RUN: /usr/share/launchpad-buildd/slavebin/slave-prep ['slave-prep'] Forking launchpad-buildd slave process... Kernel version: Linux bos01-arm64-006 4.4.0-83-generic #106-Ubuntu SMP Mon Jun 26 17:58:57 UTC 2017 aarch64 Buildd toolchain package versions: launchpad-buildd_145 python-lpbuildd_145 sbuild_0.67.0-2ubuntu7 bzr-builder_0.7.3+bzr174~ppa13~ubuntu14.10.1 bzr_2.7.0-2ubuntu3 git-build-recipe_0.3.4~git201611291343.dcee459~ubuntu16.04.1 git_1:2.7.4-0ubuntu1.1 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... 13 Jul 04:03:35 ntpdate[1839]: adjust time server 10.211.37.1 offset 0.003644 sec RUN: /usr/share/launchpad-buildd/slavebin/unpack-chroot ['unpack-chroot', 'PACKAGEBUILD-12936478', '/home/buildd/filecache-default/42e17d2fa25e748a1aa6eaeef2fe6722beaed5a9'] Unpacking chroot for build PACKAGEBUILD-12936478 RUN: /usr/share/launchpad-buildd/slavebin/mount-chroot ['mount-chroot', 'PACKAGEBUILD-12936478'] Mounting chroot for build PACKAGEBUILD-12936478 RUN: /usr/share/launchpad-buildd/slavebin/override-sources-list ['override-sources-list', 'PACKAGEBUILD-12936478', '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-12936478 RUN: /usr/share/launchpad-buildd/slavebin/add-trusted-keys ['add-trusted-keys', 'PACKAGEBUILD-12936478'] Adding trusted keys to build-PACKAGEBUILD-12936478 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-12936478', 'armhf'] Updating debian chroot for build PACKAGEBUILD-12936478 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://ftpmaster.internal/ubuntu artful-security InRelease [65.5 kB] Get:4 http://ftpmaster.internal/ubuntu artful-updates InRelease [65.5 kB] Get:5 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu artful/main armhf Packages [28.1 kB] Get:6 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu artful/main Translation-en [16.6 kB] Get:7 http://ftpmaster.internal/ubuntu artful/main armhf Packages [1101 kB] Get:8 http://ftpmaster.internal/ubuntu artful/main Translation-en [557 kB] Get:9 http://ftpmaster.internal/ubuntu artful/restricted armhf Packages [5668 B] Get:10 http://ftpmaster.internal/ubuntu artful/restricted Translation-en [2724 B] Get:11 http://ftpmaster.internal/ubuntu artful/universe armhf Packages [8016 kB] Get:12 http://ftpmaster.internal/ubuntu artful/universe Translation-en [4763 kB] Get:13 http://ftpmaster.internal/ubuntu artful/multiverse armhf Packages [131 kB] Get:14 http://ftpmaster.internal/ubuntu artful/multiverse Translation-en [109 kB] Fetched 15.1 MB in 7s (1892 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 debianutils dmsetup dpkg dpkg-dev findutils g++ g++-6 gcc gcc-6 gcc-6-base libapparmor1 libapt-pkg5.0 libasan3 libasn1-8-heimdal libatomic1 libaudit-common libaudit1 libblkid1 libcc1-0 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 libk5crypto3 libkmod2 libkrb5-26-heimdal libkrb5-3 libkrb5support0 libldap-2.4-2 libldap-common libmount1 libnpth0 libp11-kit0 libperl5.24 libpng16-16 libroken18-heimdal libselinux1 libsemanage-common libsemanage1 libsmartcols1 libsqlite3-0 libssl1.0.0 libstdc++-6-dev libstdc++6 libsystemd0 libtasn1-6 libubsan0 libudev1 libusb-0.1-4 libuuid1 libwind0-heimdal linux-libc-dev login mount openssl passwd perl perl-base perl-modules-5.24 systemd systemd-sysv tzdata util-linux 86 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 45.4 MB of archives. After this operation, 3080 kB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu artful/main armhf base-files armhf 9.6ubuntu101 [59.1 kB] Get:2 http://ftpmaster.internal/ubuntu artful/main armhf debianutils armhf 4.8.1.1 [84.3 kB] Get:3 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu artful/main armhf gcc-7-base armhf 7.1.0-9ubuntu1 [18.9 kB] Get:4 http://ftpmaster.internal/ubuntu artful/main armhf bash armhf 4.4-5ubuntu1 [527 kB] Get:5 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu artful/main armhf libgcc1 armhf 1:7.1.0-9ubuntu1 [38.4 kB] Get:6 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu artful/main armhf libstdc++6 armhf 7.1.0-9ubuntu1 [346 kB] Get:7 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu artful/main armhf binutils armhf 2.28.90.20170704-0ubuntu1 [2658 kB] Get:8 http://ftpmaster.internal/ubuntu artful/main armhf bsdutils armhf 1:2.29-1ubuntu3 [52.1 kB] Get:9 http://ftpmaster.internal/ubuntu artful/main armhf dpkg armhf 1.18.24ubuntu1 [1099 kB] Get:10 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu artful/main armhf libgomp1 armhf 7.1.0-9ubuntu1 [64.6 kB] Get:11 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu artful/main armhf libubsan0 armhf 7.1.0-9ubuntu1 [104 kB] Get:12 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu artful/main armhf libatomic1 armhf 7.1.0-9ubuntu1 [6252 B] Get:13 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu artful/main armhf libasan3 armhf 6.4.0-1ubuntu2 [292 kB] Get:14 http://ftpmaster.internal/ubuntu artful/main armhf findutils armhf 4.6.0+git+20170606-3 [277 kB] Get:15 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu artful/main armhf g++-6 armhf 6.4.0-1ubuntu2 [5925 kB] Get:16 http://ftpmaster.internal/ubuntu artful/main armhf login armhf 1:4.2-3.2ubuntu2 [301 kB] Get:17 http://ftpmaster.internal/ubuntu artful/main armhf util-linux armhf 2.29-1ubuntu3 [861 kB] Get:18 http://ftpmaster.internal/ubuntu artful/main armhf mount armhf 2.29-1ubuntu3 [124 kB] Get:19 http://ftpmaster.internal/ubuntu artful/main armhf libperl5.24 armhf 5.24.1-4ubuntu1 [2810 kB] Get:20 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu artful/main armhf libstdc++-6-dev armhf 6.4.0-1ubuntu2 [1481 kB] Get:21 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu artful/main armhf gcc-6 armhf 6.4.0-1ubuntu2 [5805 kB] Get:22 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu artful/main armhf libgcc-6-dev armhf 6.4.0-1ubuntu2 [550 kB] Get:23 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu artful/main armhf libcc1-0 armhf 7.1.0-9ubuntu1 [31.5 kB] Get:24 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu artful/main armhf cpp-6 armhf 6.4.0-1ubuntu2 [5202 kB] Get:25 http://ftpmaster.internal/ubuntu artful/main armhf perl armhf 5.24.1-4ubuntu1 [219 kB] Get:26 http://ftpmaster.internal/ubuntu artful/main armhf perl-base armhf 5.24.1-4ubuntu1 [1237 kB] Get:27 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu artful/main armhf gcc-6-base armhf 6.4.0-1ubuntu2 [17.5 kB] Get:28 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu artful/main armhf linux-libc-dev armhf 4.11.0-10.15 [903 kB] Get:29 http://ftpmaster.internal/ubuntu artful/main armhf perl-modules-5.24 all 5.24.1-4ubuntu1 [2663 kB] Get:30 http://ftpmaster.internal/ubuntu artful/main armhf libapt-pkg5.0 armhf 1.5~beta1 [722 kB] Get:31 http://ftpmaster.internal/ubuntu artful/main armhf apt-transport-https armhf 1.5~beta1 [30.7 kB] Get:32 http://ftpmaster.internal/ubuntu artful/main armhf libp11-kit0 armhf 0.23.7-2 [163 kB] Get:33 http://ftpmaster.internal/ubuntu artful/main armhf libtasn1-6 armhf 4.12-2 [30.7 kB] Get:34 http://ftpmaster.internal/ubuntu artful/main armhf libgnutls30 armhf 3.5.8-6ubuntu1 [617 kB] Get:35 http://ftpmaster.internal/ubuntu artful/main armhf apt armhf 1.5~beta1 [1067 kB] Get:36 http://ftpmaster.internal/ubuntu artful/main armhf libip4tc0 armhf 1.6.1-2ubuntu1 [17.9 kB] Get:37 http://ftpmaster.internal/ubuntu artful/main armhf libapparmor1 armhf 2.11.0-2ubuntu8 [26.0 kB] Get:38 http://ftpmaster.internal/ubuntu artful/main armhf libaudit-common all 1:2.7.7-1ubuntu1 [4118 B] Get:39 http://ftpmaster.internal/ubuntu artful/main armhf libaudit1 armhf 1:2.7.7-1ubuntu1 [35.1 kB] Get:40 http://ftpmaster.internal/ubuntu artful/main armhf libselinux1 armhf 2.6-3build1 [59.4 kB] Get:41 http://ftpmaster.internal/ubuntu artful/main armhf libsemanage-common all 2.6-2build1 [6738 B] Get:42 http://ftpmaster.internal/ubuntu artful/main armhf libsemanage1 armhf 2.6-2build1 [71.1 kB] Get:43 http://ftpmaster.internal/ubuntu artful/main armhf passwd armhf 1:4.2-3.2ubuntu2 [747 kB] Get:44 http://ftpmaster.internal/ubuntu artful/main armhf libuuid1 armhf 2.29-1ubuntu3 [14.4 kB] Get:45 http://ftpmaster.internal/ubuntu artful/main armhf libblkid1 armhf 2.29-1ubuntu3 [98.2 kB] Get:46 http://ftpmaster.internal/ubuntu artful/main armhf libgpg-error0 armhf 1.27-3 [32.0 kB] Get:47 http://ftpmaster.internal/ubuntu artful/main armhf libgcrypt20 armhf 1.7.8-2 [344 kB] Get:48 http://ftpmaster.internal/ubuntu artful/main armhf libkmod2 armhf 24-1ubuntu1 [34.8 kB] Get:49 http://ftpmaster.internal/ubuntu artful/main armhf libmount1 armhf 2.29-1ubuntu3 [106 kB] Get:50 http://ftpmaster.internal/ubuntu artful/main armhf systemd armhf 233-8ubuntu2 [2252 kB] Get:51 http://ftpmaster.internal/ubuntu artful/main armhf libsystemd0 armhf 