seer →
1.1.4-1+b1 →
armhf → 2017-11-13 00:45:33
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-04
+==============================================================================+
| seer 1.1.4-1+b1 (armhf) Mon, 13 Nov 2017 00:19:46 +0000 |
+==============================================================================+
Package: seer
Version: 1.1.4-1+b1
Source Version: 1.1.4-1
Distribution: buster-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/buster-staging-armhf-sbuild-b85b26e4-b6b9-45e4-9106-039ca182a762' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private buster-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private buster-staging/main Sources [10.3 MB]
Get:3 http://172.17.0.1/private buster-staging/main armhf Packages [12.2 MB]
Fetched 22.5 MB in 31s (725 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
W: http: aptMethod::Configuration: could not load seccomp policy: Invalid argument
W: store: aptMethod::Configuration: could not load seccomp policy: Invalid argument
+------------------------------------------------------------------------------+
| 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 981 kB of source archives.
Get:1 http://172.17.0.1/private buster-staging/main seer 1.1.4-1 (dsc) [2033 B]
Get:2 http://172.17.0.1/private buster-staging/main seer 1.1.4-1 (tar) [972 kB]
Get:3 http://172.17.0.1/private buster-staging/main seer 1.1.4-1 (diff) [6896 B]
Fetched 981 kB in 0s (3343 kB/s)
Download complete and in download only mode
W: http: aptMethod::Configuration: could not load seccomp policy: Invalid argument
I: NOTICE: Log filtering will replace 'build/seer-mMGleP/seer-1.1.4' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/seer-mMGleP' 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-bbVEx8/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-bbVEx8/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-bbVEx8/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-bbVEx8/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-bbVEx8/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-bbVEx8/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-bbVEx8/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-bbVEx8/apt_archive ./ Packages [430 B]
Fetched 2106 B in 0s (3368 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
W: copy: aptMethod::Configuration: could not load seccomp policy: Invalid argument
W: store: aptMethod::Configuration: could not load seccomp policy: Invalid argument
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:
ca-certificates e2fsprogs-l10n libsasl2-modules libssl1.1 openssl
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 13 not upgraded.
Need to get 852 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-bbVEx8/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 852 B in 0s (0 B/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 15098 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
W: copy: aptMethod::Configuration: could not load seccomp policy: Invalid argument
+------------------------------------------------------------------------------+
| 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-bbVEx8/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-bbVEx8/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-bbVEx8/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-bbVEx8/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-bbVEx8/apt_archive ./ Sources [549 B]
Get:5 copy:/<<BUILDDIR>>/resolver-bbVEx8/apt_archive ./ Packages [631 B]
Fetched 2513 B in 0s (3642 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
W: copy: aptMethod::Configuration: could not load seccomp policy: Invalid argument
W: store: aptMethod::Configuration: could not load seccomp policy: Invalid argument
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:
ca-certificates e2fsprogs-l10n libsasl2-modules libssl1.1 openssl
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils debhelper
dh-autoreconf dh-strip-nondeterminism file gettext gettext-base groff-base
hdf5-helpers intltool-debian libaec-dev libaec0 libarchive-zip-perl
libarmadillo-dev libarmadillo8 libarpack2 libarpack2-dev 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
libfile-stripnondeterminism-perl libgfortran4 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 libxml2 m4 man-db po-debconf zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
vacation dh-make dwz gettext-doc libasprintf-dev libgettextpo-dev groff
libitpp-dev 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 gfortran | fortran95-compiler gcj-jdk m4-doc less www-browser
libmail-box-perl
Recommended packages:
curl | wget | lynx-cur libarchive-cpio-perl libglib2.0-data shared-mime-info
xdg-user-dirs libltdl-dev 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 groff-base
hdf5-helpers intltool-debian libaec-dev libaec0 libarchive-zip-perl
libarmadillo-dev libarmadillo8 libarpack2 libarpack2-dev 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
libfile-stripnondeterminism-perl libgfortran4 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 libxml2 m4 man-db po-debconf
sbuild-build-depends-seer-dummy zlib1g-dev
0 upgraded, 62 newly installed, 0 to remove and 13 not upgraded.
Need to get 99.3 MB of archives.
After this operation, 331 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-bbVEx8/apt_archive ./ sbuild-build-depends-seer-dummy 0.invalid.0 [920 B]
Get:2 http://172.17.0.1/private buster-staging/main armhf groff-base armhf 1.22.3-9 [1005 kB]
Get:3 http://172.17.0.1/private buster-staging/main armhf libbsd0 armhf 0.8.6-3 [95.9 kB]
Get:4 http://172.17.0.1/private buster-staging/main armhf bsdmainutils armhf 9.0.14 [178 kB]
Get:5 http://172.17.0.1/private buster-staging/main armhf libpipeline1 armhf 1.4.2-1 [24.2 kB]
Get:6 http://172.17.0.1/private buster-staging/main armhf man-db armhf 2.7.6.1-2 [1014 kB]
Get:7 http://172.17.0.1/private buster-staging/main armhf libmagic-mgc armhf 1:5.32-1 [225 kB]
Get:8 http://172.17.0.1/private buster-staging/main armhf libmagic1 armhf 1:5.32-1 [105 kB]
Get:9 http://172.17.0.1/private buster-staging/main armhf file armhf 1:5.32-1 [63.7 kB]
Get:10 http://172.17.0.1/private buster-staging/main armhf gettext-base armhf 0.19.8.1-4 [117 kB]
Get:11 http://172.17.0.1/private buster-staging/main armhf libicu57 armhf 57.1-8 [7411 kB]
Get:12 http://172.17.0.1/private buster-staging/main armhf libxml2 armhf 2.9.4+dfsg1-5 [609 kB]
Get:13 http://172.17.0.1/private buster-staging/main armhf libsigsegv2 armhf 2.11-1 [29.3 kB]
Get:14 http://172.17.0.1/private buster-staging/main armhf m4 armhf 1.4.18-1 [185 kB]
Get:15 http://172.17.0.1/private buster-staging/main armhf autoconf all 2.69-11 [341 kB]
Get:16 http://172.17.0.1/private buster-staging/main armhf autotools-dev all 20161112.1+nmu1 [74.2 kB]
Get:17 http://172.17.0.1/private buster-staging/main armhf automake all 1:1.15.1-3 [736 kB]
Get:18 http://172.17.0.1/private buster-staging/main armhf autopoint all 0.19.8.1-4 [434 kB]
