seer →
1.1.0-1 →
armhf → 2016-04-08 08:47:14
sbuild (Debian sbuild) 0.66.0 (04 Oct 2015) on testbuildd.raspbian.org
+==============================================================================+
| seer 1.1.0-1 (armhf) 08 Apr 2016 08:10 |
+==============================================================================+
Package: seer
Version: 1.1.0-1
Source Version: 1.1.0-1
Distribution: stretch-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'build/seer-gHhqxi/seer-1.1.0' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/seer-gHhqxi' with '<<BUILDDIR>>'
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/stretch-staging-armhf-sbuild-a601e131-4865-4b77-96d7-ca12c875b6f2' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private stretch-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private stretch-staging/main Sources [8886 kB]
Get:3 http://172.17.0.1/private stretch-staging/main armhf Packages [11.0 MB]
Fetched 19.9 MB in 24s (811 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: 'seer' packaging is maintained in the 'Svn' version control system at:
svn://anonscm.debian.org/debian-med/trunk/packages/seer/trunk/
Need to get 130 kB of source archives.
Get:1 http://172.17.0.1/private stretch-staging/main seer 1.1.0-1 (dsc) [2002 B]
Get:2 http://172.17.0.1/private stretch-staging/main seer 1.1.0-1 (tar) [122 kB]
Get:3 http://172.17.0.1/private stretch-staging/main seer 1.1.0-1 (diff) [5580 B]
Fetched 130 kB in 0s (751 kB/s)
Download complete and in download only mode
Check architectures
-------------------
Check dependencies
------------------
Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<<BUILDDIR>>/resolver-G8pMUr/apt_archive/sbuild-build-depends-core-dummy.deb'.
OK
Get:1 file:/<<BUILDDIR>>/resolver-G8pMUr/apt_archive ./ InRelease
Ign:1 file:/<<BUILDDIR>>/resolver-G8pMUr/apt_archive ./ InRelease
Get:2 file:/<<BUILDDIR>>/resolver-G8pMUr/apt_archive ./ Release [2119 B]
Get:2 file:/<<BUILDDIR>>/resolver-G8pMUr/apt_archive ./ Release [2119 B]
Get:3 file:/<<BUILDDIR>>/resolver-G8pMUr/apt_archive ./ Release.gpg [299 B]
Get:3 file:/<<BUILDDIR>>/resolver-G8pMUr/apt_archive ./ Release.gpg [299 B]
Get:4 file:/<<BUILDDIR>>/resolver-G8pMUr/apt_archive ./ Sources [214 B]
Get:5 file:/<<BUILDDIR>>/resolver-G8pMUr/apt_archive ./ Packages [528 B]
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 NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 48 not upgraded.
Need to get 0 B/768 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 file:/<<BUILDDIR>>/resolver-G8pMUr/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [768 B]
debconf: delaying package configuration, since apt-utils is not installed
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ...
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 12648 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy.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
Merged Build-Depends: debhelper (>= 9), libarmadillo-dev, libdlib-dev, libhdf5-dev, libgzstream-dev, libboost-dev, libboost-program-options-dev
Filtered Build-Depends: debhelper (>= 9), libarmadillo-dev, libdlib-dev, libhdf5-dev, libgzstream-dev, libboost-dev, libboost-program-options-dev
dpkg-deb: building package 'sbuild-build-depends-seer-dummy' in '/<<BUILDDIR>>/resolver-SlLU83/apt_archive/sbuild-build-depends-seer-dummy.deb'.
OK
Get:1 file:/<<BUILDDIR>>/resolver-SlLU83/apt_archive ./ InRelease
Ign:1 file:/<<BUILDDIR>>/resolver-SlLU83/apt_archive ./ InRelease
Get:2 file:/<<BUILDDIR>>/resolver-SlLU83/apt_archive ./ Release [2119 B]
Get:2 file:/<<BUILDDIR>>/resolver-SlLU83/apt_archive ./ Release [2119 B]
Get:3 file:/<<BUILDDIR>>/resolver-SlLU83/apt_archive ./ Release.gpg [299 B]
Get:3 file:/<<BUILDDIR>>/resolver-SlLU83/apt_archive ./ Release.gpg [299 B]
Get:4 file:/<<BUILDDIR>>/resolver-SlLU83/apt_archive ./ Sources [255 B]
Get:5 file:/<<BUILDDIR>>/resolver-SlLU83/apt_archive ./ Packages [571 B]
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
+------------------------------------------------------------------------------+
| Install seer build dependencies (apt-based resolver) |
+------------------------------------------------------------------------------+
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following additional packages will be installed:
autotools-dev bsdmainutils cpp-5 debhelper dh-strip-nondeterminism file
g++-5 gcc-5 gcc-5-base gettext gettext-base gfortran gfortran-5 groff-base
hdf5-helpers intltool-debian libaec-dev libaec0 libarchive-zip-perl
libarmadillo-dev libarmadillo6 libarpack2 libarpack2-dev libasan2 libatomic1
libblas-common libblas-dev libblas3 libboost-dev
libboost-program-options-dev libboost-program-options1.58-dev
libboost-program-options1.58.0 libboost1.58-dev libbsd0 libcc1-0 libcroco3
libdlib-data libdlib-dev libdlib18 libffi6 libfile-stripnondeterminism-perl
libgcc-5-dev libgcc1 libgfortran-5-dev libgfortran3 libglib2.0-0 libgomp1
libgzstream-dev libgzstream0 libhdf5-10 libhdf5-cpp-11 libhdf5-dev libicu55
libjpeg-dev libjpeg62-turbo libjpeg62-turbo-dev liblapack-dev liblapack3
libmagic1 libpipeline1 libsqlite3-0 libstdc++-5-dev libstdc++6
libsuperlu-dev libsuperlu4 libsz2 libtimedate-perl libubsan0 libunistring0
libxml2 man-db po-debconf zlib1g-dev
Suggested packages:
wamerican | wordlist whois vacation gcc-5-locales dh-make gcc-5-doc
libstdc++6-5-dbg libgcc1-dbg libgomp1-dbg libitm1-dbg libatomic1-dbg
libasan2-dbg liblsan0-dbg libtsan0-dbg libubsan0-dbg libcilkrts5-dbg
libmpx0-dbg libquadmath0-dbg gettext-doc autopoint libasprintf-dev
libgettextpo-dev gfortran-doc gfortran-5-doc libgfortran3-dbg groff
libitpp-dev liblapack-doc-man liblapack-doc libboost-doc libboost1.58-doc
libboost-atomic1.58-dev libboost-chrono1.58-dev libboost-context1.58-dev
libboost-coroutine1.58-dev libboost-date-time1.58-dev
libboost-exception1.58-dev libboost-filesystem1.58-dev
libboost-graph1.58-dev libboost-graph-parallel1.58-dev
libboost-iostreams1.58-dev libboost-locale1.58-dev libboost-log1.58-dev
libboost-math1.58-dev libboost-mpi1.58-dev libboost-mpi-python1.58-dev
libboost-python1.58-dev libboost-random1.58-dev libboost-regex1.58-dev
libboost-serialization1.58-dev libboost-signals1.58-dev
libboost-system1.58-dev libboost-test1.58-dev libboost-thread1.58-dev
libboost-timer1.58-dev libboost-wave1.58-dev libboost1.58-tools-dev
libmpfrc++-dev libntl-dev libhdf5-doc libstdc++-5-doc libsuperlu-doc less
www-browser libmail-box-perl
Recommended packages:
curl | wget | lynx-cur libglib2.0-data shared-mime-info xdg-user-dirs
xml-core libmail-sendmail-perl
The following NEW packages will be installed:
autotools-dev bsdmainutils debhelper dh-strip-nondeterminism file gettext
gettext-base gfortran gfortran-5 groff-base hdf5-helpers intltool-debian
libaec-dev libaec0 libarchive-zip-perl libarmadillo-dev libarmadillo6
libarpack2 libarpack2-dev libblas-common libblas-dev libblas3 libboost-dev
libboost-program-options-dev libboost-program-options1.58-dev
libboost-program-options1.58.0 libboost1.58-dev libbsd0 libcroco3
libdlib-data libdlib-dev libdlib18 libffi6 libfile-stripnondeterminism-perl
libgfortran-5-dev libgfortran3 libglib2.0-0 libgzstream-dev libgzstream0
libhdf5-10 libhdf5-cpp-11 libhdf5-dev libicu55 libjpeg-dev libjpeg62-turbo
libjpeg62-turbo-dev liblapack-dev liblapack3 libmagic1 libpipeline1
libsqlite3-0 libsuperlu-dev libsuperlu4 libsz2 libtimedate-perl
libunistring0 libxml2 man-db po-debconf sbuild-build-depends-seer-dummy
zlib1g-dev
The following packages will be upgraded:
cpp-5 g++-5 gcc-5 gcc-5-base libasan2 libatomic1 libcc1-0 libgcc-5-dev
libgcc1 libgomp1 libstdc++-5-dev libstdc++6 libubsan0
13 upgraded, 61 newly installed, 0 to remove and 35 not upgraded.
Need to get 196 MB/196 MB of archives.
After this operation, 424 MB of additional disk space will be used.
