RUN: /usr/share/launchpad-buildd/slavebin/slave-prep ['slave-prep'] Forking launchpad-buildd slave process... Kernel version: Linux bos01-arm64-037 4.4.0-45-generic #66+buildd2-Ubuntu SMP Fri Oct 21 06:29:15 UTC 2016 aarch64 Buildd toolchain package versions: launchpad-buildd_140 python-lpbuildd_140 sbuild_0.67.0-2ubuntu7 bzr-builder_0.7.3+bzr174~ppa13~ubuntu14.10.1 bzr_2.7.0-2ubuntu3 git-build-recipe_0.3.2 git_1:2.7.4-0ubuntu1 dpkg-dev_1.18.4ubuntu1.1 python-debian_0.1.27ubuntu2 qemu-user-static_1:2.5+dfsg-5ubuntu10.5. Syncing the system clock with the buildd NTP service... 1 Nov 17:38:25 ntpdate[1737]: adjust time server 10.211.37.1 offset -0.010085 sec RUN: /usr/share/launchpad-buildd/slavebin/unpack-chroot ['unpack-chroot', 'PACKAGEBUILD-11110629', '/home/buildd/filecache-default/0309f704a9139dce864b78599cddd58acb3f260a'] Unpacking chroot for build PACKAGEBUILD-11110629 RUN: /usr/share/launchpad-buildd/slavebin/mount-chroot ['mount-chroot', 'PACKAGEBUILD-11110629'] Mounting chroot for build PACKAGEBUILD-11110629 RUN: /usr/share/launchpad-buildd/slavebin/override-sources-list ['override-sources-list', 'PACKAGEBUILD-11110629', '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-11110629 RUN: /usr/share/launchpad-buildd/slavebin/update-debian-chroot ['update-debian-chroot', 'PACKAGEBUILD-11110629', 'arm64'] Updating debian chroot for build PACKAGEBUILD-11110629 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 arm64 Packages [1187 kB] Get:6 http://ftpmaster.internal/ubuntu zesty/main Translation-en [583 kB] Get:7 http://ftpmaster.internal/ubuntu zesty/universe arm64 Packages [7504 kB] Get:8 http://ftpmaster.internal/ubuntu zesty/universe Translation-en [4486 kB] Get:9 http://ftpmaster.internal/ubuntu zesty-proposed/main arm64 Packages [36.4 kB] Get:10 http://ftpmaster.internal/ubuntu zesty-proposed/main Translation-en [22.3 kB] Get:11 http://ftpmaster.internal/ubuntu zesty-proposed/universe arm64 Packages [137 kB] Get:12 http://ftpmaster.internal/ubuntu zesty-proposed/universe Translation-en [69.5 kB] Fetched 14.6 MB in 4s (3127 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 libasan3 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 libubsan0 libudev1 libwind0-heimdal linux-libc-dev perl perl-base systemd systemd-sysv tzdata ubuntu-keyring xz-utils 41 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 34.0 MB of archives. After this operation, 39.5 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu zesty/main arm64 base-files arm64 9.6ubuntu6 [55.8 kB] Get:2 http://ftpmaster.internal/ubuntu zesty/main arm64 perl-modules-5.24 all 5.24.1~rc3-3 [2661 kB] Get:3 http://ftpmaster.internal/ubuntu zesty/main arm64 libperl5.24 arm64 5.24.1~rc3-3 [3226 kB] Get:4 http://ftpmaster.internal/ubuntu zesty/main arm64 perl arm64 5.24.1~rc3-3 [237 kB] Get:5 http://ftpmaster.internal/ubuntu zesty/main arm64 perl-base arm64 5.24.1~rc3-3 [1180 kB] Get:6 http://ftpmaster.internal/ubuntu zesty/main arm64 libapparmor1 arm64 2.10.95-4ubuntu5.2 [27.1 kB] Get:7 http://ftpmaster.internal/ubuntu zesty/main arm64 liblzma5 arm64 5.2.2-1.2 [81.2 kB] Get:8 http://ftpmaster.internal/ubuntu zesty/main arm64 adduser all 3.113+nmu3ubuntu5 [161 kB] Get:9 http://ftpmaster.internal/ubuntu zesty/main arm64 systemd arm64 231-10 [1934 kB] Get:10 http://ftpmaster.internal/ubuntu zesty/main arm64 libsystemd0 arm64 231-10 [171 kB] Get:11 http://ftpmaster.internal/ubuntu zesty/main arm64 systemd-sysv arm64 231-10 [14.3 kB] Get:12 http://ftpmaster.internal/ubuntu zesty/main arm64 libgomp1 arm64 6.2.0-10ubuntu1 [61.7 kB] Get:13 http://ftpmaster.internal/ubuntu zesty/main arm64 libitm1 arm64 6.2.0-10ubuntu1 [25.2 kB] Get:14 http://ftpmaster.internal/ubuntu zesty/main arm64 libcc1-0 arm64 6.2.0-10ubuntu1 [27.6 kB] Get:15 http://ftpmaster.internal/ubuntu zesty/main arm64 libatomic1 arm64 6.2.0-10ubuntu1 [6636 B] Get:16 http://ftpmaster.internal/ubuntu zesty/main arm64 libasan3 arm64 6.2.0-10ubuntu1 [267 kB] Get:17 http://ftpmaster.internal/ubuntu