sbuild (Debian sbuild) 0.79.1 (22 April 2020) on carme.larted.org.uk +==============================================================================+ | abyss 2.2.4-1 (amd64) Fri, 02 Oct 2020 22:48:25 +0000 | +==============================================================================+ Package: abyss Version: 2.2.4-1 Source Version: 2.2.4-1 Distribution: sid Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: full I: NOTICE: Log filtering will replace 'var/run/schroot/mount/sid-amd64-debomatic-bd60c713-0093-4412-9d01-3b2e0f7814bb' with '<>' +------------------------------------------------------------------------------+ | Chroot Setup Commands | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup abyss_2.2.4-1 sid amd64 ---------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup abyss_2.2.4-1 sid amd64'. Finished processing commands. -------------------------------------------------------------------------------- I: NOTICE: Log filtering will replace 'build/abyss-a85IiE/resolver-LkkBv5' with '<>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Get:1 http://localhost:3142/debian unstable InRelease [146 kB] Get:2 http://localhost:3142/debian sid InRelease [146 kB] Get:3 http://localhost:3142/debian unstable/main amd64 Packages.diff/Index [27.9 kB] Get:4 http://localhost:3142/debian unstable/main amd64 Packages 2020-10-02-0800.55.pdiff [2416 B] Get:5 http://localhost:3142/debian unstable/main amd64 Packages 2020-10-02-1400.49.pdiff [10.2 kB] Get:6 http://localhost:3142/debian unstable/main amd64 Packages 2020-10-02-2000.55.pdiff [5353 B] Get:6 http://localhost:3142/debian unstable/main amd64 Packages 2020-10-02-2000.55.pdiff [5353 B] Get:7 http://localhost:3142/debian sid/main Sources.diff/Index [27.9 kB] Get:8 http://localhost:3142/debian sid/main Sources 2020-10-02-0800.55.pdiff [2429 B] Get:9 http://localhost:3142/debian sid/main Sources 2020-10-02-1400.49.pdiff [9442 B] Get:10 http://localhost:3142/debian sid/main Sources 2020-10-02-2000.55.pdiff [7669 B] Get:10 http://localhost:3142/debian sid/main Sources 2020-10-02-2000.55.pdiff [7669 B] Fetched 386 kB in 1s (331 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- /srv/debomatic/incoming/abyss_2.2.4-1.dsc exists in /srv/debomatic/incoming; copying to chroot I: NOTICE: Log filtering will replace 'build/abyss-a85IiE/abyss-2.2.4' with '<>' I: NOTICE: Log filtering will replace 'build/abyss-a85IiE' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 12), libboost-graph-dev, libopenmpi-dev, libsparsehash-dev, libtext-multimarkdown-perl, libsqlite3-dev, pkg-config, help2man, build-essential, fakeroot Filtered Build-Depends: debhelper-compat (= 12), libboost-graph-dev, libopenmpi-dev, libsparsehash-dev, libtext-multimarkdown-perl, libsqlite3-dev, pkg-config, help2man, build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<>/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [957 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [444 B] Get:5 copy:/<>/apt_archive ./ Packages [518 B] Fetched 1919 B in 0s (144 kB/s) Reading package lists... Reading package lists... Install main 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 bsdextrautils build-essential cpp-9 debhelper dh-autoreconf dh-strip-nondeterminism dpkg-dev dwz fakeroot file g++ g++-10 gcc gcc-10 gcc-9 gettext gettext-base gfortran-9 groff-base help2man ibverbs-providers icu-devtools intltool-debian libarchive-zip-perl libasan5 libasan6 libboost-graph-dev libboost-graph1.71-dev libboost-graph1.71.0 libboost-regex1.71-dev libboost-regex1.71.0 libboost-serialization1.71-dev libboost-serialization1.71.0 libboost-test1.71-dev libboost-test1.71.0 libboost1.71-dev libbsd0 libc6-dev libcbor0 libcroco3 libcrypt-dev libdebhelper-perl libdpkg-perl libedit2 libelf1 libevent-2.1-7 libevent-core-2.1-7 libevent-dev libevent-extra-2.1-7 libevent-openssl-2.1-7 libevent-pthreads-2.1-7 libfabric1 libfakeroot libfido2-1 libfile-stripnondeterminism-perl libgcc-10-dev libgcc-9-dev libgfortran-9-dev libgfortran5 libglib2.0-0 libgssapi-krb5-2 libhtml-parser-perl libhtml-tagset-perl libhwloc-dev libhwloc-plugins libhwloc15 libibverbs-dev libibverbs1 libicu-dev libicu67 libjs-jquery libjs-jquery-ui libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblocale-gettext-perl libltdl-dev libltdl7 libmagic-mgc libmagic1 libnl-3-200 libnl-3-dev libnl-route-3-200 libnl-route-3-dev libnuma-dev libnuma1 libopenmpi-dev libopenmpi3 libpciaccess0 libperl5.30 libpipeline1 libpmix-dev libpmix2 libpsm-infinipath1 libpsm2-2 librdmacm1 libsigsegv2 libsparsehash-dev libsqlite3-dev libssl1.1 libstdc++-10-dev libstdc++-9-dev libsub-override-perl libtext-markdown-perl libtext-multimarkdown-perl libtool libubsan1 libuchardet0 libucx0 liburi-perl libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxml2 libxnvctrl0 m4 man-db node-jquery ocl-icd-libopencl1 openmpi-bin openmpi-common openssh-client perl perl-modules-5.30 pkg-config po-debconf sensible-utils zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc gcc-9-locales dh-make debian-keyring g++-multilib g++-10-multilib gcc-10-doc gcc-multilib manpages-dev flex bison gdb gcc-doc gcc-10-multilib gcc-10-locales gcc-9-multilib gcc-9-doc gettext-doc libasprintf-dev libgettextpo-dev gfortran-9-multilib gfortran-9-doc libcoarrays-dev groff graphviz libboost1.71-doc libboost-atomic1.71-dev libboost-chrono1.71-dev libboost-container1.71-dev libboost-context1.71-dev libboost-contract1.71-dev libboost-coroutine1.71-dev libboost-date-time1.71-dev libboost-exception1.71-dev libboost-fiber1.71-dev libboost-filesystem1.71-dev libboost-graph-parallel1.71-dev libboost-iostreams1.71-dev libboost-locale1.71-dev libboost-log1.71-dev libboost-math1.71-dev libboost-mpi1.71-dev libboost-mpi-python1.71-dev libboost-numpy1.71-dev libboost-program-options1.71-dev libboost-python1.71-dev libboost-random1.71-dev libboost-stacktrace1.71-dev libboost-system1.71-dev libboost-thread1.71-dev libboost-timer1.71-dev libboost-type-erasure1.71-dev libboost-wave1.71-dev libboost1.71-tools-dev libmpfrc++-dev libntl-dev glibc-doc git bzr krb5-doc krb5-user libdata-dump-perl libhwloc-contrib-plugins icu-doc libjs-jquery-ui-docs libtool-doc openmpi-doc pciutils sqlite3-doc libstdc++-10-doc libstdc++-9-doc gcj-jdk libwww-perl m4-doc apparmor less www-browser opencl-icd gfortran | fortran-compiler keychain libpam-ssh monkeysphere ssh-askpass perl-doc libterm-readline-gnu-perl | libterm-readline-perl-perl libtap-harness-archive-perl libmail-box-perl Recommended packages: libalgorithm-merge-perl curl | wget | lynx libfile-fcntllock-perl libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs libhttp-message-perl javascript-common krb5-locales libcoarrays-openmpi-dev xauth libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils build-essential cpp-9 debhelper dh-autoreconf dh-strip-nondeterminism dpkg-dev dwz fakeroot file g++ g++-10 gcc gcc-10 gcc-9 gettext gettext-base gfortran-9 groff-base help2man ibverbs-providers icu-devtools intltool-debian libarchive-zip-perl libasan5 libasan6 libboost-graph-dev libboost-graph1.71-dev libboost-graph1.71.0 libboost-regex1.71-dev libboost-regex1.71.0 libboost-serialization1.71-dev libboost-serialization1.71.0 libboost-test1.71-dev libboost-test1.71.0 libboost1.71-dev libbsd0 libc6-dev libcbor0 libcroco3 libcrypt-dev libdebhelper-perl libdpkg-perl libedit2 libelf1 libevent-2.1-7 libevent-core-2.1-7 libevent-dev libevent-extra-2.1-7 libevent-openssl-2.1-7 libevent-pthreads-2.1-7 libfabric1 libfakeroot libfido2-1 libfile-stripnondeterminism-perl libgcc-10-dev libgcc-9-dev libgfortran-9-dev libgfortran5 libglib2.0-0 libgssapi-krb5-2 libhtml-parser-perl libhtml-tagset-perl libhwloc-dev libhwloc-plugins libhwloc15 libibverbs-dev libibverbs1 libicu-dev libicu67 libjs-jquery libjs-jquery-ui libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblocale-gettext-perl libltdl-dev libltdl7 libmagic-mgc libmagic1 libnl-3-200 libnl-3-dev libnl-route-3-200 libnl-route-3-dev libnuma-dev libnuma1 libopenmpi-dev libopenmpi3 libpciaccess0 libperl5.30 libpipeline1 libpmix-dev libpmix2 libpsm-infinipath1 libpsm2-2 librdmacm1 libsigsegv2 libsparsehash-dev libsqlite3-dev libssl1.1 libstdc++-10-dev libstdc++-9-dev libsub-override-perl libtext-markdown-perl libtext-multimarkdown-perl libtool libubsan1 libuchardet0 libucx0 liburi-perl libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxml2 libxnvctrl0 m4 man-db node-jquery ocl-icd-libopencl1 openmpi-bin openmpi-common openssh-client perl perl-modules-5.30 pkg-config po-debconf sbuild-build-depends-main-dummy sensible-utils zlib1g-dev 0 upgraded, 137 newly installed, 0 to remove and 0 not upgraded. Need to get 137 MB of archives. After this operation, 673 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [952 B] Get:2 http://localhost:3142/debian unstable/main amd64 bsdextrautils amd64 2.36-3+b1 [140 kB] Get:3 http://localhost:3142/debian unstable/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get:4 http://localhost:3142/debian unstable/main amd64 groff-base amd64 1.22.4-5 [920 kB] Get:5 http://localhost:3142/debian unstable/main amd64 libpipeline1 amd64 1.5.3-1 [34.3 kB] Get:6 http://localhost:3142/debian unstable/main amd64 man-db amd64 2.9.3-2 [1314 kB] Get:7 http://localhost:3142/debian unstable/main amd64 perl-modules-5.30 all 5.30.3-4 [2806 kB] Get:8 http://localhost:3142/debian unstable/main amd64 libperl5.30 amd64 5.30.3-4 [4019 kB] Get:9 http://localhost:3142/debian unstable/main amd64 perl amd64 5.30.3-4 [290 kB] Get:10 http://localhost:3142/debian unstable/main amd64 liblocale-gettext-perl amd64 1.07-4 [18.8 kB] Get:11 http://localhost:3142/debian unstable/main amd64 sensible-utils all 0.0.12+nmu1 [16.0 kB] Get:12 http://localhost:3142/debian unstable/main amd64 libmagic-mgc amd64 1:5.38-5 [262 kB] Get:13 http://localhost:3142/debian unstable/main amd64 libmagic1 amd64 1:5.38-5 [120 kB] Get:14 http://localhost:3142/debian unstable/main amd64 file amd64 1:5.38-5 [67.9 kB] Get:15 http://localhost:3142/debian unstable/main amd64 gettext-base amd64 0.19.8.1-10 [123 kB] Get:16 http://localhost:3142/debian unstable/main amd64 libbsd0 amd64 0.10.0-1 [107 kB] Get:17 http://localhost:3142/debian unstable/main amd64 libedit2 amd64 3.1-20191231-1 [95.4 kB] Get:18 http://localhost:3142/debian unstable/main amd64 libcbor0 amd64 0.5.0+dfsg-2 [24.0 kB] Get:19 http://localhost:3142/debian unstable/main amd64 libssl1.1 amd64 1.1.1g-1 [1543 kB] Get:20 http://localhost:3142/debian unstable/main amd64 libfido2-1 amd64 1.5.0-2 [52.3 kB] Get:21 http://localhost:3142/debian unstable/main amd64 libkrb5support0 amd64 1.17-10 [64.6 kB] Get:22 http://localhost:3142/debian unstable/main amd64 libk5crypto3 amd64 1.17-10 [115 kB] Get:23 http://localhost:3142/debian unstable/main amd64 libkeyutils1 amd64 1.6.1-2 [15.4 kB] Get:24 http://localhost:3142/debian unstable/main amd64 libkrb5-3 amd64 1.17-10 [366 kB] Get:25 http://localhost:3142/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.17-10 [156 kB] Get:26 http://localhost:3142/debian unstable/main amd64 openssh-client amd64 1:8.3p1-1 [910 kB] Get:27 http://localhost:3142/debian unstable/main amd64 libsigsegv2 amd64 2.12-2 [32.8 kB] Get:28 http://localhost:3142/debian unstable/main amd64 m4 amd64 1.4.18-4 [203 kB] Get:29 http://localhost:3142/debian unstable/main amd64 autoconf all 2.69-11.1 [341 kB] Get:30 http://localhost:3142/debian unstable/main amd64 autotools-dev all 20180224.1 [77.0 kB] Get:31 http://localhost:3142/debian unstable/main amd64 automake all 1:1.16.2-4 [801 kB] Get:32 http://localhost:3142/debian unstable/main amd64 autopoint all 0.19.8.1-10 [435 kB] Get:33 http://localhost:3142/debian unstable/main amd64 libcrypt-dev amd64 1:4.4.17-1 [104 kB] Get:34 http://localhost:3142/debian unstable/main amd64 libc6-dev amd64 2.31-3 [2395 kB] Get:35 http://localhost:3142/debian unstable/main amd64 libasan6 amd64 10.2.0-13 [340 kB] Get:36 http://localhost:3142/debian unstable/main amd64 libubsan1 amd64 10.2.0-13 [134 kB] Get:37 http://localhost:3142/debian unstable/main amd64 libgcc-10-dev amd64 10.2.0-13 [2327 kB] Get:38 http://localhost:3142/debian unstable/main amd64 gcc-10 amd64 10.2.0-13 [15.9 MB] Get:39 http://localhost:3142/debian unstable/main amd64 gcc amd64 4:10.2.0-1 [5196 B] Get:40 http://localhost:3142/debian unstable/main amd64 libstdc++-10-dev amd64 10.2.0-13 [1738 kB] Get:41 http://localhost:3142/debian unstable/main amd64 g++-10 amd64 10.2.0-13 [8670 kB] Get:42 http://localhost:3142/debian unstable/main amd64 g++ amd64 4:10.2.0-1 [1644 B] Get:43 http://localhost:3142/debian unstable/main amd64 libdpkg-perl all 1.20.5 [1473 kB] Get:44 http://localhost:3142/debian unstable/main amd64 dpkg-dev all 1.20.5 [1909 kB] Get:45 http://localhost:3142/debian unstable/main amd64 build-essential amd64 12.8 [7640 