RUN: /usr/share/launchpad-buildd/slavebin/slave-prep ['slave-prep'] Forking launchpad-buildd slave process... Kernel version: Linux lcy01-11 4.4.0-64-generic #85-Ubuntu SMP Mon Feb 20 11:50:30 UTC 2017 x86_64 Buildd toolchain package versions: launchpad-buildd_142 python-lpbuildd_142 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 dpkg-dev_1.18.4ubuntu1.1 python-debian_0.1.27ubuntu2 qemu-user-static_1:2.5+dfsg-5ubuntu10.9. Syncing the system clock with the buildd NTP service... 2 Mar 06:19:06 ntpdate[1896]: adjust time server 10.211.37.1 offset -0.000151 sec RUN: /usr/share/launchpad-buildd/slavebin/unpack-chroot ['unpack-chroot', 'PACKAGEBUILD-11933282', '/home/buildd/filecache-default/94f0b0f826e99ad354ce9a7a99ba3c310ddcc327'] Unpacking chroot for build PACKAGEBUILD-11933282 RUN: /usr/share/launchpad-buildd/slavebin/mount-chroot ['mount-chroot', 'PACKAGEBUILD-11933282'] Mounting chroot for build PACKAGEBUILD-11933282 RUN: /usr/share/launchpad-buildd/slavebin/override-sources-list ['override-sources-list', 'PACKAGEBUILD-11933282', 'deb http://ftpmaster.internal/ubuntu zesty main universe', 'deb http://ftpmaster.internal/ubuntu zesty-security main universe', 'deb http://ftpmaster.internal/ubuntu zesty-updates main universe', 'deb http://ftpmaster.internal/ubuntu zesty-proposed main universe'] Overriding sources.list in build-PACKAGEBUILD-11933282 RUN: /usr/share/launchpad-buildd/slavebin/update-debian-chroot ['update-debian-chroot', 'PACKAGEBUILD-11933282', 'amd64'] Updating debian chroot for build PACKAGEBUILD-11933282 Get:1 http://ftpmaster.internal/ubuntu zesty InRelease [256 kB] Get:2 http://ftpmaster.internal/ubuntu zesty-security InRelease [102 kB] Get:3 http://ftpmaster.internal/ubuntu zesty-updates InRelease [102 kB] Get:4 http://ftpmaster.internal/ubuntu zesty-proposed InRelease [253 kB] Get:5 http://ftpmaster.internal/ubuntu zesty/main amd64 Packages [1217 kB] Get:6 http://ftpmaster.internal/ubuntu zesty/main Translation-en [583 kB] Get:7 http://ftpmaster.internal/ubuntu zesty/universe amd64 Packages [8072 kB] Get:8 http://ftpmaster.internal/ubuntu zesty/universe Translation-en [4679 kB] Get:9 http://ftpmaster.internal/ubuntu zesty-proposed/main amd64 Packages [108 kB] Get:10 http://ftpmaster.internal/ubuntu zesty-proposed/main Translation-en [46.7 kB] Get:11 http://ftpmaster.internal/ubuntu zesty-proposed/universe amd64 Packages [311 kB] Get:12 http://ftpmaster.internal/ubuntu zesty-proposed/universe Translation-en [122 kB] Fetched 15.9 MB in 5s (2977 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: libperl5.22 perl-modules-5.22 Use 'sudo apt autoremove' to remove them. The following NEW packages will be installed: libidn2-0 libldap-common libperl5.24 libpsl5 libunistring0 perl-modules-5.24 The following packages will be upgraded: adduser advancecomp apt apt-transport-https base-files base-passwd bash binutils bsdutils bzip2 ca-certificates coreutils cpp cpp-6 debianutils diffutils dmsetup e2fslibs e2fsprogs findutils g++ g++-6 gcc gcc-6 gcc-6-base grep init init-system-helpers libapparmor1 libapt-pkg5.0 libasan3 libasn1-8-heimdal libassuan0 libatomic1 libblkid1 libbz2-1.0 libc-bin libc-dev-bin libc6 libc6-dev libcc1-0 libcilkrts5 libcomerr2 libcurl3-gnutls libdevmapper1.02.1 libfdisk1 libgcc-6-dev libgcc1 libgcrypt20 libgmp10 libgnutls30 libgomp1 libgpg-error0 libgssapi-krb5-2 libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhogweed4 libhx509-5-heimdal libisl15 libitm1 libk5crypto3 libkrb5-26-heimdal libkrb5-3 libkrb5support0 libksba8 libldap-2.4-2 liblockfile-bin liblockfile1 liblsan0 liblzma5 libmount1 libmpx2 libnettle6 libnpth0 libp11-kit0 libpng16-16 libquadmath0 libroken18-heimdal libsasl2-2 libsasl2-modules-db libseccomp2 libselinux1 libsemanage-common libsemanage1 libsepol1 libslang2 libsmartcols1 libsqlite3-0 libss2 libssl1.0.0 libstdc++-6-dev libstdc++6 libsystemd0 libtasn1-6 libtsan0 libubsan0 libudev1 libustr-1.0-1 libuuid1 libwind0-heimdal linux-libc-dev make mount multiarch-support openssl perl perl-base pinentry-curses pkg-create-dbgsym sed systemd systemd-sysv tar tzdata ubuntu-keyring util-linux xz-utils zlib1g 120 upgraded, 6 newly installed, 0 to remove and 0 not upgraded. Need to get 62.1 MB of archives. After this operation, 43.9 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu zesty/main amd64 perl-modules-5.24 all 5.24.1-1 [2662 kB] Get:2 http://ftpmaster.internal/ubuntu zesty/main amd64 libperl5.24 amd64 5.24.1-1 [3473 kB] Get:3 http://ftpmaster.internal/ubuntu zesty/main amd64 perl amd64 5.24.1-1 [219 kB] Get:4 http://ftpmaster.internal/ubuntu zesty/main amd64 perl-base amd64 5.24.1-1 [1341 kB] Get:5 http://ftpmaster.internal/ubuntu zesty/main amd64 libc6-dev amd64 2.24-7ubuntu2 [2274 kB] Get:6 http://ftpmaster.internal/ubuntu zesty/main amd64 libc-dev-bin amd64 2.24-7ubuntu2 [68.5 kB] Get:7 http://ftpmaster.internal/ubuntu zesty/main amd64 linux-libc-dev amd64 4.10.0-9.11 [893 kB] Get:8 http://ftpmaster.internal/ubuntu zesty-proposed/main amd64 libitm1 amd64 6.3.0-8ubuntu1 [27.9 kB] Get:9 http://ftpmaster.internal/ubuntu zesty-proposed/main amd64 gcc-6-base amd64 6.3.0-8ubuntu1 [17.3 kB] Get:10 http://ftpmaster.internal/ubuntu zesty-proposed/main amd64 libgcc1 amd64 1:6.3.0-8ubuntu1 [38.1 kB] Get:11 http://ftpmaster.internal/ubuntu zesty-proposed/main amd64 libcc1-0 amd64 6.3.0-8ubuntu1 [31.1 kB] Get:12 http://ftpmaster.internal/ubuntu zesty-proposed/main amd64 binutils amd64 2.27.90.20170221-1ubuntu1 [2432 kB] Get:13 http://ftpmaster.internal/ubuntu zesty-proposed/main amd64 libgomp1 amd64 6.3.0-8ubuntu1 [73.9 kB] Get:14 http://ftpmaster.internal/ubuntu zesty-proposed/main amd64 libatomic1 amd64 6.3.0-8ubuntu1 [9174 B] Get:15 http://ftpmaster.internal/ubuntu zesty-proposed/main amd64 libasan3 amd64 6.3.0-8ubuntu1 [316 kB] Get:16 http://ftpmaster.internal/ubuntu zesty-proposed/main amd64 liblsan0 amd64 6.3.0-8ubuntu1 [117 kB] Get:17 http://ftpmaster.internal/ubuntu zesty-proposed/main amd64 libtsan0 amd64 6.3.0-8ubuntu1 [261 kB] Get:18 http://ftpmaster.internal/ubuntu zesty-proposed/main amd64 libubsan0 amd64 6.3.0-8ubuntu1 [108 kB] Get:19 http://ftpmaster.internal/ubuntu zesty-proposed/main amd64 libcilkrts5 amd64 6.3.0-8ubuntu1 [40.8 kB] Get:20 http://ftpmaster.internal/ubuntu zesty-proposed/main amd64 libmpx2 amd64 6.3.0-8ubuntu1 [11.5 kB] Get:21 http://ftpmaster.internal/ubuntu zesty-proposed/main amd64 libquadmath0 amd64 6.3.0-8ubuntu1 [132 kB] Get:22 http://ftpmaster.internal/ubuntu zesty-proposed/main amd64 g++-6 amd64 6.3.0-8ubuntu1 [7393 kB] Get:23 http://ftpmaster.internal/ubuntu zesty-proposed/main amd64 libstdc++-6-dev amd64 6.3.0-8ubuntu1 [1424 kB] Get:24 http://ftpmaster.internal/ubuntu zesty-proposed/main amd64 libgcc-6-dev amd64 6.3.0-8ubuntu1 [2308 kB] Get:25 http://ftpmaster.internal/ubuntu zesty-proposed/main amd64 gcc-6 amd64 6.3.0-8ubuntu1 [7175 kB] Get:26 http://ftpmaster.internal/ubuntu zesty-proposed/main amd64 cpp-6 amd64 6.3.0-8ubuntu1 [6609 kB] Get:27 http://ftpmaster.internal/ubuntu zesty-proposed/main amd64 libstdc++6 amd64 6.3.0-8ubuntu1 [403 kB] Get:28 http://ftpmaster.internal/ubuntu zesty/main amd64 zlib1g amd64 1:1.2.11.dfsg-0ubuntu1 [54.2 kB] Get:29 http://ftpmaster.internal/ubuntu zesty-proposed/main amd64 libgmp10 amd64 2:6.1.2+dfsg-1 [240 kB] Get:30 http://ftpmaster.internal/ubuntu zesty/main amd64 libisl15 amd64 0.18-1 [545 kB] Get:31 http://ftpmaster.internal/ubuntu zesty/main amd64 libc6 amd64 2.24-7ubuntu2 [2587 kB] Get:32 http://ftpmaster.internal/ubuntu zesty-proposed/main amd64 bzip2 amd64 1.0.6-8.1 [33.4 kB] Get:33 http://ftpmaster.internal/ubuntu zesty-proposed/main amd64 libbz2-1.0 amd64 1.0.6-8.1 [30.9 kB] Get:34 http://ftpmaster.internal/ubuntu zesty-proposed/main amd64 init-system-helpers all 1.47 [37.8 kB] Get:35 http://ftpmaster.internal/ubuntu zesty/main amd64 base-files amd64 9.6ubuntu12 [59.0 kB] Get:36 http://ftpmaster.internal/ubuntu zesty/main amd64 debianutils amd64 4.8.1 [85.7 kB] Get:37 http://ftpmaster.internal/ubuntu zesty/main amd64 bash amd64 4.4-2ubuntu1 [624 kB] Get:38 http://ftpmaster.internal/ubuntu zesty/main amd64 bsdutils amd64 1:2.29-1ubuntu2 [55.3 kB] Get:39 http://ftpmaster.internal/ubuntu zesty/main amd64 coreutils amd64 8.26-3ubuntu3 [1204 kB] Get:40 http://ftpmaster.internal/ubuntu zesty/main amd64 diffutils amd64 1:3.5-3 [166 kB] Get:41 http://ftpmaster.internal/ubuntu zesty/main amd64 e2fslibs amd64 1.43.4-2 [153 kB] Get:42 http://ftpmaster.internal/ubuntu zesty/main amd64 e2fsprogs amd64 1.43.4-2 [488 kB] Get:43 http://ftpmaster.internal/ubuntu zesty/main amd64 findutils amd64 4.6.0+git+20161106-2 [282 kB] Get:44 http://ftpmaster.internal/ubuntu zesty/main amd64 grep amd64 2.27-2 [154 kB] Get:45 http://ftpmaster.internal/ubuntu zesty/main amd64 libuuid1 amd64 2.29-1ubuntu2 [14.7 kB] Get:46 http://ftpmaster.internal/ubuntu zesty/main amd64 libblkid1 amd64 2.29-1ubuntu2 [110 kB] Get:47 http://ftpmaster.internal/ubuntu zesty/main amd64 libfdisk1 amd64 2.29-1ubuntu2 [144 kB] Get:48 http://ftpmaster.internal/ubuntu zesty/main amd64 libselinux1 amd64 2.6-3 [67.8 kB] Get:49 http://ftpmaster.internal/ubuntu zesty/main amd64 util-linux amd64 2.29-1ubuntu2 [911 kB] Get:50 http://ftpmaster.internal/ubuntu zesty/main amd64 mount amd64 2.29-1ubuntu2 [129 kB] Get:51 http://ftpmaster.internal/ubuntu zesty/main amd64 sed amd64 4.4-1 [182 kB] Get:52 http://ftpmaster.internal/ubuntu zesty/main amd64 tar amd64 1.29b-1.1 [232 kB] Get:53 http://ftpmaster.internal/ubuntu zesty/main amd64 base-passwd amd64 3.5.43 [48.4 kB] Get:54 http://ftpmaster.internal/ubuntu zesty/main amd64 libc-bin amd64 2.24-7ubuntu2 [635 kB] Get:55 http://ftpmaster.internal/ubuntu zesty/main amd64 liblzma5 amd64 5.2.2-1.2 [91.0 kB] Get:56 http://ftpmaster.internal/ubuntu zesty-proposed/main amd64 libapt-pkg5.0 amd64 1.4~rc2 [787 kB] Get:57 http://ftpmaster.internal/ubuntu zesty/main amd64 adduser all 3.113+nmu3ubuntu5 [161 kB] Get:58 http://ftpmaster.internal/ubuntu zesty/main amd64 ubuntu-keyring all 2016.10.27 [16.6 kB] Get:59 