RUN: /usr/share/launchpad-buildd/slavebin/slave-prep ['slave-prep'] Forking launchpad-buildd slave process... Kernel version: Linux bos01-arm64-005 4.2.0-34-generic #39-Ubuntu SMP Thu Mar 10 22:12:07 UTC 2016 aarch64 Buildd toolchain package versions: launchpad-buildd_138 python-lpbuildd_138 sbuild_0.65.2-1ubuntu2+ubuntu15.10.3 bzr-builder_0.7.3-0ubuntu1 bzr_2.6.0+bzr6602-2ubuntu4 git-build-recipe_0.3~git201603101733.90b6821~ubuntu15.10.1 git_1:2.5.0-1ubuntu0.2 dpkg-dev_1.18.2ubuntu5.1 python-debian_0.1.27ubuntu1 qemu-user-static_1:2.3+dfsg-5ubuntu9.2. Syncing the system clock with the buildd NTP service... 13 May 05:13:21 ntpdate[29517]: adjust time server 10.211.37.1 offset -0.000866 sec RUN: /usr/share/launchpad-buildd/slavebin/unpack-chroot ['unpack-chroot', 'PACKAGEBUILD-9736183', '/home/buildd/filecache-default/69d3533015def2fc9828d1a0131b60ffb6ebf960'] Unpacking chroot for build PACKAGEBUILD-9736183 RUN: /usr/share/launchpad-buildd/slavebin/mount-chroot ['mount-chroot', 'PACKAGEBUILD-9736183'] Mounting chroot for build PACKAGEBUILD-9736183 RUN: /usr/share/launchpad-buildd/slavebin/override-sources-list ['override-sources-list', 'PACKAGEBUILD-9736183', 'deb http://ftpmaster.internal/ubuntu yakkety main universe', 'deb http://ftpmaster.internal/ubuntu yakkety-security main universe', 'deb http://ftpmaster.internal/ubuntu yakkety-updates main universe', 'deb http://ftpmaster.internal/ubuntu yakkety-proposed main universe'] Overriding sources.list in build-PACKAGEBUILD-9736183 RUN: /usr/share/launchpad-buildd/slavebin/update-debian-chroot ['update-debian-chroot', 'PACKAGEBUILD-9736183', 'arm64'] Updating debian chroot for build PACKAGEBUILD-9736183 Get:1 http://ftpmaster.internal/ubuntu yakkety InRelease [247 kB] Get:2 http://ftpmaster.internal/ubuntu yakkety-security InRelease [92.2 kB] Get:3 http://ftpmaster.internal/ubuntu yakkety-updates InRelease [92.2 kB] Get:4 http://ftpmaster.internal/ubuntu yakkety-proposed InRelease [95.7 kB] Get:5 http://ftpmaster.internal/ubuntu yakkety/main arm64 Packages [1130 kB] Get:6 http://ftpmaster.internal/ubuntu yakkety/main Translation-en [568 kB] Get:7 http://ftpmaster.internal/ubuntu yakkety/universe arm64 Packages [7430 kB] Get:8 http://ftpmaster.internal/ubuntu yakkety/universe Translation-en [4425 kB] Get:9 http://ftpmaster.internal/ubuntu yakkety-security/main arm64 Packages [64 B] Get:10 http://ftpmaster.internal/ubuntu yakkety-security/main Translation-en [64 B] Get:11 http://ftpmaster.internal/ubuntu yakkety-security/universe arm64 Packages [64 B] Get:12 http://ftpmaster.internal/ubuntu yakkety-security/universe Translation-en [64 B] Get:13 http://ftpmaster.internal/ubuntu yakkety-updates/main arm64 Packages [64 B] Get:14 http://ftpmaster.internal/ubuntu yakkety-updates/main Translation-en [64 B] Get:15 http://ftpmaster.internal/ubuntu yakkety-updates/universe arm64 Packages [64 B] Get:16 http://ftpmaster.internal/ubuntu yakkety-updates/universe Translation-en [64 B] Get:17 http://ftpmaster.internal/ubuntu yakkety-proposed/main arm64 Packages [38.6 kB] Get:18 http://ftpmaster.internal/ubuntu yakkety-proposed/main Translation-en [21.4 kB] Get:19 http://ftpmaster.internal/ubuntu yakkety-proposed/universe arm64 Packages [172 kB] Get:20 http://ftpmaster.internal/ubuntu yakkety-proposed/universe Translation-en [91.1 kB] Fetched 14.4 MB in 5s (2631 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following NEW packages will be installed: libpng16-16 The following packages will be upgraded: apt apt-transport-https bash binutils bzip2 cpp-5 debconf dmsetup dpkg dpkg-dev g++-5 gcc-5 gcc-5-base gcc-6-base grep hostname init init-system-helpers initscripts libapt-pkg5.0 libasan2 libasn1-8-heimdal libatomic1 libbz2-1.0 libcc1-0 libdevmapper1.02.1 libdpkg-perl libgcc-5-dev libgcc1 libgcrypt20 libgomp1 libgpg-error0 libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhx509-5-heimdal libitm1 libkrb5-26-heimdal libldap-2.4-2 libperl5.22 libpng12-0 libroken18-heimdal librtmp1 libsasl2-2 libsasl2-modules-db libselinux1 libsemanage-common libsemanage1 libsepol1 libslang2 libstdc++-5-dev libstdc++6 libsystemd0 libtasn1-6 libubsan0 libudev1 libusb-0.1-4 libwind0-heimdal linux-libc-dev make optipng perl perl-base perl-modules-5.22 policyrcd-script-zg2 sed systemd systemd-sysv sysv-rc sysvinit-utils tar tzdata zlib1g 74 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 78.7 MB of archives. After this operation, 205 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu yakkety/main arm64 bash arm64 4.3-14ubuntu2 [518 kB] Get:2 http://ftpmaster.internal/ubuntu yakkety-proposed/main arm64 dpkg arm64 1.18.7ubuntu1 [2091 kB] Get:3 http://ftpmaster.internal/ubuntu yakkety/main arm64 grep arm64 2.25-1 [137 kB] Get:4 http://ftpmaster.internal/ubuntu yakkety/main arm64 hostname arm64 3.17ubuntu1 [11.3 kB] Get:5 http://ftpmaster.internal/ubuntu yakkety/main arm64 perl-modules-5.22 all 5.22.2-1 [2642 kB] Get:6 http://ftpmaster.internal/ubuntu yakkety/main arm64 libperl5.22 arm64 5.22.2-1 [2797 kB] Get:7 http://ftpmaster.internal/ubuntu yakkety/main arm64 perl arm64 5.22.2-1 [237 kB] Get:8 http://ftpmaster.internal/ubuntu yakkety/main arm64 perl-base arm64 5.22.2-1 [1141 kB] Get:9 http://ftpmaster.internal/ubuntu yakkety/main arm64 bzip2 arm64 1.0.6-8build1 [31.1 kB] Get:10 http://ftpmaster.internal/ubuntu yakkety/main arm64 libbz2-1.0 arm64 1.0.6-8build1 [28.6 kB] Get:11 http://ftpmaster.internal/ubuntu yakkety/main arm64 zlib1g arm64 1:1.2.8.dfsg-2ubuntu5 [45.5 kB] Get:12 http://ftpmaster.internal/ubuntu yakkety/main arm64 init-system-helpers all 1.33ubuntu1 [31.9 kB] Get:13 http://ftpmaster.internal/ubuntu yakkety/main arm64 init arm64 1.33ubuntu1 [4382 B] Get:14 http://ftpmaster.internal/ubuntu yakkety/main arm64 sed arm64 4.2.2-7.1 [134 kB] Get:15 http://ftpmaster.internal/ubuntu yakkety/main arm64 tar arm64 1.28-2.2 [183 kB] Get:16 http://ftpmaster.internal/ubuntu yakkety-proposed/main arm64 gcc-6-base arm64 6.1.1-3ubuntu11 [16.9 kB] Get:17 http://ftpmaster.internal/ubuntu yakkety-proposed/main arm64 libgcc1 arm64 1:6.1.1-3ubuntu11 [30.2 kB] Get:18 http://ftpmaster.internal/ubuntu yakkety-proposed/main arm64 libstdc++6 arm64 6.1.1-3ubuntu11 [368 kB] Get:19 http://ftpmaster.internal/ubuntu yakkety-proposed/main arm64 libapt-pkg5.0 arm64 1.3~exp1 [652 kB] Get:20 http://ftpmaster.internal/ubuntu yakkety-proposed/main arm64 apt arm64 1.3~exp1 [1010 kB] Get:21 http://ftpmaster.internal/ubuntu yakkety/main arm64 debconf all 1.5.59ubuntu1 [136 kB] Get:22 http://ftpmaster.internal/ubuntu yakkety-proposed/main arm64 libgpg-error0 arm64 1.22-2 [29.7 kB] Get:23 http://ftpmaster.internal/ubuntu yakkety/main arm64 libgcrypt20 arm64 1.7.0-2 [301 kB] Get:24 http://ftpmaster.internal/ubuntu yakkety/main arm64 sysvinit-utils arm64 2.88dsf-59.3ubuntu5 [20.9 kB] Get:25 http://ftpmaster.internal/ubuntu yakkety/main arm64 sysv-rc all 2.88dsf-59.3ubuntu5 [18.2 kB] Get:26 http://ftpmaster.internal/ubuntu yakkety/main arm64 initscripts arm64 2.88dsf-59.3ubuntu5 [24.7 kB] Get:27 http://ftpmaster.internal/ubuntu yakkety/main arm64 libselinux1 arm64 2.5-2 [53.9 kB] Get:28 http://ftpmaster.internal/ubuntu yakkety/main arm64 libsystemd0 arm64 229-6ubuntu1 [172 kB] Get:29 http://ftpmaster.internal/ubuntu yakkety/main arm64 systemd arm64 229-6ubuntu1 [2971 kB] Get:30 http://ftpmaster.internal/ubuntu yakkety/main arm64 systemd-sysv arm64 229-6ubuntu1 [17.6 kB] Get:31 http://ftpmaster.internal/ubuntu yakkety/main arm64 libudev1 arm64 229-6ubuntu1 [51.0 kB] Get:32 http://ftpmaster.internal/ubuntu yakkety/main arm64 libdevmapper1.02.1 arm64 2:1.02.122-1ubuntu1 [116 kB] Get:33 http://ftpmaster.internal/ubuntu yakkety/main arm64 libsepol1 arm64 2.5-1 [175 kB] Get:34 http://ftpmaster.internal/ubuntu yakkety-proposed/main arm64 libsemanage-common all 2.5-1 [6800 B] Get:35 http://ftpmaster.internal/ubuntu yakkety-proposed/main arm64 libsemanage1 arm64 2.5-1 [65.9 kB] Get:36 http://ftpmaster.internal/ubuntu yakkety/main arm64 libusb-0.1-4 arm64 2:0.1.12-30 [15.1 kB] Get:37 http://ftpmaster.internal/ubuntu yakkety/main arm64 tzdata all 2016d-2 [168 kB] Get:38 http://ftpmaster.internal/ubuntu yakkety/main arm64 libslang2 arm64 2.3.0-2.3ubuntu1 [357 kB] Get:39 http://ftpmaster.internal/ubuntu yakkety/main arm64 libtasn1-6 arm64 4.8-1 [37.2 kB] Get:40 http://ftpmaster.internal/ubuntu yakkety-proposed/main arm64 apt-transport-https arm64 1.3~exp1 [24.3 kB] Get:41 http://ftpmaster.internal/ubuntu yakkety-proposed/main arm64 libroken18-heimdal arm64 1.7~git20160418+dfsg-3 [34.5 kB] Get:42 http://ftpmaster.internal/ubuntu yakkety-proposed/main arm64 libasn1-8-heimdal arm64 1.7~git20160418+dfsg-3 [127 kB] Get:43 http://ftpmaster.internal/ubuntu yakkety-proposed/main arm64 libheimbase1-heimdal arm64 1.7~git20160418+dfsg-3 [24.3 kB] Get:44 http://ftpmaster.internal/ubuntu yakkety-proposed/main arm64 libhcrypto4-heimdal arm64 1.7~git20160418+dfsg-3 [74.4 kB] Get:45 http://ftpmaster.internal/ubuntu yakkety-proposed/main arm64 libwind0-heimdal arm64 1.7~git20160418+dfsg-3 [47.0 kB] Get:46 http://ftpmaster.internal/ubuntu yakkety-proposed/main arm64 libhx509-5-heimdal arm64 1.7~git20160418+dfsg-3 [86.4 kB] Get:47 http://ftpmaster.internal/ubuntu yakkety-proposed/main arm64 libkrb5-26-heimdal arm64 1.7~git20160418+dfsg-3 [163 kB] Get:48 http://ftpmaster.internal/ubuntu yakkety-proposed/main arm64 libheimntlm0-heimdal arm64 1.7~git20160418+dfsg-3 [13.2 kB] Get:49 http://ftpmaster.internal/ubuntu yakkety-proposed/main arm64 libgssapi3-heimdal arm64 1.7~git20160418+dfsg-3 [76.7 kB] Get:50 http://ftpmaster.internal/ubuntu yakkety/main arm64 libsasl2-modules-db arm64 2.1.26.dfsg1-15 [12.9 kB] Get:51 http://ftpmaster.internal/ubuntu yakkety/main arm64 libsasl2-2 arm64 2.1.26.dfsg1-15 [41.5 kB] Get:52 http://ftpmaster.internal/ubuntu yakkety/main arm64 libldap-2.4-2 arm64 2.4.42+dfsg-2ubuntu4 [135 kB] Get:53 http://ftpmaster.internal/ubuntu yakkety/main arm64 libpng16-16 arm64 1.6.21-5 [159 kB] Get:54 http://ftpmaster.internal/ubuntu yakkety/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-1 [48.2 kB] Get:55 http://ftpmaster.internal/ubuntu yakkety-proposed/main arm64 binutils arm64 2.26-9ubuntu1 [2457 kB] Get:56 http://ftpmaster.internal/ubuntu yakkety-proposed/main arm64 libgomp1 arm64 6.1.1-3ubuntu11 [61.8 kB] Get:57 http://ftpmaster.internal/ubuntu yakkety-proposed/main arm64 libitm1 arm64 6.1.1-3ubuntu11 [24.9 kB] Get:58 http://ftpmaster.internal/ubuntu yakkety-proposed/main arm64 libatomic1 arm64 6.1.1-3ubuntu11 [6586 B] Get:59 http://ftpmaster.internal/ubuntu yakkety/main arm64 libasan2 arm64 5.3.1-19ubuntu1 [232 kB] Get:60 http://ftpmaster.internal/ubuntu yakkety-proposed/main arm64 libubsan0 arm64 6.1.1-3ubuntu11 [96.9 kB] Get:61 http://ftpmaster.internal/ubuntu yakkety/main arm64 g++-5 arm64 5.3.1-19ubuntu1 [25.0 MB] Get:62 http://ftpmaster.internal/ubuntu yakkety/main arm64 gcc-5 arm64 5.3.1-19ubuntu1 [5536 kB] Get:63 http://ftpmaster.internal/ubuntu yakkety/main arm64 libstdc++-5-dev arm64 5.3.1-19ubuntu1 [1354 kB] Get:64 http://ftpmaster.internal/ubuntu yakkety/main arm64 libgcc-5-dev arm64 5.3.1-19ubuntu1 [487 kB] Get:65 http://ftpmaster.internal/ubuntu yakkety-proposed/main arm64 libcc1-0 arm64 6.1.1-3ubuntu11 [27.3 kB] Get:66 http://ftpmaster.internal/ubuntu yakkety/main arm64 cpp-5 arm64 5.3.1-19ubuntu1 [23.4 MB] Get:67 http://ftpmaster.internal/ubuntu yakkety/main arm64 gcc-5-base arm64 5.3.1-19ubuntu1 [17.3 kB] Get:68 http://ftpmaster.internal/ubuntu yakkety/main arm64 dmsetup arm64 2:1.02.122-1ubuntu1 [63.1 kB] Get:69 http://ftpmaster.internal/ubuntu yakkety-proposed/main arm64 dpkg-dev all 1.18.7ubuntu1 [666 kB] Get:70 http://ftpmaster.internal/ubuntu yakkety-proposed/main arm64 libdpkg-perl all 1.18.7ubuntu1 [202 kB] Get:71 http://ftpmaster.internal/ubuntu yakkety/main arm64 make arm64 4.1-9 [137 kB] Get:72 http://ftpmaster.internal/ubuntu yakkety/universe arm64 libpng12-0 arm64 1.2.54-6ubuntu1 [105 kB] Get:73 http://ftpmaster.internal/ubuntu yakkety/main arm64 linux-libc-dev arm64 4.4.0-22.39 [810 kB] Get:74 http://ftpmaster.internal/ubuntu yakkety/main arm64 optipng arm64 0.7.6-1build1 [77.1 kB] Get:75 http://ftpmaster.internal/ubuntu yakkety/main arm64 policyrcd-script-zg2 all 0.1-3 [5610 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 78.7 MB in 7s (9921 kB/s) (Reading database ... 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Universal Time is now: Fri May 13 05:14:11 UTC 2016. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libslang2:arm64 (2.3.0-2.3ubuntu1) ... Setting up libtasn1-6:arm64 (4.8-1) ... Setting up apt-transport-https (1.3~exp1) ... Setting up libroken18-heimdal:arm64 (1.7~git20160418+dfsg-3) ... Setting up libasn1-8-heimdal:arm64 (1.7~git20160418+dfsg-3) ... Setting up libheimbase1-heimdal:arm64 (1.7~git20160418+dfsg-3) ... Setting up libhcrypto4-heimdal:arm64 (1.7~git20160418+dfsg-3) ... Setting up libwind0-heimdal:arm64 (1.7~git20160418+dfsg-3) ... Setting up libhx509-5-heimdal:arm64 (1.7~git20160418+dfsg-3) ... Setting up libkrb5-26-heimdal:arm64 (1.7~git20160418+dfsg-3) ... Setting up libheimntlm0-heimdal:arm64 (1.7~git20160418+dfsg-3) ... Setting up libgssapi3-heimdal:arm64 (1.7~git20160418+dfsg-3) ... Setting up libsasl2-modules-db:arm64 (2.1.26.dfsg1-15) ... Setting up libsasl2-2:arm64 (2.1.26.dfsg1-15) ... Setting up libldap-2.4-2:arm64 (2.4.42+dfsg-2ubuntu4) ... Setting up libpng16-16:arm64 (1.6.21-5) ... Setting up librtmp1:arm64 (2.4+20151223.gitfa8646d.1-1) ... Setting up binutils (2.26-9ubuntu1) ... Setting up libgomp1:arm64 (6.1.1-3ubuntu11) ... Setting up libitm1:arm64 (6.1.1-3ubuntu11) ... Setting up libatomic1:arm64 (6.1.1-3ubuntu11) ... Setting up gcc-5-base:arm64 (5.3.1-19ubuntu1) ... Setting up libasan2:arm64 (5.3.1-19ubuntu1) ... Setting up libubsan0:arm64 (6.1.1-3ubuntu11) ... Setting up cpp-5 (5.3.1-19ubuntu1) ... Setting up libcc1-0:arm64 (6.1.1-3ubuntu11) ... Setting up libgcc-5-dev:arm64 (5.3.1-19ubuntu1) ... Setting up gcc-5 (5.3.1-19ubuntu1) ... Setting up libstdc++-5-dev:arm64 (5.3.1-19ubuntu1) ... Setting up g++-5 (5.3.1-19ubuntu1) ... Setting up dmsetup (2:1.02.122-1ubuntu1) ... Setting up libdpkg-perl (1.18.7ubuntu1) ... Setting up make (4.1-9) ... Setting up dpkg-dev (1.18.7ubuntu1) ... Setting up libpng12-0:arm64 (1.2.54-6ubuntu1) ... Setting up linux-libc-dev:arm64 (4.4.0-22.39) ... Setting up optipng (0.7.6-1build1) ... Setting up policyrcd-script-zg2 (0.1-3) ... Processing triggers for libc-bin (2.23-0ubuntu3) ... Processing triggers for systemd (229-6ubuntu1) ... RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package ['sbuild-package', 'PACKAGEBUILD-9736183', 'arm64', 'yakkety-proposed', '-c', 'chroot:autobuild', '--arch=arm64', '--dist=yakkety-proposed', '--purge=never', '--nolog', 'iva_1.0.6+ds-1.dsc'] Initiating build PACKAGEBUILD-9736183 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.2.0-34-generic #39-Ubuntu SMP Thu Mar 10 22:12:07 UTC 2016 aarch64 sbuild (Debian sbuild) 0.65.2 (24 Mar 2015) on bos01-arm64-005.buildd ╔══════════════════════════════════════════════════════════════════════════════╗ ║ iva 1.0.6+ds-1 (arm64) 13 May 2016 05:14 ║ ╚══════════════════════════════════════════════════════════════════════════════╝ Package: iva Version: 1.0.6+ds-1 Source Version: 1.0.6+ds-1 Distribution: yakkety-proposed Machine Architecture: arm64 Host Architecture: arm64 Build Architecture: arm64 I: NOTICE: Log filtering will replace 'build/iva-52lJSJ/iva-1.0.6+ds' with '«PKGBUILDDIR»' I: NOTICE: Log filtering will replace 'build/iva-52lJSJ' with '«BUILDDIR»' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-9736183/chroot-autobuild' with '«CHROOT»' ┌──────────────────────────────────────────────────────────────────────────────┐ │ Fetch source files │ └──────────────────────────────────────────────────────────────────────────────┘ Local sources ───────────── iva_1.0.6+ds-1.dsc exists in .; copying to chroot Check architectures ─────────────────── Check dependencies ────────────────── Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/«BUILDDIR»/resolver-1g48hg/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/«BUILDDIR»/resolver-1g48hg/apt_archive ./ InRelease Get:2 copy:/«BUILDDIR»/resolver-1g48hg/apt_archive ./ Release [2119 B] Ign:3 copy:/«BUILDDIR»/resolver-1g48hg/apt_archive ./ Release.gpg Get:4 copy:/«BUILDDIR»/resolver-1g48hg/apt_archive ./ Sources [208 B] Get:5 copy:/«BUILDDIR»/resolver-1g48hg/apt_archive ./ Packages [527 B] Fetched 2854 B in 0s (168 kB/s) Reading package lists... W: The repository 'copy:/«BUILDDIR»/resolver-1g48hg/apt_archive ./ Release' is not signed. 