RUN: /usr/share/launchpad-buildd/slavebin/slave-prep ['slave-prep'] Forking launchpad-buildd slave process... Kernel version: Linux lgw01-28 4.4.0-81-generic #104-Ubuntu SMP Wed Jun 14 08:17:06 UTC 2017 x86_64 Buildd toolchain package versions: launchpad-buildd_144 python-lpbuildd_144 sbuild_0.67.0-2ubuntu7 bzr-builder_0.7.3+bzr174~ppa13~ubuntu14.10.1 bzr_2.7.0-2ubuntu3 git-build-recipe_0.3.4~git201611291343.dcee459~ubuntu16.04.1 git_1:2.7.4-0ubuntu1.1 dpkg-dev_1.18.4ubuntu1.2 python-debian_0.1.27ubuntu2 qemu-user-static_1:2.5+dfsg-5ubuntu10.14. Syncing the system clock with the buildd NTP service... 29 Jun 17:11:30 ntpdate[1767]: adjust time server 10.211.37.1 offset -0.000637 sec RUN: /usr/share/launchpad-buildd/slavebin/unpack-chroot ['unpack-chroot', 'PACKAGEBUILD-12827438', '/home/buildd/filecache-default/e3a0751dad18cad81698aa46cb02fd9a2acf7c0b'] Unpacking chroot for build PACKAGEBUILD-12827438 RUN: /usr/share/launchpad-buildd/slavebin/mount-chroot ['mount-chroot', 'PACKAGEBUILD-12827438'] Mounting chroot for build PACKAGEBUILD-12827438 RUN: /usr/share/launchpad-buildd/slavebin/override-sources-list ['override-sources-list', 'PACKAGEBUILD-12827438', 'deb http://ftpmaster.internal/ubuntu artful main universe', 'deb http://ftpmaster.internal/ubuntu artful-security main universe', 'deb http://ftpmaster.internal/ubuntu artful-updates main universe', 'deb http://ftpmaster.internal/ubuntu artful-proposed main universe'] Overriding sources.list in build-PACKAGEBUILD-12827438 RUN: /usr/share/launchpad-buildd/slavebin/update-debian-chroot ['update-debian-chroot', 'PACKAGEBUILD-12827438', 'amd64'] Updating debian chroot for build PACKAGEBUILD-12827438 Get:1 http://ftpmaster.internal/ubuntu artful InRelease [237 kB] Get:2 http://ftpmaster.internal/ubuntu artful-security InRelease [65.5 kB] Get:3 http://ftpmaster.internal/ubuntu artful-updates InRelease [65.5 kB] Get:4 http://ftpmaster.internal/ubuntu artful-proposed InRelease [235 kB] Get:5 http://ftpmaster.internal/ubuntu artful/main amd64 Packages [1166 kB] Get:6 http://ftpmaster.internal/ubuntu artful/main Translation-en [566 kB] Get:7 http://ftpmaster.internal/ubuntu artful/universe amd64 Packages [8272 kB] Get:8 http://ftpmaster.internal/ubuntu artful/universe Translation-en [4756 kB] Get:9 http://ftpmaster.internal/ubuntu artful-proposed/main amd64 Packages [101 kB] Get:10 http://ftpmaster.internal/ubuntu artful-proposed/main Translation-en [40.7 kB] Get:11 http://ftpmaster.internal/ubuntu artful-proposed/universe amd64 Packages [166 kB] Get:12 http://ftpmaster.internal/ubuntu artful-proposed/universe Translation-en [89.4 kB] Fetched 15.8 MB in 4s (3632 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following NEW packages will be installed: gcc-7-base The following packages will be upgraded: advancecomp apt apt-transport-https base-files bash binutils bsdutils ca-certificates cpp-6 debianutils dmsetup dpkg dpkg-dev findutils g++-6 gcc-6 gcc-6-base init init-system-helpers libapparmor1 libapt-pkg5.0 libasan3 libasn1-8-heimdal libatomic1 libaudit-common libaudit1 libblkid1 libcc1-0 libcilkrts5 libdevmapper1.02.1 libdpkg-perl libfdisk1 libgcc-6-dev libgcc1 libgcrypt20 libgnutls30 libgomp1 libgpg-error0 libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhx509-5-heimdal libip4tc0 libitm1 libkmod2 libkrb5-26-heimdal libldap-2.4-2 libldap-common liblsan0 libmount1 libmpx2 libnpth0 libperl5.24 libpng16-16 libquadmath0 libroken18-heimdal libselinux1 libsemanage-common libsemanage1 libsmartcols1 libsqlite3-0 libssl1.0.0 libstdc++-6-dev libstdc++6 libsystemd0 libtasn1-6 libtsan0 libubsan0 libudev1 libusb-0.1-4 libuuid1 libwind0-heimdal linux-libc-dev login mount openssl passwd perl perl-base perl-modules-5.24 systemd systemd-sysv tzdata util-linux 85 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 53.5 MB of archives. After this operation, 579 kB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu artful/main amd64 libperl5.24 amd64 5.24.1-4ubuntu1 [3460 kB] Get:2 http://ftpmaster.internal/ubuntu artful/main amd64 perl amd64 5.24.1-4ubuntu1 [219 kB] Get:3 http://ftpmaster.internal/ubuntu artful/main amd64 perl-base amd64 5.24.1-4ubuntu1 [1343 kB] Get:4 http://ftpmaster.internal/ubuntu artful/main amd64 perl-modules-5.24 all 5.24.1-4ubuntu1 [2663 kB] Get:5 http://ftpmaster.internal/ubuntu artful-proposed/main amd64 init-system-helpers all 1.48 [37.8 kB] Get:6 http://ftpmaster.internal/ubuntu artful-proposed/main amd64 base-files amd64 9.6ubuntu101 [59.1 kB] Get:7 http://ftpmaster.internal/ubuntu artful/main amd64 debianutils amd64 4.8.1.1 [85.6 kB] Get:8 http://ftpmaster.internal/ubuntu artful/main amd64 bash amd64 4.4-5ubuntu1 [625 kB] Get:9 http://ftpmaster.internal/ubuntu artful/main amd64 bsdutils amd64 1:2.29-1ubuntu3 [55.5 kB] Get:10 http://ftpmaster.internal/ubuntu artful/main amd64 dpkg amd64 1.18.24ubuntu1 [1140 kB] Get:11 http://ftpmaster.internal/ubuntu artful/main amd64 findutils amd64 4.6.0+git+20170606-2 [293 kB] Get:12 http://ftpmaster.internal/ubuntu artful/main amd64 login amd64 1:4.2-3.2ubuntu2 [304 kB] Get:13 http://ftpmaster.internal/ubuntu artful/main amd64 util-linux amd64 2.29-1ubuntu3 [913 kB] Get:14 http://ftpmaster.internal/ubuntu artful/main amd64 mount amd64 2.29-1ubuntu3 [130 kB] Get:15 http://ftpmaster.internal/ubuntu artful/main amd64 gcc-7-base amd64 7.1.0-7ubuntu1 [18.5 kB] Get:16 http://ftpmaster.internal/ubuntu artful/main amd64 libgcc1 amd64 1:7.1.0-7ubuntu1 [39.3 kB] Get:17 http://ftpmaster.internal/ubuntu artful/main amd64 libstdc++6 amd64 7.1.0-7ubuntu1 [403 kB] Get:18 http://ftpmaster.internal/ubuntu artful-proposed/main amd64 libapt-pkg5.0 amd64 1.4.6 [783 kB] Get:19 http://ftpmaster.internal/ubuntu artful-proposed/main amd64 apt amd64 1.4.6 [1096 kB] Get:20 http://ftpmaster.internal/ubuntu artful/main amd64 libip4tc0 amd64 1.6.0+snapshot20161117-6ubuntu1 [19.4 kB] Get:21 http://ftpmaster.internal/ubuntu artful/main amd64 libapparmor1 amd64 2.11.0-2ubuntu8 [29.8 kB] Get:22 http://ftpmaster.internal/ubuntu artful/main amd64 libaudit-common all 1:2.6.6-1ubuntu2 [4626 B] Get:23 http://ftpmaster.internal/ubuntu artful/main amd64 libaudit1 amd64 1:2.6.6-1ubuntu2 [37.6 kB] Get:24 http://ftpmaster.internal/ubuntu artful/main amd64 libselinux1 amd64 2.6-3build1 [67.5 kB] Get:25 http://ftpmaster.internal/ubuntu artful/main amd64 libsemanage-common all 2.6-2build1 [6738 B] Get:26 http://ftpmaster.internal/ubuntu artful/main amd64 libsemanage1 amd64 2.6-2build1 [82.2 kB] Get:27 http://ftpmaster.internal/ubuntu artful/main amd64 passwd amd64 1:4.2-3.2ubuntu2 [781 kB] Get:28 http://ftpmaster.internal/ubuntu artful/main amd64 libuuid1 amd64 2.29-1ubuntu3 [14.8 kB] Get:29 http://ftpmaster.internal/ubuntu artful/main amd64 libblkid1 amd64 2.29-1ubuntu3 [110 kB] Get:30 http://ftpmaster.internal/ubuntu artful-proposed/main amd64 libgpg-error0 amd64 1.27-3 [36.4 kB] Get:31 http://ftpmaster.internal/ubuntu artful/main amd64 libgcrypt20 amd64 1.7.7-2 [400 kB] Get:32 http://ftpmaster.internal/ubuntu artful/main amd64 libkmod2 amd64 24-1ubuntu1 [39.9 kB] Get:33 http://ftpmaster.internal/ubuntu artful/main amd64 libmount1 amd64 2.29-1ubuntu3 [119 kB] Get:34 http://ftpmaster.internal/ubuntu artful-proposed/main amd64 systemd amd64 233-8ubuntu2 [2444 kB] Get:35 http://ftpmaster.internal/ubuntu artful-proposed/main amd64 libsystemd0 amd64 233-8ubuntu2 [211 kB] Get:36 http://ftpmaster.internal/ubuntu artful-proposed/main amd64 init amd64 1.48 [5806 B] Get:37 http://ftpmaster.internal/ubuntu artful-proposed/main amd64 systemd-sysv amd64 233-8ubuntu2 [12.4 kB] Get:38 http://ftpmaster.internal/ubuntu artful/main amd64 libfdisk1 amd64 2.29-1ubuntu3 [145 kB] Get:39 http://ftpmaster.internal/ubuntu artful/main amd64 libsmartcols1 amd64 2.29-1ubuntu3 [69.4 kB] Get:40 http://ftpmaster.internal/ubuntu artful-proposed/main amd64 libudev1 amd64 233-8ubuntu2 [56.9 kB] Get:41 http://ftpmaster.internal/ubuntu artful/main amd64 libdevmapper1.02.1 amd64 2:1.02.137-2ubuntu2 [135 kB] Get:42 http://ftpmaster.internal/ubuntu artful/main amd64 dmsetup amd64 2:1.02.137-2ubuntu2 [71.8 kB] Get:43 http://ftpmaster.internal/ubuntu artful/main amd64 libroken18-heimdal amd64 7.1.0+dfsg-13 [40.8 kB] Get:44 http://ftpmaster.internal/ubuntu artful/main amd64 libasn1-8-heimdal amd64 7.1.0+dfsg-13 [176 kB] Get:45 http://ftpmaster.internal/ubuntu artful/main amd64 libtasn1-6 amd64 4.12-2 [35.6 kB] Get:46 http://ftpmaster.internal/ubuntu artful/main amd64 libgnutls30 amd64 3.5.8-6ubuntu1 [675 kB] Get:47 http://ftpmaster.internal/ubuntu artful/main amd64 libheimbase1-heimdal amd64 7.1.0+dfsg-13 [29.1 kB] Get:48 http://ftpmaster.internal/ubuntu artful/main amd64 libhcrypto4-heimdal amd64 7.1.0+dfsg-13 [88.1 kB] Get:49 http://ftpmaster.internal/ubuntu artful/main amd64 libwind0-heimdal amd64 7.1.0+dfsg-13 [47.9 kB] Get:50 http://ftpmaster.internal/ubuntu artful/main amd64 libhx509-5-heimdal amd64 7.1.0+dfsg-13 [107 kB] Get:51 http://ftpmaster.internal/ubuntu artful/main amd64 libsqlite3-0 amd64 3.16.2-5 [486 kB] Get:52 http://ftpmaster.internal/ubuntu artful/main amd64 libkrb5-26-heimdal amd64 7.1.0+dfsg-13 [206 kB] Get:53 http://ftpmaster.internal/ubuntu artful/main amd64 libheimntlm0-heimdal amd64 7.1.0+dfsg-13 [15.1 kB] Get:54 http://ftpmaster.internal/ubuntu artful/main amd64 libgssapi3-heimdal amd64 7.1.0+dfsg-13 [97.5 kB] Get:55 http://ftpmaster.internal/ubuntu artful-proposed/main amd64 libldap-2.4-2 amd64 2.4.44+dfsg-7ubuntu1 [155 kB] Get:56 http://ftpmaster.internal/ubuntu artful-proposed/main amd64 libldap-common all 2.4.44+dfsg-7ubuntu1 [16.4 kB] Get:57 http://ftpmaster.internal/ubuntu artful/main amd64 libnpth0 amd64 1.5-2 [7622 B] Get:58 http://ftpmaster.internal/ubuntu artful/main amd64 libssl1.0.0 amd64 1.0.2g-1ubuntu13 [1081 kB] Get:59 http://ftpmaster.internal/ubuntu artful/main amd64 tzdata all 2017b-2 [203 kB] Get:60 http://ftpmaster.internal/ubuntu artful-proposed/main amd64 apt-transport-https amd64 1.4.6 [34.2 kB] Get:61 http://ftpmaster.internal/ubuntu artful/main amd64 openssl amd64 1.0.2g-1ubuntu13 [491 kB] Get:62 http://ftpmaster.internal/ubuntu artful/main amd64 ca-certificates all 20161130+nmu1 [186 kB] Get:63 http://ftpmaster.internal/ubuntu artful/main amd64 libpng16-16 amd64 1.6.29-3 [173 kB] Get:64 http://ftpmaster.internal/ubuntu artful/main amd64 advancecomp amd64 2.0-1 [198 kB] Get:65 http://ftpmaster.internal/ubuntu artful-proposed/main amd64 binutils amd64 2.28.51.20170627-1ubuntu1 [2474 kB] Get:66 http://ftpmaster.internal/ubuntu artful/main amd64 libquadmath0 amd64 7.1.0-7ubuntu1 [132 kB] Get:67 http://ftpmaster.internal/ubuntu artful/main amd64 libitm1 amd64 7.1.0-7ubuntu1 [27.6 kB] Get:68 http://ftpmaster.internal/ubuntu artful/main amd64 libmpx2 amd64 7.1.0-7ubuntu1 [11.7 kB] Get:69 http://ftpmaster.internal/ubuntu artful/main amd64 liblsan0 amd64 7.1.0-7ubuntu1 [126 kB] Get:70 http://ftpmaster.internal/ubuntu artful/main amd64 libtsan0 amd64 7.1.0-7ubuntu1 [275 kB] Get:71 http://ftpmaster.internal/ubuntu artful/main amd64 libubsan0 amd64 7.1.0-7ubuntu1 [119 kB] Get:72 http://ftpmaster.internal/ubuntu artful/main amd64 libcilkrts5 amd64 7.1.0-7ubuntu1 [42.3 kB] Get:73 http://ftpmaster.internal/ubuntu artful/main amd64 libgomp1 amd64 7.1.0-7ubuntu1 [76.3 kB] Get:74 http://ftpmaster.internal/ubuntu artful/main amd64 libatomic1 amd64 7.1.0-7ubuntu1 [8900 B] Get:75 http://ftpmaster.internal/ubuntu artful-proposed/main amd64 libasan3 amd64 6.3.0-21ubuntu1 [315 kB] Get:76 http://ftpmaster.internal/ubuntu artful-proposed/main amd64 g++-6 amd64 6.3.0-21ubuntu1 [7400 kB] Get:77 http://ftpmaster.internal/ubuntu artful-proposed/main amd64 libstdc++-6-dev amd64 6.3.0-21ubuntu1 [1409 kB] Get:78 http://ftpmaster.internal/ubuntu artful-proposed/main amd64 gcc-6 amd64 6.3.0-21ubuntu1 [7243 kB] Get:79 http://ftpmaster.internal/ubuntu artful-proposed/main amd64 libgcc-6-dev amd64 6.3.0-21ubuntu1 [2305 kB] Get:80 http://ftpmaster.internal/ubuntu artful/main amd64 libcc1-0 amd64 7.1.0-7ubuntu1 [38.5 kB] Get:81 http://ftpmaster.internal/ubuntu artful-proposed/main amd64 cpp-6 amd64 6.3.0-21ubuntu1 [6590 kB] Get:82 http://ftpmaster.internal/ubuntu artful-proposed/main amd64 gcc-6-base amd64 6.3.0-21ubuntu1 [17.8 kB] Get:83 http://ftpmaster.internal/ubuntu artful/main amd64 dpkg-dev all 1.18.24ubuntu1 [608 kB] Get:84 http://ftpmaster.internal/ubuntu artful/main amd64 libdpkg-perl all 1.18.24ubuntu1 [209 kB] Get:85 http://ftpmaster.internal/ubuntu artful/main amd64 libusb-0.1-4 amd64 2:0.1.12-31 [17.1 kB] Get:86 http://ftpmaster.internal/ubuntu artful-proposed/main amd64 linux-libc-dev amd64 4.11.0-9.14 [926 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 53.5 MB in 5s (10.4 MB/s) (Reading database ... 