abyss →
2.2.4-1+b2 →
armhf → 2020-07-21 06:50:58
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on testwandboard
+==============================================================================+
| abyss 2.2.4-1+b2 (armhf) Tue, 21 Jul 2020 05:45:07 +0000 |
+==============================================================================+
Package: abyss
Version: 2.2.4-1+b2
Source Version: 2.2.4-1
Distribution: bullseye-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/bullseye-staging-armhf-sbuild-dbc79598-9c1d-43f6-abb2-1adf45d15cc1' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private bullseye-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private bullseye-staging/main Sources [11.8 MB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf Packages [12.9 MB]
Fetched 24.6 MB in 28s (870 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 1962 kB of source archives.
Get:1 http://172.17.0.1/private bullseye-staging/main abyss 2.2.4-1 (dsc) [2318 B]
Get:2 http://172.17.0.1/private bullseye-staging/main abyss 2.2.4-1 (tar) [1204 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main abyss 2.2.4-1 (diff) [756 kB]
Fetched 1962 kB in 1s (2159 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/abyss-aB9P2p/abyss-2.2.4' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/abyss-aB9P2p' 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-IqXvI3/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-IqXvI3/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-IqXvI3/gpg/trustdb.gpg: trustdb created
gpg: key 35506D9A48F77B2E: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg: imported: 1
gpg: key 35506D9A48F77B2E: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 35506D9A48F77B2E: secret key imported
gpg: Total number processed: 1
gpg: unchanged: 1
gpg: secret keys read: 1
gpg: secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-IqXvI3/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-IqXvI3/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-IqXvI3/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-IqXvI3/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-IqXvI3/apt_archive ./ Packages [432 B]
Fetched 2108 B in 1s (2826 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
bsdextrautils libpam-cap netbase
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 21 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-IqXvI3/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 (22.9 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12329 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 (= 12), libboost-graph-dev, libopenmpi-dev, libsparsehash-dev, libtext-multimarkdown-perl, libsqlite3-dev, pkg-config, help2man
Filtered Build-Depends: debhelper-compat (= 12), 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-IqXvI3/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-IqXvI3/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-IqXvI3/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-IqXvI3/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-IqXvI3/apt_archive ./ Sources [567 B]
Get:5 copy:/<<BUILDDIR>>/resolver-IqXvI3/apt_archive ./ Packages [638 B]
Fetched 2538 B in 1s (3305 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install abyss build dependencies (apt-based resolver)
-----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
dmsetup libargon2-1 libcryptsetup12 libdevmapper1.02.1 libjson-c4 libpam-cap
netbase
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev debhelper dh-autoreconf
dh-strip-nondeterminism dwz file gettext gettext-base gfortran-9 groff-base
help2man ibverbs-providers icu-devtools intltool-debian libarchive-zip-perl
libboost-graph-dev libboost-graph1.71-dev libboost-graph1.71.0
libboost-regex1.71-dev libboost-regex1.71.0 libboost-serialization1.71-dev
libboost-serialization1.71.0 libboost-test1.71-dev libboost-test1.71.0
libboost1.71-dev libbsd0 libcbor0 libcroco3 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 libfido2-1
libfile-stripnondeterminism-perl libgfortran-9-dev libgfortran5 libglib2.0-0
libgssapi-krb5-2 libhtml-parser-perl libhtml-tagset-perl libhwloc-dev
libhwloc-plugins libhwloc15 libibverbs-dev libibverbs1 libicu-dev libicu67
libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblocale-gettext-perl
libltdl-dev libltdl7 libmagic-mgc libmagic1 libmount1 libnl-3-200
libnl-3-dev libnl-route-3-200 libnl-route-3-dev libnuma-dev libnuma1
libopenmpi-dev libopenmpi3 libpciaccess0 libpipeline1 libpmix2 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 sensible-utils zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc dh-make gettext-doc
libasprintf-dev libgettextpo-dev gfortran-9-doc libcoarrays-dev groff
graphviz libboost1.71-doc libboost-atomic1.71-dev libboost-chrono1.71-dev
libboost-container1.71-dev libboost-context1.71-dev
libboost-contract1.71-dev libboost-coroutine1.71-dev
libboost-date-time1.71-dev libboost-exception1.71-dev libboost-fiber1.71-dev
libboost-filesystem1.71-dev libboost-graph-parallel1.71-dev
libboost-iostreams1.71-dev libboost-locale1.71-dev libboost-log1.71-dev
libboost-math1.71-dev libboost-mpi1.71-dev libboost-mpi-python1.71-dev
libboost-numpy1.71-dev libboost-program-options1.71-dev
libboost-python1.71-dev libboost-random1.71-dev libboost-stacktrace1.71-dev
libboost-system1.71-dev libboost-thread1.71-dev libboost-timer1.71-dev
libboost-type-erasure1.71-dev libboost-wave1.71-dev libboost1.71-tools-dev
libmpfrc++-dev libntl-dev krb5-doc krb5-user libdata-dump-perl icu-doc
libtool-doc openmpi-doc pciutils sqlite3-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 krb5-locales libcoarrays-openmpi-dev
xauth libmail-sendmail-perl
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev debhelper dh-autoreconf
dh-strip-nondeterminism dwz file gettext gettext-base gfortran-9 groff-base
help2man ibverbs-providers icu-devtools intltool-debian libarchive-zip-perl
libboost-graph-dev libboost-graph1.71-dev libboost-graph1.71.0
libboost-regex1.71-dev libboost-regex1.71.0 libboost-serialization1.71-dev
libboost-serialization1.71.0 libboost-test1.71-dev libboost-test1.71.0
libboost1.71-dev libbsd0 libcbor0 libcroco3 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 libfido2-1
libfile-stripnondeterminism-perl libgfortran-9-dev libgfortran5 libglib2.0-0
libgssapi-krb5-2 libhtml-parser-perl libhtml-tagset-perl libhwloc-dev
libhwloc-plugins libhwloc15 libibverbs-dev libibverbs1 libicu-dev libicu67
libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblocale-gettext-perl
libltdl-dev libltdl7 libmagic-mgc libmagic1 libnl-3-200 libnl-3-dev
libnl-route-3-200 libnl-route-3-dev libnuma-dev libnuma1 libopenmpi-dev
libopenmpi3 libpciaccess0 libpipeline1 libpmix2 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:
libmount1
1 upgraded, 103 newly installed, 0 to remove and 20 not upgraded.
Need to get 59.4 MB of archives.
After this operation, 342 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-IqXvI3/apt_archive ./ sbuild-build-depends-abyss-dummy 0.invalid.0 [928 B]
Get:2 http://172.17.0.1/private bullseye-staging/main armhf liblocale-gettext-perl armhf 1.07-4 [18.1 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:4 http://172.17.0.1/private bullseye-staging/main armhf groff-base armhf 1.22.4-5 [783 kB]
Get:5 http://172.17.0.1/private bullseye-staging/main armhf libpipeline1 armhf 1.5.2-2 [29.6 kB]
Get:6 http://172.17.0.1/private bullseye-staging/main armhf man-db armhf 2.9.3-2 [1269 kB]
Get:7 http://172.17.0.1/private bullseye-staging/main armhf libmount1 armhf 2.35.2-7 [190 kB]
Get:8 http://172.17.0.1/private bullseye-staging/main armhf sensible-utils all 0.0.12+nmu1 [16.0 kB]
Get:9 http://172.17.0.1/private bullseye-staging/main armhf libmagic-mgc armhf 1:5.38-5 [262 kB]
Get:10 http://172.17.0.1/private bullseye-staging/main armhf libmagic1 armhf 1:5.38-5 [113 kB]
Get:11 http://172.17.0.1/private bullseye-staging/main armhf file armhf 1:5.38-5 [67.0 kB]
Get:12 http://172.17.0.1/private bullseye-staging/main armhf gettext-base armhf 0.19.8.1-10 [117 kB]
Get:13 http://172.17.0.1/private bullseye-staging/main armhf libbsd0 armhf 0.10.0-1 [112 kB]
Get:14 http://172.17.0.1/private bullseye-staging/main armhf libedit2 armhf 3.1-20191231-1 [79.2 kB]
Get:15 http://172.17.0.1/private bullseye-staging/main armhf libcbor0 armhf 0.5.0+dfsg-2 [19.5 kB]
Get:16 http://172.17.0.1/private bullseye-staging/main armhf libfido2-1 armhf 1.4.0-2 [43.9 kB]
Get:17 http://172.17.0.1/private bullseye-staging/main armhf libkrb5support0 armhf 1.17-10 [61.7 kB]
Get:18 http://172.17.0.1/private bullseye-staging/main armhf libk5crypto3 armhf 1.17-10 [112 kB]
Get:19 http://172.17.0.1/private bullseye-staging/main armhf libkeyutils1 armhf 1.6.1-2 [14.5 kB]
Get:20 http://172.17.0.1/private bullseye-staging/main armhf libkrb5-3 armhf 1.17-10 [320 kB]
Get:21 http://172.17.0.1/private bullseye-staging/main armhf libgssapi-krb5-2 armhf 1.17-10 [135 kB]
Get:22 http://172.17.0.1/private bullseye-staging/main armhf openssh-client armhf 1:8.3p1-1 [783 kB]
Get:23 http://172.17.0.1/private bullseye-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:24 http://172.17.0.1/private bullseye-staging/main armhf m4 armhf 1.4.18-4 [185 kB]
Get:25 http://172.17.0.1/private bullseye-staging/main armhf autoconf all 2.69-11.1 [341 kB]
Get:26 http://172.17.0.1/private bullseye-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:27 http://172.17.0.1/private bullseye-staging/main armhf automake all 1:1.16.2-3 [801 kB]
Get:28 http://172.17.0.1/private bullseye-staging/main armhf autopoint all 0.19.8.1-10 [435 kB]
Get:29 http://172.17.0.1/private bullseye-staging/main armhf libtool all 2.4.6-14 [513 kB]
Get:30 http://172.17.0.1/private bullseye-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:31 http://172.17.0.1/private bullseye-staging/main armhf libdebhelper-perl all 13.2 [187 kB]
Get:32 http://172.17.0.1/private bullseye-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:33 http://172.17.0.1/private bullseye-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:34 http://172.17.0.1/private bullseye-staging/main armhf libfile-stripnondeterminism-perl all 1.9.0-1 [25.5 kB]
Get:35 http://172.17.0.1/private bullseye-staging/main armhf dh-strip-nondeterminism all 1.9.0-1 [15.2 kB]
Get:36 http://172.17.0.1/private bullseye-staging/main armhf libelf1 armhf 0.176-1.1 [158 kB]
Get:37 http://172.17.0.1/private bullseye-staging/main armhf dwz armhf 0.13-5 [142 kB]
Get:38 http://172.17.0.1/private bullseye-staging/main armhf libglib2.0-0 armhf 2.64.4-1 [1159 kB]
Get:39 http://172.17.0.1/private bullseye-staging/main armhf libicu67 armhf 67.1-3 [8287 kB]
Get:40 http://172.17.0.1/private bullseye-staging/main armhf libxml2 armhf 2.9.10+dfsg-5+b1 [593 kB]
Get:41 http://172.17.0.1/private bullseye-staging/main armhf libcroco3 armhf 0.6.13-1 [133 kB]
Get:42 http://172.17.0.1/private bullseye-staging/main armhf gettext armhf 0.19.8.1-10 [1219 kB]
Get:43 http://172.17.0.1/private bullseye-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:44 http://172.17.0.1/private bullseye-staging/main armhf po-debconf all 1.0.21 [248 kB]
