RUN: /usr/share/launchpad-buildd/slavebin/slave-prep Forking launchpad-buildd slave process... Kernel version: Linux bos02-ppc64el-007 4.4.0-104-generic #127-Ubuntu SMP Mon Dec 11 12:16:48 UTC 2017 ppc64le Buildd toolchain package versions: launchpad-buildd_157 python-lpbuildd_157 sbuild_0.67.0-2ubuntu7.1 bzr-builder_0.7.3+bzr174~ppa13~ubuntu14.10.1 bzr_2.7.0-2ubuntu3.1 git-build-recipe_0.3.4~git201611291343.dcee459~ubuntu16.04.1 git_1:2.7.4-0ubuntu1.3 dpkg-dev_1.18.4ubuntu1.3 python-debian_0.1.27ubuntu2. Syncing the system clock with the buildd NTP service... 24 Dec 18:22:48 ntpdate[1787]: adjust time server 10.211.37.1 offset 0.000308 sec RUN: /usr/share/launchpad-buildd/slavebin/in-target unpack-chroot --backend=chroot --series=bionic --arch=ppc64el PACKAGEBUILD-13921413 /home/buildd/filecache-default/64ab4a3b1843816d631a3747c16f42fa2d8de59d Creating target for build PACKAGEBUILD-13921413 RUN: /usr/share/launchpad-buildd/slavebin/in-target mount-chroot --backend=chroot --series=bionic --arch=ppc64el PACKAGEBUILD-13921413 Starting target for build PACKAGEBUILD-13921413 RUN: /usr/share/launchpad-buildd/slavebin/in-target override-sources-list --backend=chroot --series=bionic --arch=ppc64el PACKAGEBUILD-13921413 'deb http://ftpmaster.internal/ubuntu bionic main restricted universe multiverse' 'deb http://ftpmaster.internal/ubuntu bionic-security main restricted universe multiverse' 'deb http://ftpmaster.internal/ubuntu bionic-updates main restricted universe multiverse' Overriding sources.list in build-PACKAGEBUILD-13921413 RUN: /usr/share/launchpad-buildd/slavebin/in-target update-debian-chroot --backend=chroot --series=bionic --arch=ppc64el PACKAGEBUILD-13921413 Updating target for build PACKAGEBUILD-13921413 Get:1 http://ftpmaster.internal/ubuntu bionic InRelease [235 kB] Get:2 http://ftpmaster.internal/ubuntu bionic-security InRelease [65.4 kB] Get:3 http://ftpmaster.internal/ubuntu bionic-updates InRelease [65.4 kB] Get:4 http://ftpmaster.internal/ubuntu bionic/main ppc64el Packages [972 kB] Get:5 http://ftpmaster.internal/ubuntu bionic/main Translation-en [517 kB] Get:6 http://ftpmaster.internal/ubuntu bionic/restricted Translation-en [2788 B] Get:7 http://ftpmaster.internal/ubuntu bionic/universe ppc64el Packages [8088 kB] Get:8 http://ftpmaster.internal/ubuntu bionic/universe Translation-en [4918 kB] Get:9 http://ftpmaster.internal/ubuntu bionic/multiverse ppc64el Packages [133 kB] Get:10 http://ftpmaster.internal/ubuntu bionic/multiverse Translation-en [109 kB] Fetched 15.1 MB in 3s (4735 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: libasn1-8-heimdal libcurl3-gnutls libgssapi-krb5-2 libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhx509-5-heimdal libidn2-0 libk5crypto3 libkeyutils1 libkrb5-26-heimdal libkrb5-3 libkrb5support0 libldap-2.4-2 libldap-common libnghttp2-14 libpsl5 libroken18-heimdal librtmp1 libsasl2-2 libsasl2-modules-db libunistring0 libwind0-heimdal Use 'sudo apt autoremove' to remove them. The following NEW packages will be installed: liblsan0 libnghttp2-14 libtsan0 The following packages will be upgraded: adduser apt apt-transport-https base-files base-passwd binutils binutils-common binutils-powerpc64le-linux-gnu bsdutils build-essential coreutils cpp-7 debconf debianutils dpkg dpkg-dev e2fslibs e2fsprogs fdisk findutils g++-7 gcc-7 gcc-7-base gnupg gnupg-agent gpgv libapparmor1 libapt-pkg5.0 libasan4 libasn1-8-heimdal libassuan0 libatomic1 libbinutils libblkid1 libc-bin libc-dev-bin libc6 libc6-dev libcap-ng0 libcap2 libcc1-0 libcomerr2 libcurl3-gnutls libdpkg-perl libfdisk1 libgcc-7-dev libgcc1 libgcrypt20 libgomp1 libgpg-error0 libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhogweed4 libhx509-5-heimdal libidn11 libidn2-0 libip4tc0 libitm1 libkeyutils1 libkrb5-26-heimdal liblockfile-bin liblockfile1 libmount1 libnettle6 libnpth0 libp11-kit0 libpcre3 libperl5.26 libpng16-16 libpsl5 libroken18-heimdal libseccomp2 libselinux1 libsemanage-common libsemanage1 libsmartcols1 libsqlite3-0 libss2 libssl1.0.0 libstdc++-7-dev libstdc++6 libsystemd0 libtasn1-6 libubsan0 libudev1 libuuid1 libwind0-heimdal linux-libc-dev lsb-base mount multiarch-support openssl optipng perl perl-base perl-modules-5.26 pinentry-curses sensible-utils systemd systemd-sysv sysvinit-utils tzdata util-linux 105 upgraded, 3 newly installed, 0 to remove and 0 not upgraded. Need to get 59.6 MB of archives. After this operation, 9367 kB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu bionic/main ppc64el base-files ppc64el 10ubuntu1 [55.9 kB] Get:2 http://ftpmaster.internal/ubuntu bionic/main ppc64el bsdutils ppc64el 1:2.30.2-0.1ubuntu1 [61.8 kB] Get:3 http://ftpmaster.internal/ubuntu bionic/main ppc64el coreutils ppc64el 8.26-3ubuntu4 [1251 kB] Get:4 http://ftpmaster.internal/ubuntu bionic/main ppc64el debianutils ppc64el 4.8.3 [86.0 kB] Get:5 http://ftpmaster.internal/ubuntu bionic/main ppc64el dpkg ppc64el 1.19.0.4ubuntu1 [1149 kB] Get:6 http://ftpmaster.internal/ubuntu bionic/main ppc64el libc6-dev ppc64el 2.26-0ubuntu2 [2458 kB] Get:7 http://ftpmaster.internal/ubuntu bionic/main ppc64el libc-dev-bin ppc64el 2.26-0ubuntu2 [65.4 kB] Get:8 http://ftpmaster.internal/ubuntu bionic/main ppc64el linux-libc-dev ppc64el 4.13.0-17.20 [955 kB] Get:9 http://ftpmaster.internal/ubuntu bionic/main ppc64el libgomp1 ppc64el 7.2.0-18ubuntu2 [69.2 kB] Get:10 http://ftpmaster.internal/ubuntu bionic/main ppc64el libitm1 ppc64el 7.2.0-18ubuntu2 [29.7 kB] Get:11 http://ftpmaster.internal/ubuntu bionic/main ppc64el gcc-7-base ppc64el 7.2.0-18ubuntu2 [19.0 kB] Get:12 http://ftpmaster.internal/ubuntu bionic/main ppc64el libgcc1 ppc64el 1:7.2.0-18ubuntu2 [29.8 kB] Get:13 http://ftpmaster.internal/ubuntu bionic/main ppc64el libatomic1 ppc64el 7.2.0-18ubuntu2 [8532 B] Get:14 http://ftpmaster.internal/ubuntu bionic/main ppc64el libasan4 ppc64el 7.2.0-18ubuntu2 [367 kB] Get:15 http://ftpmaster.internal/ubuntu bionic/main ppc64el liblsan0 ppc64el 7.2.0-18ubuntu2 [134 kB] Get:16 http://ftpmaster.internal/ubuntu bionic/main ppc64el libtsan0 ppc64el 7.2.0-18ubuntu2 [287 kB] Get:17 http://ftpmaster.internal/ubuntu bionic/main ppc64el libubsan0 ppc64el 7.2.0-18ubuntu2 [136 kB] Get:18 http://ftpmaster.internal/ubuntu bionic/main ppc64el cpp-7 ppc64el 7.2.0-18ubuntu2 [6260 kB] Get:19 http://ftpmaster.internal/ubuntu bionic/main ppc64el libcc1-0 ppc64el 7.2.0-18ubuntu2 [39.3 kB] Get:20 http://ftpmaster.internal/ubuntu bionic/main ppc64el g++-7 ppc64el 7.2.0-18ubuntu2 [7106 kB] Get:21 http://ftpmaster.internal/ubuntu bionic/main ppc64el gcc-7 ppc64el 7.2.0-18ubuntu2 [6903 kB] Get:22 http://ftpmaster.internal/ubuntu bionic/main ppc64el libgcc-7-dev ppc64el 7.2.0-18ubuntu2 [986 kB] Get:23 http://ftpmaster.internal/ubuntu bionic/main ppc64el libstdc++-7-dev ppc64el 7.2.0-18ubuntu2 [1524 kB] Get:24 http://ftpmaster.internal/ubuntu bionic/main ppc64el libstdc++6 ppc64el 7.2.0-18ubuntu2 [440 kB] Get:25 http://ftpmaster.internal/ubuntu bionic/main ppc64el libbinutils ppc64el 2.29.1-12ubuntu1 [457 kB] Get:26 http://ftpmaster.internal/ubuntu bionic/main ppc64el binutils ppc64el 2.29.1-12ubuntu1 [3404 B] Get:27 http://ftpmaster.internal/ubuntu bionic/main ppc64el binutils-common ppc64el 2.29.1-12ubuntu1 [190 kB] Get:28 http://ftpmaster.internal/ubuntu bionic/main ppc64el binutils-powerpc64le-linux-gnu ppc64el 2.29.1-12ubuntu1 [1969 kB] Get:29 http://ftpmaster.internal/ubuntu bionic/main ppc64el libc6 ppc64el 2.26-0ubuntu2 [2619 kB] Get:30 http://ftpmaster.internal/ubuntu bionic/main ppc64el e2fslibs ppc64el 1.43.7-1 [173 kB] Get:31 http://ftpmaster.internal/ubuntu bionic/main ppc64el e2fsprogs ppc64el 1.43.7-1 [510 kB] Get:32 http://ftpmaster.internal/ubuntu bionic/main ppc64el findutils ppc64el 4.6.0+git+20170828-2 [314 kB] Get:33 http://ftpmaster.internal/ubuntu bionic/main ppc64el perl-modules-5.26 all 5.26.1-3 [2761 kB] Get:34 http://ftpmaster.internal/ubuntu bionic/main ppc64el libperl5.26 ppc64el 5.26.1-3 [3399 kB] Get:35 http://ftpmaster.internal/ubuntu bionic/main ppc64el perl ppc64el 5.26.1-3 [201 kB] Get:36 http://ftpmaster.internal/ubuntu bionic/main ppc64el perl-base ppc64el 5.26.1-3 [1304 kB] Get:37 http://ftpmaster.internal/ubuntu bionic/main ppc64el libuuid1 ppc64el 2.30.2-0.1ubuntu1 [15.5 kB] Get:38 http://ftpmaster.internal/ubuntu bionic/main ppc64el libblkid1 ppc64el 2.30.2-0.1ubuntu1 [128 kB] Get:39 http://ftpmaster.internal/ubuntu bionic/main ppc64el libsmartcols1 ppc64el 2.30.2-0.1ubuntu1 [84.7 kB] Get:40 http://ftpmaster.internal/ubuntu bionic/main ppc64el libfdisk1 ppc64el 