abyss →
2.0.3-1 →
armhf → 2018-03-26 05:37:10
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on testwandboard
+==============================================================================+
| abyss 2.0.3-1 (armhf) Mon, 26 Mar 2018 04:43:26 +0000 |
+==============================================================================+
Package: abyss
Version: 2.0.3-1
Source Version: 2.0.3-1
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-28ed7caf-ecd6-4674-8a50-3da6ebc1af3f' 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 [10.7 MB]
Get:3 http://172.17.0.1/private buster-staging/main armhf Packages [12.4 MB]
Fetched 23.1 MB in 29s (784 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://anonscm.debian.org/git/debian-med/abyss.git
Please use:
git clone https://anonscm.debian.org/git/debian-med/abyss.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 1808 kB of source archives.
Get:1 http://172.17.0.1/private buster-staging/main abyss 2.0.3-1 (dsc) [2098 B]
Get:2 http://172.17.0.1/private buster-staging/main abyss 2.0.3-1 (tar) [1049 kB]
Get:3 http://172.17.0.1/private buster-staging/main abyss 2.0.3-1 (diff) [757 kB]
Fetched 1808 kB in 1s (2806 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/abyss-6DxsQZ/abyss-2.0.3' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/abyss-6DxsQZ' 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-YvQu8z/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-YvQu8z/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-YvQu8z/gpg/trustdb.gpg: trustdb created
gpg: key 35506D9A48F77B2E: 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 35506D9A48F77B2E: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 35506D9A48F77B2E: 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-YvQu8z/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-YvQu8z/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-YvQu8z/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-YvQu8z/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-YvQu8z/apt_archive ./ Packages [430 B]
Fetched 2106 B in 1s (3020 B/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 libexpat1
libnss-systemd libpam-systemd libsasl2-modules 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 27 not upgraded.
Need to get 852 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-YvQu8z/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 852 B in 0s (13.8 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 15694 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)
+------------------------------------------------------------------------------+
| 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-YvQu8z/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-YvQu8z/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-YvQu8z/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-YvQu8z/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-YvQu8z/apt_archive ./ Sources [560 B]
Get:5 copy:/<<BUILDDIR>>/resolver-YvQu8z/apt_archive ./ Packages [637 B]
Fetched 2530 B in 1s (3228 B/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 libnss-systemd
libpam-systemd libsasl2-modules 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 file gettext gettext-base googletest
groff-base ibverbs-providers intltool-debian libarchive-zip-perl
libboost-chrono1.62.0 libboost-graph-dev libboost-graph1.62-dev
libboost-graph1.62.0 libboost-regex1.62.0 libboost-serialization1.62-dev
libboost-serialization1.62.0 libboost-system1.62.0 libboost-test1.62-dev
libboost-test1.62.0 libboost-timer1.62.0 libboost1.62-dev libbsd0 libcroco3
libfile-stripnondeterminism-perl libgfortran4 libglib2.0-0 libgtest-dev
libhtml-parser-perl libhtml-tagset-perl libhwloc-dev libhwloc-plugins
libhwloc5 libibverbs-dev libibverbs1 libicu57 libltdl-dev libltdl7
libmagic-mgc libmagic1 libnl-3-200 libnl-route-3-200 libopenmpi-dev
libopenmpi2 libpciaccess0 libpipeline1 libpython-stdlib libpython2.7-minimal
libpython2.7-stdlib libsigsegv2 libsparsehash-dev libsqlite3-0
libsqlite3-dev libtext-markdown-perl libtext-multimarkdown-perl
libtimedate-perl libtool liburi-perl libxml2 m4 man-db mime-support
ocl-icd-libopencl1 openmpi-common po-debconf python python-markdown
python-minimal python2.7 python2.7-minimal
Suggested packages:
autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
vacation dh-make dwz gettext-doc libasprintf-dev libgettextpo-dev groff
graphviz libboost1.62-doc libboost-atomic1.62-dev libboost-chrono1.62-dev
libboost-context1.62-dev libboost-coroutine1.62-dev
libboost-date-time1.62-dev libboost-exception1.62-dev libboost-fiber1.62-dev
libboost-filesystem1.62-dev libboost-graph-parallel1.62-dev
libboost-iostreams1.62-dev libboost-locale1.62-dev libboost-log1.62-dev
libboost-math1.62-dev libboost-mpi1.62-dev libboost-mpi-python1.62-dev
libboost-program-options1.62-dev libboost-python1.62-dev
libboost-random1.62-dev libboost-regex1.62-dev libboost-signals1.62-dev
libboost-system1.62-dev libboost-thread1.62-dev libboost-timer1.62-dev
libboost-type-erasure1.62-dev libboost-wave1.62-dev libboost1.62-tools-dev
libmpfrc++-dev libntl-dev libdata-dump-perl libhwloc-contrib-plugins
libtool-doc openmpi-doc pciutils sqlite3-doc gfortran | fortran95-compiler
gcj-jdk libwww-perl m4-doc apparmor less www-browser opencl-icd
libmail-box-perl python-doc python-tk python-markdown-doc python2.7-doc
binfmt-support
Recommended packages:
curl | wget | lynx-cur libarchive-cpio-perl libglib2.0-data shared-mime-info
xdg-user-dirs libhttp-message-perl openmpi-bin 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 file gettext gettext-base googletest
groff-base ibverbs-providers intltool-debian libarchive-zip-perl
libboost-chrono1.62.0 libboost-graph-dev libboost-graph1.62-dev
libboost-graph1.62.0 libboost-regex1.62.0 libboost-serialization1.62-dev
libboost-serialization1.62.0 libboost-system1.62.0 libboost-test1.62-dev
libboost-test1.62.0 libboost-timer1.62.0 libboost1.62-dev libbsd0 libcroco3
libfile-stripnondeterminism-perl libgfortran4 libglib2.0-0 libgtest-dev
libhtml-parser-perl libhtml-tagset-perl libhwloc-dev libhwloc-plugins
libhwloc5 libibverbs-dev libibverbs1 libicu57 libltdl-dev libltdl7
libmagic-mgc libmagic1 libnl-3-200 libnl-route-3-200 libopenmpi-dev
libopenmpi2 libpciaccess0 libpipeline1 libpython-stdlib libpython2.7-minimal
libpython2.7-stdlib libsigsegv2 libsparsehash-dev libsqlite3-dev
libtext-markdown-perl libtext-multimarkdown-perl libtimedate-perl libtool
liburi-perl libxml2 m4 man-db mime-support ocl-icd-libopencl1 openmpi-common
po-debconf python python-markdown python-minimal python2.7 python2.7-minimal
sbuild-build-depends-abyss-dummy
The following packages will be upgraded:
libsqlite3-0
1 upgraded, 76 newly installed, 0 to remove and 26 not upgraded.
Need to get 18.8 MB/37.6 MB of archives.
After this operation, 233 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-YvQu8z/apt_archive ./ sbuild-build-depends-abyss-dummy 0.invalid.0 [924 B]
Get:2 http://172.17.0.1/private buster-staging/main armhf bsdmainutils armhf 11.1.2 [182 kB]
Get:3 http://172.17.0.1/private buster-staging/main armhf groff-base armhf 1.22.3-10 [1005 kB]
Get:4 http://172.17.0.1/private buster-staging/main armhf libpipeline1 armhf 1.5.0-1 [24.6 kB]
Get:5 http://172.17.0.1/private buster-staging/main armhf man-db armhf 2.8.2-1 [1145 kB]
Get:6 http://172.17.0.1/private buster-staging/main armhf libpython2.7-minimal armhf 2.7.14-7 [393 kB]
Get:7 http://172.17.0.1/private buster-staging/main armhf python2.7-minimal armhf 2.7.14-7 [1077 kB]
Get:8 http://172.17.0.1/private buster-staging/main armhf python-minimal armhf 2.7.14-4 [41.0 kB]
Get:9 http://172.17.0.1/private buster-staging/main armhf libsqlite3-0 armhf 3.22.0-2 [511 kB]
Get:10 http://172.17.0.1/private buster-staging/main armhf libpython2.7-stdlib armhf 2.7.14-7 [1842 kB]
Get:11 http://172.17.0.1/private buster-staging/main armhf python2.7 armhf 2.7.14-7 [293 kB]
Get:12 http://172.17.0.1/private buster-staging/main armhf libpython-stdlib armhf 2.7.14-4 [20.4 kB]
Get:13 http://172.17.0.1/private buster-staging/main armhf python armhf 2.7.14-4 [155 kB]
Get:14 http://172.17.0.1/private buster-staging/main armhf gettext-base armhf 0.19.8.1-4 [117 kB]
Get:15 http://172.17.0.1/private buster-staging/main armhf libsigsegv2 armhf 2.12-1 [32.2 kB]
Get:16 http://172.17.0.1/private buster-staging/main armhf m4 armhf 1.4.18-1 [185 kB]
Get:17 http://172.17.0.1/private buster-staging/main armhf autoconf all 2.69-11 [341 kB]
Get:18 http://172.17.0.1/private buster-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:19 http://172.17.0.1/private buster-staging/main armhf automake all 1:1.15.1-3 [736 kB]
Get:20 http://172.17.0.1/private buster-staging/main armhf autopoint all 0.19.8.1-4 [434 kB]
Get:21 http://172.17.0.1/private buster-staging/main armhf libtool all 2.4.6-2 [545 kB]
Get:22 http://172.17.0.1/private buster-staging/main armhf dh-autoreconf all 16 [16.3 kB]
Get:23 http://172.17.0.1/private buster-staging/main armhf libarchive-zip-perl all 1.60-1 [95.6 kB]
Get:24 http://172.17.0.1/private buster-staging/main armhf libfile-stripnondeterminism-perl all 0.040-1 [18.4 kB]
Get:25 http://172.17.0.1/private buster-staging/main armhf libtimedate-perl all 2.3000-2 [42.2 kB]
Get:26 http://172.17.0.1/private buster-staging/main armhf dh-strip-nondeterminism all 0.040-1 [11.8 kB]
Get:27 http://172.17.0.1/private buster-staging/main armhf libglib2.0-0 armhf 2.56.0-2 [2750 kB]
Get:28 http://172.17.0.1/private buster-staging/main armhf gettext armhf 0.19.8.1-4 [1218 kB]
Get:29 http://172.17.0.1/private buster-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:30 http://172.17.0.1/private buster-staging/main armhf po-debconf all 1.0.20 [247 kB]
Get:31 http://172.17.0.1/private buster-staging/main armhf debhelper all 11.1.5 [1007 kB]
Get:32 http://172.17.0.1/private buster-staging/main armhf googletest armhf 1.8.0-6 [653 kB]
Get:33 http://172.17.0.1/private buster-staging/main armhf libibverbs1 armhf 17.1-1 [38.9 kB]
Get:34 http://172.17.0.1/private buster-staging/main armhf ibverbs-providers armhf 17.1-1 [19.3 kB]
Get:35 http://172.17.0.1/private buster-staging/main armhf libboost-graph1.62.0 armhf 1.62.0+dfsg-5 [102 kB]
Get:36 http://172.17.0.1/private buster-staging/main armhf libboost-timer1.62.0 armhf 1.62.0+dfsg-5 [34.4 kB]
Get:37 http://172.17.0.1/private buster-staging/main armhf libboost-test1.62.0 armhf 1.62.0+dfsg-5 [223 kB]