zesty/main arm64 libubsan0 arm64 6.2.0-10ubuntu1 [97.1 kB] Get:18 http://ftpmaster.internal/ubuntu zesty/main arm64 gcc-6-base arm64 6.2.0-10ubuntu1 [17.3 kB] Get:19 http://ftpmaster.internal/ubuntu zesty/main arm64 libstdc++6 arm64 6.2.0-10ubuntu1 [369 kB] Get:20 http://ftpmaster.internal/ubuntu zesty/main arm64 g++-6 arm64 6.2.0-10ubuntu1 [5886 kB] Get:21 http://ftpmaster.internal/ubuntu zesty/main arm64 libstdc++-6-dev arm64 6.2.0-10ubuntu1 [1383 kB] Get:22 http://ftpmaster.internal/ubuntu zesty/main arm64 libgcc-6-dev arm64 6.2.0-10ubuntu1 [563 kB] Get:23 http://ftpmaster.internal/ubuntu zesty/main arm64 gcc-6 arm64 6.2.0-10ubuntu1 [5742 kB] Get:24 http://ftpmaster.internal/ubuntu zesty/main arm64 cpp-6 arm64 6.2.0-10ubuntu1 [5155 kB] Get:25 http://ftpmaster.internal/ubuntu zesty/main arm64 libgcc1 arm64 1:6.2.0-10ubuntu1 [30.1 kB] Get:26 http://ftpmaster.internal/ubuntu zesty-proposed/main arm64 binutils arm64 2.27-9ubuntu1 [2497 kB] Get:27 http://ftpmaster.internal/ubuntu zesty/main arm64 libudev1 arm64 231-10 [48.0 kB] Get:28 http://ftpmaster.internal/ubuntu zesty/main arm64 ubuntu-keyring all 2016.10.27 [16.6 kB] Get:29 http://ftpmaster.internal/ubuntu zesty/main arm64 tzdata all 2016h-1 [169 kB] Get:30 http://ftpmaster.internal/ubuntu zesty/main arm64 libdevmapper1.02.1 arm64 2:1.02.133-1ubuntu1 [129 kB] Get:31 http://ftpmaster.internal/ubuntu zesty/main arm64 dmsetup arm64 2:1.02.133-1ubuntu1 [69.5 kB] Get:32 http://ftpmaster.internal/ubuntu zesty-proposed/main arm64 libroken18-heimdal arm64 1.7~git20160703+dfsg-1 [34.4 kB] Get:33 http://ftpmaster.internal/ubuntu zesty-proposed/main arm64 libasn1-8-heimdal arm64 1.7~git20160703+dfsg-1 [127 kB] Get:34 http://ftpmaster.internal/ubuntu zesty-proposed/main arm64 libheimbase1-heimdal arm64 1.7~git20160703+dfsg-1 [24.2 kB] Get:35 http://ftpmaster.internal/ubuntu zesty-proposed/main arm64 libhcrypto4-heimdal arm64 1.7~git20160703+dfsg-1 [73.1 kB] Get:36 http://ftpmaster.internal/ubuntu zesty-proposed/main arm64 libwind0-heimdal arm64 1.7~git20160703+dfsg-1 [46.9 kB] Get:37 http://ftpmaster.internal/ubuntu zesty-proposed/main arm64 libhx509-5-heimdal arm64 1.7~git20160703+dfsg-1 [86.2 kB] Get:38 http://ftpmaster.internal/ubuntu zesty-proposed/main arm64 libkrb5-26-heimdal arm64 1.7~git20160703+dfsg-1 [162 kB] Get:39 http://ftpmaster.internal/ubuntu zesty-proposed/main arm64 libheimntlm0-heimdal arm64 1.7~git20160703+dfsg-1 [13.1 kB] Get:40 http://ftpmaster.internal/ubuntu zesty-proposed/main arm64 libgssapi3-heimdal arm64 1.7~git20160703+dfsg-1 [76.9 kB] Get:41 http://ftpmaster.internal/ubuntu zesty/main arm64 libldap-2.4-2 arm64 2.4.42+dfsg-2ubuntu5 [135 kB] Get:42 http://ftpmaster.internal/ubuntu zesty/main arm64 xz-utils arm64 5.2.2-1.2 [79.1 kB] Get:43 http://ftpmaster.internal/ubuntu zesty-proposed/main arm64 linux-libc-dev arm64 4.8.0-27.29 [827 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 34.0 MB in 1s (26.5 MB/s) (Reading database ... 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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:arm64 (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:arm64 (6.2.0-10ubuntu1) ... Setting up libgcc-6-dev:arm64 (6.2.0-10ubuntu1) ... Setting up libstdc++-6-dev:arm64 (6.2.0-10ubuntu1) ... Setting up libwind0-heimdal:arm64 (1.7~git20160703+dfsg-1) ... Setting up libasn1-8-heimdal:arm64 (1.7~git20160703+dfsg-1) ... Setting up libhcrypto4-heimdal:arm64 (1.7~git20160703+dfsg-1) ... Setting up libhx509-5-heimdal:arm64 (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:arm64 (1.7~git20160703+dfsg-1) ... Setting up libheimntlm0-heimdal:arm64 (1.7~git20160703+dfsg-1) ... Setting up libgssapi3-heimdal:arm64 (1.7~git20160703+dfsg-1) ... Setting up libldap-2.4-2:arm64 (2.4.42+dfsg-2ubuntu5) ... Processing triggers for libc-bin (2.24-3ubuntu1) ... RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package ['sbuild-package', 'PACKAGEBUILD-11110629', 'arm64', 'zesty-proposed', '-c', 