https://launchpad.net/ubuntu/+source/dssp/3.0.0-3/+build/15626811 RUN: /usr/share/launchpad-buildd/slavebin/slave-prep Forking launchpad-buildd slave process... Kernel version: Linux bos02-arm64-009 4.4.0-138-generic #164-Ubuntu SMP Tue Oct 2 17:15:48 UTC 2018 aarch64 Buildd toolchain package versions: launchpad-buildd_165 python-lpbuildd_165 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_1:2.7.4-0ubuntu1.5 dpkg-dev_1.18.4ubuntu1.5 python-debian_0.1.27ubuntu2. Syncing the system clock with the buildd NTP service... 9 Nov 10:59:28 ntpdate[1832]: adjust time server 10.211.37.1 offset 0.038478 sec RUN: /usr/share/launchpad-buildd/slavebin/in-target unpack-chroot --backend=chroot --series=disco --arch=armhf PACKAGEBUILD-15626811 /home/buildd/filecache-default/c94e68d26d8f9980ef1477bde7a83b553e812c5f Creating target for build PACKAGEBUILD-15626811 RUN: /usr/share/launchpad-buildd/slavebin/in-target mount-chroot --backend=chroot --series=disco --arch=armhf PACKAGEBUILD-15626811 Starting target for build PACKAGEBUILD-15626811 RUN: /usr/share/launchpad-buildd/slavebin/in-target override-sources-list --backend=chroot --series=disco --arch=armhf PACKAGEBUILD-15626811 'deb http://ftpmaster.internal/ubuntu disco main universe' 'deb http://ftpmaster.internal/ubuntu disco-security main universe' 'deb http://ftpmaster.internal/ubuntu disco-updates main universe' 'deb http://ftpmaster.internal/ubuntu disco-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-15626811 RUN: /usr/share/launchpad-buildd/slavebin/in-target update-debian-chroot --backend=chroot --series=disco --arch=armhf PACKAGEBUILD-15626811 Updating target for build PACKAGEBUILD-15626811 Get:1 http://ftpmaster.internal/ubuntu disco InRelease [243 kB] Get:2 http://ftpmaster.internal/ubuntu disco-security InRelease [65.4 kB] Get:3 http://ftpmaster.internal/ubuntu disco-updates InRelease [65.4 kB] Get:4 http://ftpmaster.internal/ubuntu disco-proposed InRelease [93.2 kB] Get:5 http://ftpmaster.internal/ubuntu disco/main armhf Packages [968 kB] Get:6 http://ftpmaster.internal/ubuntu disco/main Translation-en [513 kB] Get:7 http://ftpmaster.internal/ubuntu disco/universe armhf Packages [8427 kB] Get:8 http://ftpmaster.internal/ubuntu disco/universe Translation-en [5037 kB] Get:9 http://ftpmaster.internal/ubuntu disco-proposed/main armhf Packages [116 kB] Get:10 http://ftpmaster.internal/ubuntu disco-proposed/main Translation-en [75.6 kB] Get:11 http://ftpmaster.internal/ubuntu disco-proposed/universe armhf Packages [311 kB] Get:12 http://ftpmaster.internal/ubuntu disco-proposed/universe Translation-en [286 kB] Fetched 16.2 MB in 7s (2284 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: libgdbm5 libperl5.26 perl-modules-5.26 Use 'sudo apt autoremove' to remove them. The following NEW packages will be installed: libgdbm6 libperl5.28 perl-modules-5.28 The following packages will be upgraded: base-files binutils binutils-arm-linux-gnueabihf binutils-common cpp cpp-8 dash dmsetup findutils g++ g++-8 gcc gcc-8 gcc-8-base hostname init init-system-helpers libapparmor1 libasan5 libatomic1 libaudit-common libaudit1 libbinutils libcap-ng0 libcc1-0 libdb5.3 libdevmapper1.02.1 libgcc-8-dev libgcc1 libgdbm-compat4 libgomp1 libgpg-error0 libkmod2 libseccomp2 libselinux1 libsemanage-common libsemanage1 libsqlite3-0 libstdc++-8-dev libstdc++6 libsystemd0 libubsan1 libudev1 linux-libc-dev lockfile-progs perl perl-base sed systemd systemd-sysv tzdata 51 upgraded, 3 newly installed, 0 to remove and 0 not upgraded. Need to get 38.4 MB of archives. After this operation, 40.7 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu disco/main armhf base-files armhf 10.1ubuntu8 [59.8 kB] Get:2 http://ftpmaster.internal/ubuntu disco-proposed/main armhf dash armhf 0.5.10.2-1 [81.2 kB] Get:3 http://ftpmaster.internal/ubuntu disco-proposed/main armhf findutils armhf 4.6.0+git+20181018-1 [279 kB] Get:4 http://ftpmaster.internal/ubuntu disco/main armhf hostname armhf 3.21 [10.3 kB] Get:5 http://ftpmaster.internal/ubuntu disco/main armhf perl-modules-5.28 all 5.28.0-3 [2818 kB] Get:6 http://ftpmaster.internal/ubuntu disco/main armhf libgdbm6 armhf 1.18.1-1 [24.8 kB] Get:7 http://ftpmaster.internal/ubuntu disco/main armhf libgdbm-compat4 armhf 1.18.1-1 [5784 B] Get:8 http://ftpmaster.internal/ubuntu disco/main armhf libperl5.28 armhf 5.28.0-3 [3153 kB] Get:9 http://ftpmaster.internal/ubuntu disco/main armhf perl armhf 5.28.0-3 [204 kB] Get:10 http://ftpmaster.internal/ubuntu disco/main armhf perl-base armhf 5.28.0-3 [1397 kB] Get:11 http://ftpmaster.internal/ubuntu disco-proposed/main armhf libdb5.3 armhf 5.3.28+dfsg1-0.2 [590 kB] Get:12 http://ftpmaster.internal/ubuntu disco-proposed/main armhf sed armhf 4.5-2 [178 kB] Get:13 http://ftpmaster.internal/ubuntu disco-proposed/main armhf init-system-helpers all 1.55 [38.5 kB] Get:14 http://ftpmaster.internal/ubuntu disco-proposed/main armhf systemd-sysv armhf 239-7ubuntu10.1 [9404 B] Get:15 http://ftpmaster.internal/ubuntu disco/main armhf libapparmor1 armhf 2.12-4ubuntu10 [25.7 kB] Get:16 http://ftpmaster.internal/ubuntu disco/main armhf libaudit-common all 1:2.8.3-1ubuntu3 [4068 B] Get:17 http://ftpmaster.internal/ubuntu disco/main armhf libcap-ng0 armhf 0.7.9-1build1 [9600 B] Get:18 http://ftpmaster.internal/ubuntu disco/main armhf libaudit1 armhf 1:2.8.3-1ubuntu3 [35.5 kB] Get:19 http://ftpmaster.internal/ubuntu disco-proposed/main armhf libgpg-error0 armhf 1.32-3 [48.1 kB] Get:20 http://ftpmaster.internal/ubuntu disco-proposed/main armhf libkmod2 armhf 25-1ubuntu1.1 [35.7 kB] Get:21 http://ftpmaster.internal/ubuntu disco-proposed/main armhf systemd armhf 239-7ubuntu10.1 [2804 kB] Get:22 http://ftpmaster.internal/ubuntu disco-proposed/main armhf libsystemd0 armhf 239-7ubuntu10.1 [191 kB] Get:23 http://ftpmaster.internal/ubuntu disco-proposed/main armhf init armhf 1.55 [6476 B] Get:24 http://ftpmaster.internal/ubuntu disco/main