abyss →
2.1.5-3 →
armhf → 2019-01-12 05:03:01
sbuild (Debian sbuild) 0.72.0 (25 Oct 2016) on mb-lxc-01
+==============================================================================+
| abyss 2.1.5-3 (armhf) Sat, 12 Jan 2019 04:42:30 +0000 |
+==============================================================================+
Package: abyss
Version: 2.1.5-3
Source Version: 2.1.5-3
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-24d53753-a85a-420b-b4e9-9db5d4b89fd9' 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 24.5 MB in 9s (2814 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 1823 kB of source archives.
Get:1 http://172.17.0.1/private buster-staging/main abyss 2.1.5-3 (dsc) [2313 B]
Get:2 http://172.17.0.1/private buster-staging/main abyss 2.1.5-3 (tar) [1063 kB]
Get:3 http://172.17.0.1/private buster-staging/main abyss 2.1.5-3 (diff) [758 kB]
Fetched 1823 kB in 0s (5186 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/abyss-60YTrp/abyss-2.1.5' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/abyss-60YTrp' 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-yJrwgL/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-yJrwgL/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-yJrwgL/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-yJrwgL/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-yJrwgL/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-yJrwgL/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-yJrwgL/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-yJrwgL/apt_archive ./ Packages [428 B]
Fetched 2104 B in 0s (11.0 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 libnss-systemd libpam-systemd libssl1.1 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 11 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-yJrwgL/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 ... 15815 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 (>= 11~), python-markdown, libboost-graph-dev, libopenmpi-dev, libsparsehash-dev, libtext-multimarkdown-perl, libgtest-dev, libsqlite3-dev
Filtered Build-Depends: debhelper (>= 11~), python-markdown, libboost-graph-dev, libopenmpi-dev, libsparsehash-dev, libtext-multimarkdown-perl, libgtest-dev, libsqlite3-dev
dpkg-deb: building package 'sbuild-build-depends-abyss-dummy' in '/<<BUILDDIR>>/resolver-yJrwgL/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-yJrwgL/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-yJrwgL/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-yJrwgL/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-yJrwgL/apt_archive ./ Sources [560 B]
Get:5 copy:/<<BUILDDIR>>/resolver-yJrwgL/apt_archive ./ Packages [636 B]
Fetched 2529 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 debhelper
dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base
gfortran-8 googletest groff-base 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 libgfortran-8-dev libgfortran5 libglib2.0-0
libgtest-dev libhtml-parser-perl libhtml-tagset-perl libhwloc-dev
libhwloc-plugins libhwloc5 libibverbs-dev libibverbs1 libicu63 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 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 dh-make gettext-doc libasprintf-dev libgettextpo-dev gfortran-8-doc
libgfortran5-dbg libcoarrays-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 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
gfortran-8 googletest groff-base 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 libgfortran-8-dev libgfortran5 libglib2.0-0
libgtest-dev libhtml-parser-perl libhtml-tagset-perl libhwloc-dev
libhwloc-plugins libhwloc5 libibverbs-dev libibverbs1 libicu63 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 po-debconf python python-markdown
python-minimal python-pkg-resources python2 python2-minimal python2.7
python2.7-minimal sbuild-build-depends-abyss-dummy
0 upgraded, 93 newly installed, 0 to remove and 11 not upgraded.
Need to get 47.9 MB of archives.
After this operation, 297 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-yJrwgL/apt_archive ./ sbuild-build-depends-abyss-dummy 0.invalid.0 [924 B]
Get:2 http://172.17.0.1/private buster-staging/main armhf libbsd0 armhf 0.9.1-1 [104 kB]
Get:3 http://172.17.0.1/private buster-staging/main armhf bsdmainutils armhf 11.1.2 [182 kB]
Get:4 http://172.17.0.1/private buster-staging/main armhf libuchardet0 armhf 0.0.6-3 [62.2 kB]
Get:5 http://172.17.0.1/private buster-staging/main armhf groff-base armhf 1.22.4-2 [782 kB]
Get:6 http://172.17.0.1/private buster-staging/main armhf libpipeline1 armhf 1.5.0-2 [25.1 kB]
Get:7 http://172.17.0.1/private buster-staging/main armhf man-db armhf 2.8.5-1 [1231 kB]
Get:8 http://172.17.0.1/private buster-staging/main armhf libpython2.7-minimal armhf 2.7.15-5 [394 kB]
Get:9 http://172.17.0.1/private buster-staging/main armhf python2.7-minimal armhf 2.7.15-5 [1089 kB]
Get:10 http://172.17.0.1/private buster-staging/main armhf python2-minimal armhf 2.7.15-3 [41.3 kB]
Get:11 http://172.17.0.1/private buster-staging/main armhf python-minimal armhf 2.7.15-3 [20.9 kB]
Get:12 http://172.17.0.1/private buster-staging/main armhf mime-support all 3.61 [37.1 kB]
Get:13 http://172.17.0.1/private buster-staging/main armhf libpython2.7-stdlib armhf 2.7.15-5 [1844 kB]
Get:14 http://172.17.0.1/private buster-staging/main armhf python2.7 armhf 2.7.15-5 [299 kB]
Get:15 http://172.17.0.1/private buster-staging/main armhf libpython2-stdlib armhf 2.7.15-3 [20.7 kB]
Get:16 http://172.17.0.1/private buster-staging/main armhf libpython-stdlib armhf 2.7.15-3 [20.7 kB]
Get:17 http://172.17.0.1/private buster-staging/main armhf python2 armhf 2.7.15-3 [41.5 kB]
Get:18 http://172.17.0.1/private buster-staging/main armhf python armhf 2.7.15-3 [22.7 kB]
Get:19 http://172.17.0.1/private buster-staging/main armhf libmagic-mgc armhf 1:5.34-2 [239 kB]
Get:20 http://172.17.0.1/private buster-staging/main armhf libmagic1 armhf 1:5.34-2 [107 kB]
Get:21 http://172.17.0.1/private buster-staging/main armhf file armhf 1:5.34-2 [65.0 kB]
Get:22 http://172.17.0.1/private buster-staging/main armhf gettext-base armhf 0.19.8.1-9 [117 kB]
Get:23 http://172.17.0.1/private buster-staging/main armhf libevent-2.1-6 armhf 2.1.8-stable-4 [156 kB]
Get:24 http://172.17.0.1/private buster-staging/main armhf libedit2 armhf 3.1-20181209-1 [78.7 kB]
Get:25 http://172.17.0.1/private buster-staging/main armhf openssh-client armhf 1:7.9p1-4 [683 kB]
Get:26 http://172.17.0.1/private buster-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:27 http://172.17.0.1/private buster-staging/main armhf m4 armhf 1.4.18-2 [185 kB]
Get:28 http://172.17.0.1/private buster-staging/main armhf autoconf all 2.69-11 [341 kB]