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Unpacking libusb-0.1-4:amd64 (2:0.1.12-31) over (2:0.1.12-30) ... Preparing to unpack .../45-linux-libc-dev_4.11.0-9.14_amd64.deb ... Unpacking linux-libc-dev:amd64 (4.11.0-9.14) over (4.10.0-20.22) ... Setting up libquadmath0:amd64 (7.1.0-7ubuntu1) ... Setting up libnpth0:amd64 (1.5-2) ... Setting up libgomp1:amd64 (7.1.0-7ubuntu1) ... Setting up libatomic1:amd64 (7.1.0-7ubuntu1) ... Setting up perl-modules-5.24 (5.24.1-4ubuntu1) ... Setting up libperl5.24:amd64 (5.24.1-4ubuntu1) ... Setting up libcc1-0:amd64 (7.1.0-7ubuntu1) ... Setting up apt-transport-https (1.4.6) ... Setting up libssl1.0.0:amd64 (1.0.2g-1ubuntu13) ... Setting up libpng16-16:amd64 (1.6.29-3) ... Setting up libldap-common (2.4.44+dfsg-7ubuntu1) ... Setting up libcilkrts5:amd64 (7.1.0-7ubuntu1) ... Setting up tzdata (2017b-2) ... Current default time zone: 'Etc/UTC' Local time is now: Thu Jun 29 17:12:21 UTC 2017. Universal Time is now: Thu Jun 29 17:12:21 UTC 2017. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up systemd-sysv (233-8ubuntu2) ... Setting up libubsan0:amd64 (7.1.0-7ubuntu1) ... Setting up libtsan0:amd64 (7.1.0-7ubuntu1) ... Setting up gcc-6-base:amd64 (6.3.0-21ubuntu1) ... Setting up linux-libc-dev:amd64 (4.11.0-9.14) ... Setting up advancecomp (2.0-1) ... Setting up libroken18-heimdal:amd64 (7.1.0+dfsg-13) ... Setting up libdevmapper1.02.1:amd64 (2:1.02.137-2ubuntu2) ... Setting up libtasn1-6:amd64 (4.12-2) ... Setting up liblsan0:amd64 (7.1.0-7ubuntu1) ... Setting up perl (5.24.1-4ubuntu1) ... Setting up libmpx2:amd64 (7.1.0-7ubuntu1) ... Processing triggers for libc-bin (2.24-9ubuntu2) ... Setting up libheimbase1-heimdal:amd64 (7.1.0+dfsg-13) ... Setting up openssl (1.0.2g-1ubuntu13) ... Setting up libsqlite3-0:amd64 (3.16.2-5) ... Setting up dmsetup (2:1.02.137-2ubuntu2) ... Setting up binutils (2.28.51.20170627-1ubuntu1) ... Setting up cpp-6 (6.3.0-21ubuntu1) ... Setting up ca-certificates (20161130+nmu1) ... Updating certificates in /etc/ssl/certs... 0 added, 7 removed; done. Setting up libusb-0.1-4:amd64 (2:0.1.12-31) ... Setting up libitm1:amd64 (7.1.0-7ubuntu1) ... Setting up libasan3:amd64 (6.3.0-21ubuntu1) ... Setting up libgcc-6-dev:amd64 (6.3.0-21ubuntu1) ... Setting up libstdc++-6-dev:amd64 (6.3.0-21ubuntu1) ... Setting up libwind0-heimdal:amd64 (7.1.0+dfsg-13) ... Setting up init (1.48) ... Setting up libasn1-8-heimdal:amd64 (7.1.0+dfsg-13) ... Setting up libhcrypto4-heimdal:amd64 (7.1.0+dfsg-13) ... Setting up libgnutls30:amd64 (3.5.8-6ubuntu1) ... Setting up libdpkg-perl (1.18.24ubuntu1) ... Setting up libhx509-5-heimdal:amd64 (7.1.0+dfsg-13) ... Setting up gcc-6 (6.3.0-21ubuntu1) ... Setting up g++-6 (6.3.0-21ubuntu1) ... Setting up dpkg-dev (1.18.24ubuntu1) ... Setting up libkrb5-26-heimdal:amd64 (7.1.0+dfsg-13) ... Setting up libheimntlm0-heimdal:amd64 (7.1.0+dfsg-13) ... Setting up libgssapi3-heimdal:amd64 (7.1.0+dfsg-13) ... Setting up libldap-2.4-2:amd64 (2.4.44+dfsg-7ubuntu1) ... Processing triggers for libc-bin (2.24-9ubuntu2) ... Processing triggers for ca-certificates (20161130+nmu1) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package ['sbuild-package', 'PACKAGEBUILD-12827438', 'amd64', 'artful-proposed', '-c', 'chroot:autobuild', '--arch=amd64', '--dist=artful-proposed', '--purge=never', '--nolog', '-A', 'ariba_2.10.0+ds-1.dsc'] Initiating build PACKAGEBUILD-12827438 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.4.0-81-generic #104-Ubuntu SMP Wed Jun 14 08:17:06 UTC 2017 x86_64 sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on lgw01-28.buildd +==============================================================================+ | ariba 2.10.0+ds-1 (amd64) 29 Jun 2017 17:12 | +==============================================================================+ Package: ariba Version: 2.10.0+ds-1 Source Version: 2.10.0+ds-1 Distribution: artful-proposed Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 I: NOTICE: Log filtering will replace 'build/ariba-8tsDXb/ariba-2.10.0+ds' with '<>' I: NOTICE: Log filtering will replace 'build/ariba-8tsDXb' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-12827438/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- ariba_2.10.0+ds-1.dsc exists in .; copying to chroot Check architectures ------------------- Check dependencies ------------------ Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<>/resolver-_MN30j/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/<>/resolver-_MN30j/apt_archive ./ InRelease Get:2 copy:/<>/resolver-_MN30j/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-_MN30j/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-_MN30j/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-_MN30j/apt_archive ./ Packages [525 B] Fetched 2858 B in 0s (187 kB/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install core build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following NEW packages will be installed: sbuild-build-depends-core-dummy 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 780 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-_MN30j/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [780 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 780 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... (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 ... 12505 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_amd64.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... Merged Build-Depends: debhelper (>= 9), python3, python3-dev, python3-dendropy (>= 4.2.0), python3-setuptools, python3-pymummer (>= 0.10.2), python3-pysam (>= 0.9.1), python3-nose (>= 1.3), python3-bs4 (>= 4.1.0), python3-matplotlib, python3-tk, bowtie2 (>= 2.1.0), cd-hit, mash, libminimap-dev, libfml-dev (>= 0.1-3), mummer, fastaq (>= 3.12.0), help2man, asciidoctor Filtered Build-Depends: debhelper (>= 9), python3, python3-dev, python3-dendropy (>= 4.2.0), python3-setuptools, python3-pymummer (>= 0.10.2), python3-pysam (>= 0.9.1), python3-nose (>= 1.3), python3-bs4 (>= 4.1.0), python3-matplotlib, python3-tk, bowtie2 (>= 2.1.0), cd-hit, mash, libminimap-dev, libfml-dev (>= 0.1-3), mummer, fastaq (>= 3.12.0), help2man, asciidoctor dpkg-deb: building package 'sbuild-build-depends-ariba-dummy' in '/<>/resolver-fmV96H/apt_archive/sbuild-build-depends-ariba-dummy.deb'. Ign:1 copy:/<>/resolver-fmV96H/apt_archive ./ InRelease Get:2 copy:/<>/resolver-fmV96H/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-fmV96H/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-fmV96H/apt_archive ./ Sources [353 B] Get:5 copy:/<>/resolver-fmV96H/apt_archive ./ Packages [674 B] Fetched 3146 B in 0s (246 kB/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install ariba build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: asciidoctor autoconf automake autopoint autotools-dev blt bowtie2 bsdmainutils cd-hit debhelper dh-autoreconf dh-python dh-strip-nondeterminism fastaq file fontconfig-config fonts-lyx gawk gettext gettext-base groff-base help2man intltool-debian libarchive-zip-perl libblas-common libblas3 libbsd0 libcapnp-0.5.3 libcroco3 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl libfml-dev libfml0 libfontconfig1 libfreetype6 libgfortran3 libglib2.0-0 libgsl2 libhts1 libhts2 libicu57 libjs-jquery libjs-jquery-ui liblapack3 liblocale-gettext-perl libmagic-mgc libmagic1 libminimap-dev libminimap0 libmpdec2 libpipeline1 libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libpython3-dev libpython3-stdlib libpython3.5 libpython3.5-dev libpython3.5-minimal libpython3.5-stdlib libpython3.6-minimal libpython3.6-stdlib libruby2.3 libsigsegv2 libtbb2 libtcl8.6 libtimedate-perl libtk8.6 libtool libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxss1 libyaml-0-2 m4 man-db mash mime-support mummer po-debconf python python-matplotlib-data python-minimal python2.7 python2.7-minimal python3 python3-bs4 python3-cycler python3-dateutil python3-dendropy python3-dev python3-matplotlib python3-minimal python3-nose python3-numpy python3-pkg-resources python3-pymummer python3-pyparsing python3-pysam python3-setuptools python3-six python3-tk python3-tz python3.5 python3.5-dev python3.5-minimal python3.6 python3.6-minimal rake ruby ruby-did-you-mean ruby-minitest ruby-net-telnet ruby-power-assert ruby-test-unit ruby2.3 rubygems-integration samtools tk8.6-blt2.5 ttf-bitstream-vera ucf x11-common zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc blt-demo bowtie2-examples wamerican | wordlist whois vacation dh-make gawk-doc gettext-doc libasprintf-dev libgettextpo-dev groff gsl-ref-psdoc | gsl-doc-pdf | gsl-doc-info | gsl-ref-html libjs-jquery-ui-docs tcl8.6 tk8.6 libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc less www-browser libmail-box-perl python-doc python-tk python2.7-doc binfmt-support python3-doc python3-venv python-cycler-doc dvipng ffmpeg gir1.2-gtk-3.0 ghostscript inkscape ipython3 librsvg2-common python-matplotlib-doc python3-cairocffi python3-gi python3-gi-cairo python3-gobject python3-pyqt4 python3-scipy python3-sip python3-tornado texlive-extra-utils texlive-latex-extra ttf-staypuft python-nose-doc gfortran python-numpy-doc python3-numpy-dbg python-pyparsing-doc python-setuptools-doc tix python3-tk-dbg python3.5-venv python3.5-doc python3.6-venv python3.6-doc ri ruby-dev bundler Recommended packages: curl | wget | lynx-cur libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs javascript-common libltdl-dev xml-core libmail-sendmail-perl python3-chardet python3-lxml python3-pil zip fonts-lato The following packages will be REMOVED: pkg-create-dbgsym* The following NEW packages will be installed: asciidoctor autoconf automake autopoint autotools-dev blt bowtie2 bsdmainutils cd-hit debhelper dh-autoreconf dh-python dh-strip-nondeterminism fastaq file fontconfig-config fonts-lyx gawk gettext gettext-base groff-base help2man intltool-debian libarchive-zip-perl libblas-common libblas3 libbsd0 libcapnp-0.5.3 libcroco3 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl libfml-dev libfml0 libfontconfig1 libfreetype6 libgfortran3 libglib2.0-0 libgsl2 libhts1 libhts2 libicu57 libjs-jquery libjs-jquery-ui liblapack3 liblocale-gettext-perl libmagic-mgc libmagic1 libminimap-dev libminimap0 libmpdec2 libpipeline1 libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libpython3-dev libpython3-stdlib libpython3.5 libpython3.5-dev libpython3.5-minimal libpython3.5-stdlib libpython3.6-minimal libpython3.6-stdlib libruby2.3 libsigsegv2 libtbb2 libtcl8.6 libtimedate-perl libtk8.6 libtool libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxss1 libyaml-0-2 m4 man-db mash mime-support mummer po-debconf python python-matplotlib-data python-minimal python2.7 python2.7-minimal python3 python3-bs4 python3-cycler python3-dateutil python3-dendropy python3-dev python3-matplotlib python3-minimal python3-nose python3-numpy python3-pkg-resources python3-pymummer python3-pyparsing python3-pysam python3-setuptools python3-six python3-tk python3-tz python3.5 python3.5-dev python3.5-minimal python3.6 python3.6-minimal rake ruby ruby-did-you-mean ruby-minitest ruby-net-telnet ruby-power-assert ruby-test-unit ruby2.3 rubygems-integration samtools sbuild-build-depends-ariba-dummy tk8.6-blt2.5 ttf-bitstream-vera ucf x11-common zlib1g-dev 0 upgraded, 131 newly installed, 1 to remove and 0 not upgraded. Need to get 103 MB of archives. After this operation, 366 MB of additional disk space will be used. 