Raspbian Package Auto-Building

Build log for pbdagcon (0~20160325+ds-1) on armhf

pbdagcon0~20160325+ds-1armhf → 2016-11-01 00:24:21

sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on testwandboard

+==============================================================================+
| pbdagcon 0~20160325+ds-1 (armhf)             Tue, 01 Nov 2016 00:12:55 +0000 |
+==============================================================================+

Package: pbdagcon
Version: 0~20160325+ds-1
Source Version: 0~20160325+ds-1
Distribution: stretch-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf

I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/stretch-staging-armhf-sbuild-8cb99a62-77ca-4283-83a3-0fa90dfcd554' 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 [9419 kB]
Get:3 http://172.17.0.1/private stretch-staging/main armhf Packages [11.4 MB]
Fetched 20.8 MB in 29s (712 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: 'pbdagcon' packaging is maintained in the 'Git' version control system at:
https://anonscm.debian.org/git/debian-med/pbdagcon.git
Please use:
git clone https://anonscm.debian.org/git/debian-med/pbdagcon.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 100 kB of source archives.
Get:1 http://172.17.0.1/private stretch-staging/main pbdagcon 0~20160325+ds-1 (dsc) [2072 B]
Get:2 http://172.17.0.1/private stretch-staging/main pbdagcon 0~20160325+ds-1 (tar) [93.9 kB]
Get:3 http://172.17.0.1/private stretch-staging/main pbdagcon 0~20160325+ds-1 (diff) [4424 B]
Fetched 100 kB in 0s (407 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/pbdagcon-1KCb4u/pbdagcon-0~20160325+ds' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/pbdagcon-1KCb4u' 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-VRaC5P/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-VRaC5P/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-VRaC5P/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-VRaC5P/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-VRaC5P/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-VRaC5P/apt_archive ./ Release.gpg [342 B]
Get:4 copy:/<<BUILDDIR>>/resolver-VRaC5P/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-VRaC5P/apt_archive ./ Packages [432 B]
Fetched 2080 B in 0s (3014 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:
  dirmngr fuse2fs gnupg-l10n kbd libffi6 libfuse2 libgnutls30 libhogweed4
  libldap-2.4-2 libnettle6 libp11-kit0 libsasl2-2 libsasl2-modules
  libsasl2-modules-db libssl1.0.2 libtasn1-6 manpages netbase psmisc
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
  sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 5 not upgraded.
Need to get 764 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-VRaC5P/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [764 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 764 B in 0s (0 B/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 13408 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 (>= 9), python, libboost-dev, libtclap-dev, libpbdata-dev, libblasr-dev, libpbihdf-dev, libgtest-dev
Filtered Build-Depends: debhelper (>= 9), python, libboost-dev, libtclap-dev, libpbdata-dev, libblasr-dev, libpbihdf-dev, libgtest-dev
dpkg-deb: building package 'sbuild-build-depends-pbdagcon-dummy' in '/<<BUILDDIR>>/resolver-VRaC5P/apt_archive/sbuild-build-depends-pbdagcon-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning:   sbuild-build-depends-core-dummy sbuild-build-depends-pbdagcon-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-VRaC5P/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-VRaC5P/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-VRaC5P/apt_archive ./ Release.gpg [342 B]
Get:4 copy:/<<BUILDDIR>>/resolver-VRaC5P/apt_archive ./ Sources [528 B]
Get:5 copy:/<<BUILDDIR>>/resolver-VRaC5P/apt_archive ./ Packages [609 B]
Fetched 2442 B in 0s (3639 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...

