seer →
1.1.2-1 →
armhf → 2016-12-18 12:22:50
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on testwandboard
+==============================================================================+
| seer 1.1.2-1 (armhf) Sun, 18 Dec 2016 12:02:55 +0000 |
+==============================================================================+
Package: seer
Version: 1.1.2-1
Source Version: 1.1.2-1
Distribution: stretch-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/stretch-staging-armhf-sbuild-968cbb72-c694-4bc3-8e24-ffea0fafe629' 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 [9603 kB]
Get:3 http://172.17.0.1/private stretch-staging/main armhf Packages [11.5 MB]
Fetched 21.1 MB in 27s (768 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 977 kB of source archives.
Get:1 http://172.17.0.1/private stretch-staging/main seer 1.1.2-1 (dsc) [2033 B]
Get:2 http://172.17.0.1/private stretch-staging/main seer 1.1.2-1 (tar) [969 kB]
Get:3 http://172.17.0.1/private stretch-staging/main seer 1.1.2-1 (diff) [5736 B]
Fetched 977 kB in 0s (2014 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/seer-YPPVVe/seer-1.1.2' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/seer-YPPVVe' with '<<BUILDDIR>>'
+------------------------------------------------------------------------------+
| Install build-essential |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<<BUILDDIR>>/resolver-TrX7Mo/apt_archive/sbuild-build-depends-core-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy
dpkg-scanpackages: info: Wrote 1 entries to output Packages file.
gpg: keybox '/<<BUILDDIR>>/resolver-TrX7Mo/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-TrX7Mo/gpg/trustdb.gpg: trustdb created
gpg: key 35506D9A48F77B2E: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg: imported: 1
gpg: key 35506D9A48F77B2E: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 35506D9A48F77B2E: secret key imported
gpg: Total number processed: 1
gpg: unchanged: 1
gpg: secret keys read: 1
gpg: secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-TrX7Mo/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-TrX7Mo/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-TrX7Mo/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-TrX7Mo/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-TrX7Mo/apt_archive ./ Packages [431 B]
Fetched 2107 B in 0s (2977 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
fuse2fs gnupg-l10n kbd libfuse2 manpages netbase psmisc
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 25 not upgraded.
Need to get 776 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-TrX7Mo/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [776 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 776 B in 0s (0 B/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 13244 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper (>= 10), libarmadillo-dev (>= 1:6.700.6+dfsg-1~), libdlib-dev, libhdf5-dev, libgzstream-dev, libboost-dev, libboost-program-options-dev
Filtered Build-Depends: debhelper (>= 10), libarmadillo-dev (>= 1:6.700.6+dfsg-1~), libdlib-dev, libhdf5-dev, libgzstream-dev, libboost-dev, libboost-program-options-dev
dpkg-deb: building package 'sbuild-build-depends-seer-dummy' in '/<<BUILDDIR>>/resolver-TrX7Mo/apt_archive/sbuild-build-depends-seer-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-seer-dummy
dpkg-scanpackages: info: Wrote 2 entries to output Packages file.
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-TrX7Mo/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-TrX7Mo/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-TrX7Mo/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-TrX7Mo/apt_archive ./ Sources [549 B]
Get:5 copy:/<<BUILDDIR>>/resolver-TrX7Mo/apt_archive ./ Packages [632 B]
Fetched 2514 B in 0s (3674 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install seer build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
fuse2fs gnupg-l10n kbd libfuse2 manpages netbase psmisc
