RUN: /usr/share/launchpad-buildd/slavebin/slave-prep ['slave-prep'] Forking launchpad-buildd slave process... Kernel version: Linux bos01-arm64-033 4.4.0-87-generic #110-Ubuntu SMP Tue Jul 18 12:55:22 UTC 2017 aarch64 Buildd toolchain package versions: launchpad-buildd_147 python-lpbuildd_147 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... 29 Jul 17:42:45 ntpdate[1795]: adjust time server 10.211.37.1 offset -0.037728 sec RUN: /usr/share/launchpad-buildd/slavebin/unpack-chroot ['unpack-chroot', 'PACKAGEBUILD-13170033', '/home/buildd/filecache-default/42e17d2fa25e748a1aa6eaeef2fe6722beaed5a9'] Unpacking chroot for build PACKAGEBUILD-13170033 RUN: /usr/share/launchpad-buildd/slavebin/mount-chroot ['mount-chroot', 'PACKAGEBUILD-13170033'] Mounting chroot for build PACKAGEBUILD-13170033 RUN: /usr/share/launchpad-buildd/slavebin/override-sources-list ['override-sources-list', 'PACKAGEBUILD-13170033', 'deb http://ftpmaster.internal/ubuntu artful main universe', 'deb http://ftpmaster.internal/ubuntu artful-security main universe', 'deb http://ftpmaster.internal/ubuntu artful-updates main universe', 'deb http://ftpmaster.internal/ubuntu artful-proposed main universe'] Overriding sources.list in build-PACKAGEBUILD-13170033 RUN: /usr/share/launchpad-buildd/slavebin/update-debian-chroot ['update-debian-chroot', 'PACKAGEBUILD-13170033', 'armhf'] Updating debian chroot for build PACKAGEBUILD-13170033 Get:1 http://ftpmaster.internal/ubuntu artful InRelease [237 kB] Get:2 http://ftpmaster.internal/ubuntu artful-security InRelease [65.5 kB] Get:3 http://ftpmaster.internal/ubuntu artful-updates InRelease [65.5 kB] Get:4 http://ftpmaster.internal/ubuntu artful-proposed InRelease [235 kB] Get:5 http://ftpmaster.internal/ubuntu artful/main armhf Packages [1105 kB] Get:6 http://ftpmaster.internal/ubuntu artful/main Translation-en [558 kB] Get:7 http://ftpmaster.internal/ubuntu artful/universe armhf Packages [8028 kB] Get:8 http://ftpmaster.internal/ubuntu artful/universe Translation-en [4776 kB] Get:9 http://ftpmaster.internal/ubuntu artful-proposed/main armhf Packages [104 kB] Get:10 http://ftpmaster.internal/ubuntu artful-proposed/main Translation-en [63.8 kB] Get:11 http://ftpmaster.internal/ubuntu artful-proposed/universe armhf Packages [346 kB] Get:12 http://ftpmaster.internal/ubuntu artful-proposed/universe Translation-en [219 kB] Fetched 15.8 MB in 5s (2870 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: libperl5.24 perl-modules-5.24 Use 'sudo apt autoremove' to remove them. The following NEW packages will be installed: gcc-7-base libperl5.26 perl-modules-5.26 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 init init-system-helpers libapparmor1 libapt-pkg5.0 libasan3 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 libk5crypto3 libkmod2 libkrb5-26-heimdal libkrb5-3 libkrb5support0 libldap-2.4-2 libldap-common liblzma5 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 libubsan0 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 xz-utils 103 upgraded, 3 newly installed, 0 to remove and 0 not upgraded. Need to get 57.6 MB of archives. After this operation, 37.8 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu artful/main armhf debconf all 1.5.63 [136 kB] Get:2 http://ftpmaster.internal/ubuntu artful-proposed/main armhf perl armhf 5.26.0-4 [205 kB] Get:3 http://ftpmaster.internal/ubuntu artful-proposed/main armhf perl-modules-5.26 all 5.26.0-4 [2762 kB] Get:4 http://ftpmaster.internal/ubuntu artful/main armhf libperl5.24 armhf 5.24.1-7ubuntu1 [2794 kB] Get:5 http://ftpmaster.internal/ubuntu artful-proposed/main armhf libperl5.26 armhf 5.26.0-4 [2874 kB] Get:6 http://ftpmaster.internal/ubuntu artful-proposed/main armhf perl-base armhf 5.26.0-4 [1280 kB] Get:7 http://ftpmaster.internal/ubuntu artful/main armhf perl-modules-5.24 all 5.24.1-7ubuntu1 [2664 kB] Get:8 http://ftpmaster.internal/ubuntu artful/main armhf libc6-dev armhf 2.24-12ubuntu1 [1810 kB] Get:9 http://ftpmaster.internal/ubuntu artful/main armhf libc-dev-bin armhf 2.24-12ubuntu1 [59.4 kB] Get:10 http://ftpmaster.internal/ubuntu artful-proposed/main armhf linux-libc-dev armhf 4.11.0-11.16 [908 kB] Get:11 http://ftpmaster.internal/ubuntu artful-proposed/main armhf gcc-7-base armhf 7.1.0-10ubuntu1 [18.7 kB] Get:12 http://ftpmaster.internal/ubuntu artful-proposed/main armhf libgcc1 armhf 1:7.1.0-10ubuntu1 [38.5 kB] Get:13 http://ftpmaster.internal/ubuntu artful/main armhf libc6 armhf 2.24-12ubuntu1 [2143 kB] Get:14 http://ftpmaster.internal/ubuntu artful/main armhf libdb5.3 armhf 5.3.28-13 [589 kB] Get:15 http://ftpmaster.internal/ubuntu artful-proposed/main armhf init-system-helpers all 1.49 [37.0 kB] Get:16 http://ftpmaster.internal/ubuntu artful/main armhf base-files armhf 9.6ubuntu101 [59.1 kB] Get:17 http://ftpmaster.internal/ubuntu artful/main armhf sensible-utils all 0.0.9+nmu1 [10.2 kB] Get:18 http://ftpmaster.internal/ubuntu artful/main armhf debianutils armhf 4.8.1.1 [84.3 kB] Get:19 http://ftpmaster.internal/ubuntu artful/main armhf bash armhf 4.4-5ubuntu1 [527 kB] Get:20 http://ftpmaster.internal/ubuntu artful-proposed/main armhf bsdutils armhf 1:2.30.1-0ubuntu1 [55.3 kB] Get:21 http://ftpmaster.internal/ubuntu artful/main armhf tar armhf 1.29b-2 [209 kB] Get:22 http://ftpmaster.internal/ubuntu artful/main armhf dpkg armhf 1.18.24ubuntu1 [1099 kB] Get:23 http://ftpmaster.internal/ubuntu artful/main armhf findutils armhf 4.6.0+git+20170606-3 [277 kB] Get:24 http://ftpmaster.internal/ubuntu artful/main armhf grep armhf 3.1-2 [145 kB] Get:25 http://ftpmaster.internal/ubuntu artful/main armhf login armhf 1:4.2-3.2ubuntu2 [301 kB] Get:26 http://ftpmaster.internal/ubuntu artful-proposed/main armhf libuuid1 armhf 2.30.1-0ubuntu1 [14.1 kB] Get:27 http://ftpmaster.internal/ubuntu artful-proposed/main armhf libblkid1 armhf 2.30.1-0ubuntu1 [105 kB] Get:28 http://ftpmaster.internal/ubuntu artful/main armhf libpcre3 armhf 2:8.39-4 [208 kB] Get:29 http://ftpmaster.internal/ubuntu artful/main armhf libselinux1 armhf 2.6-3build1 [59.4 kB] Get:30 http://ftpmaster.internal/ubuntu artful-proposed/main armhf libmount1 armhf 2.30.1-0ubuntu1 [117 kB] Get:31 http://ftpmaster.internal/ubuntu artful-proposed/main armhf libfdisk1 armhf 2.30.1-0ubuntu1 [143 kB] Get:32 http://ftpmaster.internal/ubuntu artful-proposed/main armhf libsmartcols1 armhf 2.30.1-0ubuntu1 [68.5 kB] Get:33 http://ftpmaster.internal/ubuntu artful-proposed/main armhf util-linux armhf 2.30.1-0ubuntu1 [881 kB] Get:34 http://ftpmaster.internal/ubuntu artful-proposed/main armhf mount armhf 2.30.1-0ubuntu1 [123 kB] Get:35 http://ftpmaster.internal/ubuntu artful/main armhf libc-bin armhf 2.24-12ubuntu1 [491 kB] Get:36 http://ftpmaster.internal/ubuntu artful-proposed/main armhf liblzma5 armhf 5.2.2-1.3 [82.9 kB] Get:37 http://ftpmaster.internal/ubuntu artful-proposed/main armhf libstdc++6 armhf 7.1.0-10ubuntu1 [345 kB] Get:38 http://ftpmaster.internal/ubuntu artful/main armhf libapt-pkg5.0 armhf 1.5~beta1 [722 kB] Get:39 http://ftpmaster.internal/ubuntu artful/main armhf apt-transport-https armhf 1.5~beta1 [30.7 kB] Get:40 http://ftpmaster.internal/ubuntu artful/main armhf libp11-kit0 armhf 0.23.7-3 [163 kB] Get:41 http://ftpmaster.internal/ubuntu artful/main armhf libtasn1-6 armhf 4.12-2.1 [30.7 kB] Get:42 http://ftpmaster.internal/ubuntu artful/main armhf libgnutls30 armhf 3.5.8-6ubuntu1 [617 kB] Get:43 http://ftpmaster.internal/ubuntu artful/main armhf apt armhf 1.5~beta1 [1067 kB] Get:44 http://ftpmaster.internal/ubuntu artful/main armhf libip4tc0 armhf 1.6.1-2ubuntu1 [17.9 kB] Get:45 http://ftpmaster.internal/ubuntu artful-proposed/main armhf libapparmor1 armhf 2.11.0-2ubuntu10 [25.7 kB] Get:46 http://ftpmaster.internal/ubuntu artful/main armhf libaudit-common all 1:2.7.7-1ubuntu1 [4118 B] Get:47 http://ftpmaster.internal/ubuntu artful/main armhf libcap-ng0 armhf 0.7.7-3build1 [9794 B] Get:48 http://ftpmaster.internal/ubuntu artful/main armhf libaudit1 armhf 1:2.7.7-1ubuntu1 [35.1 kB] Get:49 http://ftpmaster.internal/ubuntu artful/main armhf libgpg-error0 armhf 1.27-3 [32.0 kB] Get:50 http://ftpmaster.internal/ubuntu artful/main armhf libgcrypt20 armhf 1.7.8-2 [344 kB] Get:51 http://ftpmaster.internal/ubuntu artful/main armhf libkmod2 armhf 24-1ubuntu1 [34.8 kB] Get:52 http://ftpmaster.internal/ubuntu artful-proposed/main armhf systemd armhf 234-2ubuntu1 [2643 kB] Get:53 http://ftpmaster.internal/ubuntu artful-proposed/main armhf libsystemd0 armhf 234-2ubuntu1 [195 kB] Get:54 http://ftpmaster.internal/ubuntu artful-proposed/main armhf init armhf 1.49 [6040 B] Get:55 http://ftpmaster.internal/ubuntu artful-proposed/main armhf systemd-sysv armhf 234-2ubuntu1 [13.8 kB] Get:56 http://ftpmaster.internal/ubuntu artful/main armhf libsemanage-common all 2.6-2build1 [6738 B] Get:57 http://ftpmaster.internal/ubuntu artful/main armhf libsemanage1 armhf 2.6-2build1 [71.1 kB] Get:58 http://ftpmaster.internal/ubuntu artful-proposed/main armhf libudev1 armhf 234-2ubuntu1 [51.0 kB] Get:59 http://ftpmaster.internal/ubuntu artful/main armhf passwd armhf 1:4.2-3.2ubuntu2 [747 kB] Get:60 http://ftpmaster.internal/ubuntu artful/main armhf multiarch-support armhf 2.24-12ubuntu1 [6836 B] Get:61 http://ftpmaster.internal/ubuntu artful/main armhf libdevmapper1.02.1 armhf 2:1.02.137-2ubuntu2 [125 kB] Get:62 http://ftpmaster.internal/ubuntu artful/main armhf dmsetup armhf 2:1.02.137-2ubuntu2 [71.2 kB] Get:63 http://ftpmaster.internal/ubuntu artful/main armhf libroken18-heimdal armhf 7.4.0.dfsg.1-2 [33.9 kB] Get:64 http://ftpmaster.internal/ubuntu artful/main armhf libasn1-8-heimdal armhf 7.4.0.dfsg.1-2 [138 kB] Get:65 http://ftpmaster.internal/ubuntu artful/main armhf libheimbase1-heimdal armhf 7.4.0.dfsg.1-2 [24.0 kB] Get:66 http://ftpmaster.internal/ubuntu artful/main armhf libhcrypto4-heimdal armhf 7.4.0.dfsg.1-2 [77.4 kB] Get:67 http://ftpmaster.internal/ubuntu artful/main armhf libwind0-heimdal armhf 7.4.0.dfsg.1-2 [46.9 kB] Get:68 http://ftpmaster.internal/ubuntu artful/main armhf libhx509-5-heimdal armhf 7.4.0.dfsg.1-2 [88.3 kB] Get:69 http://ftpmaster.internal/ubuntu artful/main armhf libsqlite3-0 armhf 3.19.3-3 [416 kB] Get:70 http://ftpmaster.internal/ubuntu artful/main armhf libkrb5-26-heimdal armhf 7.4.0.dfsg.1-2 [168 kB] Get:71 http://ftpmaster.internal/ubuntu artful/main armhf libheimntlm0-heimdal armhf 7.4.0.dfsg.1-2 [13.3 kB] Get:72 http://ftpmaster.internal/ubuntu artful/main armhf libgssapi3-heimdal armhf 