B] Get:46 http://localhost:3142/debian unstable/main amd64 cpp-9 amd64 9.3.0-18 [9712 kB] Get:47 http://localhost:3142/debian unstable/main amd64 libasan5 amd64 9.3.0-18 [390 kB] Get:48 http://localhost:3142/debian unstable/main amd64 libgcc-9-dev amd64 9.3.0-18 [2347 kB] Get:49 http://localhost:3142/debian unstable/main amd64 gcc-9 amd64 9.3.0-18 [10.0 MB] Get:50 http://localhost:3142/debian unstable/main amd64 libtool all 2.4.6-14 [513 kB] Get:51 http://localhost:3142/debian unstable/main amd64 dh-autoreconf all 19 [16.9 kB] Get:52 http://localhost:3142/debian unstable/main amd64 libdebhelper-perl all 13.2.1 [188 kB] Get:53 http://localhost:3142/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get:54 http://localhost:3142/debian unstable/main amd64 libsub-override-perl all 0.09-2 [10.2 kB] Get:55 http://localhost:3142/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.9.0-1 [25.5 kB] Get:56 http://localhost:3142/debian unstable/main amd64 dh-strip-nondeterminism all 1.9.0-1 [15.2 kB] Get:57 http://localhost:3142/debian unstable/main amd64 libelf1 amd64 0.181-1 [164 kB] Get:58 http://localhost:3142/debian unstable/main amd64 dwz amd64 0.13-5 [151 kB] Get:59 http://localhost:3142/debian unstable/main amd64 libglib2.0-0 amd64 2.66.0-2 [1361 kB] Get:60 http://localhost:3142/debian unstable/main amd64 libicu67 amd64 67.1-4 [8624 kB] Get:61 http://localhost:3142/debian unstable/main amd64 libxml2 amd64 2.9.10+dfsg-6 [692 kB] Get:62 http://localhost:3142/debian unstable/main amd64 libcroco3 amd64 0.6.13-1 [146 kB] Get:63 http://localhost:3142/debian unstable/main amd64 gettext amd64 0.19.8.1-10 [1303 kB] Get:64 http://localhost:3142/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get:65 http://localhost:3142/debian unstable/main amd64 po-debconf all 1.0.21 [248 kB] Get:66 http://localhost:3142/debian unstable/main amd64 debhelper all 13.2.1 [1007 kB] Get:67 http://localhost:3142/debian unstable/main amd64 libfakeroot amd64 1.25.1-1 [46.8 kB] Get:68 http://localhost:3142/debian unstable/main amd64 fakeroot amd64 1.25.1-1 [86.8 kB] Get:69 http://localhost:3142/debian unstable/main amd64 libgfortran5 amd64 10.2.0-13 [728 kB] Get:70 http://localhost:3142/debian unstable/main amd64 libgfortran-9-dev amd64 9.3.0-18 [675 kB] Get:71 http://localhost:3142/debian unstable/main amd64 gfortran-9 amd64 9.3.0-18 [10.4 MB] Get:72 http://localhost:3142/debian unstable/main amd64 help2man amd64 1.47.16 [181 kB] Get:73 http://localhost:3142/debian unstable/main amd64 libnl-3-200 amd64 3.4.0-1+b1 [63.6 kB] Get:74 http://localhost:3142/debian unstable/main amd64 libnl-route-3-200 amd64 3.4.0-1+b1 [161 kB] Get:75 http://localhost:3142/debian unstable/main amd64 libibverbs1 amd64 31.0-1 [57.2 kB] Get:76 http://localhost:3142/debian unstable/main amd64 ibverbs-providers amd64 31.0-1 [239 kB] Get:77 http://localhost:3142/debian unstable/main amd64 icu-devtools amd64 67.1-4 [201 kB] Get:78 http://localhost:3142/debian unstable/main amd64 libstdc++-9-dev amd64 9.3.0-18 [1702 kB] Get:79 http://localhost:3142/debian unstable/main amd64 libboost1.71-dev amd64 1.71.0-6+b2 [9097 kB] Get:80 http://localhost:3142/debian unstable/main amd64 libboost-regex1.71.0 amd64 1.71.0-6+b2 [496 kB] Get:81 http://localhost:3142/debian unstable/main amd64 libboost-graph1.71.0 amd64 1.71.0-6+b2 [323 kB] Get:82 http://localhost:3142/debian unstable/main amd64 libicu-dev amd64 67.1-4 [9593 kB] Get:83 http://localhost:3142/debian unstable/main amd64 libboost-regex1.71-dev amd64 1.71.0-6+b2 [583 kB] Get:84 http://localhost:3142/debian unstable/main amd64 libboost-serialization1.71.0 amd64 1.71.0-6+b2 [328 kB] Get:85 http://localhost:3142/debian unstable/main amd64 libboost-serialization1.71-dev amd64 1.71.0-6+b2 [371 kB] Get:86 http://localhost:3142/debian unstable/main amd64 libboost-test1.71.0 amd64 1.71.0-6+b2 [462 kB] Get:87 http://localhost:3142/debian unstable/main amd64 libboost-test1.71-dev amd64 1.71.0-6+b2 [539 kB] Get:88 http://localhost:3142/debian unstable/main amd64 libboost-graph1.71-dev amd64 1.71.0-6+b2 [344 kB] Get:89 http://localhost:3142/debian unstable/main amd64 libboost-graph-dev amd64 1.71.0.3 [4228 B] Get:90 http://localhost:3142/debian unstable/main amd64 libevent-2.1-7 amd64 2.1.12-stable-1 [188 kB] Get:91 http://localhost:3142/debian unstable/main amd64 libevent-core-2.1-7 amd64 2.1.12-stable-1 [139 kB] Get:92 http://localhost:3142/debian unstable/main amd64 libevent-extra-2.1-7 amd64 2.1.12-stable-1 [110 kB] Get:93 http://localhost:3142/debian unstable/main amd64 libevent-pthreads-2.1-7 amd64 2.1.12-stable-1 [57.1 kB] Get:94 http://localhost:3142/debian unstable/main amd64 libevent-openssl-2.1-7 amd64 2.1.12-stable-1 [64.1 kB] Get:95 http://localhost:3142/debian unstable/main amd64 libevent-dev amd64 2.1.12-stable-1 [311 kB] Get:96 http://localhost:3142/debian unstable/main amd64 libpsm-infinipath1 amd64 3.3+20.604758e7-6+b1 [169 kB] Get:97 http://localhost:3142/debian unstable/main amd64 libnuma1 amd64 2.0.12-1+b1 [26.3 kB] Get:98 http://localhost:3142/debian unstable/main amd64 libpsm2-2 amd64 11.2.185-1 [181 kB] Get:99 http://localhost:3142/debian unstable/main amd64 librdmacm1 amd64 31.0-1 [68.1 kB] Get:100 http://localhost:3142/debian unstable/main amd64 libfabric1 amd64 1.11.0-2 [521 kB] Get:101 http://localhost:3142/debian unstable/main amd64 libhtml-tagset-perl all 3.20-4 [13.0 kB] Get:102 http://localhost:3142/debian unstable/main amd64 liburi-perl all 1.76-2 [90.2 kB] Get:103 http://localhost:3142/debian unstable/main amd64 libhtml-parser-perl amd64 3.75-1 [105 kB] Get:104 http://localhost:3142/debian unstable/main amd64 libhwloc15 amd64 2.3.0+dfsg-1 [145 kB] Get:105 http://localhost:3142/debian unstable/main amd64 libnuma-dev amd64 2.0.12-1+b1 [39.3 kB] Get:106 http://localhost:3142/debian unstable/main amd64 libltdl7 amd64 2.4.6-14 [390 kB] Get:107 http://localhost:3142/debian unstable/main amd64 libltdl-dev amd64 2.4.6-14 [162 kB] Get:108 http://localhost:3142/debian unstable/main amd64 libhwloc-dev amd64 2.3.0+dfsg-1 [223 kB] Get:109 http://localhost:3142/debian unstable/main amd64 libpciaccess0 amd64 0.16-1 [53.6 kB] Get:110 http://localhost:3142/debian unstable/main amd64 libxau6 amd64 1:1.0.8-1+b2 [19.9 kB] Get:111 http://localhost:3142/debian unstable/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get:112 http://localhost:3142/debian unstable/main amd64 libxcb1 amd64 1.14-2 [139 kB] Get:113 http://localhost:3142/debian unstable/main amd64 libx11-data all 2:1.6.12-1 [311 kB] Get:114 http://localhost:3142/debian unstable/main amd64 libx11-6 amd64 2:1.6.12-1 [770 kB] Get:115 http://localhost:3142/debian unstable/main amd64 libxext6 amd64 2:1.3.3-1+b2 [52.5 kB] Get:116 http://localhost:3142/debian unstable/main amd64 libxnvctrl0 amd64 450.66-1 [26.5 kB] Get:117 http://localhost:3142/debian unstable/main amd64 ocl-icd-libopencl1 amd64 2.2.12-4 [37.8 kB] Get:118 http://localhost:3142/debian unstable/main amd64 libhwloc-plugins amd64 2.3.0+dfsg-1 [20.8 kB] Get:119 http://localhost:3142/debian unstable/main amd64 libnl-3-dev amd64 3.4.0-1+b1 [102 kB] Get:120 http://localhost:3142/debian unstable/main amd64 libnl-route-3-dev amd64 3.4.0-1+b1 [176 kB] Get:121 http://localhost:3142/debian unstable/main amd64 libibverbs-dev amd64 31.0-1 [534 kB] Get:122 http://localhost:3142/debian unstable/main amd64 node-jquery all 3.5.1+dfsg-4 [309 kB] Get:123 http://localhost:3142/debian unstable/main amd64 libjs-jquery all 3.5.1+dfsg-4 [3612 B] Get:124 http://localhost:3142/debian unstable/main amd64 libjs-jquery-ui all 1.12.1+dfsg-7 [232 kB] Get:125 http://localhost:3142/debian unstable/main amd64 libpmix2 amd64 3.2.0~rc1-4 [448 kB] Get:126 http://localhost:3142/debian unstable/main amd64 libucx0 amd64 1.9.0~rc1-2 [660 kB] Get:127 http://localhost:3142/debian unstable/main amd64 libopenmpi3 amd64 4.0.5-5 [2166 kB] Get:128 http://localhost:3142/debian unstable/main amd64 openmpi-common all 4.0.5-5 [73.6 kB] Get:129 http://localhost:3142/debian unstable/main amd64 libpmix-dev amd64 3.2.0~rc1-4 [551 kB] Get:130 http://localhost:3142/debian unstable/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-2 [190 kB] Get:131 http://localhost:3142/debian unstable/main amd64 openmpi-bin amd64 4.0.5-5 [127 kB] Get:132 http://localhost:3142/debian unstable/main amd64 libopenmpi-dev amd64 4.0.5-5 [1090 kB] Get:133 http://localhost:3142/debian unstable/main amd64 libsparsehash-dev all 2.0.3-2 [76.8 kB] Get:134 http://localhost:3142/debian unstable/main amd64 libsqlite3-dev amd64 3.33.0-1 [956 kB] Get:135 http://localhost:3142/debian unstable/main amd64 libtext-markdown-perl all 1.000031-3 [33.8 kB] Get:136 http://localhost:3142/debian unstable/main amd64 libtext-multimarkdown-perl all 1.000035-2 [28.6 kB] Get:137 http://localhost:3142/debian unstable/main amd64 pkg-config amd64 0.29.2-1 [65.1 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 137 MB in 1s (115 MB/s) Selecting previously unselected package bsdextrautils. 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Setting up libubsan1:amd64 (10.2.0-13) ... Setting up libnuma1:amd64 (2.0.12-1+b1) ... Setting up sensible-utils (0.0.12+nmu1) ... Setting up ocl-icd-libopencl1:amd64 (2.2.12-4) ... Setting up libboost-test1.71.0:amd64 (1.71.0-6+b2) ... Setting up libcrypt-dev:amd64 (1:4.4.17-1) ... Setting up libuchardet0:amd64 (0.0.7-1) ... Setting up libnl-3-200:amd64 (3.4.0-1+b1) ... Setting up libpsm2-2 (11.2.185-1) ... Setting up openmpi-common (4.0.5-5) ... Setting up cpp-9 (9.3.0-18) ... Setting up libperl5.30:amd64 (5.30.3-4) ... Setting up libc6-dev:amd64 (2.31-3) ... Setting up libboost-serialization1.71.0:amd64 (1.71.0-6+b2) ... Setting up libkrb5-3:amd64 (1.17-10) ... Setting up libpsm-infinipath1 (3.3+20.604758e7-6+b1) ... update-alternatives: using /usr/lib/libpsm1/libpsm_infinipath.so.1.16 to provide /usr/lib/x86_64-linux-gnu/libpsm_infinipath.so.1 (libpsm_infinipath.so.1) in auto mode Setting up libboost-graph1.71.0:amd64 (1.71.0-6+b2) ... Setting up libfido2-1:amd64 (1.5.0-2) ... 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Setting up libcroco3:amd64 (0.6.13-1) ... Setting up gcc-10 (10.2.0-13) ... Setting up libdpkg-perl (1.20.5) ... Setting up autoconf (2.69-11.1) ... Setting up zlib1g-dev:amd64 (1:1.2.11.dfsg-2) ... Setting up dwz (0.13-5) ... Setting up libnl-3-dev:amd64 (3.4.0-1+b1) ... Setting up groff-base (1.22.4-5) ... Setting up libsub-override-perl (0.09-2) ... Setting up libx11-6:amd64 (2:1.6.12-1) ... Setting up libjs-jquery (3.5.1+dfsg-4) ... Setting up liburi-perl (1.76-2) ... Setting up automake (1:1.16.2-4) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up gcc-9 (9.3.0-18) ... Setting up libtext-markdown-perl (1.000031-3) ... Setting up libibverbs1:amd64 (31.0-1) ... Setting up gettext (0.19.8.1-10) ... Setting up libstdc++-10-dev:amd64 (10.2.0-13) ... Setting up g++-10 (10.2.0-13) ... Setting up libstdc++-9-dev:amd64 (9.3.0-18) ... Setting up ibverbs-providers:amd64 (31.0-1) ... Setting up libtool (2.4.6-14) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up openssh-client (1:8.3p1-1) ... Setting up libhtml-tagset-perl (3.20-4) ... Setting up libdebhelper-perl (13.2.1) ... Setting up libboost1.71-dev:amd64 (1.71.0-6+b2) ... Setting up libxext6:amd64 (2:1.3.3-1+b2) ... Setting up libgfortran-9-dev:amd64 (9.3.0-18) ... Setting up man-db (2.9.3-2) ... Not building database; man-db/auto-update is not 'true'. Setting up gcc (4:10.2.0-1) ... Setting up dpkg-dev (1.20.5) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libxnvctrl0:amd64 (450.66-1) ... Setting up help2man (1.47.16) ... Setting up libnl-route-3-dev:amd64 (3.4.0-1+b1) ... Setting up libltdl-dev:amd64 (2.4.6-14) ... Setting up libboost-test1.71-dev:amd64 (1.71.0-6+b2) ... Setting up libjs-jquery-ui (1.12.1+dfsg-7) ... Setting up libboost-regex1.71-dev:amd64 (1.71.0-6+b2) ... Setting up libboost-serialization1.71-dev:amd64 (1.71.0-6+b2) ... Setting up pkg-config (0.29.2-1) ... Setting up g++ (4:10.2.0-1) ... update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode Setting up libhtml-parser-perl (3.75-1) ... Setting up build-essential (12.8) ... Setting up libhwloc-dev:amd64 (2.3.0+dfsg-1) ... Setting up libtext-multimarkdown-perl (1.000035-2) ... Setting up libboost-graph1.71-dev:amd64 (1.71.0-6+b2) ... Setting up libfile-stripnondeterminism-perl (1.9.0-1) ... Setting up librdmacm1:amd64 (31.0-1) ... Setting up libboost-graph-dev:amd64 (1.71.0.3) ... Setting up libucx0:amd64 (1.9.0~rc1-2) ... Setting up gfortran-9 (9.3.0-18) ... Setting up po-debconf (1.0.21) ... Setting up libibverbs-dev:amd64 (31.0-1) ... Setting up libhwloc-plugins:amd64 (2.3.0+dfsg-1) ... Setting up dh-strip-nondeterminism (1.9.0-1) ... Setting up libfabric1 (1.11.0-2) ... Setting up libpmix2:amd64 (3.2.0~rc1-4) ... Setting up