I: pbuilder: network access will be disabled during build
I: Current time: Sun Feb  9 14:35:26 +14 2025
I: pbuilder-time-stamp: 1739061326
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz]
I: copying local configuration
W: --override-config is not set; not updating apt.conf Read the manpage for details.
I: mounting /proc filesystem
I: mounting /sys filesystem
I: creating /{dev,run}/shm
I: mounting /dev/pts filesystem
I: redirecting /dev/ptmx to /dev/pts/ptmx
I: policy-rc.d already exists
I: Copying source file
I: copying [abyss_2.3.10-1.dsc]
I: copying [./abyss_2.3.10.orig.tar.xz]
I: copying [./abyss_2.3.10-1.debian.tar.xz]
I: Extracting source
dpkg-source: warning: cannot verify inline signature for ./abyss_2.3.10-1.dsc: unsupported subcommand
dpkg-source: info: extracting abyss in abyss-2.3.10
dpkg-source: info: unpacking abyss_2.3.10.orig.tar.xz
dpkg-source: info: unpacking abyss_2.3.10-1.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying abyss-pe.patch
dpkg-source: info: applying fix-privacy-breach.patch
I: Not using root during the build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/510437/tmp/hooks/D01_modify_environment starting
debug: Running on codethink04-arm64.
I: Changing host+domainname to test build reproducibility
I: Adding a custom variable just for the fun of it...
I: Changing /bin/sh to bash
'/bin/sh' -> '/bin/bash'
lrwxrwxrwx 1 root root 9 Feb  9 00:35 /bin/sh -> /bin/bash
I: Setting pbuilder2's login shell to /bin/bash
I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other
I: user script /srv/workspace/pbuilder/510437/tmp/hooks/D01_modify_environment finished
I: user script /srv/workspace/pbuilder/510437/tmp/hooks/D02_print_environment starting
I: set
  BASH=/bin/sh
  BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath
  BASH_ALIASES=()
  BASH_ARGC=()
  BASH_ARGV=()
  BASH_CMDS=()
  BASH_LINENO=([0]="12" [1]="0")
  BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:.
  BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment")
  BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu")
  BASH_VERSION='5.2.37(1)-release'
  BUILDDIR=/build/reproducible-path
  BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other'
  BUILDUSERNAME=pbuilder2
  BUILD_ARCH=arm64
  DEBIAN_FRONTEND=noninteractive
  DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 '
  DIRSTACK=()
  DISTRIBUTION=trixie
  EUID=0
  FUNCNAME=([0]="Echo" [1]="main")
  GROUPS=()
  HOME=/root
  HOSTNAME=i-capture-the-hostname
  HOSTTYPE=aarch64
  HOST_ARCH=arm64
  IFS=' 	
  '
  INVOCATION_ID=bec78ca02d524fb5bd24fe5342e94458
  LANG=C
  LANGUAGE=nl_BE:nl
  LC_ALL=C
  MACHTYPE=aarch64-unknown-linux-gnu
  MAIL=/var/mail/root
  OPTERR=1
  OPTIND=1
  OSTYPE=linux-gnu
  PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path
  PBCURRENTCOMMANDLINEOPERATION=build
  PBUILDER_OPERATION=build
  PBUILDER_PKGDATADIR=/usr/share/pbuilder
  PBUILDER_PKGLIBDIR=/usr/lib/pbuilder
  PBUILDER_SYSCONFDIR=/etc
  PIPESTATUS=([0]="0")
  POSIXLY_CORRECT=y
  PPID=510437
  PS4='+ '
  PWD=/
  SHELL=/bin/bash
  SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix
  SHLVL=3
  SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.YO30Kj1W/pbuilderrc_gD3w --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.YO30Kj1W/b2 --logfile b2/build.log abyss_2.3.10-1.dsc'
  SUDO_GID=109
  SUDO_UID=104
  SUDO_USER=jenkins
  TERM=unknown
  TZ=/usr/share/zoneinfo/Etc/GMT-14
  UID=0
  USER=root
  _='I: set'
  http_proxy=http://192.168.101.4:3128
I: uname -a
  Linux i-capture-the-hostname 6.1.0-30-cloud-arm64 #1 SMP Debian 6.1.124-1 (2025-01-12) aarch64 GNU/Linux
I: ls -l /bin
  lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin
I: user script /srv/workspace/pbuilder/510437/tmp/hooks/D02_print_environment finished
 -> Attempting to satisfy build-dependencies
 -> Creating pbuilder-satisfydepends-dummy package
Package: pbuilder-satisfydepends-dummy
Version: 0.invalid.0
Architecture: arm64
Maintainer: Debian Pbuilder Team <pbuilder-maint@lists.alioth.debian.org>
Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder
 This package was created automatically by pbuilder to satisfy the
 build-dependencies of the package being currently built.
Depends: debhelper-compat (= 13), architecture-is-64-bit, libboost-graph-dev, libbtllib-dev, libopenmpi-dev, libsparsehash-dev, libtext-multimarkdown-perl, libsqlite3-dev, pkgconf, help2man, debhelper
dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'.
Selecting previously unselected package pbuilder-satisfydepends-dummy.
(Reading database ... 19956 files and directories currently installed.)
Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ...
Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ...
dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested:
 pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however:
  Package debhelper-compat is not installed.
 pbuilder-satisfydepends-dummy depends on architecture-is-64-bit; however:
  Package architecture-is-64-bit is not installed.
 pbuilder-satisfydepends-dummy depends on libboost-graph-dev; however:
  Package libboost-graph-dev is not installed.
 pbuilder-satisfydepends-dummy depends on libbtllib-dev; however:
  Package libbtllib-dev is not installed.
 pbuilder-satisfydepends-dummy depends on libopenmpi-dev; however:
  Package libopenmpi-dev is not installed.
 pbuilder-satisfydepends-dummy depends on libsparsehash-dev; however:
  Package libsparsehash-dev is not installed.
 pbuilder-satisfydepends-dummy depends on libtext-multimarkdown-perl; however:
  Package libtext-multimarkdown-perl is not installed.
 pbuilder-satisfydepends-dummy depends on libsqlite3-dev; however:
  Package libsqlite3-dev is not installed.
 pbuilder-satisfydepends-dummy depends on pkgconf; however:
  Package pkgconf is not installed.
 pbuilder-satisfydepends-dummy depends on help2man; however:
  Package help2man is not installed.
 pbuilder-satisfydepends-dummy depends on debhelper; however:
  Package debhelper is not installed.

Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ...
Reading package lists...
Building dependency tree...
Reading state information...
Initializing package states...
Writing extended state information...
Building tag database...
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
The following NEW packages will be installed:
  architecture-properties{a} autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} ca-certificates{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} docutils-common{a} dwz{a} file{a} gettext{a} gettext-base{a} gfortran-14{a} gfortran-14-aarch64-linux-gnu{a} groff-base{a} help2man{a} ibverbs-providers{a} icu-devtools{a} intltool-debian{a} libamd-comgr2{a} libamdhip64-5{a} libarchive-zip-perl{a} libboost-graph-dev{a} libboost-graph1.83-dev{a} libboost-graph1.83.0{a} libboost-regex1.83-dev{a} libboost-regex1.83.0{a} libboost-serialization1.83-dev{a} libboost-serialization1.83.0{a} libboost-test1.83-dev{a} libboost-test1.83.0{a} libboost1.83-dev{a} libbrotli1{a} libbtllib-dev{a} libcbor0.10{a} libcom-err2{a} libcpptoml-dev{a} libcurl3t64-gnutls{a} libdebhelper-perl{a} libdeflate0{a} libdivsufsort-dev{a} libdivsufsort3{a} libdrm-amdgpu1{a} libdrm-common{a} libdrm2{a} libedit2{a} libelf1t64{a} libevent-2.1-7t64{a} libevent-core-2.1-7t64{a} libevent-dev{a} libevent-extra-2.1-7t64{a} libevent-openssl-2.1-7t64{a} libevent-pthreads-2.1-7t64{a} libexpat1{a} libfabric1{a} libffi8{a} libfido2-1{a} libfile-stripnondeterminism-perl{a} libgfortran-14-dev{a} libgfortran5{a} libgnutls30t64{a} libgssapi-krb5-2{a} libhsa-runtime64-1{a} libhsakmt1{a} libhtml-parser-perl{a} libhtml-tagset-perl{a} libhts3t64{a} libhtscodecs2{a} libhwloc-dev{a} libhwloc-plugins{a} libhwloc15{a} libibmad5{a} libibumad3{a} libibverbs-dev{a} libibverbs1{a} libicu-dev{a} libicu72{a} libidn2-0{a} libjs-d3{a} libjs-jquery{a} libjs-jquery-ui{a} libjs-sphinxdoc{a} libjs-underscore{a} libjson-perl{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libldap2{a} libllvm17t64{a} liblocale-gettext-perl{a} libltdl-dev{a} libltdl7{a} libmagic-mgc{a} libmagic1t64{a} libmunge2{a} libncurses6{a} libnghttp2-14{a} libnghttp3-9{a} libngtcp2-16{a} libngtcp2-crypto-gnutls8{a} libnl-3-200{a} libnl-3-dev{a} libnl-route-3-200{a} libnl-route-3-dev{a} libnuma-dev{a} libnuma1{a} libopenmpi-dev{a} libopenmpi40{a} libp11-kit0{a} libpciaccess0{a} libpipeline1{a} libpkgconf3{a} libpmix-dev{a} libpmix2t64{a} libpsl5t64{a} libpython3-stdlib{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} librdmacm1t64{a} libreadline8t64{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsdsl-dev{a} libsdsl3{a} libsparsehash-dev{a} libsqlite3-dev{a} libssh2-1t64{a} libtasn1-6{a} libtext-markdown-perl{a} libtext-multimarkdown-perl{a} libtool{a} libuchardet0{a} libucx0{a} libunistring5{a} liburi-perl{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxml2{a} libxnvctrl0{a} libz3-4{a} m4{a} man-db{a} media-types{a} netbase{a} ocl-icd-libopencl1{a} openmpi-bin{a} openmpi-common{a} openssh-client{a} openssl{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} python-babel-localedata{a} python3{a} python3-alabaster{a} python3-babel{a} python3-certifi{a} python3-chardet{a} python3-charset-normalizer{a} python3-defusedxml{a} python3-docutils{a} python3-idna{a} python3-imagesize{a} python3-jinja2{a} python3-markupsafe{a} python3-minimal{a} python3-packaging{a} python3-pygments{a} python3-requests{a} python3-roman{a} python3-snowballstemmer{a} python3-sphinx{a} python3-urllib3{a} python3.13{a} python3.13-minimal{a} readline-common{a} samtools{a} sensible-utils{a} sgml-base{a} sphinx-common{a} tzdata{a} wget{a} xml-core{a} zlib1g-dev{a} 
The following packages are RECOMMENDED but will NOT be installed:
  javascript-common krb5-locales libarchive-cpio-perl libcoarrays-openmpi-dev libgpm2 libhttp-message-perl libjson-xs-perl libldap-common libmail-sendmail-perl libpaper-utils libsasl2-modules publicsuffix python3-pil xauth 
0 packages upgraded, 193 newly installed, 0 to remove and 0 not upgraded.
Need to get 148 MB of archives. After unpacking 777 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian trixie/main arm64 liblocale-gettext-perl arm64 1.07-7+b1 [15.2 kB]
Get: 2 http://deb.debian.org/debian trixie/main arm64 libpython3.13-minimal arm64 3.13.1-3+b1 [852 kB]
Get: 3 http://deb.debian.org/debian trixie/main arm64 libexpat1 arm64 2.6.4-1 [90.7 kB]
Get: 4 http://deb.debian.org/debian trixie/main arm64 python3.13-minimal arm64 3.13.1-3+b1 [1987 kB]
Get: 5 http://deb.debian.org/debian trixie/main arm64 python3-minimal arm64 3.13.1-2 [27.0 kB]
Get: 6 http://deb.debian.org/debian trixie/main arm64 media-types all 10.1.0 [26.9 kB]
Get: 7 http://deb.debian.org/debian trixie/main arm64 netbase all 6.4 [12.8 kB]
Get: 8 http://deb.debian.org/debian trixie/main arm64 tzdata all 2024b-6 [257 kB]
Get: 9 http://deb.debian.org/debian trixie/main arm64 libffi8 arm64 3.4.6-1 [20.9 kB]
Get: 10 http://deb.debian.org/debian trixie/main arm64 readline-common all 8.2-6 [69.4 kB]
Get: 11 http://deb.debian.org/debian trixie/main arm64 libreadline8t64 arm64 8.2-6 [159 kB]
Get: 12 http://deb.debian.org/debian trixie/main arm64 libpython3.13-stdlib arm64 3.13.1-3+b1 [1913 kB]
Get: 13 http://deb.debian.org/debian trixie/main arm64 python3.13 arm64 3.13.1-3+b1 [740 kB]
Get: 14 http://deb.debian.org/debian trixie/main arm64 libpython3-stdlib arm64 3.13.1-2 [9952 B]
Get: 15 http://deb.debian.org/debian trixie/main arm64 python3 arm64 3.13.1-2 [28.0 kB]
Get: 16 http://deb.debian.org/debian trixie/main arm64 sgml-base all 1.31 [15.4 kB]
Get: 17 http://deb.debian.org/debian trixie/main arm64 sensible-utils all 0.0.24 [24.8 kB]
Get: 18 http://deb.debian.org/debian trixie/main arm64 openssl arm64 3.4.0-2 [1385 kB]
Get: 19 http://deb.debian.org/debian trixie/main arm64 ca-certificates all 20241223 [164 kB]
Get: 20 http://deb.debian.org/debian trixie/main arm64 libmagic-mgc arm64 1:5.45-3+b1 [314 kB]
Get: 21 http://deb.debian.org/debian trixie/main arm64 libmagic1t64 arm64 1:5.45-3+b1 [102 kB]
Get: 22 http://deb.debian.org/debian trixie/main arm64 file arm64 1:5.45-3+b1 [43.4 kB]
Get: 23 http://deb.debian.org/debian trixie/main arm64 gettext-base arm64 0.23.1-1 [241 kB]
Get: 24 http://deb.debian.org/debian trixie/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB]
Get: 25 http://deb.debian.org/debian trixie/main arm64 groff-base arm64 1.23.0-7 [1129 kB]
Get: 26 http://deb.debian.org/debian trixie/main arm64 bsdextrautils arm64 2.40.4-2 [91.5 kB]
Get: 27 http://deb.debian.org/debian trixie/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB]
Get: 28 http://deb.debian.org/debian trixie/main arm64 man-db arm64 2.13.0-1 [1404 kB]
Get: 29 http://deb.debian.org/debian trixie/main arm64 libedit2 arm64 3.1-20250104-1 [89.3 kB]
Get: 30 http://deb.debian.org/debian trixie/main arm64 libcbor0.10 arm64 0.10.2-2 [27.4 kB]
Get: 31 http://deb.debian.org/debian trixie/main arm64 libfido2-1 arm64 1.15.0-1+b1 [74.3 kB]
Get: 32 http://deb.debian.org/debian trixie/main arm64 libkrb5support0 arm64 1.21.3-4 [32.2 kB]
Get: 33 http://deb.debian.org/debian trixie/main arm64 libcom-err2 arm64 1.47.2-1 [23.9 kB]
Get: 34 http://deb.debian.org/debian trixie/main arm64 libk5crypto3 arm64 1.21.3-4 [81.5 kB]
Get: 35 http://deb.debian.org/debian trixie/main arm64 libkeyutils1 arm64 1.6.3-4 [9352 B]
Get: 36 http://deb.debian.org/debian trixie/main arm64 libkrb5-3 arm64 1.21.3-4 [308 kB]
Get: 37 http://deb.debian.org/debian trixie/main arm64 libgssapi-krb5-2 arm64 1.21.3-4 [127 kB]
Get: 38 http://deb.debian.org/debian trixie/main arm64 openssh-client arm64 1:9.9p1-3 [928 kB]
Get: 39 http://deb.debian.org/debian trixie/main arm64 libunistring5 arm64 1.3-1 [449 kB]
Get: 40 http://deb.debian.org/debian trixie/main arm64 libidn2-0 arm64 2.3.7-2+b1 [127 kB]
Get: 41 http://deb.debian.org/debian trixie/main arm64 libp11-kit0 arm64 0.25.5-3 [409 kB]
Get: 42 http://deb.debian.org/debian trixie/main arm64 libtasn1-6 arm64 4.19.0-3+b3 [46.9 kB]
Get: 43 http://deb.debian.org/debian trixie/main arm64 libgnutls30t64 arm64 3.8.8-2 [1363 kB]
Get: 44 http://deb.debian.org/debian trixie/main arm64 libpsl5t64 arm64 0.21.2-1.1+b1 [57.1 kB]
Get: 45 http://deb.debian.org/debian trixie/main arm64 wget arm64 1.24.5-2 [966 kB]
Get: 46 http://deb.debian.org/debian trixie/main arm64 architecture-properties arm64 0.2.5 [2272 B]
Get: 47 http://deb.debian.org/debian trixie/main arm64 m4 arm64 1.4.19-5 [284 kB]
Get: 48 http://deb.debian.org/debian trixie/main arm64 autoconf all 2.72-3 [493 kB]
Get: 49 http://deb.debian.org/debian trixie/main arm64 autotools-dev all 20220109.1 [51.6 kB]
Get: 50 http://deb.debian.org/debian trixie/main arm64 automake all 1:1.17-3 [862 kB]
Get: 51 http://deb.debian.org/debian trixie/main arm64 autopoint all 0.23.1-1 [770 kB]
Get: 52 http://deb.debian.org/debian trixie/main arm64 libdebhelper-perl all 13.24.1 [90.9 kB]
Get: 53 http://deb.debian.org/debian trixie/main arm64 libtool all 2.5.4-3 [539 kB]
Get: 54 http://deb.debian.org/debian trixie/main arm64 dh-autoreconf all 20 [17.1 kB]
Get: 55 http://deb.debian.org/debian trixie/main arm64 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 56 http://deb.debian.org/debian trixie/main arm64 libfile-stripnondeterminism-perl all 1.14.1-1 [19.6 kB]
Get: 57 http://deb.debian.org/debian trixie/main arm64 dh-strip-nondeterminism all 1.14.1-1 [8584 B]
Get: 58 http://deb.debian.org/debian trixie/main arm64 libelf1t64 arm64 0.192-4 [189 kB]
Get: 59 http://deb.debian.org/debian trixie/main arm64 dwz arm64 0.15-1+b1 [102 kB]
Get: 60 http://deb.debian.org/debian trixie/main arm64 libicu72 arm64 72.1-6 [9239 kB]
Get: 61 http://deb.debian.org/debian trixie/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.2+b1 [630 kB]
Get: 62 http://deb.debian.org/debian trixie/main arm64 gettext arm64 0.23.1-1 [1610 kB]
Get: 63 http://deb.debian.org/debian trixie/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 64 http://deb.debian.org/debian trixie/main arm64 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 65 http://deb.debian.org/debian trixie/main arm64 debhelper all 13.24.1 [920 kB]
Get: 66 http://deb.debian.org/debian trixie/main arm64 xml-core all 0.19 [20.1 kB]
Get: 67 http://deb.debian.org/debian trixie/main arm64 docutils-common all 0.21.2+dfsg-2 [128 kB]
Get: 68 http://deb.debian.org/debian trixie/main arm64 libgfortran5 arm64 14.2.0-12 [361 kB]