Install pbdagcon 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:
  dirmngr fuse2fs gnupg-l10n kbd libfuse2 libgnutls30 libhogweed4
  libldap-2.4-2 libnettle6 libp11-kit0 libsasl2-2 libsasl2-modules
  libsasl2-modules-db libtasn1-6 manpages netbase psmisc
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
  intltool-debian libaec0 libarchive-zip-perl libblasr libblasr-dev
  libboost-dev libboost1.61-dev libbsd0 libcroco3 libexpat1
  libfile-stripnondeterminism-perl libgfortran3 libglib2.0-0 libgtest-dev
  libhdf5-10 libhdf5-cpp-11 libicu57 libmagic-mgc libmagic1 libpbdata
  libpbdata-dev libpbihdf libpbihdf-dev libpipeline1 libpython-stdlib
  libpython2.7-minimal libpython2.7-stdlib libreadline6 libsigsegv2 libsz2
  libtclap-dev libtimedate-perl libtool libunistring0 libxml2 m4 man-db
  mime-support po-debconf python python-minimal python2.7 python2.7-minimal
Suggested packages:
  autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
  vacation dh-make gettext-doc libasprintf-dev libgettextpo-dev groff
  libboost-doc libboost1.61-doc libboost-atomic1.61-dev
  libboost-chrono1.61-dev libboost-context1.61-dev libboost-coroutine1.61-dev
  libboost-date-time1.61-dev libboost-exception1.61-dev
  libboost-filesystem1.61-dev libboost-graph1.61-dev
  libboost-graph-parallel1.61-dev libboost-iostreams1.61-dev
  libboost-locale1.61-dev libboost-log1.61-dev libboost-math1.61-dev
  libboost-mpi1.61-dev libboost-mpi-python1.61-dev
  libboost-program-options1.61-dev libboost-python1.61-dev
  libboost-random1.61-dev libboost-regex1.61-dev
  libboost-serialization1.61-dev libboost-signals1.61-dev
  libboost-system1.61-dev libboost-test1.61-dev libboost-thread1.61-dev
  libboost-timer1.61-dev libboost-wave1.61-dev libboost1.61-tools-dev
  libmpfrc++-dev libntl-dev libtool-doc gfortran | fortran95-compiler gcj-jdk
  less www-browser libmail-box-perl python-doc python-tk python2.7-doc
  binfmt-support
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 groff-base
  intltool-debian libaec0 libarchive-zip-perl libblasr libblasr-dev
  libboost-dev libboost1.61-dev libbsd0 libcroco3 libexpat1
  libfile-stripnondeterminism-perl libgfortran3 libglib2.0-0 libgtest-dev
  libhdf5-10 libhdf5-cpp-11 libicu57 libmagic-mgc libmagic1 libpbdata
  libpbdata-dev libpbihdf libpbihdf-dev libpipeline1 libpython-stdlib
  libpython2.7-minimal libpython2.7-stdlib libreadline6 libsigsegv2 libsz2
  libtclap-dev libtimedate-perl libtool libunistring0 libxml2 m4 man-db
  mime-support po-debconf python python-minimal python2.7 python2.7-minimal
  sbuild-build-depends-pbdagcon-dummy
0 upgraded, 56 newly installed, 0 to remove and 5 not upgraded.
Need to get 35.1 MB/35.2 MB of archives.
After this operation, 218 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-VRaC5P/apt_archive ./ sbuild-build-depends-pbdagcon-dummy 0.invalid.0 [806 B]
Get:2 http://172.17.0.1/private stretch-staging/main armhf groff-base armhf 1.22.3-8 [1087 kB]
Get:3 http://172.17.0.1/private stretch-staging/main armhf libbsd0 armhf 0.8.3-1 [89.0 kB]
Get:4 http://172.17.0.1/private stretch-staging/main armhf bsdmainutils armhf 9.0.12 [178 kB]
Get:5 http://172.17.0.1/private stretch-staging/main armhf libpipeline1 armhf 1.4.1-2 [23.7 kB]
Get:6 http://172.17.0.1/private stretch-staging/main armhf man-db armhf 2.7.5-1 [975 kB]
Get:7 http://172.17.0.1/private stretch-staging/main armhf libpython2.7-minimal armhf 2.7.12-3 [388 kB]
Get:8 http://172.17.0.1/private stretch-staging/main armhf python2.7-minimal armhf 2.7.12-3 [1174 kB]
Get:9 http://172.17.0.1/private stretch-staging/main armhf python-minimal armhf 2.7.11-2 [40.3 kB]
Get:10 http://172.17.0.1/private stretch-staging/main armhf mime-support all 3.60 [36.7 kB]
Get:11 http://172.17.0.1/private stretch-staging/main armhf libexpat1 armhf 2.2.0-1 [61.7 kB]
Get:12 http://172.17.0.1/private stretch-staging/main armhf libpython2.7-stdlib armhf 2.7.12-3 [1843 kB]
Get:13 http://172.17.0.1/private stretch-staging/main armhf python2.7 armhf 2.7.12-3 [279 kB]
Get:14 http://172.17.0.1/private stretch-staging/main armhf libpython-stdlib armhf 2.7.11-2 [19.8 kB]
Get:15 http://172.17.0.1/private stretch-staging/main armhf python armhf 2.7.11-2 [153 kB]
Get:16 http://172.17.0.1/private stretch-staging/main armhf libmagic-mgc armhf 1:5.29-1 [219 kB]
Get:17 http://172.17.0.1/private stretch-staging/main armhf libmagic1 armhf 1:5.29-1 [104 kB]
Get:18 http://172.17.0.1/private stretch-staging/main armhf file armhf 1:5.29-1 [63.3 kB]
Get:19 http://172.17.0.1/private stretch-staging/main armhf gettext-base armhf 0.19.8.1-1 [117 kB]
Get:20 http://172.17.0.1/private stretch-staging/main armhf libicu57 armhf 57.1-4 [7407 kB]
Get:21 http://172.17.0.1/private stretch-staging/main armhf libxml2 armhf 2.9.4+dfsg1-2 [805 kB]
Get:22 http://172.17.0.1/private stretch-staging/main armhf libsigsegv2 armhf 2.10-5 [28.4 kB]
Get:23 http://172.17.0.1/private stretch-staging/main armhf m4 armhf 1.4.17-5 [239 kB]
Get:24 http://172.17.0.1/private stretch-staging/main armhf autoconf all 2.69-10 [338 kB]
Get:25 http://172.17.0.1/private stretch-staging/main armhf autotools-dev all 20160430.1 [72.6 kB]
Get:26 http://172.17.0.1/private stretch-staging/main armhf automake all 1:1.15-4 [735 kB]
Get:27 http://172.17.0.1/private stretch-staging/main armhf autopoint all 0.19.8.1-1 [433 kB]
Get:28 http://172.17.0.1/private stretch-staging/main armhf libtool all 2.4.6-2 [545 kB]
Get:29 http://172.17.0.1/private stretch-staging/main armhf dh-autoreconf all 12 [15.8 kB]
Get:30 http://172.17.0.1/private stretch-staging/main armhf libarchive-zip-perl all 1.59-1 [95.5 kB]
Get:31 http://172.17.0.1/private stretch-staging/main armhf libfile-stripnondeterminism-perl all 0.028-1 [14.6 kB]
Get:32 http://172.17.0.1/private stretch-staging/main armhf libtimedate-perl all 2.3000-2 [42.2 kB]
Get:33 http://172.17.0.1/private stretch-staging/main armhf dh-strip-nondeterminism all 0.028-1 [9020 B]
Get:34 http://172.17.0.1/private stretch-staging/main armhf libglib2.0-0 armhf 2.50.0-2+rpi1 [2523 kB]
Get:35 http://172.17.0.1/private stretch-staging/main armhf libcroco3 armhf 0.6.11-2 [131 kB]
Get:36 http://172.17.0.1/private stretch-staging/main armhf libunistring0 armhf 0.9.6+really0.9.3-0.1 [252 kB]
Get:37 http://172.17.0.1/private stretch-staging/main armhf gettext armhf 0.19.8.1-1 [1433 kB]
Get:38 http://172.17.0.1/private stretch-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:39 http://172.17.0.1/private stretch-staging/main armhf po-debconf all 1.0.20 [247 kB]
Get:40 http://172.17.0.1/private stretch-staging/main armhf debhelper all 10.2.2 [826 kB]