libopenmpi3:amd64 (4.0.5-5) ... Setting up libpmix-dev:amd64 (3.2.0~rc1-4) ... Setting up openmpi-bin (4.0.5-5) ... update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode Setting up libopenmpi-dev:amd64 (4.0.5-5) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/openmpi/include to provide /usr/include/x86_64-linux-gnu/mpi (mpi-x86_64-linux-gnu) in auto mode Setting up dh-autoreconf (19) ... Setting up debhelper (13.2.1) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.31-3) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any-amd64 any-i386 arm64 armel armhf mips64el mipsel ppc64el s390x alpha ia64 m68k powerpcspe ppc64 riscv64 sh4 sparc64) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 5.7.0-2-amd64 #1 SMP Debian 5.7.10-1 (2020-07-26) amd64 (x86_64) Toolchain package versions: binutils_2.35.1-1 dpkg-dev_1.20.5 g++-10_10.2.0-13 gcc-10_10.2.0-13 gcc-9_9.3.0-18 libc6-dev_2.31-3 libstdc++-10-dev_10.2.0-13 libstdc++-9-dev_9.3.0-18 libstdc++6_10.2.0-13 linux-libc-dev_5.8.10-1 Package versions: adduser_3.118 apt_2.1.10 autoconf_2.69-11.1 automake_1:1.16.2-4 autopoint_0.19.8.1-10 autotools-dev_20180224.1 base-files_11 base-passwd_3.5.47 bash_5.0-7 binutils_2.35.1-1 binutils-common_2.35.1-1 binutils-x86-64-linux-gnu_2.35.1-1 bsdextrautils_2.36-3+b1 bsdutils_1:2.36-3+b1 build-essential_12.8 bzip2_1.0.8-4 coreutils_8.32-4+b1 cpp_4:10.2.0-1 cpp-10_10.2.0-13 cpp-7_7.5.0-6 cpp-9_9.3.0-18 dash_0.5.10.2-7 debconf_1.5.74 debhelper_13.2.1 debian-archive-keyring_2019.1 debianutils_4.11.2 dh-autoreconf_19 dh-strip-nondeterminism_1.9.0-1 diffutils_1:3.7-3 dirmngr_2.2.20-1 dpkg_1.20.5 dpkg-dev_1.20.5 dwz_0.13-5 e2fsprogs_1.45.6-1 eatmydata_105-9 fakeroot_1.25.1-1 fdisk_2.36-3+b1 file_1:5.38-5 findutils_4.7.0-1 g++_4:10.2.0-1 g++-10_10.2.0-13 gcc_4:10.2.0-1 gcc-10_10.2.0-13 gcc-10-base_10.2.0-13 gcc-7-base_7.5.0-6 gcc-8-base_8.4.0-4 gcc-9_9.3.0-18 gcc-9-base_9.3.0-18 gettext_0.19.8.1-10 gettext-base_0.19.8.1-10 gfortran-9_9.3.0-18 gnupg_2.2.20-1 gnupg-l10n_2.2.20-1 gnupg-utils_2.2.20-1 gpg_2.2.20-1 gpg-agent_2.2.20-1 gpg-wks-client_2.2.20-1 gpg-wks-server_2.2.20-1 gpgconf_2.2.20-1 gpgsm_2.2.20-1 gpgv_2.2.20-1 grep_3.4-1 groff-base_1.22.4-5 gzip_1.10-2 help2man_1.47.16 hostname_3.23 ibverbs-providers_31.0-1 icu-devtools_67.1-4 init-system-helpers_1.58 intltool-debian_0.35.0+20060710.5 libacl1_2.2.53-8 libapt-pkg5.0_1.8.4 libapt-pkg6.0_2.1.10 libarchive-zip-perl_1.68-1 libasan4_7.5.0-6 libasan5_9.3.0-18 libasan6_10.2.0-13 libassuan0_2.5.3-7.1 libatomic1_10.2.0-13 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-3 libaudit1_1:2.8.5-3+b1 libbinutils_2.35.1-1 libblkid1_2.36-3+b1 libboost-graph-dev_1.71.0.3 libboost-graph1.71-dev_1.71.0-6+b2 libboost-graph1.71.0_1.71.0-6+b2 libboost-regex1.71-dev_1.71.0-6+b2 libboost-regex1.71.0_1.71.0-6+b2 libboost-serialization1.71-dev_1.71.0-6+b2 libboost-serialization1.71.0_1.71.0-6+b2 libboost-test1.71-dev_1.71.0-6+b2 libboost-test1.71.0_1.71.0-6+b2 libboost1.71-dev_1.71.0-6+b2 libbsd0_0.10.0-1 libbz2-1.0_1.0.8-4 libc-bin_2.31-3 libc-dev-bin_2.31-3 libc6_2.31-3 libc6-dev_2.31-3 libcap-ng0_0.7.9-2.2 libcbor0_0.5.0+dfsg-2 libcc1-0_10.2.0-13 libcilkrts5_7.5.0-6 libcom-err2_1.45.6-1 libcroco3_0.6.13-1 libcrypt-dev_1:4.4.17-1 libcrypt1_1:4.4.17-1 libctf-nobfd0_2.35.1-1 libctf0_2.35.1-1 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.254 libdebhelper-perl_13.2.1 libdpkg-perl_1.20.5 libeatmydata1_105-9 libedit2_3.1-20191231-1 libelf1_0.181-1 libevent-2.1-7_2.1.12-stable-1 libevent-core-2.1-7_2.1.12-stable-1 libevent-dev_2.1.12-stable-1 libevent-extra-2.1-7_2.1.12-stable-1 libevent-openssl-2.1-7_2.1.12-stable-1 libevent-pthreads-2.1-7_2.1.12-stable-1 libext2fs2_1.45.6-1 libfabric1_1.11.0-2 libfakeroot_1.25.1-1 libfdisk1_2.36-3+b1 libffi6_3.2.1-9 libffi7_3.3-4 libfido2-1_1.5.0-2 libfile-stripnondeterminism-perl_1.9.0-1 libgcc-10-dev_10.2.0-13 libgcc-9-dev_9.3.0-18 libgcc-s1_10.2.0-13 libgcrypt20_1.8.6-2 libgdbm-compat4_1.18.1-5.1 libgdbm5_1.14.1-6+b1 libgdbm6_1.18.1-5.1 libgfortran-9-dev_9.3.0-18 libgfortran5_10.2.0-13 libglib2.0-0_2.66.0-2 libgmp10_2:6.2.0+dfsg-6 libgnutls30_3.6.15-4 libgomp1_10.2.0-13 libgpg-error0_1.38-2 libgssapi-krb5-2_1.17-10 libhogweed4_3.5.1+really3.4.1-1 libhogweed6_3.6-2 libhtml-parser-perl_3.75-1 libhtml-tagset-perl_3.20-4 libhwloc-dev_2.3.0+dfsg-1 libhwloc-plugins_2.3.0+dfsg-1 libhwloc15_2.3.0+dfsg-1 libibverbs-dev_31.0-1 libibverbs1_31.0-1 libicu-dev_67.1-4 libicu67_67.1-4 libidn2-0_2.3.0-1 libisl19_0.20-2 libisl22_0.22.1-1 libitm1_10.2.0-13 libjs-jquery_3.5.1+dfsg-4 libjs-jquery-ui_1.12.1+dfsg-7 libk5crypto3_1.17-10 libkeyutils1_1.6.1-2 libkrb5-3_1.17-10 libkrb5support0_1.17-10 libksba8_1.4.0-2 libldap-2.4-2_2.4.53+dfsg-1 libldap-common_2.4.53+dfsg-1 liblocale-gettext-perl_1.07-4 liblsan0_10.2.0-13 libltdl-dev_2.4.6-14 libltdl7_2.4.6-14 liblz4-1_1.9.2-2 liblzma5_5.2.4-1+b1 libmagic-mgc_1:5.38-5 libmagic1_1:5.38-5 libmount1_2.36-3+b1 libmpc3_1.2.0-1 libmpfr6_4.1.0-3 libmpx2_8.4.0-4 libncursesw6_6.2+20200918-1 libnettle6_3.5.1+really3.4.1-1 libnettle8_3.6-2 libnl-3-200_3.4.0-1+b1 libnl-3-dev_3.4.0-1+b1 libnl-route-3-200_3.4.0-1+b1 libnl-route-3-dev_3.4.0-1+b1 libnpth0_1.6-2 libnuma-dev_2.0.12-1+b1 libnuma1_2.0.12-1+b1 libopenmpi-dev_4.0.5-5 libopenmpi3_4.0.5-5 libp11-kit0_0.23.21-2 libpam-modules_1.3.1-5 libpam-modules-bin_1.3.1-5 libpam-runtime_1.3.1-5 libpam0g_1.3.1-5 libpciaccess0_0.16-1 libpcre2-8-0_10.34-7 libpcre3_2:8.39-13 libperl5.26_5.26.2-7+b1 libperl5.30_5.30.3-4 libpipeline1_1.5.3-1 libpmix-dev_3.2.0~rc1-4 libpmix2_3.2.0~rc1-4 libpsm-infinipath1_3.3+20.604758e7-6+b1 libpsm2-2_11.2.185-1 libquadmath0_10.2.0-13 librdmacm1_31.0-1 libreadline7_7.0-5 libreadline8_8.0-4 libsasl2-2_2.1.27+dfsg-2 libsasl2-modules-db_2.1.27+dfsg-2 libseccomp2_2.4.4-1 libselinux1_3.1-2 libsemanage-common_3.1-1 libsemanage1_3.1-1 libsepol1_3.1-1 libsigsegv2_2.12-2 libsmartcols1_2.36-3+b1 libsparsehash-dev_2.0.3-2 libsqlite3-0_3.33.0-1 libsqlite3-dev_3.33.0-1 libss2_1.45.6-1 libssl1.1_1.1.1g-1 libstdc++-10-dev_10.2.0-13 libstdc++-9-dev_9.3.0-18 libstdc++6_10.2.0-13 libsub-override-perl_0.09-2 libsystemd0_246.6-1 libtasn1-6_4.16.0-2 libtext-markdown-perl_1.000031-3 libtext-multimarkdown-perl_1.000035-2 libtinfo6_6.2+20200918-1 libtool_2.4.6-14 libtsan0_10.2.0-13 libubsan0_7.5.0-6 libubsan1_10.2.0-13 libuchardet0_0.0.7-1 libucx0_1.9.0~rc1-2 libudev1_246.6-1 libunistring2_0.9.10-4 liburi-perl_1.76-2 libuuid1_2.36-3+b1 libx11-6_2:1.6.12-1 libx11-data_2:1.6.12-1 libxau6_1:1.0.8-1+b2 libxcb1_1.14-2 libxdmcp6_1:1.1.2-3 libxext6_2:1.3.3-1+b2 libxml2_2.9.10+dfsg-6 libxnvctrl0_450.66-1 libzstd1_1.4.5+dfsg-4 linux-libc-dev_5.8.10-1 login_1:4.8.1-1 logsave_1.45.6-1 lsb-base_11.1.0 m4_1.4.18-4 make_4.3-4 man-db_2.9.3-2 mawk_1.3.4.20200120-2 mount_2.36-3+b1 ncurses-base_6.2+20200918-1 ncurses-bin_6.2+20200918-1 netbase_6.1 node-jquery_3.5.1+dfsg-4 ocl-icd-libopencl1_2.2.12-4 openmpi-bin_4.0.5-5 openmpi-common_4.0.5-5 openssh-client_1:8.3p1-1 passwd_1:4.8.1-1 patch_2.7.6-6 perl_5.30.3-4 perl-base_5.30.3-4 perl-modules-5.26_5.26.2-7 perl-modules-5.30_5.30.3-4 pinentry-curses_1.1.0-4 pkg-config_0.29.2-1 po-debconf_1.0.21 readline-common_8.0-4 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12+nmu1 sysvinit-utils_2.96-5 tar_1.30+dfsg-7 tzdata_2020a-1 util-linux_2.36-3+b1 xz-utils_5.2.4-1+b1 zlib1g_1:1.2.11.dfsg-2 zlib1g-dev_1:1.2.11.dfsg-2 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: abyss Binary: abyss Architecture: any-amd64 any-i386 arm64 armel armhf mips64el mipsel ppc64el s390x alpha ia64 m68k powerpcspe ppc64 riscv64 sh4 sparc64 Version: 2.2.4-1 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille , Michael R. Crusoe Homepage: https://github.com/bcgsc/abyss Standards-Version: 4.4.1 Vcs-Browser: https://salsa.debian.org/med-team/abyss Vcs-Git: https://salsa.debian.org/med-team/abyss.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 12), libboost-graph-dev, libopenmpi-dev, libsparsehash-dev, libtext-multimarkdown-perl , libsqlite3-dev, pkg-config, help2man Package-List: abyss deb science optional arch=any-amd64,arm64,armel,armhf,any-i386,mips64el,mipsel,ppc64el,s390x,alpha,ia64,m68k,powerpcspe,ppc64,riscv64,sh4,sparc64,x32 Checksums-Sha1: f4a124d99b8bb38423bce219d4ba87d1d4b1dfa1 1204110 abyss_2.2.4.orig.tar.gz 4bddb9b425d48387b9d8292dd4d63836e11786c0 755968 abyss_2.2.4-1.debian.tar.xz Checksums-Sha256: 0b3265506d448cad5bbfe16b7b3cbd88c51a9c02a96ce1ddcd0389836c317d5a 1204110 abyss_2.2.4.orig.tar.gz e781bf3654d94470948269962a6e8bdce5a71d19c56ed37e8bb2f7e5b47bea22 755968 abyss_2.2.4-1.debian.tar.xz Files: 4988af5a801864ef04a7fdf5d171e75c 1204110 abyss_2.2.4.orig.tar.gz f56f2fc3c30202b97526bb7c53611e89 755968 abyss_2.2.4-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEck1gkzcRPHEFUNdHPCZ2P2xn5uIFAl5CvMMACgkQPCZ2P2xn 5uJ2MRAAoXHwuDbTRbwZF/AXjKiRnMxfzryC2Lz1xKxxb3TgpNaPRtKO2kGSCZvR 85Mx66WW+ZOveTfon5p+XFNn5UFfkuF3N8wpZQVI90ON2MafDDDbailG1HrcvUCD kYkKAKNneChMqEDtuiiK9NZxeLis9e/b+/vboqbLEV82hQmRsTPN1izsv6OVE3X9 fDNVo5OkuRnjvLmkLhU8hdGISPJK8qipgthLahKJoEOC/5aMxXL3RV03tKeuY41a h/MCosrln9wuIM7+nrodVfbU4krfEJBJd0xM9VJf4nZypAaLRsq+ED4QEp1MqaSp SYU4KtZaEgBao6A7oZDlDoGBVM73NUy1HeFJCKFDhu9UlQEJej13f84T7zwlb4LI TdZ7mXBmufKViLZyp7tu/4wcWABWwl1SxQGWtz2qToTnaQpvH6fHS9GmUo7UiGsE 3lZE515wLfrdKFqo6nFYGoiZPOjQq/3tpNedjk0h3BnriiMfFP6eB4rDpJlha6Wz C/c9Fzali/3EXOa0DZIKbhlaAY47xJN/m317c1tpUvfw/tdqJc2E7qTw790g2shJ Xu9ghj9vtNifJqtGg+Ec39H4Iizw/jHGsrMcVh1qsIGhhjRg6dzGxfH6ScJEKM5z wKhW5TRfRjMDoibN7sJmqyBHFjhO0xxVkM1iu3aOdSUivtmNmBE= =xxno -----END PGP SIGNATURE----- gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.VsQGmiik/trustedkeys.kbx': General error gpgv: Signature made Tue Feb 11 14:40:03 2020 UTC gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./abyss_2.2.4-1.dsc dpkg-source: info: extracting abyss in /<> dpkg-source: info: unpacking abyss_2.2.4.orig.tar.gz dpkg-source: info: unpacking abyss_2.2.4-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying abyss-pe.patch Check disk space ---------------- Sufficient free space for build +------------------------------------------------------------------------------+ | Starting Timed Build Commands | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/starting-build-commands/no-network abyss_2.2.4-1 sid amd64 ---------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/starting-build-commands/no-network abyss_2.2.4-1 sid amd64'. Finished processing commands. -------------------------------------------------------------------------------- User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DBUS_SESSION_BUS_ADDRESS=unix:path=/run/user/1001/bus HOME=/sbuild-nonexistent LANG=C LC_ALL=C.UTF-8 LD_LIBRARY_PATH=/usr/lib/libeatmydata LD_PRELOAD=libeatmydata.so LOGNAME=debomatic PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games PWD=/<> SCHROOT_ALIAS_NAME=sid-amd64-debomatic SCHROOT_CHROOT_NAME=sid-amd64-debomatic SCHROOT_COMMAND=env SCHROOT_GID=112 SCHROOT_GROUP=sbuild SCHROOT_SESSION_ID=sid-amd64-debomatic-bd60c713-0093-4412-9d01-3b2e0f7814bb SCHROOT_UID=1001 SCHROOT_USER=debomatic SHELL=/bin/sh USER=debomatic XDG_RUNTIME_DIR=/run/user/1001 XDG_SESSION_CLASS=background XDG_SESSION_ID=c3817745 XDG_SESSION_TYPE=unspecified dpkg-buildpackage ----------------- Command: dpkg-buildpackage -us -uc -rfakeroot -Zxz dpkg-buildpackage: info: source package abyss dpkg-buildpackage: info: source version 2.2.4-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Michael R. Crusoe dpkg-source -Zxz --before-build . dpkg-buildpackage: info: host architecture amd64 fakeroot debian/rules clean dh clean dh_clean dpkg-source -Zxz -b . dpkg-source: info: using source format '3.0 (quilt)' dpkg-source: info: building abyss using existing ./abyss_2.2.4.orig.tar.gz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: building abyss in abyss_2.2.4-1.debian.tar.xz dpkg-source: info: building abyss in abyss_2.2.4-1.dsc debian/rules build dh build dh_update_autotools_config dh_autoreconf configure.ac:16: installing './compile' configure.ac:166: installing './config.guess' configure.ac:166: installing './config.sub' configure.ac:10: installing './install-sh' configure.ac:10: installing './missing' ABYSS/Makefile.am: installing './depcomp' parallel-tests: installing './test-driver' debian/rules override_dh_auto_configure make[1]: Entering directory '/<>' dh_auto_configure -- \ --with-mpi=/usr/lib/x86_64-linux-gnu/openmpi ./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-mpi=/usr/lib/x86_64-linux-gnu/openmpi checking for g++... g++ checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking whether g++ supports C++11 features with -std=c++11... yes checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports the include directive... yes (GNU style) checking whether make supports nested variables... yes checking dependency style of g++ -std=c++11... none checking for