abyss →
2.1.5-7 →
armhf → 2019-02-27 05:12:23
sbuild (Debian sbuild) 0.72.0 (25 Oct 2016) on mb-lxc-01
+==============================================================================+
| abyss 2.1.5-7 (armhf) Wed, 27 Feb 2019 04:49:33 +0000 |
+==============================================================================+
Package: abyss
Version: 2.1.5-7
Source Version: 2.1.5-7
Distribution: buster-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/buster-staging-armhf-sbuild-ca834cc9-f37a-4296-9058-a304782aeb5d' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private buster-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private buster-staging/main Sources [11.4 MB]
Get:3 http://172.17.0.1/private buster-staging/main armhf Packages [13.1 MB]
Fetched 24.4 MB in 9s (2760 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: 'abyss' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/abyss.git
Please use:
git clone https://salsa.debian.org/med-team/abyss.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 1826 kB of source archives.
Get:1 http://172.17.0.1/private buster-staging/main abyss 2.1.5-7 (dsc) [2356 B]
Get:2 http://172.17.0.1/private buster-staging/main abyss 2.1.5-7 (tar) [1063 kB]
Get:3 http://172.17.0.1/private buster-staging/main abyss 2.1.5-7 (diff) [760 kB]
Fetched 1826 kB in 0s (6152 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/abyss-zGwvH9/abyss-2.1.5' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/abyss-zGwvH9' with '<<BUILDDIR>>'
+------------------------------------------------------------------------------+
| Install build-essential |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<<BUILDDIR>>/resolver-tGwL1Y/apt_archive/sbuild-build-depends-core-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy
dpkg-scanpackages: info: Wrote 1 entries to output Packages file.
gpg: keybox '/<<BUILDDIR>>/resolver-tGwL1Y/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-tGwL1Y/gpg/trustdb.gpg: trustdb created
gpg: key 37145E60F90AF620: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg: imported: 1
gpg: key 37145E60F90AF620: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 37145E60F90AF620: secret key imported
gpg: Total number processed: 1
gpg: unchanged: 1
gpg: secret keys read: 1
gpg: secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-tGwL1Y/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-tGwL1Y/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-tGwL1Y/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-tGwL1Y/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-tGwL1Y/apt_archive ./ Packages [434 B]
Fetched 2110 B in 0s (10.5 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
ca-certificates dbus dbus-user-session e2fsprogs-l10n krb5-locales libexpat1
libgpg-error-l10n libgssapi-krb5-2 libk5crypto3 libkeyutils1 libkrb5-3
libkrb5support0 libnss-systemd libpam-systemd openssl systemd-sysv
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 39 not upgraded.
Need to get 848 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-tGwL1Y/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [848 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 848 B in 0s (0 B/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 15799 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any-amd64 any-i386 arm64 armel armhf mips64el mipsel ppc64el s390x alpha ia64 m68k powerpcspe ppc64 riscv64 sh4 sparc64)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper (>= 12~), python-markdown, libboost-graph-dev, libopenmpi-dev, libsparsehash-dev, libtext-multimarkdown-perl, libgtest-dev, libsqlite3-dev, pkg-config, help2man
Filtered Build-Depends: debhelper (>= 12~), python-markdown, libboost-graph-dev, libopenmpi-dev, libsparsehash-dev, libtext-multimarkdown-perl, libgtest-dev, libsqlite3-dev, pkg-config, help2man
dpkg-deb: building package 'sbuild-build-depends-abyss-dummy' in '/<<BUILDDIR>>/resolver-tGwL1Y/apt_archive/sbuild-build-depends-abyss-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-abyss-dummy sbuild-build-depends-core-dummy
dpkg-scanpackages: info: Wrote 2 entries to output Packages file.
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-tGwL1Y/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-tGwL1Y/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-tGwL1Y/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-tGwL1Y/apt_archive ./ Sources [573 B]
Get:5 copy:/<<BUILDDIR>>/resolver-tGwL1Y/apt_archive ./ Packages [654 B]
Fetched 2560 B in 0s (13.1 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install abyss build dependencies (apt-based resolver)
-----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
ca-certificates dbus dbus-user-session e2fsprogs-l10n krb5-locales
libgpg-error-l10n libnss-systemd libpam-systemd openssl systemd-sysv
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils cpp-8 debhelper
dh-autoreconf dh-strip-nondeterminism dwz file g++-8 gcc-8 gcc-8-base
gettext gettext-base googletest groff-base help2man ibverbs-providers
intltool-debian libarchive-zip-perl libasan5 libatomic1
libboost-chrono1.67.0 libboost-graph-dev libboost-graph1.67-dev
libboost-graph1.67.0 libboost-regex1.67.0 libboost-serialization1.67-dev
libboost-serialization1.67.0 libboost-system1.67.0 libboost-test1.67-dev
libboost-test1.67.0 libboost-timer1.67.0 libboost1.67-dev libbsd0 libcc1-0
libcroco3 libedit2 libelf1 libevent-2.1-6 libevent-core-2.1-6
libevent-pthreads-2.1-6 libfile-stripnondeterminism-perl libgcc-8-dev
libgcc1 libgfortran5 libglib2.0-0 libgomp1 libgtest-dev libhtml-parser-perl
libhtml-tagset-perl libhwloc-dev libhwloc-plugins libhwloc5 libibverbs-dev
libibverbs1 libicu63 liblocale-gettext-perl libltdl-dev libltdl7
libmagic-mgc libmagic1 libnl-3-200 libnl-3-dev libnl-route-3-200
libnl-route-3-dev libopenmpi-dev libopenmpi3 libpciaccess0 libpipeline1
libpmix2 libpython-stdlib libpython2-stdlib libpython2.7-minimal
libpython2.7-stdlib libsigsegv2 libsparsehash-dev libsqlite3-dev
libstdc++-8-dev libstdc++6 libtext-markdown-perl libtext-multimarkdown-perl
libtool libubsan1 libuchardet0 liburi-perl libxml2 m4 man-db mime-support
ocl-icd-libopencl1 openmpi-bin openmpi-common openssh-client pkg-config
po-debconf python python-markdown python-minimal python-pkg-resources
python2 python2-minimal python2.7 python2.7-minimal
Suggested packages:
autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
vacation gcc-8-locales dh-make gcc-8-doc libstdc++6-8-dbg libgcc1-dbg
libgomp1-dbg libitm1-dbg libatomic1-dbg libasan5-dbg liblsan0-dbg
libtsan0-dbg libubsan1-dbg libmpx2-dbg libquadmath0-dbg gettext-doc
libasprintf-dev libgettextpo-dev groff graphviz libboost1.67-doc
libboost-atomic1.67-dev libboost-chrono1.67-dev libboost-container1.67-dev
libboost-context1.67-dev libboost-coroutine1.67-dev
libboost-date-time1.67-dev libboost-exception1.67-dev libboost-fiber1.67-dev
libboost-filesystem1.67-dev libboost-graph-parallel1.67-dev
libboost-iostreams1.67-dev libboost-locale1.67-dev libboost-log1.67-dev
libboost-math1.67-dev libboost-mpi1.67-dev libboost-mpi-python1.67-dev
libboost-numpy1.67-dev libboost-program-options1.67-dev
libboost-python1.67-dev libboost-random1.67-dev libboost-regex1.67-dev
libboost-signals1.67-dev libboost-stacktrace1.67-dev libboost-system1.67-dev
libboost-thread1.67-dev libboost-timer1.67-dev libboost-type-erasure1.67-dev
libboost-wave1.67-dev libboost1.67-tools-dev libmpfrc++-dev libntl-dev
libdata-dump-perl libhwloc-contrib-plugins libtool-doc openmpi-doc pciutils
sqlite3-doc libstdc++-8-doc gfortran | fortran95-compiler gcj-jdk
libwww-perl m4-doc apparmor less www-browser opencl-icd gfortran keychain
libpam-ssh monkeysphere ssh-askpass libmail-box-perl python-doc python-tk
python-markdown-doc python-setuptools python2-doc python2.7-doc
binfmt-support
Recommended packages:
curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info
xdg-user-dirs libhttp-message-perl libcoarrays-openmpi-dev xauth
libmail-sendmail-perl python-pygments python-yaml
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils debhelper
dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base
googletest groff-base help2man ibverbs-providers intltool-debian
libarchive-zip-perl libboost-chrono1.67.0 libboost-graph-dev
libboost-graph1.67-dev libboost-graph1.67.0 libboost-regex1.67.0
libboost-serialization1.67-dev libboost-serialization1.67.0
libboost-system1.67.0 libboost-test1.67-dev libboost-test1.67.0
libboost-timer1.67.0 libboost1.67-dev libbsd0 libcroco3 libedit2 libelf1
libevent-2.1-6 libevent-core-2.1-6 libevent-pthreads-2.1-6
libfile-stripnondeterminism-perl libgfortran5 libglib2.0-0 libgtest-dev
libhtml-parser-perl libhtml-tagset-perl libhwloc-dev libhwloc-plugins
libhwloc5 libibverbs-dev libibverbs1 libicu63 liblocale-gettext-perl
libltdl-dev libltdl7 libmagic-mgc libmagic1 libnl-3-200 libnl-3-dev
libnl-route-3-200 libnl-route-3-dev libopenmpi-dev libopenmpi3 libpciaccess0
libpipeline1 libpmix2 libpython-stdlib libpython2-stdlib
libpython2.7-minimal libpython2.7-stdlib libsigsegv2 libsparsehash-dev
libsqlite3-dev libtext-markdown-perl libtext-multimarkdown-perl libtool
libuchardet0 liburi-perl libxml2 m4 man-db mime-support ocl-icd-libopencl1
openmpi-bin openmpi-common openssh-client pkg-config po-debconf python
python-markdown python-minimal python-pkg-resources python2 python2-minimal
python2.7 python2.7-minimal sbuild-build-depends-abyss-dummy
The following packages will be upgraded:
cpp-8 g++-8 gcc-8 gcc-8-base libasan5 libatomic1 libcc1-0 libgcc-8-dev
libgcc1 libgomp1 libstdc++-8-dev libstdc++6 libubsan1
13 upgraded, 94 newly installed, 0 to remove and 26 not upgraded.
Need to get 67.5 MB of archives.
After this operation, 282 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-tGwL1Y/apt_archive ./ sbuild-build-depends-abyss-dummy 0.invalid.0 [940 B]
Get:2 http://172.17.0.1/private buster-staging/main armhf liblocale-gettext-perl armhf 1.07-3+b3 [18.2 kB]
Get:3 http://172.17.0.1/private buster-staging/main armhf libbsd0 armhf 0.9.1-1 [104 kB]
Get:4 http://172.17.0.1/private buster-staging/main armhf bsdmainutils armhf 11.1.2 [182 kB]
Get:5 http://172.17.0.1/private buster-staging/main armhf libcc1-0 armhf 8.2.0-21+rpi1 [37.9 kB]
Get:6 http://172.17.0.1/private buster-staging/main armhf gcc-8-base armhf 8.2.0-21+rpi1 [190 kB]
Get:7 http://172.17.0.1/private buster-staging/main armhf libgcc1 armhf 1:8.2.0-21+rpi1 [36.6 kB]
Get:8 http://172.17.0.1/private buster-staging/main armhf libgomp1 armhf 8.2.0-21+rpi1 [64.0 kB]
Get:9 http://172.17.0.1/private buster-staging/main armhf libatomic1 armhf 8.2.0-21+rpi1 [8100 B]
Get:10 http://172.17.0.1/private buster-staging/main armhf libasan5 armhf 8.2.0-21+rpi1 [316 kB]
Get:11 http://172.17.0.1/private buster-staging/main armhf libubsan1 armhf 8.2.0-21+rpi1 [103 kB]
Get:12 http://172.17.0.1/private buster-staging/main armhf g++-8 armhf 8.2.0-21+rpi1 [7463 kB]
Get:13 http://172.17.0.1/private buster-staging/main armhf libstdc++-8-dev armhf 8.2.0-21+rpi1 [1545 kB]
Get:14 http://172.17.0.1/private buster-staging/main armhf libgcc-8-dev armhf 8.2.0-21+rpi1 [595 kB]
Get:15 http://172.17.0.1/private buster-staging/main armhf gcc-8 armhf 8.2.0-21+rpi1 [7218 kB]
Get:16 http://172.17.0.1/private buster-staging/main armhf cpp-8 armhf 8.2.0-21+rpi1 [6786 kB]
Get:17 http://172.17.0.1/private buster-staging/main armhf libstdc++6 armhf 8.2.0-21+rpi1 [325 kB]
Get:18 http://172.17.0.1/private buster-staging/main armhf libuchardet0 armhf 0.0.6-3 [62.2 kB]
Get:19 http://172.17.0.1/private buster-staging/main armhf groff-base armhf 1.22.4-2 [782 kB]
Get:20 http://172.17.0.1/private buster-staging/main armhf libpipeline1 armhf 1.5.1-2 [26.6 kB]
Get:21 http://172.17.0.1/private buster-staging/main armhf man-db armhf 2.8.5-2 [1230 kB]
Get:22 http://172.17.0.1/private buster-staging/main armhf libpython2.7-minimal armhf 2.7.15-8 [394 kB]
Get:23 http://172.17.0.1/private buster-staging/main armhf python2.7-minimal armhf 2.7.15-8 [1089 kB]
Get:24 http://172.17.0.1/private buster-staging/main armhf python2-minimal armhf 2.7.15-4 [41.4 kB]
Get:25 http://172.17.0.1/private buster-staging/main armhf python-minimal armhf 2.7.15-4 [21.0 kB]
Get:26 http://172.17.0.1/private buster-staging/main armhf mime-support all 3.62 [37.2 kB]
Get:27 http://172.17.0.1/private buster-staging/main armhf libpython2.7-stdlib armhf 2.7.15-8 [1844 kB]
Get:28 http://172.17.0.1/private buster-staging/main armhf python2.7 armhf 2.7.15-8 [299 kB]
Get:29 http://172.17.0.1/private buster-staging/main armhf libpython2-stdlib armhf 2.7.15-4 [20.8 kB]
Get:30 http://172.17.0.1/private buster-staging/main armhf libpython-stdlib armhf 2.7.15-4 [20.8 kB]
Get:31 http://172.17.0.1/private buster-staging/main armhf python2 armhf 2.7.15-4 [41.6 kB]
Get:32 http://172.17.0.1/private buster-staging/main armhf python armhf 2.7.15-4 [22.8 kB]
Get:33 http://172.17.0.1/private buster-staging/main armhf libmagic-mgc armhf 1:5.35-2 [242 kB]
Get:34 http://172.17.0.1/private buster-staging/main armhf libmagic1 armhf 1:5.35-2 [109 kB]
Get:35 http://172.17.0.1/private buster-staging/main armhf file armhf 1:5.35-2 [65.1 kB]
Get:36 http://172.17.0.1/private buster-staging/main armhf gettext-base armhf 0.19.8.1-9 [117 kB]
Get:37 http://172.17.0.1/private buster-staging/main armhf libevent-2.1-6 armhf 2.1.8-stable-4 [156 kB]
Get:38 http://172.17.0.1/private buster-staging/main armhf libedit2 armhf 3.1-20181209-1 [78.7 kB]
Get:39 http://172.17.0.1/private buster-staging/main armhf openssh-client armhf 1:7.9p1-6 [670 kB]
Get:40 http://172.17.0.1/private buster-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:41 http://172.17.0.1/private buster-staging/main armhf m4 armhf 1.4.18-2 [185 kB]
Get:42 http://172.17.0.1/private buster-staging/main armhf autoconf all 2.69-11 [341 kB]
Get:43 http://172.17.0.1/private buster-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:44 http://172.17.0.1/private buster-staging/main armhf automake all 1:1.16.1-4 [771 kB]
Get:45 http://172.17.0.1/private buster-staging/main armhf autopoint all 0.19.8.1-9 [434 kB]
Get:46 http://172.17.0.1/private buster-staging/main armhf libtool all 2.4.6-9 [547 kB]
Get:47 http://172.17.0.1/private buster-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:48 http://172.17.0.1/private buster-staging/main armhf libarchive-zip-perl all 1.64-1 [96.8 kB]
Get:49 http://172.17.0.1/private buster-staging/main armhf libfile-stripnondeterminism-perl all 1.1.1-1 [19.7 kB]
Get:50 http://172.17.0.1/private buster-staging/main armhf dh-strip-nondeterminism all 1.1.1-1 [13.0 kB]
Get:51 http://172.17.0.1/private buster-staging/main armhf libelf1 armhf 0.175-2 [157 kB]
Get:52 http://172.17.0.1/private buster-staging/main armhf dwz armhf 0.12-3 [66.0 kB]
Get:53 http://172.17.0.1/private buster-staging/main armhf libglib2.0-0 armhf 2.58.3-1 [1077 kB]
Get:54 http://172.17.0.1/private buster-staging/main armhf libicu63 armhf 63.1-6 [7973 kB]
Get:55 http://172.17.0.1/private buster-staging/main armhf libxml2 armhf 2.9.4+dfsg1-7+b1 [570 kB]
Get:56 http://172.17.0.1/private buster-staging/main armhf libcroco3 armhf 0.6.12-3 [132 kB]
Get:57 http://172.17.0.1/private buster-staging/main armhf gettext armhf 0.19.8.1-9 [1219 kB]
Get:58 http://172.17.0.1/private buster-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:59 http://172.17.0.1/private buster-staging/main armhf po-debconf all 1.0.21 [248 kB]
Get:60 http://172.17.0.1/private buster-staging/main armhf debhelper all 12.1 [1015 kB]
Get:61 http://172.17.0.1/private buster-staging/main armhf googletest armhf 1.8.1-3 [903 kB]
Get:62 http://172.17.0.1/private buster-staging/main armhf help2man armhf 1.47.8 [176 kB]
Get:63 http://172.17.0.1/private buster-staging/main armhf libnl-3-200 armhf 3.4.0-1 [55.0 kB]
Get:64 http://172.17.0.1/private buster-staging/main armhf libnl-route-3-200 armhf 3.4.0-1 [132 kB]
Get:65 http://172.17.0.1/private buster-staging/main armhf libibverbs1 armhf 22.1-1 [43.5 kB]
Get:66 http://172.17.0.1/private buster-staging/main armhf ibverbs-providers armhf 22.1-1 [20.2 kB]
Get:67 http://172.17.0.1/private buster-staging/main armhf libboost-system1.67.0 armhf 1.67.0-13 [228 kB]
Get:68 http://172.17.0.1/private buster-staging/main armhf libboost-chrono1.67.0 armhf 1.67.0-13 [231 kB]
Get:69 http://172.17.0.1/private buster-staging/main armhf libboost1.67-dev armhf 1.67.0-13 [8386 kB]
Get:70 http://172.17.0.1/private buster-staging/main armhf libboost-regex1.67.0 armhf 1.67.0-13 [430 kB]
Get:71 http://172.17.0.1/private buster-staging/main armhf libboost-graph1.67.0 armhf 1.67.0-13 [297 kB]
Get:72 http://172.17.0.1/private buster-staging/main armhf libboost-serialization1.67.0 armhf 1.67.0-13 [300 kB]
Get:73 http://172.17.0.1/private buster-staging/main armhf libboost-serialization1.67-dev armhf 1.67.0-13 [365 kB]
Get:74 http://172.17.0.1/private buster-staging/main armhf libboost-timer1.67.0 armhf 1.67.0-13 [229 kB]
Get:75 http://172.17.0.1/private buster-staging/main armhf libboost-test1.67.0 armhf 1.67.0-13 [421 kB]
Get:76 http://172.17.0.1/private buster-staging/main armhf libboost-test1.67-dev armhf 1.67.0-13 [491 kB]
Get:77 http://172.17.0.1/private buster-staging/main armhf libboost-graph1.67-dev armhf 1.67.0-13 [321 kB]
Get:78 http://172.17.0.1/private buster-staging/main armhf libboost-graph-dev armhf 1.67.0.1+b1 [4032 B]
Get:79 http://172.17.0.1/private buster-staging/main armhf libevent-core-2.1-6 armhf 2.1.8-stable-4 [117 kB]
Get:80 http://172.17.0.1/private buster-staging/main armhf libevent-pthreads-2.1-6 armhf 2.1.8-stable-4 [47.6 kB]
Get:81 http://172.17.0.1/private buster-staging/main armhf libgfortran5 armhf 8.2.0-21+rpi1 [206 kB]
Get:82 http://172.17.0.1/private buster-staging/main armhf libgtest-dev armhf 1.8.1-3 [214 kB]
Get:83 http://172.17.0.1/private buster-staging/main armhf libhtml-tagset-perl all 3.20-3 [12.7 kB]
Get:84 http://172.17.0.1/private buster-staging/main armhf liburi-perl all 1.76-1 [89.9 kB]
Get:85 http://172.17.0.1/private buster-staging/main armhf libhtml-parser-perl armhf 3.72-3+b2 [101 kB]
Get:86 http://172.17.0.1/private buster-staging/main armhf libltdl7 armhf 2.4.6-9 [387 kB]
Get:87 http://172.17.0.1/private buster-staging/main armhf libhwloc5 armhf 1.11.12-3+rpi1 [86.3 kB]
Get:88 http://172.17.0.1/private buster-staging/main armhf libltdl-dev armhf 2.4.6-9 [159 kB]
Get:89 http://172.17.0.1/private buster-staging/main armhf libhwloc-dev armhf 1.11.12-3+rpi1 [142 kB]
Get:90 http://172.17.0.1/private buster-staging/main armhf libpciaccess0 armhf 0.14-1 [51.0 kB]
Get:91 http://172.17.0.1/private buster-staging/main armhf ocl-icd-libopencl1 armhf 2.2.12-2 [35.7 kB]
Get:92 http://172.17.0.1/private buster-staging/main armhf libhwloc-plugins armhf 1.11.12-3+rpi1 [16.0 kB]
Get:93 http://172.17.0.1/private buster-staging/main armhf libnl-3-dev armhf 3.4.0-1 [92.4 kB]
Get:94 http://172.17.0.1/private buster-staging/main armhf libnl-route-3-dev armhf 3.4.0-1 [145 kB]
Get:95 http://172.17.0.1/private buster-staging/main armhf libibverbs-dev armhf 22.1-1 [149 kB]
Get:96 http://172.17.0.1/private buster-staging/main armhf libpmix2 armhf 3.1.2-2 [423 kB]
Get:97 http://172.17.0.1/private buster-staging/main armhf libopenmpi3 armhf 3.1.3-10+rpi1 [2156 kB]
Get:98 http://172.17.0.1/private buster-staging/main armhf openmpi-common all 3.1.3-10+rpi1 [164 kB]
Get:99 http://172.17.0.1/private buster-staging/main armhf openmpi-bin armhf 3.1.3-10+rpi1 [197 kB]
Get:100 http://172.17.0.1/private buster-staging/main armhf libopenmpi-dev armhf 3.1.3-10+rpi1 [964 kB]
Get:101 http://172.17.0.1/private buster-staging/main armhf libsparsehash-dev all 2.0.2-1 [76.9 kB]
Get:102 http://172.17.0.1/private buster-staging/main armhf libsqlite3-dev armhf 3.26.0+fossilbc891ac6b-2 [680 kB]
Get:103 http://172.17.0.1/private buster-staging/main armhf libtext-markdown-perl all 1.000031-2 [34.4 kB]
Get:104 http://172.17.0.1/private buster-staging/main armhf libtext-multimarkdown-perl all 1.000035-1 [29.4 kB]
Get:105 http://172.17.0.1/private buster-staging/main armhf pkg-config armhf 0.29-6 [59.8 kB]
Get:106 http://172.17.0.1/private buster-staging/main armhf python-pkg-resources all 40.7.1-1 [181 kB]
Get:107 http://172.17.0.1/private buster-staging/main armhf python-markdown all 3.0.1-3 [60.6 kB]
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Unpacking sbuild-build-depends-abyss-dummy (0.invalid.0) ...
