sbuild (Debian sbuild) 0.85.10 (30 May 2024) on carme.larted.org.uk +==============================================================================+ | abyss 2.3.8-1 (amd64) Sat, 03 Aug 2024 11:09:09 +0000 | +==============================================================================+ Package: abyss Version: 2.3.8-1 Source Version: 2.3.8-1 Distribution: perl-5.40-throwaway Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: full I: NOTICE: Log filtering will replace 'var/run/schroot/mount/perl-5.40-amd64-debomatic-5a89ef2e-bed2-4120-8aa3-8616b474863a' with '<>' +------------------------------------------------------------------------------+ | Chroot Setup Commands | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup abyss_2.3.8-1 perl-5.40-throwaway amd64 -------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup abyss_2.3.8-1 perl-5.40-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- I: NOTICE: Log filtering will replace 'build/abyss-ZwQfBi/resolver-li8tRu' with '<>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Get:1 file:/srv/reprepro perl-5.40 InRelease [3042 B] Get:2 http://deb.debian.org/debian unstable InRelease [198 kB] Get:1 file:/srv/reprepro perl-5.40 InRelease [3042 B] Get:3 http://deb.debian.org/debian unstable/main amd64 Packages.diff/Index [63.6 kB] Get:4 http://deb.debian.org/debian unstable/main amd64 Packages T-2024-08-03-0808.05-F-2024-08-03-0808.05.pdiff [10.5 kB] Get:4 http://deb.debian.org/debian unstable/main amd64 Packages T-2024-08-03-0808.05-F-2024-08-03-0808.05.pdiff [10.5 kB] Get:5 http://localhost:3142/debian sid InRelease [198 kB] Get:6 http://localhost:3142/debian sid/main Sources.diff/Index [63.6 kB] Get:7 http://localhost:3142/debian sid/main Sources T-2024-08-03-0808.05-F-2024-08-03-0808.05.pdiff [16.0 kB] Get:7 http://localhost:3142/debian sid/main Sources T-2024-08-03-0808.05-F-2024-08-03-0808.05.pdiff [16.0 kB] Fetched 550 kB in 7s (82.7 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_2.3.8-1.dsc exists in /srv/debomatic/incoming; copying to chroot I: NOTICE: Log filtering will replace 'build/abyss-ZwQfBi/abyss-2.3.8' with '<>' I: NOTICE: Log filtering will replace 'build/abyss-ZwQfBi' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), architecture-is-64-bit, libboost-graph-dev, libbtllib-dev, libopenmpi-dev, libsparsehash-dev, libtext-multimarkdown-perl, libsqlite3-dev, pkgconf, help2man, debhelper, build-essential, fakeroot Filtered Build-Depends: debhelper-compat (= 13), architecture-is-64-bit, libboost-graph-dev, libbtllib-dev, libopenmpi-dev, libsparsehash-dev, libtext-multimarkdown-perl, libsqlite3-dev, pkgconf, help2man, debhelper, 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 [609 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [794 B] Get:5 copy:/<>/apt_archive ./ Packages [817 B] Fetched 2220 B in 0s (0 B/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: architecture-properties autoconf automake autopoint autotools-dev bsdextrautils debhelper dh-autoreconf dh-strip-nondeterminism dwz fakeroot file gettext gettext-base gfortran-13 gfortran-13-x86-64-linux-gnu groff-base help2man ibverbs-providers icu-devtools intltool-debian libamd-comgr2 libamdhip64-5 libarchive-zip-perl libboost-graph-dev libboost-graph1.83-dev libboost-graph1.83.0 libboost-regex1.83-dev libboost-regex1.83.0 libboost-serialization1.83-dev libboost-serialization1.83.0 libboost-test1.83-dev libboost-test1.83.0 libboost1.83-dev libbrotli1 libbtllib-dev libcbor0.10 libcom-err2 libcpptoml-dev libcurl3t64-gnutls libdebhelper-perl libdeflate0 libdivsufsort-dev libdivsufsort3 libdrm-amdgpu1 libdrm-common libdrm2 libedit2 libelf1t64 libevent-2.1-7t64 libevent-core-2.1-7t64 libevent-dev libevent-extra-2.1-7t64 libevent-openssl-2.1-7t64 libevent-pthreads-2.1-7t64 libfabric1 libfakeroot libfido2-1 libfile-stripnondeterminism-perl libgfortran-13-dev libgfortran5 libgssapi-krb5-2 libhsa-runtime64-1 libhsakmt1 libhtml-parser-perl libhtml-tagset-perl libhts3t64 libhtscodecs2 libhwloc-dev libhwloc-plugins libhwloc15 libibmad5 libibumad3 libibverbs-dev libibverbs1 libicu-dev libicu72 libjs-d3 libjs-jquery libjs-jquery-ui libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libllvm17t64 liblocale-gettext-perl libltdl-dev libltdl7 libmagic-mgc libmagic1t64 libmunge2 libncurses6 libnghttp2-14 libnghttp3-9 libngtcp2-16 libngtcp2-crypto-gnutls8 libnl-3-200 libnl-3-dev libnl-route-3-200 libnl-route-3-dev libnuma-dev libnuma1 libopenmpi-dev libopenmpi3t64 libpciaccess0 libpipeline1 libpkgconf3 libpmix-dev libpmix2t64 libpsl5t64 libpsm-infinipath1 libpsm2-2 librdmacm1t64 librtmp1 libsdsl-dev libsdsl3 libsparsehash-dev libsqlite3-dev libssh2-1t64 libtext-markdown-perl libtext-multimarkdown-perl libtool libuchardet0 libucx0 liburi-perl libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxml2 libxnvctrl0 libz3-4 m4 man-db ocl-icd-libopencl1 openmpi-bin openmpi-common openssh-client pkgconf pkgconf-bin po-debconf samtools sensible-utils wget zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc dh-make gettext-doc libasprintf-dev libgettextpo-dev gfortran-13-multilib gfortran-13-doc libcoarrays-dev groff graphviz libboost1.83-doc libboost-atomic1.83-dev libboost-chrono1.83-dev libboost-container1.83-dev libboost-context1.83-dev libboost-contract1.83-dev libboost-coroutine1.83-dev libboost-date-time1.83-dev libboost-exception1.83-dev libboost-fiber1.83-dev libboost-filesystem1.83-dev libboost-graph-parallel1.83-dev libboost-iostreams1.83-dev libboost-json1.83-dev libboost-locale1.83-dev libboost-log1.83-dev libboost-math1.83-dev libboost-mpi-python1.83-dev libboost-mpi1.83-dev libboost-nowide1.83-dev libboost-numpy1.83-dev libboost-program-options1.83-dev libboost-python1.83-dev libboost-random1.83-dev libboost-stacktrace1.83-dev libboost-system1.83-dev libboost-thread1.83-dev libboost-timer1.83-dev libboost-type-erasure1.83-dev libboost-url1.83-dev libboost-wave1.83-dev libboost1.83-tools-dev libmpfrc++-dev libntl-dev krb5-doc krb5-user libdata-dump-perl libhwloc-contrib-plugins icu-doc libjs-jquery-ui-docs libtool-doc openmpi-doc pciutils sqlite3-doc gcj-jdk libbusiness-isbn-perl libregexp-ipv6-perl libwww-perl m4-doc apparmor less www-browser opencl-icd gfortran | fortran-compiler keychain libpam-ssh monkeysphere ssh-askpass libmail-box-perl cwltool Recommended packages: ca-certificates libarchive-cpio-perl libhttp-message-perl javascript-common krb5-locales libgpm2 libcoarrays-openmpi-dev publicsuffix xauth libmail-sendmail-perl The following NEW packages will be installed: architecture-properties autoconf automake autopoint autotools-dev bsdextrautils debhelper dh-autoreconf dh-strip-nondeterminism dwz fakeroot file gettext gettext-base gfortran-13 gfortran-13-x86-64-linux-gnu groff-base help2man ibverbs-providers icu-devtools intltool-debian libamd-comgr2 libamdhip64-5 libarchive-zip-perl libboost-graph-dev libboost-graph1.83-dev libboost-graph1.83.0 libboost-regex1.83-dev libboost-regex1.83.0 libboost-serialization1.83-dev libboost-serialization1.83.0 libboost-test1.83-dev libboost-test1.83.0 libboost1.83-dev libbrotli1 libbtllib-dev libcbor0.10 libcom-err2 libcpptoml-dev libcurl3t64-gnutls libdebhelper-perl libdeflate0 libdivsufsort-dev libdivsufsort3 libdrm-amdgpu1 libdrm-common libdrm2 libedit2 libelf1t64 libevent-2.1-7t64 libevent-core-2.1-7t64 libevent-dev libevent-extra-2.1-7t64 libevent-openssl-2.1-7t64 libevent-pthreads-2.1-7t64 libfabric1 libfakeroot libfido2-1 libfile-stripnondeterminism-perl libgfortran-13-dev libgfortran5 libgssapi-krb5-2 libhsa-runtime64-1 libhsakmt1 libhtml-parser-perl libhtml-tagset-perl libhts3t64 libhtscodecs2 libhwloc-dev libhwloc-plugins libhwloc15 libibmad5 libibumad3 libibverbs-dev libibverbs1 libicu-dev libicu72 libjs-d3 libjs-jquery libjs-jquery-ui libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libllvm17t64 liblocale-gettext-perl libltdl-dev libltdl7 libmagic-mgc libmagic1t64 libmunge2 libncurses6 libnghttp2-14 libnghttp3-9 libngtcp2-16 libngtcp2-crypto-gnutls8 libnl-3-200 libnl-3-dev libnl-route-3-200 libnl-route-3-dev libnuma-dev libnuma1 libopenmpi-dev libopenmpi3t64 libpciaccess0 libpipeline1 libpkgconf3 libpmix-dev libpmix2t64 libpsl5t64 libpsm-infinipath1 libpsm2-2 librdmacm1t64 librtmp1 libsdsl-dev libsdsl3 libsparsehash-dev libsqlite3-dev libssh2-1t64 libtext-markdown-perl libtext-multimarkdown-perl libtool libuchardet0 libucx0 liburi-perl libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxml2 libxnvctrl0 libz3-4 m4 man-db ocl-icd-libopencl1 openmpi-bin openmpi-common openssh-client pkgconf pkgconf-bin po-debconf samtools sbuild-build-depends-main-dummy sensible-utils wget zlib1g-dev 0 upgraded, 148 newly installed, 0 to remove and 0 not upgraded. Need to get 135 MB/135 MB of archives. After this operation, 690 MB of additional disk space will be used. Get:1 file:/srv/reprepro perl-5.40/main amd64 liblocale-gettext-perl amd64 1.07-7+b1 [15.3 kB] Get:2 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [972 B] Get:3 file:/srv/reprepro perl-5.40/main amd64 libhtml-parser-perl amd64 3.82-1+b1 [99.5 kB] Get:4 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get:5 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3 [314 kB] Get:6 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3 [105 kB] Get:7 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.45-3 [42.9 kB] Get:8 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.22.5-2 [200 kB] Get:9 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b1 [68.8 kB] Get:10 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-5 [1181 kB] Get:11 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40.2-1 [96.1 kB] Get:12 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.7-2 [38.0 kB] Get:13 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.12.1-2 [1411 kB] Get:14 http://deb.debian.org/debian unstable/main amd64 libedit2 amd64 3.1-20240517-1 [93.3 kB] Get:15 http://deb.debian.org/debian unstable/main amd64 libcbor0.10 amd64 0.10.2-1.2 [28.2 kB] Get:16 http://deb.debian.org/debian unstable/main amd64 libfido2-1 amd64 1.15.0-1 [78.5 kB] Get:17 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.21.3-3 [32.5 kB] Get:18 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.1-1 [22.9 kB] Get:19 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.21.3-3 [79.9 kB] Get:20 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-3 [8952 B] Get:21 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.21.3-3 [324 kB] Get:22 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.21.3-3 [136 kB] Get:23 http://deb.debian.org/debian unstable/main amd64 openssh-client amd64 1:9.8p1-2 [964 kB] Get:24 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.21.2-1.1 [56.8 kB] Get:25 http://deb.debian.org/debian unstable/main amd64 wget amd64 1.24.5-2+b1 [981 kB] Get:26 http://deb.debian.org/debian unstable/main amd64 architecture-properties amd64 0.1.1+b1 [1888 B] Get:27 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-4 [287 kB] Get:28 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.71-3 [332 kB] Get:29 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get:30 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get:31 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.22.5-2 [723 kB] Get:32 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.16 [88.6 kB] Get:33 http://deb.debian.org/debian unstable/main amd64 libtool all 2.4.7-7 [517 kB] Get:34 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get:35 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get:36 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get:37 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get:38 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.191-2 [188 kB] Get:39 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get:40 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-5 [9396 kB] Get:41 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg-3+b1 [671 kB] Get:42 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.22.5-2 [1601 kB] Get:43 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get:44 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get:45 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.16 [891 kB] Get:46 http://deb.debian.org/debian unstable/main amd64 libfakeroot amd64 1.35.1-1 [28.6 kB] Get:47 http://deb.debian.org/debian unstable/main amd64 fakeroot amd64 1.35.1-1 [74.5 kB] Get:48 http://deb.debian.org/debian unstable/main amd64 libgfortran5 amd64 14.2.0-1 [837 kB] Get:49 http://deb.debian.org/debian unstable/main amd64 libgfortran-13-dev amd64 13.3.0-4 [847 kB] Get:50 http://deb.debian.org/debian unstable/main amd64 gfortran-13-x86-64-linux-gnu amd64 13.3.0-4 [10.6 MB] Get:51 http://deb.debian.org/debian unstable/main amd64 gfortran-13 amd64 13.3.0-4 [14.1 kB] Get:52 http://deb.debian.org/debian unstable/main amd64 help2man amd64 1.49.3 [198 kB] Get:53 http://deb.debian.org/debian unstable/main amd64 libnl-3-200 amd64 3.7.0-0.3 [59.0 kB] Get:54 http://deb.debian.org/debian unstable/main amd64 libnl-route-3-200 amd64 3.7.0-0.3 [181 kB] Get:55 http://deb.debian.org/debian unstable/main amd64 libibverbs1 amd64 52.0-2 [61.6 kB] Get:56 http://deb.debian.org/debian unstable/main amd64 ibverbs-providers amd64 52.0-2 [343 kB] Get:57 http://deb.debian.org/debian unstable/main amd64 icu-devtools amd64 72.1-5 [207 kB] Get:58 http://deb.debian.org/debian unstable/main amd64 libz3-4 amd64 4.8.12-3.1+b2 [7346 kB] Get:59 http://deb.debian.org/debian unstable/main amd64 libllvm17t64 amd64 1:17.0.6-15 [23.6 MB] Get:60 http://deb.debian.org/debian unstable/main amd64 libamd-comgr2 amd64 6.0+git20231212.4510c28+dfsg-3+b1 [13.0 MB] Get:61 http://deb.debian.org/debian unstable/main amd64 libdrm-common all 2.4.122-1 [7992 B] Get:62 http://deb.debian.org/debian unstable/main amd64 libdrm2 amd64 2.4.122-1 [38.7 kB] Get:63 http://deb.debian.org/debian unstable/main amd64 libdrm-amdgpu1 amd64 2.4.122-1 [22.2 kB] Get:64 http://deb.debian.org/debian unstable/main amd64 libnuma1 amd64 2.0.18-1 [21.9 kB] Get:65 http://deb.debian.org/debian unstable/main amd64 libhsakmt1 amd64 5.7.0-1 [60.7 kB] Get:66 http://deb.debian.org/debian unstable/main amd64 libhsa-runtime64-1 amd64 5.7.1-2 [504 kB] Get:67 http://deb.debian.org/debian unstable/main amd64 libamdhip64-5 amd64 5.7.1-4 [8770 kB] Get:68 http://deb.debian.org/debian unstable/main amd64 libboost1.83-dev amd64 1.83.0-3.1 [10.6 MB] Get:69 http://deb.debian.org/debian unstable/main amd64 libboost-graph1.83.0 amd64 1.83.0-3.1 [359 kB] Get:70 http://deb.debian.org/debian unstable/main amd64 libboost-regex1.83.0 amd64 1.83.0-3.1 [328 kB] Get:71 http://deb.debian.org/debian unstable/main amd64 libicu-dev amd64 72.1-5 [10.4 MB] Get:72 http://deb.debian.org/debian unstable/main amd64 libboost-regex1.83-dev amd64 1.83.0-3.1 [346 kB] Get:73 http://deb.debian.org/debian unstable/main amd64 libboost-serialization1.83.0 amd64 1.83.0-3.1 [333 kB] Get:74 http://deb.debian.org/debian unstable/main amd64 libboost-serialization1.83-dev amd64 1.83.0-3.1 [372 kB] Get:75 http://deb.debian.org/debian unstable/main amd64 libboost-test1.83.0 amd64 1.83.0-3.1 [471 kB] Get:76 http://deb.debian.org/debian unstable/main amd64 libboost-test1.83-dev amd64 1.83.0-3.1 [541 kB] Get:77 http://deb.debian.org/debian unstable/main amd64 libboost-graph1.83-dev amd64 1.83.0-3.1 [382 kB] Get:78 http://deb.debian.org/debian unstable/main amd64 libboost-graph-dev amd64 1.83.0.2+b2 [3700 B] Get:79 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b4 [300 kB] Get:80 http://deb.debian.org/debian unstable/main amd64 libcpptoml-dev all 0.1.1-3 [180 