Get:45 http://172.17.0.1/private bullseye-staging/main armhf debhelper all 13.2 [1007 kB]
Get:46 http://172.17.0.1/private bullseye-staging/main armhf libgfortran5 armhf 10.1.0-4+rpi1 [231 kB]
Get:47 http://172.17.0.1/private bullseye-staging/main armhf libgfortran-9-dev armhf 9.3.0-14+rpi1 [278 kB]
Get:48 http://172.17.0.1/private bullseye-staging/main armhf gfortran-9 armhf 9.3.0-14+rpi1 [8112 kB]
Get:49 http://172.17.0.1/private bullseye-staging/main armhf help2man armhf 1.47.16 [181 kB]
Get:50 http://172.17.0.1/private bullseye-staging/main armhf libnl-3-200 armhf 3.4.0-1 [55.0 kB]
Get:51 http://172.17.0.1/private bullseye-staging/main armhf libnl-route-3-200 armhf 3.4.0-1 [132 kB]
Get:52 http://172.17.0.1/private bullseye-staging/main armhf libibverbs1 armhf 29.0-1 [47.5 kB]
Get:53 http://172.17.0.1/private bullseye-staging/main armhf ibverbs-providers armhf 29.0-1 [24.2 kB]
Get:54 http://172.17.0.1/private bullseye-staging/main armhf icu-devtools armhf 67.1-3 [170 kB]
Get:55 http://172.17.0.1/private bullseye-staging/main armhf libboost1.71-dev armhf 1.71.0-6+b1 [9099 kB]
Get:56 http://172.17.0.1/private bullseye-staging/main armhf libboost-regex1.71.0 armhf 1.71.0-6+b1 [435 kB]
Get:57 http://172.17.0.1/private bullseye-staging/main armhf libboost-graph1.71.0 armhf 1.71.0-6+b1 [303 kB]
Get:58 http://172.17.0.1/private bullseye-staging/main armhf libicu-dev armhf 67.1-3 [9213 kB]
Get:59 http://172.17.0.1/private bullseye-staging/main armhf libboost-regex1.71-dev armhf 1.71.0-6+b1 [571 kB]
Get:60 http://172.17.0.1/private bullseye-staging/main armhf libboost-serialization1.71.0 armhf 1.71.0-6+b1 [308 kB]
Get:61 http://172.17.0.1/private bullseye-staging/main armhf libboost-serialization1.71-dev armhf 1.71.0-6+b1 [382 kB]
Get:62 http://172.17.0.1/private bullseye-staging/main armhf libboost-test1.71.0 armhf 1.71.0-6+b1 [419 kB]
Get:63 http://172.17.0.1/private bullseye-staging/main armhf libboost-test1.71-dev armhf 1.71.0-6+b1 [519 kB]
Get:64 http://172.17.0.1/private bullseye-staging/main armhf libboost-graph1.71-dev armhf 1.71.0-6+b1 [342 kB]
Get:65 http://172.17.0.1/private bullseye-staging/main armhf libboost-graph-dev armhf 1.71.0.3+b2 [4512 B]
Get:66 http://172.17.0.1/private bullseye-staging/main armhf libevent-2.1-7 armhf 2.1.12-stable-1 [167 kB]
Get:67 http://172.17.0.1/private bullseye-staging/main armhf libevent-core-2.1-7 armhf 2.1.12-stable-1 [126 kB]
Get:68 http://172.17.0.1/private bullseye-staging/main armhf libevent-extra-2.1-7 armhf 2.1.12-stable-1 [100 kB]
Get:69 http://172.17.0.1/private bullseye-staging/main armhf libevent-pthreads-2.1-7 armhf 2.1.12-stable-1 [56.8 kB]
Get:70 http://172.17.0.1/private bullseye-staging/main armhf libevent-openssl-2.1-7 armhf 2.1.12-stable-1 [61.7 kB]
Get:71 http://172.17.0.1/private bullseye-staging/main armhf libevent-dev armhf 2.1.12-stable-1 [281 kB]
Get:72 http://172.17.0.1/private bullseye-staging/main armhf libhtml-tagset-perl all 3.20-4 [13.0 kB]
Get:73 http://172.17.0.1/private bullseye-staging/main armhf liburi-perl all 1.76-2 [90.2 kB]
Get:74 http://172.17.0.1/private bullseye-staging/main armhf libhtml-parser-perl armhf 3.72-5 [101 kB]
Get:75 http://172.17.0.1/private bullseye-staging/main armhf libhwloc15 armhf 2.2.0+dfsg-3 [113 kB]
Get:76 http://172.17.0.1/private bullseye-staging/main armhf libnuma1 armhf 2.0.12-1 [22.5 kB]
Get:77 http://172.17.0.1/private bullseye-staging/main armhf libnuma-dev armhf 2.0.12-1 [35.6 kB]
Get:78 http://172.17.0.1/private bullseye-staging/main armhf libltdl7 armhf 2.4.6-14 [388 kB]
Get:79 http://172.17.0.1/private bullseye-staging/main armhf libltdl-dev armhf 2.4.6-14 [159 kB]
Get:80 http://172.17.0.1/private bullseye-staging/main armhf libhwloc-dev armhf 2.2.0+dfsg-3 [174 kB]
Get:81 http://172.17.0.1/private bullseye-staging/main armhf libpciaccess0 armhf 0.14-1 [51.0 kB]
Get:82 http://172.17.0.1/private bullseye-staging/main armhf libxau6 armhf 1:1.0.8-1+b2 [19.1 kB]
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Get:87 http://172.17.0.1/private bullseye-staging/main armhf libxext6 armhf 2:1.3.3-1+b2 [47.8 kB]
Get:88 http://172.17.0.1/private bullseye-staging/main armhf libxnvctrl0 armhf 440.100-1 [25.3 kB]
Get:89 http://172.17.0.1/private bullseye-staging/main armhf ocl-icd-libopencl1 armhf 2.2.12-4 [36.0 kB]
Get:90 http://172.17.0.1/private bullseye-staging/main armhf libhwloc-plugins armhf 2.2.0+dfsg-3 [19.0 kB]
Get:91 http://172.17.0.1/private bullseye-staging/main armhf libnl-3-dev armhf 3.4.0-1 [92.4 kB]
Get:92 http://172.17.0.1/private bullseye-staging/main armhf libnl-route-3-dev armhf 3.4.0-1 [145 kB]
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Get:94 http://172.17.0.1/private bullseye-staging/main armhf libpmix2 armhf 3.1.5-1+b1 [378 kB]
Get:95 http://172.17.0.1/private bullseye-staging/main armhf libopenmpi3 armhf 4.0.4-1+rpi1 [1689 kB]
Get:96 http://172.17.0.1/private bullseye-staging/main armhf openmpi-common all 4.0.4-1+rpi1 [173 kB]
Get:97 http://172.17.0.1/private bullseye-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-2 [184 kB]
Get:98 http://172.17.0.1/private bullseye-staging/main armhf openmpi-bin armhf 4.0.4-1+rpi1 [189 kB]
Get:99 http://172.17.0.1/private bullseye-staging/main armhf libopenmpi-dev armhf 4.0.4-1+rpi1 [927 kB]
Get:100 http://172.17.0.1/private bullseye-staging/main armhf libsparsehash-dev all 2.0.3-2 [76.8 kB]
Get:101 http://172.17.0.1/private bullseye-staging/main armhf libsqlite3-dev armhf 3.32.3-1 [804 kB]
Get:102 http://172.17.0.1/private bullseye-staging/main armhf libtext-markdown-perl all 1.000031-3 [33.8 kB]
Get:103 http://172.17.0.1/private bullseye-staging/main armhf libtext-multimarkdown-perl all 1.000035-2 [28.6 kB]
Get:104 http://172.17.0.1/private bullseye-staging/main armhf pkg-config armhf 0.29.2-1 [61.5 kB]
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Unpacking libsqlite3-dev:armhf (3.32.3-1) ...
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Unpacking libtext-markdown-perl (1.000031-3) ...
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Unpacking libtext-multimarkdown-perl (1.000035-2) ...
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Unpacking pkg-config (0.29.2-1) ...
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Preparing to unpack .../97-sbuild-build-depends-abyss-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-abyss-dummy (0.invalid.0) ...
Setting up libpipeline1:armhf (1.5.2-2) ...
Setting up libtext-markdown-perl (1.000031-3) ...
Setting up libpciaccess0:armhf (0.14-1) ...
Setting up libxau6:armhf (1:1.0.8-1+b2) ...
Setting up libkeyutils1:armhf (1.6.1-2) ...
Setting up libicu67:armhf (67.1-3) ...
Setting up libmagic-mgc (1:5.38-5) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up libglib2.0-0:armhf (2.64.4-1) ...
No schema files found: doing nothing.
Setting up libhtml-tagset-perl (3.20-4) ...
Setting up libdebhelper-perl (13.2) ...
Setting up libboost1.71-dev:armhf (1.71.0-6+b1) ...
Setting up libcbor0:armhf (0.5.0+dfsg-2) ...
Setting up libmagic1:armhf (1:5.38-5) ...
Setting up gettext-base (0.19.8.1-10) ...
Setting up file (1:5.38-5) ...
Setting up libsparsehash-dev (2.0.3-2) ...
Setting up libkrb5support0:armhf (1.17-10) ...
Setting up autotools-dev (20180224.1) ...
Setting up libsqlite3-dev:armhf (3.32.3-1) ...
Setting up libx11-data (2:1.6.9-2) ...
Setting up libsigsegv2:armhf (2.12-2) ...
Setting up libhwloc15:armhf (2.2.0+dfsg-3) ...
Setting up libevent-core-2.1-7:armhf (2.1.12-stable-1) ...
Setting up libevent-2.1-7:armhf (2.1.12-stable-1) ...
Setting up autopoint (0.19.8.1-10) ...
Setting up icu-devtools (67.1-3) ...
Setting up pkg-config (0.29.2-1) ...
Setting up libboost-regex1.71.0:armhf (1.71.0-6+b1) ...
Setting up libk5crypto3:armhf (1.17-10) ...
Setting up libltdl7:armhf (2.4.6-14) ...
Setting up libgfortran5:armhf (10.1.0-4+rpi1) ...
Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-2) ...
Setting up libnuma1:armhf (2.0.12-1) ...
Setting up sensible-utils (0.0.12+nmu1) ...
Setting up ocl-icd-libopencl1:armhf (2.2.12-4) ...
Setting up libboost-test1.71.0:armhf (1.71.0-6+b1) ...
Setting up libuchardet0:armhf (0.0.7-1) ...
Setting up libnl-3-200:armhf (3.4.0-1) ...
Setting up openmpi-common (4.0.4-1+rpi1) ...
Setting up libsub-override-perl (0.09-2) ...
Setting up libboost-serialization1.71.0:armhf (1.71.0-6+b1) ...
Setting up libkrb5-3:armhf (1.17-10) ...
Setting up libboost-graph1.71.0:armhf (1.71.0-6+b1) ...
Setting up libfido2-1:armhf (1.4.0-2) ...
Setting up libbsd0:armhf (0.10.0-1) ...
Setting up libelf1:armhf (0.176-1.1) ...
Setting up libicu-dev:armhf (67.1-3) ...
Setting up libxml2:armhf (2.9.10+dfsg-5+b1) ...
Setting up liburi-perl (1.76-2) ...
Setting up liblocale-gettext-perl (1.07-4) ...
Setting up libevent-pthreads-2.1-7:armhf (2.1.12-stable-1) ...
Setting up libfile-stripnondeterminism-perl (1.9.0-1) ...
Setting up libxdmcp6:armhf (1:1.1.2-3) ...
Setting up libevent-extra-2.1-7:armhf (2.1.12-stable-1) ...
Setting up libxcb1:armhf (1.14-2) ...
Setting up libtool (2.4.6-14) ...
Setting up libedit2:armhf (3.1-20191231-1) ...
Setting up libgfortran-9-dev:armhf (9.3.0-14+rpi1) ...
Setting up libevent-openssl-2.1-7:armhf (2.1.12-stable-1) ...
Setting up m4 (1.4.18-4) ...
Setting up libnuma-dev:armhf (2.0.12-1) ...
Setting up libnl-route-3-200:armhf (3.4.0-1) ...
Setting up help2man (1.47.16) ...
Setting up libboost-test1.71-dev:armhf (1.71.0-6+b1) ...
Setting up libevent-dev (2.1.12-stable-1) ...
Setting up libgssapi-krb5-2:armhf (1.17-10) ...
Setting up libboost-regex1.71-dev:armhf (1.71.0-6+b1) ...
Setting up libcroco3:armhf (0.6.13-1) ...
Setting up libboost-serialization1.71-dev:armhf (1.71.0-6+b1) ...
Setting up autoconf (2.69-11.1) ...
Setting up dh-strip-nondeterminism (1.9.0-1) ...
Setting up dwz (0.13-5) ...
Setting up libnl-3-dev:armhf (3.4.0-1) ...
Setting up groff-base (1.22.4-5) ...
Setting up libhtml-parser-perl (3.72-5) ...
Setting up libx11-6:armhf (2:1.6.9-2) ...
Setting up libtext-multimarkdown-perl (1.000035-2) ...
Setting up libboost-graph1.71-dev:armhf (1.71.0-6+b1) ...
Setting up automake (1:1.16.2-3) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up libboost-graph-dev:armhf (1.71.0.3+b2) ...
Setting up libibverbs1:armhf (29.0-1) ...
Setting up gettext (0.19.8.1-10) ...
Setting up gfortran-9 (9.3.0-14+rpi1) ...
Setting up ibverbs-providers:armhf (29.0-1) ...
Setting up openssh-client (1:8.3p1-1) ...
Setting up libxext6:armhf (2:1.3.3-1+b2) ...
Setting up man-db (2.9.3-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up intltool-debian (0.35.0+20060710.5) ...
Setting up libxnvctrl0:armhf (440.100-1) ...
Setting up libnl-route-3-dev:armhf (3.4.0-1) ...
Setting up libltdl-dev:armhf (2.4.6-14) ...
Setting up libhwloc-dev:armhf (2.2.0+dfsg-3) ...
Setting up po-debconf (1.0.21) ...
Setting up libibverbs-dev:armhf (29.0-1) ...
Setting up libhwloc-plugins:armhf (2.2.0+dfsg-3) ...
Setting up libpmix2:armhf (3.1.5-1+b1) ...
Setting up libopenmpi3:armhf (4.0.4-1+rpi1) ...
Setting up openmpi-bin (4.0.4-1+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 (4.0.4-1+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 dh-autoreconf (19) ...
Setting up debhelper (13.2) ...