7.4.0.dfsg.1-2 [79.5 kB] Get:73 http://ftpmaster.internal/ubuntu artful-proposed/main armhf libldap-2.4-2 armhf 2.4.45+dfsg-1ubuntu1 [132 kB] Get:74 http://ftpmaster.internal/ubuntu artful-proposed/main armhf libldap-common all 2.4.45+dfsg-1ubuntu1 [16.6 kB] Get:75 http://ftpmaster.internal/ubuntu artful/main armhf libnpth0 armhf 1.5-2 [6582 B] Get:76 http://ftpmaster.internal/ubuntu artful/main armhf libssl1.0.0 armhf 1.0.2g-1ubuntu13 [711 kB] Get:77 http://ftpmaster.internal/ubuntu artful/main armhf tzdata all 2017b-2 [203 kB] Get:78 http://ftpmaster.internal/ubuntu artful-proposed/main armhf xz-utils armhf 5.2.2-1.3 [82.0 kB] Get:79 http://ftpmaster.internal/ubuntu artful/main armhf openssl armhf 1.0.2g-1ubuntu13 [485 kB] Get:80 http://ftpmaster.internal/ubuntu artful/main armhf ca-certificates all 20161130+nmu1 [186 kB] Get:81 http://ftpmaster.internal/ubuntu artful/main armhf libgssapi-krb5-2 armhf 1.15.1-2 [98.7 kB] Get:82 http://ftpmaster.internal/ubuntu artful/main armhf libkrb5-3 armhf 1.15.1-2 [231 kB] Get:83 http://ftpmaster.internal/ubuntu artful/main armhf libkrb5support0 armhf 1.15.1-2 [28.4 kB] Get:84 http://ftpmaster.internal/ubuntu artful/main armhf libk5crypto3 armhf 1.15.1-2 [83.3 kB] Get:85 http://ftpmaster.internal/ubuntu artful/main armhf libidn2-0 armhf 2.0.2-1 [86.6 kB] Get:86 http://ftpmaster.internal/ubuntu artful/main armhf libpng16-16 armhf 1.6.30-2 [158 kB] Get:87 http://ftpmaster.internal/ubuntu artful/main armhf libpsl5 armhf 0.17.0-5 [39.4 kB] Get:88 http://ftpmaster.internal/ubuntu artful/main armhf advancecomp armhf 2.0-1 [167 kB] Get:89 http://ftpmaster.internal/ubuntu artful-proposed/main armhf binutils armhf 2.29-1ubuntu1 [2658 kB] Get:90 http://ftpmaster.internal/ubuntu artful-proposed/main armhf libgomp1 armhf 7.1.0-10ubuntu1 [64.4 kB] Get:91 http://ftpmaster.internal/ubuntu artful-proposed/main armhf libubsan0 armhf 7.1.0-10ubuntu1 [104 kB] Get:92 http://ftpmaster.internal/ubuntu artful-proposed/main armhf libatomic1 armhf 7.1.0-10ubuntu1 [6244 B] Get:93 http://ftpmaster.internal/ubuntu artful-proposed/main armhf libasan3 armhf 6.4.0-2ubuntu1 [292 kB] Get:94 http://ftpmaster.internal/ubuntu artful-proposed/main armhf g++-6 armhf 6.4.0-2ubuntu1 [5923 kB] Get:95 http://ftpmaster.internal/ubuntu artful-proposed/main armhf libstdc++-6-dev armhf 6.4.0-2ubuntu1 [1480 kB] Get:96 http://ftpmaster.internal/ubuntu artful-proposed/main armhf gcc-6 armhf 6.4.0-2ubuntu1 [5803 kB] Get:97 http://ftpmaster.internal/ubuntu artful-proposed/main armhf libgcc-6-dev armhf 6.4.0-2ubuntu1 [550 kB] Get:98 http://ftpmaster.internal/ubuntu artful-proposed/main armhf libcc1-0 armhf 7.1.0-10ubuntu1 [31.5 kB] Get:99 http://ftpmaster.internal/ubuntu artful-proposed/main armhf cpp-6 armhf 6.4.0-2ubuntu1 [5200 kB] Get:100 http://ftpmaster.internal/ubuntu artful-proposed/main armhf gcc-6-base armhf 6.4.0-2ubuntu1 [17.4 kB] Get:101 http://ftpmaster.internal/ubuntu artful/main armhf cpp armhf 4:6.3.0-2ubuntu2 [27.5 kB] Get:102 http://ftpmaster.internal/ubuntu artful/main armhf dpkg-dev all 1.18.24ubuntu1 [608 kB] Get:103 http://ftpmaster.internal/ubuntu artful/main armhf libdpkg-perl all 1.18.24ubuntu1 [209 kB] Get:104 http://ftpmaster.internal/ubuntu artful/main armhf gcc armhf 4:6.3.0-2ubuntu2 [5276 B] Get:105 http://ftpmaster.internal/ubuntu artful/main armhf g++ armhf 4:6.3.0-2ubuntu2 [1492 B] Get:106 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 57.6 MB in 2s (27.3 MB/s) (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 14054 files and directories currently installed.) Preparing to unpack .../libpcre3_2%3a8.39-4_armhf.deb ... Unpacking libpcre3:armhf (2:8.39-4) over (2:8.39-3) ... Setting up libpcre3:armhf (2:8.39-4) ... (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 14054 files and directories currently installed.) Preparing to unpack .../util-linux_2.30.1-0ubuntu1_armhf.deb ... Unpacking util-linux (2.30.1-0ubuntu1) over (2.29-1ubuntu2) ... Setting up util-linux (2.30.1-0ubuntu1) ... update-alternatives: warning: alternative /usr/bin/pg (part of link group pager) doesn't exist; removing from list of alternatives (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 14052 files and directories currently installed.) Preparing to unpack .../libapt-pkg5.0_1.5~beta1_armhf.deb ... Unpacking libapt-pkg5.0:armhf (1.5~beta1) over (1.4.1ubuntu2) ... Setting up libapt-pkg5.0:armhf (1.5~beta1) ... (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 14054 files and directories currently installed.) Preparing to unpack .../libtasn1-6_4.12-2.1_armhf.deb ... Unpacking libtasn1-6:armhf (4.12-2.1) over (4.10-1) ... Setting up libtasn1-6:armhf (4.12-2.1) ... (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 14054 files and directories currently installed.) Preparing to unpack .../apt_1.5~beta1_armhf.deb ... Unpacking apt (1.5~beta1) over (1.4.1ubuntu2) ... Setting up apt (1.5~beta1) ... (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 ... 14053 files and directories currently installed.) Preparing to unpack .../libip4tc0_1.6.1-2ubuntu1_armhf.deb ... Unpacking libip4tc0:armhf (1.6.1-2ubuntu1) over (1.6.0-3ubuntu2) ... Preparing to unpack .../libapparmor1_2.11.0-2ubuntu10_armhf.deb ... Unpacking libapparmor1:armhf (2.11.0-2ubuntu10) over (2.11.0-2ubuntu4) ... Preparing to unpack .../libaudit-common_1%3a2.7.7-1ubuntu1_all.deb ... Unpacking libaudit-common (1:2.7.7-1ubuntu1) over (1:2.6.6-1ubuntu1) ... Setting up libaudit-common (1:2.7.7-1ubuntu1) ... (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 ... 14053 files and directories currently installed.) Preparing to unpack .../libcap-ng0_0.7.7-3build1_armhf.deb ... Unpacking libcap-ng0:armhf (0.7.7-3build1) over (0.7.7-3) ... Setting up libcap-ng0:armhf (0.7.7-3build1) ... (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 ... 14053 files and directories currently installed.) Preparing to unpack .../libaudit1_1%3a2.7.7-1ubuntu1_armhf.deb ... Unpacking libaudit1:armhf (1:2.7.7-1ubuntu1) over (1:2.6.6-1ubuntu1) ... Setting up libaudit1:armhf (1:2.7.7-1ubuntu1) ... (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 ... 14053 files and directories currently installed.) Preparing to unpack .../libgpg-error0_1.27-3_armhf.deb ... Unpacking libgpg-error0:armhf (1.27-3) over (1.26-2) ... Setting up libgpg-error0:armhf (1.27-3) ... (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 ... 14053 files and directories currently installed.) Preparing to unpack .../libgcrypt20_1.7.8-2_armhf.deb ... Unpacking libgcrypt20:armhf (1.7.8-2) over (1.7.6-1) ... Setting up libgcrypt20:armhf (1.7.8-2) ... (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 ... 14053 files and directories currently installed.) Preparing to unpack .../libkmod2_24-1ubuntu1_armhf.deb ... Unpacking libkmod2:armhf (24-1ubuntu1) over (22-1.1ubuntu1) ... Preparing to unpack .../systemd_234-2ubuntu1_armhf.deb ... Unpacking systemd (234-2ubuntu1) over (232-21ubuntu3) ... dpkg: warning: unable to delete old directory '/etc/dbus-1/system.d': Directory not empty dpkg: warning: unable to delete old directory '/etc/dbus-1': Directory not empty Preparing to unpack .../libsystemd0_234-2ubuntu1_armhf.deb ... Unpacking libsystemd0:armhf (234-2ubuntu1) over (232-21ubuntu3) ... Setting up libsystemd0:armhf (234-2ubuntu1) ... (Reading database ... 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Installing new version of config file /etc/systemd/resolved.conf ... Created symlink /etc/systemd/system/dbus-org.freedesktop.resolve1.service -> /lib/systemd/system/systemd-resolved.service. Created symlink /etc/systemd/system/multi-user.target.wants/systemd-resolved.service -> /lib/systemd/system/systemd-resolved.service. 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 ... 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Current default time zone: 'Etc/UTC' Local time is now: Sat Jul 29 17:43:28 UTC 2017. Universal Time is now: Sat Jul 29 17:43:28 UTC 2017. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up systemd-sysv (234-2ubuntu1) ... Setting up libubsan0:armhf (7.1.0-10ubuntu1) ... Setting up gcc-6-base:armhf (6.4.0-2ubuntu1) ... Setting up linux-libc-dev:armhf (4.11.0-11.16) ... Setting up advancecomp (2.0-1) ... Setting up libroken18-heimdal:armhf (7.4.0.dfsg.1-2) ... Setting up libdevmapper1.02.1:armhf (2:1.02.137-2ubuntu2) ... Setting up perl-modules-5.26 (5.26.0-4) ... Setting up libkrb5support0:armhf (1.15.1-2) ... Processing triggers for libc-bin (2.24-12ubuntu1) ... Setting up libperl5.26:armhf (5.26.0-4) ... Setting up xz-utils (5.2.2-1.3) ... Setting up libheimbase1-heimdal:armhf (7.4.0.dfsg.1-2) ... Setting up openssl (1.0.2g-1ubuntu13) ... Setting up libsqlite3-0:armhf (3.19.3-3) ... Setting up dmsetup (2:1.02.137-2ubuntu2) ... Setting up binutils (2.29-1ubuntu1) ... Setting up cpp-6 (6.4.0-2ubuntu1) ... 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:armhf (2.24-12ubuntu1) ... Setting up libusb-0.1-4:armhf (2:0.1.12-31) ... Setting up cpp (4:6.3.0-2ubuntu2) ... Setting up libk5crypto3:armhf (1.15.1-2) ... Setting up libasan3:armhf (6.4.0-2ubuntu1) ... Setting up libgcc-6-dev:armhf (6.4.0-2ubuntu1) ... Setting up libstdc++-6-dev:armhf (6.4.0-2ubuntu1) ... Setting up libwind0-heimdal:armhf (7.4.0.dfsg.1-2) ... Setting up init (1.49) ... Setting up libasn1-8-heimdal:armhf (7.4.0.dfsg.1-2) ... Setting up libhcrypto4-heimdal:armhf (7.4.0.dfsg.1-2) ... Setting up libhx509-5-heimdal:armhf (7.4.0.dfsg.1-2) ... Setting up gcc-6 (6.4.0-2ubuntu1) ... Setting up g++-6 (6.4.0-2ubuntu1) ... Setting up perl (5.26.0-4) ... Removing obsolete conffile /etc/perl/sitecustomize.pl ... Setting up libkrb5-3:armhf (1.15.1-2) ... Setting up libkrb5-26-heimdal:armhf (7.4.0.dfsg.1-2) ... Setting up libheimntlm0-heimdal:armhf (7.4.0.dfsg.1-2) ... Setting up libdpkg-perl (1.18.24ubuntu1) ... Setting up gcc (4:6.3.0-2ubuntu2) ... Setting up libgssapi-krb5-2:armhf (1.15.1-2) ... Setting up dpkg-dev (1.18.24ubuntu1) ... Setting up g++ (4:6.3.0-2ubuntu2) ... Setting up libgssapi3-heimdal:armhf (7.4.0.dfsg.1-2) ... Setting up libldap-2.4-2:armhf (2.4.45+dfsg-1ubuntu1) ... 