RUN: /usr/share/launchpad-buildd/slavebin/slave-prep ['slave-prep'] Forking launchpad-buildd slave process... Kernel version: Linux bos01-arm64-024 4.4.0-83-generic #106-Ubuntu SMP Mon Jun 26 17:58:57 UTC 2017 aarch64 Buildd toolchain package versions: launchpad-buildd_144 python-lpbuildd_144 sbuild_0.67.0-2ubuntu7 bzr-builder_0.7.3+bzr174~ppa13~ubuntu14.10.1 bzr_2.7.0-2ubuntu3 git-build-recipe_0.3.4~git201611291343.dcee459~ubuntu16.04.1 git_1:2.7.4-0ubuntu1.1 dpkg-dev_1.18.4ubuntu1.2 python-debian_0.1.27ubuntu2 qemu-user-static_1:2.5+dfsg-5ubuntu10.14. Syncing the system clock with the buildd NTP service... 1 Jul 11:06:59 ntpdate[1831]: adjust time server 10.211.37.1 offset 0.006345 sec RUN: /usr/share/launchpad-buildd/slavebin/unpack-chroot ['unpack-chroot', 'PACKAGEBUILD-12836059', '/home/buildd/filecache-default/42e17d2fa25e748a1aa6eaeef2fe6722beaed5a9'] Unpacking chroot for build PACKAGEBUILD-12836059 RUN: /usr/share/launchpad-buildd/slavebin/mount-chroot ['mount-chroot', 'PACKAGEBUILD-12836059'] Mounting chroot for build PACKAGEBUILD-12836059 RUN: /usr/share/launchpad-buildd/slavebin/override-sources-list ['override-sources-list', 'PACKAGEBUILD-12836059', 'deb http://ftpmaster.internal/ubuntu artful main restricted universe multiverse', 'deb http://ftpmaster.internal/ubuntu artful-security main restricted universe multiverse', 'deb http://ftpmaster.internal/ubuntu artful-updates main restricted universe multiverse', 'deb http://ftpmaster.internal/ubuntu artful-proposed main restricted universe multiverse'] Overriding sources.list in build-PACKAGEBUILD-12836059 RUN: /usr/share/launchpad-buildd/slavebin/update-debian-chroot ['update-debian-chroot', 'PACKAGEBUILD-12836059', 'armhf'] Updating debian chroot for build PACKAGEBUILD-12836059 Get:1 http://ftpmaster.internal/ubuntu artful InRelease [237 kB] Get:2 http://ftpmaster.internal/ubuntu artful-security InRelease [65.5 kB] Get:3 http://ftpmaster.internal/ubuntu artful-updates InRelease [65.5 kB] Get:4 http://ftpmaster.internal/ubuntu artful-proposed InRelease [235 kB] Get:5 http://ftpmaster.internal/ubuntu artful/main armhf Packages [1126 kB] Get:6 http://ftpmaster.internal/ubuntu artful/main Translation-en [566 kB] Get:7 http://ftpmaster.internal/ubuntu artful/restricted armhf Packages [5668 B] Get:8 http://ftpmaster.internal/ubuntu artful/restricted Translation-en [2724 B] Get:9 http://ftpmaster.internal/ubuntu artful/universe armhf Packages [7996 kB] Get:10 http://ftpmaster.internal/ubuntu artful/universe Translation-en [4757 kB] Get:11 http://ftpmaster.internal/ubuntu artful/multiverse armhf Packages [131 kB] Get:12 http://ftpmaster.internal/ubuntu artful/multiverse Translation-en [109 kB] Get:13 http://ftpmaster.internal/ubuntu artful-proposed/main armhf Packages [70.8 kB] Get:14 http://ftpmaster.internal/ubuntu artful-proposed/main Translation-en [37.9 kB] Get:15 http://ftpmaster.internal/ubuntu artful-proposed/universe armhf Packages [170 kB] Get:16 http://ftpmaster.internal/ubuntu artful-proposed/universe Translation-en [97.4 kB] Get:17 http://ftpmaster.internal/ubuntu artful-proposed/multiverse armhf Packages [692 B] Get:18 http://ftpmaster.internal/ubuntu artful-proposed/multiverse Translation-en [348 B] Fetched 15.7 MB in 8s (1753 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following NEW packages will be installed: gcc-7-base The following packages will be upgraded: advancecomp apt apt-transport-https base-files bash binutils bsdutils ca-certificates cpp-6 debianutils dmsetup dpkg dpkg-dev findutils g++-6 gcc-6 gcc-6-base init init-system-helpers libapparmor1 libapt-pkg5.0 libasan3 libasn1-8-heimdal libatomic1 libaudit-common libaudit1 libblkid1 libcc1-0 libdevmapper1.02.1 libdpkg-perl libfdisk1 libgcc-6-dev libgcc1 libgcrypt20 libgnutls30 libgomp1 libgpg-error0 libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhx509-5-heimdal libip4tc0 libkmod2 libkrb5-26-heimdal libldap-2.4-2 libldap-common libmount1 libnpth0 libperl5.24 libpng16-16 libroken18-heimdal libselinux1 libsemanage-common libsemanage1 libsmartcols1 libsqlite3-0 libssl1.0.0 libstdc++-6-dev libstdc++6 libsystemd0 libtasn1-6 libubsan0 libudev1 libusb-0.1-4 libuuid1 libwind0-heimdal linux-libc-dev login mount openssl passwd perl perl-base perl-modules-5.24 systemd systemd-sysv tzdata util-linux 79 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 44.7 MB of archives. After this operation, 2542 kB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu artful/main armhf libperl5.24 armhf 5.24.1-4ubuntu1 [2810 kB] Get:2 http://ftpmaster.internal/ubuntu artful/main armhf perl armhf 5.24.1-4ubuntu1 [219 kB] Get:3 http://ftpmaster.internal/ubuntu artful/main armhf perl-base armhf 5.24.1-4ubuntu1 [1237 kB] Get:4 http://ftpmaster.internal/ubuntu artful/main armhf perl-modules-5.24 all 5.24.1-4ubuntu1 [2663 kB] Get:5 http://ftpmaster.internal/ubuntu artful-proposed/main armhf init-system-helpers all 1.48 [37.8 kB] Get:6 http://ftpmaster.internal/ubuntu artful/main armhf base-files armhf 9.6ubuntu101 [59.1 kB] Get:7 http://ftpmaster.internal/ubuntu artful/main armhf debianutils armhf 4.8.1.1 [84.3 kB] Get:8 http://ftpmaster.internal/ubuntu artful/main armhf bash armhf 4.4-5ubuntu1 [527 kB] Get:9 http://ftpmaster.internal/ubuntu artful/main armhf bsdutils armhf 1:2.29-1ubuntu3 [52.1 kB] Get:10 http://ftpmaster.internal/ubuntu artful/main armhf dpkg armhf 1.18.24ubuntu1 [1099 kB] Get:11 http://ftpmaster.internal/ubuntu artful/main armhf findutils armhf 4.6.0+git+20170606-2 [277 kB] Get:12 http://ftpmaster.internal/ubuntu artful/main armhf login armhf 1:4.2-3.2ubuntu2 [301 kB] Get:13 http://ftpmaster.internal/ubuntu artful/main armhf util-linux armhf 2.29-1ubuntu3 [861 kB] Get:14 http://ftpmaster.internal/ubuntu artful/main armhf mount armhf 2.29-1ubuntu3 [124 kB] Get:15 http://ftpmaster.internal/ubuntu artful-proposed/main armhf gcc-7-base armhf 7.1.0-8ubuntu2 [18.8 kB] Get:16 http://ftpmaster.internal/ubuntu artful-proposed/main armhf libgcc1 armhf 1:7.1.0-8ubuntu2 [38.5 kB] Get:17 http://ftpmaster.internal/ubuntu artful-proposed/main armhf libstdc++6 armhf 7.1.0-8ubuntu2 [346 kB] Get:18 http://ftpmaster.internal/ubuntu artful-proposed/main armhf libapt-pkg5.0 armhf 1.5~alpha4 [722 kB] Get:19 http://ftpmaster.internal/ubuntu artful-proposed/main armhf apt-transport-https armhf 1.5~alpha4 [30.8 kB] Get:20 http://ftpmaster.internal/ubuntu artful/main armhf libtasn1-6 armhf 4.12-2 [30.7 kB] Get:21 http://ftpmaster.internal/ubuntu artful/main armhf libgnutls30 armhf 3.5.8-6ubuntu1 [617 kB] Get:22 http://ftpmaster.internal/ubuntu artful-proposed/main armhf apt armhf 1.5~alpha4 [1066 kB] Get:23 http://ftpmaster.internal/ubuntu artful/main armhf libip4tc0 armhf 1.6.0+snapshot20161117-6ubuntu1 [17.8 kB] Get:24 http://ftpmaster.internal/ubuntu artful/main armhf libapparmor1 armhf 2.11.0-2ubuntu8 [26.0 kB] Get:25 http://ftpmaster.internal/ubuntu artful/main armhf libaudit-common all 1:2.6.6-1ubuntu3 [4524 B] Get:26 http://ftpmaster.internal/ubuntu artful/main armhf libaudit1 armhf 1:2.6.6-1ubuntu3 [34.6 kB] Get:27 http://ftpmaster.internal/ubuntu artful/main armhf libselinux1 armhf 2.6-3build1 [59.4 kB] Get:28 http://ftpmaster.internal/ubuntu artful/main armhf libsemanage-common all 2.6-2build1 [6738 B] Get:29 http://ftpmaster.internal/ubuntu artful/main armhf libsemanage1 armhf 2.6-2build1 [71.1 kB] Get:30 http://ftpmaster.internal/ubuntu artful/main armhf passwd armhf 1:4.2-3.2ubuntu2 [747 kB] Get:31 http://ftpmaster.internal/ubuntu artful/main armhf libuuid1 armhf 2.29-1ubuntu3 [14.4 kB] Get:32 http://ftpmaster.internal/ubuntu artful/main armhf libblkid1 armhf 2.29-1ubuntu3 [98.2 kB] Get:33 http://ftpmaster.internal/ubuntu artful/main armhf libgpg-error0 armhf 1.27-3 [32.0 kB] Get:34 http://ftpmaster.internal/ubuntu artful/main armhf libgcrypt20 armhf 1.7.8-1 [344 kB] Get:35 http://ftpmaster.internal/ubuntu artful/main armhf libkmod2 armhf 24-1ubuntu1 [34.8 kB] Get:36 http://ftpmaster.internal/ubuntu artful/main armhf libmount1 armhf 2.29-1ubuntu3 [106 kB] Get:37 http://ftpmaster.internal/ubuntu artful-proposed/main armhf systemd armhf 233-8ubuntu2 [2252 kB] Get:38 http://ftpmaster.internal/ubuntu artful-proposed/main armhf libsystemd0 armhf 233-8ubuntu2 [190 kB] Get:39 http://ftpmaster.internal/ubuntu artful-proposed/main armhf init armhf 1.48 [5806 B] Get:40 http://ftpmaster.internal/ubuntu artful-proposed/main armhf systemd-sysv armhf 233-8ubuntu2 [12.4 kB] Get:41 http://ftpmaster.internal/ubuntu artful/main armhf libfdisk1 armhf 2.29-1ubuntu3 [132 kB] Get:42 http://ftpmaster.internal/ubuntu artful/main armhf libsmartcols1 armhf 2.29-1ubuntu3 [60.5 kB] Get:43 http://ftpmaster.internal/ubuntu artful-proposed/main armhf libudev1 armhf 233-8ubuntu2 [51.3 kB] Get:44 http://ftpmaster.internal/ubuntu artful/main armhf libdevmapper1.02.1 armhf 2:1.02.137-2ubuntu2 [125 kB] Get:45 http://ftpmaster.internal/ubuntu artful/main armhf dmsetup armhf 2:1.02.137-2ubuntu2 [71.2 kB] Get:46 http://ftpmaster.internal/ubuntu artful/main armhf libroken18-heimdal armhf 7.1.0+dfsg-13 [33.7 kB] Get:47 http://ftpmaster.internal/ubuntu artful/main armhf libasn1-8-heimdal armhf 7.1.0+dfsg-13 [138 kB] Get:48 http://ftpmaster.internal/ubuntu artful/main armhf libheimbase1-heimdal armhf 7.1.0+dfsg-13 [23.9 kB] Get:49 http://ftpmaster.internal/ubuntu artful/main armhf libhcrypto4-heimdal armhf 7.1.0+dfsg-13 [77.4 kB] Get:50 http://ftpmaster.internal/ubuntu artful/main armhf libwind0-heimdal armhf 7.1.0+dfsg-13 [47.3 kB] Get:51 http://ftpmaster.internal/ubuntu artful/main armhf libhx509-5-heimdal armhf 7.1.0+dfsg-13 [88.3 kB] Get:52 http://ftpmaster.internal/ubuntu artful/main armhf libsqlite3-0 armhf 3.16.2-5 [412 kB] Get:53 http://ftpmaster.internal/ubuntu artful/main armhf libkrb5-26-heimdal armhf 7.1.0+dfsg-13 [168 kB] Get:54 http://ftpmaster.internal/ubuntu artful/main armhf libheimntlm0-heimdal armhf 7.1.0+dfsg-13 [13.3 kB] Get:55 http://ftpmaster.internal/ubuntu artful/main armhf libgssapi3-heimdal armhf 7.1.0+dfsg-13 [79.3 kB] Get:56 http://ftpmaster.internal/ubuntu artful/main armhf libldap-2.4-2 armhf 2.4.44+dfsg-7ubuntu1 [132 kB] Get:57 http://ftpmaster.internal/ubuntu artful/main armhf libldap-common all 2.4.44+dfsg-7ubuntu1 [16.4 kB] Get:58 http://ftpmaster.internal/ubuntu artful/main armhf libnpth0 armhf 1.5-2 [6582 B] Get:59 http://ftpmaster.internal/ubuntu artful/main armhf libssl1.0.0 armhf 1.0.2g-1ubuntu13 [711 kB] Get:60 http://ftpmaster.internal/ubuntu artful/main armhf tzdata all 2017b-2 [203 kB] Get:61 http://ftpmaster.internal/ubuntu artful/main armhf openssl armhf 1.0.2g-1ubuntu13 [485 kB] Get:62 http://ftpmaster.internal/ubuntu artful/main armhf ca-certificates all 20161130+nmu1 [186 kB] Get:63 http://ftpmaster.internal/ubuntu artful/main armhf libpng16-16 armhf 1.6.29-3 [157 kB] Get:64 http://ftpmaster.internal/ubuntu artful/main armhf advancecomp armhf 2.0-1 [167 kB] Get:65 http://ftpmaster.internal/ubuntu artful-proposed/main armhf binutils armhf 2.28.51.20170627-1ubuntu1 [2653 kB] Get:66 http://ftpmaster.internal/ubuntu artful-proposed/main armhf libgomp1 armhf 7.1.0-8ubuntu2 [64.6 kB] Get:67 http://ftpmaster.internal/ubuntu artful-proposed/main armhf libubsan0 armhf 7.1.0-8ubuntu2 [104 kB] Get:68 http://ftpmaster.internal/ubuntu artful-proposed/main armhf libatomic1 armhf 7.1.0-8ubuntu2 [6250 B] Get:69 http://ftpmaster.internal/ubuntu artful-proposed/main armhf libasan3 armhf 6.3.0-21ubuntu1 [293 kB] Get:70 http://ftpmaster.internal/ubuntu artful-proposed/main armhf g++-6 armhf 6.3.0-21ubuntu1 [5925 kB] Get:71 http://ftpmaster.internal/ubuntu artful-proposed/main armhf libstdc++-6-dev armhf 6.3.0-21ubuntu1 [1481 kB] Get:72 http://ftpmaster.internal/ubuntu artful-proposed/main armhf gcc-6 armhf 6.3.0-21ubuntu1 [5801 kB] Get:73 http://ftpmaster.internal/ubuntu artful-proposed/main armhf libgcc-6-dev armhf 6.3.0-21ubuntu1 [549 kB] Get:74 http://ftpmaster.internal/ubuntu artful-proposed/main armhf libcc1-0 armhf 7.1.0-8ubuntu2 [31.5 kB] Get:75 http://ftpmaster.internal/ubuntu artful-proposed/main armhf cpp-6 armhf 6.3.0-21ubuntu1 [5204 kB] Get:76 http://ftpmaster.internal/ubuntu artful-proposed/main armhf gcc-6-base armhf 6.3.0-21ubuntu1 [18.0 kB] Get:77 http://ftpmaster.internal/ubuntu artful/main armhf dpkg-dev all 1.18.24ubuntu1 [608 kB] Get:78 http://ftpmaster.internal/ubuntu artful/main armhf libdpkg-perl all 1.18.24ubuntu1 [209 kB] Get:79 http://ftpmaster.internal/ubuntu artful/main armhf libusb-0.1-4 armhf 2:0.1.12-31 [15.6 kB] Get:80 http://ftpmaster.internal/ubuntu artful/main armhf linux-libc-dev armhf 4.10.0-26.30 [892 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 44.7 MB in 6s (7005 kB/s) (Reading database ... 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Setting up systemd (233-8ubuntu2) ... Installing new version of config file /etc/systemd/resolved.conf ... addgroup: The group `systemd-journal' already exists as a system group. Exiting. Removing obsolete conffile /etc/dbus-1/system.d/org.freedesktop.hostname1.conf ... Removing obsolete conffile /etc/dbus-1/system.d/org.freedesktop.locale1.conf ... Removing obsolete conffile /etc/dbus-1/system.d/org.freedesktop.login1.conf ... Removing obsolete conffile /etc/dbus-1/system.d/org.freedesktop.network1.conf ... Removing obsolete conffile /etc/dbus-1/system.d/org.freedesktop.resolve1.conf ... Removing obsolete conffile /etc/dbus-1/system.d/org.freedesktop.systemd1.conf ... Removing obsolete conffile /etc/dbus-1/system.d/org.freedesktop.timedate1.conf ... (Reading database ... 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Unpacking linux-libc-dev:armhf (4.10.0-26.30) over (4.10.0-20.22) ... Setting up libnpth0:armhf (1.5-2) ... Setting up libgomp1:armhf (7.1.0-8ubuntu2) ... Setting up libatomic1:armhf (7.1.0-8ubuntu2) ... Setting up perl-modules-5.24 (5.24.1-4ubuntu1) ... Setting up libperl5.24:armhf (5.24.1-4ubuntu1) ... Setting up libcc1-0:armhf (7.1.0-8ubuntu2) ... Setting up apt-transport-https (1.5~alpha4) ... Setting up libssl1.0.0:armhf (1.0.2g-1ubuntu13) ... Setting up libpng16-16:armhf (1.6.29-3) ... Setting up libldap-common (2.4.44+dfsg-7ubuntu1) ... Setting up tzdata (2017b-2) ... Current default time zone: 'Etc/UTC' Local time is now: Sat Jul 1 11:07:44 UTC 2017. Universal Time is now: Sat Jul 1 11:07:44 UTC 2017. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up systemd-sysv (233-8ubuntu2) ... Setting up libubsan0:armhf (7.1.0-8ubuntu2) ... Setting up gcc-6-base:armhf (6.3.0-21ubuntu1) ... Setting up linux-libc-dev:armhf (4.10.0-26.30) ... 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RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package ['sbuild-package', 'PACKAGEBUILD-12836059', 'armhf', 'artful-proposed', '-c', 'chroot:autobuild', '--arch=armhf', '--dist=artful-proposed', '--purge=never', '--nolog', 'abyss_2.0.2-3.dsc'] Initiating build PACKAGEBUILD-12836059 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.4.0-83-generic #106-Ubuntu SMP Mon Jun 26 17:58:57 UTC 2017 armv7l sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on bos01-arm64-024.buildd +==============================================================================+ | abyss 2.0.2-3 (armhf) 01 Jul 2017 11:07 | +==============================================================================+ Package: abyss Version: 2.0.2-3 Source Version: 2.0.2-3 Distribution: artful-proposed Machine Architecture: arm64 Host Architecture: armhf Build Architecture: armhf I: NOTICE: Log filtering will replace 'build/abyss-__2ywA/abyss-2.0.2' with '<>' I: NOTICE: Log filtering will replace 'build/abyss-__2ywA' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-12836059/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- abyss_2.0.2-3.