http://ftpmaster.internal/ubuntu zesty-proposed/main amd64 apt amd64 1.4~rc2 [1096 kB] Get:60 http://ftpmaster.internal/ubuntu zesty-proposed/main amd64 libapparmor1 amd64 2.11.0-2ubuntu2 [30.6 kB] Get:61 http://ftpmaster.internal/ubuntu zesty/main amd64 libgpg-error0 amd64 1.26-2 [34.6 kB] Get:62 http://ftpmaster.internal/ubuntu zesty/main amd64 libgcrypt20 amd64 1.7.6-1 [399 kB] Get:63 http://ftpmaster.internal/ubuntu zesty/main amd64 libmount1 amd64 2.29-1ubuntu2 [119 kB] Get:64 http://ftpmaster.internal/ubuntu zesty/main amd64 libseccomp2 amd64 2.3.1-2.1ubuntu1 [37.5 kB] Get:65 http://ftpmaster.internal/ubuntu zesty/main amd64 systemd amd64 232-18ubuntu1 [2364 kB] Get:66 http://ftpmaster.internal/ubuntu zesty/main amd64 libsystemd0 amd64 232-18ubuntu1 [208 kB] Get:67 http://ftpmaster.internal/ubuntu zesty-proposed/main amd64 init amd64 1.47 [5832 B] Get:68 http://ftpmaster.internal/ubuntu zesty/main amd64 systemd-sysv amd64 232-18ubuntu1 [12.1 kB] Get:69 http://ftpmaster.internal/ubuntu zesty/main amd64 liblockfile-bin amd64 1.14-1 [10.8 kB] Get:70 http://ftpmaster.internal/ubuntu zesty/main amd64 liblockfile1 amd64 1.14-1 [6344 B] Get:71 http://ftpmaster.internal/ubuntu zesty/main amd64 libunistring0 amd64 0.9.3-5.2ubuntu1 [279 kB] Get:72 http://ftpmaster.internal/ubuntu zesty/main amd64 libcomerr2 amd64 1.43.4-2 [9172 B] Get:73 http://ftpmaster.internal/ubuntu zesty/main amd64 libsepol1 amd64 2.6-2 [220 kB] Get:74 http://ftpmaster.internal/ubuntu zesty/main amd64 libustr-1.0-1 amd64 1.0.4-6 [66.1 kB] Get:75 http://ftpmaster.internal/ubuntu zesty/main amd64 libsemanage-common all 2.6-2 [6794 B] Get:76 http://ftpmaster.internal/ubuntu zesty/main amd64 libsemanage1 amd64 2.6-2 [82.6 kB] Get:77 http://ftpmaster.internal/ubuntu zesty/main amd64 libsmartcols1 amd64 2.29-1ubuntu2 [69.4 kB] Get:78 http://ftpmaster.internal/ubuntu zesty/main amd64 libss2 amd64 1.43.4-2 [10.7 kB] Get:79 http://ftpmaster.internal/ubuntu zesty/main amd64 libudev1 amd64 232-18ubuntu1 [55.1 kB] Get:80 http://ftpmaster.internal/ubuntu zesty/main amd64 multiarch-support amd64 2.24-7ubuntu2 [6816 B] Get:81 http://ftpmaster.internal/ubuntu zesty/main amd64 tzdata all 2016j-2 [204 kB] Get:82 http://ftpmaster.internal/ubuntu zesty/main amd64 libdevmapper1.02.1 amd64 2:1.02.136-1ubuntu1 [135 kB] Get:83 http://ftpmaster.internal/ubuntu zesty/main amd64 dmsetup amd64 2:1.02.136-1ubuntu1 [71.7 kB] Get:84 http://ftpmaster.internal/ubuntu zesty/main amd64 libroken18-heimdal amd64 7.1.0+dfsg-9ubuntu1 [41.0 kB] Get:85 http://ftpmaster.internal/ubuntu zesty/main amd64 libasn1-8-heimdal amd64 7.1.0+dfsg-9ubuntu1 [176 kB] Get:86 http://ftpmaster.internal/ubuntu zesty/main amd64 libassuan0 amd64 2.4.3-2 [34.5 kB] Get:87 http://ftpmaster.internal/ubuntu zesty/main amd64 libhogweed4 amd64 3.3-1 [135 kB] Get:88 http://ftpmaster.internal/ubuntu zesty/main amd64 libnettle6 amd64 3.3-1 [92.4 kB] Get:89 http://ftpmaster.internal/ubuntu zesty/main amd64 libp11-kit0 amd64 0.23.3-5 [107 kB] Get:90 http://ftpmaster.internal/ubuntu zesty/main amd64 libtasn1-6 amd64 4.10-1 [35.4 kB] Get:91 http://ftpmaster.internal/ubuntu zesty-proposed/main amd64 libgnutls30 amd64 3.5.6-4ubuntu3 [627 kB] Get:92 http://ftpmaster.internal/ubuntu zesty/main amd64 libheimbase1-heimdal amd64 7.1.0+dfsg-9ubuntu1 [29.4 kB] Get:93 http://ftpmaster.internal/ubuntu zesty/main amd64 libhcrypto4-heimdal amd64 7.1.0+dfsg-9ubuntu1 [87.4 kB] Get:94 http://ftpmaster.internal/ubuntu zesty/main amd64 libwind0-heimdal amd64 7.1.0+dfsg-9ubuntu1 [48.2 kB] Get:95 http://ftpmaster.internal/ubuntu zesty/main amd64 libhx509-5-heimdal amd64 7.1.0+dfsg-9ubuntu1 [108 kB] Get:96 http://ftpmaster.internal/ubuntu zesty/main amd64 libsqlite3-0 amd64 3.16.2-2 [486 kB] Get:97 http://ftpmaster.internal/ubuntu zesty/main amd64 libkrb5-26-heimdal amd64 7.1.0+dfsg-9ubuntu1 [206 kB] Get:98 http://ftpmaster.internal/ubuntu zesty/main amd64 libheimntlm0-heimdal amd64 7.1.0+dfsg-9ubuntu1 [15.1 kB] Get:99 http://ftpmaster.internal/ubuntu zesty/main amd64 libgssapi3-heimdal amd64 7.1.0+dfsg-9ubuntu1 [96.7 kB] Get:100 http://ftpmaster.internal/ubuntu zesty/main amd64 libksba8 amd64 1.3.5-2 [92.6 kB] Get:101 http://ftpmaster.internal/ubuntu zesty/main amd64 libsasl2-modules-db amd64 2.1.27~72-g88d82a3+dfsg-1 [15.1 kB] Get:102 http://ftpmaster.internal/ubuntu zesty/main amd64 libsasl2-2 amd64 2.1.27~72-g88d82a3+dfsg-1 [48.8 kB] Get:103 http://ftpmaster.internal/ubuntu zesty-proposed/main amd64 libldap-common all 2.4.44+dfsg-3ubuntu2 [16.8 kB] Get:104 http://ftpmaster.internal/ubuntu zesty-proposed/main amd64 libldap-2.4-2 amd64 2.4.44+dfsg-3ubuntu2 [155 kB] Get:105 http://ftpmaster.internal/ubuntu zesty/main amd64 libnpth0 amd64 1.3-1 [8054 B] Get:106 http://ftpmaster.internal/ubuntu zesty/main amd64 libslang2 amd64 2.3.1-5ubuntu1 [422 kB] Get:107 http://ftpmaster.internal/ubuntu zesty/main amd64 libssl1.0.0 amd64 1.0.2g-1ubuntu11 [1080 kB] Get:108 http://ftpmaster.internal/ubuntu zesty/main amd64 pinentry-curses amd64 1.0.0-2 [32.7 kB] Get:109 http://ftpmaster.internal/ubuntu zesty/main amd64 xz-utils amd64 5.2.2-1.2 [83.2 kB] Get:110 http://ftpmaster.internal/ubuntu zesty-proposed/main amd64 libgssapi-krb5-2 amd64 1.15-1 [120 kB] Get:111 http://ftpmaster.internal/ubuntu zesty-proposed/main amd64 libkrb5-3 amd64 1.15-1 [275 kB] Get:112 http://ftpmaster.internal/ubuntu zesty-proposed/main amd64 libkrb5support0 amd64 1.15-1 [31.9 kB] Get:113 http://ftpmaster.internal/ubuntu zesty-proposed/main amd64 libk5crypto3 amd64 1.15-1 [84.8 kB] Get:114 http://ftpmaster.internal/ubuntu zesty/universe amd64 libidn2-0 amd64 0.16-1 [47.6 kB] Get:115 http://ftpmaster.internal/ubuntu zesty/universe amd64 libpsl5 amd64 0.17.0-4 [39.4 kB] Get:116 http://ftpmaster.internal/ubuntu zesty-proposed/main amd64 libcurl3-gnutls amd64 7.52.1-3ubuntu1 [193 kB] Get:117 http://ftpmaster.internal/ubuntu zesty-proposed/main amd64 apt-transport-https amd64 1.4~rc2 [34.4 kB] Get:118 http://ftpmaster.internal/ubuntu zesty/main amd64 openssl amd64 1.0.2g-1ubuntu11 [491 kB] Get:119 http://ftpmaster.internal/ubuntu zesty/main amd64 ca-certificates all 20161130 [193 kB] Get:120 http://ftpmaster.internal/ubuntu zesty/main amd64 libpng16-16 amd64 1.6.28-1 [172 kB] Get:121 http://ftpmaster.internal/ubuntu zesty-proposed/main amd64 advancecomp amd64 1.23-1 [197 kB] Get:122 http://ftpmaster.internal/ubuntu zesty-proposed/main amd64 cpp amd64 4:6.3.0-1ubuntu3 [27.5 kB] Get:123 http://ftpmaster.internal/ubuntu zesty-proposed/main amd64 gcc amd64 4:6.3.0-1ubuntu3 [5172 B] Get:124 http://ftpmaster.internal/ubuntu zesty-proposed/main amd64 g++ amd64 4:6.3.0-1ubuntu3 [1472 B] Get:125 http://ftpmaster.internal/ubuntu zesty/main amd64 make amd64 4.1-9.1 [154 kB] Get:126 http://ftpmaster.internal/ubuntu zesty/main amd64 pkg-create-dbgsym all 0.73 [8952 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 62.1 MB in 6s (10.1 MB/s) (Reading database ... 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Setting up libcilkrts5:amd64 (6.3.0-8ubuntu1) ... Setting up tzdata (2016j-2) ... Current default time zone: 'Etc/UTC' Local time is now: Thu Mar 2 06:19:57 UTC 2017. Universal Time is now: Thu Mar 2 06:19:57 UTC 2017. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up systemd-sysv (232-18ubuntu1) ... Setting up libubsan0:amd64 (6.3.0-8ubuntu1) ... Setting up libtsan0:amd64 (6.3.0-8ubuntu1) ... Setting up liblockfile1:amd64 (1.14-1) ... Setting up libsasl2-modules-db:amd64 (2.1.27~72-g88d82a3+dfsg-1) ... Setting up linux-libc-dev:amd64 (4.10.0-9.11) ... Setting up advancecomp (1.23-1) ... Setting up libsasl2-2:amd64 (2.1.27~72-g88d82a3+dfsg-1) ... Setting up libroken18-heimdal:amd64 (7.1.0+dfsg-9ubuntu1) ... Setting up libksba8:amd64 (1.3.5-2) ... Setting up libdevmapper1.02.1:amd64 (2:1.02.136-1ubuntu1) ... Setting up libkrb5support0:amd64 (1.15-1) ... Setting up libtasn1-6:amd64 (4.10-1) ... Setting up bzip2 (1.0.6-8.1) ... Setting up liblsan0:amd64 (6.3.0-8ubuntu1) ... Setting up perl (5.24.1-1) ... Installing new version of config file /etc/perl/sitecustomize.pl ... Setting up libmpx2:amd64 (6.3.0-8ubuntu1) ... Setting up libgmp10:amd64 (2:6.1.2+dfsg-1) ... Processing triggers for libc-bin (2.24-7ubuntu2) ... Setting up pkg-create-dbgsym (0.73) ... Setting up libunistring0:amd64 (0.9.3-5.2ubuntu1) ... Setting up xz-utils (5.2.2-1.2) ... Setting up libheimbase1-heimdal:amd64 (7.1.0+dfsg-9ubuntu1) ... Setting up libp11-kit0:amd64 (0.23.3-5) ... Setting up openssl (1.0.2g-1ubuntu11) ... Setting up libsqlite3-0:amd64 (3.16.2-2) ... Setting up dmsetup (2:1.02.136-1ubuntu1) ... Setting up binutils (2.27.90.20170221-1ubuntu1) ... Setting up libc-dev-bin (2.24-7ubuntu2) ... Setting up ca-certificates (20161130) ... Updating certificates in /etc/ssl/certs... 10 added, 10 removed; done. Setting up libc6-dev:amd64 (2.24-7ubuntu2) ... Setting up libslang2:amd64 (2.3.1-5ubuntu1) ... Setting up libassuan0:amd64 (2.4.3-2) ... Setting up libitm1:amd64 (6.3.0-8ubuntu1) ... Setting up libk5crypto3:amd64 (1.15-1) ... Setting up libgcc-6-dev:amd64 (6.3.0-8ubuntu1) ... Setting up libidn2-0:amd64 (0.16-1) ... Setting up libstdc++-6-dev:amd64 (6.3.0-8ubuntu1) ... Setting up libwind0-heimdal:amd64 (7.1.0+dfsg-9ubuntu1) ... Setting up libpsl5:amd64 (0.17.0-4) ... Setting up init (1.47) ... Setting up libasn1-8-heimdal:amd64 (7.1.0+dfsg-9ubuntu1) ... Setting up libhcrypto4-heimdal:amd64 (7.1.0+dfsg-9ubuntu1) ... Setting up libhx509-5-heimdal:amd64 (7.1.0+dfsg-9ubuntu1) ... Setting up libhogweed4:amd64 (3.3-1) ... Setting up libisl15:amd64 (0.18-1) ... Setting up pinentry-curses (1.0.0-2) ... Setting up libkrb5-3:amd64 (1.15-1) ... Setting up cpp-6 (6.3.0-8ubuntu1) ... Setting up libkrb5-26-heimdal:amd64 (7.1.0+dfsg-9ubuntu1) ... Setting up libheimntlm0-heimdal:amd64 (7.1.0+dfsg-9ubuntu1) ... Setting up cpp (4:6.3.0-1ubuntu3) ... Setting up libgnutls30:amd64 (3.5.6-4ubuntu3) ... Setting up gcc-6 (6.3.0-8ubuntu1) ... Setting up libgssapi-krb5-2:amd64 (1.15-1) ... Setting up g++-6 (6.3.0-8ubuntu1) ... Setting up libgssapi3-heimdal:amd64 (7.1.0+dfsg-9ubuntu1) ... Setting up gcc (4:6.3.0-1ubuntu3) ... Setting up libldap-2.4-2:amd64 (2.4.44+dfsg-3ubuntu2) ... Setting up g++ (4:6.3.0-1ubuntu3) ... Setting up libcurl3-gnutls:amd64 (7.52.1-3ubuntu1) ... Setting up apt-transport-https (1.4~rc2) ... Processing triggers for libc-bin (2.24-7ubuntu2) ... Processing triggers for ca-certificates (20161130) ... 