Fri Sep 13 20:21:17 UTC 2024 I: starting to build abyss/unstable/arm64 on jenkins on '2024-09-13 20:20' Fri Sep 13 20:21:17 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_13/36448/console.log Fri Sep 13 20:21:17 UTC 2024 I: Downloading source for unstable/abyss=2.3.9-1 --2024-09-13 20:21:17-- http://deb.debian.org/debian/pool/main/a/abyss/abyss_2.3.9-1.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2302 (2.2K) [text/prs.lines.tag] Saving to: ‘abyss_2.3.9-1.dsc’ 0K .. 100% 317M=0s 2024-09-13 20:21:17 (317 MB/s) - ‘abyss_2.3.9-1.dsc’ saved [2302/2302] Fri Sep 13 20:21:17 UTC 2024 I: abyss_2.3.9-1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: abyss Binary: abyss Architecture: any Version: 2.3.9-1 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille , Michael R. Crusoe , Étienne Mollier Homepage: https://github.com/bcgsc/abyss Standards-Version: 4.7.0 Vcs-Browser: https://salsa.debian.org/med-team/abyss Vcs-Git: https://salsa.debian.org/med-team/abyss.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), architecture-is-64-bit, libboost-graph-dev, libbtllib-dev, libopenmpi-dev, libsparsehash-dev, libtext-multimarkdown-perl , libsqlite3-dev, pkgconf, help2man, debhelper Package-List: abyss deb science optional arch=any Checksums-Sha1: ec95d82f7bc7999f88c57d305dc270f71c342951 933744 abyss_2.3.9.orig.tar.xz 4211075a885a16e74b0fad03ed3e1afb99ac8d70 1497856 abyss_2.3.9-1.debian.tar.xz Checksums-Sha256: 0e41d8e0fea5674cdf21f2b53af1ec173791879486233cd28b385413ded8712d 933744 abyss_2.3.9.orig.tar.xz ff67c73eb6e72086fcd232546c81a8e7845a122e02bf83f8e47722ff82ddc218 1497856 abyss_2.3.9-1.debian.tar.xz Files: 633324e0140f6dd7934fdb4ebbf13f1a 933744 abyss_2.3.9.orig.tar.xz e1b282601dd4dd11a7bf833b3148c508 1497856 abyss_2.3.9-1.debian.tar.xz Dgit: 7625d6c097b895ae2b180b6e0c453e8ca98b7568 debian archive/debian/2.3.9-1 https://git.dgit.debian.org/abyss -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmbjViIUHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdqYJxAAlnO4YS5b9GPByZ7fvy4W4TFoQgfz Bil1q+hp006TGT5NzA9OjXvRbOptKJKK88ZEVKVfhF68nFtAh5/x6gOXrNMFWT5V 9ycIFUC1p7bIUJOyuGuosXgleZj0cOD5PRVeQ3ZXfWy5r89oTqJ2DJadvDMe10j1 ikSD1ydZKXvsnBLETR2pVt2uCanh4XKwaxfOPpjMgKJSGfJrTyzuKNMf93uZQBIG f5zmrvQ6fLgWoP35zPYFgXzxmm4YWfwdOTPEl1WFUWG3qk85B9fdfH159QfINGZ3 PBGq+RxZygGjW62yXbPbBAlfkKYF9zbriAjMwYpMUjd1eTrN2UcyEA+TlP7scvMn e6dzPdf43I97rEy4cnfzXioKQwHX57nB37xndI0cz1raW+LNXYUicajgV0QpKEYL nYBsJ6q9rgD9N+h0nMktWhp0Nt1sXsgZXHVvk82zOzfxFfo2LJK45AmZLIGxa4Kt aw4RmMS2rQwHpYORwg0AEo8Y1UtCC7iyaLNkh0kY8o9DY6OeQFMoFmsLjYtrgrdr 5wwNy4AjSx/lN9X3hxMw8i4X1ALo6yEP92DJI6en3VKXXLWn62mFUeOpbaCrfGa8 9zb1oIRLutZHGsD+Vb4R/MKJeKRW/sB1SLqt9W8c+FcjDCokP5LO+Lwq4qMHFikt NXCUoSQwCZUHzYU= =rhZ8 -----END PGP SIGNATURE----- Fri Sep 13 20:21:17 UTC 2024 I: Checking whether the package is not for us Fri Sep 13 20:21:17 UTC 2024 I: Starting 1st build on remote node codethink01-arm64.debian.net. Fri Sep 13 20:21:17 UTC 2024 I: Preparing to do remote build '1' on codethink01-arm64.debian.net. Fri Sep 13 20:27:50 UTC 2024 I: Deleting $TMPDIR on codethink01-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Thu Oct 16 14:44:18 -12 2025 I: pbuilder-time-stamp: 1760669058 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_2.3.9-1.dsc] I: copying [./abyss_2.3.9.orig.tar.xz] I: copying [./abyss_2.3.9-1.debian.tar.xz] I: Extracting source gpgv: Signature made Thu Sep 12 20:59:14 2024 gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./abyss_2.3.9-1.dsc: no acceptable signature found dpkg-source: info: extracting abyss in abyss-2.3.9 dpkg-source: info: unpacking abyss_2.3.9.orig.tar.xz dpkg-source: info: unpacking abyss_2.3.9-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying abyss-pe.patch dpkg-source: info: applying fix-privacy-breach.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2823553/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='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='4c9b90212de54fdc86ee4114ed8b994e' 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='2823553' 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.DpmzMZ4i/pbuilderrc_9mAP --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.DpmzMZ4i/b1 --logfile b1/build.log abyss_2.3.9-1.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' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink01-arm64 6.1.0-25-cloud-arm64 #1 SMP Debian 6.1.106-3 (2024-08-26) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2823553/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: arm64 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), architecture-is-64-bit, libboost-graph-dev, libbtllib-dev, libopenmpi-dev, libsparsehash-dev, libtext-multimarkdown-perl, libsqlite3-dev, pkgconf, 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 ... 19891 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 architecture-is-64-bit; however: Package architecture-is-64-bit 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 pkgconf; however: Package pkgconf 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: architecture-properties{a} autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} cpp-13{a} cpp-13-aarch64-linux-gnu{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gcc-13{a} gcc-13-aarch64-linux-gnu{a} gcc-13-base{a} gettext{a} gettext-base{a} gfortran-13{a} gfortran-13-aarch64-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} 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} libgcc-13-dev{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} libibmad5{a} libibumad3{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} libnghttp3-9{a} libngtcp2-16{a} libngtcp2-crypto-gnutls8{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} 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} 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} 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, 152 newly installed, 0 to remove and 0 not upgraded. Need to get 153 MB of archives. After unpacking 785 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main arm64 liblocale-gettext-perl arm64 1.07-7 [14.8 kB] Get: 2 http://deb.debian.org/debian unstable/main arm64 sensible-utils all 0.0.24 [24.8 kB] Get: 3 http://deb.debian.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.45-3 [314 kB] Get: 4 http://deb.debian.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.45-3 [100 kB] Get: 5 http://deb.debian.org/debian unstable/main arm64 file arm64 1:5.45-3 [43.0 kB] Get: 6 http://deb.debian.org/debian unstable/main arm64 gettext-base arm64 0.22.5-2 [198 kB] Get: 7 http://deb.debian.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-1+b1 [69.0 kB] Get: 8 http://deb.debian.org/debian unstable/main arm64 groff-base arm64 1.23.0-5 [1129 kB] Get: 9 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.40.2-8 [96.6 kB] Get: 10 http://deb.debian.org/debian unstable/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 11 http://deb.debian.org/debian unstable/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 12 http://deb.debian.org/debian unstable/main arm64 libedit2 arm64 3.1-20240808-1 [89.2 kB] Get: 13 http://deb.debian.org/debian unstable/main arm64 libcbor0.10 arm64 0.10.2-1.2 [27.2 kB] Get: 14 http://deb.debian.org/debian unstable/main arm64 libfido2-1 arm64 1.15.0-1 [74.1 kB] Get: 15 http://deb.debian.org/debian unstable/main arm64 libkrb5support0 arm64 1.21.3-3 [32.1 kB] Get: 16 http://deb.debian.org/debian unstable/main arm64 libcom-err2 arm64 1.47.1-1 [22.8 kB] Get: 17 http://deb.debian.org/debian unstable/main arm64 libk5crypto3 arm64 1.21.3-3 [80.8 kB] Get: 18 http://deb.debian.org/debian unstable/main arm64 libkeyutils1 arm64 1.6.3-3 [9112 B] Get: 19 http://deb.debian.org/debian unstable/main arm64 libkrb5-3 arm64 1.21.3-3 [310 kB] Get: 20 http://deb.debian.org/debian unstable/main arm64 libgssapi-krb5-2 arm64 1.21.3-3 [126 kB] Get: 21 http://deb.debian.org/debian unstable/main arm64 openssh-client arm64 1:9.8p1-8 [902 kB] Get: 22 http://deb.debian.org/debian unstable/main arm64 libpsl5t64 arm64 0.21.2-1.1 [56.8 kB] Get: 23 http://deb.debian.org/debian unstable/main arm64 wget arm64 1.24.5-2 [966 kB] Get: 24 http://deb.debian.org/debian unstable/main arm64 architecture-properties arm64 0.1.1+b1 [1880 B] Get: 25 http://deb.debian.org/debian unstable/main arm64 m4 arm64 1.4.19-4 [277 kB] Get: 26 http://deb.debian.org/debian unstable/main arm64 autoconf all 2.72-3 [493 kB] Get: 27 http://deb.debian.org/debian unstable/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 28 http://deb.debian.org/debian unstable/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 29 http://deb.debian.org/debian unstable/main arm64 autopoint all 0.22.5-2 [723 kB] Get: 30 http://deb.debian.org/debian unstable/main arm64 gcc-13-base arm64 13.3.0-6 [47.1 kB] Get: 31 http://deb.debian.org/debian unstable/main arm64 cpp-13-aarch64-linux-gnu arm64 13.3.0-6 [8211 kB] Get: 32 http://deb.debian.org/debian unstable/main arm64 cpp-13 arm64 13.3.0-6 [1276 B] Get: 33 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.20 [89.7 kB] Get: 34 http://deb.debian.org/debian unstable/main arm64 libgcc-13-dev arm64 13.3.0-6 [2241 kB] Get: 35 http://deb.debian.org/debian unstable/main arm64 gcc-13-aarch64-linux-gnu arm64 13.3.0-6 [15.8 MB] Get: 36 http://deb.debian.org/debian unstable/main arm64 gcc-13 arm64 13.3.0-6 [486 kB] Get: 37 http://deb.debian.org/debian unstable/main arm64 libtool all 2.4.7-7 [517 kB] Get: 38 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 39 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 40 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 41 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 42 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.191-2 [188 kB] Get: 43 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 44 http://deb.debian.org/debian unstable/main arm64 libicu72 arm64 72.1-5 [9224 kB] Get: 45 http://deb.debian.org/debian unstable/main arm64 libxml2 arm64 2.12.7+dfsg-3+b1 [609 kB] Get: 46 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.22.5-2 [1532 kB] Get: 47 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 48 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 49 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.20 [915 kB] Get: 50 http://deb.debian.org/debian unstable/main arm64 libgfortran5 arm64 14.2.0-4 [361 kB] Get: 51 http://deb.debian.org/debian unstable/main arm64 libgfortran-13-dev arm64 13.3.0-6 [404 kB] Get: 52 http://deb.debian.org/debian unstable/main arm64 gfortran-13-aarch64-linux-gnu arm64 13.3.0-6 [8834 kB] Get: 53 http://deb.debian.org/debian unstable/main arm64 gfortran-13 arm64 13.3.0-6 [14.2 kB] Get: 54 http://deb.debian.org/debian unstable/main arm64 help2man arm64 1.49.3 [198 kB] Get: 55 http://deb.debian.org/debian unstable/main arm64 libnl-3-200 arm64 3.7.0-0.3 [56.5 kB] Get: 56 http://deb.debian.org/debian unstable/main arm64 libnl-route-3-200 arm64 3.7.0-0.3 [165 kB] Get: 57 http://deb.debian.org/debian unstable/main arm64 libibverbs1 arm64 52.0-2 [58.2 kB] Get: 58 http://deb.debian.org/debian unstable/main arm64 ibverbs-providers arm64 52.0-2 [316 kB] Get: 59 http://deb.debian.org/debian unstable/main arm64 icu-devtools arm64 72.1-5 [194 kB] Get: 60 http://deb.debian.org/debian unstable/main arm64 libz3-4 arm64 4.8.12-3.1+b2 [6508 kB] Get: 61 http://deb.debian.org/debian unstable/main arm64 libllvm17t64 arm64 1:17.0.6-18 [21.3 MB] Get: 62 http://deb.debian.org/debian unstable/main arm64 libamd-comgr2 arm64 6.0+git20231212.4510c28+dfsg-3+b1 [12.1 MB] Get: 63 http://deb.debian.org/debian unstable/main arm64 libdrm-common all 2.4.123-1 [8084 B] Get: 64 http://deb.debian.org/debian unstable/main arm64 libdrm2 arm64 2.4.123-1 [38.0 kB] Get: 65 http://deb.debian.org/debian unstable/main arm64 libdrm-amdgpu1 arm64 2.4.123-1 [21.6 kB] Get: 66 http://deb.debian.org/debian unstable/main arm64 libnuma1 arm64 2.0.18-1 [21.4 kB] Get: 67 http://deb.debian.org/debian unstable/main arm64 libhsakmt1 arm64 5.7.0-1 [57.6 kB] Get: 68 http://deb.debian.org/debian unstable/main arm64 libhsa-runtime64-1 arm64 5.7.1-3 [278 kB] Get: 69 http://deb.debian.org/debian unstable/main arm64 libamdhip64-5 arm64 5.7.1-4 [8715 kB] Get: 70 http://deb.debian.org/debian unstable/main arm64 libboost1.83-dev arm64 1.83.0-3.2 [10.6 MB] Get: 71 http://deb.debian.org/debian unstable/main arm64 libboost-graph1.83.0 arm64 1.83.0-3.2 [341 kB] Get: 72 http://deb.debian.org/debian unstable/main arm64 libboost-regex1.83.0 arm64 1.83.0-3.2 [314 kB] Get: 73 http://deb.debian.org/debian unstable/main arm64 libicu-dev arm64 72.1-5 [10.2 MB] Get: 74 http://deb.debian.org/debian unstable/main arm64 libboost-regex1.83-dev arm64 1.83.0-3.2 [335 kB] Get: 75 http://deb.debian.org/debian unstable/main arm64 libboost-serialization1.83.0 arm64 1.83.0-3.2 [325 kB] Get: 76 http://deb.debian.org/debian unstable/main arm64 libboost-serialization1.83-dev arm64 1.83.0-3.2 [373 kB] Get: 77 http://deb.debian.org/debian unstable/main arm64 libboost-test1.83.0 arm64 1.83.0-3.2 [438 kB] Get: 78 http://deb.debian.org/debian unstable/main arm64 libboost-test1.83-dev arm64 1.83.0-3.2 [527 kB] Get: 79 http://deb.debian.org/debian unstable/main arm64 libboost-graph1.83-dev arm64 1.83.0-3.2 [372 kB] Get: 80 http://deb.debian.org/debian unstable/main arm64 libboost-graph-dev arm64 1.83.0.2+b2 [3688 B] Get: 81 http://deb.debian.org/debian unstable/main arm64 libbrotli1 arm64 1.1.0-2+b4 [292 kB] Get: 82 http://deb.debian.org/debian unstable/main arm64 libcpptoml-dev all 0.1.1-3 [180 kB] Get: 83 http://deb.debian.org/debian unstable/main arm64 libdivsufsort3 arm64 2.0.1-6 [39.1 kB] Get: 84 http://deb.debian.org/debian unstable/main arm64 libdivsufsort-dev arm64 2.0.1-6 [18.8 kB] Get: 85 http://deb.debian.org/debian unstable/main arm64 libjs-d3 all 3.5.17-4 [132 kB] Get: 86 http://deb.debian.org/debian unstable/main arm64 libsdsl3 arm64 2.1.1+dfsg-5 [180 kB] Get: 87 http://deb.debian.org/debian unstable/main arm64 libsdsl-dev arm64 2.1.1+dfsg-5 [428 kB] Get: 88 http://deb.debian.org/debian unstable/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-8 [20.0 kB] Get: 89 http://deb.debian.org/debian unstable/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-8 [55.4 kB] Get: 90 http://deb.debian.org/debian unstable/main arm64 libldap-2.5-0 arm64 2.5.18+dfsg-3 [174 kB] Get: 91 http://deb.debian.org/debian unstable/main arm64 libnghttp2-14 arm64 1.63.0-1 [71.2 kB] Get: 92 http://deb.debian.org/debian unstable/main arm64 libnghttp3-9 arm64 1.4.0-1 [59.5 kB] Get: 93 http://deb.debian.org/debian unstable/main arm64 libngtcp2-16 arm64 1.6.0-1 [112 kB] Get: 94 http://deb.debian.org/debian unstable/main arm64 libngtcp2-crypto-gnutls8 arm64 1.6.0-1 [18.5 kB] Get: 95 http://deb.debian.org/debian unstable/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b4 [56.7 kB] Get: 96 http://deb.debian.org/debian unstable/main arm64 libssh2-1t64 arm64 1.11.0-7 [208 kB] Get: 97 http://deb.debian.org/debian unstable/main arm64 libcurl3t64-gnutls arm64 8.10.0-2 [329 kB] Get: 98 http://deb.debian.org/debian unstable/main arm64 libdeflate0 arm64 1.21-1 [42.2 kB] Get: 99 http://deb.debian.org/debian unstable/main arm64 libhtscodecs2 arm64 1.6.1-1 [74.6 kB] Get: 100 http://deb.debian.org/debian unstable/main arm64 libhts3t64 arm64 1.20+ds-1 [416 kB] Get: 101 http://deb.debian.org/debian unstable/main arm64 libncurses6 arm64 6.5-2 [95.7 kB] Get: 102 http://deb.debian.org/debian unstable/main arm64 samtools arm64 1.20-3 [624 kB] Get: 103 http://deb.debian.org/debian unstable/main arm64 libbtllib-dev arm64 1.4.10+dfsg-1 [165 kB] Get: 104 http://deb.debian.org/debian unstable/main arm64 libevent-2.1-7t64 arm64 2.1.12-stable-10 [169 kB] Get: 105 http://deb.debian.org/debian unstable/main arm64 libevent-core-2.1-7t64 arm64 2.1.12-stable-10 [125 kB] Get: 106 http://deb.debian.org/debian unstable/main arm64 libevent-extra-2.1-7t64 arm64 2.1.12-stable-10 [102 kB] Get: 107 http://deb.debian.org/debian unstable/main arm64 libevent-pthreads-2.1-7t64 arm64 2.1.12-stable-10 [54.1 kB] Get: 108 http://deb.debian.org/debian unstable/main arm64 libevent-openssl-2.1-7t64 arm64 2.1.12-stable-10 [60.0 kB] Get: 109 http://deb.debian.org/debian unstable/main arm64 libevent-dev arm64 2.1.12-stable-10 [303 kB] Get: 110 http://deb.debian.org/debian unstable/main arm64 librdmacm1t64 arm64 52.0-2 [66.5 kB] Get: 111 http://deb.debian.org/debian unstable/main arm64 libfabric1 arm64 1.17.0-3+b1 [479 kB] Get: 112 http://deb.debian.org/debian unstable/main arm64 libhtml-tagset-perl all 3.24-1 [14.7 kB] Get: 113 http://deb.debian.org/debian unstable/main arm64 liburi-perl all 5.29-1 [103 kB] Get: 114 http://deb.debian.org/debian unstable/main arm64 libhtml-parser-perl arm64 3.83-1 [97.2 kB] Get: 115 http://deb.debian.org/debian unstable/main arm64 libhwloc15 arm64 2.11.0-2 [140 kB] Get: 116 http://deb.debian.org/debian unstable/main arm64 libnuma-dev arm64 2.0.18-1 [37.4 kB] Get: 117 http://deb.debian.org/debian unstable/main arm64 libltdl7 arm64 2.4.7-7+b1 [393 kB] Get: 118 http://deb.debian.org/debian unstable/main arm64 libltdl-dev arm64 2.4.7-7+b1 [165 kB] Get: 119 http://deb.debian.org/debian unstable/main arm64 libhwloc-dev arm64 2.11.0-2 [235 kB] Get: 120 http://deb.debian.org/debian unstable/main arm64 libpciaccess0 arm64 0.17-3+b1 [51.1 kB] Get: 121 http://deb.debian.org/debian unstable/main arm64 libxau6 arm64 1:1.0.9-1+b1 [18.1 kB] Get: 122 http://deb.debian.org/debian unstable/main arm64 libxdmcp6 arm64 1:1.1.2-3+b1 [24.3 kB] Get: 123 http://deb.debian.org/debian unstable/main arm64 libxcb1 arm64 1.17.0-2 [143 kB] Get: 124 http://deb.debian.org/debian unstable/main arm64 libx11-data all 2:1.8.7-1 [328 kB] Get: 125 http://deb.debian.org/debian unstable/main arm64 libx11-6 arm64 2:1.8.7-1+b1 [775 kB] Get: 126 http://deb.debian.org/debian unstable/main arm64 libxext6 arm64 2:1.3.4-1+b1 [51.7 kB] Get: 127 http://deb.debian.org/debian unstable/main arm64 libxnvctrl0 arm64 535.171.04-1 [13.8 kB] Get: 128 http://deb.debian.org/debian unstable/main arm64 ocl-icd-libopencl1 arm64 2.3.2-1+b1 [39.3 kB] Get: 129 http://deb.debian.org/debian unstable/main arm64 libhwloc-plugins arm64 2.11.0-2 [17.8 kB] Get: 130 http://deb.debian.org/debian unstable/main arm64 libibumad3 arm64 52.0-2 [26.9 kB] Get: 131 http://deb.debian.org/debian unstable/main arm64 libibmad5 arm64 52.0-2 [41.3 kB] Get: 132 http://deb.debian.org/debian unstable/main arm64 libnl-3-dev arm64 3.7.0-0.3 [101 kB] Get: 133 http://deb.debian.org/debian unstable/main arm64 libnl-route-3-dev arm64 3.7.0-0.3 [197 kB] Get: 134 http://deb.debian.org/debian unstable/main arm64 libibverbs-dev arm64 52.0-2 [630 kB] Get: 135 http://deb.debian.org/debian unstable/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 136 http://deb.debian.org/debian unstable/main arm64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get: 137 http://deb.debian.org/debian unstable/main arm64 libmunge2 arm64 0.5.15-4 [19.2 kB] Get: 138 http://deb.debian.org/debian unstable/main arm64 libpmix2t64 arm64 5.0.3-2 [581 kB] Get: 139 http://deb.debian.org/debian unstable/main arm64 libucx0 arm64 1.17.0+ds-3 [959 kB] Get: 140 http://deb.debian.org/debian unstable/main arm64 libopenmpi3t64 arm64 4.1.6-13.3 [2170 kB] Get: 141 http://deb.debian.org/debian unstable/main arm64 openmpi-common all 4.1.6-13.3 [169 kB] Get: 142 http://deb.debian.org/debian unstable/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1 [916 kB] Get: 143 http://deb.debian.org/debian unstable/main arm64 libpmix-dev arm64 5.0.3-2 [3921 kB] Get: 144 http://deb.debian.org/debian unstable/main arm64 openmpi-bin arm64 4.1.6-13.3 [225 kB] Get: 145 http://deb.debian.org/debian unstable/main arm64 libopenmpi-dev arm64 4.1.6-13.3 [972 kB] Get: 146 http://deb.debian.org/debian unstable/main arm64 libpkgconf3 arm64 1.8.1-3 [35.3 kB] Get: 147 http://deb.debian.org/debian unstable/main arm64 libsparsehash-dev all 2.0.3-2 [76.8 kB] Get: 148 http://deb.debian.org/debian unstable/main arm64 libsqlite3-dev arm64 3.46.1-1 [1058 kB] Get: 149 http://deb.debian.org/debian unstable/main arm64 libtext-markdown-perl all 1.000031-4 [32.1 kB] Get: 150 http://deb.debian.org/debian unstable/main arm64 libtext-multimarkdown-perl all 1.000035-3 [28.5 kB] Get: 151 http://deb.debian.org/debian unstable/main arm64 pkgconf-bin arm64 1.8.1-3 [29.4 kB] Get: 152 http://deb.debian.org/debian unstable/main arm64 pkgconf arm64 1.8.1-3 [26.0 kB] Fetched 153 MB in 1s (223 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 ... 