233-8ubuntu2 [190 kB] Get:52 http://ftpmaster.internal/ubuntu artful/main armhf systemd-sysv armhf 233-8ubuntu2 [12.4 kB] Get:53 http://ftpmaster.internal/ubuntu artful/main armhf libfdisk1 armhf 2.29-1ubuntu3 [132 kB] Get:54 http://ftpmaster.internal/ubuntu artful/main armhf libsmartcols1 armhf 2.29-1ubuntu3 [60.5 kB] Get:55 http://ftpmaster.internal/ubuntu artful/main armhf libudev1 armhf 233-8ubuntu2 [51.3 kB] Get:56 http://ftpmaster.internal/ubuntu artful/main armhf libdevmapper1.02.1 armhf 2:1.02.137-2ubuntu2 [125 kB] Get:57 http://ftpmaster.internal/ubuntu artful/main armhf dmsetup armhf 2:1.02.137-2ubuntu2 [71.2 kB] Get:58 http://ftpmaster.internal/ubuntu artful/main armhf libroken18-heimdal armhf 7.1.0+dfsg-13 [33.7 kB] Get:59 http://ftpmaster.internal/ubuntu artful/main armhf libasn1-8-heimdal armhf 7.1.0+dfsg-13 [138 kB] Get:60 http://ftpmaster.internal/ubuntu artful/main armhf libheimbase1-heimdal armhf 7.1.0+dfsg-13 [23.9 kB] Get:61 http://ftpmaster.internal/ubuntu artful/main armhf libhcrypto4-heimdal armhf 7.1.0+dfsg-13 [77.4 kB] Get:62 http://ftpmaster.internal/ubuntu artful/main armhf libwind0-heimdal armhf 7.1.0+dfsg-13 [47.3 kB] Get:63 http://ftpmaster.internal/ubuntu artful/main armhf libhx509-5-heimdal armhf 7.1.0+dfsg-13 [88.3 kB] Get:64 http://ftpmaster.internal/ubuntu artful/main armhf libsqlite3-0 armhf 3.19.3-2 [416 kB] Get:65 http://ftpmaster.internal/ubuntu artful/main armhf libkrb5-26-heimdal armhf 7.1.0+dfsg-13 [168 kB] Get:66 http://ftpmaster.internal/ubuntu artful/main armhf libheimntlm0-heimdal armhf 7.1.0+dfsg-13 [13.3 kB] Get:67 http://ftpmaster.internal/ubuntu artful/main armhf libgssapi3-heimdal armhf 7.1.0+dfsg-13 [79.3 kB] Get:68 http://ftpmaster.internal/ubuntu artful/main armhf libldap-2.4-2 armhf 2.4.44+dfsg-7ubuntu1 [132 kB] Get:69 http://ftpmaster.internal/ubuntu artful/main armhf libldap-common all 2.4.44+dfsg-7ubuntu1 [16.4 kB] Get:70 http://ftpmaster.internal/ubuntu artful/main armhf libnpth0 armhf 1.5-2 [6582 B] Get:71 http://ftpmaster.internal/ubuntu artful/main armhf libssl1.0.0 armhf 1.0.2g-1ubuntu13 [711 kB] Get:72 http://ftpmaster.internal/ubuntu artful/main armhf tzdata all 2017b-2 [203 kB] Get:73 http://ftpmaster.internal/ubuntu artful/main armhf openssl armhf 1.0.2g-1ubuntu13 [485 kB] Get:74 http://ftpmaster.internal/ubuntu artful/main armhf ca-certificates all 20161130+nmu1 [186 kB] Get:75 http://ftpmaster.internal/ubuntu artful/main armhf libgssapi-krb5-2 armhf 1.15.1-1 [98.7 kB] Get:76 http://ftpmaster.internal/ubuntu artful/main armhf libkrb5-3 armhf 1.15.1-1 [231 kB] Get:77 http://ftpmaster.internal/ubuntu artful/main armhf libkrb5support0 armhf 1.15.1-1 [28.2 kB] Get:78 http://ftpmaster.internal/ubuntu artful/main armhf libk5crypto3 armhf 1.15.1-1 [82.8 kB] Get:79 http://ftpmaster.internal/ubuntu artful/main armhf libidn2-0 armhf 2.0.2-1 [86.6 kB] Get:80 http://ftpmaster.internal/ubuntu artful/main armhf libpng16-16 armhf 1.6.29-3 [157 kB] Get:81 http://ftpmaster.internal/ubuntu artful/main armhf advancecomp armhf 2.0-1 [167 kB] Get:82 http://ftpmaster.internal/ubuntu artful/main armhf cpp armhf 4:6.3.0-2ubuntu2 [27.5 kB] Get:83 http://ftpmaster.internal/ubuntu artful/main armhf dpkg-dev all 1.18.24ubuntu1 [608 kB] Get:84 http://ftpmaster.internal/ubuntu artful/main armhf libdpkg-perl all 1.18.24ubuntu1 [209 kB] Get:85 http://ftpmaster.internal/ubuntu artful/main armhf gcc armhf 4:6.3.0-2ubuntu2 [5276 B] Get:86 http://ftpmaster.internal/ubuntu artful/main armhf g++ armhf 4:6.3.0-2ubuntu2 [1492 B] Get:87 http://ftpmaster.internal/ubuntu artful/main armhf libusb-0.1-4 armhf 2:0.1.12-31 [15.6 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 45.4 MB in 3s (15.1 MB/s) (Reading database ... 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RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package ['sbuild-package', 'PACKAGEBUILD-12936478', 'armhf', 'artful', '-c', 'chroot:autobuild', '--arch=armhf', '--dist=artful', '--purge=never', '--nolog', 'samtools_1.3.1-3.dsc'] Initiating build PACKAGEBUILD-12936478 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.4.0-83-generic #106-Ubuntu SMP Mon Jun 26 17:58:57 UTC 2017 armv7l sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on bos01-arm64-006.buildd +==============================================================================+ | samtools 1.3.1-3 (armhf) 13 Jul 2017 04:06 | +==============================================================================+ Package: samtools Version: 1.3.1-3 Source Version: 1.3.1-3 Distribution: artful Machine Architecture: arm64 Host Architecture: armhf Build Architecture: armhf I: NOTICE: Log filtering will replace 'build/samtools-HxjocH/samtools-1.3.1' with '<>' I: NOTICE: Log filtering will replace 'build/samtools-HxjocH' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-12936478/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- samtools_1.3.1-3.dsc exists in .; copying to chroot Check architectures ------------------- Check dependencies ------------------ Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<>/resolver-voyAEd/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/<>/resolver-voyAEd/apt_archive ./ InRelease Get:2 copy:/<>/resolver-voyAEd/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-voyAEd/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-voyAEd/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-voyAEd/apt_archive ./ Packages [526 B] Fetched 2859 B in 0s (26.0 kB/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install core build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following 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-voyAEd/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 ... 12255 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... Merged Build-Depends: debhelper (>= 9), bash-completion, libio-pty-perl, libncurses5-dev, libhts-dev (>= 1.3.1), zlib1g-dev, automake, autoconf-archive, pkg-config, tabix (>= 1.0) Filtered Build-Depends: debhelper (>= 9), bash-completion, libio-pty-perl, libncurses5-dev, libhts-dev (>= 1.3.1), zlib1g-dev, automake, autoconf-archive, pkg-config, tabix (>= 1.0) dpkg-deb: building package 'sbuild-build-depends-samtools-dummy' in '/<>/resolver-B9KxGZ/apt_archive/sbuild-build-depends-samtools-dummy.deb'. Ign:1 copy:/<>/resolver-B9KxGZ/apt_archive ./ InRelease Get:2 copy:/<>/resolver-B9KxGZ/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-B9KxGZ/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-B9KxGZ/apt_archive ./ Sources [289 B] Get:5 copy:/<>/resolver-B9KxGZ/apt_archive ./ Packages [606 B] Fetched 3014 B in 0s (68.8 kB/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install samtools 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 autoconf-archive automake autopoint autotools-dev bash-completion bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libbsd0 libcroco3 libfile-stripnondeterminism-perl libglib2.0-0 libhts-dev libhts1 libicu57 libio-pty-perl libmagic-mgc libmagic1 libncurses5-dev libpipeline1 libsigsegv2 libtimedate-perl libtinfo-dev libtool libxml2 m4 man-db pkg-config po-debconf tabix zlib1g-dev Suggested packages: gnu-standards autoconf-doc wamerican | wordlist whois vacation dh-make gettext-doc libasprintf-dev libgettextpo-dev groff ncurses-doc libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc less www-browser libmail-box-perl Recommended packages: curl | wget | lynx-cur libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs libltdl-dev xml-core libmail-sendmail-perl The following packages will be REMOVED: pkg-create-dbgsym* The following NEW packages will be installed: autoconf autoconf-archive automake autopoint autotools-dev bash-completion bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libbsd0 libcroco3 libfile-stripnondeterminism-perl libglib2.0-0 libhts-dev libhts1 libicu57 libio-pty-perl libmagic-mgc libmagic1 libncurses5-dev libpipeline1 libsigsegv2 libtimedate-perl libtinfo-dev libtool libxml2 m4 man-db pkg-config po-debconf sbuild-build-depends-samtools-dummy tabix zlib1g-dev 0 upgraded, 40 newly installed, 1 to remove and 0 not upgraded. Need to get 17.5 MB of archives. After this operation, 67.3 MB of additional disk space will be used. 