abyss →
2.3.1-1 →
armhf → 2021-10-05 00:26:51
sbuild (Debian sbuild) 0.72.0 (25 Oct 2016) on mb-lxc-01
+==============================================================================+
| abyss 2.3.1-1 (armhf) Tue, 05 Oct 2021 00:02:04 +0000 |
+==============================================================================+
Package: abyss
Version: 2.3.1-1
Source Version: 2.3.1-1
Distribution: bookworm-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/bookworm-staging-armhf-sbuild-e89a8e59-39f6-4209-ab2c-f32d65bf3dbe' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private bookworm-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private bookworm-staging/main Sources [12.4 MB]
Get:3 http://172.17.0.1/private bookworm-staging/main armhf Packages [13.4 MB]
Fetched 25.8 MB in 10s (2647 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: 'abyss' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/abyss.git
Please use:
git clone https://salsa.debian.org/med-team/abyss.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 1823 kB of source archives.
Get:1 http://172.17.0.1/private bookworm-staging/main abyss 2.3.1-1 (dsc) [2336 B]
Get:2 http://172.17.0.1/private bookworm-staging/main abyss 2.3.1-1 (tar) [1064 kB]
Get:3 http://172.17.0.1/private bookworm-staging/main abyss 2.3.1-1 (diff) [757 kB]
Fetched 1823 kB in 0s (4698 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/abyss-s8KY1t/abyss-2.3.1' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/abyss-s8KY1t' 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-9zVo1V/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-9zVo1V/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-9zVo1V/gpg/trustdb.gpg: trustdb created
gpg: key 37145E60F90AF620: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg: imported: 1
gpg: key 37145E60F90AF620: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 37145E60F90AF620: secret key imported
gpg: Total number processed: 1
gpg: unchanged: 1
gpg: secret keys read: 1
gpg: secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-9zVo1V/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-9zVo1V/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-9zVo1V/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-9zVo1V/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-9zVo1V/apt_archive ./ Packages [432 B]
Fetched 2108 B in 0s (9782 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 package was automatically installed and is no longer required:
netbase
Use 'apt autoremove' to remove it.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 22 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-9zVo1V/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 (67.2 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12484 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any-amd64 any-i386 arm64 armel armhf mips64el mipsel ppc64el s390x alpha ia64 m68k powerpcspe ppc64 riscv64 sh4 sparc64)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper-compat (= 13), libboost-graph-dev, libopenmpi-dev, libsparsehash-dev, libtext-multimarkdown-perl, libsqlite3-dev, pkg-config, help2man
Filtered Build-Depends: debhelper-compat (= 13), libboost-graph-dev, libopenmpi-dev, libsparsehash-dev, libtext-multimarkdown-perl, libsqlite3-dev, pkg-config, help2man
dpkg-deb: building package 'sbuild-build-depends-abyss-dummy' in '/<<BUILDDIR>>/resolver-9zVo1V/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-9zVo1V/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-9zVo1V/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-9zVo1V/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-9zVo1V/apt_archive ./ Sources [568 B]
Get:5 copy:/<<BUILDDIR>>/resolver-9zVo1V/apt_archive ./ Packages [638 B]
Fetched 2539 B in 0s (11.8 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install abyss build dependencies (apt-based resolver)
-----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following package was automatically installed and is no longer required:
netbase
Use 'apt autoremove' to remove it.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdextrautils cpp-10 debhelper
dh-autoreconf dh-strip-nondeterminism dwz file g++-10 gcc-10 gcc-10-base
gcc-11-base gettext gettext-base gfortran-10 groff-base help2man
ibverbs-providers icu-devtools intltool-debian libarchive-zip-perl libasan6
libatomic1 libboost-graph-dev libboost-graph1.74-dev libboost-graph1.74.0
libboost-regex1.74-dev libboost-regex1.74.0 libboost-serialization1.74-dev
libboost-serialization1.74.0 libboost-test1.74-dev libboost-test1.74.0
libboost1.74-dev libbsd0 libcbor0 libcc1-0 libdebhelper-perl libedit2
libelf1 libevent-2.1-7 libevent-core-2.1-7 libevent-dev libevent-extra-2.1-7
libevent-openssl-2.1-7 libevent-pthreads-2.1-7 libfabric1 libffi8 libfido2-1
libfile-stripnondeterminism-perl libgcc-10-dev libgcc-s1 libgfortran-10-dev
libgfortran5 libglib2.0-0 libgomp1 libhtml-parser-perl libhtml-tagset-perl
libhwloc-dev libhwloc-plugins libhwloc15 libibverbs-dev libibverbs1
libicu-dev libicu67 libjs-jquery libjs-jquery-ui libltdl-dev libltdl7
libmagic-mgc libmagic1 libmd0 libnl-3-200 libnl-3-dev libnl-route-3-200
libnl-route-3-dev libnuma-dev libnuma1 libopenmpi-dev libopenmpi3
libpciaccess0 libpipeline1 libpmix-dev libpmix2 librdmacm1 libsigsegv2
libsparsehash-dev libsqlite3-dev libstdc++-10-dev libstdc++6
libsub-override-perl libtext-markdown-perl libtext-multimarkdown-perl
libtool libubsan1 libuchardet0 liburi-perl libx11-6 libx11-data libxau6
libxcb1 libxdmcp6 libxext6 libxml2 libxnvctrl0 m4 man-db ocl-icd-libopencl1
openmpi-bin openmpi-common openssh-client pkg-config po-debconf
sensible-utils zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc gcc-10-locales dh-make
gcc-10-doc gettext-doc libasprintf-dev libgettextpo-dev gfortran-10-doc
libcoarrays-dev groff graphviz libboost1.74-doc libboost-atomic1.74-dev
libboost-chrono1.74-dev libboost-container1.74-dev libboost-context1.74-dev
libboost-contract1.74-dev libboost-coroutine1.74-dev
libboost-date-time1.74-dev libboost-exception1.74-dev libboost-fiber1.74-dev
libboost-filesystem1.74-dev libboost-graph-parallel1.74-dev
libboost-iostreams1.74-dev libboost-locale1.74-dev libboost-log1.74-dev
libboost-math1.74-dev libboost-mpi1.74-dev libboost-mpi-python1.74-dev
libboost-numpy1.74-dev libboost-program-options1.74-dev
libboost-python1.74-dev libboost-random1.74-dev libboost-stacktrace1.74-dev
libboost-system1.74-dev libboost-thread1.74-dev libboost-timer1.74-dev
libboost-type-erasure1.74-dev libboost-wave1.74-dev libboost1.74-tools-dev
libmpfrc++-dev libntl-dev libboost-nowide1.74-dev libdata-dump-perl icu-doc
libjs-jquery-ui-docs libtool-doc openmpi-doc pciutils sqlite3-doc
libstdc++-10-doc gcj-jdk libwww-perl m4-doc apparmor less www-browser
opencl-icd gfortran | fortran-compiler keychain libpam-ssh monkeysphere
ssh-askpass libmail-box-perl
Recommended packages:
curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info
xdg-user-dirs libhttp-message-perl javascript-common libcoarrays-openmpi-dev
xauth libmail-sendmail-perl
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdextrautils debhelper
dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base
gfortran-10 groff-base help2man ibverbs-providers icu-devtools
intltool-debian libarchive-zip-perl libboost-graph-dev
libboost-graph1.74-dev libboost-graph1.74.0 libboost-regex1.74-dev
libboost-regex1.74.0 libboost-serialization1.74-dev
libboost-serialization1.74.0 libboost-test1.74-dev libboost-test1.74.0
libboost1.74-dev libbsd0 libcbor0 libdebhelper-perl libedit2 libelf1
libevent-2.1-7 libevent-core-2.1-7 libevent-dev libevent-extra-2.1-7
libevent-openssl-2.1-7 libevent-pthreads-2.1-7 libfabric1 libffi8 libfido2-1
libfile-stripnondeterminism-perl libgfortran-10-dev libgfortran5
libglib2.0-0 libhtml-parser-perl libhtml-tagset-perl libhwloc-dev
libhwloc-plugins libhwloc15 libibverbs-dev libibverbs1 libicu-dev libicu67
libjs-jquery libjs-jquery-ui libltdl-dev libltdl7 libmagic-mgc libmagic1
libmd0 libnl-3-200 libnl-3-dev libnl-route-3-200 libnl-route-3-dev
libnuma-dev libnuma1 libopenmpi-dev libopenmpi3 libpciaccess0 libpipeline1
libpmix-dev libpmix2 librdmacm1 libsigsegv2 libsparsehash-dev libsqlite3-dev
libsub-override-perl libtext-markdown-perl libtext-multimarkdown-perl
libtool libuchardet0 liburi-perl libx11-6 libx11-data libxau6 libxcb1
libxdmcp6 libxext6 libxml2 libxnvctrl0 m4 man-db ocl-icd-libopencl1
openmpi-bin openmpi-common openssh-client pkg-config po-debconf
sbuild-build-depends-abyss-dummy sensible-utils zlib1g-dev
The following packages will be upgraded:
cpp-10 g++-10 gcc-10 gcc-10-base gcc-11-base libasan6 libatomic1 libcc1-0
libgcc-10-dev libgcc-s1 libgomp1 libstdc++-10-dev libstdc++6 libubsan1
14 upgraded, 104 newly installed, 0 to remove and 8 not upgraded.
Need to get 94.2 MB of archives.
After this operation, 353 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-9zVo1V/apt_archive ./ sbuild-build-depends-abyss-dummy 0.invalid.0 [928 B]
Get:2 http://172.17.0.1/private bookworm-staging/main armhf bsdextrautils armhf 2.37.2-1 [135 kB]
Get:3 http://172.17.0.1/private bookworm-staging/main armhf libasan6 armhf 11.2.0-7+rpi1 [1944 kB]
Get:4 http://172.17.0.1/private bookworm-staging/main armhf libubsan1 armhf 11.2.0-7+rpi1 [797 kB]
Get:5 http://172.17.0.1/private bookworm-staging/main armhf libgomp1 armhf 11.2.0-7+rpi1 [88.1 kB]
Get:6 http://172.17.0.1/private bookworm-staging/main armhf gcc-11-base armhf 11.2.0-7+rpi1 [205 kB]
Get:7 http://172.17.0.1/private bookworm-staging/main armhf libgcc-s1 armhf 11.2.0-7+rpi1 [36.2 kB]
Get:8 http://172.17.0.1/private bookworm-staging/main armhf libcc1-0 armhf 11.2.0-7+rpi1 [37.7 kB]
Get:9 http://172.17.0.1/private bookworm-staging/main armhf libatomic1 armhf 11.2.0-7+rpi1 [8188 B]
Get:10 http://172.17.0.1/private bookworm-staging/main armhf libstdc++6 armhf 11.2.0-7+rpi1 [465 kB]
Get:11 http://172.17.0.1/private bookworm-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:12 http://172.17.0.1/private bookworm-staging/main armhf groff-base armhf 1.22.4-7 [793 kB]
Get:13 http://172.17.0.1/private bookworm-staging/main armhf libpipeline1 armhf 1.5.3-1 [29.9 kB]
Get:14 http://172.17.0.1/private bookworm-staging/main armhf man-db armhf 2.9.4-2 [1307 kB]
Get:15 http://172.17.0.1/private bookworm-staging/main armhf g++-10 armhf 10.3.0-11+rpi1 [7350 kB]
Get:16 http://172.17.0.1/private bookworm-staging/main armhf gcc-10 armhf 10.3.0-11+rpi1 [13.4 MB]
Get:17 http://172.17.0.1/private bookworm-staging/main armhf libstdc++-10-dev armhf 10.3.0-11+rpi1 [1755 kB]
Get:18 http://172.17.0.1/private bookworm-staging/main armhf libgcc-10-dev armhf 10.3.0-11+rpi1 [678 kB]
Get:19 http://172.17.0.1/private bookworm-staging/main armhf cpp-10 armhf 10.3.0-11+rpi1 [6690 kB]
Get:20 http://172.17.0.1/private bookworm-staging/main armhf gcc-10-base armhf 10.3.0-11+rpi1 [206 kB]
Get:21 http://172.17.0.1/private bookworm-staging/main armhf sensible-utils all 0.0.17 [21.5 kB]
Get:22 http://172.17.0.1/private bookworm-staging/main armhf libmagic-mgc armhf 1:5.39-3 [273 kB]
Get:23 http://172.17.0.1/private bookworm-staging/main armhf libmagic1 armhf 1:5.39-3 [117 kB]
Get:24 http://172.17.0.1/private bookworm-staging/main armhf file armhf 1:5.39-3 [68.0 kB]
Get:25 http://172.17.0.1/private bookworm-staging/main armhf gettext-base armhf 0.21-4 [171 kB]
Get:26 http://172.17.0.1/private bookworm-staging/main armhf libmd0 armhf 1.0.3-3 [27.2 kB]
Get:27 http://172.17.0.1/private bookworm-staging/main armhf libbsd0 armhf 0.11.3-1 [103 kB]
Get:28 http://172.17.0.1/private bookworm-staging/main armhf libedit2 armhf 3.1-20210910-1 [81.2 kB]
Get:29 http://172.17.0.1/private bookworm-staging/main armhf libcbor0 armhf 0.5.0+dfsg-2 [19.5 kB]
Get:30 http://172.17.0.1/private bookworm-staging/main armhf libfido2-1 armhf 1.8.0-1 [55.9 kB]
Get:31 http://172.17.0.1/private bookworm-staging/main armhf openssh-client armhf 1:8.4p1-6 [794 kB]
Get:32 http://172.17.0.1/private bookworm-staging/main armhf libsigsegv2 armhf 2.13-1 [34.3 kB]
Get:33 http://172.17.0.1/private bookworm-staging/main armhf m4 armhf 1.4.18-5 [186 kB]
Get:34 http://172.17.0.1/private bookworm-staging/main armhf autoconf all 2.71-2 [343 kB]
Get:35 http://172.17.0.1/private bookworm-staging/main armhf autotools-dev all 20180224.1+nmu1 [77.1 kB]
Get:36 http://172.17.0.1/private bookworm-staging/main armhf automake all 1:1.16.4-2 [819 kB]
Get:37 http://172.17.0.1/private bookworm-staging/main armhf autopoint all 0.21-4 [510 kB]
Get:38 http://172.17.0.1/private bookworm-staging/main armhf libdebhelper-perl all 13.5.2 [192 kB]
Get:39 http://172.17.0.1/private bookworm-staging/main armhf libtool all 2.4.6-15 [513 kB]
Get:40 http://172.17.0.1/private bookworm-staging/main armhf dh-autoreconf all 20 [17.1 kB]
Get:41 http://172.17.0.1/private bookworm-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:42 http://172.17.0.1/private bookworm-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:43 http://172.17.0.1/private bookworm-staging/main armhf libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB]
Get:44 http://172.17.0.1/private bookworm-staging/main armhf dh-strip-nondeterminism all 1.12.0-1 [15.4 kB]
Get:45 http://172.17.0.1/private bookworm-staging/main armhf libelf1 armhf 0.185-2 [168 kB]
Get:46 http://172.17.0.1/private bookworm-staging/main armhf dwz armhf 0.14-1 [83.0 kB]
Get:47 http://172.17.0.1/private bookworm-staging/main armhf libicu67 armhf 67.1-7 [8291 kB]
Get:48 http://172.17.0.1/private bookworm-staging/main armhf libxml2 armhf 2.9.12+dfsg-5 [584 kB]
Get:49 http://172.17.0.1/private bookworm-staging/main armhf gettext armhf 0.21-4 [1215 kB]
Get:50 http://172.17.0.1/private bookworm-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:51 http://172.17.0.1/private bookworm-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:52 http://172.17.0.1/private bookworm-staging/main armhf debhelper all 13.5.2 [1056 kB]
Get:53 http://172.17.0.1/private bookworm-staging/main armhf libgfortran5 armhf 11.2.0-7+rpi1 [235 kB]
Get:54 http://172.17.0.1/private bookworm-staging/main armhf libgfortran-10-dev armhf 10.3.0-11+rpi1 [277 kB]
Get:55 http://172.17.0.1/private bookworm-staging/main armhf gfortran-10 armhf 10.3.0-11+rpi1 [7201 kB]
