seer →
1.1.2-3 →
armhf → 2017-03-29 05:25:41
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-02
+==============================================================================+
| seer 1.1.2-3 (armhf) Wed, 29 Mar 2017 05:01:48 +0000 |
+==============================================================================+
Package: seer
Version: 1.1.2-3
Source Version: 1.1.2-3
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-f176abcc-7435-4d0b-a1db-80570fdd882a' 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 [9732 kB]
Get:3 http://172.17.0.1/private stretch-staging/main armhf Packages [11.7 MB]
Fetched 21.4 MB in 23s (905 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 978 kB of source archives.
Get:1 http://172.17.0.1/private stretch-staging/main seer 1.1.2-3 (dsc) [2033 B]
Get:2 http://172.17.0.1/private stretch-staging/main seer 1.1.2-3 (tar) [969 kB]
Get:3 http://172.17.0.1/private stretch-staging/main seer 1.1.2-3 (diff) [6868 B]
Fetched 978 kB in 0s (5493 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/seer-J224bT/seer-1.1.2' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/seer-J224bT' 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-aIAK1p/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-aIAK1p/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-aIAK1p/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-aIAK1p/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-aIAK1p/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-aIAK1p/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-aIAK1p/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-aIAK1p/apt_archive ./ Packages [433 B]
Fetched 2109 B in 0s (3035 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 libfuse2 manpages
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 43 not upgraded.
Need to get 772 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-aIAK1p/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [772 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 772 B in 0s (0 B/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 13959 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-aIAK1p/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-aIAK1p/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-aIAK1p/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-aIAK1p/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-aIAK1p/apt_archive ./ Sources [549 B]
Get:5 copy:/<<BUILDDIR>>/resolver-aIAK1p/apt_archive ./ Packages [631 B]
Fetched 2513 B in 0s (3736 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 libfuse2 manpages
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev binutils bsdmainutils cpp cpp-6
debhelper dh-autoreconf dh-strip-nondeterminism file g++-6 gcc gcc-6
gcc-6-base gettext gettext-base gfortran gfortran-6 groff-base hdf5-helpers
intltool-debian libaec-dev libaec0 libarchive-zip-perl libarmadillo-dev
libarmadillo7 libarpack2 libarpack2-dev libasan3 libatomic1 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 libcc1-0 libcroco3 libdlib-data libdlib-dev
libdlib18 libffi6 libfile-stripnondeterminism-perl libgcc-6-dev libgcc1
libgfortran-6-dev libgfortran3 libglib2.0-0 libgomp1 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 libpng16-16 libsigsegv2 libstdc++-6-dev libstdc++6
libsuperlu-dev libsuperlu5 libsz2 libtool libubsan0 libunistring0 libxml2 m4
man-db po-debconf zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc binutils-doc wamerican
| wordlist whois vacation cpp-doc gcc-6-locales dh-make gcc-6-doc
libstdc++6-6-dbg gcc-multilib manpages-dev flex bison gdb gcc-doc
libgcc1-dbg libgomp1-dbg libitm1-dbg libatomic1-dbg libasan3-dbg
liblsan0-dbg libtsan0-dbg libubsan0-dbg libcilkrts5-dbg libmpx2-dbg
libquadmath0-dbg 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 libstdc++-6-doc
libsuperlu-doc libtool-doc gcj-jdk m4-doc 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 libpng16-16 libsigsegv2 libsuperlu-dev libsuperlu5 libsz2
libtool libunistring0 libxml2 m4 man-db po-debconf
sbuild-build-depends-seer-dummy zlib1g-dev
The following packages will be upgraded:
binutils cpp cpp-6 g++-6 gcc gcc-6 gcc-6-base libasan3 libatomic1 libcc1-0
libgcc-6-dev libgcc1 libgomp1 libstdc++-6-dev libstdc++6 libubsan0
16 upgraded, 68 newly installed, 0 to remove and 27 not upgraded.
Need to get 128 MB/128 MB of archives.