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Preparing to unpack .../38-zlib1g-dev_1%3a1.2.11.dfsg-0ubuntu1_armhf.deb ... Unpacking zlib1g-dev:armhf (1:1.2.11.dfsg-0ubuntu1) ... Selecting previously unselected package sbuild-build-depends-samtools-dummy. Preparing to unpack .../39-sbuild-build-depends-samtools-dummy_0.invalid.0_armhf.deb ... Unpacking sbuild-build-depends-samtools-dummy (0.invalid.0) ... Setting up libhts1:armhf (1.3.2-2ubuntu1) ... Setting up libarchive-zip-perl (1.59-1) ... Setting up libio-pty-perl (1:1.08-1.1build3) ... Setting up libtimedate-perl (2.3000-2) ... Setting up libsigsegv2:armhf (2.11-1) ... Setting up libhts-dev:armhf (1.3.2-2ubuntu1) ... Setting up bash-completion (1:2.1-4.3ubuntu1) ... Setting up groff-base (1.22.3-9) ... Setting up libglib2.0-0:armhf (2.53.3-1) ... No schema files found: doing nothing. Setting up libtinfo-dev:armhf (6.0+20160625-1ubuntu1) ... Setting up gettext-base (0.19.8.1-2ubuntu1) ... Setting up libpipeline1:armhf (1.4.2-1) ... Setting up m4 (1.4.18-1) ... Setting up libicu57:armhf (57.1-6) ... Setting up libbsd0:armhf (0.8.5-1) ... Setting up libxml2:armhf (2.9.4+dfsg1-2.2ubuntu1) ... Setting up libmagic-mgc (1:5.30-1) ... Setting up libmagic1:armhf (1:5.30-1) ... Setting up libcroco3:armhf (0.6.12-1) ... Setting up libncurses5-dev:armhf (6.0+20160625-1ubuntu1) ... Setting up pkg-config (0.29.1-0ubuntu2) ... Setting up autoconf-archive (20160916-1ubuntu1) ... Processing triggers for libc-bin (2.24-9ubuntu2) ... Setting up autotools-dev (20161112.1) ... Setting up tabix (1.3.2-2ubuntu1) ... Setting up bsdmainutils (9.0.12ubuntu1) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up autopoint (0.19.8.1-2ubuntu1) ... Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-0ubuntu1) ... Setting up libfile-stripnondeterminism-perl (0.038-1~build2) ... Setting up gettext (0.19.8.1-2ubuntu1) ... Setting up autoconf (2.69-10) ... Setting up file (1:5.30-1) ... Setting up intltool-debian (0.35.0+20060710.4) ... Setting up automake (1:1.15-6ubuntu1) ... update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode Setting up man-db (2.7.6.1-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libtool (2.4.6-2) ... Setting up po-debconf (1.0.20) ... Setting up dh-autoreconf (14) ... Setting up dh-strip-nondeterminism (0.038-1~build2) ... Setting up debhelper (10.4ubuntu3) ... Setting up sbuild-build-depends-samtools-dummy (0.invalid.0) ... (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 ... 15952 files and directories currently installed.) Purging configuration files for pkg-create-dbgsym (0.73) ... Processing triggers for libc-bin (2.24-9ubuntu2) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.4.0-83-generic arm64 (armv7l) 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_2.24-9ubuntu2 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 autoconf-archive_20160916-1ubuntu1 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 bash-completion_1:2.1-4.3ubuntu1 binutils_2.28.90.20170704-0ubuntu1 bsdmainutils_9.0.12ubuntu1 bsdutils_1:2.29-1ubuntu3 build-essential_12.1ubuntu2 bzip2_1.0.6-8.1 ca-certificates_20161130+nmu1 coreutils_8.26-3ubuntu3 cpp_4:6.3.0-2ubuntu2 cpp-6_6.4.0-1ubuntu2 dash_0.5.8-2.3ubuntu1 debconf_1.5.60ubuntu1 debhelper_10.4ubuntu3 debianutils_4.8.1.1 dh-autoreconf_14 dh-strip-nondeterminism_0.038-1~build2 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_2.27-2 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 libasan3_6.4.0-1ubuntu2 libasn1-8-heimdal_7.1.0+dfsg-13 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_2.29-1ubuntu3 libbsd0_0.8.5-1 libbz2-1.0_1.0.6-8.1 libc-bin_2.24-9ubuntu2 libc-dev-bin_2.24-9ubuntu2 libc6_2.24-9ubuntu2 libc6-dev_2.24-9ubuntu2 libcap-ng0_0.7.7-3 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-gnutls_7.52.1-5ubuntu1 libdb5.3_5.3.28-12 libdebconfclient0_0.213ubuntu1 libdevmapper1.02.1_2:1.02.137-2ubuntu2 libdpkg-perl_1.18.24ubuntu1 libfakeroot_1.21-1ubuntu2 libfdisk1_2.29-1ubuntu3 libffi6_3.2.1-6 libfile-stripnondeterminism-perl_0.038-1~build2 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_2.53.3-1 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_1.15.1-1 libgssapi3-heimdal_7.1.0+dfsg-13 libhcrypto4-heimdal_7.1.0+dfsg-13 libheimbase1-heimdal_7.1.0+dfsg-13 libheimntlm0-heimdal_7.1.0+dfsg-13 libhogweed4_3.3-1 libhts-dev_1.3.2-2ubuntu1 libhts1_1.3.2-2ubuntu1 libhx509-5-heimdal_7.1.0+dfsg-13 libicu57_57.1-6 libidn11_1.33-1 libidn2-0_2.0.2-1 libio-pty-perl_1:1.08-1.1build3 libip4tc0_1.6.1-2ubuntu1 libisl15_0.18-1 libk5crypto3_1.15.1-1 libkeyutils1_1.5.9-9ubuntu1 libkmod2_24-1ubuntu1 libkrb5-26-heimdal_7.1.0+dfsg-13 libkrb5-3_1.15.1-1 libkrb5support0_1.15.1-1 libksba8_1.3.5-2 libldap-2.4-2_2.4.44+dfsg-7ubuntu1 libldap-common_2.4.44+dfsg-7ubuntu1 liblockfile-bin_1.14-1 liblockfile1_1.14-1 liblz4-1_0.0~r131-2ubuntu2 liblzma5_5.2.2-1.2 libmagic-mgc_1:5.30-1 libmagic1_1:5.30-1 libmount1_2.29-1ubuntu3 libmpc3_1.0.3-1 libmpfr4_3.1.5-1 libncurses5_6.0+20160625-1ubuntu1 libncurses5-dev_6.0+20160625-1ubuntu1 libncursesw5_6.0+20160625-1ubuntu1 libnettle6_3.3-1 libnpth0_1.5-2 libp11-kit0_0.23.7-2 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_2:8.39-3 libperl5.24_5.24.1-4ubuntu1 libpipeline1_1.4.2-1 libpng16-16_1.6.29-3 libprocps6_2:3.3.12-1ubuntu2 libpsl5_0.17.0-4 libreadline7_7.0-0ubuntu2 libroken18-heimdal_7.1.0+dfsg-13 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_2.29-1ubuntu3 libsqlite3-0_3.19.3-2 libss2_1.43.4-2 libssl1.0.0_1.0.2g-1ubuntu13 libstdc++-6-dev_6.4.0-1ubuntu2 libstdc++6_7.1.0-9ubuntu1 libsystemd0_233-8ubuntu2 libtasn1-6_4.12-2 libtimedate-perl_2.3000-2 libtinfo-dev_6.0+20160625-1ubuntu1 libtinfo5_6.0+20160625-1ubuntu1 libtool_2.4.6-2 libubsan0_7.1.0-9ubuntu1 libudev1_233-8ubuntu2 libunistring0_0.9.3-5.2ubuntu1 libusb-0.1-4_2:0.1.12-31 libustr-1.0-1_1.0.4-6 libuuid1_2.29-1ubuntu3 libwind0-heimdal_7.1.0+dfsg-13 libxml2_2.9.4+dfsg1-2.2ubuntu1 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 mount_2.29-1ubuntu3 multiarch-support_2.24-9ubuntu2 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_5.24.1-4ubuntu1 perl-base_5.24.1-4ubuntu1 perl-modules-5.24_5.24.1-4ubuntu1 pinentry-curses_1.0.0-2 pkg-config_0.29.1-0ubuntu2 pkgbinarymangler_131 po-debconf_1.0.20 policyrcd-script-zg2_0.1-3 procps_2:3.3.12-1ubuntu2 readline-common_7.0-0ubuntu2 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-samtools-dummy_0.invalid.0 sed_4.4-1 sensible-utils_0.0.9 systemd_233-8ubuntu2 systemd-sysv_233-8ubuntu2 sysv-rc_2.88dsf-59.3ubuntu2 sysvinit-utils_2.88dsf-59.8git1 tabix_1.3.2-2ubuntu1 tar_1.29b-1.1 tzdata_2017b-2 ubuntu-keyring_2016.10.27 util-linux_2.29-1ubuntu3 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 Mon Oct 24 17:33:47 2016 UTC gpgv: using RSA key gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./samtools_1.3.1-3.dsc dpkg-source: info: extracting samtools in samtools-1.3.1 dpkg-source: info: unpacking samtools_1.3.1.orig.tar.gz dpkg-source: info: unpacking samtools_1.3.1-3.debian.tar.xz dpkg-source: info: applying spelling.patch dpkg-source: info: applying literal_version.patch dpkg-source: info: applying mayhem.patch dpkg-source: info: applying fix-test.patch Check disc space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=4 HOME=/home/buildd LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd MAIL=/var/mail/buildd OLDPWD=/ PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games PWD=/<> SHELL=/bin/sh SUDO_COMMAND=/usr/sbin/chroot /<> su buildd -s /bin/sh -c cd '/<>' && 'env' SUDO_GID=2501 SUDO_UID=2001 SUDO_USER=buildd TERM=unknown USER=buildd USERNAME=root dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package samtools dpkg-buildpackage: info: source version 1.3.1-3 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build samtools-1.3.1 dpkg-buildpackage: info: host architecture armhf dpkg-source: info: using options from samtools-1.3.1/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis.*|README.md)$ fakeroot debian/rules clean dh clean --parallel dh_testdir -O--parallel debian/rules override_dh_auto_clean make[1]: Entering directory '/<>' rm -f config.mk touch config.mk dh_auto_clean -- make -j4 distclean make[2]: Entering directory '/<>' rm -f test/*.new test/*.tmp test/*/*.new test/*/*.tmp test/*/*.tmp.* cd test/dat && rm -f test_input_*.bam.bai cd test/mpileup && rm -f FAIL-*.out* PASS-*.out* anomalous.[bc]*am indels.[bc]*am mpileup.*.[cs]*am mpileup.*.crai overlap50.[bc]*am expected/1.out xx#depth[12].bam* rm -f *.o misc/*.o test/*.o test/*/*.o version.h rm -f samtools libbam.a misc/ace2sam misc/maq2sam-long misc/maq2sam-short misc/md5fa misc/md5sum-lite misc/wgsim test/merge/test_bam_translate test/merge/test_rtrans_build test/merge/test_trans_tbl_init test/split/test_count_rg test/split/test_expand_format_string test/split/test_filter_header_rg test/split/test_parse_args test/vcf-miniview rm -f config.cache config.h config.log config.mk config.status rm -f TAGS make[2]: Leaving directory '/<>' make[1]: Leaving directory '/<>' dh_clean -O--parallel rm -f debian/debhelper-build-stamp rm -f debian/samtools.substvars rm -f debian/samtools.*.debhelper rm -rf debian/samtools/ rm -f debian/samtools-test.substvars rm -f debian/samtools-test.