pbdagcon →
0.3+20161121+ds-1 →
armhf → 2017-02-01 00:43:02
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-02
+==============================================================================+
| pbdagcon 0.3+20161121+ds-1 (armhf) Wed, 01 Feb 2017 00:23:27 +0000 |
+==============================================================================+
Package: pbdagcon
Version: 0.3+20161121+ds-1
Source Version: 0.3+20161121+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-440d0824-4156-47e3-8442-8357b9e5213e' 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 [9728 kB]
Get:3 http://172.17.0.1/private stretch-staging/main armhf Packages [11.7 MB]
Fetched 21.4 MB in 23s (921 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 263 kB of source archives.
Get:1 http://172.17.0.1/private stretch-staging/main pbdagcon 0.3+20161121+ds-1 (dsc) [2097 B]
Get:2 http://172.17.0.1/private stretch-staging/main pbdagcon 0.3+20161121+ds-1 (tar) [256 kB]
Get:3 http://172.17.0.1/private stretch-staging/main pbdagcon 0.3+20161121+ds-1 (diff) [4872 B]
Fetched 263 kB in 0s (1759 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/pbdagcon-HMOu0Y/pbdagcon-0.3+20161121+ds' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/pbdagcon-HMOu0Y' 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-ii7dDo/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-ii7dDo/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-ii7dDo/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-ii7dDo/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-ii7dDo/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-ii7dDo/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-ii7dDo/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-ii7dDo/apt_archive ./ Packages [434 B]
Fetched 2110 B in 0s (3583 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
fuse2fs gnupg-l10n libfuse2 manpages
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 83 not upgraded.
Need to get 770 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-ii7dDo/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [770 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 770 B in 0s (0 B/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 13928 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper (>= 10), python, zlib1g-dev, libhdf5-dev, libboost-dev, libtclap-dev, libpbseq-dev, libpbbam-dev, googletest
Filtered Build-Depends: debhelper (>= 10), python, zlib1g-dev, libhdf5-dev, libboost-dev, libtclap-dev, libpbseq-dev, libpbbam-dev, googletest
dpkg-deb: building package 'sbuild-build-depends-pbdagcon-dummy' in '/<<BUILDDIR>>/resolver-ii7dDo/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-ii7dDo/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-ii7dDo/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-ii7dDo/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-ii7dDo/apt_archive ./ Sources [537 B]
Get:5 copy:/<<BUILDDIR>>/resolver-ii7dDo/apt_archive ./ Packages [620 B]
Fetched 2490 B in 0s (4181 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:
fuse2fs gnupg-l10n libfuse2 manpages
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev binutils bsdmainutils cpp-6
debhelper dh-autoreconf dh-strip-nondeterminism file g++-6 gcc-6 gcc-6-base
gettext gettext-base googletest groff-base hdf5-helpers intltool-debian
libaec-dev libaec0 libarchive-zip-perl libasan3 libatomic1 libblasr
libblasr-dev libboost-dev libboost1.62-dev libbsd0 libcc1-0 libcroco3
