seer →
1.1.1-2 →
armhf → 2016-04-25 06:02:01
sbuild (Debian sbuild) 0.66.0 (04 Oct 2015) on testwandboard
+==============================================================================+
| seer 1.1.1-2 (armhf) 25 Apr 2016 05:29 |
+==============================================================================+
Package: seer
Version: 1.1.1-2
Source Version: 1.1.1-2
Distribution: stretch-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'build/seer-ubVIya/seer-1.1.1' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/seer-ubVIya' with '<<BUILDDIR>>'
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/stretch-staging-armhf-sbuild-856aa61d-c354-488a-b77f-1cc7c37eb694' 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 [8925 kB]
Get:3 http://172.17.0.1/private stretch-staging/main armhf Packages [11.0 MB]
Fetched 19.9 MB in 24s (821 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 'Git' version control system at:
https://anonscm.debian.org/git/debian-med/seer.git
Please use:
git clone https://anonscm.debian.org/git/debian-med/seer.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 267 kB of source archives.
Get:1 http://172.17.0.1/private stretch-staging/main seer 1.1.1-2 (dsc) [1970 B]
Get:2 http://172.17.0.1/private stretch-staging/main seer 1.1.1-2 (tar) [260 kB]
Get:3 http://172.17.0.1/private stretch-staging/main seer 1.1.1-2 (diff) [5688 B]
Fetched 267 kB in 0s (1132 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-5s2xxC/apt_archive/sbuild-build-depends-core-dummy.deb'.
OK
Get:1 file:/<<BUILDDIR>>/resolver-5s2xxC/apt_archive ./ InRelease
Ign:1 file:/<<BUILDDIR>>/resolver-5s2xxC/apt_archive ./ InRelease
Get:2 file:/<<BUILDDIR>>/resolver-5s2xxC/apt_archive ./ Release [2119 B]
Get:2 file:/<<BUILDDIR>>/resolver-5s2xxC/apt_archive ./ Release [2119 B]
Get:3 file:/<<BUILDDIR>>/resolver-5s2xxC/apt_archive ./ Release.gpg [299 B]
Get:3 file:/<<BUILDDIR>>/resolver-5s2xxC/apt_archive ./ Release.gpg [299 B]
Get:4 file:/<<BUILDDIR>>/resolver-5s2xxC/apt_archive ./ Sources [194 B]
Get:5 file:/<<BUILDDIR>>/resolver-5s2xxC/apt_archive ./ Packages [507 B]
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
W: file:///<<BUILDDIR>>/resolver-5s2xxC/apt_archive/./Release.gpg: Signature by key 3493EC2B8E6DC280C121C60435506D9A48F77B2E uses weak digest algorithm (SHA1)
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 22 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-5s2xxC/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.
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(Reading database ... 13813 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-dfRCwO/apt_archive/sbuild-build-depends-seer-dummy.deb'.
