I: pbuilder: network access will be disabled during build I: Current time: Sun Aug 30 13:04:31 -12 2020 I: pbuilder-time-stamp: 1598835871 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz] I: copying local configuration 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_2.1.5-7.dsc] I: copying [./abyss_2.1.5.orig.tar.gz] I: copying [./abyss_2.1.5-7.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/var/lib/jenkins/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Sun Feb 17 01:20:28 2019 -12 gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./abyss_2.1.5-7.dsc dpkg-source: info: extracting abyss in abyss-2.1.5 dpkg-source: info: unpacking abyss_2.1.5.orig.tar.gz dpkg-source: info: unpacking abyss_2.1.5-7.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying abyss-pe.patch dpkg-source: info: applying abyss-32-bit.patch dpkg-source: info: applying fix_bash_script.patch dpkg-source: info: applying big_endian.patch dpkg-source: info: applying strict_alignment.patch dpkg-source: info: applying hurd.patch dpkg-source: info: applying fix_implicit-function-declaration dpkg-source: info: applying spelling I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2361/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' 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=8' DISTRIBUTION='' HOME='/var/lib/jenkins' HOST_ARCH='arm64' IFS=' ' 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='2361' 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/tmp.uqIpINyM6l/pbuilderrc_XfAU --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.uqIpINyM6l/b1 --logfile b1/build.log abyss_2.1.5-7.dsc' SUDO_GID='117' SUDO_UID='110' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' USERNAME='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.16:3128' I: uname -a Linux codethink-sled14-arm64 4.4.0-187-generic #217-Ubuntu SMP Tue Jul 21 04:16:35 UTC 2020 aarch64 GNU/Linux I: ls -l /bin total 4928 -rwxr-xr-x 1 root root 1216928 Apr 17 2019 bash -rwxr-xr-x 3 root root 34808 Jul 10 2019 bunzip2 -rwxr-xr-x 3 root root 34808 Jul 10 2019 bzcat lrwxrwxrwx 1 root root 6 Jul 10 2019 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2227 Jul 10 2019 bzdiff lrwxrwxrwx 1 root root 6 Jul 10 2019 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Jun 24 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 10 2019 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3641 Jul 10 2019 bzgrep -rwxr-xr-x 3 root root 34808 Jul 10 2019 bzip2 -rwxr-xr-x 1 root root 14264 Jul 10 2019 bzip2recover lrwxrwxrwx 1 root root 6 Jul 10 2019 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 10 2019 bzmore -rwxr-xr-x 1 root root 35576 Feb 28 2019 cat -rwxr-xr-x 1 root root 60256 Feb 28 2019 chgrp -rwxr-xr-x 1 root root 56096 Feb 28 2019 chmod -rwxr-xr-x 1 root root 64368 Feb 28 2019 chown -rwxr-xr-x 1 root root 134632 Feb 28 2019 cp -rwxr-xr-x 1 root root 129536 Jan 17 2019 dash -rwxr-xr-x 1 root root 97136 Feb 28 2019 date -rwxr-xr-x 1 root root 76736 Feb 28 2019 dd -rwxr-xr-x 1 root root 93752 Feb 28 2019 df -rwxr-xr-x 1 root root 138848 Feb 28 2019 dir -rwxr-xr-x 1 root root 75984 Jan 9 2019 dmesg lrwxrwxrwx 1 root root 8 Sep 26 2018 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Sep 26 2018 domainname -> hostname -rwxr-xr-x 1 root root 31368 Feb 28 2019 echo -rwxr-xr-x 1 root root 28 Jan 7 2019 egrep -rwxr-xr-x 1 root root 27256 Feb 28 2019 false -rwxr-xr-x 1 root root 28 Jan 7 2019 fgrep -rwxr-xr-x 1 root root 68792 Jan 9 2019 findmnt -rwsr-xr-x 1 root root 34824 Apr 22 07:38 fusermount -rwxr-xr-x 1 root root 174304 Jan 7 2019 grep -rwxr-xr-x 2 root root 2345 Jan 5 2019 gunzip -rwxr-xr-x 1 root root 6375 Jan 5 2019 gzexe -rwxr-xr-x 1 root root 89656 Jan 5 2019 gzip -rwxr-xr-x 1 root root 18440 Sep 26 2018 hostname -rwxr-xr-x 1 root root 64472 Feb 28 2019 ln -rwxr-xr-x 1 root root 52544 Jul 26 2018 login -rwxr-xr-x 1 root root 138848 Feb 28 2019 ls -rwxr-xr-x 1 root root 108552 Jan 9 2019 lsblk -rwxr-xr-x 1 root root 76840 Feb 28 2019 mkdir -rwxr-xr-x 1 root root 64480 Feb 28 2019 mknod -rwxr-xr-x 1 root root 39736 Feb 28 2019 mktemp -rwxr-xr-x 1 root root 38840 Jan 9 2019 more -rwsr-xr-x 1 root root 47112 Jan 9 2019 mount -rwxr-xr-x 1 root root 14344 Jan 9 2019 mountpoint -rwxr-xr-x 1 root root 138736 Feb 28 2019 mv lrwxrwxrwx 1 root root 8 Sep 26 2018 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Feb 14 2019 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 35560 Feb 28 2019 pwd lrwxrwxrwx 1 root root 4 Apr 17 2019 rbash -> bash -rwxr-xr-x 1 root root 43712 Feb 28 2019 readlink -rwxr-xr-x 1 root root 68440 Feb 28 2019 rm -rwxr-xr-x 1 root root 39624 Feb 28 2019 rmdir -rwxr-xr-x 1 root root 19144 Jan 21 2019 run-parts -rwxr-xr-x 1 root root 114016 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Aug 23 20:27 sh -> dash -rwxr-xr-x 1 root root 31384 Feb 28 2019 sleep -rwxr-xr-x 1 root root 72480 Feb 28 2019 stty -rwsr-xr-x 1 root root 59424 Jan 9 2019 su -rwxr-xr-x 1 root root 31416 Feb 28 2019 sync -rwxr-xr-x 1 root root 449416 Apr 23 2019 tar -rwxr-xr-x 1 root root 10560 Jan 21 2019 tempfile -rwxr-xr-x 1 root root 88968 Feb 28 2019 touch -rwxr-xr-x 1 root root 27256 Feb 28 2019 true -rwxr-xr-x 1 root root 14264 Apr 22 07:38 ulockmgr_server -rwsr-xr-x 1 root root 30728 Jan 9 2019 umount -rwxr-xr-x 1 root root 31384 Feb 28 2019 uname -rwxr-xr-x 2 root root 2345 Jan 5 2019 uncompress -rwxr-xr-x 1 root root 138848 Feb 28 2019 vdir -rwxr-xr-x 1 root root 34824 Jan 9 2019 wdctl -rwxr-xr-x 1 root root 946 Jan 21 2019 which lrwxrwxrwx 1 root root 8 Sep 26 2018 ypdomainname -> hostname -rwxr-xr-x 1 root root 1983 Jan 5 2019 zcat -rwxr-xr-x 1 root root 1677 Jan 5 2019 zcmp -rwxr-xr-x 1 root root 5879 Jan 5 2019 zdiff -rwxr-xr-x 1 root root 29 Jan 5 2019 zegrep -rwxr-xr-x 1 root root 29 Jan 5 2019 zfgrep -rwxr-xr-x 1 root root 2080 Jan 5 2019 zforce -rwxr-xr-x 1 root root 7584 Jan 5 2019 zgrep -rwxr-xr-x 1 root root 2205 Jan 5 2019 zless -rwxr-xr-x 1 root root 1841 Jan 5 2019 zmore -rwxr-xr-x 1 root root 4552 Jan 5 2019 znew I: user script /srv/workspace/pbuilder/2361/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 (>= 12~), python-markdown, libboost-graph-dev, libopenmpi-dev, libsparsehash-dev, libtext-multimarkdown-perl, libgtest-dev, libsqlite3-dev, pkg-config, help2man dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19168 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 (>= 12~); however: Package debhelper is not installed. pbuilder-satisfydepends-dummy depends on python-markdown; however: Package python-markdown is not installed. pbuilder-satisfydepends-dummy depends on libboost-graph-dev; however: Package libboost-graph-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 libgtest-dev; however: Package libgtest-dev is not installed. pbuilder-satisfydepends-dummy depends on libsqlite3-dev; however: Package libsqlite3-dev is not installed. pbuilder-satisfydepends-dummy depends on pkg-config; however: Package pkg-config is not installed. pbuilder-satisfydepends-dummy depends on help2man; however: Package help2man is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdmainutils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} googletest{a} groff-base{a} help2man{a} ibverbs-providers{a} intltool-debian{a} libarchive-zip-perl{a} libboost-chrono1.67.0{a} libboost-graph-dev{a} libboost-graph1.67-dev{a} libboost-graph1.67.0{a} libboost-regex1.67.0{a} libboost-serialization1.67-dev{a} libboost-serialization1.67.0{a} libboost-test1.67-dev{a} libboost-test1.67.0{a} libboost-timer1.67.0{a} libboost1.67-dev{a} libbsd0{a} libcroco3{a} libedit2{a} libelf1{a} libevent-2.1-6{a} libevent-core-2.1-6{a} libevent-pthreads-2.1-6{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libglib2.0-0{a} libgssapi-krb5-2{a} libgtest-dev{a} libhtml-parser-perl{a} libhtml-tagset-perl{a} libhwloc-dev{a} libhwloc-plugins{a} libhwloc5{a} libibverbs-dev{a} libibverbs1{a} libicu63{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblocale-gettext-perl{a} libltdl-dev{a} libltdl7{a} libmagic-mgc{a} libmagic1{a} libncurses6{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} libopenmpi3{a} libpciaccess0{a} libpipeline1{a} libpmix2{a} libpython-stdlib{a} libpython2-stdlib{a} libpython2.7-minimal{a} libpython2.7-stdlib{a} libreadline7{a} libsigsegv2{a} libsparsehash-dev{a} libsqlite3-dev{a} libssl1.1{a} libtext-markdown-perl{a} libtext-multimarkdown-perl{a} libtool{a} libuchardet0{a} liburi-perl{a} libxml2{a} m4{a} man-db{a} mime-support{a} ocl-icd-libopencl1{a} openmpi-bin{a} openmpi-common{a} openssh-client{a} pkg-config{a} po-debconf{a} python{a} python-markdown{a} python-minimal{a} python-pkg-resources{a} python2{a} python2-minimal{a} python2.7{a} python2.7-minimal{a} readline-common{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: curl krb5-locales libarchive-cpio-perl libcoarrays-openmpi-dev libglib2.0-data libgpm2 libhttp-message-perl libmail-sendmail-perl lynx python-pygments python-yaml shared-mime-info wget xauth xdg-user-dirs 0 packages upgraded, 105 newly installed, 0 to remove and 0 not upgraded. Need to get 46.6 MB of archives. After unpacking 296 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian buster/main arm64 libbsd0 arm64 0.9.1-2 [97.4 kB] Get: 2 http://deb.debian.org/debian buster/main arm64 bsdmainutils arm64 11.1.2+b1 [185 kB] Get: 3 http://deb.debian.org/debian buster/main arm64 libuchardet0 arm64 0.0.6-3 [65.0 kB] Get: 4 http://deb.debian.org/debian buster/main arm64 groff-base arm64 1.22.4-3 [869 kB] Get: 5 http://deb.debian.org/debian buster/main arm64 libpipeline1 arm64 1.5.1-2 [29.8 kB] Get: 6 http://deb.debian.org/debian buster/main arm64 man-db arm64 2.8.5-2 [1258 kB] Get: 7 http://deb.debian.org/debian buster/main arm64 libpython2.7-minimal arm64 2.7.16-2+deb10u1 [395 kB] Get: 8 http://deb.debian.org/debian buster/main arm64 python2.7-minimal arm64 2.7.16-2+deb10u1 [1292 kB] Get: 9 http://deb.debian.org/debian buster/main arm64 python2-minimal arm64 2.7.16-1 [41.4 kB] Get: 10 http://deb.debian.org/debian buster/main arm64 python-minimal arm64 2.7.16-1 [21.0 kB] Get: 11 http://deb.debian.org/debian buster/main arm64 libssl1.1 arm64 1.1.1d-0+deb10u3 [1382 kB] Get: 12 http://deb.debian.org/debian buster/main arm64 mime-support all 3.62 [37.2 kB] Get: 13 http://deb.debian.org/debian buster/main arm64 libexpat1 arm64 2.2.6-2+deb10u1 [85.4 kB] Get: 14 http://deb.debian.org/debian buster/main arm64 readline-common all 7.0-5 [70.6 kB] Get: 15 http://deb.debian.org/debian buster/main arm64 libreadline7 arm64 7.0-5 [134 kB] Get: 16 http://deb.debian.org/debian buster/main arm64 libpython2.7-stdlib arm64 2.7.16-2+deb10u1 [1890 kB] Get: 17 http://deb.debian.org/debian buster/main arm64 python2.7 arm64 2.7.16-2+deb10u1 [305 kB] Get: 18 http://deb.debian.org/debian buster/main arm64 libpython2-stdlib arm64 2.7.16-1 [20.8 kB] Get: 19 http://deb.debian.org/debian buster/main arm64 libpython-stdlib arm64 2.7.16-1 [20.8 kB] Get: 20 http://deb.debian.org/debian buster/main arm64 python2 arm64 2.7.16-1 [41.6 kB] Get: 21 http://deb.debian.org/debian buster/main arm64 python arm64 2.7.16-1 [22.8 kB] Get: 22 http://deb.debian.org/debian buster/main arm64 liblocale-gettext-perl arm64 1.07-3+b4 [18.8 kB] Get: 23 http://deb.debian.org/debian buster/main arm64 sensible-utils all 0.0.12 [15.8 kB] Get: 24 http://deb.debian.org/debian buster/main arm64 libmagic-mgc arm64 1:5.35-4+deb10u1 [242 kB] Get: 25 http://deb.debian.org/debian buster/main arm64 libmagic1 arm64 1:5.35-4+deb10u1 [115 kB] Get: 26 http://deb.debian.org/debian buster/main arm64 file arm64 1:5.35-4+deb10u1 [66.4 kB] Get: 27 http://deb.debian.org/debian buster/main arm64 gettext-base arm64 0.19.8.1-9 [120 kB] Get: 28 http://deb.debian.org/debian buster/main arm64 libedit2 arm64 3.1-20181209-1 [91.2 kB] Get: 29 http://deb.debian.org/debian buster/main arm64 libkeyutils1 arm64 1.6-6 [14.9 kB] Get: 30 http://deb.debian.org/debian buster/main arm64 libkrb5support0 arm64 1.17-3 [64.7 kB] Get: 31 http://deb.debian.org/debian buster/main arm64 libk5crypto3 arm64 1.17-3 [122 kB] Get: 32 http://deb.debian.org/debian buster/main arm64 libkrb5-3 arm64 1.17-3 [353 kB] Get: 33 http://deb.debian.org/debian buster/main arm64 libgssapi-krb5-2 arm64 1.17-3 [150 kB] Get: 34 http://deb.debian.org/debian buster/main arm64 openssh-client arm64 1:7.9p1-10+deb10u2 [757 kB] Get: 35 http://deb.debian.org/debian buster/main arm64 libsigsegv2 arm64 2.12-2 [32.3 kB] Get: 36 http://deb.debian.org/debian buster/main arm64 m4 arm64 1.4.18-2 [198 kB] Get: 37 http://deb.debian.org/debian buster/main arm64 autoconf all 2.69-11 [341 kB] Get: 38 http://deb.debian.org/debian buster/main arm64 autotools-dev all 20180224.1 [77.0 kB] Get: 39 http://deb.debian.org/debian