RUN: /usr/share/launchpad-buildd/slavebin/slave-prep ['slave-prep'] Forking launchpad-buildd slave process... Kernel version: Linux bos01-arm64-037 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 22:33:46 ntpdate[2179]: adjust time server 10.211.37.1 offset 0.000340 sec RUN: /usr/share/launchpad-buildd/slavebin/unpack-chroot ['unpack-chroot', 'PACKAGEBUILD-12929070', '/home/buildd/filecache-default/42e17d2fa25e748a1aa6eaeef2fe6722beaed5a9'] Unpacking chroot for build PACKAGEBUILD-12929070 RUN: /usr/share/launchpad-buildd/slavebin/mount-chroot ['mount-chroot', 'PACKAGEBUILD-12929070'] Mounting chroot for build PACKAGEBUILD-12929070 RUN: /usr/share/launchpad-buildd/slavebin/override-sources-list ['override-sources-list', 'PACKAGEBUILD-12929070', 'deb http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu artful main', 'deb http://ftpmaster.internal/ubuntu artful main restricted universe multiverse', 'deb http://ftpmaster.internal/ubuntu artful-security main restricted universe multiverse', 'deb http://ftpmaster.internal/ubuntu artful-updates main restricted universe multiverse'] Overriding sources.list in build-PACKAGEBUILD-12929070 RUN: /usr/share/launchpad-buildd/slavebin/add-trusted-keys ['add-trusted-keys', 'PACKAGEBUILD-12929070'] Adding trusted keys to build-PACKAGEBUILD-12929070 Warning: apt-key output should not be parsed (stdout is not a terminal) OK Warning: apt-key output should not be parsed (stdout is not a terminal) /etc/apt/trusted.gpg -------------------- pub rsa1024 2009-10-22 [SC] 60C3 1780 3A41 BA51 845E 371A 1E93 77A2 BA9E F27F uid [ unknown] Launchpad Toolchain builds /etc/apt/trusted.gpg.d/ubuntu-keyring-2012-archive.gpg ------------------------------------------------------ pub rsa4096 2012-05-11 [SC] 790B C727 7767 219C 42C8 6F93 3B4F E6AC C0B2 1F32 uid [ unknown] Ubuntu Archive Automatic Signing Key (2012) /etc/apt/trusted.gpg.d/ubuntu-keyring-2012-cdimage.gpg ------------------------------------------------------ pub rsa4096 2012-05-11 [SC] 8439 38DF 228D 22F7 B374 2BC0 D94A A3F0 EFE2 1092 uid [ unknown] Ubuntu CD Image Automatic Signing Key (2012) RUN: /usr/share/launchpad-buildd/slavebin/update-debian-chroot ['update-debian-chroot', 'PACKAGEBUILD-12929070', 'armhf'] Updating debian chroot for build PACKAGEBUILD-12929070 Get:1 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu artful InRelease [15.4 kB] Get:2 http://ftpmaster.internal/ubuntu artful InRelease [237 kB] Get:3 http://ftpmaster.internal/ubuntu artful-security InRelease [65.5 kB] Get:4 http://ftpmaster.internal/ubuntu artful-updates InRelease [65.5 kB] Get:5 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu artful/main armhf Packages [28.1 kB] Get:6 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu artful/main Translation-en [16.6 kB] Get:7 http://ftpmaster.internal/ubuntu artful/main armhf Packages [1105 kB] Get:8 http://ftpmaster.internal/ubuntu artful/main Translation-en [558 kB] Get:9 http://ftpmaster.internal/ubuntu artful/restricted armhf Packages [5668 B] Get:10 http://ftpmaster.internal/ubuntu artful/restricted Translation-en [2724 B] Get:11 http://ftpmaster.internal/ubuntu artful/universe armhf Packages [8028 kB] Get:12 http://ftpmaster.internal/ubuntu artful/universe Translation-en [4776 kB] Get:13 http://ftpmaster.internal/ubuntu artful/multiverse armhf Packages [131 kB] Get:14 http://ftpmaster.internal/ubuntu artful/multiverse Translation-en [109 kB] Fetched 15.1 MB in 5s (2615 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following NEW packages will be installed: gcc-7-base The following packages will be upgraded: advancecomp apt apt-transport-https base-files bash binutils bsdutils ca-certificates cpp cpp-6 debconf debianutils dmsetup dpkg dpkg-dev findutils g++ g++-6 gcc gcc-6 gcc-6-base grep libapparmor1 libapt-pkg5.0 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 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 99 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 51.2 MB of archives. After this operation, 3006 kB of additional disk space will be used. Get:1 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu artful/main armhf linux-libc-dev armhf 4.11.0-10.15 [903 kB] Get:2 http://ftpmaster.internal/ubuntu artful/main armhf base-files armhf 9.6ubuntu101 [59.1 kB] Get:3 http://ftpmaster.internal/ubuntu artful/main armhf sensible-utils all 0.0.9+nmu1 [10.2 kB] Get:4 http://ftpmaster.internal/ubuntu artful/main armhf debianutils armhf 4.8.1.1 [84.3 kB] Get:5 http://ftpmaster.internal/ubuntu artful/main armhf bash armhf 4.4-5ubuntu1 [527 kB] Get:6 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu artful/main armhf gcc-7-base armhf 7.1.0-9ubuntu1 [18.9 kB] Get:7 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu artful/main armhf libgcc1 armhf 1:7.1.0-9ubuntu1 [38.4 kB] Get:8 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu artful/main armhf libstdc++6 armhf 7.1.0-9ubuntu1 [346 kB] Get:9 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu artful/main armhf binutils armhf 2.28.90.20170704-0ubuntu1 [2658 kB] Get:10 http://ftpmaster.internal/ubuntu artful/main armhf bsdutils armhf 1:2.29.2-2ubuntu1 [52.4 kB] Get:11 http://ftpmaster.internal/ubuntu artful/main armhf tar armhf 1.29b-2 [209 kB] Get:12 http://ftpmaster.internal/ubuntu artful/main armhf dpkg armhf 1.18.24ubuntu1 [1099 kB] Get:13 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu artful/main armhf libgomp1 armhf 7.1.0-9ubuntu1 [64.6 kB] Get:14 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu artful/main armhf libubsan0 armhf 7.1.0-9ubuntu1 [104 kB] Get:15 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu artful/main armhf libatomic1 armhf 7.1.0-9ubuntu1 [6252 B] Get:16 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu artful/main armhf libasan3 armhf 6.4.0-1ubuntu2 [292 kB] Get:17 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu artful/main armhf g++-6 armhf 6.4.0-1ubuntu2 [5925 kB] Get:18 http://ftpmaster.internal/ubuntu artful/main armhf findutils armhf 4.6.0+git+20170606-3 [277 kB] Get:19 http://ftpmaster.internal/ubuntu artful/main armhf grep armhf 3.1-2 [145 kB] Get:20 http://ftpmaster.internal/ubuntu artful/main armhf login armhf 1:4.2-3.2ubuntu2 [301 kB] Get:21 http://ftpmaster.internal/ubuntu artful/main armhf util-linux armhf 2.29.2-2ubuntu1 [842 kB] Get:22 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu artful/main armhf libstdc++-6-dev armhf 6.4.0-1ubuntu2 [1481 kB] Get:23 http://ftpmaster.internal/ubuntu artful/main armhf mount armhf 2.29.2-2ubuntu1 [124 kB] Get:24 http://ftpmaster.internal/ubuntu artful/main armhf libperl5.24 armhf 5.24.1-7ubuntu1 [2794 kB] Get:25 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu artful/main armhf gcc-6 armhf 6.4.0-1ubuntu2 [5805 kB] Get:26 http://ftpmaster.internal/ubuntu artful/main armhf perl armhf 5.24.1-7ubuntu1 [219 kB] Get:27 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu artful/main armhf libgcc-6-dev armhf 6.4.0-1ubuntu2 [550 kB] Get:28 http://ftpmaster.internal/ubuntu artful/main armhf perl-base armhf 5.24.1-7ubuntu1 [1239 kB] Get:29 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu artful/main armhf libcc1-0 armhf 7.1.0-9ubuntu1 [31.5 kB] Get:30 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu artful/main armhf cpp-6 armhf 6.4.0-1ubuntu2 [5202 kB] Get:31 http://ftpmaster.internal/ubuntu artful/main armhf perl-modules-5.24 all 5.24.1-7ubuntu1 [2664 kB] Get:32 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu artful/main armhf gcc-6-base armhf 6.4.0-1ubuntu2 [17.5 kB] Get:33 http://ftpmaster.internal/ubuntu artful/main armhf libc6-dev armhf 2.24-12ubuntu1 [1810 kB] Get:34 http://ftpmaster.internal/ubuntu artful/main armhf libc-dev-bin armhf 2.24-12ubuntu1 [59.4 kB] Get:35 http://ftpmaster.internal/ubuntu artful/main armhf libc6 armhf 2.24-12ubuntu1 [2143 kB] Get:36 http://ftpmaster.internal/ubuntu artful/main armhf libdb5.3 armhf 5.3.28-13 [589 kB] Get:37 http://ftpmaster.internal/ubuntu artful/main armhf libc-bin armhf 2.24-12ubuntu1 [491 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 debconf all 1.5.63 [136 kB] Get:45 http://ftpmaster.internal/ubuntu artful/main