After this operation, 351 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-aIAK1p/apt_archive ./ sbuild-build-depends-seer-dummy 0.invalid.0 [832 B]
Get:2 http://172.17.0.1/private stretch-staging/main armhf libgomp1 armhf 6.3.0-10+rpi1 [63.9 kB]
Get:3 http://172.17.0.1/private stretch-staging/main armhf gcc-6-base armhf 6.3.0-10+rpi1 [179 kB]
Get:4 http://172.17.0.1/private stretch-staging/main armhf libgcc1 armhf 1:6.3.0-10+rpi1 [38.3 kB]
Get:5 http://172.17.0.1/private stretch-staging/main armhf libcc1-0 armhf 6.3.0-10+rpi1 [24.9 kB]
Get:6 http://172.17.0.1/private stretch-staging/main armhf binutils armhf 2.28-2 [3612 kB]
Get:7 http://172.17.0.1/private stretch-staging/main armhf libatomic1 armhf 6.3.0-10+rpi1 [6834 B]
Get:8 http://172.17.0.1/private stretch-staging/main armhf libasan3 armhf 6.3.0-10+rpi1 [268 kB]
Get:9 http://172.17.0.1/private stretch-staging/main armhf libubsan0 armhf 6.3.0-10+rpi1 [91.6 kB]
Get:10 http://172.17.0.1/private stretch-staging/main armhf g++-6 armhf 6.3.0-10+rpi1 [5549 kB]
Get:11 http://172.17.0.1/private stretch-staging/main armhf libstdc++-6-dev armhf 6.3.0-10+rpi1 [1446 kB]
Get:12 http://172.17.0.1/private stretch-staging/main armhf libgcc-6-dev armhf 6.3.0-10+rpi1 [512 kB]
Get:13 http://172.17.0.1/private stretch-staging/main armhf gcc-6 armhf 6.3.0-10+rpi1 [5403 kB]
Get:14 http://172.17.0.1/private stretch-staging/main armhf cpp-6 armhf 6.3.0-10+rpi1 [5131 kB]
Get:15 http://172.17.0.1/private stretch-staging/main armhf libstdc++6 armhf 6.3.0-10+rpi1 [334 kB]
Get:16 http://172.17.0.1/private stretch-staging/main armhf groff-base armhf 1.22.3-9 [1005 kB]
Get:17 http://172.17.0.1/private stretch-staging/main armhf libbsd0 armhf 0.8.3-1 [89.0 kB]
Get:18 http://172.17.0.1/private stretch-staging/main armhf bsdmainutils armhf 9.0.12 [178 kB]
Get:19 http://172.17.0.1/private stretch-staging/main armhf libpipeline1 armhf 1.4.1-2 [23.7 kB]
Get:20 http://172.17.0.1/private stretch-staging/main armhf man-db armhf 2.7.6.1-2 [1014 kB]
Get:21 http://172.17.0.1/private stretch-staging/main armhf libmagic-mgc armhf 1:5.29-3 [221 kB]
Get:22 http://172.17.0.1/private stretch-staging/main armhf libmagic1 armhf 1:5.29-3 [104 kB]
Get:23 http://172.17.0.1/private stretch-staging/main armhf file armhf 1:5.29-3 [63.2 kB]
Get:24 http://172.17.0.1/private stretch-staging/main armhf gettext-base armhf 0.19.8.1-2 [116 kB]
Get:25 http://172.17.0.1/private stretch-staging/main armhf libicu57 armhf 57.1-5 [7427 kB]
Get:26 http://172.17.0.1/private stretch-staging/main armhf libxml2 armhf 2.9.4+dfsg1-2.2 [806 kB]
Get:27 http://172.17.0.1/private stretch-staging/main armhf libsigsegv2 armhf 2.10-5 [28.4 kB]
Get:28 http://172.17.0.1/private stretch-staging/main armhf m4 armhf 1.4.18-1 [185 kB]
Get:29 http://172.17.0.1/private stretch-staging/main armhf autoconf all 2.69-10 [338 kB]
Get:30 http://172.17.0.1/private stretch-staging/main armhf autotools-dev all 20161112.1 [73.4 kB]
Get:31 http://172.17.0.1/private stretch-staging/main armhf automake all 1:1.15-6 [733 kB]
Get:32 http://172.17.0.1/private stretch-staging/main armhf autopoint all 0.19.8.1-2 [433 kB]
Get:33 http://172.17.0.1/private stretch-staging/main armhf cpp armhf 4:6.3.0-2 [18.6 kB]
Get:34 http://172.17.0.1/private stretch-staging/main armhf gcc armhf 4:6.3.0-2 [5208 B]
Get:35 http://172.17.0.1/private stretch-staging/main armhf libtool all 2.4.6-2 [545 kB]