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-mnPDTu/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/<>/resolver-mnPDTu/apt_archive ./ InRelease Get:2 copy:/<>/resolver-mnPDTu/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-mnPDTu/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-mnPDTu/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-mnPDTu/apt_archive ./ Packages [529 B] Fetched 2862 B in 0s (147 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 778 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-mnPDTu/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [778 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 778 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12239 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 (>= 10), dh-autoreconf, python-markdown, libboost-graph-dev, libopenmpi-dev, libsparsehash-dev, libtext-multimarkdown-perl, libgtest-dev, libsqlite3-dev Filtered Build-Depends: debhelper (>= 10), dh-autoreconf, python-markdown, libboost-graph-dev, libopenmpi-dev, libsparsehash-dev, libtext-multimarkdown-perl, libgtest-dev, libsqlite3-dev dpkg-deb: building package 'sbuild-build-depends-abyss-dummy' in '/<>/resolver-8m982T/apt_archive/sbuild-build-depends-abyss-dummy.deb'. Ign:1 copy:/<>/resolver-8m982T/apt_archive ./ InRelease Get:2 copy:/<>/resolver-8m982T/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-8m982T/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-8m982T/apt_archive ./ Sources [285 B] Get:5 copy:/<>/resolver-8m982T/apt_archive ./ Packages [609 B] Fetched 3013 B in 0s (135 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 file gettext gettext-base googletest groff-base intltool-debian libarchive-zip-perl libboost-graph-dev libboost-graph1.62-dev libboost-graph1.62.0 libboost-regex1.62.0 libboost-serialization1.62-dev libboost-serialization1.62.0 libboost-test1.62-dev libboost-test1.62.0 libboost1.62-dev libbsd0 libcroco3 libexpat1 libfile-stripnondeterminism-perl libglib2.0-0 libgtest-dev libhtml-parser-perl libhtml-tagset-perl libhwloc-dev libhwloc-plugins libhwloc5 libibverbs-dev libibverbs1 libicu57 libltdl-dev libltdl7 libmagic-mgc libmagic1 libnl-3-200 libnl-route-3-200 libopenmpi-dev libopenmpi2 libpciaccess0 libpipeline1 libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libsigsegv2 libsparsehash-dev libsqlite3-dev libtext-markdown-perl libtext-multimarkdown-perl libtimedate-perl libtool liburi-perl libxml2 m4 man-db mime-support ocl-icd-libopencl1 openmpi-common po-debconf python python-markdown python-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 libboost1.62-doc libboost-atomic1.62-dev libboost-chrono1.62-dev libboost-context1.62-dev libboost-coroutine1.62-dev libboost-date-time1.62-dev libboost-exception1.62-dev libboost-fiber1.62-dev libboost-filesystem1.62-dev libboost-graph-parallel1.62-dev libboost-iostreams1.62-dev libboost-locale1.62-dev libboost-log1.62-dev libboost-math1.62-dev libboost-mpi1.62-dev libboost-mpi-python1.62-dev libboost-program-options1.62-dev libboost-python1.62-dev libboost-random1.62-dev libboost-regex1.62-dev libboost-signals1.62-dev libboost-system1.62-dev libboost-thread1.62-dev libboost-timer1.62-dev libboost-type-erasure1.62-dev libboost-wave1.62-dev libboost1.62-tools-dev libmpfrc++-dev libntl-dev libdata-dump-perl libhwloc-contrib-plugins libtool-doc openmpi-doc pciutils sqlite3-doc gfortran | fortran95-compiler gcj-jdk libwww-perl m4-doc less www-browser opencl-icd libmail-box-perl python-doc python-tk python-markdown-doc python2.7-doc binfmt-support Recommended packages: curl | wget | lynx-cur libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs libhttp-message-perl openmpi-bin xml-core libmail-sendmail-perl python-pygments python-yaml The following packages will be REMOVED: pkg-create-dbgsym* The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism file gettext gettext-base googletest groff-base intltool-debian libarchive-zip-perl libboost-graph-dev libboost-graph1.62-dev libboost-graph1.62.0 libboost-regex1.62.0 libboost-serialization1.62-dev libboost-serialization1.62.0 libboost-test1.62-dev libboost-test1.62.0 libboost1.62-dev libbsd0 libcroco3 libexpat1 libfile-stripnondeterminism-perl libglib2.0-0 libgtest-dev libhtml-parser-perl libhtml-tagset-perl libhwloc-dev libhwloc-plugins libhwloc5 libibverbs-dev libibverbs1 libicu57 libltdl-dev libltdl7 libmagic-mgc libmagic1 libnl-3-200 libnl-route-3-200 libopenmpi-dev libopenmpi2 libpciaccess0 libpipeline1 libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libsigsegv2 libsparsehash-dev libsqlite3-dev libtext-markdown-perl libtext-multimarkdown-perl libtimedate-perl libtool liburi-perl libxml2 m4 man-db mime-support ocl-icd-libopencl1 openmpi-common po-debconf python python-markdown python-minimal python2.7 python2.7-minimal sbuild-build-depends-abyss-dummy 0 upgraded, 72 newly installed, 1 to remove and 0 not upgraded. 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armhf 1.2.1-2ubuntu1 [94.7 kB] Get:71 http://ftpmaster.internal/ubuntu artful/universe armhf libopenmpi2 armhf 2.1.1-6 [1797 kB] Get:72 http://ftpmaster.internal/ubuntu artful/universe armhf libopenmpi-dev armhf 2.1.1-6 [914 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 32.7 MB in 16s (1923 kB/s) (Reading database ... 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Setting up libhtml-tagset-perl (3.20-3) ... Setting up libboost-serialization1.62.0:armhf (1.62.0+dfsg-4build2) ... Setting up libsparsehash-dev (2.0.2-1) ... Setting up libexpat1:armhf (2.2.1-2) ... Setting up libarchive-zip-perl (1.59-1) ... Setting up mime-support (3.60ubuntu1) ... Setting up libtext-markdown-perl (1.000031-2) ... Setting up libboost1.62-dev:armhf (1.62.0+dfsg-4build2) ... Setting up libsqlite3-dev:armhf (3.16.2-5) ... Setting up libtimedate-perl (2.3000-2) ... Setting up libsigsegv2:armhf (2.11-1) ... Setting up groff-base (1.22.3-9) ... Setting up libglib2.0-0:armhf (2.53.3-1) ... No schema files found: doing nothing. Setting up gettext-base (0.19.8.1-2ubuntu1) ... Setting up libpipeline1:armhf (1.4.1-2) ... Setting up m4 (1.4.18-1) ... Setting up libicu57:armhf (57.1-6) ... Setting up libbsd0:armhf (0.8.5-1) ... Setting up libboost-serialization1.62-dev:armhf (1.62.0+dfsg-4build2) ... Setting up libxml2:armhf (2.9.4+dfsg1-2.2ubuntu1) ... Setting up libmagic-mgc (1:5.30-1) ... Setting up libmagic1:armhf (1:5.30-1) ... Setting up libcroco3:armhf (0.6.11-3) ... Setting up openmpi-common (2.1.1-6) ... Processing triggers for libc-bin (2.24-9ubuntu2) ... Setting up autotools-dev (20161112.1) ... Setting up liburi-perl (1.71-1) ... Setting up libboost-test1.62.0:armhf (1.62.0+dfsg-4build2) ... Setting up libltdl7:armhf (2.4.6-2) ... Setting up libhtml-parser-perl (3.72-3) ... Setting up libpciaccess0:armhf (0.13.4-1ubuntu1) ... Setting up ocl-icd-libopencl1:armhf (2.2.11-1ubuntu1) ... Setting up bsdmainutils (9.0.12ubuntu1) ... 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 libnl-3-200:armhf (3.2.29-0ubuntu3) ... Setting up libpython2.7-stdlib:armhf (2.7.13-2) ... Setting up autopoint (0.19.8.1-2ubuntu1) ... Setting up libfile-stripnondeterminism-perl (0.035-2) ... Setting up libltdl-dev:armhf (2.4.6-2) ... Setting up gettext (0.19.8.1-2ubuntu1) ... Setting up libboost-regex1.62.0:armhf (1.62.0+dfsg-4build2) ... Setting up python2.7 (2.7.13-2) ... Setting up libnl-route-3-200:armhf (3.2.29-0ubuntu3) ... Setting up autoconf (2.69-10) ... Setting up file (1:5.30-1) ... Setting up libhwloc5:armhf (1.11.5-1) ... Setting up libboost-test1.62-dev:armhf (1.62.0+dfsg-4build2) ... Setting up libtext-multimarkdown-perl (1.000035-1) ... Setting up libpython-stdlib:armhf (2.7.13-2) ... Setting up libhwloc-plugins (1.11.5-1) ... Setting up intltool-debian (0.35.0+20060710.4) ... Setting up automake (1:1.15-6ubuntu1) ... update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode Setting up man-db (2.7.6.1-2) ... Not building database; man-db/auto-update is not 'true'. Setting up python (2.7.13-2) ... Setting up python-markdown (2.6.8-1) ... Setting up libtool (2.4.6-2) ... Setting up libibverbs1 (1.2.1-2ubuntu1) ... Setting up po-debconf (1.0.20) ... Setting up libhwloc-dev:armhf (1.11.5-1) ... Setting up libboost-graph1.62.0:armhf (1.62.0+dfsg-4build2) ... Setting up libboost-graph1.62-dev:armhf (1.62.0+dfsg-4build2) ... Setting up googletest:armhf (1.8.0-6) ... Setting up libgtest-dev:armhf (1.8.0-6) ... Setting up libopenmpi2:armhf (2.1.1-6) ... Setting up libibverbs-dev (1.2.1-2ubuntu1) ... Setting up libboost-graph-dev:armhf (1.62.0.1) ... Setting up libopenmpi-dev (2.1.1-6) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/openmpi/include to provide /usr/include/mpi (mpi) in auto mode Setting up dh-autoreconf (14) ... Setting up dh-strip-nondeterminism (0.035-2) ... Setting up debhelper (10.4ubuntu3) ... Setting up sbuild-build-depends-abyss-dummy (0.invalid.0) ... (Reading database ... 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Processing triggers for libc-bin (2.24-9ubuntu2) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.4.0-83-generic arm64 (armv7l) Toolchain package versions: binutils_2.28.51.20170627-1ubuntu1 dpkg-dev_1.18.24ubuntu1 g++-6_6.3.0-21ubuntu1 gcc-6_6.3.0-21ubuntu1 libc6-dev_2.24-9ubuntu2 libstdc++-6-dev_6.3.0-21ubuntu1 libstdc++6_7.1.0-8ubuntu2 linux-libc-dev_4.10.0-26.30 Package versions: adduser_3.113+nmu3ubuntu5 advancecomp_2.0-1 apt_1.5~alpha4 apt-transport-https_1.5~alpha4 autoconf_2.69-10 automake_1:1.15-6ubuntu1 autopoint_0.19.8.1-2ubuntu1 autotools-dev_20161112.1 base-files_9.6ubuntu101 base-passwd_3.5.43 bash_4.4-5ubuntu1 binutils_2.28.51.20170627-1ubuntu1 bsdmainutils_9.0.12ubuntu1 bsdutils_1:2.29-1ubuntu3 build-essential_12.1ubuntu2 bzip2_1.0.6-8.1 ca-certificates_20161130+nmu1 coreutils_8.26-3ubuntu3 cpp_4:6.3.0-2ubuntu1 cpp-6_6.3.0-21ubuntu1 dash_0.5.8-2.3ubuntu1 debconf_1.5.60ubuntu1 debhelper_10.4ubuntu3 debianutils_4.8.1.1 dh-autoreconf_14 dh-strip-nondeterminism_0.035-2 diffutils_1:3.5-3 dmsetup_2:1.02.137-2ubuntu2 dpkg_1.18.24ubuntu1 dpkg-dev_1.18.24ubuntu1 e2fslibs_1.43.4-2 e2fsprogs_1.43.4-2 fakeroot_1.21-1ubuntu2 file_1:5.30-1 findutils_4.6.0+git+20170606-2 g++_4:6.3.0-2ubuntu1 g++-6_6.3.0-21ubuntu1 gcc_4:6.3.0-2ubuntu1 gcc-6_6.3.0-21ubuntu1 gcc-6-base_6.3.0-21ubuntu1 gcc-7-base_7.1.0-8ubuntu2 gettext_0.19.8.1-2ubuntu1 gettext-base_0.19.8.1-2ubuntu1 gnupg_2.1.15-1ubuntu7 gnupg-agent_2.1.15-1ubuntu7 googletest_1.8.0-6 gpgv_2.1.15-1ubuntu7 grep_2.27-2 groff-base_1.22.3-9 gzip_1.6-5ubuntu1 hostname_3.18 init_1.48 init-system-helpers_1.48 initscripts_2.88dsf-59.3ubuntu2 insserv_1.14.0-5ubuntu3 intltool-debian_0.35.0+20060710.4 libacl1_2.2.52-3build1 libapparmor1_2.11.0-2ubuntu8 libapt-pkg5.0_1.5~alpha4 libarchive-zip-perl_1.59-1 libasan3_6.3.0-21ubuntu1 libasn1-8-heimdal_7.1.0+dfsg-13 libassuan0_2.4.3-2 libatomic1_7.1.0-8ubuntu2 libattr1_1:2.4.47-2build1 libaudit-common_1:2.6.6-1ubuntu3 libaudit1_1:2.6.6-1ubuntu3 libblkid1_2.29-1ubuntu3 libboost-graph-dev_1.62.0.1 libboost-graph1.62-dev_1.62.0+dfsg-4build2 libboost-graph1.62.0_1.62.0+dfsg-4build2 libboost-regex1.62.0_1.62.0+dfsg-4build2 libboost-serialization1.62-dev_1.62.0+dfsg-4build2 libboost-serialization1.62.0_1.62.0+dfsg-4build2 libboost-test1.62-dev_1.62.0+dfsg-4build2 libboost-test1.62.0_1.62.0+dfsg-4build2 libboost1.62-dev_1.62.0+dfsg-4build2 libbsd0_0.8.5-1 libbz2-1.0_1.0.6-8.1 libc-bin_2.24-9ubuntu2 libc-dev-bin_2.24-9ubuntu2 libc6_2.24-9ubuntu2 libc6-dev_2.24-9ubuntu2 libcap-ng0_0.7.7-3 libcap2_1:2.25-1 libcc1-0_7.1.0-8ubuntu2 libcomerr2_1.43.4-2 libcroco3_0.6.11-3 libcryptsetup4_2:1.7.2-0ubuntu1 libcurl3-gnutls_7.52.1-5ubuntu1 libdb5.3_5.3.28-12 libdebconfclient0_0.213ubuntu1 libdevmapper1.02.1_2:1.02.137-2ubuntu2 libdpkg-perl_1.18.24ubuntu1 libexpat1_2.2.1-2 libfakeroot_1.21-1ubuntu2 libfdisk1_2.29-1ubuntu3 libffi6_3.2.1-6 libfile-stripnondeterminism-perl_0.035-2 libgcc-6-dev_6.3.0-21ubuntu1 libgcc1_1:7.1.0-8ubuntu2 libgcrypt20_1.7.8-1 libgdbm3_1.8.3-14 libglib2.0-0_2.53.3-1 libgmp10_2:6.1.2+dfsg-1 libgnutls30_3.5.8-6ubuntu1 libgomp1_7.1.0-8ubuntu2 libgpg-error0_1.27-3 libgssapi-krb5-2_1.15-2 libgssapi3-heimdal_7.1.0+dfsg-13 libgtest-dev_1.8.0-6 libhcrypto4-heimdal_7.1.0+dfsg-13 libheimbase1-heimdal_7.1.0+dfsg-13 libheimntlm0-heimdal_7.1.0+dfsg-13 libhogweed4_3.3-1 libhtml-parser-perl_3.72-3 libhtml-tagset-perl_3.20-3 libhwloc-dev_1.11.5-1 libhwloc-plugins_1.11.5-1 libhwloc5_1.11.5-1 libhx509-5-heimdal_7.1.0+dfsg-13 libibverbs-dev_1.2.1-2ubuntu1 libibverbs1_1.2.1-2ubuntu1 libicu57_57.1-6 libidn11_1.33-1 libidn2-0_0.16-1 libip4tc0_1.6.0+snapshot20161117-6ubuntu1 libisl15_0.18-1 libk5crypto3_1.15-2 libkeyutils1_1.5.9-9ubuntu1 libkmod2_24-1ubuntu1 libkrb5-26-heimdal_7.1.0+dfsg-13 libkrb5-3_1.15-2 libkrb5support0_1.15-2 libksba8_1.3.5-2 libldap-2.4-2_2.4.44+dfsg-7ubuntu1 libldap-common_2.4.44+dfsg-7ubuntu1 liblockfile-bin_1.14-1 liblockfile1_1.14-1 libltdl-dev_2.4.6-2 libltdl7_2.4.6-2 liblz4-1_0.0~r131-2ubuntu2 liblzma5_5.2.2-1.2 libmagic-mgc_1:5.30-1 libmagic1_1:5.30-1 libmount1_2.29-1ubuntu3 libmpc3_1.0.3-1 libmpfr4_3.1.5-1 libncurses5_6.0+20160625-1ubuntu1 libncursesw5_6.0+20160625-1ubuntu1 libnettle6_3.3-1 libnl-3-200_3.2.29-0ubuntu3 libnl-route-3-200_3.2.29-0ubuntu3 libnpth0_1.5-2 libopenmpi-dev_2.1.1-6 libopenmpi2_2.1.1-6 libp11-kit0_0.23.3-5 libpam-modules_1.1.8-3.2ubuntu3 libpam-modules-bin_1.1.8-3.2ubuntu3 libpam-runtime_1.1.8-3.2ubuntu3 libpam0g_1.1.8-3.2ubuntu3 libpciaccess0_0.13.4-1ubuntu1 libpcre3_2:8.39-3 libperl5.24_5.24.1-4ubuntu1 libpipeline1_1.4.1-2 libpng16-16_1.6.29-3 libprocps6_2:3.3.12-1ubuntu2 libpsl5_0.17.0-4 libpython-stdlib_2.7.13-2 libpython2.7-minimal_2.7.13-2 libpython2.7-stdlib_2.7.13-2 libreadline7_7.0-0ubuntu2 libroken18-heimdal_7.1.0+dfsg-13 librtmp1_2.4+20151223.gitfa8646d.1-1 libsasl2-2_2.1.27~101-g0780600+dfsg-2ubuntu1 libsasl2-modules-db_2.1.27~101-g0780600+dfsg-2ubuntu1 libseccomp2_2.3.1-2.1ubuntu1 libselinux1_2.6-3build1 libsemanage-common_2.6-2build1 libsemanage1_2.6-2build1 libsepol1_2.6-2 libsigsegv2_2.11-1 libslang2_2.3.1-5ubuntu1 libsmartcols1_2.29-1ubuntu3 libsparsehash-dev_2.0.2-1 libsqlite3-0_3.16.2-5 libsqlite3-dev_3.16.2-5 libss2_1.43.4-2 libssl1.0.0_1.0.2g-1ubuntu13 libstdc++-6-dev_6.3.0-21ubuntu1 libstdc++6_7.1.0-8ubuntu2 libsystemd0_233-8ubuntu2 libtasn1-6_4.12-2 libtext-markdown-perl_1.000031-2 libtext-multimarkdown-perl_1.000035-1 libtimedate-perl_2.3000-2 libtinfo5_6.0+20160625-1ubuntu1 libtool_2.4.6-2 libubsan0_7.1.0-8ubuntu2 libudev1_233-8ubuntu2 libunistring0_0.9.3-5.2ubuntu1 liburi-perl_1.71-1 libusb-0.1-4_2:0.1.12-31 libustr-1.0-1_1.0.4-6 libuuid1_2.29-1ubuntu3 libwind0-heimdal_7.1.0+dfsg-13 libxml2_2.9.4+dfsg1-2.2ubuntu1 linux-libc-dev_4.10.0-26.30 lockfile-progs_0.1.17build1 login_1:4.2-3.2ubuntu2 lsb-base_9.20160110ubuntu5 m4_1.4.18-1 make_4.1-9.1 man-db_2.7.6.1-2 mawk_1.3.3-17ubuntu2 mime-support_3.60ubuntu1 mount_2.29-1ubuntu3 multiarch-support_2.24-9ubuntu2 ncurses-base_6.0+20160625-1ubuntu1 ncurses-bin_6.0+20160625-1ubuntu1 ocl-icd-libopencl1_2.2.11-1ubuntu1 openmpi-common_2.1.1-6 openssl_1.0.2g-1ubuntu13 optipng_0.7.6-1build1 passwd_1:4.2-3.2ubuntu2 patch_2.7.5-1build1 perl_5.24.1-4ubuntu1 perl-base_5.24.1-4ubuntu1 perl-modules-5.24_5.24.1-4ubuntu1 pinentry-curses_1.0.0-2 pkgbinarymangler_131 po-debconf_1.0.20 policyrcd-script-zg2_0.1-3 procps_2:3.3.12-1ubuntu2 python_2.7.13-2 python-markdown_2.6.8-1 python-minimal_2.7.13-2 python2.7_2.7.13-2 python2.7-minimal_2.7.13-2 readline-common_7.0-0ubuntu2 sbuild-build-depends-abyss-dummy_0.invalid.0 sbuild-build-depends-core-dummy_0.invalid.0 sed_4.4-1 sensible-utils_0.0.9 systemd_233-8ubuntu2 systemd-sysv_233-8ubuntu2 sysv-rc_2.88dsf-59.3ubuntu2 sysvinit-utils_2.88dsf-59.8git1 tar_1.29b-1.1 tzdata_2017b-2 ubuntu-keyring_2016.10.27 util-linux_2.29-1ubuntu3 xz-utils_5.2.2-1.2 zlib1g_1:1.2.11.dfsg-0ubuntu1 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Sat Jul 1 00:18:01 2017 UTC gpgv: using RSA key gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./abyss_2.0.2-3.dsc dpkg-source: info: extracting abyss in abyss-2.0.2 dpkg-source: info: unpacking abyss_2.0.2.orig.tar.gz dpkg-source: info: unpacking abyss_2.0.2-3.debian.tar.xz dpkg-source: info: applying abyss-pe.patch dpkg-source: info: applying abyss-32-bit.patch dpkg-source: info: applying fix_bash_script.patch dpkg-source: info: applying big_endian.patch Check disc space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=4 HOME=/home/buildd LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd MAIL=/var/mail/buildd OLDPWD=/ PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games PWD=/<> SHELL=/bin/sh SUDO_COMMAND=/usr/sbin/chroot /<> su buildd -s /bin/sh -c cd '/<>' && 'env' SUDO_GID=2501 SUDO_UID=2001 SUDO_USER=buildd TERM=unknown USER=buildd USERNAME=root dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package abyss dpkg-buildpackage: info: source version 2.0.2-3 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build abyss-2.0.2 dpkg-buildpackage: info: host architecture armhf fakeroot debian/rules clean dh clean --with autoreconf dh_testdir dh_auto_clean dh_autoreconf_clean dh_clean debian/rules build-arch dh build-arch --with autoreconf dh_testdir -a dh_update_autotools_config -a dh_autoreconf -a configure.ac:11: installing './compile' configure.ac:161: installing './config.guess' configure.ac:161: installing './config.sub' configure.ac:5: installing './install-sh' configure.ac:5: 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/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 --libexecdir=\${prefix}/lib/arm-linux-gnueabihf --disable-maintainer-mode --disable-dependency-tracking --with-mpi=/usr/lib/openmpi configure: WARNING: unrecognized options: --disable-maintainer-mode checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking for gawk... (cached) mawk checking for gcc... gcc 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 gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... yes checking for style of include used by make... GNU checking dependency style of gcc... none checking how to run the C preprocessor... gcc -E checking for g++... g++ checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking dependency style of g++... none checking for ranlib... ranlib checking for ghc... no checking for ghc-pkg... no ./configure: line 5332: : 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... no checking mpi.h presence... no checking for mpi.h... no 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++ -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++ 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 Misc/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 lib/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 lib/bloomfilter/Makefile config.status: creating lib/rolling-hash/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++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/<> -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libcommon_a-ContigID.o `test -f 'ContigID.cpp' || echo './'`ContigID.