Get: 69 http://deb.debian.org/debian trixie/main arm64 libgfortran-14-dev arm64 14.2.0-12 [427 kB]
Get: 70 http://deb.debian.org/debian trixie/main arm64 gfortran-14-aarch64-linux-gnu arm64 14.2.0-12 [9791 kB]
Get: 71 http://deb.debian.org/debian trixie/main arm64 gfortran-14 arm64 14.2.0-12 [13.4 kB]
Get: 72 http://deb.debian.org/debian trixie/main arm64 help2man arm64 1.49.3+b1 [198 kB]
Get: 73 http://deb.debian.org/debian trixie/main arm64 libnl-3-200 arm64 3.7.0-0.3+b1 [57.0 kB]
Get: 74 http://deb.debian.org/debian trixie/main arm64 libnl-route-3-200 arm64 3.7.0-0.3+b1 [167 kB]
Get: 75 http://deb.debian.org/debian trixie/main arm64 libibverbs1 arm64 55.0-1 [58.6 kB]
Get: 76 http://deb.debian.org/debian trixie/main arm64 ibverbs-providers arm64 55.0-1 [328 kB]
Get: 77 http://deb.debian.org/debian trixie/main arm64 icu-devtools arm64 72.1-6 [196 kB]
Get: 78 http://deb.debian.org/debian trixie/main arm64 libz3-4 arm64 4.13.3-1 [7507 kB]
Get: 79 http://deb.debian.org/debian trixie/main arm64 libllvm17t64 arm64 1:17.0.6-20+b2 [21.3 MB]
Get: 80 http://deb.debian.org/debian trixie/main arm64 libamd-comgr2 arm64 6.0+git20231212.4510c28+dfsg-3+b2 [12.1 MB]
Get: 81 http://deb.debian.org/debian trixie/main arm64 libdrm-common all 2.4.123-1 [8084 B]
Get: 82 http://deb.debian.org/debian trixie/main arm64 libdrm2 arm64 2.4.123-1 [38.0 kB]
Get: 83 http://deb.debian.org/debian trixie/main arm64 libdrm-amdgpu1 arm64 2.4.123-1 [21.6 kB]
Get: 84 http://deb.debian.org/debian trixie/main arm64 libnuma1 arm64 2.0.18-1+b1 [21.8 kB]
Get: 85 http://deb.debian.org/debian trixie/main arm64 libhsakmt1 arm64 6.1.2+ds-1 [56.9 kB]
Get: 86 http://deb.debian.org/debian trixie/main arm64 libhsa-runtime64-1 arm64 5.7.1-3 [278 kB]
Get: 87 http://deb.debian.org/debian trixie/main arm64 libamdhip64-5 arm64 5.7.1-5 [8823 kB]
Get: 88 http://deb.debian.org/debian trixie/main arm64 libboost1.83-dev arm64 1.83.0-4 [10.6 MB]
Get: 89 http://deb.debian.org/debian trixie/main arm64 libboost-graph1.83.0 arm64 1.83.0-4 [341 kB]
Get: 90 http://deb.debian.org/debian trixie/main arm64 libboost-regex1.83.0 arm64 1.83.0-4 [314 kB]
Get: 91 http://deb.debian.org/debian trixie/main arm64 libicu-dev arm64 72.1-6 [10.3 MB]
Get: 92 http://deb.debian.org/debian trixie/main arm64 libboost-regex1.83-dev arm64 1.83.0-4 [338 kB]
Get: 93 http://deb.debian.org/debian trixie/main arm64 libboost-serialization1.83.0 arm64 1.83.0-4 [325 kB]
Get: 94 http://deb.debian.org/debian trixie/main arm64 libboost-serialization1.83-dev arm64 1.83.0-4 [375 kB]
Get: 95 http://deb.debian.org/debian trixie/main arm64 libboost-test1.83.0 arm64 1.83.0-4 [438 kB]
Get: 96 http://deb.debian.org/debian trixie/main arm64 libboost-test1.83-dev arm64 1.83.0-4 [531 kB]
Get: 97 http://deb.debian.org/debian trixie/main arm64 libboost-graph1.83-dev arm64 1.83.0-4 [377 kB]
Get: 98 http://deb.debian.org/debian trixie/main arm64 libboost-graph-dev arm64 1.83.0.2+b2 [3688 B]
Get: 99 http://deb.debian.org/debian trixie/main arm64 libbrotli1 arm64 1.1.0-2+b6 [297 kB]
Get: 100 http://deb.debian.org/debian trixie/main arm64 libcpptoml-dev all 0.1.1-3 [180 kB]
Get: 101 http://deb.debian.org/debian trixie/main arm64 libdivsufsort3 arm64 2.0.1-6+b1 [39.9 kB]
Get: 102 http://deb.debian.org/debian trixie/main arm64 libdivsufsort-dev arm64 2.0.1-6+b1 [19.1 kB]
Get: 103 http://deb.debian.org/debian trixie/main arm64 libjs-d3 all 3.5.17-4 [132 kB]
Get: 104 http://deb.debian.org/debian trixie/main arm64 libsdsl3 arm64 2.1.1+dfsg-5 [180 kB]
Get: 105 http://deb.debian.org/debian trixie/main arm64 libsdsl-dev arm64 2.1.1+dfsg-5 [428 kB]
Get: 106 http://deb.debian.org/debian trixie/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-8+b1 [20.3 kB]
Get: 107 http://deb.debian.org/debian trixie/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-8+b1 [55.7 kB]
Get: 108 http://deb.debian.org/debian trixie/main arm64 libldap2 arm64 2.6.9+dfsg-1 [179 kB]
Get: 109 http://deb.debian.org/debian trixie/main arm64 libnghttp2-14 arm64 1.64.0-1 [71.3 kB]
Get: 110 http://deb.debian.org/debian trixie/main arm64 libnghttp3-9 arm64 1.6.0-2 [60.5 kB]
Get: 111 http://deb.debian.org/debian trixie/main arm64 libngtcp2-16 arm64 1.9.1-1 [109 kB]
Get: 112 http://deb.debian.org/debian trixie/main arm64 libngtcp2-crypto-gnutls8 arm64 1.9.1-1 [17.3 kB]
Get: 113 http://deb.debian.org/debian trixie/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b5 [56.8 kB]
Get: 114 http://deb.debian.org/debian trixie/main arm64 libssh2-1t64 arm64 1.11.1-1 [235 kB]
Get: 115 http://deb.debian.org/debian trixie/main arm64 libcurl3t64-gnutls arm64 8.11.1-1+b1 [331 kB]
Get: 116 http://deb.debian.org/debian trixie/main arm64 libdeflate0 arm64 1.23-1+b1 [42.5 kB]
Get: 117 http://deb.debian.org/debian trixie/main arm64 libhtscodecs2 arm64 1.6.1-1 [74.6 kB]
Get: 118 http://deb.debian.org/debian trixie/main arm64 libhts3t64 arm64 1.20+ds-2 [420 kB]
Get: 119 http://deb.debian.org/debian trixie/main arm64 libncurses6 arm64 6.5-2+b1 [96.1 kB]
Get: 120 http://deb.debian.org/debian trixie/main arm64 samtools arm64 1.20-3+b1 [629 kB]
Get: 121 http://deb.debian.org/debian trixie/main arm64 libbtllib-dev arm64 1.4.10+dfsg-1+b1 [185 kB]
Get: 122 http://deb.debian.org/debian trixie/main arm64 libevent-2.1-7t64 arm64 2.1.12-stable-10+b1 [170 kB]
Get: 123 http://deb.debian.org/debian trixie/main arm64 libevent-core-2.1-7t64 arm64 2.1.12-stable-10+b1 [126 kB]
Get: 124 http://deb.debian.org/debian trixie/main arm64 libevent-extra-2.1-7t64 arm64 2.1.12-stable-10+b1 [102 kB]
Get: 125 http://deb.debian.org/debian trixie/main arm64 libevent-pthreads-2.1-7t64 arm64 2.1.12-stable-10+b1 [54.4 kB]
Get: 126 http://deb.debian.org/debian trixie/main arm64 libevent-openssl-2.1-7t64 arm64 2.1.12-stable-10+b1 [60.4 kB]
Get: 127 http://deb.debian.org/debian trixie/main arm64 libevent-dev arm64 2.1.12-stable-10+b1 [304 kB]
Get: 128 http://deb.debian.org/debian trixie/main arm64 librdmacm1t64 arm64 55.0-1 [67.0 kB]
Get: 129 http://deb.debian.org/debian trixie/main arm64 libfabric1 arm64 1.17.0-3.1 [480 kB]
Get: 130 http://deb.debian.org/debian trixie/main arm64 libhtml-tagset-perl all 3.24-1 [14.7 kB]
Get: 131 http://deb.debian.org/debian trixie/main arm64 liburi-perl all 5.30-1 [105 kB]
Get: 132 http://deb.debian.org/debian trixie/main arm64 libhtml-parser-perl arm64 3.83-1+b2 [97.5 kB]
Get: 133 http://deb.debian.org/debian trixie/main arm64 libhwloc15 arm64 2.11.2-1 [141 kB]
Get: 134 http://deb.debian.org/debian trixie/main arm64 libnuma-dev arm64 2.0.18-1+b1 [37.8 kB]
Get: 135 http://deb.debian.org/debian trixie/main arm64 libltdl7 arm64 2.5.4-3 [415 kB]
Get: 136 http://deb.debian.org/debian trixie/main arm64 libltdl-dev arm64 2.5.4-3 [168 kB]
Get: 137 http://deb.debian.org/debian trixie/main arm64 libhwloc-dev arm64 2.11.2-1 [237 kB]
Get: 138 http://deb.debian.org/debian trixie/main arm64 libpciaccess0 arm64 0.17-3+b3 [51.2 kB]
Get: 139 http://deb.debian.org/debian trixie/main arm64 libxau6 arm64 1:1.0.11-1 [20.6 kB]
Get: 140 http://deb.debian.org/debian trixie/main arm64 libxdmcp6 arm64 1:1.1.5-1 [27.8 kB]
Get: 141 http://deb.debian.org/debian trixie/main arm64 libxcb1 arm64 1.17.0-2+b1 [143 kB]
Get: 142 http://deb.debian.org/debian trixie/main arm64 libx11-data all 2:1.8.10-2 [337 kB]
Get: 143 http://deb.debian.org/debian trixie/main arm64 libx11-6 arm64 2:1.8.10-2 [789 kB]
Get: 144 http://deb.debian.org/debian trixie/main arm64 libxext6 arm64 2:1.3.4-1+b3 [49.2 kB]
Get: 145 http://deb.debian.org/debian trixie/main arm64 libxnvctrl0 arm64 535.171.04-1+b2 [14.0 kB]
Get: 146 http://deb.debian.org/debian trixie/main arm64 ocl-icd-libopencl1 arm64 2.3.2-1+b2 [39.3 kB]
Get: 147 http://deb.debian.org/debian trixie/main arm64 libhwloc-plugins arm64 2.11.2-1 [17.9 kB]
Get: 148 http://deb.debian.org/debian trixie/main arm64 libibumad3 arm64 55.0-1 [27.2 kB]
Get: 149 http://deb.debian.org/debian trixie/main arm64 libibmad5 arm64 55.0-1 [41.3 kB]
Get: 150 http://deb.debian.org/debian trixie/main arm64 libnl-3-dev arm64 3.7.0-0.3+b1 [101 kB]
Get: 151 http://deb.debian.org/debian trixie/main arm64 libnl-route-3-dev arm64 3.7.0-0.3+b1 [198 kB]
Get: 152 http://deb.debian.org/debian trixie/main arm64 libibverbs-dev arm64 55.0-1 [637 kB]
Get: 153 http://deb.debian.org/debian trixie/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB]
Get: 154 http://deb.debian.org/debian trixie/main arm64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB]
Get: 155 http://deb.debian.org/debian trixie/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB]
Get: 156 http://deb.debian.org/debian trixie/main arm64 libjs-sphinxdoc all 8.1.3-4 [30.4 kB]
Get: 157 http://deb.debian.org/debian trixie/main arm64 libjson-perl all 4.10000-1 [87.5 kB]
Get: 158 http://deb.debian.org/debian trixie/main arm64 libmunge2 arm64 0.5.16-1 [19.2 kB]
Get: 159 http://deb.debian.org/debian trixie/main arm64 libpmix2t64 arm64 5.0.6-1 [577 kB]
Get: 160 http://deb.debian.org/debian trixie/main arm64 libucx0 arm64 1.17.0+ds-3 [959 kB]
Get: 161 http://deb.debian.org/debian trixie/main arm64 libopenmpi40 arm64 5.0.6-3 [2087 kB]
Get: 162 http://deb.debian.org/debian trixie/main arm64 openmpi-common all 5.0.6-3 [97.0 kB]
Get: 163 http://deb.debian.org/debian trixie/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1+b1 [917 kB]
Get: 164 http://deb.debian.org/debian trixie/main arm64 python3-defusedxml all 0.7.1-3 [43.4 kB]
Get: 165 http://deb.debian.org/debian trixie/main arm64 sphinx-common all 8.1.3-4 [616 kB]
Get: 166 http://deb.debian.org/debian trixie/main arm64 python3-alabaster all 0.7.16-0.1 [27.9 kB]
Get: 167 http://deb.debian.org/debian trixie/main arm64 python-babel-localedata all 2.17.0-1 [6050 kB]
Get: 168 http://deb.debian.org/debian trixie/main arm64 python3-babel all 2.17.0-1 [117 kB]
Get: 169 http://deb.debian.org/debian trixie/main arm64 python3-roman all 5.0-1 [10.6 kB]
Get: 170 http://deb.debian.org/debian trixie/main arm64 python3-docutils all 0.21.2+dfsg-2 [403 kB]
Get: 171 http://deb.debian.org/debian trixie/main arm64 python3-imagesize all 1.4.1-1 [6688 B]
Get: 172 http://deb.debian.org/debian trixie/main arm64 python3-markupsafe arm64 2.1.5-1+b3 [14.0 kB]
Get: 173 http://deb.debian.org/debian trixie/main arm64 python3-jinja2 all 3.1.5-2 [107 kB]
Get: 174 http://deb.debian.org/debian trixie/main arm64 python3-packaging all 24.2-1 [55.3 kB]
Get: 175 http://deb.debian.org/debian trixie/main arm64 python3-pygments all 2.18.0+dfsg-2 [836 kB]
Get: 176 http://deb.debian.org/debian trixie/main arm64 python3-certifi all 2024.12.14+ds-1 [9624 B]
Get: 177 http://deb.debian.org/debian trixie/main arm64 python3-charset-normalizer arm64 3.4.0-1+b1 [129 kB]
Get: 178 http://deb.debian.org/debian trixie/main arm64 python3-idna all 3.8-2 [41.6 kB]
Get: 179 http://deb.debian.org/debian trixie/main arm64 python3-urllib3 all 2.3.0-1 [114 kB]
Get: 180 http://deb.debian.org/debian trixie/main arm64 python3-chardet all 5.2.0+dfsg-2 [108 kB]
Get: 181 http://deb.debian.org/debian trixie/main arm64 python3-requests all 2.32.3+dfsg-1 [71.9 kB]
Get: 182 http://deb.debian.org/debian trixie/main arm64 python3-snowballstemmer all 2.2.0-4 [58.0 kB]
Get: 183 http://deb.debian.org/debian trixie/main arm64 python3-sphinx all 8.1.3-4 [468 kB]
Get: 184 http://deb.debian.org/debian trixie/main arm64 libpmix-dev arm64 5.0.6-1 [3933 kB]
Get: 185 http://deb.debian.org/debian trixie/main arm64 openmpi-bin arm64 5.0.6-3 [180 kB]
Get: 186 http://deb.debian.org/debian trixie/main arm64 libopenmpi-dev arm64 5.0.6-3 [1088 kB]
Get: 187 http://deb.debian.org/debian trixie/main arm64 libpkgconf3 arm64 1.8.1-4 [35.3 kB]
Get: 188 http://deb.debian.org/debian trixie/main arm64 libsparsehash-dev all 2.0.3-2 [76.8 kB]
Get: 189 http://deb.debian.org/debian trixie/main arm64 libsqlite3-dev arm64 3.46.1-1 [1058 kB]
Get: 190 http://deb.debian.org/debian trixie/main arm64 libtext-markdown-perl all 1.000031-5 [31.4 kB]
Get: 191 http://deb.debian.org/debian trixie/main arm64 libtext-multimarkdown-perl all 1.000035-3 [28.5 kB]
Get: 192 http://deb.debian.org/debian trixie/main arm64 pkgconf-bin arm64 1.8.1-4 [29.6 kB]
Get: 193 http://deb.debian.org/debian trixie/main arm64 pkgconf arm64 1.8.1-4 [26.1 kB]
Fetched 148 MB in 1s (259 MB/s)
Preconfiguring packages ...
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Unpacking libpython3.13-minimal:arm64 (3.13.1-3+b1) ...
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Setting up libpython3.13-minimal:arm64 (3.13.1-3+b1) ...
Setting up libexpat1:arm64 (2.6.4-1) ...
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Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8 to /lib/aarch64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64'
Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8.2 to /lib/aarch64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64'
Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8 to /lib/aarch64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64'
Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8.2 to /lib/aarch64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64'
Unpacking libreadline8t64:arm64 (8.2-6) ...
Selecting previously unselected package libpython3.13-stdlib:arm64.
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Setting up python3-minimal (3.13.1-2) ...
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Unpacking python3 (3.13.1-2) ...
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Unpacking gettext-base (0.23.1-1) ...
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Unpacking libuchardet0:arm64 (0.0.8-1+b2) ...
Selecting previously unselected package groff-base.
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Unpacking groff-base (1.23.0-7) ...
Selecting previously unselected package bsdextrautils.
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Unpacking bsdextrautils (2.40.4-2) ...
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Unpacking libcbor0.10:arm64 (0.10.2-2) ...
Selecting previously unselected package libfido2-1:arm64.
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Unpacking libk5crypto3:arm64 (1.21.3-4) ...
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Unpacking libkeyutils1:arm64 (1.6.3-4) ...
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Unpacking libgssapi-krb5-2:arm64 (1.21.3-4) ...
Selecting previously unselected package openssh-client.
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Unpacking openssh-client (1:9.9p1-3) ...
Selecting previously unselected package libunistring5:arm64.
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Unpacking libunistring5:arm64 (1.3-1) ...
Selecting previously unselected package libidn2-0:arm64.
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Unpacking libidn2-0:arm64 (2.3.7-2+b1) ...
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Setting up tzdata (2024b-6) ...

Current default time zone: 'Etc/UTC'
Local time is now:      Sun Feb  9 00:36:00 UTC 2025.
Universal Time is now:  Sun Feb  9 00:36:00 UTC 2025.
Run 'dpkg-reconfigure tzdata' if you wish to change it.

Setting up libboost-serialization1.83.0:arm64 (1.83.0-4) ...
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Not building database; man-db/auto-update is not 'true'.
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update-alternatives: using /usr/bin/pybabel-python3 to provide /usr/bin/pybabel (pybabel) in auto mode
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Setting up python3-requests (2.32.3+dfsg-1) ...
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Setting up openmpi-bin (5.0.6-3) ...
update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode
update-alternatives: warning: skip creation of /usr/share/man/man1/mpiexec.1.gz because associated file /usr/share/man/man1/mpiexec.openmpi.1.gz (of link group mpirun) doesn't exist
update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode
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update-alternatives: using /usr/lib/aarch64-linux-gnu/openmpi/include to provide /usr/include/aarch64-linux-gnu/mpi (mpi-aarch64-linux-gnu) in auto mode
Processing triggers for ca-certificates (20241223) ...
Updating certificates in /etc/ssl/certs...
0 added, 0 removed; done.
Running hooks in /etc/ca-certificates/update.d...
done.
Reading package lists...
Building dependency tree...
Reading state information...
Reading extended state information...
Initializing package states...
Writing extended state information...
Building tag database...