buster/main arm64 automake all 1:1.16.1-4 [771 kB] Get: 40 http://deb.debian.org/debian buster/main arm64 autopoint all 0.19.8.1-9 [434 kB] Get: 41 http://deb.debian.org/debian buster/main arm64 libtool all 2.4.6-9 [547 kB] Get: 42 http://deb.debian.org/debian buster/main arm64 dh-autoreconf all 19 [16.9 kB] Get: 43 http://deb.debian.org/debian buster/main arm64 libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 44 http://deb.debian.org/debian buster/main arm64 libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 45 http://deb.debian.org/debian buster/main arm64 dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 46 http://deb.debian.org/debian buster/main arm64 libelf1 arm64 0.176-1.1 [160 kB] Get: 47 http://deb.debian.org/debian buster/main arm64 dwz arm64 0.12-3 [71.7 kB] Get: 48 http://deb.debian.org/debian buster/main arm64 libglib2.0-0 arm64 2.58.3-2+deb10u2 [1185 kB] Get: 49 http://deb.debian.org/debian buster/main arm64 libicu63 arm64 63.1-6+deb10u1 [8151 kB] Get: 50 http://deb.debian.org/debian buster/main arm64 libxml2 arm64 2.9.4+dfsg1-7+b3 [623 kB] Get: 51 http://deb.debian.org/debian buster/main arm64 libcroco3 arm64 0.6.12-3 [140 kB] Get: 52 http://deb.debian.org/debian buster/main arm64 libncurses6 arm64 6.1+20181013-2+deb10u2 [92.6 kB] Get: 53 http://deb.debian.org/debian buster/main arm64 gettext arm64 0.19.8.1-9 [1261 kB] Get: 54 http://deb.debian.org/debian buster/main arm64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 55 http://deb.debian.org/debian buster/main arm64 po-debconf all 1.0.21 [248 kB] Get: 56 http://deb.debian.org/debian buster/main arm64 debhelper all 12.1.1 [1016 kB] Get: 57 http://deb.debian.org/debian buster/main arm64 googletest arm64 1.8.1-3 [903 kB] Get: 58 http://deb.debian.org/debian buster/main arm64 help2man arm64 1.47.8 [177 kB] Get: 59 http://deb.debian.org/debian buster/main arm64 libnl-3-200 arm64 3.4.0-1 [54.9 kB] Get: 60 http://deb.debian.org/debian buster/main arm64 libnl-route-3-200 arm64 3.4.0-1 [134 kB] Get: 61 http://deb.debian.org/debian buster/main arm64 libibverbs1 arm64 22.1-1 [47.8 kB] Get: 62 http://deb.debian.org/debian buster/main arm64 ibverbs-providers arm64 22.1-1 [174 kB] Get: 63 http://deb.debian.org/debian buster/main arm64 libboost-chrono1.67.0 arm64 1.67.0-13+deb10u1 [233 kB] Get: 64 http://deb.debian.org/debian buster/main arm64 libboost1.67-dev arm64 1.67.0-13+deb10u1 [8388 kB] Get: 65 http://deb.debian.org/debian buster/main arm64 libboost-regex1.67.0 arm64 1.67.0-13+deb10u1 [458 kB] Get: 66 http://deb.debian.org/debian buster/main arm64 libboost-graph1.67.0 arm64 1.67.0-13+deb10u1 [310 kB] Get: 67 http://deb.debian.org/debian buster/main arm64 libboost-serialization1.67.0 arm64 1.67.0-13+deb10u1 [311 kB] Get: 68 http://deb.debian.org/debian buster/main arm64 libboost-serialization1.67-dev arm64 1.67.0-13+deb10u1 [358 kB] Get: 69 http://deb.debian.org/debian buster/main arm64 libboost-timer1.67.0 arm64 1.67.0-13+deb10u1 [231 kB] Get: 70 http://deb.debian.org/debian buster/main arm64 libboost-test1.67.0 arm64 1.67.0-13+deb10u1 [433 kB] Get: 71 http://deb.debian.org/debian buster/main arm64 libboost-test1.67-dev arm64 1.67.0-13+deb10u1 [503 kB] Get: 72 http://deb.debian.org/debian buster/main arm64 libboost-graph1.67-dev arm64 1.67.0-13+deb10u1 [323 kB] Get: 73 http://deb.debian.org/debian buster/main arm64 libboost-graph-dev arm64 1.67.0.1 [3752 B] Get: 74 http://deb.debian.org/debian buster/main arm64 libevent-2.1-6 arm64 2.1.8-stable-4 [150 kB] Get: 75 http://deb.debian.org/debian buster/main arm64 libevent-core-2.1-6 arm64 2.1.8-stable-4 [112 kB] Get: 76 http://deb.debian.org/debian buster/main arm64 libevent-pthreads-2.1-6 arm64 2.1.8-stable-4 [47.7 kB] Get: 77 http://deb.debian.org/debian buster/main arm64 libgfortran5 arm64 8.3.0-6 [298 kB] Get: 78 http://deb.debian.org/debian buster/main arm64 libgtest-dev arm64 1.8.1-3 [218 kB] Get: 79 http://deb.debian.org/debian buster/main arm64 libhtml-tagset-perl all 3.20-3 [12.7 kB] Get: 80 http://deb.debian.org/debian buster/main arm64 liburi-perl all 1.76-1 [89.9 kB] Get: 81 http://deb.debian.org/debian buster/main arm64 libhtml-parser-perl arm64 3.72-3+b3 [103 kB] Get: 82 http://deb.debian.org/debian buster/main arm64 libltdl7 arm64 2.4.6-9 [389 kB] Get: 83 http://deb.debian.org/debian buster/main arm64 libnuma1 arm64 2.0.12-1 [25.6 kB] Get: 84 http://deb.debian.org/debian buster/main arm64 libhwloc5 arm64 1.11.12-3 [97.9 kB] Get: 85 http://deb.debian.org/debian buster/main arm64 libnuma-dev arm64 2.0.12-1 [40.0 kB] Get: 86 http://deb.debian.org/debian buster/main arm64 libltdl-dev arm64 2.4.6-9 [162 kB] Get: 87 http://deb.debian.org/debian buster/main arm64 libhwloc-dev arm64 1.11.12-3 [165 kB] Get: 88 http://deb.debian.org/debian buster/main arm64 libpciaccess0 arm64 0.14-1 [51.0 kB] Get: 89 http://deb.debian.org/debian buster/main arm64 ocl-icd-libopencl1 arm64 2.2.12-2 [37.4 kB] Get: 90 http://deb.debian.org/debian buster/main arm64 libhwloc-plugins arm64 1.11.12-3 [16.9 kB] Get: 91 http://deb.debian.org/debian buster/main arm64 libnl-3-dev arm64 3.4.0-1 [98.2 kB] Get: 92 http://deb.debian.org/debian buster/main arm64 libnl-route-3-dev arm64 3.4.0-1 [162 kB] Get: 93 http://deb.debian.org/debian buster/main arm64 libibverbs-dev arm64 22.1-1 [356 kB] Get: 94 http://deb.debian.org/debian buster/main arm64 libpmix2 arm64 3.1.2-3 [455 kB] Get: 95 http://deb.debian.org/debian buster/main arm64 libopenmpi3 arm64 3.1.3-11 [1996 kB] Get: 96 http://deb.debian.org/debian buster/main arm64 openmpi-common all 3.1.3-11 [165 kB] Get: 97 http://deb.debian.org/debian buster/main arm64 openmpi-bin arm64 3.1.3-11 [199 kB] Get: 98 http://deb.debian.org/debian buster/main arm64 libopenmpi-dev arm64 3.1.3-11 [974 kB] Get: 99 http://deb.debian.org/debian buster/main arm64 libsparsehash-dev all 2.0.2-1 [76.9 kB] Get: 100 http://deb.debian.org/debian buster/main arm64 libsqlite3-dev arm64 3.27.2-3 [745 kB] Get: 101 http://deb.debian.org/debian buster/main arm64 libtext-markdown-perl all 1.000031-2 [34.4 kB] Get: 102 http://deb.debian.org/debian buster/main arm64 libtext-multimarkdown-perl all 1.000035-1 [29.4 kB] Get: 103 http://deb.debian.org/debian buster/main arm64 pkg-config arm64 0.29-6 [62.2 kB] Get: 104 http://deb.debian.org/debian buster/main arm64 python-pkg-resources all 40.8.0-1 [182 kB] Get: 105 http://deb.debian.org/debian buster/main arm64 python-markdown all 3.0.1-3 [60.6 kB] Fetched 46.6 MB in 8s (5798 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:arm64. (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 ... 19168 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.9.1-2_arm64.deb ... Unpacking libbsd0:arm64 (0.9.1-2) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2+b1_arm64.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../02-libuchardet0_0.0.6-3_arm64.deb ... 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Selecting previously unselected package python2. (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 ... 20631 files and directories currently installed.) Preparing to unpack .../python2_2.7.16-1_arm64.deb ... Unpacking python2 (2.7.16-1) ... Setting up python-minimal (2.7.16-1) ... Selecting previously unselected package python. (Reading database ... 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Setting up libssl1.1:arm64 (1.1.1d-0+deb10u3) ... Setting up libhtml-tagset-perl (3.20-3) ... Setting up libmagic1:arm64 (1:5.35-4+deb10u1) ... Setting up gettext-base (0.19.8.1-9) ... Setting up file (1:5.35-4+deb10u1) ... Setting up libsparsehash-dev (2.0.2-1) ... Setting up googletest:arm64 (1.8.1-3) ... Setting up libicu63:arm64 (63.1-6+deb10u1) ... Setting up libkrb5support0:arm64 (1.17-3) ... Setting up autotools-dev (20180224.1) ... Setting up libsqlite3-dev:arm64 (3.27.2-3) ... Setting up libncurses6:arm64 (6.1+20181013-2+deb10u2) ... Setting up libsigsegv2:arm64 (2.12-2) ... Setting up autopoint (0.19.8.1-9) ... Setting up pkg-config (0.29-6) ... Setting up libk5crypto3:arm64 (1.17-3) ... Setting up libltdl7:arm64 (2.4.6-9) ... Setting up libevent-core-2.1-6:arm64 (2.1.8-stable-4) ... Setting up libgfortran5:arm64 (8.3.0-6) ... Setting up libevent-2.1-6:arm64 (2.1.8-stable-4) ... Setting up libnuma1:arm64 (2.0.12-1) ... Setting up sensible-utils (0.0.12) ... Setting up ocl-icd-libopencl1:arm64 (2.2.12-2) ... Setting up libuchardet0:arm64 (0.0.6-3) ... Setting up libboost-timer1.67.0:arm64 (1.67.0-13+deb10u1) ... Setting up libnl-3-200:arm64 (3.4.0-1) ... Setting up openmpi-common (3.1.3-11) ... Setting up libkrb5-3:arm64 (1.17-3) ... Setting up libboost-serialization1.67.0:arm64 (1.67.0-13+deb10u1) ... Setting up libbsd0:arm64 (0.9.1-2) ... Setting up libelf1:arm64 (0.176-1.1) ... Setting up readline-common (7.0-5) ... Setting up libxml2:arm64 (2.9.4+dfsg1-7+b3) ... Setting up liburi-perl (1.76-1) ... Setting up liblocale-gettext-perl (1.07-3+b4) ... Setting up libreadline7:arm64 (7.0-5) ... Setting up libfile-stripnondeterminism-perl (1.1.2-1) ... Setting up libboost-serialization1.67-dev:arm64 (1.67.0-13+deb10u1) ... Setting up libevent-pthreads-2.1-6:arm64 (2.1.8-stable-4) ... Setting up libboost-regex1.67.0:arm64 (1.67.0-13+deb10u1) ... Setting up libgtest-dev:arm64 (1.8.1-3) ... Setting up libtool (2.4.6-9) ... Setting up libhwloc5:arm64 (1.11.12-3) ... Setting up libedit2:arm64 (3.1-20181209-1) ... Setting up libboost-test1.67.0:arm64 (1.67.0-13+deb10u1) ... Setting up m4 (1.4.18-2) ... Setting up libboost-graph1.67.0:arm64 (1.67.0-13+deb10u1) ... Setting up libhwloc-plugins:arm64 (1.11.12-3) ... Setting up libnuma-dev:arm64 (2.0.12-1) ... Setting up libboost-test1.67-dev:arm64 (1.67.0-13+deb10u1) ... Setting up libnl-route-3-200:arm64 (3.4.0-1) ... Setting up libpython2.7-stdlib:arm64 (2.7.16-2+deb10u1) ... Setting up help2man (1.47.8) ... Setting up bsdmainutils (11.1.2+b1) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up libgssapi-krb5-2:arm64 (1.17-3) ... Setting up libcroco3:arm64 (0.6.12-3) ... Setting up autoconf (2.69-11) ... Setting up dwz (0.12-3) ... Setting up libnl-3-dev:arm64 (3.4.0-1) ... Setting up groff-base (1.22.4-3) ... Setting up libhtml-parser-perl (3.72-3+b3) ... Setting up libboost-graph1.67-dev:arm64 (1.67.0-13+deb10u1) ... Setting up libtext-multimarkdown-perl (1.000035-1) ... Setting up automake (1:1.16.1-4) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libboost-graph-dev:arm64 (1.67.0.1) ... Setting up libibverbs1:arm64 (22.1-1) ... Setting up gettext (0.19.8.1-9) ... Setting up python2.7 (2.7.16-2+deb10u1) ... Setting up libpmix2:arm64 (3.1.2-3) ... Setting up ibverbs-providers:arm64 (22.1-1) ... Setting up libpython2-stdlib:arm64 (2.7.16-1) ... Setting up openssh-client (1:7.9p1-10+deb10u2) ... Setting up libopenmpi3:arm64 (3.1.3-11) ... Setting up man-db (2.8.5-2) ... Not building database; man-db/auto-update is not 'true'. Setting up python2 (2.7.16-1) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libnl-route-3-dev:arm64 (3.4.0-1) ... Setting up libltdl-dev:arm64 (2.4.6-9) ... Setting up libpython-stdlib:arm64 (2.7.16-1) ... Setting up libhwloc-dev:arm64 (1.11.12-3) ... Setting up python (2.7.16-1) ... Setting up openmpi-bin (3.1.3-11) ... 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 python-pkg-resources (40.8.0-1) ... Setting up po-debconf (1.0.21) ... Setting up python-markdown (3.0.1-3) ... Setting up libibverbs-dev:arm64 (22.1-1) ... Setting up libopenmpi-dev:arm64 (3.1.3-11) ... 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 Setting up debhelper (12.1.1) ... Setting up dh-autoreconf (19) ... Setting up dh-strip-nondeterminism (1.1.2-1) ... Processing triggers for libc-bin (2.28-10) ... 