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils cpp debhelper
dh-autoreconf dh-strip-nondeterminism file gcc 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-options1.62-dev
libboost-program-options1.62.0 libboost1.62-dev libbsd0 libcroco3
libdlib-data libdlib-dev libdlib18 libffi6 libfile-stripnondeterminism-perl
libgfortran-6-dev libgfortran3 libglib2.0-0 libgzstream-dev libgzstream0
libhdf5-100 libhdf5-cpp-100 libhdf5-dev libicu57 libjpeg-dev libjpeg62-turbo
libjpeg62-turbo-dev liblapack-dev liblapack3 libmagic-mgc libmagic1
libpipeline1 libsigsegv2 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 cpp-doc dh-make gcc-multilib manpages-dev flex bison gdb gcc-doc
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 libboost1.62-doc libboost-atomic1.62-dev
libboost-chrono1.62-dev libboost-context1.62-dev libboost-coroutine1.62-dev
libboost-date-time1.62-dev libboost-exception1.62-dev libboost-fiber1.62-dev
libboost-filesystem1.62-dev libboost-graph1.62-dev
libboost-graph-parallel1.62-dev libboost-iostreams1.62-dev
libboost-locale1.62-dev libboost-log1.62-dev libboost-math1.62-dev
libboost-mpi1.62-dev libboost-mpi-python1.62-dev libboost-python1.62-dev
libboost-random1.62-dev libboost-regex1.62-dev
libboost-serialization1.62-dev libboost-signals1.62-dev
libboost-system1.62-dev libboost-test1.62-dev libboost-thread1.62-dev
libboost-timer1.62-dev libboost-type-erasure1.62-dev libboost-wave1.62-dev
libboost1.62-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-options1.62-dev
libboost-program-options1.62.0 libboost1.62-dev libbsd0 libcroco3
libdlib-data libdlib-dev libdlib18 libffi6 libfile-stripnondeterminism-perl
libgfortran-6-dev libgfortran3 libglib2.0-0 libgzstream-dev libgzstream0
libhdf5-100 libhdf5-cpp-100 libhdf5-dev libicu57 libjpeg-dev libjpeg62-turbo
libjpeg62-turbo-dev liblapack-dev liblapack3 libmagic-mgc libmagic1
libpipeline1 libsigsegv2 libsuperlu-dev libsuperlu5 libsz2 libtimedate-perl
libtool libunistring0 libxml2 m4 man-db po-debconf
sbuild-build-depends-seer-dummy zlib1g-dev
The following packages will be upgraded:
cpp gcc
2 upgraded, 68 newly installed, 0 to remove and 23 not upgraded.
Need to get 105 MB/105 MB of archives.
After this operation, 346 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-TrX7Mo/apt_archive ./ sbuild-build-depends-seer-dummy 0.invalid.0 [838 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 9.0.12 [178 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 2.7.5-2 [971 kB]
Get:7 http://172.17.0.1/private stretch-staging/main armhf libmagic-mgc armhf 1:5.29-1 [219 kB]
Get:8 http://172.17.0.1/private stretch-staging/main armhf libmagic1 armhf 1:5.29-1 [104 kB]
Get:9 http://172.17.0.1/private stretch-staging/main armhf file armhf 1:5.29-1 [63.3 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 libicu57 armhf 57.1-5 [7427 kB]
Get:12 http://172.17.0.1/private stretch-staging/main armhf libxml2 armhf 2.9.4+dfsg1-2.1 [804 kB]
Get:13 http://172.17.0.1/private stretch-staging/main armhf libsigsegv2 armhf 2.10-5 [28.4 kB]
Get:14 http://172.17.0.1/private stretch-staging/main armhf m4 armhf 1.4.17-5 [239 kB]
Get:15 http://172.17.0.1/private stretch-staging/main armhf autoconf all 2.69-10 [338 kB]
Get:16 http://172.17.0.1/private stretch-staging/main armhf autotools-dev all 20161112.1 [73.4 kB]
Get:17 http://172.17.0.1/private stretch-staging/main armhf automake all 1:1.15-5 [733 kB]
Get:18 http://172.17.0.1/private stretch-staging/main armhf autopoint all 0.19.8.1-1 [433 kB]
Get:19 http://172.17.0.1/private stretch-staging/main armhf cpp armhf 4:6.2.1-1 [18.5 kB]
Get:20 http://172.17.0.1/private stretch-staging/main armhf gcc armhf 4:6.2.1-1 [5188 B]
Get:21 http://172.17.0.1/private stretch-staging/main armhf libtool all 2.4.6-2 [545 kB]
Get:22 http://172.17.0.1/private stretch-staging/main armhf dh-autoreconf all 12 [15.8 kB]
Get:23 http://172.17.0.1/private stretch-staging/main armhf libarchive-zip-perl all 1.59-1 [95.5 kB]
Get:24 http://172.17.0.1/private stretch-staging/main armhf libfile-stripnondeterminism-perl all 0.028-1 [14.6 kB]