Get:56 http://172.17.0.1/private bookworm-staging/main armhf help2man armhf 1.48.5 [143 kB]
Get:57 http://172.17.0.1/private bookworm-staging/main armhf libnl-3-200 armhf 3.4.0-1 [55.0 kB]
Get:58 http://172.17.0.1/private bookworm-staging/main armhf libnl-route-3-200 armhf 3.4.0-1 [132 kB]
Get:59 http://172.17.0.1/private bookworm-staging/main armhf libibverbs1 armhf 36.0-1 [53.2 kB]
Get:60 http://172.17.0.1/private bookworm-staging/main armhf ibverbs-providers armhf 36.0-1 [27.3 kB]
Get:61 http://172.17.0.1/private bookworm-staging/main armhf icu-devtools armhf 67.1-7 [172 kB]
Get:62 http://172.17.0.1/private bookworm-staging/main armhf libboost1.74-dev armhf 1.74.0-9 [9534 kB]
Get:63 http://172.17.0.1/private bookworm-staging/main armhf libboost-regex1.74.0 armhf 1.74.0-9 [448 kB]
Get:64 http://172.17.0.1/private bookworm-staging/main armhf libboost-graph1.74.0 armhf 1.74.0-9 [307 kB]
Get:65 http://172.17.0.1/private bookworm-staging/main armhf libicu-dev armhf 67.1-7 [9228 kB]
Get:66 http://172.17.0.1/private bookworm-staging/main armhf libboost-regex1.74-dev armhf 1.74.0-9 [553 kB]
Get:67 http://172.17.0.1/private bookworm-staging/main armhf libboost-serialization1.74.0 armhf 1.74.0-9 [319 kB]
Get:68 http://172.17.0.1/private bookworm-staging/main armhf libboost-serialization1.74-dev armhf 1.74.0-9 [388 kB]
Get:69 http://172.17.0.1/private bookworm-staging/main armhf libboost-test1.74.0 armhf 1.74.0-9 [427 kB]
Get:70 http://172.17.0.1/private bookworm-staging/main armhf libboost-test1.74-dev armhf 1.74.0-9 [516 kB]
Get:71 http://172.17.0.1/private bookworm-staging/main armhf libboost-graph1.74-dev armhf 1.74.0-9 [338 kB]
Get:72 http://172.17.0.1/private bookworm-staging/main armhf libboost-graph-dev armhf 1.74.0.3+b1 [4708 B]
Get:73 http://172.17.0.1/private bookworm-staging/main armhf libevent-2.1-7 armhf 2.1.12-stable-1 [167 kB]
Get:74 http://172.17.0.1/private bookworm-staging/main armhf libevent-core-2.1-7 armhf 2.1.12-stable-1 [126 kB]
Get:75 http://172.17.0.1/private bookworm-staging/main armhf libevent-extra-2.1-7 armhf 2.1.12-stable-1 [100 kB]
Get:76 http://172.17.0.1/private bookworm-staging/main armhf libevent-pthreads-2.1-7 armhf 2.1.12-stable-1 [56.8 kB]
Get:77 http://172.17.0.1/private bookworm-staging/main armhf libevent-openssl-2.1-7 armhf 2.1.12-stable-1 [61.7 kB]
Get:78 http://172.17.0.1/private bookworm-staging/main armhf libevent-dev armhf 2.1.12-stable-1 [281 kB]
Get:79 http://172.17.0.1/private bookworm-staging/main armhf librdmacm1 armhf 36.0-1 [60.1 kB]
Get:80 http://172.17.0.1/private bookworm-staging/main armhf libfabric1 armhf 1.11.0-2 [311 kB]
Get:81 http://172.17.0.1/private bookworm-staging/main armhf libffi8 armhf 3.4.2-2 [21.2 kB]
Get:82 http://172.17.0.1/private bookworm-staging/main armhf libglib2.0-0 armhf 2.70.0-1 [1208 kB]
Get:83 http://172.17.0.1/private bookworm-staging/main armhf libhtml-tagset-perl all 3.20-4 [13.0 kB]
Get:84 http://172.17.0.1/private bookworm-staging/main armhf liburi-perl all 5.08-1 [90.6 kB]
Get:85 http://172.17.0.1/private bookworm-staging/main armhf libhtml-parser-perl armhf 3.76-1 [102 kB]
Get:86 http://172.17.0.1/private bookworm-staging/main armhf libhwloc15 armhf 2.5.0+dfsg-2 [126 kB]
Get:87 http://172.17.0.1/private bookworm-staging/main armhf libnuma1 armhf 2.0.14-3 [21.8 kB]
Get:88 http://172.17.0.1/private bookworm-staging/main armhf libnuma-dev armhf 2.0.14-3 [34.7 kB]
Get:89 http://172.17.0.1/private bookworm-staging/main armhf libltdl7 armhf 2.4.6-15 [388 kB]
Get:90 http://172.17.0.1/private bookworm-staging/main armhf libltdl-dev armhf 2.4.6-15 [159 kB]
Get:91 http://172.17.0.1/private bookworm-staging/main armhf libhwloc-dev armhf 2.5.0+dfsg-2 [197 kB]
Get:92 http://172.17.0.1/private bookworm-staging/main armhf libpciaccess0 armhf 0.16-1 [51.0 kB]
Get:93 http://172.17.0.1/private bookworm-staging/main armhf libxau6 armhf 1:1.0.9-1 [19.1 kB]
Get:94 http://172.17.0.1/private bookworm-staging/main armhf libxdmcp6 armhf 1:1.1.2-3 [25.0 kB]
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Get:96 http://172.17.0.1/private bookworm-staging/main armhf libx11-data all 2:1.7.2-2 [311 kB]
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Get:98 http://172.17.0.1/private bookworm-staging/main armhf libxext6 armhf 2:1.3.4-1 [48.0 kB]
Get:99 http://172.17.0.1/private bookworm-staging/main armhf libxnvctrl0 armhf 470.57.02-2 [26.0 kB]
Get:100 http://172.17.0.1/private bookworm-staging/main armhf ocl-icd-libopencl1 armhf 2.2.14-2 [39.9 kB]
Get:101 http://172.17.0.1/private bookworm-staging/main armhf libhwloc-plugins armhf 2.5.0+dfsg-2 [20.0 kB]
Get:102 http://172.17.0.1/private bookworm-staging/main armhf libnl-3-dev armhf 3.4.0-1 [92.4 kB]
Get:103 http://172.17.0.1/private bookworm-staging/main armhf libnl-route-3-dev armhf 3.4.0-1 [145 kB]
Get:104 http://172.17.0.1/private bookworm-staging/main armhf libibverbs-dev armhf 36.0-1 [186 kB]
Get:105 http://172.17.0.1/private bookworm-staging/main armhf libjs-jquery all 3.5.1+dfsg+~3.5.5-7 [315 kB]
Get:106 http://172.17.0.1/private bookworm-staging/main armhf libjs-jquery-ui all 1.12.1+dfsg-8 [232 kB]
Get:107 http://172.17.0.1/private bookworm-staging/main armhf libpmix2 armhf 4.1.1~rc2-1 [476 kB]
Get:108 http://172.17.0.1/private bookworm-staging/main armhf libopenmpi3 armhf 4.1.1-5+rpi1 [1772 kB]
Get:109 http://172.17.0.1/private bookworm-staging/main armhf openmpi-common all 4.1.1-5+rpi1 [179 kB]
Get:110 http://172.17.0.1/private bookworm-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-2 [184 kB]
Get:111 http://172.17.0.1/private bookworm-staging/main armhf libpmix-dev armhf 4.1.1~rc2-1 [640 kB]
Get:112 http://172.17.0.1/private bookworm-staging/main armhf openmpi-bin armhf 4.1.1-5+rpi1 [207 kB]
Get:113 http://172.17.0.1/private bookworm-staging/main armhf libopenmpi-dev armhf 4.1.1-5+rpi1 [1145 kB]
Get:114 http://172.17.0.1/private bookworm-staging/main armhf libsparsehash-dev all 2.0.3-2 [76.8 kB]
Get:115 http://172.17.0.1/private bookworm-staging/main armhf libsqlite3-dev armhf 3.36.0-2 [873 kB]
Get:116 http://172.17.0.1/private bookworm-staging/main armhf libtext-markdown-perl all 1.000031-3 [33.8 kB]
Get:117 http://172.17.0.1/private bookworm-staging/main armhf libtext-multimarkdown-perl all 1.000035-2 [28.6 kB]
Get:118 http://172.17.0.1/private bookworm-staging/main armhf pkg-config armhf 0.29.2-1 [61.5 kB]
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Setting up libpipeline1:armhf (1.5.3-1) ...
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Setting up libpciaccess0:armhf (0.16-1) ...
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Setting up libsqlite3-dev:armhf (3.36.0-2) ...
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Setting up libx11-6:armhf (2:1.7.2-2) ...
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Setting up libtext-multimarkdown-perl (1.000035-2) ...
Setting up automake (1:1.16.4-2) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
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Setting up libboost1.74-dev:armhf (1.74.0-9) ...
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Setting up man-db (2.9.4-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libxnvctrl0:armhf (470.57.02-2) ...
Setting up dh-autoreconf (20) ...
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Setting up libboost-test1.74-dev:armhf (1.74.0-9) ...
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Setting up libfabric1 (1.11.0-2) ...
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Setting up libpmix2:armhf (4.1.1~rc2-1) ...
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Setting up libpmix-dev:armhf (4.1.1~rc2-1) ...
Setting up openmpi-bin (4.1.1-5+rpi1) ...
update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode
update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode
Setting up libopenmpi-dev:armhf (4.1.1-5+rpi1) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/openmpi/include to provide /usr/include/arm-linux-gnueabihf/mpi (mpi-arm-linux-gnueabihf) in auto mode
Setting up sbuild-build-depends-abyss-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.32-4+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.15.0-76-generic armhf (armv8l)
Toolchain package versions: binutils_2.37-5+rpi1 dpkg-dev_1.20.9+rpi1 g++-10_10.3.0-11+rpi1 gcc-10_10.3.0-11+rpi1 libc6-dev_2.32-4+rpi1 libstdc++-10-dev_10.3.0-11+rpi1 libstdc++6_11.2.0-7+rpi1 linux-libc-dev_5.10.46-4+rpi1
Package versions: adduser_3.118 apt_2.3.9 autoconf_2.71-2 automake_1:1.16.4-2 autopoint_0.21-4 autotools-dev_20180224.1+nmu1 base-files_12+rpi1 base-passwd_3.5.51 bash_5.1-3 binutils_2.37-5+rpi1 binutils-arm-linux-gnueabihf_2.37-5+rpi1 binutils-common_2.37-5+rpi1 bsdextrautils_2.37.2-1 bsdutils_1:2.37.2-1 build-essential_12.9 bzip2_1.0.8-4 coreutils_8.32-4 cpp_4:10.2.1-1+rpi1 cpp-10_10.3.0-11+rpi1 dash_0.5.11+git20210120+802ebd4-1 debconf_1.5.77 debhelper_13.5.2 debianutils_4.11.2 dh-autoreconf_20 dh-strip-nondeterminism_1.12.0-1 diffutils_1:3.7-5 dirmngr_2.2.27-2 dpkg_1.20.9+rpi1 dpkg-dev_1.20.9+rpi1 dwz_0.14-1 e2fsprogs_1.46.4-1 fakeroot_1.25.3-1.1 file_1:5.39-3 findutils_4.8.0-1 g++_4:10.2.1-1+rpi1 g++-10_10.3.0-11+rpi1 gcc_4:10.2.1-1+rpi1 gcc-10_10.3.0-11+rpi1 gcc-10-base_10.3.0-11+rpi1 gcc-11-base_11.2.0-7+rpi1 gcc-7-base_7.5.0-6+rpi1+b2 gcc-8-base_8.4.0-7+rpi1 gcc-9-base_9.4.0-2+rpi1 gettext_0.21-4 gettext-base_0.21-4 gfortran-10_10.3.0-11+rpi1 gnupg_2.2.27-2 gnupg-l10n_2.2.27-2 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libgssapi-krb5-2_1.18.3-7 libhogweed6_3.7.3-1 libhtml-parser-perl_3.76-1 libhtml-tagset-perl_3.20-4 libhwloc-dev_2.5.0+dfsg-2 libhwloc-plugins_2.5.0+dfsg-2 libhwloc15_2.5.0+dfsg-2 libibverbs-dev_36.0-1 libibverbs1_36.0-1 libicu-dev_67.1-7 libicu67_67.1-7 libidn2-0_2.3.2-2 libisl23_0.23-1 libjs-jquery_3.5.1+dfsg+~3.5.5-7 libjs-jquery-ui_1.12.1+dfsg-8 libk5crypto3_1.18.3-7 libkeyutils1_1.6.1-2 libkrb5-3_1.18.3-7 libkrb5support0_1.18.3-7 libksba8_1.6.0-2 libldap-2.4-2_2.4.59+dfsg-1 liblocale-gettext-perl_1.07-4+b1 libltdl-dev_2.4.6-15 libltdl7_2.4.6-15 liblz4-1_1.9.3-2 liblzma5_5.2.5-2 libmagic-mgc_1:5.39-3 libmagic1_1:5.39-3 libmd0_1.0.3-3 libmount1_2.37.2-1 libmpc3_1.2.0-1 libmpfr6_4.1.0-3 libncursesw6_6.2+20201114-4 libnettle8_3.7.3-1 libnl-3-200_3.4.0-1 libnl-3-dev_3.4.0-1 libnl-route-3-200_3.4.0-1 libnl-route-3-dev_3.4.0-1 libnpth0_1.6-3 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libnuma-dev_2.0.14-3 libnuma1_2.0.14-3 libopenmpi-dev_4.1.1-5+rpi1 libopenmpi3_4.1.1-5+rpi1 libp11-kit0_0.24.0-2 libpam-modules_1.4.0-10 libpam-modules-bin_1.4.0-10 libpam-runtime_1.4.0-10 libpam0g_1.4.0-10 libpciaccess0_0.16-1 libpcre2-8-0_10.36-2 libpcre3_2:8.39-13 libperl5.32_5.32.1-5 libpipeline1_1.5.3-1 libpmix-dev_4.1.1~rc2-1 libpmix2_4.1.1~rc2-1 librdmacm1_36.0-1 libreadline8_8.1-2 libsasl2-2_2.1.27+dfsg-2.1 libsasl2-modules-db_2.1.27+dfsg-2.1 libseccomp2_2.5.1-1+rpi1 libselinux1_3.1-3 libsemanage-common_3.1-1 libsemanage1_3.1-1+b1 libsepol1_3.1-1 libsigsegv2_2.13-1 libsmartcols1_2.37.2-1 libsparsehash-dev_2.0.3-2 libsqlite3-0_3.36.0-2 libsqlite3-dev_3.36.0-2 libss2_1.46.4-1 libssl1.1_1.1.1l-1 libstdc++-10-dev_10.3.0-11+rpi1 libstdc++6_11.2.0-7+rpi1 libsub-override-perl_0.09-2 libsystemd0_247.9-1+rpi1 libtasn1-6_4.17.0-2 libtext-charwidth-perl_0.04-10+b1 libtext-iconv-perl_1.7-7+b1 libtext-markdown-perl_1.000031-3 libtext-multimarkdown-perl_1.000035-2 libtinfo6_6.2+20201114-4 libtirpc-common_1.3.2-2 libtirpc-dev_1.3.2-2 libtirpc3_1.3.2-2 libtool_2.4.6-15 libubsan1_11.2.0-7+rpi1 libuchardet0_0.0.7-1 libudev1_247.9-1+rpi1 libunistring2_0.9.10-6 liburi-perl_5.08-1 libuuid1_2.37.2-1 libx11-6_2:1.7.2-2 libx11-data_2:1.7.2-2 libxau6_1:1.0.9-1 libxcb1_1.14-3 libxdmcp6_1:1.1.2-3 libxext6_2:1.3.4-1 libxml2_2.9.12+dfsg-5 libxnvctrl0_470.57.02-2 libxxhash0_0.8.0-2+rpi1 libzstd1_1.4.8+dfsg-2.1+rpi1 linux-libc-dev_5.10.46-4+rpi1 login_1:4.8.1-1 logsave_1.46.4-1 lsb-base_11.1.0+rpi1 m4_1.4.18-5 make_4.3-4.1 man-db_2.9.4-2 mawk_1.3.4.20200120-2 mount_2.37.2-1 ncurses-base_6.2+20201114-4 ncurses-bin_6.2+20201114-4 netbase_6.3 ocl-icd-libopencl1_2.2.14-2 openmpi-bin_4.1.1-5+rpi1 openmpi-common_4.1.1-5+rpi1 openssh-client_1:8.4p1-6 passwd_1:4.8.1-1 patch_2.7.6-7 perl_5.32.1-5 perl-base_5.32.1-5 perl-modules-5.32_5.32.1-5 pinentry-curses_1.1.0-4 pkg-config_0.29.2-1 po-debconf_1.0.21+nmu1 raspbian-archive-keyring_20120528.2 readline-common_8.1-2 rpcsvc-proto_1.4.2-4 sbuild-build-depends-abyss-dummy_0.invalid.0 sbuild-build-depends-core-dummy_0.invalid.0 sed_4.8-1 sensible-utils_0.0.17 sysvinit-utils_3.00-1 tar_1.34+dfsg-1 tzdata_2021a-1 util-linux_2.37.2-1 xz-utils_5.2.5-2 zlib1g_1:1.2.11.dfsg-2 zlib1g-dev_1:1.2.11.dfsg-2
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/tmp/dpkg-verify-sig.RDoaKjEM/trustedkeys.kbx': General error
gpgv: Signature made Fri Oct 1 14:18:50 2021 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_2.3.1-1.dsc
dpkg-source: info: extracting abyss in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking abyss_2.3.1.orig.tar.xz
dpkg-source: info: unpacking abyss_2.3.1-1.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying abyss-pe.patch
Check disk space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=bookworm-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bookworm-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=112
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bookworm-staging-armhf-sbuild-e89a8e59-39f6-4209-ab2c-f32d65bf3dbe
SCHROOT_UID=107
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package abyss
dpkg-buildpackage: info: source version 2.3.1-1
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
debian/rules clean
dh clean
dh_clean
debian/rules binary-arch
dh binary-arch
dh_update_autotools_config -a
dh_autoreconf -a
configure.ac:12: warning: The macro `AC_CONFIG_HEADER' is obsolete.
configure.ac:12: You should run autoupdate.
./lib/autoconf/status.m4:719: AC_CONFIG_HEADER is expanded from...
configure.ac:12: the top level
configure.ac:31: warning: The macro `AC_HEADER_STDC' is obsolete.
configure.ac:31: You should run autoupdate.
./lib/autoconf/headers.m4:704: AC_HEADER_STDC is expanded from...
configure.ac:31: the top level
configure.ac:84: warning: The macro `AC_FUNC_SETVBUF_REVERSED' is obsolete. Remove it and all references to SETVBUF_REVERSED.