Get:19 http://172.17.0.1/private buster-staging/main armhf libtool all 2.4.6-2 [545 kB]
Get:20 http://172.17.0.1/private buster-staging/main armhf dh-autoreconf all 14 [15.9 kB]
Get:21 http://172.17.0.1/private buster-staging/main armhf libarchive-zip-perl all 1.59-1 [95.5 kB]
Get:22 http://172.17.0.1/private buster-staging/main armhf libfile-stripnondeterminism-perl all 0.040-1 [18.4 kB]
Get:23 http://172.17.0.1/private buster-staging/main armhf libtimedate-perl all 2.3000-2 [42.2 kB]
Get:24 http://172.17.0.1/private buster-staging/main armhf dh-strip-nondeterminism all 0.040-1 [11.8 kB]
Get:25 http://172.17.0.1/private buster-staging/main armhf libglib2.0-0 armhf 2.54.1-1 [2653 kB]
Get:26 http://172.17.0.1/private buster-staging/main armhf libcroco3 armhf 0.6.12-1 [132 kB]
Get:27 http://172.17.0.1/private buster-staging/main armhf gettext armhf 0.19.8.1-4 [1218 kB]
Get:28 http://172.17.0.1/private buster-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:29 http://172.17.0.1/private buster-staging/main armhf po-debconf all 1.0.20 [247 kB]
Get:30 http://172.17.0.1/private buster-staging/main armhf debhelper all 10.10.5 [978 kB]
Get:31 http://172.17.0.1/private buster-staging/main armhf hdf5-helpers armhf 1.10.0-patch1+docs-4 [36.0 kB]
Get:32 http://172.17.0.1/private buster-staging/main armhf libaec0 armhf 0.3.2-2 [19.3 kB]
Get:33 http://172.17.0.1/private buster-staging/main armhf libgfortran4 armhf 7.2.0-12 [191 kB]
Get:34 http://172.17.0.1/private buster-staging/main armhf libblas3 armhf 3.7.1-4 [103 kB]
Get:35 http://172.17.0.1/private buster-staging/main armhf liblapack3 armhf 3.7.1-4 [1508 kB]
Get:36 http://172.17.0.1/private buster-staging/main armhf libarpack2 armhf 3.5.0+real-1 [80.2 kB]
Get:37 http://172.17.0.1/private buster-staging/main armhf libsuperlu5 armhf 5.2.1+dfsg1-3 [125 kB]
Get:38 http://172.17.0.1/private buster-staging/main armhf libarmadillo8 armhf 1:8.200.0+dfsg-3 [80.8 kB]
Get:39 http://172.17.0.1/private buster-staging/main armhf libblas-dev armhf 3.7.1-4 [112 kB]
Get:40 http://172.17.0.1/private buster-staging/main armhf liblapack-dev armhf 3.7.1-4 [1564 kB]
Get:41 http://172.17.0.1/private buster-staging/main armhf libarpack2-dev armhf 3.5.0+real-1 [86.6 kB]
Get:42 http://172.17.0.1/private buster-staging/main armhf libsz2 armhf 0.3.2-2 [6080 B]
Get:43 http://172.17.0.1/private buster-staging/main armhf libhdf5-100 armhf 1.10.0-patch1+docs-4 [1220 kB]
Get:44 http://172.17.0.1/private buster-staging/main armhf zlib1g-dev armhf 1:1.2.8.dfsg-5 [198 kB]
Get:45 http://172.17.0.1/private buster-staging/main armhf libjpeg62-turbo armhf 1:1.5.2-2 [110 kB]
Get:46 http://172.17.0.1/private buster-staging/main armhf libjpeg62-turbo-dev armhf 1:1.5.2-2 [178 kB]
Get:47 http://172.17.0.1/private buster-staging/main armhf libjpeg-dev all 1:1.5.2-2 [57.5 kB]
Get:48 http://172.17.0.1/private buster-staging/main armhf libaec-dev armhf 0.3.2-2 [17.3 kB]
Get:49 http://172.17.0.1/private buster-staging/main armhf libhdf5-cpp-100 armhf 1.10.0-patch1+docs-4 [118 kB]
Get:50 http://172.17.0.1/private buster-staging/main armhf libhdf5-dev armhf 1.10.0-patch1+docs-4 [2109 kB]
Get:51 http://172.17.0.1/private buster-staging/main armhf libsuperlu-dev armhf 5.2.1+dfsg1-3 [18.2 kB]
Get:52 http://172.17.0.1/private buster-staging/main armhf libarmadillo-dev armhf 1:8.200.0+dfsg-3 [334 kB]
Get:53 http://172.17.0.1/private buster-staging/main armhf libboost1.62-dev armhf 1.62.0+dfsg-4+b2 [7053 kB]
Get:54 http://172.17.0.1/private buster-staging/main armhf libboost-dev armhf 1.62.0.1+b8 [3918 B]
Get:55 http://172.17.0.1/private buster-staging/main armhf libboost-program-options1.62.0 armhf 1.62.0+dfsg-4+b2 [137 kB]
Get:56 http://172.17.0.1/private buster-staging/main armhf libboost-program-options1.62-dev armhf 1.62.0+dfsg-4+b2 [178 kB]
Get:57 http://172.17.0.1/private buster-staging/main armhf libboost-program-options-dev armhf 1.62.0.1+b8 [3716 B]
Get:58 http://172.17.0.1/private buster-staging/main armhf libdlib-data all 18.18-2 [63.4 MB]
Get:59 http://172.17.0.1/private buster-staging/main armhf libdlib18 armhf 18.18-2 [223 kB]
Get:60 http://172.17.0.1/private buster-staging/main armhf libdlib-dev armhf 18.18-2 [1356 kB]
Get:61 http://172.17.0.1/private buster-staging/main armhf libgzstream0 armhf 1.5+dfsg-2 [5764 B]
Get:62 http://172.17.0.1/private buster-staging/main armhf libgzstream-dev armhf 1.5+dfsg-2 [6172 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 99.3 MB in 13s (7479 kB/s)
Selecting previously unselected package groff-base.
(Reading database ... 15098 files and directories currently installed.)
Preparing to unpack .../00-groff-base_1.22.3-9_armhf.deb ...
Unpacking groff-base (1.22.3-9) ...
Selecting previously unselected package libbsd0:armhf.
Preparing to unpack .../01-libbsd0_0.8.6-3_armhf.deb ...
Unpacking libbsd0:armhf (0.8.6-3) ...
Selecting previously unselected package bsdmainutils.
Preparing to unpack .../02-bsdmainutils_9.0.14_armhf.deb ...
Unpacking bsdmainutils (9.0.14) ...
Selecting previously unselected package libpipeline1:armhf.
Preparing to unpack .../03-libpipeline1_1.4.2-1_armhf.deb ...
Unpacking libpipeline1:armhf (1.4.2-1) ...
Selecting previously unselected package man-db.
Preparing to unpack .../04-man-db_2.7.6.1-2_armhf.deb ...
Unpacking man-db (2.7.6.1-2) ...
Selecting previously unselected package libmagic-mgc.
Preparing to unpack .../05-libmagic-mgc_1%3a5.32-1_armhf.deb ...
Unpacking libmagic-mgc (1:5.32-1) ...
Selecting previously unselected package libmagic1:armhf.
Preparing to unpack .../06-libmagic1_1%3a5.32-1_armhf.deb ...
Unpacking libmagic1:armhf (1:5.32-1) ...
Selecting previously unselected package file.
Preparing to unpack .../07-file_1%3a5.32-1_armhf.deb ...
Unpacking file (1:5.32-1) ...
Selecting previously unselected package gettext-base.
Preparing to unpack .../08-gettext-base_0.19.8.1-4_armhf.deb ...
Unpacking gettext-base (0.19.8.1-4) ...
Selecting previously unselected package libicu57:armhf.
Preparing to unpack .../09-libicu57_57.1-8_armhf.deb ...
Unpacking libicu57:armhf (57.1-8) ...
Selecting previously unselected package libxml2:armhf.
Preparing to unpack .../10-libxml2_2.9.4+dfsg1-5_armhf.deb ...
Unpacking libxml2:armhf (2.9.4+dfsg1-5) ...
Selecting previously unselected package libsigsegv2:armhf.
Preparing to unpack .../11-libsigsegv2_2.11-1_armhf.deb ...
Unpacking libsigsegv2:armhf (2.11-1) ...
Selecting previously unselected package m4.
Preparing to unpack .../12-m4_1.4.18-1_armhf.deb ...
Unpacking m4 (1.4.18-1) ...
Selecting previously unselected package autoconf.
Preparing to unpack .../13-autoconf_2.69-11_all.deb ...
Unpacking autoconf (2.69-11) ...
Selecting previously unselected package autotools-dev.
Preparing to unpack .../14-autotools-dev_20161112.1+nmu1_all.deb ...
Unpacking autotools-dev (20161112.1+nmu1) ...
Selecting previously unselected package automake.
Preparing to unpack .../15-automake_1%3a1.15.1-3_all.deb ...
Unpacking automake (1:1.15.1-3) ...