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/<> -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libcommon_a-Fcontrol.o `test -f 'Fcontrol.cpp' || echo './'`Fcontrol.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/<> -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libcommon_a-Histogram.o `test -f 'Histogram.cpp' || echo './'`Histogram.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/<> -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libcommon_a-Kmer.o `test -f 'Kmer.cpp' || echo './'`Kmer.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/<> -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libcommon_a-Log.o `test -f 'Log.cpp' || echo './'`Log.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/<> -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libcommon_a-Options.o `test -f 'Options.cpp' || echo './'`Options.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/<> -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libcommon_a-Sequence.o `test -f 'Sequence.cpp' || echo './'`Sequence.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/<> -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libcommon_a-SignalHandler.o `test -f 'SignalHandler.cpp' || echo './'`SignalHandler.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/<> -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libcommon_a-Timer.o `test -f 'Timer.cpp' || echo './'`Timer.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/<> -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libcommon_a-Uncompress.o `test -f 'Uncompress.cpp' || echo './'`Uncompress.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/<> -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -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++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/<> -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_gc-gc.o `test -f 'gc.cc' || echo './'`gc.cc g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/<> -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_todot-todot.o `test -f 'todot.cc' || echo './'`todot.cc g++ -Wall -Wextra -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o abyss-gc abyss_gc-gc.o ../Common/libcommon.a -ldl -lm g++ -Wall -Wextra -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L. -Wl,-Bsymbolic-functions -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++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/<> -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libdatalayer_a-FastaReader.o `test -f 'FastaReader.cpp' || echo './'`FastaReader.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/<> -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libdatalayer_a-FastaWriter.o `test -f 'FastaWriter.cpp' || echo './'`FastaWriter.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/<> -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_fac-fac.o `test -f 'fac.cc' || echo './'`fac.cc g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/<> -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -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++ -Wall -Wextra -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o abyss-tofastq abyss_tofastq-abyss-tofastq.o libdatalayer.a ../Common/libcommon.a -ldl -lm g++ -Wall -Wextra -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -Wl,-Bsymbolic-functions -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++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/<> -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libdb_a-DB.o `test -f 'DB.cc' || echo './'`DB.cc g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/<> -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_db_csv-DB.o `test -f 'DB.cc' || echo './'`DB.cc g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/<> -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_db_csv-db-csv.o `test -f 'db-csv.cc' || echo './'`db-csv.cc 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 g++ -Wall -Wextra -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o abyss-db-csv abyss_db_csv-DB.o abyss_db_csv-db-csv.o -lsqlite3 -ldl -lm make[4]: Leaving directory '/<>/DataBase' Making all in FMIndex make[4]: Entering directory '/<>/FMIndex' g++ -DHAVE_CONFIG_H -I. -I.. -I../Common -I/<> -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libfmindex_a-bit_array.o `test -f 'bit_array.cc' || echo './'`bit_array.cc g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/<> -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_count-count.o `test -f 'count.cc' || echo './'`count.cc g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/<> -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -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 In file included from /usr/include/c++/6/vector:69:0, from bit_array.h:24, from BitArrays.h:4, from FMIndex.h:5, from DAWG.h:5, from abyss-dawg.cc:2: /usr/include/c++/6/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = wat_array::BitArray; _Alloc = std::allocator]’: /usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type ‘std::vector::iterator {aka __gnu_cxx::__normal_iterator >}’ will change in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/6/vector:69:0, from bit_array.h:24, from BitArrays.h:4, from FMIndex.h:5, from DAWG.h:5, from count.cc:2: /usr/include/c++/6/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = wat_array::BitArray; _Alloc = std::allocator]’: /usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type ‘std::vector::iterator {aka __gnu_cxx::__normal_iterator >}’ will change in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/6/vector:64:0, from bit_array.h:24, from BitArrays.h:4, from FMIndex.h:5, from DAWG.h:5, from abyss-dawg.cc:2: /usr/include/c++/6/bits/stl_vector.h: In member function ‘void FMIndex::assign(It, It) [with It = __gnu_cxx::__normal_iterator >]’: /usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ will change in GCC 7.1 _M_fill_insert(begin() + __offset, __n, __x); ^~~~~~~~~~~~~~ In file included from /usr/include/c++/6/map:60:0, from abyss-dawg.cc:14: /usr/include/c++/6/bits/stl_tree.h: In function ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple&>, std::tuple<>}; _Key = std::pair; _Val = std::pair, boost::default_color_type>; _KeyOfValue = std::_Select1st, boost::default_color_type> >; _Compare = std::less >; _Alloc = std::allocator, boost::default_color_type> >]’: /usr/include/c++/6/bits/stl_tree.h:2193:7: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, boost::default_color_type>, std::_Select1st, boost::default_color_type> >, std::less >, std::allocator, boost::default_color_type> > >::const_iterator {aka std::_Rb_tree_const_iterator, boost::default_color_type> >}’ will change in GCC 7.1 _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from abyss-dawg.cc:5:0: /usr/include/boost/graph/depth_first_search.hpp: In function ‘void boost::detail::depth_first_visit_impl(const IncidenceGraph&, typename boost::graph_traits::vertex_descriptor, DFSVisitor&, ColorMap, TerminatorFunc) [with IncidenceGraph = FMIndex; DFSVisitor = DAWGVisitor; ColorMap = boost::associative_property_map, boost::default_color_type> >; TerminatorFunc = boost::detail::nontruth2]’: /usr/include/boost/graph/depth_first_search.hpp:109:10: note: parameter passing for argument of type ‘boost::associative_property_map, boost::default_color_type> >’ will change in GCC 7.1 void depth_first_visit_impl ^~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/6/map:61:0, from abyss-dawg.cc:14: /usr/include/c++/6/bits/stl_map.h:483:4: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, boost::default_color_type>, std::_Select1st, boost::default_color_type> >, std::less >, std::allocator, boost::default_color_type> > >::const_iterator {aka std::_Rb_tree_const_iterator, boost::default_color_type> >}’ will change in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, ^~~ /usr/include/c++/6/bits/stl_map.h:483:4: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, boost::default_color_type>, std::_Select1st, boost::default_color_type> >, std::less >, std::allocator, boost::default_color_type> > >::const_iterator {aka std::_Rb_tree_const_iterator, boost::default_color_type> >}’ will change in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, ^~~ /usr/include/c++/6/bits/stl_map.h:483:4: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, boost::default_color_type>, std::_Select1st, boost::default_color_type> >, std::less >, std::allocator, boost::default_color_type> > >::const_iterator {aka std::_Rb_tree_const_iterator, boost::default_color_type> >}’ will change in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, ^~~ /usr/include/c++/6/bits/stl_map.h:483:4: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, boost::default_color_type>, std::_Select1st, boost::default_color_type> >, std::less >, std::allocator, boost::default_color_type> > >::const_iterator {aka std::_Rb_tree_const_iterator, boost::default_color_type> >}’ will change in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, ^~~ In file included from /usr/include/c++/6/vector:64:0, from bit_array.h:24, from BitArrays.h:4, from FMIndex.h:5, from DAWG.h:5, from count.cc:2: /usr/include/c++/6/bits/stl_vector.h: In member function ‘void FMIndex::assign(It, It) [with It = __gnu_cxx::__normal_iterator >]’: /usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ will change in GCC 7.1 _M_fill_insert(begin() + __offset, __n, __x); ^~~~~~~~~~~~~~ In file included from abyss-dawg.cc:5:0: /usr/include/boost/graph/depth_first_search.hpp: In function ‘int main(int, char**)’: /usr/include/boost/graph/depth_first_search.hpp:354:5: note: parameter passing for argument of type ‘boost::associative_property_map, boost::default_color_type> >’ will change in GCC 7.1 detail::depth_first_visit_impl(g, u, vis, color, detail::nontruth2()); ^~~~~~ g++ -Wall -Wextra -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o abyss-count abyss_count-count.o libfmindex.a ../Common/libcommon.a -ldl -lm g++ -Wall -Wextra -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -Wl,-Bsymbolic-functions -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++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/<> -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libassembly_a-AssemblyAlgorithms.o `test -f 'AssemblyAlgorithms.cc' || echo './'`AssemblyAlgorithms.cc g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/<> -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -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/<> -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o alig.o alig.c gcc -DHAVE_CONFIG_H -I. -I.. -I/<> -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o assemble.o assemble.c gcc -DHAVE_CONFIG_H -I. -I.. -I/<> -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o diag.o diag.c gcc -DHAVE_CONFIG_H -I. -I.. -I/<> -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o io.o io.c alig.c:15:20: warning: inline function ‘calc_ov_weight’ declared but never defined 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 extern inline void calc_weight(struct diag* dg, struct scr_matrix* smatrix, ^~~~~~~~~~~ assemble.c:40:20: warning: inline function ‘align_diag’ declared but never defined extern inline char align_diag(struct alignment *algn, struct scr_matrix *smatrix, struct diag* dg); ^~~~~~~~~~ diag.c:1456:3: warning: ‘real_calc_weight’ is static but used in inline function ‘find_diags_dyn’ which is not static real_calc_weight(dg, smatrix, pdist,1,tmp_dist,algn); ^~~~~~~~~~~~~~~~ assemble.c:37:32: warning: inline function ‘find_eqc’ declared but never defined 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 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 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 extern inline void calc_weight(struct diag* dg, struct scr_matrix* smatrix, ^~~~~~~~~~~ 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] fscanf( fp, "%i", &is); ^~~~~~~~~~~~~~~~~~~~~~ io.c:282:5: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 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] fscanf( fp, "%li %li %Le\n", &ti,&tscr,&weight ); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I.. -I/<> -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o orf.o orf.c gcc -DHAVE_CONFIG_H -I. -I.. -I/<> -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o parameters.o parameters.c gcc -DHAVE_CONFIG_H -I. -I.. -I/<> -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o prob.o prob.c gcc -DHAVE_CONFIG_H -I. -I.. -I/<> -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o translate.o translate.c gcc -DHAVE_CONFIG_H -I. -I.. -I/<> -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o museq.o museq.c museq.c: In function ‘main’: museq.c:168:2: warning: implicit declaration of function ‘free_diag’ [-Wimplicit-function-declaration] free_diag(adcol.diags[i]); ^~~~~~~~~ museq.c:278:27: warning: implicit declaration of function ‘free_alignment’ [-Wimplicit-function-declaration] if(! para->FAST_MODE) free_alignment(algn); ^~~~~~~~~~~~~~ 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 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o dialign museq.o libdialign.a -ldl -lm make[4]: Leaving directory '/<>/dialign' Making all in Align make[4]: Entering directory '/<>/Align' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/<> -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libalign_a-alignGlobal.o `test -f 'alignGlobal.cc' || echo './'`alignGlobal.cc g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/<> -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libalign_a-dialign.o `test -f 'dialign.cpp' || echo './'`dialign.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/<> -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libalign_a-dna_diag_prob.o `test -f 'dna_diag_prob.cc' || echo './'`dna_diag_prob.cc g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/<> -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libalign_a-smith_waterman.o `test -f 'smith_waterman.cpp' || echo './'`smith_waterman.