Setting up libhtml-tagset-perl (3.20-3) ...
Setting up cpp-8 (8.2.0-21+rpi1) ...
Setting up libgomp1:armhf (8.2.0-21+rpi1) ...
Setting up libatomic1:armhf (8.2.0-21+rpi1) ...
Setting up libsparsehash-dev (2.0.2-1) ...
Setting up libcc1-0:armhf (8.2.0-21+rpi1) ...
Setting up libevent-2.1-6:armhf (2.1.8-stable-4) ...
Setting up libevent-core-2.1-6:armhf (2.1.8-stable-4) ...
Setting up libarchive-zip-perl (1.64-1) ...
Setting up mime-support (3.62) ...
Installing new version of config file /etc/mime.types ...
Setting up libicu63:armhf (63.1-6) ...
Setting up libtext-markdown-perl (1.000031-2) ...
Setting up libsqlite3-dev:armhf (3.26.0+fossilbc891ac6b-2) ...
Setting up libsigsegv2:armhf (2.12-2) ...
Setting up libelf1:armhf (0.175-2) ...
Setting up libglib2.0-0:armhf (2.58.3-1) ...
No schema files found: removed existing output file.
Setting up gettext-base (0.19.8.1-9) ...
Setting up libpipeline1:armhf (1.5.1-2) ...
Setting up m4 (1.4.18-2) ...
Setting up libbsd0:armhf (0.9.1-1) ...
Setting up libxml2:armhf (2.9.4+dfsg1-7+b1) ...
Setting up libuchardet0:armhf (0.0.6-3) ...
Setting up libmagic-mgc (1:5.35-2) ...
Setting up libmagic1:armhf (1:5.35-2) ...
Setting up libcroco3:armhf (0.6.12-3) ...
Setting up pkg-config (0.29-6) ...
Setting up googletest:armhf (1.8.1-3) ...
Setting up libevent-pthreads-2.1-6:armhf (2.1.8-stable-4) ...
Setting up openmpi-common (3.1.3-10+rpi1) ...
Processing triggers for libc-bin (2.28-6+rpi1) ...
Setting up dwz (0.12-3) ...
Setting up autotools-dev (20180224.1) ...
Setting up liburi-perl (1.76-1) ...
Setting up libltdl7:armhf (2.4.6-9) ...
Setting up libhtml-parser-perl (3.72-3+b2) ...
Setting up libgtest-dev:armhf (1.8.1-3) ...
Setting up liblocale-gettext-perl (1.07-3+b3) ...
Setting up libpciaccess0:armhf (0.14-1) ...
Setting up libboost-serialization1.67.0:armhf (1.67.0-13) ...
Setting up ocl-icd-libopencl1:armhf (2.2.12-2) ...
Setting up bsdmainutils (11.1.2) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
Setting up libnl-3-200:armhf (3.4.0-1) ...
Setting up libboost-system1.67.0:armhf (1.67.0-13) ...
Setting up libasan5:armhf (8.2.0-21+rpi1) ...
Setting up libgfortran5:armhf (8.2.0-21+rpi1) ...
Setting up libboost-regex1.67.0:armhf (1.67.0-13) ...
Setting up libpython2.7-stdlib:armhf (2.7.15-8) ...
Setting up autopoint (0.19.8.1-9) ...
Setting up libfile-stripnondeterminism-perl (1.1.1-1) ...
Setting up libubsan1:armhf (8.2.0-21+rpi1) ...
Setting up libedit2:armhf (3.1-20181209-1) ...
Setting up gettext (0.19.8.1-9) ...
Setting up groff-base (1.22.4-2) ...
Setting up libnl-3-dev:armhf (3.4.0-1) ...
Setting up python2.7 (2.7.15-8) ...
Setting up libnl-route-3-200:armhf (3.4.0-1) ...
Setting up autoconf (2.69-11) ...
Setting up file (1:5.35-2) ...
Setting up libboost-graph1.67.0:armhf (1.67.0-13) ...
Setting up libhwloc5:armhf (1.11.12-3+rpi1) ...
Setting up libtext-multimarkdown-perl (1.000035-1) ...
Setting up libhwloc-plugins:armhf (1.11.12-3+rpi1) ...
Setting up intltool-debian (0.35.0+20060710.5) ...
Setting up libboost-chrono1.67.0:armhf (1.67.0-13) ...
Setting up automake (1:1.16.1-4) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up help2man (1.47.8) ...
Setting up man-db (2.8.5-2) ...
Not building database; man-db/auto-update is not 'true'.
Created symlink /etc/systemd/system/timers.target.wants/man-db.timer -> /lib/systemd/system/man-db.timer.
Setting up libpython2-stdlib:armhf (2.7.15-4) ...
Setting up libgcc-8-dev:armhf (8.2.0-21+rpi1) ...
Setting up openssh-client (1:7.9p1-6) ...
Setting up libtool (2.4.6-9) ...
Setting up libibverbs1:armhf (22.1-1) ...
Setting up libstdc++-8-dev:armhf (8.2.0-21+rpi1) ...
Setting up libboost-timer1.67.0:armhf (1.67.0-13) ...
Setting up libltdl-dev:armhf (2.4.6-9) ...
Setting up po-debconf (1.0.21) ...
Setting up libhwloc-dev:armhf (1.11.12-3+rpi1) ...
Setting up libnl-route-3-dev:armhf (3.4.0-1) ...
Setting up libpmix2:armhf (3.1.2-2) ...
Setting up python2 (2.7.15-4) ...
Setting up gcc-8 (8.2.0-21+rpi1) ...
Setting up g++-8 (8.2.0-21+rpi1) ...
Setting up libpython-stdlib:armhf (2.7.15-4) ...
Setting up libboost1.67-dev:armhf (1.67.0-13) ...
Setting up ibverbs-providers:armhf (22.1-1) ...
Setting up libibverbs-dev:armhf (22.1-1) ...
Setting up libboost-test1.67.0:armhf (1.67.0-13) ...
Setting up python (2.7.15-4) ...
Setting up libopenmpi3:armhf (3.1.3-10+rpi1) ...
Setting up libboost-serialization1.67-dev:armhf (1.67.0-13) ...
Setting up libboost-test1.67-dev:armhf (1.67.0-13) ...
Setting up python-pkg-resources (40.7.1-1) ...
Setting up openmpi-bin (3.1.3-10+rpi1) ...
update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode
update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode
Setting up python-markdown (3.0.1-3) ...
Setting up libopenmpi-dev:armhf (3.1.3-10+rpi1) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/openmpi/include to provide /usr/include/arm-linux-gnueabihf/mpi (mpi-arm-linux-gnueabihf) in auto mode
Setting up libboost-graph1.67-dev:armhf (1.67.0-13) ...
Setting up libboost-graph-dev:armhf (1.67.0.1+b1) ...
Setting up dh-autoreconf (19) ...
Setting up dh-strip-nondeterminism (1.1.1-1) ...
Setting up debhelper (12.1) ...
Setting up sbuild-build-depends-abyss-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.28-6+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.4.0-124-generic armhf (armv8l)
Toolchain package versions: binutils_2.31.1-11+rpi1 dpkg-dev_1.19.2 g++-8_8.2.0-21+rpi1 gcc-8_8.2.0-21+rpi1 libc6-dev_2.28-6+rpi1 libstdc++-8-dev_8.2.0-21+rpi1 libstdc++6_8.2.0-21+rpi1 linux-libc-dev_4.18.20-2+rpi1
Package versions: adduser_3.118 apt_1.8.0~rc3 autoconf_2.69-11 automake_1:1.16.1-4 autopoint_0.19.8.1-9 autotools-dev_20180224.1 base-files_10.1+rpi1 base-passwd_3.5.46 bash_5.0-2 binutils_2.31.1-11+rpi1 binutils-arm-linux-gnueabihf_2.31.1-11+rpi1 binutils-common_2.31.1-11+rpi1 bsdmainutils_11.1.2 bsdutils_1:2.33.1-0.1 build-essential_12.5 bzip2_1.0.6-9 ca-certificates_20190110 coreutils_8.30-1 cpio_2.12+dfsg-6 cpp_4:8.2.0-2+rpi1 cpp-8_8.2.0-21+rpi1 dash_0.5.10.2-5 dbus_1.12.12-1 dbus-user-session_1.12.12-1 debconf_1.5.70 debhelper_12.1 debianutils_4.8.6.1 dh-autoreconf_19 dh-strip-nondeterminism_1.1.1-1 diffutils_1:3.6-1 dirmngr_2.2.12-1+rpi1 dmsetup_2:1.02.155-2 dpkg_1.19.2 dpkg-dev_1.19.2 dwz_0.12-3 e2fslibs_1.44.5-1 e2fsprogs_1.44.5-1 e2fsprogs-l10n_1.44.5-1 fakeroot_1.23-1 fdisk_2.33.1-0.1 file_1:5.35-2 findutils_4.6.0+git+20190105-2 g++_4:8.2.0-2+rpi1 g++-8_8.2.0-21+rpi1 gcc_4:8.2.0-2+rpi1 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8-base_4.8.5-4 gcc-4.9-base_4.9.4-2+rpi1+b19 gcc-5-base_5.5.0-8 gcc-8_8.2.0-21+rpi1 gcc-8-base_8.2.0-21+rpi1 gettext_0.19.8.1-9 gettext-base_0.19.8.1-9 gnupg_2.2.12-1+rpi1 gnupg-agent_2.2.12-1+rpi1 gnupg-l10n_2.2.12-1+rpi1 gnupg-utils_2.2.12-1+rpi1 googletest_1.8.1-3 gpg_2.2.12-1+rpi1 gpg-agent_2.2.12-1+rpi1 gpg-wks-client_2.2.12-1+rpi1 gpg-wks-server_2.2.12-1+rpi1 gpgconf_2.2.12-1+rpi1 gpgsm_2.2.12-1+rpi1 gpgv_2.2.12-1+rpi1 grep_3.3-1 groff-base_1.22.4-2 gzip_1.9-3 help2man_1.47.8 hostname_3.21 ibverbs-providers_22.1-1 inetutils-ping_2:1.9.4-5 init-system-helpers_1.56+nmu1 initramfs-tools_0.133 initramfs-tools-core_0.133 intltool-debian_0.35.0+20060710.5 klibc-utils_2.0.6-1+rpi1 kmod_26-1 krb5-locales_1.17-1 libacl1_2.2.52-3 libapparmor1_2.13.2-7 libapt-pkg5.0_1.8.0~rc3 libarchive-zip-perl_1.64-1 libargon2-1_0~20171227-0.2 libasan5_8.2.0-21+rpi1 libassuan0_2.5.2-1 libatomic1_8.2.0-21+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.8.4-2 libaudit1_1:2.8.4-2+b1 libbinutils_2.31.1-11+rpi1 libblkid1_2.33.1-0.1 libboost-chrono1.67.0_1.67.0-13 libboost-graph-dev_1.67.0.1+b1 libboost-graph1.67-dev_1.67.0-13 libboost-graph1.67.0_1.67.0-13 libboost-regex1.67.0_1.67.0-13 libboost-serialization1.67-dev_1.67.0-13 libboost-serialization1.67.0_1.67.0-13 libboost-system1.67.0_1.67.0-13 libboost-test1.67-dev_1.67.0-13 libboost-test1.67.0_1.67.0-13 libboost-timer1.67.0_1.67.0-13 libboost1.67-dev_1.67.0-13 libbsd0_0.9.1-1 libbz2-1.0_1.0.6-9 libc-bin_2.28-6+rpi1 libc-dev-bin_2.28-6+rpi1 libc6_2.28-6+rpi1 libc6-dev_2.28-6+rpi1 libcap-ng0_0.7.9-2 libcap2_1:2.25-2 libcc1-0_8.2.0-21+rpi1 libcom-err2_1.44.5-1 libcroco3_0.6.12-3 libcryptsetup12_2:2.1.0-1 libcryptsetup4_2:1.7.5-1 libdb5.3_5.3.28+dfsg1-0.3 libdbus-1-3_1.12.12-1 libdebconfclient0_0.247 libdevmapper1.02.1_2:1.02.155-2 libdpkg-perl_1.19.2 libdrm-common_2.4.97-1+rpi1 libdrm2_2.4.97-1+rpi1 libedit2_3.1-20181209-1 libelf1_0.175-2 libevent-2.1-6_2.1.8-stable-4 libevent-core-2.1-6_2.1.8-stable-4 libevent-pthreads-2.1-6_2.1.8-stable-4 libexpat1_2.2.6-1 libext2fs2_1.44.5-1 libfakeroot_1.23-1 libfdisk1_2.33.1-0.1 libffi6_3.2.1-9 libfile-stripnondeterminism-perl_1.1.1-1 libgcc-8-dev_8.2.0-21+rpi1 libgcc1_1:8.2.0-21+rpi1 libgcrypt20_1.8.4-5 libgdbm-compat4_1.18.1-2 libgdbm3_1.8.3-14 libgdbm6_1.18.1-2 libgfortran5_8.2.0-21+rpi1 libglib2.0-0_2.58.3-1 libgmp10_2:6.1.2+dfsg-4 libgnutls30_3.6.6-2 libgomp1_8.2.0-21+rpi1 libgpg-error-l10n_1.35-1 libgpg-error0_1.35-1 libgssapi-krb5-2_1.17-1 libgtest-dev_1.8.1-3 libhogweed4_3.4.1-1 libhtml-parser-perl_3.72-3+b2 libhtml-tagset-perl_3.20-3 libhwloc-dev_1.11.12-3+rpi1 libhwloc-plugins_1.11.12-3+rpi1 libhwloc5_1.11.12-3+rpi1 libibverbs-dev_22.1-1 libibverbs1_22.1-1 libicu63_63.1-6 libidn11_1.33-2.2 libidn2-0_2.0.5-1 libip4tc0_1.8.2-3 libisl19_0.20-2 libjson-c3_0.12.1+ds-2 libk5crypto3_1.17-1 libkeyutils1_1.6-2 libklibc_2.0.6-1+rpi1 libkmod2_26-1 libkrb5-3_1.17-1 libkrb5support0_1.17-1 libksba8_1.3.5-2 libldap-2.4-2_2.4.47+dfsg-3+rpi1 libldap-common_2.4.47+dfsg-3+rpi1 liblocale-gettext-perl_1.07-3+b3 libltdl-dev_2.4.6-9 libltdl7_2.4.6-9 liblz4-1_1.8.3-1 liblzma5_5.2.4-1 libmagic-mgc_1:5.35-2 libmagic1_1:5.35-2 libmount1_2.33.1-0.1 libmpc3_1.1.0-1 libmpfr6_4.0.2-1 libncurses5_6.1+20181013-2 libncurses6_6.1+20181013-2 libncursesw5_6.1+20181013-2 libncursesw6_6.1+20181013-2 libnettle6_3.4.1-1 libnl-3-200_3.4.0-1 libnl-3-dev_3.4.0-1 libnl-route-3-200_3.4.0-1 libnl-route-3-dev_3.4.0-1 libnpth0_1.6-1 libnss-systemd_240-5+rpi1 libopenmpi-dev_3.1.3-10+rpi1 libopenmpi3_3.1.3-10+rpi1 libp11-kit0_0.23.14-2 libpam-modules_1.1.8-4 libpam-modules-bin_1.1.8-4 libpam-runtime_1.1.8-4 libpam-systemd_240-5+rpi1 libpam0g_1.1.8-4 libpciaccess0_0.14-1 libpcre3_2:8.39-11+rpi1 libperl5.24_5.24.1-7 libperl5.28_5.28.1-4 libpipeline1_1.5.1-2 libplymouth4_0.9.4-1 libpmix2_3.1.2-2 libpng16-16_1.6.36-5 libprocps7_2:3.3.15-2 libpython-stdlib_2.7.15-4 libpython2-stdlib_2.7.15-4 libpython2.7-minimal_2.7.15-8 libpython2.7-stdlib_2.7.15-8 libreadline7_7.0-5 libsasl2-2_2.1.27+dfsg-1 libsasl2-modules-db_2.1.27+dfsg-1 libseccomp2_2.3.3-4 libselinux1_2.8-1+b1 libsemanage-common_2.8-2 libsemanage1_2.8-2 libsepol1_2.8-1 libsigsegv2_2.12-2 libsmartcols1_2.33.1-0.1 libsparsehash-dev_2.0.2-1 libsqlite3-0_3.26.0+fossilbc891ac6b-2 libsqlite3-dev_3.26.0+fossilbc891ac6b-2 libss2_1.44.5-1 libssl1.1_1.1.1a-1 libstdc++-8-dev_8.2.0-21+rpi1 libstdc++6_8.2.0-21+rpi1 libsystemd0_240-5+rpi1 libtasn1-6_4.13-3 libtext-markdown-perl_1.000031-2 libtext-multimarkdown-perl_1.000035-1 libtinfo5_6.1+20181013-2 libtinfo6_6.1+20181013-2 libtool_2.4.6-9 libubsan1_8.2.0-21+rpi1 libuchardet0_0.0.6-3 libudev1_240-5+rpi1 libunistring2_0.9.10-1 liburi-perl_1.76-1 libustr-1.0-1_1.0.4-6 libuuid1_2.33.1-0.1 libxml2_2.9.4+dfsg1-7+b1 libzstd1_1.3.8+dfsg-3+rpi1 linux-base_4.5 linux-libc-dev_4.18.20-2+rpi1 login_1:4.5-1.1 lsb-base_10.2018112800+rpi1 m4_1.4.18-2 make_4.2.1-1.2 makedev_2.3.1-94 man-db_2.8.5-2 mawk_1.3.3-17 mime-support_3.62 mount_2.33.1-0.1 multiarch-support_2.28-6+rpi1 nano_3.2-1 ncurses-base_6.1+20181013-2 ncurses-bin_6.1+20181013-2 netbase_5.6 ocl-icd-libopencl1_2.2.12-2 openmpi-bin_3.1.3-10+rpi1 openmpi-common_3.1.3-10+rpi1 openssh-client_1:7.9p1-6 openssl_1.1.1a-1 passwd_1:4.5-1.1 patch_2.7.6-3 perl_5.28.1-4 perl-base_5.28.1-4 perl-modules-5.24_5.24.1-7 perl-modules-5.28_5.28.1-4 pinentry-curses_1.1.0-1 pkg-config_0.29-6 plymouth_0.9.4-1 po-debconf_1.0.21 procps_2:3.3.15-2 python_2.7.15-4 python-markdown_3.0.1-3 python-minimal_2.7.15-4 python-pkg-resources_40.7.1-1 python2_2.7.15-4 python2-minimal_2.7.15-4 python2.7_2.7.15-8 python2.7-minimal_2.7.15-8 raspbian-archive-keyring_20120528.2 readline-common_7.0-5 sbuild-build-depends-abyss-dummy_0.invalid.0 sbuild-build-depends-core-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12 systemd_240-5+rpi1 systemd-sysv_240-5+rpi1 sysvinit-utils_2.93-6 tar_1.30+dfsg-5 tzdata_2018i-1 udev_240-5+rpi1 util-linux_2.33.1-0.1 xz-utils_5.2.4-1 zlib1g_1:1.2.11.dfsg-1
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Sun Feb 17 13:20:28 2019 UTC
gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./abyss_2.1.5-7.dsc
dpkg-source: info: extracting abyss in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking abyss_2.1.5.orig.tar.gz
dpkg-source: info: unpacking abyss_2.1.5-7.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying abyss-pe.patch
dpkg-source: info: applying abyss-32-bit.patch
dpkg-source: info: applying fix_bash_script.patch
dpkg-source: info: applying big_endian.patch
dpkg-source: info: applying strict_alignment.patch
dpkg-source: info: applying hurd.patch
dpkg-source: info: applying fix_implicit-function-declaration
dpkg-source: info: applying spelling
Check disk space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=buster-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=buster-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=112
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=buster-staging-armhf-sbuild-ca834cc9-f37a-4296-9058-a304782aeb5d
SCHROOT_UID=107
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package abyss
dpkg-buildpackage: info: source version 2.1.5-7
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
fakeroot debian/rules clean
dh clean
dh_clean
debian/rules build-arch
dh build-arch
dh_update_autotools_config -a
dh_autoreconf -a
configure.ac:11: installing './compile'
configure.ac:161: installing './config.guess'
configure.ac:161: installing './config.sub'
configure.ac:5: installing './install-sh'
configure.ac:5: installing './missing'
ABYSS/Makefile.am: installing './depcomp'
parallel-tests: installing './test-driver'
debian/rules override_dh_auto_configure
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_configure -- \
--with-mpi=/usr/lib/arm-linux-gnueabihf/openmpi
./configure --build=arm-linux-gnueabihf --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-silent-rules --libdir=\${prefix}/lib/arm-linux-gnueabihf --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-mpi=/usr/lib/arm-linux-gnueabihf/openmpi
configure: WARNING: unrecognized options: --disable-maintainer-mode
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
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checking whether make sets $(MAKE)... yes
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checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
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checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking whether gcc understands -c and -o together... yes
checking whether make supports the include directive... yes (GNU style)
checking dependency style of gcc... none
checking how to run the C preprocessor... gcc -E
checking for g++... g++
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
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checking for ranlib... ranlib
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checking build system type... arm-unknown-linux-gnueabihf
checking host system type... arm-unknown-linux-gnueabihf
checking if compiler needs -Werror to reject unknown flags... no
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checking functional usability... yes
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checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating ABYSS/Makefile
config.status: creating Align/Makefile
config.status: creating Assembly/Makefile
config.status: creating Common/Makefile
config.status: creating DataLayer/Makefile
config.status: creating FMIndex/Makefile
config.status: creating Graph/Makefile
config.status: creating Parallel/Makefile
config.status: creating bin/Makefile
config.status: creating doc/Makefile
config.status: creating dialign/Makefile
config.status: creating kmerprint/Makefile
config.status: creating AdjList/Makefile
config.status: creating Konnector/Makefile
config.status: creating DAssembler/Makefile
config.status: creating DistanceEst/Makefile
config.status: creating Layout/Makefile
config.status: creating Map/Makefile
config.status: creating Misc/Makefile
config.status: creating Overlap/Makefile
config.status: creating PopBubbles/Makefile
config.status: creating Scaffold/Makefile
config.status: creating SimpleGraph/Makefile
config.status: creating MergePaths/Makefile
config.status: creating KAligner/Makefile
config.status: creating PairedDBG/Makefile
config.status: creating ParseAligns/Makefile
config.status: creating PathOverlap/Makefile
config.status: creating Consensus/Makefile
config.status: creating FilterGraph/Makefile
config.status: creating GapFiller/Makefile
config.status: creating Sealer/Makefile
config.status: creating lib/gtest-1.7.0/Makefile
config.status: creating Unittest/Makefile
config.status: creating LogKmerCount/Makefile
config.status: creating Bloom/Makefile
config.status: creating BloomDBG/Makefile
config.status: creating DataBase/Makefile
config.status: creating lib/bloomfilter/Makefile
config.status: creating lib/nthash/Makefile
config.status: creating config.h
config.status: executing depfiles commands
configure: WARNING: unrecognized options: --disable-maintainer-mode
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
debian/rules override_dh_auto_build
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_build
make -j4
make[2]: Entering directory '/<<PKGBUILDDIR>>'
make all-recursive
make[3]: Entering directory '/<<PKGBUILDDIR>>'
Making all in bin
make[4]: Entering directory '/<<PKGBUILDDIR>>/bin'
make[4]: Nothing to be done for 'all'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/bin'
Making all in doc
make[4]: Entering directory '/<<PKGBUILDDIR>>/doc'
make[4]: Nothing to be done for 'all'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/doc'
Making all in Common
make[4]: Entering directory '/<<PKGBUILDDIR>>/Common'
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libcommon_a-ContigID.o `test -f 'ContigID.cpp' || echo './'`ContigID.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libcommon_a-Fcontrol.o `test -f 'Fcontrol.cpp' || echo './'`Fcontrol.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libcommon_a-Histogram.o `test -f 'Histogram.cpp' || echo './'`Histogram.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libcommon_a-Kmer.o `test -f 'Kmer.cpp' || echo './'`Kmer.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libcommon_a-Log.o `test -f 'Log.cpp' || echo './'`Log.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libcommon_a-Options.o `test -f 'Options.cpp' || echo './'`Options.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libcommon_a-Sequence.o `test -f 'Sequence.cpp' || echo './'`Sequence.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libcommon_a-SignalHandler.o `test -f 'SignalHandler.cpp' || echo './'`SignalHandler.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libcommon_a-Timer.o `test -f 'Timer.cpp' || echo './'`Timer.cpp
