Tue May 7 11:52:11 UTC 2024 I: starting to build abyss/unstable/amd64 on jenkins on '2024-05-07 11:51' Tue May 7 11:52:11 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_33/11166/console.log Tue May 7 11:52:11 UTC 2024 I: Downloading source for unstable/abyss=2.3.7-3 --2024-05-07 11:52:12-- http://deb.debian.org/debian/pool/main/a/abyss/abyss_2.3.7-3.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2318 (2.3K) [text/prs.lines.tag] Saving to: ‘abyss_2.3.7-3.dsc’ 0K .. 100% 353M=0s 2024-05-07 11:52:12 (353 MB/s) - ‘abyss_2.3.7-3.dsc’ saved [2318/2318] Tue May 7 11:52:12 UTC 2024 I: abyss_2.3.7-3.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: abyss Binary: abyss Architecture: any-amd64 arm64 loong64 mips64el ppc64el s390x ia64 ppc64 riscv64 sparc64 alpha Version: 2.3.7-3 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille , Michael R. Crusoe , Étienne Mollier Homepage: https://github.com/bcgsc/abyss Standards-Version: 4.6.2 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), libboost-graph-dev, libbtllib-dev, libopenmpi-dev, libsparsehash-dev, libtext-multimarkdown-perl , libsqlite3-dev, pkg-config, help2man, debhelper Package-List: abyss deb science optional arch=any-amd64,arm64,loong64,mips64el,ppc64el,s390x,ia64,ppc64,riscv64,sparc64,alpha Checksums-Sha1: 38dbf86f0ebda69e7ab633e92ba66b99e8179dec 933440 abyss_2.3.7.orig.tar.xz 271de11e45f2d1a876d87592be40502ceb7e6930 1497704 abyss_2.3.7-3.debian.tar.xz Checksums-Sha256: 70ef428552d234c2ee51a430b7092d5952ba12251bbaeb6373a5f62a4a8702cb 933440 abyss_2.3.7.orig.tar.xz d7a0af8f3f26ef190722aaad2b484af6b7ef881878f9ea4673dbd6819aa7a1eb 1497704 abyss_2.3.7-3.debian.tar.xz Files: a234694ce7d1781632123845208119f9 933440 abyss_2.3.7.orig.tar.xz de18961d29398836e298289e10449797 1497704 abyss_2.3.7-3.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmV93GgRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtETPQ/9EMC9JgHp4SZKOuQOBlO2tCQfBSjOMFCP JU6A9qlO5CVBbR0QybRYSswG4Czv/cxEyJ5bXeE7FSdX5cKKJ0Ijgru8MyBymlzJ ET26Ps58UdiHBpCZ2sMBdI4MlyfMfV7v+8yzFyGIDZe24E+R3YEPeLl+5H4ToTI7 91YrG5SkmliYIr1zX9m1jmWV5YV8/HxINi1jPyxtW5eJTlGQpQphqKguIRBclDVL jDMtvMYtMqluqh6ggP2x+AjeqaW1pm5mrJG2NCT2aD01T8ur+X2SdAC1GS6NP6sG US5Hb2G/4UCRsI6jMw7lRfTNTY/x7uZQNaj/klpq5VO8UdenIdYzu1BNemPXDaxa OBLjI1qXrRuT+Tlgl4dCkKqQz+9ncANJP6q9HgoEUElGr6+kUhQ2wHCQUS8dhOzO 38x8+sgXqgaJHp5UkZJGdRqjwr54Dj4HbVaERkTOl+snizXHafH81KofBVuDb0cz BV1f2sBC3NYeu7VBIHNFVF5B8K77sv2cOiB3Vsu4HF7e3L1bbgoFbLKJeSUJZcOa f4zDWkB8pXahGpGlAVmBgHkqkVjmVRs5iHvbrFvpDhnQWSJDtgalMl4+DNgitgsn aglbdN1i5/rtOS4t3S6ILHdFxdsi/VqjgGJZXxS8yTsqHAq1A9VReY0YdLGRQGxi frbDrO+1Wz8= =xEhP -----END PGP SIGNATURE----- Tue May 7 11:52:12 UTC 2024 I: Checking whether the package is not for us Tue May 7 11:52:12 UTC 2024 I: Starting 1st build on remote node infom01-amd64.debian.net. Tue May 7 11:52:12 UTC 2024 I: Preparing to do remote build '1' on infom01-amd64.debian.net. Tue May 7 11:59:23 UTC 2024 I: Deleting $TMPDIR on infom01-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Mon May 6 23:52:14 -12 2024 I: pbuilder-time-stamp: 1715082734 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [abyss_2.3.7-3.dsc] I: copying [./abyss_2.3.7.orig.tar.xz] I: copying [./abyss_2.3.7-3.debian.tar.xz] I: Extracting source gpgv: Signature made Sat Dec 16 17:20:40 2023 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./abyss_2.3.7-3.dsc: no acceptable signature found dpkg-source: info: extracting abyss in abyss-2.3.7 dpkg-source: info: unpacking abyss_2.3.7.orig.tar.xz dpkg-source: info: unpacking abyss_2.3.7-3.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 I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1207255/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='172d13e02f4e4b45ba80504ac18c649a' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='1207255' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.bstw1hvP/pbuilderrc_xefe --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.bstw1hvP/b1 --logfile b1/build.log abyss_2.3.7-3.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' I: uname -a Linux infom01-amd64 6.1.0-21-cloud-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.90-1 (2024-05-03) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 6 07:42 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1207255/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), libboost-graph-dev, libbtllib-dev, libopenmpi-dev, libsparsehash-dev, libtext-multimarkdown-perl, libsqlite3-dev, pkg-config, help2man, debhelper dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19699 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on libboost-graph-dev; however: Package libboost-graph-dev is not installed. pbuilder-satisfydepends-dummy depends on libbtllib-dev; however: Package libbtllib-dev is not installed. pbuilder-satisfydepends-dummy depends on libopenmpi-dev; however: Package libopenmpi-dev is not installed. pbuilder-satisfydepends-dummy depends on libsparsehash-dev; however: Package libsparsehash-dev is not installed. pbuilder-satisfydepends-dummy depends on libtext-multimarkdown-perl; however: Package libtext-multimarkdown-perl is not installed. pbuilder-satisfydepends-dummy depends on libsqlite3-dev; however: Package libsqlite3-dev is not installed. pbuilder-satisfydepends-dummy depends on pkg-config; however: Package pkg-config is not installed. pbuilder-satisfydepends-dummy depends on help2man; however: Package help2man is not installed. pbuilder-satisfydepends-dummy depends on debhelper; however: Package debhelper is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} gfortran-13{a} gfortran-13-x86-64-linux-gnu{a} groff-base{a} help2man{a} ibverbs-providers{a} icu-devtools{a} intltool-debian{a} libamd-comgr2{a} libamdhip64-5{a} libarchive-zip-perl{a} libboost-graph-dev{a} libboost-graph1.83-dev{a} libboost-graph1.83.0{a} libboost-regex1.83-dev{a} libboost-regex1.83.0{a} libboost-serialization1.83-dev{a} libboost-serialization1.83.0{a} libboost-test1.83-dev{a} libboost-test1.83.0{a} libboost1.83-dev{a} libbrotli1{a} libbsd0{a} libbtllib-dev{a} libcbor0.10{a} libcom-err2{a} libcpptoml-dev{a} libcurl3t64-gnutls{a} libdebhelper-perl{a} libdeflate0{a} libdivsufsort-dev{a} libdivsufsort3{a} libdrm-amdgpu1{a} libdrm-common{a} libdrm2{a} libedit2{a} libelf1t64{a} libevent-2.1-7t64{a} libevent-core-2.1-7t64{a} libevent-dev{a} libevent-extra-2.1-7t64{a} libevent-openssl-2.1-7t64{a} libevent-pthreads-2.1-7t64{a} libfabric1{a} libfido2-1{a} libfile-stripnondeterminism-perl{a} libgfortran-13-dev{a} libgfortran5{a} libgssapi-krb5-2{a} libhsa-runtime64-1{a} libhsakmt1{a} libhtml-parser-perl{a} libhtml-tagset-perl{a} libhts3t64{a} libhtscodecs2{a} libhwloc-dev{a} libhwloc-plugins{a} libhwloc15{a} libibverbs-dev{a} libibverbs1{a} libicu-dev{a} libicu72{a} libjs-d3{a} libjs-jquery{a} libjs-jquery-ui{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libldap-2.5-0{a} libllvm17t64{a} liblocale-gettext-perl{a} libltdl-dev{a} libltdl7{a} libmagic-mgc{a} libmagic1t64{a} libmunge2{a} libncurses6{a} libnghttp2-14{a} libnl-3-200{a} libnl-3-dev{a} libnl-route-3-200{a} libnl-route-3-dev{a} libnuma-dev{a} libnuma1{a} libopenmpi-dev{a} libopenmpi3t64{a} libpciaccess0{a} libpipeline1{a} libpkgconf3{a} libpmix-dev{a} libpmix2t64{a} libpsl5t64{a} libpsm-infinipath1{a} libpsm2-2{a} librdmacm1t64{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsdsl-dev{a} libsdsl3{a} libsparsehash-dev{a} libsqlite3-dev{a} libssh2-1t64{a} libsub-override-perl{a} libtext-markdown-perl{a} libtext-multimarkdown-perl{a} libtool{a} libuchardet0{a} libucx0{a} liburi-perl{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxml2{a} libxnvctrl0{a} libz3-4{a} m4{a} man-db{a} ocl-icd-libopencl1{a} openmpi-bin{a} openmpi-common{a} openssh-client{a} pkg-config{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} samtools{a} sensible-utils{a} wget{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates javascript-common krb5-locales libarchive-cpio-perl libcoarrays-openmpi-dev libgpm2 libhttp-message-perl libldap-common libmail-sendmail-perl libsasl2-modules publicsuffix xauth 0 packages upgraded, 145 newly installed, 0 to remove and 0 not upgraded. Need to get 135 MB of archives. After unpacking 692 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 liblocale-gettext-perl amd64 1.07-7 [15.0 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.22 [22.4 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3 [314 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3 [105 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.45-3 [42.9 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.21-14+b1 [161 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b1 [68.8 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-4 [1180 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40-8 [92.8 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.7-2 [38.0 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.12.1-1 [1411 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 libbsd0 amd64 0.12.2-1 [131 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 libedit2 amd64 3.1-20230828-1+b1 [93.5 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 libcbor0.10 amd64 0.10.2-1.2 [28.2 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 libfido2-1 amd64 1.14.0-1+b2 [77.7 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.20.1-6+b1 [33.3 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.1~rc2-1 [22.6 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.20.1-6+b1 [79.8 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-3 [8952 B] Get: 20 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.20.1-6+b1 [333 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.20.1-6+b1 [135 kB] Get: 22 http://deb.debian.org/debian unstable/main amd64 openssh-client amd64 1:9.7p1-4 [965 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.21.2-1.1 [56.8 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 wget amd64 1.24.5-1 [979 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.71-3 [332 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.21-14 [496 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 libtool all 2.4.7-7 [517 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 33 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 34 http://deb.debian.org/debian unstable/main amd64 libsub-override-perl all 0.10-1 [10.6 kB] Get: 35 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 36 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 37 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.191-1+b1 [189 kB] Get: 38 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 39 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-4+b1 [9395 kB] Get: 40 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.9.14+dfsg-1.3+b3 [692 kB] Get: 41 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.21-14+b1 [1301 kB] Get: 42 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 43 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 44 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.15.3 [901 kB] Get: 45 http://deb.debian.org/debian unstable/main amd64 libgfortran5 amd64 14-20240429-1 [836 kB] Get: 46 http://deb.debian.org/debian unstable/main amd64 libgfortran-13-dev amd64 13.2.0-24 [847 kB] Get: 47 http://deb.debian.org/debian unstable/main amd64 gfortran-13-x86-64-linux-gnu amd64 13.2.0-24 [10.7 MB] Get: 48 http://deb.debian.org/debian unstable/main amd64 gfortran-13 amd64 13.2.0-24 [12.2 kB] Get: 49 http://deb.debian.org/debian unstable/main amd64 help2man amd64 1.49.3 [198 kB] Get: 50 http://deb.debian.org/debian unstable/main amd64 libnl-3-200 amd64 3.7.0-0.3 [59.0 kB] Get: 51 http://deb.debian.org/debian unstable/main amd64 libnl-route-3-200 amd64 3.7.0-0.3 [181 kB] Get: 52 http://deb.debian.org/debian unstable/main amd64 libibverbs1 amd64 50.0-2+b1 [61.7 kB] Get: 53 http://deb.debian.org/debian unstable/main amd64 ibverbs-providers amd64 50.0-2+b1 [342 kB] Get: 54 http://deb.debian.org/debian unstable/main amd64 icu-devtools amd64 72.1-4+b1 [208 kB] Get: 55 http://deb.debian.org/debian unstable/main amd64 libz3-4 amd64 4.8.12-3.1+b2 [7346 kB] Get: 56 http://deb.debian.org/debian unstable/main amd64 libllvm17t64 amd64 1:17.0.6-12 [23.7 MB] Get: 57 http://deb.debian.org/debian unstable/main amd64 libamd-comgr2 amd64 6.0+git20231212.4510c28+dfsg-3+b1 [13.0 MB] Get: 58 http://deb.debian.org/debian unstable/main amd64 libdrm-common all 2.4.120-2 [7688 B] Get: 59 http://deb.debian.org/debian unstable/main amd64 libdrm2 amd64 2.4.120-2 [38.1 kB] Get: 60 http://deb.debian.org/debian unstable/main amd64 libdrm-amdgpu1 amd64 2.4.120-2 [21.4 kB] Get: 61 http://deb.debian.org/debian unstable/main amd64 libnuma1 amd64 2.0.18-1 [21.9 kB] Get: 62 http://deb.debian.org/debian unstable/main amd64 libhsakmt1 amd64 5.7.0-1 [60.7 kB] Get: 63 http://deb.debian.org/debian