I: pbuilder: network access will be disabled during build I: Current time: Fri Aug 21 13:06:21 -12 2020 I: pbuilder-time-stamp: 1598058381 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 '/root/.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/29195/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='armhf' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3' DISTRIBUTION='' HOME='/root' HOST_ARCH='armhf' IFS=' ' INVOCATION_ID='722a251350084353bf03dccb47aba17f' 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='29195' 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.60vk7OTpIf/pbuilderrc_gBW6 --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.60vk7OTpIf/b1 --logfile b1/build.log abyss_2.1.5-7.dsc' SUDO_GID='114' SUDO_UID='109' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://10.0.0.15:8000/' I: uname -a Linux odu3a 4.19.0-10-armmp #1 SMP Debian 4.19.132-1 (2020-07-24) armv7l GNU/Linux I: ls -l /bin total 3328 -rwxr-xr-x 1 root root 767656 Apr 17 2019 bash -rwxr-xr-x 3 root root 26052 Jul 10 2019 bunzip2 -rwxr-xr-x 3 root root 26052 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 26052 Jul 10 2019 bzip2 -rwxr-xr-x 1 root root 9636 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 22432 Feb 28 2019 cat -rwxr-xr-x 1 root root 38868 Feb 28 2019 chgrp -rwxr-xr-x 1 root root 38836 Feb 28 2019 chmod -rwxr-xr-x 1 root root 42972 Feb 28 2019 chown -rwxr-xr-x 1 root root 88376 Feb 28 2019 cp -rwxr-xr-x 1 root root 75516 Jan 17 2019 dash -rwxr-xr-x 1 root root 71648 Feb 28 2019 date -rwxr-xr-x 1 root root 51212 Feb 28 2019 dd -rwxr-xr-x 1 root root 55672 Feb 28 2019 df -rwxr-xr-x 1 root root 88444 Feb 28 2019 dir -rwxr-xr-x 1 root root 54872 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 22364 Feb 28 2019 echo -rwxr-xr-x 1 root root 28 Jan 7 2019 egrep -rwxr-xr-x 1 root root 18260 Feb 28 2019 false -rwxr-xr-x 1 root root 28 Jan 7 2019 fgrep -rwxr-xr-x 1 root root 47356 Jan 9 2019 findmnt -rwsr-xr-x 1 root root 21980 Apr 22 07:38 fusermount -rwxr-xr-x 1 root root 124508 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 64232 Jan 5 2019 gzip -rwxr-xr-x 1 root root 13784 Sep 26 2018 hostname -rwxr-xr-x 1 root root 43044 Feb 28 2019 ln -rwxr-xr-x 1 root root 34932 Jul 26 2018 login -rwxr-xr-x 1 root root 88444 Feb 28 2019 ls -rwxr-xr-x 1 root root 67036 Jan 9 2019 lsblk -rwxr-xr-x 1 root root 47168 Feb 28 2019 mkdir -rwxr-xr-x 1 root root 43040 Feb 28 2019 mknod -rwxr-xr-x 1 root root 26552 Feb 28 2019 mktemp -rwxr-xr-x 1 root root 26024 Jan 9 2019 more -rwsr-xr-x 1 root root 34268 Jan 9 2019 mount -rwxr-xr-x 1 root root 9688 Jan 9 2019 mountpoint -rwxr-xr-x 1 root root 84284 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 22416 Feb 28 2019 pwd lrwxrwxrwx 1 root root 4 Apr 17 2019 rbash -> bash -rwxr-xr-x 1 root root 26504 Feb 28 2019 readlink -rwxr-xr-x 1 root root 42968 Feb 28 2019 rm -rwxr-xr-x 1 root root 26496 Feb 28 2019 rmdir -rwxr-xr-x 1 root root 14136 Jan 21 2019 run-parts -rwxr-xr-x 1 root root 76012 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Aug 18 20:27 sh -> dash -rwxr-xr-x 1 root root 22384 Feb 28 2019 sleep -rwxr-xr-x 1 root root 51124 Feb 28 2019 stty -rwsr-xr-x 1 root root 42472 Jan 9 2019 su -rwxr-xr-x 1 root root 22392 Feb 28 2019 sync -rwxr-xr-x 1 root root 283324 Apr 23 2019 tar -rwxr-xr-x 1 root root 9808 Jan 21 2019 tempfile -rwxr-xr-x 1 root root 63464 Feb 28 2019 touch -rwxr-xr-x 1 root root 18260 Feb 28 2019 true -rwxr-xr-x 1 root root 9636 Apr 22 07:38 ulockmgr_server -rwsr-xr-x 1 root root 21976 Jan 9 2019 umount -rwxr-xr-x 1 root root 22380 Feb 28 2019 uname -rwxr-xr-x 2 root root 2345 Jan 5 2019 uncompress -rwxr-xr-x 1 root root 88444 Feb 28 2019 vdir -rwxr-xr-x 1 root root 21980 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/29195/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: armhf 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 ... 18932 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} 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, 103 newly installed, 0 to remove and 0 not upgraded. Need to get 45.1 MB of archives. After unpacking 276 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian buster/main armhf libbsd0 armhf 0.9.1-2 [103 kB] Get: 2 http://deb.debian.org/debian buster/main armhf bsdmainutils armhf 11.1.2+b1 [186 kB] Get: 3 http://deb.debian.org/debian buster/main armhf libuchardet0 armhf 0.0.6-3 [62.2 kB] Get: 4 http://deb.debian.org/debian buster/main armhf groff-base armhf 1.22.4-3 [828 kB] Get: 5 http://deb.debian.org/debian buster/main armhf libpipeline1 armhf 1.5.1-2 [26.8 kB] Get: 6 http://deb.debian.org/debian buster/main armhf man-db armhf 2.8.5-2 [1240 kB] Get: 7 http://deb.debian.org/debian buster/main armhf libpython2.7-minimal armhf 2.7.16-2+deb10u1 [395 kB] Get: 8 http://deb.debian.org/debian buster/main armhf python2.7-minimal armhf 2.7.16-2+deb10u1 [1171 kB] Get: 9 http://deb.debian.org/debian buster/main armhf python2-minimal armhf 2.7.16-1 [41.4 kB] Get: 10 http://deb.debian.org/debian buster/main armhf python-minimal armhf 2.7.16-1 [21.0 kB] Get: 11 http://deb.debian.org/debian buster/main armhf libssl1.1 armhf 1.1.1d-0+deb10u3 [1299 kB] Get: 12 http://deb.debian.org/debian buster/main armhf mime-support all 3.62 [37.2 kB] Get: 13 http://deb.debian.org/debian buster/main armhf libexpat1 armhf 2.2.6-2+deb10u1 [78.0 kB] Get: 14 http://deb.debian.org/debian buster/main armhf readline-common all 7.0-5 [70.6 kB] Get: 15 http://deb.debian.org/debian buster/main armhf libreadline7 armhf 7.0-5 [131 kB] Get: 16 http://deb.debian.org/debian buster/main armhf libpython2.7-stdlib armhf 2.7.16-2+deb10u1 [1837 kB] Get: 17 http://deb.debian.org/debian buster/main armhf python2.7 armhf 2.7.16-2+deb10u1 [305 kB] Get: 18 http://deb.debian.org/debian buster/main armhf libpython2-stdlib armhf 2.7.16-1 [20.8 kB] Get: 19 http://deb.debian.org/debian buster/main armhf libpython-stdlib armhf 2.7.16-1 [20.8 kB] Get: 20 http://deb.debian.org/debian buster/main armhf python2 armhf 2.7.16-1 [41.6 kB] Get: 21 http://deb.debian.org/debian buster/main armhf python armhf 2.7.16-1 [22.8 kB] Get: 22 http://deb.debian.org/debian buster/main armhf liblocale-gettext-perl armhf 1.07-3+b4 [18.4 kB] Get: 23 http://deb.debian.org/debian buster/main armhf sensible-utils all 0.0.12 [15.8 kB] Get: 24 http://deb.debian.org/debian buster/main armhf libmagic-mgc armhf 1:5.35-4+deb10u1 [242 kB] Get: 25 http://deb.debian.org/debian buster/main armhf libmagic1 armhf 1:5.35-4+deb10u1 [110 kB] Get: 26 http://deb.debian.org/debian buster/main armhf file armhf 1:5.35-4+deb10u1 [65.5 kB] Get: 27 http://deb.debian.org/debian buster/main armhf gettext-base armhf 0.19.8.1-9 [118 kB] Get: 28 http://deb.debian.org/debian buster/main armhf libedit2 