19891 files and directories currently installed.) Preparing to unpack .../000-liblocale-gettext-perl_1.07-7_arm64.deb ... Unpacking liblocale-gettext-perl (1.07-7) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../001-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../002-libmagic-mgc_1%3a5.45-3_arm64.deb ... Unpacking libmagic-mgc (1:5.45-3) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../003-libmagic1t64_1%3a5.45-3_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.45-3) ... Selecting previously unselected package file. Preparing to unpack .../004-file_1%3a5.45-3_arm64.deb ... Unpacking file (1:5.45-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../005-gettext-base_0.22.5-2_arm64.deb ... Unpacking gettext-base (0.22.5-2) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../006-libuchardet0_0.0.8-1+b1_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../007-groff-base_1.23.0-5_arm64.deb ... Unpacking groff-base (1.23.0-5) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../008-bsdextrautils_2.40.2-8_arm64.deb ... Unpacking bsdextrautils (2.40.2-8) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../009-libpipeline1_1.5.8-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../010-man-db_2.13.0-1_arm64.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package libedit2:arm64. Preparing to unpack .../011-libedit2_3.1-20240808-1_arm64.deb ... Unpacking libedit2:arm64 (3.1-20240808-1) ... Selecting previously unselected package libcbor0.10:arm64. Preparing to unpack .../012-libcbor0.10_0.10.2-1.2_arm64.deb ... Unpacking libcbor0.10:arm64 (0.10.2-1.2) ... Selecting previously unselected package libfido2-1:arm64. Preparing to unpack .../013-libfido2-1_1.15.0-1_arm64.deb ... Unpacking libfido2-1:arm64 (1.15.0-1) ... Selecting previously unselected package libkrb5support0:arm64. Preparing to unpack .../014-libkrb5support0_1.21.3-3_arm64.deb ... Unpacking libkrb5support0:arm64 (1.21.3-3) ... Selecting previously unselected package libcom-err2:arm64. Preparing to unpack .../015-libcom-err2_1.47.1-1_arm64.deb ... Unpacking libcom-err2:arm64 (1.47.1-1) ... Selecting previously unselected package libk5crypto3:arm64. Preparing to unpack .../016-libk5crypto3_1.21.3-3_arm64.deb ... Unpacking libk5crypto3:arm64 (1.21.3-3) ... Selecting previously unselected package libkeyutils1:arm64. Preparing to unpack .../017-libkeyutils1_1.6.3-3_arm64.deb ... Unpacking libkeyutils1:arm64 (1.6.3-3) ... Selecting previously unselected package libkrb5-3:arm64. Preparing to unpack .../018-libkrb5-3_1.21.3-3_arm64.deb ... Unpacking libkrb5-3:arm64 (1.21.3-3) ... Selecting previously unselected package libgssapi-krb5-2:arm64. Preparing to unpack .../019-libgssapi-krb5-2_1.21.3-3_arm64.deb ... Unpacking libgssapi-krb5-2:arm64 (1.21.3-3) ... Selecting previously unselected package openssh-client. Preparing to unpack .../020-openssh-client_1%3a9.8p1-8_arm64.deb ... Unpacking openssh-client (1:9.8p1-8) ... Selecting previously unselected package libpsl5t64:arm64. Preparing to unpack .../021-libpsl5t64_0.21.2-1.1_arm64.deb ... Unpacking libpsl5t64:arm64 (0.21.2-1.1) ... Selecting previously unselected package wget. Preparing to unpack .../022-wget_1.24.5-2_arm64.deb ... Unpacking wget (1.24.5-2) ... Selecting previously unselected package architecture-properties:arm64. Preparing to unpack .../023-architecture-properties_0.1.1+b1_arm64.deb ... Unpacking architecture-properties:arm64 (0.1.1+b1) ... Selecting previously unselected package m4. Preparing to unpack .../024-m4_1.4.19-4_arm64.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../025-autoconf_2.72-3_all.deb ... Unpacking autoconf (2.72-3) ... 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_0.22.5-2_all.deb ... Unpacking autopoint (0.22.5-2) ... Selecting previously unselected package gcc-13-base:arm64. Preparing to unpack .../029-gcc-13-base_13.3.0-6_arm64.deb ... Unpacking gcc-13-base:arm64 (13.3.0-6) ... Selecting previously unselected package cpp-13-aarch64-linux-gnu. Preparing to unpack .../030-cpp-13-aarch64-linux-gnu_13.3.0-6_arm64.deb ... Unpacking cpp-13-aarch64-linux-gnu (13.3.0-6) ... Selecting previously unselected package cpp-13. Preparing to unpack .../031-cpp-13_13.3.0-6_arm64.deb ... Unpacking cpp-13 (13.3.0-6) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../032-libdebhelper-perl_13.20_all.deb ... Unpacking libdebhelper-perl (13.20) ... Selecting previously unselected package libgcc-13-dev:arm64. Preparing to unpack .../033-libgcc-13-dev_13.3.0-6_arm64.deb ... Unpacking libgcc-13-dev:arm64 (13.3.0-6) ... Selecting previously unselected package gcc-13-aarch64-linux-gnu. Preparing to unpack .../034-gcc-13-aarch64-linux-gnu_13.3.0-6_arm64.deb ... Unpacking gcc-13-aarch64-linux-gnu (13.3.0-6) ... Selecting previously unselected package gcc-13. Preparing to unpack .../035-gcc-13_13.3.0-6_arm64.deb ... Unpacking gcc-13 (13.3.0-6) ... Selecting previously unselected package libtool. Preparing to unpack .../036-libtool_2.4.7-7_all.deb ... Unpacking libtool (2.4.7-7) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../037-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../038-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../039-libfile-stripnondeterminism-perl_1.14.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../040-dh-strip-nondeterminism_1.14.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.14.0-1) ... Selecting previously unselected package libelf1t64:arm64. Preparing to unpack .../041-libelf1t64_0.191-2_arm64.deb ... Unpacking libelf1t64:arm64 (0.191-2) ... Selecting previously unselected package dwz. Preparing to unpack .../042-dwz_0.15-1+b1_arm64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libicu72:arm64. Preparing to unpack .../043-libicu72_72.1-5_arm64.deb ... Unpacking libicu72:arm64 (72.1-5) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../044-libxml2_2.12.7+dfsg-3+b1_arm64.deb ... Unpacking libxml2:arm64 (2.12.7+dfsg-3+b1) ... Selecting previously unselected package gettext. Preparing to unpack .../045-gettext_0.22.5-2_arm64.deb ... Unpacking gettext (0.22.5-2) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../046-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 .../047-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../048-debhelper_13.20_all.deb ... Unpacking debhelper (13.20) ... Selecting previously unselected package libgfortran5:arm64. Preparing to unpack .../049-libgfortran5_14.2.0-4_arm64.deb ... Unpacking libgfortran5:arm64 (14.2.0-4) ... Selecting previously unselected package libgfortran-13-dev:arm64. Preparing to unpack .../050-libgfortran-13-dev_13.3.0-6_arm64.deb ... Unpacking libgfortran-13-dev:arm64 (13.3.0-6) ... Selecting previously unselected package gfortran-13-aarch64-linux-gnu. Preparing to unpack .../051-gfortran-13-aarch64-linux-gnu_13.3.0-6_arm64.deb ... Unpacking gfortran-13-aarch64-linux-gnu (13.3.0-6) ... Selecting previously unselected package gfortran-13. Preparing to unpack .../052-gfortran-13_13.3.0-6_arm64.deb ... Unpacking gfortran-13 (13.3.0-6) ... Selecting previously unselected package help2man. Preparing to unpack .../053-help2man_1.49.3_arm64.deb ... Unpacking help2man (1.49.3) ... Selecting previously unselected package libnl-3-200:arm64. Preparing to unpack .../054-libnl-3-200_3.7.0-0.3_arm64.deb ... Unpacking libnl-3-200:arm64 (3.7.0-0.3) ... Selecting previously unselected package libnl-route-3-200:arm64. Preparing to unpack .../055-libnl-route-3-200_3.7.0-0.3_arm64.deb ... Unpacking libnl-route-3-200:arm64 (3.7.0-0.3) ... Selecting previously unselected package libibverbs1:arm64. Preparing to unpack .../056-libibverbs1_52.0-2_arm64.deb ... Unpacking libibverbs1:arm64 (52.0-2) ... Selecting previously unselected package ibverbs-providers:arm64. Preparing to unpack .../057-ibverbs-providers_52.0-2_arm64.deb ... Unpacking ibverbs-providers:arm64 (52.0-2) ... Selecting previously unselected package icu-devtools. Preparing to unpack .../058-icu-devtools_72.1-5_arm64.deb ... Unpacking icu-devtools (72.1-5) ... Selecting previously unselected package libz3-4:arm64. Preparing to unpack .../059-libz3-4_4.8.12-3.1+b2_arm64.deb ... Unpacking libz3-4:arm64 (4.8.12-3.1+b2) ... Selecting previously unselected package libllvm17t64:arm64. Preparing to unpack .../060-libllvm17t64_1%3a17.0.6-18_arm64.deb ... Unpacking libllvm17t64:arm64 (1:17.0.6-18) ... Selecting previously unselected package libamd-comgr2:arm64. Preparing to unpack .../061-libamd-comgr2_6.0+git20231212.4510c28+dfsg-3+b1_arm64.deb ... Unpacking libamd-comgr2:arm64 (6.0+git20231212.4510c28+dfsg-3+b1) ... Selecting previously unselected package libdrm-common. Preparing to unpack .../062-libdrm-common_2.4.123-1_all.deb ... Unpacking libdrm-common (2.4.123-1) ... Selecting previously unselected package libdrm2:arm64. Preparing to unpack .../063-libdrm2_2.4.123-1_arm64.deb ... Unpacking libdrm2:arm64 (2.4.123-1) ... Selecting previously unselected package libdrm-amdgpu1:arm64. Preparing to unpack .../064-libdrm-amdgpu1_2.4.123-1_arm64.deb ... Unpacking libdrm-amdgpu1:arm64 (2.4.123-1) ... Selecting previously unselected package libnuma1:arm64. Preparing to unpack .../065-libnuma1_2.0.18-1_arm64.deb ... Unpacking libnuma1:arm64 (2.0.18-1) ... Selecting previously unselected package libhsakmt1:arm64. Preparing to unpack .../066-libhsakmt1_5.7.0-1_arm64.deb ... Unpacking libhsakmt1:arm64 (5.7.0-1) ... Selecting previously unselected package libhsa-runtime64-1:arm64. Preparing to unpack .../067-libhsa-runtime64-1_5.7.1-3_arm64.deb ... Unpacking libhsa-runtime64-1:arm64 (5.7.1-3) ... Selecting previously unselected package libamdhip64-5. Preparing to unpack .../068-libamdhip64-5_5.7.1-4_arm64.deb ... Unpacking libamdhip64-5 (5.7.1-4) ... Selecting previously unselected package libboost1.83-dev:arm64. Preparing to unpack .../069-libboost1.83-dev_1.83.0-3.2_arm64.deb ... Unpacking libboost1.83-dev:arm64 (1.83.0-3.2) ... Selecting previously unselected package libboost-graph1.83.0:arm64. Preparing to unpack .../070-libboost-graph1.83.0_1.83.0-3.2_arm64.deb ... Unpacking libboost-graph1.83.0:arm64 (1.83.0-3.2) ... Selecting previously unselected package libboost-regex1.83.0:arm64. Preparing to unpack .../071-libboost-regex1.83.0_1.83.0-3.2_arm64.deb ... Unpacking libboost-regex1.83.0:arm64 (1.83.0-3.2) ... Selecting previously unselected package libicu-dev:arm64. Preparing to unpack .../072-libicu-dev_72.1-5_arm64.deb ... Unpacking libicu-dev:arm64 (72.1-5) ... Selecting previously unselected package libboost-regex1.83-dev:arm64. Preparing to unpack .../073-libboost-regex1.83-dev_1.83.0-3.2_arm64.deb ... Unpacking libboost-regex1.83-dev:arm64 (1.83.0-3.2) ... Selecting previously unselected package libboost-serialization1.83.0:arm64. Preparing to unpack .../074-libboost-serialization1.83.0_1.83.0-3.2_arm64.deb ... Unpacking libboost-serialization1.83.0:arm64 (1.83.0-3.2) ... Selecting previously unselected package libboost-serialization1.83-dev:arm64. Preparing to unpack .../075-libboost-serialization1.83-dev_1.83.0-3.2_arm64.deb ... Unpacking libboost-serialization1.83-dev:arm64 (1.83.0-3.2) ... Selecting previously unselected package libboost-test1.83.0:arm64. Preparing to unpack .../076-libboost-test1.83.0_1.83.0-3.2_arm64.deb ... Unpacking libboost-test1.83.0:arm64 (1.83.0-3.2) ... Selecting previously unselected package libboost-test1.83-dev:arm64. Preparing to unpack .../077-libboost-test1.83-dev_1.83.0-3.2_arm64.deb ... Unpacking libboost-test1.83-dev:arm64 (1.83.0-3.2) ... Selecting previously unselected package libboost-graph1.83-dev:arm64. Preparing to unpack .../078-libboost-graph1.83-dev_1.83.0-3.2_arm64.deb ... Unpacking libboost-graph1.83-dev:arm64 (1.83.0-3.2) ... Selecting previously unselected package libboost-graph-dev:arm64. Preparing to unpack .../079-libboost-graph-dev_1.83.0.2+b2_arm64.deb ... Unpacking libboost-graph-dev:arm64 (1.83.0.2+b2) ... Selecting previously unselected package libbrotli1:arm64. Preparing to unpack .../080-libbrotli1_1.1.0-2+b4_arm64.deb ... Unpacking libbrotli1:arm64 (1.1.0-2+b4) ... Selecting previously unselected package libcpptoml-dev. Preparing to unpack .../081-libcpptoml-dev_0.1.1-3_all.deb ... Unpacking libcpptoml-dev (0.1.1-3) ... Selecting previously unselected package libdivsufsort3:arm64. Preparing to unpack .../082-libdivsufsort3_2.0.1-6_arm64.deb ... Unpacking libdivsufsort3:arm64 (2.0.1-6) ... Selecting previously unselected package libdivsufsort-dev:arm64. Preparing to unpack .../083-libdivsufsort-dev_2.0.1-6_arm64.deb ... Unpacking libdivsufsort-dev:arm64 (2.0.1-6) ... Selecting previously unselected package libjs-d3. Preparing to unpack .../084-libjs-d3_3.5.17-4_all.deb ... Unpacking libjs-d3 (3.5.17-4) ... Selecting previously unselected package libsdsl3:arm64. Preparing to unpack .../085-libsdsl3_2.1.1+dfsg-5_arm64.deb ... Unpacking libsdsl3:arm64 (2.1.1+dfsg-5) ... Selecting previously unselected package libsdsl-dev:arm64. Preparing to unpack .../086-libsdsl-dev_2.1.1+dfsg-5_arm64.deb ... Unpacking libsdsl-dev:arm64 (2.1.1+dfsg-5) ... Selecting previously unselected package libsasl2-modules-db:arm64. Preparing to unpack .../087-libsasl2-modules-db_2.1.28+dfsg1-8_arm64.deb ... Unpacking libsasl2-modules-db:arm64 (2.1.28+dfsg1-8) ... Selecting previously unselected package libsasl2-2:arm64. Preparing to unpack .../088-libsasl2-2_2.1.28+dfsg1-8_arm64.deb ... Unpacking libsasl2-2:arm64 (2.1.28+dfsg1-8) ... Selecting previously unselected package libldap-2.5-0:arm64. Preparing to unpack .../089-libldap-2.5-0_2.5.18+dfsg-3_arm64.deb ... Unpacking libldap-2.5-0:arm64 (2.5.18+dfsg-3) ... Selecting previously unselected package libnghttp2-14:arm64. Preparing to unpack .../090-libnghttp2-14_1.63.0-1_arm64.deb ... Unpacking libnghttp2-14:arm64 (1.63.0-1) ... Selecting previously unselected package libnghttp3-9:arm64. Preparing to unpack .../091-libnghttp3-9_1.4.0-1_arm64.deb ... Unpacking libnghttp3-9:arm64 (1.4.0-1) ... Selecting previously unselected package libngtcp2-16:arm64. Preparing to unpack .../092-libngtcp2-16_1.6.0-1_arm64.deb ... Unpacking libngtcp2-16:arm64 (1.6.0-1) ... Selecting previously unselected package libngtcp2-crypto-gnutls8:arm64. Preparing to unpack .../093-libngtcp2-crypto-gnutls8_1.6.0-1_arm64.deb ... Unpacking libngtcp2-crypto-gnutls8:arm64 (1.6.0-1) ... Selecting previously unselected package librtmp1:arm64. Preparing to unpack .../094-librtmp1_2.4+20151223.gitfa8646d.1-2+b4_arm64.deb ... Unpacking librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2+b4) ... Selecting previously unselected package libssh2-1t64:arm64. Preparing to unpack .../095-libssh2-1t64_1.11.0-7_arm64.deb ... Unpacking libssh2-1t64:arm64 (1.11.0-7) ... Selecting previously unselected package libcurl3t64-gnutls:arm64. Preparing to unpack .../096-libcurl3t64-gnutls_8.10.0-2_arm64.deb ... Unpacking libcurl3t64-gnutls:arm64 (8.10.0-2) ... Selecting previously unselected package libdeflate0:arm64. Preparing to unpack .../097-libdeflate0_1.21-1_arm64.deb ... Unpacking libdeflate0:arm64 (1.21-1) ... Selecting previously unselected package libhtscodecs2:arm64. Preparing to unpack .../098-libhtscodecs2_1.6.1-1_arm64.deb ... Unpacking libhtscodecs2:arm64 (1.6.1-1) ... Selecting previously unselected package libhts3t64:arm64. Preparing to unpack .../099-libhts3t64_1.20+ds-1_arm64.deb ... Unpacking libhts3t64:arm64 (1.20+ds-1) ... Selecting previously unselected package libncurses6:arm64. Preparing to unpack .../100-libncurses6_6.5-2_arm64.deb ... Unpacking libncurses6:arm64 (6.5-2) ... Selecting previously unselected package samtools. Preparing to unpack .../101-samtools_1.20-3_arm64.deb ... Unpacking samtools (1.20-3) ... Selecting previously unselected package libbtllib-dev. Preparing