Get:25 http://172.17.0.1/private stretch-staging/main armhf libtimedate-perl all 2.3000-2 [42.2 kB]
Get:26 http://172.17.0.1/private stretch-staging/main armhf dh-strip-nondeterminism all 0.028-1 [9020 B]
Get:27 http://172.17.0.1/private stretch-staging/main armhf libglib2.0-0 armhf 2.50.2-2 [2527 kB]
Get:28 http://172.17.0.1/private stretch-staging/main armhf libcroco3 armhf 0.6.11-2 [131 kB]
Get:29 http://172.17.0.1/private stretch-staging/main armhf libunistring0 armhf 0.9.6+really0.9.3-0.1 [252 kB]
Get:30 http://172.17.0.1/private stretch-staging/main armhf gettext armhf 0.19.8.1-1 [1433 kB]
Get:31 http://172.17.0.1/private stretch-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:32 http://172.17.0.1/private stretch-staging/main armhf po-debconf all 1.0.20 [247 kB]
Get:33 http://172.17.0.1/private stretch-staging/main armhf debhelper all 10.2.2 [826 kB]
Get:34 http://172.17.0.1/private stretch-staging/main armhf libgfortran3 armhf 6.2.1-5+rpi1 [166 kB]
Get:35 http://172.17.0.1/private stretch-staging/main armhf libgfortran-6-dev armhf 6.2.1-5+rpi1 [199 kB]
Get:36 http://172.17.0.1/private stretch-staging/main armhf gfortran-6 armhf 6.2.1-5+rpi1 [5414 kB]
Get:37 http://172.17.0.1/private stretch-staging/main armhf gfortran armhf 4:6.2.1-1 [1340 B]
Get:38 http://172.17.0.1/private stretch-staging/main armhf hdf5-helpers armhf 1.10.0-patch1+docs-3 [35.9 kB]
Get:39 http://172.17.0.1/private stretch-staging/main armhf libaec0 armhf 0.3.2-1 [19.4 kB]
Get:40 http://172.17.0.1/private stretch-staging/main armhf libblas-common armhf 3.6.1-2 [13.9 kB]
Get:41 http://172.17.0.1/private stretch-staging/main armhf libblas3 armhf 3.6.1-2 [112 kB]
Get:42 http://172.17.0.1/private stretch-staging/main armhf liblapack3 armhf 3.6.1-2 [1392 kB]
Get:43 http://172.17.0.1/private stretch-staging/main armhf libarpack2 armhf 3.4.0-1+b1 [78.4 kB]
Get:44 http://172.17.0.1/private stretch-staging/main armhf libsuperlu5 armhf 5.2.1+dfsg1-2 [126 kB]
Get:45 http://172.17.0.1/private stretch-staging/main armhf libarmadillo7 armhf 1:7.500.2+dfsg-1 [80.3 kB]
Get:46 http://172.17.0.1/private stretch-staging/main armhf libblas-dev armhf 3.6.1-2 [18.9 kB]
Get:47 http://172.17.0.1/private stretch-staging/main armhf liblapack-dev armhf 3.6.1-2 [1379 kB]
Get:48 http://172.17.0.1/private stretch-staging/main armhf libarpack2-dev armhf 3.4.0-1+b1 [90.5 kB]
Get:49 http://172.17.0.1/private stretch-staging/main armhf libsz2 armhf 0.3.2-1 [5836 B]
Get:50 http://172.17.0.1/private stretch-staging/main armhf libhdf5-100 armhf 1.10.0-patch1+docs-3 [1203 kB]
Get:51 http://172.17.0.1/private stretch-staging/main armhf zlib1g-dev armhf 1:1.2.8.dfsg-2+b1 [197 kB]
Get:52 http://172.17.0.1/private stretch-staging/main armhf libjpeg62-turbo armhf 1:1.5.1-2 [109 kB]
Get:53 http://172.17.0.1/private stretch-staging/main armhf libjpeg62-turbo-dev armhf 1:1.5.1-2 [181 kB]
Get:54 http://172.17.0.1/private stretch-staging/main armhf libjpeg-dev all 1:1.5.1-2 [56.1 kB]
Get:55 http://172.17.0.1/private stretch-staging/main armhf libaec-dev armhf 0.3.2-1 [17.6 kB]
Get:56 http://172.17.0.1/private stretch-staging/main armhf libhdf5-cpp-100 armhf 1.10.0-patch1+docs-3 [118 kB]
Get:57 http://172.17.0.1/private stretch-staging/main armhf libhdf5-dev armhf 1.10.0-patch1+docs-3 [2093 kB]
Get:58 http://172.17.0.1/private stretch-staging/main armhf libsuperlu-dev armhf 5.2.1+dfsg1-2 [18.0 kB]
Get:59 http://172.17.0.1/private stretch-staging/main armhf libarmadillo-dev armhf 1:7.500.2+dfsg-1 [321 kB]
Get:60 http://172.17.0.1/private stretch-staging/main armhf libboost1.62-dev armhf 1.62.0+dfsg-4 [7009 kB]
Get:61 http://172.17.0.1/private stretch-staging/main armhf libboost-dev armhf 1.62.0.1 [3632 B]
Get:62 http://172.17.0.1/private stretch-staging/main armhf libboost-program-options1.62.0 armhf 1.62.0+dfsg-4 [136 kB]
Get:63 http://172.17.0.1/private stretch-staging/main armhf libboost-program-options1.62-dev armhf 1.62.0+dfsg-4 [178 kB]