gawk... (cached) mawk checking for gcc... gcc checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... none checking how to run the C preprocessor... gcc -E checking whether we are using the GNU C++ compiler... (cached) yes checking whether g++ -std=c++11 accepts -g... (cached) yes checking for ranlib... ranlib checking for ghc... no ./configure: line 5896: : command not found checking for pandoc... no checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking dlfcn.h usability... yes checking dlfcn.h presence... yes checking for dlfcn.h... yes checking fcntl.h usability... yes checking fcntl.h presence... yes checking for fcntl.h... yes checking float.h usability... yes checking float.h presence... yes checking for float.h... yes checking limits.h usability... yes checking limits.h presence... yes checking for limits.h... yes checking stddef.h usability... yes checking stddef.h presence... yes checking for stddef.h... yes checking for stdint.h... (cached) yes checking for stdlib.h... (cached) yes checking sys/param.h usability... yes checking sys/param.h presence... yes checking for sys/param.h... yes checking for stdbool.h that conforms to C99... yes checking for _Bool... yes checking for ANSI C header files... (cached) yes checking whether byte ordering is bigendian... no checking for an ANSI C-conforming const... yes checking for inline... inline checking for ptrdiff_t... yes checking for mode_t... yes checking for pid_t... yes checking for size_t... yes checking for ssize_t... yes checking for int64_t... yes checking for uint8_t... yes checking for uint16_t... yes checking for uint32_t... yes checking for uint64_t... yes checking for std::hash... yes checking for std::tr1::hash... yes checking for std::tr1::tuple... yes checking for dup2... yes checking for gethostname... yes checking for getopt_long... yes checking for getpagesize... yes checking for memset... yes checking for strdup... yes checking for strerror... yes checking for strtoul... yes checking vfork.h usability... no checking vfork.h presence... no checking for vfork.h... no checking for fork... yes checking for vfork... yes checking for working fork... yes checking for working vfork... (cached) yes checking for stdlib.h... (cached) yes checking for GNU libc compatible malloc... yes checking for working memcmp... yes checking for stdlib.h... (cached) yes checking for GNU libc compatible realloc... yes checking for vprintf... yes checking for _doprnt... no checking whether HOST_NAME_MAX is declared... yes checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking if compiler needs -Werror to reject unknown flags... no checking for the pthreads library -lpthreads... no checking whether pthreads work without any flags... no checking whether pthreads work with -Kthread... no checking whether pthreads work with -kthread... no checking for the pthreads library -llthread... no checking whether pthreads work with -pthread... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for PTHREAD_PRIO_INHERIT... yes checking mpi.h usability... yes checking mpi.h presence... yes checking for mpi.h... yes checking for MPI_Init in -lmpi... yes checking for sqrt in -lm... yes checking for pow... yes checking for sqrt... yes checking for ceilf... yes checking for dlsym in -ldl... yes checking how to run the C++ preprocessor... g++ -std=c++11 -E checking functional usability... yes checking functional presence... yes checking for functional... yes checking tr1/functional usability... yes checking tr1/functional presence... yes checking for tr1/functional... yes checking boost/functional/hash.hpp usability... yes checking boost/functional/hash.hpp presence... yes checking for boost/functional/hash.hpp... yes checking boost/property_map/property_map.hpp usability... yes checking boost/property_map/property_map.hpp presence... yes checking for boost/property_map/property_map.hpp... yes checking google/sparse_hash_map usability... yes checking google/sparse_hash_map presence... yes checking for google/sparse_hash_map... yes checking unordered_map usability... yes checking unordered_map presence... yes checking for unordered_map... yes checking tr1/unordered_map usability... yes checking tr1/unordered_map presence... yes checking for tr1/unordered_map... yes checking unordered_set usability... yes checking unordered_set presence... yes checking for unordered_set... yes checking tr1/unordered_set usability... yes checking tr1/unordered_set presence... yes checking for tr1/unordered_set... yes checking boost/unordered_set.hpp usability... yes checking boost/unordered_set.hpp presence... yes checking for boost/unordered_set.hpp... yes checking sqlite3.h usability... yes checking sqlite3.h presence... yes checking for sqlite3.h... yes checking for main in -lsqlite3... yes checking for g++ -std=c++11 option to support OpenMP... -fopenmp checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating ABYSS/Makefile config.status: creating Align/Makefile config.status: creating Assembly/Makefile config.status: creating Common/Makefile config.status: creating DataLayer/Makefile config.status: creating FMIndex/Makefile config.status: creating Graph/Makefile config.status: creating Parallel/Makefile config.status: creating bin/Makefile config.status: creating doc/Makefile config.status: creating dialign/Makefile config.status: creating kmerprint/Makefile config.status: creating AdjList/Makefile config.status: creating Konnector/Makefile config.status: creating DAssembler/Makefile config.status: creating DistanceEst/Makefile config.status: creating Layout/Makefile config.status: creating Map/Makefile config.status: creating Overlap/Makefile config.status: creating PopBubbles/Makefile config.status: creating Scaffold/Makefile config.status: creating SimpleGraph/Makefile config.status: creating MergePaths/Makefile config.status: creating KAligner/Makefile config.status: creating PairedDBG/Makefile config.status: creating ParseAligns/Makefile config.status: creating PathOverlap/Makefile config.status: creating Consensus/Makefile config.status: creating FilterGraph/Makefile config.status: creating GapFiller/Makefile config.status: creating Sealer/Makefile config.status: creating vendor/gtest-1.7.0/Makefile config.status: creating Unittest/Makefile config.status: creating LogKmerCount/Makefile config.status: creating Bloom/Makefile config.status: creating BloomDBG/Makefile config.status: creating DataBase/Makefile config.status: creating vendor/Makefile config.status: creating vendor/nthash/Makefile config.status: creating config.h config.status: executing depfiles commands make[1]: Leaving directory '/<>' debian/rules override_dh_auto_build make[1]: Entering directory '/<>' dh_auto_build make -j4 make[2]: Entering directory '/<>' make all-recursive make[3]: Entering directory '/<>' Making all in bin make[4]: Entering directory '/<>/bin' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/<>/bin' Making all in doc make[4]: Entering directory '/<>/doc' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/<>/doc' Making all in Common make[4]: Entering directory '/<>/Common' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -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++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -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++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -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++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -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++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -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++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -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++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -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++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -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++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -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++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -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++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -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++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -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++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -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++ -std=c++11 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-gc abyss_gc-gc.o ../Common/libcommon.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L. -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-todot abyss_todot-todot.o ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/<>/Graph' Making all in DataLayer make[4]: Entering directory '/<>/DataLayer' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -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++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -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++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -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++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -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++ -std=c++11 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-tofastq abyss_tofastq-abyss-tofastq.o libdatalayer.a ../Common/libcommon.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-fac abyss_fac-fac.o libdatalayer.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/<>/DataLayer' Making all in DataBase make[4]: Entering directory '/<>/DataBase' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -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++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -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 g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -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++ -std=c++11 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-db-csv abyss_db_csv-DB.o abyss_db_csv-db-csv.o -lsqlite3 -ldl -lm rm -f libdb.a ar cru libdb.a libdb_a-DB.o ../Common/libcommon.a ar: `u' modifier ignored since `D' is the default (see `U') ranlib libdb.a make[4]: Leaving directory '/<>/DataBase' Making all in FMIndex make[4]: Entering directory '/<>/FMIndex' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -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++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I../Common -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -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++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -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 g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-count abyss_count-count.o libfmindex.a ../Common/libcommon.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-dawg abyss_dawg-abyss-dawg.o libfmindex.