In file included from /usr/include/c++/8/vector:69,
from VectorUtil.h:4,
from Histogram.h:6,
from Histogram.cpp:1:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long unsigned int&}; _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from VectorUtil.h:4,
from Histogram.h:6,
from Histogram.cpp:1:
/usr/include/c++/8/bits/stl_vector.h: In member function 'Histogram::Bins Histogram::bin(unsigned int) const':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libcommon_a-Uncompress.o `test -f 'Uncompress.cpp' || echo './'`Uncompress.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libcommon_a-city.o `test -f 'city.cc' || echo './'`city.cc
rm -f libcommon.a
ar cru libcommon.a libcommon_a-ContigID.o libcommon_a-Fcontrol.o libcommon_a-Histogram.o libcommon_a-Kmer.o libcommon_a-Log.o libcommon_a-Options.o libcommon_a-Sequence.o libcommon_a-SignalHandler.o libcommon_a-Timer.o libcommon_a-Uncompress.o libcommon_a-city.o
ar: `u' modifier ignored since `D' is the default (see `U')
ranlib libcommon.a
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Common'
Making all in Graph
make[4]: Entering directory '/<<PKGBUILDDIR>>/Graph'
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_gc-gc.o `test -f 'gc.cc' || echo './'`gc.cc
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_todot-todot.o `test -f 'todot.cc' || echo './'`todot.cc
g++ -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-gc abyss_gc-gc.o ../Common/libcommon.a -ldl -lm
g++ -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L. -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-todot abyss_todot-todot.o ../Common/libcommon.a -ldl -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Graph'
Making all in DataLayer
make[4]: Entering directory '/<<PKGBUILDDIR>>/DataLayer'
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_fac-fac.o `test -f 'fac.cc' || echo './'`fac.cc
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libdatalayer_a-FastaReader.o `test -f 'FastaReader.cpp' || echo './'`FastaReader.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libdatalayer_a-FastaWriter.o `test -f 'FastaWriter.cpp' || echo './'`FastaWriter.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_tofastq-abyss-tofastq.o `test -f 'abyss-tofastq.cc' || echo './'`abyss-tofastq.cc
rm -f libdatalayer.a
ar cru libdatalayer.a libdatalayer_a-FastaReader.o libdatalayer_a-FastaWriter.o
ar: `u' modifier ignored since `D' is the default (see `U')
ranlib libdatalayer.a
g++ -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-tofastq abyss_tofastq-abyss-tofastq.o libdatalayer.a ../Common/libcommon.a -ldl -lm
g++ -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-fac abyss_fac-fac.o libdatalayer.a ../Common/libcommon.a -ldl -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/DataLayer'
Making all in DataBase
make[4]: Entering directory '/<<PKGBUILDDIR>>/DataBase'
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_db_csv-DB.o `test -f 'DB.cc' || echo './'`DB.cc
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_db_csv-db-csv.o `test -f 'db-csv.cc' || echo './'`db-csv.cc
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libdb_a-DB.o `test -f 'DB.cc' || echo './'`DB.cc
g++ -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-db-csv abyss_db_csv-DB.o abyss_db_csv-db-csv.o -lsqlite3 -ldl -lm
rm -f libdb.a
ar cru libdb.a libdb_a-DB.o ../Common/libcommon.a
ar: `u' modifier ignored since `D' is the default (see `U')
ranlib libdb.a
make[4]: Leaving directory '/<<PKGBUILDDIR>>/DataBase'
Making all in FMIndex
make[4]: Entering directory '/<<PKGBUILDDIR>>/FMIndex'
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_count-count.o `test -f 'count.cc' || echo './'`count.cc
g++ -DHAVE_CONFIG_H -I. -I.. -I../Common -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libfmindex_a-bit_array.o `test -f 'bit_array.cc' || echo './'`bit_array.cc
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_dawg-abyss-dawg.o `test -f 'abyss-dawg.cc' || echo './'`abyss-dawg.cc
rm -f libfmindex.a
ar cru libfmindex.a libfmindex_a-bit_array.o
ar: `u' modifier ignored since `D' is the default (see `U')
ranlib libfmindex.a
In file included from /usr/include/c++/8/vector:69,
from bit_array.h:24,
from BitArrays.h:4,
from FMIndex.h:5,
from DAWG.h:5,
from count.cc:2:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {std::pair<std::pair<long long unsigned int, long long unsigned int>, std::pair<boost::optional<std::pair<std::pair<long long unsigned int, long long unsigned int>, std::pair<long long unsigned int, long long unsigned int> > >, std::pair<boost::graph_traits<FMIndex>::out_edge_iterator, boost::graph_traits<FMIndex>::out_edge_iterator> > >}; _Tp = std::pair<std::pair<long long unsigned int, long long unsigned int>, std::pair<boost::optional<std::pair<std::pair<long long unsigned int, long long unsigned int>, std::pair<long long unsigned int, long long unsigned int> > >, std::pair<boost::graph_traits<FMIndex>::out_edge_iterator, boost::graph_traits<FMIndex>::out_edge_iterator> > >; _Alloc = std::allocator<std::pair<std::pair<long long unsigned int, long long unsigned int>, std::pair<boost::optional<std::pair<std::pair<long long unsigned int, long long unsigned int>, std::pair<long long unsigned int, long long unsigned int> > >, std::pair<boost::graph_traits<FMIndex>::out_edge_iterator, boost::graph_traits<FMIndex>::out_edge_iterator> > > >]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<std::pair<std::pair<long long unsigned int, long long unsigned int>, std::pair<boost::optional<std::pair<std::pair<long long unsigned int, long long unsigned int>, std::pair<long long unsigned int, long long unsigned int> > >, std::pair<boost::graph_traits<FMIndex>::out_edge_iterator, boost::graph_traits<FMIndex>::out_edge_iterator> > >, std::allocator<std::pair<std::pair<long long unsigned int, long long unsigned int>, std::pair<boost::optional<std::pair<std::pair<long long unsigned int, long long unsigned int>, std::pair<long long unsigned int, long long unsigned int> > >, std::pair<boost::graph_traits<FMIndex>::out_edge_iterator, boost::graph_traits<FMIndex>::out_edge_iterator> > > > >::iterator' {aka '__gnu_cxx::__normal_iterator<std::pair<std::pair<long long unsigned int, long long unsigned int>, std::pair<boost::optional<std::pair<std::pair<long long unsigned int, long long unsigned int>, std::pair<long long unsigned int, long long unsigned int> > >, std::pair<boost::graph_traits<FMIndex>::out_edge_iterator, boost::graph_traits<FMIndex>::out_edge_iterator> > >*, std::vector<std::pair<std::pair<long long unsigned int, long long unsigned int>, std::pair<boost::optional<std::pair<std::pair<long long unsigned int, long long unsigned int>, std::pair<long long unsigned int, long long unsigned int> > >, std::pair<boost::graph_traits<FMIndex>::out_edge_iterator, boost::graph_traits<FMIndex>::out_edge_iterator> > >, std::allocator<std::pair<std::pair<long long unsigned int, long long unsigned int>, std::pair<boost::optional<std::pair<std::pair<long long unsigned int, long long unsigned int>, std::pair<long long unsigned int, long long unsigned int> > >, std::pair<boost::graph_traits<FMIndex>::out_edge_iterator, boost::graph_traits<FMIndex>::out_edge_iterator> > > > > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::pair<std::pair<long long unsigned int, long long unsigned int>, std::pair<boost::optional<std::pair<std::pair<long long unsigned int, long long unsigned int>, std::pair<long long unsigned int, long long unsigned int> > >, std::pair<boost::graph_traits<FMIndex>::out_edge_iterator, boost::graph_traits<FMIndex>::out_edge_iterator> > >}; _Tp = std::pair<std::pair<long long unsigned int, long long unsigned int>, std::pair<boost::optional<std::pair<std::pair<long long unsigned int, long long unsigned int>, std::pair<long long unsigned int, long long unsigned int> > >, std::pair<boost::graph_traits<FMIndex>::out_edge_iterator, boost::graph_traits<FMIndex>::out_edge_iterator> > >; _Alloc = std::allocator<std::pair<std::pair<long long unsigned int, long long unsigned int>, std::pair<boost::optional<std::pair<std::pair<long long unsigned int, long long unsigned int>, std::pair<long long unsigned int, long long unsigned int> > >, std::pair<boost::graph_traits<FMIndex>::out_edge_iterator, boost::graph_traits<FMIndex>::out_edge_iterator> > > >]':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<std::pair<long long unsigned int, long long unsigned int>, std::pair<boost::optional<std::pair<std::pair<long long unsigned int, long long unsigned int>, std::pair<long long unsigned int, long long unsigned int> > >, std::pair<boost::graph_traits<FMIndex>::out_edge_iterator, boost::graph_traits<FMIndex>::out_edge_iterator> > >*, std::vector<std::pair<std::pair<long long unsigned int, long long unsigned int>, std::pair<boost::optional<std::pair<std::pair<long long unsigned int, long long unsigned int>, std::pair<long long unsigned int, long long unsigned int> > >, std::pair<boost::graph_traits<FMIndex>::out_edge_iterator, boost::graph_traits<FMIndex>::out_edge_iterator> > >, std::allocator<std::pair<std::pair<long long unsigned int, long long unsigned int>, std::pair<boost::optional<std::pair<std::pair<long long unsigned int, long long unsigned int>, std::pair<long long unsigned int, long long unsigned int> > >, std::pair<boost::graph_traits<FMIndex>::out_edge_iterator, boost::graph_traits<FMIndex>::out_edge_iterator> > > > > >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from bit_array.h:24,
from BitArrays.h:4,
from FMIndex.h:5,
from DAWG.h:5,
from abyss-dawg.cc:2:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {std::pair<std::pair<long long unsigned int, long long unsigned int>, std::pair<boost::optional<std::pair<std::pair<long long unsigned int, long long unsigned int>, std::pair<long long unsigned int, long long unsigned int> > >, std::pair<boost::graph_traits<FMIndex>::out_edge_iterator, boost::graph_traits<FMIndex>::out_edge_iterator> > >}; _Tp = std::pair<std::pair<long long unsigned int, long long unsigned int>, std::pair<boost::optional<std::pair<std::pair<long long unsigned int, long long unsigned int>, std::pair<long long unsigned int, long long unsigned int> > >, std::pair<boost::graph_traits<FMIndex>::out_edge_iterator, boost::graph_traits<FMIndex>::out_edge_iterator> > >; _Alloc = std::allocator<std::pair<std::pair<long long unsigned int, long long unsigned int>, std::pair<boost::optional<std::pair<std::pair<long long unsigned int, long long unsigned int>, std::pair<long long unsigned int, long long unsigned int> > >, std::pair<boost::graph_traits<FMIndex>::out_edge_iterator, boost::graph_traits<FMIndex>::out_edge_iterator> > > >]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<std::pair<std::pair<long long unsigned int, long long unsigned int>, std::pair<boost::optional<std::pair<std::pair<long long unsigned int, long long unsigned int>, std::pair<long long unsigned int, long long unsigned int> > >, std::pair<boost::graph_traits<FMIndex>::out_edge_iterator, boost::graph_traits<FMIndex>::out_edge_iterator> > >, std::allocator<std::pair<std::pair<long long unsigned int, long long unsigned int>, std::pair<boost::optional<std::pair<std::pair<long long unsigned int, long long unsigned int>, std::pair<long long unsigned int, long long unsigned int> > >, std::pair<boost::graph_traits<FMIndex>::out_edge_iterator, boost::graph_traits<FMIndex>::out_edge_iterator> > > > >::iterator' {aka '__gnu_cxx::__normal_iterator<std::pair<std::pair<long long unsigned int, long long unsigned int>, std::pair<boost::optional<std::pair<std::pair<long long unsigned int, long long unsigned int>, std::pair<long long unsigned int, long long unsigned int> > >, std::pair<boost::graph_traits<FMIndex>::out_edge_iterator, boost::graph_traits<FMIndex>::out_edge_iterator> > >*, std::vector<std::pair<std::pair<long long unsigned int, long long unsigned int>, std::pair<boost::optional<std::pair<std::pair<long long unsigned int, long long unsigned int>, std::pair<long long unsigned int, long long unsigned int> > >, std::pair<boost::graph_traits<FMIndex>::out_edge_iterator, boost::graph_traits<FMIndex>::out_edge_iterator> > >, std::allocator<std::pair<std::pair<long long unsigned int, long long unsigned int>, std::pair<boost::optional<std::pair<std::pair<long long unsigned int, long long unsigned int>, std::pair<long long unsigned int, long long unsigned int> > >, std::pair<boost::graph_traits<FMIndex>::out_edge_iterator, boost::graph_traits<FMIndex>::out_edge_iterator> > > > > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::pair<std::pair<long long unsigned int, long long unsigned int>, std::pair<boost::optional<std::pair<std::pair<long long unsigned int, long long unsigned int>, std::pair<long long unsigned int, long long unsigned int> > >, std::pair<boost::graph_traits<FMIndex>::out_edge_iterator, boost::graph_traits<FMIndex>::out_edge_iterator> > >}; _Tp = std::pair<std::pair<long long unsigned int, long long unsigned int>, std::pair<boost::optional<std::pair<std::pair<long long unsigned int, long long unsigned int>, std::pair<long long unsigned int, long long unsigned int> > >, std::pair<boost::graph_traits<FMIndex>::out_edge_iterator, boost::graph_traits<FMIndex>::out_edge_iterator> > >; _Alloc = std::allocator<std::pair<std::pair<long long unsigned int, long long unsigned int>, std::pair<boost::optional<std::pair<std::pair<long long unsigned int, long long unsigned int>, std::pair<long long unsigned int, long long unsigned int> > >, std::pair<boost::graph_traits<FMIndex>::out_edge_iterator, boost::graph_traits<FMIndex>::out_edge_iterator> > > >]':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<std::pair<long long unsigned int, long long unsigned int>, std::pair<boost::optional<std::pair<std::pair<long long unsigned int, long long unsigned int>, std::pair<long long unsigned int, long long unsigned int> > >, std::pair<boost::graph_traits<FMIndex>::out_edge_iterator, boost::graph_traits<FMIndex>::out_edge_iterator> > >*, std::vector<std::pair<std::pair<long long unsigned int, long long unsigned int>, std::pair<boost::optional<std::pair<std::pair<long long unsigned int, long long unsigned int>, std::pair<long long unsigned int, long long unsigned int> > >, std::pair<boost::graph_traits<FMIndex>::out_edge_iterator, boost::graph_traits<FMIndex>::out_edge_iterator> > >, std::allocator<std::pair<std::pair<long long unsigned int, long long unsigned int>, std::pair<boost::optional<std::pair<std::pair<long long unsigned int, long long unsigned int>, std::pair<long long unsigned int, long long unsigned int> > >, std::pair<boost::graph_traits<FMIndex>::out_edge_iterator, boost::graph_traits<FMIndex>::out_edge_iterator> > > > > >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = wat_array::BitArray; _Alloc = std::allocator<wat_array::BitArray>]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<wat_array::BitArray>::iterator' {aka '__gnu_cxx::__normal_iterator<wat_array::BitArray*, std::vector<wat_array::BitArray> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = wat_array::BitArray; _Alloc = std::allocator<wat_array::BitArray>]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<wat_array::BitArray>::iterator' {aka '__gnu_cxx::__normal_iterator<wat_array::BitArray*, std::vector<wat_array::BitArray> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from bit_array.h:24,
from BitArrays.h:4,
from FMIndex.h:5,
from DAWG.h:5,
from abyss-dawg.cc:2:
/usr/include/c++/8/bits/stl_vector.h: In member function 'void FMIndex::assign(It, It) [with It = __gnu_cxx::__normal_iterator<unsigned char*, std::vector<unsigned char> >]':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<wat_array::BitArray*, std::vector<wat_array::BitArray> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
In file included from /usr/include/c++/8/map:60,
from abyss-dawg.cc:14:
/usr/include/c++/8/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple<const std::pair<long long unsigned int, long long unsigned int>&>, std::tuple<>}; _Key = std::pair<long long unsigned int, long long unsigned int>; _Val = std::pair<const std::pair<long long unsigned int, long long unsigned int>, boost::default_color_type>; _KeyOfValue = std::_Select1st<std::pair<const std::pair<long long unsigned int, long long unsigned int>, boost::default_color_type> >; _Compare = std::less<std::pair<long long unsigned int, long long unsigned int> >; _Alloc = std::allocator<std::pair<const std::pair<long long unsigned int, long long unsigned int>, boost::default_color_type> >]':
/usr/include/c++/8/bits/stl_tree.h:2411:7: note: parameter passing for argument of type 'std::_Rb_tree<std::pair<long long unsigned int, long long unsigned int>, std::pair<const std::pair<long long unsigned int, long long unsigned int>, boost::default_color_type>, std::_Select1st<std::pair<const std::pair<long long unsigned int, long long unsigned int>, boost::default_color_type> >, std::less<std::pair<long long unsigned int, long long unsigned int> >, std::allocator<std::pair<const std::pair<long long unsigned int, long long unsigned int>, boost::default_color_type> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const std::pair<long long unsigned int, long long unsigned int>, boost::default_color_type> >'} changed in GCC 7.1
_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from abyss-dawg.cc:5:
/usr/include/boost/graph/depth_first_search.hpp: In function 'void boost::detail::depth_first_visit_impl(const IncidenceGraph&, typename boost::graph_traits<Graph>::vertex_descriptor, DFSVisitor&, ColorMap, TerminatorFunc) [with IncidenceGraph = FMIndex; DFSVisitor = DAWGVisitor; ColorMap = boost::associative_property_map<std::map<std::pair<long long unsigned int, long long unsigned int>, boost::default_color_type> >; TerminatorFunc = boost::detail::nontruth2]':
/usr/include/boost/graph/depth_first_search.hpp:109:10: note: parameter passing for argument of type 'boost::associative_property_map<std::map<std::pair<long long unsigned int, long long unsigned int>, boost::default_color_type> >' changed in GCC 7.1
void depth_first_visit_impl
^~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/map:61,
from abyss-dawg.cc:14:
/usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<std::pair<long long unsigned int, long long unsigned int>, std::pair<const std::pair<long long unsigned int, long long unsigned int>, boost::default_color_type>, std::_Select1st<std::pair<const std::pair<long long unsigned int, long long unsigned int>, boost::default_color_type> >, std::less<std::pair<long long unsigned int, long long unsigned int> >, std::allocator<std::pair<const std::pair<long long unsigned int, long long unsigned int>, boost::default_color_type> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const std::pair<long long unsigned int, long long unsigned int>, boost::default_color_type> >'} changed in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<std::pair<long long unsigned int, long long unsigned int>, std::pair<const std::pair<long long unsigned int, long long unsigned int>, boost::default_color_type>, std::_Select1st<std::pair<const std::pair<long long unsigned int, long long unsigned int>, boost::default_color_type> >, std::less<std::pair<long long unsigned int, long long unsigned int> >, std::allocator<std::pair<const std::pair<long long unsigned int, long long unsigned int>, boost::default_color_type> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const std::pair<long long unsigned int, long long unsigned int>, boost::default_color_type> >'} changed in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<std::pair<long long unsigned int, long long unsigned int>, std::pair<const std::pair<long long unsigned int, long long unsigned int>, boost::default_color_type>, std::_Select1st<std::pair<const std::pair<long long unsigned int, long long unsigned int>, boost::default_color_type> >, std::less<std::pair<long long unsigned int, long long unsigned int> >, std::allocator<std::pair<const std::pair<long long unsigned int, long long unsigned int>, boost::default_color_type> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const std::pair<long long unsigned int, long long unsigned int>, boost::default_color_type> >'} changed in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<std::pair<long long unsigned int, long long unsigned int>, std::pair<const std::pair<long long unsigned int, long long unsigned int>, boost::default_color_type>, std::_Select1st<std::pair<const std::pair<long long unsigned int, long long unsigned int>, boost::default_color_type> >, std::less<std::pair<long long unsigned int, long long unsigned int> >, std::allocator<std::pair<const std::pair<long long unsigned int, long long unsigned int>, boost::default_color_type> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const std::pair<long long unsigned int, long long unsigned int>, boost::default_color_type> >'} changed in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
In file included from /usr/include/c++/8/vector:64,
from bit_array.h:24,
from BitArrays.h:4,
from FMIndex.h:5,
from DAWG.h:5,
from count.cc:2:
/usr/include/c++/8/bits/stl_vector.h: In member function 'void FMIndex::assign(It, It) [with It = __gnu_cxx::__normal_iterator<unsigned char*, std::vector<unsigned char> >]':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<wat_array::BitArray*, std::vector<wat_array::BitArray> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
In file included from abyss-dawg.cc:5:
/usr/include/boost/graph/depth_first_search.hpp: In function 'int main(int, char**)':
/usr/include/boost/graph/depth_first_search.hpp:354:35: note: parameter passing for argument of type 'boost::associative_property_map<std::map<std::pair<long long unsigned int, long long unsigned int>, boost::default_color_type> >' changed in GCC 7.1
detail::depth_first_visit_impl(g, u, vis, color, detail::nontruth2());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-count abyss_count-count.o libfmindex.a ../Common/libcommon.a -ldl -lm
g++ -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-dawg abyss_dawg-abyss-dawg.o libfmindex.a ../Common/libcommon.a -ldl -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/FMIndex'
Making all in Assembly
make[4]: Entering directory '/<<PKGBUILDDIR>>/Assembly'
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libassembly_a-AssemblyAlgorithms.o `test -f 'AssemblyAlgorithms.cc' || echo './'`AssemblyAlgorithms.cc
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libassembly_a-Options.o `test -f 'Options.cc' || echo './'`Options.cc
rm -f libassembly.a
ar cru libassembly.a libassembly_a-AssemblyAlgorithms.o libassembly_a-Options.o ../Common/libcommon.a
ar: `u' modifier ignored since `D' is the default (see `U')
ranlib libassembly.a
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Assembly'
Making all in dialign
make[4]: Entering directory '/<<PKGBUILDDIR>>/dialign'
gcc -DHAVE_CONFIG_H -I. -I.. -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o museq.o museq.c
gcc -DHAVE_CONFIG_H -I. -I.. -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o alig.o alig.c
gcc -DHAVE_CONFIG_H -I. -I.. -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o assemble.o assemble.c
gcc -DHAVE_CONFIG_H -I. -I.. -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o diag.o diag.c
alig.c:15:20: warning: inline function 'calc_ov_weight' declared but never defined
extern inline void calc_ov_weight(struct diag* dg, struct diag_col *dcol, struct scr_matrix* smatrix,
^~~~~~~~~~~~~~
alig.c:13:20: warning: inline function 'calc_weight' declared but never defined
extern inline void calc_weight(struct diag* dg, struct scr_matrix* smatrix,
^~~~~~~~~~~
assemble.c:40:20: warning: inline function 'align_diag' declared but never defined
extern inline char align_diag(struct alignment *algn, struct scr_matrix *smatrix, struct diag* dg);
^~~~~~~~~~
assemble.c:37:32: warning: inline function 'find_eqc' declared but never defined
extern inline struct algn_pos *find_eqc(struct algn_pos **ap, int seqnum, int pos);
^~~~~~~~
assemble.c:25:39: warning: inline function 'find_diags_guided' declared but never defined
extern inline struct simple_diag_col* find_diags_guided(struct scr_matrix *smatrix,
^~~~~~~~~~~~~~~~~
assemble.c:15:20: warning: inline function 'calc_ov_weight' declared but never defined
extern inline void calc_ov_weight(struct diag* dg, struct diag_col *dcol, struct scr_matrix* smatrix,
^~~~~~~~~~~~~~
assemble.c:13:20: warning: inline function 'calc_weight' declared but never defined
extern inline void calc_weight(struct diag* dg, struct scr_matrix* smatrix,
^~~~~~~~~~~
diag.c:1456:3: warning: 'real_calc_weight' is static but used in inline function 'find_diags_dyn' which is not static
real_calc_weight(dg, smatrix, pdist,1,tmp_dist,algn);
^~~~~~~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -I.. -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o io.o io.c
io.c: In function 'read_scr_matrix':
io.c:270:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf( fp, "%i", &is);
^~~~~~~~~~~~~~~~~~~~~~
io.c:282:5: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(fp, "%s\n", rline);
^~~~~~~~~~~~~~~~~~~~~~~~~
io.c: In function 'read_diag_prob_dist':
io.c:371:7: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf( fp, "%li %li %Le\n", &ti,&tscr,&weight );
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -I.. -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o orf.o orf.c
gcc -DHAVE_CONFIG_H -I. -I.. -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o parameters.o parameters.c
gcc -DHAVE_CONFIG_H -I. -I.. -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o prob.o prob.c
gcc -DHAVE_CONFIG_H -I. -I.. -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o translate.o translate.c
rm -f libdialign.a
ar cru libdialign.a alig.o assemble.o diag.o io.o orf.o parameters.o prob.o translate.o
ar: `u' modifier ignored since `D' is the default (see `U')
ranlib libdialign.a
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o dialign museq.o libdialign.a -ldl -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/dialign'
Making all in Align
make[4]: Entering directory '/<<PKGBUILDDIR>>/Align'
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_align-align.o `test -f 'align.cc' || echo './'`align.cc
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libalign_a-alignGlobal.o `test -f 'alignGlobal.cc' || echo './'`alignGlobal.cc
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libalign_a-dialign.o `test -f 'dialign.cpp' || echo './'`dialign.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libalign_a-dna_diag_prob.o `test -f 'dna_diag_prob.cc' || echo './'`dna_diag_prob.cc
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libalign_a-smith_waterman.o `test -f 'smith_waterman.cpp' || echo './'`smith_waterman.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_mergepairs-mergepairs.o `test -f 'mergepairs.cc' || echo './'`mergepairs.cc
rm -f libalign.a
ar cru libalign.a libalign_a-alignGlobal.o libalign_a-dialign.o libalign_a-dna_diag_prob.o libalign_a-smith_waterman.o
ar: `u' modifier ignored since `D' is the default (see `U')
ranlib libalign.a
g++ -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-align abyss_align-align.o ./libalign.a ../dialign/libdialign.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm
g++ -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-mergepairs abyss_mergepairs-mergepairs.o ./libalign.a ../dialign/libdialign.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Align'
Making all in ABYSS
make[4]: Entering directory '/<<PKGBUILDDIR>>/ABYSS'
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o ABYSS-abyss.o `test -f 'abyss.cc' || echo './'`abyss.cc
g++ -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o ABYSS ABYSS-abyss.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../Assembly/libassembly.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/ABYSS'
Making all in Parallel
make[4]: Entering directory '/<<PKGBUILDDIR>>/Parallel'
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o ABYSS_P-parallelAbyss.o `test -f 'parallelAbyss.cpp' || echo './'`parallelAbyss.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o ABYSS_P-CommLayer.o `test -f 'CommLayer.cpp' || echo './'`CommLayer.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o ABYSS_P-NetworkSequenceCollection.o `test -f 'NetworkSequenceCollection.cpp' || echo './'`NetworkSequenceCollection.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o ABYSS_P-MessageBuffer.o `test -f 'MessageBuffer.cpp' || echo './'`MessageBuffer.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o ABYSS_P-Messages.o `test -f 'Messages.cpp' || echo './'`Messages.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -DPAIRED_DBG -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_paired_dbg_mpi-parallelAbyss.o `test -f 'parallelAbyss.cpp' || echo './'`parallelAbyss.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -DPAIRED_DBG -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_paired_dbg_mpi-CommLayer.o `test -f 'CommLayer.cpp' || echo './'`CommLayer.cpp
In file included from /usr/include/c++/8/map:60,
from ../Assembly/BranchGroup.h:7,
from NetworkSequenceCollection.h:7,
from NetworkSequenceCollection.cpp:1:
/usr/include/c++/8/bits/stl_tree.h: In member function 'void std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_erase_aux(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator) [with _Key = long long unsigned int; _Val = std::pair<const long long unsigned int, BranchGroup>; _KeyOfValue = std::_Select1st<std::pair<const long long unsigned int, BranchGroup> >; _Compare = std::less<long long unsigned int>; _Alloc = std::allocator<std::pair<const long long unsigned int, BranchGroup> >]':
/usr/include/c++/8/bits/stl_tree.h:2486:5: note: parameter passing for argument of type 'std::_Rb_tree<long long unsigned int, std::pair<const long long unsigned int, BranchGroup>, std::_Select1st<std::pair<const long long unsigned int, BranchGroup> >, std::less<long long unsigned int>, std::allocator<std::pair<const long long unsigned int, BranchGroup> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const long long unsigned int, BranchGroup> >'} changed in GCC 7.1
_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_tree.h: In member function 'bool NetworkSequenceCollection::processBranchesDiscoverBubbles()':
/usr/include/c++/8/bits/stl_tree.h:1141:2: note: parameter passing for argument of type 'std::_Rb_tree<long long unsigned int, std::pair<const long long unsigned int, BranchGroup>, std::_Select1st<std::pair<const long long unsigned int, BranchGroup> >, std::less<long long unsigned int>, std::allocator<std::pair<const long long unsigned int, BranchGroup> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const long long unsigned int, BranchGroup> >'} changed in GCC 7.1
_M_erase_aux(__position);
^~~~~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -DPAIRED_DBG -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_paired_dbg_mpi-NetworkSequenceCollection.o `test -f 'NetworkSequenceCollection.cpp' || echo './'`NetworkSequenceCollection.cpp
/usr/include/c++/8/bits/stl_tree.h: In member function 'std::pair<unsigned int, unsigned int> NetworkSequenceCollection::processBranchesAssembly(FastaWriter*, unsigned int)':
/usr/include/c++/8/bits/stl_tree.h:1141:2: note: parameter passing for argument of type 'std::_Rb_tree<long long unsigned int, std::pair<const long long unsigned int, BranchGroup>, std::_Select1st<std::pair<const long long unsigned int, BranchGroup> >, std::less<long long unsigned int>, std::allocator<std::pair<const long long unsigned int, BranchGroup> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const long long unsigned int, BranchGroup> >'} changed in GCC 7.1
_M_erase_aux(__position);
^~~~~~~~~~~~
/usr/include/c++/8/bits/stl_tree.h: In member function 'size_t NetworkSequenceCollection::processBranchesTrim()':
/usr/include/c++/8/bits/stl_tree.h:1141:2: note: parameter passing for argument of type 'std::_Rb_tree<long long unsigned int, std::pair<const long long unsigned int, BranchGroup>, std::_Select1st<std::pair<const long long unsigned int, BranchGroup> >, std::less<long long unsigned int>, std::allocator<std::pair<const long long unsigned int, BranchGroup> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const long long unsigned int, BranchGroup> >'} changed in GCC 7.1
_M_erase_aux(__position);
^~~~~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -DPAIRED_DBG -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_paired_dbg_mpi-MessageBuffer.o `test -f 'MessageBuffer.cpp' || echo './'`MessageBuffer.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -DPAIRED_DBG -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_paired_dbg_mpi-Messages.o `test -f 'Messages.cpp' || echo './'`Messages.cpp
g++ -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o ABYSS-P ABYSS_P-parallelAbyss.o ABYSS_P-CommLayer.o ABYSS_P-NetworkSequenceCollection.o ABYSS_P-MessageBuffer.o ABYSS_P-Messages.o ../Assembly/libassembly.a ../Common/libcommon.a ../DataLayer/libdatalayer.a ../DataBase/libdb.a -lsqlite3 -ldl -lm -lmpi -ldl -lm
In file included from /usr/include/c++/8/map:60,
from ../Assembly/BranchGroup.h:7,
from NetworkSequenceCollection.h:7,
from NetworkSequenceCollection.cpp:1:
/usr/include/c++/8/bits/stl_tree.h: In member function 'void std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_erase_aux(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator) [with _Key = long long unsigned int; _Val = std::pair<const long long unsigned int, BranchGroup>; _KeyOfValue = std::_Select1st<std::pair<const long long unsigned int, BranchGroup> >; _Compare = std::less<long long unsigned int>; _Alloc = std::allocator<std::pair<const long long unsigned int, BranchGroup> >]':
/usr/include/c++/8/bits/stl_tree.h:2486:5: note: parameter passing for argument of type 'std::_Rb_tree<long long unsigned int, std::pair<const long long unsigned int, BranchGroup>, std::_Select1st<std::pair<const long long unsigned int, BranchGroup> >, std::less<long long unsigned int>, std::allocator<std::pair<const long long unsigned int, BranchGroup> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const long long unsigned int, BranchGroup> >'} changed in GCC 7.1
_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_tree.h: In member function 'bool NetworkSequenceCollection::processBranchesDiscoverBubbles()':
/usr/include/c++/8/bits/stl_tree.h:1141:2: note: parameter passing for argument of type 'std::_Rb_tree<long long unsigned int, std::pair<const long long unsigned int, BranchGroup>, std::_Select1st<std::pair<const long long unsigned int, BranchGroup> >, std::less<long long unsigned int>, std::allocator<std::pair<const long long unsigned int, BranchGroup> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const long long unsigned int, BranchGroup> >'} changed in GCC 7.1
_M_erase_aux(__position);
^~~~~~~~~~~~
/usr/include/c++/8/bits/stl_tree.h: In member function 'std::pair<unsigned int, unsigned int> NetworkSequenceCollection::processBranchesAssembly(FastaWriter*, unsigned int)':
/usr/include/c++/8/bits/stl_tree.h:1141:2: note: parameter passing for argument of type 'std::_Rb_tree<long long unsigned int, std::pair<const long long unsigned int, BranchGroup>, std::_Select1st<std::pair<const long long unsigned int, BranchGroup> >, std::less<long long unsigned int>, std::allocator<std::pair<const long long unsigned int, BranchGroup> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const long long unsigned int, BranchGroup> >'} changed in GCC 7.1
_M_erase_aux(__position);
^~~~~~~~~~~~
/usr/include/c++/8/bits/stl_tree.h: In member function 'size_t NetworkSequenceCollection::processBranchesTrim()':
/usr/include/c++/8/bits/stl_tree.h:1141:2: note: parameter passing for argument of type 'std::_Rb_tree<long long unsigned int, std::pair<const long long unsigned int, BranchGroup>, std::_Select1st<std::pair<const long long unsigned int, BranchGroup> >, std::less<long long unsigned int>, std::allocator<std::pair<const long long unsigned int, BranchGroup> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const long long unsigned int, BranchGroup> >'} changed in GCC 7.1
_M_erase_aux(__position);
^~~~~~~~~~~~
g++ -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-paired-dbg-mpi abyss_paired_dbg_mpi-parallelAbyss.o abyss_paired_dbg_mpi-CommLayer.o abyss_paired_dbg_mpi-NetworkSequenceCollection.o abyss_paired_dbg_mpi-MessageBuffer.o abyss_paired_dbg_mpi-Messages.o ../Assembly/libassembly.a ../Common/libcommon.a ../DataLayer/libdatalayer.a ../DataBase/libdb.a -lsqlite3 -ldl -lm -lmpi -ldl -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Parallel'
Making all in Bloom
make[4]: Entering directory '/<<PKGBUILDDIR>>/Bloom'
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_bloom-bloom.o `test -f 'bloom.cc' || echo './'`bloom.cc
g++ -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-bloom abyss_bloom-bloom.o ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a -ldl -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Bloom'
Making all in BloomDBG
make[4]: Entering directory '/<<PKGBUILDDIR>>/BloomDBG'
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_bloom_dbg-bloom-dbg.o `test -f 'bloom-dbg.cc' || echo './'`bloom-dbg.cc