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 770 B of archives. After this operation, 0 B of additional disk space will be used. WARNING: The following packages cannot be authenticated! sbuild-build-depends-core-dummy Authentication warning overridden. Get:1 copy:/«BUILDDIR»/resolver-1g48hg/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [770 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 770 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 ... 12080 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_arm64.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... Merged Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, init, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, tar, util-linux, libc6-dev | libc-dev, gcc (>= 4:5.2), g++ (>= 4:5.2), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), libssl-dev, bioperl, fastaq (>= 1.6), kmc, help2man, mummer, python3, python3-setuptools, python3-numpy, python3-nose, python3-networkx, python3-pysam, samtools, smalt, default-jdk-headless Filtered Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, init, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, tar, util-linux, libc6-dev | libc-dev, gcc (>= 4:5.2), g++ (>= 4:5.2), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), libssl-dev, bioperl, fastaq (>= 1.6), kmc, help2man, mummer, python3, python3-setuptools, python3-numpy, python3-nose, python3-networkx, python3-pysam, samtools, smalt, default-jdk-headless dpkg-deb: building package 'sbuild-build-depends-iva-dummy' in '/«BUILDDIR»/resolver-OUcC3K/apt_archive/sbuild-build-depends-iva-dummy.deb'. Ign:1 copy:/«BUILDDIR»/resolver-OUcC3K/apt_archive ./ InRelease Get:2 copy:/«BUILDDIR»/resolver-OUcC3K/apt_archive ./ Release [2119 B] Ign:3 copy:/«BUILDDIR»/resolver-OUcC3K/apt_archive ./ Release.gpg Get:4 copy:/«BUILDDIR»/resolver-OUcC3K/apt_archive ./ Sources [510 B] Get:5 copy:/«BUILDDIR»/resolver-OUcC3K/apt_archive ./ Packages [775 B] Fetched 3404 B in 0s (197 kB/s) Reading package lists... W: The repository 'copy:/«BUILDDIR»/resolver-OUcC3K/apt_archive ./ Release' is not signed. Reading package lists... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Install iva 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 bioperl bsdmainutils ca-certificates-java debhelper default-jdk-headless default-jre-headless dh-autoreconf dh-python dh-strip-nondeterminism fastaq file fontconfig-config fonts-dejavu-core gawk gettext gettext-base groff-base help2man intltool-debian java-common kmc libarchive-zip-perl libasprintf0v5 libavahi-client3 libavahi-common-data libavahi-common3 libbambamc0 libbio-perl-perl libblas-common libblas3 libcroco3 libcups2 libdata-stag-perl libdbus-1-3 libexpat1 libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libgfortran3 libglib2.0-0 libhts1 libicu57 libio-string-perl libjpeg-turbo8 libjpeg8 liblapack3 liblcms2-2 liblocale-gettext-perl libmagic1 libmpdec2 libnspr4 libnss3 libnss3-nssdb libpcsclite1 libpipeline1 libpython3-stdlib libpython3.5-minimal libpython3.5-stdlib libsigsegv2 libssl-dev libtimedate-perl libtool libunistring0 libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxi6 libxml2 libxrender1 libxtst6 m4 man-db mime-support mummer openjdk-8-jdk-headless openjdk-8-jre-headless po-debconf python3 python3-decorator python3-minimal python3-networkx python3-nose python3-numpy python3-pkg-resources python3-pysam python3-setuptools python3.5 python3.5-minimal samtools smalt ucf x11-common zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois vacation dh-make default-jre gawk-doc gettext-doc groff libxml-sax-expatxs-perl cups-common liblcms2-utils pcscd libtool-doc gfortran | fortran95-compiler gcj-jdk less www-browser openjdk-8-demo openjdk-8-source libnss-mdns fonts-dejavu-extra fonts-ipafont-gothic fonts-ipafont-mincho ttf-wqy-microhei | ttf-wqy-zenhei fonts-indic libmail-box-perl python3-doc python3-tk python3-venv python3-scipy python-nose-doc gfortran python-numpy-doc python3-dev python3-numpy-dbg python-setuptools-doc python3.5-venv python3.5-doc binfmt-support Recommended packages: bioperl-run perl-doc libhttp-message-perl libwww-perl libcache-cache-perl libbio-perl-run-perl libdbi-perl libgd-gd2-perl libapache-dbi-perl liburi-perl libxml-simple-perl libyaml-perl libace-perl liblist-moreutils-perl libxml-twig-perl libset-scalar-perl curl | wget | lynx-cur libasprintf-dev libgettextpo-dev bioperl-run | libbio-perl-run-perl libalgorithm-munkres-perl libarray-compare-perl libbio-asn1-entrezgene-perl libclone-perl libconvert-binary-c-perl libdbd-sqlite3-perl libdbd-mysql-perl libdbd-pg-perl libgd-perl libgraph-perl libgraphviz-perl libhtml-parser-perl libhtml-tableextract-perl libpostscript-perl libsoap-lite-perl libsort-naturally-perl libspreadsheet-parseexcel-perl libspreadsheet-writeexcel-perl libsvg-perl libsvg-graph-perl libxml-dom-xpath-perl libxml-parser-perl libxml-sax-perl libxml-sax-writer-perl libxml-writer-perl libxml-libxml-perl perl-tk libgd-gd2-perl | libgd-gd2-noxpm-perl libxml-libxslt-perl libmldbm-perl libxml-perl dbus libglib2.0-data shared-mime-info xdg-user-dirs libssl-doc libltdl-dev xml-core libmail-sendmail-perl python3-yaml python The following NEW packages will be installed: autoconf automake autopoint autotools-dev bioperl bsdmainutils ca-certificates-java debhelper default-jdk-headless default-jre-headless dh-autoreconf dh-python dh-strip-nondeterminism fastaq file fontconfig-config fonts-dejavu-core gawk gettext gettext-base groff-base help2man intltool-debian java-common kmc libarchive-zip-perl libasprintf0v5 libavahi-client3 libavahi-common-data libavahi-common3 libbambamc0 libbio-perl-perl libblas-common libblas3 libcroco3 libcups2 libdata-stag-perl libdbus-1-3 libexpat1 libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libgfortran3 libglib2.0-0 libhts1 libicu57 libio-string-perl libjpeg-turbo8 libjpeg8 liblapack3 liblcms2-2 liblocale-gettext-perl libmagic1 libmpdec2 libnspr4 libnss3 libnss3-nssdb libpcsclite1 libpipeline1 libpython3-stdlib libpython3.5-minimal libpython3.5-stdlib libsigsegv2 libssl-dev libtimedate-perl libtool libunistring0 libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxi6 libxml2 libxrender1 libxtst6 m4 man-db mime-support mummer openjdk-8-jdk-headless openjdk-8-jre-headless po-debconf python3 python3-decorator python3-minimal python3-networkx python3-nose python3-numpy python3-pkg-resources python3-pysam python3-setuptools python3.5 python3.5-minimal samtools sbuild-build-depends-iva-dummy smalt ucf x11-common zlib1g-dev 0 upgraded, 101 newly installed, 0 to remove and 0 not upgraded. Need to get 69.2 MB of archives. After this operation, 288 MB of additional disk space will be used. WARNING: The following packages cannot be authenticated! sbuild-build-depends-iva-dummy Authentication warning overridden. Get:1 copy:/«BUILDDIR»/resolver-OUcC3K/apt_archive ./ sbuild-build-depends-iva-dummy 0.invalid.0 [1020 B] Get:2 http://ftpmaster.internal/ubuntu yakkety/main arm64 liblocale-gettext-perl arm64 1.07-1build1 [16.8 kB] Get:3 http://ftpmaster.internal/ubuntu yakkety/main arm64 libpython3.5-minimal arm64 3.5.1-12 [513 kB] Get:4 http://ftpmaster.internal/ubuntu yakkety/main arm64 libexpat1 arm64 2.1.1-1 [58.0 kB] Get:5 http://ftpmaster.internal/ubuntu yakkety/main arm64 python3.5-minimal arm64 3.5.1-12 [1160 kB] Get:6 http://ftpmaster.internal/ubuntu yakkety/main arm64 python3-minimal arm64 3.5.1-3 [23.4 kB] Get:7 http://ftpmaster.internal/ubuntu yakkety/main arm64 mime-support all 3.59ubuntu1 [31.0 kB] Get:8 http://ftpmaster.internal/ubuntu yakkety/main arm64 libmpdec2 arm64 2.4.2-1 [74.3 kB] Get:9 http://ftpmaster.internal/ubuntu yakkety/main arm64 libpython3.5-stdlib arm64 3.5.1-12 [2001 kB] Get:10 http://ftpmaster.internal/ubuntu yakkety/main arm64 python3.5 arm64 3.5.1-12 [160 kB] Get:11 http://ftpmaster.internal/ubuntu yakkety/main arm64 libpython3-stdlib arm64 3.5.1-3 [6850 B] Get:12 http://ftpmaster.internal/ubuntu yakkety/main arm64 dh-python all 2.20151103ubuntu2 [74.2 kB] Get:13 http://ftpmaster.internal/ubuntu yakkety/main arm64 python3 arm64 3.5.1-3 [8710 B] Get:14 http://ftpmaster.internal/ubuntu yakkety/main arm64 libxau6 arm64 1:1.0.8-1 [7590 B] Get:15 http://ftpmaster.internal/ubuntu yakkety/main arm64 libxdmcp6 arm64 1:1.1.2-1.1 [10.1 kB] Get:16 http://ftpmaster.internal/ubuntu yakkety/main arm64 libxcb1 arm64 1.11.1-1ubuntu1 [33.3 kB] Get:17 http://ftpmaster.internal/ubuntu yakkety/main arm64 libx11-data all 2:1.6.3-1ubuntu2 [113 kB] Get:18 http://ftpmaster.internal/ubuntu yakkety/main arm64 libx11-6 arm64 2:1.6.3-1ubuntu2 [512 kB] Get:19 http://ftpmaster.internal/ubuntu yakkety/main arm64 libxext6 arm64 2:1.3.3-1 [25.4 kB] Get:20 http://ftpmaster.internal/ubuntu yakkety/main arm64 groff-base arm64 1.22.3-7 [1122 kB] Get:21 http://ftpmaster.internal/ubuntu yakkety/main arm64 bsdmainutils arm64 9.0.6ubuntu3 [170 kB] Get:22 http://ftpmaster.internal/ubuntu yakkety/main arm64 libpipeline1 arm64 1.4.1-2 [21.9 kB] Get:23 http://ftpmaster.internal/ubuntu yakkety/main arm64 man-db arm64 2.7.5-1 [832 kB] Get:24 http://ftpmaster.internal/ubuntu yakkety/main arm64 libsigsegv2 arm64 2.10-5 [13.3 kB] Get:25 http://ftpmaster.internal/ubuntu yakkety/main arm64 gawk arm64 1:4.1.3+dfsg-0.1 [344 kB] Get:26 http://ftpmaster.internal/ubuntu yakkety/main arm64 libjpeg-turbo8 arm64 1.4.2-0ubuntu3 [86.3 kB] Get:27 http://ftpmaster.internal/ubuntu yakkety/main arm64 libunistring0 arm64 0.9.3-5.2ubuntu1 [251 kB] Get:28 http://ftpmaster.internal/ubuntu yakkety/main arm64 x11-common all 1:7.7+13ubuntu3 [22.4 kB] Get:29 http://ftpmaster.internal/ubuntu yakkety/main arm64 libxtst6 arm64 2:1.2.2-1 [12.7 kB] Get:30 http://ftpmaster.internal/ubuntu yakkety/main arm64 java-common all 0.56ubuntu2 [7742 B] Get:31 http://ftpmaster.internal/ubuntu yakkety/main arm64 default-jre-headless arm64 2:1.8-56ubuntu2 [4394 B] Get:32 http://ftpmaster.internal/ubuntu yakkety/main arm64 libnspr4 arm64 2:4.11-1ubuntu1 [91.8 kB] Get:33 http://ftpmaster.internal/ubuntu yakkety/main arm64 libnss3-nssdb all 2:3.21-1ubuntu4 [10.6 kB] Get:34 http://ftpmaster.internal/ubuntu yakkety/main arm64 libnss3 arm64 2:3.21-1ubuntu4 [930 kB] Get:35 http://ftpmaster.internal/ubuntu yakkety/main arm64 ca-certificates-java all 20160321 [12.9 kB] Get:36 http://ftpmaster.internal/ubuntu yakkety/main arm64 libavahi-common-data arm64 0.6.32~rc+dfsg-1ubuntu2 [21.7 kB] Get:37 http://ftpmaster.internal/ubuntu yakkety/main arm64 libavahi-common3 arm64 0.6.32~rc+dfsg-1ubuntu2 [18.0 kB] Get:38 http://ftpmaster.internal/ubuntu yakkety/main arm64 libdbus-1-3 arm64 1.10.6-1ubuntu3 [137 kB] Get:39 http://ftpmaster.internal/ubuntu yakkety/main arm64 libavahi-client3 arm64 0.6.32~rc+dfsg-1ubuntu2 [21.0 kB] Get:40 http://ftpmaster.internal/ubuntu yakkety/main arm64 libcups2 arm64 2.1.3-5 [163 kB] Get:41 http://ftpmaster.internal/ubuntu yakkety/main arm64 liblcms2-2 arm64 2.7-1ubuntu1 [110 kB] Get:42 http://ftpmaster.internal/ubuntu yakkety/main arm64 libjpeg8 arm64 8c-2ubuntu8 [2198 B] Get:43 http://ftpmaster.internal/ubuntu yakkety/main arm64 fonts-dejavu-core all 2.35-1 [1039 kB] Get:44 http://ftpmaster.internal/ubuntu yakkety/main arm64 ucf all 3.0036 [52.9 kB] Get:45 http://ftpmaster.internal/ubuntu yakkety/main arm64 fontconfig-config all 2.11.94-0ubuntu1 [49.9 kB] Get:46 http://ftpmaster.internal/ubuntu yakkety/main arm64 libfreetype6 arm64 2.6.3-3ubuntu1 [271 kB] Get:47 http://ftpmaster.internal/ubuntu yakkety/main arm64 libfontconfig1 arm64 2.11.94-0ubuntu1 [116 kB] Get:48 http://ftpmaster.internal/ubuntu yakkety/main arm64 libpcsclite1 arm64 1.8.14-1ubuntu1 [18.4 kB] Get:49 http://ftpmaster.internal/ubuntu yakkety/main arm64 libxi6 arm64 2:1.7.6-1 [24.9 kB] Get:50 http://ftpmaster.internal/ubuntu yakkety/main arm64 libxrender1 arm64 1:0.9.9-0ubuntu1 [16.0 kB] Get:51 http://ftpmaster.internal/ubuntu yakkety/main arm64 openjdk-8-jre-headless arm64 8u91-b14-2ubuntu1 [25.9 MB] Get:52 http://ftpmaster.internal/ubuntu yakkety/main arm64 libmagic1 arm64 1:5.25-2ubuntu1 [209 kB] Get:53 http://ftpmaster.internal/ubuntu yakkety/main arm64 file arm64 1:5.25-2ubuntu1 [21.2 kB] Get:54 http://ftpmaster.internal/ubuntu yakkety/main arm64 libasprintf0v5 arm64 0.19.7-2ubuntu3 [6420 B] Get:55 http://ftpmaster.internal/ubuntu yakkety/main arm64 gettext-base arm64 0.19.7-2ubuntu3 [45.0 kB] Get:56 http://ftpmaster.internal/ubuntu yakkety-proposed/main arm64 libglib2.0-0 arm64 2.48.1-1 [926 kB] Get:57 http://ftpmaster.internal/ubuntu yakkety/main arm64 libicu57 arm64 57.1-1 [7529 kB] Get:58 http://ftpmaster.internal/ubuntu yakkety/main arm64 libxml2 arm64 2.9.3+dfsg1-1build1 [565 kB] Get:59 http://ftpmaster.internal/ubuntu yakkety/main arm64 m4 arm64 1.4.17-5 [184 kB] Get:60 http://ftpmaster.internal/ubuntu yakkety-proposed/main arm64 autoconf all 2.69-10 [321 kB] Get:61 http://ftpmaster.internal/ubuntu yakkety-proposed/main arm64 autotools-dev all 20160430.1 [39.6 kB] Get:62 http://ftpmaster.internal/ubuntu yakkety/main arm64 automake all 1:1.15-4ubuntu1 [510 kB] Get:63 http://ftpmaster.internal/ubuntu yakkety/main arm64 autopoint all 0.19.7-2ubuntu3 [406 kB] Get:64 http://ftpmaster.internal/ubuntu yakkety/main arm64 libio-string-perl all 1.08-3 [11.1 kB] Get:65 http://ftpmaster.internal/ubuntu yakkety/universe arm64 libdata-stag-perl all 0.14-1ubuntu2 [366 kB] Get:66 http://ftpmaster.internal/ubuntu yakkety/universe arm64 libbio-perl-perl all 1.6.924-3 [4721 kB] Get:67 http://ftpmaster.internal/ubuntu yakkety/universe arm64 bioperl all 1.6.924-3 [387 kB] Get:68 http://ftpmaster.internal/ubuntu yakkety/main arm64 libcroco3 arm64 0.6.11-1 [66.0 kB] Get:69 http://ftpmaster.internal/ubuntu yakkety/main arm64 gettext arm64 0.19.7-2ubuntu3 [1015 kB] Get:70 http://ftpmaster.internal/ubuntu yakkety/main arm64 intltool-debian all 0.35.0+20060710.4 [24.9 kB] Get:71 http://ftpmaster.internal/ubuntu