kB] Get:81 http://deb.debian.org/debian unstable/main amd64 libdivsufsort3 amd64 2.0.1-6 [45.6 kB] Get:82 http://deb.debian.org/debian unstable/main amd64 libdivsufsort-dev amd64 2.0.1-6 [18.8 kB] Get:83 http://deb.debian.org/debian unstable/main amd64 libjs-d3 all 3.5.17-4 [132 kB] Get:84 http://deb.debian.org/debian unstable/main amd64 libsdsl3 amd64 2.1.1+dfsg-5 [214 kB] Get:85 http://deb.debian.org/debian unstable/main amd64 libsdsl-dev amd64 2.1.1+dfsg-5 [451 kB] Get:86 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.62.1-2 [74.9 kB] Get:87 http://deb.debian.org/debian unstable/main amd64 libnghttp3-9 amd64 1.4.0-1 [63.1 kB] Get:88 http://deb.debian.org/debian unstable/main amd64 libngtcp2-16 amd64 1.6.0-1 [122 kB] Get:89 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls8 amd64 1.6.0-1 [19.6 kB] Get:90 http://deb.debian.org/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b4 [58.5 kB] Get:91 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.0-7 [216 kB] Get:92 http://deb.debian.org/debian unstable/main amd64 libcurl3t64-gnutls amd64 8.9.1-1 [470 kB] Get:93 http://deb.debian.org/debian unstable/main amd64 libdeflate0 amd64 1.20-1 [46.0 kB] Get:94 http://deb.debian.org/debian unstable/main amd64 libhtscodecs2 amd64 1.6.0-1+b1 [93.0 kB] Get:95 http://deb.debian.org/debian unstable/main amd64 libhts3t64 amd64 1.20+ds-1 [452 kB] Get:96 http://deb.debian.org/debian unstable/main amd64 libncurses6 amd64 6.5-2 [104 kB] Get:97 http://deb.debian.org/debian unstable/main amd64 samtools amd64 1.20-3 [653 kB] Get:98 http://deb.debian.org/debian unstable/main amd64 libbtllib-dev amd64 1.4.10+dfsg-1 [173 kB] Get:99 http://deb.debian.org/debian unstable/main amd64 libevent-2.1-7t64 amd64 2.1.12-stable-10 [181 kB] Get:100 http://deb.debian.org/debian unstable/main amd64 libevent-core-2.1-7t64 amd64 2.1.12-stable-10 [131 kB] Get:101 http://deb.debian.org/debian unstable/main amd64 libevent-extra-2.1-7t64 amd64 2.1.12-stable-10 [107 kB] Get:102 http://deb.debian.org/debian unstable/main amd64 libevent-pthreads-2.1-7t64 amd64 2.1.12-stable-10 [53.9 kB] Get:103 http://deb.debian.org/debian unstable/main amd64 libevent-openssl-2.1-7t64 amd64 2.1.12-stable-10 [60.8 kB] Get:104 http://deb.debian.org/debian unstable/main amd64 libevent-dev amd64 2.1.12-stable-10 [305 kB] Get:105 http://deb.debian.org/debian unstable/main amd64 libpsm-infinipath1 amd64 3.3+20.604758e7-6.3 [170 kB] Get:106 http://deb.debian.org/debian unstable/main amd64 libpsm2-2 amd64 11.2.185-2.1 [181 kB] Get:107 http://deb.debian.org/debian unstable/main amd64 librdmacm1t64 amd64 52.0-2 [70.2 kB] Get:108 http://deb.debian.org/debian unstable/main amd64 libfabric1 amd64 1.17.0-3+b1 [628 kB] Get:109 http://deb.debian.org/debian unstable/main amd64 libhtml-tagset-perl all 3.24-1 [14.7 kB] Get:110 http://deb.debian.org/debian unstable/main amd64 liburi-perl all 5.28-1 [98.6 kB] Get:111 http://deb.debian.org/debian unstable/main amd64 libhwloc15 amd64 2.11.0-2 [162 kB] Get:112 http://deb.debian.org/debian unstable/main amd64 libnuma-dev amd64 2.0.18-1 [36.2 kB] Get:113 http://deb.debian.org/debian unstable/main amd64 libltdl7 amd64 2.4.7-7+b1 [393 kB] Get:114 http://deb.debian.org/debian unstable/main amd64 libltdl-dev amd64 2.4.7-7+b1 [164 kB] Get:115 http://deb.debian.org/debian unstable/main amd64 libhwloc-dev amd64 2.11.0-2 [251 kB] Get:116 http://deb.debian.org/debian unstable/main amd64 libpciaccess0 amd64 0.17-3+b1 [51.9 kB] Get:117 http://deb.debian.org/debian unstable/main amd64 libxau6 amd64 1:1.0.9-1+b1 [18.1 kB] Get:118 http://deb.debian.org/debian unstable/main amd64 libxdmcp6 amd64 1:1.1.2-3+b1 [24.3 kB] Get:119 http://deb.debian.org/debian unstable/main amd64 libxcb1 amd64 1.17.0-2 [144 kB] Get:120 http://deb.debian.org/debian unstable/main amd64 libx11-data all 2:1.8.7-1 [328 kB] Get:121 http://deb.debian.org/debian unstable/main amd64 libx11-6 amd64 2:1.8.7-1+b1 [799 kB] Get:122 http://deb.debian.org/debian unstable/main amd64 libxext6 amd64 2:1.3.4-1+b1 [52.9 kB] Get:123 http://deb.debian.org/debian unstable/main amd64 libxnvctrl0 amd64 535.171.04-1 [13.8 kB] Get:124 http://deb.debian.org/debian unstable/main amd64 ocl-icd-libopencl1 amd64 2.3.2-1+b1 [40.3 kB] Get:125 http://deb.debian.org/debian unstable/main amd64 libhwloc-plugins amd64 2.11.0-2 [17.9 kB] Get:126 http://deb.debian.org/debian unstable/main amd64 libibumad3 amd64 52.0-2 [27.7 kB] Get:127 http://deb.debian.org/debian unstable/main amd64 libibmad5 amd64 52.0-2 [43.3 kB] Get:128 http://deb.debian.org/debian unstable/main amd64 libnl-3-dev amd64 3.7.0-0.3 [99.4 kB] Get:129 http://deb.debian.org/debian unstable/main amd64 libnl-route-3-dev amd64 3.7.0-0.3 [199 kB] Get:130 http://deb.debian.org/debian unstable/main amd64 libibverbs-dev amd64 52.0-2 [647 kB] Get:131 http://deb.debian.org/debian unstable/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get:132 http://deb.debian.org/debian unstable/main amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get:133 http://deb.debian.org/debian unstable/main amd64 libmunge2 amd64 0.5.15-4 [19.8 kB] Get:134 http://deb.debian.org/debian unstable/main amd64 libpmix2t64 amd64 5.0.3-2 [658 kB] Get:135 http://deb.debian.org/debian unstable/main amd64 libucx0 amd64 1.17.0+ds-3 [1130 kB] Get:136 http://deb.debian.org/debian unstable/main amd64 libopenmpi3t64 amd64 4.1.6-13.3 [2426 kB] Get:137 http://deb.debian.org/debian unstable/main amd64 openmpi-common all 4.1.6-13.3 [169 kB] Get:138 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1 [919 kB] Get:139 http://deb.debian.org/debian unstable/main amd64 libpmix-dev amd64 5.0.3-2 [3954 kB] Get:140 http://deb.debian.org/debian unstable/main amd64 openmpi-bin amd64 4.1.6-13.3 [226 kB] Get:141 http://deb.debian.org/debian unstable/main amd64 libopenmpi-dev amd64 4.1.6-13.3 [972 kB] Get:142 http://deb.debian.org/debian unstable/main amd64 libpkgconf3 amd64 1.8.1-3 [36.2 kB] Get:143 http://deb.debian.org/debian unstable/main amd64 libsparsehash-dev all 2.0.3-2 [76.8 kB] Get:144 http://deb.debian.org/debian unstable/main amd64 libsqlite3-dev amd64 3.46.0-1 [1096 kB] Get:145 http://deb.debian.org/debian unstable/main amd64 libtext-markdown-perl all 1.000031-4 [32.1 kB] Get:146 http://deb.debian.org/debian unstable/main amd64 libtext-multimarkdown-perl all 1.000035-3 [28.5 kB] Get:147 http://deb.debian.org/debian unstable/main amd64 pkgconf-bin amd64 1.8.1-3 [29.9 kB] Get:148 http://deb.debian.org/debian unstable/main amd64 pkgconf amd64 1.8.1-3 [26.1 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 135 MB in 1s (115 MB/s) Selecting previously unselected package liblocale-gettext-perl. 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Unpacking sbuild-build-depends-main-dummy (0.invalid.0) ... Setting up libhtscodecs2:amd64 (1.6.0-1+b1) ... Setting up libpipeline1:amd64 (1.5.7-2) ... Setting up libtext-markdown-perl (1.000031-4) ... Setting up libpciaccess0:amd64 (0.17-3+b1) ... Setting up libxau6:amd64 (1:1.0.9-1+b1) ... Setting up libxdmcp6:amd64 (1:1.1.2-3+b1) ... Setting up libkeyutils1:amd64 (1.6.3-3) ... Setting up libboost1.83-dev:amd64 (1.83.0-3.1) ... Setting up libxcb1:amd64 (1.17.0-2) ... Setting up libicu72:amd64 (72.1-5) ... Setting up bsdextrautils (2.40.2-1) ... Setting up libmagic-mgc (1:5.45-3) ... Setting up libcbor0.10:amd64 (0.10.2-1.2) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up architecture-properties:amd64 (0.1.1+b1) ... Setting up libhtml-tagset-perl (3.24-1) ... Setting up libboost-regex1.83.0:amd64 (1.83.0-3.1) ... Setting up libdebhelper-perl (13.16) ... Setting up libbrotli1:amd64 (1.1.0-2+b4) ... Setting up libedit2:amd64 (3.1-20240517-1) ... 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Setting up libmunge2:amd64 (0.5.15-4) ... Setting up libsqlite3-dev:amd64 (3.46.0-1) ... Setting up libx11-data (2:1.8.7-1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b4) ... Setting up libcpptoml-dev (0.1.1-3) ... Setting up libncurses6:amd64 (6.5-2) ... Setting up libjs-d3 (3.5.17-4) ... Setting up libhwloc15:amd64 (2.11.0-2) ... Setting up autopoint (0.22.5-2) ... Setting up icu-devtools (72.1-5) ... Setting up pkgconf-bin (1.8.1-3) ... Setting up libk5crypto3:amd64 (1.21.3-3) ... Setting up libltdl7:amd64 (2.4.7-7+b1) ... Setting up libboost-test1.83.0:amd64 (1.83.0-3.1) ... Setting up libgfortran5:amd64 (14.2.0-1) ... Setting up autoconf (2.71-3) ... Setting up libsdsl3:amd64 (2.1.1+dfsg-5) ... Setting up libnghttp3-9:amd64 (1.4.0-1) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1) ... Setting up libnuma1:amd64 (2.0.18-1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up ocl-icd-libopencl1:amd64 (2.3.2-1+b1) ... Setting up libuchardet0:amd64 (0.0.8-1+b1) ... Setting up libnl-3-200:amd64 (3.7.0-0.3) ... Setting up libboost-graph1.83.0:amd64 (1.83.0-3.1) ... Setting up libpsm2-2 (11.2.185-2.1) ... Setting up openmpi-common (4.1.6-13.3) ... Setting up libx11-6:amd64 (2:1.8.7-1+b1) ... Setting up libngtcp2-16:amd64 (1.6.0-1) ... Setting up libkrb5-3:amd64 (1.21.3-3) ... Setting up libevent-core-2.1-7t64:amd64 (2.1.12-stable-10) ... Setting up libpsm-infinipath1 (3.3+20.604758e7-6.3) ... 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 libssh2-1t64:amd64 (1.11.0-7) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up libfido2-1:amd64 (1.15.0-1) ... Setting up libgfortran-13-dev:amd64 (13.3.0-4) ... Setting up libdivsufsort3:amd64 (2.0.1-6) ... Setting up libdrm-common (2.4.122-1) ... Setting up libicu-dev:amd64 (72.1-5) ... Setting up libxml2:amd64 (2.12.7+dfsg-3+b1) ... Setting up liburi-perl (5.28-1) ... Setting up liblocale-gettext-perl (1.07-7+b1) ... Setting up libngtcp2-crypto-gnutls8:amd64 (1.6.0-1) ... Setting up libdivsufsort-dev:amd64 (2.0.1-6) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up gettext (0.22.5-2) ... Setting up libsdsl-dev:amd64 (2.1.1+dfsg-5) ... Setting up wget (1.24.5-2+b1) ... Setting up libtool (2.4.7-7) ... Setting up libevent-pthreads-2.1-7t64:amd64 (2.1.12-stable-10) ... Setting up libevent-openssl-2.1-7t64:amd64 (2.1.12-stable-10) ... Setting up libboost-serialization1.83-dev:amd64 (1.83.0-3.1) ... Setting up libxext6:amd64 (2:1.3.4-1+b1) ... Setting up libboost-test1.83-dev:amd64 (1.83.0-3.1) ... Setting up gfortran-13-x86-64-linux-gnu (13.3.0-4) ... Setting up pkgconf:amd64 (1.8.1-3) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up libnuma-dev:amd64 (2.0.18-1) ... Setting up libnl-route-3-200:amd64 (3.7.0-0.3) ... Setting up libxnvctrl0:amd64 (535.171.04-1) ... Setting up help2man (1.49.3) ... Setting up dh-autoreconf (20) ... Setting up libltdl-dev:amd64 (2.4.7-7+b1) ... Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... Setting up libllvm17t64:amd64 (1:17.0.6-15) ... Setting up gfortran-13 (13.3.0-4) ... Setting up libgssapi-krb5-2:amd64 (1.21.3-3) ... Setting up libboost-regex1.83-dev:amd64 (1.83.0-3.1) ... Setting up libevent-extra-2.1-7t64:amd64 (2.1.12-stable-10) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up libdrm2:amd64 (2.4.122-1) ... Setting up libnl-3-dev:amd64 (3.7.0-0.3) ... Setting up groff-base (1.23.0-5) ... Setting up libhtml-parser-perl:amd64 (3.82-1+b1) ... Setting up libhwloc-dev:amd64 (2.11.0-2) ... Setting up libamd-comgr2:amd64 (6.0+git20231212.4510c28+dfsg-3+b1) ... Setting up libtext-multimarkdown-perl (1.000035-3) ... Setting up libdrm-amdgpu1:amd64 (2.4.122-1) ... Setting up libibverbs1:amd64 (52.0-2) ... Setting up ibverbs-providers:amd64 (52.0-2) ... Setting up openssh-client (1:9.8p1-2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libcurl3t64-gnutls:amd64 (8.9.1-1) ... Setting up libhwloc-plugins:amd64 (2.11.0-2) ... Setting up man-db (2.12.1-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libboost-graph1.83-dev:amd64 (1.83.0-3.1) ... Setting up libnl-route-3-dev:amd64 (3.7.0-0.3) ... Setting up libevent-dev (2.1.12-stable-10) ... Setting up libpmix2t64:amd64 (5.0.3-2) ... Setting up libhts3t64:amd64 (1.20+ds-1) ... Setting up librdmacm1t64:amd64 (52.0-2) ... Setting up libpmix-dev:amd64 (5.0.3-2) ... Setting up libhsakmt1:amd64 (5.7.0-1) ... Setting up libfabric1:amd64 (1.17.0-3+b1) ... Setting up libboost-graph-dev:amd64 (1.83.0.2+b2) ... Setting up debhelper (13.16) ... Setting up libibverbs-dev:amd64 (52.0-2) ... Setting up samtools (1.20-3) ... Setting up libhsa-runtime64-1 (5.7.1-2) ... Setting up libbtllib-dev (1.4.10+dfsg-1) ... Setting up libamdhip64-5 (5.7.1-4) ... Setting up libucx0:amd64 (1.17.0+ds-3) ... Setting up libopenmpi3t64:amd64 (4.1.6-13.3) ... Setting up openmpi-bin (4.1.6-13.3) ... 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 (4.1.6-13.3) ... 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 sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.39-6) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 6.9.7-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.9.7-1 (2024-06-27) amd64 (x86_64) Toolchain package versions: binutils_2.42.90.20240720-2 dpkg-dev_1.22.11 g++-13_13.3.0-4 g++-14_14.2.0-1 gcc-13_13.3.0-4 gcc-14_14.2.0-1 libc6-dev_2.39-6 libstdc++-13-dev_13.3.0-4 libstdc++-14-dev_14.2.0-1 libstdc++6_14.2.0-1 linux-libc-dev_6.9.12-1 Package versions: adduser_3.137 apt_2.9.7 architecture-properties_0.1.1+b1 autoconf_2.71-3 automake_1:1.16.5-1.3 autopoint_0.22.5-2 autotools-dev_20220109.1 base-files_13.4 base-passwd_3.6.4 bash_5.2.21-2.1 binutils_2.42.90.20240720-2 binutils-common_2.42.90.20240720-2 binutils-x86-64-linux-gnu_2.42.90.20240720-2 bsdextrautils_2.40.2-1 bsdutils_1:2.40.2-1 build-essential_12.10 bzip2_1.0.8-5.1 coreutils_9.4-3.1 cpp_4:14.1.0-2 cpp-13_13.3.0-4 cpp-13-x86-64-linux-gnu_13.3.0-4 cpp-14_14.2.0-1 cpp-14-x86-64-linux-gnu_14.2.0-1 cpp-x86-64-linux-gnu_4:14.1.0-2 dash_0.5.12-9 debconf_1.5.87 debhelper_13.16 debian-archive-keyring_2023.4 debianutils_5.20 dh-autoreconf_20 dh-strip-nondeterminism_1.14.0-1 diffutils_1:3.10-1 dirmngr_2.2.43-8 dpkg_1.22.11 dpkg-dev_1.22.11 dwz_0.15-1+b1 eatmydata_131-2 fakeroot_1.35.1-1 file_1:5.45-3 findutils_4.10.0-2 g++_4:14.1.0-2 g++-13_13.3.0-4 g++-13-x86-64-linux-gnu_13.3.0-4 g++-14_14.2.0-1 g++-14-x86-64-linux-gnu_14.2.0-1 g++-x86-64-linux-gnu_4:14.1.0-2 gcc_4:14.1.0-2 gcc-13_13.3.0-4 gcc-13-base_13.3.0-4 gcc-13-x86-64-linux-gnu_13.3.0-4 gcc-14_14.2.0-1 gcc-14-base_14.2.0-1 gcc-14-x86-64-linux-gnu_14.2.0-1 gcc-x86-64-linux-gnu_4:14.1.0-2 gettext_0.22.5-2 gettext-base_0.22.5-2 gfortran-13_13.3.0-4 gfortran-13-x86-64-linux-gnu_13.3.0-4 gnupg_2.2.43-8 gnupg-l10n_2.2.43-8 gnupg-utils_2.2.43-8 gpg_2.2.43-8 gpg-agent_2.2.43-8 gpg-wks-client_2.2.43-8 gpgconf_2.2.43-8 gpgsm_2.2.43-8 gpgv_2.2.43-8 grep_3.11-4 groff-base_1.23.0-5 gzip_1.12-1.1 help2man_1.49.3 hostname_3.23+nmu2 ibverbs-providers_52.0-2 icu-devtools_72.1-5 init-system-helpers_1.66 intltool-debian_0.35.0+20060710.6 libacl1_2.3.2-2 libamd-comgr2_6.0+git20231212.4510c28+dfsg-3+b1 libamdhip64-5_5.7.1-4 libapt-pkg6.0t64_2.9.7 libarchive-zip-perl_1.68-1 libasan8_14.2.0-1 libassuan0_2.5.6-1+b1 libatomic1_14.2.0-1 libattr1_1:2.5.2-1 libaudit-common_1:3.1.2-4 libaudit1_1:3.1.2-4+b1 libbinutils_2.42.90.20240720-2 libblkid1_2.40.2-1 libboost-graph-dev_1.83.0.2+b2 libboost-graph1.83-dev_1.83.0-3.1 libboost-graph1.83.0_1.83.0-3.1 libboost-regex1.83-dev_1.83.0-3.1 libboost-regex1.83.0_1.83.0-3.1 libboost-serialization1.83-dev_1.83.0-3.1 libboost-serialization1.83.0_1.83.0-3.1 libboost-test1.83-dev_1.83.0-3.1 libboost-test1.83.0_1.83.0-3.1 libboost1.83-dev_1.83.0-3.1 libbrotli1_1.1.0-2+b4 libbsd0_0.12.2-1 libbtllib-dev_1.4.10+dfsg-1 libbz2-1.0_1.0.8-5.1 libc-bin_2.39-6 libc-dev-bin_2.39-6 libc-l10n_2.39-6 libc6_2.39-6 libc6-dev_2.39-6 libcap-ng0_0.8.5-1+b1 libcap2_1:2.66-5 libcbor0.10_0.10.2-1.2 