./lib/autoconf/functions.m4:1766: AC_FUNC_SETVBUF_REVERSED is expanded from...
configure.ac:84: the top level
configure.ac:25: installing './ar-lib'
configure.ac:16: installing './compile'
configure.ac:81: installing './config.guess'
configure.ac:81: installing './config.sub'
configure.ac:10: installing './install-sh'
configure.ac:10: installing './missing'
ABYSS/Makefile.am: installing './depcomp'
parallel-tests: installing './test-driver'
debian/rules override_dh_auto_configure
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_configure -- \
--with-mpi=/usr/lib/arm-linux-gnueabihf/openmpi
./configure --build=arm-linux-gnueabihf --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/arm-linux-gnueabihf --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-mpi=/usr/lib/arm-linux-gnueabihf/openmpi
checking for g++... g++
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 the compiler supports GNU C++... yes
checking whether g++ accepts -g... yes
checking for g++ option to enable C++11 features... none needed
checking whether g++ supports C++11 features with -std=c++11... yes
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a race-free mkdir -p... /bin/mkdir -p
checking for gawk... no
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checking whether make sets $(MAKE)... yes
checking whether make supports the include directive... yes (GNU style)
checking whether make supports nested variables... yes
checking dependency style of g++ -std=c++11... none
checking for gawk... (cached) mawk
checking for gcc... gcc
checking whether the compiler supports GNU C... yes
checking whether gcc accepts -g... yes
checking for gcc option to enable C11 features... none needed
checking whether gcc understands -c and -o together... yes
checking dependency style of gcc... none
checking how to run the C preprocessor... gcc -E
checking whether the compiler supports GNU C++... (cached) yes
checking whether g++ -std=c++11 accepts -g... (cached) yes
checking for g++ -std=c++11 option to enable C++11 features... (cached) none needed
checking for ranlib... ranlib
checking for ghc... no
./configure: line 6915: : command not found
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checking for ar... ar
checking the archiver (ar) interface... ar
checking for stdio.h... yes
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checking for string.h... yes
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checking for egrep... /bin/grep -E
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checking for inline... inline
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checking for strtoul... yes
checking for fork... yes
checking for vfork... yes
checking for vprintf... yes
checking for working fork... yes
checking for working vfork... (cached) yes
checking build system type... arm-unknown-linux-gnueabihf
checking host system type... arm-unknown-linux-gnueabihf
checking for GNU libc compatible malloc... yes
checking for working memcmp... yes
checking for GNU libc compatible realloc... yes
checking for gcc options needed to detect all undeclared functions... none needed
checking whether HOST_NAME_MAX is declared... yes
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 for mpi.h... yes
checking for MPI_Init in -lmpi... yes
checking for sqrt in -lm... yes
checking for pow... yes
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checking for ceilf... yes
checking for dlsym in -ldl... yes
checking for functional... yes
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checking for boost/functional/hash.hpp... yes
checking for boost/property_map/property_map.hpp... yes
checking for google/sparse_hash_map... yes
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checking for boost/unordered_set.hpp... yes
checking for sqlite3.h... yes
checking for main in -lsqlite3... yes
checking for g++ -std=c++11 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 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 vendor/gtest-1.7.0/Makefile
config.status: creating RResolver/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 vendor/Makefile
config.status: creating config.h
config.status: executing depfiles commands
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
debian/rules override_dh_auto_build
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_build
make -j4
make[2]: Entering directory '/<<PKGBUILDDIR>>'
make all-recursive
make[3]: Entering directory '/<<PKGBUILDDIR>>'
Making all in bin
make[4]: Entering directory '/<<PKGBUILDDIR>>/bin'
make[4]: Nothing to be done for 'all'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/bin'
Making all in doc
make[4]: Entering directory '/<<PKGBUILDDIR>>/doc'
make[4]: Nothing to be done for 'all'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/doc'
Making all in Common
make[4]: Entering directory '/<<PKGBUILDDIR>>/Common'
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libcommon_a-ContigID.o `test -f 'ContigID.cpp' || echo './'`ContigID.cpp
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libcommon_a-Fcontrol.o `test -f 'Fcontrol.cpp' || echo './'`Fcontrol.cpp
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libcommon_a-Histogram.o `test -f 'Histogram.cpp' || echo './'`Histogram.cpp
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libcommon_a-Kmer.o `test -f 'Kmer.cpp' || echo './'`Kmer.cpp
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libcommon_a-Log.o `test -f 'Log.cpp' || echo './'`Log.cpp
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libcommon_a-Options.o `test -f 'Options.cpp' || echo './'`Options.cpp
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libcommon_a-Sequence.o `test -f 'Sequence.cpp' || echo './'`Sequence.cpp
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libcommon_a-SignalHandler.o `test -f 'SignalHandler.cpp' || echo './'`SignalHandler.cpp
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libcommon_a-Timer.o `test -f 'Timer.cpp' || echo './'`Timer.cpp
In file included from /usr/include/c++/10/vector:72,
from VectorUtil.h:4,
from Histogram.h:6,
from Histogram.cpp:1:
/usr/include/c++/10/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++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from VectorUtil.h:4,
from Histogram.h:6,
from Histogram.cpp:1:
/usr/include/c++/10/bits/stl_vector.h: In member function 'Histogram::Bins Histogram::bin(unsigned int) const':
/usr/include/c++/10/bits/stl_vector.h:1198:21: 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
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: 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
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libcommon_a-Uncompress.o `test -f 'Uncompress.cpp' || echo './'`Uncompress.cpp
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libcommon_a-city.o `test -f 'city.cc' || echo './'`city.cc
rm -f libcommon.a
ar cru libcommon.a libcommon_a-ContigID.o libcommon_a-Fcontrol.o libcommon_a-Histogram.o libcommon_a-Kmer.o libcommon_a-Log.o libcommon_a-Options.o libcommon_a-Sequence.o libcommon_a-SignalHandler.o libcommon_a-Timer.o libcommon_a-Uncompress.o libcommon_a-city.o
ar: `u' modifier ignored since `D' is the default (see `U')
ranlib libcommon.a
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Common'
Making all in Graph
make[4]: Entering directory '/<<PKGBUILDDIR>>/Graph'
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_gc-gc.o `test -f 'gc.cc' || echo './'`gc.cc
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_todot-todot.o `test -f 'todot.cc' || echo './'`todot.cc
g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-gc abyss_gc-gc.o ../Common/libcommon.a -ldl -lm
g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L. -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-todot abyss_todot-todot.o ../Common/libcommon.a -ldl -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Graph'
Making all in DataLayer
make[4]: Entering directory '/<<PKGBUILDDIR>>/DataLayer'
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_fac-fac.o `test -f 'fac.cc' || echo './'`fac.cc
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libdatalayer_a-FastaReader.o `test -f 'FastaReader.cpp' || echo './'`FastaReader.cpp
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libdatalayer_a-FastaWriter.o `test -f 'FastaWriter.cpp' || echo './'`FastaWriter.cpp
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_tofastq-abyss-tofastq.o `test -f 'abyss-tofastq.cc' || echo './'`abyss-tofastq.cc
rm -f libdatalayer.a
ar cru libdatalayer.a libdatalayer_a-FastaReader.o libdatalayer_a-FastaWriter.o
ar: `u' modifier ignored since `D' is the default (see `U')
ranlib libdatalayer.a
g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-fac abyss_fac-fac.o libdatalayer.a ../Common/libcommon.a -ldl -lm
g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-tofastq abyss_tofastq-abyss-tofastq.o libdatalayer.a ../Common/libcommon.a -ldl -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/DataLayer'
Making all in DataBase
make[4]: Entering directory '/<<PKGBUILDDIR>>/DataBase'
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_db_csv-DB.o `test -f 'DB.cc' || echo './'`DB.cc
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_db_csv-db-csv.o `test -f 'db-csv.cc' || echo './'`db-csv.cc
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libdb_a-DB.o `test -f 'DB.cc' || echo './'`DB.cc
rm -f libdb.a
ar cru libdb.a libdb_a-DB.o ../Common/libcommon.a
ar: `u' modifier ignored since `D' is the default (see `U')
ranlib libdb.a
g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-db-csv abyss_db_csv-DB.o abyss_db_csv-db-csv.o -lsqlite3 -ldl -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/DataBase'
Making all in FMIndex
make[4]: Entering directory '/<<PKGBUILDDIR>>/FMIndex'
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_count-count.o `test -f 'count.cc' || echo './'`count.cc
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I../Common -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libfmindex_a-bit_array.o `test -f 'bit_array.cc' || echo './'`bit_array.cc
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_dawg-abyss-dawg.o `test -f 'abyss-dawg.cc' || echo './'`abyss-dawg.cc
rm -f libfmindex.a
ar cru libfmindex.a libfmindex_a-bit_array.o
ar: `u' modifier ignored since `D' is the default (see `U')
ranlib libfmindex.a
In file included from /usr/include/c++/10/vector:66,
from bit_array.h:24,
from BitArrays.h:4,
from FMIndex.h:5,
from DAWG.h:5,
from count.cc:2:
/usr/include/c++/10/bits/stl_uninitialized.h: In 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++/10/bits/stl_uninitialized.h:84:9: note: parameter passing for argument of type 'std::move_iterator<wat_array::BitArray*>' changed in GCC 7.1
84 | __uninit_copy(_InputIterator __first, _InputIterator __last,
| ^~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_uninitialized.h:84:9: 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++/10/vector:66,
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++/10/bits/stl_uninitialized.h: In 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++/10/bits/stl_uninitialized.h:84:9: note: parameter passing for argument of type 'std::move_iterator<wat_array::BitArray*>' changed in GCC 7.1
84 | __uninit_copy(_InputIterator __first, _InputIterator __last,
| ^~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_uninitialized.h:84:9: 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++/10/vector:72,
from bit_array.h:24,
from BitArrays.h:4,
from FMIndex.h:5,
from DAWG.h:5,
from count.cc:2:
/usr/include/c++/10/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++/10/bits/vector.tcc:426:7: 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' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
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++/10/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++/10/bits/vector.tcc:426:7: 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' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/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++/10/bits/vector.tcc:121:21: 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
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/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++/10/bits/vector.tcc:121:21: 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
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/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++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<wat_array::BitArray>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:66,
from bit_array.h:24,
from BitArrays.h:4,
from FMIndex.h:5,
from DAWG.h:5,
from count.cc:2:
/usr/include/c++/10/bits/stl_uninitialized.h:150:15: note: parameter passing for argument of type 'std::move_iterator<wat_array::BitArray*>' changed in GCC 7.1
147 | return std::__uninitialized_copy<__is_trivial(_ValueType1)
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
148 | && __is_trivial(_ValueType2)
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
149 | && __assignable>::
| ~~~~~~~~~~~~~~~~~~
150 | __uninit_copy(__first, __last, __result);
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_uninitialized.h:150:15: note: parameter passing for argument of type 'std::move_iterator<wat_array::BitArray*>' changed in GCC 7.1
147 | return std::__uninitialized_copy<__is_trivial(_ValueType1)
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
148 | && __is_trivial(_ValueType2)
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
149 | && __assignable>::
| ~~~~~~~~~~~~~~~~~~
150 | __uninit_copy(__first, __last, __result);
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/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++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<wat_array::BitArray>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:66,
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++/10/bits/stl_uninitialized.h:150:15: note: parameter passing for argument of type 'std::move_iterator<wat_array::BitArray*>' changed in GCC 7.1
147 | return std::__uninitialized_copy<__is_trivial(_ValueType1)
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
148 | && __is_trivial(_ValueType2)
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
149 | && __assignable>::
| ~~~~~~~~~~~~~~~~~~
150 | __uninit_copy(__first, __last, __result);
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_uninitialized.h:150:15: note: parameter passing for argument of type 'std::move_iterator<wat_array::BitArray*>' changed in GCC 7.1
147 | return std::__uninitialized_copy<__is_trivial(_ValueType1)
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
148 | && __is_trivial(_ValueType2)
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
149 | && __assignable>::
| ~~~~~~~~~~~~~~~~~~
150 | __uninit_copy(__first, __last, __result);
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from bit_array.h:24,
from BitArrays.h:4,
from FMIndex.h:5,
from DAWG.h:5,
from count.cc:2:
/usr/include/c++/10/bits/stl_vector.h: In member function 'void BitArrays::assign(It, It) [with It = __gnu_cxx::__normal_iterator<unsigned char*, std::vector<unsigned char> >]':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<wat_array::BitArray*, std::vector<wat_array::BitArray> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
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++/10/bits/stl_vector.h: In member function 'void BitArrays::assign(It, It) [with It = __gnu_cxx::__normal_iterator<unsigned char*, std::vector<unsigned char> >]':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<wat_array::BitArray*, std::vector<wat_array::BitArray> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/map:60,
from abyss-dawg.cc:14:
/usr/include/c++/10/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++/10/bits/stl_tree.h:2460:7: 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' changed in GCC 7.1
2460 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/map:61,
from abyss-dawg.cc:14:
/usr/include/c++/10/bits/stl_map.h: In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = std::pair<long long unsigned int, long long unsigned int>; _Tp = 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++/10/bits/stl_map.h:501:37: 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' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_map.h: In function 'int main(int, char**)':
/usr/include/c++/10/bits/stl_map.h:501:37: 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' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_map.h:501:37: 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' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_map.h:501:37: 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' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-count abyss_count-count.o libfmindex.a ../Common/libcommon.a -ldl -lm
g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-dawg abyss_dawg-abyss-dawg.o libfmindex.a ../Common/libcommon.a -ldl -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/FMIndex'
Making all in Assembly
make[4]: Entering directory '/<<PKGBUILDDIR>>/Assembly'
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libassembly_a-AssemblyAlgorithms.o `test -f 'AssemblyAlgorithms.cc' || echo './'`AssemblyAlgorithms.cc
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libassembly_a-Options.o `test -f 'Options.cc' || echo './'`Options.cc
rm -f libassembly.a
ar cru libassembly.a libassembly_a-AssemblyAlgorithms.o libassembly_a-Options.o ../Common/libcommon.a
ar: `u' modifier ignored since `D' is the default (see `U')
ranlib libassembly.a
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Assembly'
Making all in dialign
make[4]: Entering directory '/<<PKGBUILDDIR>>/dialign'
gcc -DHAVE_CONFIG_H -I. -I.. -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o museq.o museq.c
gcc -DHAVE_CONFIG_H -I. -I.. -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o alig.o alig.c
gcc -DHAVE_CONFIG_H -I. -I.. -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o assemble.o assemble.c
gcc -DHAVE_CONFIG_H -I. -I.. -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o diag.o diag.c
alig.c:15:20: warning: inline function 'calc_ov_weight' declared but never defined
15 | extern inline void calc_ov_weight(struct diag* dg, struct diag_col *dcol, struct scr_matrix* smatrix,
| ^~~~~~~~~~~~~~
alig.c:13:20: warning: inline function 'calc_weight' declared but never defined
13 | extern inline void calc_weight(struct diag* dg, struct scr_matrix* smatrix,
| ^~~~~~~~~~~
assemble.c:40:20: warning: inline function 'align_diag' declared but never defined
40 | extern inline char align_diag(struct alignment *algn, struct scr_matrix *smatrix, struct diag* dg);
| ^~~~~~~~~~
assemble.c:37:32: warning: inline function 'find_eqc' declared but never defined
37 | extern inline struct algn_pos *find_eqc(struct algn_pos **ap, int seqnum, int pos);
| ^~~~~~~~
assemble.c:25:39: warning: inline function 'find_diags_guided' declared but never defined
25 | extern inline struct simple_diag_col* find_diags_guided(struct scr_matrix *smatrix,
| ^~~~~~~~~~~~~~~~~
assemble.c:15:20: warning: inline function 'calc_ov_weight' declared but never defined
15 | extern inline void calc_ov_weight(struct diag* dg, struct diag_col *dcol, struct scr_matrix* smatrix,
| ^~~~~~~~~~~~~~
assemble.c:13:20: warning: inline function 'calc_weight' declared but never defined
13 | extern inline void calc_weight(struct diag* dg, struct scr_matrix* smatrix,
| ^~~~~~~~~~~
diag.c:1456:3: warning: 'real_calc_weight' is static but used in inline function 'find_diags_dyn' which is not static
1456 | real_calc_weight(dg, smatrix, pdist,1,tmp_dist,algn);
| ^~~~~~~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -I.. -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -g -O2 -ffile-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]
270 | fscanf( fp, "%i", &is);
| ^~~~~~~~~~~~~~~~~~~~~~
io.c:282:5: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result]
282 | fscanf(fp, "%s\n", rline);
| ^~~~~~~~~~~~~~~~~~~~~~~~~
io.c: In function 'read_diag_prob_dist':
io.c:371:7: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result]
371 | fscanf( fp, "%li %li %Le\n", &ti,&tscr,&weight );
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -I.. -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o orf.o orf.c
gcc -DHAVE_CONFIG_H -I. -I.. -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o parameters.o parameters.c
gcc -DHAVE_CONFIG_H -I. -I.. -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o prob.o prob.c
gcc -DHAVE_CONFIG_H -I. -I.. -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o translate.o translate.c
rm -f libdialign.a
ar cru libdialign.a alig.o assemble.o diag.o io.o orf.o parameters.o prob.o translate.o
ar: `u' modifier ignored since `D' is the default (see `U')
ranlib libdialign.a
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o dialign museq.o libdialign.a -ldl -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/dialign'
Making all in Align
make[4]: Entering directory '/<<PKGBUILDDIR>>/Align'
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_align-align.o `test -f 'align.cc' || echo './'`align.cc
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libalign_a-alignGlobal.o `test -f 'alignGlobal.cc' || echo './'`alignGlobal.cc
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libalign_a-dialign.o `test -f 'dialign.cpp' || echo './'`dialign.cpp
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libalign_a-dna_diag_prob.o `test -f 'dna_diag_prob.cc' || echo './'`dna_diag_prob.cc
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libalign_a-smith_waterman.o `test -f 'smith_waterman.cpp' || echo './'`smith_waterman.cpp
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_mergepairs-mergepairs.o `test -f 'mergepairs.cc' || echo './'`mergepairs.cc
rm -f libalign.a
ar cru libalign.a libalign_a-alignGlobal.o libalign_a-dialign.o libalign_a-dna_diag_prob.o libalign_a-smith_waterman.o
ar: `u' modifier ignored since `D' is the default (see `U')
ranlib libalign.a
g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-align abyss_align-align.o ./libalign.a ../dialign/libdialign.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm
g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-mergepairs abyss_mergepairs-mergepairs.o ./libalign.a ../dialign/libdialign.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Align'
Making all in ABYSS
make[4]: Entering directory '/<<PKGBUILDDIR>>/ABYSS'
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o ABYSS-abyss.o `test -f 'abyss.cc' || echo './'`abyss.cc
g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o ABYSS ABYSS-abyss.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../Assembly/libassembly.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/ABYSS'
Making all in Parallel
make[4]: Entering directory '/<<PKGBUILDDIR>>/Parallel'