2.30.2-0.1ubuntu1 [160 kB] Get:41 http://ftpmaster.internal/ubuntu bionic/main ppc64el libpcre3 ppc64el 2:8.39-8 [224 kB] Get:42 http://ftpmaster.internal/ubuntu bionic/main ppc64el libselinux1 ppc64el 2.7-2 [78.6 kB] Get:43 http://ftpmaster.internal/ubuntu bionic/main ppc64el libmount1 ppc64el 2.30.2-0.1ubuntu1 [139 kB] Get:44 http://ftpmaster.internal/ubuntu bionic/main ppc64el fdisk ppc64el 2.30.2-0.1ubuntu1 [108 kB] Get:45 http://ftpmaster.internal/ubuntu bionic/main ppc64el util-linux ppc64el 2.30.2-0.1ubuntu1 [881 kB] Get:46 http://ftpmaster.internal/ubuntu bionic/main ppc64el base-passwd ppc64el 3.5.44 [50.1 kB] Get:47 http://ftpmaster.internal/ubuntu bionic/main ppc64el libc-bin ppc64el 2.26-0ubuntu2 [573 kB] Get:48 http://ftpmaster.internal/ubuntu bionic/main ppc64el sysvinit-utils ppc64el 2.88dsf-59.10ubuntu1 [20.6 kB] Get:49 http://ftpmaster.internal/ubuntu bionic/main ppc64el libudev1 ppc64el 235-3ubuntu2 [60.8 kB] Get:50 http://ftpmaster.internal/ubuntu bionic/main ppc64el libapt-pkg5.0 ppc64el 1.6~alpha5 [878 kB] Get:51 http://ftpmaster.internal/ubuntu bionic/main ppc64el debconf all 1.5.65 [124 kB] Get:52 http://ftpmaster.internal/ubuntu bionic/main ppc64el adduser all 3.116ubuntu1 [163 kB] Get:53 http://ftpmaster.internal/ubuntu bionic/main ppc64el libgpg-error0 ppc64el 1.27-5 [42.1 kB] Get:54 http://ftpmaster.internal/ubuntu bionic/main ppc64el libgcrypt20 ppc64el 1.8.1-4 [448 kB] Get:55 http://ftpmaster.internal/ubuntu bionic/main ppc64el gpgv ppc64el 2.1.15-1ubuntu8 [218 kB] Get:56 http://ftpmaster.internal/ubuntu bionic/main ppc64el libseccomp2 ppc64el 2.3.1-2.1ubuntu3 [47.2 kB] Get:57 http://ftpmaster.internal/ubuntu bionic/main ppc64el apt ppc64el 1.6~alpha5 [1191 kB] Get:58 http://ftpmaster.internal/ubuntu bionic/main ppc64el libapparmor1 ppc64el 2.11.0-2ubuntu18 [29.9 kB] Get:59 http://ftpmaster.internal/ubuntu bionic/main ppc64el libcap2 ppc64el 1:2.25-1.2 [13.5 kB] Get:60 http://ftpmaster.internal/ubuntu bionic/main ppc64el libidn11 ppc64el 1.33-2.1 [46.4 kB] Get:61 http://ftpmaster.internal/ubuntu bionic/main ppc64el libip4tc0 ppc64el 1.6.1-2ubuntu2 [23.6 kB] Get:62 http://ftpmaster.internal/ubuntu bionic/main ppc64el mount ppc64el 2.30.2-0.1ubuntu1 [111 kB] Get:63 http://ftpmaster.internal/ubuntu bionic/main ppc64el systemd ppc64el 235-3ubuntu2 [2962 kB] Get:64 http://ftpmaster.internal/ubuntu bionic/main ppc64el libsystemd0 ppc64el 235-3ubuntu2 [213 kB] Get:65 http://ftpmaster.internal/ubuntu bionic/main ppc64el systemd-sysv ppc64el 235-3ubuntu2 [13.1 kB] Get:66 http://ftpmaster.internal/ubuntu bionic/main ppc64el libcap-ng0 ppc64el 0.7.7-3.1 [11.6 kB] Get:67 http://ftpmaster.internal/ubuntu bionic/main ppc64el libcomerr2 ppc64el 1.43.7-1 [11.6 kB] Get:68 http://ftpmaster.internal/ubuntu bionic/main ppc64el libsemanage-common all 2.7-2 [6916 B] Get:69 http://ftpmaster.internal/ubuntu bionic/main ppc64el libsemanage1 ppc64el 2.7-2 [85.4 kB] Get:70 http://ftpmaster.internal/ubuntu bionic/main ppc64el libss2 ppc64el 1.43.7-1 [11.4 kB] Get:71 http://ftpmaster.internal/ubuntu bionic/main ppc64el libnettle6 ppc64el 3.3-2 [120 kB] Get:72 http://ftpmaster.internal/ubuntu bionic/main ppc64el libhogweed4 ppc64el 3.3-2 [134 kB] Get:73 http://ftpmaster.internal/ubuntu bionic/main ppc64el libp11-kit0 ppc64el 0.23.9-2 [167 kB] Get:74 http://ftpmaster.internal/ubuntu bionic/main ppc64el libtasn1-6 ppc64el 4.12-3 [39.8 kB] Get:75 http://ftpmaster.internal/ubuntu bionic/main ppc64el lsb-base all 9.20170808ubuntu1 [12.5 kB] Get:76 http://ftpmaster.internal/ubuntu bionic/main ppc64el sensible-utils all 0.0.11 [14.8 kB] Get:77 http://ftpmaster.internal/ubuntu bionic/main ppc64el libassuan0 ppc64el 2.5.1-1 [33.9 kB] Get:78 http://ftpmaster.internal/ubuntu bionic/main ppc64el pinentry-curses ppc64el 1.0.0-3 [37.5 kB] Get:79 http://ftpmaster.internal/ubuntu bionic/main ppc64el libnpth0 ppc64el 1.5-3 [7780 B] Get:80 http://ftpmaster.internal/ubuntu bionic/main ppc64el gnupg ppc64el 2.1.15-1ubuntu8 [847 kB] Get:81 http://ftpmaster.internal/ubuntu bionic/main ppc64el gnupg-agent ppc64el 2.1.15-1ubuntu8 [291 kB] Get:82 http://ftpmaster.internal/ubuntu bionic/main ppc64el libsqlite3-0 ppc64el 3.21.0-1 [464 kB] Get:83 http://ftpmaster.internal/ubuntu bionic/main ppc64el libroken18-heimdal ppc64el 7.5.0+dfsg-1 [42.2 kB] Get:84 http://ftpmaster.internal/ubuntu bionic/main ppc64el libasn1-8-heimdal ppc64el 7.5.0+dfsg-1 [140 kB] Get:85 http://ftpmaster.internal/ubuntu bionic/main ppc64el libheimbase1-heimdal ppc64el 7.5.0+dfsg-1 [30.5 kB] Get:86 http://ftpmaster.internal/ubuntu bionic/main ppc64el libhcrypto4-heimdal ppc64el 7.5.0+dfsg-1 [100 kB] Get:87 http://ftpmaster.internal/ubuntu bionic/main ppc64el libwind0-heimdal ppc64el 7.5.0+dfsg-1 [48.0 kB] Get:88 http://ftpmaster.internal/ubuntu bionic/main ppc64el libhx509-5-heimdal ppc64el 7.5.0+dfsg-1 [108 kB] Get:89 http://ftpmaster.internal/ubuntu bionic/main ppc64el libkrb5-26-heimdal ppc64el 7.5.0+dfsg-1 [216 kB] Get:90 http://ftpmaster.internal/ubuntu bionic/main ppc64el libheimntlm0-heimdal ppc64el 7.5.0+dfsg-1 [16.4 kB] Get:91 http://ftpmaster.internal/ubuntu bionic/main ppc64el libgssapi3-heimdal ppc64el 7.5.0+dfsg-1 [92.6 kB] Get:92 http://ftpmaster.internal/ubuntu bionic/main ppc64el libssl1.0.0 ppc64el 1.0.2g-1ubuntu14 [880 kB] Get:93 http://ftpmaster.internal/ubuntu bionic/main ppc64el multiarch-support ppc64el 2.26-0ubuntu2 [6832 B] Get:94 http://ftpmaster.internal/ubuntu bionic/main ppc64el openssl ppc64el 1.0.2g-1ubuntu14 [520 kB] Get:95 http://ftpmaster.internal/ubuntu bionic/main ppc64el tzdata all 2017c-1 [188 kB] Get:96 http://ftpmaster.internal/ubuntu bionic/main ppc64el libidn2-0 ppc64el 2.0.4-1 [95.7 kB] Get:97 http://ftpmaster.internal/ubuntu bionic/main ppc64el libkeyutils1 ppc64el 1.5.9-9.2ubuntu1 [9736 B] Get:98 http://ftpmaster.internal/ubuntu bionic/main ppc64el libpng16-16 ppc64el 1.6.34-1 [200 kB] Get:99 http://ftpmaster.internal/ubuntu bionic/universe ppc64el apt-transport-https all 1.6~alpha5 [1692 B] Get:100 http://ftpmaster.internal/ubuntu bionic/main ppc64el dpkg-dev all 1.19.0.4ubuntu1 [607 kB] Get:101 http://ftpmaster.internal/ubuntu bionic/main ppc64el libdpkg-perl all 1.19.0.4ubuntu1 [211 kB] Get:102 http://ftpmaster.internal/ubuntu bionic/main ppc64el build-essential ppc64el 12.4ubuntu1 [4754 B] Get:103 http://ftpmaster.internal/ubuntu bionic/main ppc64el libnghttp2-14 ppc64el 1.28.0-1 [84.7 kB] Get:104 http://ftpmaster.internal/ubuntu bionic/main ppc64el libpsl5 ppc64el 0.19.1-4 [43.0 kB] Get:105 http://ftpmaster.internal/ubuntu bionic/main ppc64el libcurl3-gnutls ppc64el 7.57.0-1ubuntu1 [215 kB] Get:106 http://ftpmaster.internal/ubuntu bionic/main ppc64el liblockfile-bin ppc64el 1.14-1.1 [12.0 kB] Get:107 http://ftpmaster.internal/ubuntu bionic/main ppc64el liblockfile1 ppc64el 1.14-1.1 [6988 B] Get:108 http://ftpmaster.internal/ubuntu bionic/main ppc64el optipng ppc64el 0.7.6-1.1 [86.8 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 59.6 MB in 1s (54.3 MB/s) (Reading database ... 12537 files and directories currently installed.) Preparing to unpack .../base-files_10ubuntu1_ppc64el.deb ... Unpacking base-files (10ubuntu1) over (9.6ubuntu101) ... Setting up base-files (10ubuntu1) ... Installing new version of config file /etc/debian_version ... Installing new version of config file /etc/issue ... Installing new version of config file /etc/issue.net ... Installing new version of config file /etc/lsb-release ... (Reading database ... 12537 files and directories currently installed.) Preparing to unpack .../bsdutils_1%3a2.30.2-0.1ubuntu1_ppc64el.deb ... Unpacking bsdutils (1:2.30.2-0.1ubuntu1) over (1:2.30.1-0ubuntu4) ... Setting up bsdutils (1:2.30.2-0.1ubuntu1) ... (Reading database ... 12537 files and directories currently installed.) Preparing to unpack .../coreutils_8.26-3ubuntu4_ppc64el.deb ... Unpacking coreutils (8.26-3ubuntu4) over (8.26-3ubuntu3) ... Setting up coreutils (8.26-3ubuntu4) ... (Reading database ... 12537 files and directories currently installed.) Preparing to unpack .../debianutils_4.8.3_ppc64el.deb ... Unpacking debianutils (4.8.3) over (4.8.2) ... Setting up debianutils (4.8.3) ... (Reading database ... 12537 files and directories currently installed.) Preparing to unpack .../dpkg_1.19.0.4ubuntu1_ppc64el.deb ... Unpacking dpkg (1.19.0.4ubuntu1) over (1.18.24ubuntu1) ... Setting up dpkg (1.19.0.4ubuntu1) ... Installing new version of config file /etc/alternatives/README ... Installing new version of config file /etc/cron.daily/dpkg ... Installing new version of config file /etc/logrotate.d/dpkg ... (Reading database ... 