armhf libcc1-0 armhf 8.2.0-9ubuntu1 [32.5 kB] Get:25 http://ftpmaster.internal/ubuntu disco/main armhf libgomp1 armhf 8.2.0-9ubuntu1 [66.6 kB] Get:26 http://ftpmaster.internal/ubuntu disco/main armhf libatomic1 armhf 8.2.0-9ubuntu1 [7068 B] Get:27 http://ftpmaster.internal/ubuntu disco/main armhf libasan5 armhf 8.2.0-9ubuntu1 [349 kB] Get:28 http://ftpmaster.internal/ubuntu disco/main armhf libubsan1 armhf 8.2.0-9ubuntu1 [109 kB] Get:29 http://ftpmaster.internal/ubuntu disco/main armhf gcc-8-base armhf 8.2.0-9ubuntu1 [18.6 kB] Get:30 http://ftpmaster.internal/ubuntu disco/main armhf libstdc++6 armhf 8.2.0-9ubuntu1 [350 kB] Get:31 http://ftpmaster.internal/ubuntu disco/main armhf g++-8 armhf 8.2.0-9ubuntu1 [6431 kB] Get:32 http://ftpmaster.internal/ubuntu disco/main armhf libstdc++-8-dev armhf 8.2.0-9ubuntu1 [1594 kB] Get:33 http://ftpmaster.internal/ubuntu disco/main armhf libgcc-8-dev armhf 8.2.0-9ubuntu1 [632 kB] Get:34 http://ftpmaster.internal/ubuntu disco/main armhf gcc-8 armhf 8.2.0-9ubuntu1 [6349 kB] Get:35 http://ftpmaster.internal/ubuntu disco/main armhf cpp-8 armhf 8.2.0-9ubuntu1 [5643 kB] Get:36 http://ftpmaster.internal/ubuntu disco/main armhf libgcc1 armhf 1:8.2.0-9ubuntu1 [37.1 kB] Get:37 http://ftpmaster.internal/ubuntu disco/main armhf libbinutils armhf 2.31.1-7ubuntu1 [309 kB] Get:38 http://ftpmaster.internal/ubuntu disco/main armhf binutils-common armhf 2.31.1-7ubuntu1 [194 kB] Get:39 http://ftpmaster.internal/ubuntu disco/main armhf binutils armhf 2.31.1-7ubuntu1 [3360 B] Get:40 http://ftpmaster.internal/ubuntu disco/main armhf binutils-arm-linux-gnueabihf armhf 2.31.1-7ubuntu1 [2144 kB] Get:41 http://ftpmaster.internal/ubuntu disco/main armhf libselinux1 armhf 2.8-1build2 [59.1 kB] Get:42 http://ftpmaster.internal/ubuntu disco/main armhf libsemanage-common all 2.8-1build2 [6892 B] Get:43 http://ftpmaster.internal/ubuntu disco/main armhf libsemanage1 armhf 2.8-1build2 [72.5 kB] Get:44 http://ftpmaster.internal/ubuntu disco-proposed/main armhf libudev1 armhf 239-7ubuntu10.1 [48.3 kB] Get:45 http://ftpmaster.internal/ubuntu disco-proposed/main armhf libseccomp2 armhf 2.3.3-3ubuntu2 [30.5 kB] Get:46 http://ftpmaster.internal/ubuntu disco-proposed/main armhf libdevmapper1.02.1 armhf 2:1.02.145-4.1ubuntu4 [118 kB] Get:47 http://ftpmaster.internal/ubuntu disco-proposed/main armhf dmsetup armhf 2:1.02.145-4.1ubuntu4 [73.6 kB] Get:48 http://ftpmaster.internal/ubuntu disco-proposed/main armhf libsqlite3-0 armhf 3.25.3-1 [447 kB] Get:49 http://ftpmaster.internal/ubuntu disco/main armhf tzdata all 2018g-1 [188 kB] Get:50 http://ftpmaster.internal/ubuntu disco/main armhf g++ armhf 4:8.2.0-2ubuntu2 [1616 B] Get:51 http://ftpmaster.internal/ubuntu disco/main armhf gcc armhf 4:8.2.0-2ubuntu2 [5236 B] Get:52 http://ftpmaster.internal/ubuntu disco/main armhf cpp armhf 4:8.2.0-2ubuntu2 [27.6 kB] Get:53 http://ftpmaster.internal/ubuntu disco-proposed/main armhf linux-libc-dev armhf 4.18.0-11.12 [1022 kB] Get:54 http://ftpmaster.internal/ubuntu disco/main armhf lockfile-progs armhf 0.1.18 [9372 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 38.4 MB in 3s (12.8 MB/s) (Reading database ... 12387 files and directories currently installed.) Preparing to unpack .../base-files_10.1ubuntu8_armhf.deb ... Unpacking base-files (10.1ubuntu8) over (10.1ubuntu7) ... Setting up base-files (10.1ubuntu8) ... Installing new version of config file /etc/issue ... Installing new version of config file /etc/issue.net ... Installing new version of config file /etc/lsb-release ... (Reading database ... 12387 files and directories currently installed.) Preparing to unpack .../dash_0.5.10.2-1_armhf.deb ... Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by bash' Unpacking dash (0.5.10.2-1) over (0.5.8-2.10) ... Setting up dash (0.5.10.2-1) ... Removing 'diversion of /bin/sh to /bin/sh.distrib by bash' Adding 'diversion of /bin/sh to /bin/sh.distrib by dash' Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by bash' Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' (Reading database ... 12387 files and directories currently installed.) Preparing to unpack .../findutils_4.6.0+git+20181018-1_armhf.deb ... Unpacking findutils (4.6.0+git+20181018-1) over (4.6.0+git+20180808-2) ... Setting up findutils (4.6.0+git+20181018-1) ... (Reading database ... 12387 files and directories currently installed.) Preparing to unpack .../hostname_3.21_armhf.deb ... Unpacking hostname (3.21) over (3.20) ... Setting up hostname (3.21) ... (Reading database ... 12387 files and directories currently installed.) Preparing to unpack .../0-perl_5.28.0-3_armhf.deb ... Unpacking perl (5.28.0-3) over (5.26.2-7) ... 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Preparing to unpack .../2-libsqlite3-0_3.25.3-1_armhf.deb ... Unpacking libsqlite3-0:armhf (3.25.3-1) over (3.24.0-1) ... Preparing to unpack .../3-tzdata_2018g-1_all.deb ... Unpacking tzdata (2018g-1) over (2018e-1) ... Preparing to unpack .../4-g++_4%3a8.2.0-2ubuntu2_armhf.deb ... Unpacking g++ (4:8.2.0-2ubuntu2) over (4:8.2.0-1ubuntu1) ... Preparing to unpack .../5-gcc_4%3a8.2.0-2ubuntu2_armhf.deb ... Unpacking gcc (4:8.2.0-2ubuntu2) over (4:8.2.0-1ubuntu1) ... Preparing to unpack .../6-cpp_4%3a8.2.0-2ubuntu2_armhf.deb ... Unpacking cpp (4:8.2.0-2ubuntu2) over (4:8.2.0-1ubuntu1) ... Preparing to unpack .../7-linux-libc-dev_4.18.0-11.12_armhf.deb ... Unpacking linux-libc-dev:armhf (4.18.0-11.12) over (4.18.0-10.11) ... Preparing to unpack .../8-lockfile-progs_0.1.18_armhf.deb ... Unpacking lockfile-progs (0.1.18) over (0.1.17build1) ... Setting up cpp-8 (8.2.0-9ubuntu1) ... Setting up libgomp1:armhf (8.2.0-9ubuntu1) ... Setting up libatomic1:armhf (8.2.0-9ubuntu1) ... Setting up cpp (4:8.2.0-2ubuntu2) ... Setting up libcc1-0:armhf (8.2.0-9ubuntu1) ... Setting up tzdata (2018g-1) ... Current default time zone: 'Etc/UTC' Local time is now: Fri Nov 9 11:00:12 UTC 2018. Universal Time is now: Fri Nov 9 11:00:12 UTC 2018. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up init (1.55) ... Setting up linux-libc-dev:armhf (4.18.0-11.12) ... Setting up libdevmapper1.02.1:armhf (2:1.02.145-4.1ubuntu4) ... Setting up libgdbm6:armhf (1.18.1-1) ... Setting up binutils-common:armhf (2.31.1-7ubuntu1) ... Setting up perl-modules-5.28 (5.28.0-3) ... Processing triggers for libc-bin (2.28-0ubuntu1) ... Setting up libsqlite3-0:armhf (3.25.3-1) ... Setting up dmsetup (2:1.02.145-4.1ubuntu4) ... Setting up libgdbm-compat4:armhf (1.18.1-1) ... Setting up lockfile-progs (0.1.18) ... Setting up libasan5:armhf (8.2.0-9ubuntu1) ... Setting up libubsan1:armhf (8.2.0-9ubuntu1) ... Setting up libbinutils:armhf (2.31.1-7ubuntu1) ... Setting up libperl5.28:armhf (5.28.0-3) ... Setting up binutils-arm-linux-gnueabihf (2.31.1-7ubuntu1) ... Setting up perl (5.28.0-3) ... Setting up libgcc-8-dev:armhf (8.2.0-9ubuntu1) ... Setting up binutils (2.31.1-7ubuntu1) ... Setting up libstdc++-8-dev:armhf (8.2.0-9ubuntu1) ... Setting up gcc-8 (8.2.0-9ubuntu1) ... Setting up g++-8 (8.2.0-9ubuntu1) ... Setting up gcc (4:8.2.0-2ubuntu2) ... Setting up g++ (4:8.2.0-2ubuntu2) ... Processing triggers for libc-bin (2.28-0ubuntu1) ... RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package PACKAGEBUILD-15626811 armhf disco-proposed -c chroot:build-PACKAGEBUILD-15626811 --arch=armhf --dist=disco-proposed --nolog dssp_3.0.0-3.dsc Initiating build PACKAGEBUILD-15626811 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.4.0-138-generic #164-Ubuntu SMP Tue Oct 2 17:15:48 UTC 2018 armv7l sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on bos02-arm64-009.buildd +==============================================================================+ | dssp 3.0.0-3 (armhf) 09 Nov 2018 11:00 | +==============================================================================+ Package: dssp Version: 3.0.0-3 Source Version: 3.0.0-3 Distribution: disco-proposed Machine Architecture: arm64 Host Architecture: armhf Build Architecture: armhf I: NOTICE: Log filtering will replace 'build/dssp-tooEWJ/dssp-3.0.0' with '<>' I: NOTICE: Log filtering will replace 'build/dssp-tooEWJ' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-15626811/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- dssp_3.0.0-3.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-5pU4IN/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/<>/resolver-5pU4IN/apt_archive ./ InRelease Get:2 copy:/<>/resolver-5pU4IN/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-5pU4IN/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-5pU4IN/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-5pU4IN/apt_archive ./ Packages [528 B] Fetched 2861 B in 0s (123 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: libgdbm5 libperl5.26 perl-modules-5.26 Use 'apt autoremove' to remove them. The following NEW packages will be installed: sbuild-build-depends-core-dummy 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 852 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-5pU4IN/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 ... 14274 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... Merged Build-Depends: debhelper (>= 11~), libboost-filesystem-dev, libboost-iostreams-dev, libboost-program-options-dev, libboost-system-dev, libboost-thread-dev Filtered Build-Depends: debhelper (>= 11~), libboost-filesystem-dev, libboost-iostreams-dev, libboost-program-options-dev, libboost-system-dev, libboost-thread-dev dpkg-deb: building package 'sbuild-build-depends-dssp-dummy' in '/<>/resolver-NXdHBL/apt_archive/sbuild-build-depends-dssp-dummy.deb'. Ign:1 copy:/<>/resolver-NXdHBL/apt_archive ./ InRelease Get:2 copy:/<>/resolver-NXdHBL/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-NXdHBL/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-NXdHBL/apt_archive ./ Sources [255 B] Get:5 copy:/<>/resolver-NXdHBL/apt_archive ./ Packages [574 B] Fetched 2948 B in 0s (128 kB/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install dssp 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: libgdbm5 libperl5.26 perl-modules-5.26 Use 'apt autoremove' to remove them. The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base gir1.2-glib-2.0 gir1.2-harfbuzz-0.0 groff-base icu-devtools intltool-debian libarchive-zip-perl libboost-atomic1.67-dev libboost-atomic1.67.0 libboost-chrono1.67-dev libboost-chrono1.67.0 libboost-date-time1.67-dev libboost-date-time1.67.0 libboost-filesystem-dev libboost-filesystem1.67-dev libboost-filesystem1.67.0 libboost-iostreams-dev libboost-iostreams1.67-dev libboost-iostreams1.67.0 libboost-program-options-dev libboost-program-options1.67-dev libboost-program-options1.67.0 libboost-regex1.67-dev libboost-regex1.67.0 libboost-serialization1.67-dev libboost-serialization1.67.0 libboost-system-dev libboost-system1.67-dev libboost-system1.67.0 libboost-thread-dev libboost-thread1.67-dev libboost-thread1.67.0 libboost1.67-dev libbsd0 libcroco3 libelf1 libexpat1 libfile-stripnondeterminism-perl libfreetype6 libgirepository-1.0-1 libglib2.0-0 libglib2.0-bin libglib2.0-data libglib2.0-dev libglib2.0-dev-bin libgraphite2-3 libgraphite2-dev libharfbuzz-dev libharfbuzz-gobject0 libharfbuzz-icu0 libharfbuzz0b libicu-dev libicu-le-hb-dev libicu-le-hb0 libicu60 libiculx60 libmagic-mgc libmagic1 libmpdec2 libpcre16-3 libpcre3-dev libpcre32-3 libpcrecpp0v5 libpipeline1 libpython3-stdlib libpython3.7-minimal libpython3.7-stdlib libsigsegv2 libtool libxml2 m4 man-db mime-support pkg-config po-debconf python3 python3-distutils python3-lib2to3 python3-minimal python3.7 python3.7-minimal zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois vacation dh-make gettext-doc libasprintf-dev libgettextpo-dev groff libboost1.67-doc libboost-container1.67-dev libboost-context1.67-dev libboost-coroutine1.67-dev libboost-exception1.67-dev