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/<>/FMIndex' Making all in Assembly make[4]: Entering directory '/<>/Assembly' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -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++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -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/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -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 gcc -DHAVE_CONFIG_H -I. -I.. -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -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/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -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/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -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 alig.c:15:20: warning: inline function ‘calc_ov_weight’ declared but never defined 15 | extern inline void calc_ov_weight(struct diag* dg, struct diag_col *dcol, struct scr_matrix* smatrix, | ^~~~~~~~~~~~~~ alig.c:13:20: warning: inline function ‘calc_weight’ declared but never defined 13 | extern inline void calc_weight(struct diag* dg, struct scr_matrix* smatrix, | ^~~~~~~~~~~ assemble.c:40:20: warning: inline function ‘align_diag’ declared but never defined 40 | extern inline char align_diag(struct alignment *algn, struct scr_matrix *smatrix, struct diag* dg); | ^~~~~~~~~~ assemble.c:37:32: warning: inline function ‘find_eqc’ declared but never defined 37 | extern inline struct algn_pos *find_eqc(struct algn_pos **ap, int seqnum, int pos); | ^~~~~~~~ assemble.c:25:39: warning: inline function ‘find_diags_guided’ declared but never defined 25 | extern inline struct simple_diag_col* find_diags_guided(struct scr_matrix *smatrix, | ^~~~~~~~~~~~~~~~~ assemble.c:15:20: warning: inline function ‘calc_ov_weight’ declared but never defined 15 | extern inline void calc_ov_weight(struct diag* dg, struct diag_col *dcol, struct scr_matrix* smatrix, | ^~~~~~~~~~~~~~ assemble.c:13:20: warning: inline function ‘calc_weight’ declared but never defined 13 | extern inline void calc_weight(struct diag* dg, struct scr_matrix* smatrix, | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I.. -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -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 diag.c:1456:3: warning: ‘real_calc_weight’ is static but used in inline function ‘find_diags_dyn’ which is not static 1456 | real_calc_weight(dg, smatrix, pdist,1,tmp_dist,algn); | ^~~~~~~~~~~~~~~~ io.c: In function ‘read_scr_matrix’: io.c:270:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 270 | fscanf( fp, "%i", &is); | ^~~~~~~~~~~~~~~~~~~~~~ io.c:282:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 282 | fscanf(fp, "%s\n", rline); | ^~~~~~~~~~~~~~~~~~~~~~~~~ io.c: In function ‘read_diag_prob_dist’: io.c:371:7: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 371 | fscanf( fp, "%li %li %Le\n", &ti,&tscr,&weight ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I.. -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -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/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -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/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -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/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -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 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 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -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++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -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++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -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++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -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++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -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++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -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++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -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++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-align abyss_align-align.o ./libalign.a ../dialign/libdialign.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -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++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -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++ -std=c++11 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -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 Parallel make[4]: Entering directory '/<>/Parallel' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o ABYSS_P-parallelAbyss.o `test -f 'parallelAbyss.cpp' || echo './'`parallelAbyss.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o ABYSS_P-CommLayer.o `test -f 'CommLayer.cpp' || echo './'`CommLayer.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o ABYSS_P-NetworkSequenceCollection.o `test -f 'NetworkSequenceCollection.cpp' || echo './'`NetworkSequenceCollection.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o ABYSS_P-MessageBuffer.o `test -f 'MessageBuffer.cpp' || echo './'`MessageBuffer.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o ABYSS_P-Messages.o `test -f 'Messages.cpp' || echo './'`Messages.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -DPAIRED_DBG -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_paired_dbg_mpi-parallelAbyss.o `test -f 'parallelAbyss.cpp' || echo './'`parallelAbyss.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -DPAIRED_DBG -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_paired_dbg_mpi-CommLayer.o `test -f 'CommLayer.cpp' || echo './'`CommLayer.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -DPAIRED_DBG -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_paired_dbg_mpi-NetworkSequenceCollection.o `test -f 'NetworkSequenceCollection.cpp' || echo './'`NetworkSequenceCollection.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -DPAIRED_DBG -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_paired_dbg_mpi-MessageBuffer.o `test -f 'MessageBuffer.cpp' || echo './'`MessageBuffer.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -DPAIRED_DBG -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_paired_dbg_mpi-Messages.o `test -f 'Messages.cpp' || echo './'`Messages.cpp g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o ABYSS-P ABYSS_P-parallelAbyss.o ABYSS_P-CommLayer.o ABYSS_P-NetworkSequenceCollection.o ABYSS_P-MessageBuffer.o ABYSS_P-Messages.o ../Assembly/libassembly.a ../Common/libcommon.a ../DataLayer/libdatalayer.a ../DataBase/libdb.a -lsqlite3 -ldl -lm -lmpi -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-paired-dbg-mpi abyss_paired_dbg_mpi-parallelAbyss.o abyss_paired_dbg_mpi-CommLayer.o abyss_paired_dbg_mpi-NetworkSequenceCollection.o abyss_paired_dbg_mpi-MessageBuffer.o abyss_paired_dbg_mpi-Messages.o ../Assembly/libassembly.a ../Common/libcommon.a ../DataLayer/libdatalayer.a ../DataBase/libdb.a -lsqlite3 -ldl -lm -lmpi -ldl -lm make[4]: Leaving directory '/<>/Parallel' Making all in Bloom make[4]: Entering directory '/<>/Bloom' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../vendor -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -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++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -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++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../vendor -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -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 g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -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++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -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++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -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++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -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++ -std=c++11 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -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++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -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++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -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++ -std=c++11 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -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++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -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++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -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++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -D SAM_SEQ_QUAL=1 -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -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++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -D SAM_SEQ_QUAL=1 -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -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++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -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 g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -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 make[4]: Leaving directory '/<>/DistanceEst' Making all in KAligner make[4]: Entering directory '/<>/KAligner' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -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++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -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++ -std=c++11 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -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++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -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++ -std=c++11 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -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++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -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++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -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++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../FMIndex -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -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++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../FMIndex -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -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++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../FMIndex -D SAM_SEQ_QUAL=1 -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -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++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../FMIndex -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -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 g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-index abyss_index-index.o ../FMIndex/libfmindex.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -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 g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -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++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -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++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -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++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Align -I../Common -I../DataLayer -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -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++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Align -I../Common -I../DataLayer -I../SimpleGraph -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -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++ -std=c++11 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -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++ -std=c++11 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -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++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -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 Overlap make[4]: Entering directory '/<>/Overlap' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -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++ -std=c++11 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -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++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -DPAIRED_DBG -I.. -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -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++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -DPAIRED_DBG -I.. -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -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 g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o KmerPair.o 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++ -std=c++11 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -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++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -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++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -D SAM_SEQ_QUAL=1 -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -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++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -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++ -std=c++11 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -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 g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -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++ -std=c++11 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o ParseAligns ParseAligns-ParseAligns.o ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/<>/ParseAligns' Making all in PathOverlap make[4]: Entering directory '/<>/PathOverlap' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -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++ -std=c++11 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -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++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Align -I../Common -I../DataLayer -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -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++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -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++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -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++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -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++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -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++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -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 g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-junction abyss_junction-junction.o ../Common/libcommon.