RUN: /usr/share/launchpad-buildd/slavebin/slave-prep Forking launchpad-buildd slave process... Kernel version: Linux lcy01-10 4.4.0-97-generic #120-Ubuntu SMP Tue Sep 19 17:28:18 UTC 2017 x86_64 Buildd toolchain package versions: launchpad-buildd_154 python-lpbuildd_154 sbuild_0.67.0-2ubuntu7.1 bzr-builder_0.7.3+bzr174~ppa13~ubuntu14.10.1 bzr_2.7.0-2ubuntu3.1 git-build-recipe_0.3.4~git201611291343.dcee459~ubuntu16.04.1 git_1:2.7.4-0ubuntu1.3 dpkg-dev_1.18.4ubuntu1.2 python-debian_0.1.27ubuntu2. Syncing the system clock with the buildd NTP service... 27 Oct 23:41:28 ntpdate[1825]: adjust time server 10.211.37.1 offset 0.002877 sec RUN: /usr/share/launchpad-buildd/slavebin/in-target unpack-chroot --backend=chroot --series=bionic --arch=amd64 PACKAGEBUILD-13634426 /home/buildd/filecache-default/f027e517e95d0e91684230ee23be60d709f816c0 Creating target for build PACKAGEBUILD-13634426 RUN: /usr/share/launchpad-buildd/slavebin/in-target mount-chroot --backend=chroot --series=bionic --arch=amd64 PACKAGEBUILD-13634426 Starting target for build PACKAGEBUILD-13634426 RUN: /usr/share/launchpad-buildd/slavebin/in-target override-sources-list --backend=chroot --series=bionic --arch=amd64 PACKAGEBUILD-13634426 'deb http://ftpmaster.internal/ubuntu bionic main restricted universe multiverse' 'deb http://ftpmaster.internal/ubuntu bionic-security main restricted universe multiverse' 'deb http://ftpmaster.internal/ubuntu bionic-updates main restricted universe multiverse' 'deb http://ftpmaster.internal/ubuntu bionic-proposed main restricted universe multiverse' Overriding sources.list in build-PACKAGEBUILD-13634426 RUN: /usr/share/launchpad-buildd/slavebin/in-target update-debian-chroot --backend=chroot --series=bionic --arch=amd64 PACKAGEBUILD-13634426 Updating target for build PACKAGEBUILD-13634426 Get:1 http://ftpmaster.internal/ubuntu bionic InRelease [235 kB] Get:2 http://ftpmaster.internal/ubuntu bionic-security InRelease [65.4 kB] Get:3 http://ftpmaster.internal/ubuntu bionic-updates InRelease [65.4 kB] Get:4 http://ftpmaster.internal/ubuntu bionic-proposed InRelease [85.4 kB] Get:5 http://ftpmaster.internal/ubuntu bionic/main amd64 Packages [1070 kB] Get:6 http://ftpmaster.internal/ubuntu bionic/main Translation-en [542 kB] Get:7 http://ftpmaster.internal/ubuntu bionic/restricted amd64 Packages [8852 B] Get:8 http://ftpmaster.internal/ubuntu bionic/restricted Translation-en [2788 B] Get:9 http://ftpmaster.internal/ubuntu bionic/universe amd64 Packages [8102 kB] Get:10 http://ftpmaster.internal/ubuntu bionic/universe Translation-en [4788 kB] Get:11 http://ftpmaster.internal/ubuntu bionic/multiverse amd64 Packages [150 kB] Get:12 http://ftpmaster.internal/ubuntu bionic/multiverse Translation-en [108 kB] Get:13 http://ftpmaster.internal/ubuntu bionic-proposed/main amd64 Packages [134 kB] Get:14 http://ftpmaster.internal/ubuntu bionic-proposed/main Translation-en [58.4 kB] Get:15 http://ftpmaster.internal/ubuntu bionic-proposed/universe amd64 Packages [404 kB] Get:16 http://ftpmaster.internal/ubuntu bionic-proposed/universe Translation-en [214 kB] Get:17 http://ftpmaster.internal/ubuntu bionic-proposed/multiverse amd64 Packages [7556 B] Get:18 http://ftpmaster.internal/ubuntu bionic-proposed/multiverse Translation-en [5488 B] Fetched 16.0 MB in 3s (4767 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following package was automatically installed and is no longer required: libustr-1.0-1 Use 'sudo apt autoremove' to remove it. The following packages will be upgraded: apt apt-transport-https base-files binutils binutils-common binutils-x86-64-linux-gnu build-essential coreutils cpp-7 dpkg dpkg-dev g++-7 gcc-7 gcc-7-base gnupg gnupg-agent gpgv libapt-pkg5.0 libasan4 libatomic1 libbinutils libc-bin libc-dev-bin libc6 libc6-dev libcap2 libcc1-0 libcilkrts5 libcurl3-gnutls libdpkg-perl libgcc-7-dev libgcc1 libgomp1 libhogweed4 libitm1 libkeyutils1 liblsan0 libmpx2 libnettle6 libpcre3 libpng16-16 libquadmath0 libseccomp2 libsemanage-common libsemanage1 libsqlite3-0 libstdc++-7-dev libstdc++6 libsystemd0 libtsan0 libubsan0 libudev1 linux-libc-dev multiarch-support systemd systemd-sysv tzdata 57 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 47.8 MB of archives. After this operation, 318 kB of additional disk space will be used. 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Get:20 http://ftpmaster.internal/ubuntu bionic-proposed/main amd64 libcc1-0 amd64 7.2.0-12ubuntu1 [38.7 kB] Get:21 http://ftpmaster.internal/ubuntu bionic-proposed/main amd64 g++-7 amd64 7.2.0-12ubuntu1 [7554 kB] Get:22 http://ftpmaster.internal/ubuntu bionic-proposed/main amd64 gcc-7 amd64 7.2.0-12ubuntu1 [7414 kB] Get:23 http://ftpmaster.internal/ubuntu bionic-proposed/main amd64 libgcc-7-dev amd64 7.2.0-12ubuntu1 [2377 kB] Get:24 http://ftpmaster.internal/ubuntu bionic-proposed/main amd64 libstdc++-7-dev amd64 7.2.0-12ubuntu1 [1457 kB] Get:25 http://ftpmaster.internal/ubuntu bionic-proposed/main amd64 libstdc++6 amd64 7.2.0-12ubuntu1 [405 kB] Get:26 http://ftpmaster.internal/ubuntu bionic-proposed/main amd64 libbinutils amd64 2.29.1-6ubuntu1 [502 kB] Get:27 http://ftpmaster.internal/ubuntu bionic-proposed/main amd64 binutils amd64 2.29.1-6ubuntu1 [3344 B] Get:28 http://ftpmaster.internal/ubuntu bionic-proposed/main amd64 binutils-common amd64 2.29.1-6ubuntu1 [190 kB] Get:29 http://ftpmaster.internal/ubuntu bionic-proposed/main amd64 binutils-x86-64-linux-gnu amd64 2.29.1-6ubuntu1 [1825 kB] Get:30 http://ftpmaster.internal/ubuntu bionic/main amd64 libc6 amd64 2.26-0ubuntu2 [2778 kB] Get:31 http://ftpmaster.internal/ubuntu bionic/main amd64 libc-bin amd64 2.26-0ubuntu2 [593 kB] Get:32 http://ftpmaster.internal/ubuntu bionic/main amd64 libudev1 amd64 234-2ubuntu12 [51.7 kB] Get:33 http://ftpmaster.internal/ubuntu bionic-proposed/main amd64 libapt-pkg5.0 amd64 1.5.1 [781 kB] Get:34 http://ftpmaster.internal/ubuntu bionic/main amd64 gpgv amd64 2.1.15-1ubuntu8 [186 kB] Get:35 http://ftpmaster.internal/ubuntu bionic-proposed/main amd64 apt amd64 1.5.1 [1121 kB] Get:36 http://ftpmaster.internal/ubuntu bionic/main amd64 libcap2 amd64 1:2.25-1.1 [13.2 kB] Get:37 http://ftpmaster.internal/ubuntu bionic/main amd64 libseccomp2 amd64 2.3.1-2.1ubuntu3 [37.3 kB] Get:38 http://ftpmaster.internal/ubuntu bionic/main amd64 systemd amd64 234-2ubuntu12 [2780 kB] Get:39 http://ftpmaster.internal/ubuntu bionic/main amd64 libsystemd0 amd64 234-2ubuntu12 [208 kB] Get:40 http://ftpmaster.internal/ubuntu bionic/main amd64 systemd-sysv amd64 234-2ubuntu12 [10.8 kB] Get:41 http://ftpmaster.internal/ubuntu bionic/main amd64 libpcre3 amd64 2:8.39-5ubuntu3 [229 kB] Get:42 http://ftpmaster.internal/ubuntu bionic/main amd64 libsemanage-common all 2.7-2 [6916 B] Get:43 http://ftpmaster.internal/ubuntu bionic/main amd64 libsemanage1 amd64 2.7-2 [84.6 kB] Get:44 http://ftpmaster.internal/ubuntu bionic/main amd64 libnettle6 amd64 3.3-2 [91.7 kB] Get:45 http://ftpmaster.internal/ubuntu bionic/main amd64 libhogweed4 amd64 3.3-2 [135 kB] Get:46 http://ftpmaster.internal/ubuntu bionic/main amd64 gnupg amd64 2.1.15-1ubuntu8 [780 kB] Get:47 http://ftpmaster.internal/ubuntu bionic/main amd64 gnupg-agent amd64 2.1.15-1ubuntu8 [255 kB] Get:48 http://ftpmaster.internal/ubuntu bionic-proposed/main amd64 libsqlite3-0 amd64 3.20.1-2 [491 kB] Get:49 http://ftpmaster.internal/ubuntu bionic/main amd64 multiarch-support amd64 2.26-0ubuntu2 [6832 B] Get:50 http://ftpmaster.internal/ubuntu bionic-proposed/main amd64 tzdata all 2017c-1 [188 kB] Get:51 http://ftpmaster.internal/ubuntu bionic-proposed/main amd64 libkeyutils1 amd64 1.5.9-9.1ubuntu1 [9488 B] Get:52 http://ftpmaster.internal/ubuntu bionic/main amd64 libpng16-16 amd64 1.6.34-1 [176 kB] Get:53 http://ftpmaster.internal/ubuntu bionic-proposed/main amd64 libcurl3-gnutls amd64 7.55.1-1ubuntu2.1 [193 kB] Get:54 http://ftpmaster.internal/ubuntu bionic-proposed/main amd64 apt-transport-https amd64 1.5.1 [34.7 kB] Get:55 http://ftpmaster.internal/ubuntu bionic-proposed/main amd64 dpkg-dev all 1.19.0.4ubuntu1 [607 kB] Get:56 http://ftpmaster.internal/ubuntu bionic-proposed/main amd64 libdpkg-perl all 1.19.0.4ubuntu1 [211 kB] Get:57 http://ftpmaster.internal/ubuntu bionic/main amd64 build-essential amd64 12.4ubuntu1 [4758 B] debconf: delaying package configuration, since apt-utils is 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Current default time zone: 'Etc/UTC' Local time is now: Fri Oct 27 23:41:53 UTC 2017. Universal Time is now: Fri Oct 27 23:41:53 UTC 2017. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up systemd-sysv (234-2ubuntu12) ... Setting up libubsan0:amd64 (7.2.0-12ubuntu1) ... Setting up libtsan0:amd64 (7.2.0-12ubuntu1) ... Setting up linux-libc-dev:amd64 (4.13.0-16.19) ... Setting up libdpkg-perl (1.19.0.4ubuntu1) ... Setting up cpp-7 (7.2.0-12ubuntu1) ... Setting up liblsan0:amd64 (7.2.0-12ubuntu1) ... Setting up binutils-common:amd64 (2.29.1-6ubuntu1) ... Setting up libmpx2:amd64 (7.2.0-12ubuntu1) ... Processing triggers for libc-bin (2.26-0ubuntu2) ... Setting up libsqlite3-0:amd64 (3.20.1-2) ... Setting up libc-dev-bin (2.26-0ubuntu2) ... Setting up libkeyutils1:amd64 (1.5.9-9.1ubuntu1) ... Setting up gnupg-agent (2.1.15-1ubuntu8) ... Setting up libc6-dev:amd64 (2.26-0ubuntu2) ... Setting up libitm1:amd64 (7.2.0-12ubuntu1) ... Setting up apt-transport-https (1.5.1) ... Setting up libbinutils:amd64 (2.29.1-6ubuntu1) ... Setting up gnupg (2.1.15-1ubuntu8) ... Setting up libgcc-7-dev:amd64 (7.2.0-12ubuntu1) ... Setting up libstdc++-7-dev:amd64 (7.2.0-12ubuntu1) ... Setting up binutils-x86-64-linux-gnu (2.29.1-6ubuntu1) ... Setting up binutils (2.29.1-6ubuntu1) ... Setting up gcc-7 (7.2.0-12ubuntu1) ... Setting up g++-7 (7.2.0-12ubuntu1) ... Setting up dpkg-dev (1.19.0.4ubuntu1) ... Setting up build-essential (12.4ubuntu1) ... Processing triggers for libc-bin (2.26-0ubuntu2) ... RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package PACKAGEBUILD-13634426 amd64 bionic-proposed -c chroot:build-PACKAGEBUILD-13634426 --arch=amd64 --dist=bionic-proposed --nolog -A cufflinks_2.2.1+dfsg.1-1.dsc Initiating build PACKAGEBUILD-13634426 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.4.0-97-generic #120-Ubuntu SMP Tue Sep 19 17:28:18 UTC 2017 x86_64 sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on lcy01-10.buildd +==============================================================================+ | cufflinks 2.2.1+dfsg.1-1 (amd64) 27 Oct 2017 23:41 | +==============================================================================+ Package: cufflinks Version: 2.2.1+dfsg.1-1 Source Version: 2.2.1+dfsg.1-1 Distribution: bionic-proposed Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 I: NOTICE: Log filtering will replace 'build/cufflinks-fDtriC/cufflinks-2.2.1+dfsg.1' with '<>' I: NOTICE: Log filtering will replace 