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-13170033', 'armhf', 'artful-proposed', '-c', 'chroot:autobuild', '--arch=armhf', '--dist=artful-proposed', '--purge=never', '--nolog', 'samtools_1.4.1-1build1.dsc'] Initiating build PACKAGEBUILD-13170033 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.4.0-87-generic #110-Ubuntu SMP Tue Jul 18 12:55:22 UTC 2017 armv7l sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on bos01-arm64-033.buildd +==============================================================================+ | samtools 1.4.1-1build1 (armhf) 29 Jul 2017 17:43 | +==============================================================================+ Package: samtools Version: 1.4.1-1build1 Source Version: 1.4.1-1build1 Distribution: artful-proposed Machine Architecture: arm64 Host Architecture: armhf Build Architecture: armhf I: NOTICE: Log filtering will replace 'build/samtools-xJO80b/samtools-1.4.1' with '<>' I: NOTICE: Log filtering will replace 'build/samtools-xJO80b' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-13170033/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- samtools_1.4.1-1build1.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-TssMFn/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/<>/resolver-TssMFn/apt_archive ./ InRelease Get:2 copy:/<>/resolver-TssMFn/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-TssMFn/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-TssMFn/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-TssMFn/apt_archive ./ Packages [526 B] Fetched 2859 B in 0s (148 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 packages were automatically installed and are no longer required: libperl5.24 perl-modules-5.24 Use 'sudo apt autoremove' to remove them. The following NEW packages will be installed: sbuild-build-depends-core-dummy 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 780 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-TssMFn/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [780 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 780 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 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Merged Build-Depends: debhelper (>= 9), bash-completion, libio-pty-perl, libncurses5-dev, libhts-dev (>= 1.4), zlib1g-dev, automake, autoconf-archive, pkg-config, tabix (>= 1.0) Filtered Build-Depends: debhelper (>= 9), bash-completion, libio-pty-perl, libncurses5-dev, libhts-dev (>= 1.4), zlib1g-dev, automake, autoconf-archive, pkg-config, tabix (>= 1.0) dpkg-deb: building package 'sbuild-build-depends-samtools-dummy' in '/<>/resolver-yybFGv/apt_archive/sbuild-build-depends-samtools-dummy.deb'. Ign:1 copy:/<>/resolver-yybFGv/apt_archive ./ InRelease Get:2 copy:/<>/resolver-yybFGv/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-yybFGv/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-yybFGv/apt_archive ./ Sources [288 B] Get:5 copy:/<>/resolver-yybFGv/apt_archive ./ Packages [607 B] Fetched 3014 B in 0s (150 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 packages were automatically installed and are no longer required: libperl5.24 perl-modules-5.24 Use 'sudo apt autoremove' to remove them. 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 libhts2 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 libhts2 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 17.6 MB of archives. After this operation, 67.9 MB of additional disk space will be used. Get:1 copy:/<>/resolver-yybFGv/apt_archive ./ sbuild-build-depends-samtools-dummy 0.invalid.0 [858 B] Get:2 http://ftpmaster.internal/ubuntu artful/main armhf bash-completion all 1:2.1-4.3ubuntu1 [150 kB] Get:3 http://ftpmaster.internal/ubuntu artful/main armhf groff-base armhf 1.22.3-9 [1013 kB] Get:4 http://ftpmaster.internal/ubuntu artful/main armhf libbsd0 armhf 0.8.6-1 [50.6 kB] Get:5 http://ftpmaster.internal/ubuntu artful/main armhf bsdmainutils armhf 9.0.12+nmu1ubuntu1 [173 kB] Get:6 http://ftpmaster.internal/ubuntu artful/main armhf libpipeline1 armhf 1.4.2-1 [21.0 kB] Get:7 http://ftpmaster.internal/ubuntu artful/main armhf man-db armhf 2.7.6.1-2 [873 kB] Get:8 http://ftpmaster.internal/ubuntu artful/universe armhf autoconf-archive all 20160916-1ubuntu1 [649 kB] Get:9 http://ftpmaster.internal/ubuntu artful/main armhf libmagic-mgc armhf 1:5.30-1 [181 kB] Get:10 http://ftpmaster.internal/ubuntu artful/main armhf libmagic1 armhf 1:5.30-1 [63.0 kB] Get:11 http://ftpmaster.internal/ubuntu artful/main armhf file armhf 1:5.30-1 [21.5 kB] Get:12 http://ftpmaster.internal/ubuntu artful/main armhf gettext-base armhf 0.19.8.1-2ubuntu1 [44.8 kB] Get:13 http://ftpmaster.internal/ubuntu artful/main armhf libglib2.0-0 armhf 2.53.4-1 [1012 kB] Get:14 http://ftpmaster.internal/ubuntu artful/main armhf libicu57 armhf 57.1-6 [7442 kB] Get:15 http://ftpmaster.internal/ubuntu artful/main armhf libxml2 armhf 2.9.4+dfsg1-3build1 [562 kB] Get:16 http://ftpmaster.internal/ubuntu artful/main armhf libsigsegv2 armhf 2.11-1 [12.6 kB] Get:17 http://ftpmaster.internal/ubuntu artful/main armhf m4 armhf 1.4.18-1 [181 kB] Get:18 http://ftpmaster.internal/ubuntu artful/main armhf autoconf all 2.69-10 [321 kB] Get:19 http://ftpmaster.internal/ubuntu artful/main armhf autotools-dev all 20161112.1 [39.5 kB] Get:20 http://ftpmaster.internal/ubuntu artful/main armhf automake all 1:1.15-6ubuntu1 [509 kB] Get:21 http://ftpmaster.internal/ubuntu artful/main armhf autopoint all 0.19.8.1-2ubuntu1 [411 kB] Get:22 http://ftpmaster.internal/ubuntu artful/main armhf libtool all 2.4.6-2 [194 kB] Get:23 http://ftpmaster.internal/ubuntu artful/main armhf dh-autoreconf all 14 [15.5 kB] Get:24 http://ftpmaster.internal/ubuntu artful/main armhf libarchive-zip-perl all 1.59-1 [84.0 kB] Get:25 http://ftpmaster.internal/ubuntu artful/main armhf libfile-stripnondeterminism-perl all 0.038-1 [13.3 kB] Get:26 http://ftpmaster.internal/ubuntu artful/main armhf libtimedate-perl all 2.3000-2 [37.5 kB] Get:27 http://ftpmaster.internal/ubuntu artful/main armhf dh-strip-nondeterminism all 0.038-1 [5026 B] Get:28 http://ftpmaster.internal/ubuntu artful/main armhf libcroco3 armhf 0.6.12-1 [69.7 kB] Get:29 http://ftpmaster.internal/ubuntu artful/main armhf gettext armhf 0.19.8.1-2ubuntu1 [1018 kB] Get:30 http://ftpmaster.internal/ubuntu artful/main armhf intltool-debian all 0.35.0+20060710.4 [24.9 kB] Get:31 http://ftpmaster.internal/ubuntu artful/main armhf po-debconf all 1.0.20 [232 kB] Get:32 http://ftpmaster.internal/ubuntu artful/main armhf debhelper all 10.6.4ubuntu1 [875 kB] Get:33 http://ftpmaster.internal/ubuntu artful-proposed/universe armhf libhts2 armhf 1.4.1-5 [246 kB] Get:34 http://ftpmaster.internal/ubuntu artful-proposed/universe armhf libhts-dev armhf 1.4.1-5 [351 kB] Get:35 http://ftpmaster.internal/ubuntu artful-proposed/main armhf libio-pty-perl armhf 1:1.08-1.1build4 [29.3 kB] Get:36 http://ftpmaster.internal/ubuntu artful/main armhf libtinfo-dev armhf 6.0+20160625-1ubuntu1 [66.4 kB] Get:37 http://ftpmaster.internal/ubuntu artful/main armhf libncurses5-dev armhf 6.0+20160625-1ubuntu1 [154 kB] Get:38 http://ftpmaster.internal/ubuntu artful/main armhf pkg-config armhf 0.29.1-0ubuntu2 [42.0 kB] Get:39 http://ftpmaster.internal/ubuntu artful-proposed/universe armhf tabix armhf 1.4.1-5 [260 kB] Get:40 http://ftpmaster.internal/ubuntu artful/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-0ubuntu1 [166 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 17.6 MB in 0s (26.7 MB/s) (Reading database ... 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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 (2.24-12ubuntu1) ... Setting up autotools-dev (20161112.1) ... Setting up tabix (1.4.1-5) ... 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:armhf (1.4.1-5) ... 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) ... Setting up gettext (0.19.8.1-2ubuntu1) ... Setting up libhts-dev:armhf (1.4.1-5) ... 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) ... Setting up debhelper (10.6.4ubuntu1) ... Setting up sbuild-build-depends-samtools-dummy (0.invalid.0) ... (Reading database ... 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Processing triggers for libc-bin (2.24-12ubuntu1) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.4.0-87-generic arm64 (armv7l) Toolchain package versions: binutils_2.29-1ubuntu1 dpkg-dev_1.18.24ubuntu1 g++-6_6.4.0-2ubuntu1 gcc-6_6.4.0-2ubuntu1 libc6-dev_2.24-12ubuntu1 libstdc++-6-dev_6.4.0-2ubuntu1 libstdc++6_7.1.0-10ubuntu1 linux-libc-dev_4.11.0-11.16 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_2.29-1ubuntu1 bsdmainutils_9.0.12+nmu1ubuntu1 bsdutils_1:2.30.1-0ubuntu1 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_6.4.0-2ubuntu1 dash_0.5.8-2.3ubuntu1 debconf_1.5.63 debhelper_10.6.4ubuntu1 debianutils_4.8.1.1 dh-autoreconf_14 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_6.4.0-2ubuntu1 gcc_4:6.3.0-2ubuntu2 gcc-6_6.4.0-2ubuntu1 gcc-6-base_6.4.0-2ubuntu1 gcc-7-base_7.1.0-10ubuntu1 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_1.49 init-system-helpers_1.49 initscripts_2.88dsf-59.3ubuntu2 insserv_1.14.0-5ubuntu3 intltool-debian_0.35.0+20060710.4 libacl1_2.2.52-3build1 libapparmor1_2.11.0-2ubuntu10 libapt-pkg5.0_1.5~beta1 libarchive-zip-perl_1.59-1 libasan3_6.4.0-2ubuntu1 libasn1-8-heimdal_7.4.0.dfsg.1-2 libassuan0_2.4.3-2 libatomic1_7.1.0-10ubuntu1 libattr1_1:2.4.47-2build1 libaudit-common_1:2.7.7-1ubuntu1 libaudit1_1:2.7.7-1ubuntu1 libblkid1_2.30.1-0ubuntu1 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_7.1.0-10ubuntu1 libcomerr2_1.43.4-2 libcroco3_0.6.12-1 libcryptsetup4_2:1.7.2-0ubuntu1 libcurl3-gnutls_7.52.1-5ubuntu1 libdb5.3_5.3.28-13 libdebconfclient0_0.213ubuntu1 libdevmapper1.02.1_2:1.02.137-2ubuntu2 libdpkg-perl_1.18.24ubuntu1 libfakeroot_1.21-1ubuntu2 libfdisk1_2.30.1-0ubuntu1 libffi6_3.2.1-6 libfile-stripnondeterminism-perl_0.038-1 libgcc-6-dev_6.4.0-2ubuntu1 libgcc1_1:7.1.0-10ubuntu1 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_7.1.0-10ubuntu1 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 libio-pty-perl_1:1.08-1.1build4 libip4tc0_1.6.1-2ubuntu1 libisl15_0.18-1 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_2.4.45+dfsg-1ubuntu1 libldap-common_2.4.45+dfsg-1ubuntu1 liblockfile-bin_1.14-1 liblockfile1_1.14-1 liblz4-1_0.0~r131-2ubuntu2 liblzma5_5.2.2-1.3 libmagic-mgc_1:5.30-1 libmagic1_1:5.30-1 libmount1_2.30.1-0ubuntu1 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_0.23.7-3 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 libperl5.26_5.26.0-4 libpipeline1_1.4.2-1 libpng16-16_1.6.30-2 libprocps6_2:3.3.12-1ubuntu2 libpsl5_0.17.0-5 libreadline7_7.0-0ubuntu2 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_2.30.1-0ubuntu1 libsqlite3-0_3.19.3-3 libss2_1.43.4-2 libssl1.0.0_1.0.2g-1ubuntu13 libstdc++-6-dev_6.4.0-2ubuntu1 libstdc++6_7.1.0-10ubuntu1 libsystemd0_234-2ubuntu1 libtasn1-6_4.12-2.1 libtimedate-perl_2.3000-2 libtinfo-dev_6.0+20160625-1ubuntu1 libtinfo5_6.0+20160625-1ubuntu1 libtool_2.4.6-2 libubsan0_7.1.0-10ubuntu1 libudev1_234-2ubuntu1 libunistring0_0.9.3-5.2ubuntu1 libusb-0.1-4_2:0.1.12-31 libustr-1.0-1_1.0.4-6 libuuid1_2.30.1-0ubuntu1 libwind0-heimdal_7.4.0.dfsg.1-2 libxml2_2.9.4+dfsg1-3build1 linux-libc-dev_4.11.0-11.16 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_2.30.1-0ubuntu1 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_5.26.0-4 perl-base_5.26.0-4 perl-modules-5.24_5.24.1-7ubuntu1 perl-modules-5.26_5.26.0-4 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+nmu1 systemd_234-2ubuntu1 systemd-sysv_234-2ubuntu1 sysv-rc_2.88dsf-59.3ubuntu2 sysvinit-utils_2.88dsf-59.8git1 tabix_1.4.1-5 tar_1.29b-2 tzdata_2017b-2 ubuntu-keyring_2016.10.27 util-linux_2.30.1-0ubuntu1 xz-utils_5.2.2-1.3 zlib1g_1:1.2.11.dfsg-0ubuntu1 zlib1g-dev_1:1.2.11.dfsg-0ubuntu1 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Sat Jul 29 17:41:38 2017 UTC gpgv: using RSA key gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./samtools_1.4.1-1build1.dsc dpkg-source: info: extracting samtools in samtools-1.4.1 dpkg-source: info: unpacking samtools_1.4.1.orig.tar.gz dpkg-source: info: unpacking samtools_1.4.1-1build1.debian.tar.xz dpkg-source: info: applying spelling.patch dpkg-source: info: applying literal_version.patch dpkg-source: info: applying mayhem.