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 Reading package lists... Building dependency tree... Reading state information... fakeroot is already the newest version (1.23-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: Running cd /build/abyss-2.1.5/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package abyss dpkg-buildpackage: info: source version 2.1.5-7 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Michael R. Crusoe dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 fakeroot debian/rules clean dh clean dh_clean debian/rules build dh build dh_update_autotools_config dh_autoreconf configure.ac:11: installing './compile' configure.ac:161: installing './config.guess' configure.ac:161: installing './config.sub' configure.ac:5: installing './install-sh' configure.ac:5: installing './missing' ABYSS/Makefile.am: installing './depcomp' parallel-tests: installing './test-driver' debian/rules override_dh_auto_configure make[1]: Entering directory '/build/abyss-2.1.5' 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-silent-rules --libdir=\${prefix}/lib/aarch64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-mpi=/usr/lib/aarch64-linux-gnu/openmpi configure: WARNING: unrecognized options: --disable-maintainer-mode checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking for gawk... (cached) mawk checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... yes checking whether make supports the include directive... yes (GNU style) checking dependency style of gcc... none checking how to run the C preprocessor... gcc -E checking for g++... g++ checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking dependency style of g++... none checking for ranlib... ranlib checking for ghc... no ./configure: line 5208: : command not found checking for pandoc... no checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking dlfcn.h usability... yes checking dlfcn.h presence... yes checking for dlfcn.h... yes checking fcntl.h usability... yes checking fcntl.h presence... yes checking for fcntl.h... yes checking float.h usability... yes checking float.h presence... yes checking for float.h... yes checking limits.h usability... yes checking limits.h presence... yes checking for limits.h... yes checking stddef.h usability... yes checking stddef.h presence... yes checking for stddef.h... yes checking for stdint.h... (cached) yes checking for stdlib.h... (cached) yes checking sys/param.h usability... yes checking sys/param.h presence... yes checking for sys/param.h... yes checking for stdbool.h that conforms to C99... yes checking for _Bool... yes checking for ANSI C header files... (cached) yes checking whether byte ordering is bigendian... no checking for an ANSI C-conforming const... yes checking for inline... inline checking for ptrdiff_t... yes checking for mode_t... yes checking for pid_t... yes checking for size_t... yes checking for ssize_t... yes checking for int64_t... yes checking for uint8_t... yes checking for uint16_t... yes checking for uint32_t... yes checking for uint64_t... yes checking for std::hash... yes checking for std::tr1::hash... yes checking for std::tr1::tuple... yes checking for dup2... yes checking for gethostname... yes checking for getopt_long... yes checking for getpagesize... yes checking for memset... yes checking for strdup... yes checking for strerror... yes checking for strtoul... yes checking vfork.h usability... no checking vfork.h presence... no checking for vfork.h... no checking for fork... yes checking for vfork... yes checking for working fork... yes checking for working vfork... (cached) yes checking for stdlib.h... (cached) yes checking for GNU libc compatible malloc... yes checking for working memcmp... yes checking for stdlib.h... (cached) yes checking for GNU libc compatible realloc... yes checking for vprintf... yes checking for _doprnt... no checking whether HOST_NAME_MAX is declared... yes checking build system type... aarch64-unknown-linux-gnu checking host system type... aarch64-unknown-linux-gnu checking if compiler needs -Werror to reject unknown flags... no checking for the pthreads library -lpthreads... no checking whether pthreads work without any flags... no checking whether pthreads work with -Kthread... no checking whether pthreads work with -kthread... no checking for the pthreads library -llthread... no checking whether pthreads work with -pthread... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for PTHREAD_PRIO_INHERIT... yes checking mpi.h usability... yes checking mpi.h presence... yes checking for mpi.h... yes checking for MPI_Init in -lmpi... yes checking for sqrt in -lm... yes checking for pow... yes checking for sqrt... yes checking for ceilf... yes checking for dlsym in -ldl... yes checking how to run the C++ preprocessor... g++ -E checking functional usability... yes checking functional presence... yes checking for functional... yes checking tr1/functional usability... yes checking tr1/functional presence... yes checking for tr1/functional... yes checking boost/functional/hash.hpp usability... yes checking boost/functional/hash.hpp presence... yes checking for boost/functional/hash.hpp... yes checking boost/property_map/property_map.hpp usability... yes checking boost/property_map/property_map.hpp presence... yes checking for boost/property_map/property_map.hpp... yes checking google/sparse_hash_map usability... yes checking google/sparse_hash_map presence... yes checking for google/sparse_hash_map... yes checking unordered_map usability... yes checking unordered_map presence... yes checking for unordered_map... yes checking tr1/unordered_map usability... yes checking tr1/unordered_map presence... yes checking for tr1/unordered_map... yes checking unordered_set usability... yes checking unordered_set presence... yes checking for unordered_set... yes checking tr1/unordered_set usability... yes checking tr1/unordered_set presence... yes checking for tr1/unordered_set... yes checking boost/unordered_set.hpp usability... yes checking boost/unordered_set.hpp presence... yes checking for boost/unordered_set.hpp... yes checking sqlite3.h usability... yes checking sqlite3.h presence... yes checking for sqlite3.h... yes checking for main in -lsqlite3... yes checking for g++ option to support OpenMP... -fopenmp checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating ABYSS/Makefile config.status: creating Align/Makefile config.status: creating Assembly/Makefile config.status: creating Common/Makefile config.status: creating DataLayer/Makefile config.status: creating FMIndex/Makefile config.status: creating Graph/Makefile config.status: creating Parallel/Makefile config.status: creating bin/Makefile config.status: creating doc/Makefile config.status: creating dialign/Makefile config.status: creating kmerprint/Makefile config.status: creating AdjList/Makefile config.status: creating Konnector/Makefile config.status: creating DAssembler/Makefile config.status: creating DistanceEst/Makefile config.status: creating Layout/Makefile config.status: creating Map/Makefile config.status: creating Misc/Makefile config.status: creating Overlap/Makefile config.status: creating PopBubbles/Makefile config.status: creating Scaffold/Makefile config.status: creating SimpleGraph/Makefile config.status: creating MergePaths/Makefile config.status: creating KAligner/Makefile config.status: creating PairedDBG/Makefile config.status: creating ParseAligns/Makefile config.status: creating PathOverlap/Makefile config.status: creating Consensus/Makefile config.status: creating FilterGraph/Makefile config.status: creating GapFiller/Makefile config.status: creating Sealer/Makefile config.status: creating lib/gtest-1.7.0/Makefile config.status: creating Unittest/Makefile config.status: creating LogKmerCount/Makefile config.status: creating Bloom/Makefile config.status: creating BloomDBG/Makefile config.status: creating DataBase/Makefile config.status: creating lib/bloomfilter/Makefile config.status: creating lib/nthash/Makefile config.status: creating config.h config.status: executing depfiles commands configure: WARNING: unrecognized options: --disable-maintainer-mode make[1]: Leaving directory '/build/abyss-2.1.5' debian/rules override_dh_auto_build make[1]: Entering directory '/build/abyss-2.1.5' dh_auto_build make -j8 make[2]: Entering directory '/build/abyss-2.1.5' make all-recursive make[3]: Entering directory '/build/abyss-2.1.5' Making all in bin make[4]: Entering directory '/build/abyss-2.1.5/bin' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/build/abyss-2.1.5/bin' Making all in doc make[4]: Entering directory '/build/abyss-2.1.5/doc' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/build/abyss-2.1.5/doc' Making all in Common make[4]: Entering directory '/build/abyss-2.1.5/Common' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-2.1.5 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libcommon_a-ContigID.o `test -f 'ContigID.cpp' || echo './'`ContigID.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-2.1.5 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libcommon_a-Fcontrol.o `test -f 'Fcontrol.cpp' || echo './'`Fcontrol.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-2.1.5 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libcommon_a-Histogram.o `test -f 'Histogram.cpp' || echo './'`Histogram.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-2.1.5 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libcommon_a-Kmer.o `test -f 'Kmer.cpp' || echo './'`Kmer.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-2.1.5 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libcommon_a-Log.o `test -f 'Log.cpp' || echo './'`Log.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-2.1.5 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libcommon_a-Options.o `test -f 'Options.cpp' || echo './'`Options.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-2.1.5 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libcommon_a-Sequence.o `test -f 'Sequence.cpp' || echo './'`Sequence.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-2.1.5 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libcommon_a-SignalHandler.o `test -f 'SignalHandler.cpp' || echo './'`SignalHandler.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-2.1.5 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libcommon_a-Timer.o `test -f 'Timer.cpp' || echo './'`Timer.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-2.1.5 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libcommon_a-Uncompress.o `test -f 'Uncompress.cpp' || echo './'`Uncompress.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-2.1.5 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libcommon_a-city.o `test -f 'city.cc' || echo './'`city.cc rm -f libcommon.a ar cru libcommon.a libcommon_a-ContigID.o libcommon_a-Fcontrol.o libcommon_a-Histogram.o libcommon_a-Kmer.o libcommon_a-Log.o libcommon_a-Options.o libcommon_a-Sequence.o libcommon_a-SignalHandler.o libcommon_a-Timer.o libcommon_a-Uncompress.o libcommon_a-city.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libcommon.a make[4]: Leaving directory '/build/abyss-2.1.5/Common' Making all in Graph make[4]: Entering directory '/build/abyss-2.1.5/Graph' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-2.1.5 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_gc-gc.o `test -f 'gc.cc' || echo './'`gc.cc g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-2.1.5 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_todot-todot.o `test -f 'todot.cc' || echo './'`todot.cc g++ -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -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++ -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -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/abyss-2.1.5/Graph' Making all in DataLayer make[4]: Entering directory '/build/abyss-2.1.5/DataLayer' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-2.1.5 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_fac-fac.o `test -f 'fac.cc' || echo './'`fac.cc g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-2.1.5 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libdatalayer_a-FastaReader.o `test -f 'FastaReader.cpp' || echo './'`FastaReader.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-2.1.5 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libdatalayer_a-FastaWriter.o `test -f 'FastaWriter.cpp' || echo './'`FastaWriter.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-2.1.5 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_tofastq-abyss-tofastq.o `test -f 'abyss-tofastq.cc' || echo './'`abyss-tofastq.cc rm -f libdatalayer.a ar cru libdatalayer.a libdatalayer_a-FastaReader.o libdatalayer_a-FastaWriter.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libdatalayer.a g++ -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -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 g++ -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -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 make[4]: Leaving directory '/build/abyss-2.1.5/DataLayer' Making all in DataBase make[4]: Entering directory '/build/abyss-2.1.5/DataBase' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-2.1.5 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_db_csv-DB.o `test -f 'DB.cc' || echo './'`DB.cc g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-2.1.5 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_db_csv-db-csv.o `test -f 'db-csv.cc' || echo './'`db-csv.cc g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-2.1.5 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libdb_a-DB.o `test -f 'DB.cc' || echo './'`DB.cc rm -f libdb.a ar cru libdb.a libdb_a-DB.o ../Common/libcommon.a ar: `u' modifier ignored since `D' is the default (see `U') ranlib libdb.a g++ -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -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/abyss-2.1.5/DataBase' Making all in FMIndex make[4]: Entering directory '/build/abyss-2.1.5/FMIndex' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-2.1.5 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_count-count.o `test -f 'count.cc' || echo './'`count.cc g++ -DHAVE_CONFIG_H -I. -I.. -I../Common -I/build/abyss-2.1.5 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libfmindex_a-bit_array.o `test -f 'bit_array.cc' || echo './'`bit_array.cc g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-2.1.5 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_dawg-abyss-dawg.o `test -f 'abyss-dawg.cc' || echo './'`abyss-dawg.cc rm -f libfmindex.a ar cru libfmindex.a libfmindex_a-bit_array.