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-11933282', 'amd64', 'zesty-proposed', '-c', 'chroot:autobuild', '--arch=amd64', '--dist=zesty-proposed', '--purge=never', '--nolog', '-A', 'ariba_2.7.1+ds-1.dsc'] Initiating build PACKAGEBUILD-11933282 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.4.0-64-generic #85-Ubuntu SMP Mon Feb 20 11:50:30 UTC 2017 x86_64 sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on lcy01-11.buildd +==============================================================================+ | ariba 2.7.1+ds-1 (amd64) 02 Mar 2017 06:20 | +==============================================================================+ Package: ariba Version: 2.7.1+ds-1 Source Version: 2.7.1+ds-1 Distribution: zesty-proposed Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 I: NOTICE: Log filtering will replace 'build/ariba-jXw0WU/ariba-2.7.1+ds' with '<>' I: NOTICE: Log filtering will replace 'build/ariba-jXw0WU' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-11933282/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- ariba_2.7.1+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-KMMl_p/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/<>/resolver-KMMl_p/apt_archive ./ InRelease Get:2 copy:/<>/resolver-KMMl_p/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-KMMl_p/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-KMMl_p/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-KMMl_p/apt_archive ./ Packages [525 B] Fetched 2858 B in 0s (240 kB/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install core build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: libperl5.22 perl-modules-5.22 Use 'sudo apt autoremove' to remove them. The following NEW packages will be installed: sbuild-build-depends-core-dummy 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 770 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-KMMl_p/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [770 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 770 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 14170 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 (>= 0.10.1), python3-pysam (>= 0.9.1), python3-nose (>= 1.3), python3-bs4 (>= 4.1.0), bowtie2 (>= 2.1.0), cd-hit, mash, libminimap-dev, libfml-dev, mummer, fastaq (>= 3.12.0), help2man, asciidoctor Filtered Build-Depends: debhelper (>= 9), python3, python3-dev, python3-dendropy (>= 4.2.0), python3-setuptools, python3-pymummer (>= 0.10.1), python3-pysam (>= 0.9.1), python3-nose (>= 1.3), python3-bs4 (>= 4.1.0), bowtie2 (>= 2.1.0), cd-hit, mash, libminimap-dev, libfml-dev, mummer, fastaq (>= 3.12.0), help2man, asciidoctor dpkg-deb: building package 'sbuild-build-depends-ariba-dummy' in '/<>/resolver-eUhNps/apt_archive/sbuild-build-depends-ariba-dummy.deb'. Ign:1 copy:/<>/resolver-eUhNps/apt_archive ./ InRelease Get:2 copy:/<>/resolver-eUhNps/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-eUhNps/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-eUhNps/apt_archive ./ Sources [335 B] Get:5 copy:/<>/resolver-eUhNps/apt_archive ./ Packages [653 B] Fetched 3107 B in 0s (250 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 packages were automatically installed and are no longer required: libperl5.22 perl-modules-5.22 Use 'sudo apt autoremove' to remove them. The following additional packages will be installed: asciidoctor autoconf automake autopoint autotools-dev bowtie2 bsdmainutils cd-hit debhelper dh-autoreconf dh-python dh-strip-nondeterminism fastaq file gawk gettext gettext-base groff-base help2man intltool-debian libarchive-zip-perl libbsd0 libcapnp-0.5.3 libcroco3 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl libfml-dev libfml0 libglib2.0-0 libgsl2 libhts1 libicu57 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 libruby2.3 libsigsegv2 libtbb2 libtimedate-perl libtool libxml2 libyaml-0-2 m4 man-db mash mime-support mummer po-debconf python python-minimal python2.7 python2.7-minimal python3 python3-bs4 python3-dendropy python3-dev python3-minimal python3-nose python3-pkg-resources python3-pymummer python3-pysam python3-setuptools python3.5 python3.5-dev python3.5-minimal rake ruby ruby-did-you-mean ruby-minitest ruby-net-telnet ruby-power-assert ruby-test-unit ruby2.3 rubygems-integration samtools zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc 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 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-tk python3-venv python-nose-doc python-setuptools-doc python3.5-venv python3.5-doc ri ruby-dev bundler Recommended packages: curl | wget | lynx-cur libglib2.0-data shared-mime-info xdg-user-dirs libltdl-dev xml-core libmail-sendmail-perl python3-chardet python3-lxml zip fonts-lato libjs-jquery The following NEW packages will be installed: asciidoctor autoconf automake autopoint autotools-dev bowtie2 bsdmainutils cd-hit debhelper dh-autoreconf dh-python dh-strip-nondeterminism fastaq file gawk gettext gettext-base groff-base help2man intltool-debian libarchive-zip-perl libbsd0 libcapnp-0.5.3 libcroco3 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl libfml-dev libfml0 libglib2.0-0 libgsl2 libhts1 libicu57 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 libruby2.3 libsigsegv2 libtbb2 libtimedate-perl libtool libxml2 libyaml-0-2 m4 man-db mash mime-support mummer po-debconf python python-minimal python2.7 python2.7-minimal python3 python3-bs4 python3-dendropy python3-dev python3-minimal python3-nose python3-pkg-resources python3-pymummer python3-pysam python3-setuptools python3.5 python3.5-dev python3.5-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 zlib1g-dev 0 upgraded, 91 newly installed, 0 to remove and 0 not upgraded. Need to get 83.0 MB of archives. After this operation, 276 MB of additional disk space will be used. Get:1 copy:/<>/resolver-eUhNps/apt_archive ./ sbuild-build-depends-ariba-dummy 0.invalid.0 [900 B] Get:2 http://ftpmaster.internal/ubuntu zesty/main amd64 liblocale-gettext-perl amd64 1.07-3build1 [16.7 kB] Get:3 http://ftpmaster.internal/ubuntu zesty/main amd64 libpython3.5-minimal amd64 3.5.3-1 [531 kB] Get:4 http://ftpmaster.internal/ubuntu zesty/main amd64 libexpat1 amd64 2.2.0-2 [72.2 kB] Get:5 http://ftpmaster.internal/ubuntu zesty/main amd64 python3.5-minimal amd64 3.5.3-1 [1634 kB] Get:6 http://ftpmaster.internal/ubuntu zesty-proposed/main amd64 python3-minimal amd64 3.5.3-1 [23.4 kB] Get:7 http://ftpmaster.internal/ubuntu zesty/main amd64 mime-support all 3.60ubuntu1 [30.1 kB] Get:8 http://ftpmaster.internal/ubuntu zesty/main amd64 libmpdec2 amd64 2.4.2-1 [82.6 kB] Get:9 http://ftpmaster.internal/ubuntu zesty/main amd64 libpython3.5-stdlib amd64 3.5.3-1 [2163 kB] Get:10 http://ftpmaster.internal/ubuntu zesty/main amd64 python3.5 amd64 3.5.3-1 [175 kB] Get:11 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amd64 libpython2.7-minimal amd64 2.7.13-2 [338 kB] Get:22 http://ftpmaster.internal/ubuntu zesty/main amd64 python2.7-minimal amd64 2.7.13-2 [1327 kB] Get:23 http://ftpmaster.internal/ubuntu zesty/main amd64 python-minimal amd64 2.7.13-2 [28.2 kB] Get:24 http://ftpmaster.internal/ubuntu zesty/main amd64 libpython2.7-stdlib amd64 2.7.13-2 [1898 kB] Get:25 http://ftpmaster.internal/ubuntu zesty/main amd64 python2.7 amd64 2.7.13-2 [229 kB] Get:26 http://ftpmaster.internal/ubuntu zesty/main amd64 libpython-stdlib amd64 2.7.13-2 [7774 B] Get:27 http://ftpmaster.internal/ubuntu zesty/main amd64 python amd64 2.7.13-2 [139 kB] Get:28 http://ftpmaster.internal/ubuntu zesty/main amd64 libmagic-mgc amd64 1:5.29-3 [181 kB] Get:29 http://ftpmaster.internal/ubuntu zesty/main amd64 libmagic1 amd64 1:5.29-3 [68.3 kB] Get:30 http://ftpmaster.internal/ubuntu zesty/main amd64 file amd64 1:5.29-3 [21.8 kB] Get:31 http://ftpmaster.internal/ubuntu zesty/main amd64 gettext-base amd64 0.19.8.1-1ubuntu2 [48.7 kB] Get:32 http://ftpmaster.internal/ubuntu zesty/main amd64 libglib2.0-0 amd64 2.51.2-1 [1144 kB] Get:33 http://ftpmaster.internal/ubuntu zesty/main amd64 libicu57 amd64 57.1-5 [7674 kB] Get:34 http://ftpmaster.internal/ubuntu zesty/main amd64 libxml2 amd64 2.9.4+dfsg1-2.2 [698 kB] Get:35 http://ftpmaster.internal/ubuntu zesty/main amd64 libyaml-0-2 amd64 0.1.7-2 [47.2 kB] Get:36 http://ftpmaster.internal/ubuntu zesty/main amd64 rubygems-integration all 1.11 [4994 B] Get:37 http://ftpmaster.internal/ubuntu zesty/main amd64 rake all 10.5.0-2 [48.2 kB] Get:38 http://ftpmaster.internal/ubuntu zesty/main amd64 ruby-did-you-mean all 1.0.0-2 [8390 B] Get:39 http://ftpmaster.internal/ubuntu zesty/main amd64 ruby-minitest all 5.9.0-1 [37.0 kB] Get:40 http://ftpmaster.internal/ubuntu zesty/main amd64 ruby-net-telnet all 0.1.1-2 [12.6 kB] Get:41 http://ftpmaster.internal/ubuntu zesty/main amd64 ruby-power-assert all 0.3.0-1 [7952 B] Get:42 http://ftpmaster.internal/ubuntu zesty/main amd64 ruby-test-unit all 3.1.7-2 [60.3 kB] Get:43 http://ftpmaster.internal/ubuntu zesty/main amd64 libruby2.3 amd64 2.3.3-1 [2954 kB] Get:44 http://ftpmaster.internal/ubuntu zesty/main amd64 ruby2.3 amd64 2.3.3-1 [40.9 kB] Get:45 http://ftpmaster.internal/ubuntu zesty-proposed/main amd64 ruby amd64 1:2.3.3 [5636 B] Get:46 http://ftpmaster.internal/ubuntu zesty/universe amd64 asciidoctor all 1.5.4-2 [148 kB] Get:47 http://ftpmaster.internal/ubuntu zesty/main amd64 m4 amd64 1.4.18-1 [197 kB] Get:48 http://ftpmaster.internal/ubuntu zesty/main amd64 autoconf all 2.69-10 [321 kB] Get:49 http://ftpmaster.internal/ubuntu zesty/main amd64 autotools-dev all 20161112.1 [39.5 kB] Get:50 http://ftpmaster.internal/ubuntu zesty/main amd64 automake all 1:1.15-5ubuntu1 [509 kB] Get:51 