RUN: /usr/share/launchpad-buildd/slavebin/slave-prep ['slave-prep'] Forking launchpad-buildd slave process... Kernel version: Linux z13-025 4.4.0-43-generic #63-Ubuntu SMP Wed Oct 12 13:54:32 UTC 2016 s390x Buildd toolchain package versions: launchpad-buildd_140 python-lpbuildd_140 sbuild_0.67.0-2ubuntu7 dpkg-dev_1.18.4ubuntu1.1 python-debian_0.1.27ubuntu2 qemu-user-static_1:2.5+dfsg-5ubuntu10.5. Syncing the system clock with the buildd NTP service... 1 Nov 17:19:40 ntpdate[64715]: adjust time server 10.211.37.1 offset -0.000648 sec RUN: /usr/share/launchpad-buildd/slavebin/unpack-chroot ['unpack-chroot', 'PACKAGEBUILD-11110634', '/home/buildd/filecache-default/309330829b4f61930f4191d7be733906953ac6c4'] Unpacking chroot for build PACKAGEBUILD-11110634 RUN: /usr/share/launchpad-buildd/slavebin/mount-chroot ['mount-chroot', 'PACKAGEBUILD-11110634'] Mounting chroot for build PACKAGEBUILD-11110634 RUN: /usr/share/launchpad-buildd/slavebin/override-sources-list ['override-sources-list', 'PACKAGEBUILD-11110634', '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-11110634 RUN: /usr/share/launchpad-buildd/slavebin/update-debian-chroot ['update-debian-chroot', 'PACKAGEBUILD-11110634', 's390x'] Updating debian chroot for build PACKAGEBUILD-11110634 Get:1 http://ftpmaster.internal/ubuntu zesty InRelease [247 kB] Get:2 http://ftpmaster.internal/ubuntu zesty-security InRelease [92.2 kB] Get:3 http://ftpmaster.internal/ubuntu zesty-updates InRelease [92.1 kB] Get:4 http://ftpmaster.internal/ubuntu zesty-proposed InRelease [95.6 kB] Get:5 http://ftpmaster.internal/ubuntu zesty/main s390x Packages [1145 kB] Get:6 http://ftpmaster.internal/ubuntu zesty/main Translation-en [583 kB] Get:7 http://ftpmaster.internal/ubuntu zesty/universe s390x Packages [7435 kB] Get:8 http://ftpmaster.internal/ubuntu zesty/universe Translation-en [4486 kB] Get:9 http://ftpmaster.internal/ubuntu zesty-proposed/main s390x Packages [32.4 kB] Get:10 http://ftpmaster.internal/ubuntu zesty-proposed/main Translation-en [22.3 kB] Get:11 http://ftpmaster.internal/ubuntu zesty-proposed/universe s390x Packages [129 kB] Get:12 http://ftpmaster.internal/ubuntu zesty-proposed/universe Translation-en [69.5 kB] Fetched 14.4 MB in 22s (647 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: libperl5.24 perl-modules-5.24 The following packages will be upgraded: adduser base-files binutils cpp-6 dmsetup g++-6 gcc-6 gcc-6-base libapparmor1 libasn1-8-heimdal libatomic1 libcc1-0 libdevmapper1.02.1 libgcc-6-dev libgcc1 libgomp1 libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhx509-5-heimdal libitm1 libkrb5-26-heimdal libldap-2.4-2 liblzma5 libroken18-heimdal libstdc++-6-dev libstdc++6 libsystemd0 libudev1 libwind0-heimdal linux-libc-dev perl perl-base systemd systemd-sysv tzdata ubuntu-keyring xz-utils 39 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 32.3 MB of archives. After this operation, 39.4 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu zesty/main s390x base-files s390x 9.6ubuntu6 [55.8 kB] Get:2 http://ftpmaster.internal/ubuntu zesty/main s390x perl-modules-5.24 all 5.24.1~rc3-3 [2661 kB] Get:3 http://ftpmaster.internal/ubuntu zesty/main s390x libperl5.24 s390x 5.24.1~rc3-3 [3314 kB] Get:4 http://ftpmaster.internal/ubuntu zesty/main s390x perl s390x 5.24.1~rc3-3 [237 kB] Get:5 http://ftpmaster.internal/ubuntu zesty/main s390x perl-base s390x 5.24.1~rc3-3 [1271 kB] Get:6 http://ftpmaster.internal/ubuntu zesty/main s390x libapparmor1 s390x 2.10.95-4ubuntu5.2 [29.5 kB] Get:7 http://ftpmaster.internal/ubuntu zesty/main s390x liblzma5 s390x 5.2.2-1.2 [90.8 kB] Get:8 http://ftpmaster.internal/ubuntu zesty/main s390x adduser all 3.113+nmu3ubuntu5 [161 kB] Get:9 http://ftpmaster.internal/ubuntu zesty/main s390x systemd s390x 231-10 [2172 kB] Get:10 http://ftpmaster.internal/ubuntu zesty/main s390x libsystemd0 s390x 231-10 [192 kB] Get:11 http://ftpmaster.internal/ubuntu zesty/main s390x systemd-sysv s390x 231-10 [14.3 kB] Get:12 http://ftpmaster.internal/ubuntu zesty/main s390x libgomp1 s390x 6.2.0-10ubuntu1 [71.1 kB] Get:13 http://ftpmaster.internal/ubuntu zesty/main s390x libitm1 s390x 6.2.0-10ubuntu1 [27.2 kB] Get:14 http://ftpmaster.internal/ubuntu zesty/main s390x libcc1-0 s390x 6.2.0-10ubuntu1 [31.0 kB] Get:15 http://ftpmaster.internal/ubuntu zesty/main s390x libatomic1 s390x 6.2.0-10ubuntu1 [8150 B] Get:16 http://ftpmaster.internal/ubuntu zesty/main s390x gcc-6-base s390x 6.2.0-10ubuntu1 [17.4 kB] Get:17 http://ftpmaster.internal/ubuntu zesty/main s390x libstdc++6 s390x 6.2.0-10ubuntu1 [403 kB] Get:18 http://ftpmaster.internal/ubuntu zesty/main s390x g++-6 s390x 6.2.0-10ubuntu1 [5822 kB] Get:19 http://ftpmaster.internal/ubuntu zesty/main s390x libstdc++-6-dev s390x 6.2.0-10ubuntu1 [1391 kB] Get:20 http://ftpmaster.internal/ubuntu zesty/main s390x libgcc-6-dev s390x 6.2.0-10ubuntu1 [268 kB] Get:21 http://ftpmaster.internal/ubuntu zesty/main s390x gcc-6 s390x 6.2.0-10ubuntu1 [5612 kB] Get:22 http://ftpmaster.internal/ubuntu zesty/main s390x cpp-6 s390x 6.2.0-10ubuntu1 [5069 kB] Get:23 http://ftpmaster.internal/ubuntu zesty/main s390x libgcc1 s390x 1:6.2.0-10ubuntu1 [24.5 kB] Get:24 http://ftpmaster.internal/ubuntu zesty-proposed/main s390x binutils s390x 2.27-9ubuntu1 [1057 kB] Get:25 http://ftpmaster.internal/ubuntu zesty/main s390x libudev1 s390x 231-10 [53.9 kB] Get:26 http://ftpmaster.internal/ubuntu zesty/main s390x ubuntu-keyring all 2016.10.27 [16.6 kB] Get:27 http://ftpmaster.internal/ubuntu zesty/main s390x tzdata all 2016h-1 [169 kB] Get:28 http://ftpmaster.internal/ubuntu zesty/main s390x libdevmapper1.02.1 s390x 2:1.02.133-1ubuntu1 [148 kB] Get:29 http://ftpmaster.internal/ubuntu zesty/main s390x dmsetup s390x 2:1.02.133-1ubuntu1 [75.4 kB] Get:30 http://ftpmaster.internal/ubuntu zesty-proposed/main s390x libroken18-heimdal s390x 