OK
Get:1 file:/<<BUILDDIR>>/resolver-dfRCwO/apt_archive ./ InRelease
Ign:1 file:/<<BUILDDIR>>/resolver-dfRCwO/apt_archive ./ InRelease
Get:2 file:/<<BUILDDIR>>/resolver-dfRCwO/apt_archive ./ Release [2119 B]
Get:2 file:/<<BUILDDIR>>/resolver-dfRCwO/apt_archive ./ Release [2119 B]
Get:3 file:/<<BUILDDIR>>/resolver-dfRCwO/apt_archive ./ Release.gpg [299 B]
Get:3 file:/<<BUILDDIR>>/resolver-dfRCwO/apt_archive ./ Release.gpg [299 B]
Get:4 file:/<<BUILDDIR>>/resolver-dfRCwO/apt_archive ./ Sources [235 B]
Get:5 file:/<<BUILDDIR>>/resolver-dfRCwO/apt_archive ./ Packages [551 B]
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
W: file:///<<BUILDDIR>>/resolver-dfRCwO/apt_archive/./Release.gpg: Signature by key 3493EC2B8E6DC280C121C60435506D9A48F77B2E uses weak digest algorithm (SHA1)
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:
autoconf automake autopoint autotools-dev bsdmainutils debhelper
dh-autoreconf 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
libsigsegv2 libsqlite3-0 libsuperlu-dev libsuperlu4 libsz2 libtimedate-perl
libtool libunistring0 libxml2 m4 man-db po-debconf zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
vacation dh-make gettext-doc 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 libsuperlu-doc libtool-doc gcj-jdk
less www-browser libmail-box-perl
Recommended packages:
curl | wget | lynx-cur libglib2.0-data shared-mime-info xdg-user-dirs
libltdl-dev xml-core libmail-sendmail-perl
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils debhelper
dh-autoreconf 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
libsigsegv2 libsqlite3-0 libsuperlu-dev libsuperlu4 libsz2 libtimedate-perl
libtool libunistring0 libxml2 m4 man-db po-debconf
sbuild-build-depends-seer-dummy zlib1g-dev
0 upgraded, 68 newly installed, 0 to remove and 22 not upgraded.
Need to get 117 MB/125 MB of archives.
After this operation, 430 MB of additional disk space will be used.
Get:1 file:/<<BUILDDIR>>/resolver-dfRCwO/apt_archive ./ sbuild-build-depends-seer-dummy 0.invalid.0 [808 B]
Get:2 http://172.17.0.1/private stretch-staging/main armhf groff-base armhf 1.22.3-7 [1083 kB]
Get:3 http://172.17.0.1/private stretch-staging/main armhf libbsd0 armhf 0.8.2-1 [88.0 kB]
Get:4 http://172.17.0.1/private stretch-staging/main armhf bsdmainutils armhf 9.0.10 [177 kB]
Get:5 http://172.17.0.1/private stretch-staging/main armhf libpipeline1 armhf 1.4.1-2 [23.7 kB]
Get:6 http://172.17.0.1/private stretch-staging/main armhf man-db armhf 2.7.5-1 [975 kB]
Get:7 http://172.17.0.1/private stretch-staging/main armhf libgfortran3 armhf 5.3.1-14 [153 kB]
Get:8 http://172.17.0.1/private stretch-staging/main armhf libblas-common armhf 3.6.0-2 [13.5 kB]
Get:9 http://172.17.0.1/private stretch-staging/main armhf libblas3 armhf 3.6.0-2 [110 kB]
Get:10 http://172.17.0.1/private stretch-staging/main armhf libsuperlu4 armhf 4.3+dfsg-3 [136 kB]
Get:11 http://172.17.0.1/private stretch-staging/main armhf libunistring0 armhf 0.9.3-5.2 [253 kB]
Get:12 http://172.17.0.1/private stretch-staging/main armhf libmagic1 armhf 1:5.25-2 [250 kB]
Get:13 http://172.17.0.1/private stretch-staging/main armhf file armhf 1:5.25-2 [61.2 kB]
Get:14 http://172.17.0.1/private stretch-staging/main armhf gettext-base armhf 0.19.7-2 [111 kB]
Get:15 http://172.17.0.1/private stretch-staging/main armhf libsqlite3-0 armhf 3.12.1-1 [463 kB]
