https://launchpad.net/ubuntu/+archive/test-rebuild-20190906-lto/+build/17632304 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux bos02-arm64-049 4.4.0-161-generic #189-Ubuntu SMP Tue Aug 27 08:12:37 UTC 2019 aarch64 Buildd toolchain package versions: launchpad-buildd_177 python-lpbuildd_177 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_0.3.6~git201906051340.ff11471~ubuntu16.04.1 git_1:2.7.4-0ubuntu1.6 dpkg-dev_1.18.4ubuntu1.6 python-debian_0.1.27ubuntu2. Syncing the system clock with the buildd NTP service... 18 Sep 01:48:02 ntpdate[1857]: adjust time server 10.211.37.1 offset 0.033678 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=eoan --arch=armhf PACKAGEBUILD-17632304 --image-type chroot /home/buildd/filecache-default/136db2b044b6db4888594b9f3f4be8b15ba46e35 Creating target for build PACKAGEBUILD-17632304 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=eoan --arch=armhf PACKAGEBUILD-17632304 Starting target for build PACKAGEBUILD-17632304 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=eoan --arch=armhf PACKAGEBUILD-17632304 'deb http://ppa.launchpad.net/ubuntu-toolchain-r/volatile/ubuntu eoan main' 'deb http://ppa.launchpad.net/ubuntu-toolchain-r/dpkg-lto/ubuntu eoan main' 'deb http://ftpmaster.internal/ubuntu eoan main restricted universe multiverse' Overriding sources.list in build-PACKAGEBUILD-17632304 RUN: /usr/share/launchpad-buildd/bin/in-target add-trusted-keys --backend=chroot --series=eoan --arch=armhf PACKAGEBUILD-17632304 Adding trusted keys to build-PACKAGEBUILD-17632304 Warning: apt-key output should not be parsed (stdout is not a terminal) OK Warning: apt-key output should not be parsed (stdout is not a terminal) /etc/apt/trusted.gpg -------------------- pub rsa1024 2009-10-22 [SC] 60C3 1780 3A41 BA51 845E 371A 1E93 77A2 BA9E F27F uid [ unknown] Launchpad Toolchain builds /etc/apt/trusted.gpg.d/ubuntu-keyring-2012-archive.gpg ------------------------------------------------------ pub rsa4096 2012-05-11 [SC] 790B C727 7767 219C 42C8 6F93 3B4F E6AC C0B2 1F32 uid [ unknown] Ubuntu Archive Automatic Signing Key (2012) /etc/apt/trusted.gpg.d/ubuntu-keyring-2012-cdimage.gpg ------------------------------------------------------ pub rsa4096 2012-05-11 [SC] 8439 38DF 228D 22F7 B374 2BC0 D94A A3F0 EFE2 1092 uid [ unknown] Ubuntu CD Image Automatic Signing Key (2012) /etc/apt/trusted.gpg.d/ubuntu-keyring-2018-archive.gpg ------------------------------------------------------ pub rsa4096 2018-09-17 [SC] F6EC B376 2474 EDA9 D21B 7022 8719 20D1 991B C93C uid [ unknown] Ubuntu Archive Automatic Signing Key (2018) RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=eoan --arch=armhf PACKAGEBUILD-17632304 Updating target for build PACKAGEBUILD-17632304 Get:1 http://ftpmaster.internal/ubuntu eoan InRelease [255 kB] Get:2 http://ppa.launchpad.net/ubuntu-toolchain-r/volatile/ubuntu eoan InRelease [15.4 kB] Get:3 http://ppa.launchpad.net/ubuntu-toolchain-r/dpkg-lto/ubuntu eoan InRelease [20.8 kB] Get:4 http://ppa.launchpad.net/ubuntu-toolchain-r/volatile/ubuntu eoan/main armhf Packages [3200 B] Get:5 http://ppa.launchpad.net/ubuntu-toolchain-r/volatile/ubuntu eoan/main Translation-en [4848 B] Get:6 http://ftpmaster.internal/ubuntu eoan/main armhf Packages [931 kB] Get:7 http://ppa.launchpad.net/ubuntu-toolchain-r/dpkg-lto/ubuntu eoan/main armhf Packages [1696 B] Get:8 http://ftpmaster.internal/ubuntu eoan/main Translation-en [504 kB] Get:9 http://ppa.launchpad.net/ubuntu-toolchain-r/dpkg-lto/ubuntu eoan/main Translation-en [1760 B] Get:10 http://ftpmaster.internal/ubuntu eoan/restricted armhf Packages [6800 B] Get:11 http://ftpmaster.internal/ubuntu eoan/restricted Translation-en [4836 B] Get:12 http://ftpmaster.internal/ubuntu eoan/universe armhf Packages [8599 kB] Get:13 http://ftpmaster.internal/ubuntu eoan/universe Translation-en [5224 kB] Get:14 http://ftpmaster.internal/ubuntu eoan/multiverse armhf Packages [122 kB] Get:15 http://ftpmaster.internal/ubuntu eoan/multiverse Translation-en [111 kB] Fetched 15.8 MB in 7s (2251 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following NEW packages will be installed: logsave The following packages will be upgraded: binutils binutils-arm-linux-gnueabihf binutils-common build-essential coreutils cpp cpp-9 dpkg dpkg-dev e2fsprogs g++ g++-9 gcc gcc-9 gcc-9-base libapparmor1 libasan5 libatomic1 libbinutils libc-bin libc-dev-bin libc6 libc6-dev libcc1-0 libcom-err2 libdevmapper1.02.1 libdpkg-perl libext2fs2 libgcc-9-dev libgcc1 libgnutls30 libgomp1 libip4tc2 libisl21 libp11-kit0 libsqlite3-0 libss2 libstdc++-9-dev libstdc++6 libubsan1 linux-libc-dev login passwd tzdata 44 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 44.8 MB of archives. After this operation, 346 kB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu eoan/main armhf coreutils armhf 8.30-3ubuntu2 [1132 kB] Get:2 http://ppa.launchpad.net/ubuntu-toolchain-r/dpkg-lto/ubuntu eoan/main armhf dpkg armhf 1.19.7ubuntu77 [2196 kB] Get:3 http://ftpmaster.internal/ubuntu eoan/main armhf login armhf 1:4.5-1.1ubuntu4 [261 kB] Get:4 http://ftpmaster.internal/ubuntu eoan/main armhf libc6-dev armhf 2.30-0ubuntu1 [1943 kB] Get:5 http://ppa.launchpad.net/ubuntu-toolchain-r/dpkg-lto/ubuntu eoan/main armhf dpkg-dev all 1.19.7ubuntu77 [1793 kB] Get:6 http://ftpmaster.internal/ubuntu eoan/main armhf libc-dev-bin armhf 2.30-0ubuntu1 [63.7 kB] Get:7 http://ftpmaster.internal/ubuntu eoan/main armhf linux-libc-dev armhf 5.3.0-10.11 [1044 kB] Get:8 http://ppa.launchpad.net/ubuntu-toolchain-r/dpkg-lto/ubuntu eoan/main armhf libdpkg-perl all 1.19.7ubuntu77 [1434 kB] Get:9 http://ftpmaster.internal/ubuntu eoan/main armhf libcc1-0 armhf 9.2.1-8ubuntu1 [41.6 kB] Get:10 http://ftpmaster.internal/ubuntu eoan/main armhf binutils-arm-linux-gnueabihf armhf 2.32.51.20190905-0ubuntu1 [2102 kB] Get:11 http://ftpmaster.internal/ubuntu eoan/main armhf libbinutils armhf 2.32.51.20190905-0ubuntu1 [315 kB] Get:12 http://ftpmaster.internal/ubuntu eoan/main armhf binutils-common armhf 2.32.51.20190905-0ubuntu1 [203 kB] Get:13 http://ftpmaster.internal/ubuntu eoan/main armhf binutils armhf 2.32.51.20190905-0ubuntu1 [3356 B] Get:14 http://ftpmaster.internal/ubuntu eoan/main armhf gcc-9-base armhf 9.2.1-8ubuntu1 [19.2 kB] Get:15 http://ftpmaster.internal/ubuntu eoan/main armhf libgcc1 armhf 1:9.2.1-8ubuntu1 [37.4 kB] Get:16 http://ftpmaster.internal/ubuntu eoan/main armhf libgomp1 armhf 9.2.1-8ubuntu1 [77.4 kB] Get:17 http://ftpmaster.internal/ubuntu eoan/main armhf libatomic1 armhf 9.2.1-8ubuntu1 [7100 B] Get:18 http://ftpmaster.internal/ubuntu eoan/main armhf libasan5 armhf 9.2.1-8ubuntu1 [386 kB] Get:19 http://ftpmaster.internal/ubuntu eoan/main armhf libubsan1 armhf 9.2.1-8ubuntu1 [118 kB] Get:20 http://ftpmaster.internal/ubuntu eoan/main armhf g++-9 armhf 9.2.1-8ubuntu1 [7931 kB] Get:21 http://ftpmaster.internal/ubuntu eoan/main armhf libstdc++-9-dev armhf 9.2.1-8ubuntu1 [1774 kB] Get:22 http://ftpmaster.internal/ubuntu eoan/main armhf libgcc-9-dev armhf 9.2.1-8ubuntu1 [687 kB] Get:23 http://ftpmaster.internal/ubuntu eoan/main armhf gcc-9 armhf 9.2.1-8ubuntu1 [7594 kB] Get:24 http://ftpmaster.internal/ubuntu eoan/main armhf cpp-9 armhf 9.2.1-8ubuntu1 [6905 kB] Get:25 http://ftpmaster.internal/ubuntu eoan/main armhf libstdc++6 armhf 9.2.1-8ubuntu1 [451 kB] Get:26 http://ftpmaster.internal/ubuntu eoan/main armhf libisl21 armhf 0.21-2 [446 kB] Get:27 http://ftpmaster.internal/ubuntu eoan/main armhf libc6 armhf 2.30-0ubuntu1 [2146 kB] Get:28 http://ftpmaster.internal/ubuntu eoan/main armhf libc-bin armhf 2.30-0ubuntu1 [486 kB] Get:29 http://ftpmaster.internal/ubuntu eoan/main armhf libext2fs2 armhf 1.45.3-4ubuntu1 [167 kB] Get:30 http://ftpmaster.internal/ubuntu eoan/main armhf e2fsprogs armhf 1.45.3-4ubuntu1 [507 kB] Get:31 http://ftpmaster.internal/ubuntu eoan/main armhf logsave armhf 1.45.3-4ubuntu1 [9076 B] Get:32 http://ftpmaster.internal/ubuntu eoan/main armhf passwd armhf 1:4.5-1.1ubuntu4 [772 kB] Get:33 http://ftpmaster.internal/ubuntu eoan/main armhf libp11-kit0 armhf 0.23.17-2 [166 kB] Get:34 http://ftpmaster.internal/ubuntu eoan/main armhf libgnutls30 armhf 3.6.9-4build1 [734 kB] Get:35 http://ftpmaster.internal/ubuntu eoan/main armhf libcom-err2 armhf 1.45.3-4ubuntu1 [8032 B] Get:36 http://ftpmaster.internal/ubuntu eoan/main armhf libss2 armhf 1.45.3-4ubuntu1 [9372 B] Get:37 http://ftpmaster.internal/ubuntu eoan/main armhf libapparmor1 armhf 2.13.3-5ubuntu1 [30.5 kB] Get:38 http://ftpmaster.internal/ubuntu eoan/main armhf libdevmapper1.02.1 armhf 2:1.02.155-2ubuntu6 [118 kB] Get:39 http://ftpmaster.internal/ubuntu eoan/main armhf libsqlite3-0 armhf 3.29.0-2 [456 kB] Get:40 http://ftpmaster.internal/ubuntu eoan/main armhf tzdata all 2019c-1 [188 kB] Get:41 http://ftpmaster.internal/ubuntu eoan/main armhf g++ armhf 4:9.2.1-3.1ubuntu1 [1616 B] Get:42 http://ftpmaster.internal/ubuntu eoan/main armhf gcc armhf 4:9.2.1-3.1ubuntu1 [5224 B] Get:43 http://ftpmaster.internal/ubuntu eoan/main armhf cpp armhf 4:9.2.1-3.1ubuntu1 [27.6 kB] Get:44 http://ftpmaster.internal/ubuntu eoan/main armhf build-essential armhf 12.7ubuntu1 [4644 B] Get:45 http://ftpmaster.internal/ubuntu eoan/main armhf libip4tc2 armhf 1.8.3-2ubuntu4 [18.5 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 44.8 MB in 3s (13.7 MB/s) (Reading database ... 