Get:29 http://172.17.0.1/private buster-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:30 http://172.17.0.1/private buster-staging/main armhf automake all 1:1.16.1-4 [771 kB]
Get:31 http://172.17.0.1/private buster-staging/main armhf autopoint all 0.19.8.1-9 [434 kB]
Get:32 http://172.17.0.1/private buster-staging/main armhf libtool all 2.4.6-6 [547 kB]
Get:33 http://172.17.0.1/private buster-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:34 http://172.17.0.1/private buster-staging/main armhf libarchive-zip-perl all 1.64-1 [96.8 kB]
Get:35 http://172.17.0.1/private buster-staging/main armhf libfile-stripnondeterminism-perl all 1.0.0-1 [19.5 kB]
Get:36 http://172.17.0.1/private buster-staging/main armhf dh-strip-nondeterminism all 1.0.0-1 [12.5 kB]
Get:37 http://172.17.0.1/private buster-staging/main armhf libelf1 armhf 0.175-2 [157 kB]
Get:38 http://172.17.0.1/private buster-staging/main armhf dwz armhf 0.12-3 [66.0 kB]
Get:39 http://172.17.0.1/private buster-staging/main armhf libglib2.0-0 armhf 2.58.2-3 [1076 kB]
Get:40 http://172.17.0.1/private buster-staging/main armhf libicu63 armhf 63.1-5 [7976 kB]
Get:41 http://172.17.0.1/private buster-staging/main armhf libxml2 armhf 2.9.4+dfsg1-7+b1 [570 kB]
Get:42 http://172.17.0.1/private buster-staging/main armhf libcroco3 armhf 0.6.12-3 [132 kB]
Get:43 http://172.17.0.1/private buster-staging/main armhf gettext armhf 0.19.8.1-9 [1219 kB]
Get:44 http://172.17.0.1/private buster-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:45 http://172.17.0.1/private buster-staging/main armhf po-debconf all 1.0.21 [248 kB]
Get:46 http://172.17.0.1/private buster-staging/main armhf debhelper all 12 [1002 kB]
Get:47 http://172.17.0.1/private buster-staging/main armhf libgfortran5 armhf 8.2.0-13+rpi1 [205 kB]
Get:48 http://172.17.0.1/private buster-staging/main armhf libgfortran-8-dev armhf 8.2.0-13+rpi1 [248 kB]
Get:49 http://172.17.0.1/private buster-staging/main armhf gfortran-8 armhf 8.2.0-13+rpi1 [5816 kB]
Get:50 http://172.17.0.1/private buster-staging/main armhf googletest armhf 1.8.0-10.1 [648 kB]
Get:51 http://172.17.0.1/private buster-staging/main armhf libnl-3-200 armhf 3.4.0-1 [55.0 kB]
Get:52 http://172.17.0.1/private buster-staging/main armhf libnl-route-3-200 armhf 3.4.0-1 [132 kB]
Get:53 http://172.17.0.1/private buster-staging/main armhf libibverbs1 armhf 21.0-1 [43.5 kB]
Get:54 http://172.17.0.1/private buster-staging/main armhf ibverbs-providers armhf 21.0-1 [20.1 kB]
Get:55 http://172.17.0.1/private buster-staging/main armhf libboost-system1.67.0 armhf 1.67.0-11 [228 kB]
Get:56 http://172.17.0.1/private buster-staging/main armhf libboost-chrono1.67.0 armhf 1.67.0-11 [231 kB]
Get:57 http://172.17.0.1/private buster-staging/main armhf libboost1.67-dev armhf 1.67.0-11 [8386 kB]
Get:58 http://172.17.0.1/private buster-staging/main armhf libboost-regex1.67.0 armhf 1.67.0-11 [429 kB]
Get:59 http://172.17.0.1/private buster-staging/main armhf libboost-graph1.67.0 armhf 1.67.0-11 [297 kB]
Get:60 http://172.17.0.1/private buster-staging/main armhf libboost-serialization1.67.0 armhf 1.67.0-11 [300 kB]
Get:61 http://172.17.0.1/private buster-staging/main armhf libboost-serialization1.67-dev armhf 1.67.0-11 [364 kB]
Get:62 http://172.17.0.1/private buster-staging/main armhf libboost-timer1.67.0 armhf 1.67.0-11 [229 kB]
Get:63 http://172.17.0.1/private buster-staging/main armhf libboost-test1.67.0 armhf 1.67.0-11 [420 kB]
Get:64 http://172.17.0.1/private buster-staging/main armhf libboost-test1.67-dev armhf 1.67.0-11 [491 kB]
Get:65 http://172.17.0.1/private buster-staging/main armhf libboost-graph1.67-dev armhf 1.67.0-11 [321 kB]
Get:66 http://172.17.0.1/private buster-staging/main armhf libboost-graph-dev armhf 1.67.0.1+b1 [4032 B]
Get:67 http://172.17.0.1/private buster-staging/main armhf libevent-core-2.1-6 armhf 2.1.8-stable-4 [117 kB]
Get:68 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:69 http://172.17.0.1/private buster-staging/main armhf libgtest-dev armhf 1.8.0-10.1 [203 kB]
Get:70 http://172.17.0.1/private buster-staging/main armhf libhtml-tagset-perl all 3.20-3 [12.7 kB]
Get:71 http://172.17.0.1/private buster-staging/main armhf liburi-perl all 1.74-1 [89.4 kB]
Get:72 http://172.17.0.1/private buster-staging/main armhf libhtml-parser-perl armhf 3.72-3+b2 [101 kB]
Get:73 http://172.17.0.1/private buster-staging/main armhf libltdl7 armhf 2.4.6-6 [387 kB]
Get:74 http://172.17.0.1/private buster-staging/main armhf libhwloc5 armhf 1.11.12-1+rpi1 [86.5 kB]
Get:75 http://172.17.0.1/private buster-staging/main armhf libltdl-dev armhf 2.4.6-6 [159 kB]
Get:76 http://172.17.0.1/private buster-staging/main armhf libhwloc-dev armhf 1.11.12-1+rpi1 [142 kB]
Get:77 http://172.17.0.1/private buster-staging/main armhf libpciaccess0 armhf 0.14-1 [51.0 kB]
Get:78 http://172.17.0.1/private buster-staging/main armhf ocl-icd-libopencl1 armhf 2.2.12-2 [35.7 kB]
Get:79 http://172.17.0.1/private buster-staging/main armhf libhwloc-plugins armhf 1.11.12-1+rpi1 [15.9 kB]
Get:80 http://172.17.0.1/private buster-staging/main armhf libnl-3-dev armhf 3.4.0-1 [92.4 kB]
Get:81 http://172.17.0.1/private buster-staging/main armhf libnl-route-3-dev armhf 3.4.0-1 [145 kB]
Get:82 http://172.17.0.1/private buster-staging/main armhf libibverbs-dev armhf 21.0-1 [147 kB]
Get:83 http://172.17.0.1/private buster-staging/main armhf libpmix2 armhf 3.0.2-2+b1 [344 kB]
Get:84 http://172.17.0.1/private buster-staging/main armhf libopenmpi3 armhf 3.1.3-3+rpi1 [1805 kB]
Get:85 http://172.17.0.1/private buster-staging/main armhf openmpi-common all 3.1.3-3+rpi1 [164 kB]
Get:86 http://172.17.0.1/private buster-staging/main armhf openmpi-bin armhf 3.1.3-3+rpi1 [196 kB]
Get:87 http://172.17.0.1/private buster-staging/main armhf libopenmpi-dev armhf 3.1.3-3+rpi1 [963 kB]
Get:88 http://172.17.0.1/private buster-staging/main armhf libsparsehash-dev all 2.0.2-1 [76.9 kB]
Get:89 http://172.17.0.1/private buster-staging/main armhf libsqlite3-dev armhf 3.26.0+fossilbc891ac6b-1 [680 kB]
Get:90 http://172.17.0.1/private buster-staging/main armhf libtext-markdown-perl all 1.000031-2 [34.4 kB]
Get:91 http://172.17.0.1/private buster-staging/main armhf libtext-multimarkdown-perl all 1.000035-1 [29.4 kB]
Get:92 http://172.17.0.1/private buster-staging/main armhf python-pkg-resources all 40.6.2-1 [181 kB]
Get:93 http://172.17.0.1/private buster-staging/main armhf python-markdown all 3.0.1-2 [60.5 kB]
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Setting up libnl-route-3-200:armhf (3.4.0-1) ...
Setting up autoconf (2.69-11) ...
Setting up file (1:5.34-2) ...
Setting up libboost-graph1.67.0:armhf (1.67.0-11) ...