Get:41 http://172.17.0.1/private stretch-staging/main armhf libaec0 armhf 0.3.2-1 [19.4 kB]
Get:42 http://172.17.0.1/private stretch-staging/main armhf libpbdata armhf 0~20160705-1 [104 kB]
Get:43 http://172.17.0.1/private stretch-staging/main armhf libgfortran3 armhf 6.2.0-6+rpi1 [165 kB]
Get:44 http://172.17.0.1/private stretch-staging/main armhf libsz2 armhf 0.3.2-1 [5836 B]
Get:45 http://172.17.0.1/private stretch-staging/main armhf libhdf5-10 armhf 1.8.16+docs-8+b1 [977 kB]
Get:46 http://172.17.0.1/private stretch-staging/main armhf libhdf5-cpp-11 armhf 1.8.16+docs-8+b1 [116 kB]
Get:47 http://172.17.0.1/private stretch-staging/main armhf libpbihdf armhf 0~20160705-1 [103 kB]
Get:48 http://172.17.0.1/private stretch-staging/main armhf libblasr armhf 0~20160705-1 [792 kB]
Get:49 http://172.17.0.1/private stretch-staging/main armhf libblasr-dev armhf 0~20160705-1 [1627 kB]
Get:50 http://172.17.0.1/private stretch-staging/main armhf libboost1.61-dev armhf 1.61.0+dfsg-3 [6843 kB]
Get:51 http://172.17.0.1/private stretch-staging/main armhf libboost-dev armhf 1.61.0.2 [3758 B]
Get:52 http://172.17.0.1/private stretch-staging/main armhf libgtest-dev armhf 1.7.0-4 [200 kB]
Get:53 http://172.17.0.1/private stretch-staging/main armhf libpbdata-dev armhf 0~20160705-1 [175 kB]
Get:54 http://172.17.0.1/private stretch-staging/main armhf libpbihdf-dev armhf 0~20160705-1 [193 kB]
Get:55 http://172.17.0.1/private stretch-staging/main armhf libtclap-dev armhf 1.2.1-1 [727 kB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 35.1 MB in 14s (2492 kB/s)
Selecting previously unselected package groff-base.
(Reading database ... 13408 files and directories currently installed.)
Preparing to unpack .../00-groff-base_1.22.3-8_armhf.deb ...
Unpacking groff-base (1.22.3-8) ...
Selecting previously unselected package libbsd0:armhf.
Preparing to unpack .../01-libbsd0_0.8.3-1_armhf.deb ...
Unpacking libbsd0:armhf (0.8.3-1) ...
Selecting previously unselected package bsdmainutils.
Preparing to unpack .../02-bsdmainutils_9.0.12_armhf.deb ...
Unpacking bsdmainutils (9.0.12) ...
Selecting previously unselected package libpipeline1:armhf.
Preparing to unpack .../03-libpipeline1_1.4.1-2_armhf.deb ...
Unpacking libpipeline1:armhf (1.4.1-2) ...
Selecting previously unselected package man-db.
Preparing to unpack .../04-man-db_2.7.5-1_armhf.deb ...
Unpacking man-db (2.7.5-1) ...
Selecting previously unselected package libpython2.7-minimal:armhf.
Preparing to unpack .../05-libpython2.7-minimal_2.7.12-3_armhf.deb ...
Unpacking libpython2.7-minimal:armhf (2.7.12-3) ...
Selecting previously unselected package python2.7-minimal.
Preparing to unpack .../06-python2.7-minimal_2.7.12-3_armhf.deb ...
Unpacking python2.7-minimal (2.7.12-3) ...
Selecting previously unselected package python-minimal.
Preparing to unpack .../07-python-minimal_2.7.11-2_armhf.deb ...
Unpacking python-minimal (2.7.11-2) ...
Selecting previously unselected package mime-support.
Preparing to unpack .../08-mime-support_3.60_all.deb ...
Unpacking mime-support (3.60) ...
Selecting previously unselected package libexpat1:armhf.
Preparing to unpack .../09-libexpat1_2.2.0-1_armhf.deb ...
Unpacking libexpat1:armhf (2.2.0-1) ...
Selecting previously unselected package libreadline6:armhf.
Preparing to unpack .../10-libreadline6_6.3-9_armhf.deb ...
Unpacking libreadline6:armhf (6.3-9) ...
Selecting previously unselected package libpython2.7-stdlib:armhf.
Preparing to unpack .../11-libpython2.7-stdlib_2.7.12-3_armhf.deb ...
Unpacking libpython2.7-stdlib:armhf (2.7.12-3) ...
Selecting previously unselected package python2.7.
Preparing to unpack .../12-python2.7_2.7.12-3_armhf.deb ...
Unpacking python2.7 (2.7.12-3) ...
Selecting previously unselected package libpython-stdlib:armhf.
Preparing to unpack .../13-libpython-stdlib_2.7.11-2_armhf.deb ...
Unpacking libpython-stdlib:armhf (2.7.11-2) ...
Setting up libpython2.7-minimal:armhf (2.7.12-3) ...
Setting up python2.7-minimal (2.7.12-3) ...
Setting up python-minimal (2.7.11-2) ...
Selecting previously unselected package python.
(Reading database ... 14756 files and directories currently installed.)
Preparing to unpack .../00-python_2.7.11-2_armhf.deb ...
Unpacking python (2.7.11-2) ...
Selecting previously unselected package libmagic-mgc.
Preparing to unpack .../01-libmagic-mgc_1%3a5.29-1_armhf.deb ...
Unpacking libmagic-mgc (1:5.29-1) ...
Selecting previously unselected package libmagic1:armhf.
Preparing to unpack .../02-libmagic1_1%3a5.29-1_armhf.deb ...
Unpacking libmagic1:armhf (1:5.29-1) ...
Selecting previously unselected package file.
Preparing to unpack .../03-file_1%3a5.29-1_armhf.deb ...
Unpacking file (1:5.29-1) ...
Selecting previously unselected package gettext-base.
Preparing to unpack .../04-gettext-base_0.19.8.1-1_armhf.deb ...
Unpacking gettext-base (0.19.8.1-1) ...
Selecting previously unselected package libicu57:armhf.
Preparing to unpack .../05-libicu57_57.1-4_armhf.deb ...
Unpacking libicu57:armhf (57.1-4) ...
Selecting previously unselected package libxml2:armhf.
Preparing to unpack .../06-libxml2_2.9.4+dfsg1-2_armhf.deb ...
Unpacking libxml2:armhf (2.9.4+dfsg1-2) ...
Selecting previously unselected package libsigsegv2:armhf.
Preparing to unpack .../07-libsigsegv2_2.10-5_armhf.deb ...
Unpacking libsigsegv2:armhf (2.10-5) ...
Selecting previously unselected package m4.
Preparing to unpack .../08-m4_1.4.17-5_armhf.deb ...
Unpacking m4 (1.4.17-5) ...
Selecting previously unselected package autoconf.
Preparing to unpack .../09-autoconf_2.69-10_all.deb ...
Unpacking autoconf (2.69-10) ...
Selecting previously unselected package autotools-dev.
Preparing to unpack .../10-autotools-dev_20160430.1_all.deb ...
Unpacking autotools-dev (20160430.1) ...
Selecting previously unselected package automake.
Preparing to unpack .../11-automake_1%3a1.15-4_all.deb ...
Unpacking automake (1:1.15-4) ...
Selecting previously unselected package autopoint.
Preparing to unpack .../12-autopoint_0.19.8.1-1_all.deb ...
Unpacking autopoint (0.19.8.1-1) ...
Selecting previously unselected package libtool.
Preparing to unpack .../13-libtool_2.4.6-2_all.deb ...
Unpacking libtool (2.4.6-2) ...
Selecting previously unselected package dh-autoreconf.
Preparing to unpack .../14-dh-autoreconf_12_all.deb ...
Unpacking dh-autoreconf (12) ...
Selecting previously unselected package libarchive-zip-perl.
Preparing to unpack .../15-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 .../16-libfile-stripnondeterminism-perl_0.028-1_all.deb ...
Unpacking libfile-stripnondeterminism-perl (0.028-1) ...
Selecting previously unselected package libtimedate-perl.
Preparing to unpack .../17-libtimedate-perl_2.3000-2_all.deb ...