Get:1 file:/<<BUILDDIR>>/resolver-SlLU83/apt_archive ./ sbuild-build-depends-seer-dummy 0.invalid.0 [814 B]
Get:2 http://172.17.0.1/private stretch-staging/main armhf libgomp1 armhf 5.3.1-13 [47.3 kB]
Get:3 http://172.17.0.1/private stretch-staging/main armhf libatomic1 armhf 5.3.1-13 [6562 B]
Get:4 http://172.17.0.1/private stretch-staging/main armhf gcc-5-base armhf 5.3.1-13 [170 kB]
Get:5 http://172.17.0.1/private stretch-staging/main armhf libgcc1 armhf 1:5.3.1-13 [38.5 kB]
Get:6 http://172.17.0.1/private stretch-staging/main armhf libasan2 armhf 5.3.1-13 [227 kB]
Get:7 http://172.17.0.1/private stretch-staging/main armhf libubsan0 armhf 5.3.1-13 [84.3 kB]
Get:8 http://172.17.0.1/private stretch-staging/main armhf cpp-5 armhf 5.3.1-13 [22.9 MB]
Get:9 http://172.17.0.1/private stretch-staging/main armhf libcc1-0 armhf 5.3.1-13 [24.8 kB]
Get:10 http://172.17.0.1/private stretch-staging/main armhf g++-5 armhf 5.3.1-13 [24.5 MB]
Get:11 http://172.17.0.1/private stretch-staging/main armhf gcc-5 armhf 5.3.1-13 [22.9 MB]
Get:12 http://172.17.0.1/private stretch-staging/main armhf libgcc-5-dev armhf 5.3.1-13 [450 kB]
Get:13 http://172.17.0.1/private stretch-staging/main armhf libstdc++-5-dev armhf 5.3.1-13 [1431 kB]
Get:14 http://172.17.0.1/private stretch-staging/main armhf libstdc++6 armhf 5.3.1-13 [326 kB]
Get:15 http://172.17.0.1/private stretch-staging/main armhf groff-base armhf 1.22.3-7 [1083 kB]
Get:16 http://172.17.0.1/private stretch-staging/main armhf libbsd0 armhf 0.8.2-1 [88.0 kB]
Get:17 http://172.17.0.1/private stretch-staging/main armhf bsdmainutils armhf 9.0.10 [177 kB]
Get:18 http://172.17.0.1/private stretch-staging/main armhf libpipeline1 armhf 1.4.1-2 [23.7 kB]
Get:19 http://172.17.0.1/private stretch-staging/main armhf man-db armhf 2.7.5-1 [975 kB]
Get:20 http://172.17.0.1/private stretch-staging/main armhf libgfortran3 armhf 5.3.1-13 [153 kB]
Get:21 http://172.17.0.1/private stretch-staging/main armhf libblas-common armhf 3.6.0-2 [13.5 kB]
Get:22 http://172.17.0.1/private stretch-staging/main armhf libblas3 armhf 3.6.0-2 [110 kB]
Get:23 http://172.17.0.1/private stretch-staging/main armhf libsuperlu4 armhf 4.3+dfsg-3 [136 kB]
Get:24 http://172.17.0.1/private stretch-staging/main armhf libunistring0 armhf 0.9.3-5.2 [253 kB]
Get:25 http://172.17.0.1/private stretch-staging/main armhf libmagic1 armhf 1:5.25-2 [250 kB]
Get:26 http://172.17.0.1/private stretch-staging/main armhf file armhf 1:5.25-2 [61.2 kB]
Get:27 http://172.17.0.1/private stretch-staging/main armhf gettext-base armhf 0.19.7-2 [111 kB]
Get:28 http://172.17.0.1/private stretch-staging/main armhf libsqlite3-0 armhf 3.11.1-1 [457 kB]
Get:29 http://172.17.0.1/private stretch-staging/main armhf libicu55 armhf 55.1-7 [7380 kB]
Get:30 http://172.17.0.1/private stretch-staging/main armhf libxml2 armhf 2.9.3+dfsg1-1 [800 kB]
Get:31 http://172.17.0.1/private stretch-staging/main armhf autotools-dev all 20150820.1 [71.7 kB]
Get:32 http://172.17.0.1/private stretch-staging/main armhf libffi6 armhf 3.2.1-4 [18.5 kB]
Get:33 http://172.17.0.1/private stretch-staging/main armhf libglib2.0-0 armhf 2.48.0-1 [2540 kB]
Get:34 http://172.17.0.1/private stretch-staging/main armhf libcroco3 armhf 0.6.11-1 [131 kB]
Get:35 http://172.17.0.1/private stretch-staging/main armhf gettext armhf 0.19.7-2 [1400 kB]
Get:36 http://172.17.0.1/private stretch-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:37 http://172.17.0.1/private stretch-staging/main armhf po-debconf all 1.0.19 [249 kB]
Get:38 http://172.17.0.1/private stretch-staging/main armhf libarchive-zip-perl all 1.57-1 [95.1 kB]
Get:39 http://172.17.0.1/private stretch-staging/main armhf libfile-stripnondeterminism-perl all 0.016-1 [11.9 kB]
Get:40 http://172.17.0.1/private stretch-staging/main armhf libtimedate-perl all 2.3000-2 [42.2 kB]
Get:41 http://172.17.0.1/private stretch-staging/main armhf dh-strip-nondeterminism all 0.016-1 [6998 B]
Get:42 http://172.17.0.1/private stretch-staging/main armhf debhelper all 9.20160313 [808 kB]
Get:43 http://172.17.0.1/private stretch-staging/main armhf libgfortran-5-dev armhf 5.3.1-13 [182 kB]
Get:44 http://172.17.0.1/private stretch-staging/main armhf gfortran-5 armhf 5.3.1-13 [23.7 MB]
Get:45 http://172.17.0.1/private stretch-staging/main armhf gfortran armhf 4:5.3.1-1+rpi1 [1362 B]
Get:46 http://172.17.0.1/private stretch-staging/main armhf hdf5-helpers armhf 1.8.16+docs-6+b1 [35.5 kB]
Get:47 http://172.17.0.1/private stretch-staging/main armhf libaec0 armhf 0.3.2-1 [19.4 kB]
Get:48 http://172.17.0.1/private stretch-staging/main armhf liblapack3 armhf 3.6.0-2 [1382 kB]
Get:49 http://172.17.0.1/private stretch-staging/main armhf libarpack2 armhf 3.3.0-1+b1 [78.1 kB]
Get:50 http://172.17.0.1/private stretch-staging/main armhf libarmadillo6 armhf 1:6.500.5+dfsg-1 [76.5 kB]
Get:51 http://172.17.0.1/private stretch-staging/main armhf libblas-dev armhf 3.6.0-2 [116 kB]
Get:52 http://172.17.0.1/private stretch-staging/main armhf liblapack-dev armhf 3.6.0-2 [1355 kB]
Get:53 http://172.17.0.1/private stretch-staging/main armhf libarpack2-dev armhf 3.3.0-1+b1 [89.3 kB]
Get:54 http://172.17.0.1/private stretch-staging/main armhf libsz2 armhf 0.3.2-1 [5836 B]
Get:55 http://172.17.0.1/private stretch-staging/main armhf libhdf5-10 armhf 1.8.16+docs-6+b1 [980 kB]
Get:56 http://172.17.0.1/private stretch-staging/main armhf zlib1g-dev armhf 1:1.2.8.dfsg-2+b1 [197 kB]
Get:57 http://172.17.0.1/private stretch-staging/main armhf libjpeg62-turbo armhf 1:1.4.2-2 [104 kB]
Get:58 http://172.17.0.1/private stretch-staging/main armhf libjpeg62-turbo-dev armhf 1:1.4.2-2 [413 kB]
Get:59 http://172.17.0.1/private stretch-staging/main armhf libjpeg-dev all 1:1.4.2-2 [51.7 kB]
Get:60 http://172.17.0.1/private stretch-staging/main armhf libaec-dev armhf 0.3.2-1 [17.6 kB]
Get:61 http://172.17.0.1/private stretch-staging/main armhf libhdf5-cpp-11 armhf 1.8.16+docs-6+b1 [116 kB]
Get:62 http://172.17.0.1/private stretch-staging/main armhf libhdf5-dev armhf 1.8.16+docs-6+b1 [4906 kB]
Get:63 http://172.17.0.1/private stretch-staging/main armhf libsuperlu-dev armhf 4.3+dfsg-3 [150 kB]
Get:64 http://172.17.0.1/private stretch-staging/main armhf libarmadillo-dev armhf 1:6.500.5+dfsg-1 [299 kB]
Get:65 http://172.17.0.1/private stretch-staging/main armhf libboost1.58-dev armhf 1.58.0+dfsg-5+b1 [6232 kB]
Get:66 http://172.17.0.1/private stretch-staging/main armhf libboost-dev armhf 1.58.0.1+b1 [3748 B]
Get:67 http://172.17.0.1/private stretch-staging/main armhf libboost-program-options1.58.0 armhf 1.58.0+dfsg-5+b1 [137 kB]
Get:68 http://172.17.0.1/private stretch-staging/main armhf libboost-program-options1.58-dev armhf 1.58.0+dfsg-5+b1 [182 kB]
Get:69 http://172.17.0.1/private stretch-staging/main armhf libboost-program-options-dev armhf 1.58.0.1+b1 [3404 B]
Get:70 http://172.17.0.1/private stretch-staging/main armhf libdlib-data all 18.18-1 [63.3 MB]
Get:71 http://172.17.0.1/private stretch-staging/main armhf libdlib18 armhf 18.18-1 [223 kB]
Get:72 http://172.17.0.1/private stretch-staging/main armhf libdlib-dev armhf 18.18-1 [1067 kB]
Get:73 http://172.17.0.1/private stretch-staging/main armhf libgzstream0 armhf 1.5+dfsg-1 [5682 B]
Get:74 http://172.17.0.1/private stretch-staging/main armhf libgzstream-dev armhf 1.5+dfsg-1 [6060 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 196 MB in 1min 14s (2614 kB/s)
(Reading database ...
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 12648 files and directories currently installed.)
Preparing to unpack .../libgomp1_5.3.1-13_armhf.deb ...
Unpacking libgomp1:armhf (5.3.1-13) over (5.3.1-11) ...
Preparing to unpack .../libatomic1_5.3.1-13_armhf.deb ...
Unpacking libatomic1:armhf (5.3.1-13) over (5.3.1-11) ...