Setting up sbuild-build-depends-abyss-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.30-8+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.9.0-0.bpo.6-armmp armhf (armv7l)
Toolchain package versions: binutils_2.34-8+rpi1 dpkg-dev_1.19.7 g++-9_9.3.0-14+rpi1 gcc-9_9.3.0-14+rpi1 libc6-dev_2.30-8+rpi1 libstdc++-9-dev_9.3.0-14+rpi1 libstdc++6_10.1.0-4+rpi1 linux-libc-dev_5.2.17-1+rpi1+b2
Package versions: adduser_3.118 apt_2.1.6 autoconf_2.69-11.1 automake_1:1.16.2-3 autopoint_0.19.8.1-10 autotools-dev_20180224.1 base-files_11+rpi1 base-passwd_3.5.47 bash_5.0-6 binutils_2.34-8+rpi1 binutils-arm-linux-gnueabihf_2.34-8+rpi1 binutils-common_2.34-8+rpi1 bsdextrautils_2.35.2-6 bsdutils_1:2.35.2-6 build-essential_12.8 bzip2_1.0.8-3 coreutils_8.30-3 cpp_4:9.2.1-3.1+rpi1 cpp-9_9.3.0-14+rpi1 dash_0.5.10.2-7 debconf_1.5.74 debhelper_13.2 debianutils_4.9.1 dh-autoreconf_19 dh-strip-nondeterminism_1.9.0-1 diffutils_1:3.7-3 dirmngr_2.2.20-1 dmsetup_2:1.02.167-1+b2 dpkg_1.19.7 dpkg-dev_1.19.7 dwz_0.13-5 e2fsprogs_1.45.6-1 fakeroot_1.24-1 fdisk_2.35.2-6 file_1:5.38-5 findutils_4.7.0-1 g++_4:9.2.1-3.1+rpi1 g++-9_9.3.0-14+rpi1 gcc_4:9.2.1-3.1+rpi1 gcc-10-base_10.1.0-4+rpi1 gcc-9_9.3.0-14+rpi1 gcc-9-base_9.3.0-14+rpi1 gettext_0.19.8.1-10 gettext-base_0.19.8.1-10 gfortran-9_9.3.0-14+rpi1 gnupg_2.2.20-1 gnupg-l10n_2.2.20-1 gnupg-utils_2.2.20-1 gpg_2.2.20-1 gpg-agent_2.2.20-1 gpg-wks-client_2.2.20-1 gpg-wks-server_2.2.20-1 gpgconf_2.2.20-1 gpgsm_2.2.20-1 gpgv_2.2.20-1 grep_3.4-1 groff-base_1.22.4-5 gzip_1.10-2 help2man_1.47.16 hostname_3.23 ibverbs-providers_29.0-1 icu-devtools_67.1-3 init-system-helpers_1.58 intltool-debian_0.35.0+20060710.5 iputils-ping_3:20190709-3 libacl1_2.2.53-8 libapt-pkg6.0_2.1.6 libarchive-zip-perl_1.68-1 libargon2-1_0~20171227-0.2 libasan5_9.3.0-14+rpi1 libassuan0_2.5.3-7.1 libatomic1_10.1.0-4+rpi1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-3 libaudit1_1:2.8.5-3 libbinutils_2.34-8+rpi1 libblkid1_2.35.2-6 libboost-graph-dev_1.71.0.3+b2 libboost-graph1.71-dev_1.71.0-6+b1 libboost-graph1.71.0_1.71.0-6+b1 libboost-regex1.71-dev_1.71.0-6+b1 libboost-regex1.71.0_1.71.0-6+b1 libboost-serialization1.71-dev_1.71.0-6+b1 libboost-serialization1.71.0_1.71.0-6+b1 libboost-test1.71-dev_1.71.0-6+b1 libboost-test1.71.0_1.71.0-6+b1 libboost1.71-dev_1.71.0-6+b1 libbsd0_0.10.0-1 libbz2-1.0_1.0.8-3 libc-bin_2.30-8+rpi1 libc-dev-bin_2.30-8+rpi1 libc6_2.30-8+rpi1 libc6-dev_2.30-8+rpi1 libcap-ng0_0.7.9-2.2 libcap2_1:2.36-1 libcap2-bin_1:2.36-1 libcbor0_0.5.0+dfsg-2 libcc1-0_10.1.0-4+rpi1 libcom-err2_1.45.6-1 libcroco3_0.6.13-1 libcrypt-dev_1:4.4.16-1 libcrypt1_1:4.4.16-1 libcryptsetup12_2:2.3.3-1 libctf-nobfd0_2.34-8+rpi1 libctf0_2.34-8+rpi1 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.252 libdebhelper-perl_13.2 libdevmapper1.02.1_2:1.02.167-1+b2 libdpkg-perl_1.19.7 libedit2_3.1-20191231-1 libelf1_0.176-1.1 libevent-2.1-7_2.1.12-stable-1 libevent-core-2.1-7_2.1.12-stable-1 libevent-dev_2.1.12-stable-1 libevent-extra-2.1-7_2.1.12-stable-1 libevent-openssl-2.1-7_2.1.12-stable-1 libevent-pthreads-2.1-7_2.1.12-stable-1 libext2fs2_1.45.6-1 libfakeroot_1.24-1 libfdisk1_2.35.2-6 libffi7_3.3-4 libfido2-1_1.4.0-2 libfile-stripnondeterminism-perl_1.9.0-1 libgcc-9-dev_9.3.0-14+rpi1 libgcc-s1_10.1.0-4+rpi1 libgcrypt20_1.8.5-5 libgdbm-compat4_1.18.1-5 libgdbm6_1.18.1-5 libgfortran-9-dev_9.3.0-14+rpi1 libgfortran5_10.1.0-4+rpi1 libglib2.0-0_2.64.4-1 libgmp10_2:6.2.0+dfsg-6 libgnutls30_3.6.14-2 libgomp1_10.1.0-4+rpi1 libgpg-error0_1.38-2 libgssapi-krb5-2_1.17-10 libhogweed5_3.5.1+really3.5.1-2 libhtml-parser-perl_3.72-5 libhtml-tagset-perl_3.20-4 libhwloc-dev_2.2.0+dfsg-3 libhwloc-plugins_2.2.0+dfsg-3 libhwloc15_2.2.0+dfsg-3 libibverbs-dev_29.0-1 libibverbs1_29.0-1 libicu-dev_67.1-3 libicu67_67.1-3 libidn2-0_2.3.0-1 libisl22_0.22.1-1 libjson-c4_0.13.1+dfsg-9 libk5crypto3_1.17-10 libkeyutils1_1.6.1-2 libkrb5-3_1.17-10 libkrb5support0_1.17-10 libksba8_1.4.0-2 libldap-2.4-2_2.4.50+dfsg-1 libldap-common_2.4.50+dfsg-1 liblocale-gettext-perl_1.07-4 libltdl-dev_2.4.6-14 libltdl7_2.4.6-14 liblz4-1_1.9.2-2 liblzma5_5.2.4-1 libmagic-mgc_1:5.38-5 libmagic1_1:5.38-5 libmount1_2.35.2-7 libmpc3_1.1.0-1 libmpfr6_4.0.2-1 libncursesw6_6.2-1 libnettle7_3.5.1+really3.5.1-2 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_1.6-2 libnuma-dev_2.0.12-1 libnuma1_2.0.12-1 libopenmpi-dev_4.0.4-1+rpi1 libopenmpi3_4.0.4-1+rpi1 libp11-kit0_0.23.20-1 libpam-cap_1:2.36-1 libpam-modules_1.3.1-5 libpam-modules-bin_1.3.1-5 libpam-runtime_1.3.1-5 libpam0g_1.3.1-5 libpciaccess0_0.14-1 libpcre2-8-0_10.34-7 libpcre3_2:8.39-13 libperl5.30_5.30.3-4 libpipeline1_1.5.2-2 libpmix2_3.1.5-1+b1 libreadline7_7.0-5 libreadline8_8.0-4 librust-rand-core-dev_0.5.1-1 libsasl2-2_2.1.27+dfsg-2 libsasl2-modules-db_2.1.27+dfsg-2 libseccomp2_2.4.3-1+rpi1 libselinux1_3.0-1+b1 libsemanage-common_3.0-1 libsemanage1_3.0-1+b1 libsepol1_3.0-1 libsigsegv2_2.12-2 libsmartcols1_2.35.2-6 libsparsehash-dev_2.0.3-2 libsqlite3-0_3.32.3-1 libsqlite3-dev_3.32.3-1 libss2_1.45.6-1 libssl1.1_1.1.1g-1 libstdc++-9-dev_9.3.0-14+rpi1 libstdc++6_10.1.0-4+rpi1 libsub-override-perl_0.09-2 libsystemd0_245.6-2+rpi1 libtasn1-6_4.16.0-2 libtext-markdown-perl_1.000031-3 libtext-multimarkdown-perl_1.000035-2 libtinfo6_6.2-1 libtool_2.4.6-14 libubsan1_10.1.0-4+rpi1 libuchardet0_0.0.7-1 libudev1_245.6-2+rpi1 libunistring2_0.9.10-4 liburi-perl_1.76-2 libuuid1_2.35.2-6 libx11-6_2:1.6.9-2 libx11-data_2:1.6.9-2 libxau6_1:1.0.8-1+b2 libxcb1_1.14-2 libxdmcp6_1:1.1.2-3 libxext6_2:1.3.3-1+b2 libxml2_2.9.10+dfsg-5+b1 libxnvctrl0_440.100-1 libzstd1_1.4.5+dfsg-3+rpi1 linux-libc-dev_5.2.17-1+rpi1+b2 login_1:4.8.1-1 logsave_1.45.6-1 lsb-base_11.1.0+rpi1 m4_1.4.18-4 make_4.2.1-2 man-db_2.9.3-2 mawk_1.3.4.20200120-2 mount_2.35.2-6 ncurses-base_6.2-1 ncurses-bin_6.2-1 netbase_6.1 ocl-icd-libopencl1_2.2.12-4 openmpi-bin_4.0.4-1+rpi1 openmpi-common_4.0.4-1+rpi1 openssh-client_1:8.3p1-1 passwd_1:4.8.1-1 patch_2.7.6-6 perl_5.30.3-4 perl-base_5.30.3-4 perl-modules-5.30_5.30.3-4 pinentry-curses_1.1.0-4 pkg-config_0.29.2-1 po-debconf_1.0.21 raspbian-archive-keyring_20120528.2 readline-common_8.0-4 sbuild-build-depends-abyss-dummy_0.invalid.0 sbuild-build-depends-core-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12+nmu1 sysvinit-utils_2.96-3 tar_1.30+dfsg-7 tzdata_2020a-1 util-linux_2.35.2-6 xz-utils_5.2.4-1 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 '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Tue Feb 11 14:40:03 2020 UTC
gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./abyss_2.2.4-1.dsc
dpkg-source: info: extracting abyss in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking abyss_2.2.4.orig.tar.gz
dpkg-source: info: unpacking abyss_2.2.4-1.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying abyss-pe.patch
Check disc space
----------------
Sufficient free space for build
Hack binNMU version
-------------------
Created changelog entry for binNMU version 2.2.4-1+b2
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=bullseye-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bullseye-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bullseye-staging-armhf-sbuild-dbc79598-9c1d-43f6-abb2-1adf45d15cc1
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package abyss
dpkg-buildpackage: info: source version 2.2.4-1+b2
dpkg-buildpackage: info: source distribution bullseye-staging
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
fakeroot debian/rules clean
dh clean
dh_clean
debian/rules build-arch
dh build-arch
dh_update_autotools_config -a
dh_autoreconf -a
configure.ac:16: installing './compile'
configure.ac:166: installing './config.guess'
configure.ac:166: 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 we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
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 thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... no
checking for mawk... mawk
checking whether make sets $(MAKE)... yes
checking whether make supports 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 we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking whether gcc understands -c and -o together... yes
checking dependency style of gcc... none
checking how to run the C preprocessor... gcc -E
checking whether we are using the GNU C++ compiler... (cached) yes
checking whether g++ -std=c++11 accepts -g... (cached) yes
checking for ranlib... ranlib
checking for ghc... no
./configure: line 5896: : command not found
checking for pandoc... no
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
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make[1]: Leaving directory '/<<PKGBUILDDIR>>'
debian/rules override_dh_auto_build
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make -j4
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Making all in Common
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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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libcommon_a-ContigID.o `test -f 'ContigID.cpp' || echo './'`ContigID.cpp
g++ -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libcommon_a-Fcontrol.o `test -f 'Fcontrol.cpp' || echo './'`Fcontrol.cpp
g++ -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libcommon_a-Histogram.o `test -f 'Histogram.cpp' || echo './'`Histogram.cpp
g++ -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libcommon_a-Kmer.o `test -f 'Kmer.cpp' || echo './'`Kmer.cpp
g++ -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libcommon_a-Log.o `test -f 'Log.cpp' || echo './'`Log.cpp
g++ -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libcommon_a-Options.o `test -f 'Options.cpp' || echo './'`Options.cpp
g++ -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libcommon_a-Sequence.o `test -f 'Sequence.cpp' || echo './'`Sequence.cpp
g++ -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libcommon_a-SignalHandler.o `test -f 'SignalHandler.cpp' || echo './'`SignalHandler.cpp
g++ -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libcommon_a-Timer.o `test -f 'Timer.cpp' || echo './'`Timer.cpp
In file included from /usr/include/c++/9/vector:72,
from VectorUtil.h:4,
from Histogram.h:6,
from Histogram.cpp:1:
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from VectorUtil.h:4,
from Histogram.h:6,
from Histogram.cpp:1:
/usr/include/c++/9/bits/stl_vector.h: In member function 'Histogram::Bins Histogram::bin(unsigned int) const':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
1195 | _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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libcommon_a-Uncompress.o `test -f 'Uncompress.cpp' || echo './'`Uncompress.cpp
g++ -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libcommon_a-city.o `test -f 'city.cc' || echo './'`city.cc
rm -f libcommon.a
ar cru libcommon.a libcommon_a-ContigID.o libcommon_a-Fcontrol.o libcommon_a-Histogram.o libcommon_a-Kmer.o libcommon_a-Log.o libcommon_a-Options.o libcommon_a-Sequence.o libcommon_a-SignalHandler.o libcommon_a-Timer.o libcommon_a-Uncompress.o libcommon_a-city.o
ar: `u' modifier ignored since `D' is the default (see `U')
ranlib libcommon.a
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Common'
Making all in Graph
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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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_gc-gc.o `test -f 'gc.cc' || echo './'`gc.cc
g++ -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_todot-todot.o `test -f 'todot.cc' || echo './'`todot.cc
g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-gc abyss_gc-gc.o ../Common/libcommon.a -ldl -lm
g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L. -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-todot abyss_todot-todot.o ../Common/libcommon.a -ldl -lm
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Making all in DataLayer
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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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_fac-fac.o `test -f 'fac.cc' || echo './'`fac.cc
g++ -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libdatalayer_a-FastaReader.o `test -f 'FastaReader.cpp' || echo './'`FastaReader.cpp
g++ -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libdatalayer_a-FastaWriter.o `test -f 'FastaWriter.cpp' || echo './'`FastaWriter.cpp
g++ -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_tofastq-abyss-tofastq.o `test -f 'abyss-tofastq.cc' || echo './'`abyss-tofastq.cc
rm -f libdatalayer.a
ar cru libdatalayer.a libdatalayer_a-FastaReader.o libdatalayer_a-FastaWriter.o
ar: `u' modifier ignored since `D' is the default (see `U')
ranlib libdatalayer.a
g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-tofastq abyss_tofastq-abyss-tofastq.o libdatalayer.a ../Common/libcommon.a -ldl -lm
g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-fac abyss_fac-fac.o libdatalayer.a ../Common/libcommon.a -ldl -lm
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Making all in DataBase
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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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_db_csv-DB.o `test -f 'DB.cc' || echo './'`DB.cc
g++ -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_db_csv-db-csv.o `test -f 'db-csv.cc' || echo './'`db-csv.cc
g++ -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libdb_a-DB.o `test -f 'DB.cc' || echo './'`DB.cc
g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-db-csv abyss_db_csv-DB.o abyss_db_csv-db-csv.o -lsqlite3 -ldl -lm
rm -f libdb.a
ar cru libdb.a libdb_a-DB.o ../Common/libcommon.a
ar: `u' modifier ignored since `D' is the default (see `U')
ranlib libdb.a
make[4]: Leaving directory '/<<PKGBUILDDIR>>/DataBase'
Making all in FMIndex
make[4]: Entering directory '/<<PKGBUILDDIR>>/FMIndex'
g++ -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_count-count.o `test -f 'count.cc' || echo './'`count.cc
g++ -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libfmindex_a-bit_array.o `test -f 'bit_array.cc' || echo './'`bit_array.cc
g++ -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_dawg-abyss-dawg.o `test -f 'abyss-dawg.cc' || echo './'`abyss-dawg.cc
rm -f libfmindex.a
ar cru libfmindex.a libfmindex_a-bit_array.o
ar: `u' modifier ignored since `D' is the default (see `U')
ranlib libfmindex.a
