seer →
1.1.1-2+b1 →
armhf → 2016-09-16 04:57:59
sbuild (Debian sbuild) 0.66.0 (04 Oct 2015) on bm-wb-03
+==============================================================================+
| seer 1.1.1-2+b1 (armhf) 16 Sep 2016 04:21 |
+==============================================================================+
Package: seer
Version: 1.1.1-2+b1
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-dXN6nr/seer-1.1.1' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/seer-dXN6nr' with '<<BUILDDIR>>'
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/stretch-staging-armhf-sbuild-1371bdb2-19db-458c-91bc-0ae39cf4b104' 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 [9284 kB]
Get:3 http://172.17.0.1/private stretch-staging/main armhf Packages [11.2 MB]
Fetched 20.5 MB in 22s (925 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 (2706 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-riWQ3j/apt_archive/sbuild-build-depends-core-dummy.deb'.
Warning: apt-key output should not be parsed (stdout is not a terminal)
OK
Get:1 file:/<<BUILDDIR>>/resolver-riWQ3j/apt_archive ./ InRelease
Ign:1 file:/<<BUILDDIR>>/resolver-riWQ3j/apt_archive ./ InRelease
Get:2 file:/<<BUILDDIR>>/resolver-riWQ3j/apt_archive ./ Release [2119 B]
Get:2 file:/<<BUILDDIR>>/resolver-riWQ3j/apt_archive ./ Release [2119 B]
Get:3 file:/<<BUILDDIR>>/resolver-riWQ3j/apt_archive ./ Release.gpg [299 B]
Get:3 file:/<<BUILDDIR>>/resolver-riWQ3j/apt_archive ./ Release.gpg [299 B]
Get:4 file:/<<BUILDDIR>>/resolver-riWQ3j/apt_archive ./ Sources [214 B]
Get:5 file:/<<BUILDDIR>>/resolver-riWQ3j/apt_archive ./ Packages [525 B]
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
W: file:///<<BUILDDIR>>/resolver-riWQ3j/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 33 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-riWQ3j/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 ... 13920 files and directories currently installed.)
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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-kv2lPW/apt_archive/sbuild-build-depends-seer-dummy.deb'.
Warning: apt-key output should not be parsed (stdout is not a terminal)
OK
Get:1 file:/<<BUILDDIR>>/resolver-kv2lPW/apt_archive ./ InRelease
Ign:1 file:/<<BUILDDIR>>/resolver-kv2lPW/apt_archive ./ InRelease
Get:2 file:/<<BUILDDIR>>/resolver-kv2lPW/apt_archive ./ Release [2119 B]
Get:2 file:/<<BUILDDIR>>/resolver-kv2lPW/apt_archive ./ Release [2119 B]
Get:3 file:/<<BUILDDIR>>/resolver-kv2lPW/apt_archive ./ Release.gpg [299 B]
Get:3 file:/<<BUILDDIR>>/resolver-kv2lPW/apt_archive ./ Release.gpg [299 B]
Get:4 file:/<<BUILDDIR>>/resolver-kv2lPW/apt_archive ./ Sources [255 B]
Get:5 file:/<<BUILDDIR>>/resolver-kv2lPW/apt_archive ./ Packages [568 B]
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
W: file:///<<BUILDDIR>>/resolver-kv2lPW/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-6 groff-base hdf5-helpers intltool-debian libaec-dev libaec0
libarchive-zip-perl libarmadillo-dev libarmadillo7 libarpack2 libarpack2-dev
libblas-common libblas-dev libblas3 libboost-dev