12477 files and directories currently installed.) Preparing to unpack .../coreutils_8.30-3ubuntu2_armhf.deb ... Unpacking coreutils (8.30-3ubuntu2) over (8.30-3ubuntu1) ... Setting up coreutils (8.30-3ubuntu2) ... (Reading database ... 12477 files and directories currently installed.) Preparing to unpack .../dpkg_1.19.7ubuntu77_armhf.deb ... Unpacking dpkg (1.19.7ubuntu77) over (1.19.7ubuntu1) ... Setting up dpkg (1.19.7ubuntu77) ... (Reading database ... 12478 files and directories currently installed.) Preparing to unpack .../login_1%3a4.5-1.1ubuntu4_armhf.deb ... Unpacking login (1:4.5-1.1ubuntu4) over (1:4.5-1.1ubuntu3) ... Setting up login (1:4.5-1.1ubuntu4) ... (Reading database ... 12478 files and directories currently installed.) Preparing to unpack .../0-libc6-dev_2.30-0ubuntu1_armhf.deb ... Unpacking libc6-dev:armhf (2.30-0ubuntu1) over (2.29-0ubuntu3) ... Preparing to unpack .../1-libc-dev-bin_2.30-0ubuntu1_armhf.deb ... Unpacking libc-dev-bin (2.30-0ubuntu1) over (2.29-0ubuntu3) ... 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Unpacking libcom-err2:armhf (1.45.3-4ubuntu1) over (1.45.2-1ubuntu1) ... Preparing to unpack .../01-libss2_1.45.3-4ubuntu1_armhf.deb ... Unpacking libss2:armhf (1.45.3-4ubuntu1) over (1.45.2-1ubuntu1) ... Preparing to unpack .../02-libapparmor1_2.13.3-5ubuntu1_armhf.deb ... Unpacking libapparmor1:armhf (2.13.3-5ubuntu1) over (2.13.2-9ubuntu7) ... Preparing to unpack .../03-libdevmapper1.02.1_2%3a1.02.155-2ubuntu6_armhf.deb ... Unpacking libdevmapper1.02.1:armhf (2:1.02.155-2ubuntu6) over (2:1.02.155-2ubuntu5) ... Preparing to unpack .../04-libsqlite3-0_3.29.0-2_armhf.deb ... Unpacking libsqlite3-0:armhf (3.29.0-2) over (3.29.0-1) ... Preparing to unpack .../05-tzdata_2019c-1_all.deb ... Unpacking tzdata (2019c-1) over (2019b-2) ... Preparing to unpack .../06-g++_4%3a9.2.1-3.1ubuntu1_armhf.deb ... Unpacking g++ (4:9.2.1-3.1ubuntu1) over (4:9.2.1-2ubuntu2) ... Preparing to unpack .../07-gcc_4%3a9.2.1-3.1ubuntu1_armhf.deb ... Unpacking gcc (4:9.2.1-3.1ubuntu1) over (4:9.2.1-2ubuntu2) ... 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Setting up libcom-err2:armhf (1.45.3-4ubuntu1) ... Setting up libgomp1:armhf (9.2.1-8ubuntu1) ... Setting up tzdata (2019c-1) ... Current default time zone: 'Etc/UTC' Local time is now: Wed Sep 18 01:48:49 UTC 2019. Universal Time is now: Wed Sep 18 01:48:49 UTC 2019. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libasan5:armhf (9.2.1-8ubuntu1) ... Setting up libatomic1:armhf (9.2.1-8ubuntu1) ... Setting up libss2:armhf (1.45.3-4ubuntu1) ... Setting up libdpkg-perl (1.19.7ubuntu77) ... Setting up logsave (1.45.3-4ubuntu1) ... Setting up libubsan1:armhf (9.2.1-8ubuntu1) ... Setting up libdevmapper1.02.1:armhf (2:1.02.155-2ubuntu6) ... Setting up cpp-9 (9.2.1-8ubuntu1) ... Setting up libbinutils:armhf (2.32.51.20190905-0ubuntu1) ... Setting up libc-dev-bin (2.30-0ubuntu1) ... Setting up binutils-arm-linux-gnueabihf (2.32.51.20190905-0ubuntu1) ... Setting up libcc1-0:armhf (9.2.1-8ubuntu1) ... Setting up e2fsprogs (1.45.3-4ubuntu1) ... Installing new version of config file /etc/cron.d/e2scrub_all ... Installing new version of config file /etc/e2scrub.conf ... Setting up binutils (2.32.51.20190905-0ubuntu1) ... Setting up dpkg-dev (1.19.7ubuntu77) ... Setting up libgcc-9-dev:armhf (9.2.1-8ubuntu1) ... Setting up cpp (4:9.2.1-3.1ubuntu1) ... Setting up libc6-dev:armhf (2.30-0ubuntu1) ... Setting up gcc-9 (9.2.1-8ubuntu1) ... Setting up libstdc++-9-dev:armhf (9.2.1-8ubuntu1) ... Setting up gcc (4:9.2.1-3.1ubuntu1) ... Setting up g++-9 (9.2.1-8ubuntu1) ... Setting up g++ (4:9.2.1-3.1ubuntu1) ... Setting up build-essential (12.7ubuntu1) ... Processing triggers for libc-bin (2.30-0ubuntu1) ... RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-17632304 armhf eoan -c chroot:build-PACKAGEBUILD-17632304 --arch=armhf --dist=eoan --nolog abyss_2.2.2-1.dsc Initiating build PACKAGEBUILD-17632304 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.4.0-161-generic #189-Ubuntu SMP Tue Aug 27 08:12:37 UTC 2019 armv7l sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on bos02-arm64-049.buildd +==============================================================================+ | abyss 2.2.2-1 (armhf) 18 Sep 2019 01:48 | +==============================================================================+ Package: abyss Version: 2.2.2-1 Source Version: 2.2.2-1 Distribution: eoan Machine Architecture: arm64 Host Architecture: armhf Build Architecture: armhf I: NOTICE: Log filtering will replace 'build/abyss-9dJBVG/abyss-2.2.2' with '<>' I: NOTICE: Log filtering will replace 'build/abyss-9dJBVG' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-17632304/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- abyss_2.2.2-1.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-rcFtp6/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/<>/resolver-rcFtp6/apt_archive ./ InRelease Get:2 copy:/<>/resolver-rcFtp6/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-rcFtp6/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-rcFtp6/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-rcFtp6/apt_archive ./ Packages [528 B] Fetched 2861 B in 0s (107 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 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-rcFtp6/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 ... 12500 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-compat (= 12), python-markdown, libboost-graph-dev, libopenmpi-dev, libsparsehash-dev, libtext-multimarkdown-perl, libsqlite3-dev, pkg-config, help2man Filtered Build-Depends: debhelper-compat (= 12), python-markdown, libboost-graph-dev, libopenmpi-dev, libsparsehash-dev, libtext-multimarkdown-perl, libsqlite3-dev, pkg-config, help2man dpkg-deb: building package 'sbuild-build-depends-abyss-dummy' in '/<>/resolver-ujMCkA/apt_archive/sbuild-build-depends-abyss-dummy.deb'. Ign:1 copy:/<>/resolver-ujMCkA/apt_archive ./ InRelease Get:2 copy:/<>/resolver-ujMCkA/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-ujMCkA/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-ujMCkA/apt_archive ./ Sources [284 B] Get:5 copy:/<>/resolver-ujMCkA/apt_archive ./ Packages [608 B] Fetched 3011 B in 0s (108 kB/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install abyss build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base help2man ibverbs-providers intltool-debian libarchive-zip-perl libboost-graph-dev libboost-graph1.67-dev libboost-graph1.67.0 libboost-regex1.67.0 libboost-serialization1.67-dev libboost-serialization1.67.0 libboost-test1.67-dev libboost-test1.67.0 libboost1.67-dev libbsd0 libcroco3 libedit2 libelf1 libevent-2.1-6 libevent-core-2.1-6 libevent-pthreads-2.1-6 libexpat1 libfile-stripnondeterminism-perl libglib2.0-0 libgssapi-krb5-2 libhtml-parser-perl libhtml-tagset-perl libhwloc-dev libhwloc-plugins libhwloc5 libibverbs-dev libibverbs1 libicu63 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblocale-gettext-perl libltdl-dev libltdl7 libmagic-mgc libmagic1 libnl-3-200 libnl-3-dev libnl-route-3-200 libnl-route-3-dev libopenmpi-dev libopenmpi3 libpciaccess0 libpipeline1 libpmix2 libpython-stdlib libpython2-stdlib libpython2.7-minimal libpython2.7-stdlib libsigsegv2 libsparsehash-dev libsqlite3-dev libsub-override-perl libtext-markdown-perl libtext-multimarkdown-perl libtool libuchardet0 liburi-perl libxml2 m4 man-db mime-support ocl-icd-libopencl1 openmpi-bin openmpi-common openssh-client pkg-config po-debconf python python-attr python-markdown python-minimal python-packaging python-pkg-resources python-pyparsing python-six python2 python2-minimal python2.7 python2.7-minimal Suggested packages: autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois vacation dh-make gettext-doc libasprintf-dev libgettextpo-dev groff graphviz libboost1.67-doc libboost-atomic1.67-dev libboost-chrono1.67-dev libboost-container1.67-dev libboost-context1.67-dev libboost-contract1.67-dev libboost-coroutine1.67-dev libboost-date-time1.67-dev libboost-exception1.67-dev libboost-fiber1.67-dev libboost-filesystem1.67-dev libboost-graph-parallel1.67-dev libboost-iostreams1.67-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-program-options1.67-dev libboost-python1.67-dev libboost-random1.67-dev libboost-regex1.67-dev libboost-signals1.67-dev libboost-stacktrace1.67-dev libboost-system1.67-dev libboost-thread1.67-dev libboost-timer1.67-dev libboost-type-erasure1.67-dev libboost-wave1.67-dev libboost1.67-tools-dev libmpfrc++-dev libntl-dev krb5-doc krb5-user libdata-dump-perl libhwloc-contrib-plugins libtool-doc openmpi-doc pciutils sqlite3-doc gfortran | fortran95-compiler gcj-jdk libwww-perl