yakkety/main arm64 po-debconf all 1.0.19 [234 kB] Get:72 http://ftpmaster.internal/ubuntu yakkety/main arm64 libarchive-zip-perl all 1.57-1 [84.0 kB] Get:73 http://ftpmaster.internal/ubuntu yakkety/main arm64 libfile-stripnondeterminism-perl all 0.016-1 [11.0 kB] Get:74 http://ftpmaster.internal/ubuntu yakkety/main arm64 libtimedate-perl all 2.3000-2 [37.5 kB] Get:75 http://ftpmaster.internal/ubuntu yakkety/main arm64 dh-strip-nondeterminism all 0.016-1 [4858 B] Get:76 http://ftpmaster.internal/ubuntu yakkety/main arm64 libtool all 2.4.6-0.1 [193 kB] Get:77 http://ftpmaster.internal/ubuntu yakkety/main arm64 dh-autoreconf all 12 [15.8 kB] Get:78 http://ftpmaster.internal/ubuntu yakkety/main arm64 debhelper all 9.20160403ubuntu1 [711 kB] Get:79 http://ftpmaster.internal/ubuntu yakkety/main arm64 openjdk-8-jdk-headless arm64 8u91-b14-2ubuntu1 [6200 kB] Get:80 http://ftpmaster.internal/ubuntu yakkety/main arm64 default-jdk-headless arm64 2:1.8-56ubuntu2 [980 B] Get:81 http://ftpmaster.internal/ubuntu yakkety/main arm64 python3-pkg-resources all 20.10.1-1 [79.0 kB] Get:82 http://ftpmaster.internal/ubuntu yakkety/universe arm64 libhts1 arm64 1.3.1-1ubuntu1 [211 kB] Get:83 http://ftpmaster.internal/ubuntu yakkety-proposed/universe arm64 samtools arm64 1.3.1-2 [227 kB] Get:84 http://ftpmaster.internal/ubuntu yakkety/universe arm64 fastaq all 3.12.1-1 [45.8 kB] Get:85 http://ftpmaster.internal/ubuntu yakkety/universe arm64 help2man arm64 1.47.4 [155 kB] Get:86 http://ftpmaster.internal/ubuntu yakkety/universe arm64 kmc arm64 2.3+dfsg-5 [454 kB] Get:87 http://ftpmaster.internal/ubuntu yakkety/universe arm64 libbambamc0 arm64 0.0.50-1 [27.6 kB] Get:88 http://ftpmaster.internal/ubuntu yakkety/main arm64 libblas-common arm64 3.6.0-2ubuntu2 [5338 B] Get:89 http://ftpmaster.internal/ubuntu yakkety/main arm64 libblas3 arm64 3.6.0-2ubuntu2 [87.5 kB] Get:90 http://ftpmaster.internal/ubuntu yakkety-proposed/main arm64 libgfortran3 arm64 6.1.1-3ubuntu11 [200 kB] Get:91 http://ftpmaster.internal/ubuntu yakkety/main arm64 liblapack3 arm64 3.6.0-2ubuntu2 [1268 kB] Get:92 http://ftpmaster.internal/ubuntu yakkety/main arm64 zlib1g-dev arm64 1:1.2.8.dfsg-2ubuntu5 [162 kB] Get:93 http://ftpmaster.internal/ubuntu yakkety/main arm64 libssl-dev arm64 1.0.2g-1ubuntu4 [1046 kB] Get:94 http://ftpmaster.internal/ubuntu yakkety/universe arm64 mummer arm64 3.23~dfsg-3 [278 kB] Get:95 http://ftpmaster.internal/ubuntu yakkety/universe arm64 python3-decorator all 4.0.6-1 [9388 B] Get:96 http://ftpmaster.internal/ubuntu yakkety/universe arm64 python3-networkx all 1.11-1ubuntu1 [608 kB] Get:97 http://ftpmaster.internal/ubuntu yakkety/main arm64 python3-nose all 1.3.7-1 [116 kB] Get:98 http://ftpmaster.internal/ubuntu yakkety/main arm64 python3-numpy arm64 1:1.11.0-1ubuntu1 [1590 kB] Get:99 http://ftpmaster.internal/ubuntu yakkety-proposed/universe arm64 python3-pysam arm64 0.9.0+ds-1 [896 kB] Get:100 http://ftpmaster.internal/ubuntu yakkety/main arm64 python3-setuptools all 20.10.1-1 [88.3 kB] Get:101 http://ftpmaster.internal/ubuntu yakkety/universe arm64 smalt arm64 0.7.6-4 [92.5 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 69.2 MB in 2s (26.2 MB/s) Selecting previously unselected package liblocale-gettext-perl. 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Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Setting up liblocale-gettext-perl (1.07-1build1) ... Setting up mime-support (3.59ubuntu1) ... Setting up libmpdec2:arm64 (2.4.2-1) ... Setting up libpython3.5-stdlib:arm64 (3.5.1-12) ... Setting up python3.5 (3.5.1-12) ... Setting up libpython3-stdlib:arm64 (3.5.1-3) ... Setting up libxau6:arm64 (1:1.0.8-1) ... Setting up libxdmcp6:arm64 (1:1.1.2-1.1) ... Setting up libxcb1:arm64 (1.11.1-1ubuntu1) ... Setting up libx11-data (2:1.6.3-1ubuntu2) ... Setting up libx11-6:arm64 (2:1.6.3-1ubuntu2) ... Setting up libxext6:arm64 (2:1.3.3-1) ... Setting up groff-base (1.22.3-7) ... Setting up bsdmainutils (9.0.6ubuntu3) ... 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 libpipeline1:arm64 (1.4.1-2) ... Setting up man-db (2.7.5-1) ... Not building database; man-db/auto-update is not 'true'. Setting up gawk (1:4.1.3+dfsg-0.1) ... Setting up libjpeg-turbo8:arm64 (1.4.2-0ubuntu3) ... Setting up libunistring0:arm64 (0.9.3-5.2ubuntu1) ... Setting up x11-common (1:7.7+13ubuntu3) ... update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults Running in chroot, ignoring request. invoke-rc.d: policy-rc.d denied execution of start. Setting up libxtst6:arm64 (2:1.2.2-1) ... Setting up java-common (0.56ubuntu2) ... Setting up libnspr4:arm64 (2:4.11-1ubuntu1) ... Setting up libavahi-common-data:arm64 (0.6.32~rc+dfsg-1ubuntu2) ... Setting up libavahi-common3:arm64 (0.6.32~rc+dfsg-1ubuntu2) ... Setting up libdbus-1-3:arm64 (1.10.6-1ubuntu3) ... Setting up libavahi-client3:arm64 (0.6.32~rc+dfsg-1ubuntu2) ... Setting up libcups2:arm64 (2.1.3-5) ... Setting up liblcms2-2:arm64 (2.7-1ubuntu1) ... Setting up libjpeg8:arm64 (8c-2ubuntu8) ... Setting up fonts-dejavu-core (2.35-1) ... Setting up ucf (3.0036) ... Setting up fontconfig-config (2.11.94-0ubuntu1) ... Setting up libfreetype6:arm64 (2.6.3-3ubuntu1) ... Setting up libfontconfig1:arm64 (2.11.94-0ubuntu1) ... Setting up libpcsclite1:arm64 (1.8.14-1ubuntu1) ... Setting up libxi6:arm64 (2:1.7.6-1) ... Setting up libxrender1:arm64 (1:0.9.9-0ubuntu1) ... Setting up libmagic1:arm64 (1:5.25-2ubuntu1) ... Setting up file (1:5.25-2ubuntu1) ... Setting up libasprintf0v5:arm64 (0.19.7-2ubuntu3) ... Setting up gettext-base (0.19.7-2ubuntu3) ... Setting up libglib2.0-0:arm64 (2.48.1-1) ... No schema files found: doing nothing. Setting up libicu57:arm64 (57.1-1) ... Setting up libxml2:arm64 (2.9.3+dfsg1-1build1) ... Setting up m4 (1.4.17-5) ... Setting up autoconf (2.69-10) ... Setting up autotools-dev (20160430.1) ... Setting up automake (1:1.15-4ubuntu1) ... update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode Setting up autopoint (0.19.7-2ubuntu3) ... Setting up libio-string-perl (1.08-3) ... Setting up libdata-stag-perl (0.14-1ubuntu2) ... Setting up libbio-perl-perl (1.6.924-3) ... Setting up bioperl (1.6.924-3) ... Setting up libcroco3:arm64 (0.6.11-1) ... Setting up gettext (0.19.7-2ubuntu3) ... Setting up intltool-debian (0.35.0+20060710.4) ... Setting up po-debconf (1.0.19) ... Setting up libarchive-zip-perl (1.57-1) ... Setting up libfile-stripnondeterminism-perl (0.016-1) ... Setting up libtimedate-perl (2.3000-2) ... Setting up libtool (2.4.6-0.1) ... Setting up libhts1:arm64 (1.3.1-1ubuntu1) ... Setting up samtools (1.3.1-2) ... Setting up help2man (1.47.4) ... Setting up kmc (2.3+dfsg-5) ... Setting up libbambamc0 (0.0.50-1) ... Setting up libblas-common (3.6.0-2ubuntu2) ... Setting up libblas3 (3.6.0-2ubuntu2) ... update-alternatives: using /usr/lib/libblas/libblas.so.3 to provide /usr/lib/libblas.so.3 (libblas.so.3) in auto mode Setting up libgfortran3:arm64 (6.1.1-3ubuntu11) ... Setting up liblapack3 (3.6.0-2ubuntu2) ... update-alternatives: using /usr/lib/lapack/liblapack.so.3 to provide /usr/lib/liblapack.so.3 (liblapack.so.3) in auto mode Setting up zlib1g-dev:arm64 (1:1.2.8.dfsg-2ubuntu5) ... Setting up libssl-dev:arm64 (1.0.2g-1ubuntu4) ... Setting up mummer (3.23~dfsg-3) ... Setting up smalt (0.7.6-4) ... Setting up dh-python (2.20151103ubuntu2) ... Setting up python3 (3.5.1-3) ... Setting up libnss3-nssdb (2:3.21-1ubuntu4) ... Setting up dh-autoreconf (12) ... Setting up python3-pkg-resources (20.10.1-1) ... Setting up fastaq (3.12.1-1) ... Setting up python3-decorator (4.0.6-1) ... Setting up python3-networkx (1.11-1ubuntu1) ... Setting up python3-nose (1.3.7-1) ... Setting up python3-numpy (1:1.11.0-1ubuntu1) ... Setting up python3-pysam (0.9.0+ds-1) ... Setting up python3-setuptools (20.10.1-1) ... Setting up libnss3:arm64 (2:3.21-1ubuntu4) ... Setting up openjdk-8-jre-headless:arm64 (8u91-b14-2ubuntu1) ... update-alternatives: using /usr/lib/jvm/java-8-openjdk-arm64/jre/bin/rmid to provide /usr/bin/rmid (rmid) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-arm64/jre/bin/java to provide /usr/bin/java (java) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-arm64/jre/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-arm64/jre/bin/jjs to provide /usr/bin/jjs (jjs) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-arm64/jre/bin/pack200 to provide /usr/bin/pack200 (pack200) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-arm64/jre/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-arm64/jre/bin/unpack200 to provide /usr/bin/unpack200 (unpack200) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-arm64/jre/bin/orbd to provide /usr/bin/orbd (orbd) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-arm64/jre/bin/servertool to provide /usr/bin/servertool (servertool) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-arm64/jre/bin/tnameserv to provide /usr/bin/tnameserv (tnameserv) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-arm64/jre/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode Setting up ca-certificates-java (20160321) ... Adding debian:Verisign_Class_3_Public_Primary_Certification_Authority_-_G3.pem Adding debian:GeoTrust_Primary_Certification_Authority_-_G3.pem Adding debian:Verisign_Class_1_Public_Primary_Certification_Authority.pem Adding debian:QuoVadis_Root_CA_2_G3.pem Adding debian:QuoVadis_Root_CA.pem Adding debian:Verisign_Class_1_Public_Primary_Certification_Authority_-_G2.pem Adding debian:DigiCert_Global_Root_CA.pem Adding debian:SwissSign_Silver_CA_-_G2.pem Adding debian:UTN_USERFirst_Email_Root_CA.pem Adding debian:CFCA_EV_ROOT.pem Adding debian:CNNIC_ROOT.pem Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem Adding debian:S-TRUST_Universal_Root_CA.pem Adding debian:Taiwan_GRCA.pem Adding debian:TÜRKTRUST_Elektronik_Sertifika_Hizmet_Sağlayıcısı_H6.pem Adding debian:Verisign_Class_3_Public_Primary_Certification_Authority.pem Adding debian:StartCom_Certification_Authority_G2.pem Adding debian:SwissSign_Gold_CA_-_G2.pem Adding debian:AffirmTrust_Networking.pem Adding debian:Equifax_Secure_CA.pem Adding debian:GeoTrust_Primary_Certification_Authority_-_G2.pem Adding debian:NetLock_Notary_=Class_A=_Root.pem Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem Adding debian:Entrust_Root_Certification_Authority_-_G2.pem Adding debian:CA_WoSign_ECC_Root.pem Adding debian:Deutsche_Telekom_Root_CA_2.pem Adding debian:Buypass_Class_2_CA_1.pem Adding debian:TURKTRUST_Certificate_Services_Provider_Root_2007.pem Adding debian:Entrust_Root_Certification_Authority.pem Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem Adding debian:RSA_Security_2048_v3.pem Adding debian:TÜBİTAK_UEKAE_Kök_Sertifika_Hizmet_Sağlayıcısı_-_Sürüm_3.pem Adding debian:DigiCert_Global_Root_G3.pem Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem Adding debian:DST_Root_CA_X3.pem Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem Adding debian:AddTrust_Qualified_Certificates_Root.pem Adding debian:GeoTrust_Universal_CA_2.pem Adding debian:COMODO_Certification_Authority.pem Adding debian:ComSign_CA.pem Adding debian:Go_Daddy_Class_2_CA.pem Adding debian:Certification_Authority_of_WoSign_G2.pem Adding debian:Equifax_Secure_Global_eBusiness_CA.pem Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem Adding debian:USERTrust_RSA_Certification_Authority.pem Adding debian:Microsec_e-Szigno_Root_CA_2009.pem Adding debian:ApplicationCA_-_Japanese_Government.pem Adding debian:COMODO_ECC_Certification_Authority.pem Adding debian:COMODO_RSA_Certification_Authority.pem Adding debian:WoSign.pem Adding debian:China_Internet_Network_Information_Center_EV_Certificates_Root.pem Adding debian:Chambers_of_Commerce_Root_-_2008.pem Adding debian:DigiCert_Trusted_Root_G4.pem Adding debian:StartCom_Certification_Authority_2.pem Adding debian:Certum_Root_CA.pem Adding debian:Hongkong_Post_Root_CA_1.pem Adding debian:VeriSign_Class_3_Public_Primary_Certification_Authority_-_G5.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2011.pem Adding debian:IdenTrust_Commercial_Root_CA_1.pem Adding debian:PSCProcert.pem Adding debian:thawte_Primary_Root_CA_-_G2.pem Adding debian:Buypass_Class_2_Root_CA.pem Adding debian:Comodo_Secure_Services_root.pem Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem Adding debian:TWCA_Global_Root_CA.pem Adding debian:Certinomis_-_Autorité_Racine.pem Adding debian:DigiCert_Assured_ID_Root_G3.pem Adding debian:EC-ACC.pem Adding debian:DigiCert_Assured_ID_Root_CA.pem Adding debian:Comodo_Trusted_Services_root.pem Adding debian:Actalis_Authentication_Root_CA.pem Adding debian:Secure_Global_CA.pem Adding debian:IGC_A.pem Adding debian:GlobalSign_Root_CA_-_R3.pem Adding debian:Sonera_Class_1_Root_CA.pem Adding debian:S-TRUST_Authentication_and_Encryption_Root_CA_2005_PN.pem Adding debian:TWCA_Root_Certification_Authority.pem Adding debian:Swisscom_Root_EV_CA_2.pem Adding debian:TeliaSonera_Root_CA_v1.pem Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem Adding debian:Security_Communication_EV_RootCA1.pem Adding debian:Staat_der_Nederlanden_Root_CA_-_G2.pem Adding debian:AffirmTrust_Premium_ECC.pem Adding debian:NetLock_Business_=Class_B=_Root.pem Adding debian:Staat_der_Nederlanden_EV_Root_CA.pem Adding debian:NetLock_Qualified_=Class_QA=_Root.pem Adding debian:AddTrust_External_Root.pem Adding debian:GeoTrust_Global_CA.pem Adding debian:GeoTrust_Primary_Certification_Authority.pem Adding debian:DST_ACES_CA_X6.pem Adding debian:VeriSign_Class_3_Public_Primary_Certification_Authority_-_G4.pem Adding debian:Camerfirma_Global_Chambersign_Root.pem Adding debian:Global_Chambersign_Root_-_2008.pem Adding debian:SwissSign_Platinum_CA_-_G2.pem Adding debian:Visa_eCommerce_Root.pem Adding debian:GlobalSign_Root_CA.pem Adding debian:Starfield_Class_2_CA.pem Adding debian:TÜRKTRUST_Elektronik_Sertifika_Hizmet_Sağlayıcısı_H5.pem Adding debian:QuoVadis_Root_CA_3.pem Adding debian:Trustis_FPS_Root_CA.pem Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem Adding debian:CA_Disig.pem Adding debian:DigiCert_Global_Root_G2.pem Adding debian:SecureTrust_CA.pem Adding debian:WellsSecure_Public_Root_Certificate_Authority.pem Adding debian:Verisign_Class_3_Public_Primary_Certification_Authority_-_G2.pem Adding debian:ACCVRAIZ1.pem Adding debian:AC_Raíz_Certicámara_S.A..pem Adding debian:Security_Communication_Root_CA.pem Adding debian:ePKI_Root_Certification_Authority.pem Adding debian:Certplus_Class_2_Primary_CA.pem Adding debian:Swisscom_Root_CA_1.pem Adding debian:T-TeleSec_GlobalRoot_Class_2.pem Adding debian:AffirmTrust_Commercial.pem Adding debian:VeriSign_Universal_Root_Certification_Authority.pem Adding debian:Verisign_Class_2_Public_Primary_Certification_Authority_-_G3.pem Adding debian:EBG_Elektronik_Sertifika_Hizmet_Sağlayıcısı.pem Adding debian:XRamp_Global_CA_Root.pem Adding debian:Atos_TrustedRoot_2011.pem Adding debian:NetLock_Express_=Class_C=_Root.pem Adding debian:Certinomis_-_Root_CA.pem Adding debian:TC_TrustCenter_Class_3_CA_II.pem Adding debian:QuoVadis_Root_CA_2.pem Adding debian:Equifax_Secure_eBusiness_CA_1.pem Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem Adding debian:Verisign_Class_3_Public_Primary_Certification_Authority_2.pem