armhf libip4tc0 armhf 1.6.1-2ubuntu1 [17.9 kB] Get:46 http://ftpmaster.internal/ubuntu artful/main armhf libapparmor1 armhf 2.11.0-2ubuntu8 [26.0 kB] Get:47 http://ftpmaster.internal/ubuntu artful/main armhf libaudit-common all 1:2.7.7-1ubuntu1 [4118 B] Get:48 http://ftpmaster.internal/ubuntu artful/main armhf libcap-ng0 armhf 0.7.7-3build1 [9794 B] Get:49 http://ftpmaster.internal/ubuntu artful/main armhf libaudit1 armhf 1:2.7.7-1ubuntu1 [35.1 kB] Get:50 http://ftpmaster.internal/ubuntu artful/main armhf libuuid1 armhf 2.29.2-2ubuntu1 [14.2 kB] Get:51 http://ftpmaster.internal/ubuntu artful/main armhf libblkid1 armhf 2.29.2-2ubuntu1 [98.4 kB] Get:52 http://ftpmaster.internal/ubuntu artful/main armhf libgpg-error0 armhf 1.27-3 [32.0 kB] Get:53 http://ftpmaster.internal/ubuntu artful/main armhf libgcrypt20 armhf 1.7.8-2 [344 kB] Get:54 http://ftpmaster.internal/ubuntu artful/main armhf libkmod2 armhf 24-1ubuntu1 [34.8 kB] Get:55 http://ftpmaster.internal/ubuntu artful/main armhf libpcre3 armhf 2:8.39-4 [208 kB] Get:56 http://ftpmaster.internal/ubuntu artful/main armhf libselinux1 armhf 2.6-3build1 [59.4 kB] Get:57 http://ftpmaster.internal/ubuntu artful/main armhf libmount1 armhf 2.29.2-2ubuntu1 [106 kB] Get:58 http://ftpmaster.internal/ubuntu artful/main armhf systemd armhf 233-8ubuntu3 [2250 kB] Get:59 http://ftpmaster.internal/ubuntu artful/main armhf libsystemd0 armhf 233-8ubuntu3 [191 kB] Get:60 http://ftpmaster.internal/ubuntu artful/main armhf systemd-sysv armhf 233-8ubuntu3 [12.3 kB] Get:61 http://ftpmaster.internal/ubuntu artful/main armhf libfdisk1 armhf 2.29.2-2ubuntu1 [132 kB] Get:62 http://ftpmaster.internal/ubuntu artful/main armhf libsemanage-common all 2.6-2build1 [6738 B] Get:63 http://ftpmaster.internal/ubuntu artful/main armhf libsemanage1 armhf 2.6-2build1 [71.1 kB] Get:64 http://ftpmaster.internal/ubuntu artful/main armhf libsmartcols1 armhf 2.29.2-2ubuntu1 [60.8 kB] Get:65 http://ftpmaster.internal/ubuntu artful/main armhf libudev1 armhf 233-8ubuntu3 [51.3 kB] Get:66 http://ftpmaster.internal/ubuntu artful/main armhf passwd armhf 1:4.2-3.2ubuntu2 [747 kB] Get:67 http://ftpmaster.internal/ubuntu artful/main armhf multiarch-support armhf 2.24-12ubuntu1 [6836 B] Get:68 http://ftpmaster.internal/ubuntu artful/main armhf libdevmapper1.02.1 armhf 2:1.02.137-2ubuntu2 [125 kB] Get:69 http://ftpmaster.internal/ubuntu artful/main armhf dmsetup armhf 2:1.02.137-2ubuntu2 [71.2 kB] Get:70 http://ftpmaster.internal/ubuntu artful/main armhf libroken18-heimdal armhf 7.4.0.dfsg.1-2 [33.9 kB] Get:71 http://ftpmaster.internal/ubuntu artful/main armhf libasn1-8-heimdal armhf 7.4.0.dfsg.1-2 [138 kB] Get:72 http://ftpmaster.internal/ubuntu artful/main armhf libheimbase1-heimdal armhf 7.4.0.dfsg.1-2 [24.0 kB] Get:73 http://ftpmaster.internal/ubuntu artful/main armhf libhcrypto4-heimdal armhf 7.4.0.dfsg.1-2 [77.4 kB] Get:74 http://ftpmaster.internal/ubuntu artful/main armhf libwind0-heimdal armhf 7.4.0.dfsg.1-2 [46.9 kB] Get:75 http://ftpmaster.internal/ubuntu artful/main armhf libhx509-5-heimdal armhf 7.4.0.dfsg.1-2 [88.3 kB] Get:76 http://ftpmaster.internal/ubuntu artful/main armhf libsqlite3-0 armhf 3.19.3-3 [416 kB] Get:77 http://ftpmaster.internal/ubuntu artful/main armhf libkrb5-26-heimdal armhf 7.4.0.dfsg.1-2 [168 kB] Get:78 http://ftpmaster.internal/ubuntu artful/main armhf libheimntlm0-heimdal armhf 7.4.0.dfsg.1-2 [13.3 kB] Get:79 http://ftpmaster.internal/ubuntu artful/main armhf libgssapi3-heimdal armhf 7.4.0.dfsg.1-2 [79.5 kB] Get:80 http://ftpmaster.internal/ubuntu artful/main armhf libldap-2.4-2 armhf 2.4.44+dfsg-8ubuntu1 [132 kB] Get:81 http://ftpmaster.internal/ubuntu artful/main armhf libldap-common all 2.4.44+dfsg-8ubuntu1 [16.4 kB] Get:82 http://ftpmaster.internal/ubuntu artful/main armhf libnpth0 armhf 1.5-2 [6582 B] Get:83 http://ftpmaster.internal/ubuntu artful/main armhf libssl1.0.0 armhf 1.0.2g-1ubuntu13 [711 kB] Get:84 http://ftpmaster.internal/ubuntu artful/main armhf tzdata all 2017b-2 [203 kB] Get:85 http://ftpmaster.internal/ubuntu artful/main armhf openssl armhf 1.0.2g-1ubuntu13 [485 kB] Get:86 http://ftpmaster.internal/ubuntu artful/main armhf ca-certificates all 20161130+nmu1 [186 kB] Get:87 http://ftpmaster.internal/ubuntu artful/main armhf libgssapi-krb5-2 armhf 1.15.1-2 [98.7 kB] Get:88 http://ftpmaster.internal/ubuntu artful/main armhf libkrb5-3 armhf 1.15.1-2 [231 kB] Get:89 http://ftpmaster.internal/ubuntu artful/main armhf libkrb5support0 armhf 1.15.1-2 [28.4 kB] Get:90 http://ftpmaster.internal/ubuntu artful/main armhf libk5crypto3 armhf 1.15.1-2 [83.3 kB] Get:91 http://ftpmaster.internal/ubuntu artful/main armhf libidn2-0 armhf 2.0.2-1 [86.6 kB] Get:92 http://ftpmaster.internal/ubuntu artful/main armhf libpng16-16 armhf 1.6.30-2 [158 kB] Get:93 http://ftpmaster.internal/ubuntu artful/main armhf libpsl5 armhf 0.17.0-5 [39.4 kB] Get:94 http://ftpmaster.internal/ubuntu artful/main armhf advancecomp armhf 2.0-1 [167 kB] Get:95 http://ftpmaster.internal/ubuntu artful/main armhf cpp armhf 4:6.3.0-2ubuntu2 [27.5 kB] Get:96 http://ftpmaster.internal/ubuntu artful/main armhf dpkg-dev all 1.18.24ubuntu1 [608 kB] Get:97 http://ftpmaster.internal/ubuntu artful/main armhf libdpkg-perl all 1.18.24ubuntu1 [209 kB] Get:98 http://ftpmaster.internal/ubuntu artful/main armhf gcc armhf 4:6.3.0-2ubuntu2 [5276 B] Get:99 http://ftpmaster.internal/ubuntu artful/main armhf g++ armhf 4:6.3.0-2ubuntu2 [1492 B] Get:100 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 51.2 MB in 3s (13.6 MB/s) (Reading database ... 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Setting up perl-base (5.24.1-7ubuntu1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12204 files and directories currently installed.) Preparing to unpack .../perl-modules-5.24_5.24.1-7ubuntu1_all.deb ... Unpacking perl-modules-5.24 (5.24.1-7ubuntu1) over (5.24.1-2ubuntu1) ... Preparing to unpack .../libc6-dev_2.24-12ubuntu1_armhf.deb ... Unpacking libc6-dev:armhf (2.24-12ubuntu1) over (2.24-9ubuntu2) ... Preparing to unpack .../libc-dev-bin_2.24-12ubuntu1_armhf.deb ... 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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 ... 12226 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 ... 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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 ... 12226 files and directories currently installed.) Preparing to unpack .../libselinux1_2.6-3build1_armhf.deb ... Unpacking libselinux1:armhf (2.6-3build1) over (2.6-3) ... Setting up libselinux1:armhf (2.6-3build1) ... (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 ... 12226 files and directories currently installed.) Preparing to unpack .../systemd_233-8ubuntu3_armhf.deb ... Unpacking systemd (233-8ubuntu3) 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_233-8ubuntu3_armhf.deb ... Unpacking libsystemd0:armhf (233-8ubuntu3) over (232-21ubuntu3) ... Setting up libsystemd0:armhf (233-8ubuntu3) ... Setting up libapparmor1:armhf (2.11.0-2ubuntu8) ... Setting up libip4tc0:armhf (1.6.1-2ubuntu1) ... Setting up libkmod2:armhf (24-1ubuntu1) ... Setting up systemd (233-8ubuntu3) ... Installing new version of config file /etc/systemd/resolved.conf ... addgroup: The group `systemd-journal' already exists as a system group. Exiting. Removing obsolete conffile /etc/dbus-1/system.d/org.freedesktop.hostname1.conf ... Removing obsolete conffile /etc/dbus-1/system.d/org.freedesktop.locale1.conf ... Removing obsolete conffile /etc/dbus-1/system.d/org.freedesktop.login1.conf ... Removing obsolete conffile /etc/dbus-1/system.d/org.freedesktop.network1.conf ... Removing obsolete conffile /etc/dbus-1/system.d/org.freedesktop.resolve1.conf ... Removing obsolete conffile /etc/dbus-1/system.d/org.freedesktop.systemd1.conf ... Removing obsolete conffile /etc/dbus-1/system.d/org.freedesktop.timedate1.conf ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12252 files and directories currently installed.) Preparing to unpack .../systemd-sysv_233-8ubuntu3_armhf.deb ... Unpacking systemd-sysv (233-8ubuntu3) over (232-21ubuntu3) ... Preparing to unpack .../libfdisk1_2.29.2-2ubuntu1_armhf.deb ... Unpacking libfdisk1:armhf (2.29.2-2ubuntu1) over (2.29-1ubuntu2) ... Setting up libfdisk1:armhf (2.29.2-2ubuntu1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12252 files and directories currently installed.) Preparing to unpack .../libsemanage-common_2.6-2build1_all.deb ... Unpacking libsemanage-common (2.6-2build1) over (2.6-2) ... Setting up libsemanage-common (2.6-2build1) ... (Reading database ... (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 ... 