Get:64 http://172.17.0.1/private stretch-staging/main armhf libboost-program-options-dev armhf 1.62.0.1 [3430 B]
Get:65 http://172.17.0.1/private stretch-staging/main armhf libdlib-data all 18.18-1 [63.3 MB]
Get:66 http://172.17.0.1/private stretch-staging/main armhf libdlib18 armhf 18.18-1 [223 kB]
Get:67 http://172.17.0.1/private stretch-staging/main armhf libdlib-dev armhf 18.18-1 [1067 kB]
Get:68 http://172.17.0.1/private stretch-staging/main armhf libgzstream0 armhf 1.5+dfsg-2 [5764 B]
Get:69 http://172.17.0.1/private stretch-staging/main armhf libgzstream-dev armhf 1.5+dfsg-2 [6172 B]
debconf: delaying package configuration, since apt-utils is not installed
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Processing triggers for libc-bin (2.24-7+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.4.0-1-armmp armhf (armv7l)
Toolchain package versions: binutils_2.27.51.20161127-1 dpkg-dev_1.18.15 g++-6_6.2.1-5+rpi1 gcc-6_6.2.1-5+rpi1 libc6-dev_2.24-7+rpi1 libstdc++-6-dev_6.2.1-5+rpi1 libstdc++6_6.2.1-5+rpi1 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch
Package versions: adduser_3.115 apt_1.4~beta1 autoconf_2.69-10 automake_1:1.15-5 autopoint_0.19.8.1-1 autotools-dev_20161112.1 base-files_9.7+rpi1 base-passwd_3.5.41 bash_4.4-2 binutils_2.27.51.20161127-1 bsdmainutils_9.0.12 bsdutils_1:2.29-1 build-essential_12.2 bzip2_1.0.6-8 coreutils_8.25-2 cpio_2.11+dfsg-6 cpp_4:6.2.1-1 cpp-6_6.2.1-5+rpi1 dash_0.5.8-2.3 debconf_1.5.59 debfoster_2.7-2.1 debhelper_10.2.2 debianutils_4.8.1 dh-autoreconf_12 dh-strip-nondeterminism_0.028-1 diffutils_1:3.5-1 dmsetup_2:1.02.136-1 dpkg_1.18.15 dpkg-dev_1.18.15 e2fslibs_1.43.3-1 e2fsprogs_1.43.3-1 fakeroot_1.21-2 file_1:5.29-1 findutils_4.6.0+git+20161106-1 fuse2fs_1.43.3-1 g++_4:6.1.1-1 g++-6_6.2.1-5+rpi1 gcc_4:6.2.1-1 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-6_6.2.1-5+rpi1 gcc-6-base_6.2.1-5+rpi1 gettext_0.19.8.1-1 gettext-base_0.19.8.1-1 gfortran_4:6.2.1-1 gfortran-6_6.2.1-5+rpi1 gnupg_2.1.16-2 gnupg-agent_2.1.16-2 gnupg-l10n_2.1.16-2 gpgv_2.1.16-2 grep_2.26-1 groff-base_1.22.3-8 gzip_1.6-5 hdf5-helpers_1.10.0-patch1+docs-3 hostname_3.18 init_1.46 init-system-helpers_1.46 initscripts_2.88dsf-59.8 insserv_1.14.0-5.4 intltool-debian_0.35.0+20060710.4 kbd_2.0.3-2 klibc-utils_2.0.4-9+rpi1 kmod_23-1 libacl1_2.2.52-3 libaec-dev_0.3.2-1 libaec0_0.3.2-1 libapparmor1_2.10.95-6 libapt-pkg5.0_1.4~beta1 libarchive-zip-perl_1.59-1 libarmadillo-dev_1:7.500.2+dfsg-1 libarmadillo7_1:7.500.2+dfsg-1 libarpack2_3.4.0-1+b1 libarpack2-dev_3.4.0-1+b1 libasan3_6.2.1-5+rpi1 libassuan0_2.4.3-2 libatomic1_6.2.1-5+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.6.7-1 libaudit1_1:2.6.7-1 libblas-common_3.6.1-2 libblas-dev_3.6.1-2 libblas3_3.6.1-2 libblkid1_2.29-1 libboost-dev_1.62.0.1 libboost-program-options-dev_1.62.0.1 libboost-program-options1.62-dev_1.62.0+dfsg-4 libboost-program-options1.62.0_1.62.0+dfsg-4 libboost1.62-dev_1.62.0+dfsg-4 libbsd0_0.8.3-1 libbz2-1.0_1.0.6-8 libc-bin_2.24-7+rpi1 libc-dev-bin_2.24-7+rpi1 libc6_2.24-7+rpi1 libc6-dev_2.24-7+rpi1 libcap-ng0_0.7.7-3 libcap2_1:2.25-1 libcap2-bin_1:2.25-1 libcc1-0_6.2.1-5+rpi1 libcomerr2_1.43.3-1 libcroco3_0.6.11-2 libcryptsetup4_2:1.7.3-2 libdb5.3_5.3.28-12 libdbus-1-3_1.10.14-1 libdebconfclient0_0.218 libdevmapper1.02.1_2:1.02.136-1 libdlib-data_18.18-1 libdlib-dev_18.18-1 libdlib18_18.18-1 libdpkg-perl_1.18.15 libdrm2_2.4.74-1 libfakeroot_1.21-2 libfdisk1_2.29-1 libffi6_3.2.1-6 libfile-stripnondeterminism-perl_0.028-1 libfuse2_2.9.7-1 libgc1c2_1:7.4.2-8 libgcc-6-dev_6.2.1-5+rpi1 libgcc1_1:6.2.1-5+rpi1 libgcrypt20_1.7.3-2 libgdbm3_1.8.3-14 libgfortran-6-dev_6.2.1-5+rpi1 libgfortran3_6.2.1-5+rpi1 libglib2.0-0_2.50.2-2 libgmp10_2:6.1.1+dfsg-1 libgomp1_6.2.1-5+rpi1 libgpg-error0_1.25-1 libgzstream-dev_1.5+dfsg-2 libgzstream0_1.5+dfsg-2 libhdf5-100_1.10.0-patch1+docs-3 libhdf5-cpp-100_1.10.0-patch1+docs-3 libhdf5-dev_1.10.0-patch1+docs-3 libicu57_57.1-5 libidn11_1.33-1 libip4tc0_1.6.0-4 libisl15_0.17.1-1 libjpeg-dev_1:1.5.1-2 libjpeg62-turbo_1:1.5.1-2 