12539 files and directories currently installed.) Preparing to unpack .../0-libc6-dev_2.26-0ubuntu2_ppc64el.deb ... Unpacking libc6-dev:ppc64el (2.26-0ubuntu2) over (2.26-0ubuntu1) ... Preparing to unpack .../1-libc-dev-bin_2.26-0ubuntu2_ppc64el.deb ... Unpacking libc-dev-bin (2.26-0ubuntu2) over (2.26-0ubuntu1) ... Preparing to unpack .../2-linux-libc-dev_4.13.0-17.20_ppc64el.deb ... 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Setting up libheimntlm0-heimdal:ppc64el (7.5.0+dfsg-1) ... Setting up gcc-7 (7.2.0-18ubuntu2) ... Setting up g++-7 (7.2.0-18ubuntu2) ... Setting up gnupg (2.1.15-1ubuntu8) ... Setting up libdpkg-perl (1.19.0.4ubuntu1) ... Setting up dpkg-dev (1.19.0.4ubuntu1) ... Setting up libgssapi3-heimdal:ppc64el (7.5.0+dfsg-1) ... Setting up build-essential (12.4ubuntu1) ... Processing triggers for libc-bin (2.26-0ubuntu2) ... RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package PACKAGEBUILD-13921413 ppc64el bionic -c chroot:build-PACKAGEBUILD-13921413 --arch=ppc64el --dist=bionic --nolog kineticstools_0.6.1+20161222-1ubuntu1.dsc Initiating build PACKAGEBUILD-13921413 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.4.0-104-generic #127-Ubuntu SMP Mon Dec 11 12:16:48 UTC 2017 ppc64le sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on bos02-ppc64el-007.buildd +==============================================================================+ | kineticstools 0.6.1+20161222-1ubuntu1 (ppc64el) 24 Dec 2017 18:23 | +==============================================================================+ Package: kineticstools Version: 0.6.1+20161222-1ubuntu1 Source Version: 0.6.1+20161222-1ubuntu1 Distribution: bionic Machine Architecture: ppc64el Host Architecture: ppc64el Build Architecture: ppc64el I: NOTICE: Log filtering will replace 'build/kineticstools-Tkr2H4/kineticstools-0.6.1+20161222' with '<>' I: NOTICE: Log filtering will replace 'build/kineticstools-Tkr2H4' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-13921413/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- kineticstools_0.6.1+20161222-1ubuntu1.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-A6db7L/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/<>/resolver-A6db7L/apt_archive ./ InRelease Get:2 copy:/<>/resolver-A6db7L/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-A6db7L/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-A6db7L/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-A6db7L/apt_archive ./ Packages [527 B] Fetched 2860 B in 0s (162 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: libasn1-8-heimdal libcurl3-gnutls libgssapi-krb5-2 libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhx509-5-heimdal libidn2-0 libk5crypto3 libkeyutils1 libkrb5-26-heimdal libkrb5-3 libkrb5support0 libldap-2.4-2 libldap-common libnghttp2-14 libpsl5 libroken18-heimdal librtmp1 libsasl2-2 libsasl2-modules-db libunistring0 libwind0-heimdal Use '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 852 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-A6db7L/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 852 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 12553 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_ppc64el.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... Merged Build-Depends: debhelper (>= 9), dh-python, python-all, python-setuptools, python-docutils, python-pbcore (>= 1.2.8), python-pbcommand (>= 0.3.22), python-numpy (>= 1.6.0), python-h5py (>= 1.3.0), python-scipy (>= 0.9.0), python-nose Filtered Build-Depends: debhelper (>= 9), dh-python, python-all, python-setuptools, python-docutils, python-pbcore (>= 1.2.8), python-pbcommand (>= 0.3.22), python-numpy (>= 1.6.0), python-h5py (>= 1.3.0), python-scipy (>= 0.9.0), python-nose dpkg-deb: building package 'sbuild-build-depends-kineticstools-dummy' in '/<>/resolver-GI3TDp/apt_archive/sbuild-build-depends-kineticstools-dummy.deb'. Ign:1 copy:/<>/resolver-GI3TDp/apt_archive ./ InRelease Get:2 copy:/<>/resolver-GI3TDp/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-GI3TDp/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-GI3TDp/apt_archive ./ Sources [290 B] Get:5 copy:/<>/resolver-GI3TDp/apt_archive ./ Packages [610 B] Fetched 3019 B in 0s (172 kB/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install kineticstools build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils debhelper dh-autoreconf dh-python dh-strip-nondeterminism docutils-common file gettext gettext-base groff-base intltool-debian libaec0 libarchive-zip-perl libblas3 libbsd0 libcroco3 libexpat1 libfile-stripnondeterminism-perl libfreetype6 libgfortran4 libglib2.0-0 libgraphite2-3 libharfbuzz0b libhdf5-100 libhts2 libicu-le-hb0 libicu60 liblapack3 libmagic-mgc libmagic1 libmpdec2 libpipeline1 libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libpython3-stdlib libpython3.6-minimal libpython3.6-stdlib libsigsegv2 libsz2 libtimedate-perl libtool libxml2 m4 man-db mime-support po-debconf python python-all python-avro python-certifi python-chardet python-decorator python-docutils python-h5py python-idna python-iso8601 python-minimal python-nose python-numpy python-pbcommand python-pbcore python-pkg-resources python-pysam python-requests python-roman python-scipy python-setuptools python-six python-urllib3 python2.7 python2.7-minimal python3 python3-distutils python3-minimal python3.6 python3.6-2to3 python3.6-minimal sgml-base xml-core Suggested packages: autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois vacation dh-make dwz gettext-doc libasprintf-dev libgettextpo-dev groff libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc less www-browser apparmor libmail-box-perl python-doc python-tk fonts-linuxlibertine | ttf-linux-libertine texlive-lang-french texlive-latex-base texlive-latex-recommended python-h5py-doc python-coverage python-nose-doc gfortran python-dev python-numpy-dbg python-numpy-doc python-pbcore-doc python-cryptography python-openssl python-socks python-scipy-doc python-setuptools-doc python-ntlm python2.7-doc binfmt-support python3-doc python3-tk python3-venv python3.6-venv python3.6-doc sgml-base-doc Recommended packages: curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs libltdl-dev libmail-sendmail-perl docutils-doc libpaper-utils python-pil python-pygments python-dev python-imaging python-cryptography python-ipaddress python-openssl The following packages will be REMOVED: pkg-create-dbgsym* The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils debhelper dh-autoreconf dh-python dh-strip-nondeterminism docutils-common file gettext gettext-base groff-base intltool-debian libaec0 libarchive-zip-perl libblas3 libbsd0 libcroco3 libexpat1 libfile-stripnondeterminism-perl libfreetype6 libgfortran4 libglib2.0-0 libgraphite2-3 libharfbuzz0b libhdf5-100 libhts2 libicu-le-hb0 libicu60 liblapack3 libmagic-mgc libmagic1 libmpdec2 libpipeline1 libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libpython3-stdlib libpython3.6-minimal libpython3.6-stdlib libsigsegv2 libsz2 libtimedate-perl libtool libxml2 m4 man-db mime-support po-debconf python python-all python-avro python-certifi python-chardet python-decorator python-docutils python-h5py python-idna python-iso8601 python-minimal python-nose python-numpy python-pbcommand python-pbcore python-pkg-resources python-pysam python-requests python-roman python-scipy python-setuptools python-six python-urllib3 python2.7 python2.7-minimal python3 python3-distutils python3-minimal python3.6 python3.6-2to3 python3.6-minimal sbuild-build-depends-kineticstools-dummy sgml-base xml-core 0 upgraded, 85 newly installed, 1 to remove and 0 not upgraded. Need to get 53.8 MB of archives. After this operation, 228 MB of additional disk space will be used. 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Get:80 http://ftpmaster.internal/ubuntu bionic/main ppc64el python-requests all 2.18.1-1 [57.9 kB] Get:81 http://ftpmaster.internal/ubuntu bionic/universe ppc64el python-pbcommand all 0.5.3-1 [79.6 kB] Get:82 http://ftpmaster.internal/ubuntu bionic/universe ppc64el python-pysam ppc64el 0.13.0+ds-1 [1400 kB] Get:83 http://ftpmaster.internal/ubuntu bionic/universe ppc64el python-pbcore all 1.2.11+dfsg-1ubuntu1 [9084 kB] Get:84 http://ftpmaster.internal/ubuntu bionic/main ppc64el python-setuptools all 36.2.7-2 [260 kB] Get:85 http://ftpmaster.internal/ubuntu bionic/universe ppc64el python-scipy ppc64el 0.19.1-1ubuntu1 [9357 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 53.8 MB in 2s (25.5 MB/s) (Reading database ... 