'chroot:autobuild', '--arch=arm64', '--dist=zesty-proposed', '--purge=never', '--nolog', 'berkeley-express_1.5.1-3build1.dsc'] Initiating build PACKAGEBUILD-11110629 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.4.0-45-generic #66+buildd2-Ubuntu SMP Fri Oct 21 06:29:15 UTC 2016 aarch64 sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on bos01-arm64-037.buildd +==============================================================================+ | berkeley-express 1.5.1-3build1 (arm64) 01 Nov 2016 17:38 | +==============================================================================+ Package: berkeley-express Version: 1.5.1-3build1 Source Version: 1.5.1-3build1 Distribution: zesty-proposed Machine Architecture: arm64 Host Architecture: arm64 Build Architecture: arm64 I: NOTICE: Log filtering will replace 'build/berkeley-express-V0vsiN/berkeley-express-1.5.1' with '<>' I: NOTICE: Log filtering will replace 'build/berkeley-express-V0vsiN' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-11110629/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-GLYB_H/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/<>/resolver-GLYB_H/apt_archive ./ InRelease Get:2 copy:/<>/resolver-GLYB_H/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-GLYB_H/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-GLYB_H/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-GLYB_H/apt_archive ./ Packages [526 B] Fetched 2859 B in 0s (94.9 kB/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install core build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: libperl5.22 perl-modules-5.22 Use 'sudo apt autoremove' to remove them. The following NEW packages will be installed: sbuild-build-depends-core-dummy 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 772 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-GLYB_H/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, libgoogle-perftools-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, libgoogle-perftools-dev, cmake, libprotobuf-dev, protobuf-compiler dpkg-deb: building package 'sbuild-build-depends-berkeley-express-dummy' in '/<>/resolver-Di30vr/apt_archive/sbuild-build-depends-berkeley-express-dummy.deb'. Ign:1 copy:/<>/resolver-Di30vr/apt_archive ./ InRelease Get:2 copy:/<>/resolver-Di30vr/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-Di30vr/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-Di30vr/apt_archive ./ Sources [331 B] Get:5 copy:/<>/resolver-Di30vr/apt_archive ./ Packages [620 B] Fetched 3070 B in 0s (192 kB/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 libgoogle-perftools-dev libgoogle-perftools4 libicu57 libjsoncpp1 liblzo2-2 libmagic1 libpipeline1 libprotobuf-dev libprotobuf-lite10 libprotobuf10 libprotoc10 libsigsegv2 libtcmalloc-minimal4 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-context1.62-dev libboost-coroutine1.62-dev libboost-exception1.62-dev libboost-fiber1.62-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 libgoogle-perftools-dev libgoogle-perftools4 libicu57 libjsoncpp1 liblzo2-2 libmagic1 libpipeline1 libprotobuf-dev libprotobuf-lite10 libprotobuf10 libprotoc10 libsigsegv2 libtcmalloc-minimal4 libtimedate-perl libtool libunistring0 libxml2 m4 man-db po-debconf protobuf-compiler sbuild-build-depends-berkeley-express-dummy zlib1g-dev 0 upgraded, 71 newly installed, 0 to remove and 0 not upgraded. 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Processing triggers for libc-bin (2.24-3ubuntu1) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.4.0-45-generic arm64 (aarch64) 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 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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 arm64 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 -- Found GPERFTOOLS_TCMALLOC: /usr/lib/libtcmalloc.so -- Found Protobuf: /usr/lib/aarch64-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-aarch64-linux-gnu dh_auto_build -a -O--parallel make -j4 make[1]: Entering