12252 files and directories currently installed.) Preparing to unpack .../libsemanage1_2.6-2build1_armhf.deb ... Unpacking libsemanage1:armhf (2.6-2build1) over (2.6-2) ... Setting up libsemanage1:armhf (2.6-2build1) ... (Reading database ... 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Unpacking libusb-0.1-4:armhf (2:0.1.12-31) over (2:0.1.12-30) ... Setting up libnpth0:armhf (1.5-2) ... Setting up libgomp1:armhf (7.1.0-9ubuntu1) ... Setting up libatomic1:armhf (7.1.0-9ubuntu1) ... Setting up perl-modules-5.24 (5.24.1-7ubuntu1) ... Setting up libperl5.24:armhf (5.24.1-7ubuntu1) ... Setting up libcc1-0:armhf (7.1.0-9ubuntu1) ... Setting up apt-transport-https (1.5~beta1) ... Setting up libidn2-0:armhf (2.0.2-1) ... Setting up libssl1.0.0:armhf (1.0.2g-1ubuntu13) ... Setting up libpng16-16:armhf (1.6.30-2) ... Setting up libldap-common (2.4.44+dfsg-8ubuntu1) ... Setting up libpsl5:armhf (0.17.0-5) ... Setting up multiarch-support (2.24-12ubuntu1) ... Setting up tzdata (2017b-2) ... Current default time zone: 'Etc/UTC' Local time is now: Sat Jul 29 22:34:33 UTC 2017. Universal Time is now: Sat Jul 29 22:34:33 UTC 2017. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up systemd-sysv (233-8ubuntu3) ... Setting up libubsan0:armhf (7.1.0-9ubuntu1) ... Setting up gcc-6-base:armhf (6.4.0-1ubuntu2) ... Setting up linux-libc-dev:armhf (4.11.0-10.15) ... 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 libkrb5support0:armhf (1.15.1-2) ... Setting up perl (5.24.1-7ubuntu1) ... Processing triggers for libc-bin (2.24-12ubuntu1) ... 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 (2.28.90.20170704-0ubuntu1) ... Setting up cpp-6 (6.4.0-1ubuntu2) ... Setting up libc-dev-bin (2.24-12ubuntu1) ... Setting up ca-certificates (20161130+nmu1) ... Updating certificates in /etc/ssl/certs... 0 added, 7 removed; done. Setting up libc6-dev: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 (6.4.0-1ubuntu2) ... Setting up libgcc-6-dev:armhf (6.4.0-1ubuntu2) ... Setting up libstdc++-6-dev:armhf (6.4.0-1ubuntu2) ... Setting up libwind0-heimdal:armhf (7.4.0.dfsg.1-2) ... 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 libdpkg-perl (1.18.24ubuntu1) ... Setting up libhx509-5-heimdal:armhf (7.4.0.dfsg.1-2) ... Setting up gcc-6 (6.4.0-1ubuntu2) ... Setting up g++-6 (6.4.0-1ubuntu2) ... Setting up dpkg-dev (1.18.24ubuntu1) ... Setting up libkrb5-3: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 gcc (4:6.3.0-2ubuntu2) ... Setting up libgssapi-krb5-2:armhf (1.15.1-2) ... 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 (2.4.44+dfsg-8ubuntu1) ... Processing triggers for libc-bin (2.24-12ubuntu1) ... Processing triggers for ca-certificates (20161130+nmu1) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package ['sbuild-package', 'PACKAGEBUILD-12929070', 'armhf', 'artful', '-c', 'chroot:autobuild', '--arch=armhf', '--dist=artful', '--purge=never', '--nolog', 'python-pysam_0.10.0+ds-2build1.dsc'] Initiating build PACKAGEBUILD-12929070 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-arm64-037.buildd +==============================================================================+ | python-pysam 0.10.0+ds-2build1 (armhf) 29 Jul 2017 22:34 | +==============================================================================+ Package: python-pysam Version: 0.10.0+ds-2build1 Source Version: 0.10.0+ds-2build1 Distribution: artful Machine Architecture: arm64 Host Architecture: armhf Build Architecture: armhf I: NOTICE: Log filtering will replace 'build/python-pysam-_mqI0X/python-pysam-0.10.0+ds' with '<>' I: NOTICE: Log filtering will replace 'build/python-pysam-_mqI0X' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-12929070/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- python-pysam_0.10.0+ds-2build1.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-FTxIVp/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/<>/resolver-FTxIVp/apt_archive ./ InRelease Get:2 copy:/<>/resolver-FTxIVp/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-FTxIVp/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-FTxIVp/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-FTxIVp/apt_archive ./ Packages [529 B] Fetched 2862 B in 0s (127 kB/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install core build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following NEW packages will be installed: sbuild-build-depends-core-dummy 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 776 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-FTxIVp/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [776 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 776 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12246 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... Merged Build-Depends: debhelper (>= 9), dh-python, libhts-dev (>= 1.3.2), zlib1g-dev, python-all-dev, python-setuptools, cython (>= 0.23), python3-all-dev, python3-setuptools, cython3 (>= 0.23), tabix, samtools (>= 1.3.1), bcftools (>= 1.3.1), python-nose, python3-nose Filtered Build-Depends: debhelper (>= 9), dh-python, libhts-dev (>= 1.3.2), zlib1g-dev, python-all-dev, python-setuptools, cython (>= 0.23), python3-all-dev, python3-setuptools, cython3 (>= 0.23), tabix, samtools (>= 1.3.1), bcftools (>= 1.3.1), python-nose, python3-nose dpkg-deb: building package 'sbuild-build-depends-python-pysam-dummy' in '/<>/resolver-7lcoKp/apt_archive/sbuild-build-depends-python-pysam-dummy.deb'. Ign:1 copy:/<>/resolver-7lcoKp/apt_archive ./ InRelease Get:2 copy:/<>/resolver-7lcoKp/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-7lcoKp/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-7lcoKp/apt_archive ./ Sources [299 B] Get:5 copy:/<>/resolver-7lcoKp/apt_archive ./ Packages [619 B] Fetched 3037 B in 0s (144 kB/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install python-pysam build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: autoconf automake autopoint autotools-dev bcftools bsdmainutils cython cython3 debhelper dh-autoreconf dh-python dh-strip-nondeterminism file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libbsd0 libcroco3 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl libglib2.0-0 libgsl2 libhts-dev libhts2 libicu57 libmagic-mgc libmagic1 libmpdec2 libpipeline1 libpython-all-dev libpython-dev libpython-stdlib libpython2.7 libpython2.7-dev libpython2.7-minimal libpython2.7-stdlib libpython3-all-dev libpython3-dev libpython3-stdlib libpython3.5 libpython3.5-dev libpython3.5-minimal libpython3.5-stdlib libpython3.6 libpython3.6-dev libpython3.6-minimal libpython3.6-stdlib libsigsegv2 libtimedate-perl libtool libxml2 m4 man-db mime-support po-debconf python python-all python-all-dev python-dev python-minimal python-nose python-pkg-resources python-setuptools python2.7 python2.7-dev python2.7-minimal python3 python3-all python3-all-dev python3-dev python3-minimal python3-nose python3-pkg-resources python3-setuptools python3.5 python3.5-dev python3.5-minimal python3.6 python3.6-dev python3.6-minimal samtools tabix zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc python-numpy python-matplotlib texlive-latex-recommended wamerican | wordlist whois vacation cython-doc dh-make gettext-doc libasprintf-dev libgettextpo-dev groff gsl-ref-psdoc | gsl-doc-pdf | gsl-doc-info | gsl-ref-html libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc less www-browser libmail-box-perl python-doc python-tk python-coverage python-nose-doc python-setuptools-doc python2.7-doc binfmt-support python3-doc python3-tk python3-venv python3.5-venv python3.5-doc python3.6-venv python3.6-doc 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 automake