12553 files and directories currently installed.) 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Setting up libblas3:ppc64el (3.7.1-4ubuntu1) ... update-alternatives: using /usr/lib/powerpc64le-linux-gnu/blas/libblas.so.3 to provide /usr/lib/powerpc64le-linux-gnu/libblas.so.3 (libblas.so.3-powerpc64le-linux-gnu) in auto mode Processing triggers for libc-bin (2.26-0ubuntu2) ... Setting up autotools-dev (20171216.1) ... Setting up xml-core (0.18) ... Setting up bsdmainutils (9.0.14ubuntu1) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up libhts2:ppc64el (1.6-4) ... Setting up libpython2.7-stdlib:ppc64el (2.7.14-4) ... Setting up autopoint (0.19.8.1-4ubuntu2) ... Setting up libmpdec2:ppc64el (2.4.2-1) ... Setting up libsz2:ppc64el (0.3.2-2) ... Setting up libfile-stripnondeterminism-perl (0.040-1) ... Setting up libpython3.6-stdlib:ppc64el (3.6.4-1) ... Setting up libhdf5-100:ppc64el (1.10.0-patch1+docs-4) ... Setting up liblapack3:ppc64el (3.7.1-4ubuntu1) ... update-alternatives: using /usr/lib/powerpc64le-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/powerpc64le-linux-gnu/liblapack.so.3 (liblapack.so.3-powerpc64le-linux-gnu) in auto mode Setting up python2.7 (2.7.14-4) ... Setting up libharfbuzz0b:ppc64el (1.7.2-1) ... Setting up autoconf (2.69-11) ... Setting up file (1:5.32-1) ... Setting up libpython-stdlib:ppc64el (2.7.14-2ubuntu1) ... Setting up automake (1:1.15.1-3ubuntu1) ... update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode Setting up man-db (2.7.6.1-4) ... Not building database; man-db/auto-update is not 'true'. Setting up python (2.7.14-2ubuntu1) ... Setting up python-idna (2.5-1) ... Setting up libtool (2.4.6-2) ... Setting up libpython3-stdlib:ppc64el (3.6.3-0ubuntu2) ... Setting up python-pysam (0.13.0+ds-1) ... Setting up python-certifi (2017.7.27.1-2) ... Setting up python-avro (1.8.2+dfsg-1) ... Setting up python-pkg-resources (36.2.7-2) ... Setting up python-roman (2.0.0-2) ... Setting up python-numpy (1:1.13.3-2ubuntu1) ... Setting up python-six (1.11.0-1) ... Setting up python-iso8601 (0.1.11-1) ... Setting up python-decorator (4.1.2-1) ... Setting up python-nose (1.3.7-3) ... Setting up python-all (2.7.14-2ubuntu1) ... Setting up python-setuptools (36.2.7-2) ... Setting up python-urllib3 (1.21.1-1) ... Setting up python-h5py (2.7.1-2) ... Setting up python-chardet (3.0.4-1) ... Setting up python-scipy (0.19.1-1ubuntu1) ... Setting up python-pbcore (1.2.11+dfsg-1ubuntu1) ... Setting up python-requests (2.18.1-1) ... Setting up python-pbcommand (0.5.3-1) ... Processing triggers for sgml-base (1.29) ... Setting up docutils-common (0.14+dfsg-1) ... Processing triggers for sgml-base (1.29) ... Setting up python-docutils (0.14+dfsg-1) ... update-alternatives: using /usr/share/docutils/scripts/python2/rst-buildhtml to provide /usr/bin/rst-buildhtml (rst-buildhtml) in auto mode update-alternatives: using /usr/share/docutils/scripts/python2/rst2html to provide /usr/bin/rst2html (rst2html) in auto mode update-alternatives: using /usr/share/docutils/scripts/python2/rst2html4 to provide /usr/bin/rst2html4 (rst2html4) in auto mode update-alternatives: using /usr/share/docutils/scripts/python2/rst2html5 to provide /usr/bin/rst2html5 (rst2html5) in auto mode update-alternatives: using /usr/share/docutils/scripts/python2/rst2latex to provide /usr/bin/rst2latex (rst2latex) in auto mode update-alternatives: using /usr/share/docutils/scripts/python2/rst2man to provide /usr/bin/rst2man (rst2man) in auto mode update-alternatives: using /usr/share/docutils/scripts/python2/rst2odt to provide /usr/bin/rst2odt (rst2odt) in auto mode update-alternatives: using /usr/share/docutils/scripts/python2/rst2odt_prepstyles to provide /usr/bin/rst2odt_prepstyles (rst2odt_prepstyles) in auto mode update-alternatives: using /usr/share/docutils/scripts/python2/rst2pseudoxml to provide /usr/bin/rst2pseudoxml (rst2pseudoxml) in auto mode update-alternatives: using /usr/share/docutils/scripts/python2/rst2s5 to provide /usr/bin/rst2s5 (rst2s5) in auto mode update-alternatives: using /usr/share/docutils/scripts/python2/rst2xetex to provide /usr/bin/rst2xetex (rst2xetex) in auto mode update-alternatives: using /usr/share/docutils/scripts/python2/rst2xml to provide /usr/bin/rst2xml (rst2xml) in auto mode update-alternatives: using /usr/share/docutils/scripts/python2/rstpep2html to provide /usr/bin/rstpep2html (rstpep2html) in auto mode Setting up python3.6 (3.6.4-1) ... Setting up dh-autoreconf (15) ... Setting up python3 (3.6.3-0ubuntu2) ... Setting up libicu-le-hb0:ppc64el (1.0.3+git161113-4) ... Setting up python3.6-2to3 (3.6.4-1) ... Setting up dh-python (2.20170125) ... Setting up python3-distutils (3.6.4~rc1-6) ... Setting up libicu60:ppc64el (60.2-1ubuntu1) ... Setting up libxml2:ppc64el (2.9.4+dfsg1-5.2ubuntu1) ... Setting up libcroco3:ppc64el (0.6.12-2) ... Setting up gettext (0.19.8.1-4ubuntu2) ... Setting up intltool-debian (0.35.0+20060710.4) ... Setting up po-debconf (1.0.20) ... Setting up debhelper (11ubuntu1) ... Setting up sbuild-build-depends-kineticstools-dummy (0.invalid.0) ... Setting up dh-strip-nondeterminism (0.040-1) ... (Reading database ... 18630 files and directories currently installed.) Purging configuration files for pkg-create-dbgsym (0.73) ... Processing triggers for libc-bin (2.26-0ubuntu2) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.4.0-104-generic ppc64el (ppc64le) Toolchain package versions: binutils_2.29.1-12ubuntu1 dpkg-dev_1.19.0.4ubuntu1 g++-7_7.2.0-18ubuntu2 gcc-7_7.2.0-18ubuntu2 libc6-dev_2.26-0ubuntu2 libstdc++-7-dev_7.2.0-18ubuntu2 libstdc++6_7.2.0-18ubuntu2 linux-libc-dev_4.13.0-17.20 Package versions: adduser_3.116ubuntu1 advancecomp_2.0-1 apt_1.6~alpha5 apt-transport-https_1.6~alpha5 autoconf_2.69-11 automake_1:1.15.1-3ubuntu1 autopoint_0.19.8.1-4ubuntu2 autotools-dev_20171216.1 base-files_10ubuntu1 base-passwd_3.5.44 bash_4.4-5ubuntu1 binutils_2.29.1-12ubuntu1 binutils-common_2.29.1-12ubuntu1 binutils-powerpc64le-linux-gnu_2.29.1-12ubuntu1 bsdmainutils_9.0.14ubuntu1 bsdutils_1:2.30.2-0.1ubuntu1 build-essential_12.4ubuntu1 bzip2_1.0.6-8.1 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perl-base_5.26.1-3 perl-modules-5.26_5.26.1-3 pinentry-curses_1.0.0-3 pkgbinarymangler_131 po-debconf_1.0.20 policyrcd-script-zg2_0.1-3 procps_2:3.3.12-1ubuntu2 python_2.7.14-2ubuntu1 python-all_2.7.14-2ubuntu1 python-avro_1.8.2+dfsg-1 python-certifi_2017.7.27.1-2 python-chardet_3.0.4-1 python-decorator_4.1.2-1 python-docutils_0.14+dfsg-1 python-h5py_2.7.1-2 python-idna_2.5-1 python-iso8601_0.1.11-1 python-minimal_2.7.14-2ubuntu1 python-nose_1.3.7-3 python-numpy_1:1.13.3-2ubuntu1 python-pbcommand_0.5.3-1 python-pbcore_1.2.11+dfsg-1ubuntu1 python-pkg-resources_36.2.7-2 python-pysam_0.13.0+ds-1 python-requests_2.18.1-1 python-roman_2.0.0-2 python-scipy_0.19.1-1ubuntu1 python-setuptools_36.2.7-2 python-six_1.11.0-1 python-urllib3_1.21.1-1 python2.7_2.7.14-4 python2.7-minimal_2.7.14-4 python3_3.6.3-0ubuntu2 python3-distutils_3.6.4~rc1-6 python3-minimal_3.6.3-0ubuntu2 python3.6_3.6.4-1 python3.6-2to3_3.6.4-1 python3.6-minimal_3.6.4-1 readline-common_7.0-0ubuntu2 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-kineticstools-dummy_0.invalid.0 sed_4.4-1 sensible-utils_0.0.11 sgml-base_1.29 systemd_235-3ubuntu2 systemd-sysv_235-3ubuntu2 sysv-rc_2.88dsf-59.3ubuntu2 sysvinit-utils_2.88dsf-59.10ubuntu1 tar_1.29b-2 tzdata_2017c-1 ubuntu-keyring_2016.10.27 util-linux_2.30.2-0.1ubuntu1 xml-core_0.18 xz-utils_5.2.2-1.3 zlib1g_1:1.2.11.dfsg-0ubuntu2 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Tue Feb 21 02:47:59 2017 UTC gpgv: using RSA key gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./kineticstools_0.6.1+20161222-1ubuntu1.dsc dpkg-source: info: extracting kineticstools in kineticstools-0.6.1+20161222 dpkg-source: info: unpacking kineticstools_0.6.1+20161222.orig.tar.gz dpkg-source: info: unpacking kineticstools_0.6.1+20161222-1ubuntu1.debian.tar.xz dpkg-source: info: applying man-pages.patch dpkg-source: info: applying tests-import.patch dpkg-source: info: applying verbose-testing.patch dpkg-source: info: applying deactivate-tests-requiring-unavailable-data.patch dpkg-source: info: applying compiled-extension.patch dpkg-source: info: applying spelling.patch Check disc space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=noautodbgsym parallel=4 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=build-PACKAGEBUILD-13921413 