Selecting previously unselected package autopoint.
Preparing to unpack .../16-autopoint_0.19.8.1-4_all.deb ...
Unpacking autopoint (0.19.8.1-4) ...
Selecting previously unselected package libtool.
Preparing to unpack .../17-libtool_2.4.6-2_all.deb ...
Unpacking libtool (2.4.6-2) ...
Selecting previously unselected package dh-autoreconf.
Preparing to unpack .../18-dh-autoreconf_14_all.deb ...
Unpacking dh-autoreconf (14) ...
Selecting previously unselected package libarchive-zip-perl.
Preparing to unpack .../19-libarchive-zip-perl_1.59-1_all.deb ...
Unpacking libarchive-zip-perl (1.59-1) ...
Selecting previously unselected package libfile-stripnondeterminism-perl.
Preparing to unpack .../20-libfile-stripnondeterminism-perl_0.040-1_all.deb ...
Unpacking libfile-stripnondeterminism-perl (0.040-1) ...
Selecting previously unselected package libtimedate-perl.
Preparing to unpack .../21-libtimedate-perl_2.3000-2_all.deb ...
Unpacking libtimedate-perl (2.3000-2) ...
Selecting previously unselected package dh-strip-nondeterminism.
Preparing to unpack .../22-dh-strip-nondeterminism_0.040-1_all.deb ...
Unpacking dh-strip-nondeterminism (0.040-1) ...
Selecting previously unselected package libglib2.0-0:armhf.
Preparing to unpack .../23-libglib2.0-0_2.54.1-1_armhf.deb ...
Unpacking libglib2.0-0:armhf (2.54.1-1) ...
Selecting previously unselected package libcroco3:armhf.
Preparing to unpack .../24-libcroco3_0.6.12-1_armhf.deb ...
Unpacking libcroco3:armhf (0.6.12-1) ...
Selecting previously unselected package gettext.
Preparing to unpack .../25-gettext_0.19.8.1-4_armhf.deb ...
Unpacking gettext (0.19.8.1-4) ...
Selecting previously unselected package intltool-debian.
Preparing to unpack .../26-intltool-debian_0.35.0+20060710.4_all.deb ...
Unpacking intltool-debian (0.35.0+20060710.4) ...
Selecting previously unselected package po-debconf.
Preparing to unpack .../27-po-debconf_1.0.20_all.deb ...
Unpacking po-debconf (1.0.20) ...
Selecting previously unselected package debhelper.
Preparing to unpack .../28-debhelper_10.10.5_all.deb ...
Unpacking debhelper (10.10.5) ...
Selecting previously unselected package hdf5-helpers.
Preparing to unpack .../29-hdf5-helpers_1.10.0-patch1+docs-4_armhf.deb ...
Unpacking hdf5-helpers (1.10.0-patch1+docs-4) ...
Selecting previously unselected package libaec0:armhf.
Preparing to unpack .../30-libaec0_0.3.2-2_armhf.deb ...
Unpacking libaec0:armhf (0.3.2-2) ...
Selecting previously unselected package libgfortran4:armhf.
Preparing to unpack .../31-libgfortran4_7.2.0-12_armhf.deb ...
Unpacking libgfortran4:armhf (7.2.0-12) ...
Selecting previously unselected package libblas3:armhf.
Preparing to unpack .../32-libblas3_3.7.1-4_armhf.deb ...
Unpacking libblas3:armhf (3.7.1-4) ...
Selecting previously unselected package liblapack3:armhf.
Preparing to unpack .../33-liblapack3_3.7.1-4_armhf.deb ...
Unpacking liblapack3:armhf (3.7.1-4) ...
Selecting previously unselected package libarpack2:armhf.
Preparing to unpack .../34-libarpack2_3.5.0+real-1_armhf.deb ...
Unpacking libarpack2:armhf (3.5.0+real-1) ...
Selecting previously unselected package libsuperlu5:armhf.
Preparing to unpack .../35-libsuperlu5_5.2.1+dfsg1-3_armhf.deb ...
Unpacking libsuperlu5:armhf (5.2.1+dfsg1-3) ...
Selecting previously unselected package libarmadillo8.
Preparing to unpack .../36-libarmadillo8_1%3a8.200.0+dfsg-3_armhf.deb ...
Unpacking libarmadillo8 (1:8.200.0+dfsg-3) ...
Selecting previously unselected package libblas-dev:armhf.
Preparing to unpack .../37-libblas-dev_3.7.1-4_armhf.deb ...
Unpacking libblas-dev:armhf (3.7.1-4) ...
Selecting previously unselected package liblapack-dev:armhf.
Preparing to unpack .../38-liblapack-dev_3.7.1-4_armhf.deb ...
Unpacking liblapack-dev:armhf (3.7.1-4) ...
Selecting previously unselected package libarpack2-dev:armhf.
Preparing to unpack .../39-libarpack2-dev_3.5.0+real-1_armhf.deb ...
Unpacking libarpack2-dev:armhf (3.5.0+real-1) ...
Selecting previously unselected package libsz2:armhf.
Preparing to unpack .../40-libsz2_0.3.2-2_armhf.deb ...
Unpacking libsz2:armhf (0.3.2-2) ...
Selecting previously unselected package libhdf5-100:armhf.
Preparing to unpack .../41-libhdf5-100_1.10.0-patch1+docs-4_armhf.deb ...
Unpacking libhdf5-100:armhf (1.10.0-patch1+docs-4) ...
Selecting previously unselected package zlib1g-dev:armhf.
Preparing to unpack .../42-zlib1g-dev_1%3a1.2.8.dfsg-5_armhf.deb ...
Unpacking zlib1g-dev:armhf (1:1.2.8.dfsg-5) ...
Selecting previously unselected package libjpeg62-turbo:armhf.
Preparing to unpack .../43-libjpeg62-turbo_1%3a1.5.2-2_armhf.deb ...
Unpacking libjpeg62-turbo:armhf (1:1.5.2-2) ...
Selecting previously unselected package libjpeg62-turbo-dev:armhf.
Preparing to unpack .../44-libjpeg62-turbo-dev_1%3a1.5.2-2_armhf.deb ...
Unpacking libjpeg62-turbo-dev:armhf (1:1.5.2-2) ...
Selecting previously unselected package libjpeg-dev.
Preparing to unpack .../45-libjpeg-dev_1%3a1.5.2-2_all.deb ...
Unpacking libjpeg-dev (1:1.5.2-2) ...
Selecting previously unselected package libaec-dev:armhf.
Preparing to unpack .../46-libaec-dev_0.3.2-2_armhf.deb ...
Unpacking libaec-dev:armhf (0.3.2-2) ...
Selecting previously unselected package libhdf5-cpp-100:armhf.
Preparing to unpack .../47-libhdf5-cpp-100_1.10.0-patch1+docs-4_armhf.deb ...
Unpacking libhdf5-cpp-100:armhf (1.10.0-patch1+docs-4) ...
Selecting previously unselected package libhdf5-dev.
Preparing to unpack .../48-libhdf5-dev_1.10.0-patch1+docs-4_armhf.deb ...
Unpacking libhdf5-dev (1.10.0-patch1+docs-4) ...
Selecting previously unselected package libsuperlu-dev:armhf.
Preparing to unpack .../49-libsuperlu-dev_5.2.1+dfsg1-3_armhf.deb ...
Unpacking libsuperlu-dev:armhf (5.2.1+dfsg1-3) ...
Selecting previously unselected package libarmadillo-dev.
Preparing to unpack .../50-libarmadillo-dev_1%3a8.200.0+dfsg-3_armhf.deb ...
Unpacking libarmadillo-dev (1:8.200.0+dfsg-3) ...
Selecting previously unselected package libboost1.62-dev:armhf.