libboost-program-options-dev libboost-program-options1.61-dev
libboost-program-options1.61.0 libboost1.61-dev libbsd0 libcroco3
libdlib-data libdlib-dev libdlib18 libffi6 libfile-stripnondeterminism-perl
libgfortran-6-dev libgfortran3 libglib2.0-0 libgzstream-dev libgzstream0
libhdf5-10 libhdf5-cpp-11 libhdf5-dev libicu57 libjpeg-dev libjpeg62-turbo
libjpeg62-turbo-dev liblapack-dev liblapack3 libmagic-mgc libmagic1
libpipeline1 libsigsegv2 libsqlite3-0 libsuperlu-dev libsuperlu5 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-6-doc libgfortran3-dbg libcoarrays-dev groff libitpp-dev
liblapack-doc-man liblapack-doc libboost-doc libboost1.61-doc
libboost-atomic1.61-dev libboost-chrono1.61-dev libboost-context1.61-dev
libboost-coroutine1.61-dev libboost-date-time1.61-dev
libboost-exception1.61-dev libboost-filesystem1.61-dev
libboost-graph1.61-dev libboost-graph-parallel1.61-dev
libboost-iostreams1.61-dev libboost-locale1.61-dev libboost-log1.61-dev
libboost-math1.61-dev libboost-mpi1.61-dev libboost-mpi-python1.61-dev
libboost-python1.61-dev libboost-random1.61-dev libboost-regex1.61-dev
libboost-serialization1.61-dev libboost-signals1.61-dev
libboost-system1.61-dev libboost-test1.61-dev libboost-thread1.61-dev
libboost-timer1.61-dev libboost-wave1.61-dev libboost1.61-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-6 groff-base hdf5-helpers intltool-debian libaec-dev libaec0
libarchive-zip-perl libarmadillo-dev libarmadillo7 libarpack2 libarpack2-dev
libblas-common libblas-dev libblas3 libboost-dev
libboost-program-options-dev libboost-program-options1.61-dev
libboost-program-options1.61.0 libboost1.61-dev libbsd0 libcroco3
libdlib-data libdlib-dev libdlib18 libffi6 libfile-stripnondeterminism-perl
libgfortran-6-dev libgfortran3 libglib2.0-0 libgzstream-dev libgzstream0
libhdf5-10 libhdf5-cpp-11 libhdf5-dev libicu57 libjpeg-dev libjpeg62-turbo
libjpeg62-turbo-dev liblapack-dev liblapack3 libmagic-mgc libmagic1
libpipeline1 libsigsegv2 libsqlite3-0 libsuperlu-dev libsuperlu5 libsz2
libtimedate-perl libtool libunistring0 libxml2 m4 man-db po-debconf
sbuild-build-depends-seer-dummy zlib1g-dev
0 upgraded, 69 newly installed, 0 to remove and 33 not upgraded.
Need to get 130 MB/130 MB of archives.
After this operation, 455 MB of additional disk space will be used.
Get:1 file:/<<BUILDDIR>>/resolver-kv2lPW/apt_archive ./ sbuild-build-depends-seer-dummy 0.invalid.0 [806 B]
Get:2 http://172.17.0.1/private stretch-staging/main armhf groff-base armhf 1.22.3-8 [1087 kB]
Get:3 http://172.17.0.1/private stretch-staging/main armhf libbsd0 armhf 0.8.3-1 [89.0 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 libmagic-mgc armhf 1:5.28-4 [210 kB]
Get:8 http://172.17.0.1/private stretch-staging/main armhf libmagic1 armhf 1:5.28-4 [104 kB]
Get:9 http://172.17.0.1/private stretch-staging/main armhf file armhf 1:5.28-4 [62.7 kB]
Get:10 http://172.17.0.1/private stretch-staging/main armhf gettext-base armhf 0.19.8.1-1 [117 kB]
Get:11 http://172.17.0.1/private stretch-staging/main armhf libsqlite3-0 armhf 3.14.1-1 [483 kB]
Get:12 http://172.17.0.1/private stretch-staging/main armhf libicu57 armhf 57.1-4 [7407 kB]