libjpeg62-turbo-dev_1:1.5.1-2 libklibc_2.0.4-9+rpi1 libkmod2_23-1 libksba8_1.3.5-2 liblapack-dev_3.6.1-2 liblapack3_3.6.1-2 liblz4-1_0.0~r131-2 liblzma5_5.2.2-1.2 libmagic-mgc_1:5.29-1 libmagic1_1:5.29-1 libmount1_2.29-1 libmpc3_1.0.3-1 libmpfr4_3.1.5-1 libncurses5_6.0+20160917-1 libncursesw5_6.0+20160917-1 libnpth0_1.3-1 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_2:8.39-2 libperl5.24_5.24.1~rc4-1 libpipeline1_1.4.1-2 libplymouth4_0.9.2-3 libpng12-0_1.2.54-6 libprocps6_2:3.3.12-3 libreadline7_7.0-1 libseccomp2_2.3.1-2.1 libselinux1_2.6-3 libsemanage-common_2.6-1 libsemanage1_2.6-1 libsepol1_2.6-1 libsigsegv2_2.10-5 libsmartcols1_2.29-1 libsqlite3-0_3.15.2-1 libss2_1.43.3-1 libstdc++-6-dev_6.2.1-5+rpi1 libstdc++6_6.2.1-5+rpi1 libsuperlu-dev_5.2.1+dfsg1-2 libsuperlu5_5.2.1+dfsg1-2 libsystemd0_232-6 libsz2_0.3.2-1 libtimedate-perl_2.3000-2 libtinfo5_6.0+20160917-1 libtool_2.4.6-2 libubsan0_6.2.1-5+rpi1 libudev1_232-6 libunistring0_0.9.6+really0.9.3-0.1 libusb-0.1-4_2:0.1.12-30 libustr-1.0-1_1.0.4-6 libuuid1_2.29-1 libxml2_2.9.4+dfsg1-2.1 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch login_1:4.2-3.3 lsb-base_9.20161125+rpi1 m4_1.4.17-5 make_4.1-9 makedev_2.3.1-93 man-db_2.7.5-2 manpages_4.08-1 mawk_1.3.3-17 mount_2.29-1 multiarch-support_2.24-7+rpi1 ncurses-base_6.0+20160917-1 ncurses-bin_6.0+20160917-1 netbase_5.3 passwd_1:4.2-3.3 patch_2.7.5-1 perl_5.24.1~rc4-1 perl-base_5.24.1~rc4-1 perl-modules-5.24_5.24.1~rc4-1 pinentry-curses_0.9.7-9 po-debconf_1.0.20 procps_2:3.3.12-3 psmisc_22.21-2.1 raspbian-archive-keyring_20120528.2 readline-common_7.0-1 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-seer-dummy_0.invalid.0 sed_4.2.2-8 sensible-utils_0.0.9 startpar_0.59-3.1 systemd_232-6 systemd-sysv_232-6 sysv-rc_2.88dsf-59.8 sysvinit-utils_2.88dsf-59.8 tar_1.29b-1.1 tzdata_2016j-2 udev_232-6 util-linux_2.29-1 xz-utils_5.2.2-1.2 zlib1g_1:1.2.8.dfsg-2+b1 zlib1g-dev_1:1.2.8.dfsg-2+b1
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Wed Dec 7 22:08:16 2016 UTC
gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv: issuer "tille@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./seer_1.1.2-1.dsc
dpkg-source: info: extracting seer in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking seer_1.1.2.orig.tar.gz
dpkg-source: info: unpacking seer_1.1.2-1.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
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=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-968cbb72-c694-4bc3-8e24-ffea0fafe629
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package seer
dpkg-buildpackage: info: source version 1.1.2-1
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build seer-1.1.2
dpkg-buildpackage: info: host architecture armhf
fakeroot debian/rules clean
dh clean
dh_testdir
dh_auto_clean
make -j4 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_autoreconf_clean
dh_clean
debian/rules build-arch
dh build-arch
dh_testdir -a
dh_update_autotools_config -a
dh_autoreconf -a
dh_auto_configure -a
dh_auto_build -a
make -j4
make[1]: Entering directory '/<<PKGBUILDDIR>>'
cd src && make all
make[2]: Entering directory '/<<PKGBUILDDIR>>/src'
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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>>=. -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>>=. -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>>=. -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>>=. -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
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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>>=. -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>>=. -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
seerCommon.cpp: In function 'arma::vec dlib_to_arma(const column_vector&)':