Adding debian:Swisscom_Root_CA_2.pem Adding debian:E-Tugra_Certification_Authority.pem Adding debian:Staat_der_Nederlanden_Root_CA.pem Adding debian:Comodo_AAA_Services_root.pem Adding debian:QuoVadis_Root_CA_1_G3.pem Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem Adding debian:Network_Solutions_Certificate_Authority.pem Adding debian:DigiCert_Assured_ID_Root_G2.pem Adding debian:AddTrust_Public_Services_Root.pem Adding debian:Microsec_e-Szigno_Root_CA.pem Adding debian:SecureSign_RootCA11.pem Adding debian:Verisign_Class_2_Public_Primary_Certification_Authority_-_G2.pem Adding debian:CA_Disig_Root_R2.pem Adding debian:Sonera_Class_2_Root_CA.pem Adding debian:thawte_Primary_Root_CA_-_G3.pem Adding debian:StartCom_Certification_Authority.pem Adding debian:Certigna.pem Adding debian:Juur-SK.pem Adding debian:Cybertrust_Global_Root.pem Adding debian:AddTrust_Low-Value_Services_Root.pem Adding debian:CA_Disig_Root_R1.pem Adding debian:ACEDICOM_Root.pem Adding debian:Buypass_Class_3_Root_CA.pem Adding debian:certSIGN_ROOT_CA.pem Adding debian:OISTE_WISeKey_Global_Root_GA_CA.pem Adding debian:T-TeleSec_GlobalRoot_Class_3.pem Adding debian:Izenpe.com.pem Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem Adding debian:WoSign_China.pem Adding debian:GeoTrust_Global_CA_2.pem Adding debian:Verisign_Class_1_Public_Primary_Certification_Authority_-_G3.pem Adding debian:Certum_Trusted_Network_CA.pem Adding debian:Baltimore_CyberTrust_Root.pem Adding debian:GlobalSign_Root_CA_-_R2.pem Adding debian:AffirmTrust_Premium.pem Adding debian:Staat_der_Nederlanden_Root_CA_-_G3.pem Adding debian:USERTrust_ECC_Certification_Authority.pem Adding debian:QuoVadis_Root_CA_3_G3.pem Adding debian:EE_Certification_Centre_Root_CA.pem Adding debian:UTN_USERFirst_Hardware_Root_CA.pem Adding debian:GeoTrust_Universal_CA.pem Adding debian:thawte_Primary_Root_CA.pem Adding debian:Security_Communication_RootCA2.pem Adding debian:Root_CA_Generalitat_Valenciana.pem Adding debian:Camerfirma_Chambers_of_Commerce_Root.pem done. Setting up default-jre-headless (2:1.8-56ubuntu2) ... Setting up debhelper (9.20160403ubuntu1) ... Setting up openjdk-8-jdk-headless:arm64 (8u91-b14-2ubuntu1) ... update-alternatives: using /usr/lib/jvm/java-8-openjdk-arm64/bin/idlj to provide /usr/bin/idlj (idlj) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-arm64/bin/jdeps to provide /usr/bin/jdeps (jdeps) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-arm64/bin/wsimport to provide /usr/bin/wsimport (wsimport) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-arm64/bin/jinfo to provide /usr/bin/jinfo (jinfo) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-arm64/bin/jsadebugd to provide /usr/bin/jsadebugd (jsadebugd) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-arm64/bin/native2ascii to provide /usr/bin/native2ascii (native2ascii) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-arm64/bin/jstat to provide /usr/bin/jstat (jstat) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-arm64/bin/javac to provide /usr/bin/javac (javac) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-arm64/bin/javah to provide /usr/bin/javah (javah) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-arm64/bin/jstack to provide /usr/bin/jstack (jstack) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-arm64/bin/jrunscript to provide /usr/bin/jrunscript (jrunscript) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-arm64/bin/javadoc to provide /usr/bin/javadoc (javadoc) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-arm64/bin/jhat to provide /usr/bin/jhat (jhat) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-arm64/bin/javap to provide /usr/bin/javap (javap) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-arm64/bin/jar to provide /usr/bin/jar (jar) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-arm64/bin/extcheck to provide /usr/bin/extcheck (extcheck) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-arm64/bin/schemagen to provide /usr/bin/schemagen (schemagen) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-arm64/bin/jps to provide /usr/bin/jps (jps) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-arm64/bin/xjc to provide /usr/bin/xjc (xjc) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-arm64/bin/rmic to provide /usr/bin/rmic (rmic) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-arm64/bin/jstatd to provide /usr/bin/jstatd (jstatd) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-arm64/bin/jdb to provide /usr/bin/jdb (jdb) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-arm64/bin/serialver to provide /usr/bin/serialver (serialver) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-arm64/bin/wsgen to provide /usr/bin/wsgen (wsgen) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-arm64/bin/jcmd to provide /usr/bin/jcmd (jcmd) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-arm64/bin/jarsigner to provide /usr/bin/jarsigner (jarsigner) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-arm64/bin/jmap to provide /usr/bin/jmap (jmap) in auto mode Setting up default-jdk-headless (2:1.8-56ubuntu2) ... Setting up sbuild-build-depends-iva-dummy (0.invalid.0) ... Setting up dh-strip-nondeterminism (0.016-1) ... Processing triggers for libc-bin (2.23-0ubuntu3) ... Processing triggers for systemd (229-6ubuntu1) ... Processing triggers for ca-certificates (20160104ubuntu1) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. done. ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build environment │ └──────────────────────────────────────────────────────────────────────────────┘ Kernel: Linux 4.2.0-34-generic arm64 (aarch64) Toolchain package versions: binutils_2.26-9ubuntu1 dpkg-dev_1.18.7ubuntu1 g++-5_5.3.1-19ubuntu1 gcc-5_5.3.1-19ubuntu1 libc6-dev_2.23-0ubuntu3 libstdc++-5-dev_5.3.1-19ubuntu1 libstdc++6_6.1.1-3ubuntu11 linux-libc-dev_4.4.0-22.39 Package versions: adduser_3.113+nmu3ubuntu4 advancecomp_1.20-1 apt_1.3~exp1 apt-transport-https_1.3~exp1 autoconf_2.69-10 automake_1:1.15-4ubuntu1 autopoint_0.19.7-2ubuntu3 autotools-dev_20160430.1 base-files_9.6ubuntu1 base-passwd_3.5.39 bash_4.3-14ubuntu2 binutils_2.26-9ubuntu1 bioperl_1.6.924-3 bsdmainutils_9.0.6ubuntu3 bsdutils_1:2.27.1-6ubuntu3 build-essential_12.1ubuntu2 bzip2_1.0.6-8build1 ca-certificates_20160104ubuntu1 ca-certificates-java_20160321 coreutils_8.25-2ubuntu2 cpp_4:5.3.1-1ubuntu1 cpp-5_5.3.1-19ubuntu1 dash_0.5.8-2.1ubuntu2 debconf_1.5.59ubuntu1 debhelper_9.20160403ubuntu1 debianutils_4.7 default-jdk-headless_2:1.8-56ubuntu2 default-jre-headless_2:1.8-56ubuntu2 dh-autoreconf_12 dh-python_2.20151103ubuntu2 dh-strip-nondeterminism_0.016-1 diffutils_1:3.3-3 dmsetup_2:1.02.122-1ubuntu1 dpkg_1.18.7ubuntu1 dpkg-dev_1.18.7ubuntu1 e2fslibs_1.42.13-1ubuntu1 e2fsprogs_1.42.13-1ubuntu1 fakeroot_1.20.2-1ubuntu1 fastaq_3.12.1-1 file_1:5.25-2ubuntu1 findutils_4.6.0+git+20160126-2 fontconfig-config_2.11.94-0ubuntu1 fonts-dejavu-core_2.35-1 g++_4:5.3.1-1ubuntu1 g++-5_5.3.1-19ubuntu1 gawk_1:4.1.3+dfsg-0.1 gcc_4:5.3.1-1ubuntu1 gcc-5_5.3.1-19ubuntu1 gcc-5-base_5.3.1-19ubuntu1 gcc-6-base_6.1.1-3ubuntu11 gettext_0.19.7-2ubuntu3 gettext-base_0.19.7-2ubuntu3 gnupg_1.4.20-1ubuntu3 gpgv_1.4.20-1ubuntu3 grep_2.25-1 groff-base_1.22.3-7 gzip_1.6-4ubuntu1 help2man_1.47.4 hostname_3.17ubuntu1 init_1.33ubuntu1 init-system-helpers_1.33ubuntu1 initscripts_2.88dsf-59.3ubuntu5 insserv_1.14.0-5ubuntu3 intltool-debian_0.35.0+20060710.4 java-common_0.56ubuntu2 kmc_2.3+dfsg-5 libacl1_2.2.52-3 libapparmor1_2.10.95-0ubuntu2 libapt-pkg5.0_1.3~exp1 libarchive-zip-perl_1.57-1 libasan2_5.3.1-19ubuntu1 libasn1-8-heimdal_1.7~git20160418+dfsg-3 libasprintf0v5_0.19.7-2ubuntu3 libatomic1_6.1.1-3ubuntu11 libattr1_1:2.4.47-2 libaudit-common_1:2.4.5-1ubuntu2 libaudit1_1:2.4.5-1ubuntu2 libavahi-client3_0.6.32~rc+dfsg-1ubuntu2 libavahi-common-data_0.6.32~rc+dfsg-1ubuntu2 libavahi-common3_0.6.32~rc+dfsg-1ubuntu2 libbambamc0_0.0.50-1 libbio-perl-perl_1.6.924-3 libblas-common_3.6.0-2ubuntu2 libblas3_3.6.0-2ubuntu2 libblkid1_2.27.1-6ubuntu3 libbz2-1.0_1.0.6-8build1 libc-bin_2.23-0ubuntu3 libc-dev-bin_2.23-0ubuntu3 libc6_2.23-0ubuntu3 libc6-dev_2.23-0ubuntu3 libcap2_1:2.24-12 libcap2-bin_1:2.24-12 libcc1-0_6.1.1-3ubuntu11 libcomerr2_1.42.13-1ubuntu1 libcroco3_0.6.11-1 libcryptsetup4_2:1.6.6-5ubuntu2 libcups2_2.1.3-5 libcurl3-gnutls_7.47.0-1ubuntu2 libdata-stag-perl_0.14-1ubuntu2 libdb5.3_5.3.28-11 libdbus-1-3_1.10.6-1ubuntu3 libdebconfclient0_0.198ubuntu1 libdevmapper1.02.1_2:1.02.122-1ubuntu1 libdpkg-perl_1.18.7ubuntu1 libexpat1_2.1.1-1 libfakeroot_1.20.2-1ubuntu1 libfdisk1_2.27.1-6ubuntu3 libffi6_3.2.1-4 libfile-stripnondeterminism-perl_0.016-1 libfontconfig1_2.11.94-0ubuntu1 libfreetype6_2.6.3-3ubuntu1 libgcc-5-dev_5.3.1-19ubuntu1 libgcc1_1:6.1.1-3ubuntu11 libgcrypt20_1.7.0-2 libgdbm3_1.8.3-13.1 libgfortran3_6.1.1-3ubuntu11 libglib2.0-0_2.48.1-1 libgmp10_2:6.1.0+dfsg-2 libgnutls30_3.4.10-4ubuntu1 libgomp1_6.1.1-3ubuntu11 libgpg-error0_1.22-2 libgssapi-krb5-2_1.13.2+dfsg-5 libgssapi3-heimdal_1.7~git20160418+dfsg-3 libhcrypto4-heimdal_1.7~git20160418+dfsg-3 libheimbase1-heimdal_1.7~git20160418+dfsg-3 libheimntlm0-heimdal_1.7~git20160418+dfsg-3 libhogweed4_3.2-1 libhts1_1.3.1-1ubuntu1 libhx509-5-heimdal_1.7~git20160418+dfsg-3 libicu57_57.1-1 libidn11_1.32-3ubuntu1 libio-string-perl_1.08-3 libisl15_0.16.1-1 libitm1_6.1.1-3ubuntu11 libjpeg-turbo8_1.4.2-0ubuntu3 libjpeg8_8c-2ubuntu8 libk5crypto3_1.13.2+dfsg-5 libkeyutils1_1.5.9-8ubuntu1 libkmod2_22-1ubuntu4 libkrb5-26-heimdal_1.7~git20160418+dfsg-3 libkrb5-3_1.13.2+dfsg-5 libkrb5support0_1.13.2+dfsg-5 liblapack3_3.6.0-2ubuntu2 liblcms2-2_2.7-1ubuntu1 libldap-2.4-2_2.4.42+dfsg-2ubuntu4 liblocale-gettext-perl_1.07-1build1 liblockfile-bin_1.09-6ubuntu1 liblockfile1_1.09-6ubuntu1 liblz4-1_0.0~r131-2ubuntu2 liblzma5_5.1.1alpha+20120614-2ubuntu2 libmagic1_1:5.25-2ubuntu1 libmount1_2.27.1-6ubuntu3 libmpc3_1.0.3-1 libmpdec2_2.4.2-1 libmpfr4_3.1.4-1 libncurses5_6.0+20160213-1ubuntu1 libncursesw5_6.0+20160213-1ubuntu1 libnettle6_3.2-1 libnspr4_2:4.11-1ubuntu1 libnss3_2:3.21-1ubuntu4 libnss3-nssdb_2:3.21-1ubuntu4 libp11-kit0_0.23.2-3 libpam-modules_1.1.8-3.2ubuntu2 libpam-modules-bin_1.1.8-3.2ubuntu2 libpam-runtime_1.1.8-3.2ubuntu2 libpam0g_1.1.8-3.2ubuntu2 libpcre3_2:8.38-3.1 libpcsclite1_1.8.14-1ubuntu1 libperl5.22_5.22.2-1 libpipeline1_1.4.1-2 libpng12-0_1.2.54-6ubuntu1 libpng16-16_1.6.21-5 libprocps4_2:3.3.10-4ubuntu2 libpython3-stdlib_3.5.1-3 libpython3.5-minimal_3.5.1-12 libpython3.5-stdlib_3.5.1-12 libreadline6_6.3-8ubuntu2 libroken18-heimdal_1.7~git20160418+dfsg-3 librtmp1_2.4+20151223.gitfa8646d.1-1 libsasl2-2_2.1.26.dfsg1-15 libsasl2-modules-db_2.1.26.dfsg1-15 libseccomp2_2.2.3-3ubuntu3 libselinux1_2.5-2 libsemanage-common_2.5-1 libsemanage1_2.5-1 libsepol1_2.5-1 libsigsegv2_2.10-5 libslang2_2.3.0-2.3ubuntu1 libsmartcols1_2.27.1-6ubuntu3 libsqlite3-0_3.11.0-1ubuntu1 libss2_1.42.13-1ubuntu1 libssl-dev_1.0.2g-1ubuntu4 libssl1.0.0_1.0.2g-1ubuntu4 libstdc++-5-dev_5.3.1-19ubuntu1 libstdc++6_6.1.1-3ubuntu11 libsystemd0_229-6ubuntu1 libtasn1-6_4.8-1 libtimedate-perl_2.3000-2 libtinfo5_6.0+20160213-1ubuntu1 libtool_2.4.6-0.1 libubsan0_6.1.1-3ubuntu11 libudev1_229-6ubuntu1 libunistring0_0.9.3-5.2ubuntu1 libusb-0.1-4_2:0.1.12-30 libustr-1.0-1_1.0.4-5 libuuid1_2.27.1-6ubuntu3 libwind0-heimdal_1.7~git20160418+dfsg-3 libx11-6_2:1.6.3-1ubuntu2 libx11-data_2:1.6.3-1ubuntu2 libxau6_1:1.0.8-1 libxcb1_1.11.1-1ubuntu1 libxdmcp6_1:1.1.2-1.1 libxext6_2:1.3.3-1 libxi6_2:1.7.6-1 libxml2_2.9.3+dfsg1-1build1 libxrender1_1:0.9.9-0ubuntu1 libxtst6_2:1.2.2-1 linux-libc-dev_4.4.0-22.39 lockfile-progs_0.1.17 login_1:4.2-3.1ubuntu5 lsb-base_9.20160110 m4_1.4.17-5 make_4.1-9 man-db_2.7.5-1 mawk_1.3.3-17ubuntu2 mime-support_3.59ubuntu1 mount_2.27.1-6ubuntu3 multiarch-support_2.23-0ubuntu3 mummer_3.23~dfsg-3 ncurses-base_6.0+20160213-1ubuntu1 ncurses-bin_6.0+20160213-1ubuntu1 openjdk-8-jdk-headless_8u91-b14-2ubuntu1 openjdk-8-jre-headless_8u91-b14-2ubuntu1 openssl_1.0.2g-1ubuntu4 optipng_0.7.6-1build1 passwd_1:4.2-3.1ubuntu5 patch_2.7.5-1 perl_5.22.2-1 perl-base_5.22.2-1 perl-modules-5.22_5.22.2-1 pkg-create-dbgsym_0.72 pkgbinarymangler_129 po-debconf_1.0.19 policyrcd-script-zg2_0.1-3 procps_2:3.3.10-4ubuntu2 python3_3.5.1-3 python3-decorator_4.0.6-1 python3-minimal_3.5.1-3 python3-networkx_1.11-1ubuntu1 python3-nose_1.3.7-1 python3-numpy_1:1.11.0-1ubuntu1 python3-pkg-resources_20.10.1-1 python3-pysam_0.9.0+ds-1 python3-setuptools_20.10.1-1 python3.5_3.5.1-12 python3.5-minimal_3.5.1-12 readline-common_6.3-8ubuntu2 samtools_1.3.1-2 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-iva-dummy_0.invalid.0 sed_4.2.2-7.1 sensible-utils_0.0.9 smalt_0.7.6-4 systemd_229-6ubuntu1 systemd-sysv_229-6ubuntu1 sysv-rc_2.88dsf-59.3ubuntu5 sysvinit-utils_2.88dsf-59.3ubuntu5 tar_1.28-2.2 tzdata_2016d-2 ubuntu-keyring_2012.05.19 ucf_3.0036 util-linux_2.27.1-6ubuntu3 x11-common_1:7.7+13ubuntu3 xz-utils_5.1.1alpha+20120614-2ubuntu2 zlib1g_1:1.2.8.dfsg-2ubuntu5 zlib1g-dev_1:1.2.8.dfsg-2ubuntu5 ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build │ └──────────────────────────────────────────────────────────────────────────────┘ Unpack source ───────────── gpgv: Signature made Thu May 12 10:02:15 2016 UTC using RSA key ID F09F4872 gpgv: Can't check signature: public key not found dpkg-source: warning: failed to verify signature on ./iva_1.0.6+ds-1.dsc dpkg-source: info: extracting iva in iva-1.0.6+ds dpkg-source: info: unpacking iva_1.0.6+ds.orig.tar.xz dpkg-source: info: unpacking iva_1.0.6+ds-1.debian.tar.xz dpkg-source: info: applying add-shebang-line-to-getMummerStats dpkg-source: info: applying adjust_required_pysam_version.patch Check disc space ──────────────── Sufficient free space for build User Environment ──────────────── DEB_BUILD_OPTIONS=parallel=4 HOME=/home/buildd LANG=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=/«BUILDDIR»/iva-1.0.6+ds SHELL=/bin/sh SUDO_COMMAND=/usr/sbin/chroot /«CHROOT» su buildd -s /bin/sh -c cd '/«BUILDDIR»/iva-1.0.6+ds' && 'env' SUDO_GID=2501 SUDO_UID=2001 SUDO_USER=buildd TERM=unknown USER=buildd USERNAME=root dpkg-buildpackage ───────────────── dpkg-buildpackage: info: source package iva dpkg-buildpackage: info: source version 1.0.6+ds-1 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build iva-1.0.6+ds dpkg-buildpackage: info: host architecture arm64 fakeroot debian/rules clean dh clean --with python3 --buildsystem=pybuild dh_testdir -O--buildsystem=pybuild debian/rules override_dh_auto_clean make[1]: Entering directory '/«BUILDDIR»/iva-1.0.6+ds' rm -rf .pybuild rm -f iva/gage/*.class rm -rf /«BUILDDIR»/iva-1.0.6+ds/debian/man find . -name __pycache__ | xargs rm -rf make[1]: Leaving directory '/«BUILDDIR»/iva-1.0.6+ds' dh_clean -O--buildsystem=pybuild debian/rules build-arch dh build-arch --with 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: python3.5 setup.py config Checking dependencies found in path: OK kmc OK kmc_dump OK nucmer OK delta-filter OK show-coords OK samtools OK smalt running config debian/rules override_dh_auto_build make[1]: Entering directory '/«BUILDDIR»/iva-1.0.6+ds' chmod a-x /«BUILDDIR»/iva-1.0.6+ds/iva/read_trim/adapters.fasta chmod a+x /«BUILDDIR»/iva-1.0.6+ds/iva/gage/getCorrectnessStats.sh chmod a+x /«BUILDDIR»/iva-1.0.6+ds/iva/ratt/main.ratt.pl chmod a+x scripts/* javac -verbose /«BUILDDIR»/iva-1.0.6+ds/iva/gage/*.java [parsing started RegularFileObject[/«BUILDDIR»/iva-1.0.6+ds/iva/gage/GetFastaStats.java]] [parsing completed 101ms] [parsing started RegularFileObject[/«BUILDDIR»/iva-1.0.6+ds/iva/gage/SizeFasta.java]] [parsing completed 7ms] [parsing started RegularFileObject[/«BUILDDIR»/iva-1.0.6+ds/iva/gage/SplitFastaByLetter.java]] [parsing completed 4ms] [parsing started RegularFileObject[/«BUILDDIR»/iva-1.0.6+ds/iva/gage/Utils.java]] [parsing completed 16ms] [parsing started RegularFileObject[/«BUILDDIR»/iva-1.0.6+ds/iva/gage/getScaffoldStats.java]] [parsing completed 48ms] [search path for source files: .] [search path for class files: /usr/lib/jvm/java-8-openjdk-arm64/jre/lib/resources.jar,/usr/lib/jvm/java-8-openjdk-arm64/jre/lib/rt.jar,/usr/lib/jvm/java-8-openjdk-arm64/jre/lib/sunrsasign.jar,/usr/lib/jvm/java-8-openjdk-arm64/jre/lib/jsse.jar,/usr/lib/jvm/java-8-openjdk-arm64/jre/lib/jce.jar,/usr/lib/jvm/java-8-openjdk-arm64/jre/lib/charsets.jar,/usr/lib/jvm/java-8-openjdk-arm64/jre/lib/jfr.jar,/usr/lib/jvm/java-8-openjdk-arm64/jre/classes,/usr/lib/jvm/java-8-openjdk-arm64/jre/lib/ext/sunpkcs11.jar,/usr/lib/jvm/java-8-openjdk-arm64/jre/lib/ext/sunec.jar,/usr/lib/jvm/java-8-openjdk-arm64/jre/lib/ext/dnsns.jar,/usr/lib/jvm/java-8-openjdk-arm64/jre/lib/ext/icedtea-sound.jar,/usr/lib/jvm/java-8-openjdk-arm64/jre/lib/ext/jaccess.jar,/usr/lib/jvm/java-8-openjdk-arm64/jre/lib/ext/cldrdata.jar,/usr/lib/jvm/java-8-openjdk-arm64/jre/lib/ext/sunjce_provider.jar,/usr/lib/jvm/java-8-openjdk-arm64/jre/lib/ext/nashorn.jar,/usr/lib/jvm/java-8-openjdk-arm64/jre/lib/ext/localedata.jar,/usr/lib/jvm/java-8-openjdk-arm64/jre/lib/ext/zipfs.jar,.] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-arm64/lib/ct.sym(META-INF/sym/rt.jar/java/io/BufferedReader.class)]] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-arm64/lib/ct.sym(META-INF/sym/rt.jar/java/io/FileInputStream.class)]] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-arm64/lib/ct.sym(META-INF/sym/rt.jar/java/io/InputStreamReader.class)]] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-arm64/lib/ct.sym(META-INF/sym/rt.jar/java/text/DecimalFormat.class)]] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-arm64/lib/ct.sym(META-INF/sym/rt.jar/java/text/NumberFormat.class)]] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-arm64/lib/ct.sym(META-INF/sym/rt.jar/java/util/ArrayList.class)]] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-arm64/lib/ct.sym(META-INF/sym/rt.jar/java/util/Arrays.class)]] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-arm64/lib/ct.sym(META-INF/sym/rt.jar/java/util/HashMap.class)]] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-arm64/lib/ct.sym(META-INF/sym/rt.jar/java/lang/Object.class)]] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-arm64/lib/ct.sym(META-INF/sym/rt.jar/java/lang/String.class)]] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-arm64/lib/ct.sym(META-INF/sym/rt.jar/java/lang/Integer.class)]] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-arm64/lib/ct.sym(META-INF/sym/rt.jar/java/lang/Exception.class)]] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-arm64/lib/ct.sym(META-INF/sym/rt.jar/java/lang/StringBuffer.class)]] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-arm64/lib/ct.sym(META-INF/sym/rt.jar/java/lang/management/ManagementFactory.class)]] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-arm64/lib/ct.sym(META-INF/sym/rt.jar/java/lang/management/MemoryMXBean.class)]] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-arm64/lib/ct.sym(META-INF/sym/rt.jar/java/io/File.class)]] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-arm64/lib/ct.sym(META-INF/sym/rt.jar/java/io/FileReader.class)]] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-arm64/lib/ct.sym(META-INF/sym/rt.jar/java/lang/Boolean.class)]] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-arm64/lib/ct.sym(META-INF/sym/rt.jar/java/lang/Enum.class)]] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-arm64/lib/ct.sym(META-INF/sym/rt.jar/java/lang/Comparable.class)]] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-arm64/lib/ct.sym(META-INF/sym/rt.jar/java/io/Serializable.class)]] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-arm64/lib/ct.sym(META-INF/sym/rt.jar/java/util/Collections.class)]] [checking GetFastaStats] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-arm64/lib/ct.sym(META-INF/sym/rt.jar/java/lang/AutoCloseable.class)]] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-arm64/lib/ct.sym(META-INF/sym/rt.jar/java/lang/Byte.class)]] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-arm64/lib/ct.sym(META-INF/sym/rt.jar/java/lang/Character.class)]] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-arm64/lib/ct.sym(META-INF/sym/rt.jar/java/lang/Short.class)]] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-arm64/lib/ct.sym(META-INF/sym/rt.jar/java/lang/Long.class)]] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-arm64/lib/ct.sym(META-INF/sym/rt.jar/java/lang/Float.class)]] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-arm64/lib/ct.sym(META-INF/sym/rt.jar/java/lang/Double.class)]] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-arm64/lib/ct.sym(META-INF/sym/rt.jar/java/lang/Void.class)]] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-arm64/lib/ct.sym(META-INF/sym/rt.jar/java/util/Map.class)]] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-arm64/lib/ct.sym(META-INF/sym/rt.jar/java/lang/Throwable.class)]] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-arm64/lib/ct.sym(META-INF/sym/rt.jar/java/lang/CharSequence.class)]] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-arm64/lib/ct.sym(META-INF/sym/rt.jar/java/io/Reader.class)]] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-arm64/lib/ct.sym(META-INF/sym/rt.jar/java/lang/Readable.class)]] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-arm64/lib/ct.sym(META-INF/sym/rt.jar/java/io/Closeable.class)]] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-arm64/lib/ct.sym(META-INF/sym/rt.jar/java/lang/Number.class)]] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-arm64/lib/ct.sym(META-INF/sym/rt.jar/java/lang/Cloneable.class)]] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-arm64/lib/ct.sym(META-INF/sym/rt.jar/java/util/AbstractMap.class)]] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-arm64/lib/ct.sym(META-INF/sym/rt.jar/java/lang/AbstractStringBuilder.class)]] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-arm64/lib/ct.sym(META-INF/sym/rt.jar/java/lang/Appendable.class)]] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-arm64/lib/ct.sym(META-INF/sym/rt.jar/java/io/FileDescriptor.class)]] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-arm64/lib/ct.sym(META-INF/sym/rt.jar/java/lang/System.class)]] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-arm64/lib/ct.sym(META-INF/sym/rt.jar/java/io/PrintStream.class)]] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-arm64/lib/ct.sym(META-INF/sym/rt.jar/java/io/FilterOutputStream.class)]] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-arm64/lib/ct.sym(META-INF/sym/rt.jar/java/io/OutputStream.class)]] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-arm64/lib/ct.sym(META-INF/sym/rt.jar/java/io/Flushable.class)]] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-arm64/lib/ct.sym(META-INF/sym/rt.jar/java/util/Set.class)]] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-arm64/lib/ct.sym(META-INF/sym/rt.jar/java/lang/Iterable.class)]] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-arm64/lib/ct.sym(META-INF/sym/rt.jar/java/util/Collection.class)]] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-arm64/lib/ct.sym(META-INF/sym/rt.jar/java/lang/Math.class)]] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-arm64/lib/ct.sym(META-INF/sym/rt.jar/java/util/List.class)]] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-arm64/lib/ct.sym(META-INF/sym/rt.jar/java/util/RandomAccess.class)]] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-arm64/lib/ct.sym(META-INF/sym/rt.jar/java/util/AbstractList.class)]] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-arm64/lib/ct.sym(META-INF/sym/rt.jar/java/util/AbstractCollection.class)]] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-arm64/lib/ct.sym(META-INF/sym/rt.jar/java/util/Comparator.class)]] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-arm64/lib/ct.sym(META-INF/sym/rt.jar/java/text/Format.class)]] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-arm64/lib/ct.sym(META-INF/sym/rt.jar/java/lang/Error.class)]] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-arm64/lib/ct.sym(META-INF/sym/rt.jar/java/lang/RuntimeException.class)]] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-arm64/lib/ct.sym(META-INF/sym/rt.jar/java/io/IOException.class)]] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-arm64/lib/ct.sym(META-INF/sym/rt.jar/java/lang/NumberFormatException.class)]] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-arm64/lib/ct.sym(META-INF/sym/rt.jar/java/lang/IllegalArgumentException.class)]] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-arm64/lib/ct.sym(META-INF/sym/rt.jar/java/io/FileNotFoundException.class)]] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-arm64/lib/ct.sym(META-INF/sym/rt.jar/java/util/Iterator.class)]] [wrote RegularFileObject[/«BUILDDIR»/iva-1.0.6+ds/iva/gage/GetFastaStats$ContigAt.class]] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-arm64/lib/ct.sym(META-INF/sym/rt.jar/java/lang/StringBuilder.class)]] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-arm64/lib/ct.sym(META-INF/sym/rt.jar/java/io/InputStream.class)]] [wrote RegularFileObject[/«BUILDDIR»/iva-1.0.6+ds/iva/gage/GetFastaStats.class]] [checking SizeFasta] [wrote RegularFileObject[/«BUILDDIR»/iva-1.0.6+ds/iva/gage/SizeFasta.class]] [checking SplitFastaByLetter] [wrote RegularFileObject[/«BUILDDIR»/iva-1.0.6+ds/iva/gage/SplitFastaByLetter.class]] [checking Utils] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-arm64/lib/ct.sym(META-INF/sym/rt.jar/java/lang/CloneNotSupportedException.class)]] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-arm64/lib/ct.sym(META-INF/sym/rt.jar/java/lang/Class.class)]] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-arm64/lib/ct.sym(META-INF/sym/rt.jar/java/net/URI.class)]] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-arm64/lib/ct.sym(META-INF/sym/rt.jar/java/lang/Process.class)]] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-arm64/lib/ct.sym(META-INF/sym/rt.jar/java/lang/Runtime.class)]] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-arm64/lib/ct.sym(META-INF/sym/rt.jar/java/lang/reflect/GenericDeclaration.class)]] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-arm64/lib/ct.sym(META-INF/sym/rt.jar/java/lang/reflect/AnnotatedElement.class)]] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-arm64/lib/ct.sym(META-INF/sym/rt.jar/java/lang/reflect/Type.class)]] [loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-arm64/lib/ct.sym(META-INF/sym/rt.jar/java/lang/AssertionError.class)]] [wrote RegularFileObject[/«BUILDDIR»/iva-1.0.6+ds/iva/gage/Utils$Pair.class]] [wrote RegularFileObject[/«BUILDDIR»/iva-1.0.6+ds/iva/gage/Utils$Translate.class]] [wrote RegularFileObject[/«BUILDDIR»/iva-1.0.6+ds/iva/gage/Utils$ToProtein.class]] [wrote RegularFileObject[/«BUILDDIR»/iva-1.0.6+ds/iva/gage/Utils.class]] [checking getScaffoldStats] [wrote RegularFileObject[/«BUILDDIR»/iva-1.0.6+ds/iva/gage/getScaffoldStats$Scaffold.class]] [wrote RegularFileObject[/«BUILDDIR»/iva-1.0.6+ds/iva/gage/getScaffoldStats$1.class]] [wrote RegularFileObject[/«BUILDDIR»/iva-1.0.6+ds/iva/gage/getScaffoldStats.class]] [total 1937ms] dh_auto_build -- I: pybuild base:184: /usr/bin/python3 setup.py build Checking dependencies found in path: OK kmc OK kmc_dump OK nucmer OK delta-filter OK show-coords OK samtools OK smalt running build running build_py creating /«BUILDDIR»/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva copying iva/assembly.py -> /«BUILDDIR»/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva copying iva/graph.py -> /«BUILDDIR»/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva copying iva/kcount.py -> /«BUILDDIR»/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva copying iva/test_data_runner.py -> /«BUILDDIR»/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva copying iva/qc.py -> /«BUILDDIR»/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva copying iva/kmers.py -> /«BUILDDIR»/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva copying iva/mapping.py -> /«BUILDDIR»/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva copying iva/contig.py -> /«BUILDDIR»/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva copying iva/contig_trim.py -> /«BUILDDIR»/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva copying iva/edge.py -> /«BUILDDIR»/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva copying iva/egg_extract.py -> /«BUILDDIR»/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva copying iva/__init__.py -> /«BUILDDIR»/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva copying iva/common.py -> /«BUILDDIR»/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva copying iva/mummer.py -> /«BUILDDIR»/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva copying iva/seed_processor.py -> /«BUILDDIR»/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva copying iva/kraken.py -> /«BUILDDIR»/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva copying iva/seed.py -> /«BUILDDIR»/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva copying iva/external_progs.py -> /«BUILDDIR»/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva copying iva/qc_external.py -> /«BUILDDIR»/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva copying iva/read_trim.py -> /«BUILDDIR»/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva creating /«BUILDDIR»/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva/gage copying iva/gage/getMummerStats.sh -> /«BUILDDIR»/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva/gage copying iva/gage/getScaffoldStats.java -> /«BUILDDIR»/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva/gage copying iva/gage/GetFastaStats.class -> /«BUILDDIR»/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva/gage copying iva/gage/getScaffoldStats$Scaffold.class -> /«BUILDDIR»/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva/gage copying iva/gage/SizeFasta.class -> /«BUILDDIR»/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva/gage copying iva/gage/getCorrectnessStats.sh -> /«BUILDDIR»/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva/gage copying iva/gage/Utils$Translate.class -> /«BUILDDIR»/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva/gage copying iva/gage/SizeFasta.java -> /«BUILDDIR»/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva/gage copying iva/gage/getScaffoldStats.class -> /«BUILDDIR»/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva/gage copying iva/gage/colsum.pl -> /«BUILDDIR»/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva/gage