1.7~git20160703+dfsg-1 [39.3 kB] Get:31 http://ftpmaster.internal/ubuntu zesty-proposed/main s390x libasn1-8-heimdal s390x 1.7~git20160703+dfsg-1 [147 kB] Get:32 http://ftpmaster.internal/ubuntu zesty-proposed/main s390x libheimbase1-heimdal s390x 1.7~git20160703+dfsg-1 [27.5 kB] Get:33 http://ftpmaster.internal/ubuntu zesty-proposed/main s390x libhcrypto4-heimdal s390x 1.7~git20160703+dfsg-1 [84.4 kB] Get:34 http://ftpmaster.internal/ubuntu zesty-proposed/main s390x libwind0-heimdal s390x 1.7~git20160703+dfsg-1 [48.2 kB] Get:35 http://ftpmaster.internal/ubuntu zesty-proposed/main s390x libhx509-5-heimdal s390x 1.7~git20160703+dfsg-1 [100.0 kB] Get:36 http://ftpmaster.internal/ubuntu zesty-proposed/main s390x libkrb5-26-heimdal s390x 1.7~git20160703+dfsg-1 [188 kB] Get:37 http://ftpmaster.internal/ubuntu zesty-proposed/main s390x libheimntlm0-heimdal s390x 1.7~git20160703+dfsg-1 [14.7 kB] Get:38 http://ftpmaster.internal/ubuntu zesty-proposed/main s390x libgssapi3-heimdal s390x 1.7~git20160703+dfsg-1 [89.0 kB] Get:39 http://ftpmaster.internal/ubuntu zesty/main s390x libldap-2.4-2 s390x 2.4.42+dfsg-2ubuntu5 [151 kB] Get:40 http://ftpmaster.internal/ubuntu zesty/main s390x xz-utils s390x 5.2.2-1.2 [82.1 kB] Get:41 http://ftpmaster.internal/ubuntu zesty-proposed/main s390x linux-libc-dev s390x 4.8.0-27.29 [844 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 32.3 MB in 51s (624 kB/s) (Reading database ... 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Unpacking xz-utils (5.2.2-1.2) over (5.1.1alpha+20120614-2.1ubuntu1) ... Preparing to unpack .../14-linux-libc-dev_4.8.0-27.29_s390x.deb ... Unpacking linux-libc-dev:s390x (4.8.0-27.29) over (4.8.0-22.24) ... Setting up libgomp1:s390x (6.2.0-10ubuntu1) ... Setting up libatomic1:s390x (6.2.0-10ubuntu1) ... Setting up perl-modules-5.24 (5.24.1~rc3-3) ... Setting up libperl5.24:s390x (5.24.1~rc3-3) ... Setting up libcc1-0:s390x (6.2.0-10ubuntu1) ... Setting up tzdata (2016h-1) ... Current default time zone: 'Etc/UTC' Local time is now: Tue Nov 1 17:21:07 UTC 2016. Universal Time is now: Tue Nov 1 17:21:07 UTC 2016. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up systemd-sysv (231-10) ... Setting up linux-libc-dev:s390x (4.8.0-27.29) ... Setting up libroken18-heimdal:s390x (1.7~git20160703+dfsg-1) ... Setting up libdevmapper1.02.1:s390x (2:1.02.133-1ubuntu1) ... Setting up perl (5.24.1~rc3-3) ... Installing new version of config file /etc/perl/sitecustomize.pl ... Processing triggers for libc-bin (2.24-3ubuntu1) ... Setting up xz-utils (5.2.2-1.2) ... Setting up libheimbase1-heimdal:s390x (1.7~git20160703+dfsg-1) ... Setting up dmsetup (2:1.02.133-1ubuntu1) ... Setting up binutils (2.27-9ubuntu1) ... Setting up cpp-6 (6.2.0-10ubuntu1) ... Setting up libitm1:s390x (6.2.0-10ubuntu1) ... Setting up libgcc-6-dev:s390x (6.2.0-10ubuntu1) ... Setting up libstdc++-6-dev:s390x (6.2.0-10ubuntu1) ... Setting up libwind0-heimdal:s390x (1.7~git20160703+dfsg-1) ... Setting up libasn1-8-heimdal:s390x (1.7~git20160703+dfsg-1) ... Setting up libhcrypto4-heimdal:s390x (1.7~git20160703+dfsg-1) ... Setting up libhx509-5-heimdal:s390x (1.7~git20160703+dfsg-1) ... Setting up gcc-6 (6.2.0-10ubuntu1) ... Setting up g++-6 (6.2.0-10ubuntu1) ... Setting up libkrb5-26-heimdal:s390x (1.7~git20160703+dfsg-1) ... Setting up libheimntlm0-heimdal:s390x (1.7~git20160703+dfsg-1) ... Setting up libgssapi3-heimdal:s390x (1.7~git20160703+dfsg-1) ... Setting up libldap-2.4-2:s390x (2.4.42+dfsg-2ubuntu5) ... Processing triggers for libc-bin (2.24-3ubuntu1) ... RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package ['sbuild-package', 'PACKAGEBUILD-11110634', 's390x', 'zesty-proposed', '-c', 'chroot:autobuild', '--arch=s390x', '--dist=zesty-proposed', '--purge=never', '--nolog', 'berkeley-express_1.5.1-3build1.dsc'] Initiating build PACKAGEBUILD-11110634 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.4.0-43-generic #63-Ubuntu SMP Wed Oct 12 13:54:32 UTC 2016 s390x sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on z13-025.buildd +==============================================================================+ | berkeley-express 1.5.1-3build1 (s390x) 01 Nov 2016 17:21 | +==============================================================================+ Package: berkeley-express Version: 1.5.1-3build1 Source Version: 1.5.1-3build1 Distribution: zesty-proposed Machine Architecture: s390x Host Architecture: s390x Build Architecture: s390x I: NOTICE: Log filtering will replace 'build/berkeley-express-WPEWWc/berkeley-express-1.5.1' with '<>' I: NOTICE: Log filtering will replace 'build/berkeley-express-WPEWWc' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-11110634/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- berkeley-express_1.5.1-3build1.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-L_67tx/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/<>/resolver-L_67tx/apt_archive ./ InRelease Get:2 copy:/<>/resolver-L_67tx/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-L_67tx/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-L_67tx/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-L_67tx/apt_archive ./ Packages [527 B] Fetched 2860 B in 0s (0 B/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 772 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-L_67tx/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [772 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 772 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 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Merged Build-Depends: debhelper (>= 9), libboost-thread-dev, libboost-system-dev, libboost-filesystem-dev, libboost-program-options-dev, libboost-date-time-dev, libbamtools-dev, libboost-tools-dev, cmake, libprotobuf-dev, protobuf-compiler Filtered Build-Depends: debhelper (>= 