g++ -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-bloom-dbg abyss_bloom_dbg-bloom-dbg.o ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/BloomDBG'
Making all in Konnector
make[4]: Entering directory '/<<PKGBUILDDIR>>/Konnector'
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o konnector-konnector.o `test -f 'konnector.cc' || echo './'`konnector.cc
g++ -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o konnector konnector-konnector.o ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a -ldl -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Konnector'
Making all in Consensus
make[4]: Entering directory '/<<PKGBUILDDIR>>/Consensus'
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Consensus-Consensus.o `test -f 'Consensus.cpp' || echo './'`Consensus.cpp
g++ -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o Consensus Consensus-Consensus.o ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Consensus'
Making all in DAssembler
make[4]: Entering directory '/<<PKGBUILDDIR>>/DAssembler'
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o DAssembler-DAssembler.o `test -f 'DAssembler.cpp' || echo './'`DAssembler.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o DAssembler-RotatedRead.o `test -f 'RotatedRead.cpp' || echo './'`RotatedRead.cpp
g++ -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o DAssembler DAssembler-DAssembler.o DAssembler-RotatedRead.o ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/DAssembler'
Making all in DistanceEst
make[4]: Entering directory '/<<PKGBUILDDIR>>/DistanceEst'
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o DistanceEst-DistanceEst.o `test -f 'DistanceEst.cpp' || echo './'`DistanceEst.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o DistanceEst-MLE.o `test -f 'MLE.cpp' || echo './'`MLE.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -D SAM_SEQ_QUAL=1 -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o DistanceEst_ssq-DistanceEst.o `test -f 'DistanceEst.cpp' || echo './'`DistanceEst.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -D SAM_SEQ_QUAL=1 -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o DistanceEst_ssq-MLE.o `test -f 'MLE.cpp' || echo './'`MLE.cpp
In file included from /usr/include/c++/8/vector:69,
from MLE.h:4,
from MLE.cpp:1:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from MLE.h:4,
from MLE.cpp:1:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from MLE.h:4,
from MLE.cpp:1:
/usr/include/c++/8/bits/stl_vector.h: In function 'std::pair<int, unsigned int> maximumLikelihoodEstimate(int, int, const Histogram&, const PMF&, unsigned int, unsigned int)':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from MLE.h:4,
from MLE.cpp:1:
/usr/include/c++/8/bits/stl_vector.h: In function 'std::pair<int, unsigned int> maximumLikelihoodEstimate(int, int, const Histogram&, const PMF&, unsigned int, unsigned int)':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
g++ -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o DistanceEst DistanceEst-DistanceEst.o DistanceEst-MLE.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../Common/libcommon.a -ldl -lm
g++ -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o DistanceEst-ssq DistanceEst_ssq-DistanceEst.o DistanceEst_ssq-MLE.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../Common/libcommon.a -ldl -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/DistanceEst'
Making all in KAligner
make[4]: Entering directory '/<<PKGBUILDDIR>>/KAligner'
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o KAligner-KAligner.o `test -f 'KAligner.cpp' || echo './'`KAligner.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o KAligner-Aligner.o `test -f 'Aligner.cpp' || echo './'`Aligner.cpp
g++ -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o KAligner KAligner-KAligner.o KAligner-Aligner.o ../DataLayer/libdatalayer.a ../Common/libcommon.a -lpthread -ldl -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/KAligner'
Making all in Layout
make[4]: Entering directory '/<<PKGBUILDDIR>>/Layout'
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_layout-layout.o `test -f 'layout.cc' || echo './'`layout.cc
g++ -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-layout abyss_layout-layout.o ../Common/libcommon.a -ldl -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Layout'
Making all in LogKmerCount
make[4]: Entering directory '/<<PKGBUILDDIR>>/LogKmerCount'
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o logcounter-logcounter.o `test -f 'logcounter.cc' || echo './'`logcounter.cc
g++ -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o logcounter logcounter-logcounter.o ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a -ldl -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/LogKmerCount'
Making all in Map
make[4]: Entering directory '/<<PKGBUILDDIR>>/Map'
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../FMIndex -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_index-index.o `test -f 'index.cc' || echo './'`index.cc
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../FMIndex -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_map-map.o `test -f 'map.cc' || echo './'`map.cc
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../FMIndex -D SAM_SEQ_QUAL=1 -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_map_ssq-map.o `test -f 'map.cc' || echo './'`map.cc
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../FMIndex -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_overlap-overlap.o `test -f 'overlap.cc' || echo './'`overlap.cc
index.cc: In function 'void buildFMIndex(FMIndex&, const string&)':
index.cc:149:64: warning: unsigned conversion from 'long long int' to 'size_t' {aka 'unsigned int'} changes value from '9223372036854775807' to '4294967295' [-Woverflow]
size_t MAX_SIZE = numeric_limits<FMIndex::sais_size_type>::max();
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~
overlap.cc: In function 'void buildFMIndex(FMIndex&, const char*)':
overlap.cc:296:64: warning: unsigned conversion from 'long long int' to 'size_t' {aka 'unsigned int'} changes value from '9223372036854775807' to '4294967295' [-Woverflow]
size_t MAX_SIZE = numeric_limits<FMIndex::sais_size_type>::max();
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~
map.cc: In function 'void buildFMIndex(FMIndex&, const char*)':
map.cc:508:64: warning: unsigned conversion from 'long long int' to 'size_t' {aka 'unsigned int'} changes value from '9223372036854775807' to '4294967295' [-Woverflow]
size_t MAX_SIZE = numeric_limits<FMIndex::sais_size_type>::max();
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~
map.cc: In function 'void buildFMIndex(FMIndex&, const char*)':
map.cc:508:64: warning: unsigned conversion from 'long long int' to 'size_t' {aka 'unsigned int'} changes value from '9223372036854775807' to '4294967295' [-Woverflow]
size_t MAX_SIZE = numeric_limits<FMIndex::sais_size_type>::max();
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~
In file included from /usr/include/c++/8/vector:69,
from ../DataLayer/FastaIndex.h:11,
from index.cc:3:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = wat_array::BitArray; _Alloc = std::allocator<wat_array::BitArray>]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<wat_array::BitArray>::iterator' {aka '__gnu_cxx::__normal_iterator<wat_array::BitArray*, std::vector<wat_array::BitArray> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from ../DataLayer/FastaIndex.h:11,
from index.cc:3:
/usr/include/c++/8/bits/stl_vector.h: In member function 'void FMIndex::assign(It, It) [with It = __gnu_cxx::__normal_iterator<unsigned char*, std::vector<unsigned char> >]':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<wat_array::BitArray*, std::vector<wat_array::BitArray> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In member function 'void FMIndex::assignBWT(It, It) [with It = __gnu_cxx::__normal_iterator<unsigned char*, std::vector<unsigned char> >]':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<wat_array::BitArray*, std::vector<wat_array::BitArray> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
g++ -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-index abyss_index-index.o ../FMIndex/libfmindex.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm
In file included from /usr/include/c++/8/vector:69,
from ../Common/Dictionary.h:10,
from ../Common/ContigID.h:5,
from ../Common/ContigNode.h:5,
from ../Common/ContigProperties.h:4,
from overlap.cc:10:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {FMIndex::Match}; _Tp = FMIndex::Match; _Alloc = std::allocator<FMIndex::Match>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<FMIndex::Match>::iterator' {aka '__gnu_cxx::__normal_iterator<FMIndex::Match*, std::vector<FMIndex::Match> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {FMIndex::Match}; _Tp = FMIndex::Match; _Alloc = std::allocator<FMIndex::Match>]':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<FMIndex::Match*, std::vector<FMIndex::Match> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from ../FMIndex/bit_array.h:24,
from ../FMIndex/BitArrays.h:4,
from ../FMIndex/FMIndex.h:5,
from map.cc:3:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = wat_array::BitArray; _Alloc = std::allocator<wat_array::BitArray>]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<wat_array::BitArray>::iterator' {aka '__gnu_cxx::__normal_iterator<wat_array::BitArray*, std::vector<wat_array::BitArray> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from ../FMIndex/bit_array.h:24,
from ../FMIndex/BitArrays.h:4,
from ../FMIndex/FMIndex.h:5,
from map.cc:3:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = wat_array::BitArray; _Alloc = std::allocator<wat_array::BitArray>]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<wat_array::BitArray>::iterator' {aka '__gnu_cxx::__normal_iterator<wat_array::BitArray*, std::vector<wat_array::BitArray> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from ../FMIndex/bit_array.h:24,
from ../FMIndex/BitArrays.h:4,
from ../FMIndex/FMIndex.h:5,
from map.cc:3:
/usr/include/c++/8/bits/stl_vector.h: In member function 'void FMIndex::assign(It, It) [with It = __gnu_cxx::__normal_iterator<unsigned char*, std::vector<unsigned char> >]':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<wat_array::BitArray*, std::vector<wat_array::BitArray> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from ../FMIndex/bit_array.h:24,
from ../FMIndex/BitArrays.h:4,
from ../FMIndex/FMIndex.h:5,
from map.cc:3:
/usr/include/c++/8/bits/stl_vector.h: In member function 'void FMIndex::assign(It, It) [with It = __gnu_cxx::__normal_iterator<unsigned char*, std::vector<unsigned char> >]':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<wat_array::BitArray*, std::vector<wat_array::BitArray> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:63,
from ../Common/Dictionary.h:10,
from ../Common/ContigID.h:5,
from ../Common/ContigNode.h:5,
from ../Common/ContigProperties.h:4,
from overlap.cc:10:
/usr/include/c++/8/bits/stl_uninitialized.h: In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator<wat_array::BitArray*>; _ForwardIterator = wat_array::BitArray*; bool _TrivialValueTypes = false]':
/usr/include/c++/8/bits/stl_uninitialized.h:76:9: note: parameter passing for argument of type 'std::move_iterator<wat_array::BitArray*>' changed in GCC 7.1
__uninit_copy(_InputIterator __first, _InputIterator __last,
^~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_uninitialized.h:76:9: note: parameter passing for argument of type 'std::move_iterator<wat_array::BitArray*>' changed in GCC 7.1
In file included from /usr/include/c++/8/vector:69,
from ../Common/Dictionary.h:10,
from ../Common/ContigID.h:5,
from ../Common/ContigNode.h:5,
from ../Common/ContigProperties.h:4,
from overlap.cc:10:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = wat_array::BitArray; _Alloc = std::allocator<wat_array::BitArray>]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<wat_array::BitArray>::iterator' {aka '__gnu_cxx::__normal_iterator<wat_array::BitArray*, std::vector<wat_array::BitArray> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:63,
from ../Common/Dictionary.h:10,
from ../Common/ContigID.h:5,
from ../Common/ContigNode.h:5,
from ../Common/ContigProperties.h:4,
from overlap.cc:10:
/usr/include/c++/8/bits/stl_uninitialized.h:134:15: note: parameter passing for argument of type 'std::move_iterator<wat_array::BitArray*>' changed in GCC 7.1
return std::__uninitialized_copy<__is_trivial(_ValueType1)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
&& __is_trivial(_ValueType2)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
&& __assignable>::
~~~~~~~~~~~~~~~~~~
__uninit_copy(__first, __last, __result);
~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_uninitialized.h:134:15: note: parameter passing for argument of type 'std::move_iterator<wat_array::BitArray*>' changed in GCC 7.1
return std::__uninitialized_copy<__is_trivial(_ValueType1)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
&& __is_trivial(_ValueType2)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
&& __assignable>::
~~~~~~~~~~~~~~~~~~
__uninit_copy(__first, __last, __result);
~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from ../Common/Dictionary.h:10,
from ../Common/ContigID.h:5,
from ../Common/ContigNode.h:5,
from ../Common/ContigProperties.h:4,
from overlap.cc:10:
/usr/include/c++/8/bits/stl_vector.h: In member function 'void FMIndex::assign(It, It) [with It = __gnu_cxx::__normal_iterator<unsigned char*, std::vector<unsigned char> >]':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<wat_array::BitArray*, std::vector<wat_array::BitArray> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
g++ -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-map abyss_map-map.o ../FMIndex/libfmindex.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../DataBase/libdb.a -lsqlite3 -ldl -lm -ldl -lm
g++ -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-map-ssq abyss_map_ssq-map.o ../FMIndex/libfmindex.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../DataBase/libdb.a -lsqlite3 -ldl -lm -ldl -lm
g++ -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-overlap abyss_overlap-overlap.o ../FMIndex/libfmindex.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Map'
Making all in MergePaths
make[4]: Entering directory '/<<PKGBUILDDIR>>/MergePaths'
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o MergePaths-MergePaths.o `test -f 'MergePaths.cpp' || echo './'`MergePaths.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Align -I../Common -I../DataLayer -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o MergeContigs-MergeContigs.o `test -f 'MergeContigs.cpp' || echo './'`MergeContigs.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Align -I../Common -I../DataLayer -I../SimpleGraph -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o PathConsensus-PathConsensus.o `test -f 'PathConsensus.cpp' || echo './'`PathConsensus.cpp
g++ -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o MergeContigs MergeContigs-MergeContigs.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a -ldl -lm
g++ -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o PathConsensus PathConsensus-PathConsensus.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a ../dialign/libdialign.a -ldl -lm
g++ -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o MergePaths MergePaths-MergePaths.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/MergePaths'
Making all in Misc
make[4]: Entering directory '/<<PKGBUILDDIR>>/Misc'
make[4]: Nothing to be done for 'all'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Misc'
Making all in Overlap
make[4]: Entering directory '/<<PKGBUILDDIR>>/Overlap'
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Overlap-Overlap.o `test -f 'Overlap.cpp' || echo './'`Overlap.cpp
g++ -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o Overlap Overlap-Overlap.o ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Overlap'
Making all in PairedDBG
make[4]: Entering directory '/<<PKGBUILDDIR>>/PairedDBG'
g++ -DHAVE_CONFIG_H -I. -I.. -DPAIRED_DBG -I.. -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_paired_dbg-abyss-paired-dbg.o `test -f 'abyss-paired-dbg.cc' || echo './'`abyss-paired-dbg.cc
g++ -DHAVE_CONFIG_H -I. -I.. -DPAIRED_DBG -I.. -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_paired_dbg-KmerPair.o `test -f 'KmerPair.cc' || echo './'`KmerPair.cc
g++ -DHAVE_CONFIG_H -I. -I.. -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o KmerPair.o KmerPair.cc
rm -f libpaireddbg.a
ar cru libpaireddbg.a KmerPair.o
ar: `u' modifier ignored since `D' is the default (see `U')
ranlib libpaireddbg.a
g++ -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-paired-dbg abyss_paired_dbg-abyss-paired-dbg.o abyss_paired_dbg-KmerPair.o ../Assembly/libassembly.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../DataBase/libdb.a -lsqlite3 -ldl -lm -ldl -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/PairedDBG'
Making all in ParseAligns
make[4]: Entering directory '/<<PKGBUILDDIR>>/ParseAligns'
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_fixmate-abyss-fixmate.o `test -f 'abyss-fixmate.cc' || echo './'`abyss-fixmate.cc
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -D SAM_SEQ_QUAL=1 -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_fixmate_ssq-abyss-fixmate.o `test -f 'abyss-fixmate.cc' || echo './'`abyss-fixmate.cc
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o ParseAligns-ParseAligns.o `test -f 'ParseAligns.cpp' || echo './'`ParseAligns.cpp
g++ -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o ParseAligns ParseAligns-ParseAligns.o ../Common/libcommon.a -ldl -lm
g++ -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-fixmate abyss_fixmate-abyss-fixmate.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../Common/libcommon.a -ldl -lm
g++ -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-fixmate-ssq abyss_fixmate_ssq-abyss-fixmate.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../Common/libcommon.a -ldl -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/ParseAligns'
Making all in PathOverlap
make[4]: Entering directory '/<<PKGBUILDDIR>>/PathOverlap'
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o PathOverlap-PathOverlap.o `test -f 'PathOverlap.cpp' || echo './'`PathOverlap.cpp
g++ -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o PathOverlap PathOverlap-PathOverlap.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/PathOverlap'
Making all in PopBubbles
make[4]: Entering directory '/<<PKGBUILDDIR>>/PopBubbles'
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Align -I../Common -I../DataLayer -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o PopBubbles-PopBubbles.o `test -f 'PopBubbles.cpp' || echo './'`PopBubbles.cpp