armhf 3.1-20181209-1 [79.5 kB] Get: 29 http://deb.debian.org/debian buster/main armhf libkeyutils1 armhf 1.6-6 [13.9 kB] Get: 30 http://deb.debian.org/debian buster/main armhf libkrb5support0 armhf 1.17-3 [62.3 kB] Get: 31 http://deb.debian.org/debian buster/main armhf libk5crypto3 armhf 1.17-3 [119 kB] Get: 32 http://deb.debian.org/debian buster/main armhf libkrb5-3 armhf 1.17-3 [323 kB] Get: 33 http://deb.debian.org/debian buster/main armhf libgssapi-krb5-2 armhf 1.17-3 [137 kB] Get: 34 http://deb.debian.org/debian buster/main armhf openssh-client armhf 1:7.9p1-10+deb10u2 [704 kB] Get: 35 http://deb.debian.org/debian buster/main armhf libsigsegv2 armhf 2.12-2 [32.1 kB] Get: 36 http://deb.debian.org/debian buster/main armhf m4 armhf 1.4.18-2 [190 kB] Get: 37 http://deb.debian.org/debian buster/main armhf autoconf all 2.69-11 [341 kB] Get: 38 http://deb.debian.org/debian buster/main armhf autotools-dev all 20180224.1 [77.0 kB] Get: 39 http://deb.debian.org/debian buster/main armhf automake all 1:1.16.1-4 [771 kB] Get: 40 http://deb.debian.org/debian buster/main armhf autopoint all 0.19.8.1-9 [434 kB] Get: 41 http://deb.debian.org/debian buster/main armhf libtool all 2.4.6-9 [547 kB] Get: 42 http://deb.debian.org/debian buster/main armhf dh-autoreconf all 19 [16.9 kB] Get: 43 http://deb.debian.org/debian buster/main armhf libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 44 http://deb.debian.org/debian buster/main armhf libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 45 http://deb.debian.org/debian buster/main armhf dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 46 http://deb.debian.org/debian buster/main armhf libelf1 armhf 0.176-1.1 [158 kB] Get: 47 http://deb.debian.org/debian buster/main armhf dwz armhf 0.12-3 [72.0 kB] Get: 48 http://deb.debian.org/debian buster/main armhf libglib2.0-0 armhf 2.58.3-2+deb10u2 [1101 kB] Get: 49 http://deb.debian.org/debian buster/main armhf libicu63 armhf 63.1-6+deb10u1 [8005 kB] Get: 50 http://deb.debian.org/debian buster/main armhf libxml2 armhf 2.9.4+dfsg1-7+b3 [595 kB] Get: 51 http://deb.debian.org/debian buster/main armhf libcroco3 armhf 0.6.12-3 [133 kB] Get: 52 http://deb.debian.org/debian buster/main armhf libncurses6 armhf 6.1+20181013-2+deb10u2 [79.8 kB] Get: 53 http://deb.debian.org/debian buster/main armhf gettext armhf 0.19.8.1-9 [1242 kB] Get: 54 http://deb.debian.org/debian buster/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 55 http://deb.debian.org/debian buster/main armhf po-debconf all 1.0.21 [248 kB] Get: 56 http://deb.debian.org/debian buster/main armhf debhelper all 12.1.1 [1016 kB] Get: 57 http://deb.debian.org/debian buster/main armhf googletest armhf 1.8.1-3 [903 kB] Get: 58 http://deb.debian.org/debian buster/main armhf help2man armhf 1.47.8 [176 kB] Get: 59 http://deb.debian.org/debian buster/main armhf libnl-3-200 armhf 3.4.0-1 [55.6 kB] Get: 60 http://deb.debian.org/debian buster/main armhf libnl-route-3-200 armhf 3.4.0-1 [136 kB] Get: 61 http://deb.debian.org/debian buster/main armhf libibverbs1 armhf 22.1-1 [44.1 kB] Get: 62 http://deb.debian.org/debian buster/main armhf ibverbs-providers armhf 22.1-1 [20.2 kB] Get: 63 http://deb.debian.org/debian buster/main armhf libboost-chrono1.67.0 armhf 1.67.0-13+deb10u1 [231 kB] Get: 64 http://deb.debian.org/debian buster/main armhf libboost1.67-dev armhf 1.67.0-13+deb10u1 [8388 kB] Get: 65 http://deb.debian.org/debian buster/main armhf libboost-regex1.67.0 armhf 1.67.0-13+deb10u1 [438 kB] Get: 66 http://deb.debian.org/debian buster/main armhf libboost-graph1.67.0 armhf 1.67.0-13+deb10u1 [299 kB] Get: 67 http://deb.debian.org/debian buster/main armhf libboost-serialization1.67.0 armhf 1.67.0-13+deb10u1 [303 kB] Get: 68 http://deb.debian.org/debian buster/main armhf libboost-serialization1.67-dev armhf 1.67.0-13+deb10u1 [370 kB] Get: 69 http://deb.debian.org/debian buster/main armhf libboost-timer1.67.0 armhf 1.67.0-13+deb10u1 [229 kB] Get: 70 http://deb.debian.org/debian buster/main armhf libboost-test1.67.0 armhf 1.67.0-13+deb10u1 [426 kB] Get: 71 http://deb.debian.org/debian buster/main armhf libboost-test1.67-dev armhf 1.67.0-13+deb10u1 [513 kB] Get: 72 http://deb.debian.org/debian buster/main armhf libboost-graph1.67-dev armhf 1.67.0-13+deb10u1 [325 kB] Get: 73 http://deb.debian.org/debian buster/main armhf libboost-graph-dev armhf 1.67.0.1 [3752 B] Get: 74 http://deb.debian.org/debian buster/main armhf libevent-2.1-6 armhf 2.1.8-stable-4 [159 kB] Get: 75 http://deb.debian.org/debian buster/main armhf libevent-core-2.1-6 armhf 2.1.8-stable-4 [118 kB] Get: 76 http://deb.debian.org/debian buster/main armhf libevent-pthreads-2.1-6 armhf 2.1.8-stable-4 [47.6 kB] Get: 77 http://deb.debian.org/debian buster/main armhf libgfortran5 armhf 8.3.0-6 [213 kB] Get: 78 http://deb.debian.org/debian buster/main armhf libgtest-dev armhf 1.8.1-3 [214 kB] Get: 79 http://deb.debian.org/debian buster/main armhf libhtml-tagset-perl all 3.20-3 [12.7 kB] Get: 80 http://deb.debian.org/debian buster/main armhf liburi-perl all 1.76-1 [89.9 kB] Get: 81 http://deb.debian.org/debian buster/main armhf libhtml-parser-perl armhf 3.72-3+b3 [102 kB] Get: 82 http://deb.debian.org/debian buster/main armhf libltdl7 armhf 2.4.6-9 [387 kB] Get: 83 http://deb.debian.org/debian buster/main armhf libhwloc5 armhf 1.11.12-3 [87.6 kB] Get: 84 http://deb.debian.org/debian buster/main armhf libltdl-dev armhf 2.4.6-9 [160 kB] Get: 85 http://deb.debian.org/debian buster/main armhf libhwloc-dev armhf 1.11.12-3 [153 kB] Get: 86 http://deb.debian.org/debian buster/main armhf libpciaccess0 armhf 0.14-1 [51.0 kB] Get: 87 http://deb.debian.org/debian buster/main armhf ocl-icd-libopencl1 armhf 2.2.12-2 [35.6 kB] Get: 88 http://deb.debian.org/debian buster/main armhf libhwloc-plugins armhf 1.11.12-3 [15.7 kB] Get: 89 http://deb.debian.org/debian buster/main armhf libnl-3-dev armhf 3.4.0-1 [96.9 kB] Get: 90 http://deb.debian.org/debian buster/main armhf libnl-route-3-dev armhf 3.4.0-1 [162 kB] Get: 91 http://deb.debian.org/debian buster/main armhf libibverbs-dev armhf 22.1-1 [151 kB] Get: 92 http://deb.debian.org/debian buster/main armhf libpmix2 armhf 3.1.2-3 [449 kB] Get: 93 http://deb.debian.org/debian buster/main armhf libopenmpi3 armhf 3.1.3-11 [1890 kB] Get: 94 http://deb.debian.org/debian buster/main armhf openmpi-common all 3.1.3-11 [165 kB] Get: 95 http://deb.debian.org/debian buster/main armhf openmpi-bin armhf 3.1.3-11 [198 kB] Get: 96 http://deb.debian.org/debian buster/main armhf libopenmpi-dev armhf 3.1.3-11 [964 kB] Get: 97 http://deb.debian.org/debian buster/main armhf libsparsehash-dev all 2.0.2-1 [76.9 kB] Get: 98 http://deb.debian.org/debian buster/main armhf libsqlite3-dev armhf 3.27.2-3 [722 kB] Get: 99 http://deb.debian.org/debian buster/main armhf libtext-markdown-perl all 1.000031-2 [34.4 kB] Get: 100 http://deb.debian.org/debian buster/main armhf libtext-multimarkdown-perl all 1.000035-1 [29.4 kB] Get: 101 http://deb.debian.org/debian buster/main armhf pkg-config armhf 0.29-6 [60.7 kB] Get: 102 http://deb.debian.org/debian buster/main armhf python-pkg-resources all 40.8.0-1 [182 kB] Get: 103 http://deb.debian.org/debian buster/main armhf python-markdown all 3.0.1-3 [60.6 kB] Fetched 45.1 MB in 8s (5654 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:armhf. (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 ... 