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-drawgraph abyss_drawgraph-drawgraph.o ../Common/libcommon.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-longseqdist abyss_longseqdist-longseqdist.o ../Common/libcommon.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -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++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -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++ -std=c++11 -Wall -Wextra -Werror -Wno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -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++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Assembly -I../Common -I../DataLayer -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -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++ -std=c++11 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -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++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -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++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -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++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../Align -D SAM_SEQ_QUAL=1 -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -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++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -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++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -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++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -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++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -DPAIRED_DBG -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -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++ -std=c++11 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -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 vendor make[4]: Entering directory '/<>/vendor' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/<>/vendor' Making all in vendor/nthash make[4]: Entering directory '/<>/vendor/nthash' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/<>/vendor/nthash' Making all in vendor/gtest-1.7.0 make[4]: Entering directory '/<>/vendor/gtest-1.7.0' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/<>/vendor/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 README.md > README.html make[1]: Leaving directory '/<>' dh_auto_test 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 Parallel make[2]: Entering directory '/<>/Parallel' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/<>/Parallel' 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 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 vendor make[2]: Entering directory '/<>/vendor' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/<>/vendor' Making check in vendor/nthash make[2]: Entering directory '/<>/vendor/nthash' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/<>/vendor/nthash' Making check in vendor/gtest-1.7.0 make[2]: Entering directory '/<>/vendor/gtest-1.7.0' make libgtest.a libgtest_main.a make[3]: Entering directory '/<>/vendor/gtest-1.7.0' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I../.. -I../.. -isystem ../../vendor/gtest-1.7.0/include -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -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++ -std=c++11 -DHAVE_CONFIG_H -I. -I../.. -I../.. -isystem ../../vendor/gtest-1.7.0/include -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -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++ -std=c++11 -DHAVE_CONFIG_H -I. -I../.. -I../.. -isystem ../../vendor/gtest-1.7.0/include -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -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.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 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 make[3]: Leaving directory '/<>/vendor/gtest-1.7.0' make[2]: Leaving directory '/<>/vendor/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_CountingBloomFilter BloomDBG_RollingBloomDBG BloomDBG_MaskedKmer BloomDBG_SpacedSeed BloomDBG_LightweightKmer make[3]: Entering directory '/<>/Unittest' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../Common -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -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-konnectorTest.o `test -f 'Konnector/konnectorTest.cpp' || echo './'`Konnector/konnectorTest.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -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++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -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++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -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++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -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++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -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++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -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++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -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++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../Common -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -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++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../Common -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -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/DBGBloom-DBGBloomTest.o `test -f 'Konnector/DBGBloomTest.cpp' || echo './'`Konnector/DBGBloomTest.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../Common -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -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/DBGBloomAlgorithms-DBGBloomAlgorithmsTest.o `test -f 'Konnector/DBGBloomAlgorithmsTest.cpp' || echo './'`Konnector/DBGBloomAlgorithmsTest.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../Common -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -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++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../Common -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -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++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../Common -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -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++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../Common -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -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++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../Common -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -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++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../Common -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -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++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../Common -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -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++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -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++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o Konnector_konnector Konnector/konnector-konnectorTest.o ../Align/libalign.a ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../DataLayer -I../Common -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -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/LoadAlgorithm-LoadAlgorithmTest.o `test -f 'DBG/LoadAlgorithmTest.cpp' || echo './'`DBG/LoadAlgorithmTest.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../DataLayer -I../Common -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -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/LoadAlgorithm-LoadAlgorithmTest.o `test -f 'PairedDBG/LoadAlgorithmTest.cpp' || echo './'`PairedDBG/LoadAlgorithmTest.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../DataLayer -I../Common -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -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/KmerPair-KmerPairTest.o `test -f 'PairedDBG/KmerPairTest.cc' || echo './'`PairedDBG/KmerPairTest.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../DataLayer -I../Common -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -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/Dinuc-DinucTest.o `test -f 'PairedDBG/DinucTest.cc' || echo './'`PairedDBG/DinucTest.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../DataLayer -I../Common -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -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/BranchRecord-BranchRecordTest.o `test -f 'PairedDBG/BranchRecordTest.cpp' || echo './'`PairedDBG/BranchRecordTest.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../Common -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -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-BloomDBGTest.o `test -f 'BloomDBG/BloomDBGTest.cpp' || echo './'`BloomDBG/BloomDBGTest.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -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++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -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++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -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/HashAgnosticCascadingBloom-HashAgnosticCascadingBloomTest.o `test -f 'BloomDBG/HashAgnosticCascadingBloomTest.cpp' || echo './'`BloomDBG/HashAgnosticCascadingBloomTest.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../Common -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -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/CountingBloomFilter-CountingBloomFilterTest.o `test -f 'BloomDBG/CountingBloomFilterTest.cpp' || echo './'`BloomDBG/CountingBloomFilterTest.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -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/RollingBloomDBG-RollingBloomDBGTest.o `test -f 'BloomDBG/RollingBloomDBGTest.cpp' || echo './'`BloomDBG/RollingBloomDBGTest.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -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++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -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++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o BloomDBG/LightweightKmerTest.o BloomDBG/LightweightKmerTest.cpp g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o common_stringutil Common/StringUtilTest.o ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o common_histogram Common/HistogramTest.o ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o common_bitutil Common/BitUtilTest.o ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o common_kmer Common/KmerTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o common_sequence Common/Sequence.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o common_KmerIterator Common/KmerIteratorTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o common_sam Common/SAM.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o BloomFilter Konnector/BloomFilter-BloomFilter.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o Konnector_DBGBloom Konnector/DBGBloom-DBGBloomTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o Konnector_DBGBloomAlgorithms Konnector/DBGBloomAlgorithms-DBGBloomAlgorithmsTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o graph_ConstrainedBFSVisitor Graph/graph_ConstrainedBFSVisitor-ConstrainedBFSVisitorTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o graph_BidirectionalBFS Graph/graph_BidirectionalBFS-BidirectionalBFSTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o graph_AllPathsSearch Graph/graph_AllPathsSearch-AllPathsSearchTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o graph_HashGraph Graph/graph_HashGraph-HashGraphTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o graph_ConstrainedBidiBFSVisitor Graph/graph_ConstrainedBidiBFSVisitor-ConstrainedBidiBFSVisitorTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o graph_ExtendPath Graph/graph_ExtendPath-ExtendPathTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o graph_DotIO Graph/graph_DotIO-DotIOTest.o ../Assembly/libassembly.