http://ftpmaster.internal/ubuntu zesty/main amd64 autopoint all 0.19.8.1-1ubuntu2 [412 kB] Get:52 http://ftpmaster.internal/ubuntu zesty/universe amd64 cd-hit amd64 4.6.6-2 [851 kB] Get:53 http://ftpmaster.internal/ubuntu zesty/main amd64 libtool all 2.4.6-2 [194 kB] Get:54 http://ftpmaster.internal/ubuntu zesty/main amd64 dh-autoreconf all 13 [15.6 kB] Get:55 http://ftpmaster.internal/ubuntu zesty/main amd64 libarchive-zip-perl all 1.59-1 [84.0 kB] Get:56 http://ftpmaster.internal/ubuntu zesty/main amd64 libfile-stripnondeterminism-perl all 0.031-1 [12.8 kB] Get:57 http://ftpmaster.internal/ubuntu zesty/main amd64 libtimedate-perl all 2.3000-2 [37.5 kB] Get:58 http://ftpmaster.internal/ubuntu zesty/main amd64 dh-strip-nondeterminism all 0.031-1 [4884 B] Get:59 http://ftpmaster.internal/ubuntu zesty/main amd64 libcroco3 amd64 0.6.11-2 [81.1 kB] Get:60 http://ftpmaster.internal/ubuntu zesty/main amd64 gettext amd64 0.19.8.1-1ubuntu2 [1083 kB] Get:61 http://ftpmaster.internal/ubuntu zesty/main amd64 intltool-debian all 0.35.0+20060710.4 [24.9 kB] Get:62 http://ftpmaster.internal/ubuntu zesty/main amd64 po-debconf all 1.0.20 [232 kB] Get:63 http://ftpmaster.internal/ubuntu zesty/main amd64 debhelper all 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http://ftpmaster.internal/ubuntu zesty/main amd64 libgsl2 amd64 2.3+dfsg-1 [871 kB] Get:75 http://ftpmaster.internal/ubuntu zesty/universe amd64 libminimap0 amd64 0.2-3 [22.2 kB] Get:76 http://ftpmaster.internal/ubuntu zesty/universe amd64 libminimap-dev amd64 0.2-3 [32.8 kB] Get:77 http://ftpmaster.internal/ubuntu zesty/main amd64 libpython3.5 amd64 3.5.3-1 [1372 kB] Get:78 http://ftpmaster.internal/ubuntu zesty/main amd64 libpython3.5-dev amd64 3.5.3-1 [37.7 MB] Get:79 http://ftpmaster.internal/ubuntu zesty-proposed/main amd64 libpython3-dev amd64 3.5.3-1 [6932 B] Get:80 http://ftpmaster.internal/ubuntu zesty/universe amd64 mash amd64 1.1.1-1 [127 kB] Get:81 http://ftpmaster.internal/ubuntu zesty/universe amd64 mummer amd64 3.23+dfsg-2 [811 kB] Get:82 http://ftpmaster.internal/ubuntu zesty/main amd64 python3-bs4 all 4.5.3-1 [66.6 kB] Get:83 http://ftpmaster.internal/ubuntu zesty/universe amd64 python3-dendropy all 4.2.0+dfsg-1 [7307 kB] Get:84 http://ftpmaster.internal/ubuntu zesty/main amd64 python3.5-dev amd64 3.5.3-1 [413 kB] Get:85 http://ftpmaster.internal/ubuntu zesty-proposed/main amd64 python3-dev amd64 3.5.3-1 [1190 B] Get:86 http://ftpmaster.internal/ubuntu zesty/universe amd64 python3-nose all 1.3.7-2 [116 kB] Get:87 http://ftpmaster.internal/ubuntu zesty/universe amd64 python3-pymummer all 0.10.2-1 [9030 B] Get:88 http://ftpmaster.internal/ubuntu zesty/universe amd64 python3-pysam amd64 0.10.0+ds-1ubuntu1 [1298 kB] Get:89 http://ftpmaster.internal/ubuntu zesty/main amd64 python3-setuptools all 33.1.1-1 [175 kB] Get:90 http://ftpmaster.internal/ubuntu zesty/universe amd64 libtbb2 amd64 4.4~20160526-0ubuntu1 [111 kB] Get:91 http://ftpmaster.internal/ubuntu zesty/universe amd64 bowtie2 amd64 2.3.0-2ubuntu1 [1163 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 83.0 MB in 4s (17.4 MB/s) Selecting previously unselected package liblocale-gettext-perl. 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Setting up libxml2:amd64 (2.9.4+dfsg1-2.2) ... Setting up libmagic-mgc (1:5.29-3) ... Setting up libmagic1:amd64 (1:5.29-3) ... Setting up libcroco3:amd64 (0.6.11-2) ... Setting up ruby-did-you-mean (1.0.0-2) ... Setting up libyaml-0-2:amd64 (0.1.7-2) ... Setting up libminimap0 (0.2-3) ... Processing triggers for libc-bin (2.24-7ubuntu2) ... Setting up autotools-dev (20161112.1) ... Setting up libfml0 (0.1-2) ... 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 (2.2.0-2) ... 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 samtools (1.3.1-3) ... Setting up ruby-minitest (5.9.0-1) ... Setting up libpython2.7-stdlib:amd64 (2.7.13-2) ... Setting up autopoint (0.19.8.1-1ubuntu2) ... Setting up libmpdec2:amd64 (2.4.2-1) ... Setting up ruby-power-assert (0.3.0-1) ... Setting up zlib1g-dev:amd64 (1:1.2.11.dfsg-0ubuntu1) ... Setting up libfile-stripnondeterminism-perl (0.031-1) ... Setting up mash (1.1.1-1) ... Setting up ruby-test-unit (3.1.7-2) ... Setting up gettext (0.19.8.1-1ubuntu2) ... Setting up mummer (3.23+dfsg-2) ... Setting up libpython3.5-stdlib:amd64 (3.5.3-1) ... Setting up python2.7 (2.7.13-2) ... Setting up libminimap-dev (0.2-3) ... Setting up libfml-dev (0.1-2) ... Setting up autoconf (2.69-10) ... Setting up file (1:5.29-3) ... Setting up libpython-stdlib:amd64 (2.7.13-2) ... Setting up intltool-debian (0.35.0+20060710.4) ... Setting up automake (1:1.15-5ubuntu1) ... 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 python (2.7.13-2) ... Setting up libtool (2.4.6-2) ... Setting up python3.5 (3.5.3-1) ... Setting up libpython3-stdlib:amd64 (3.5.3-1) ... Setting up po-debconf (1.0.20) ... Setting up libpython3.5:amd64 (3.5.3-1) ... Setting up libpython3.5-dev:amd64 (3.5.3-1) ... Setting up bowtie2 (2.3.0-2ubuntu1) ... Setting up python3.5-dev (3.5.3-1) ... Setting up libpython3-dev:amd64 (3.5.3-1) ... Setting up python3 (3.5.3-1) ... Setting up rake (10.5.0-2) ... Setting up python3-dev (3.5.3-1) ... Setting up python3-pkg-resources (33.1.1-1) ... Setting up python3-bs4 (4.5.3-1) ... Setting up fastaq (3.14.0-1) ... Setting up dh-strip-nondeterminism (0.031-1) ... Setting up python3-pysam (0.10.0+ds-1ubuntu1) ... Setting up python3-nose (1.3.7-2) ... Setting up python3-setuptools (33.1.1-1) ... Setting up python3-pymummer (0.10.2-1) ... Setting up python3-dendropy (4.2.0+dfsg-1) ... Setting up libruby2.3:amd64 (2.3.3-1) ... Setting up dh-python (2.20170125) ... Setting up debhelper (10.2.2ubuntu1) ... Setting up dh-autoreconf (13) ... Setting up ruby2.3 (2.3.3-1) ... Setting up ruby (1:2.3.3) ... Setting up asciidoctor (1.5.4-2) ... Setting up sbuild-build-depends-ariba-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.24-7ubuntu2) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.4.0-64-generic amd64 (x86_64) Toolchain package versions: binutils_2.27.90.20170221-1ubuntu1 dpkg-dev_1.18.10ubuntu1 g++-6_6.3.0-8ubuntu1 gcc-6_6.3.0-8ubuntu1 libc6-dev_2.24-7ubuntu2 libstdc++-6-dev_6.3.0-8ubuntu1 libstdc++6_6.3.0-8ubuntu1 linux-libc-dev_4.10.0-9.11 Package versions: adduser_3.113+nmu3ubuntu5 advancecomp_1.23-1 apt_1.4~rc2 apt-transport-https_1.4~rc2 asciidoctor_1.5.4-2 autoconf_2.69-10 automake_1:1.15-5ubuntu1 autopoint_0.19.8.1-1ubuntu2 autotools-dev_20161112.1 base-files_9.6ubuntu12 base-passwd_3.5.43 bash_4.4-2ubuntu1 binutils_2.27.90.20170221-1ubuntu1 bowtie2_2.3.0-2ubuntu1 bsdmainutils_9.0.12ubuntu1 bsdutils_1:2.29-1ubuntu2 build-essential_12.1ubuntu2 bzip2_1.0.6-8.1 ca-certificates_20161130 cd-hit_4.6.6-2 coreutils_8.26-3ubuntu3 cpp_4:6.3.0-1ubuntu3 cpp-6_6.3.0-8ubuntu1 dash_0.5.8-2.3ubuntu1 debconf_1.5.59ubuntu1 debhelper_10.2.2ubuntu1 debianutils_4.8.1 dh-autoreconf_13 dh-python_2.20170125 dh-strip-nondeterminism_0.031-1 diffutils_1:3.5-3 dmsetup_2:1.02.136-1ubuntu1 dpkg_1.18.10ubuntu1 dpkg-dev_1.18.10ubuntu1 e2fslibs_1.43.4-2 e2fsprogs_1.43.4-2 fakeroot_1.21-1ubuntu2 fastaq_3.14.0-1 file_1:5.29-3 findutils_4.6.0+git+20161106-2 g++_4:6.3.0-1ubuntu3 g++-6_6.3.0-8ubuntu1 gawk_1:4.1.4+dfsg-1 gcc_4:6.3.0-1ubuntu3 gcc-6_6.3.0-8ubuntu1 gcc-6-base_6.3.0-8ubuntu1 gettext_0.19.8.1-1ubuntu2 gettext-base_0.19.8.1-1ubuntu2 gnupg_2.1.15-1ubuntu6 gnupg-agent_2.1.15-1ubuntu6 gpgv_2.1.15-1ubuntu6 grep_2.27-2 groff-base_1.22.3-9 gzip_1.6-4ubuntu1 help2man_1.47.4 hostname_3.18 init_1.47 init-system-helpers_1.47 initscripts_2.88dsf-59.3ubuntu2 insserv_1.14.0-5ubuntu3 intltool-debian_0.35.0+20060710.4 libacl1_2.2.52-3 libapparmor1_2.11.0-2ubuntu2 libapt-pkg5.0_1.4~rc2 libarchive-zip-perl_1.59-1 libasan3_6.3.0-8ubuntu1 libasn1-8-heimdal_7.1.0+dfsg-9ubuntu1 libassuan0_2.4.3-2 libatomic1_6.3.0-8ubuntu1 libattr1_1:2.4.47-2 libaudit-common_1:2.6.6-1ubuntu1 libaudit1_1:2.6.6-1ubuntu1 libblkid1_2.29-1ubuntu2 libbsd0_0.8.3-1 libbz2-1.0_1.0.6-8.1 libc-bin_2.24-7ubuntu2 libc-dev-bin_2.24-7ubuntu2 libc6_2.24-7ubuntu2 libc6-dev_2.24-7ubuntu2 libcap-ng0_0.7.7-3 libcap2_1:2.25-1 libcapnp-0.5.3_0.5.3-2ubuntu1 libcc1-0_6.3.0-8ubuntu1 libcilkrts5_6.3.0-8ubuntu1 libcomerr2_1.43.4-2 libcroco3_0.6.11-2 libcryptsetup4_2:1.7.2-0ubuntu1 libcurl3-gnutls_7.52.1-3ubuntu1 libdb5.3_5.3.28-12 libdebconfclient0_0.213ubuntu1 libdevmapper1.02.1_2:1.02.136-1ubuntu1 libdpkg-perl_1.18.10ubuntu1 libexpat1_2.2.0-2 libexpat1-dev_2.2.0-2 libfakeroot_1.21-1ubuntu2 libfdisk1_2.29-1ubuntu2 libffi6_3.2.1-6 libfile-stripnondeterminism-perl_0.031-1 libfml-dev_0.1-2 libfml0_0.1-2 libgcc-6-dev_6.3.0-8ubuntu1 libgcc1_1:6.3.0-8ubuntu1 libgcrypt20_1.7.6-1 libgdbm3_1.8.3-14 libglib2.0-0_2.51.2-1 libgmp10_2:6.1.2+dfsg-1 libgnutls30_3.5.6-4ubuntu3 libgomp1_6.3.0-8ubuntu1 libgpg-error0_1.26-2 libgsl2_2.3+dfsg-1 libgssapi-krb5-2_1.15-1 libgssapi3-heimdal_7.1.0+dfsg-9ubuntu1 libhcrypto4-heimdal_7.1.0+dfsg-9ubuntu1 libheimbase1-heimdal_7.1.0+dfsg-9ubuntu1 libheimntlm0-heimdal_7.1.0+dfsg-9ubuntu1 libhogweed4_3.3-1 libhts1_1.3.2-2ubuntu1 libhx509-5-heimdal_7.1.0+dfsg-9ubuntu1 libicu57_57.1-5 libidn11_1.33-1 libidn2-0_0.16-1 libip4tc0_1.6.0-3ubuntu2 libisl15_0.18-1 libitm1_6.3.0-8ubuntu1 libk5crypto3_1.15-1 libkeyutils1_1.5.9-9ubuntu1 libkmod2_22-1.1ubuntu1 libkrb5-26-heimdal_7.1.0+dfsg-9ubuntu1 libkrb5-3_1.15-1 libkrb5support0_1.15-1 libksba8_1.3.5-2 libldap-2.4-2_2.4.44+dfsg-3ubuntu2 libldap-common_2.4.44+dfsg-3ubuntu2 liblocale-gettext-perl_1.07-3build1 liblockfile-bin_1.14-1 liblockfile1_1.14-1 liblsan0_6.3.0-8ubuntu1 liblz4-1_0.0~r131-2ubuntu2 liblzma5_5.2.2-1.2 libmagic-mgc_1:5.29-3 libmagic1_1:5.29-3 libminimap-dev_0.2-3 libminimap0_0.2-3 libmount1_2.29-1ubuntu2 libmpc3_1.0.3-1 libmpdec2_2.4.2-1 libmpfr4_3.1.5-1 libmpx2_6.3.0-8ubuntu1 libncurses5_6.0+20160625-1ubuntu1 libncursesw5_6.0+20160625-1ubuntu1 libnettle6_3.3-1 libnpth0_1.3-1 libp11-kit0_0.23.3-5 libpam-modules_1.1.8-3.2ubuntu2 libpam-modules-bin_1.1.8-3.2ubuntu2 libpam-runtime_1.1.8-3.2ubuntu2 libpam0g_1.1.8-3.2ubuntu2 libpcre3_2:8.39-2 