9), libboost-thread-dev, libboost-system-dev, libboost-filesystem-dev, libboost-program-options-dev, libboost-date-time-dev, libbamtools-dev, libboost-tools-dev, cmake, libprotobuf-dev, protobuf-compiler dpkg-deb: building package 'sbuild-build-depends-berkeley-express-dummy' in '/<>/resolver-8MWVKf/apt_archive/sbuild-build-depends-berkeley-express-dummy.deb'. Ign:1 copy:/<>/resolver-8MWVKf/apt_archive ./ InRelease Get:2 copy:/<>/resolver-8MWVKf/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-8MWVKf/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-8MWVKf/apt_archive ./ Sources [331 B] Get:5 copy:/<>/resolver-8MWVKf/apt_archive ./ Packages [608 B] Fetched 3058 B in 0s (0 B/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install berkeley-express 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: autoconf automake autopoint autotools-dev bsdmainutils cmake cmake-data debhelper dh-autoreconf dh-strip-nondeterminism file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libarchive13 libbamtools-dev libbamtools2.4.0 libboost-atomic1.62-dev libboost-atomic1.62.0 libboost-chrono1.62-dev libboost-chrono1.62.0 libboost-date-time-dev libboost-date-time1.62-dev libboost-date-time1.62.0 libboost-filesystem-dev libboost-filesystem1.62-dev libboost-filesystem1.62.0 libboost-program-options-dev libboost-program-options1.62-dev libboost-program-options1.62.0 libboost-serialization1.62-dev libboost-serialization1.62.0 libboost-system-dev libboost-system1.62-dev libboost-system1.62.0 libboost-thread-dev libboost-thread1.62-dev libboost-thread1.62.0 libboost-tools-dev libboost1.62-dev libboost1.62-tools-dev libcroco3 libcurl3 libexpat1 libfile-stripnondeterminism-perl libglib2.0-0 libicu57 libjsoncpp1 liblzo2-2 libmagic1 libpipeline1 libprotobuf-dev libprotobuf-lite10 libprotobuf10 libprotoc10 libsigsegv2 libtimedate-perl libtool libunistring0 libxml2 m4 man-db po-debconf protobuf-compiler zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois vacation codeblocks eclipse ninja-build dh-make gettext-doc libasprintf-dev libgettextpo-dev groff lrzip libbamtools-doc libboost1.62-doc libboost-exception1.62-dev libboost-graph1.62-dev libboost-graph-parallel1.62-dev libboost-iostreams1.62-dev libboost-locale1.62-dev libboost-log1.62-dev libboost-math1.62-dev libboost-mpi1.62-dev libboost-mpi-python1.62-dev libboost-python1.62-dev libboost-random1.62-dev libboost-regex1.62-dev libboost-signals1.62-dev libboost-test1.62-dev libboost-timer1.62-dev libboost-type-erasure1.62-dev libboost-wave1.62-dev libmpfrc++-dev libntl-dev xsltproc doxygen docbook-xml docbook-xsl default-jdk fop libtool-doc gfortran | fortran95-compiler gcj-jdk less www-browser libmail-box-perl Recommended packages: curl | wget | lynx-cur libglib2.0-data shared-mime-info xdg-user-dirs libltdl-dev xml-core libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils cmake cmake-data debhelper dh-autoreconf dh-strip-nondeterminism file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libarchive13 libbamtools-dev libbamtools2.4.0 libboost-atomic1.62-dev libboost-atomic1.62.0 libboost-chrono1.62-dev libboost-chrono1.62.0 libboost-date-time-dev libboost-date-time1.62-dev libboost-date-time1.62.0 libboost-filesystem-dev libboost-filesystem1.62-dev libboost-filesystem1.62.0 libboost-program-options-dev libboost-program-options1.62-dev libboost-program-options1.62.0 libboost-serialization1.62-dev libboost-serialization1.62.0 libboost-system-dev libboost-system1.62-dev libboost-system1.62.0 libboost-thread-dev libboost-thread1.62-dev libboost-thread1.62.0 libboost-tools-dev libboost1.62-dev libboost1.62-tools-dev libcroco3 libcurl3 libexpat1 libfile-stripnondeterminism-perl libglib2.0-0 libicu57 libjsoncpp1 liblzo2-2 libmagic1 libpipeline1 libprotobuf-dev libprotobuf-lite10 libprotobuf10 libprotoc10 libsigsegv2 libtimedate-perl libtool libunistring0 libxml2 m4 man-db po-debconf protobuf-compiler sbuild-build-depends-berkeley-express-dummy zlib1g-dev 0 upgraded, 68 newly installed, 0 to remove and 0 not upgraded. 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1.62.0.0ubuntu1 [3032 B] Get:59 http://ftpmaster.internal/ubuntu zesty/universe s390x libboost-thread1.62.0 s390x 1.62.0+dfsg-2 [44.4 kB] Get:60 http://ftpmaster.internal/ubuntu zesty/universe s390x libboost-thread1.62-dev s390x 1.62.0+dfsg-2 [44.6 kB] Get:61 http://ftpmaster.internal/ubuntu zesty-proposed/main s390x libboost-thread-dev s390x 1.62.0.0ubuntu1 [2900 B] Get:62 http://ftpmaster.internal/ubuntu zesty/universe s390x libboost1.62-tools-dev s390x 1.62.0+dfsg-2 [1120 kB] Get:63 http://ftpmaster.internal/ubuntu zesty-proposed/universe s390x libboost-tools-dev s390x 1.62.0.0ubuntu1 [3060 B] Get:64 http://ftpmaster.internal/ubuntu zesty/main s390x libprotobuf-lite10 s390x 3.0.0-7ubuntu3 [93.4 kB] Get:65 http://ftpmaster.internal/ubuntu zesty/main s390x libprotobuf10 s390x 3.0.0-7ubuntu3 [594 kB] Get:66 http://ftpmaster.internal/ubuntu zesty/main s390x libprotoc10 s390x 3.0.0-7ubuntu3 [519 kB] Get:67 http://ftpmaster.internal/ubuntu zesty/main s390x libprotobuf-dev s390x 3.0.0-7ubuntu3 [904 kB] Get:68 http://ftpmaster.internal/ubuntu zesty/main s390x protobuf-compiler s390x 3.0.0-7ubuntu3 [24.6 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 31.8 MB in 46s (687 kB/s) Selecting previously unselected package groff-base. 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Setting up libarchive13:s390x (3.2.1-2) ... Setting up libboost-thread1.62.0:s390x (1.62.0+dfsg-2) ... Setting up libprotobuf-dev:s390x (3.0.0-7ubuntu3) ... Setting up libbamtools-dev (2.4.0+dfsg-6) ... Setting up autoconf (2.69-10) ... Setting up libboost-date-time-dev:s390x (1.62.0.0ubuntu1) ... Setting up file (1:5.28-2ubuntu1) ... Setting up intltool-debian (0.35.0+20060710.4) ... Setting up libboost-system1.62-dev:s390x (1.62.0+dfsg-2) ... Setting up libboost-filesystem1.62.0:s390x (1.62.0+dfsg-2) ... Setting up automake (1:1.15-4ubuntu1) ... update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode Setting up man-db (2.7.5-1) ... Not building database; man-db/auto-update is not 'true'. Setting up cmake (3.6.2-2ubuntu1) ... Setting up libboost-chrono1.62.0:s390x (1.62.0+dfsg-2) ... Setting up libtool (2.4.6-1) ... Setting up libboost-filesystem1.62-dev:s390x (1.62.0+dfsg-2) ... Setting up po-debconf (1.0.19) ... 