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o graph_UndirectedGraph Graph/UndirectedGraphTest.o ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o DBG_LoadAlgorithm DBG/LoadAlgorithm-LoadAlgorithmTest.o ../Assembly/libassembly.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o PairedDBG_LoadAlgorithm PairedDBG/LoadAlgorithm-LoadAlgorithmTest.o ../PairedDBG/libpaireddbg.a ../Assembly/libassembly.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o PairedDBG_KmerPair PairedDBG/KmerPair-KmerPairTest.o ../PairedDBG/libpaireddbg.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o PairedDBG_Dinuc PairedDBG/Dinuc-DinucTest.o ../PairedDBG/libpaireddbg.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o PairedDBG_BranchRecord PairedDBG/BranchRecord-BranchRecordTest.o ../PairedDBG/libpaireddbg.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o BloomDBG_BloomDBG BloomDBG/BloomDBG-BloomDBGTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o BloomDBG_RollingHash BloomDBG/RollingHashTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o BloomDBG_RollingHashIterator BloomDBG/RollingHashIteratorTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o BloomDBG_HashAgnosticCascadingBloom BloomDBG/HashAgnosticCascadingBloom-HashAgnosticCascadingBloomTest.o ../DataLayer/libdatalayer.a ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o BloomDBG_CountingBloomFilter BloomDBG/CountingBloomFilter-CountingBloomFilterTest.o ../DataLayer/libdatalayer.a ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o BloomDBG_RollingBloomDBG BloomDBG/RollingBloomDBG-RollingBloomDBGTest.o ../DataLayer/libdatalayer.a ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o BloomDBG_MaskedKmer BloomDBG/MaskedKmerTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o BloomDBG_SpacedSeed BloomDBG/SpacedSeedTest.o ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o BloomDBG_LightweightKmer BloomDBG/LightweightKmerTest.o ../Common/libcommon.a ../vendor/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_stringutil PASS: common_kmer PASS: common_KmerIterator PASS: common_bitutil PASS: common_sequence PASS: common_sam PASS: Konnector_DBGBloom PASS: BloomFilter PASS: graph_ConstrainedBFSVisitor PASS: Konnector_DBGBloomAlgorithms PASS: graph_HashGraph PASS: graph_BidirectionalBFS PASS: graph_AllPathsSearch PASS: graph_ConstrainedBidiBFSVisitor PASS: graph_DotIO PASS: graph_ExtendPath PASS: Konnector_konnector PASS: graph_UndirectedGraph PASS: PairedDBG_KmerPair PASS: PairedDBG_Dinuc PASS: PairedDBG_BranchRecord PASS: BloomDBG_BloomDBG PASS: BloomDBG_RollingHash PASS: BloomDBG_RollingHashIterator PASS: BloomDBG_HashAgnosticCascadingBloom PASS: BloomDBG_CountingBloomFilter PASS: BloomDBG_RollingBloomDBG PASS: BloomDBG_MaskedKmer PASS: BloomDBG_SpacedSeed PASS: BloomDBG_LightweightKmer PASS: DBG_LoadAlgorithm PASS: PairedDBG_LoadAlgorithm ============================================================================ Testsuite summary for ABySS 2.2.4 ============================================================================ # TOTAL: 33 # PASS: 33 # 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 dh binary dh_testroot dh_prep 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 abyss-stack-size '/<>/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' /bin/mkdir -p '/<>/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/<>/debian/tmp/usr/bin' /usr/bin/install -c abyss-db-txt '/<>/debian/tmp/usr/bin' /usr/bin/install -c abyss-db-csv '/<>/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 Parallel make[3]: Entering directory '/<>/Parallel' make[4]: Entering directory '/<>/Parallel' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/<>/debian/tmp/usr/bin' /usr/bin/install -c ABYSS-P abyss-paired-dbg-mpi '/<>/debian/tmp/usr/bin' make[4]: Leaving directory '/<>/Parallel' make[3]: Leaving directory '/<>/Parallel' 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 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 vendor make[3]: Entering directory '/<>/vendor' make[4]: Entering directory '/<>/vendor' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/<>/vendor' make[3]: Leaving directory '/<>/vendor' Making install in vendor/nthash make[3]: Entering directory '/<>/vendor/nthash' make[4]: Entering directory '/<>/vendor/nthash' 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 README.md '/<>/debian/tmp/usr/share/doc/abyss' make[4]: Leaving directory '/<>/vendor/nthash' make[3]: Leaving directory '/<>/vendor/nthash' Making install in vendor/gtest-1.7.0 make[3]: Entering directory '/<>/vendor/gtest-1.7.0' make[4]: Entering directory '/<>/vendor/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 '/<>/vendor/gtest-1.7.0' make[3]: Leaving directory '/<>/vendor/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 '/<>' PATH=debian/tmp/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games help2man --no-info \ -n "Estimate distances between contigs using paired-end alignments." \ DistanceEst > debian/tmp/usr/share/man/man1/DistanceEst.1 PATH=debian/tmp/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games help2man --no-info \ -n "Fill the paired-end fields of SAM alignments" abyss-fixmate \ > debian/tmp/usr/share/man/man1/abyss-fixmate.1 make[1]: Leaving directory '/<>' debian/rules override_dh_install make[1]: Entering directory '/<>' dh_install for pl in `grep -Rl '#!/usr/bin/env[[:space:]]\+perl' debian/*/usr/*` ; do \ sed -i '1s?^#!/usr/bin/env[[:space:]]\+perl?#!/usr/bin/perl?' ${pl} ; \ done make[1]: Leaving directory '/<>' dh_installdocs dh_installchangelogs dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz dh_strip dh_makeshlibs dh_shlibdeps dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'abyss' in '../abyss_2.2.4-1_amd64.deb'. dpkg-deb: building package 'abyss-dbgsym' in '../abyss-dbgsym_2.2.4-1_amd64.deb'. dpkg-genbuildinfo dpkg-genchanges >../abyss_2.2.4-1_amd64.changes dpkg-genchanges: info: including full source code in upload dpkg-source -Zxz --after-build . dpkg-buildpackage: info: full upload (original source is included) -------------------------------------------------------------------------------- Build finished at 2020-10-02T22:55:01Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ abyss_2.2.4-1_amd64.changes: ---------------------------- Format: 1.8 Date: Tue, 11 Feb 2020 15:39:45 +0100 Source: abyss Binary: abyss abyss-dbgsym Architecture: source amd64 Version: 2.2.4-1 Distribution: sid Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Michael R. Crusoe Description: abyss - de novo, parallel, sequence assembler for short reads Changes: abyss (2.2.4-1) unstable; urgency=medium . * New upstream version * spelling patch incorporated upstream, removed it * Remove markdown from the nodoc build profile, to allow for cross-building Checksums-Sha1: c9ce93cbd2b53b8e91f2a77e954bedd0fe7d09be 1435 abyss_2.2.4-1.dsc f4a124d99b8bb38423bce219d4ba87d1d4b1dfa1 1204110 abyss_2.2.4.orig.tar.gz 4bddb9b425d48387b9d8292dd4d63836e11786c0 755968 abyss_2.2.4-1.debian.tar.xz 76febf0e935c03fc0b8dcc60b68f5f30b8fafefa 27417440 abyss-dbgsym_2.2.4-1_amd64.deb b6bd4fb9f00afc52c9df9afd5ffb0772154a0627 7640 abyss_2.2.4-1_amd64.buildinfo 2468885b7a90af58563bc690fb6cebbcb7f3103d 3006744 abyss_2.2.4-1_amd64.deb Checksums-Sha256: fe76aea22d27d3ff11267ac5f67357c5d56b7e5f587635ff4a8f52c7df864aaf 1435 abyss_2.2.4-1.dsc 0b3265506d448cad5bbfe16b7b3cbd88c51a9c02a96ce1ddcd0389836c317d5a 1204110 abyss_2.2.4.orig.tar.gz e781bf3654d94470948269962a6e8bdce5a71d19c56ed37e8bb2f7e5b47bea22 755968 abyss_2.2.4-1.debian.tar.xz 524a0b047249be06dc201585fa13750704f2c07a422fce048e2452d81955bf73 27417440 abyss-dbgsym_2.2.4-1_amd64.deb 64b004cdd8da760490ff26559bfc9acae5ee8e88622ca3312c0f15f98ce571d0 7640 abyss_2.2.4-1_amd64.buildinfo f2d6ea59c9fae0172b7aca3067f943e5b628e3ce8077c7ed97380c77f2c4ae09 3006744 abyss_2.2.4-1_amd64.deb Files: ff597d261f3516e703450b25829f9b42 1435 science optional abyss_2.2.4-1.dsc 4988af5a801864ef04a7fdf5d171e75c 1204110 science optional abyss_2.2.4.orig.tar.gz f56f2fc3c30202b97526bb7c53611e89 755968 science optional abyss_2.2.4-1.debian.tar.xz 9f5abd7da19aea781f00455c4bbc7ee4 27417440 debug optional abyss-dbgsym_2.2.4-1_amd64.deb 8443fecd1c8f39ff2e5fa95a065cc3e0 7640 science optional abyss_2.2.4-1_amd64.buildinfo e4b67538a89aa89e91328335daa6906d 3006744 science optional abyss_2.2.4-1_amd64.deb /<>/abyss_2.2.4-1_amd64.changes.new could not be renamed to /<>/abyss_2.2.4-1_amd64.changes: Illegal seek Distribution field may be wrong!!! +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: abyss Binary: abyss abyss-dbgsym Architecture: amd64 source Version: 2.2.4-1 Checksums-Md5: ff597d261f3516e703450b25829f9b42 1435 abyss_2.2.4-1.dsc 9f5abd7da19aea781f00455c4bbc7ee4 27417440 abyss-dbgsym_2.2.4-1_amd64.deb e4b67538a89aa89e91328335daa6906d 3006744 abyss_2.2.4-1_amd64.deb Checksums-Sha1: c9ce93cbd2b53b8e91f2a77e954bedd0fe7d09be 1435 abyss_2.2.4-1.dsc 76febf0e935c03fc0b8dcc60b68f5f30b8fafefa 27417440 abyss-dbgsym_2.2.4-1_amd64.deb 2468885b7a90af58563bc690fb6cebbcb7f3103d 3006744 abyss_2.2.4-1_amd64.deb Checksums-Sha256: fe76aea22d27d3ff11267ac5f67357c5d56b7e5f587635ff4a8f52c7df864aaf 1435 abyss_2.2.4-1.dsc 524a0b047249be06dc201585fa13750704f2c07a422fce048e2452d81955bf73 27417440 abyss-dbgsym_2.2.4-1_amd64.deb f2d6ea59c9fae0172b7aca3067f943e5b628e3ce8077c7ed97380c77f2c4ae09 3006744 abyss_2.2.4-1_amd64.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Fri, 02 Oct 2020 22:55:00 +0000 Build-Path: /<> Build-Tainted-By: usr-local-has-programs Installed-Build-Depends: adduser (= 3.118), autoconf (= 2.69-11.1), automake (= 1:1.16.2-4), autopoint (= 0.19.8.1-10), autotools-dev (= 20180224.1), base-files (= 11), base-passwd (= 3.5.47), bash (= 5.0-7), binutils (= 2.35.1-1), binutils-common (= 2.35.1-1), binutils-x86-64-linux-gnu (= 2.35.1-1), bsdextrautils (= 2.36-3+b1), bsdutils (= 1:2.36-3+b1), build-essential (= 12.8), bzip2 (= 1.0.8-4), coreutils (= 8.32-4+b1), cpp (= 4:10.2.0-1), cpp-10 (= 10.2.0-13), cpp-9 (= 9.3.0-18), dash (= 0.5.10.2-7), debconf (= 1.5.74), debhelper (= 13.2.1), debianutils (= 4.11.2), dh-autoreconf (= 19), dh-strip-nondeterminism (= 1.9.0-1), diffutils (= 1:3.7-3), dpkg (= 1.20.5), dpkg-dev (= 1.20.5), dwz (= 0.13-5), file (= 1:5.38-5), findutils (= 4.7.0-1), g++ (= 4:10.2.0-1), g++-10 (= 10.2.0-13), gcc (= 4:10.2.0-1), gcc-10 (= 10.2.0-13), gcc-10-base (= 10.2.0-13), gcc-9 (= 9.3.0-18), gcc-9-base (= 9.3.0-18), gettext (= 0.19.8.1-10), gettext-base (= 0.19.8.1-10), gfortran-9 (= 9.3.0-18), grep (= 3.4-1), groff-base (= 1.22.4-5), gzip (= 1.10-2), help2man (= 1.47.16), hostname (= 3.23), ibverbs-providers (= 31.0-1), icu-devtools (= 67.1-4), init-system-helpers (= 1.58), intltool-debian (= 0.35.0+20060710.5), libacl1 (= 2.2.53-8), libarchive-zip-perl (= 1.68-1), libasan5 (= 9.3.0-18), libasan6 (= 10.2.0-13), libatomic1 (= 10.2.0-13), libattr1 (= 1:2.4.48-5), libaudit-common (= 1:2.8.5-3), libaudit1 (= 1:2.8.5-3+b1), libbinutils (= 2.35.1-1), libblkid1 (= 2.36-3+b1), libboost-graph-dev (= 1.71.0.3), libboost-graph1.71-dev (= 1.71.0-6+b2), libboost-graph1.71.0 (= 1.71.0-6+b2), libboost-regex1.71-dev (= 1.71.0-6+b2), libboost-regex1.71.0 (= 1.71.0-6+b2), libboost-serialization1.71-dev (= 1.71.0-6+b2), libboost-serialization1.71.0 (= 1.71.0-6+b2), libboost-test1.71-dev (= 1.71.0-6+b2), libboost-test1.71.0 (= 1.71.0-6+b2), libboost1.71-dev (= 1.71.0-6+b2), libbsd0 (= 0.10.0-1), libbz2-1.0 (= 1.0.8-4), libc-bin (= 2.31-3), libc-dev-bin (= 2.31-3), libc6 (= 2.31-3), libc6-dev (= 2.31-3), libcap-ng0 (= 0.7.9-2.2), libcbor0 (= 0.5.0+dfsg-2), libcc1-0 (= 10.2.0-13), libcom-err2 (= 1.45.6-1), libcroco3 (= 0.6.13-1), libcrypt-dev (= 1:4.4.17-1), libcrypt1 (= 1:4.4.17-1), libctf-nobfd0 (= 2.35.1-1), libctf0 (= 2.35.1-1), libdb5.3 (= 5.3.28+dfsg1-0.6), libdebconfclient0 (= 0.254), libdebhelper-perl (= 13.2.1), libdpkg-perl (= 1.20.5), libedit2 (= 3.1-20191231-1), libelf1 (= 0.181-1), libevent-2.1-7 (= 2.1.12-stable-1), libevent-core-2.1-7 (= 2.1.12-stable-1), libevent-dev (= 2.1.12-stable-1), libevent-extra-2.1-7 (= 2.1.12-stable-1), libevent-openssl-2.1-7 (= 2.1.12-stable-1), libevent-pthreads-2.1-7 (= 2.1.12-stable-1), libfabric1 (= 1.11.0-2), libffi7 (= 3.3-4), libfido2-1 (= 1.5.0-2), libfile-stripnondeterminism-perl (= 1.9.0-1), libgcc-10-dev (= 10.2.0-13), libgcc-9-dev (= 9.3.0-18), libgcc-s1 (= 10.2.0-13), libgcrypt20 (= 1.8.6-2), libgdbm-compat4 (= 1.18.1-5.1), libgdbm6 (= 1.18.1-5.1), libgfortran-9-dev (= 9.3.0-18), libgfortran5 (= 10.2.0-13), libglib2.0-0 (= 2.66.0-2), libgmp10 (= 2:6.2.0+dfsg-6), libgomp1 (= 10.2.0-13), libgpg-error0 (= 1.38-2), libgssapi-krb5-2 (= 1.17-10), libhtml-parser-perl (= 3.75-1), libhtml-tagset-perl (= 3.20-4), libhwloc-dev (= 2.3.0+dfsg-1), libhwloc-plugins (= 2.3.0+dfsg-1), libhwloc15 (= 2.3.0+dfsg-1), libibverbs-dev (= 31.0-1), libibverbs1 (= 31.0-1), libicu-dev (= 67.1-4), libicu67 (= 67.1-4), libisl22 (= 0.22.1-1), libitm1 (= 10.2.0-13), libjs-jquery (= 3.5.1+dfsg-4), libjs-jquery-ui (= 1.12.1+dfsg-7), libk5crypto3 (= 1.17-10), libkeyutils1 (= 1.6.1-2), libkrb5-3 (= 1.17-10), libkrb5support0 (= 1.17-10), liblocale-gettext-perl (= 1.07-4), liblsan0 (= 10.2.0-13), libltdl-dev (= 2.4.6-14), libltdl7 (= 2.4.6-14), liblz4-1 (= 1.9.2-2), liblzma5 (= 5.2.4-1+b1), libmagic-mgc (= 1:5.38-5), libmagic1 (= 1:5.38-5), libmount1 (= 2.36-3+b1), libmpc3 (= 1.2.0-1), libmpfr6 (= 4.1.0-3), libnl-3-200 (= 3.4.0-1+b1), libnl-3-dev (= 3.4.0-1+b1), libnl-route-3-200 (= 3.4.0-1+b1), libnl-route-3-dev (= 3.4.0-1+b1), libnuma-dev (= 2.0.12-1+b1), libnuma1 (= 2.0.12-1+b1), libopenmpi-dev (= 4.0.5-5), libopenmpi3 (= 4.0.5-5), libpam-modules (= 1.3.1-5), libpam-modules-bin (= 1.3.1-5), libpam-runtime (= 1.3.1-5), libpam0g (= 1.3.1-5), libpciaccess0 (= 0.16-1), libpcre2-8-0 (= 10.34-7), libpcre3 (= 2:8.39-13), libperl5.30 (= 5.30.3-4), libpipeline1 (= 1.5.3-1), libpmix-dev (= 3.2.0~rc1-4), libpmix2 (= 3.2.0~rc1-4), libpsm-infinipath1 (= 3.3+20.604758e7-6+b1), libpsm2-2 (= 11.2.185-1), libquadmath0 (= 10.2.0-13), librdmacm1 (= 31.0-1), libseccomp2 (= 2.4.4-1), libselinux1 (= 3.1-2), libsemanage-common (= 3.1-1), libsemanage1 (= 3.1-1), libsepol1 (= 3.1-1), libsigsegv2 (= 2.12-2), libsmartcols1 (= 2.36-3+b1), libsparsehash-dev (= 2.0.3-2), libsqlite3-0 (= 3.33.0-1), libsqlite3-dev (= 3.33.0-1), libssl1.1 (= 1.1.1g-1), libstdc++-10-dev (= 10.2.0-13), libstdc++-9-dev (= 9.3.0-18), libstdc++6 (= 10.2.0-13), libsub-override-perl (= 0.09-2), libsystemd0 (= 246.6-1), libtext-markdown-perl (= 1.000031-3), libtext-multimarkdown-perl (= 1.000035-2), libtinfo6 (= 6.2+20200918-1), libtool (= 2.4.6-14), libtsan0 (= 10.2.0-13), libubsan1 (= 10.2.0-13), libuchardet0 (= 0.0.7-1), libucx0 (= 1.9.0~rc1-2), libudev1 (= 246.6-1), libunistring2 (= 0.9.10-4), liburi-perl (= 1.76-2), libuuid1 (= 2.36-3+b1), libx11-6 (= 2:1.6.12-1), libx11-data (= 2:1.6.12-1), libxau6 (= 1:1.0.8-1+b2), libxcb1 (= 1.14-2), libxdmcp6 (= 1:1.1.2-3), libxext6 (= 2:1.3.3-1+b2), libxml2 (= 2.9.10+dfsg-6), libxnvctrl0 (= 450.66-1), libzstd1 (= 1.4.5+dfsg-4), linux-libc-dev (= 5.8.10-1), login (= 1:4.8.1-1), lsb-base (= 11.1.0), m4 (= 1.4.18-4), make (= 4.3-4), man-db (= 2.9.3-2), mawk (= 1.3.4.20200120-2), ncurses-base (= 6.2+20200918-1), ncurses-bin (= 6.2+20200918-1), node-jquery (= 3.5.1+dfsg-4), ocl-icd-libopencl1 (= 2.2.12-4), openmpi-bin (= 4.0.5-5), openmpi-common (= 4.0.5-5), openssh-client (= 1:8.3p1-1), passwd (= 1:4.8.1-1), patch (= 2.7.6-6), perl (= 5.30.3-4), perl-base (= 5.30.3-4), perl-modules-5.30 (= 5.30.3-4), pkg-config (= 0.29.2-1), po-debconf (= 1.0.21), sed (= 4.7-1), sensible-utils (= 0.0.12+nmu1), sysvinit-utils (= 2.96-5), tar (= 1.30+dfsg-7), util-linux (= 2.36-3+b1), xz-utils (= 5.2.4-1+b1), zlib1g (= 1:1.2.11.dfsg-2), zlib1g-dev (= 1:1.2.11.dfsg-2) Environment: DEB_BUILD_OPTIONS="parallel=4" LANG="C" LC_ALL="C.UTF-8" LD_LIBRARY_PATH="/usr/lib/libeatmydata" SOURCE_DATE_EPOCH="1581431985" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ abyss-dbgsym_2.2.4-1_amd64.deb ------------------------------ new Debian package, version 2.0. size 27417440 bytes: control archive=2480 bytes. 2045 bytes, 12 lines control 4534 bytes, 43 lines md5sums Package: abyss-dbgsym Source: abyss Version: 2.2.4-1 Auto-Built-Package: debug-symbols Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 28486 Depends: abyss (= 2.2.4-1) Section: debug Priority: optional Description: debug symbols for abyss Build-Ids: 03c9afcf32452487c5d7f425af56ed9968197648 0e4646c23fcd9f10943a223249e15a429378d0d8 16e637366a18fb4b471d5c08f461455cc9569204 183206649506a02e8c04c95ad08756acecd73e3a 2874fc72bb17459db2f29107a4bc3ba58546c756 2bc454b0434b4ff949425162f40176f9487a0676 2ecda7713db1378f8d46eb4d7976a62b3fe932e9 39b32407cf32544ce1d2899c4d1fff791fdf8997 46000c8b29c94d037039da36945136214583ccab 4abd59840964916ccfccf824007b1259082a2f0b 4b21bf22f1f41580748f73e0ec0e114939589f10 502d77533f2a2fb9eb01af6e39161bde53eeb49c 529911a30fb242cf808e3d77b4c813ce0c33f875 57dfdd4b413656ef3f0776ed7bd8fc38c8aa83f5 64b903651fc0af97ca81d6126772033ca4a98955 64bae5426b6bc90802bcedc50652124ad899d536 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./usr/lib/debug/.build-id/f7/edc19dec3b8c1721d768bca965428284222212.debug drwxr-xr-x root/root 0 2020-02-11 14:39 ./usr/lib/debug/.build-id/f9/ -rw-r--r-- root/root 252440 2020-02-11 14:39 ./usr/lib/debug/.build-id/f9/d65d13ab32909bda6d70f9e6b9aa6436249666.debug drwxr-xr-x root/root 0 2020-02-11 14:39 ./usr/lib/debug/.dwz/ drwxr-xr-x root/root 0 2020-02-11 14:39 ./usr/lib/debug/.dwz/x86_64-linux-gnu/ -rw-r--r-- root/root 1014792 2020-02-11 14:39 ./usr/lib/debug/.dwz/x86_64-linux-gnu/abyss.debug drwxr-xr-x root/root 0 2020-02-11 14:39 ./usr/share/ drwxr-xr-x root/root 0 2020-02-11 14:39 ./usr/share/doc/ lrwxrwxrwx root/root 0 2020-02-11 14:39 ./usr/share/doc/abyss-dbgsym -> abyss abyss_2.2.4-1_amd64.deb ----------------------- new Debian package, version 2.0. size 3006744 bytes: control archive=2676 bytes. 705 bytes, 14 lines control 4907 bytes, 78 lines md5sums Package: abyss Version: 2.2.4-1 Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 9004 Depends: make, libc6 (>= 2.29), libgcc-s1 (>= 3.0), libgomp1 (>= 4.9), libopenmpi3 (>= 4.0.5), libsqlite3-0 (>= 3.5.9), libstdc++6 (>= 9), perl:any, bsdmainutils, openmpi-common, openmpi-bin Section: science Priority: optional Homepage: https://github.com/bcgsc/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 2020-02-11 14:39 ./ drwxr-xr-x root/root 0 2020-02-11 14:39 ./usr/ drwxr-xr-x root/root 0 2020-02-11 14:39 ./usr/bin/ -rwxr-xr-x root/root 141664 2020-02-11 14:39 ./usr/bin/DistanceEst -rwxr-xr-x root/root 129352 2020-02-11 14:39 ./usr/bin/abyss-fixmate -rwxr-xr-x root/root 22460 2020-02-11 14:39 ./usr/bin/abyss-pe drwxr-xr-x root/root 0 2020-02-11 14:39 ./usr/lib/ drwxr-xr-x root/root 0 2020-02-11 14:39 ./usr/lib/abyss/ -rwxr-xr-x root/root 256368 2020-02-11 14:39 ./usr/lib/abyss/ABYSS -rwxr-xr-x root/root 309616 2020-02-11 14:39 ./usr/lib/abyss/ABYSS-P -rwxr-xr-x root/root 170328 2020-02-11 14:39 ./usr/lib/abyss/AdjList -rwxr-xr-x root/root 76112 2020-02-11 14:39 ./usr/lib/abyss/Consensus -rwxr-xr-x root/root 96608 2020-02-11 14:39 ./usr/lib/abyss/DAssembler -rwxr-xr-x root/root 141664 2020-02-11 14:39 ./usr/lib/abyss/DistanceEst -rwxr-xr-x root/root 141664 2020-02-11 14:39 ./usr/lib/abyss/DistanceEst-ssq -rwxr-xr-x root/root 182624 2020-02-11 14:39 ./usr/lib/abyss/KAligner -rwxr-xr-x root/root 223592 2020-02-11 14:39 ./usr/lib/abyss/MergeContigs -rwxr-xr-x root/root 190800 2020-02-11 14:39 ./usr/lib/abyss/MergePaths -rwxr-xr-x root/root 186720 2020-02-11 14:39 ./usr/lib/abyss/Overlap -rwxr-xr-x root/root 100672 2020-02-11 14:39 ./usr/lib/abyss/ParseAligns -rwxr-xr-x root/root 342368 2020-02-11 14:39 ./usr/lib/abyss/PathConsensus -rwxr-xr-x root/root 178496 2020-02-11 14:39 ./usr/lib/abyss/PathOverlap -rwxr-xr-x root/root 190816 2020-02-11 14:39 ./usr/lib/abyss/PopBubbles -rwxr-xr-x root/root 174432 2020-02-11 14:39 ./usr/lib/abyss/SimpleGraph -rwxr-xr-x root/root 186704 2020-02-11 14:39 ./usr/lib/abyss/abyss-align -rwxr-xr-x root/root 317896 2020-02-11 14:39 ./usr/lib/abyss/abyss-bloom -rwxr-xr-x root/root 342440 2020-02-11 14:39 ./usr/lib/abyss/abyss-bloom-dbg -rwxr-xr-x root/root 6491 2020-02-11 14:39 ./usr/lib/abyss/abyss-bloom-dist.mk -rwxr-xr-x root/root 1135 2020-02-11 14:39 ./usr/lib/abyss/abyss-bowtie -rwxr-xr-x root/root 1192 2020-02-11 14:39 ./usr/lib/abyss/abyss-bowtie2 -rwxr-xr-x root/root 1208 2020-02-11 14:39 ./usr/lib/abyss/abyss-bwa -rwxr-xr-x root/root 1454 2020-02-11 14:39 ./usr/lib/abyss/abyss-bwamem -rwxr-xr-x root/root 1362 2020-02-11 14:39 ./usr/lib/abyss/abyss-bwasw -rwxr-xr-x root/root 67904 2020-02-11 14:39 ./usr/lib/abyss/abyss-db-csv -rwxr-xr-x root/root 703 2020-02-11 14:39 ./usr/lib/abyss/abyss-db-txt -rwxr-xr-x root/root 2739 2020-02-11 14:39 ./usr/lib/abyss/abyss-dida -rwxr-xr-x root/root 80216 2020-02-11 14:39 ./usr/lib/abyss/abyss-fac -rwxr-xr-x root/root 2058 2020-02-11 14:39 ./usr/lib/abyss/abyss-fatoagp -rwxr-xr-x root/root 170336 2020-02-11 14:39 ./usr/lib/abyss/abyss-filtergraph -rwxr-xr-x root/root 129352 2020-02-11 14:39 ./usr/lib/abyss/abyss-fixmate -rwxr-xr-x root/root 129352 2020-02-11 14:39 ./usr/lib/abyss/abyss-fixmate-ssq -rwxr-xr-x root/root 96608 2020-02-11 14:39 ./usr/lib/abyss/abyss-gapfill -rwxr-xr-x root/root 80192 2020-02-11 14:39 ./usr/lib/abyss/abyss-gc -rwxr-xr-x root/root 88392 2020-02-11 14:39 ./usr/lib/abyss/abyss-index -rwxr-xr-x root/root 92488 2020-02-11 14:39 ./usr/lib/abyss/abyss-junction -rwxr-xr-x root/root 39 2020-02-11 14:39 ./usr/lib/abyss/abyss-kaligner -rwxr-xr-x root/root 125256 2020-02-11 14:39 ./usr/lib/abyss/abyss-layout -rwxr-xr-x root/root 92496 2020-02-11 14:39 ./usr/lib/abyss/abyss-longseqdist -rwxr-xr-x root/root 170328 2020-02-11 14:39 ./usr/lib/abyss/abyss-map -rwxr-xr-x root/root 174424 2020-02-11 14:39 ./usr/lib/abyss/abyss-map-ssq -rwxr-xr-x root/root 80232 2020-02-11 14:39 ./usr/lib/abyss/abyss-mergepairs -rwxr-xr-x root/root 190824 2020-02-11 14:39 ./usr/lib/abyss/abyss-overlap -rwxr-xr-x root/root 276856 2020-02-11 14:39 ./usr/lib/abyss/abyss-paired-dbg -rwxr-xr-x root/root 317808 2020-02-11 14:39 ./usr/lib/abyss/abyss-paired-dbg-mpi -rwxr-xr-x root/root 22460 2020-02-11 14:39 ./usr/lib/abyss/abyss-pe -rwxr-xr-x root/root 4501 2020-02-11 14:39 ./usr/lib/abyss/abyss-samtoafg -rwxr-xr-x root/root 231768 2020-02-11 14:39 ./usr/lib/abyss/abyss-scaffold -rwxr-xr-x root/root 215480 2020-02-11 14:39 ./usr/lib/abyss/abyss-sealer -rwxr-xr-x root/root 671 2020-02-11 14:39 ./usr/lib/abyss/abyss-stack-size -rwxr-xr-x root/root 209 2020-02-11 14:39 ./usr/lib/abyss/abyss-tabtomd -rwxr-xr-x root/root 162120 2020-02-11 14:39 ./usr/lib/abyss/abyss-todot -rwxr-xr-x root/root 67928 2020-02-11 14:39 ./usr/lib/abyss/abyss-tofastq -rwxr-xr-x root/root 240088 2020-02-11 14:39 ./usr/lib/abyss/konnector -rwxr-xr-x root/root 76128 2020-02-11 14:39 ./usr/lib/abyss/logcounter drwxr-xr-x root/root 0 2020-02-11 14:39 ./usr/share/ drwxr-xr-x root/root 0 2020-02-11 14:39 ./usr/share/doc-base/ -rw-r--r-- root/root 226 2019-08-08 14:47 ./usr/share/doc-base/abyss-flowcharts drwxr-xr-x root/root 0 2020-02-11 14:39 ./usr/share/doc/ drwxr-xr-x root/root 0 2020-02-11 14:39 ./usr/share/doc/abyss/ -rw-r--r-- root/root 556 2020-02-11 14:39 ./usr/share/doc/abyss/CITATION.bib -rw-r--r-- root/root 1861 2020-02-11 14:39 ./usr/share/doc/abyss/CITATION.md -rw-r--r-- root/root 31249 2020-02-11 14:39 ./usr/share/doc/abyss/README.html -rw-r--r-- root/root 9171 2020-02-11 14:39 ./usr/share/doc/abyss/README.md.gz -rw-r--r-- root/root 182 2019-08-08 14:47 ./usr/share/doc/abyss/README.test -rw-r--r-- root/root 3496 2020-02-11 14:39 ./usr/share/doc/abyss/changelog.Debian.gz -rw-r--r-- root/root 15647 2020-01-30 18:48 ./usr/share/doc/abyss/changelog.gz -rw-r--r-- root/root 7012 2020-01-30 19:54 ./usr/share/doc/abyss/copyright -rw-r--r-- root/root 66778 2020-02-11 14:39 ./usr/share/doc/abyss/flowchart.pdf.gz -rw-r--r-- root/root 22664 2020-02-11 14:39 ./usr/share/doc/abyss/flowchart_simplified.pdf.gz -rw-r--r-- root/root 672 2019-08-08 14:47 ./usr/share/doc/abyss/run-unit-test drwxr-xr-x root/root 0 2020-02-11 14:39 ./usr/share/doc/abyss/test-data/ -rw-r--r-- root/root 743013 2019-08-08 14:47 ./usr/share/doc/abyss/test-data/reads1.fastq.gz -rw-r--r-- root/root 743377 2019-08-08 14:47 ./usr/share/doc/abyss/test-data/reads2.fastq.gz drwxr-xr-x root/root 0 2020-02-11 14:39 ./usr/share/man/ drwxr-xr-x root/root 0 2020-02-11 14:39 ./usr/share/man/man1/ -rw-r--r-- root/root 1200 2020-02-11 14:39 ./usr/share/man/man1/ABYSS.1.gz -rw-r--r-- root/root 1023 2020-02-11 14:39 ./usr/share/man/man1/DistanceEst.1.gz -rw-r--r-- root/root 792 2020-02-11 14:39 ./usr/share/man/man1/abyss-fixmate.1.gz -rw-r--r-- root/root 3562 2020-02-11 14:39 ./usr/share/man/man1/abyss-pe.1.gz -rw-r--r-- root/root 408 2020-02-11 14:39 ./usr/share/man/man1/abyss-tofastq.1.gz +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: full Build-Space: 927916 Build-Time: 370 Distribution: sid Host Architecture: amd64 Install-Time: 21 Job: /srv/debomatic/incoming/abyss_2.2.4-1.dsc Machine Architecture: amd64 Package: abyss Package-Time: 396 Source-Version: 2.2.4-1 Space: 927916 Status: successful Version: 2.2.4-1 -------------------------------------------------------------------------------- Finished at 2020-10-02T22:55:01Z Build needed 00:06:36, 927916k disk space