g++ -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o PopBubbles PopBubbles-PopBubbles.o ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a ../dialign/libdialign.a -ldl -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/PopBubbles'
Making all in Scaffold
make[4]: Entering directory '/<<PKGBUILDDIR>>/Scaffold'
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_scaffold-scaffold.o `test -f 'scaffold.cc' || echo './'`scaffold.cc
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_junction-junction.o `test -f 'junction.cc' || echo './'`junction.cc
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_longseqdist-longseqdist.o `test -f 'longseqdist.cpp' || echo './'`longseqdist.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_drawgraph-drawgraph.o `test -f 'drawgraph.cc' || echo './'`drawgraph.cc
In file included from /usr/include/c++/8/vector:69,
from ../Common/Dictionary.h:10,
from ../Common/ContigID.h:5,
from ../Common/ContigNode.h:5,
from ../Common/ContigProperties.h:4,
from drawgraph.cc:10:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {std::pair<double, ContigNode>}; _Tp = std::pair<double, ContigNode>; _Alloc = std::allocator<std::pair<double, ContigNode> >]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<std::pair<double, ContigNode> >::iterator' {aka '__gnu_cxx::__normal_iterator<std::pair<double, ContigNode>*, std::vector<std::pair<double, ContigNode> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/algorithm:62,
from /usr/include/boost/type_traits/is_nothrow_swappable.hpp:33,
from /usr/include/boost/type_traits.hpp:117,
from /usr/include/boost/pending/property.hpp:13,
from /usr/include/boost/graph/properties.hpp:15,
from ../Graph/Properties.h:6,
from ../Common/ContigNode.h:6,
from ../Common/ContigProperties.h:4,
from drawgraph.cc:10:
/usr/include/c++/8/bits/stl_algo.h: In function 'void std::__move_median_to_first(_Iterator, _Iterator, _Iterator, _Iterator, _Compare) [with _Iterator = __gnu_cxx::__normal_iterator<std::pair<double, ContigNode>*, std::vector<std::pair<double, ContigNode> > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/8/bits/stl_algo.h:78:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, ContigNode>*, std::vector<std::pair<double, ContigNode> > >' changed in GCC 7.1
__move_median_to_first(_Iterator __result,_Iterator __a, _Iterator __b,
^~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:78:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, ContigNode>*, std::vector<std::pair<double, ContigNode> > >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:78:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, ContigNode>*, std::vector<std::pair<double, ContigNode> > >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:78:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, ContigNode>*, std::vector<std::pair<double, ContigNode> > >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<double, ContigNode>*, std::vector<std::pair<double, ContigNode> > >; _Compare = __gnu_cxx::__ops::_Val_less_iter]':
/usr/include/c++/8/bits/stl_algo.h:1821:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, ContigNode>*, std::vector<std::pair<double, ContigNode> > >' changed in GCC 7.1
__unguarded_linear_insert(_RandomAccessIterator __last,
^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<double, ContigNode>*, std::vector<std::pair<double, ContigNode> > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, ContigNode>*, std::vector<std::pair<double, ContigNode> > >' changed in GCC 7.1
__insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, ContigNode>*, std::vector<std::pair<double, ContigNode> > >' changed in GCC 7.1
In file included from /usr/include/c++/8/bits/stl_algo.h:61,
from /usr/include/c++/8/algorithm:62,
from /usr/include/boost/type_traits/is_nothrow_swappable.hpp:33,
from /usr/include/boost/type_traits.hpp:117,
from /usr/include/boost/pending/property.hpp:13,
from /usr/include/boost/graph/properties.hpp:15,
from ../Graph/Properties.h:6,
from ../Common/ContigNode.h:6,
from ../Common/ContigProperties.h:4,
from drawgraph.cc:10:
/usr/include/c++/8/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<double, ContigNode>*, std::vector<std::pair<double, ContigNode> > >; _Distance = int; _Tp = std::pair<double, ContigNode>; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, ContigNode>*, std::vector<std::pair<double, ContigNode> > >' changed in GCC 7.1
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
In file included from /usr/include/c++/8/algorithm:62,
from /usr/include/boost/type_traits/is_nothrow_swappable.hpp:33,
from /usr/include/boost/type_traits.hpp:117,
from /usr/include/boost/pending/property.hpp:13,
from /usr/include/boost/graph/properties.hpp:15,
from ../Graph/Properties.h:6,
from ../Common/ContigNode.h:6,
from ../Common/ContigProperties.h:4,
from drawgraph.cc:10:
/usr/include/c++/8/bits/stl_algo.h: In function 'void std::__heap_select(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<double, ContigNode>*, std::vector<std::pair<double, ContigNode> > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/8/bits/stl_algo.h:1668:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, ContigNode>*, std::vector<std::pair<double, ContigNode> > >' changed in GCC 7.1
__heap_select(_RandomAccessIterator __first,
^~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1668:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, ContigNode>*, std::vector<std::pair<double, ContigNode> > >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1668:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, ContigNode>*, std::vector<std::pair<double, ContigNode> > >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1668:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, ContigNode>*, std::vector<std::pair<double, ContigNode> > >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<double, ContigNode>*, std::vector<std::pair<double, ContigNode> > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, ContigNode>*, std::vector<std::pair<double, ContigNode> > >' changed in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, ContigNode>*, std::vector<std::pair<double, ContigNode> > >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, ContigNode>*, std::vector<std::pair<double, ContigNode> > >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1921:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, ContigNode>*, std::vector<std::pair<double, ContigNode> > >' changed in GCC 7.1
std::__move_median_to_first(__first, __first + 1, __mid, __last - 1,
~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1921:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, ContigNode>*, std::vector<std::pair<double, ContigNode> > >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, ContigNode>*, std::vector<std::pair<double, ContigNode> > >' changed in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1933:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, ContigNode>*, std::vector<std::pair<double, ContigNode> > >' changed in GCC 7.1
std::__heap_select(__first, __middle, __last, __comp);
~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from ../Common/Dictionary.h:10,
from ../Common/ContigID.h:5,
from ../Common/ContigNode.h:5,
from ../Common/ContigProperties.h:4,
from drawgraph.cc:10:
/usr/include/c++/8/bits/vector.tcc: In function 'int main(int, char**)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, ContigNode>*, std::vector<std::pair<double, ContigNode> > >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/algorithm:62,
from /usr/include/boost/type_traits/is_nothrow_swappable.hpp:33,
from /usr/include/boost/type_traits.hpp:117,
from /usr/include/boost/pending/property.hpp:13,
from /usr/include/boost/graph/properties.hpp:15,
from ../Graph/Properties.h:6,
from ../Common/ContigNode.h:6,
from ../Common/ContigProperties.h:4,
from drawgraph.cc:10:
/usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, ContigNode>*, std::vector<std::pair<double, ContigNode> > >' changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, ContigNode>*, std::vector<std::pair<double, ContigNode> > >' changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, ContigNode>*, std::vector<std::pair<double, ContigNode> > >' changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
g++ -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-longseqdist abyss_longseqdist-longseqdist.o ../Common/libcommon.a -ldl -lm
g++ -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-drawgraph abyss_drawgraph-drawgraph.o ../Common/libcommon.a -ldl -lm
g++ -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-junction abyss_junction-junction.o ../Common/libcommon.a -ldl -lm
g++ -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-scaffold abyss_scaffold-scaffold.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../Common/libcommon.a -ldl -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Scaffold'
Making all in SimpleGraph
make[4]: Entering directory '/<<PKGBUILDDIR>>/SimpleGraph'
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Wno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o SimpleGraph-SimpleGraph.o `test -f 'SimpleGraph.cpp' || echo './'`SimpleGraph.cpp
g++ -Wall -Wextra -Wno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o SimpleGraph SimpleGraph-SimpleGraph.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../Common/libcommon.a -lpthread -ldl -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/SimpleGraph'
Making all in kmerprint
make[4]: Entering directory '/<<PKGBUILDDIR>>/kmerprint'
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Assembly -I../Common -I../DataLayer -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o kmerprint-kmerprint.o `test -f 'kmerprint.cc' || echo './'`kmerprint.cc
g++ -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o kmerprint kmerprint-kmerprint.o ../Assembly/libassembly.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/kmerprint'
Making all in FilterGraph
make[4]: Entering directory '/<<PKGBUILDDIR>>/FilterGraph'
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_filtergraph-FilterGraph.o `test -f 'FilterGraph.cc' || echo './'`FilterGraph.cc
g++ -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-filtergraph abyss_filtergraph-FilterGraph.o ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/FilterGraph'
Making all in GapFiller
make[4]: Entering directory '/<<PKGBUILDDIR>>/GapFiller'
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../Align -D SAM_SEQ_QUAL=1 -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_gapfill-gapfill.o `test -f 'gapfill.cpp' || echo './'`gapfill.cpp
g++ -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-gapfill abyss_gapfill-gapfill.o ../Align/libalign.a ../dialign/libdialign.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/GapFiller'
Making all in Sealer
make[4]: Entering directory '/<<PKGBUILDDIR>>/Sealer'
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_sealer-sealer.o `test -f 'sealer.cc' || echo './'`sealer.cc
g++ -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-sealer abyss_sealer-sealer.o ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a -ldl -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Sealer'
Making all in AdjList
make[4]: Entering directory '/<<PKGBUILDDIR>>/AdjList'
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -DPAIRED_DBG -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o AdjList-AdjList.o `test -f 'AdjList.cpp' || echo './'`AdjList.cpp
g++ -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o AdjList AdjList-AdjList.o ../DataLayer/libdatalayer.a ../Common/libcommon.a ../PairedDBG/libpaireddbg.a ../DataBase/libdb.a -lsqlite3 -ldl -lm -ldl -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/AdjList'
Making all in lib/bloomfilter
make[4]: Entering directory '/<<PKGBUILDDIR>>/lib/bloomfilter'
make[4]: Nothing to be done for 'all'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/lib/bloomfilter'
Making all in lib/nthash
make[4]: Entering directory '/<<PKGBUILDDIR>>/lib/nthash'
make[4]: Nothing to be done for 'all'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/lib/nthash'
Making all in lib/gtest-1.7.0
make[4]: Entering directory '/<<PKGBUILDDIR>>/lib/gtest-1.7.0'
make[4]: Nothing to be done for 'all'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/lib/gtest-1.7.0'
Making all in Unittest
make[4]: Entering directory '/<<PKGBUILDDIR>>/Unittest'
make[4]: Nothing to be done for 'all'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Unittest'
make[4]: Entering directory '/<<PKGBUILDDIR>>'
make[4]: Leaving directory '/<<PKGBUILDDIR>>'
make[3]: Leaving directory '/<<PKGBUILDDIR>>'
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
markdown_py -f README.html README.md
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dh_auto_test -a
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Making check in lib/gtest-1.7.0
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make libgtest.a libgtest_main.a
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g++ -DHAVE_CONFIG_H -I. -I../.. -I../.. -isystem ../../lib/gtest-1.7.0/include -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Wno-missing-field-initializers -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o src/libgtest_a-gtest-all.o `test -f 'src/gtest-all.cc' || echo './'`src/gtest-all.cc
g++ -DHAVE_CONFIG_H -I. -I../.. -I../.. -isystem ../../lib/gtest-1.7.0/include -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Wno-missing-field-initializers -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o src/libgtest_main_a-gtest_main.o `test -f 'src/gtest_main.cc' || echo './'`src/gtest_main.cc
g++ -DHAVE_CONFIG_H -I. -I../.. -I../.. -isystem ../../lib/gtest-1.7.0/include -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Wno-missing-field-initializers -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o src/libgtest_main_a-gtest-all.o `test -f 'src/gtest-all.cc' || echo './'`src/gtest-all.cc
rm -f libgtest_main.a
ar cru libgtest_main.a src/libgtest_main_a-gtest_main.o src/libgtest_main_a-gtest-all.o
ar: `u' modifier ignored since `D' is the default (see `U')
ranlib libgtest_main.a
rm -f libgtest.a
ar cru libgtest.a src/libgtest_a-gtest-all.o
ar: `u' modifier ignored since `D' is the default (see `U')
ranlib libgtest.a
make[3]: Leaving directory '/<<PKGBUILDDIR>>/lib/gtest-1.7.0'
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Making check in Unittest
make[2]: Entering directory '/<<PKGBUILDDIR>>/Unittest'
make common_stringutil common_histogram common_bitutil common_kmer common_sequence common_KmerIterator common_sam BloomFilter Konnector_DBGBloom Konnector_DBGBloomAlgorithms graph_ConstrainedBFSVisitor graph_BidirectionalBFS graph_AllPathsSearch graph_HashGraph graph_ConstrainedBidiBFSVisitor graph_ExtendPath graph_DotIO graph_UndirectedGraph Konnector_konnector DBG_LoadAlgorithm PairedDBG_LoadAlgorithm PairedDBG_KmerPair PairedDBG_Dinuc PairedDBG_BranchRecord BloomDBG_BloomDBG BloomDBG_RollingHash BloomDBG_RollingHashIterator BloomDBG_HashAgnosticCascadingBloom BloomDBG_RollingBloomDBG BloomDBG_MaskedKmer BloomDBG_SpacedSeed BloomDBG_LightweightKmer
make[3]: Entering directory '/<<PKGBUILDDIR>>/Unittest'
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Common/StringUtilTest.o Common/StringUtilTest.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Common/HistogramTest.o Common/HistogramTest.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Common/BitUtilTest.o Common/BitUtilTest.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Common/KmerTest.o Common/KmerTest.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Common/Sequence.o Common/Sequence.cc
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Common/KmerIteratorTest.o Common/KmerIteratorTest.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Common/SAM.o Common/SAM.cc
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../Common -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Konnector/BloomFilter-BloomFilter.o `test -f 'Konnector/BloomFilter.cc' || echo './'`Konnector/BloomFilter.cc
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../Common -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Konnector/DBGBloom-DBGBloomTest.o `test -f 'Konnector/DBGBloomTest.cpp' || echo './'`Konnector/DBGBloomTest.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../Common -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Konnector/DBGBloomAlgorithms-DBGBloomAlgorithmsTest.o `test -f 'Konnector/DBGBloomAlgorithmsTest.cpp' || echo './'`Konnector/DBGBloomAlgorithmsTest.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../Common -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Graph/graph_ConstrainedBFSVisitor-ConstrainedBFSVisitorTest.o `test -f 'Graph/ConstrainedBFSVisitorTest.cpp' || echo './'`Graph/ConstrainedBFSVisitorTest.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../Common -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Graph/graph_BidirectionalBFS-BidirectionalBFSTest.o `test -f 'Graph/BidirectionalBFSTest.cpp' || echo './'`Graph/BidirectionalBFSTest.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../Common -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Graph/graph_AllPathsSearch-AllPathsSearchTest.o `test -f 'Graph/AllPathsSearchTest.cpp' || echo './'`Graph/AllPathsSearchTest.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../Common -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Graph/graph_HashGraph-HashGraphTest.o `test -f 'Graph/HashGraphTest.cpp' || echo './'`Graph/HashGraphTest.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../Common -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Graph/graph_ConstrainedBidiBFSVisitor-ConstrainedBidiBFSVisitorTest.o `test -f 'Graph/ConstrainedBidiBFSVisitorTest.cpp' || echo './'`Graph/ConstrainedBidiBFSVisitorTest.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../Common -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Graph/graph_ExtendPath-ExtendPathTest.o `test -f 'Graph/ExtendPathTest.cpp' || echo './'`Graph/ExtendPathTest.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../Common -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Graph/graph_DotIO-DotIOTest.o `test -f 'Graph/DotIOTest.cpp' || echo './'`Graph/DotIOTest.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Graph/UndirectedGraphTest.o Graph/UndirectedGraphTest.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../Common -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Konnector/konnector-konnectorTest.o `test -f 'Konnector/konnectorTest.cpp' || echo './'`Konnector/konnectorTest.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../DataLayer -I../Common -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o DBG/LoadAlgorithm-LoadAlgorithmTest.o `test -f 'DBG/LoadAlgorithmTest.cpp' || echo './'`DBG/LoadAlgorithmTest.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../DataLayer -I../Common -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o PairedDBG/LoadAlgorithm-LoadAlgorithmTest.o `test -f 'PairedDBG/LoadAlgorithmTest.cpp' || echo './'`PairedDBG/LoadAlgorithmTest.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../DataLayer -I../Common -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o PairedDBG/KmerPair-KmerPairTest.o `test -f 'PairedDBG/KmerPairTest.cc' || echo './'`PairedDBG/KmerPairTest.cc