Unpacking libtimedate-perl (2.3000-2) ...
Selecting previously unselected package dh-strip-nondeterminism.
Preparing to unpack .../18-dh-strip-nondeterminism_0.028-1_all.deb ...
Unpacking dh-strip-nondeterminism (0.028-1) ...
Selecting previously unselected package libglib2.0-0:armhf.
Preparing to unpack .../19-libglib2.0-0_2.50.0-2+rpi1_armhf.deb ...
Unpacking libglib2.0-0:armhf (2.50.0-2+rpi1) ...
Selecting previously unselected package libcroco3:armhf.
Preparing to unpack .../20-libcroco3_0.6.11-2_armhf.deb ...
Unpacking libcroco3:armhf (0.6.11-2) ...
Selecting previously unselected package libunistring0:armhf.
Preparing to unpack .../21-libunistring0_0.9.6+really0.9.3-0.1_armhf.deb ...
Unpacking libunistring0:armhf (0.9.6+really0.9.3-0.1) ...
Selecting previously unselected package gettext.
Preparing to unpack .../22-gettext_0.19.8.1-1_armhf.deb ...
Unpacking gettext (0.19.8.1-1) ...
Selecting previously unselected package intltool-debian.
Preparing to unpack .../23-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 .../24-po-debconf_1.0.20_all.deb ...
Unpacking po-debconf (1.0.20) ...
Selecting previously unselected package debhelper.
Preparing to unpack .../25-debhelper_10.2.2_all.deb ...
Unpacking debhelper (10.2.2) ...
Selecting previously unselected package libaec0:armhf.
Preparing to unpack .../26-libaec0_0.3.2-1_armhf.deb ...
Unpacking libaec0:armhf (0.3.2-1) ...
Selecting previously unselected package libpbdata:armhf.
Preparing to unpack .../27-libpbdata_0~20160705-1_armhf.deb ...
Unpacking libpbdata:armhf (0~20160705-1) ...
Selecting previously unselected package libgfortran3:armhf.
Preparing to unpack .../28-libgfortran3_6.2.0-6+rpi1_armhf.deb ...
Unpacking libgfortran3:armhf (6.2.0-6+rpi1) ...
Selecting previously unselected package libsz2:armhf.
Preparing to unpack .../29-libsz2_0.3.2-1_armhf.deb ...
Unpacking libsz2:armhf (0.3.2-1) ...
Selecting previously unselected package libhdf5-10:armhf.
Preparing to unpack .../30-libhdf5-10_1.8.16+docs-8+b1_armhf.deb ...
Unpacking libhdf5-10:armhf (1.8.16+docs-8+b1) ...
Selecting previously unselected package libhdf5-cpp-11:armhf.
Preparing to unpack .../31-libhdf5-cpp-11_1.8.16+docs-8+b1_armhf.deb ...
Unpacking libhdf5-cpp-11:armhf (1.8.16+docs-8+b1) ...
Selecting previously unselected package libpbihdf:armhf.
Preparing to unpack .../32-libpbihdf_0~20160705-1_armhf.deb ...
Unpacking libpbihdf:armhf (0~20160705-1) ...
Selecting previously unselected package libblasr:armhf.
Preparing to unpack .../33-libblasr_0~20160705-1_armhf.deb ...
Unpacking libblasr:armhf (0~20160705-1) ...
Selecting previously unselected package libblasr-dev:armhf.
Preparing to unpack .../34-libblasr-dev_0~20160705-1_armhf.deb ...
Unpacking libblasr-dev:armhf (0~20160705-1) ...
Selecting previously unselected package libboost1.61-dev:armhf.
Preparing to unpack .../35-libboost1.61-dev_1.61.0+dfsg-3_armhf.deb ...
Unpacking libboost1.61-dev:armhf (1.61.0+dfsg-3) ...
Selecting previously unselected package libboost-dev:armhf.
Preparing to unpack .../36-libboost-dev_1.61.0.2_armhf.deb ...
Unpacking libboost-dev:armhf (1.61.0.2) ...
Selecting previously unselected package libgtest-dev:armhf.
Preparing to unpack .../37-libgtest-dev_1.7.0-4_armhf.deb ...
Unpacking libgtest-dev:armhf (1.7.0-4) ...
Selecting previously unselected package libpbdata-dev:armhf.
Preparing to unpack .../38-libpbdata-dev_0~20160705-1_armhf.deb ...
Unpacking libpbdata-dev:armhf (0~20160705-1) ...
Selecting previously unselected package libpbihdf-dev:armhf.
Preparing to unpack .../39-libpbihdf-dev_0~20160705-1_armhf.deb ...
Unpacking libpbihdf-dev:armhf (0~20160705-1) ...
Selecting previously unselected package libtclap-dev.
Preparing to unpack .../40-libtclap-dev_1.2.1-1_armhf.deb ...
Unpacking libtclap-dev (1.2.1-1) ...
Selecting previously unselected package sbuild-build-depends-pbdagcon-dummy.
Preparing to unpack .../41-sbuild-build-depends-pbdagcon-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-pbdagcon-dummy (0.invalid.0) ...
Setting up libaec0:armhf (0.3.2-1) ...
Setting up libexpat1:armhf (2.2.0-1) ...
Setting up libarchive-zip-perl (1.59-1) ...
Setting up mime-support (3.60) ...
Setting up libtimedate-perl (2.3000-2) ...
Setting up libsigsegv2:armhf (2.10-5) ...
Setting up libgfortran3:armhf (6.2.0-6+rpi1) ...
Setting up groff-base (1.22.3-8) ...
Setting up libglib2.0-0:armhf (2.50.0-2+rpi1) ...
No schema files found: doing nothing.
Setting up libtclap-dev (1.2.1-1) ...
Setting up gettext-base (0.19.8.1-1) ...
Setting up libpipeline1:armhf (1.4.1-2) ...
Setting up m4 (1.4.17-5) ...
Setting up libicu57:armhf (57.1-4) ...
Setting up libboost1.61-dev:armhf (1.61.0+dfsg-3) ...
Setting up libbsd0:armhf (0.8.3-1) ...
Setting up libxml2:armhf (2.9.4+dfsg1-2) ...
Setting up libmagic-mgc (1:5.29-1) ...
Setting up libmagic1:armhf (1:5.29-1) ...
Setting up libcroco3:armhf (0.6.11-2) ...
Processing triggers for libc-bin (2.24-5+rpi1) ...
Setting up autotools-dev (20160430.1) ...
Setting up libunistring0:armhf (0.9.6+really0.9.3-0.1) ...
Setting up libpbdata:armhf (0~20160705-1) ...
Setting up libgtest-dev:armhf (1.7.0-4) ...
Setting up libboost-dev:armhf (1.61.0.2) ...
Setting up bsdmainutils (9.0.12) ...
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 autopoint (0.19.8.1-1) ...
Setting up libreadline6:armhf (6.3-9) ...
Setting up libsz2:armhf (0.3.2-1) ...
Setting up libfile-stripnondeterminism-perl (0.028-1) ...
Setting up libhdf5-10:armhf (1.8.16+docs-8+b1) ...
Setting up libhdf5-cpp-11:armhf (1.8.16+docs-8+b1) ...
Setting up gettext (0.19.8.1-1) ...
Setting up libpbdata-dev:armhf (0~20160705-1) ...
Setting up autoconf (2.69-10) ...
Setting up file (1:5.29-1) ...
Setting up intltool-debian (0.35.0+20060710.4) ...
Setting up libpbihdf:armhf (0~20160705-1) ...
Setting up automake (1:1.15-4) ...
update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode
Setting up man-db (2.7.5-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libpython2.7-stdlib:armhf (2.7.12-3) ...
Setting up libtool (2.4.6-2) ...
Setting up libblasr:armhf (0~20160705-1) ...
Setting up po-debconf (1.0.20) ...
Setting up libpbihdf-dev:armhf (0~20160705-1) ...
Setting up libblasr-dev:armhf (0~20160705-1) ...
Setting up python2.7 (2.7.12-3) ...
Setting up libpython-stdlib:armhf (2.7.11-2) ...
Setting up python (2.7.11-2) ...
Setting up dh-autoreconf (12) ...
Setting up debhelper (10.2.2) ...
Setting up sbuild-build-depends-pbdagcon-dummy (0.invalid.0) ...
Setting up dh-strip-nondeterminism (0.028-1) ...
Processing triggers for libc-bin (2.24-5+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges

+------------------------------------------------------------------------------+
| Build environment                                                            |
+------------------------------------------------------------------------------+

Kernel: Linux 4.5.0-1-armmp armhf (armv7l)
Toolchain package versions: binutils_2.27-9 dpkg-dev_1.18.10 g++-6_6.2.0-6+rpi1 gcc-6_6.2.0-6+rpi1 libc6-dev_2.24-5+rpi1 libstdc++-6-dev_6.2.0-6+rpi1 libstdc++6_6.2.0-6+rpi1 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch
Package versions: adduser_3.115 apt_1.3.1 autoconf_2.69-10 automake_1:1.15-4 autopoint_0.19.8.1-1 autotools-dev_20160430.1 base-files_9.6+rpi1 base-passwd_3.5.40 bash_4.4-1 binutils_2.27-9 bsdmainutils_9.0.12 bsdutils_1:2.28.2-1 build-essential_12.2 bzip2_1.0.6-8 coreutils_8.25-2 cpio_2.11+dfsg-5 cpp_4:6.1.1-1 cpp-6_6.2.0-6+rpi1 dash_0.5.8-2.3 debconf_1.5.59 debfoster_2.7-2.1 debhelper_10.2.2 debianutils_4.8 dh-autoreconf_12 dh-strip-nondeterminism_0.028-1 diffutils_1:3.5-1 dirmngr_2.1.15-4 dmsetup_2:1.02.133-1 dpkg_1.18.10 dpkg-dev_1.18.10 e2fslibs_1.43.3-1 e2fsprogs_1.43.3-1 fakeroot_1.21-2 file_1:5.29-1 findutils_4.6.0+git+20160703-2 fuse2fs_1.43.3-1 g++_4:6.1.1-1 g++-6_6.2.0-6+rpi1 gcc_4:6.1.1-1 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8-base_4.8.5-4 gcc-4.9-base_4.9.3-14 gcc-6_6.2.0-6+rpi1 gcc-6-base_6.2.0-6+rpi1 gettext_0.19.8.1-1 gettext-base_0.19.8.1-1 gnupg_2.1.15-4 gnupg-agent_2.1.15-4 gnupg-l10n_2.1.15-4 gpgv_2.1.15-4 grep_2.26-1 groff-base_1.22.3-8 gzip_1.6-5 hostname_3.18 init_1.45 init-system-helpers_1.45 initscripts_2.88dsf-59.8 insserv_1.14.0-5.4 intltool-debian_0.35.0+20060710.4 kbd_2.0.3-2 klibc-utils_2.0.4-9+rpi1 kmod_22-1.1 libacl1_2.2.52-3 libaec0_0.3.2-1 libapparmor1_2.10.95-5 libapt-pkg5.0_1.3.1 libarchive-zip-perl_1.59-1 libasan3_6.2.0-6+rpi1 libassuan0_2.4.3-1 libatomic1_6.2.0-6+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.6.7-1 libaudit1_1:2.6.7-1 libblasr_0~20160705-1 libblasr-dev_0~20160705-1 libblkid1_2.28.2-1 libboost-dev_1.61.0.2 libboost1.61-dev_1.61.0+dfsg-3 libbsd0_0.8.3-1 libbz2-1.0_1.0.6-8 libc-bin_2.24-5+rpi1 libc-dev-bin_2.24-5+rpi1 libc6_2.24-5+rpi1 libc6-dev_2.24-5+rpi1 libcap-ng0_0.7.7-3 libcap2_1:2.25-1 libcap2-bin_1:2.25-1 libcc1-0_6.2.0-6+rpi1 libcomerr2_1.43.3-1 libcroco3_0.6.11-2 libcryptsetup4_2:1.7.2-5 libdb5.3_5.3.28-12 libdbus-1-3_1.10.12-1 libdebconfclient0_0.218 libdevmapper1.02.1_2:1.02.133-1 libdpkg-perl_1.18.10 libdrm2_2.4.71-1 libexpat1_2.2.0-1 libfakeroot_1.21-2 libfdisk1_2.28.2-1 libffi6_3.2.1-6 libfile-stripnondeterminism-perl_0.028-1 libfuse2_2.9.7-1 libgc1c2_1:7.4.2-8 libgcc-6-dev_6.2.0-6+rpi1 libgcc1_1:6.2.0-6+rpi1 libgcrypt20_1.7.3-2 libgdbm3_1.8.3-14 libgfortran3_6.2.0-6+rpi1 libglib2.0-0_2.50.0-2+rpi1 libgmp10_2:6.1.1+dfsg-1 libgnutls30_3.5.5-2 libgomp1_6.2.0-6+rpi1 libgpg-error0_1.24-1 libgtest-dev_1.7.0-4 libhdf5-10_1.8.16+docs-8+b1 libhdf5-cpp-11_1.8.16+docs-8+b1 libhogweed4_3.3-1 libicu57_57.1-4 libidn11_1.33-1 libip4tc0_1.6.0-4 libisl15_0.17.1-1 libklibc_2.0.4-9+rpi1 libkmod2_22-1.1 libksba8_1.3.5-2 libldap-2.4-2_2.4.42+dfsg-2+rpi1+b3 liblz4-1_0.0~r131-2 liblzma5_5.2.2-1.2 libmagic-mgc_1:5.29-1 libmagic1_1:5.29-1 libmount1_2.28.2-1 libmpc3_1.0.3-1 libmpfr4_3.1.5-1 libncurses5_6.0+20160917-1 libncursesw5_6.0+20160917-1 libnettle6_3.3-1 libnpth0_1.2-3 libp11-kit0_0.23.2-5 libpam-modules_1.1.8-3.3 libpam-modules-bin_1.1.8-3.3 libpam-runtime_1.1.8-3.3 libpam0g_1.1.8-3.3 libpbdata_0~20160705-1 libpbdata-dev_0~20160705-1 libpbihdf_0~20160705-1 libpbihdf-dev_0~20160705-1 libpcre3_2:8.39-2 libperl5.24_5.24.1~rc3-3 libpipeline1_1.4.1-2 libplymouth4_0.9.2-3 libpng12-0_1.2.54-6 libprocps6_2:3.3.12-2 libpython-stdlib_2.7.11-2 libpython2.7-minimal_2.7.12-3 libpython2.7-stdlib_2.7.12-3 libreadline6_6.3-9 libreadline7_7.0-1 libsasl2-2_2.1.26.dfsg1-15 libsasl2-modules_2.1.26.dfsg1-15 libsasl2-modules-db_2.1.26.dfsg1-15 libseccomp2_2.3.1-2 libselinux1_2.5-3 libsemanage-common_2.5-1 libsemanage1_2.5-1 libsepol1_2.5-1 libsigsegv2_2.10-5 libsmartcols1_2.28.2-1 libsqlite3-0_3.14.2-1 libss2_1.43.3-1 libssl1.0.2_1.0.2j-1 libstdc++-6-dev_6.2.0-6+rpi1 libstdc++6_6.2.0-6+rpi1 libsystemd0_231-9 libsz2_0.3.2-1 libtasn1-6_4.9-4 libtclap-dev_1.2.1-1 libtimedate-perl_2.3000-2 libtinfo5_6.0+20160917-1 libtool_2.4.6-2 libubsan0_6.2.0-6+rpi1 libudev1_231-9 libunistring0_0.9.6+really0.9.3-0.1 libusb-0.1-4_2:0.1.12-30 libustr-1.0-1_1.0.4-5 libuuid1_2.28.2-1 libxml2_2.9.4+dfsg1-2 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch login_1:4.2-3.2 lsb-base_9.20160629+rpi1 m4_1.4.17-5 make_4.1-9 makedev_2.3.1-93 man-db_2.7.5-1 manpages_4.08-1 mawk_1.3.3-17 mime-support_3.60 mount_2.28.2-1 multiarch-support_2.24-5+rpi1 ncurses-base_6.0+20160917-1 ncurses-bin_6.0+20160917-1 netbase_5.3 passwd_1:4.2-3.2 patch_2.7.5-1 perl_5.24.1~rc3-3 perl-base_5.24.1~rc3-3 perl-modules-5.24_5.24.1~rc3-3 pinentry-curses_0.9.7-6 po-debconf_1.0.20 procps_2:3.3.12-2 psmisc_22.21-2.1 python_2.7.11-2 python-minimal_2.7.11-2 python2.7_2.7.12-3 python2.7-minimal_2.7.12-3 raspbian-archive-keyring_20120528.2 readline-common_7.0-1 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-pbdagcon-dummy_0.invalid.0 sed_4.2.2-8 sensible-utils_0.0.9 startpar_0.59-3.1 systemd_231-9 systemd-sysv_231-9 sysv-rc_2.88dsf-59.8 sysvinit-utils_2.88dsf-59.8 tar_1.29b-1 tzdata_2016h-1 udev_231-9 util-linux_2.28.2-1 xz-utils_5.2.2-1.2 zlib1g_1:1.2.8.dfsg-2+b1