libperl5.22_5.22.2-3 libperl5.24_5.24.1-1 libpipeline1_1.4.1-2 libpng16-16_1.6.28-1 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_3.5.3-1 libpython3-stdlib_3.5.3-1 libpython3.5_3.5.3-1 libpython3.5-dev_3.5.3-1 libpython3.5-minimal_3.5.3-1 libpython3.5-stdlib_3.5.3-1 libquadmath0_6.3.0-8ubuntu1 libreadline7_7.0-0ubuntu2 libroken18-heimdal_7.1.0+dfsg-9ubuntu1 librtmp1_2.4+20151223.gitfa8646d.1-1 libruby2.3_2.3.3-1 libsasl2-2_2.1.27~72-g88d82a3+dfsg-1 libsasl2-modules-db_2.1.27~72-g88d82a3+dfsg-1 libseccomp2_2.3.1-2.1ubuntu1 libselinux1_2.6-3 libsemanage-common_2.6-2 libsemanage1_2.6-2 libsepol1_2.6-2 libsigsegv2_2.10-5 libslang2_2.3.1-5ubuntu1 libsmartcols1_2.29-1ubuntu2 libsqlite3-0_3.16.2-2 libss2_1.43.4-2 libssl1.0.0_1.0.2g-1ubuntu11 libstdc++-6-dev_6.3.0-8ubuntu1 libstdc++6_6.3.0-8ubuntu1 libsystemd0_232-18ubuntu1 libtasn1-6_4.10-1 libtbb2_4.4~20160526-0ubuntu1 libtimedate-perl_2.3000-2 libtinfo5_6.0+20160625-1ubuntu1 libtool_2.4.6-2 libtsan0_6.3.0-8ubuntu1 libubsan0_6.3.0-8ubuntu1 libudev1_232-18ubuntu1 libunistring0_0.9.3-5.2ubuntu1 libusb-0.1-4_2:0.1.12-30 libustr-1.0-1_1.0.4-6 libuuid1_2.29-1ubuntu2 libwind0-heimdal_7.1.0+dfsg-9ubuntu1 libxml2_2.9.4+dfsg1-2.2 libyaml-0-2_0.1.7-2 linux-libc-dev_4.10.0-9.11 lockfile-progs_0.1.17 login_1:4.2-3.2ubuntu1 lsb-base_9.20160110ubuntu5 m4_1.4.18-1 make_4.1-9.1 man-db_2.7.6.1-2 mash_1.1.1-1 mawk_1.3.3-17ubuntu2 mime-support_3.60ubuntu1 mount_2.29-1ubuntu2 multiarch-support_2.24-7ubuntu2 mummer_3.23+dfsg-2 ncurses-base_6.0+20160625-1ubuntu1 ncurses-bin_6.0+20160625-1ubuntu1 openssl_1.0.2g-1ubuntu11 optipng_0.7.6-1build1 passwd_1:4.2-3.2ubuntu1 patch_2.7.5-1 perl_5.24.1-1 perl-base_5.24.1-1 perl-modules-5.22_5.22.2-3 perl-modules-5.24_5.24.1-1 pinentry-curses_1.0.0-2 pkg-create-dbgsym_0.73 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-minimal_2.7.13-2 python2.7_2.7.13-2 python2.7-minimal_2.7.13-2 python3_3.5.3-1 python3-bs4_4.5.3-1 python3-dendropy_4.2.0+dfsg-1 python3-dev_3.5.3-1 python3-minimal_3.5.3-1 python3-nose_1.3.7-2 python3-pkg-resources_33.1.1-1 python3-pymummer_0.10.2-1 python3-pysam_0.10.0+ds-1ubuntu1 python3-setuptools_33.1.1-1 python3.5_3.5.3-1 python3.5-dev_3.5.3-1 python3.5-minimal_3.5.3-1 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_2.3.3-1 rubygems-integration_1.11 samtools_1.3.1-3 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_232-18ubuntu1 systemd-sysv_232-18ubuntu1 sysv-rc_2.88dsf-59.3ubuntu2 sysvinit-utils_2.88dsf-59.8git1 tar_1.29b-1.1 tzdata_2016j-2 ubuntu-keyring_2016.10.27 util-linux_2.29-1ubuntu2 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 Fri Jan 27 16:57:20 2017 UTC gpgv: using RSA key gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./ariba_2.7.1+ds-1.dsc dpkg-source: info: extracting ariba in ariba-2.7.1+ds dpkg-source: info: unpacking ariba_2.7.1+ds.orig.tar.xz dpkg-source: info: unpacking ariba_2.7.1+ds-1.debian.tar.xz dpkg-source: info: applying use_debian_packaged_libs_for_extension.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-2.7.1+ds SHELL=/bin/sh SUDO_COMMAND=/usr/sbin/chroot /<> su buildd -s /bin/sh -c cd '/<>/ariba-2.7.1+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 2.7.1+ds-1 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build ariba-2.7.1+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-2.7.1+ds' rm -rf /<>/ariba-2.7.1+ds/debian/man dh_auto_clean -- I: pybuild base:184: python3.5 setup.py clean running clean removing '/<>/ariba-2.7.1+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-2.7.1+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-2.7.1+ds/.pybuild/pythonX.Y_3.5/build/ariba copying ariba/mapping.py -> /<>/ariba-2.7.1+ds/.pybuild/pythonX.Y_3.5/build/ariba copying ariba/ref_preparer.py -> /<>/ariba-2.7.1+ds/.pybuild/pythonX.Y_3.5/build/ariba copying ariba/flag.py -> /<>/ariba-2.7.1+ds/.pybuild/pythonX.Y_3.5/build/ariba copying ariba/clusters.py -> /<>/ariba-2.7.1+ds/.pybuild/pythonX.Y_3.5/build/ariba copying ariba/ref_genes_getter.py -> /<>/ariba-2.7.1+ds/.pybuild/pythonX.Y_3.5/build/ariba copying ariba/cluster.py -> /<>/ariba-2.7.1+ds/.pybuild/pythonX.Y_3.5/build/ariba copying ariba/assembly_variants.py -> /<>/ariba-2.7.1+ds/.pybuild/pythonX.Y_3.5/build/ariba copying ariba/bam_parse.py -> /<>/ariba-2.7.1+ds/.pybuild/pythonX.Y_3.5/build/ariba copying ariba/assembly.py -> /<>/ariba-2.7.1+ds/.pybuild/pythonX.Y_3.5/build/ariba copying ariba/pubmlst_getter.py -> /<>/ariba-2.7.1+ds/.pybuild/pythonX.Y_3.5/build/ariba copying ariba/scaffold_graph.py -> /<>/ariba-2.7.1+ds/.pybuild/pythonX.Y_3.5/build/ariba copying ariba/link.py -> /<>/ariba-2.7.1+ds/.pybuild/pythonX.Y_3.5/build/ariba copying ariba/pubmlst_ref_preparer.py -> /<>/ariba-2.7.1+ds/.pybuild/pythonX.Y_3.5/build/ariba copying ariba/cdhit.py -> /<>/ariba-2.7.1+ds/.pybuild/pythonX.Y_3.5/build/ariba copying ariba/vfdb_parser.py -> /<>/ariba-2.7.1+ds/.pybuild/pythonX.Y_3.5/build/ariba copying ariba/megares_data_finder.py -> /<>/ariba-2.7.1+ds/.pybuild/pythonX.Y_3.5/build/ariba copying ariba/samtools_variants.py -> /<>/ariba-2.7.1+ds/.pybuild/pythonX.Y_3.5/build/ariba copying ariba/external_progs.py -> /<>/ariba-2.7.1+ds/.pybuild/pythonX.Y_3.5/build/ariba copying ariba/report_filter.py -> /<>/ariba-2.7.1+ds/.pybuild/pythonX.Y_3.5/build/ariba copying ariba/refdata_query.py -> /<>/ariba-2.7.1+ds/.pybuild/pythonX.Y_3.5/build/ariba copying ariba/summary_cluster_variant.py -> /<>/ariba-2.7.1+ds/.pybuild/pythonX.Y_3.5/build/ariba copying ariba/sequence_variant.py -> /<>/ariba-2.7.1+ds/.pybuild/pythonX.Y_3.5/build/ariba copying ariba/mlst_profile.py -> /<>/ariba-2.7.1+ds/.pybuild/pythonX.Y_3.5/build/ariba copying ariba/read_store.py -> /<>/ariba-2.7.1+ds/.pybuild/pythonX.Y_3.5/build/ariba copying ariba/summary.py -> /<>/ariba-2.7.1+ds/.pybuild/pythonX.Y_3.5/build/ariba copying ariba/ref_seq_chooser.py -> /<>/ariba-2.7.1+ds/.pybuild/pythonX.Y_3.5/build/ariba copying ariba/histogram.py -> /<>/ariba-2.7.1+ds/.pybuild/pythonX.Y_3.5/build/ariba copying ariba/card_record.py -> /<>/ariba-2.7.1+ds/.pybuild/pythonX.Y_3.5/build/ariba copying ariba/megares_zip_parser.py -> /<>/ariba-2.7.1+ds/.pybuild/pythonX.Y_3.5/build/ariba copying ariba/reference_data.py -> /<>/ariba-2.7.1+ds/.pybuild/pythonX.Y_3.5/build/ariba copying ariba/summary_cluster.py -> /<>/ariba-2.7.1+ds/.pybuild/pythonX.Y_3.5/build/ariba copying ariba/faidx.py -> /<>/ariba-2.7.1+ds/.pybuild/pythonX.Y_3.5/build/ariba copying ariba/common.py -> /<>/ariba-2.7.1+ds/.pybuild/pythonX.Y_3.5/build/ariba copying ariba/assembly_compare.py -> /<>/ariba-2.7.1+ds/.pybuild/pythonX.Y_3.5/build/ariba copying ariba/__init__.py -> /<>/ariba-2.7.1+ds/.pybuild/pythonX.Y_3.5/build/ariba copying ariba/aln_to_metadata.py -> /<>/ariba-2.7.1+ds/.pybuild/pythonX.Y_3.5/build/ariba copying ariba/versions.py -> /<>/ariba-2.7.1+ds/.pybuild/pythonX.Y_3.5/build/ariba copying ariba/sequence_metadata.py -> /<>/ariba-2.7.1+ds/.pybuild/pythonX.Y_3.5/build/ariba copying ariba/mlst_reporter.py -> /<>/ariba-2.7.1+ds/.pybuild/pythonX.Y_3.5/build/ariba copying ariba/read_filter.py -> /<>/ariba-2.7.1+ds/.pybuild/pythonX.Y_3.5/build/ariba copying ariba/report.py -> /<>/ariba-2.7.1+ds/.pybuild/pythonX.Y_3.5/build/ariba copying ariba/summary_sample.py -> /<>/ariba-2.7.1+ds/.pybuild/pythonX.Y_3.5/build/ariba creating /<>/ariba-2.7.1+ds/.pybuild/pythonX.Y_3.5/build/ariba/tasks copying ariba/tasks/flag.py -> /<>/ariba-2.7.1+ds/.pybuild/pythonX.Y_3.5/build/ariba/tasks copying ariba/tasks/reportfilter.py -> /<>/ariba-2.7.1+ds/.pybuild/pythonX.Y_3.5/build/ariba/tasks copying ariba/tasks/version.py -> /<>/ariba-2.7.1+ds/.pybuild/pythonX.Y_3.5/build/ariba/tasks copying ariba/tasks/prepareref.py -> /<>/ariba-2.7.1+ds/.pybuild/pythonX.Y_3.5/build/ariba/tasks copying ariba/tasks/aln2meta.py -> /<>/ariba-2.7.1+ds/.pybuild/pythonX.Y_3.5/build/ariba/tasks copying ariba/tasks/pubmlstget.py -> /<>/ariba-2.7.1+ds/.pybuild/pythonX.Y_3.5/build/ariba/tasks copying ariba/tasks/getref.py -> /<>/ariba-2.7.1+ds/.pybuild/pythonX.Y_3.5/build/ariba/tasks copying ariba/tasks/pubmlstspecies.py -> /<>/ariba-2.7.1+ds/.pybuild/pythonX.Y_3.5/build/ariba/tasks copying ariba/tasks/summary.py -> /<>/ariba-2.7.1+ds/.pybuild/pythonX.Y_3.5/build/ariba/tasks copying ariba/tasks/test.py -> /<>/ariba-2.7.1+ds/.pybuild/pythonX.Y_3.5/build/ariba/tasks copying ariba/tasks/refquery.py -> /<>/ariba-2.7.1+ds/.pybuild/pythonX.Y_3.5/build/ariba/tasks copying ariba/tasks/__init__.py -> /<>/ariba-2.7.1+ds/.pybuild/pythonX.Y_3.5/build/ariba/tasks copying ariba/tasks/run.py -> /<>/ariba-2.7.1+ds/.pybuild/pythonX.Y_3.5/build/ariba/tasks creating /<>/ariba-2.7.1+ds/.pybuild/pythonX.Y_3.5/build/ariba/test_run_data copying ariba/test_run_data/metadata.tsv -> /<>/ariba-2.7.1+ds/.pybuild/pythonX.Y_3.5/build/ariba/test_run_data copying ariba/test_run_data/reads_2.fq -> /<>/ariba-2.7.1+ds/.pybuild/pythonX.Y_3.5/build/ariba/test_run_data copying ariba/test_run_data/ref_fasta_to_make_reads_from.fa -> /<>/ariba-2.7.1+ds/.pybuild/pythonX.Y_3.5/build/ariba/test_run_data copying ariba/test_run_data/reads_1.fq -> /<>/ariba-2.7.1+ds/.pybuild/pythonX.Y_3.5/build/ariba/test_run_data copying ariba/test_run_data/ref_seqs.fa -> /<>/ariba-2.7.1+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-2.7.1+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-2.7.1+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-2.7.1+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-2.7.1+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-2.7.1+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-2.7.1+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-2.7.1+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-2.7.1+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-2.7.1+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-2.7.1+ds' python3 setup.py nosetests running nosetests running egg_info creating ariba.egg-info writing ariba.egg-info/PKG-INFO writing dependency_links to ariba.egg-info/dependency_links.txt writing requirements to ariba.egg-info/requires.txt writing top-level