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 1.4.1-1build1 dpkg-buildpackage: info: source distribution artful dpkg-source --before-build samtools-1.4.1 dpkg-buildpackage: info: host architecture armhf dpkg-source: info: using options from samtools-1.4.1/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*.bam* rm -f *.o misc/*.o test/*.o test/*/*.o version.h rm -f samtools libbam.a libst.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 -rf debian/.debhelper/ rm -f debian/samtools-test.debhelper.log debian/samtools.debhelper.log rm -f -- debian/samtools.substvars debian/samtools-test.substvars debian/files rm -fr -- debian/samtools/ debian/samtools-test/ 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 \ \( -type d -a -name autom4te.cache -prune -exec rm -rf {} + \) \) 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:45: warning: AC_CONFIG_SUBDIRS: you should use literals ../../lib/autoconf/status.m4:1097: AC_CONFIG_SUBDIRS is expanded from... m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from... configure.ac:45: the top level autoconf configure.ac:45: warning: AC_CONFIG_SUBDIRS: you should use literals ../../lib/autoconf/status.m4:1097: AC_CONFIG_SUBDIRS is expanded from... m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from... configure.ac:45: 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 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 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 "1.4.1"' > 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 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 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 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 sam_utils.o sam_utils.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') ar -rcs libst.a sam_opts.o sam_utils.o gcc -Wl,-Bsymbolic-functions -Wl,-z,relro -o misc/ace2sam misc/ace2sam.o -lz gcc -Wl,-Bsymbolic-functions -Wl,-z,relro -o misc/maq2sam-long misc/maq2sam-long.o -lz gcc -Wl,-Bsymbolic-functions -Wl,-z,relro -o misc/maq2sam-short misc/maq2sam-short.o -lz gcc -Wl,-Bsymbolic-functions -Wl,-z,relro -o misc/md5fa misc/md5fa.o -lhts -lz gcc -Wl,-Bsymbolic-functions -Wl,-z,relro -o misc/md5sum-lite misc/md5sum-lite.o -lhts -lz gcc -Wl,-Bsymbolic-functions -Wl,-z,relro -o misc/wgsim misc/wgsim.o -lm -lz gcc -Wl,-Bsymbolic-functions -Wl,-z,relro -o test/merge/test_bam_translate test/merge/test_bam_translate.o test/test.o libst.a -lhts -lz -lpthread gcc -Wl,-Bsymbolic-functions -Wl,-z,relro -o test/merge/test_rtrans_build test/merge/test_rtrans_build.o libst.a -lhts -lz -lpthread gcc -Wl,-Bsymbolic-functions -Wl,-z,relro -o test/split/test_count_rg test/split/test_count_rg.o test/test.o libst.a -lhts -lz -lpthread gcc -Wl,-Bsymbolic-functions -Wl,-z,relro -o test/split/test_expand_format_string test/split/test_expand_format_string.o test/test.o libst.a -lhts -lz -lpthread gcc -Wl,-Bsymbolic-functions -Wl,-z,relro -o test/split/test_filter_header_rg test/split/test_filter_header_rg.o test/test.o libst.a -lhts -lz -lpthread gcc -Wl,-Bsymbolic-functions -Wl,-z,relro -o test/split/test_parse_args test/split/test_parse_args.o test/test.o libst.a -lhts -lz -lpthread gcc -Wl,-Bsymbolic-functions -Wl,-z,relro -o test/vcf-miniview test/vcf-miniview.o -lhts -lz -lpthread gcc -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 bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o bam2bcf.o bam2bcf_indel.o sample.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 libst.a -lhts -lcurses -lm -lz -lpthread gcc -Wl,-Bsymbolic-functions -Wl,-z,relro -o test/merge/test_trans_tbl_init test/merge/test_trans_tbl_init.o libst.a -lhts -lz -lpthread 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/ZQIkjsGhPT/bgzip.dat.gz .. ok /usr/bin/bgzip -c -b 979200 -s 6 /tmp/ZQIkjsGhPT/bgzip.dat.gz .. ok /usr/bin/bgzip -c -b 652804 -s 6 /tmp/ZQIkjsGhPT/bgzip.dat.gz .. ok /<>/samtools faidx /tmp/ZQIkjsGhPT/faidx.fa 3:11-13 | grep -v '^>' .. ok /<>/samtools faidx /tmp/ZQIkjsGhPT/faidx.fa.gz 3:11-13 | grep -v '^>' .. ok /<>/samtools faidx /tmp/ZQIkjsGhPT/faidx.fa 2:998-1003 | grep -v '^>' .. ok /<>/samtools faidx /tmp/ZQIkjsGhPT/faidx.fa.gz 2:998-1003 | grep -v '^>' .. ok /<>/samtools faidx /tmp/ZQIkjsGhPT/faidx.fa 1:100-104 | grep -v '^>' .. ok /<>/samtools faidx /tmp/ZQIkjsGhPT/faidx.fa.gz 1:100-104 | grep -v '^>' .. ok /<>/samtools faidx /tmp/ZQIkjsGhPT/faidx.fa 1:99998-100007 | grep -v '^>' .. ok /<>/samtools faidx /tmp/ZQIkjsGhPT/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/ZQIkjsGhPT/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 view /tmp/ZQIkjsGhPT/large_chrom.bam ref2 .. ok test_index: /<>/samtools view /tmp/ZQIkjsGhPT/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_index: /<>/samtools view -@ 2 /tmp/ZQIkjsGhPT/large_chrom.bam ref2 .. ok test_index: /<>/samtools view -@ 2 /tmp/ZQIkjsGhPT/large_chrom.bam ref2:1-541556283 .. ok test_index: /<>/samtools index -@ 2 /<>/test/dat/test_input_1_a.bam && cat /<>/test/dat/test_input_1_a.bam.bai .. ok test_mpileup: /<>/samtools mpileup -b /tmp/ZQIkjsGhPT/mpileup.bam.list -f /tmp/ZQIkjsGhPT/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: /<>/samtools mpileup -b /tmp/ZQIkjsGhPT/mpileup.cram.list -f /tmp/ZQIkjsGhPT/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: /<>/samtools mpileup -b /tmp/ZQIkjsGhPT/mpileup.bam.urllist -f /tmp/ZQIkjsGhPT/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: /<>/samtools mpileup -b /tmp/ZQIkjsGhPT/mpileup.cram.urllist -f /tmp/ZQIkjsGhPT/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: /<>/samtools mpileup -uvDV -b /tmp/ZQIkjsGhPT/mpileup.bam.list -f /tmp/ZQIkjsGhPT/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref .. ok test_mpileup: /<>/samtools mpileup -uvDV -b /tmp/ZQIkjsGhPT/mpileup.cram.list -f /tmp/ZQIkjsGhPT/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/ZQIkjsGhPT/mpileup.cram.list -f /tmp/ZQIkjsGhPT/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/ZQIkjsGhPT/mpileup.cram.list -f /tmp/ZQIkjsGhPT/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref .. ok test_mpileup: /<>/samtools mpileup -B --ff 0x14 -f /tmp/ZQIkjsGhPT/mpileup.ref.fa.gz -r17:1050-1060 /tmp/ZQIkjsGhPT/mpileup.1.bam | grep -v mpileup .. ok test_mpileup: /<>/samtools mpileup -B --ff 0x14 -f /tmp/ZQIkjsGhPT/mpileup.ref.fa.gz -r17:1050-1060 /tmp/ZQIkjsGhPT/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 .. ok 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 .. ok 2: SAM -> uncompressed BAM .. ok 3: uncompressed BAM -> SAM and compare .. ok 4: SAM -> fast compressed BAM .. ok 5: fast compressed BAM -> SAM and compare .. ok 6: SAM -> CRAM -> SAM (UR header tags) .. ok 7: SAM -> CRAM -> SAM (M5 header tags) .. ok 8: BAM -> CRAM with UR -> SAM .. ok 9: SAM -> BAM (M5 header tags) .. ok 10: SAM -> BAM -> CRAM -> SAM (M5 header tags) .. ok 11: CRAM -> BAM with UR .. ok 12: CRAM -> BAM with M5 .. ok 13: SAM -> SAM via stdout .. ok 14: SAM -> BAM via stdout .. ok 15: SAM -> CRAM via stdout .. ok 16: SAM from stdin -> SAM .. ok 17: BAM from stdin -> SAM .. ok 18: CRAM from stdin -> SAM .. ok 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) .. ok 23: No headers (BAM input) .. ok 24: No headers (CRAM input) .. ok 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) .. ok 32: Count -F 128 (SAM input) .. ok 33: Filter -F 128 (BAM input) .. ok 34: Count -F 128 (BAM input) .. ok 35: Filter -F 128 (CRAM input) .. ok 36: Count -F 128 (CRAM input) .. ok 37: Filter -F 128 -f 2 (SAM input) .. ok 38: Count -F 128 -f 2 (SAM input) .. ok 39: Filter -F 128 -f 2 (BAM input) .. ok 40: Count -F 128 -f 2 (BAM input) .. ok 41: Filter -F 128 -f 2 (CRAM input) .. ok 42: Count -F 128 -f 2 (CRAM input) .. ok 43: Filter -r grp2 (SAM input) .. ok 44: Count -r grp2 (SAM input) .. ok 45: Filter -r grp2 (BAM input) .. ok 46: Count -r grp2 (BAM input) .. ok 47: Filter -r grp2 (CRAM input) .. ok 48: Count -r grp2 (CRAM input) .. ok 49: Filter -R /tmp/ZQIkjsGhPT/view.001.fogn (SAM input) .. ok 50: Count -R /tmp/ZQIkjsGhPT/view.001.fogn (SAM input) .. ok 51: Filter -R /tmp/ZQIkjsGhPT/view.001.fogn (BAM input) .. ok 52: Count -R /tmp/ZQIkjsGhPT/view.001.fogn (BAM input) .. ok 53: Filter -R /tmp/ZQIkjsGhPT/view.001.fogn (CRAM input) .. ok 54: Count -R /tmp/ZQIkjsGhPT/view.001.fogn (CRAM input) .. ok 55: Filter -R /tmp/ZQIkjsGhPT/view.001.fogn -r grp2 (SAM input).. ok 56: Count -R /tmp/ZQIkjsGhPT/view.001.fogn -r grp2 (SAM input).. ok 57: Filter -R /tmp/ZQIkjsGhPT/view.001.fogn -r grp2 (BAM input).. ok 58: Count -R /tmp/ZQIkjsGhPT/view.001.fogn -r grp2 (BAM input).. ok 59: Filter -R /tmp/ZQIkjsGhPT/view.001.fogn -r grp2 (CRAM input).. ok 60: Count -R /tmp/ZQIkjsGhPT/view.001.fogn -r grp2 (CRAM input).. ok 61: Filter -r grp2 -R /tmp/ZQIkjsGhPT/view.001.fogn (SAM input).. ok 62: Count -r grp2 -R /tmp/ZQIkjsGhPT/view.001.fogn (SAM input).. ok 63: Filter -r grp2 -R /tmp/ZQIkjsGhPT/view.001.fogn (BAM input).. ok 64: Count -r grp2 -R /tmp/ZQIkjsGhPT/view.001.fogn (BAM input).. ok 65: Filter -r grp2 -R /tmp/ZQIkjsGhPT/view.001.fogn (CRAM input).. ok 66: Count -r grp2 -R /tmp/ZQIkjsGhPT/view.001.fogn (CRAM input).. ok 67: Filter -l Library 2 (SAM input) .. ok 68: Count -l Library 2 (SAM input) .. ok 69: Filter -l Library 2 (BAM input) .. ok 70: Count -l Library 2 (BAM input) .. ok 71: Filter -l Library 2 (CRAM input) .. ok 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) .. ok 116: Count -x RG -r grp2 (SAM input) .. ok 117: Filter -x RG -r grp2 (BAM input) .. ok 118: Count -x RG -r grp2 (BAM input) .. ok 119: Filter -x RG -r grp2 (CRAM input) .. ok 120: Count -x RG -r grp2 (CRAM input) .. ok 121: Filter -m 10 (SAM input) .. ok 122: Count -m 10 (SAM input) .. ok 123: Filter -m 10 (BAM input) .. ok 124: Count -m 10 (BAM input) .. ok 125: Filter -m 10 (CRAM input) .. ok 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) .. ok 159: Count ref1 (BAM input) .. ok 160: Region ref1 (CRAM input) .. ok 161: Count ref1 (CRAM input) .. ok 162: Region ref1:15 (BAM input) .. ok 163: Count ref1:15 (BAM input) .. ok 164: Region ref1:15 (CRAM input) .. ok 165: Count ref1:15 (CRAM input) .. ok 166: Region ref1:15-45 (BAM input) .. ok 167: Count ref1:15-45 (BAM input) .. ok 168: Region ref1:15-45 (CRAM input) .. ok 169: Count ref1:15-45 (CRAM input) .. ok 170: Region ref1:15-45 ref2 (BAM input) .. ok 171: Count ref1:15-45 ref2 (BAM input) .. ok 172: Region ref1:15-45 ref2 (CRAM input) .. ok 173: Count ref1:15-45 ref2 (CRAM input) .. ok 174: Region ref1:15-45 ref2:16 (BAM input) .. ok 175: Count ref1:15-45 ref2:16 (BAM input) .. ok 176: Region ref1:15-45 ref2:16 (CRAM input) .. ok 177: Count ref1:15-45 ref2:16 (CRAM input) .. ok 178: Region ref1:15-45 ref2:16-31 (BAM input) .. ok 179: Count ref1:15-45 ref2:16-31 (BAM input) .. ok 180: Region ref1:15-45 ref2:16-31 (CRAM input) .. ok 181: Count ref1:15-45 ref2:16-31 (CRAM input) .. ok 182: Region ref1:15-15 ref1:45-45 (BAM input) .. ok 183: Count ref1:15-15 ref1:45-45 (BAM input) .. ok 184: Region ref1:15-15 ref1:45-45 (CRAM input) .. ok 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) .. ok 195: Count -r grp2 ref1:15-45 (BAM input) .. ok 196: Region -r grp2 ref1:15-45 (CRAM input) .. ok 197: Count -r grp2 ref1:15-45 (CRAM input) .. ok 198: Region * (BAM input) .. ok 199: Count * (BAM input) .. ok 200: Region * (CRAM input) .. ok 201: Count * (CRAM input) .. ok 202: Region -L /<>/test/dat/view.002.01.bed (BAM input).. ok 203: Count -L /<>/test/dat/view.002.01.bed (BAM input).. ok 204: Region -L /<>/test/dat/view.002.01.bed (CRAM input).. ok 205: Count -L /<>/test/dat/view.002.01.bed (CRAM input).. ok 206: Region -L /<>/test/dat/view.002.02.bed (BAM input).. ok 207: Count -L /<>/test/dat/view.002.02.bed (BAM input).. ok 208: Region -L /<>/test/dat/view.002.02.bed (CRAM input).. ok 209: Count -L /<>/test/dat/view.002.02.bed (CRAM input).. ok 210: Region -L /<>/test/dat/view.001.01.bed (BAM input).. ok 211: Count -L /<>/test/dat/view.001.01.bed (BAM input).. ok 212: Region -L /<>/test/dat/view.001.01.bed (CRAM input).. ok 213: Count -L /<>/test/dat/view.001.01.bed (CRAM input).. ok 214: Region -L /<>/test/dat/view.001.02.bed (BAM input).. ok 215: Count -L /<>/test/dat/view.001.02.bed (BAM input).. ok 216: Region -L /<>/test/dat/view.001.02.bed (CRAM input).. ok 217: Count -L /<>/test/dat/view.001.02.bed (CRAM input).. ok 218: Region -L /<>/test/dat/view.002.01.bed Z (BAM input).. ok 219: Count -L /<>/test/dat/view.002.01.bed Z (BAM input).. ok 220: Region -L /<>/test/dat/view.002.01.bed Z (CRAM input).. ok 221: Count -L /<>/test/dat/view.002.01.bed Z (CRAM input).. ok 222: Region -L /<>/test/dat/view.002.01.bed Z:30 (BAM input).. ok 223: Count -L /<>/test/dat/view.002.01.bed Z:30 (BAM input).. ok 224: Region -L /<>/test/dat/view.002.01.bed Z:30 (CRAM input).. ok 225: Count -L /<>/test/dat/view.002.01.bed Z:30 (CRAM input).. ok 226: Region -L /<>/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok 227: Count -L /<>/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok 228: Region -L /<>/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok 229: Count -L /<>/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok 230: Region -L /<>/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok 231: Count -L /<>/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok 232: Region -L /<>/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok 233: Count -L /<>/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok 234: Region -L /<>/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok 235: Count -L /<>/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok 236: Region -L /<>/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok 237: Count -L /<>/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok 238: Region -L /<>/test/dat/view.001.01.bed ref2 (BAM input).. ok 239: Count -L /<>/test/dat/view.001.01.bed ref2 (BAM input).. ok 240: Region -L /<>/test/dat/view.001.01.bed ref2 (CRAM input).. ok 241: Count -L /<>/test/dat/view.001.01.bed ref2 (CRAM input).. ok 242: Region -L /<>/test/dat/view.001.01.bed -r grp1 (BAM input).. ok 243: Count -L /<>/test/dat/view.001.01.bed -r grp1 (BAM input).. ok 244: Region -L /<>/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok 245: Count -L /<>/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok 246: Region -L /<>/test/dat/view.001.01.bed -f 128 (BAM input).. ok 247: Count -L /<>/test/dat/view.001.01.bed -f 128 (BAM input).. ok 248: Region -L /<>/test/dat/view.001.01.bed -f 128 (CRAM input).. ok 249: Count -L /<>/test/dat/view.001.01.bed -f 128 (CRAM input).. ok 250: Region -L /<>/test/dat/view.001.01.bed -q 5 (BAM input).. ok 251: Count -L /<>/test/dat/view.001.01.bed -q 5 (BAM input).. ok 252: Region -L /<>/test/dat/view.001.01.bed -q 5 (CRAM input).. ok 253: Count -L /<>/test/dat/view.001.01.bed -q 5 (CRAM input).. ok 254: Region -L /<>/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok 255: Count -L /<>/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok 256: Region -L /<>/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok 257: Count -L /<>/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok 258: Make BAM with no M5/UR tags .. ok 259: Add @SQ with -t (SAM -> SAM) .. ok 260: Add @SQ with -T (SAM -> SAM) .. ok 261: Add @SQ with -t (BAM -> SAM) .. ok 262: Add @SQ with -T (BAM -> SAM) .. ok 263: Add @SQ with -t (SAM -> BAM) .. ok 264: Add @SQ with -T (SAM -> BAM) .. ok 265: Add @SQ with -t (BAM -> BAM) .. ok 266: Add @SQ with -T (BAM -> BAM) .. ok 267: Add @SQ with -t (SAM -> CRAM) .. ok 268: Add @SQ with -T (SAM -> CRAM) .. ok 269: Add @SQ with -t (BAM -> CRAM) .. ok 270: Add @SQ with -T (BAM -> CRAM) .. ok 271: Make CRAM with no UR field .. ok 272: Decoding CRAM with no UR field via -T .. ok 273: CIGAR B-operator removal .. ok 274: Big SAM -> BAM .. ok 275: Big SAM -> BAM (2 threads) .. ok 276: Big SAM -> BAM (4 threads) .. ok 277: Big SAM -> CRAM .. ok 278: Big SAM -> CRAM (2 threads) .. ok 279: Big SAM -> CRAM (4 threads) .. ok 280: Subsample 0.2 (SAM input) ............ ok 281: Subsample 0.5 (SAM input) ............ ok 282: Subsample 0.8 (SAM input) ............ ok 283: Subsample 0.2 (BAM input) ............ ok 284: Subsample 0.5 (BAM input) ............ ok 285: Subsample 0.8 (BAM input) ............ ok 286: Subsample 0.2 (CRAM input) ............ ok 287: Subsample 0.5 (CRAM input) ............ ok 288: 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 .. ok Generate CRAM file .. ok 1: fastq (SAM input) [M::bam2fq_mainloop] processed 36 reads .. ok 2: fastq -n (SAM input) [M::bam2fq_mainloop] processed 36 reads .. ok 3: fastq (BAM input) [M::bam2fq_mainloop] processed 36 reads .. ok 4: fastq -n (BAM input) [M::bam2fq_mainloop] processed 36 reads .. ok 5: fastq (CRAM input) [M::bam2fq_mainloop] processed 36 reads .. ok 6: fastq -n (CRAM input) [M::bam2fq_mainloop] processed 36 reads .. ok test_bam2fq: /<>/samtools fastq -1 /<>/test/1.fq -2 /<>/test/2.fq /<>/test/dat/bam2fq.001.sam .. ok test_bam2fq: /<>/samtools fastq -s /<>/test/s.fq -1 /<>/test/1.fq -2 /<>/test/2.fq /<>/test/dat/bam2fq.001.sam .. ok test_bam2fq: /<>/samtools fastq -s /<>/test/s.fq -1 /<>/test/1.fq -2 /<>/test/2.fq /<>/test/dat/bam2fq.002.sam .. ok test_bam2fq: /<>/samtools fastq -s /<>/test/s.fq -1 /<>/test/1.fq -2 /<>/test/2.fq /<>/test/dat/bam2fq.003.sam .. ok test_bam2fq: /<>/samtools fastq --barcode-tag BC --index-format 'n2i2' --i1 /<>/test/bc.fq -s /<>/test/s.fq -1 /<>/test/1.fq -2 /<>/test/2.fq /<>/test/dat/bam2fq.004.sam .. ok test_bam2fq: /<>/samtools fastq --barcode-tag BC -N --index-format 'n*i*' --i1 /<>/test/bc_split.fq -s /<>/test/s.fq -1 /<>/test/1.fq -2 /<>/test/2.fq /<>/test/dat/bam2fq.005.sam .. ok test_bam2fq: Generate BAM file (2 threads) .. ok Generate CRAM file (2 threads) .. ok 1: fastq (SAM input) (2 threads) [M::bam2fq_mainloop] processed 36 reads .. ok 2: fastq -n (SAM input) (2 threads) [M::bam2fq_mainloop] processed 36 reads .. ok 3: fastq (BAM input) (2 threads) [M::bam2fq_mainloop] processed 36 reads .. ok 4: fastq -n (BAM input) (2 threads) [M::bam2fq_mainloop] processed 36 reads .. ok 5: fastq (CRAM input) (2 threads) [M::bam2fq_mainloop] processed 36 reads .. ok 6: fastq -n (CRAM input) (2 threads) [M::bam2fq_mainloop] processed 36 reads .. ok test_bam2fq: /<>/samtools fastq -@ 2 -1 /<>/test/1.fq -2 /<>/test/2.fq /<>/test/dat/bam2fq.001.sam .. ok test_bam2fq: /<>/samtools fastq -@ 2 -s /<>/test/s.fq -1 /<>/test/1.fq -2 /<>/test/2.fq /<>/test/dat/bam2fq.001.sam .. ok test_bam2fq: /<>/samtools fastq -@ 2 -s /<>/test/s.fq -1 /<>/test/1.fq -2 /<>/test/2.fq /<>/test/dat/bam2fq.002.sam .. ok test_bam2fq: /<>/samtools fastq -@ 2 -s /<>/test/s.fq -1 /<>/test/1.fq -2 /<>/test/2.fq /<>/test/dat/bam2fq.003.sam .. ok test_bam2fq: /<>/samtools fastq -@ 2 --barcode-tag BC --index-format 'n2i2' --i1 /<>/test/bc.fq -s /<>/test/s.fq -1 /<>/test/1.fq -2 /<>/test/2.fq /<>/test/dat/bam2fq.004.sam .. ok test_bam2fq: /<>/samtools fastq -@ 2 --barcode-tag BC -N --index-format 'n*i*' --i1 /<>/test/bc_split.fq -s /<>/test/s.fq -1 /<>/test/1.fq -2 /<>/test/2.fq /<>/test/dat/bam2fq.005.sam .. ok test_depad: Generate BAM file .. ok depad (SAM input) .. ok depad -s (SAM input) .. ok depad -u (SAM input) .. ok depad -1 (SAM input) .. ok depad (BAM input) .. ok depad -s (BAM input) .. ok depad -u (BAM input) .. ok depad -1 (BAM input) .. ok test_stats: /<>/samtools