Get:13 http://172.17.0.1/private stretch-staging/main armhf libxml2 armhf 2.9.4+dfsg1-1+b1 [803 kB]
Get:14 http://172.17.0.1/private stretch-staging/main armhf libsigsegv2 armhf 2.10-5 [28.4 kB]
Get:15 http://172.17.0.1/private stretch-staging/main armhf m4 armhf 1.4.17-5 [239 kB]
Get:16 http://172.17.0.1/private stretch-staging/main armhf autoconf all 2.69-10 [338 kB]
Get:17 http://172.17.0.1/private stretch-staging/main armhf autotools-dev all 20160430.1 [72.6 kB]
Get:18 http://172.17.0.1/private stretch-staging/main armhf automake all 1:1.15-4 [735 kB]
Get:19 http://172.17.0.1/private stretch-staging/main armhf autopoint all 0.19.8.1-1 [433 kB]
Get:20 http://172.17.0.1/private stretch-staging/main armhf libtool all 2.4.6-2 [545 kB]
Get:21 http://172.17.0.1/private stretch-staging/main armhf dh-autoreconf all 12 [15.8 kB]
Get:22 http://172.17.0.1/private stretch-staging/main armhf libarchive-zip-perl all 1.59-1 [95.5 kB]
Get:23 http://172.17.0.1/private stretch-staging/main armhf libfile-stripnondeterminism-perl all 0.023-2 [13.4 kB]
Get:24 http://172.17.0.1/private stretch-staging/main armhf libtimedate-perl all 2.3000-2 [42.2 kB]
Get:25 http://172.17.0.1/private stretch-staging/main armhf dh-strip-nondeterminism all 0.023-2 [8202 B]
Get:26 http://172.17.0.1/private stretch-staging/main armhf libglib2.0-0 armhf 2.49.6-1 [2518 kB]
Get:27 http://172.17.0.1/private stretch-staging/main armhf libcroco3 armhf 0.6.11-1 [131 kB]
Get:28 http://172.17.0.1/private stretch-staging/main armhf libunistring0 armhf 0.9.6+really0.9.3-0.1 [252 kB]
Get:29 http://172.17.0.1/private stretch-staging/main armhf gettext armhf 0.19.8.1-1 [1433 kB]
Get:30 http://172.17.0.1/private stretch-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:31 http://172.17.0.1/private stretch-staging/main armhf po-debconf all 1.0.19 [249 kB]
Get:32 http://172.17.0.1/private stretch-staging/main armhf debhelper all 10 [823 kB]
Get:33 http://172.17.0.1/private stretch-staging/main armhf libgfortran3 armhf 6.1.1-11+rpi1 [166 kB]
Get:34 http://172.17.0.1/private stretch-staging/main armhf libgfortran-6-dev armhf 6.1.1-11+rpi1 [200 kB]
Get:35 http://172.17.0.1/private stretch-staging/main armhf gfortran-6 armhf 6.1.1-11+rpi1 [27.9 MB]
Get:36 http://172.17.0.1/private stretch-staging/main armhf gfortran armhf 4:6.1.1-1 [1370 B]
Get:37 http://172.17.0.1/private stretch-staging/main armhf hdf5-helpers armhf 1.8.16+docs-8 [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 libblas-common armhf 3.6.1-2 [13.9 kB]
Get:40 http://172.17.0.1/private stretch-staging/main armhf libblas3 armhf 3.6.1-2 [112 kB]
Get:41 http://172.17.0.1/private stretch-staging/main armhf liblapack3 armhf 3.6.1-2 [1392 kB]
Get:42 http://172.17.0.1/private stretch-staging/main armhf libarpack2 armhf 3.4.0-1 [78.4 kB]
Get:43 http://172.17.0.1/private stretch-staging/main armhf libsuperlu5 armhf 5.2.1+dfsg1-2 [126 kB]
Get:44 http://172.17.0.1/private stretch-staging/main armhf libarmadillo7 armhf 1:7.400.1+dfsg-2 [80.0 kB]
Get:45 http://172.17.0.1/private stretch-staging/main armhf libblas-dev armhf 3.6.1-2 [18.9 kB]