Get:38 http://172.17.0.1/private buster-staging/main armhf libboost-test1.62-dev armhf 1.62.0+dfsg-5 [288 kB]
Get:39 http://172.17.0.1/private buster-staging/main armhf libboost-graph1.62-dev armhf 1.62.0+dfsg-5 [122 kB]
Get:40 http://172.17.0.1/private buster-staging/main armhf libboost-graph-dev armhf 1.62.0.1+b8 [3800 B]
Get:41 http://172.17.0.1/private buster-staging/main armhf libgfortran4 armhf 7.3.0-11 [191 kB]
Get:42 http://172.17.0.1/private buster-staging/main armhf libhtml-tagset-perl all 3.20-3 [12.7 kB]
Get:43 http://172.17.0.1/private buster-staging/main armhf liburi-perl all 1.73-1 [89.3 kB]
Get:44 http://172.17.0.1/private buster-staging/main armhf libhtml-parser-perl armhf 3.72-3+b1 [101 kB]
Get:45 http://172.17.0.1/private buster-staging/main armhf libltdl-dev armhf 2.4.6-2 [159 kB]
Get:46 http://172.17.0.1/private buster-staging/main armhf libhwloc-dev armhf 1.11.9-1+rpi1 [140 kB]
Get:47 http://172.17.0.1/private buster-staging/main armhf libpciaccess0 armhf 0.14-1 [51.0 kB]
Get:48 http://172.17.0.1/private buster-staging/main armhf libibverbs-dev armhf 17.1-1 [89.8 kB]
Get:49 http://172.17.0.1/private buster-staging/main armhf libsparsehash-dev all 2.0.2-1 [76.9 kB]
Get:50 http://172.17.0.1/private buster-staging/main armhf libsqlite3-dev armhf 3.22.0-2 [638 kB]
Get:51 http://172.17.0.1/private buster-staging/main armhf libtext-markdown-perl all 1.000031-2 [34.4 kB]
Get:52 http://172.17.0.1/private buster-staging/main armhf libtext-multimarkdown-perl all 1.000035-1 [29.4 kB]
Get:53 http://172.17.0.1/private buster-staging/main armhf python-markdown all 2.6.9-1 [57.9 kB]
Get:54 http://172.17.0.1/private buster-staging/main armhf libgtest-dev armhf 1.8.0-6 [5110 B]
Get:55 http://172.17.0.1/private buster-staging/main armhf libopenmpi-dev armhf 2.1.1-8+rpi1 [1024 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Processing triggers for libc-bin (2.27-2+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.8.0-0.bpo.2-armmp armhf (armv7l)
Toolchain package versions: binutils_2.30-7+rpi1 dpkg-dev_1.19.0.5 g++-7_7.3.0-11 gcc-7_7.3.0-11 libc6-dev_2.27-2+rpi1 libstdc++-7-dev_7.3.0-11 libstdc++6_8-20180218-1+rpi1 linux-libc-dev_4.15.4-1+rpi1
Package versions: adduser_3.117 apt_1.6~beta1 autoconf_2.69-11 automake_1:1.15.1-3 autopoint_0.19.8.1-4 autotools-dev_20180224.1 base-files_10.1+rpi1 base-passwd_3.5.44 bash_4.4.18-1.1 binutils_2.30-7+rpi1 binutils-arm-linux-gnueabihf_2.30-7+rpi1 binutils-common_2.30-7+rpi1 bsdmainutils_11.1.2 bsdutils_1:2.31.1-0.4 build-essential_12.4 bzip2_1.0.6-8.1 ca-certificates_20170717 coreutils_8.28-1 cpio_2.12+dfsg-6 cpp_4:7.2.0-1d1 cpp-7_7.3.0-11 dash_0.5.8-2.10 dbus_1.12.6-2 dbus-user-session_1.12.6-2 debconf_1.5.66 debhelper_11.1.5 debianutils_4.8.4 dh-autoreconf_16 dh-strip-nondeterminism_0.040-1 diffutils_1:3.6-1 dirmngr_2.2.5-1 dmsetup_2:1.02.145-4.1 dpkg_1.19.0.5 dpkg-dev_1.19.0.5 e2fslibs_1.44.0-1 e2fsprogs_1.44.0-1 e2fsprogs-l10n_1.44.0-1 fakeroot_1.22-2 fdisk_2.31.1-0.4 file_1:5.32-2 findutils_4.6.0+git+20170828-2 g++_4:7.2.0-1d1 g++-7_7.3.0-11 gcc_4:7.2.0-1d1 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 gcc-5-base_5.5.0-8 gcc-7_7.3.0-11 gcc-7-base_7.3.0-11 gcc-8-base_8-20180218-1+rpi1 gettext_0.19.8.1-4 gettext-base_0.19.8.1-4 gnupg_2.2.5-1 gnupg-agent_2.2.5-1 gnupg-l10n_2.2.5-1 gnupg-utils_2.2.5-1 googletest_1.8.0-6 gpg_2.2.5-1 gpg-agent_2.2.5-1 gpg-wks-client_2.2.5-1 gpg-wks-server_2.2.5-1 gpgconf_2.2.5-1 gpgsm_2.2.5-1 gpgv_2.2.5-1 grep_3.1-2 groff-base_1.22.3-10 gzip_1.6-5 hostname_3.20 ibverbs-providers_17.1-1 init-system-helpers_1.51 initramfs-tools_0.130 initramfs-tools-core_0.130 intltool-debian_0.35.0+20060710.4 klibc-utils_2.0.4-11+rpi1 kmod_25-1 libacl1_2.2.52-3 libapparmor1_2.12-3 libapt-pkg5.0_1.6~beta1 libarchive-zip-perl_1.60-1 libargon2-0_0~20161029-1.1 libasan4_7.3.0-11 libassuan0_2.5.1-2 libatomic1_8-20180218-1+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.8.2-1 libaudit1_1:2.8.2-1 libbinutils_2.30-7+rpi1 libblkid1_2.31.1-0.4 libboost-chrono1.62.0_1.62.0+dfsg-5 libboost-graph-dev_1.62.0.1+b8 libboost-graph1.62-dev_1.62.0+dfsg-5 libboost-graph1.62.0_1.62.0+dfsg-5 libboost-regex1.62.0_1.62.0+dfsg-5 libboost-serialization1.62-dev_1.62.0+dfsg-5 libboost-serialization1.62.0_1.62.0+dfsg-5 libboost-system1.62.0_1.62.0+dfsg-5 libboost-test1.62-dev_1.62.0+dfsg-5 libboost-test1.62.0_1.62.0+dfsg-5 libboost-timer1.62.0_1.62.0+dfsg-5 libboost1.62-dev_1.62.0+dfsg-5 libbsd0_0.8.7-1 libbz2-1.0_1.0.6-8.1 libc-bin_2.27-2+rpi1 libc-dev-bin_2.27-2+rpi1 libc6_2.27-2+rpi1 libc6-dev_2.27-2+rpi1 libcap-ng0_0.7.7-3.1+b1 libcap2_1:2.25-1.2 libcc1-0_8-20180218-1+rpi1 libcilkrts5_7.3.0-11 libcom-err2_1.44.0-1 libcroco3_0.6.12-2 libcryptsetup12_2:2.0.1-1 libcryptsetup4_2:1.7.5-1 libdb5.3_5.3.28-13.1 libdbus-1-3_1.12.6-2 libdebconfclient0_0.241 libdevmapper1.02.1_2:1.02.145-4.1 libdpkg-perl_1.19.0.5 libdrm-common_2.4.90-1+rpi1 libdrm2_2.4.90-1+rpi1 libexpat1_2.2.5-3 libext2fs2_1.44.0-1 libfakeroot_1.22-2 libfdisk1_2.31.1-0.4 libffi6_3.2.1-8 libfile-stripnondeterminism-perl_0.040-1 libgcc-7-dev_7.3.0-11 libgcc1_1:8-20180218-1+rpi1 libgcrypt20_1.8.1-4 libgdbm-compat4_1.14.1-4 libgdbm3_1.8.3-14 libgdbm5_1.14.1-4 libgfortran4_7.3.0-11 libglib2.0-0_2.56.0-2 libgmp10_2:6.1.2+dfsg-3 libgnutls30_3.5.18-1 libgomp1_8-20180218-1+rpi1 libgpg-error0_1.27-6 libgtest-dev_1.8.0-6 libhogweed4_3.4-1 libhtml-parser-perl_3.72-3+b1 libhtml-tagset-perl_3.20-3 libhwloc-dev_1.11.9-1+rpi1 libhwloc-plugins_1.11.9-1+rpi1 libhwloc5_1.11.9-1+rpi1 libibverbs-dev_17.1-1 libibverbs1_17.1-1 libicu57_57.1-9 libidn11_1.33-2.1 libidn2-0_2.0.4-1.1 libip4tc0_1.6.2-1 libisl15_0.18-1 libjson-c3_0.12.1-1.3 libklibc_2.0.4-11+rpi1 libkmod2_25-1 libksba8_1.3.5-2 libldap-2.4-2_2.4.45+dfsg-1 libldap-common_2.4.45+dfsg-1 liblocale-gettext-perl_1.07-3+b2 libltdl-dev_2.4.6-2 libltdl7_2.4.6-2 liblz4-1_0.0~r131-2 liblzma5_5.2.2-1.3 libmagic-mgc_1:5.32-2 libmagic1_1:5.32-2 libmount1_2.31.1-0.4 libmpc3_1.1.0-1 libmpfr6_4.0.1-1 libncurses5_6.1-1 libncursesw5_6.1-1 libnettle6_3.4-1 libnl-3-200_3.2.27-2 libnl-route-3-200_3.2.27-2 libnpth0_1.5-3 libnss-systemd_238-2 libopenmpi-dev_2.1.1-8+rpi1 libopenmpi2_2.1.1-8+rpi1 libp11-kit0_0.23.9-2 libpam-modules_1.1.8-3.7 libpam-modules-bin_1.1.8-3.7 libpam-runtime_1.1.8-3.7 libpam-systemd_238-2 libpam0g_1.1.8-3.7 libpciaccess0_0.14-1 libpcre3_2:8.39-9 libperl5.24_5.24.1-4 libperl5.26_5.26.1-5 libpipeline1_1.5.0-1 libplymouth4_0.9.3-2 libpng16-16_1.6.34-1 libprocps6_2:3.3.12-4 libpython-stdlib_2.7.14-4 libpython2.7-minimal_2.7.14-7 libpython2.7-stdlib_2.7.14-7 libreadline7_7.0-3 libsasl2-2_2.1.27~101-g0780600+dfsg-3 libsasl2-modules_2.1.27~101-g0780600+dfsg-3 libsasl2-modules-db_2.1.27~101-g0780600+dfsg-3 libseccomp2_2.3.1-2.1 libselinux1_2.7-2 libsemanage-common_2.7-2 libsemanage1_2.7-2 libsepol1_2.7-1 libsigsegv2_2.12-1 libsmartcols1_2.31.1-0.4 libsparsehash-dev_2.0.2-1 libsqlite3-0_3.22.0-2 libsqlite3-dev_3.22.0-2 libss2_1.44.0-1 libssl1.1_1.1.0g-2 libstdc++-7-dev_7.3.0-11 libstdc++6_8-20180218-1+rpi1 libsystemd0_238-2 libtasn1-6_4.13-2 libtext-charwidth-perl_0.04-7.1 libtext-iconv-perl_1.7-5+b9 libtext-markdown-perl_1.000031-2 libtext-multimarkdown-perl_1.000035-1 libtext-wrapi18n-perl_0.06-7.1 libtimedate-perl_2.3000-2 libtinfo5_6.1-1 libtool_2.4.6-2 libubsan0_7.3.0-11 libudev1_238-2 libunistring2_0.9.8-1 liburi-perl_1.73-1 libustr-1.0-1_1.0.4-6 libuuid1_2.31.1-0.4 libxml2_2.9.4+dfsg1-6.1 linux-base_4.5 linux-libc-dev_4.15.4-1+rpi1 login_1:4.5-1 lsb-base_9.20170808+rpi1 m4_1.4.18-1 make_4.1-9.1 makedev_2.3.1-93 man-db_2.8.2-1 mawk_1.3.3-17 mime-support_3.60 mount_2.31.1-0.4 multiarch-support_2.27-2+rpi1 nano_2.9.4-1 ncurses-base_6.1-1 ncurses-bin_6.1-1 ocl-icd-libopencl1_2.2.12-1 openmpi-common_2.1.1-8+rpi1 openssl_1.1.0g-2 passwd_1:4.5-1 patch_2.7.6-1 perl_5.26.1-5 perl-base_5.26.1-5 perl-modules-5.24_5.24.1-7 perl-modules-5.26_5.26.1-5 pinentry-curses_1.1.0-1 plymouth_0.9.3-2 po-debconf_1.0.20 procps_2:3.3.12-4 python_2.7.14-4 python-markdown_2.6.9-1 python-minimal_2.7.14-4 python2.7_2.7.14-7 python2.7-minimal_2.7.14-7 raspbian-archive-keyring_20120528.2 readline-common_7.0-3 sbuild-build-depends-abyss-dummy_0.invalid.0 sbuild-build-depends-core-dummy_0.invalid.0 sed_4.4-2 sensible-utils_0.0.12 systemd_238-2 systemd-sysv_238-2 sysvinit-utils_2.88dsf-59.10 tar_1.29b-2 tzdata_2018c-1 udev_238-2 util-linux_2.31.1-0.4 xz-utils_5.2.2-1.3 zlib1g_1:1.2.8.dfsg-5
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Tue Mar 20 13:48:25 2018 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_2.0.3-1.dsc
dpkg-source: info: extracting abyss in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking abyss_2.0.3.orig.tar.gz
dpkg-source: info: unpacking abyss_2.0.3-1.debian.tar.xz
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
Check disc 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=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=buster-staging-armhf-sbuild-28ed7caf-ecd6-4674-8a50-3da6ebc1af3f
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package abyss
dpkg-buildpackage: info: source version 2.0.3-1
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build abyss-2.0.3
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 for style of include used by make... GNU
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
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checking for unistd.h... yes
checking dlfcn.h usability... yes
checking dlfcn.h presence... yes
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checking fcntl.h usability... yes
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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
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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
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checking for ssize_t... yes
checking for int64_t... yes
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checking for std::tr1::hash<int>... yes
checking for std::tr1::tuple<int>... yes
checking for dup2... yes
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checking for getopt_long... yes
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checking for strdup... yes
checking for strerror... yes
checking for strtoul... yes
checking vfork.h usability... no
checking vfork.h presence... no
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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/rolling-hash/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 -O
make all-recursive
Making all in bin
make[4]: Nothing to be done for 'all'.