unstable/main amd64 libhsa-runtime64-1 amd64 5.7.1-2 [504 kB] Get: 64 http://deb.debian.org/debian unstable/main amd64 libamdhip64-5 amd64 5.7.1-3 [8760 kB] Get: 65 http://deb.debian.org/debian unstable/main amd64 libboost1.83-dev amd64 1.83.0-2.1+b1 [10.6 MB] Get: 66 http://deb.debian.org/debian unstable/main amd64 libboost-graph1.83.0 amd64 1.83.0-2.1+b1 [358 kB] Get: 67 http://deb.debian.org/debian unstable/main amd64 libboost-regex1.83.0 amd64 1.83.0-2.1+b1 [325 kB] Get: 68 http://deb.debian.org/debian unstable/main amd64 libicu-dev amd64 72.1-4+b1 [10.4 MB] Get: 69 http://deb.debian.org/debian unstable/main amd64 libboost-regex1.83-dev amd64 1.83.0-2.1+b1 [342 kB] Get: 70 http://deb.debian.org/debian unstable/main amd64 libboost-serialization1.83.0 amd64 1.83.0-2.1+b1 [332 kB] Get: 71 http://deb.debian.org/debian unstable/main amd64 libboost-serialization1.83-dev amd64 1.83.0-2.1+b1 [372 kB] Get: 72 http://deb.debian.org/debian unstable/main amd64 libboost-test1.83.0 amd64 1.83.0-2.1+b1 [466 kB] Get: 73 http://deb.debian.org/debian unstable/main amd64 libboost-test1.83-dev amd64 1.83.0-2.1+b1 [537 kB] Get: 74 http://deb.debian.org/debian unstable/main amd64 libboost-graph1.83-dev amd64 1.83.0-2.1+b1 [383 kB] Get: 75 http://deb.debian.org/debian unstable/main amd64 libboost-graph-dev amd64 1.83.0.2+b2 [3700 B] Get: 76 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b3 [305 kB] Get: 77 http://deb.debian.org/debian unstable/main amd64 libcpptoml-dev all 0.1.1-3 [180 kB] Get: 78 http://deb.debian.org/debian unstable/main amd64 libdivsufsort3 amd64 2.0.1-6 [45.6 kB] Get: 79 http://deb.debian.org/debian unstable/main amd64 libdivsufsort-dev amd64 2.0.1-6 [18.8 kB] Get: 80 http://deb.debian.org/debian unstable/main amd64 libjs-d3 all 3.5.17-4 [132 kB] Get: 81 http://deb.debian.org/debian unstable/main amd64 libsdsl3 amd64 2.1.1+dfsg-4+b1 [208 kB] Get: 82 http://deb.debian.org/debian unstable/main amd64 libsdsl-dev amd64 2.1.1+dfsg-4+b1 [445 kB] Get: 83 http://deb.debian.org/debian unstable/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-6 [19.5 kB] Get: 84 http://deb.debian.org/debian unstable/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-6 [56.9 kB] Get: 85 http://deb.debian.org/debian unstable/main amd64 libldap-2.5-0 amd64 2.5.17+dfsg-1 [186 kB] Get: 86 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.61.0-1+b1 [75.6 kB] Get: 87 http://deb.debian.org/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b4 [58.5 kB] Get: 88 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.0-4.1+b2 [215 kB] Get: 89 http://deb.debian.org/debian unstable/main amd64 libcurl3t64-gnutls amd64 8.7.1-5 [433 kB] Get: 90 http://deb.debian.org/debian unstable/main amd64 libdeflate0 amd64 1.20-1 [46.0 kB] Get: 91 http://deb.debian.org/debian unstable/main amd64 libhtscodecs2 amd64 1.6.0-1+b1 [93.0 kB] Get: 92 http://deb.debian.org/debian unstable/main amd64 libhts3t64 amd64 1.19+ds-1.1+b1 [448 kB] Get: 93 http://deb.debian.org/debian unstable/main amd64 libncurses6 amd64 6.4+20240414-1 [104 kB] Get: 94 http://deb.debian.org/debian unstable/main amd64 samtools amd64 1.19.2-1+b1 [645 kB] Get: 95 http://deb.debian.org/debian unstable/main amd64 libbtllib-dev amd64 1.4.10+dfsg-1 [173 kB] Get: 96 http://deb.debian.org/debian unstable/main amd64 libevent-2.1-7t64 amd64 2.1.12-stable-8.1+b3 [181 kB] Get: 97 http://deb.debian.org/debian unstable/main amd64 libevent-core-2.1-7t64 amd64 2.1.12-stable-8.1+b3 [132 kB] Get: 98 http://deb.debian.org/debian unstable/main amd64 libevent-extra-2.1-7t64 amd64 2.1.12-stable-8.1+b3 [107 kB] Get: 99 http://deb.debian.org/debian unstable/main amd64 libevent-pthreads-2.1-7t64 amd64 2.1.12-stable-8.1+b3 [54.1 kB] Get: 100 http://deb.debian.org/debian unstable/main amd64 libevent-openssl-2.1-7t64 amd64 2.1.12-stable-8.1+b3 [61.1 kB] Get: 101 http://deb.debian.org/debian unstable/main amd64 libevent-dev amd64 2.1.12-stable-8.1+b3 [305 kB] Get: 102 http://deb.debian.org/debian unstable/main amd64 libpsm-infinipath1 amd64 3.3+20.604758e7-6.3 [170 kB] Get: 103 http://deb.debian.org/debian unstable/main amd64 libpsm2-2 amd64 11.2.185-2 [180 kB] Get: 104 http://deb.debian.org/debian unstable/main amd64 librdmacm1t64 amd64 50.0-2+b1 [70.2 kB] Get: 105 http://deb.debian.org/debian unstable/main amd64 libfabric1 amd64 1.17.0-3+b1 [628 kB] Get: 106 http://deb.debian.org/debian unstable/main amd64 libhtml-tagset-perl all 3.24-1 [14.7 kB] Get: 107 http://deb.debian.org/debian unstable/main amd64 liburi-perl all 5.28-1 [98.6 kB] Get: 108 http://deb.debian.org/debian unstable/main amd64 libhtml-parser-perl amd64 3.82-1 [98.9 kB] Get: 109 http://deb.debian.org/debian unstable/main amd64 libhwloc15 amd64 2.10.0-1+b1 [161 kB] Get: 110 http://deb.debian.org/debian unstable/main amd64 libnuma-dev amd64 2.0.18-1 [36.2 kB] Get: 111 http://deb.debian.org/debian unstable/main amd64 libltdl7 amd64 2.4.7-7+b1 [393 kB] Get: 112 http://deb.debian.org/debian unstable/main amd64 libltdl-dev amd64 2.4.7-7+b1 [164 kB] Get: 113 http://deb.debian.org/debian unstable/main amd64 libhwloc-dev amd64 2.10.0-1+b1 [250 kB] Get: 114 http://deb.debian.org/debian unstable/main amd64 libpciaccess0 amd64 0.17-3+b1 [51.9 kB] Get: 115 http://deb.debian.org/debian unstable/main amd64 libxau6 amd64 1:1.0.9-1+b1 [18.1 kB] Get: 116 http://deb.debian.org/debian unstable/main amd64 libxdmcp6 amd64 1:1.1.2-3+b1 [24.3 kB] Get: 117 http://deb.debian.org/debian unstable/main amd64 libxcb1 amd64 1.17.0-1 [144 kB] Get: 118 http://deb.debian.org/debian unstable/main amd64 libx11-data all 2:1.8.7-1 [328 kB] Get: 119 http://deb.debian.org/debian unstable/main amd64 libx11-6 amd64 2:1.8.7-1+b1 [799 kB] Get: 120 http://deb.debian.org/debian unstable/main amd64 libxext6 amd64 2:1.3.4-1+b1 [52.9 kB] Get: 121 http://deb.debian.org/debian unstable/main amd64 libxnvctrl0 amd64 535.171.04-1 [13.8 kB] Get: 122 http://deb.debian.org/debian unstable/main amd64 ocl-icd-libopencl1 amd64 2.3.2-1+b1 [40.3 kB] Get: 123 http://deb.debian.org/debian unstable/main amd64 libhwloc-plugins amd64 2.10.0-1+b1 [18.0 kB] Get: 124 http://deb.debian.org/debian unstable/main amd64 libnl-3-dev amd64 3.7.0-0.3 [99.4 kB] Get: 125 http://deb.debian.org/debian unstable/main amd64 libnl-route-3-dev amd64 3.7.0-0.3 [199 kB] Get: 126 http://deb.debian.org/debian unstable/main amd64 libibverbs-dev amd64 50.0-2+b1 [642 kB] Get: 127 http://deb.debian.org/debian unstable/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 128 http://deb.debian.org/debian unstable/main amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get: 129 http://deb.debian.org/debian unstable/main amd64 libmunge2 amd64 0.5.15-4 [19.8 kB] Get: 130 http://deb.debian.org/debian unstable/main amd64 libpmix2t64 amd64 5.0.2-3 [652 kB] Get: 131 http://deb.debian.org/debian unstable/main amd64 libucx0 amd64 1.16.0+ds-5 [1109 kB] Get: 132 http://deb.debian.org/debian unstable/main amd64 libopenmpi3t64 amd64 4.1.6-13.3 [2426 kB] Get: 133 http://deb.debian.org/debian unstable/main amd64 openmpi-common all 4.1.6-13.3 [169 kB] Get: 134 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg-3.1 [918 kB] Get: 135 http://deb.debian.org/debian unstable/main amd64 libpmix-dev amd64 5.0.2-3 [3940 kB] Get: 136 http://deb.debian.org/debian unstable/main amd64 openmpi-bin amd64 4.1.6-13.3 [226 kB] Get: 137 http://deb.debian.org/debian unstable/main amd64 libopenmpi-dev amd64 4.1.6-13.3 [972 kB] Get: 138 http://deb.debian.org/debian unstable/main amd64 libpkgconf3 amd64 1.8.1-1+b2 [36.4 kB] Get: 139 http://deb.debian.org/debian unstable/main amd64 libsparsehash-dev all 2.0.3-2 [76.8 kB] Get: 140 http://deb.debian.org/debian unstable/main amd64 libsqlite3-dev amd64 3.45.3-1 [1088 kB] Get: 141 http://deb.debian.org/debian unstable/main amd64 libtext-markdown-perl all 1.000031-4 [32.1 kB] Get: 142 http://deb.debian.org/debian unstable/main amd64 libtext-multimarkdown-perl all 1.000035-3 [28.5 kB] Get: 143 http://deb.debian.org/debian unstable/main amd64 pkgconf-bin amd64 1.8.1-1+b2 [29.7 kB] Get: 144 http://deb.debian.org/debian unstable/main amd64 pkgconf amd64 1.8.1-1+b2 [26.2 kB] Get: 145 http://deb.debian.org/debian unstable/main amd64 pkg-config amd64 1.8.1-1+b2 [14.0 kB] Fetched 135 MB in 1s (115 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package liblocale-gettext-perl. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19699 files and directories currently installed.) Preparing to unpack .../000-liblocale-gettext-perl_1.07-7_amd64.deb ... Unpacking liblocale-gettext-perl (1.07-7) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../001-sensible-utils_0.0.22_all.deb ... Unpacking sensible-utils (0.0.22) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../002-libmagic-mgc_1%3a5.45-3_amd64.deb ... Unpacking libmagic-mgc (1:5.45-3) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../003-libmagic1t64_1%3a5.45-3_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.45-3) ... Selecting previously unselected package file. Preparing to unpack .../004-file_1%3a5.45-3_amd64.deb ... Unpacking file (1:5.45-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../005-gettext-base_0.21-14+b1_amd64.deb ... Unpacking gettext-base (0.21-14+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../006-libuchardet0_0.0.8-1+b1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../007-groff-base_1.23.0-4_amd64.deb ... Unpacking groff-base (1.23.0-4) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../008-bsdextrautils_2.40-8_amd64.deb ... Unpacking bsdextrautils (2.40-8) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../009-libpipeline1_1.5.7-2_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.7-2) ... Selecting previously unselected package man-db. Preparing to unpack .../010-man-db_2.12.1-1_amd64.deb ... Unpacking man-db (2.12.1-1) ... Selecting previously unselected package libbsd0:amd64. Preparing to unpack .../011-libbsd0_0.12.2-1_amd64.deb ... Unpacking libbsd0:amd64 (0.12.2-1) ... Selecting previously unselected package libedit2:amd64. Preparing to unpack .../012-libedit2_3.1-20230828-1+b1_amd64.deb ... Unpacking libedit2:amd64 (3.1-20230828-1+b1) ... Selecting previously unselected package libcbor0.10:amd64. Preparing to unpack .../013-libcbor0.10_0.10.2-1.2_amd64.deb ... Unpacking libcbor0.10:amd64 (0.10.2-1.2) ... Selecting previously unselected package libfido2-1:amd64. Preparing to unpack .../014-libfido2-1_1.14.0-1+b2_amd64.deb ... Unpacking libfido2-1:amd64 (1.14.0-1+b2) ... Selecting previously unselected package libkrb5support0:amd64. Preparing to unpack .../015-libkrb5support0_1.20.1-6+b1_amd64.deb ... Unpacking libkrb5support0:amd64 (1.20.1-6+b1) ... Selecting previously unselected package libcom-err2:amd64. Preparing to unpack .../016-libcom-err2_1.47.1~rc2-1_amd64.deb ... Unpacking libcom-err2:amd64 (1.47.1~rc2-1) ... Selecting previously unselected package libk5crypto3:amd64. Preparing to unpack .../017-libk5crypto3_1.20.1-6+b1_amd64.deb ... Unpacking libk5crypto3:amd64 (1.20.1-6+b1) ... Selecting previously unselected package libkeyutils1:amd64. Preparing to unpack .../018-libkeyutils1_1.6.3-3_amd64.deb ... Unpacking libkeyutils1:amd64 (1.6.3-3) ... Selecting previously unselected package libkrb5-3:amd64. Preparing to unpack .../019-libkrb5-3_1.20.1-6+b1_amd64.deb ... Unpacking libkrb5-3:amd64 (1.20.1-6+b1) ... Selecting previously unselected package libgssapi-krb5-2:amd64. Preparing to unpack .../020-libgssapi-krb5-2_1.20.1-6+b1_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.20.1-6+b1) ... Selecting previously unselected package openssh-client. Preparing to unpack .../021-openssh-client_1%3a9.7p1-4_amd64.deb ... Unpacking openssh-client (1:9.7p1-4) ... Selecting previously unselected package libpsl5t64:amd64. Preparing to unpack .../022-libpsl5t64_0.21.2-1.1_amd64.deb ... Unpacking libpsl5t64:amd64 (0.21.2-1.1) ... Selecting previously unselected package wget. Preparing to unpack .../023-wget_1.24.5-1_amd64.deb ... Unpacking wget (1.24.5-1) ... Selecting previously unselected package m4. Preparing to unpack .../024-m4_1.4.19-4_amd64.