Get:16 http://172.17.0.1/private stretch-staging/main armhf libsigsegv2 armhf 2.10-5 [28.4 kB]
Get:17 http://172.17.0.1/private stretch-staging/main armhf m4 armhf 1.4.17-5 [239 kB]
Get:18 http://172.17.0.1/private stretch-staging/main armhf autoconf all 2.69-10 [338 kB]
Get:19 http://172.17.0.1/private stretch-staging/main armhf autotools-dev all 20150820.1 [71.7 kB]
Get:20 http://172.17.0.1/private stretch-staging/main armhf automake all 1:1.15-4 [735 kB]
Get:21 http://172.17.0.1/private stretch-staging/main armhf autopoint all 0.19.7-2 [424 kB]
Get:22 http://172.17.0.1/private stretch-staging/main armhf libglib2.0-0 armhf 2.48.0-1 [2540 kB]
Get:23 http://172.17.0.1/private stretch-staging/main armhf libcroco3 armhf 0.6.11-1 [131 kB]
Get:24 http://172.17.0.1/private stretch-staging/main armhf gettext armhf 0.19.7-2 [1400 kB]
Get:25 http://172.17.0.1/private stretch-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:26 http://172.17.0.1/private stretch-staging/main armhf po-debconf all 1.0.19 [249 kB]
Get:27 http://172.17.0.1/private stretch-staging/main armhf libarchive-zip-perl all 1.57-1 [95.1 kB]
Get:28 http://172.17.0.1/private stretch-staging/main armhf libfile-stripnondeterminism-perl all 0.016-1 [11.9 kB]
Get:29 http://172.17.0.1/private stretch-staging/main armhf libtimedate-perl all 2.3000-2 [42.2 kB]
Get:30 http://172.17.0.1/private stretch-staging/main armhf dh-strip-nondeterminism all 0.016-1 [6998 B]
Get:31 http://172.17.0.1/private stretch-staging/main armhf libtool all 2.4.6-0.1 [200 kB]
Get:32 http://172.17.0.1/private stretch-staging/main armhf dh-autoreconf all 12 [15.8 kB]
Get:33 http://172.17.0.1/private stretch-staging/main armhf debhelper all 9.20160403 [800 kB]
Get:34 http://172.17.0.1/private stretch-staging/main armhf libgfortran-5-dev armhf 5.3.1-14 [182 kB]
Get:35 http://172.17.0.1/private stretch-staging/main armhf gfortran-5 armhf 5.3.1-14 [23.7 MB]
Get:36 http://172.17.0.1/private stretch-staging/main armhf gfortran armhf 4:5.3.1-1+rpi1 [1362 B]
Get:37 http://172.17.0.1/private stretch-staging/main armhf hdf5-helpers armhf 1.8.16+docs-7 [35.3 kB]
Get:38 http://172.17.0.1/private stretch-staging/main armhf libaec0 armhf 0.3.2-1 [19.4 kB]
Get:39 http://172.17.0.1/private stretch-staging/main armhf liblapack3 armhf 3.6.0-2 [1382 kB]
Get:40 http://172.17.0.1/private stretch-staging/main armhf libarpack2 armhf 3.3.0-1+b1 [78.1 kB]
Get:41 http://172.17.0.1/private stretch-staging/main armhf libarmadillo6 armhf 1:6.700.3+dfsg-1 [78.0 kB]
Get:42 http://172.17.0.1/private stretch-staging/main armhf libblas-dev armhf 3.6.0-2 [116 kB]
Get:43 http://172.17.0.1/private stretch-staging/main armhf liblapack-dev armhf 3.6.0-2 [1355 kB]
Get:44 http://172.17.0.1/private stretch-staging/main armhf libarpack2-dev armhf 3.3.0-1+b1 [89.3 kB]
Get:45 http://172.17.0.1/private stretch-staging/main armhf libsz2 armhf 0.3.2-1 [5836 B]
Get:46 http://172.17.0.1/private stretch-staging/main armhf libhdf5-10 armhf 1.8.16+docs-7 [978 kB]
Get:47 http://172.17.0.1/private stretch-staging/main armhf zlib1g-dev armhf 1:1.2.8.dfsg-2+b1 [197 kB]
Get:48 http://172.17.0.1/private stretch-staging/main armhf libjpeg62-turbo armhf 1:1.4.2-2 [104 kB]
Get:49 http://172.17.0.1/private stretch-staging/main armhf libjpeg62-turbo-dev armhf 1:1.4.2-2 [413 kB]
Get:50 http://172.17.0.1/private stretch-staging/main armhf libjpeg-dev all 1:1.4.2-2 [51.7 kB]