Making all in doc
make[4]: Nothing to be done for 'all'.
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-Fcontrol.o `test -f 'Fcontrol.cpp' || echo './'`Fcontrol.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/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-Log.o `test -f 'Log.cpp' || echo './'`Log.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/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-Options.o `test -f 'Options.cpp' || echo './'`Options.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/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-Kmer.o `test -f 'Kmer.cpp' || echo './'`Kmer.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/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
make[4]: Leaving directory '/<<PKGBUILDDIR>>/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-Sequence.o `test -f 'Sequence.cpp' || echo './'`Sequence.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/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-SignalHandler.o `test -f 'SignalHandler.cpp' || echo './'`SignalHandler.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/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-Histogram.o `test -f 'Histogram.cpp' || echo './'`Histogram.cpp
In file included from /usr/include/c++/7/vector:69:0,
from VectorUtil.h:4,
from Histogram.h:5,
from Histogram.cpp:1:
/usr/include/c++/7/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++/7/bits/vector.tcc:394:7: 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++/7/vector:64:0,
from VectorUtil.h:4,
from Histogram.h:5,
from Histogram.cpp:1:
/usr/include/c++/7/bits/stl_vector.h: In member function 'Histogram::Bins Histogram::bin(unsigned int) const':
/usr/include/c++/7/bits/stl_vector.h:948:21: 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++/7/bits/stl_vector.h:948:21: 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);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
make[4]: Leaving directory '/<<PKGBUILDDIR>>/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-Timer.o `test -f 'Timer.cpp' || echo './'`Timer.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/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-city.o `test -f 'city.cc' || echo './'`city.cc
make[4]: Leaving directory '/<<PKGBUILDDIR>>/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-Uncompress.o `test -f 'Uncompress.cpp' || echo './'`Uncompress.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Common'
make[4]: Entering directory '/<<PKGBUILDDIR>>/Common'
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
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Graph'
make[4]: Entering directory '/<<PKGBUILDDIR>>/Graph'
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
make[4]: Leaving directory '/<<PKGBUILDDIR>>/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_todot-todot.o `test -f 'todot.cc' || echo './'`todot.cc
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Graph'
make[4]: Entering directory '/<<PKGBUILDDIR>>/Graph'
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 libdatalayer_a-FastaWriter.o `test -f 'FastaWriter.cpp' || echo './'`FastaWriter.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/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_tofastq-abyss-tofastq.o `test -f 'abyss-tofastq.cc' || echo './'`abyss-tofastq.cc
make[4]: Leaving directory '/<<PKGBUILDDIR>>/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 libdatalayer_a-FastaReader.o `test -f 'FastaReader.cpp' || echo './'`FastaReader.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/DataLayer'
make[4]: Entering directory '/<<PKGBUILDDIR>>/DataLayer'
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
make[4]: Leaving directory '/<<PKGBUILDDIR>>/DataLayer'
make[4]: Entering directory '/<<PKGBUILDDIR>>/DataLayer'
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
make[4]: Leaving directory '/<<PKGBUILDDIR>>/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
make[4]: Leaving directory '/<<PKGBUILDDIR>>/DataLayer'
make[4]: Entering directory '/<<PKGBUILDDIR>>/DataLayer'
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-csv.o `test -f 'db-csv.cc' || echo './'`db-csv.cc
make[4]: Leaving directory '/<<PKGBUILDDIR>>/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
make[4]: Leaving directory '/<<PKGBUILDDIR>>/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 libdb_a-DB.o `test -f 'DB.cc' || echo './'`DB.cc
make[4]: Leaving directory '/<<PKGBUILDDIR>>/DataBase'
make[4]: Entering directory '/<<PKGBUILDDIR>>/DataBase'
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'
make[4]: Entering directory '/<<PKGBUILDDIR>>/DataBase'
rm -f libdb.a
ar cru libdb.a libdb_a-DB.o ../Common/libcommon.a
ar: `u' modifier ignored since `D' is the default (see `U')
ranlib libdb.a
make[4]: Leaving directory '/<<PKGBUILDDIR>>/DataBase'
Making all in FMIndex
make[4]: Entering directory '/<<PKGBUILDDIR>>/FMIndex'
g++ -DHAVE_CONFIG_H -I. -I.. -I../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
make[4]: Leaving directory '/<<PKGBUILDDIR>>/FMIndex'
make[4]: Entering directory '/<<PKGBUILDDIR>>/FMIndex'
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
make[4]: Leaving directory '/<<PKGBUILDDIR>>/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_dawg-abyss-dawg.o `test -f 'abyss-dawg.cc' || echo './'`abyss-dawg.cc
In file included from /usr/include/c++/7/vector:69:0,
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++/7/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++/7/bits/vector.tcc:394:7: 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++/7/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++/7/bits/vector.tcc:105:21: 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++/7/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++/7/bits/vector.tcc:458:5: 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++/7/vector:64:0,
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++/7/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++/7/bits/stl_vector.h:712:18: 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++/7/map:60:0,
from abyss-dawg.cc:14:
/usr/include/c++/7/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++/7/bits/stl_tree.h:2395:7: 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:5:0:
/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++/7/map:61:0,
from abyss-dawg.cc:14:
/usr/include/c++/7/bits/stl_map.h:493:4: 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++/7/bits/stl_map.h:493:4: 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++/7/bits/stl_map.h:493:4: 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++/7/bits/stl_map.h:493:4: 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 abyss-dawg.cc:5:0:
/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());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
make[4]: Leaving directory '/<<PKGBUILDDIR>>/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
In file included from /usr/include/c++/7/vector:69:0,
from bit_array.h:24,
from BitArrays.h:4,
from FMIndex.h:5,
from DAWG.h:5,
from count.cc:2:
/usr/include/c++/7/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++/7/bits/vector.tcc:394:7: 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++/7/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++/7/bits/vector.tcc:105:21: 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++/7/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++/7/bits/vector.tcc:458:5: 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++/7/vector:64:0,
from bit_array.h:24,
from BitArrays.h:4,
from FMIndex.h:5,
from DAWG.h:5,
from count.cc:2:
/usr/include/c++/7/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++/7/bits/stl_vector.h:712:18: 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);
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
make[4]: Leaving directory '/<<PKGBUILDDIR>>/FMIndex'
make[4]: Entering directory '/<<PKGBUILDDIR>>/FMIndex'
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'
make[4]: Entering directory '/<<PKGBUILDDIR>>/FMIndex'
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
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-Options.o `test -f 'Options.cc' || echo './'`Options.cc
make[4]: Leaving directory '/<<PKGBUILDDIR>>/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
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Assembly'
make[4]: Entering directory '/<<PKGBUILDDIR>>/Assembly'
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 alig.o alig.c
alig.c:15:20: warning: inline function 'calc_ov_weight' declared but never defined
extern inline void calc_ov_weight(struct diag* dg, struct diag_col *dcol, struct scr_matrix* smatrix,
^~~~~~~~~~~~~~
alig.c:13:20: warning: inline function 'calc_weight' declared but never defined
extern inline void calc_weight(struct diag* dg, struct scr_matrix* smatrix,
^~~~~~~~~~~
make[4]: Leaving directory '/<<PKGBUILDDIR>>/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 assemble.o assemble.c
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,
^~~~~~~~~~~
make[4]: Leaving directory '/<<PKGBUILDDIR>>/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 diag.o diag.c
diag.c:1456:3: warning: 'real_calc_weight' is static but used in inline function 'find_diags_dyn' which is not static
real_calc_weight(dg, smatrix, pdist,1,tmp_dist,algn);
^~~~~~~~~~~~~~~~
make[4]: Leaving directory '/<<PKGBUILDDIR>>/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 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 );
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
make[4]: Leaving directory '/<<PKGBUILDDIR>>/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 parameters.o parameters.c
make[4]: Leaving directory '/<<PKGBUILDDIR>>/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 prob.o prob.c
make[4]: Leaving directory '/<<PKGBUILDDIR>>/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 translate.o translate.c
make[4]: Leaving directory '/<<PKGBUILDDIR>>/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
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);
^~~~~~~~~~~~~~
make[4]: Leaving directory '/<<PKGBUILDDIR>>/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 orf.o orf.c
make[4]: Leaving directory '/<<PKGBUILDDIR>>/dialign'
make[4]: Entering directory '/<<PKGBUILDDIR>>/dialign'
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
make[4]: Leaving directory '/<<PKGBUILDDIR>>/dialign'
make[4]: Entering directory '/<<PKGBUILDDIR>>/dialign'
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/<<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
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Align'
make[4]: Entering directory '/<<PKGBUILDDIR>>/Align'
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
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Align'
make[4]: Entering directory '/<<PKGBUILDDIR>>/Align'
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
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Align'
make[4]: Entering directory '/<<PKGBUILDDIR>>/Align'
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
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Align'
make[4]: Entering directory '/<<PKGBUILDDIR>>/Align'
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
make[4]: Leaving directory '/<<PKGBUILDDIR>>/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
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Align'
make[4]: Entering directory '/<<PKGBUILDDIR>>/Align'
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
make[4]: Leaving directory '/<<PKGBUILDDIR>>/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_mergepairs-mergepairs.o `test -f 'mergepairs.cc' || echo './'`mergepairs.cc
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Align'
make[4]: Entering directory '/<<PKGBUILDDIR>>/Align'
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
make[4]: Leaving directory '/<<PKGBUILDDIR>>/ABYSS'
make[4]: Entering directory '/<<PKGBUILDDIR>>/ABYSS'
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
bloom.cc: In function 'void parseGlobalOpts(int, char**)':
bloom.cc:226:21: warning: this statement may fall through [-Wimplicit-fallthrough=]
dieWithUsageError();
~~~~~~~~~~~~~~~~~^~
bloom.cc:227:5: note: here
case 'k':
^~~~
bloom.cc: In function 'int build(int, char**)':
bloom.cc:511:21: warning: this statement may fall through [-Wimplicit-fallthrough=]
dieWithUsageError();
~~~~~~~~~~~~~~~~~^~
bloom.cc:512:5: note: here
case 'b':
^~~~
bloom.cc: In function 'int compare(int, char**)':
bloom.cc:726:22: warning: this statement may fall through [-Wimplicit-fallthrough=]
dieWithUsageError();
~~~~~~~~~~~~~~~~~^~
bloom.cc:727:4: note: here
case 'm':
^~~~
bloom.cc: In function 'int memberOf(int, char**)':
bloom.cc:858:22: warning: this statement may fall through [-Wimplicit-fallthrough=]
dieWithUsageError();
~~~~~~~~~~~~~~~~~^~
bloom.cc:859:4: note: here
case 'r':
^~~~
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Bloom'
make[4]: Entering directory '/<<PKGBUILDDIR>>/Bloom'
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
In file included from /usr/include/c++/7/vector:69:0,
from ../BloomDBG/RollingHashIterator.h:5,
from ../BloomDBG/bloom-dbg.h:6,
from bloom-dbg.cc:3:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const RollingBloomDBGVertex&}; _Tp = RollingBloomDBGVertex; _Alloc = std::allocator<RollingBloomDBGVertex>]':
/usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type 'std::vector<RollingBloomDBGVertex, std::allocator<RollingBloomDBGVertex> >::iterator {aka __gnu_cxx::__normal_iterator<RollingBloomDBGVertex*, std::vector<RollingBloomDBGVertex, std::allocator<RollingBloomDBGVertex> > >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
from ../BloomDBG/RollingHashIterator.h:5,
from ../BloomDBG/bloom-dbg.h:6,
from bloom-dbg.cc:3:
/usr/include/c++/7/bits/stl_vector.h: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = RollingBloomDBGVertex; _Alloc = std::allocator<RollingBloomDBGVertex>]':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<RollingBloomDBGVertex*, std::vector<RollingBloomDBGVertex, std::allocator<RollingBloomDBGVertex> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/7/algorithm:62:0,