copying iva/gage/Utils$Pair.class -> /«BUILDDIR»/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva/gage copying iva/gage/Utils.class -> /«BUILDDIR»/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva/gage copying iva/gage/GetFastaStats$ContigAt.class -> /«BUILDDIR»/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva/gage copying iva/gage/GetFastaStats.java -> /«BUILDDIR»/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva/gage copying iva/gage/Utils$ToProtein.class -> /«BUILDDIR»/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva/gage copying iva/gage/Utils.java -> /«BUILDDIR»/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva/gage copying iva/gage/SplitFastaByLetter.class -> /«BUILDDIR»/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva/gage copying iva/gage/SplitFastaByLetter.java -> /«BUILDDIR»/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva/gage copying iva/gage/getScaffoldStats$1.class -> /«BUILDDIR»/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva/gage creating /«BUILDDIR»/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva/ratt copying iva/ratt/main.ratt.pl -> /«BUILDDIR»/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva/ratt copying iva/ratt/embl2gff.pl -> /«BUILDDIR»/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva/ratt copying iva/ratt/ratt.config -> /«BUILDDIR»/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva/ratt copying iva/ratt/ratt_correction.pm -> /«BUILDDIR»/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva/ratt copying iva/ratt/genbank2embl.pl -> /«BUILDDIR»/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva/ratt copying iva/ratt/ratt.config.hiv -> /«BUILDDIR»/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva/ratt copying iva/ratt/start.ratt.sh -> /«BUILDDIR»/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva/ratt creating /«BUILDDIR»/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva/read_trim copying iva/read_trim/adapters.fasta -> /«BUILDDIR»/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva/read_trim creating /«BUILDDIR»/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva/test_run_data copying iva/test_run_data/reads_2.fq.gz -> /«BUILDDIR»/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva/test_run_data copying iva/test_run_data/reads_1.fq.gz -> /«BUILDDIR»/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva/test_run_data copying iva/test_run_data/hiv_pcr_primers.fa -> /«BUILDDIR»/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva/test_run_data copying iva/test_run_data/iva_contigs_with_trimmomatic.fasta -> /«BUILDDIR»/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva/test_run_data copying iva/test_run_data/reference.fasta -> /«BUILDDIR»/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva/test_run_data copying iva/test_run_data/iva_contigs_no_trimmomatic.fasta -> /«BUILDDIR»/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva/test_run_data running build_scripts creating build creating build/scripts-3.5 copying and adjusting scripts/iva -> build/scripts-3.5 copying and adjusting scripts/iva_qc -> build/scripts-3.5 copying and adjusting scripts/iva_qc_make_db -> build/scripts-3.5 changing mode of build/scripts-3.5/iva from 664 to 775 changing mode of build/scripts-3.5/iva_qc from 664 to 775 changing mode of build/scripts-3.5/iva_qc_make_db from 664 to 775 make[1]: Leaving directory '/«BUILDDIR»/iva-1.0.6+ds' debian/rules override_dh_auto_test make[1]: Entering directory '/«BUILDDIR»/iva-1.0.6+ds' python3 setup.py test Checking dependencies found in path: OK kmc OK kmc_dump OK nucmer OK delta-filter OK show-coords OK samtools OK smalt running test running egg_info creating iva.egg-info writing dependency_links to iva.egg-info/dependency_links.txt writing requirements to iva.egg-info/requires.txt writing top-level names to iva.egg-info/top_level.txt writing iva.egg-info/PKG-INFO writing manifest file 'iva.egg-info/SOURCES.txt' reading manifest file 'iva.egg-info/SOURCES.txt' writing manifest file 'iva.egg-info/SOURCES.txt' running build_ext test_add_new_seed_contig (assembly_test.TestAssembly) Test add_new_seed_contig ... ok test_contig_contained_in_nucmer_hits (assembly_test.TestAssembly) Test _contig_contained_in_nucmer_hits ... ok test_contig_names_size_order (assembly_test.TestAssembly) Test _contig_names_size_order ... ok test_contig_worth_extending (assembly_test.TestAssembly) Test _contig_worth_extending ... ok test_coords_to_new_contig (assembly_test.TestAssembly) Test _coords_to_new_contig ... ok test_extend_contigs_with_bam (assembly_test.TestAssembly) test _extend_contigs_with_bam ... ok test_get_contig_order_by_orfs (assembly_test.TestAssembly) Test get_contig_order_by_orfs ... ok test_get_ref_length (assembly_test.TestAssembly) Test _get_ref_length ... ok test_get_ref_length_sam_pair (assembly_test.TestAssembly) Test _get_ref_length_sam_pair ... ok test_get_unmapped_pairs (assembly_test.TestAssembly) Test _get_unmapped_pairs ... ok test_good_intervals_from_strand_coverage (assembly_test.TestAssembly) Test good_intervals_from_strand_coverage ... ok test_init_and_write (assembly_test.TestAssembly) test assembly initialise and write to file ... ok test_map_reads (assembly_test.TestAssembly) test _map_reads ... ok test_merge_overlapping_contigs (assembly_test.TestAssembly) Test _merge_overlapping_contigs ... ok test_read_pair_extend (assembly_test.TestAssembly) Test read_pair_extend ... ok test_remove_contained_contigs (assembly_test.TestAssembly) Test _remove_contained_contigs ... ok test_remove_contig (assembly_test.TestAssembly) Test _remove_contig ... ok test_remove_contig_from_nucmer_hits (assembly_test.TestAssembly) Test _remove_contig_from_nucmer_hits ... ok test_subcontigs_from_strand_bias (assembly_test.TestAssembly) Test _subcontigs_from_strand_bias ... ok test_trim_contig_for_strand_bias (assembly_test.TestAssembly) Test _trim_contig_for_strand_bias ... ok test_trim_contigs (assembly_test.TestAssembly) Test trim_contigs ... ok test_trim_strand_biased_ends (assembly_test.TestAssembly) Test _trim_strand_biased_ends ... ok test_worth_extending (assembly_test.TestAssembly) Test worth_extending ... ok test_add_left_kmer (contig_test.TestContig) Test add_left_kmer ... ok test_add_right_kmer (contig_test.TestContig) Test add_right_kmer ... ok test_extend (contig_test.TestContig) Test extend ... ok test_init (contig_test.TestContig) Test init ... ok test_len (contig_test.TestContig) Test len ... ok test_coverage_to_trimmed_coords (contig_trim_test.TestContigTrim) Test _coverage_to_trimmed_coords ... ok test_trim_ends (contig_trim_test.TestContigTrim) Test _trim_ends ... ok test_trim_primers_and_adapters (contig_trim_test.TestContigTrim) Test trim_primers_and_adapters ... ok test_change_hit_coords_with_intersection (edge_test.TestEdge) test test_change_hit_coords_with_intersection ... ok test_make_contig_first (edge_test.TestEdge) test make_contig_first ... ok test_make_contig_forwards (edge_test.TestEdge) test make_contig_forwards ... ok test_merge_into (edge_test.TestEdge) test merge_into ... ok test_open_end (edge_test.TestEdge) test open_end ... ok test_reverse (edge_test.TestEdge) test reverse ... ok test_copy_dir (egg_extract_test.TestEggExtract) test copy_dir ... ok test_copy_dir_unzipped (egg_extract_test.TestEggExtract) test copy_dir_unzipped ... ok test_copy_dir_zipped (egg_extract_test.TestEggExtract) test copy_dir_zipped ... ok test_copy_file (egg_extract_test.TestEggExtract) test copy_file ... ok test_copy_file_unzipped (egg_extract_test.TestEggExtract) test _copy_file_unzipped ... ok test_copy_file_zipped (egg_extract_test.TestEggExtract) test _copy_file_zipped ... ok test_init_and_write (egg_extract_test.TestEggExtract) test __init__ ... ok test_delta_filter_in_path (external_progs_test.TestExternalProgs) Test delta-filter in path ... ok test_kmc_dump_in_path (external_progs_test.TestExternalProgs) Test kmc_dump in path ... ok test_kmc_in_path (external_progs_test.TestExternalProgs) Test kmc in path ... ok test_nucmer_in_path (external_progs_test.TestExternalProgs) Test nucmer in path ... ok test_samtools_in_path (external_progs_test.TestExternalProgs) Test samtools in path ... ok test_show_coords_in_path (external_progs_test.TestExternalProgs) Test show-coords in path ... ok test_smalt_in_path (external_progs_test.TestExternalProgs) Test smalt in path ... ok test_add_and_get_edges (graph_test.TestGraph) test adding and getting edges ... ok test_connected_components (graph_test.TestGraph) test connected_components ... ok test_degree (graph_test.TestGraph) test degree ... ok test_edges_are_consistent (graph_test.TestGraph) test edges_are_consistent ... ok test_find_simple_path (graph_test.TestGraph) test find_simple_path ... ok test_get_nodes (graph_test.TestGraph) test get_nodes ... ok test_merged_coords_from_simple_nonredundant_path (graph_test.TestGraph) test merged_coords_from_simple_nonredundant_path ... ok test_node_to_coords (graph_test.TestGraph) test _node_to_coords ... ok test_remove_middle_node (graph_test.TestGraph) test remove_middle_node ... ok test_remove_node (graph_test.TestGraph) test remove_node ... ok test_remove_redundant_nodes_from_simple_path (graph_test.TestGraph) test remove_redundant_nodes_from_simple_path ... ok test_simple_path_is_consistent (graph_test.TestGraph) test simple_path_is_consistent ... ok test_counts_file_to_fasta (kcount_test.TestKcount) Test _counts_file_to_fasta ... ok test_get_most_common_kmers (kcount_test.TestKcount) Test get_most_common_kmers ... ok test_head_fastaq_fa (kcount_test.TestKcount) Test head_fastaq with FASTA input ... ok test_head_fastaq_fq (kcount_test.TestKcount) Test head_fastaq with FASTQ input ... ok test_kmc_to_kmer_counts (kcount_test.TestKcount) Test _kmc_to_kmer_counts ... ok test_median (kcount_test.TestKcount) Test _median() ... ok test_run_kmc (kcount_test.TestKcount) Test test_run_kmc ... ok test_run_kmc_two_threads (kcount_test.TestKcount) Test test_run_kmc with two threads ... ok test_append (kmers_test.TestKmers) Test append ... ok test_commonest_kmers (kmers_test.TestKmers) ... ok test_extend (kmers_test.TestKmers) Test extend ... ok test_extension (kmers_test.TestKmers) Test extension ... ok test_init (kmers_test.TestKmers) Test __init__ ... ok test_kmer_dict (kmers_test.TestKmers) Test kmer_dict ... ok test_append_to_file (kraken_test.TestKraken) test _append_to_file ... ok test_genbank_to_taxon_and_gi (kraken_test.TestKraken) test _genbank_to_taxon_and_gi ... ok test_get_most_common_species_dir (kraken_test.TestKraken) Test get_most_common_species ... ok test_get_parent_taxons (kraken_test.TestKraken) test _get_parent_taxons ... ok test_load_extra_ref_info (kraken_test.TestKraken) test _load_extra_ref_info ... ok test_replace_fasta_header (kraken_test.TestKraken) test _replace_fasta_header ... ok test_species_to_dir (kraken_test.TestKraken) test species_to_dir ... ok test_bam_file_to_fasta_pair_files (mapping_test.TestMapping) Test bam_file_to_fasta_pair_files ... ok test_bam_file_to_fasta_pair_files_region (mapping_test.TestMapping) Test bam_file_to_fasta_pair_files with a region ... ok test_bam_file_to_region_fasta (mapping_test.TestMapping) Test bam_file_to_region_fasta ... ok test_bam_to_fasta (mapping_test.TestMapping) Test bam_to_fasta ... ok test_can_extend (mapping_test.TestMapping) Test can_extend ... ok test_consensus_base (mapping_test.TestMapping) Test consensus_base ... ok test_consensus_base_both_strands (mapping_test.TestMapping) Test consensus_base_both_strands ... ok test_find_incorrect_ref_bases (mapping_test.TestMapping) Test find_incorrect_ref_bases ... ok test_get_bam_region_coverage_fwd (mapping_test.TestMapping) Test get_bam_region_coverage forward strand ... ok test_get_bam_region_coverage_fwd_And_rev (mapping_test.TestMapping) Test get_bam_region_coverage both strands ... ok test_get_bam_region_coverage_rev (mapping_test.TestMapping) Test get_bam_region_coverage reverse strand ... ok test_get_pair_type (mapping_test.TestMapping) Test get_pair_type ... ok test_get_ref_name (mapping_test.TestMapping) Test get_ref_name ... ok test_map_reads (mapping_test.TestMapping) Test mapping reads ... ok test_map_reads_and_sort (mapping_test.TestMapping) Test mapping reads and sort BAM ... ok test_map_reads_wth_flag (mapping_test.TestMapping) Test map_reads with required flag ... ok test_remove_indels (mapping_test.TestMapping) Test _remove_indels ... ok test_sam_to_fasta (mapping_test.TestMapping) Test sam_to_fasta ... ok test_smalt_in_path (mapping_test.TestMapping) Test that samtools is in the user's path ... ok test_soft_clipped (mapping_test.TestMapping) Test soft_clipped ... ok test_strip_mpileup_coverage_string (mapping_test.TestMapping) Test strip_mpileup_coverage_string ... ok test_total_ref_length_from_bam (mapping_test.TestMapping) Test _total_ref_length_from_bam ... ok test_file_read (mummer_test.TestMummer) test file_read ... ok test_is_at_ends (mummer_test.TestMummer) Test is_at_ends ... ok test_is_self_hit (mummer_test.TestMummer) Test is_self_hit ... ok test_on_same_strand (mummer_test.TestMummer) test on_same_strand ... ok test_qry_coords (mummer_test.TestMummer) Test qry_coords ... ok test_ref_coords (mummer_test.TestMummer) Test ref_coords ... ok test_run_nucmer (mummer_test.TestMummer) test run_nucmer ... ok test_sort (mummer_test.TestMummer) test sort ... ok test_swap (mummer_test.TestMummer) test swap ... ok test_to_graph_edge (mummer_test.TestMummer) Test to_graph_edge ... ok test_run_gage (qc_external_test.TestQcExternal) test run_gage ... ok test_run_ratt (qc_external_test.TestQcExternal) test run_ratt ... ok test_calculate_cds_assembly_stats (qc_test.TestQc) test _calculate_cds_assembly_stats ... ok test_calculate_contig_placement (qc_test.TestQc) test calculate_contig_placement ... ok test_calculate_ref_positions_covered_by_contigs (qc_test.TestQc) test _calculate_ref_positions_covered_by_contigs ... ok test_calculate_ref_read_coverage (qc_test.TestQc) test _calculate_ref_read_coverage ... ok test_calculate_ref_read_region_coverage (qc_test.TestQc) test _calculate_ref_read_region_coverage ... ok test_calculate_refseq_assembly_stats (qc_test.TestQc) test _calculate_refseq_assembly_stats ... ok test_calculate_should_have_assembled (qc_test.TestQc) test _calculate_should_have_assembled ... ok test_contig_placement_in_reference (qc_test.TestQc) test _contig_placement_in_reference ... ok test_contigs_and_bases_that_hit_ref (qc_test.TestQc) test _contigs_and_bases_that_hit_ref ... ok test_cov_to_R_string (qc_test.TestQc) test _cov_to_R_string ... ok test_coverage_list_to_low_cov_intervals (qc_test.TestQc) test _coverage_list_to_low_cov_intervals ... ok test_get_R_plot_contig_order_from_contig_placement (qc_test.TestQc) test _get_R_plot_contig_order_from_contig_placement ... ok test_get_contig_hits_to_reference (qc_test.TestQc) test _get_contig_hits_to_reference ... ok test_get_overlapping_qry_hits (qc_test.TestQc) test _get_overlapping_qry_hits ... ok test_get_ref_cds_from_gff (qc_test.TestQc) test _get_ref_cds_from_gff ... ok test_get_unique_and_repetitive_from_contig_hits (qc_test.TestQc) test _get_unique_and_repetitive_from_contig_hits ... ok test_gff_and_fasta_to_cds (qc_test.TestQc) test _gff_and_fasta_to_cds ... ok test_has_orf (qc_test.TestQc) test _has_orf ... ok test_hash_nucmer_hits_by_ref (qc_test.TestQc) test _hash_nucmer_hits_by_ref ... ok test_ids_in_order_from_fai (qc_test.TestQc) test _ids_in_order_from_fai ... ok test_invert_list (qc_test.TestQc) test _invert_list ... ok test_map_cds_to_assembly (qc_test.TestQc) test _map_cds_to_assembly ... ok test_mummer_coords_file_to_dict (qc_test.TestQc) test _mummer_coords_file_to_dict ... ok test_write_cds_seqs (qc_test.TestQc) test _write_cds_seqs ... ok test_write_fasta_contigs_hit_ref (qc_test.TestQc) test _write_fasta_contigs_hit_ref ... ok test_write_fasta_contigs_not_hit_ref (qc_test.TestQc) test _write_fasta_contigs_not_hit_ref ... ok test_write_ref_coverage_to_files_for_R (qc_test.TestQc) test _write_ref_coverage_to_files_for_R ... ok test_run_trimmomatic (read_trim_test.TestReadTrim) Test run_trimmomatic ... ok test_process_seeds (seed_processor_test.TestSeedProcessor) Test process_seeds ... ok test_extend (seed_test.TestSeed) Test extend ... ok test_extend_with_reads_as_single_end (seed_test.TestSeed) Test _extend_with_reads_as_single_end ... ok test_extension_from_read (seed_test.TestSeed) Test _test_extension_from_read ... ok test_extensions_from_reads_file (seed_test.TestSeed) Test _extensions_from_reads_file ... ok test_init (seed_test.TestSeed) test init ... ok test_kmc_in_path (seed_test.TestSeed) Test that kmc is in the user's path ... ok test_len (seed_test.TestSeed) Test len ... ok test_write_fasta (seed_test.TestSeed) Test write_fasta ... ok ---------------------------------------------------------------------- Ran 155 tests in 19.478s OK make[1]: Leaving directory '/«BUILDDIR»/iva-1.0.6+ds' fakeroot debian/rules binary-arch dh binary-arch --with python3 --buildsystem=pybuild dh_testroot -a -O--buildsystem=pybuild dh_prep -a -O--buildsystem=pybuild dh_auto_install -a -O--buildsystem=pybuild I: pybuild base:184: /usr/bin/python3 setup.py install --root /«BUILDDIR»/iva-1.0.6+ds/debian/iva Checking dependencies found in path: OK kmc OK kmc_dump OK nucmer OK delta-filter OK show-coords OK samtools OK smalt running install running build running build_py running build_scripts running install_lib creating /«BUILDDIR»/iva-1.0.6+ds/debian/iva/usr creating /«BUILDDIR»/iva-1.0.6+ds/debian/iva/usr/lib creating /«BUILDDIR»/iva-1.0.6+ds/debian/iva/usr/lib/python3.5 creating /«BUILDDIR»/iva-1.0.6+ds/debian/iva/usr/lib/python3.5/dist-packages creating /«BUILDDIR»/iva-1.0.6+ds/debian/iva/usr/lib/python3.5/dist-packages/iva copying /«BUILDDIR»/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva/assembly.py -> /«BUILDDIR»/iva-1.0.6+ds/debian/iva/usr/lib/python3.5/dist-packages/iva copying /«BUILDDIR»/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva/graph.py -> /«BUILDDIR»/iva-1.0.6+ds/debian/iva/usr/lib/python3.5/dist-packages/iva creating /«BUILDDIR»/iva-1.0.6+ds/debian/iva/usr/lib/python3.5/dist-packages/iva/test_run_data copying /«BUILDDIR»/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva/test_run_data/reads_2.fq.gz -> /«BUILDDIR»/iva-1.0.6+ds/debian/iva/usr/lib/python3.5/dist-packages/iva/test_run_data copying /«BUILDDIR»/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva/test_run_data/reads_1.fq.gz -> /«BUILDDIR»/iva-1.0.6+ds/debian/iva/usr/lib/python3.5/dist-packages/iva/test_run_data copying /«BUILDDIR»/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva/test_run_data/hiv_pcr_primers.fa -> /«BUILDDIR»/iva-1.0.6+ds/debian/iva/usr/lib/python3.5/dist-packages/iva/test_run_data copying /«BUILDDIR»/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva/test_run_data/iva_contigs_with_trimmomatic.fasta -> /«BUILDDIR»/iva-1.0.6+ds/debian/iva/usr/lib/python3.5/dist-packages/iva/test_run_data copying /«BUILDDIR»/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva/test_run_data/reference.fasta -> /«BUILDDIR»/iva-1.0.6+ds/debian/iva/usr/lib/python3.5/dist-packages/iva/test_run_data copying /«BUILDDIR»/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva/test_run_data/iva_contigs_no_trimmomatic.fasta -> /«BUILDDIR»/iva-1.0.6+ds/debian/iva/usr/lib/python3.5/dist-packages/iva/test_run_data copying /«BUILDDIR»/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva/kcount.py -> /«BUILDDIR»/iva-1.0.6+ds/debian/iva/usr/lib/python3.5/dist-packages/iva copying /«BUILDDIR»/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva/test_data_runner.py -> /«BUILDDIR»/iva-1.0.6+ds/debian/iva/usr/lib/python3.5/dist-packages/iva creating /«BUILDDIR»/iva-1.0.6+ds/debian/iva/usr/lib/python3.5/dist-packages/iva/ratt copying /«BUILDDIR»/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva/ratt/main.ratt.pl -> /«BUILDDIR»/iva-1.0.6+ds/debian/iva/usr/lib/python3.5/dist-packages/iva/ratt copying /«BUILDDIR»/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva/ratt/embl2gff.pl -> /«BUILDDIR»/iva-1.0.6+ds/debian/iva/usr/lib/python3.5/dist-packages/iva/ratt copying /«BUILDDIR»/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva/ratt/ratt.config -> /«BUILDDIR»/iva-1.0.6+ds/debian/iva/usr/lib/python3.5/dist-packages/iva/ratt copying /«BUILDDIR»/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva/ratt/ratt_correction.pm -> /«BUILDDIR»/iva-1.0.6+ds/debian/iva/usr/lib/python3.5/dist-packages/iva/ratt copying /«BUILDDIR»/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva/ratt/genbank2embl.pl -> /«BUILDDIR»/iva-1.0.6+ds/debian/iva/usr/lib/python3.5/dist-packages/iva/ratt copying /«BUILDDIR»/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva/ratt/ratt.config.hiv -> /«BUILDDIR»/iva-1.0.6+ds/debian/iva/usr/lib/python3.5/dist-packages/iva/ratt copying /«BUILDDIR»/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva/ratt/start.ratt.sh -> /«BUILDDIR»/iva-1.0.6+ds/debian/iva/usr/lib/python3.5/dist-packages/iva/ratt copying /«BUILDDIR»/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva/qc.py -> /«BUILDDIR»/iva-1.0.6+ds/debian/iva/usr/lib/python3.5/dist-packages/iva copying /«BUILDDIR»/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva/kmers.py -> /«BUILDDIR»/iva-1.0.6+ds/debian/iva/usr/lib/python3.5/dist-packages/iva creating /«BUILDDIR»/iva-1.0.6+ds/debian/iva/usr/lib/python3.5/dist-packages/iva/gage copying /«BUILDDIR»/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva/gage/getMummerStats.sh -> /«BUILDDIR»/iva-1.0.6+ds/debian/iva/usr/lib/python3.5/dist-packages/iva/gage copying /«BUILDDIR»/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva/gage/getScaffoldStats.java -> /«BUILDDIR»/iva-1.0.6+ds/debian/iva/usr/lib/python3.5/dist-packages/iva/gage copying /«BUILDDIR»/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva/gage/GetFastaStats.class -> /«BUILDDIR»/iva-1.0.6+ds/debian/iva/usr/lib/python3.5/dist-packages/iva/gage copying /«BUILDDIR»/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva/gage/getScaffoldStats$Scaffold.class -> /«BUILDDIR»/iva-1.0.6+ds/debian/iva/usr/lib/python3.5/dist-packages/iva/gage copying /«BUILDDIR»/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva/gage/SizeFasta.class -> /«BUILDDIR»/iva-1.0.6+ds/debian/iva/usr/lib/python3.5/dist-packages/iva/gage copying /«BUILDDIR»/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva/gage/getCorrectnessStats.sh -> /«BUILDDIR»/iva-1.0.6+ds/debian/iva/usr/lib/python3.5/dist-packages/iva/gage copying /«BUILDDIR»/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva/gage/Utils$Translate.class -> /«BUILDDIR»/iva-1.0.6+ds/debian/iva/usr/lib/python3.5/dist-packages/iva/gage copying /«BUILDDIR»/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva/gage/SizeFasta.java -> /«BUILDDIR»/iva-1.0.6+ds/debian/iva/usr/lib/python3.5/dist-packages/iva/gage copying /«BUILDDIR»/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva/gage/getScaffoldStats.class -> /«BUILDDIR»/iva-1.0.6+ds/debian/iva/usr/lib/python3.5/dist-packages/iva/gage copying /«BUILDDIR»/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva/gage/colsum.pl -> /«BUILDDIR»/iva-1.0.6+ds/debian/iva/usr/lib/python3.5/dist-packages/iva/gage copying /«BUILDDIR»/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva/gage/Utils$Pair.class -> /«BUILDDIR»/iva-1.0.6+ds/debian/iva/usr/lib/python3.5/dist-packages/iva/gage copying /«BUILDDIR»/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva/gage/Utils.class -> /«BUILDDIR»/iva-1.0.6+ds/debian/iva/usr/lib/python3.5/dist-packages/iva/gage copying /«BUILDDIR»/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva/gage/GetFastaStats$ContigAt.class -> /«BUILDDIR»/iva-1.0.6+ds/debian/iva/usr/lib/python3.5/dist-packages/iva/gage copying /«BUILDDIR»/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva/gage/GetFastaStats.java -> /«BUILDDIR»/iva-1.0.6+ds/debian/iva/usr/lib/python3.5/dist-packages/iva/gage copying /«BUILDDIR»/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva/gage/Utils$ToProtein.class -> /«BUILDDIR»/iva-1.0.6+ds/debian/iva/usr/lib/python3.5/dist-packages/iva/gage copying /«BUILDDIR»/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva/gage/Utils.java -> /«BUILDDIR»/iva-1.0.6+ds/debian/iva/usr/lib/python3.5/dist-packages/iva/gage copying /«BUILDDIR»/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva/gage/SplitFastaByLetter.class -> /«BUILDDIR»/iva-1.0.6+ds/debian/iva/usr/lib/python3.5/dist-packages/iva/gage copying /«BUILDDIR»/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva/gage/SplitFastaByLetter.java -> /«BUILDDIR»/iva-1.0.6+ds/debian/iva/usr/lib/python3.5/dist-packages/iva/gage copying /«BUILDDIR»/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva/gage/getScaffoldStats$1.class -> /«BUILDDIR»/iva-1.0.6+ds/debian/iva/usr/lib/python3.5/dist-packages/iva/gage copying /«BUILDDIR»/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva/mapping.py -> /«BUILDDIR»/iva-1.0.6+ds/debian/iva/usr/lib/python3.5/dist-packages/iva copying /«BUILDDIR»/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva/contig.py -> /«BUILDDIR»/iva-1.0.6+ds/debian/iva/usr/lib/python3.5/dist-packages/iva copying /«BUILDDIR»/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva/contig_trim.py -> /«BUILDDIR»/iva-1.0.6+ds/debian/iva/usr/lib/python3.5/dist-packages/iva copying /«BUILDDIR»/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva/edge.py -> /«BUILDDIR»/iva-1.0.6+ds/debian/iva/usr/lib/python3.5/dist-packages/iva copying /«BUILDDIR»/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva/egg_extract.py -> /«BUILDDIR»/iva-1.0.6+ds/debian/iva/usr/lib/python3.5/dist-packages/iva copying /«BUILDDIR»/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva/__init__.py -> /«BUILDDIR»/iva-1.0.6+ds/debian/iva/usr/lib/python3.5/dist-packages/iva copying /«BUILDDIR»/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva/common.py -> /«BUILDDIR»/iva-1.0.6+ds/debian/iva/usr/lib/python3.5/dist-packages/iva creating /«BUILDDIR»/iva-1.0.6+ds/debian/iva/usr/lib/python3.5/dist-packages/iva/read_trim copying /«BUILDDIR»/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva/read_trim/adapters.fasta -> /«BUILDDIR»/iva-1.0.6+ds/debian/iva/usr/lib/python3.5/dist-packages/iva/read_trim copying /«BUILDDIR»/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva/mummer.py -> /«BUILDDIR»/iva-1.0.6+ds/debian/iva/usr/lib/python3.5/dist-packages/iva copying /«BUILDDIR»/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva/seed_processor.py -> /«BUILDDIR»/iva-1.0.6+ds/debian/iva/usr/lib/python3.5/dist-packages/iva copying /«BUILDDIR»/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva/kraken.py -> /«BUILDDIR»/iva-1.0.6+ds/debian/iva/usr/lib/python3.5/dist-packages/iva copying /«BUILDDIR»/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva/seed.py -> /«BUILDDIR»/iva-1.0.6+ds/debian/iva/usr/lib/python3.5/dist-packages/iva copying /«BUILDDIR»/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva/external_progs.py -> /«BUILDDIR»/iva-1.0.6+ds/debian/iva/usr/lib/python3.5/dist-packages/iva copying /«BUILDDIR»/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva/qc_external.py -> /«BUILDDIR»/iva-1.0.6+ds/debian/iva/usr/lib/python3.5/dist-packages/iva copying /«BUILDDIR»/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva/read_trim.py -> /«BUILDDIR»/iva-1.0.6+ds/debian/iva/usr/lib/python3.5/dist-packages/iva byte-compiling /«BUILDDIR»/iva-1.0.6+ds/debian/iva/usr/lib/python3.5/dist-packages/iva/assembly.py to assembly.cpython-35.pyc byte-compiling /«BUILDDIR»/iva-1.0.6+ds/debian/iva/usr/lib/python3.5/dist-packages/iva/graph.py to graph.cpython-35.pyc byte-compiling /«BUILDDIR»/iva-1.0.6+ds/debian/iva/usr/lib/python3.5/dist-packages/iva/kcount.py to kcount.cpython-35.pyc byte-compiling /«BUILDDIR»/iva-1.0.6+ds/debian/iva/usr/lib/python3.5/dist-packages/iva/test_data_runner.py to test_data_runner.cpython-35.pyc byte-compiling /«BUILDDIR»/iva-1.0.6+ds/debian/iva/usr/lib/python3.5/dist-packages/iva/qc.py to qc.cpython-35.pyc byte-compiling /«BUILDDIR»/iva-1.0.6+ds/debian/iva/usr/lib/python3.5/dist-packages/iva/kmers.py to kmers.cpython-35.pyc byte-compiling /«BUILDDIR»/iva-1.0.6+ds/debian/iva/usr/lib/python3.5/dist-packages/iva/mapping.py to mapping.cpython-35.pyc byte-compiling /«BUILDDIR»/iva-1.0.6+ds/debian/iva/usr/lib/python3.5/dist-packages/iva/contig.py to contig.cpython-35.pyc byte-compiling /«BUILDDIR»/iva-1.0.6+ds/debian/iva/usr/lib/python3.5/dist-packages/iva/contig_trim.py to contig_trim.cpython-35.pyc byte-compiling /«BUILDDIR»/iva-1.0.6+ds/debian/iva/usr/lib/python3.5/dist-packages/iva/edge.py to edge.cpython-35.pyc byte-compiling /«BUILDDIR»/iva-1.0.6+ds/debian/iva/usr/lib/python3.5/dist-packages/iva/egg_extract.py to egg_extract.cpython-35.pyc byte-compiling /«BUILDDIR»/iva-1.0.6+ds/debian/iva/usr/lib/python3.5/dist-packages/iva/__init__.py to __init__.cpython-35.pyc byte-compiling /«BUILDDIR»/iva-1.0.6+ds/debian/iva/usr/lib/python3.5/dist-packages/iva/common.py to common.cpython-35.pyc byte-compiling /«BUILDDIR»/iva-1.0.6+ds/debian/iva/usr/lib/python3.5/dist-packages/iva/mummer.py to mummer.cpython-35.pyc byte-compiling /«BUILDDIR»/iva-1.0.6+ds/debian/iva/usr/lib/python3.5/dist-packages/iva/seed_processor.py to seed_processor.cpython-35.pyc byte-compiling /«BUILDDIR»/iva-1.0.6+ds/debian/iva/usr/lib/python3.5/dist-packages/iva/kraken.py to kraken.cpython-35.pyc byte-compiling /«BUILDDIR»/iva-1.0.6+ds/debian/iva/usr/lib/python3.5/dist-packages/iva/seed.py to seed.cpython-35.pyc byte-compiling /«BUILDDIR»/iva-1.0.6+ds/debian/iva/usr/lib/python3.5/dist-packages/iva/external_progs.py to external_progs.cpython-35.pyc byte-compiling /«BUILDDIR»/iva-1.0.6+ds/debian/iva/usr/lib/python3.5/dist-packages/iva/qc_external.py to qc_external.cpython-35.pyc byte-compiling /«BUILDDIR»/iva-1.0.6+ds/debian/iva/usr/lib/python3.5/dist-packages/iva/read_trim.py to read_trim.cpython-35.pyc running install_egg_info running egg_info writing requirements to iva.egg-info/requires.txt writing dependency_links to iva.egg-info/dependency_links.txt writing iva.egg-info/PKG-INFO writing top-level names to iva.egg-info/top_level.txt reading manifest file 'iva.egg-info/SOURCES.txt' writing manifest file 'iva.egg-info/SOURCES.txt' Copying iva.egg-info to /«BUILDDIR»/iva-1.0.6+ds/debian/iva/usr/lib/python3.5/dist-packages/iva-1.0.6.egg-info