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Processing triggers for libc-bin (2.24-3ubuntu1) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.4.0-43-generic s390x (s390x) Toolchain package versions: binutils_2.27-9ubuntu1 dpkg-dev_1.18.10ubuntu1 g++-6_6.2.0-10ubuntu1 gcc-6_6.2.0-10ubuntu1 libc6-dev_2.24-3ubuntu1 libstdc++-6-dev_6.2.0-10ubuntu1 libstdc++6_6.2.0-10ubuntu1 linux-libc-dev_4.8.0-27.29 Package versions: adduser_3.113+nmu3ubuntu5 advancecomp_1.20-1 apt_1.3.1 apt-transport-https_1.3.1 autoconf_2.69-10 automake_1:1.15-4ubuntu1 autopoint_0.19.8.1-1ubuntu2 autotools-dev_20160430.1 base-files_9.6ubuntu6 base-passwd_3.5.40 bash_4.3-15ubuntu1 binutils_2.27-9ubuntu1 bsdmainutils_9.0.6ubuntu3 bsdutils_1:2.28.2-1ubuntu1 build-essential_12.1ubuntu2 bzip2_1.0.6-8build1 ca-certificates_20160104ubuntu1 cmake_3.6.2-2ubuntu1 cmake-data_3.6.2-2ubuntu1 coreutils_8.25-2ubuntu2 cpp_4:6.1.1-1ubuntu2 cpp-6_6.2.0-10ubuntu1 dash_0.5.8-2.3ubuntu1 debconf_1.5.59ubuntu1 debhelper_10.2.2ubuntu1 debianutils_4.8 dh-autoreconf_12 dh-strip-nondeterminism_0.028-1 diffutils_1:3.3-3 dmsetup_2:1.02.133-1ubuntu1 dpkg_1.18.10ubuntu1 dpkg-dev_1.18.10ubuntu1 e2fslibs_1.43.3-1 e2fsprogs_1.43.3-1 fakeroot_1.21-1ubuntu2 file_1:5.28-2ubuntu1 findutils_4.6.0+git+20160703-2 g++_4:6.1.1-1ubuntu2 g++-6_6.2.0-10ubuntu1 gcc_4:6.1.1-1ubuntu2 gcc-6_6.2.0-10ubuntu1 gcc-6-base_6.2.0-10ubuntu1 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_2.25-6 groff-base_1.22.3-8 gzip_1.6-4ubuntu1 hostname_3.18 init_1.45 init-system-helpers_1.45 initscripts_2.88dsf-59.3ubuntu2 insserv_1.14.0-5ubuntu3 intltool-debian_0.35.0+20060710.4 libacl1_2.2.52-3 libapparmor1_2.10.95-4ubuntu5.2 libapt-pkg5.0_1.3.1 libarchive-zip-perl_1.59-1 libarchive13_3.2.1-2 libasn1-8-heimdal_1.7~git20160703+dfsg-1 libassuan0_2.4.3-1 libatomic1_6.2.0-10ubuntu1 libattr1_1:2.4.47-2 libaudit-common_1:2.6.6-1ubuntu1 libaudit1_1:2.6.6-1ubuntu1 libbamtools-dev_2.4.0+dfsg-6 libbamtools2.4.0_2.4.0+dfsg-6 libblkid1_2.28.2-1ubuntu1 libboost-atomic1.62-dev_1.62.0+dfsg-2 libboost-atomic1.62.0_1.62.0+dfsg-2 libboost-chrono1.62-dev_1.62.0+dfsg-2 libboost-chrono1.62.0_1.62.0+dfsg-2 libboost-date-time-dev_1.62.0.0ubuntu1 libboost-date-time1.62-dev_1.62.0+dfsg-2 libboost-date-time1.62.0_1.62.0+dfsg-2 libboost-filesystem-dev_1.62.0.0ubuntu1 libboost-filesystem1.62-dev_1.62.0+dfsg-2 libboost-filesystem1.62.0_1.62.0+dfsg-2 libboost-program-options-dev_1.62.0.0ubuntu1 libboost-program-options1.62-dev_1.62.0+dfsg-2 libboost-program-options1.62.0_1.62.0+dfsg-2 libboost-serialization1.62-dev_1.62.0+dfsg-2 libboost-serialization1.62.0_1.62.0+dfsg-2 libboost-system-dev_1.62.0.0ubuntu1 libboost-system1.62-dev_1.62.0+dfsg-2 libboost-system1.62.0_1.62.0+dfsg-2 libboost-thread-dev_1.62.0.0ubuntu1 libboost-thread1.62-dev_1.62.0+dfsg-2 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libhcrypto4-heimdal_1.7~git20160703+dfsg-1 libheimbase1-heimdal_1.7~git20160703+dfsg-1 libheimntlm0-heimdal_1.7~git20160703+dfsg-1 libhogweed4_3.2-1 libhx509-5-heimdal_1.7~git20160703+dfsg-1 libicu57_57.1-4 libidn11_1.33-1 libip4tc0_1.6.0-3ubuntu2 libisl15_0.17.1-1 libitm1_6.2.0-10ubuntu1 libjsoncpp1_1.7.2-1 libk5crypto3_1.14.3+dfsg-2 libkeyutils1_1.5.9-9ubuntu1 libkmod2_22-1.1ubuntu1 libkrb5-26-heimdal_1.7~git20160703+dfsg-1 libkrb5-3_1.14.3+dfsg-2 libkrb5support0_1.14.3+dfsg-2 libksba8_1.3.4-4 libldap-2.4-2_2.4.42+dfsg-2ubuntu5 liblockfile-bin_1.09-6ubuntu1 liblockfile1_1.09-6ubuntu1 liblz4-1_0.0~r131-2ubuntu2 liblzma5_5.2.2-1.2 liblzo2-2_2.08-1.2 libmagic1_1:5.28-2ubuntu1 libmount1_2.28.2-1ubuntu1 libmpc3_1.0.3-1 libmpfr4_3.1.5-1 libncurses5_6.0+20160625-1ubuntu1 libncursesw5_6.0+20160625-1ubuntu1 libnettle6_3.2-1 libnpth0_1.2-3 libp11-kit0_0.23.2-5 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~rc3-3 libpipeline1_1.4.1-2 libpng16-16_1.6.25-1 libprocps6_2:3.3.12-1ubuntu2 libprotobuf-dev_3.0.0-7ubuntu3 libprotobuf-lite10_3.0.0-7ubuntu3 libprotobuf10_3.0.0-7ubuntu3 libprotoc10_3.0.0-7ubuntu3 libreadline7_7.0-0ubuntu2 libroken18-heimdal_1.7~git20160703+dfsg-1 librtmp1_2.4+20151223.gitfa8646d.1-1 libsasl2-2_2.1.26.dfsg1-15 libsasl2-modules-db_2.1.26.dfsg1-15 libseccomp2_2.3.1-2ubuntu2 libselinux1_2.5-3 libsemanage-common_2.5-1 libsemanage1_2.5-1 libsepol1_2.5-1 libsigsegv2_2.10-5 libslang2_2.3.0-2.3ubuntu1 libsmartcols1_2.28.2-1ubuntu1 libsqlite3-0_3.14.1-1build1 libss2_1.43.3-1 libssl1.0.0_1.0.2g-1ubuntu9 libstdc++-6-dev_6.2.0-10ubuntu1 libstdc++6_6.2.0-10ubuntu1 libsystemd0_231-10 libtasn1-6_4.9-4 libtimedate-perl_2.3000-2 libtinfo5_6.0+20160625-1ubuntu1 libtool_2.4.6-1 libudev1_231-10 libunistring0_0.9.3-5.2ubuntu1 libusb-0.1-4_2:0.1.12-30 libustr-1.0-1_1.0.4-5 libuuid1_2.28.2-1ubuntu1 libwind0-heimdal_1.7~git20160703+dfsg-1 libxml2_2.9.4+dfsg1-2 linux-libc-dev_4.8.0-27.29 lockfile-progs_0.1.17 login_1:4.2-3.2ubuntu1 lsb-base_9.20160110ubuntu5 m4_1.4.17-5 make_4.1-9 man-db_2.7.5-1 mawk_1.3.3-17ubuntu2 mount_2.28.2-1ubuntu1 multiarch-support_2.24-3ubuntu1 ncurses-base_6.0+20160625-1ubuntu1 ncurses-bin_6.0+20160625-1ubuntu1 openssl_1.0.2g-1ubuntu9 optipng_0.7.6-1build1 passwd_1:4.2-3.2ubuntu1 patch_2.7.5-1 perl_5.24.1~rc3-3 perl-base_5.24.1~rc3-3 perl-modules-5.22_5.22.2-3 perl-modules-5.24_5.24.1~rc3-3 pinentry-curses_0.9.7-5 pkg-create-dbgsym_0.72 pkgbinarymangler_131 po-debconf_1.0.19 policyrcd-script-zg2_0.1-3 procps_2:3.3.12-1ubuntu2 protobuf-compiler_3.0.0-7ubuntu3 