libcc1-0_14.2.0-1 libcom-err2_1.47.1-1 libcpptoml-dev_0.1.1-3 libcrypt-dev_1:4.4.36-4 libcrypt1_1:4.4.36-4 libctf-nobfd0_2.42.90.20240720-2 libctf0_2.42.90.20240720-2 libcurl3t64-gnutls_8.9.1-1 libdb5.3t64_5.3.28+dfsg2-7 libdebconfclient0_0.272 libdebhelper-perl_13.16 libdeflate0_1.20-1 libdivsufsort-dev_2.0.1-6 libdivsufsort3_2.0.1-6 libdpkg-perl_1.22.11 libdrm-amdgpu1_2.4.122-1 libdrm-common_2.4.122-1 libdrm2_2.4.122-1 libeatmydata1_131-2 libedit2_3.1-20240517-1 libelf1t64_0.191-2 libevent-2.1-7t64_2.1.12-stable-10 libevent-core-2.1-7t64_2.1.12-stable-10 libevent-dev_2.1.12-stable-10 libevent-extra-2.1-7t64_2.1.12-stable-10 libevent-openssl-2.1-7t64_2.1.12-stable-10 libevent-pthreads-2.1-7t64_2.1.12-stable-10 libfabric1_1.17.0-3+b1 libfakeroot_1.35.1-1 libffi8_3.4.6-1 libfido2-1_1.15.0-1 libfile-stripnondeterminism-perl_1.14.0-1 libgcc-13-dev_13.3.0-4 libgcc-14-dev_14.2.0-1 libgcc-s1_14.2.0-1 libgcrypt20_1.11.0-5 libgdbm-compat4t64_1.23-6 libgdbm6t64_1.23-6 libgfortran-13-dev_13.3.0-4 libgfortran5_14.2.0-1 libgmp10_2:6.3.0+dfsg-2+b1 libgnutls30t64_3.8.6-2 libgomp1_14.2.0-1 libgpg-error0_1.49-2 libgprofng0_2.42.90.20240720-2 libgssapi-krb5-2_1.21.3-3 libhogweed6t64_3.10-1 libhsa-runtime64-1_5.7.1-2 libhsakmt1_5.7.0-1 libhtml-parser-perl_3.82-1+b1 libhtml-tagset-perl_3.24-1 libhts3t64_1.20+ds-1 libhtscodecs2_1.6.0-1+b1 libhwasan0_14.2.0-1 libhwloc-dev_2.11.0-2 libhwloc-plugins_2.11.0-2 libhwloc15_2.11.0-2 libibmad5_52.0-2 libibumad3_52.0-2 libibverbs-dev_52.0-2 libibverbs1_52.0-2 libicu-dev_72.1-5 libicu72_72.1-5 libidn2-0_2.3.7-2 libisl23_0.26-3+b2 libitm1_14.2.0-1 libjansson4_2.14-2+b2 libjs-d3_3.5.17-4 libjs-jquery_3.6.1+dfsg+~3.5.14-1 libjs-jquery-ui_1.13.2+dfsg-1 libk5crypto3_1.21.3-3 libkeyutils1_1.6.3-3 libkrb5-3_1.21.3-3 libkrb5support0_1.21.3-3 libksba8_1.6.7-2 libldap-2.5-0_2.5.18+dfsg-2+b1 libllvm17t64_1:17.0.6-15 liblocale-gettext-perl_1.07-7+b1 liblsan0_14.2.0-1 libltdl-dev_2.4.7-7+b1 libltdl7_2.4.7-7+b1 liblz4-1_1.9.4-3 liblzma5_5.6.2-2 libmagic-mgc_1:5.45-3 libmagic1t64_1:5.45-3 libmd0_1.1.0-2 libmount1_2.40.2-1 libmpc3_1.3.1-1+b2 libmpfr6_4.2.1-1+b1 libmunge2_0.5.15-4 libncurses6_6.5-2 libncursesw6_6.5-2 libnettle8t64_3.10-1 libnghttp2-14_1.62.1-2 libnghttp3-9_1.4.0-1 libngtcp2-16_1.6.0-1 libngtcp2-crypto-gnutls8_1.6.0-1 libnl-3-200_3.7.0-0.3 libnl-3-dev_3.7.0-0.3 libnl-route-3-200_3.7.0-0.3 libnl-route-3-dev_3.7.0-0.3 libnpth0t64_1.6-3.1 libnuma-dev_2.0.18-1 libnuma1_2.0.18-1 libopenmpi-dev_4.1.6-13.3 libopenmpi3t64_4.1.6-13.3 libp11-kit0_0.25.5-2 libpam-modules_1.5.3-7 libpam-modules-bin_1.5.3-7 libpam-runtime_1.5.3-7 libpam0g_1.5.3-7 libpciaccess0_0.17-3+b1 libpcre2-8-0_10.42-4+b1 libperl5.38t64_5.38.2-5 libperl5.40_5.40.0-1 libpipeline1_1.5.7-2 libpkgconf3_1.8.1-3 libpmix-dev_5.0.3-2 libpmix2t64_5.0.3-2 libpsl5t64_0.21.2-1.1 libpsm-infinipath1_3.3+20.604758e7-6.3 libpsm2-2_11.2.185-2.1 libquadmath0_14.2.0-1 librdmacm1t64_52.0-2 libreadline8t64_8.2-4 librtmp1_2.4+20151223.gitfa8646d.1-2+b4 libsasl2-2_2.1.28+dfsg1-6 libsasl2-modules-db_2.1.28+dfsg1-6 libsdsl-dev_2.1.1+dfsg-5 libsdsl3_2.1.1+dfsg-5 libseccomp2_2.5.5-1+b1 libselinux1_3.5-2+b3 libsemanage-common_3.5-1 libsemanage2_3.5-1+b4 libsepol2_3.5-2+b1 libsframe1_2.42.90.20240720-2 libsmartcols1_2.40.2-1 libsparsehash-dev_2.0.3-2 libsqlite3-0_3.46.0-1 libsqlite3-dev_3.46.0-1 libssh2-1t64_1.11.0-7 libssl3t64_3.2.2-1 libstdc++-13-dev_13.3.0-4 libstdc++-14-dev_14.2.0-1 libstdc++6_14.2.0-1 libsystemd0_256.4-2 libtasn1-6_4.19.0-3+b2 libtext-markdown-perl_1.000031-4 libtext-multimarkdown-perl_1.000035-3 libtinfo6_6.5-2 libtool_2.4.7-7 libtsan2_14.2.0-1 libubsan1_14.2.0-1 libuchardet0_0.0.8-1+b1 libucx0_1.17.0+ds-3 libudev1_256.4-2 libunistring5_1.2-1 liburi-perl_5.28-1 libuuid1_2.40.2-1 libx11-6_2:1.8.7-1+b1 libx11-data_2:1.8.7-1 libxau6_1:1.0.9-1+b1 libxcb1_1.17.0-2 libxdmcp6_1:1.1.2-3+b1 libxext6_2:1.3.4-1+b1 libxml2_2.12.7+dfsg-3+b1 libxnvctrl0_535.171.04-1 libxxhash0_0.8.2-2+b1 libz3-4_4.8.12-3.1+b2 libzstd1_1.5.6+dfsg-1 linux-libc-dev_6.9.12-1 locales-all_2.39-6 login_1:4.15.3-3 m4_1.4.19-4 make_4.3-4.1 man-db_2.12.1-2 mawk_1.3.4.20240622-2 ncurses-base_6.5-2 ncurses-bin_6.5-2 ocl-icd-libopencl1_2.3.2-1+b1 openmpi-bin_4.1.6-13.3 openmpi-common_4.1.6-13.3 openssh-client_1:9.8p1-2 passwd_1:4.15.3-3 patch_2.7.6-7 perl_5.40.0-1 perl-base_5.40.0-1 perl-modules-5.38_5.38.2-5 perl-modules-5.40_5.40.0-1 pinentry-curses_1.2.1-3+b2 pkgconf_1.8.1-3 pkgconf-bin_1.8.1-3 po-debconf_1.0.21+nmu1 readline-common_8.2-4 rpcsvc-proto_1.4.3-1 samtools_1.20-3 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-2 sensible-utils_0.0.24 sysvinit-utils_3.09-2 tar_1.35+dfsg-3 usr-is-merged_39 util-linux_2.40.2-1 wget_1.24.5-2+b1 xz-utils_5.6.2-2 zlib1g_1:1.3.dfsg+really1.3.1-1 zlib1g-dev_1:1.3.dfsg+really1.3.1-1 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: abyss Binary: abyss Architecture: any Version: 2.3.8-1 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille , Michael R. Crusoe , Étienne Mollier Homepage: https://github.com/bcgsc/abyss Standards-Version: 4.7.0 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 (= 13), architecture-is-64-bit, libboost-graph-dev, libbtllib-dev, libopenmpi-dev, libsparsehash-dev, libtext-multimarkdown-perl , libsqlite3-dev, pkgconf, help2man, debhelper Package-List: abyss deb science optional arch=any Checksums-Sha1: 586529353ae31330aed86e8b08aba80caee07963 933896 abyss_2.3.8.orig.tar.xz af58c248cd7efb774841b60670d02ff1f843a204 1497808 abyss_2.3.8-1.debian.tar.xz Checksums-Sha256: 1cd5ba90b67dc8369621a4388429c3d2a1b31def0012b4a56a7df275f868e2b7 933896 abyss_2.3.8.orig.tar.xz ae62b91061c2ed3cab7caf6798c1d600ddd9cd51d837956ac648512e1f7f101d 1497808 abyss_2.3.8-1.debian.tar.xz Files: 46d01630215512be64c4c01aac97ecba 933896 abyss_2.3.8.orig.tar.xz 0dfe8ce001050aeb1890af4c3d4dba97 1497808 abyss_2.3.8-1.debian.tar.xz Dgit: ccf4d8a7eb7748402c9eb5a02ee6a452f362e4c9 debian archive/debian/2.3.8-1 https://git.dgit.debian.org/abyss -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmalQDYUHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdp15g//WHGCuVfIr923Nf2CuR4CE/TbweIu oI28wk4/e9g9VXS1E2azMAdOKidXRdwCgbOVR539U9Tz/4hVLAE9VxNPCw+VygvC YrK7nhYia/yxexCe6ITqgML6Mqfgo/ws1kUjP1ZXSeO3x8rgemX0GO4TYF5GKjPK GD/VYGf/ZRt9w45m8JDw2tLgzlzS+3qfpuJdeBrQwLN+MbvIKpcQVrXiTP3u+Xqh yKO0PhC/m0lp6QKGDpxYtZSuU1D1NX8Hq0vY4yCcj2GzjGIbFVmVd96jvrMxCw0o JxMtZxv8LoiF73le2KJujOFY5UfLCR6cIz2unyhcQ6RzFEg3/Hda8ZmKxktUEaAu /ulea9lJOyVNSaD4aD1qBDVlWyaEfE1sLZRCHW7WB+djLArvEoNflG+iWcbHyjWB pMfuMyS8+VBQO/JfLCIOB36+2XihCUkoJdRXYP8weuHGKXoRNkl4Gdj0ImSDPARe OeF6Rie3C14y/+NVubYPpOa6WJ1zUgRw8nPInqVA5hCzAs+tbcPZcpA7qSOZ7ECy CnSGd/6n8xjg40g3MmImJBr5Ug8mUGfNAJ1Ppv1zJUUeqVzeHkGWHmoABtIEsZ4k FSulNFA6uIpL+68fq9BCBbefO8Q/uudMbHETBuPuLLpkJp2J4iRsDWZX+8zk73jc rZEwCvd3tR3gqz8= =vSg7 -----END PGP SIGNATURE----- gpgv: Signature made Sat Jul 27 18:45:10 2024 UTC gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./abyss_2.3.8-1.dsc: no acceptable signature found dpkg-source: info: extracting abyss in /<> dpkg-source: info: unpacking abyss_2.3.8.orig.tar.xz dpkg-source: info: unpacking abyss_2.3.8-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying abyss-pe.patch dpkg-source: info: applying fix-privacy-breach.patch Check disk space ---------------- Sufficient free space for build +------------------------------------------------------------------------------+ | Starting Timed Build Commands | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/starting-build-commands/no-network abyss_2.3.8-1 perl-5.40-throwaway amd64 -------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/starting-build-commands/no-network abyss_2.3.8-1 perl-5.40-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf HOME=/sbuild-nonexistent LANG=en_GB.UTF-8 LANGUAGE=en_GB:en 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=perl-5.40-throwaway-amd64-debomatic SCHROOT_CHROOT_NAME=perl-5.40-amd64-debomatic SCHROOT_COMMAND=env SCHROOT_GID=110 SCHROOT_GROUP=sbuild SCHROOT_SESSION_ID=perl-5.40-amd64-debomatic-5a89ef2e-bed2-4120-8aa3-8616b474863a SCHROOT_UID=1002 SCHROOT_USER=debomatic SHELL=/bin/sh USER=debomatic dpkg-buildpackage ----------------- Command: dpkg-buildpackage --sanitize-env -us -uc -rfakeroot -Zxz dpkg-buildpackage: info: source package abyss dpkg-buildpackage: info: source version 2.3.8-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source -Zxz --before-build . dpkg-buildpackage: info: host architecture amd64 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_2.3.8.orig.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: building abyss in abyss_2.3.8-1.debian.tar.xz dpkg-source: info: building abyss in abyss_2.3.8-1.dsc debian/rules binary dh binary dh_update_autotools_config dh_autoreconf configure.ac:25: installing './ar-lib' configure.ac:16: installing './compile' configure.ac:80: installing './config.guess' configure.ac:80: 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 the compiler supports GNU C++... yes checking whether g++ accepts -g... yes checking for g++ option to enable C++11 features... none needed 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 race-free mkdir -p... /usr/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 whether UID '1002' is supported by ustar format... yes checking whether GID '110' is supported by ustar format... yes checking how to create a ustar tar archive... gnutar checking dependency style of g++ -std=c++11... none checking for gawk... (cached) mawk checking for gcc... gcc checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... 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 the compiler supports GNU C++... (cached) yes checking whether g++ -std=c++11 accepts -g... (cached) yes checking for g++ -std=c++11 option to enable C++11 features... (cached) none needed checking for ranlib... ranlib checking for ghc... no checking for pandoc... no checking for ar... ar checking the archiver (ar) interface... ar checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for vfork.h... no checking for dlfcn.h... yes checking for fcntl.h... yes checking for float.h... yes checking for limits.h... yes checking for stddef.h... yes checking for stdint.h... (cached) yes checking for stdlib.h... (cached) yes checking for sys/param.h... yes checking for _Bool... yes checking for stdbool.h that conforms to C99... 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 for fork... yes checking for vfork... yes checking for vprintf... yes checking for working fork... yes checking for working vfork... (cached) yes checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking for GNU libc compatible malloc... yes checking for working memcmp... yes checking for GNU libc compatible realloc... yes checking for gcc options needed to detect all undeclared functions... none needed checking whether HOST_NAME_MAX is declared... yes checking if compiler needs -Werror to reject unknown flags... no checking for the pthreads library -lpthreads... no checking whether pthreads work without any flags... 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 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 for functional... yes checking for tr1/functional... yes checking for boost/functional/hash.hpp... yes checking for boost/property_map/property_map.hpp... yes checking for google/sparse_hash_map... yes checking for unordered_map... yes checking for tr1/unordered_map... yes checking for unordered_set... yes checking for tr1/unordered_set... yes checking for boost/unordered_set.hpp... yes checking for btllib/bloom_filter.hpp... 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 RResolver/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 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 -j2 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 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -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 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -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 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -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 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -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 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -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 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -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 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -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 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -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 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -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 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -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 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -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 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -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 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o abyss_todot-todot.o `test -f 'todot.cc' || echo './'`todot.cc In file included from GraphIO.h:8, from todot.cc:9: DotIO.h: In instantiation of ‘void write_edges(std::ostream&, const Graph&, typename boost::graph_traits::vertex_descriptor, const EdgeProp*) [with Graph = ContigGraph >; EdgeProp = DistanceEst; std::ostream = std::basic_ostream; typename boost::graph_traits::vertex_descriptor = ContigNode]’: DotIO.h:110:14: required from ‘std::ostream& write_dot(std::ostream&, const Graph&, const std::string&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream; std::string = std::__cxx11::basic_string]’ 110 | write_edges(out, g, *u, (edge_property_type*)NULL); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ DotIO.h:77:18: required from ‘std::ostream& write_dot(std::ostream&, const Graph&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream]’ 77 | return write_dot(out, g, "adj"); | ~~~~~~~~~^~~~~~~~~~~~~~~ DotIO.h:125:26: required from ‘std::ostream& operator<<(std::ostream&, const DotWriter > >&)’ 125 | return write_dot(out, o.g); | ~~~~~~~~~~~~~~~~^~~~~~~~~~ GraphIO.h:33:14: required from ‘std::ostream& write_graph(std::ostream&, const Graph&, const std::string&, const std::string&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream; std::string = std::__cxx11::basic_string]’ 33 | return out << dot_writer(g); | ~~~~^~~~~~~~~~~~~~~~ todot.cc:186:14: required from here 186 | write_graph(cout, g, PROGRAM, commandLine); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ DotIO.h:44:43: warning: possibly dangling reference to a temporary [-Wdangling-reference] 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ^~ DotIO.h:44:51: note: the temporary was destroyed at the end of the full expression ‘get >(boost::edge_bundle, (* & g), DirectedGraph::out_edge_iterator(e))’ 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ~~~^~~~~~~~~~~~~~~~~~~ DotIO.h: In instantiation of ‘void write_edges(std::ostream&, const Graph&, typename boost::graph_traits::vertex_descriptor, const EdgeProp*) [with Graph = ContigGraph >; EdgeProp = Distance; std::ostream = std::basic_ostream; typename boost::graph_traits::vertex_descriptor = ContigNode]’: DotIO.h:110:14: required from ‘std::ostream& write_dot(std::ostream&, const Graph&, const std::string&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream; std::string = std::__cxx11::basic_string]’ 110 | write_edges(out, g, *u, (edge_property_type*)NULL); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ DotIO.h:77:18: required