Setting up libhwloc5:armhf (1.11.12-1+rpi1) ...
Setting up libtext-multimarkdown-perl (1.000035-1) ...
Setting up libhwloc-plugins:armhf (1.11.12-1+rpi1) ...
Setting up intltool-debian (0.35.0+20060710.4) ...
Setting up libboost-chrono1.67.0:armhf (1.67.0-11) ...
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 man-db (2.8.5-1) ...
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 (2.7.15-3) ...
Setting up libgfortran-8-dev:armhf (8.2.0-13+rpi1) ...
Setting up openssh-client (1:7.9p1-4) ...
Setting up libtool (2.4.6-6) ...
Setting up libibverbs1:armhf (21.0-1) ...
Setting up libboost-timer1.67.0:armhf (1.67.0-11) ...
Setting up libltdl-dev:armhf (2.4.6-6) ...
Setting up po-debconf (1.0.21) ...
Setting up libhwloc-dev:armhf (1.11.12-1+rpi1) ...
Setting up gfortran-8 (8.2.0-13+rpi1) ...
Setting up libnl-route-3-dev:armhf (3.4.0-1) ...
Setting up libpmix2:armhf (3.0.2-2+b1) ...
Setting up python2 (2.7.15-3) ...
Setting up libpython-stdlib:armhf (2.7.15-3) ...
Setting up ibverbs-providers:armhf (21.0-1) ...
Setting up libibverbs-dev:armhf (21.0-1) ...
Setting up libboost-test1.67.0:armhf (1.67.0-11) ...
Setting up python (2.7.15-3) ...
Setting up libopenmpi3:armhf (3.1.3-3+rpi1) ...
Setting up libboost-test1.67-dev:armhf (1.67.0-11) ...
Setting up python-pkg-resources (40.6.2-1) ...
Setting up openmpi-bin (3.1.3-3+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 (3.0.1-2) ...
Setting up libopenmpi-dev:armhf (3.1.3-3+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 (1.67.0-11) ...
Setting up libboost-graph-dev:armhf (1.67.0.1+b1) ...
Setting up dh-autoreconf (19) ...
Setting up dh-strip-nondeterminism (1.0.0-1) ...
Setting up debhelper (12) ...
Setting up sbuild-build-depends-abyss-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.28-2) ...
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_8.2.0-13+rpi1 gcc-8_8.2.0-13+rpi1 libc6-dev_2.28-2 libstdc++-8-dev_8.2.0-13+rpi1 libstdc++6_8.2.0-13+rpi1 linux-libc-dev_4.18.20-2+rpi1
Package versions: adduser_3.118 apt_1.8.0~alpha3 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_3.5.45 bash_4.4.18-3.1 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_1:2.33-0.2 build-essential_12.5 bzip2_1.0.6-9 ca-certificates_20170717 coreutils_8.30-1 cpio_2.12+dfsg-6 cpp_4:8.2.0-2+rpi1 cpp-8_8.2.0-13+rpi1 dash_0.5.10.2-4 dbus_1.12.12-1 dbus-user-session_1.12.12-1 debconf_1.5.69 debhelper_12 debianutils_4.8.6 dh-autoreconf_19 dh-strip-nondeterminism_1.0.0-1 diffutils_1:3.6-1 dirmngr_2.2.12-1+rpi1 dmsetup_2:1.02.145-4.1+b5 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_2.33-0.2 file_1:5.34-2 findutils_4.6.0+git+20181018-1 g++_4:8.2.0-2+rpi1 g++-8_8.2.0-13+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_8.2.0-13+rpi1 gcc-8-base_8.2.0-13+rpi1 gettext_0.19.8.1-9 gettext-base_0.19.8.1-9 gfortran-8_8.2.0-13+rpi1 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_1.8.0-10.1 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_3.1-3 groff-base_1.22.4-2 gzip_1.9-2.1 hostname_3.21 ibverbs-providers_21.0-1 inetutils-ping_2:1.9.4-5 init-system-helpers_1.56+nmu1 initramfs-tools_0.132 initramfs-tools-core_0.132 intltool-debian_0.35.0+20060710.4 klibc-utils_2.0.4-14+rpi1 kmod_25-2 krb5-locales_1.16.2-1 libacl1_2.2.52-3 libapparmor1_2.13.1-3+b1 libapt-pkg5.0_1.8.0~alpha3 libarchive-zip-perl_1.64-1 libargon2-1_0~20171227-0.1 libasan5_8.2.0-13+rpi1 libassuan0_2.5.2-1 libatomic1_8.2.0-13+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_2.33-0.2 libboost-chrono1.67.0_1.67.0-11 libboost-graph-dev_1.67.0.1+b1 libboost-graph1.67-dev_1.67.0-11 libboost-graph1.67.0_1.67.0-11 libboost-regex1.67.0_1.67.0-11 libboost-serialization1.67-dev_1.67.0-11 libboost-serialization1.67.0_1.67.0-11 libboost-system1.67.0_1.67.0-11 libboost-test1.67-dev_1.67.0-11 libboost-test1.67.0_1.67.0-11 libboost-timer1.67.0_1.67.0-11 libboost1.67-dev_1.67.0-11 libbsd0_0.9.1-1 libbz2-1.0_1.0.6-9 libc-bin_2.28-2 libc-dev-bin_2.28-2 libc6_2.28-2 libc6-dev_2.28-2 libcap-ng0_0.7.9-1+b1 libcap2_1:2.25-1.2 libcc1-0_8.2.0-13+rpi1 libcom-err2_1.44.5-1 libcroco3_0.6.12-3 libcryptsetup12_2:2.0.6-1 libcryptsetup4_2:1.7.5-1 libdb5.3_5.3.28+dfsg1-0.2 libdbus-1-3_1.12.12-1 libdebconfclient0_0.246 libdevmapper1.02.1_2:1.02.145-4.1+b5 libdpkg-perl_1.19.2 libdrm-common_2.4.95-1+rpi1 libdrm2_2.4.95-1+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_2.33-0.2 libffi6_3.2.1-9 libfile-stripnondeterminism-perl_1.0.0-1 libgcc-8-dev_8.2.0-13+rpi1 libgcc1_1:8.2.0-13+rpi1 libgcrypt20_1.8.4-4 libgdbm-compat4_1.18.1-2 libgdbm3_1.8.3-14 libgdbm6_1.18.1-2 libgfortran-8-dev_8.2.0-13+rpi1 libgfortran5_8.2.0-13+rpi1 libglib2.0-0_2.58.2-3 libgmp10_2:6.1.2+dfsg-4 libgnutls30_3.6.5-2+rpi1 libgomp1_8.2.0-13+rpi1 libgpg-error-l10n_1.33-3 libgpg-error0_1.33-3 libgssapi-krb5-2_1.16.2-1 libgtest-dev_1.8.0-10.1 libhogweed4_3.4.1~rc1-1 libhtml-parser-perl_3.72-3+b2 libhtml-tagset-perl_3.20-3 libhwloc-dev_1.11.12-1+rpi1 libhwloc-plugins_1.11.12-1+rpi1 libhwloc5_1.11.12-1+rpi1 libibverbs-dev_21.0-1 libibverbs1_21.0-1 libicu63_63.1-5 libidn11_1.33-2.2 libidn2-0_2.0.5-1 libip4tc0_1.8.2-3 libisl19_0.20-2 libjson-c3_0.12.1-1.3 libk5crypto3_1.16.2-1 libkeyutils1_1.5.9-9.3 libklibc_2.0.4-14+rpi1 libkmod2_25-2 libkrb5-3_1.16.2-1 libkrb5support0_1.16.2-1 libksba8_1.3.5-2 libldap-2.4-2_2.4.47+dfsg-1 libldap-common_2.4.47+dfsg-1 libltdl-dev_2.4.6-6 libltdl7_2.4.6-6 liblz4-1_1.8.2-1+rpi1 liblzma5_5.2.2-1.3 libmagic-mgc_1:5.34-2 libmagic1_1:5.34-2 libmount1_2.33-0.2 libmpc3_1.1.0-1 libmpfr6_4.0.1-2 libncurses5_6.1+20181013-1 libncurses6_6.1+20181013-1 libncursesw5_6.1+20181013-1 libncursesw6_6.1+20181013-1 libnettle6_3.4.1~rc1-1 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_240-2+rpi1 libopenmpi-dev_3.1.3-3+rpi1 libopenmpi3_3.1.3-3+rpi1 libp11-kit0_0.23.14-2 libpam-modules_1.1.8-3.8 libpam-modules-bin_1.1.8-3.8 libpam-runtime_1.1.8-3.8 libpam-systemd_240-2+rpi1 libpam0g_1.1.8-3.8 libpciaccess0_0.14-1 libpcre3_2:8.39-11+rpi1 libperl5.24_5.24.1-7 libperl5.28_5.28.1-3 libpipeline1_1.5.0-2 libplymouth4_0.9.4-1 libpmix2_3.0.2-2+b1 libpng16-16_1.6.34-2+rpi1 libprocps7_2:3.3.15-2 libpython-stdlib_2.7.15-3 libpython2-stdlib_2.7.15-3 libpython2.7-minimal_2.7.15-5 libpython2.7-stdlib_2.7.15-5 libreadline7_7.0-5 libsasl2-2_2.1.27~rc8-1 libsasl2-modules-db_2.1.27~rc8-1 libseccomp2_2.3.3-3+b1 libselinux1_2.8-1+b1 libsemanage-common_2.8-1 libsemanage1_2.8-1+b1 libsepol1_2.8-1 libsigsegv2_2.12-2 libsmartcols1_2.33-0.2 libsparsehash-dev_2.0.2-1 libsqlite3-0_3.26.0+fossilbc891ac6b-1 libsqlite3-dev_3.26.0+fossilbc891ac6b-1 libss2_1.44.5-1 libssl1.1_1.1.1a-1 libstdc++-8-dev_8.2.0-13+rpi1 libstdc++6_8.2.0-13+rpi1 libsystemd0_240-2+rpi1 libtasn1-6_4.13-3 libtext-markdown-perl_1.000031-2 libtext-multimarkdown-perl_1.000035-1 libtinfo5_6.1+20181013-1 libtinfo6_6.1+20181013-1 libtool_2.4.6-6 libubsan1_8.2.0-13+rpi1 libuchardet0_0.0.6-3 libudev1_240-2+rpi1 libunistring2_0.9.10-1 liburi-perl_1.74-1 libustr-1.0-1_1.0.4-6 libuuid1_2.33-0.2 libxml2_2.9.4+dfsg1-7+b1 libzstd1_1.3.5+dfsg-2+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_2.8.5-1 mawk_1.3.3-17 mime-support_3.61 mount_2.33-0.2 multiarch-support_2.28-2 nano_3.2-1 ncurses-base_6.1+20181013-1 ncurses-bin_6.1+20181013-1 netbase_5.5 ocl-icd-libopencl1_2.2.12-2 openmpi-bin_3.1.3-3+rpi1 openmpi-common_3.1.3-3+rpi1 openssh-client_1:7.9p1-4 openssl_1.1.1a-1 passwd_1:4.5-1.1 patch_2.7.6-3 perl_5.28.1-3 perl-base_5.28.1-3 perl-modules-5.24_5.24.1-7 perl-modules-5.28_5.28.1-3 pinentry-curses_1.1.0-1 plymouth_0.9.4-1 po-debconf_1.0.21 procps_2:3.3.15-2 python_2.7.15-3 python-markdown_3.0.1-2 python-minimal_2.7.15-3 python-pkg-resources_40.6.2-1 python2_2.7.15-3 python2-minimal_2.7.15-3 python2.7_2.7.15-5 python2.7-minimal_2.7.15-5 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_240-2+rpi1 systemd-sysv_240-2+rpi1 sysvinit-utils_2.93-2 tar_1.30+dfsg-3+rpi1 tzdata_2018i-1 udev_240-2+rpi1 util-linux_2.33-0.2 xz-utils_5.2.2-1.3 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 Wed Jan 9 20:31:30 2019 UTC
gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv: issuer "tille@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./abyss_2.1.5-3.dsc
dpkg-source: info: extracting abyss in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking abyss_2.1.5.orig.tar.gz
dpkg-source: info: unpacking abyss_2.1.5-3.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