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../DataLayer -I../Common -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o PairedDBG/Dinuc-DinucTest.o `test -f 'PairedDBG/DinucTest.cc' || echo './'`PairedDBG/DinucTest.cc
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../DataLayer -I../Common -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o PairedDBG/BranchRecord-BranchRecordTest.o `test -f 'PairedDBG/BranchRecordTest.cpp' || echo './'`PairedDBG/BranchRecordTest.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../Common -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o BloomDBG/BloomDBG-BloomDBGTest.o `test -f 'BloomDBG/BloomDBGTest.cpp' || echo './'`BloomDBG/BloomDBGTest.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o BloomDBG/RollingHashTest.o BloomDBG/RollingHashTest.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o BloomDBG/RollingHashIteratorTest.o BloomDBG/RollingHashIteratorTest.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o BloomDBG/HashAgnosticCascadingBloom-HashAgnosticCascadingBloomTest.o `test -f 'BloomDBG/HashAgnosticCascadingBloomTest.cpp' || echo './'`BloomDBG/HashAgnosticCascadingBloomTest.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o BloomDBG/RollingBloomDBG-RollingBloomDBGTest.o `test -f 'BloomDBG/RollingBloomDBGTest.cpp' || echo './'`BloomDBG/RollingBloomDBGTest.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o BloomDBG/MaskedKmerTest.o BloomDBG/MaskedKmerTest.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o BloomDBG/SpacedSeedTest.o BloomDBG/SpacedSeedTest.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o BloomDBG/LightweightKmerTest.o BloomDBG/LightweightKmerTest.cpp
g++ -Wall -Wextra -pthread -Wno-error -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o common_stringutil Common/StringUtilTest.o ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm
g++ -Wall -Wextra -pthread -Wno-error -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o common_histogram Common/HistogramTest.o ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm
g++ -Wall -Wextra -pthread -Wno-error -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o common_bitutil Common/BitUtilTest.o ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm
g++ -Wall -Wextra -pthread -Wno-error -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o common_kmer Common/KmerTest.o ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm
g++ -Wall -Wextra -pthread -Wno-error -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o common_sequence Common/Sequence.o ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm
g++ -Wall -Wextra -pthread -Wno-error -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o common_KmerIterator Common/KmerIteratorTest.o ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm
g++ -Wall -Wextra -pthread -Wno-error -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o common_sam Common/SAM.o ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm
g++ -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o BloomFilter Konnector/BloomFilter-BloomFilter.o ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm
g++ -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o Konnector_DBGBloom Konnector/DBGBloom-DBGBloomTest.o ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm
g++ -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o Konnector_DBGBloomAlgorithms Konnector/DBGBloomAlgorithms-DBGBloomAlgorithmsTest.o ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm
g++ -Wall -Wextra -pthread -Wno-error -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o graph_ConstrainedBFSVisitor Graph/graph_ConstrainedBFSVisitor-ConstrainedBFSVisitorTest.o ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm
g++ -Wall -Wextra -pthread -Wno-error -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o graph_BidirectionalBFS Graph/graph_BidirectionalBFS-BidirectionalBFSTest.o ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm
g++ -Wall -Wextra -pthread -Wno-error -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o graph_AllPathsSearch Graph/graph_AllPathsSearch-AllPathsSearchTest.o ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm
g++ -Wall -Wextra -pthread -Wno-error -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o graph_HashGraph Graph/graph_HashGraph-HashGraphTest.o ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm
g++ -Wall -Wextra -pthread -Wno-error -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o graph_ConstrainedBidiBFSVisitor Graph/graph_ConstrainedBidiBFSVisitor-ConstrainedBidiBFSVisitorTest.o ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm
g++ -Wall -Wextra -pthread -Wno-error -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o graph_ExtendPath Graph/graph_ExtendPath-ExtendPathTest.o ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm
g++ -Wall -Wextra -pthread -Wno-error -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o graph_DotIO Graph/graph_DotIO-DotIOTest.o ../Assembly/libassembly.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm
g++ -Wall -Wextra -pthread -Wno-error -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o graph_UndirectedGraph Graph/UndirectedGraphTest.o ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm
g++ -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o Konnector_konnector Konnector/konnector-konnectorTest.o ../Align/libalign.a ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm
g++ -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o DBG_LoadAlgorithm DBG/LoadAlgorithm-LoadAlgorithmTest.o ../Assembly/libassembly.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm
g++ -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o PairedDBG_LoadAlgorithm PairedDBG/LoadAlgorithm-LoadAlgorithmTest.o ../PairedDBG/libpaireddbg.a ../Assembly/libassembly.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm
g++ -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o PairedDBG_KmerPair PairedDBG/KmerPair-KmerPairTest.o ../PairedDBG/libpaireddbg.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm
g++ -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o PairedDBG_Dinuc PairedDBG/Dinuc-DinucTest.o ../PairedDBG/libpaireddbg.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm
g++ -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o PairedDBG_BranchRecord PairedDBG/BranchRecord-BranchRecordTest.o ../PairedDBG/libpaireddbg.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm
g++ -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o BloomDBG_BloomDBG BloomDBG/BloomDBG-BloomDBGTest.o ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm
g++ -Wall -Wextra -pthread -Wno-error -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o BloomDBG_RollingHash BloomDBG/RollingHashTest.o ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm
g++ -Wall -Wextra -pthread -Wno-error -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o BloomDBG_RollingHashIterator BloomDBG/RollingHashIteratorTest.o ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm
g++ -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o BloomDBG_HashAgnosticCascadingBloom BloomDBG/HashAgnosticCascadingBloom-HashAgnosticCascadingBloomTest.o ../DataLayer/libdatalayer.a ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm
In file included from /usr/include/c++/8/unordered_set:46,
from ../Common/UnorderedSet.h:8,
from BloomDBG/RollingBloomDBGTest.cpp:3:
/usr/include/c++/8/bits/hashtable.h: In member function 'std::_Hashtable<_Key, _Value, _Alloc, _ExtractKey, _Equal, _H1, _H2, _Hash, _RehashPolicy, _Traits>::iterator std::_Hashtable<_Key, _Value, _Alloc, _ExtractKey, _Equal, _H1, _H2, _Hash, _RehashPolicy, _Traits>::erase(std::_Hashtable<_Key, _Value, _Alloc, _ExtractKey, _Equal, _H1, _H2, _Hash, _RehashPolicy, _Traits>::const_iterator) [with _Key = RollingBloomDBGVertex; _Value = RollingBloomDBGVertex; _Alloc = std::allocator<RollingBloomDBGVertex>; _ExtractKey = std::__detail::_Identity; _Equal = std::equal_to<RollingBloomDBGVertex>; _H1 = std::hash<RollingBloomDBGVertex>; _H2 = std::__detail::_Mod_range_hashing; _Hash = std::__detail::_Default_ranged_hash; _RehashPolicy = std::__detail::_Prime_rehash_policy; _Traits = std::__detail::_Hashtable_traits<true, true, true>]':
/usr/include/c++/8/bits/hashtable.h:1871:5: note: parameter passing for argument of type 'std::_Hashtable<RollingBloomDBGVertex, RollingBloomDBGVertex, std::allocator<RollingBloomDBGVertex>, std::__detail::_Identity, std::equal_to<RollingBloomDBGVertex>, std::hash<RollingBloomDBGVertex>, std::__detail::_Mod_range_hashing, std::__detail::_Default_ranged_hash, std::__detail::_Prime_rehash_policy, std::__detail::_Hashtable_traits<true, true, true> >::const_iterator' {aka 'std::__detail::_Node_const_iterator<RollingBloomDBGVertex, true, true>'} changed in GCC 7.1
_Hashtable<_Key, _Value, _Alloc, _ExtractKey, _Equal,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
_H1, _H2, _Hash, _RehashPolicy, _Traits>::
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -Wall -Wextra -pthread -Wno-error -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o BloomDBG_MaskedKmer BloomDBG/MaskedKmerTest.o ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm
g++ -Wall -Wextra -pthread -Wno-error -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o BloomDBG_SpacedSeed BloomDBG/SpacedSeedTest.o ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm
g++ -Wall -Wextra -pthread -Wno-error -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o BloomDBG_LightweightKmer BloomDBG/LightweightKmerTest.o ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm
/usr/include/c++/8/bits/hashtable.h: In member function 'virtual void RollingBloomDBGTest_out_edge_iterator_Test::TestBody()':
/usr/include/c++/8/bits/hashtable.h:767:42: note: parameter passing for argument of type 'std::_Hashtable<RollingBloomDBGVertex, RollingBloomDBGVertex, std::allocator<RollingBloomDBGVertex>, std::__detail::_Identity, std::equal_to<RollingBloomDBGVertex>, std::hash<RollingBloomDBGVertex>, std::__detail::_Mod_range_hashing, std::__detail::_Default_ranged_hash, std::__detail::_Prime_rehash_policy, std::__detail::_Hashtable_traits<true, true, true> >::const_iterator' {aka 'std::__detail::_Node_const_iterator<RollingBloomDBGVertex, true, true>'} changed in GCC 7.1
{ return erase(const_iterator(__it)); }
^
/usr/include/c++/8/bits/hashtable.h: In member function 'virtual void RollingBloomDBGSpacedSeedTest_out_edge_iterator_Test::TestBody()':
/usr/include/c++/8/bits/hashtable.h:767:42: note: parameter passing for argument of type 'std::_Hashtable<RollingBloomDBGVertex, RollingBloomDBGVertex, std::allocator<RollingBloomDBGVertex>, std::__detail::_Identity, std::equal_to<RollingBloomDBGVertex>, std::hash<RollingBloomDBGVertex>, std::__detail::_Mod_range_hashing, std::__detail::_Default_ranged_hash, std::__detail::_Prime_rehash_policy, std::__detail::_Hashtable_traits<true, true, true> >::const_iterator' {aka 'std::__detail::_Node_const_iterator<RollingBloomDBGVertex, true, true>'} changed in GCC 7.1
{ return erase(const_iterator(__it)); }
^
/usr/include/c++/8/bits/hashtable.h: In member function 'virtual void RollingBloomDBGTest_adjacency_iterator_Test::TestBody()':
/usr/include/c++/8/bits/hashtable.h:767:42: note: parameter passing for argument of type 'std::_Hashtable<RollingBloomDBGVertex, RollingBloomDBGVertex, std::allocator<RollingBloomDBGVertex>, std::__detail::_Identity, std::equal_to<RollingBloomDBGVertex>, std::hash<RollingBloomDBGVertex>, std::__detail::_Mod_range_hashing, std::__detail::_Default_ranged_hash, std::__detail::_Prime_rehash_policy, std::__detail::_Hashtable_traits<true, true, true> >::const_iterator' {aka 'std::__detail::_Node_const_iterator<RollingBloomDBGVertex, true, true>'} changed in GCC 7.1
{ return erase(const_iterator(__it)); }
^
/usr/include/c++/8/bits/hashtable.h: In member function 'virtual void RollingBloomDBGTest_in_edges_Test::TestBody()':
/usr/include/c++/8/bits/hashtable.h:767:42: note: parameter passing for argument of type 'std::_Hashtable<RollingBloomDBGVertex, RollingBloomDBGVertex, std::allocator<RollingBloomDBGVertex>, std::__detail::_Identity, std::equal_to<RollingBloomDBGVertex>, std::hash<RollingBloomDBGVertex>, std::__detail::_Mod_range_hashing, std::__detail::_Default_ranged_hash, std::__detail::_Prime_rehash_policy, std::__detail::_Hashtable_traits<true, true, true> >::const_iterator' {aka 'std::__detail::_Node_const_iterator<RollingBloomDBGVertex, true, true>'} changed in GCC 7.1
{ return erase(const_iterator(__it)); }
^
g++ -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o BloomDBG_RollingBloomDBG BloomDBG/RollingBloomDBG-RollingBloomDBGTest.o ../DataLayer/libdatalayer.a ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm
make[3]: Leaving directory '/<<PKGBUILDDIR>>/Unittest'
make check-TESTS
make[3]: Entering directory '/<<PKGBUILDDIR>>/Unittest'
make[4]: Entering directory '/<<PKGBUILDDIR>>/Unittest'
PASS: common_histogram
PASS: common_bitutil
PASS: common_stringutil
PASS: common_kmer
PASS: common_sequence
PASS: common_KmerIterator
PASS: BloomFilter
PASS: common_sam
PASS: Konnector_DBGBloom
PASS: graph_BidirectionalBFS
PASS: Konnector_DBGBloomAlgorithms
PASS: graph_ConstrainedBFSVisitor
PASS: graph_ConstrainedBidiBFSVisitor
PASS: graph_ExtendPath
PASS: graph_AllPathsSearch
PASS: graph_HashGraph
PASS: graph_UndirectedGraph
PASS: graph_DotIO
PASS: Konnector_konnector
PASS: PairedDBG_Dinuc
PASS: PairedDBG_KmerPair
PASS: BloomDBG_BloomDBG
PASS: PairedDBG_BranchRecord
PASS: BloomDBG_RollingHash
PASS: BloomDBG_RollingHashIterator
PASS: BloomDBG_HashAgnosticCascadingBloom
PASS: BloomDBG_RollingBloomDBG
PASS: BloomDBG_MaskedKmer
PASS: BloomDBG_SpacedSeed
PASS: BloomDBG_LightweightKmer
PASS: DBG_LoadAlgorithm
PASS: PairedDBG_LoadAlgorithm
============================================================================
Testsuite summary for ABySS 2.1.5
============================================================================
# TOTAL: 32
# PASS: 32
# SKIP: 0
# XFAIL: 0
# FAIL: 0
# XPASS: 0
# ERROR: 0
============================================================================
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Unittest'
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make[2]: Entering directory '/<<PKGBUILDDIR>>'
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
create-stamp debian/debhelper-build-stamp
fakeroot debian/rules binary-arch
dh binary-arch
dh_testroot -a
dh_prep -a
debian/rules override_dh_auto_install
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_install --destdir=debian/tmp
make -j4 install DESTDIR=/<<PKGBUILDDIR>>/debian/tmp AM_UPDATE_INFO_DIR=no
make[2]: Entering directory '/<<PKGBUILDDIR>>'
Making install in bin
make[3]: Entering directory '/<<PKGBUILDDIR>>/bin'
make[4]: Entering directory '/<<PKGBUILDDIR>>/bin'
make[4]: Nothing to be done for 'install-data-am'.
/bin/mkdir -p '/<<PKGBUILDDIR>>/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 '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/bin'
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Making install in doc
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make[4]: Nothing to be done for 'install-exec-am'.
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/share/doc/abyss'
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man1'
/usr/bin/install -c -m 644 flowchart.pdf flowchart_simplified.pdf '/<<PKGBUILDDIR>>/debian/tmp/usr/share/doc/abyss'
/usr/bin/install -c -m 644 ABYSS.1 abyss-pe.1 abyss-tofastq.1 '/<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man1'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/doc'
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Making install in Common
make[3]: Entering directory '/<<PKGBUILDDIR>>/Common'
make[4]: Entering directory '/<<PKGBUILDDIR>>/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 '/<<PKGBUILDDIR>>/Common'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/Common'
Making install in Graph
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make[4]: Entering directory '/<<PKGBUILDDIR>>/Graph'
make[4]: Nothing to be done for 'install-data-am'.
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
/usr/bin/install -c abyss-gc abyss-todot '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Graph'
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Making install in DataLayer
make[3]: Entering directory '/<<PKGBUILDDIR>>/DataLayer'
make[4]: Entering directory '/<<PKGBUILDDIR>>/DataLayer'
make[4]: Nothing to be done for 'install-data-am'.
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
/usr/bin/install -c abyss-fac abyss-tofastq '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/DataLayer'
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Making install in DataBase
make[3]: Entering directory '/<<PKGBUILDDIR>>/DataBase'
make[4]: Entering directory '/<<PKGBUILDDIR>>/DataBase'
make[4]: Nothing to be done for 'install-data-am'.
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
/usr/bin/install -c abyss-db-csv '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
/usr/bin/install -c abyss-db-txt '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/DataBase'
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Making install in FMIndex
make[3]: Entering directory '/<<PKGBUILDDIR>>/FMIndex'
make[4]: Entering directory '/<<PKGBUILDDIR>>/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 '/<<PKGBUILDDIR>>/FMIndex'
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Making install in Assembly
make[3]: Entering directory '/<<PKGBUILDDIR>>/Assembly'
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make[4]: Nothing to be done for 'install-exec-am'.
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Making install in dialign
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make[4]: Nothing to be done for 'install-exec-am'.
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Making install in Align
make[3]: Entering directory '/<<PKGBUILDDIR>>/Align'
make[4]: Entering directory '/<<PKGBUILDDIR>>/Align'
make[4]: Nothing to be done for 'install-data-am'.
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
/usr/bin/install -c abyss-align abyss-mergepairs '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Align'
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Making install in ABYSS
make[3]: Entering directory '/<<PKGBUILDDIR>>/ABYSS'
make[4]: Entering directory '/<<PKGBUILDDIR>>/ABYSS'
make[4]: Nothing to be done for 'install-data-am'.