Get:51 http://172.17.0.1/private stretch-staging/main armhf libaec-dev armhf 0.3.2-1 [17.6 kB]
Get:52 http://172.17.0.1/private stretch-staging/main armhf libhdf5-cpp-11 armhf 1.8.16+docs-7 [115 kB]
Get:53 http://172.17.0.1/private stretch-staging/main armhf libhdf5-dev armhf 1.8.16+docs-7 [4907 kB]
Get:54 http://172.17.0.1/private stretch-staging/main armhf libsuperlu-dev armhf 4.3+dfsg-3 [150 kB]
Get:55 http://172.17.0.1/private stretch-staging/main armhf libarmadillo-dev armhf 1:6.700.3+dfsg-1 [307 kB]
Get:56 http://172.17.0.1/private stretch-staging/main armhf libboost1.58-dev armhf 1.58.0+dfsg-5+b1 [6232 kB]
Get:57 http://172.17.0.1/private stretch-staging/main armhf libboost-dev armhf 1.58.0.1+b1 [3748 B]
Get:58 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:59 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:60 http://172.17.0.1/private stretch-staging/main armhf libboost-program-options-dev armhf 1.58.0.1+b1 [3404 B]
Get:61 http://172.17.0.1/private stretch-staging/main armhf libdlib-data all 18.18-1 [63.3 MB]
Get:62 http://172.17.0.1/private stretch-staging/main armhf libdlib18 armhf 18.18-1 [223 kB]
Get:63 http://172.17.0.1/private stretch-staging/main armhf libdlib-dev armhf 18.18-1 [1067 kB]
Get:64 http://172.17.0.1/private stretch-staging/main armhf libgzstream0 armhf 1.5+dfsg-2 [5764 B]
Get:65 http://172.17.0.1/private stretch-staging/main armhf libgzstream-dev armhf 1.5+dfsg-2 [6172 B]
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Processing triggers for libc-bin (2.22-5) ...
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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
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Setting up libpipeline1:armhf (1.4.1-2) ...
Setting up man-db (2.7.5-1) ...
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Setting up libunistring0:armhf (0.9.3-5.2) ...
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Setting up gettext-base (0.19.7-2) ...
Setting up libsqlite3-0:armhf (3.12.1-1) ...
Setting up libicu55:armhf (55.1-7) ...
Setting up libxml2:armhf (2.9.3+dfsg1-1) ...
Setting up libsigsegv2:armhf (2.10-5) ...
Setting up m4 (1.4.17-5) ...
Setting up autoconf (2.69-10) ...
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Setting up libffi6:armhf (3.2.1-4) ...
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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 libtool (2.4.6-0.1) ...
Setting up libgfortran-5-dev:armhf (5.3.1-14) ...
Setting up gfortran-5 (5.3.1-14) ...
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-7) ...
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 (1:6.700.3+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
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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-7) ...
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-7) ...
Setting up libhdf5-dev (1.8.16+docs-7) ...
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 (1:6.700.3+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) ...
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Setting up libgzstream0 (1.5+dfsg-2) ...
Setting up libgzstream-dev (1.5+dfsg-2) ...
Setting up dh-autoreconf (12) ...
Setting up debhelper (9.20160403) ...
Setting up sbuild-build-depends-seer-dummy (0.invalid.0) ...
Setting up dh-strip-nondeterminism (0.016-1) ...