In file included from /usr/include/c++/9/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++/9/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++/9/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' {aka '__gnu_cxx::__normal_iterator<std::pair<std::pair<long long unsigned int, long long unsigned int>, std::pair<boost::optional<std::pair<std::pair<long long unsigned int, long long unsigned int>, std::pair<long long unsigned int, long long unsigned int> > >, std::pair<boost::graph_traits<FMIndex>::out_edge_iterator, boost::graph_traits<FMIndex>::out_edge_iterator> > >*, std::vector<std::pair<std::pair<long long unsigned int, long long unsigned int>, std::pair<boost::optional<std::pair<std::pair<long long unsigned int, long long unsigned int>, std::pair<long long unsigned int, long long unsigned int> > >, std::pair<boost::graph_traits<FMIndex>::out_edge_iterator, boost::graph_traits<FMIndex>::out_edge_iterator> > >, std::allocator<std::pair<std::pair<long long unsigned int, long long unsigned int>, std::pair<boost::optional<std::pair<std::pair<long long unsigned int, long long unsigned int>, std::pair<long long unsigned int, long long unsigned int> > >, std::pair<boost::graph_traits<FMIndex>::out_edge_iterator, boost::graph_traits<FMIndex>::out_edge_iterator> > > > > >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/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++/9/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++/9/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' {aka '__gnu_cxx::__normal_iterator<std::pair<std::pair<long long unsigned int, long long unsigned int>, std::pair<boost::optional<std::pair<std::pair<long long unsigned int, long long unsigned int>, std::pair<long long unsigned int, long long unsigned int> > >, std::pair<boost::graph_traits<FMIndex>::out_edge_iterator, boost::graph_traits<FMIndex>::out_edge_iterator> > >*, std::vector<std::pair<std::pair<long long unsigned int, long long unsigned int>, std::pair<boost::optional<std::pair<std::pair<long long unsigned int, long long unsigned int>, std::pair<long long unsigned int, long long unsigned int> > >, std::pair<boost::graph_traits<FMIndex>::out_edge_iterator, boost::graph_traits<FMIndex>::out_edge_iterator> > >, std::allocator<std::pair<std::pair<long long unsigned int, long long unsigned int>, std::pair<boost::optional<std::pair<std::pair<long long unsigned int, long long unsigned int>, std::pair<long long unsigned int, long long unsigned int> > >, std::pair<boost::graph_traits<FMIndex>::out_edge_iterator, boost::graph_traits<FMIndex>::out_edge_iterator> > > > > >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/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++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<std::pair<long long unsigned int, long long unsigned int>, std::pair<boost::optional<std::pair<std::pair<long long unsigned int, long long unsigned int>, std::pair<long long unsigned int, long long unsigned int> > >, std::pair<boost::graph_traits<FMIndex>::out_edge_iterator, boost::graph_traits<FMIndex>::out_edge_iterator> > >*, std::vector<std::pair<std::pair<long long unsigned int, long long unsigned int>, std::pair<boost::optional<std::pair<std::pair<long long unsigned int, long long unsigned int>, std::pair<long long unsigned int, long long unsigned int> > >, std::pair<boost::graph_traits<FMIndex>::out_edge_iterator, boost::graph_traits<FMIndex>::out_edge_iterator> > >, std::allocator<std::pair<std::pair<long long unsigned int, long long unsigned int>, std::pair<boost::optional<std::pair<std::pair<long long unsigned int, long long unsigned int>, std::pair<long long unsigned int, long long unsigned int> > >, std::pair<boost::graph_traits<FMIndex>::out_edge_iterator, boost::graph_traits<FMIndex>::out_edge_iterator> > > > > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/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++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<std::pair<long long unsigned int, long long unsigned int>, std::pair<boost::optional<std::pair<std::pair<long long unsigned int, long long unsigned int>, std::pair<long long unsigned int, long long unsigned int> > >, std::pair<boost::graph_traits<FMIndex>::out_edge_iterator, boost::graph_traits<FMIndex>::out_edge_iterator> > >*, std::vector<std::pair<std::pair<long long unsigned int, long long unsigned int>, std::pair<boost::optional<std::pair<std::pair<long long unsigned int, long long unsigned int>, std::pair<long long unsigned int, long long unsigned int> > >, std::pair<boost::graph_traits<FMIndex>::out_edge_iterator, boost::graph_traits<FMIndex>::out_edge_iterator> > >, std::allocator<std::pair<std::pair<long long unsigned int, long long unsigned int>, std::pair<boost::optional<std::pair<std::pair<long long unsigned int, long long unsigned int>, std::pair<long long unsigned int, long long unsigned int> > >, std::pair<boost::graph_traits<FMIndex>::out_edge_iterator, boost::graph_traits<FMIndex>::out_edge_iterator> > > > > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/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++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<wat_array::BitArray>::iterator' {aka '__gnu_cxx::__normal_iterator<wat_array::BitArray*, std::vector<wat_array::BitArray> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/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++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<wat_array::BitArray>::iterator' {aka '__gnu_cxx::__normal_iterator<wat_array::BitArray*, std::vector<wat_array::BitArray> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/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++/9/bits/stl_vector.h: In member function 'void FMIndex::assign(It, It) [with It = __gnu_cxx::__normal_iterator<unsigned char*, std::vector<unsigned char> >]':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<wat_array::BitArray*, std::vector<wat_array::BitArray> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
In file included from /usr/include/c++/9/map:60,
from abyss-dawg.cc:14:
/usr/include/c++/9/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++/9/bits/stl_tree.h:2452:7: note: parameter passing for argument of type 'std::_Rb_tree<std::pair<long long unsigned int, long long unsigned int>, std::pair<const std::pair<long long unsigned int, long long unsigned int>, boost::default_color_type>, std::_Select1st<std::pair<const std::pair<long long unsigned int, long long unsigned int>, boost::default_color_type> >, std::less<std::pair<long long unsigned int, long long unsigned int> >, std::allocator<std::pair<const std::pair<long long unsigned int, long long unsigned int>, boost::default_color_type> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const std::pair<long long unsigned int, long long unsigned int>, boost::default_color_type> >'} changed in GCC 7.1
2452 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/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++/9/bits/stl_vector.h: In member function 'void FMIndex::assign(It, It) [with It = __gnu_cxx::__normal_iterator<unsigned char*, std::vector<unsigned char> >]':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<wat_array::BitArray*, std::vector<wat_array::BitArray> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
In file included from abyss-dawg.cc:5:
/usr/include/boost/graph/depth_first_search.hpp: In function 'void boost::detail::depth_first_visit_impl(const IncidenceGraph&, typename boost::graph_traits<Graph>::vertex_descriptor, DFSVisitor&, ColorMap, TerminatorFunc) [with IncidenceGraph = FMIndex; DFSVisitor = DAWGVisitor; ColorMap = boost::associative_property_map<std::map<std::pair<long long unsigned int, long long unsigned int>, boost::default_color_type> >; TerminatorFunc = boost::detail::nontruth2]':
/usr/include/boost/graph/depth_first_search.hpp:110:10: note: parameter passing for argument of type 'boost::associative_property_map<std::map<std::pair<long long unsigned int, long long unsigned int>, boost::default_color_type> >' changed in GCC 7.1
110 | void depth_first_visit_impl
| ^~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/map:61,
from abyss-dawg.cc:14:
/usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<std::pair<long long unsigned int, long long unsigned int>, std::pair<const std::pair<long long unsigned int, long long unsigned int>, boost::default_color_type>, std::_Select1st<std::pair<const std::pair<long long unsigned int, long long unsigned int>, boost::default_color_type> >, std::less<std::pair<long long unsigned int, long long unsigned int> >, std::allocator<std::pair<const std::pair<long long unsigned int, long long unsigned int>, boost::default_color_type> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const std::pair<long long unsigned int, long long unsigned int>, boost::default_color_type> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<std::pair<long long unsigned int, long long unsigned int>, std::pair<const std::pair<long long unsigned int, long long unsigned int>, boost::default_color_type>, std::_Select1st<std::pair<const std::pair<long long unsigned int, long long unsigned int>, boost::default_color_type> >, std::less<std::pair<long long unsigned int, long long unsigned int> >, std::allocator<std::pair<const std::pair<long long unsigned int, long long unsigned int>, boost::default_color_type> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const std::pair<long long unsigned int, long long unsigned int>, boost::default_color_type> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<std::pair<long long unsigned int, long long unsigned int>, std::pair<const std::pair<long long unsigned int, long long unsigned int>, boost::default_color_type>, std::_Select1st<std::pair<const std::pair<long long unsigned int, long long unsigned int>, boost::default_color_type> >, std::less<std::pair<long long unsigned int, long long unsigned int> >, std::allocator<std::pair<const std::pair<long long unsigned int, long long unsigned int>, boost::default_color_type> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const std::pair<long long unsigned int, long long unsigned int>, boost::default_color_type> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<std::pair<long long unsigned int, long long unsigned int>, std::pair<const std::pair<long long unsigned int, long long unsigned int>, boost::default_color_type>, std::_Select1st<std::pair<const std::pair<long long unsigned int, long long unsigned int>, boost::default_color_type> >, std::less<std::pair<long long unsigned int, long long unsigned int> >, std::allocator<std::pair<const std::pair<long long unsigned int, long long unsigned int>, boost::default_color_type> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const std::pair<long long unsigned int, long long unsigned int>, boost::default_color_type> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
In file included from abyss-dawg.cc:5:
/usr/include/boost/graph/depth_first_search.hpp: In function 'int main(int, char**)':
/usr/include/boost/graph/depth_first_search.hpp:355:35: note: parameter passing for argument of type 'boost::associative_property_map<std::map<std::pair<long long unsigned int, long long unsigned int>, boost::default_color_type> >' changed in GCC 7.1
355 | detail::depth_first_visit_impl(g, u, vis, color, detail::nontruth2());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-count abyss_count-count.o libfmindex.a ../Common/libcommon.a -ldl -lm
g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-dawg abyss_dawg-abyss-dawg.o libfmindex.a ../Common/libcommon.a -ldl -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/FMIndex'
Making all in Assembly
make[4]: Entering directory '/<<PKGBUILDDIR>>/Assembly'
g++ -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libassembly_a-AssemblyAlgorithms.o `test -f 'AssemblyAlgorithms.cc' || echo './'`AssemblyAlgorithms.cc
g++ -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libassembly_a-Options.o `test -f 'Options.cc' || echo './'`Options.cc
rm -f libassembly.a
ar cru libassembly.a libassembly_a-AssemblyAlgorithms.o libassembly_a-Options.o ../Common/libcommon.a
ar: `u' modifier ignored since `D' is the default (see `U')
ranlib libassembly.a
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Assembly'
Making all in dialign
make[4]: Entering directory '/<<PKGBUILDDIR>>/dialign'
gcc -DHAVE_CONFIG_H -I. -I.. -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o museq.o museq.c
gcc -DHAVE_CONFIG_H -I. -I.. -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o alig.o alig.c
gcc -DHAVE_CONFIG_H -I. -I.. -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o assemble.o assemble.c
gcc -DHAVE_CONFIG_H -I. -I.. -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o diag.o diag.c
alig.c:15:20: warning: inline function 'calc_ov_weight' declared but never defined
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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o io.o io.c
io.c: In function 'read_scr_matrix':
io.c:270:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o orf.o orf.c
gcc -DHAVE_CONFIG_H -I. -I.. -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o parameters.o parameters.c
gcc -DHAVE_CONFIG_H -I. -I.. -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o prob.o prob.c
gcc -DHAVE_CONFIG_H -I. -I.. -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o translate.o translate.c
rm -f libdialign.a
ar cru libdialign.a alig.o assemble.o diag.o io.o orf.o parameters.o prob.o translate.o
ar: `u' modifier ignored since `D' is the default (see `U')
ranlib libdialign.a
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o dialign museq.o libdialign.a -ldl -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/dialign'
Making all in Align
make[4]: Entering directory '/<<PKGBUILDDIR>>/Align'
g++ -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_align-align.o `test -f 'align.cc' || echo './'`align.cc
g++ -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libalign_a-alignGlobal.o `test -f 'alignGlobal.cc' || echo './'`alignGlobal.cc
g++ -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libalign_a-dialign.o `test -f 'dialign.cpp' || echo './'`dialign.cpp
g++ -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libalign_a-dna_diag_prob.o `test -f 'dna_diag_prob.cc' || echo './'`dna_diag_prob.cc
g++ -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libalign_a-smith_waterman.o `test -f 'smith_waterman.cpp' || echo './'`smith_waterman.cpp
g++ -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_mergepairs-mergepairs.o `test -f 'mergepairs.cc' || echo './'`mergepairs.cc
rm -f libalign.a
ar cru libalign.a libalign_a-alignGlobal.o libalign_a-dialign.o libalign_a-dna_diag_prob.o libalign_a-smith_waterman.o
ar: `u' modifier ignored since `D' is the default (see `U')
ranlib libalign.a
g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-align abyss_align-align.o ./libalign.a ../dialign/libdialign.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm
g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-mergepairs abyss_mergepairs-mergepairs.o ./libalign.a ../dialign/libdialign.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Align'
Making all in ABYSS
make[4]: Entering directory '/<<PKGBUILDDIR>>/ABYSS'
g++ -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o ABYSS-abyss.o `test -f 'abyss.cc' || echo './'`abyss.cc
g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o ABYSS ABYSS-abyss.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../Assembly/libassembly.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/ABYSS'
Making all in Parallel
make[4]: Entering directory '/<<PKGBUILDDIR>>/Parallel'
g++ -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o ABYSS_P-parallelAbyss.o `test -f 'parallelAbyss.cpp' || echo './'`parallelAbyss.cpp
g++ -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o ABYSS_P-CommLayer.o `test -f 'CommLayer.cpp' || echo './'`CommLayer.cpp
g++ -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o ABYSS_P-NetworkSequenceCollection.o `test -f 'NetworkSequenceCollection.cpp' || echo './'`NetworkSequenceCollection.cpp
g++ -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o ABYSS_P-MessageBuffer.o `test -f 'MessageBuffer.cpp' || echo './'`MessageBuffer.cpp
g++ -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o ABYSS_P-Messages.o `test -f 'Messages.cpp' || echo './'`Messages.cpp
g++ -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_paired_dbg_mpi-parallelAbyss.o `test -f 'parallelAbyss.cpp' || echo './'`parallelAbyss.cpp
g++ -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_paired_dbg_mpi-CommLayer.o `test -f 'CommLayer.cpp' || echo './'`CommLayer.cpp
In file included from /usr/include/c++/9/map:60,
from ../Assembly/BranchGroup.h:7,
from NetworkSequenceCollection.h:7,
from NetworkSequenceCollection.cpp:1:
/usr/include/c++/9/bits/stl_tree.h: In member function 'void std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_erase_aux(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator) [with _Key = long long unsigned int; _Val = std::pair<const long long unsigned int, BranchGroup>; _KeyOfValue = std::_Select1st<std::pair<const long long unsigned int, BranchGroup> >; _Compare = std::less<long long unsigned int>; _Alloc = std::allocator<std::pair<const long long unsigned int, BranchGroup> >]':
/usr/include/c++/9/bits/stl_tree.h:2504:5: note: parameter passing for argument of type 'std::_Rb_tree<long long unsigned int, std::pair<const long long unsigned int, BranchGroup>, std::_Select1st<std::pair<const long long unsigned int, BranchGroup> >, std::less<long long unsigned int>, std::allocator<std::pair<const long long unsigned int, BranchGroup> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const long long unsigned int, BranchGroup> >'} changed in GCC 7.1