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libfmindex.a g++ -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -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++ -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -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/abyss-2.1.5/FMIndex' Making all in Assembly make[4]: Entering directory '/build/abyss-2.1.5/Assembly' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-2.1.5 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libassembly_a-AssemblyAlgorithms.o `test -f 'AssemblyAlgorithms.cc' || echo './'`AssemblyAlgorithms.cc g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-2.1.5 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libassembly_a-Options.o `test -f 'Options.cc' || echo './'`Options.cc rm -f libassembly.a ar cru libassembly.a libassembly_a-AssemblyAlgorithms.o libassembly_a-Options.o ../Common/libcommon.a ar: `u' modifier ignored since `D' is the default (see `U') ranlib libassembly.a make[4]: Leaving directory '/build/abyss-2.1.5/Assembly' Making all in dialign make[4]: Entering directory '/build/abyss-2.1.5/dialign' gcc -DHAVE_CONFIG_H -I. -I.. -I/build/abyss-2.1.5 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -c -o museq.o museq.c gcc -DHAVE_CONFIG_H -I. -I.. -I/build/abyss-2.1.5 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -c -o alig.o alig.c gcc -DHAVE_CONFIG_H -I. -I.. -I/build/abyss-2.1.5 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -c -o assemble.o assemble.c gcc -DHAVE_CONFIG_H -I. -I.. -I/build/abyss-2.1.5 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -c -o diag.o diag.c gcc -DHAVE_CONFIG_H -I. -I.. -I/build/abyss-2.1.5 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -c -o io.o io.c gcc -DHAVE_CONFIG_H -I. -I.. -I/build/abyss-2.1.5 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -c -o orf.o orf.c gcc -DHAVE_CONFIG_H -I. -I.. -I/build/abyss-2.1.5 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -c -o parameters.o parameters.c gcc -DHAVE_CONFIG_H -I. -I.. -I/build/abyss-2.1.5 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -c -o prob.o prob.c alig.c:15:20: warning: inline function 'calc_ov_weight' declared but never defined extern inline void calc_ov_weight(struct diag* dg, struct diag_col *dcol, struct scr_matrix* smatrix, ^~~~~~~~~~~~~~ alig.c:13:20: warning: inline function 'calc_weight' declared but never defined extern inline void calc_weight(struct diag* dg, struct scr_matrix* smatrix, ^~~~~~~~~~~ assemble.c:40:20: warning: inline function 'align_diag' declared but never defined extern inline char align_diag(struct alignment *algn, struct scr_matrix *smatrix, struct diag* dg); ^~~~~~~~~~ assemble.c:37:32: warning: inline function 'find_eqc' declared but never defined extern inline struct algn_pos *find_eqc(struct algn_pos **ap, int seqnum, int pos); ^~~~~~~~ assemble.c:25:39: warning: inline function 'find_diags_guided' declared but never defined extern inline struct simple_diag_col* find_diags_guided(struct scr_matrix *smatrix, ^~~~~~~~~~~~~~~~~ assemble.c:15:20: warning: inline function 'calc_ov_weight' declared but never defined extern inline void calc_ov_weight(struct diag* dg, struct diag_col *dcol, struct scr_matrix* smatrix, ^~~~~~~~~~~~~~ assemble.c:13:20: warning: inline function 'calc_weight' declared but never defined extern inline void calc_weight(struct diag* dg, struct scr_matrix* smatrix, ^~~~~~~~~~~ diag.c:1456:3: warning: 'real_calc_weight' is static but used in inline function 'find_diags_dyn' which is not static real_calc_weight(dg, smatrix, pdist,1,tmp_dist,algn); ^~~~~~~~~~~~~~~~ io.c: In function 'read_scr_matrix': io.c:270:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf( fp, "%i", &is); ^~~~~~~~~~~~~~~~~~~~~~ io.c:282:5: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf(fp, "%s\n", rline); ^~~~~~~~~~~~~~~~~~~~~~~~~ io.c: In function 'read_diag_prob_dist': io.c:371:7: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf( fp, "%li %li %Le\n", &ti,&tscr,&weight ); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I.. -I/build/abyss-2.1.5 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -c -o translate.o translate.c rm -f libdialign.a ar cru libdialign.a alig.o assemble.o diag.o io.o orf.o parameters.o prob.o translate.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libdialign.a gcc -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -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/abyss-2.1.5/dialign' Making all in Align make[4]: Entering directory '/build/abyss-2.1.5/Align' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/abyss-2.1.5 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_align-align.o `test -f 'align.cc' || echo './'`align.cc g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-2.1.5 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libalign_a-alignGlobal.o `test -f 'alignGlobal.cc' || echo './'`alignGlobal.cc g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-2.1.5 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libalign_a-dialign.o `test -f 'dialign.cpp' || echo './'`dialign.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-2.1.5 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libalign_a-dna_diag_prob.o `test -f 'dna_diag_prob.cc' || echo './'`dna_diag_prob.cc g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-2.1.5 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libalign_a-smith_waterman.o `test -f 'smith_waterman.cpp' || echo './'`smith_waterman.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/abyss-2.1.5 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_mergepairs-mergepairs.o `test -f 'mergepairs.cc' || echo './'`mergepairs.cc rm -f libalign.a ar cru libalign.a libalign_a-alignGlobal.o libalign_a-dialign.o libalign_a-dna_diag_prob.o libalign_a-smith_waterman.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libalign.a g++ -Wall -Wextra -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -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++ -Wall -Wextra -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -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/abyss-2.1.5/Align' Making all in ABYSS make[4]: Entering directory '/build/abyss-2.1.5/ABYSS' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-2.1.5 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o ABYSS-abyss.o `test -f 'abyss.cc' || echo './'`abyss.cc g++ -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -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/abyss-2.1.5/ABYSS' Making all in Parallel make[4]: Entering directory '/build/abyss-2.1.5/Parallel' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-2.1.5 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o ABYSS_P-parallelAbyss.o `test -f 'parallelAbyss.cpp' || echo './'`parallelAbyss.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-2.1.5 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o ABYSS_P-CommLayer.o `test -f 'CommLayer.cpp' || echo './'`CommLayer.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-2.1.5 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o ABYSS_P-NetworkSequenceCollection.o `test -f 'NetworkSequenceCollection.cpp' || echo './'`NetworkSequenceCollection.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-2.1.5 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o ABYSS_P-MessageBuffer.o `test -f 'MessageBuffer.cpp' || echo './'`MessageBuffer.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-2.1.5 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o ABYSS_P-Messages.o `test -f 'Messages.cpp' || echo './'`Messages.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -DPAIRED_DBG -I/build/abyss-2.1.5 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_paired_dbg_mpi-parallelAbyss.o `test -f 'parallelAbyss.cpp' || echo './'`parallelAbyss.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -DPAIRED_DBG -I/build/abyss-2.1.5 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_paired_dbg_mpi-CommLayer.o `test -f 'CommLayer.cpp' || echo './'`CommLayer.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -DPAIRED_DBG -I/build/abyss-2.1.5 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_paired_dbg_mpi-NetworkSequenceCollection.o `test -f 'NetworkSequenceCollection.cpp' || echo './'`NetworkSequenceCollection.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -DPAIRED_DBG -I/build/abyss-2.1.5 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_paired_dbg_mpi-MessageBuffer.o `test -f 'MessageBuffer.cpp' || echo './'`MessageBuffer.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -DPAIRED_DBG -I/build/abyss-2.1.5 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_paired_dbg_mpi-Messages.o `test -f 'Messages.cpp' || echo './'`Messages.cpp g++ -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -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++ -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -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/abyss-2.1.5/Parallel' Making all in Bloom make[4]: Entering directory '/build/abyss-2.1.5/Bloom' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/abyss-2.1.5 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_bloom-bloom.o `test -f 'bloom.cc' || echo './'`bloom.cc g++ -Wall -Wextra -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -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/abyss-2.1.5/Bloom' Making all in BloomDBG make[4]: Entering directory '/build/abyss-2.1.5/BloomDBG' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/abyss-2.1.5 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_bloom_dbg-bloom-dbg.o `test -f 'bloom-dbg.cc' || echo './'`bloom-dbg.cc g++ -Wall -Wextra -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -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/abyss-2.1.5/BloomDBG' Making all in Konnector make[4]: Entering directory '/build/abyss-2.1.5/Konnector' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/abyss-2.1.5 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o konnector-konnector.o `test -f 'konnector.cc' || echo './'`konnector.cc g++ -Wall -Wextra -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -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/abyss-2.1.5/Konnector' Making all in Consensus make[4]: Entering directory '/build/abyss-2.1.5/Consensus' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/abyss-2.1.5 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Consensus-Consensus.o `test -f 'Consensus.cpp' || echo './'`Consensus.cpp g++ -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -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/abyss-2.1.5/Consensus' Making all in DAssembler make[4]: Entering directory '/build/abyss-2.1.5/DAssembler' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/abyss-2.1.5 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o DAssembler-DAssembler.o `test -f 'DAssembler.cpp' || echo './'`DAssembler.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/abyss-2.1.5 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o DAssembler-RotatedRead.o `test -f 'RotatedRead.cpp' || echo './'`RotatedRead.cpp g++ -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -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/abyss-2.1.5/DAssembler' Making all in DistanceEst make[4]: Entering directory '/build/abyss-2.1.5/DistanceEst' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-2.1.5 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o DistanceEst-DistanceEst.o `test -f 'DistanceEst.cpp' || echo './'`DistanceEst.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-2.1.5 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o DistanceEst-MLE.o `test -f 'MLE.cpp' || echo './'`MLE.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -D SAM_SEQ_QUAL=1 -I/build/abyss-2.1.5 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o DistanceEst_ssq-DistanceEst.o `test -f 'DistanceEst.cpp' || echo './'`DistanceEst.