Processing triggers for libc-bin (2.22-5) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.5.0-1-armmp armhf (armv7l)
Toolchain package versions: binutils_2.26-8 dpkg-dev_1.18.4 g++-5_5.3.1-14 gcc-5_5.3.1-14 libc6-dev_2.22-5 libstdc++-5-dev_5.3.1-14 libstdc++6_5.3.1-14 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch
Package versions: adduser_3.114 apt_1.2.10 autoconf_2.69-10 automake_1:1.15-4 autopoint_0.19.7-2 autotools-dev_20150820.1 base-files_9.6+rpi1 base-passwd_3.5.39 bash_4.3-14 binutils_2.26-8 bsdmainutils_9.0.10 bsdutils_1:2.27.1-6 build-essential_11.7 bzip2_1.0.6-8 console-setup_1.141 console-setup-linux_1.141 coreutils_8.25-2 cpio_2.11+dfsg-5 cpp_4:5.3.1-1+rpi1 cpp-5_5.3.1-14 dash_0.5.8-2.2 debconf_1.5.59 debfoster_2.7-2 debhelper_9.20160403 debianutils_4.7 dh-autoreconf_12 dh-strip-nondeterminism_0.016-1 diffutils_1:3.3-3 dmsetup_2:1.02.120-1 dpkg_1.18.4 dpkg-dev_1.18.4 e2fslibs_1.43~WIP.2016.03.15-2 e2fsprogs_1.43~WIP.2016.03.15-2 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_5.3.1-14 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_5.3.1-14 gcc-5-base_5.3.1-14 gettext_0.19.7-2 gettext-base_0.19.7-2 gfortran_4:5.3.1-1+rpi1 gfortran-5_5.3.1-14 gnupg_1.4.20-5 gpgv_1.4.20-5 grep_2.22-1 groff-base_1.22.3-7 gzip_1.6-5 hdf5-helpers_1.8.16+docs-7 hostname_3.17 ifupdown_0.8.10 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 iproute2_4.3.0-1 kbd_2.0.3-2 keyboard-configuration_1.141 klibc-utils_2.0.4-8+rpi1 kmod_22-1.1 libacl1_2.2.52-3 libaec-dev_0.3.2-1 libaec0_0.3.2-1 libapparmor1_2.10-4 libapt-pkg5.0_1.2.10 libarchive-zip-perl_1.57-1 libarmadillo-dev_1:6.700.3+dfsg-1 libarmadillo6_1:6.700.3+dfsg-1 libarpack2_3.3.0-1+b1 libarpack2-dev_3.3.0-1+b1 libasan2_5.3.1-14 libatm1_1:2.5.1-1.5 libatomic1_5.3.1-14 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_2.22-5 libc-dev-bin_2.22-5 libc6_2.22-5 libc6-dev_2.22-5 libcap2_1:2.24-12 libcap2-bin_1:2.24-12 libcc1-0_5.3.1-14 libcomerr2_1.43~WIP.2016.03.15-2 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_0.208 libdevmapper1.02.1_2:1.02.120-1 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_1:7.4.2-7.4 libgcc-5-dev_5.3.1-14 libgcc1_1:5.3.1-14 libgcrypt20_1.6.5-2 libgdbm3_1.8.3-13.1 libgfortran-5-dev_5.3.1-14 libgfortran3_5.3.1-14 libglib2.0-0_2.48.0-1 libgmp10_2:6.1.0+dfsg-2 libgomp1_5.3.1-14 libgpg-error0_1.21-2 libgzstream-dev_1.5+dfsg-2 libgzstream0_1.5+dfsg-2 libhdf5-10_1.8.16+docs-7 libhdf5-cpp-11_1.8.16+docs-7 libhdf5-dev_1.8.16+docs-7 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_22-1.1 liblapack-dev_3.6.0-2 liblapack3_3.6.0-2 liblocale-gettext-perl_1.07-1+b1 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+20160319-1 libncursesw5_6.0+20160319-1 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_2:8.38-3.1 libperl5.22_5.22.1-9 libpipeline1_1.4.1-2 libplymouth4_0.9.2-3 libpng12-0_1.2.54-6 libprocps5_2:3.3.11-3 libreadline6_6.3-8+b3 libseccomp2_2.3.0-1 libselinux1_2.4-3 libsemanage-common_2.4-3 libsemanage1_2.4-3 libsepol1_2.4-2 libsigsegv2_2.10-5 libsmartcols1_2.27.1-6 libsqlite3-0_3.12.1-1 libss2_1.43~WIP.2016.03.15-2 libstdc++-5-dev_5.3.1-14 libstdc++6_5.3.1-14 libsuperlu-dev_4.3+dfsg-3 libsuperlu4_4.3+dfsg-3 libsystemd0_229-4 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+20160319-1 libtool_2.4.6-0.1 libubsan0_5.3.1-14 libudev1_229-4 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 m4_1.4.17-5 make_4.1-9 makedev_2.3.1-93 man-db_2.7.5-1 manpages_4.05-1 mawk_1.3.3-17 mount_2.27.1-6 multiarch-support_2.22-5 ncurses-base_6.0+20160319-1 ncurses-bin_6.0+20160319-1 netbase_5.3 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 psmisc_22.21-2.1 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_229-4 systemd-sysv_229-4 sysv-rc_2.88dsf-59.3 sysvinit-utils_2.88dsf-59.3 tar_1.28-2.1 tzdata_2016c-0+deb8u1 udev_229-4 util-linux_2.27.1-6 xkb-data_2.17-1 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 Tue Apr 19 08:44:13 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_1.1.1-2.dsc
dpkg-source: info: extracting seer in seer-1.1.1
dpkg-source: info: unpacking seer_1.1.1.orig.tar.gz
dpkg-source: info: unpacking seer_1.1.1-2.debian.tar.xz
dpkg-source: info: applying fix_lib_location.patch
dpkg-source: info: applying hardening.patch
Check disc space
----------------
Sufficient free space for build
User Environment
----------------
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LOGNAME=buildd
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=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=stretch-staging-armhf-sbuild-856aa61d-c354-488a-b77f-1cc7c37eb694
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: source package seer
dpkg-buildpackage: source version 1.1.1-2