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-13921413 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-13921413 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package kineticstools dpkg-buildpackage: info: source version 0.6.1+20161222-1ubuntu1 dpkg-buildpackage: info: source distribution zesty dpkg-source --before-build kineticstools-0.6.1+20161222 dpkg-buildpackage: info: host architecture ppc64el fakeroot debian/rules clean dh clean --with python2 --buildsystem=pybuild dh_auto_clean -O--buildsystem=pybuild I: pybuild base:184: python2.7 setup.py clean running clean removing '/<>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build' (and everything under it) 'build/bdist.linux-ppc64el' does not exist -- can't clean it 'build/scripts-2.7' does not exist -- can't clean it dh_clean -O--buildsystem=pybuild debian/rules build-arch dh build-arch --with python2 --buildsystem=pybuild dh_update_autotools_config -a -O--buildsystem=pybuild dh_auto_configure -a -O--buildsystem=pybuild I: pybuild base:184: python2.7 setup.py config running config dh_auto_build -a -O--buildsystem=pybuild I: pybuild base:184: /usr/bin/python setup.py build running build running build_py creating /<>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools copying kineticsTools/PositiveControlEnricher.py -> /<>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools copying kineticsTools/ipdSummary.py -> /<>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools copying kineticsTools/MultiSiteDetection.py -> /<>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools copying kineticsTools/MedakaLdaEnricher.py -> /<>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools copying kineticsTools/WorkerProcess.py -> /<>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools copying kineticsTools/BasicLdaEnricher.py -> /<>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools copying kineticsTools/ResultWriter.py -> /<>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools copying kineticsTools/pipelineTools.py -> /<>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools copying kineticsTools/MultiSiteCommon.py -> /<>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools copying kineticsTools/summarizeModifications.py -> /<>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools copying kineticsTools/ModificationDecode.py -> /<>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools copying kineticsTools/ipdModel.py -> /<>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools copying kineticsTools/KineticWorker.py -> /<>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools copying kineticsTools/__init__.py -> /<>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools copying kineticsTools/ReferenceUtils.py -> /<>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools copying kineticsTools/sharedArray.py -> /<>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools copying kineticsTools/MixtureEstimationMethods.py -> /<>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools creating /<>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools/tasks copying kineticsTools/tasks/__init__.py -> /<>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools/tasks copying kineticsTools/tasks/gather_kinetics_h5.py -> /<>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools/tasks creating /<>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools/resources copying kineticsTools/resources/P5-C3.h5 -> /<>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools/resources copying kineticsTools/resources/C2.h5 -> /<>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools/resources copying kineticsTools/resources/P6-C4.h5 -> /<>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools/resources copying kineticsTools/resources/XL-C2.h5 -> /<>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools/resources copying kineticsTools/resources/XL-XL.h5 -> /<>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools/resources copying kineticsTools/resources/unknown.h5 -> /<>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools/resources copying kineticsTools/resources/P4-C2.h5 -> /<>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools/resources running build_ext building 'kineticsTools/tree_predict' extension creating build creating build/temp.linux-ppc64el-2.7 creating build/temp.linux-ppc64el-2.7/kineticsTools powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O3 -fdebug-prefix-map=/<>/kineticstools-0.6.1+20161222=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python2.7 -c kineticsTools/tree_predict.c -o build/temp.linux-ppc64el-2.7/kineticsTools/tree_predict.o -O3 -shared -std=c99 powerpc64le-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-b3XMKw/python2.7-2.7.14=. -fstack-protector-strong -Wformat -Werror=format-security -fexceptions -Wl,-Bsymbolic-functions -specs=/usr/share/dpkg/no-pie-link.specs -Wl,-z,relro -Wl,-z,now -g -O3 -fdebug-prefix-map=/<>/kineticstools-0.6.1+20161222=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-ppc64el-2.7/kineticsTools/tree_predict.o -o /<>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools/tree_predict.so dh_auto_test -a -O--buildsystem=pybuild I: pybuild base:184: cd /<>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build; python2.7 -m nose test Check the null model against a few hard-coded contexts ... ok Test a modification decode around a known modification in lambda ... ok runTest (test.TestSetup) ... ok test_bam (test_ReferenceUtils.ReferenceUtilsTest) ... SKIP: Shared data folder missing test_cmph5 (test_ReferenceUtils.ReferenceUtilsTest) ... SKIP: Shared data folder missing test_createReferenceWindows (test_ReferenceUtils.ReferenceUtilsTest) ... SKIP: Shared data folder missing test_dataset (test_ReferenceUtils.ReferenceUtilsTest) ... SKIP: Shared data folder missing test_enumerateChunks (test_ReferenceUtils.ReferenceUtilsTest) ... SKIP: Shared data folder missing test_parseReferenceWindow (test_ReferenceUtils.ReferenceUtilsTest) ... SKIP: Shared data folder missing test_run_e2e (test_gather_h5.TestGatherH5ToolContract) ... ok test_gather_kinetics_h5 (test_gather_h5.TestGatherHDF5) ... ok test_gather_kinetics_h5 (test_gather_h5.TestGatherHDF5Flat) ... ok test_private_api (test_inputs.TestBam) ... SKIP: Missing test data directory Test for known modifications near the start of H. pylori genome ... SKIP: Missing test data directory test_small_decode (test_inputs.TestChunkedDataset) ... SKIP: Missing test data directory test_private_api (test_inputs.TestDataset) ... SKIP: Missing test data directory Test for known modifications near the start of H. pylori genome ... SKIP: Missing test data directory test_small_decode (test_inputs.TestNonStochastic) ... SKIP: Missing test data directory test_private_api (test_inputs.TestSplitDataset) ... SKIP: Missing test data directory Test for known modifications near the start of H. pylori genome ... SKIP: Missing test data directory SKIP: /pbi/dept/secondary/siv/testdata/kineticsTools or /pbi/dept/secondary/siv/references/Helicobacter_pylori_J99 not available test_run_e2e (test_tool_contract.TestIpdSummary) ... SKIP: /pbi/dept/secondary/siv/testdata/kineticsTools or /pbi/dept/secondary/siv/references/Helicobacter_pylori_J99 not available test_run_e2e (test_tool_contract.TestIpdSummaryChunk) ... SKIP: FIXME test_run_e2e (test_tool_contract.TestSummarizeModifications) ... SKIP: /pbi/dept/secondary/siv/testdata/kineticsTools or /pbi/dept/secondary/siv/references/Helicobacter_pylori_J99 not available ---------------------------------------------------------------------- Ran 23 tests in 65.008s OK (SKIP=18) Pos: 3, TplStrand: 0 Got ctx: NGGGCGGCGACCTCG Lut prediction: 0.692615 Gbm prediction: 0.692615 Gbm prediction fast: 0.692615 Gbm pred via predictIpdFuncModel: 0.692615 Methylated prediction: NGGGJGGCGACCTCG -> 0.809961 Methylated prediction: NGGGCGGCGJCCTCG -> 0.481690 Methylated prediction fast: NGGGJGGCGACCTCG -> 0.809961 Methylated prediction fast: NGGGCGGCGJCCTCG -> 0.481690 Pos: 10, TplStrand: 0 Got ctx: CGACCTCGCGGGTTT Lut prediction: 0.439837 Gbm prediction: 0.439837 Gbm prediction fast: 0.439837 Gbm pred via predictIpdFuncModel: 0.439837 Methylated prediction: CGACJTCGCGGGTTT -> 1.806269 Methylated prediction: CGACCTCGCJGGTTT -> 0.418073 Methylated prediction fast: CGACJTCGCGGGTTT -> 1.806269 Methylated prediction fast: CGACCTCGCJGGTTT -> 0.418073 Pos: 20, TplStrand: 0 Got ctx: GGTTTTCGCTATTTA Lut prediction: 0.803713 Gbm prediction: 0.803713 Gbm prediction