names to ariba.egg-info/top_level.txt 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-2.7.1+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-2.7.1+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-2.7.1+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-2.7.1+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-2.7.1+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-2.7.1+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. ........The following command failed with exit code 139 /usr/bin/bowtie2-build -q /<>/ariba-2.7.1+ds/tmp.cluster_test_full_run_ok_samtools_snp_known_position_var_only_noncoding/assembly.fa /<>/ariba-2.7.1+ds/tmp.cluster_test_full_run_ok_samtools_snp_known_position_var_only_noncoding/assembly.reads_mapped.map_index The output was: Segmentation fault (core dumped) EThe following command failed with exit code 139 /usr/bin/bowtie2-build -q /<>/ariba-2.7.1+ds/tmp.cluster_test_full_run_ok_samtools_snp_known_position_var_only_noncoding/tmp.cluster_test_full_delete_codon/assembly.fa /<>/ariba-2.7.1+ds/tmp.cluster_test_full_run_ok_samtools_snp_known_position_var_only_noncoding/tmp.cluster_test_full_delete_codon/assembly.reads_mapped.map_index The output was: Segmentation fault (core dumped) EThe following command failed with exit code 139 /usr/bin/bowtie2-build -q /<>/ariba-2.7.1+ds/tmp.cluster_test_full_run_ok_samtools_snp_known_position_var_only_noncoding/tmp.cluster_test_full_delete_codon/tmp.cluster_test_full_insert_codon/assembly.fa /<>/ariba-2.7.1+ds/tmp.cluster_test_full_run_ok_samtools_snp_known_position_var_only_noncoding/tmp.cluster_test_full_delete_codon/tmp.cluster_test_full_insert_codon/assembly.reads_mapped.map_index The output was: Segmentation fault (core dumped) EThe following command failed with exit code 139 /usr/bin/bowtie2-build -q /<>/ariba-2.7.1+ds/tmp.cluster_test_full_run_ok_samtools_snp_known_position_var_only_noncoding/tmp.cluster_test_full_delete_codon/tmp.cluster_test_full_insert_codon/tmp.cluster_test_full_run_ok_samtools_snp_known_position_pres_abs_gene/assembly.fa /<>/ariba-2.7.1+ds/tmp.cluster_test_full_run_ok_samtools_snp_known_position_var_only_noncoding/tmp.cluster_test_full_delete_codon/tmp.cluster_test_full_insert_codon/tmp.cluster_test_full_run_ok_samtools_snp_known_position_pres_abs_gene/assembly.reads_mapped.map_index The output was: Segmentation fault (core dumped) EThe following command failed with exit code 139 /usr/bin/bowtie2-build -q /<>/ariba-2.7.1+ds/tmp.cluster_test_full_run_ok_samtools_snp_known_position_var_only_noncoding/tmp.cluster_test_full_delete_codon/tmp.cluster_test_full_insert_codon/tmp.cluster_test_full_run_ok_samtools_snp_known_position_pres_abs_gene/tmp.cluster_test_full_run_ok_samtools_snp_known_position_pres_abs_noncoding/assembly.fa /<>/ariba-2.7.1+ds/tmp.cluster_test_full_run_ok_samtools_snp_known_position_var_only_noncoding/tmp.cluster_test_full_delete_codon/tmp.cluster_test_full_insert_codon/tmp.cluster_test_full_run_ok_samtools_snp_known_position_pres_abs_gene/tmp.cluster_test_full_run_ok_samtools_snp_known_position_pres_abs_noncoding/assembly.reads_mapped.map_index The output was: Segmentation fault (core dumped) EThe following command failed with exit code 139 /usr/bin/bowtie2-build -q /<>/ariba-2.7.1+ds/tmp.cluster_test_full_run_ok_samtools_snp_known_position_var_only_noncoding/tmp.cluster_test_full_delete_codon/tmp.cluster_test_full_insert_codon/tmp.cluster_test_full_run_ok_samtools_snp_known_position_pres_abs_gene/tmp.cluster_test_full_run_ok_samtools_snp_known_position_pres_abs_noncoding/tmp.cluster_test_full_run_multiple_vars/assembly.fa /<>/ariba-2.7.1+ds/tmp.cluster_test_full_run_ok_samtools_snp_known_position_var_only_noncoding/tmp.cluster_test_full_delete_codon/tmp.cluster_test_full_insert_codon/tmp.cluster_test_full_run_ok_samtools_snp_known_position_pres_abs_gene/tmp.cluster_test_full_run_ok_samtools_snp_known_position_pres_abs_noncoding/tmp.cluster_test_full_run_multiple_vars/assembly.reads_mapped.map_index The output was: Segmentation fault (core dumped) E..The following command failed with exit code 139 /usr/bin/bowtie2-build -q /<>/ariba-2.7.1+ds/tmp.cluster_test_full_run_ok_samtools_snp_known_position_var_only_noncoding/tmp.cluster_test_full_delete_codon/tmp.cluster_test_full_insert_codon/tmp.cluster_test_full_run_ok_samtools_snp_known_position_pres_abs_gene/tmp.cluster_test_full_run_ok_samtools_snp_known_position_pres_abs_noncoding/tmp.cluster_test_full_run_multiple_vars/tmp.test_full_run_ok_non_coding/assembly.fa /<>/ariba-2.7.1+ds/tmp.cluster_test_full_run_ok_samtools_snp_known_position_var_only_noncoding/tmp.cluster_test_full_delete_codon/tmp.cluster_test_full_insert_codon/tmp.cluster_test_full_run_ok_samtools_snp_known_position_pres_abs_gene/tmp.cluster_test_full_run_ok_samtools_snp_known_position_pres_abs_noncoding/tmp.cluster_test_full_run_multiple_vars/tmp.test_full_run_ok_non_coding/assembly.reads_mapped.map_index The output was: Segmentation fault (core dumped) E.........The following command failed with exit code 139 /usr/bin/bowtie2-build -q /<>/ariba-2.7.1+ds/tmp.cluster_test_full_run_ok_samtools_snp_known_position_var_only_noncoding/tmp.cluster_test_full_delete_codon/tmp.cluster_test_full_insert_codon/tmp.cluster_test_full_run_ok_samtools_snp_known_position_pres_abs_gene/tmp.cluster_test_full_run_ok_samtools_snp_known_position_pres_abs_noncoding/tmp.cluster_test_full_run_multiple_vars/tmp.test_full_run_ok_non_coding/tmp.cluster_test_full_run_ok_samtools_snp_known_position_var_only_gene_does_have_var/assembly.fa /<>/ariba-2.7.1+ds/tmp.cluster_test_full_run_ok_samtools_snp_known_position_var_only_noncoding/tmp.cluster_test_full_delete_codon/tmp.cluster_test_full_insert_codon/tmp.cluster_test_full_run_ok_samtools_snp_known_position_pres_abs_gene/tmp.cluster_test_full_run_ok_samtools_snp_known_position_pres_abs_noncoding/tmp.cluster_test_full_run_multiple_vars/tmp.test_full_run_ok_non_coding/tmp.cluster_test_full_run_ok_samtools_snp_known_position_var_only_gene_does_have_var/assembly.reads_mapped.map_index The output was: Segmentation fault (core dumped) EThe following command failed with exit code 139 /usr/bin/bowtie2-build -q /<>/ariba-2.7.1+ds/tmp.cluster_test_full_run_ok_samtools_snp_known_position_var_only_noncoding/tmp.cluster_test_full_delete_codon/tmp.cluster_test_full_insert_codon/tmp.cluster_test_full_run_ok_samtools_snp_known_position_pres_abs_gene/tmp.cluster_test_full_run_ok_samtools_snp_known_position_pres_abs_noncoding/tmp.cluster_test_full_run_multiple_vars/tmp.test_full_run_ok_non_coding/tmp.cluster_test_full_run_ok_samtools_snp_known_position_var_only_gene_does_have_var/tmp.cluster_full_run_smtls_snp_varonly_gene_2/assembly.fa /<>/ariba-2.7.1+ds/tmp.cluster_test_full_run_ok_samtools_snp_known_position_var_only_noncoding/tmp.cluster_test_full_delete_codon/tmp.cluster_test_full_insert_codon/tmp.cluster_test_full_run_ok_samtools_snp_known_position_pres_abs_gene/tmp.cluster_test_full_run_ok_samtools_snp_known_position_pres_abs_noncoding/tmp.cluster_test_full_run_multiple_vars/tmp.test_full_run_ok_non_coding/tmp.cluster_test_full_run_ok_samtools_snp_known_position_var_only_gene_does_have_var/tmp.cluster_full_run_smtls_snp_varonly_gene_2/assembly.reads_mapped.map_index The output was: Segmentation fault (core dumped) EThe following command failed with exit code 139 /usr/bin/bowtie2-build -q /<>/ariba-2.7.1+ds/tmp.cluster_test_full_run_ok_samtools_snp_known_position_var_only_noncoding/tmp.cluster_test_full_delete_codon/tmp.cluster_test_full_insert_codon/tmp.cluster_test_full_run_ok_samtools_snp_known_position_pres_abs_gene/tmp.cluster_test_full_run_ok_samtools_snp_known_position_pres_abs_noncoding/tmp.cluster_test_full_run_multiple_vars/tmp.test_full_run_ok_non_coding/tmp.cluster_test_full_run_ok_samtools_snp_known_position_var_only_gene_does_have_var/tmp.cluster_full_run_smtls_snp_varonly_gene_2/tmp.cluster_test_full_run_smtls_snp_varonly_gene_no_snp/assembly.fa /<>/ariba-2.7.1+ds/tmp.cluster_test_full_run_ok_samtools_snp_known_position_var_only_noncoding/tmp.cluster_test_full_delete_codon/tmp.cluster_test_full_insert_codon/tmp.cluster_test_full_run_ok_samtools_snp_known_position_pres_abs_gene/tmp.cluster_test_full_run_ok_samtools_snp_known_position_pres_abs_noncoding/tmp.cluster_test_full_run_multiple_vars/tmp.test_full_run_ok_non_coding/tmp.cluster_test_full_run_ok_samtools_snp_known_position_var_only_gene_does_have_var/tmp.cluster_full_run_smtls_snp_varonly_gene_2/tmp.cluster_test_full_run_smtls_snp_varonly_gene_no_snp/assembly.reads_mapped.map_index The output was: Segmentation fault (core dumped) EThe following command failed with exit code 139 /usr/bin/bowtie2-build -q /<>/ariba-2.7.1+ds/tmp.cluster_test_full_run_ok_samtools_snp_known_position_var_only_noncoding/tmp.cluster_test_full_delete_codon/tmp.cluster_test_full_insert_codon/tmp.cluster_test_full_run_ok_samtools_snp_known_position_pres_abs_gene/tmp.cluster_test_full_run_ok_samtools_snp_known_position_pres_abs_noncoding/tmp.cluster_test_full_run_multiple_vars/tmp.test_full_run_ok_non_coding/tmp.cluster_test_full_run_ok_samtools_snp_known_position_var_only_gene_does_have_var/tmp.cluster_full_run_smtls_snp_varonly_gene_2/tmp.cluster_test_full_run_smtls_snp_varonly_gene_no_snp/tmp.cluster_full_run_smtls_snp_varonly_nonc/assembly.fa /<>/ariba-2.7.1+ds/tmp.cluster_test_full_run_ok_samtools_snp_known_position_var_only_noncoding/tmp.cluster_test_full_delete_codon/tmp.cluster_test_full_insert_codon/tmp.cluster_test_full_run_ok_samtools_snp_known_position_pres_abs_gene/tmp.cluster_test_full_run_ok_samtools_snp_known_position_pres_abs_noncoding/tmp.cluster_test_full_run_multiple_vars/tmp.test_full_run_ok_non_coding/tmp.cluster_test_full_run_ok_samtools_snp_known_position_var_only_gene_does_have_var/tmp.cluster_full_run_smtls_snp_varonly_gene_2/tmp.cluster_test_full_run_smtls_snp_varonly_gene_no_snp/tmp.cluster_full_run_smtls_snp_varonly_nonc/assembly.reads_mapped.map_index The output was: Segmentation fault (core dumped) EThe