Get:46 http://172.17.0.1/private stretch-staging/main armhf liblapack-dev armhf 3.6.1-2 [1379 kB]
Get:47 http://172.17.0.1/private stretch-staging/main armhf libarpack2-dev armhf 3.4.0-1 [89.6 kB]
Get:48 http://172.17.0.1/private stretch-staging/main armhf libsz2 armhf 0.3.2-1 [5836 B]
Get:49 http://172.17.0.1/private stretch-staging/main armhf libhdf5-10 armhf 1.8.16+docs-8 [981 kB]
Get:50 http://172.17.0.1/private stretch-staging/main armhf zlib1g-dev armhf 1:1.2.8.dfsg-2+b1 [197 kB]
Get:51 http://172.17.0.1/private stretch-staging/main armhf libjpeg62-turbo armhf 1:1.5.0-1 [109 kB]
Get:52 http://172.17.0.1/private stretch-staging/main armhf libjpeg62-turbo-dev armhf 1:1.5.0-1 [181 kB]
Get:53 http://172.17.0.1/private stretch-staging/main armhf libjpeg-dev all 1:1.5.0-1 [54.8 kB]
Get:54 http://172.17.0.1/private stretch-staging/main armhf libaec-dev armhf 0.3.2-1 [17.6 kB]
Get:55 http://172.17.0.1/private stretch-staging/main armhf libhdf5-cpp-11 armhf 1.8.16+docs-8 [115 kB]
Get:56 http://172.17.0.1/private stretch-staging/main armhf libhdf5-dev armhf 1.8.16+docs-8 [4909 kB]
Get:57 http://172.17.0.1/private stretch-staging/main armhf libsuperlu-dev armhf 5.2.1+dfsg1-2 [18.0 kB]
Get:58 http://172.17.0.1/private stretch-staging/main armhf libarmadillo-dev armhf 1:7.400.1+dfsg-2 [319 kB]
Get:59 http://172.17.0.1/private stretch-staging/main armhf libboost1.61-dev armhf 1.61.0+dfsg-2.1 [6851 kB]
Get:60 http://172.17.0.1/private stretch-staging/main armhf libboost-dev armhf 1.61.0.2 [3758 B]
Get:61 http://172.17.0.1/private stretch-staging/main armhf libboost-program-options1.61.0 armhf 1.61.0+dfsg-2.1 [137 kB]
Get:62 http://172.17.0.1/private stretch-staging/main armhf libboost-program-options1.61-dev armhf 1.61.0+dfsg-2.1 [177 kB]
Get:63 http://172.17.0.1/private stretch-staging/main armhf libboost-program-options-dev armhf 1.61.0.2 [3416 B]
Get:64 http://172.17.0.1/private stretch-staging/main armhf libdlib-data all 18.18-1 [63.3 MB]
Get:65 http://172.17.0.1/private stretch-staging/main armhf libdlib18 armhf 18.18-1 [223 kB]
Get:66 http://172.17.0.1/private stretch-staging/main armhf libdlib-dev armhf 18.18-1 [1067 kB]
Get:67 http://172.17.0.1/private stretch-staging/main armhf libgzstream0 armhf 1.5+dfsg-2 [5764 B]
Get:68 http://172.17.0.1/private stretch-staging/main armhf libgzstream-dev armhf 1.5+dfsg-2 [6172 B]
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+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 3.19.0-trunk-armmp armhf (armv7l)
Toolchain package versions: binutils_2.26.1-1 dpkg-dev_1.18.10 g++-6_6.1.1-11+rpi1 gcc-6_6.1.1-11+rpi1 libc6-dev_2.23-4 libstdc++-6-dev_6.1.1-11+rpi1 libstdc++6_6.1.1-11+rpi1 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch
Package versions: adduser_3.115 apt_1.3~pre3 autoconf_2.69-10 automake_1:1.15-4 autopoint_0.19.8.1-1 autotools-dev_20160430.1 base-files_9.6+rpi1 base-passwd_3.5.39 bash_4.3-15 binutils_2.26.1-1 bsdmainutils_9.0.10 bsdutils_1:2.28-6 build-essential_12.2 bzip2_1.0.6-8 console-setup_1.147 console-setup-linux_1.147 coreutils_8.25-2 cpio_2.11+dfsg-5 cpp_4:6.1.1-1 cpp-6_6.1.1-11+rpi1 dash_0.5.8-2.3 debconf_1.5.59 debfoster_2.7-2.1 debhelper_10 debianutils_4.8 dh-autoreconf_12 dh-strip-nondeterminism_0.023-2 diffutils_1:3.3-3 dmsetup_2:1.02.130-1 dpkg_1.18.10 dpkg-dev_1.18.10 e2fslibs_1.43.1-1 e2fsprogs_1.43.1-1 fakeroot_1.21-1 file_1:5.28-4 findutils_4.6.0+git+20160703-2 fuse2fs_1.43.1-1 g++_4:6.1.1-1 g++-6_6.1.1-11+rpi1 gcc_4:6.1.1-1 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_4.9.3-14 gcc-5-base_5.4.0-4 gcc-6_6.1.1-11+rpi1 gcc-6-base_6.1.1-11+rpi1 gettext_0.19.8.1-1 gettext-base_0.19.8.1-1 gfortran_4:6.1.1-1 gfortran-6_6.1.1-11+rpi1 gnupg_1.4.20-6 gpgv_1.4.20-6 grep_2.25-6 groff-base_1.22.3-8 gzip_1.6-5 hdf5-helpers_1.8.16+docs-8 hostname_3.18 ifupdown_0.8.13 init_1.42 init-system-helpers_1.42 initscripts_2.88dsf-59.8 insserv_1.14.0-5.4 intltool-debian_0.35.0+20060710.4 iproute2_4.6.0-1 kbd_2.0.3-2 keyboard-configuration_1.147 klibc-utils_2.0.4-9+rpi1 kmod_22-1.1 libacl1_2.2.52-3 libaec-dev_0.3.2-1 libaec0_0.3.2-1 libapparmor1_2.10.95-4 libapt-pkg5.0_1.3~pre3 libarchive-zip-perl_1.59-1 libarmadillo-dev_1:7.400.1+dfsg-2 libarmadillo7_1:7.400.1+dfsg-2 libarpack2_3.4.0-1 libarpack2-dev_3.4.0-1 libasan3_6.1.1-11+rpi1 libatm1_1:2.5.1-1.6 libatomic1_6.1.1-11+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.6.5-1 libaudit1_1:2.6.5-1 libblas-common_3.6.1-2 libblas-dev_3.6.1-2 libblas3_3.6.1-2 libblkid1_2.28-6 libboost-dev_1.61.0.2 libboost-program-options-dev_1.61.0.2 libboost-program-options1.61-dev_1.61.0+dfsg-2.1 libboost-program-options1.61.0_1.61.0+dfsg-2.1 libboost1.61-dev_1.61.0+dfsg-2.1 libbsd0_0.8.3-1 libbz2-1.0_1.0.6-8 libc-bin_2.23-4 libc-dev-bin_2.23-4 libc6_2.23-4 libc6-dev_2.23-4 libcap-ng0_0.7.7-3 libcap2_1:2.25-1 libcap2-bin_1:2.25-1 libcc1-0_6.1.1-11+rpi1 libcomerr2_1.43.1-1 libcroco3_0.6.11-1 libcryptsetup4_2:1.7.0-2 libdb5.3_5.3.28-12 libdbus-1-3_1.10.8-1 libdebconfclient0_0.215 libdevmapper1.02.1_2:1.02.130-1 libdlib-data_18.18-1 libdlib-dev_18.18-1 libdlib18_18.18-1 libdpkg-perl_1.18.10 libdrm2_2.4.70-1 libfakeroot_1.21-1 libfdisk1_2.28-6 libffi6_3.2.1-4 libfile-stripnondeterminism-perl_0.023-2 libfuse2_2.9.7-1 libgc1c2_1:7.4.2-8 libgcc-6-dev_6.1.1-11+rpi1 libgcc1_1:6.1.1-11+rpi1 libgcrypt20_1.7.2-2 libgdbm3_1.8.3-14 libgfortran-6-dev_6.1.1-11+rpi1 libgfortran3_6.1.1-11+rpi1 libglib2.0-0_2.49.6-1 libgmp10_2:6.1.1+dfsg-1 libgomp1_6.1.1-11+rpi1 libgpg-error0_1.24-1 libgzstream-dev_1.5+dfsg-2 libgzstream0_1.5+dfsg-2 libhdf5-10_1.8.16+docs-8 libhdf5-cpp-11_1.8.16+docs-8 libhdf5-dev_1.8.16+docs-8 libicu57_57.1-4 libidn11_1.33-1 libisl15_0.17.1-1 libjpeg-dev_1:1.5.0-1 libjpeg62-turbo_1:1.5.0-1 libjpeg62-turbo-dev_1:1.5.0-1 libklibc_2.0.4-9+rpi1 libkmod2_22-1.1 liblapack-dev_3.6.1-2 liblapack3_3.6.1-2 liblocale-gettext-perl_1.07-3 liblz4-1_0.0~r131-2 liblzma5_5.1.1alpha+20120614-2.1 libmagic-mgc_1:5.28-4 libmagic1_1:5.28-4 libmount1_2.28-6 libmpc3_1.0.3-1 libmpfr4_3.1.4-2 libncurses5_6.0+20160625-1 libncursesw5_6.0+20160625-1 libpam-modules_1.1.8-3.3 libpam-modules-bin_1.1.8-3.3 libpam-runtime_1.1.8-3.3 libpam0g_1.1.8-3.3 libpcre3_2:8.39-1 libperl5.22_5.22.2-3 libpipeline1_1.4.1-2 