18932 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.9.1-2_armhf.deb ... Unpacking libbsd0:armhf (0.9.1-2) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2+b1_armhf.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:armhf. Preparing to unpack .../02-libuchardet0_0.0.6-3_armhf.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 ... 20397 files and directories currently installed.) Preparing to unpack .../python2_2.7.16-1_armhf.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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Unpacking libboost-timer1.67.0:armhf (1.67.0-13+deb10u1) ... Selecting previously unselected package libboost-test1.67.0:armhf. Preparing to unpack .../49-libboost-test1.67.0_1.67.0-13+deb10u1_armhf.deb ... Unpacking libboost-test1.67.0:armhf (1.67.0-13+deb10u1) ... Selecting previously unselected package libboost-test1.67-dev:armhf. Preparing to unpack .../50-libboost-test1.67-dev_1.67.0-13+deb10u1_armhf.deb ... Unpacking libboost-test1.67-dev:armhf (1.67.0-13+deb10u1) ... Selecting previously unselected package libboost-graph1.67-dev:armhf. Preparing to unpack .../51-libboost-graph1.67-dev_1.67.0-13+deb10u1_armhf.deb ... Unpacking libboost-graph1.67-dev:armhf (1.67.0-13+deb10u1) ... Selecting previously unselected package libboost-graph-dev:armhf. Preparing to unpack .../52-libboost-graph-dev_1.67.0.1_armhf.deb ... Unpacking libboost-graph-dev:armhf (1.67.0.1) ... Selecting previously unselected package libevent-2.1-6:armhf. Preparing to unpack .../53-libevent-2.1-6_2.1.8-stable-4_armhf.deb ... Unpacking libevent-2.1-6:armhf (2.1.8-stable-4) ... Selecting previously unselected package libevent-core-2.1-6:armhf. Preparing to unpack .../54-libevent-core-2.1-6_2.1.8-stable-4_armhf.deb ... Unpacking libevent-core-2.1-6:armhf (2.1.8-stable-4) ... Selecting previously unselected package libevent-pthreads-2.1-6:armhf. Preparing to unpack .../55-libevent-pthreads-2.1-6_2.1.8-stable-4_armhf.deb ... Unpacking libevent-pthreads-2.1-6:armhf (2.1.8-stable-4) ... Selecting previously unselected package libgfortran5:armhf. Preparing to unpack .../56-libgfortran5_8.3.0-6_armhf.deb ... Unpacking libgfortran5:armhf (8.3.0-6) ... Selecting previously unselected package libgtest-dev:armhf. Preparing to unpack .../57-libgtest-dev_1.8.1-3_armhf.deb ... Unpacking libgtest-dev:armhf (1.8.1-3) ... Selecting previously unselected package libhtml-tagset-perl. Preparing to unpack .../58-libhtml-tagset-perl_3.20-3_all.deb ... 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Setting up libboost-test1.67-dev:armhf (1.67.0-13+deb10u1) ... Setting up libnl-route-3-200:armhf (3.4.0-1) ... Setting up libpython2.7-stdlib:armhf (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:armhf (1.17-3) ... Setting up libcroco3:armhf (0.6.12-3) ... Setting up autoconf (2.69-11) ... Setting up dwz (0.12-3) ... Setting up libnl-3-dev:armhf (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:armhf (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:armhf (1.67.0.1) ... Setting up libibverbs1:armhf (22.1-1) ... Setting up gettext (0.19.8.1-9) ... Setting up python2.7 (2.7.16-2+deb10u1) ... Setting up libpmix2:armhf (3.1.2-3) ... Setting up ibverbs-providers:armhf (22.1-1) ... Setting up libpython2-stdlib:armhf (2.7.16-1) ... Setting up openssh-client (1:7.9p1-10+deb10u2) ... Setting up libopenmpi3:armhf (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:armhf (3.4.0-1) ... Setting up libltdl-dev:armhf (2.4.6-9) ... Setting up libpython-stdlib:armhf (2.7.16-1) ... Setting up libhwloc-dev:armhf (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:armhf (22.1-1) ... Setting up libopenmpi-dev:armhf (3.1.3-11) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/openmpi/include to provide /usr/include/arm-linux-gnueabihf/mpi (mpi-arm-linux-gnueabihf) 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 armhf 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/arm-linux-gnueabihf/openmpi ./configure --build=arm-linux-gnueabihf --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-silent-rules --libdir=\${prefix}/lib/arm-linux-gnueabihf --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-mpi=/usr/lib/arm-linux-gnueabihf/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... arm-unknown-linux-gnueabihf checking host system type... arm-unknown-linux-gnueabihf 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 -j3 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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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 In file included from /usr/include/c++/8/vector:69, from VectorUtil.h:4, from Histogram.h:6, from Histogram.cpp:1: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long unsigned int&}; _Tp = long long unsigned int; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from VectorUtil.h:4, from Histogram.h:6, from Histogram.cpp:1: /usr/include/c++/8/bits/stl_vector.h: In member function 'Histogram::Bins Histogram::bin(unsigned int) const': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-2.1.5 -isystem/usr/lib/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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 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/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-db-csv abyss_db_csv-DB.o abyss_db_csv-db-csv.o -lsqlite3 -ldl -lm rm -f libdb.a ar cru libdb.a libdb_a-DB.o ../Common/libcommon.a ar: `u' modifier ignored since `D' is the default (see `U') ranlib libdb.a make[4]: Leaving directory '/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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 In file included from /usr/include/c++/8/vector:69, from bit_array.h:24, from BitArrays.h:4, from FMIndex.h:5, from DAWG.h:5, from count.cc:2: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {std::pair, std::pair, std::pair > >, std::pair::out_edge_iterator, boost::graph_traits::out_edge_iterator> > >}; _Tp = std::pair, std::pair, std::pair > >, std::pair::out_edge_iterator, boost::graph_traits::out_edge_iterator> > >; _Alloc = std::allocator, std::pair, std::pair > >, std::pair::out_edge_iterator, boost::graph_traits::out_edge_iterator> > > >]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector, std::pair, std::pair > >, std::pair::out_edge_iterator, boost::graph_traits::out_edge_iterator> > >, std::allocator, std::pair, std::pair > >, std::pair::out_edge_iterator, boost::graph_traits::out_edge_iterator> > > > >::iterator' {aka '__gnu_cxx::__normal_iterator, std::pair, std::pair > >, std::pair::out_edge_iterator, boost::graph_traits::out_edge_iterator> > >*, std::vector, std::pair, std::pair > >, std::pair::out_edge_iterator, boost::graph_traits::out_edge_iterator> > >, std::allocator, std::pair, std::pair > >, std::pair::out_edge_iterator, boost::graph_traits::out_edge_iterator> > > > > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::pair, std::pair, std::pair > >, std::pair::out_edge_iterator, boost::graph_traits::out_edge_iterator> > >}; _Tp = std::pair, std::pair, std::pair > >, std::pair::out_edge_iterator, boost::graph_traits::out_edge_iterator> > >; _Alloc = std::allocator, std::pair, std::pair > >, std::pair::out_edge_iterator, boost::graph_traits::out_edge_iterator> > > >]': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator, std::pair, std::pair > >, std::pair::out_edge_iterator, boost::graph_traits::out_edge_iterator> > >*, std::vector, std::pair, std::pair > >, std::pair::out_edge_iterator, boost::graph_traits::out_edge_iterator> > >, std::allocator, std::pair, std::pair > >, std::pair::out_edge_iterator, boost::graph_traits::out_edge_iterator> > > > > >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from bit_array.h:24, from BitArrays.h:4, from FMIndex.h:5, from DAWG.h:5, from abyss-dawg.cc:2: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {std::pair, std::pair, std::pair > >, std::pair::out_edge_iterator, boost::graph_traits::out_edge_iterator> > >}; _Tp = std::pair, std::pair, std::pair > >, std::pair::out_edge_iterator, boost::graph_traits::out_edge_iterator> > >; _Alloc = std::allocator, std::pair, std::pair > >, std::pair::out_edge_iterator, boost::graph_traits::out_edge_iterator> > > >]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector, std::pair, std::pair > >, std::pair::out_edge_iterator, boost::graph_traits::out_edge_iterator> > >, std::allocator, std::pair, std::pair > >, std::pair::out_edge_iterator, boost::graph_traits::out_edge_iterator> > > > >::iterator' {aka '__gnu_cxx::__normal_iterator, std::pair, std::pair > >, std::pair::out_edge_iterator, boost::graph_traits::out_edge_iterator> > >*, std::vector, std::pair, std::pair > >, std::pair::out_edge_iterator, boost::graph_traits::out_edge_iterator> > >, std::allocator, std::pair, std::pair > >, std::pair::out_edge_iterator, boost::graph_traits::out_edge_iterator> > > > > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::pair, std::pair, std::pair > >, std::pair::out_edge_iterator, boost::graph_traits::out_edge_iterator> > >}; _Tp = std::pair, std::pair, std::pair > >, std::pair::out_edge_iterator, boost::graph_traits::out_edge_iterator> > >; _Alloc = std::allocator, std::pair, std::pair > >, std::pair::out_edge_iterator, boost::graph_traits::out_edge_iterator> > > >]': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator, std::pair, std::pair > >, std::pair::out_edge_iterator, boost::graph_traits::out_edge_iterator> > >*, std::vector, std::pair, std::pair > >, std::pair::out_edge_iterator, boost::graph_traits::out_edge_iterator> > >, std::allocator, std::pair, std::pair > >, std::pair::out_edge_iterator, boost::graph_traits::out_edge_iterator> > > > > >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = wat_array::BitArray; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from bit_array.h:24, from BitArrays.h:4, from FMIndex.h:5, from DAWG.h:5, from abyss-dawg.cc:2: /usr/include/c++/8/bits/stl_vector.h: In member function 'void FMIndex::assign(It, It) [with It = __gnu_cxx::__normal_iterator >]': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = wat_array::BitArray; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/map:60, from abyss-dawg.cc:14: /usr/include/c++/8/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple&>, std::tuple<>}; _Key = std::pair; _Val = std::pair, boost::default_color_type>; _KeyOfValue = std::_Select1st, boost::default_color_type> >; _Compare = std::less >; _Alloc = std::allocator, boost::default_color_type> >]': /usr/include/c++/8/bits/stl_tree.h:2411:7: note: parameter passing for argument of type 'std::_Rb_tree, std::pair, boost::default_color_type>, std::_Select1st, boost::default_color_type> >, std::less >, std::allocator, boost::default_color_type> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator, boost::default_color_type> >'} changed in GCC 7.1 _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from abyss-dawg.cc:5: /usr/include/boost/graph/depth_first_search.hpp: In function 'void boost::detail::depth_first_visit_impl(const IncidenceGraph&, typename boost::graph_traits::vertex_descriptor, DFSVisitor&, ColorMap, TerminatorFunc) [with IncidenceGraph = FMIndex; DFSVisitor = DAWGVisitor; ColorMap = boost::associative_property_map, boost::default_color_type> >; TerminatorFunc = boost::detail::nontruth2]': /usr/include/boost/graph/depth_first_search.hpp:109:10: note: parameter passing for argument of type 'boost::associative_property_map, boost::default_color_type> >' changed in GCC 7.1 void depth_first_visit_impl ^~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/map:61, from abyss-dawg.cc:14: /usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree, std::pair, boost::default_color_type>, std::_Select1st, boost::default_color_type> >, std::less >, std::allocator, boost::default_color_type> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator, boost::default_color_type> >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree, std::pair, boost::default_color_type>, std::_Select1st, boost::default_color_type> >, std::less >, std::allocator, boost::default_color_type> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator, boost::default_color_type> >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree, std::pair, boost::default_color_type>, std::_Select1st, boost::default_color_type> >, std::less >, std::allocator, boost::default_color_type> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator, boost::default_color_type> >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree, std::pair, boost::default_color_type>, std::_Select1st, boost::default_color_type> >, std::less >, std::allocator, boost::default_color_type> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator, boost::default_color_type> >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, In file included from /usr/include/c++/8/vector:64, from bit_array.h:24, from BitArrays.h:4, from FMIndex.h:5, from DAWG.h:5, from count.cc:2: /usr/include/c++/8/bits/stl_vector.h: In member function 'void FMIndex::assign(It, It) [with It = __gnu_cxx::__normal_iterator >]': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ In file included from abyss-dawg.cc:5: /usr/include/boost/graph/depth_first_search.hpp: In function 'int main(int, char**)': /usr/include/boost/graph/depth_first_search.hpp:354:35: note: parameter passing for argument of type 'boost::associative_property_map, boost::default_color_type> >' changed in GCC 7.1 detail::depth_first_visit_impl(g, u, vis, color, detail::nontruth2()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-dawg abyss_dawg-abyss-dawg.