from ‘std::ostream& write_dot(std::ostream&, const Graph&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream]’ 77 | return write_dot(out, g, "adj"); | ~~~~~~~~~^~~~~~~~~~~~~~~ DotIO.h:125:26: required from ‘std::ostream& operator<<(std::ostream&, const DotWriter > >&)’ 125 | return write_dot(out, o.g); | ~~~~~~~~~~~~~~~~^~~~~~~~~~ GraphIO.h:33:14: required from ‘std::ostream& write_graph(std::ostream&, const Graph&, const std::string&, const std::string&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream; std::string = std::__cxx11::basic_string]’ 33 | return out << dot_writer(g); | ~~~~^~~~~~~~~~~~~~~~ todot.cc:191:14: required from here 191 | write_graph(cout, g, PROGRAM, commandLine); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ DotIO.h:44:43: warning: possibly dangling reference to a temporary [-Wdangling-reference] 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ^~ DotIO.h:44:51: note: the temporary was destroyed at the end of the full expression ‘get >(boost::edge_bundle, (* & g), DirectedGraph::out_edge_iterator(e))’ 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ~~~^~~~~~~~~~~~~~~~~~~ g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -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 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -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 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -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 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -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 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -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 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -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 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -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 g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -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 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 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -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 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -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 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o libdb_a-DB.o `test -f 'DB.cc' || echo './'`DB.cc g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -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-ContigID.o ../Common/libcommon_a-Fcontrol.o ../Common/libcommon_a-Histogram.o ../Common/libcommon_a-Kmer.o ../Common/libcommon_a-Log.o ../Common/libcommon_a-Options.o ../Common/libcommon_a-Sequence.o ../Common/libcommon_a-SignalHandler.o ../Common/libcommon_a-Timer.o ../Common/libcommon_a-Uncompress.o ../Common/libcommon_a-city.o 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 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -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 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -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 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -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 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -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 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -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 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -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 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -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-ContigID.o ../Common/libcommon_a-Fcontrol.o ../Common/libcommon_a-Histogram.o ../Common/libcommon_a-Kmer.o ../Common/libcommon_a-Log.o ../Common/libcommon_a-Options.o ../Common/libcommon_a-Sequence.o ../Common/libcommon_a-SignalHandler.o ../Common/libcommon_a-Timer.o ../Common/libcommon_a-Uncompress.o ../Common/libcommon_a-city.o 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 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o alig.o alig.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, | ^~~~~~~~~~~ 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 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o assemble.o assemble.c assemble.c:40:20: warning: inline function ‘align_diag’ declared but never defined 40 | extern inline char align_diag(struct alignment *algn, struct scr_matrix *smatrix, struct diag* dg); | ^~~~~~~~~~ assemble.c:37:32: warning: inline function ‘find_eqc’ declared but never defined 37 | extern inline struct algn_pos *find_eqc(struct algn_pos **ap, int seqnum, int pos); | ^~~~~~~~ assemble.c:25:39: warning: inline function ‘find_diags_guided’ declared but never defined 25 | extern inline struct simple_diag_col* find_diags_guided(struct scr_matrix *smatrix, | ^~~~~~~~~~~~~~~~~ assemble.c:15:20: warning: inline function ‘calc_ov_weight’ declared but never defined 15 | extern inline void calc_ov_weight(struct diag* dg, struct diag_col *dcol, struct scr_matrix* smatrix, | ^~~~~~~~~~~~~~ assemble.c:13:20: warning: inline function ‘calc_weight’ declared but never defined 13 | extern inline void calc_weight(struct diag* dg, struct scr_matrix* smatrix, | ^~~~~~~~~~~ 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 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o diag.o diag.c diag.c:1456:17: 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); | ^~~~~~~~~~~~~~~~ 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 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o io.o io.c io.c: In function ‘read_scr_matrix’: io.c:270:17: 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 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -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 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -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 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -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 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -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 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -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 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -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 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -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 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -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 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o ABYSS-abyss.o `test -f 'abyss.cc' || echo './'`abyss.cc g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -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 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -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 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -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 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -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 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -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 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -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 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -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 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -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 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -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 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -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 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o abyss_paired_dbg_mpi-Messages.o `test -f 'Messages.cpp' || echo './'`Messages.cpp g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -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 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -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 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o abyss_bloom-bloom.o `test -f 'bloom.cc' || echo './'`bloom.cc g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -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 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -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 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -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 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o konnector-konnector.o `test -f 'konnector.cc' || echo './'`konnector.cc g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -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 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o Consensus-Consensus.o `test -f 'Consensus.cpp' || echo './'`Consensus.cpp g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -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 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -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 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o DAssembler-RotatedRead.o `test -f 'RotatedRead.cpp' || echo './'`RotatedRead.cpp g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -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 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -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 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -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 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -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 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o DistanceEst_ssq-MLE.o `test -f 'MLE.cpp' || echo './'`MLE.cpp g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -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 g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -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 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 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -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 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o KAligner-Aligner.o `test -f 'Aligner.cpp' || echo './'`Aligner.cpp g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -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 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o abyss_layout-layout.o `test -f 'layout.cc' || echo './'`layout.cc In file included from ../Graph/GraphIO.h:8, from layout.cc:8: ../Graph/DotIO.h: In instantiation of ‘void write_edges(std::ostream&, const Graph&, typename boost::graph_traits::vertex_descriptor, const EdgeProp*) [with Graph = ContigGraph >; EdgeProp = Distance; std::ostream = std::basic_ostream; typename boost::graph_traits::vertex_descriptor = ContigNode]’: ../Graph/DotIO.h:110:14: required from ‘std::ostream& write_dot(std::ostream&, const Graph&, const std::string&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream; std::string = std::__cxx11::basic_string]’ 110 | write_edges(out, g, *u, (edge_property_type*)NULL); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../Graph/DotIO.h:77:18: required from ‘std::ostream& write_dot(std::ostream&, const Graph&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream]’ 77 | return write_dot(out, g, "adj"); | ~~~~~~~~~^~~~~~~~~~~~~~~ layout.cc:314:12: required from here 314 | write_dot(out, g); | ~~~~~~~~~^~~~~~~~ ../Graph/DotIO.h:44:43: warning: possibly dangling reference to a temporary [-Wdangling-reference] 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ^~ ../Graph/DotIO.h:44:51: note: the temporary was destroyed at the end of the full expression ‘get >(boost::edge_bundle, (* & g), DirectedGraph::out_edge_iterator(e))’ 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ~~~^~~~~~~~~~~~~~~~~~~ g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -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 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o logcounter-logcounter.o `test -f 'logcounter.cc' || echo './'`logcounter.cc g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -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 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -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 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -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 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -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 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o abyss_overlap-overlap.o `test -f 'overlap.cc' || echo './'`overlap.cc In file included from ../Graph/GraphIO.h:8, from overlap.cc:23: ../Graph/DotIO.h: In instantiation of ‘void write_edges(std::ostream&, const Graph&, typename boost::graph_traits::vertex_descriptor, const EdgeProp*) [with Graph = ContigGraph >; EdgeProp = Distance; std::ostream = std::basic_ostream; typename boost::graph_traits::vertex_descriptor = ContigNode]’: ../Graph/DotIO.h:110:14: required from ‘std::ostream& write_dot(std::ostream&, const Graph&, const std::string&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream; std::string = std::__cxx11::basic_string]’ 110 | write_edges(out, g, *u, (edge_property_type*)NULL); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../Graph/DotIO.h:77:18: required from ‘std::ostream& write_dot(std::ostream&, const Graph&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream]’ 77 | return write_dot(out, g, "adj"); | ~~~~~~~~~^~~~~~~~~~~~~~~ ../Graph/DotIO.h:125:26: required from ‘std::ostream& operator<<(std::ostream&, const DotWriter > >&)’ 125 | return write_dot(out, o.g); | ~~~~~~~~~~~~~~~~^~~~~~~~~~ ../Graph/GraphIO.h:33:14: required from ‘std::ostream& write_graph(std::ostream&, const Graph&, const std::string&, const std::string&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream; std::string = std::__cxx11::basic_string]’ 33 | return out << dot_writer(g); | ~~~~^~~~~~~~~~~~~~~~ overlap.cc:502:13: required from here 502 | write_graph(cout, g, PROGRAM, commandLine); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../Graph/DotIO.h:44:43: warning: possibly dangling reference to a temporary [-Wdangling-reference] 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ^~ ../Graph/DotIO.h:44:51: note: the temporary was destroyed at the end of the full expression ‘get >(boost::edge_bundle, (* & g), DirectedGraph::out_edge_iterator(e))’ 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ~~~^~~~~~~~~~~~~~~~~~~ g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -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 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -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 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -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 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -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 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -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 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o MergeContigs-MergeContigs.o `test -f 'MergeContigs.cpp' || echo './'`MergeContigs.cpp In file included from ../Graph/GraphIO.h:8, from MergeContigs.cpp:13: ../Graph/DotIO.h: In instantiation of ‘void write_edges(std::ostream&, const Graph&, typename boost::graph_traits::vertex_descriptor, const EdgeProp*) [with Graph = ContigGraph >; EdgeProp = Distance; std::ostream = std::basic_ostream; typename