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/<> -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_align-align.o `test -f 'align.cc' || echo './'`align.cc g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/<> -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -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++ -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -Wl,-Bsymbolic-functions -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++ -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -Wl,-Bsymbolic-functions -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 make[4]: Leaving directory '/<>/Align' Making all in ABYSS make[4]: Entering directory '/<>/ABYSS' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/<> -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o ABYSS-abyss.o `test -f 'abyss.cc' || echo './'`abyss.cc g++ -Wall -Wextra -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o ABYSS ABYSS-abyss.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../Assembly/libassembly.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/<>/ABYSS' Making all in Bloom make[4]: Entering directory '/<>/Bloom' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/<> -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_bloom-bloom.o `test -f 'bloom.cc' || echo './'`bloom.cc g++ -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o abyss-bloom abyss_bloom-bloom.o ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/<>/Bloom' Making all in BloomDBG make[4]: Entering directory '/<>/BloomDBG' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/<> -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_bloom_dbg-bloom-dbg.o `test -f 'bloom-dbg.cc' || echo './'`bloom-dbg.cc In file included from /usr/include/c++/6/algorithm:62:0, from ../BloomDBG/RollingHashIterator.h:9, from ../BloomDBG/bloom-dbg.h:4, from bloom-dbg.cc:3: /usr/include/c++/6/bits/stl_algo.h: In function ‘_RandomAccessIterator std::__find_if(_RandomAccessIterator, _RandomAccessIterator, _Predicate, std::random_access_iterator_tag) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator > >; _Predicate = __gnu_cxx::__ops::_Iter_equals_val]’: /usr/include/c++/6/bits/stl_algo.h:112:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ will change in GCC 7.1 __find_if(_RandomAccessIterator __first, _RandomAccessIterator __last, ^~~~~~~~~ /usr/include/c++/6/bits/stl_algo.h:112:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ will change in GCC 7.1 /usr/include/c++/6/bits/stl_algo.h: In function ‘PathExtensionResult extendPath(Path::vertex_descriptor>&, Direction, const BidirectionalGraph&, std::unordered_set::vertex_descriptor, std::hash::vertex_descriptor> >&, const ExtendPathParams&) [with BidirectionalGraph = RollingBloomDBG]’: /usr/include/c++/6/bits/stl_algo.h:162:43: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ will change in GCC 7.1 std::__iterator_category(__first)); ^ /usr/include/c++/6/bits/stl_algo.h: In function ‘’: /usr/include/c++/6/bits/stl_algo.h:162:43: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ will change in GCC 7.1 std::__iterator_category(__first)); ^ /usr/include/c++/6/bits/stl_algo.h:162:43: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ will change in GCC 7.1 std::__iterator_category(__first)); ^ g++ -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o abyss-bloom-dbg abyss_bloom_dbg-bloom-dbg.o ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/<>/BloomDBG' Making all in Konnector make[4]: Entering directory '/<>/Konnector' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/<> -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o konnector-konnector.o `test -f 'konnector.cc' || echo './'`konnector.cc g++ -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o konnector konnector-konnector.o ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/<>/Konnector' Making all in Consensus make[4]: Entering directory '/<>/Consensus' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/<> -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Consensus-Consensus.o `test -f 'Consensus.cpp' || echo './'`Consensus.cpp g++ -Wall -Wextra -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o Consensus Consensus-Consensus.o ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/<>/Consensus' Making all in DAssembler make[4]: Entering directory '/<>/DAssembler' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/<> -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o DAssembler-DAssembler.o `test -f 'DAssembler.cpp' || echo './'`DAssembler.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/<> -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o DAssembler-RotatedRead.o `test -f 'RotatedRead.cpp' || echo './'`RotatedRead.cpp g++ -Wall -Wextra -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o DAssembler DAssembler-DAssembler.o DAssembler-RotatedRead.o ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/<>/DAssembler' Making all in DistanceEst make[4]: Entering directory '/<>/DistanceEst' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/<> -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o DistanceEst-DistanceEst.o `test -f 'DistanceEst.cpp' || echo './'`DistanceEst.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/<> -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o DistanceEst-MLE.o `test -f 'MLE.cpp' || echo './'`MLE.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -D SAM_SEQ_QUAL=1 -I/<> -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o DistanceEst_ssq-DistanceEst.o `test -f 'DistanceEst.cpp' || echo './'`DistanceEst.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -D SAM_SEQ_QUAL=1 -I/<> -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o DistanceEst_ssq-MLE.o `test -f 'MLE.cpp' || echo './'`MLE.cpp g++ -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o DistanceEst DistanceEst-DistanceEst.o DistanceEst-MLE.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../Common/libcommon.a -ldl -lm g++ -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o DistanceEst-ssq DistanceEst_ssq-DistanceEst.o DistanceEst_ssq-MLE.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/<>/DistanceEst' Making all in KAligner make[4]: Entering directory '/<>/KAligner' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/<> -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o KAligner-KAligner.o `test -f 'KAligner.cpp' || echo './'`KAligner.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/<> -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o KAligner-Aligner.o `test -f 'Aligner.cpp' || echo './'`Aligner.cpp g++ -Wall -Wextra -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o KAligner KAligner-KAligner.o KAligner-Aligner.o ../DataLayer/libdatalayer.a ../Common/libcommon.a -lpthread -ldl -lm make[4]: Leaving directory '/<>/KAligner' Making all in Layout make[4]: Entering directory '/<>/Layout' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/<> -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_layout-layout.o `test -f 'layout.cc' || echo './'`layout.cc g++ -Wall -Wextra -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o abyss-layout abyss_layout-layout.o ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/<>/Layout' Making all in LogKmerCount make[4]: Entering directory '/<>/LogKmerCount' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/<> -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o logcounter-logcounter.o `test -f 'logcounter.cc' || echo './'`logcounter.cc g++ -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o logcounter logcounter-logcounter.o ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/<>/LogKmerCount' Making all in Map make[4]: Entering directory '/<>/Map' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../FMIndex -I/<> -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_index-index.o `test -f 'index.cc' || echo './'`index.cc g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../FMIndex -I/<> -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_map-map.o `test -f 'map.cc' || echo './'`map.cc g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../FMIndex -D SAM_SEQ_QUAL=1 -I/<> -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_map_ssq-map.o `test -f 'map.cc' || echo './'`map.cc g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../FMIndex -I/<> -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_overlap-overlap.o `test -f 'overlap.cc' || echo './'`overlap.cc index.cc: In function ‘void buildFMIndex(FMIndex&, const string&)’: index.cc:149:64: warning: large integer implicitly truncated to unsigned type [-Woverflow] size_t MAX_SIZE = numeric_limits::max(); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ overlap.cc: In function ‘void buildFMIndex(FMIndex&, const char*)’: overlap.cc:296:64: warning: large integer implicitly truncated to unsigned type [-Woverflow] size_t MAX_SIZE = numeric_limits::max(); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ map.cc: In function ‘void buildFMIndex(FMIndex&, const char*)’: map.cc:492:64: warning: large integer implicitly truncated to unsigned type [-Woverflow] size_t MAX_SIZE = numeric_limits::max(); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ map.cc: In function ‘void buildFMIndex(FMIndex&, const char*)’: map.cc:492:64: warning: large integer implicitly truncated to unsigned type [-Woverflow] size_t MAX_SIZE = numeric_limits::max(); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ In file included from /usr/include/c++/6/vector:69:0, from ../DataLayer/FastaIndex.h:11, from index.cc:3: /usr/include/c++/6/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = wat_array::BitArray; _Alloc = std::allocator]’: /usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type ‘std::vector::iterator {aka __gnu_cxx::__normal_iterator >}’ will change in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/6/vector:64:0, from ../DataLayer/FastaIndex.h:11, from index.cc:3: /usr/include/c++/6/bits/stl_vector.h: In member function ‘void FMIndex::assign(It, It) [with It = __gnu_cxx::__normal_iterator >]’: /usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ will change in GCC 7.1 _M_fill_insert(begin() + __offset, __n, __x); ^~~~~~~~~~~~~~ /usr/include/c++/6/bits/stl_vector.h: In member function ‘void FMIndex::assignBWT(It, It) [with It = __gnu_cxx::__normal_iterator >]’: /usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ will change in GCC 7.1 _M_fill_insert(begin() + __offset, __n, __x); ^~~~~~~~~~~~~~ g++ -Wall -Wextra -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o abyss-index abyss_index-index.o ../FMIndex/libfmindex.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm In file included from /usr/include/c++/6/vector:69:0, from ../FMIndex/bit_array.h:24, from ../FMIndex/BitArrays.h:4, from ../FMIndex/FMIndex.h:5, from map.cc:3: /usr/include/c++/6/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = wat_array::BitArray; _Alloc = std::allocator]’: /usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type ‘std::vector::iterator {aka __gnu_cxx::__normal_iterator >}’ will change in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/6/vector:64:0, from ../FMIndex/bit_array.h:24, from ../FMIndex/BitArrays.h:4, from ../FMIndex/FMIndex.h:5, from map.cc:3: /usr/include/c++/6/bits/stl_vector.h: In member function ‘void FMIndex::assign(It, It) [with It = __gnu_cxx::__normal_iterator >]’: /usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ will change in GCC 7.1 _M_fill_insert(begin() + __offset, __n, __x); ^~~~~~~~~~~~~~ In file included from /usr/include/c++/6/vector:69:0, from ../FMIndex/bit_array.h:24, from ../FMIndex/BitArrays.h:4, from ../FMIndex/FMIndex.h:5, from map.cc:3: /usr/include/c++/6/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = wat_array::BitArray; _Alloc = std::allocator]’: /usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type ‘std::vector::iterator {aka __gnu_cxx::__normal_iterator >}’ will change in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/6/vector:64:0, from ../FMIndex/bit_array.h:24, from ../FMIndex/BitArrays.h:4, from ../FMIndex/FMIndex.h:5, from map.cc:3: /usr/include/c++/6/bits/stl_vector.h: In member function ‘void FMIndex::assign(It, It) [with It = __gnu_cxx::__normal_iterator >]’: /usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ will change in GCC 7.1 _M_fill_insert(begin() + __offset, __n, __x); ^~~~~~~~~~~~~~ g++ -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o abyss-map abyss_map-map.o ../FMIndex/libfmindex.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../DataBase/libdb.a -lsqlite3 -ldl -lm -ldl -lm In file included from /usr/include/c++/6/vector:63:0, from ../Common/Dictionary.h:10, from ../Common/ContigID.h:5, from ../Common/ContigNode.h:5, from ../Common/ContigProperties.h:4, from overlap.cc:10: /usr/include/c++/6/bits/stl_uninitialized.h: In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator; _ForwardIterator = wat_array::BitArray*; bool _TrivialValueTypes = false]’: /usr/include/c++/6/bits/stl_uninitialized.h:68:9: note: parameter passing for argument of type ‘std::move_iterator’ will change in GCC 7.1 __uninit_copy(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~ /usr/include/c++/6/bits/stl_uninitialized.h:68:9: note: parameter passing for argument of type ‘std::move_iterator’ will change in GCC 7.1 In file included from /usr/include/c++/6/vector:69:0, from ../Common/Dictionary.h:10, from ../Common/ContigID.h:5, from ../Common/ContigNode.h:5, from ../Common/ContigProperties.h:4, from overlap.cc:10: /usr/include/c++/6/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = wat_array::BitArray; _Alloc = std::allocator]’: /usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type ‘std::vector::iterator {aka __gnu_cxx::__normal_iterator >}’ will change in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/6/vector:63:0, from ../Common/Dictionary.h:10, from ../Common/ContigID.h:5, from ../Common/ContigNode.h:5, from ../Common/ContigProperties.h:4, from overlap.cc:10: /usr/include/c++/6/bits/stl_uninitialized.h:126:41: note: parameter passing for argument of type ‘std::move_iterator’ will change in GCC 7.1 __uninit_copy(__first, __last, __result); ^ /usr/include/c++/6/bits/stl_uninitialized.h:126:41: note: parameter passing for argument of type ‘std::move_iterator’ will change in GCC 7.1 __uninit_copy(__first, __last, __result); ^ In file included from /usr/include/c++/6/vector:64:0, from ../Common/Dictionary.h:10, from ../Common/ContigID.h:5, from ../Common/ContigNode.h:5, from ../Common/ContigProperties.h:4, from overlap.cc:10: /usr/include/c++/6/bits/stl_vector.h: In member function ‘void FMIndex::assign(It, It) [with It = __gnu_cxx::__normal_iterator >]’: /usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ will change in GCC 7.1 _M_fill_insert(begin() + __offset, __n, __x); ^~~~~~~~~~~~~~ g++ -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o abyss-map-ssq abyss_map_ssq-map.o ../FMIndex/libfmindex.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../DataBase/libdb.a -lsqlite3 -ldl -lm -ldl -lm g++ -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o abyss-overlap abyss_overlap-overlap.o ../FMIndex/libfmindex.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/<>/Map' Making all in MergePaths make[4]: Entering directory '/<>/MergePaths' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/<> -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o MergePaths-MergePaths.o `test -f 'MergePaths.cpp' || echo './'`MergePaths.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Align -I../Common -I../DataLayer -I/<> -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o MergeContigs-MergeContigs.o `test -f 'MergeContigs.cpp' || echo './'`MergeContigs.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Align -I../Common -I../DataLayer -I../SimpleGraph -I/<> -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o PathConsensus-PathConsensus.o `test -f 'PathConsensus.cpp' || echo './'`PathConsensus.cpp g++ -Wall -Wextra -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o MergeContigs MergeContigs-MergeContigs.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a -ldl -lm g++ -Wall -Wextra -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o PathConsensus PathConsensus-PathConsensus.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a ../dialign/libdialign.a -ldl -lm g++ -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o MergePaths MergePaths-MergePaths.