autopoint autotools-dev bcftools bsdmainutils cython cython3 debhelper dh-autoreconf dh-python dh-strip-nondeterminism file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libbsd0 libcroco3 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl libglib2.0-0 libgsl2 libhts-dev libhts2 libicu57 libmagic-mgc libmagic1 libmpdec2 libpipeline1 libpython-all-dev libpython-dev libpython-stdlib libpython2.7 libpython2.7-dev libpython2.7-minimal libpython2.7-stdlib libpython3-all-dev libpython3-dev libpython3-stdlib libpython3.5 libpython3.5-dev libpython3.5-minimal libpython3.5-stdlib libpython3.6 libpython3.6-dev libpython3.6-minimal libpython3.6-stdlib libsigsegv2 libtimedate-perl libtool libxml2 m4 man-db mime-support po-debconf python python-all python-all-dev python-dev python-minimal python-nose python-pkg-resources python-setuptools python2.7 python2.7-dev python2.7-minimal python3 python3-all python3-all-dev python3-dev python3-minimal python3-nose python3-pkg-resources python3-setuptools python3.5 python3.5-dev python3.5-minimal python3.6 python3.6-dev python3.6-minimal samtools sbuild-build-depends-python-pysam-dummy tabix zlib1g-dev 0 upgraded, 87 newly installed, 1 to remove and 0 not upgraded. Need to get 107 MB of archives. After this operation, 245 MB of additional disk space will be used. Get:1 copy:/<>/resolver-7lcoKp/apt_archive ./ sbuild-build-depends-python-pysam-dummy 0.invalid.0 [872 B] Get:2 http://ftpmaster.internal/ubuntu artful/main armhf libpython3.6-minimal armhf 3.6.2-1 [534 kB] Get:3 http://ftpmaster.internal/ubuntu artful/main armhf libexpat1 armhf 2.2.2-2 [53.4 kB] Get:4 http://ftpmaster.internal/ubuntu artful/main armhf python3.6-minimal armhf 3.6.2-1 [1198 kB] Get:5 http://ftpmaster.internal/ubuntu artful/main armhf python3-minimal armhf 3.6.1-0ubuntu2 [23.5 kB] Get:6 http://ftpmaster.internal/ubuntu artful/main armhf mime-support all 3.60ubuntu1 [30.1 kB] Get:7 http://ftpmaster.internal/ubuntu artful/main armhf libmpdec2 armhf 2.4.2-1 [66.9 kB] Get:8 http://ftpmaster.internal/ubuntu artful/main armhf libpython3.6-stdlib armhf 3.6.2-1 [2030 kB] Get:9 http://ftpmaster.internal/ubuntu artful/main armhf python3.6 armhf 3.6.2-1 [168 kB] Get:10 http://ftpmaster.internal/ubuntu artful/main armhf libpython3-stdlib armhf 3.6.1-0ubuntu2 [7012 B] Get:11 http://ftpmaster.internal/ubuntu artful/main armhf dh-python all 2.20170125 [83.7 kB] Get:12 http://ftpmaster.internal/ubuntu artful/main armhf python3 armhf 3.6.1-0ubuntu2 [8714 B] Get:13 http://ftpmaster.internal/ubuntu artful/main armhf groff-base armhf 1.22.3-9 [1013 kB] Get:14 http://ftpmaster.internal/ubuntu artful/main armhf libbsd0 armhf 0.8.6-1 [50.6 kB] Get:15 http://ftpmaster.internal/ubuntu artful/main armhf bsdmainutils armhf 9.0.12+nmu1ubuntu1 [173 kB] Get:16 http://ftpmaster.internal/ubuntu artful/main armhf libpipeline1 armhf 1.4.2-1 [21.0 kB] Get:17 http://ftpmaster.internal/ubuntu artful/main armhf man-db armhf 2.7.6.1-2 [873 kB] Get:18 http://ftpmaster.internal/ubuntu artful/main armhf libpython2.7-minimal armhf 2.7.13-2 [338 kB] Get:19 http://ftpmaster.internal/ubuntu artful/main armhf python2.7-minimal armhf 2.7.13-2 [1118 kB] Get:20 http://ftpmaster.internal/ubuntu artful/main armhf python-minimal armhf 2.7.13-2 [28.2 kB] Get:21 http://ftpmaster.internal/ubuntu artful/main armhf libpython2.7-stdlib armhf 2.7.13-2 [1839 kB] Get:22 http://ftpmaster.internal/ubuntu artful/main armhf python2.7 armhf 2.7.13-2 [229 kB] Get:23 http://ftpmaster.internal/ubuntu artful/main armhf libpython-stdlib armhf 2.7.13-2 [7774 B] Get:24 http://ftpmaster.internal/ubuntu artful/main armhf python armhf 2.7.13-2 [139 kB] Get:25 http://ftpmaster.internal/ubuntu artful/main armhf libpython3.5-minimal armhf 3.5.3-3 [526 kB] Get:26 http://ftpmaster.internal/ubuntu artful/main armhf python3.5-minimal armhf 3.5.3-3 [1390 kB] Get:27 http://ftpmaster.internal/ubuntu artful/main armhf libmagic-mgc armhf 1:5.30-1 [181 kB] Get:28 http://ftpmaster.internal/ubuntu artful/main armhf libmagic1 armhf 1:5.30-1 [63.0 kB] Get:29 http://ftpmaster.internal/ubuntu artful/main armhf file armhf 1:5.30-1 [21.5 kB] Get:30 http://ftpmaster.internal/ubuntu artful/main armhf gettext-base armhf 0.19.8.1-2ubuntu1 [44.8 kB] Get:31 http://ftpmaster.internal/ubuntu artful/main armhf libglib2.0-0 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Get:73 http://ftpmaster.internal/ubuntu artful/main armhf python-pkg-resources all 36.0.1-1ubuntu1 [128 kB] Get:74 http://ftpmaster.internal/ubuntu artful/universe armhf python-nose all 1.3.7-2 [116 kB] Get:75 http://ftpmaster.internal/ubuntu artful/main armhf python-setuptools all 36.0.1-1ubuntu1 [260 kB] Get:76 http://ftpmaster.internal/ubuntu artful/main armhf python3.5 armhf 3.5.3-3 [179 kB] Get:77 http://ftpmaster.internal/ubuntu artful/main armhf python3-all armhf 3.6.1-0ubuntu2 [994 B] Get:78 http://ftpmaster.internal/ubuntu artful/main armhf python3.6-dev armhf 3.6.2-1 [501 kB] Get:79 http://ftpmaster.internal/ubuntu artful/main armhf python3-dev armhf 3.6.1-0ubuntu2 [1214 B] Get:80 http://ftpmaster.internal/ubuntu artful/main armhf python3.5-dev armhf 3.5.3-3 [413 kB] Get:81 http://ftpmaster.internal/ubuntu artful/main armhf python3-all-dev armhf 3.6.1-0ubuntu2 [1020 B] Get:82 http://ftpmaster.internal/ubuntu artful/main armhf python3-pkg-resources all 36.0.1-1ubuntu1 [98.4 kB] Get:83 http://ftpmaster.internal/ubuntu artful/universe armhf python3-nose all 1.3.7-2 [116 kB] Get:84 http://ftpmaster.internal/ubuntu artful/main armhf python3-setuptools all 36.0.1-1ubuntu1 [178 kB] Get:85 http://ftpmaster.internal/ubuntu artful/universe armhf samtools armhf 1.4.1-1build1 [225 kB] Get:86 http://ftpmaster.internal/ubuntu artful/universe armhf tabix armhf 1.4.1-5 [260 kB] Get:87 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 107 MB in 4s (24.0 MB/s) (Reading database ... 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Setting up m4 (1.4.18-1) ... Setting up libicu57:armhf (57.1-6) ... Setting up libbsd0:armhf (0.8.6-1) ... Setting up libxml2:armhf (2.9.4+dfsg1-3build1) ... Setting up libmagic-mgc (1:5.30-1) ... Setting up libmagic1:armhf (1:5.30-1) ... Setting up libcroco3:armhf (0.6.12-1) ... Processing triggers for libc-bin (2.24-12ubuntu1) ... Setting up autotools-dev (20161112.1) ... Setting up libexpat1-dev:armhf (2.2.2-2) ... 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 libpython2.7-stdlib:armhf (2.7.13-2) ... Setting up autopoint (0.19.8.1-2ubuntu1) ... Setting up libmpdec2:armhf (2.4.2-1) ... Setting up libpython3.5-minimal:armhf (3.5.3-3) ... Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-0ubuntu1) ... Setting up libfile-stripnondeterminism-perl (0.038-1) ... Setting up libpython3.6-stdlib:armhf (3.6.2-1) ... Setting up python3.6 (3.6.2-1) ... Setting up gettext (0.19.8.1-2ubuntu1) ... Setting up libhts-dev:armhf (1.4.1-5) ... Setting up libpython3.5-stdlib:armhf (3.5.3-3) ... Setting up python2.7 (2.7.13-2) ... Setting up autoconf (2.69-10) ... Setting up file (1:5.30-1) ... Setting up python3.5-minimal (3.5.3-3) ... Setting up libpython-stdlib:armhf (2.7.13-2) ... Setting up intltool-debian (0.35.0+20060710.4) ... Setting up libpython2.7:armhf (2.7.13-2) ... 