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o ABYSS_P-parallelAbyss.o `test -f 'parallelAbyss.cpp' || echo './'`parallelAbyss.cpp
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o ABYSS_P-CommLayer.o `test -f 'CommLayer.cpp' || echo './'`CommLayer.cpp
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o ABYSS_P-NetworkSequenceCollection.o `test -f 'NetworkSequenceCollection.cpp' || echo './'`NetworkSequenceCollection.cpp
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o ABYSS_P-MessageBuffer.o `test -f 'MessageBuffer.cpp' || echo './'`MessageBuffer.cpp
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o ABYSS_P-Messages.o `test -f 'Messages.cpp' || echo './'`Messages.cpp
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -DPAIRED_DBG -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_paired_dbg_mpi-parallelAbyss.o `test -f 'parallelAbyss.cpp' || echo './'`parallelAbyss.cpp
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -DPAIRED_DBG -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_paired_dbg_mpi-CommLayer.o `test -f 'CommLayer.cpp' || echo './'`CommLayer.cpp
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -DPAIRED_DBG -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_paired_dbg_mpi-NetworkSequenceCollection.o `test -f 'NetworkSequenceCollection.cpp' || echo './'`NetworkSequenceCollection.cpp
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -DPAIRED_DBG -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_paired_dbg_mpi-MessageBuffer.o `test -f 'MessageBuffer.cpp' || echo './'`MessageBuffer.cpp
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -DPAIRED_DBG -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_paired_dbg_mpi-Messages.o `test -f 'Messages.cpp' || echo './'`Messages.cpp
g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o ABYSS-P ABYSS_P-parallelAbyss.o ABYSS_P-CommLayer.o ABYSS_P-NetworkSequenceCollection.o ABYSS_P-MessageBuffer.o ABYSS_P-Messages.o ../Assembly/libassembly.a ../Common/libcommon.a ../DataLayer/libdatalayer.a ../DataBase/libdb.a -lsqlite3 -ldl -lm -lmpi -ldl -lm
g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-paired-dbg-mpi abyss_paired_dbg_mpi-parallelAbyss.o abyss_paired_dbg_mpi-CommLayer.o abyss_paired_dbg_mpi-NetworkSequenceCollection.o abyss_paired_dbg_mpi-MessageBuffer.o abyss_paired_dbg_mpi-Messages.o ../Assembly/libassembly.a ../Common/libcommon.a ../DataLayer/libdatalayer.a ../DataBase/libdb.a -lsqlite3 -ldl -lm -lmpi -ldl -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Parallel'
Making all in Bloom
make[4]: Entering directory '/<<PKGBUILDDIR>>/Bloom'
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../vendor -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_bloom-bloom.o `test -f 'bloom.cc' || echo './'`bloom.cc
g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-bloom abyss_bloom-bloom.o ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a -ldl -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Bloom'
Making all in BloomDBG
make[4]: Entering directory '/<<PKGBUILDDIR>>/BloomDBG'
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../vendor -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_bloom_dbg-bloom-dbg.o `test -f 'bloom-dbg.cc' || echo './'`bloom-dbg.cc
g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-bloom-dbg abyss_bloom_dbg-bloom-dbg.o ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/BloomDBG'
Making all in Konnector
make[4]: Entering directory '/<<PKGBUILDDIR>>/Konnector'
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o konnector-konnector.o `test -f 'konnector.cc' || echo './'`konnector.cc
g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o konnector konnector-konnector.o ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a -ldl -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Konnector'
Making all in Consensus
make[4]: Entering directory '/<<PKGBUILDDIR>>/Consensus'
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Consensus-Consensus.o `test -f 'Consensus.cpp' || echo './'`Consensus.cpp
g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o Consensus Consensus-Consensus.o ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Consensus'
Making all in DAssembler
make[4]: Entering directory '/<<PKGBUILDDIR>>/DAssembler'
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o DAssembler-DAssembler.o `test -f 'DAssembler.cpp' || echo './'`DAssembler.cpp
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o DAssembler-RotatedRead.o `test -f 'RotatedRead.cpp' || echo './'`RotatedRead.cpp
g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o DAssembler DAssembler-DAssembler.o DAssembler-RotatedRead.o ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/DAssembler'
Making all in DistanceEst
make[4]: Entering directory '/<<PKGBUILDDIR>>/DistanceEst'
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o DistanceEst-DistanceEst.o `test -f 'DistanceEst.cpp' || echo './'`DistanceEst.cpp
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o DistanceEst-MLE.o `test -f 'MLE.cpp' || echo './'`MLE.cpp
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -D SAM_SEQ_QUAL=1 -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o DistanceEst_ssq-DistanceEst.o `test -f 'DistanceEst.cpp' || echo './'`DistanceEst.cpp
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -D SAM_SEQ_QUAL=1 -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-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++/10/vector:72,
from MLE.h:4,
from MLE.cpp:1:
/usr/include/c++/10/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++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from MLE.h:4,
from MLE.cpp:1:
/usr/include/c++/10/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++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from MLE.h:4,
from MLE.cpp:1:
/usr/include/c++/10/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++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from MLE.h:4,
from MLE.cpp:1:
/usr/include/c++/10/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++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o DistanceEst DistanceEst-DistanceEst.o DistanceEst-MLE.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../Common/libcommon.a -ldl -lm
g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o DistanceEst-ssq DistanceEst_ssq-DistanceEst.o DistanceEst_ssq-MLE.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../Common/libcommon.a -ldl -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/DistanceEst'
Making all in KAligner
make[4]: Entering directory '/<<PKGBUILDDIR>>/KAligner'
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o KAligner-KAligner.o `test -f 'KAligner.cpp' || echo './'`KAligner.cpp
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o KAligner-Aligner.o `test -f 'Aligner.cpp' || echo './'`Aligner.cpp
g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o KAligner KAligner-KAligner.o KAligner-Aligner.o ../DataLayer/libdatalayer.a ../Common/libcommon.a -lpthread -ldl -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/KAligner'
Making all in Layout
make[4]: Entering directory '/<<PKGBUILDDIR>>/Layout'
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_layout-layout.o `test -f 'layout.cc' || echo './'`layout.cc
g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-layout abyss_layout-layout.o ../Common/libcommon.a -ldl -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Layout'
Making all in LogKmerCount
make[4]: Entering directory '/<<PKGBUILDDIR>>/LogKmerCount'
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o logcounter-logcounter.o `test -f 'logcounter.cc' || echo './'`logcounter.cc
g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o logcounter logcounter-logcounter.o ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a -ldl -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/LogKmerCount'
Making all in Map
make[4]: Entering directory '/<<PKGBUILDDIR>>/Map'
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../FMIndex -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_index-index.o `test -f 'index.cc' || echo './'`index.cc
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../FMIndex -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_map-map.o `test -f 'map.cc' || echo './'`map.cc
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../FMIndex -D SAM_SEQ_QUAL=1 -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_map_ssq-map.o `test -f 'map.cc' || echo './'`map.cc
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../FMIndex -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-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
In file included from /usr/include/c++/10/vector:66,
from ../DataLayer/FastaIndex.h:11,
from index.cc:3:
/usr/include/c++/10/bits/stl_uninitialized.h: In 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++/10/bits/stl_uninitialized.h:84:9: note: parameter passing for argument of type 'std::move_iterator<wat_array::BitArray*>' changed in GCC 7.1
84 | __uninit_copy(_InputIterator __first, _InputIterator __last,
| ^~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_uninitialized.h:84:9: 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++/10/vector:66,
from ../FMIndex/bit_array.h:24,
from ../FMIndex/BitArrays.h:4,
from ../FMIndex/FMIndex.h:5,
from map.cc:3:
/usr/include/c++/10/bits/stl_uninitialized.h: In 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++/10/bits/stl_uninitialized.h:84:9: note: parameter passing for argument of type 'std::move_iterator<wat_array::BitArray*>' changed in GCC 7.1
84 | __uninit_copy(_InputIterator __first, _InputIterator __last,
| ^~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_uninitialized.h:84:9: 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++/10/vector:66,
from ../FMIndex/bit_array.h:24,
from ../FMIndex/BitArrays.h:4,
from ../FMIndex/FMIndex.h:5,
from map.cc:3:
/usr/include/c++/10/bits/stl_uninitialized.h: In 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++/10/bits/stl_uninitialized.h:84:9: note: parameter passing for argument of type 'std::move_iterator<wat_array::BitArray*>' changed in GCC 7.1
84 | __uninit_copy(_InputIterator __first, _InputIterator __last,
| ^~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_uninitialized.h:84:9: 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++/10/vector:72,
from ../DataLayer/FastaIndex.h:11,
from index.cc:3:
/usr/include/c++/10/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++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<wat_array::BitArray>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:66,
from ../DataLayer/FastaIndex.h:11,
from index.cc:3:
/usr/include/c++/10/bits/stl_uninitialized.h:150:15: note: parameter passing for argument of type 'std::move_iterator<wat_array::BitArray*>' changed in GCC 7.1
147 | return std::__uninitialized_copy<__is_trivial(_ValueType1)
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
148 | && __is_trivial(_ValueType2)
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
149 | && __assignable>::
| ~~~~~~~~~~~~~~~~~~
150 | __uninit_copy(__first, __last, __result);
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_uninitialized.h:150:15: note: parameter passing for argument of type 'std::move_iterator<wat_array::BitArray*>' changed in GCC 7.1
147 | return std::__uninitialized_copy<__is_trivial(_ValueType1)
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
148 | && __is_trivial(_ValueType2)
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
149 | && __assignable>::
| ~~~~~~~~~~~~~~~~~~
150 | __uninit_copy(__first, __last, __result);
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from ../DataLayer/FastaIndex.h:11,
from index.cc:3:
/usr/include/c++/10/bits/stl_vector.h: In member function 'void BitArrays::assign(It, It) [with It = __gnu_cxx::__normal_iterator<unsigned char*, std::vector<unsigned char> >]':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<wat_array::BitArray*, std::vector<wat_array::BitArray> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:66,
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++/10/bits/stl_uninitialized.h: In 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++/10/bits/stl_uninitialized.h:84:9: note: parameter passing for argument of type 'std::move_iterator<wat_array::BitArray*>' changed in GCC 7.1
84 | __uninit_copy(_InputIterator __first, _InputIterator __last,
| ^~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_uninitialized.h:84:9: note: parameter passing for argument of type 'std::move_iterator<wat_array::BitArray*>' changed in GCC 7.1
g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-index abyss_index-index.o ../FMIndex/libfmindex.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm
In file included from /usr/include/c++/10/vector:72,
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++/10/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++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<FMIndex::Match>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/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++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<FMIndex::Match*, std::vector<FMIndex::Match> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from ../FMIndex/bit_array.h:24,
from ../FMIndex/BitArrays.h:4,
from ../FMIndex/FMIndex.h:5,
from map.cc:3:
/usr/include/c++/10/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++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<wat_array::BitArray>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:66,
from ../FMIndex/bit_array.h:24,
from ../FMIndex/BitArrays.h:4,
from ../FMIndex/FMIndex.h:5,
from map.cc:3:
/usr/include/c++/10/bits/stl_uninitialized.h:150:15: note: parameter passing for argument of type 'std::move_iterator<wat_array::BitArray*>' changed in GCC 7.1
147 | return std::__uninitialized_copy<__is_trivial(_ValueType1)
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
148 | && __is_trivial(_ValueType2)
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
149 | && __assignable>::
| ~~~~~~~~~~~~~~~~~~
150 | __uninit_copy(__first, __last, __result);
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_uninitialized.h:150:15: note: parameter passing for argument of type 'std::move_iterator<wat_array::BitArray*>' changed in GCC 7.1
147 | return std::__uninitialized_copy<__is_trivial(_ValueType1)
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
148 | && __is_trivial(_ValueType2)
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
149 | && __assignable>::
| ~~~~~~~~~~~~~~~~~~
150 | __uninit_copy(__first, __last, __result);
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from ../FMIndex/bit_array.h:24,
from ../FMIndex/BitArrays.h:4,
from ../FMIndex/FMIndex.h:5,
from map.cc:3:
/usr/include/c++/10/bits/stl_vector.h: In member function 'void BitArrays::assign(It, It) [with It = __gnu_cxx::__normal_iterator<unsigned char*, std::vector<unsigned char> >]':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<wat_array::BitArray*, std::vector<wat_array::BitArray> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from ../FMIndex/bit_array.h:24,
from ../FMIndex/BitArrays.h:4,
from ../FMIndex/FMIndex.h:5,
from map.cc:3:
/usr/include/c++/10/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++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<wat_array::BitArray>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:66,
from ../FMIndex/bit_array.h:24,
from ../FMIndex/BitArrays.h:4,
from ../FMIndex/FMIndex.h:5,
from map.cc:3:
/usr/include/c++/10/bits/stl_uninitialized.h:150:15: note: parameter passing for argument of type 'std::move_iterator<wat_array::BitArray*>' changed in GCC 7.1
147 | return std::__uninitialized_copy<__is_trivial(_ValueType1)
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
148 | && __is_trivial(_ValueType2)
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
149 | && __assignable>::
| ~~~~~~~~~~~~~~~~~~
150 | __uninit_copy(__first, __last, __result);
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_uninitialized.h:150:15: note: parameter passing for argument of type 'std::move_iterator<wat_array::BitArray*>' changed in GCC 7.1
147 | return std::__uninitialized_copy<__is_trivial(_ValueType1)
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
148 | && __is_trivial(_ValueType2)
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
149 | && __assignable>::
| ~~~~~~~~~~~~~~~~~~
150 | __uninit_copy(__first, __last, __result);
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from ../FMIndex/bit_array.h:24,
from ../FMIndex/BitArrays.h:4,
from ../FMIndex/FMIndex.h:5,
from map.cc:3:
/usr/include/c++/10/bits/stl_vector.h: In member function 'void BitArrays::assign(It, It) [with It = __gnu_cxx::__normal_iterator<unsigned char*, std::vector<unsigned char> >]':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<wat_array::BitArray*, std::vector<wat_array::BitArray> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/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++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<wat_array::BitArray>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:66,
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++/10/bits/stl_uninitialized.h:150:15: note: parameter passing for argument of type 'std::move_iterator<wat_array::BitArray*>' changed in GCC 7.1
147 | return std::__uninitialized_copy<__is_trivial(_ValueType1)
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
148 | && __is_trivial(_ValueType2)
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
149 | && __assignable>::
| ~~~~~~~~~~~~~~~~~~
150 | __uninit_copy(__first, __last, __result);
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_uninitialized.h:150:15: note: parameter passing for argument of type 'std::move_iterator<wat_array::BitArray*>' changed in GCC 7.1
147 | return std::__uninitialized_copy<__is_trivial(_ValueType1)
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
148 | && __is_trivial(_ValueType2)
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
149 | && __assignable>::
| ~~~~~~~~~~~~~~~~~~
150 | __uninit_copy(__first, __last, __result);
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
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++/10/bits/stl_vector.h: In member function 'void BitArrays::assign(It, It) [with It = __gnu_cxx::__normal_iterator<unsigned char*, std::vector<unsigned char> >]':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<wat_array::BitArray*, std::vector<wat_array::BitArray> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-map abyss_map-map.o ../FMIndex/libfmindex.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../DataBase/libdb.a -lsqlite3 -ldl -lm -ldl -lm
g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-map-ssq abyss_map_ssq-map.o ../FMIndex/libfmindex.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../DataBase/libdb.a -lsqlite3 -ldl -lm -ldl -lm
g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-overlap abyss_overlap-overlap.o ../FMIndex/libfmindex.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Map'
Making all in MergePaths
make[4]: Entering directory '/<<PKGBUILDDIR>>/MergePaths'
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o MergePaths-MergePaths.o `test -f 'MergePaths.cpp' || echo './'`MergePaths.cpp
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Align -I../Common -I../DataLayer -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o MergeContigs-MergeContigs.o `test -f 'MergeContigs.cpp' || echo './'`MergeContigs.cpp
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Align -I../Common -I../DataLayer -I../SimpleGraph -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o PathConsensus-PathConsensus.o `test -f 'PathConsensus.cpp' || echo './'`PathConsensus.cpp
g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o MergeContigs MergeContigs-MergeContigs.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a -ldl -lm
g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o PathConsensus PathConsensus-PathConsensus.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a ../dialign/libdialign.a -ldl -lm
g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o MergePaths MergePaths-MergePaths.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/MergePaths'
Making all in Overlap
make[4]: Entering directory '/<<PKGBUILDDIR>>/Overlap'
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Overlap-Overlap.o `test -f 'Overlap.cpp' || echo './'`Overlap.cpp
g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o Overlap Overlap-Overlap.o ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Overlap'
Making all in PairedDBG
make[4]: Entering directory '/<<PKGBUILDDIR>>/PairedDBG'
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -DPAIRED_DBG -I.. -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_paired_dbg-abyss-paired-dbg.o `test -f 'abyss-paired-dbg.cc' || echo './'`abyss-paired-dbg.cc
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -DPAIRED_DBG -I.. -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_paired_dbg-KmerPair.o `test -f 'KmerPair.cc' || echo './'`KmerPair.cc
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o KmerPair.o KmerPair.cc
rm -f libpaireddbg.a
ar cru libpaireddbg.a KmerPair.o
ar: `u' modifier ignored since `D' is the default (see `U')
ranlib libpaireddbg.a
g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-paired-dbg abyss_paired_dbg-abyss-paired-dbg.o abyss_paired_dbg-KmerPair.o ../Assembly/libassembly.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../DataBase/libdb.a -lsqlite3 -ldl -lm -ldl -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/PairedDBG'
Making all in ParseAligns
make[4]: Entering directory '/<<PKGBUILDDIR>>/ParseAligns'
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_fixmate-abyss-fixmate.o `test -f 'abyss-fixmate.cc' || echo './'`abyss-fixmate.cc
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -D SAM_SEQ_QUAL=1 -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_fixmate_ssq-abyss-fixmate.o `test -f 'abyss-fixmate.cc' || echo './'`abyss-fixmate.cc
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o ParseAligns-ParseAligns.o `test -f 'ParseAligns.cpp' || echo './'`ParseAligns.cpp
g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o ParseAligns ParseAligns-ParseAligns.o ../Common/libcommon.a -ldl -lm
g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-fixmate abyss_fixmate-abyss-fixmate.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../Common/libcommon.a -ldl -lm
g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-fixmate-ssq abyss_fixmate_ssq-abyss-fixmate.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../Common/libcommon.a -ldl -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/ParseAligns'
Making all in PathOverlap
make[4]: Entering directory '/<<PKGBUILDDIR>>/PathOverlap'
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o PathOverlap-PathOverlap.o `test -f 'PathOverlap.cpp' || echo './'`PathOverlap.cpp