dpkg-buildpackage: source distribution unstable
dpkg-source --before-build seer-1.1.1
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
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 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=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 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=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 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o kmer.o kmer.cpp
g++ -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=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 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o seerCommon.o seerCommon.cpp
seerCommon.cpp: In function 'arma::vec dlib_to_arma(const column_vector&)':
seerCommon.cpp:183:31: 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 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o seerErr.o seerErr.cpp
g++ -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o seerFilter.o seerFilter.cpp
g++ -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o seerIO.o seerIO.cpp
g++ -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o seerChiFilter.o seerChiFilter.cpp
g++ -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o seerMain.o seerMain.cpp
g++ -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o seerCmdLine.o seerCmdLine.cpp
g++ -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o seerContinuousAssoc.o seerContinuousAssoc.cpp
g++ -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o seerBinaryAssoc.o seerBinaryAssoc.cpp
g++ -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o logitFunction.o logitFunction.cpp
g++ -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o linearFunction.o linearFunction.cpp
g++ -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=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 -lpthread -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 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o kmdsMain.o kmdsMain.cpp
g++ -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o kmdsStruct.o kmdsStruct.cpp
g++ -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o kmdsCmdLine.o kmdsCmdLine.cpp
g++ -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=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 -lpthread -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 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=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 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=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 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o mapCmdLine.o mapCmdLine.cpp
g++ -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -fPIE -pie -Wl,-z,relro -Wl,-z,now fasta.o significant_kmer.o mapMain.o mapCmdLine.o -lboost_program_options -lpthread -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 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=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 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=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 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o combineKmers.o combineKmers.cpp
g++ -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=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 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=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 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o filterCmdLine.o filterCmdLine.cpp
g++ -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=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'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
debian/rules override_dh_auto_test
make[1]: Entering directory '/<<PKGBUILDDIR>>'
if dh_auto_test ; then echo Test passed ; else echo '****************************** TEST FAILED. Please contact upstream *******************************' ; fi
make -j1 test
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 test
make[3]: Entering directory '/<<PKGBUILDDIR>>/test'
./run_test.pl && touch tests_passed
FAILED test 1, basic filters
Makefile:2: recipe for target 'all' failed
make[3]: *** [all] Error 1
make[3]: Leaving directory '/<<PKGBUILDDIR>>/test'
Makefile:15: recipe for target 'test' failed
make[2]: *** [test] Error 2
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_test: make -j1 test returned exit code 2
****************************** TEST FAILED. Please contact upstream *******************************
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
fakeroot debian/rules binary-arch
seer: sequence element enrichment analysis
Detected binary phenotype
sequence maf unadj_p_val p_val beta se comments
Done.