to unpack .../102-libbtllib-dev_1.4.10+dfsg-1_arm64.deb ... Unpacking libbtllib-dev (1.4.10+dfsg-1) ... Selecting previously unselected package libevent-2.1-7t64:arm64. Preparing to unpack .../103-libevent-2.1-7t64_2.1.12-stable-10_arm64.deb ... Unpacking libevent-2.1-7t64:arm64 (2.1.12-stable-10) ... Selecting previously unselected package libevent-core-2.1-7t64:arm64. Preparing to unpack .../104-libevent-core-2.1-7t64_2.1.12-stable-10_arm64.deb ... Unpacking libevent-core-2.1-7t64:arm64 (2.1.12-stable-10) ... Selecting previously unselected package libevent-extra-2.1-7t64:arm64. Preparing to unpack .../105-libevent-extra-2.1-7t64_2.1.12-stable-10_arm64.deb ... Unpacking libevent-extra-2.1-7t64:arm64 (2.1.12-stable-10) ... Selecting previously unselected package libevent-pthreads-2.1-7t64:arm64. Preparing to unpack .../106-libevent-pthreads-2.1-7t64_2.1.12-stable-10_arm64.deb ... Unpacking libevent-pthreads-2.1-7t64:arm64 (2.1.12-stable-10) ... Selecting previously unselected package libevent-openssl-2.1-7t64:arm64. Preparing to unpack .../107-libevent-openssl-2.1-7t64_2.1.12-stable-10_arm64.deb ... Unpacking libevent-openssl-2.1-7t64:arm64 (2.1.12-stable-10) ... Selecting previously unselected package libevent-dev. Preparing to unpack .../108-libevent-dev_2.1.12-stable-10_arm64.deb ... Unpacking libevent-dev (2.1.12-stable-10) ... Selecting previously unselected package librdmacm1t64:arm64. Preparing to unpack .../109-librdmacm1t64_52.0-2_arm64.deb ... Unpacking librdmacm1t64:arm64 (52.0-2) ... Selecting previously unselected package libfabric1:arm64. Preparing to unpack .../110-libfabric1_1.17.0-3+b1_arm64.deb ... Unpacking libfabric1:arm64 (1.17.0-3+b1) ... Selecting previously unselected package libhtml-tagset-perl. Preparing to unpack .../111-libhtml-tagset-perl_3.24-1_all.deb ... Unpacking libhtml-tagset-perl (3.24-1) ... Selecting previously unselected package liburi-perl. Preparing to unpack .../112-liburi-perl_5.29-1_all.deb ... Unpacking liburi-perl (5.29-1) ... Selecting previously unselected package libhtml-parser-perl:arm64. Preparing to unpack .../113-libhtml-parser-perl_3.83-1_arm64.deb ... Unpacking libhtml-parser-perl:arm64 (3.83-1) ... Selecting previously unselected package libhwloc15:arm64. Preparing to unpack .../114-libhwloc15_2.11.0-2_arm64.deb ... Unpacking libhwloc15:arm64 (2.11.0-2) ... Selecting previously unselected package libnuma-dev:arm64. Preparing to unpack .../115-libnuma-dev_2.0.18-1_arm64.deb ... Unpacking libnuma-dev:arm64 (2.0.18-1) ... Selecting previously unselected package libltdl7:arm64. Preparing to unpack .../116-libltdl7_2.4.7-7+b1_arm64.deb ... Unpacking libltdl7:arm64 (2.4.7-7+b1) ... Selecting previously unselected package libltdl-dev:arm64. Preparing to unpack .../117-libltdl-dev_2.4.7-7+b1_arm64.deb ... Unpacking libltdl-dev:arm64 (2.4.7-7+b1) ... Selecting previously unselected package libhwloc-dev:arm64. Preparing to unpack .../118-libhwloc-dev_2.11.0-2_arm64.deb ... Unpacking libhwloc-dev:arm64 (2.11.0-2) ... Selecting previously unselected package libpciaccess0:arm64. Preparing to unpack .../119-libpciaccess0_0.17-3+b1_arm64.deb ... Unpacking libpciaccess0:arm64 (0.17-3+b1) ... Selecting previously unselected package libxau6:arm64. Preparing to unpack .../120-libxau6_1%3a1.0.9-1+b1_arm64.deb ... Unpacking libxau6:arm64 (1:1.0.9-1+b1) ... Selecting previously unselected package libxdmcp6:arm64. Preparing to unpack .../121-libxdmcp6_1%3a1.1.2-3+b1_arm64.deb ... Unpacking libxdmcp6:arm64 (1:1.1.2-3+b1) ... Selecting previously unselected package libxcb1:arm64. Preparing to unpack .../122-libxcb1_1.17.0-2_arm64.deb ... Unpacking libxcb1:arm64 (1.17.0-2) ... Selecting previously unselected package libx11-data. Preparing to unpack .../123-libx11-data_2%3a1.8.7-1_all.deb ... Unpacking libx11-data (2:1.8.7-1) ... Selecting previously unselected package libx11-6:arm64. Preparing to unpack .../124-libx11-6_2%3a1.8.7-1+b1_arm64.deb ... Unpacking libx11-6:arm64 (2:1.8.7-1+b1) ... Selecting previously unselected package libxext6:arm64. Preparing to unpack .../125-libxext6_2%3a1.3.4-1+b1_arm64.deb ... Unpacking libxext6:arm64 (2:1.3.4-1+b1) ... Selecting previously unselected package libxnvctrl0:arm64. Preparing to unpack .../126-libxnvctrl0_535.171.04-1_arm64.deb ... Unpacking libxnvctrl0:arm64 (535.171.04-1) ... Selecting previously unselected package ocl-icd-libopencl1:arm64. Preparing to unpack .../127-ocl-icd-libopencl1_2.3.2-1+b1_arm64.deb ... Unpacking ocl-icd-libopencl1:arm64 (2.3.2-1+b1) ... Selecting previously unselected package libhwloc-plugins:arm64. Preparing to unpack .../128-libhwloc-plugins_2.11.0-2_arm64.deb ... Unpacking libhwloc-plugins:arm64 (2.11.0-2) ... Selecting previously unselected package libibumad3:arm64. Preparing to unpack .../129-libibumad3_52.0-2_arm64.deb ... Unpacking libibumad3:arm64 (52.0-2) ... Selecting previously unselected package libibmad5:arm64. Preparing to unpack .../130-libibmad5_52.0-2_arm64.deb ... Unpacking libibmad5:arm64 (52.0-2) ... Selecting previously unselected package libnl-3-dev:arm64. Preparing to unpack .../131-libnl-3-dev_3.7.0-0.3_arm64.deb ... Unpacking libnl-3-dev:arm64 (3.7.0-0.3) ... Selecting previously unselected package libnl-route-3-dev:arm64. Preparing to unpack .../132-libnl-route-3-dev_3.7.0-0.3_arm64.deb ... Unpacking libnl-route-3-dev:arm64 (3.7.0-0.3) ... Selecting previously unselected package libibverbs-dev:arm64. Preparing to unpack .../133-libibverbs-dev_52.0-2_arm64.deb ... Unpacking libibverbs-dev:arm64 (52.0-2) ... Selecting previously unselected package libjs-jquery. Preparing to unpack .../134-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Selecting previously unselected package libjs-jquery-ui. Preparing to unpack .../135-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ... Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ... Selecting previously unselected package libmunge2:arm64. Preparing to unpack .../136-libmunge2_0.5.15-4_arm64.deb ... Unpacking libmunge2:arm64 (0.5.15-4) ... Selecting previously unselected package libpmix2t64:arm64. Preparing to unpack .../137-libpmix2t64_5.0.3-2_arm64.deb ... Unpacking libpmix2t64:arm64 (5.0.3-2) ... Selecting previously unselected package libucx0:arm64. Preparing to unpack .../138-libucx0_1.17.0+ds-3_arm64.deb ... Unpacking libucx0:arm64 (1.17.0+ds-3) ... Selecting previously unselected package libopenmpi3t64:arm64. Preparing to unpack .../139-libopenmpi3t64_4.1.6-13.3_arm64.deb ... Unpacking libopenmpi3t64:arm64 (4.1.6-13.3) ... Selecting previously unselected package openmpi-common. Preparing to unpack .../140-openmpi-common_4.1.6-13.3_all.deb ... Unpacking openmpi-common (4.1.6-13.3) ... Selecting previously unselected package zlib1g-dev:arm64. Preparing to unpack .../141-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1_arm64.deb ... Unpacking zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1) ... Selecting previously unselected package libpmix-dev:arm64. Preparing to unpack .../142-libpmix-dev_5.0.3-2_arm64.deb ... Unpacking libpmix-dev:arm64 (5.0.3-2) ... Selecting previously unselected package openmpi-bin. Preparing to unpack .../143-openmpi-bin_4.1.6-13.3_arm64.deb ... Unpacking openmpi-bin (4.1.6-13.3) ... Selecting previously unselected package libopenmpi-dev:arm64. Preparing to unpack .../144-libopenmpi-dev_4.1.6-13.3_arm64.deb ... Unpacking libopenmpi-dev:arm64 (4.1.6-13.3) ... Selecting previously unselected package libpkgconf3:arm64. Preparing to unpack .../145-libpkgconf3_1.8.1-3_arm64.deb ... Unpacking libpkgconf3:arm64 (1.8.1-3) ... Selecting previously unselected package libsparsehash-dev. Preparing to unpack .../146-libsparsehash-dev_2.0.3-2_all.deb ... Unpacking libsparsehash-dev (2.0.3-2) ... Selecting previously unselected package libsqlite3-dev:arm64. Preparing to unpack .../147-libsqlite3-dev_3.46.1-1_arm64.deb ... Unpacking libsqlite3-dev:arm64 (3.46.1-1) ... Selecting previously unselected package libtext-markdown-perl. Preparing to unpack .../148-libtext-markdown-perl_1.000031-4_all.deb ... Unpacking libtext-markdown-perl (1.000031-4) ... Selecting previously unselected package libtext-multimarkdown-perl. Preparing to unpack .../149-libtext-multimarkdown-perl_1.000035-3_all.deb ... Unpacking libtext-multimarkdown-perl (1.000035-3) ... Selecting previously unselected package pkgconf-bin. Preparing to unpack .../150-pkgconf-bin_1.8.1-3_arm64.deb ... Unpacking pkgconf-bin (1.8.1-3) ... Selecting previously unselected package pkgconf:arm64. Preparing to unpack .../151-pkgconf_1.8.1-3_arm64.deb ... Unpacking pkgconf:arm64 (1.8.1-3) ... Setting up libhtscodecs2:arm64 (1.6.1-1) ... Setting up libpipeline1:arm64 (1.5.8-1) ... Setting up libtext-markdown-perl (1.000031-4) ... Setting up libpciaccess0:arm64 (0.17-3+b1) ... Setting up libxau6:arm64 (1:1.0.9-1+b1) ... Setting up libxdmcp6:arm64 (1:1.1.2-3+b1) ... Setting up libkeyutils1:arm64 (1.6.3-3) ... Setting up libboost1.83-dev:arm64 (1.83.0-3.2) ... Setting up libxcb1:arm64 (1.17.0-2) ... Setting up libicu72:arm64 (72.1-5) ... Setting up bsdextrautils (2.40.2-8) ... Setting up libmagic-mgc (1:5.45-3) ... Setting up libcbor0.10:arm64 (0.10.2-1.2) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up architecture-properties:arm64 (0.1.1+b1) ... Setting up libhtml-tagset-perl (3.24-1) ... Setting up libboost-regex1.83.0:arm64 (1.83.0-3.2) ... Setting up libdebhelper-perl (13.20) ... Setting up libbrotli1:arm64 (1.1.0-2+b4) ... Setting up libedit2:arm64 (3.1-20240808-1) ... Setting up libmagic1t64:arm64 (1:5.45-3) ... Setting up libpsl5t64:arm64 (0.21.2-1.1) ... Setting up libnghttp2-14:arm64 (1.63.0-1) ... Setting up libibumad3:arm64 (52.0-2) ... Setting up libdeflate0:arm64 (1.21-1) ... Setting up gettext-base (0.22.5-2) ... Setting up m4 (1.4.19-4) ... Setting up libevent-2.1-7t64:arm64 (2.1.12-stable-10) ... Setting up libibmad5:arm64 (52.0-2) ... Setting up libcom-err2:arm64 (1.47.1-1) ... Setting up file (1:5.45-3) ... Setting up libsparsehash-dev (2.0.3-2) ... Setting up libelf1t64:arm64 (0.191-2) ... Setting up libkrb5support0:arm64 (1.21.3-3) ... Setting up libsasl2-modules-db:arm64 (2.1.28+dfsg1-8) ... Setting up libboost-serialization1.83.0:arm64 (1.83.0-3.2) ... Setting up autotools-dev (20220109.1) ... Setting up libz3-4:arm64 (4.8.12-3.1+b2) ... Setting up libpkgconf3:arm64 (1.8.1-3) ... Setting up gcc-13-base:arm64 (13.3.0-6) ... Setting up libmunge2:arm64 (0.5.15-4) ... Setting up libsqlite3-dev:arm64 (3.46.1-1) ... Setting up libx11-data (2:1.8.7-1) ... Setting up librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2+b4) ... Setting up libcpptoml-dev (0.1.1-3) ... Setting up libncurses6:arm64 (6.5-2) ... Setting up libjs-d3 (3.5.17-4) ... Setting up libhwloc15:arm64 (2.11.0-2) ... Setting up autopoint (0.22.5-2) ... Setting up icu-devtools (72.1-5) ... Setting up pkgconf-bin (1.8.1-3) ... Setting up libk5crypto3:arm64 (1.21.3-3) ... Setting up libltdl7:arm64 (2.4.7-7+b1) ... Setting up libboost-test1.83.0:arm64 (1.83.0-3.2) ... Setting up libsasl2-2:arm64 (2.1.28+dfsg1-8) ... Setting up libgfortran5:arm64 (14.2.0-4) ... Setting up autoconf (2.72-3) ... Setting up libsdsl3:arm64 (2.1.1+dfsg-5) ... Setting up libnghttp3-9:arm64 (1.4.0-1) ... Setting up zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1) ... Setting up libnuma1:arm64 (2.0.18-1) ... Setting up dwz (0.15-1+b1) ... Setting up libgcc-13-dev:arm64 (13.3.0-6) ... Setting up sensible-utils (0.0.24) ... Setting up ocl-icd-libopencl1:arm64 (2.3.2-1+b1) ... Setting up libuchardet0:arm64 (0.0.8-1+b1) ... Setting up libnl-3-200:arm64 (3.7.0-0.3) ... Setting up libboost-graph1.83.0:arm64 (1.83.0-3.2) ... Setting up openmpi-common (4.1.6-13.3) ... Setting up libx11-6:arm64 (2:1.8.7-1+b1) ... Setting up libngtcp2-16:arm64 (1.6.0-1) ... Setting up libkrb5-3:arm64 (1.21.3-3) ... Setting up libevent-core-2.1-7t64:arm64 (2.1.12-stable-10) ... Setting up libssh2-1t64:arm64 (1.11.0-7) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up libfido2-1:arm64 (1.15.0-1) ... Setting up libgfortran-13-dev:arm64 (13.3.0-6) ... Setting up libdivsufsort3:arm64 (2.0.1-6) ... Setting up libdrm-common (2.4.123-1) ... Setting up libicu-dev:arm64 (72.1-5) ... Setting up libxml2:arm64 (2.12.7+dfsg-3+b1) ... Setting up liburi-perl (5.29-1) ... Setting up liblocale-gettext-perl (1.07-7) ... Setting up libngtcp2-crypto-gnutls8:arm64 (1.6.0-1) ... Setting up libdivsufsort-dev:arm64 (2.0.1-6) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up gettext (0.22.5-2) ... Setting up libsdsl-dev:arm64 (2.1.1+dfsg-5) ... Setting up wget (1.24.5-2) ... Setting up cpp-13-aarch64-linux-gnu (13.3.0-6) ... Setting up libtool (2.4.7-7) ... Setting up libevent-pthreads-2.1-7t64:arm64 (2.1.12-stable-10) ... Setting up libevent-openssl-2.1-7t64:arm64 (2.1.12-stable-10) ... Setting up libboost-serialization1.83-dev:arm64 (1.83.0-3.2) ... Setting up libxext6:arm64 (2:1.3.4-1+b1) ... Setting up libboost-test1.83-dev:arm64 (1.83.0-3.2) ... Setting up gcc-13-aarch64-linux-gnu (13.3.0-6) ... Setting up libldap-2.5-0:arm64 (2.5.18+dfsg-3) ... Setting up pkgconf:arm64 (1.8.1-3) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up libnuma-dev:arm64 (2.0.18-1) ... Setting up libnl-route-3-200:arm64 (3.7.0-0.3) ... Setting up libxnvctrl0:arm64 (535.171.04-1) ... Setting up help2man (1.49.3) ... Setting up dh-autoreconf (20) ... Setting up libltdl-dev:arm64 (2.4.7-7+b1) ... Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... Setting up libllvm17t64:arm64 (1:17.0.6-18) ... Setting up libgssapi-krb5-2:arm64 (1.21.3-3) ... Setting up libboost-regex1.83-dev:arm64 (1.83.0-3.2) ... Setting up libevent-extra-2.1-7t64:arm64 (2.1.12-stable-10) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up libdrm2:arm64 (2.4.123-1) ... Setting up libnl-3-dev:arm64 (3.7.0-0.3) ... Setting up groff-base (1.23.0-5) ... Setting up libhtml-parser-perl:arm64 (3.83-1) ... Setting up libhwloc-dev:arm64 (2.11.0-2) ... Setting up libamd-comgr2:arm64 (6.0+git20231212.4510c28+dfsg-3+b1) ... Setting up libtext-multimarkdown-perl (1.000035-3) ... Setting up libdrm-amdgpu1:arm64 (2.4.123-1) ... Setting up libibverbs1:arm64 (52.0-2) ... Setting up cpp-13 (13.3.0-6) ... Setting up ibverbs-providers:arm64 (52.0-2) ... Setting up openssh-client (1:9.8p1-8) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libcurl3t64-gnutls:arm64 (8.10.0-2) ... Setting up gfortran-13-aarch64-linux-gnu (13.3.0-6) ... Setting up libhwloc-plugins:arm64 (2.11.0-2) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libboost-graph1.83-dev:arm64 (1.83.0-3.2) ... Setting up libnl-route-3-dev:arm64 (3.7.0-0.3) ... Setting up libevent-dev (2.1.12-stable-10) ... Setting up gcc-13 (13.3.0-6) ... Setting up libpmix2t64:arm64 (5.0.3-2) ... Setting up libhts3t64:arm64 (1.20+ds-1) ... Setting up librdmacm1t64:arm64 (52.0-2) ... Setting up libpmix-dev:arm64 (5.0.3-2) ... Setting up libhsakmt1:arm64 (5.7.0-1) ... Setting up libfabric1:arm64 (1.17.0-3+b1) ... Setting up libboost-graph-dev:arm64 (1.83.0.2+b2) ... Setting up debhelper (13.20) ... Setting up libibverbs-dev:arm64 (52.0-2) ... Setting up samtools (1.20-3) ... Setting up gfortran-13 (13.3.0-6) ... Setting up libhsa-runtime64-1:arm64 (5.7.1-3) ... Setting up libbtllib-dev (1.4.10+dfsg-1) ... Setting up libamdhip64-5 (5.7.1-4) ... Setting up libucx0:arm64 (1.17.0+ds-3) ... Setting up libopenmpi3t64:arm64 (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:arm64 (4.1.6-13.3) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/openmpi/include to provide /usr/include/aarch64-linux-gnu/mpi (mpi-aarch64-linux-gnu) in auto mode Processing triggers for libc-bin (2.40-2) ... 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-2.3.9/ && 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_2.3.9-1_source.changes dpkg-buildpackage: info: source package abyss dpkg-buildpackage: info: source version 2.3.9-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 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-2.3.9' dh_auto_configure -- \ --with-mpi=/usr/lib/aarch64-linux-gnu/openmpi ./configure --build=aarch64-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/aarch64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-mpi=/usr/lib/aarch64-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 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 or later... 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... aarch64-unknown-linux-gnu checking host system type... aarch64-unknown-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-2.3.9' debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/abyss-2.3.9' dh_auto_build make -j12 make[2]: Entering directory '/build/reproducible-path/abyss-2.3.9' make all-recursive make[3]: Entering directory '/build/reproducible-path/abyss-2.3.9' Making all in bin make[4]: Entering directory '/build/reproducible-path/abyss-2.3.9/bin' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.9/bin' Making all in doc make[4]: Entering directory '/build/reproducible-path/abyss-2.3.9/doc' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.9/doc' Making all in Common make[4]: Entering directory '/build/reproducible-path/abyss-2.3.9/Common' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/reproducible-path/abyss-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.3.9/Common' Making all in Graph make[4]: Entering directory '/build/reproducible-path/abyss-2.3.9/Graph' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/reproducible-path/abyss-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o abyss_gc-gc.o `test -f 'gc.cc' || echo './'`gc.