stats -r /<>/test/stat/test.fa /<>/test/stat/1_map_cigar.sam | tail -n+4 .. ok test_stats: /<>/samtools stats -r /<>/test/stat/test.fa /<>/test/stat/2_equal_cigar_full_seq.sam | tail -n+4 .. ok test_stats: /<>/samtools stats -r /<>/test/stat/test.fa /<>/test/stat/3_map_cigar_equal_seq.sam | tail -n+4 .. ok test_stats: /<>/samtools stats -r /<>/test/stat/test.fa /<>/test/stat/4_X_cigar_full_seq.sam | tail -n+4 .. ok test_stats: /<>/samtools stats -r /<>/test/stat/test.fa /<>/test/stat/5_insert_cigar.sam | tail -n+4 .. ok test_stats: /<>/samtools stats -r /<>/test/stat/test.fa -i 0 /<>/test/stat/5_insert_cigar.sam | tail -n+4 .. ok test_stats: /<>/samtools stats -r /<>/test/stat/test.fa /<>/test/stat/7_supp.sam | tail -n+4 .. ok test_stats: /<>/samtools stats -r /<>/test/stat/test.fa /<>/test/stat/8_secondary.sam | tail -n+4 .. ok test_stats: /<>/samtools stats -S RG -r /<>/test/stat/test.fa /<>/test/stat/1_map_cigar.sam | tail -n+4 .. ok test_stats: /<>/samtools stats -S RG -r /<>/test/stat/test.fa /<>/test/stat/10_map_cigar.sam | tail -n+4 .. ok test_merge: /<>/samtools merge -s 1 - /<>/test/dat/test_input_1_a.sam /<>/test/dat/test_input_1_b.sam /<>/test/dat/test_input_1_c.sam .. ok test_merge: /<>/samtools merge -s 1 - /<>/test/dat/test_input_1_a.bam /<>/test/dat/test_input_1_b.bam /<>/test/dat/test_input_1_c.bam .. ok test_merge: /<>/samtools merge -s 1 -b /tmp/RFlZI0ba1q - /<>/test/dat/test_input_1_a.bam .. ok test_merge: /<>/samtools merge -s 1 - /<>/test/dat/test_input_1_b.bam .. ok test_merge: /<>/samtools merge -r -s 1 - /<>/test/dat/test_input_1_a.sam /<>/test/dat/test_input_1_b.sam /<>/test/dat/test_input_1_c.sam .. ok test_merge: /<>/samtools merge -cp -s 1 - /<>/test/dat/test_input_1_a.sam /<>/test/dat/test_input_1_b.sam .. ok test_merge: /<>/samtools merge -s 1 - /<>/test/dat/test_input_1_a_regex.sam /<>/test/dat/test_input_1_b_regex.sam .. ok test_merge: /<>/samtools merge -@ 2 -s 1 - /<>/test/dat/test_input_1_a.sam /<>/test/dat/test_input_1_b.sam /<>/test/dat/test_input_1_c.sam .. ok test_merge: /<>/samtools merge -@ 2 -s 1 - /<>/test/dat/test_input_1_a.bam /<>/test/dat/test_input_1_b.bam /<>/test/dat/test_input_1_c.bam .. ok test_merge: /<>/samtools merge -@ 2 -s 1 -b /tmp/yeK2ucGccq - /<>/test/dat/test_input_1_a.bam .. ok test_merge: /<>/samtools merge -@ 2 -s 1 - /<>/test/dat/test_input_1_b.bam .. ok test_merge: /<>/samtools merge -@ 2 -r -s 1 - /<>/test/dat/test_input_1_a.sam /<>/test/dat/test_input_1_b.sam /<>/test/dat/test_input_1_c.sam .. ok test_merge: /<>/samtools merge -@ 2 -cp -s 1 - /<>/test/dat/test_input_1_a.sam /<>/test/dat/test_input_1_b.sam .. ok test_merge: /<>/samtools merge -@ 2 -s 1 - /<>/test/dat/test_input_1_a_regex.sam /<>/test/dat/test_input_1_b_regex.sam .. ok test_sort: /<>/samtools sort /<>/test/dat/test_input_1_a.bam /tmp/ZQIkjsGhPT/sortout .. ok test_sort: /<>/samtools sort -f /<>/test/dat/test_input_1_a.bam /tmp/ZQIkjsGhPT/sortout.bam .. ok test_sort: /<>/samtools sort -o /<>/test/dat/test_input_1_a.bam /tmp/ZQIkjsGhPT/sorttmp .. ok test_sort: /<>/samtools sort -@ 2 /<>/test/dat/test_input_1_a.bam /tmp/ZQIkjsGhPT/sortout .. ok test_sort: /<>/samtools sort -@ 2 -f /<>/test/dat/test_input_1_a.bam /tmp/ZQIkjsGhPT/sortout.bam .. ok test_sort: /<>/samtools sort -@ 2 -o /<>/test/dat/test_input_1_a.bam /tmp/ZQIkjsGhPT/sorttmp .. ok test_fixmate: /<>/samtools fixmate -O sam /<>/test/fixmate/1_coord_sort.sam - ERR: [bam_mating_core] ERROR: Coordinate sorted, require grouped/sorted by queryname. .. expected failure test_fixmate: /<>/samtools fixmate -O sam /<>/test/fixmate/2_isize_overflow.sam - .. ok test_fixmate: /<>/samtools fixmate -O sam /<>/test/fixmate/3_reverse_read_pp_lt.sam - .. ok test_fixmate: /<>/samtools fixmate -O sam /<>/test/fixmate/4_reverse_read_pp_equal.sam - .. ok test_fixmate: /<>/samtools fixmate -cO sam /<>/test/fixmate/5_ct.sam - .. ok test_fixmate: /<>/samtools fixmate -cO sam /<>/test/fixmate/6_ct_replace.sam - .. ok test_fixmate: /<>/samtools fixmate -O sam /<>/test/fixmate/7_two_read_mapped.sam - .. ok test_fixmate: /<>/samtools fixmate -@ 2 -O sam /<>/test/fixmate/1_coord_sort.sam - ERR: [bam_mating_core] ERROR: Coordinate sorted, require grouped/sorted by queryname. .. expected failure test_fixmate: /<>/samtools fixmate -@ 2 -O sam /<>/test/fixmate/2_isize_overflow.sam - .. ok test_fixmate: /<>/samtools fixmate -@ 2 -O sam /<>/test/fixmate/3_reverse_read_pp_lt.sam - .. ok test_fixmate: /<>/samtools fixmate -@ 2 -O sam /<>/test/fixmate/4_reverse_read_pp_equal.sam - .. ok test_fixmate: /<>/samtools fixmate -@ 2 -cO sam /<>/test/fixmate/5_ct.sam - .. ok test_fixmate: /<>/samtools fixmate -@ 2 -cO sam /<>/test/fixmate/6_ct_replace.sam - .. ok test_fixmate: /<>/samtools fixmate -@ 2 -O sam /<>/test/fixmate/7_two_read_mapped.sam - .. ok /<>/samtools calmd -uAr /<>/test/dat/mpileup.1.sam /<>/test/dat/mpileup.ref.fa .. ok /<>/samtools calmd -@ 2 -uAr /<>/test/dat/mpileup.1.sam /<>/test/dat/mpileup.ref.fa .. ok test_idxstat: /<>/samtools idxstats /<>/test/dat/test_input_1_a.bam .. ok test_quickcheck: /<>/samtools quickcheck /<>/test/quickcheck/1.quickcheck.badeof.bam .. ok test_quickcheck: /<>/samtools quickcheck /<>/test/quickcheck/2.quickcheck.badheader.bam .. ok test_quickcheck: /<>/samtools quickcheck /<>/test/quickcheck/3.quickcheck.ok.bam .. ok test_quickcheck: /<>/samtools quickcheck /<>/test/quickcheck/4.quickcheck.ok.bam .. ok test_quickcheck: /<>/samtools quickcheck /<>/test/quickcheck/5.quickcheck.scramble30.truncated.cram .. ok test_quickcheck: /<>/samtools quickcheck /<>/test/quickcheck/6.quickcheck.cram21.ok.cram .. ok test_quickcheck: /<>/samtools quickcheck /<>/test/quickcheck/7.quickcheck.cram30.ok.cram .. ok test_quickcheck: /<>/samtools quickcheck /<>/test/quickcheck/8.quickcheck.cram21.truncated.cram .. ok test_quickcheck: /<>/samtools quickcheck /<>/test/quickcheck/9.quickcheck.cram30.truncated.cram .. ok test_quickcheck: /<>/samtools quickcheck -v /<>/test/quickcheck/1.quickcheck.badeof.bam /<>/test/quickcheck/2.quickcheck.badheader.bam /<>/test/quickcheck/3.quickcheck.ok.bam /<>/test/quickcheck/4.quickcheck.ok.bam /<>/test/quickcheck/5.quickcheck.scramble30.truncated.cram /<>/test/quickcheck/6.quickcheck.cram21.ok.cram /<>/test/quickcheck/7.quickcheck.cram30.ok.cram /<>/test/quickcheck/8.quickcheck.cram21.truncated.cram /<>/test/quickcheck/9.quickcheck.cram30.truncated.cram | sed 's,.*/quickcheck/,,' .. ok test_reheader: /<>/samtools reheader /<>/test/reheader/hdr.sam /<>/test/dat/view.001.tmp.bam | /<>/samtools view -h | perl -pe 's/ VN:.*//' .. ok test_reheader: /<>/samtools reheader /<>/test/reheader/hdr.sam /<>/test/dat/view.001.tmp.v21.cram | /<>/samtools view -h | perl -pe 's/ VN:.*//' .. ok test_reheader: /<>/samtools reheader /<>/test/reheader/hdr.sam /<>/test/dat/view.001.tmp.v30.cram | /<>/samtools view -h | perl -pe 's/ VN:.*//' .. ok test_reheader: /<>/samtools reheader --in-place /<>/test/reheader/hdr.sam /<>/test/dat/view.001.tmp.v21.cram && /<>/samtools view -h /<>/test/dat/view.001.tmp.v21.cram | perl -pe 's/ VN:.*//' .. ok test_reheader: /<>/samtools reheader --in-place /<>/test/reheader/hdr.sam /<>/test/dat/view.001.tmp.v30.cram && /<>/samtools view -h /<>/test/dat/view.001.tmp.v30.cram | perl -pe 's/ VN:.*//' .. ok test_addrprg: /<>/samtools addreplacerg -O sam -m overwrite_all /<>/test/addrprg/1_fixup.sam .. ok test_addrprg: /<>/samtools addreplacerg -O sam -m orphan_only /<>/test/addrprg/2_fixup_orphan.sam .. ok test_addrprg: /<>/samtools addreplacerg -O sam -R '1#7' /<>/test/addrprg/1_fixup.sam .. ok test_addrprg: /<>/samtools addreplacerg -O sam -r '@RG\tID:1#8\tCN:SC' /<>/test/addrprg/4_fixup_norg.sam .. ok test_addrprg: /<>/samtools addreplacerg -O sam -m overwrite_all -R '1#8' /<>/test/addrprg/1_fixup.sam .. ok test_addrprg: /<>/samtools addreplacerg -O sam -r 'ID:1#8' -r 'CN:SC' /<>/test/addrprg/4_fixup_norg.sam .. ok test_addrprg: /<>/samtools addreplacerg -@ 2 -O sam -m overwrite_all /<>/test/addrprg/1_fixup.sam .. ok test_addrprg: /<>/samtools addreplacerg -@ 2 -O sam -m orphan_only /<>/test/addrprg/2_fixup_orphan.sam .. ok test_addrprg: /<>/samtools addreplacerg -@ 2 -O sam -R '1#7' /<>/test/addrprg/1_fixup.sam .. ok test_addrprg: /<>/samtools addreplacerg -@ 2 -O sam -r '@RG\tID:1#8\tCN:SC' /<>/test/addrprg/4_fixup_norg.sam .. ok test_addrprg: /<>/samtools addreplacerg -@ 2 -O sam -m overwrite_all -R '1#8' /<>/test/addrprg/1_fixup.sam .. ok test_addrprg: /<>/samtools addreplacerg -@ 2 -O sam -r 'ID:1#8' -r 'CN:SC' /<>/test/addrprg/4_fixup_norg.sam .. ok Number of tests: total .. 476 passed .. 459 failed .. 0 expected failure .. 17 unexpected pass .. 0 test/merge/test_bam_translate test/merge/test_bam_translate.tmp test/merge/test_rtrans_build test/merge/test_trans_tbl_init cd test/mpileup && ./regression.sh mpileup.reg === Testing mpileup.reg regressions === EXPECTED FAIL: Task failed, but expected to fail; when running $samtools mpileup -Q0 -x -f c1.fa c1#pad1.bam EXPECTED FAIL: Task failed, but expected to fail; when running $samtools mpileup -Q0 -x -f c1.fa c1#pad2.bam EXPECTED FAIL: Task failed, but expected to fail; when running $samtools mpileup -ABQ0 -a -l xx.bed3 xx#depth3.bam Expected passes: 153 Unexpected passes: 0 Expected failures: 3 Unexpected failures: 0 => PASS cd test/mpileup && ./regression.sh depth.reg === Testing depth.reg regressions === EXPECTED FAIL: Task failed, but expected to fail; when running $samtools depth -a -b xx.bed3 xx#depth3.bam Expected passes: 43 Unexpected passes: 0 Expected failures: 1 Unexpected failures: 0 => PASS test/split/test_count_rg test/split/test_expand_format_string test/split/test_filter_header_rg test/split/test_parse_args make[2]: Leaving directory '/<>' make[1]: Leaving directory '/<>' fakeroot debian/rules binary-arch dh binary-arch --parallel dh_testroot -a -O--parallel dh_prep -a -O--parallel rm -f -- debian/samtools.substvars rm -fr -- debian/.debhelper/generated/samtools/ debian/samtools/ debian/rules override_dh_auto_install make[1]: Entering directory '/<>' dh_auto_install -- \ prefix=/usr install -d debian/samtools make -j4 install DESTDIR=/<>/debian/tmp AM_UPDATE_INFO_DIR=no prefix=/usr make[2]: Entering directory '/<>' mkdir -p -m 755 /<>/debian/tmp/usr/bin /<>/debian/tmp/usr/bin /<>/debian/tmp/usr/share/man/man1 install -p samtools /<>/debian/tmp/usr/bin install -p misc/ace2sam misc/maq2sam-long misc/maq2sam-short misc/md5fa misc/md5sum-lite misc/wgsim /<>/debian/tmp/usr/bin install -p misc/blast2sam.pl misc/bowtie2sam.pl misc/export2sam.pl misc/interpolate_sam.pl misc/novo2sam.pl misc/plot-bamstats misc/psl2sam.pl misc/sam2vcf.pl misc/samtools.pl misc/seq_cache_populate.pl misc/soap2sam.pl misc/varfilter.py misc/wgsim_eval.pl misc/zoom2sam.pl /<>/debian/tmp/usr/bin install -p -m 644 samtools.1 misc/wgsim.1 /<>/debian/tmp/usr/share/man/man1 make[2]: Leaving directory '/<>' make clean 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*.bam* rm -f *.o misc/*.o test/*.o test/*/*.o version.h rm -f samtools libbam.a libst.