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/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-count abyss_count-count.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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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 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, ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I.. -I/build/abyss-2.1.5 -isystem/usr/lib/arm-linux-gnueabihf/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 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); ^~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I.. -I/build/abyss-2.1.5 -isystem/usr/lib/arm-linux-gnueabihf/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 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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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 gcc -DHAVE_CONFIG_H -I. -I.. -I/build/abyss-2.1.5 -isystem/usr/lib/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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 In file included from /usr/include/c++/8/map:60, from ../Assembly/BranchGroup.h:7, from NetworkSequenceCollection.h:7, from NetworkSequenceCollection.cpp:1: /usr/include/c++/8/bits/stl_tree.h: In member function 'void std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_erase_aux(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator) [with _Key = long long unsigned int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': /usr/include/c++/8/bits/stl_tree.h:2486:5: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_tree.h: In member function 'bool NetworkSequenceCollection::processBranchesDiscoverBubbles()': /usr/include/c++/8/bits/stl_tree.h:1141:2: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 _M_erase_aux(__position); ^~~~~~~~~~~~ /usr/include/c++/8/bits/stl_tree.h: In member function 'std::pair NetworkSequenceCollection::processBranchesAssembly(FastaWriter*, unsigned int)': /usr/include/c++/8/bits/stl_tree.h:1141:2: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 _M_erase_aux(__position); ^~~~~~~~~~~~ /usr/include/c++/8/bits/stl_tree.h: In member function 'size_t NetworkSequenceCollection::processBranchesTrim()': /usr/include/c++/8/bits/stl_tree.h:1141:2: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 _M_erase_aux(__position); ^~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I.. -I.. -DPAIRED_DBG -I/build/abyss-2.1.5 -isystem/usr/lib/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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 In file included from /usr/include/c++/8/map:60, from ../Assembly/BranchGroup.h:7, from NetworkSequenceCollection.h:7, from NetworkSequenceCollection.cpp:1: /usr/include/c++/8/bits/stl_tree.h: In member function 'void std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_erase_aux(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator) [with _Key = long long unsigned int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': /usr/include/c++/8/bits/stl_tree.h:2486:5: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_tree.h: In member function 'bool NetworkSequenceCollection::processBranchesDiscoverBubbles()': /usr/include/c++/8/bits/stl_tree.h:1141:2: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 _M_erase_aux(__position); ^~~~~~~~~~~~ /usr/include/c++/8/bits/stl_tree.h: In member function 'std::pair NetworkSequenceCollection::processBranchesAssembly(FastaWriter*, unsigned int)': /usr/include/c++/8/bits/stl_tree.h:1141:2: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 _M_erase_aux(__position); ^~~~~~~~~~~~ /usr/include/c++/8/bits/stl_tree.h: In member function 'size_t NetworkSequenceCollection::processBranchesTrim()': /usr/include/c++/8/bits/stl_tree.h:1141:2: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 _M_erase_aux(__position); ^~~~~~~~~~~~ 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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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 In file included from /usr/include/c++/8/vector:69, from MLE.h:4, from MLE.cpp:1: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from MLE.h:4, from MLE.cpp:1: /usr/include/c++/8/bits/stl_vector.h: In function 'std::pair maximumLikelihoodEstimate(int, int, const Histogram&, const PMF&, unsigned int, unsigned int)': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -D SAM_SEQ_QUAL=1 -I/build/abyss-2.1.5 -isystem/usr/lib/arm-linux-gnueabihf/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 In file included from /usr/include/c++/8/vector:69, from MLE.h:4, from MLE.cpp:1: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from MLE.h:4, from MLE.cpp:1: /usr/include/c++/8/bits/stl_vector.h: In function 'std::pair maximumLikelihoodEstimate(int, int, const Histogram&, const PMF&, unsigned int, unsigned int)': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ 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/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o DistanceEst DistanceEst-DistanceEst.o DistanceEst-MLE.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../Common/libcommon.a -ldl -lm g++ -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/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o DistanceEst-ssq DistanceEst_ssq-DistanceEst.o DistanceEst_ssq-MLE.