following command failed with exit code 139 /usr/bin/bowtie2-build -q /<>/ariba-2.7.1+ds/tmp.cluster_test_full_run_ok_samtools_snp_known_position_var_only_noncoding/tmp.cluster_test_full_delete_codon/tmp.cluster_test_full_insert_codon/tmp.cluster_test_full_run_ok_samtools_snp_known_position_pres_abs_gene/tmp.cluster_test_full_run_ok_samtools_snp_known_position_pres_abs_noncoding/tmp.cluster_test_full_run_multiple_vars/tmp.test_full_run_ok_non_coding/tmp.cluster_test_full_run_ok_samtools_snp_known_position_var_only_gene_does_have_var/tmp.cluster_full_run_smtls_snp_varonly_gene_2/tmp.cluster_test_full_run_smtls_snp_varonly_gene_no_snp/tmp.cluster_full_run_smtls_snp_varonly_nonc/tmp.cluster_test_full_run_ok_samtools_snp_known_position_var_only_noncoding/assembly.fa /<>/ariba-2.7.1+ds/tmp.cluster_test_full_run_ok_samtools_snp_known_position_var_only_noncoding/tmp.cluster_test_full_delete_codon/tmp.cluster_test_full_insert_codon/tmp.cluster_test_full_run_ok_samtools_snp_known_position_pres_abs_gene/tmp.cluster_test_full_run_ok_samtools_snp_known_position_pres_abs_noncoding/tmp.cluster_test_full_run_multiple_vars/tmp.test_full_run_ok_non_coding/tmp.cluster_test_full_run_ok_samtools_snp_known_position_var_only_gene_does_have_var/tmp.cluster_full_run_smtls_snp_varonly_gene_2/tmp.cluster_test_full_run_smtls_snp_varonly_gene_no_snp/tmp.cluster_full_run_smtls_snp_varonly_nonc/tmp.cluster_test_full_run_ok_samtools_snp_known_position_var_only_noncoding/assembly.reads_mapped.map_index The output was: Segmentation fault (core dumped) E........................................The following command failed with exit code 139 /usr/bin/bowtie2-build -q tmp.test_bowtie2_index.ref.fa tmp.test_bowtie2_index.ref.out The output was: Segmentation fault (core dumped) E.The following command failed with exit code 139 /usr/bin/bowtie2-build -q /<>/ariba-2.7.1+ds/ariba/tests/data/mapping_test_bowtie2_ref.fa tmp.out.bowtie2.map_index The output was: Segmentation fault (core dumped) EThe following command failed with exit code 139 /usr/bin/bowtie2-build -q /<>/ariba-2.7.1+ds/ariba/tests/data/mapping_test_bowtie2_ref.fa tmp.out.bowtie2.map_index The output was: Segmentation fault (core dumped) EThe following command failed with exit code 139 /usr/bin/bowtie2-build -q /<>/ariba-2.7.1+ds/ariba/tests/data/mapping_test_bowtie2_ref.fa tmp.out.bowtie2_remove_both_unmapped.map_index The output was: Segmentation fault (core dumped) E........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 seq1 has length 1 which is too long or short. Removing. WARNING: Median sequence length is 5 but seq5 has length 14 which is too long or short. Removing. .........................WARNING: sequence "non_coding_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 "presence_absence_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. .................................................................................................................... ====================================================================== ERROR: test complete run where samtools calls a snp at a known snp location in a presence/absence noncoding and sample has the var ---------------------------------------------------------------------- Traceback (most recent call last): File "/<>/ariba-2.7.1+ds/ariba/tests/cluster_test.py", line 471, in test_full_run_cluster_test_full_run_smtls_snp_varonly_nonc c.run() File "/<>/ariba-2.7.1+ds/ariba/cluster.py", line 283, in run self._run() File "/<>/ariba-2.7.1+ds/ariba/cluster.py", line 329, in _run self.assembly.run() File "/<>/ariba-2.7.1+ds/ariba/assembly.py", line 215, in run verbose_filehandle=self.log_fh File "/<>/ariba-2.7.1+ds/ariba/mapping.py", line 62, in run_bowtie2 bowtie2_index(ref_fa, map_index, bowtie2=bowtie2, verbose=verbose, verbose_filehandle=verbose_filehandle) File "/<>/ariba-2.7.1+ds/ariba/mapping.py", line 29, in bowtie2_index common.syscall(cmd, verbose=verbose, verbose_filehandle=verbose_filehandle) File "/<>/ariba-2.7.1+ds/ariba/common.py", line 28, in syscall sys.exit(1) SystemExit: 1 ====================================================================== ERROR: Test complete run where there is a deleted codon ---------------------------------------------------------------------- Traceback (most recent call last): File "/<>/ariba-2.7.1+ds/ariba/tests/cluster_test.py", line 525, in test_full_run_delete_codon c.run() File "/<>/ariba-2.7.1+ds/ariba/cluster.py", line 283, in run self._run() File "/<>/ariba-2.7.1+ds/ariba/cluster.py", line 329, in _run self.assembly.run() File "/<>/ariba-2.7.1+ds/ariba/assembly.py", line 215, in run verbose_filehandle=self.log_fh File "/<>/ariba-2.7.1+ds/ariba/mapping.py", line 62, in run_bowtie2 bowtie2_index(ref_fa, map_index, bowtie2=bowtie2, verbose=verbose, verbose_filehandle=verbose_filehandle) File "/<>/ariba-2.7.1+ds/ariba/mapping.py", line 29, in bowtie2_index common.syscall(cmd, verbose=verbose, verbose_filehandle=verbose_filehandle) File "/<>/ariba-2.7.1+ds/ariba/common.py", line 28, in syscall sys.exit(1) SystemExit: 1 ====================================================================== ERROR: Test complete run where there is a inserted codon ---------------------------------------------------------------------- Traceback (most recent call last): File "/<>/ariba-2.7.1+ds/ariba/tests/cluster_test.py", line 542, in test_full_run_insert_codon c.run() File "/<>/ariba-2.7.1+ds/ariba/cluster.py", line 283, in run self._run() File "/<>/ariba-2.7.1+ds/ariba/cluster.py", line 329, in _run self.assembly.run() File "/<>/ariba-2.7.1+ds/ariba/assembly.py", line 215, in run verbose_filehandle=self.log_fh File "/<>/ariba-2.7.1+ds/ariba/mapping.py", line 62, in run_bowtie2 bowtie2_index(ref_fa, map_index, bowtie2=bowtie2, verbose=verbose, verbose_filehandle=verbose_filehandle) File "/<>/ariba-2.7.1+ds/ariba/mapping.py", line 29, in bowtie2_index common.syscall(cmd, verbose=verbose, verbose_filehandle=verbose_filehandle) File "/<>/ariba-2.7.1+ds/ariba/common.py", line 28, in syscall sys.exit(1) SystemExit: 1 ====================================================================== ERROR: test complete run where samtools calls a snp at a known snp location in a presence/absence gene ---------------------------------------------------------------------- Traceback (most recent call last): File "/<>/ariba-2.7.1+ds/ariba/tests/cluster_test.py", line 328, in test_full_run_known_smtls_snp_presabs_gene c.run() File "/<>/ariba-2.7.1+ds/ariba/cluster.py", line 283, in run self._run() File "/<>/ariba-2.7.1+ds/ariba/cluster.py", line 329, in _run self.assembly.run() File "/<>/ariba-2.7.1+ds/ariba/assembly.py", line 215, in run verbose_filehandle=self.log_fh File "/<>/ariba-2.7.1+ds/ariba/mapping.py", line 62, in run_bowtie2 bowtie2_index(ref_fa, map_index, bowtie2=bowtie2, verbose=verbose, verbose_filehandle=verbose_filehandle) File "/<>/ariba-2.7.1+ds/ariba/mapping.py", line 29, in bowtie2_index common.syscall(cmd, verbose=verbose, verbose_filehandle=verbose_filehandle) File "/<>/ariba-2.7.1+ds/ariba/common.py", line 28, in syscall sys.exit(1) SystemExit: 1 ====================================================================== ERROR: test complete run where samtools calls a snp at a known snp location in a presence/absence noncoding ---------------------------------------------------------------------- Traceback (most recent call last): File "/<>/ariba-2.7.1+ds/ariba/tests/cluster_test.py", line 433, in test_full_run_known_smtls_snp_presabs_nonc c.run() File "/<>/ariba-2.7.1+ds/ariba/cluster.py", line 283, in run self._run() File "/<>/ariba-2.7.1+ds/ariba/cluster.py", line 329, in _run self.assembly.run() File "/<>/ariba-2.7.1+ds/ariba/assembly.py", line 215, in run verbose_filehandle=self.log_fh File "/<>/ariba-2.7.1+ds/ariba/mapping.py", line 62, in run_bowtie2 bowtie2_index(ref_fa, map_index, bowtie2=bowtie2, verbose=verbose, verbose_filehandle=verbose_filehandle) File "/<>/ariba-2.7.1+ds/ariba/mapping.py", line 29, in bowtie2_index common.syscall(cmd, verbose=verbose, verbose_filehandle=verbose_filehandle) File "/<>/ariba-2.7.1+ds/ariba/common.py", line 28, in syscall sys.exit(1) SystemExit: 1 ====================================================================== ERROR: Test complete run where there is a codon with a SNP and an indel ---------------------------------------------------------------------- Traceback (most recent call last): File "/<>/ariba-2.7.1+ds/ariba/tests/cluster_test.py", line 507, in test_full_run_multiple_vars_in_codon c.run() File "/<>/ariba-2.7.1+ds/ariba/cluster.py", line 283, in run self._run() File "/<>/ariba-2.7.1+ds/ariba/cluster.py", line 329, in _run self.assembly.run() File "/<>/ariba-2.7.1+ds/ariba/assembly.py", line 215, in run verbose_filehandle=self.log_fh File "/<>/ariba-2.7.1+ds/ariba/mapping.py", line 62, in run_bowtie2 bowtie2_index(ref_fa, map_index, bowtie2=bowtie2, verbose=verbose, verbose_filehandle=verbose_filehandle) File "/<>/ariba-2.7.1+ds/ariba/mapping.py", line 29, in bowtie2_index common.syscall(cmd, verbose=verbose, verbose_filehandle=verbose_filehandle) File "/<>/ariba-2.7.1+ds/ariba/common.py", line 28, in syscall sys.exit(1) SystemExit: 1 ====================================================================== ERROR: test complete run of cluster on a noncoding sequence ---------------------------------------------------------------------- Traceback (most recent call last): File "/<>/ariba-2.7.1+ds/ariba/tests/cluster_test.py", line 179, in test_full_run_ok_non_coding c.run() File "/<>/ariba-2.7.1+ds/ariba/cluster.py", line 283, in run self._run() File "/<>/ariba-2.7.1+ds/ariba/cluster.py", line 329, in _run self.assembly.run() File "/<>/ariba-2.7.1+ds/ariba/assembly.py", line 215, in run verbose_filehandle=self.log_fh File "/<>/ariba-2.7.1+ds/ariba/mapping.py", line 62, in run_bowtie2 bowtie2_index(ref_fa, map_index, bowtie2=bowtie2, verbose=verbose, verbose_filehandle=verbose_filehandle) File "/<>/ariba-2.7.1+ds/ariba/mapping.py", line 29, in bowtie2_index