 -> Finished parsing the build-deps
I: Building the package
I: user script /srv/workspace/pbuilder/510437/tmp/hooks/A99_set_merged_usr starting
Not re-configuring usrmerge for trixie
I: user script /srv/workspace/pbuilder/510437/tmp/hooks/A99_set_merged_usr finished
hostname: Name or service not known
I: Running cd /build/reproducible-path/abyss-2.3.10/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S  > ../abyss_2.3.10-1_source.changes
dpkg-buildpackage: info: source package abyss
dpkg-buildpackage: info: source version 2.3.10-1
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Étienne Mollier <emollier@debian.org>
 dpkg-source --before-build .
dpkg-buildpackage: info: host architecture arm64
 debian/rules clean
dh  clean
   dh_clean
 debian/rules binary
dh  binary
   dh_update_autotools_config
   dh_autoreconf
configure.ac:25: installing './ar-lib'
configure.ac:16: installing './compile'
configure.ac:80: installing './config.guess'
configure.ac:80: installing './config.sub'
configure.ac:10: installing './install-sh'
configure.ac:10: installing './missing'
ABYSS/Makefile.am: installing './depcomp'
parallel-tests: installing './test-driver'
   debian/rules override_dh_auto_configure
make[1]: Entering directory '/build/reproducible-path/abyss-2.3.10'
dh_auto_configure -- \
	--with-mpi=/usr/lib/aarch64-linux-gnu/openmpi
	./configure --build=aarch64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/aarch64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-mpi=/usr/lib/aarch64-linux-gnu/openmpi
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configure: creating ./config.status
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config.status: executing depfiles commands
make[1]: Leaving directory '/build/reproducible-path/abyss-2.3.10'
   debian/rules override_dh_auto_build
make[1]: Entering directory '/build/reproducible-path/abyss-2.3.10'
dh_auto_build
	make -j12
make[2]: Entering directory '/build/reproducible-path/abyss-2.3.10'
make  all-recursive
make[3]: Entering directory '/build/reproducible-path/abyss-2.3.10'
Making all in bin
make[4]: Entering directory '/build/reproducible-path/abyss-2.3.10/bin'
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Making all in doc
make[4]: Entering directory '/build/reproducible-path/abyss-2.3.10/doc'
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make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.10/doc'
Making all in Common
make[4]: Entering directory '/build/reproducible-path/abyss-2.3.10/Common'
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o libcommon_a-ContigID.o `test -f 'ContigID.cpp' || echo './'`ContigID.cpp
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o libcommon_a-Fcontrol.o `test -f 'Fcontrol.cpp' || echo './'`Fcontrol.cpp
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o libcommon_a-Histogram.o `test -f 'Histogram.cpp' || echo './'`Histogram.cpp
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o libcommon_a-Kmer.o `test -f 'Kmer.cpp' || echo './'`Kmer.cpp
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o libcommon_a-Log.o `test -f 'Log.cpp' || echo './'`Log.cpp
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o libcommon_a-Options.o `test -f 'Options.cpp' || echo './'`Options.cpp
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o libcommon_a-Sequence.o `test -f 'Sequence.cpp' || echo './'`Sequence.cpp
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o libcommon_a-SignalHandler.o `test -f 'SignalHandler.cpp' || echo './'`SignalHandler.cpp
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o libcommon_a-Timer.o `test -f 'Timer.cpp' || echo './'`Timer.cpp
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o libcommon_a-Uncompress.o `test -f 'Uncompress.cpp' || echo './'`Uncompress.cpp
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o libcommon_a-city.o `test -f 'city.cc' || echo './'`city.cc
rm -f libcommon.a
ar cr 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 
ranlib libcommon.a
make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.10/Common'
Making all in Graph
make[4]: Entering directory '/build/reproducible-path/abyss-2.3.10/Graph'
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I../Common -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o abyss_gc-gc.o `test -f 'gc.cc' || echo './'`gc.cc
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I../Common -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o abyss_todot-todot.o `test -f 'todot.cc' || echo './'`todot.cc
In file included from GraphIO.h:8,
                 from todot.cc:9:
DotIO.h: In instantiation of 'void write_edges(std::ostream&, const Graph&, typename boost::graph_traits<Graph>::vertex_descriptor, const EdgeProp*) [with Graph = ContigGraph<DirectedGraph<ContigProperties, DistanceEst> >; EdgeProp = DistanceEst; std::ostream = std::basic_ostream<char>; typename boost::graph_traits<Graph>::vertex_descriptor = ContigNode]':
DotIO.h:110:14:   required from 'std::ostream& write_dot(std::ostream&, const Graph&, const std::string&) [with Graph = ContigGraph<DirectedGraph<ContigProperties, DistanceEst> >; std::ostream = std::basic_ostream<char>; std::string = std::__cxx11::basic_string<char>]'
  110 |                 write_edges(out, g, *u, (edge_property_type*)NULL);
      |                 ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
DotIO.h:77:18:   required from 'std::ostream& write_dot(std::ostream&, const Graph&) [with Graph = ContigGraph<DirectedGraph<ContigProperties, DistanceEst> >; std::ostream = std::basic_ostream<char>]'
   77 |         return write_dot(out, g, "adj");
      |                ~~~~~~~~~^~~~~~~~~~~~~~~
DotIO.h:125:26:   required from 'std::ostream& operator<<(std::ostream&, const DotWriter<ContigGraph<DirectedGraph<ContigProperties, DistanceEst> > >&)'
  125 |                 return write_dot<Graph>(out, o.g);
      |                        ~~~~~~~~~~~~~~~~^~~~~~~~~~
GraphIO.h:33:14:   required from 'std::ostream& write_graph(std::ostream&, const Graph&, const std::string&, const std::string&) [with Graph = ContigGraph<DirectedGraph<ContigProperties, DistanceEst> >; std::ostream = std::basic_ostream<char>; std::string = std::__cxx11::basic_string<char>]'
   33 |                 return out << dot_writer(g);
      |                        ~~~~^~~~~~~~~~~~~~~~
todot.cc:186:14:   required from here
  186 |                 write_graph(cout, g, PROGRAM, commandLine);
      |                 ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
DotIO.h:44:43: warning: possibly dangling reference to a temporary [-Wdangling-reference]
   44 |                 const edge_property_type& ep = get(edge_bundle, g, e);
      |                                           ^~
DotIO.h:44:51: note: the temporary was destroyed at the end of the full expression 'get<DirectedGraph<ContigProperties, DistanceEst> >(boost::edge_bundle, (* & g), DirectedGraph<ContigProperties, DistanceEst>::out_edge_iterator(e))'
   44 |                 const edge_property_type& ep = get(edge_bundle, g, e);
      |                                                ~~~^~~~~~~~~~~~~~~~~~~
DotIO.h: In instantiation of 'void write_edges(std::ostream&, const Graph&, typename boost::graph_traits<Graph>::vertex_descriptor, const EdgeProp*) [with Graph = ContigGraph<DirectedGraph<ContigProperties, Distance> >; EdgeProp = Distance; std::ostream = std::basic_ostream<char>; typename boost::graph_traits<Graph>::vertex_descriptor = ContigNode]':
DotIO.h:110:14:   required from 'std::ostream& write_dot(std::ostream&, const Graph&, const std::string&) [with Graph = ContigGraph<DirectedGraph<ContigProperties, Distance> >; std::ostream = std::basic_ostream<char>; std::string = std::__cxx11::basic_string<char>]'
  110 |                 write_edges(out, g, *u, (edge_property_type*)NULL);
      |                 ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
DotIO.h:77:18:   required from 'std::ostream& write_dot(std::ostream&, const Graph&) [with Graph = ContigGraph<DirectedGraph<ContigProperties, Distance> >; std::ostream = std::basic_ostream<char>]'
   77 |         return write_dot(out, g, "adj");
      |                ~~~~~~~~~^~~~~~~~~~~~~~~
DotIO.h:125:26:   required from 'std::ostream& operator<<(std::ostream&, const DotWriter<ContigGraph<DirectedGraph<ContigProperties, Distance> > >&)'
  125 |                 return write_dot<Graph>(out, o.g);
      |                        ~~~~~~~~~~~~~~~~^~~~~~~~~~
GraphIO.h:33:14:   required from 'std::ostream& write_graph(std::ostream&, const Graph&, const std::string&, const std::string&) [with Graph = ContigGraph<DirectedGraph<ContigProperties, Distance> >; std::ostream = std::basic_ostream<char>; std::string = std::__cxx11::basic_string<char>]'
   33 |                 return out << dot_writer(g);
      |                        ~~~~^~~~~~~~~~~~~~~~
todot.cc:191:14:   required from here
  191 |                 write_graph(cout, g, PROGRAM, commandLine);
      |                 ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
DotIO.h:44:43: warning: possibly dangling reference to a temporary [-Wdangling-reference]
   44 |                 const edge_property_type& ep = get(edge_bundle, g, e);
      |                                           ^~
DotIO.h:44:51: note: the temporary was destroyed at the end of the full expression 'get<DirectedGraph<ContigProperties, Distance> >(boost::edge_bundle, (* & g), DirectedGraph<ContigProperties, Distance>::out_edge_iterator(e))'
   44 |                 const edge_property_type& ep = get(edge_bundle, g, e);
      |                                                ~~~^~~~~~~~~~~~~~~~~~~
g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations  -L/usr/lib/aarch64-linux-gnu/openmpi/lib    -Wl,-z,relro -Wl,-z,now -o abyss-gc abyss_gc-gc.o ../Common/libcommon.a -ldl -lm 
g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -L. -L/usr/lib/aarch64-linux-gnu/openmpi/lib    -Wl,-z,relro -Wl,-z,now -o abyss-todot abyss_todot-todot.o ../Common/libcommon.a -ldl -lm 
make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.10/Graph'
Making all in DataLayer
make[4]: Entering directory '/build/reproducible-path/abyss-2.3.10/DataLayer'
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o abyss_fac-fac.o `test -f 'fac.cc' || echo './'`fac.cc
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o libdatalayer_a-FastaReader.o `test -f 'FastaReader.cpp' || echo './'`FastaReader.cpp
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o libdatalayer_a-FastaWriter.o `test -f 'FastaWriter.cpp' || echo './'`FastaWriter.cpp
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o abyss_tofastq-abyss-tofastq.o `test -f 'abyss-tofastq.cc' || echo './'`abyss-tofastq.cc
rm -f libdatalayer.a
ar cr libdatalayer.a libdatalayer_a-FastaReader.o libdatalayer_a-FastaWriter.o 
ranlib libdatalayer.a
g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference  -L/usr/lib/aarch64-linux-gnu/openmpi/lib    -Wl,-z,relro -Wl,-z,now -o abyss-fac abyss_fac-fac.o libdatalayer.a ../Common/libcommon.a -ldl -lm 
g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference  -L/usr/lib/aarch64-linux-gnu/openmpi/lib    -Wl,-z,relro -Wl,-z,now -o abyss-tofastq abyss_tofastq-abyss-tofastq.o libdatalayer.a ../Common/libcommon.a -ldl -lm 
make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.10/DataLayer'
Making all in DataBase
make[4]: Entering directory '/build/reproducible-path/abyss-2.3.10/DataBase'
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o abyss_db_csv-DB.o `test -f 'DB.cc' || echo './'`DB.cc
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o abyss_db_csv-db-csv.o `test -f 'db-csv.cc' || echo './'`db-csv.cc
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o libdb_a-DB.o `test -f 'DB.cc' || echo './'`DB.cc
rm -f libdb.a
ar cr libdb.a libdb_a-DB.o ../Common/libcommon_a-ContigID.o ../Common/libcommon_a-Fcontrol.o ../Common/libcommon_a-Histogram.o ../Common/libcommon_a-Kmer.o ../Common/libcommon_a-Log.o ../Common/libcommon_a-Options.o ../Common/libcommon_a-Sequence.o ../Common/libcommon_a-SignalHandler.o ../Common/libcommon_a-Timer.o ../Common/libcommon_a-Uncompress.o ../Common/libcommon_a-city.o
ranlib libdb.a
g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference  -L/usr/lib/aarch64-linux-gnu/openmpi/lib    -Wl,-z,relro -Wl,-z,now -o abyss-db-csv abyss_db_csv-DB.o abyss_db_csv-db-csv.o -lsqlite3 -ldl -lm 
make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.10/DataBase'
Making all in FMIndex
make[4]: Entering directory '/build/reproducible-path/abyss-2.3.10/FMIndex'
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I../Common -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o abyss_count-count.o `test -f 'count.cc' || echo './'`count.cc
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I../Common -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o libfmindex_a-bit_array.o `test -f 'bit_array.cc' || echo './'`bit_array.cc
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I../Common -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o abyss_dawg-abyss-dawg.o `test -f 'abyss-dawg.cc' || echo './'`abyss-dawg.cc
rm -f libfmindex.a
ar cr libfmindex.a libfmindex_a-bit_array.o 
ranlib libfmindex.a
g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations  -L/usr/lib/aarch64-linux-gnu/openmpi/lib    -Wl,-z,relro -Wl,-z,now -o abyss-count abyss_count-count.o libfmindex.a ../Common/libcommon.a -ldl -lm 
g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations  -L/usr/lib/aarch64-linux-gnu/openmpi/lib    -Wl,-z,relro -Wl,-z,now -o abyss-dawg abyss_dawg-abyss-dawg.o libfmindex.a ../Common/libcommon.a -ldl -lm 
make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.10/FMIndex'
Making all in Assembly
make[4]: Entering directory '/build/reproducible-path/abyss-2.3.10/Assembly'
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o libassembly_a-AssemblyAlgorithms.o `test -f 'AssemblyAlgorithms.cc' || echo './'`AssemblyAlgorithms.cc
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o libassembly_a-Options.o `test -f 'Options.cc' || echo './'`Options.cc
rm -f libassembly.a
ar cr libassembly.a libassembly_a-AssemblyAlgorithms.o libassembly_a-Options.o ../Common/libcommon_a-ContigID.o ../Common/libcommon_a-Fcontrol.o ../Common/libcommon_a-Histogram.o ../Common/libcommon_a-Kmer.o ../Common/libcommon_a-Log.o ../Common/libcommon_a-Options.o ../Common/libcommon_a-Sequence.o ../Common/libcommon_a-SignalHandler.o ../Common/libcommon_a-Timer.o ../Common/libcommon_a-Uncompress.o ../Common/libcommon_a-city.o
ranlib libassembly.a
make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.10/Assembly'
Making all in dialign
make[4]: Entering directory '/build/reproducible-path/abyss-2.3.10/dialign'
gcc -DHAVE_CONFIG_H -I. -I..   -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0  -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o museq.o museq.c
gcc -DHAVE_CONFIG_H -I. -I..   -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0  -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o alig.o alig.c
gcc -DHAVE_CONFIG_H -I. -I..   -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0  -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o assemble.o assemble.c
gcc -DHAVE_CONFIG_H -I. -I..   -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0  -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o diag.o diag.c
gcc -DHAVE_CONFIG_H -I. -I..   -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0  -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o io.o io.c
gcc -DHAVE_CONFIG_H -I. -I..   -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0  -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o orf.o orf.c
gcc -DHAVE_CONFIG_H -I. -I..   -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0  -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o parameters.o parameters.c
gcc -DHAVE_CONFIG_H -I. -I..   -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0  -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o prob.o prob.c
gcc -DHAVE_CONFIG_H -I. -I..   -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0  -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o translate.o translate.c
assemble.c:40:20: warning: inline function 'align_diag' declared but never defined
   40 | extern inline char align_diag(struct alignment *algn, struct scr_matrix *smatrix, struct diag* dg);
      |                    ^~~~~~~~~~
assemble.c:37:32: warning: inline function 'find_eqc' declared but never defined
   37 | extern inline struct algn_pos *find_eqc(struct algn_pos **ap, int seqnum, int pos);
      |                                ^~~~~~~~
assemble.c:25:39: warning: inline function 'find_diags_guided' declared but never defined
   25 | extern inline struct simple_diag_col* find_diags_guided(struct scr_matrix *smatrix,
      |                                       ^~~~~~~~~~~~~~~~~
assemble.c:15:20: warning: inline function 'calc_ov_weight' declared but never defined
   15 | extern inline void calc_ov_weight(struct diag* dg, struct diag_col *dcol, struct scr_matrix* smatrix,
      |                    ^~~~~~~~~~~~~~
assemble.c:13:20: warning: inline function 'calc_weight' declared but never defined
   13 | extern inline void calc_weight(struct diag* dg, struct scr_matrix* smatrix,
      |                    ^~~~~~~~~~~
alig.c:15:20: warning: inline function 'calc_ov_weight' declared but never defined
   15 | extern inline void calc_ov_weight(struct diag* dg, struct diag_col *dcol, struct scr_matrix* smatrix,
      |                    ^~~~~~~~~~~~~~
alig.c:13:20: warning: inline function 'calc_weight' declared but never defined
   13 | extern inline void calc_weight(struct diag* dg, struct scr_matrix* smatrix,
      |                    ^~~~~~~~~~~
diag.c:1456:17: warning: 'real_calc_weight' is static but used in inline function 'find_diags_dyn' which is not static
 1456 |                 real_calc_weight(dg, smatrix, pdist,1,tmp_dist,algn);
      |                 ^~~~~~~~~~~~~~~~
io.c: In function 'read_scr_matrix':
io.c:270:17: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result]
  270 |                 fscanf( fp, "%i", &is);
      |                 ^~~~~~~~~~~~~~~~~~~~~~
io.c:282:5: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result]
  282 |     fscanf(fp, "%s\n", rline);
      |     ^~~~~~~~~~~~~~~~~~~~~~~~~
io.c: In function 'read_diag_prob_dist':
io.c:371:7: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result]
  371 |       fscanf( fp, "%li %li %Le\n", &ti,&tscr,&weight );
      |       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
rm -f libdialign.a
ar cr libdialign.a alig.o assemble.o diag.o io.o orf.o parameters.o prob.o translate.o 
ranlib libdialign.a
gcc  -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard  -L/usr/lib/aarch64-linux-gnu/openmpi/lib    -Wl,-z,relro -Wl,-z,now -o dialign museq.o libdialign.a -ldl -lm 
make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.10/dialign'
Making all in Align
make[4]: Entering directory '/build/reproducible-path/abyss-2.3.10/Align'
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I../Common -I../DataLayer -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o abyss_align-align.o `test -f 'align.cc' || echo './'`align.cc
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I../Common -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o libalign_a-alignGlobal.o `test -f 'alignGlobal.cc' || echo './'`alignGlobal.cc
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I../Common -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o libalign_a-dialign.o `test -f 'dialign.cpp' || echo './'`dialign.cpp
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I../Common -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o libalign_a-dna_diag_prob.o `test -f 'dna_diag_prob.cc' || echo './'`dna_diag_prob.cc
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I../Common -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o libalign_a-smith_waterman.o `test -f 'smith_waterman.cpp' || echo './'`smith_waterman.cpp
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I../Common -I../DataLayer -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o abyss_mergepairs-mergepairs.o `test -f 'mergepairs.cc' || echo './'`mergepairs.cc
rm -f libalign.a
ar cr libalign.a libalign_a-alignGlobal.o libalign_a-dialign.o libalign_a-dna_diag_prob.o libalign_a-smith_waterman.o 
ranlib libalign.a
g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference  -L/usr/lib/aarch64-linux-gnu/openmpi/lib    -Wl,-z,relro -Wl,-z,now -o abyss-align abyss_align-align.o ./libalign.a ../dialign/libdialign.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm 
g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference  -L/usr/lib/aarch64-linux-gnu/openmpi/lib    -Wl,-z,relro -Wl,-z,now -o abyss-mergepairs abyss_mergepairs-mergepairs.o ./libalign.a ../dialign/libdialign.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm 
make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.10/Align'
Making all in ABYSS
make[4]: Entering directory '/build/reproducible-path/abyss-2.3.10/ABYSS'
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o ABYSS-abyss.o `test -f 'abyss.cc' || echo './'`abyss.cc
g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations  -L/usr/lib/aarch64-linux-gnu/openmpi/lib    -Wl,-z,relro -Wl,-z,now -o ABYSS ABYSS-abyss.o ../DataBase/libdb.a -lsqlite3 -ldl -lm  ../Assembly/libassembly.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm 
make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.10/ABYSS'
Making all in Parallel
make[4]: Entering directory '/build/reproducible-path/abyss-2.3.10/Parallel'
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o ABYSS_P-parallelAbyss.o `test -f 'parallelAbyss.cpp' || echo './'`parallelAbyss.cpp
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o ABYSS_P-CommLayer.o `test -f 'CommLayer.cpp' || echo './'`CommLayer.cpp
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o ABYSS_P-NetworkSequenceCollection.o `test -f 'NetworkSequenceCollection.cpp' || echo './'`NetworkSequenceCollection.cpp
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o ABYSS_P-MessageBuffer.o `test -f 'MessageBuffer.cpp' || echo './'`MessageBuffer.cpp