libcurl3-gnutls libexpat1 libffi6 libfile-stripnondeterminism-perl
libgcc-6-dev libgcc1 libgfortran3 libglib2.0-0 libgnutls30 libgomp1
libgssapi-krb5-2 libhdf5-100 libhdf5-cpp-100 libhdf5-dev libhogweed4
libhts-dev libhts1 libicu57 libidn2-0 libjpeg-dev libjpeg62-turbo
libjpeg62-turbo-dev libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0
libldap-2.4-2 libldap-common libmagic-mgc libmagic1 libnettle6 libnghttp2-14
libp11-kit0 libpbbam libpbbam-dev libpbdata libpbdata-dev libpbihdf
libpbihdf-dev libpbseq-dev libpipeline1 libpsl5 libpython-stdlib
libpython2.7-minimal libpython2.7-stdlib librtmp1 libsasl2-2
libsasl2-modules-db libsigsegv2 libssh2-1 libssl1.1 libstdc++-6-dev
libstdc++6 libsz2 libtasn1-6 libtclap-dev libtool libubsan0 libunistring0
libxml2 m4 man-db mime-support po-debconf python python-minimal python2.7
python2.7-minimal zlib1g zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc binutils-doc wamerican
| wordlist whois vacation gcc-6-locales dh-make gcc-6-doc libstdc++6-6-dbg
libgcc1-dbg libgomp1-dbg libitm1-dbg libatomic1-dbg libasan3-dbg
liblsan0-dbg libtsan0-dbg libubsan0-dbg libcilkrts5-dbg libmpx2-dbg
libquadmath0-dbg gettext-doc libasprintf-dev libgettextpo-dev groff
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-program-options1.62-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 gnutls-bin krb5-doc
krb5-user libhdf5-doc libstdc++-6-doc libtool-doc gfortran
| fortran95-compiler gcj-jdk m4-doc less www-browser libmail-box-perl
python-doc python-tk python2.7-doc binfmt-support
Recommended packages:
curl | wget | lynx-cur ca-certificates libglib2.0-data shared-mime-info
xdg-user-dirs krb5-locales publicsuffix libsasl2-modules 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 googletest
groff-base hdf5-helpers intltool-debian libaec-dev libaec0
libarchive-zip-perl libblasr libblasr-dev libboost-dev libboost1.62-dev
libbsd0 libcroco3 libcurl3-gnutls libexpat1 libffi6
libfile-stripnondeterminism-perl libgfortran3 libglib2.0-0 libgnutls30
libgssapi-krb5-2 libhdf5-100 libhdf5-cpp-100 libhdf5-dev libhogweed4
libhts-dev libhts1 libicu57 libidn2-0 libjpeg-dev libjpeg62-turbo
libjpeg62-turbo-dev libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0
libldap-2.4-2 libldap-common libmagic-mgc libmagic1 libnettle6 libnghttp2-14
libp11-kit0 libpbbam libpbbam-dev libpbdata libpbdata-dev libpbihdf
libpbihdf-dev libpbseq-dev libpipeline1 libpsl5 libpython-stdlib
libpython2.7-minimal libpython2.7-stdlib librtmp1 libsasl2-2
libsasl2-modules-db libsigsegv2 libssh2-1 libssl1.1 libsz2 libtasn1-6
libtclap-dev libtool libunistring0 libxml2 m4 man-db mime-support po-debconf
python python-minimal python2.7 python2.7-minimal
sbuild-build-depends-pbdagcon-dummy zlib1g-dev
The following packages will be upgraded:
binutils cpp-6 g++-6 gcc-6 gcc-6-base libasan3 libatomic1 libcc1-0
libgcc-6-dev libgcc1 libgomp1 libstdc++-6-dev libstdc++6 libubsan0 zlib1g
15 upgraded, 88 newly installed, 0 to remove and 68 not upgraded.
Need to get 66.1 MB/66.4 MB of archives.
After this operation, 251 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-ii7dDo/apt_archive ./ sbuild-build-depends-pbdagcon-dummy 0.invalid.0 [822 B]
Get:2 http://172.17.0.1/private stretch-staging/main armhf libgomp1 armhf 6.3.0-5+rpi1 [63.9 kB]
Get:3 http://172.17.0.1/private stretch-staging/main armhf gcc-6-base armhf 6.3.0-5+rpi1 [178 kB]
Get:4 http://172.17.0.1/private stretch-staging/main armhf libgcc1 armhf 1:6.3.0-5+rpi1 [38.3 kB]