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 libpython2.7-dev:armhf (2.7.13-2) ... Setting up samtools (1.4.1-1build1) ... Setting up bcftools (1.4.1-2ubuntu2) ... Setting up python2.7-dev (2.7.13-2) ... Setting up python (2.7.13-2) ... Setting up libpython3.6:armhf (3.6.2-1) ... Setting up libtool (2.4.6-2) ... Setting up python3.5 (3.5.3-3) ... Setting up libpython3-stdlib:armhf (3.6.1-0ubuntu2) ... Setting up libpython-dev:armhf (2.7.13-2) ... Setting up po-debconf (1.0.20) ... Setting up libpython3.5:armhf (3.5.3-3) ... Setting up python-dev (2.7.13-2) ... Setting up libpython-all-dev:armhf (2.7.13-2) ... Setting up python-pkg-resources (36.0.1-1ubuntu1) ... Setting up libpython3.6-dev:armhf (3.6.2-1) ... Setting up libpython3.5-dev:armhf (3.5.3-3) ... Setting up cython (0.25.2-1build1) ... Setting up python3.6-dev (3.6.2-1) ... Setting up python3.5-dev (3.5.3-3) ... Setting up python-nose (1.3.7-2) ... Setting up python-all (2.7.13-2) ... Setting up libpython3-dev:armhf (3.6.1-0ubuntu2) ... Setting up python-setuptools (36.0.1-1ubuntu1) ... Setting up python-all-dev (2.7.13-2) ... Setting up libpython3-all-dev:armhf (3.6.1-0ubuntu2) ... Setting up dh-autoreconf (14) ... Setting up python3 (3.6.1-0ubuntu2) ... Setting up python3-dev (3.6.1-0ubuntu2) ... Setting up python3-pkg-resources (36.0.1-1ubuntu1) ... Setting up dh-strip-nondeterminism (0.038-1) ... Setting up python3-nose (1.3.7-2) ... Setting up python3-all (3.6.1-0ubuntu2) ... Setting up cython3 (0.25.2-1build1) ... Setting up python3-setuptools (36.0.1-1ubuntu1) ... Setting up dh-python (2.20170125) ... Setting up debhelper (10.6.4ubuntu1) ... Setting up python3-all-dev (3.6.1-0ubuntu2) ... Setting up sbuild-build-depends-python-pysam-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_2.28.90.20170704-0ubuntu1 dpkg-dev_1.18.24ubuntu1 g++-6_6.4.0-1ubuntu2 gcc-6_6.4.0-1ubuntu2 libc6-dev_2.24-12ubuntu1 libstdc++-6-dev_6.4.0-1ubuntu2 libstdc++6_7.1.0-9ubuntu1 linux-libc-dev_4.11.0-10.15 Package versions: adduser_3.113+nmu3ubuntu5 advancecomp_2.0-1 apt_1.5~beta1 apt-transport-https_1.5~beta1 autoconf_2.69-10 automake_1:1.15-6ubuntu1 autopoint_0.19.8.1-2ubuntu1 autotools-dev_20161112.1 base-files_9.6ubuntu101 base-passwd_3.5.43 bash_4.4-5ubuntu1 bcftools_1.4.1-2ubuntu2 binutils_2.28.90.20170704-0ubuntu1 bsdmainutils_9.0.12+nmu1ubuntu1 bsdutils_1:2.29.2-2ubuntu1 build-essential_12.1ubuntu2 bzip2_1.0.6-8.1 ca-certificates_20161130+nmu1 coreutils_8.26-3ubuntu3 cpp_4:6.3.0-2ubuntu2 cpp-6_6.4.0-1ubuntu2 cython_0.25.2-1build1 cython3_0.25.2-1build1 dash_0.5.8-2.3ubuntu1 debconf_1.5.63 debhelper_10.6.4ubuntu1 debianutils_4.8.1.1 dh-autoreconf_14 dh-python_2.20170125 dh-strip-nondeterminism_0.038-1 diffutils_1:3.5-3 dmsetup_2:1.02.137-2ubuntu2 dpkg_1.18.24ubuntu1 dpkg-dev_1.18.24ubuntu1 e2fslibs_1.43.4-2 e2fsprogs_1.43.4-2 fakeroot_1.21-1ubuntu2 file_1:5.30-1 findutils_4.6.0+git+20170606-3 g++_4:6.3.0-2ubuntu2 g++-6_6.4.0-1ubuntu2 gcc_4:6.3.0-2ubuntu2 gcc-6_6.4.0-1ubuntu2 gcc-6-base_6.4.0-1ubuntu2 gcc-7-base_7.1.0-9ubuntu1 gettext_0.19.8.1-2ubuntu1 gettext-base_0.19.8.1-2ubuntu1 gnupg_2.1.15-1ubuntu7 gnupg-agent_2.1.15-1ubuntu7 gpgv_2.1.15-1ubuntu7 grep_3.1-2 groff-base_1.22.3-9 gzip_1.6-5ubuntu1 hostname_3.18 init_1.47 init-system-helpers_1.47 initscripts_2.88dsf-59.3ubuntu2 insserv_1.14.0-5ubuntu3 intltool-debian_0.35.0+20060710.4 libacl1_2.2.52-3build1 libapparmor1_2.11.0-2ubuntu8 libapt-pkg5.0_1.5~beta1 libarchive-zip-perl_1.59-1 libasan3_6.4.0-1ubuntu2 libasn1-8-heimdal_7.4.0.dfsg.1-2 libassuan0_2.4.3-2 libatomic1_7.1.0-9ubuntu1 libattr1_1:2.4.47-2build1 libaudit-common_1:2.7.7-1ubuntu1 libaudit1_1:2.7.7-1ubuntu1 libblkid1_2.29.2-2ubuntu1 libbsd0_0.8.6-1 libbz2-1.0_1.0.6-8.1 libc-bin_2.24-12ubuntu1 libc-dev-bin_2.24-12ubuntu1 libc6_2.24-12ubuntu1 libc6-dev_2.24-12ubuntu1 libcap-ng0_0.7.7-3build1 libcap2_1:2.25-1 libcc1-0_7.1.0-9ubuntu1 libcomerr2_1.43.4-2 libcroco3_0.6.12-1 libcryptsetup4_2:1.7.2-0ubuntu1 libcurl3-gnutls_7.52.1-5ubuntu1 libdb5.3_5.3.28-13 libdebconfclient0_0.213ubuntu1 libdevmapper1.02.1_2:1.02.137-2ubuntu2 libdpkg-perl_1.18.24ubuntu1 libexpat1_2.2.2-2 libexpat1-dev_2.2.2-2 libfakeroot_1.21-1ubuntu2 libfdisk1_2.29.2-2ubuntu1 libffi6_3.2.1-6 libfile-stripnondeterminism-perl_0.038-1 libgcc-6-dev_6.4.0-1ubuntu2 libgcc1_1:7.1.0-9ubuntu1 libgcrypt20_1.7.8-2 libgdbm3_1.8.3-14 libglib2.0-0_2.53.4-1 libgmp10_2:6.1.2+dfsg-1 libgnutls30_3.5.8-6ubuntu1 libgomp1_7.1.0-9ubuntu1 libgpg-error0_1.27-3 libgsl2_2.4+dfsg-2 libgssapi-krb5-2_1.15.1-2 libgssapi3-heimdal_7.4.0.dfsg.1-2 libhcrypto4-heimdal_7.4.0.dfsg.1-2 libheimbase1-heimdal_7.4.0.dfsg.1-2 libheimntlm0-heimdal_7.4.0.dfsg.1-2 libhogweed4_3.3-1 libhts-dev_1.4.1-5 libhts2_1.4.1-5 libhx509-5-heimdal_7.4.0.dfsg.1-2 libicu57_57.1-6 libidn11_1.33-1 libidn2-0_2.0.2-1 libip4tc0_1.6.1-2ubuntu1 libisl15_0.18-1 libk5crypto3_1.15.1-2 libkeyutils1_1.5.9-9ubuntu1 libkmod2_24-1ubuntu1 libkrb5-26-heimdal_7.4.0.dfsg.1-2 libkrb5-3_1.15.1-2 libkrb5support0_1.15.1-2 libksba8_1.3.5-2 libldap-2.4-2_2.4.44+dfsg-8ubuntu1 libldap-common_2.4.44+dfsg-8ubuntu1 liblockfile-bin_1.14-1 liblockfile1_1.14-1 liblz4-1_0.0~r131-2ubuntu2 liblzma5_5.2.2-1.2 libmagic-mgc_1:5.30-1 libmagic1_1:5.30-1 libmount1_2.29.2-2ubuntu1 libmpc3_1.0.3-1 libmpdec2_2.4.2-1 libmpfr4_3.1.5-1 libncurses5_6.0+20160625-1ubuntu1 libncursesw5_6.0+20160625-1ubuntu1 libnettle6_3.3-1 libnpth0_1.5-2 libp11-kit0_0.23.7-3 libpam-modules_1.1.8-3.2ubuntu3 libpam-modules-bin_1.1.8-3.2ubuntu3 libpam-runtime_1.1.8-3.2ubuntu3 libpam0g_1.1.8-3.2ubuntu3 libpcre3_2:8.39-4 libperl5.24_5.24.1-7ubuntu1 libpipeline1_1.4.2-1 libpng16-16_1.6.30-2 libprocps6_2:3.3.12-1ubuntu2 libpsl5_0.17.0-5 libpython-all-dev_2.7.13-2 libpython-dev_2.7.13-2 libpython-stdlib_2.7.13-2 libpython2.7_2.7.13-2 libpython2.7-dev_2.7.13-2 libpython2.7-minimal_2.7.13-2 libpython2.7-stdlib_2.7.13-2 libpython3-all-dev_3.6.1-0ubuntu2 libpython3-dev_3.6.1-0ubuntu2 libpython3-stdlib_3.6.1-0ubuntu2 libpython3.5_3.5.3-3 libpython3.5-dev_3.5.3-3 libpython3.5-minimal_3.5.3-3 libpython3.5-stdlib_3.5.3-3 libpython3.6_3.6.2-1 libpython3.6-dev_3.6.2-1 libpython3.6-minimal_3.6.2-1 libpython3.6-stdlib_3.6.2-1 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_2.29.2-2ubuntu1 libsqlite3-0_3.19.3-3 libss2_1.43.4-2 libssl1.0.0_1.0.2g-1ubuntu13 libstdc++-6-dev_6.4.0-1ubuntu2 libstdc++6_7.1.0-9ubuntu1 libsystemd0_233-8ubuntu3 libtasn1-6_4.12-2.1 libtimedate-perl_2.3000-2 libtinfo5_6.0+20160625-1ubuntu1 libtool_2.4.6-2 libubsan0_7.1.0-9ubuntu1 libudev1_233-8ubuntu3 libunistring0_0.9.3-5.2ubuntu1 libusb-0.1-4_2:0.1.12-31 libustr-1.0-1_1.0.4-6 libuuid1_2.29.2-2ubuntu1 libwind0-heimdal_7.4.0.dfsg.1-2 libxml2_2.9.4+dfsg1-3build1 linux-libc-dev_4.11.0-10.15 lockfile-progs_0.1.17build1 login_1:4.2-3.2ubuntu2 lsb-base_9.20160110ubuntu5 m4_1.4.18-1 make_4.1-9.1 man-db_2.7.6.1-2 mawk_1.3.3-17ubuntu2 mime-support_3.60ubuntu1 mount_2.29.2-2ubuntu1 multiarch-support_2.24-12ubuntu1 ncurses-base_6.0+20160625-1ubuntu1 ncurses-bin_6.0+20160625-1ubuntu1 openssl_1.0.2g-1ubuntu13 optipng_0.7.6-1build1 passwd_1:4.2-3.2ubuntu2 patch_2.7.5-1build1 perl_5.24.1-7ubuntu1 perl-base_5.24.1-7ubuntu1 perl-modules-5.24_5.24.1-7ubuntu1 pinentry-curses_1.0.0-2 pkgbinarymangler_131 po-debconf_1.0.20 policyrcd-script-zg2_0.1-3 procps_2:3.3.12-1ubuntu2 python_2.7.13-2 python-all_2.7.13-2 python-all-dev_2.7.13-2 python-dev_2.7.13-2 python-minimal_2.7.13-2 python-nose_1.3.7-2 python-pkg-resources_36.0.1-1ubuntu1 python-setuptools_36.0.1-1ubuntu1 python2.7_2.7.13-2 python2.7-dev_2.7.13-2 python2.7-minimal_2.7.13-2 python3_3.6.1-0ubuntu2 python3-all_3.6.1-0ubuntu2 python3-all-dev_3.6.1-0ubuntu2 python3-dev_3.6.1-0ubuntu2 python3-minimal_3.6.1-0ubuntu2 python3-nose_1.3.7-2 python3-pkg-resources_36.0.1-1ubuntu1 python3-setuptools_36.0.1-1ubuntu1 python3.5_3.5.3-3 python3.5-dev_3.5.3-3 python3.5-minimal_3.5.3-3 python3.6_3.6.2-1 python3.6-dev_3.6.2-1 python3.6-minimal_3.6.2-1 readline-common_7.0-0ubuntu2 samtools_1.4.1-1build1 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-python-pysam-dummy_0.invalid.0 sed_4.4-1 sensible-utils_0.0.9+nmu1 systemd_233-8ubuntu3 systemd-sysv_233-8ubuntu3 sysv-rc_2.88dsf-59.3ubuntu2 sysvinit-utils_2.88dsf-59.8git1 tabix_1.4.1-5 tar_1.29b-2 tzdata_2017b-2 ubuntu-keyring_2016.10.27 util-linux_2.29.2-2ubuntu1 xz-utils_5.2.2-1.2 zlib1g_1:1.2.11.dfsg-0ubuntu1 zlib1g-dev_1:1.2.11.dfsg-0ubuntu1 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Sun May 14 14:33:10 2017 UTC gpgv: using RSA key gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./python-pysam_0.10.0+ds-2build1.dsc dpkg-source: info: extracting python-pysam in python-pysam-0.10.0+ds dpkg-source: info: unpacking python-pysam_0.10.0+ds.orig.tar.gz dpkg-source: info: unpacking python-pysam_0.10.0+ds-2build1.debian.tar.xz dpkg-source: info: applying rpath.patch dpkg-source: info: applying htslib-external-config.patch dpkg-source: info: applying exclude_test_tyring_to_access_remote_ftpserver.