Get:36 http://172.17.0.1/private stretch-staging/main armhf dh-autoreconf all 13 [15.8 kB]
Get:37 http://172.17.0.1/private stretch-staging/main armhf libarchive-zip-perl all 1.59-1 [95.5 kB]
Get:38 http://172.17.0.1/private stretch-staging/main armhf libfile-stripnondeterminism-perl all 0.032-1 [15.8 kB]
Get:39 http://172.17.0.1/private stretch-staging/main armhf dh-strip-nondeterminism all 0.032-1 [9888 B]
Get:40 http://172.17.0.1/private stretch-staging/main armhf libglib2.0-0 armhf 2.50.3-1 [2527 kB]
Get:41 http://172.17.0.1/private stretch-staging/main armhf libcroco3 armhf 0.6.11-2 [131 kB]
Get:42 http://172.17.0.1/private stretch-staging/main armhf libunistring0 armhf 0.9.6+really0.9.3-0.1 [252 kB]
Get:43 http://172.17.0.1/private stretch-staging/main armhf gettext armhf 0.19.8.1-2 [1434 kB]
Get:44 http://172.17.0.1/private stretch-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:45 http://172.17.0.1/private stretch-staging/main armhf po-debconf all 1.0.20 [247 kB]
Get:46 http://172.17.0.1/private stretch-staging/main armhf debhelper all 10.2.5 [961 kB]
Get:47 http://172.17.0.1/private stretch-staging/main armhf libgfortran3 armhf 6.3.0-10+rpi1 [166 kB]
Get:48 http://172.17.0.1/private stretch-staging/main armhf libgfortran-6-dev armhf 6.3.0-10+rpi1 [199 kB]
Get:49 http://172.17.0.1/private stretch-staging/main armhf gfortran-6 armhf 6.3.0-10+rpi1 [5413 kB]
Get:50 http://172.17.0.1/private stretch-staging/main armhf gfortran armhf 4:6.3.0-2 [1350 B]
Get:51 http://172.17.0.1/private stretch-staging/main armhf hdf5-helpers armhf 1.10.0-patch1+docs-3 [35.9 kB]
Get:52 http://172.17.0.1/private stretch-staging/main armhf libaec0 armhf 0.3.2-1 [19.4 kB]
Get:53 http://172.17.0.1/private stretch-staging/main armhf libblas-common armhf 3.7.0-1 [14.0 kB]
Get:54 http://172.17.0.1/private stretch-staging/main armhf libblas3 armhf 3.7.0-1 [107 kB]
Get:55 http://172.17.0.1/private stretch-staging/main armhf liblapack3 armhf 3.7.0-1 [1503 kB]
Get:56 http://172.17.0.1/private stretch-staging/main armhf libarpack2 armhf 3.4.0-1+b1 [78.4 kB]
Get:57 http://172.17.0.1/private stretch-staging/main armhf libsuperlu5 armhf 5.2.1+dfsg1-2 [126 kB]
Get:58 http://172.17.0.1/private stretch-staging/main armhf libarmadillo7 armhf 1:7.600.2+dfsg-2 [80.6 kB]
Get:59 http://172.17.0.1/private stretch-staging/main armhf libblas-dev armhf 3.7.0-1 [19.0 kB]
Get:60 http://172.17.0.1/private stretch-staging/main armhf liblapack-dev armhf 3.7.0-1 [1483 kB]
Get:61 http://172.17.0.1/private stretch-staging/main armhf libarpack2-dev armhf 3.4.0-1+b1 [90.5 kB]
Get:62 http://172.17.0.1/private stretch-staging/main armhf libsz2 armhf 0.3.2-1 [5836 B]
Get:63 http://172.17.0.1/private stretch-staging/main armhf libhdf5-100 armhf 1.10.0-patch1+docs-3 [1203 kB]
Get:64 http://172.17.0.1/private stretch-staging/main armhf zlib1g-dev armhf 1:1.2.8.dfsg-5 [198 kB]
Get:65 http://172.17.0.1/private stretch-staging/main armhf libjpeg62-turbo armhf 1:1.5.1-2 [109 kB]
Get:66 http://172.17.0.1/private stretch-staging/main armhf libjpeg62-turbo-dev armhf 1:1.5.1-2 [181 kB]
Get:67 http://172.17.0.1/private stretch-staging/main armhf libjpeg-dev all 1:1.5.1-2 [56.1 kB]
Get:68 http://172.17.0.1/private stretch-staging/main armhf libaec-dev armhf 0.3.2-1 [17.6 kB]
Get:69 http://172.17.0.1/private stretch-staging/main armhf libhdf5-cpp-100 armhf 1.10.0-patch1+docs-3 [118 kB]