Preparing to unpack .../gcc-5-base_5.3.1-13_armhf.deb ...
Unpacking gcc-5-base:armhf (5.3.1-13) over (5.3.1-11) ...
Processing triggers for libc-bin (2.22-3) ...
Setting up gcc-5-base:armhf (5.3.1-13) ...
(Reading database ...
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 12648 files and directories currently installed.)
Preparing to unpack .../libgcc1_1%3a5.3.1-13_armhf.deb ...
Unpacking libgcc1:armhf (1:5.3.1-13) over (1:5.3.1-11) ...
Processing triggers for libc-bin (2.22-3) ...
Setting up libgcc1:armhf (1:5.3.1-13) ...
Processing triggers for libc-bin (2.22-3) ...
(Reading database ...
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 12648 files and directories currently installed.)
Preparing to unpack .../libasan2_5.3.1-13_armhf.deb ...
Unpacking libasan2:armhf (5.3.1-13) over (5.3.1-11) ...
Preparing to unpack .../libubsan0_5.3.1-13_armhf.deb ...
Unpacking libubsan0:armhf (5.3.1-13) over (5.3.1-11) ...
Preparing to unpack .../cpp-5_5.3.1-13_armhf.deb ...
Unpacking cpp-5 (5.3.1-13) over (5.3.1-11) ...
Preparing to unpack .../libcc1-0_5.3.1-13_armhf.deb ...
Unpacking libcc1-0:armhf (5.3.1-13) over (5.3.1-11) ...
Preparing to unpack .../g++-5_5.3.1-13_armhf.deb ...
Unpacking g++-5 (5.3.1-13) over (5.3.1-11) ...
Preparing to unpack .../gcc-5_5.3.1-13_armhf.deb ...
Unpacking gcc-5 (5.3.1-13) over (5.3.1-11) ...
Preparing to unpack .../libgcc-5-dev_5.3.1-13_armhf.deb ...
Unpacking libgcc-5-dev:armhf (5.3.1-13) over (5.3.1-11) ...
Preparing to unpack .../libstdc++-5-dev_5.3.1-13_armhf.deb ...
Unpacking libstdc++-5-dev:armhf (5.3.1-13) over (5.3.1-11) ...
Preparing to unpack .../libstdc++6_5.3.1-13_armhf.deb ...
Unpacking libstdc++6:armhf (5.3.1-13) over (5.3.1-11) ...
Processing triggers for libc-bin (2.22-3) ...
Setting up libstdc++6:armhf (5.3.1-13) ...
Processing triggers for libc-bin (2.22-3) ...
Selecting previously unselected package groff-base.
(Reading database ...
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 12648 files and directories currently installed.)
Preparing to unpack .../groff-base_1.22.3-7_armhf.deb ...
Unpacking groff-base (1.22.3-7) ...
Selecting previously unselected package libbsd0:armhf.
Preparing to unpack .../libbsd0_0.8.2-1_armhf.deb ...
Unpacking libbsd0:armhf (0.8.2-1) ...
Selecting previously unselected package bsdmainutils.
Preparing to unpack .../bsdmainutils_9.0.10_armhf.deb ...
Unpacking bsdmainutils (9.0.10) ...
Selecting previously unselected package libpipeline1:armhf.
Preparing to unpack .../libpipeline1_1.4.1-2_armhf.deb ...
Unpacking libpipeline1:armhf (1.4.1-2) ...
Selecting previously unselected package man-db.
Preparing to unpack .../man-db_2.7.5-1_armhf.deb ...
Unpacking man-db (2.7.5-1) ...
Selecting previously unselected package libgfortran3:armhf.
Preparing to unpack .../libgfortran3_5.3.1-13_armhf.deb ...
Unpacking libgfortran3:armhf (5.3.1-13) ...
Selecting previously unselected package libblas-common.
Preparing to unpack .../libblas-common_3.6.0-2_armhf.deb ...
Unpacking libblas-common (3.6.0-2) ...
Selecting previously unselected package libblas3.
Preparing to unpack .../libblas3_3.6.0-2_armhf.deb ...
Unpacking libblas3 (3.6.0-2) ...
Selecting previously unselected package libsuperlu4:armhf.
Preparing to unpack .../libsuperlu4_4.3+dfsg-3_armhf.deb ...
Unpacking libsuperlu4:armhf (4.3+dfsg-3) ...
Selecting previously unselected package libunistring0:armhf.
Preparing to unpack .../libunistring0_0.9.3-5.2_armhf.deb ...
Unpacking libunistring0:armhf (0.9.3-5.2) ...
Selecting previously unselected package libmagic1:armhf.
Preparing to unpack .../libmagic1_1%3a5.25-2_armhf.deb ...
Unpacking libmagic1:armhf (1:5.25-2) ...
Selecting previously unselected package file.
Preparing to unpack .../file_1%3a5.25-2_armhf.deb ...
Unpacking file (1:5.25-2) ...
Selecting previously unselected package gettext-base.
Preparing to unpack .../gettext-base_0.19.7-2_armhf.deb ...
Unpacking gettext-base (0.19.7-2) ...
Selecting previously unselected package libsqlite3-0:armhf.
Preparing to unpack .../libsqlite3-0_3.11.1-1_armhf.deb ...
Unpacking libsqlite3-0:armhf (3.11.1-1) ...
Selecting previously unselected package libicu55:armhf.
Preparing to unpack .../libicu55_55.1-7_armhf.deb ...
Unpacking libicu55:armhf (55.1-7) ...
Selecting previously unselected package libxml2:armhf.
Preparing to unpack .../libxml2_2.9.3+dfsg1-1_armhf.deb ...
Unpacking libxml2:armhf (2.9.3+dfsg1-1) ...
Selecting previously unselected package autotools-dev.
Preparing to unpack .../autotools-dev_20150820.1_all.deb ...
Unpacking autotools-dev (20150820.1) ...
Selecting previously unselected package libffi6:armhf.
Preparing to unpack .../libffi6_3.2.1-4_armhf.deb ...
Unpacking libffi6:armhf (3.2.1-4) ...
Selecting previously unselected package libglib2.0-0:armhf.
Preparing to unpack .../libglib2.0-0_2.48.0-1_armhf.deb ...
Unpacking libglib2.0-0:armhf (2.48.0-1) ...
Selecting previously unselected package libcroco3:armhf.
Preparing to unpack .../libcroco3_0.6.11-1_armhf.deb ...
Unpacking libcroco3:armhf (0.6.11-1) ...
Selecting previously unselected package gettext.
Preparing to unpack .../gettext_0.19.7-2_armhf.deb ...
Unpacking gettext (0.19.7-2) ...
Selecting previously unselected package intltool-debian.
Preparing to unpack .../intltool-debian_0.35.0+20060710.4_all.deb ...
Unpacking intltool-debian (0.35.0+20060710.4) ...
Selecting previously unselected package po-debconf.
Preparing to unpack .../po-debconf_1.0.19_all.deb ...
Unpacking po-debconf (1.0.19) ...
Selecting previously unselected package libarchive-zip-perl.
Preparing to unpack .../libarchive-zip-perl_1.57-1_all.deb ...
Unpacking libarchive-zip-perl (1.57-1) ...
Selecting previously unselected package libfile-stripnondeterminism-perl.
Preparing to unpack .../libfile-stripnondeterminism-perl_0.016-1_all.deb ...
Unpacking libfile-stripnondeterminism-perl (0.016-1) ...
Selecting previously unselected package libtimedate-perl.
Preparing to unpack .../libtimedate-perl_2.3000-2_all.deb ...
Unpacking libtimedate-perl (2.3000-2) ...
Selecting previously unselected package dh-strip-nondeterminism.
Preparing to unpack .../dh-strip-nondeterminism_0.016-1_all.deb ...
Unpacking dh-strip-nondeterminism (0.016-1) ...
Selecting previously unselected package debhelper.
Preparing to unpack .../debhelper_9.20160313_all.deb ...
Unpacking debhelper (9.20160313) ...
Selecting previously unselected package libgfortran-5-dev:armhf.
Preparing to unpack .../libgfortran-5-dev_5.3.1-13_armhf.deb ...
Unpacking libgfortran-5-dev:armhf (5.3.1-13) ...
Selecting previously unselected package gfortran-5.
Preparing to unpack .../gfortran-5_5.3.1-13_armhf.deb ...
Unpacking gfortran-5 (5.3.1-13) ...
Selecting previously unselected package gfortran.
Preparing to unpack .../gfortran_4%3a5.3.1-1+rpi1_armhf.deb ...
Unpacking gfortran (4:5.3.1-1+rpi1) ...
Selecting previously unselected package hdf5-helpers.
Preparing to unpack .../hdf5-helpers_1.8.16+docs-6+b1_armhf.deb ...
Unpacking hdf5-helpers (1.8.16+docs-6+b1) ...
Selecting previously unselected package libaec0:armhf.
Preparing to unpack .../libaec0_0.3.2-1_armhf.deb ...
Unpacking libaec0:armhf (0.3.2-1) ...
Selecting previously unselected package liblapack3.
Preparing to unpack .../liblapack3_3.6.0-2_armhf.deb ...
Unpacking liblapack3 (3.6.0-2) ...
Selecting previously unselected package libarpack2.
Preparing to unpack .../libarpack2_3.3.0-1+b1_armhf.deb ...
Unpacking libarpack2 (3.3.0-1+b1) ...
Selecting previously unselected package libarmadillo6.
Preparing to unpack .../libarmadillo6_1%3a6.500.5+dfsg-1_armhf.deb ...
Unpacking libarmadillo6 (1:6.500.5+dfsg-1) ...
Selecting previously unselected package libblas-dev.
Preparing to unpack .../libblas-dev_3.6.0-2_armhf.deb ...
Unpacking libblas-dev (3.6.0-2) ...