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
/usr/bin/install -c ABYSS '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/ABYSS'
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Making install in Parallel
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make[4]: Entering directory '/<<PKGBUILDDIR>>/Parallel'
make[4]: Nothing to be done for 'install-data-am'.
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
/usr/bin/install -c ABYSS-P abyss-paired-dbg-mpi '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Parallel'
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Making install in Bloom
make[3]: Entering directory '/<<PKGBUILDDIR>>/Bloom'
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make[4]: Nothing to be done for 'install-data-am'.
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
/usr/bin/install -c abyss-bloom '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Bloom'
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Making install in BloomDBG
make[3]: Entering directory '/<<PKGBUILDDIR>>/BloomDBG'
make[4]: Entering directory '/<<PKGBUILDDIR>>/BloomDBG'
make[4]: Nothing to be done for 'install-data-am'.
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
/usr/bin/install -c abyss-bloom-dbg '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/BloomDBG'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/BloomDBG'
Making install in Konnector
make[3]: Entering directory '/<<PKGBUILDDIR>>/Konnector'
make[4]: Entering directory '/<<PKGBUILDDIR>>/Konnector'
make[4]: Nothing to be done for 'install-data-am'.
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
/usr/bin/install -c konnector '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Konnector'
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Making install in Consensus
make[3]: Entering directory '/<<PKGBUILDDIR>>/Consensus'
make[4]: Entering directory '/<<PKGBUILDDIR>>/Consensus'
make[4]: Nothing to be done for 'install-data-am'.
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
/usr/bin/install -c Consensus '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Consensus'
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Making install in DAssembler
make[3]: Entering directory '/<<PKGBUILDDIR>>/DAssembler'
make[4]: Entering directory '/<<PKGBUILDDIR>>/DAssembler'
make[4]: Nothing to be done for 'install-data-am'.
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
/usr/bin/install -c DAssembler '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/DAssembler'
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Making install in DistanceEst
make[3]: Entering directory '/<<PKGBUILDDIR>>/DistanceEst'
make[4]: Entering directory '/<<PKGBUILDDIR>>/DistanceEst'
make[4]: Nothing to be done for 'install-data-am'.
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
/usr/bin/install -c DistanceEst DistanceEst-ssq '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/DistanceEst'
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Making install in KAligner
make[3]: Entering directory '/<<PKGBUILDDIR>>/KAligner'
make[4]: Entering directory '/<<PKGBUILDDIR>>/KAligner'
make[4]: Nothing to be done for 'install-data-am'.
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
/usr/bin/install -c KAligner '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/KAligner'
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Making install in Layout
make[3]: Entering directory '/<<PKGBUILDDIR>>/Layout'
make[4]: Entering directory '/<<PKGBUILDDIR>>/Layout'
make[4]: Nothing to be done for 'install-data-am'.
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
/usr/bin/install -c abyss-layout '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Layout'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/Layout'
Making install in LogKmerCount
make[3]: Entering directory '/<<PKGBUILDDIR>>/LogKmerCount'
make[4]: Entering directory '/<<PKGBUILDDIR>>/LogKmerCount'
make[4]: Nothing to be done for 'install-data-am'.
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
/usr/bin/install -c logcounter '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/LogKmerCount'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/LogKmerCount'
Making install in Map
make[3]: Entering directory '/<<PKGBUILDDIR>>/Map'
make[4]: Entering directory '/<<PKGBUILDDIR>>/Map'
make[4]: Nothing to be done for 'install-data-am'.
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
/usr/bin/install -c abyss-index abyss-map abyss-map-ssq abyss-overlap '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Map'
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Making install in MergePaths
make[3]: Entering directory '/<<PKGBUILDDIR>>/MergePaths'
make[4]: Entering directory '/<<PKGBUILDDIR>>/MergePaths'
make[4]: Nothing to be done for 'install-data-am'.
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
/usr/bin/install -c MergePaths MergeContigs PathConsensus '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/MergePaths'
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Making install in Misc
make[3]: Entering directory '/<<PKGBUILDDIR>>/Misc'
make[4]: Entering directory '/<<PKGBUILDDIR>>/Misc'
make[4]: Nothing to be done for 'install-data-am'.
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Making install in Overlap
make[3]: Entering directory '/<<PKGBUILDDIR>>/Overlap'
make[4]: Entering directory '/<<PKGBUILDDIR>>/Overlap'
make[4]: Nothing to be done for 'install-data-am'.
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
/usr/bin/install -c Overlap '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Overlap'
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Making install in PairedDBG
make[3]: Entering directory '/<<PKGBUILDDIR>>/PairedDBG'
make[4]: Entering directory '/<<PKGBUILDDIR>>/PairedDBG'
make[4]: Nothing to be done for 'install-data-am'.
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
/usr/bin/install -c abyss-paired-dbg '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/PairedDBG'
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Making install in ParseAligns
make[3]: Entering directory '/<<PKGBUILDDIR>>/ParseAligns'
make[4]: Entering directory '/<<PKGBUILDDIR>>/ParseAligns'
make[4]: Nothing to be done for 'install-data-am'.
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
/usr/bin/install -c abyss-fixmate abyss-fixmate-ssq ParseAligns '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/ParseAligns'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/ParseAligns'
Making install in PathOverlap
make[3]: Entering directory '/<<PKGBUILDDIR>>/PathOverlap'
make[4]: Entering directory '/<<PKGBUILDDIR>>/PathOverlap'
make[4]: Nothing to be done for 'install-data-am'.
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
/usr/bin/install -c PathOverlap '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/PathOverlap'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/PathOverlap'
Making install in PopBubbles
make[3]: Entering directory '/<<PKGBUILDDIR>>/PopBubbles'
make[4]: Entering directory '/<<PKGBUILDDIR>>/PopBubbles'
make[4]: Nothing to be done for 'install-data-am'.
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
/usr/bin/install -c PopBubbles '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/PopBubbles'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/PopBubbles'
Making install in Scaffold
make[3]: Entering directory '/<<PKGBUILDDIR>>/Scaffold'
make[4]: Entering directory '/<<PKGBUILDDIR>>/Scaffold'
make[4]: Nothing to be done for 'install-data-am'.
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
/usr/bin/install -c abyss-scaffold abyss-junction abyss-longseqdist '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Scaffold'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/Scaffold'
Making install in SimpleGraph
make[3]: Entering directory '/<<PKGBUILDDIR>>/SimpleGraph'
make[4]: Entering directory '/<<PKGBUILDDIR>>/SimpleGraph'
make[4]: Nothing to be done for 'install-data-am'.
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
/usr/bin/install -c SimpleGraph '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/SimpleGraph'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/SimpleGraph'
Making install in kmerprint
make[3]: Entering directory '/<<PKGBUILDDIR>>/kmerprint'
make[4]: Entering directory '/<<PKGBUILDDIR>>/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 '/<<PKGBUILDDIR>>/kmerprint'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/kmerprint'
Making install in FilterGraph
make[3]: Entering directory '/<<PKGBUILDDIR>>/FilterGraph'
make[4]: Entering directory '/<<PKGBUILDDIR>>/FilterGraph'
make[4]: Nothing to be done for 'install-data-am'.
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
/usr/bin/install -c abyss-filtergraph '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/FilterGraph'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/FilterGraph'
Making install in GapFiller
make[3]: Entering directory '/<<PKGBUILDDIR>>/GapFiller'
make[4]: Entering directory '/<<PKGBUILDDIR>>/GapFiller'
make[4]: Nothing to be done for 'install-data-am'.
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
/usr/bin/install -c abyss-gapfill '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/GapFiller'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/GapFiller'
Making install in Sealer
make[3]: Entering directory '/<<PKGBUILDDIR>>/Sealer'
make[4]: Entering directory '/<<PKGBUILDDIR>>/Sealer'
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
/usr/bin/install -c abyss-sealer '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Sealer'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/Sealer'
Making install in AdjList
make[3]: Entering directory '/<<PKGBUILDDIR>>/AdjList'
make[4]: Entering directory '/<<PKGBUILDDIR>>/AdjList'
make[4]: Nothing to be done for 'install-data-am'.
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
/usr/bin/install -c AdjList '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/AdjList'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/AdjList'
Making install in lib/bloomfilter
make[3]: Entering directory '/<<PKGBUILDDIR>>/lib/bloomfilter'
make[4]: Entering directory '/<<PKGBUILDDIR>>/lib/bloomfilter'
make[4]: Nothing to be done for 'install-exec-am'.
make[4]: Nothing to be done for 'install-data-am'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/lib/bloomfilter'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/lib/bloomfilter'
Making install in lib/nthash
make[3]: Entering directory '/<<PKGBUILDDIR>>/lib/nthash'
make[4]: Entering directory '/<<PKGBUILDDIR>>/lib/nthash'
make[4]: Nothing to be done for 'install-exec-am'.
make[4]: Nothing to be done for 'install-data-am'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/lib/nthash'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/lib/nthash'
Making install in lib/gtest-1.7.0
make[3]: Entering directory '/<<PKGBUILDDIR>>/lib/gtest-1.7.0'
make[4]: Entering directory '/<<PKGBUILDDIR>>/lib/gtest-1.7.0'
make[4]: Nothing to be done for 'install-exec-am'.
make[4]: Nothing to be done for 'install-data-am'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/lib/gtest-1.7.0'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/lib/gtest-1.7.0'
Making install in Unittest
make[3]: Entering directory '/<<PKGBUILDDIR>>/Unittest'
make[4]: Entering directory '/<<PKGBUILDDIR>>/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 '/<<PKGBUILDDIR>>/Unittest'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/Unittest'
make[3]: Entering directory '/<<PKGBUILDDIR>>'
make[4]: Entering directory '/<<PKGBUILDDIR>>'
make[4]: Nothing to be done for 'install-exec-am'.
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/share/doc/abyss'
/usr/bin/install -c -m 644 ChangeLog CITATION.bib CITATION.md COPYRIGHT LICENSE README.md '/<<PKGBUILDDIR>>/debian/tmp/usr/share/doc/abyss'
make[4]: Leaving directory '/<<PKGBUILDDIR>>'
make[3]: Leaving directory '/<<PKGBUILDDIR>>'
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
PATH=debian/tmp/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games help2man --no-info \
-n "Estimate distances between contigs using paired-end alignments." \
DistanceEst > debian/tmp/usr/share/man/man1/DistanceEst.1
PATH=debian/tmp/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games help2man --no-info \
-n "Fill the paired-end fields of SAM alignments" abyss-fixmate \
> debian/tmp/usr/share/man/man1/abyss-fixmate.1
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
debian/rules override_dh_install
make[1]: Entering directory '/<<PKGBUILDDIR>>'
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 '/<<PKGBUILDDIR>>'
dh_installdocs -a
dh_installchangelogs -a
dh_installman -a
dh_perl -a
dh_link -a
dh_strip_nondeterminism -a
dh_compress -a
dh_fixperms -a
dh_missing -a
dh_dwz -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/Consensus contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/DAssembler contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/abyss-filtergraph contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/abyss-junction contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/ABYSS contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/abyss-paired-dbg contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/MergePaths contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/AdjList contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/abyss-fac contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/DistanceEst-ssq contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/abyss-layout contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/abyss-bloom-dbg contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/MergeContigs contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/abyss-sealer contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/konnector contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/ParseAligns contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/PathConsensus contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/abyss/usr/bin/abyss-fixmate contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/Overlap contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/PathOverlap contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/DistanceEst contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/abyss-map contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/SimpleGraph contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/abyss-db-csv contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/KAligner contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/abyss-paired-dbg-mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/abyss-align contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/abyss/usr/bin/DistanceEst contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/abyss-longseqdist contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/logcounter contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/abyss-mergepairs contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/ABYSS-P contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/abyss-scaffold contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/abyss-fixmate-ssq contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/abyss-tofastq contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/abyss-gapfill contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/abyss-overlap contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/abyss-fixmate contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/PopBubbles contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/abyss-map-ssq contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/abyss-todot contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/abyss-gc contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/abyss-index contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/abyss-bloom contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/abyss/usr/lib/abyss/Consensus debian/abyss/usr/lib/abyss/DAssembler debian/abyss/usr/lib/abyss/abyss-filtergraph debian/abyss/usr/lib/abyss/abyss-junction debian/abyss/usr/lib/abyss/ABYSS debian/abyss/usr/lib/abyss/abyss-paired-dbg debian/abyss/usr/lib/abyss/MergePaths debian/abyss/usr/lib/abyss/AdjList debian/abyss/usr/lib/abyss/abyss-fac debian/abyss/usr/lib/abyss/DistanceEst-ssq debian/abyss/usr/lib/abyss/abyss-layout debian/abyss/usr/lib/abyss/abyss-bloom-dbg debian/abyss/usr/lib/abyss/MergeContigs debian/abyss/usr/lib/abyss/abyss-sealer debian/abyss/usr/lib/abyss/konnector debian/abyss/usr/lib/abyss/ParseAligns debian/abyss/usr/lib/abyss/PathConsensus debian/abyss/usr/bin/abyss-fixmate debian/abyss/usr/lib/abyss/Overlap debian/abyss/usr/lib/abyss/PathOverlap debian/abyss/usr/lib/abyss/DistanceEst debian/abyss/usr/lib/abyss/abyss-map debian/abyss/usr/lib/abyss/SimpleGraph debian/abyss/usr/lib/abyss/abyss-db-csv debian/abyss/usr/lib/abyss/KAligner debian/abyss/usr/lib/abyss/abyss-paired-dbg-mpi debian/abyss/usr/lib/abyss/abyss-align debian/abyss/usr/bin/DistanceEst debian/abyss/usr/lib/abyss/abyss-longseqdist debian/abyss/usr/lib/abyss/logcounter debian/abyss/usr/lib/abyss/abyss-mergepairs debian/abyss/usr/lib/abyss/ABYSS-P debian/abyss/usr/lib/abyss/abyss-scaffold debian/abyss/usr/lib/abyss/abyss-fixmate-ssq debian/abyss/usr/lib/abyss/abyss-tofastq debian/abyss/usr/lib/abyss/abyss-gapfill debian/abyss/usr/lib/abyss/abyss-overlap debian/abyss/usr/lib/abyss/abyss-fixmate debian/abyss/usr/lib/abyss/PopBubbles debian/abyss/usr/lib/abyss/abyss-map-ssq debian/abyss/usr/lib/abyss/abyss-todot debian/abyss/usr/lib/abyss/abyss-gc debian/abyss/usr/lib/abyss/abyss-index debian/abyss/usr/lib/abyss/abyss-bloom were not linked against ld-linux-armhf.so.3 (they use none of the library's symbols)
dh_installdeb -a
dh_gencontrol -a
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package 'abyss' in '../abyss_2.1.5-7_armhf.deb'.
dpkg-deb: building package 'abyss-dbgsym' in '../abyss-dbgsym_2.1.5-7_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian mythic lxc autobuilder 1 <root@raspbian.org> >../abyss_2.1.5-7_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2019-02-27T05:12:15Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
abyss_2.1.5-7_armhf.changes:
----------------------------
Format: 1.8
Date: Sun, 17 Feb 2019 05:19:54 -0800
Source: abyss
Binary: abyss
Architecture: armhf
Version: 2.1.5-7
Distribution: buster-staging
Urgency: medium
Maintainer: Raspbian mythic lxc autobuilder 1 <root@raspbian.org>
Changed-By: Michael R. Crusoe <michael.crusoe@gmail.com>
Description:
abyss - de novo, parallel, sequence assembler for short reads
Changes:
abyss (2.1.5-7) unstable; urgency=medium
.
* Add myself as an uploader.
* The package openmpi-bin is now a required dependency for the abyss
binary package. Many thanks to ci.debian.org for bringing this to light.
* Fix "implicit declaration of function"s in dialign/museq.c
* Fix some spelling typos
* Register the flowchart PDFs with doc-base
Checksums-Sha1:
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68dfd60fbc90d4dd9de8eec0334d4e2aa57db044 6899 abyss_2.1.5-7_armhf.buildinfo
dbe40eb603ba0702fd0a6715c971dc54160b9d0f 2653888 abyss_2.1.5-7_armhf.deb
Checksums-Sha256:
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c7d7657b7f68f9fb2c51226af1775d3ffa13a75ef0f32c1df919d224b11625de 6899 abyss_2.1.5-7_armhf.buildinfo
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Files:
cb19db2abdf4cdf8e3d1354acfddc4f7 28154512 debug optional abyss-dbgsym_2.1.5-7_armhf.deb
1ba62144a60d01bb9bdf9c2e82d666f8 6899 science optional abyss_2.1.5-7_armhf.buildinfo
02c712f45e8a165a5055a9100dc78ab9 2653888 science optional abyss_2.1.5-7_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
abyss-dbgsym_2.1.5-7_armhf.deb
------------------------------
new Debian package, version 2.0.
size 28154512 bytes: control archive=2468 bytes.
2045 bytes, 12 lines control
4537 bytes, 43 lines md5sums
Package: abyss-dbgsym
Source: abyss
Version: 2.1.5-7
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 29221
Depends: abyss (= 2.1.5-7)
Section: debug
Priority: optional
Description: debug symbols for abyss
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lrwxrwxrwx root/root 0 2019-02-17 13:19 ./usr/share/doc/abyss-dbgsym -> abyss
abyss_2.1.5-7_armhf.deb
-----------------------
new Debian package, version 2.0.
size 2653888 bytes: control archive=2696 bytes.
717 bytes, 14 lines control
4907 bytes, 78 lines md5sums
Package: abyss
Version: 2.1.5-7
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 7502
Depends: make, libc6 (>= 2.28), libgcc1 (>= 1:3.5), libgomp1 (>= 4.9), libopenmpi3, libsqlite3-0 (>= 3.5.9), libstdc++6 (>= 5.2), perl:any, bsdmainutils, openmpi-common, openmpi-bin
Section: science
Priority: optional
Homepage: http://www.bcgsc.ca/platform/bioinfo/software/abyss
Description: de novo, parallel, sequence assembler for short reads
ABySS is a de novo, parallel, sequence assembler that is designed for
short reads. It may be used to assemble genome or transcriptome
sequence data. Parallelization is achieved using MPI, OpenMP and
pthread.
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drwxr-xr-x root/root 0 2019-02-17 13:19 ./usr/share/doc/abyss/test-data/
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drwxr-xr-x root/root 0 2019-02-17 13:19 ./usr/share/man/
drwxr-xr-x root/root 0 2019-02-17 13:19 ./usr/share/man/man1/
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-rw-r--r-- root/root 3564 2019-02-17 13:19 ./usr/share/man/man1/abyss-pe.1.gz
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| Post Build |
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| Cleanup |
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Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
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| Summary |
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Build Architecture: armhf
Build-Space: 621760
Build-Time: 798
Distribution: buster-staging
Host Architecture: armhf
Install-Time: 548
Job: abyss_2.1.5-7
Machine Architecture: armhf
Package: abyss
Package-Time: 1362
Source-Version: 2.1.5-7
Space: 621760
Status: successful
Version: 2.1.5-7
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Finished at 2019-02-27T05:12:15Z
Build needed 00:22:42, 621760k disk space