m4-doc apparmor less www-browser opencl-icd gfortran | fortran-compiler keychain libpam-ssh monkeysphere ssh-askpass libmail-box-perl python-doc python-tk python-attr-doc python-markdown-doc python-setuptools python-pyparsing-doc python2-doc python2.7-doc binfmt-support Recommended packages: curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs libhttp-message-perl krb5-locales libcoarrays-openmpi-dev xauth libmail-sendmail-perl python-pygments python-yaml The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base help2man ibverbs-providers intltool-debian libarchive-zip-perl libboost-graph-dev libboost-graph1.67-dev libboost-graph1.67.0 libboost-regex1.67.0 libboost-serialization1.67-dev libboost-serialization1.67.0 libboost-test1.67-dev libboost-test1.67.0 libboost1.67-dev libbsd0 libcroco3 libedit2 libelf1 libevent-2.1-6 libevent-core-2.1-6 libevent-pthreads-2.1-6 libexpat1 libfile-stripnondeterminism-perl libglib2.0-0 libgssapi-krb5-2 libhtml-parser-perl libhtml-tagset-perl libhwloc-dev libhwloc-plugins libhwloc5 libibverbs-dev libibverbs1 libicu63 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblocale-gettext-perl libltdl-dev libltdl7 libmagic-mgc libmagic1 libnl-3-200 libnl-3-dev libnl-route-3-200 libnl-route-3-dev libopenmpi-dev libopenmpi3 libpciaccess0 libpipeline1 libpmix2 libpython-stdlib libpython2-stdlib libpython2.7-minimal libpython2.7-stdlib libsigsegv2 libsparsehash-dev libsqlite3-dev libsub-override-perl libtext-markdown-perl libtext-multimarkdown-perl libtool libuchardet0 liburi-perl libxml2 m4 man-db mime-support ocl-icd-libopencl1 openmpi-bin openmpi-common openssh-client pkg-config po-debconf python python-attr python-markdown python-minimal python-packaging python-pkg-resources python-pyparsing python-six python2 python2-minimal python2.7 python2.7-minimal sbuild-build-depends-abyss-dummy 0 upgraded, 99 newly installed, 0 to remove and 0 not upgraded. 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python-pyparsing all 2.2.0+dfsg1-2 [52.1 kB] Get:93 http://ftpmaster.internal/ubuntu eoan/universe armhf python-six all 1.12.0-2 [11.6 kB] Get:94 http://ftpmaster.internal/ubuntu eoan/universe armhf python-packaging all 19.1-2 [21.6 kB] Get:95 http://ftpmaster.internal/ubuntu eoan/universe armhf python-pkg-resources all 41.1.0-1 [129 kB] Get:96 http://ftpmaster.internal/ubuntu eoan/universe armhf python-markdown all 3.1.1-2 [60.5 kB] Get:97 http://ftpmaster.internal/ubuntu eoan/universe armhf libhwloc-dev armhf 1.11.13-1 [150 kB] Get:98 http://ftpmaster.internal/ubuntu eoan/main armhf libibverbs-dev armhf 24.0-2 [189 kB] Get:99 http://ftpmaster.internal/ubuntu eoan/universe armhf libopenmpi-dev armhf 3.1.3-11build1 [851 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 37.9 MB in 2s (24.3 MB/s) Selecting previously unselected package liblocale-gettext-perl. 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Setting up libevent-2.1-6:armhf (2.1.8-stable-4build1) ... Setting up ocl-icd-libopencl1:armhf (2.2.11-1ubuntu1) ... Setting up libuchardet0:armhf (0.0.6-3) ... Setting up libnl-3-200:armhf (3.4.0-1) ... Setting up openmpi-common (3.1.3-11build1) ... Setting up libsub-override-perl (0.09-2) ... Setting up libkrb5-3:armhf (1.17-6) ... Setting up libboost-serialization1.67.0:armhf (1.67.0-13ubuntu1) ... Setting up libbsd0:armhf (0.10.0-1) ... Setting up libelf1:armhf (0.176-1.1) ... Setting up libxml2:armhf (2.9.4+dfsg1-7ubuntu3) ... Setting up liburi-perl (1.76-1) ... Setting up liblocale-gettext-perl (1.07-3build3) ... Setting up libfile-stripnondeterminism-perl (1.6.0-1) ... Setting up libboost-serialization1.67-dev:armhf (1.67.0-13ubuntu1) ... Setting up libevent-pthreads-2.1-6:armhf (2.1.8-stable-4build1) ... Setting up libboost-regex1.67.0:armhf (1.67.0-13ubuntu1) ... Setting up python2.7 (2.7.16-4) ... Setting up libtool (2.4.6-11) ... Setting up libpython2-stdlib:armhf (2.7.16-1) ... Setting up libhwloc5:armhf (1.11.13-1) ... Setting up libedit2:armhf (3.1-20190324-1) ... Setting up m4 (1.4.18-2) ... Setting up libboost-graph1.67.0:armhf (1.67.0-13ubuntu1) ... Setting up libhwloc-plugins:armhf (1.11.13-1) ... Setting up python2 (2.7.16-1) ... Setting up libnl-route-3-200:armhf (3.4.0-1) ... Setting up help2man (1.47.11) ... Setting up libpython-stdlib:armhf (2.7.16-1) ... Setting up bsdmainutils (11.1.2ubuntu2) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up libgssapi-krb5-2:armhf (1.17-6) ... Setting up libcroco3:armhf (0.6.13-1) ... Setting up autoconf (2.69-11) ... Setting up dwz (0.13-1) ... Setting up libnl-3-dev:armhf (3.4.0-1) ... Setting up groff-base (1.22.4-3) ... Setting up libhtml-parser-perl (3.72-3build2) ... Setting up libboost-graph1.67-dev:armhf (1.67.0-13ubuntu1) ... Setting up libtext-multimarkdown-perl (1.000035-1) ... Setting up python (2.7.16-1) ... Setting up automake (1:1.16.1-4ubuntu3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libboost-graph-dev:armhf (1.67.0.2) ... Setting up libibverbs1:armhf (24.0-2) ... Setting up gettext (0.19.8.1-9) ... Setting up libpmix2:armhf (3.1.4-1) ... Setting up ibverbs-providers:armhf (24.0-2) ... Setting up python-pkg-resources (41.1.0-1) ... Setting up openssh-client (1:8.0p1-6build1) ... Setting up libopenmpi3:armhf (3.1.3-11build1) ... Setting up python-attr (18.2.0-1) ... Setting up man-db (2.8.7-3) ... Not building database; man-db/auto-update is not 'true'. Created symlink /etc/systemd/system/timers.target.wants/man-db.timer → /lib/systemd/system/man-db.timer. Setting up intltool-debian (0.35.0+20060710.5) ... Setting up python-six (1.12.0-2) ... Setting up libnl-route-3-dev:armhf (3.4.0-1) ... Setting up libltdl-dev:armhf (2.4.6-11) ... Setting up python-pyparsing (2.2.0+dfsg1-2) ... Setting up libhwloc-dev:armhf (1.11.13-1) ... Setting up openmpi-bin (3.1.3-11build1) ... update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode Setting up python-packaging (19.1-2) ... Setting up po-debconf (1.0.21) ... Setting up python-markdown (3.1.1-2) ... Setting up libibverbs-dev:armhf (24.0-2) ... Setting up libopenmpi-dev:armhf (3.1.3-11build1) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/openmpi/include to provide /usr/include/arm-linux-gnueabihf/mpi (mpi-arm-linux-gnueabihf) in auto mode Setting up debhelper (12.4ubuntu1) ... Setting up dh-autoreconf (19) ... Setting up dh-strip-nondeterminism (1.6.0-1) ... Setting up sbuild-build-depends-abyss-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.30-0ubuntu1) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.4.0-161-generic arm64 (armv7l) Toolchain package versions: binutils_2.32.51.20190905-0ubuntu1 dpkg-dev_1.19.7ubuntu77 g++-9_9.2.1-8ubuntu1 gcc-9_9.2.1-8ubuntu1 libc6-dev_2.30-0ubuntu1 libstdc++-9-dev_9.2.1-8ubuntu1 libstdc++6_9.2.1-8ubuntu1 linux-libc-dev_5.3.0-10.11 Package versions: adduser_3.118ubuntu1 advancecomp_2.1-2.1 apt_1.9.3 autoconf_2.69-11 automake_1:1.16.1-4ubuntu3 autopoint_0.19.8.1-9 autotools-dev_20180224.1 base-files_10.2ubuntu6 base-passwd_3.5.46 bash_5.0-4ubuntu1 binutils_2.32.51.20190905-0ubuntu1 binutils-arm-linux-gnueabihf_2.32.51.20190905-0ubuntu1 binutils-common_2.32.51.20190905-0ubuntu1 bsdmainutils_11.1.2ubuntu2 bsdutils_1:2.34-0.1ubuntu2 build-essential_12.7ubuntu1 bzip2_1.0.6-9.2 ca-certificates_20190110 coreutils_8.30-3ubuntu2 cpp_4:9.2.1-3.1ubuntu1 cpp-9_9.2.1-8ubuntu1 dash_0.5.10.2-6 debconf_1.5.73 debhelper_12.4ubuntu1 debianutils_4.8.6.3 dh-autoreconf_19 dh-strip-nondeterminism_1.6.0-1 diffutils_1:3.7-3 dpkg_1.19.7ubuntu77 dpkg-dev_1.19.7ubuntu77 dwz_0.13-1 e2fsprogs_1.45.3-4ubuntu1 fakeroot_1.23-1 fdisk_2.34-0.1ubuntu2 file_1:5.37-5 findutils_4.6.0+git+20190209-2ubuntu1 g++_4:9.2.1-3.1ubuntu1 g++-9_9.2.1-8ubuntu1 gcc_4:9.2.1-3.1ubuntu1 gcc-9_9.2.1-8ubuntu1 gcc-9-base_9.2.1-8ubuntu1 gettext_0.19.8.1-9 gettext-base_0.19.8.1-9 gpg_2.2.12-1ubuntu3 gpg-agent_2.2.12-1ubuntu3 gpgconf_2.2.12-1ubuntu3 gpgv_2.2.12-1ubuntu3 grep_3.3-1 groff-base_1.22.4-3 gzip_1.10-0ubuntu3 help2man_1.47.11 hostname_3.22 ibverbs-providers_24.0-2 init_1.57 init-system-helpers_1.57 intltool-debian_0.35.0+20060710.5 libacl1_2.2.53-4 libapparmor1_2.13.3-5ubuntu1 libapt-pkg5.90_1.9.3 libarchive-zip-perl_1.65-1 libargon2-1_0~20171227-0.2 libasan5_9.2.1-8ubuntu1 libassuan0_2.5.3-7ubuntu1 libatomic1_9.2.1-8ubuntu1 libattr1_1:2.4.48-4 libaudit-common_1:2.8.5-2ubuntu1 libaudit1_1:2.8.5-2ubuntu1 libbinutils_2.32.51.20190905-0ubuntu1 libblkid1_2.34-0.1ubuntu2 libboost-graph-dev_1.67.0.2 libboost-graph1.67-dev_1.67.0-13ubuntu1 libboost-graph1.67.0_1.67.0-13ubuntu1 libboost-regex1.67.0_1.67.0-13ubuntu1 libboost-serialization1.67-dev_1.67.0-13ubuntu1 libboost-serialization1.67.0_1.67.0-13ubuntu1 libboost-test1.67-dev_1.67.0-13ubuntu1 libboost-test1.67.0_1.67.0-13ubuntu1 libboost1.67-dev_1.67.0-13ubuntu1 libbsd0_0.10.0-1 libbz2-1.0_1.0.6-9.2 libc-bin_2.30-0ubuntu1 libc-dev-bin_2.30-0ubuntu1 libc6_2.30-0ubuntu1 libc6-dev_2.30-0ubuntu1 libcap-ng0_0.7.9-2 libcap2_1:2.25-2 libcc1-0_9.2.1-8ubuntu1 libcom-err2_1.45.3-4ubuntu1 libcroco3_0.6.13-1 