g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o PathOverlap PathOverlap-PathOverlap.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/PathOverlap'
Making all in PopBubbles
make[4]: Entering directory '/<<PKGBUILDDIR>>/PopBubbles'
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Align -I../Common -I../DataLayer -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o PopBubbles-PopBubbles.o `test -f 'PopBubbles.cpp' || echo './'`PopBubbles.cpp
g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o PopBubbles PopBubbles-PopBubbles.o ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a ../dialign/libdialign.a -ldl -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/PopBubbles'
Making all in Scaffold
make[4]: Entering directory '/<<PKGBUILDDIR>>/Scaffold'
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_scaffold-scaffold.o `test -f 'scaffold.cc' || echo './'`scaffold.cc
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_junction-junction.o `test -f 'junction.cc' || echo './'`junction.cc
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_longseqdist-longseqdist.o `test -f 'longseqdist.cpp' || echo './'`longseqdist.cpp
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-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++/10/algorithm:62,
from /usr/include/boost/type_traits/is_nothrow_swappable.hpp:33,
from /usr/include/boost/type_traits.hpp:122,
from /usr/include/boost/pending/property.hpp:13,
from /usr/include/boost/graph/properties.hpp:15,
from ../Graph/Properties.h:6,
from ../Common/ContigNode.h:6,
from ../Common/ContigProperties.h:4,
from drawgraph.cc:10:
/usr/include/c++/10/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++/10/bits/stl_algo.h:1824:5: 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
1824 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
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++/10/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++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<std::pair<double, ContigNode> >::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
from /usr/include/boost/type_traits/is_nothrow_swappable.hpp:33,
from /usr/include/boost/type_traits.hpp:122,
from /usr/include/boost/pending/property.hpp:13,
from /usr/include/boost/graph/properties.hpp:15,
from ../Graph/Properties.h:6,
from ../Common/ContigNode.h:6,
from ../Common/ContigProperties.h:4,
from drawgraph.cc:10:
/usr/include/c++/10/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++/10/bits/stl_algo.h:1844:5: 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
1844 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1844:5: 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++/10/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++/10/bits/stl_algo.h:79:5: 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
79 | __move_median_to_first(_Iterator __result,_Iterator __a, _Iterator __b,
| ^~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:79:5: 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++/10/bits/stl_algo.h:79:5: 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++/10/bits/stl_algo.h:79:5: 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++/10/bits/stl_algo.h:61,
from /usr/include/c++/10/algorithm:62,
from /usr/include/boost/type_traits/is_nothrow_swappable.hpp:33,
from /usr/include/boost/type_traits.hpp:122,
from /usr/include/boost/pending/property.hpp:13,
from /usr/include/boost/graph/properties.hpp:15,
from ../Graph/Properties.h:6,
from ../Common/ContigNode.h:6,
from ../Common/ContigProperties.h:4,
from drawgraph.cc:10:
/usr/include/c++/10/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++/10/bits/stl_heap.h:223:5: 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
223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
from /usr/include/boost/type_traits/is_nothrow_swappable.hpp:33,
from /usr/include/boost/type_traits.hpp:122,
from /usr/include/boost/pending/property.hpp:13,
from /usr/include/boost/graph/properties.hpp:15,
from ../Graph/Properties.h:6,
from ../Common/ContigNode.h:6,
from ../Common/ContigProperties.h:4,
from drawgraph.cc:10:
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__heap_select(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<double, ContigNode>*, std::vector<std::pair<double, ContigNode> > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/10/bits/stl_algo.h:1667:5: 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
1667 | __heap_select(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1667:5: 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++/10/bits/stl_algo.h:1667:5: 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++/10/bits/stl_algo.h:1667:5: 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++/10/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++/10/bits/stl_algo.h:1950:5: 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
1950 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1950:5: 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++/10/bits/stl_algo.h:1929:34: 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
1929 | std::__move_median_to_first(__first, __first + 1, __mid, __last - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1930 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1929:34: 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++/10/bits/stl_algo.h:1964:25: 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
1964 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1942:25: 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
1942 | std::__heap_select(__first, __middle, __last, __comp);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
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++/10/bits/vector.tcc: In function 'int main(int, char**)':
/usr/include/c++/10/bits/vector.tcc:121:21: 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
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
from /usr/include/boost/type_traits/is_nothrow_swappable.hpp:33,
from /usr/include/boost/type_traits.hpp:122,
from /usr/include/boost/pending/property.hpp:13,
from /usr/include/boost/graph/properties.hpp:15,
from ../Graph/Properties.h:6,
from ../Common/ContigNode.h:6,
from ../Common/ContigProperties.h:4,
from drawgraph.cc:10:
/usr/include/c++/10/bits/stl_algo.h:1979:25: 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
1979 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1980 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1981 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1891:25: 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
1891 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1896:23: 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
1896 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-longseqdist abyss_longseqdist-longseqdist.o ../Common/libcommon.a -ldl -lm
g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-junction abyss_junction-junction.o ../Common/libcommon.a -ldl -lm
g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-drawgraph abyss_drawgraph-drawgraph.o ../Common/libcommon.a -ldl -lm
g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-scaffold abyss_scaffold-scaffold.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../Common/libcommon.a -ldl -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Scaffold'
Making all in SimpleGraph
make[4]: Entering directory '/<<PKGBUILDDIR>>/SimpleGraph'
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -Wno-strict-aliasing -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o SimpleGraph-SimpleGraph.o `test -f 'SimpleGraph.cpp' || echo './'`SimpleGraph.cpp
g++ -std=c++11 -Wall -Wextra -Werror -Wno-strict-aliasing -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o SimpleGraph SimpleGraph-SimpleGraph.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../Common/libcommon.a -lpthread -ldl -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/SimpleGraph'
Making all in kmerprint
make[4]: Entering directory '/<<PKGBUILDDIR>>/kmerprint'
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Assembly -I../Common -I../DataLayer -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o kmerprint-kmerprint.o `test -f 'kmerprint.cc' || echo './'`kmerprint.cc
g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o kmerprint kmerprint-kmerprint.o ../Assembly/libassembly.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/kmerprint'
Making all in FilterGraph
make[4]: Entering directory '/<<PKGBUILDDIR>>/FilterGraph'
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_filtergraph-FilterGraph.o `test -f 'FilterGraph.cc' || echo './'`FilterGraph.cc
g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-filtergraph abyss_filtergraph-FilterGraph.o ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/FilterGraph'
Making all in GapFiller
make[4]: Entering directory '/<<PKGBUILDDIR>>/GapFiller'
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../Align -D SAM_SEQ_QUAL=1 -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_gapfill-gapfill.o `test -f 'gapfill.cpp' || echo './'`gapfill.cpp
g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-gapfill abyss_gapfill-gapfill.o ../Align/libalign.a ../dialign/libdialign.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/GapFiller'
Making all in Sealer
make[4]: Entering directory '/<<PKGBUILDDIR>>/Sealer'
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_sealer-sealer.o `test -f 'sealer.cc' || echo './'`sealer.cc
g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-sealer abyss_sealer-sealer.o ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a -ldl -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Sealer'
Making all in RResolver
make[4]: Entering directory '/<<PKGBUILDDIR>>/RResolver'
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -I.. -I../Common -I../DataLayer -I../RResolver/btllib/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_rresolver_short-RResolverShort.o `test -f 'RResolverShort.cpp' || echo './'`RResolverShort.cpp
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -I.. -I../Common -I../DataLayer -I../RResolver/btllib/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_rresolver_short-Contigs.o `test -f 'Contigs.cpp' || echo './'`Contigs.cpp
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -I.. -I../Common -I../DataLayer -I../RResolver/btllib/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libralgorithmsshort_a-RAlgorithmsShort.o `test -f 'RAlgorithmsShort.cpp' || echo './'`RAlgorithmsShort.cpp
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -I.. -I../Common -I../DataLayer -I../RResolver/btllib/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libralgorithmsshort_a-BloomFilters.o `test -f 'BloomFilters.cpp' || echo './'`BloomFilters.cpp
In file included from /usr/include/c++/10/vector:72,
from ../RResolver/btllib/include/btllib/nthash.hpp:14,
from ../RResolver/btllib/include/btllib/bloom_filter.hpp:4,
from BloomFilters.h:4,
from RAlgorithmsShort.h:4,
from RResolverShort.cpp:7:
/usr/include/c++/10/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++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from ../RResolver/btllib/include/btllib/nthash.hpp:14,
from ../RResolver/btllib/include/btllib/bloom_filter.hpp:4,
from BloomFilters.h:4,
from RAlgorithmsShort.h:4,
from RResolverShort.cpp:7:
/usr/include/c++/10/bits/stl_vector.h: In function 'int main(int, char**)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -I.. -I../Common -I../DataLayer -I../RResolver/btllib/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libralgorithmsshort_a-Contigs.o `test -f 'Contigs.cpp' || echo './'`Contigs.cpp
In file included from /usr/include/c++/10/bits/stl_algo.h:61,
from /usr/include/c++/10/algorithm:62,
from ../RResolver/btllib/include/btllib/../external/cpptoml.hpp:10,
from ../RResolver/btllib/include/btllib/bloom_filter.hpp:7,
from BloomFilters.h:4,
from RAlgorithmsShort.h:4,
from RAlgorithmsShort.cpp:1:
/usr/include/c++/10/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
from ../RResolver/btllib/include/btllib/../external/cpptoml.hpp:10,
from ../RResolver/btllib/include/btllib/bloom_filter.hpp:7,
from BloomFilters.h:4,
from RAlgorithmsShort.h:4,
from RAlgorithmsShort.cpp:1:
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/10/bits/stl_algo.h:1844:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1844 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1844:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/10/bits/stl_algo.h:1950:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1950 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1950:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1964:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1964 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<ReadSize*, std::vector<ReadSize> >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<determineShortReadStats(const std::vector<std::__cxx11::basic_string<char> >&)::<lambda(ReadSize, ReadSize)> >]':
/usr/include/c++/10/bits/stl_algo.h:1824:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ReadSize*, std::vector<ReadSize> >' changed in GCC 7.1
1824 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<ReadSize*, std::vector<ReadSize> >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<determineShortReadStats(const std::vector<std::__cxx11::basic_string<char> >&)::<lambda(ReadSize, ReadSize)> >]':
/usr/include/c++/10/bits/stl_algo.h:1824:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ReadSize*, std::vector<ReadSize> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<ReadSize*, std::vector<ReadSize> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<determineShortReadStats(const std::vector<std::__cxx11::basic_string<char> >&)::<lambda(ReadSize, ReadSize)> >]':
/usr/include/c++/10/bits/stl_algo.h:1844:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ReadSize*, std::vector<ReadSize> >' changed in GCC 7.1
1844 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1844:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ReadSize*, std::vector<ReadSize> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<ReadSize*, std::vector<ReadSize> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<determineShortReadStats(const std::vector<std::__cxx11::basic_string<char> >&)::<lambda(ReadSize, ReadSize)> >]':
/usr/include/c++/10/bits/stl_algo.h:1844:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ReadSize*, std::vector<ReadSize> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1844:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ReadSize*, std::vector<ReadSize> >' changed in GCC 7.1
In file included from /usr/include/c++/10/bits/stl_algo.h:61,
from /usr/include/c++/10/algorithm:62,
from ../RResolver/btllib/include/btllib/../external/cpptoml.hpp:10,
from ../RResolver/btllib/include/btllib/bloom_filter.hpp:7,
from BloomFilters.h:4,
from RAlgorithmsShort.h:4,
from RAlgorithmsShort.cpp:1:
/usr/include/c++/10/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<ReadSize*, std::vector<ReadSize> >; _Distance = int; _Tp = ReadSize; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<determineShortReadStats(const std::vector<std::__cxx11::basic_string<char> >&)::<lambda(ReadSize, ReadSize)> >]':
/usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ReadSize*, std::vector<ReadSize> >' changed in GCC 7.1
223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<ReadSize*, std::vector<ReadSize> >; _Distance = int; _Tp = ReadSize; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<determineShortReadStats(const std::vector<std::__cxx11::basic_string<char> >&)::<lambda(ReadSize, ReadSize)> >]':
/usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ReadSize*, std::vector<ReadSize> >' changed in GCC 7.1
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -I.. -I../Common -I../DataLayer -I../RResolver/btllib/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libralgorithmsshort_a-SequenceTree.o `test -f 'SequenceTree.cpp' || echo './'`SequenceTree.cpp
In file included from /usr/include/c++/10/bits/stl_algobase.h:71,
from /usr/include/c++/10/bits/char_traits.h:39,
from /usr/include/c++/10/string:40,
from ../RResolver/btllib/include/btllib/nthash.hpp:13,
from ../RResolver/btllib/include/btllib/bloom_filter.hpp:4,
from BloomFilters.h:4,
from RAlgorithmsShort.h:4,
from RAlgorithmsShort.cpp:1:
/usr/include/c++/10/bits/predefined_ops.h: In function 'bool __gnu_cxx::__ops::_Iter_comp_iter<_Compare>::operator()(_Iterator1, _Iterator2) [with _Iterator1 = __gnu_cxx::__normal_iterator<ReadSize*, std::vector<ReadSize> >; _Iterator2 = __gnu_cxx::__normal_iterator<ReadSize*, std::vector<ReadSize> >; _Compare = determineShortReadStats(const std::vector<std::__cxx11::basic_string<char> >&)::<lambda(ReadSize, ReadSize)>]':
/usr/include/c++/10/bits/predefined_ops.h:155:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ReadSize*, std::vector<ReadSize> >' changed in GCC 7.1
155 | operator()(_Iterator1 __it1, _Iterator2 __it2)
| ^~~~~~~~
/usr/include/c++/10/bits/predefined_ops.h:155:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ReadSize*, std::vector<ReadSize> >' changed in GCC 7.1
/usr/include/c++/10/bits/predefined_ops.h: In function 'bool __gnu_cxx::__ops::_Iter_comp_iter<_Compare>::operator()(_Iterator1, _Iterator2) [with _Iterator1 = __gnu_cxx::__normal_iterator<ReadSize*, std::vector<ReadSize> >; _Iterator2 = __gnu_cxx::__normal_iterator<ReadSize*, std::vector<ReadSize> >; _Compare = determineShortReadStats(const std::vector<std::__cxx11::basic_string<char> >&)::<lambda(ReadSize, ReadSize)>]':
/usr/include/c++/10/bits/predefined_ops.h:155:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ReadSize*, std::vector<ReadSize> >' changed in GCC 7.1
/usr/include/c++/10/bits/predefined_ops.h:155:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ReadSize*, std::vector<ReadSize> >' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from ../RResolver/btllib/include/btllib/nthash.hpp:14,
from ../RResolver/btllib/include/btllib/bloom_filter.hpp:4,
from BloomFilters.h:4,
from RAlgorithmsShort.h:4,
from RAlgorithmsShort.cpp:1:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const ReadSize&}; _Tp = ReadSize; _Alloc = std::allocator<ReadSize>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<ReadSize>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -I.. -I../Common -I../DataLayer -I../RResolver/btllib/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libralgorithmsshort_a-RUtils.o `test -f 'RUtils.cpp' || echo './'`RUtils.cpp
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {ReadSize}; _Tp = ReadSize; _Alloc = std::allocator<ReadSize>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<ReadSize>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In function '_ZL23determineShortReadStatsRKSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE._omp_fn.1':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ReadSize*, std::vector<ReadSize> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
from ../RResolver/btllib/include/btllib/../external/cpptoml.hpp:10,
from ../RResolver/btllib/include/btllib/bloom_filter.hpp:7,
from BloomFilters.h:4,
from RAlgorithmsShort.h:4,
from RAlgorithmsShort.cpp:1:
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<ReadSize*, std::vector<ReadSize> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<determineShortReadStats(const std::vector<std::__cxx11::basic_string<char> >&)::<lambda(ReadSize, ReadSize)> >]':
/usr/include/c++/10/bits/stl_algo.h:1950:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ReadSize*, std::vector<ReadSize> >' changed in GCC 7.1
1950 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1950:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ReadSize*, std::vector<ReadSize> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:86:19: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ReadSize*, std::vector<ReadSize> >' changed in GCC 7.1
86 | else if (__comp(__a, __c))
| ~~~~~~^~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:93:22: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ReadSize*, std::vector<ReadSize> >' changed in GCC 7.1
93 | else if (__comp(__b, __c))
| ~~~~~~^~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1964:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ReadSize*, std::vector<ReadSize> >' changed in GCC 7.1
1964 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<ReadSize*, std::vector<ReadSize> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<determineShortReadStats(const std::vector<std::__cxx11::basic_string<char> >&)::<lambda(ReadSize, ReadSize)> >]':
/usr/include/c++/10/bits/stl_algo.h:1950:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ReadSize*, std::vector<ReadSize> >' changed in GCC 7.1
1950 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1950:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ReadSize*, std::vector<ReadSize> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:86:19: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ReadSize*, std::vector<ReadSize> >' changed in GCC 7.1
86 | else if (__comp(__a, __c))
| ~~~~~~^~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:93:22: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ReadSize*, std::vector<ReadSize> >' changed in GCC 7.1
93 | else if (__comp(__b, __c))
| ~~~~~~^~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1964:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ReadSize*, std::vector<ReadSize> >' changed in GCC 7.1
1964 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h: In function 'bool determineShortReadStats(const std::vector<std::__cxx11::basic_string<char> >&)':
/usr/include/c++/10/bits/stl_algo.h:1891:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ReadSize*, std::vector<ReadSize> >' changed in GCC 7.1
1891 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1896:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ReadSize*, std::vector<ReadSize> >' changed in GCC 7.1
1896 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from ../RResolver/btllib/include/btllib/nthash.hpp:14,
from ../RResolver/btllib/include/btllib/bloom_filter.hpp:4,
from BloomFilters.h:4,
from RAlgorithmsShort.h:4,
from RAlgorithmsShort.cpp:1:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ReadSize*, std::vector<ReadSize> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
from ../RResolver/btllib/include/btllib/../external/cpptoml.hpp:10,
from ../RResolver/btllib/include/btllib/bloom_filter.hpp:7,
from BloomFilters.h:4,
from RAlgorithmsShort.h:4,
from RAlgorithmsShort.cpp:1:
/usr/include/c++/10/bits/stl_algo.h:1979:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ReadSize*, std::vector<ReadSize> >' changed in GCC 7.1
1979 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1980 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1981 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1891:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ReadSize*, std::vector<ReadSize> >' changed in GCC 7.1