readline-common_7.0-0ubuntu2 sbuild-build-depends-berkeley-express-dummy_0.invalid.0 sbuild-build-depends-core-dummy_0.invalid.0 sed_4.2.2-8 sensible-utils_0.0.9 systemd_231-10 systemd-sysv_231-10 sysv-rc_2.88dsf-59.3ubuntu2 sysvinit-utils_2.88dsf-59.8git1 tar_1.29b-1 tzdata_2016h-1 ubuntu-keyring_2016.10.27 util-linux_2.28.2-1ubuntu1 xz-utils_5.2.2-1.2 zlib1g_1:1.2.8.dfsg-2ubuntu5 zlib1g-dev_1:1.2.8.dfsg-2ubuntu5 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Tue Nov 1 17:00:50 2016 UTC gpgv: using RSA key gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./berkeley-express_1.5.1-3build1.dsc dpkg-source: info: extracting berkeley-express in berkeley-express-1.5.1 dpkg-source: info: unpacking berkeley-express_1.5.1.orig.tar.gz dpkg-source: info: unpacking berkeley-express_1.5.1-3build1.debian.tar.xz dpkg-source: info: applying spelling-fixes dpkg-source: info: applying fix-bamtools-path dpkg-source: info: applying drop-zlib dpkg-source: info: applying gcc-6.patch dpkg-source: info: applying correct-debug-flags.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=/<> SHELL=/bin/sh SUDO_COMMAND=/usr/sbin/chroot /<> su buildd -s /bin/sh -c cd '/<>' && 'env' SUDO_GID=2501 SUDO_UID=2001 SUDO_USER=buildd TERM=unknown USER=buildd USERNAME=root dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package berkeley-express dpkg-buildpackage: info: source version 1.5.1-3build1 dpkg-buildpackage: info: source distribution zesty dpkg-source --before-build berkeley-express-1.5.1 dpkg-buildpackage: info: host architecture s390x fakeroot debian/rules clean dh clean --parallel dh_testdir -O--parallel dh_auto_clean -O--parallel debian/rules override_dh_clean make[1]: Entering directory '/<>' dh_clean src/config.h make[1]: Leaving directory '/<>' debian/rules build-arch dh build-arch --parallel dh_testdir -a -O--parallel dh_update_autotools_config -a -O--parallel dh_auto_configure -a -O--parallel cmake .. -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -- The C compiler identification is GNU 6.2.0 -- The CXX compiler identification is GNU 6.2.0 -- Check for working C compiler: /usr/bin/cc -- Check for working C compiler: /usr/bin/cc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done CMake Warning at /usr/share/cmake-3.6/Modules/FindBoost.cmake:743 (message): Imported targets not available for Boost version 106200 Call Stack (most recent call first): /usr/share/cmake-3.6/Modules/FindBoost.cmake:842 (_Boost_COMPONENT_DEPENDENCIES) /usr/share/cmake-3.6/Modules/FindBoost.cmake:1411 (_Boost_MISSING_DEPENDENCIES) CMakeLists.txt:17 (find_package) CMake Warning at /usr/share/cmake-3.6/Modules/FindBoost.cmake:743 (message): Imported targets not available for Boost version 106200 Call Stack (most recent call first): /usr/share/cmake-3.6/Modules/FindBoost.cmake:842 (_Boost_COMPONENT_DEPENDENCIES) /usr/share/cmake-3.6/Modules/FindBoost.cmake:1411 (_Boost_MISSING_DEPENDENCIES) CMakeLists.txt:17 (find_package) CMake Warning at /usr/share/cmake-3.6/Modules/FindBoost.cmake:743 (message): Imported targets not available for Boost version 106200 Call Stack (most recent call first): /usr/share/cmake-3.6/Modules/FindBoost.cmake:842 (_Boost_COMPONENT_DEPENDENCIES) /usr/share/cmake-3.6/Modules/FindBoost.cmake:1411 (_Boost_MISSING_DEPENDENCIES) CMakeLists.txt:17 (find_package) CMake Warning at /usr/share/cmake-3.6/Modules/FindBoost.cmake:743 (message): Imported targets not available for Boost version 106200 Call Stack (most recent call first): /usr/share/cmake-3.6/Modules/FindBoost.cmake:842 (_Boost_COMPONENT_DEPENDENCIES) /usr/share/cmake-3.6/Modules/FindBoost.cmake:1411 (_Boost_MISSING_DEPENDENCIES) CMakeLists.txt:17 (find_package) CMake Warning at /usr/share/cmake-3.6/Modules/FindBoost.cmake:743 (message): Imported targets not available for Boost version 106200 Call Stack (most recent call first): /usr/share/cmake-3.6/Modules/FindBoost.cmake:842 (_Boost_COMPONENT_DEPENDENCIES) /usr/share/cmake-3.6/Modules/FindBoost.cmake:1411 (_Boost_MISSING_DEPENDENCIES) CMakeLists.txt:17 (find_package) -- Looking for pthread.h -- Looking for pthread.h - found -- Looking for pthread_create -- Looking for pthread_create - not found -- Looking for pthread_create in pthreads -- Looking for pthread_create in pthreads - not found -- Looking for pthread_create in pthread -- Looking for pthread_create in pthread - found -- Found Threads: TRUE -- Boost version: 1.62.0 -- Found the following Boost libraries: -- thread -- system -- filesystem -- program_options -- date_time -- Could NOT find GPERFTOOLS_TCMALLOC: Install to improve speed. -- Found Protobuf: /usr/lib/s390x-linux-gnu/libprotobuf.so;-lpthread (found version "3.0.0") -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_SYSCONFDIR -- Build files have been written to: /<>/obj-s390x-linux-gnu dh_auto_build -a -O--parallel make -j4 make[1]: Entering directory '/<>/obj-s390x-linux-gnu' /usr/bin/cmake -H/<> -B/<>/obj-s390x-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /<>/obj-s390x-linux-gnu/CMakeFiles /<>/obj-s390x-linux-gnu/CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/<>/obj-s390x-linux-gnu' make -f src/CMakeFiles/express.dir/build.make src/CMakeFiles/express.dir/depend make[3]: Entering directory '/<>/obj-s390x-linux-gnu' [ 5%] Running C++ protocol buffer compiler on /<>/src/alignments.proto cd /<>/obj-s390x-linux-gnu/src && /usr/bin/protoc --cpp_out /<>/obj-s390x-linux-gnu/src -I /<>/src /<>/src/alignments.proto [ 11%] Running C++ protocol buffer compiler on /<>/src/targets.proto cd /<>/obj-s390x-linux-gnu/src && /usr/bin/protoc --cpp_out /<>/obj-s390x-linux-gnu/src -I /<>/src /<>/src/targets.proto [libprotobuf WARNING google/protobuf/compiler/parser.cc:547] No syntax specified for the proto file: alignments.proto. Please use 'syntax = "proto2";' or 'syntax = "proto3";' to