Selecting previously unselected package liblapack-dev.
Preparing to unpack .../liblapack-dev_3.6.0-2_armhf.deb ...
Unpacking liblapack-dev (3.6.0-2) ...
Selecting previously unselected package libarpack2-dev.
Preparing to unpack .../libarpack2-dev_3.3.0-1+b1_armhf.deb ...
Unpacking libarpack2-dev (3.3.0-1+b1) ...
Selecting previously unselected package libsz2:armhf.
Preparing to unpack .../libsz2_0.3.2-1_armhf.deb ...
Unpacking libsz2:armhf (0.3.2-1) ...
Selecting previously unselected package libhdf5-10:armhf.
Preparing to unpack .../libhdf5-10_1.8.16+docs-6+b1_armhf.deb ...
Unpacking libhdf5-10:armhf (1.8.16+docs-6+b1) ...
Selecting previously unselected package zlib1g-dev:armhf.
Preparing to unpack .../zlib1g-dev_1%3a1.2.8.dfsg-2+b1_armhf.deb ...
Unpacking zlib1g-dev:armhf (1:1.2.8.dfsg-2+b1) ...
Selecting previously unselected package libjpeg62-turbo:armhf.
Preparing to unpack .../libjpeg62-turbo_1%3a1.4.2-2_armhf.deb ...
Unpacking libjpeg62-turbo:armhf (1:1.4.2-2) ...
Selecting previously unselected package libjpeg62-turbo-dev:armhf.
Preparing to unpack .../libjpeg62-turbo-dev_1%3a1.4.2-2_armhf.deb ...
Unpacking libjpeg62-turbo-dev:armhf (1:1.4.2-2) ...
Selecting previously unselected package libjpeg-dev.
Preparing to unpack .../libjpeg-dev_1%3a1.4.2-2_all.deb ...
Unpacking libjpeg-dev (1:1.4.2-2) ...
Selecting previously unselected package libaec-dev:armhf.
Preparing to unpack .../libaec-dev_0.3.2-1_armhf.deb ...
Unpacking libaec-dev:armhf (0.3.2-1) ...
Selecting previously unselected package libhdf5-cpp-11:armhf.
Preparing to unpack .../libhdf5-cpp-11_1.8.16+docs-6+b1_armhf.deb ...
Unpacking libhdf5-cpp-11:armhf (1.8.16+docs-6+b1) ...
Selecting previously unselected package libhdf5-dev.
Preparing to unpack .../libhdf5-dev_1.8.16+docs-6+b1_armhf.deb ...
Unpacking libhdf5-dev (1.8.16+docs-6+b1) ...
Selecting previously unselected package libsuperlu-dev:armhf.
Preparing to unpack .../libsuperlu-dev_4.3+dfsg-3_armhf.deb ...
Unpacking libsuperlu-dev:armhf (4.3+dfsg-3) ...
Selecting previously unselected package libarmadillo-dev.
Preparing to unpack .../libarmadillo-dev_1%3a6.500.5+dfsg-1_armhf.deb ...
Unpacking libarmadillo-dev (1:6.500.5+dfsg-1) ...
Selecting previously unselected package libboost1.58-dev:armhf.
Preparing to unpack .../libboost1.58-dev_1.58.0+dfsg-5+b1_armhf.deb ...
Unpacking libboost1.58-dev:armhf (1.58.0+dfsg-5+b1) ...
Selecting previously unselected package libboost-dev:armhf.
Preparing to unpack .../libboost-dev_1.58.0.1+b1_armhf.deb ...
Unpacking libboost-dev:armhf (1.58.0.1+b1) ...
Selecting previously unselected package libboost-program-options1.58.0:armhf.
Preparing to unpack .../libboost-program-options1.58.0_1.58.0+dfsg-5+b1_armhf.deb ...
Unpacking libboost-program-options1.58.0:armhf (1.58.0+dfsg-5+b1) ...
Selecting previously unselected package libboost-program-options1.58-dev:armhf.
Preparing to unpack .../libboost-program-options1.58-dev_1.58.0+dfsg-5+b1_armhf.deb ...
Unpacking libboost-program-options1.58-dev:armhf (1.58.0+dfsg-5+b1) ...
Selecting previously unselected package libboost-program-options-dev:armhf.
Preparing to unpack .../libboost-program-options-dev_1.58.0.1+b1_armhf.deb ...
Unpacking libboost-program-options-dev:armhf (1.58.0.1+b1) ...
Selecting previously unselected package libdlib-data.
Preparing to unpack .../libdlib-data_18.18-1_all.deb ...
Unpacking libdlib-data (18.18-1) ...
Selecting previously unselected package libdlib18.
Preparing to unpack .../libdlib18_18.18-1_armhf.deb ...
Unpacking libdlib18 (18.18-1) ...
Selecting previously unselected package libdlib-dev.
Preparing to unpack .../libdlib-dev_18.18-1_armhf.deb ...
Unpacking libdlib-dev (18.18-1) ...
Selecting previously unselected package libgzstream0.
Preparing to unpack .../libgzstream0_1.5+dfsg-1_armhf.deb ...
Unpacking libgzstream0 (1.5+dfsg-1) ...
Selecting previously unselected package libgzstream-dev.
Preparing to unpack .../libgzstream-dev_1.5+dfsg-1_armhf.deb ...
Unpacking libgzstream-dev (1.5+dfsg-1) ...
Selecting previously unselected package sbuild-build-depends-seer-dummy.
Preparing to unpack .../sbuild-build-depends-seer-dummy.deb ...
Unpacking sbuild-build-depends-seer-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.22-3) ...
Setting up libgomp1:armhf (5.3.1-13) ...
Setting up libatomic1:armhf (5.3.1-13) ...
Setting up libasan2:armhf (5.3.1-13) ...
Setting up libubsan0:armhf (5.3.1-13) ...
Setting up cpp-5 (5.3.1-13) ...
Setting up libcc1-0:armhf (5.3.1-13) ...
Setting up libgcc-5-dev:armhf (5.3.1-13) ...
Setting up gcc-5 (5.3.1-13) ...
Setting up libstdc++-5-dev:armhf (5.3.1-13) ...
Setting up g++-5 (5.3.1-13) ...
Setting up groff-base (1.22.3-7) ...
Setting up libbsd0:armhf (0.8.2-1) ...
Setting up bsdmainutils (9.0.10) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
Setting up libpipeline1:armhf (1.4.1-2) ...
Setting up man-db (2.7.5-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libgfortran3:armhf (5.3.1-13) ...
Setting up libblas-common (3.6.0-2) ...
Setting up libblas3 (3.6.0-2) ...
update-alternatives: using /usr/lib/libblas/libblas.so.3 to provide /usr/lib/libblas.so.3 (libblas.so.3) in auto mode
Setting up libsuperlu4:armhf (4.3+dfsg-3) ...
Setting up libunistring0:armhf (0.9.3-5.2) ...
Setting up libmagic1:armhf (1:5.25-2) ...
Setting up file (1:5.25-2) ...
Setting up gettext-base (0.19.7-2) ...
Setting up libsqlite3-0:armhf (3.11.1-1) ...
Setting up libicu55:armhf (55.1-7) ...
Setting up libxml2:armhf (2.9.3+dfsg1-1) ...
Setting up autotools-dev (20150820.1) ...
Setting up libffi6:armhf (3.2.1-4) ...
Setting up libglib2.0-0:armhf (2.48.0-1) ...
No schema files found: doing nothing.
Setting up libcroco3:armhf (0.6.11-1) ...
Setting up gettext (0.19.7-2) ...
Setting up intltool-debian (0.35.0+20060710.4) ...
Setting up po-debconf (1.0.19) ...
Setting up libarchive-zip-perl (1.57-1) ...
Setting up libfile-stripnondeterminism-perl (0.016-1) ...
Setting up libtimedate-perl (2.3000-2) ...
Setting up libgfortran-5-dev:armhf (5.3.1-13) ...
Setting up gfortran-5 (5.3.1-13) ...
Setting up gfortran (4:5.3.1-1+rpi1) ...
update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode
update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode
Setting up hdf5-helpers (1.8.16+docs-6+b1) ...
Setting up libaec0:armhf (0.3.2-1) ...
Setting up liblapack3 (3.6.0-2) ...
update-alternatives: using /usr/lib/lapack/liblapack.so.3 to provide /usr/lib/liblapack.so.3 (liblapack.so.3) in auto mode
Setting up libarpack2 (3.3.0-1+b1) ...
Setting up libarmadillo6 (1:6.500.5+dfsg-1) ...
Setting up libblas-dev (3.6.0-2) ...
update-alternatives: using /usr/lib/libblas/libblas.so to provide /usr/lib/libblas.so (libblas.so) in auto mode
Setting up liblapack-dev (3.6.0-2) ...
update-alternatives: using /usr/lib/lapack/liblapack.so to provide /usr/lib/liblapack.so (liblapack.so) in auto mode
Setting up libarpack2-dev (3.3.0-1+b1) ...
Setting up libsz2:armhf (0.3.2-1) ...
Setting up libhdf5-10:armhf (1.8.16+docs-6+b1) ...
Setting up zlib1g-dev:armhf (1:1.2.8.dfsg-2+b1) ...
Setting up libjpeg62-turbo:armhf (1:1.4.2-2) ...
Setting up libjpeg62-turbo-dev:armhf (1:1.4.2-2) ...
Setting up libjpeg-dev (1:1.4.2-2) ...
Setting up libaec-dev:armhf (0.3.2-1) ...
Setting up libhdf5-cpp-11:armhf (1.8.16+docs-6+b1) ...
Setting up libhdf5-dev (1.8.16+docs-6+b1) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/pkgconfig/hdf5-serial.pc to provide /usr/lib/arm-linux-gnueabihf/pkgconfig/hdf5.pc (hdf5.pc) in auto mode
Setting up libsuperlu-dev:armhf (4.3+dfsg-3) ...