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 make[2]: Leaving directory '/<>' make[1]: Leaving directory '/<>' dh_install -a -O--parallel install -d debian/samtools//usr cp --reflink=auto -a debian/tmp/usr/bin debian/samtools//usr/ install -d debian/samtools//usr/share/man cp --reflink=auto -a debian/tmp/usr/share/man/man1 debian/samtools//usr/share/man/ install -d debian/samtools/usr/share/commonwl/ cp --reflink=auto -a ./debian/samtools-faidx.cwl ./debian/samtools-index.cwl ./debian/samtools-rmdup.cwl ./debian/samtools-sort.cwl ./debian/samtools-view.cwl debian/samtools/usr/share/commonwl// cp --reflink=auto -a ./debian/mans/ace2sam.1 ./debian/mans/samtools.pl.1 ./debian/mans/wgsim.1 debian/samtools/usr/share/man/man1/ install -d debian/.debhelper/generated/samtools install -d debian/.debhelper/generated/samtools-test dh_installdocs -a -O--parallel install -d debian/samtools/usr/share/doc/samtools cp --reflink=auto -a ./AUTHORS debian/samtools/usr/share/doc/samtools cp --reflink=auto -a ./debian/reference debian/samtools/usr/share/doc/samtools chown -R 0:0 debian/samtools/usr/share/doc chmod -R go=rX debian/samtools/usr/share/doc chmod -R u\+rw debian/samtools/usr/share/doc install -p -m0644 debian/README.Debian debian/samtools/usr/share/doc/samtools/README.Debian install -p -m0644 debian/copyright debian/samtools/usr/share/doc/samtools/copyright dh_installchangelogs -a -O--parallel install -p -m0644 debian/changelog debian/samtools/usr/share/doc/samtools/changelog.Debian install -p -m0644 debian/NEWS debian/samtools/usr/share/doc/samtools/NEWS.Debian dh_installman -a -O--parallel man --recode UTF-8 \.\/debian\/samtools\/usr\/share\/man\/man1\/ace2sam\.1 > debian\/samtools\/usr\/share\/man\/man1\/ace2sam\.1\.dh\-new man --recode UTF-8 \.\/debian\/samtools\/usr\/share\/man\/man1\/samtools\.1 > debian\/samtools\/usr\/share\/man\/man1\/samtools\.1\.dh\-new man --recode UTF-8 \.\/debian\/samtools\/usr\/share\/man\/man1\/samtools\.pl\.1 > debian\/samtools\/usr\/share\/man\/man1\/samtools\.pl\.1\.dh\-new man --recode UTF-8 \.\/debian\/samtools\/usr\/share\/man\/man1\/wgsim\.1 > debian\/samtools\/usr\/share\/man\/man1\/wgsim\.1\.dh\-new mv debian/samtools/usr/share/man/man1/samtools.pl.1.dh-new debian/samtools/usr/share/man/man1/samtools.pl.1 chmod 0644 -- debian/samtools/usr/share/man/man1/samtools.pl.1 mv debian/samtools/usr/share/man/man1/samtools.1.dh-new debian/samtools/usr/share/man/man1/samtools.1 chmod 0644 -- debian/samtools/usr/share/man/man1/samtools.1 mv debian/samtools/usr/share/man/man1/ace2sam.1.dh-new debian/samtools/usr/share/man/man1/ace2sam.1 chmod 0644 -- debian/samtools/usr/share/man/man1/ace2sam.1 mv debian/samtools/usr/share/man/man1/wgsim.1.dh-new debian/samtools/usr/share/man/man1/wgsim.1 chmod 0644 -- debian/samtools/usr/share/man/man1/wgsim.1 dh_lintian -a -O--parallel install -d debian/samtools/usr/share/lintian/overrides install -p -m0644 debian/samtools.lintian-overrides debian/samtools/usr/share/lintian/overrides/samtools dh_perl -a -O--parallel (grep -a -s -v perl:Depends debian/samtools.substvars; echo perl:Depends=perl:any) > debian/samtools.substvars.new mv debian/samtools.substvars.new debian/samtools.substvars dh_link -a -O--parallel dh_strip_nondeterminism -a -O--parallel dh_compress -a -O--parallel cd debian/samtools chmod a-x usr/share/doc/samtools/NEWS.Debian usr/share/doc/samtools/changelog.Debian usr/share/man/man1/ace2sam.1 usr/share/man/man1/samtools.1 usr/share/man/man1/samtools.pl.1 usr/share/man/man1/wgsim.1 gzip -9nf usr/share/doc/samtools/NEWS.Debian usr/share/doc/samtools/changelog.Debian usr/share/man/man1/ace2sam.1 usr/share/man/man1/samtools.1 usr/share/man/man1/samtools.pl.1 usr/share/man/man1/wgsim.1 cd '/<>' dh_fixperms -a -O--parallel find debian/samtools -true -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0 find debian/samtools ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/samtools/usr/share/doc -type f -a -true -a ! -regex 'debian/samtools/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/samtools/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/samtools/usr/share/man debian/samtools/usr/share/lintian/overrides -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/samtools -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/samtools/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x dh_missing -a -O--parallel dh_strip -a -O--parallel install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/82 objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/ace2sam debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/82/5a0d076ff5b061ee83e2ad99e0a030ab2bd952.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/82/5a0d076ff5b061ee83e2ad99e0a030ab2bd952.debug chown 0:0 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/82/5a0d076ff5b061ee83e2ad99e0a030ab2bd952.debug strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/ace2sam objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/82/5a0d076ff5b061ee83e2ad99e0a030ab2bd952.debug debian/samtools/usr/bin/ace2sam install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/b1 objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5sum-lite debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/b1/d3d47091bb144b02f08128ff0aa57d2f05bc46.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/b1/d3d47091bb144b02f08128ff0aa57d2f05bc46.debug chown 0:0 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/b1/d3d47091bb144b02f08128ff0aa57d2f05bc46.debug strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/md5sum-lite objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/b1/d3d47091bb144b02f08128ff0aa57d2f05bc46.debug debian/samtools/usr/bin/md5sum-lite install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/1a objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5fa debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/1a/0851c402e8e0c990cf9e71b2e8c164e007fb78.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/1a/0851c402e8e0c990cf9e71b2e8c164e007fb78.debug chown 0:0 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/1a/0851c402e8e0c990cf9e71b2e8c164e007fb78.debug strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/md5fa objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/1a/0851c402e8e0c990cf9e71b2e8c164e007fb78.debug debian/samtools/usr/bin/md5fa install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/d6 objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-short debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/d6/e25fedcfeb31d5b5ae63cac7dcd85d5124efe4.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/d6/e25fedcfeb31d5b5ae63cac7dcd85d5124efe4.debug chown 0:0 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/d6/e25fedcfeb31d5b5ae63cac7dcd85d5124efe4.debug strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/maq2sam-short objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/d6/e25fedcfeb31d5b5ae63cac7dcd85d5124efe4.debug debian/samtools/usr/bin/maq2sam-short install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/31 objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/wgsim debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/31/0f81fa5f2e141087c3445a05f67ae4fd7c2428.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/31/0f81fa5f2e141087c3445a05f67ae4fd7c2428.debug chown 0:0 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/31/0f81fa5f2e141087c3445a05f67ae4fd7c2428.debug strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/wgsim objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/31/0f81fa5f2e141087c3445a05f67ae4fd7c2428.debug debian/samtools/usr/bin/wgsim install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/23 objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-long debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/23/b5855b9c27b3fd5bcd95f6264c29fffc5112c0.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/23/b5855b9c27b3fd5bcd95f6264c29fffc5112c0.debug chown 0:0 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/23/b5855b9c27b3fd5bcd95f6264c29fffc5112c0.debug strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/maq2sam-long objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/23/b5855b9c27b3fd5bcd95f6264c29fffc5112c0.debug debian/samtools/usr/bin/maq2sam-long install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/72 objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/samtools debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/72/0c6e81db0ec92109392a1eb46480c8ff6a92b9.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/72/0c6e81db0ec92109392a1eb46480c8ff6a92b9.debug chown 0:0 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/72/0c6e81db0ec92109392a1eb46480c8ff6a92b9.debug strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/samtools objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/72/0c6e81db0ec92109392a1eb46480c8ff6a92b9.debug debian/samtools/usr/bin/samtools install -d debian/.debhelper/samtools/dbgsym-root/usr/share/doc ln -s samtools debian/.debhelper/samtools/dbgsym-root/usr/share/doc/samtools-dbgsym dh_makeshlibs -a -O--parallel rm -f debian/samtools/DEBIAN/shlibs dh_shlibdeps -a -O--parallel install -d debian/samtools/DEBIAN dpkg-shlibdeps -Tdebian/samtools.substvars debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/wgsim debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/samtools dh_installdeb -a -O--parallel dh_gencontrol -a -O--parallel echo misc:Depends= >> debian/samtools.substvars echo misc:Pre-Depends= >> debian/samtools.substvars install -d debian/.debhelper/samtools/dbgsym-root/DEBIAN dpkg-gencontrol -psamtools -ldebian/changelog -Tdebian/samtools.substvars -Pdebian/.debhelper/samtools/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=extra -UHomepage -DAuto-Built-Package=debug-symbols -DPackage=samtools-dbgsym "-DDepends=samtools (= \${binary:Version})" "-DDescription=Debug symbols for samtools" "-DBuild-Ids=1a0851c402e8e0c990cf9e71b2e8c164e007fb78 23b5855b9c27b3fd5bcd95f6264c29fffc5112c0 310f81fa5f2e141087c3445a05f67ae4fd7c2428 720c6e81db0ec92109392a1eb46480c8ff6a92b9 825a0d076ff5b061ee83e2ad99e0a030ab2bd952 b1d3d47091bb144b02f08128ff0aa57d2f05bc46 d6e25fedcfeb31d5b5ae63cac7dcd85d5124efe4" -DSection=debug -DPackage-Type=ddeb -UMulti-Arch -UReplaces -UBreaks dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:Depends} chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/DEBIAN/control chown 0:0 -- debian/.debhelper/samtools/dbgsym-root/DEBIAN/control dpkg-gencontrol -psamtools -ldebian/changelog -Tdebian/samtools.substvars -Pdebian/samtools -UMulti-Arch dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:Depends} chmod 0644 -- debian/samtools/DEBIAN/control chown 0:0 -- debian/samtools/DEBIAN/control dh_md5sums -a -O--parallel (cd debian/samtools >/dev/null ; find . -type f ! -regex './DEBIAN/.