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../025-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../026-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../027-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../028-autopoint_0.21-14_all.deb ... Unpacking autopoint (0.21-14) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../029-libdebhelper-perl_13.15.3_all.deb ... Unpacking libdebhelper-perl (13.15.3) ... Selecting previously unselected package libtool. Preparing to unpack .../030-libtool_2.4.7-7_all.deb ... Unpacking libtool (2.4.7-7) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../031-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../032-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../033-libsub-override-perl_0.10-1_all.deb ... Unpacking libsub-override-perl (0.10-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../034-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../035-dh-strip-nondeterminism_1.13.1-1_all.deb ... Unpacking dh-strip-nondeterminism (1.13.1-1) ... Selecting previously unselected package libelf1t64:amd64. Preparing to unpack .../036-libelf1t64_0.191-1+b1_amd64.deb ... Unpacking libelf1t64:amd64 (0.191-1+b1) ... Selecting previously unselected package dwz. Preparing to unpack .../037-dwz_0.15-1+b1_amd64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libicu72:amd64. Preparing to unpack .../038-libicu72_72.1-4+b1_amd64.deb ... Unpacking libicu72:amd64 (72.1-4+b1) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../039-libxml2_2.9.14+dfsg-1.3+b3_amd64.deb ... Unpacking libxml2:amd64 (2.9.14+dfsg-1.3+b3) ... Selecting previously unselected package gettext. Preparing to unpack .../040-gettext_0.21-14+b1_amd64.deb ... Unpacking gettext (0.21-14+b1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../041-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../042-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../043-debhelper_13.15.3_all.deb ... Unpacking debhelper (13.15.3) ... Selecting previously unselected package libgfortran5:amd64. Preparing to unpack .../044-libgfortran5_14-20240429-1_amd64.deb ... Unpacking libgfortran5:amd64 (14-20240429-1) ... Selecting previously unselected package libgfortran-13-dev:amd64. Preparing to unpack .../045-libgfortran-13-dev_13.2.0-24_amd64.deb ... Unpacking libgfortran-13-dev:amd64 (13.2.0-24) ... Selecting previously unselected package gfortran-13-x86-64-linux-gnu. Preparing to unpack .../046-gfortran-13-x86-64-linux-gnu_13.2.0-24_amd64.deb ... Unpacking gfortran-13-x86-64-linux-gnu (13.2.0-24) ... Selecting previously unselected package gfortran-13. Preparing to unpack .../047-gfortran-13_13.2.0-24_amd64.deb ... Unpacking gfortran-13 (13.2.0-24) ... Selecting previously unselected package help2man. Preparing to unpack .../048-help2man_1.49.3_amd64.deb ... Unpacking help2man (1.49.3) ... Selecting previously unselected package libnl-3-200:amd64. Preparing to unpack .../049-libnl-3-200_3.7.0-0.3_amd64.deb ... Unpacking libnl-3-200:amd64 (3.7.0-0.3) ... Selecting previously unselected package libnl-route-3-200:amd64. Preparing to unpack .../050-libnl-route-3-200_3.7.0-0.3_amd64.deb ... Unpacking libnl-route-3-200:amd64 (3.7.0-0.3) ... Selecting previously unselected package libibverbs1:amd64. Preparing to unpack .../051-libibverbs1_50.0-2+b1_amd64.deb ... Unpacking libibverbs1:amd64 (50.0-2+b1) ... Selecting previously unselected package ibverbs-providers:amd64. Preparing to unpack .../052-ibverbs-providers_50.0-2+b1_amd64.deb ... Unpacking ibverbs-providers:amd64 (50.0-2+b1) ... Selecting previously unselected package icu-devtools. Preparing to unpack .../053-icu-devtools_72.1-4+b1_amd64.deb ... Unpacking icu-devtools (72.1-4+b1) ... Selecting previously unselected package libz3-4:amd64. Preparing to unpack .../054-libz3-4_4.8.12-3.1+b2_amd64.deb ... Unpacking libz3-4:amd64 (4.8.12-3.1+b2) ... Selecting previously unselected package libllvm17t64:amd64. Preparing to unpack .../055-libllvm17t64_1%3a17.0.6-12_amd64.deb ... Unpacking libllvm17t64:amd64 (1:17.0.6-12) ... Selecting previously unselected package libamd-comgr2:amd64. Preparing to unpack .../056-libamd-comgr2_6.0+git20231212.4510c28+dfsg-3+b1_amd64.deb ... Unpacking libamd-comgr2:amd64 (6.0+git20231212.4510c28+dfsg-3+b1) ... Selecting previously unselected package libdrm-common. Preparing to unpack .../057-libdrm-common_2.4.120-2_all.deb ... Unpacking libdrm-common (2.4.120-2) ... Selecting previously unselected package libdrm2:amd64. Preparing to unpack .../058-libdrm2_2.4.120-2_amd64.deb ... Unpacking libdrm2:amd64 (2.4.120-2) ... Selecting previously unselected package libdrm-amdgpu1:amd64. Preparing to unpack .../059-libdrm-amdgpu1_2.4.120-2_amd64.deb ... Unpacking libdrm-amdgpu1:amd64 (2.4.120-2) ... Selecting previously unselected package libnuma1:amd64. Preparing to unpack .../060-libnuma1_2.0.18-1_amd64.deb ... Unpacking libnuma1:amd64 (2.0.18-1) ... Selecting previously unselected package libhsakmt1:amd64. 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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 (1.83.0-2.1+b1) ... Setting up libpsm2-2 (11.2.185-2) ... Setting up openmpi-common (4.1.6-13.3) ... Setting up libsub-override-perl (0.10-1) ... Setting up libkrb5-3:amd64 (1.20.1-6+b1) ... Setting up libevent-core-2.1-7t64:amd64 (2.1.12-stable-8.1+b3) ... 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 (1.11.0-4.1+b2) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up libfido2-1:amd64 (1.14.0-1+b2) ... Setting up libgfortran-13-dev:amd64 (13.2.0-24) ... Setting up libdivsufsort3:amd64 (2.0.1-6) ... Setting up libbsd0:amd64 (0.12.2-1) ... Setting up libdrm-common (2.4.120-2) ... Setting up libicu-dev:amd64 (72.1-4+b1) ... Setting up libxml2:amd64 (2.9.14+dfsg-1.3+b3) ... Setting up liburi-perl (5.28-1) ... Setting up liblocale-gettext-perl (1.07-7) ... 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 (1.13.1-1) ... Setting up libxdmcp6:amd64 (1:1.1.2-3+b1) ... Setting up libxcb1:amd64 (1.17.0-1) ... Setting up gettext (0.21-14+b1) ... Setting up libsdsl-dev:amd64 (2.1.1+dfsg-4+b1) ... Setting up wget (1.24.5-1) ... Setting up libtool (2.4.7-7) ... Setting up libevent-pthreads-2.1-7t64:amd64 (2.1.12-stable-8.1+b3) ... Setting up libedit2:amd64 (3.1-20230828-1+b1) ... Setting up libevent-openssl-2.1-7t64:amd64 (2.1.12-stable-8.1+b3) ... Setting up libboost-serialization1.83-dev:amd64 (1.83.0-2.1+b1) ... Setting up libboost-test1.83-dev:amd64 (1.83.0-2.1+b1) ... Setting up gfortran-13-x86-64-linux-gnu (13.2.0-24) ... Setting up libldap-2.5-0:amd64 (2.5.17+dfsg-1) ... Setting up pkgconf:amd64 (1.8.1-1+b2) ... 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 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 (1:17.0.6-12) ... Setting up gfortran-13 (13.2.0-24) ... Setting up libgssapi-krb5-2:amd64 (1.20.1-6+b1) ... Setting up libboost-regex1.83-dev:amd64 (1.83.0-2.1+b1) ... Setting up pkg-config:amd64 (1.8.1-1+b2) ... Setting up libevent-extra-2.1-7t64:amd64 (2.1.12-stable-8.1+b3) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up libdrm2:amd64 (2.4.120-2) ... Setting up libnl-3-dev:amd64 (3.7.0-0.3) ... Setting up groff-base (1.23.0-4) ... Setting up libhtml-parser-perl:amd64 (3.82-1) ... Setting up libx11-6:amd64 (2:1.8.7-1+b1) ... Setting up libhwloc-dev:amd64 (2.10.0-1+b1) ... 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 (2.4.120-2) ... Setting up libibverbs1:amd64 (50.0-2+b1) ... Setting up ibverbs-providers:amd64 (50.0-2+b1) ... Setting up openssh-client (1:9.7p1-4) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libcurl3t64-gnutls:amd64 (8.7.1-5) ... Setting up libxext6:amd64 (2:1.3.4-1+b1) ... Setting up man-db (2.12.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libboost-graph1.83-dev:amd64 (1.83.0-2.1+b1) ... Setting up libxnvctrl0:amd64 (535.171.04-1) ... Setting up libnl-route-3-dev:amd64 (3.7.0-0.3) ... Setting up libevent-dev (2.1.12-stable-8.1+b3) ... Setting up libhts3t64:amd64 (1.19+ds-1.1+b1) ... Setting up librdmacm1t64:amd64 (50.0-2+b1) ... 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 (13.15.3) ... Setting up libibverbs-dev:amd64 (50.0-2+b1) ... Setting up libhwloc-plugins:amd64 (2.10.0-1+b1) ... Setting up samtools (1.19.2-1+b1) ... Setting up libpmix2t64:amd64 (5.0.2-3) ... Setting up libhsa-runtime64-1 (5.7.1-2) ... Setting up libpmix-dev:amd64 (5.0.2-3) ... Setting up libbtllib-dev (1.4.10+dfsg-1) ... Setting up libamdhip64-5 (5.7.1-3) ... Setting up libucx0:amd64 (1.16.0+ds-5) ... 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 Processing triggers for libc-bin (2.38-8) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/abyss-2.3.7/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../abyss_2.3.7-3_source.changes dpkg-buildpackage: info: source package abyss dpkg-buildpackage: info: source version 2.3.7-3 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean dh_clean 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 '/build/reproducible-path/abyss-2.3.7' 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 '1111' is supported by ustar format... yes checking whether GID '1111' 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 ./configure: line 7032: : command not found 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 '/build/reproducible-path/abyss-2.3.7' debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/abyss-2.3.7' dh_auto_build make -j12 make[2]: Entering directory '/build/reproducible-path/abyss-2.3.7' make all-recursive make[3]: Entering directory '/build/reproducible-path/abyss-2.3.7' Making all in bin make[4]: Entering directory '/build/reproducible-path/abyss-2.3.7/bin' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.7/bin' Making all in doc make[4]: Entering directory '/build/reproducible-path/abyss-2.3.7/doc' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.7/doc' Making all in Common make[4]: Entering directory '/build/reproducible-path/abyss-2.3.7/Common' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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 '/build/reproducible-path/abyss-2.3.7/Common' Making all in Graph make[4]: Entering directory '/build/reproducible-path/abyss-2.3.7/Graph' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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_gc-gc.o `test -f 'gc.cc' || echo './'`gc.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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_todot-todot.o `test -f 'todot.cc' || echo './'`todot.cc In file included from GraphIO.h:10, from todot.cc:9: GfaIO.h: In instantiation of 'std::ostream& write_gfa2_edges(std::ostream&, const Graph&, const DistanceEst*) [with Graph = ContigGraph >; std::ostream = std::basic_ostream]': GfaIO.h:216:25: required from 'std::ostream& write_gfa2(std::ostream&, Graph&) [with Graph = const ContigGraph >; std::ostream = std::basic_ostream]' GraphIO.h:37:20: 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]' todot.cc:186:14: required from here GfaIO.h:182:27: warning: possibly dangling reference to a temporary [-Wdangling-reference] 182 | const EP& ep = get(edge_bundle, g, eit); | ^~ GfaIO.h:182:35: note: the temporary was destroyed at the end of the full expression 'get(boost::edge_bundle, g.ContigGraph >::, DirectedGraph::edge_iterator(eit))' 182 | const EP& ep = get(edge_bundle, g, eit); | ~~~^~~~~~~~~~~~~~~~~~~~~ In file included from GraphIO.h:8: 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]' DotIO.h:77:18: required from 'std::ostream& write_dot(std::ostream&, const Graph&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream]' DotIO.h:125:26: required from 'std::ostream& operator<<(std::ostream&, const DotWriter > >&)' 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]' todot.cc:186:14: required from here 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]' DotIO.h:77:18: required from 'std::ostream& write_dot(std::ostream&, const Graph&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream]' DotIO.h:125:26: required from 'std::ostream& operator<<(std::ostream&, const DotWriter > >&)' 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]' todot.cc:191:14: required from here 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=/build/reproducible-path/abyss-2.3.7=. -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-gc abyss_gc-gc.o ../Common/libcommon.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -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 '/build/reproducible-path/abyss-2.3.7/Graph' Making all in DataLayer make[4]: Entering directory '/build/reproducible-path/abyss-2.3.7/DataLayer' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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=/build/reproducible-path/abyss-2.3.7=. -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 g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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 make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.7/DataLayer' Making all in DataBase make[4]: Entering directory '/build/reproducible-path/abyss-2.3.7/DataBase' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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=/build/reproducible-path/abyss-2.3.7=. -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 '/build/reproducible-path/abyss-2.3.7/DataBase' Making all in FMIndex make[4]: Entering directory '/build/reproducible-path/abyss-2.3.7/FMIndex' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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_count-count.o `test -f 'count.cc' || echo './'`count.