Setting up libarmadillo-dev (1:6.500.5+dfsg-1) ...
Setting up libboost1.58-dev:armhf (1.58.0+dfsg-5+b1) ...
Setting up libboost-dev:armhf (1.58.0.1+b1) ...
Setting up libboost-program-options1.58.0:armhf (1.58.0+dfsg-5+b1) ...
Setting up libboost-program-options1.58-dev:armhf (1.58.0+dfsg-5+b1) ...
Setting up libboost-program-options-dev:armhf (1.58.0.1+b1) ...
Setting up libdlib-data (18.18-1) ...
Setting up libdlib18 (18.18-1) ...
Setting up libdlib-dev (18.18-1) ...
Setting up libgzstream0 (1.5+dfsg-1) ...
Setting up libgzstream-dev (1.5+dfsg-1) ...
Setting up debhelper (9.20160313) ...
Setting up sbuild-build-depends-seer-dummy (0.invalid.0) ...
Setting up dh-strip-nondeterminism (0.016-1) ...
Processing triggers for libc-bin (2.22-3) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 3.19.0-trunk-armmp armhf (armv7l)
Toolchain package versions: binutils_2.26-5 dpkg-dev_1.18.4 g++-5_5.3.1-13 gcc-5_5.3.1-13 libc6-dev_2.22-3 libstdc++-5-dev_5.3.1-13 libstdc++6_5.3.1-13 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch
Package versions: adduser_3.114 apt_1.2.6 autotools-dev_20150820.1 base-files_9.5+rpi1 base-passwd_3.5.39 bash_4.3-14 binutils_2.26-5 bsdmainutils_9.0.10 bsdutils_1:2.27.1-6 build-essential_11.7 bzip2_1.0.6-8 coreutils_8.25-2 cpio_2.11+dfsg-5 cpp_4:5.3.1-1+rpi1 cpp-5_5.3.1-13 dash_0.5.8-2.1 debconf_1.5.59 debfoster_2.7-2 debhelper_9.20160313 debianutils_4.7 dh-strip-nondeterminism_0.016-1 diffutils_1:3.3-3 dmsetup_2:1.02.116-1 dpkg_1.18.4 dpkg-dev_1.18.4 e2fslibs_1.42.13-1 e2fsprogs_1.42.13-1 fakeroot_1.20.2-1 file_1:5.25-2 findutils_4.6.0+git+20160126-2 g++_4:5.3.1-1+rpi1 g++-5_5.3.1-13 gcc_4:5.3.1-1+rpi1 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8-base_4.8.5-4 gcc-4.9-base_4.9.3-12 gcc-5_5.3.1-13 gcc-5-base_5.3.1-13 gettext_0.19.7-2 gettext-base_0.19.7-2 gfortran_4:5.3.1-1+rpi1 gfortran-5_5.3.1-13 gnupg_1.4.20-4 gpgv_1.4.20-4 grep_2.22-1 groff-base_1.22.3-7 gzip_1.6-4 hdf5-helpers_1.8.16+docs-6+b1 hostname_3.17 init_1.29 init-system-helpers_1.29 initscripts_2.88dsf-59.3 insserv_1.14.0-5.3 intltool-debian_0.35.0+20060710.4 klibc-utils_2.0.4-8+rpi1 kmod_22-1 libacl1_2.2.52-3 libaec-dev_0.3.2-1 libaec0_0.3.2-1 libapparmor1_2.10-3 libapt-pkg5.0_1.2.6 libarchive-zip-perl_1.57-1 libarmadillo-dev_1:6.500.5+dfsg-1 libarmadillo6_1:6.500.5+dfsg-1 libarpack2_3.3.0-1+b1 libarpack2-dev_3.3.0-1+b1 libasan2_5.3.1-13 libatomic1_5.3.1-13 libattr1_1:2.4.47-2 libaudit-common_1:2.4.5-1 libaudit1_1:2.4.5-1 libblas-common_3.6.0-2 libblas-dev_3.6.0-2 libblas3_3.6.0-2 libblkid1_2.27.1-6 libboost-dev_1.58.0.1+b1 libboost-program-options-dev_1.58.0.1+b1 libboost-program-options1.58-dev_1.58.0+dfsg-5+b1 libboost-program-options1.58.0_1.58.0+dfsg-5+b1 libboost1.58-dev_1.58.0+dfsg-5+b1 libbsd0_0.8.2-1 libbz2-1.0_1.0.6-8 libc-bin_2.22-3 libc-dev-bin_2.22-3 libc6_2.22-3 libc6-dev_2.22-3 libcap2_1:2.24-12 libcap2-bin_1:2.24-12 libcc1-0_5.3.1-13 libcomerr2_1.42.13-1 libcroco3_0.6.11-1 libcryptsetup4_2:1.7.0-2 libdb5.3_5.3.28-11 libdbus-1-3_1.10.8-1 libdebconfclient0_0.207 libdevmapper1.02.1_2:1.02.116-1 libdlib-data_18.18-1 libdlib-dev_18.18-1 libdlib18_18.18-1 libdpkg-perl_1.18.4 libdrm2_2.4.67-1 libfakeroot_1.20.2-1 libfdisk1_2.27.1-6 libffi6_3.2.1-4 libfile-stripnondeterminism-perl_0.016-1 libgc1c2_1:7.4.2-7.3 libgcc-5-dev_5.3.1-13 libgcc1_1:5.3.1-13 libgcrypt20_1.6.5-2 libgdbm3_1.8.3-13.1 libgfortran-5-dev_5.3.1-13 libgfortran3_5.3.1-13 libglib2.0-0_2.48.0-1 libgmp10_2:6.1.0+dfsg-2 libgomp1_5.3.1-13 libgpg-error0_1.21-2 libgzstream-dev_1.5+dfsg-1 libgzstream0_1.5+dfsg-1 libhdf5-10_1.8.16+docs-6+b1 libhdf5-cpp-11_1.8.16+docs-6+b1 libhdf5-dev_1.8.16+docs-6+b1 libicu55_55.1-7 libisl15_0.16.1-1 libjpeg-dev_1:1.4.2-2 libjpeg62-turbo_1:1.4.2-2 libjpeg62-turbo-dev_1:1.4.2-2 libklibc_2.0.4-8+rpi1 libkmod2_22-1 liblapack-dev_3.6.0-2 liblapack3_3.6.0-2 liblz4-1_0.0~r131-2 liblzma5_5.1.1alpha+20120614-2.1 libmagic1_1:5.25-2 libmount1_2.27.1-6 libmpc3_1.0.3-1 libmpfr4_3.1.4-1 libncurses5_6.0+20160213-1 libncursesw5_6.0+20160213-1 libpam-modules_1.1.8-3.2 libpam-modules-bin_1.1.8-3.2 libpam-runtime_1.1.8-3.2 libpam0g_1.1.8-3.2 libpcre3_2:8.38-3 libperl5.22_5.22.1-9 libpipeline1_1.4.1-2 libpng12-0_1.2.54-4 libprocps5_2:3.3.11-3 libreadline6_6.3-8+b3 libseccomp2_2.2.3-3 libselinux1_2.4-3 libsemanage-common_2.4-3 libsemanage1_2.4-3 libsepol1_2.4-2 libsmartcols1_2.27.1-6 libsqlite3-0_3.11.1-1 libss2_1.42.13-1 libstdc++-5-dev_5.3.1-13 libstdc++6_5.3.1-13 libsuperlu-dev_4.3+dfsg-3 libsuperlu4_4.3+dfsg-3 libsystemd0_229-2 libsz2_0.3.2-1 libtext-charwidth-perl_0.04-7+b6 libtext-iconv-perl_1.7-5+b7 libtext-wrapi18n-perl_0.06-7.1 libtimedate-perl_2.3000-2 libtinfo5_6.0+20160213-1 libubsan0_5.3.1-13 libudev1_229-2 libunistring0_0.9.3-5.2 libusb-0.1-4_2:0.1.12-28 libustr-1.0-1_1.0.4-5 libuuid1_2.27.1-6 libxml2_2.9.3+dfsg1-1 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch login_1:4.2-3.1 lsb-base_9.20160110+rpi1 make_4.1-6 makedev_2.3.1-93 man-db_2.7.5-1 manpages_4.04-2 mawk_1.3.3-17 mount_2.27.1-6 multiarch-support_2.22-3 nano_2.5.3-2 ncurses-base_6.0+20160213-1 ncurses-bin_6.0+20160213-1 passwd_1:4.2-3.1 patch_2.7.5-1 perl_5.22.1-9 perl-base_5.22.1-9 perl-modules-5.22_5.22.1-9 po-debconf_1.0.19 procps_2:3.3.11-3 raspbian-archive-keyring_20120528.2 readline-common_6.3-8 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-seer-dummy_0.invalid.0 sed_4.2.2-7.1 sensible-utils_0.0.9 startpar_0.59-3 systemd_229-2 systemd-sysv_229-2 sysv-rc_2.88dsf-59.3 sysvinit-utils_2.88dsf-59.3 tar_1.28-2.1 tzdata_2016a-1 udev_229-2 util-linux_2.27.1-6 xz-utils_5.1.1alpha+20120614-2.1 zlib1g_1:1.2.8.dfsg-2+b1 zlib1g-dev_1:1.2.8.dfsg-2+b1
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error
gpgv: Signature made Fri Apr 1 06:22:50 2016 UTC using RSA key ID D1C646D1
gpgv: Can't check signature: public key not found
dpkg-source: warning: failed to verify signature on ./seer_1.1.0-1.dsc
dpkg-source: info: extracting seer in seer-1.1.0
dpkg-source: info: unpacking seer_1.1.0.orig.tar.gz
dpkg-source: info: unpacking seer_1.1.0-1.debian.tar.xz
dpkg-source: info: applying fix_lib_location.patch
dpkg-source: info: applying hardening.patch
dpkg-source: info: applying debug_hardening.patch
Check disc space
----------------
Sufficient free space for build
User Environment
----------------
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LOGNAME=root
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=stretch-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=stretch-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=111
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=stretch-staging-armhf-sbuild-a601e131-4865-4b77-96d7-ca12c875b6f2
SCHROOT_UID=106
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=xterm
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: source package seer
dpkg-buildpackage: source version 1.1.0-1
dpkg-buildpackage: source distribution unstable
dpkg-source --before-build seer-1.1.0
dpkg-buildpackage: host architecture armhf
fakeroot debian/rules clean
dh clean
dh_testdir
dh_auto_clean
make -j1 clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
cd src && make clean
make[2]: Entering directory '/<<PKGBUILDDIR>>/src'
rm -f *.o ~* seer kmds map_back combineKmers filter_seer
make[2]: Leaving directory '/<<PKGBUILDDIR>>/src'
cd test && make clean
make[2]: Entering directory '/<<PKGBUILDDIR>>/test'
rm -f *.o ~* tests_passed.txt
make[2]: Leaving directory '/<<PKGBUILDDIR>>/test'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_clean
debian/rules build-arch
dh build-arch
dh_testdir -a
dh_update_autotools_config -a
dh_auto_configure -a
dh_auto_build -a
make -j1
make[1]: Entering directory '/<<PKGBUILDDIR>>'
cd src && make all
make[2]: Entering directory '/<<PKGBUILDDIR>>/src'
g++ -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I/sbuild-nonexistent/software/include -I../gzstream -I../dlib -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -c -o sample.o sample.cpp