Get:70 http://172.17.0.1/private stretch-staging/main armhf libhdf5-dev armhf 1.10.0-patch1+docs-3 [2093 kB]
Get:71 http://172.17.0.1/private stretch-staging/main armhf libsuperlu-dev armhf 5.2.1+dfsg1-2 [18.0 kB]
Get:72 http://172.17.0.1/private stretch-staging/main armhf libarmadillo-dev armhf 1:7.600.2+dfsg-2 [323 kB]
Get:73 http://172.17.0.1/private stretch-staging/main armhf libboost1.62-dev armhf 1.62.0+dfsg-4 [7009 kB]
Get:74 http://172.17.0.1/private stretch-staging/main armhf libboost-dev armhf 1.62.0.1+b4 [3920 B]
Get:75 http://172.17.0.1/private stretch-staging/main armhf libboost-program-options1.62.0 armhf 1.62.0+dfsg-4 [136 kB]
Get:76 http://172.17.0.1/private stretch-staging/main armhf libboost-program-options1.62-dev armhf 1.62.0+dfsg-4 [178 kB]
Get:77 http://172.17.0.1/private stretch-staging/main armhf libboost-program-options-dev armhf 1.62.0.1+b4 [3716 B]
Get:78 http://172.17.0.1/private stretch-staging/main armhf libdlib-data all 18.18-2 [63.4 MB]
Get:79 http://172.17.0.1/private stretch-staging/main armhf libpng16-16 armhf 1.6.28-1 [263 kB]
Get:80 http://172.17.0.1/private stretch-staging/main armhf libdlib18 armhf 18.18-2 [223 kB]
Get:81 http://172.17.0.1/private stretch-staging/main armhf libdlib-dev armhf 18.18-2 [1356 kB]
Get:82 http://172.17.0.1/private stretch-staging/main armhf libgzstream0 armhf 1.5+dfsg-2 [5764 B]
Get:83 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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(Reading database ... 13959 files and directories currently installed.)
Preparing to unpack .../libgomp1_6.3.0-10+rpi1_armhf.deb ...
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Setting up libgcc1:armhf (1:6.3.0-10+rpi1) ...
(Reading database ... 13959 files and directories currently installed.)
Preparing to unpack .../00-libcc1-0_6.3.0-10+rpi1_armhf.deb ...
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Processing triggers for libc-bin (2.24-9) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 3.19.0-trunk-armmp armhf (armv7l)
Toolchain package versions: binutils_2.28-2 dpkg-dev_1.18.22 g++-6_6.3.0-10+rpi1 gcc-6_6.3.0-10+rpi1 libc6-dev_2.24-9 libstdc++-4.9-dev_4.9.3-14 libstdc++-6-dev_6.3.0-10+rpi1 libstdc++6_6.3.0-10+rpi1 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch
Package versions: acl_2.2.52-3 adduser_3.115 apt_1.4~rc1 autoconf_2.69-10 automake_1:1.15-6 autopoint_0.19.8.1-2 autotools-dev_20161112.1 base-files_9.8+rpi1 base-passwd_3.5.43 bash_4.4-4 binutils_2.28-2 bsdmainutils_9.0.12 bsdutils_1:2.29.1-1 build-essential_12.3 bzip2_1.0.6-8.1 coreutils_8.26-2 cpio_2.11+dfsg-6 cpp_4:6.3.0-2 cpp-6_6.3.0-10+rpi1 dash_0.5.8-2.4 debconf_1.5.60 debfoster_2.7-2.1 debhelper_10.2.5 debianutils_4.8.1 dh-autoreconf_13 dh-strip-nondeterminism_0.032-1 diffutils_1:3.5-3 dmsetup_2:1.02.137-1 dpkg_1.18.22 dpkg-dev_1.18.22 e2fslibs_1.43.4-2 e2fsprogs_1.43.4-2 fakeroot_1.21-3.1 file_1:5.29-3 findutils_4.6.0+git+20161106-2 fuse2fs_1.43.4-2 g++_4:6.3.0-1 g++-6_6.3.0-10+rpi1 gcc_4:6.3.0-2 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_6.3.0-10+rpi1 gcc-6-base_6.3.0-10+rpi1 gettext_0.19.8.1-2 gettext-base_0.19.8.1-2 gfortran_4:6.3.0-2 gfortran-6_6.3.0-10+rpi1 gnupg_2.1.18-3 gnupg-agent_2.1.18-3 gnupg-l10n_2.1.18-3 gpgv_2.1.18-3 grep_2.27-2 groff-base_1.22.3-9 gzip_1.6-5 hdf5-helpers_1.10.0-patch1+docs-3 