*.debhelper rm -rf debian/samtools-test/ rm -rf debian/.debhelper/ rm -f debian/*.debhelper.log rm -f debian/files find . \( \( \ \( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS \) -prune -o -type f -a \ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \ \) -exec rm -f {} + \) -o \ \( -type d -a -name autom4te.cache -prune -exec rm -rf {} + \) \) rm -f *-stamp debian/rules build-arch dh build-arch --parallel dh_testdir -a -O--parallel dh_update_autotools_config -a -O--parallel debian/rules override_dh_auto_configure make[1]: Entering directory '/<>' touch config.mk aclocal --force -I debian/ -I /usr/share/aclocal configure.ac:42: warning: AC_CONFIG_SUBDIRS: you should use literals ../../lib/autoconf/status.m4:1097: AC_CONFIG_SUBDIRS is expanded from... debian/ax_with_htslib.m4:53: AX_WITH_HTSLIB is expanded from... configure.ac:42: the top level autoconf configure.ac:42: warning: AC_CONFIG_SUBDIRS: you should use literals ../../lib/autoconf/status.m4:1097: AC_CONFIG_SUBDIRS is expanded from... debian/ax_with_htslib.m4:53: AX_WITH_HTSLIB is expanded from... configure.ac:42: the top level dh_auto_configure -- --with-htslib=system ./configure --build=arm-linux-gnueabihf --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-silent-rules --libdir=\${prefix}/lib/arm-linux-gnueabihf --libexecdir=\${prefix}/lib/arm-linux-gnueabihf --disable-maintainer-mode --disable-dependency-tracking --with-htslib=system checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... 64 checking for htslib/sam.h... yes checking for hts_version in -lhts... yes checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for Curses library... yes checking for working curses.h... yes checking for X/Open Enhanced Curses conformance... no checking for Curses color functions... yes checking for obsolete Curses functions... yes checking for zlib.h... yes checking for inflate in -lz... yes configure: creating ./config.status config.status: creating config.mk config.status: creating config.h make[1]: Leaving directory '/<>' debian/rules override_dh_auto_build make[1]: Entering directory '/<>' dh_auto_build -- \ CFLAGS="$(dpkg-buildflags --get CFLAGS)" \ CPPFLAGS="\$(DFLAGS) \$(INCLUDES) $(dpkg-buildflags --get CPPFLAGS)" \ LDFLAGS="$(dpkg-buildflags --get LDFLAGS)" make -j4 "CFLAGS=-g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security" "CPPFLAGS=\$(DFLAGS) \$(INCLUDES) -Wdate-time -D_FORTIFY_SOURCE=2" "LDFLAGS=-Wl,-Bsymbolic-functions -Wl,-z,relro" make[2]: Entering directory '/<>' gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_index.o bam_index.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_plcmd.o bam_plcmd.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_view.o sam_view.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_cat.o bam_cat.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_md.o bam_md.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_reheader.o bam_reheader.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_sort.o bam_sort.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bedidx.o bedidx.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kprobaln.o kprobaln.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_rmdup.o bam_rmdup.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_rmdupse.o bam_rmdupse.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_mate.o bam_mate.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_stat.o bam_stat.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_color.o bam_color.c echo '#define SAMTOOLS_VERSION "1.3.1"' > version.h gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf.o bam2bcf.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf_indel.o bam2bcf_indel.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o errmod.o errmod.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sample.o sample.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_opts.o sam_opts.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cut_target.o cut_target.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o phase.o phase.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2depth.o bam2depth.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o padding.o padding.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bedcov.o bedcov.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bamshuf.o bamshuf.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o faidx.o faidx.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o dict.o dict.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o stats.o stats.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o stats_isize.o stats_isize.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_flags.o bam_flags.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_split.o bam_split.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_tview.o bam_tview.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_tview_curses.o bam_tview_curses.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_tview_html.o bam_tview_html.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_lpileup.o bam_lpileup.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_quickcheck.o bam_quickcheck.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_addrprg.o bam_addrprg.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_aux.o bam_aux.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam.o bam.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_import.o bam_import.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam.o sam.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_header.o sam_header.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_plbuf.o bam_plbuf.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/ace2sam.o misc/ace2sam.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DMAQ_LONGREADS -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/maq2sam-long.o misc/maq2sam.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/maq2sam-short.o misc/maq2sam.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/md5fa.o misc/md5fa.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/md5sum-lite.o misc/md5sum-lite.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/wgsim.o misc/wgsim.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/merge/test_bam_translate.o test/merge/test_bam_translate.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test.o test/test.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/merge/test_rtrans_build.o test/merge/test_rtrans_build.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/merge/test_trans_tbl_init.o test/merge/test_trans_tbl_init.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_count_rg.o test/split/test_count_rg.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_expand_format_string.o test/split/test_expand_format_string.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_filter_header_rg.o test/split/test_filter_header_rg.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_parse_args.o test/split/test_parse_args.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/vcf-miniview.o test/vcf-miniview.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bamtk.o bamtk.c ar -csru libbam.a bam_aux.o bam.o bam_import.o sam.o sam_header.o bam_plbuf.o ar: `u' modifier ignored since `D' is the default (see `U') gcc -Wl,-Bsymbolic-functions -Wl,-z,relro -o misc/ace2sam misc/ace2sam.o -lz -ldl gcc -Wl,-Bsymbolic-functions -Wl,-z,relro -o misc/maq2sam-long misc/maq2sam-long.o -lz -ldl gcc -Wl,-Bsymbolic-functions -Wl,-z,relro -o misc/maq2sam-short misc/maq2sam-short.o -lz -ldl gcc -rdynamic -Wl,-Bsymbolic-functions -Wl,-z,relro -o misc/md5fa misc/md5fa.o -lhts -lz -ldl gcc -rdynamic -Wl,-Bsymbolic-functions -Wl,-z,relro -o misc/md5sum-lite misc/md5sum-lite.o -lhts -lz -ldl gcc -Wl,-Bsymbolic-functions -Wl,-z,relro -o misc/wgsim misc/wgsim.o -lm -lz -ldl gcc -pthread -rdynamic -Wl,-Bsymbolic-functions -Wl,-z,relro -o test/merge/test_rtrans_build test/merge/test_rtrans_build.o sam_opts.o -lhts -lz -ldl gcc -pthread -rdynamic -Wl,-Bsymbolic-functions -Wl,-z,relro -o test/merge/test_trans_tbl_init test/merge/test_trans_tbl_init.o sam_opts.o -lhts -lz -ldl gcc -pthread -rdynamic -Wl,-Bsymbolic-functions -Wl,-z,relro -o test/split/test_count_rg test/split/test_count_rg.o test/test.o sam_opts.o -lhts -lz -ldl gcc -pthread -rdynamic -Wl,-Bsymbolic-functions -Wl,-z,relro -o test/split/test_expand_format_string test/split/test_expand_format_string.o test/test.o sam_opts.o -lhts -lz -ldl gcc -pthread -rdynamic -Wl,-Bsymbolic-functions -Wl,-z,relro -o test/split/test_filter_header_rg test/split/test_filter_header_rg.o test/test.o sam_opts.o -lhts -lz -ldl gcc -pthread -rdynamic -Wl,-Bsymbolic-functions -Wl,-z,relro -o test/split/test_parse_args test/split/test_parse_args.o test/test.o sam_opts.o -lhts -lz -ldl gcc -pthread -rdynamic -Wl,-Bsymbolic-functions -Wl,-z,relro -o test/vcf-miniview test/vcf-miniview.o -lhts -lz -ldl gcc -pthread -rdynamic -Wl,-Bsymbolic-functions -Wl,-z,relro -o samtools bam_index.o bam_plcmd.o sam_view.o bam_cat.o bam_md.o bam_reheader.o bam_sort.o bedidx.o kprobaln.