Preparing to unpack .../51-libboost1.62-dev_1.62.0+dfsg-4+b2_armhf.deb ...
Unpacking libboost1.62-dev:armhf (1.62.0+dfsg-4+b2) ...
Selecting previously unselected package libboost-dev:armhf.
Preparing to unpack .../52-libboost-dev_1.62.0.1+b8_armhf.deb ...
Unpacking libboost-dev:armhf (1.62.0.1+b8) ...
Selecting previously unselected package libboost-program-options1.62.0:armhf.
Preparing to unpack .../53-libboost-program-options1.62.0_1.62.0+dfsg-4+b2_armhf.deb ...
Unpacking libboost-program-options1.62.0:armhf (1.62.0+dfsg-4+b2) ...
Selecting previously unselected package libboost-program-options1.62-dev:armhf.
Preparing to unpack .../54-libboost-program-options1.62-dev_1.62.0+dfsg-4+b2_armhf.deb ...
Unpacking libboost-program-options1.62-dev:armhf (1.62.0+dfsg-4+b2) ...
Selecting previously unselected package libboost-program-options-dev:armhf.
Preparing to unpack .../55-libboost-program-options-dev_1.62.0.1+b8_armhf.deb ...
Unpacking libboost-program-options-dev:armhf (1.62.0.1+b8) ...
Selecting previously unselected package libdlib-data.
Preparing to unpack .../56-libdlib-data_18.18-2_all.deb ...
Unpacking libdlib-data (18.18-2) ...
Selecting previously unselected package libdlib18.
Preparing to unpack .../57-libdlib18_18.18-2_armhf.deb ...
Unpacking libdlib18 (18.18-2) ...
Selecting previously unselected package libdlib-dev.
Preparing to unpack .../58-libdlib-dev_18.18-2_armhf.deb ...
Unpacking libdlib-dev (18.18-2) ...
Selecting previously unselected package libgzstream0.
Preparing to unpack .../59-libgzstream0_1.5+dfsg-2_armhf.deb ...
Unpacking libgzstream0 (1.5+dfsg-2) ...
Selecting previously unselected package libgzstream-dev.
Preparing to unpack .../60-libgzstream-dev_1.5+dfsg-2_armhf.deb ...
Unpacking libgzstream-dev (1.5+dfsg-2) ...
Selecting previously unselected package sbuild-build-depends-seer-dummy.
Preparing to unpack .../61-sbuild-build-depends-seer-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-seer-dummy (0.invalid.0) ...
Setting up libdlib-data (18.18-2) ...
Setting up libaec0:armhf (0.3.2-2) ...
Setting up libjpeg62-turbo:armhf (1:1.5.2-2) ...
Setting up libarchive-zip-perl (1.59-1) ...
Setting up libgfortran4:armhf (7.2.0-12) ...
Setting up libgzstream0 (1.5+dfsg-2) ...
Setting up libboost1.62-dev:armhf (1.62.0+dfsg-4+b2) ...
Setting up libgzstream-dev (1.5+dfsg-2) ...
Setting up libtimedate-perl (2.3000-2) ...
Setting up libsigsegv2:armhf (2.11-1) ...
Setting up libboost-program-options1.62.0:armhf (1.62.0+dfsg-4+b2) ...
Setting up groff-base (1.22.3-9) ...
Setting up libglib2.0-0:armhf (2.54.1-1) ...
No schema files found: doing nothing.
Setting up libboost-program-options1.62-dev:armhf (1.62.0+dfsg-4+b2) ...
Setting up gettext-base (0.19.8.1-4) ...
Setting up libpipeline1:armhf (1.4.2-1) ...
Setting up m4 (1.4.18-1) ...
Setting up libicu57:armhf (57.1-8) ...
Setting up libbsd0:armhf (0.8.6-3) ...
Setting up libxml2:armhf (2.9.4+dfsg1-5) ...
Setting up libmagic-mgc (1:5.32-1) ...
Setting up libmagic1:armhf (1:5.32-1) ...
Setting up libcroco3:armhf (0.6.12-1) ...
Setting up libblas3:armhf (3.7.1-4) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode
Processing triggers for libc-bin (2.24-17) ...
Setting up autotools-dev (20161112.1+nmu1) ...
Setting up libboost-dev:armhf (1.62.0.1+b8) ...
Setting up libjpeg62-turbo-dev:armhf (1:1.5.2-2) ...
Setting up bsdmainutils (9.0.14) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
Setting up hdf5-helpers (1.10.0-patch1+docs-4) ...
Setting up autopoint (0.19.8.1-4) ...
Setting up libboost-program-options-dev:armhf (1.62.0.1+b8) ...
Setting up libsz2:armhf (0.3.2-2) ...
Setting up zlib1g-dev:armhf (1:1.2.8.dfsg-5) ...
Setting up libfile-stripnondeterminism-perl (0.040-1) ...
Setting up libhdf5-100:armhf (1.10.0-patch1+docs-4) ...
Setting up gettext (0.19.8.1-4) ...
Setting up libblas-dev:armhf (3.7.1-4) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so to provide /usr/lib/arm-linux-gnueabihf/libblas.so (libblas.so-arm-linux-gnueabihf) in auto mode
Setting up liblapack3:armhf (3.7.1-4) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode
Setting up libaec-dev:armhf (0.3.2-2) ...
Setting up autoconf (2.69-11) ...
Setting up file (1:5.32-1) ...
Setting up libdlib18 (18.18-2) ...
Setting up libsuperlu5:armhf (5.2.1+dfsg1-3) ...
Setting up intltool-debian (0.35.0+20060710.4) ...
Setting up libsuperlu-dev:armhf (5.2.1+dfsg1-3) ...
Setting up libjpeg-dev (1:1.5.2-2) ...
Setting up automake (1:1.15.1-3) ...
update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode
Setting up libdlib-dev (18.18-2) ...
Setting up libarpack2:armhf (3.5.0+real-1) ...
Setting up man-db (2.7.6.1-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up liblapack-dev:armhf (3.7.1-4) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so to provide /usr/lib/arm-linux-gnueabihf/liblapack.so (liblapack.so-arm-linux-gnueabihf) in auto mode
Setting up libtool (2.4.6-2) ...
Setting up libhdf5-cpp-100:armhf (1.10.0-patch1+docs-4) ...
Setting up po-debconf (1.0.20) ...
Setting up libhdf5-dev (1.10.0-patch1+docs-4) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/pkgconfig/hdf5-serial.pc to provide /usr/lib/arm-linux-gnueabihf/pkgconfig/hdf5.pc (hdf5.pc) in auto mode
Setting up libarmadillo8 (1:8.200.0+dfsg-3) ...
Setting up libarpack2-dev:armhf (3.5.0+real-1) ...
Setting up libarmadillo-dev (1:8.200.0+dfsg-3) ...
Setting up dh-autoreconf (14) ...
Setting up debhelper (10.10.5) ...
Setting up sbuild-build-depends-seer-dummy (0.invalid.0) ...
Setting up dh-strip-nondeterminism (0.040-1) ...
Processing triggers for libc-bin (2.24-17) ...