fast: 0.803713 Gbm pred via predictIpdFuncModel: 0.803713 Pos: 30, TplStrand: 0 Got ctx: ATTTATGAAAATTTT Lut prediction: 0.497546 Gbm prediction: 0.497546 Gbm prediction fast: 0.497546 Gbm pred via predictIpdFuncModel: 0.497546 Methylated prediction: ATTTHTGAAAATTTT -> 3.467282 Methylated prediction: ATTTATGAAHATTTT -> 0.462962 Methylated prediction fast: ATTTHTGAAAATTTT -> 3.467282 Methylated prediction fast: ATTTATGAAHATTTT -> 0.462962 Pos: 31, TplStrand: 0 Got ctx: TTTATGAAAATTTTC Lut prediction: 0.425639 Gbm prediction: 0.425639 Gbm prediction fast: 0.425639 Gbm pred via predictIpdFuncModel: 0.425639 Pos: 32, TplStrand: 0 Got ctx: TTATGAAAATTTTCC Lut prediction: 0.387926 Gbm prediction: 0.387926 Gbm prediction fast: 0.387926 Gbm pred via predictIpdFuncModel: 0.387926 Pos: 33, TplStrand: 0 Got ctx: TATGAAAATTTTCCG Lut prediction: 1.008767 Gbm prediction: 1.008767 Gbm prediction fast: 1.008767 Gbm pred via predictIpdFuncModel: 1.008767 Methylated prediction: TATGHAAATTTTCCG -> 6.857647 Methylated prediction: TATGAAAATHTTCCG -> 1.047730 Methylated prediction fast: TATGHAAATTTTCCG -> 6.857647 Methylated prediction fast: TATGAAAATHTTCCG -> 1.047730 Pos: 34, TplStrand: 0 Got ctx: ATGAAAATTTTCCGG Lut prediction: 1.700875 Gbm prediction: 1.700875 Gbm prediction fast: 1.700875 Gbm pred via predictIpdFuncModel: 1.700875 Methylated prediction: ATGAHAATTTTCCGG -> 9.737025 Methylated prediction: ATGAAAATTHTCCGG -> 2.211950 Methylated prediction fast: ATGAHAATTTTCCGG -> 9.737025 Methylated prediction fast: ATGAAAATTHTCCGG -> 2.211950 [{'LLR': 44.9363980691445, 'tpl': 14982, 'Mask': [-5, 0], 'modification': 'm6A', 'strand': 0, 'QMod': 195.15629718037397}, {'LLR': 0.7833812384793148, 'tpl': 15040, 'Mask': [-1, 3], 'modification': 'm6A', 'strand': 1, 'QMod': 5.0363556562304366}, {'LLR': 45.588426682175815, 'tpl': 14991, 'Mask': [-5, 0, 1], 'modification': 'm6A', 'strand': 1, 'QMod': 197.98802146719927}, {'LLR': 12.04025630132049, 'tpl': 14997, 'Mask': [-8, -5, 1, 2, 3], 'modification': 'm4C', 'strand': 1, 'QMod': 52.290194354679265}, {'LLR': 5.787841909938088, 'tpl': 14996, 'Mask': [-6, -3, 1, 2], 'modification': 'm4C', 'strand': 1, 'QMod': 25.14956702352173}] fakeroot debian/rules binary-arch dh binary-arch --with python2 --buildsystem=pybuild dh_testroot -a -O--buildsystem=pybuild dh_prep -a -O--buildsystem=pybuild debian/rules override_dh_auto_install make[1]: Entering directory '/<>/kineticstools-0.6.1+20161222' dh_auto_install I: pybuild base:184: /usr/bin/python setup.py install --root /<>/kineticstools-0.6.1+20161222/debian/python-kineticstools running install running build running build_py running build_ext running install_lib creating /<>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr creating /<>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib creating /<>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7 creating /<>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages creating /<>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools copying /<>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools/pipelineTools.pyc -> /<>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools copying /<>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools/PositiveControlEnricher.py -> /<>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools copying /<>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools/ipdSummary.py -> /<>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools copying /<>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools/sharedArray.pyc -> /<>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools copying /<>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools/MultiSiteDetection.py -> /<>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools copying /<>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools/WorkerProcess.pyc -> /<>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools copying /<>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools/__init__.pyc -> /<>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools copying /<>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools/MedakaLdaEnricher.py -> /<>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools copying /<>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools/ModificationDecode.pyc -> /<>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools copying /<>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools/WorkerProcess.py -> /<>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools copying /<>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools/BasicLdaEnricher.py -> /<>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools copying /<>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools/ipdModel.pyc -> /<>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools copying /<>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools/ResultWriter.py -> /<>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools copying /<>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools/pipelineTools.py -> /<>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools copying /<>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools/MultiSiteCommon.py -> /<>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools copying /<>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools/MedakaLdaEnricher.pyc -> /<>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools copying /<>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools/tree_predict.so -> /<>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools copying /<>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools/summarizeModifications.py -> /<>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools copying /<>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools/ModificationDecode.py -> /<>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools copying /<>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools/ResultWriter.pyc -> /<>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools copying /<>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools/MultiSiteDetection.pyc -> /<>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools copying /<>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools/BasicLdaEnricher.pyc -> /<>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools copying /<>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools/ipdModel.py -> /<>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools copying /<>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools/MultiSiteCommon.pyc -> /<>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools copying /<>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools/PositiveControlEnricher.pyc -> /<>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools copying /<>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools/KineticWorker.py -> /<>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools copying /<>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools/KineticWorker.pyc -> /<>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools copying /<>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools/ReferenceUtils.pyc -> /<>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools copying /<>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools/__init__.py -> /<>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools copying /<>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools/MixtureEstimationMethods.pyc -> /<>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools creating /<>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/resources copying /<>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools/resources/P5-C3.h5 -> /<>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/resources copying /<>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools/resources/C2.h5 -> /<>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/resources copying /<>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools/resources/P6-C4.h5 -> /<>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/resources copying /<>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools/resources/XL-C2.h5 -> /<>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/resources copying /<>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools/resources/XL-XL.h5 -> /<>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/resources copying /<>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools/resources/unknown.h5 -> /<>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/resources copying /<>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools/resources/P4-C2.h5 -> /<>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/resources creating /<>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/tasks copying /<>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools/tasks/__init__.pyc -> /<>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/tasks copying /<>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools/tasks/gather_kinetics_h5.pyc -> /<>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/tasks copying /<>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools/tasks/__init__.py -> /<>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/tasks copying /<>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools/tasks/gather_kinetics_h5.py -> /<>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/tasks copying /<>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools/ReferenceUtils.py -> /<>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools copying /<>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools/sharedArray.py -> /<>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools copying /<>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools/MixtureEstimationMethods.py -> /<>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools byte-compiling /<>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/PositiveControlEnricher.py to PositiveControlEnricher.pyc byte-compiling /<>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/ipdSummary.py to ipdSummary.pyc byte-compiling /<>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/MultiSiteDetection.py to MultiSiteDetection.pyc byte-compiling /<>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/MedakaLdaEnricher.py to MedakaLdaEnricher.pyc byte-compiling /<>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/WorkerProcess.py to WorkerProcess.pyc byte-compiling /<>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/BasicLdaEnricher.py to BasicLdaEnricher.pyc byte-compiling /<>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/ResultWriter.py to ResultWriter.pyc byte-compiling /<>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/pipelineTools.py to pipelineTools.pyc byte-compiling /<>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/MultiSiteCommon.py to MultiSiteCommon.pyc byte-compiling /<>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/summarizeModifications.py to summarizeModifications.pyc byte-compiling /<>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/ModificationDecode.py to ModificationDecode.pyc byte-compiling /<>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/ipdModel.py to ipdModel.pyc byte-compiling /<>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/KineticWorker.py to KineticWorker.pyc byte-compiling /<>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/__init__.py to __init__.pyc byte-compiling /<>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/tasks/__init__.py to __init__.pyc byte-compiling /<>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/tasks/gather_kinetics_h5.py to gather_kinetics_h5.pyc byte-compiling /<>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/ReferenceUtils.py to ReferenceUtils.pyc byte-compiling /<>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/sharedArray.py to sharedArray.pyc byte-compiling /<>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/MixtureEstimationMethods.py to MixtureEstimationMethods.pyc running install_egg_info running egg_info creating kineticsTools.egg-info writing requirements to kineticsTools.egg-info/requires.txt writing kineticsTools.egg-info/PKG-INFO writing top-level names to kineticsTools.egg-info/top_level.txt writing dependency_links to kineticsTools.egg-info/dependency_links.txt writing entry points to kineticsTools.egg-info/entry_points.txt writing manifest file 'kineticsTools.egg-info/SOURCES.txt' reading manifest file 'kineticsTools.egg-info/SOURCES.txt' writing manifest file 'kineticsTools.egg-info/SOURCES.txt' Copying kineticsTools.egg-info to /<>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools-0.6.1.egg-info Skipping SOURCES.txt running install_scripts Installing ipdSummary script to /<>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/bin Installing summarizeModifications script to /<>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/bin mkdir -p /<>/kineticstools-0.6.1+20161222/debian/kineticstools/usr/bin mv debian/python-kineticstools/usr/bin/* /<>/kineticstools-0.6.1+20161222/debian/kineticstools/usr/bin mkdir -p /<>/kineticstools-0.6.1+20161222/debian/kineticstools/usr/share/man//man1 rst2man doc/manual.rst > /<>/kineticstools-0.6.1+20161222/debian/kineticstools/usr/share/man//man1/ipdSummary.1 doc/manual.rst:114: (ERROR/3) Malformed table. Text in column margin in table line 2. ================ =========== Column Description ================ =========== seqid Fasta contig name source Name of tool -- 'kinModCall' type Modification type -- in identification mode this will be m6A, m4C, or m5C for identified bases, or the generic tag 'modified_base' if a kinetic event was detected that does not match a known modification signature start Modification position on contig end Modification position on contig score Phred transformed p-value of detection - this is the single-site detection p-value strand Sample strand containing modification phase Not applicable attributes Extra fields relevant to base mods. IPDRatio is traditional IPDRatio, context is the reference sequence -20bp to +20bp around the modification, and coverage level is the number of IPD observations used after Mapping QV filtering and accuracy filtering. If the row results from an identified modification we also include an identificationQv tag with the from the modification identification procedure. identificationQv is the phred-transformed probability of an incorrect identification, for bases that were identified as having a particular modification. frac, fracLow, fracUp are the estimated fraction of molecules carrying the modification, and the 5% confidence intervals of the estimate. The methylated fraction estimation is a beta-level feature, and should only be used for exploratory purposes. ================ =========== doc/manual.rst:46: (WARNING/2) "math" role not supported doc/manual.rst:48: (WARNING/2) "math" role not supported doc/manual.rst:48: (WARNING/2) "math" role not supported mkdir -p debian/kineticstools-data/usr/share/kineticstools mv debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/resources debian/kineticstools-data/usr/share/kineticstools/ make[1]: Leaving directory '/<>/kineticstools-0.6.1+20161222' dh_installdocs -a -O--buildsystem=pybuild dh_installchangelogs -a -O--buildsystem=pybuild dh_installexamples -a -O--buildsystem=pybuild dh_installman -a -O--buildsystem=pybuild dh_python2 -a -O--buildsystem=pybuild I: dh_python2 fs:322: renaming tree_predict.so to tree_predict.powerpc64le-linux-gnu.so dh_perl -a -O--buildsystem=pybuild dh_link -a -O--buildsystem=pybuild dh_strip_nondeterminism -a -O--buildsystem=pybuild dh_compress -a -O--buildsystem=pybuild dh_fixperms -a -O--buildsystem=pybuild dh_missing -a -O--buildsystem=pybuild dh_strip -a -O--buildsystem=pybuild dh_makeshlibs -a -O--buildsystem=pybuild dh_shlibdeps -a -O--buildsystem=pybuild dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/tree_predict.powerpc64le-linux-gnu.so was not linked against libpthread.so.0 (it uses none of the library's symbols) dh_installdeb -a -O--buildsystem=pybuild dh_gencontrol -a -O--buildsystem=pybuild dpkg-gencontrol: warning: package python-kineticstools: unused substitution variable ${python:Provides} dpkg-gencontrol: warning: package python-kineticstools: unused substitution variable ${python:Versions} dh_md5sums -a -O--buildsystem=pybuild dh_builddeb -a -O--buildsystem=pybuild INFO: pkgstriptranslations version 131 pkgstriptranslations: processing python-kineticstools (in debian/python-kineticstools); do_strip: , oemstrip: pkgmaintainermangler: Not overriding Maintainer for domain lists.ubuntu.com pkgstripfiles: processing control file: debian/python-kineticstools/DEBIAN/control, package python-kineticstools, directory debian/python-kineticstools pkgstripfiles: Running PNG optimization (using 4 cpus) for package python-kineticstools ... pkgstripfiles: No PNG files. dpkg-deb: building package 'python-kineticstools' in '../python-kineticstools_0.6.1+20161222-1ubuntu1_ppc64el.