specify a syntax version. (Defaulted to proto2 syntax.) [libprotobuf WARNING google/protobuf/compiler/parser.cc:547] No syntax specified for the proto file: targets.proto. Please use 'syntax = "proto2";' or 'syntax = "proto3";' to specify a syntax version. (Defaulted to proto2 syntax.) cd /<>/obj-s390x-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src /<>/obj-s390x-linux-gnu /<>/obj-s390x-linux-gnu/src /<>/obj-s390x-linux-gnu/src/CMakeFiles/express.dir/DependInfo.cmake --color= Scanning dependencies of target express make[3]: Leaving directory '/<>/obj-s390x-linux-gnu' make -f src/CMakeFiles/express.dir/build.make src/CMakeFiles/express.dir/build make[3]: Entering directory '/<>/obj-s390x-linux-gnu' [ 16%] Building CXX object src/CMakeFiles/express.dir/biascorrection.cpp.o cd /<>/obj-s390x-linux-gnu/src && /usr/bin/c++ -I/usr/include/bamtools -g -O2 -fdebug-prefix-map=/<>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D__FILE__=\"\" -o CMakeFiles/express.dir/biascorrection.cpp.o -c /<>/src/biascorrection.cpp [ 22%] Building CXX object src/CMakeFiles/express.dir/fragments.cpp.o cd /<>/obj-s390x-linux-gnu/src && /usr/bin/c++ -I/usr/include/bamtools -g -O2 -fdebug-prefix-map=/<>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D__FILE__=\"\" -o CMakeFiles/express.dir/fragments.cpp.o -c /<>/src/fragments.cpp [ 27%] Building CXX object src/CMakeFiles/express.dir/directiondetector.cpp.o cd /<>/obj-s390x-linux-gnu/src && /usr/bin/c++ -I/usr/include/bamtools -g -O2 -fdebug-prefix-map=/<>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D__FILE__=\"\" -o CMakeFiles/express.dir/directiondetector.cpp.o -c /<>/src/directiondetector.cpp [ 33%] Building CXX object src/CMakeFiles/express.dir/bundles.cpp.o :0:0: warning: "__FILE__" redefined [-Wbuiltin-macro-redefined] :0:0: warning: "__FILE__" redefined [-Wbuiltin-macro-redefined] cd /<>/obj-s390x-linux-gnu/src && /usr/bin/c++ -I/usr/include/bamtools -g -O2 -fdebug-prefix-map=/<>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D__FILE__=\"\" -o CMakeFiles/express.dir/bundles.cpp.o -c /<>/src/bundles.cpp :0:0: warning: "__FILE__" redefined [-Wbuiltin-macro-redefined] :0:0: warning: "__FILE__" redefined [-Wbuiltin-macro-redefined] [ 38%] Building CXX object src/CMakeFiles/express.dir/lengthdistribution.cpp.o cd /<>/obj-s390x-linux-gnu/src && /usr/bin/c++ -I/usr/include/bamtools -g -O2 -fdebug-prefix-map=/<>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D__FILE__=\"\" -o CMakeFiles/express.dir/lengthdistribution.cpp.o -c /<>/src/lengthdistribution.cpp :0:0: warning: "__FILE__" redefined [-Wbuiltin-macro-redefined] [ 44%] Building CXX object src/CMakeFiles/express.dir/main.cpp.o cd /<>/obj-s390x-linux-gnu/src && /usr/bin/c++ -I/usr/include/bamtools -g -O2 -fdebug-prefix-map=/<>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D__FILE__=\"\" -o CMakeFiles/express.dir/main.cpp.o -c /<>/src/main.cpp :0:0: warning: "__FILE__" redefined [-Wbuiltin-macro-redefined] [ 50%] Building CXX object src/CMakeFiles/express.dir/mapparser.cpp.o cd /<>/obj-s390x-linux-gnu/src && /usr/bin/c++ -I/usr/include/bamtools -g -O2 -fdebug-prefix-map=/<>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D__FILE__=\"\" -o CMakeFiles/express.dir/mapparser.cpp.o -c /<>/src/mapparser.cpp :0:0: warning: "__FILE__" redefined [-Wbuiltin-macro-redefined] [ 55%] Building CXX object src/CMakeFiles/express.dir/markovmodel.cpp.o cd /<>/obj-s390x-linux-gnu/src && /usr/bin/c++ -I/usr/include/bamtools -g -O2 -fdebug-prefix-map=/<>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D__FILE__=\"\" -o CMakeFiles/express.dir/markovmodel.cpp.o -c /<>/src/markovmodel.cpp :0:0: warning: "__FILE__" redefined [-Wbuiltin-macro-redefined] [ 61%] Building CXX object src/CMakeFiles/express.dir/mismatchmodel.cpp.o cd /<>/obj-s390x-linux-gnu/src && /usr/bin/c++ -I/usr/include/bamtools -g -O2 -fdebug-prefix-map=/<>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D__FILE__=\"\" -o CMakeFiles/express.dir/mismatchmodel.cpp.o -c /<>/src/mismatchmodel.cpp :0:0: warning: "__FILE__" redefined [-Wbuiltin-macro-redefined] [ 66%] Building CXX object src/CMakeFiles/express.dir/robertsfilter.cpp.o cd /<>/obj-s390x-linux-gnu/src && /usr/bin/c++ -I/usr/include/bamtools -g -O2 -fdebug-prefix-map=/<>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D__FILE__=\"\" -o CMakeFiles/express.dir/robertsfilter.cpp.o -c /<>/src/robertsfilter.cpp :0:0: warning: "__FILE__" redefined [-Wbuiltin-macro-redefined] [ 72%] Building CXX object src/CMakeFiles/express.dir/sequence.cpp.o cd /<>/obj-s390x-linux-gnu/src && /usr/bin/c++ -I/usr/include/bamtools -g -O2 -fdebug-prefix-map=/<>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D__FILE__=\"\" -o CMakeFiles/express.dir/sequence.cpp.o -c /<>/src/sequence.cpp :0:0: warning: "__FILE__" redefined [-Wbuiltin-macro-redefined] [ 77%] Building CXX object src/CMakeFiles/express.dir/targets.cpp.o cd /<>/obj-s390x-linux-gnu/src && /usr/bin/c++ -I/usr/include/bamtools -g -O2 -fdebug-prefix-map=/<>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D__FILE__=\"\" -o CMakeFiles/express.dir/targets.cpp.o -c /<>/src/targets.cpp :0:0: warning: "__FILE__" redefined [-Wbuiltin-macro-redefined] [ 83%] Building CXX object src/CMakeFiles/express.dir/threadsafety.cpp.o cd /<>/obj-s390x-linux-gnu/src && /usr/bin/c++ -I/usr/include/bamtools -g -O2 -fdebug-prefix-map=/<>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D__FILE__=\"\" -o CMakeFiles/express.dir/threadsafety.cpp.o -c /<>/src/threadsafety.cpp :0:0: warning: "__FILE__" redefined [-Wbuiltin-macro-redefined] [ 88%] Building CXX object src/CMakeFiles/express.dir/alignments.pb.cc.o cd /<>/obj-s390x-linux-gnu/src && /usr/bin/c++ -I/usr/include/bamtools -g -O2 -fdebug-prefix-map=/<>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D__FILE__=\"\" -o