1891 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1896:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ReadSize*, std::vector<ReadSize> >' changed in GCC 7.1
1896 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1979:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1979 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1980 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1981 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1891:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1891 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1896:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1896 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1979:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ReadSize*, std::vector<ReadSize> >' changed in GCC 7.1
1979 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1980 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1981 | __comp);
| ~~~~~~~
rm -f libralgorithmsshort.a
ar cru libralgorithmsshort.a libralgorithmsshort_a-RAlgorithmsShort.o libralgorithmsshort_a-BloomFilters.o libralgorithmsshort_a-Contigs.o libralgorithmsshort_a-SequenceTree.o libralgorithmsshort_a-RUtils.o ../DataLayer/libdatalayer.a ../Common/libcommon.a
ar: `u' modifier ignored since `D' is the default (see `U')
ranlib libralgorithmsshort.a
g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -I.. -I../Common -I../DataLayer -I../RResolver/btllib/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -pthread -o abyss-rresolver-short abyss_rresolver_short-RResolverShort.o abyss_rresolver_short-Contigs.o ../DataLayer/libdatalayer.a ../Common/libcommon.a libralgorithmsshort.a -ldl -lm
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ar: `u' modifier ignored since `D' is the default (see `U')
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make common_stringutil common_histogram common_bitutil common_kmer common_sequence common_KmerIterator common_sam common_sam_ssq BloomFilter Konnector_DBGBloom Konnector_DBGBloomAlgorithms graph_ConstrainedBFSVisitor graph_BidirectionalBFS graph_AllPathsSearch graph_HashGraph graph_ConstrainedBidiBFSVisitor graph_ExtendPath graph_DotIO graph_UndirectedGraph Konnector_konnector DBG_LoadAlgorithm PairedDBG_LoadAlgorithm PairedDBG_KmerPair PairedDBG_Dinuc PairedDBG_BranchRecord BloomDBG_BloomDBG BloomDBG_RollingHash BloomDBG_RollingHashIterator BloomDBG_HashAgnosticCascadingBloom BloomDBG_CountingBloomFilter BloomDBG_RollingBloomDBG BloomDBG_MaskedKmer BloomDBG_SpacedSeed BloomDBG_LightweightKmer
make[3]: Entering directory '/<<PKGBUILDDIR>>/Unittest'
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Common/StringUtilTest.o Common/StringUtilTest.cpp
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Common/HistogramTest.o Common/HistogramTest.cpp
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Common/BitUtilTest.o Common/BitUtilTest.cpp
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Common/KmerTest.o Common/KmerTest.cpp
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Common/Sequence.o Common/Sequence.cc
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Common/KmerIteratorTest.o Common/KmerIteratorTest.cpp
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Common/SAM.o Common/SAM.cc
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -DSAM_SEQ_QUAL -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Common/common_sam_ssq-SAM.o `test -f 'Common/SAM.cc' || echo './'`Common/SAM.cc
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../Common -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -pthread -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Konnector/BloomFilter-BloomFilter.o `test -f 'Konnector/BloomFilter.cc' || echo './'`Konnector/BloomFilter.cc
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../Common -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -pthread -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Konnector/DBGBloom-DBGBloomTest.o `test -f 'Konnector/DBGBloomTest.cpp' || echo './'`Konnector/DBGBloomTest.cpp
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../Common -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -pthread -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Konnector/DBGBloomAlgorithms-DBGBloomAlgorithmsTest.o `test -f 'Konnector/DBGBloomAlgorithmsTest.cpp' || echo './'`Konnector/DBGBloomAlgorithmsTest.cpp
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../Common -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Graph/graph_ConstrainedBFSVisitor-ConstrainedBFSVisitorTest.o `test -f 'Graph/ConstrainedBFSVisitorTest.cpp' || echo './'`Graph/ConstrainedBFSVisitorTest.cpp
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../Common -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Graph/graph_BidirectionalBFS-BidirectionalBFSTest.o `test -f 'Graph/BidirectionalBFSTest.cpp' || echo './'`Graph/BidirectionalBFSTest.cpp
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../Common -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Graph/graph_AllPathsSearch-AllPathsSearchTest.o `test -f 'Graph/AllPathsSearchTest.cpp' || echo './'`Graph/AllPathsSearchTest.cpp
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../Common -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Graph/graph_HashGraph-HashGraphTest.o `test -f 'Graph/HashGraphTest.cpp' || echo './'`Graph/HashGraphTest.cpp
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../Common -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Graph/graph_ConstrainedBidiBFSVisitor-ConstrainedBidiBFSVisitorTest.o `test -f 'Graph/ConstrainedBidiBFSVisitorTest.cpp' || echo './'`Graph/ConstrainedBidiBFSVisitorTest.cpp
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../Common -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Graph/graph_ExtendPath-ExtendPathTest.o `test -f 'Graph/ExtendPathTest.cpp' || echo './'`Graph/ExtendPathTest.cpp
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../Common -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Graph/graph_DotIO-DotIOTest.o `test -f 'Graph/DotIOTest.cpp' || echo './'`Graph/DotIOTest.cpp
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Graph/UndirectedGraphTest.o Graph/UndirectedGraphTest.cpp
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../Common -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -pthread -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Konnector/konnector-konnectorTest.o `test -f 'Konnector/konnectorTest.cpp' || echo './'`Konnector/konnectorTest.cpp
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../DataLayer -I../Common -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -pthread -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o DBG/LoadAlgorithm-LoadAlgorithmTest.o `test -f 'DBG/LoadAlgorithmTest.cpp' || echo './'`DBG/LoadAlgorithmTest.cpp
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../DataLayer -I../Common -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -pthread -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o PairedDBG/LoadAlgorithm-LoadAlgorithmTest.o `test -f 'PairedDBG/LoadAlgorithmTest.cpp' || echo './'`PairedDBG/LoadAlgorithmTest.cpp
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../DataLayer -I../Common -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -pthread -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o PairedDBG/KmerPair-KmerPairTest.o `test -f 'PairedDBG/KmerPairTest.cc' || echo './'`PairedDBG/KmerPairTest.cc
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../DataLayer -I../Common -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -pthread -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o PairedDBG/Dinuc-DinucTest.o `test -f 'PairedDBG/DinucTest.cc' || echo './'`PairedDBG/DinucTest.cc
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../DataLayer -I../Common -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -pthread -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o PairedDBG/BranchRecord-BranchRecordTest.o `test -f 'PairedDBG/BranchRecordTest.cpp' || echo './'`PairedDBG/BranchRecordTest.cpp
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../Common -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -pthread -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o BloomDBG/BloomDBG-BloomDBGTest.o `test -f 'BloomDBG/BloomDBGTest.cpp' || echo './'`BloomDBG/BloomDBGTest.cpp
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o BloomDBG/RollingHashTest.o BloomDBG/RollingHashTest.cpp
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o BloomDBG/RollingHashIteratorTest.o BloomDBG/RollingHashIteratorTest.cpp
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -pthread -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o BloomDBG/HashAgnosticCascadingBloom-HashAgnosticCascadingBloomTest.o `test -f 'BloomDBG/HashAgnosticCascadingBloomTest.cpp' || echo './'`BloomDBG/HashAgnosticCascadingBloomTest.cpp
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../Common -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -pthread -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o BloomDBG/CountingBloomFilter-CountingBloomFilterTest.o `test -f 'BloomDBG/CountingBloomFilterTest.cpp' || echo './'`BloomDBG/CountingBloomFilterTest.cpp
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -pthread -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o BloomDBG/RollingBloomDBG-RollingBloomDBGTest.o `test -f 'BloomDBG/RollingBloomDBGTest.cpp' || echo './'`BloomDBG/RollingBloomDBGTest.cpp
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o BloomDBG/MaskedKmerTest.o BloomDBG/MaskedKmerTest.cpp
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o BloomDBG/SpacedSeedTest.o BloomDBG/SpacedSeedTest.cpp
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o BloomDBG/LightweightKmerTest.o BloomDBG/LightweightKmerTest.cpp
g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o common_stringutil Common/StringUtilTest.o ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm
g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o common_histogram Common/HistogramTest.o ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm
g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o common_bitutil Common/BitUtilTest.o ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm
g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o common_kmer Common/KmerTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm
g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o common_sequence Common/Sequence.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm
g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o common_KmerIterator Common/KmerIteratorTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm
g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o common_sam Common/SAM.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm
g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o common_sam_ssq Common/common_sam_ssq-SAM.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm
g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o BloomFilter Konnector/BloomFilter-BloomFilter.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm
g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o Konnector_DBGBloom Konnector/DBGBloom-DBGBloomTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm
g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o Konnector_DBGBloomAlgorithms Konnector/DBGBloomAlgorithms-DBGBloomAlgorithmsTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm
g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o graph_ConstrainedBFSVisitor Graph/graph_ConstrainedBFSVisitor-ConstrainedBFSVisitorTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm
g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o graph_BidirectionalBFS Graph/graph_BidirectionalBFS-BidirectionalBFSTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm
g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o graph_AllPathsSearch Graph/graph_AllPathsSearch-AllPathsSearchTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm
g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o graph_HashGraph Graph/graph_HashGraph-HashGraphTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm
g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o graph_ConstrainedBidiBFSVisitor Graph/graph_ConstrainedBidiBFSVisitor-ConstrainedBidiBFSVisitorTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm
g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o graph_ExtendPath Graph/graph_ExtendPath-ExtendPathTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm
g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o graph_DotIO Graph/graph_DotIO-DotIOTest.o ../Assembly/libassembly.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm
g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o graph_UndirectedGraph Graph/UndirectedGraphTest.o ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm
g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o Konnector_konnector Konnector/konnector-konnectorTest.o ../Align/libalign.a ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm
g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o DBG_LoadAlgorithm DBG/LoadAlgorithm-LoadAlgorithmTest.o ../Assembly/libassembly.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm
g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o PairedDBG_LoadAlgorithm PairedDBG/LoadAlgorithm-LoadAlgorithmTest.o ../PairedDBG/libpaireddbg.a ../Assembly/libassembly.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm
g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o PairedDBG_KmerPair PairedDBG/KmerPair-KmerPairTest.o ../PairedDBG/libpaireddbg.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm
g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o PairedDBG_Dinuc PairedDBG/Dinuc-DinucTest.o ../PairedDBG/libpaireddbg.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm
In file included from /usr/include/c++/10/unordered_map:46,
from ../vendor/btl_bloomfilter/vendor/cpptoml/include/cpptoml.h:22,
from ../vendor/btl_bloomfilter/BloomFilter.hpp:13,
from ../BloomDBG/RollingBloomDBG.h:15,
from BloomDBG/RollingBloomDBGTest.cpp:1:
/usr/include/c++/10/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++/10/bits/hashtable.h:1886:5: 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::_Hashtable_base<RollingBloomDBGVertex, RollingBloomDBGVertex, std::__detail::_Identity, std::equal_to<RollingBloomDBGVertex>, std::hash<RollingBloomDBGVertex>, std::__detail::_Mod_range_hashing, std::__detail::_Default_ranged_hash, std::__detail::_Hashtable_traits<true, true, true> >::const_iterator'} changed in GCC 7.1
1886 | _Hashtable<_Key, _Value, _Alloc, _ExtractKey, _Equal,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1887 | _H1, _H2, _Hash, _RehashPolicy, _Traits>::
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o PairedDBG_BranchRecord PairedDBG/BranchRecord-BranchRecordTest.o ../PairedDBG/libpaireddbg.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm
g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o BloomDBG_BloomDBG BloomDBG/BloomDBG-BloomDBGTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm
g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o BloomDBG_RollingHash BloomDBG/RollingHashTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm
g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o BloomDBG_RollingHashIterator BloomDBG/RollingHashIteratorTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm
g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o BloomDBG_HashAgnosticCascadingBloom BloomDBG/HashAgnosticCascadingBloom-HashAgnosticCascadingBloomTest.o ../DataLayer/libdatalayer.a ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm
g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o BloomDBG_CountingBloomFilter BloomDBG/CountingBloomFilter-CountingBloomFilterTest.o ../DataLayer/libdatalayer.a ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm
g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o BloomDBG_MaskedKmer BloomDBG/MaskedKmerTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm
g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o BloomDBG_SpacedSeed BloomDBG/SpacedSeedTest.o ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm
g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o BloomDBG_LightweightKmer BloomDBG/LightweightKmerTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm
/usr/include/c++/10/bits/hashtable.h: In member function 'virtual void RollingBloomDBGTest_adjacency_iterator_Test::TestBody()':
/usr/include/c++/10/bits/hashtable.h:839:21: 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::_Hashtable_base<RollingBloomDBGVertex, RollingBloomDBGVertex, std::__detail::_Identity, std::equal_to<RollingBloomDBGVertex>, std::hash<RollingBloomDBGVertex>, std::__detail::_Mod_range_hashing, std::__detail::_Default_ranged_hash, std::__detail::_Hashtable_traits<true, true, true> >::const_iterator'} changed in GCC 7.1
839 | { return erase(const_iterator(__it)); }
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/hashtable.h: In member function 'virtual void RollingBloomDBGTest_out_edge_iterator_Test::TestBody()':
/usr/include/c++/10/bits/hashtable.h:839:21: 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::_Hashtable_base<RollingBloomDBGVertex, RollingBloomDBGVertex, std::__detail::_Identity, std::equal_to<RollingBloomDBGVertex>, std::hash<RollingBloomDBGVertex>, std::__detail::_Mod_range_hashing, std::__detail::_Default_ranged_hash, std::__detail::_Hashtable_traits<true, true, true> >::const_iterator'} changed in GCC 7.1
839 | { return erase(const_iterator(__it)); }
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/hashtable.h: In member function 'virtual void RollingBloomDBGSpacedSeedTest_out_edge_iterator_Test::TestBody()':
/usr/include/c++/10/bits/hashtable.h:839:21: 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::_Hashtable_base<RollingBloomDBGVertex, RollingBloomDBGVertex, std::__detail::_Identity, std::equal_to<RollingBloomDBGVertex>, std::hash<RollingBloomDBGVertex>, std::__detail::_Mod_range_hashing, std::__detail::_Default_ranged_hash, std::__detail::_Hashtable_traits<true, true, true> >::const_iterator'} changed in GCC 7.1
839 | { return erase(const_iterator(__it)); }
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/hashtable.h: In member function 'virtual void RollingBloomDBGTest_in_edges_Test::TestBody()':
/usr/include/c++/10/bits/hashtable.h:839:21: 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::_Hashtable_base<RollingBloomDBGVertex, RollingBloomDBGVertex, std::__detail::_Identity, std::equal_to<RollingBloomDBGVertex>, std::hash<RollingBloomDBGVertex>, std::__detail::_Mod_range_hashing, std::__detail::_Default_ranged_hash, std::__detail::_Hashtable_traits<true, true, true> >::const_iterator'} changed in GCC 7.1
839 | { return erase(const_iterator(__it)); }
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~
g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o BloomDBG_RollingBloomDBG BloomDBG/RollingBloomDBG-RollingBloomDBGTest.o ../DataLayer/libdatalayer.a ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm
make[3]: Leaving directory '/<<PKGBUILDDIR>>/Unittest'
make check-TESTS
make[3]: Entering directory '/<<PKGBUILDDIR>>/Unittest'
make[4]: Entering directory '/<<PKGBUILDDIR>>/Unittest'
PASS: common_bitutil
PASS: common_histogram
PASS: common_kmer
PASS: common_stringutil
PASS: common_sequence
PASS: common_KmerIterator
PASS: common_sam
PASS: common_sam_ssq
PASS: BloomFilter
PASS: Konnector_DBGBloom
PASS: Konnector_DBGBloomAlgorithms
PASS: graph_ConstrainedBFSVisitor
PASS: graph_BidirectionalBFS
PASS: graph_AllPathsSearch
PASS: graph_HashGraph
PASS: graph_ConstrainedBidiBFSVisitor
PASS: graph_ExtendPath
PASS: graph_DotIO
PASS: graph_UndirectedGraph
PASS: Konnector_konnector
PASS: PairedDBG_KmerPair
PASS: PairedDBG_Dinuc
PASS: PairedDBG_BranchRecord
PASS: BloomDBG_BloomDBG
PASS: BloomDBG_RollingHash
PASS: BloomDBG_RollingHashIterator
PASS: BloomDBG_HashAgnosticCascadingBloom
PASS: BloomDBG_CountingBloomFilter
PASS: BloomDBG_RollingBloomDBG
PASS: BloomDBG_MaskedKmer
PASS: BloomDBG_SpacedSeed
PASS: BloomDBG_LightweightKmer
PASS: PairedDBG_LoadAlgorithm
PASS: DBG_LoadAlgorithm
============================================================================
Testsuite summary for ABySS 2.3.1
============================================================================
# TOTAL: 34
# PASS: 34
# SKIP: 0
# XFAIL: 0
# FAIL: 0
# XPASS: 0
# ERROR: 0
============================================================================
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Unittest'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/Unittest'
make[2]: Leaving directory '/<<PKGBUILDDIR>>/Unittest'
make[2]: Entering directory '/<<PKGBUILDDIR>>'
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
create-stamp debian/debhelper-build-stamp
dh_prep -a
debian/rules override_dh_auto_install
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_install --destdir=debian/tmp
make -j4 install DESTDIR=/<<PKGBUILDDIR>>/debian/tmp AM_UPDATE_INFO_DIR=no
make[2]: Entering directory '/<<PKGBUILDDIR>>'
Making install in bin
make[3]: Entering directory '/<<PKGBUILDDIR>>/bin'
make[4]: Entering directory '/<<PKGBUILDDIR>>/bin'
make[4]: Nothing to be done for 'install-data-am'.
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
/usr/bin/install -c abyss-bowtie abyss-bowtie2 abyss-bwa abyss-bwasw abyss-bwamem abyss-fatoagp abyss-kaligner abyss-pe abyss-samtoafg abyss-tabtomd abyss-bloom-dist.mk abyss-dida abyss-stack-size '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/bin'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/bin'
Making install in doc
make[3]: Entering directory '/<<PKGBUILDDIR>>/doc'
make[4]: Entering directory '/<<PKGBUILDDIR>>/doc'
make[4]: Nothing to be done for 'install-exec-am'.
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/share/doc/abyss'
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man1'
/usr/bin/install -c -m 644 flowchart.pdf flowchart_simplified.pdf '/<<PKGBUILDDIR>>/debian/tmp/usr/share/doc/abyss'
/usr/bin/install -c -m 644 ABYSS.1 abyss-pe.1 abyss-tofastq.1 '/<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man1'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/doc'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/doc'
Making install in Common
make[3]: Entering directory '/<<PKGBUILDDIR>>/Common'
make[4]: Entering directory '/<<PKGBUILDDIR>>/Common'
make[4]: Nothing to be done for 'install-exec-am'.
make[4]: Nothing to be done for 'install-data-am'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Common'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/Common'
Making install in Graph
make[3]: Entering directory '/<<PKGBUILDDIR>>/Graph'
make[4]: Entering directory '/<<PKGBUILDDIR>>/Graph'
make[4]: Nothing to be done for 'install-data-am'.