g++ -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I/sbuild-nonexistent/software/include -I../gzstream -I../dlib -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -c -o significant_kmer.o significant_kmer.cpp
g++ -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I/sbuild-nonexistent/software/include -I../gzstream -I../dlib -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -c -o kmer.o kmer.cpp
In file included from /usr/include/armadillo:50:0,
from kmer.hpp:13,
from kmer.cpp:8:
/usr/include/armadillo_bits/compiler_setup.hpp:90:106: note: #pragma message: WARNING: disabled use of 64 bit integers, as std::size_t is smaller than 64 bits
#pragma message ("WARNING: disabled use of 64 bit integers, as std::size_t is smaller than 64 bits")
^
g++ -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I/sbuild-nonexistent/software/include -I../gzstream -I../dlib -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -c -o covar.o covar.cpp
g++ -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I/sbuild-nonexistent/software/include -I../gzstream -I../dlib -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -c -o seerCommon.o seerCommon.cpp
In file included from /usr/include/armadillo:50:0,
from seercommon.hpp:35,
from seerCommon.cpp:9:
/usr/include/armadillo_bits/compiler_setup.hpp:90:106: note: #pragma message: WARNING: disabled use of 64 bit integers, as std::size_t is smaller than 64 bits
#pragma message ("WARNING: disabled use of 64 bit integers, as std::size_t is smaller than 64 bits")
^
seerCommon.cpp: In function 'arma::vec dlib_to_arma(const column_vector&)':
seerCommon.cpp:179:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (unsigned int i = 0; i < dlib_vec.nr(); ++i)
^
g++ -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I/sbuild-nonexistent/software/include -I../gzstream -I../dlib -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -c -o seerErr.o seerErr.cpp
In file included from /usr/include/armadillo:50:0,
from seercommon.hpp:35,
from seerErr.cpp:8:
/usr/include/armadillo_bits/compiler_setup.hpp:90:106: note: #pragma message: WARNING: disabled use of 64 bit integers, as std::size_t is smaller than 64 bits
#pragma message ("WARNING: disabled use of 64 bit integers, as std::size_t is smaller than 64 bits")
^
g++ -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I/sbuild-nonexistent/software/include -I../gzstream -I../dlib -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -c -o seerFilter.o seerFilter.cpp
In file included from /usr/include/armadillo:50:0,
from seercommon.hpp:35,
from seerFilter.cpp:9:
/usr/include/armadillo_bits/compiler_setup.hpp:90:106: note: #pragma message: WARNING: disabled use of 64 bit integers, as std::size_t is smaller than 64 bits
#pragma message ("WARNING: disabled use of 64 bit integers, as std::size_t is smaller than 64 bits")
^
g++ -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I/sbuild-nonexistent/software/include -I../gzstream -I../dlib -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -c -o seerIO.o seerIO.cpp
In file included from /usr/include/armadillo:50:0,
from seercommon.hpp:35,
from seerIO.cpp:12:
/usr/include/armadillo_bits/compiler_setup.hpp:90:106: note: #pragma message: WARNING: disabled use of 64 bit integers, as std::size_t is smaller than 64 bits
#pragma message ("WARNING: disabled use of 64 bit integers, as std::size_t is smaller than 64 bits")
^
g++ -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I/sbuild-nonexistent/software/include -I../gzstream -I../dlib -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -c -o seerChiFilter.o seerChiFilter.cpp
In file included from /usr/include/armadillo:50:0,
from seercommon.hpp:35,
from seerChiFilter.cpp:8:
/usr/include/armadillo_bits/compiler_setup.hpp:90:106: note: #pragma message: WARNING: disabled use of 64 bit integers, as std::size_t is smaller than 64 bits
#pragma message ("WARNING: disabled use of 64 bit integers, as std::size_t is smaller than 64 bits")
^
g++ -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I/sbuild-nonexistent/software/include -I../gzstream -I../dlib -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -c -o seerMain.o seerMain.cpp
In file included from /usr/include/armadillo:50:0,
from seercommon.hpp:35,
from linkFunction.hpp:6,
from seer.hpp:10,
from seerMain.cpp:8:
/usr/include/armadillo_bits/compiler_setup.hpp:90:106: note: #pragma message: WARNING: disabled use of 64 bit integers, as std::size_t is smaller than 64 bits
#pragma message ("WARNING: disabled use of 64 bit integers, as std::size_t is smaller than 64 bits")
^
g++ -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I/sbuild-nonexistent/software/include -I../gzstream -I../dlib -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -c -o seerCmdLine.o seerCmdLine.cpp
In file included from /usr/include/armadillo:50:0,
from seercommon.hpp:35,
from linkFunction.hpp:6,
from seer.hpp:10,
from seerCmdLine.cpp:9:
/usr/include/armadillo_bits/compiler_setup.hpp:90:106: note: #pragma message: WARNING: disabled use of 64 bit integers, as std::size_t is smaller than 64 bits
#pragma message ("WARNING: disabled use of 64 bit integers, as std::size_t is smaller than 64 bits")
^
g++ -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I/sbuild-nonexistent/software/include -I../gzstream -I../dlib -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -c -o seerContinuousAssoc.o seerContinuousAssoc.cpp
In file included from /usr/include/armadillo:50:0,
from seercommon.hpp:35,
from linkFunction.hpp:6,
from seer.hpp:10,
from seerContinuousAssoc.cpp:8:
/usr/include/armadillo_bits/compiler_setup.hpp:90:106: note: #pragma message: WARNING: disabled use of 64 bit integers, as std::size_t is smaller than 64 bits
#pragma message ("WARNING: disabled use of 64 bit integers, as std::size_t is smaller than 64 bits")
^
g++ -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I/sbuild-nonexistent/software/include -I../gzstream -I../dlib -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -c -o seerBinaryAssoc.o seerBinaryAssoc.cpp
In file included from /usr/include/armadillo:50:0,
from seercommon.hpp:35,
from linkFunction.hpp:6,
from seer.hpp:10,
from seerBinaryAssoc.cpp:8:
/usr/include/armadillo_bits/compiler_setup.hpp:90:106: note: #pragma message: WARNING: disabled use of 64 bit integers, as std::size_t is smaller than 64 bits
#pragma message ("WARNING: disabled use of 64 bit integers, as std::size_t is smaller than 64 bits")
^
g++ -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I/sbuild-nonexistent/software/include -I../gzstream -I../dlib -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -c -o logitFunction.o logitFunction.cpp
In file included from /usr/include/armadillo:50:0,
from seercommon.hpp:35,
from linkFunction.hpp:6,
from logitFunction.cpp:8:
/usr/include/armadillo_bits/compiler_setup.hpp:90:106: note: #pragma message: WARNING: disabled use of 64 bit integers, as std::size_t is smaller than 64 bits
#pragma message ("WARNING: disabled use of 64 bit integers, as std::size_t is smaller than 64 bits")
^
g++ -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I/sbuild-nonexistent/software/include -I../gzstream -I../dlib -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -c -o linearFunction.o linearFunction.cpp
In file included from /usr/include/armadillo:50:0,
from seercommon.hpp:35,
from linkFunction.hpp:6,
from linearFunction.cpp:8:
/usr/include/armadillo_bits/compiler_setup.hpp:90:106: note: #pragma message: WARNING: disabled use of 64 bit integers, as std::size_t is smaller than 64 bits
#pragma message ("WARNING: disabled use of 64 bit integers, as std::size_t is smaller than 64 bits")
^
echo "debug seer: SEER_LDLIBS = -lhdf5 -lgzstream -lz -larmadillo -lboost_program_options -llapack -lblas -pthread -fPIE -pie -Wl,-z,relro -Wl,-z,now / -fPIE -pie -Wl,-z,relro -Wl,-z,now"
debug seer: SEER_LDLIBS = -lhdf5 -lgzstream -lz -larmadillo -lboost_program_options -llapack -lblas -pthread -fPIE -pie -Wl,-z,relro -Wl,-z,now / -fPIE -pie -Wl,-z,relro -Wl,-z,now