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o sam_opts.o cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o faidx.o dict.o stats.o stats_isize.o bam_flags.o bam_split.o bam_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o bam_quickcheck.o bam_addrprg.o libbam.a -lhts -lcurses -lm -lz -ldl gcc -pthread -rdynamic -Wl,-Bsymbolic-functions -Wl,-z,relro -o test/merge/test_bam_translate test/merge/test_bam_translate.o test/test.o sam_opts.o -lhts -lz -ldl make[2]: Leaving directory '/<>' make[1]: Leaving directory '/<>' debian/rules override_dh_auto_test make[1]: Entering directory '/<>' dh_auto_test -- \ BGZIP=/usr/bin/bgzip make -j4 test VERBOSE=1 BGZIP=/usr/bin/bgzip make[2]: Entering directory '/<>' REF_PATH=: test/test.pl --exec bgzip=/usr/bin/bgzip /usr/bin/bgzip -c -b 65272 -s 5 /tmp/eK_ZuA6n59/bgzip.dat.gz .. ok /usr/bin/bgzip -c -b 979200 -s 6 /tmp/eK_ZuA6n59/bgzip.dat.gz .. ok /usr/bin/bgzip -c -b 652804 -s 6 /tmp/eK_ZuA6n59/bgzip.dat.gz .. ok /<>/samtools faidx /tmp/eK_ZuA6n59/faidx.fa 3:11-13 | grep -v '^>' .. ok /<>/samtools faidx /tmp/eK_ZuA6n59/faidx.fa.gz 3:11-13 | grep -v '^>' .. ok /<>/samtools faidx /tmp/eK_ZuA6n59/faidx.fa 2:998-1003 | grep -v '^>' .. ok /<>/samtools faidx /tmp/eK_ZuA6n59/faidx.fa.gz 2:998-1003 | grep -v '^>' .. ok /<>/samtools faidx /tmp/eK_ZuA6n59/faidx.fa 1:100-104 | grep -v '^>' .. ok /<>/samtools faidx /tmp/eK_ZuA6n59/faidx.fa.gz 1:100-104 | grep -v '^>' .. ok /<>/samtools faidx /tmp/eK_ZuA6n59/faidx.fa 1:99998-100007 | grep -v '^>' .. ok /<>/samtools faidx /tmp/eK_ZuA6n59/faidx.fa.gz 1:99998-100007 | grep -v '^>' .. ok test_dict: /<>/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://orthanc.org/hf37d5.fa.gz /<>/test/dat/dict.fa .. ok test_dict: /<>/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://orthanc.org/hf37d5.fa.gz /tmp/eK_ZuA6n59/dict.fa.gz .. ok test_dict: cat /<>/test/dat/dict.fa | /<>/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://orthanc.org/hf37d5.fa.gz .. ok test_index: /<>/samtools index /tmp/eK_ZuA6n59/large_chrom.bam ERR: .. expected failure test_index: /<>/samtools view /tmp/eK_ZuA6n59/large_chrom.bam ref2 .. ok test_index: /<>/samtools view /tmp/eK_ZuA6n59/large_chrom.bam ref2:1-541556283 .. ok test_index: /<>/samtools index /<>/test/dat/test_input_1_a.bam && cat /<>/test/dat/test_input_1_a.bam.bai .. ok test_mpileup: /<>/samtools mpileup -b /tmp/eK_ZuA6n59/mpileup.bam.list -f /tmp/eK_ZuA6n59/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: /<>/samtools mpileup -b /tmp/eK_ZuA6n59/mpileup.cram.list -f /tmp/eK_ZuA6n59/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: /<>/samtools mpileup -uvDV -b /tmp/eK_ZuA6n59/mpileup.bam.list -f /tmp/eK_ZuA6n59/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref .. ok test_mpileup: /<>/samtools mpileup -uvDV -b /tmp/eK_ZuA6n59/mpileup.cram.list -f /tmp/eK_ZuA6n59/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref .. ok test_mpileup: /<>/samtools mpileup -uv -t DP,DPR,DV,DP4,INFO/DPR,SP -b /tmp/eK_ZuA6n59/mpileup.cram.list -f /tmp/eK_ZuA6n59/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref .. ok test_mpileup: /<>/samtools mpileup -uv -t DP,DPR,DV,DP4,INFO/DPR,SP -b /tmp/eK_ZuA6n59/mpileup.cram.list -f /tmp/eK_ZuA6n59/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref .. ok test_mpileup: /<>/samtools mpileup -B --ff 0x14 -f /tmp/eK_ZuA6n59/mpileup.ref.fa.gz -r17:1050-1060 /tmp/eK_ZuA6n59/mpileup.1.bam | grep -v mpileup .. ok test_mpileup: /<>/samtools mpileup -B --ff 0x14 -f /tmp/eK_ZuA6n59/mpileup.ref.fa.gz -r17:1050-1060 /tmp/eK_ZuA6n59/mpileup.1.cram | grep -v mpileup .. ok test_usage: samtools samtools has subcommands: dict, faidx, index, calmd, fixmate, reheader, rmdup, targetcut, addreplacerg, collate, cat, merge, mpileup, sort, split, quickcheck, fastq, fasta, bedcov, depth, flagstat, idxstats, phase, stats, flags, tview, view, depad .. ok test_usage_subcommand: samtools dict Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools faidx Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools index .. ok test_usage_subcommand: samtools calmd Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools fixmate .. ok test_usage_subcommand: samtools reheader Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools rmdup Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools targetcut Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools addreplacerg .. ok test_usage_subcommand: samtools collate Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools cat Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools merge .. ok test_usage_subcommand: samtools mpileup Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools sort .. ok test_usage_subcommand: samtools split .. ok test_usage_subcommand: samtools quickcheck .. ok test_usage_subcommand: samtools fastq .. ok test_usage_subcommand: samtools fasta .. ok test_usage_subcommand: samtools bedcov Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools depth Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools flagstat .. ok test_usage_subcommand: samtools idxstats Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools phase Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools stats .. ok test_usage_subcommand: samtools flags Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools tview Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools view .. ok test_usage_subcommand: samtools depad Usage on stderr rather than stdout .. expected failure test_view: Generating test data file .................. done 1: SAM -> BAM -> SAM Failed command: /<>/samtools view -o /tmp/eK_ZuA6n59/view.test001.bam -b /tmp/eK_ZuA6n59/view.001.sam && /<>/samtools view -h -o /tmp/eK_ZuA6n59/view.test001.bam.sam /tmp/eK_ZuA6n59/view.test001.bam .. failed ... 2: SAM -> uncompressed BAM .. ok 3: uncompressed BAM -> SAM and compare Failed command: /<>/samtools view -o /tmp/eK_ZuA6n59/view.test003.sam -h /tmp/eK_ZuA6n59/view.test002.bam .. failed ... 4: SAM -> fast compressed BAM .. ok 5: fast compressed BAM -> SAM and compare Failed command: /<>/samtools view -o /tmp/eK_ZuA6n59/view.test005.sam -h /tmp/eK_ZuA6n59/view.test004.bam .. failed ... 6: SAM -> CRAM -> SAM (UR header tags) Failed command: /<>/samtools view -o /tmp/eK_ZuA6n59/view.test006.cram -C /tmp/eK_ZuA6n59/view.001.sam && /<>/samtools view -h -o /tmp/eK_ZuA6n59/view.test006.cram.sam /tmp/eK_ZuA6n59/view.test006.cram .. failed ... 7: SAM -> CRAM -> SAM (M5 header tags) Failed command: /<>/samtools view -o /tmp/eK_ZuA6n59/view.test007.cram -C /<>/test/dat/view.001.sam && /<>/samtools view -h -o /tmp/eK_ZuA6n59/view.test007.cram.sam /tmp/eK_ZuA6n59/view.test007.cram .. failed ... 8: BAM -> CRAM with UR -> SAM Failed command: /<>/samtools view -o /tmp/eK_ZuA6n59/view.test008.cram -C /tmp/eK_ZuA6n59/view.test001.bam && /<>/samtools view -h -o /tmp/eK_ZuA6n59/view.test008.cram.sam /tmp/eK_ZuA6n59/view.test008.cram .. failed ... 9: SAM -> BAM (M5 header tags) Failed command: /<>/samtools view -o /tmp/eK_ZuA6n59/view.test009.bam -b /<>/test/dat/view.001.sam && /<>/samtools view -h -o /tmp/eK_ZuA6n59/view.test009.bam.sam /tmp/eK_ZuA6n59/view.test009.bam .. failed ... 10: SAM -> BAM -> CRAM -> SAM (M5 header tags) Failed command: /<>/samtools view -o /tmp/eK_ZuA6n59/view.test010.cram -C /tmp/eK_ZuA6n59/view.test009.bam && /<>/samtools view -h -o /tmp/eK_ZuA6n59/view.test010.cram.sam /tmp/eK_ZuA6n59/view.test010.cram .. failed ... 11: CRAM -> BAM with UR Failed command: /<>/samtools view -o /tmp/eK_ZuA6n59/view.test011.bam -b /tmp/eK_ZuA6n59/view.test008.cram && /<>/samtools view -h -o /tmp/eK_ZuA6n59/view.test011.bam.sam /tmp/eK_ZuA6n59/view.test011.bam .. failed ... 12: CRAM -> BAM with M5 Failed command: /<>/samtools view -o /tmp/eK_ZuA6n59/view.test012.bam -b /tmp/eK_ZuA6n59/view.test010.cram && /<>/samtools view -h -o /tmp/eK_ZuA6n59/view.test012.bam.sam /tmp/eK_ZuA6n59/view.test012.bam .. failed ... 13: SAM -> SAM via stdout Failed command: /<>/samtools view -h /tmp/eK_ZuA6n59/view.001.sam .. failed ... 14: SAM -> BAM via stdout .. ok 15: SAM -> CRAM via stdout Failed command: /<>/samtools view -C /tmp/eK_ZuA6n59/view.001.sam && /<>/samtools view -h -o /tmp/eK_ZuA6n59/view.test015.cram.sam /tmp/eK_ZuA6n59/view.test015.cram .. failed ... 