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o ABYSS_P-Messages.o `test -f 'Messages.cpp' || echo './'`Messages.cpp
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -DPAIRED_DBG -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o abyss_paired_dbg_mpi-parallelAbyss.o `test -f 'parallelAbyss.cpp' || echo './'`parallelAbyss.cpp
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -DPAIRED_DBG -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o abyss_paired_dbg_mpi-CommLayer.o `test -f 'CommLayer.cpp' || echo './'`CommLayer.cpp
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -DPAIRED_DBG -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o abyss_paired_dbg_mpi-NetworkSequenceCollection.o `test -f 'NetworkSequenceCollection.cpp' || echo './'`NetworkSequenceCollection.cpp
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -DPAIRED_DBG -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o abyss_paired_dbg_mpi-MessageBuffer.o `test -f 'MessageBuffer.cpp' || echo './'`MessageBuffer.cpp
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -DPAIRED_DBG -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o abyss_paired_dbg_mpi-Messages.o `test -f 'Messages.cpp' || echo './'`Messages.cpp
g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations  -L/usr/lib/aarch64-linux-gnu/openmpi/lib    -Wl,-z,relro -Wl,-z,now -o ABYSS-P ABYSS_P-parallelAbyss.o ABYSS_P-CommLayer.o ABYSS_P-NetworkSequenceCollection.o ABYSS_P-MessageBuffer.o ABYSS_P-Messages.o ../Assembly/libassembly.a ../Common/libcommon.a ../DataLayer/libdatalayer.a ../DataBase/libdb.a -lsqlite3 -ldl -lm  -lmpi  -ldl -lm 
g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations  -L/usr/lib/aarch64-linux-gnu/openmpi/lib    -Wl,-z,relro -Wl,-z,now -o abyss-paired-dbg-mpi abyss_paired_dbg_mpi-parallelAbyss.o abyss_paired_dbg_mpi-CommLayer.o abyss_paired_dbg_mpi-NetworkSequenceCollection.o abyss_paired_dbg_mpi-MessageBuffer.o abyss_paired_dbg_mpi-Messages.o ../Assembly/libassembly.a ../Common/libcommon.a ../DataLayer/libdatalayer.a ../DataBase/libdb.a -lsqlite3 -ldl -lm  -lmpi  -ldl -lm 
make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.10/Parallel'
Making all in Bloom
make[4]: Entering directory '/build/reproducible-path/abyss-2.3.10/Bloom'
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I../Common -I../DataLayer -I../vendor -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o abyss_bloom-bloom.o `test -f 'bloom.cc' || echo './'`bloom.cc
g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations  -L/usr/lib/aarch64-linux-gnu/openmpi/lib    -Wl,-z,relro -Wl,-z,now -o abyss-bloom abyss_bloom-bloom.o ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a -ldl -lm 
make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.10/Bloom'
Making all in BloomDBG
make[4]: Entering directory '/build/reproducible-path/abyss-2.3.10/BloomDBG'
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I../Common -I../DataLayer -I../vendor -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o abyss_bloom_dbg-bloom-dbg.o `test -f 'bloom-dbg.cc' || echo './'`bloom-dbg.cc
g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations  -L/usr/lib/aarch64-linux-gnu/openmpi/lib    -Wl,-z,relro -Wl,-z,now -o abyss-bloom-dbg abyss_bloom_dbg-bloom-dbg.o ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm 
make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.10/BloomDBG'
Making all in Konnector
make[4]: Entering directory '/build/reproducible-path/abyss-2.3.10/Konnector'
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I../Common -I../DataLayer -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o konnector-konnector.o `test -f 'konnector.cc' || echo './'`konnector.cc
g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations  -L/usr/lib/aarch64-linux-gnu/openmpi/lib    -Wl,-z,relro -Wl,-z,now -o konnector konnector-konnector.o ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a -ldl -lm 
make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.10/Konnector'
Making all in Consensus
make[4]: Entering directory '/build/reproducible-path/abyss-2.3.10/Consensus'
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I../Common -I../DataLayer -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o Consensus-Consensus.o `test -f 'Consensus.cpp' || echo './'`Consensus.cpp
g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference  -L/usr/lib/aarch64-linux-gnu/openmpi/lib    -Wl,-z,relro -Wl,-z,now -o Consensus Consensus-Consensus.o ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm 
make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.10/Consensus'
Making all in DAssembler
make[4]: Entering directory '/build/reproducible-path/abyss-2.3.10/DAssembler'
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I../Common -I../DataLayer -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o DAssembler-DAssembler.o `test -f 'DAssembler.cpp' || echo './'`DAssembler.cpp
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I../Common -I../DataLayer -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o DAssembler-RotatedRead.o `test -f 'RotatedRead.cpp' || echo './'`RotatedRead.cpp
g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference  -L/usr/lib/aarch64-linux-gnu/openmpi/lib    -Wl,-z,relro -Wl,-z,now -o DAssembler DAssembler-DAssembler.o DAssembler-RotatedRead.o ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm 
make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.10/DAssembler'
Making all in DistanceEst
make[4]: Entering directory '/build/reproducible-path/abyss-2.3.10/DistanceEst'
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I../Common -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o DistanceEst-DistanceEst.o `test -f 'DistanceEst.cpp' || echo './'`DistanceEst.cpp
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I../Common -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o DistanceEst-MLE.o `test -f 'MLE.cpp' || echo './'`MLE.cpp
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I../Common -D SAM_SEQ_QUAL=1 -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o DistanceEst_ssq-DistanceEst.o `test -f 'DistanceEst.cpp' || echo './'`DistanceEst.cpp
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I../Common -D SAM_SEQ_QUAL=1 -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o DistanceEst_ssq-MLE.o `test -f 'MLE.cpp' || echo './'`MLE.cpp
g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference  -L/usr/lib/aarch64-linux-gnu/openmpi/lib    -Wl,-z,relro -Wl,-z,now -o DistanceEst-ssq DistanceEst_ssq-DistanceEst.o DistanceEst_ssq-MLE.o ../DataBase/libdb.a -lsqlite3 -ldl -lm  ../Common/libcommon.a -ldl -lm 
g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference  -L/usr/lib/aarch64-linux-gnu/openmpi/lib    -Wl,-z,relro -Wl,-z,now -o DistanceEst DistanceEst-DistanceEst.o DistanceEst-MLE.o ../DataBase/libdb.a -lsqlite3 -ldl -lm  ../Common/libcommon.a -ldl -lm 
make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.10/DistanceEst'
Making all in KAligner
make[4]: Entering directory '/build/reproducible-path/abyss-2.3.10/KAligner'
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I../Common -I../DataLayer -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o KAligner-KAligner.o `test -f 'KAligner.cpp' || echo './'`KAligner.cpp
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I../Common -I../DataLayer -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o KAligner-Aligner.o `test -f 'Aligner.cpp' || echo './'`Aligner.cpp
g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations  -L/usr/lib/aarch64-linux-gnu/openmpi/lib    -Wl,-z,relro -Wl,-z,now -o KAligner KAligner-KAligner.o KAligner-Aligner.o ../DataLayer/libdatalayer.a ../Common/libcommon.a -lpthread -ldl -lm 
make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.10/KAligner'
Making all in Layout
make[4]: Entering directory '/build/reproducible-path/abyss-2.3.10/Layout'
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I../Common -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o abyss_layout-layout.o `test -f 'layout.cc' || echo './'`layout.cc
In file included from ../Graph/GraphIO.h:8,
                 from layout.cc:8:
../Graph/DotIO.h: In instantiation of 'void write_edges(std::ostream&, const Graph&, typename boost::graph_traits<Graph>::vertex_descriptor, const EdgeProp*) [with Graph = ContigGraph<DirectedGraph<Length, Distance> >; EdgeProp = Distance; std::ostream = std::basic_ostream<char>; typename boost::graph_traits<Graph>::vertex_descriptor = ContigNode]':
../Graph/DotIO.h:110:14:   required from 'std::ostream& write_dot(std::ostream&, const Graph&, const std::string&) [with Graph = ContigGraph<DirectedGraph<Length, Distance> >; std::ostream = std::basic_ostream<char>; std::string = std::__cxx11::basic_string<char>]'
  110 |                 write_edges(out, g, *u, (edge_property_type*)NULL);
      |                 ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../Graph/DotIO.h:77:18:   required from 'std::ostream& write_dot(std::ostream&, const Graph&) [with Graph = ContigGraph<DirectedGraph<Length, Distance> >; std::ostream = std::basic_ostream<char>]'
   77 |         return write_dot(out, g, "adj");
      |                ~~~~~~~~~^~~~~~~~~~~~~~~
layout.cc:314:12:   required from here
  314 |                 write_dot(out, g);
      |                 ~~~~~~~~~^~~~~~~~
../Graph/DotIO.h:44:43: warning: possibly dangling reference to a temporary [-Wdangling-reference]
   44 |                 const edge_property_type& ep = get(edge_bundle, g, e);
      |                                           ^~
../Graph/DotIO.h:44:51: note: the temporary was destroyed at the end of the full expression 'get<DirectedGraph<Length, Distance> >(boost::edge_bundle, (* & g), DirectedGraph<Length, Distance>::out_edge_iterator(e))'
   44 |                 const edge_property_type& ep = get(edge_bundle, g, e);
      |                                                ~~~^~~~~~~~~~~~~~~~~~~
g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations  -L/usr/lib/aarch64-linux-gnu/openmpi/lib    -Wl,-z,relro -Wl,-z,now -o abyss-layout abyss_layout-layout.o ../Common/libcommon.a -ldl -lm 
make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.10/Layout'
Making all in LogKmerCount
make[4]: Entering directory '/build/reproducible-path/abyss-2.3.10/LogKmerCount'
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I../Common -I../DataLayer -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o logcounter-logcounter.o `test -f 'logcounter.cc' || echo './'`logcounter.cc
g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference  -L/usr/lib/aarch64-linux-gnu/openmpi/lib    -Wl,-z,relro -Wl,-z,now -o logcounter logcounter-logcounter.o ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a -ldl -lm 
make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.10/LogKmerCount'
Making all in Map
make[4]: Entering directory '/build/reproducible-path/abyss-2.3.10/Map'
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I../Common -I../DataLayer -I../FMIndex -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o abyss_index-index.o `test -f 'index.cc' || echo './'`index.cc
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I../Common -I../DataLayer -I../FMIndex -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o abyss_map-map.o `test -f 'map.cc' || echo './'`map.cc
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I../Common -I../DataLayer -I../FMIndex -D SAM_SEQ_QUAL=1 -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o abyss_map_ssq-map.o `test -f 'map.cc' || echo './'`map.cc
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I../Common -I../DataLayer -I../FMIndex -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o abyss_overlap-overlap.o `test -f 'overlap.cc' || echo './'`overlap.cc
In file included from ../Graph/GraphIO.h:8,
                 from overlap.cc:23:
../Graph/DotIO.h: In instantiation of 'void write_edges(std::ostream&, const Graph&, typename boost::graph_traits<Graph>::vertex_descriptor, const EdgeProp*) [with Graph = ContigGraph<DirectedGraph<ContigProperties, Distance> >; EdgeProp = Distance; std::ostream = std::basic_ostream<char>; typename boost::graph_traits<Graph>::vertex_descriptor = ContigNode]':
../Graph/DotIO.h:110:14:   required from 'std::ostream& write_dot(std::ostream&, const Graph&, const std::string&) [with Graph = ContigGraph<DirectedGraph<ContigProperties, Distance> >; std::ostream = std::basic_ostream<char>; std::string = std::__cxx11::basic_string<char>]'
  110 |                 write_edges(out, g, *u, (edge_property_type*)NULL);
      |                 ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../Graph/DotIO.h:77:18:   required from 'std::ostream& write_dot(std::ostream&, const Graph&) [with Graph = ContigGraph<DirectedGraph<ContigProperties, Distance> >; std::ostream = std::basic_ostream<char>]'
   77 |         return write_dot(out, g, "adj");
      |                ~~~~~~~~~^~~~~~~~~~~~~~~
../Graph/DotIO.h:125:26:   required from 'std::ostream& operator<<(std::ostream&, const DotWriter<ContigGraph<DirectedGraph<ContigProperties, Distance> > >&)'
  125 |                 return write_dot<Graph>(out, o.g);
      |                        ~~~~~~~~~~~~~~~~^~~~~~~~~~
../Graph/GraphIO.h:33:14:   required from 'std::ostream& write_graph(std::ostream&, const Graph&, const std::string&, const std::string&) [with Graph = ContigGraph<DirectedGraph<ContigProperties, Distance> >; std::ostream = std::basic_ostream<char>; std::string = std::__cxx11::basic_string<char>]'
   33 |                 return out << dot_writer(g);
      |                        ~~~~^~~~~~~~~~~~~~~~
overlap.cc:502:13:   required from here
  502 |         write_graph(cout, g, PROGRAM, commandLine);
      |         ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../Graph/DotIO.h:44:43: warning: possibly dangling reference to a temporary [-Wdangling-reference]
   44 |                 const edge_property_type& ep = get(edge_bundle, g, e);
      |                                           ^~
../Graph/DotIO.h:44:51: note: the temporary was destroyed at the end of the full expression 'get<DirectedGraph<ContigProperties, Distance> >(boost::edge_bundle, (* & g), DirectedGraph<ContigProperties, Distance>::out_edge_iterator(e))'
   44 |                 const edge_property_type& ep = get(edge_bundle, g, e);
      |                                                ~~~^~~~~~~~~~~~~~~~~~~
g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations  -L/usr/lib/aarch64-linux-gnu/openmpi/lib    -Wl,-z,relro -Wl,-z,now -o abyss-index abyss_index-index.o ../FMIndex/libfmindex.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm 
g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations  -L/usr/lib/aarch64-linux-gnu/openmpi/lib    -Wl,-z,relro -Wl,-z,now -o abyss-map abyss_map-map.o ../FMIndex/libfmindex.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../DataBase/libdb.a -lsqlite3 -ldl -lm  -ldl -lm 
g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations  -L/usr/lib/aarch64-linux-gnu/openmpi/lib    -Wl,-z,relro -Wl,-z,now -o abyss-map-ssq abyss_map_ssq-map.o ../FMIndex/libfmindex.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../DataBase/libdb.a -lsqlite3 -ldl -lm  -ldl -lm 
g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations  -L/usr/lib/aarch64-linux-gnu/openmpi/lib    -Wl,-z,relro -Wl,-z,now -o abyss-overlap abyss_overlap-overlap.o ../FMIndex/libfmindex.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm 
make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.10/Map'
Making all in MergePaths
make[4]: Entering directory '/build/reproducible-path/abyss-2.3.10/MergePaths'
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I../Common -I../DataLayer -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o MergePaths-MergePaths.o `test -f 'MergePaths.cpp' || echo './'`MergePaths.cpp
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I../Align -I../Common -I../DataLayer -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o MergeContigs-MergeContigs.o `test -f 'MergeContigs.cpp' || echo './'`MergeContigs.cpp
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I../Align -I../Common -I../DataLayer -I../SimpleGraph -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o PathConsensus-PathConsensus.o `test -f 'PathConsensus.cpp' || echo './'`PathConsensus.cpp
In file included from ../Graph/GraphIO.h:8,
                 from MergeContigs.cpp:13:
../Graph/DotIO.h: In instantiation of 'void write_edges(std::ostream&, const Graph&, typename boost::graph_traits<Graph>::vertex_descriptor, const EdgeProp*) [with Graph = ContigGraph<DirectedGraph<ContigProperties, Distance> >; EdgeProp = Distance; std::ostream = std::basic_ostream<char>; typename boost::graph_traits<Graph>::vertex_descriptor = ContigNode]':
../Graph/DotIO.h:110:14:   required from 'std::ostream& write_dot(std::ostream&, const Graph&, const std::string&) [with Graph = ContigGraph<DirectedGraph<ContigProperties, Distance> >; std::ostream = std::basic_ostream<char>; std::string = std::__cxx11::basic_string<char>]'
  110 |                 write_edges(out, g, *u, (edge_property_type*)NULL);
      |                 ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../Graph/DotIO.h:77:18:   required from 'std::ostream& write_dot(std::ostream&, const Graph&) [with Graph = ContigGraph<DirectedGraph<ContigProperties, Distance> >; std::ostream = std::basic_ostream<char>]'
   77 |         return write_dot(out, g, "adj");
      |                ~~~~~~~~~^~~~~~~~~~~~~~~
../Graph/DotIO.h:125:26:   required from 'std::ostream& operator<<(std::ostream&, const DotWriter<ContigGraph<DirectedGraph<ContigProperties, Distance> > >&)'
  125 |                 return write_dot<Graph>(out, o.g);
      |                        ~~~~~~~~~~~~~~~~^~~~~~~~~~
../Graph/GraphIO.h:33:14:   required from 'std::ostream& write_graph(std::ostream&, const Graph&, const std::string&, const std::string&) [with Graph = ContigGraph<DirectedGraph<ContigProperties, Distance> >; std::ostream = std::basic_ostream<char>; std::string = std::__cxx11::basic_string<char>]'
   33 |                 return out << dot_writer(g);
      |                        ~~~~^~~~~~~~~~~~~~~~
MergeContigs.cpp:428:13:   required from here
  428 |         write_graph(fout, g, PROGRAM, commandLine);
      |         ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../Graph/DotIO.h:44:43: warning: possibly dangling reference to a temporary [-Wdangling-reference]
   44 |                 const edge_property_type& ep = get(edge_bundle, g, e);
      |                                           ^~
../Graph/DotIO.h:44:51: note: the temporary was destroyed at the end of the full expression 'get<DirectedGraph<ContigProperties, Distance> >(boost::edge_bundle, (* & g), DirectedGraph<ContigProperties, Distance>::out_edge_iterator(e))'
   44 |                 const edge_property_type& ep = get(edge_bundle, g, e);
      |                                                ~~~^~~~~~~~~~~~~~~~~~~
In file included from ../Graph/GraphIO.h:8,
                 from PathConsensus.cpp:16:
../Graph/DotIO.h: In instantiation of 'void write_edges(std::ostream&, const Graph&, typename boost::graph_traits<Graph>::vertex_descriptor, const EdgeProp*) [with Graph = ContigGraph<DirectedGraph<ContigProperties, Distance> >; EdgeProp = Distance; std::ostream = std::basic_ostream<char>; typename boost::graph_traits<Graph>::vertex_descriptor = ContigNode]':
../Graph/DotIO.h:110:14:   required from 'std::ostream& write_dot(std::ostream&, const Graph&, const std::string&) [with Graph = ContigGraph<DirectedGraph<ContigProperties, Distance> >; std::ostream = std::basic_ostream<char>; std::string = std::__cxx11::basic_string<char>]'
  110 |                 write_edges(out, g, *u, (edge_property_type*)NULL);
      |                 ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../Graph/DotIO.h:77:18:   required from 'std::ostream& write_dot(std::ostream&, const Graph&) [with Graph = ContigGraph<DirectedGraph<ContigProperties, Distance> >; std::ostream = std::basic_ostream<char>]'
   77 |         return write_dot(out, g, "adj");
      |                ~~~~~~~~~^~~~~~~~~~~~~~~
../Graph/DotIO.h:125:26:   required from 'std::ostream& operator<<(std::ostream&, const DotWriter<ContigGraph<DirectedGraph<ContigProperties, Distance> > >&)'
  125 |                 return write_dot<Graph>(out, o.g);
      |                        ~~~~~~~~~~~~~~~~^~~~~~~~~~
../Graph/GraphIO.h:33:14:   required from 'std::ostream& write_graph(std::ostream&, const Graph&, const std::string&, const std::string&) [with Graph = ContigGraph<DirectedGraph<ContigProperties, Distance> >; std::ostream = std::basic_ostream<char>; std::string = std::__cxx11::basic_string<char>]'
   33 |                 return out << dot_writer(g);
      |                        ~~~~^~~~~~~~~~~~~~~~
PathConsensus.cpp:999:14:   required from here
  999 |                 write_graph(fout, g, PROGRAM, commandLine);
      |                 ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../Graph/DotIO.h:44:43: warning: possibly dangling reference to a temporary [-Wdangling-reference]
   44 |                 const edge_property_type& ep = get(edge_bundle, g, e);
      |                                           ^~
../Graph/DotIO.h:44:51: note: the temporary was destroyed at the end of the full expression 'get<DirectedGraph<ContigProperties, Distance> >(boost::edge_bundle, (* & g), DirectedGraph<ContigProperties, Distance>::out_edge_iterator(e))'
   44 |                 const edge_property_type& ep = get(edge_bundle, g, e);
      |                                                ~~~^~~~~~~~~~~~~~~~~~~
g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations  -L/usr/lib/aarch64-linux-gnu/openmpi/lib    -Wl,-z,relro -Wl,-z,now -o MergeContigs MergeContigs-MergeContigs.o ../DataBase/libdb.a -lsqlite3 -ldl -lm  ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a -ldl -lm 
g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations  -L/usr/lib/aarch64-linux-gnu/openmpi/lib    -Wl,-z,relro -Wl,-z,now -o PathConsensus PathConsensus-PathConsensus.o ../DataBase/libdb.a -lsqlite3 -ldl -lm  ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a ../dialign/libdialign.a -ldl -lm 