from ../BloomDBG/RollingHashIterator.h:9,
from ../BloomDBG/bloom-dbg.h:6,
from bloom-dbg.cc:3:
/usr/include/c++/7/bits/stl_algo.h: In function '_RandomAccessIterator std::__find_if(_RandomAccessIterator, _RandomAccessIterator, _Predicate, std::random_access_iterator_tag) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<RollingBloomDBGVertex*, std::vector<RollingBloomDBGVertex, std::allocator<RollingBloomDBGVertex> > >; _Predicate = __gnu_cxx::__ops::_Iter_equals_val<const RollingBloomDBGVertex>]':
/usr/include/c++/7/bits/stl_algo.h:112:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<RollingBloomDBGVertex*, std::vector<RollingBloomDBGVertex, std::allocator<RollingBloomDBGVertex> > >' changed in GCC 7.1
__find_if(_RandomAccessIterator __first, _RandomAccessIterator __last,
^~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:112:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<RollingBloomDBGVertex*, std::vector<RollingBloomDBGVertex, std::allocator<RollingBloomDBGVertex> > >' changed in GCC 7.1
In file included from /usr/include/c++/7/vector:64:0,
from ../BloomDBG/RollingHashIterator.h:5,
from ../BloomDBG/bloom-dbg.h:6,
from bloom-dbg.cc:3:
/usr/include/c++/7/bits/stl_vector.h: In function 'std::vector<typename boost::graph_traits<G>::vertex_descriptor> trueBranches(const typename boost::graph_traits<Graph>::vertex_descriptor&, Direction, const BidirectionalGraph&, unsigned int) [with BidirectionalGraph = RollingBloomDBG<HashAgnosticCascadingBloom>]':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<RollingBloomDBGVertex*, std::vector<RollingBloomDBGVertex, std::allocator<RollingBloomDBGVertex> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/7/algorithm:62:0,
from ../BloomDBG/RollingHashIterator.h:9,
from ../BloomDBG/bloom-dbg.h:6,
from bloom-dbg.cc:3:
/usr/include/c++/7/bits/stl_algo.h: In function 'PathExtensionResult extendPath(Path<typename boost::graph_traits<Graph>::vertex_descriptor>&, Direction, const BidirectionalGraph&, std::unordered_set<typename boost::graph_traits<Graph>::vertex_descriptor, std::hash<typename boost::graph_traits<Graph>::vertex_descriptor> >&, const ExtendPathParams&) [with BidirectionalGraph = RollingBloomDBG<HashAgnosticCascadingBloom>]':
/usr/include/c++/7/bits/stl_algo.h:162:43: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<RollingBloomDBGVertex*, std::vector<RollingBloomDBGVertex, std::allocator<RollingBloomDBGVertex> > >' changed in GCC 7.1
std::__iterator_category(__first));
^
/usr/include/c++/7/bits/stl_algo.h: In function '_ZN8BloomDBGL8assembleI26HashAgnosticCascadingBloomN3BTL11BloomFilterE11FastaConcatEEvRKT_RT0_RNS_16AssemblyCountersERKNS_14AssemblyParamsERNS_15AssemblyStreamsIT1_EE._omp_fn.1':
/usr/include/c++/7/bits/stl_algo.h:162:43: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<RollingBloomDBGVertex*, std::vector<RollingBloomDBGVertex, std::allocator<RollingBloomDBGVertex> > >' changed in GCC 7.1
std::__iterator_category(__first));
^
/usr/include/c++/7/bits/stl_algo.h:162:43: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<RollingBloomDBGVertex*, std::vector<RollingBloomDBGVertex, std::allocator<RollingBloomDBGVertex> > >' changed in GCC 7.1
std::__iterator_category(__first));
^
make[4]: Leaving directory '/<<PKGBUILDDIR>>/BloomDBG'
make[4]: Entering directory '/<<PKGBUILDDIR>>/BloomDBG'
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
In file included from konnector.cc:8:0:
konnector.h: In function 'ExtendSeqResult extendSeq(Sequence&, Direction, unsigned int, unsigned int, const Graph&, unsigned int, unsigned int, bool, bool, bool) [with Graph = DBGBloom<BloomFilter>]':
konnector.h:814:3: warning: this statement may fall through [-Wimplicit-fallthrough=]
if (seq.length() > origSeqLen)
^~
konnector.h:818:2: note: here
case DEAD_END:
^~~~
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Konnector'
make[4]: Entering directory '/<<PKGBUILDDIR>>/Konnector'
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
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Consensus'
make[4]: Entering directory '/<<PKGBUILDDIR>>/Consensus'
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-RotatedRead.o `test -f 'RotatedRead.cpp' || echo './'`RotatedRead.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/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
make[4]: Leaving directory '/<<PKGBUILDDIR>>/DAssembler'
make[4]: Entering directory '/<<PKGBUILDDIR>>/DAssembler'
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 -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++/7/vector:69:0,
from MLE.h:4,
from MLE.cpp:1:
/usr/include/c++/7/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++/7/bits/vector.tcc:394:7: 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++/7/vector:64:0,
from MLE.h:4,
from MLE.cpp:1:
/usr/include/c++/7/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++/7/bits/stl_vector.h:948:21: 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);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
make[4]: Leaving directory '/<<PKGBUILDDIR>>/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-MLE.o `test -f 'MLE.cpp' || echo './'`MLE.cpp
In file included from /usr/include/c++/7/vector:69:0,
from MLE.h:4,
from MLE.cpp:1:
/usr/include/c++/7/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++/7/bits/vector.tcc:394:7: 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++/7/vector:64:0,
from MLE.h:4,
from MLE.cpp:1:
/usr/include/c++/7/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++/7/bits/stl_vector.h:948:21: 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);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
make[4]: Leaving directory '/<<PKGBUILDDIR>>/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
make[4]: Leaving directory '/<<PKGBUILDDIR>>/DistanceEst'
make[4]: Entering directory '/<<PKGBUILDDIR>>/DistanceEst'
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
make[4]: Leaving directory '/<<PKGBUILDDIR>>/DistanceEst'
make[4]: Entering directory '/<<PKGBUILDDIR>>/DistanceEst'
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
make[4]: Leaving directory '/<<PKGBUILDDIR>>/DistanceEst'
make[4]: Entering directory '/<<PKGBUILDDIR>>/DistanceEst'
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
In file included from KAligner.cpp:5:0:
../DataLayer/FastaReader.h: In member function 'std::pair<T, unsigned int> PipeMux<T>::nextValue() [with T = FastaRecord]':
../DataLayer/FastaReader.h:123:8: warning: '<anonymous>.FastaRecord::anchor' is used uninitialized in this function [-Wuninitialized]
struct FastaRecord
^~~~~~~~~~~
make[4]: Leaving directory '/<<PKGBUILDDIR>>/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-Aligner.o `test -f 'Aligner.cpp' || echo './'`Aligner.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/KAligner'
make[4]: Entering directory '/<<PKGBUILDDIR>>/KAligner'
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
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Layout'
make[4]: Entering directory '/<<PKGBUILDDIR>>/Layout'
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
make[4]: Leaving directory '/<<PKGBUILDDIR>>/LogKmerCount'
make[4]: Entering directory '/<<PKGBUILDDIR>>/LogKmerCount'
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
index.cc: In function 'void buildFMIndex(FMIndex&, const string&)':
index.cc:149:64: warning: large integer implicitly truncated to unsigned type [-Woverflow]
size_t MAX_SIZE = numeric_limits<FMIndex::sais_size_type>::max();
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~
In file included from /usr/include/c++/7/vector:69:0,
from ../DataLayer/FastaIndex.h:11,
from index.cc:3:
/usr/include/c++/7/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++/7/bits/vector.tcc:458:5: 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++/7/vector:64:0,
from ../DataLayer/FastaIndex.h:11,
from index.cc:3:
/usr/include/c++/7/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++/7/bits/stl_vector.h:712:18: 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++/7/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++/7/bits/stl_vector.h:712:18: 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);
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Map'
make[4]: Entering directory '/<<PKGBUILDDIR>>/Map'
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
make[4]: Leaving directory '/<<PKGBUILDDIR>>/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 -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
map.cc: In function 'void buildFMIndex(FMIndex&, const char*)':
map.cc:508:64: warning: large integer implicitly truncated to unsigned type [-Woverflow]
size_t MAX_SIZE = numeric_limits<FMIndex::sais_size_type>::max();
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~
In file included from /usr/include/c++/7/vector:69:0,
from ../FMIndex/bit_array.h:24,
from ../FMIndex/BitArrays.h:4,
from ../FMIndex/FMIndex.h:5,
from map.cc:3:
/usr/include/c++/7/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++/7/bits/vector.tcc:458:5: 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++/7/vector:64:0,
from ../FMIndex/bit_array.h:24,
from ../FMIndex/BitArrays.h:4,
from ../FMIndex/FMIndex.h:5,
from map.cc:3:
/usr/include/c++/7/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++/7/bits/stl_vector.h:712:18: 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);
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Map'
make[4]: Entering directory '/<<PKGBUILDDIR>>/Map'
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
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Map'
make[4]: Entering directory '/<<PKGBUILDDIR>>/Map'
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
map.cc: In function 'void buildFMIndex(FMIndex&, const char*)':
map.cc:508:64: warning: large integer implicitly truncated to unsigned type [-Woverflow]
size_t MAX_SIZE = numeric_limits<FMIndex::sais_size_type>::max();
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~
In file included from /usr/include/c++/7/vector:69:0,
from ../FMIndex/bit_array.h:24,
from ../FMIndex/BitArrays.h:4,
from ../FMIndex/FMIndex.h:5,
from map.cc:3:
/usr/include/c++/7/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++/7/bits/vector.tcc:458:5: 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++/7/vector:64:0,
from ../FMIndex/bit_array.h:24,
from ../FMIndex/BitArrays.h:4,
from ../FMIndex/FMIndex.h:5,
from map.cc:3:
/usr/include/c++/7/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++/7/bits/stl_vector.h:712:18: 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);
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Map'
make[4]: Entering directory '/<<PKGBUILDDIR>>/Map'
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
make[4]: Leaving directory '/<<PKGBUILDDIR>>/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 -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
overlap.cc: In function 'void buildFMIndex(FMIndex&, const char*)':
overlap.cc:296:64: warning: large integer implicitly truncated to unsigned type [-Woverflow]
size_t MAX_SIZE = numeric_limits<FMIndex::sais_size_type>::max();
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~
In file included from /usr/include/c++/7/vector:69:0,
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++/7/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++/7/bits/vector.tcc:394:7: 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++/7/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++/7/bits/vector.tcc:105:21: 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++/7/vector:63:0,
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++/7/bits/stl_uninitialized.h: In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator<wat_array::BitArray*>; _ForwardIterator = wat_array::BitArray*; bool _TrivialValueTypes = false]':
/usr/include/c++/7/bits/stl_uninitialized.h:76:9: note: parameter passing for argument of type 'std::move_iterator<wat_array::BitArray*>' changed in GCC 7.1
__uninit_copy(_InputIterator __first, _InputIterator __last,
^~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_uninitialized.h:76:9: note: parameter passing for argument of type 'std::move_iterator<wat_array::BitArray*>' changed in GCC 7.1
In file included from /usr/include/c++/7/vector:69:0,
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++/7/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++/7/bits/vector.tcc:458:5: 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++/7/vector:63:0,
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++/7/bits/stl_uninitialized.h:134:41: note: parameter passing for argument of type 'std::move_iterator<wat_array::BitArray*>' changed in GCC 7.1
__uninit_copy(__first, __last, __result);
^
/usr/include/c++/7/bits/stl_uninitialized.h:134:41: note: parameter passing for argument of type 'std::move_iterator<wat_array::BitArray*>' changed in GCC 7.1
__uninit_copy(__first, __last, __result);
^
In file included from /usr/include/c++/7/vector:64:0,
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++/7/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++/7/bits/stl_vector.h:712:18: 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);
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Map'
make[4]: Entering directory '/<<PKGBUILDDIR>>/Map'
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../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
make[4]: Leaving directory '/<<PKGBUILDDIR>>/MergePaths'
make[4]: Entering directory '/<<PKGBUILDDIR>>/MergePaths'
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
make[4]: Leaving directory '/<<PKGBUILDDIR>>/MergePaths'
make[4]: Entering directory '/<<PKGBUILDDIR>>/MergePaths'
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
make[4]: Leaving directory '/<<PKGBUILDDIR>>/MergePaths'
make[4]: Entering directory '/<<PKGBUILDDIR>>/MergePaths'
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
make[4]: Leaving directory '/<<PKGBUILDDIR>>/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
make[4]: Leaving directory '/<<PKGBUILDDIR>>/MergePaths'
make[4]: Entering directory '/<<PKGBUILDDIR>>/MergePaths'
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]: Nothing to be done for 'all'.