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/reproducible-path/abyss-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o abyss_todot-todot.o `test -f 'todot.cc' || echo './'`todot.cc In file included from GraphIO.h:8, from todot.cc:9: DotIO.h: In instantiation of 'void write_edges(std::ostream&, const Graph&, typename boost::graph_traits::vertex_descriptor, const EdgeProp*) [with Graph = ContigGraph >; EdgeProp = DistanceEst; std::ostream = std::basic_ostream; typename boost::graph_traits::vertex_descriptor = ContigNode]': DotIO.h:110:14: required from 'std::ostream& write_dot(std::ostream&, const Graph&, const std::string&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream; std::string = std::__cxx11::basic_string]' 110 | write_edges(out, g, *u, (edge_property_type*)NULL); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ DotIO.h:77:18: required from 'std::ostream& write_dot(std::ostream&, const Graph&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream]' 77 | return write_dot(out, g, "adj"); | ~~~~~~~~~^~~~~~~~~~~~~~~ DotIO.h:125:26: required from 'std::ostream& operator<<(std::ostream&, const DotWriter > >&)' 125 | return write_dot(out, o.g); | ~~~~~~~~~~~~~~~~^~~~~~~~~~ GraphIO.h:33:14: required from 'std::ostream& write_graph(std::ostream&, const Graph&, const std::string&, const std::string&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream; std::string = std::__cxx11::basic_string]' 33 | return out << dot_writer(g); | ~~~~^~~~~~~~~~~~~~~~ todot.cc:186:14: required from here 186 | write_graph(cout, g, PROGRAM, commandLine); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ DotIO.h:44:43: warning: possibly dangling reference to a temporary [-Wdangling-reference] 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ^~ DotIO.h:44:51: note: the temporary was destroyed at the end of the full expression 'get >(boost::edge_bundle, (* & g), DirectedGraph::out_edge_iterator(e))' 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ~~~^~~~~~~~~~~~~~~~~~~ DotIO.h: In instantiation of 'void write_edges(std::ostream&, const Graph&, typename boost::graph_traits::vertex_descriptor, const EdgeProp*) [with Graph = ContigGraph >; EdgeProp = Distance; std::ostream = std::basic_ostream; typename boost::graph_traits::vertex_descriptor = ContigNode]': DotIO.h:110:14: required from 'std::ostream& write_dot(std::ostream&, const Graph&, const std::string&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream; std::string = std::__cxx11::basic_string]' 110 | write_edges(out, g, *u, (edge_property_type*)NULL); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ DotIO.h:77:18: required from 'std::ostream& write_dot(std::ostream&, const Graph&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream]' 77 | return write_dot(out, g, "adj"); | ~~~~~~~~~^~~~~~~~~~~~~~~ DotIO.h:125:26: required from 'std::ostream& operator<<(std::ostream&, const DotWriter > >&)' 125 | return write_dot(out, o.g); | ~~~~~~~~~~~~~~~~^~~~~~~~~~ GraphIO.h:33:14: required from 'std::ostream& write_graph(std::ostream&, const Graph&, const std::string&, const std::string&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream; std::string = std::__cxx11::basic_string]' 33 | return out << dot_writer(g); | ~~~~^~~~~~~~~~~~~~~~ todot.cc:191:14: required from here 191 | write_graph(cout, g, PROGRAM, commandLine); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ DotIO.h:44:43: warning: possibly dangling reference to a temporary [-Wdangling-reference] 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ^~ DotIO.h:44:51: note: the temporary was destroyed at the end of the full expression 'get >(boost::edge_bundle, (* & g), DirectedGraph::out_edge_iterator(e))' 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ~~~^~~~~~~~~~~~~~~~~~~ g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -L/usr/lib/aarch64-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-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -L. -L/usr/lib/aarch64-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-2.3.9/Graph' Making all in DataLayer make[4]: Entering directory '/build/reproducible-path/abyss-2.3.9/DataLayer' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/reproducible-path/abyss-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/aarch64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-fac abyss_fac-fac.o libdatalayer.a ../Common/libcommon.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/aarch64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-tofastq abyss_tofastq-abyss-tofastq.o libdatalayer.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.9/DataLayer' Making all in DataBase make[4]: Entering directory '/build/reproducible-path/abyss-2.3.9/DataBase' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/reproducible-path/abyss-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o libdb_a-DB.o `test -f 'DB.cc' || echo './'`DB.cc 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 g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/aarch64-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 make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.9/DataBase' Making all in FMIndex make[4]: Entering directory '/build/reproducible-path/abyss-2.3.9/FMIndex' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/reproducible-path/abyss-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o abyss_count-count.o `test -f 'count.cc' || echo './'`count.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I../Common -I/build/reproducible-path/abyss-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o libfmindex_a-bit_array.o `test -f 'bit_array.cc' || echo './'`bit_array.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/reproducible-path/abyss-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o abyss_dawg-abyss-dawg.o `test -f 'abyss-dawg.cc' || echo './'`abyss-dawg.cc rm -f libfmindex.a ar cru libfmindex.a libfmindex_a-bit_array.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libfmindex.a g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -L/usr/lib/aarch64-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-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -L/usr/lib/aarch64-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-2.3.9/FMIndex' Making all in Assembly make[4]: Entering directory '/build/reproducible-path/abyss-2.3.9/Assembly' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/reproducible-path/abyss-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.3.9/Assembly' Making all in dialign make[4]: Entering directory '/build/reproducible-path/abyss-2.3.9/dialign' gcc -DHAVE_CONFIG_H -I. -I.. -I/build/reproducible-path/abyss-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/boost_1_56_0 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o museq.o museq.c gcc -DHAVE_CONFIG_H -I. -I.. -I/build/reproducible-path/abyss-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/boost_1_56_0 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o alig.o alig.c gcc -DHAVE_CONFIG_H -I. -I.. -I/build/reproducible-path/abyss-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/boost_1_56_0 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o assemble.o assemble.c gcc -DHAVE_CONFIG_H -I. -I.. -I/build/reproducible-path/abyss-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/boost_1_56_0 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o diag.o diag.c gcc -DHAVE_CONFIG_H -I. -I.. -I/build/reproducible-path/abyss-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/boost_1_56_0 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o io.o io.c gcc -DHAVE_CONFIG_H -I. -I.. -I/build/reproducible-path/abyss-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/boost_1_56_0 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o orf.o orf.c gcc -DHAVE_CONFIG_H -I. -I.. -I/build/reproducible-path/abyss-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/boost_1_56_0 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o parameters.o parameters.c gcc -DHAVE_CONFIG_H -I. -I.. -I/build/reproducible-path/abyss-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/boost_1_56_0 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o prob.o prob.c gcc -DHAVE_CONFIG_H -I. -I.. -I/build/reproducible-path/abyss-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/boost_1_56_0 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o translate.o translate.c alig.c:15:20: warning: inline function 'calc_ov_weight' declared but never defined 15 | extern inline void calc_ov_weight(struct diag* dg, struct diag_col *dcol, struct scr_matrix* smatrix, | ^~~~~~~~~~~~~~ alig.c:13:20: warning: inline function 'calc_weight' declared but never defined 13 | extern inline void calc_weight(struct diag* dg, struct scr_matrix* smatrix, | ^~~~~~~~~~~ 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 ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ assemble.c:40:20: warning: inline function 'align_diag' declared but never defined 40 | extern inline char align_diag(struct alignment *algn, struct scr_matrix *smatrix, struct diag* dg); | ^~~~~~~~~~ assemble.c:37:32: warning: inline function 'find_eqc' declared but never defined 37 | extern inline struct algn_pos *find_eqc(struct algn_pos **ap, int seqnum, int pos); | ^~~~~~~~ assemble.c:25:39: warning: inline function 'find_diags_guided' declared but never defined 25 | extern inline struct simple_diag_col* find_diags_guided(struct scr_matrix *smatrix, | ^~~~~~~~~~~~~~~~~ assemble.c:15:20: warning: inline function 'calc_ov_weight' declared but never defined 15 | extern inline void calc_ov_weight(struct diag* dg, struct diag_col *dcol, struct scr_matrix* smatrix, | ^~~~~~~~~~~~~~ assemble.c:13:20: warning: inline function 'calc_weight' declared but never defined 13 | extern inline void calc_weight(struct diag* dg, struct scr_matrix* smatrix, | ^~~~~~~~~~~ diag.c:1456:17: 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-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -L/usr/lib/aarch64-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-2.3.9/dialign' Making all in Align make[4]: Entering directory '/build/reproducible-path/abyss-2.3.9/Align' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/reproducible-path/abyss-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/aarch64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-align abyss_align-align.o ./libalign.a ../dialign/libdialign.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/aarch64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-mergepairs abyss_mergepairs-mergepairs.o ./libalign.a ../dialign/libdialign.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.9/Align' Making all in ABYSS make[4]: Entering directory '/build/reproducible-path/abyss-2.3.9/ABYSS' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/reproducible-path/abyss-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o ABYSS-abyss.o `test -f 'abyss.cc' || echo './'`abyss.cc g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -L/usr/lib/aarch64-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-2.3.9/ABYSS' Making all in Parallel make[4]: Entering directory '/build/reproducible-path/abyss-2.3.9/Parallel' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/reproducible-path/abyss-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o ABYSS_P-parallelAbyss.o `test -f 'parallelAbyss.cpp' || echo './'`parallelAbyss.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/reproducible-path/abyss-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o ABYSS_P-CommLayer.o `test -f 'CommLayer.cpp' || echo './'`CommLayer.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/reproducible-path/abyss-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o ABYSS_P-NetworkSequenceCollection.o `test -f 'NetworkSequenceCollection.cpp' || echo './'`NetworkSequenceCollection.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/reproducible-path/abyss-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o ABYSS_P-MessageBuffer.o `test -f 'MessageBuffer.cpp' || echo './'`MessageBuffer.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/reproducible-path/abyss-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o ABYSS_P-Messages.o `test -f 'Messages.cpp' || echo './'`Messages.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -DPAIRED_DBG -I/build/reproducible-path/abyss-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o abyss_paired_dbg_mpi-parallelAbyss.o `test -f 'parallelAbyss.cpp' || echo './'`parallelAbyss.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -DPAIRED_DBG -I/build/reproducible-path/abyss-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o abyss_paired_dbg_mpi-CommLayer.o `test -f 'CommLayer.cpp' || echo './'`CommLayer.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -DPAIRED_DBG -I/build/reproducible-path/abyss-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o abyss_paired_dbg_mpi-NetworkSequenceCollection.o `test -f 'NetworkSequenceCollection.cpp' || echo './'`NetworkSequenceCollection.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -DPAIRED_DBG -I/build/reproducible-path/abyss-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o abyss_paired_dbg_mpi-MessageBuffer.o `test -f 'MessageBuffer.cpp' || echo './'`MessageBuffer.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -DPAIRED_DBG -I/build/reproducible-path/abyss-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o abyss_paired_dbg_mpi-Messages.o `test -f 'Messages.cpp' || echo './'`Messages.cpp g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -L/usr/lib/aarch64-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-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -L/usr/lib/aarch64-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-2.3.9/Parallel' Making all in Bloom make[4]: Entering directory '/build/reproducible-path/abyss-2.3.9/Bloom' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../vendor -I/build/reproducible-path/abyss-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o abyss_bloom-bloom.o `test -f 'bloom.cc' || echo './'`bloom.cc g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -L/usr/lib/aarch64-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-2.3.9/Bloom' Making all in BloomDBG make[4]: Entering directory '/build/reproducible-path/abyss-2.3.9/BloomDBG' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../vendor -I/build/reproducible-path/abyss-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o abyss_bloom_dbg-bloom-dbg.o `test -f 'bloom-dbg.cc' || echo './'`bloom-dbg.cc g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -L/usr/lib/aarch64-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-2.3.9/BloomDBG' Making all in Konnector make[4]: Entering directory '/build/reproducible-path/abyss-2.3.9/Konnector' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/reproducible-path/abyss-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o konnector-konnector.o `test -f 'konnector.cc' || echo './'`konnector.cc g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -L/usr/lib/aarch64-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-2.3.9/Konnector' Making all in Consensus make[4]: Entering directory '/build/reproducible-path/abyss-2.3.9/Consensus' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/reproducible-path/abyss-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/aarch64-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-2.3.9/Consensus' Making all in DAssembler make[4]: Entering directory '/build/reproducible-path/abyss-2.3.9/DAssembler' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/reproducible-path/abyss-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/aarch64-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-2.3.9/DAssembler' Making all in DistanceEst make[4]: Entering directory '/build/reproducible-path/abyss-2.3.9/DistanceEst' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/reproducible-path/abyss-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/aarch64-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-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/aarch64-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-2.3.9/DistanceEst' Making all in KAligner make[4]: Entering directory '/build/reproducible-path/abyss-2.3.9/KAligner' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/reproducible-path/abyss-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o KAligner-KAligner.o `test -f 'KAligner.cpp' || echo './'`KAligner.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/reproducible-path/abyss-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o KAligner-Aligner.o `test -f 'Aligner.cpp' || echo './'`Aligner.cpp g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -L/usr/lib/aarch64-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-2.3.9/KAligner' Making all in Layout make[4]: Entering directory '/build/reproducible-path/abyss-2.3.9/Layout' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/reproducible-path/abyss-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o abyss_layout-layout.o `test -f 'layout.cc' || echo './'`layout.cc In file included from ../Graph/GraphIO.h:8, from layout.cc:8: ../Graph/DotIO.h: In instantiation of 'void write_edges(std::ostream&, const Graph&, typename boost::graph_traits::vertex_descriptor, const EdgeProp*) [with Graph = ContigGraph >; EdgeProp = Distance; std::ostream = std::basic_ostream; typename boost::graph_traits::vertex_descriptor = ContigNode]': ../Graph/DotIO.h:110:14: required from 'std::ostream& write_dot(std::ostream&, const Graph&, const std::string&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream; std::string = std::__cxx11::basic_string]' 110 | write_edges(out, g, *u, (edge_property_type*)NULL); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../Graph/DotIO.h:77:18: required from 'std::ostream& write_dot(std::ostream&, const Graph&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream]' 77 | return write_dot(out, g, "adj"); | ~~~~~~~~~^~~~~~~~~~~~~~~ layout.cc:314:12: required from here 314 | write_dot(out, g); | ~~~~~~~~~^~~~~~~~ ../Graph/DotIO.h:44:43: warning: possibly dangling reference to a temporary [-Wdangling-reference] 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ^~ ../Graph/DotIO.h:44:51: note: the temporary was destroyed at the end of the full expression 'get >(boost::edge_bundle, (* & g), DirectedGraph::out_edge_iterator(e))' 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ~~~^~~~~~~~~~~~~~~~~~~ g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -L/usr/lib/aarch64-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-2.3.9/Layout' Making all in LogKmerCount make[4]: Entering directory '/build/reproducible-path/abyss-2.3.9/LogKmerCount' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/reproducible-path/abyss-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/aarch64-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-2.3.9/LogKmerCount' Making all in Map make[4]: Entering directory '/build/reproducible-path/abyss-2.3.9/Map' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../FMIndex -I/build/reproducible-path/abyss-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o abyss_index-index.o `test -f 'index.cc' || echo './'`index.