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Setting up libglib2.0-0:amd64 (2.53.3-1) ... No schema files found: doing nothing. Setting up libcapnp-0.5.3:amd64 (0.5.3-2ubuntu2) ... Setting up gettext-base (0.19.8.1-2ubuntu1) ... Setting up libpipeline1:amd64 (1.4.1-2) ... Setting up libgsl2:amd64 (2.3+dfsg-1) ... Setting up m4 (1.4.18-1) ... Setting up gawk (1:4.1.4+dfsg-1) ... Setting up libicu57:amd64 (57.1-6) ... Setting up libbsd0:amd64 (0.8.5-1) ... Setting up ucf (3.0036) ... Setting up libxml2:amd64 (2.9.4+dfsg1-2.2ubuntu1) ... Setting up libfreetype6:amd64 (2.6.3-3.2ubuntu1) ... Setting up libmagic-mgc (1:5.30-1) ... Setting up libmagic1:amd64 (1:5.30-1) ... Setting up libcroco3:amd64 (0.6.11-3) ... Setting up libpython3.6-minimal:amd64 (3.6.2~rc1-1) ... Setting up ruby-did-you-mean (1.0.0-2) ... Setting up libyaml-0-2:amd64 (0.1.7-2ubuntu2) ... Setting up libblas3 (3.7.0-2) ... update-alternatives: using /usr/lib/libblas/libblas.so.3 to provide /usr/lib/libblas.so.3 (libblas.so.3) in auto mode Setting up libminimap0 (0.2-3) ... Processing triggers for libc-bin (2.24-9ubuntu2) ... Setting up autotools-dev (20161112.1) ... Setting up libjs-jquery-ui (1.12.1+dfsg-4) ... Processing triggers for systemd (233-8ubuntu2) ... Setting up libfml0 (0.1-4) ... Setting up ruby-net-telnet (0.1.1-2) ... Setting up liblocale-gettext-perl (1.07-3build1) ... Setting up rubygems-integration (1.11) ... Setting up libexpat1-dev:amd64 (2.2.1-2) ... Setting up ttf-bitstream-vera (1.10-8) ... Setting up libtcl8.6:amd64 (8.6.6+dfsg-1) ... Setting up libxdmcp6:amd64 (1:1.1.2-3) ... Setting up bsdmainutils (9.0.12ubuntu1) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up ruby-minitest (5.9.0-1) ... Setting up x11-common (1:7.7+19ubuntu1) ... 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 libhts2:amd64 (1.4.1-2ubuntu1) ... Setting up libx11-data (2:1.6.4-3) ... Setting up libpython2.7-stdlib:amd64 (2.7.13-2) ... Setting up libxau6:amd64 (1:1.0.8-1) ... Setting up autopoint (0.19.8.1-2ubuntu1) ... Setting up libmpdec2:amd64 (2.4.2-1) ... Setting up ruby-power-assert (0.3.0-1) ... Setting up fonts-lyx (2.2.3-1) ... Setting up zlib1g-dev:amd64 (1:1.2.11.dfsg-0ubuntu1) ... Setting up libfile-stripnondeterminism-perl (0.035-2) ... Setting up libpython3.6-stdlib:amd64 (3.6.2~rc1-1) ... Setting up fontconfig-config (2.11.94-0ubuntu2) ... Setting up mash (1.1.1-2) ... Setting up python-matplotlib-data (2.0.0+dfsg1-2ubuntu2) ... Setting up ruby-test-unit (3.1.7-2) ... Setting up gettext (0.19.8.1-2ubuntu1) ... Setting up mummer (3.23+dfsg-2) ... Setting up liblapack3 (3.7.0-2) ... update-alternatives: using /usr/lib/lapack/liblapack.so.3 to provide /usr/lib/liblapack.so.3 (liblapack.so.3) in auto mode Setting up libpython3.5-stdlib:amd64 (3.5.3-3) ... Setting up python3.6-minimal (3.6.2~rc1-1) ... Setting up python2.7 (2.7.13-2) ... Setting up libminimap-dev (0.2-3) ... Setting up libfml-dev (0.1-4) ... Setting up autoconf (2.69-10) ... Setting up file (1:5.30-1) ... Setting up libpython-stdlib:amd64 (2.7.13-2) ... Setting up intltool-debian (0.35.0+20060710.4) ... Setting up automake (1:1.15-6ubuntu1) ... update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode Setting up help2man (1.47.4) ... Setting up man-db (2.7.6.1-2) ... Not building database; man-db/auto-update is not 'true'. Setting up samtools (1.4.1-1) ... Setting up libxcb1:amd64 (1.11.1-1ubuntu1) ... Setting up python (2.7.13-2) ... Setting up libtool (2.4.6-2) ... Setting up python3.5 (3.5.3-3) ... Setting up libpython3-stdlib:amd64 (3.5.3-1ubuntu3) ... Setting up libfontconfig1:amd64 (2.11.94-0ubuntu2) ... Setting up python3.6 (3.6.2~rc1-1) ... Setting up po-debconf (1.0.20) ... Setting up libpython3.5:amd64 (3.5.3-3) ... Setting up libx11-6:amd64 (2:1.6.4-3) ... Setting up libpython3.5-dev:amd64 (3.5.3-3) ... Setting up bowtie2 (2.3.1-1) ... Setting up libxrender1:amd64 (1:0.9.10-1) ... Setting up libxft2:amd64 (2.3.2-1) ... Setting up python3.5-dev (3.5.3-3) ... Setting up libpython3-dev:amd64 (3.5.3-1ubuntu3) ... Setting up libxext6:amd64 (2:1.3.3-1) ... Setting up libxss1:amd64 (1:1.2.2-1) ... Setting up libtk8.6:amd64 (8.6.6-1) ... Setting up tk8.6-blt2.5 (2.5.3+dfsg-3) ... Setting up blt (2.5.3+dfsg-3) ... Setting up python3 (3.5.3-1ubuntu3) ... Setting up python3-numpy (1:1.12.1-3ubuntu1) ... Setting up rake (10.5.0-2) ... Setting up python3-six (1.10.0-4) ... Setting up python3-pyparsing (2.1.10+dfsg1-1) ... Setting up python3-cycler (0.10.0-1) ... Setting up python3-dev (3.5.3-1ubuntu3) ... Setting up python3-pkg-resources (36.0.1-1) ... Setting up python3-bs4 (4.6.0-1) ... Setting up fastaq (3.15.0-2) ... Setting up dh-strip-nondeterminism (0.035-2) ... Setting up python3-pysam (0.10.0+ds-2build1) ... Setting up python3-nose (1.3.7-2) ... Setting up python3-tk:amd64 (3.5.3-2) ... Setting up python3-setuptools (36.0.1-1) ... Setting up python3-pymummer (0.10.2-1) ... Setting up python3-dendropy (4.2.0+dfsg-1) ... Setting up libruby2.3:amd64 (2.3.3-1ubuntu1) ... Setting up dh-python (2.20170125) ... Setting up python3-tz (2017.2-2) ... Setting up python3-dateutil (2.5.3-2) ... Setting up debhelper (10.4ubuntu3) ... Setting up dh-autoreconf (14) ... Setting up ruby2.3 (2.3.3-1ubuntu1) ... Setting up ruby (1:2.3.3) ... Setting up python3-matplotlib (2.0.0+dfsg1-2ubuntu2) ... Setting up asciidoctor (1.5.4-2) ... Setting up sbuild-build-depends-ariba-dummy (0.invalid.0) ... 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Processing triggers for systemd (233-8ubuntu2) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.4.0-81-generic amd64 (x86_64) Toolchain package versions: binutils_2.28.51.20170627-1ubuntu1 dpkg-dev_1.18.24ubuntu1 g++-6_6.3.0-21ubuntu1 gcc-6_6.3.0-21ubuntu1 libc6-dev_2.24-9ubuntu2 libstdc++-6-dev_6.3.0-21ubuntu1 libstdc++6_7.1.0-7ubuntu1 linux-libc-dev_4.11.0-9.14 Package versions: adduser_3.113+nmu3ubuntu5 advancecomp_2.0-1 apt_1.4.6 apt-transport-https_1.4.6 asciidoctor_1.5.4-2 autoconf_2.69-10 automake_1:1.15-6ubuntu1 autopoint_0.19.8.1-2ubuntu1 autotools-dev_20161112.1 base-files_9.6ubuntu101 base-passwd_3.5.43 bash_4.4-5ubuntu1 binutils_2.28.51.20170627-1ubuntu1 blt_2.5.3+dfsg-3 bowtie2_2.3.1-1 bsdmainutils_9.0.12ubuntu1 bsdutils_1:2.29-1ubuntu3 build-essential_12.1ubuntu2 bzip2_1.0.6-8.1 ca-certificates_20161130+nmu1 cd-hit_4.6.7-1 coreutils_8.26-3ubuntu3 cpp_4:6.3.0-2ubuntu1 cpp-6_6.3.0-21ubuntu1 dash_0.5.8-2.3ubuntu1 debconf_1.5.60ubuntu1 debhelper_10.4ubuntu3 debianutils_4.8.1.1 dh-autoreconf_14 dh-python_2.20170125 dh-strip-nondeterminism_0.035-2 diffutils_1:3.5-3 dmsetup_2:1.02.137-2ubuntu2 dpkg_1.18.24ubuntu1 dpkg-dev_1.18.24ubuntu1 e2fslibs_1.43.4-2 e2fsprogs_1.43.4-2 fakeroot_1.21-1ubuntu2 fastaq_3.15.0-2 file_1:5.30-1 findutils_4.6.0+git+20170606-2 fontconfig-config_2.11.94-0ubuntu2 fonts-lyx_2.2.3-1 g++_4:6.3.0-2ubuntu1 g++-6_6.3.0-21ubuntu1 gawk_1:4.1.4+dfsg-1 gcc_4:6.3.0-2ubuntu1 gcc-6_6.3.0-21ubuntu1 gcc-6-base_6.3.0-21ubuntu1 gcc-7-base_7.1.0-7ubuntu1 gettext_0.19.8.1-2ubuntu1 gettext-base_0.19.8.1-2ubuntu1 gnupg_2.1.15-1ubuntu7 gnupg-agent_2.1.15-1ubuntu7 gpgv_2.1.15-1ubuntu7 grep_2.27-2 groff-base_1.22.3-9 gzip_1.6-5ubuntu1 help2man_1.47.4 hostname_3.18 init_1.48 init-system-helpers_1.48 initscripts_2.88dsf-59.3ubuntu2 insserv_1.14.0-5ubuntu3 intltool-debian_0.35.0+20060710.4 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libfontconfig1_2.11.94-0ubuntu2 libfreetype6_2.6.3-3.2ubuntu1 libgcc-6-dev_6.3.0-21ubuntu1 libgcc1_1:7.1.0-7ubuntu1 libgcrypt20_1.7.7-2 libgdbm3_1.8.3-14 libgfortran3_6.3.0-21ubuntu1 libglib2.0-0_2.53.3-1 libgmp10_2:6.1.2+dfsg-1 libgnutls30_3.5.8-6ubuntu1 libgomp1_7.1.0-7ubuntu1 libgpg-error0_1.27-3 libgsl2_2.3+dfsg-1 libgssapi-krb5-2_1.15-2 libgssapi3-heimdal_7.1.0+dfsg-13 libhcrypto4-heimdal_7.1.0+dfsg-13 libheimbase1-heimdal_7.1.0+dfsg-13 libheimntlm0-heimdal_7.1.0+dfsg-13 libhogweed4_3.3-1 libhts1_1.3.2-2ubuntu1 libhts2_1.4.1-2ubuntu1 libhx509-5-heimdal_7.1.0+dfsg-13 libicu57_57.1-6 libidn11_1.33-1 libidn2-0_0.16-1 libip4tc0_1.6.0+snapshot20161117-6ubuntu1 libisl15_0.18-1 libitm1_7.1.0-7ubuntu1 libjs-jquery_3.1.1-2 libjs-jquery-ui_1.12.1+dfsg-4 libk5crypto3_1.15-2 libkeyutils1_1.5.9-9ubuntu1 libkmod2_24-1ubuntu1 libkrb5-26-heimdal_7.1.0+dfsg-13 libkrb5-3_1.15-2 libkrb5support0_1.15-2 libksba8_1.3.5-2 liblapack3_3.7.0-2 libldap-2.4-2_2.4.44+dfsg-7ubuntu1 libldap-common_2.4.44+dfsg-7ubuntu1 liblocale-gettext-perl_1.07-3build1 liblockfile-bin_1.14-1 liblockfile1_1.14-1 liblsan0_7.1.0-7ubuntu1 liblz4-1_0.0~r131-2ubuntu2 liblzma5_5.2.2-1.2 libmagic-mgc_1:5.30-1 libmagic1_1:5.30-1 libminimap-dev_0.2-3 libminimap0_0.2-3 libmount1_2.29-1ubuntu3 libmpc3_1.0.3-1 libmpdec2_2.4.2-1 libmpfr4_3.1.5-1 libmpx2_7.1.0-7ubuntu1 libncurses5_6.0+20160625-1ubuntu1 libncursesw5_6.0+20160625-1ubuntu1 libnettle6_3.3-1 libnpth0_1.5-2 libp11-kit0_0.23.3-5 libpam-modules_1.1.8-3.2ubuntu3 libpam-modules-bin_1.1.8-3.2ubuntu3 libpam-runtime_1.1.8-3.2ubuntu3 libpam0g_1.1.8-3.2ubuntu3 libpcre3_2:8.39-3 libperl5.24_5.24.1-4ubuntu1 libpipeline1_1.4.1-2 libpng16-16_1.6.29-3 libprocps6_2:3.3.12-1ubuntu2 libpsl5_0.17.0-4 libpython-stdlib_2.7.13-2 libpython2.7-minimal_2.7.13-2 libpython2.7-stdlib_2.7.13-2 libpython3-dev_3.5.3-1ubuntu3 libpython3-stdlib_3.5.3-1ubuntu3 libpython3.5_3.5.3-3 libpython3.5-dev_3.5.3-3 libpython3.5-minimal_3.5.3-3 libpython3.5-stdlib_3.5.3-3 libpython3.6-minimal_3.6.2~rc1-1 libpython3.6-stdlib_3.6.2~rc1-1 libquadmath0_7.1.0-7ubuntu1 libreadline7_7.0-0ubuntu2 libroken18-heimdal_7.1.0+dfsg-13 librtmp1_2.4+20151223.gitfa8646d.1-1 libruby2.3_2.3.3-1ubuntu1 libsasl2-2_2.1.27~101-g0780600+dfsg-2ubuntu1 libsasl2-modules-db_2.1.27~101-g0780600+dfsg-2ubuntu1 libseccomp2_2.3.1-2.1ubuntu1 libselinux1_2.6-3build1 libsemanage-common_2.6-2build1 libsemanage1_2.6-2build1 libsepol1_2.6-2 libsigsegv2_2.10-5 libslang2_2.3.1-5ubuntu1 libsmartcols1_2.29-1ubuntu3 libsqlite3-0_3.16.2-5 libss2_1.43.4-2 libssl1.0.0_1.0.2g-1ubuntu13 libstdc++-6-dev_6.3.0-21ubuntu1 libstdc++6_7.1.0-7ubuntu1 libsystemd0_233-8ubuntu2 libtasn1-6_4.12-2 libtbb2_4.4~20160526-0ubuntu2 libtcl8.6_8.6.6+dfsg-1 libtimedate-perl_2.3000-2 libtinfo5_6.0+20160625-1ubuntu1 