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
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Overlap'
make[4]: Entering directory '/<<PKGBUILDDIR>>/Overlap'
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.. -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
make[4]: Leaving directory '/<<PKGBUILDDIR>>/PairedDBG'
make[4]: Entering directory '/<<PKGBUILDDIR>>/PairedDBG'
rm -f libpaireddbg.a
ar cru libpaireddbg.a KmerPair.o
ar: `u' modifier ignored since `D' is the default (see `U')
ranlib libpaireddbg.a
make[4]: Leaving directory '/<<PKGBUILDDIR>>/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-KmerPair.o `test -f 'KmerPair.cc' || echo './'`KmerPair.cc
make[4]: Leaving directory '/<<PKGBUILDDIR>>/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
make[4]: Leaving directory '/<<PKGBUILDDIR>>/PairedDBG'
make[4]: Entering directory '/<<PKGBUILDDIR>>/PairedDBG'
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 ParseAligns-ParseAligns.o `test -f 'ParseAligns.cpp' || echo './'`ParseAligns.cpp
In file included from ParseAligns.cpp:6:0:
../Common/SAM.h: In static member function 'static Alignment SAMAlignment::parseCigar(const string&, bool)':
../Common/SAM.h:174:11: warning: this statement may fall through [-Wimplicit-fallthrough=]
clip1 += len;
~~~~~~^~~~~~
../Common/SAM.h:175:6: note: here
case 'D': case 'N': case 'P':
^~~~
../Common/SAM.h:184:5: warning: this statement may fall through [-Wimplicit-fallthrough=]
if ((unsigned)a.align_length < len) {
^~
../Common/SAM.h:191:6: note: here
case 'H': case 'S':
^~~~
make[4]: Leaving directory '/<<PKGBUILDDIR>>/ParseAligns'
make[4]: Entering directory '/<<PKGBUILDDIR>>/ParseAligns'
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
make[4]: Leaving directory '/<<PKGBUILDDIR>>/ParseAligns'
make[4]: Entering directory '/<<PKGBUILDDIR>>/ParseAligns'
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
make[4]: Leaving directory '/<<PKGBUILDDIR>>/ParseAligns'
make[4]: Entering directory '/<<PKGBUILDDIR>>/ParseAligns'
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'
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
make[4]: Leaving directory '/<<PKGBUILDDIR>>/ParseAligns'
make[4]: Entering directory '/<<PKGBUILDDIR>>/ParseAligns'
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
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
make[4]: Leaving directory '/<<PKGBUILDDIR>>/PathOverlap'
make[4]: Entering directory '/<<PKGBUILDDIR>>/PathOverlap'
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
make[4]: Leaving directory '/<<PKGBUILDDIR>>/PopBubbles'
make[4]: Entering directory '/<<PKGBUILDDIR>>/PopBubbles'
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_longseqdist-longseqdist.o `test -f 'longseqdist.cpp' || echo './'`longseqdist.cpp
In file included from longseqdist.cpp:12:0:
../Common/SAM.h: In static member function 'static Alignment SAMAlignment::parseCigar(const string&, bool)':
../Common/SAM.h:174:11: warning: this statement may fall through [-Wimplicit-fallthrough=]
clip1 += len;
~~~~~~^~~~~~
../Common/SAM.h:175:6: note: here
case 'D': case 'N': case 'P':
^~~~
../Common/SAM.h:184:5: warning: this statement may fall through [-Wimplicit-fallthrough=]
if ((unsigned)a.align_length < len) {
^~
../Common/SAM.h:191:6: note: here
case 'H': case 'S':
^~~~
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Scaffold'
make[4]: Entering directory '/<<PKGBUILDDIR>>/Scaffold'
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
make[4]: Leaving directory '/<<PKGBUILDDIR>>/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_junction-junction.o `test -f 'junction.cc' || echo './'`junction.cc
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Scaffold'
make[4]: Entering directory '/<<PKGBUILDDIR>>/Scaffold'
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
make[4]: Leaving directory '/<<PKGBUILDDIR>>/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 -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++/7/algorithm:62:0,
from /usr/include/boost/smart_ptr/shared_ptr.hpp:38,
from /usr/include/boost/shared_ptr.hpp:17,
from /usr/include/boost/property_map/vector_property_map.hpp:14,
from /usr/include/boost/property_map/property_map.hpp:600,
from /usr/include/boost/graph/properties.hpp:19,
from ../Graph/Properties.h:6,
from ../Common/ContigNode.h:6,
from ../Common/ContigProperties.h:4,
from drawgraph.cc:10:
/usr/include/c++/7/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++/7/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,
^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:69:0,
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++/7/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++/7/bits/vector.tcc:394:7: 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++/7/algorithm:62:0,
from /usr/include/boost/smart_ptr/shared_ptr.hpp:38,
from /usr/include/boost/shared_ptr.hpp:17,
from /usr/include/boost/property_map/vector_property_map.hpp:14,
from /usr/include/boost/property_map/property_map.hpp:600,
from /usr/include/boost/graph/properties.hpp:19,
from ../Graph/Properties.h:6,
from ../Common/ContigNode.h:6,
from ../Common/ContigProperties.h:4,
from drawgraph.cc:10:
/usr/include/c++/7/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++/7/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++/7/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
/usr/include/c++/7/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++/7/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++/7/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++/7/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++/7/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
In file included from /usr/include/c++/7/bits/stl_algo.h:61:0,
from /usr/include/c++/7/algorithm:62,
from /usr/include/boost/smart_ptr/shared_ptr.hpp:38,
from /usr/include/boost/shared_ptr.hpp:17,
from /usr/include/boost/property_map/vector_property_map.hpp:14,
from /usr/include/boost/property_map/property_map.hpp:600,
from /usr/include/boost/graph/properties.hpp:19,
from ../Graph/Properties.h:6,
from ../Common/ContigNode.h:6,
from ../Common/ContigProperties.h:4,
from drawgraph.cc:10:
/usr/include/c++/7/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++/7/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++/7/algorithm:62:0,
from /usr/include/boost/smart_ptr/shared_ptr.hpp:38,
from /usr/include/boost/shared_ptr.hpp:17,
from /usr/include/boost/property_map/vector_property_map.hpp:14,
from /usr/include/boost/property_map/property_map.hpp:600,
from /usr/include/boost/graph/properties.hpp:19,
from ../Graph/Properties.h:6,
from ../Common/ContigNode.h:6,
from ../Common/ContigProperties.h:4,
from drawgraph.cc:10:
/usr/include/c++/7/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++/7/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++/7/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++/7/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++/7/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++/7/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++/7/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);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:69:0,
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++/7/bits/vector.tcc: In function 'int main(int, char**)':
/usr/include/c++/7/bits/vector.tcc:105:21: 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++/7/algorithm:62:0,
from /usr/include/boost/smart_ptr/shared_ptr.hpp:38,
from /usr/include/boost/shared_ptr.hpp:17,
from /usr/include/boost/property_map/vector_property_map.hpp:14,
from /usr/include/boost/property_map/property_map.hpp:600,
from /usr/include/boost/graph/properties.hpp:19,
from ../Graph/Properties.h:6,
from ../Common/ContigNode.h:6,
from ../Common/ContigProperties.h:4,
from drawgraph.cc:10:
/usr/include/c++/7/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++/7/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++/7/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);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Scaffold'
make[4]: Entering directory '/<<PKGBUILDDIR>>/Scaffold'
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
make[4]: Leaving directory '/<<PKGBUILDDIR>>/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
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Scaffold'
make[4]: Entering directory '/<<PKGBUILDDIR>>/Scaffold'
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
make[4]: Leaving directory '/<<PKGBUILDDIR>>/SimpleGraph'
make[4]: Entering directory '/<<PKGBUILDDIR>>/SimpleGraph'
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
make[4]: Leaving directory '/<<PKGBUILDDIR>>/kmerprint'
make[4]: Entering directory '/<<PKGBUILDDIR>>/kmerprint'
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
make[4]: Leaving directory '/<<PKGBUILDDIR>>/FilterGraph'
make[4]: Entering directory '/<<PKGBUILDDIR>>/FilterGraph'
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
make[4]: Leaving directory '/<<PKGBUILDDIR>>/GapFiller'
make[4]: Entering directory '/<<PKGBUILDDIR>>/GapFiller'
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
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Sealer'
make[4]: Entering directory '/<<PKGBUILDDIR>>/Sealer'
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
make[4]: Leaving directory '/<<PKGBUILDDIR>>/AdjList'
make[4]: Entering directory '/<<PKGBUILDDIR>>/AdjList'
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
make[4]: Nothing to be done for 'all'.
Making all in lib/rolling-hash
make[4]: Nothing to be done for 'all'.
Making all in lib/gtest-1.7.0
make[4]: Nothing to be done for 'all'.
Making all in Unittest
make[4]: Nothing to be done for 'all'.
markdown_py -f README.html README.md
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_test -a
make -j4 -O check VERBOSE=1
Making check in bin
make[2]: Nothing to be done for 'check'.
Making check in doc
make[2]: Nothing to be done for 'check'.
Making check in Common
make[2]: Nothing to be done for 'check'.
Making check in Graph
make[2]: Nothing to be done for 'check'.
Making check in DataLayer
make[2]: Nothing to be done for 'check'.
Making check in DataBase
make[2]: Nothing to be done for 'check'.
Making check in FMIndex
make[2]: Nothing to be done for 'check'.
Making check in Assembly
make[2]: Nothing to be done for 'check'.
Making check in dialign
make[2]: Nothing to be done for 'check'.
Making check in Align
make[2]: Nothing to be done for 'check'.
Making check in ABYSS
make[2]: Nothing to be done for 'check'.
Making check in Bloom
make[2]: Nothing to be done for 'check'.
Making check in BloomDBG
make[2]: Nothing to be done for 'check'.
Making check in Konnector
make[2]: Nothing to be done for 'check'.
Making check in Consensus
make[2]: Nothing to be done for 'check'.
Making check in DAssembler
make[2]: Nothing to be done for 'check'.
Making check in DistanceEst
make[2]: Nothing to be done for 'check'.
Making check in KAligner
make[2]: Nothing to be done for 'check'.
Making check in Layout
make[2]: Nothing to be done for 'check'.
Making check in LogKmerCount
make[2]: Nothing to be done for 'check'.
Making check in Map
make[2]: Nothing to be done for 'check'.
Making check in MergePaths
make[2]: Nothing to be done for 'check'.
Making check in Misc
make[2]: Nothing to be done for 'check'.
Making check in Overlap
make[2]: Nothing to be done for 'check'.
Making check in PairedDBG
make[2]: Nothing to be done for 'check'.
Making check in ParseAligns
make[2]: Nothing to be done for 'check'.
Making check in PathOverlap
make[2]: Nothing to be done for 'check'.
Making check in PopBubbles
make[2]: Nothing to be done for 'check'.
Making check in Scaffold
make[2]: Nothing to be done for 'check'.
Making check in SimpleGraph
make[2]: Nothing to be done for 'check'.
Making check in kmerprint
make[2]: Nothing to be done for 'check'.
Making check in FilterGraph
make[2]: Nothing to be done for 'check'.
Making check in GapFiller
make[2]: Nothing to be done for 'check'.
Making check in Sealer
make[2]: Nothing to be done for 'check'.
Making check in AdjList
make[2]: Nothing to be done for 'check'.
Making check in lib/bloomfilter
make[2]: Nothing to be done for 'check'.
Making check in lib/rolling-hash
make[2]: Nothing to be done for 'check'.
