cpp.o -c /<>/pbbam-0.7.4+ds/src/ProgramInfo.cpp [ 55%] Building CXX object src/CMakeFiles/pbbam.dir/QNameQuery.cpp.o cd /<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/QNameQuery.cpp.o -c /<>/pbbam-0.7.4+ds/src/QNameQuery.cpp [ 56%] Building CXX object src/CMakeFiles/pbbam.dir/QualityValue.cpp.o cd /<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/QualityValue.cpp.o -c /<>/pbbam-0.7.4+ds/src/QualityValue.cpp [ 57%] Building CXX object src/CMakeFiles/pbbam.dir/ReadAccuracyQuery.cpp.o cd /<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/ReadAccuracyQuery.cpp.o -c /<>/pbbam-0.7.4+ds/src/ReadAccuracyQuery.cpp In file included from /<>/pbbam-0.7.4+ds/src/PbiIndexIO.cpp:38:0: /<>/pbbam-0.7.4+ds/src/PbiIndexIO.h: In static member function ‘static void PacBio::BAM::internal::PbiIndexIO::LoadBgzfVector(BGZF*, std::vector&, uint32_t) [with T = short int]’: /<>/pbbam-0.7.4+ds/src/PbiIndexIO.h:121:5: warning: ignoring return value of ‘ssize_t bgzf_read(BGZF*, void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] bgzf_read(fp, &data[0], numReads*sizeof(T)); ^~~~~~~~~ /<>/pbbam-0.7.4+ds/src/PbiIndexIO.h: In static member function ‘static void PacBio::BAM::internal::PbiIndexIO::LoadBgzfVector(BGZF*, std::vector&, uint32_t) [with T = signed char]’: /<>/pbbam-0.7.4+ds/src/PbiIndexIO.h:121:5: warning: ignoring return value of ‘ssize_t bgzf_read(BGZF*, void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] /<>/pbbam-0.7.4+ds/src/PbiIndexIO.cpp: In static member function ‘static void PacBio::BAM::internal::PbiIndexIO::LoadHeader(PacBio::BAM::PbiRawData&, BGZF*)’: /<>/pbbam-0.7.4+ds/src/PbiIndexIO.cpp:237:46: warning: ignoring return value of ‘ssize_t bgzf_read(BGZF*, void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] bgzf_read(fp, &version, sizeof(version)); ^ /<>/pbbam-0.7.4+ds/src/PbiIndexIO.cpp:238:47: warning: ignoring return value of ‘ssize_t bgzf_read(BGZF*, void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] bgzf_read(fp, §ions, sizeof(sections)); ^ /<>/pbbam-0.7.4+ds/src/PbiIndexIO.cpp:239:47: warning: ignoring return value of ‘ssize_t bgzf_read(BGZF*, void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] bgzf_read(fp, &numReads, sizeof(numReads)); ^ In file included from /<>/pbbam-0.7.4+ds/src/PbiIndexIO.cpp:38:0: /<>/pbbam-0.7.4+ds/src/PbiIndexIO.h: In static member function ‘static void PacBio::BAM::internal::PbiIndexIO::LoadBgzfVector(BGZF*, std::vector&, uint32_t) [with T = int]’: /<>/pbbam-0.7.4+ds/src/PbiIndexIO.h:121:5: warning: ignoring return value of ‘ssize_t bgzf_read(BGZF*, void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] bgzf_read(fp, &data[0], numReads*sizeof(T)); ^~~~~~~~~ /<>/pbbam-0.7.4+ds/src/PbiIndexIO.h: In static member function ‘static void PacBio::BAM::internal::PbiIndexIO::LoadBgzfVector(BGZF*, std::vector&, uint32_t) [with T = unsigned int]’: /<>/pbbam-0.7.4+ds/src/PbiIndexIO.h:121:5: warning: ignoring return value of ‘ssize_t bgzf_read(BGZF*, void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] /<>/pbbam-0.7.4+ds/src/PbiIndexIO.h: In static member function ‘static void PacBio::BAM::internal::PbiIndexIO::LoadBgzfVector(BGZF*, std::vector&, uint32_t) [with T = unsigned char]’: /<>/pbbam-0.7.4+ds/src/PbiIndexIO.h:121:5: warning: ignoring return value of ‘ssize_t bgzf_read(BGZF*, void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] /<>/pbbam-0.7.4+ds/src/PbiIndexIO.cpp: In static member function ‘static void PacBio::BAM::internal::PbiIndexIO::LoadReferenceData(PacBio::BAM::PbiRawReferenceData&, BGZF*)’: /<>/pbbam-0.7.4+ds/src/PbiIndexIO.cpp:293:31: warning: ignoring return value of ‘ssize_t bgzf_read(BGZF*, void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] bgzf_read(fp, &numRefs, 4); ^ /<>/pbbam-0.7.4+ds/src/PbiIndexIO.cpp:302:43: warning: ignoring return value of ‘ssize_t bgzf_read(BGZF*, void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] bgzf_read(fp, &entry.tId_, 4); ^ /<>/pbbam-0.7.4+ds/src/PbiIndexIO.cpp:303:43: warning: ignoring return value of ‘ssize_t bgzf_read(BGZF*, void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] bgzf_read(fp, &entry.beginRow_, 4); ^ /<>/pbbam-0.7.4+ds/src/PbiIndexIO.cpp:304:43: warning: ignoring return value of ‘ssize_t bgzf_read(BGZF*, void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] bgzf_read(fp, &entry.endRow_, 4); ^ In file included from /<>/pbbam-0.7.4+ds/src/PbiIndexIO.cpp:38:0: /<>/pbbam-0.7.4+ds/src/PbiIndexIO.h: In static member function ‘static void PacBio::BAM::internal::PbiIndexIO::LoadBgzfVector(BGZF*, std::vector&, uint32_t) [with T = float]’: /<>/pbbam-0.7.4+ds/src/PbiIndexIO.h:121:5: warning: ignoring return value of ‘ssize_t bgzf_read(BGZF*, void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] bgzf_read(fp, &data[0], numReads*sizeof(T)); ^~~~~~~~~ /<>/pbbam-0.7.4+ds/src/PbiIndexIO.h: In static member function ‘static void PacBio::BAM::internal::PbiIndexIO::LoadBgzfVector(BGZF*, std::vector&, uint32_t) [with T = long int]’: /<>/pbbam-0.7.4+ds/src/PbiIndexIO.h:121:5: warning: ignoring return value of ‘ssize_t bgzf_read(BGZF*, void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] /<>/pbbam-0.7.4+ds/src/PbiIndexIO.h: In static member function ‘static void PacBio::BAM::internal::PbiIndexIO::WriteBgzfVector(BGZF*, const std::vector&) [with T = short int]’: /<>/pbbam-0.7.4+ds/src/PbiIndexIO.h:158:5: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] bgzf_write(fp, &output[0], data.size()*sizeof(T)); ^~~~~~~~~~ /<>/pbbam-0.7.4+ds/src/PbiIndexIO.h: In static member function ‘static void PacBio::BAM::internal::PbiIndexIO::WriteBgzfVector(BGZF*, const std::vector&) [with T = signed char]’: /<>/pbbam-0.7.4+ds/src/PbiIndexIO.h:158:5: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] /<>/pbbam-0.7.4+ds/src/PbiIndexIO.cpp: In static member function ‘static void PacBio::BAM::internal::PbiIndexIO::WriteHeader(const PacBio::BAM::PbiRawData&, BGZF*)’: /<>/pbbam-0.7.4+ds/src/PbiIndexIO.cpp:380:29: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] bgzf_write(fp, magic, 4); ^ /<>/pbbam-0.7.4+ds/src/PbiIndexIO.cpp:391:34: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] bgzf_write(fp, &version, 4); ^ /<>/pbbam-0.7.4+ds/src/PbiIndexIO.cpp:392:34: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] bgzf_write(fp, &pbi_flags, 2); ^ /<>/pbbam-0.7.4+ds/src/PbiIndexIO.cpp:393:34: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] bgzf_write(fp, &numReads, 4); ^ /<>/pbbam-0.7.4+ds/src/PbiIndexIO.cpp:398:33: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] bgzf_write(fp, reserved, 18); ^ In file included from /<>/pbbam-0.7.4+ds/src/PbiIndexIO.cpp:38:0: /<>/pbbam-0.7.4+ds/src/PbiIndexIO.h: In static member function ‘static void PacBio::BAM::internal::PbiIndexIO::WriteBgzfVector(BGZF*, const std::vector&) [with T = int]’: /<>/pbbam-0.7.4+ds/src/PbiIndexIO.h:158:5: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] bgzf_write(fp, &output[0], data.size()*sizeof(T)); ^~~~~~~~~~ /<>/pbbam-0.7.4+ds/src/PbiIndexIO.h: In static member function ‘static void PacBio::BAM::internal::PbiIndexIO::WriteBgzfVector(BGZF*, const std::vector&) [with T = unsigned int]’: /<>/pbbam-0.7.4+ds/src/PbiIndexIO.h:158:5: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] /<>/pbbam-0.7.4+ds/src/PbiIndexIO.h: In static member function ‘static void PacBio::BAM::internal::PbiIndexIO::WriteBgzfVector(BGZF*, const std::vector&) [with T = unsigned char]’: /<>/pbbam-0.7.4+ds/src/PbiIndexIO.h:158:5: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] /<>/pbbam-0.7.4+ds/src/PbiIndexIO.cpp: In static member function ‘static void PacBio::BAM::internal::PbiIndexIO::WriteReferenceData(const PacBio::BAM::PbiRawReferenceData&, BGZF*)’: /<>/pbbam-0.7.4+ds/src/PbiIndexIO.cpp:434:32: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] bgzf_write(fp, &numRefs, 4); ^ /<>/pbbam-0.7.4+ds/src/PbiIndexIO.cpp:448:37: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] bgzf_write(fp, &tId, 4); ^ /<>/pbbam-0.7.4+ds/src/PbiIndexIO.cpp:449:37: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] bgzf_write(fp, &beginRow, 4); ^ /<>/pbbam-0.7.4+ds/src/PbiIndexIO.cpp:450:37: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] bgzf_write(fp, &endRow, 4); ^ In file included from /<>/pbbam-0.7.4+ds/src/PbiIndexIO.cpp:38:0: /<>/pbbam-0.7.4+ds/src/PbiIndexIO.h: In static member function ‘static void PacBio::BAM::internal::PbiIndexIO::WriteBgzfVector(BGZF*, const std::vector&) [with T = float]’: /<>/pbbam-0.7.4+ds/src/PbiIndexIO.h:158:5: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] bgzf_write(fp, &output[0], data.size()*sizeof(T)); ^~~~~~~~~~ /<>/pbbam-0.7.4+ds/src/PbiIndexIO.h: In static member function ‘static void PacBio::BAM::internal::PbiIndexIO::WriteBgzfVector(BGZF*, const std::vector&) [with T = long int]’: /<>/pbbam-0.7.4+ds/src/PbiIndexIO.h:158:5: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] [ 58%] Building CXX object src/CMakeFiles/pbbam.dir/ReadGroupInfo.cpp.o cd /<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/ReadGroupInfo.cpp.o -c /<>/pbbam-0.7.4+ds/src/ReadGroupInfo.cpp [ 59%] Building CXX object src/CMakeFiles/pbbam.dir/SamTagCodec.cpp.o cd /<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/SamTagCodec.cpp.o -c /<>/pbbam-0.7.4+ds/src/SamTagCodec.cpp [ 60%] Building CXX object src/CMakeFiles/pbbam.dir/SamWriter.cpp.o cd /<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/SamWriter.cpp.o -c /<>/pbbam-0.7.4+ds/src/SamWriter.cpp [ 62%] Building CXX object src/CMakeFiles/pbbam.dir/SequenceInfo.cpp.o cd /<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/SequenceInfo.cpp.o -c /<>/pbbam-0.7.4+ds/src/SequenceInfo.cpp [ 63%] Building CXX object src/CMakeFiles/pbbam.dir/SubreadLengthQuery.cpp.o cd /<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/SubreadLengthQuery.cpp.o -c /<>/pbbam-0.7.4+ds/src/SubreadLengthQuery.cpp [ 64%] Building CXX object src/CMakeFiles/pbbam.dir/Tag.cpp.o cd /<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/Tag.cpp.o -c /<>/pbbam-0.7.4+ds/src/Tag.cpp [ 65%] Building CXX object src/CMakeFiles/pbbam.dir/TagCollection.cpp.o cd /<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/TagCollection.cpp.o -c /<>/pbbam-0.7.4+ds/src/TagCollection.cpp [ 66%] Building CXX object src/CMakeFiles/pbbam.dir/Validator.cpp.o cd /<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/Validator.cpp.o -c /<>/pbbam-0.7.4+ds/src/Validator.cpp [ 67%] Building CXX object src/CMakeFiles/pbbam.dir/ValidationErrors.cpp.o cd /<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/ValidationErrors.cpp.o -c /<>/pbbam-0.7.4+ds/src/ValidationErrors.cpp [ 68%] Building CXX object src/CMakeFiles/pbbam.dir/ValidationException.cpp.o cd /<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/ValidationException.cpp.o -c /<>/pbbam-0.7.4+ds/src/ValidationException.cpp [ 70%] Building CXX object src/CMakeFiles/pbbam.dir/Version.cpp.o cd /<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/Version.cpp.o -c /<>/pbbam-0.7.4+ds/src/Version.cpp [ 71%] Building CXX object src/CMakeFiles/pbbam.dir/VirtualZmwBamRecord.cpp.o cd /<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/VirtualZmwBamRecord.cpp.o -c /<>/pbbam-0.7.4+ds/src/VirtualZmwBamRecord.cpp [ 72%] Building CXX object src/CMakeFiles/pbbam.dir/VirtualZmwReader.cpp.o cd /<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/VirtualZmwReader.cpp.o -c /<>/pbbam-0.7.4+ds/src/VirtualZmwReader.cpp [ 73%] Building CXX object src/CMakeFiles/pbbam.dir/VirtualZmwCompositeReader.cpp.o cd /<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/VirtualZmwCompositeReader.cpp.o -c /<>/pbbam-0.7.4+ds/src/VirtualZmwCompositeReader.cpp [ 74%] Building CXX object src/CMakeFiles/pbbam.dir/VirtualRegionTypeMap.cpp.o cd /<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/VirtualRegionTypeMap.cpp.o -c /<>/pbbam-0.7.4+ds/src/VirtualRegionTypeMap.cpp [ 75%] Building CXX object src/CMakeFiles/pbbam.dir/XmlReader.cpp.o cd /<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/XmlReader.cpp.o -c /<>/pbbam-0.7.4+ds/src/XmlReader.cpp [ 77%] Building CXX object src/CMakeFiles/pbbam.dir/XmlWriter.cpp.o cd /<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/XmlWriter.cpp.o -c /<>/pbbam-0.7.4+ds/src/XmlWriter.cpp [ 78%] Building CXX object src/CMakeFiles/pbbam.dir/WhitelistedZmwReadStitcher.cpp.o cd /<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/WhitelistedZmwReadStitcher.cpp.o -c /<>/pbbam-0.7.4+ds/src/WhitelistedZmwReadStitcher.cpp [ 79%] Building CXX object src/CMakeFiles/pbbam.dir/ZmwGroupQuery.cpp.o cd /<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/ZmwGroupQuery.cpp.o -c /<>/pbbam-0.7.4+ds/src/ZmwGroupQuery.cpp [ 80%] Building CXX object src/CMakeFiles/pbbam.dir/ZmwReadStitcher.cpp.o cd /<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/ZmwReadStitcher.cpp.o -c /<>/pbbam-0.7.4+ds/src/ZmwReadStitcher.cpp [ 81%] Building CXX object src/CMakeFiles/pbbam.dir/ZmwQuery.cpp.o cd /<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/ZmwQuery.cpp.o -c /<>/pbbam-0.7.4+ds/src/ZmwQuery.cpp [ 82%] Building CXX object src/CMakeFiles/pbbam.dir/ZmwTypeMap.cpp.o cd /<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/ZmwTypeMap.cpp.o -c /<>/pbbam-0.7.4+ds/src/ZmwTypeMap.cpp [ 83%] Building CXX object src/CMakeFiles/pbbam.dir/pugixml/pugixml.cpp.o cd /<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/pugixml/pugixml.cpp.o -c /<>/pbbam-0.7.4+ds/src/pugixml/pugixml.cpp [ 85%] Linking CXX shared library ../lib/libpbbam.so cd /<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/pbbam.