Get:5 http://172.17.0.1/private stretch-staging/main armhf libcc1-0 armhf 6.3.0-5+rpi1 [24.9 kB]
Get:6 http://172.17.0.1/private stretch-staging/main armhf binutils armhf 2.27.90.20170124-2 [3605 kB]
Get:7 http://172.17.0.1/private stretch-staging/main armhf libatomic1 armhf 6.3.0-5+rpi1 [6838 B]
Get:8 http://172.17.0.1/private stretch-staging/main armhf libasan3 armhf 6.3.0-5+rpi1 [268 kB]
Get:9 http://172.17.0.1/private stretch-staging/main armhf libubsan0 armhf 6.3.0-5+rpi1 [91.6 kB]
Get:10 http://172.17.0.1/private stretch-staging/main armhf g++-6 armhf 6.3.0-5+rpi1 [5543 kB]
Get:11 http://172.17.0.1/private stretch-staging/main armhf libstdc++-6-dev armhf 6.3.0-5+rpi1 [1442 kB]
Get:12 http://172.17.0.1/private stretch-staging/main armhf libgcc-6-dev armhf 6.3.0-5+rpi1 [512 kB]
Get:13 http://172.17.0.1/private stretch-staging/main armhf gcc-6 armhf 6.3.0-5+rpi1 [5380 kB]
Get:14 http://172.17.0.1/private stretch-staging/main armhf cpp-6 armhf 6.3.0-5+rpi1 [5137 kB]
Get:15 http://172.17.0.1/private stretch-staging/main armhf libstdc++6 armhf 6.3.0-5+rpi1 [334 kB]
Get:16 http://172.17.0.1/private stretch-staging/main armhf zlib1g armhf 1:1.2.8.dfsg-4 [81.6 kB]
Get:17 http://172.17.0.1/private stretch-staging/main armhf groff-base armhf 1.22.3-9 [1005 kB]
Get:18 http://172.17.0.1/private stretch-staging/main armhf libbsd0 armhf 0.8.3-1 [89.0 kB]
Get:19 http://172.17.0.1/private stretch-staging/main armhf bsdmainutils armhf 9.0.12 [178 kB]
Get:20 http://172.17.0.1/private stretch-staging/main armhf libpipeline1 armhf 1.4.1-2 [23.7 kB]
Get:21 http://172.17.0.1/private stretch-staging/main armhf man-db armhf 2.7.6.1-2 [1014 kB]
Get:22 http://172.17.0.1/private stretch-staging/main armhf libpython2.7-minimal armhf 2.7.13-1 [389 kB]
Get:23 http://172.17.0.1/private stretch-staging/main armhf python2.7-minimal armhf 2.7.13-1 [1180 kB]
Get:24 http://172.17.0.1/private stretch-staging/main armhf python-minimal armhf 2.7.13-1 [40.5 kB]
Get:25 http://172.17.0.1/private stretch-staging/main armhf mime-support all 3.60 [36.7 kB]
Get:26 http://172.17.0.1/private stretch-staging/main armhf libexpat1 armhf 2.2.0-2 [62.2 kB]
Get:27 http://172.17.0.1/private stretch-staging/main armhf libssl1.1 armhf 1.1.0c-2 [1101 kB]
Get:28 http://172.17.0.1/private stretch-staging/main armhf libpython2.7-stdlib armhf 2.7.13-1 [1828 kB]
Get:29 http://172.17.0.1/private stretch-staging/main armhf python2.7 armhf 2.7.13-1 [285 kB]
Get:30 http://172.17.0.1/private stretch-staging/main armhf libpython-stdlib armhf 2.7.13-1 [19.9 kB]
Get:31 http://172.17.0.1/private stretch-staging/main armhf python armhf 2.7.13-1 [154 kB]
Get:32 http://172.17.0.1/private stretch-staging/main armhf libmagic-mgc armhf 1:5.29-2 [221 kB]
Get:33 http://172.17.0.1/private stretch-staging/main armhf libmagic1 armhf 1:5.29-2 [104 kB]
Get:34 http://172.17.0.1/private stretch-staging/main armhf file armhf 1:5.29-2 [63.1 kB]
Get:35 http://172.17.0.1/private stretch-staging/main armhf gettext-base armhf 0.19.8.1-1 [117 kB]
Get:36 http://172.17.0.1/private stretch-staging/main armhf libp11-kit0 armhf 0.23.3-2 [94.4 kB]
Get:37 http://172.17.0.1/private stretch-staging/main armhf libtasn1-6 armhf 4.10-1 [45.3 kB]
Get:38 http://172.17.0.1/private stretch-staging/main armhf libgnutls30 armhf 3.5.8-1 [823 kB]
Get:39 http://172.17.0.1/private stretch-staging/main armhf libkeyutils1 armhf 1.5.9-9 [11.9 kB]
Get:40 http://172.17.0.1/private stretch-staging/main armhf libkrb5support0 armhf 1.15-1 [57.9 kB]