+------------------------------------------------------------------------------+
| Build                                                                        |
+------------------------------------------------------------------------------+


Unpack source
-------------

gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Mon Oct 24 04:04:54 2016 UTC
gpgv:                using RSA key 59B2306F3AF9DDC1
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./pbdagcon_0~20160325+ds-1.dsc
dpkg-source: info: extracting pbdagcon in /<<BUILDDIR>>/pbdagcon-0~20160325+ds
dpkg-source: info: unpacking pbdagcon_0~20160325+ds.orig.tar.gz
dpkg-source: info: unpacking pbdagcon_0~20160325+ds-1.debian.tar.xz
dpkg-source: info: applying compiler-flags.patch
dpkg-source: info: applying dazcon.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=root
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=stretch-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=stretch-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=stretch-staging-armhf-sbuild-8cb99a62-77ca-4283-83a3-0fa90dfcd554
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=xterm
USER=buildd

dpkg-buildpackage
-----------------

dpkg-buildpackage: info: source package pbdagcon
dpkg-buildpackage: info: source version 0~20160325+ds-1
dpkg-buildpackage: info: source distribution unstable
 dpkg-source --before-build pbdagcon-0~20160325+ds
dpkg-buildpackage: info: host architecture armhf
 fakeroot debian/rules clean
dh clean --parallel
   dh_testdir -O--parallel
   dh_auto_clean -O--parallel
	make -j4 clean
make[1]: Entering directory '/<<BUILDDIR>>/pbdagcon-0~20160325+ds'
make -C src/cpp clean
make[2]: Entering directory '/<<BUILDDIR>>/pbdagcon-0~20160325+ds/src/cpp'
rm -f *.d
rm -f *.o
rm -f pbdagcon
rm -f dazcon
make[2]: Leaving directory '/<<BUILDDIR>>/pbdagcon-0~20160325+ds/src/cpp'
make -C test/cpp clean
make[2]: Entering directory '/<<BUILDDIR>>/pbdagcon-0~20160325+ds/test/cpp'
rm -f .//*.o
rm -f *.o
rm -f test_*
make[2]: Leaving directory '/<<BUILDDIR>>/pbdagcon-0~20160325+ds/test/cpp'
make[1]: Leaving directory '/<<BUILDDIR>>/pbdagcon-0~20160325+ds'
   dh_clean -O--parallel
 debian/rules build-arch
dh build-arch --parallel
   dh_testdir -a -O--parallel
   dh_update_autotools_config -a -O--parallel
   debian/rules override_dh_auto_configure
make[1]: Entering directory '/<<BUILDDIR>>/pbdagcon-0~20160325+ds'
./configure.py --no-pbbam --shared
uname -s
uname='Linux'
writing to '/<<BUILDDIR>>/pbdagcon-0~20160325+ds/defines.mk'
"""
DALIGNER_INCLUDE     ?= ${DALIGNER_SRC}
DALIGNER_SRC         ?= /<<BUILDDIR>>/pbdagcon-0~20160325+ds/../DALIGNER
DAZZ_DB_INCLUDE      ?= ${DAZZ_DB_SRC}
DAZZ_DB_SRC          ?= /<<BUILDDIR>>/pbdagcon-0~20160325+ds/../DAZZ_DB
GTEST_INCLUDE        ?= /usr/src/gtest
LIBBLASR_LIBFLAGS    ?= -lblasr
LIBPBDATA_LIBFLAGS   ?= -lpbdata
PTHREAD_LIBFLAGS     ?= -lpthread
LDLIBS+=-lrt
"""
make[1]: Leaving directory '/<<BUILDDIR>>/pbdagcon-0~20160325+ds'
   dh_auto_build -a -O--parallel
	make -j4
make[1]: Entering directory '/<<BUILDDIR>>/pbdagcon-0~20160325+ds'
make -C src/cpp
make[2]: Entering directory '/<<BUILDDIR>>/pbdagcon-0~20160325+ds/src/cpp'
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbdagcon-0~20160325+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -Wall -Wuninitialized -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq/alignment -I/usr/include/pbseq/pbdata -I/usr/include/pbseq/hdf -MMD -MP -I/<<BUILDDIR>>/pbdagcon-0~20160325+ds/../DAZZ_DB -I/<<BUILDDIR>>/pbdagcon-0~20160325+ds/../DALIGNER -isystem.//third-party  -c -o Alignment.o Alignment.cpp
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbdagcon-0~20160325+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -Wall -Wuninitialized -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq/alignment -I/usr/include/pbseq/pbdata -I/usr/include/pbseq/hdf -MMD -MP -I/<<BUILDDIR>>/pbdagcon-0~20160325+ds/../DAZZ_DB -I/<<BUILDDIR>>/pbdagcon-0~20160325+ds/../DALIGNER -isystem.//third-party  -c -o AlnGraphBoost.o AlnGraphBoost.cpp
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbdagcon-0~20160325+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -Wall -Wuninitialized -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq/alignment -I/usr/include/pbseq/pbdata -I/usr/include/pbseq/hdf -MMD -MP -I/<<BUILDDIR>>/pbdagcon-0~20160325+ds/../DAZZ_DB -I/<<BUILDDIR>>/pbdagcon-0~20160325+ds/../DALIGNER -isystem.//third-party  -c -o BlasrM5AlnProvider.o BlasrM5AlnProvider.cpp
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbdagcon-0~20160325+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -Wall -Wuninitialized -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq/alignment -I/usr/include/pbseq/pbdata -I/usr/include/pbseq/hdf -MMD -MP -I/<<BUILDDIR>>/pbdagcon-0~20160325+ds/../DAZZ_DB -I/<<BUILDDIR>>/pbdagcon-0~20160325+ds/../DALIGNER -isystem.//third-party  -c -o main.o main.cpp
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbdagcon-0~20160325+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -Wall -Wuninitialized -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq/alignment -I/usr/include/pbseq/pbdata -I/usr/include/pbseq/hdf -MMD -MP -I/<<BUILDDIR>>/pbdagcon-0~20160325+ds/../DAZZ_DB -I/<<BUILDDIR>>/pbdagcon-0~20160325+ds/../DALIGNER -isystem.//third-party  -c -o SimpleAligner.o SimpleAligner.cpp
g++ -o pbdagcon Alignment.o AlnGraphBoost.o BlasrM5AlnProvider.o main.o SimpleAligner.o -Wl,-z,relro   -lrt -lblasr -lpbdata      -lpthread 
make[2]: Leaving directory '/<<BUILDDIR>>/pbdagcon-0~20160325+ds/src/cpp'
make[1]: Leaving directory '/<<BUILDDIR>>/pbdagcon-0~20160325+ds'
   debian/rules override_dh_auto_test
make[1]: Entering directory '/<<BUILDDIR>>/pbdagcon-0~20160325+ds'
src/cpp/pbdagcon --help