'build/cufflinks-fDtriC' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-13634426/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- cufflinks_2.2.1+dfsg.1-1.dsc exists in .; copying to chroot Check architectures ------------------- Check dependencies ------------------ Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<>/resolver-Z_Ofwq/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/<>/resolver-Z_Ofwq/apt_archive ./ InRelease Get:2 copy:/<>/resolver-Z_Ofwq/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-Z_Ofwq/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-Z_Ofwq/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-Z_Ofwq/apt_archive ./ Packages [525 B] Fetched 2858 B in 0s (266 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 package was automatically installed and is no longer required: libustr-1.0-1 Use 'apt autoremove' to remove it. The following NEW packages will be installed: sbuild-build-depends-core-dummy 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 852 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-Z_Ofwq/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 852 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 12683 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_amd64.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... Merged Build-Depends: debhelper (>= 9), help2man, autotools-dev, libboost-dev, libboost-serialization-dev, libboost-system-dev, libboost-thread-dev, libbam-dev, zlib1g-dev, dh-autoreconf, python, libeigen3-dev Filtered Build-Depends: debhelper (>= 9), help2man, autotools-dev, libboost-dev, libboost-serialization-dev, libboost-system-dev, libboost-thread-dev, libbam-dev, zlib1g-dev, dh-autoreconf, python, libeigen3-dev dpkg-deb: building package 'sbuild-build-depends-cufflinks-dummy' in '/<>/resolver-iSjBGp/apt_archive/sbuild-build-depends-cufflinks-dummy.deb'. Ign:1 copy:/<>/resolver-iSjBGp/apt_archive ./ InRelease Get:2 copy:/<>/resolver-iSjBGp/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-iSjBGp/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-iSjBGp/apt_archive ./ Sources [284 B] Get:5 copy:/<>/resolver-iSjBGp/apt_archive ./ Packages [600 B] Fetched 3003 B in 0s (0 B/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install cufflinks build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following package was automatically installed and is no longer required: libustr-1.0-1 Use 'apt autoremove' to remove it. The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism file gettext gettext-base groff-base help2man intltool-debian libarchive-zip-perl libbam-dev libboost-atomic1.65-dev libboost-atomic1.65.1 libboost-chrono1.65-dev libboost-chrono1.65.1 libboost-date-time1.65-dev libboost-date-time1.65.1 libboost-dev libboost-serialization-dev libboost-serialization1.65-dev libboost-serialization1.65.1 libboost-system-dev libboost-system1.65-dev libboost-system1.65.1 libboost-thread-dev libboost-thread1.65-dev libboost-thread1.65.1 libboost1.65-dev libbsd0 libcroco3 libeigen3-dev libexpat1 libfile-stripnondeterminism-perl libglib2.0-0 libicu59 liblocale-gettext-perl libmagic-mgc libmagic1 libpipeline1 libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libsigsegv2 libtimedate-perl libtool libxml2 m4 man-db mime-support pkg-config po-debconf python python-minimal python2.7 python2.7-minimal zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois vacation dh-make dwz gettext-doc libasprintf-dev libgettextpo-dev groff libboost-doc libboost1.65-doc libboost-container1.65-dev libboost-context1.65-dev libboost-coroutine1.65-dev libboost-exception1.65-dev libboost-fiber1.65-dev libboost-filesystem1.65-dev libboost-graph1.65-dev libboost-graph-parallel1.65-dev libboost-iostreams1.65-dev libboost-locale1.65-dev libboost-log1.65-dev libboost-math1.65-dev libboost-mpi1.65-dev libboost-mpi-python1.65-dev libboost-numpy1.65-dev libboost-program-options1.65-dev libboost-python1.65-dev libboost-random1.65-dev libboost-regex1.65-dev libboost-signals1.65-dev libboost-stacktrace1.65-dev libboost-test1.65-dev libboost-timer1.65-dev libboost-type-erasure1.65-dev libboost-wave1.65-dev libboost1.65-tools-dev libmpfrc++-dev libntl-dev libeigen3-doc libmrpt-dev libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc less www-browser libmail-box-perl python-doc python-tk python2.7-doc binfmt-support Recommended packages: curl | wget | lynx-cur libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs libltdl-dev libmail-sendmail-perl The following packages will be REMOVED: pkg-create-dbgsym* The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism file gettext gettext-base groff-base help2man intltool-debian libarchive-zip-perl libbam-dev libboost-atomic1.65-dev libboost-atomic1.65.1 libboost-chrono1.65-dev libboost-chrono1.65.1 libboost-date-time1.65-dev libboost-date-time1.65.1 libboost-dev libboost-serialization-dev libboost-serialization1.65-dev libboost-serialization1.65.1 libboost-system-dev libboost-system1.65-dev libboost-system1.65.1 libboost-thread-dev libboost-thread1.65-dev libboost-thread1.65.1 libboost1.65-dev libbsd0 libcroco3 libeigen3-dev libexpat1 libfile-stripnondeterminism-perl libglib2.0-0 libicu59 liblocale-gettext-perl libmagic-mgc libmagic1 libpipeline1 libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libsigsegv2 libtimedate-perl libtool libxml2 m4 man-db mime-support pkg-config po-debconf python python-minimal python2.7 python2.7-minimal sbuild-build-depends-cufflinks-dummy zlib1g-dev 0 upgraded, 62 newly installed, 1 to remove and 0 not upgraded. 