hostname_3.18 init_1.47 init-system-helpers_1.47 initscripts_2.88dsf-59.9 insserv_1.14.0-5.4 intltool-debian_0.35.0+20060710.4 klibc-utils_2.0.4-9+rpi1 kmod_23-2 libacl1_2.2.52-3 libaec-dev_0.3.2-1 libaec0_0.3.2-1 libapparmor1_2.11.0-2 libapt-pkg4.12_1.0.9.10 libapt-pkg5.0_1.4~rc1 libarchive-zip-perl_1.59-1 libarmadillo-dev_1:7.600.2+dfsg-2 libarmadillo7_1:7.600.2+dfsg-2 libarpack2_3.4.0-1+b1 libarpack2-dev_3.4.0-1+b1 libasan1_4.9.3-14 libasan3_6.3.0-10+rpi1 libassuan0_2.4.3-2 libatomic1_6.3.0-10+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.6.7-1 libaudit1_1:2.6.7-1 libblas-common_3.7.0-1 libblas-dev_3.7.0-1 libblas3_3.7.0-1 libblkid1_2.29.1-1 libboost-dev_1.62.0.1+b4 libboost-program-options-dev_1.62.0.1+b4 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_1.0.6-8.1 libc-bin_2.24-9 libc-dev-bin_2.24-9 libc6_2.24-9 libc6-dev_2.24-9 libcap-ng0_0.7.7-3 libcap2_1:2.25-1 libcap2-bin_1:2.25-1 libcc1-0_6.3.0-10+rpi1 libcomerr2_1.43.4-2 libcroco3_0.6.11-2 libcryptsetup4_2:1.7.3-3 libdb5.3_5.3.28-12 libdbus-1-3_1.10.16-1 libdebconfclient0_0.220 libdevmapper1.02.1_2:1.02.137-1 libdlib-data_18.18-2 libdlib-dev_18.18-2 libdlib18_18.18-2 libdpkg-perl_1.18.22 libdrm2_2.4.74-1 libfakeroot_1.21-3.1 libfdisk1_2.29.1-1 libffi6_3.2.1-6 libfile-stripnondeterminism-perl_0.032-1 libfuse2_2.9.7-1 libgc1c2_1:7.4.2-8 libgcc-4.9-dev_4.9.3-14 libgcc-6-dev_6.3.0-10+rpi1 libgcc1_1:6.3.0-10+rpi1 libgcrypt20_1.7.6-1 libgdbm3_1.8.3-14 libgfortran-6-dev_6.3.0-10+rpi1 libgfortran3_6.3.0-10+rpi1 libglib2.0-0_2.50.3-1 libgmp10_2:6.1.2+dfsg-1 libgomp1_6.3.0-10+rpi1 libgpg-error0_1.26-2 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+snapshot20161117-5 libisl15_0.18-1 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_23-2 libksba8_1.3.5-2 liblapack-dev_3.7.0-1 liblapack3_3.7.0-1 liblz4-1_0.0~r131-2 liblzma5_5.2.2-1.2 libmagic-mgc_1:5.29-3 libmagic1_1:5.29-3 libmount1_2.29.1-1 libmpc3_1.0.3-1 libmpfr4_3.1.5-1 libncurses5_6.0+20161126-1 libncursesw5_6.0+20161126-1 libnpth0_1.3-1 libpam-modules_1.1.8-3.5 libpam-modules-bin_1.1.8-3.5 libpam-runtime_1.1.8-3.5 libpam0g_1.1.8-3.5 libpcre3_2:8.39-2 libperl5.24_5.24.1-1 libpipeline1_1.4.1-2 libpng12-0_1.2.54-6 libpng16-16_1.6.28-1 libprocps3_2:3.3.9-9 libprocps6_2:3.3.12-3 libreadline7_7.0-2 libseccomp2_2.3.1-2.1 libselinux1_2.6-3 libsemanage-common_2.6-2 libsemanage1_2.6-2 libsepol1_2.6-2 libsigsegv2_2.10-5 libslang2_2.3.1-5 libsmartcols1_2.29.1-1 libsqlite3-0_3.16.2-2 libss2_1.43.4-2 libstdc++-4.9-dev_4.9.3-14 libstdc++-6-dev_6.3.0-10+rpi1 libstdc++6_6.3.0-10+rpi1 libsuperlu-dev_5.2.1+dfsg1-2 libsuperlu5_5.2.1+dfsg1-2 libsystemd0_232-18 libsz2_0.3.2-1 libtimedate-perl_2.3000-2 libtinfo5_6.0+20161126-1 libtool_2.4.6-2 libubsan0_6.3.0-10+rpi1 libudev1_232-18 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_2.29.1-1 libxml2_2.9.4+dfsg1-2.2 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch login_1:4.4-3 lsb-base_9.20161125+rpi1 m4_1.4.18-1 make_4.1-9.1 makedev_2.3.1-93 man-db_2.7.6.1-2 manpages_4.09-2 mawk_1.3.3-17 mount_2.29.1-1 multiarch-support_2.24-9 nano_2.7.4-1 ncurses-base_6.0+20161126-1 ncurses-bin_6.0+20161126-1 passwd_1:4.4-3 patch_2.7.5-1 perl_5.24.1-1 perl-base_5.24.1-1 perl-modules-5.24_5.24.1-1 pinentry-curses_1.0.0-2 po-debconf_1.0.20 procps_2:3.3.12-3 raspbian-archive-keyring_20120528.2 readline-common_7.0-2 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-seer-dummy_0.invalid.0 sed_4.4-1 sensible-utils_0.0.9 startpar_0.59-3.1 systemd_232-18 systemd-sysv_232-18 sysv-rc_2.88dsf-59.9 sysvinit-utils_2.88dsf-59.9 tar_1.29b-1.1 tzdata_2016j-2 udev_232-18 util-linux_2.29.1-1 xz-utils_5.2.2-1.2 zlib1g_1:1.2.8.dfsg-5 zlib1g-dev_1:1.2.8.dfsg-5