libplymouth4_0.9.2-3 libpng12-0_1.2.54-6 libprocps6_2:3.3.12-2 libreadline6_6.3-8+b3 libseccomp2_2.3.1-2 libselinux1_2.5-3 libsemanage-common_2.5-1 libsemanage1_2.5-1 libsepol1_2.5-1 libsigsegv2_2.10-5 libsmartcols1_2.28-6 libsqlite3-0_3.14.1-1 libss2_1.43.1-1 libstdc++-6-dev_6.1.1-11+rpi1 libstdc++6_6.1.1-11+rpi1 libsuperlu-dev_5.2.1+dfsg1-2 libsuperlu5_5.2.1+dfsg1-2 libsystemd0_230-7+b1 libsz2_0.3.2-1 libtimedate-perl_2.3000-2 libtinfo5_6.0+20160625-1 libtool_2.4.6-2 libubsan0_6.1.1-11+rpi1 libudev1_230-7+b1 libunistring0_0.9.6+really0.9.3-0.1 libusb-0.1-4_2:0.1.12-30 libustr-1.0-1_1.0.4-5 libuuid1_2.28-6 libxml2_2.9.4+dfsg1-1+b1 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch login_1:4.2-3.1 lsb-base_9.20160629+rpi1 m4_1.4.17-5 make_4.1-9 makedev_2.3.1-93 man-db_2.7.5-1 manpages_4.07-1 mawk_1.3.3-17 mount_2.28-6 multiarch-support_2.23-4 ncurses-base_6.0+20160625-1 ncurses-bin_6.0+20160625-1 netbase_5.3 passwd_1:4.2-3.1 patch_2.7.5-1 perl_5.22.2-3 perl-base_5.22.2-3 perl-modules-5.22_5.22.2-3 po-debconf_1.0.19 procps_2:3.3.12-2 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_0.59-3.1 systemd_230-7+b1 systemd-sysv_230-7+b1 sysv-rc_2.88dsf-59.8 sysvinit-utils_2.88dsf-59.8 tar_1.29b-1 tzdata_2016f-1 udev_230-7+b1 util-linux_2.28-6 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
Hack binNMU version
-------------------
Created changelog entry for binNMU version 1.1.1-2+b1
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=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=stretch-staging-armhf-sbuild-1371bdb2-19db-458c-91bc-0ae39cf4b104
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=vt102
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package seer
dpkg-buildpackage: info: source version 1.1.1-2+b1
dpkg-buildpackage: info: source distribution stretch-staging
dpkg-source --before-build seer-1.1.1
dpkg-buildpackage: info: 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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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/seer debian/seer/usr/bin/kmds 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/seer debian/seer/usr/bin/kmds debian/seer/usr/bin/combineKmers 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_1.1.1-2+b1_armhf.deb'.
dpkg-deb: building package 'seer' in '../seer_1.1.1-2+b1_armhf.deb'.
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../seer_1.1.1-2+b1_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build seer-1.1.1
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 20160916-0456
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
seer_1.1.1-2+b1_armhf.changes:
------------------------------
Format: 1.8
Date: Tue, 19 Apr 2016 10:39:15 +0200
Source: seer (1.1.1-2)
Binary: seer
Binary-Only: yes
Architecture: armhf
Version: 1.1.1-2+b1
Distribution: stretch-staging
Urgency: low
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Raspbian wandboard test autobuilder <root@raspbian.org>
Description:
seer - genomic sequence element (kmer) enrichment analysis
Changes:
seer (1.1.1-2+b1) stretch-staging; urgency=low, binary-only=yes
.