g++ -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I/sbuild-nonexistent/software/include -I../gzstream -I../dlib -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -fPIE -pie -Wl,-z,relro -Wl,-z,now sample.o significant_kmer.o kmer.o covar.o seerCommon.o seerErr.o seerFilter.o seerIO.o seerChiFilter.o seerMain.o seerCmdLine.o seerContinuousAssoc.o seerBinaryAssoc.o logitFunction.o linearFunction.o -lhdf5 -lgzstream -lz -larmadillo -lboost_program_options -llapack -lblas -pthread -fPIE -pie -Wl,-z,relro -Wl,-z,now -o seer
g++ -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I/sbuild-nonexistent/software/include -I../gzstream -I../dlib -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -c -o kmdsMain.o kmdsMain.cpp
In file included from /usr/include/armadillo:50:0,
from seercommon.hpp:35,
from kmds.hpp:9,
from kmdsMain.cpp:8:
/usr/include/armadillo_bits/compiler_setup.hpp:90:106: note: #pragma message: WARNING: disabled use of 64 bit integers, as std::size_t is smaller than 64 bits
#pragma message ("WARNING: disabled use of 64 bit integers, as std::size_t is smaller than 64 bits")
^
g++ -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I/sbuild-nonexistent/software/include -I../gzstream -I../dlib -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -c -o kmdsStruct.o kmdsStruct.cpp
In file included from /usr/include/armadillo:50:0,
from seercommon.hpp:35,
from kmds.hpp:9,
from kmdsStruct.cpp:8:
/usr/include/armadillo_bits/compiler_setup.hpp:90:106: note: #pragma message: WARNING: disabled use of 64 bit integers, as std::size_t is smaller than 64 bits
#pragma message ("WARNING: disabled use of 64 bit integers, as std::size_t is smaller than 64 bits")
^
g++ -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I/sbuild-nonexistent/software/include -I../gzstream -I../dlib -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -c -o kmdsCmdLine.o kmdsCmdLine.cpp
In file included from /usr/include/armadillo:50:0,
from seercommon.hpp:35,
from kmds.hpp:9,
from kmdsCmdLine.cpp:8:
/usr/include/armadillo_bits/compiler_setup.hpp:90:106: note: #pragma message: WARNING: disabled use of 64 bit integers, as std::size_t is smaller than 64 bits
#pragma message ("WARNING: disabled use of 64 bit integers, as std::size_t is smaller than 64 bits")
^
echo "debug kmds: SEER_LDLIBS = -lhdf5 -lgzstream -lz -larmadillo -lboost_program_options -llapack -lblas -pthread -fPIE -pie -Wl,-z,relro -Wl,-z,now / -fPIE -pie -Wl,-z,relro -Wl,-z,now"
debug kmds: SEER_LDLIBS = -lhdf5 -lgzstream -lz -larmadillo -lboost_program_options -llapack -lblas -pthread -fPIE -pie -Wl,-z,relro -Wl,-z,now / -fPIE -pie -Wl,-z,relro -Wl,-z,now
g++ -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I/sbuild-nonexistent/software/include -I../gzstream -I../dlib -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -fPIE -pie -Wl,-z,relro -Wl,-z,now sample.o significant_kmer.o kmer.o covar.o seerCommon.o seerErr.o seerFilter.o seerIO.o seerChiFilter.o kmdsMain.o kmdsStruct.o kmdsCmdLine.o -lhdf5 -lgzstream -lz -larmadillo -lboost_program_options -llapack -lblas -pthread -fPIE -pie -Wl,-z,relro -Wl,-z,now -o kmds
g++ -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I/sbuild-nonexistent/software/include -I../gzstream -I../dlib -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -c -o fasta.o fasta.cpp
g++ -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I/sbuild-nonexistent/software/include -I../gzstream -I../dlib -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -c -o mapMain.o mapMain.cpp
g++ -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I/sbuild-nonexistent/software/include -I../gzstream -I../dlib -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -c -o mapCmdLine.o mapCmdLine.cpp
echo "debug map_back: MAP_LDLIBS = -lboost_program_options -pthread -fPIE -pie -Wl,-z,relro -Wl,-z,now / -fPIE -pie -Wl,-z,relro -Wl,-z,now"
debug map_back: MAP_LDLIBS = -lboost_program_options -pthread -fPIE -pie -Wl,-z,relro -Wl,-z,now / -fPIE -pie -Wl,-z,relro -Wl,-z,now
g++ -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I/sbuild-nonexistent/software/include -I../gzstream -I../dlib -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -fPIE -pie -Wl,-z,relro -Wl,-z,now fasta.o significant_kmer.o mapMain.o mapCmdLine.o -lboost_program_options -pthread -fPIE -pie -Wl,-z,relro -Wl,-z,now -fPIE -pie -Wl,-z,relro -Wl,-z,now -o map_back
g++ -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I/sbuild-nonexistent/software/include -I../gzstream -I../dlib -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -c -o combineInit.o combineInit.cpp
g++ -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I/sbuild-nonexistent/software/include -I../gzstream -I../dlib -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -c -o combineCmdLine.o combineCmdLine.cpp
g++ -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I/sbuild-nonexistent/software/include -I../gzstream -I../dlib -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -c -o combineKmers.o combineKmers.cpp
echo "debug combineKmers: COMBINE_LDLIBS = -lgzstream -lz -lboost_program_options -fPIE -pie -Wl,-z,relro -Wl,-z,now / -fPIE -pie -Wl,-z,relro -Wl,-z,now"
debug combineKmers: COMBINE_LDLIBS = -lgzstream -lz -lboost_program_options -fPIE -pie -Wl,-z,relro -Wl,-z,now / -fPIE -pie -Wl,-z,relro -Wl,-z,now
g++ -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I/sbuild-nonexistent/software/include -I../gzstream -I../dlib -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -fPIE -pie -Wl,-z,relro -Wl,-z,now combineInit.o combineCmdLine.o combineKmers.o -lgzstream -lz -lboost_program_options -fPIE -pie -Wl,-z,relro -Wl,-z,now -fPIE -pie -Wl,-z,relro -Wl,-z,now -o combineKmers
g++ -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I/sbuild-nonexistent/software/include -I../gzstream -I../dlib -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -c -o filter_seer.o filter_seer.cpp
g++ -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I/sbuild-nonexistent/software/include -I../gzstream -I../dlib -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -c -o filterCmdLine.o filterCmdLine.cpp
echo "debug filter_seer: FILTER_LDLIBS = -lboost_program_options -fPIE -pie -Wl,-z,relro -Wl,-z,now / -fPIE -pie -Wl,-z,relro -Wl,-z,now"
debug filter_seer: FILTER_LDLIBS = -lboost_program_options -fPIE -pie -Wl,-z,relro -Wl,-z,now / -fPIE -pie -Wl,-z,relro -Wl,-z,now
g++ -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I/sbuild-nonexistent/software/include -I../gzstream -I../dlib -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -fPIE -pie -Wl,-z,relro -Wl,-z,now significant_kmer.o filter_seer.o filterCmdLine.o -lboost_program_options -fPIE -pie -Wl,-z,relro -Wl,-z,now -fPIE -pie -Wl,-z,relro -Wl,-z,now -o filter_seer
make[2]: Leaving directory '/<<PKGBUILDDIR>>/src'
cd test && make all
make[2]: Entering directory '/<<PKGBUILDDIR>>/test'
echo "Tests not yet implemented" > tests_passed.txt
make[2]: Leaving directory '/<<PKGBUILDDIR>>/test'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_test -a
make -j1 test
make[1]: Entering directory '/<<PKGBUILDDIR>>'
cd src && make all
make[2]: Entering directory '/<<PKGBUILDDIR>>/src'
make[2]: Nothing to be done for 'all'.
make[2]: Leaving directory '/<<PKGBUILDDIR>>/src'
cd test && make all
make[2]: Entering directory '/<<PKGBUILDDIR>>/test'
echo "Tests not yet implemented" > tests_passed.txt
make[2]: Leaving directory '/<<PKGBUILDDIR>>/test'
cd test && make test
make[2]: Entering directory '/<<PKGBUILDDIR>>/test'
echo "Tests not yet implemented" > tests_passed.txt
make[2]: Leaving directory '/<<PKGBUILDDIR>>/test'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
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 -- PREFIX=/<<PKGBUILDDIR>>/debian/seer/usr
make -j1 install DESTDIR=/<<PKGBUILDDIR>>/debian/seer AM_UPDATE_INFO_DIR=no PREFIX=/<<PKGBUILDDIR>>/debian/seer/usr
make[2]: Entering directory '/<<PKGBUILDDIR>>'
cd src && make all
make[3]: Entering directory '/<<PKGBUILDDIR>>/src'
make[3]: Nothing to be done for 'all'.