Skipping SOURCES.txt running install_scripts creating /«BUILDDIR»/iva-1.0.6+ds/debian/iva/usr/bin copying build/scripts-3.5/iva -> /«BUILDDIR»/iva-1.0.6+ds/debian/iva/usr/bin copying build/scripts-3.5/iva_qc -> /«BUILDDIR»/iva-1.0.6+ds/debian/iva/usr/bin copying build/scripts-3.5/iva_qc_make_db -> /«BUILDDIR»/iva-1.0.6+ds/debian/iva/usr/bin changing mode of /«BUILDDIR»/iva-1.0.6+ds/debian/iva/usr/bin/iva to 775 changing mode of /«BUILDDIR»/iva-1.0.6+ds/debian/iva/usr/bin/iva_qc to 775 changing mode of /«BUILDDIR»/iva-1.0.6+ds/debian/iva/usr/bin/iva_qc_make_db to 775 dh_installdocs -a -O--buildsystem=pybuild dh_installchangelogs -a -O--buildsystem=pybuild debian/rules override_dh_installman make[1]: Entering directory '/«BUILDDIR»/iva-1.0.6+ds' mkdir -p /«BUILDDIR»/iva-1.0.6+ds/debian/man PYTHONPATH=. help2man -N -o /«BUILDDIR»/iva-1.0.6+ds/debian/man/iva.1 \ -n 'iterative virus assembler' \ --no-discard-stderr ./scripts/iva PYTHONPATH=. help2man -N -o /«BUILDDIR»/iva-1.0.6+ds/debian/man/iva_qc.1 \ -n 'compare an assembly to a reference' \ --no-discard-stderr ./scripts/iva_qc PYTHONPATH=. help2man -N -o /«BUILDDIR»/iva-1.0.6+ds/debian/man/iva_qc_make_db.1 \ -n 'make a database as input for iva_qc' \ --no-discard-stderr ./scripts/iva_qc_make_db dh_installman -- make[1]: Leaving directory '/«BUILDDIR»/iva-1.0.6+ds' dh_python3 -a -O--buildsystem=pybuild dh_lintian -a -O--buildsystem=pybuild dh_perl -a -O--buildsystem=pybuild dh_link -a -O--buildsystem=pybuild dh_strip_nondeterminism -a -O--buildsystem=pybuild dh_compress -a -O--buildsystem=pybuild dh_fixperms -a -O--buildsystem=pybuild dh_strip -a -O--buildsystem=pybuild dh_strip debug symbol extraction: enabling -a due to Build-Debug-Symbols: yes in /CurrentlyBuilding dh_strip debug symbol extraction: all non-arch-all packages for this build platform arm64: iva dh_strip debug symbol extraction: packages to act on: iva dh_strip debug symbol extraction: ignored packages: Using buildid for compat level >= 9 iva has no unstripped objects, ignoring find: ‘/«BUILDDIR»/iva-1.0.6+ds/debian/iva-dbgsym’: No such file or directory /usr/bin/pkg_create_dbgsym: nothing in /«BUILDDIR»/iva-1.0.6+ds/debian/iva-dbgsym and no dbgdepends, ignoring dh_makeshlibs -a -O--buildsystem=pybuild dh_shlibdeps -a -O--buildsystem=pybuild dh_installdeb -a -O--buildsystem=pybuild dh_gencontrol -a -O--buildsystem=pybuild dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe dpkg-gencontrol: warning: package iva: unused substitution variable ${perl:Depends} dh_gencontrol debug symbol wrapper: all non-arch-all packages for this build platform arm64: iva dh_gencontrol debug symbol wrapper: packages to act on: iva dh_gencontrol debug symbol wrapper: ignored packages: dh_gencontrol debug symbol wrapper: no debian/iva-dbgsym, skipping package iva dh_md5sums -a -O--buildsystem=pybuild dh_builddeb -a -O--buildsystem=pybuild INFO: pkgstriptranslations version 129 pkgstriptranslations: processing iva (in debian/iva); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/iva/DEBIAN/control, package iva, directory debian/iva pkgstripfiles: Running PNG optimization (using 4 cpus) for package iva ... pkgstripfiles: No PNG files. dpkg-deb: building package 'iva' in '../iva_1.0.6+ds-1_arm64.deb'. dpkg-genchanges --build=any -mLaunchpad Build Daemon >../iva_1.0.6+ds-1_arm64.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build iva-1.0.6+ds dpkg-buildpackage: info: binary-only upload (no source included) ──────────────────────────────────────────────────────────────────────────────── Build finished at 20160513-0515 Finished ──────── I: Built successfully ┌──────────────────────────────────────────────────────────────────────────────┐ │ Post Build Chroot │ └──────────────────────────────────────────────────────────────────────────────┘ ┌──────────────────────────────────────────────────────────────────────────────┐ │ Changes │ └──────────────────────────────────────────────────────────────────────────────┘ iva_1.0.6+ds-1_arm64.changes: ───────────────────────────── Format: 1.8 Date: Thu, 12 May 2016 09:50:41 +0000 Source: iva Binary: iva Architecture: arm64 Version: 1.0.6+ds-1 Distribution: yakkety-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Sascha Steinbiss Description: iva - iterative virus sequence assembler Changes: iva (1.0.6+ds-1) unstable; urgency=medium . * New upstream release. * Change orig tarball compression. * Add missing repack suffix to package. Checksums-Sha1: dc7f97c2d781d6980224bae3cb72780c8f91a70d 8577210 iva_1.0.6+ds-1_arm64.deb Checksums-Sha256: cd7542eab1d171ed10b8621aaf10f0d980753c362479e04be88239f660b7c594 8577210 iva_1.0.6+ds-1_arm64.deb Files: 5f6475f17b5fb79a80351bbaa4d2a247 8577210 science optional iva_1.0.6+ds-1_arm64.deb ┌──────────────────────────────────────────────────────────────────────────────┐ │ Package contents │ └──────────────────────────────────────────────────────────────────────────────┘ iva_1.0.6+ds-1_arm64.deb ──────────────────────── new debian package, version 2.0. size 8577210 bytes: control archive=3190 bytes. 1023 bytes, 22 lines control 5641 bytes, 66 lines md5sums 160 bytes, 9 lines * postinst #!/bin/sh 379 bytes, 12 lines * prerm #!/bin/sh Package: iva Version: 1.0.6+ds-1 Architecture: arm64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 8769 Depends: fastaq (>= 1.6), python3-networkx, python3-pysam, python3:any (>= 3.3.2-2~), kmc, mummer, smalt, samtools, python3-numpy, default-jre-headless Recommends: r-base-core, bioperl, trimmomatic Section: science Priority: optional Homepage: https://github.com/sanger-pathogens/iva Description: iterative virus sequence assembler IVA is a de novo assembler designed to assemble virus genomes that have no repeat sequences, using Illumina read pairs sequenced from mixed populations at extremely high depth. . IVA's main algorithm works by iteratively extending contigs using aligned read pairs. Its input can be just read pairs, or additionally you can provide an existing set of contigs to be extended. Alternatively, it can take reads together with a reference sequence. drwxr-xr-x root/root 0 2016-05-13 05:15 ./ drwxr-xr-x root/root 0 2016-05-13 05:15 ./usr/ drwxr-xr-x root/root 0 2016-05-13 05:15 ./usr/bin/ -rwxr-xr-x root/root 17240 2016-05-13 05:15 ./usr/bin/iva -rwxr-xr-x root/root 6228 2016-05-13 05:15 ./usr/bin/iva_qc -rwxr-xr-x root/root 2407 2016-05-13 05:15 ./usr/bin/iva_qc_make_db drwxr-xr-x root/root 0 2016-05-13 05:15 ./usr/lib/ drwxr-xr-x root/root 0 2016-05-13 05:15 ./usr/lib/python3/ drwxr-xr-x root/root 0 2016-05-13 05:15 ./usr/lib/python3/dist-packages/ drwxr-xr-x root/root 0 2016-05-13 05:15 ./usr/lib/python3/dist-packages/iva-1.0.6.egg-info/ -rw-r--r-- root/root 483 2016-05-13 05:15 ./usr/lib/python3/dist-packages/iva-1.0.6.egg-info/PKG-INFO -rw-r--r-- root/root 1 2016-05-13 05:15 ./usr/lib/python3/dist-packages/iva-1.0.6.egg-info/dependency_links.txt -rw-r--r-- root/root 0 2016-05-13 05:15 ./usr/lib/python3/dist-packages/iva-1.0.6.egg-info/requires.txt -rw-r--r-- root/root 4 2016-05-13 05:15 ./usr/lib/python3/dist-packages/iva-1.0.6.egg-info/top_level.txt drwxr-xr-x root/root 0 2016-05-13 05:15 ./usr/lib/python3/dist-packages/iva/ -rw-r--r-- root/root 1033 2016-05-12 07:37 ./usr/lib/python3/dist-packages/iva/__init__.py -rw-r--r-- root/root 28055 2016-05-12 07:37 ./usr/lib/python3/dist-packages/iva/assembly.py -rw-r--r-- root/root 1856 2016-05-12 07:37 ./usr/lib/python3/dist-packages/iva/common.py -rw-r--r-- root/root 1960 2016-05-12 07:37 ./usr/lib/python3/dist-packages/iva/contig.py -rw-r--r-- root/root 4391 2016-05-12 07:37 ./usr/lib/python3/dist-packages/iva/contig_trim.py -rw-r--r-- root/root 4903 2016-05-12 07:37 ./usr/lib/python3/dist-packages/iva/edge.py -rw-r--r-- root/root 3077 2016-05-12 07:37 ./usr/lib/python3/dist-packages/iva/egg_extract.py -rw-r--r-- root/root 4110 2016-05-12 07:37 ./usr/lib/python3/dist-packages/iva/external_progs.py drwxr-xr-x root/root 0 2016-05-13 05:15 ./usr/lib/python3/dist-packages/iva/gage/ -rw-r--r-- root/root 489 2016-05-13 05:15 ./usr/lib/python3/dist-packages/iva/gage/GetFastaStats$ContigAt.class -rw-r--r-- root/root 10191 2016-05-13 05:15 ./usr/lib/python3/dist-packages/iva/gage/GetFastaStats.class -rw-r--r-- root/root 14839 2016-05-12 07:37 ./usr/lib/python3/dist-packages/iva/gage/GetFastaStats.java -rw-r--r-- root/root 3408 2016-05-13 05:15 ./usr/lib/python3/dist-packages/iva/gage/SizeFasta.class -rw-r--r-- root/root 3611 2016-05-12 07:37 ./usr/lib/python3/dist-packages/iva/gage/SizeFasta.java -rw-r--r-- root/root 2621 2016-05-13 05:15 ./usr/lib/python3/dist-packages/iva/gage/SplitFastaByLetter.class -rw-r--r-- root/root 2229 2016-05-12 07:37 ./usr/lib/python3/dist-packages/iva/gage/SplitFastaByLetter.java -rw-r--r-- root/root 621 2016-05-13 05:15 ./usr/lib/python3/dist-packages/iva/gage/Utils$Pair.class -rw-r--r-- root/root 4564 2016-05-13 05:15 ./usr/lib/python3/dist-packages/iva/gage/Utils$ToProtein.class -rw-r--r-- root/root 1225 2016-05-13 05:15 ./usr/lib/python3/dist-packages/iva/gage/Utils$Translate.class -rw-r--r-- root/root 5575 2016-05-13 05:15 ./usr/lib/python3/dist-packages/iva/gage/Utils.class -rw-r--r-- root/root 9230 2016-05-12 07:37 ./usr/lib/python3/dist-packages/iva/gage/Utils.java -rwxr-xr-x root/root 80 2016-05-12 07:37 ./usr/lib/python3/dist-packages/iva/gage/colsum.pl -rwxr-xr-x root/root 1773 2016-05-12 07:37 ./usr/lib/python3/dist-packages/iva/gage/getCorrectnessStats.sh -rwxr-xr-x root/root 1430 2016-05-13 05:15 ./usr/lib/python3/dist-packages/iva/gage/getMummerStats.sh -rw-r--r-- root/root 196 2016-05-13 05:15 ./usr/lib/python3/dist-packages/iva/gage/getScaffoldStats$1.class -rw-r--r-- root/root 1229 2016-05-13 05:15 ./usr/lib/python3/dist-packages/iva/gage/getScaffoldStats$Scaffold.class -rw-r--r-- root/root 13399 2016-05-13 05:15 ./usr/lib/python3/dist-packages/iva/gage/getScaffoldStats.class -rw-r--r-- root/root 19111 2016-05-12 07:37 ./usr/lib/python3/dist-packages/iva/gage/getScaffoldStats.java -rw-r--r-- root/root 7133 2016-05-12 07:37 ./usr/lib/python3/dist-packages/iva/graph.py -rw-r--r-- root/root 9487 2016-05-12 07:37 ./usr/lib/python3/dist-packages/iva/kcount.py -rw-r--r-- root/root 3466 2016-05-12 07:37 ./usr/lib/python3/dist-packages/iva/kmers.py -rw-r--r-- root/root 16417 2016-05-12 07:37 ./usr/lib/python3/dist-packages/iva/kraken.py -rw-r--r-- root/root 13238 2016-05-12 07:37 ./usr/lib/python3/dist-packages/iva/mapping.py -rw-r--r-- root/root 8365 2016-05-12 07:37 ./usr/lib/python3/dist-packages/iva/mummer.py -rw-r--r-- root/root 36646 2016-05-12 07:37 ./usr/lib/python3/dist-packages/iva/qc.py -rw-r--r-- root/root 8190 2016-05-12 07:37 ./usr/lib/python3/dist-packages/iva/qc_external.py drwxr-xr-x root/root 0 2016-05-13 05:15 ./usr/lib/python3/dist-packages/iva/ratt/ -rwxr-xr-x root/root 1012 2016-05-12 07:37 ./usr/lib/python3/dist-packages/iva/ratt/embl2gff.pl -rwxr-xr-x root/root 1049 2016-05-12 07:37 ./usr/lib/python3/dist-packages/iva/ratt/genbank2embl.pl -rwxr-xr-x root/root 41988 2016-05-12 07:37 ./usr/lib/python3/dist-packages/iva/ratt/main.ratt.pl -rw-r--r-- root/root 90 2016-05-12 07:37 ./usr/lib/python3/dist-packages/iva/ratt/ratt.config -rw-r--r-- root/root 90 2016-05-12 07:37 ./usr/lib/python3/dist-packages/iva/ratt/ratt.config.hiv -rw-r--r-- root/root 57611 2016-05-12 07:37 ./usr/lib/python3/dist-packages/iva/ratt/ratt_correction.pm -rwxr-xr-x root/root 13201 2016-05-12 07:37 ./usr/lib/python3/dist-packages/iva/ratt/start.ratt.sh -rw-r--r-- root/root 1428 2016-05-12 07:37 ./usr/lib/python3/dist-packages/iva/read_trim.py drwxr-xr-x root/root 0 2016-05-13 05:15 ./usr/lib/python3/dist-packages/iva/read_trim/ -rw-r--r-- root/root 3143 2016-05-12 07:37 ./usr/lib/python3/dist-packages/iva/read_trim/adapters.fasta -rw-r--r-- root/root 6056 2016-05-12 07:37 ./usr/lib/python3/dist-packages/iva/seed.py -rw-r--r-- root/root 5586 2016-05-12 07:37 ./usr/lib/python3/dist-packages/iva/seed_processor.py -rw-r--r-- root/root 2443 2016-05-12 07:37 ./usr/lib/python3/dist-packages/iva/test_data_runner.py drwxr-xr-x root/root 0 2016-05-13 05:15 ./usr/lib/python3/dist-packages/iva/test_run_data/ -rw-r--r-- root/root 672 2016-05-12 07:37 ./usr/lib/python3/dist-packages/iva/test_run_data/hiv_pcr_primers.fa -rw-r--r-- root/root 9981 2016-05-12 07:37 ./usr/lib/python3/dist-packages/iva/test_run_data/iva_contigs_no_trimmomatic.fasta -rw-r--r-- root/root 9200 2016-05-12 07:37 ./usr/lib/python3/dist-packages/iva/test_run_data/iva_contigs_with_trimmomatic.fasta -rw-r--r-- root/root 3813239 2016-05-13 05:15 ./usr/lib/python3/dist-packages/iva/test_run_data/reads_1.fq.gz -rw-r--r-- root/root 4661713 2016-05-13 05:15 ./usr/lib/python3/dist-packages/iva/test_run_data/reads_2.fq.gz -rw-r--r-- root/root 9217 2016-05-12 07:37 ./usr/lib/python3/dist-packages/iva/test_run_data/reference.fasta drwxr-xr-x root/root 0 2016-05-13 05:15 ./usr/share/ drwxr-xr-x root/root 0 2016-05-13 05:15 ./usr/share/doc/ drwxr-xr-x root/root 0 2016-05-13 05:15 ./usr/share/doc/iva/ -rw-r--r-- root/root 247 2016-05-12 09:52 ./usr/share/doc/iva/changelog.Debian.gz -rw-r--r-- root/root 1487 2016-05-05 09:17 ./usr/share/doc/iva/copyright drwxr-xr-x root/root 0 2016-05-13 05:15 ./usr/share/lintian/ drwxr-xr-x root/root 0 2016-05-13 05:15 ./usr/share/lintian/overrides/ -rw-r--r-- root/root 93 2016-05-05 09:17 ./usr/share/lintian/overrides/iva drwxr-xr-x root/root 0 2016-05-13 05:15 ./usr/share/man/ drwxr-xr-x root/root 0 2016-05-13 05:15 ./usr/share/man/man1/ -rw-r--r-- root/root 2252 2016-05-13 05:15 ./usr/share/man/man1/iva.1.gz -rw-r--r-- root/root 1279 2016-05-13 05:15 ./usr/share/man/man1/iva_qc.1.gz -rw-r--r-- root/root 641 2016-05-13 05:15 ./usr/share/man/man1/iva_qc_make_db.1.gz ┌──────────────────────────────────────────────────────────────────────────────┐ │ Post Build │ └──────────────────────────────────────────────────────────────────────────────┘ ┌──────────────────────────────────────────────────────────────────────────────┐ │ Cleanup │ └──────────────────────────────────────────────────────────────────────────────┘ Not removing build depends: as requested Keeping session: ┌──────────────────────────────────────────────────────────────────────────────┐ │ Summary │ └──────────────────────────────────────────────────────────────────────────────┘ Build Architecture: arm64 Build-Space: 37324 Build-Time: 53 Distribution: yakkety-proposed Host Architecture: arm64 Install-Time: 52 Job: iva_1.0.6+ds-1.dsc Machine Architecture: arm64 Package: iva Package-Time: 107 Source-Version: 1.0.6+ds-1 Space: 37324 Status: successful Version: 1.0.6+ds-1 ──────────────────────────────────────────────────────────────────────────────── Finished at 20160513-0515 Build needed 00:01:47, 37324k disc space RUN: /usr/share/launchpad-buildd/slavebin/scan-for-processes ['scan-for-processes', 'PACKAGEBUILD-9736183'] Scanning for processes to kill in build /home/buildd/build-PACKAGEBUILD-9736183/chroot-autobuild... RUN: /usr/share/launchpad-buildd/slavebin/umount-chroot ['umount-chroot', 'PACKAGEBUILD-9736183'] Unmounting chroot for build PACKAGEBUILD-9736183... RUN: /usr/share/launchpad-buildd/slavebin/remove-build ['remove-build', 'PACKAGEBUILD-9736183'] Removing build PACKAGEBUILD-9736183