libboost-fiber1.67-dev libboost-graph1.67-dev libboost-graph-parallel1.67-dev libboost-locale1.67-dev libboost-log1.67-dev libboost-math1.67-dev libboost-mpi1.67-dev libboost-mpi-python1.67-dev libboost-numpy1.67-dev libboost-python1.67-dev libboost-random1.67-dev libboost-signals1.67-dev libboost-stacktrace1.67-dev libboost-test1.67-dev libboost-timer1.67-dev libboost-type-erasure1.67-dev libboost-wave1.67-dev libboost1.67-tools-dev libmpfrc++-dev libntl-dev libglib2.0-doc libgdk-pixbuf2.0-bin | libgdk-pixbuf2.0-dev libxml2-utils libgraphite2-utils icu-doc libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl python3-doc python3-tk python3-venv python3.7-venv python3.7-doc binfmt-support Recommended packages: curl | wget | lynx libarchive-cpio-perl shared-mime-info xdg-user-dirs libltdl-dev libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base gir1.2-glib-2.0 gir1.2-harfbuzz-0.0 groff-base icu-devtools intltool-debian libarchive-zip-perl libboost-atomic1.67-dev libboost-atomic1.67.0 libboost-chrono1.67-dev libboost-chrono1.67.0 libboost-date-time1.67-dev libboost-date-time1.67.0 libboost-filesystem-dev libboost-filesystem1.67-dev libboost-filesystem1.67.0 libboost-iostreams-dev libboost-iostreams1.67-dev libboost-iostreams1.67.0 libboost-program-options-dev libboost-program-options1.67-dev libboost-program-options1.67.0 libboost-regex1.67-dev libboost-regex1.67.0 libboost-serialization1.67-dev libboost-serialization1.67.0 libboost-system-dev libboost-system1.67-dev libboost-system1.67.0 libboost-thread-dev libboost-thread1.67-dev libboost-thread1.67.0 libboost1.67-dev libbsd0 libcroco3 libelf1 libexpat1 libfile-stripnondeterminism-perl libfreetype6 libgirepository-1.0-1 libglib2.0-0 libglib2.0-bin libglib2.0-data libglib2.0-dev libglib2.0-dev-bin libgraphite2-3 libgraphite2-dev libharfbuzz-dev libharfbuzz-gobject0 libharfbuzz-icu0 libharfbuzz0b libicu-dev libicu-le-hb-dev libicu-le-hb0 libicu60 libiculx60 libmagic-mgc libmagic1 libmpdec2 libpcre16-3 libpcre3-dev libpcre32-3 libpcrecpp0v5 libpipeline1 libpython3-stdlib libpython3.7-minimal libpython3.7-stdlib libsigsegv2 libtool libxml2 m4 man-db mime-support pkg-config po-debconf python3 python3-distutils python3-lib2to3 python3-minimal python3.7 python3.7-minimal sbuild-build-depends-dssp-dummy zlib1g-dev 0 upgraded, 94 newly installed, 0 to remove and 0 not upgraded. Need to get 46.4 MB of archives. After this operation, 314 MB of additional disk space will be used. Get:1 copy:/<>/resolver-NXdHBL/apt_archive ./ sbuild-build-depends-dssp-dummy 0.invalid.0 [900 B] Get:2 http://ftpmaster.internal/ubuntu disco/main armhf libpython3.7-minimal armhf 3.7.1-1 [537 kB] Get:3 http://ftpmaster.internal/ubuntu disco/main armhf libexpat1 armhf 2.2.6-1 [60.1 kB] Get:4 http://ftpmaster.internal/ubuntu disco/main armhf python3.7-minimal armhf 3.7.1-1 [1410 kB] Get:5 http://ftpmaster.internal/ubuntu disco/main armhf python3-minimal armhf 3.7.1-1ubuntu1 [23.6 kB] Get:6 http://ftpmaster.internal/ubuntu disco/main armhf mime-support all 3.60ubuntu1 [30.1 kB] Get:7 http://ftpmaster.internal/ubuntu disco/main armhf libmpdec2 armhf 2.4.2-2 [66.4 kB] Get:8 http://ftpmaster.internal/ubuntu disco/main armhf libpython3.7-stdlib armhf 3.7.1-1 [1660 kB] Get:9 http://ftpmaster.internal/ubuntu disco/main armhf python3.7 armhf 3.7.1-1 [272 kB] Get:10 http://ftpmaster.internal/ubuntu disco/main armhf libpython3-stdlib armhf 3.7.1-1ubuntu1 [7128 B] Get:11 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libgirepository-1.0-1 armhf 1.58.0-1build1 [69.6 kB] Get:22 http://ftpmaster.internal/ubuntu disco/main armhf gir1.2-glib-2.0 armhf 1.58.0-1build1 [132 kB] Get:23 http://ftpmaster.internal/ubuntu disco/main armhf libelf1 armhf 0.170-0.5.0ubuntu1 [40.8 kB] Get:24 http://ftpmaster.internal/ubuntu disco/main armhf libglib2.0-data all 2.58.1-2 [5476 B] Get:25 http://ftpmaster.internal/ubuntu disco/main armhf libicu60 armhf 60.2-6ubuntu1 [7801 kB] Get:26 http://ftpmaster.internal/ubuntu disco/main armhf libxml2 armhf 2.9.4+dfsg1-7ubuntu2 [533 kB] Get:27 http://ftpmaster.internal/ubuntu disco/main armhf gettext-base armhf 0.19.8.1-8 [45.9 kB] Get:28 http://ftpmaster.internal/ubuntu disco/main armhf libsigsegv2 armhf 2.12-2 [13.1 kB] Get:29 http://ftpmaster.internal/ubuntu disco/main armhf m4 armhf 1.4.18-1ubuntu1 [186 kB] Get:30 http://ftpmaster.internal/ubuntu disco/main armhf autoconf all 2.69-11 [322 kB] Get:31 http://ftpmaster.internal/ubuntu disco/main armhf autotools-dev all 20180224.1 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[201 kB] Get:52 http://ftpmaster.internal/ubuntu disco-proposed/main armhf libboost-atomic1.67-dev armhf 1.67.0-9 [199 kB] Get:53 http://ftpmaster.internal/ubuntu disco-proposed/main armhf libboost-system1.67.0 armhf 1.67.0-9 [204 kB] Get:54 http://ftpmaster.internal/ubuntu disco-proposed/main armhf libboost-chrono1.67.0 armhf 1.67.0-9 [205 kB] Get:55 http://ftpmaster.internal/ubuntu disco-proposed/main armhf libboost-chrono1.67-dev armhf 1.67.0-9 [208 kB] Get:56 http://ftpmaster.internal/ubuntu disco-proposed/main armhf libboost-date-time1.67.0 armhf 1.67.0-9 [212 kB] Get:57 http://ftpmaster.internal/ubuntu disco-proposed/main armhf libboost-serialization1.67.0 armhf 1.67.0-9 [276 kB] Get:58 http://ftpmaster.internal/ubuntu disco-proposed/main armhf libboost-serialization1.67-dev armhf 1.67.0-9 [343 kB] Get:59 http://ftpmaster.internal/ubuntu disco-proposed/main armhf libboost-date-time1.67-dev armhf 1.67.0-9 [222 kB] Get:60 http://ftpmaster.internal/ubuntu disco-proposed/main armhf libboost-filesystem1.67.0 armhf 1.67.0-9 [229 kB] Get:61 http://ftpmaster.internal/ubuntu disco-proposed/main armhf libboost-system1.67-dev armhf 1.67.0-9 [206 kB] Get:62 http://ftpmaster.internal/ubuntu disco-proposed/main armhf libboost-filesystem1.67-dev armhf 1.67.0-9 [236 kB] Get:63 http://ftpmaster.internal/ubuntu disco/main armhf libboost-filesystem-dev