libcryptsetup12_2:2.2.0-3ubuntu1 libdb5.3_5.3.28+dfsg1-0.6ubuntu1 libdebconfclient0_0.249ubuntu1 libdevmapper1.02.1_2:1.02.155-2ubuntu6 libdpkg-perl_1.19.7ubuntu77 libedit2_3.1-20190324-1 libelf1_0.176-1.1 libevent-2.1-6_2.1.8-stable-4build1 libevent-core-2.1-6_2.1.8-stable-4build1 libevent-pthreads-2.1-6_2.1.8-stable-4build1 libexpat1_2.2.7-2 libext2fs2_1.45.3-4ubuntu1 libfakeroot_1.23-1 libfdisk1_2.34-0.1ubuntu2 libffi6_3.2.1-9 libfile-stripnondeterminism-perl_1.6.0-1 libgcc-9-dev_9.2.1-8ubuntu1 libgcc1_1:9.2.1-8ubuntu1 libgcrypt20_1.8.4-5ubuntu1 libgdbm-compat4_1.18.1-5 libgdbm6_1.18.1-5 libglib2.0-0_2.62.0-1 libgmp10_2:6.1.2+dfsg-4 libgnutls30_3.6.9-4build1 libgomp1_9.2.1-8ubuntu1 libgpg-error0_1.36-7 libgssapi-krb5-2_1.17-6 libhogweed4_3.4.1-1 libhtml-parser-perl_3.72-3build2 libhtml-tagset-perl_3.20-3 libhwloc-dev_1.11.13-1 libhwloc-plugins_1.11.13-1 libhwloc5_1.11.13-1 libibverbs-dev_24.0-2 libibverbs1_24.0-2 libicu63_63.2-2 libidn11_1.33-2.2ubuntu2 libidn2-0_2.2.0-1 libip4tc2_1.8.3-2ubuntu4 libisl21_0.21-2 libjson-c4_0.13.1+dfsg-4 libk5crypto3_1.17-6 libkeyutils1_1.6-6 libkmod2_26-1ubuntu1 libkrb5-3_1.17-6 libkrb5support0_1.17-6 liblocale-gettext-perl_1.07-3build3 liblockfile-bin_1.15-1 liblockfile1_1.15-1 libltdl-dev_2.4.6-11 libltdl7_2.4.6-11 liblz4-1_1.9.1-1 liblzma5_5.2.4-1 libmagic-mgc_1:5.37-5 libmagic1_1:5.37-5 libmount1_2.34-0.1ubuntu2 libmpc3_1.1.0-1 libmpfr6_4.0.2-1 libncurses6_6.1+20190803-1ubuntu1 libncursesw6_6.1+20190803-1ubuntu1 libnettle6_3.4.1-1 libnl-3-200_3.4.0-1 libnl-3-dev_3.4.0-1 libnl-route-3-200_3.4.0-1 libnl-route-3-dev_3.4.0-1 libnpth0_1.6-1 libopenmpi-dev_3.1.3-11build1 libopenmpi3_3.1.3-11build1 libp11-kit0_0.23.17-2 libpam-modules_1.3.1-5ubuntu1 libpam-modules-bin_1.3.1-5ubuntu1 libpam-runtime_1.3.1-5ubuntu1 libpam0g_1.3.1-5ubuntu1 libpciaccess0_0.16-0ubuntu1 libpcre2-8-0_10.32-5 libpcre3_2:8.39-12 libperl5.28_5.28.1-6 libpipeline1_1.5.1-2 libpmix2_3.1.4-1 libpng16-16_1.6.37-1 libprocps7_2:3.3.15-2ubuntu3 libpython-stdlib_2.7.16-1 libpython2-stdlib_2.7.16-1 libpython2.7-minimal_2.7.16-4 libpython2.7-stdlib_2.7.16-4 libreadline8_8.0-3 libseccomp2_2.4.1-0ubuntu0.19.10.3 libselinux1_2.9-2 libsemanage-common_2.9-3 libsemanage1_2.9-3 libsepol1_2.9-2 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openssh-client_1:8.0p1-6build1 openssl_1.1.1c-1ubuntu4 optipng_0.7.7-1 passwd_1:4.5-1.1ubuntu4 patch_2.7.6-6 perl_5.28.1-6 perl-base_5.28.1-6 perl-modules-5.28_5.28.1-6 pinentry-curses_1.1.0-3 pkg-config_0.29.1-0ubuntu3 pkgbinarymangler_144 po-debconf_1.0.21 policyrcd-script-zg2_0.1-3 procps_2:3.3.15-2ubuntu3 python_2.7.16-1 python-attr_18.2.0-1 python-markdown_3.1.1-2 python-minimal_2.7.16-1 python-packaging_19.1-2 python-pkg-resources_41.1.0-1 python-pyparsing_2.2.0+dfsg1-2 python-six_1.12.0-2 python2_2.7.16-1 python2-minimal_2.7.16-1 python2.7_2.7.16-4 python2.7-minimal_2.7.16-4 readline-common_8.0-3 sbuild-build-depends-abyss-dummy_0.invalid.0 sbuild-build-depends-core-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12 systemd_241-7ubuntu1 systemd-sysv_241-7ubuntu1 sysvinit-utils_2.95-5ubuntu2 tar_1.30+dfsg-6 tzdata_2019c-1 ubuntu-keyring_2018.09.18.1 util-linux_2.34-0.1ubuntu2 xz-utils_5.2.4-1 zlib1g_1:1.2.11.dfsg-1ubuntu3 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Sat Aug 17 07:23:59 2019 UTC gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./abyss_2.2.2-1.dsc dpkg-source: info: extracting abyss in abyss-2.2.2 dpkg-source: info: unpacking abyss_2.2.2.orig.tar.gz dpkg-source: info: unpacking abyss_2.2.2-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying abyss-pe.patch dpkg-source: info: applying abyss-32-bit.patch dpkg-source: info: applying strict_alignment.patch dpkg-source: info: applying spelling Check disc space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=noautodbgsym parallel=4 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=build-PACKAGEBUILD-17632304 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-17632304 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-17632304 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package abyss dpkg-buildpackage: info: source version 2.2.2-1 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf fakeroot debian/rules clean dh clean dh_clean debian/rules build-arch dh build-arch dh_update_autotools_config -a dh_autoreconf -a configure.ac:16: installing './compile' configure.ac:166: installing './config.guess' configure.ac:166: installing './config.sub' configure.ac:10: installing './install-sh' configure.ac:10: installing './missing' ABYSS/Makefile.am: installing './depcomp' parallel-tests: installing './test-driver' debian/rules override_dh_auto_configure make[1]: Entering directory '/<>' dh_auto_configure -- \ --with-mpi=/usr/lib/arm-linux-gnueabihf/openmpi ./configure --build=arm-linux-gnueabihf --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-silent-rules --libdir=\${prefix}/lib/arm-linux-gnueabihf --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-mpi=/usr/lib/arm-linux-gnueabihf/openmpi configure: WARNING: unrecognized options: --disable-maintainer-mode 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 whether g++ supports C++11 features with -std=c++11... yes 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 the include directive... yes (GNU style) checking whether make supports nested variables... yes checking dependency style of g++ -std=c++11... none checking for gawk... (cached) mawk 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 how to run the C preprocessor... gcc -E checking whether we are using the GNU C++ compiler... (cached) yes checking whether g++ -std=c++11 accepts -g... (cached) yes checking for ranlib... ranlib checking for ghc... no ./configure: line 5896: : command not found checking for pandoc... no 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 dlfcn.h usability... yes checking dlfcn.h presence... yes checking for dlfcn.h... yes checking fcntl.h usability... yes checking fcntl.h presence... yes checking for fcntl.h... yes checking float.h usability... yes checking float.h presence... yes checking for float.h... yes checking limits.h usability... yes checking limits.h presence... yes checking for limits.h... yes checking stddef.h usability... yes checking stddef.h presence... yes checking for stddef.h... yes checking for stdint.h... (cached) yes checking for stdlib.h... (cached) yes checking sys/param.h usability... yes checking sys/param.h presence... yes checking for sys/param.h... yes checking for stdbool.h that conforms to C99... yes checking for _Bool... yes checking for ANSI C header files... (cached) yes checking whether byte ordering is bigendian... no checking for an ANSI C-conforming const... yes checking for inline... inline checking for ptrdiff_t... yes checking for mode_t... yes checking for pid_t... yes checking for size_t... yes checking for ssize_t... yes checking for int64_t... yes checking for uint8_t... yes checking for uint16_t... yes checking for uint32_t... yes checking for uint64_t... yes checking for std::hash... yes checking for std::tr1::hash... yes checking for std::tr1::tuple... yes checking for dup2... yes checking for gethostname... yes checking for getopt_long... yes checking for getpagesize... yes checking for memset... yes checking for strdup... yes checking for strerror... yes checking for strtoul... yes checking vfork.h usability... no checking vfork.h presence... no checking for vfork.h... no checking for fork... yes checking for vfork... yes checking for working fork... yes checking for working vfork... (cached) yes checking for stdlib.h... (cached) yes checking for GNU libc compatible malloc... yes checking for working memcmp... yes checking for stdlib.h... (cached) yes checking for GNU libc compatible realloc... yes checking for vprintf... yes checking for _doprnt... no checking whether HOST_NAME_MAX is declared... yes checking build system type... arm-unknown-linux-gnueabihf checking host system type... arm-unknown-linux-gnueabihf checking if compiler needs -Werror to reject unknown flags... no checking for the pthreads library -lpthreads... no checking whether pthreads work without any flags... no checking whether pthreads work with -Kthread... no checking whether pthreads work with -kthread... no checking for the pthreads library -llthread... no checking whether pthreads work with -pthread... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for PTHREAD_PRIO_INHERIT... yes checking mpi.h usability... yes checking mpi.h presence... yes checking for mpi.h... yes checking for MPI_Init in -lmpi... yes checking for sqrt in -lm... yes checking for pow... yes checking for sqrt... yes checking for ceilf... yes checking for dlsym in -ldl... yes checking how to run the C++ preprocessor... g++ -std=c++11 -E checking functional usability... yes checking functional presence... yes checking for functional... yes checking tr1/functional usability... yes checking tr1/functional presence... yes checking for tr1/functional... yes checking boost/functional/hash.hpp usability... yes checking boost/functional/hash.hpp presence... yes checking for boost/functional/hash.hpp... yes checking boost/property_map/property_map.hpp usability... yes checking boost/property_map/property_map.hpp presence... yes checking for boost/property_map/property_map.hpp... yes checking google/sparse_hash_map usability... yes checking google/sparse_hash_map presence... yes checking for google/sparse_hash_map... yes checking unordered_map usability... yes checking unordered_map presence... yes checking for unordered_map... yes checking tr1/unordered_map usability... yes checking tr1/unordered_map presence... yes checking for tr1/unordered_map... yes checking unordered_set usability... yes checking unordered_set presence... yes checking for unordered_set... yes checking tr1/unordered_set usability... yes checking tr1/unordered_set presence... yes checking for tr1/unordered_set... yes checking boost/unordered_set.hpp usability... yes checking boost/unordered_set.hpp presence... yes checking for boost/unordered_set.hpp... yes checking sqlite3.h usability... yes checking sqlite3.h presence... yes checking for sqlite3.h... yes checking for main in -lsqlite3... yes checking for g++ -std=c++11 option to support OpenMP... -fopenmp checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating ABYSS/Makefile config.status: creating Align/Makefile config.status: creating Assembly/Makefile config.status: creating Common/Makefile config.status: creating DataLayer/Makefile config.status: creating FMIndex/Makefile config.status: creating Graph/Makefile config.status: creating Parallel/Makefile config.status: creating bin/Makefile config.status: creating doc/Makefile config.status: creating dialign/Makefile config.status: creating kmerprint/Makefile config.status: creating AdjList/Makefile config.status: creating Konnector/Makefile config.status: creating DAssembler/Makefile config.status: creating DistanceEst/Makefile config.status: creating Layout/Makefile config.status: creating Map/Makefile config.status: creating Overlap/Makefile config.status: creating PopBubbles/Makefile config.status: creating Scaffold/Makefile config.status: creating SimpleGraph/Makefile config.status: creating MergePaths/Makefile config.status: creating KAligner/Makefile config.status: creating PairedDBG/Makefile config.status: creating ParseAligns/Makefile config.status: creating PathOverlap/Makefile config.status: creating Consensus/Makefile config.status: creating FilterGraph/Makefile config.status: creating GapFiller/Makefile config.status: creating Sealer/Makefile config.status: creating vendor/gtest-1.7.0/Makefile config.status: creating Unittest/Makefile config.status: creating LogKmerCount/Makefile config.status: creating Bloom/Makefile config.status: creating BloomDBG/Makefile config.status: creating DataBase/Makefile config.status: creating vendor/Makefile config.status: creating vendor/nthash/Makefile config.status: creating config.h config.status: executing depfiles commands configure: WARNING: unrecognized options: --disable-maintainer-mode make[1]: Leaving directory '/<>' debian/rules override_dh_auto_build make[1]: Entering directory '/<>' dh_auto_build make -j4 make[2]: Entering directory '/<>' make all-recursive make[3]: Entering directory '/<>' Making all in bin make[4]: Entering directory '/<>/bin' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/<>/bin' Making all in doc make[4]: Entering directory '/<>/doc' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/<>/doc' Making all in Common make[4]: Entering directory '/<>/Common' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/<> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -flto=auto -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=deprecated-copy -Wno-error=array-bounds -c -o libcommon_a-ContigID.o `test -f 'ContigID.cpp' || echo './'`ContigID.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/<> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -flto=auto -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=deprecated-copy -Wno-error=array-bounds -c -o libcommon_a-Fcontrol.o `test -f 'Fcontrol.cpp' || echo './'`Fcontrol.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/<> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -flto=auto -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=deprecated-copy -Wno-error=array-bounds -c -o libcommon_a-Histogram.o `test -f 'Histogram.cpp' || echo './'`Histogram.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/<> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -flto=auto -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=deprecated-copy -Wno-error=array-bounds -c -o libcommon_a-Kmer.o `test -f 'Kmer.cpp' || echo './'`Kmer.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/<> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -flto=auto -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=deprecated-copy -Wno-error=array-bounds -c -o libcommon_a-Log.o `test -f 'Log.cpp' || echo './'`Log.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/<> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -flto=auto -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=deprecated-copy -Wno-error=array-bounds -c -o libcommon_a-Options.o `test -f 'Options.cpp' || echo './'`Options.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/<> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -flto=auto -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=deprecated-copy -Wno-error=array-bounds -c -o libcommon_a-Sequence.o `test -f 'Sequence.cpp' || echo './'`Sequence.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/<> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -flto=auto -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=deprecated-copy -Wno-error=array-bounds -c -o libcommon_a-SignalHandler.o `test -f 'SignalHandler.cpp' || echo './'`SignalHandler.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/<> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -flto=auto -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=deprecated-copy -Wno-error=array-bounds -c -o libcommon_a-Timer.o `test -f 'Timer.cpp' || echo './'`Timer.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/<> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -flto=auto -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=deprecated-copy -Wno-error=array-bounds -c -o libcommon_a-Uncompress.o `test -f 'Uncompress.cpp' || echo './'`Uncompress.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/<> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -flto=auto -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=deprecated-copy -Wno-error=array-bounds -c -o libcommon_a-city.o `test -f 'city.cc' || echo './'`city.cc rm -f libcommon.a ar cru libcommon.a libcommon_a-ContigID.o libcommon_a-Fcontrol.o libcommon_a-Histogram.o libcommon_a-Kmer.o libcommon_a-Log.o libcommon_a-Options.o libcommon_a-Sequence.o libcommon_a-SignalHandler.o libcommon_a-Timer.o libcommon_a-Uncompress.o libcommon_a-city.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libcommon.a make[4]: Leaving directory '/<>/Common' Making all in Graph make[4]: Entering directory '/<>/Graph' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/<> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -flto=auto -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=deprecated-copy -Wno-error=array-bounds -c -o abyss_gc-gc.o `test -f 'gc.cc' || echo './'`gc.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/<> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -flto=auto -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=deprecated-copy -Wno-error=array-bounds -c -o abyss_todot-todot.o `test -f 'todot.cc' || echo './'`todot.cc In file included from todot.cc:7: ../Common/Estimate.h: In function ‘std::istream& operator>>(std::istream&, EstimateRecord&)’: ../Common/Estimate.h:188:44: warning: implicitly-declared ‘ContigNode& ContigNode::operator=(const ContigNode&)’ is deprecated [-Wdeprecated-copy] 188 | ep.first = find_vertex(s, g_contigNames); | ^ In file included from ../Common/ContigProperties.h:4, from todot.cc:5: ../Common/ContigNode.h:25:1: note: because ‘ContigNode’ has user-provided ‘ContigNode::ContigNode(const ContigNode&)’ 25 | ContigNode(const ContigNode& o) : m_index(o.m_index) { } | ^~~~~~~~~~ In file included from GraphIO.h:8, from gc.cc:6: DotIO.h: In instantiation of ‘std::istream& read_dot_id(std::istream&, const Graph&, typename boost::graph_traits::vertex_descriptor&) [with Graph = DirectedGraph; std::istream = std::basic_istream; typename boost::graph_traits::vertex_descriptor = ContigNode]’: DotIO.h:259:42: required from ‘std::istream& read_dot(std::istream&, Graph&, BetterEP) [with Graph = DirectedGraph; BetterEP = DisallowParallelEdges; std::istream = std::basic_istream]’ GraphIO.h:60:25: required from ‘std::istream& read_graph(std::istream&, ContigGraph&, BetterEP) [with Graph = DirectedGraph; BetterEP = DisallowParallelEdges; std::istream = std::basic_istream]’ gc.cc:61:12: required from ‘void readGraph(const string&, Graph&, BetterEP) [with Graph = ContigGraph >; BetterEP = DisallowParallelEdges; std::string = std::__cxx11::basic_string]’ gc.cc:73:13: required from ‘void readGraphs(Graph&, It, It, BetterEP) [with Graph = ContigGraph >; It = char**; BetterEP = DisallowParallelEdges]’ gc.cc:109:27: required from here DotIO.h:155:5: warning: implicitly-declared ‘ContigNode& ContigNode::operator=(const ContigNode&)’ is deprecated [-Wdeprecated-copy] 155 | u = find_vertex(s, g); | ~~^~~~~~~~~~~~~~~~~~~ In file included from DirectedGraph.h:4, from gc.cc:5: ../Common/ContigNode.h:25:1: note: because ‘ContigNode’ has user-provided ‘ContigNode::ContigNode(const ContigNode&)’ 25 | ContigNode(const ContigNode& o) : m_index(o.m_index) { } | ^~~~~~~~~~ In file included from GraphIO.h:5, from gc.cc:6: AdjIO.h: In instantiation of ‘std::istream& readDistEdges(std::istream&, ContigGraph&, typename boost::graph_traits::vertex_descriptor, BetterEP) [with Graph = DirectedGraph; BetterEP = DisallowParallelEdges; std::istream = std::basic_istream; typename boost::graph_traits::vertex_descriptor = ContigNode]’: AdjIO.h:170:18: required from ‘std::istream& read_adj(std::istream&, ContigGraph&, BetterEP) [with Graph = DirectedGraph; BetterEP = DisallowParallelEdges; std::istream = std::basic_istream]’ GraphIO.h:80:18: required from ‘std::istream& read_graph(std::istream&, ContigGraph&, BetterEP) [with Graph = DirectedGraph; BetterEP = DisallowParallelEdges; std::istream = std::basic_istream]’ gc.cc:61:12: required from ‘void readGraph(const string&, Graph&, BetterEP) [with Graph = ContigGraph >; BetterEP = DisallowParallelEdges; std::string = std::__cxx11::basic_string]’ gc.cc:73:13: required from ‘void readGraphs(Graph&, It, It, BetterEP) [with Graph = ContigGraph >; It = char**; BetterEP = DisallowParallelEdges]’ gc.cc:109:27: required from here AdjIO.h:76:5: warning: implicitly-declared ‘ContigNode& ContigNode::operator=(const ContigNode&)’ is deprecated [-Wdeprecated-copy] 76 | v = v ^ get(vertex_sense, g, u); | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from DirectedGraph.h:4, from gc.cc:5: ../Common/ContigNode.h:25:1: note: because ‘ContigNode’ has user-provided ‘ContigNode::ContigNode(const ContigNode&)’ 25 | ContigNode(const ContigNode& o) : m_index(o.m_index) { } | ^~~~~~~~~~ In file included from GraphIO.h:8, from todot.cc:9: DotIO.h: In instantiation of ‘std::istream& read_dot_id(std::istream&, const Graph&, typename boost::graph_traits::vertex_descriptor&) [with Graph = DirectedGraph; std::istream = std::basic_istream; typename boost::graph_traits::vertex_descriptor = ContigNode]’: DotIO.h:259:42: required from ‘std::istream& read_dot(std::istream&, Graph&, BetterEP) [with Graph = DirectedGraph; BetterEP = BetterDistanceEst; std::istream = std::basic_istream]’ GraphIO.h:60:25: required from ‘std::istream& read_graph(std::istream&, ContigGraph&, BetterEP) [with Graph = DirectedGraph; BetterEP = BetterDistanceEst; std::istream = std::basic_istream]’ todot.cc:105:12: required from ‘void readGraph(const string&, Graph&, BetterEP) [with Graph = ContigGraph >; BetterEP = BetterDistanceEst; std::string = std::__cxx11::basic_string]’ todot.cc:118:13: required from ‘void readGraphs(Graph&, It, It, BetterEP) [with Graph = ContigGraph >; It = char**; BetterEP = BetterDistanceEst]’ todot.cc:185:24: required from here DotIO.h:155:5: warning: implicitly-declared ‘ContigNode& ContigNode::operator=(const ContigNode&)’ is deprecated [-Wdeprecated-copy] 155 | u = find_vertex(s, g); | ~~^~~~~~~~~~~~~~~~~~~ In file included from ../Common/ContigProperties.h:4, from todot.cc:5: ../Common/ContigNode.h:25:1: note: because ‘ContigNode’ has user-provided ‘ContigNode::ContigNode(const ContigNode&)’ 25 | ContigNode(const ContigNode& o) : m_index(o.m_index) { } | ^~~~~~~~~~ In file included from GraphIO.h:5, from todot.cc:9: AdjIO.h: In instantiation of ‘std::istream& readDistEdges(std::istream&, ContigGraph&, typename boost::graph_traits::vertex_descriptor, BetterEP) [with Graph = DirectedGraph; BetterEP = BetterDistanceEst; std::istream = std::basic_istream; typename boost::graph_traits::vertex_descriptor = ContigNode]’: AdjIO.h:170:18: required from ‘std::istream& read_adj(std::istream&, ContigGraph&, BetterEP) [with Graph = DirectedGraph; BetterEP = BetterDistanceEst; std::istream = std::basic_istream]’ GraphIO.h:80:18: required from ‘std::istream& read_graph(std::istream&, ContigGraph&, BetterEP) [with Graph = DirectedGraph; BetterEP = BetterDistanceEst; std::istream = std::basic_istream]’ todot.cc:105:12: required from ‘void readGraph(const string&, Graph&, BetterEP) [with Graph = ContigGraph >; BetterEP = BetterDistanceEst; std::string = std::__cxx11::basic_string]’ todot.cc:118:13: required from ‘void readGraphs(Graph&, It, It, BetterEP) [with Graph = ContigGraph >; It = char**; BetterEP = BetterDistanceEst]’ todot.cc:185:24: required from here AdjIO.h:76:5: warning: implicitly-declared ‘ContigNode& ContigNode::operator=(const ContigNode&)’ is deprecated [-Wdeprecated-copy] 76 | v = v ^ get(vertex_sense, g, u); | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../Common/ContigProperties.h:4, from todot.cc:5: ../Common/ContigNode.h:25:1: note: because ‘ContigNode’ has user-provided ‘ContigNode::ContigNode(const ContigNode&)’ 25 | ContigNode(const ContigNode& o) : m_index(o.m_index) { } | ^~~~~~~~~~ In file included from GraphIO.h:8, from todot.cc:9: DotIO.h: In instantiation of ‘std::istream& read_dot_id(std::istream&, const Graph&, typename boost::graph_traits::vertex_descriptor&) [with Graph = DirectedGraph; std::istream = std::basic_istream; typename boost::graph_traits::vertex_descriptor = ContigNode]’: DotIO.h:259:42: required from ‘std::istream& read_dot(std::istream&, Graph&, BetterEP) [with Graph = DirectedGraph; BetterEP = DisallowParallelEdges; std::istream = std::basic_istream]’ GraphIO.h:60:25: required from ‘std::istream& read_graph(std::istream&, ContigGraph&, BetterEP) [with Graph = DirectedGraph; BetterEP = DisallowParallelEdges; std::istream = std::basic_istream]’ todot.cc:105:12: required from ‘void readGraph(const string&, Graph&, BetterEP) [with Graph = ContigGraph >; BetterEP = DisallowParallelEdges; std::string = std::__cxx11::basic_string]’ todot.cc:118:13: required from ‘void readGraphs(Graph&, It, It, BetterEP) [with Graph = ContigGraph >; It = char**; BetterEP = DisallowParallelEdges]’ todot.cc:190:28: required from here DotIO.h:155:5: warning: implicitly-declared ‘ContigNode& ContigNode::operator=(const ContigNode&)’ is deprecated [-Wdeprecated-copy] 155 | u = find_vertex(s, g); | ~~^~~~~~~~~~~~~~~~~~~ In file included from ../Common/ContigProperties.h:4, from todot.cc:5: ../Common/ContigNode.h:25:1: note: because ‘ContigNode’ has user-provided ‘ContigNode::ContigNode(const ContigNode&)’ 25 | ContigNode(const ContigNode& o) : m_index(o.m_index) { } | ^~~~~~~~~~ In file included from GraphIO.h:5, from todot.cc:9: AdjIO.h: In instantiation of ‘std::istream& readDistEdges(std::istream&, ContigGraph&, typename boost::graph_traits::vertex_descriptor, BetterEP) [with Graph = DirectedGraph; BetterEP = DisallowParallelEdges; std::istream = std::basic_istream; typename boost::graph_traits::vertex_descriptor = ContigNode]’: AdjIO.h:170:18: required from ‘std::istream& read_adj(std::istream&, ContigGraph&, BetterEP) [with Graph = DirectedGraph; BetterEP = DisallowParallelEdges; std::istream = std::basic_istream]’ GraphIO.h:80:18: required from ‘std::istream& read_graph(std::istream&, ContigGraph&, BetterEP) [with Graph = DirectedGraph; BetterEP = DisallowParallelEdges; std::istream = std::basic_istream]’ todot.cc:105:12: required from ‘void readGraph(const string&, Graph&, BetterEP) [with Graph = ContigGraph >; BetterEP = DisallowParallelEdges; std::string = std::__cxx11::basic_string]’ todot.cc:118:13: required from ‘void readGraphs(Graph&, It, It, BetterEP) [with Graph = ContigGraph >; It = char**; BetterEP = DisallowParallelEdges]’ todot.cc:190:28: required from here AdjIO.h:76:5: warning: implicitly-declared ‘ContigNode& ContigNode::operator=(const ContigNode&)’ is deprecated [-Wdeprecated-copy] 76 | v = v ^ get(vertex_sense, g, u); | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../Common/ContigProperties.h:4, from todot.cc:5: ../Common/ContigNode.h:25:1: note: because ‘ContigNode’ has user-provided ‘ContigNode::ContigNode(const ContigNode&)’ 25 | ContigNode(const ContigNode& o) : m_index(o.m_index) { } | ^~~~~~~~~~ g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -flto=auto -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=deprecated-copy -Wno-error=array-bounds -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-Bsymbolic-functions -flto=auto -Wl,-z,relro -Wl,-z,now -o abyss-gc abyss_gc-gc.o ../Common/libcommon.