16: SAM from stdin -> SAM Failed command: /<>/samtools view -o /tmp/eK_ZuA6n59/view.test016.sam -h - .. failed ... 17: BAM from stdin -> SAM Failed command: /<>/samtools view -o /tmp/eK_ZuA6n59/view.test017.sam -h - .. failed ... 18: CRAM from stdin -> SAM Failed command: /<>/samtools view -o /tmp/eK_ZuA6n59/view.test018.sam -h - .. failed ... 19: samtools view -H (SAM input) .. ok 20: samtools view -H (BAM input) .. ok 21: samtools view -H (CRAM input) .. ok 22: No headers (SAM input) Failed command: /<>/samtools view -o /tmp/eK_ZuA6n59/view.test022.body /tmp/eK_ZuA6n59/view.001.sam .. failed ... 23: No headers (BAM input) Failed command: /<>/samtools view -o /tmp/eK_ZuA6n59/view.test023.body /tmp/eK_ZuA6n59/view.test001.bam .. failed ... 24: No headers (CRAM input) Failed command: /<>/samtools view -o /tmp/eK_ZuA6n59/view.test024.body /tmp/eK_ZuA6n59/view.test006.cram .. failed ... 25: Filter -f 128 (SAM input) .. ok 26: Count -f 128 (SAM input) .. ok 27: Filter -f 128 (BAM input) .. ok 28: Count -f 128 (BAM input) .. ok 29: Filter -f 128 (CRAM input) .. ok 30: Count -f 128 (CRAM input) .. ok 31: Filter -F 128 (SAM input) Failed command: /<>/samtools view -o /tmp/eK_ZuA6n59/view.test031.sam -h -F 128 /tmp/eK_ZuA6n59/view.001.sam .. failed ... 32: Count -F 128 (SAM input) .. ok 33: Filter -F 128 (BAM input) Failed command: /<>/samtools view -o /tmp/eK_ZuA6n59/view.test033.sam -h -F 128 /tmp/eK_ZuA6n59/view.test001.bam .. failed ... 34: Count -F 128 (BAM input) .. ok 35: Filter -F 128 (CRAM input) Failed command: /<>/samtools view -o /tmp/eK_ZuA6n59/view.test035.sam -h -F 128 /tmp/eK_ZuA6n59/view.test006.cram .. failed ... 36: Count -F 128 (CRAM input) .. ok 37: Filter -F 128 -f 2 (SAM input) Failed command: /<>/samtools view -o /tmp/eK_ZuA6n59/view.test037.sam -h -F 128 -f 2 /tmp/eK_ZuA6n59/view.001.sam .. failed ... 38: Count -F 128 -f 2 (SAM input) .. ok 39: Filter -F 128 -f 2 (BAM input) Failed command: /<>/samtools view -o /tmp/eK_ZuA6n59/view.test039.sam -h -F 128 -f 2 /tmp/eK_ZuA6n59/view.test001.bam .. failed ... 40: Count -F 128 -f 2 (BAM input) .. ok 41: Filter -F 128 -f 2 (CRAM input) Failed command: /<>/samtools view -o /tmp/eK_ZuA6n59/view.test041.sam -h -F 128 -f 2 /tmp/eK_ZuA6n59/view.test006.cram .. failed ... 42: Count -F 128 -f 2 (CRAM input) .. ok 43: Filter -r grp2 (SAM input) Failed command: /<>/samtools view -o /tmp/eK_ZuA6n59/view.test043.sam -h -r grp2 /tmp/eK_ZuA6n59/view.001.sam .. failed ... 44: Count -r grp2 (SAM input) .. ok 45: Filter -r grp2 (BAM input) Failed command: /<>/samtools view -o /tmp/eK_ZuA6n59/view.test045.sam -h -r grp2 /tmp/eK_ZuA6n59/view.test001.bam .. failed ... 46: Count -r grp2 (BAM input) .. ok 47: Filter -r grp2 (CRAM input) Failed command: /<>/samtools view -o /tmp/eK_ZuA6n59/view.test047.sam -h -r grp2 /tmp/eK_ZuA6n59/view.test006.cram .. failed ... 48: Count -r grp2 (CRAM input) .. ok 49: Filter -R /tmp/eK_ZuA6n59/view.001.fogn (SAM input) Failed command: /<>/samtools view -o /tmp/eK_ZuA6n59/view.test049.sam -h -R /tmp/eK_ZuA6n59/view.001.fogn /tmp/eK_ZuA6n59/view.001.sam .. failed ... 50: Count -R /tmp/eK_ZuA6n59/view.001.fogn (SAM input) .. ok 51: Filter -R /tmp/eK_ZuA6n59/view.001.fogn (BAM input) Failed command: /<>/samtools view -o /tmp/eK_ZuA6n59/view.test051.sam -h -R /tmp/eK_ZuA6n59/view.001.fogn /tmp/eK_ZuA6n59/view.test001.bam .. failed ... 52: Count -R /tmp/eK_ZuA6n59/view.001.fogn (BAM input) .. ok 53: Filter -R /tmp/eK_ZuA6n59/view.001.fogn (CRAM input) Failed command: /<>/samtools view -o /tmp/eK_ZuA6n59/view.test053.sam -h -R /tmp/eK_ZuA6n59/view.001.fogn /tmp/eK_ZuA6n59/view.test006.cram .. failed ... 54: Count -R /tmp/eK_ZuA6n59/view.001.fogn (CRAM input) .. ok 55: Filter -R /tmp/eK_ZuA6n59/view.001.fogn -r grp2 (SAM input) Failed command: /<>/samtools view -o /tmp/eK_ZuA6n59/view.test055.sam -h -R /tmp/eK_ZuA6n59/view.001.fogn -r grp2 /tmp/eK_ZuA6n59/view.001.sam .. failed ... 56: Count -R /tmp/eK_ZuA6n59/view.001.fogn -r grp2 (SAM input).. ok 57: Filter -R /tmp/eK_ZuA6n59/view.001.fogn -r grp2 (BAM input) Failed command: /<>/samtools view -o /tmp/eK_ZuA6n59/view.test057.sam -h -R /tmp/eK_ZuA6n59/view.001.fogn -r grp2 /tmp/eK_ZuA6n59/view.test001.bam .. failed ... 58: Count -R /tmp/eK_ZuA6n59/view.001.fogn -r grp2 (BAM input).. ok 59: Filter -R /tmp/eK_ZuA6n59/view.001.fogn -r grp2 (CRAM input) Failed command: /<>/samtools view -o /tmp/eK_ZuA6n59/view.test059.sam -h -R /tmp/eK_ZuA6n59/view.001.fogn -r grp2 /tmp/eK_ZuA6n59/view.test006.cram .. failed ... 60: Count -R /tmp/eK_ZuA6n59/view.001.fogn -r grp2 (CRAM input).. ok 61: Filter -r grp2 -R /tmp/eK_ZuA6n59/view.001.fogn (SAM input) Failed command: /<>/samtools view -o /tmp/eK_ZuA6n59/view.test061.sam -h -r grp2 -R /tmp/eK_ZuA6n59/view.001.fogn /tmp/eK_ZuA6n59/view.001.sam .. failed ... 62: Count -r grp2 -R /tmp/eK_ZuA6n59/view.001.fogn (SAM input).. ok 63: Filter -r grp2 -R /tmp/eK_ZuA6n59/view.001.fogn (BAM input) Failed command: /<>/samtools view -o /tmp/eK_ZuA6n59/view.test063.sam -h -r grp2 -R /tmp/eK_ZuA6n59/view.001.fogn /tmp/eK_ZuA6n59/view.test001.bam .. failed ... 64: Count -r grp2 -R /tmp/eK_ZuA6n59/view.001.fogn (BAM input).. ok 65: Filter -r grp2 -R /tmp/eK_ZuA6n59/view.001.fogn (CRAM input) Failed command: /<>/samtools view -o /tmp/eK_ZuA6n59/view.test065.sam -h -r grp2 -R /tmp/eK_ZuA6n59/view.001.fogn /tmp/eK_ZuA6n59/view.test006.cram .. failed ... 66: Count -r grp2 -R /tmp/eK_ZuA6n59/view.001.fogn (CRAM input).. ok 67: Filter -l Library 2 (SAM input) Failed command: /<>/samtools view -o /tmp/eK_ZuA6n59/view.test067.sam -h -l Library 2 /tmp/eK_ZuA6n59/view.001.sam .. failed ... 68: Count -l Library 2 (SAM input) .. ok 69: Filter -l Library 2 (BAM input) Failed command: /<>/samtools view -o /tmp/eK_ZuA6n59/view.test069.sam -h -l Library 2 /tmp/eK_ZuA6n59/view.test001.bam .. failed ... 70: Count -l Library 2 (BAM input) .. ok 71: Filter -l Library 2 (CRAM input) Failed command: /<>/samtools view -o /tmp/eK_ZuA6n59/view.test071.sam -h -l Library 2 /tmp/eK_ZuA6n59/view.test006.cram .. failed ... 72: Count -l Library 2 (CRAM input) .. ok 73: Filter -l Library 3 (SAM input) .. ok 74: Count -l Library 3 (SAM input) .. ok 75: Filter -l Library 3 (BAM input) .. ok 76: Count -l Library 3 (BAM input) .. ok 77: Filter -l Library 3 (CRAM input) .. ok 78: Count -l Library 3 (CRAM input) .. ok 79: Filter -q 50 (SAM input) .. ok 80: Count -q 50 (SAM input) .. ok 81: Filter -q 50 (BAM input) .. ok 82: Count -q 50 (BAM input) .. ok 83: Filter -q 50 (CRAM input) .. ok 84: Count -q 50 (CRAM input) .. ok 85: Filter -q 99 (SAM input) .. ok 86: Count -q 99 (SAM input) .. ok 87: Filter -q 99 (BAM input) .. ok 88: Count -q 99 (BAM input) .. ok 89: Filter -q 99 (CRAM input) .. ok 90: Count -q 99 (CRAM input) .. ok 91: Filter -q 100 (SAM input) .. ok 92: Count -q 100 (SAM input) .. ok 93: Filter -q 100 (BAM input) .. ok 94: Count -q 100 (BAM input) .. ok 95: Filter -q 100 (CRAM input) .. ok 96: Count -q 100 (CRAM input) .. ok 97: Filter -x fa (SAM input) .. ok 98: Count -x fa (SAM input) .. ok 99: Filter -x fa (BAM input) .. ok 100: Count -x fa (BAM input) .. ok 101: Filter -x fa (CRAM input) .. ok 102: Count -x fa (CRAM input) .. ok 103: Filter -x fa -x ha (SAM input) .. ok 104: Count -x fa -x ha (SAM input) .. ok 105: Filter -x fa -x ha (BAM input) .. ok 106: Count -x fa -x ha (BAM input) .. ok 107: Filter -x fa -x ha (CRAM input) .. ok 108: Count -x fa -x ha (CRAM input) .. ok 109: Filter -x fa -r grp2 (SAM input) .. ok 110: Count -x fa -r grp2 (SAM input) .. ok 111: Filter -x fa -r grp2 (BAM input) .. ok 112: Count -x fa -r grp2 (BAM input) .. ok 113: Filter -x fa -r grp2 (CRAM input) .. ok 114: Count -x fa -r grp2 (CRAM input) .. ok 115: Filter -x RG -r grp2 (SAM input) Failed command: /<>/samtools view -o /tmp/eK_ZuA6n59/view.test115.sam -h -x RG -r grp2 /tmp/eK_ZuA6n59/view.001.sam .. failed ... 116: Count -x RG -r grp2 (SAM input) .. ok 117: Filter -x RG -r grp2 (BAM input) Failed command: /<>/samtools view -o /tmp/eK_ZuA6n59/view.test117.sam -h -x RG -r grp2 /tmp/eK_ZuA6n59/view.test001.bam .. failed ... 118: Count -x RG -r grp2 (BAM input) .. ok 119: Filter -x RG -r grp2 (CRAM input) Failed command: /<>/samtools view -o /tmp/eK_ZuA6n59/view.test119.sam -h -x RG -r grp2 /tmp/eK_ZuA6n59/view.test006.cram .. failed ... 120: Count -x RG -r grp2 (CRAM input) .. ok 121: Filter -m 10 (SAM input) Failed command: /<>/samtools view -o /tmp/eK_ZuA6n59/view.test121.sam -h -m 10 /tmp/eK_ZuA6n59/view.001.sam .. failed ... 122: Count -m 10 (SAM input) .. ok 123: Filter -m 10 (BAM input) Failed command: /<>/samtools view -o /tmp/eK_ZuA6n59/view.test123.sam -h -m 10 /tmp/eK_ZuA6n59/view.test001.bam .. failed ... 