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../FMIndex -I/build/reproducible-path/abyss-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o abyss_map-map.o `test -f 'map.cc' || echo './'`map.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../FMIndex -D SAM_SEQ_QUAL=1 -I/build/reproducible-path/abyss-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o abyss_map_ssq-map.o `test -f 'map.cc' || echo './'`map.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../FMIndex -I/build/reproducible-path/abyss-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o abyss_overlap-overlap.o `test -f 'overlap.cc' || echo './'`overlap.cc In file included from ../Graph/GraphIO.h:8, from overlap.cc:23: ../Graph/DotIO.h: In instantiation of 'void write_edges(std::ostream&, const Graph&, typename boost::graph_traits::vertex_descriptor, const EdgeProp*) [with Graph = ContigGraph >; EdgeProp = Distance; std::ostream = std::basic_ostream; typename boost::graph_traits::vertex_descriptor = ContigNode]': ../Graph/DotIO.h:110:14: required from 'std::ostream& write_dot(std::ostream&, const Graph&, const std::string&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream; std::string = std::__cxx11::basic_string]' 110 | write_edges(out, g, *u, (edge_property_type*)NULL); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../Graph/DotIO.h:77:18: required from 'std::ostream& write_dot(std::ostream&, const Graph&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream]' 77 | return write_dot(out, g, "adj"); | ~~~~~~~~~^~~~~~~~~~~~~~~ ../Graph/DotIO.h:125:26: required from 'std::ostream& operator<<(std::ostream&, const DotWriter > >&)' 125 | return write_dot(out, o.g); | ~~~~~~~~~~~~~~~~^~~~~~~~~~ ../Graph/GraphIO.h:33:14: required from 'std::ostream& write_graph(std::ostream&, const Graph&, const std::string&, const std::string&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream; std::string = std::__cxx11::basic_string]' 33 | return out << dot_writer(g); | ~~~~^~~~~~~~~~~~~~~~ overlap.cc:502:13: required from here 502 | write_graph(cout, g, PROGRAM, commandLine); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../Graph/DotIO.h:44:43: warning: possibly dangling reference to a temporary [-Wdangling-reference] 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ^~ ../Graph/DotIO.h:44:51: note: the temporary was destroyed at the end of the full expression 'get >(boost::edge_bundle, (* & g), DirectedGraph::out_edge_iterator(e))' 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ~~~^~~~~~~~~~~~~~~~~~~ g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -L/usr/lib/aarch64-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-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -L/usr/lib/aarch64-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-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -L/usr/lib/aarch64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-map-ssq abyss_map_ssq-map.o ../FMIndex/libfmindex.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../DataBase/libdb.a -lsqlite3 -ldl -lm -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -L/usr/lib/aarch64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-overlap abyss_overlap-overlap.o ../FMIndex/libfmindex.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.9/Map' Making all in MergePaths make[4]: Entering directory '/build/reproducible-path/abyss-2.3.9/MergePaths' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/reproducible-path/abyss-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o MergePaths-MergePaths.o `test -f 'MergePaths.cpp' || echo './'`MergePaths.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Align -I../Common -I../DataLayer -I/build/reproducible-path/abyss-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o MergeContigs-MergeContigs.o `test -f 'MergeContigs.cpp' || echo './'`MergeContigs.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Align -I../Common -I../DataLayer -I../SimpleGraph -I/build/reproducible-path/abyss-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o PathConsensus-PathConsensus.o `test -f 'PathConsensus.cpp' || echo './'`PathConsensus.cpp In file included from ../Graph/GraphIO.h:8, from MergeContigs.cpp:13: ../Graph/DotIO.h: In instantiation of 'void write_edges(std::ostream&, const Graph&, typename boost::graph_traits::vertex_descriptor, const EdgeProp*) [with Graph = ContigGraph >; EdgeProp = Distance; std::ostream = std::basic_ostream; typename boost::graph_traits::vertex_descriptor = ContigNode]': ../Graph/DotIO.h:110:14: required from 'std::ostream& write_dot(std::ostream&, const Graph&, const std::string&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream; std::string = std::__cxx11::basic_string]' 110 | write_edges(out, g, *u, (edge_property_type*)NULL); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../Graph/DotIO.h:77:18: required from 'std::ostream& write_dot(std::ostream&, const Graph&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream]' 77 | return write_dot(out, g, "adj"); | ~~~~~~~~~^~~~~~~~~~~~~~~ ../Graph/DotIO.h:125:26: required from 'std::ostream& operator<<(std::ostream&, const DotWriter > >&)' 125 | return write_dot(out, o.g); | ~~~~~~~~~~~~~~~~^~~~~~~~~~ ../Graph/GraphIO.h:33:14: required from 'std::ostream& write_graph(std::ostream&, const Graph&, const std::string&, const std::string&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream; std::string = std::__cxx11::basic_string]' 33 | return out << dot_writer(g); | ~~~~^~~~~~~~~~~~~~~~ MergeContigs.cpp:428:13: required from here 428 | write_graph(fout, g, PROGRAM, commandLine); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../Graph/DotIO.h:44:43: warning: possibly dangling reference to a temporary [-Wdangling-reference] 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ^~ ../Graph/DotIO.h:44:51: note: the temporary was destroyed at the end of the full expression 'get >(boost::edge_bundle, (* & g), DirectedGraph::out_edge_iterator(e))' 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ~~~^~~~~~~~~~~~~~~~~~~ In file included from ../Graph/GraphIO.h:8, from PathConsensus.cpp:16: ../Graph/DotIO.h: In instantiation of 'void write_edges(std::ostream&, const Graph&, typename boost::graph_traits::vertex_descriptor, const EdgeProp*) [with Graph = ContigGraph >; EdgeProp = Distance; std::ostream = std::basic_ostream; typename boost::graph_traits::vertex_descriptor = ContigNode]': ../Graph/DotIO.h:110:14: required from 'std::ostream& write_dot(std::ostream&, const Graph&, const std::string&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream; std::string = std::__cxx11::basic_string]' 110 | write_edges(out, g, *u, (edge_property_type*)NULL); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../Graph/DotIO.h:77:18: required from 'std::ostream& write_dot(std::ostream&, const Graph&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream]' 77 | return write_dot(out, g, "adj"); | ~~~~~~~~~^~~~~~~~~~~~~~~ ../Graph/DotIO.h:125:26: required from 'std::ostream& operator<<(std::ostream&, const DotWriter > >&)' 125 | return write_dot(out, o.g); | ~~~~~~~~~~~~~~~~^~~~~~~~~~ ../Graph/GraphIO.h:33:14: required from 'std::ostream& write_graph(std::ostream&, const Graph&, const std::string&, const std::string&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream; std::string = std::__cxx11::basic_string]' 33 | return out << dot_writer(g); | ~~~~^~~~~~~~~~~~~~~~ PathConsensus.cpp:999:14: required from here 999 | write_graph(fout, g, PROGRAM, commandLine); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../Graph/DotIO.h:44:43: warning: possibly dangling reference to a temporary [-Wdangling-reference] 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ^~ ../Graph/DotIO.h:44:51: note: the temporary was destroyed at the end of the full expression 'get >(boost::edge_bundle, (* & g), DirectedGraph::out_edge_iterator(e))' 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ~~~^~~~~~~~~~~~~~~~~~~ g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -L/usr/lib/aarch64-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-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -L/usr/lib/aarch64-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-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -L/usr/lib/aarch64-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-2.3.9/MergePaths' Making all in Overlap make[4]: Entering directory '/build/reproducible-path/abyss-2.3.9/Overlap' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/reproducible-path/abyss-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o Overlap-Overlap.o `test -f 'Overlap.cpp' || echo './'`Overlap.cpp Overlap.cpp: In function 'int main(int, char**)': Overlap.cpp:513:40: warning: possibly dangling reference to a temporary [-Wdangling-reference] 513 | const Overlap& ep = get(edge_bundle, scaffoldGraph, e); | ^~ Overlap.cpp:513:48: note: the temporary was destroyed at the end of the full expression 'get >(boost::edge_bundle, scaffoldGraph, DirectedGraph::out_edge_iterator(e))' 513 | const Overlap& ep = get(edge_bundle, scaffoldGraph, e); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../Graph/GraphIO.h:8, from Overlap.cpp:16: ../Graph/DotIO.h: In instantiation of 'void write_edges(std::ostream&, const Graph&, typename boost::graph_traits::vertex_descriptor, const EdgeProp*) [with Graph = ContigGraph >; EdgeProp = Overlap; std::ostream = std::basic_ostream; typename boost::graph_traits::vertex_descriptor = ContigNode]': ../Graph/DotIO.h:110:14: required from 'std::ostream& write_dot(std::ostream&, const Graph&, const std::string&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream; std::string = std::__cxx11::basic_string]' 110 | write_edges(out, g, *u, (edge_property_type*)NULL); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../Graph/DotIO.h:77:18: required from 'std::ostream& write_dot(std::ostream&, const Graph&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream]' 77 | return write_dot(out, g, "adj"); | ~~~~~~~~~^~~~~~~~~~~~~~~ ../Graph/DotIO.h:125:26: required from 'std::ostream& operator<<(std::ostream&, const DotWriter > >&)' 125 | return write_dot(out, o.g); | ~~~~~~~~~~~~~~~~^~~~~~~~~~ Overlap.cpp:481:35: required from here 481 | cout << dot_writer(scaffoldGraph); | ^ ../Graph/DotIO.h:44:43: warning: possibly dangling reference to a temporary [-Wdangling-reference] 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ^~ ../Graph/DotIO.h:44:51: note: the temporary was destroyed at the end of the full expression 'get >(boost::edge_bundle, (* & g), DirectedGraph::out_edge_iterator(e))' 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ~~~^~~~~~~~~~~~~~~~~~~ ../Graph/DotIO.h: In instantiation of 'void write_edges(std::ostream&, const Graph&, typename boost::graph_traits::vertex_descriptor, const EdgeProp*) [with Graph = ContigGraph >; EdgeProp = Distance; std::ostream = std::basic_ostream; typename boost::graph_traits::vertex_descriptor = ContigNode]': ../Graph/DotIO.h:110:14: required from 'std::ostream& write_dot(std::ostream&, const Graph&, const std::string&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream; std::string = std::__cxx11::basic_string]' 110 | write_edges(out, g, *u, (edge_property_type*)NULL); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../Graph/DotIO.h:77:18: required from 'std::ostream& write_dot(std::ostream&, const Graph&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream]' 77 | return write_dot(out, g, "adj"); | ~~~~~~~~~^~~~~~~~~~~~~~~ ../Graph/DotIO.h:125:26: required from 'std::ostream& operator<<(std::ostream&, const DotWriter > >&)' 125 | return write_dot(out, o.g); | ~~~~~~~~~~~~~~~~^~~~~~~~~~ ../Graph/GraphIO.h:33:14: required from 'std::ostream& write_graph(std::ostream&, const Graph&, const std::string&, const std::string&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream; std::string = std::__cxx11::basic_string]' 33 | return out << dot_writer(g); | ~~~~^~~~~~~~~~~~~~~~ Overlap.cpp:587:14: required from here 587 | write_graph(fout, graph, PROGRAM, commandLine); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../Graph/DotIO.h:44:43: warning: possibly dangling reference to a temporary [-Wdangling-reference] 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ^~ ../Graph/DotIO.h:44:51: note: the temporary was destroyed at the end of the full expression 'get >(boost::edge_bundle, (* & g), DirectedGraph::out_edge_iterator(e))' 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ~~~^~~~~~~~~~~~~~~~~~~ g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -L/usr/lib/aarch64-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-2.3.9/Overlap' Making all in PairedDBG make[4]: Entering directory '/build/reproducible-path/abyss-2.3.9/PairedDBG' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -DPAIRED_DBG -I.. -I/build/reproducible-path/abyss-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o abyss_paired_dbg-abyss-paired-dbg.o `test -f 'abyss-paired-dbg.cc' || echo './'`abyss-paired-dbg.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -DPAIRED_DBG -I.. -I/build/reproducible-path/abyss-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o abyss_paired_dbg-KmerPair.o `test -f 'KmerPair.cc' || echo './'`KmerPair.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I/build/reproducible-path/abyss-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o KmerPair.o KmerPair.cc rm -f libpaireddbg.a ar cru libpaireddbg.a KmerPair.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libpaireddbg.a g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -L/usr/lib/aarch64-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-2.3.9/PairedDBG' Making all in ParseAligns make[4]: Entering directory '/build/reproducible-path/abyss-2.3.9/ParseAligns' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/reproducible-path/abyss-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/aarch64-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-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/aarch64-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-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/aarch64-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-2.3.9/ParseAligns' Making all in PathOverlap make[4]: Entering directory '/build/reproducible-path/abyss-2.3.9/PathOverlap' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/reproducible-path/abyss-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o PathOverlap-PathOverlap.o `test -f 'PathOverlap.cpp' || echo './'`PathOverlap.cpp In file included from ../Graph/GraphIO.h:8, from PathOverlap.cpp:10: ../Graph/DotIO.h: In instantiation of 'void write_edges(std::ostream&, const Graph&, typename boost::graph_traits::vertex_descriptor, const EdgeProp*) [with Graph = ContigGraph >; EdgeProp = Distance; std::ostream = std::basic_ostream; typename boost::graph_traits::vertex_descriptor = ContigNode]': ../Graph/DotIO.h:110:14: required from 'std::ostream& write_dot(std::ostream&, const Graph&, const std::string&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream; std::string = std::__cxx11::basic_string]' 110 | write_edges(out, g, *u, (edge_property_type*)NULL); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../Graph/DotIO.h:77:18: required from 'std::ostream& write_dot(std::ostream&, const Graph&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream]' 77 | return write_dot(out, g, "adj"); | ~~~~~~~~~^~~~~~~~~~~~~~~ ../Graph/DotIO.h:125:26: required from 'std::ostream& operator<<(std::ostream&, const DotWriter > >&)' 125 | return write_dot(out, o.g); | ~~~~~~~~~~~~~~~~^~~~~~~~~~ ../Graph/GraphIO.h:33:14: required from 'std::ostream& write_graph(std::ostream&, const Graph&, const std::string&, const std::string&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream; std::string = std::__cxx11::basic_string]' 33 | return out << dot_writer(g); | ~~~~^~~~~~~~~~~~~~~~ PathOverlap.cpp:709:14: required from here 709 | write_graph(out, g, PROGRAM, commandLine); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../Graph/DotIO.h:44:43: warning: possibly dangling reference to a temporary [-Wdangling-reference] 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ^~ ../Graph/DotIO.h:44:51: note: the temporary was destroyed at the end of the full expression 'get >(boost::edge_bundle, (* & g), DirectedGraph::out_edge_iterator(e))' 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ~~~^~~~~~~~~~~~~~~~~~~ g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -L/usr/lib/aarch64-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-2.3.9/PathOverlap' Making all in PopBubbles make[4]: Entering directory '/build/reproducible-path/abyss-2.3.9/PopBubbles' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Align -I../Common -I../DataLayer -I/build/reproducible-path/abyss-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o PopBubbles-PopBubbles.o `test -f 'PopBubbles.cpp' || echo './'`PopBubbles.cpp In file included from ../Graph/GraphIO.h:8, from PopBubbles.cpp:16: ../Graph/DotIO.h: In instantiation of 'void write_edges(std::ostream&, const Graph&, typename boost::graph_traits::vertex_descriptor, const EdgeProp*) [with Graph = ContigGraph >; EdgeProp = Distance; std::ostream = std::basic_ostream; typename boost::graph_traits::vertex_descriptor = ContigNode]': ../Graph/DotIO.h:110:14: required from 'std::ostream& write_dot(std::ostream&, const Graph&, const std::string&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream; std::string = std::__cxx11::basic_string]' 110 | write_edges(out, g, *u, (edge_property_type*)NULL); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../Graph/DotIO.h:77:18: required from 'std::ostream& write_dot(std::ostream&, const Graph&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream]' 77 | return write_dot(out, g, "adj"); | ~~~~~~~~~^~~~~~~~~~~~~~~ ../Graph/DotIO.h:125:26: required from 'std::ostream& operator<<(std::ostream&, const DotWriter > >&)' 125 | return write_dot(out, o.g); | ~~~~~~~~~~~~~~~~^~~~~~~~~~ ../Graph/GraphIO.h:33:14: required from 'std::ostream& write_graph(std::ostream&, const Graph&, const std::string&, const std::string&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream; std::string = std::__cxx11::basic_string]' 33 | return out << dot_writer(g); | ~~~~^~~~~~~~~~~~~~~~ PopBubbles.cpp:723:14: required from here 723 | write_graph(fout, g, PROGRAM, commandLine); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../Graph/DotIO.h:44:43: warning: possibly dangling reference to a temporary [-Wdangling-reference] 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ^~ ../Graph/DotIO.h:44:51: note: the temporary was destroyed at the end of the full expression 'get >(boost::edge_bundle, (* & g), DirectedGraph::out_edge_iterator(e))' 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ~~~^~~~~~~~~~~~~~~~~~~ g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -L/usr/lib/aarch64-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-2.3.9/PopBubbles' Making all in Scaffold make[4]: Entering directory '/build/reproducible-path/abyss-2.3.9/Scaffold' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/reproducible-path/abyss-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o abyss_scaffold-scaffold.o `test -f 'scaffold.cc' || echo './'`scaffold.