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-24d53753-a85a-420b-b4e9-9db5d4b89fd9
SCHROOT_UID=107
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package abyss
dpkg-buildpackage: info: source version 2.1.5-3
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/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 --libexecdir=\${prefix}/lib/arm-linux-gnueabihf --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-mpi=/usr/lib/openmpi
configure: WARNING: unrecognized options: --disable-maintainer-mode
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... no
checking for mawk... mawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking for gawk... (cached) mawk
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking whether gcc understands -c and -o together... yes
checking whether make supports the include directive... yes (GNU style)
checking dependency style of gcc... none
checking how to run the C preprocessor... gcc -E
checking for g++... g++
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking dependency style of g++... none
checking for ranlib... ranlib
checking for ghc... no
./configure: line 5241: : command not found
checking for pandoc... no
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking dlfcn.h usability... yes
checking dlfcn.h presence... yes
checking for dlfcn.h... yes
checking fcntl.h usability... yes
checking fcntl.h presence... yes
checking for fcntl.h... yes
checking float.h usability... yes
checking float.h presence... yes
checking for float.h... yes
checking limits.h usability... yes
checking limits.h presence... yes
checking for limits.h... yes
checking stddef.h usability... yes
checking stddef.h presence... yes
checking for stddef.h... yes
checking for stdint.h... (cached) yes
checking for stdlib.h... (cached) yes
checking sys/param.h usability... yes
checking sys/param.h presence... yes
checking for sys/param.h... yes
checking for stdbool.h that conforms to C99... yes
checking for _Bool... yes
checking for ANSI C header files... (cached) yes
checking whether byte ordering is bigendian... no
checking for an ANSI C-conforming const... yes
checking for inline... inline
checking for ptrdiff_t... yes
checking for mode_t... yes
checking for pid_t... yes
checking for size_t... yes
checking for ssize_t... yes
checking for int64_t... yes
checking for uint8_t... yes
checking for uint16_t... yes
checking for uint32_t... yes
checking for uint64_t... yes
checking for std::hash<int>... yes
checking for std::tr1::hash<int>... yes
checking for std::tr1::tuple<int>... yes
checking for dup2... yes
checking for gethostname... yes
checking for getopt_long... yes
checking for getpagesize... yes
checking for memset... yes
checking for strdup... yes
checking for strerror... yes
checking for strtoul... yes
checking vfork.h usability... no
checking vfork.h presence... no
checking for vfork.h... no
checking for fork... yes
checking for vfork... yes
checking for working fork... yes
checking for working vfork... (cached) yes
checking for stdlib.h... (cached) yes
checking for GNU libc compatible malloc... yes
checking for working memcmp... yes
checking for stdlib.h... (cached) yes
checking for GNU libc compatible realloc... yes
checking for vprintf... yes
checking for _doprnt... no
checking whether HOST_NAME_MAX is declared... yes
checking build system type... arm-unknown-linux-gnueabihf
checking host system type... arm-unknown-linux-gnueabihf
checking if compiler needs -Werror to reject unknown flags... no
checking for the pthreads library -lpthreads... no
checking whether pthreads work without any flags... no
checking whether pthreads work with -Kthread... no
checking whether pthreads work with -kthread... no
checking for the pthreads library -llthread... no
checking whether pthreads work with -pthread... yes
checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE
checking if more special flags are required for pthreads... no
checking for PTHREAD_PRIO_INHERIT... yes
checking mpi.h usability... no
checking mpi.h presence... no
checking for mpi.h... no
checking for MPI_Init in -lmpi... yes
checking for sqrt in -lm... yes
checking for pow... yes
checking for sqrt... yes
checking for ceilf... yes
checking for dlsym in -ldl... yes
checking how to run the C++ preprocessor... g++ -E
checking functional usability... yes
checking functional presence... yes
checking for functional... yes
checking tr1/functional usability... yes
checking tr1/functional presence... yes
checking for tr1/functional... yes
checking boost/functional/hash.hpp usability... yes
checking boost/functional/hash.hpp presence... yes
checking for boost/functional/hash.hpp... yes
checking boost/property_map/property_map.hpp usability... yes
checking boost/property_map/property_map.hpp presence... yes
checking for boost/property_map/property_map.hpp... yes
checking google/sparse_hash_map usability... yes
checking google/sparse_hash_map presence... yes
checking for google/sparse_hash_map... yes
checking unordered_map usability... yes
checking unordered_map presence... yes
checking for unordered_map... yes
checking tr1/unordered_map usability... yes
checking tr1/unordered_map presence... yes
checking for tr1/unordered_map... yes
checking unordered_set usability... yes
checking unordered_set presence... yes
checking for unordered_set... yes
checking tr1/unordered_set usability... yes
checking tr1/unordered_set presence... yes
checking for tr1/unordered_set... yes
checking boost/unordered_set.hpp usability... yes
checking boost/unordered_set.hpp presence... yes
checking for boost/unordered_set.hpp... yes
checking sqlite3.h usability... yes
checking sqlite3.h presence... yes
checking for sqlite3.h... yes
checking for main in -lsqlite3... yes
checking for g++ option to support OpenMP... -fopenmp
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating ABYSS/Makefile
config.status: creating Align/Makefile
config.status: creating Assembly/Makefile
config.status: creating Common/Makefile
config.status: creating DataLayer/Makefile
config.status: creating FMIndex/Makefile
config.status: creating Graph/Makefile
config.status: creating Parallel/Makefile
config.status: creating bin/Makefile
config.status: creating doc/Makefile
config.status: creating dialign/Makefile
config.status: creating kmerprint/Makefile
config.status: creating AdjList/Makefile
config.status: creating Konnector/Makefile
config.status: creating DAssembler/Makefile
config.status: creating DistanceEst/Makefile
config.status: creating Layout/Makefile
config.status: creating Map/Makefile
config.status: creating Misc/Makefile
config.status: creating Overlap/Makefile
config.status: creating PopBubbles/Makefile
config.status: creating Scaffold/Makefile
config.status: creating SimpleGraph/Makefile
config.status: creating MergePaths/Makefile
config.status: creating KAligner/Makefile
config.status: creating PairedDBG/Makefile
config.status: creating ParseAligns/Makefile
config.status: creating PathOverlap/Makefile
config.status: creating Consensus/Makefile
config.status: creating FilterGraph/Makefile
config.status: creating GapFiller/Makefile
config.status: creating Sealer/Makefile
config.status: creating lib/gtest-1.7.0/Makefile
config.status: creating Unittest/Makefile
config.status: creating LogKmerCount/Makefile
config.status: creating Bloom/Makefile
config.status: creating BloomDBG/Makefile
config.status: creating DataBase/Makefile
config.status: creating lib/bloomfilter/Makefile
config.status: creating lib/nthash/Makefile
config.status: creating config.h
config.status: executing depfiles commands
configure: WARNING: unrecognized options: --disable-maintainer-mode
make[1]: Leaving directory '/<<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'
cp ../bin/abyss-nompi ABYSS-P