124: Count -m 10 (BAM input) .. ok 125: Filter -m 10 (CRAM input) Failed command: /<>/samtools view -o /tmp/eK_ZuA6n59/view.test125.sam -h -m 10 /tmp/eK_ZuA6n59/view.test006.cram .. failed ... 126: Count -m 10 (CRAM input) .. ok 127: Filter -m 11 (SAM input) .. ok 128: Count -m 11 (SAM input) .. ok 129: Filter -m 11 (BAM input) .. ok 130: Count -m 11 (BAM input) .. ok 131: Filter -m 11 (CRAM input) .. ok 132: Count -m 11 (CRAM input) .. ok 133: Filter -m 15 (SAM input) .. ok 134: Count -m 15 (SAM input) .. ok 135: Filter -m 15 (BAM input) .. ok 136: Count -m 15 (BAM input) .. ok 137: Filter -m 15 (CRAM input) .. ok 138: Count -m 15 (CRAM input) .. ok 139: Filter -m 16 (SAM input) .. ok 140: Count -m 16 (SAM input) .. ok 141: Filter -m 16 (BAM input) .. ok 142: Count -m 16 (BAM input) .. ok 143: Filter -m 16 (CRAM input) .. ok 144: Count -m 16 (CRAM input) .. ok 145: 1bp reads file SAM -> BAM -> SAM .. ok 146: 1bp reads file SAM -> CRAM -> SAM .. ok 146: Region Z (BAM input) .. ok 147: Count Z (BAM input) .. ok 148: Region Z (CRAM input) .. ok 149: Count Z (CRAM input) .. ok 150: Region Z:30 (BAM input) .. ok 151: Count Z:30 (BAM input) .. ok 152: Region Z:30 (CRAM input) .. ok 153: Count Z:30 (CRAM input) .. ok 154: Region Z:20-40 (BAM input) .. ok 155: Count Z:20-40 (BAM input) .. ok 156: Region Z:20-40 (CRAM input) .. ok 157: Count Z:20-40 (CRAM input) .. ok 158: Region ref1 (BAM input) Failed command: /<>/samtools view -o /tmp/eK_ZuA6n59/view.test158.sam -h /tmp/eK_ZuA6n59/view.test001.bam ref1 .. failed ... 159: Count ref1 (BAM input) .. ok 160: Region ref1 (CRAM input) Failed command: /<>/samtools view -o /tmp/eK_ZuA6n59/view.test160.sam -h /tmp/eK_ZuA6n59/view.test006.cram ref1 .. failed ... 161: Count ref1 (CRAM input) .. ok 162: Region ref1:15 (BAM input) Failed command: /<>/samtools view -o /tmp/eK_ZuA6n59/view.test162.sam -h /tmp/eK_ZuA6n59/view.test001.bam ref1:15 .. failed ... 163: Count ref1:15 (BAM input) .. ok 164: Region ref1:15 (CRAM input) Failed command: /<>/samtools view -o /tmp/eK_ZuA6n59/view.test164.sam -h /tmp/eK_ZuA6n59/view.test006.cram ref1:15 .. failed ... 165: Count ref1:15 (CRAM input) .. ok 166: Region ref1:15-45 (BAM input) Failed command: /<>/samtools view -o /tmp/eK_ZuA6n59/view.test166.sam -h /tmp/eK_ZuA6n59/view.test001.bam ref1:15-45 .. failed ... 167: Count ref1:15-45 (BAM input) .. ok 168: Region ref1:15-45 (CRAM input) Failed command: /<>/samtools view -o /tmp/eK_ZuA6n59/view.test168.sam -h /tmp/eK_ZuA6n59/view.test006.cram ref1:15-45 .. failed ... 169: Count ref1:15-45 (CRAM input) .. ok 170: Region ref1:15-45 ref2 (BAM input) Failed command: /<>/samtools view -o /tmp/eK_ZuA6n59/view.test170.sam -h /tmp/eK_ZuA6n59/view.test001.bam ref1:15-45 ref2 .. failed ... 171: Count ref1:15-45 ref2 (BAM input) .. ok 172: Region ref1:15-45 ref2 (CRAM input) Failed command: /<>/samtools view -o /tmp/eK_ZuA6n59/view.test172.sam -h /tmp/eK_ZuA6n59/view.test006.cram ref1:15-45 ref2 .. failed ... 173: Count ref1:15-45 ref2 (CRAM input) .. ok 174: Region ref1:15-45 ref2:16 (BAM input) Failed command: /<>/samtools view -o /tmp/eK_ZuA6n59/view.test174.sam -h /tmp/eK_ZuA6n59/view.test001.bam ref1:15-45 ref2:16 .. failed ... 175: Count ref1:15-45 ref2:16 (BAM input) .. ok 176: Region ref1:15-45 ref2:16 (CRAM input) Failed command: /<>/samtools view -o /tmp/eK_ZuA6n59/view.test176.sam -h /tmp/eK_ZuA6n59/view.test006.cram ref1:15-45 ref2:16 .. failed ... 177: Count ref1:15-45 ref2:16 (CRAM input) .. ok 178: Region ref1:15-45 ref2:16-31 (BAM input) Failed command: /<>/samtools view -o /tmp/eK_ZuA6n59/view.test178.sam -h /tmp/eK_ZuA6n59/view.test001.bam ref1:15-45 ref2:16-31 .. failed ... 179: Count ref1:15-45 ref2:16-31 (BAM input) .. ok 180: Region ref1:15-45 ref2:16-31 (CRAM input) Failed command: /<>/samtools view -o /tmp/eK_ZuA6n59/view.test180.sam -h /tmp/eK_ZuA6n59/view.test006.cram ref1:15-45 ref2:16-31 .. failed ... 181: Count ref1:15-45 ref2:16-31 (CRAM input) .. ok 182: Region ref1:15-15 ref1:45-45 (BAM input) Failed command: /<>/samtools view -o /tmp/eK_ZuA6n59/view.test182.sam -h /tmp/eK_ZuA6n59/view.test001.bam ref1:15-15 ref1:45-45 .. failed ... 183: Count ref1:15-15 ref1:45-45 (BAM input) .. ok 184: Region ref1:15-15 ref1:45-45 (CRAM input) Failed command: /<>/samtools view -o /tmp/eK_ZuA6n59/view.test184.sam -h /tmp/eK_ZuA6n59/view.test006.cram ref1:15-15 ref1:45-45 .. failed ... 185: Count ref1:15-15 ref1:45-45 (CRAM input) .. ok 186: Region -f 128 ref1 (BAM input) .. ok 187: Count -f 128 ref1 (BAM input) .. ok 188: Region -f 128 ref1 (CRAM input) .. ok 189: Count -f 128 ref1 (CRAM input) .. ok 190: Region -q 50 ref1:15-45 (BAM input) .. ok 191: Count -q 50 ref1:15-45 (BAM input) .. ok 192: Region -q 50 ref1:15-45 (CRAM input) .. ok 193: Count -q 50 ref1:15-45 (CRAM input) .. ok 194: Region -r grp2 ref1:15-45 (BAM input) Failed command: /<>/samtools view -o /tmp/eK_ZuA6n59/view.test194.sam -h -r grp2 /tmp/eK_ZuA6n59/view.test001.bam ref1:15-45 .. failed ... 195: Count -r grp2 ref1:15-45 (BAM input) .. ok 196: Region -r grp2 ref1:15-45 (CRAM input) Failed command: /<>/samtools view -o /tmp/eK_ZuA6n59/view.test196.sam -h -r grp2 /tmp/eK_ZuA6n59/view.test006.cram ref1:15-45 .. failed ... 197: Count -r grp2 ref1:15-45 (CRAM input) .. ok 198: Region -L /<>/test/dat/view.002.01.bed (BAM input).. ok 199: Count -L /<>/test/dat/view.002.01.bed (BAM input).. ok 200: Region -L /<>/test/dat/view.002.01.bed (CRAM input).. ok 201: Count -L /<>/test/dat/view.002.01.bed (CRAM input).. ok 202: Region -L /<>/test/dat/view.002.02.bed (BAM input).. ok 203: Count -L /<>/test/dat/view.002.02.bed (BAM input).. ok 204: Region -L /<>/test/dat/view.002.02.bed (CRAM input).. ok 205: Count -L /<>/test/dat/view.002.02.bed (CRAM input).. ok 206: Region -L /<>/test/dat/view.001.01.bed (BAM input) Failed command: /<>/samtools view -o /tmp/eK_ZuA6n59/view.test206.sam -h -L /<>/test/dat/view.001.01.bed /tmp/eK_ZuA6n59/view.test001.bam .. failed ... 207: Count -L /<>/test/dat/view.001.01.bed (BAM input).. ok 208: Region -L /<>/test/dat/view.001.01.bed (CRAM input) Failed command: /<>/samtools view -o /tmp/eK_ZuA6n59/view.test208.sam -h -L /<>/test/dat/view.001.01.bed /tmp/eK_ZuA6n59/view.test006.cram .. failed ... 209: Count -L /<>/test/dat/view.001.01.bed (CRAM input).. ok 210: Region -L /<>/test/dat/view.001.02.bed (BAM input) Failed command: /<>/samtools view -o /tmp/eK_ZuA6n59/view.test210.sam -h -L /<>/test/dat/view.001.02.bed /tmp/eK_ZuA6n59/view.test001.bam .. failed ... 211: Count -L /<>/test/dat/view.001.02.bed (BAM input).. ok 212: Region -L /<>/test/dat/view.001.02.bed (CRAM input) Failed command: /<>/samtools view -o /tmp/eK_ZuA6n59/view.test212.sam -h -L /<>/test/dat/view.001.02.bed /tmp/eK_ZuA6n59/view.test006.cram .. failed ... 213: Count -L /<>/test/dat/view.001.02.bed (CRAM input).. ok 214: Region -L /<>/test/dat/view.002.01.bed Z (BAM input).. ok 215: Count -L /<>/test/dat/view.002.01.bed Z (BAM input).. ok 216: Region -L /<>/test/dat/view.002.01.bed Z (CRAM input).. ok 217: Count -L /<>/test/dat/view.002.01.bed Z (CRAM input).. ok 218: Region -L /<>/test/dat/view.002.01.bed Z:30 (BAM input).. ok 219: Count -L /<>/test/dat/view.002.01.bed Z:30 (BAM input).. ok 220: Region -L /<>/test/dat/view.002.01.bed Z:30 (CRAM input).. ok 221: Count -L /<>/test/dat/view.002.01.bed Z:30 (CRAM input).. ok 222: Region -L /<>/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok 223: Count -L /<>/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok 224: Region -L /<>/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok 225: Count -L /<>/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok 226: Region -L /<>/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok 227: Count -L /<>/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok 228: Region -L /<>/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok 229: Count -L /<>/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok 230: Region -L /<>/test/dat/view.001.01.bed ref1:11-16 (BAM input) Failed command: /<>/samtools view -o /tmp/eK_ZuA6n59/view.test230.sam -h -L /<>/test/dat/view.001.01.bed /tmp/eK_ZuA6n59/view.test001.bam ref1:11-16 .. failed ... 231: Count -L /<>/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok 232: Region -L /<>/test/dat/view.001.01.bed ref1:11-16 (CRAM input) Failed command: /<>/samtools view -o /tmp/eK_ZuA6n59/view.test232.sam -h -L /<>/test/dat/view.001.01.bed /tmp/eK_ZuA6n59/view.test006.cram ref1:11-16 .. failed ... 233: Count -L /<>/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok 234: Region -L /<>/test/dat/view.001.01.bed ref2 (BAM input).. ok 235: Count -L /<>/test/dat/view.001.01.bed ref2 (BAM input).. ok 236: Region -L /<>/test/dat/view.001.01.bed ref2 (CRAM input).. ok 237: Count -L /<>/test/dat/view.001.01.bed ref2 (CRAM input).. ok 238: Region -L /<>/test/dat/view.001.01.bed -r grp1 (BAM input) Failed command: /<>/samtools view -o /tmp/eK_ZuA6n59/view.test238.sam -h -L /<>/test/dat/view.001.01.bed -r grp1 /tmp/eK_ZuA6n59/view.test001.bam .. failed ... 