USAGE: 

   src/cpp/pbdagcon  [-v] [-a] [-t <uint>] [-m <uint>] [-c <uint>] [-j
                     <int>] [--] [--version] [-h] <either file path or
                     stdin>


Where: 

   -v,  --verbose
     Turns on verbose logging

   -a,  --align
     Align sequences before adding to consensus

   -t <uint>,  --trim <uint>
     Trim alignments on either size

   -m <uint>,  --min-length <uint>
     Minimum length for correction

   -c <uint>,  --min-coverage <uint>
     Minimum coverage for correction

   -j <int>,  --threads <int>
     Number of consensus threads

   --,  --ignore_rest
     Ignores the rest of the labeled arguments following this flag.

   --version
     Displays version information and exits.

   -h,  --help
     Displays usage information and exits.

   <either file path or stdin>
     (required)  Input data


   PBI consensus module

make[1]: Leaving directory '/<<BUILDDIR>>/pbdagcon-0~20160325+ds'
 fakeroot debian/rules binary-arch
dh binary-arch --parallel
   dh_testroot -a -O--parallel
   dh_prep -a -O--parallel
   dh_auto_install -a -O--parallel
   dh_install -a -O--parallel
   dh_installdocs -a -O--parallel
   dh_installchangelogs -a -O--parallel
   dh_installexamples -a -O--parallel
   dh_installman -a -O--parallel
   dh_perl -a -O--parallel
   dh_link -a -O--parallel
   dh_strip_nondeterminism -a -O--parallel
   dh_compress -a -O--parallel
   dh_fixperms -a -O--parallel
   dh_strip -a -O--parallel
   dh_makeshlibs -a -O--parallel
   dh_shlibdeps -a -O--parallel
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbdata.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbdata.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libblasr.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libblasr.so'
dpkg-shlibdeps: warning: debian/pbdagcon/usr/bin/pbdagcon 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/pbdagcon/usr/bin/pbdagcon was not linked against librt.so.1 (it uses none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/pbdagcon/usr/bin/pbdagcon was not linked against ld-linux-armhf.so.3 (it uses none of the library's symbols)
   dh_installdeb -a -O--parallel
   dh_gencontrol -a -O--parallel
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
   dh_md5sums -a -O--parallel
   dh_builddeb -a -O--parallel
dpkg-deb: building package 'pbdagcon-dbgsym' in '../pbdagcon-dbgsym_0~20160325+ds-1_armhf.deb'.
dpkg-deb: building package 'pbdagcon' in '../pbdagcon_0~20160325+ds-1_armhf.deb'.
 dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../pbdagcon_0~20160325+ds-1_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
 dpkg-source --after-build pbdagcon-0~20160325+ds
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2016-11-01T00:24:12Z

Finished
--------

I: Built successfully

+------------------------------------------------------------------------------+
| Post Build Chroot                                                            |
+------------------------------------------------------------------------------+


+------------------------------------------------------------------------------+
| Changes                                                                      |
+------------------------------------------------------------------------------+


pbdagcon_0~20160325+ds-1_armhf.changes:
---------------------------------------

Format: 1.8
Date: Sun, 23 Oct 2016 19:43:31 -0700
Source: pbdagcon
Binary: pbdagcon
Architecture: armhf
Version: 0~20160325+ds-1
Distribution: stretch-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Afif Elghraoui <afif@debian.org>
Description:
 pbdagcon   - sequence consensus using directed acyclic graphs
Changes:
 pbdagcon (0~20160325+ds-1) unstable; urgency=medium
 .
   * Imported Upstream version 0~20160325+ds
     (upstream git revision f19aed1)
   * Do not use rpath for pbseqlib
   * Update patches
   * d/rules: update for changes to build system and dependencies
   * Do not build dazcon for now (needs additional sources)
   * d/copyright: Remove obsolete declarations
Checksums-Sha1:
 50eaba3b9be001bb2f3e99100011c3eb4f3c14a8 2157242 pbdagcon-dbgsym_0~20160325+ds-1_armhf.deb
 809ee6c44bfea876612802309db02bb7a33a19e9 154014 pbdagcon_0~20160325+ds-1_armhf.deb
Checksums-Sha256:
 086f3ac7d29956c93dc59e4c355e43b07200f870c9be38cf4107af17972b4233 2157242 pbdagcon-dbgsym_0~20160325+ds-1_armhf.deb
 1bbd4382020dec0b8ce9f4c5e78220818e78d46ead435e977f509c712eef77e9 154014 pbdagcon_0~20160325+ds-1_armhf.deb
Files:
 815a7ace77bdedab494c2186e7f18e9a 2157242 debug extra pbdagcon-dbgsym_0~20160325+ds-1_armhf.deb
 1c24d656ae323b828506989f41a37f72 154014 science optional pbdagcon_0~20160325+ds-1_armhf.deb