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/reproducible-path/abyss-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o abyss_junction-junction.o `test -f 'junction.cc' || echo './'`junction.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/reproducible-path/abyss-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o abyss_longseqdist-longseqdist.o `test -f 'longseqdist.cpp' || echo './'`longseqdist.cpp In file included from ../Graph/GraphIO.h:8, from longseqdist.cpp:9: ../Graph/DotIO.h: In instantiation of 'void write_edges(std::ostream&, const Graph&, typename boost::graph_traits::vertex_descriptor, const EdgeProp*) [with Graph = ContigGraph >; EdgeProp = DistanceEst; std::ostream = std::basic_ostream; typename boost::graph_traits::vertex_descriptor = ContigNode]': ../Graph/DotIO.h:110:14: required from 'std::ostream& write_dot(std::ostream&, const Graph&, const std::string&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream; std::string = std::__cxx11::basic_string]' 110 | write_edges(out, g, *u, (edge_property_type*)NULL); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../Graph/DotIO.h:77:18: required from 'std::ostream& write_dot(std::ostream&, const Graph&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream]' 77 | return write_dot(out, g, "adj"); | ~~~~~~~~~^~~~~~~~~~~~~~~ longseqdist.cpp:208:11: required from here 208 | write_dot(cout, g); | ~~~~~~~~~^~~~~~~~~ ../Graph/DotIO.h:44:43: warning: possibly dangling reference to a temporary [-Wdangling-reference] 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ^~ ../Graph/DotIO.h:44:51: note: the temporary was destroyed at the end of the full expression 'get >(boost::edge_bundle, (* & g), DirectedGraph::out_edge_iterator(e))' 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ~~~^~~~~~~~~~~~~~~~~~~ In file included from ../Graph/GraphIO.h:8, from scaffold.cc:13: ../Graph/DotIO.h: In instantiation of 'void write_edges(std::ostream&, const Graph&, typename boost::graph_traits::vertex_descriptor, const EdgeProp*) [with Graph = ContigGraph >; EdgeProp = DistanceEst; std::ostream = std::basic_ostream; typename boost::graph_traits::vertex_descriptor = ContigNode]': ../Graph/DotIO.h:110:14: required from 'std::ostream& write_dot(std::ostream&, const Graph&, const std::string&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream; std::string = std::__cxx11::basic_string]' 110 | write_edges(out, g, *u, (edge_property_type*)NULL); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../Graph/DotIO.h:77:18: required from 'std::ostream& write_dot(std::ostream&, const Graph&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream]' 77 | return write_dot(out, g, "adj"); | ~~~~~~~~~^~~~~~~~~~~~~~~ scaffold.cc:824:13: required from here 824 | write_dot(out, g); | ~~~~~~~~~^~~~~~~~ ../Graph/DotIO.h:44:43: warning: possibly dangling reference to a temporary [-Wdangling-reference] 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ^~ ../Graph/DotIO.h:44:51: note: the temporary was destroyed at the end of the full expression 'get >(boost::edge_bundle, (* & g), DirectedGraph::out_edge_iterator(e))' 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ~~~^~~~~~~~~~~~~~~~~~~ g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -L/usr/lib/aarch64-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-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -L/usr/lib/aarch64-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-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -L/usr/lib/aarch64-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-2.3.9/Scaffold' Making all in SimpleGraph make[4]: Entering directory '/build/reproducible-path/abyss-2.3.9/SimpleGraph' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/reproducible-path/abyss-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/boost_1_56_0 -Wall -Wextra -Werror -Wno-strict-aliasing -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o SimpleGraph-SimpleGraph.o `test -f 'SimpleGraph.cpp' || echo './'`SimpleGraph.cpp g++ -std=c++11 -Wall -Wextra -Werror -Wno-strict-aliasing -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -L/usr/lib/aarch64-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-2.3.9/SimpleGraph' Making all in kmerprint make[4]: Entering directory '/build/reproducible-path/abyss-2.3.9/kmerprint' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Assembly -I../Common -I../DataLayer -I/build/reproducible-path/abyss-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o kmerprint-kmerprint.o `test -f 'kmerprint.cc' || echo './'`kmerprint.cc g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -L/usr/lib/aarch64-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-2.3.9/kmerprint' Making all in FilterGraph make[4]: Entering directory '/build/reproducible-path/abyss-2.3.9/FilterGraph' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/reproducible-path/abyss-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o abyss_filtergraph-FilterGraph.o `test -f 'FilterGraph.cc' || echo './'`FilterGraph.cc In file included from ../Graph/GraphIO.h:8, from FilterGraph.cc:15: ../Graph/DotIO.h: In instantiation of 'void write_edges(std::ostream&, const Graph&, typename boost::graph_traits::vertex_descriptor, const EdgeProp*) [with Graph = ContigGraph >; EdgeProp = Distance; std::ostream = std::basic_ostream; typename boost::graph_traits::vertex_descriptor = ContigNode]': ../Graph/DotIO.h:110:14: required from 'std::ostream& write_dot(std::ostream&, const Graph&, const std::string&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream; std::string = std::__cxx11::basic_string]' 110 | write_edges(out, g, *u, (edge_property_type*)NULL); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../Graph/DotIO.h:77:18: required from 'std::ostream& write_dot(std::ostream&, const Graph&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream]' 77 | return write_dot(out, g, "adj"); | ~~~~~~~~~^~~~~~~~~~~~~~~ ../Graph/DotIO.h:125:26: required from 'std::ostream& operator<<(std::ostream&, const DotWriter > >&)' 125 | return write_dot(out, o.g); | ~~~~~~~~~~~~~~~~^~~~~~~~~~ ../Graph/GraphIO.h:33:14: required from 'std::ostream& write_graph(std::ostream&, const Graph&, const std::string&, const std::string&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream; std::string = std::__cxx11::basic_string]' 33 | return out << dot_writer(g); | ~~~~^~~~~~~~~~~~~~~~ FilterGraph.cc:825:14: required from here 825 | write_graph(fout, g, PROGRAM, commandLine); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../Graph/DotIO.h:44:43: warning: possibly dangling reference to a temporary [-Wdangling-reference] 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ^~ ../Graph/DotIO.h:44:51: note: the temporary was destroyed at the end of the full expression 'get >(boost::edge_bundle, (* & g), DirectedGraph::out_edge_iterator(e))' 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ~~~^~~~~~~~~~~~~~~~~~~ g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -L/usr/lib/aarch64-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-2.3.9/FilterGraph' Making all in GapFiller make[4]: Entering directory '/build/reproducible-path/abyss-2.3.9/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-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/aarch64-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-2.3.9/GapFiller' Making all in Sealer make[4]: Entering directory '/build/reproducible-path/abyss-2.3.9/Sealer' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/reproducible-path/abyss-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o abyss_sealer-sealer.o `test -f 'sealer.cc' || echo './'`sealer.cc g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -L/usr/lib/aarch64-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-2.3.9/Sealer' Making all in RResolver make[4]: Entering directory '/build/reproducible-path/abyss-2.3.9/RResolver' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I/build/reproducible-path/abyss-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/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-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/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-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/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-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/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-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/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-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/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-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/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-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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]' 110 | write_edges(out, g, *u, (edge_property_type*)NULL); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../Graph/DotIO.h:77:18: required from 'std::ostream& write_dot(std::ostream&, const Graph&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream]' 77 | return write_dot(out, g, "adj"); | ~~~~~~~~~^~~~~~~~~~~~~~~ ../Graph/DotIO.h:125:26: required from 'std::ostream& operator<<(std::ostream&, const DotWriter > >&)' 125 | return write_dot(out, o.g); | ~~~~~~~~~~~~~~~~^~~~~~~~~~ ../Graph/GraphIO.h:33:14: required from 'std::ostream& write_graph(std::ostream&, const Graph&, const std::string&, const std::string&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream; std::string = std::__cxx11::basic_string]' 33 | return out << dot_writer(g); | ~~~~^~~~~~~~~~~~~~~~ Contigs.cpp:140:13: required from here 140 | write_graph(fout, g_contigGraph, program, commandLine); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../Graph/DotIO.h:44:43: warning: possibly dangling reference to a temporary [-Wdangling-reference] 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ^~ ../Graph/DotIO.h:44:51: note: the temporary was destroyed at the end of the full expression 'get >(boost::edge_bundle, (* & g), DirectedGraph::out_edge_iterator(e))' 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ~~~^~~~~~~~~~~~~~~~~~~ In file included from ../Graph/GraphIO.h:8, from Contigs.h:17, from Contigs.cpp:1: ../Graph/DotIO.h: In instantiation of 'void write_edges(std::ostream&, const Graph&, typename boost::graph_traits::vertex_descriptor, const EdgeProp*) [with Graph = ContigGraph >; EdgeProp = Distance; std::ostream = std::basic_ostream; typename boost::graph_traits::vertex_descriptor = ContigNode]': ../Graph/DotIO.h:110:14: required from 'std::ostream& write_dot(std::ostream&, const Graph&, const std::string&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream; std::string = std::__cxx11::basic_string]' 110 | write_edges(out, g, *u, (edge_property_type*)NULL); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../Graph/DotIO.h:77:18: required from 'std::ostream& write_dot(std::ostream&, const Graph&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream]' 77 | return write_dot(out, g, "adj"); | ~~~~~~~~~^~~~~~~~~~~~~~~ ../Graph/DotIO.h:125:26: required from 'std::ostream& operator<<(std::ostream&, const DotWriter > >&)' 125 | return write_dot(out, o.g); | ~~~~~~~~~~~~~~~~^~~~~~~~~~ ../Graph/GraphIO.h:33:14: required from 'std::ostream& write_graph(std::ostream&, const Graph&, const std::string&, const std::string&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream; std::string = std::__cxx11::basic_string]' 33 | return out << dot_writer(g); | ~~~~^~~~~~~~~~~~~~~~ Contigs.cpp:140:13: required from here 140 | write_graph(fout, g_contigGraph, program, commandLine); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../Graph/DotIO.h:44:43: warning: possibly dangling reference to a temporary [-Wdangling-reference] 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ^~ ../Graph/DotIO.h:44:51: note: the temporary was destroyed at the end of the full expression 'get >(boost::edge_bundle, (* & g), DirectedGraph::out_edge_iterator(e))' 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ~~~^~~~~~~~~~~~~~~~~~~ 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-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/aarch64-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-2.3.9/RResolver' Making all in AdjList make[4]: Entering directory '/build/reproducible-path/abyss-2.3.9/AdjList' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -DPAIRED_DBG -I/build/reproducible-path/abyss-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o AdjList-AdjList.o `test -f 'AdjList.cpp' || echo './'`AdjList.cpp In file included from ../Graph/GraphIO.h:8, from AdjList.cpp:15: ../Graph/DotIO.h: In instantiation of 'void write_edges(std::ostream&, const Graph&, typename boost::graph_traits::vertex_descriptor, const EdgeProp*) [with Graph = ContigGraph >; EdgeProp = Distance; std::ostream = std::basic_ostream; typename boost::graph_traits::vertex_descriptor = ContigNode]': ../Graph/DotIO.h:110:14: required from 'std::ostream& write_dot(std::ostream&, const Graph&, const std::string&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream; std::string = std::__cxx11::basic_string]' 110 | write_edges(out, g, *u, (edge_property_type*)NULL); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../Graph/DotIO.h:77:18: required from 'std::ostream& write_dot(std::ostream&, const Graph&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream]' 77 | return write_dot(out, g, "adj"); | ~~~~~~~~~^~~~~~~~~~~~~~~ ../Graph/DotIO.h:125:26: required from 'std::ostream& operator<<(std::ostream&, const DotWriter > >&)' 125 | return write_dot(out, o.g); | ~~~~~~~~~~~~~~~~^~~~~~~~~~ ../Graph/GraphIO.h:33:14: required from 'std::ostream& write_graph(std::ostream&, const Graph&, const std::string&, const std::string&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream; std::string = std::__cxx11::basic_string]' 33 | return out << dot_writer(g); | ~~~~^~~~~~~~~~~~~~~~ AdjList.cpp:401:13: required from here 401 | write_graph(cout, g, PROGRAM, commandLine); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../Graph/DotIO.h:44:43: warning: possibly dangling reference to a temporary [-Wdangling-reference] 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ^~ ../Graph/DotIO.h:44:51: note: the temporary was destroyed at the end of the full expression 'get >(boost::edge_bundle, (* & g), DirectedGraph::out_edge_iterator(e))' 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ~~~^~~~~~~~~~~~~~~~~~~ g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -L/usr/lib/aarch64-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-2.3.9/AdjList' Making all in vendor make[4]: Entering directory '/build/reproducible-path/abyss-2.3.9/vendor' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.9/vendor' Making all in vendor/gtest-1.7.0 make[4]: Entering directory '/build/reproducible-path/abyss-2.3.9/vendor/gtest-1.7.0' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.9/vendor/gtest-1.7.0' Making all in Unittest make[4]: Entering directory '/build/reproducible-path/abyss-2.3.9/Unittest' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.9/Unittest' make[4]: Entering directory '/build/reproducible-path/abyss-2.3.9' make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.9' make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.9' make[2]: Leaving directory '/build/reproducible-path/abyss-2.3.9' markdown README.md > README.html make[1]: Leaving directory '/build/reproducible-path/abyss-2.3.9' dh_auto_test make -j12 check "TESTSUITEFLAGS=-j12 --verbose" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/abyss-2.3.9' Making check in bin make[2]: Entering directory '/build/reproducible-path/abyss-2.3.9/bin' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/abyss-2.3.9/bin' Making check in doc make[2]: Entering directory '/build/reproducible-path/abyss-2.3.9/doc' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/abyss-2.3.9/doc' Making check in Common make[2]: Entering directory '/build/reproducible-path/abyss-2.3.9/Common' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/abyss-2.3.9/Common' Making check in Graph make[2]: Entering directory '/build/reproducible-path/abyss-2.3.9/Graph' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/abyss-2.3.9/Graph' Making