libtk8.6_8.6.6-1 libtool_2.4.6-2 libtsan0_7.1.0-7ubuntu1 libubsan0_7.1.0-7ubuntu1 libudev1_233-8ubuntu2 libunistring0_0.9.3-5.2ubuntu1 libusb-0.1-4_2:0.1.12-31 libustr-1.0-1_1.0.4-6 libuuid1_2.29-1ubuntu3 libwind0-heimdal_7.1.0+dfsg-13 libx11-6_2:1.6.4-3 libx11-data_2:1.6.4-3 libxau6_1:1.0.8-1 libxcb1_1.11.1-1ubuntu1 libxdmcp6_1:1.1.2-3 libxext6_2:1.3.3-1 libxft2_2.3.2-1 libxml2_2.9.4+dfsg1-2.2ubuntu1 libxrender1_1:0.9.10-1 libxss1_1:1.2.2-1 libyaml-0-2_0.1.7-2ubuntu2 linux-libc-dev_4.11.0-9.14 lockfile-progs_0.1.17build1 login_1:4.2-3.2ubuntu2 lsb-base_9.20160110ubuntu5 m4_1.4.18-1 make_4.1-9.1 man-db_2.7.6.1-2 mash_1.1.1-2 mawk_1.3.3-17ubuntu2 mime-support_3.60ubuntu1 mount_2.29-1ubuntu3 multiarch-support_2.24-9ubuntu2 mummer_3.23+dfsg-2 ncurses-base_6.0+20160625-1ubuntu1 ncurses-bin_6.0+20160625-1ubuntu1 openssl_1.0.2g-1ubuntu13 optipng_0.7.6-1build1 passwd_1:4.2-3.2ubuntu2 patch_2.7.5-1build1 perl_5.24.1-4ubuntu1 perl-base_5.24.1-4ubuntu1 perl-modules-5.24_5.24.1-4ubuntu1 pinentry-curses_1.0.0-2 pkgbinarymangler_131 po-debconf_1.0.20 policyrcd-script-zg2_0.1-3 procps_2:3.3.12-1ubuntu2 python_2.7.13-2 python-matplotlib-data_2.0.0+dfsg1-2ubuntu2 python-minimal_2.7.13-2 python2.7_2.7.13-2 python2.7-minimal_2.7.13-2 python3_3.5.3-1ubuntu3 python3-bs4_4.6.0-1 python3-cycler_0.10.0-1 python3-dateutil_2.5.3-2 python3-dendropy_4.2.0+dfsg-1 python3-dev_3.5.3-1ubuntu3 python3-matplotlib_2.0.0+dfsg1-2ubuntu2 python3-minimal_3.5.3-1ubuntu3 python3-nose_1.3.7-2 python3-numpy_1:1.12.1-3ubuntu1 python3-pkg-resources_36.0.1-1 python3-pymummer_0.10.2-1 python3-pyparsing_2.1.10+dfsg1-1 python3-pysam_0.10.0+ds-2build1 python3-setuptools_36.0.1-1 python3-six_1.10.0-4 python3-tk_3.5.3-2 python3-tz_2017.2-2 python3.5_3.5.3-3 python3.5-dev_3.5.3-3 python3.5-minimal_3.5.3-3 python3.6_3.6.2~rc1-1 python3.6-minimal_3.6.2~rc1-1 rake_10.5.0-2 readline-common_7.0-0ubuntu2 ruby_1:2.3.3 ruby-did-you-mean_1.0.0-2 ruby-minitest_5.9.0-1 ruby-net-telnet_0.1.1-2 ruby-power-assert_0.3.0-1 ruby-test-unit_3.1.7-2 ruby2.3_2.3.3-1ubuntu1 rubygems-integration_1.11 samtools_1.4.1-1 sbuild-build-depends-ariba-dummy_0.invalid.0 sbuild-build-depends-core-dummy_0.invalid.0 sed_4.4-1 sensible-utils_0.0.9 systemd_233-8ubuntu2 systemd-sysv_233-8ubuntu2 sysv-rc_2.88dsf-59.3ubuntu2 sysvinit-utils_2.88dsf-59.8git1 tar_1.29b-1.1 tk8.6-blt2.5_2.5.3+dfsg-3 ttf-bitstream-vera_1.10-8 tzdata_2017b-2 ubuntu-keyring_2016.10.27 ucf_3.0036 util-linux_2.29-1ubuntu3 x11-common_1:7.7+19ubuntu1 xz-utils_5.2.2-1.2 zlib1g_1:1.2.11.dfsg-0ubuntu1 zlib1g-dev_1:1.2.11.dfsg-0ubuntu1 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Wed Jun 28 21:08:24 2017 UTC gpgv: using RSA key gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./ariba_2.10.0+ds-1.dsc dpkg-source: info: extracting ariba in ariba-2.10.0+ds dpkg-source: info: unpacking ariba_2.10.0+ds.orig.tar.xz dpkg-source: info: unpacking ariba_2.10.0+ds-1.debian.tar.xz dpkg-source: info: applying use_debian_packaged_libs_for_extension.patch dpkg-source: info: applying use_bwa_compatible_fermi-lite.patch Check disc space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=4 HOME=/home/buildd LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd MAIL=/var/mail/buildd OLDPWD=/ PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games PWD=/<>/ariba-2.10.0+ds SHELL=/bin/sh SUDO_COMMAND=/usr/sbin/chroot /<> su buildd -s /bin/sh -c cd '/<>/ariba-2.10.0+ds' && 'env' SUDO_GID=2501 SUDO_UID=2001 SUDO_USER=buildd TERM=unknown USER=buildd USERNAME=root dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package ariba dpkg-buildpackage: info: source version 2.10.0+ds-1 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build ariba-2.10.0+ds dpkg-buildpackage: info: host architecture amd64 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 '/<>/ariba-2.10.0+ds' rm -rf /<>/ariba-2.10.0+ds/debian/man dh_auto_clean -- I: pybuild base:184: python3.5 setup.py clean running clean removing '/<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build' (and everything under it) 'build/bdist.linux-amd64' does not exist -- can't clean it 'build/scripts-3.5' does not exist -- can't clean it make[1]: Leaving directory '/<>/ariba-2.10.0+ds' dh_clean -O--buildsystem=pybuild debian/rules build dh build --with python3 --buildsystem=pybuild dh_testdir -O--buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild I: pybuild base:184: python3.5 setup.py config running config dh_auto_build -O--buildsystem=pybuild I: pybuild base:184: /usr/bin/python3 setup.py build running build running build_py creating /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba copying ariba/aln_to_metadata.py -> /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba copying ariba/vfdb_parser.py -> /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba copying ariba/mlst_profile.py -> /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba copying ariba/mic_plotter.py -> /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba copying ariba/cdhit.py -> /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba copying ariba/ref_seq_chooser.py -> /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba copying ariba/samtools_variants.py -> /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba copying ariba/histogram.py -> /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba copying ariba/external_progs.py -> /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba copying ariba/report.py -> /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba copying ariba/assembly_compare.py -> /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba copying ariba/read_store.py -> /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba copying ariba/scaffold_graph.py -> /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba copying ariba/summary.py -> /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba copying ariba/versions.py -> /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba copying ariba/summary_cluster_variant.py -> /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba copying ariba/ref_genes_getter.py -> /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba copying ariba/refdata_query.py -> /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba copying ariba/sequence_metadata.py -> /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba copying ariba/summary_sample.py -> /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba copying ariba/mlst_reporter.py -> /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba copying ariba/flag.py -> /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba copying ariba/common.py -> /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba copying ariba/clusters.py -> /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba copying ariba/bam_parse.py -> /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba copying ariba/__init__.py -> /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba copying ariba/report_filter.py -> /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba copying ariba/assembly_variants.py -> /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba copying ariba/read_filter.py -> /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba copying ariba/reference_data.py -> /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba copying ariba/pubmlst_ref_preparer.py -> /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba copying ariba/cluster.py -> /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba copying ariba/link.py -> /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba copying ariba/summary_cluster.py -> /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba copying ariba/megares_zip_parser.py -> /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba copying ariba/megares_data_finder.py -> /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba copying ariba/assembly.py -> /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba copying ariba/pubmlst_getter.py -> /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba copying ariba/ref_preparer.py -> /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba copying ariba/card_record.py -> /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba copying ariba/mapping.py -> /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba copying ariba/sequence_variant.py -> /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba copying ariba/faidx.py -> /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba copying ariba/report_flag_expander.py -> /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba creating /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/tasks copying ariba/tasks/run.py -> /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/tasks copying ariba/tasks/summary.py -> /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/tasks copying ariba/tasks/expandflag.py -> /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/tasks copying ariba/tasks/aln2meta.py -> /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/tasks copying ariba/tasks/reportfilter.py -> /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/tasks copying ariba/tasks/flag.py -> /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/tasks copying ariba/tasks/prepareref.py -> /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/tasks copying ariba/tasks/pubmlstget.py -> /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/tasks copying ariba/tasks/__init__.py -> /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/tasks copying ariba/tasks/getref.py -> /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/tasks copying ariba/tasks/micplot.py -> /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/tasks copying ariba/tasks/pubmlstspecies.py -> /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/tasks copying ariba/tasks/test.py -> /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/tasks copying ariba/tasks/refquery.py -> /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/tasks copying ariba/tasks/version.py -> /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/tasks creating /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/test_run_data copying ariba/test_run_data/ref_seqs.fa -> /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/test_run_data copying ariba/test_run_data/reads_2.fq -> /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/test_run_data copying ariba/test_run_data/ref_fasta_to_make_reads_from.fa -> /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/test_run_data copying ariba/test_run_data/metadata.tsv -> /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/test_run_data copying ariba/test_run_data/reads_1.fq -> /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/test_run_data running build_ext building 'minimap_ariba' extension creating build creating build/temp.linux-amd64-3.5 creating build/temp.linux-amd64-3.5/ariba creating build/temp.linux-amd64-3.5/ariba/ext x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/ariba-2.