g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations  -L/usr/lib/aarch64-linux-gnu/openmpi/lib    -Wl,-z,relro -Wl,-z,now -o MergePaths MergePaths-MergePaths.o ../DataBase/libdb.a -lsqlite3 -ldl -lm  ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm 
make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.10/MergePaths'
Making all in Overlap
make[4]: Entering directory '/build/reproducible-path/abyss-2.3.10/Overlap'
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I../Common -I../DataLayer -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o Overlap-Overlap.o `test -f 'Overlap.cpp' || echo './'`Overlap.cpp
Overlap.cpp: In function 'int main(int, char**)':
Overlap.cpp:513:40: warning: possibly dangling reference to a temporary [-Wdangling-reference]
  513 |                         const Overlap& ep = get(edge_bundle, scaffoldGraph, e);
      |                                        ^~
Overlap.cpp:513:48: note: the temporary was destroyed at the end of the full expression 'get<DirectedGraph<NoProperty, Overlap> >(boost::edge_bundle, scaffoldGraph, DirectedGraph<NoProperty, Overlap>::out_edge_iterator(e))'
  513 |                         const Overlap& ep = get(edge_bundle, scaffoldGraph, e);
      |                                             ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../Graph/GraphIO.h:8,
                 from Overlap.cpp:16:
../Graph/DotIO.h: In instantiation of 'void write_edges(std::ostream&, const Graph&, typename boost::graph_traits<Graph>::vertex_descriptor, const EdgeProp*) [with Graph = ContigGraph<DirectedGraph<NoProperty, Overlap> >; EdgeProp = Overlap; std::ostream = std::basic_ostream<char>; typename boost::graph_traits<Graph>::vertex_descriptor = ContigNode]':
../Graph/DotIO.h:110:14:   required from 'std::ostream& write_dot(std::ostream&, const Graph&, const std::string&) [with Graph = ContigGraph<DirectedGraph<NoProperty, Overlap> >; std::ostream = std::basic_ostream<char>; std::string = std::__cxx11::basic_string<char>]'
  110 |                 write_edges(out, g, *u, (edge_property_type*)NULL);
      |                 ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../Graph/DotIO.h:77:18:   required from 'std::ostream& write_dot(std::ostream&, const Graph&) [with Graph = ContigGraph<DirectedGraph<NoProperty, Overlap> >; std::ostream = std::basic_ostream<char>]'
   77 |         return write_dot(out, g, "adj");
      |                ~~~~~~~~~^~~~~~~~~~~~~~~
../Graph/DotIO.h:125:26:   required from 'std::ostream& operator<<(std::ostream&, const DotWriter<ContigGraph<DirectedGraph<NoProperty, Overlap> > >&)'
  125 |                 return write_dot<Graph>(out, o.g);
      |                        ~~~~~~~~~~~~~~~~^~~~~~~~~~
Overlap.cpp:481:35:   required from here
  481 |                 cout << dot_writer(scaffoldGraph);
      |                                                 ^
../Graph/DotIO.h:44:43: warning: possibly dangling reference to a temporary [-Wdangling-reference]
   44 |                 const edge_property_type& ep = get(edge_bundle, g, e);
      |                                           ^~
../Graph/DotIO.h:44:51: note: the temporary was destroyed at the end of the full expression 'get<DirectedGraph<NoProperty, Overlap> >(boost::edge_bundle, (* & g), DirectedGraph<NoProperty, Overlap>::out_edge_iterator(e))'
   44 |                 const edge_property_type& ep = get(edge_bundle, g, e);
      |                                                ~~~^~~~~~~~~~~~~~~~~~~
../Graph/DotIO.h: In instantiation of 'void write_edges(std::ostream&, const Graph&, typename boost::graph_traits<Graph>::vertex_descriptor, const EdgeProp*) [with Graph = ContigGraph<DirectedGraph<ContigProperties, Distance> >; EdgeProp = Distance; std::ostream = std::basic_ostream<char>; typename boost::graph_traits<Graph>::vertex_descriptor = ContigNode]':
../Graph/DotIO.h:110:14:   required from 'std::ostream& write_dot(std::ostream&, const Graph&, const std::string&) [with Graph = ContigGraph<DirectedGraph<ContigProperties, Distance> >; std::ostream = std::basic_ostream<char>; std::string = std::__cxx11::basic_string<char>]'
  110 |                 write_edges(out, g, *u, (edge_property_type*)NULL);
      |                 ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../Graph/DotIO.h:77:18:   required from 'std::ostream& write_dot(std::ostream&, const Graph&) [with Graph = ContigGraph<DirectedGraph<ContigProperties, Distance> >; std::ostream = std::basic_ostream<char>]'
   77 |         return write_dot(out, g, "adj");
      |                ~~~~~~~~~^~~~~~~~~~~~~~~
../Graph/DotIO.h:125:26:   required from 'std::ostream& operator<<(std::ostream&, const DotWriter<ContigGraph<DirectedGraph<ContigProperties, Distance> > >&)'
  125 |                 return write_dot<Graph>(out, o.g);
      |                        ~~~~~~~~~~~~~~~~^~~~~~~~~~
../Graph/GraphIO.h:33:14:   required from 'std::ostream& write_graph(std::ostream&, const Graph&, const std::string&, const std::string&) [with Graph = ContigGraph<DirectedGraph<ContigProperties, Distance> >; std::ostream = std::basic_ostream<char>; std::string = std::__cxx11::basic_string<char>]'
   33 |                 return out << dot_writer(g);
      |                        ~~~~^~~~~~~~~~~~~~~~
Overlap.cpp:587:14:   required from here
  587 |                 write_graph(fout, graph, PROGRAM, commandLine);
      |                 ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../Graph/DotIO.h:44:43: warning: possibly dangling reference to a temporary [-Wdangling-reference]
   44 |                 const edge_property_type& ep = get(edge_bundle, g, e);
      |                                           ^~
../Graph/DotIO.h:44:51: note: the temporary was destroyed at the end of the full expression 'get<DirectedGraph<ContigProperties, Distance> >(boost::edge_bundle, (* & g), DirectedGraph<ContigProperties, Distance>::out_edge_iterator(e))'
   44 |                 const edge_property_type& ep = get(edge_bundle, g, e);
      |                                                ~~~^~~~~~~~~~~~~~~~~~~
g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations  -L/usr/lib/aarch64-linux-gnu/openmpi/lib    -Wl,-z,relro -Wl,-z,now -o Overlap Overlap-Overlap.o ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm 
make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.10/Overlap'
Making all in PairedDBG
make[4]: Entering directory '/build/reproducible-path/abyss-2.3.10/PairedDBG'
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -DPAIRED_DBG -I.. -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o abyss_paired_dbg-abyss-paired-dbg.o `test -f 'abyss-paired-dbg.cc' || echo './'`abyss-paired-dbg.cc
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -DPAIRED_DBG -I.. -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o abyss_paired_dbg-KmerPair.o `test -f 'KmerPair.cc' || echo './'`KmerPair.cc
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..   -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o KmerPair.o KmerPair.cc
rm -f libpaireddbg.a
ar cr libpaireddbg.a KmerPair.o 
ranlib libpaireddbg.a
g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations  -L/usr/lib/aarch64-linux-gnu/openmpi/lib    -Wl,-z,relro -Wl,-z,now -o abyss-paired-dbg abyss_paired_dbg-abyss-paired-dbg.o abyss_paired_dbg-KmerPair.o ../Assembly/libassembly.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../DataBase/libdb.a -lsqlite3 -ldl -lm  -ldl -lm 
make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.10/PairedDBG'
Making all in ParseAligns
make[4]: Entering directory '/build/reproducible-path/abyss-2.3.10/ParseAligns'
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I../Common -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o abyss_fixmate-abyss-fixmate.o `test -f 'abyss-fixmate.cc' || echo './'`abyss-fixmate.cc
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I../Common -D SAM_SEQ_QUAL=1 -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o abyss_fixmate_ssq-abyss-fixmate.o `test -f 'abyss-fixmate.cc' || echo './'`abyss-fixmate.cc
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I../Common -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o ParseAligns-ParseAligns.o `test -f 'ParseAligns.cpp' || echo './'`ParseAligns.cpp
g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference  -L/usr/lib/aarch64-linux-gnu/openmpi/lib    -Wl,-z,relro -Wl,-z,now -o ParseAligns ParseAligns-ParseAligns.o ../Common/libcommon.a -ldl -lm 
g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference  -L/usr/lib/aarch64-linux-gnu/openmpi/lib    -Wl,-z,relro -Wl,-z,now -o abyss-fixmate abyss_fixmate-abyss-fixmate.o ../DataBase/libdb.a -lsqlite3 -ldl -lm  ../Common/libcommon.a -ldl -lm 
g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference  -L/usr/lib/aarch64-linux-gnu/openmpi/lib    -Wl,-z,relro -Wl,-z,now -o abyss-fixmate-ssq abyss_fixmate_ssq-abyss-fixmate.o ../DataBase/libdb.a -lsqlite3 -ldl -lm  ../Common/libcommon.a -ldl -lm 
make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.10/ParseAligns'
Making all in PathOverlap
make[4]: Entering directory '/build/reproducible-path/abyss-2.3.10/PathOverlap'
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I../Common -I../DataLayer -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o PathOverlap-PathOverlap.o `test -f 'PathOverlap.cpp' || echo './'`PathOverlap.cpp
In file included from ../Graph/GraphIO.h:8,
                 from PathOverlap.cpp:10:
../Graph/DotIO.h: In instantiation of 'void write_edges(std::ostream&, const Graph&, typename boost::graph_traits<Graph>::vertex_descriptor, const EdgeProp*) [with Graph = ContigGraph<DirectedGraph<ContigProperties, Distance> >; EdgeProp = Distance; std::ostream = std::basic_ostream<char>; typename boost::graph_traits<Graph>::vertex_descriptor = ContigNode]':
../Graph/DotIO.h:110:14:   required from 'std::ostream& write_dot(std::ostream&, const Graph&, const std::string&) [with Graph = ContigGraph<DirectedGraph<ContigProperties, Distance> >; std::ostream = std::basic_ostream<char>; std::string = std::__cxx11::basic_string<char>]'
  110 |                 write_edges(out, g, *u, (edge_property_type*)NULL);
      |                 ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../Graph/DotIO.h:77:18:   required from 'std::ostream& write_dot(std::ostream&, const Graph&) [with Graph = ContigGraph<DirectedGraph<ContigProperties, Distance> >; std::ostream = std::basic_ostream<char>]'
   77 |         return write_dot(out, g, "adj");
      |                ~~~~~~~~~^~~~~~~~~~~~~~~
../Graph/DotIO.h:125:26:   required from 'std::ostream& operator<<(std::ostream&, const DotWriter<ContigGraph<DirectedGraph<ContigProperties, Distance> > >&)'
  125 |                 return write_dot<Graph>(out, o.g);
      |                        ~~~~~~~~~~~~~~~~^~~~~~~~~~
../Graph/GraphIO.h:33:14:   required from 'std::ostream& write_graph(std::ostream&, const Graph&, const std::string&, const std::string&) [with Graph = ContigGraph<DirectedGraph<ContigProperties, Distance> >; std::ostream = std::basic_ostream<char>; std::string = std::__cxx11::basic_string<char>]'
   33 |                 return out << dot_writer(g);
      |                        ~~~~^~~~~~~~~~~~~~~~
PathOverlap.cpp:709:14:   required from here
  709 |                 write_graph(out, g, PROGRAM, commandLine);
      |                 ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../Graph/DotIO.h:44:43: warning: possibly dangling reference to a temporary [-Wdangling-reference]
   44 |                 const edge_property_type& ep = get(edge_bundle, g, e);
      |                                           ^~
../Graph/DotIO.h:44:51: note: the temporary was destroyed at the end of the full expression 'get<DirectedGraph<ContigProperties, Distance> >(boost::edge_bundle, (* & g), DirectedGraph<ContigProperties, Distance>::out_edge_iterator(e))'
   44 |                 const edge_property_type& ep = get(edge_bundle, g, e);
      |                                                ~~~^~~~~~~~~~~~~~~~~~~
g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations  -L/usr/lib/aarch64-linux-gnu/openmpi/lib    -Wl,-z,relro -Wl,-z,now -o PathOverlap PathOverlap-PathOverlap.o ../DataBase/libdb.a -lsqlite3 -ldl -lm  ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm 
make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.10/PathOverlap'
Making all in PopBubbles
make[4]: Entering directory '/build/reproducible-path/abyss-2.3.10/PopBubbles'
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I../Align -I../Common -I../DataLayer -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o PopBubbles-PopBubbles.o `test -f 'PopBubbles.cpp' || echo './'`PopBubbles.cpp
In file included from ../Graph/GraphIO.h:8,
                 from PopBubbles.cpp:16:
../Graph/DotIO.h: In instantiation of 'void write_edges(std::ostream&, const Graph&, typename boost::graph_traits<Graph>::vertex_descriptor, const EdgeProp*) [with Graph = ContigGraph<DirectedGraph<ContigProperties, Distance> >; EdgeProp = Distance; std::ostream = std::basic_ostream<char>; typename boost::graph_traits<Graph>::vertex_descriptor = ContigNode]':
../Graph/DotIO.h:110:14:   required from 'std::ostream& write_dot(std::ostream&, const Graph&, const std::string&) [with Graph = ContigGraph<DirectedGraph<ContigProperties, Distance> >; std::ostream = std::basic_ostream<char>; std::string = std::__cxx11::basic_string<char>]'
  110 |                 write_edges(out, g, *u, (edge_property_type*)NULL);
      |                 ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../Graph/DotIO.h:77:18:   required from 'std::ostream& write_dot(std::ostream&, const Graph&) [with Graph = ContigGraph<DirectedGraph<ContigProperties, Distance> >; std::ostream = std::basic_ostream<char>]'
   77 |         return write_dot(out, g, "adj");
      |                ~~~~~~~~~^~~~~~~~~~~~~~~
../Graph/DotIO.h:125:26:   required from 'std::ostream& operator<<(std::ostream&, const DotWriter<ContigGraph<DirectedGraph<ContigProperties, Distance> > >&)'
  125 |                 return write_dot<Graph>(out, o.g);
      |                        ~~~~~~~~~~~~~~~~^~~~~~~~~~
../Graph/GraphIO.h:33:14:   required from 'std::ostream& write_graph(std::ostream&, const Graph&, const std::string&, const std::string&) [with Graph = ContigGraph<DirectedGraph<ContigProperties, Distance> >; std::ostream = std::basic_ostream<char>; std::string = std::__cxx11::basic_string<char>]'
   33 |                 return out << dot_writer(g);
      |                        ~~~~^~~~~~~~~~~~~~~~
PopBubbles.cpp:723:14:   required from here
  723 |                 write_graph(fout, g, PROGRAM, commandLine);
      |                 ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../Graph/DotIO.h:44:43: warning: possibly dangling reference to a temporary [-Wdangling-reference]
   44 |                 const edge_property_type& ep = get(edge_bundle, g, e);
      |                                           ^~
../Graph/DotIO.h:44:51: note: the temporary was destroyed at the end of the full expression 'get<DirectedGraph<ContigProperties, Distance> >(boost::edge_bundle, (* & g), DirectedGraph<ContigProperties, Distance>::out_edge_iterator(e))'
   44 |                 const edge_property_type& ep = get(edge_bundle, g, e);
      |                                                ~~~^~~~~~~~~~~~~~~~~~~
g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations  -L/usr/lib/aarch64-linux-gnu/openmpi/lib    -Wl,-z,relro -Wl,-z,now -o PopBubbles PopBubbles-PopBubbles.o ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a ../dialign/libdialign.a -ldl -lm 
make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.10/PopBubbles'
Making all in Scaffold
make[4]: Entering directory '/build/reproducible-path/abyss-2.3.10/Scaffold'
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I../Common -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o abyss_scaffold-scaffold.o `test -f 'scaffold.cc' || echo './'`scaffold.cc
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I../Common -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o abyss_junction-junction.o `test -f 'junction.cc' || echo './'`junction.cc
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I../Common -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o abyss_longseqdist-longseqdist.o `test -f 'longseqdist.cpp' || echo './'`longseqdist.cpp
In file included from ../Graph/GraphIO.h:8,
                 from longseqdist.cpp:9:
../Graph/DotIO.h: In instantiation of 'void write_edges(std::ostream&, const Graph&, typename boost::graph_traits<Graph>::vertex_descriptor, const EdgeProp*) [with Graph = ContigGraph<DirectedGraph<Length, DistanceEst> >; EdgeProp = DistanceEst; std::ostream = std::basic_ostream<char>; typename boost::graph_traits<Graph>::vertex_descriptor = ContigNode]':
../Graph/DotIO.h:110:14:   required from 'std::ostream& write_dot(std::ostream&, const Graph&, const std::string&) [with Graph = ContigGraph<DirectedGraph<Length, DistanceEst> >; std::ostream = std::basic_ostream<char>; std::string = std::__cxx11::basic_string<char>]'
  110 |                 write_edges(out, g, *u, (edge_property_type*)NULL);
      |                 ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../Graph/DotIO.h:77:18:   required from 'std::ostream& write_dot(std::ostream&, const Graph&) [with Graph = ContigGraph<DirectedGraph<Length, DistanceEst> >; std::ostream = std::basic_ostream<char>]'
   77 |         return write_dot(out, g, "adj");
      |                ~~~~~~~~~^~~~~~~~~~~~~~~
longseqdist.cpp:208:11:   required from here
  208 |         write_dot(cout, g);
      |         ~~~~~~~~~^~~~~~~~~
../Graph/DotIO.h:44:43: warning: possibly dangling reference to a temporary [-Wdangling-reference]
   44 |                 const edge_property_type& ep = get(edge_bundle, g, e);
      |                                           ^~
../Graph/DotIO.h:44:51: note: the temporary was destroyed at the end of the full expression 'get<DirectedGraph<Length, DistanceEst> >(boost::edge_bundle, (* & g), DirectedGraph<Length, DistanceEst>::out_edge_iterator(e))'
   44 |                 const edge_property_type& ep = get(edge_bundle, g, e);
      |                                                ~~~^~~~~~~~~~~~~~~~~~~
In file included from ../Graph/GraphIO.h:8,
                 from scaffold.cc:13:
../Graph/DotIO.h: In instantiation of 'void write_edges(std::ostream&, const Graph&, typename boost::graph_traits<Graph>::vertex_descriptor, const EdgeProp*) [with Graph = ContigGraph<DirectedGraph<Length, DistanceEst> >; EdgeProp = DistanceEst; std::ostream = std::basic_ostream<char>; typename boost::graph_traits<Graph>::vertex_descriptor = ContigNode]':
../Graph/DotIO.h:110:14:   required from 'std::ostream& write_dot(std::ostream&, const Graph&, const std::string&) [with Graph = ContigGraph<DirectedGraph<Length, DistanceEst> >; std::ostream = std::basic_ostream<char>; std::string = std::__cxx11::basic_string<char>]'
  110 |                 write_edges(out, g, *u, (edge_property_type*)NULL);
      |                 ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../Graph/DotIO.h:77:18:   required from 'std::ostream& write_dot(std::ostream&, const Graph&) [with Graph = ContigGraph<DirectedGraph<Length, DistanceEst> >; std::ostream = std::basic_ostream<char>]'
   77 |         return write_dot(out, g, "adj");
      |                ~~~~~~~~~^~~~~~~~~~~~~~~
scaffold.cc:824:13:   required from here
  824 |                         write_dot(out, g);
      |                         ~~~~~~~~~^~~~~~~~
../Graph/DotIO.h:44:43: warning: possibly dangling reference to a temporary [-Wdangling-reference]
   44 |                 const edge_property_type& ep = get(edge_bundle, g, e);
      |                                           ^~
../Graph/DotIO.h:44:51: note: the temporary was destroyed at the end of the full expression 'get<DirectedGraph<Length, DistanceEst> >(boost::edge_bundle, (* & g), DirectedGraph<Length, DistanceEst>::out_edge_iterator(e))'
   44 |                 const edge_property_type& ep = get(edge_bundle, g, e);
      |                                                ~~~^~~~~~~~~~~~~~~~~~~
g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations  -L/usr/lib/aarch64-linux-gnu/openmpi/lib    -Wl,-z,relro -Wl,-z,now -o abyss-longseqdist abyss_longseqdist-longseqdist.o ../Common/libcommon.a -ldl -lm 
g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations  -L/usr/lib/aarch64-linux-gnu/openmpi/lib    -Wl,-z,relro -Wl,-z,now -o abyss-junction abyss_junction-junction.o ../Common/libcommon.a -ldl -lm 
g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations  -L/usr/lib/aarch64-linux-gnu/openmpi/lib    -Wl,-z,relro -Wl,-z,now -o abyss-scaffold abyss_scaffold-scaffold.o ../DataBase/libdb.a -lsqlite3 -ldl -lm  ../Common/libcommon.a -ldl -lm 
make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.10/Scaffold'
Making all in SimpleGraph
make[4]: Entering directory '/build/reproducible-path/abyss-2.3.10/SimpleGraph'
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I../Common -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -Wno-strict-aliasing -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o SimpleGraph-SimpleGraph.o `test -f 'SimpleGraph.cpp' || echo './'`SimpleGraph.cpp
g++ -std=c++11 -Wall -Wextra -Werror -Wno-strict-aliasing -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations  -L/usr/lib/aarch64-linux-gnu/openmpi/lib    -Wl,-z,relro -Wl,-z,now -o SimpleGraph SimpleGraph-SimpleGraph.o ../DataBase/libdb.a -lsqlite3 -ldl -lm  ../Common/libcommon.a -lpthread -ldl -lm 
make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.10/SimpleGraph'
Making all in kmerprint
make[4]: Entering directory '/build/reproducible-path/abyss-2.3.10/kmerprint'
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I../Assembly -I../Common -I../DataLayer -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o kmerprint-kmerprint.o `test -f 'kmerprint.cc' || echo './'`kmerprint.cc
g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations  -L/usr/lib/aarch64-linux-gnu/openmpi/lib    -Wl,-z,relro -Wl,-z,now -o kmerprint kmerprint-kmerprint.o ../Assembly/libassembly.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm 