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
/usr/bin/install -c abyss-gc abyss-todot '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Graph'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/Graph'
Making install in DataLayer
make[3]: Entering directory '/<<PKGBUILDDIR>>/DataLayer'
make[4]: Entering directory '/<<PKGBUILDDIR>>/DataLayer'
make[4]: Nothing to be done for 'install-data-am'.
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
/usr/bin/install -c abyss-fac abyss-tofastq '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/DataLayer'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/DataLayer'
Making install in DataBase
make[3]: Entering directory '/<<PKGBUILDDIR>>/DataBase'
make[4]: Entering directory '/<<PKGBUILDDIR>>/DataBase'
make[4]: Nothing to be done for 'install-data-am'.
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
/usr/bin/install -c abyss-db-csv '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
/usr/bin/install -c abyss-db-txt '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/DataBase'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/DataBase'
Making install in FMIndex
make[3]: Entering directory '/<<PKGBUILDDIR>>/FMIndex'
make[4]: Entering directory '/<<PKGBUILDDIR>>/FMIndex'
make[4]: Nothing to be done for 'install-exec-am'.
make[4]: Nothing to be done for 'install-data-am'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/FMIndex'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/FMIndex'
Making install in Assembly
make[3]: Entering directory '/<<PKGBUILDDIR>>/Assembly'
make[4]: Entering directory '/<<PKGBUILDDIR>>/Assembly'
make[4]: Nothing to be done for 'install-exec-am'.
make[4]: Nothing to be done for 'install-data-am'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Assembly'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/Assembly'
Making install in dialign
make[3]: Entering directory '/<<PKGBUILDDIR>>/dialign'
make[4]: Entering directory '/<<PKGBUILDDIR>>/dialign'
make[4]: Nothing to be done for 'install-exec-am'.
make[4]: Nothing to be done for 'install-data-am'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/dialign'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/dialign'
Making install in Align
make[3]: Entering directory '/<<PKGBUILDDIR>>/Align'
make[4]: Entering directory '/<<PKGBUILDDIR>>/Align'
make[4]: Nothing to be done for 'install-data-am'.
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
/usr/bin/install -c abyss-align abyss-mergepairs '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Align'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/Align'
Making install in ABYSS
make[3]: Entering directory '/<<PKGBUILDDIR>>/ABYSS'
make[4]: Entering directory '/<<PKGBUILDDIR>>/ABYSS'
make[4]: Nothing to be done for 'install-data-am'.
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
/usr/bin/install -c ABYSS '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/ABYSS'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/ABYSS'
Making install in Parallel
make[3]: Entering directory '/<<PKGBUILDDIR>>/Parallel'
make[4]: Entering directory '/<<PKGBUILDDIR>>/Parallel'
make[4]: Nothing to be done for 'install-data-am'.
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
/usr/bin/install -c ABYSS-P abyss-paired-dbg-mpi '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Parallel'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/Parallel'
Making install in Bloom
make[3]: Entering directory '/<<PKGBUILDDIR>>/Bloom'
make[4]: Entering directory '/<<PKGBUILDDIR>>/Bloom'
make[4]: Nothing to be done for 'install-data-am'.
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
/usr/bin/install -c abyss-bloom '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Bloom'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/Bloom'
Making install in BloomDBG
make[3]: Entering directory '/<<PKGBUILDDIR>>/BloomDBG'
make[4]: Entering directory '/<<PKGBUILDDIR>>/BloomDBG'
make[4]: Nothing to be done for 'install-data-am'.
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
/usr/bin/install -c abyss-bloom-dbg '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/BloomDBG'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/BloomDBG'
Making install in Konnector
make[3]: Entering directory '/<<PKGBUILDDIR>>/Konnector'
make[4]: Entering directory '/<<PKGBUILDDIR>>/Konnector'
make[4]: Nothing to be done for 'install-data-am'.
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
/usr/bin/install -c konnector '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Konnector'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/Konnector'
Making install in Consensus
make[3]: Entering directory '/<<PKGBUILDDIR>>/Consensus'
make[4]: Entering directory '/<<PKGBUILDDIR>>/Consensus'
make[4]: Nothing to be done for 'install-data-am'.
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
/usr/bin/install -c Consensus '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Consensus'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/Consensus'
Making install in DAssembler
make[3]: Entering directory '/<<PKGBUILDDIR>>/DAssembler'
make[4]: Entering directory '/<<PKGBUILDDIR>>/DAssembler'
make[4]: Nothing to be done for 'install-data-am'.
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
/usr/bin/install -c DAssembler '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/DAssembler'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/DAssembler'
Making install in DistanceEst
make[3]: Entering directory '/<<PKGBUILDDIR>>/DistanceEst'
make[4]: Entering directory '/<<PKGBUILDDIR>>/DistanceEst'
make[4]: Nothing to be done for 'install-data-am'.
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
/usr/bin/install -c DistanceEst DistanceEst-ssq '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/DistanceEst'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/DistanceEst'
Making install in KAligner
make[3]: Entering directory '/<<PKGBUILDDIR>>/KAligner'
make[4]: Entering directory '/<<PKGBUILDDIR>>/KAligner'
make[4]: Nothing to be done for 'install-data-am'.
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
/usr/bin/install -c KAligner '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/KAligner'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/KAligner'
Making install in Layout
make[3]: Entering directory '/<<PKGBUILDDIR>>/Layout'
make[4]: Entering directory '/<<PKGBUILDDIR>>/Layout'
make[4]: Nothing to be done for 'install-data-am'.
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
/usr/bin/install -c abyss-layout '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Layout'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/Layout'
Making install in LogKmerCount
make[3]: Entering directory '/<<PKGBUILDDIR>>/LogKmerCount'
make[4]: Entering directory '/<<PKGBUILDDIR>>/LogKmerCount'
make[4]: Nothing to be done for 'install-data-am'.
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
/usr/bin/install -c logcounter '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/LogKmerCount'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/LogKmerCount'
Making install in Map
make[3]: Entering directory '/<<PKGBUILDDIR>>/Map'
make[4]: Entering directory '/<<PKGBUILDDIR>>/Map'
make[4]: Nothing to be done for 'install-data-am'.
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
/usr/bin/install -c abyss-index abyss-map abyss-map-ssq abyss-overlap '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Map'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/Map'
Making install in MergePaths
make[3]: Entering directory '/<<PKGBUILDDIR>>/MergePaths'
make[4]: Entering directory '/<<PKGBUILDDIR>>/MergePaths'
make[4]: Nothing to be done for 'install-data-am'.
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
/usr/bin/install -c MergePaths MergeContigs PathConsensus '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/MergePaths'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/MergePaths'
Making install in Overlap
make[3]: Entering directory '/<<PKGBUILDDIR>>/Overlap'
make[4]: Entering directory '/<<PKGBUILDDIR>>/Overlap'
make[4]: Nothing to be done for 'install-data-am'.
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
/usr/bin/install -c Overlap '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Overlap'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/Overlap'
Making install in PairedDBG
make[3]: Entering directory '/<<PKGBUILDDIR>>/PairedDBG'
make[4]: Entering directory '/<<PKGBUILDDIR>>/PairedDBG'
make[4]: Nothing to be done for 'install-data-am'.
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
/usr/bin/install -c abyss-paired-dbg '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/PairedDBG'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/PairedDBG'
Making install in ParseAligns
make[3]: Entering directory '/<<PKGBUILDDIR>>/ParseAligns'
make[4]: Entering directory '/<<PKGBUILDDIR>>/ParseAligns'
make[4]: Nothing to be done for 'install-data-am'.
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
/usr/bin/install -c abyss-fixmate abyss-fixmate-ssq ParseAligns '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/ParseAligns'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/ParseAligns'
Making install in PathOverlap
make[3]: Entering directory '/<<PKGBUILDDIR>>/PathOverlap'
make[4]: Entering directory '/<<PKGBUILDDIR>>/PathOverlap'
make[4]: Nothing to be done for 'install-data-am'.
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
/usr/bin/install -c PathOverlap '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/PathOverlap'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/PathOverlap'
Making install in PopBubbles
make[3]: Entering directory '/<<PKGBUILDDIR>>/PopBubbles'
make[4]: Entering directory '/<<PKGBUILDDIR>>/PopBubbles'
make[4]: Nothing to be done for 'install-data-am'.
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
/usr/bin/install -c PopBubbles '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/PopBubbles'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/PopBubbles'
Making install in Scaffold
make[3]: Entering directory '/<<PKGBUILDDIR>>/Scaffold'
make[4]: Entering directory '/<<PKGBUILDDIR>>/Scaffold'
make[4]: Nothing to be done for 'install-data-am'.
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
/usr/bin/install -c abyss-scaffold abyss-junction abyss-longseqdist '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Scaffold'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/Scaffold'
Making install in SimpleGraph
make[3]: Entering directory '/<<PKGBUILDDIR>>/SimpleGraph'
make[4]: Entering directory '/<<PKGBUILDDIR>>/SimpleGraph'
make[4]: Nothing to be done for 'install-data-am'.
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
/usr/bin/install -c SimpleGraph '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/SimpleGraph'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/SimpleGraph'
Making install in kmerprint
make[3]: Entering directory '/<<PKGBUILDDIR>>/kmerprint'
make[4]: Entering directory '/<<PKGBUILDDIR>>/kmerprint'
make[4]: Nothing to be done for 'install-exec-am'.
make[4]: Nothing to be done for 'install-data-am'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/kmerprint'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/kmerprint'
Making install in FilterGraph
make[3]: Entering directory '/<<PKGBUILDDIR>>/FilterGraph'
make[4]: Entering directory '/<<PKGBUILDDIR>>/FilterGraph'
make[4]: Nothing to be done for 'install-data-am'.
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
/usr/bin/install -c abyss-filtergraph '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/FilterGraph'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/FilterGraph'
Making install in GapFiller
make[3]: Entering directory '/<<PKGBUILDDIR>>/GapFiller'
make[4]: Entering directory '/<<PKGBUILDDIR>>/GapFiller'
make[4]: Nothing to be done for 'install-data-am'.
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
/usr/bin/install -c abyss-gapfill '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/GapFiller'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/GapFiller'
Making install in Sealer
make[3]: Entering directory '/<<PKGBUILDDIR>>/Sealer'
make[4]: Entering directory '/<<PKGBUILDDIR>>/Sealer'
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
/usr/bin/install -c abyss-sealer '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Sealer'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/Sealer'
Making install in RResolver
make[3]: Entering directory '/<<PKGBUILDDIR>>/RResolver'
make[4]: Entering directory '/<<PKGBUILDDIR>>/RResolver'
make[4]: Nothing to be done for 'install-data-am'.
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
/usr/bin/install -c abyss-rresolver-short '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/RResolver'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/RResolver'
Making install in AdjList
make[3]: Entering directory '/<<PKGBUILDDIR>>/AdjList'
make[4]: Entering directory '/<<PKGBUILDDIR>>/AdjList'
make[4]: Nothing to be done for 'install-data-am'.
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
/usr/bin/install -c AdjList '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/AdjList'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/AdjList'
Making install in vendor
make[3]: Entering directory '/<<PKGBUILDDIR>>/vendor'
make[4]: Entering directory '/<<PKGBUILDDIR>>/vendor'
make[4]: Nothing to be done for 'install-exec-am'.
make[4]: Nothing to be done for 'install-data-am'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/vendor'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/vendor'
Making install in vendor/gtest-1.7.0
make[3]: Entering directory '/<<PKGBUILDDIR>>/vendor/gtest-1.7.0'
make[4]: Entering directory '/<<PKGBUILDDIR>>/vendor/gtest-1.7.0'
make[4]: Nothing to be done for 'install-exec-am'.
make[4]: Nothing to be done for 'install-data-am'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/vendor/gtest-1.7.0'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/vendor/gtest-1.7.0'
Making install in Unittest
make[3]: Entering directory '/<<PKGBUILDDIR>>/Unittest'
make[4]: Entering directory '/<<PKGBUILDDIR>>/Unittest'
make[4]: Nothing to be done for 'install-exec-am'.
make[4]: Nothing to be done for 'install-data-am'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Unittest'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/Unittest'
make[3]: Entering directory '/<<PKGBUILDDIR>>'
make[4]: Entering directory '/<<PKGBUILDDIR>>'
make[4]: Nothing to be done for 'install-exec-am'.
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/share/doc/abyss'
/usr/bin/install -c -m 644 ChangeLog CITATION.bib CITATION.md COPYRIGHT LICENSE README.md '/<<PKGBUILDDIR>>/debian/tmp/usr/share/doc/abyss'
make[4]: Leaving directory '/<<PKGBUILDDIR>>'
make[3]: Leaving directory '/<<PKGBUILDDIR>>'
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
PATH=debian/tmp/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games help2man --no-info \
-n "Estimate distances between contigs using paired-end alignments." \
DistanceEst > debian/tmp/usr/share/man/man1/DistanceEst.1
PATH=debian/tmp/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games help2man --no-info \
-n "Fill the paired-end fields of SAM alignments" abyss-fixmate \
> debian/tmp/usr/share/man/man1/abyss-fixmate.1
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
debian/rules override_dh_install
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_install
for pl in `grep -Rl '#!/usr/bin/env[[:space:]]\+perl' debian/*/usr/*` ; do \
sed -i '1s?^#!/usr/bin/env[[:space:]]\+perl?#!/usr/bin/perl?' ${pl} ; \
done
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_installdocs -a
dh_installchangelogs -a
dh_installman -a
dh_perl -a
dh_link -a
dh_strip_nondeterminism -a
dh_compress -a
dh_fixperms -a
dh_missing -a
dh_dwz -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/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/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-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-paired-dbg-mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/konnector contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/ParseAligns contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/abyss-scaffold contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/ABYSS 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/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-rresolver-short contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/abyss-db-csv contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/PathConsensus contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/abyss-junction contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/abyss-paired-dbg contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/abyss-filtergraph contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/abyss-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-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/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-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/DAssembler contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/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-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-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/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/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-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-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/PopBubbles contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/abyss-map contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/PathOverlap contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/abyss-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/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-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-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/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/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/AdjList contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/ABYSS-P contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/abyss-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/MergeContigs contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/abyss-sealer contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/abyss-bloom contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/MergePaths 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/KAligner debian/abyss/usr/lib/abyss/DistanceEst-ssq debian/abyss/usr/lib/abyss/abyss-fixmate-ssq debian/abyss/usr/lib/abyss/abyss-paired-dbg-mpi debian/abyss/usr/lib/abyss/konnector debian/abyss/usr/lib/abyss/ParseAligns debian/abyss/usr/lib/abyss/abyss-scaffold debian/abyss/usr/lib/abyss/ABYSS debian/abyss/usr/bin/abyss-fixmate debian/abyss/usr/lib/abyss/abyss-mergepairs debian/abyss/usr/lib/abyss/abyss-rresolver-short debian/abyss/usr/lib/abyss/abyss-db-csv debian/abyss/usr/lib/abyss/PathConsensus debian/abyss/usr/lib/abyss/abyss-junction debian/abyss/usr/lib/abyss/abyss-paired-dbg debian/abyss/usr/lib/abyss/abyss-filtergraph debian/abyss/usr/lib/abyss/abyss-fac debian/abyss/usr/lib/abyss/abyss-map-ssq debian/abyss/usr/lib/abyss/SimpleGraph debian/abyss/usr/lib/abyss/abyss-bloom-dbg debian/abyss/usr/lib/abyss/DAssembler debian/abyss/usr/lib/abyss/DistanceEst debian/abyss/usr/lib/abyss/abyss-gc debian/abyss/usr/lib/abyss/abyss-align debian/abyss/usr/lib/abyss/abyss-longseqdist debian/abyss/usr/lib/abyss/Consensus debian/abyss/usr/lib/abyss/logcounter debian/abyss/usr/lib/abyss/abyss-todot debian/abyss/usr/lib/abyss/abyss-index debian/abyss/usr/lib/abyss/PopBubbles debian/abyss/usr/lib/abyss/abyss-map debian/abyss/usr/lib/abyss/PathOverlap debian/abyss/usr/lib/abyss/abyss-fixmate debian/abyss/usr/lib/abyss/abyss-overlap debian/abyss/usr/lib/abyss/abyss-tofastq debian/abyss/usr/lib/abyss/abyss-layout debian/abyss/usr/lib/abyss/Overlap debian/abyss/usr/bin/DistanceEst debian/abyss/usr/lib/abyss/AdjList debian/abyss/usr/lib/abyss/ABYSS-P debian/abyss/usr/lib/abyss/abyss-gapfill debian/abyss/usr/lib/abyss/MergeContigs debian/abyss/usr/lib/abyss/abyss-sealer debian/abyss/usr/lib/abyss/abyss-bloom debian/abyss/usr/lib/abyss/MergePaths 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_2.3.1-1_armhf.deb'.
dpkg-deb: building package 'abyss-dbgsym' in '../abyss-dbgsym_2.3.1-1_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian mythic lxc autobuilder 1 <root@raspbian.org> >../abyss_2.3.1-1_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2021-10-05T00:26:46Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
abyss_2.3.1-1_armhf.changes:
----------------------------
Format: 1.8
Date: Fri, 01 Oct 2021 16:10:22 +0200
Source: abyss
Binary: abyss abyss-dbgsym
Architecture: armhf
Version: 2.3.1-1
Distribution: bookworm-staging
Urgency: medium
Maintainer: Raspbian mythic lxc autobuilder 1 <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
abyss - de novo, parallel, sequence assembler for short reads
Changes:
abyss (2.3.1-1) unstable; urgency=medium
.