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Processing triggers for libc-bin (2.26-0ubuntu2) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.4.0-97-generic amd64 (x86_64) Toolchain package versions: binutils_2.29.1-6ubuntu1 dpkg-dev_1.19.0.4ubuntu1 g++-7_7.2.0-12ubuntu1 gcc-7_7.2.0-12ubuntu1 libc6-dev_2.26-0ubuntu2 libstdc++-7-dev_7.2.0-12ubuntu1 libstdc++6_7.2.0-12ubuntu1 linux-libc-dev_4.13.0-16.19 Package versions: adduser_3.113+nmu3ubuntu5 advancecomp_2.0-1 apt_1.5.1 apt-transport-https_1.5.1 autoconf_2.69-11 automake_1:1.15.1-3ubuntu1 autopoint_0.19.8.1-4ubuntu1 autotools-dev_20161112.1 base-files_10ubuntu1 base-passwd_3.5.43 bash_4.4-5ubuntu1 binutils_2.29.1-6ubuntu1 binutils-common_2.29.1-6ubuntu1 binutils-x86-64-linux-gnu_2.29.1-6ubuntu1 bsdmainutils_9.0.12+nmu1ubuntu1 bsdutils_1:2.30.1-0ubuntu4 build-essential_12.4ubuntu1 bzip2_1.0.6-8.1 ca-certificates_20170717 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libhx509-5-heimdal_7.4.0.dfsg.1-2 libicu59_59.1-3ubuntu1 libidn11_1.33-2 libidn2-0_2.0.2-5 libip4tc0_1.6.1-2ubuntu1 libisl15_0.18-1 libitm1_7.2.0-12ubuntu1 libk5crypto3_1.15.1-2 libkeyutils1_1.5.9-9.1ubuntu1 libkmod2_24-1ubuntu2 libkrb5-26-heimdal_7.4.0.dfsg.1-2 libkrb5-3_1.15.1-2 libkrb5support0_1.15.1-2 libksba8_1.3.5-2 libldap-2.4-2_2.4.45+dfsg-1ubuntu1 libldap-common_2.4.45+dfsg-1ubuntu1 liblocale-gettext-perl_1.07-3build2 liblockfile-bin_1.14-1 liblockfile1_1.14-1 liblsan0_7.2.0-12ubuntu1 liblz4-1_0.0~r131-2ubuntu2 liblzma5_5.2.2-1.3 libmagic-mgc_1:5.32-1 libmagic1_1:5.32-1 libmount1_2.30.1-0ubuntu4 libmpc3_1.0.3-2 libmpfr4_3.1.6-1 libmpx2_7.2.0-12ubuntu1 libncurses5_6.0+20160625-1ubuntu1 libncursesw5_6.0+20160625-1ubuntu1 libnettle6_3.3-2 libnpth0_1.5-2 libp11-kit0_0.23.7-3 libpam-modules_1.1.8-3.2ubuntu3 libpam-modules-bin_1.1.8-3.2ubuntu3 libpam-runtime_1.1.8-3.2ubuntu3 libpam0g_1.1.8-3.2ubuntu3 libpcre3_2:8.39-5ubuntu3 libperl5.26_5.26.0-8ubuntu1 libpipeline1_1.4.2-1 libpng16-16_1.6.34-1 libprocps6_2:3.3.12-1ubuntu2 libpsl5_0.18.0-2 libpython-stdlib_2.7.14-2ubuntu1 libpython2.7-minimal_2.7.14-2ubuntu2 libpython2.7-stdlib_2.7.14-2ubuntu2 libquadmath0_7.2.0-12ubuntu1 libreadline7_7.0-0ubuntu2 libroken18-heimdal_7.4.0.dfsg.1-2 librtmp1_2.4+20151223.gitfa8646d.1-1 libsasl2-2_2.1.27~101-g0780600+dfsg-3ubuntu1 libsasl2-modules-db_2.1.27~101-g0780600+dfsg-3ubuntu1 libseccomp2_2.3.1-2.1ubuntu3 libselinux1_2.7-1 libsemanage-common_2.7-2 libsemanage1_2.7-2 libsepol1_2.7-1 libsigsegv2_2.11-1 libslang2_2.3.1-5ubuntu1 libsmartcols1_2.30.1-0ubuntu4 libsqlite3-0_3.20.1-2 libss2_1.43.5-1 libssl1.0.0_1.0.2g-1ubuntu13 libstdc++-7-dev_7.2.0-12ubuntu1 libstdc++6_7.2.0-12ubuntu1 libsystemd0_234-2ubuntu12 libtasn1-6_4.12-2.1 libtimedate-perl_2.3000-2 libtinfo5_6.0+20160625-1ubuntu1 libtool_2.4.6-2 libtsan0_7.2.0-12ubuntu1 libubsan0_7.2.0-12ubuntu1 libudev1_234-2ubuntu12 libunistring0_0.9.3-5.2ubuntu1 libusb-0.1-4_2:0.1.12-31 libustr-1.0-1_1.0.4-6 libuuid1_2.30.1-0ubuntu4 libwind0-heimdal_7.4.0.dfsg.1-2 libxml2_2.9.4+dfsg1-5ubuntu1 linux-libc-dev_4.13.0-16.19 lockfile-progs_0.1.17build1 login_1:4.2-3.2ubuntu4 lsb-base_9.20160110ubuntu5 m4_1.4.18-1 make_4.1-9.1 man-db_2.7.6.1-2 mawk_1.3.3-17ubuntu2 mime-support_3.60ubuntu1 mount_2.30.1-0ubuntu4 multiarch-support_2.26-0ubuntu2 ncurses-base_6.0+20160625-1ubuntu1 ncurses-bin_6.0+20160625-1ubuntu1 openssl_1.0.2g-1ubuntu13 optipng_0.7.6-1build1 passwd_1:4.2-3.2ubuntu4 patch_2.7.5-1build1 perl_5.26.0-8ubuntu1 perl-base_5.26.0-8ubuntu1 perl-modules-5.26_5.26.0-8ubuntu1 pinentry-curses_1.0.0-2 pkg-config_0.29.1-0ubuntu2 pkgbinarymangler_131 po-debconf_1.0.20 policyrcd-script-zg2_0.1-3 procps_2:3.3.12-1ubuntu2 python_2.7.14-2ubuntu1 python-minimal_2.7.14-2ubuntu1 python2.7_2.7.14-2ubuntu2 python2.7-minimal_2.7.14-2ubuntu2 readline-common_7.0-0ubuntu2 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-cufflinks-dummy_0.invalid.0 sed_4.4-1 sensible-utils_0.0.10 systemd_234-2ubuntu12 systemd-sysv_234-2ubuntu12 sysv-rc_2.88dsf-59.3ubuntu2 sysvinit-utils_2.88dsf-59.8git1 tar_1.29b-2 tzdata_2017c-1 ubuntu-keyring_2016.10.27 util-linux_2.30.1-0ubuntu4 xz-utils_5.2.2-1.3 zlib1g_1:1.2.11.dfsg-0ubuntu2 zlib1g-dev_1:1.2.11.dfsg-0ubuntu2 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Tue Sep 5 21:58:05 2017 UTC gpgv: using RSA key gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./cufflinks_2.2.1+dfsg.1-1.dsc dpkg-source: info: extracting cufflinks in cufflinks-2.2.1+dfsg.1 dpkg-source: info: unpacking cufflinks_2.2.1+dfsg.1.orig.tar.gz dpkg-source: info: unpacking cufflinks_2.2.1+dfsg.1-1.debian.tar.xz dpkg-source: info: applying fix_gcc-7_ftbfs.patch dpkg-source: info: applying gffread_show_usage.patch dpkg-source: info: applying 0004-fix-m64-usage-and-lfs.patch dpkg-source: info: applying 0001-fix_spelling.patch dpkg-source: info: applying 0002-bam2samtools.patch dpkg-source: info: applying 0003-fix_includes_path.patch dpkg-source: info: applying format-security.patch dpkg-source: info: applying lib_eigen.patch dpkg-source: info: applying fix_gcc-6.1_issue_in_liblemon_code_copy.patch Check disc space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=4 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=build-PACKAGEBUILD-13634426 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-13634426 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-13634426 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package