2504 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_tree.h: In member function 'size_t NetworkSequenceCollection::processBranchesTrim()':
/usr/include/c++/9/bits/stl_tree.h:1220:2: note: parameter passing for argument of type 'std::_Rb_tree<long long unsigned int, std::pair<const long long unsigned int, BranchGroup>, std::_Select1st<std::pair<const long long unsigned int, BranchGroup> >, std::less<long long unsigned int>, std::allocator<std::pair<const long long unsigned int, BranchGroup> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const long long unsigned int, BranchGroup> >'} changed in GCC 7.1
1220 | _M_erase_aux(__position);
| ^~~~~~~~~~~~
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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_paired_dbg_mpi-NetworkSequenceCollection.o `test -f 'NetworkSequenceCollection.cpp' || echo './'`NetworkSequenceCollection.cpp
/usr/include/c++/9/bits/stl_tree.h: In member function 'bool NetworkSequenceCollection::processBranchesDiscoverBubbles()':
/usr/include/c++/9/bits/stl_tree.h:1220:2: note: parameter passing for argument of type 'std::_Rb_tree<long long unsigned int, std::pair<const long long unsigned int, BranchGroup>, std::_Select1st<std::pair<const long long unsigned int, BranchGroup> >, std::less<long long unsigned int>, std::allocator<std::pair<const long long unsigned int, BranchGroup> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const long long unsigned int, BranchGroup> >'} changed in GCC 7.1
1220 | _M_erase_aux(__position);
| ^~~~~~~~~~~~
/usr/include/c++/9/bits/stl_tree.h: In member function 'std::pair<unsigned int, unsigned int> NetworkSequenceCollection::processBranchesAssembly(FastaWriter*, unsigned int)':
/usr/include/c++/9/bits/stl_tree.h:1220:2: note: parameter passing for argument of type 'std::_Rb_tree<long long unsigned int, std::pair<const long long unsigned int, BranchGroup>, std::_Select1st<std::pair<const long long unsigned int, BranchGroup> >, std::less<long long unsigned int>, std::allocator<std::pair<const long long unsigned int, BranchGroup> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const long long unsigned int, BranchGroup> >'} changed in GCC 7.1
1220 | _M_erase_aux(__position);
| ^~~~~~~~~~~~
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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_paired_dbg_mpi-MessageBuffer.o `test -f 'MessageBuffer.cpp' || echo './'`MessageBuffer.cpp
g++ -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_paired_dbg_mpi-Messages.o `test -f 'Messages.cpp' || echo './'`Messages.cpp
In file included from /usr/include/c++/9/map:60,
from ../Assembly/BranchGroup.h:7,
from NetworkSequenceCollection.h:7,
from NetworkSequenceCollection.cpp:1:
/usr/include/c++/9/bits/stl_tree.h: In member function 'void std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_erase_aux(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator) [with _Key = long long unsigned int; _Val = std::pair<const long long unsigned int, BranchGroup>; _KeyOfValue = std::_Select1st<std::pair<const long long unsigned int, BranchGroup> >; _Compare = std::less<long long unsigned int>; _Alloc = std::allocator<std::pair<const long long unsigned int, BranchGroup> >]':
/usr/include/c++/9/bits/stl_tree.h:2504:5: note: parameter passing for argument of type 'std::_Rb_tree<long long unsigned int, std::pair<const long long unsigned int, BranchGroup>, std::_Select1st<std::pair<const long long unsigned int, BranchGroup> >, std::less<long long unsigned int>, std::allocator<std::pair<const long long unsigned int, BranchGroup> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const long long unsigned int, BranchGroup> >'} changed in GCC 7.1
2504 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_tree.h: In member function 'size_t NetworkSequenceCollection::processBranchesTrim()':
/usr/include/c++/9/bits/stl_tree.h:1220:2: note: parameter passing for argument of type 'std::_Rb_tree<long long unsigned int, std::pair<const long long unsigned int, BranchGroup>, std::_Select1st<std::pair<const long long unsigned int, BranchGroup> >, std::less<long long unsigned int>, std::allocator<std::pair<const long long unsigned int, BranchGroup> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const long long unsigned int, BranchGroup> >'} changed in GCC 7.1
1220 | _M_erase_aux(__position);
| ^~~~~~~~~~~~
/usr/include/c++/9/bits/stl_tree.h: In member function 'bool NetworkSequenceCollection::processBranchesDiscoverBubbles()':
/usr/include/c++/9/bits/stl_tree.h:1220:2: note: parameter passing for argument of type 'std::_Rb_tree<long long unsigned int, std::pair<const long long unsigned int, BranchGroup>, std::_Select1st<std::pair<const long long unsigned int, BranchGroup> >, std::less<long long unsigned int>, std::allocator<std::pair<const long long unsigned int, BranchGroup> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const long long unsigned int, BranchGroup> >'} changed in GCC 7.1
1220 | _M_erase_aux(__position);
| ^~~~~~~~~~~~
/usr/include/c++/9/bits/stl_tree.h: In member function 'std::pair<unsigned int, unsigned int> NetworkSequenceCollection::processBranchesAssembly(FastaWriter*, unsigned int)':
/usr/include/c++/9/bits/stl_tree.h:1220:2: note: parameter passing for argument of type 'std::_Rb_tree<long long unsigned int, std::pair<const long long unsigned int, BranchGroup>, std::_Select1st<std::pair<const long long unsigned int, BranchGroup> >, std::less<long long unsigned int>, std::allocator<std::pair<const long long unsigned int, BranchGroup> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const long long unsigned int, BranchGroup> >'} changed in GCC 7.1
1220 | _M_erase_aux(__position);
| ^~~~~~~~~~~~
g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o ABYSS-P ABYSS_P-parallelAbyss.o ABYSS_P-CommLayer.o ABYSS_P-NetworkSequenceCollection.o ABYSS_P-MessageBuffer.o ABYSS_P-Messages.o ../Assembly/libassembly.a ../Common/libcommon.a ../DataLayer/libdatalayer.a ../DataBase/libdb.a -lsqlite3 -ldl -lm -lmpi -ldl -lm
g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-paired-dbg-mpi abyss_paired_dbg_mpi-parallelAbyss.o abyss_paired_dbg_mpi-CommLayer.o abyss_paired_dbg_mpi-NetworkSequenceCollection.o abyss_paired_dbg_mpi-MessageBuffer.o abyss_paired_dbg_mpi-Messages.o ../Assembly/libassembly.a ../Common/libcommon.a ../DataLayer/libdatalayer.a ../DataBase/libdb.a -lsqlite3 -ldl -lm -lmpi -ldl -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Parallel'
Making all in Bloom
make[4]: Entering directory '/<<PKGBUILDDIR>>/Bloom'
g++ -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_bloom-bloom.o `test -f 'bloom.cc' || echo './'`bloom.cc
g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-bloom abyss_bloom-bloom.o ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a -ldl -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Bloom'
Making all in BloomDBG
make[4]: Entering directory '/<<PKGBUILDDIR>>/BloomDBG'
g++ -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_bloom_dbg-bloom-dbg.o `test -f 'bloom-dbg.cc' || echo './'`bloom-dbg.cc
g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-bloom-dbg abyss_bloom_dbg-bloom-dbg.o ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/BloomDBG'
Making all in Konnector
make[4]: Entering directory '/<<PKGBUILDDIR>>/Konnector'
g++ -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o konnector-konnector.o `test -f 'konnector.cc' || echo './'`konnector.cc
g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o konnector konnector-konnector.o ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a -ldl -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Konnector'
Making all in Consensus
make[4]: Entering directory '/<<PKGBUILDDIR>>/Consensus'
g++ -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Consensus-Consensus.o `test -f 'Consensus.cpp' || echo './'`Consensus.cpp
g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o Consensus Consensus-Consensus.o ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Consensus'
Making all in DAssembler
make[4]: Entering directory '/<<PKGBUILDDIR>>/DAssembler'
g++ -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o DAssembler-DAssembler.o `test -f 'DAssembler.cpp' || echo './'`DAssembler.cpp
g++ -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o DAssembler-RotatedRead.o `test -f 'RotatedRead.cpp' || echo './'`RotatedRead.cpp
g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o DAssembler DAssembler-DAssembler.o DAssembler-RotatedRead.o ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/DAssembler'
Making all in DistanceEst
make[4]: Entering directory '/<<PKGBUILDDIR>>/DistanceEst'
g++ -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o DistanceEst-DistanceEst.o `test -f 'DistanceEst.cpp' || echo './'`DistanceEst.cpp
g++ -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o DistanceEst-MLE.o `test -f 'MLE.cpp' || echo './'`MLE.cpp
g++ -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o DistanceEst_ssq-DistanceEst.o `test -f 'DistanceEst.cpp' || echo './'`DistanceEst.cpp
g++ -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o DistanceEst_ssq-MLE.o `test -f 'MLE.cpp' || echo './'`MLE.cpp
In file included from /usr/include/c++/9/vector:72,
from MLE.h:4,
from MLE.cpp:1:
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from MLE.h:4,
from MLE.cpp:1:
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from MLE.h:4,
from MLE.cpp:1:
/usr/include/c++/9/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++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from MLE.h:4,
from MLE.cpp:1:
/usr/include/c++/9/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++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o DistanceEst DistanceEst-DistanceEst.o DistanceEst-MLE.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../Common/libcommon.a -ldl -lm
g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o DistanceEst-ssq DistanceEst_ssq-DistanceEst.o DistanceEst_ssq-MLE.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../Common/libcommon.a -ldl -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/DistanceEst'
Making all in KAligner
make[4]: Entering directory '/<<PKGBUILDDIR>>/KAligner'
g++ -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o KAligner-KAligner.o `test -f 'KAligner.cpp' || echo './'`KAligner.cpp
g++ -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o KAligner-Aligner.o `test -f 'Aligner.cpp' || echo './'`Aligner.cpp
g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o KAligner KAligner-KAligner.o KAligner-Aligner.o ../DataLayer/libdatalayer.a ../Common/libcommon.a -lpthread -ldl -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/KAligner'
Making all in Layout
make[4]: Entering directory '/<<PKGBUILDDIR>>/Layout'
g++ -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_layout-layout.o `test -f 'layout.cc' || echo './'`layout.cc
g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-layout abyss_layout-layout.o ../Common/libcommon.a -ldl -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Layout'
Making all in LogKmerCount
make[4]: Entering directory '/<<PKGBUILDDIR>>/LogKmerCount'
g++ -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o logcounter-logcounter.o `test -f 'logcounter.cc' || echo './'`logcounter.cc
g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o logcounter logcounter-logcounter.o ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a -ldl -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/LogKmerCount'
Making all in Map
make[4]: Entering directory '/<<PKGBUILDDIR>>/Map'
g++ -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_index-index.o `test -f 'index.cc' || echo './'`index.cc
g++ -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_map-map.o `test -f 'map.cc' || echo './'`map.cc
g++ -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_map_ssq-map.o `test -f 'map.cc' || echo './'`map.cc
g++ -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_overlap-overlap.o `test -f 'overlap.cc' || echo './'`overlap.cc
In file included from /usr/include/c++/9/vector:72,
from ../DataLayer/FastaIndex.h:11,
from index.cc:3:
/usr/include/c++/9/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++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<wat_array::BitArray>::iterator' {aka '__gnu_cxx::__normal_iterator<wat_array::BitArray*, std::vector<wat_array::BitArray> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from ../DataLayer/FastaIndex.h:11,
from index.cc:3:
/usr/include/c++/9/bits/stl_vector.h: In member function 'void FMIndex::assign(It, It) [with It = __gnu_cxx::__normal_iterator<unsigned char*, std::vector<unsigned char> >]':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<wat_array::BitArray*, std::vector<wat_array::BitArray> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In member function 'void FMIndex::assignBWT(It, It) [with It = __gnu_cxx::__normal_iterator<unsigned char*, std::vector<unsigned char> >]':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<wat_array::BitArray*, std::vector<wat_array::BitArray> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-index abyss_index-index.o ../FMIndex/libfmindex.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm
In file included from /usr/include/c++/9/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++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<FMIndex::Match>::iterator' {aka '__gnu_cxx::__normal_iterator<FMIndex::Match*, std::vector<FMIndex::Match> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/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++/9/bits/vector.tcc:121:4: 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++/9/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++/9/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++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<wat_array::BitArray>::iterator' {aka '__gnu_cxx::__normal_iterator<wat_array::BitArray*, std::vector<wat_array::BitArray> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/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++/9/bits/stl_vector.h: In member function 'void FMIndex::assign(It, It) [with It = __gnu_cxx::__normal_iterator<unsigned char*, std::vector<unsigned char> >]':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<wat_array::BitArray*, std::vector<wat_array::BitArray> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
In file included from /usr/include/c++/9/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++/9/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++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<wat_array::BitArray>::iterator' {aka '__gnu_cxx::__normal_iterator<wat_array::BitArray*, std::vector<wat_array::BitArray> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/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++/9/bits/stl_vector.h: In member function 'void FMIndex::assign(It, It) [with It = __gnu_cxx::__normal_iterator<unsigned char*, std::vector<unsigned char> >]':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<wat_array::BitArray*, std::vector<wat_array::BitArray> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/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++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<wat_array::BitArray>::iterator' {aka '__gnu_cxx::__normal_iterator<wat_array::BitArray*, std::vector<wat_array::BitArray> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-map abyss_map-map.o ../FMIndex/libfmindex.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../DataBase/libdb.a -lsqlite3 -ldl -lm -ldl -lm
In file included from /usr/include/c++/9/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++/9/bits/stl_vector.h: In member function 'void FMIndex::assign(It, It) [with It = __gnu_cxx::__normal_iterator<unsigned char*, std::vector<unsigned char> >]':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<wat_array::BitArray*, std::vector<wat_array::BitArray> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-map-ssq abyss_map_ssq-map.o ../FMIndex/libfmindex.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../DataBase/libdb.a -lsqlite3 -ldl -lm -ldl -lm