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Thu Mar 23 13:36:29 2017 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_1.1.2-3.dsc
dpkg-source: info: extracting seer in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking seer_1.1.2.orig.tar.gz
dpkg-source: info: unpacking seer_1.1.2-3.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-f176abcc-7435-4d0b-a1db-80570fdd882a
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=xterm
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package seer
dpkg-buildpackage: info: source version 1.1.2-3
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>>'
create-stamp debian/debhelper-build-stamp
fakeroot debian/rules binary-arch
dh binary-arch
dh_testroot -a
dh_prep -a
debian/rules override_dh_auto_install
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_install -- 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>>'
for pl in scripts/*.pl ; do \
plbase=`basename ${pl} .pl` ; \
sed "s+Usage: ./${plbase}.pl+Usage: ${plbase}+" ${pl} > /<<PKGBUILDDIR>>/debian/seer/usr/bin/${plbase} ; \
done
# Fix broken usage hint:
sed -i "s+Usage: ./hits_to_matrix.pl+Usage: reformat_output+" /<<PKGBUILDDIR>>/debian/seer/usr/bin/reformat_output
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: tried to merge the same object (ld-linux-armhf.so.3) twice in a symfile
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: tried to merge the same object (ld-linux-armhf.so.3) twice in a symfile
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: tried to merge the same object (ld-linux-armhf.so.3) twice in a symfile
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: tried to merge the same object (ld-linux-armhf.so.3) twice in a symfile
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: tried to merge the same object (ld-linux-armhf.so.3) twice in a symfile
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: package could avoid a useless dependency if debian/seer/usr/bin/combineKmers debian/seer/usr/bin/seer debian/seer/usr/bin/kmds were not linked against libz.so.1 (they use none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/seer/usr/bin/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/map_back debian/seer/usr/bin/combineKmers debian/seer/usr/bin/seer debian/seer/usr/bin/kmds debian/seer/usr/bin/filter_seer were not linked against ld-linux-armhf.so.3 (they use none of the library's symbols)
dh_installdeb -a
dh_gencontrol -a
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package 'seer-dbgsym' in '../seer-dbgsym_1.1.2-3_armhf.deb'.
dpkg-deb: building package 'seer' in '../seer_1.1.2-3_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../seer_1.1.2-3_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 2017-03-29T05:23:24Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
seer_1.1.2-3_armhf.changes:
---------------------------
Format: 1.8
Date: Thu, 23 Mar 2017 14:33:36 +0100
Source: seer
Binary: seer
Architecture: armhf
Version: 1.1.2-3
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 (1.1.2-3) unstable; urgency=medium
.