* Binary-only non-maintainer upload for armhf; no source changes.
* rebuild due to debcheck failure
Checksums-Sha1:
bd9fe5592b88d8030dad036df16d163535c8514a 7728076 seer-dbgsym_1.1.1-2+b1_armhf.deb
5d9223003c1d0c6233dea53682fc6b826466b7c8 313842 seer_1.1.1-2+b1_armhf.deb
Checksums-Sha256:
838151f7ef41b572d3db0dc8579adb1bdaa1b1356b8863b81bf5f092e425195b 7728076 seer-dbgsym_1.1.1-2+b1_armhf.deb
0fcdb3d5a15afbacaf00dd865b124abe9022c3d79abc34338c26e053611ec7ac 313842 seer_1.1.1-2+b1_armhf.deb
Files:
04efa3686afd4e0b7c68cd39aec9c02a 7728076 debug extra seer-dbgsym_1.1.1-2+b1_armhf.deb
a6fca6b0e7c31afabce8380ccc600c6d 313842 science optional seer_1.1.1-2+b1_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
seer-dbgsym_1.1.1-2+b1_armhf.deb
--------------------------------
new debian package, version 2.0.
size 7728076 bytes: control archive=716 bytes.
579 bytes, 13 lines control
530 bytes, 5 lines md5sums
Package: seer-dbgsym
Source: seer (1.1.1-2)
Version: 1.1.1-2+b1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 8082
Depends: seer (= 1.1.1-2+b1)
Section: debug
Priority: extra
Homepage: https://github.com/johnlees/seer
Description: Debug symbols for seer
Auto-Built-Package: debug-symbols
Build-Ids: 2552fbadb37ebcc17c7019d35a9a9920e50cb2ad 639bdc0c6777f3b3985df6bf151253188543fc14 7211f0068ff12fadb1b9d547b30a7a0ef0fe6cd6 c46b30140072023106dccf81f1617473ddaea6da c5f95158366ae26fc78a64c0a466709856f8fb8e
drwxr-xr-x root/root 0 2016-04-19 08:39 ./
drwxr-xr-x root/root 0 2016-04-19 08:39 ./usr/
drwxr-xr-x root/root 0 2016-04-19 08:39 ./usr/lib/
drwxr-xr-x root/root 0 2016-04-19 08:39 ./usr/lib/debug/
drwxr-xr-x root/root 0 2016-04-19 08:39 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2016-04-19 08:39 ./usr/lib/debug/.build-id/25/
-rw-r--r-- root/root 3452972 2016-04-19 08:39 ./usr/lib/debug/.build-id/25/52fbadb37ebcc17c7019d35a9a9920e50cb2ad.debug
drwxr-xr-x root/root 0 2016-04-19 08:39 ./usr/lib/debug/.build-id/63/
-rw-r--r-- root/root 339744 2016-04-19 08:39 ./usr/lib/debug/.build-id/63/9bdc0c6777f3b3985df6bf151253188543fc14.debug
drwxr-xr-x root/root 0 2016-04-19 08:39 ./usr/lib/debug/.build-id/72/
-rw-r--r-- root/root 476752 2016-04-19 08:39 ./usr/lib/debug/.build-id/72/11f0068ff12fadb1b9d547b30a7a0ef0fe6cd6.debug
drwxr-xr-x root/root 0 2016-04-19 08:39 ./usr/lib/debug/.build-id/c4/
-rw-r--r-- root/root 3186380 2016-04-19 08:39 ./usr/lib/debug/.build-id/c4/6b30140072023106dccf81f1617473ddaea6da.debug
drwxr-xr-x root/root 0 2016-04-19 08:39 ./usr/lib/debug/.build-id/c5/
-rw-r--r-- root/root 803232 2016-04-19 08:39 ./usr/lib/debug/.build-id/c5/f95158366ae26fc78a64c0a466709856f8fb8e.debug
drwxr-xr-x root/root 0 2016-04-19 08:39 ./usr/share/
drwxr-xr-x root/root 0 2016-04-19 08:39 ./usr/share/doc/
lrwxrwxrwx root/root 0 2016-04-19 08:39 ./usr/share/doc/seer-dbgsym -> seer
seer_1.1.1-2+b1_armhf.deb
-------------------------
new debian package, version 2.0.
size 313842 bytes: control archive=1541 bytes.