boost::graph_traits::vertex_descriptor = ContigNode]’: ../Graph/DotIO.h:110:14: required from ‘std::ostream& write_dot(std::ostream&, const Graph&, const std::string&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream; std::string = std::__cxx11::basic_string]’ 110 | write_edges(out, g, *u, (edge_property_type*)NULL); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../Graph/DotIO.h:77:18: required from ‘std::ostream& write_dot(std::ostream&, const Graph&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream]’ 77 | return write_dot(out, g, "adj"); | ~~~~~~~~~^~~~~~~~~~~~~~~ ../Graph/DotIO.h:125:26: required from ‘std::ostream& operator<<(std::ostream&, const DotWriter > >&)’ 125 | return write_dot(out, o.g); | ~~~~~~~~~~~~~~~~^~~~~~~~~~ ../Graph/GraphIO.h:33:14: required from ‘std::ostream& write_graph(std::ostream&, const Graph&, const std::string&, const std::string&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream; std::string = std::__cxx11::basic_string]’ 33 | return out << dot_writer(g); | ~~~~^~~~~~~~~~~~~~~~ MergeContigs.cpp:428:13: required from here 428 | write_graph(fout, g, PROGRAM, commandLine); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../Graph/DotIO.h:44:43: warning: possibly dangling reference to a temporary [-Wdangling-reference] 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ^~ ../Graph/DotIO.h:44:51: note: the temporary was destroyed at the end of the full expression ‘get >(boost::edge_bundle, (* & g), DirectedGraph::out_edge_iterator(e))’ 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ~~~^~~~~~~~~~~~~~~~~~~ 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 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o PathConsensus-PathConsensus.o `test -f 'PathConsensus.cpp' || echo './'`PathConsensus.cpp In file included from ../Graph/GraphIO.h:8, from PathConsensus.cpp:16: ../Graph/DotIO.h: In instantiation of ‘void write_edges(std::ostream&, const Graph&, typename boost::graph_traits::vertex_descriptor, const EdgeProp*) [with Graph = ContigGraph >; EdgeProp = Distance; std::ostream = std::basic_ostream; typename boost::graph_traits::vertex_descriptor = ContigNode]’: ../Graph/DotIO.h:110:14: required from ‘std::ostream& write_dot(std::ostream&, const Graph&, const std::string&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream; std::string = std::__cxx11::basic_string]’ 110 | write_edges(out, g, *u, (edge_property_type*)NULL); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../Graph/DotIO.h:77:18: required from ‘std::ostream& write_dot(std::ostream&, const Graph&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream]’ 77 | return write_dot(out, g, "adj"); | ~~~~~~~~~^~~~~~~~~~~~~~~ ../Graph/DotIO.h:125:26: required from ‘std::ostream& operator<<(std::ostream&, const DotWriter > >&)’ 125 | return write_dot(out, o.g); | ~~~~~~~~~~~~~~~~^~~~~~~~~~ ../Graph/GraphIO.h:33:14: required from ‘std::ostream& write_graph(std::ostream&, const Graph&, const std::string&, const std::string&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream; std::string = std::__cxx11::basic_string]’ 33 | return out << dot_writer(g); | ~~~~^~~~~~~~~~~~~~~~ PathConsensus.cpp:999:14: required from here 999 | write_graph(fout, g, PROGRAM, commandLine); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../Graph/DotIO.h:44:43: warning: possibly dangling reference to a temporary [-Wdangling-reference] 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ^~ ../Graph/DotIO.h:44:51: note: the temporary was destroyed at the end of the full expression ‘get >(boost::edge_bundle, (* & g), DirectedGraph::out_edge_iterator(e))’ 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ~~~^~~~~~~~~~~~~~~~~~~ g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -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 g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -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 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -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 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 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o Overlap-Overlap.o `test -f 'Overlap.cpp' || echo './'`Overlap.cpp Overlap.cpp: In function ‘int main(int, char**)’: Overlap.cpp:513:40: warning: possibly dangling reference to a temporary [-Wdangling-reference] 513 | const Overlap& ep = get(edge_bundle, scaffoldGraph, e); | ^~ Overlap.cpp:513:48: note: the temporary was destroyed at the end of the full expression ‘get >(boost::edge_bundle, scaffoldGraph, DirectedGraph::out_edge_iterator(e))’ 513 | const Overlap& ep = get(edge_bundle, scaffoldGraph, e); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../Graph/GraphIO.h:8, from Overlap.cpp:16: ../Graph/DotIO.h: In instantiation of ‘void write_edges(std::ostream&, const Graph&, typename boost::graph_traits::vertex_descriptor, const EdgeProp*) [with Graph = ContigGraph >; EdgeProp = Overlap; std::ostream = std::basic_ostream; typename boost::graph_traits::vertex_descriptor = ContigNode]’: ../Graph/DotIO.h:110:14: required from ‘std::ostream& write_dot(std::ostream&, const Graph&, const std::string&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream; std::string = std::__cxx11::basic_string]’ 110 | write_edges(out, g, *u, (edge_property_type*)NULL); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../Graph/DotIO.h:77:18: required from ‘std::ostream& write_dot(std::ostream&, const Graph&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream]’ 77 | return write_dot(out, g, "adj"); | ~~~~~~~~~^~~~~~~~~~~~~~~ ../Graph/DotIO.h:125:26: required from ‘std::ostream& operator<<(std::ostream&, const DotWriter > >&)’ 125 | return write_dot(out, o.g); | ~~~~~~~~~~~~~~~~^~~~~~~~~~ Overlap.cpp:481:35: required from here 481 | cout << dot_writer(scaffoldGraph); | ^ ../Graph/DotIO.h:44:43: warning: possibly dangling reference to a temporary [-Wdangling-reference] 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ^~ ../Graph/DotIO.h:44:51: note: the temporary was destroyed at the end of the full expression ‘get >(boost::edge_bundle, (* & g), DirectedGraph::out_edge_iterator(e))’ 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ~~~^~~~~~~~~~~~~~~~~~~ ../Graph/DotIO.h: In instantiation of ‘void write_edges(std::ostream&, const Graph&, typename boost::graph_traits::vertex_descriptor, const EdgeProp*) [with Graph = ContigGraph >; EdgeProp = Distance; std::ostream = std::basic_ostream; typename boost::graph_traits::vertex_descriptor = ContigNode]’: ../Graph/DotIO.h:110:14: required from ‘std::ostream& write_dot(std::ostream&, const Graph&, const std::string&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream; std::string = std::__cxx11::basic_string]’ 110 | write_edges(out, g, *u, (edge_property_type*)NULL); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../Graph/DotIO.h:77:18: required from ‘std::ostream& write_dot(std::ostream&, const Graph&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream]’ 77 | return write_dot(out, g, "adj"); | ~~~~~~~~~^~~~~~~~~~~~~~~ ../Graph/DotIO.h:125:26: required from ‘std::ostream& operator<<(std::ostream&, const DotWriter > >&)’ 125 | return write_dot(out, o.g); | ~~~~~~~~~~~~~~~~^~~~~~~~~~ ../Graph/GraphIO.h:33:14: required from ‘std::ostream& write_graph(std::ostream&, const Graph&, const std::string&, const std::string&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream; std::string = std::__cxx11::basic_string]’ 33 | return out << dot_writer(g); | ~~~~^~~~~~~~~~~~~~~~ Overlap.cpp:587:14: required from here 587 | write_graph(fout, graph, PROGRAM, commandLine); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../Graph/DotIO.h:44:43: warning: possibly dangling reference to a temporary [-Wdangling-reference] 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ^~ ../Graph/DotIO.h:44:51: note: the temporary was destroyed at the end of the full expression ‘get >(boost::edge_bundle, (* & g), DirectedGraph::out_edge_iterator(e))’ 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ~~~^~~~~~~~~~~~~~~~~~~ g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -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 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -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 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -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 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -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 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -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 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -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 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -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 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o ParseAligns-ParseAligns.o `test -f 'ParseAligns.cpp' || echo './'`ParseAligns.cpp g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -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 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -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 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -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 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o PathOverlap-PathOverlap.o `test -f 'PathOverlap.cpp' || echo './'`PathOverlap.cpp In file included from ../Graph/GraphIO.h:8, from PathOverlap.cpp:10: ../Graph/DotIO.h: In instantiation of ‘void write_edges(std::ostream&, const Graph&, typename boost::graph_traits::vertex_descriptor, const EdgeProp*) [with Graph = ContigGraph >; EdgeProp = Distance; std::ostream = std::basic_ostream; typename boost::graph_traits::vertex_descriptor = ContigNode]’: ../Graph/DotIO.h:110:14: required from ‘std::ostream& write_dot(std::ostream&, const Graph&, const std::string&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream; std::string = std::__cxx11::basic_string]’ 110 | write_edges(out, g, *u, (edge_property_type*)NULL); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../Graph/DotIO.h:77:18: required from ‘std::ostream& write_dot(std::ostream&, const Graph&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream]’ 77 | return write_dot(out, g, "adj"); | ~~~~~~~~~^~~~~~~~~~~~~~~ ../Graph/DotIO.h:125:26: required from ‘std::ostream& operator<<(std::ostream&, const DotWriter > >&)’ 125 | return write_dot(out, o.g); | ~~~~~~~~~~~~~~~~^~~~~~~~~~ ../Graph/GraphIO.h:33:14: required from ‘std::ostream& write_graph(std::ostream&, const Graph&, const std::string&, const std::string&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream; std::string = std::__cxx11::basic_string]’ 33 | return out << dot_writer(g); | ~~~~^~~~~~~~~~~~~~~~ PathOverlap.cpp:709:14: required from here 709 | write_graph(out, g, PROGRAM, commandLine); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../Graph/DotIO.h:44:43: warning: possibly dangling reference to a temporary [-Wdangling-reference] 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ^~ ../Graph/DotIO.h:44:51: note: the temporary was destroyed at the end of the full expression ‘get >(boost::edge_bundle, (* & g), DirectedGraph::out_edge_iterator(e))’ 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ~~~^~~~~~~~~~~~~~~~~~~ g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -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 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o PopBubbles-PopBubbles.o `test -f 'PopBubbles.cpp' || echo './'`PopBubbles.cpp In file included from ../Graph/GraphIO.h:8, from PopBubbles.cpp:16: ../Graph/DotIO.h: In instantiation of ‘void write_edges(std::ostream&, const Graph&, typename boost::graph_traits::vertex_descriptor, const EdgeProp*) [with Graph = ContigGraph >; EdgeProp = Distance; std::ostream = std::basic_ostream; typename boost::graph_traits::vertex_descriptor = ContigNode]’: ../Graph/DotIO.h:110:14: required from ‘std::ostream& write_dot(std::ostream&, const Graph&, const std::string&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream; std::string = std::__cxx11::basic_string]’ 110 | write_edges(out, g, *u, (edge_property_type*)NULL); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../Graph/DotIO.h:77:18: required from ‘std::ostream& write_dot(std::ostream&, const Graph&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream]’ 77 | return write_dot(out, g, "adj"); | ~~~~~~~~~^~~~~~~~~~~~~~~ ../Graph/DotIO.h:125:26: required from ‘std::ostream& operator<<(std::ostream&, const DotWriter > >&)’ 125 | return write_dot(out, o.g); | ~~~~~~~~~~~~~~~~^~~~~~~~~~ ../Graph/GraphIO.h:33:14: required from ‘std::ostream& write_graph(std::ostream&, const Graph&, const std::string&, const std::string&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream; std::string = std::__cxx11::basic_string]’ 33 | return out << dot_writer(g); | ~~~~^~~~~~~~~~~~~~~~ PopBubbles.cpp:723:14: required from here 723 | write_graph(fout, g, PROGRAM, commandLine); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../Graph/DotIO.h:44:43: warning: possibly dangling reference to a temporary [-Wdangling-reference] 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ^~ ../Graph/DotIO.h:44:51: note: the temporary was destroyed at the end of the full expression ‘get >(boost::edge_bundle, (* & g), DirectedGraph::out_edge_iterator(e))’ 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ~~~^~~~~~~~~~~~~~~~~~~ g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -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 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -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 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o abyss_junction-junction.o `test -f 'junction.cc' || echo './'`junction.cc In file included from ../Graph/GraphIO.h:8, from scaffold.cc:13: ../Graph/DotIO.h: In instantiation of ‘void write_edges(std::ostream&, const Graph&, typename boost::graph_traits::vertex_descriptor, const EdgeProp*) [with Graph = ContigGraph >; EdgeProp = DistanceEst; std::ostream = std::basic_ostream; typename boost::graph_traits::vertex_descriptor = ContigNode]’: ../Graph/DotIO.h:110:14: required from ‘std::ostream& write_dot(std::ostream&, const Graph&, const std::string&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream; std::string = std::__cxx11::basic_string]’ 110 | write_edges(out, g, *u, (edge_property_type*)NULL); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../Graph/DotIO.h:77:18: required from ‘std::ostream& write_dot(std::ostream&, const Graph&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream]’ 77 | return write_dot(out, g, "adj"); | ~~~~~~~~~^~~~~~~~~~~~~~~ scaffold.cc:824:13: required from here 824 | write_dot(out, g); | ~~~~~~~~~^~~~~~~~ ../Graph/DotIO.h:44:43: warning: possibly dangling reference to a temporary [-Wdangling-reference] 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ^~ ../Graph/DotIO.h:44:51: note: the temporary was destroyed at the end of the full expression ‘get >(boost::edge_bundle, (* & g), DirectedGraph::out_edge_iterator(e))’ 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ~~~^~~~~~~~~~~~~~~~~~~ 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 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o abyss_longseqdist-longseqdist.o `test -f 'longseqdist.cpp' || echo './'`longseqdist.cpp In file included from ../Graph/GraphIO.h:8, from longseqdist.cpp:9: ../Graph/DotIO.h: In instantiation of ‘void write_edges(std::ostream&, const Graph&, typename boost::graph_traits::vertex_descriptor, const EdgeProp*) [with