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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 index.cc: In function 'void buildFMIndex(FMIndex&, const string&)': index.cc:149:64: warning: unsigned conversion from 'long long int' to 'size_t' {aka 'unsigned int'} changes value from '9223372036854775807' to '4294967295' [-Woverflow] size_t MAX_SIZE = numeric_limits::max(); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ map.cc: In function 'void buildFMIndex(FMIndex&, const char*)': map.cc:508:64: warning: unsigned conversion from 'long long int' to 'size_t' {aka 'unsigned int'} changes value from '9223372036854775807' to '4294967295' [-Woverflow] size_t MAX_SIZE = numeric_limits::max(); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ map.cc: In function 'void buildFMIndex(FMIndex&, const char*)': map.cc:508:64: warning: unsigned conversion from 'long long int' to 'size_t' {aka 'unsigned int'} changes value from '9223372036854775807' to '4294967295' [-Woverflow] size_t MAX_SIZE = numeric_limits::max(); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ In file included from /usr/include/c++/8/vector:69, from ../DataLayer/FastaIndex.h:11, from index.cc:3: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = wat_array::BitArray; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from ../DataLayer/FastaIndex.h:11, from index.cc:3: /usr/include/c++/8/bits/stl_vector.h: In member function 'void FMIndex::assign(It, It) [with It = __gnu_cxx::__normal_iterator >]': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In member function 'void FMIndex::assignBWT(It, It) [with It = __gnu_cxx::__normal_iterator >]': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../FMIndex -I/build/abyss-2.1.5 -isystem/usr/lib/arm-linux-gnueabihf/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 In file included from /usr/include/c++/8/vector:69, from ../FMIndex/bit_array.h:24, from ../FMIndex/BitArrays.h:4, from ../FMIndex/FMIndex.h:5, from map.cc:3: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = wat_array::BitArray; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from ../FMIndex/bit_array.h:24, from ../FMIndex/BitArrays.h:4, from ../FMIndex/FMIndex.h:5, from map.cc:3: /usr/include/c++/8/bits/stl_vector.h: In member function 'void FMIndex::assign(It, It) [with It = __gnu_cxx::__normal_iterator >]': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from ../FMIndex/bit_array.h:24, from ../FMIndex/BitArrays.h:4, from ../FMIndex/FMIndex.h:5, from map.cc:3: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = wat_array::BitArray; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from ../FMIndex/bit_array.h:24, from ../FMIndex/BitArrays.h:4, from ../FMIndex/FMIndex.h:5, from map.cc:3: /usr/include/c++/8/bits/stl_vector.h: In member function 'void FMIndex::assign(It, It) [with It = __gnu_cxx::__normal_iterator >]': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ overlap.cc: In function 'void buildFMIndex(FMIndex&, const char*)': overlap.cc:296:64: warning: unsigned conversion from 'long long int' to 'size_t' {aka 'unsigned int'} changes value from '9223372036854775807' to '4294967295' [-Woverflow] size_t MAX_SIZE = numeric_limits::max(); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ 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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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 In file included from /usr/include/c++/8/vector:69, from ../Common/Dictionary.h:10, from ../Common/ContigID.h:5, from ../Common/ContigNode.h:5, from ../Common/ContigProperties.h:4, from overlap.cc:10: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {FMIndex::Match}; _Tp = FMIndex::Match; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {FMIndex::Match}; _Tp = FMIndex::Match; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:63, from ../Common/Dictionary.h:10, from ../Common/ContigID.h:5, from ../Common/ContigNode.h:5, from ../Common/ContigProperties.h:4, from overlap.cc:10: /usr/include/c++/8/bits/stl_uninitialized.h: In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator; _ForwardIterator = wat_array::BitArray*; bool _TrivialValueTypes = false]': /usr/include/c++/8/bits/stl_uninitialized.h:76:9: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 __uninit_copy(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:76:9: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 In file included from /usr/include/c++/8/vector:69, from ../Common/Dictionary.h:10, from ../Common/ContigID.h:5, from ../Common/ContigNode.h:5, from ../Common/ContigProperties.h:4, from overlap.cc:10: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = wat_array::BitArray; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:63, from ../Common/Dictionary.h:10, from ../Common/ContigID.h:5, from ../Common/ContigNode.h:5, from ../Common/ContigProperties.h:4, from overlap.cc:10: /usr/include/c++/8/bits/stl_uninitialized.h:134:15: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 return std::__uninitialized_copy<__is_trivial(_ValueType1) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && __is_trivial(_ValueType2) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && __assignable>:: ~~~~~~~~~~~~~~~~~~ __uninit_copy(__first, __last, __result); ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:134:15: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 return std::__uninitialized_copy<__is_trivial(_ValueType1) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && __is_trivial(_ValueType2) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && __assignable>:: ~~~~~~~~~~~~~~~~~~ __uninit_copy(__first, __last, __result); ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from ../Common/Dictionary.h:10, from ../Common/ContigID.h:5, from ../Common/ContigNode.h:5, from ../Common/ContigProperties.h:4, from overlap.cc:10: /usr/include/c++/8/bits/stl_vector.h: In member function 'void FMIndex::assign(It, It) [with It = __gnu_cxx::__normal_iterator >]': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ 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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-longseqdist abyss_longseqdist-longseqdist.o ../Common/libcommon.a -ldl -lm In file included from /usr/include/c++/8/vector:69, from ../Common/Dictionary.h:10, from ../Common/ContigID.h:5, from ../Common/ContigNode.h:5, from ../Common/ContigProperties.h:4, from drawgraph.cc:10: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {std::pair}; _Tp = std::pair; _Alloc = std::allocator >]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/algorithm:62, from /usr/include/boost/type_traits/is_nothrow_swappable.hpp:33, from /usr/include/boost/type_traits.hpp:117, from /usr/include/boost/pending/property.hpp:13, from /usr/include/boost/graph/properties.hpp:15, from ../Graph/Properties.h:6, from ../Common/ContigNode.h:6, from ../Common/ContigProperties.h:4, from drawgraph.cc:10: /usr/include/c++/8/bits/stl_algo.h: In function 'void std::__move_median_to_first(_Iterator, _Iterator, _Iterator, _Iterator, _Compare) [with _Iterator = __gnu_cxx::__normal_iterator*, std::vector > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/8/bits/stl_algo.h:78:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 __move_median_to_first(_Iterator __result,_Iterator __a, _Iterator __b, ^~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:78:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:78:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:78:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, std::vector > >; _Compare = __gnu_cxx::__ops::_Val_less_iter]': /usr/include/c++/8/bits/stl_algo.h:1821:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 __unguarded_linear_insert(_RandomAccessIterator __last, ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, std::vector > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 __insertion_sort(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 In file included from /usr/include/c++/8/bits/stl_algo.h:61, from /usr/include/c++/8/algorithm:62, from /usr/include/boost/type_traits/is_nothrow_swappable.hpp:33, from /usr/include/boost/type_traits.hpp:117, from /usr/include/boost/pending/property.hpp:13, from /usr/include/boost/graph/properties.hpp:15, from ../Graph/Properties.h:6, from ../Common/ContigNode.h:6, from ../Common/ContigProperties.h:4, from drawgraph.cc:10: /usr/include/c++/8/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, std::vector > >; _Distance = int; _Tp = std::pair; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, ^~~~~~~~~~~~~ In file included from /usr/include/c++/8/algorithm:62, from /usr/include/boost/type_traits/is_nothrow_swappable.hpp:33, from /usr/include/boost/type_traits.hpp:117, from /usr/include/boost/pending/property.hpp:13, from /usr/include/boost/graph/properties.hpp:15, from ../Graph/Properties.h:6, from ../Common/ContigNode.h:6, from ../Common/ContigProperties.h:4, from drawgraph.cc:10: /usr/include/c++/8/bits/stl_algo.h: In function 'void std::__heap_select(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, std::vector > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/8/bits/stl_algo.h:1668:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 __heap_select(_RandomAccessIterator __first, ^~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1668:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:1668:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:1668:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, std::vector > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 __introsort_loop(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:1921:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 std::__move_median_to_first(__first, __first + 1, __mid, __last - 1, ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1921:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 std::__introsort_loop(__cut, __last, __depth_limit, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1933:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 std::__heap_select(__first, __middle, __last, __comp); ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from ../Common/Dictionary.h:10, from ../Common/ContigID.h:5, from ../Common/ContigNode.h:5, from ../Common/ContigProperties.h:4, from drawgraph.cc:10: /usr/include/c++/8/bits/vector.tcc: In function 'int main(int, char**)': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/algorithm:62, from /usr/include/boost/type_traits/is_nothrow_swappable.hpp:33, from /usr/include/boost/type_traits.hpp:117, from /usr/include/boost/pending/property.hpp:13, from /usr/include/boost/graph/properties.hpp:15, from ../Graph/Properties.h:6, from ../Common/ContigNode.h:6, from ../Common/ContigProperties.h:4, from drawgraph.cc:10: /usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 std::__introsort_loop(__first, __last, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 std::__insertion_sort(__first, __first + int(_S_threshold), __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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 -j3 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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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_main.a ar cru libgtest_main.a src/libgtest_main_a-gtest_main.o src/libgtest_main_a-gtest-all.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libgtest_main.a rm -f libgtest.a ar cru libgtest.a src/libgtest_a-gtest-all.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libgtest.a make[3]: Leaving directory '/build/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../Common -I/build/abyss-2.1.5 -isystem/usr/lib/arm-linux-gnueabihf/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/build/abyss-2.1.5 -isystem/usr/lib/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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++ -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/arm-linux-gnueabihf/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++ -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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o common_bitutil Common/BitUtilTest.o ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm In file included from /usr/include/c++/8/unordered_set:46, from ../Common/UnorderedSet.h:8, from BloomDBG/RollingBloomDBGTest.cpp:3: /usr/include/c++/8/bits/hashtable.h: In member function 'std::_Hashtable<_Key, _Value, _Alloc, _ExtractKey, _Equal, _H1, _H2, _Hash, _RehashPolicy, _Traits>::iterator std::_Hashtable<_Key, _Value, _Alloc, _ExtractKey, _Equal, _H1, _H2, _Hash, _RehashPolicy, _Traits>::erase(std::_Hashtable<_Key, _Value, _Alloc, _ExtractKey, _Equal, _H1, _H2, _Hash, _RehashPolicy, _Traits>::const_iterator) [with _Key = RollingBloomDBGVertex; _Value = RollingBloomDBGVertex; _Alloc = std::allocator; _ExtractKey = std::__detail::_Identity; _Equal = std::equal_to; _H1 = std::hash; _H2 = std::__detail::_Mod_range_hashing; _Hash = std::__detail::_Default_ranged_hash; _RehashPolicy = std::__detail::_Prime_rehash_policy; _Traits = std::__detail::_Hashtable_traits]': /usr/include/c++/8/bits/hashtable.h:1871:5: note: parameter passing for argument of type 'std::_Hashtable, std::__detail::_Identity, std::equal_to, std::hash, std::__detail::_Mod_range_hashing, std::__detail::_Default_ranged_hash, std::__detail::_Prime_rehash_policy, std::__detail::_Hashtable_traits >::const_iterator' {aka 'std::__detail::_Node_const_iterator'} changed in GCC 7.1 _Hashtable<_Key, _Value, _Alloc, _ExtractKey, _Equal, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ _H1, _H2, _Hash, _RehashPolicy, _Traits>:: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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 /usr/include/c++/8/bits/hashtable.h: In member function 'virtual void RollingBloomDBGTest_out_edge_iterator_Test::TestBody()': /usr/include/c++/8/bits/hashtable.h:767:42: note: parameter passing for argument of type 'std::_Hashtable, std::__detail::_Identity, std::equal_to, std::hash, std::__detail::_Mod_range_hashing, std::__detail::_Default_ranged_hash, std::__detail::_Prime_rehash_policy, std::__detail::_Hashtable_traits >::const_iterator' {aka 'std::__detail::_Node_const_iterator'} changed in GCC 7.1 { return