1437 bytes, 25 lines control
1084 bytes, 17 lines md5sums
Package: seer
Source: seer (1.1.1-2)
Version: 1.1.1-2+b1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1416
Depends: libarmadillo7, libblas3 | libblas.so.3, libboost-program-options1.61.0, libc6 (>= 2.4), libgcc1 (>= 1:3.5), libgzstream0, libhdf5-10, liblapack3 | liblapack.so.3, libstdc++6 (>= 6), 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.
drwxr-xr-x root/root 0 2016-04-19 08:39 ./
drwxr-xr-x root/root 0 2016-04-19 08:39 ./usr/
drwxr-xr-x root/root 0 2016-04-19 08:39 ./usr/bin/
-rwxr-xr-x root/root 3799 2016-03-31 08:55 ./usr/bin/blast_top_hits
-rwxr-xr-x root/root 103988 2016-04-19 08:39 ./usr/bin/combineKmers
-rwxr-xr-x root/root 71220 2016-04-19 08:39 ./usr/bin/filter_seer
-rwxr-xr-x root/root 497748 2016-04-19 08:39 ./usr/bin/kmds
-rwxr-xr-x root/root 181812 2016-04-19 08:39 ./usr/bin/map_back
-rwxr-xr-x root/root 563284 2016-04-19 08:39 ./usr/bin/seer
drwxr-xr-x root/root 0 2016-04-19 08:39 ./usr/share/
drwxr-xr-x root/root 0 2016-04-19 08:39 ./usr/share/doc/
drwxr-xr-x root/root 0 2016-04-19 08:39 ./usr/share/doc/seer/
-rw-r--r-- root/root 293 2016-04-19 08:39 ./usr/share/doc/seer/README.Debian
-rw-r--r-- root/root 218 2016-04-19 08:39 ./usr/share/doc/seer/changelog.Debian.armhf.gz
-rw-r--r-- root/root 316 2016-04-19 08:39 ./usr/share/doc/seer/changelog.Debian.gz
-rw-r--r-- root/root 1008 2016-04-19 08:39 ./usr/share/doc/seer/copyright
drwxr-xr-x root/root 0 2016-04-19 08:39 ./usr/share/doc/seer/examples/
-rw-r--r-- root/root 2110 2016-03-31 08:55 ./usr/share/doc/seer/examples/example_wrapper.py.gz
drwxr-xr-x root/root 0 2016-04-19 08:39 ./usr/share/man/
drwxr-xr-x root/root 0 2016-04-19 08:39 ./usr/share/man/man1/
-rw-r--r-- root/root 551 2016-04-19 08:39 ./usr/share/man/man1/blast_top_hits.1.gz
-rw-r--r-- root/root 509 2016-04-19 08:39 ./usr/share/man/man1/combineKmers.1.gz
-rw-r--r-- root/root 590 2016-04-19 08:39 ./usr/share/man/man1/filter_seer.1.gz
-rw-r--r-- root/root 993 2016-04-19 08:39 ./usr/share/man/man1/kmds.1.gz
-rw-r--r-- root/root 486 2016-04-19 08:39 ./usr/share/man/man1/map_back.1.gz
-rw-r--r-- root/root 1064 2016-04-19 08:39 ./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: 77436
Build-Time: 1642
Distribution: stretch-staging
Host Architecture: armhf
Install-Time: 418
Job: seer_1.1.1-2
Machine Architecture: armhf
Package: seer
Package-Time: 2102
Source-Version: 1.1.1-2
Space: 77436
Status: successful
Version: 1.1.1-2+b1
--------------------------------------------------------------------------------
Finished at 20160916-0456
Build needed 00:35:02, 77436k disc space