make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.10/kmerprint'
Making all in FilterGraph
make[4]: Entering directory '/build/reproducible-path/abyss-2.3.10/FilterGraph'
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I../Common -I../DataLayer -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o abyss_filtergraph-FilterGraph.o `test -f 'FilterGraph.cc' || echo './'`FilterGraph.cc
In file included from ../Graph/GraphIO.h:8,
                 from FilterGraph.cc:15:
../Graph/DotIO.h: In instantiation of 'void write_edges(std::ostream&, const Graph&, typename boost::graph_traits<Graph>::vertex_descriptor, const EdgeProp*) [with Graph = ContigGraph<DirectedGraph<ContigProperties, Distance> >; EdgeProp = Distance; std::ostream = std::basic_ostream<char>; typename boost::graph_traits<Graph>::vertex_descriptor = ContigNode]':
../Graph/DotIO.h:110:14:   required from 'std::ostream& write_dot(std::ostream&, const Graph&, const std::string&) [with Graph = ContigGraph<DirectedGraph<ContigProperties, Distance> >; std::ostream = std::basic_ostream<char>; std::string = std::__cxx11::basic_string<char>]'
  110 |                 write_edges(out, g, *u, (edge_property_type*)NULL);
      |                 ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../Graph/DotIO.h:77:18:   required from 'std::ostream& write_dot(std::ostream&, const Graph&) [with Graph = ContigGraph<DirectedGraph<ContigProperties, Distance> >; std::ostream = std::basic_ostream<char>]'
   77 |         return write_dot(out, g, "adj");
      |                ~~~~~~~~~^~~~~~~~~~~~~~~
../Graph/DotIO.h:125:26:   required from 'std::ostream& operator<<(std::ostream&, const DotWriter<ContigGraph<DirectedGraph<ContigProperties, Distance> > >&)'
  125 |                 return write_dot<Graph>(out, o.g);
      |                        ~~~~~~~~~~~~~~~~^~~~~~~~~~
../Graph/GraphIO.h:33:14:   required from 'std::ostream& write_graph(std::ostream&, const Graph&, const std::string&, const std::string&) [with Graph = ContigGraph<DirectedGraph<ContigProperties, Distance> >; std::ostream = std::basic_ostream<char>; std::string = std::__cxx11::basic_string<char>]'
   33 |                 return out << dot_writer(g);
      |                        ~~~~^~~~~~~~~~~~~~~~
FilterGraph.cc:825:14:   required from here
  825 |                 write_graph(fout, g, PROGRAM, commandLine);
      |                 ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../Graph/DotIO.h:44:43: warning: possibly dangling reference to a temporary [-Wdangling-reference]
   44 |                 const edge_property_type& ep = get(edge_bundle, g, e);
      |                                           ^~
../Graph/DotIO.h:44:51: note: the temporary was destroyed at the end of the full expression 'get<DirectedGraph<ContigProperties, Distance> >(boost::edge_bundle, (* & g), DirectedGraph<ContigProperties, Distance>::out_edge_iterator(e))'
   44 |                 const edge_property_type& ep = get(edge_bundle, g, e);
      |                                                ~~~^~~~~~~~~~~~~~~~~~~
g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations  -L/usr/lib/aarch64-linux-gnu/openmpi/lib    -Wl,-z,relro -Wl,-z,now -o abyss-filtergraph abyss_filtergraph-FilterGraph.o ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm 
make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.10/FilterGraph'
Making all in GapFiller
make[4]: Entering directory '/build/reproducible-path/abyss-2.3.10/GapFiller'
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I../Common -I../DataLayer -I../Align -D SAM_SEQ_QUAL=1 -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o abyss_gapfill-gapfill.o `test -f 'gapfill.cpp' || echo './'`gapfill.cpp
g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference  -L/usr/lib/aarch64-linux-gnu/openmpi/lib    -Wl,-z,relro -Wl,-z,now -o abyss-gapfill abyss_gapfill-gapfill.o ../Align/libalign.a ../dialign/libdialign.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm 
make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.10/GapFiller'
Making all in Sealer
make[4]: Entering directory '/build/reproducible-path/abyss-2.3.10/Sealer'
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I../Common -I../DataLayer -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o abyss_sealer-sealer.o `test -f 'sealer.cc' || echo './'`sealer.cc
g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations  -L/usr/lib/aarch64-linux-gnu/openmpi/lib    -Wl,-z,relro -Wl,-z,now -o abyss-sealer abyss_sealer-sealer.o ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a -ldl -lm 
make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.10/Sealer'
Making all in RResolver
make[4]: Entering directory '/build/reproducible-path/abyss-2.3.10/RResolver'
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..   -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror  -Wno-deprecated-declarations -fopenmp -I.. -I../Common -I../DataLayer -I../RResolver/btllib/include -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o abyss_rresolver_short-RResolverShort.o `test -f 'RResolverShort.cpp' || echo './'`RResolverShort.cpp
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..   -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror  -Wno-deprecated-declarations -fopenmp -I.. -I../Common -I../DataLayer -I../RResolver/btllib/include -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o abyss_rresolver_short-Contigs.o `test -f 'Contigs.cpp' || echo './'`Contigs.cpp
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..   -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror  -Wno-deprecated-declarations -fopenmp -I.. -I../Common -I../DataLayer -I../RResolver/btllib/include -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o libralgorithmsshort_a-RAlgorithmsShort.o `test -f 'RAlgorithmsShort.cpp' || echo './'`RAlgorithmsShort.cpp
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..   -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror  -Wno-deprecated-declarations -fopenmp -I.. -I../Common -I../DataLayer -I../RResolver/btllib/include -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o libralgorithmsshort_a-BloomFilters.o `test -f 'BloomFilters.cpp' || echo './'`BloomFilters.cpp
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..   -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror  -Wno-deprecated-declarations -fopenmp -I.. -I../Common -I../DataLayer -I../RResolver/btllib/include -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o libralgorithmsshort_a-Contigs.o `test -f 'Contigs.cpp' || echo './'`Contigs.cpp
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..   -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror  -Wno-deprecated-declarations -fopenmp -I.. -I../Common -I../DataLayer -I../RResolver/btllib/include -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o libralgorithmsshort_a-SequenceTree.o `test -f 'SequenceTree.cpp' || echo './'`SequenceTree.cpp
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..   -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror  -Wno-deprecated-declarations -fopenmp -I.. -I../Common -I../DataLayer -I../RResolver/btllib/include -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o libralgorithmsshort_a-RUtils.o `test -f 'RUtils.cpp' || echo './'`RUtils.cpp
In file included from ../Graph/GraphIO.h:8,
                 from Contigs.h:17,
                 from Contigs.cpp:1:
../Graph/DotIO.h: In instantiation of 'void write_edges(std::ostream&, const Graph&, typename boost::graph_traits<Graph>::vertex_descriptor, const EdgeProp*) [with Graph = ContigGraph<DirectedGraph<ContigProperties, Distance> >; EdgeProp = Distance; std::ostream = std::basic_ostream<char>; typename boost::graph_traits<Graph>::vertex_descriptor = ContigNode]':
../Graph/DotIO.h:110:14:   required from 'std::ostream& write_dot(std::ostream&, const Graph&, const std::string&) [with Graph = ContigGraph<DirectedGraph<ContigProperties, Distance> >; std::ostream = std::basic_ostream<char>; std::string = std::__cxx11::basic_string<char>]'
  110 |                 write_edges(out, g, *u, (edge_property_type*)NULL);
      |                 ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../Graph/DotIO.h:77:18:   required from 'std::ostream& write_dot(std::ostream&, const Graph&) [with Graph = ContigGraph<DirectedGraph<ContigProperties, Distance> >; std::ostream = std::basic_ostream<char>]'
   77 |         return write_dot(out, g, "adj");
      |                ~~~~~~~~~^~~~~~~~~~~~~~~
../Graph/DotIO.h:125:26:   required from 'std::ostream& operator<<(std::ostream&, const DotWriter<ContigGraph<DirectedGraph<ContigProperties, Distance> > >&)'
  125 |                 return write_dot<Graph>(out, o.g);
      |                        ~~~~~~~~~~~~~~~~^~~~~~~~~~
../Graph/GraphIO.h:33:14:   required from 'std::ostream& write_graph(std::ostream&, const Graph&, const std::string&, const std::string&) [with Graph = ContigGraph<DirectedGraph<ContigProperties, Distance> >; std::ostream = std::basic_ostream<char>; std::string = std::__cxx11::basic_string<char>]'
   33 |                 return out << dot_writer(g);
      |                        ~~~~^~~~~~~~~~~~~~~~
Contigs.cpp:140:13:   required from here
  140 |         write_graph(fout, g_contigGraph, program, commandLine);
      |         ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../Graph/DotIO.h:44:43: warning: possibly dangling reference to a temporary [-Wdangling-reference]
   44 |                 const edge_property_type& ep = get(edge_bundle, g, e);
      |                                           ^~
../Graph/DotIO.h:44:51: note: the temporary was destroyed at the end of the full expression 'get<DirectedGraph<ContigProperties, Distance> >(boost::edge_bundle, (* & g), DirectedGraph<ContigProperties, Distance>::out_edge_iterator(e))'
   44 |                 const edge_property_type& ep = get(edge_bundle, g, e);
      |                                                ~~~^~~~~~~~~~~~~~~~~~~
In file included from ../Graph/GraphIO.h:8,
                 from Contigs.h:17,
                 from Contigs.cpp:1:
../Graph/DotIO.h: In instantiation of 'void write_edges(std::ostream&, const Graph&, typename boost::graph_traits<Graph>::vertex_descriptor, const EdgeProp*) [with Graph = ContigGraph<DirectedGraph<ContigProperties, Distance> >; EdgeProp = Distance; std::ostream = std::basic_ostream<char>; typename boost::graph_traits<Graph>::vertex_descriptor = ContigNode]':
../Graph/DotIO.h:110:14:   required from 'std::ostream& write_dot(std::ostream&, const Graph&, const std::string&) [with Graph = ContigGraph<DirectedGraph<ContigProperties, Distance> >; std::ostream = std::basic_ostream<char>; std::string = std::__cxx11::basic_string<char>]'
  110 |                 write_edges(out, g, *u, (edge_property_type*)NULL);
      |                 ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../Graph/DotIO.h:77:18:   required from 'std::ostream& write_dot(std::ostream&, const Graph&) [with Graph = ContigGraph<DirectedGraph<ContigProperties, Distance> >; std::ostream = std::basic_ostream<char>]'
   77 |         return write_dot(out, g, "adj");
      |                ~~~~~~~~~^~~~~~~~~~~~~~~
../Graph/DotIO.h:125:26:   required from 'std::ostream& operator<<(std::ostream&, const DotWriter<ContigGraph<DirectedGraph<ContigProperties, Distance> > >&)'
  125 |                 return write_dot<Graph>(out, o.g);
      |                        ~~~~~~~~~~~~~~~~^~~~~~~~~~
../Graph/GraphIO.h:33:14:   required from 'std::ostream& write_graph(std::ostream&, const Graph&, const std::string&, const std::string&) [with Graph = ContigGraph<DirectedGraph<ContigProperties, Distance> >; std::ostream = std::basic_ostream<char>; std::string = std::__cxx11::basic_string<char>]'
   33 |                 return out << dot_writer(g);
      |                        ~~~~^~~~~~~~~~~~~~~~
Contigs.cpp:140:13:   required from here
  140 |         write_graph(fout, g_contigGraph, program, commandLine);
      |         ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../Graph/DotIO.h:44:43: warning: possibly dangling reference to a temporary [-Wdangling-reference]
   44 |                 const edge_property_type& ep = get(edge_bundle, g, e);
      |                                           ^~
../Graph/DotIO.h:44:51: note: the temporary was destroyed at the end of the full expression 'get<DirectedGraph<ContigProperties, Distance> >(boost::edge_bundle, (* & g), DirectedGraph<ContigProperties, Distance>::out_edge_iterator(e))'
   44 |                 const edge_property_type& ep = get(edge_bundle, g, e);
      |                                                ~~~^~~~~~~~~~~~~~~~~~~
rm -f libralgorithmsshort.a
ar cr libralgorithmsshort.a libralgorithmsshort_a-RAlgorithmsShort.o libralgorithmsshort_a-BloomFilters.o libralgorithmsshort_a-Contigs.o libralgorithmsshort_a-SequenceTree.o libralgorithmsshort_a-RUtils.o ../DataLayer/abyss_fac-fac.o ../DataLayer/abyss_tofastq-abyss-tofastq.o ../DataLayer/libdatalayer_a-FastaReader.o ../DataLayer/libdatalayer_a-FastaWriter.o ../Common/libcommon_a-ContigID.o ../Common/libcommon_a-Fcontrol.o ../Common/libcommon_a-Histogram.o ../Common/libcommon_a-Kmer.o ../Common/libcommon_a-Log.o ../Common/libcommon_a-Options.o ../Common/libcommon_a-Sequence.o ../Common/libcommon_a-SignalHandler.o ../Common/libcommon_a-Timer.o ../Common/libcommon_a-Uncompress.o ../Common/libcommon_a-city.o
ranlib libralgorithmsshort.a
g++ -std=c++11 -Wall -Wextra -Werror  -Wno-deprecated-declarations -fopenmp -I.. -I../Common -I../DataLayer -I../RResolver/btllib/include -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference  -L/usr/lib/aarch64-linux-gnu/openmpi/lib    -Wl,-z,relro -Wl,-z,now -pthread -o abyss-rresolver-short abyss_rresolver_short-RResolverShort.o abyss_rresolver_short-Contigs.o ../DataLayer/libdatalayer.a ../Common/libcommon.a libralgorithmsshort.a -lbtllib -ldl -lm 
make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.10/RResolver'
Making all in AdjList
make[4]: Entering directory '/build/reproducible-path/abyss-2.3.10/AdjList'
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I../Common -I../DataLayer -DPAIRED_DBG -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o AdjList-AdjList.o `test -f 'AdjList.cpp' || echo './'`AdjList.cpp
In file included from ../Graph/GraphIO.h:8,
                 from AdjList.cpp:15:
../Graph/DotIO.h: In instantiation of 'void write_edges(std::ostream&, const Graph&, typename boost::graph_traits<Graph>::vertex_descriptor, const EdgeProp*) [with Graph = ContigGraph<DirectedGraph<ContigProperties, Distance> >; EdgeProp = Distance; std::ostream = std::basic_ostream<char>; typename boost::graph_traits<Graph>::vertex_descriptor = ContigNode]':
../Graph/DotIO.h:110:14:   required from 'std::ostream& write_dot(std::ostream&, const Graph&, const std::string&) [with Graph = ContigGraph<DirectedGraph<ContigProperties, Distance> >; std::ostream = std::basic_ostream<char>; std::string = std::__cxx11::basic_string<char>]'
  110 |                 write_edges(out, g, *u, (edge_property_type*)NULL);
      |                 ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../Graph/DotIO.h:77:18:   required from 'std::ostream& write_dot(std::ostream&, const Graph&) [with Graph = ContigGraph<DirectedGraph<ContigProperties, Distance> >; std::ostream = std::basic_ostream<char>]'
   77 |         return write_dot(out, g, "adj");
      |                ~~~~~~~~~^~~~~~~~~~~~~~~
../Graph/DotIO.h:125:26:   required from 'std::ostream& operator<<(std::ostream&, const DotWriter<ContigGraph<DirectedGraph<ContigProperties, Distance> > >&)'
  125 |                 return write_dot<Graph>(out, o.g);
      |                        ~~~~~~~~~~~~~~~~^~~~~~~~~~
../Graph/GraphIO.h:33:14:   required from 'std::ostream& write_graph(std::ostream&, const Graph&, const std::string&, const std::string&) [with Graph = ContigGraph<DirectedGraph<ContigProperties, Distance> >; std::ostream = std::basic_ostream<char>; std::string = std::__cxx11::basic_string<char>]'
   33 |                 return out << dot_writer(g);
      |                        ~~~~^~~~~~~~~~~~~~~~
AdjList.cpp:401:13:   required from here
  401 |         write_graph(cout, g, PROGRAM, commandLine);
      |         ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../Graph/DotIO.h:44:43: warning: possibly dangling reference to a temporary [-Wdangling-reference]
   44 |                 const edge_property_type& ep = get(edge_bundle, g, e);
      |                                           ^~
../Graph/DotIO.h:44:51: note: the temporary was destroyed at the end of the full expression 'get<DirectedGraph<ContigProperties, Distance> >(boost::edge_bundle, (* & g), DirectedGraph<ContigProperties, Distance>::out_edge_iterator(e))'
   44 |                 const edge_property_type& ep = get(edge_bundle, g, e);
      |                                                ~~~^~~~~~~~~~~~~~~~~~~
g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations  -L/usr/lib/aarch64-linux-gnu/openmpi/lib    -Wl,-z,relro -Wl,-z,now -o AdjList AdjList-AdjList.o ../DataLayer/libdatalayer.a ../Common/libcommon.a ../PairedDBG/libpaireddbg.a ../DataBase/libdb.a -lsqlite3 -ldl -lm  -ldl -lm 
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markdown README.md > README.html
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   dh_auto_test
	make -j12 check "TESTSUITEFLAGS=-j12 --verbose" VERBOSE=1
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Making check in Scaffold
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Making check in SimpleGraph
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Making check in kmerprint
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Making check in FilterGraph
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Making check in vendor
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Making check in vendor/gtest-1.7.0
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make  libgtest.a libgtest_main.a
make[3]: Entering directory '/build/reproducible-path/abyss-2.3.10/vendor/gtest-1.7.0'
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I../..  -I../.. -isystem ../../vendor/gtest-1.7.0/include -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -Wno-missing-field-initializers -Wno-uninitialized -Wno-error=unused-result -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o src/libgtest_a-gtest-all.o `test -f 'src/gtest-all.cc' || echo './'`src/gtest-all.cc
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I../..  -I../.. -isystem ../../vendor/gtest-1.7.0/include -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -Wno-missing-field-initializers -Wno-uninitialized -Wno-error=unused-result -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o src/libgtest_main_a-gtest_main.o `test -f 'src/gtest_main.cc' || echo './'`src/gtest_main.cc
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I../..  -I../.. -isystem ../../vendor/gtest-1.7.0/include -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -Wno-missing-field-initializers -Wno-uninitialized -Wno-error=unused-result -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o src/libgtest_main_a-gtest-all.o `test -f 'src/gtest-all.cc' || echo './'`src/gtest-all.cc
rm -f libgtest_main.a
ar cr libgtest_main.a src/libgtest_main_a-gtest_main.o src/libgtest_main_a-gtest-all.o 
ranlib libgtest_main.a
rm -f libgtest.a
ar cr libgtest.a src/libgtest_a-gtest-all.o 
ranlib libgtest.a
make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.10/vendor/gtest-1.7.0'
make[2]: Leaving directory '/build/reproducible-path/abyss-2.3.10/vendor/gtest-1.7.0'
Making check in Unittest
make[2]: Entering directory '/build/reproducible-path/abyss-2.3.10/Unittest'
make  common_stringutil common_histogram common_bitutil common_kmer common_sequence common_KmerIterator common_sam common_sam_ssq BloomFilter Konnector_DBGBloom Konnector_DBGBloomAlgorithms graph_ConstrainedBFSVisitor graph_BidirectionalBFS graph_AllPathsSearch graph_HashGraph graph_ConstrainedBidiBFSVisitor graph_ExtendPath graph_DotIO graph_UndirectedGraph Konnector_konnector DBG_LoadAlgorithm PairedDBG_LoadAlgorithm PairedDBG_KmerPair PairedDBG_Dinuc PairedDBG_BranchRecord BloomDBG_BloomDBG BloomDBG_RollingHash BloomDBG_RollingHashIterator BloomDBG_HashAgnosticCascadingBloom BloomDBG_CountingBloomFilter BloomDBG_RollingBloomDBG BloomDBG_MaskedKmer BloomDBG_SpacedSeed BloomDBG_LightweightKmer
make[3]: Entering directory '/build/reproducible-path/abyss-2.3.10/Unittest'
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror  -Wno-error -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o Common/StringUtilTest.o Common/StringUtilTest.cpp
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror  -Wno-error -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o Common/HistogramTest.o Common/HistogramTest.cpp
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror  -Wno-error -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o Common/BitUtilTest.o Common/BitUtilTest.cpp
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror  -Wno-error -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o Common/KmerTest.o Common/KmerTest.cpp
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror  -Wno-error -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o Common/Sequence.o Common/Sequence.cc
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror  -Wno-error -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o Common/KmerIteratorTest.o Common/KmerIteratorTest.cpp
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror  -Wno-error -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o Common/SAM.o Common/SAM.cc
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0  -DSAM_SEQ_QUAL -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror  -Wno-error -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o Common/common_sam_ssq-SAM.o `test -f 'Common/SAM.cc' || echo './'`Common/SAM.cc
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../Common -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror  -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o Konnector/BloomFilter-BloomFilter.o `test -f 'Konnector/BloomFilter.cc' || echo './'`Konnector/BloomFilter.cc