erase(const_iterator(__it)); } ^ /usr/include/c++/8/bits/hashtable.h: In member function 'virtual void RollingBloomDBGSpacedSeedTest_out_edge_iterator_Test::TestBody()': /usr/include/c++/8/bits/hashtable.h:767:42: note: parameter passing for argument of type 'std::_Hashtable, std::__detail::_Identity, std::equal_to, std::hash, std::__detail::_Mod_range_hashing, std::__detail::_Default_ranged_hash, std::__detail::_Prime_rehash_policy, std::__detail::_Hashtable_traits >::const_iterator' {aka 'std::__detail::_Node_const_iterator'} changed in GCC 7.1 { return erase(const_iterator(__it)); } ^ 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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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 /usr/include/c++/8/bits/hashtable.h: In member function 'virtual void RollingBloomDBGTest_adjacency_iterator_Test::TestBody()': /usr/include/c++/8/bits/hashtable.h:767:42: note: parameter passing for argument of type 'std::_Hashtable, std::__detail::_Identity, std::equal_to, std::hash, std::__detail::_Mod_range_hashing, std::__detail::_Default_ranged_hash, std::__detail::_Prime_rehash_policy, std::__detail::_Hashtable_traits >::const_iterator' {aka 'std::__detail::_Node_const_iterator'} changed in GCC 7.1 { return erase(const_iterator(__it)); } ^ 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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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 /usr/include/c++/8/bits/hashtable.h: In member function 'virtual void RollingBloomDBGTest_in_edges_Test::TestBody()': /usr/include/c++/8/bits/hashtable.h:767:42: note: parameter passing for argument of type 'std::_Hashtable, std::__detail::_Identity, std::equal_to, std::hash, std::__detail::_Mod_range_hashing, std::__detail::_Default_ranged_hash, std::__detail::_Prime_rehash_policy, std::__detail::_Hashtable_traits >::const_iterator' {aka 'std::__detail::_Node_const_iterator'} changed in GCC 7.1 { return erase(const_iterator(__it)); } ^ 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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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_histogram PASS: common_stringutil PASS: common_bitutil PASS: common_kmer PASS: common_sequence PASS: common_KmerIterator PASS: BloomFilter PASS: common_sam PASS: Konnector_DBGBloom PASS: Konnector_DBGBloomAlgorithms PASS: graph_BidirectionalBFS PASS: graph_ConstrainedBFSVisitor PASS: graph_AllPathsSearch PASS: graph_HashGraph PASS: graph_ConstrainedBidiBFSVisitor PASS: graph_ExtendPath PASS: graph_UndirectedGraph PASS: graph_DotIO PASS: Konnector_konnector PASS: PairedDBG_KmerPair PASS: PairedDBG_Dinuc PASS: PairedDBG_BranchRecord PASS: BloomDBG_BloomDBG PASS: BloomDBG_RollingHash PASS: BloomDBG_RollingHashIterator PASS: BloomDBG_HashAgnosticCascadingBloom PASS: BloomDBG_RollingBloomDBG PASS: BloomDBG_MaskedKmer PASS: BloomDBG_SpacedSeed PASS: BloomDBG_LightweightKmer 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 -j3 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' /bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/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-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 dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/abyss-bloom-dbg contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/DistanceEst contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/abyss/usr/bin/abyss-fixmate contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/DAssembler contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/abyss-map-ssq contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/DistanceEst-ssq contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/abyss-layout contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/PathConsensus contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/abyss-bloom contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/konnector contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/AdjList contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/ABYSS-P contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/abyss-overlap contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/abyss-sealer contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/abyss-fac contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/abyss-mergepairs contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/abyss-scaffold contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/abyss-gc contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/abyss-index contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/Consensus contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/abyss-fixmate contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/ParseAligns contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/Overlap contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/abyss-paired-dbg contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/PopBubbles contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/KAligner contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/abyss-longseqdist contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/MergePaths contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/logcounter contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/abyss-align contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/abyss-junction contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/PathOverlap contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/abyss-map contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/abyss-paired-dbg-mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/abyss/usr/bin/DistanceEst contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/SimpleGraph contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/abyss-gapfill contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/abyss-fixmate-ssq contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/abyss-tofastq contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/abyss-todot contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/abyss-filtergraph contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/MergeContigs contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/abyss-db-csv contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/ABYSS contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'abyss-dbgsym' in '../abyss-dbgsym_2.1.5-7_armhf.deb'. dpkg-deb: building package 'abyss' in '../abyss_2.1.5-7_armhf.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../abyss_2.1.5-7_armhf.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/29195 and its subdirectories I: Current time: Fri Aug 21 13:43:12 -12 2020 I: pbuilder-time-stamp: 1598060592