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -D SAM_SEQ_QUAL=1 -I/build/abyss-2.1.5 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o DistanceEst_ssq-MLE.o `test -f 'MLE.cpp' || echo './'`MLE.cpp g++ -Wall -Wextra -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -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++ -Wall -Wextra -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -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/abyss-2.1.5/DistanceEst' Making all in KAligner make[4]: Entering directory '/build/abyss-2.1.5/KAligner' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/abyss-2.1.5 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o KAligner-KAligner.o `test -f 'KAligner.cpp' || echo './'`KAligner.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/abyss-2.1.5 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o KAligner-Aligner.o `test -f 'Aligner.cpp' || echo './'`Aligner.cpp g++ -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -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/abyss-2.1.5/KAligner' Making all in Layout make[4]: Entering directory '/build/abyss-2.1.5/Layout' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-2.1.5 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_layout-layout.o `test -f 'layout.cc' || echo './'`layout.cc g++ -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -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/abyss-2.1.5/Layout' Making all in LogKmerCount make[4]: Entering directory '/build/abyss-2.1.5/LogKmerCount' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/abyss-2.1.5 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o logcounter-logcounter.o `test -f 'logcounter.cc' || echo './'`logcounter.cc g++ -Wall -Wextra -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -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/abyss-2.1.5/LogKmerCount' Making all in Map make[4]: Entering directory '/build/abyss-2.1.5/Map' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../FMIndex -I/build/abyss-2.1.5 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_index-index.o `test -f 'index.cc' || echo './'`index.cc g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../FMIndex -I/build/abyss-2.1.5 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_map-map.o `test -f 'map.cc' || echo './'`map.cc g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../FMIndex -D SAM_SEQ_QUAL=1 -I/build/abyss-2.1.5 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_map_ssq-map.o `test -f 'map.cc' || echo './'`map.cc g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../FMIndex -I/build/abyss-2.1.5 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_overlap-overlap.o `test -f 'overlap.cc' || echo './'`overlap.cc g++ -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -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++ -Wall -Wextra -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -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++ -Wall -Wextra -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -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++ -Wall -Wextra -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -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/abyss-2.1.5/Map' Making all in MergePaths make[4]: Entering directory '/build/abyss-2.1.5/MergePaths' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/abyss-2.1.5 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o MergePaths-MergePaths.o `test -f 'MergePaths.cpp' || echo './'`MergePaths.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Align -I../Common -I../DataLayer -I/build/abyss-2.1.5 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o MergeContigs-MergeContigs.o `test -f 'MergeContigs.cpp' || echo './'`MergeContigs.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Align -I../Common -I../DataLayer -I../SimpleGraph -I/build/abyss-2.1.5 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o PathConsensus-PathConsensus.o `test -f 'PathConsensus.cpp' || echo './'`PathConsensus.cpp g++ -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -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++ -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -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++ -Wall -Wextra -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -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/abyss-2.1.5/MergePaths' Making all in Misc make[4]: Entering directory '/build/abyss-2.1.5/Misc' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/build/abyss-2.1.5/Misc' Making all in Overlap make[4]: Entering directory '/build/abyss-2.1.5/Overlap' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/abyss-2.1.5 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Overlap-Overlap.o `test -f 'Overlap.cpp' || echo './'`Overlap.cpp g++ -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -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/abyss-2.1.5/Overlap' Making all in PairedDBG make[4]: Entering directory '/build/abyss-2.1.5/PairedDBG' g++ -DHAVE_CONFIG_H -I. -I.. -DPAIRED_DBG -I.. -I/build/abyss-2.1.5 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_paired_dbg-abyss-paired-dbg.o `test -f 'abyss-paired-dbg.cc' || echo './'`abyss-paired-dbg.cc g++ -DHAVE_CONFIG_H -I. -I.. -DPAIRED_DBG -I.. -I/build/abyss-2.1.5 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_paired_dbg-KmerPair.o `test -f 'KmerPair.cc' || echo './'`KmerPair.cc g++ -DHAVE_CONFIG_H -I. -I.. -I/build/abyss-2.1.5 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o KmerPair.o KmerPair.cc rm -f libpaireddbg.a ar cru libpaireddbg.a KmerPair.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libpaireddbg.a g++ -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -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/abyss-2.1.5/PairedDBG' Making all in ParseAligns make[4]: Entering directory '/build/abyss-2.1.5/ParseAligns' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-2.1.5 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_fixmate-abyss-fixmate.o `test -f 'abyss-fixmate.cc' || echo './'`abyss-fixmate.cc g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -D SAM_SEQ_QUAL=1 -I/build/abyss-2.1.5 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_fixmate_ssq-abyss-fixmate.o `test -f 'abyss-fixmate.cc' || echo './'`abyss-fixmate.cc g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-2.1.5 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o ParseAligns-ParseAligns.o `test -f 'ParseAligns.cpp' || echo './'`ParseAligns.cpp g++ -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -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++ -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -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 g++ -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -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 make[4]: Leaving directory '/build/abyss-2.1.5/ParseAligns' Making all in PathOverlap make[4]: Entering directory '/build/abyss-2.1.5/PathOverlap' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/abyss-2.1.5 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o PathOverlap-PathOverlap.o `test -f 'PathOverlap.cpp' || echo './'`PathOverlap.cpp g++ -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -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/abyss-2.1.5/PathOverlap' Making all in PopBubbles make[4]: Entering directory '/build/abyss-2.1.5/PopBubbles' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Align -I../Common -I../DataLayer -I/build/abyss-2.1.5 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o PopBubbles-PopBubbles.o `test -f 'PopBubbles.cpp' || echo './'`PopBubbles.cpp g++ -Wall -Wextra -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -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/abyss-2.1.5/PopBubbles' Making all in Scaffold make[4]: Entering directory '/build/abyss-2.1.5/Scaffold' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-2.1.5 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_scaffold-scaffold.o `test -f 'scaffold.cc' || echo './'`scaffold.cc g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-2.1.5 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_junction-junction.o `test -f 'junction.cc' || echo './'`junction.cc g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-2.1.5 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_longseqdist-longseqdist.o `test -f 'longseqdist.cpp' || echo './'`longseqdist.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-2.1.5 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_drawgraph-drawgraph.o `test -f 'drawgraph.cc' || echo './'`drawgraph.cc g++ -Wall -Wextra -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -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++ -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/aarch64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-drawgraph abyss_drawgraph-drawgraph.o ../Common/libcommon.a -ldl -lm g++ -Wall -Wextra -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -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++ -Wall -Wextra -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -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/abyss-2.1.5/Scaffold' Making all in SimpleGraph make[4]: Entering directory '/build/abyss-2.1.5/SimpleGraph' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-2.1.5 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -Wno-strict-aliasing -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o SimpleGraph-SimpleGraph.o `test -f 'SimpleGraph.cpp' || echo './'`SimpleGraph.cpp g++ -Wall -Wextra -Wno-strict-aliasing -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -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/abyss-2.1.5/SimpleGraph' Making all in kmerprint make[4]: Entering directory '/build/abyss-2.1.5/kmerprint' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Assembly -I../Common -I../DataLayer -I/build/abyss-2.1.5 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o kmerprint-kmerprint.o `test -f 'kmerprint.cc' || echo './'`kmerprint.cc g++ -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -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/abyss-2.1.5/kmerprint' Making all in FilterGraph make[4]: Entering directory '/build/abyss-2.1.5/FilterGraph' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/abyss-2.1.5 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_filtergraph-FilterGraph.o `test -f 'FilterGraph.cc' || echo './'`FilterGraph.cc g++ -Wall -Wextra -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -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/abyss-2.1.5/FilterGraph' Making all in GapFiller make[4]: Entering directory '/build/abyss-2.1.5/GapFiller' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../Align -D SAM_SEQ_QUAL=1 -I/build/abyss-2.1.5 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_gapfill-gapfill.o `test -f 'gapfill.cpp' || echo './'`gapfill.cpp g++ -Wall -Wextra -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -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/abyss-2.1.5/GapFiller' Making all in Sealer make[4]: Entering directory '/build/abyss-2.1.5/Sealer' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/abyss-2.1.5 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_sealer-sealer.o `test -f 'sealer.cc' || echo './'`sealer.cc g++ -Wall -Wextra -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -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/abyss-2.1.5/Sealer' Making all in AdjList make[4]: Entering directory '/build/abyss-2.1.5/AdjList' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -DPAIRED_DBG -I/build/abyss-2.1.5 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o AdjList-AdjList.o `test -f 'AdjList.cpp' || echo './'`AdjList.cpp g++ -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -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/abyss-2.1.5/AdjList' Making all in lib/bloomfilter make[4]: Entering directory '/build/abyss-2.1.5/lib/bloomfilter' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/build/abyss-2.1.5/lib/bloomfilter' Making all in lib/nthash make[4]: Entering directory '/build/abyss-2.1.5/lib/nthash' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/build/abyss-2.1.5/lib/nthash' Making all in lib/gtest-1.7.0 make[4]: Entering directory '/build/abyss-2.1.5/lib/gtest-1.7.0' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/build/abyss-2.1.5/lib/gtest-1.7.0' Making all in Unittest make[4]: Entering directory '/build/abyss-2.1.5/Unittest' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/build/abyss-2.1.5/Unittest' make[4]: Entering directory '/build/abyss-2.1.5' make[4]: Leaving directory '/build/abyss-2.1.5' make[3]: Leaving directory '/build/abyss-2.1.5' make[2]: Leaving directory '/build/abyss-2.1.5' markdown_py -f README.html README.md make[1]: Leaving directory '/build/abyss-2.1.5' dh_auto_test make -j8 check VERBOSE=1 make[1]: Entering directory '/build/abyss-2.1.5' Making check in bin make[2]: Entering directory '/build/abyss-2.1.5/bin' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.1.5/bin' Making check in doc make[2]: Entering directory '/build/abyss-2.1.5/doc' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.1.5/doc' Making check in Common make[2]: Entering directory '/build/abyss-2.1.5/Common' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.1.5/Common' Making check in Graph make[2]: Entering directory '/build/abyss-2.1.5/Graph' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.1.5/Graph' Making check in DataLayer make[2]: Entering directory '/build/abyss-2.1.5/DataLayer' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.1.5/DataLayer' Making check in DataBase make[2]: Entering directory '/build/abyss-2.1.5/DataBase' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.1.5/DataBase' Making check in FMIndex make[2]: Entering directory '/build/abyss-2.1.5/FMIndex' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.1.5/FMIndex' Making check in Assembly make[2]: Entering directory '/build/abyss-2.1.5/Assembly' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.1.5/Assembly' Making check in dialign make[2]: Entering directory '/build/abyss-2.1.5/dialign' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.1.5/dialign' Making check in Align make[2]: Entering directory '/build/abyss-2.1.5/Align' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.1.5/Align' Making check in ABYSS make[2]: Entering directory '/build/abyss-2.1.5/ABYSS' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.1.5/ABYSS' Making check in Parallel make[2]: Entering directory '/build/abyss-2.1.5/Parallel' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.1.5/Parallel' Making check in Bloom make[2]: Entering directory '/build/abyss-2.1.5/Bloom' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.1.5/Bloom' Making check in BloomDBG make[2]: Entering directory '/build/abyss-2.1.5/BloomDBG' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.1.5/BloomDBG' Making check in Konnector make[2]: Entering directory '/build/abyss-2.1.5/Konnector' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.1.5/Konnector' Making check in Consensus make[2]: Entering directory '/build/abyss-2.1.5/Consensus' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.1.5/Consensus' Making check in DAssembler make[2]: Entering directory '/build/abyss-2.1.5/DAssembler' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.1.5/DAssembler' Making check in DistanceEst make[2]: Entering directory '/build/abyss-2.1.5/DistanceEst' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.1.5/DistanceEst' Making check in KAligner make[2]: Entering directory '/build/abyss-2.1.5/KAligner' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.1.5/KAligner' Making check in Layout make[2]: Entering directory '/build/abyss-2.1.5/Layout' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.1.5/Layout' Making check in LogKmerCount make[2]: Entering directory '/build/abyss-2.1.5/LogKmerCount' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.1.5/LogKmerCount' Making check in Map make[2]: Entering directory '/build/abyss-2.1.5/Map' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.1.5/Map' Making check in MergePaths make[2]: Entering directory '/build/abyss-2.1.5/MergePaths' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.1.5/MergePaths' Making check in Misc make[2]: Entering directory '/build/abyss-2.1.5/Misc' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.1.5/Misc' Making check in Overlap make[2]: Entering directory '/build/abyss-2.1.5/Overlap' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.1.5/Overlap' Making check in PairedDBG make[2]: Entering directory '/build/abyss-2.1.5/PairedDBG' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.1.5/PairedDBG' Making check in ParseAligns make[2]: Entering directory '/build/abyss-2.1.5/ParseAligns' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.1.5/ParseAligns' Making check in PathOverlap make[2]: Entering directory '/build/abyss-2.1.5/PathOverlap' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.1.5/PathOverlap' Making check in PopBubbles make[2]: Entering directory '/build/abyss-2.1.5/PopBubbles' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.1.5/PopBubbles' Making check in Scaffold make[2]: Entering directory '/build/abyss-2.1.5/Scaffold' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.1.5/Scaffold' Making check in SimpleGraph make[2]: Entering directory '/build/abyss-2.1.5/SimpleGraph' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.1.5/SimpleGraph' Making check in kmerprint make[2]: Entering directory '/build/abyss-2.1.5/kmerprint' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.1.5/kmerprint' Making check in FilterGraph make[2]: Entering directory '/build/abyss-2.1.5/FilterGraph' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.1.5/FilterGraph' Making check in GapFiller make[2]: Entering directory '/build/abyss-2.1.5/GapFiller' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.1.5/GapFiller' Making check in Sealer make[2]: Entering directory '/build/abyss-2.1.5/Sealer' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.1.5/Sealer' Making check in AdjList make[2]: Entering directory '/build/abyss-2.1.5/AdjList' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.1.5/AdjList' Making check in lib/bloomfilter make[2]: Entering directory '/build/abyss-2.1.5/lib/bloomfilter' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.1.5/lib/bloomfilter' Making check in lib/nthash make[2]: Entering directory '/build/abyss-2.1.5/lib/nthash' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.1.5/lib/nthash' Making check in lib/gtest-1.7.0 make[2]: Entering directory '/build/abyss-2.1.5/lib/gtest-1.7.0' make libgtest.a libgtest_main.a make[3]: Entering directory '/build/abyss-2.1.5/lib/gtest-1.7.0' g++ -DHAVE_CONFIG_H -I. -I../.. -I../.. -isystem ../../lib/gtest-1.7.0/include -I/build/abyss-2.1.5 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -Wno-missing-field-initializers -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o src/libgtest_a-gtest-all.o `test -f 'src/gtest-all.cc' || echo './'`src/gtest-all.cc g++ -DHAVE_CONFIG_H -I. -I../.. -I../.. -isystem ../../lib/gtest-1.7.0/include -I/build/abyss-2.1.5 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -Wno-missing-field-initializers -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o src/libgtest_main_a-gtest_main.o `test -f 'src/gtest_main.cc' || echo './'`src/gtest_main.cc g++ -DHAVE_CONFIG_H -I. -I../.. -I../.. -isystem ../../lib/gtest-1.7.0/include -I/build/abyss-2.1.5 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -Wno-missing-field-initializers -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o src/libgtest_main_a-gtest-all.o `test -f 'src/gtest-all.cc' || echo './'`src/gtest-all.cc rm -f libgtest.a ar cru libgtest.a src/libgtest_a-gtest-all.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libgtest.a rm -f libgtest_main.a ar cru libgtest_main.a src/libgtest_main_a-gtest_main.o src/libgtest_main_a-gtest-all.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libgtest_main.a make[3]: Leaving directory '/build/abyss-2.1.5/lib/gtest-1.7.0' make[2]: Leaving directory '/build/abyss-2.1.5/lib/gtest-1.7.0' Making check in Unittest make[2]: Entering directory '/build/abyss-2.1.5/Unittest' make common_stringutil common_histogram common_bitutil common_kmer common_sequence common_KmerIterator common_sam BloomFilter Konnector_DBGBloom Konnector_DBGBloomAlgorithms graph_ConstrainedBFSVisitor graph_BidirectionalBFS graph_AllPathsSearch graph_HashGraph graph_ConstrainedBidiBFSVisitor graph_ExtendPath graph_DotIO graph_UndirectedGraph Konnector_konnector DBG_LoadAlgorithm PairedDBG_LoadAlgorithm PairedDBG_KmerPair PairedDBG_Dinuc PairedDBG_BranchRecord BloomDBG_BloomDBG BloomDBG_RollingHash BloomDBG_RollingHashIterator BloomDBG_HashAgnosticCascadingBloom BloomDBG_RollingBloomDBG BloomDBG_MaskedKmer BloomDBG_SpacedSeed BloomDBG_LightweightKmer make[3]: Entering directory '/build/abyss-2.1.5/Unittest' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/build/abyss-2.1.5 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Common/StringUtilTest.o Common/StringUtilTest.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/build/abyss-2.1.5 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Common/HistogramTest.o Common/HistogramTest.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/build/abyss-2.1.5 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Common/BitUtilTest.o Common/BitUtilTest.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/build/abyss-2.1.5 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Common/KmerTest.o Common/KmerTest.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/build/abyss-2.1.5 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Common/Sequence.o Common/Sequence.cc g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/build/abyss-2.1.5 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Common/KmerIteratorTest.o Common/KmerIteratorTest.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/build/abyss-2.1.5 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Common/SAM.o Common/SAM.cc g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../Common -I/build/abyss-2.1.5 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Konnector/BloomFilter-BloomFilter.o `test -f 'Konnector/BloomFilter.cc' || echo './'`Konnector/BloomFilter.cc g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../Common -I/build/abyss-2.1.5 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Konnector/DBGBloom-DBGBloomTest.o `test -f 'Konnector/DBGBloomTest.cpp' || echo './'`Konnector/DBGBloomTest.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../Common -I/build/abyss-2.1.5 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Konnector/DBGBloomAlgorithms-DBGBloomAlgorithmsTest.o `test -f 'Konnector/DBGBloomAlgorithmsTest.cpp' || echo './'`Konnector/DBGBloomAlgorithmsTest.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../Common -I/build/abyss-2.1.5 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Graph/graph_ConstrainedBFSVisitor-ConstrainedBFSVisitorTest.o `test -f 'Graph/ConstrainedBFSVisitorTest.cpp' || echo './'`Graph/ConstrainedBFSVisitorTest.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../Common -I/build/abyss-2.1.5 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Graph/graph_BidirectionalBFS-BidirectionalBFSTest.o `test -f 'Graph/BidirectionalBFSTest.cpp' || echo './'`Graph/BidirectionalBFSTest.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../Common -I/build/abyss-2.1.5 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Graph/graph_AllPathsSearch-AllPathsSearchTest.o `test -f 'Graph/AllPathsSearchTest.cpp' || echo './'`Graph/AllPathsSearchTest.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../Common -I/build/abyss-2.1.5 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Graph/graph_HashGraph-HashGraphTest.o `test -f 'Graph/HashGraphTest.cpp' || echo './'`Graph/HashGraphTest.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../Common -I/build/abyss-2.1.5 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Graph/graph_ConstrainedBidiBFSVisitor-ConstrainedBidiBFSVisitorTest.o `test -f 'Graph/ConstrainedBidiBFSVisitorTest.cpp' || echo './'`Graph/ConstrainedBidiBFSVisitorTest.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../Common -I/build/abyss-2.1.5 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Graph/graph_ExtendPath-ExtendPathTest.o `test -f 'Graph/ExtendPathTest.cpp' || echo './'`Graph/ExtendPathTest.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../Common -I/build/abyss-2.1.5 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Graph/graph_DotIO-DotIOTest.o `test -f 'Graph/DotIOTest.cpp' || echo './'`Graph/DotIOTest.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/build/abyss-2.1.5 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Graph/UndirectedGraphTest.o Graph/UndirectedGraphTest.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../Common -I/build/abyss-2.1.5 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Konnector/konnector-konnectorTest.o `test -f 'Konnector/konnectorTest.cpp' || echo './'`Konnector/konnectorTest.