seerCommon.cpp:174:31: 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>>=. -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>>=. -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>>=. -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>>=. -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>>=. -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>>=. -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>>=. -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>>=. -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>>=. -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>>=. -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>>=. -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>>=. -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>>=. -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>>=. -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>>=. -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>>=. -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>>=. -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>>=. -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>>=. -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 -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 -Wl,-z,relro -Wl,-z,now -o seer
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -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 -Wl,-z,relro -Wl,-z,now -o kmds
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -Wl,-z,relro -Wl,-z,now fasta.o significant_kmer.o mapMain.o mapCmdLine.o -lboost_program_options -lpthread -Wl,-z,relro -Wl,-z,now -Wl,-z,relro -Wl,-z,now -o map_back
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -Wl,-z,relro -Wl,-z,now combineInit.o combineCmdLine.o combineKmers.o -lgzstream -lz -lboost_program_options -Wl,-z,relro -Wl,-z,now -Wl,-z,relro -Wl,-z,now -o combineKmers
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -Wl,-z,relro -Wl,-z,now significant_kmer.o filter_seer.o filterCmdLine.o -lboost_program_options -Wl,-z,relro -Wl,-z,now -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 -j4 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
PASSED test 1, basic filters
PASSED test 2, binary phenotype assocation
PASSED test 3, print output
PASSED test 4, continuous phenotype assocation
PASSED test 5, assocation with population structure
PASSED test 6, assocation with covariates
PASSED test 7, filter output
PASSED test 8, map k-mers
make[3]: Leaving directory '/<<PKGBUILDDIR>>/test'
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
Test passed
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
fakeroot debian/rules binary-arch
dh binary-arch
dh_testroot -a
dh_prep -a
debian/rules override_dh_auto_install
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_install -- PREFIX=/<<PKGBUILDDIR>>/debian/seer/usr
make -j4 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: debian/seer/usr/bin/map_back contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/seer/usr/bin/kmds contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/seer/usr/bin/filter_seer contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/seer/usr/bin/combineKmers contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/seer/usr/bin/seer contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/seer/usr/bin/kmds debian/seer/usr/bin/seer were not linked against liblapack.so.3 (they use none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/seer/usr/bin/map_back debian/seer/usr/bin/kmds debian/seer/usr/bin/filter_seer debian/seer/usr/bin/combineKmers debian/seer/usr/bin/seer were not linked against ld-linux-armhf.so.3 (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/combineKmers debian/seer/usr/bin/seer were not linked against libz.so.1 (they use none of the library's symbols)
dh_installdeb -a
dh_gencontrol -a
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-gencontrol: warning: package seer: unused substitution variable ${perl:Depends}
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-gencontrol: warning: package seer: unused substitution variable ${perl:Depends}
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package 'seer-dbgsym' in '../seer-dbgsym_1.1.2-1_armhf.deb'.