g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-overlap abyss_overlap-overlap.o ../FMIndex/libfmindex.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Map'
Making all in MergePaths
make[4]: Entering directory '/<<PKGBUILDDIR>>/MergePaths'
g++ -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o MergePaths-MergePaths.o `test -f 'MergePaths.cpp' || echo './'`MergePaths.cpp
g++ -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o MergeContigs-MergeContigs.o `test -f 'MergeContigs.cpp' || echo './'`MergeContigs.cpp
g++ -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o PathConsensus-PathConsensus.o `test -f 'PathConsensus.cpp' || echo './'`PathConsensus.cpp
g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o MergeContigs MergeContigs-MergeContigs.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a -ldl -lm
g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o PathConsensus PathConsensus-PathConsensus.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a ../dialign/libdialign.a -ldl -lm
g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o MergePaths MergePaths-MergePaths.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/MergePaths'
Making all in 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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Overlap-Overlap.o `test -f 'Overlap.cpp' || echo './'`Overlap.cpp
g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o Overlap Overlap-Overlap.o ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Overlap'
Making all in PairedDBG
make[4]: Entering directory '/<<PKGBUILDDIR>>/PairedDBG'
g++ -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_paired_dbg-abyss-paired-dbg.o `test -f 'abyss-paired-dbg.cc' || echo './'`abyss-paired-dbg.cc
g++ -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_paired_dbg-KmerPair.o `test -f 'KmerPair.cc' || echo './'`KmerPair.cc
g++ -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o KmerPair.o KmerPair.cc
rm -f libpaireddbg.a
ar cru libpaireddbg.a KmerPair.o
ar: `u' modifier ignored since `D' is the default (see `U')
ranlib libpaireddbg.a
g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-paired-dbg abyss_paired_dbg-abyss-paired-dbg.o abyss_paired_dbg-KmerPair.o ../Assembly/libassembly.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../DataBase/libdb.a -lsqlite3 -ldl -lm -ldl -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/PairedDBG'
Making all in ParseAligns
make[4]: Entering directory '/<<PKGBUILDDIR>>/ParseAligns'
g++ -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_fixmate-abyss-fixmate.o `test -f 'abyss-fixmate.cc' || echo './'`abyss-fixmate.cc
g++ -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_fixmate_ssq-abyss-fixmate.o `test -f 'abyss-fixmate.cc' || echo './'`abyss-fixmate.cc
g++ -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o ParseAligns-ParseAligns.o `test -f 'ParseAligns.cpp' || echo './'`ParseAligns.cpp
g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o ParseAligns ParseAligns-ParseAligns.o ../Common/libcommon.a -ldl -lm
g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-fixmate-ssq abyss_fixmate_ssq-abyss-fixmate.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../Common/libcommon.a -ldl -lm
g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-fixmate abyss_fixmate-abyss-fixmate.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../Common/libcommon.a -ldl -lm
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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o PathOverlap-PathOverlap.o `test -f 'PathOverlap.cpp' || echo './'`PathOverlap.cpp
g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o PathOverlap PathOverlap-PathOverlap.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/PathOverlap'
Making all in PopBubbles
make[4]: Entering directory '/<<PKGBUILDDIR>>/PopBubbles'
g++ -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o PopBubbles-PopBubbles.o `test -f 'PopBubbles.cpp' || echo './'`PopBubbles.cpp
g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o PopBubbles PopBubbles-PopBubbles.o ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a ../dialign/libdialign.a -ldl -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/PopBubbles'
Making all in Scaffold
make[4]: Entering directory '/<<PKGBUILDDIR>>/Scaffold'
g++ -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_scaffold-scaffold.o `test -f 'scaffold.cc' || echo './'`scaffold.cc
g++ -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_junction-junction.o `test -f 'junction.cc' || echo './'`junction.cc
g++ -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_longseqdist-longseqdist.o `test -f 'longseqdist.cpp' || echo './'`longseqdist.cpp
g++ -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_drawgraph-drawgraph.o `test -f 'drawgraph.cc' || echo './'`drawgraph.cc
In file included from /usr/include/c++/9/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++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<std::pair<double, ContigNode> >::iterator' {aka '__gnu_cxx::__normal_iterator<std::pair<double, ContigNode>*, std::vector<std::pair<double, ContigNode> > >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/algorithm:62,
from /usr/include/boost/type_traits/is_nothrow_swappable.hpp:33,
from /usr/include/boost/type_traits.hpp:120,
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++/9/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++/9/bits/stl_algo.h:78:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, ContigNode>*, std::vector<std::pair<double, ContigNode> > >' changed in GCC 7.1
78 | __move_median_to_first(_Iterator __result,_Iterator __a, _Iterator __b,
| ^~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:78:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, ContigNode>*, std::vector<std::pair<double, ContigNode> > >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:78:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, ContigNode>*, std::vector<std::pair<double, ContigNode> > >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:78:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, ContigNode>*, std::vector<std::pair<double, ContigNode> > >' changed in GCC 7.1
/usr/include/c++/9/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++/9/bits/stl_algo.h:1820:5: 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
1820 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/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++/9/bits/stl_algo.h:1839:5: 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
1839 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1839:5: 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++/9/bits/stl_algo.h:61,
from /usr/include/c++/9/algorithm:62,
from /usr/include/boost/type_traits/is_nothrow_swappable.hpp:33,
from /usr/include/boost/type_traits.hpp:120,
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++/9/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++/9/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, ContigNode>*, std::vector<std::pair<double, ContigNode> > >' changed in GCC 7.1
214 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
In file included from /usr/include/c++/9/algorithm:62,
from /usr/include/boost/type_traits/is_nothrow_swappable.hpp:33,
from /usr/include/boost/type_traits.hpp:120,
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++/9/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++/9/bits/stl_algo.h:1939:5: 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
1939 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1939:5: 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++/9/bits/stl_algo.h:1939:5: 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++/9/bits/stl_algo.h:1920:34: 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
1920 | std::__move_median_to_first(__first, __first + 1, __mid, __last - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1921 | __comp);
| ~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1920:34: 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++/9/bits/stl_algo.h:1953:25: 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
1953 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/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++/9/bits/vector.tcc: In function 'int main(int, char**)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, ContigNode>*, std::vector<std::pair<double, ContigNode> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/algorithm:62,
from /usr/include/boost/type_traits/is_nothrow_swappable.hpp:33,
from /usr/include/boost/type_traits.hpp:120,
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++/9/bits/stl_algo.h:1967:25: 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
1967 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1968 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1969 | __comp);
| ~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1884:25: 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
1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1889:23: 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
1889 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-longseqdist abyss_longseqdist-longseqdist.o ../Common/libcommon.a -ldl -lm
g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-drawgraph abyss_drawgraph-drawgraph.o ../Common/libcommon.a -ldl -lm
g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-junction abyss_junction-junction.o ../Common/libcommon.a -ldl -lm
g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-scaffold abyss_scaffold-scaffold.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../Common/libcommon.a -ldl -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Scaffold'
Making all in SimpleGraph
make[4]: Entering directory '/<<PKGBUILDDIR>>/SimpleGraph'
g++ -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o SimpleGraph-SimpleGraph.o `test -f 'SimpleGraph.cpp' || echo './'`SimpleGraph.cpp
g++ -std=c++11 -Wall -Wextra -Werror -Wno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o SimpleGraph SimpleGraph-SimpleGraph.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../Common/libcommon.a -lpthread -ldl -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/SimpleGraph'
Making all in kmerprint
make[4]: Entering directory '/<<PKGBUILDDIR>>/kmerprint'
g++ -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o kmerprint-kmerprint.o `test -f 'kmerprint.cc' || echo './'`kmerprint.cc
g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o kmerprint kmerprint-kmerprint.o ../Assembly/libassembly.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/kmerprint'
Making all in FilterGraph
make[4]: Entering directory '/<<PKGBUILDDIR>>/FilterGraph'
g++ -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_filtergraph-FilterGraph.o `test -f 'FilterGraph.cc' || echo './'`FilterGraph.cc
g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-filtergraph abyss_filtergraph-FilterGraph.o ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm
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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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_gapfill-gapfill.o `test -f 'gapfill.cpp' || echo './'`gapfill.cpp
g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-gapfill abyss_gapfill-gapfill.o ../Align/libalign.a ../dialign/libdialign.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm
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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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_sealer-sealer.o `test -f 'sealer.cc' || echo './'`sealer.cc
g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-sealer abyss_sealer-sealer.o ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a -ldl -lm
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g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -DPAIRED_DBG -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o AdjList-AdjList.o `test -f 'AdjList.cpp' || echo './'`AdjList.cpp
g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o AdjList AdjList-AdjList.o ../DataLayer/libdatalayer.a ../Common/libcommon.a ../PairedDBG/libpaireddbg.a ../DataBase/libdb.a -lsqlite3 -ldl -lm -ldl -lm
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markdown README.md > README.html
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dh_auto_test -a
make -j4 check VERBOSE=1
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Making check in PairedDBG
make[2]: Entering directory '/<<PKGBUILDDIR>>/PairedDBG'
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make[2]: Leaving directory '/<<PKGBUILDDIR>>/PairedDBG'
Making check in ParseAligns
make[2]: Entering directory '/<<PKGBUILDDIR>>/ParseAligns'
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Making check in PathOverlap
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Making check in PopBubbles
make[2]: Entering directory '/<<PKGBUILDDIR>>/PopBubbles'
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Making check in Scaffold
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Making check in SimpleGraph
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Making check in kmerprint
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Making check in FilterGraph
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Making check in GapFiller
make[2]: Entering directory '/<<PKGBUILDDIR>>/GapFiller'
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Making check in Sealer
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Making check in AdjList
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Making check in vendor
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Making check in vendor/nthash
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Making check in vendor/gtest-1.7.0
make[2]: Entering directory '/<<PKGBUILDDIR>>/vendor/gtest-1.7.0'
make libgtest.a libgtest_main.a
make[3]: Entering directory '/<<PKGBUILDDIR>>/vendor/gtest-1.7.0'
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I../.. -I../.. -isystem ../../vendor/gtest-1.7.0/include -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -Wno-missing-field-initializers -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o src/libgtest_a-gtest-all.o `test -f 'src/gtest-all.cc' || echo './'`src/gtest-all.cc
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I../.. -I../.. -isystem ../../vendor/gtest-1.7.0/include -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -Wno-missing-field-initializers -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o src/libgtest_main_a-gtest_main.o `test -f 'src/gtest_main.cc' || echo './'`src/gtest_main.cc
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I../.. -I../.. -isystem ../../vendor/gtest-1.7.0/include -I/<<PKGBUILDDIR>> -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -Wno-missing-field-initializers -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o src/libgtest_main_a-gtest-all.o `test -f 'src/gtest-all.cc' || echo './'`src/gtest-all.cc
rm -f libgtest.a
ar cru libgtest.a src/libgtest_a-gtest-all.o
ar: `u' modifier ignored since `D' is the default (see `U')
ranlib libgtest.a
rm -f libgtest_main.a
ar cru libgtest_main.a src/libgtest_main_a-gtest_main.o src/libgtest_main_a-gtest-all.o
ar: `u' modifier ignored since `D' is the default (see `U')
ranlib libgtest_main.a
make[3]: Leaving directory '/<<PKGBUILDDIR>>/vendor/gtest-1.7.0'
make[2]: Leaving directory '/<<PKGBUILDDIR>>/vendor/gtest-1.7.0'
Making check in Unittest
make[2]: Entering directory '/<<PKGBUILDDIR>>/Unittest'
make common_stringutil common_histogram common_bitutil common_kmer common_sequence common_KmerIterator common_sam BloomFilter Konnector_DBGBloom Konnector_DBGBloomAlgorithms graph_ConstrainedBFSVisitor graph_BidirectionalBFS graph_AllPathsSearch graph_HashGraph graph_ConstrainedBidiBFSVisitor graph_ExtendPath graph_DotIO graph_UndirectedGraph Konnector_konnector DBG_LoadAlgorithm PairedDBG_LoadAlgorithm PairedDBG_KmerPair PairedDBG_Dinuc PairedDBG_BranchRecord BloomDBG_BloomDBG BloomDBG_RollingHash BloomDBG_RollingHashIterator BloomDBG_HashAgnosticCascadingBloom BloomDBG_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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Common/StringUtilTest.o Common/StringUtilTest.cpp