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I../Common -I/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -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/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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_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=/build/reproducible-path/abyss-2.3.7=. -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-count abyss_count-count.o libfmindex.a ../Common/libcommon.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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-dawg abyss_dawg-abyss-dawg.o libfmindex.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.7/FMIndex' Making all in Assembly make[4]: Entering directory '/build/reproducible-path/abyss-2.3.7/Assembly' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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 '/build/reproducible-path/abyss-2.3.7/Assembly' Making all in dialign make[4]: Entering directory '/build/reproducible-path/abyss-2.3.7/dialign' gcc -DHAVE_CONFIG_H -I. -I.. -I/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o alig.o alig.c gcc -DHAVE_CONFIG_H -I. -I.. -I/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o assemble.o assemble.c gcc -DHAVE_CONFIG_H -I. -I.. -I/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o diag.o diag.c gcc -DHAVE_CONFIG_H -I. -I.. -I/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o io.o io.c gcc -DHAVE_CONFIG_H -I. -I.. -I/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o translate.o translate.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, | ^~~~~~~~~~~ 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, | ^~~~~~~~~~~ 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 ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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); | ^~~~~~~~~~~~~~~~ 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=/build/reproducible-path/abyss-2.3.7=. -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 '/build/reproducible-path/abyss-2.3.7/dialign' Making all in Align make[4]: Entering directory '/build/reproducible-path/abyss-2.3.7/Align' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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=/build/reproducible-path/abyss-2.3.7=. -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 g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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 make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.7/Align' Making all in ABYSS make[4]: Entering directory '/build/reproducible-path/abyss-2.3.7/ABYSS' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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-abyss.o `test -f 'abyss.cc' || echo './'`abyss.cc g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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 ABYSS-abyss.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../Assembly/libassembly.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.7/ABYSS' Making all in Parallel make[4]: Entering directory '/build/reproducible-path/abyss-2.3.7/Parallel' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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_P-parallelAbyss.o `test -f 'parallelAbyss.cpp' || echo './'`parallelAbyss.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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_P-CommLayer.o `test -f 'CommLayer.cpp' || echo './'`CommLayer.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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_P-NetworkSequenceCollection.o `test -f 'NetworkSequenceCollection.cpp' || echo './'`NetworkSequenceCollection.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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_P-MessageBuffer.o `test -f 'MessageBuffer.cpp' || echo './'`MessageBuffer.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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_P-Messages.o `test -f 'Messages.cpp' || echo './'`Messages.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -DPAIRED_DBG -I/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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_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/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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_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/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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_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/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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_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/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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_paired_dbg_mpi-Messages.o `test -f 'Messages.cpp' || echo './'`Messages.cpp g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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-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=/build/reproducible-path/abyss-2.3.7=. -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-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 '/build/reproducible-path/abyss-2.3.7/Parallel' Making all in Bloom make[4]: Entering directory '/build/reproducible-path/abyss-2.3.7/Bloom' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../vendor -I/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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_bloom-bloom.o `test -f 'bloom.cc' || echo './'`bloom.cc g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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-bloom abyss_bloom-bloom.o ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.7/Bloom' Making all in BloomDBG make[4]: Entering directory '/build/reproducible-path/abyss-2.3.7/BloomDBG' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../vendor -I/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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_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=/build/reproducible-path/abyss-2.3.7=. -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-bloom-dbg abyss_bloom_dbg-bloom-dbg.o ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.7/BloomDBG' Making all in Konnector make[4]: Entering directory '/build/reproducible-path/abyss-2.3.7/Konnector' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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.o `test -f 'konnector.cc' || echo './'`konnector.cc g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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.o ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.7/Konnector' Making all in Consensus make[4]: Entering directory '/build/reproducible-path/abyss-2.3.7/Consensus' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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=/build/reproducible-path/abyss-2.3.7=. -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 '/build/reproducible-path/abyss-2.3.7/Consensus' Making all in DAssembler make[4]: Entering directory '/build/reproducible-path/abyss-2.3.7/DAssembler' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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=/build/reproducible-path/abyss-2.3.7=. -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 '/build/reproducible-path/abyss-2.3.7/DAssembler' Making all in DistanceEst make[4]: Entering directory '/build/reproducible-path/abyss-2.3.7/DistanceEst' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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=/build/reproducible-path/abyss-2.3.7=. -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 g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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 make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.7/DistanceEst' Making all in KAligner make[4]: Entering directory '/build/reproducible-path/abyss-2.3.7/KAligner' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -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/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o KAligner-Aligner.o `test -f 'Aligner.cpp' || echo './'`Aligner.cpp g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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 KAligner KAligner-KAligner.o KAligner-Aligner.o ../DataLayer/libdatalayer.a ../Common/libcommon.a -lpthread -ldl -lm make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.7/KAligner' Making all in Layout make[4]: Entering directory '/build/reproducible-path/abyss-2.3.7/Layout' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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_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]' ../Graph/DotIO.h:77:18: required from 'std::ostream& write_dot(std::ostream&, const Graph&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream]' layout.cc:314:12: required from here ../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=/build/reproducible-path/abyss-2.3.7=. -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-layout abyss_layout-layout.o ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.7/Layout' Making all in LogKmerCount make[4]: Entering directory '/build/reproducible-path/abyss-2.3.7/LogKmerCount' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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=/build/reproducible-path/abyss-2.3.7=. -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 '/build/reproducible-path/abyss-2.3.7/LogKmerCount' Making all in Map make[4]: Entering directory '/build/reproducible-path/abyss-2.3.7/Map' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../FMIndex -I/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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_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/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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_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/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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_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/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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_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]' ../Graph/DotIO.h:77:18: required from 'std::ostream& write_dot(std::ostream&, const Graph&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream]' ../Graph/DotIO.h:125:26: required from 'std::ostream& operator<<(std::ostream&, const DotWriter > >&)' ../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]' overlap.cc:502:13: required from here ../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=/build/reproducible-path/abyss-2.3.7=. -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-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=/build/reproducible-path/abyss-2.3.7=. -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-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=/build/reproducible-path/abyss-2.3.7=. -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-overlap abyss_overlap-overlap.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=/build/reproducible-path/abyss-2.3.7=. -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-map-ssq abyss_map_ssq-map.o ../FMIndex/libfmindex.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../DataBase/libdb.a -lsqlite3 -ldl -lm -ldl -lm make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.7/Map' Making all in MergePaths make[4]: Entering directory '/build/reproducible-path/abyss-2.3.7/MergePaths' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -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/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o MergeContigs-MergeContigs.o `test -f 'MergeContigs.cpp' || echo './'`MergeContigs.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Align -I../Common -I../DataLayer -I../SimpleGraph -I/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o PathConsensus-PathConsensus.o `test -f 'PathConsensus.cpp' || echo './'`PathConsensus.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]' ../Graph/DotIO.h:77:18: required from 'std::ostream& write_dot(std::ostream&, const Graph&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream]' ../Graph/DotIO.h:125:26: required from 'std::ostream& operator<<(std::ostream&, const DotWriter > >&)' ../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]' MergeContigs.cpp:428:13: required from here ../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); | ~~~^~~~~~~~~~~~~~~~~~~ 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]' ../Graph/DotIO.h:77:18: required from 'std::ostream& write_dot(std::ostream&, const Graph&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream]' ../Graph/DotIO.h:125:26: required from 'std::ostream& operator<<(std::ostream&, const DotWriter > >&)' ../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]' PathConsensus.cpp:999:14: required from here ../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=/build/reproducible-path/abyss-2.3.7=. -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 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=/build/reproducible-path/abyss-2.3.7=. -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 PathConsensus PathConsensus-PathConsensus.