Making check in 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_main_a-gtest_main.o `test -f 'src/gtest_main.cc' || echo './'`src/gtest_main.cc
make[3]: Leaving directory '/<<PKGBUILDDIR>>/lib/gtest-1.7.0'
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_main_a-gtest-all.o `test -f 'src/gtest-all.cc' || echo './'`src/gtest-all.cc
make[3]: Leaving directory '/<<PKGBUILDDIR>>/lib/gtest-1.7.0'
make[3]: Entering directory '/<<PKGBUILDDIR>>/lib/gtest-1.7.0'
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[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
make[3]: Leaving directory '/<<PKGBUILDDIR>>/lib/gtest-1.7.0'
make[3]: Entering directory '/<<PKGBUILDDIR>>/lib/gtest-1.7.0'
rm -f libgtest.a
ar cru libgtest.a src/libgtest_a-gtest-all.o
ar: `u' modifier ignored since `D' is the default (see `U')
ranlib libgtest.a
make[3]: Leaving directory '/<<PKGBUILDDIR>>/lib/gtest-1.7.0'
Making check in 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
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/KmerTest.o Common/KmerTest.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/Unittest'
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/HistogramTest.o Common/HistogramTest.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/Unittest'
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/BitUtilTest.o Common/BitUtilTest.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/Unittest'
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/Sequence.o Common/Sequence.cc
make[3]: Leaving directory '/<<PKGBUILDDIR>>/Unittest'
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/KmerIteratorTest.o Common/KmerIteratorTest.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/Unittest'
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
make[3]: Leaving directory '/<<PKGBUILDDIR>>/Unittest'
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/SAM.o Common/SAM.cc
In file included from Common/SAM.cc:1:0:
../Common/SAM.h: In static member function 'static Alignment SAMAlignment::parseCigar(const string&, bool)':
../Common/SAM.h:174:11: warning: this statement may fall through [-Wimplicit-fallthrough=]
clip1 += len;
~~~~~~^~~~~~
../Common/SAM.h:175:6: note: here
case 'D': case 'N': case 'P':
^~~~
../Common/SAM.h:184:5: warning: this statement may fall through [-Wimplicit-fallthrough=]
if ((unsigned)a.align_length < len) {
^~
../Common/SAM.h:191:6: note: here
case 'H': case 'S':
^~~~
make[3]: Leaving directory '/<<PKGBUILDDIR>>/Unittest'
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../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_DBGBloom-DBGBloomTest.o `test -f 'Konnector/DBGBloomTest.cpp' || echo './'`Konnector/DBGBloomTest.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/Unittest'
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../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
make[3]: Leaving directory '/<<PKGBUILDDIR>>/Unittest'
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../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_DBGBloomAlgorithms-DBGBloomAlgorithmsTest.o `test -f 'Konnector/DBGBloomAlgorithmsTest.cpp' || echo './'`Konnector/DBGBloomAlgorithmsTest.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/Unittest'
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../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
make[3]: Leaving directory '/<<PKGBUILDDIR>>/Unittest'
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../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
make[3]: Leaving directory '/<<PKGBUILDDIR>>/Unittest'
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../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
Graph/HashGraphTest.cpp: In member function 'virtual void {anonymous}::HashGraphTest_vertex_iterator_Test::TestBody()':
Graph/HashGraphTest.cpp:78:6: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else]
if (vi != vi_begin)
^
make[3]: Leaving directory '/<<PKGBUILDDIR>>/Unittest'
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../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
make[3]: Leaving directory '/<<PKGBUILDDIR>>/Unittest'
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../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
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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
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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
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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
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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/PairedDBG_KmerPair-KmerPairTest.o `test -f 'PairedDBG/KmerPairTest.cc' || echo './'`PairedDBG/KmerPairTest.cc
make[3]: Leaving directory '/<<PKGBUILDDIR>>/Unittest'
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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/DBG_LoadAlgorithm-LoadAlgorithmTest.o `test -f 'DBG/LoadAlgorithmTest.cpp' || echo './'`DBG/LoadAlgorithmTest.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/Unittest'
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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/PairedDBG_Dinuc-DinucTest.o `test -f 'PairedDBG/DinucTest.cc' || echo './'`PairedDBG/DinucTest.cc
make[3]: Leaving directory '/<<PKGBUILDDIR>>/Unittest'
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../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_konnector-konnectorTest.o `test -f 'Konnector/konnectorTest.cpp' || echo './'`Konnector/konnectorTest.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/Unittest'
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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/PairedDBG_LoadAlgorithm-LoadAlgorithmTest.o `test -f 'PairedDBG/LoadAlgorithmTest.cpp' || echo './'`PairedDBG/LoadAlgorithmTest.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/Unittest'
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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/PairedDBG_BranchRecord-BranchRecordTest.o `test -f 'PairedDBG/BranchRecordTest.cpp' || echo './'`PairedDBG/BranchRecordTest.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/Unittest'
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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
make[3]: Leaving directory '/<<PKGBUILDDIR>>/Unittest'
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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
make[3]: Leaving directory '/<<PKGBUILDDIR>>/Unittest'
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 -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o BloomDBG/BloomDBG_HashAgnosticCascadingBloom-HashAgnosticCascadingBloomTest.o `test -f 'BloomDBG/HashAgnosticCascadingBloomTest.cpp' || echo './'`BloomDBG/HashAgnosticCascadingBloomTest.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/Unittest'
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 BloomDBG/MaskedKmerTest.o BloomDBG/MaskedKmerTest.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/Unittest'
make[3]: Entering directory '/<<PKGBUILDDIR>>/Unittest'
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
make[3]: Leaving directory '/<<PKGBUILDDIR>>/Unittest'
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../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_BloomDBG-BloomDBGTest.o `test -f 'BloomDBG/BloomDBGTest.cpp' || echo './'`BloomDBG/BloomDBGTest.cpp
In file included from /usr/include/c++/7/vector:69:0,
from ../BloomDBG/RollingHashIterator.h:5,
from ../BloomDBG/bloom-dbg.h:6,
from BloomDBG/BloomDBGTest.cpp:2:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const RollingBloomDBGVertex&}; _Tp = RollingBloomDBGVertex; _Alloc = std::allocator<RollingBloomDBGVertex>]':
/usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type 'std::vector<RollingBloomDBGVertex, std::allocator<RollingBloomDBGVertex> >::iterator {aka __gnu_cxx::__normal_iterator<RollingBloomDBGVertex*, std::vector<RollingBloomDBGVertex, std::allocator<RollingBloomDBGVertex> > >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/algorithm:62:0,
from ../BloomDBG/RollingHashIterator.h:9,
from ../BloomDBG/bloom-dbg.h:6,
from BloomDBG/BloomDBGTest.cpp:2:
/usr/include/c++/7/bits/stl_algo.h: In function '_RandomAccessIterator std::__find_if(_RandomAccessIterator, _RandomAccessIterator, _Predicate, std::random_access_iterator_tag) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<RollingBloomDBGVertex*, std::vector<RollingBloomDBGVertex, std::allocator<RollingBloomDBGVertex> > >; _Predicate = __gnu_cxx::__ops::_Iter_equals_val<const RollingBloomDBGVertex>]':
/usr/include/c++/7/bits/stl_algo.h:112:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<RollingBloomDBGVertex*, std::vector<RollingBloomDBGVertex, std::allocator<RollingBloomDBGVertex> > >' changed in GCC 7.1
__find_if(_RandomAccessIterator __first, _RandomAccessIterator __last,
^~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:112:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<RollingBloomDBGVertex*, std::vector<RollingBloomDBGVertex, std::allocator<RollingBloomDBGVertex> > >' changed in GCC 7.1
/usr/include/c++/7/bits/stl_algo.h:112:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<RollingBloomDBGVertex*, std::vector<RollingBloomDBGVertex, std::allocator<RollingBloomDBGVertex> > >' changed in GCC 7.1
In file included from /usr/include/c++/7/vector:64:0,
from ../BloomDBG/RollingHashIterator.h:5,
from ../BloomDBG/bloom-dbg.h:6,
from BloomDBG/BloomDBGTest.cpp:2:
/usr/include/c++/7/bits/stl_vector.h: In function 'std::vector<std::__cxx11::basic_string<char> > BloomDBG::splitSeq(const Sequence&, unsigned int, unsigned int, const GraphT&, unsigned int) [with GraphT = RollingBloomDBG<BTL::BloomFilter>]':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<RollingBloomDBGVertex*, std::vector<RollingBloomDBGVertex, std::allocator<RollingBloomDBGVertex> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/7/algorithm:62:0,
from ../BloomDBG/RollingHashIterator.h:9,
from ../BloomDBG/bloom-dbg.h:6,
from BloomDBG/BloomDBGTest.cpp:2:
/usr/include/c++/7/bits/stl_algo.h:162:43: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<RollingBloomDBGVertex*, std::vector<RollingBloomDBGVertex, std::allocator<RollingBloomDBGVertex> > >' changed in GCC 7.1
std::__iterator_category(__first));
^
In file included from /usr/include/c++/7/vector:64:0,
from ../BloomDBG/RollingHashIterator.h:5,
from ../BloomDBG/bloom-dbg.h:6,
from BloomDBG/BloomDBGTest.cpp:2:
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<RollingBloomDBGVertex*, std::vector<RollingBloomDBGVertex, std::allocator<RollingBloomDBGVertex> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/7/algorithm:62:0,
from ../BloomDBG/RollingHashIterator.h:9,
from ../BloomDBG/bloom-dbg.h:6,
from BloomDBG/BloomDBGTest.cpp:2:
/usr/include/c++/7/bits/stl_algo.h:162:43: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<RollingBloomDBGVertex*, std::vector<RollingBloomDBGVertex, std::allocator<RollingBloomDBGVertex> > >' changed in GCC 7.1
std::__iterator_category(__first));
^
make[3]: Leaving directory '/<<PKGBUILDDIR>>/Unittest'
make[3]: Entering directory '/<<PKGBUILDDIR>>/Unittest'
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
make[3]: Leaving directory '/<<PKGBUILDDIR>>/Unittest'
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 BloomDBG/SpacedSeedTest.o BloomDBG/SpacedSeedTest.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/Unittest'
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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
make[3]: Leaving directory '/<<PKGBUILDDIR>>/Unittest'
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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
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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
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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
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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
make[3]: Leaving directory '/<<PKGBUILDDIR>>/Unittest'
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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
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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/Konnector_DBGBloom-DBGBloomTest.o ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm
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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/Konnector_DBGBloomAlgorithms-DBGBloomAlgorithmsTest.o ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm
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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
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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
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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
make[3]: Leaving directory '/<<PKGBUILDDIR>>/Unittest'
make[3]: Entering directory '/<<PKGBUILDDIR>>/Unittest'
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
make[3]: Leaving directory '/<<PKGBUILDDIR>>/Unittest'
make[3]: Entering directory '/<<PKGBUILDDIR>>/Unittest'
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
make[3]: Leaving directory '/<<PKGBUILDDIR>>/Unittest'
make[3]: Entering directory '/<<PKGBUILDDIR>>/Unittest'
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
make[3]: Leaving directory '/<<PKGBUILDDIR>>/Unittest'
make[3]: Entering directory '/<<PKGBUILDDIR>>/Unittest'
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
make[3]: Leaving directory '/<<PKGBUILDDIR>>/Unittest'
make[3]: Entering directory '/<<PKGBUILDDIR>>/Unittest'
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
make[3]: Leaving directory '/<<PKGBUILDDIR>>/Unittest'
make[3]: Entering directory '/<<PKGBUILDDIR>>/Unittest'
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_konnector-konnectorTest.o ../Align/libalign.a ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm
make[3]: Leaving directory '/<<PKGBUILDDIR>>/Unittest'
make[3]: Entering directory '/<<PKGBUILDDIR>>/Unittest'
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/DBG_LoadAlgorithm-LoadAlgorithmTest.o ../Assembly/libassembly.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm
make[3]: Leaving directory '/<<PKGBUILDDIR>>/Unittest'
make[3]: Entering directory '/<<PKGBUILDDIR>>/Unittest'
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/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
make[3]: Leaving directory '/<<PKGBUILDDIR>>/Unittest'
make[3]: Entering directory '/<<PKGBUILDDIR>>/Unittest'
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/PairedDBG_Dinuc-DinucTest.o ../PairedDBG/libpaireddbg.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm
make[3]: Leaving directory '/<<PKGBUILDDIR>>/Unittest'
make[3]: Entering directory '/<<PKGBUILDDIR>>/Unittest'
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/PairedDBG_BranchRecord-BranchRecordTest.o ../PairedDBG/libpaireddbg.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm
make[3]: Leaving directory '/<<PKGBUILDDIR>>/Unittest'
make[3]: Entering directory '/<<PKGBUILDDIR>>/Unittest'