CMakeFiles/express.dir/alignments.pb.cc.o -c /<>/obj-s390x-linux-gnu/src/alignments.pb.cc :0:0: warning: "__FILE__" redefined [-Wbuiltin-macro-redefined] [ 94%] Building CXX object src/CMakeFiles/express.dir/targets.pb.cc.o cd /<>/obj-s390x-linux-gnu/src && /usr/bin/c++ -I/usr/include/bamtools -g -O2 -fdebug-prefix-map=/<>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D__FILE__=\"\" -o CMakeFiles/express.dir/targets.pb.cc.o -c /<>/obj-s390x-linux-gnu/src/targets.pb.cc :0:0: warning: "__FILE__" redefined [-Wbuiltin-macro-redefined] [100%] Linking CXX executable express cd /<>/obj-s390x-linux-gnu/src && /usr/bin/cmake -E cmake_link_script 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-lbamtools -lpthread -lprotobuf make[3]: Leaving directory '/<>/obj-s390x-linux-gnu' [100%] Built target express make[2]: Leaving directory '/<>/obj-s390x-linux-gnu' /usr/bin/cmake -E cmake_progress_start /<>/obj-s390x-linux-gnu/CMakeFiles 0 make[1]: Leaving directory '/<>/obj-s390x-linux-gnu' dh_auto_test -a -O--parallel fakeroot debian/rules binary-arch dh binary-arch --parallel dh_testroot -a -O--parallel dh_prep -a -O--parallel dh_installdirs -a -O--parallel dh_auto_install -a -O--parallel make -j4 install DESTDIR=/<>/debian/tmp AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/<>/obj-s390x-linux-gnu' /usr/bin/cmake -H/<> -B/<>/obj-s390x-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /<>/obj-s390x-linux-gnu/CMakeFiles /<>/obj-s390x-linux-gnu/CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/<>/obj-s390x-linux-gnu' make -f src/CMakeFiles/express.dir/build.make 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/usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /<>/debian/tmp/usr/bin/express make[1]: Leaving directory '/<>/obj-s390x-linux-gnu' dh_install -a -O--parallel dh_installdocs -a -O--parallel dh_installchangelogs -a -O--parallel dh_installman -a -O--parallel dh_perl -a -O--parallel dh_link -a -O--parallel dh_strip_nondeterminism -a -O--parallel debian/rules override_dh_compress make[1]: Entering directory '/<>' dh_compress --exclude=express-doc.pdf make[1]: Leaving directory '/<>' dh_fixperms -a -O--parallel dh_strip -a -O--parallel dh_strip debug symbol extraction: enabling -a due to Build-Debug-Symbols: yes in /CurrentlyBuilding dh_strip debug symbol extraction: all non-arch-all packages for this build platform s390x: berkeley-express dh_strip debug symbol extraction: packages to act on: berkeley-express dh_strip debug symbol extraction: ignored packages: Using buildid for compat level >= 9 dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe /usr/bin/pkg_create_dbgsym: deferring build of .ddeb to dh_gencontrol dh_makeshlibs -a -O--parallel dh_shlibdeps -a -O--parallel dh_installdeb -a -O--parallel dh_gencontrol -a -O--parallel dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe dh_gencontrol debug symbol wrapper: all non-arch-all packages for this build platform s390x: berkeley-express dh_gencontrol debug symbol wrapper: packages to act on: berkeley-express dh_gencontrol debug symbol wrapper: ignored packages: dh_gencontrol debug symbol wrapper: processing package berkeley-express (pkgdir debian/berkeley-express, ddeb package dir debian/berkeley-express-dbgsym) dh_gencontrol debug symbol wrapper: building berkeley-express-dbgsym_1.5.1-3build1_s390x.ddeb dpkg-deb: building package 'berkeley-express-dbgsym' in '../berkeley-express-dbgsym_1.5.1-3build1_s390x.ddeb'. dh_gencontrol debug symbol wrapper: dpkg-distaddfile berkeley-express-dbgsym_1.5.1-3build1_s390x.ddeb science extra dpkg-distaddfile: warning: File::FcntlLock not available; using flock which is not NFS-safe dh_md5sums -a -O--parallel dh_builddeb -a -O--parallel INFO: pkgstriptranslations version 131 pkgstriptranslations: processing berkeley-express (in debian/berkeley-express); do_strip: , oemstrip: pkgmaintainermangler: Not overriding Maintainer for domain lists.ubuntu.com pkgstripfiles: processing control file: debian/berkeley-express/DEBIAN/control, package berkeley-express, directory debian/berkeley-express pkgstripfiles: Running PNG optimization (using 4 cpus) for package berkeley-express ... pkgstripfiles: No PNG files. dpkg-deb: building package 'berkeley-express' in '../berkeley-express_1.5.1-3build1_s390x.deb'. dpkg-genchanges --build=any -mLaunchpad Build Daemon >../berkeley-express_1.5.1-3build1_s390x.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build berkeley-express-1.5.1 dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 20161101-1722 Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Post Build Chroot | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ berkeley-express_1.5.1-3build1_s390x.changes: --------------------------------------------- Format: 1.8 Date: Tue, 01 Nov 2016 16:09:43 +0000 Source: berkeley-express Binary: berkeley-express berkeley-express-doc Architecture: s390x Version: 1.5.1-3build1 Distribution: zesty-proposed Urgency: high Maintainer: Launchpad Build Daemon Changed-By: Dimitri John Ledkov Description: berkeley-express - Streaming quantification for high-throughput sequencing berkeley-express-doc - Documentation for RNA-Seq tool eXpress Changes: berkeley-express (1.5.1-3build1) zesty; urgency=high . * No change rebuild against boost1.62. Checksums-Sha1: aedacd438d7407b0813c51d3ffe927dfb1993d17 2493164 berkeley-express-dbgsym_1.5.1-3build1_s390x.ddeb a8c03bd9c82050978e863a067ec5b6f4b4d6b7a9 222014 berkeley-express_1.5.1-3build1_s390x.deb Checksums-Sha256: 1dc9b2cc7365652fbdb9f0885272aa3a148cde12caad92547a8930270d6bf49e 2493164 berkeley-express-dbgsym_1.5.1-3build1_s390x.ddeb 6b1cac8c4869f449e909bed9a28cae4858f071821c0813ebd4518e0a52f421f4 222014 berkeley-express_1.5.1-3build1_s390x.deb Files: 780d28e74fce7d7abc071d712643afc9 2493164 science extra berkeley-express-dbgsym_1.5.1-3build1_s390x.ddeb ae1ac75338457682404627f8edf70373 222014 science optional berkeley-express_1.5.1-3build1_s390x.deb Original-Maintainer: Debian Med Packaging Team +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ berkeley-express_1.5.1-3build1_s390x.deb ---------------------------------------- new debian package, version 2.0. size 222014 bytes: control archive=1877 bytes. 