Graph = ContigGraph >; EdgeProp = DistanceEst; std::ostream = std::basic_ostream; typename boost::graph_traits::vertex_descriptor = ContigNode]’: ../Graph/DotIO.h:110:14: required from ‘std::ostream& write_dot(std::ostream&, const Graph&, const std::string&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream; std::string = std::__cxx11::basic_string]’ 110 | write_edges(out, g, *u, (edge_property_type*)NULL); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../Graph/DotIO.h:77:18: required from ‘std::ostream& write_dot(std::ostream&, const Graph&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream]’ 77 | return write_dot(out, g, "adj"); | ~~~~~~~~~^~~~~~~~~~~~~~~ longseqdist.cpp:208:11: required from here 208 | write_dot(cout, g); | ~~~~~~~~~^~~~~~~~~ ../Graph/DotIO.h:44:43: warning: possibly dangling reference to a temporary [-Wdangling-reference] 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ^~ ../Graph/DotIO.h:44:51: note: the temporary was destroyed at the end of the full expression ‘get >(boost::edge_bundle, (* & g), DirectedGraph::out_edge_iterator(e))’ 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ~~~^~~~~~~~~~~~~~~~~~~ g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -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 -fopenmp -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -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 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -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 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o SimpleGraph-SimpleGraph.o `test -f 'SimpleGraph.cpp' || echo './'`SimpleGraph.cpp g++ -std=c++11 -Wall -Wextra -Werror -Wno-strict-aliasing -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -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 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o kmerprint-kmerprint.o `test -f 'kmerprint.cc' || echo './'`kmerprint.cc g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -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 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o abyss_filtergraph-FilterGraph.o `test -f 'FilterGraph.cc' || echo './'`FilterGraph.cc In file included from ../Graph/GraphIO.h:8, from FilterGraph.cc:15: ../Graph/DotIO.h: In instantiation of ‘void write_edges(std::ostream&, const Graph&, typename boost::graph_traits::vertex_descriptor, const EdgeProp*) [with Graph = ContigGraph >; EdgeProp = Distance; std::ostream = std::basic_ostream; typename boost::graph_traits::vertex_descriptor = ContigNode]’: ../Graph/DotIO.h:110:14: required from ‘std::ostream& write_dot(std::ostream&, const Graph&, const std::string&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream; std::string = std::__cxx11::basic_string]’ 110 | write_edges(out, g, *u, (edge_property_type*)NULL); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../Graph/DotIO.h:77:18: required from ‘std::ostream& write_dot(std::ostream&, const Graph&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream]’ 77 | return write_dot(out, g, "adj"); | ~~~~~~~~~^~~~~~~~~~~~~~~ ../Graph/DotIO.h:125:26: required from ‘std::ostream& operator<<(std::ostream&, const DotWriter > >&)’ 125 | return write_dot(out, o.g); | ~~~~~~~~~~~~~~~~^~~~~~~~~~ ../Graph/GraphIO.h:33:14: required from ‘std::ostream& write_graph(std::ostream&, const Graph&, const std::string&, const std::string&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream; std::string = std::__cxx11::basic_string]’ 33 | return out << dot_writer(g); | ~~~~^~~~~~~~~~~~~~~~ FilterGraph.cc:825:14: required from here 825 | write_graph(fout, g, PROGRAM, commandLine); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../Graph/DotIO.h:44:43: warning: possibly dangling reference to a temporary [-Wdangling-reference] 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ^~ ../Graph/DotIO.h:44:51: note: the temporary was destroyed at the end of the full expression ‘get >(boost::edge_bundle, (* & g), DirectedGraph::out_edge_iterator(e))’ 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ~~~^~~~~~~~~~~~~~~~~~~ g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -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 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o abyss_gapfill-gapfill.o `test -f 'gapfill.cpp' || echo './'`gapfill.cpp g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -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 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o abyss_sealer-sealer.o `test -f 'sealer.cc' || echo './'`sealer.cc g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -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 RResolver make[4]: Entering directory '/<>/RResolver' 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 -Wno-deprecated-declarations -fopenmp -I.. -I../Common -I../DataLayer -I../RResolver/btllib/include -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o abyss_rresolver_short-RResolverShort.o `test -f 'RResolverShort.cpp' || echo './'`RResolverShort.cpp 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 -Wno-deprecated-declarations -fopenmp -I.. -I../Common -I../DataLayer -I../RResolver/btllib/include -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o abyss_rresolver_short-Contigs.o `test -f 'Contigs.cpp' || echo './'`Contigs.cpp In file included from ../Graph/GraphIO.h:8, from Contigs.h:17, from Contigs.cpp:1: ../Graph/DotIO.h: In instantiation of ‘void write_edges(std::ostream&, const Graph&, typename boost::graph_traits::vertex_descriptor, const EdgeProp*) [with Graph = ContigGraph >; EdgeProp = Distance; std::ostream = std::basic_ostream; typename boost::graph_traits::vertex_descriptor = ContigNode]’: ../Graph/DotIO.h:110:14: required from ‘std::ostream& write_dot(std::ostream&, const Graph&, const std::string&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream; std::string = std::__cxx11::basic_string]’ 110 | write_edges(out, g, *u, (edge_property_type*)NULL); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../Graph/DotIO.h:77:18: required from ‘std::ostream& write_dot(std::ostream&, const Graph&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream]’ 77 | return write_dot(out, g, "adj"); | ~~~~~~~~~^~~~~~~~~~~~~~~ ../Graph/DotIO.h:125:26: required from ‘std::ostream& operator<<(std::ostream&, const DotWriter > >&)’ 125 | return write_dot(out, o.g); | ~~~~~~~~~~~~~~~~^~~~~~~~~~ ../Graph/GraphIO.h:33:14: required from ‘std::ostream& write_graph(std::ostream&, const Graph&, const std::string&, const std::string&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream; std::string = std::__cxx11::basic_string]’ 33 | return out << dot_writer(g); | ~~~~^~~~~~~~~~~~~~~~ Contigs.cpp:140:13: required from here 140 | write_graph(fout, g_contigGraph, program, commandLine); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../Graph/DotIO.h:44:43: warning: possibly dangling reference to a temporary [-Wdangling-reference] 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ^~ ../Graph/DotIO.h:44:51: note: the temporary was destroyed at the end of the full expression ‘get >(boost::edge_bundle, (* & g), DirectedGraph::out_edge_iterator(e))’ 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ~~~^~~~~~~~~~~~~~~~~~~ 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 -Wno-deprecated-declarations -fopenmp -I.. -I../Common -I../DataLayer -I../RResolver/btllib/include -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o libralgorithmsshort_a-RAlgorithmsShort.o `test -f 'RAlgorithmsShort.cpp' || echo './'`RAlgorithmsShort.cpp 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 -Wno-deprecated-declarations -fopenmp -I.. -I../Common -I../DataLayer -I../RResolver/btllib/include -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o libralgorithmsshort_a-BloomFilters.o `test -f 'BloomFilters.cpp' || echo './'`BloomFilters.cpp 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 -Wno-deprecated-declarations -fopenmp -I.. -I../Common -I../DataLayer -I../RResolver/btllib/include -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o libralgorithmsshort_a-Contigs.o `test -f 'Contigs.cpp' || echo './'`Contigs.cpp In file included from ../Graph/GraphIO.h:8, from Contigs.h:17, from Contigs.cpp:1: ../Graph/DotIO.h: In instantiation of ‘void write_edges(std::ostream&, const Graph&, typename boost::graph_traits::vertex_descriptor, const EdgeProp*) [with Graph = ContigGraph >; EdgeProp = Distance; std::ostream = std::basic_ostream; typename boost::graph_traits::vertex_descriptor = ContigNode]’: ../Graph/DotIO.h:110:14: required from ‘std::ostream& write_dot(std::ostream&, const Graph&, const std::string&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream; std::string = std::__cxx11::basic_string]’ 110 | write_edges(out, g, *u, (edge_property_type*)NULL); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../Graph/DotIO.h:77:18: required from ‘std::ostream& write_dot(std::ostream&, const Graph&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream]’ 77 | return write_dot(out, g, "adj"); | ~~~~~~~~~^~~~~~~~~~~~~~~ ../Graph/DotIO.h:125:26: required from ‘std::ostream& operator<<(std::ostream&, const DotWriter > >&)’ 125 | return write_dot(out, o.g); | ~~~~~~~~~~~~~~~~^~~~~~~~~~ ../Graph/GraphIO.h:33:14: required from ‘std::ostream& write_graph(std::ostream&, const Graph&, const std::string&, const std::string&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream; std::string = std::__cxx11::basic_string]’ 33 | return out << dot_writer(g); | ~~~~^~~~~~~~~~~~~~~~ Contigs.cpp:140:13: required from here 140 | write_graph(fout, g_contigGraph, program, commandLine); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../Graph/DotIO.h:44:43: warning: possibly dangling reference to a temporary [-Wdangling-reference] 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ^~ ../Graph/DotIO.h:44:51: note: the temporary was destroyed at the end of the full expression ‘get >(boost::edge_bundle, (* & g), DirectedGraph::out_edge_iterator(e))’ 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ~~~^~~~~~~~~~~~~~~~~~~ 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 -Wno-deprecated-declarations -fopenmp -I.. -I../Common -I../DataLayer -I../RResolver/btllib/include -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o libralgorithmsshort_a-SequenceTree.o `test -f 'SequenceTree.cpp' || echo './'`SequenceTree.cpp 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 -Wno-deprecated-declarations -fopenmp -I.. -I../Common -I../DataLayer -I../RResolver/btllib/include -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o libralgorithmsshort_a-RUtils.o `test -f 'RUtils.cpp' || echo './'`RUtils.cpp rm -f libralgorithmsshort.a ar cru libralgorithmsshort.a libralgorithmsshort_a-RAlgorithmsShort.o libralgorithmsshort_a-BloomFilters.o libralgorithmsshort_a-Contigs.o libralgorithmsshort_a-SequenceTree.o libralgorithmsshort_a-RUtils.o ../DataLayer/abyss_fac-fac.o ../DataLayer/abyss_tofastq-abyss-tofastq.o ../DataLayer/libdatalayer_a-FastaReader.o ../DataLayer/libdatalayer_a-FastaWriter.o ../Common/libcommon_a-ContigID.o ../Common/libcommon_a-Fcontrol.o ../Common/libcommon_a-Histogram.o ../Common/libcommon_a-Kmer.o ../Common/libcommon_a-Log.o ../Common/libcommon_a-Options.o ../Common/libcommon_a-Sequence.o ../Common/libcommon_a-SignalHandler.o ../Common/libcommon_a-Timer.o ../Common/libcommon_a-Uncompress.o ../Common/libcommon_a-city.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libralgorithmsshort.a g++ -std=c++11 -Wall -Wextra -Werror -Wno-deprecated-declarations -fopenmp -I.. -I../Common -I../DataLayer -I../RResolver/btllib/include -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -pthread -o abyss-rresolver-short abyss_rresolver_short-RResolverShort.o abyss_rresolver_short-Contigs.o ../DataLayer/libdatalayer.a ../Common/libcommon.a libralgorithmsshort.a -lbtllib -ldl -lm make[4]: Leaving directory '/<>/RResolver' 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 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o AdjList-AdjList.o `test -f 'AdjList.cpp' || echo './'`AdjList.cpp In file included from ../Graph/GraphIO.h:8, from AdjList.cpp:15: ../Graph/DotIO.h: In instantiation of ‘void write_edges(std::ostream&, const Graph&, typename boost::graph_traits::vertex_descriptor, const EdgeProp*) [with Graph = ContigGraph >; EdgeProp = Distance; std::ostream = std::basic_ostream; typename boost::graph_traits::vertex_descriptor = ContigNode]’: ../Graph/DotIO.h:110:14: required from ‘std::ostream& write_dot(std::ostream&, const Graph&, const std::string&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream; std::string = std::__cxx11::basic_string]’ 110 | write_edges(out, g, *u, (edge_property_type*)NULL); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../Graph/DotIO.h:77:18: required from ‘std::ostream& write_dot(std::ostream&, const Graph&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream]’ 77 | return write_dot(out, g, "adj"); | ~~~~~~~~~^~~~~~~~~~~~~~~ ../Graph/DotIO.h:125:26: required from ‘std::ostream& operator<<(std::ostream&, const DotWriter > >&)’ 125 | return write_dot(out, o.g); | ~~~~~~~~~~~~~~~~^~~~~~~~~~ ../Graph/GraphIO.h:33:14: required from ‘std::ostream& write_graph(std::ostream&, const Graph&, const std::string&, const std::string&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream; std::string = std::__cxx11::basic_string]’ 33 | return out << dot_writer(g); | ~~~~^~~~~~~~~~~~~~~~ AdjList.cpp:401:13: required from here 401 | write_graph(cout, g, PROGRAM, commandLine); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../Graph/DotIO.h:44:43: warning: possibly dangling reference to a temporary [-Wdangling-reference] 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ^~ ../Graph/DotIO.h:44:51: note: the temporary was destroyed at the end of the full expression ‘get >(boost::edge_bundle, (* & g), DirectedGraph::out_edge_iterator(e))’ 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ~~~^~~~~~~~~~~~~~~~~~~ g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -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/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 -j2 check "TESTSUITEFLAGS=-j2 --verbose" VERBOSE=1 make[1]: Entering directory '/<>' Making check in bin make[2]: Entering directory '/<>/bin' make[2]: 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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 RResolver make[2]: Entering directory '/<>/RResolver' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/<>/RResolver' 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/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 -Wno-uninitialized -Wno-error=unused-result -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -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 -Wno-uninitialized -Wno-error=unused-result -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -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 -Wno-uninitialized -Wno-error=unused-result -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -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 common_sam_ssq 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 -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -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 -Wno-error -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -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 -Wno-error -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -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 -Wno-error -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -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 -Wno-error -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -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 -Wno-error -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -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 -Wno-error -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -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 -Wno-error -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -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 -DSAM_SEQ_QUAL -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-error -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o Common/common_sam_ssq-SAM.o `test -f 'Common/SAM.cc' || echo './'`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 -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -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 -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -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 -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -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 -Wno-error -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -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 -Wno-error -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -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 -Wno-error -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -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 -Wno-error -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -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 -Wno-error -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -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 -Wno-error -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -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 -Wno-error -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -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 -Wno-error -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o Graph/UndirectedGraphTest.o Graph/UndirectedGraphTest.cpp g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -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 -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -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 -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -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 -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -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 -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -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 -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -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 -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -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 -Wno-error -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -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 -Wno-error -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -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 -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -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 -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -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 -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -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 -Wno-error -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -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 -Wno-error -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -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 -Wno-error -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o BloomDBG/LightweightKmerTest.o BloomDBG/LightweightKmerTest.cpp g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -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 -Wno-error -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -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 -Wno-error -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -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 -Wno-error -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -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 -Wno-error -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -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 -Wno-error -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -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 -Wno-error -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -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 -Wno-error -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o common_sam_ssq Common/common_sam_ssq-SAM.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -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 -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -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 -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -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 -Wno-error -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -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 -Wno-error -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -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 -Wno-error -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -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 -Wno-error -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -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 -Wno-error -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -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 -Wno-error -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -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 -Wno-error -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -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 -Wno-error -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -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 -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -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 -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -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 -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -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 -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -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 -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -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 -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -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 -Wno-error -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -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 -Wno-error -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -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 -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -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 -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -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 -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -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 -Wno-error -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -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 -Wno-error -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -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 -Wno-error -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -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_bitutil PASS: common_kmer PASS: common_sequence PASS: common_KmerIterator PASS: common_sam PASS: common_sam_ssq PASS: Konnector_DBGBloom PASS: BloomFilter PASS: graph_ConstrainedBFSVisitor PASS: Konnector_DBGBloomAlgorithms PASS: graph_AllPathsSearch PASS: graph_BidirectionalBFS PASS: graph_ConstrainedBidiBFSVisitor PASS: graph_HashGraph PASS: graph_ExtendPath PASS: graph_DotIO PASS: graph_UndirectedGraph PASS: Konnector_konnector PASS: DBG_LoadAlgorithm PASS: PairedDBG_KmerPair PASS: PairedDBG_LoadAlgorithm PASS: PairedDBG_Dinuc PASS: PairedDBG_BranchRecord PASS: BloomDBG_BloomDBG PASS: BloomDBG_RollingHash PASS: BloomDBG_HashAgnosticCascadingBloom PASS: BloomDBG_RollingHashIterator PASS: BloomDBG_RollingBloomDBG PASS: BloomDBG_CountingBloomFilter PASS: BloomDBG_MaskedKmer PASS: BloomDBG_SpacedSeed PASS: BloomDBG_LightweightKmer ============================================================================ Testsuite summary for ABySS 2.3.8 ============================================================================ # TOTAL: 34 # PASS: 34 # 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 dh_prep debian/rules override_dh_auto_install make[1]: Entering directory '/<>' dh_auto_install --destdir=debian/tmp make -j2 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' /usr/bin/mkdir -p '/<>/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. /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'. /usr/bin/mkdir -p '/<>/debian/tmp/usr/share/doc/abyss' /usr/bin/install -c -m 644 flowchart.pdf flowchart_simplified.pdf '/<>/debian/tmp/usr/share/doc/abyss' 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'. /usr/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' /usr/bin/mkdir -p '/<>/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. /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' /usr/bin/mkdir -p '/<>/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/<>/debian/tmp/usr/bin' /usr/bin/install -c abyss-db-csv '/<>/debian/tmp/usr/bin' /usr/bin/install -c abyss-db-txt '/<>/debian/tmp/usr/bin' make[4]: Leaving directory '/<>/DataBase' make[3]: Leaving directory '/<>/DataBase' Making install in FMIndex make[3]: Entering directory '/<>/FMIndex' make[4]: Entering directory '/<>/FMIndex' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/<>/FMIndex' make[3]: Leaving directory '/<>/FMIndex' Making install in Assembly make[3]: Entering directory '/<>/Assembly' make[4]: Entering directory '/<>/Assembly' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/<>/Assembly' make[3]: Leaving directory '/<>/Assembly' Making install in dialign make[3]: Entering directory '/<>/dialign' make[4]: Entering directory '/<>/dialign' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/<>/dialign' make[3]: Leaving directory '/<>/dialign' Making install in Align make[3]: Entering directory '/<>/Align' make[4]: Entering directory '/<>/Align' /usr/bin/mkdir -p '/<>/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. /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' /usr/bin/mkdir -p '/<>/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. /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'. /usr/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' /usr/bin/mkdir -p '/<>/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. /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' /usr/bin/mkdir -p '/<>/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. /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' /usr/bin/mkdir -p '/<>/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. /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' /usr/bin/mkdir -p '/<>/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. /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' /usr/bin/mkdir -p '/<>/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. /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' /usr/bin/mkdir -p '/<>/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. /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' /usr/bin/mkdir -p '/<>/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. /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' /usr/bin/mkdir -p '/<>/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. /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' /usr/bin/mkdir -p '/<>/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. /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' /usr/bin/mkdir -p '/<>/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. /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'. /usr/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' /usr/bin/mkdir -p '/<>/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. /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' /usr/bin/mkdir -p '/<>/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. /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' /usr/bin/mkdir -p '/<>/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. /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' /usr/bin/mkdir -p '/<>/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. /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' /usr/bin/mkdir -p '/<>/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. /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' /usr/bin/mkdir -p '/<>/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. /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'. /usr/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' /usr/bin/mkdir -p '/<>/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. /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' /usr/bin/mkdir -p '/<>/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. /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' /usr/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 RResolver make[3]: Entering directory '/<>/RResolver' make[4]: Entering directory '/<>/RResolver' /usr/bin/mkdir -p '/<>/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c abyss-rresolver-short '/<>/debian/tmp/usr/bin' make[4]: Leaving directory '/<>/RResolver' make[3]: Leaving directory '/<>/RResolver' Making install in AdjList make[3]: Entering directory '/<>/AdjList' make[4]: Entering directory '/<>/AdjList' /usr/bin/mkdir -p '/<>/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. /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/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'. /usr/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 '/<>' mkdir -p debian/tmp/usr/share/man/man1 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 -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib64/ld-linux-x86-64.so.2 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib64/ld-linux-x86-64.so.2.usr-is-merged dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'abyss' in '../abyss_2.3.8-1_amd64.deb'. dpkg-deb: building package 'abyss-dbgsym' in '../abyss-dbgsym_2.3.8-1_amd64.deb'. dpkg-genbuildinfo -O../abyss_2.3.8-1_amd64.buildinfo dpkg-genchanges -O../abyss_2.3.8-1_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 2024-08-03T11:18:47Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ abyss_2.3.8-1_amd64.changes: ---------------------------- Format: 1.8 Date: Sat, 27 Jul 2024 18:59:57 +0200 Source: abyss Binary: abyss abyss-dbgsym Architecture: source amd64 Version: 2.3.8-1 Distribution: perl-5.40-throwaway Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Étienne Mollier Description: abyss - de novo, parallel, sequence assembler for short reads Changes: abyss (2.3.8-1) unstable; urgency=medium . [ Michael R. Crusoe ] * d/control: simplify architecture specifications by using provisions from the architecture-properties package. . [ Étienne Mollier ] * New upstream version 2.3.8 * fix-privacy-breach.patch: freshen. * d/copyright: bump copyright years. * d/control: declare compliance to standards version 4.7.0. * d/{control,rules}: migrate from pkg-config to pkgconf. 