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/PairedDBG_KmerPair-KmerPairTest.o ../PairedDBG/libpaireddbg.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm
make[3]: Leaving directory '/<<PKGBUILDDIR>>/Unittest'
make[3]: Entering directory '/<<PKGBUILDDIR>>/Unittest'
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
make[3]: Leaving directory '/<<PKGBUILDDIR>>/Unittest'
make[3]: Entering directory '/<<PKGBUILDDIR>>/Unittest'
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_BloomDBG-BloomDBGTest.o ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm
make[3]: Leaving directory '/<<PKGBUILDDIR>>/Unittest'
make[3]: Entering directory '/<<PKGBUILDDIR>>/Unittest'
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
make[3]: Leaving directory '/<<PKGBUILDDIR>>/Unittest'
make[3]: Entering directory '/<<PKGBUILDDIR>>/Unittest'
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/BloomDBG_HashAgnosticCascadingBloom-HashAgnosticCascadingBloomTest.o ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm
make[3]: Leaving directory '/<<PKGBUILDDIR>>/Unittest'
make[3]: Entering directory '/<<PKGBUILDDIR>>/Unittest'
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
make[3]: Leaving directory '/<<PKGBUILDDIR>>/Unittest'
make[3]: Entering directory '/<<PKGBUILDDIR>>/Unittest'
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
make[3]: Leaving directory '/<<PKGBUILDDIR>>/Unittest'
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 -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o BloomDBG/BloomDBG_RollingBloomDBG-RollingBloomDBGTest.o `test -f 'BloomDBG/RollingBloomDBGTest.cpp' || echo './'`BloomDBG/RollingBloomDBGTest.cpp
In file included from /usr/include/c++/7/unordered_set:47:0,
from ../Common/UnorderedSet.h:8,
from BloomDBG/RollingBloomDBGTest.cpp:3:
/usr/include/c++/7/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++/7/bits/hashtable.h:1850:5: 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>::
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/hashtable.h: In member function 'virtual void RollingBloomDBGTest_out_edge_iterator_Test::TestBody()':
/usr/include/c++/7/bits/hashtable.h:755:42: 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++/7/bits/hashtable.h: In member function 'virtual void RollingBloomDBGSpacedSeedTest_out_edge_iterator_Test::TestBody()':
/usr/include/c++/7/bits/hashtable.h:755:42: 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++/7/bits/hashtable.h: In member function 'virtual void RollingBloomDBGTest_adjacency_iterator_Test::TestBody()':
/usr/include/c++/7/bits/hashtable.h:755:42: 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++/7/bits/hashtable.h: In member function 'virtual void RollingBloomDBGTest_in_edges_Test::TestBody()':
/usr/include/c++/7/bits/hashtable.h:755:42: 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)); }
^
make[3]: Leaving directory '/<<PKGBUILDDIR>>/Unittest'
make[3]: Entering directory '/<<PKGBUILDDIR>>/Unittest'
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/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[4]: Entering directory '/<<PKGBUILDDIR>>/Unittest'
PASS: common_kmer
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Unittest'
make[4]: Entering directory '/<<PKGBUILDDIR>>/Unittest'
PASS: common_bitutil
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Unittest'
make[4]: Entering directory '/<<PKGBUILDDIR>>/Unittest'
PASS: common_histogram
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Unittest'
make[4]: Entering directory '/<<PKGBUILDDIR>>/Unittest'
PASS: common_stringutil
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Unittest'
make[4]: Entering directory '/<<PKGBUILDDIR>>/Unittest'
PASS: common_KmerIterator
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Unittest'
make[4]: Entering directory '/<<PKGBUILDDIR>>/Unittest'
PASS: common_sequence
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Unittest'
make[4]: Entering directory '/<<PKGBUILDDIR>>/Unittest'
PASS: common_sam
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Unittest'
make[4]: Entering directory '/<<PKGBUILDDIR>>/Unittest'
PASS: BloomFilter
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Unittest'
make[4]: Entering directory '/<<PKGBUILDDIR>>/Unittest'
PASS: Konnector_DBGBloom
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Unittest'
make[4]: Entering directory '/<<PKGBUILDDIR>>/Unittest'
PASS: Konnector_DBGBloomAlgorithms
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Unittest'
make[4]: Entering directory '/<<PKGBUILDDIR>>/Unittest'
PASS: graph_ConstrainedBFSVisitor
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Unittest'
make[4]: Entering directory '/<<PKGBUILDDIR>>/Unittest'
PASS: graph_BidirectionalBFS
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Unittest'
make[4]: Entering directory '/<<PKGBUILDDIR>>/Unittest'
PASS: graph_AllPathsSearch
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Unittest'
make[4]: Entering directory '/<<PKGBUILDDIR>>/Unittest'
PASS: graph_HashGraph
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Unittest'
make[4]: Entering directory '/<<PKGBUILDDIR>>/Unittest'
PASS: graph_ConstrainedBidiBFSVisitor
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Unittest'
make[4]: Entering directory '/<<PKGBUILDDIR>>/Unittest'
PASS: graph_DotIO
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Unittest'
make[4]: Entering directory '/<<PKGBUILDDIR>>/Unittest'
PASS: graph_ExtendPath
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Unittest'
make[4]: Entering directory '/<<PKGBUILDDIR>>/Unittest'
PASS: graph_UndirectedGraph
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Unittest'
make[4]: Entering directory '/<<PKGBUILDDIR>>/Unittest'
PASS: Konnector_konnector
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Unittest'
make[4]: Entering directory '/<<PKGBUILDDIR>>/Unittest'
PASS: PairedDBG_KmerPair
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Unittest'
make[4]: Entering directory '/<<PKGBUILDDIR>>/Unittest'
PASS: PairedDBG_Dinuc
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Unittest'
make[4]: Entering directory '/<<PKGBUILDDIR>>/Unittest'
PASS: PairedDBG_BranchRecord
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Unittest'
make[4]: Entering directory '/<<PKGBUILDDIR>>/Unittest'
PASS: BloomDBG_BloomDBG
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Unittest'
make[4]: Entering directory '/<<PKGBUILDDIR>>/Unittest'
PASS: BloomDBG_RollingHash
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Unittest'
make[4]: Entering directory '/<<PKGBUILDDIR>>/Unittest'
PASS: BloomDBG_RollingHashIterator
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Unittest'
make[4]: Entering directory '/<<PKGBUILDDIR>>/Unittest'
PASS: BloomDBG_RollingBloomDBG
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Unittest'
make[4]: Entering directory '/<<PKGBUILDDIR>>/Unittest'
PASS: BloomDBG_HashAgnosticCascadingBloom
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Unittest'
make[4]: Entering directory '/<<PKGBUILDDIR>>/Unittest'
PASS: BloomDBG_MaskedKmer
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Unittest'
make[4]: Entering directory '/<<PKGBUILDDIR>>/Unittest'
PASS: BloomDBG_SpacedSeed
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Unittest'
make[4]: Entering directory '/<<PKGBUILDDIR>>/Unittest'
PASS: PairedDBG_LoadAlgorithm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Unittest'
make[4]: Entering directory '/<<PKGBUILDDIR>>/Unittest'
PASS: DBG_LoadAlgorithm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Unittest'
make[4]: Entering directory '/<<PKGBUILDDIR>>/Unittest'
============================================================================
Testsuite summary for ABySS 2.0.3
============================================================================
# TOTAL: 31
# PASS: 31
# SKIP: 0
# XFAIL: 0
# FAIL: 0
# XPASS: 0
# ERROR: 0
============================================================================
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Unittest'
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 -O install DESTDIR=/<<PKGBUILDDIR>>/debian/tmp AM_UPDATE_INFO_DIR=no
Making install in bin
make[4]: Nothing to be done for 'install-data-am'.
make[4]: Entering directory '/<<PKGBUILDDIR>>/bin'
/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 '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/bin'
Making install in doc
make[4]: Nothing to be done for 'install-exec-am'.
make[4]: Entering directory '/<<PKGBUILDDIR>>/doc'
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/share/doc/abyss'
/usr/bin/install -c -m 644 flowchart.pdf flowchart_simplified.pdf '/<<PKGBUILDDIR>>/debian/tmp/usr/share/doc/abyss'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/doc'
make[4]: Entering directory '/<<PKGBUILDDIR>>/doc'
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man1'
/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'
Making install in Common
make[4]: Nothing to be done for 'install-exec-am'.
make[4]: Nothing to be done for 'install-data-am'.
Making install in Graph
make[4]: Nothing to be done for 'install-data-am'.
make[4]: Entering directory '/<<PKGBUILDDIR>>/Graph'
/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'
Making install in DataLayer
make[4]: Nothing to be done for 'install-data-am'.
make[4]: Entering directory '/<<PKGBUILDDIR>>/DataLayer'
/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'
Making install in DataBase
make[4]: Nothing to be done for 'install-data-am'.
make[4]: Entering directory '/<<PKGBUILDDIR>>/DataBase'
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
/usr/bin/install -c abyss-db-csv '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/DataBase'
make[4]: Entering directory '/<<PKGBUILDDIR>>/DataBase'
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
/usr/bin/install -c abyss-db-txt '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/DataBase'
Making install in FMIndex
make[4]: Nothing to be done for 'install-exec-am'.
make[4]: Nothing to be done for 'install-data-am'.
Making install in Assembly
make[4]: Nothing to be done for 'install-exec-am'.
make[4]: Nothing to be done for 'install-data-am'.
Making install in dialign
make[4]: Nothing to be done for 'install-exec-am'.
make[4]: Nothing to be done for 'install-data-am'.
Making install in Align
make[4]: Nothing to be done for 'install-data-am'.
make[4]: Entering directory '/<<PKGBUILDDIR>>/Align'
/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'
Making install in ABYSS
make[4]: Nothing to be done for 'install-data-am'.
make[4]: Entering directory '/<<PKGBUILDDIR>>/ABYSS'
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
/usr/bin/install -c ABYSS '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/ABYSS'
Making install in Bloom
make[4]: Nothing to be done for 'install-data-am'.
make[4]: Entering directory '/<<PKGBUILDDIR>>/Bloom'
/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'
Making install in BloomDBG
make[4]: Nothing to be done for 'install-data-am'.
make[4]: Entering directory '/<<PKGBUILDDIR>>/BloomDBG'
/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'
Making install in Konnector
make[4]: Nothing to be done for 'install-data-am'.
make[4]: Entering directory '/<<PKGBUILDDIR>>/Konnector'
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
/usr/bin/install -c konnector '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Konnector'
Making install in Consensus
make[4]: Nothing to be done for 'install-data-am'.
make[4]: Entering directory '/<<PKGBUILDDIR>>/Consensus'
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
/usr/bin/install -c Consensus '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Consensus'
Making install in DAssembler
make[4]: Nothing to be done for 'install-data-am'.
make[4]: Entering directory '/<<PKGBUILDDIR>>/DAssembler'
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
/usr/bin/install -c DAssembler '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/DAssembler'
Making install in DistanceEst
make[4]: Nothing to be done for 'install-data-am'.
make[4]: Entering directory '/<<PKGBUILDDIR>>/DistanceEst'
/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'
Making install in KAligner
make[4]: Nothing to be done for 'install-data-am'.
make[4]: Entering directory '/<<PKGBUILDDIR>>/KAligner'
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
/usr/bin/install -c KAligner '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/KAligner'
Making install in Layout
make[4]: Nothing to be done for 'install-data-am'.
make[4]: Entering directory '/<<PKGBUILDDIR>>/Layout'
/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'
Making install in LogKmerCount
make[4]: Nothing to be done for 'install-data-am'.
make[4]: Entering directory '/<<PKGBUILDDIR>>/LogKmerCount'
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
/usr/bin/install -c logcounter '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/LogKmerCount'
Making install in Map
make[4]: Nothing to be done for 'install-data-am'.
make[4]: Entering directory '/<<PKGBUILDDIR>>/Map'
/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'
Making install in MergePaths
make[4]: Nothing to be done for 'install-data-am'.
make[4]: Entering directory '/<<PKGBUILDDIR>>/MergePaths'
/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'
Making install in Misc
make[4]: Nothing to be done for 'install-data-am'.
Making install in Overlap
make[4]: Nothing to be done for 'install-data-am'.
make[4]: Entering directory '/<<PKGBUILDDIR>>/Overlap'
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
/usr/bin/install -c Overlap '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Overlap'
Making install in PairedDBG
make[4]: Nothing to be done for 'install-data-am'.
make[4]: Entering directory '/<<PKGBUILDDIR>>/PairedDBG'
/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'
Making install in ParseAligns
make[4]: Nothing to be done for 'install-data-am'.
make[4]: Entering directory '/<<PKGBUILDDIR>>/ParseAligns'
/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'
Making install in PathOverlap
make[4]: Nothing to be done for 'install-data-am'.
make[4]: Entering directory '/<<PKGBUILDDIR>>/PathOverlap'
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
/usr/bin/install -c PathOverlap '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/PathOverlap'
Making install in PopBubbles
make[4]: Nothing to be done for 'install-data-am'.
make[4]: Entering directory '/<<PKGBUILDDIR>>/PopBubbles'
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
/usr/bin/install -c PopBubbles '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/PopBubbles'
Making install in Scaffold
make[4]: Nothing to be done for 'install-data-am'.
make[4]: Entering directory '/<<PKGBUILDDIR>>/Scaffold'
/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'
Making install in SimpleGraph
make[4]: Nothing to be done for 'install-data-am'.
make[4]: Entering directory '/<<PKGBUILDDIR>>/SimpleGraph'
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
/usr/bin/install -c SimpleGraph '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/SimpleGraph'
Making install in kmerprint
make[4]: Nothing to be done for 'install-exec-am'.
make[4]: Nothing to be done for 'install-data-am'.