+------------------------------------------------------------------------------+
| Package contents                                                             |
+------------------------------------------------------------------------------+


pbdagcon-dbgsym_0~20160325+ds-1_armhf.deb
-----------------------------------------

 new debian package, version 2.0.
 size 2157242 bytes: control archive=502 bytes.
     445 bytes,    13 lines      control              
     106 bytes,     1 lines      md5sums              
 Package: pbdagcon-dbgsym
 Source: pbdagcon
 Version: 0~20160325+ds-1
 Architecture: armhf
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 2280
 Depends: pbdagcon (= 0~20160325+ds-1)
 Section: debug
 Priority: extra
 Homepage: https://github.com/PacificBiosciences/pbdagcon
 Description: Debug symbols for pbdagcon
 Auto-Built-Package: debug-symbols
 Build-Ids: 30def9b2e79d9ca6c4d0c8b2dce95c6b83582aa4

drwxr-xr-x root/root         0 2016-10-24 02:43 ./
drwxr-xr-x root/root         0 2016-10-24 02:43 ./usr/
drwxr-xr-x root/root         0 2016-10-24 02:43 ./usr/lib/
drwxr-xr-x root/root         0 2016-10-24 02:43 ./usr/lib/debug/
drwxr-xr-x root/root         0 2016-10-24 02:43 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root         0 2016-10-24 02:43 ./usr/lib/debug/.build-id/30/
-rw-r--r-- root/root   2323920 2016-10-24 02:43 ./usr/lib/debug/.build-id/30/def9b2e79d9ca6c4d0c8b2dce95c6b83582aa4.debug
drwxr-xr-x root/root         0 2016-10-24 02:43 ./usr/share/
drwxr-xr-x root/root         0 2016-10-24 02:43 ./usr/share/doc/
lrwxrwxrwx root/root         0 2016-10-24 02:43 ./usr/share/doc/pbdagcon-dbgsym -> pbdagcon


pbdagcon_0~20160325+ds-1_armhf.deb
----------------------------------

 new debian package, version 2.0.
 size 154014 bytes: control archive=1330 bytes.
    1593 bytes,    30 lines      control              
     720 bytes,    10 lines      md5sums              
 Package: pbdagcon
 Version: 0~20160325+ds-1
 Architecture: armhf
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 424
 Depends: libc6 (>= 2.4), libgcc1 (>= 1:3.5), libstdc++6 (>= 6), libpbdata, libblasr
 Suggests: blasr
 Section: science
 Priority: optional
 Homepage: https://github.com/PacificBiosciences/pbdagcon
 Description: sequence consensus using directed acyclic graphs
  pbdagcon is a tool that implements DAGCon (Directed Acyclic Graph Consensus)
  which is a sequence consensus algorithm based on using directed acyclic
  graphs to encode multiple sequence alignment.
  .
  It uses the alignment information from blasr to align sequence reads to a
  "backbone" sequence. Based on the underlying alignment directed acyclic graph
  (DAG), it will be able to use the new information from the reads to find the
  discrepancies between the reads and the "backbone" sequences. A dynamic
  programming process is then applied to the DAG to find the optimum sequence
  of bases as the consensus. The new consensus can be used as a new backbone
  sequence to iteratively improve the consensus quality.
  .
  While the code is developed for processing PacBio(TM) raw sequence data,
  the algorithm can be used for general consensus purpose. Currently, it only
  takes FASTA input. For shorter read sequences, one might need to adjust the
  blasr alignment parameters to get the alignment string properly.
  .
  The code and the underlying graphical data structure have been used for some
  algorithm development prototyping including phasing reads and pre-assembly.

drwxr-xr-x root/root         0 2016-10-24 02:43 ./
drwxr-xr-x root/root         0 2016-10-24 02:43 ./usr/
drwxr-xr-x root/root         0 2016-10-24 02:43 ./usr/bin/
-rwxr-xr-x root/root    403768 2016-10-24 02:43 ./usr/bin/pbdagcon
drwxr-xr-x root/root         0 2016-10-24 02:43 ./usr/share/
drwxr-xr-x root/root         0 2016-10-24 02:43 ./usr/share/doc/
drwxr-xr-x root/root         0 2016-10-24 02:43 ./usr/share/doc/pbdagcon/
-rw-r--r-- root/root      2365 2016-03-25 14:00 ./usr/share/doc/pbdagcon/README.md.gz
-rw-r--r-- root/root       102 2016-10-24 02:40 ./usr/share/doc/pbdagcon/TODO.Debian
-rw-r--r-- root/root       565 2016-10-24 02:43 ./usr/share/doc/pbdagcon/changelog.Debian.gz
-rw-r--r-- root/root      3257 2016-10-24 02:42 ./usr/share/doc/pbdagcon/copyright
drwxr-xr-x root/root         0 2016-10-24 02:43 ./usr/share/doc/pbdagcon/examples/
-rwxr-xr-x root/root      1588 2016-03-25 14:00 ./usr/share/doc/pbdagcon/examples/filterm4.py
-rw-r--r-- root/root      2224 2016-03-25 14:00 ./usr/share/doc/pbdagcon/examples/m4topre.py.gz
-rwxr-xr-x root/root      1145 2016-03-25 14:00 ./usr/share/doc/pbdagcon/examples/pbdagcon_wf.sh
-rw-r--r-- root/root      1771 2016-03-25 14:00 ./usr/share/doc/pbdagcon/examples/q-sense.py.gz
drwxr-xr-x root/root         0 2016-10-24 02:43 ./usr/share/man/
drwxr-xr-x root/root         0 2016-10-24 02:43 ./usr/share/man/man1/
-rw-r--r-- root/root       775 2016-10-24 02:43 ./usr/share/man/man1/pbdagcon.1.gz


+------------------------------------------------------------------------------+
| Post Build                                                                   |
+------------------------------------------------------------------------------+


+------------------------------------------------------------------------------+
| Cleanup                                                                      |
+------------------------------------------------------------------------------+

Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use

+------------------------------------------------------------------------------+
| Summary                                                                      |
+------------------------------------------------------------------------------+

Build Architecture: armhf
Build-Space: 26276
Build-Time: 261
Distribution: stretch-staging
Host Architecture: armhf
Install-Time: 364
Job: pbdagcon_0~20160325+ds-1
Machine Architecture: armhf
Package: pbdagcon
Package-Time: 677
Source-Version: 0~20160325+ds-1
Space: 26276
Status: successful
Version: 0~20160325+ds-1
--------------------------------------------------------------------------------
Finished at 2016-11-01T00:24:12Z
Build needed 00:11:17, 26276k disc space