dpkg-deb: building package 'seer' in '../seer_1.1.2-1_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genbuildinfo: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../seer_1.1.2-1_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build seer-1.1.2
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2016-12-18T12:22:35Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
seer_1.1.2-1_armhf.changes:
---------------------------
Format: 1.8
Date: Wed, 07 Dec 2016 23:05:02 +0100
Source: seer
Binary: seer
Architecture: armhf
Version: 1.1.2-1
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 (1.1.2-1) unstable; urgency=medium
.
* New upstream version
* Add versioned Build-Depends libarmadillo-dev
* debhelper 10
* d/watch: version=4
Checksums-Sha1:
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840fe8d959d4fee0a704795ea0b00b0f61a5fdbd 5571 seer_1.1.2-1_armhf.buildinfo
8c85703869fa14bfca2061504eafb981a503dbc8 293334 seer_1.1.2-1_armhf.deb
Checksums-Sha256:
63d2a41136d0d2beb51543daa597d48cac1a886927daabc1e78fad1a90ddd1f1 7518466 seer-dbgsym_1.1.2-1_armhf.deb
02836372a34c5e50c09c2ec1348dc73d7543483e72ee25cb6b5036ee096bcaf4 5571 seer_1.1.2-1_armhf.buildinfo
656acf18dc6df8f9240cd5ed59291e27633e06c32aa2098616701ae4af1689d9 293334 seer_1.1.2-1_armhf.deb
Files:
3c62703dfbe7f45dd632d607bf1e14af 7518466 debug extra seer-dbgsym_1.1.2-1_armhf.deb
efb514e5d0dd326decd4a16c0b0f94ac 5571 science optional seer_1.1.2-1_armhf.buildinfo
67ea73ecb8dde8bcd81f029b6465d19f 293334 science optional seer_1.1.2-1_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
seer-dbgsym_1.1.2-1_armhf.deb
-----------------------------
new debian package, version 2.0.
size 7518466 bytes: control archive=709 bytes.
563 bytes, 13 lines control
530 bytes, 5 lines md5sums
Package: seer-dbgsym
Source: seer
Version: 1.1.2-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 7842
Depends: seer (= 1.1.2-1)
Section: debug
Priority: extra
Homepage: https://github.com/johnlees/seer
Description: Debug symbols for seer
Auto-Built-Package: debug-symbols
Build-Ids: 2b5c4015a130b83b6e749523a5b4c983e4a2cf16 653675ad5a33b4ce3aa8d984b613abb6889dfac6 6d9923aed13d5a09242aeeb5fc74c02e964e8e3a ea60f0e132dcaeeb710bfb159da40c1e4d187fcd fa889b6c7afb2559a6ce15c0888c78ecbb648b9d
drwxr-xr-x root/root 0 2016-12-07 22:05 ./
drwxr-xr-x root/root 0 2016-12-07 22:05 ./usr/
drwxr-xr-x root/root 0 2016-12-07 22:05 ./usr/lib/
drwxr-xr-x root/root 0 2016-12-07 22:05 ./usr/lib/debug/
drwxr-xr-x root/root 0 2016-12-07 22:05 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2016-12-07 22:05 ./usr/lib/debug/.build-id/2b/
-rw-r--r-- root/root 478560 2016-12-07 22:05 ./usr/lib/debug/.build-id/2b/5c4015a130b83b6e749523a5b4c983e4a2cf16.debug
drwxr-xr-x root/root 0 2016-12-07 22:05 ./usr/lib/debug/.build-id/65/
-rw-r--r-- root/root 3062824 2016-12-07 22:05 ./usr/lib/debug/.build-id/65/3675ad5a33b4ce3aa8d984b613abb6889dfac6.debug
drwxr-xr-x root/root 0 2016-12-07 22:05 ./usr/lib/debug/.build-id/6d/
-rw-r--r-- root/root 808952 2016-12-07 22:05 ./usr/lib/debug/.build-id/6d/9923aed13d5a09242aeeb5fc74c02e964e8e3a.debug
drwxr-xr-x root/root 0 2016-12-07 22:05 ./usr/lib/debug/.build-id/ea/
-rw-r--r-- root/root 3315560 2016-12-07 22:05 ./usr/lib/debug/.build-id/ea/60f0e132dcaeeb710bfb159da40c1e4d187fcd.debug
drwxr-xr-x root/root 0 2016-12-07 22:05 ./usr/lib/debug/.build-id/fa/
-rw-r--r-- root/root 347444 2016-12-07 22:05 ./usr/lib/debug/.build-id/fa/889b6c7afb2559a6ce15c0888c78ecbb648b9d.debug
drwxr-xr-x root/root 0 2016-12-07 22:05 ./usr/share/
drwxr-xr-x root/root 0 2016-12-07 22:05 ./usr/share/doc/
lrwxrwxrwx root/root 0 2016-12-07 22:05 ./usr/share/doc/seer-dbgsym -> seer
seer_1.1.2-1_armhf.deb
----------------------
new debian package, version 2.0.