3174 bytes, 51 lines control 454 bytes, 6 lines md5sums Package: berkeley-express Version: 1.5.1-3build1 Architecture: s390x Maintainer: Ubuntu Developers Installed-Size: 849 Depends: libbamtools2.4.0, libboost-date-time1.62.0, libboost-filesystem1.62.0, libboost-program-options1.62.0, libboost-system1.62.0, libboost-thread1.62.0, libc6 (>= 2.4), libgcc1 (>= 1:3.0), libprotobuf10, libstdc++6 (>= 5.2) Recommends: med-config (>= 2.1) Section: science Priority: optional Homepage: http://bio.math.berkeley.edu/eXpress/index.html Description: Streaming quantification for high-throughput sequencing eXpress is a streaming tool for quantifying the abundances of a set of target sequences from sampled subsequences. Example applications include transcript-level RNA-Seq quantification, allele-specific/haplotype expression analysis (from RNA-Seq), transcription factor binding quantification in ChIP-Seq, and analysis of metagenomic data. It is based on an online-EM algorithm that results in space (memory) requirements proportional to the total size of the target sequences and time requirements that are proportional to the number of sampled fragments. Thus, in applications such as RNA-Seq, eXpress can accurately quantify much larger samples than other currently available tools greatly reducing computing infrastructure requirements. eXpress can be used to build lightweight high-throughput sequencing processing pipelines when coupled with a streaming aligner (such as Bowtie), as output can be piped directly into eXpress, effectively eliminating the need to store read alignments in memory or on disk. . In an analysis of the performance of eXpress for RNA-Seq data, it was observed that this efficiency does not come at a cost of accuracy. eXpress is more accurate than other available tools, even when limited to smaller datasets that do not require such efficiency. Moreover, like the Cufflinks program, eXpress can be used to estimate transcript abundances in multi-isoform genes. eXpress is also able to resolve multi-mappings of reads across gene families, and does not require a reference genome so that it can be used in conjunction with de novo assemblers such as Trinity, Oases, or Trans-ABySS. The underlying model is based on previously described probabilistic models developed for RNA-Seq but is applicable to other settings where target sequences are sampled, and includes parameters for fragment length distributions, errors in reads, and sequence-specific fragment bias. . eXpress can be used to resolve ambiguous mappings in other high-throughput sequencing based applications. The only required inputs to eXpress are a set of target sequences and a set of sequenced fragments multiply-aligned to them. While these target sequences will often be gene isoforms, they need not be. Haplotypes can be used as the reference for allele-specific expression analysis, binding regions for ChIP-Seq, or target genomes in metagenomics experiments. eXpress is useful in any analysis where reads multi-map to sequences that differ in abundance. Original-Maintainer: Debian Med Packaging Team drwxr-xr-x root/root 0 2016-11-01 16:09 ./ drwxr-xr-x root/root 0 2016-11-01 16:09 ./usr/ drwxr-xr-x root/root 0 2016-11-01 16:09 ./usr/bin/ lrwxrwxrwx root/root 0 2016-11-01 16:09 ./usr/bin/berkeley-express -> ../lib/debian-med/bin/express drwxr-xr-x root/root 0 2016-11-01 16:09 ./usr/lib/ drwxr-xr-x root/root 0 2016-11-01 16:09 ./usr/lib/debian-med/ drwxr-xr-x root/root 0 2016-11-01 16:09 ./usr/lib/debian-med/bin/ -rwxr-xr-x root/root 846256 2016-11-01 16:09 ./usr/lib/debian-med/bin/express drwxr-xr-x root/root 0 2016-11-01 16:09 ./usr/share/ drwxr-xr-x root/root 0 2016-11-01 16:09 ./usr/share/doc/ drwxr-xr-x root/root 0 2016-11-01 16:09 ./usr/share/doc/berkeley-express/ -rw-r--r-- root/root 987 2016-09-19 18:26 ./usr/share/doc/berkeley-express/README.Debian -rw-r--r-- root/root 1540 2013-12-08 19:09 ./usr/share/doc/berkeley-express/README.gz -rw-r--r-- root/root 609 2016-11-01 16:09 ./usr/share/doc/berkeley-express/changelog.Debian.gz -rw-r--r-- root/root 2668 2016-09-19 18:26 ./usr/share/doc/berkeley-express/copyright drwxr-xr-x root/root 0 2016-11-01 16:09 ./usr/share/man/ drwxr-xr-x root/root 0 2016-11-01 16:09 ./usr/share/man/man1/ -rw-r--r-- root/root 1192 2016-11-01 16:09 ./usr/share/man/man1/berkeley-express.1.gz +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Not removing build depends: as requested Keeping session: +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: s390x Build-Space: 74236 Build-Time: 31 Distribution: zesty-proposed Host Architecture: s390x Install-Time: 65 Job: berkeley-express_1.5.1-3build1.dsc Machine Architecture: s390x Package: berkeley-express Package-Time: 97 Source-Version: 1.5.1-3build1 Space: 74236 Status: successful Version: 1.5.1-3build1 -------------------------------------------------------------------------------- Finished at 20161101-1722 Build needed 00:01:37, 74236k disc space RUN: /usr/share/launchpad-buildd/slavebin/scan-for-processes ['scan-for-processes', 'PACKAGEBUILD-11110634'] Scanning for processes to kill in build /home/buildd/build-PACKAGEBUILD-11110634/chroot-autobuild... RUN: /usr/share/launchpad-buildd/slavebin/umount-chroot ['umount-chroot', 'PACKAGEBUILD-11110634'] Unmounting chroot for build PACKAGEBUILD-11110634... RUN: /usr/share/launchpad-buildd/slavebin/remove-build ['remove-build', 'PACKAGEBUILD-11110634'] Removing build PACKAGEBUILD-11110634