*' -printf '%P\0' | LC_ALL=C sort -z | xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums) >/dev/null chmod 0644 -- debian/samtools/DEBIAN/md5sums chown 0:0 -- debian/samtools/DEBIAN/md5sums (cd debian/.debhelper/samtools/dbgsym-root >/dev/null ; find . -type f ! -regex './DEBIAN/.*' -printf '%P\0' | LC_ALL=C sort -z | xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums) >/dev/null chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/DEBIAN/md5sums chown 0:0 -- debian/.debhelper/samtools/dbgsym-root/DEBIAN/md5sums dh_builddeb -a -O--parallel dpkg-deb --build debian/samtools .. install -d debian/.debhelper/scratch-space/build-samtools dpkg-deb -z1 -Zxz -Sextreme --build debian/.debhelper/samtools/dbgsym-root debian/.debhelper/scratch-space/build-samtools INFO: pkgstriptranslations version 131 INFO: pkgstriptranslations version 131 pkgstriptranslations: processing samtools (in debian/samtools); do_strip: , oemstrip: pkgstriptranslations: processing samtools-dbgsym (in debian/.debhelper/samtools/dbgsym-root); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/samtools/DEBIAN/control, package samtools, directory debian/samtools pkgstripfiles: Truncating usr/share/doc/samtools/changelog.Debian.gz to topmost ten records pkgstripfiles: Running PNG optimization (using 4 cpus) for package samtools ... pkgstripfiles: No PNG files. dpkg-deb: building package 'samtools' in '../samtools_1.4.1-1build1_armhf.deb'. pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/.debhelper/samtools/dbgsym-root/DEBIAN/control, package samtools-dbgsym, directory debian/.debhelper/samtools/dbgsym-root pkgstripfiles: Running PNG optimization (using 4 cpus) for package samtools-dbgsym ... pkgstripfiles: No PNG files. dpkg-deb: building package 'samtools-dbgsym' in 'debian/.debhelper/scratch-space/build-samtools/samtools-dbgsym_1.4.1-1build1_armhf.deb'. Renaming samtools-dbgsym_1.4.1-1build1_armhf.deb to samtools-dbgsym_1.4.1-1build1_armhf.ddeb mv debian/.debhelper/scratch-space/build-samtools/samtools-dbgsym_1.4.1-1build1_armhf.deb ../samtools-dbgsym_1.4.1-1build1_armhf.ddeb dpkg-genbuildinfo --build=any dpkg-genchanges --build=any -mLaunchpad Build Daemon >../samtools_1.4.1-1build1_armhf.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build samtools-1.4.1 dpkg-source: info: using options from samtools-1.4.1/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis.*|README.md)$ dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 20170729-1746 Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Post Build Chroot | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ samtools_1.4.1-1build1_armhf.changes: ------------------------------------- Format: 1.8 Date: Sat, 29 Jul 2017 19:41:36 +0200 Source: samtools Binary: samtools samtools-test Architecture: armhf Version: 1.4.1-1build1 Distribution: artful-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Gianfranco Costamagna Description: samtools - processing sequence alignments in SAM and BAM formats samtools-test - test files for the samtools package Changes: samtools (1.4.1-1build1) artful; urgency=medium . * Rebuild against new libhts2. Checksums-Sha1: d338c41286608eb9a440a7bc78b0bc99fa22d0b2 472680 samtools-dbgsym_1.4.1-1build1_armhf.ddeb 235370c74c750cfedd7b1cef9118d293caa6935d 6168 samtools_1.4.1-1build1_armhf.buildinfo 73357087387fa1168eb8c9e7e0e831b51d5093df 225010 samtools_1.4.1-1build1_armhf.deb Checksums-Sha256: d060949d7349dd17c8472077787b19ab9599876cabee17896e53fb1030be7776 472680 samtools-dbgsym_1.4.1-1build1_armhf.ddeb 432178183f39c8752d9b67263b378cdaa59005d9e5dcade44cee71706db4e07d 6168 samtools_1.4.1-1build1_armhf.buildinfo aff0e82c7841ef8a29bd59ff08747151b95f7e60c41447e0b468acd944c2d762 225010 samtools_1.4.1-1build1_armhf.deb Files: 4a74653ba32ea5315b9a053c51172f6c 472680 debug extra samtools-dbgsym_1.4.1-1build1_armhf.ddeb 97b4f683e1aae414d24545c9e5847ea5 6168 science optional samtools_1.4.1-1build1_armhf.buildinfo e0dbc0fe829003cd6942543138bf6688 225010 science optional samtools_1.4.1-1build1_armhf.deb +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ samtools_1.4.1-1build1_armhf.deb -------------------------------- new debian package, version 2.0. size 225010 bytes: control archive=1826 bytes. 884 bytes, 18 lines control 2258 bytes, 37 lines md5sums Package: samtools Version: 1.4.1-1build1 Architecture: armhf Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 567 Depends: libc6 (>= 2.7), libhts2, libncurses5 (>= 6), libtinfo5 (>= 6), zlib1g (>= 1:1.2.3.3) Recommends: python Section: science Priority: optional Homepage: http://www.htslib.org/ Description: processing sequence alignments in SAM and BAM formats Samtools is a set of utilities that manipulate nucleotide sequence alignments in the binary BAM format. It imports from and exports to the ascii SAM (Sequence Alignment/Map) format, does sorting, merging and indexing, and allows one to retrieve reads in any regions swiftly. It is designed to work on a stream, and is able to open a BAM (not SAM) file on a remote FTP or HTTP server. drwxr-xr-x root/root 0 2017-07-29 17:41 ./ drwxr-xr-x root/root 0 2017-07-29 17:41 ./usr/ drwxr-xr-x root/root 0 2017-07-29 17:41 ./usr/bin/ -rwxr-xr-x root/root 13776 2017-07-29 17:41 ./usr/bin/ace2sam -rwxr-xr-x root/root 5328 2017-05-08 10:07 ./usr/bin/blast2sam.pl -rwxr-xr-x root/root 3364 2017-05-08 10:07 ./usr/bin/bowtie2sam.pl -rwxr-xr-x root/root 18032 2017-05-08 10:07 ./usr/bin/export2sam.pl -rwxr-xr-x root/root 6125 2017-05-08 10:07 ./usr/bin/interpolate_sam.pl -rwxr-xr-x root/root 9680 2017-07-29 17:41 ./usr/bin/maq2sam-long -rwxr-xr-x root/root 9680 2017-07-29 17:41 ./usr/bin/maq2sam-short -rwxr-xr-x root/root 9680 2017-07-29 17:41 ./usr/bin/md5fa -rwxr-xr-x root/root 5584 2017-07-29 17:41 ./usr/bin/md5sum-lite -rwxr-xr-x root/root 6773 2017-05-08 10:07 ./usr/bin/novo2sam.pl -rwxr-xr-x root/root 48659 2017-05-08 10:07 ./usr/bin/plot-bamstats -rwxr-xr-x root/root 3208 2017-05-08 10:07 ./usr/bin/psl2sam.pl -rwxr-xr-x root/root 8961 2017-05-08 10:07 ./usr/bin/sam2vcf.pl -rwxr-xr-x root/root 280128 2017-07-29 17:41 ./usr/bin/samtools -rwxr-xr-x root/root 16478 2017-05-08 10:07 ./usr/bin/samtools.pl -rwxr-xr-x root/root 11105 2017-05-08 10:07 ./usr/bin/seq_cache_populate.pl -rwxr-xr-x root/root 3909 2017-05-08 10:07 ./usr/bin/soap2sam.pl -rwxr-xr-x root/root 7888 2017-05-08 10:07 ./usr/bin/varfilter.py -rwxr-xr-x root/root 17912 2017-07-29 17:41 ./usr/bin/wgsim -rwxr-xr-x root/root 12540 2017-05-08 10:07 ./usr/bin/wgsim_eval.pl -rwxr-xr-x root/root 3583 2017-05-08 10:07 ./usr/bin/zoom2sam.pl drwxr-xr-x root/root 0 2017-07-29 17:41 ./usr/share/ drwxr-xr-x root/root 0 2017-07-29 17:41 ./usr/share/commonwl/ -rwxr-xr-x root/root 1910 2017-06-18 19:11 ./usr/share/commonwl/samtools-faidx.cwl -rwxr-xr-x root/root 1983 2017-06-18 19:11 ./usr/share/commonwl/samtools-index.cwl -rwxr-xr-x root/root 1631 2017-06-18 19:11 ./usr/share/commonwl/samtools-rmdup.cwl -rwxr-xr-x root/root 2838 2017-06-18 19:11 ./usr/share/commonwl/samtools-sort.cwl -rwxr-xr-x root/root 6228 2017-06-18 19:11 ./usr/share/commonwl/samtools-view.cwl drwxr-xr-x root/root 0 2017-07-29 17:41 ./usr/share/doc/ drwxr-xr-x root/root 0 2017-07-29 17:41 ./usr/share/doc/samtools/ -rw-r--r-- root/root 828 2017-05-08 10:07 ./usr/share/doc/samtools/AUTHORS -rw-r--r-- root/root 295 2017-06-18 19:11 ./usr/share/doc/samtools/NEWS.Debian.gz -rw-r--r-- root/root 721 2017-06-18 19:11 ./usr/share/doc/samtools/README.Debian -rw-r--r-- root/root 1139 2017-07-29 17:41 ./usr/share/doc/samtools/changelog.Debian.gz -rw-r--r-- root/root 3451 2017-06-18 19:11 ./usr/share/doc/samtools/copyright -rw-r--r-- root/root 592 2017-06-18 19:11 ./usr/share/doc/samtools/reference drwxr-xr-x root/root 0 2017-07-29 17:41 ./usr/share/lintian/ drwxr-xr-x root/root 0 2017-07-29 17:41 ./usr/share/lintian/overrides/ -rw-r--r-- root/root 219 2017-06-18 19:11 ./usr/share/lintian/overrides/samtools drwxr-xr-x root/root 0 2017-07-29 17:41 ./usr/share/man/ drwxr-xr-x root/root 0 2017-07-29 17:41 ./usr/share/man/man1/ -rw-r--r-- root/root 462 2017-07-29 17:41 ./usr/share/man/man1/ace2sam.1.gz -rw-r--r-- root/root 20580 2017-07-29 17:41 ./usr/share/man/man1/samtools.1.gz -rw-r--r-- root/root 410 2017-07-29 17:41 ./usr/share/man/man1/samtools.pl.1.gz -rw-r--r-- root/root 518 2017-07-29 17:41 ./usr/share/man/man1/wgsim.1.gz +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Not removing build depends: as requested Keeping session: +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: armhf Build-Space: 17484 Build-Time: 156 Distribution: artful-proposed Host Architecture: armhf Install-Time: 20 Job: samtools_1.4.1-1build1.dsc Machine Architecture: arm64 Package: samtools Package-Time: 178 Source-Version: 1.4.1-1build1 Space: 17484 Status: successful Version: 1.4.1-1build1 -------------------------------------------------------------------------------- Finished at 20170729-1746 Build needed 00:02:58, 17484k disc space RUN: /usr/share/launchpad-buildd/slavebin/scan-for-processes ['scan-for-processes', 'PACKAGEBUILD-13170033'] Scanning for processes to kill in build /home/buildd/build-PACKAGEBUILD-13170033/chroot-autobuild... RUN: /usr/share/launchpad-buildd/slavebin/umount-chroot ['umount-chroot', 'PACKAGEBUILD-13170033'] Unmounting chroot for build PACKAGEBUILD-13170033... RUN: /usr/share/launchpad-buildd/slavebin/remove-build ['remove-build', 'PACKAGEBUILD-13170033'] Removing build PACKAGEBUILD-13170033