size 293334 bytes: control archive=1501 bytes.
1412 bytes, 24 lines control
1005 bytes, 16 lines md5sums
Package: seer
Version: 1.1.2-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1291
Depends: libarmadillo7, libblas3 | libblas.so.3, libboost-program-options1.62.0, libc6 (>= 2.4), libgcc1 (>= 1:3.5), libgzstream0, libhdf5-100, 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 2016-12-07 22:05 ./
drwxr-xr-x root/root 0 2016-12-07 22:05 ./usr/
drwxr-xr-x root/root 0 2016-12-07 22:05 ./usr/bin/
-rwxr-xr-x root/root 3799 2016-10-03 13:35 ./usr/bin/blast_top_hits
-rwxr-xr-x root/root 95744 2016-12-07 22:05 ./usr/bin/combineKmers
-rwxr-xr-x root/root 71168 2016-12-07 22:05 ./usr/bin/filter_seer
-rwxr-xr-x root/root 444448 2016-12-07 22:05 ./usr/bin/kmds
-rwxr-xr-x root/root 173568 2016-12-07 22:05 ./usr/bin/map_back
-rwxr-xr-x root/root 505888 2016-12-07 22:05 ./usr/bin/seer
drwxr-xr-x root/root 0 2016-12-07 22:05 ./usr/share/
drwxr-xr-x root/root 0 2016-12-07 22:05 ./usr/share/doc/
drwxr-xr-x root/root 0 2016-12-07 22:05 ./usr/share/doc/seer/
-rw-r--r-- root/root 293 2016-12-07 22:05 ./usr/share/doc/seer/README.Debian
-rw-r--r-- root/root 395 2016-12-07 22:05 ./usr/share/doc/seer/changelog.Debian.gz
-rw-r--r-- root/root 1008 2016-12-07 22:05 ./usr/share/doc/seer/copyright
drwxr-xr-x root/root 0 2016-12-07 22:05 ./usr/share/doc/seer/examples/
-rw-r--r-- root/root 2110 2016-10-03 13:35 ./usr/share/doc/seer/examples/example_wrapper.py.gz
drwxr-xr-x root/root 0 2016-12-07 22:05 ./usr/share/man/
drwxr-xr-x root/root 0 2016-12-07 22:05 ./usr/share/man/man1/
-rw-r--r-- root/root 551 2016-12-07 22:05 ./usr/share/man/man1/blast_top_hits.1.gz
-rw-r--r-- root/root 509 2016-12-07 22:05 ./usr/share/man/man1/combineKmers.1.gz
-rw-r--r-- root/root 590 2016-12-07 22:05 ./usr/share/man/man1/filter_seer.1.gz
-rw-r--r-- root/root 993 2016-12-07 22:05 ./usr/share/man/man1/kmds.1.gz
-rw-r--r-- root/root 486 2016-12-07 22:05 ./usr/share/man/man1/map_back.1.gz
-rw-r--r-- root/root 1064 2016-12-07 22:05 ./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: 77800
Build-Time: 736
Distribution: stretch-staging
Host Architecture: armhf
Install-Time: 394
Job: seer_1.1.2-1
Machine Architecture: armhf
Package: seer
Package-Time: 1180
Source-Version: 1.1.2-1
Space: 77800
Status: successful
Version: 1.1.2-1
--------------------------------------------------------------------------------
Finished at 2016-12-18T12:22:35Z
Build needed 00:19:40, 77800k disc space