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=/<>/python-pysam-0.10.0+ds SHELL=/bin/sh SUDO_COMMAND=/usr/sbin/chroot /<> su buildd -s /bin/sh -c cd '/<>/python-pysam-0.10.0+ds' && 'env' SUDO_GID=2501 SUDO_UID=2001 SUDO_USER=buildd TERM=unknown USER=buildd USERNAME=root dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package python-pysam dpkg-buildpackage: info: source version 0.10.0+ds-2build1 dpkg-buildpackage: info: source distribution artful dpkg-source --before-build python-pysam-0.10.0+ds dpkg-buildpackage: info: host architecture armhf fakeroot debian/rules clean cd tests/pysam_data && /usr/bin/make clean make[1]: Entering directory '/<>/python-pysam-0.10.0+ds/tests/pysam_data' rm -fr *.bam *.bai *.fai *.pileup* *.cram \ *~ calDepth *.dSYM pysam_*.sam \ ex2.sam ex2.sam.gz ex1.sam \ *.fq.gz make[1]: Leaving directory '/<>/python-pysam-0.10.0+ds/tests/pysam_data' cd tests/cbcf_data && /usr/bin/make clean make[1]: Entering directory '/<>/python-pysam-0.10.0+ds/tests/cbcf_data' rm -f *.gz *.tbi *.csi *.bcf make[1]: Leaving directory '/<>/python-pysam-0.10.0+ds/tests/cbcf_data' find . -name "*.pyc" -delete find . -name "*.pyxbldc" -delete find . -name "tmp_*" -delete find . -name "*.bai*" -delete find . -name "*.cram*" -delete find . -name "*.bam" -delete rm -rf tests/pysam_test_work \ tests/example_htslib.gtf.gz.tbi \ tests/log.txt \ tests/test.bam \ tests/_compile_test.c \ tests/pysam_ex2.sam \ tests/__pycache__ \ pysam/calignmentfile.c \ pysam/cbcf.c \ tests/GRCh38_full_analysis_set_plus_decoy_hla.fa.fai \ tests/pysam_data/ex1.fa.gz \ tests/pysam_data/ex1.fa.gz.gzi \ tests/pysam_data/ex1_csi.bam.csi dh clean --with python2,python3 --buildsystem=pybuild dh_testdir -O--buildsystem=pybuild debian/rules override_dh_auto_clean make[1]: Entering directory '/<>/python-pysam-0.10.0+ds' dh_auto_clean I: pybuild base:184: python2.7 setup.py clean # pysam: cython is available - using cythonize if necessary # pysam: htslib mode is external # pysam: HTSLIB_CONFIGURE_OPTIONS=None running clean removing '/<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build' (and everything under it) 'build/bdist.linux-armhf' does not exist -- can't clean it 'build/scripts-2.7' does not exist -- can't clean it I: pybuild base:184: python3.5 setup.py clean # pysam: cython is available - using cythonize if necessary # pysam: htslib mode is external # pysam: HTSLIB_CONFIGURE_OPTIONS=None running clean removing '/<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build' (and everything under it) 'build/bdist.linux-armhf' does not exist -- can't clean it 'build/scripts-3.5' does not exist -- can't clean it I: pybuild base:184: python3.6 setup.py clean # pysam: cython is available - using cythonize if necessary # pysam: htslib mode is external # pysam: HTSLIB_CONFIGURE_OPTIONS=None running clean removing '/<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build' (and everything under it) 'build/bdist.linux-armhf' does not exist -- can't clean it 'build/scripts-3.6' does not exist -- can't clean it rm -f \ pysam/config.py \ pysam/config.h \ pysam/lib*.c \ samtools/config.h rm -rf pysam.egg-info make[1]: Leaving directory '/<>/python-pysam-0.10.0+ds' dh_clean -O--buildsystem=pybuild debian/rules build-arch dh build-arch --with python2,python3 --buildsystem=pybuild dh_testdir -a -O--buildsystem=pybuild dh_update_autotools_config -a -O--buildsystem=pybuild dh_auto_configure -a -O--buildsystem=pybuild I: pybuild base:184: python2.7 setup.py config # pysam: cython is available - using cythonize if necessary # pysam: htslib mode is external # pysam: HTSLIB_CONFIGURE_OPTIONS=None running config I: pybuild base:184: python3.5 setup.py config # pysam: cython is available - using cythonize if necessary # pysam: htslib mode is external # pysam: HTSLIB_CONFIGURE_OPTIONS=None running config I: pybuild base:184: python3.6 setup.py config # pysam: cython is available - using cythonize if necessary # pysam: htslib mode is external # pysam: HTSLIB_CONFIGURE_OPTIONS=None running config dh_auto_build -a -O--buildsystem=pybuild I: pybuild base:184: /usr/bin/python setup.py build # pysam: cython is available - using cythonize if necessary # pysam: htslib mode is external # pysam: HTSLIB_CONFIGURE_OPTIONS=None running build running build_py creating /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam copying pysam/config.py -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam copying pysam/samtools.py -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam copying pysam/bcftools.py -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam copying pysam/namedtuple.py -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam copying pysam/Pileup.py -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam copying pysam/version.py -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam copying pysam/__init__.py -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam copying pysam/utils.py -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam creating /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include copying pysam/include/__init__.py -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include package init file 'samtools/__init__.py' not found (or not a regular file) package init file 'bcftools/__init__.py' not found (or not a regular file) package init file 'samtools/win32/__init__.py' not found (or not a regular file) copying pysam/libcalignmentfile.pxd -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam copying pysam/libctabixproxies.pxd -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam copying pysam/libcfaidx.pxd -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam copying pysam/libctabix.pxd -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam copying pysam/libcbcf.pxd -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam copying pysam/libcutils.pxd -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam copying pysam/libchtslib.pxd -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam copying pysam/libcvcf.pxd -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam copying pysam/libcalignedsegment.pxd -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam copying pysam/libcsamfile.pxd -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam copying pysam/samfile_util.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam copying pysam/htslib_util.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam copying pysam/tabix_util.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam copying pysam/pysam_util.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam copying pysam/pysam_stream.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam creating /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools copying samtools/bam_tview.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools copying samtools/bam2bcf.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools copying samtools/sam.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools copying samtools/bam.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools copying samtools/sam_header.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools copying samtools/sample.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools copying samtools/version.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools copying samtools/samtools.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools copying samtools/bam_endian.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools copying samtools/bam_lpileup.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools copying samtools/kprobaln.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools copying samtools/config.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools copying samtools/sam_opts.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools copying samtools/pysam.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools copying samtools/bam_plbuf.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools copying samtools/errmod.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools copying samtools/stats_isize.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools creating /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools copying bcftools/prob1.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools copying bcftools/bcftools.