Making install in FilterGraph
make[4]: Nothing to be done for 'install-data-am'.
make[4]: Entering directory '/<<PKGBUILDDIR>>/FilterGraph'
/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'
Making install in GapFiller
make[4]: Nothing to be done for 'install-data-am'.
make[4]: Entering directory '/<<PKGBUILDDIR>>/GapFiller'
/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'
Making install in 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'
Making install in AdjList
make[4]: Nothing to be done for 'install-data-am'.
make[4]: Entering directory '/<<PKGBUILDDIR>>/AdjList'
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
/usr/bin/install -c AdjList '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/AdjList'
Making install in lib/bloomfilter
make[4]: Nothing to be done for 'install-exec-am'.
make[4]: Nothing to be done for 'install-data-am'.
Making install in lib/rolling-hash
make[4]: Nothing to be done for 'install-exec-am'.
make[4]: Nothing to be done for 'install-data-am'.
Making install in 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'.
Making install in Unittest
make[4]: Nothing to be done for 'install-exec-am'.
make[4]: Nothing to be done for 'install-data-am'.
make[4]: Nothing to be done for 'install-exec-am'.
make[4]: Entering directory '/<<PKGBUILDDIR>>'
/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[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_install -a
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/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-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/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-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-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-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/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/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/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-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/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 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/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/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/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-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-sealer contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/abyss-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-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-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/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-gc contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/abyss-tofastq contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/abyss-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/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/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/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-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/logcounter contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/abyss-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-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/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-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/MergeContigs contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/abyss-longseqdist contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/MergePaths contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/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-bloom contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/abyss/usr/lib/abyss/abyss-db-csv debian/abyss/usr/lib/abyss/abyss-paired-dbg debian/abyss/usr/bin/DistanceEst debian/abyss/usr/lib/abyss/abyss-align debian/abyss/usr/lib/abyss/abyss-bloom-dbg debian/abyss/usr/lib/abyss/abyss-map-ssq debian/abyss/usr/lib/abyss/Overlap debian/abyss/usr/lib/abyss/KAligner debian/abyss/usr/lib/abyss/ParseAligns debian/abyss/usr/lib/abyss/abyss-scaffold debian/abyss/usr/lib/abyss/konnector debian/abyss/usr/lib/abyss/ABYSS debian/abyss/usr/lib/abyss/PathOverlap debian/abyss/usr/lib/abyss/PopBubbles debian/abyss/usr/lib/abyss/PathConsensus debian/abyss/usr/lib/abyss/SimpleGraph debian/abyss/usr/lib/abyss/abyss-mergepairs debian/abyss/usr/lib/abyss/abyss-sealer debian/abyss/usr/lib/abyss/abyss-fixmate-ssq debian/abyss/usr/lib/abyss/abyss-fac debian/abyss/usr/lib/abyss/abyss-overlap debian/abyss/usr/lib/abyss/abyss-layout debian/abyss/usr/lib/abyss/DistanceEst debian/abyss/usr/lib/abyss/abyss-gc debian/abyss/usr/lib/abyss/abyss-tofastq debian/abyss/usr/lib/abyss/abyss-index debian/abyss/usr/lib/abyss/DAssembler debian/abyss/usr/bin/abyss-fixmate debian/abyss/usr/lib/abyss/Consensus debian/abyss/usr/lib/abyss/abyss-junction debian/abyss/usr/lib/abyss/logcounter debian/abyss/usr/lib/abyss/abyss-gapfill debian/abyss/usr/lib/abyss/DistanceEst-ssq debian/abyss/usr/lib/abyss/abyss-filtergraph debian/abyss/usr/lib/abyss/AdjList debian/abyss/usr/lib/abyss/abyss-todot debian/abyss/usr/lib/abyss/abyss-fixmate debian/abyss/usr/lib/abyss/MergeContigs debian/abyss/usr/lib/abyss/abyss-longseqdist debian/abyss/usr/lib/abyss/MergePaths debian/abyss/usr/lib/abyss/abyss-map debian/abyss/usr/lib/abyss/abyss-bloom were not linked against ld-linux-armhf.so.3 (they use none of the library's symbols)
dh_installdeb -a
dh_gencontrol -a
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package 'abyss' in '../abyss_2.0.3-1_armhf.deb'.
dpkg-deb: building package 'abyss-dbgsym' in '../abyss-dbgsym_2.0.3-1_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../abyss_2.0.3-1_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build abyss-2.0.3
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2018-03-26T05:36:56Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
abyss_2.0.3-1_armhf.changes:
----------------------------
Format: 1.8
Date: Tue, 20 Mar 2018 14:33:26 +0100
Source: abyss
Binary: abyss
Architecture: armhf
Version: 2.0.3-1
Distribution: buster-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
abyss - de novo, parallel, sequence assembler for short reads
Changes:
abyss (2.0.3-1) unstable; urgency=medium
.
[ Steffen Moeller ]
* debian/upstream/metadata: RRID -> SciCrunch
.
[ Andreas Tille ]
* New upstream version
* Standards-Version: 4.1.3
* debhelper 11
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1b80303cbb32829df0c66f600b2fcdb1264a99d8e49ecfb4165efdc0979e1fd8 2532540 abyss_2.0.3-1_armhf.deb
Files:
e8b39d1f41da57f015b6ba006517fa4f 21586680 debug optional abyss-dbgsym_2.0.3-1_armhf.deb
0e818e6c6cb51a256d1d97fda63ccb2c 6220 science optional abyss_2.0.3-1_armhf.buildinfo
94f4597e7bd8bc5a9ee9586ea6378277 2532540 science optional abyss_2.0.3-1_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
abyss-dbgsym_2.0.3-1_armhf.deb
------------------------------
new Debian package, version 2.0.
size 21586680 bytes: control archive=2336 bytes.
1963 bytes, 12 lines control
4240 bytes, 40 lines md5sums
Package: abyss-dbgsym
Source: abyss
Version: 2.0.3-1
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 22620
Depends: abyss (= 2.0.3-1)
Section: debug
Priority: optional
Description: debug symbols for abyss
Build-Ids: 0e8c9c3004e6b7bba4d74a719200d088c8ef1552 0f5d15c50f3b52b12a4b4ded2c0fe5da82cf5133 132ff9cb027fa099ae967c98a67e95fe6f079b7b 1352011d71e6098aa1c24c3bd12832d6c51273c8 13826e335d0b366b3c8ee3d140102d6b7eba07a7 1912cf2bc1f2e648c62600d4b1a738a8cabd1b5a 247bdbb641261efa342719dcef4b90e6c95be51c 34a013731c1d9e29462eb31de8426cfade96bc4c 409d40ecc09b6a58a20e6986a6589b7011b4699a 40b9509c06f1d561f96cda586172865b5e1a3773 4656dfb8ef6af9236365f74ebea864dc8c47cb71 477c4cb5893ede7465af111b0f365597d76c364c 48c9695d0d33d50182f4948a083ec8f663cf938b 4d0f74cc5522582807c963164400f6fbe5491e71 4d5af5a9356c0f58932b216bfbbd50f124cff166 4e28ac1f30c22d8d4e0bda9d69eef1ad5d0d9f35 506e74114dbe20761a46cee2b96a5dd1790077b1 515957911368ccbcf1c22d7aa54d46a3b2383334 54cbe93b8e40efbfaf76ad37fe2fc72a0c1241a9 5be357e78eb096bf1f03ca275cd57efa35686975 609074ba6005d248613e1ce1abbe4162cf0eee5d 666067be83346ad5dbd8e85cfa7a1409dc1f7aee 66621de30d00b59df487c4a05f340e96ffbac8e5 6bf0a22ef151e76a3e29d9238f2fb7b85ce636d2 6ceff9ffa69b133cf49bb625e89939a77904d9fb 743fbb2264b315129b17afa50350bd061b291409 75fa125a7e7a1f4729d16b361c3408843d46dfd6 76de6a26afb6e88543704fe8b734f7127719b68d 79861af48671e1c6858134c7a4a5b155b1ae0325 8dfedfa64e4eb912057e535e7a67fa9e65e62e44 917846c7d00dfcc0101b309d3b5e7970b4a71374 a60707c69de9a8322b684c3b6ed52b9372c7a4a2 b124b6b62f558194cec4e053e8bcac21e7625029 b4a67d43c8d7ea0f2d2082158da9011408ef5a76 b6aaa8be906b26007405e131ba7e5bb4646d4b25 ba9b134cc85f7e1ae2d7e32fc51d7143a6c8a284 c0795a44b65390df9a22ccc52f692534e3a5dd88 d104f7a5d0a55ae608ec87f34f12fb2506c474dc e46f0d6d3deea342bb1293a30560e511d23467b3 e7e83f5b1005a61b0e31c0615da2de26baf12946
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lrwxrwxrwx root/root 0 2018-03-20 13:33 ./usr/share/doc/abyss-dbgsym -> abyss
abyss_2.0.3-1_armhf.deb
-----------------------
new Debian package, version 2.0.
size 2532540 bytes: control archive=2460 bytes.
696 bytes, 15 lines control
4290 bytes, 69 lines md5sums
Package: abyss
Version: 2.0.3-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 7030
Depends: make, libc6 (>= 2.7), 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 2018-03-20 13:33 ./
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-rwxr-xr-x root/root 1135 2018-03-20 13:33 ./usr/lib/abyss/abyss-bowtie
-rwxr-xr-x root/root 1192 2018-03-20 13:33 ./usr/lib/abyss/abyss-bowtie2
-rwxr-xr-x root/root 1208 2018-03-20 13:33 ./usr/lib/abyss/abyss-bwa
-rwxr-xr-x root/root 1454 2018-03-20 13:33 ./usr/lib/abyss/abyss-bwamem
-rwxr-xr-x root/root 1362 2018-03-20 13:33 ./usr/lib/abyss/abyss-bwasw
-rwxr-xr-x root/root 54792 2018-03-20 13:33 ./usr/lib/abyss/abyss-db-csv
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-rw-r--r-- root/root 182 2018-03-20 13:33 ./usr/share/doc/abyss/README.test
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-rw-r--r-- root/root 6121 2018-03-20 13:33 ./usr/share/doc/abyss/copyright
-rw-r--r-- root/root 66778 2018-03-14 21:55 ./usr/share/doc/abyss/flowchart.pdf.gz
-rw-r--r-- root/root 299 2018-03-20 13:33 ./usr/share/doc/abyss/run-unit-test
drwxr-xr-x root/root 0 2018-03-20 13:33 ./usr/share/doc/abyss/test-data/
-rw-r--r-- root/root 743013 2018-03-20 13:33 ./usr/share/doc/abyss/test-data/reads1.fastq.gz
-rw-r--r-- root/root 743377 2018-03-20 13:33 ./usr/share/doc/abyss/test-data/reads2.fastq.gz
drwxr-xr-x root/root 0 2018-03-20 13:33 ./usr/share/man/
drwxr-xr-x root/root 0 2018-03-20 13:33 ./usr/share/man/man1/
-rw-r--r-- root/root 1200 2018-03-20 13:33 ./usr/share/man/man1/ABYSS.1.gz
-rw-r--r-- root/root 3567 2018-03-20 13:33 ./usr/share/man/man1/abyss-pe.1.gz
-rw-r--r-- root/root 408 2018-03-20 13:33 ./usr/share/man/man1/abyss-tofastq.1.gz
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 420016
Build-Time: 2555
Distribution: buster-staging
Host Architecture: armhf
Install-Time: 600
Job: abyss_2.0.3-1
Machine Architecture: armhf
Package: abyss
Package-Time: 3210
Source-Version: 2.0.3-1
Space: 420016
Status: successful
Version: 2.0.3-1
--------------------------------------------------------------------------------
Finished at 2018-03-26T05:36:56Z
Build needed 00:53:30, 420016k disc space