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 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/combineKmers debian/seer/usr/bin/seer were not linked against libz.so.1 (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)
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_1.1.1-2_armhf.deb'.
dpkg-deb: building package 'seer' in '../seer_1.1.1-2_armhf.deb'.
dpkg-genchanges -B -mRaspbian wandboard test autobuilder <root@raspbian.org> >../seer_1.1.1-2_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-1.1.1
dpkg-buildpackage: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 20160425-0601
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
seer_1.1.1-2_armhf.changes:
---------------------------
Format: 1.8
Date: Tue, 19 Apr 2016 10:39:15 +0200
Source: seer
Binary: seer
Architecture: armhf
Version: 1.1.1-2
Distribution: stretch-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
seer - genomic sequence element (kmer) enrichment analysis
Changes:
seer (1.1.1-2) unstable; urgency=medium
.
* use -DARMA_USE_HDF5=1
Checksums-Sha1:
2f53ec6ea539a605ca1864c0720a398b74def6a9 7259098 seer-dbgsym_1.1.1-2_armhf.deb
d60478e5091247d24f1149d2aff81c1fd820161e 301504 seer_1.1.1-2_armhf.deb
Checksums-Sha256:
9fe6293733b339d318f9cfb717981035ebd90e09db848f5481c5634735957506 7259098 seer-dbgsym_1.1.1-2_armhf.deb
ecadc7584c981f32cd67d510e6bd372fd399d223ffd59dc364c9d0afa3b74994 301504 seer_1.1.1-2_armhf.deb
Files:
6ce30d06046e079c2d70e0e4388067fc 7259098 debug extra seer-dbgsym_1.1.1-2_armhf.deb
b086a3d2f7f5778536e261b1026abcbc 301504 science optional seer_1.1.1-2_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
seer-dbgsym_1.1.1-2_armhf.deb
-----------------------------
new debian package, version 2.0.
size 7259098 bytes: control archive=714 bytes.
563 bytes, 13 lines control
530 bytes, 5 lines md5sums
Package: seer-dbgsym
Source: seer
Version: 1.1.1-2
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 7621
Depends: seer (= 1.1.1-2)
Section: debug
Priority: extra
Homepage: https://github.com/johnlees/seer
Description: Debug symbols for seer
Auto-Built-Package: debug-symbols
Build-Ids: 1ecafe4f0541fda6e905f12cbd3ddd29f34a2cc5 32614c8ad02d88cf636feb421d06a04d384fdbff 4b87f661131193a25d0e4fdfa8c9ca2157e28cb7 7b5c7f8819820293cde86151ca532c5b8896cb7c 7db649f9ace90956fd4eabc533bbb919a83cd23d
drwxr-xr-x root/root 0 2016-04-25 06:01 ./
drwxr-xr-x root/root 0 2016-04-25 06:01 ./usr/
drwxr-xr-x root/root 0 2016-04-25 06:00 ./usr/lib/
drwxr-xr-x root/root 0 2016-04-25 06:00 ./usr/lib/debug/
drwxr-xr-x root/root 0 2016-04-25 06:01 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2016-04-25 06:01 ./usr/lib/debug/.build-id/1e/
-rw-r--r-- root/root 461920 2016-04-25 06:01 ./usr/lib/debug/.build-id/1e/cafe4f0541fda6e905f12cbd3ddd29f34a2cc5.debug
drwxr-xr-x root/root 0 2016-04-25 06:01 ./usr/lib/debug/.build-id/32/