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>> -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>> -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>> -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>> -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>> -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>> -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>> -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>> -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>> -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>> -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>> -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>> -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>> -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 -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. -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>> -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>> -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>> -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>> -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 -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 -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>> -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>> -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>> -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
rm -f libdb.a
ar cru libdb.a libdb_a-DB.o ../Common/libcommon.a
ar: `u' modifier ignored since `D' is the default (see `U')
ranlib libdb.a
g++ -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -Wl,-z,relro -Wl,-z,now -o abyss-db-csv abyss_db_csv-DB.o abyss_db_csv-db-csv.o -lsqlite3 -ldl -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/DataBase'
Making all in FMIndex
make[4]: Entering directory '/<<PKGBUILDDIR>>/FMIndex'
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/<<PKGBUILDDIR>> -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>> -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>> -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 -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 -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>> -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>> -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>> -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>> -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>> -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>> -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
museq.c: In function 'main':
museq.c:168:2: warning: implicit declaration of function 'free_diag'; did you mean 'free_diag_col'? [-Wimplicit-function-declaration]
free_diag(adcol.diags[i]);
^~~~~~~~~
free_diag_col
museq.c:278:27: warning: implicit declaration of function 'free_alignment' [-Wimplicit-function-declaration]
if(! para->FAST_MODE) free_alignment(algn);
^~~~~~~~~~~~~~
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,
^~~~~~~~~~~
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,
^~~~~~~~~~~
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>> -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>> -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>> -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>> -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>> -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 -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>> -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>> -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>> -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>> -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>> -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>> -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 -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 -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>> -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 -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 Bloom
make[4]: Entering directory '/<<PKGBUILDDIR>>/Bloom'
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/<<PKGBUILDDIR>> -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 -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>> -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 -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>> -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 -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>> -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 -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>> -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>> -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 -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>> -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>> -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>> -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>> -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 -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 -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>> -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>> -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 -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>> -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 -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>> -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 -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>> -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>> -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>> -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>> -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::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);
^~~~~~~~~~~~~~
/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 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -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: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: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);
^~~~~~~~~~~~~~
/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 ../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 -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 -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 -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>> -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>> -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>> -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 -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 -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 -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>> -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 -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>> -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>> -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>> -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 -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>> -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>> -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>> -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 -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 -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 -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>> -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 -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>> -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 -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>> -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>> -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>> -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>> -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 -Wl,-z,relro -Wl,-z,now -o abyss-longseqdist abyss_longseqdist-longseqdist.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 -Wl,-z,relro -Wl,-z,now -o abyss-junction abyss_junction-junction.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 -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 -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>> -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 -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>> -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 -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>> -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 -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>> -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 -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>> -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 -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>> -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 -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
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make[4]: Nothing to be done for 'all'.