* Fix watchfile to detect new versions on github
* New upstream version
* Standards-Version: 4.6.0 (routine-update)
Checksums-Sha1:
8dcaf7110e08cf5acacef3b8b36e371791bd3fdf 29273396 abyss-dbgsym_2.3.1-1_armhf.deb
349c14d3a7540085e714e9fe976b9893508d0b0e 7289 abyss_2.3.1-1_armhf.buildinfo
7ce0e1fe5933b8c2712785b9d580f277f820fd11 2822524 abyss_2.3.1-1_armhf.deb
Checksums-Sha256:
9d9470bfee9399a8870b19993be9e8d4b30a7e485b31028c39371f2be6b914b0 29273396 abyss-dbgsym_2.3.1-1_armhf.deb
fe7c8bc1d174075ee93388b3f6eafedf0a339e3ffcdf7613e57b8b3c0ec716aa 7289 abyss_2.3.1-1_armhf.buildinfo
c84649f5c3d9cddbaa0bd28afdd0f495a132f11d571278cdfd7116b063b41495 2822524 abyss_2.3.1-1_armhf.deb
Files:
69fb4f45eb2622b23cba676cd39b49fe 29273396 debug optional abyss-dbgsym_2.3.1-1_armhf.deb
710de0c3a2583a5b543292e48be1b789 7289 science optional abyss_2.3.1-1_armhf.buildinfo
1b850c7bb925c24520d332dc6708ba38 2822524 science optional abyss_2.3.1-1_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
abyss-dbgsym_2.3.1-1_armhf.deb
------------------------------
new Debian package, version 2.0.
size 29273396 bytes: control archive=2528 bytes.
2086 bytes, 12 lines control
4643 bytes, 44 lines md5sums
Package: abyss-dbgsym
Source: abyss
Version: 2.3.1-1
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 30297
Depends: abyss (= 2.3.1-1)
Section: debug
Priority: optional
Description: debug symbols for abyss
Build-Ids: 03204b122747a26adabc708a51b567b85de62343 08a1848c776d9af933345b765d6d47f942d2d13f 1479f6dd77e8c12c8bd0e1597e9b10d17c264f74 170453a4cb7f8a48aaf133917ae3586c1453ad02 1848477636da3b828a71c8d6bf675eccbe448f5f 1e1517c15b49208d4829737bd6b1ccafbdab2321 1e2b1091f759d5d60ca66f8895fec3e7d9dc0097 2740d0ae1ee751f00ede4ffc94c7c76c30efa314 27ccdb4a6c4af62aba83a314577c1d678a813256 2d2036901d8306f7ee2ced41c541143393632f78 30593dcbce00df9c1f90c4f5183d51c7f6a681a0 363c8d3503fed01ac58e163b04293456276e7fb8 366581974f6156485b1532c29d27c19cefa06201 391c315c2f8f6291e1f34e37d7449bf865bcbb18 572698441d16ea72c80dc5a8be4e550afdbb8a09 6e028529b46ea5ced748339e8b840800100320d4 78be93d2edcbf40e7f8e5a5c8fb3627638639035 7959989bed17afa500ac0ad2c9cace740bd01540 846d81f29fef44d16eacf337b2c58bc58254edc8 86ea1aef3ff2f09f99f3cb6fd002a889174a91ee 8a0fc2a092e42acb7d74aab26ac675665414ea91 8a2848ea5cb4a7f5cfc16e31c2c4fd8bbfbdb5cc 90b010815d50b478e32d82aeae60763beff94b11 94dceaaecf41bb31bf07d3695cec85fa28b58aa6 9acf2f53ab3651329a182c5f892b324011be6c04 b29e3a8b46e1948cb6a36dc4d67faa0494cc3ff7 b51c77c011e3bb904ec2e44ce9991f9a70579180 bb847b8a1da7b70240d5eb0a173fc44a2243144a bf98a1d8827fe1d82da856dcdd1b01ae929f8b73 c5434aa55fa62ee06c5c939bcb5a9185f3a073cf ce375ea1eb9be306275ba6c7ee6b004488f7d36b cf25835b386b33d6494c28dc2987bb5218523f83 cfb2e5db372846bd2bb956023ddab4d3940c56c6 d5f83fe335eb42142076dce00617a89dcbec3c8d d90466166a38482b4d71d85b979aff1c58f24048 e07127853794cc7795e418debf4b28fa024bf2c6 ed6d1162f9ce0c7815f842b79386236974ab912a eedcdffe048a3934af7e4f3039b796d9d951d9e1 f0ed0c408969614d50ad6bb61ddf5e6470d25645 f520fb0945d27b609f55725802bb2b30e8a4b617 f8097e24ba59e145701d5d50454b434729891f30 fa93e7d4f11531fddc12c5ef007700ebba82f030 fb616894fad52a51a353647dc919cddcaad43ece
drwxr-xr-x root/root 0 2021-10-01 14:10 ./
drwxr-xr-x root/root 0 2021-10-01 14:10 ./usr/
drwxr-xr-x root/root 0 2021-10-01 14:10 ./usr/lib/
drwxr-xr-x root/root 0 2021-10-01 14:10 ./usr/lib/debug/
drwxr-xr-x root/root 0 2021-10-01 14:10 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2021-10-01 14:10 ./usr/lib/debug/.build-id/03/
-rw-r--r-- root/root 1338256 2021-10-01 14:10 ./usr/lib/debug/.build-id/03/204b122747a26adabc708a51b567b85de62343.debug
drwxr-xr-x root/root 0 2021-10-01 14:10 ./usr/lib/debug/.build-id/08/
-rw-r--r-- root/root 445656 2021-10-01 14:10 ./usr/lib/debug/.build-id/08/a1848c776d9af933345b765d6d47f942d2d13f.debug
drwxr-xr-x root/root 0 2021-10-01 14:10 ./usr/lib/debug/.build-id/14/
-rw-r--r-- root/root 433304 2021-10-01 14:10 ./usr/lib/debug/.build-id/14/79f6dd77e8c12c8bd0e1597e9b10d17c264f74.debug
drwxr-xr-x root/root 0 2021-10-01 14:10 ./usr/lib/debug/.build-id/17/
-rw-r--r-- root/root 499632 2021-10-01 14:10 ./usr/lib/debug/.build-id/17/0453a4cb7f8a48aaf133917ae3586c1453ad02.debug
drwxr-xr-x root/root 0 2021-10-01 14:10 ./usr/lib/debug/.build-id/18/
-rw-r--r-- root/root 197532 2021-10-01 14:10 ./usr/lib/debug/.build-id/18/48477636da3b828a71c8d6bf675eccbe448f5f.debug
drwxr-xr-x root/root 0 2021-10-01 14:10 ./usr/lib/debug/.build-id/1e/
-rw-r--r-- root/root 263412 2021-10-01 14:10 ./usr/lib/debug/.build-id/1e/1517c15b49208d4829737bd6b1ccafbdab2321.debug
-rw-r--r-- root/root 798836 2021-10-01 14:10 ./usr/lib/debug/.build-id/1e/2b1091f759d5d60ca66f8895fec3e7d9dc0097.debug
drwxr-xr-x root/root 0 2021-10-01 14:10 ./usr/lib/debug/.build-id/27/
-rw-r--r-- root/root 1338692 2021-10-01 14:10 ./usr/lib/debug/.build-id/27/40d0ae1ee751f00ede4ffc94c7c76c30efa314.debug
-rw-r--r-- root/root 1249120 2021-10-01 14:10 ./usr/lib/debug/.build-id/27/ccdb4a6c4af62aba83a314577c1d678a813256.debug
drwxr-xr-x root/root 0 2021-10-01 14:10 ./usr/lib/debug/.build-id/2d/
-rw-r--r-- root/root 232640 2021-10-01 14:10 ./usr/lib/debug/.build-id/2d/2036901d8306f7ee2ced41c541143393632f78.debug
drwxr-xr-x root/root 0 2021-10-01 14:10 ./usr/lib/debug/.build-id/30/
-rw-r--r-- root/root 580968 2021-10-01 14:10 ./usr/lib/debug/.build-id/30/593dcbce00df9c1f90c4f5183d51c7f6a681a0.debug
drwxr-xr-x root/root 0 2021-10-01 14:10 ./usr/lib/debug/.build-id/36/
-rw-r--r-- root/root 753164 2021-10-01 14:10 ./usr/lib/debug/.build-id/36/3c8d3503fed01ac58e163b04293456276e7fb8.debug
-rw-r--r-- root/root 245264 2021-10-01 14:10 ./usr/lib/debug/.build-id/36/6581974f6156485b1532c29d27c19cefa06201.debug
drwxr-xr-x root/root 0 2021-10-01 14:10 ./usr/lib/debug/.build-id/39/
-rw-r--r-- root/root 763084 2021-10-01 14:10 ./usr/lib/debug/.build-id/39/1c315c2f8f6291e1f34e37d7449bf865bcbb18.debug
drwxr-xr-x root/root 0 2021-10-01 14:10 ./usr/lib/debug/.build-id/57/
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-rw-r--r-- root/root 1054860 2021-10-01 14:10 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/abyss.debug
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lrwxrwxrwx root/root 0 2021-10-01 14:10 ./usr/share/doc/abyss-dbgsym -> abyss
abyss_2.3.1-1_armhf.deb
-----------------------
new Debian package, version 2.0.
size 2822524 bytes: control archive=2720 bytes.
706 bytes, 14 lines control
4983 bytes, 79 lines md5sums
Package: abyss
Version: 2.3.1-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 8140
Depends: make, libc6 (>= 2.29), libgcc-s1 (>= 3.5), libgomp1 (>= 4.9), libopenmpi3 (>= 4.1.1), libsqlite3-0 (>= 3.5.9), libstdc++6 (>= 6), perl:any, bsdextrautils, openmpi-common, openmpi-bin
Section: science
Priority: optional
Homepage: https://github.com/bcgsc/abyss
Description: de novo, parallel, sequence assembler for short reads
ABySS is a de novo, parallel, sequence assembler that is designed for
short reads. It may be used to assemble genome or transcriptome
sequence data. Parallelization is achieved using MPI, OpenMP and
pthread.
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drwxr-xr-x root/root 0 2021-10-01 14:10 ./usr/bin/
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-rwxr-xr-x root/root 22809 2021-10-01 14:10 ./usr/bin/abyss-pe
drwxr-xr-x root/root 0 2021-10-01 14:10 ./usr/lib/
drwxr-xr-x root/root 0 2021-10-01 14:10 ./usr/lib/abyss/
-rwxr-xr-x root/root 218816 2021-10-01 14:10 ./usr/lib/abyss/ABYSS
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-rwxr-xr-x root/root 59036 2021-10-01 14:10 ./usr/lib/abyss/Consensus
-rwxr-xr-x root/root 79532 2021-10-01 14:10 ./usr/lib/abyss/DAssembler
-rwxr-xr-x root/root 116392 2021-10-01 14:10 ./usr/lib/abyss/DistanceEst
-rwxr-xr-x root/root 120488 2021-10-01 14:10 ./usr/lib/abyss/DistanceEst-ssq
-rwxr-xr-x root/root 161448 2021-10-01 14:10 ./usr/lib/abyss/KAligner
-rwxr-xr-x root/root 181936 2021-10-01 14:10 ./usr/lib/abyss/MergeContigs
-rwxr-xr-x root/root 153244 2021-10-01 14:10 ./usr/lib/abyss/MergePaths
-rwxr-xr-x root/root 157356 2021-10-01 14:10 ./usr/lib/abyss/Overlap
-rwxr-xr-x root/root 83596 2021-10-01 14:10 ./usr/lib/abyss/ParseAligns
-rwxr-xr-x root/root 292524 2021-10-01 14:10 ./usr/lib/abyss/PathConsensus
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-rwxr-xr-x root/root 161452 2021-10-01 14:10 ./usr/lib/abyss/PopBubbles
-rwxr-xr-x root/root 145064 2021-10-01 14:10 ./usr/lib/abyss/SimpleGraph
-rwxr-xr-x root/root 153244 2021-10-01 14:10 ./usr/lib/abyss/abyss-align
-rwxr-xr-x root/root 272084 2021-10-01 14:10 ./usr/lib/abyss/abyss-bloom
-rwxr-xr-x root/root 292536 2021-10-01 14:10 ./usr/lib/abyss/abyss-bloom-dbg
-rwxr-xr-x root/root 6491 2021-10-01 14:10 ./usr/lib/abyss/abyss-bloom-dist.mk
-rwxr-xr-x root/root 1135 2021-10-01 14:10 ./usr/lib/abyss/abyss-bowtie
-rwxr-xr-x root/root 1192 2021-10-01 14:10 ./usr/lib/abyss/abyss-bowtie2
-rwxr-xr-x root/root 1208 2021-10-01 14:10 ./usr/lib/abyss/abyss-bwa
-rwxr-xr-x root/root 1454 2021-10-01 14:10 ./usr/lib/abyss/abyss-bwamem
-rwxr-xr-x root/root 1362 2021-10-01 14:10 ./usr/lib/abyss/abyss-bwasw
-rwxr-xr-x root/root 46732 2021-10-01 14:10 ./usr/lib/abyss/abyss-db-csv
-rwxr-xr-x root/root 703 2021-10-01 14:10 ./usr/lib/abyss/abyss-db-txt
-rwxr-xr-x root/root 2739 2021-10-01 14:10 ./usr/lib/abyss/abyss-dida
-rwxr-xr-x root/root 59044 2021-10-01 14:10 ./usr/lib/abyss/abyss-fac
-rwxr-xr-x root/root 2058 2021-10-01 14:10 ./usr/lib/abyss/abyss-fatoagp
-rwxr-xr-x root/root 145064 2021-10-01 14:10 ./usr/lib/abyss/abyss-filtergraph
-rwxr-xr-x root/root 104080 2021-10-01 14:10 ./usr/lib/abyss/abyss-fixmate
-rwxr-xr-x root/root 104080 2021-10-01 14:10 ./usr/lib/abyss/abyss-fixmate-ssq
-rwxr-xr-x root/root 79532 2021-10-01 14:10 ./usr/lib/abyss/abyss-gapfill
-rwxr-xr-x root/root 67212 2021-10-01 14:10 ./usr/lib/abyss/abyss-gc
-rwxr-xr-x root/root 79508 2021-10-01 14:10 ./usr/lib/abyss/abyss-index
-rwxr-xr-x root/root 79504 2021-10-01 14:10 ./usr/lib/abyss/abyss-junction
-rwxr-xr-x root/root 39 2021-10-01 14:10 ./usr/lib/abyss/abyss-kaligner
-rwxr-xr-x root/root 104084 2021-10-01 14:10 ./usr/lib/abyss/abyss-layout
-rwxr-xr-x root/root 79512 2021-10-01 14:10 ./usr/lib/abyss/abyss-longseqdist
-rwxr-xr-x root/root 145056 2021-10-01 14:10 ./usr/lib/abyss/abyss-map
-rwxr-xr-x root/root 153248 2021-10-01 14:10 ./usr/lib/abyss/abyss-map-ssq
-rwxr-xr-x root/root 63156 2021-10-01 14:10 ./usr/lib/abyss/abyss-mergepairs
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-rwxr-xr-x root/root 22809 2021-10-01 14:10 ./usr/lib/abyss/abyss-pe
-rwxr-xr-x root/root 374504 2021-10-01 14:10 ./usr/lib/abyss/abyss-rresolver-short
-rwxr-xr-x root/root 4501 2021-10-01 14:10 ./usr/lib/abyss/abyss-samtoafg
-rwxr-xr-x root/root 190116 2021-10-01 14:10 ./usr/lib/abyss/abyss-scaffold
-rwxr-xr-x root/root 177888 2021-10-01 14:10 ./usr/lib/abyss/abyss-sealer
-rwxr-xr-x root/root 671 2021-10-01 14:10 ./usr/lib/abyss/abyss-stack-size
-rwxr-xr-x root/root 209 2021-10-01 14:10 ./usr/lib/abyss/abyss-tabtomd
-rwxr-xr-x root/root 136848 2021-10-01 14:10 ./usr/lib/abyss/abyss-todot
-rwxr-xr-x root/root 50848 2021-10-01 14:10 ./usr/lib/abyss/abyss-tofastq
-rwxr-xr-x root/root 194276 2021-10-01 14:10 ./usr/lib/abyss/konnector
-rwxr-xr-x root/root 59044 2021-10-01 14:10 ./usr/lib/abyss/logcounter
drwxr-xr-x root/root 0 2021-10-01 14:10 ./usr/share/
drwxr-xr-x root/root 0 2021-10-01 14:10 ./usr/share/doc-base/
-rw-r--r-- root/root 226 2021-10-01 14:10 ./usr/share/doc-base/abyss.abyss-flowcharts
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-rw-r--r-- root/root 556 2021-10-01 14:10 ./usr/share/doc/abyss/CITATION.bib
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-rw-r--r-- root/root 182 2021-10-01 14:10 ./usr/share/doc/abyss/README.test
-rw-r--r-- root/root 3721 2021-10-01 14:10 ./usr/share/doc/abyss/changelog.Debian.gz
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-rw-r--r-- root/root 7148 2021-10-01 14:10 ./usr/share/doc/abyss/copyright
-rw-r--r-- root/root 66778 2021-10-01 14:10 ./usr/share/doc/abyss/flowchart.pdf.gz
-rw-r--r-- root/root 22664 2021-10-01 14:10 ./usr/share/doc/abyss/flowchart_simplified.pdf.gz
-rw-r--r-- root/root 672 2021-10-01 14:10 ./usr/share/doc/abyss/run-unit-test
drwxr-xr-x root/root 0 2021-10-01 14:10 ./usr/share/doc/abyss/test-data/
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drwxr-xr-x root/root 0 2021-10-01 14:10 ./usr/share/man/
drwxr-xr-x root/root 0 2021-10-01 14:10 ./usr/share/man/man1/
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-rw-r--r-- root/root 789 2021-10-01 14:10 ./usr/share/man/man1/abyss-fixmate.1.gz
-rw-r--r-- root/root 3561 2021-10-01 14:10 ./usr/share/man/man1/abyss-pe.1.gz
-rw-r--r-- root/root 407 2021-10-01 14:10 ./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: 728704
Build-Time: 1009
Distribution: bookworm-staging
Host Architecture: armhf
Install-Time: 455
Job: abyss_2.3.1-1
Machine Architecture: armhf
Package: abyss
Package-Time: 1482
Source-Version: 2.3.1-1
Space: 728704
Status: successful
Version: 2.3.1-1
--------------------------------------------------------------------------------
Finished at 2021-10-05T00:26:46Z
Build needed 00:24:42, 728704k disk space