239: Count -L /<>/test/dat/view.001.01.bed -r grp1 (BAM input).. ok 240: Region -L /<>/test/dat/view.001.01.bed -r grp1 (CRAM input) Failed command: /<>/samtools view -o /tmp/eK_ZuA6n59/view.test240.sam -h -L /<>/test/dat/view.001.01.bed -r grp1 /tmp/eK_ZuA6n59/view.test006.cram .. failed ... 241: Count -L /<>/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok 242: Region -L /<>/test/dat/view.001.01.bed -f 128 (BAM input).. ok 243: Count -L /<>/test/dat/view.001.01.bed -f 128 (BAM input).. ok 244: Region -L /<>/test/dat/view.001.01.bed -f 128 (CRAM input).. ok 245: Count -L /<>/test/dat/view.001.01.bed -f 128 (CRAM input).. ok 246: Region -L /<>/test/dat/view.001.01.bed -q 5 (BAM input) Failed command: /<>/samtools view -o /tmp/eK_ZuA6n59/view.test246.sam -h -L /<>/test/dat/view.001.01.bed -q 5 /tmp/eK_ZuA6n59/view.test001.bam .. failed ... 247: Count -L /<>/test/dat/view.001.01.bed -q 5 (BAM input).. ok 248: Region -L /<>/test/dat/view.001.01.bed -q 5 (CRAM input) Failed command: /<>/samtools view -o /tmp/eK_ZuA6n59/view.test248.sam -h -L /<>/test/dat/view.001.01.bed -q 5 /tmp/eK_ZuA6n59/view.test006.cram .. failed ... 249: Count -L /<>/test/dat/view.001.01.bed -q 5 (CRAM input).. ok 250: Region -L /<>/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input) Failed command: /<>/samtools view -o /tmp/eK_ZuA6n59/view.test250.sam -h -L /<>/test/dat/view.001.01.bed -r grp1 /tmp/eK_ZuA6n59/view.test001.bam ref1:11-16 .. failed ... 251: Count -L /<>/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok 252: Region -L /<>/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input) Failed command: /<>/samtools view -o /tmp/eK_ZuA6n59/view.test252.sam -h -L /<>/test/dat/view.001.01.bed -r grp1 /tmp/eK_ZuA6n59/view.test006.cram ref1:11-16 .. failed ... 253: Count -L /<>/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok 254: Make BAM with no M5/UR tags Failed command: /<>/samtools view -o /tmp/eK_ZuA6n59/view.001.no_sq.bam -b /tmp/eK_ZuA6n59/view.001.no_m5.sam && /<>/samtools view -h -o /tmp/eK_ZuA6n59/view.001.no_sq.bam.sam /tmp/eK_ZuA6n59/view.001.no_sq.bam .. failed ... 255: Add @SQ with -t (SAM -> SAM) Failed command: /<>/samtools view -o /tmp/eK_ZuA6n59/view.test255.sam -h -t /<>/test/dat/view.001.fa.fai /tmp/eK_ZuA6n59/view.001.no_sq.sam .. failed ... 256: Add @SQ with -T (SAM -> SAM) Failed command: /<>/samtools view -o /tmp/eK_ZuA6n59/view.test256.sam -h -T /<>/test/dat/view.001.fa /tmp/eK_ZuA6n59/view.001.no_sq.sam .. failed ... 257: Add @SQ with -t (BAM -> SAM) Failed command: /<>/samtools view -o /tmp/eK_ZuA6n59/view.test257.sam -h -t /<>/test/dat/view.001.fa.fai /tmp/eK_ZuA6n59/view.001.no_sq.bam .. failed ... 258: Add @SQ with -T (BAM -> SAM) Failed command: /<>/samtools view -o /tmp/eK_ZuA6n59/view.test258.sam -h -T /<>/test/dat/view.001.fa /tmp/eK_ZuA6n59/view.001.no_sq.bam .. failed ... 259: Add @SQ with -t (SAM -> BAM) Failed command: /<>/samtools view -o /tmp/eK_ZuA6n59/view.test259.bam -b -t /<>/test/dat/view.001.fa.fai /tmp/eK_ZuA6n59/view.001.no_sq.sam && /<>/samtools view -h -o /tmp/eK_ZuA6n59/view.test259.bam.sam /tmp/eK_ZuA6n59/view.test259.bam .. failed ... 260: Add @SQ with -T (SAM -> BAM) Failed command: /<>/samtools view -o /tmp/eK_ZuA6n59/view.test260.bam -b -T /<>/test/dat/view.001.fa /tmp/eK_ZuA6n59/view.001.no_sq.sam && /<>/samtools view -h -o /tmp/eK_ZuA6n59/view.test260.bam.sam /tmp/eK_ZuA6n59/view.test260.bam .. failed ... 261: Add @SQ with -t (BAM -> BAM) Failed command: /<>/samtools view -o /tmp/eK_ZuA6n59/view.test261.bam -b -t /<>/test/dat/view.001.fa.fai /tmp/eK_ZuA6n59/view.001.no_sq.bam && /<>/samtools view -h -o /tmp/eK_ZuA6n59/view.test261.bam.sam /tmp/eK_ZuA6n59/view.test261.bam .. failed ... 262: Add @SQ with -T (BAM -> BAM) Failed command: /<>/samtools view -o /tmp/eK_ZuA6n59/view.test262.bam -b -T /<>/test/dat/view.001.fa /tmp/eK_ZuA6n59/view.001.no_sq.bam && /<>/samtools view -h -o /tmp/eK_ZuA6n59/view.test262.bam.sam /tmp/eK_ZuA6n59/view.test262.bam .. failed ... 263: Add @SQ with -t (SAM -> CRAM) Failed command: /<>/samtools view -o /tmp/eK_ZuA6n59/view.test263.cram -C -t /<>/test/dat/view.001.fa.fai /tmp/eK_ZuA6n59/view.001.no_sq.sam && /<>/samtools view -h -o /tmp/eK_ZuA6n59/view.test263.cram.sam /tmp/eK_ZuA6n59/view.test263.cram .. failed ... 264: Add @SQ with -T (SAM -> CRAM) Failed command: /<>/samtools view -o /tmp/eK_ZuA6n59/view.test264.cram -C -T /<>/test/dat/view.001.fa /tmp/eK_ZuA6n59/view.001.no_sq.sam && /<>/samtools view -h -o /tmp/eK_ZuA6n59/view.test264.cram.sam /tmp/eK_ZuA6n59/view.test264.cram .. failed ... 265: Add @SQ with -t (BAM -> CRAM) Failed command: /<>/samtools view -o /tmp/eK_ZuA6n59/view.test265.cram -C -t /<>/test/dat/view.001.fa.fai /tmp/eK_ZuA6n59/view.001.no_sq.bam && /<>/samtools view -h -o /tmp/eK_ZuA6n59/view.test265.cram.sam /tmp/eK_ZuA6n59/view.test265.cram .. failed ... 266: Add @SQ with -T (BAM -> CRAM) Failed command: /<>/samtools view -o /tmp/eK_ZuA6n59/view.test266.cram -C -T /<>/test/dat/view.001.fa /tmp/eK_ZuA6n59/view.001.no_sq.bam && /<>/samtools view -h -o /tmp/eK_ZuA6n59/view.test266.cram.sam /tmp/eK_ZuA6n59/view.test266.cram .. failed ... 267: Make CRAM with no UR field .. ok 268: Decoding CRAM with no UR field via -T Failed command: /<>/samtools view -o /tmp/eK_ZuA6n59/view.test268.sam -T /<>/test/dat/view.001.fa /tmp/eK_ZuA6n59/view.test267.cram .. failed ... 269: CIGAR B-operator removal .. ok 270: Big SAM -> BAM .. ok 271: Big SAM -> BAM (2 threads) .. ok 272: Big SAM -> BAM (4 threads) .. ok 273: Big SAM -> CRAM .. ok 274: Big SAM -> CRAM (2 threads) .. ok 275: Big SAM -> CRAM (4 threads) .. ok 276: Subsample 0.2 (SAM input) ............ ok 277: Subsample 0.5 (SAM input) ............ ok 278: Subsample 0.8 (SAM input) ............ ok 279: Subsample 0.2 (BAM input) ............ ok 280: Subsample 0.5 (BAM input) ............ ok 281: Subsample 0.8 (BAM input) ............ ok 282: Subsample 0.2 (CRAM input) ............ ok 283: Subsample 0.5 (CRAM input) ............ ok 284: Subsample 0.8 (CRAM input) ............ ok test_cat: Generating test data file .................. done Generate BAM file #1 .. ok Generate CRAM file #1 .. ok Generating test data file .................. done Generate BAM file #2 .. ok Generate CRAM file #2 .. ok Generating test data file .................. done Generate BAM file #3 .. ok Generate CRAM file #3 .. ok Generating test data file .................. done Generate BAM file #4 .. ok Generate CRAM file #4 .. ok 1: cat BAM files .. ok 2: cat recompressed BAM files .. ok 3: cat CRAM files .. ok 4: cat BAM files to stdout .. ok 5: cat recompressed BAM files to stdout .. ok 6: cat CRAM files to stdout .. ok 7: cat BAM files with new header .. ok 8: cat recompressed BAM files with new header .. ok 9: cat CRAM files with new header .. ok test_bam2fq: Generate BAM file Error reading GLOB(0xab8fc1c0): Makefile:201: recipe for target 'test' failed make[2]: *** [test] Error 255 make[2]: Leaving directory '/<>' dh_auto_test: make -j4 test VERBOSE=1 BGZIP=/usr/bin/bgzip returned exit code 2 debian/rules:27: recipe for target 'override_dh_auto_test' failed make[1]: *** [override_dh_auto_test] Error 2 make[1]: Leaving directory '/<>' debian/rules:7: 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 20170713-0409 Finished -------- E: Build failure (dpkg-buildpackage died) +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Not removing build depends: as requested Keeping session: +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: armhf Build-Space: 19176 Build-Time: 190 Distribution: artful Fail-Stage: build Host Architecture: armhf Install-Time: 40 Job: samtools_1.3.1-3.dsc Machine Architecture: arm64 Package: samtools Package-Time: 233 Source-Version: 1.3.1-3 Space: 19176 Status: attempted Version: 1.3.1-3 -------------------------------------------------------------------------------- Finished at 20170713-0409 Build needed 00:03:53, 19176k disc space RUN: /usr/share/launchpad-buildd/slavebin/scan-for-processes ['scan-for-processes', 'PACKAGEBUILD-12936478'] Scanning for processes to kill in build /home/buildd/build-PACKAGEBUILD-12936478/chroot-autobuild... RUN: /usr/share/launchpad-buildd/slavebin/umount-chroot ['umount-chroot', 'PACKAGEBUILD-12936478'] Unmounting chroot for build PACKAGEBUILD-12936478... RUN: /usr/share/launchpad-buildd/slavebin/remove-build ['remove-build', 'PACKAGEBUILD-12936478'] Removing build PACKAGEBUILD-12936478