armhf 1.67.0.0ubuntu1 [2972 B] Get:64 http://ftpmaster.internal/ubuntu disco-proposed/universe armhf libboost-regex1.67.0 armhf 1.67.0-9 [410 kB] Get:65 http://ftpmaster.internal/ubuntu disco/main armhf libicu-le-hb0 armhf 1.0.3+git161113-5 [12.6 kB] Get:66 http://ftpmaster.internal/ubuntu disco/main armhf libiculx60 armhf 60.2-6ubuntu1 [16.1 kB] Get:67 http://ftpmaster.internal/ubuntu disco-proposed/main armhf libharfbuzz-icu0 armhf 1.9.0-1 [5284 B] Get:68 http://ftpmaster.internal/ubuntu disco-proposed/main armhf libharfbuzz-gobject0 armhf 1.9.0-1 [12.2 kB] Get:69 http://ftpmaster.internal/ubuntu disco/main armhf libglib2.0-bin armhf 2.58.1-2 [65.3 kB] Get:70 http://ftpmaster.internal/ubuntu disco/main armhf python3-lib2to3 all 3.7.1-1ubuntu3 [76.5 kB] Get:71 http://ftpmaster.internal/ubuntu disco/main armhf python3-distutils all 3.7.1-1ubuntu3 [141 kB] Get:72 http://ftpmaster.internal/ubuntu disco/main armhf libglib2.0-dev-bin armhf 2.58.1-2 [102 kB] Get:73 http://ftpmaster.internal/ubuntu disco/main armhf libpcre16-3 armhf 2:8.39-11 [128 kB] Get:74 http://ftpmaster.internal/ubuntu disco/main armhf libpcre32-3 armhf 2:8.39-11 [120 kB] Get:75 http://ftpmaster.internal/ubuntu disco/main armhf libpcrecpp0v5 armhf 2:8.39-11 [13.2 kB] Get:76 http://ftpmaster.internal/ubuntu disco/main armhf libpcre3-dev armhf 2:8.39-11 [474 kB] Get:77 http://ftpmaster.internal/ubuntu disco/main armhf pkg-config armhf 0.29.1-0ubuntu2 [42.0 kB] Get:78 http://ftpmaster.internal/ubuntu disco/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-0ubuntu2 [168 kB] Get:79 http://ftpmaster.internal/ubuntu disco/main armhf libglib2.0-dev armhf 2.58.1-2 [1301 kB] Get:80 http://ftpmaster.internal/ubuntu disco/main armhf libgraphite2-dev armhf 1.3.12-1 [14.7 kB] Get:81 http://ftpmaster.internal/ubuntu disco-proposed/main armhf libharfbuzz-dev armhf 1.9.0-1 [321 kB] Get:82 http://ftpmaster.internal/ubuntu disco/main armhf libicu-le-hb-dev armhf 1.0.3+git161113-5 [27.8 kB] Get:83 http://ftpmaster.internal/ubuntu disco/main armhf libicu-dev armhf 60.2-6ubuntu1 [8712 kB] Get:84 http://ftpmaster.internal/ubuntu disco-proposed/universe armhf libboost-regex1.67-dev armhf 1.67.0-9 [512 kB] Get:85 http://ftpmaster.internal/ubuntu disco-proposed/main armhf libboost-iostreams1.67.0 armhf 1.67.0-9 [220 kB] Get:86 http://ftpmaster.internal/ubuntu disco-proposed/universe armhf libboost-iostreams1.67-dev armhf 1.67.0-9 [228 kB] Get:87 http://ftpmaster.internal/ubuntu disco/universe armhf libboost-iostreams-dev armhf 1.67.0.0ubuntu1 [2920 B] Get:88 http://ftpmaster.internal/ubuntu disco-proposed/main armhf libboost-program-options1.67.0 armhf 1.67.0-9 [310 kB] Get:89 http://ftpmaster.internal/ubuntu disco-proposed/main armhf libboost-program-options1.67-dev armhf 1.67.0-9 [358 kB] Get:90 http://ftpmaster.internal/ubuntu disco/main armhf libboost-program-options-dev armhf 1.67.0.0ubuntu1 [2948 B] Get:91 http://ftpmaster.internal/ubuntu disco/main armhf libboost-system-dev armhf 1.67.0.0ubuntu1 [3080 B] Get:92 http://ftpmaster.internal/ubuntu disco-proposed/main armhf libboost-thread1.67.0 armhf 1.67.0-9 [234 kB] Get:93 http://ftpmaster.internal/ubuntu disco-proposed/main armhf libboost-thread1.67-dev armhf 1.67.0-9 [244 kB] Get:94 http://ftpmaster.internal/ubuntu disco/main armhf libboost-thread-dev armhf 1.67.0.0ubuntu1 [2964 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 46.4 MB in 3s (18.2 MB/s) Selecting previously unselected package libpython3.7-minimal:armhf. 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Setting up libboost-filesystem1.67.0:armhf (1.67.0-9) ... Setting up libboost-thread1.67.0:armhf (1.67.0-9) ... Setting up libharfbuzz0b:armhf (1.9.0-1) ... Setting up python3.7 (3.7.1-1) ... Setting up autoconf (2.69-11) ... Setting up file (1:5.34-2) ... Setting up intltool-debian (0.35.0+20060710.4) ... Setting up libboost-program-options1.67-dev:armhf (1.67.0-9) ... Setting up libboost-atomic1.67-dev:armhf (1.67.0-9) ... Setting up gir1.2-harfbuzz-0.0:armhf (1.9.0-1) ... Setting up libboost-chrono1.67.0:armhf (1.67.0-9) ... Setting up automake (1:1.16.1-4) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libboost-system1.67-dev:armhf (1.67.0-9) ... Setting up man-db (2.8.4-3) ... Not building database; man-db/auto-update is not 'true'. Setting up libboost-chrono1.67-dev:armhf (1.67.0-9) ... Setting up libboost-date-time1.67-dev:armhf (1.67.0-9) ... Setting up libharfbuzz-gobject0:armhf (1.9.0-1) ... Setting up libboost-program-options-dev:armhf (1.67.0.0ubuntu1) ... Setting up libtool (2.4.6-6) ... Setting up libpython3-stdlib:armhf (3.7.1-1ubuntu1) ... Setting up libboost-filesystem1.67-dev:armhf (1.67.0-9) ... Setting up libharfbuzz-icu0:armhf (1.9.0-1) ... Setting up po-debconf (1.0.20) ... Setting up python3 (3.7.1-1ubuntu1) ... Setting up libboost-thread1.67-dev:armhf (1.67.0-9) ... Setting up libboost-system-dev:armhf (1.67.0.0ubuntu1) ... Setting up libicu-le-hb0:armhf (1.0.3+git161113-5) ... Setting up libboost-filesystem-dev:armhf (1.67.0.0ubuntu1) ... Setting up libiculx60:armhf (60.2-6ubuntu1) ... Setting up python3-lib2to3 (3.7.1-1ubuntu3) ... Setting up python3-distutils (3.7.1-1ubuntu3) ... Setting up libboost-thread-dev:armhf (1.67.0.0ubuntu1) ... Setting up libglib2.0-dev-bin (2.58.1-2) ... Setting up libglib2.0-dev:armhf (2.58.1-2) ... Setting up libharfbuzz-dev:armhf (1.9.0-1) ... Setting up dh-autoreconf (19) ... Setting up libicu-le-hb-dev:armhf (1.0.3+git161113-5) ... Setting up libicu-dev (60.2-6ubuntu1) ... Setting up dh-strip-nondeterminism (0.044-1) ... Setting up debhelper (11.3.2ubuntu1) ... Setting up libboost-regex1.67-dev:armhf (1.67.0-9) ... Setting up libboost-iostreams1.67-dev:armhf (1.67.0-9) ... Setting up libboost-iostreams-dev:armhf (1.67.0.0ubuntu1) ... Setting up sbuild-build-depends-dssp-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.28-0ubuntu1) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.4.0-138-generic