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools copying bcftools/HMM.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools copying bcftools/vcmp.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools copying bcftools/filter.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools copying bcftools/version.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools copying bcftools/gvcf.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools copying bcftools/convert.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools copying bcftools/rbuf.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools copying bcftools/pysam.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools copying bcftools/call.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools copying bcftools/kmin.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools copying bcftools/khash_str2str.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools copying bcftools/tsv2vcf.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools copying bcftools/ploidy.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools creating /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/win32 copying samtools/win32/zlib.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/win32 copying samtools/win32/xcurses.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/win32 copying samtools/win32/zconf.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/win32 running build_ext cythoning pysam/libchtslib.pyx to pysam/libchtslib.c building 'pysam.libchtslib' extension creating build creating build/temp.linux-armhf-2.7 creating build/temp.linux-armhf-2.7/pysam arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c pysam/libchtslib.c -o build/temp.linux-armhf-2.7/pysam/libchtslib.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c pysam/htslib_util.c -o build/temp.linux-armhf-2.7/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-EVqH4j/python2.7-2.7.13=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-2.7/pysam/libchtslib.o build/temp.linux-armhf-2.7/pysam/htslib_util.o -L/usr/lib/arm-linux-gnueabihf -lz -lhts -o /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/libchtslib.so cythoning pysam/libcsamfile.pyx to pysam/libcsamfile.c building 'pysam.libcsamfile' extension creating build/temp.linux-armhf-2.7/samtools arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python2.7 -c pysam/libcsamfile.c -o build/temp.linux-armhf-2.7/pysam/libcsamfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python2.7 -c pysam/htslib_util.c -o build/temp.linux-armhf-2.7/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python2.7 -c pysam/samfile_util.c -o build/temp.linux-armhf-2.7/pysam/samfile_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python2.7 -c samtools/kprobaln.c -o build/temp.linux-armhf-2.7/samtools/kprobaln.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-EVqH4j/python2.7-2.7.13=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-2.7/pysam/libcsamfile.o build/temp.linux-armhf-2.7/pysam/htslib_util.o build/temp.linux-armhf-2.7/pysam/samfile_util.o build/temp.linux-armhf-2.7/samtools/kprobaln.o -L/usr/lib/arm-linux-gnueabihf -lz -lhts -o /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/libcsamfile.so cythoning pysam/libcalignmentfile.pyx to pysam/libcalignmentfile.c building 'pysam.libcalignmentfile' extension arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I/usr/include -I/usr/include/python2.7 -c pysam/libcalignmentfile.c -o build/temp.linux-armhf-2.7/pysam/libcalignmentfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement pysam/libcalignmentfile.c: In function ‘__pyx_f_5pysam_17libcalignmentfile_14IteratorColumn_cnext’: pysam/libcalignmentfile.c:23298:21: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] __pyx_v_self->plp = bam_plp_auto(__pyx_v_self->pileup_iter, (&__pyx_v_self->tid), (&__pyx_v_self->pos), (&__pyx_v_self->n_plp)); ^ pysam/libcalignmentfile.c: In function ‘__pyx_f_5pysam_17libcalignmentfile_20IteratorRowSelection_cnext’: pysam/libcalignmentfile.c:21854:9: warning: ignoring return value of ‘bgzf_seek’, declared with attribute warn_unused_result [-Wunused-result] bgzf_seek(hts_get_bgzfp(__pyx_v_self->__pyx_base.htsfile), __pyx_v_pos, 0); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pysam/libcalignmentfile.c: In function ‘__pyx_pf_5pysam_17libcalignmentfile_13AlignmentFile_6_open’: pysam/libcalignmentfile.c:7271:13: warning: ignoring return value of ‘sam_hdr_write’, declared with attribute warn_unused_result [-Wunused-result] sam_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_self->header); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I/usr/include -I/usr/include/python2.7 -c pysam/htslib_util.c -o build/temp.linux-armhf-2.7/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I/usr/include -I/usr/include/python2.7 -c pysam/samfile_util.c -o build/temp.linux-armhf-2.7/pysam/samfile_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I/usr/include -I/usr/include/python2.7 -c samtools/kprobaln.c -o build/temp.linux-armhf-2.7/samtools/kprobaln.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-EVqH4j/python2.7-2.7.13=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-2.7/pysam/libcalignmentfile.o build/temp.linux-armhf-2.7/pysam/htslib_util.o build/temp.linux-armhf-2.7/pysam/samfile_util.o build/temp.linux-armhf-2.7/samtools/kprobaln.o -L/usr/lib/arm-linux-gnueabihf -lz -lhts -o /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/libcalignmentfile.so cythoning pysam/libcalignedsegment.pyx to pysam/libcalignedsegment.c building 'pysam.libcalignedsegment' extension arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python2.7 -c pysam/libcalignedsegment.c -o build/temp.linux-armhf-2.7/pysam/libcalignedsegment.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python2.7 -c pysam/htslib_util.c -o build/temp.linux-armhf-2.7/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python2.7 -c pysam/samfile_util.c -o build/temp.linux-armhf-2.7/pysam/samfile_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python2.7 -c samtools/kprobaln.c -o build/temp.linux-armhf-2.7/samtools/kprobaln.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-EVqH4j/python2.7-2.7.13=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-2.7/pysam/libcalignedsegment.o build/temp.linux-armhf-2.7/pysam/htslib_util.o build/temp.linux-armhf-2.7/pysam/samfile_util.o build/temp.linux-armhf-2.7/samtools/kprobaln.o -L/usr/lib/arm-linux-gnueabihf -lz -lhts -o /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/libcalignedsegment.so cythoning pysam/libctabix.pyx to pysam/libctabix.c building 'pysam.libctabix' extension arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c pysam/libctabix.c -o build/temp.linux-armhf-2.7/pysam/libctabix.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement pysam/libctabix.c: In function ‘__pyx_pf_5pysam_9libctabix_9TabixFile_7contigs___get__’: pysam/libctabix.c:5979:27: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types] __pyx_v_sequences = tbx_seqnames(__pyx_v_self->index, (&__pyx_v_nsequences)); ^ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c pysam/tabix_util.c -o build/temp.linux-armhf-2.7/pysam/tabix_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-EVqH4j/python2.7-2.7.13=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-2.7/pysam/libctabix.o build/temp.linux-armhf-2.7/pysam/tabix_util.o -Lpysam -L/usr/lib/arm-linux-gnueabihf -lz -lhts -o /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/libctabix.so cythoning pysam/libctabixproxies.pyx to pysam/libctabixproxies.c building 'pysam.libctabixproxies' extension arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python2.7 -c pysam/libctabixproxies.c -o build/temp.linux-armhf-2.7/pysam/libctabixproxies.