* Better documentation of scripts
Checksums-Sha1:
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0c13243d71da39655a7082b62401c2a18fbb11b7 5704 seer_1.1.2-3_armhf.buildinfo
d7494d0519825b3c62c69b7e9a79e7cdd3e69748 299100 seer_1.1.2-3_armhf.deb
Checksums-Sha256:
8049c7445f1dda54b86e50a6a756029cd7b93f8484ac474ac52afe4509f5ce55 7501376 seer-dbgsym_1.1.2-3_armhf.deb
2de07da78d98356f27365723e6838b6134e51ead6604f2a545065723c93220a1 5704 seer_1.1.2-3_armhf.buildinfo
8fe76829a3fda92d86c7e34cf059028369fa3c8cc14ed7bf49c0beb3a88dcdbc 299100 seer_1.1.2-3_armhf.deb
Files:
bf537d5e57341fa88a7dccf8cc08e90e 7501376 debug extra seer-dbgsym_1.1.2-3_armhf.deb
dc2889bb7603c4abbc0020af6e823ca2 5704 science optional seer_1.1.2-3_armhf.buildinfo
b3e788c40a796bc70beac98e3edcb95f 299100 science optional seer_1.1.2-3_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
seer-dbgsym_1.1.2-3_armhf.deb
-----------------------------
new debian package, version 2.0.
size 7501376 bytes: control archive=711 bytes.
563 bytes, 13 lines control
530 bytes, 5 lines md5sums
Package: seer-dbgsym
Source: seer
Version: 1.1.2-3
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 7825
Depends: seer (= 1.1.2-3)
Section: debug
Priority: extra
Homepage: https://github.com/johnlees/seer
Description: Debug symbols for seer
Build-Ids: 26fabe772f166e4a01899d24662576e3823e5433 4569696a5272f5d55ab41ca63a0e3e674fc91ae1 9b9c62e1a2c686135173efe8e3d575678f4b02bc c67570bed753880c8492db1e7490939fc090e73f d8dac8691d720f534fb4b5d985d8dd5178c67f74
drwxr-xr-x root/root 0 2017-03-23 13:33 ./
drwxr-xr-x root/root 0 2017-03-23 13:33 ./usr/
drwxr-xr-x root/root 0 2017-03-23 13:33 ./usr/lib/
drwxr-xr-x root/root 0 2017-03-23 13:33 ./usr/lib/debug/
drwxr-xr-x root/root 0 2017-03-23 13:33 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2017-03-23 13:33 ./usr/lib/debug/.build-id/26/
-rw-r--r-- root/root 800096 2017-03-23 13:33 ./usr/lib/debug/.build-id/26/fabe772f166e4a01899d24662576e3823e5433.debug
drwxr-xr-x root/root 0 2017-03-23 13:33 ./usr/lib/debug/.build-id/45/
-rw-r--r-- root/root 348436 2017-03-23 13:33 ./usr/lib/debug/.build-id/45/69696a5272f5d55ab41ca63a0e3e674fc91ae1.debug
drwxr-xr-x root/root 0 2017-03-23 13:33 ./usr/lib/debug/.build-id/9b/
-rw-r--r-- root/root 3053164 2017-03-23 13:33 ./usr/lib/debug/.build-id/9b/9c62e1a2c686135173efe8e3d575678f4b02bc.debug
drwxr-xr-x root/root 0 2017-03-23 13:33 ./usr/lib/debug/.build-id/c6/
-rw-r--r-- root/root 3315332 2017-03-23 13:33 ./usr/lib/debug/.build-id/c6/7570bed753880c8492db1e7490939fc090e73f.debug
drwxr-xr-x root/root 0 2017-03-23 13:33 ./usr/lib/debug/.build-id/d8/
-rw-r--r-- root/root 478604 2017-03-23 13:33 ./usr/lib/debug/.build-id/d8/dac8691d720f534fb4b5d985d8dd5178c67f74.debug
drwxr-xr-x root/root 0 2017-03-23 13:33 ./usr/share/
drwxr-xr-x root/root 0 2017-03-23 13:33 ./usr/share/doc/
lrwxrwxrwx root/root 0 2017-03-23 13:33 ./usr/share/doc/seer-dbgsym -> seer
seer_1.1.2-3_armhf.deb
----------------------
new debian package, version 2.0.
size 299100 bytes: control archive=1787 bytes.