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Making all in lib/nthash
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markdown_py -f README.html README.md
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dh_auto_test -a
make -j4 check VERBOSE=1
make[1]: Entering directory '/<<PKGBUILDDIR>>'
Making check in bin
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Making check in Graph
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Making check in DataBase
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Making check in FMIndex
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Making check in Assembly
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Making check in DAssembler
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Making check in KAligner
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Making check in Layout
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Making check in LogKmerCount
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Making check in Map
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Making check in Overlap
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Making check in PairedDBG
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Making check in ParseAligns
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Making check in SimpleGraph
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Making check in kmerprint
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Making check in FilterGraph
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Making check in GapFiller
make[2]: Entering directory '/<<PKGBUILDDIR>>/GapFiller'
make[2]: Nothing to be done for 'check'.
make[2]: Leaving directory '/<<PKGBUILDDIR>>/GapFiller'
Making check in Sealer
make[2]: Entering directory '/<<PKGBUILDDIR>>/Sealer'
make[2]: Nothing to be done for 'check'.
make[2]: Leaving directory '/<<PKGBUILDDIR>>/Sealer'
Making check in AdjList
make[2]: Entering directory '/<<PKGBUILDDIR>>/AdjList'
make[2]: Nothing to be done for 'check'.
make[2]: Leaving directory '/<<PKGBUILDDIR>>/AdjList'
Making check in lib/bloomfilter
make[2]: Entering directory '/<<PKGBUILDDIR>>/lib/bloomfilter'
make[2]: Nothing to be done for 'check'.
make[2]: Leaving directory '/<<PKGBUILDDIR>>/lib/bloomfilter'
Making check in lib/nthash
make[2]: Entering directory '/<<PKGBUILDDIR>>/lib/nthash'
make[2]: Nothing to be done for 'check'.
make[2]: Leaving directory '/<<PKGBUILDDIR>>/lib/nthash'
Making check in lib/gtest-1.7.0
make[2]: Entering directory '/<<PKGBUILDDIR>>/lib/gtest-1.7.0'
make libgtest.a libgtest_main.a
make[3]: Entering directory '/<<PKGBUILDDIR>>/lib/gtest-1.7.0'
g++ -DHAVE_CONFIG_H -I. -I../.. -I../.. -isystem ../../lib/gtest-1.7.0/include -I/<<PKGBUILDDIR>> -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>> -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>> -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.a
ar cru libgtest.a src/libgtest_a-gtest-all.o
ar: `u' modifier ignored since `D' is the default (see `U')
ranlib libgtest.a
rm -f libgtest_main.a
ar cru libgtest_main.a src/libgtest_main_a-gtest_main.o src/libgtest_main_a-gtest-all.o
ar: `u' modifier ignored since `D' is the default (see `U')
ranlib libgtest_main.a
make[3]: Leaving directory '/<<PKGBUILDDIR>>/lib/gtest-1.7.0'
make[2]: Leaving directory '/<<PKGBUILDDIR>>/lib/gtest-1.7.0'
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>> -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>> -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>> -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>> -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>> -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>> -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>> -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>> -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>> -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>> -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>> -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>> -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>> -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>> -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>> -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>> -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>> -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>> -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>> -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>> -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>> -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>> -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>> -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>> -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>> -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>> -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>> -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>> -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>> -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>> -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>> -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>> -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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_stringutil
PASS: common_kmer
PASS: common_bitutil
PASS: common_sequence
PASS: common_KmerIterator
PASS: common_sam
PASS: BloomFilter
PASS: Konnector_DBGBloom
PASS: Konnector_DBGBloomAlgorithms
PASS: graph_ConstrainedBFSVisitor
PASS: graph_BidirectionalBFS
PASS: graph_AllPathsSearch
PASS: graph_HashGraph
PASS: graph_ConstrainedBidiBFSVisitor
PASS: graph_ExtendPath
PASS: graph_UndirectedGraph
PASS: Konnector_konnector
PASS: graph_DotIO
PASS: PairedDBG_Dinuc
PASS: PairedDBG_KmerPair
PASS: PairedDBG_BranchRecord
PASS: BloomDBG_BloomDBG
PASS: BloomDBG_RollingHashIterator
PASS: BloomDBG_RollingHash
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'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/Unittest'
make[2]: Leaving directory '/<<PKGBUILDDIR>>/Unittest'
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 ABYSS-P '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/bin'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/bin'
Making install in doc
make[3]: Entering directory '/<<PKGBUILDDIR>>/doc'
make[4]: Entering directory '/<<PKGBUILDDIR>>/doc'
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'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/doc'
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
make[3]: Entering directory '/<<PKGBUILDDIR>>/Graph'
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'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/Graph'
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'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/DataLayer'
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'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/DataBase'
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'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/FMIndex'
Making install in Assembly
make[3]: Entering directory '/<<PKGBUILDDIR>>/Assembly'
make[4]: Entering directory '/<<PKGBUILDDIR>>/Assembly'
make[4]: Nothing to be done for 'install-exec-am'.
make[4]: Nothing to be done for 'install-data-am'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Assembly'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/Assembly'
Making install in dialign
make[3]: Entering directory '/<<PKGBUILDDIR>>/dialign'
make[4]: Entering directory '/<<PKGBUILDDIR>>/dialign'
make[4]: Nothing to be done for 'install-exec-am'.
make[4]: Nothing to be done for 'install-data-am'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/dialign'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/dialign'
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'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/Align'
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'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/ABYSS'
Making install in Bloom
make[3]: Entering directory '/<<PKGBUILDDIR>>/Bloom'
make[4]: Entering directory '/<<PKGBUILDDIR>>/Bloom'
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'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/Bloom'
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'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/Konnector'
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'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/Consensus'
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'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/DAssembler'
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'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/DistanceEst'
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'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/KAligner'
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'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/Map'
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'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/MergePaths'
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'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Misc'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/Misc'
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'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/Overlap'
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'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/PairedDBG'
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>>'
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_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
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/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/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-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/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-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-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/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-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/PathConsensus contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/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 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/PopBubbles contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/KAligner contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/Consensus contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/abyss-fixmate contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/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-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-db-csv contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/abyss-align contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/abyss-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-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/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/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-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-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/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-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-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-bloom contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/abyss-map contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/abyss-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/PathOverlap contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/abyss-fac contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/abyss-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/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/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/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-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/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/MergeContigs 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/ParseAligns debian/abyss/usr/lib/abyss/abyss-bloom-dbg debian/abyss/usr/lib/abyss/abyss-mergepairs debian/abyss/usr/lib/abyss/abyss-junction debian/abyss/usr/lib/abyss/DistanceEst debian/abyss/usr/lib/abyss/abyss-overlap debian/abyss/usr/lib/abyss/abyss-layout debian/abyss/usr/bin/DistanceEst debian/abyss/usr/lib/abyss/abyss-tofastq debian/abyss/usr/lib/abyss/PathConsensus debian/abyss/usr/lib/abyss/Overlap debian/abyss/usr/lib/abyss/ABYSS debian/abyss/usr/lib/abyss/MergePaths debian/abyss/usr/lib/abyss/PopBubbles debian/abyss/usr/lib/abyss/KAligner debian/abyss/usr/lib/abyss/Consensus debian/abyss/usr/lib/abyss/abyss-fixmate debian/abyss/usr/lib/abyss/SimpleGraph debian/abyss/usr/lib/abyss/abyss-index debian/abyss/usr/lib/abyss/abyss-db-csv debian/abyss/usr/lib/abyss/abyss-align debian/abyss/usr/lib/abyss/abyss-filtergraph debian/abyss/usr/lib/abyss/abyss-paired-dbg debian/abyss/usr/lib/abyss/logcounter debian/abyss/usr/lib/abyss/AdjList debian/abyss/usr/lib/abyss/abyss-todot debian/abyss/usr/lib/abyss/abyss-gapfill debian/abyss/usr/lib/abyss/DistanceEst-ssq debian/abyss/usr/lib/abyss/abyss-scaffold debian/abyss/usr/lib/abyss/abyss-map-ssq debian/abyss/usr/lib/abyss/abyss-bloom debian/abyss/usr/lib/abyss/abyss-map debian/abyss/usr/lib/abyss/abyss-sealer debian/abyss/usr/lib/abyss/PathOverlap debian/abyss/usr/lib/abyss/abyss-fac debian/abyss/usr/lib/abyss/abyss-gc debian/abyss/usr/bin/abyss-fixmate debian/abyss/usr/lib/abyss/konnector debian/abyss/usr/lib/abyss/abyss-fixmate-ssq debian/abyss/usr/lib/abyss/abyss-longseqdist debian/abyss/usr/lib/abyss/DAssembler debian/abyss/usr/lib/abyss/MergeContigs 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_2.1.5-3_armhf.deb'.
dpkg-deb: building package 'abyss-dbgsym' in '../abyss-dbgsym_2.1.5-3_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian mythic lxc autobuilder 1 <root@raspbian.org> >../abyss_2.1.5-3_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 2019-01-12T05:02:57Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
abyss_2.1.5-3_armhf.changes:
----------------------------
Format: 1.8
Date: Wed, 09 Jan 2019 21:23:43 +0100
Source: abyss
Binary: abyss
Architecture: armhf
Version: 2.1.5-3
Distribution: buster-staging
Urgency: medium
Maintainer: Raspbian mythic lxc autobuilder 1 <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
abyss - de novo, parallel, sequence assembler for short reads
Closes: 918735
Changes:
abyss (2.1.5-3) unstable; urgency=medium
.