check in DataLayer make[2]: Entering directory '/build/reproducible-path/abyss-2.3.9/DataLayer' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/abyss-2.3.9/DataLayer' Making check in DataBase make[2]: Entering directory '/build/reproducible-path/abyss-2.3.9/DataBase' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/abyss-2.3.9/DataBase' Making check in FMIndex make[2]: Entering directory '/build/reproducible-path/abyss-2.3.9/FMIndex' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/abyss-2.3.9/FMIndex' Making check in Assembly make[2]: Entering directory '/build/reproducible-path/abyss-2.3.9/Assembly' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/abyss-2.3.9/Assembly' Making check in dialign make[2]: Entering directory '/build/reproducible-path/abyss-2.3.9/dialign' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/abyss-2.3.9/dialign' Making check in Align make[2]: Entering directory '/build/reproducible-path/abyss-2.3.9/Align' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/abyss-2.3.9/Align' Making check in ABYSS make[2]: Entering directory '/build/reproducible-path/abyss-2.3.9/ABYSS' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/abyss-2.3.9/ABYSS' Making check in Parallel make[2]: Entering directory '/build/reproducible-path/abyss-2.3.9/Parallel' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/abyss-2.3.9/Parallel' Making check in Bloom make[2]: Entering directory '/build/reproducible-path/abyss-2.3.9/Bloom' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/abyss-2.3.9/Bloom' Making check in BloomDBG make[2]: Entering directory '/build/reproducible-path/abyss-2.3.9/BloomDBG' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/abyss-2.3.9/BloomDBG' Making check in Konnector make[2]: Entering directory '/build/reproducible-path/abyss-2.3.9/Konnector' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/abyss-2.3.9/Konnector' Making check in Consensus make[2]: Entering directory '/build/reproducible-path/abyss-2.3.9/Consensus' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/abyss-2.3.9/Consensus' Making check in DAssembler make[2]: Entering directory '/build/reproducible-path/abyss-2.3.9/DAssembler' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/abyss-2.3.9/DAssembler' Making check in DistanceEst make[2]: Entering directory '/build/reproducible-path/abyss-2.3.9/DistanceEst' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/abyss-2.3.9/DistanceEst' Making check in KAligner make[2]: Entering directory '/build/reproducible-path/abyss-2.3.9/KAligner' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/abyss-2.3.9/KAligner' Making check in Layout make[2]: Entering directory '/build/reproducible-path/abyss-2.3.9/Layout' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/abyss-2.3.9/Layout' Making check in LogKmerCount make[2]: Entering directory '/build/reproducible-path/abyss-2.3.9/LogKmerCount' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/abyss-2.3.9/LogKmerCount' Making check in Map make[2]: Entering directory '/build/reproducible-path/abyss-2.3.9/Map' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/abyss-2.3.9/Map' Making check in MergePaths make[2]: Entering directory '/build/reproducible-path/abyss-2.3.9/MergePaths' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/abyss-2.3.9/MergePaths' Making check in Overlap make[2]: Entering directory '/build/reproducible-path/abyss-2.3.9/Overlap' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/abyss-2.3.9/Overlap' Making check in PairedDBG make[2]: Entering directory '/build/reproducible-path/abyss-2.3.9/PairedDBG' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/abyss-2.3.9/PairedDBG' Making check in ParseAligns make[2]: Entering directory '/build/reproducible-path/abyss-2.3.9/ParseAligns' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/abyss-2.3.9/ParseAligns' Making check in PathOverlap make[2]: Entering directory '/build/reproducible-path/abyss-2.3.9/PathOverlap' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/abyss-2.3.9/PathOverlap' Making check in PopBubbles make[2]: Entering directory '/build/reproducible-path/abyss-2.3.9/PopBubbles' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/abyss-2.3.9/PopBubbles' Making check in Scaffold make[2]: Entering directory '/build/reproducible-path/abyss-2.3.9/Scaffold' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/abyss-2.3.9/Scaffold' Making check in SimpleGraph make[2]: Entering directory '/build/reproducible-path/abyss-2.3.9/SimpleGraph' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/abyss-2.3.9/SimpleGraph' Making check in kmerprint make[2]: Entering directory '/build/reproducible-path/abyss-2.3.9/kmerprint' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/abyss-2.3.9/kmerprint' Making check in FilterGraph make[2]: Entering directory '/build/reproducible-path/abyss-2.3.9/FilterGraph' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/abyss-2.3.9/FilterGraph' Making check in GapFiller make[2]: Entering directory '/build/reproducible-path/abyss-2.3.9/GapFiller' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/abyss-2.3.9/GapFiller' Making check in Sealer make[2]: Entering directory '/build/reproducible-path/abyss-2.3.9/Sealer' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/abyss-2.3.9/Sealer' Making check in RResolver make[2]: Entering directory '/build/reproducible-path/abyss-2.3.9/RResolver' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/abyss-2.3.9/RResolver' Making check in AdjList make[2]: Entering directory '/build/reproducible-path/abyss-2.3.9/AdjList' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/abyss-2.3.9/AdjList' Making check in vendor make[2]: Entering directory '/build/reproducible-path/abyss-2.3.9/vendor' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/abyss-2.3.9/vendor' Making check in vendor/gtest-1.7.0 make[2]: Entering directory '/build/reproducible-path/abyss-2.3.9/vendor/gtest-1.7.0' make libgtest.a libgtest_main.a make[3]: Entering directory '/build/reproducible-path/abyss-2.3.9/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-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/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-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/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-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/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-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o src/libgtest_main_a-gtest-all.o `test -f 'src/gtest-all.cc' || echo './'`src/gtest-all.cc rm -f libgtest.a ar cru libgtest.a src/libgtest_a-gtest-all.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libgtest.a rm -f libgtest_main.a ar cru libgtest_main.a src/libgtest_main_a-gtest_main.o src/libgtest_main_a-gtest-all.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libgtest_main.a make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.9/vendor/gtest-1.7.0' make[2]: Leaving directory '/build/reproducible-path/abyss-2.3.9/vendor/gtest-1.7.0' Making check in Unittest make[2]: Entering directory '/build/reproducible-path/abyss-2.3.9/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-2.3.9/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-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.3.9 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.9/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/aarch64-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-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/aarch64-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-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/aarch64-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-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/aarch64-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-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/aarch64-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-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/aarch64-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-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/aarch64-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-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/aarch64-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-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/aarch64-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-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/aarch64-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-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/aarch64-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-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/aarch64-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-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/aarch64-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-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/aarch64-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-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/aarch64-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-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/aarch64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o graph_ConstrainedBidiBFSVisitor Graph/graph_ConstrainedBidiBFSVisitor-ConstrainedBidiBFSVisitorTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/aarch64-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-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/aarch64-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-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/aarch64-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-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/aarch64-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-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/aarch64-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-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/aarch64-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-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/aarch64-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-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/aarch64-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-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/aarch64-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-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/aarch64-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-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/aarch64-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-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/aarch64-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-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/aarch64-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 -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/aarch64-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-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/aarch64-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-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/aarch64-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-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/aarch64-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-2.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/aarch64-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-2.3.9/Unittest' make check-TESTS make[3]: Entering directory '/build/reproducible-path/abyss-2.3.9/Unittest' make[4]: Entering directory '/build/reproducible-path/abyss-2.3.9/Unittest' PASS: common_stringutil PASS: common_bitutil PASS: common_histogram PASS: common_KmerIterator PASS: common_kmer PASS: common_sam PASS: common_sam_ssq PASS: BloomFilter PASS: Konnector_DBGBloom PASS: graph_ConstrainedBFSVisitor PASS: common_sequence PASS: Konnector_DBGBloomAlgorithms PASS: graph_BidirectionalBFS PASS: graph_HashGraph PASS: graph_AllPathsSearch PASS: graph_ExtendPath PASS: graph_ConstrainedBidiBFSVisitor PASS: graph_UndirectedGraph PASS: Konnector_konnector PASS: PairedDBG_KmerPair PASS: PairedDBG_BranchRecord PASS: graph_DotIO PASS: BloomDBG_BloomDBG PASS: PairedDBG_Dinuc PASS: BloomDBG_RollingHashIterator PASS: BloomDBG_RollingHash PASS: BloomDBG_HashAgnosticCascadingBloom PASS: BloomDBG_RollingBloomDBG PASS: BloomDBG_CountingBloomFilter PASS: BloomDBG_MaskedKmer PASS: BloomDBG_SpacedSeed PASS: BloomDBG_LightweightKmer PASS: DBG_LoadAlgorithm PASS: PairedDBG_LoadAlgorithm ============================================================================ Testsuite summary for ABySS 2.3.9 ============================================================================ # TOTAL: 34 # PASS: 34 # SKIP: 0 # XFAIL: 0 # FAIL: 0 # XPASS: 0 # ERROR: 0 ============================================================================ make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.9/Unittest' make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.9/Unittest' make[2]: Leaving directory '/build/reproducible-path/abyss-2.3.9/Unittest' make[2]: Entering directory '/build/reproducible-path/abyss-2.3.9' make[2]: Leaving directory '/build/reproducible-path/abyss-2.3.9' make[1]: Leaving directory '/build/reproducible-path/abyss-2.3.9' create-stamp debian/debhelper-build-stamp dh_prep debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/abyss-2.3.9' dh_auto_install --destdir=debian/tmp make -j12 install DESTDIR=/build/reproducible-path/abyss-2.3.9/debian/tmp AM_UPDATE_INFO_DIR=no make[2]: Entering directory '/build/reproducible-path/abyss-2.3.9' Making install in bin make[3]: Entering directory '/build/reproducible-path/abyss-2.3.9/bin' make[4]: Entering directory '/build/reproducible-path/abyss-2.3.9/bin' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/abyss-2.3.9/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-2.3.9/debian/tmp/usr/bin' make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.9/bin' make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.9/bin' Making install in doc make[3]: Entering directory '/build/reproducible-path/abyss-2.3.9/doc' make[4]: Entering directory '/build/reproducible-path/abyss-2.3.9/doc' make[4]: Nothing to be done for 'install-exec-am'. /usr/bin/mkdir -p '/build/reproducible-path/abyss-2.3.9/debian/tmp/usr/share/doc/abyss' /usr/bin/install -c -m 644 flowchart.pdf flowchart_simplified.pdf '/build/reproducible-path/abyss-2.3.9/debian/tmp/usr/share/doc/abyss' make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.9/doc' make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.9/doc' Making install in Common make[3]: Entering directory '/build/reproducible-path/abyss-2.3.9/Common' make[4]: Entering directory '/build/reproducible-path/abyss-2.3.9/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-2.3.9/Common' make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.9/Common' Making install in Graph make[3]: Entering directory '/build/reproducible-path/abyss-2.3.9/Graph' make[4]: Entering directory '/build/reproducible-path/abyss-2.3.9/Graph' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/abyss-2.3.9/debian/tmp/usr/bin' /usr/bin/install -c abyss-gc abyss-todot '/build/reproducible-path/abyss-2.3.9/debian/tmp/usr/bin' make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.9/Graph' make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.9/Graph' Making install in DataLayer make[3]: Entering directory '/build/reproducible-path/abyss-2.3.9/DataLayer' make[4]: Entering directory '/build/reproducible-path/abyss-2.3.9/DataLayer' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/abyss-2.3.9/debian/tmp/usr/bin' /usr/bin/install -c abyss-fac abyss-tofastq '/build/reproducible-path/abyss-2.3.9/debian/tmp/usr/bin' make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.9/DataLayer' make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.9/DataLayer' Making install in DataBase make[3]: Entering directory '/build/reproducible-path/abyss-2.3.9/DataBase' make[4]: Entering directory '/build/reproducible-path/abyss-2.3.9/DataBase' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/abyss-2.3.9/debian/tmp/usr/bin' /usr/bin/mkdir -p '/build/reproducible-path/abyss-2.3.9/debian/tmp/usr/bin' /usr/bin/install -c abyss-db-txt '/build/reproducible-path/abyss-2.3.9/debian/tmp/usr/bin' /usr/bin/install -c abyss-db-csv '/build/reproducible-path/abyss-2.3.9/debian/tmp/usr/bin' make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.9/DataBase' make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.9/DataBase' Making install in FMIndex make[3]: Entering directory '/build/reproducible-path/abyss-2.3.9/FMIndex' make[4]: Entering directory '/build/reproducible-path/abyss-2.3.9/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-2.3.9/FMIndex' make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.9/FMIndex' Making install in Assembly make[3]: Entering directory '/build/reproducible-path/abyss-2.3.9/Assembly' make[4]: Entering directory '/build/reproducible-path/abyss-2.3.9/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-2.3.9/Assembly' make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.9/Assembly' Making install in dialign make[3]: Entering directory '/build/reproducible-path/abyss-2.3.9/dialign' make[4]: Entering directory '/build/reproducible-path/abyss-2.3.9/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-2.3.9/dialign' make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.9/dialign' Making install in Align make[3]: Entering directory '/build/reproducible-path/abyss-2.3.9/Align' make[4]: Entering directory '/build/reproducible-path/abyss-2.3.9/Align' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/abyss-2.3.9/debian/tmp/usr/bin' /usr/bin/install -c abyss-align abyss-mergepairs '/build/reproducible-path/abyss-2.3.9/debian/tmp/usr/bin' make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.9/Align' make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.9/Align' Making install in ABYSS make[3]: Entering directory '/build/reproducible-path/abyss-2.3.9/ABYSS' make[4]: Entering directory '/build/reproducible-path/abyss-2.3.9/ABYSS' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/abyss-2.3.9/debian/tmp/usr/bin' /usr/bin/install -c ABYSS '/build/reproducible-path/abyss-2.3.9/debian/tmp/usr/bin' make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.9/ABYSS' make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.9/ABYSS' Making install in Parallel make[3]: Entering directory '/build/reproducible-path/abyss-2.3.9/Parallel' make[4]: Entering directory '/build/reproducible-path/abyss-2.3.9/Parallel' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/abyss-2.3.9/debian/tmp/usr/bin' /usr/bin/install -c ABYSS-P abyss-paired-dbg-mpi '/build/reproducible-path/abyss-2.3.9/debian/tmp/usr/bin' make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.9/Parallel' make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.9/Parallel' Making install in Bloom make[3]: Entering directory '/build/reproducible-path/abyss-2.3.9/Bloom' make[4]: Entering directory '/build/reproducible-path/abyss-2.3.9/Bloom' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/abyss-2.3.9/debian/tmp/usr/bin' /usr/bin/install -c abyss-bloom '/build/reproducible-path/abyss-2.3.9/debian/tmp/usr/bin' make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.9/Bloom' make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.9/Bloom' Making install in BloomDBG make[3]: Entering directory '/build/reproducible-path/abyss-2.3.9/BloomDBG' make[4]: Entering directory '/build/reproducible-path/abyss-2.3.9/BloomDBG' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/abyss-2.3.9/debian/tmp/usr/bin' /usr/bin/install -c abyss-bloom-dbg '/build/reproducible-path/abyss-2.3.9/debian/tmp/usr/bin' make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.9/BloomDBG' make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.9/BloomDBG' Making install in Konnector make[3]: Entering directory '/build/reproducible-path/abyss-2.3.9/Konnector' make[4]: Entering directory '/build/reproducible-path/abyss-2.3.9/Konnector' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/abyss-2.3.9/debian/tmp/usr/bin' /usr/bin/install -c konnector '/build/reproducible-path/abyss-2.3.9/debian/tmp/usr/bin' make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.9/Konnector' make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.9/Konnector' Making install in Consensus make[3]: Entering directory '/build/reproducible-path/abyss-2.3.9/Consensus' make[4]: Entering directory '/build/reproducible-path/abyss-2.3.9/Consensus' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/abyss-2.3.9/debian/tmp/usr/bin' /usr/bin/install -c Consensus '/build/reproducible-path/abyss-2.3.9/debian/tmp/usr/bin' make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.9/Consensus' make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.9/Consensus' Making install in DAssembler make[3]: Entering directory '/build/reproducible-path/abyss-2.3.9/DAssembler' make[4]: Entering directory '/build/reproducible-path/abyss-2.3.9/DAssembler' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/abyss-2.3.9/debian/tmp/usr/bin' /usr/bin/install -c DAssembler '/build/reproducible-path/abyss-2.3.9/debian/tmp/usr/bin' make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.9/DAssembler' make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.9/DAssembler' Making install in DistanceEst make[3]: Entering directory '/build/reproducible-path/abyss-2.3.9/DistanceEst' make[4]: Entering directory '/build/reproducible-path/abyss-2.3.9/DistanceEst' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/abyss-2.3.9/debian/tmp/usr/bin' /usr/bin/install -c DistanceEst DistanceEst-ssq '/build/reproducible-path/abyss-2.3.9/debian/tmp/usr/bin' make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.9/DistanceEst' make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.9/DistanceEst' Making install in KAligner make[3]: Entering directory '/build/reproducible-path/abyss-2.3.9/KAligner' make[4]: Entering directory '/build/reproducible-path/abyss-2.3.9/KAligner' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/abyss-2.3.9/debian/tmp/usr/bin' /usr/bin/install -c KAligner '/build/reproducible-path/abyss-2.3.9/debian/tmp/usr/bin' make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.9/KAligner' make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.9/KAligner' Making install in Layout make[3]: Entering directory '/build/reproducible-path/abyss-2.3.9/Layout' make[4]: Entering directory '/build/reproducible-path/abyss-2.3.9/Layout' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/abyss-2.3.9/debian/tmp/usr/bin' /usr/bin/install -c abyss-layout '/build/reproducible-path/abyss-2.3.9/debian/tmp/usr/bin' make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.9/Layout' make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.9/Layout' Making install in LogKmerCount make[3]: Entering directory '/build/reproducible-path/abyss-2.3.9/LogKmerCount' make[4]: Entering directory '/build/reproducible-path/abyss-2.3.9/LogKmerCount' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/abyss-2.3.9/debian/tmp/usr/bin' /usr/bin/install -c logcounter '/build/reproducible-path/abyss-2.3.9/debian/tmp/usr/bin' make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.9/LogKmerCount' make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.9/LogKmerCount' Making install in Map make[3]: Entering directory '/build/reproducible-path/abyss-2.3.9/Map' make[4]: Entering directory '/build/reproducible-path/abyss-2.3.9/Map' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/abyss-2.3.9/debian/tmp/usr/bin' /usr/bin/install -c abyss-index abyss-map abyss-map-ssq abyss-overlap '/build/reproducible-path/abyss-2.3.9/debian/tmp/usr/bin' make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.9/Map' make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.9/Map' Making install in MergePaths make[3]: Entering directory '/build/reproducible-path/abyss-2.3.9/MergePaths' make[4]: Entering directory '/build/reproducible-path/abyss-2.3.9/MergePaths' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/abyss-2.3.9/debian/tmp/usr/bin' /usr/bin/install -c MergePaths MergeContigs PathConsensus '/build/reproducible-path/abyss-2.3.9/debian/tmp/usr/bin' make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.9/MergePaths' make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.9/MergePaths' Making install in Overlap make[3]: Entering directory '/build/reproducible-path/abyss-2.3.9/Overlap' make[4]: Entering directory '/build/reproducible-path/abyss-2.3.9/Overlap' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/abyss-2.3.9/debian/tmp/usr/bin' /usr/bin/install -c Overlap '/build/reproducible-path/abyss-2.3.9/debian/tmp/usr/bin' make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.9/Overlap' make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.9/Overlap' Making install in PairedDBG make[3]: Entering directory '/build/reproducible-path/abyss-2.3.9/PairedDBG' make[4]: Entering directory '/build/reproducible-path/abyss-2.3.9/PairedDBG' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/abyss-2.3.9/debian/tmp/usr/bin' /usr/bin/install -c abyss-paired-dbg '/build/reproducible-path/abyss-2.3.9/debian/tmp/usr/bin' make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.9/PairedDBG' make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.9/PairedDBG' Making install in ParseAligns make[3]: Entering directory '/build/reproducible-path/abyss-2.3.9/ParseAligns' make[4]: Entering directory '/build/reproducible-path/abyss-2.3.9/ParseAligns' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/abyss-2.3.9/debian/tmp/usr/bin' /usr/bin/install -c abyss-fixmate abyss-fixmate-ssq ParseAligns '/build/reproducible-path/abyss-2.3.9/debian/tmp/usr/bin' make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.9/ParseAligns' make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.9/ParseAligns' Making install in PathOverlap make[3]: Entering directory '/build/reproducible-path/abyss-2.3.9/PathOverlap' make[4]: Entering directory '/build/reproducible-path/abyss-2.3.9/PathOverlap' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/abyss-2.3.9/debian/tmp/usr/bin' /usr/bin/install -c PathOverlap '/build/reproducible-path/abyss-2.3.9/debian/tmp/usr/bin' make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.9/PathOverlap' make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.9/PathOverlap' Making install in PopBubbles make[3]: Entering directory '/build/reproducible-path/abyss-2.3.9/PopBubbles' make[4]: Entering directory '/build/reproducible-path/abyss-2.3.9/PopBubbles' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/abyss-2.3.9/debian/tmp/usr/bin' /usr/bin/install -c PopBubbles '/build/reproducible-path/abyss-2.3.9/debian/tmp/usr/bin' make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.9/PopBubbles' make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.9/PopBubbles' Making install in Scaffold make[3]: Entering directory '/build/reproducible-path/abyss-2.3.9/Scaffold' make[4]: Entering directory '/build/reproducible-path/abyss-2.3.9/Scaffold' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/abyss-2.3.9/debian/tmp/usr/bin' /usr/bin/install -c abyss-scaffold abyss-junction abyss-longseqdist '/build/reproducible-path/abyss-2.3.9/debian/tmp/usr/bin' make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.9/Scaffold' make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.9/Scaffold' Making install in SimpleGraph make[3]: Entering directory '/build/reproducible-path/abyss-2.3.9/SimpleGraph' make[4]: Entering directory '/build/reproducible-path/abyss-2.3.9/SimpleGraph' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/abyss-2.3.9/debian/tmp/usr/bin' /usr/bin/install -c SimpleGraph '/build/reproducible-path/abyss-2.3.9/debian/tmp/usr/bin' make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.9/SimpleGraph' make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.9/SimpleGraph' Making install in kmerprint make[3]: Entering directory '/build/reproducible-path/abyss-2.3.9/kmerprint' make[4]: Entering directory '/build/reproducible-path/abyss-2.3.9/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-2.3.9/kmerprint' make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.9/kmerprint' Making install in FilterGraph make[3]: Entering directory '/build/reproducible-path/abyss-2.3.9/FilterGraph' make[4]: Entering directory '/build/reproducible-path/abyss-2.3.9/FilterGraph' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/abyss-2.3.9/debian/tmp/usr/bin' /usr/bin/install -c abyss-filtergraph '/build/reproducible-path/abyss-2.3.9/debian/tmp/usr/bin' make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.9/FilterGraph' make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.9/FilterGraph' Making install in GapFiller make[3]: Entering directory '/build/reproducible-path/abyss-2.3.9/GapFiller' make[4]: Entering directory '/build/reproducible-path/abyss-2.3.9/GapFiller' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/abyss-2.3.9/debian/tmp/usr/bin' /usr/bin/install -c abyss-gapfill '/build/reproducible-path/abyss-2.3.9/debian/tmp/usr/bin' make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.9/GapFiller' make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.9/GapFiller' Making install in Sealer make[3]: Entering directory '/build/reproducible-path/abyss-2.3.9/Sealer' make[4]: Entering directory '/build/reproducible-path/abyss-2.3.9/Sealer' /usr/bin/mkdir -p '/build/reproducible-path/abyss-2.3.9/debian/tmp/usr/bin' /usr/bin/install -c abyss-sealer '/build/reproducible-path/abyss-2.3.9/debian/tmp/usr/bin' make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.9/Sealer' make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.9/Sealer' Making install in RResolver make[3]: Entering directory '/build/reproducible-path/abyss-2.3.9/RResolver' make[4]: Entering directory '/build/reproducible-path/abyss-2.3.9/RResolver' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/abyss-2.3.9/debian/tmp/usr/bin' /usr/bin/install -c abyss-rresolver-short '/build/reproducible-path/abyss-2.3.9/debian/tmp/usr/bin' make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.9/RResolver' make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.9/RResolver' Making install in AdjList make[3]: Entering directory '/build/reproducible-path/abyss-2.3.9/AdjList' make[4]: Entering directory '/build/reproducible-path/abyss-2.3.9/AdjList' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/abyss-2.3.9/debian/tmp/usr/bin' /usr/bin/install -c AdjList '/build/reproducible-path/abyss-2.3.9/debian/tmp/usr/bin' make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.9/AdjList' make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.9/AdjList' Making install in vendor make[3]: Entering directory '/build/reproducible-path/abyss-2.3.9/vendor' make[4]: Entering directory '/build/reproducible-path/abyss-2.3.9/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-2.3.9/vendor' make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.9/vendor' Making install in vendor/gtest-1.7.0 make[3]: Entering directory '/build/reproducible-path/abyss-2.3.9/vendor/gtest-1.7.0' make[4]: Entering directory '/build/reproducible-path/abyss-2.3.9/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-2.3.9/vendor/gtest-1.7.0' make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.9/vendor/gtest-1.7.0' Making install in Unittest make[3]: Entering directory '/build/reproducible-path/abyss-2.3.9/Unittest' make[4]: Entering directory '/build/reproducible-path/abyss-2.3.9/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-2.3.9/Unittest' make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.9/Unittest' make[3]: Entering directory '/build/reproducible-path/abyss-2.3.9' make[4]: Entering directory '/build/reproducible-path/abyss-2.3.9' make[4]: Nothing to be done for 'install-exec-am'. /usr/bin/mkdir -p '/build/reproducible-path/abyss-2.3.9/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-2.3.9/debian/tmp/usr/share/doc/abyss' make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.9' make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.9' make[2]: Leaving directory '/build/reproducible-path/abyss-2.3.9' 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-2.3.9' debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/abyss-2.3.9' 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-2.3.9' dh_installdocs dh_installchangelogs dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'abyss' in '../abyss_2.3.9-1_arm64.deb'. dpkg-deb: building package 'abyss-dbgsym' in '../abyss-dbgsym_2.3.9-1_arm64.deb'. dpkg-genbuildinfo --build=binary -O../abyss_2.3.9-1_arm64.buildinfo dpkg-genchanges --build=binary -O../abyss_2.3.9-1_arm64.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: including full 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/2823553 and its subdirectories I: Current time: Thu Oct 16 14:50:45 -12 2025 I: pbuilder-time-stamp: 1760669445 Fri Sep 13 20:27:51 UTC 2024 I: 1st build successful. Starting 2nd build on remote node codethink02-arm64.debian.net. Fri Sep 13 20:27:51 UTC 2024 I: Preparing to do remote build '2' on codethink02-arm64.debian.net. Fri Sep 13 20:39:10 UTC 2024 I: Deleting $TMPDIR on codethink02-arm64.debian.net. Fri Sep 13 20:39:11 UTC 2024 I: abyss_2.3.9-1_arm64.changes: Format: 1.8 Date: Thu, 12 Sep 2024 22:44:04 +0200 Source: abyss Binary: abyss abyss-dbgsym Architecture: arm64 Version: 2.3.9-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Étienne Mollier Description: abyss - de novo, parallel, sequence assembler for short reads Closes: 1080071 Changes: abyss (2.3.9-1) unstable; urgency=medium . * New upstream version 2.3.9 (Closes: #1080071) * fix-privacy-breach.patch: refresh. Checksums-Sha1: 47dfdf8133fed3d6362ad2c4ab4fe57034e75a13 29394436 abyss-dbgsym_2.3.9-1_arm64.deb f4598f11eb1100a452ad1e6ec66e15ab4d9bc24b 9073 abyss_2.3.9-1_arm64.buildinfo 4446d0c1fa08b1b2d13108291a6c26dee65fc6d9 3065144 abyss_2.3.9-1_arm64.deb Checksums-Sha256: efa95abf7f8e589d5293317c9db1586e9c9aa6dcf9f2a38d4262f97090bcd697 29394436 abyss-dbgsym_2.3.9-1_arm64.deb 5c53ce58ba3137a6df1e76489190286cb527e71c0d4d062947fbddbfbbf8f5a3 9073 abyss_2.3.9-1_arm64.buildinfo e8d9b08ef5d52ee85d8e7343b62e5d7db8e27f16855617ff5bdfc501e3fdbd6d 3065144 abyss_2.3.9-1_arm64.deb Files: 7f8d6dbfc9442d451c69aefec61cacc7 29394436 debug optional abyss-dbgsym_2.3.9-1_arm64.deb a53dd339240a10ffe63ebe74f97d8c6a 9073 science optional abyss_2.3.9-1_arm64.buildinfo 776ea6499cd355fd246e6b4f72ade611 3065144 science optional abyss_2.3.9-1_arm64.deb Fri Sep 13 20:39:12 UTC 2024 I: diffoscope 277 will be used to compare the two builds: Running as unit: rb-diffoscope-arm64_13-36448.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.DpmzMZ4i/abyss_2.3.9-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.DpmzMZ4i/abyss_2.3.9-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.DpmzMZ4i/abyss_2.3.9-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.DpmzMZ4i/b1/abyss_2.3.9-1_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.DpmzMZ4i/b2/abyss_2.3.9-1_arm64.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: 0.729s) 0.729s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.355s) 0.355s 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: 1.076s CPU time consumed: 1.075s Fri Sep 13 20:39:14 UTC 2024 I: diffoscope 277 found no differences in the changes files, and a .buildinfo file also exists. Fri Sep 13 20:39:14 UTC 2024 I: abyss from unstable built successfully and reproducibly on arm64. Fri Sep 13 20:39:15 UTC 2024 I: Submitting .buildinfo files to external archives: Fri Sep 13 20:39:15 UTC 2024 I: Submitting 12K b1/abyss_2.3.9-1_arm64.buildinfo.asc Fri Sep 13 20:39:16 UTC 2024 I: Submitting 12K b2/abyss_2.3.9-1_arm64.buildinfo.asc Fri Sep 13 20:39:17 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Fri Sep 13 20:39:17 UTC 2024 I: Done submitting .buildinfo files. Fri Sep 13 20:39:17 UTC 2024 I: Removing signed abyss_2.3.9-1_arm64.buildinfo.asc files: removed './b1/abyss_2.3.9-1_arm64.buildinfo.asc' removed './b2/abyss_2.3.9-1_arm64.buildinfo.asc'