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any -mLaunchpad Build Daemon >../kineticstools_0.6.1+20161222-1ubuntu1_ppc64el.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build kineticstools-0.6.1+20161222 dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 20171224-1824 Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Post Build Chroot | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ kineticstools_0.6.1+20161222-1ubuntu1_ppc64el.changes: ------------------------------------------------------ Format: 1.8 Date: Tue, 21 Feb 2017 07:56:17 +0530 Source: kineticstools Binary: kineticstools kineticstools-data python-kineticstools Architecture: ppc64el Version: 0.6.1+20161222-1ubuntu1 Distribution: bionic Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Bhavani Shankar Description: kineticstools - detection of DNA modifications kineticstools-data - detection of DNA modifications -- data files python-kineticstools - detection of DNA modifications (Python 2 library) Changes: kineticstools (0.6.1+20161222-1ubuntu1) zesty; urgency=medium . * Disable PIE during build so that python linkage doesnt break. Checksums-Sha1: dd29c061ee345ce9c1dfca3e244561b2d289ca68 7702 kineticstools_0.6.1+20161222-1ubuntu1_ppc64el.buildinfo 457ba5bfde0b04176f247c4a8f677adf4d2c7880 49528 python-kineticstools_0.6.1+20161222-1ubuntu1_ppc64el.deb Checksums-Sha256: ffc778ca010d1ac80ba68e0e54d91c690f0feb8d882068efe6db31f8f7502e1d 7702 kineticstools_0.6.1+20161222-1ubuntu1_ppc64el.buildinfo 663f0cbc76696057151b24c5edaa53d863973fb1cfae08dd47c4a9cace793154 49528 python-kineticstools_0.6.1+20161222-1ubuntu1_ppc64el.deb Files: 1c094dfaf46b1856de33c31873269f71 7702 science optional kineticstools_0.6.1+20161222-1ubuntu1_ppc64el.buildinfo 03fadc3aee3307e4f12bb4c011885a43 49528 python optional python-kineticstools_0.6.1+20161222-1ubuntu1_ppc64el.deb Original-Maintainer: Debian Med Packaging Team +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ python-kineticstools_0.6.1+20161222-1ubuntu1_ppc64el.deb -------------------------------------------------------- new debian package, version 2.0. size 49528 bytes: control archive=2020 bytes. 1198 bytes, 22 lines control 2832 bytes, 28 lines md5sums 170 bytes, 9 lines * postinst #!/bin/sh 277 bytes, 14 lines * prerm #!/bin/sh Package: python-kineticstools Source: kineticstools Version: 0.6.1+20161222-1ubuntu1 Architecture: ppc64el Maintainer: Ubuntu Developers Installed-Size: 318 Depends: libc6 (>= 2.17), python (<< 2.8), python (>= 2.7~), python-h5py, python-numpy, python-pbcommand, python-pbcore, python-scipy, python:any (<< 2.8), python:any (>= 2.7.5-5~), kineticstools-data (= 0.6.1+20161222-1ubuntu1) Suggests: python-pybigwig Section: python Priority: optional Homepage: https://github.com/PacificBiosciences/kineticsTools Description: detection of DNA modifications (Python 2 library) Tools for detecting DNA modifications from single molecule, real-time (SMRT®) sequencing data. This tool implements the P_ModificationDetection module in SMRT® Portal, used by the RS_Modification_Detection and RS_Modifications_and_Motif_Detection protocol. Researchers interested in understanding or extending the modification detection algorithms can use these tools as a starting point. . This package is part of the SMRTAnalysis suite and contains the backend Python 2 library. Original-Maintainer: Debian Med Packaging Team drwxr-xr-x root/root 0 2017-02-21 02:26 ./ drwxr-xr-x root/root 0 2017-02-21 02:26 ./usr/ drwxr-xr-x root/root 0 2017-02-21 02:26 ./usr/lib/ drwxr-xr-x root/root 0 2017-02-21 02:26 ./usr/lib/python2.7/ drwxr-xr-x root/root 0 2017-02-21 02:26 ./usr/lib/python2.7/dist-packages/ drwxr-xr-x root/root 0 2017-02-21 02:26 ./usr/lib/python2.7/dist-packages/kineticsTools-0.6.1.egg-info/ -rw-r--r-- root/root 1831 2017-02-21 02:26 ./usr/lib/python2.7/dist-packages/kineticsTools-0.6.1.egg-info/PKG-INFO -rw-r--r-- root/root 1 2017-02-21 02:26 ./usr/lib/python2.7/dist-packages/kineticsTools-0.6.1.egg-info/dependency_links.txt -rw-r--r-- root/root 129 2017-02-21 02:26 ./usr/lib/python2.7/dist-packages/kineticsTools-0.6.1.egg-info/entry_points.txt -rw-r--r-- root/root 1 2017-02-21 02:26 ./usr/lib/python2.7/dist-packages/kineticsTools-0.6.1.egg-info/not-zip-safe -rw-r--r-- root/root 0 2017-02-21 02:26 ./usr/lib/python2.7/dist-packages/kineticsTools-0.6.1.egg-info/requires.txt -rw-r--r-- root/root 41 2017-02-21 02:26 ./usr/lib/python2.7/dist-packages/kineticsTools-0.6.1.egg-info/top_level.txt drwxr-xr-x root/root 0 2017-02-21 02:26 ./usr/lib/python2.7/dist-packages/kineticsTools/ -rw-r--r-- root/root 2638 2016-12-22 19:12 ./usr/lib/python2.7/dist-packages/kineticsTools/BasicLdaEnricher.py -rw-r--r-- root/root 35840 2016-12-22 19:12 ./usr/lib/python2.7/dist-packages/kineticsTools/KineticWorker.py -rw-r--r-- root/root 3628 2016-12-22 19:12 ./usr/lib/python2.7/dist-packages/kineticsTools/MedakaLdaEnricher.py -rw-r--r-- root/root 12627 2016-12-22 19:12 ./usr/lib/python2.7/dist-packages/kineticsTools/MixtureEstimationMethods.py -rw-r--r-- root/root 15729 2016-12-22 19:12 ./usr/lib/python2.7/dist-packages/kineticsTools/ModificationDecode.py -rw-r--r-- root/root 6939 2016-12-22 19:12 ./usr/lib/python2.7/dist-packages/kineticsTools/MultiSiteCommon.py -rw-r--r-- root/root 11759 2016-12-22 19:12 ./usr/lib/python2.7/dist-packages/kineticsTools/MultiSiteDetection.py -rw-r--r-- root/root 4918 2016-12-22 19:12 ./usr/lib/python2.7/dist-packages/kineticsTools/PositiveControlEnricher.py -rw-r--r-- root/root 6585 2016-12-22 19:12 ./usr/lib/python2.7/dist-packages/kineticsTools/ReferenceUtils.py -rw-r--r-- root/root 38161 2016-12-22 19:12 ./usr/lib/python2.7/dist-packages/kineticsTools/ResultWriter.py -rw-r--r-- root/root 9249 2016-12-22 19:12 ./usr/lib/python2.7/dist-packages/kineticsTools/WorkerProcess.py -rw-r--r-- root/root 1829 2016-12-22 19:12 ./usr/lib/python2.7/dist-packages/kineticsTools/__init__.py -rw-r--r-- root/root 22765 2017-02-21 02:26 ./usr/lib/python2.7/dist-packages/kineticsTools/ipdModel.py -rw-r--r-- root/root 32019 2016-12-22 19:12 ./usr/lib/python2.7/dist-packages/kineticsTools/ipdSummary.py -rw-r--r-- root/root 2182 2016-12-22 19:12 ./usr/lib/python2.7/dist-packages/kineticsTools/pipelineTools.py lrwxrwxrwx root/root 0 2017-02-21 02:26 ./usr/lib/python2.7/dist-packages/kineticsTools/resources -> ../../../../share/kineticstools/resources -rw-r--r-- root/root 2399 2016-12-22 19:12 ./usr/lib/python2.7/dist-packages/kineticsTools/sharedArray.py -rw-r--r-- root/root 7874 2016-12-22 19:12 ./usr/lib/python2.7/dist-packages/kineticsTools/summarizeModifications.py drwxr-xr-x root/root 0 2017-02-21 02:26 ./usr/lib/python2.7/dist-packages/kineticsTools/tasks/ -rw-r--r-- root/root 0 2016-12-22 19:12 ./usr/lib/python2.7/dist-packages/kineticsTools/tasks/__init__.py -rw-r--r-- root/root 6205 2016-12-22 19:12 ./usr/lib/python2.7/dist-packages/kineticsTools/tasks/gather_kinetics_h5.py -rw-r--r-- root/root 67368 2017-02-21 02:26 ./usr/lib/python2.7/dist-packages/kineticsTools/tree_predict.powerpc64le-linux-gnu.so drwxr-xr-x root/root 0 2017-02-21 02:26 ./usr/share/ drwxr-xr-x root/root 0 2017-02-21 02:26 ./usr/share/doc/ drwxr-xr-x root/root 0 2017-02-21 02:26 ./usr/share/doc/python-kineticstools/ -rw-r--r-- root/root 911 2017-02-21 02:26 ./usr/share/doc/python-kineticstools/changelog.Debian.gz -rw-r--r-- root/root 2036 2017-01-15 22:24 ./usr/share/doc/python-kineticstools/copyright +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: ppc64el Build-Space: 327604 Build-Time: 72 Distribution: bionic Host Architecture: ppc64el Install-Time: 21 Job: kineticstools_0.6.1+20161222-1ubuntu1.dsc Machine Architecture: ppc64el Package: kineticstools Package-Time: 96 Source-Version: 0.6.1+20161222-1ubuntu1 Space: 327604 Status: successful Version: 0.6.1+20161222-1ubuntu1 -------------------------------------------------------------------------------- Finished at 20171224-1824 Build needed 00:01:36, 327604k disc space RUN: /usr/share/launchpad-buildd/slavebin/in-target scan-for-processes --backend=chroot --series=bionic --arch=ppc64el PACKAGEBUILD-13921413 Scanning for processes to kill in build PACKAGEBUILD-13921413 RUN: /usr/share/launchpad-buildd/slavebin/in-target umount-chroot --backend=chroot --series=bionic --arch=ppc64el PACKAGEBUILD-13921413 Stopping target for build PACKAGEBUILD-13921413 RUN: /usr/share/launchpad-buildd/slavebin/in-target remove-build --backend=chroot --series=bionic --arch=ppc64el PACKAGEBUILD-13921413 Removing build PACKAGEBUILD-13921413