arm64 (armv7l) Toolchain package versions: binutils_2.31.1-7ubuntu1 dpkg-dev_1.19.0.5ubuntu5 g++-8_8.2.0-9ubuntu1 gcc-8_8.2.0-9ubuntu1 libc6-dev_2.28-0ubuntu1 libstdc++-8-dev_8.2.0-9ubuntu1 libstdc++6_8.2.0-9ubuntu1 linux-libc-dev_4.18.0-11.12 Package versions: adduser_3.117ubuntu1 advancecomp_2.1-1 apt_1.7.0 autoconf_2.69-11 automake_1:1.16.1-4 autopoint_0.19.8.1-8 autotools-dev_20180224.1 base-files_10.1ubuntu8 base-passwd_3.5.45 bash_4.4.18-2ubuntu3 binutils_2.31.1-7ubuntu1 binutils-arm-linux-gnueabihf_2.31.1-7ubuntu1 binutils-common_2.31.1-7ubuntu1 bsdmainutils_11.1.2ubuntu2 bsdutils_1:2.32-0.1ubuntu2 build-essential_12.5ubuntu2 bzip2_1.0.6-9 ca-certificates_20180409 coreutils_8.28-1ubuntu2 cpp_4:8.2.0-2ubuntu2 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libzstd1_1.3.5+dfsg-1ubuntu1 linux-libc-dev_4.18.0-11.12 lockfile-progs_0.1.18 login_1:4.5-1ubuntu1 lsb-base_9.20170808ubuntu1 m4_1.4.18-1ubuntu1 make_4.2.1-1.2 man-db_2.8.4-3 mawk_1.3.3-17ubuntu3 mime-support_3.60ubuntu1 mount_2.32-0.1ubuntu2 multiarch-support_2.28-0ubuntu1 ncurses-base_6.1+20180210-4ubuntu1 ncurses-bin_6.1+20180210-4ubuntu1 openssl_1.1.1-1ubuntu2 optipng_0.7.6-1.1 passwd_1:4.5-1ubuntu1 patch_2.7.6-3 perl_5.28.0-3 perl-base_5.28.0-3 perl-modules-5.26_5.26.2-7 perl-modules-5.28_5.28.0-3 pinentry-curses_1.1.0-1build2 pkg-config_0.29.1-0ubuntu2 pkgbinarymangler_143 po-debconf_1.0.20 policyrcd-script-zg2_0.1-3 procps_2:3.3.15-2ubuntu1 python3_3.7.1-1ubuntu1 python3-distutils_3.7.1-1ubuntu3 python3-lib2to3_3.7.1-1ubuntu3 python3-minimal_3.7.1-1ubuntu1 python3.7_3.7.1-1 python3.7-minimal_3.7.1-1 readline-common_7.0-5 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-dssp-dummy_0.invalid.0 sed_4.5-2 sensible-utils_0.0.12 systemd_239-7ubuntu10.1 systemd-sysv_239-7ubuntu10.1 sysv-rc_2.88dsf-59.3ubuntu2 sysvinit-utils_2.88dsf-59.10ubuntu2 tar_1.30+dfsg-2 tzdata_2018g-1 ubuntu-keyring_2018.09.18.1 util-linux_2.32-0.1ubuntu2 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 Sun Oct 28 10:22:14 2018 UTC gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./dssp_3.0.0-3.dsc dpkg-source: info: extracting dssp in dssp-3.0.0 dpkg-source: info: unpacking dssp_3.0.0.orig.tar.gz dpkg-source: info: unpacking dssp_3.0.0-3.debian.tar.xz dpkg-source: info: applying makefile dpkg-source: info: applying hardening.patch dpkg-source: info: applying boost1.65.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-15626811 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-15626811 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-15626811 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package dssp dpkg-buildpackage: info: source version 3.0.0-3 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build dssp-3.0.0 dpkg-buildpackage: info: host architecture armhf fakeroot debian/rules clean dh clean dh_auto_clean make -j4 clean make[1]: Entering directory '/<>' rm -rf obj/* mkdssp make[1]: Leaving directory '/<>' dh_clean debian/rules build-arch dh build-arch dh_update_autotools_config -a dh_autoreconf -a dh_auto_configure -a dh_auto_build -a make -j4 "INSTALL=install --strip-program=true" make[1]: Entering directory '/<>' mkdir -p obj g++ -MD -c -o obj/mkdssp.o src/mkdssp.cpp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -iquote src -g -Wall -Wno-multichar -pthread -O3 -DUSE_COMPRESSION -DLINUX -DVERSION='"2.2.1"' -DNDEBUG g++ -MD -c -o obj/dssp.o src/dssp.cpp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -iquote src -g -Wall -Wno-multichar -pthread -O3 -DUSE_COMPRESSION -DLINUX -DVERSION='"2.2.1"' -DNDEBUG g++ -MD -c -o obj/primitives-3d.o src/primitives-3d.cpp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -iquote src -g -Wall -Wno-multichar -pthread -O3 -DUSE_COMPRESSION -DLINUX -DVERSION='"2.2.1"' -DNDEBUG g++ -MD -c -o obj/structure.o src/structure.cpp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -iquote src -g -Wall -Wno-multichar -pthread -O3 -DUSE_COMPRESSION -DLINUX -DVERSION='"2.2.1"' -DNDEBUG g++ -MD -c -o obj/utils.o src/utils.cpp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -iquote src -g -Wall -Wno-multichar -pthread -O3 -DUSE_COMPRESSION -DLINUX -DVERSION='"2.2.1"' -DNDEBUG In file included from src/structure.cpp:9: src/structure.h: In constructor ‘MResidue::MResidue(int32, char, MResidue*)’: src/structure.h:283:17: warning: ‘MResidue::mRadius’ will be initialized after [-Wreorder] double mRadius; ^~~~~~~ src/structure.h:274:33: warning: ‘MAtom MResidue::mH’ [-Wreorder] MAtom mC, mN, mCA, mO, mH; ^~ src/structure.cpp:440:1: warning: when initialized here [-Wreorder] MResidue::MResidue(int32 inNumber, char inTypeCode, MResidue* inPrevious) ^~~~~~~~ In file included from src/structure.cpp:9: src/structure.h: In constructor ‘MProtein::MProtein(const string&, MChain*)’: src/structure.h:430:40: warning: ‘MProtein::mNrOfHBondsInAntiparallelBridges’ will be initialized after [-Wreorder] uint32 mNrOfHBondsInParallelBridges, mNrOfHBondsInAntiparallelBridges; ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/structure.h:424:17: warning: ‘uint32 MProtein::mResidueCount’ [-Wreorder] uint32 mResidueCount, mChainBreaks; ^~~~~~~~~~~~~ src/structure.cpp:1031:1: warning: when initialized here [-Wreorder] MProtein::MProtein(const std::string& inID, MChain* inChain) ^~~~~~~~ g++ -MD -c -o obj/mas.o src/mas.cpp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -iquote src -g -Wall -Wno-multichar -pthread -O3 -DUSE_COMPRESSION -DLINUX -DVERSION='"2.2.1"' -DNDEBUG g++ -MD -c -o obj/iocif.o src/iocif.cpp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -iquote src -g -Wall -Wno-multichar -pthread -O3 -DUSE_COMPRESSION -DLINUX -DVERSION='"2.2.1"' -DNDEBUG In file included from /usr/include/c++/8/bits/stl_algo.h:61, from /usr/include/c++/8/algorithm:62, from src/align-2d.h:14, from src/structure.h:9, from src/structure.cpp:9: /usr/include/c++/8/bits/stl_heap.h: In function ‘void std::push_heap(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]’: /usr/include/c++/8/bits/stl_heap.h:154:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 push_heap(_RandomAccessIterator __first, _RandomAccessIterator __last) ^~~~~~~~~ /usr/include/c++/8/bits/stl_heap.h:154:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/8/bits/stl_heap.h: In function ‘void std::sort_heap(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]’: /usr/include/c++/8/bits/stl_heap.h:422:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 sort_heap(_RandomAccessIterator __first, _RandomAccessIterator __last) ^~~~~~~~~ /usr/include/c++/8/bits/stl_heap.h:422:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 In file included from /usr/include/c++/8/vector:69, from src/align-2d.h:16, from src/structure.h:9, from src/structure.cpp:9: /usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const MPoint&}; _Tp = MPoint; _Alloc = std::allocator]’: /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from src/align-2d.h:16, from src/structure.h:9, from src/structure.cpp:9: /usr/include/c++/8/bits/stl_vector.h: In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = MPoint; _Alloc = std::allocator]’: /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In member function ‘void MResidue::GetPoints(std::vector&) const’: /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In member function ‘void MProtein::GetCAlphaLocations(const string&, std::vector&) const’: /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In static member function ‘static {anonymous}::MSurfaceDots& {anonymous}::MSurfaceDots::Instance()’: /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from src/align-2d.h:16, from src/structure.h:9, from src/structure.cpp:9: /usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const MAtom&}; _Tp = MAtom; _Alloc = std::allocator]’: /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const MAccumulator::candidate&}; _Tp = MAccumulator::candidate; _Alloc = std::allocator]’: /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 In file included from /usr/include/c++/8/vector:64, from src/align-2d.h:16, from src/structure.h:9, from src/structure.cpp:9: /usr/include/c++/8/bits/stl_vector.h: In member function ‘void MAccumulator::operator()(const MPoint&, const MPoint&, double, double)’: /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ src/structure.cpp:811:16: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 push_heap(m_x.begin(), m_x.end()); ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ src/structure.cpp: In function ‘double MResidue::CalculateSurface(const MAtom&, double, const std::vector&)’: src/structure.cpp:817:14: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 sort_heap(m_x.begin(), m_x.end()); ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from src/align-2d.h:16, from src/structure.h:9, from src/structure.cpp:9: /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ src/structure.cpp:811:16: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 push_heap(m_x.begin(), m_x.end()); ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ src/structure.cpp: In member function ‘double MResidue::CalculateSurface(const MAtom&, double, const std::vector&)’: src/structure.cpp:817:14: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 sort_heap(m_x.begin(), m_x.end()); ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from src/align-2d.h:16, from src/structure.h:9, from src/structure.cpp:9: /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ src/structure.cpp:811:16: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 push_heap(m_x.begin(), m_x.end()); ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from src/align-2d.h:16, from src/structure.h:9, from src/structure.cpp:9: /usr/include/c++/8/bits/stl_vector.h: In function ‘void MAccumulator::operator()(const MPoint&, const MPoint&, double, double)’: /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ src/structure.cpp:811:16: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 push_heap(m_x.begin(), m_x.end()); ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ src/structure.cpp: In member function ‘void MResidue::CalculateSurface(const std::vector&)’: src/structure.cpp:817:14: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 sort_heap(m_x.begin(), m_x.end()); ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from src/align-2d.h:16, from src/structure.h:9, from src/structure.cpp:9: /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ src/structure.cpp:811:16: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 push_heap(m_x.begin(), m_x.end()); ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from src/align-2d.h:16, from src/structure.h:9, from src/structure.cpp:9: /usr/include/c++/8/bits/stl_vector.h: In constructor ‘MResidue::MResidue(int32, MResidue*, const std::vector&)’: /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In member function ‘void MProtein::ReadPDB(std::istream&, bool)’: /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In member function ‘void MProtein::ReadmmCIF(std::istream&, bool)’: /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ g++ -o mkdssp obj/mkdssp.o obj/dssp.o obj/primitives-3d.o obj/structure.o obj/utils.o obj/mas.o obj/iocif.o -Wl,-Bsymbolic-functions -Wl,-z,relro -lboost_thread -lboost_program_options -lboost_iostreams -lboost_system -g -pthread -Wl,-Bsymbolic-functions -Wl,-z,relro make[1]: Leaving directory '/<>' dh_auto_test -a create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary-arch dh binary-arch dh_testroot -a dh_prep -a dh_auto_install -a make -j4 install DESTDIR=/<>/debian/dssp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/<>' install -d /<>/debian/dssp/usr/bin /<>/debian/dssp/usr/share/man/man1 install -m 755 mkdssp /<>/debian/dssp/usr/bin/mkdssp install doc/mkdssp.1 /<>/debian/dssp/usr/share/man/man1/mkdssp.1 make[1]: Leaving directory '/<>' dh_installdocs -a dh_installchangelogs -a dh_installexamples -a dh_installman -a dh_perl -a dh_link -a dh_strip_nondeterminism -a dh_compress -a dh_fixperms -a dh_missing -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb -a dh_gencontrol -a dh_md5sums -a dh_builddeb -a INFO: pkgstriptranslations version 143 INFO: pkgstriptranslations version 143 pkgstriptranslations: processing dssp (in debian/dssp); do_strip: , oemstrip: pkgstriptranslations: processing dssp-dbgsym (in debian/.debhelper/dssp/dbgsym-root); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/dssp/DEBIAN/control, package dssp, directory debian/dssp pkgstripfiles: Running PNG optimization (using 4 cpus) for package dssp ... pkgstripfiles: No PNG files. dpkg-deb: building package 'dssp' in '../dssp_3.0.0-3_armhf.deb'. pkgstripfiles: processing control file: debian/.debhelper/dssp/dbgsym-root/DEBIAN/control, package dssp-dbgsym, directory debian/.debhelper/dssp/dbgsym-root dpkg-deb: building package 'dssp-dbgsym' in 'debian/.debhelper/scratch-space/build-dssp/dssp-dbgsym_3.0.0-3_armhf.deb'. Renaming dssp-dbgsym_3.0.0-3_armhf.deb to dssp-dbgsym_3.0.0-3_armhf.ddeb dpkg-genbuildinfo --build=any dpkg-genchanges --build=any -mLaunchpad Build Daemon >../dssp_3.0.0-3_armhf.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build dssp-3.0.0 dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 20181109-1102 Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Post Build Chroot | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ dssp_3.0.0-3_armhf.changes: --------------------------- Format: 1.8 Date: Sun, 28 Oct 2018 11:18:40 +0100 Source: dssp Binary: dssp Architecture: armhf Version: 3.0.0-3 Distribution: disco-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Andreas Tille Description: dssp - protein secondary structure assignment based on 3D structure Changes: dssp (3.0.0-3) unstable; urgency=medium . * debhelper 11 * Point Vcs fields to salsa.debian.org * Standards-Version: 4.2.1 * Secure URI in copyright format * Remove trailing whitespace in debian/copyright Checksums-Sha1: 8ad5d569024c5c8c90eba0b2404fb89357427c7f 2697564 dssp-dbgsym_3.0.0-3_armhf.ddeb 9e47f9291280d4bc8117d83b12317982cd74fda8 7086 dssp_3.0.0-3_armhf.buildinfo 44c444375de2dfb681d03b35104bf3203584459a 222888 dssp_3.0.0-3_armhf.deb Checksums-Sha256: b28a3ed61092943ed3c8513467d6615ff1e675ae94d7d47a0d81cf371d14606c 2697564 dssp-dbgsym_3.0.0-3_armhf.ddeb ddd370d37b5f91ec123075aaf9d7f2a3f1c9679bdbec2344cd3f20cd14223c2e 7086 dssp_3.0.0-3_armhf.buildinfo 071241277964d9d912fcc7025edf17ae04047dc20f2d4ce20e808238f0c52b6d 222888 dssp_3.0.0-3_armhf.deb Files: bfe767af3ced0cb4d2c954f6867d58a1 2697564 debug optional dssp-dbgsym_3.0.0-3_armhf.ddeb fb3ea3c6f7e8f6f5f0d90abb427d19bc 7086 science optional dssp_3.0.0-3_armhf.buildinfo 36cb69fc3bc4ee0eb6eea74a84d727f8 222888 science optional dssp_3.0.0-3_armhf.deb +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ dssp_3.0.0-3_armhf.deb ---------------------- new debian package, version 2.0. size 222888 bytes: control archive=1056 bytes. 826 bytes, 17 lines control 607 bytes, 9 lines md5sums Package: dssp Version: 3.0.0-3 Architecture: armhf Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 434 Depends: libboost-program-options1.67.0, libboost-system1.67.0, libboost-thread1.67.0, libc6 (>= 2.4), libgcc1 (>= 1:4.0), libstdc++6 (>= 5.2) Section: science Priority: optional Homepage: http://www.cmbi.ru.nl/dssp.html Description: protein secondary structure assignment based on 3D structure DSSP is an application you use to assign the secondary structure of a protein based on its solved three dimensional (3D) structure. . This version (2) of DSSP is a rewrite that produces the same output as the original DSSP, but deals better with exceptions in PDB files and is much faster. drwxr-xr-x root/root 0 2018-10-28 10:18 ./ drwxr-xr-x root/root 0 2018-10-28 10:18 ./usr/ drwxr-xr-x root/root 0 2018-10-28 10:18 ./usr/bin/ lrwxrwxrwx root/root 0 2018-10-28 10:18 ./usr/bin/dssp -> mkdssp -rwxr-xr-x root/root 333324 2018-10-28 10:18 ./usr/bin/mkdssp drwxr-xr-x root/root 0 2018-10-28 10:18 ./usr/share/ drwxr-xr-x root/root 0 2018-10-28 10:18 ./usr/share/doc/ drwxr-xr-x root/root 0 2018-10-28 10:18 ./usr/share/doc/dssp/ -rw-r--r-- root/root 1318 2018-10-28 10:18 ./usr/share/doc/dssp/README.test -rw-r--r-- root/root 533 2017-09-21 09:25 ./usr/share/doc/dssp/README.txt -rw-r--r-- root/root 1440 2018-10-28 10:18 ./usr/share/doc/dssp/changelog.Debian.gz -rw-r--r-- root/root 3716 2018-10-28 10:18 ./usr/share/doc/dssp/copyright drwxr-xr-x root/root 0 2018-10-28 10:18 ./usr/share/doc/dssp/examples/ -rw-r--r-- root/root 1447 2018-10-28 10:18 ./usr/share/doc/dssp/examples/2OSL_fragment.pdb.gz -rw-r--r-- root/root 82571 2018-10-28 10:18 ./usr/share/doc/dssp/examples/5bmg.pdb.gz -rw-r--r-- root/root 756 2018-10-28 10:18 ./usr/share/doc/dssp/installation-test drwxr-xr-x root/root 0 2018-10-28 10:18 ./usr/share/man/ drwxr-xr-x root/root 0 2018-10-28 10:18 ./usr/share/man/man1/ lrwxrwxrwx root/root 0 2018-10-28 10:18 ./usr/share/man/man1/dssp.1.gz -> mkdssp.1.gz -rw-r--r-- root/root 2550 2018-10-28 10:18 ./usr/share/man/man1/mkdssp.1.gz +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: armhf Build-Space: 31892 Build-Time: 86 Distribution: disco-proposed Host Architecture: armhf Install-Time: 51 Job: dssp_3.0.0-3.dsc Machine Architecture: arm64 Package: dssp Package-Time: 139 Source-Version: 3.0.0-3 Space: 31892 Status: successful Version: 3.0.0-3 -------------------------------------------------------------------------------- Finished at 20181109-1102 Build needed 00:02:19, 31892k disc space RUN: /usr/share/launchpad-buildd/slavebin/in-target scan-for-processes --backend=chroot --series=disco --arch=armhf PACKAGEBUILD-15626811 Scanning for processes to kill in build PACKAGEBUILD-15626811