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -Wl,-Bsymbolic-functions -Wl,-z,relro -shared -Wl,-soname,libpbbam.so -o ../lib/libpbbam.so CMakeFiles/pbbam.dir/Accuracy.cpp.o CMakeFiles/pbbam.dir/AlignmentPrinter.cpp.o CMakeFiles/pbbam.dir/AssertUtils.cpp.o CMakeFiles/pbbam.dir/BaiIndexedBamReader.cpp.o CMakeFiles/pbbam.dir/BamFile.cpp.o CMakeFiles/pbbam.dir/BamHeader.cpp.o CMakeFiles/pbbam.dir/BamReader.cpp.o CMakeFiles/pbbam.dir/BamRecord.cpp.o CMakeFiles/pbbam.dir/BamRecordBuilder.cpp.o CMakeFiles/pbbam.dir/BamRecordImpl.cpp.o CMakeFiles/pbbam.dir/BamRecordTags.cpp.o CMakeFiles/pbbam.dir/BamTagCodec.cpp.o CMakeFiles/pbbam.dir/BamWriter.cpp.o CMakeFiles/pbbam.dir/BarcodeQuery.cpp.o CMakeFiles/pbbam.dir/ChemistryTable.cpp.o CMakeFiles/pbbam.dir/Cigar.cpp.o CMakeFiles/pbbam.dir/CigarOperation.cpp.o CMakeFiles/pbbam.dir/Compare.cpp.o CMakeFiles/pbbam.dir/Config.cpp.o CMakeFiles/pbbam.dir/DataSet.cpp.o CMakeFiles/pbbam.dir/DataSetBaseTypes.cpp.o CMakeFiles/pbbam.dir/DataSetElement.cpp.o CMakeFiles/pbbam.dir/DataSetIO.cpp.o CMakeFiles/pbbam.dir/DataSetTypes.cpp.o CMakeFiles/pbbam.dir/DataSetXsd.cpp.o CMakeFiles/pbbam.dir/EntireFileQuery.cpp.o CMakeFiles/pbbam.dir/FastaReader.cpp.o CMakeFiles/pbbam.dir/FileProducer.cpp.o CMakeFiles/pbbam.dir/FileUtils.cpp.o CMakeFiles/pbbam.dir/FofnReader.cpp.o CMakeFiles/pbbam.dir/Frames.cpp.o CMakeFiles/pbbam.dir/GenomicInterval.cpp.o CMakeFiles/pbbam.dir/GenomicIntervalQuery.cpp.o CMakeFiles/pbbam.dir/IndexedFastaReader.cpp.o CMakeFiles/pbbam.dir/IRecordWriter.cpp.o CMakeFiles/pbbam.dir/MD5.cpp.o CMakeFiles/pbbam.dir/MemoryUtils.cpp.o CMakeFiles/pbbam.dir/PbiBuilder.cpp.o CMakeFiles/pbbam.dir/PbiFile.cpp.o CMakeFiles/pbbam.dir/PbiFilter.cpp.o CMakeFiles/pbbam.dir/PbiFilterQuery.cpp.o CMakeFiles/pbbam.dir/PbiFilterTypes.cpp.o CMakeFiles/pbbam.dir/PbiIndex.cpp.o CMakeFiles/pbbam.dir/PbiIndexedBamReader.cpp.o CMakeFiles/pbbam.dir/PbiIndexIO.cpp.o CMakeFiles/pbbam.dir/PbiRawData.cpp.o CMakeFiles/pbbam.dir/ProgramInfo.cpp.o CMakeFiles/pbbam.dir/QNameQuery.cpp.o CMakeFiles/pbbam.dir/QualityValue.cpp.o CMakeFiles/pbbam.dir/ReadAccuracyQuery.cpp.o CMakeFiles/pbbam.dir/ReadGroupInfo.cpp.o CMakeFiles/pbbam.dir/SamTagCodec.cpp.o CMakeFiles/pbbam.dir/SamWriter.cpp.o CMakeFiles/pbbam.dir/SequenceInfo.cpp.o CMakeFiles/pbbam.dir/SubreadLengthQuery.cpp.o CMakeFiles/pbbam.dir/Tag.cpp.o CMakeFiles/pbbam.dir/TagCollection.cpp.o CMakeFiles/pbbam.dir/Validator.cpp.o CMakeFiles/pbbam.dir/ValidationErrors.cpp.o CMakeFiles/pbbam.dir/ValidationException.cpp.o CMakeFiles/pbbam.dir/Version.cpp.o CMakeFiles/pbbam.dir/VirtualZmwBamRecord.cpp.o CMakeFiles/pbbam.dir/VirtualZmwCompositeReader.cpp.o CMakeFiles/pbbam.dir/VirtualZmwReader.cpp.o CMakeFiles/pbbam.dir/VirtualRegionTypeMap.cpp.o CMakeFiles/pbbam.dir/XmlReader.cpp.o CMakeFiles/pbbam.dir/XmlWriter.cpp.o CMakeFiles/pbbam.dir/WhitelistedZmwReadStitcher.cpp.o CMakeFiles/pbbam.dir/ZmwGroupQuery.cpp.o CMakeFiles/pbbam.dir/ZmwReadStitcher.cpp.o CMakeFiles/pbbam.dir/ZmwQuery.cpp.o CMakeFiles/pbbam.dir/ZmwTypeMap.cpp.o CMakeFiles/pbbam.dir/pugixml/pugixml.cpp.o -lssl -lcrypto -lhts -lz -lpthread make[3]: Leaving directory '/<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu' [ 85%] Built target pbbam make -f tools/pbindex/CMakeFiles/pbindex.dir/build.make tools/pbindex/CMakeFiles/pbindex.dir/depend make -f tools/pbindexdump/CMakeFiles/pbindexdump.dir/build.make tools/pbindexdump/CMakeFiles/pbindexdump.dir/depend make -f tools/pbmerge/CMakeFiles/pbmerge.dir/build.make tools/pbmerge/CMakeFiles/pbmerge.dir/depend make[3]: Entering directory '/<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu' cd /<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/pbbam-0.7.4+ds /<>/pbbam-0.7.4+ds/tools/pbindex /<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu /<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu/tools/pbindex /<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu/tools/pbindex/CMakeFiles/pbindex.dir/DependInfo.cmake --color= make[3]: Entering directory '/<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu' cd /<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/pbbam-0.7.4+ds /<>/pbbam-0.7.4+ds/tools/pbmerge /<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu /<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu/tools/pbmerge /<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu/tools/pbmerge/CMakeFiles/pbmerge.dir/DependInfo.cmake --color= make[3]: Entering directory '/<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu' cd /<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/pbbam-0.7.4+ds /<>/pbbam-0.7.4+ds/tools/pbindexdump /<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu /<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu/tools/pbindexdump /<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu/tools/pbindexdump/CMakeFiles/pbindexdump.dir/DependInfo.cmake --color= Scanning dependencies of target pbindex make[3]: Leaving directory '/<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu' make -f tools/pbindex/CMakeFiles/pbindex.dir/build.make tools/pbindex/CMakeFiles/pbindex.dir/build Scanning dependencies of target pbindexdump make[3]: Entering directory '/<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu' Scanning dependencies of target pbmerge make[3]: Leaving directory '/<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu' make[3]: Leaving directory '/<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu' make -f tools/pbindexdump/CMakeFiles/pbindexdump.dir/build.make tools/pbindexdump/CMakeFiles/pbindexdump.dir/build make -f tools/pbmerge/CMakeFiles/pbmerge.dir/build.make tools/pbmerge/CMakeFiles/pbmerge.dir/build make[3]: Entering directory '/<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu' make[3]: Entering directory '/<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu' [ 86%] Building CXX object tools/pbindex/CMakeFiles/pbindex.dir/__/common/OptionParser.cpp.o cd /<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu/tools/pbindex && /usr/bin/c++ -I/<>/pbbam-0.7.4+ds/tools/common -I/<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu/generated -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -Wno-unused-private-field -std=gnu++11 -o CMakeFiles/pbindex.dir/__/common/OptionParser.cpp.o -c /<>/pbbam-0.7.4+ds/tools/common/OptionParser.cpp [ 87%] Building CXX object tools/pbindex/CMakeFiles/pbindex.dir/src/main.cpp.o cd /<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu/tools/pbindex && /usr/bin/c++ -I/<>/pbbam-0.7.4+ds/tools/common -I/<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu/generated -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -Wno-unused-private-field -std=gnu++11 -o CMakeFiles/pbindex.dir/src/main.cpp.o -c /<>/pbbam-0.7.4+ds/tools/pbindex/src/main.cpp [ 88%] Building CXX object tools/pbmerge/CMakeFiles/pbmerge.dir/__/common/OptionParser.cpp.o [ 89%] Building CXX object tools/pbindexdump/CMakeFiles/pbindexdump.dir/__/common/OptionParser.cpp.o cd /<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu/tools/pbindexdump && /usr/bin/c++ -I/<>/pbbam-0.7.4+ds/tools/common -I/<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu/generated -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -Wno-unused-private-field -std=gnu++11 -o CMakeFiles/pbindexdump.dir/__/common/OptionParser.cpp.o -c /<>/pbbam-0.7.4+ds/tools/common/OptionParser.cpp cd /<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu/tools/pbmerge && /usr/bin/c++ -I/<>/pbbam-0.7.4+ds/tools/common -I/<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu/generated -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -Wno-unused-private-field -std=gnu++11 -o CMakeFiles/pbmerge.dir/__/common/OptionParser.cpp.o -c /<>/pbbam-0.7.4+ds/tools/common/OptionParser.cpp [ 90%] Building CXX object tools/pbmerge/CMakeFiles/pbmerge.dir/src/main.cpp.o cd /<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu/tools/pbmerge && /usr/bin/c++ -I/<>/pbbam-0.7.4+ds/tools/common -I/<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu/generated -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -Wno-unused-private-field -std=gnu++11 -o CMakeFiles/pbmerge.dir/src/main.cpp.o -c /<>/pbbam-0.7.4+ds/tools/pbmerge/src/main.cpp [ 91%] Building CXX object tools/pbindex/CMakeFiles/pbindex.dir/src/PbIndex.cpp.o cd /<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu/tools/pbindex && /usr/bin/c++ -I/<>/pbbam-0.7.4+ds/tools/common -I/<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu/generated -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -Wno-unused-private-field -std=gnu++11 -o CMakeFiles/pbindex.dir/src/PbIndex.cpp.o -c /<>/pbbam-0.7.4+ds/tools/pbindex/src/PbIndex.cpp [ 93%] Linking CXX executable ../../bin/pbindex cd /<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu/tools/pbindex && /usr/bin/cmake -E cmake_link_script CMakeFiles/pbindex.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -Wno-unused-private-field -Wl,-Bsymbolic-functions -Wl,-z,relro -rdynamic CMakeFiles/pbindex.dir/__/common/OptionParser.cpp.o CMakeFiles/pbindex.dir/src/main.cpp.o CMakeFiles/pbindex.dir/src/PbIndex.cpp.o -o ../../bin/pbindex ../../lib/libpbbam.so -lssl -lcrypto -lhts -lz -lpthread make[3]: Leaving directory '/<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu' [ 93%] Built target pbindex [ 94%] Building CXX object tools/pbindexdump/CMakeFiles/pbindexdump.dir/src/CppFormatter.cpp.o [ 95%] Building CXX object tools/pbindexdump/CMakeFiles/pbindexdump.dir/src/JsonFormatter.cpp.o cd /<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu/tools/pbindexdump && /usr/bin/c++ -I/<>/pbbam-0.7.4+ds/tools/common -I/<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu/generated -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -Wno-unused-private-field -std=gnu++11 -o CMakeFiles/pbindexdump.dir/src/JsonFormatter.cpp.o -c /<>/pbbam-0.7.4+ds/tools/pbindexdump/src/JsonFormatter.cpp cd /<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu/tools/pbindexdump && /usr/bin/c++ -I/<>/pbbam-0.7.4+ds/tools/common -I/<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu/generated -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -Wno-unused-private-field -std=gnu++11 -o CMakeFiles/pbindexdump.dir/src/CppFormatter.cpp.o -c /<>/pbbam-0.7.4+ds/tools/pbindexdump/src/CppFormatter.cpp [ 96%] Building CXX object tools/pbindexdump/CMakeFiles/pbindexdump.dir/src/PbIndexDump.cpp.o cd /<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu/tools/pbindexdump && /usr/bin/c++ -I/<>/pbbam-0.7.4+ds/tools/common -I/<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu/generated -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -Wno-unused-private-field -std=gnu++11 -o CMakeFiles/pbindexdump.dir/src/PbIndexDump.cpp.o -c /<>/pbbam-0.7.4+ds/tools/pbindexdump/src/PbIndexDump.cpp [ 97%] Building CXX object tools/pbindexdump/CMakeFiles/pbindexdump.dir/src/main.cpp.o cd /<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu/tools/pbindexdump && /usr/bin/c++ -I/<>/pbbam-0.7.4+ds/tools/common -I/<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu/generated -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -Wno-unused-private-field -std=gnu++11 -o CMakeFiles/pbindexdump.dir/src/main.cpp.o -c /<>/pbbam-0.7.4+ds/tools/pbindexdump/src/main.cpp [ 98%] Linking CXX executable ../../bin/pbindexdump cd /<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu/tools/pbindexdump && /usr/bin/cmake -E cmake_link_script CMakeFiles/pbindexdump.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -Wno-unused-private-field -Wl,-Bsymbolic-functions -Wl,-z,relro -rdynamic CMakeFiles/pbindexdump.dir/__/common/OptionParser.cpp.o CMakeFiles/pbindexdump.dir/src/CppFormatter.cpp.o CMakeFiles/pbindexdump.dir/src/JsonFormatter.cpp.o CMakeFiles/pbindexdump.dir/src/PbIndexDump.cpp.o CMakeFiles/pbindexdump.dir/src/main.cpp.o -o ../../bin/pbindexdump ../../lib/libpbbam.so -lssl -lcrypto -lhts -lz -lpthread make[3]: Leaving directory '/<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu' [ 98%] Built target pbindexdump [100%] Linking CXX executable ../../bin/pbmerge cd /<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu/tools/pbmerge && /usr/bin/cmake -E cmake_link_script CMakeFiles/pbmerge.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -Wno-unused-private-field -Wl,-Bsymbolic-functions -Wl,-z,relro -rdynamic CMakeFiles/pbmerge.dir/__/common/OptionParser.cpp.o CMakeFiles/pbmerge.dir/src/main.cpp.o -o ../../bin/pbmerge ../../lib/libpbbam.so -lssl -lcrypto -lhts -lz -lpthread make[3]: Leaving directory '/<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu' [100%] Built target pbmerge make[2]: Leaving directory '/<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu' /usr/bin/cmake -E cmake_progress_start /<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu/CMakeFiles 0 make[1]: Leaving directory '/<>/pbbam-0.7.4+ds/obj-s390x-linux-gnu' debian/rules override_dh_auto_test make[1]: Entering directory '/<>/pbbam-0.7.4+ds' sed \ -e 's/$BAM2SAM/samtools view/g' \ -e 's/\-\-header\-only/-H/g' \ -e 's/\-\-no\-header//g' \ -e 's|@PacBioBAM_BinDir@/||g' \ -e 's|$TOOLS_BIN/||g' \ -e 's|@PacBioBAM_TestsDir@|/<>/pbbam-0.7.4+ds/tests|g' \ -e 's|@PacBioBAM_VERSION@|0.7.4|g' \ -e 's|@GeneratedTestDataDir@|/<>/pbbam-0.7.4+ds/gendata|g' \ tests/src/cram/pbmerge_pacbio_ordering.t.in > tests/src/cram/pbmerge_pacbio_ordering.deb.t sed \ -e 's/$BAM2SAM/samtools view/g' \ -e 's/\-\-header\-only/-H/g' \ -e 's/\-\-no\-header//g' \ -e 's|@PacBioBAM_BinDir@/||g' \ -e 's|$TOOLS_BIN/||g' \ -e 's|@PacBioBAM_TestsDir@|/<>/pbbam-0.7.4+ds/tests|g' \ -e 's|@PacBioBAM_VERSION@|0.7.4|g' \ -e 's|@GeneratedTestDataDir@|/<>/pbbam-0.7.4+ds/gendata|g' \ tests/src/cram/pbmerge_mixed_ordering.t.in > tests/src/cram/pbmerge_mixed_ordering.deb.t sed \ -e 's/$BAM2SAM/samtools view/g' \ -e 's/\-\-header\-only/-H/g' \ -e 's/\-\-no\-header//g' \ -e 's|@PacBioBAM_BinDir@/||g' \ -e 's|$TOOLS_BIN/||g' \ -e 's|@PacBioBAM_TestsDir@|/<>/pbbam-0.7.4+ds/tests|g' \ -e 's|@PacBioBAM_VERSION@|0.7.4|g' \ -e 's|@GeneratedTestDataDir@|/<>/pbbam-0.7.4+ds/gendata|g' \ tests/src/cram/pbmerge_aligned_ordering.t.in > tests/src/cram/pbmerge_aligned_ordering.deb.t sed \ -e 's/$BAM2SAM/samtools view/g' \ -e 's/\-\-header\-only/-H/g' \ -e 's/\-\-no\-header//g' \ -e 's|@PacBioBAM_BinDir@/||g' \ -e 's|$TOOLS_BIN/||g' \ -e 's|@PacBioBAM_TestsDir@|/<>/pbbam-0.7.4+ds/tests|g' \ -e 's|@PacBioBAM_VERSION@|0.7.4|g' \ -e 's|@GeneratedTestDataDir@|/<>/pbbam-0.7.4+ds/gendata|g' \ tests/src/cram/pbindexdump_json.t.in > tests/src/cram/pbindexdump_json.deb.t sed \ -e 's/$BAM2SAM/samtools view/g' \ -e 's/\-\-header\-only/-H/g' \ -e 's/\-\-no\-header//g' \ -e 's|@PacBioBAM_BinDir@/||g' \ -e 's|$TOOLS_BIN/||g' \ -e 's|@PacBioBAM_TestsDir@|/<>/pbbam-0.7.4+ds/tests|g' \ -e 's|@PacBioBAM_VERSION@|0.7.4|g' \ -e 's|@GeneratedTestDataDir@|/<>/pbbam-0.7.4+ds/gendata|g' \ tests/src/cram/pbindexdump_cpp.t.in > tests/src/cram/pbindexdump_cpp.deb.t sed \ -e 's/$BAM2SAM/samtools view/g' \ -e 's/\-\-header\-only/-H/g' \ -e 's/\-\-no\-header//g' \ -e 's|@PacBioBAM_BinDir@/||g' \ -e 's|$TOOLS_BIN/||g' \ -e 's|@PacBioBAM_TestsDir@|/<>/pbbam-0.7.4+ds/tests|g' \ -e 's|@PacBioBAM_VERSION@|0.7.4|g' \ -e 's|@GeneratedTestDataDir@|/<>/pbbam-0.7.4+ds/gendata|g' \ tests/src/cram/pbmerge_fofn.t.in > tests/src/cram/pbmerge_fofn.deb.t sed \ -e 's/$BAM2SAM/samtools view/g' \ -e 's/\-\-header\-only/-H/g' \ -e 's/\-\-no\-header//g' \ -e 's|@PacBioBAM_BinDir@/||g' \ -e 's|$TOOLS_BIN/||g' \ -e 's|@PacBioBAM_TestsDir@|/<>/pbbam-0.7.4+ds/tests|g' \ -e 's|@PacBioBAM_VERSION@|0.7.4|g' \ -e 's|@GeneratedTestDataDir@|/<>/pbbam-0.7.4+ds/gendata|g' \ tests/src/cram/pbmerge_dataset.t.in > tests/src/cram/pbmerge_dataset.deb.t mkdir -p /<>/pbbam-0.7.4+ds/gendata python tests/scripts/generate_data.py /<>/pbbam-0.7.4+ds/tests/data /<>/pbbam-0.7.4+ds/gendata Generating test data in /<>/pbbam-0.7.4+ds/gendata - Creating file: truncated.bam...done. - Creating file: normal.fa...done. - Creating file: chunking_missingfilters.subreadset.xml...done. - Creating file: chunking_emptyfilters.subreadset.xml...done. - Creating symlink: missing_pbi.bam...done. - Creating symlink: aligned.bam.bai...done. - Creating symlink: m150404_101626_42267_c100807920800000001823174110291514_s1_p0.2.subreads.bam.pbi...done. - Creating symlink: m150404_101626_42267_c100807920800000001823174110291514_s1_p0.1.subreads.bam...done. - Creating symlink: m150404_101626_42267_c100807920800000001823174110291514_s1_p0.2.subreads.bam...done. - Creating symlink: aligned2.bam.pbi...done. - Creating symlink: m150404_101626_42267_c100807920800000001823174110291514_s1_p0.3.subreads.bam.pbi...done. - Creating symlink: aligned2.bam.bai...done. - Creating symlink: aligned2.bam...done. - Creating symlink: aligned.bam...done. - Creating symlink: aligned.bam.pbi...done. - Creating symlink: m150404_101626_42267_c100807920800000001823174110291514_s1_p0.1.subreads.bam.pbi...done. - Creating symlink: m150404_101626_42267_c100807920800000001823174110291514_s1_p0.3.subreads.bam...done. BINDIR=`find $PWD -name bin -type d`; \ LIBDIR=`find $PWD -name lib -type d`; \ PATH="$BINDIR:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games" LD_LIBRARY_PATH="$LIBDIR:" \ cram -v tests/src/cram/pbmerge_pacbio_ordering.deb.t tests/src/cram/pbmerge_mixed_ordering.deb.t tests/src/cram/pbmerge_aligned_ordering.deb.t tests/src/cram/pbindexdump_json.deb.t tests/src/cram/pbindexdump_cpp.deb.t tests/src/cram/pbmerge_fofn.deb.t tests/src/cram/pbmerge_dataset.deb.t tests/src/cram/pbmerge_pacbio_ordering.deb.t: failed --- tests/src/cram/pbmerge_pacbio_ordering.deb.t +++ tests/src/cram/pbmerge_pacbio_ordering.deb.t.err @@ -104,354 +104,70 @@ Normal Merge: $ $PBMERGE $HQREGION_BAM $SCRAPS_BAM > $MERGED_BAM + ERROR: read group ID not found + [1] $ samtools view -H $MERGED_BAM - @HD\tVN:1.1\tSO:unknown\tpb:3.0.1 (esc) - @RG\tID:ca75d884\tPL:PACBIO\tDS:READTYPE=HQREGION;DeletionQV=dq;DeletionTag=dt;InsertionQV=iq;MergeQV=mq;SubstitutionQV=sq;SubstitutionTag=st;Ipd:Frames=ip;PulseWidth:Frames=pw;PkMid=pm;PkMean=pa;LabelQV=pq;AltLabel=pt;AltLabelQV=pv;PulseMergeQV=pg;PulseCall=pc;PrePulseFrames=pd;PulseCallWidth=px;BINDINGKIT=100372700;SEQUENCINGKIT=100356200;BASECALLERVERSION=0.1;FRAMERATEHZ=100.000000\tPU:ArminsFakeMovie\tPM:SEQUEL (esc) - @RG\tID:e83fc9c6\tPL:PACBIO\tDS:READTYPE=SCRAP;DeletionQV=dq;DeletionTag=dt;InsertionQV=iq;MergeQV=mq;SubstitutionQV=sq;SubstitutionTag=st;Ipd:Frames=ip;PulseWidth:Frames=pw;PkMid=pm;PkMean=pa;LabelQV=pq;AltLabel=pt;AltLabelQV=pv;PulseMergeQV=pg;PulseCall=pc;PrePulseFrames=pd;PulseCallWidth=px;BINDINGKIT=100372700;SEQUENCINGKIT=100356200;BASECALLERVERSION=0.1;FRAMERATEHZ=100.000000\tPU:ArminsFakeMovie\tPM:SEQUEL (esc) - @PG\tID:baz2bam-0.15.0\tPN:baz2bam\tVN:0.15.0 (esc) - @PG\tID:bazFormat-0.3.0\tPN:bazFormat\tVN:0.3.0 (esc) - @PG\tID:bazwriter-0.15.0\tPN:bazwriter\tVN:0.15.0 (esc) - @PG\tID:pbmerge-0.7.4\tPN:pbmerge\tVN:0.7.4 (esc) $ samtools view $MERGED_BAM | cut -f 1 - ArminsFakeMovie/100000/0_2659 - ArminsFakeMovie/100000/2659_7034 - ArminsFakeMovie/100000/3025_3047 - ArminsFakeMovie/100000/3047_3095 - ArminsFakeMovie/100000/3095_3116 - ArminsFakeMovie/100000/3628_3650 - ArminsFakeMovie/100000/3650_3700 - ArminsFakeMovie/100000/3700_3722 - ArminsFakeMovie/100000/4267_4289 - ArminsFakeMovie/100000/4289_4335 - ArminsFakeMovie/100000/4335_4356 - ArminsFakeMovie/100000/4864_4888 - ArminsFakeMovie/100000/4888_4939 - ArminsFakeMovie/100000/4939_4960 - ArminsFakeMovie/100000/5477_5498 - ArminsFakeMovie/100000/5498_5546 - ArminsFakeMovie/100000/5546_5571 - ArminsFakeMovie/100000/6087_6116 - ArminsFakeMovie/100000/6116_6173 - ArminsFakeMovie/100000/6173_6199 - ArminsFakeMovie/100000/6719_6740 - ArminsFakeMovie/100000/6740_6790 - ArminsFakeMovie/100000/6790_6812 - ArminsFakeMovie/100000/7034_7035 - ArminsFakeMovie/200000/0_2659 - ArminsFakeMovie/200000/3025_3047 - ArminsFakeMovie/200000/3047_3095 - ArminsFakeMovie/200000/3095_3116 - ArminsFakeMovie/200000/3628_3650 - ArminsFakeMovie/200000/3650_3700 - ArminsFakeMovie/200000/3700_3722 - ArminsFakeMovie/200000/4267_4289 - ArminsFakeMovie/200000/4289_4335 - ArminsFakeMovie/200000/4335_4356 - ArminsFakeMovie/200000/4864_4888 - ArminsFakeMovie/200000/4888_4939 - ArminsFakeMovie/200000/4939_4960 - ArminsFakeMovie/200000/5477_5498 - ArminsFakeMovie/200000/5498_5546 - ArminsFakeMovie/200000/5546_5571 - ArminsFakeMovie/200000/6087_6116 - ArminsFakeMovie/200000/6116_6173 - ArminsFakeMovie/200000/6173_6199 - ArminsFakeMovie/200000/6719_6740 - ArminsFakeMovie/200000/6740_6790 - ArminsFakeMovie/200000/6790_6812 - ArminsFakeMovie/200000/7034_7035 - ArminsFakeMovie/300000/0_2659 - ArminsFakeMovie/300000/3025_3047 - ArminsFakeMovie/300000/3047_3095 - ArminsFakeMovie/300000/3095_3116 - ArminsFakeMovie/300000/3628_3650 - ArminsFakeMovie/300000/3650_3700 - ArminsFakeMovie/300000/3700_3722 - ArminsFakeMovie/300000/4267_4289 - ArminsFakeMovie/300000/4289_4335 - ArminsFakeMovie/300000/4335_4356 - ArminsFakeMovie/300000/4864_4888 - ArminsFakeMovie/300000/4888_4939 - ArminsFakeMovie/300000/4939_4960 - ArminsFakeMovie/300000/5477_5498 - ArminsFakeMovie/300000/5498_5546 - ArminsFakeMovie/300000/5546_5571 - ArminsFakeMovie/300000/6087_6116 - ArminsFakeMovie/300000/6116_6173 - ArminsFakeMovie/300000/6173_6199 - ArminsFakeMovie/300000/6719_6740 - ArminsFakeMovie/300000/6740_6790 - ArminsFakeMovie/300000/6790_6812 - ArminsFakeMovie/300000/7034_7035 $ rm $MERGED_BAM Shuffle Input: $ $PBMERGE $SCRAPS_BAM $HQREGION_BAM > $MERGED_BAM + ERROR: read group ID not found + [1] $ samtools view -H $MERGED_BAM - @HD\tVN:1.1\tSO:unknown\tpb:3.0.1 (esc) - @RG\tID:ca75d884\tPL:PACBIO\tDS:READTYPE=HQREGION;DeletionQV=dq;DeletionTag=dt;InsertionQV=iq;MergeQV=mq;SubstitutionQV=sq;SubstitutionTag=st;Ipd:Frames=ip;PulseWidth:Frames=pw;PkMid=pm;PkMean=pa;LabelQV=pq;AltLabel=pt;AltLabelQV=pv;PulseMergeQV=pg;PulseCall=pc;PrePulseFrames=pd;PulseCallWidth=px;BINDINGKIT=100372700;SEQUENCINGKIT=100356200;BASECALLERVERSION=0.1;FRAMERATEHZ=100.000000\tPU:ArminsFakeMovie\tPM:SEQUEL (esc) - @RG\tID:e83fc9c6\tPL:PACBIO\tDS:READTYPE=SCRAP;DeletionQV=dq;DeletionTag=dt;InsertionQV=iq;MergeQV=mq;SubstitutionQV=sq;SubstitutionTag=st;Ipd:Frames=ip;PulseWidth:Frames=pw;PkMid=pm;PkMean=pa;LabelQV=pq;AltLabel=pt;AltLabelQV=pv;PulseMergeQV=pg;PulseCall=pc;PrePulseFrames=pd;PulseCallWidth=px;BINDINGKIT=100372700;SEQUENCINGKIT=100356200;BASECALLERVERSION=0.1;FRAMERATEHZ=100.000000\tPU:ArminsFakeMovie\tPM:SEQUEL (esc) - @PG\tID:baz2bam-0.15.0\tPN:baz2bam\tVN:0.15.0 (esc) - @PG\tID:bazFormat-0.3.0\tPN:bazFormat\tVN:0.3.0 (esc) - @PG\tID:bazwriter-0.15.0\tPN:bazwriter\tVN:0.15.0 (esc) - @PG\tID:pbmerge-0.7.4\tPN:pbmerge\tVN:0.7.4 (esc) $ samtools view $MERGED_BAM | cut -f 1 - ArminsFakeMovie/100000/0_2659 - ArminsFakeMovie/100000/2659_7034 - ArminsFakeMovie/100000/3025_3047 - ArminsFakeMovie/100000/3047_3095 - ArminsFakeMovie/100000/3095_3116 - ArminsFakeMovie/100000/3628_3650 - ArminsFakeMovie/100000/3650_3700 - ArminsFakeMovie/100000/3700_3722 - ArminsFakeMovie/100000/4267_4289 - ArminsFakeMovie/100000/4289_4335 - ArminsFakeMovie/100000/4335_4356 - ArminsFakeMovie/100000/4864_4888 - ArminsFakeMovie/100000/4888_4939 - ArminsFakeMovie/100000/4939_4960 - ArminsFakeMovie/100000/5477_5498 - ArminsFakeMovie/100000/5498_5546 - ArminsFakeMovie/100000/5546_5571 - ArminsFakeMovie/100000/6087_6116 - ArminsFakeMovie/100000/6116_6173 - ArminsFakeMovie/100000/6173_6199 - ArminsFakeMovie/100000/6719_6740 - ArminsFakeMovie/100000/6740_6790 - ArminsFakeMovie/100000/6790_6812 - ArminsFakeMovie/100000/7034_7035 - ArminsFakeMovie/200000/0_2659 - ArminsFakeMovie/200000/3025_3047 - ArminsFakeMovie/200000/3047_3095 - ArminsFakeMovie/200000/3095_3116 - ArminsFakeMovie/200000/3628_3650 - ArminsFakeMovie/200000/3650_3700 - ArminsFakeMovie/200000/3700_3722 - ArminsFakeMovie/200000/4267_4289 - ArminsFakeMovie/200000/4289_4335 - ArminsFakeMovie/200000/4335_4356 - ArminsFakeMovie/200000/4864_4888 - ArminsFakeMovie/200000/4888_4939 - ArminsFakeMovie/200000/4939_4960 - ArminsFakeMovie/200000/5477_5498 - ArminsFakeMovie/200000/5498_5546 - ArminsFakeMovie/200000/5546_5571 - ArminsFakeMovie/200000/6087_6116 - ArminsFakeMovie/200000/6116_6173 - ArminsFakeMovie/200000/6173_6199 - ArminsFakeMovie/200000/6719_6740 - ArminsFakeMovie/200000/6740_6790 - ArminsFakeMovie/200000/6790_6812 - ArminsFakeMovie/200000/7034_7035 - ArminsFakeMovie/300000/0_2659 - ArminsFakeMovie/300000/3025_3047 - ArminsFakeMovie/300000/3047_3095 - ArminsFakeMovie/300000/3095_3116 - ArminsFakeMovie/300000/3628_3650 - ArminsFakeMovie/300000/3650_3700 - ArminsFakeMovie/300000/3700_3722 - ArminsFakeMovie/300000/4267_4289 - ArminsFakeMovie/300000/4289_4335 - ArminsFakeMovie/300000/4335_4356 - ArminsFakeMovie/300000/4864_4888 - ArminsFakeMovie/300000/4888_4939 - ArminsFakeMovie/300000/4939_4960 - ArminsFakeMovie/300000/5477_5498 - ArminsFakeMovie/300000/5498_5546 - ArminsFakeMovie/300000/5546_5571 - ArminsFakeMovie/300000/6087_6116 - ArminsFakeMovie/300000/6116_6173 - ArminsFakeMovie/300000/6173_6199 - ArminsFakeMovie/300000/6719_6740 - ArminsFakeMovie/300000/6740_6790 - ArminsFakeMovie/300000/6790_6812 - ArminsFakeMovie/300000/7034_7035 $ rm $MERGED_BAM Explicit Output Filename (also enables PBI): $ $PBMERGE -o $MERGED_BAM $HQREGION_BAM $SCRAPS_BAM + ERROR: read group ID not found + [1] $ samtools view -H $MERGED_BAM - @HD\tVN:1.1\tSO:unknown\tpb:3.0.1 (esc) - @RG\tID:ca75d884\tPL:PACBIO\tDS:READTYPE=HQREGION;DeletionQV=dq;DeletionTag=dt;InsertionQV=iq;MergeQV=mq;SubstitutionQV=sq;SubstitutionTag=st;Ipd:Frames=ip;PulseWidth:Frames=pw;PkMid=pm;PkMean=pa;LabelQV=pq;AltLabel=pt;AltLabelQV=pv;PulseMergeQV=pg;PulseCall=pc;PrePulseFrames=pd;PulseCallWidth=px;BINDINGKIT=100372700;SEQUENCINGKIT=100356200;BASECALLERVERSION=0.1;FRAMERATEHZ=100.000000\tPU:ArminsFakeMovie\tPM:SEQUEL (esc) - @RG\tID:e83fc9c6\tPL:PACBIO\tDS:READTYPE=SCRAP;DeletionQV=dq;DeletionTag=dt;InsertionQV=iq;MergeQV=mq;SubstitutionQV=sq;SubstitutionTag=st;Ipd:Frames=ip;PulseWidth:Frames=pw;PkMid=pm;PkMean=pa;LabelQV=pq;AltLabel=pt;AltLabelQV=pv;PulseMergeQV=pg;PulseCall=pc;PrePulseFrames=pd;PulseCallWidth=px;BINDINGKIT=100372700;SEQUENCINGKIT=100356200;BASECALLERVERSION=0.1;FRAMERATEHZ=100.000000\tPU:ArminsFakeMovie\tPM:SEQUEL (esc) - @PG\tID:baz2bam-0.15.0\tPN:baz2bam\tVN:0.15.0 (esc) - @PG\tID:bazFormat-0.3.0\tPN:bazFormat\tVN:0.3.0 (esc) - @PG\tID:bazwriter-0.15.0\tPN:bazwriter\tVN:0.15.0 (esc) - @PG\tID:pbmerge-0.7.4\tPN:pbmerge\tVN:0.7.4 (esc) + [E::hts_open_format] fail to open file '/<>/pbbam-0.7.4+ds/gendata/pacbio_ordering_merged.bam' + samtools view: failed to open "/<>/pbbam-0.7.4+ds/gendata/pacbio_ordering_merged.bam" for reading: No such file or directory + [1] $ samtools view $MERGED_BAM | cut -f 1 - ArminsFakeMovie/100000/0_2659 - ArminsFakeMovie/100000/2659_7034 - ArminsFakeMovie/100000/3025_3047 - ArminsFakeMovie/100000/3047_3095 - ArminsFakeMovie/100000/3095_3116 - ArminsFakeMovie/100000/3628_3650 - ArminsFakeMovie/100000/3650_3700 - ArminsFakeMovie/100000/3700_3722 - ArminsFakeMovie/100000/4267_4289 - ArminsFakeMovie/100000/4289_4335 - ArminsFakeMovie/100000/4335_4356 - ArminsFakeMovie/100000/4864_4888 - ArminsFakeMovie/100000/4888_4939 - ArminsFakeMovie/100000/4939_4960 - ArminsFakeMovie/100000/5477_5498 - ArminsFakeMovie/100000/5498_5546 - ArminsFakeMovie/100000/5546_5571 - ArminsFakeMovie/100000/6087_6116 - ArminsFakeMovie/100000/6116_6173 - ArminsFakeMovie/100000/6173_6199 - ArminsFakeMovie/100000/6719_6740 - ArminsFakeMovie/100000/6740_6790 - ArminsFakeMovie/100000/6790_6812 - ArminsFakeMovie/100000/7034_7035 - ArminsFakeMovie/200000/0_2659 - ArminsFakeMovie/200000/3025_3047 - ArminsFakeMovie/200000/3047_3095 - ArminsFakeMovie/200000/3095_3116 - ArminsFakeMovie/200000/3628_3650 - ArminsFakeMovie/200000/3650_3700 - ArminsFakeMovie/200000/3700_3722 - ArminsFakeMovie/200000/4267_4289 - ArminsFakeMovie/200000/4289_4335 - ArminsFakeMovie/200000/4335_4356 - ArminsFakeMovie/200000/4864_4888 - ArminsFakeMovie/200000/4888_4939 - ArminsFakeMovie/200000/4939_4960 - ArminsFakeMovie/200000/5477_5498 - ArminsFakeMovie/200000/5498_5546 - ArminsFakeMovie/200000/5546_5571 - ArminsFakeMovie/200000/6087_6116 - ArminsFakeMovie/200000/6116_6173 - ArminsFakeMovie/200000/6173_6199 - ArminsFakeMovie/200000/6719_6740 - ArminsFakeMovie/200000/6740_6790 - ArminsFakeMovie/200000/6790_6812 - ArminsFakeMovie/200000/7034_7035 - ArminsFakeMovie/300000/0_2659 - ArminsFakeMovie/300000/3025_3047 - ArminsFakeMovie/300000/3047_3095 - ArminsFakeMovie/300000/3095_3116 - ArminsFakeMovie/300000/3628_3650 - ArminsFakeMovie/300000/3650_3700 - ArminsFakeMovie/300000/3700_3722 - ArminsFakeMovie/300000/4267_4289 - ArminsFakeMovie/300000/4289_4335 - ArminsFakeMovie/300000/4335_4356 - ArminsFakeMovie/300000/4864_4888 - ArminsFakeMovie/300000/4888_4939 - ArminsFakeMovie/300000/4939_4960 - ArminsFakeMovie/300000/5477_5498 - ArminsFakeMovie/300000/5498_5546 - ArminsFakeMovie/300000/5546_5571 - ArminsFakeMovie/300000/6087_6116 - ArminsFakeMovie/300000/6116_6173 - ArminsFakeMovie/300000/6173_6199 - ArminsFakeMovie/300000/6719_6740 - ArminsFakeMovie/300000/6740_6790 - ArminsFakeMovie/300000/6790_6812 - ArminsFakeMovie/300000/7034_7035 - - $ [ -f $MERGED_BAM_PBI ] && echo "Found" || echo "Not found" - Found - - $ rm $MERGED_BAM - $ rm $MERGED_BAM_PBI - -Explicit Output Filename (with disabled PBI): - - $ $PBMERGE -o $MERGED_BAM --no-pbi $HQREGION_BAM $SCRAPS_BAM - - $ samtools view -H $MERGED_BAM - @HD\tVN:1.1\tSO:unknown\tpb:3.0.1 (esc) - @RG\tID:ca75d884\tPL:PACBIO\tDS:READTYPE=HQREGION;DeletionQV=dq;DeletionTag=dt;InsertionQV=iq;MergeQV=mq;SubstitutionQV=sq;SubstitutionTag=st;Ipd:Frames=ip;PulseWidth:Frames=pw;PkMid=pm;PkMean=pa;LabelQV=pq;AltLabel=pt;AltLabelQV=pv;PulseMergeQV=pg;PulseCall=pc;PrePulseFrames=pd;PulseCallWidth=px;BINDINGKIT=100372700;SEQUENCINGKIT=100356200;BASECALLERVERSION=0.1;FRAMERATEHZ=100.000000\tPU:ArminsFakeMovie\tPM:SEQUEL (esc) - @RG\tID:e83fc9c6\tPL:PACBIO\tDS:READTYPE=SCRAP;DeletionQV=dq;DeletionTag=dt;InsertionQV=iq;MergeQV=mq;SubstitutionQV=sq;SubstitutionTag=st;Ipd:Frames=ip;PulseWidth:Frames=pw;PkMid=pm;PkMean=pa;LabelQV=pq;AltLabel=pt;AltLabelQV=pv;PulseMergeQV=pg;PulseCall=pc;PrePulseFrames=pd;PulseCallWidth=px;BINDINGKIT=100372700;SEQUENCINGKIT=100356200;BASECALLERVERSION=0.1;FRAMERATEHZ=100.000000\tPU:ArminsFakeMovie\tPM:SEQUEL (esc) - @PG\tID:baz2bam-0.15.0\tPN:baz2bam\tVN:0.15.0 (esc) - @PG\tID:bazFormat-0.3.0\tPN:bazFormat\tVN:0.3.0 (esc) - @PG\tID:bazwriter-0.15.0\tPN:bazwriter\tVN:0.15.0 (esc) - @PG\tID:pbmerge-0.7.4\tPN:pbmerge\tVN:0.7.4 (esc) - - $ samtools view $MERGED_BAM | cut -f 1 - ArminsFakeMovie/100000/0_2659 - ArminsFakeMovie/100000/2659_7034 - ArminsFakeMovie/100000/3025_3047 - ArminsFakeMovie/100000/3047_3095 - ArminsFakeMovie/100000/3095_3116 - ArminsFakeMovie/100000/3628_3650 - ArminsFakeMovie/100000/3650_3700 - ArminsFakeMovie/100000/3700_3722 - ArminsFakeMovie/100000/4267_4289 - ArminsFakeMovie/100000/4289_4335 - ArminsFakeMovie/100000/4335_4356 - ArminsFakeMovie/100000/4864_4888 - ArminsFakeMovie/100000/4888_4939 - ArminsFakeMovie/100000/4939_4960 - ArminsFakeMovie/100000/5477_5498 - ArminsFakeMovie/100000/5498_5546 - ArminsFakeMovie/100000/5546_5571 - ArminsFakeMovie/100000/6087_6116 - ArminsFakeMovie/100000/6116_6173 - ArminsFakeMovie/100000/6173_6199 - ArminsFakeMovie/100000/6719_6740 - ArminsFakeMovie/100000/6740_6790 - ArminsFakeMovie/100000/6790_6812 - ArminsFakeMovie/100000/7034_7035 - ArminsFakeMovie/200000/0_2659 - ArminsFakeMovie/200000/3025_3047 - ArminsFakeMovie/200000/3047_3095 - ArminsFakeMovie/200000/3095_3116 - ArminsFakeMovie/200000/3628_3650 - ArminsFakeMovie/200000/3650_3700 - ArminsFakeMovie/200000/3700_3722 - ArminsFakeMovie/200000/4267_4289 - ArminsFakeMovie/200000/4289_4335 - ArminsFakeMovie/200000/4335_4356 - ArminsFakeMovie/200000/4864_4888 - ArminsFakeMovie/200000/4888_4939 - ArminsFakeMovie/200000/4939_4960 - ArminsFakeMovie/200000/5477_5498 - ArminsFakeMovie/200000/5498_5546 - ArminsFakeMovie/200000/5546_5571 - ArminsFakeMovie/200000/6087_6116 - ArminsFakeMovie/200000/6116_6173 - ArminsFakeMovie/200000/6173_6199 - ArminsFakeMovie/200000/6719_6740 - ArminsFakeMovie/200000/6740_6790 - ArminsFakeMovie/200000/6790_6812 - ArminsFakeMovie/200000/7034_7035 - ArminsFakeMovie/300000/0_2659 - ArminsFakeMovie/300000/3025_3047 - ArminsFakeMovie/300000/3047_3095 - ArminsFakeMovie/300000/3095_3116 - ArminsFakeMovie/300000/3628_3650 - ArminsFakeMovie/300000/3650_3700 - ArminsFakeMovie/300000/3700_3722 - ArminsFakeMovie/300000/4267_4289 - ArminsFakeMovie/300000/4289_4335 - ArminsFakeMovie/300000/4335_4356 - ArminsFakeMovie/300000/4864_4888 - ArminsFakeMovie/300000/4888_4939 - ArminsFakeMovie/300000/4939_4960 - ArminsFakeMovie/300000/5477_5498 - ArminsFakeMovie/300000/5498_5546 - ArminsFakeMovie/300000/5546_5571 - ArminsFakeMovie/300000/6087_6116 - ArminsFakeMovie/300000/6116_6173 - ArminsFakeMovie/300000/6173_6199 - ArminsFakeMovie/300000/6719_6740 - ArminsFakeMovie/300000/6740_6790 - ArminsFakeMovie/300000/6790_6812 - ArminsFakeMovie/300000/7034_7035 + [E::hts_open_format] fail to open file '/<>/pbbam-0.7.4+ds/gendata/pacbio_ordering_merged.bam' + samtools view: failed to open "/<>/pbbam-0.7.4+ds/gendata/pacbio_ordering_merged.bam" for reading: No such file or directory $ [ -f $MERGED_BAM_PBI ] && echo "Found" || echo "Not found" Not found $ rm $MERGED_BAM + rm: cannot remove '/<>/pbbam-0.7.4+ds/gendata/pacbio_ordering_merged.bam': No such file or directory + [1] + $ rm $MERGED_BAM_PBI + rm: cannot remove '/<>/pbbam-0.7.4+ds/gendata/pacbio_ordering_merged.bam.pbi': No such file or directory + [1] + +Explicit Output Filename (with disabled PBI): + + $ $PBMERGE -o $MERGED_BAM --no-pbi $HQREGION_BAM $SCRAPS_BAM + ERROR: read group ID not found + [1] + + $ samtools view -H $MERGED_BAM + [E::hts_open_format] fail to open file '/<>/pbbam-0.7.4+ds/gendata/pacbio_ordering_merged.bam' + samtools view: failed to open "/<>/pbbam-0.7.4+ds/gendata/pacbio_ordering_merged.bam" for reading: No such file or directory + [1] + + $ samtools view $MERGED_BAM | cut -f 1 + [E::hts_open_format] fail to open file '/<>/pbbam-0.7.4+ds/gendata/pacbio_ordering_merged.bam' + samtools view: failed to open "/<>/pbbam-0.7.4+ds/gendata/pacbio_ordering_merged.bam" for reading: No such file or directory + + $ [ -f $MERGED_BAM_PBI ] && echo "Found" || echo "Not found" + Not found + + $ rm $MERGED_BAM + rm: cannot remove '/<>/pbbam-0.7.4+ds/gendata/pacbio_ordering_merged.bam': No such file or directory + [1] tests/src/cram/pbmerge_mixed_ordering.deb.t: passed tests/src/cram/pbmerge_aligned_ordering.deb.t: passed tests/src/cram/pbindexdump_json.deb.t: passed tests/src/cram/pbindexdump_cpp.deb.t: passed tests/src/cram/pbmerge_fofn.deb.t: passed tests/src/cram/pbmerge_dataset.deb.t: failed --- tests/src/cram/pbmerge_dataset.deb.t +++ tests/src/cram/pbmerge_dataset.deb.t.err @@ -52,38 +52,61 @@ Normal Merge from XML: $ $PBMERGE -o $MERGED_BAM $INPUT_XML + ERROR: read group ID not found + [1] $ [ -f $MERGED_BAM ] && echo "Found" || echo "Not found" - Found + Not found $ [ -f $MERGED_BAM_PBI ] && echo "Found" || echo "Not found" - Found + Not found $ samtools view -H $MERGED_BAM - @HD\tVN:1.1\tSO:unknown\tpb:3.0.1 (esc) - @RG\tID:8aaede36\tPL:PACBIO\tDS:READTYPE=SUBREAD;DeletionQV=dq;DeletionTag=dt;InsertionQV=iq;MergeQV=mq;SubstitutionQV=sq;SubstitutionTag=st;Ipd:CodecV1=ip;BINDINGKIT=FakeBindKit;SEQUENCINGKIT=FakeSeqKit;BASECALLERVERSION=0.2.0;FRAMERATEHZ=100.000000\tPU:ArminsFakeMovie\tPM:SEQUEL (esc) - @RG\tID:e83fc9c6\tPL:PACBIO\tDS:READTYPE=SCRAP;DeletionQV=dq;DeletionTag=dt;InsertionQV=iq;MergeQV=mq;SubstitutionQV=sq;SubstitutionTag=st;Ipd:CodecV1=ip;BINDINGKIT=FakeBindKit;SEQUENCINGKIT=FakeSeqKit;BASECALLERVERSION=0.2.0;FRAMERATEHZ=100.000000\tPU:ArminsFakeMovie\tPM:SEQUEL (esc) - @PG\tID:BAZ_FORMAT\tVN:0.3.0 (esc) - @PG\tID:PPA-BAZ2BAM\tVN:0.1.0 (esc) - @PG\tID:PPA-BAZWRITER\tVN:0.2.0 (esc) - @PG\tID:pbmerge-0.7.4\tPN:pbmerge\tVN:0.7.4 (esc) + [E::hts_open_format] fail to open file '/<>/pbbam-0.7.4+ds/gendata/merged.bam' + samtools view: failed to open "/<>/pbbam-0.7.4+ds/gendata/merged.bam" for reading: No such file or directory + [1] $ samtools view $MERGED_BAM | cut -f 1 - ArminsFakeMovie/0/4267_4289 - ArminsFakeMovie/0/4289_4335 - ArminsFakeMovie/0/4335_4356 - ArminsFakeMovie/0/4356_4864 - ArminsFakeMovie/0/4864_4888 - ArminsFakeMovie/0/4888_4939 - ArminsFakeMovie/0/4939_4960 - ArminsFakeMovie/0/4960_5477 + [E::hts_open_format] fail to open file '/<>/pbbam-0.7.4+ds/gendata/merged.bam' + samtools view: failed to open "/<>/pbbam-0.7.4+ds/gendata/merged.bam" for reading: No such file or directory $ rm $MERGED_BAM + rm: cannot remove '/<>/pbbam-0.7.4+ds/gendata/merged.bam': No such file or directory + [1] $ rm $MERGED_BAM_PBI + rm: cannot remove '/<>/pbbam-0.7.4+ds/gendata/merged.bam.pbi': No such file or directory + [1] Normal Merge from XML (disabled PBI): $ $PBMERGE --no-pbi -o $MERGED_BAM $INPUT_XML + ERROR: read group ID not found + [1] + + $ [ -f $MERGED_BAM ] && echo "Found" || echo "Not found" + Not found + + $ [ -f $MERGED_BAM_PBI ] && echo "Found" || echo "Not found" + Not found + + $ samtools view -H $MERGED_BAM + [E::hts_open_format] fail to open file '/<>/pbbam-0.7.4+ds/gendata/merged.bam' + samtools view: failed to open "/<>/pbbam-0.7.4+ds/gendata/merged.bam" for reading: No such file or directory + [1] + + $ samtools view $MERGED_BAM | cut -f 1 + [E::hts_open_format] fail to open file '/<>/pbbam-0.7.4+ds/gendata/merged.bam' + samtools view: failed to open "/<>/pbbam-0.7.4+ds/gendata/merged.bam" for reading: No such file or directory + + $ rm $MERGED_BAM + rm: cannot remove '/<>/pbbam-0.7.4+ds/gendata/merged.bam': No such file or directory + [1] + +Write to stdout: + + $ $PBMERGE --no-pbi $INPUT_XML > $MERGED_BAM + ERROR: read group ID not found + [1] $ [ -f $MERGED_BAM ] && echo "Found" || echo "Not found" Found @@ -92,53 +115,7 @@ Not found $ samtools view -H $MERGED_BAM - @HD\tVN:1.1\tSO:unknown\tpb:3.0.1 (esc) - @RG\tID:8aaede36\tPL:PACBIO\tDS:READTYPE=SUBREAD;DeletionQV=dq;DeletionTag=dt;InsertionQV=iq;MergeQV=mq;SubstitutionQV=sq;SubstitutionTag=st;Ipd:CodecV1=ip;BINDINGKIT=FakeBindKit;SEQUENCINGKIT=FakeSeqKit;BASECALLERVERSION=0.2.0;FRAMERATEHZ=100.000000\tPU:ArminsFakeMovie\tPM:SEQUEL (esc) - @RG\tID:e83fc9c6\tPL:PACBIO\tDS:READTYPE=SCRAP;DeletionQV=dq;DeletionTag=dt;InsertionQV=iq;MergeQV=mq;SubstitutionQV=sq;SubstitutionTag=st;Ipd:CodecV1=ip;BINDINGKIT=FakeBindKit;SEQUENCINGKIT=FakeSeqKit;BASECALLERVERSION=0.2.0;FRAMERATEHZ=100.000000\tPU:ArminsFakeMovie\tPM:SEQUEL (esc) - @PG\tID:BAZ_FORMAT\tVN:0.3.0 (esc) - @PG\tID:PPA-BAZ2BAM\tVN:0.1.0 (esc) - @PG\tID:PPA-BAZWRITER\tVN:0.2.0 (esc) - @PG\tID:pbmerge-0.7.4\tPN:pbmerge\tVN:0.7.4 (esc) $ samtools view $MERGED_BAM | cut -f 1 - ArminsFakeMovie/0/4267_4289 - ArminsFakeMovie/0/4289_4335 - ArminsFakeMovie/0/4335_4356 - ArminsFakeMovie/0/4356_4864 - ArminsFakeMovie/0/4864_4888 - ArminsFakeMovie/0/4888_4939 - ArminsFakeMovie/0/4939_4960 - ArminsFakeMovie/0/4960_5477 $ rm $MERGED_BAM - -Write to stdout: - - $ $PBMERGE --no-pbi $INPUT_XML > $MERGED_BAM - - $ [ -f $MERGED_BAM ] && echo "Found" || echo "Not found" - Found - - $ [ -f $MERGED_BAM_PBI ] && echo "Found" || echo "Not found" - Not found - - $ samtools view -H $MERGED_BAM - @HD\tVN:1.1\tSO:unknown\tpb:3.0.1 (esc) - @RG\tID:8aaede36\tPL:PACBIO\tDS:READTYPE=SUBREAD;DeletionQV=dq;DeletionTag=dt;InsertionQV=iq;MergeQV=mq;SubstitutionQV=sq;SubstitutionTag=st;Ipd:CodecV1=ip;BINDINGKIT=FakeBindKit;SEQUENCINGKIT=FakeSeqKit;BASECALLERVERSION=0.2.0;FRAMERATEHZ=100.000000\tPU:ArminsFakeMovie\tPM:SEQUEL (esc) - @RG\tID:e83fc9c6\tPL:PACBIO\tDS:READTYPE=SCRAP;DeletionQV=dq;DeletionTag=dt;InsertionQV=iq;MergeQV=mq;SubstitutionQV=sq;SubstitutionTag=st;Ipd:CodecV1=ip;BINDINGKIT=FakeBindKit;SEQUENCINGKIT=FakeSeqKit;BASECALLERVERSION=0.2.0;FRAMERATEHZ=100.000000\tPU:ArminsFakeMovie\tPM:SEQUEL (esc) - @PG\tID:BAZ_FORMAT\tVN:0.3.0 (esc) - @PG\tID:PPA-BAZ2BAM\tVN:0.1.0 (esc) - @PG\tID:PPA-BAZWRITER\tVN:0.2.0 (esc) - @PG\tID:pbmerge-0.7.4\tPN:pbmerge\tVN:0.7.4 (esc) - - $ samtools view $MERGED_BAM | cut -f 1 - ArminsFakeMovie/0/4267_4289 - ArminsFakeMovie/0/4289_4335 - ArminsFakeMovie/0/4335_4356 - ArminsFakeMovie/0/4356_4864 - ArminsFakeMovie/0/4864_4888 - ArminsFakeMovie/0/4888_4939 - ArminsFakeMovie/0/4939_4960 - ArminsFakeMovie/0/4960_5477 - - $ rm $MERGED_BAM # Ran 7 tests, 0 skipped, 2 failed. debian/rules:26: recipe for target 'override_dh_auto_test' failed make[1]: *** [override_dh_auto_test] Error 1 make[1]: Leaving directory '/<>/pbbam-0.7.4+ds' 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 20170729-2236 Finished -------- E: Build failure (dpkg-buildpackage died) +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Not removing build depends: as requested Keeping session: +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: s390x Build-Space: 168148 Build-Time: 78 Distribution: artful Fail-Stage: build Host Architecture: s390x Install-Time: 24 Job: pbbam_0.7.4+ds-1.dsc Machine Architecture: s390x Package: pbbam Package-Time: 102 Source-Version: 0.7.4+ds-1 Space: 168148 Status: attempted Version: 0.7.4+ds-1 -------------------------------------------------------------------------------- Finished at 20170729-2236 Build needed 00:01:42, 168148k disc space RUN: /usr/share/launchpad-buildd/slavebin/scan-for-processes ['scan-for-processes', 'PACKAGEBUILD-12921756'] Scanning for processes to kill in build /home/buildd/build-PACKAGEBUILD-12921756/chroot-autobuild... RUN: /usr/share/launchpad-buildd/slavebin/umount-chroot ['umount-chroot', 'PACKAGEBUILD-12921756'] Unmounting chroot for build PACKAGEBUILD-12921756... RUN: /usr/share/launchpad-buildd/slavebin/remove-build ['remove-build', 'PACKAGEBUILD-12921756'] Removing build PACKAGEBUILD-12921756