-rw-r--r-- root/root 330000 2016-04-25 06:01 ./usr/lib/debug/.build-id/32/614c8ad02d88cf636feb421d06a04d384fdbff.debug
drwxr-xr-x root/root 0 2016-04-25 06:01 ./usr/lib/debug/.build-id/4b/
-rw-r--r-- root/root 3235828 2016-04-25 06:01 ./usr/lib/debug/.build-id/4b/87f661131193a25d0e4fdfa8c9ca2157e28cb7.debug
drwxr-xr-x root/root 0 2016-04-25 06:01 ./usr/lib/debug/.build-id/7b/
-rw-r--r-- root/root 778704 2016-04-25 06:01 ./usr/lib/debug/.build-id/7b/5c7f8819820293cde86151ca532c5b8896cb7c.debug
drwxr-xr-x root/root 0 2016-04-25 06:01 ./usr/lib/debug/.build-id/7d/
-rw-r--r-- root/root 2980576 2016-04-25 06:01 ./usr/lib/debug/.build-id/7d/b649f9ace90956fd4eabc533bbb919a83cd23d.debug
drwxr-xr-x root/root 0 2016-04-25 06:01 ./usr/share/
drwxr-xr-x root/root 0 2016-04-25 06:01 ./usr/share/doc/
lrwxrwxrwx root/root 0 2016-04-25 06:01 ./usr/share/doc/seer-dbgsym -> seer
seer_1.1.1-2_armhf.deb
----------------------
new debian package, version 2.0.
size 301504 bytes: control archive=1504 bytes.
1413 bytes, 24 lines control
1005 bytes, 16 lines md5sums
Package: seer
Version: 1.1.1-2
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1383
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
Suggests: fsm-lite
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.
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-rwxr-xr-x root/root 3799 2016-03-31 08:55 ./usr/bin/blast_top_hits
-rwxr-xr-x root/root 108084 2016-04-25 06:01 ./usr/bin/combineKmers
-rwxr-xr-x root/root 71220 2016-04-25 06:01 ./usr/bin/filter_seer
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-rw-r--r-- root/root 293 2016-04-19 08:40 ./usr/share/doc/seer/README.Debian
-rw-r--r-- root/root 316 2016-04-19 08:40 ./usr/share/doc/seer/changelog.Debian.gz
-rw-r--r-- root/root 1008 2016-04-19 08:40 ./usr/share/doc/seer/copyright
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-rw-r--r-- root/root 2110 2016-03-31 08:55 ./usr/share/doc/seer/examples/example_wrapper.py.gz
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drwxr-xr-x root/root 0 2016-04-25 06:00 ./usr/share/man/man1/
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-rw-r--r-- root/root 509 2016-04-25 06:00 ./usr/share/man/man1/combineKmers.1.gz
-rw-r--r-- root/root 590 2016-04-25 06:00 ./usr/share/man/man1/filter_seer.1.gz
-rw-r--r-- root/root 993 2016-04-25 06:00 ./usr/share/man/man1/kmds.1.gz
-rw-r--r-- root/root 486 2016-04-25 06:00 ./usr/share/man/man1/map_back.1.gz
-rw-r--r-- root/root 1064 2016-04-25 06:00 ./usr/share/man/man1/seer.1.gz
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Build Architecture: armhf
Build-Space: 73808
Build-Time: 1537
Distribution: stretch-staging
Host Architecture: armhf
Install-Time: 373
Job: seer_1.1.1-2
Machine Architecture: armhf
Package: seer
Package-Time: 1953
Source-Version: 1.1.1-2
Space: 73808
Status: successful
Version: 1.1.1-2
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Finished at 20160425-0601
Build needed 00:32:33, 73808k disc space