directory '/<>/obj-aarch64-linux-gnu' /usr/bin/cmake -H/<> -B/<>/obj-aarch64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /<>/obj-aarch64-linux-gnu/CMakeFiles /<>/obj-aarch64-linux-gnu/CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/<>/obj-aarch64-linux-gnu' make -f src/CMakeFiles/express.dir/build.make src/CMakeFiles/express.dir/depend make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' [ 11%] Running C++ protocol buffer compiler on /<>/src/alignments.proto [ 11%] Running C++ protocol buffer compiler on /<>/src/targets.proto cd /<>/obj-aarch64-linux-gnu/src && /usr/bin/protoc --cpp_out /<>/obj-aarch64-linux-gnu/src -I /<>/src /<>/src/targets.proto cd /<>/obj-aarch64-linux-gnu/src && /usr/bin/protoc --cpp_out /<>/obj-aarch64-linux-gnu/src -I /<>/src /<>/src/alignments.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-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/src /<>/obj-aarch64-linux-gnu/src/CMakeFiles/express.dir/DependInfo.cmake --color= Scanning dependencies of target express make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f src/CMakeFiles/express.dir/build.make src/CMakeFiles/express.dir/build make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' [ 27%] Building CXX object src/CMakeFiles/express.dir/fragments.cpp.o [ 27%] Building CXX object src/CMakeFiles/express.dir/biascorrection.cpp.o [ 27%] Building CXX object src/CMakeFiles/express.dir/bundles.cpp.o [ 33%] Building CXX object src/CMakeFiles/express.dir/directiondetector.cpp.o cd /<>/obj-aarch64-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 cd /<>/obj-aarch64-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 cd /<>/obj-aarch64-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 cd /<>/obj-aarch64-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 :0:0: warning: "__FILE__" redefined [-Wbuiltin-macro-redefined] :0:0: warning: "__FILE__" redefined [-Wbuiltin-macro-redefined] :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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-linux-gnu/src/targets.pb.cc :0:0: warning: "__FILE__" redefined [-Wbuiltin-macro-redefined] [100%] Linking CXX executable express cd /<>/obj-aarch64-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/express.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D__FILE__=\"\" -Wl,-Bsymbolic-functions -fPIE -pie -Wl,-z,relro -Wl,-z,now CMakeFiles/express.dir/biascorrection.cpp.o CMakeFiles/express.dir/bundles.cpp.o CMakeFiles/express.dir/directiondetector.cpp.o CMakeFiles/express.dir/fragments.cpp.o CMakeFiles/express.dir/lengthdistribution.cpp.o CMakeFiles/express.dir/main.cpp.o CMakeFiles/express.dir/mapparser.cpp.o CMakeFiles/express.dir/markovmodel.cpp.o CMakeFiles/express.dir/mismatchmodel.cpp.o CMakeFiles/express.dir/robertsfilter.cpp.o CMakeFiles/express.dir/sequence.cpp.o CMakeFiles/express.dir/targets.cpp.o CMakeFiles/express.dir/threadsafety.cpp.o CMakeFiles/express.dir/alignments.pb.cc.o CMakeFiles/express.dir/targets.pb.cc.o -o express -rdynamic -lboost_thread -lboost_system -lboost_filesystem -lboost_program_options -lboost_date_time -lpthread -lbamtools -lpthread -lprotobuf make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' [100%] Built target express make[2]: Leaving directory '/<>/obj-aarch64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /<>/obj-aarch64-linux-gnu/CMakeFiles 0 make[1]: Leaving directory '/<>/obj-aarch64-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-aarch64-linux-gnu' /usr/bin/cmake -H/<> -B/<>/obj-aarch64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /<>/obj-aarch64-linux-gnu/CMakeFiles /<>/obj-aarch64-linux-gnu/CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/<>/obj-aarch64-linux-gnu' make -f src/CMakeFiles/express.dir/build.make src/CMakeFiles/express.dir/depend make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/src /<>/obj-aarch64-linux-gnu/src/CMakeFiles/express.dir/DependInfo.cmake --color= make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f