g++ -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Common/HistogramTest.o Common/HistogramTest.cpp
g++ -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Common/BitUtilTest.o Common/BitUtilTest.cpp
g++ -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Common/KmerTest.o Common/KmerTest.cpp
g++ -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Common/Sequence.o Common/Sequence.cc
g++ -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Common/KmerIteratorTest.o Common/KmerIteratorTest.cpp
g++ -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Common/SAM.o Common/SAM.cc
g++ -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Konnector/BloomFilter-BloomFilter.o `test -f 'Konnector/BloomFilter.cc' || echo './'`Konnector/BloomFilter.cc
g++ -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Konnector/DBGBloom-DBGBloomTest.o `test -f 'Konnector/DBGBloomTest.cpp' || echo './'`Konnector/DBGBloomTest.cpp
g++ -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Konnector/DBGBloomAlgorithms-DBGBloomAlgorithmsTest.o `test -f 'Konnector/DBGBloomAlgorithmsTest.cpp' || echo './'`Konnector/DBGBloomAlgorithmsTest.cpp
g++ -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Graph/graph_ConstrainedBFSVisitor-ConstrainedBFSVisitorTest.o `test -f 'Graph/ConstrainedBFSVisitorTest.cpp' || echo './'`Graph/ConstrainedBFSVisitorTest.cpp
g++ -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Graph/graph_BidirectionalBFS-BidirectionalBFSTest.o `test -f 'Graph/BidirectionalBFSTest.cpp' || echo './'`Graph/BidirectionalBFSTest.cpp
g++ -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Graph/graph_AllPathsSearch-AllPathsSearchTest.o `test -f 'Graph/AllPathsSearchTest.cpp' || echo './'`Graph/AllPathsSearchTest.cpp
g++ -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Graph/graph_HashGraph-HashGraphTest.o `test -f 'Graph/HashGraphTest.cpp' || echo './'`Graph/HashGraphTest.cpp
g++ -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Graph/graph_ConstrainedBidiBFSVisitor-ConstrainedBidiBFSVisitorTest.o `test -f 'Graph/ConstrainedBidiBFSVisitorTest.cpp' || echo './'`Graph/ConstrainedBidiBFSVisitorTest.cpp
g++ -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Graph/graph_ExtendPath-ExtendPathTest.o `test -f 'Graph/ExtendPathTest.cpp' || echo './'`Graph/ExtendPathTest.cpp
g++ -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Graph/graph_DotIO-DotIOTest.o `test -f 'Graph/DotIOTest.cpp' || echo './'`Graph/DotIOTest.cpp
g++ -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Graph/UndirectedGraphTest.o Graph/UndirectedGraphTest.cpp
g++ -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Konnector/konnector-konnectorTest.o `test -f 'Konnector/konnectorTest.cpp' || echo './'`Konnector/konnectorTest.cpp
g++ -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o DBG/LoadAlgorithm-LoadAlgorithmTest.o `test -f 'DBG/LoadAlgorithmTest.cpp' || echo './'`DBG/LoadAlgorithmTest.cpp
g++ -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o PairedDBG/LoadAlgorithm-LoadAlgorithmTest.o `test -f 'PairedDBG/LoadAlgorithmTest.cpp' || echo './'`PairedDBG/LoadAlgorithmTest.cpp
g++ -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o PairedDBG/KmerPair-KmerPairTest.o `test -f 'PairedDBG/KmerPairTest.cc' || echo './'`PairedDBG/KmerPairTest.cc
g++ -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o PairedDBG/Dinuc-DinucTest.o `test -f 'PairedDBG/DinucTest.cc' || echo './'`PairedDBG/DinucTest.cc
g++ -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o PairedDBG/BranchRecord-BranchRecordTest.o `test -f 'PairedDBG/BranchRecordTest.cpp' || echo './'`PairedDBG/BranchRecordTest.cpp
g++ -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o BloomDBG/BloomDBG-BloomDBGTest.o `test -f 'BloomDBG/BloomDBGTest.cpp' || echo './'`BloomDBG/BloomDBGTest.cpp
g++ -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o BloomDBG/RollingHashTest.o BloomDBG/RollingHashTest.cpp
g++ -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o BloomDBG/RollingHashIteratorTest.o BloomDBG/RollingHashIteratorTest.cpp
g++ -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o BloomDBG/HashAgnosticCascadingBloom-HashAgnosticCascadingBloomTest.o `test -f 'BloomDBG/HashAgnosticCascadingBloomTest.cpp' || echo './'`BloomDBG/HashAgnosticCascadingBloomTest.cpp
g++ -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 -fdebug-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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o BloomDBG/RollingBloomDBG-RollingBloomDBGTest.o `test -f 'BloomDBG/RollingBloomDBGTest.cpp' || echo './'`BloomDBG/RollingBloomDBGTest.cpp
g++ -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o BloomDBG/MaskedKmerTest.o BloomDBG/MaskedKmerTest.cpp
g++ -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o BloomDBG/SpacedSeedTest.o BloomDBG/SpacedSeedTest.cpp
g++ -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o BloomDBG/LightweightKmerTest.o BloomDBG/LightweightKmerTest.cpp
g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o common_stringutil Common/StringUtilTest.o ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm
g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o common_histogram Common/HistogramTest.o ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm
g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o common_bitutil Common/BitUtilTest.o ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm
g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o common_kmer Common/KmerTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm
g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o common_sequence Common/Sequence.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm
g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o common_KmerIterator Common/KmerIteratorTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm
g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o common_sam Common/SAM.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm
g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o BloomFilter Konnector/BloomFilter-BloomFilter.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm
g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o Konnector_DBGBloom Konnector/DBGBloom-DBGBloomTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm
g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o Konnector_DBGBloomAlgorithms Konnector/DBGBloomAlgorithms-DBGBloomAlgorithmsTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm
g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o graph_ConstrainedBFSVisitor Graph/graph_ConstrainedBFSVisitor-ConstrainedBFSVisitorTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm
g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o graph_BidirectionalBFS Graph/graph_BidirectionalBFS-BidirectionalBFSTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm
g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o graph_AllPathsSearch Graph/graph_AllPathsSearch-AllPathsSearchTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm
g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o graph_HashGraph Graph/graph_HashGraph-HashGraphTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm
g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o graph_ConstrainedBidiBFSVisitor Graph/graph_ConstrainedBidiBFSVisitor-ConstrainedBidiBFSVisitorTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm
g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o graph_ExtendPath Graph/graph_ExtendPath-ExtendPathTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm
g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o graph_DotIO Graph/graph_DotIO-DotIOTest.o ../Assembly/libassembly.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm
g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o graph_UndirectedGraph Graph/UndirectedGraphTest.o ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm
g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o Konnector_konnector Konnector/konnector-konnectorTest.o ../Align/libalign.a ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm
g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o DBG_LoadAlgorithm DBG/LoadAlgorithm-LoadAlgorithmTest.o ../Assembly/libassembly.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm
g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o PairedDBG_LoadAlgorithm PairedDBG/LoadAlgorithm-LoadAlgorithmTest.o ../PairedDBG/libpaireddbg.a ../Assembly/libassembly.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm
In file included from /usr/include/c++/9/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++/9/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++/9/bits/hashtable.h:1849:5: note: parameter passing for argument of type 'std::_Hashtable<RollingBloomDBGVertex, RollingBloomDBGVertex, std::allocator<RollingBloomDBGVertex>, std::__detail::_Identity, std::equal_to<RollingBloomDBGVertex>, std::hash<RollingBloomDBGVertex>, std::__detail::_Mod_range_hashing, std::__detail::_Default_ranged_hash, std::__detail::_Prime_rehash_policy, std::__detail::_Hashtable_traits<true, true, true> >::const_iterator' {aka 'std::__detail::_Node_const_iterator<RollingBloomDBGVertex, true, true>'} changed in GCC 7.1
1849 | _Hashtable<_Key, _Value, _Alloc, _ExtractKey, _Equal,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1850 | _H1, _H2, _Hash, _RehashPolicy, _Traits>::
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o PairedDBG_KmerPair PairedDBG/KmerPair-KmerPairTest.o ../PairedDBG/libpaireddbg.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm
g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o PairedDBG_Dinuc PairedDBG/Dinuc-DinucTest.o ../PairedDBG/libpaireddbg.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm
g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o PairedDBG_BranchRecord PairedDBG/BranchRecord-BranchRecordTest.o ../PairedDBG/libpaireddbg.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm
g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o BloomDBG_BloomDBG BloomDBG/BloomDBG-BloomDBGTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm
g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o BloomDBG_RollingHash BloomDBG/RollingHashTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm
g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o BloomDBG_RollingHashIterator BloomDBG/RollingHashIteratorTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm
g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o BloomDBG_HashAgnosticCascadingBloom BloomDBG/HashAgnosticCascadingBloom-HashAgnosticCascadingBloomTest.o ../DataLayer/libdatalayer.a ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm
g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o BloomDBG_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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o BloomDBG_MaskedKmer BloomDBG/MaskedKmerTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm
g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o BloomDBG_SpacedSeed BloomDBG/SpacedSeedTest.o ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm
g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o BloomDBG_LightweightKmer BloomDBG/LightweightKmerTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm
/usr/include/c++/9/bits/hashtable.h: In member function 'virtual void RollingBloomDBGTest_out_edge_iterator_Test::TestBody()':
/usr/include/c++/9/bits/hashtable.h:768:42: note: parameter passing for argument of type 'std::_Hashtable<RollingBloomDBGVertex, RollingBloomDBGVertex, std::allocator<RollingBloomDBGVertex>, std::__detail::_Identity, std::equal_to<RollingBloomDBGVertex>, std::hash<RollingBloomDBGVertex>, std::__detail::_Mod_range_hashing, std::__detail::_Default_ranged_hash, std::__detail::_Prime_rehash_policy, std::__detail::_Hashtable_traits<true, true, true> >::const_iterator' {aka 'std::__detail::_Node_const_iterator<RollingBloomDBGVertex, true, true>'} changed in GCC 7.1
768 | { return erase(const_iterator(__it)); }
| ^
/usr/include/c++/9/bits/hashtable.h: In member function 'virtual void RollingBloomDBGSpacedSeedTest_out_edge_iterator_Test::TestBody()':
/usr/include/c++/9/bits/hashtable.h:768:42: note: parameter passing for argument of type 'std::_Hashtable<RollingBloomDBGVertex, RollingBloomDBGVertex, std::allocator<RollingBloomDBGVertex>, std::__detail::_Identity, std::equal_to<RollingBloomDBGVertex>, std::hash<RollingBloomDBGVertex>, std::__detail::_Mod_range_hashing, std::__detail::_Default_ranged_hash, std::__detail::_Prime_rehash_policy, std::__detail::_Hashtable_traits<true, true, true> >::const_iterator' {aka 'std::__detail::_Node_const_iterator<RollingBloomDBGVertex, true, true>'} changed in GCC 7.1
768 | { return erase(const_iterator(__it)); }
| ^
/usr/include/c++/9/bits/hashtable.h: In member function 'virtual void RollingBloomDBGTest_adjacency_iterator_Test::TestBody()':
/usr/include/c++/9/bits/hashtable.h:768:42: note: parameter passing for argument of type 'std::_Hashtable<RollingBloomDBGVertex, RollingBloomDBGVertex, std::allocator<RollingBloomDBGVertex>, std::__detail::_Identity, std::equal_to<RollingBloomDBGVertex>, std::hash<RollingBloomDBGVertex>, std::__detail::_Mod_range_hashing, std::__detail::_Default_ranged_hash, std::__detail::_Prime_rehash_policy, std::__detail::_Hashtable_traits<true, true, true> >::const_iterator' {aka 'std::__detail::_Node_const_iterator<RollingBloomDBGVertex, true, true>'} changed in GCC 7.1
768 | { return erase(const_iterator(__it)); }
| ^
/usr/include/c++/9/bits/hashtable.h: In member function 'virtual void RollingBloomDBGTest_in_edges_Test::TestBody()':
/usr/include/c++/9/bits/hashtable.h:768:42: note: parameter passing for argument of type 'std::_Hashtable<RollingBloomDBGVertex, RollingBloomDBGVertex, std::allocator<RollingBloomDBGVertex>, std::__detail::_Identity, std::equal_to<RollingBloomDBGVertex>, std::hash<RollingBloomDBGVertex>, std::__detail::_Mod_range_hashing, std::__detail::_Default_ranged_hash, std::__detail::_Prime_rehash_policy, std::__detail::_Hashtable_traits<true, true, true> >::const_iterator' {aka 'std::__detail::_Node_const_iterator<RollingBloomDBGVertex, true, true>'} changed in GCC 7.1
768 | { return erase(const_iterator(__it)); }
| ^
g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o BloomDBG_RollingBloomDBG BloomDBG/RollingBloomDBG-RollingBloomDBGTest.o ../DataLayer/libdatalayer.a ../Common/libcommon.a ../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_kmer
PASS: common_bitutil
PASS: common_histogram
PASS: common_stringutil
PASS: common_sequence
PASS: common_sam
PASS: common_KmerIterator
PASS: BloomFilter
PASS: Konnector_DBGBloomAlgorithms
PASS: graph_ConstrainedBFSVisitor
PASS: Konnector_DBGBloom
PASS: graph_BidirectionalBFS
PASS: graph_HashGraph
PASS: graph_ConstrainedBidiBFSVisitor
PASS: graph_ExtendPath
PASS: graph_AllPathsSearch
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: DBG_LoadAlgorithm
PASS: PairedDBG_LoadAlgorithm
============================================================================
Testsuite summary for ABySS 2.2.4
============================================================================
# TOTAL: 33
# PASS: 33
# SKIP: 0
# XFAIL: 0
# FAIL: 0
# XPASS: 0
# ERROR: 0
============================================================================
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Unittest'
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make[2]: Entering directory '/<<PKGBUILDDIR>>'
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
create-stamp debian/debhelper-build-stamp
fakeroot debian/rules binary-arch
dh binary-arch
dh_testroot -a
dh_prep -a
debian/rules override_dh_auto_install
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_install --destdir=debian/tmp
make -j4 install DESTDIR=/<<PKGBUILDDIR>>/debian/tmp AM_UPDATE_INFO_DIR=no
make[2]: Entering directory '/<<PKGBUILDDIR>>'
Making install in bin
make[3]: Entering directory '/<<PKGBUILDDIR>>/bin'
make[4]: Entering directory '/<<PKGBUILDDIR>>/bin'
make[4]: Nothing to be done for 'install-data-am'.