W: No sandbox user '_apt' on the system, can not drop privileges
W: copy: aptMethod::Configuration: could not load seccomp policy: Invalid argument
W: http: aptMethod::Configuration: could not load seccomp policy: Invalid argument
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 3.19.0-trunk-armmp armhf (armv7l)
Toolchain package versions: binutils_2.29.1-6+rpi1 dpkg-dev_1.19.0.4 g++-7_7.2.0-12 gcc-7_7.2.0-12 libc6-dev_2.24-17 libstdc++-7-dev_7.2.0-12 libstdc++6_7.2.0-12 linux-libc-dev_4.9.51-1+rpi3+b1
Package versions: adduser_3.116 apt_1.6~alpha3 autoconf_2.69-11 automake_1:1.15.1-3 autopoint_0.19.8.1-4 autotools-dev_20161112.1+nmu1 base-files_10+rpi1 base-passwd_3.5.44 bash_4.4-5 binutils_2.29.1-6+rpi1 binutils-arm-linux-gnueabihf_2.29.1-6+rpi1 binutils-common_2.29.1-6+rpi1 bsdmainutils_9.0.14 bsdutils_1:2.30.2-0.1 build-essential_12.4 bzip2_1.0.6-8.1 ca-certificates_20170717 coreutils_8.28-1 cpio_2.11+dfsg-6 cpp_4:7.2.0-1d1 cpp-7_7.2.0-12 dash_0.5.8-2.5 debconf_1.5.64 debhelper_10.10.5 debianutils_4.8.2 dh-autoreconf_14 dh-strip-nondeterminism_0.040-1 diffutils_1:3.6-1 dirmngr_2.2.1-5 dmsetup_2:1.02.142-1 dpkg_1.19.0.4 dpkg-dev_1.19.0.4 e2fslibs_1.43.7-1 e2fsprogs_1.43.7-1 e2fsprogs-l10n_1.43.7-1 fakeroot_1.22-1 fdisk_2.30.2-0.1 file_1:5.32-1 findutils_4.6.0+git+20170729-2 g++_4:7.2.0-1d1 g++-7_7.2.0-12 gcc_4:7.2.0-1d1 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8-base_4.8.5-4 gcc-4.9-base_4.9.3-14 gcc-5-base_5.4.1-4 gcc-7_7.2.0-12 gcc-7-base_7.2.0-12 gettext_0.19.8.1-4 gettext-base_0.19.8.1-4 gnupg_2.2.1-5 gnupg-agent_2.2.1-5 gnupg-l10n_2.2.1-5 gnupg-utils_2.2.1-5 gpg_2.2.1-5 gpg-agent_2.2.1-5 gpg-wks-client_2.2.1-5 gpg-wks-server_2.2.1-5 gpgconf_2.2.1-5 gpgsm_2.2.1-5 gpgv_2.2.1-5 grep_3.1-2 groff-base_1.22.3-9 gzip_1.6-5 hdf5-helpers_1.10.0-patch1+docs-4 hostname_3.18 init-system-helpers_1.51 initramfs-tools_0.130 initramfs-tools-core_0.130 intltool-debian_0.35.0+20060710.4 klibc-utils_2.0.4-9+rpi1 kmod_24-1 libacl1_2.2.52-3 libaec-dev_0.3.2-2 libaec0_0.3.2-2 libapparmor1_2.11.1-2 libapt-pkg5.0_1.6~alpha3 libarchive-zip-perl_1.59-1 libarmadillo-dev_1:8.200.0+dfsg-3 libarmadillo8_1:8.200.0+dfsg-3 libarpack2_3.5.0+real-1 libarpack2-dev_3.5.0+real-1 libasan4_7.2.0-12 libassuan0_2.4.3-3 libatomic1_7.2.0-12 libattr1_1:2.4.47-2 libaudit-common_1:2.8.1-1 libaudit1_1:2.8.1-1 libbinutils_2.29.1-6+rpi1 libblas-dev_3.7.1-4 libblas3_3.7.1-4 libblkid1_2.30.2-0.1 libboost-dev_1.62.0.1+b8 libboost-program-options-dev_1.62.0.1+b8 libboost-program-options1.62-dev_1.62.0+dfsg-4+b2 libboost-program-options1.62.0_1.62.0+dfsg-4+b2 libboost1.62-dev_1.62.0+dfsg-4+b2 libbsd0_0.8.6-3 libbz2-1.0_1.0.6-8.1 libc-bin_2.24-17 libc-dev-bin_2.24-17 libc6_2.24-17 libc6-dev_2.24-17 libcap-ng0_0.7.7-3.1+b1 libcap2_1:2.25-1.1 libcc1-0_7.2.0-12 libcilkrts5_7.2.0-12 libcomerr2_1.43.7-1 libcroco3_0.6.12-1 libcryptsetup4_2:1.7.5-1 libdb5.3_5.3.28-13.1 libdbus-1-3_1.11.22-1 libdebconfclient0_0.232 libdevmapper1.02.1_2:1.02.142-1 libdlib-data_18.18-2 libdlib-dev_18.18-2 libdlib18_18.18-2 libdpkg-perl_1.19.0.4 libdrm-common_2.4.84-2+rpi1 libdrm2_2.4.84-2+rpi1 libfakeroot_1.22-1 libfdisk1_2.30.2-0.1 libffi6_3.2.1-6 libfile-stripnondeterminism-perl_0.040-1 libgcc-7-dev_7.2.0-12 libgcc1_1:7.2.0-12 libgcrypt20_1.7.9-1 libgdbm3_1.8.3-14 libgfortran4_7.2.0-12 libglib2.0-0_2.54.1-1 libgmp10_2:6.1.2+dfsg-1.1 libgnutls30_3.5.16-1 libgomp1_7.2.0-12 libgpg-error0_1.27-4 libgzstream-dev_1.5+dfsg-2 libgzstream0_1.5+dfsg-2 libhdf5-100_1.10.0-patch1+docs-4 libhdf5-cpp-100_1.10.0-patch1+docs-4 libhdf5-dev_1.10.0-patch1+docs-4 libhogweed4_3.3-2 libicu57_57.1-8 libidn11_1.33-2 libidn2-0_2.0.2-5 libip4tc0_1.6.1-2+b1 libisl15_0.18-1 libjpeg-dev_1:1.5.2-2 libjpeg62-turbo_1:1.5.2-2 libjpeg62-turbo-dev_1:1.5.2-2 libklibc_2.0.4-9+rpi1 libkmod2_24-1 libksba8_1.3.5-2 liblapack-dev_3.7.1-4 liblapack3_3.7.1-4 libldap-2.4-2_2.4.45+dfsg-1 libldap-common_2.4.45+dfsg-1 liblz4-1_0.0~r131-2 liblzma5_5.2.2-1.3 libmagic-mgc_1:5.32-1 libmagic1_1:5.32-1 libmount1_2.30.2-0.1 libmpc3_1.0.3-2 libmpfr4_3.1.6-1 libncurses5_6.0+20170902-1 libncursesw5_6.0+20170902-1 libnettle6_3.3-2 libnih-dbus1_1.0.3-8 libnih1_1.0.3-8 libnpth0_1.5-2 libp11-kit0_0.23.9-2 libpam-modules_1.1.8-3.6 libpam-modules-bin_1.1.8-3.6 libpam-runtime_1.1.8-3.6 libpam0g_1.1.8-3.6 libpcre3_2:8.39-4 libperl5.24_5.24.1-7 libperl5.26_5.26.1-2 libpipeline1_1.4.2-1 libplymouth4_0.9.3-1 libpng16-16_1.6.34-1 libprocps6_2:3.3.12-3 libreadline7_7.0-3 libsasl2-2_2.1.27~101-g0780600+dfsg-3 libsasl2-modules_2.1.27~101-g0780600+dfsg-3 libsasl2-modules-db_2.1.27~101-g0780600+dfsg-3 libseccomp2_2.3.1-2.1 libselinux1_2.7-2 libsemanage-common_2.7-2 libsemanage1_2.7-2 libsepol1_2.7-1 libsigsegv2_2.11-1 libsmartcols1_2.30.2-0.1 libsqlite3-0_3.20.1-2 libss2_1.43.7-1 libssl1.1_1.1.0f-5 libstdc++-7-dev_7.2.0-12 libstdc++6_7.2.0-12 libsuperlu-dev_5.2.1+dfsg1-3 libsuperlu5_5.2.1+dfsg1-3 libsystemd0_235-2 libsz2_0.3.2-2 libtasn1-6_4.12-2.1 libtimedate-perl_2.3000-2 libtinfo5_6.0+20170902-1 libtool_2.4.6-2 libubsan0_7.2.0-12 libudev1_235-2 libunistring2_0.9.7-2 libustr-1.0-1_1.0.4-6 libuuid1_2.30.2-0.1 libxml2_2.9.4+dfsg1-5 linux-base_4.5 linux-libc-dev_4.9.51-1+rpi3+b1 login_1:4.5-1 lsb-base_9.20170808+rpi1 m4_1.4.18-1 make_4.1-9.1 makedev_2.3.1-93 man-db_2.7.6.1-2 mawk_1.3.3-17 mount_2.30.2-0.1 mountall_2.54 multiarch-support_2.24-17 ncurses-base_6.0+20170902-1 ncurses-bin_6.0+20170902-1 openssl_1.1.0f-5 passwd_1:4.5-1 patch_2.7.5-1 perl_5.26.1-2 perl-base_5.26.1-2 perl-modules-5.24_5.24.1-7 perl-modules-5.26_5.26.1-2 pinentry-curses_1.0.0-3 plymouth_0.9.3-1 po-debconf_1.0.20 procps_2:3.3.12-3 raspbian-archive-keyring_20120528.2 readline-common_7.0-3 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-seer-dummy_0.invalid.0 sed_4.4-1 sensible-utils_0.0.10 systemd_235-2 sysvinit-utils_2.88dsf-59.10 tar_1.29b-2 tzdata_2017c-1 udev_235-2 util-linux_2.30.2-0.1 xz-utils_5.2.2-1.3 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 Sep 28 14:04:26 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_1.1.4-1.dsc
dpkg-source: info: extracting seer in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking seer_1.1.4.orig.tar.gz
dpkg-source: info: unpacking seer_1.1.4-1.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
Hack binNMU version
-------------------
Created changelog entry for binNMU version 1.1.4-1+b1
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=buster-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=buster-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=buster-staging-armhf-sbuild-b85b26e4-b6b9-45e4-9106-039ca182a762
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 1.1.4-1+b1
dpkg-buildpackage: info: source distribution buster-staging
dpkg-source --before-build seer-1.1.4
dpkg-buildpackage: info: host architecture armhf
fakeroot debian/rules clean
dh clean
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_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 seerIO.o seerIO.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 seerBasicFilter.o seerBasicFilter.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 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 seerStats.o seerStats.cpp
In file included from /usr/include/c++/7/vector:69:0,
from seercommon.hpp:18,
from seerIO.cpp:12:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const Sample&}; _Tp = Sample; _Alloc = std::allocator<Sample>]':
/usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type 'std::vector<Sample>::iterator {aka __gnu_cxx::__normal_iterator<Sample*, std::vector<Sample> >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator<long long int>]':
/usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type 'std::vector<long long int, std::allocator<long long int> >::iterator {aka __gnu_cxx::__normal_iterator<long long int*, std::vector<long long int, std::allocator<long long int> > >}' changed in GCC 7.1
In file included from /usr/include/c++/7/vector:64:0,
from seercommon.hpp:18,
from seerIO.cpp:12:
/usr/include/c++/7/bits/stl_vector.h: In static member function 'static bool arma::diskio::save_hdf5_binary(const arma::Mat<eT>&, const arma::hdf5_name&) [with eT = double]':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int, std::allocator<long long int> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/7/bits/stl_algobase.h:71:0,
from /usr/include/c++/7/bits/char_traits.h:39,
from /usr/include/c++/7/ios:40,
from /usr/include/c++/7/ostream:38,
from /usr/include/c++/7/iostream:39,
from seercommon.hpp:10,
from seerIO.cpp:12:
/usr/include/c++/7/bits/predefined_ops.h: In member function 'bool __gnu_cxx::__ops::_Iter_comp_iter<_Compare>::operator()(_Iterator1, _Iterator2) [with _Iterator1 = __gnu_cxx::__normal_iterator<Sample*, std::vector<Sample> >; _Iterator2 = __gnu_cxx::__normal_iterator<Sample*, std::vector<Sample> >; _Compare = bool (*)(Sample, Sample)]':
/usr/include/c++/7/bits/predefined_ops.h:142:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sample*, std::vector<Sample> >' changed in GCC 7.1
operator()(_Iterator1 __it1, _Iterator2 __it2)
^~~~~~~~
/usr/include/c++/7/bits/predefined_ops.h:142:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sample*, std::vector<Sample> >' changed in GCC 7.1
In file included from /usr/include/c++/7/algorithm:62:0,
from seercommon.hpp:15,
from seerIO.cpp:12:
/usr/include/c++/7/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Sample*, std::vector<Sample> >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<bool (*)(Sample, Sample)>]':
/usr/include/c++/7/bits/stl_algo.h:1821:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sample*, std::vector<Sample> >' changed in GCC 7.1
__unguarded_linear_insert(_RandomAccessIterator __last,
^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Sample*, std::vector<Sample> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(Sample, Sample)>]':
/usr/include/c++/7/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sample*, std::vector<Sample> >' changed in GCC 7.1
__insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sample*, std::vector<Sample> >' changed in GCC 7.1
/usr/include/c++/7/bits/stl_algo.h:1847:14: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sample*, std::vector<Sample> >' changed in GCC 7.1
if (__comp(__i, __first))
~~~~~~^~~~~~~~~~~~~~
In file included from /usr/include/c++/7/bits/stl_algo.h:61:0,
from /usr/include/c++/7/algorithm:62,
from seercommon.hpp:15,
from seerIO.cpp:12:
/usr/include/c++/7/bits/stl_heap.h: In function 'void std::__push_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Sample*, std::vector<Sample> >; _Distance = int; _Tp = Sample; _Compare = __gnu_cxx::__ops::_Iter_comp_val<bool (*)(Sample, Sample)>]':
/usr/include/c++/7/bits/stl_heap.h:128:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sample*, std::vector<Sample> >' changed in GCC 7.1
__push_heap(_RandomAccessIterator __first,
^~~~~~~~~~~
/usr/include/c++/7/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Sample*, std::vector<Sample> >; _Distance = int; _Tp = Sample; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(Sample, Sample)>]':
/usr/include/c++/7/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sample*, std::vector<Sample> >' changed in GCC 7.1
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_heap.h:222:14: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sample*, std::vector<Sample> >' changed in GCC 7.1
if (__comp(__first + __secondChild,
~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
__first + (__secondChild - 1)))
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_heap.h: In function 'void std::__make_heap(_RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Sample*, std::vector<Sample> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(Sample, Sample)>]':
/usr/include/c++/7/bits/stl_heap.h:326:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sample*, std::vector<Sample> >' changed in GCC 7.1
__make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
^~~~~~~~~~~
/usr/include/c++/7/bits/stl_heap.h:326:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sample*, std::vector<Sample> >' changed in GCC 7.1
In file included from /usr/include/c++/7/algorithm:62:0,
from seercommon.hpp:15,
from seerIO.cpp:12:
/usr/include/c++/7/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Sample*, std::vector<Sample> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(Sample, Sample)>]':
/usr/include/c++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sample*, std::vector<Sample> >' changed in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sample*, std::vector<Sample> >' changed in GCC 7.1
/usr/include/c++/7/bits/stl_algo.h:81:17: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sample*, std::vector<Sample> >' changed in GCC 7.1
if (__comp(__a, __b))
~~~~~~^~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:83:14: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sample*, std::vector<Sample> >' changed in GCC 7.1
if (__comp(__b, __c))
~~~~~~^~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:85:19: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sample*, std::vector<Sample> >' changed in GCC 7.1
else if (__comp(__a, __c))
~~~~~~^~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:90:22: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sample*, std::vector<Sample> >' changed in GCC 7.1
else if (__comp(__a, __c))
~~~~~~^~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:92:22: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sample*, std::vector<Sample> >' changed in GCC 7.1
else if (__comp(__b, __c))
~~~~~~^~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sample*, std::vector<Sample> >' changed in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1672:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sample*, std::vector<Sample> >' changed in GCC 7.1
std::__make_heap(__first, __middle, __comp);
~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
from seercommon.hpp:18,
from seerIO.cpp:12:
/usr/include/c++/7/bits/stl_vector.h: In function 'void readPheno(const string&, std::vector<Sample>&, std::unordered_map<std::__cxx11::basic_string<char>, int>&)':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sample*, std::vector<Sample> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/7/algorithm:62:0,
from seercommon.hpp:15,
from seerIO.cpp:12:
/usr/include/c++/7/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sample*, std::vector<Sample> >' changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sample*, std::vector<Sample> >' changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sample*, std::vector<Sample> >' changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:69:0,
from seercommon.hpp:18,
from linkFunction.hpp:6,