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src'
cd test && make all
make[3]: Entering directory '/<<PKGBUILDDIR>>/test'
echo "Tests not yet implemented" > tests_passed.txt
make[3]: Leaving directory '/<<PKGBUILDDIR>>/test'
cd src && make install
make[3]: Entering directory '/<<PKGBUILDDIR>>/src'
install -d /<<PKGBUILDDIR>>/debian/seer/usr/bin
install seer kmds map_back combineKmers filter_seer /<<PKGBUILDDIR>>/debian/seer/usr/bin
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
cp -a scripts/blast_top_hits.pl /<<PKGBUILDDIR>>/debian/seer/usr/bin/blast_top_hits
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_installdocs -a
dh_installchangelogs -a
dh_installexamples -a
dh_installman -a
dh_perl -a
dh_link -a
dh_strip_nondeterminism -a
dh_compress -a
dh_fixperms -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/seer/usr/bin/kmds debian/seer/usr/bin/seer were not linked against libhdf5_serial.so.10 (they use none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/seer/usr/bin/kmds debian/seer/usr/bin/seer were not linked against liblapack.so.3 (they use none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/seer/usr/bin/combineKmers debian/seer/usr/bin/kmds debian/seer/usr/bin/seer were not linked against libz.so.1 (they use none of the library's symbols)
dh_installdeb -a
dh_gencontrol -a
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-gencontrol: warning: package seer: unused substitution variable ${perl:Depends}
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-gencontrol: warning: package seer: unused substitution variable ${perl:Depends}
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package 'seer-dbgsym' in '../seer-dbgsym_1.1.0-1_armhf.deb'.
dpkg-deb: building package 'seer' in '../seer_1.1.0-1_armhf.deb'.
dpkg-genchanges -B -mRaspbian nitrogen6x test autobuilder <root@raspbian.org> >../seer_1.1.0-1_armhf.changes
dpkg-genchanges: warning: package seer-dbgsym listed in files list but not in control info
dpkg-genchanges: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build seer-1.1.0
dpkg-buildpackage: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 20160408-0845
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
seer_1.1.0-1_armhf.changes:
---------------------------
Format: 1.8
Date: Thu, 31 Mar 2016 22:35:05 +0200
Source: seer
Binary: seer
Architecture: armhf
Version: 1.1.0-1
Distribution: stretch-staging
Urgency: medium
Maintainer: Raspbian nitrogen6x test autobuilder <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
seer - genomic sequence element (kmer) enrichment analysis
Closes: 819674
Changes:
seer (1.1.0-1) unstable; urgency=medium
.
* Initial release (Closes: #819674)
Checksums-Sha1:
dbcad13cd2f9b44e68bd12541e5d52f0bf71b303 6720970 seer-dbgsym_1.1.0-1_armhf.deb
3c276b9cd684ea7cd9f8c4810bb86c6e8ed7f9bb 291526 seer_1.1.0-1_armhf.deb
Checksums-Sha256:
9745c50f2557cbe795a5800df5cf427b768aa1c876aa8a88934df42557d1e74f 6720970 seer-dbgsym_1.1.0-1_armhf.deb
8639983f9190c82b9b362785918f4d9496a8b70ce22c4c064949031cd6385730 291526 seer_1.1.0-1_armhf.deb
Files:
ed7bdd9450bbe2fe8218a7c0cbdc63de 6720970 debug extra seer-dbgsym_1.1.0-1_armhf.deb
9a2aaf181edf78d7f212b1677c5dd567 291526 science optional seer_1.1.0-1_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
seer-dbgsym_1.1.0-1_armhf.deb
-----------------------------
new debian package, version 2.0.
size 6720970 bytes: control archive=714 bytes.
563 bytes, 13 lines control
530 bytes, 5 lines md5sums
Package: seer-dbgsym
Source: seer
Version: 1.1.0-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 7083
Depends: seer (= 1.1.0-1)
Section: debug
Priority: extra
Homepage: https://github.com/johnlees/seer
Description: Debug symbols for seer
Auto-Built-Package: debug-symbols
Build-Ids: e0af9ae846c2c9435fb60c98cd02c586c4ff4100 e1458876c9d7ceb557107be887414c189b5c54bf f52ed161de684b6d96971970a5aca312079a47d2 f6ac54daebd7eb5246fbdd2a4fe992dbd272a74d ffd24d4740458b99836db3652680539337a29cb0
drwxr-xr-x root/root 0 2016-04-08 08:45 ./
drwxr-xr-x root/root 0 2016-04-08 08:44 ./usr/
drwxr-xr-x root/root 0 2016-04-08 08:44 ./usr/lib/
drwxr-xr-x root/root 0 2016-04-08 08:44 ./usr/lib/debug/
drwxr-xr-x root/root 0 2016-04-08 08:44 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2016-04-08 08:44 ./usr/lib/debug/.build-id/e0/
-rw-r--r-- root/root 2721876 2016-04-08 08:44 ./usr/lib/debug/.build-id/e0/af9ae846c2c9435fb60c98cd02c586c4ff4100.debug
drwxr-xr-x root/root 0 2016-04-08 08:44 ./usr/lib/debug/.build-id/e1/
-rw-r--r-- root/root 764408 2016-04-08 08:44 ./usr/lib/debug/.build-id/e1/458876c9d7ceb557107be887414c189b5c54bf.debug
drwxr-xr-x root/root 0 2016-04-08 08:44 ./usr/lib/debug/.build-id/f5/
-rw-r--r-- root/root 2978152 2016-04-08 08:44 ./usr/lib/debug/.build-id/f5/2ed161de684b6d96971970a5aca312079a47d2.debug
drwxr-xr-x root/root 0 2016-04-08 08:44 ./usr/lib/debug/.build-id/f6/
-rw-r--r-- root/root 308856 2016-04-08 08:44 ./usr/lib/debug/.build-id/f6/ac54daebd7eb5246fbdd2a4fe992dbd272a74d.debug
drwxr-xr-x root/root 0 2016-04-08 08:44 ./usr/lib/debug/.build-id/ff/
-rw-r--r-- root/root 461908 2016-04-08 08:44 ./usr/lib/debug/.build-id/ff/d24d4740458b99836db3652680539337a29cb0.debug
drwxr-xr-x root/root 0 2016-04-08 08:44 ./usr/share/
drwxr-xr-x root/root 0 2016-04-08 08:44 ./usr/share/doc/
lrwxrwxrwx root/root 0 2016-04-08 08:44 ./usr/share/doc/seer-dbgsym -> seer
seer_1.1.0-1_armhf.deb
----------------------
new debian package, version 2.0.
size 291526 bytes: control archive=1481 bytes.
1394 bytes, 23 lines control
1005 bytes, 16 lines md5sums
Package: seer
Version: 1.1.0-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1343
Depends: libarmadillo6, libblas3 | libblas.so.3, libboost-program-options1.58.0, libc6 (>= 2.4), libgcc1 (>= 1:3.5), libgzstream0, libhdf5-10, liblapack3 | liblapack.so.3, libstdc++6 (>= 5.2), zlib1g (>= 1:1.1.4), libtext-csv-perl
Section: science
Priority: optional
Homepage: https://github.com/johnlees/seer
Description: genomic sequence element (kmer) enrichment analysis
Bacterial genomes vary extensively in terms of both gene content and
gene sequence - this plasticity hampers the use of traditional SNP-based
methods for identifying all genetic associations with phenotypic
variation. SEER provides a computationally scalable and widely
applicable statistical method for the identification of sequence
elements that are significantly enriched in a phenotype of interest.
SEER is applicable to even tens of thousands of genomes by counting variable-
length k-mers using a distributed string-mining algorithm. Robust
options are provided for association analysis that also correct for the
clonal population structure of bacteria. Using large collections of
genomes of the major human pathogen Streptococcus pneumoniae, SEER
identifies relevant previously characterised resistance determinants for
several antibiotics.
drwxr-xr-x root/root 0 2016-04-08 08:44 ./
drwxr-xr-x root/root 0 2016-04-08 08:44 ./usr/
drwxr-xr-x root/root 0 2016-04-08 08:44 ./usr/bin/
-rwxr-xr-x root/root 3799 2015-11-05 19:38 ./usr/bin/blast_top_hits
-rwxr-xr-x root/root 108084 2016-04-08 08:44 ./usr/bin/combineKmers
-rwxr-xr-x root/root 71220 2016-04-08 08:44 ./usr/bin/filter_seer
-rwxr-xr-x root/root 460880 2016-04-08 08:44 ./usr/bin/kmds
-rwxr-xr-x root/root 181812 2016-04-08 08:44 ./usr/bin/map_back
-rwxr-xr-x root/root 522320 2016-04-08 08:44 ./usr/bin/seer
drwxr-xr-x root/root 0 2016-04-08 08:44 ./usr/share/
drwxr-xr-x root/root 0 2016-04-08 08:44 ./usr/share/doc/
drwxr-xr-x root/root 0 2016-04-08 08:44 ./usr/share/doc/seer/
-rw-r--r-- root/root 293 2016-03-31 06:59 ./usr/share/doc/seer/README.Debian
-rw-r--r-- root/root 154 2016-03-31 20:35 ./usr/share/doc/seer/changelog.Debian.gz
-rw-r--r-- root/root 1008 2016-03-31 18:01 ./usr/share/doc/seer/copyright
drwxr-xr-x root/root 0 2016-04-08 08:44 ./usr/share/doc/seer/examples/
-rw-r--r-- root/root 2110 2015-11-05 19:38 ./usr/share/doc/seer/examples/example_wrapper.py.gz
drwxr-xr-x root/root 0 2016-04-08 08:44 ./usr/share/man/
drwxr-xr-x root/root 0 2016-04-08 08:44 ./usr/share/man/man1/
-rw-r--r-- root/root 551 2016-04-08 08:44 ./usr/share/man/man1/blast_top_hits.1.gz
-rw-r--r-- root/root 509 2016-04-08 08:44 ./usr/share/man/man1/combineKmers.1.gz
-rw-r--r-- root/root 590 2016-04-08 08:44 ./usr/share/man/man1/filter_seer.1.gz
-rw-r--r-- root/root 993 2016-04-08 08:44 ./usr/share/man/man1/kmds.1.gz
-rw-r--r-- root/root 486 2016-04-08 08:44 ./usr/share/man/man1/map_back.1.gz
-rw-r--r-- root/root 1064 2016-04-08 08:44 ./usr/share/man/man1/seer.1.gz
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 69012
Build-Time: 1493
Distribution: stretch-staging
Host Architecture: armhf
Install-Time: 568
Job: seer_1.1.0-1
Machine Architecture: armhf
Package: seer
Package-Time: 2104
Source-Version: 1.1.0-1
Space: 69012
Status: successful
Version: 1.1.0-1
--------------------------------------------------------------------------------
Finished at 20160408-0845
Build needed 00:35:04, 69012k disc space