1412 bytes, 24 lines control
1643 bytes, 26 lines md5sums
Package: seer
Version: 1.1.2-3
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1309
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 2017-03-23 13:33 ./
drwxr-xr-x root/root 0 2017-03-23 13:33 ./usr/
drwxr-xr-x root/root 0 2017-03-23 13:33 ./usr/bin/
-rwxr-xr-x root/root 3872 2017-03-23 13:33 ./usr/bin/R_mds
-rwxr-xr-x root/root 3794 2017-03-23 13:33 ./usr/bin/blast_top_hits
-rwxr-xr-x root/root 95796 2017-03-23 13:33 ./usr/bin/combineKmers
-rwxr-xr-x root/root 71220 2017-03-23 13:33 ./usr/bin/filter_seer
-rwxr-xr-x root/root 1869 2017-03-23 13:33 ./usr/bin/hits_to_fastq
-rwxr-xr-x root/root 444500 2017-03-23 13:33 ./usr/bin/kmds
-rwxr-xr-x root/root 173620 2017-03-23 13:33 ./usr/bin/map_back
-rwxr-xr-x root/root 2751 2017-03-23 13:33 ./usr/bin/mapping_to_phandango
-rwxr-xr-x root/root 1208 2017-03-23 13:33 ./usr/bin/mash2matrix
-rwxr-xr-x root/root 2295 2017-03-23 13:33 ./usr/bin/reformat_output
-rwxr-xr-x root/root 505940 2017-03-23 13:33 ./usr/bin/seer
drwxr-xr-x root/root 0 2017-03-23 13:33 ./usr/share/
drwxr-xr-x root/root 0 2017-03-23 13:33 ./usr/share/doc/
drwxr-xr-x root/root 0 2017-03-23 13:33 ./usr/share/doc/seer/
-rw-r--r-- root/root 684 2017-03-23 13:33 ./usr/share/doc/seer/README.Debian
-rw-r--r-- root/root 490 2017-03-23 13:33 ./usr/share/doc/seer/changelog.Debian.gz
-rw-r--r-- root/root 1008 2017-03-23 13:33 ./usr/share/doc/seer/copyright
drwxr-xr-x root/root 0 2017-03-23 13:33 ./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 2017-03-23 13:33 ./usr/share/man/
drwxr-xr-x root/root 0 2017-03-23 13:33 ./usr/share/man/man1/
-rw-r--r-- root/root 506 2017-03-23 13:33 ./usr/share/man/man1/R_mds.1.gz
-rw-r--r-- root/root 501 2017-03-23 13:33 ./usr/share/man/man1/blast_top_hits.1.gz
-rw-r--r-- root/root 461 2017-03-23 13:33 ./usr/share/man/man1/combineKmers.1.gz
-rw-r--r-- root/root 543 2017-03-23 13:33 ./usr/share/man/man1/filter_seer.1.gz
-rw-r--r-- root/root 408 2017-03-23 13:33 ./usr/share/man/man1/hits_to_fastq.1.gz
-rw-r--r-- root/root 906 2017-03-23 13:33 ./usr/share/man/man1/kmds.1.gz
-rw-r--r-- root/root 458 2017-03-23 13:33 ./usr/share/man/man1/map_back.1.gz
-rw-r--r-- root/root 432 2017-03-23 13:33 ./usr/share/man/man1/mapping_to_phandango.1.gz
-rw-r--r-- root/root 466 2017-03-23 13:33 ./usr/share/man/man1/mash2matrix.1.gz
-rw-r--r-- root/root 422 2017-03-23 13:33 ./usr/share/man/man1/reformat_output.1.gz
-rw-r--r-- root/root 995 2017-03-23 13:33 ./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: 77652
Build-Time: 740
Distribution: stretch-staging
Host Architecture: armhf
Install-Time: 508
Job: seer_1.1.2-3
Machine Architecture: armhf
Package: seer
Package-Time: 1296
Source-Version: 1.1.2-3
Space: 77652
Status: successful
Version: 1.1.2-3
--------------------------------------------------------------------------------
Finished at 2017-03-29T05:23:24Z
Build needed 00:21:36, 77652k disc space