src/CMakeFiles/express.dir/build.make src/CMakeFiles/express.dir/build make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' make[3]: Nothing to be done for 'src/CMakeFiles/express.dir/build'. make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' [100%] Built target express make[2]: Leaving directory '/<>/obj-aarch64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /<>/obj-aarch64-linux-gnu/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/<>/obj-aarch64-linux-gnu' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/<>/obj-aarch64-linux-gnu' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /<>/debian/tmp/usr/bin/express make[1]: Leaving directory '/<>/obj-aarch64-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 arm64: 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 arm64: 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_arm64.ddeb dpkg-deb: building package 'berkeley-express-dbgsym' in '../berkeley-express-dbgsym_1.5.1-3build1_arm64.ddeb'. dh_gencontrol debug symbol wrapper: dpkg-distaddfile berkeley-express-dbgsym_1.5.1-3build1_arm64.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_arm64.deb'. dpkg-genchanges --build=any -mLaunchpad Build Daemon >../berkeley-express_1.5.1-3build1_arm64.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 20161101-1741 Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Post Build Chroot | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ berkeley-express_1.5.1-3build1_arm64.changes: --------------------------------------------- Format: 1.8 Date: Tue, 01 Nov 2016 16:09:43 +0000 Source: berkeley-express Binary: berkeley-express berkeley-express-doc Architecture: arm64 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: d952739631a4e20e4d0f625f929feada6c049b7d 2583368 berkeley-express-dbgsym_1.5.1-3build1_arm64.ddeb 4a77fa5493d1581bae8f7a4183d4ff20d9ddbf4f 221134 berkeley-express_1.5.1-3build1_arm64.deb Checksums-Sha256: 141d78fc5da16cf552a58c5ac6a9b8d75a2ec6d2086d4f92910c9c90c3caf5b6 2583368 berkeley-express-dbgsym_1.5.1-3build1_arm64.ddeb 93e99b7b720073d879b0d8f620bea2f224aaf43210b990da6ca28550606b9241 221134 berkeley-express_1.5.1-3build1_arm64.deb Files: defa97533f402c4832e5d7b676746367 2583368 science extra berkeley-express-dbgsym_1.5.1-3build1_arm64.ddeb 33c6167b5ba8d4de6d19304a51922a60 221134 science optional berkeley-express_1.5.1-3build1_arm64.deb Original-Maintainer: Debian Med Packaging Team +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ berkeley-express_1.5.1-3build1_arm64.deb ---------------------------------------- new debian package, version 2.0. size 221134 bytes: control archive=1873 bytes. 3175 bytes, 51 lines control 454 bytes, 6 lines md5sums Package: berkeley-express Version: 1.5.1-3build1 Architecture: arm64 Maintainer: Ubuntu Developers Installed-Size: 801 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 (>= 2.17), libgcc1 (>= 1:4.5), 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 797096 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: arm64 Build-Space: 70776 Build-Time: 97 Distribution: zesty-proposed Host Architecture: arm64 Install-Time: 29 Job: berkeley-express_1.5.1-3build1.dsc Machine Architecture: arm64 Package: berkeley-express Package-Time: 128 Source-Version: 1.5.1-3build1 Space: 70776 Status: successful Version: 1.5.1-3build1 -------------------------------------------------------------------------------- Finished at 20161101-1741 Build needed 00:02:08, 70776k disc space RUN: /usr/share/launchpad-buildd/slavebin/scan-for-processes ['scan-for-processes', 'PACKAGEBUILD-11110629'] Scanning for processes to kill in build /home/buildd/build-PACKAGEBUILD-11110629/chroot-autobuild... RUN: /usr/share/launchpad-buildd/slavebin/umount-chroot ['umount-chroot', 'PACKAGEBUILD-11110629'] Unmounting chroot for build PACKAGEBUILD-11110629... RUN: /usr/share/launchpad-buildd/slavebin/remove-build ['remove-build', 'PACKAGEBUILD-11110629'] Removing build PACKAGEBUILD-11110629