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/<>/MergePaths' Making all in Misc make[4]: Entering directory '/<>/Misc' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/<>/Misc' Making all in Overlap make[4]: Entering directory '/<>/Overlap' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/<> -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Overlap-Overlap.o `test -f 'Overlap.cpp' || echo './'`Overlap.cpp g++ -Wall -Wextra -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o Overlap Overlap-Overlap.o ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/<>/Overlap' Making all in PairedDBG make[4]: Entering directory '/<>/PairedDBG' g++ -DHAVE_CONFIG_H -I. -I.. -I/<> -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o KmerPair.o KmerPair.cc g++ -DHAVE_CONFIG_H -I. -I.. -DPAIRED_DBG -I.. -I/<> -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_paired_dbg-abyss-paired-dbg.o `test -f 'abyss-paired-dbg.cc' || echo './'`abyss-paired-dbg.cc g++ -DHAVE_CONFIG_H -I. -I.. -DPAIRED_DBG -I.. -I/<> -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_paired_dbg-KmerPair.o `test -f 'KmerPair.cc' || echo './'`KmerPair.cc rm -f libpaireddbg.a ar cru libpaireddbg.a KmerPair.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libpaireddbg.a g++ -Wall -Wextra -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o abyss-paired-dbg abyss_paired_dbg-abyss-paired-dbg.o abyss_paired_dbg-KmerPair.o ../Assembly/libassembly.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../DataBase/libdb.a -lsqlite3 -ldl -lm -ldl -lm make[4]: Leaving directory '/<>/PairedDBG' Making all in ParseAligns make[4]: Entering directory '/<>/ParseAligns' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/<> -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_fixmate-abyss-fixmate.o `test -f 'abyss-fixmate.cc' || echo './'`abyss-fixmate.cc g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -D SAM_SEQ_QUAL=1 -I/<> -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_fixmate_ssq-abyss-fixmate.o `test -f 'abyss-fixmate.cc' || echo './'`abyss-fixmate.cc g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/<> -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o ParseAligns-ParseAligns.o `test -f 'ParseAligns.cpp' || echo './'`ParseAligns.cpp g++ -Wall -Wextra -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o ParseAligns ParseAligns-ParseAligns.o ../Common/libcommon.a -ldl -lm g++ -Wall -Wextra -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o abyss-fixmate abyss_fixmate-abyss-fixmate.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../Common/libcommon.a -ldl -lm g++ -Wall -Wextra -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o abyss-fixmate-ssq abyss_fixmate_ssq-abyss-fixmate.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/<>/ParseAligns' Making all in PathOverlap make[4]: Entering directory '/<>/PathOverlap' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/<> -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o PathOverlap-PathOverlap.o `test -f 'PathOverlap.cpp' || echo './'`PathOverlap.cpp g++ -Wall -Wextra -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o PathOverlap PathOverlap-PathOverlap.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/<>/PathOverlap' Making all in PopBubbles make[4]: Entering directory '/<>/PopBubbles' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Align -I../Common -I../DataLayer -I/<> -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o PopBubbles-PopBubbles.o `test -f 'PopBubbles.cpp' || echo './'`PopBubbles.cpp g++ -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o PopBubbles PopBubbles-PopBubbles.o ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a ../dialign/libdialign.a -ldl -lm make[4]: Leaving directory '/<>/PopBubbles' Making all in Scaffold make[4]: Entering directory '/<>/Scaffold' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/<> -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_scaffold-scaffold.o `test -f 'scaffold.cc' || echo './'`scaffold.cc g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/<> -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_junction-junction.o `test -f 'junction.cc' || echo './'`junction.cc g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/<> -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_longseqdist-longseqdist.o `test -f 'longseqdist.cpp' || echo './'`longseqdist.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/<> -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_drawgraph-drawgraph.o `test -f 'drawgraph.cc' || echo './'`drawgraph.cc In file included from /usr/include/c++/6/algorithm:62:0, from /usr/include/boost/smart_ptr/shared_ptr.hpp:38, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/property_map/vector_property_map.hpp:14, from /usr/include/boost/property_map/property_map.hpp:600, from /usr/include/boost/graph/properties.hpp:19, from ../Graph/Properties.h:6, from ../Common/ContigNode.h:6, from ../Common/ContigProperties.h:4, from drawgraph.cc:10: /usr/include/c++/6/bits/stl_algo.h: In function ‘void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, std::vector > >; _Compare = __gnu_cxx::__ops::_Val_less_iter]’: /usr/include/c++/6/bits/stl_algo.h:1818:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ will change in GCC 7.1 __unguarded_linear_insert(_RandomAccessIterator __last, ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/6/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, std::vector > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: /usr/include/c++/6/bits/stl_algo.h:1837:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ will change in GCC 7.1 __insertion_sort(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/6/bits/stl_algo.h:1837:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ will change in GCC 7.1 /usr/include/c++/6/bits/stl_algo.h: In function ‘void std::__move_median_to_first(_Iterator, _Iterator, _Iterator, _Iterator, _Compare) [with _Iterator = __gnu_cxx::__normal_iterator*, std::vector > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: /usr/include/c++/6/bits/stl_algo.h:78:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ will change in GCC 7.1 __move_median_to_first(_Iterator __result,_Iterator __a, _Iterator __b, ^~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/6/bits/stl_algo.h:78:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ will change in GCC 7.1 /usr/include/c++/6/bits/stl_algo.h:78:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ will change in GCC 7.1 /usr/include/c++/6/bits/stl_algo.h:78:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ will change in GCC 7.1 /usr/include/c++/6/bits/stl_algo.h:78:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ will change in GCC 7.1 /usr/include/c++/6/bits/stl_algo.h:78:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ will change in GCC 7.1 In file included from /usr/include/c++/6/bits/stl_algo.h:61:0, from /usr/include/c++/6/algorithm:62, from /usr/include/boost/smart_ptr/shared_ptr.hpp:38, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/property_map/vector_property_map.hpp:14, from /usr/include/boost/property_map/property_map.hpp:600, from /usr/include/boost/graph/properties.hpp:19, from ../Graph/Properties.h:6, from ../Common/ContigNode.h:6, from ../Common/ContigProperties.h:4, from drawgraph.cc:10: /usr/include/c++/6/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, std::vector > >; _Distance = int; _Tp = std::pair; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: /usr/include/c++/6/bits/stl_heap.h:209:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ will change in GCC 7.1 __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, ^~~~~~~~~~~~~ In file included from /usr/include/c++/6/algorithm:62:0, from /usr/include/boost/smart_ptr/shared_ptr.hpp:38, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/property_map/vector_property_map.hpp:14, from /usr/include/boost/property_map/property_map.hpp:600, from /usr/include/boost/graph/properties.hpp:19, from ../Graph/Properties.h:6, from ../Common/ContigNode.h:6, from ../Common/ContigProperties.h:4, from drawgraph.cc:10: /usr/include/c++/6/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, std::vector > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: /usr/include/c++/6/bits/stl_algo.h:1937:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ will change in GCC 7.1 __introsort_loop(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/6/bits/stl_algo.h:1937:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ will change in GCC 7.1 /usr/include/c++/6/bits/stl_algo.h:1918:7: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ will change in GCC 7.1 std::__move_median_to_first(__first, __first + 1, __mid, __last - 1, ^~~ /usr/include/c++/6/bits/stl_algo.h:1918:7: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ will change in GCC 7.1 /usr/include/c++/6/bits/stl_algo.h:1918:7: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ will change in GCC 7.1 /usr/include/c++/6/bits/stl_algo.h:1918:7: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ will change in GCC 7.1 /usr/include/c++/6/bits/stl_algo.h:1951:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ will change in GCC 7.1 std::__introsort_loop(__cut, __last, __depth_limit, __comp); ^~~ /usr/include/c++/6/bits/stl_algo.h: In function ‘int main(int, char**)’: /usr/include/c++/6/bits/stl_algo.h:1965:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ will change in GCC 7.1 std::__introsort_loop(__first, __last, ^~~ /usr/include/c++/6/bits/stl_algo.h:1882:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ will change in GCC 7.1 std::__insertion_sort(__first, __first + int(_S_threshold), __comp); ^~~ /usr/include/c++/6/bits/stl_algo.h:1887:2: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ will change in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ^~~ g++ -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o abyss-longseqdist abyss_longseqdist-longseqdist.o ../Common/libcommon.a -ldl -lm g++ -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o abyss-junction abyss_junction-junction.o ../Common/libcommon.a -ldl -lm g++ -Wall -Wextra -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o abyss-drawgraph abyss_drawgraph-drawgraph.o ../Common/libcommon.a -ldl -lm g++ -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o abyss-scaffold abyss_scaffold-scaffold.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/<>/Scaffold' Making all in SimpleGraph make[4]: Entering directory '/<>/SimpleGraph' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/<> -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Wno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o SimpleGraph-SimpleGraph.o `test -f 'SimpleGraph.cpp' || echo './'`SimpleGraph.cpp g++ -Wall -Wextra -Wno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o SimpleGraph SimpleGraph-SimpleGraph.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../Common/libcommon.a -lpthread -ldl -lm make[4]: Leaving directory '/<>/SimpleGraph' Making all in kmerprint make[4]: Entering directory '/<>/kmerprint' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Assembly -I../Common -I../DataLayer -I/<> -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o kmerprint-kmerprint.o `test -f 'kmerprint.cc' || echo './'`kmerprint.cc g++ -Wall -Wextra -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o kmerprint kmerprint-kmerprint.o ../Assembly/libassembly.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/<>/kmerprint' Making all in FilterGraph make[4]: Entering directory '/<>/FilterGraph' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/<> -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_filtergraph-FilterGraph.o `test -f 'FilterGraph.cc' || echo './'`FilterGraph.cc g++ -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o abyss-filtergraph abyss_filtergraph-FilterGraph.o ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/<>/FilterGraph' Making all in GapFiller make[4]: Entering directory '/<>/GapFiller' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../Align -D SAM_SEQ_QUAL=1 -I/<> -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_gapfill-gapfill.o `test -f 'gapfill.cpp' || echo './'`gapfill.cpp g++ -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o abyss-gapfill abyss_gapfill-gapfill.o ../Align/libalign.a ../dialign/libdialign.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/<>/GapFiller' Making all in Sealer make[4]: Entering directory '/<>/Sealer' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/<> -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_sealer-sealer.o `test -f 'sealer.cc' || echo './'`sealer.cc g++ -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o abyss-sealer abyss_sealer-sealer.o ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/<>/Sealer' Making all in AdjList make[4]: Entering directory '/<>/AdjList' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -DPAIRED_DBG -I/<> -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o AdjList-AdjList.o `test -f 'AdjList.cpp' || echo './'`AdjList.cpp g++ -Wall -Wextra -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o AdjList AdjList-AdjList.o ../DataLayer/libdatalayer.a ../Common/libcommon.a ../PairedDBG/libpaireddbg.a ../DataBase/libdb.a -lsqlite3 -ldl -lm -ldl -lm make[4]: Leaving directory '/<>/AdjList' Making all in lib/bloomfilter make[4]: Entering directory '/<>/lib/bloomfilter' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/<>/lib/bloomfilter' Making all in lib/rolling-hash make[4]: Entering directory '/<>/lib/rolling-hash' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/<>/lib/rolling-hash' Making all in lib/gtest-1.7.0 make[4]: Entering directory '/<>/lib/gtest-1.7.0' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/<>/lib/gtest-1.7.0' Making all in Unittest make[4]: Entering directory '/<>/Unittest' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/<>/Unittest' make[4]: Entering directory '/<>' make[4]: Leaving directory '/<>' make[3]: Leaving directory '/<>' make[2]: Leaving directory '/<>' markdown_py -f README.html README.md make[1]: Leaving directory '/<>' dh_auto_test -a make -j4 check VERBOSE=1 make[1]: Entering directory '/<>' Making check in bin make[2]: Entering directory '/<>/bin' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/<>/bin' Making check in doc make[2]: Entering directory '/<>/doc' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/<>/doc' Making check in Common make[2]: Entering directory '/<>/Common' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/<>/Common' Making check in Graph make[2]: Entering directory '/<>/Graph' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/<>/Graph' Making check in DataLayer make[2]: Entering directory '/<>/DataLayer' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/<>/DataLayer' Making check in DataBase make[2]: Entering directory '/<>/DataBase' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/<>/DataBase' Making check in FMIndex make[2]: Entering directory '/<>/FMIndex' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/<>/FMIndex' Making check in Assembly make[2]: Entering directory '/<>/Assembly' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/<>/Assembly' Making check in dialign make[2]: Entering directory '/<>/dialign' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/<>/dialign' Making check in Align make[2]: Entering directory '/<>/Align' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/<>/Align' Making check in ABYSS make[2]: Entering directory '/<>/ABYSS' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/<>/ABYSS' Making check in Bloom make[2]: Entering directory '/<>/Bloom' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/<>/Bloom' Making check in BloomDBG make[2]: Entering directory '/<>/BloomDBG' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/<>/BloomDBG' Making check in Konnector make[2]: Entering directory '/<>/Konnector' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/<>/Konnector' Making check in Consensus make[2]: Entering directory '/<>/Consensus' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/<>/Consensus' Making check in DAssembler make[2]: Entering directory '/<>/DAssembler' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/<>/DAssembler' Making check in DistanceEst make[2]: Entering directory '/<>/DistanceEst' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/<>/DistanceEst' Making check in KAligner make[2]: Entering directory '/<>/KAligner' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/<>/KAligner' Making check in Layout make[2]: Entering directory '/<>/Layout' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/<>/Layout' Making check in LogKmerCount make[2]: Entering directory '/<>/LogKmerCount' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/<>/LogKmerCount' Making check in Map make[2]: Entering directory '/<>/Map' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/<>/Map' Making check in MergePaths make[2]: Entering directory '/<>/MergePaths' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/<>/MergePaths' Making check in Misc make[2]: Entering directory '/<>/Misc' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/<>/Misc' Making check in Overlap make[2]: Entering directory '/<>/Overlap' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/<>/Overlap' Making check in PairedDBG make[2]: Entering directory '/<>/PairedDBG' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/<>/PairedDBG' Making check in ParseAligns make[2]: Entering directory '/<>/ParseAligns' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/<>/ParseAligns' Making check in PathOverlap make[2]: Entering directory '/<>/PathOverlap' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/<>/PathOverlap' Making check in PopBubbles make[2]: Entering directory '/<>/PopBubbles' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/<>/PopBubbles' Making check in Scaffold make[2]: Entering directory '/<>/Scaffold' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/<>/Scaffold' Making check in SimpleGraph make[2]: Entering directory '/<>/SimpleGraph' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/<>/SimpleGraph' Making check in kmerprint make[2]: Entering directory '/<>/kmerprint' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/<>/kmerprint' Making check in FilterGraph make[2]: Entering directory '/<>/FilterGraph' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/<>/FilterGraph' Making check in GapFiller make[2]: Entering directory '/<>/GapFiller' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/<>/GapFiller' Making check in Sealer make[2]: Entering directory '/<>/Sealer' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/<>/Sealer' Making check in AdjList make[2]: Entering directory '/<>/AdjList' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/<>/AdjList' Making check in lib/bloomfilter make[2]: Entering directory '/<>/lib/bloomfilter' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/<>/lib/bloomfilter' Making check in lib/rolling-hash make[2]: Entering directory '/<>/lib/rolling-hash' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/<>/lib/rolling-hash' Making check in lib/gtest-1.7.0 make[2]: Entering directory '/<>/lib/gtest-1.7.0' make libgtest.a libgtest_main.a make[3]: Entering directory '/<>/lib/gtest-1.7.0' g++ -DHAVE_CONFIG_H -I. -I../.. -I../.. -isystem ../../lib/gtest-1.7.0/include -I/<> -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Wno-missing-field-initializers -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o src/libgtest_a-gtest-all.o `test -f 'src/gtest-all.cc' || echo './'`src/gtest-all.cc g++ -DHAVE_CONFIG_H -I. -I../.. -I../.. -isystem ../../lib/gtest-1.7.0/include -I/<> -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Wno-missing-field-initializers -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o src/libgtest_main_a-gtest_main.o `test -f 'src/gtest_main.cc' || echo './'`src/gtest_main.cc g++ -DHAVE_CONFIG_H -I. -I../.. -I../.. -isystem ../../lib/gtest-1.7.0/include -I/<> -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Wno-missing-field-initializers -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o src/libgtest_main_a-gtest-all.o `test -f 'src/gtest-all.cc' || echo './'`src/gtest-all.cc rm -f libgtest_main.a ar cru libgtest_main.a src/libgtest_main_a-gtest_main.o src/libgtest_main_a-gtest-all.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libgtest_main.a rm -f libgtest.a ar cru libgtest.a src/libgtest_a-gtest-all.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libgtest.a make[3]: Leaving directory '/<>/lib/gtest-1.7.0' make[2]: Leaving directory '/<>/lib/gtest-1.7.0' Making check in Unittest make[2]: Entering directory '/<>/Unittest' make common_stringutil common_histogram common_bitutil common_kmer common_sequence common_KmerIterator common_sam BloomFilter Konnector_DBGBloom Konnector_DBGBloomAlgorithms graph_ConstrainedBFSVisitor graph_BidirectionalBFS graph_AllPathsSearch graph_HashGraph graph_ConstrainedBidiBFSVisitor graph_ExtendPath graph_DotIO graph_UndirectedGraph Konnector_konnector DBG_LoadAlgorithm PairedDBG_LoadAlgorithm PairedDBG_KmerPair PairedDBG_Dinuc PairedDBG_BranchRecord BloomDBG_BloomDBG BloomDBG_RollingHash BloomDBG_RollingHashIterator BloomDBG_HashAgnosticCascadingBloom BloomDBG_RollingBloomDBG BloomDBG_MaskedKmer BloomDBG_SpacedSeed make[3]: Entering directory '/<>/Unittest' g++ -DHAVE_CONFIG_H -I. -I.. -DGTEST_USE_OWN_TR1_TUPLE=0 -I.. -I../lib/gtest-1.7.0/include -I/<> -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Common/StringUtilTest.o Common/StringUtilTest.cpp g++ -DHAVE_CONFIG_H -I. -I.. -DGTEST_USE_OWN_TR1_TUPLE=0 -I.. -I../lib/gtest-1.7.0/include -I/<> -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Common/HistogramTest.o Common/HistogramTest.cpp g++ -DHAVE_CONFIG_H -I. -I.. -DGTEST_USE_OWN_TR1_TUPLE=0 -I.. -I../lib/gtest-1.7.0/include -I/<> -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Common/BitUtilTest.o Common/BitUtilTest.cpp g++ -DHAVE_CONFIG_H -I. -I.. -DGTEST_USE_OWN_TR1_TUPLE=0 -I.. -I../lib/gtest-1.7.0/include -I/<> -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Common/KmerTest.o Common/KmerTest.cpp g++ -DHAVE_CONFIG_H -I. -I.. -DGTEST_USE_OWN_TR1_TUPLE=0 -I.. -I../lib/gtest-1.7.0/include -I/<> -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Common/Sequence.o Common/Sequence.cc g++ -DHAVE_CONFIG_H -I. -I.. -DGTEST_USE_OWN_TR1_TUPLE=0 -I.. -I../lib/gtest-1.7.0/include -I/<> -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Common/KmerIteratorTest.o Common/KmerIteratorTest.cpp g++ -DHAVE_CONFIG_H -I. -I.. -DGTEST_USE_OWN_TR1_TUPLE=0 -I.. -I../lib/gtest-1.7.0/include -I/<> -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Common/SAM.o Common/SAM.cc g++ -DHAVE_CONFIG_H -I. -I.. -DGTEST_USE_OWN_TR1_TUPLE=0 -I.. -I../lib/gtest-1.7.0/include -I../Common -I/<> -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Konnector/BloomFilter-BloomFilter.o `test -f 'Konnector/BloomFilter.cc' || echo './'`Konnector/BloomFilter.cc g++ -DHAVE_CONFIG_H -I. -I.. -DGTEST_USE_OWN_TR1_TUPLE=0 -I.. -I../lib/gtest-1.7.0/include -I../Common -I/<> -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Konnector/Konnector_DBGBloom-DBGBloomTest.o `test -f 'Konnector/DBGBloomTest.cpp' || echo './'`Konnector/DBGBloomTest.cpp g++ -DHAVE_CONFIG_H -I. -I.. -DGTEST_USE_OWN_TR1_TUPLE=0 -I.. -I../lib/gtest-1.7.0/include -I../Common -I/<> -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Konnector/Konnector_DBGBloomAlgorithms-DBGBloomAlgorithmsTest.o `test -f 'Konnector/DBGBloomAlgorithmsTest.cpp' || echo './'`Konnector/DBGBloomAlgorithmsTest.cpp g++ -DHAVE_CONFIG_H -I. -I.. -DGTEST_USE_OWN_TR1_TUPLE=0 -I.. -I../lib/gtest-1.7.0/include -I../Common -I/<> -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Graph/graph_ConstrainedBFSVisitor-ConstrainedBFSVisitorTest.o `test -f 'Graph/ConstrainedBFSVisitorTest.cpp' || echo './'`Graph/ConstrainedBFSVisitorTest.cpp g++ -DHAVE_CONFIG_H -I. -I.. -DGTEST_USE_OWN_TR1_TUPLE=0 -I.. -I../lib/gtest-1.7.0/include -I../Common -I/<> -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Graph/graph_BidirectionalBFS-BidirectionalBFSTest.o `test -f 'Graph/BidirectionalBFSTest.cpp' || echo './'`Graph/BidirectionalBFSTest.cpp g++ -DHAVE_CONFIG_H -I. -I.. -DGTEST_USE_OWN_TR1_TUPLE=0 -I.. -I../lib/gtest-1.7.0/include -I../Common -I/<> -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Graph/graph_AllPathsSearch-AllPathsSearchTest.o `test -f 'Graph/AllPathsSearchTest.cpp' || echo './'`Graph/AllPathsSearchTest.cpp g++ -DHAVE_CONFIG_H -I. -I.. -DGTEST_USE_OWN_TR1_TUPLE=0 -I.. -I../lib/gtest-1.7.0/include -I../Common -I/<> -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Graph/graph_HashGraph-HashGraphTest.o `test -f 'Graph/HashGraphTest.cpp' || echo './'`Graph/HashGraphTest.cpp g++ -DHAVE_CONFIG_H -I. -I.. -DGTEST_USE_OWN_TR1_TUPLE=0 -I.. -I../lib/gtest-1.7.0/include -I../Common -I/<> -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Graph/graph_ConstrainedBidiBFSVisitor-ConstrainedBidiBFSVisitorTest.o `test -f 'Graph/ConstrainedBidiBFSVisitorTest.cpp' || echo './'`Graph/ConstrainedBidiBFSVisitorTest.cpp g++ -DHAVE_CONFIG_H -I. -I.. -DGTEST_USE_OWN_TR1_TUPLE=0 -I.. -I../lib/gtest-1.7.0/include -I../Common -I/<> -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Graph/graph_ExtendPath-ExtendPathTest.o `test -f 'Graph/ExtendPathTest.cpp' || echo './'`Graph/ExtendPathTest.cpp g++ -DHAVE_CONFIG_H -I. -I.. -DGTEST_USE_OWN_TR1_TUPLE=0 -I.. -I../lib/gtest-1.7.0/include -I../Common -I/<> -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Graph/graph_DotIO-DotIOTest.o `test -f 'Graph/DotIOTest.cpp' || echo './'`Graph/DotIOTest.cpp g++ -DHAVE_CONFIG_H -I. -I.. -DGTEST_USE_OWN_TR1_TUPLE=0 -I.. -I../lib/gtest-1.7.0/include -I/<> -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Graph/UndirectedGraphTest.o Graph/UndirectedGraphTest.cpp g++ -DHAVE_CONFIG_H -I. -I.. -DGTEST_USE_OWN_TR1_TUPLE=0 -I.. -I../lib/gtest-1.7.0/include -I../Common -I/<> -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Konnector/Konnector_konnector-konnectorTest.o `test -f 'Konnector/konnectorTest.cpp' || echo './'`Konnector/konnectorTest.cpp g++ -DHAVE_CONFIG_H -I. -I.. -DGTEST_USE_OWN_TR1_TUPLE=0 -I.. -I../lib/gtest-1.7.0/include -I../DataLayer -I../Common -I/<> -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o DBG/DBG_LoadAlgorithm-LoadAlgorithmTest.o `test -f 'DBG/LoadAlgorithmTest.cpp' || echo './'`DBG/LoadAlgorithmTest.cpp g++ -DHAVE_CONFIG_H -I. -I.. -DGTEST_USE_OWN_TR1_TUPLE=0 -I.. -I../lib/gtest-1.7.0/include -I../DataLayer -I../Common -I/<> -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o PairedDBG/PairedDBG_LoadAlgorithm-LoadAlgorithmTest.o `test -f 'PairedDBG/LoadAlgorithmTest.cpp' || echo './'`PairedDBG/LoadAlgorithmTest.cpp g++ -DHAVE_CONFIG_H -I. -I.. -DGTEST_USE_OWN_TR1_TUPLE=0 -I.. -I../lib/gtest-1.7.0/include -I../DataLayer -I../Common -I/<> -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o PairedDBG/PairedDBG_KmerPair-KmerPairTest.o `test -f 'PairedDBG/KmerPairTest.cc' || echo './'`PairedDBG/KmerPairTest.cc g++ -DHAVE_CONFIG_H -I. -I.. -DGTEST_USE_OWN_TR1_TUPLE=0 -I.. -I../lib/gtest-1.7.0/include -I../DataLayer -I../Common -I/<> -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o PairedDBG/PairedDBG_Dinuc-DinucTest.o `test -f 'PairedDBG/DinucTest.cc' || echo './'`PairedDBG/DinucTest.cc g++ -DHAVE_CONFIG_H -I. -I.. -DGTEST_USE_OWN_TR1_TUPLE=0 -I.. -I../lib/gtest-1.7.0/include -I../DataLayer -I../Common -I/<> -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o PairedDBG/PairedDBG_BranchRecord-BranchRecordTest.o `test -f 'PairedDBG/BranchRecordTest.cpp' || echo './'`PairedDBG/BranchRecordTest.cpp g++ -DHAVE_CONFIG_H -I. -I.. -DGTEST_USE_OWN_TR1_TUPLE=0 -I.. -I../lib/gtest-1.7.0/include -I../Common -I/<> -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o BloomDBG/BloomDBG_BloomDBG-BloomDBGTest.o `test -f 'BloomDBG/BloomDBGTest.cpp' || echo './'`BloomDBG/BloomDBGTest.cpp g++ -DHAVE_CONFIG_H -I. -I.. -DGTEST_USE_OWN_TR1_TUPLE=0 -I.. -I../lib/gtest-1.7.0/include -I/<> -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o BloomDBG/RollingHashTest.o BloomDBG/RollingHashTest.cpp g++ -DHAVE_CONFIG_H -I. -I.. -DGTEST_USE_OWN_TR1_TUPLE=0 -I.. -I../lib/gtest-1.7.0/include -I/<> -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o BloomDBG/RollingHashIteratorTest.o BloomDBG/RollingHashIteratorTest.cpp g++ -DHAVE_CONFIG_H -I. -I.. -DGTEST_USE_OWN_TR1_TUPLE=0 -I.. -I../lib/gtest-1.7.0/include -I/<> -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o BloomDBG/BloomDBG_HashAgnosticCascadingBloom-HashAgnosticCascadingBloomTest.o `test -f 'BloomDBG/HashAgnosticCascadingBloomTest.cpp' || echo './'`BloomDBG/HashAgnosticCascadingBloomTest.cpp In file included from /usr/include/c++/6/algorithm:62:0, from ../BloomDBG/RollingHashIterator.h:9, from ../BloomDBG/bloom-dbg.h:4, from BloomDBG/BloomDBGTest.cpp:2: /usr/include/c++/6/bits/stl_algo.h: In function ‘_RandomAccessIterator std::__find_if(_RandomAccessIterator, _RandomAccessIterator, _Predicate, std::random_access_iterator_tag) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator > >; _Predicate = __gnu_cxx::__ops::_Iter_equals_val]’: /usr/include/c++/6/bits/stl_algo.h:112:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ will change in GCC 7.1 __find_if(_RandomAccessIterator __first, _RandomAccessIterator __last, ^~~~~~~~~ /usr/include/c++/6/bits/stl_algo.h:112:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ will change in GCC 7.1 g++ -DHAVE_CONFIG_H -I. -I.. -DGTEST_USE_OWN_TR1_TUPLE=0 -I.. -I../lib/gtest-1.7.0/include -I/<> -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o BloomDBG/BloomDBG_RollingBloomDBG-RollingBloomDBGTest.o `test -f 'BloomDBG/RollingBloomDBGTest.cpp' || echo './'`BloomDBG/RollingBloomDBGTest.cpp /usr/include/c++/6/bits/stl_algo.h: In function ‘std::vector > BloomDBG::splitSeq(const Sequence&, unsigned int, unsigned int, const GraphT&, unsigned int) [with GraphT = RollingBloomDBG]’: /usr/include/c++/6/bits/stl_algo.h:162:43: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ will change in GCC 7.1 std::__iterator_category(__first)); ^ /usr/include/c++/6/bits/stl_algo.h:162:43: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ will change in GCC 7.1 std::__iterator_category(__first)); ^ g++ -DHAVE_CONFIG_H -I. -I.. -DGTEST_USE_OWN_TR1_TUPLE=0 -I.. -I../lib/gtest-1.7.0/include -I/<> -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o BloomDBG/MaskedKmerTest.o BloomDBG/MaskedKmerTest.cpp g++ -DHAVE_CONFIG_H -I. -I.. -DGTEST_USE_OWN_TR1_TUPLE=0 -I.. -I../lib/gtest-1.7.0/include -I/<> -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o BloomDBG/SpacedSeedTest.o BloomDBG/SpacedSeedTest.cpp g++ -Wall -Wextra -pthread -Wno-error -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o common_stringutil Common/StringUtilTest.o ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -Wall -Wextra -pthread -Wno-error -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o common_histogram Common/HistogramTest.o ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -Wall -Wextra -pthread -Wno-error -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o common_bitutil Common/BitUtilTest.o ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -Wall -Wextra -pthread -Wno-error -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o common_kmer Common/KmerTest.o ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -Wall -Wextra -pthread -Wno-error -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o common_sequence Common/Sequence.o ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -Wall -Wextra -pthread -Wno-error -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o common_KmerIterator Common/KmerIteratorTest.o ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -Wall -Wextra -pthread -Wno-error -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o common_sam Common/SAM.o ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o BloomFilter Konnector/BloomFilter-BloomFilter.o ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o Konnector_DBGBloom Konnector/Konnector_DBGBloom-DBGBloomTest.o ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o Konnector_DBGBloomAlgorithms Konnector/Konnector_DBGBloomAlgorithms-DBGBloomAlgorithmsTest.o ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -Wall -Wextra -pthread -Wno-error -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o graph_ConstrainedBFSVisitor Graph/graph_ConstrainedBFSVisitor-ConstrainedBFSVisitorTest.o ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -Wall -Wextra -pthread -Wno-error -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o graph_BidirectionalBFS Graph/graph_BidirectionalBFS-BidirectionalBFSTest.o ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -Wall -Wextra -pthread -Wno-error -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o graph_AllPathsSearch Graph/graph_AllPathsSearch-AllPathsSearchTest.o ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -Wall -Wextra -pthread -Wno-error -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o graph_HashGraph Graph/graph_HashGraph-HashGraphTest.o ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -Wall -Wextra -pthread -Wno-error -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o graph_ConstrainedBidiBFSVisitor Graph/graph_ConstrainedBidiBFSVisitor-ConstrainedBidiBFSVisitorTest.o ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -Wall -Wextra -pthread -Wno-error -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o graph_ExtendPath Graph/graph_ExtendPath-ExtendPathTest.o ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -Wall -Wextra -pthread -Wno-error -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o graph_DotIO Graph/graph_DotIO-DotIOTest.o ../Assembly/libassembly.