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/minimap -I/usr/include/python3.5m -c ariba/ext/minimap_ariba.cpp -o build/temp.linux-amd64-3.5/ariba/ext/minimap_ariba.o cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ ariba/ext/minimap_ariba.cpp: In function ‘bool readMappingOk(const mm_reg1_t*, const mm_idx_t*, const kseq_t*, uint32_t)’: ariba/ext/minimap_ariba.cpp:371:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if (r->qe - r->qs < std::min((unsigned) 50, (int) 0.5 * ks->seq.l)) ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ariba/ext/minimap_ariba.cpp:381:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] startOk = (r->qs < endTolerance || refLength - r->re < endTolerance); ~~~~~~^~~~~~~~~~~~~~ ariba/ext/minimap_ariba.cpp:382:60: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] endOk = (ks->seq.l - r->qe < endTolerance || r->rs < endTolerance); ~~~~~~^~~~~~~~~~~~~~ ariba/ext/minimap_ariba.cpp:386:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] startOk = (r->qs < endTolerance || r->rs < endTolerance); ~~~~~~^~~~~~~~~~~~~~ ariba/ext/minimap_ariba.cpp:386:50: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] startOk = (r->qs < endTolerance || r->rs < endTolerance); ~~~~~~^~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/ariba-2.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-amd64-3.5/ariba/ext/minimap_ariba.o -o /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/minimap_ariba.cpython-35m-x86_64-linux-gnu.so -lz -lminimap building 'fermilite_ariba' extension x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/ariba-2.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.5m -c ariba/ext/fml-asm_ariba.cpp -o build/temp.linux-amd64-3.5/ariba/ext/fml-asm_ariba.o cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ x86_64-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/ariba-2.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-amd64-3.5/ariba/ext/fml-asm_ariba.o -o /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/fermilite_ariba.cpython-35m-x86_64-linux-gnu.so -lz -lfml building 'vcfcall_ariba' extension x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/ariba-2.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.5m -c ariba/ext/vcfcall_ariba.cpp -o build/temp.linux-amd64-3.5/ariba/ext/vcfcall_ariba.o cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ x86_64-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/ariba-2.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-amd64-3.5/ariba/ext/vcfcall_ariba.o -o /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/vcfcall_ariba.cpython-35m-x86_64-linux-gnu.so running build_scripts creating build/scripts-3.5 copying and adjusting scripts/ariba -> build/scripts-3.5 changing mode of build/scripts-3.5/ariba from 664 to 775 debian/rules override_dh_auto_test make[1]: Entering directory '/<>/ariba-2.10.0+ds' python3 setup.py nosetests running nosetests running egg_info creating ariba.egg-info writing top-level names to ariba.egg-info/top_level.txt writing requirements to ariba.egg-info/requires.txt writing dependency_links to ariba.egg-info/dependency_links.txt writing ariba.egg-info/PKG-INFO writing manifest file 'ariba.egg-info/SOURCES.txt' reading manifest file 'ariba.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching '*.h' under directory 'third_party' writing manifest file 'ariba.egg-info/SOURCES.txt' building 'minimap_ariba' extension creating build/temp.linux-x86_64-3.5 creating build/temp.linux-x86_64-3.5/ariba creating build/temp.linux-x86_64-3.5/ariba/ext x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/ariba-2.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/minimap -I/usr/include/python3.5m -c ariba/ext/minimap_ariba.cpp -o build/temp.linux-x86_64-3.5/ariba/ext/minimap_ariba.o cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ ariba/ext/minimap_ariba.cpp: In function ‘bool readMappingOk(const mm_reg1_t*, const mm_idx_t*, const kseq_t*, uint32_t)’: ariba/ext/minimap_ariba.cpp:371:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if (r->qe - r->qs < std::min((unsigned) 50, (int) 0.5 * ks->seq.l)) ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ariba/ext/minimap_ariba.cpp:381:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] startOk = (r->qs < endTolerance || refLength - r->re < endTolerance); ~~~~~~^~~~~~~~~~~~~~ ariba/ext/minimap_ariba.cpp:382:60: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] endOk = (ks->seq.l - r->qe < endTolerance || r->rs < endTolerance); ~~~~~~^~~~~~~~~~~~~~ ariba/ext/minimap_ariba.cpp:386:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] startOk = (r->qs < endTolerance || r->rs < endTolerance); ~~~~~~^~~~~~~~~~~~~~ ariba/ext/minimap_ariba.cpp:386:50: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] startOk = (r->qs < endTolerance || r->rs < endTolerance); ~~~~~~^~~~~~~~~~~~~~ creating build/lib.linux-x86_64-3.5 x86_64-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/ariba-2.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.5/ariba/ext/minimap_ariba.o -o build/lib.linux-x86_64-3.5/minimap_ariba.cpython-35m-x86_64-linux-gnu.so -lz -lminimap building 'fermilite_ariba' extension x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/ariba-2.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.5m -c ariba/ext/fml-asm_ariba.cpp -o build/temp.linux-x86_64-3.5/ariba/ext/fml-asm_ariba.o cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ x86_64-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/ariba-2.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.5/ariba/ext/fml-asm_ariba.o -o build/lib.linux-x86_64-3.5/fermilite_ariba.cpython-35m-x86_64-linux-gnu.so -lz -lfml building 'vcfcall_ariba' extension x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/ariba-2.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.5m -c ariba/ext/vcfcall_ariba.cpp -o build/temp.linux-x86_64-3.5/ariba/ext/vcfcall_ariba.o cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ x86_64-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/ariba-2.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.5/ariba/ext/vcfcall_ariba.o -o build/lib.linux-x86_64-3.5/vcfcall_ariba.cpython-35m-x86_64-linux-gnu.so copying build/lib.linux-x86_64-3.5/minimap_ariba.cpython-35m-x86_64-linux-gnu.so -> copying build/lib.linux-x86_64-3.5/fermilite_ariba.cpython-35m-x86_64-linux-gnu.so -> copying build/lib.linux-x86_64-3.5/vcfcall_ariba.cpython-35m-x86_64-linux-gnu.so -> ..............Warning: position has a gap in sequence seq3 corresponding to variant A2D (id1) in sequence seq1 ... Ignoring for seq3 Warning: position has a gap in sequence seq1 corresponding to variant F2E (id2) in sequence seq5 ... Ignoring for seq1 Warning: position has a gap in sequence seq2 corresponding to variant F2E (id2) in sequence seq5 ... Ignoring for seq2 .Warning: position has a gap in sequence seq3 corresponding to variant C5T (id1) in sequence seq1 ... Ignoring for seq3 Warning: position has a gap in sequence seq1 corresponding to variant A5T (id2) in sequence seq5 ... Ignoring for seq1 Warning: position has a gap in sequence seq2 corresponding to variant A5T (id2) in sequence seq5 ... Ignoring for seq2 ...Warning: position has a gap in sequence seq3 corresponding to variant A2D (id1) in sequence seq1 ... Ignoring for seq3 Warning: position has a gap in sequence seq1 corresponding to variant F2E (id2) in sequence seq5 ... Ignoring for seq1 Warning: position has a gap in sequence seq2 corresponding to variant F2E (id2) in sequence seq5 ... Ignoring for seq2 .Warning: position has a gap in sequence seq3 corresponding to variant C5T (id1) in sequence seq1 ... Ignoring for seq3 Warning: position has a gap in sequence seq1 corresponding to variant A5T (id2) in sequence seq5 ... Ignoring for seq1 Warning: position has a gap in sequence seq2 corresponding to variant A5T (id2) in sequence seq5 ... Ignoring for seq2 .............................................Missing data from foo Missing data from foo Missing data from foo Missing data from foo Missing data from foo Missing data from foo Missing data from foo .........WARNING: ignoring sequence seq6 from clusters file because not in fasta file. This probably means it failed sanity checks - see the log files 01.filter.check_genes.log, 01.filter.check_metadata.log. .....................................................................................WARNING: sequence "Only_in_fasta_file" has no record in annotations file WARNING: sequence "Only_in_fasta_file" has no record in header mappings file ................WARNING: Same profile found twice in input file, but two different STs. Going to use the ST with the smaller number (2) ... STs are 2 3 and alleles are nusA:1, rpoB:26, eno:2, gltB:4, lepA:59, nuoL:2, nrdA:5 ..........WARNING: Median sequence length is 5 but seq5 has length 14 which is too long or short. Removing. WARNING: Median sequence length is 5 but seq1 has length 1 which is too long or short. Removing. ............WARNING. 1 sequence(s) excluded. Please see the log file 01.filter.check_genes.log for details. This will show them: grep REMOVE tmp.ref_preparer_test_run/01.filter.check_genes.log WARNING. Problem with at least one variant. Problem variants are rmoved. Please see the file tmp.ref_preparer_test_run/01.filter.check_metadata.log for details. .............WARNING: sequence "non_coding_not_in_fasta" found in metadata, but not in fasta file. Ignoring it. WARNING: sequence "presence_absence_not_in_fasta" found in metadata, but not in fasta file. Ignoring it. WARNING: sequence "variants_only_not_in_fasta" found in metadata, but not in fasta file. Ignoring it. .......WARNING: sequence "seq3" found in metadata, but not in fasta file. Ignoring it. ....................................................................................................................... ---------------------------------------------------------------------- Ran 335 tests in 108.226s OK dh_auto_test -- I: pybuild base:184: cd /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build; python3.5 -m nose ---------------------------------------------------------------------- Ran 0 tests in 1.162s OK make[1]: Leaving directory '/<>/ariba-2.10.0+ds' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary --with python3 --buildsystem=pybuild create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild dh_auto_install -O--buildsystem=pybuild I: pybuild base:184: /usr/bin/python3 setup.py install --root /<>/ariba-2.10.0+ds/debian/ariba running install running build running build_py running build_ext running build_scripts running install_lib creating /<>/ariba-2.10.0+ds/debian/ariba/usr creating /<>/ariba-2.10.0+ds/debian/ariba/usr/lib creating /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5 creating /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages copying /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/vcfcall_ariba.cpython-35m-x86_64-linux-gnu.so -> /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages creating /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba copying /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/aln_to_metadata.py -> /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba copying /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/vfdb_parser.py -> /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba copying /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/mlst_profile.py -> /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba copying /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/mic_plotter.py -> /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba copying /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/cdhit.py -> /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba copying /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/ref_seq_chooser.py -> /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba copying /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/samtools_variants.py -> /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba copying /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/histogram.py -> /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba copying /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/external_progs.py -> /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba copying /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/report.py -> /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba copying /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/assembly_compare.py -> /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba copying /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/read_store.py -> /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba copying /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/scaffold_graph.py -> /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba copying /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/summary.py -> /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba copying /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/versions.py -> /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba copying /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/summary_cluster_variant.py -> /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba copying /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/ref_genes_getter.py -> /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba creating /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/tasks copying /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/tasks/run.py -> /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/tasks copying /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/tasks/summary.py -> /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/tasks copying /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/tasks/expandflag.py -> /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/tasks copying /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/tasks/aln2meta.py -> /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/tasks copying /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/tasks/reportfilter.py -> /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/tasks copying /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/tasks/flag.py -> /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/tasks copying /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/tasks/prepareref.py -> /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/tasks copying /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/tasks/pubmlstget.py -> /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/tasks copying /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/tasks/__init__.py -> /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/tasks copying /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/tasks/getref.py -> /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/tasks copying /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/tasks/micplot.py -> /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/tasks copying /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/tasks/pubmlstspecies.py -> /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/tasks creating /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/tasks/__pycache__ copying /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/tasks/__pycache__/aln2meta.cpython-35.pyc -> /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/tasks/__pycache__ copying /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/tasks/__pycache__/reportfilter.cpython-35.pyc -> /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/tasks/__pycache__ copying /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/tasks/__pycache__/version.cpython-35.pyc -> /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/tasks/__pycache__ copying /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/tasks/__pycache__/micplot.cpython-35.pyc -> /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/tasks/__pycache__ copying /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/tasks/__pycache__/pubmlstget.cpython-35.pyc -> /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/tasks/__pycache__ copying /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/tasks/__pycache__/test.cpython-35.pyc -> /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/tasks/__pycache__ copying /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/tasks/__pycache__/__init__.cpython-35.pyc -> /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/tasks/__pycache__ copying /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/tasks/__pycache__/getref.cpython-35.pyc -> /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/tasks/__pycache__ copying /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/tasks/__pycache__/pubmlstspecies.cpython-35.pyc -> /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/tasks/__pycache__ copying /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/tasks/__pycache__/expandflag.cpython-35.pyc -> /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/tasks/__pycache__ copying /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/tasks/__pycache__/summary.cpython-35.pyc -> /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/tasks/__pycache__ copying /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/tasks/__pycache__/flag.cpython-35.pyc -> /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/tasks/__pycache__ copying /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/tasks/__pycache__/refquery.cpython-35.pyc -> /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/tasks/__pycache__ copying /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/tasks/__pycache__/prepareref.cpython-35.pyc -> /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/tasks/__pycache__ copying /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/tasks/__pycache__/run.cpython-35.pyc -> /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/tasks/__pycache__ copying /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/tasks/test.py -> /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/tasks copying /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/tasks/refquery.py -> /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/tasks copying /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/tasks/version.py -> /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/tasks copying /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/refdata_query.py -> /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba copying /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/sequence_metadata.py -> /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba copying /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/summary_sample.py -> /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba copying /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/mlst_reporter.py -> /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba copying /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/flag.py -> /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba copying /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/common.py -> /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba copying /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/clusters.py -> /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba copying /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/bam_parse.py -> /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba copying /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/__init__.py -> /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba copying /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/report_filter.py -> /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba creating /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/test_run_data copying /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/test_run_data/ref_seqs.fa -> /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/test_run_data copying /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/test_run_data/reads_2.fq -> /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/test_run_data copying /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/test_run_data/ref_fasta_to_make_reads_from.fa -> /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/test_run_data copying /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/test_run_data/metadata.tsv -> /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/test_run_data copying /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/test_run_data/reads_1.fq -> /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/test_run_data copying /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/assembly_variants.py -> /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba copying /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/read_filter.py -> /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba copying /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/reference_data.py -> /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba copying /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/pubmlst_ref_preparer.py -> /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba copying /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/cluster.py -> /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba copying /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/link.py -> /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba copying /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/summary_cluster.py -> /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba copying /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/megares_zip_parser.py -> /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba creating /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/__pycache__ copying /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/__pycache__/mic_plotter.cpython-35.pyc -> /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/__pycache__ copying /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/__pycache__/versions.cpython-35.pyc -> /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/__pycache__ copying /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/__pycache__/cdhit.cpython-35.pyc -> /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/__pycache__ copying /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/__pycache__/read_store.cpython-35.pyc -> /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/__pycache__ copying /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/__pycache__/report.cpython-35.pyc -> /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/__pycache__ copying /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/__pycache__/assembly.cpython-35.pyc -> /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/__pycache__ copying /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/__pycache__/vfdb_parser.cpython-35.pyc -> /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/__pycache__ copying /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/__pycache__/aln_to_metadata.cpython-35.pyc -> /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/__pycache__ copying /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/__pycache__/ref_preparer.cpython-35.pyc -> /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/__pycache__ copying /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/__pycache__/read_filter.cpython-35.pyc -> /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/__pycache__ copying /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/__pycache__/mlst_reporter.cpython-35.pyc -> /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/__pycache__ copying /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/__pycache__/bam_parse.cpython-35.pyc -> /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/__pycache__ copying /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/__pycache__/megares_data_finder.cpython-35.pyc -> /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/__pycache__ copying /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/__pycache__/samtools_variants.cpython-35.pyc -> /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/__pycache__ copying /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/__pycache__/common.cpython-35.pyc -> /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/__pycache__ copying /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/__pycache__/refdata_query.cpython-35.pyc -> /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/__pycache__ copying /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/__pycache__/cluster.cpython-35.pyc -> /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/__pycache__ copying /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/__pycache__/summary_sample.cpython-35.pyc -> /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/__pycache__ copying /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/__pycache__/__init__.cpython-35.pyc -> /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/__pycache__ copying /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/__pycache__/link.cpython-35.pyc -> /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/__pycache__ copying /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/__pycache__/mlst_profile.cpython-35.pyc -> /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/__pycache__ copying /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/__pycache__/ref_genes_getter.cpython-35.pyc -> /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/__pycache__ copying /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/__pycache__/faidx.cpython-35.pyc -> /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/__pycache__ copying /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/__pycache__/reference_data.cpython-35.pyc -> /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/__pycache__ copying /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/__pycache__/pubmlst_getter.cpython-35.pyc -> /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/__pycache__ copying /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/__pycache__/summary.cpython-35.pyc -> /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/__pycache__ copying /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/__pycache__/ref_seq_chooser.cpython-35.pyc -> /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/__pycache__ copying /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/__pycache__/scaffold_graph.cpython-35.pyc -> /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/__pycache__ copying /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/__pycache__/clusters.cpython-35.pyc -> /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/__pycache__ copying /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/__pycache__/flag.cpython-35.pyc -> /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/__pycache__ copying /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/__pycache__/sequence_variant.cpython-35.pyc -> /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/__pycache__ copying /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/__pycache__/pubmlst_ref_preparer.cpython-35.pyc -> /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/__pycache__ copying /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/__pycache__/sequence_metadata.cpython-35.pyc -> /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/__pycache__ copying /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/__pycache__/assembly_compare.cpython-35.pyc -> /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/__pycache__ copying /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/__pycache__/report_flag_expander.cpython-35.pyc -> /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/__pycache__ copying /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/__pycache__/histogram.cpython-35.pyc -> /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/__pycache__ copying /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/__pycache__/summary_cluster.cpython-35.pyc -> /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/__pycache__ copying /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/__pycache__/mapping.cpython-35.pyc -> /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/__pycache__ copying /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/__pycache__/megares_zip_parser.cpython-35.pyc -> /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/__pycache__ copying /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/__pycache__/summary_cluster_variant.cpython-35.pyc -> /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/__pycache__ copying /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/__pycache__/card_record.cpython-35.pyc -> /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/__pycache__ copying /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/__pycache__/assembly_variants.cpython-35.pyc -> /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/__pycache__ copying /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/__pycache__/report_filter.cpython-35.pyc -> /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/__pycache__ copying /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/__pycache__/external_progs.cpython-35.pyc -> /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/__pycache__ copying /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/megares_data_finder.py -> /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba copying /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/assembly.py -> /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba copying /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/pubmlst_getter.py -> /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba copying /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/ref_preparer.py -> /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba copying /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/card_record.py -> /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba copying /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/mapping.py -> /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba copying /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/sequence_variant.py -> /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba copying /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/faidx.py -> /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba copying /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/ariba/report_flag_expander.py -> /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba copying /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/minimap_ariba.cpython-35m-x86_64-linux-gnu.so -> /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages copying /<>/ariba-2.10.0+ds/.pybuild/pythonX.Y_3.5/build/fermilite_ariba.cpython-35m-x86_64-linux-gnu.so -> /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages byte-compiling /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/aln_to_metadata.py to aln_to_metadata.cpython-35.pyc byte-compiling /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/vfdb_parser.py to vfdb_parser.cpython-35.pyc byte-compiling /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/mlst_profile.py to mlst_profile.cpython-35.pyc byte-compiling /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/mic_plotter.py to mic_plotter.cpython-35.pyc byte-compiling /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/cdhit.py to cdhit.cpython-35.pyc byte-compiling /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/ref_seq_chooser.py to ref_seq_chooser.cpython-35.pyc byte-compiling /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/samtools_variants.py to samtools_variants.cpython-35.pyc byte-compiling /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/histogram.py to histogram.cpython-35.pyc byte-compiling /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/external_progs.py to external_progs.cpython-35.pyc byte-compiling /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/report.py to report.cpython-35.pyc byte-compiling /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/assembly_compare.py to assembly_compare.cpython-35.pyc byte-compiling /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/read_store.py to read_store.cpython-35.pyc byte-compiling /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/scaffold_graph.py to scaffold_graph.cpython-35.pyc byte-compiling /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/summary.py to summary.cpython-35.pyc byte-compiling /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/versions.py to versions.cpython-35.pyc byte-compiling /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/summary_cluster_variant.py to summary_cluster_variant.cpython-35.pyc byte-compiling /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/ref_genes_getter.py to ref_genes_getter.cpython-35.pyc byte-compiling /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/tasks/run.py to run.cpython-35.pyc byte-compiling /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/tasks/summary.py to summary.cpython-35.pyc byte-compiling /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/tasks/expandflag.py to expandflag.cpython-35.pyc byte-compiling /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/tasks/aln2meta.py to aln2meta.cpython-35.pyc byte-compiling /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/tasks/reportfilter.py to reportfilter.cpython-35.pyc byte-compiling /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/tasks/flag.py to flag.cpython-35.pyc byte-compiling /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/tasks/prepareref.py to prepareref.cpython-35.pyc byte-compiling /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/tasks/pubmlstget.py to pubmlstget.cpython-35.pyc byte-compiling /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/tasks/__init__.py to __init__.cpython-35.pyc byte-compiling /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/tasks/getref.py to getref.cpython-35.pyc byte-compiling /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/tasks/micplot.py to micplot.cpython-35.pyc byte-compiling /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/tasks/pubmlstspecies.py to pubmlstspecies.cpython-35.pyc byte-compiling /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/tasks/test.py to test.cpython-35.pyc byte-compiling /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/tasks/refquery.py to refquery.cpython-35.pyc byte-compiling /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/tasks/version.py to version.cpython-35.pyc byte-compiling /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/refdata_query.py to refdata_query.cpython-35.pyc byte-compiling /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/sequence_metadata.py to sequence_metadata.cpython-35.pyc byte-compiling /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/summary_sample.py to summary_sample.cpython-35.pyc byte-compiling /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/mlst_reporter.py to mlst_reporter.cpython-35.pyc byte-compiling /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/flag.py to flag.cpython-35.pyc byte-compiling /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/common.py to common.cpython-35.pyc byte-compiling /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/clusters.py to clusters.cpython-35.pyc byte-compiling /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/bam_parse.py to bam_parse.cpython-35.pyc byte-compiling /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/__init__.py to __init__.cpython-35.pyc byte-compiling /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/report_filter.py to report_filter.cpython-35.pyc byte-compiling /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/assembly_variants.py to assembly_variants.cpython-35.pyc byte-compiling /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/read_filter.py to read_filter.cpython-35.pyc byte-compiling /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/reference_data.py to reference_data.cpython-35.pyc byte-compiling /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/pubmlst_ref_preparer.py to pubmlst_ref_preparer.cpython-35.pyc byte-compiling /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/cluster.py to cluster.cpython-35.pyc byte-compiling /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/link.py to link.cpython-35.pyc byte-compiling /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/summary_cluster.py to summary_cluster.cpython-35.pyc byte-compiling /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/megares_zip_parser.py to megares_zip_parser.cpython-35.pyc byte-compiling /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/megares_data_finder.py to megares_data_finder.cpython-35.pyc byte-compiling /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/assembly.py to assembly.cpython-35.pyc byte-compiling /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/pubmlst_getter.py to pubmlst_getter.cpython-35.pyc byte-compiling /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/ref_preparer.py to ref_preparer.cpython-35.pyc byte-compiling /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/card_record.py to card_record.cpython-35.pyc byte-compiling /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/mapping.py to mapping.cpython-35.pyc byte-compiling /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/sequence_variant.py to sequence_variant.cpython-35.pyc byte-compiling /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/faidx.py to faidx.cpython-35.pyc byte-compiling /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba/report_flag_expander.py to report_flag_expander.cpython-35.pyc running install_egg_info running egg_info writing top-level names to ariba.egg-info/top_level.txt writing dependency_links to ariba.egg-info/dependency_links.txt writing requirements to ariba.egg-info/requires.txt writing ariba.egg-info/PKG-INFO reading manifest file 'ariba.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching '*.h' under directory 'third_party' writing manifest file 'ariba.egg-info/SOURCES.txt' Copying ariba.egg-info to /<>/ariba-2.10.0+ds/debian/ariba/usr/lib/python3.5/dist-packages/ariba-2.10.0.egg-info Skipping SOURCES.txt running install_scripts creating /<>/ariba-2.10.0+ds/debian/ariba/usr/bin copying build/scripts-3.5/ariba -> /<>/ariba-2.10.0+ds/debian/ariba/usr/bin changing mode of /<>/ariba-2.10.0+ds/debian/ariba/usr/bin/ariba to 775 dh_installdocs -O--buildsystem=pybuild dh_installchangelogs -O--buildsystem=pybuild debian/rules override_dh_installman make[1]: Entering directory '/<>/ariba-2.10.0+ds' mkdir -p /<>/ariba-2.10.0+ds/debian/man asciidoctor -a docdate='' -b manpage -o /<>/ariba-2.10.0+ds/debian/man/ariba.1 /<>/ariba-2.10.0+ds/debian/ariba.1.adoc #PYTHONPATH=. scripts/ariba 2>&1 | tail -n +10 | head -n 14 | /<>/ariba-2.10.0+ds/debian/make_man dh_installman -- make[1]: Leaving directory '/<>/ariba-2.10.0+ds' dh_python3 -O--buildsystem=pybuild dh_perl -O--buildsystem=pybuild dh_link -O--buildsystem=pybuild dh_strip_nondeterminism -O--buildsystem=pybuild dh_compress -O--buildsystem=pybuild dh_fixperms -O--buildsystem=pybuild dh_missing -O--buildsystem=pybuild dh_strip -O--buildsystem=pybuild dh_makeshlibs -O--buildsystem=pybuild dh_shlibdeps -O--buildsystem=pybuild dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/ariba/usr/lib/python3/dist-packages/vcfcall_ariba.cpython-35m-x86_64-linux-gnu.so was not linked against libpthread.so.0 (it uses none of the library's symbols) dh_installdeb -O--buildsystem=pybuild dh_gencontrol -O--buildsystem=pybuild dpkg-gencontrol: warning: package ariba: unused substitution variable ${python3:Versions} dpkg-gencontrol: warning: package ariba: unused substitution variable ${python3:Versions} dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild INFO: pkgstriptranslations version 131 pkgstriptranslations: processing ariba-dbgsym (in debian/.debhelper/ariba/dbgsym-root); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/.debhelper/ariba/dbgsym-root/DEBIAN/control, package ariba-dbgsym, directory debian/.debhelper/ariba/dbgsym-root pkgstripfiles: Running PNG optimization (using 4 cpus) for package ariba-dbgsym ... pkgstripfiles: No PNG files. dpkg-deb: building package 'ariba-dbgsym' in 'debian/.debhelper/scratch-space/build-ariba/ariba-dbgsym_2.10.0+ds-1_amd64.deb'. Renaming ariba-dbgsym_2.10.0+ds-1_amd64.deb to ariba-dbgsym_2.10.0+ds-1_amd64.ddeb INFO: pkgstriptranslations version 131 pkgstriptranslations: processing ariba (in debian/ariba); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/ariba/DEBIAN/control, package ariba, directory debian/ariba pkgstripfiles: Truncating usr/share/doc/ariba/changelog.Debian.gz to topmost ten records pkgstripfiles: Running PNG optimization (using 4 cpus) for package ariba ... pkgstripfiles: No PNG files. dpkg-deb: building package 'ariba' in '../ariba_2.10.0+ds-1_amd64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary -mLaunchpad Build Daemon >../ariba_2.10.0+ds-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build ariba-2.10.0+ds dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 20170629-1715 Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Post Build Chroot | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ ariba_2.10.0+ds-1_amd64.changes: -------------------------------- Format: 1.8 Date: Wed, 28 Jun 2017 22:59:02 +0200 Source: ariba Binary: ariba Architecture: amd64 Version: 2.10.0+ds-1 Distribution: artful-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Sascha Steinbiss Description: ariba - Antibiotic Resistance Identification By Assembly Changes: ariba (2.10.0+ds-1) unstable; urgency=medium . * New upstream release. * Bump Standards-Version. Checksums-Sha1: 16bd1947f88597035acb80a0f68a57c2df804894 332292 ariba-dbgsym_2.10.0+ds-1_amd64.ddeb 21627b810874671e6c35edc33968c819d7b549b3 9316 ariba_2.10.0+ds-1_amd64.buildinfo 279c200949ff0ef259104405f1fc4b43f64b5366 114010 ariba_2.10.0+ds-1_amd64.deb Checksums-Sha256: 4453b8902c9e4e42d7ff9ed5ffd38371dc6a4561230198d2991a39267e39241d 332292 ariba-dbgsym_2.10.0+ds-1_amd64.ddeb a2bbdd405bd242c7372b17b35647ebe81f3741ade30cfee1e6b827d855831aba 9316 ariba_2.10.0+ds-1_amd64.buildinfo 145b7a407b1c457a4b5cd8428097128896431ea6fabc8ff015f13671ed79308f 114010 ariba_2.10.0+ds-1_amd64.deb Files: dc3ce2defed68e0a3b5a888449134fd1 332292 debug extra ariba-dbgsym_2.10.0+ds-1_amd64.ddeb b0c1ad340171cc03fe7619e6c4d887ff 9316 science optional ariba_2.10.0+ds-1_amd64.buildinfo f626ac5f6209acb55023e333eb6a8a31 114010 science optional ariba_2.10.0+ds-1_amd64.deb +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ ariba_2.10.0+ds-1_amd64.deb --------------------------- new debian package, version 2.0. size 114010 bytes: control archive=3437 bytes. 1120 bytes, 17 lines control 6588 bytes, 75 lines md5sums 157 bytes, 9 lines * postinst #!/bin/sh 385 bytes, 12 lines * prerm #!/bin/sh Package: ariba Version: 2.10.0+ds-1 Architecture: amd64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 743 Depends: fastaq (>= 3.12.0), python3 (<< 3.6), python3 (>= 3.5~), python3-bs4 (>= 4.1.0), python3-dendropy (>= 4.2.0), python3-matplotlib, python3-pymummer (>= 0.10.2), python3-pysam (>= 0.9.1), python3:any (>= 3.3.2-2~), libc6 (>= 2.14), libfml0, libgcc1 (>= 1:3.0), libminimap0, libstdc++6 (>= 5.2), zlib1g (>= 1:1.1.4), bowtie2 (>= 2.1.0), cd-hit, mash, mummer, python3-tk Section: science Priority: optional Homepage: https://github.com/sanger-pathogens/ariba Description: Antibiotic Resistance Identification By Assembly ARIBA is a tool that identifies antibiotic resistance genes by running local assemblies. The input is a FASTA file of reference genes and paired sequencing reads. ARIBA reports which of the reference genes were found, plus detailed information on the quality of the assemblies and any variants between the sequencing reads and the reference genes. drwxr-xr-x root/root 0 2017-06-28 20:59 ./ drwxr-xr-x root/root 0 2017-06-28 20:59 ./usr/ drwxr-xr-x root/root 0 2017-06-28 20:59 ./usr/bin/ -rwxr-xr-x root/root 23957 2017-06-28 20:59 ./usr/bin/ariba drwxr-xr-x root/root 0 2017-06-28 20:59 ./usr/lib/ drwxr-xr-x root/root 0 2017-06-28 20:59 ./usr/lib/python3/ drwxr-xr-x root/root 0 2017-06-28 20:59 ./usr/lib/python3/dist-packages/ drwxr-xr-x root/root 0 2017-06-28 20:59 ./usr/lib/python3/dist-packages/ariba-2.10.0.egg-info/ -rw-r--r-- root/root 518 2017-06-28 20:59 ./usr/lib/python3/dist-packages/ariba-2.10.0.egg-info/PKG-INFO -rw-r--r-- root/root 1 2017-06-28 20:59 ./usr/lib/python3/dist-packages/ariba-2.10.0.egg-info/dependency_links.txt -rw-r--r-- root/root 0 2017-06-28 20:59 ./usr/lib/python3/dist-packages/ariba-2.10.0.egg-info/requires.txt 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Keeping session: +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build-Space: 18260 Build-Time: 142 Distribution: artful-proposed Host Architecture: amd64 Install-Time: 62 Job: ariba_2.10.0+ds-1.dsc Machine Architecture: amd64 Package: ariba Package-Time: 204 Source-Version: 2.10.0+ds-1 Space: 18260 Status: successful Version: 2.10.0+ds-1 -------------------------------------------------------------------------------- Finished at 20170629-1715 Build needed 00:03:24, 18260k disc space RUN: /usr/share/launchpad-buildd/slavebin/scan-for-processes ['scan-for-processes', 'PACKAGEBUILD-12827438'] Scanning for processes to kill in build /home/buildd/build-PACKAGEBUILD-12827438/chroot-autobuild... RUN: /usr/share/launchpad-buildd/slavebin/umount-chroot ['umount-chroot', 'PACKAGEBUILD-12827438'] Unmounting chroot for build PACKAGEBUILD-12827438... RUN: /usr/share/launchpad-buildd/slavebin/remove-build ['remove-build', 'PACKAGEBUILD-12827438'] Removing build PACKAGEBUILD-12827438