* Re-add armel architecture
Closes: #918735
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Checksums-Sha256:
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df11404a41e02f6088338dec6156aef27a81f853a372d2d0c72510c2e1b30d0c 6893 abyss_2.1.5-3_armhf.buildinfo
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Files:
e7a88d5364540cdefca4e7fc6098315c 30180700 debug optional abyss-dbgsym_2.1.5-3_armhf.deb
1534b86581968f8fcb0b604408d6a526 6893 science optional abyss_2.1.5-3_armhf.buildinfo
175273a3314694a3d15f27ba6f68a9fc 2545240 science optional abyss_2.1.5-3_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
abyss-dbgsym_2.1.5-3_armhf.deb
------------------------------
new Debian package, version 2.0.
size 30180700 bytes: control archive=2356 bytes.
1963 bytes, 12 lines control
4240 bytes, 40 lines md5sums
Package: abyss-dbgsym
Source: abyss
Version: 2.1.5-3
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 31028
Depends: abyss (= 2.1.5-3)
Section: debug
Priority: optional
Description: debug symbols for abyss
Build-Ids: 0552cd6b004c76b473b0e89ce5fc29e937790cbd 0b6fbb5e01a68b4ecde74955e826aca3d2873d7f 0f9e82448b740c1d2f4d65f54233246aab5ffa80 165fbb5570ceb8ec821fb7d7b298566998242d3a 1ffe65cd63442a3c96df75fe7ecd9b549d586837 2d945efb053d0338a86f5139ea99f6ac294103f4 35ba130661830c8086357ec94056b38c0ef5544b 377d43c6a5812d36da1d6a28ce20fb26ac7709e3 380b7b399b89b374971cb40182fd26c5b2aa707c 3bed1990270ac035d045d2843b2eb3f7709a9e3f 4195184646ef5d3fcd7028c1bce214b52b4a66ce 43649fee7eba198a05128dcb8ee54aa5e99121d4 4444b201b5e3805f9261d5ab66b79d70af888b1a 456c61410a4e05dd11dbc9c3eba76a372aa9e2e5 46157b59ffd3d8c8e1fa7c7e9f1d7e6cbc06b8e5 4e9c4031b9fb1dda8c4a10fa0f6aa6af5b0d9eb8 6066fca092c0383e74846268eb7d3d254e940245 644133398e02104d59b1be95c160882859a6a18f 651d661abada153fd27f9b65b9fa2ee2499a2c95 6d200e882e948dd11f9625c6a488e88410222d17 81d3d53b3f127b1f4d0a308831b2338bc99197b5 821bd8241954e65375fb541f32fdb38a84ceb11f 839b782aad89f31f3b7c4c582739c163b4e04853 8724928fc53818533c3d8d7351f8395497710d9b 9343b5c042ed5fbafdc5f333ac951c71425484ed 9930b1286a1a1e811b9330659251568dca051ef2 aee07bcb158bd181fbd977e6ba01213536da73a1 b908531612ed7479b80ce9664a6e5ddd1e888445 bc73924e41a716bf693eed260dd03e1acf4d58d8 c1398b31d76d893d74a9e11a910f644969774570 cb47b7bca4932c6bfd95cc2cc73e028dc1fd987a d0df0250de1622cc52dd2b96355c56026c619791 deca42fedfc28f146678c48678fc3e4a58d4f75f e1c1abc654ff37a505b5999471971a3f94747738 e37271bda575bdb5cd7b59262a556c9b74937a3a e44d4851c24587f49b7be4c55623f6d74fd1c797 e7533c8f923e08fd0a0b3d0a031c09084a92a934 ee9cef991f8d01a9312e7f92e933a3be8299f699 f5c6ebc2b7ce31b826b0f71ac47747dd5fb55cd5 fd0ab4e7123fe7b54db2e033ab87e155014f3a20
drwxr-xr-x root/root 0 2019-01-09 20:23 ./
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drwxr-xr-x root/root 0 2019-01-09 20:23 ./usr/share/
drwxr-xr-x root/root 0 2019-01-09 20:23 ./usr/share/doc/
lrwxrwxrwx root/root 0 2019-01-09 20:23 ./usr/share/doc/abyss-dbgsym -> abyss
abyss_2.1.5-3_armhf.deb
-----------------------
new Debian package, version 2.0.
size 2545240 bytes: control archive=2516 bytes.
697 bytes, 15 lines control
4411 bytes, 71 lines md5sums
Package: abyss
Version: 2.1.5-3
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 6988
Depends: make, libc6 (>= 2.28), libgcc1 (>= 1:3.5), libgomp1 (>= 4.9), libsqlite3-0 (>= 3.5.9), libstdc++6 (>= 5.2), perl:any, bsdmainutils
Suggests: 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.