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
/usr/bin/install -c abyss-bowtie abyss-bowtie2 abyss-bwa abyss-bwasw abyss-bwamem abyss-fatoagp abyss-kaligner abyss-pe abyss-samtoafg abyss-tabtomd abyss-bloom-dist.mk abyss-dida abyss-stack-size '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/bin'
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Making install in doc
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make[4]: 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
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make[4]: Entering directory '/<<PKGBUILDDIR>>/Graph'
make[4]: Nothing to be done for 'install-data-am'.
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
/usr/bin/install -c abyss-gc abyss-todot '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Graph'
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-txt '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
/usr/bin/install -c abyss-db-csv '/<<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
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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
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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'
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Making install in Align
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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'
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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 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/nthash
make[3]: Entering directory '/<<PKGBUILDDIR>>/vendor/nthash'
make[4]: Entering directory '/<<PKGBUILDDIR>>/vendor/nthash'
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 README.md '/<<PKGBUILDDIR>>/debian/tmp/usr/share/doc/abyss'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/vendor/nthash'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/vendor/nthash'
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/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-gapfill contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/ABYSS-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/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-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/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/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/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/MergePaths contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/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 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-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/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/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/logcounter contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/abyss-mergepairs contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/abyss-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-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/KAligner contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/abyss-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-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-fixmate contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/Overlap contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/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/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/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-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-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-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-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/DAssembler contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/abyss-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/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-db-csv contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/abyss-map contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/abyss-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/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-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-overlap contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/abyss-layout contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/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/DistanceEst-ssq contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/abyss/usr/lib/abyss/abyss-filtergraph debian/abyss/usr/lib/abyss/abyss-gapfill debian/abyss/usr/lib/abyss/ABYSS-P debian/abyss/usr/lib/abyss/AdjList debian/abyss/usr/lib/abyss/abyss-bloom-dbg debian/abyss/usr/lib/abyss/konnector debian/abyss/usr/lib/abyss/PathOverlap debian/abyss/usr/lib/abyss/Consensus debian/abyss/usr/lib/abyss/MergePaths debian/abyss/usr/lib/abyss/DistanceEst debian/abyss/usr/lib/abyss/ABYSS debian/abyss/usr/lib/abyss/PathConsensus debian/abyss/usr/lib/abyss/abyss-gc debian/abyss/usr/lib/abyss/PopBubbles debian/abyss/usr/lib/abyss/SimpleGraph debian/abyss/usr/lib/abyss/logcounter debian/abyss/usr/lib/abyss/abyss-mergepairs debian/abyss/usr/lib/abyss/abyss-tofastq debian/abyss/usr/lib/abyss/abyss-longseqdist debian/abyss/usr/lib/abyss/KAligner debian/abyss/usr/lib/abyss/abyss-align debian/abyss/usr/lib/abyss/abyss-fixmate-ssq debian/abyss/usr/lib/abyss/abyss-fixmate debian/abyss/usr/lib/abyss/Overlap debian/abyss/usr/lib/abyss/abyss-scaffold debian/abyss/usr/bin/DistanceEst debian/abyss/usr/lib/abyss/ParseAligns debian/abyss/usr/lib/abyss/abyss-todot debian/abyss/usr/lib/abyss/abyss-paired-dbg debian/abyss/usr/lib/abyss/abyss-fac debian/abyss/usr/lib/abyss/abyss-bloom debian/abyss/usr/lib/abyss/DAssembler debian/abyss/usr/lib/abyss/abyss-paired-dbg-mpi debian/abyss/usr/lib/abyss/MergeContigs debian/abyss/usr/lib/abyss/abyss-sealer debian/abyss/usr/lib/abyss/abyss-db-csv debian/abyss/usr/lib/abyss/abyss-map debian/abyss/usr/lib/abyss/abyss-index debian/abyss/usr/bin/abyss-fixmate debian/abyss/usr/lib/abyss/abyss-junction debian/abyss/usr/lib/abyss/abyss-overlap debian/abyss/usr/lib/abyss/abyss-layout debian/abyss/usr/lib/abyss/abyss-map-ssq debian/abyss/usr/lib/abyss/DistanceEst-ssq 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-dbgsym' in '../abyss-dbgsym_2.2.4-1+b2_armhf.deb'.
dpkg-deb: building package 'abyss' in '../abyss_2.2.4-1+b2_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../abyss_2.2.4-1+b2_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 2020-07-21T06:50:43Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
abyss_2.2.4-1+b2_armhf.changes:
-------------------------------
Format: 1.8
Date: Tue, 11 Feb 2020 15:39:45 +0100
Source: abyss (2.2.4-1)
Binary: abyss abyss-dbgsym
Binary-Only: yes
Architecture: armhf
Version: 2.2.4-1+b2
Distribution: bullseye-staging
Urgency: low
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Raspbian wandboard test autobuilder <root@raspbian.org>
Description:
abyss - de novo, parallel, sequence assembler for short reads
Changes:
abyss (2.2.4-1+b2) bullseye-staging; urgency=low, binary-only=yes
.
* Binary-only non-maintainer upload for armhf; no source changes.
* rebuild due to debcheck failure
Checksums-Sha1:
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3cf2b361a12dcf01991fb01a25ed602ace5ebd0b 7226 abyss_2.2.4-1+b2_armhf.buildinfo
55a8454735d0cf8b9cbdd7fe3b3bf43a1a87b5c2 2742732 abyss_2.2.4-1+b2_armhf.deb
Checksums-Sha256:
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4f9fdd775b7723f7fec9899a6ee4e356f4a961ad7831c9942f1b269906323856 7226 abyss_2.2.4-1+b2_armhf.buildinfo
2998fde938c6bdff03eba73e72244855f081938d82c815ae4638a4eb70cc0055 2742732 abyss_2.2.4-1+b2_armhf.deb
Files:
907d2811d547e6d5f4d6719308092475 26445512 debug optional abyss-dbgsym_2.2.4-1+b2_armhf.deb
aecfdf9bb5768f526efb68850a794156 7226 science optional abyss_2.2.4-1+b2_armhf.buildinfo
d8b98c88fb35f98aa85738e013342bf5 2742732 science optional abyss_2.2.4-1+b2_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
abyss-dbgsym_2.2.4-1+b2_armhf.deb
---------------------------------
new Debian package, version 2.0.
size 26445512 bytes: control archive=2488 bytes.
2061 bytes, 12 lines control
4537 bytes, 43 lines md5sums
Package: abyss-dbgsym
Source: abyss (2.2.4-1)
Version: 2.2.4-1+b2
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 27463
Depends: abyss (= 2.2.4-1+b2)
Section: debug
Priority: optional
Description: debug symbols for abyss
Build-Ids: 02cfc00da2b2affe40efb3447d27f9b7f24114e9 092b3b1fbdd5db6937baa54b04ab80d340cb95ac 0cc79b378002d42be50c61b4931e7f31e0993524 0e8375a6598075b07fc9dc627d0d1b284d95d354 0f44b7aecae98fe1553556bcd0801eb1a6cf1c62 170e2261b7fc495617aadce91dff4543ecce6ffd 1ac7db79aa8a727e64ef262332d7fc3978721bb4 1bd662453badcf581a3cb4442bf80da697c3bc50 1c99f00b3a5c31ece08ebffd74b38df4682096ab 23111f2353c6998376148ce46f01e8f02d8c6365 284cf24b6c3ed2a554e2bc6e863b9f1b45c2e8c8 2c4757d66cda2873841d0a893b467b082b060a9a 2f04d70db3861bfa9d607ca5e935115414da0bae 362f57e85d2f31af22c5c295a84cfdc451c88974 408b0ff1b6f3eb2122097985bf73179d8fa86ce9 47d06123eb37c6e7799e917b3b38494e8908a696 47d11ba0a90d9aad00ca3f1e9051a520f56e31fc 485ac542c7105f8581e346cf827a037f85e3df83 4c02d82d97735b5e742f647186b195f36a9aa3a3 4fd0158f0908bc26ffbd848f5565b5257b76ea49 51ff6eafaccf266c9a47639875c2bc7f3036e237 592775fcd589ccb5616240ec7baaa35f5ffa6c1b 5d219aa934b77a7242ce8788f338846579d3c19b 5e7edb2b154ce373227c1944157d4204db378558 6bb39317865b9626977f9cb8842b83454e592cda 72b6fbf735dc2b4f28e2b53846f29cabc29feaaf 76361ce33cb03543dde15b51787018c996fe6831 78fb5f9c59dad301e044739edab86d2672170022 822dca8cdaca2f4103b246cd4b68c1afdb44b205 86ce89aec8bd88391c452368cfa814048a3de57d 8bc0dd9f1d4f12f834e34d9b4f23c361f5e65cd6 92fc04d3fa9672cf5d3eb7039a36c070d1455d24 932881a12d7b9dc64b1aed46162c79c49ba27c54 a304a6609749fc075fd6c24f8b86426b78ce1c41 bfeb165b2688e8dcdd679a5c8118280e554c8a15 c4407976d19e2e72117048b2f6021499eba98a38 c878c1b70856f4db019d8d69ebc497293d797d40 cb8feb5dceab16a742b645172c6f7dfdabce4aef ce12603c5cfee3aec6980e286a4e1c62f1242c9a d0e7cfa8d79381daba5ec524eeae28a39e37bf97 d4b583177379524a301c7eaf18c347df6f201e72 f0949a16e6de03016a4c09ba863fe61d85655ce4
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lrwxrwxrwx root/root 0 2020-02-11 14:39 ./usr/share/doc/abyss-dbgsym -> abyss
abyss_2.2.4-1+b2_armhf.deb
--------------------------
new Debian package, version 2.0.
size 2742732 bytes: control archive=2720 bytes.
732 bytes, 15 lines control
4987 bytes, 79 lines md5sums
Package: abyss
Source: abyss (2.2.4-1)
Version: 2.2.4-1+b2
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 7925
Depends: make, libc6 (>= 2.29), libgcc-s1 (>= 3.5), libgomp1 (>= 4.9), libopenmpi3 (>= 4.0.4), libsqlite3-0 (>= 3.5.9), libstdc++6 (>= 9), perl:any, bsdmainutils, 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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-rw-r--r-- root/root 7012 2020-01-30 19:54 ./usr/share/doc/abyss/copyright
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-rw-r--r-- root/root 672 2019-08-08 14:47 ./usr/share/doc/abyss/run-unit-test
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drwxr-xr-x root/root 0 2020-02-11 14:39 ./usr/share/man/
drwxr-xr-x root/root 0 2020-02-11 14:39 ./usr/share/man/man1/
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-rw-r--r-- root/root 1023 2020-02-11 14:39 ./usr/share/man/man1/DistanceEst.1.gz
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-rw-r--r-- root/root 3562 2020-02-11 14:39 ./usr/share/man/man1/abyss-pe.1.gz
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+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 681944
Build-Time: 3211
Distribution: bullseye-staging
Host Architecture: armhf
Install-Time: 674
Job: abyss_2.2.4-1
Machine Architecture: armhf
Package: abyss
Package-Time: 3936
Source-Version: 2.2.4-1
Space: 681944
Status: successful
Version: 2.2.4-1+b2
--------------------------------------------------------------------------------
Finished at 2020-07-21T06:50:43Z
Build needed 01:05:36, 681944k disc space