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../DataLayer -I../Common -I/build/abyss-2.1.5 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o DBG/LoadAlgorithm-LoadAlgorithmTest.o `test -f 'DBG/LoadAlgorithmTest.cpp' || echo './'`DBG/LoadAlgorithmTest.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../DataLayer -I../Common -I/build/abyss-2.1.5 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o PairedDBG/LoadAlgorithm-LoadAlgorithmTest.o `test -f 'PairedDBG/LoadAlgorithmTest.cpp' || echo './'`PairedDBG/LoadAlgorithmTest.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../DataLayer -I../Common -I/build/abyss-2.1.5 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o PairedDBG/KmerPair-KmerPairTest.o `test -f 'PairedDBG/KmerPairTest.cc' || echo './'`PairedDBG/KmerPairTest.cc g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../DataLayer -I../Common -I/build/abyss-2.1.5 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o PairedDBG/Dinuc-DinucTest.o `test -f 'PairedDBG/DinucTest.cc' || echo './'`PairedDBG/DinucTest.cc g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../DataLayer -I../Common -I/build/abyss-2.1.5 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o PairedDBG/BranchRecord-BranchRecordTest.o `test -f 'PairedDBG/BranchRecordTest.cpp' || echo './'`PairedDBG/BranchRecordTest.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../Common -I/build/abyss-2.1.5 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o BloomDBG/BloomDBG-BloomDBGTest.o `test -f 'BloomDBG/BloomDBGTest.cpp' || echo './'`BloomDBG/BloomDBGTest.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/build/abyss-2.1.5 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o BloomDBG/RollingHashTest.o BloomDBG/RollingHashTest.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/build/abyss-2.1.5 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o BloomDBG/RollingHashIteratorTest.o BloomDBG/RollingHashIteratorTest.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/build/abyss-2.1.5 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o BloomDBG/HashAgnosticCascadingBloom-HashAgnosticCascadingBloomTest.o `test -f 'BloomDBG/HashAgnosticCascadingBloomTest.cpp' || echo './'`BloomDBG/HashAgnosticCascadingBloomTest.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/build/abyss-2.1.5 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o BloomDBG/RollingBloomDBG-RollingBloomDBGTest.o `test -f 'BloomDBG/RollingBloomDBGTest.cpp' || echo './'`BloomDBG/RollingBloomDBGTest.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/build/abyss-2.1.5 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o BloomDBG/MaskedKmerTest.o BloomDBG/MaskedKmerTest.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/build/abyss-2.1.5 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o BloomDBG/SpacedSeedTest.o BloomDBG/SpacedSeedTest.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/build/abyss-2.1.5 -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o BloomDBG/LightweightKmerTest.o BloomDBG/LightweightKmerTest.cpp g++ -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/aarch64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o common_stringutil Common/StringUtilTest.o ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/aarch64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o common_histogram Common/HistogramTest.o ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/aarch64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o common_bitutil Common/BitUtilTest.o ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/aarch64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o common_kmer Common/KmerTest.o ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/aarch64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o common_sequence Common/Sequence.o ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/aarch64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o common_KmerIterator Common/KmerIteratorTest.o ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/aarch64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o common_sam Common/SAM.o ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/aarch64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o BloomFilter Konnector/BloomFilter-BloomFilter.o ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/aarch64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o Konnector_DBGBloom Konnector/DBGBloom-DBGBloomTest.o ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/aarch64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o Konnector_DBGBloomAlgorithms Konnector/DBGBloomAlgorithms-DBGBloomAlgorithmsTest.o ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -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 ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -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 ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -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 ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -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 ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -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 ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -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 ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -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 ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/aarch64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o graph_UndirectedGraph Graph/UndirectedGraphTest.o ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -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 ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -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 ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -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 ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -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 ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -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 ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -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 ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/aarch64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o BloomDBG_BloomDBG BloomDBG/BloomDBG-BloomDBGTest.o ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/aarch64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o BloomDBG_RollingHash BloomDBG/RollingHashTest.o ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/aarch64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o BloomDBG_RollingHashIterator BloomDBG/RollingHashIteratorTest.o ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -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 ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/aarch64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o BloomDBG_MaskedKmer BloomDBG/MaskedKmerTest.o ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/aarch64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o BloomDBG_SpacedSeed BloomDBG/SpacedSeedTest.o ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/aarch64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o BloomDBG_LightweightKmer BloomDBG/LightweightKmerTest.o ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -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 ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm make[3]: Leaving directory '/build/abyss-2.1.5/Unittest' make check-TESTS make[3]: Entering directory '/build/abyss-2.1.5/Unittest' make[4]: Entering directory '/build/abyss-2.1.5/Unittest' PASS: common_sequence PASS: common_stringutil PASS: common_kmer PASS: common_histogram PASS: common_KmerIterator PASS: Konnector_DBGBloom PASS: common_sam PASS: Konnector_DBGBloomAlgorithms PASS: common_bitutil PASS: BloomFilter PASS: graph_AllPathsSearch PASS: graph_HashGraph PASS: graph_ConstrainedBFSVisitor PASS: graph_BidirectionalBFS PASS: graph_ConstrainedBidiBFSVisitor PASS: graph_DotIO PASS: graph_UndirectedGraph PASS: graph_ExtendPath PASS: Konnector_konnector PASS: PairedDBG_KmerPair PASS: PairedDBG_Dinuc PASS: PairedDBG_BranchRecord PASS: BloomDBG_BloomDBG PASS: BloomDBG_RollingHash PASS: BloomDBG_HashAgnosticCascadingBloom PASS: BloomDBG_RollingHashIterator PASS: BloomDBG_RollingBloomDBG PASS: BloomDBG_LightweightKmer PASS: BloomDBG_MaskedKmer PASS: BloomDBG_SpacedSeed PASS: PairedDBG_LoadAlgorithm PASS: DBG_LoadAlgorithm ============================================================================ Testsuite summary for ABySS 2.1.5 ============================================================================ # TOTAL: 32 # PASS: 32 # SKIP: 0 # XFAIL: 0 # FAIL: 0 # XPASS: 0 # ERROR: 0 ============================================================================ make[4]: Leaving directory '/build/abyss-2.1.5/Unittest' make[3]: Leaving directory '/build/abyss-2.1.5/Unittest' make[2]: Leaving directory '/build/abyss-2.1.5/Unittest' make[2]: Entering directory '/build/abyss-2.1.5' make[2]: Leaving directory '/build/abyss-2.1.5' make[1]: Leaving directory '/build/abyss-2.1.5' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary dh_testroot dh_prep debian/rules override_dh_auto_install make[1]: Entering directory '/build/abyss-2.1.5' dh_auto_install --destdir=debian/tmp make -j8 install DESTDIR=/build/abyss-2.1.5/debian/tmp AM_UPDATE_INFO_DIR=no make[2]: Entering directory '/build/abyss-2.1.5' Making install in bin make[3]: Entering directory '/build/abyss-2.1.5/bin' make[4]: Entering directory '/build/abyss-2.1.5/bin' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/build/abyss-2.1.5/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/abyss-2.1.5/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.1.5/bin' make[3]: Leaving directory '/build/abyss-2.1.5/bin' Making install in doc make[3]: Entering directory '/build/abyss-2.1.5/doc' make[4]: Entering directory '/build/abyss-2.1.5/doc' make[4]: Nothing to be done for 'install-exec-am'. /bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/share/doc/abyss' /bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/share/man/man1' /usr/bin/install -c -m 644 flowchart.pdf flowchart_simplified.pdf '/build/abyss-2.1.5/debian/tmp/usr/share/doc/abyss' /usr/bin/install -c -m 644 ABYSS.1 abyss-pe.1 abyss-tofastq.1 '/build/abyss-2.1.5/debian/tmp/usr/share/man/man1' make[4]: Leaving directory '/build/abyss-2.1.5/doc' make[3]: Leaving directory '/build/abyss-2.1.5/doc' Making install in Common make[3]: Entering directory '/build/abyss-2.1.5/Common' make[4]: Entering directory '/build/abyss-2.1.5/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/abyss-2.1.5/Common' make[3]: Leaving directory '/build/abyss-2.1.5/Common' Making install in Graph make[3]: Entering directory '/build/abyss-2.1.5/Graph' make[4]: Entering directory '/build/abyss-2.1.5/Graph' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/bin' /usr/bin/install -c abyss-gc abyss-todot '/build/abyss-2.1.5/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.1.5/Graph' make[3]: Leaving directory '/build/abyss-2.1.5/Graph' Making install in DataLayer make[3]: Entering directory '/build/abyss-2.1.5/DataLayer' make[4]: Entering directory '/build/abyss-2.1.5/DataLayer' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/bin' /usr/bin/install -c abyss-fac abyss-tofastq '/build/abyss-2.1.5/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.1.5/DataLayer' make[3]: Leaving directory '/build/abyss-2.1.5/DataLayer' Making install in DataBase make[3]: Entering directory '/build/abyss-2.1.5/DataBase' make[4]: Entering directory '/build/abyss-2.1.5/DataBase' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/bin' /bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/bin' /usr/bin/install -c abyss-db-csv '/build/abyss-2.1.5/debian/tmp/usr/bin' /usr/bin/install -c abyss-db-txt '/build/abyss-2.1.5/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.1.5/DataBase' make[3]: Leaving directory '/build/abyss-2.1.5/DataBase' Making install in FMIndex make[3]: Entering directory '/build/abyss-2.1.5/FMIndex' make[4]: Entering directory '/build/abyss-2.1.5/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/abyss-2.1.5/FMIndex' make[3]: Leaving directory '/build/abyss-2.1.5/FMIndex' Making install in Assembly make[3]: Entering directory '/build/abyss-2.1.5/Assembly' make[4]: Entering directory '/build/abyss-2.1.5/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/abyss-2.1.5/Assembly' make[3]: Leaving directory '/build/abyss-2.1.5/Assembly' Making install in dialign make[3]: Entering directory '/build/abyss-2.1.5/dialign' make[4]: Entering directory '/build/abyss-2.1.5/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/abyss-2.1.5/dialign' make[3]: Leaving directory '/build/abyss-2.1.5/dialign' Making install in Align make[3]: Entering directory '/build/abyss-2.1.5/Align' make[4]: Entering directory '/build/abyss-2.1.5/Align' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/bin' /usr/bin/install -c abyss-align abyss-mergepairs '/build/abyss-2.1.5/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.1.5/Align' make[3]: Leaving directory '/build/abyss-2.1.5/Align' Making install in ABYSS make[3]: Entering directory '/build/abyss-2.1.5/ABYSS' make[4]: Entering directory '/build/abyss-2.1.5/ABYSS' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/bin' /usr/bin/install -c ABYSS '/build/abyss-2.1.5/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.1.5/ABYSS' make[3]: Leaving directory '/build/abyss-2.1.5/ABYSS' Making install in Parallel make[3]: Entering directory '/build/abyss-2.1.5/Parallel' make[4]: Entering directory '/build/abyss-2.1.5/Parallel' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/bin' /usr/bin/install -c ABYSS-P abyss-paired-dbg-mpi '/build/abyss-2.1.5/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.1.5/Parallel' make[3]: Leaving directory '/build/abyss-2.1.5/Parallel' Making install in Bloom make[3]: Entering directory '/build/abyss-2.1.5/Bloom' make[4]: Entering directory '/build/abyss-2.1.5/Bloom' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/bin' /usr/bin/install -c abyss-bloom '/build/abyss-2.1.5/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.1.5/Bloom' make[3]: Leaving directory '/build/abyss-2.1.5/Bloom' Making install in BloomDBG make[3]: Entering directory '/build/abyss-2.1.5/BloomDBG' make[4]: Entering directory '/build/abyss-2.1.5/BloomDBG' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/bin' /usr/bin/install -c abyss-bloom-dbg '/build/abyss-2.1.5/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.1.5/BloomDBG' make[3]: Leaving directory '/build/abyss-2.1.5/BloomDBG' Making install in Konnector make[3]: Entering directory '/build/abyss-2.1.5/Konnector' make[4]: Entering directory '/build/abyss-2.1.5/Konnector' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/bin' /usr/bin/install -c konnector '/build/abyss-2.1.5/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.1.5/Konnector' make[3]: Leaving directory '/build/abyss-2.1.5/Konnector' Making install in Consensus make[3]: Entering directory '/build/abyss-2.1.5/Consensus' make[4]: Entering directory '/build/abyss-2.1.5/Consensus' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/bin' /usr/bin/install -c Consensus '/build/abyss-2.1.5/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.1.5/Consensus' make[3]: Leaving directory '/build/abyss-2.1.5/Consensus' Making install in DAssembler make[3]: Entering directory '/build/abyss-2.1.5/DAssembler' make[4]: Entering directory '/build/abyss-2.1.5/DAssembler' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/bin' /usr/bin/install -c DAssembler '/build/abyss-2.1.5/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.1.5/DAssembler' make[3]: Leaving directory '/build/abyss-2.1.5/DAssembler' Making install in DistanceEst make[3]: Entering directory '/build/abyss-2.1.5/DistanceEst' make[4]: Entering directory '/build/abyss-2.1.5/DistanceEst' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/bin' /usr/bin/install -c DistanceEst DistanceEst-ssq '/build/abyss-2.1.5/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.1.5/DistanceEst' make[3]: Leaving directory '/build/abyss-2.1.5/DistanceEst' Making install in KAligner make[3]: Entering directory '/build/abyss-2.1.5/KAligner' make[4]: Entering directory '/build/abyss-2.1.5/KAligner' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/bin' /usr/bin/install -c KAligner '/build/abyss-2.1.5/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.1.5/KAligner' make[3]: Leaving directory '/build/abyss-2.1.5/KAligner' Making install in Layout make[3]: Entering directory '/build/abyss-2.1.5/Layout' make[4]: Entering directory '/build/abyss-2.1.5/Layout' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/bin' /usr/bin/install -c abyss-layout '/build/abyss-2.1.5/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.1.5/Layout' make[3]: Leaving directory '/build/abyss-2.1.5/Layout' Making install in LogKmerCount make[3]: Entering directory '/build/abyss-2.1.5/LogKmerCount' make[4]: Entering directory '/build/abyss-2.1.5/LogKmerCount' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/bin' /usr/bin/install -c logcounter '/build/abyss-2.1.5/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.1.5/LogKmerCount' make[3]: Leaving directory '/build/abyss-2.1.5/LogKmerCount' Making install in Map make[3]: Entering directory '/build/abyss-2.1.5/Map' make[4]: Entering directory '/build/abyss-2.1.5/Map' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/bin' /usr/bin/install -c abyss-index abyss-map abyss-map-ssq abyss-overlap '/build/abyss-2.1.5/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.1.5/Map' make[3]: Leaving directory '/build/abyss-2.1.5/Map' Making install in MergePaths make[3]: Entering directory '/build/abyss-2.1.5/MergePaths' make[4]: Entering directory '/build/abyss-2.1.5/MergePaths' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/bin' /usr/bin/install -c MergePaths MergeContigs PathConsensus '/build/abyss-2.1.5/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.1.5/MergePaths' make[3]: Leaving directory '/build/abyss-2.1.5/MergePaths' Making install in Misc make[3]: Entering directory '/build/abyss-2.1.5/Misc' make[4]: Entering directory '/build/abyss-2.1.5/Misc' make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/abyss-2.1.5/Misc' make[3]: Leaving directory '/build/abyss-2.1.5/Misc' Making install in Overlap make[3]: Entering directory '/build/abyss-2.1.5/Overlap' make[4]: Entering directory '/build/abyss-2.1.5/Overlap' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/bin' /usr/bin/install -c Overlap '/build/abyss-2.1.5/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.1.5/Overlap' make[3]: Leaving directory '/build/abyss-2.1.5/Overlap' Making install in PairedDBG make[3]: Entering directory '/build/abyss-2.1.5/PairedDBG' make[4]: Entering directory '/build/abyss-2.1.5/PairedDBG' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/bin' /usr/bin/install -c abyss-paired-dbg '/build/abyss-2.1.5/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.1.5/PairedDBG' make[3]: Leaving directory '/build/abyss-2.1.5/PairedDBG' Making install in ParseAligns make[3]: Entering directory '/build/abyss-2.1.5/ParseAligns' make[4]: Entering directory '/build/abyss-2.1.5/ParseAligns' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/bin' /usr/bin/install -c abyss-fixmate abyss-fixmate-ssq ParseAligns '/build/abyss-2.1.5/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.1.5/ParseAligns' make[3]: Leaving directory '/build/abyss-2.1.5/ParseAligns' Making install in PathOverlap make[3]: Entering directory '/build/abyss-2.1.5/PathOverlap' make[4]: Entering directory '/build/abyss-2.1.5/PathOverlap' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/bin' /usr/bin/install -c PathOverlap '/build/abyss-2.1.5/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.1.5/PathOverlap' make[3]: Leaving directory '/build/abyss-2.1.5/PathOverlap' Making install in PopBubbles make[3]: Entering directory '/build/abyss-2.1.5/PopBubbles' make[4]: Entering directory '/build/abyss-2.1.5/PopBubbles' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/bin' /usr/bin/install -c PopBubbles '/build/abyss-2.1.5/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.1.5/PopBubbles' make[3]: Leaving directory '/build/abyss-2.1.5/PopBubbles' Making install in Scaffold make[3]: Entering directory '/build/abyss-2.1.5/Scaffold' make[4]: Entering directory '/build/abyss-2.1.5/Scaffold' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/bin' /usr/bin/install -c abyss-scaffold abyss-junction abyss-longseqdist '/build/abyss-2.1.5/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.1.5/Scaffold' make[3]: Leaving directory '/build/abyss-2.1.5/Scaffold' Making install in SimpleGraph make[3]: Entering directory '/build/abyss-2.1.5/SimpleGraph' make[4]: Entering directory '/build/abyss-2.1.5/SimpleGraph' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/bin' /usr/bin/install -c SimpleGraph '/build/abyss-2.1.5/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.1.5/SimpleGraph' make[3]: Leaving directory '/build/abyss-2.1.5/SimpleGraph' Making install in kmerprint make[3]: Entering directory '/build/abyss-2.1.5/kmerprint' make[4]: Entering directory '/build/abyss-2.1.5/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/abyss-2.1.5/kmerprint' make[3]: Leaving directory '/build/abyss-2.1.5/kmerprint' Making install in FilterGraph make[3]: Entering directory '/build/abyss-2.1.5/FilterGraph' make[4]: Entering directory '/build/abyss-2.1.5/FilterGraph' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/bin' /usr/bin/install -c abyss-filtergraph '/build/abyss-2.1.5/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.1.5/FilterGraph' make[3]: Leaving directory '/build/abyss-2.1.5/FilterGraph' Making install in GapFiller make[3]: Entering directory '/build/abyss-2.1.5/GapFiller' make[4]: Entering directory '/build/abyss-2.1.5/GapFiller' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/bin' /usr/bin/install -c abyss-gapfill '/build/abyss-2.1.5/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.1.5/GapFiller' make[3]: Leaving directory '/build/abyss-2.1.5/GapFiller' Making install in Sealer make[3]: Entering directory '/build/abyss-2.1.5/Sealer' make[4]: Entering directory '/build/abyss-2.1.5/Sealer' /bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/bin' /usr/bin/install -c abyss-sealer '/build/abyss-2.1.5/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.1.5/Sealer' make[3]: Leaving directory '/build/abyss-2.1.5/Sealer' Making install in AdjList make[3]: Entering directory '/build/abyss-2.1.5/AdjList' make[4]: Entering directory '/build/abyss-2.1.5/AdjList' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/bin' /usr/bin/install -c AdjList '/build/abyss-2.1.5/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.1.5/AdjList' make[3]: Leaving directory '/build/abyss-2.1.5/AdjList' Making install in lib/bloomfilter make[3]: Entering directory '/build/abyss-2.1.5/lib/bloomfilter' make[4]: Entering directory '/build/abyss-2.1.5/lib/bloomfilter' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/abyss-2.1.5/lib/bloomfilter' make[3]: Leaving directory '/build/abyss-2.1.5/lib/bloomfilter' Making install in lib/nthash make[3]: Entering directory '/build/abyss-2.1.5/lib/nthash' make[4]: Entering directory '/build/abyss-2.1.5/lib/nthash' 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/abyss-2.1.5/lib/nthash' make[3]: Leaving directory '/build/abyss-2.1.5/lib/nthash' Making install in lib/gtest-1.7.0 make[3]: Entering directory '/build/abyss-2.1.5/lib/gtest-1.7.0' make[4]: Entering directory '/build/abyss-2.1.5/lib/gtest-1.7.0' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/abyss-2.1.5/lib/gtest-1.7.0' make[3]: Leaving directory '/build/abyss-2.1.5/lib/gtest-1.7.0' Making install in Unittest make[3]: Entering directory '/build/abyss-2.1.5/Unittest' make[4]: Entering directory '/build/abyss-2.1.5/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/abyss-2.1.5/Unittest' make[3]: Leaving directory '/build/abyss-2.1.5/Unittest' make[3]: Entering directory '/build/abyss-2.1.5' make[4]: Entering directory '/build/abyss-2.1.5' make[4]: Nothing to be done for 'install-exec-am'. /bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/share/doc/abyss' /usr/bin/install -c -m 644 ChangeLog CITATION.bib CITATION.md COPYRIGHT LICENSE README.md '/build/abyss-2.1.5/debian/tmp/usr/share/doc/abyss' make[4]: Leaving directory '/build/abyss-2.1.5' make[3]: Leaving directory '/build/abyss-2.1.5' make[2]: Leaving directory '/build/abyss-2.1.5' 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/abyss-2.1.5' debian/rules override_dh_install make[1]: Entering directory '/build/abyss-2.1.5' 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/abyss-2.1.5' dh_installdocs dh_installchangelogs dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz dh_strip dh_makeshlibs dh_shlibdeps dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'abyss' in '../abyss_2.1.5-7_arm64.deb'. dpkg-deb: building package 'abyss-dbgsym' in '../abyss-dbgsym_2.1.5-7_arm64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../abyss_2.1.5-7_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) 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/2361 and its subdirectories I: Current time: Sun Aug 30 13:18:46 -12 2020 I: pbuilder-time-stamp: 1598836726