from seer.hpp:10,
from seerMain.cpp:8:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const Kmer&}; _Tp = Kmer; _Alloc = std::allocator<Kmer>]':
/usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type 'std::vector<Kmer>::iterator {aka __gnu_cxx::__normal_iterator<Kmer*, std::vector<Kmer> >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type 'std::vector<Kmer>::iterator {aka __gnu_cxx::__normal_iterator<Kmer*, std::vector<Kmer> >}' changed in GCC 7.1
In file included from /usr/include/c++/7/vector:64:0,
from seercommon.hpp:18,
from linkFunction.hpp:6,
from seer.hpp:10,
from seerMain.cpp:8:
/usr/include/c++/7/bits/stl_vector.h: In function 'int main(int, char**)':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Kmer*, std::vector<Kmer> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Kmer*, std::vector<Kmer> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
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
In file included from /usr/include/c++/7/vector:69:0,
from seercommon.hpp:18,
from linkFunction.hpp:6,
from seer.hpp:10,
from seerContinuousAssoc.cpp:8:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:69:0,
from seercommon.hpp:18,
from linkFunction.hpp:6,
from seer.hpp:10,
from seerBinaryAssoc.cpp:8:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const arma::Col<double>&}; _Tp = arma::Col<double>; _Alloc = std::allocator<arma::Col<double> >]':
/usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type 'std::vector<arma::Col<double> >::iterator {aka __gnu_cxx::__normal_iterator<arma::Col<double>*, std::vector<arma::Col<double> > >}' changed in GCC 7.1
In file included from /usr/include/c++/7/vector:64:0,
from seercommon.hpp:18,
from linkFunction.hpp:6,
from seer.hpp:10,
from seerContinuousAssoc.cpp:8:
/usr/include/c++/7/bits/stl_vector.h: In function 'void doLinear(Kmer&, const vec&, const mat&)':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
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
In file included from /usr/include/c++/7/vector:64:0,
from seercommon.hpp:18,
from linkFunction.hpp:6,
from seer.hpp:10,
from seerBinaryAssoc.cpp:8:
/usr/include/c++/7/bits/stl_vector.h: In function 'void newtonRaphson(Kmer&, const vec&, const mat&, bool)':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<arma::Col<double>*, std::vector<arma::Col<double> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<arma::Col<double>*, std::vector<arma::Col<double> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h: In function 'void doLogit(Kmer&, const vec&, const mat&)':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
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
In file included from /usr/include/c++/7/vector:69:0,
from seercommon.hpp:18,
from kmds.hpp:9,
from kmdsStruct.cpp:8:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const DistanceElement&}; _Tp = DistanceElement; _Alloc = std::allocator<DistanceElement>]':
/usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type 'std::vector<DistanceElement>::iterator {aka __gnu_cxx::__normal_iterator<DistanceElement*, std::vector<DistanceElement> >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type 'std::vector<DistanceElement>::iterator {aka __gnu_cxx::__normal_iterator<DistanceElement*, std::vector<DistanceElement> >}' changed in GCC 7.1
In file included from /usr/include/c++/7/vector:64:0,
from seercommon.hpp:18,
from kmds.hpp:9,
from kmdsStruct.cpp:8:
/usr/include/c++/7/bits/stl_vector.h: In function 'arma::mat dissimiliarityMatrix(const mat&, unsigned int)':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<DistanceElement*, std::vector<DistanceElement> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:69:0,
from seercommon.hpp:18,
from kmds.hpp:9,
from kmdsMain.cpp:8:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {arma::Col<double>}; _Tp = arma::Col<double>; _Alloc = std::allocator<arma::Col<double> >]':
/usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type 'std::vector<arma::Col<double> >::iterator {aka __gnu_cxx::__normal_iterator<arma::Col<double>*, std::vector<arma::Col<double> > >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
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
/usr/include/c++/7/bits/vector.tcc: In function 'int main(int, char**)':
/usr/include/c++/7/bits/vector.tcc:105:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<arma::Col<double>*, std::vector<arma::Col<double> > >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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 seerIO.o seerBasicFilter.o seerMain.o seerCmdLine.o seerStats.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 seerIO.o seerBasicFilter.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_missing -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
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/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/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/map_back 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/combineKmers debian/seer/usr/bin/kmds debian/seer/usr/bin/seer were not linked against libz.so.1 (they use none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/seer/usr/bin/combineKmers debian/seer/usr/bin/kmds debian/seer/usr/bin/filter_seer debian/seer/usr/bin/seer debian/seer/usr/bin/map_back 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_1.1.4-1+b1_armhf.deb'.
dpkg-deb: building package 'seer' in '../seer_1.1.4-1+b1_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../seer_1.1.4-1+b1_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build seer-1.1.4
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2017-11-13T00:43:55Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
seer_1.1.4-1+b1_armhf.changes:
------------------------------
Format: 1.8
Date: Thu, 28 Sep 2017 13:20:25 +0200
Source: seer (1.1.4-1)
Binary: seer
Binary-Only: yes
Architecture: armhf
Version: 1.1.4-1+b1
Distribution: buster-staging
Urgency: low
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Raspbian wandboard test autobuilder <root@raspbian.org>
Description:
seer - genomic sequence element (kmer) enrichment analysis
Changes:
seer (1.1.4-1+b1) buster-staging; urgency=low, binary-only=yes
.
* Binary-only non-maintainer upload for armhf; no source changes.
* rebuild due to debcheck failure
Checksums-Sha1:
528647af764f4d5774b4ac293ee50eac00aa60a7 7133744 seer-dbgsym_1.1.4-1+b1_armhf.deb
351666cbba5280fe1a6e1ca8f931f052f877d4d0 5743 seer_1.1.4-1+b1_armhf.buildinfo
87f05e3fc311d8b3e61023b67c6a75a950ff1822 297868 seer_1.1.4-1+b1_armhf.deb
Checksums-Sha256:
420d52506e2c5c10597526e8d73a90c88dee2c8a9c1cabd0faf891e52784ca77 7133744 seer-dbgsym_1.1.4-1+b1_armhf.deb
254acc205b455f9b8948bf8c5da5d41175aac0cbc21cef0c30e2c30d31e7dc2f 5743 seer_1.1.4-1+b1_armhf.buildinfo
f28e1786e53bea9fca74357a90957c5e630ce83615eec9f016ccb3be828f96f4 297868 seer_1.1.4-1+b1_armhf.deb
Files:
6510c3027071c2d3c8ed309a0bba1a43 7133744 debug optional seer-dbgsym_1.1.4-1+b1_armhf.deb
3898038cb71643569842a6d3169adb95 5743 science optional seer_1.1.4-1+b1_armhf.buildinfo
574a0ec7b8e2541e2937e5caef684b96 297868 science optional seer_1.1.4-1+b1_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
seer-dbgsym_1.1.4-1+b1_armhf.deb
--------------------------------
new Debian package, version 2.0.
size 7133744 bytes: control archive=764 bytes.