cufflinks dpkg-buildpackage: info: source version 2.2.1+dfsg.1-1 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build cufflinks-2.2.1+dfsg.1 dpkg-buildpackage: info: host architecture amd64 fakeroot debian/rules clean dh clean --with autoreconf --parallel debian/rules override_dh_auto_clean make[1]: Entering directory '/<>/cufflinks-2.2.1+dfsg.1' dh_auto_clean rm -rf autom4te.cache make[1]: Leaving directory '/<>/cufflinks-2.2.1+dfsg.1' dh_autoreconf_clean -O--parallel dh_clean -O--parallel debian/rules build dh build --with autoreconf --parallel dh_update_autotools_config -O--parallel dh_autoreconf -O--parallel sh: 1: svnversion: not found configure.ac:39: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body ../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from... ../../lib/autoconf/general.m4:2601: _AC_COMPILE_IFELSE is expanded from... ../../lib/autoconf/general.m4:2617: AC_COMPILE_IFELSE is expanded from... ../../lib/m4sugar/m4sh.m4:639: AS_IF is expanded from... ../../lib/autoconf/general.m4:2042: AC_CACHE_VAL is expanded from... ../../lib/autoconf/general.m4:2063: AC_CACHE_CHECK is expanded from... ax_boost_system.m4:33: AX_BOOST_SYSTEM is expanded from... configure.ac:39: the top level configure.ac:40: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body ../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from... ../../lib/autoconf/general.m4:2601: _AC_COMPILE_IFELSE is expanded from... ../../lib/autoconf/general.m4:2617: AC_COMPILE_IFELSE is expanded from... ../../lib/m4sugar/m4sh.m4:639: AS_IF is expanded from... ../../lib/autoconf/general.m4:2042: AC_CACHE_VAL is expanded from... ../../lib/autoconf/general.m4:2063: AC_CACHE_CHECK is expanded from... ax_boost_serialization.m4:33: AX_BOOST_SERIALIZATION is expanded from... configure.ac:40: the top level configure.ac:41: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body ../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from... ../../lib/autoconf/general.m4:2601: _AC_COMPILE_IFELSE is expanded from... ../../lib/autoconf/general.m4:2617: AC_COMPILE_IFELSE is expanded from... ../../lib/m4sugar/m4sh.m4:639: AS_IF is expanded from... ../../lib/autoconf/general.m4:2042: AC_CACHE_VAL is expanded from... ../../lib/autoconf/general.m4:2063: AC_CACHE_CHECK is expanded from... ax_boost_thread.m4:33: AX_BOOST_THREAD is expanded from... configure.ac:41: the top level sh: 1: svnversion: not found configure.ac:39: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body ../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from... ../../lib/autoconf/general.m4:2601: _AC_COMPILE_IFELSE is expanded from... ../../lib/autoconf/general.m4:2617: AC_COMPILE_IFELSE is expanded from... ../../lib/m4sugar/m4sh.m4:639: AS_IF is expanded from... ../../lib/autoconf/general.m4:2042: AC_CACHE_VAL is expanded from... ../../lib/autoconf/general.m4:2063: AC_CACHE_CHECK is expanded from... ax_boost_system.m4:33: AX_BOOST_SYSTEM is expanded from... configure.ac:39: the top level configure.ac:40: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body ../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from... ../../lib/autoconf/general.m4:2601: _AC_COMPILE_IFELSE is expanded from... ../../lib/autoconf/general.m4:2617: AC_COMPILE_IFELSE is expanded from... ../../lib/m4sugar/m4sh.m4:639: AS_IF is expanded from... ../../lib/autoconf/general.m4:2042: AC_CACHE_VAL is expanded from... ../../lib/autoconf/general.m4:2063: AC_CACHE_CHECK is expanded from... ax_boost_serialization.m4:33: AX_BOOST_SERIALIZATION is expanded from... configure.ac:40: the top level configure.ac:41: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body ../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from... ../../lib/autoconf/general.m4:2601: _AC_COMPILE_IFELSE is expanded from... ../../lib/autoconf/general.m4:2617: AC_COMPILE_IFELSE is expanded from... ../../lib/m4sugar/m4sh.m4:639: AS_IF is expanded from... ../../lib/autoconf/general.m4:2042: AC_CACHE_VAL is expanded from... ../../lib/autoconf/general.m4:2063: AC_CACHE_CHECK is expanded from... ax_boost_thread.m4:33: AX_BOOST_THREAD is expanded from... configure.ac:41: the top level sh: 1: svnversion: not found configure.ac:39: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body ../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from... ../../lib/autoconf/general.m4:2601: _AC_COMPILE_IFELSE is expanded from... ../../lib/autoconf/general.m4:2617: AC_COMPILE_IFELSE is expanded from... ../../lib/m4sugar/m4sh.m4:639: AS_IF is expanded from... ../../lib/autoconf/general.m4:2042: AC_CACHE_VAL is expanded from... ../../lib/autoconf/general.m4:2063: AC_CACHE_CHECK is expanded from... ax_boost_system.m4:33: AX_BOOST_SYSTEM is expanded from... configure.ac:39: the top level configure.ac:40: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body ../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from... ../../lib/autoconf/general.m4:2601: _AC_COMPILE_IFELSE is expanded from... ../../lib/autoconf/general.m4:2617: AC_COMPILE_IFELSE is expanded from... ../../lib/m4sugar/m4sh.m4:639: AS_IF is expanded from... ../../lib/autoconf/general.m4:2042: AC_CACHE_VAL is expanded from... ../../lib/autoconf/general.m4:2063: AC_CACHE_CHECK is expanded from... ax_boost_serialization.m4:33: AX_BOOST_SERIALIZATION is expanded from... configure.ac:40: the top level configure.ac:41: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body ../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from... ../../lib/autoconf/general.m4:2601: _AC_COMPILE_IFELSE is expanded from... ../../lib/autoconf/general.m4:2617: AC_COMPILE_IFELSE is expanded from... ../../lib/m4sugar/m4sh.m4:639: AS_IF is expanded from... ../../lib/autoconf/general.m4:2042: AC_CACHE_VAL is expanded from... ../../lib/autoconf/general.m4:2063: AC_CACHE_CHECK is expanded from... ax_boost_thread.m4:33: AX_BOOST_THREAD is expanded from... configure.ac:41: the top level sh: 1: svnversion: not found configure.ac:39: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body ../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from... ../../lib/autoconf/general.m4:2601: _AC_COMPILE_IFELSE is expanded from... ../../lib/autoconf/general.m4:2617: AC_COMPILE_IFELSE is expanded from... ../../lib/m4sugar/m4sh.m4:639: AS_IF is expanded from... ../../lib/autoconf/general.m4:2042: AC_CACHE_VAL is expanded from... ../../lib/autoconf/general.m4:2063: AC_CACHE_CHECK is expanded from... ax_boost_system.m4:33: AX_BOOST_SYSTEM is expanded from... configure.ac:39: the top level configure.ac:40: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body ../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from... ../../lib/autoconf/general.m4:2601: _AC_COMPILE_IFELSE is expanded from... ../../lib/autoconf/general.m4:2617: AC_COMPILE_IFELSE is expanded from... ../../lib/m4sugar/m4sh.m4:639: AS_IF is expanded from... ../../lib/autoconf/general.m4:2042: AC_CACHE_VAL is expanded from... ../../lib/autoconf/general.m4:2063: AC_CACHE_CHECK is expanded from... ax_boost_serialization.m4:33: AX_BOOST_SERIALIZATION is expanded from... configure.ac:40: the top level configure.ac:41: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body ../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from... ../../lib/autoconf/general.m4:2601: _AC_COMPILE_IFELSE is expanded from... ../../lib/autoconf/general.m4:2617: AC_COMPILE_IFELSE is expanded from... ../../lib/m4sugar/m4sh.m4:639: AS_IF is expanded from... ../../lib/autoconf/general.m4:2042: AC_CACHE_VAL is expanded from... ../../lib/autoconf/general.m4:2063: AC_CACHE_CHECK is expanded from... ax_boost_thread.m4:33: AX_BOOST_THREAD is expanded from... configure.ac:41: the top level sh: 1: svnversion: not found configure.ac:39: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body ../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from... ../../lib/autoconf/general.m4:2601: _AC_COMPILE_IFELSE is expanded from... ../../lib/autoconf/general.m4:2617: AC_COMPILE_IFELSE is expanded from... ../../lib/m4sugar/m4sh.m4:639: AS_IF is expanded from... ../../lib/autoconf/general.m4:2042: AC_CACHE_VAL is expanded from... ../../lib/autoconf/general.m4:2063: AC_CACHE_CHECK is expanded from... ax_boost_system.m4:33: AX_BOOST_SYSTEM is expanded from... configure.ac:39: the top level configure.ac:40: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body ../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from... ../../lib/autoconf/general.m4:2601: _AC_COMPILE_IFELSE is expanded from... ../../lib/autoconf/general.m4:2617: AC_COMPILE_IFELSE is expanded from... ../../lib/m4sugar/m4sh.m4:639: AS_IF is expanded from... ../../lib/autoconf/general.m4:2042: AC_CACHE_VAL is expanded from... ../../lib/autoconf/general.m4:2063: AC_CACHE_CHECK is expanded from... ax_boost_serialization.m4:33: AX_BOOST_SERIALIZATION is expanded from... configure.ac:40: the top level configure.ac:41: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body ../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from... ../../lib/autoconf/general.m4:2601: _AC_COMPILE_IFELSE is expanded from... ../../lib/autoconf/general.m4:2617: AC_COMPILE_IFELSE is expanded from... ../../lib/m4sugar/m4sh.m4:639: AS_IF is expanded from... ../../lib/autoconf/general.m4:2042: AC_CACHE_VAL is expanded from... ../../lib/autoconf/general.m4:2063: AC_CACHE_CHECK is expanded from... ax_boost_thread.m4:33: AX_BOOST_THREAD is expanded from... configure.ac:41: the top level configure.ac:35: installing 'build-aux/ar-lib' configure.ac:31: installing 'build-aux/compile' configure.ac:39: installing 'build-aux/config.guess' configure.ac:39: installing 'build-aux/config.sub' configure.ac:16: installing 'build-aux/install-sh' configure.ac:16: installing 'build-aux/missing' src/Makefile.am:113: warning: source file 'locfit/adap.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled automake: warning: possible forward-incompatibility. automake: At least a source file is in a subdirectory, but the 'subdir-objects' automake: automake option hasn't been enabled. For now, the corresponding output automake: object file(s) will be placed in the top-level directory. However, automake: this behaviour will change in future Automake versions: they will automake: unconditionally cause object files to be placed in the same subdirectory automake: of the corresponding sources. automake: You are advised to start using 'subdir-objects' option throughout your automake: project, to avoid future incompatibilities. src/Makefile.am:113: warning: source file 'locfit/ar_funs.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/arith.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/band.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/c_args.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/c_plot.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/cmd.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/dens_haz.