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -flto=auto -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=deprecated-copy -Wno-error=array-bounds -L. -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-Bsymbolic-functions -flto=auto -Wl,-z,relro -Wl,-z,now -o abyss-todot abyss_todot-todot.o ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/<>/Graph' Making all in DataLayer make[4]: Entering directory '/<>/DataLayer' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/<> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -flto=auto -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=deprecated-copy -Wno-error=array-bounds -c -o abyss_fac-fac.o `test -f 'fac.cc' || echo './'`fac.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/<> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -flto=auto -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=deprecated-copy -Wno-error=array-bounds -c -o libdatalayer_a-FastaReader.o `test -f 'FastaReader.cpp' || echo './'`FastaReader.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/<> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -flto=auto -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=deprecated-copy -Wno-error=array-bounds -c -o libdatalayer_a-FastaWriter.o `test -f 'FastaWriter.cpp' || echo './'`FastaWriter.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/<> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -flto=auto -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=deprecated-copy -Wno-error=array-bounds -c -o abyss_tofastq-abyss-tofastq.o `test -f 'abyss-tofastq.cc' || echo './'`abyss-tofastq.cc rm -f libdatalayer.a ar cru libdatalayer.a libdatalayer_a-FastaReader.o libdatalayer_a-FastaWriter.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libdatalayer.a g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -flto=auto -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=deprecated-copy -Wno-error=array-bounds -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-Bsymbolic-functions -flto=auto -Wl,-z,relro -Wl,-z,now -o abyss-tofastq abyss_tofastq-abyss-tofastq.o libdatalayer.a ../Common/libcommon.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -flto=auto -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=deprecated-copy -Wno-error=array-bounds -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-Bsymbolic-functions -flto=auto -Wl,-z,relro -Wl,-z,now -o abyss-fac abyss_fac-fac.o libdatalayer.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/<>/DataLayer' Making all in DataBase make[4]: Entering directory '/<>/DataBase' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/<> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -flto=auto -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=deprecated-copy -Wno-error=array-bounds -c -o abyss_db_csv-DB.o `test -f 'DB.cc' || echo './'`DB.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/<> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -flto=auto -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=deprecated-copy -Wno-error=array-bounds -c -o abyss_db_csv-db-csv.o `test -f 'db-csv.cc' || echo './'`db-csv.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/<> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -flto=auto -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=deprecated-copy -Wno-error=array-bounds -c -o libdb_a-DB.o `test -f 'DB.cc' || echo './'`DB.cc g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -flto=auto -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=deprecated-copy -Wno-error=array-bounds -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-Bsymbolic-functions -flto=auto -Wl,-z,relro -Wl,-z,now -o abyss-db-csv abyss_db_csv-DB.o abyss_db_csv-db-csv.o -lsqlite3 -ldl -lm rm -f libdb.a ar cru libdb.a libdb_a-DB.o ../Common/libcommon.a ar: `u' modifier ignored since `D' is the default (see `U') ranlib libdb.a make[4]: Leaving directory '/<>/DataBase' Making all in FMIndex make[4]: Entering directory '/<>/FMIndex' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/<> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -flto=auto -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=deprecated-copy -Wno-error=array-bounds -c -o abyss_count-count.o `test -f 'count.cc' || echo './'`count.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I../Common -I/<> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -flto=auto -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=deprecated-copy -Wno-error=array-bounds -c -o libfmindex_a-bit_array.o `test -f 'bit_array.cc' || echo './'`bit_array.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/<> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -flto=auto -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=deprecated-copy -Wno-error=array-bounds -c -o abyss_dawg-abyss-dawg.o `test -f 'abyss-dawg.cc' || echo './'`abyss-dawg.cc rm -f libfmindex.a ar cru libfmindex.a libfmindex_a-bit_array.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libfmindex.a g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -flto=auto -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=deprecated-copy -Wno-error=array-bounds -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-Bsymbolic-functions -flto=auto -Wl,-z,relro -Wl,-z,now -o abyss-count abyss_count-count.o libfmindex.a ../Common/libcommon.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -flto=auto -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=deprecated-copy -Wno-error=array-bounds -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-Bsymbolic-functions -flto=auto -Wl,-z,relro -Wl,-z,now -o abyss-dawg abyss_dawg-abyss-dawg.o libfmindex.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/<>/FMIndex' Making all in Assembly make[4]: Entering directory '/<>/Assembly' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/<> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -flto=auto -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=deprecated-copy -Wno-error=array-bounds -c -o libassembly_a-AssemblyAlgorithms.o `test -f 'AssemblyAlgorithms.cc' || echo './'`AssemblyAlgorithms.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/<> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -flto=auto -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=deprecated-copy -Wno-error=array-bounds -c -o libassembly_a-Options.o `test -f 'Options.cc' || echo './'`Options.cc rm -f libassembly.a ar cru libassembly.a libassembly_a-AssemblyAlgorithms.o libassembly_a-Options.o ../Common/libcommon.a ar: `u' modifier ignored since `D' is the default (see `U') ranlib libassembly.a make[4]: Leaving directory '/<>/Assembly' Making all in dialign make[4]: Entering directory '/<>/dialign' gcc -DHAVE_CONFIG_H -I. -I.. -I/<> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -g -O2 -flto=auto -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o museq.o museq.c gcc -DHAVE_CONFIG_H -I. -I.. -I/<> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -g -O2 -flto=auto -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o alig.o alig.c gcc -DHAVE_CONFIG_H -I. -I.. -I/<> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -g -O2 -flto=auto -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o assemble.o assemble.c gcc -DHAVE_CONFIG_H -I. -I.. -I/<> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -g -O2 -flto=auto -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o diag.o diag.c assemble.c:40:20: warning: inline function ‘align_diag’ declared but never defined 40 | extern inline char align_diag(struct alignment *algn, struct scr_matrix *smatrix, struct diag* dg); | ^~~~~~~~~~ assemble.c:37:32: warning: inline function ‘find_eqc’ declared but never defined 37 | extern inline struct algn_pos *find_eqc(struct algn_pos **ap, int seqnum, int pos); | ^~~~~~~~ assemble.c:25:39: warning: inline function ‘find_diags_guided’ declared but never defined 25 | extern inline struct simple_diag_col* find_diags_guided(struct scr_matrix *smatrix, | ^~~~~~~~~~~~~~~~~ assemble.c:15:20: warning: inline function ‘calc_ov_weight’ declared but never defined 15 | extern inline void calc_ov_weight(struct diag* dg, struct diag_col *dcol, struct scr_matrix* smatrix, | ^~~~~~~~~~~~~~ assemble.c:13:20: warning: inline function ‘calc_weight’ declared but never defined 13 | extern inline void calc_weight(struct diag* dg, struct scr_matrix* smatrix, | ^~~~~~~~~~~ diag.c:1456:3: warning: ‘real_calc_weight’ is static but used in inline function ‘find_diags_dyn’ which is not static 1456 | real_calc_weight(dg, smatrix, pdist,1,tmp_dist,algn); | ^~~~~~~~~~~~~~~~ alig.c:15:20: warning: inline function ‘calc_ov_weight’ declared but never defined 15 | extern inline void calc_ov_weight(struct diag* dg, struct diag_col *dcol, struct scr_matrix* smatrix, | ^~~~~~~~~~~~~~ alig.c:13:20: warning: inline function ‘calc_weight’ declared but never defined 13 | extern inline void calc_weight(struct diag* dg, struct scr_matrix* smatrix, | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I.. -I/<> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -g -O2 -flto=auto -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o io.o io.c gcc -DHAVE_CONFIG_H -I. -I.. -I/<> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -g -O2 -flto=auto -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o orf.o orf.c gcc -DHAVE_CONFIG_H -I. -I.. -I/<> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -g -O2 -flto=auto -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o parameters.o parameters.c io.c: In function ‘read_scr_matrix’: io.c:270:3: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 270 | fscanf( fp, "%i", &is); | ^~~~~~~~~~~~~~~~~~~~~~ io.c:282:5: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 282 | fscanf(fp, "%s\n", rline); | ^~~~~~~~~~~~~~~~~~~~~~~~~ io.c: In function ‘read_diag_prob_dist’: io.c:371:7: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 371 | fscanf( fp, "%li %li %Le\n", &ti,&tscr,&weight ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I.. -I/<> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -g -O2 -flto=auto -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o prob.o prob.c gcc -DHAVE_CONFIG_H -I. -I.. -I/<> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -g -O2 -flto=auto -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o translate.o translate.c rm -f libdialign.a ar cru libdialign.a alig.o assemble.o diag.o io.o orf.o parameters.o prob.o translate.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libdialign.a gcc -g -O2 -flto=auto -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-Bsymbolic-functions -flto=auto -Wl,-z,relro -Wl,-z,now -o dialign museq.o libdialign.a -ldl -lm museq.c:58:13: warning: type of ‘simple_aligner’ does not match original declaration [-Wlto-type-mismatch] 58 | extern int simple_aligner(struct seq_col *scol, struct diag_col *dcol, | ^ assemble.c:398:6: note: return value type mismatch 398 | char simple_aligner(struct seq_col *scol, struct diag_col *dcol, | ^ assemble.c:398:6: note: type ‘char’ should match type ‘int’ assemble.c:398:6: note: ‘simple_aligner’ was previously declared here make[4]: Leaving directory '/<>/dialign' Making all in Align make[4]: Entering directory '/<>/Align' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/<> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -flto=auto -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=deprecated-copy -Wno-error=array-bounds -c -o abyss_align-align.o `test -f 'align.cc' || echo './'`align.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/<> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -flto=auto -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=deprecated-copy -Wno-error=array-bounds -c -o libalign_a-alignGlobal.o `test -f 'alignGlobal.cc' || echo './'`alignGlobal.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/<> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -flto=auto -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=deprecated-copy -Wno-error=array-bounds -c -o libalign_a-dialign.o `test -f 'dialign.cpp' || echo './'`dialign.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/<> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -flto=auto -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=deprecated-copy -Wno-error=array-bounds -c -o libalign_a-dna_diag_prob.o `test -f 'dna_diag_prob.cc' || echo './'`dna_diag_prob.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/<> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -flto=auto -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=deprecated-copy -Wno-error=array-bounds -c -o libalign_a-smith_waterman.o `test -f 'smith_waterman.cpp' || echo './'`smith_waterman.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/<> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -flto=auto -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=deprecated-copy -Wno-error=array-bounds -c -o abyss_mergepairs-mergepairs.o `test -f 'mergepairs.cc' || echo './'`mergepairs.cc rm -f libalign.a ar cru libalign.a libalign_a-alignGlobal.o libalign_a-dialign.o libalign_a-dna_diag_prob.o libalign_a-smith_waterman.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libalign.a g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -flto=auto -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=deprecated-copy -Wno-error=array-bounds -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-Bsymbolic-functions -flto=auto -Wl,-z,relro -Wl,-z,now -o abyss-align abyss_align-align.o ./libalign.a ../dialign/libdialign.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -flto=auto -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=deprecated-copy -Wno-error=array-bounds -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-Bsymbolic-functions -flto=auto -Wl,-z,relro -Wl,-z,now -o abyss-mergepairs abyss_mergepairs-mergepairs.o ./libalign.a ../dialign/libdialign.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm mergepairs.cc: In function ‘main’: smith_waterman.cpp:38:33: error: ‘MEM[(unsigned int *)&align_pos + 12B]’ may be used uninitialized in this function [-Werror=maybe-uninitialized] 38 | unsigned bstart = alignPos[2], bend = alignPos[3] + 1; | ^ smith_waterman.cpp:264:12: note: ‘MEM[(unsigned int *)&align_pos + 12B]’ was declared here 264 | unsigned align_pos[4]; | ^ smith_waterman.cpp:40:2: error: ‘MEM[(unsigned int *)&align_pos + 8B]’ may be used uninitialized in this function [-Werror=maybe-uninitialized] 40 | assert(bstart == 0); | ^ smith_waterman.cpp:264:12: note: ‘MEM[(unsigned int *)&align_pos + 8B]’ was declared here 264 | unsigned align_pos[4]; | ^ smith_waterman.cpp:37:33: error: ‘MEM[(unsigned int *)&align_pos + 4B]’ may be used uninitialized in this function [-Werror=maybe-uninitialized] 37 | unsigned astart = alignPos[0], aend = alignPos[1] + 1; | ^ smith_waterman.cpp:264:12: note: ‘MEM[(unsigned int *)&align_pos + 4B]’ was declared here 264 | unsigned align_pos[4]; | ^ smith_waterman.cpp:264:12: error: ‘MEM[(unsigned int *)&align_pos]’ may be used uninitialized in this function [-Werror=maybe-uninitialized] lto1: all warnings being treated as errors make[5]: *** [/tmp/ccLjjU6j.mk:2: /tmp/abyss-mergepairs.Kqf8uj.ltrans0.ltrans.o] Error 1 lto-wrapper: fatal error: make returned 2 exit status compilation terminated. /usr/bin/ld: error: lto-wrapper failed collect2: error: ld returned 1 exit status make[4]: *** [Makefile:450: abyss-mergepairs] Error 1 make[4]: *** Waiting for unfinished jobs.... assemble.c: In function ‘adapt_diag’: assemble.c:214:68: error: ‘succF’ may be used uninitialized in this function [-Werror=maybe-uninitialized] assemble.c:187:14: note: ‘succF’ was declared here assemble.c:214:54: error: ‘predF’ may be used uninitialized in this function [-Werror=maybe-uninitialized] assemble.c:187:7: note: ‘predF’ was declared here diag.c: In function ‘find_all_diags’: diag.c:1122:12: error: ‘ap’ may be used uninitialized in this function [-Werror=maybe-uninitialized] diag.c:1005:21: note: ‘ap’ was declared here assemble.c: In function ‘simple_aligner.constprop’: assemble.c:533:43: error: ‘tclock’ may be used uninitialized in this function [-Werror=maybe-uninitialized] assemble.c:423:10: note: ‘tclock’ was declared here assemble.c: In function ‘guided_aligner_rec.constprop’: assemble.c:725:7: error: ‘sF2’ may be used uninitialized in this function [-Werror=maybe-uninitialized] assemble.c:606:22: note: ‘sF2’ was declared here lto1: all warnings being treated as errors make[5]: *** [/tmp/ccI155ZW.mk:2: /tmp/abyss-align.xpXKIZ.ltrans0.ltrans.o] Error 1 lto-wrapper: fatal error: make returned 2 exit status compilation terminated. /usr/bin/ld: error: lto-wrapper failed collect2: error: ld returned 1 exit status make[4]: *** [Makefile:446: abyss-align] Error 1 make[4]: Leaving directory '/<>/Align' make[3]: *** [Makefile:487: all-recursive] Error 1 make[3]: Leaving directory '/<>' make[2]: *** [Makefile:407: all] Error 2 make[2]: Leaving directory '/<>' dh_auto_build: make -j4 returned exit code 2 make[1]: *** [debian/rules:17: override_dh_auto_build] Error 255 make[1]: Leaving directory '/<>' make: *** [debian/rules:10: build-arch] Error 2 dpkg-buildpackage: error: debian/rules build-arch subprocess returned exit status 2 -------------------------------------------------------------------------------- Build finished at 20190918-0152 Finished -------- E: Build failure (dpkg-buildpackage died) +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: armhf Build-Space: 47164 Build-Time: 151 Distribution: eoan Fail-Stage: build Host Architecture: armhf Install-Time: 53 Job: abyss_2.2.2-1.dsc Machine Architecture: arm64 Package: abyss Package-Time: 208 Source-Version: 2.2.2-1 Space: 47164 Status: attempted Version: 2.2.2-1 -------------------------------------------------------------------------------- Finished at 20190918-0152 Build needed 00:03:28, 47164k disc space RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=eoan --arch=armhf PACKAGEBUILD-17632304 Scanning for processes to kill in build PACKAGEBUILD-17632304