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -Wall -Wextra -pthread -Wno-error -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o graph_UndirectedGraph Graph/UndirectedGraphTest.o ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o Konnector_konnector Konnector/Konnector_konnector-konnectorTest.o ../Align/libalign.a ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o DBG_LoadAlgorithm DBG/DBG_LoadAlgorithm-LoadAlgorithmTest.o ../Assembly/libassembly.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o PairedDBG_LoadAlgorithm PairedDBG/PairedDBG_LoadAlgorithm-LoadAlgorithmTest.o ../PairedDBG/libpaireddbg.a ../Assembly/libassembly.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o PairedDBG_KmerPair PairedDBG/PairedDBG_KmerPair-KmerPairTest.o ../PairedDBG/libpaireddbg.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o PairedDBG_Dinuc PairedDBG/PairedDBG_Dinuc-DinucTest.o ../PairedDBG/libpaireddbg.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o PairedDBG_BranchRecord PairedDBG/PairedDBG_BranchRecord-BranchRecordTest.o ../PairedDBG/libpaireddbg.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o BloomDBG_BloomDBG BloomDBG/BloomDBG_BloomDBG-BloomDBGTest.o ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -Wall -Wextra -pthread -Wno-error -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o BloomDBG_RollingHash BloomDBG/RollingHashTest.o ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -Wall -Wextra -pthread -Wno-error -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o BloomDBG_RollingHashIterator BloomDBG/RollingHashIteratorTest.o ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o BloomDBG_HashAgnosticCascadingBloom BloomDBG/BloomDBG_HashAgnosticCascadingBloom-HashAgnosticCascadingBloomTest.o ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -Wall -Wextra -pthread -Wno-error -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o BloomDBG_MaskedKmer BloomDBG/MaskedKmerTest.o ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -Wall -Wextra -pthread -Wno-error -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o BloomDBG_SpacedSeed BloomDBG/SpacedSeedTest.o ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm In file included from /usr/include/c++/6/unordered_set:47:0, from ../Common/UnorderedSet.h:8, from BloomDBG/RollingBloomDBGTest.cpp:3: /usr/include/c++/6/bits/hashtable.h: In member function ‘std::_Hashtable<_Key, _Value, _Alloc, _ExtractKey, _Equal, _H1, _H2, _Hash, _RehashPolicy, _Traits>::iterator std::_Hashtable<_Key, _Value, _Alloc, _ExtractKey, _Equal, _H1, _H2, _Hash, _RehashPolicy, _Traits>::erase(std::_Hashtable<_Key, _Value, _Alloc, _ExtractKey, _Equal, _H1, _H2, _Hash, _RehashPolicy, _Traits>::const_iterator) [with _Key = RollingBloomDBGVertex; _Value = RollingBloomDBGVertex; _Alloc = std::allocator; _ExtractKey = std::__detail::_Identity; _Equal = std::equal_to; _H1 = std::hash; _H2 = std::__detail::_Mod_range_hashing; _Hash = std::__detail::_Default_ranged_hash; _RehashPolicy = std::__detail::_Prime_rehash_policy; _Traits = std::__detail::_Hashtable_traits]’: /usr/include/c++/6/bits/hashtable.h:1722:5: note: parameter passing for argument of type ‘std::_Hashtable, std::__detail::_Identity, std::equal_to, std::hash, std::__detail::_Mod_range_hashing, std::__detail::_Default_ranged_hash, std::__detail::_Prime_rehash_policy, std::__detail::_Hashtable_traits >::const_iterator {aka std::__detail::_Node_const_iterator}’ will change in GCC 7.1 _Hashtable<_Key, _Value, _Alloc, _ExtractKey, _Equal, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ _H1, _H2, _Hash, _RehashPolicy, _Traits>:: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/6/bits/hashtable.h: In member function ‘virtual void RollingBloomDBGTest_out_edge_iterator_Test::TestBody()’: /usr/include/c++/6/bits/hashtable.h:747:42: note: parameter passing for argument of type ‘std::_Hashtable, std::__detail::_Identity, std::equal_to, std::hash, std::__detail::_Mod_range_hashing, std::__detail::_Default_ranged_hash, std::__detail::_Prime_rehash_policy, std::__detail::_Hashtable_traits >::const_iterator {aka std::__detail::_Node_const_iterator}’ will change in GCC 7.1 { return erase(const_iterator(__it)); } ^ /usr/include/c++/6/bits/hashtable.h: In member function ‘virtual void RollingBloomDBGSpacedSeedTest_out_edge_iterator_Test::TestBody()’: /usr/include/c++/6/bits/hashtable.h:747:42: note: parameter passing for argument of type ‘std::_Hashtable, std::__detail::_Identity, std::equal_to, std::hash, std::__detail::_Mod_range_hashing, std::__detail::_Default_ranged_hash, std::__detail::_Prime_rehash_policy, std::__detail::_Hashtable_traits >::const_iterator {aka std::__detail::_Node_const_iterator}’ will change in GCC 7.1 { return erase(const_iterator(__it)); } ^ /usr/include/c++/6/bits/hashtable.h: In member function ‘virtual void RollingBloomDBGTest_adjacency_iterator_Test::TestBody()’: /usr/include/c++/6/bits/hashtable.h:747:42: note: parameter passing for argument of type ‘std::_Hashtable, std::__detail::_Identity, std::equal_to, std::hash, std::__detail::_Mod_range_hashing, std::__detail::_Default_ranged_hash, std::__detail::_Prime_rehash_policy, std::__detail::_Hashtable_traits >::const_iterator {aka std::__detail::_Node_const_iterator}’ will change in GCC 7.1 { return erase(const_iterator(__it)); } ^ /usr/include/c++/6/bits/hashtable.h: In member function ‘virtual void RollingBloomDBGTest_in_edges_Test::TestBody()’: /usr/include/c++/6/bits/hashtable.h:747:42: note: parameter passing for argument of type ‘std::_Hashtable, std::__detail::_Identity, std::equal_to, std::hash, std::__detail::_Mod_range_hashing, std::__detail::_Default_ranged_hash, std::__detail::_Prime_rehash_policy, std::__detail::_Hashtable_traits >::const_iterator {aka std::__detail::_Node_const_iterator}’ will change in GCC 7.1 { return erase(const_iterator(__it)); } ^ g++ -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o BloomDBG_RollingBloomDBG BloomDBG/BloomDBG_RollingBloomDBG-RollingBloomDBGTest.o ../DataLayer/libdatalayer.a ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm make[3]: Leaving directory '/<>/Unittest' make check-TESTS make[3]: Entering directory '/<>/Unittest' make[4]: Entering directory '/<>/Unittest' PASS: common_histogram PASS: common_kmer PASS: common_bitutil PASS: common_stringutil PASS: common_sequence PASS: common_KmerIterator PASS: common_sam PASS: BloomFilter PASS: Konnector_DBGBloom PASS: graph_ConstrainedBFSVisitor PASS: graph_BidirectionalBFS PASS: Konnector_DBGBloomAlgorithms PASS: graph_AllPathsSearch PASS: graph_HashGraph PASS: graph_ConstrainedBidiBFSVisitor PASS: graph_ExtendPath PASS: graph_UndirectedGraph PASS: Konnector_konnector PASS: graph_DotIO PASS: PairedDBG_KmerPair PASS: PairedDBG_Dinuc PASS: PairedDBG_BranchRecord PASS: BloomDBG_BloomDBG PASS: BloomDBG_RollingHash PASS: BloomDBG_RollingHashIterator PASS: BloomDBG_HashAgnosticCascadingBloom PASS: BloomDBG_RollingBloomDBG PASS: BloomDBG_MaskedKmer PASS: BloomDBG_SpacedSeed PASS: PairedDBG_LoadAlgorithm PASS: DBG_LoadAlgorithm ============================================================================ Testsuite summary for ABySS 2.0.2 ============================================================================ # TOTAL: 31 # PASS: 31 # SKIP: 0 # XFAIL: 0 # FAIL: 0 # XPASS: 0 # ERROR: 0 ============================================================================ make[4]: Leaving directory '/<>/Unittest' make[3]: Leaving directory '/<>/Unittest' make[2]: Leaving directory '/<>/Unittest' make[2]: Entering directory '/<>' make[2]: Leaving directory '/<>' make[1]: Leaving directory '/<>' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary-arch dh binary-arch --with autoreconf dh_testroot -a dh_prep -a debian/rules override_dh_auto_install make[1]: Entering directory '/<>' dh_auto_install --destdir=debian/tmp make -j4 install DESTDIR=/<>/debian/tmp AM_UPDATE_INFO_DIR=no make[2]: Entering directory '/<>' Making install in bin make[3]: Entering directory '/<>/bin' make[4]: Entering directory '/<>/bin' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/<>/debian/tmp/usr/bin' /usr/bin/install -c abyss-bowtie abyss-bowtie2 abyss-bwa abyss-bwasw abyss-bwamem abyss-fatoagp abyss-kaligner abyss-pe abyss-samtoafg abyss-tabtomd abyss-bloom-dist.mk abyss-dida '/<>/debian/tmp/usr/bin' make[4]: Leaving directory '/<>/bin' make[3]: Leaving directory '/<>/bin' Making install in doc make[3]: Entering directory '/<>/doc' make[4]: Entering directory '/<>/doc' make[4]: Nothing to be done for 'install-exec-am'. /bin/mkdir -p '/<>/debian/tmp/usr/share/doc/abyss' /bin/mkdir -p '/<>/debian/tmp/usr/share/man/man1' /usr/bin/install -c -m 644 flowchart.pdf flowchart_simplified.pdf '/<>/debian/tmp/usr/share/doc/abyss' /usr/bin/install -c -m 644 ABYSS.1 abyss-pe.1 abyss-tofastq.1 '/<>/debian/tmp/usr/share/man/man1' make[4]: Leaving directory '/<>/doc' make[3]: Leaving directory '/<>/doc' Making install in Common make[3]: Entering directory '/<>/Common' make[4]: Entering directory '/<>/Common' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/<>/Common' make[3]: Leaving directory '/<>/Common' Making install in Graph make[3]: Entering directory '/<>/Graph' make[4]: Entering directory '/<>/Graph' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/<>/debian/tmp/usr/bin' /usr/bin/install -c abyss-gc abyss-todot '/<>/debian/tmp/usr/bin' make[4]: Leaving directory '/<>/Graph' make[3]: Leaving directory '/<>/Graph' Making install in DataLayer make[3]: Entering directory '/<>/DataLayer' make[4]: Entering directory '/<>/DataLayer' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/<>/debian/tmp/usr/bin' /usr/bin/install -c abyss-fac abyss-tofastq '/<>/debian/tmp/usr/bin' make[4]: Leaving directory '/<>/DataLayer' make[3]: Leaving directory '/<>/DataLayer' Making install in DataBase make[3]: Entering directory '/<>/DataBase' make[4]: Entering directory '/<>/DataBase' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/<>/debian/tmp/usr/bin' /bin/mkdir -p '/<>/debian/tmp/usr/bin' /usr/bin/install -c abyss-db-csv '/<>/debian/tmp/usr/bin' /usr/bin/install -c abyss-db-txt '/<>/debian/tmp/usr/bin' make[4]: Leaving directory '/<>/DataBase' make[3]: Leaving directory '/<>/DataBase' Making install in FMIndex make[3]: Entering directory '/<>/FMIndex' make[4]: Entering directory '/<>/FMIndex' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/<>/FMIndex' make[3]: Leaving directory '/<>/FMIndex' Making install in Assembly make[3]: Entering directory '/<>/Assembly' make[4]: Entering directory '/<>/Assembly' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/<>/Assembly' make[3]: Leaving directory '/<>/Assembly' Making install in dialign make[3]: Entering directory '/<>/dialign' make[4]: Entering directory '/<>/dialign' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/<>/dialign' make[3]: Leaving directory '/<>/dialign' Making install in Align make[3]: Entering directory '/<>/Align' make[4]: Entering directory '/<>/Align' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/<>/debian/tmp/usr/bin' /usr/bin/install -c abyss-align abyss-mergepairs '/<>/debian/tmp/usr/bin' make[4]: Leaving directory '/<>/Align' make[3]: Leaving directory '/<>/Align' Making install in ABYSS make[3]: Entering directory '/<>/ABYSS' make[4]: Entering directory '/<>/ABYSS' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/<>/debian/tmp/usr/bin' /usr/bin/install -c ABYSS '/<>/debian/tmp/usr/bin' make[4]: Leaving directory '/<>/ABYSS' make[3]: Leaving directory '/<>/ABYSS' Making install in Bloom make[3]: Entering directory '/<>/Bloom' make[4]: Entering directory '/<>/Bloom' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/<>/debian/tmp/usr/bin' /usr/bin/install -c abyss-bloom '/<>/debian/tmp/usr/bin' make[4]: Leaving directory '/<>/Bloom' make[3]: Leaving directory '/<>/Bloom' Making install in BloomDBG make[3]: Entering directory '/<>/BloomDBG' make[4]: Entering directory '/<>/BloomDBG' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/<>/debian/tmp/usr/bin' /usr/bin/install -c abyss-bloom-dbg '/<>/debian/tmp/usr/bin' make[4]: Leaving directory '/<>/BloomDBG' make[3]: Leaving directory '/<>/BloomDBG' Making install in Konnector make[3]: Entering directory '/<>/Konnector' make[4]: Entering directory '/<>/Konnector' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/<>/debian/tmp/usr/bin' /usr/bin/install -c konnector '/<>/debian/tmp/usr/bin' make[4]: Leaving directory '/<>/Konnector' make[3]: Leaving directory '/<>/Konnector' Making install in Consensus make[3]: Entering directory '/<>/Consensus' make[4]: Entering directory '/<>/Consensus' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/<>/debian/tmp/usr/bin' /usr/bin/install -c Consensus '/<>/debian/tmp/usr/bin' make[4]: Leaving directory '/<>/Consensus' make[3]: Leaving directory '/<>/Consensus' Making install in DAssembler make[3]: Entering directory '/<>/DAssembler' make[4]: Entering directory '/<>/DAssembler' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/<>/debian/tmp/usr/bin' /usr/bin/install -c DAssembler '/<>/debian/tmp/usr/bin' make[4]: Leaving directory '/<>/DAssembler' make[3]: Leaving directory '/<>/DAssembler' Making install in DistanceEst make[3]: Entering directory '/<>/DistanceEst' make[4]: Entering directory '/<>/DistanceEst' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/<>/debian/tmp/usr/bin' /usr/bin/install -c DistanceEst DistanceEst-ssq '/<>/debian/tmp/usr/bin' make[4]: Leaving directory '/<>/DistanceEst' make[3]: Leaving directory '/<>/DistanceEst' Making install in KAligner make[3]: Entering directory '/<>/KAligner' make[4]: Entering directory '/<>/KAligner' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/<>/debian/tmp/usr/bin' /usr/bin/install -c KAligner '/<>/debian/tmp/usr/bin' make[4]: Leaving directory '/<>/KAligner' make[3]: Leaving directory '/<>/KAligner' Making install in Layout make[3]: Entering directory '/<>/Layout' make[4]: Entering directory '/<>/Layout' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/<>/debian/tmp/usr/bin' /usr/bin/install -c abyss-layout '/<>/debian/tmp/usr/bin' make[4]: Leaving directory '/<>/Layout' make[3]: Leaving directory '/<>/Layout' Making install in LogKmerCount make[3]: Entering directory '/<>/LogKmerCount' make[4]: Entering directory '/<>/LogKmerCount' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/<>/debian/tmp/usr/bin' /usr/bin/install -c logcounter '/<>/debian/tmp/usr/bin' make[4]: Leaving directory '/<>/LogKmerCount' make[3]: Leaving directory '/<>/LogKmerCount' Making install in Map make[3]: Entering directory '/<>/Map' make[4]: Entering directory '/<>/Map' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/<>/debian/tmp/usr/bin' /usr/bin/install -c abyss-index abyss-map abyss-map-ssq abyss-overlap '/<>/debian/tmp/usr/bin' make[4]: Leaving directory '/<>/Map' make[3]: Leaving directory '/<>/Map' Making install in MergePaths make[3]: Entering directory '/<>/MergePaths' make[4]: Entering directory '/<>/MergePaths' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/<>/debian/tmp/usr/bin' /usr/bin/install -c MergePaths MergeContigs PathConsensus '/<>/debian/tmp/usr/bin' make[4]: Leaving directory '/<>/MergePaths' make[3]: Leaving directory '/<>/MergePaths' Making install in Misc make[3]: Entering directory '/<>/Misc' make[4]: Entering directory '/<>/Misc' make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/<>/Misc' make[3]: Leaving directory '/<>/Misc' Making install in Overlap make[3]: Entering directory '/<>/Overlap' make[4]: Entering directory '/<>/Overlap' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/<>/debian/tmp/usr/bin' /usr/bin/install -c Overlap '/<>/debian/tmp/usr/bin' make[4]: Leaving directory '/<>/Overlap' make[3]: Leaving directory '/<>/Overlap' Making install in PairedDBG make[3]: Entering directory '/<>/PairedDBG' make[4]: Entering directory '/<>/PairedDBG' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/<>/debian/tmp/usr/bin' /usr/bin/install -c abyss-paired-dbg '/<>/debian/tmp/usr/bin' make[4]: Leaving directory '/<>/PairedDBG' make[3]: Leaving directory '/<>/PairedDBG' Making install in ParseAligns make[3]: Entering directory '/<>/ParseAligns' make[4]: Entering directory '/<>/ParseAligns' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/<>/debian/tmp/usr/bin' /usr/bin/install -c abyss-fixmate abyss-fixmate-ssq ParseAligns '/<>/debian/tmp/usr/bin' make[4]: Leaving directory '/<>/ParseAligns' make[3]: Leaving directory '/<>/ParseAligns' Making install in PathOverlap make[3]: Entering directory '/<>/PathOverlap' make[4]: Entering directory '/<>/PathOverlap' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/<>/debian/tmp/usr/bin' /usr/bin/install -c PathOverlap '/<>/debian/tmp/usr/bin' make[4]: Leaving directory '/<>/PathOverlap' make[3]: Leaving directory '/<>/PathOverlap' Making install in PopBubbles make[3]: Entering directory '/<>/PopBubbles' make[4]: Entering directory '/<>/PopBubbles' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/<>/debian/tmp/usr/bin' /usr/bin/install -c PopBubbles '/<>/debian/tmp/usr/bin' make[4]: Leaving directory '/<>/PopBubbles' make[3]: Leaving directory '/<>/PopBubbles' Making install in Scaffold make[3]: Entering directory '/<>/Scaffold' make[4]: Entering directory '/<>/Scaffold' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/<>/debian/tmp/usr/bin' /usr/bin/install -c abyss-scaffold abyss-junction abyss-longseqdist '/<>/debian/tmp/usr/bin' make[4]: Leaving directory '/<>/Scaffold' make[3]: Leaving directory '/<>/Scaffold' Making install in SimpleGraph make[3]: Entering directory '/<>/SimpleGraph' make[4]: Entering directory '/<>/SimpleGraph' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/<>/debian/tmp/usr/bin' /usr/bin/install -c SimpleGraph '/<>/debian/tmp/usr/bin' make[4]: Leaving directory '/<>/SimpleGraph' make[3]: Leaving directory '/<>/SimpleGraph' Making install in kmerprint make[3]: Entering directory '/<>/kmerprint' make[4]: Entering directory '/<>/kmerprint' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/<>/kmerprint' make[3]: Leaving directory '/<>/kmerprint' Making install in FilterGraph make[3]: Entering directory '/<>/FilterGraph' make[4]: Entering directory '/<>/FilterGraph' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/<>/debian/tmp/usr/bin' /usr/bin/install -c abyss-filtergraph '/<>/debian/tmp/usr/bin' make[4]: Leaving directory '/<>/FilterGraph' make[3]: Leaving directory '/<>/FilterGraph' Making install in GapFiller make[3]: Entering directory '/<>/GapFiller' make[4]: Entering directory '/<>/GapFiller' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/<>/debian/tmp/usr/bin' /usr/bin/install -c abyss-gapfill '/<>/debian/tmp/usr/bin' make[4]: Leaving directory '/<>/GapFiller' make[3]: Leaving directory '/<>/GapFiller' Making install in Sealer make[3]: Entering directory '/<>/Sealer' make[4]: Entering directory '/<>/Sealer' /bin/mkdir -p '/<>/debian/tmp/usr/bin' /usr/bin/install -c abyss-sealer '/<>/debian/tmp/usr/bin' make[4]: Leaving directory '/<>/Sealer' make[3]: Leaving directory '/<>/Sealer' Making install in AdjList make[3]: Entering directory '/<>/AdjList' make[4]: Entering directory '/<>/AdjList' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/<>/debian/tmp/usr/bin' /usr/bin/install -c AdjList '/<>/debian/tmp/usr/bin' make[4]: Leaving directory '/<>/AdjList' make[3]: Leaving directory '/<>/AdjList' Making install in lib/bloomfilter make[3]: Entering directory '/<>/lib/bloomfilter' make[4]: Entering directory '/<>/lib/bloomfilter' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/<>/lib/bloomfilter' make[3]: Leaving directory '/<>/lib/bloomfilter' Making install in lib/rolling-hash make[3]: Entering directory '/<>/lib/rolling-hash' make[4]: Entering directory '/<>/lib/rolling-hash' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/<>/lib/rolling-hash' make[3]: Leaving directory '/<>/lib/rolling-hash' Making install in lib/gtest-1.7.0 make[3]: Entering directory '/<>/lib/gtest-1.7.0' make[4]: Entering directory '/<>/lib/gtest-1.7.0' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/<>/lib/gtest-1.7.0' make[3]: Leaving directory '/<>/lib/gtest-1.7.0' Making install in Unittest make[3]: Entering directory '/<>/Unittest' make[4]: Entering directory '/<>/Unittest' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/<>/Unittest' make[3]: Leaving directory '/<>/Unittest' make[3]: Entering directory '/<>' make[4]: Entering directory '/<>' make[4]: Nothing to be done for 'install-exec-am'. /bin/mkdir -p '/<>/debian/tmp/usr/share/doc/abyss' /usr/bin/install -c -m 644 ChangeLog CITATION.bib CITATION.md COPYRIGHT LICENSE README.md '/<>/debian/tmp/usr/share/doc/abyss' make[4]: Leaving directory '/<>' make[3]: Leaving directory '/<>' make[2]: Leaving directory '/<>' make[1]: Leaving directory '/<>' dh_install -a dh_installdocs -a dh_installchangelogs -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 131 pkgstriptranslations: processing abyss-dbgsym (in debian/.debhelper/abyss/dbgsym-root); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/.debhelper/abyss/dbgsym-root/DEBIAN/control, package abyss-dbgsym, directory debian/.debhelper/abyss/dbgsym-root pkgstripfiles: Running PNG optimization (using 4 cpus) for package abyss-dbgsym ... pkgstripfiles: No PNG files. dpkg-deb: building package 'abyss-dbgsym' in 'debian/.debhelper/scratch-space/build-abyss/abyss-dbgsym_2.0.2-3_armhf.deb'. Renaming abyss-dbgsym_2.0.2-3_armhf.deb to abyss-dbgsym_2.0.2-3_armhf.ddeb INFO: pkgstriptranslations version 131 pkgstriptranslations: processing abyss (in debian/abyss); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/abyss/DEBIAN/control, package abyss, directory debian/abyss pkgstripfiles: Truncating usr/share/doc/abyss/changelog.Debian.gz to topmost ten records pkgstripfiles: Running PNG optimization (using 4 cpus) for package abyss ... pkgstripfiles: No PNG files. dpkg-deb: building package 'abyss' in '../abyss_2.0.2-3_armhf.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any -mLaunchpad Build Daemon >../abyss_2.0.2-3_armhf.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build abyss-2.0.2 dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 20170701-1120 Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Post Build Chroot | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ abyss_2.0.2-3_armhf.changes: ---------------------------- Format: 1.8 Date: Fri, 30 Jun 2017 16:56:26 -0400 Source: abyss Binary: abyss Architecture: armhf Version: 2.0.2-3 Distribution: artful-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Nadiya Sitdykova Description: abyss - de novo, parallel, sequence assembler for short reads Changes: abyss (2.0.2-3) unstable; urgency=medium . * Team upload. . [ Nadiya Sitdykova ] * Add simple autopkgtest test-suite. . [ Steffen Moeller ] * [debian/upstream/metadata] Added references to bio.tools, OMICtools and RRID . [ Sascha Steinbiss ] * Add missing dependency on bsdmainutils. * Use HTTPS URL for Format entry in d/copyright. * Bump Standards-Version. Checksums-Sha1: 1cd49d261abb9748b05a6dc19b1ba2ff573f39ae 21443450 abyss-dbgsym_2.0.2-3_armhf.ddeb 9d8ac92446977b5beb9e91c86203c8f36951b338 6430 abyss_2.0.2-3_armhf.buildinfo 31ee9344ab79d9d81d10bc37be654660cf68fea1 2637002 abyss_2.0.2-3_armhf.deb Checksums-Sha256: 2611f4550bc1917d91690c95eb7a51e51246e34d20ab65a2155bbf4499d90e76 21443450 abyss-dbgsym_2.0.2-3_armhf.ddeb 080a969db22e1bc4c8a84328a1e11e1f5ae261c500aa191427907458abf563c9 6430 abyss_2.0.2-3_armhf.buildinfo 5583782d15aeb0f4fec14dd9ca58d50fab74e52a357ff7ab5ad4ba6a53f5a4a4 2637002 abyss_2.0.2-3_armhf.deb Files: d97f765683c8bcbb0e08a04aa5ab2ff2 21443450 debug extra abyss-dbgsym_2.0.2-3_armhf.ddeb 4f96af1b942496d4cc931974ccefe515 6430 science optional abyss_2.0.2-3_armhf.buildinfo 9fe065d2cd90b840ad064e357bffba30 2637002 science optional abyss_2.0.2-3_armhf.deb +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ abyss_2.0.2-3_armhf.deb ----------------------- new debian package, version 2.0. size 2637002 bytes: control archive=2509 bytes. 775 bytes, 16 lines control 4223 bytes, 68 lines md5sums Package: abyss Version: 2.0.2-3 Architecture: armhf Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 6044 Depends: make, libc6 (>= 2.7), libgcc1 (>= 1:3.5), libgomp1 (>= 4.9), libsqlite3-0 (>= 3.5.9), libstdc++6 (>= 5.2), perl:any, bsdmainutils Suggests: openmpi-bin Section: science Priority: optional Homepage: http://www.bcgsc.ca/platform/bioinfo/software/abyss Description: de novo, parallel, sequence assembler for short reads ABySS is a de novo, parallel, sequence assembler that is designed for short reads. It may be used to assemble genome or transcriptome sequence data. Parallelization is achieved using MPI, OpenMP and pthread. drwxr-xr-x root/root 0 2017-06-30 20:56 ./ drwxr-xr-x root/root 0 2017-06-30 20:56 ./usr/ drwxr-xr-x root/root 0 2017-06-30 20:56 ./usr/bin/ -rwxr-xr-x root/root 99924 2017-06-30 20:56 ./usr/bin/DistanceEst -rwxr-xr-x root/root 95804 2017-06-30 20:56 ./usr/bin/abyss-fixmate -rwxr-xr-x root/root 17831 2017-06-30 20:56 ./usr/bin/abyss-pe drwxr-xr-x root/root 0 2017-06-30 20:56 ./usr/lib/ drwxr-xr-x root/root 0 2017-06-30 20:56 ./usr/lib/abyss/ -rwxr-xr-x root/root 181868 2017-06-30 20:56 ./usr/lib/abyss/ABYSS -rwxr-xr-x root/root 120396 2017-06-30 20:56 ./usr/lib/abyss/AdjList -rwxr-xr-x root/root 50760 2017-06-30 20:56 ./usr/lib/abyss/Consensus -rwxr-xr-x root/root 67160 2017-06-30 20:56 ./usr/lib/abyss/DAssembler -rwxr-xr-x root/root 99924 2017-06-30 20:56 ./usr/lib/abyss/DistanceEst -rwxr-xr-x root/root 99924 2017-06-30 20:56 ./usr/lib/abyss/DistanceEst-ssq -rwxr-xr-x root/root 140884 2017-06-30 20:56 ./usr/lib/abyss/KAligner -rwxr-xr-x root/root 149084 2017-06-30 20:56 ./usr/lib/abyss/MergeContigs -rwxr-xr-x root/root 124488 2017-06-30 20:56 ./usr/lib/abyss/MergePaths -rwxr-xr-x root/root 120408 2017-06-30 20:56 ./usr/lib/abyss/Overlap -rwxr-xr-x root/root 67128 2017-06-30 20:56 ./usr/lib/abyss/ParseAligns -rwxr-xr-x root/root 243288 2017-06-30 20:56 ./usr/lib/abyss/PathConsensus -rwxr-xr-x root/root 116280 2017-06-30 20:56 ./usr/lib/abyss/PathOverlap -rwxr-xr-x root/root 124504 2017-06-30 20:56 ./usr/lib/abyss/PopBubbles -rwxr-xr-x root/root 120404 2017-06-30 20:56 ./usr/lib/abyss/SimpleGraph -rwxr-xr-x root/root 132680 2017-06-30 20:56 ./usr/lib/abyss/abyss-align -rwxr-xr-x root/root 99960 2017-06-30 20:56 ./usr/lib/abyss/abyss-bloom -rwxr-xr-x root/root 132704 2017-06-30 20:56 ./usr/lib/abyss/abyss-bloom-dbg -rwxr-xr-x root/root 6491 2017-06-30 20:56 ./usr/lib/abyss/abyss-bloom-dist.mk -rwxr-xr-x root/root 1135 2017-06-30 20:56 ./usr/lib/abyss/abyss-bowtie -rwxr-xr-x root/root 1192 2017-06-30 20:56 ./usr/lib/abyss/abyss-bowtie2 -rwxr-xr-x root/root 1208 2017-06-30 20:56 ./usr/lib/abyss/abyss-bwa -rwxr-xr-x root/root 1454 2017-06-30 20:56 ./usr/lib/abyss/abyss-bwamem -rwxr-xr-x root/root 1362 2017-06-30 20:56 ./usr/lib/abyss/abyss-bwasw -rwxr-xr-x root/root 42500 2017-06-30 20:56 ./usr/lib/abyss/abyss-db-csv -rwxr-xr-x root/root 703 2017-06-30 20:56 ./usr/lib/abyss/abyss-db-txt -rwxr-xr-x root/root 2739 2017-06-30 20:56 ./usr/lib/abyss/abyss-dida -rwxr-xr-x root/root 54864 2017-06-30 20:56 ./usr/lib/abyss/abyss-fac -rwxr-xr-x root/root 1872 2017-06-30 20:56 ./usr/lib/abyss/abyss-fatoagp -rwxr-xr-x root/root 112212 2017-06-30 20:56 ./usr/lib/abyss/abyss-filtergraph -rwxr-xr-x root/root 95804 2017-06-30 20:56 ./usr/lib/abyss/abyss-fixmate -rwxr-xr-x root/root 95804 2017-06-30 20:56 ./usr/lib/abyss/abyss-fixmate-ssq -rwxr-xr-x root/root 58968 2017-06-30 20:56 ./usr/lib/abyss/abyss-gapfill -rwxr-xr-x root/root 63032 2017-06-30 20:56 ./usr/lib/abyss/abyss-gc -rwxr-xr-x root/root 67136 2017-06-30 20:56 ./usr/lib/abyss/abyss-index -rwxr-xr-x root/root 75324 2017-06-30 20:56 ./usr/lib/abyss/abyss-junction -rwxr-xr-x root/root 39 2017-06-30 20:56 ./usr/lib/abyss/abyss-kaligner -rwxr-xr-x root/root 83520 2017-06-30 20:56 ./usr/lib/abyss/abyss-layout -rwxr-xr-x root/root 75332 2017-06-30 20:56 ./usr/lib/abyss/abyss-longseqdist -rwxr-xr-x root/root 128588 2017-06-30 20:56 ./usr/lib/abyss/abyss-map -rwxr-xr-x root/root 128588 2017-06-30 20:56 ./usr/lib/abyss/abyss-map-ssq -rwxr-xr-x root/root 50784 2017-06-30 20:56 ./usr/lib/abyss/abyss-mergepairs -rwxr-xr-x root/root 136800 2017-06-30 20:56 ./usr/lib/abyss/abyss-overlap -rwxr-xr-x root/root 190064 2017-06-30 20:56 ./usr/lib/abyss/abyss-paired-dbg -rwxr-xr-x root/root 17831 2017-06-30 20:56 ./usr/lib/abyss/abyss-pe -rwxr-xr-x root/root 4505 2017-06-30 20:56 ./usr/lib/abyss/abyss-samtoafg -rwxr-xr-x root/root 149072 2017-06-30 20:56 ./usr/lib/abyss/abyss-scaffold -rwxr-xr-x root/root 132740 2017-06-30 20:56 ./usr/lib/abyss/abyss-sealer -rwxr-xr-x root/root 209 2017-06-30 20:56 ./usr/lib/abyss/abyss-tabtomd -rwxr-xr-x root/root 103996 2017-06-30 20:56 ./usr/lib/abyss/abyss-todot -rwxr-xr-x root/root 42572 2017-06-30 20:56 ./usr/lib/abyss/abyss-tofastq -rwxr-xr-x root/root 153224 2017-06-30 20:56 ./usr/lib/abyss/konnector -rwxr-xr-x root/root 54864 2017-06-30 20:56 ./usr/lib/abyss/logcounter drwxr-xr-x root/root 0 2017-06-30 20:56 ./usr/share/ drwxr-xr-x root/root 0 2017-06-30 20:56 ./usr/share/doc/ drwxr-xr-x root/root 0 2017-06-30 20:56 ./usr/share/doc/abyss/ -rw-r--r-- root/root 25913 2017-06-30 20:56 ./usr/share/doc/abyss/README.html -rw-r--r-- root/root 7730 2016-10-21 21:48 ./usr/share/doc/abyss/README.md.gz -rw-r--r-- root/root 182 2017-06-30 20:56 ./usr/share/doc/abyss/README.test -rw-r--r-- root/root 1701 2017-06-30 20:56 ./usr/share/doc/abyss/changelog.Debian.gz -rw-r--r-- root/root 6121 2017-06-30 20:56 ./usr/share/doc/abyss/copyright -rw-r--r-- root/root 66778 2016-10-21 21:48 ./usr/share/doc/abyss/flowchart.pdf.gz -rw-r--r-- root/root 299 2017-06-30 20:56 ./usr/share/doc/abyss/run-unit-test drwxr-xr-x root/root 0 2017-06-30 20:56 ./usr/share/doc/abyss/test-data/ -rw-r--r-- root/root 743013 2017-06-30 20:56 ./usr/share/doc/abyss/test-data/reads1.fastq.gz -rw-r--r-- root/root 743377 2017-06-30 20:56 ./usr/share/doc/abyss/test-data/reads2.fastq.gz drwxr-xr-x root/root 0 2017-06-30 20:56 ./usr/share/man/ drwxr-xr-x root/root 0 2017-06-30 20:56 ./usr/share/man/man1/ -rw-r--r-- root/root 1200 2017-06-30 20:56 ./usr/share/man/man1/ABYSS.1.gz -rw-r--r-- root/root 3567 2017-06-30 20:56 ./usr/share/man/man1/abyss-pe.1.gz -rw-r--r-- root/root 408 2017-06-30 20:56 ./usr/share/man/man1/abyss-tofastq.1.gz +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Not removing build depends: as requested Keeping session: +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: armhf Build-Space: 412632 Build-Time: 712 Distribution: artful-proposed Host Architecture: armhf Install-Time: 48 Job: abyss_2.0.2-3.dsc Machine Architecture: arm64 Package: abyss Package-Time: 762 Source-Version: 2.0.2-3 Space: 412632 Status: successful Version: 2.0.2-3 -------------------------------------------------------------------------------- Finished at 20170701-1120 Build needed 00:12:42, 412632k disc space RUN: /usr/share/launchpad-buildd/slavebin/scan-for-processes ['scan-for-processes', 'PACKAGEBUILD-12836059'] Scanning for processes to kill in build /home/buildd/build-PACKAGEBUILD-12836059/chroot-autobuild... RUN: /usr/share/launchpad-buildd/slavebin/umount-chroot ['umount-chroot', 'PACKAGEBUILD-12836059'] Unmounting chroot for build PACKAGEBUILD-12836059... RUN: /usr/share/launchpad-buildd/slavebin/remove-build ['remove-build', 'PACKAGEBUILD-12836059'] Removing build PACKAGEBUILD-12836059