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/dens_int.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/dens_odi.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/density.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/dist.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/ev_atree.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/ev_interp.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/ev_kdtre.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/ev_main.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/ev_trian.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/family.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/fitted.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/frend.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/help.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/lf_dercor.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/lf_fitfun.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/lf_robust.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/lf_vari.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/lfd.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/lfstr.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/linalg.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/locfit.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/m_chol.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/m_eigen.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/m_jacob.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/m_max.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/makecmd.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/math.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/minmax.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/nbhd.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/pcomp.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/pout.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/preplot.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/random.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/readfile.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/scb.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/scb_cons.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/simul.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/solve.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/startlf.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/strings.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/vari.cpp' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/wdiag.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/weight.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am: installing 'build-aux/depcomp' debian/rules override_dh_auto_configure make[1]: Entering directory '/<>/cufflinks-2.2.1+dfsg.1' dh_auto_configure -- LIBS="-lboost_system -lboost_thread -lboost_serialization" ./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --libexecdir=\${prefix}/lib/x86_64-linux-gnu --disable-maintainer-mode --disable-dependency-tracking "LIBS=-lboost_system -lboost_thread -lboost_serialization" configure: WARNING: unrecognized options: --disable-maintainer-mode checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking for gawk... (cached) mawk checking for g++... g++ checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking for style of include used by make... GNU checking dependency style of g++... none checking for gcc... gcc checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... none checking whether make sets $(MAKE)... (cached) yes checking for ranlib... ranlib checking for ar... ar checking the archiver (ar) interface... ar checking for a Python interpreter with version >= 2.4... python checking for python... /usr/bin/python checking for python version... 2.7 checking for python platform... linux2 checking for python script directory... ${prefix}/lib/python2.7/dist-packages checking for python extension module directory... ${exec_prefix}/lib/python2.7/dist-packages checking for boostlib >= 1.47.0... yes checking for bamlib... yes checking build system type... x86_64-pc-linux-gnu checking whether the Boost::System library is available... yes checking whether the Boost::Serialization library is available... yes checking whether the Boost::Thread library is available... yes checking how to run the C preprocessor... gcc -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking if zlib is wanted... yes checking for inflateEnd in -lz... yes checking zlib.h usability... yes checking zlib.h presence... yes checking for zlib.h... yes checking for inflateEnd in -lz... (cached) yes checking zlib in /usr... ok checking for eigenlib... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for unistd.h... (cached) yes checking for stdbool.h that conforms to C99... yes checking for _Bool... yes checking for inline... inline checking for pid_t... yes checking for size_t... yes checking for ptrdiff_t... yes checking host system type... x86_64-pc-linux-gnu checking for struct sysinfo.totalram... yes checking whether sysctl is declared... yes checking whether CTL_HW is declared... no checking whether HW_PHYSMEM is declared... no checking how to create a pax tar archive... gnutar checking dependency style of gcc... (cached) none checking dependency style of g++... (cached) none checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating config.h config.status: executing depfiles commands configure: WARNING: unrecognized options: --disable-maintainer-mode -- cufflinks 2.2.1 Configuration Results -- C++ compiler: g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -g -O2 -fdebug-prefix-map=/<>/cufflinks-2.2.1+dfsg.1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now GCC version: gcc (Ubuntu 7.2.0-12ubuntu1) 7.2.0 Host System type: x86_64-pc-linux-gnu Install prefix: /usr Install eprefix: ${prefix} See config.h for further configuration information. Email with questions and bug reports. make[1]: Leaving directory '/<>/cufflinks-2.2.1+dfsg.1' dh_auto_build -O--parallel make -j4 make[1]: Entering directory '/<>/cufflinks-2.2.1+dfsg.1' make all-recursive make[2]: Entering directory '/<>/cufflinks-2.2.1+dfsg.1' Making all in src make[3]: Entering directory '/<>/cufflinks-2.2.1+dfsg.1/src' g++ -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -g -O2 -fdebug-prefix-map=/<>/cufflinks-2.2.1+dfsg.1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o clustering.o clustering.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -g -O2 -fdebug-prefix-map=/<>/cufflinks-2.2.1+dfsg.1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o differential.o differential.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -g -O2 -fdebug-prefix-map=/<>/cufflinks-2.2.1+dfsg.1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o common.o common.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -g -O2 -fdebug-prefix-map=/<>/cufflinks-2.2.1+dfsg.1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o assemble.o assemble.cpp In file included from abundances.h:26:0, from differential.cpp:20: biascorrection.h:18:10: fatal error: boost/tr1/unordered_map.hpp: No such file or directory #include ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ compilation terminated. Makefile:1627: recipe for target 'differential.o' failed make[3]: *** [differential.o] Error 1 make[3]: *** Waiting for unfinished jobs.... In file included from abundances.h:26:0, from clustering.h:38, from clustering.cpp:10: biascorrection.h:18:10: fatal error: boost/tr1/unordered_map.hpp: No such file or directory #include ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ compilation terminated. Makefile:1627: recipe for target 'clustering.o' failed make[3]: *** [clustering.o] Error 1 In file included from abundances.h:26:0, from clustering.h:38, from assemble.cpp:54: biascorrection.h:18:10: fatal error: boost/tr1/unordered_map.hpp: No such file or directory #include ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ compilation terminated. Makefile:1627: recipe for target 'assemble.o' failed make[3]: *** [assemble.o] Error 1 In file included from bundles.h:20:0, from replicates.h:10, from common.cpp:28: hits.h: In constructor ‘PrecomputedExpressionHitFactory::PrecomputedExpressionHitFactory(const string&, ReadTable&, RefSequenceTable&)’: hits.h:928:12: warning: ‘PrecomputedExpressionHitFactory::_expression_file_name’ will be initialized after [-Wreorder] string _expression_file_name; ^~~~~~~~~~~~~~~~~~~~~ hits.h:927:19: warning: ‘std::ifstream PrecomputedExpressionHitFactory::_ifs’ [-Wreorder] std::ifstream _ifs; ^~~~ In file included from bundles.h:20:0, from replicates.h:10, from common.cpp:28: hits.h:814:5: warning: when initialized here [-Wreorder] PrecomputedExpressionHitFactory(const string& expression_file_name, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from common.cpp:28:0: replicates.h: In member function ‘bool ReplicatedBundleFactory::next_bundle(HitBundle&, bool)’: replicates.h:224:57: warning: unused variable ‘s2’ [-Wunused-variable] const vector >& s2 = bundles[i-1]->ref_scaffolds(); ^~ make[3]: Leaving directory '/<>/cufflinks-2.2.1+dfsg.1/src' Makefile:400: recipe for target 'all-recursive' failed make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory '/<>/cufflinks-2.2.1+dfsg.1' Makefile:341: recipe for target 'all' failed make[1]: *** [all] Error 2 make[1]: Leaving directory '/<>/cufflinks-2.2.1+dfsg.1' dh_auto_build: make -j4 returned exit code 2 debian/rules:10: recipe for target 'build' failed make: *** [build] Error 2 dpkg-buildpackage: error: debian/rules build subprocess returned exit status 2 -------------------------------------------------------------------------------- Build finished at 20171027-2342 Finished -------- E: Build failure (dpkg-buildpackage died) +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build-Space: 9600 Build-Time: 27 Distribution: bionic-proposed Fail-Stage: build Host Architecture: amd64 Install-Time: 16 Job: cufflinks_2.2.1+dfsg.1-1.dsc Machine Architecture: amd64 Package: cufflinks Package-Time: 43 Source-Version: 2.2.1+dfsg.1-1 Space: 9600 Status: attempted Version: 2.2.1+dfsg.1-1 -------------------------------------------------------------------------------- Finished at 20171027-2342 Build needed 00:00:43, 9600k disc space RUN: /usr/share/launchpad-buildd/slavebin/in-target scan-for-processes --backend=chroot --series=bionic --arch=amd64 PACKAGEBUILD-13634426 Scanning for processes to kill in build PACKAGEBUILD-13634426 RUN: /usr/share/launchpad-buildd/slavebin/in-target umount-chroot --backend=chroot --series=bionic --arch=amd64 PACKAGEBUILD-13634426 Stopping target for build PACKAGEBUILD-13634426 RUN: /usr/share/launchpad-buildd/slavebin/in-target remove-build --backend=chroot --series=bionic --arch=amd64 PACKAGEBUILD-13634426 Removing build PACKAGEBUILD-13634426