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-EVqH4j/python2.7-2.7.13=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-2.7/pysam/libctabixproxies.o -L/usr/lib/arm-linux-gnueabihf -lz -lhts -o /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/libctabixproxies.so cythoning pysam/libcvcf.pyx to pysam/libcvcf.c warning: pysam/libcvcf.pyx:1083:27: Unreachable code building 'pysam.libcvcf' extension arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -I. -I/usr/include -I/usr/include/python2.7 -c pysam/libcvcf.c -o build/temp.linux-armhf-2.7/pysam/libcvcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement pysam/libcvcf.c: In function ‘__pyx_pf_5pysam_7libcvcf_3VCF_32parse_data.isra.66’: pysam/libcvcf.c:23985:16: warning: ‘__pyx_v_qual’ may be used uninitialized in this function [-Wmaybe-uninitialized] __pyx_t_10 = PyFloat_FromDouble(__pyx_v_qual); if (unlikely(!__pyx_t_10)) __PYX_ERR(0, 873, __pyx_L1_error) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-EVqH4j/python2.7-2.7.13=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-2.7/pysam/libcvcf.o -L/usr/lib/arm-linux-gnueabihf -lz -lhts -o /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/libcvcf.so cythoning pysam/libcbcf.pyx to pysam/libcbcf.c building 'pysam.libcbcf' extension arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -I. -I/usr/include -I/usr/include/python2.7 -c pysam/libcbcf.c -o build/temp.linux-armhf-2.7/pysam/libcbcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement pysam/libcbcf.c: In function ‘__pyx_pf_5pysam_7libcbcf_13VariantHeader_12__str__’: pysam/libcbcf.c:28476:3: warning: ‘bcf_hdr_fmt_text’ is deprecated: use bcf_hdr_format() instead [-Wdeprecated-declarations] __pyx_v_hstr = bcf_hdr_fmt_text(__pyx_v_self->ptr, 0, (&__pyx_v_hlen)); ^~~~~~~~~~~~ In file included from pysam/htslib_util.h:5:0, from pysam/libcbcf.c:438: /usr/include/htslib/vcf.h:439:11: note: declared here char *bcf_hdr_fmt_text(const bcf_hdr_t *hdr, int is_bcf, int *len) ^~~~~~~~~~~~~~~~ arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-EVqH4j/python2.7-2.7.13=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-2.7/pysam/libcbcf.o -L/usr/lib/arm-linux-gnueabihf -lz -lhts -o /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/libcbcf.so cythoning pysam/libcbgzf.pyx to pysam/libcbgzf.c building 'pysam.libcbgzf' extension arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -I. -I/usr/include -I/usr/include/python2.7 -c pysam/libcbgzf.c -o build/temp.linux-armhf-2.7/pysam/libcbgzf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-EVqH4j/python2.7-2.7.13=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-2.7/pysam/libcbgzf.o -L/usr/lib/arm-linux-gnueabihf -lz -lhts -o /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/libcbgzf.so cythoning pysam/libcfaidx.pyx to pysam/libcfaidx.c building 'pysam.libcfaidx' extension arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c pysam/libcfaidx.c -o build/temp.linux-armhf-2.7/pysam/libcfaidx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-EVqH4j/python2.7-2.7.13=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-2.7/pysam/libcfaidx.o -Lpysam -L/usr/lib/arm-linux-gnueabihf -lz -lhts -o /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/libcfaidx.so cythoning pysam/libcutils.pyx to pysam/libcutils.c building 'pysam.libcutils' extension creating build/temp.linux-armhf-2.7/bcftools arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c pysam/libcutils.c -o build/temp.linux-armhf-2.7/pysam/libcutils.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement pysam/libcutils.c: In function ‘__pyx_pf_5pysam_9libcutils_8_pysam_dispatch’: pysam/libcutils.c:6730:22: warning: implicit declaration of function ‘samtools_main’ [-Wimplicit-function-declaration] __pyx_v_retval = samtools_main((__pyx_v_n + 2), __pyx_v_cargs); ^~~~~~~~~~~~~ pysam/libcutils.c:6759:22: warning: implicit declaration of function ‘bcftools_main’ [-Wimplicit-function-declaration] __pyx_v_retval = bcftools_main((__pyx_v_n + 2), __pyx_v_cargs); ^~~~~~~~~~~~~ pysam/libcutils.c: In function ‘__pyx_pw_5pysam_9libcutils_9_pysam_dispatch’: pysam/libcutils.c:10530:20: warning: ‘__pyx_v_retval’ may be used uninitialized in this function [-Wmaybe-uninitialized] return PyInt_FromLong((long) value); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ pysam/libcutils.c:5467:7: note: ‘__pyx_v_retval’ was declared here int __pyx_v_retval; ^~~~~~~~~~~~~~ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c pysam/pysam_util.c -o build/temp.linux-armhf-2.7/pysam/pysam_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_tview_html.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam_tview_html.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement In file included from samtools/bam2bcf.h:31:0, from samtools/bam_tview.h:35, from samtools/bam_tview_html.c.pysam.c:30: samtools/errmod.h:36:3: error: conflicting types for ‘errmod_t’ } errmod_t; ^~~~~~~~ In file included from /usr/include/htslib/sam.h:31:0, from samtools/bam_tview.h:34, from samtools/bam_tview_html.c.pysam.c:30: /usr/include/htslib/hts.h:659:25: note: previous declaration of ‘errmod_t’ was here typedef struct errmod_t errmod_t; ^~~~~~~~ In file included from samtools/bam2bcf.h:31:0, from samtools/bam_tview.h:35, from samtools/bam_tview_html.c.pysam.c:30: samtools/errmod.h:38:11: error: conflicting types for ‘errmod_init’ errmod_t *errmod_init(double depcorr); ^~~~~~~~~~~ In file included from /usr/include/htslib/sam.h:31:0, from samtools/bam_tview.h:34, from samtools/bam_tview_html.c.pysam.c:30: /usr/include/htslib/hts.h:661:11: note: previous declaration of ‘errmod_init’ was here errmod_t *errmod_init(double depcorr); ^~~~~~~~~~~ In file included from samtools/bam2bcf.h:31:0, from samtools/bam_tview.h:35, from samtools/bam_tview_html.c.pysam.c:30: samtools/errmod.h:39:6: error: conflicting types for ‘errmod_destroy’ void errmod_destroy(errmod_t *em); ^~~~~~~~~~~~~~ In file included from /usr/include/htslib/sam.h:31:0, from samtools/bam_tview.h:34, from samtools/bam_tview_html.c.pysam.c:30: /usr/include/htslib/hts.h:662:6: note: previous declaration of ‘errmod_destroy’ was here void errmod_destroy(errmod_t *em); ^~~~~~~~~~~~~~ In file included from samtools/bam2bcf.h:31:0, from samtools/bam_tview.h:35, from samtools/bam_tview_html.c.pysam.c:30: samtools/errmod.h:47:5: error: conflicting types for ‘errmod_cal’ int errmod_cal(const errmod_t *em, int n, int m, uint16_t *bases, float *q); ^~~~~~~~~~ In file included from /usr/include/htslib/sam.h:31:0, from samtools/bam_tview.h:34, from samtools/bam_tview_html.c.pysam.c:30: /usr/include/htslib/hts.h:670:5: note: previous declaration of ‘errmod_cal’ was here int errmod_cal(const errmod_t *em, int n, int m, uint16_t *bases, float *q); ^~~~~~~~~~ error: command 'arm-linux-gnueabihf-gcc' failed with exit status 1 E: pybuild pybuild:283: build: plugin distutils failed with: exit code=1: /usr/bin/python setup.py build dh_auto_build: pybuild --build -i python{version} -p 2.7 returned exit code 13 debian/rules:32: recipe for target 'build-arch' failed make: *** [build-arch] Error 25 dpkg-buildpackage: error: debian/rules build-arch gave error exit status 2 -------------------------------------------------------------------------------- Build finished at 20170729-2240 Finished -------- E: Build failure (dpkg-buildpackage died) +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Not removing build depends: as requested Keeping session: +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: armhf Build-Space: 48404 Build-Time: 315 Distribution: artful Fail-Stage: build Host Architecture: armhf Install-Time: 56 Job: python-pysam_0.10.0+ds-2build1.dsc Machine Architecture: arm64 Package: python-pysam Package-Time: 373 Source-Version: 0.10.0+ds-2build1 Space: 48404 Status: attempted Version: 0.10.0+ds-2build1 -------------------------------------------------------------------------------- Finished at 20170729-2240 Build needed 00:06:13, 48404k disc space RUN: /usr/share/launchpad-buildd/slavebin/scan-for-processes ['scan-for-processes', 'PACKAGEBUILD-12929070'] Scanning for processes to kill in build /home/buildd/build-PACKAGEBUILD-12929070/chroot-autobuild... RUN: /usr/share/launchpad-buildd/slavebin/umount-chroot ['umount-chroot', 'PACKAGEBUILD-12929070'] Unmounting chroot for build PACKAGEBUILD-12929070... RUN: /usr/share/launchpad-buildd/slavebin/remove-build ['remove-build', 'PACKAGEBUILD-12929070'] Removing build PACKAGEBUILD-12929070