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a ../dialign/libdialign.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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 MergePaths MergePaths-MergePaths.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.7/MergePaths' Making all in Overlap make[4]: Entering directory '/build/reproducible-path/abyss-2.3.7/Overlap' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -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]' ../Graph/DotIO.h:77:18: required from 'std::ostream& write_dot(std::ostream&, const Graph&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream]' ../Graph/DotIO.h:125:26: required from 'std::ostream& operator<<(std::ostream&, const DotWriter > >&)' Overlap.cpp:481:35: required from here ../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]' ../Graph/DotIO.h:77:18: required from 'std::ostream& write_dot(std::ostream&, const Graph&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream]' ../Graph/DotIO.h:125:26: required from 'std::ostream& operator<<(std::ostream&, const DotWriter > >&)' ../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]' Overlap.cpp:587:14: required from here ../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=/build/reproducible-path/abyss-2.3.7=. -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 Overlap Overlap-Overlap.o ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.7/Overlap' Making all in PairedDBG make[4]: Entering directory '/build/reproducible-path/abyss-2.3.7/PairedDBG' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -DPAIRED_DBG -I.. -I/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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_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/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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_paired_dbg-KmerPair.o `test -f 'KmerPair.cc' || echo './'`KmerPair.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -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=/build/reproducible-path/abyss-2.3.7=. -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-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 '/build/reproducible-path/abyss-2.3.7/PairedDBG' Making all in ParseAligns make[4]: Entering directory '/build/reproducible-path/abyss-2.3.7/ParseAligns' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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=/build/reproducible-path/abyss-2.3.7=. -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 g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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=/build/reproducible-path/abyss-2.3.7=. -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 make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.7/ParseAligns' Making all in PathOverlap make[4]: Entering directory '/build/reproducible-path/abyss-2.3.7/PathOverlap' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -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]' ../Graph/DotIO.h:77:18: required from 'std::ostream& write_dot(std::ostream&, const Graph&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream]' ../Graph/DotIO.h:125:26: required from 'std::ostream& operator<<(std::ostream&, const DotWriter > >&)' ../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]' PathOverlap.cpp:709:14: required from here ../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=/build/reproducible-path/abyss-2.3.7=. -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 PathOverlap PathOverlap-PathOverlap.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.7/PathOverlap' Making all in PopBubbles make[4]: Entering directory '/build/reproducible-path/abyss-2.3.7/PopBubbles' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Align -I../Common -I../DataLayer -I/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -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]' ../Graph/DotIO.h:77:18: required from 'std::ostream& write_dot(std::ostream&, const Graph&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream]' ../Graph/DotIO.h:125:26: required from 'std::ostream& operator<<(std::ostream&, const DotWriter > >&)' ../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]' PopBubbles.cpp:723:14: required from here ../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=/build/reproducible-path/abyss-2.3.7=. -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 PopBubbles PopBubbles-PopBubbles.o ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a ../dialign/libdialign.a -ldl -lm make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.7/PopBubbles' Making all in Scaffold make[4]: Entering directory '/build/reproducible-path/abyss-2.3.7/Scaffold' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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_scaffold-scaffold.o `test -f 'scaffold.cc' || echo './'`scaffold.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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_junction-junction.o `test -f 'junction.cc' || echo './'`junction.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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_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]' ../Graph/DotIO.h:77:18: required from 'std::ostream& write_dot(std::ostream&, const Graph&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream]' longseqdist.cpp:208:11: required from here ../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); | ~~~^~~~~~~~~~~~~~~~~~~ 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]' ../Graph/DotIO.h:77:18: required from 'std::ostream& write_dot(std::ostream&, const Graph&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream]' scaffold.cc:824:13: required from here ../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=/build/reproducible-path/abyss-2.3.7=. -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-junction abyss_junction-junction.o ../Common/libcommon.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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-longseqdist abyss_longseqdist-longseqdist.o ../Common/libcommon.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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-scaffold abyss_scaffold-scaffold.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.7/Scaffold' Making all in SimpleGraph make[4]: Entering directory '/build/reproducible-path/abyss-2.3.7/SimpleGraph' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -Wno-strict-aliasing -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -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=/build/reproducible-path/abyss-2.3.7=. -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 SimpleGraph SimpleGraph-SimpleGraph.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../Common/libcommon.a -lpthread -ldl -lm make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.7/SimpleGraph' Making all in kmerprint make[4]: Entering directory '/build/reproducible-path/abyss-2.3.7/kmerprint' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Assembly -I../Common -I../DataLayer -I/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o kmerprint-kmerprint.o `test -f 'kmerprint.cc' || echo './'`kmerprint.cc g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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 kmerprint kmerprint-kmerprint.o ../Assembly/libassembly.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.7/kmerprint' Making all in FilterGraph make[4]: Entering directory '/build/reproducible-path/abyss-2.3.7/FilterGraph' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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_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]' ../Graph/DotIO.h:77:18: required from 'std::ostream& write_dot(std::ostream&, const Graph&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream]' ../Graph/DotIO.h:125:26: required from 'std::ostream& operator<<(std::ostream&, const DotWriter > >&)' ../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]' FilterGraph.cc:825:14: required from here ../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=/build/reproducible-path/abyss-2.3.7=. -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-filtergraph abyss_filtergraph-FilterGraph.o ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.7/FilterGraph' Making all in GapFiller make[4]: Entering directory '/build/reproducible-path/abyss-2.3.7/GapFiller' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../Align -D SAM_SEQ_QUAL=1 -I/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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=/build/reproducible-path/abyss-2.3.7=. -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 '/build/reproducible-path/abyss-2.3.7/GapFiller' Making all in Sealer make[4]: Entering directory '/build/reproducible-path/abyss-2.3.7/Sealer' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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_sealer-sealer.o `test -f 'sealer.cc' || echo './'`sealer.cc g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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-sealer abyss_sealer-sealer.o ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.7/Sealer' Making all in RResolver make[4]: Entering directory '/build/reproducible-path/abyss-2.3.7/RResolver' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/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=/build/reproducible-path/abyss-2.3.7=. -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/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/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=/build/reproducible-path/abyss-2.3.7=. -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 g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/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=/build/reproducible-path/abyss-2.3.7=. -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/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/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=/build/reproducible-path/abyss-2.3.7=. -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/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/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=/build/reproducible-path/abyss-2.3.7=. -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 g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/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=/build/reproducible-path/abyss-2.3.7=. -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/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/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=/build/reproducible-path/abyss-2.3.7=. -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 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]' ../Graph/DotIO.h:77:18: required from 'std::ostream& write_dot(std::ostream&, const Graph&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream]' ../Graph/DotIO.h:125:26: required from 'std::ostream& operator<<(std::ostream&, const DotWriter > >&)' ../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]' Contigs.cpp:140:13: required from here ../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); | ~~~^~~~~~~~~~~~~~~~~~~ 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]' ../Graph/DotIO.h:77:18: required from 'std::ostream& write_dot(std::ostream&, const Graph&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream]' ../Graph/DotIO.h:125:26: required from 'std::ostream& operator<<(std::ostream&, const DotWriter > >&)' ../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]' Contigs.cpp:140:13: required from here ../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); | ~~~^~~~~~~~~~~~~~~~~~~ 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=/build/reproducible-path/abyss-2.3.7=. -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 '/build/reproducible-path/abyss-2.3.7/RResolver' Making all in AdjList make[4]: Entering directory '/build/reproducible-path/abyss-2.3.7/AdjList' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -DPAIRED_DBG -I/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -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]' ../Graph/DotIO.h:77:18: required from 'std::ostream& write_dot(std::ostream&, const Graph&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream]' ../Graph/DotIO.h:125:26: required from 'std::ostream& operator<<(std::ostream&, const DotWriter > >&)' ../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]' AdjList.cpp:401:13: required from here ../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=/build/reproducible-path/abyss-2.3.7=. -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 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 '/build/reproducible-path/abyss-2.3.7/AdjList' Making all in vendor make[4]: Entering directory '/build/reproducible-path/abyss-2.3.7/vendor' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.7/vendor' Making all in vendor/gtest-1.7.0 make[4]: Entering directory '/build/reproducible-path/abyss-2.3.7/vendor/gtest-1.7.0' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.7/vendor/gtest-1.7.0' Making all in Unittest make[4]: Entering directory '/build/reproducible-path/abyss-2.3.7/Unittest' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.7/Unittest' make[4]: Entering directory '/build/reproducible-path/abyss-2.3.7' make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.7' make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.7' make[2]: Leaving directory '/build/reproducible-path/abyss-2.3.7' markdown README.md > README.html make[1]: Leaving directory '/build/reproducible-path/abyss-2.3.7' dh_auto_test make -j12 check "TESTSUITEFLAGS=-j12 --verbose" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/abyss-2.3.7' Making check in bin make[2]: Entering directory '/build/reproducible-path/abyss-2.3.7/bin' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/abyss-2.3.7/bin' Making check in doc make[2]: Entering directory '/build/reproducible-path/abyss-2.3.7/doc' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/abyss-2.3.7/doc' Making check in Common make[2]: Entering directory '/build/reproducible-path/abyss-2.3.7/Common' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/abyss-2.3.7/Common' Making check in Graph make[2]: Entering directory '/build/reproducible-path/abyss-2.3.7/Graph' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/abyss-2.3.7/Graph' Making check in DataLayer make[2]: Entering directory '/build/reproducible-path/abyss-2.3.7/DataLayer' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/abyss-2.3.7/DataLayer' Making check in DataBase make[2]: Entering directory '/build/reproducible-path/abyss-2.3.7/DataBase' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/abyss-2.3.7/DataBase' Making check in FMIndex make[2]: Entering directory '/build/reproducible-path/abyss-2.3.7/FMIndex' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/abyss-2.3.7/FMIndex' Making check in Assembly make[2]: Entering directory '/build/reproducible-path/abyss-2.3.7/Assembly' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/abyss-2.3.7/Assembly' Making check in dialign make[2]: Entering directory '/build/reproducible-path/abyss-2.3.7/dialign' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/abyss-2.3.7/dialign' Making check in Align make[2]: Entering directory '/build/reproducible-path/abyss-2.3.7/Align' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/abyss-2.3.7/Align' Making check in ABYSS make[2]: Entering directory '/build/reproducible-path/abyss-2.3.7/ABYSS' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/abyss-2.3.7/ABYSS' Making check in Parallel make[2]: Entering directory '/build/reproducible-path/abyss-2.3.7/Parallel' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/abyss-2.3.7/Parallel' Making check in Bloom make[2]: Entering directory '/build/reproducible-path/abyss-2.3.7/Bloom' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/abyss-2.3.7/Bloom' Making check in BloomDBG make[2]: Entering directory '/build/reproducible-path/abyss-2.3.7/BloomDBG' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/abyss-2.3.7/BloomDBG' Making check in Konnector make[2]: Entering directory '/build/reproducible-path/abyss-2.3.7/Konnector' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/abyss-2.3.7/Konnector' Making check in Consensus make[2]: Entering directory '/build/reproducible-path/abyss-2.3.7/Consensus' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/abyss-2.3.7/Consensus' Making check in DAssembler make[2]: Entering directory '/build/reproducible-path/abyss-2.3.7/DAssembler' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/abyss-2.3.7/DAssembler' Making check in DistanceEst make[2]: Entering directory '/build/reproducible-path/abyss-2.3.7/DistanceEst' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/abyss-2.3.7/DistanceEst' Making check in KAligner make[2]: Entering directory '/build/reproducible-path/abyss-2.3.7/KAligner' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/abyss-2.3.7/KAligner' Making check in Layout make[2]: Entering directory '/build/reproducible-path/abyss-2.3.7/Layout' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/abyss-2.3.7/Layout' Making check in LogKmerCount make[2]: Entering directory '/build/reproducible-path/abyss-2.3.7/LogKmerCount' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/abyss-2.3.7/LogKmerCount' Making check in Map make[2]: Entering directory '/build/reproducible-path/abyss-2.3.7/Map' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/abyss-2.3.7/Map' Making check in MergePaths make[2]: Entering directory '/build/reproducible-path/abyss-2.3.7/MergePaths' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/abyss-2.3.7/MergePaths' Making check in Overlap make[2]: Entering directory '/build/reproducible-path/abyss-2.3.7/Overlap' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/abyss-2.3.7/Overlap' Making check in PairedDBG make[2]: Entering directory '/build/reproducible-path/abyss-2.3.7/PairedDBG' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/abyss-2.3.7/PairedDBG' Making check in ParseAligns make[2]: Entering directory '/build/reproducible-path/abyss-2.3.7/ParseAligns' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/abyss-2.3.7/ParseAligns' Making check in PathOverlap make[2]: Entering directory '/build/reproducible-path/abyss-2.3.7/PathOverlap' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/abyss-2.3.7/PathOverlap' Making check in PopBubbles make[2]: Entering directory '/build/reproducible-path/abyss-2.3.7/PopBubbles' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/abyss-2.3.7/PopBubbles' Making check in Scaffold make[2]: Entering directory '/build/reproducible-path/abyss-2.3.7/Scaffold' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/abyss-2.3.7/Scaffold' Making check in SimpleGraph make[2]: Entering directory '/build/reproducible-path/abyss-2.3.7/SimpleGraph' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/abyss-2.3.7/SimpleGraph' Making check in kmerprint make[2]: Entering directory '/build/reproducible-path/abyss-2.3.7/kmerprint' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/abyss-2.3.7/kmerprint' Making check in FilterGraph make[2]: Entering directory '/build/reproducible-path/abyss-2.3.7/FilterGraph' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/abyss-2.3.7/FilterGraph' Making check in GapFiller make[2]: Entering directory '/build/reproducible-path/abyss-2.3.7/GapFiller' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/abyss-2.3.7/GapFiller' Making check in Sealer make[2]: Entering directory '/build/reproducible-path/abyss-2.3.7/Sealer' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/abyss-2.3.7/Sealer' Making check in RResolver make[2]: Entering directory '/build/reproducible-path/abyss-2.3.7/RResolver' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/abyss-2.3.7/RResolver' Making check in AdjList make[2]: Entering directory '/build/reproducible-path/abyss-2.3.7/AdjList' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/abyss-2.3.7/AdjList' Making check in vendor make[2]: Entering directory '/build/reproducible-path/abyss-2.3.7/vendor' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/abyss-2.3.7/vendor' Making check in vendor/gtest-1.7.0 make[2]: Entering directory '/build/reproducible-path/abyss-2.3.7/vendor/gtest-1.7.0' make libgtest.a libgtest_main.a make[3]: Entering directory '/build/reproducible-path/abyss-2.3.7/vendor/gtest-1.7.0' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I../.. -I../.. -isystem ../../vendor/gtest-1.7.0/include -I/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -Wno-missing-field-initializers -Wno-uninitialized -Wno-error=unused-result -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -Wno-missing-field-initializers -Wno-uninitialized -Wno-error=unused-result -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -Wno-missing-field-initializers -Wno-uninitialized -Wno-error=unused-result -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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_main.a ar cru libgtest_main.a src/libgtest_main_a-gtest_main.o src/libgtest_main_a-gtest-all.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libgtest_main.a rm -f libgtest.a ar cru libgtest.a src/libgtest_a-gtest-all.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libgtest.a make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.7/vendor/gtest-1.7.0' make[2]: Leaving directory '/build/reproducible-path/abyss-2.3.7/vendor/gtest-1.7.0' Making check in Unittest make[2]: Entering directory '/build/reproducible-path/abyss-2.3.7/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 '/build/reproducible-path/abyss-2.3.7/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/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../Common -I/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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../DataLayer -I../Common -I/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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=/build/reproducible-path/abyss-2.3.7=. -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=/build/reproducible-path/abyss-2.3.7=. -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=/build/reproducible-path/abyss-2.3.7=. -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=/build/reproducible-path/abyss-2.3.7=. -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=/build/reproducible-path/abyss-2.3.7=. -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=/build/reproducible-path/abyss-2.3.7=. -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=/build/reproducible-path/abyss-2.3.7=. -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=/build/reproducible-path/abyss-2.3.7=. -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=/build/reproducible-path/abyss-2.3.7=. -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=/build/reproducible-path/abyss-2.3.7=. -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=/build/reproducible-path/abyss-2.3.7=. -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=/build/reproducible-path/abyss-2.3.7=. -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=/build/reproducible-path/abyss-2.3.7=. -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=/build/reproducible-path/abyss-2.3.7=. -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=/build/reproducible-path/abyss-2.3.7=. -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=/build/reproducible-path/abyss-2.3.7=. -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=/build/reproducible-path/abyss-2.3.7=. -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=/build/reproducible-path/abyss-2.3.7=. -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=/build/reproducible-path/abyss-2.3.7=. -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=/build/reproducible-path/abyss-2.3.7=. -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=/build/reproducible-path/abyss-2.3.7=. -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=/build/reproducible-path/abyss-2.3.7=. -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=/build/reproducible-path/abyss-2.3.7=. -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 -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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=/build/reproducible-path/abyss-2.3.7=. -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 -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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=/build/reproducible-path/abyss-2.3.7=. -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=/build/reproducible-path/abyss-2.3.7=. -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 g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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 -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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=/build/reproducible-path/abyss-2.3.7=. -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 -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -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=/build/reproducible-path/abyss-2.3.7=. -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 make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.7/Unittest' make check-TESTS make[3]: Entering directory '/build/reproducible-path/abyss-2.3.7/Unittest' make[4]: Entering directory '/build/reproducible-path/abyss-2.3.7/Unittest' PASS: common_histogram PASS: common_bitutil PASS: common_stringutil PASS: common_KmerIterator PASS: common_sequence PASS: common_kmer PASS: common_sam PASS: BloomFilter PASS: graph_AllPathsSearch PASS: graph_HashGraph PASS: Konnector_DBGBloomAlgorithms PASS: graph_ConstrainedBFSVisitor PASS: Konnector_DBGBloom PASS: common_sam_ssq PASS: graph_BidirectionalBFS PASS: graph_DotIO PASS: graph_ExtendPath PASS: graph_UndirectedGraph PASS: graph_ConstrainedBidiBFSVisitor PASS: Konnector_konnector PASS: PairedDBG_KmerPair PASS: PairedDBG_Dinuc PASS: BloomDBG_BloomDBG PASS: PairedDBG_BranchRecord PASS: BloomDBG_HashAgnosticCascadingBloom PASS: BloomDBG_RollingHashIterator PASS: BloomDBG_CountingBloomFilter PASS: BloomDBG_RollingHash PASS: BloomDBG_MaskedKmer PASS: BloomDBG_SpacedSeed PASS: BloomDBG_LightweightKmer PASS: BloomDBG_RollingBloomDBG PASS: DBG_LoadAlgorithm PASS: PairedDBG_LoadAlgorithm ============================================================================ Testsuite summary for ABySS 2.3.7 ============================================================================ # TOTAL: 34 # PASS: 34 # SKIP: 0 # XFAIL: 0 # FAIL: 0 # XPASS: 0 # ERROR: 0 ============================================================================ make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.7/Unittest' make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.7/Unittest' make[2]: Leaving directory '/build/reproducible-path/abyss-2.3.7/Unittest' make[2]: Entering directory '/build/reproducible-path/abyss-2.3.7' make[2]: Leaving directory '/build/reproducible-path/abyss-2.3.7' make[1]: Leaving directory '/build/reproducible-path/abyss-2.3.7' create-stamp debian/debhelper-build-stamp dh_prep debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/abyss-2.3.7' dh_auto_install --destdir=debian/tmp make -j12 install DESTDIR=/build/reproducible-path/abyss-2.3.7/debian/tmp AM_UPDATE_INFO_DIR=no make[2]: Entering directory '/build/reproducible-path/abyss-2.3.7' Making install in bin make[3]: Entering directory '/build/reproducible-path/abyss-2.3.7/bin' make[4]: Entering directory '/build/reproducible-path/abyss-2.3.7/bin' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/abyss-2.3.7/debian/tmp/usr/bin' /usr/bin/install -c abyss-bowtie abyss-bowtie2 abyss-bwa abyss-bwasw abyss-bwamem abyss-fatoagp abyss-kaligner abyss-pe abyss-samtoafg abyss-tabtomd abyss-bloom-dist.mk abyss-dida abyss-stack-size '/build/reproducible-path/abyss-2.3.7/debian/tmp/usr/bin' make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.7/bin' make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.7/bin' Making install in doc make[3]: Entering directory '/build/reproducible-path/abyss-2.3.7/doc' make[4]: Entering directory '/build/reproducible-path/abyss-2.3.7/doc' make[4]: Nothing to be done for 'install-exec-am'. /usr/bin/mkdir -p '/build/reproducible-path/abyss-2.3.7/debian/tmp/usr/share/doc/abyss' /usr/bin/install -c -m 644 flowchart.pdf flowchart_simplified.pdf '/build/reproducible-path/abyss-2.3.7/debian/tmp/usr/share/doc/abyss' make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.7/doc' make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.7/doc' Making install in Common make[3]: Entering directory '/build/reproducible-path/abyss-2.3.7/Common' make[4]: Entering directory '/build/reproducible-path/abyss-2.3.7/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 '/build/reproducible-path/abyss-2.3.7/Common' make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.7/Common' Making install in Graph make[3]: Entering directory '/build/reproducible-path/abyss-2.3.7/Graph' make[4]: Entering directory '/build/reproducible-path/abyss-2.3.7/Graph' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/abyss-2.3.7/debian/tmp/usr/bin' /usr/bin/install -c abyss-gc abyss-todot '/build/reproducible-path/abyss-2.3.7/debian/tmp/usr/bin' make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.7/Graph' make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.7/Graph' Making install in DataLayer make[3]: Entering directory '/build/reproducible-path/abyss-2.3.7/DataLayer' make[4]: Entering directory '/build/reproducible-path/abyss-2.3.7/DataLayer' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/abyss-2.3.7/debian/tmp/usr/bin' /usr/bin/install -c abyss-fac abyss-tofastq '/build/reproducible-path/abyss-2.3.7/debian/tmp/usr/bin' make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.7/DataLayer' make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.7/DataLayer' Making install in DataBase make[3]: Entering directory '/build/reproducible-path/abyss-2.3.7/DataBase' make[4]: Entering directory '/build/reproducible-path/abyss-2.3.7/DataBase' /usr/bin/mkdir -p '/build/reproducible-path/abyss-2.3.7/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/abyss-2.3.7/debian/tmp/usr/bin' /usr/bin/install -c abyss-db-txt '/build/reproducible-path/abyss-2.3.7/debian/tmp/usr/bin' /usr/bin/install -c abyss-db-csv '/build/reproducible-path/abyss-2.3.7/debian/tmp/usr/bin' make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.7/DataBase' make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.7/DataBase' Making install in FMIndex make[3]: Entering directory '/build/reproducible-path/abyss-2.3.7/FMIndex' make[4]: Entering directory '/build/reproducible-path/abyss-2.3.7/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 '/build/reproducible-path/abyss-2.3.7/FMIndex' make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.7/FMIndex' Making install in Assembly make[3]: Entering directory '/build/reproducible-path/abyss-2.3.7/Assembly' make[4]: Entering directory '/build/reproducible-path/abyss-2.3.7/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 '/build/reproducible-path/abyss-2.3.7/Assembly' make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.7/Assembly' Making install in dialign make[3]: Entering directory '/build/reproducible-path/abyss-2.3.7/dialign' make[4]: Entering directory '/build/reproducible-path/abyss-2.3.7/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 '/build/reproducible-path/abyss-2.3.7/dialign' make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.7/dialign' Making install in Align make[3]: Entering directory '/build/reproducible-path/abyss-2.3.7/Align' make[4]: Entering directory '/build/reproducible-path/abyss-2.3.7/Align' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/abyss-2.3.7/debian/tmp/usr/bin' /usr/bin/install -c abyss-align abyss-mergepairs '/build/reproducible-path/abyss-2.3.7/debian/tmp/usr/bin' make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.7/Align' make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.7/Align' Making install in ABYSS make[3]: Entering directory '/build/reproducible-path/abyss-2.3.7/ABYSS' make[4]: Entering directory '/build/reproducible-path/abyss-2.3.7/ABYSS' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/abyss-2.3.7/debian/tmp/usr/bin' /usr/bin/install -c ABYSS '/build/reproducible-path/abyss-2.3.7/debian/tmp/usr/bin' make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.7/ABYSS' make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.7/ABYSS' Making install in Parallel make[3]: Entering directory '/build/reproducible-path/abyss-2.3.7/Parallel' make[4]: Entering directory '/build/reproducible-path/abyss-2.3.7/Parallel' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/abyss-2.3.7/debian/tmp/usr/bin' /usr/bin/install -c ABYSS-P abyss-paired-dbg-mpi '/build/reproducible-path/abyss-2.3.7/debian/tmp/usr/bin' make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.7/Parallel' make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.7/Parallel' Making install in Bloom make[3]: Entering directory '/build/reproducible-path/abyss-2.3.7/Bloom' make[4]: Entering directory '/build/reproducible-path/abyss-2.3.7/Bloom' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/abyss-2.3.7/debian/tmp/usr/bin' /usr/bin/install -c abyss-bloom '/build/reproducible-path/abyss-2.3.7/debian/tmp/usr/bin' make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.7/Bloom' make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.7/Bloom' Making install in BloomDBG make[3]: Entering directory '/build/reproducible-path/abyss-2.3.7/BloomDBG' make[4]: Entering directory '/build/reproducible-path/abyss-2.3.7/BloomDBG' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/abyss-2.3.7/debian/tmp/usr/bin' /usr/bin/install -c abyss-bloom-dbg '/build/reproducible-path/abyss-2.3.7/debian/tmp/usr/bin' make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.7/BloomDBG' make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.7/BloomDBG' Making install in Konnector make[3]: Entering directory '/build/reproducible-path/abyss-2.3.7/Konnector' make[4]: Entering directory '/build/reproducible-path/abyss-2.3.7/Konnector' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/abyss-2.3.7/debian/tmp/usr/bin' /usr/bin/install -c konnector '/build/reproducible-path/abyss-2.3.7/debian/tmp/usr/bin' make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.7/Konnector' make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.7/Konnector' Making install in Consensus make[3]: Entering directory '/build/reproducible-path/abyss-2.3.7/Consensus' make[4]: Entering directory '/build/reproducible-path/abyss-2.3.7/Consensus' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/abyss-2.3.7/debian/tmp/usr/bin' /usr/bin/install -c Consensus '/build/reproducible-path/abyss-2.3.7/debian/tmp/usr/bin' make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.7/Consensus' make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.7/Consensus' Making install in DAssembler make[3]: Entering directory '/build/reproducible-path/abyss-2.3.7/DAssembler' make[4]: Entering directory '/build/reproducible-path/abyss-2.3.7/DAssembler' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/abyss-2.3.7/debian/tmp/usr/bin' /usr/bin/install -c DAssembler '/build/reproducible-path/abyss-2.3.7/debian/tmp/usr/bin' make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.7/DAssembler' make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.7/DAssembler' Making install in DistanceEst make[3]: Entering directory '/build/reproducible-path/abyss-2.3.7/DistanceEst' make[4]: Entering directory '/build/reproducible-path/abyss-2.3.7/DistanceEst' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/abyss-2.3.7/debian/tmp/usr/bin' /usr/bin/install -c DistanceEst DistanceEst-ssq '/build/reproducible-path/abyss-2.3.7/debian/tmp/usr/bin' make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.7/DistanceEst' make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.7/DistanceEst' Making install in KAligner make[3]: Entering directory '/build/reproducible-path/abyss-2.3.7/KAligner' make[4]: Entering directory '/build/reproducible-path/abyss-2.3.7/KAligner' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/abyss-2.3.7/debian/tmp/usr/bin' /usr/bin/install -c KAligner '/build/reproducible-path/abyss-2.3.7/debian/tmp/usr/bin' make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.7/KAligner' make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.7/KAligner' Making install in Layout make[3]: Entering directory '/build/reproducible-path/abyss-2.3.7/Layout' make[4]: Entering directory '/build/reproducible-path/abyss-2.3.7/Layout' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/abyss-2.3.7/debian/tmp/usr/bin' /usr/bin/install -c abyss-layout '/build/reproducible-path/abyss-2.3.7/debian/tmp/usr/bin' make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.7/Layout' make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.7/Layout' Making install in LogKmerCount make[3]: Entering directory '/build/reproducible-path/abyss-2.3.7/LogKmerCount' make[4]: Entering directory '/build/reproducible-path/abyss-2.3.7/LogKmerCount' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/abyss-2.3.7/debian/tmp/usr/bin' /usr/bin/install -c logcounter '/build/reproducible-path/abyss-2.3.7/debian/tmp/usr/bin' make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.7/LogKmerCount' make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.7/LogKmerCount' Making install in Map make[3]: Entering directory '/build/reproducible-path/abyss-2.3.7/Map' make[4]: Entering directory '/build/reproducible-path/abyss-2.3.7/Map' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/abyss-2.3.7/debian/tmp/usr/bin' /usr/bin/install -c abyss-index abyss-map abyss-map-ssq abyss-overlap '/build/reproducible-path/abyss-2.3.7/debian/tmp/usr/bin' make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.7/Map' make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.7/Map' Making install in MergePaths make[3]: Entering directory '/build/reproducible-path/abyss-2.3.7/MergePaths' make[4]: Entering directory '/build/reproducible-path/abyss-2.3.7/MergePaths' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/abyss-2.3.7/debian/tmp/usr/bin' /usr/bin/install -c MergePaths MergeContigs PathConsensus '/build/reproducible-path/abyss-2.3.7/debian/tmp/usr/bin' make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.7/MergePaths' make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.7/MergePaths' Making install in Overlap make[3]: Entering directory '/build/reproducible-path/abyss-2.3.7/Overlap' make[4]: Entering directory '/build/reproducible-path/abyss-2.3.7/Overlap' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/abyss-2.3.7/debian/tmp/usr/bin' /usr/bin/install -c Overlap '/build/reproducible-path/abyss-2.3.7/debian/tmp/usr/bin' make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.7/Overlap' make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.7/Overlap' Making install in PairedDBG make[3]: Entering directory '/build/reproducible-path/abyss-2.3.7/PairedDBG' make[4]: Entering directory '/build/reproducible-path/abyss-2.3.7/PairedDBG' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/abyss-2.3.7/debian/tmp/usr/bin' /usr/bin/install -c abyss-paired-dbg '/build/reproducible-path/abyss-2.3.7/debian/tmp/usr/bin' make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.7/PairedDBG' make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.7/PairedDBG' Making install in ParseAligns make[3]: Entering directory '/build/reproducible-path/abyss-2.3.7/ParseAligns' make[4]: Entering directory '/build/reproducible-path/abyss-2.3.7/ParseAligns' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/abyss-2.3.7/debian/tmp/usr/bin' /usr/bin/install -c abyss-fixmate abyss-fixmate-ssq ParseAligns '/build/reproducible-path/abyss-2.3.7/debian/tmp/usr/bin' make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.7/ParseAligns' make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.7/ParseAligns' Making install in PathOverlap make[3]: Entering directory '/build/reproducible-path/abyss-2.3.7/PathOverlap' make[4]: Entering directory '/build/reproducible-path/abyss-2.3.7/PathOverlap' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/abyss-2.3.7/debian/tmp/usr/bin' /usr/bin/install -c PathOverlap '/build/reproducible-path/abyss-2.3.7/debian/tmp/usr/bin' make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.7/PathOverlap' make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.7/PathOverlap' Making install in PopBubbles make[3]: Entering directory '/build/reproducible-path/abyss-2.3.7/PopBubbles' make[4]: Entering directory '/build/reproducible-path/abyss-2.3.7/PopBubbles' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/abyss-2.3.7/debian/tmp/usr/bin' /usr/bin/install -c PopBubbles '/build/reproducible-path/abyss-2.3.7/debian/tmp/usr/bin' make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.7/PopBubbles' make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.7/PopBubbles' Making install in Scaffold make[3]: Entering directory '/build/reproducible-path/abyss-2.3.7/Scaffold' make[4]: Entering directory '/build/reproducible-path/abyss-2.3.7/Scaffold' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/abyss-2.3.7/debian/tmp/usr/bin' /usr/bin/install -c abyss-scaffold abyss-junction abyss-longseqdist '/build/reproducible-path/abyss-2.3.7/debian/tmp/usr/bin' make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.7/Scaffold' make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.7/Scaffold' Making install in SimpleGraph make[3]: Entering directory '/build/reproducible-path/abyss-2.3.7/SimpleGraph' make[4]: Entering directory '/build/reproducible-path/abyss-2.3.7/SimpleGraph' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/abyss-2.3.7/debian/tmp/usr/bin' /usr/bin/install -c SimpleGraph '/build/reproducible-path/abyss-2.3.7/debian/tmp/usr/bin' make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.7/SimpleGraph' make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.7/SimpleGraph' Making install in kmerprint make[3]: Entering directory '/build/reproducible-path/abyss-2.3.7/kmerprint' make[4]: Entering directory '/build/reproducible-path/abyss-2.3.7/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 '/build/reproducible-path/abyss-2.3.7/kmerprint' make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.7/kmerprint' Making install in FilterGraph make[3]: Entering directory '/build/reproducible-path/abyss-2.3.7/FilterGraph' make[4]: Entering directory '/build/reproducible-path/abyss-2.3.7/FilterGraph' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/abyss-2.3.7/debian/tmp/usr/bin' /usr/bin/install -c abyss-filtergraph '/build/reproducible-path/abyss-2.3.7/debian/tmp/usr/bin' make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.7/FilterGraph' make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.7/FilterGraph' Making install in GapFiller make[3]: Entering directory '/build/reproducible-path/abyss-2.3.7/GapFiller' make[4]: Entering directory '/build/reproducible-path/abyss-2.3.7/GapFiller' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/abyss-2.3.7/debian/tmp/usr/bin' /usr/bin/install -c abyss-gapfill '/build/reproducible-path/abyss-2.3.7/debian/tmp/usr/bin' make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.7/GapFiller' make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.7/GapFiller' Making install in Sealer make[3]: Entering directory '/build/reproducible-path/abyss-2.3.7/Sealer' make[4]: Entering directory '/build/reproducible-path/abyss-2.3.7/Sealer' /usr/bin/mkdir -p '/build/reproducible-path/abyss-2.3.7/debian/tmp/usr/bin' /usr/bin/install -c abyss-sealer '/build/reproducible-path/abyss-2.3.7/debian/tmp/usr/bin' make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.7/Sealer' make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.7/Sealer' Making install in RResolver make[3]: Entering directory '/build/reproducible-path/abyss-2.3.7/RResolver' make[4]: Entering directory '/build/reproducible-path/abyss-2.3.7/RResolver' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/abyss-2.3.7/debian/tmp/usr/bin' /usr/bin/install -c abyss-rresolver-short '/build/reproducible-path/abyss-2.3.7/debian/tmp/usr/bin' make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.7/RResolver' make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.7/RResolver' Making install in AdjList make[3]: Entering directory '/build/reproducible-path/abyss-2.3.7/AdjList' make[4]: Entering directory '/build/reproducible-path/abyss-2.3.7/AdjList' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/abyss-2.3.7/debian/tmp/usr/bin' /usr/bin/install -c AdjList '/build/reproducible-path/abyss-2.3.7/debian/tmp/usr/bin' make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.7/AdjList' make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.7/AdjList' Making install in vendor make[3]: Entering directory '/build/reproducible-path/abyss-2.3.7/vendor' make[4]: Entering directory '/build/reproducible-path/abyss-2.3.7/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 '/build/reproducible-path/abyss-2.3.7/vendor' make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.7/vendor' Making install in vendor/gtest-1.7.0 make[3]: Entering directory '/build/reproducible-path/abyss-2.3.7/vendor/gtest-1.7.0' make[4]: Entering directory '/build/reproducible-path/abyss-2.3.7/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 '/build/reproducible-path/abyss-2.3.7/vendor/gtest-1.7.0' make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.7/vendor/gtest-1.7.0' Making install in Unittest make[3]: Entering directory '/build/reproducible-path/abyss-2.3.7/Unittest' make[4]: Entering directory '/build/reproducible-path/abyss-2.3.7/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 '/build/reproducible-path/abyss-2.3.7/Unittest' make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.7/Unittest' make[3]: Entering directory '/build/reproducible-path/abyss-2.3.7' make[4]: Entering directory '/build/reproducible-path/abyss-2.3.7' make[4]: Nothing to be done for 'install-exec-am'. /usr/bin/mkdir -p '/build/reproducible-path/abyss-2.3.7/debian/tmp/usr/share/doc/abyss' /usr/bin/install -c -m 644 ChangeLog CITATION.bib CITATION.md COPYRIGHT LICENSE README.md '/build/reproducible-path/abyss-2.3.7/debian/tmp/usr/share/doc/abyss' make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.7' make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.7' make[2]: Leaving directory '/build/reproducible-path/abyss-2.3.7' mkdir -p debian/tmp/usr/share/man/man1 PATH=debian/tmp/usr/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/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 '/build/reproducible-path/abyss-2.3.7' debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/abyss-2.3.7' 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 '/build/reproducible-path/abyss-2.3.7' 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 dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'abyss-dbgsym' in '../abyss-dbgsym_2.3.7-3_amd64.deb'. dpkg-deb: building package 'abyss' in '../abyss_2.3.7-3_amd64.deb'. dpkg-genbuildinfo --build=binary -O../abyss_2.3.7-3_amd64.buildinfo dpkg-genchanges --build=binary -O../abyss_2.3.7-3_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/1207255 and its subdirectories I: Current time: Mon May 6 23:59:21 -12 2024 I: pbuilder-time-stamp: 1715083161 Tue May 7 11:59:23 UTC 2024 I: 1st build successful. Starting 2nd build on remote node infom02-amd64.debian.net. Tue May 7 11:59:23 UTC 2024 I: Preparing to do remote build '2' on infom02-amd64.debian.net. Tue May 7 12:06:17 UTC 2024 I: Deleting $TMPDIR on infom02-amd64.debian.net. Tue May 7 12:06:17 UTC 2024 I: abyss_2.3.7-3_amd64.changes: Format: 1.8 Date: Sat, 16 Dec 2023 18:14:36 +0100 Source: abyss Binary: abyss abyss-dbgsym Architecture: amd64 Version: 2.3.7-3 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: abyss - de novo, parallel, sequence assembler for short reads Closes: 1058457 Changes: abyss (2.3.7-3) unstable; urgency=medium . * Add build support for loongarch64 Closes: #1058457 Checksums-Sha1: b548ec75ca28d66c6a346279a7ec9ee637afbdd4 29862368 abyss-dbgsym_2.3.7-3_amd64.deb c16e11799142385848b81fb531733b66b02bc3a8 9233 abyss_2.3.7-3_amd64.buildinfo 893f07d0c056344695d2ba7d07f78fe80552477d 3265204 abyss_2.3.7-3_amd64.deb Checksums-Sha256: dbfabf88ace8bbcc0c96d4e7b9df39ad5404dc533d8c19c0124aac4c652eb20f 29862368 abyss-dbgsym_2.3.7-3_amd64.deb 870a7d514de9e39a71cabd24694253a2b773743091a593d592f412b38b807be8 9233 abyss_2.3.7-3_amd64.buildinfo 7baab453465f3f1b23f4a9765aed927b7e3d803160e469d52c26a97240608aed 3265204 abyss_2.3.7-3_amd64.deb Files: ad19d9c9a620ae7b31ebe5c0dc3c15ba 29862368 debug optional abyss-dbgsym_2.3.7-3_amd64.deb b5c49cad6d43fcaba4f7c328a8ff7051 9233 science optional abyss_2.3.7-3_amd64.buildinfo b5318d7b6c2aee36f73868c525b63253 3265204 science optional abyss_2.3.7-3_amd64.deb Tue May 7 12:06:19 UTC 2024 I: diffoscope 265 will be used to compare the two builds: Running as unit: rb-diffoscope-amd64_33-11166.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.bstw1hvP/abyss_2.3.7-3.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.bstw1hvP/abyss_2.3.7-3.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.bstw1hvP/abyss_2.3.7-3.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.bstw1hvP/b1/abyss_2.3.7-3_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.bstw1hvP/b2/abyss_2.3.7-3_amd64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.719s) 0.719s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.362s) 0.362s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 1.081s CPU time consumed: 1.079s Tue May 7 12:06:20 UTC 2024 I: diffoscope 265 found no differences in the changes files, and a .buildinfo file also exists. Tue May 7 12:06:20 UTC 2024 I: abyss from unstable built successfully and reproducibly on amd64. Tue May 7 12:06:22 UTC 2024 I: Submitting .buildinfo files to external archives: Tue May 7 12:06:22 UTC 2024 I: Submitting 12K b1/abyss_2.3.7-3_amd64.buildinfo.asc Tue May 7 12:06:22 UTC 2024 I: Submitting 12K b2/abyss_2.3.7-3_amd64.buildinfo.asc Tue May 7 12:06:23 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Tue May 7 12:06:23 UTC 2024 I: Done submitting .buildinfo files. Tue May 7 12:06:23 UTC 2024 I: Removing signed abyss_2.3.7-3_amd64.buildinfo.asc files: removed './b1/abyss_2.3.7-3_amd64.buildinfo.asc' removed './b2/abyss_2.3.7-3_amd64.buildinfo.asc'