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../Common -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror  -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o Konnector/DBGBloom-DBGBloomTest.o `test -f 'Konnector/DBGBloomTest.cpp' || echo './'`Konnector/DBGBloomTest.cpp
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../Common -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror  -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o Konnector/DBGBloomAlgorithms-DBGBloomAlgorithmsTest.o `test -f 'Konnector/DBGBloomAlgorithmsTest.cpp' || echo './'`Konnector/DBGBloomAlgorithmsTest.cpp
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../Common -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror  -Wno-error -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o Graph/graph_ConstrainedBFSVisitor-ConstrainedBFSVisitorTest.o `test -f 'Graph/ConstrainedBFSVisitorTest.cpp' || echo './'`Graph/ConstrainedBFSVisitorTest.cpp
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../Common -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror  -Wno-error -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o Graph/graph_BidirectionalBFS-BidirectionalBFSTest.o `test -f 'Graph/BidirectionalBFSTest.cpp' || echo './'`Graph/BidirectionalBFSTest.cpp
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../Common -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror  -Wno-error -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o Graph/graph_AllPathsSearch-AllPathsSearchTest.o `test -f 'Graph/AllPathsSearchTest.cpp' || echo './'`Graph/AllPathsSearchTest.cpp
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../Common -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror  -Wno-error -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o Graph/graph_HashGraph-HashGraphTest.o `test -f 'Graph/HashGraphTest.cpp' || echo './'`Graph/HashGraphTest.cpp
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../Common -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror  -Wno-error -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o Graph/graph_ConstrainedBidiBFSVisitor-ConstrainedBidiBFSVisitorTest.o `test -f 'Graph/ConstrainedBidiBFSVisitorTest.cpp' || echo './'`Graph/ConstrainedBidiBFSVisitorTest.cpp
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../Common -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror  -Wno-error -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o Graph/graph_ExtendPath-ExtendPathTest.o `test -f 'Graph/ExtendPathTest.cpp' || echo './'`Graph/ExtendPathTest.cpp
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../Common -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror  -Wno-error -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o Graph/graph_DotIO-DotIOTest.o `test -f 'Graph/DotIOTest.cpp' || echo './'`Graph/DotIOTest.cpp
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror  -Wno-error -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o Graph/UndirectedGraphTest.o Graph/UndirectedGraphTest.cpp
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../Common -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror  -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o Konnector/konnector-konnectorTest.o `test -f 'Konnector/konnectorTest.cpp' || echo './'`Konnector/konnectorTest.cpp
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../DataLayer -I../Common -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror  -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o DBG/LoadAlgorithm-LoadAlgorithmTest.o `test -f 'DBG/LoadAlgorithmTest.cpp' || echo './'`DBG/LoadAlgorithmTest.cpp
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../DataLayer -I../Common -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror  -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o PairedDBG/LoadAlgorithm-LoadAlgorithmTest.o `test -f 'PairedDBG/LoadAlgorithmTest.cpp' || echo './'`PairedDBG/LoadAlgorithmTest.cpp
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../DataLayer -I../Common -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror  -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o PairedDBG/KmerPair-KmerPairTest.o `test -f 'PairedDBG/KmerPairTest.cc' || echo './'`PairedDBG/KmerPairTest.cc
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../DataLayer -I../Common -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror  -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o PairedDBG/Dinuc-DinucTest.o `test -f 'PairedDBG/DinucTest.cc' || echo './'`PairedDBG/DinucTest.cc
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../DataLayer -I../Common -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror  -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o PairedDBG/BranchRecord-BranchRecordTest.o `test -f 'PairedDBG/BranchRecordTest.cpp' || echo './'`PairedDBG/BranchRecordTest.cpp
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../Common -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror  -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o BloomDBG/BloomDBG-BloomDBGTest.o `test -f 'BloomDBG/BloomDBGTest.cpp' || echo './'`BloomDBG/BloomDBGTest.cpp
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror  -Wno-error -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o BloomDBG/RollingHashTest.o BloomDBG/RollingHashTest.cpp
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror  -Wno-error -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o BloomDBG/RollingHashIteratorTest.o BloomDBG/RollingHashIteratorTest.cpp
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror  -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o BloomDBG/HashAgnosticCascadingBloom-HashAgnosticCascadingBloomTest.o `test -f 'BloomDBG/HashAgnosticCascadingBloomTest.cpp' || echo './'`BloomDBG/HashAgnosticCascadingBloomTest.cpp
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../Common -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror  -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o BloomDBG/CountingBloomFilter-CountingBloomFilterTest.o `test -f 'BloomDBG/CountingBloomFilterTest.cpp' || echo './'`BloomDBG/CountingBloomFilterTest.cpp
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror  -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o BloomDBG/RollingBloomDBG-RollingBloomDBGTest.o `test -f 'BloomDBG/RollingBloomDBGTest.cpp' || echo './'`BloomDBG/RollingBloomDBGTest.cpp
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror  -Wno-error -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o BloomDBG/MaskedKmerTest.o BloomDBG/MaskedKmerTest.cpp
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror  -Wno-error -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o BloomDBG/SpacedSeedTest.o BloomDBG/SpacedSeedTest.cpp
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror  -Wno-error -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o BloomDBG/LightweightKmerTest.o BloomDBG/LightweightKmerTest.cpp
g++ -std=c++11 -Wall -Wextra -Werror  -Wno-error -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference  -L/usr/lib/aarch64-linux-gnu/openmpi/lib    -Wl,-z,relro -Wl,-z,now -o common_stringutil Common/StringUtilTest.o ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm 
g++ -std=c++11 -Wall -Wextra -Werror  -Wno-error -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference  -L/usr/lib/aarch64-linux-gnu/openmpi/lib    -Wl,-z,relro -Wl,-z,now -o common_histogram Common/HistogramTest.o ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm 
g++ -std=c++11 -Wall -Wextra -Werror  -Wno-error -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference  -L/usr/lib/aarch64-linux-gnu/openmpi/lib    -Wl,-z,relro -Wl,-z,now -o common_bitutil Common/BitUtilTest.o ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm 
g++ -std=c++11 -Wall -Wextra -Werror  -Wno-error -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference  -L/usr/lib/aarch64-linux-gnu/openmpi/lib    -Wl,-z,relro -Wl,-z,now -o common_kmer Common/KmerTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm 
g++ -std=c++11 -Wall -Wextra -Werror  -Wno-error -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference  -L/usr/lib/aarch64-linux-gnu/openmpi/lib    -Wl,-z,relro -Wl,-z,now -o common_sequence Common/Sequence.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm 
g++ -std=c++11 -Wall -Wextra -Werror  -Wno-error -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference  -L/usr/lib/aarch64-linux-gnu/openmpi/lib    -Wl,-z,relro -Wl,-z,now -o common_KmerIterator Common/KmerIteratorTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm 
g++ -std=c++11 -Wall -Wextra -Werror  -Wno-error -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference  -L/usr/lib/aarch64-linux-gnu/openmpi/lib    -Wl,-z,relro -Wl,-z,now -o common_sam Common/SAM.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm 
g++ -std=c++11 -Wall -Wextra -Werror  -Wno-error -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference  -L/usr/lib/aarch64-linux-gnu/openmpi/lib    -Wl,-z,relro -Wl,-z,now -o common_sam_ssq Common/common_sam_ssq-SAM.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm 
g++ -std=c++11 -Wall -Wextra -Werror  -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference  -L/usr/lib/aarch64-linux-gnu/openmpi/lib    -Wl,-z,relro -Wl,-z,now -o BloomFilter Konnector/BloomFilter-BloomFilter.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm 
g++ -std=c++11 -Wall -Wextra -Werror  -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference  -L/usr/lib/aarch64-linux-gnu/openmpi/lib    -Wl,-z,relro -Wl,-z,now -o Konnector_DBGBloom Konnector/DBGBloom-DBGBloomTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm 
g++ -std=c++11 -Wall -Wextra -Werror  -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference  -L/usr/lib/aarch64-linux-gnu/openmpi/lib    -Wl,-z,relro -Wl,-z,now -o Konnector_DBGBloomAlgorithms Konnector/DBGBloomAlgorithms-DBGBloomAlgorithmsTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm 
g++ -std=c++11 -Wall -Wextra -Werror  -Wno-error -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference  -L/usr/lib/aarch64-linux-gnu/openmpi/lib    -Wl,-z,relro -Wl,-z,now -o graph_ConstrainedBFSVisitor Graph/graph_ConstrainedBFSVisitor-ConstrainedBFSVisitorTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm 
g++ -std=c++11 -Wall -Wextra -Werror  -Wno-error -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference  -L/usr/lib/aarch64-linux-gnu/openmpi/lib    -Wl,-z,relro -Wl,-z,now -o graph_BidirectionalBFS Graph/graph_BidirectionalBFS-BidirectionalBFSTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm 
g++ -std=c++11 -Wall -Wextra -Werror  -Wno-error -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference  -L/usr/lib/aarch64-linux-gnu/openmpi/lib    -Wl,-z,relro -Wl,-z,now -o graph_AllPathsSearch Graph/graph_AllPathsSearch-AllPathsSearchTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm 
g++ -std=c++11 -Wall -Wextra -Werror  -Wno-error -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference  -L/usr/lib/aarch64-linux-gnu/openmpi/lib    -Wl,-z,relro -Wl,-z,now -o graph_HashGraph Graph/graph_HashGraph-HashGraphTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm 
g++ -std=c++11 -Wall -Wextra -Werror  -Wno-error -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference  -L/usr/lib/aarch64-linux-gnu/openmpi/lib    -Wl,-z,relro -Wl,-z,now -o graph_ConstrainedBidiBFSVisitor Graph/graph_ConstrainedBidiBFSVisitor-ConstrainedBidiBFSVisitorTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm 
g++ -std=c++11 -Wall -Wextra -Werror  -Wno-error -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference  -L/usr/lib/aarch64-linux-gnu/openmpi/lib    -Wl,-z,relro -Wl,-z,now -o graph_DotIO Graph/graph_DotIO-DotIOTest.o ../Assembly/libassembly.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm 
g++ -std=c++11 -Wall -Wextra -Werror  -Wno-error -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference  -L/usr/lib/aarch64-linux-gnu/openmpi/lib    -Wl,-z,relro -Wl,-z,now -o graph_UndirectedGraph Graph/UndirectedGraphTest.o ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm 
g++ -std=c++11 -Wall -Wextra -Werror  -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference  -L/usr/lib/aarch64-linux-gnu/openmpi/lib    -Wl,-z,relro -Wl,-z,now -o DBG_LoadAlgorithm DBG/LoadAlgorithm-LoadAlgorithmTest.o ../Assembly/libassembly.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm 
g++ -std=c++11 -Wall -Wextra -Werror  -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference  -L/usr/lib/aarch64-linux-gnu/openmpi/lib    -Wl,-z,relro -Wl,-z,now -o PairedDBG_LoadAlgorithm PairedDBG/LoadAlgorithm-LoadAlgorithmTest.o ../PairedDBG/libpaireddbg.a ../Assembly/libassembly.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm 
g++ -std=c++11 -Wall -Wextra -Werror  -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference  -L/usr/lib/aarch64-linux-gnu/openmpi/lib    -Wl,-z,relro -Wl,-z,now -o PairedDBG_KmerPair PairedDBG/KmerPair-KmerPairTest.o ../PairedDBG/libpaireddbg.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm 
g++ -std=c++11 -Wall -Wextra -Werror  -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference  -L/usr/lib/aarch64-linux-gnu/openmpi/lib    -Wl,-z,relro -Wl,-z,now -o PairedDBG_Dinuc PairedDBG/Dinuc-DinucTest.o ../PairedDBG/libpaireddbg.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm 
g++ -std=c++11 -Wall -Wextra -Werror  -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference  -L/usr/lib/aarch64-linux-gnu/openmpi/lib    -Wl,-z,relro -Wl,-z,now -o PairedDBG_BranchRecord PairedDBG/BranchRecord-BranchRecordTest.o ../PairedDBG/libpaireddbg.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm 
g++ -std=c++11 -Wall -Wextra -Werror  -Wno-error -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference  -L/usr/lib/aarch64-linux-gnu/openmpi/lib    -Wl,-z,relro -Wl,-z,now -o BloomDBG_RollingHash BloomDBG/RollingHashTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm 
g++ -std=c++11 -Wall -Wextra -Werror  -Wno-error -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference  -L/usr/lib/aarch64-linux-gnu/openmpi/lib    -Wl,-z,relro -Wl,-z,now -o BloomDBG_RollingHashIterator BloomDBG/RollingHashIteratorTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm 
g++ -std=c++11 -Wall -Wextra -Werror  -Wno-error -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference  -L/usr/lib/aarch64-linux-gnu/openmpi/lib    -Wl,-z,relro -Wl,-z,now -o BloomDBG_MaskedKmer BloomDBG/MaskedKmerTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm 
g++ -std=c++11 -Wall -Wextra -Werror  -Wno-error -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference  -L/usr/lib/aarch64-linux-gnu/openmpi/lib    -Wl,-z,relro -Wl,-z,now -o BloomDBG_SpacedSeed BloomDBG/SpacedSeedTest.o ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm 
g++ -std=c++11 -Wall -Wextra -Werror  -Wno-error -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference  -L/usr/lib/aarch64-linux-gnu/openmpi/lib    -Wl,-z,relro -Wl,-z,now -o BloomDBG_LightweightKmer BloomDBG/LightweightKmerTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm 
g++ -std=c++11 -Wall -Wextra -Werror  -Wno-error -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference  -L/usr/lib/aarch64-linux-gnu/openmpi/lib    -Wl,-z,relro -Wl,-z,now -o graph_ExtendPath Graph/graph_ExtendPath-ExtendPathTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm 
g++ -std=c++11 -Wall -Wextra -Werror  -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference  -L/usr/lib/aarch64-linux-gnu/openmpi/lib    -Wl,-z,relro -Wl,-z,now -o BloomDBG_HashAgnosticCascadingBloom BloomDBG/HashAgnosticCascadingBloom-HashAgnosticCascadingBloomTest.o ../DataLayer/libdatalayer.a ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm 
g++ -std=c++11 -Wall -Wextra -Werror  -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference  -L/usr/lib/aarch64-linux-gnu/openmpi/lib    -Wl,-z,relro -Wl,-z,now -o BloomDBG_CountingBloomFilter BloomDBG/CountingBloomFilter-CountingBloomFilterTest.o ../DataLayer/libdatalayer.a ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm 
g++ -std=c++11 -Wall -Wextra -Werror  -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference  -L/usr/lib/aarch64-linux-gnu/openmpi/lib    -Wl,-z,relro -Wl,-z,now -o BloomDBG_BloomDBG BloomDBG/BloomDBG-BloomDBGTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm 
g++ -std=c++11 -Wall -Wextra -Werror  -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference  -L/usr/lib/aarch64-linux-gnu/openmpi/lib    -Wl,-z,relro -Wl,-z,now -o Konnector_konnector Konnector/konnector-konnectorTest.o ../Align/libalign.a ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm 
g++ -std=c++11 -Wall -Wextra -Werror  -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference  -L/usr/lib/aarch64-linux-gnu/openmpi/lib    -Wl,-z,relro -Wl,-z,now -o BloomDBG_RollingBloomDBG BloomDBG/RollingBloomDBG-RollingBloomDBGTest.o ../DataLayer/libdatalayer.a ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm 
make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.10/Unittest'
make  check-TESTS
make[3]: Entering directory '/build/reproducible-path/abyss-2.3.10/Unittest'
make[4]: Entering directory '/build/reproducible-path/abyss-2.3.10/Unittest'
PASS: common_stringutil
PASS: common_histogram
PASS: common_bitutil
PASS: common_KmerIterator
PASS: common_sequence
PASS: BloomFilter
PASS: common_kmer
PASS: common_sam
PASS: graph_ConstrainedBFSVisitor
PASS: Konnector_DBGBloom
PASS: Konnector_DBGBloomAlgorithms
PASS: graph_ConstrainedBidiBFSVisitor
PASS: common_sam_ssq
PASS: graph_BidirectionalBFS
PASS: graph_ExtendPath
PASS: graph_AllPathsSearch
PASS: graph_UndirectedGraph
PASS: graph_DotIO
PASS: graph_HashGraph
PASS: PairedDBG_KmerPair
PASS: Konnector_konnector
PASS: PairedDBG_BranchRecord
PASS: PairedDBG_Dinuc
PASS: BloomDBG_BloomDBG
PASS: BloomDBG_RollingHashIterator
PASS: BloomDBG_RollingHash
PASS: BloomDBG_SpacedSeed
PASS: BloomDBG_LightweightKmer
PASS: BloomDBG_RollingBloomDBG
PASS: BloomDBG_HashAgnosticCascadingBloom
PASS: BloomDBG_MaskedKmer
PASS: BloomDBG_CountingBloomFilter
PASS: PairedDBG_LoadAlgorithm
PASS: DBG_LoadAlgorithm
============================================================================
Testsuite summary for ABySS 2.3.10
============================================================================
# TOTAL: 34
# PASS:  34
# SKIP:  0
# XFAIL: 0
# FAIL:  0
# XPASS: 0
# ERROR: 0
============================================================================
make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.10/Unittest'
make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.10/Unittest'
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make[2]: Entering directory '/build/reproducible-path/abyss-2.3.10'
make[2]: Leaving directory '/build/reproducible-path/abyss-2.3.10'
make[1]: Leaving directory '/build/reproducible-path/abyss-2.3.10'
   create-stamp debian/debhelper-build-stamp
   dh_prep
   debian/rules override_dh_auto_install
make[1]: Entering directory '/build/reproducible-path/abyss-2.3.10'
dh_auto_install --destdir=debian/tmp
	make -j12 install DESTDIR=/build/reproducible-path/abyss-2.3.10/debian/tmp AM_UPDATE_INFO_DIR=no
make[2]: Entering directory '/build/reproducible-path/abyss-2.3.10'
Making install in bin
make[3]: Entering directory '/build/reproducible-path/abyss-2.3.10/bin'
make[4]: Entering directory '/build/reproducible-path/abyss-2.3.10/bin'
make[4]: Nothing to be done for 'install-data-am'.
 /usr/bin/mkdir -p '/build/reproducible-path/abyss-2.3.10/debian/tmp/usr/bin'
 /usr/bin/install -c abyss-bowtie abyss-bowtie2 abyss-bwa abyss-bwasw abyss-bwamem abyss-fatoagp abyss-kaligner abyss-pe abyss-samtoafg abyss-tabtomd abyss-bloom-dist.mk abyss-dida abyss-stack-size '/build/reproducible-path/abyss-2.3.10/debian/tmp/usr/bin'
make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.10/bin'
make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.10/bin'
Making install in doc
make[3]: Entering directory '/build/reproducible-path/abyss-2.3.10/doc'
make[4]: Entering directory '/build/reproducible-path/abyss-2.3.10/doc'
make[4]: Nothing to be done for 'install-exec-am'.
 /usr/bin/mkdir -p '/build/reproducible-path/abyss-2.3.10/debian/tmp/usr/share/doc/abyss'
 /usr/bin/install -c -m 644 flowchart.pdf flowchart_simplified.pdf '/build/reproducible-path/abyss-2.3.10/debian/tmp/usr/share/doc/abyss'
make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.10/doc'
make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.10/doc'
Making install in Common
make[3]: Entering directory '/build/reproducible-path/abyss-2.3.10/Common'
make[4]: Entering directory '/build/reproducible-path/abyss-2.3.10/Common'
make[4]: Nothing to be done for 'install-exec-am'.
make[4]: Nothing to be done for 'install-data-am'.
make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.10/Common'
make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.10/Common'
Making install in Graph
make[3]: Entering directory '/build/reproducible-path/abyss-2.3.10/Graph'
make[4]: Entering directory '/build/reproducible-path/abyss-2.3.10/Graph'
make[4]: Nothing to be done for 'install-data-am'.
 /usr/bin/mkdir -p '/build/reproducible-path/abyss-2.3.10/debian/tmp/usr/bin'
  /usr/bin/install -c abyss-gc abyss-todot '/build/reproducible-path/abyss-2.3.10/debian/tmp/usr/bin'
make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.10/Graph'
make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.10/Graph'
Making install in DataLayer
make[3]: Entering directory '/build/reproducible-path/abyss-2.3.10/DataLayer'
make[4]: Entering directory '/build/reproducible-path/abyss-2.3.10/DataLayer'
make[4]: Nothing to be done for 'install-data-am'.
 /usr/bin/mkdir -p '/build/reproducible-path/abyss-2.3.10/debian/tmp/usr/bin'
  /usr/bin/install -c abyss-fac abyss-tofastq '/build/reproducible-path/abyss-2.3.10/debian/tmp/usr/bin'
make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.10/DataLayer'
make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.10/DataLayer'
Making install in DataBase
make[3]: Entering directory '/build/reproducible-path/abyss-2.3.10/DataBase'
make[4]: Entering directory '/build/reproducible-path/abyss-2.3.10/DataBase'
make[4]: Nothing to be done for 'install-data-am'.