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abyss-dbgsym_2.3.8-1_amd64.deb 9c83fa637c6eabb9dfc4cfd87694c7e5 3320148 abyss_2.3.8-1_amd64.deb Checksums-Sha1: ab03940f9e0d90f049572a4e50ebfb24753738d5 1279 abyss_2.3.8-1.dsc f8ddcff056d56bdf0b90588da3850784fc5c3dd2 30190128 abyss-dbgsym_2.3.8-1_amd64.deb ba1a937a4a48dc7f60f60a8823685d543b529514 3320148 abyss_2.3.8-1_amd64.deb Checksums-Sha256: aeabcf3d394502ea5d3732bada68a090eb0ec9b16c041f73b237ebd4ea7c90dd 1279 abyss_2.3.8-1.dsc bc78f12ff76ff6cb9b6d73f99708b6c7c5b045141b4fd05f70ad88e76bfc93e0 30190128 abyss-dbgsym_2.3.8-1_amd64.deb 80131b69c6e5d56d540f26a245447f7e3f9058fa7a3ff49e6f768902010410c8 3320148 abyss_2.3.8-1_amd64.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Sat, 03 Aug 2024 11:18:46 +0000 Build-Path: /<> Build-Tainted-By: merged-usr-via-aliased-dirs usr-local-has-programs Installed-Build-Depends: adduser (= 3.137), architecture-properties (= 0.1.1+b1), autoconf (= 2.71-3), automake (= 1:1.16.5-1.3), autopoint (= 0.22.5-2), autotools-dev (= 20220109.1), base-files (= 13.4), base-passwd (= 3.6.4), bash (= 5.2.21-2.1), binutils (= 2.42.90.20240720-2), binutils-common (= 2.42.90.20240720-2), binutils-x86-64-linux-gnu (= 2.42.90.20240720-2), bsdextrautils (= 2.40.2-1), bsdutils (= 1:2.40.2-1), build-essential (= 12.10), bzip2 (= 1.0.8-5.1), coreutils (= 9.4-3.1), cpp (= 4:14.1.0-2), cpp-13 (= 13.3.0-4), cpp-13-x86-64-linux-gnu (= 13.3.0-4), cpp-14 (= 14.2.0-1), cpp-14-x86-64-linux-gnu (= 14.2.0-1), cpp-x86-64-linux-gnu (= 4:14.1.0-2), dash (= 0.5.12-9), debconf (= 1.5.87), debhelper (= 13.16), debianutils (= 5.20), dh-autoreconf (= 20), dh-strip-nondeterminism (= 1.14.0-1), diffutils (= 1:3.10-1), dpkg (= 1.22.11), dpkg-dev (= 1.22.11), dwz (= 0.15-1+b1), file (= 1:5.45-3), findutils (= 4.10.0-2), g++ (= 4:14.1.0-2), g++-14 (= 14.2.0-1), g++-14-x86-64-linux-gnu (= 14.2.0-1), g++-x86-64-linux-gnu (= 4:14.1.0-2), gcc (= 4:14.1.0-2), gcc-13 (= 13.3.0-4), gcc-13-base (= 13.3.0-4), gcc-13-x86-64-linux-gnu (= 13.3.0-4), gcc-14 (= 14.2.0-1), gcc-14-base (= 14.2.0-1), gcc-14-x86-64-linux-gnu (= 14.2.0-1), gcc-x86-64-linux-gnu (= 4:14.1.0-2), gettext (= 0.22.5-2), gettext-base (= 0.22.5-2), gfortran-13 (= 13.3.0-4), gfortran-13-x86-64-linux-gnu (= 13.3.0-4), grep (= 3.11-4), groff-base (= 1.23.0-5), gzip (= 1.12-1.1), help2man (= 1.49.3), hostname (= 3.23+nmu2), ibverbs-providers (= 52.0-2), icu-devtools (= 72.1-5), init-system-helpers (= 1.66), intltool-debian (= 0.35.0+20060710.6), libacl1 (= 2.3.2-2), libamd-comgr2 (= 6.0+git20231212.4510c28+dfsg-3+b1), libamdhip64-5 (= 5.7.1-4), libarchive-zip-perl (= 1.68-1), libasan8 (= 14.2.0-1), libatomic1 (= 14.2.0-1), libattr1 (= 1:2.5.2-1), libaudit-common (= 1:3.1.2-4), libaudit1 (= 1:3.1.2-4+b1), libbinutils (= 2.42.90.20240720-2), libblkid1 (= 2.40.2-1), libboost-graph-dev (= 1.83.0.2+b2), libboost-graph1.83-dev (= 1.83.0-3.1), libboost-graph1.83.0 (= 1.83.0-3.1), libboost-regex1.83-dev (= 1.83.0-3.1), libboost-regex1.83.0 (= 1.83.0-3.1), libboost-serialization1.83-dev (= 1.83.0-3.1), libboost-serialization1.83.0 (= 1.83.0-3.1), libboost-test1.83-dev (= 1.83.0-3.1), libboost-test1.83.0 (= 1.83.0-3.1), libboost1.83-dev (= 1.83.0-3.1), libbrotli1 (= 1.1.0-2+b4), libbsd0 (= 0.12.2-1), libbtllib-dev (= 1.4.10+dfsg-1), libbz2-1.0 (= 1.0.8-5.1), libc-bin (= 2.39-6), libc-dev-bin (= 2.39-6), libc6 (= 2.39-6), libc6-dev (= 2.39-6), libcap-ng0 (= 0.8.5-1+b1), libcap2 (= 1:2.66-5), libcbor0.10 (= 0.10.2-1.2), libcc1-0 (= 14.2.0-1), libcom-err2 (= 1.47.1-1), libcpptoml-dev (= 0.1.1-3), libcrypt-dev (= 1:4.4.36-4), libcrypt1 (= 1:4.4.36-4), libctf-nobfd0 (= 2.42.90.20240720-2), libctf0 (= 2.42.90.20240720-2), libcurl3t64-gnutls (= 8.9.1-1), libdb5.3t64 (= 5.3.28+dfsg2-7), libdebconfclient0 (= 0.272), libdebhelper-perl (= 13.16), libdeflate0 (= 1.20-1), libdivsufsort-dev (= 2.0.1-6), libdivsufsort3 (= 2.0.1-6), libdpkg-perl (= 1.22.11), libdrm-amdgpu1 (= 2.4.122-1), libdrm-common (= 2.4.122-1), libdrm2 (= 2.4.122-1), libedit2 (= 3.1-20240517-1), libelf1t64 (= 0.191-2), libevent-2.1-7t64 (= 2.1.12-stable-10), libevent-core-2.1-7t64 (= 2.1.12-stable-10), libevent-dev (= 2.1.12-stable-10), libevent-extra-2.1-7t64 (= 2.1.12-stable-10), libevent-openssl-2.1-7t64 (= 2.1.12-stable-10), libevent-pthreads-2.1-7t64 (= 2.1.12-stable-10), libfabric1 (= 1.17.0-3+b1), libffi8 (= 3.4.6-1), libfido2-1 (= 1.15.0-1), libfile-stripnondeterminism-perl (= 1.14.0-1), libgcc-13-dev (= 13.3.0-4), libgcc-14-dev (= 14.2.0-1), libgcc-s1 (= 14.2.0-1), libgdbm-compat4t64 (= 1.23-6), libgdbm6t64 (= 1.23-6), libgfortran-13-dev (= 13.3.0-4), libgfortran5 (= 14.2.0-1), libgmp10 (= 2:6.3.0+dfsg-2+b1), libgnutls30t64 (= 3.8.6-2), libgomp1 (= 14.2.0-1), libgprofng0 (= 2.42.90.20240720-2), libgssapi-krb5-2 (= 1.21.3-3), libhogweed6t64 (= 3.10-1), libhsa-runtime64-1 (= 5.7.1-2), libhsakmt1 (= 5.7.0-1), libhtml-parser-perl (= 3.82-1+b1), libhtml-tagset-perl (= 3.24-1), libhts3t64 (= 1.20+ds-1), libhtscodecs2 (= 1.6.0-1+b1), libhwasan0 (= 14.2.0-1), libhwloc-dev (= 2.11.0-2), libhwloc-plugins (= 2.11.0-2), libhwloc15 (= 2.11.0-2), libibmad5 (= 52.0-2), libibumad3 (= 52.0-2), libibverbs-dev (= 52.0-2), libibverbs1 (= 52.0-2), libicu-dev (= 72.1-5), libicu72 (= 72.1-5), libidn2-0 (= 2.3.7-2), libisl23 (= 0.26-3+b2), libitm1 (= 14.2.0-1), libjansson4 (= 2.14-2+b2), libjs-d3 (= 3.5.17-4), libjs-jquery (= 3.6.1+dfsg+~3.5.14-1), libjs-jquery-ui (= 1.13.2+dfsg-1), libk5crypto3 (= 1.21.3-3), libkeyutils1 (= 1.6.3-3), libkrb5-3 (= 1.21.3-3), libkrb5support0 (= 1.21.3-3), libldap-2.5-0 (= 2.5.18+dfsg-2+b1), libllvm17t64 (= 1:17.0.6-15), liblocale-gettext-perl (= 1.07-7+b1), liblsan0 (= 14.2.0-1), libltdl-dev (= 2.4.7-7+b1), libltdl7 (= 2.4.7-7+b1), liblzma5 (= 5.6.2-2), libmagic-mgc (= 1:5.45-3), libmagic1t64 (= 1:5.45-3), libmd0 (= 1.1.0-2), libmount1 (= 2.40.2-1), libmpc3 (= 1.3.1-1+b2), libmpfr6 (= 4.2.1-1+b1), libmunge2 (= 0.5.15-4), libncurses6 (= 6.5-2), libnettle8t64 (= 3.10-1), libnghttp2-14 (= 1.62.1-2), libnghttp3-9 (= 1.4.0-1), libngtcp2-16 (= 1.6.0-1), libngtcp2-crypto-gnutls8 (= 1.6.0-1), libnl-3-200 (= 3.7.0-0.3), libnl-3-dev (= 3.7.0-0.3), libnl-route-3-200 (= 3.7.0-0.3), libnl-route-3-dev (= 3.7.0-0.3), libnuma-dev (= 2.0.18-1), libnuma1 (= 2.0.18-1), libopenmpi-dev (= 4.1.6-13.3), libopenmpi3t64 (= 4.1.6-13.3), libp11-kit0 (= 0.25.5-2), libpam-modules (= 1.5.3-7), libpam-modules-bin (= 1.5.3-7), libpam-runtime (= 1.5.3-7), libpam0g (= 1.5.3-7), libpciaccess0 (= 0.17-3+b1), libpcre2-8-0 (= 10.42-4+b1), libperl5.40 (= 5.40.0-1), libpipeline1 (= 1.5.7-2), libpkgconf3 (= 1.8.1-3), libpmix-dev (= 5.0.3-2), libpmix2t64 (= 5.0.3-2), libpsl5t64 (= 0.21.2-1.1), libpsm-infinipath1 (= 3.3+20.604758e7-6.3), libpsm2-2 (= 11.2.185-2.1), libquadmath0 (= 14.2.0-1), librdmacm1t64 (= 52.0-2), librtmp1 (= 2.4+20151223.gitfa8646d.1-2+b4), libsasl2-2 (= 2.1.28+dfsg1-6), libsasl2-modules-db (= 2.1.28+dfsg1-6), libsdsl-dev (= 2.1.1+dfsg-5), libsdsl3 (= 2.1.1+dfsg-5), libseccomp2 (= 2.5.5-1+b1), libselinux1 (= 3.5-2+b3), libsemanage-common (= 3.5-1), libsemanage2 (= 3.5-1+b4), libsepol2 (= 3.5-2+b1), libsframe1 (= 2.42.90.20240720-2), libsmartcols1 (= 2.40.2-1), libsparsehash-dev (= 2.0.3-2), libsqlite3-0 (= 3.46.0-1), libsqlite3-dev (= 3.46.0-1), libssh2-1t64 (= 1.11.0-7), libssl3t64 (= 3.2.2-1), libstdc++-14-dev (= 14.2.0-1), libstdc++6 (= 14.2.0-1), libsystemd0 (= 256.4-2), libtasn1-6 (= 4.19.0-3+b2), libtext-markdown-perl (= 1.000031-4), libtext-multimarkdown-perl (= 1.000035-3), libtinfo6 (= 6.5-2), libtool (= 2.4.7-7), libtsan2 (= 14.2.0-1), libubsan1 (= 14.2.0-1), libuchardet0 (= 0.0.8-1+b1), libucx0 (= 1.17.0+ds-3), libudev1 (= 256.4-2), libunistring5 (= 1.2-1), liburi-perl (= 5.28-1), libuuid1 (= 2.40.2-1), libx11-6 (= 2:1.8.7-1+b1), libx11-data (= 2:1.8.7-1), libxau6 (= 1:1.0.9-1+b1), libxcb1 (= 1.17.0-2), libxdmcp6 (= 1:1.1.2-3+b1), libxext6 (= 2:1.3.4-1+b1), libxml2 (= 2.12.7+dfsg-3+b1), libxnvctrl0 (= 535.171.04-1), libz3-4 (= 4.8.12-3.1+b2), libzstd1 (= 1.5.6+dfsg-1), linux-libc-dev (= 6.9.12-1), login (= 1:4.15.3-3), m4 (= 1.4.19-4), make (= 4.3-4.1), man-db (= 2.12.1-2), mawk (= 1.3.4.20240622-2), ncurses-base (= 6.5-2), ncurses-bin (= 6.5-2), ocl-icd-libopencl1 (= 2.3.2-1+b1), openmpi-bin (= 4.1.6-13.3), openmpi-common (= 4.1.6-13.3), openssh-client (= 1:9.8p1-2), passwd (= 1:4.15.3-3), patch (= 2.7.6-7), perl (= 5.40.0-1), perl-base (= 5.40.0-1), perl-modules-5.40 (= 5.40.0-1), pkgconf (= 1.8.1-3), pkgconf-bin (= 1.8.1-3), po-debconf (= 1.0.21+nmu1), rpcsvc-proto (= 1.4.3-1), samtools (= 1.20-3), sed (= 4.9-2), sensible-utils (= 0.0.24), sysvinit-utils (= 3.09-2), tar (= 1.35+dfsg-3), usr-is-merged (= 39), util-linux (= 2.40.2-1), wget (= 1.24.5-2+b1), xz-utils (= 5.6.2-2), zlib1g (= 1:1.3.dfsg+really1.3.1-1), zlib1g-dev (= 1:1.3.dfsg+really1.3.1-1) Environment: DEB_BUILD_OPTIONS="parallel=2" LANG="C.UTF-8" LC_COLLATE="C.UTF-8" LC_CTYPE="C.UTF-8" LD_LIBRARY_PATH="/usr/lib/libeatmydata" SOURCE_DATE_EPOCH="1722099597" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ abyss-dbgsym_2.3.8-1_amd64.deb ------------------------------ new Debian package, version 2.0. size 30190128 bytes: control archive=2516 bytes. 2086 bytes, 12 lines control 4640 bytes, 44 lines md5sums Package: abyss-dbgsym Source: abyss Version: 2.3.8-1 Auto-Built-Package: debug-symbols Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 31018 Depends: abyss (= 2.3.8-1) Section: debug Priority: optional Description: debug symbols for abyss Build-Ids: 07cb32958c32cb15830f15db7ab489957aef5804 11518f031287355efa45abd02ecaa4ebc9a76458 18e80969e6d3b12cfdf6b20f3f5225e55eb6417a 1cb654266aa1714393f754a024f21bb114a460ae 24a9d29a616e07da23058d5874aa110216431b49 2c627dde5dcc58eddd1a3f9bd933b3dd60404741 2f0315c24064eafdaf0383e5afedcd56ceca5aed 3972a34331b33f92e3bc264df4e8a044a4bec2c7 3acb9d70fb6f308da6e17bc96b2bbdc178d6435b 3c8b0b013133ad44f347c9067b413e7d668f8d85 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./usr/lib/debug/.dwz/ drwxr-xr-x root/root 0 2024-07-27 16:59 ./usr/lib/debug/.dwz/x86_64-linux-gnu/ -rw-r--r-- root/root 1128456 2024-07-27 16:59 ./usr/lib/debug/.dwz/x86_64-linux-gnu/abyss.debug drwxr-xr-x root/root 0 2024-07-27 16:59 ./usr/share/ drwxr-xr-x root/root 0 2024-07-27 16:59 ./usr/share/doc/ lrwxrwxrwx root/root 0 2024-07-27 16:59 ./usr/share/doc/abyss-dbgsym -> abyss abyss_2.3.8-1_amd64.deb ----------------------- new Debian package, version 2.0. size 3320148 bytes: control archive=2656 bytes. 711 bytes, 14 lines control 4780 bytes, 76 lines md5sums Package: abyss Version: 2.3.8-1 Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 10011 Depends: make, libc6 (>= 2.38), libgcc-s1 (>= 3.0), libgomp1 (>= 4.9), libopenmpi3t64 (>= 4.1.6), libsqlite3-0 (>= 3.5.9), libstdc++6 (>= 14), perl:any, bsdextrautils, 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 2024-07-27 16:59 ./ drwxr-xr-x root/root 0 2024-07-27 16:59 ./usr/ drwxr-xr-x root/root 0 2024-07-27 16:59 ./usr/bin/ -rwxr-xr-x root/root 145840 2024-07-27 16:59 ./usr/bin/DistanceEst -rwxr-xr-x root/root 134192 2024-07-27 16:59 ./usr/bin/abyss-fixmate -rwxr-xr-x root/root 23148 2024-07-27 16:59 ./usr/bin/abyss-pe drwxr-xr-x root/root 0 2024-07-27 16:59 ./usr/lib/ drwxr-xr-x root/root 0 2024-07-27 16:59 ./usr/lib/abyss/ -rwxr-xr-x root/root 268736 2024-07-27 16:59 ./usr/lib/abyss/ABYSS -rwxr-xr-x root/root 321984 2024-07-27 16:59 ./usr/lib/abyss/ABYSS-P -rwxr-xr-x root/root 182696 2024-07-27 16:59 ./usr/lib/abyss/AdjList -rwxr-xr-x root/root 80288 2024-07-27 16:59 ./usr/lib/abyss/Consensus -rwxr-xr-x root/root 108976 2024-07-27 16:59 ./usr/lib/abyss/DAssembler -rwxr-xr-x root/root 145840 2024-07-27 16:59 ./usr/lib/abyss/DistanceEst -rwxr-xr-x root/root 145840 2024-07-27 16:59 ./usr/lib/abyss/DistanceEst-ssq -rwxr-xr-x root/root 190896 2024-07-27 16:59 ./usr/lib/abyss/KAligner -rwxr-xr-x root/root 227768 2024-07-27 16:59 ./usr/lib/abyss/MergeContigs -rwxr-xr-x root/root 199072 2024-07-27 16:59 ./usr/lib/abyss/MergePaths -rwxr-xr-x root/root 186800 2024-07-27 16:59 ./usr/lib/abyss/Overlap -rwxr-xr-x root/root 100752 2024-07-27 16:59 ./usr/lib/abyss/ParseAligns -rwxr-xr-x root/root 354736 2024-07-27 16:59 ./usr/lib/abyss/PathConsensus -rwxr-xr-x root/root 174480 2024-07-27 16:59 ./usr/lib/abyss/PathOverlap -rwxr-xr-x root/root 194992 2024-07-27 16:59 ./usr/lib/abyss/PopBubbles -rwxr-xr-x root/root 174512 2024-07-27 16:59 ./usr/lib/abyss/SimpleGraph -rwxr-xr-x root/root 190880 2024-07-27 16:59 ./usr/lib/abyss/abyss-align -rwxr-xr-x root/root 363032 2024-07-27 16:59 ./usr/lib/abyss/abyss-bloom -rwxr-xr-x root/root 379384 2024-07-27 16:59 ./usr/lib/abyss/abyss-bloom-dbg -rwxr-xr-x root/root 6491 2024-07-27 16:59 ./usr/lib/abyss/abyss-bloom-dist.mk -rwxr-xr-x root/root 1135 2024-07-27 16:59 ./usr/lib/abyss/abyss-bowtie -rwxr-xr-x root/root 1192 2024-07-27 16:59 ./usr/lib/abyss/abyss-bowtie2 -rwxr-xr-x root/root 1208 2024-07-27 16:59 ./usr/lib/abyss/abyss-bwa -rwxr-xr-x root/root 1454 2024-07-27 16:59 ./usr/lib/abyss/abyss-bwamem -rwxr-xr-x root/root 1362 2024-07-27 16:59 ./usr/lib/abyss/abyss-bwasw -rwxr-xr-x root/root 67984 2024-07-27 16:59 ./usr/lib/abyss/abyss-db-csv -rwxr-xr-x root/root 703 2024-07-27 16:59 ./usr/lib/abyss/abyss-db-txt -rwxr-xr-x root/root 2739 2024-07-27 16:59 ./usr/lib/abyss/abyss-dida -rwxr-xr-x root/root 84392 2024-07-27 16:59 ./usr/lib/abyss/abyss-fac -rwxr-xr-x root/root 2058 2024-07-27 16:59 ./usr/lib/abyss/abyss-fatoagp -rwxr-xr-x root/root 174512 2024-07-27 16:59 ./usr/lib/abyss/abyss-filtergraph -rwxr-xr-x root/root 134192 2024-07-27 16:59 ./usr/lib/abyss/abyss-fixmate -rwxr-xr-x root/root 134192 2024-07-27 16:59 ./usr/lib/abyss/abyss-fixmate-ssq -rwxr-xr-x root/root 108976 2024-07-27 16:59 ./usr/lib/abyss/abyss-gapfill -rwxr-xr-x root/root 84368 2024-07-27 16:59 ./usr/lib/abyss/abyss-gc -rwxr-xr-x root/root 92568 2024-07-27 16:59 ./usr/lib/abyss/abyss-index -rwxr-xr-x root/root 100760 2024-07-27 16:59 ./usr/lib/abyss/abyss-junction -rwxr-xr-x root/root 39 2024-07-27 16:59 ./usr/lib/abyss/abyss-kaligner -rwxr-xr-x root/root 129432 2024-07-27 16:59 ./usr/lib/abyss/abyss-layout -rwxr-xr-x root/root 96672 2024-07-27 16:59 ./usr/lib/abyss/abyss-longseqdist -rwxr-xr-x root/root 182696 2024-07-27 16:59 ./usr/lib/abyss/abyss-map -rwxr-xr-x root/root 190888 2024-07-27 16:59 ./usr/lib/abyss/abyss-map-ssq -rwxr-xr-x root/root 88504 2024-07-27 16:59 ./usr/lib/abyss/abyss-mergepairs -rwxr-xr-x root/root 199096 2024-07-27 16:59 ./usr/lib/abyss/abyss-overlap -rwxr-xr-x root/root 285128 2024-07-27 16:59 ./usr/lib/abyss/abyss-paired-dbg -rwxr-xr-x root/root 334272 2024-07-27 16:59 ./usr/lib/abyss/abyss-paired-dbg-mpi -rwxr-xr-x root/root 23148 2024-07-27 16:59 ./usr/lib/abyss/abyss-pe 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./usr/share/doc/abyss/test-data/ -rw-r--r-- root/root 743013 2024-07-27 16:59 ./usr/share/doc/abyss/test-data/reads1.fastq.gz -rw-r--r-- root/root 743377 2024-07-27 16:59 ./usr/share/doc/abyss/test-data/reads2.fastq.gz drwxr-xr-x root/root 0 2024-07-27 16:59 ./usr/share/man/ drwxr-xr-x root/root 0 2024-07-27 16:59 ./usr/share/man/man1/ -rw-r--r-- root/root 1019 2024-07-27 16:59 ./usr/share/man/man1/DistanceEst.1.gz -rw-r--r-- root/root 788 2024-07-27 16:59 ./usr/share/man/man1/abyss-fixmate.1.gz +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: full Build-Space: 753720 Build-Time: 542 Distribution: perl-5.40-throwaway Host Architecture: amd64 Install-Time: 24 Job: /srv/debomatic/incoming/abyss_2.3.8-1.dsc Machine Architecture: amd64 Package: abyss Package-Time: 578 Source-Version: 2.3.8-1 Space: 753720 Status: successful Version: 2.3.8-1 -------------------------------------------------------------------------------- Finished at 2024-08-03T11:18:47Z Build needed 00:09:38, 753720k disk space