common.syscall(cmd, verbose=verbose, verbose_filehandle=verbose_filehandle) File "/<>/ariba-2.7.1+ds/ariba/common.py", line 28, in syscall sys.exit(1) SystemExit: 1 ====================================================================== ERROR: test complete run where samtools calls a snp at a known snp location in a variant only gene, gene does have variant ---------------------------------------------------------------------- Traceback (most recent call last): File "/<>/ariba-2.7.1+ds/ariba/tests/cluster_test.py", line 366, in test_full_run_smtls_snp_varonly_gene c.run() File "/<>/ariba-2.7.1+ds/ariba/cluster.py", line 283, in run self._run() File "/<>/ariba-2.7.1+ds/ariba/cluster.py", line 329, in _run self.assembly.run() File "/<>/ariba-2.7.1+ds/ariba/assembly.py", line 215, in run verbose_filehandle=self.log_fh File "/<>/ariba-2.7.1+ds/ariba/mapping.py", line 62, in run_bowtie2 bowtie2_index(ref_fa, map_index, bowtie2=bowtie2, verbose=verbose, verbose_filehandle=verbose_filehandle) File "/<>/ariba-2.7.1+ds/ariba/mapping.py", line 29, in bowtie2_index common.syscall(cmd, verbose=verbose, verbose_filehandle=verbose_filehandle) File "/<>/ariba-2.7.1+ds/ariba/common.py", line 28, in syscall sys.exit(1) SystemExit: 1 ====================================================================== ERROR: test complete run where samtools calls a snp in a variant only gene ---------------------------------------------------------------------- Traceback (most recent call last): File "/<>/ariba-2.7.1+ds/ariba/tests/cluster_test.py", line 312, in test_full_run_smtls_snp_varonly_gene_2 c.run() File "/<>/ariba-2.7.1+ds/ariba/cluster.py", line 283, in run self._run() File "/<>/ariba-2.7.1+ds/ariba/cluster.py", line 329, in _run self.assembly.run() File "/<>/ariba-2.7.1+ds/ariba/assembly.py", line 215, in run verbose_filehandle=self.log_fh File "/<>/ariba-2.7.1+ds/ariba/mapping.py", line 62, in run_bowtie2 bowtie2_index(ref_fa, map_index, bowtie2=bowtie2, verbose=verbose, verbose_filehandle=verbose_filehandle) File "/<>/ariba-2.7.1+ds/ariba/mapping.py", line 29, in bowtie2_index common.syscall(cmd, verbose=verbose, verbose_filehandle=verbose_filehandle) File "/<>/ariba-2.7.1+ds/ariba/common.py", line 28, in syscall sys.exit(1) SystemExit: 1 ====================================================================== ERROR: test complete run where samtools calls a snp at a known snp location in a variant only gene, gene does not have variant ---------------------------------------------------------------------- Traceback (most recent call last): File "/<>/ariba-2.7.1+ds/ariba/tests/cluster_test.py", line 347, in test_full_run_smtls_snp_varonly_gene_no_snp c.run() File "/<>/ariba-2.7.1+ds/ariba/cluster.py", line 283, in run self._run() File "/<>/ariba-2.7.1+ds/ariba/cluster.py", line 329, in _run self.assembly.run() File "/<>/ariba-2.7.1+ds/ariba/assembly.py", line 215, in run verbose_filehandle=self.log_fh File "/<>/ariba-2.7.1+ds/ariba/mapping.py", line 62, in run_bowtie2 bowtie2_index(ref_fa, map_index, bowtie2=bowtie2, verbose=verbose, verbose_filehandle=verbose_filehandle) File "/<>/ariba-2.7.1+ds/ariba/mapping.py", line 29, in bowtie2_index common.syscall(cmd, verbose=verbose, verbose_filehandle=verbose_filehandle) File "/<>/ariba-2.7.1+ds/ariba/common.py", line 28, in syscall sys.exit(1) SystemExit: 1 ====================================================================== ERROR: test complete run where samtools calls a snp in a presence/absence noncoding sequence ---------------------------------------------------------------------- Traceback (most recent call last): File "/<>/ariba-2.7.1+ds/ariba/tests/cluster_test.py", line 417, in test_full_run_smtls_snp_varonly_nonc c.run() File "/<>/ariba-2.7.1+ds/ariba/cluster.py", line 283, in run self._run() File "/<>/ariba-2.7.1+ds/ariba/cluster.py", line 329, in _run self.assembly.run() File "/<>/ariba-2.7.1+ds/ariba/assembly.py", line 215, in run verbose_filehandle=self.log_fh File "/<>/ariba-2.7.1+ds/ariba/mapping.py", line 62, in run_bowtie2 bowtie2_index(ref_fa, map_index, bowtie2=bowtie2, verbose=verbose, verbose_filehandle=verbose_filehandle) File "/<>/ariba-2.7.1+ds/ariba/mapping.py", line 29, in bowtie2_index common.syscall(cmd, verbose=verbose, verbose_filehandle=verbose_filehandle) File "/<>/ariba-2.7.1+ds/ariba/common.py", line 28, in syscall sys.exit(1) SystemExit: 1 ====================================================================== ERROR: test complete run where samtools calls a snp at a known snp location in a presence/absence noncoding and sample does not have the var ---------------------------------------------------------------------- Traceback (most recent call last): File "/<>/ariba-2.7.1+ds/ariba/tests/cluster_test.py", line 452, in test_full_run_smtls_snp_varonly_nonc_no_snp c.run() File "/<>/ariba-2.7.1+ds/ariba/cluster.py", line 283, in run self._run() File "/<>/ariba-2.7.1+ds/ariba/cluster.py", line 329, in _run self.assembly.run() File "/<>/ariba-2.7.1+ds/ariba/assembly.py", line 215, in run verbose_filehandle=self.log_fh File "/<>/ariba-2.7.1+ds/ariba/mapping.py", line 62, in run_bowtie2 bowtie2_index(ref_fa, map_index, bowtie2=bowtie2, verbose=verbose, verbose_filehandle=verbose_filehandle) File "/<>/ariba-2.7.1+ds/ariba/mapping.py", line 29, in bowtie2_index common.syscall(cmd, verbose=verbose, verbose_filehandle=verbose_filehandle) File "/<>/ariba-2.7.1+ds/ariba/common.py", line 28, in syscall sys.exit(1) SystemExit: 1 ====================================================================== ERROR: test bowtie2_index ---------------------------------------------------------------------- Traceback (most recent call last): File "/<>/ariba-2.7.1+ds/ariba/tests/mapping_test.py", line 35, in test_bowtie2_index mapping.bowtie2_index(tmp_ref, tmp_out, bowtie2=extern_progs.exe('bowtie2')) File "/<>/ariba-2.7.1+ds/ariba/mapping.py", line 29, in bowtie2_index common.syscall(cmd, verbose=verbose, verbose_filehandle=verbose_filehandle) File "/<>/ariba-2.7.1+ds/ariba/common.py", line 28, in syscall sys.exit(1) SystemExit: 1 ====================================================================== ERROR: Test run_bowtie2 unsorted ---------------------------------------------------------------------- Traceback (most recent call last): File "/<>/ariba-2.7.1+ds/ariba/tests/mapping_test.py", line 57, in test_run_bowtie2 bowtie2=extern_progs.exe('bowtie2'), File "/<>/ariba-2.7.1+ds/ariba/mapping.py", line 62, in run_bowtie2 bowtie2_index(ref_fa, map_index, bowtie2=bowtie2, verbose=verbose, verbose_filehandle=verbose_filehandle) File "/<>/ariba-2.7.1+ds/ariba/mapping.py", line 29, in bowtie2_index common.syscall(cmd, verbose=verbose, verbose_filehandle=verbose_filehandle) File "/<>/ariba-2.7.1+ds/ariba/common.py", line 28, in syscall sys.exit(1) SystemExit: 1 ====================================================================== ERROR: Test run_bowtie2 sorted ---------------------------------------------------------------------- Traceback (most recent call last): File "/<>/ariba-2.7.1+ds/ariba/tests/mapping_test.py", line 98, in test_run_bowtie2_and_sort bowtie2=extern_progs.exe('bowtie2'), File "/<>/ariba-2.7.1+ds/ariba/mapping.py", line 62, in run_bowtie2 bowtie2_index(ref_fa, map_index, bowtie2=bowtie2, verbose=verbose, verbose_filehandle=verbose_filehandle) File "/<>/ariba-2.7.1+ds/ariba/mapping.py", line 29, in bowtie2_index common.syscall(cmd, verbose=verbose, verbose_filehandle=verbose_filehandle) File "/<>/ariba-2.7.1+ds/ariba/common.py", line 28, in syscall sys.exit(1) SystemExit: 1 ====================================================================== ERROR: Test run_bowtie2 unsorted remove both unmapped ---------------------------------------------------------------------- Traceback (most recent call last): File "/<>/ariba-2.7.1+ds/ariba/tests/mapping_test.py", line 78, in test_run_bowtie2_remove_both_unmapped remove_both_unmapped=True, File "/<>/ariba-2.7.1+ds/ariba/mapping.py", line 62, in run_bowtie2 bowtie2_index(ref_fa, map_index, bowtie2=bowtie2, verbose=verbose, verbose_filehandle=verbose_filehandle) File "/<>/ariba-2.7.1+ds/ariba/mapping.py", line 29, in bowtie2_index common.syscall(cmd, verbose=verbose, verbose_filehandle=verbose_filehandle) File "/<>/ariba-2.7.1+ds/ariba/common.py", line 28, in syscall sys.exit(1) SystemExit: 1 ---------------------------------------------------------------------- Ran 317 tests in 71.046s FAILED (errors=16) debian/rules:23: recipe for target 'override_dh_auto_test' failed make[1]: *** [override_dh_auto_test] Error 1 make[1]: Leaving directory '/<>/ariba-2.7.1+ds' debian/rules:10: recipe for target 'build' failed make: *** [build] Error 2 dpkg-buildpackage: error: debian/rules build gave error exit status 2 -------------------------------------------------------------------------------- Build finished at 20170302-0622 Finished -------- E: Build failure (dpkg-buildpackage died) +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Not removing build depends: as requested Keeping session: +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build-Space: 16700 Build-Time: 90 Distribution: zesty-proposed Fail-Stage: build Host Architecture: amd64 Install-Time: 32 Job: ariba_2.7.1+ds-1.dsc Machine Architecture: amd64 Package: ariba Package-Time: 124 Source-Version: 2.7.1+ds-1 Space: 16700 Status: attempted Version: 2.7.1+ds-1 -------------------------------------------------------------------------------- Finished at 20170302-0622 Build needed 00:02:04, 16700k disc space RUN: /usr/share/launchpad-buildd/slavebin/scan-for-processes ['scan-for-processes', 'PACKAGEBUILD-11933282'] Scanning for processes to kill in build /home/buildd/build-PACKAGEBUILD-11933282/chroot-autobuild... RUN: /usr/share/launchpad-buildd/slavebin/umount-chroot ['umount-chroot', 'PACKAGEBUILD-11933282'] Unmounting chroot for build PACKAGEBUILD-11933282... RUN: /usr/share/launchpad-buildd/slavebin/remove-build ['remove-build', 'PACKAGEBUILD-11933282'] Removing build PACKAGEBUILD-11933282