539 bytes, 12 lines control
530 bytes, 5 lines md5sums
Package: seer-dbgsym
Source: seer (1.1.4-1)
Version: 1.1.4-1+b1
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 7492
Depends: seer (= 1.1.4-1+b1)
Section: debug
Priority: optional
Description: debug symbols for seer
Build-Ids: 069b9141d2dd91a642b2e70b5392fd6a228f5f2f 36a0c03eeb4b263cce89f794456d54cedf65d57d d38b8f4f66dc59f221596ab96fa3bbd12cb9e9e2 d38fd9df46b145883aaf0c6eba5c52d255116127 eab3193e441f30210d22f679baf67e28c80ade7d
drwxr-xr-x root/root 0 2017-09-28 11:20 ./
drwxr-xr-x root/root 0 2017-09-28 11:20 ./usr/
drwxr-xr-x root/root 0 2017-09-28 11:20 ./usr/lib/
drwxr-xr-x root/root 0 2017-09-28 11:20 ./usr/lib/debug/
drwxr-xr-x root/root 0 2017-09-28 11:20 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2017-09-28 11:20 ./usr/lib/debug/.build-id/06/
-rw-r--r-- root/root 481280 2017-09-28 11:20 ./usr/lib/debug/.build-id/06/9b9141d2dd91a642b2e70b5392fd6a228f5f2f.debug
drwxr-xr-x root/root 0 2017-09-28 11:20 ./usr/lib/debug/.build-id/36/
-rw-r--r-- root/root 2725676 2017-09-28 11:20 ./usr/lib/debug/.build-id/36/a0c03eeb4b263cce89f794456d54cedf65d57d.debug
drwxr-xr-x root/root 0 2017-09-28 11:20 ./usr/lib/debug/.build-id/d3/
-rw-r--r-- root/root 3303532 2017-09-28 11:20 ./usr/lib/debug/.build-id/d3/8b8f4f66dc59f221596ab96fa3bbd12cb9e9e2.debug
-rw-r--r-- root/root 795520 2017-09-28 11:20 ./usr/lib/debug/.build-id/d3/8fd9df46b145883aaf0c6eba5c52d255116127.debug
drwxr-xr-x root/root 0 2017-09-28 11:20 ./usr/lib/debug/.build-id/ea/
-rw-r--r-- root/root 350464 2017-09-28 11:20 ./usr/lib/debug/.build-id/ea/b3193e441f30210d22f679baf67e28c80ade7d.debug
drwxr-xr-x root/root 0 2017-09-28 11:20 ./usr/share/
drwxr-xr-x root/root 0 2017-09-28 11:20 ./usr/share/doc/
lrwxrwxrwx root/root 0 2017-09-28 11:20 ./usr/share/doc/seer-dbgsym -> seer
seer_1.1.4-1+b1_armhf.deb
-------------------------
new Debian package, version 2.0.
size 297868 bytes: control archive=1884 bytes.
1438 bytes, 25 lines control
1784 bytes, 28 lines md5sums
Package: seer
Source: seer (1.1.4-1)
Version: 1.1.4-1+b1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1263
Depends: libarmadillo8, 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 (>= 7), 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 2017-09-28 11:20 ./
drwxr-xr-x root/root 0 2017-09-28 11:20 ./usr/
drwxr-xr-x root/root 0 2017-09-28 11:20 ./usr/bin/
-rwxr-xr-x root/root 4597 2017-09-28 11:20 ./usr/bin/R_mds
-rwxr-xr-x root/root 3794 2017-09-28 11:20 ./usr/bin/blast_top_hits
-rwxr-xr-x root/root 2152 2017-09-28 11:20 ./usr/bin/blastn_to_phandango
-rwxr-xr-x root/root 103944 2017-09-28 11:20 ./usr/bin/combineKmers
-rwxr-xr-x root/root 71176 2017-09-28 11:20 ./usr/bin/filter_seer
-rwxr-xr-x root/root 1869 2017-09-28 11:20 ./usr/bin/hits_to_fastq
-rwxr-xr-x root/root 374792 2017-09-28 11:20 ./usr/bin/kmds
-rwxr-xr-x root/root 177672 2017-09-28 11:20 ./usr/bin/map_back
-rwxr-xr-x root/root 3200 2017-09-28 11:20 ./usr/bin/mapping_to_phandango
-rwxr-xr-x root/root 1208 2017-09-28 11:20 ./usr/bin/mash2matrix
-rwxr-xr-x root/root 2295 2017-09-28 11:20 ./usr/bin/reformat_output
-rwxr-xr-x root/root 509992 2017-09-28 11:20 ./usr/bin/seer
drwxr-xr-x root/root 0 2017-09-28 11:20 ./usr/share/
drwxr-xr-x root/root 0 2017-09-28 11:20 ./usr/share/doc/
drwxr-xr-x root/root 0 2017-09-28 11:20 ./usr/share/doc/seer/
-rw-r--r-- root/root 684 2017-09-28 11:20 ./usr/share/doc/seer/README.Debian
-rw-r--r-- root/root 218 2017-09-28 11:20 ./usr/share/doc/seer/changelog.Debian.armhf.gz
-rw-r--r-- root/root 537 2017-09-28 11:20 ./usr/share/doc/seer/changelog.Debian.gz
-rw-r--r-- root/root 1008 2017-09-28 11:20 ./usr/share/doc/seer/copyright
drwxr-xr-x root/root 0 2017-09-28 11:20 ./usr/share/doc/seer/examples/
-rw-r--r-- root/root 2110 2017-06-20 09:43 ./usr/share/doc/seer/examples/example_wrapper.py.gz
drwxr-xr-x root/root 0 2017-09-28 11:20 ./usr/share/man/
drwxr-xr-x root/root 0 2017-09-28 11:20 ./usr/share/man/man1/
-rw-r--r-- root/root 506 2017-09-28 11:20 ./usr/share/man/man1/R_mds.1.gz
-rw-r--r-- root/root 501 2017-09-28 11:20 ./usr/share/man/man1/blast_top_hits.1.gz
-rw-r--r-- root/root 461 2017-09-28 11:20 ./usr/share/man/man1/combineKmers.1.gz
-rw-r--r-- root/root 543 2017-09-28 11:20 ./usr/share/man/man1/filter_seer.1.gz
-rw-r--r-- root/root 408 2017-09-28 11:20 ./usr/share/man/man1/hits_to_fastq.1.gz
-rw-r--r-- root/root 906 2017-09-28 11:20 ./usr/share/man/man1/kmds.1.gz
-rw-r--r-- root/root 458 2017-09-28 11:20 ./usr/share/man/man1/map_back.1.gz
-rw-r--r-- root/root 432 2017-09-28 11:20 ./usr/share/man/man1/mapping_to_phandango.1.gz
-rw-r--r-- root/root 466 2017-09-28 11:20 ./usr/share/man/man1/mash2matrix.1.gz
-rw-r--r-- root/root 422 2017-09-28 11:20 ./usr/share/man/man1/reformat_output.1.gz
-rw-r--r-- root/root 995 2017-09-28 11:20 ./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: 75668
Build-Time: 800
Distribution: buster-staging
Host Architecture: armhf
Install-Time: 584
Job: seer_1.1.4-1
Machine Architecture: armhf
Package: seer
Package-Time: 1449
Source-Version: 1.1.4-1
Space: 75668
Status: successful
Version: 1.1.4-1+b1
--------------------------------------------------------------------------------
Finished at 2017-11-13T00:43:55Z
Build needed 00:24:09, 75668k disc space