 /usr/bin/mkdir -p '/build/reproducible-path/abyss-2.3.10/debian/tmp/usr/bin'
 /usr/bin/mkdir -p '/build/reproducible-path/abyss-2.3.10/debian/tmp/usr/bin'
  /usr/bin/install -c abyss-db-csv '/build/reproducible-path/abyss-2.3.10/debian/tmp/usr/bin'
 /usr/bin/install -c abyss-db-txt '/build/reproducible-path/abyss-2.3.10/debian/tmp/usr/bin'
make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.10/DataBase'
make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.10/DataBase'
Making install in FMIndex
make[3]: Entering directory '/build/reproducible-path/abyss-2.3.10/FMIndex'
make[4]: Entering directory '/build/reproducible-path/abyss-2.3.10/FMIndex'
make[4]: Nothing to be done for 'install-exec-am'.
make[4]: Nothing to be done for 'install-data-am'.
make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.10/FMIndex'
make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.10/FMIndex'
Making install in Assembly
make[3]: Entering directory '/build/reproducible-path/abyss-2.3.10/Assembly'
make[4]: Entering directory '/build/reproducible-path/abyss-2.3.10/Assembly'
make[4]: Nothing to be done for 'install-exec-am'.
make[4]: Nothing to be done for 'install-data-am'.
make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.10/Assembly'
make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.10/Assembly'
Making install in dialign
make[3]: Entering directory '/build/reproducible-path/abyss-2.3.10/dialign'
make[4]: Entering directory '/build/reproducible-path/abyss-2.3.10/dialign'
make[4]: Nothing to be done for 'install-exec-am'.
make[4]: Nothing to be done for 'install-data-am'.
make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.10/dialign'
make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.10/dialign'
Making install in Align
make[3]: Entering directory '/build/reproducible-path/abyss-2.3.10/Align'
make[4]: Entering directory '/build/reproducible-path/abyss-2.3.10/Align'
make[4]: Nothing to be done for 'install-data-am'.
 /usr/bin/mkdir -p '/build/reproducible-path/abyss-2.3.10/debian/tmp/usr/bin'
  /usr/bin/install -c abyss-align abyss-mergepairs '/build/reproducible-path/abyss-2.3.10/debian/tmp/usr/bin'
make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.10/Align'
make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.10/Align'
Making install in ABYSS
make[3]: Entering directory '/build/reproducible-path/abyss-2.3.10/ABYSS'
make[4]: Entering directory '/build/reproducible-path/abyss-2.3.10/ABYSS'
make[4]: Nothing to be done for 'install-data-am'.
 /usr/bin/mkdir -p '/build/reproducible-path/abyss-2.3.10/debian/tmp/usr/bin'
  /usr/bin/install -c ABYSS '/build/reproducible-path/abyss-2.3.10/debian/tmp/usr/bin'
make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.10/ABYSS'
make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.10/ABYSS'
Making install in Parallel
make[3]: Entering directory '/build/reproducible-path/abyss-2.3.10/Parallel'
make[4]: Entering directory '/build/reproducible-path/abyss-2.3.10/Parallel'
make[4]: Nothing to be done for 'install-data-am'.
 /usr/bin/mkdir -p '/build/reproducible-path/abyss-2.3.10/debian/tmp/usr/bin'
  /usr/bin/install -c ABYSS-P abyss-paired-dbg-mpi '/build/reproducible-path/abyss-2.3.10/debian/tmp/usr/bin'
make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.10/Parallel'
make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.10/Parallel'
Making install in Bloom
make[3]: Entering directory '/build/reproducible-path/abyss-2.3.10/Bloom'
make[4]: Entering directory '/build/reproducible-path/abyss-2.3.10/Bloom'
make[4]: Nothing to be done for 'install-data-am'.
 /usr/bin/mkdir -p '/build/reproducible-path/abyss-2.3.10/debian/tmp/usr/bin'
  /usr/bin/install -c abyss-bloom '/build/reproducible-path/abyss-2.3.10/debian/tmp/usr/bin'
make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.10/Bloom'
make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.10/Bloom'
Making install in BloomDBG
make[3]: Entering directory '/build/reproducible-path/abyss-2.3.10/BloomDBG'
make[4]: Entering directory '/build/reproducible-path/abyss-2.3.10/BloomDBG'
make[4]: Nothing to be done for 'install-data-am'.
 /usr/bin/mkdir -p '/build/reproducible-path/abyss-2.3.10/debian/tmp/usr/bin'
  /usr/bin/install -c abyss-bloom-dbg '/build/reproducible-path/abyss-2.3.10/debian/tmp/usr/bin'
make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.10/BloomDBG'
make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.10/BloomDBG'
Making install in Konnector
make[3]: Entering directory '/build/reproducible-path/abyss-2.3.10/Konnector'
make[4]: Entering directory '/build/reproducible-path/abyss-2.3.10/Konnector'
make[4]: Nothing to be done for 'install-data-am'.
 /usr/bin/mkdir -p '/build/reproducible-path/abyss-2.3.10/debian/tmp/usr/bin'
  /usr/bin/install -c konnector '/build/reproducible-path/abyss-2.3.10/debian/tmp/usr/bin'
make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.10/Konnector'
make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.10/Konnector'
Making install in Consensus
make[3]: Entering directory '/build/reproducible-path/abyss-2.3.10/Consensus'
make[4]: Entering directory '/build/reproducible-path/abyss-2.3.10/Consensus'
make[4]: Nothing to be done for 'install-data-am'.
 /usr/bin/mkdir -p '/build/reproducible-path/abyss-2.3.10/debian/tmp/usr/bin'
  /usr/bin/install -c Consensus '/build/reproducible-path/abyss-2.3.10/debian/tmp/usr/bin'
make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.10/Consensus'
make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.10/Consensus'
Making install in DAssembler
make[3]: Entering directory '/build/reproducible-path/abyss-2.3.10/DAssembler'
make[4]: Entering directory '/build/reproducible-path/abyss-2.3.10/DAssembler'
make[4]: Nothing to be done for 'install-data-am'.
 /usr/bin/mkdir -p '/build/reproducible-path/abyss-2.3.10/debian/tmp/usr/bin'
  /usr/bin/install -c DAssembler '/build/reproducible-path/abyss-2.3.10/debian/tmp/usr/bin'
make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.10/DAssembler'
make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.10/DAssembler'
Making install in DistanceEst
make[3]: Entering directory '/build/reproducible-path/abyss-2.3.10/DistanceEst'
make[4]: Entering directory '/build/reproducible-path/abyss-2.3.10/DistanceEst'
make[4]: Nothing to be done for 'install-data-am'.
 /usr/bin/mkdir -p '/build/reproducible-path/abyss-2.3.10/debian/tmp/usr/bin'
  /usr/bin/install -c DistanceEst DistanceEst-ssq '/build/reproducible-path/abyss-2.3.10/debian/tmp/usr/bin'
make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.10/DistanceEst'
make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.10/DistanceEst'
Making install in KAligner
make[3]: Entering directory '/build/reproducible-path/abyss-2.3.10/KAligner'
make[4]: Entering directory '/build/reproducible-path/abyss-2.3.10/KAligner'
make[4]: Nothing to be done for 'install-data-am'.
 /usr/bin/mkdir -p '/build/reproducible-path/abyss-2.3.10/debian/tmp/usr/bin'
  /usr/bin/install -c KAligner '/build/reproducible-path/abyss-2.3.10/debian/tmp/usr/bin'
make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.10/KAligner'
make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.10/KAligner'
Making install in Layout
make[3]: Entering directory '/build/reproducible-path/abyss-2.3.10/Layout'
make[4]: Entering directory '/build/reproducible-path/abyss-2.3.10/Layout'
make[4]: Nothing to be done for 'install-data-am'.
 /usr/bin/mkdir -p '/build/reproducible-path/abyss-2.3.10/debian/tmp/usr/bin'
  /usr/bin/install -c abyss-layout '/build/reproducible-path/abyss-2.3.10/debian/tmp/usr/bin'
make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.10/Layout'
make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.10/Layout'
Making install in LogKmerCount
make[3]: Entering directory '/build/reproducible-path/abyss-2.3.10/LogKmerCount'
make[4]: Entering directory '/build/reproducible-path/abyss-2.3.10/LogKmerCount'
make[4]: Nothing to be done for 'install-data-am'.
 /usr/bin/mkdir -p '/build/reproducible-path/abyss-2.3.10/debian/tmp/usr/bin'
  /usr/bin/install -c logcounter '/build/reproducible-path/abyss-2.3.10/debian/tmp/usr/bin'
make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.10/LogKmerCount'
make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.10/LogKmerCount'
Making install in Map
make[3]: Entering directory '/build/reproducible-path/abyss-2.3.10/Map'
make[4]: Entering directory '/build/reproducible-path/abyss-2.3.10/Map'
make[4]: Nothing to be done for 'install-data-am'.
 /usr/bin/mkdir -p '/build/reproducible-path/abyss-2.3.10/debian/tmp/usr/bin'
  /usr/bin/install -c abyss-index abyss-map abyss-map-ssq abyss-overlap '/build/reproducible-path/abyss-2.3.10/debian/tmp/usr/bin'
make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.10/Map'
make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.10/Map'
Making install in MergePaths
make[3]: Entering directory '/build/reproducible-path/abyss-2.3.10/MergePaths'
make[4]: Entering directory '/build/reproducible-path/abyss-2.3.10/MergePaths'
make[4]: Nothing to be done for 'install-data-am'.
 /usr/bin/mkdir -p '/build/reproducible-path/abyss-2.3.10/debian/tmp/usr/bin'
  /usr/bin/install -c MergePaths MergeContigs PathConsensus '/build/reproducible-path/abyss-2.3.10/debian/tmp/usr/bin'
make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.10/MergePaths'
make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.10/MergePaths'
Making install in Overlap
make[3]: Entering directory '/build/reproducible-path/abyss-2.3.10/Overlap'
make[4]: Entering directory '/build/reproducible-path/abyss-2.3.10/Overlap'
make[4]: Nothing to be done for 'install-data-am'.
 /usr/bin/mkdir -p '/build/reproducible-path/abyss-2.3.10/debian/tmp/usr/bin'
  /usr/bin/install -c Overlap '/build/reproducible-path/abyss-2.3.10/debian/tmp/usr/bin'
make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.10/Overlap'
make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.10/Overlap'
Making install in PairedDBG
make[3]: Entering directory '/build/reproducible-path/abyss-2.3.10/PairedDBG'
make[4]: Entering directory '/build/reproducible-path/abyss-2.3.10/PairedDBG'
make[4]: Nothing to be done for 'install-data-am'.
 /usr/bin/mkdir -p '/build/reproducible-path/abyss-2.3.10/debian/tmp/usr/bin'
  /usr/bin/install -c abyss-paired-dbg '/build/reproducible-path/abyss-2.3.10/debian/tmp/usr/bin'
make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.10/PairedDBG'
make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.10/PairedDBG'
Making install in ParseAligns
make[3]: Entering directory '/build/reproducible-path/abyss-2.3.10/ParseAligns'
make[4]: Entering directory '/build/reproducible-path/abyss-2.3.10/ParseAligns'
make[4]: Nothing to be done for 'install-data-am'.
 /usr/bin/mkdir -p '/build/reproducible-path/abyss-2.3.10/debian/tmp/usr/bin'
  /usr/bin/install -c abyss-fixmate abyss-fixmate-ssq ParseAligns '/build/reproducible-path/abyss-2.3.10/debian/tmp/usr/bin'
make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.10/ParseAligns'
make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.10/ParseAligns'
Making install in PathOverlap
make[3]: Entering directory '/build/reproducible-path/abyss-2.3.10/PathOverlap'
make[4]: Entering directory '/build/reproducible-path/abyss-2.3.10/PathOverlap'
make[4]: Nothing to be done for 'install-data-am'.
 /usr/bin/mkdir -p '/build/reproducible-path/abyss-2.3.10/debian/tmp/usr/bin'
  /usr/bin/install -c PathOverlap '/build/reproducible-path/abyss-2.3.10/debian/tmp/usr/bin'
make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.10/PathOverlap'
make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.10/PathOverlap'
Making install in PopBubbles
make[3]: Entering directory '/build/reproducible-path/abyss-2.3.10/PopBubbles'
make[4]: Entering directory '/build/reproducible-path/abyss-2.3.10/PopBubbles'
make[4]: Nothing to be done for 'install-data-am'.
 /usr/bin/mkdir -p '/build/reproducible-path/abyss-2.3.10/debian/tmp/usr/bin'
  /usr/bin/install -c PopBubbles '/build/reproducible-path/abyss-2.3.10/debian/tmp/usr/bin'
make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.10/PopBubbles'
make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.10/PopBubbles'
Making install in Scaffold
make[3]: Entering directory '/build/reproducible-path/abyss-2.3.10/Scaffold'
make[4]: Entering directory '/build/reproducible-path/abyss-2.3.10/Scaffold'
make[4]: Nothing to be done for 'install-data-am'.
 /usr/bin/mkdir -p '/build/reproducible-path/abyss-2.3.10/debian/tmp/usr/bin'
  /usr/bin/install -c abyss-scaffold abyss-junction abyss-longseqdist '/build/reproducible-path/abyss-2.3.10/debian/tmp/usr/bin'
make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.10/Scaffold'
make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.10/Scaffold'
Making install in SimpleGraph
make[3]: Entering directory '/build/reproducible-path/abyss-2.3.10/SimpleGraph'
make[4]: Entering directory '/build/reproducible-path/abyss-2.3.10/SimpleGraph'
make[4]: Nothing to be done for 'install-data-am'.
 /usr/bin/mkdir -p '/build/reproducible-path/abyss-2.3.10/debian/tmp/usr/bin'
  /usr/bin/install -c SimpleGraph '/build/reproducible-path/abyss-2.3.10/debian/tmp/usr/bin'
make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.10/SimpleGraph'
make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.10/SimpleGraph'
Making install in kmerprint
make[3]: Entering directory '/build/reproducible-path/abyss-2.3.10/kmerprint'
make[4]: Entering directory '/build/reproducible-path/abyss-2.3.10/kmerprint'
make[4]: Nothing to be done for 'install-exec-am'.
make[4]: Nothing to be done for 'install-data-am'.
make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.10/kmerprint'
make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.10/kmerprint'
Making install in FilterGraph
make[3]: Entering directory '/build/reproducible-path/abyss-2.3.10/FilterGraph'
make[4]: Entering directory '/build/reproducible-path/abyss-2.3.10/FilterGraph'
make[4]: Nothing to be done for 'install-data-am'.
 /usr/bin/mkdir -p '/build/reproducible-path/abyss-2.3.10/debian/tmp/usr/bin'
  /usr/bin/install -c abyss-filtergraph '/build/reproducible-path/abyss-2.3.10/debian/tmp/usr/bin'
make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.10/FilterGraph'
make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.10/FilterGraph'
Making install in GapFiller
make[3]: Entering directory '/build/reproducible-path/abyss-2.3.10/GapFiller'
make[4]: Entering directory '/build/reproducible-path/abyss-2.3.10/GapFiller'
make[4]: Nothing to be done for 'install-data-am'.
 /usr/bin/mkdir -p '/build/reproducible-path/abyss-2.3.10/debian/tmp/usr/bin'
  /usr/bin/install -c abyss-gapfill '/build/reproducible-path/abyss-2.3.10/debian/tmp/usr/bin'
make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.10/GapFiller'
make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.10/GapFiller'
Making install in Sealer
make[3]: Entering directory '/build/reproducible-path/abyss-2.3.10/Sealer'
make[4]: Entering directory '/build/reproducible-path/abyss-2.3.10/Sealer'
 /usr/bin/mkdir -p '/build/reproducible-path/abyss-2.3.10/debian/tmp/usr/bin'
  /usr/bin/install -c abyss-sealer '/build/reproducible-path/abyss-2.3.10/debian/tmp/usr/bin'
make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.10/Sealer'
make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.10/Sealer'
Making install in RResolver
make[3]: Entering directory '/build/reproducible-path/abyss-2.3.10/RResolver'
make[4]: Entering directory '/build/reproducible-path/abyss-2.3.10/RResolver'
make[4]: Nothing to be done for 'install-data-am'.
 /usr/bin/mkdir -p '/build/reproducible-path/abyss-2.3.10/debian/tmp/usr/bin'
  /usr/bin/install -c abyss-rresolver-short '/build/reproducible-path/abyss-2.3.10/debian/tmp/usr/bin'
make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.10/RResolver'
make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.10/RResolver'
Making install in AdjList
make[3]: Entering directory '/build/reproducible-path/abyss-2.3.10/AdjList'
make[4]: Entering directory '/build/reproducible-path/abyss-2.3.10/AdjList'
make[4]: Nothing to be done for 'install-data-am'.
 /usr/bin/mkdir -p '/build/reproducible-path/abyss-2.3.10/debian/tmp/usr/bin'
  /usr/bin/install -c AdjList '/build/reproducible-path/abyss-2.3.10/debian/tmp/usr/bin'
make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.10/AdjList'
make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.10/AdjList'
Making install in vendor
make[3]: Entering directory '/build/reproducible-path/abyss-2.3.10/vendor'
make[4]: Entering directory '/build/reproducible-path/abyss-2.3.10/vendor'
make[4]: Nothing to be done for 'install-exec-am'.
make[4]: Nothing to be done for 'install-data-am'.
make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.10/vendor'
make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.10/vendor'
Making install in vendor/gtest-1.7.0
make[3]: Entering directory '/build/reproducible-path/abyss-2.3.10/vendor/gtest-1.7.0'
make[4]: Entering directory '/build/reproducible-path/abyss-2.3.10/vendor/gtest-1.7.0'
make[4]: Nothing to be done for 'install-exec-am'.
make[4]: Nothing to be done for 'install-data-am'.
make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.10/vendor/gtest-1.7.0'
make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.10/vendor/gtest-1.7.0'
Making install in Unittest
make[3]: Entering directory '/build/reproducible-path/abyss-2.3.10/Unittest'
make[4]: Entering directory '/build/reproducible-path/abyss-2.3.10/Unittest'
make[4]: Nothing to be done for 'install-exec-am'.
make[4]: Nothing to be done for 'install-data-am'.
make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.10/Unittest'
make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.10/Unittest'
make[3]: Entering directory '/build/reproducible-path/abyss-2.3.10'
make[4]: Entering directory '/build/reproducible-path/abyss-2.3.10'
make[4]: Nothing to be done for 'install-exec-am'.
 /usr/bin/mkdir -p '/build/reproducible-path/abyss-2.3.10/debian/tmp/usr/share/doc/abyss'
 /usr/bin/install -c -m 644 ChangeLog CITATION.bib CITATION.md COPYRIGHT LICENSE README.md '/build/reproducible-path/abyss-2.3.10/debian/tmp/usr/share/doc/abyss'
make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.10'
make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.10'
make[2]: Leaving directory '/build/reproducible-path/abyss-2.3.10'
mkdir -p debian/tmp/usr/share/man/man1
PATH=debian/tmp/usr/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path 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:/i/capture/the/path help2man --no-info \
     -n "Fill the paired-end fields of SAM alignments" abyss-fixmate \
     > debian/tmp/usr/share/man/man1/abyss-fixmate.1
make[1]: Leaving directory '/build/reproducible-path/abyss-2.3.10'
   debian/rules override_dh_install
make[1]: Entering directory '/build/reproducible-path/abyss-2.3.10'
dh_install
for pl in `grep -Rl '#!/usr/bin/env[[:space:]]\+perl' debian/*/usr/*` ; do \
    sed -i '1s?^#!/usr/bin/env[[:space:]]\+perl?#!/usr/bin/perl?' ${pl} ; \
done
make[1]: Leaving directory '/build/reproducible-path/abyss-2.3.10'
   dh_installdocs
   dh_installchangelogs
   dh_installman
   dh_perl
   dh_link
   dh_strip_nondeterminism
   dh_compress
   dh_fixperms
   dh_missing
   dh_dwz -a
   dh_strip -a
   dh_makeshlibs -a
   dh_shlibdeps -a
dpkg-shlibdeps: warning: diversions involved - output may be incorrect
 diversion by libc6 from: /lib/ld-linux-aarch64.so.1
dpkg-shlibdeps: warning: diversions involved - output may be incorrect
 diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged
   dh_installdeb
   dh_gencontrol
   dh_md5sums
   dh_builddeb
dpkg-deb: building package 'abyss' in '../abyss_2.3.10-1_arm64.deb'.
dpkg-deb: building package 'abyss-dbgsym' in '../abyss-dbgsym_2.3.10-1_arm64.deb'.
 dpkg-genbuildinfo --build=binary -O../abyss_2.3.10-1_arm64.buildinfo
 dpkg-genchanges --build=binary -O../abyss_2.3.10-1_arm64.changes
dpkg-genchanges: info: binary-only upload (no source code included)
 dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
dpkg-genchanges: info: including full source code in upload
I: copying local configuration
I: user script /srv/workspace/pbuilder/510437/tmp/hooks/B01_cleanup starting
I: user script /srv/workspace/pbuilder/510437/tmp/hooks/B01_cleanup finished
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/510437 and its subdirectories
I: Current time: Sun Feb  9 14:41:59 +14 2025
I: pbuilder-time-stamp: 1739061719