drwxr-xr-x root/root 0 2019-01-09 20:23 ./
drwxr-xr-x root/root 0 2019-01-09 20:23 ./usr/
drwxr-xr-x root/root 0 2019-01-09 20:23 ./usr/bin/
-rwxr-xr-x root/root 120356 2019-01-09 20:23 ./usr/bin/DistanceEst
-rwxr-xr-x root/root 112140 2019-01-09 20:23 ./usr/bin/abyss-fixmate
-rwxr-xr-x root/root 22460 2019-01-09 20:23 ./usr/bin/abyss-pe
drwxr-xr-x root/root 0 2019-01-09 20:23 ./usr/lib/
drwxr-xr-x root/root 0 2019-01-09 20:23 ./usr/lib/abyss/
-rwxr-xr-x root/root 210492 2019-01-09 20:23 ./usr/lib/abyss/ABYSS
-rwxr-xr-x root/root 232 2019-01-09 20:23 ./usr/lib/abyss/ABYSS-P
-rwxr-xr-x root/root 144924 2019-01-09 20:23 ./usr/lib/abyss/AdjList
-rwxr-xr-x root/root 54808 2019-01-09 20:23 ./usr/lib/abyss/Consensus
-rwxr-xr-x root/root 83496 2019-01-09 20:23 ./usr/lib/abyss/DAssembler
-rwxr-xr-x root/root 120356 2019-01-09 20:23 ./usr/lib/abyss/DistanceEst
-rwxr-xr-x root/root 120356 2019-01-09 20:23 ./usr/lib/abyss/DistanceEst-ssq
-rwxr-xr-x root/root 169508 2019-01-09 20:23 ./usr/lib/abyss/KAligner
-rwxr-xr-x root/root 177708 2019-01-09 20:23 ./usr/lib/abyss/MergeContigs
-rwxr-xr-x root/root 153112 2019-01-09 20:23 ./usr/lib/abyss/MergePaths
-rwxr-xr-x root/root 144936 2019-01-09 20:23 ./usr/lib/abyss/Overlap
-rwxr-xr-x root/root 79368 2019-01-09 20:23 ./usr/lib/abyss/ParseAligns
-rwxr-xr-x root/root 284200 2019-01-09 20:23 ./usr/lib/abyss/PathConsensus
-rwxr-xr-x root/root 140808 2019-01-09 20:23 ./usr/lib/abyss/PathOverlap
-rwxr-xr-x root/root 153128 2019-01-09 20:23 ./usr/lib/abyss/PopBubbles
-rwxr-xr-x root/root 144932 2019-01-09 20:23 ./usr/lib/abyss/SimpleGraph
-rwxr-xr-x root/root 153112 2019-01-09 20:23 ./usr/lib/abyss/abyss-align
-rwxr-xr-x root/root 157264 2019-01-09 20:23 ./usr/lib/abyss/abyss-bloom
-rwxr-xr-x root/root 190004 2019-01-09 20:23 ./usr/lib/abyss/abyss-bloom-dbg
-rwxr-xr-x root/root 6491 2019-01-09 20:23 ./usr/lib/abyss/abyss-bloom-dist.mk
-rwxr-xr-x root/root 1135 2019-01-09 20:23 ./usr/lib/abyss/abyss-bowtie
-rwxr-xr-x root/root 1192 2019-01-09 20:23 ./usr/lib/abyss/abyss-bowtie2
-rwxr-xr-x root/root 1208 2019-01-09 20:23 ./usr/lib/abyss/abyss-bwa
-rwxr-xr-x root/root 1454 2019-01-09 20:23 ./usr/lib/abyss/abyss-bwamem
-rwxr-xr-x root/root 1362 2019-01-09 20:23 ./usr/lib/abyss/abyss-bwasw
-rwxr-xr-x root/root 50696 2019-01-09 20:23 ./usr/lib/abyss/abyss-db-csv
-rwxr-xr-x root/root 703 2019-01-09 20:23 ./usr/lib/abyss/abyss-db-txt
-rwxr-xr-x root/root 2739 2019-01-09 20:23 ./usr/lib/abyss/abyss-dida
-rwxr-xr-x root/root 63008 2019-01-09 20:23 ./usr/lib/abyss/abyss-fac
-rwxr-xr-x root/root 2058 2019-01-09 20:23 ./usr/lib/abyss/abyss-fatoagp
-rwxr-xr-x root/root 136740 2019-01-09 20:23 ./usr/lib/abyss/abyss-filtergraph
-rwxr-xr-x root/root 112140 2019-01-09 20:23 ./usr/lib/abyss/abyss-fixmate
-rwxr-xr-x root/root 112140 2019-01-09 20:23 ./usr/lib/abyss/abyss-fixmate-ssq
-rwxr-xr-x root/root 75304 2019-01-09 20:23 ./usr/lib/abyss/abyss-gapfill
-rwxr-xr-x root/root 83464 2019-01-09 20:23 ./usr/lib/abyss/abyss-gc
-rwxr-xr-x root/root 83472 2019-01-09 20:23 ./usr/lib/abyss/abyss-index
-rwxr-xr-x root/root 87564 2019-01-09 20:23 ./usr/lib/abyss/abyss-junction
-rwxr-xr-x root/root 39 2019-01-09 20:23 ./usr/lib/abyss/abyss-kaligner
-rwxr-xr-x root/root 95760 2019-01-09 20:23 ./usr/lib/abyss/abyss-layout
-rwxr-xr-x root/root 83476 2019-01-09 20:23 ./usr/lib/abyss/abyss-longseqdist
-rwxr-xr-x root/root 149020 2019-01-09 20:23 ./usr/lib/abyss/abyss-map
-rwxr-xr-x root/root 153116 2019-01-09 20:23 ./usr/lib/abyss/abyss-map-ssq
-rwxr-xr-x root/root 58928 2019-01-09 20:23 ./usr/lib/abyss/abyss-mergepairs
-rwxr-xr-x root/root 169520 2019-01-09 20:23 ./usr/lib/abyss/abyss-overlap
-rwxr-xr-x root/root 218688 2019-01-09 20:23 ./usr/lib/abyss/abyss-paired-dbg
-rwxr-xr-x root/root 22460 2019-01-09 20:23 ./usr/lib/abyss/abyss-pe
-rwxr-xr-x root/root 4501 2019-01-09 20:23 ./usr/lib/abyss/abyss-samtoafg
-rwxr-xr-x root/root 185888 2019-01-09 20:23 ./usr/lib/abyss/abyss-scaffold
-rwxr-xr-x root/root 161372 2019-01-09 20:23 ./usr/lib/abyss/abyss-sealer
-rwxr-xr-x root/root 671 2019-01-09 20:23 ./usr/lib/abyss/abyss-stack-size
-rwxr-xr-x root/root 209 2019-01-09 20:23 ./usr/lib/abyss/abyss-tabtomd
-rwxr-xr-x root/root 128524 2019-01-09 20:23 ./usr/lib/abyss/abyss-todot
-rwxr-xr-x root/root 50716 2019-01-09 20:23 ./usr/lib/abyss/abyss-tofastq
-rwxr-xr-x root/root 177760 2019-01-09 20:23 ./usr/lib/abyss/konnector
-rwxr-xr-x root/root 63008 2019-01-09 20:23 ./usr/lib/abyss/logcounter
drwxr-xr-x root/root 0 2019-01-09 20:23 ./usr/share/
drwxr-xr-x root/root 0 2019-01-09 20:23 ./usr/share/doc/
drwxr-xr-x root/root 0 2019-01-09 20:23 ./usr/share/doc/abyss/
-rw-r--r-- root/root 30189 2019-01-09 20:23 ./usr/share/doc/abyss/README.html
-rw-r--r-- root/root 8866 2018-12-05 00:05 ./usr/share/doc/abyss/README.md.gz
-rw-r--r-- root/root 182 2019-01-09 20:23 ./usr/share/doc/abyss/README.test
-rw-r--r-- root/root 2558 2019-01-09 20:23 ./usr/share/doc/abyss/changelog.Debian.gz
-rw-r--r-- root/root 15369 2018-12-05 00:05 ./usr/share/doc/abyss/changelog.gz
-rw-r--r-- root/root 6120 2019-01-09 20:23 ./usr/share/doc/abyss/copyright
-rw-r--r-- root/root 66778 2018-12-05 00:05 ./usr/share/doc/abyss/flowchart.pdf.gz
-rw-r--r-- root/root 299 2019-01-09 20:23 ./usr/share/doc/abyss/run-unit-test
drwxr-xr-x root/root 0 2019-01-09 20:23 ./usr/share/doc/abyss/test-data/
-rw-r--r-- root/root 743013 2019-01-09 20:23 ./usr/share/doc/abyss/test-data/reads1.fastq.gz
-rw-r--r-- root/root 743377 2019-01-09 20:23 ./usr/share/doc/abyss/test-data/reads2.fastq.gz
drwxr-xr-x root/root 0 2019-01-09 20:23 ./usr/share/man/
drwxr-xr-x root/root 0 2019-01-09 20:23 ./usr/share/man/man1/
-rw-r--r-- root/root 1200 2019-01-09 20:23 ./usr/share/man/man1/ABYSS.1.gz
-rw-r--r-- root/root 3565 2019-01-09 20:23 ./usr/share/man/man1/abyss-pe.1.gz
-rw-r--r-- root/root 407 2019-01-09 20:23 ./usr/share/man/man1/abyss-tofastq.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: 592636
Build-Time: 792
Distribution: buster-staging
Host Architecture: armhf
Install-Time: 419
Job: abyss_2.1.5-3
Machine Architecture: armhf
Package: abyss
Package-Time: 1227
Source-Version: 2.1.5-3
Space: 592636
Status: successful
Version: 2.1.5-3
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Finished at 2019-01-12T05:02:57Z
Build needed 00:20:27, 592636k disk space