Get:41 http://172.17.0.1/private stretch-staging/main armhf libk5crypto3 armhf 1.15-1 [115 kB]
Get:42 http://172.17.0.1/private stretch-staging/main armhf libkrb5-3 armhf 1.15-1 [262 kB]
Get:43 http://172.17.0.1/private stretch-staging/main armhf libgssapi-krb5-2 armhf 1.15-1 [132 kB]
Get:44 http://172.17.0.1/private stretch-staging/main armhf libsasl2-modules-db armhf 2.1.27~101-g0780600+dfsg-2 [66.8 kB]
Get:45 http://172.17.0.1/private stretch-staging/main armhf libsasl2-2 armhf 2.1.27~101-g0780600+dfsg-2 [98.0 kB]
Get:46 http://172.17.0.1/private stretch-staging/main armhf libldap-common all 2.4.44+dfsg-3 [84.5 kB]
Get:47 http://172.17.0.1/private stretch-staging/main armhf libldap-2.4-2 armhf 2.4.44+dfsg-3 [194 kB]
Get:48 http://172.17.0.1/private stretch-staging/main armhf libicu57 armhf 57.1-5 [7427 kB]
Get:49 http://172.17.0.1/private stretch-staging/main armhf libxml2 armhf 2.9.4+dfsg1-2.1 [804 kB]
Get:50 http://172.17.0.1/private stretch-staging/main armhf libsigsegv2 armhf 2.10-5 [28.4 kB]
Get:51 http://172.17.0.1/private stretch-staging/main armhf m4 armhf 1.4.18-1 [185 kB]
Get:52 http://172.17.0.1/private stretch-staging/main armhf autoconf all 2.69-10 [338 kB]
Get:53 http://172.17.0.1/private stretch-staging/main armhf autotools-dev all 20161112.1 [73.4 kB]
Get:54 http://172.17.0.1/private stretch-staging/main armhf automake all 1:1.15-5 [733 kB]
Get:55 http://172.17.0.1/private stretch-staging/main armhf autopoint all 0.19.8.1-1 [433 kB]
Get:56 http://172.17.0.1/private stretch-staging/main armhf libtool all 2.4.6-2 [545 kB]
Get:57 http://172.17.0.1/private stretch-staging/main armhf dh-autoreconf all 13 [15.8 kB]
Get:58 http://172.17.0.1/private stretch-staging/main armhf libarchive-zip-perl all 1.59-1 [95.5 kB]
Get:59 http://172.17.0.1/private stretch-staging/main armhf libfile-stripnondeterminism-perl all 0.029-2 [15.3 kB]
Get:60 http://172.17.0.1/private stretch-staging/main armhf dh-strip-nondeterminism all 0.029-2 [9330 B]
Get:61 http://172.17.0.1/private stretch-staging/main armhf libglib2.0-0 armhf 2.50.2-2 [2527 kB]
Get:62 http://172.17.0.1/private stretch-staging/main armhf libcroco3 armhf 0.6.11-2 [131 kB]
Get:63 http://172.17.0.1/private stretch-staging/main armhf libunistring0 armhf 0.9.6+really0.9.3-0.1 [252 kB]
Get:64 http://172.17.0.1/private stretch-staging/main armhf gettext armhf 0.19.8.1-1 [1433 kB]
Get:65 http://172.17.0.1/private stretch-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:66 http://172.17.0.1/private stretch-staging/main armhf po-debconf all 1.0.20 [247 kB]
Get:67 http://172.17.0.1/private stretch-staging/main armhf debhelper all 10.2.3 [829 kB]
Get:68 http://172.17.0.1/private stretch-staging/main armhf googletest armhf 1.8.0-5 [652 kB]
Get:69 http://172.17.0.1/private stretch-staging/main armhf hdf5-helpers armhf 1.10.0-patch1+docs-3 [35.9 kB]
Get:70 http://172.17.0.1/private stretch-staging/main armhf libaec0 armhf 0.3.2-1 [19.4 kB]
Get:71 http://172.17.0.1/private stretch-staging/main armhf libidn2-0 armhf 0.16-1 [59.3 kB]
Get:72 http://172.17.0.1/private stretch-staging/main armhf libnghttp2-14 armhf 1.18.1-1 [68.0 kB]
Get:73 http://172.17.0.1/private stretch-staging/main armhf libpsl5 armhf 0.16.1-1 [41.2 kB]
Get:74 http://172.17.0.1/private stretch-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-1 [54.2 kB]
Get:75 http://172.17.0.1/private stretch-staging/main armhf libssh2-1 armhf 1.7.0-1 [125 kB]
Get:76 http://172.17.0.1/private stretch-staging/main armhf libcurl3-gnutls armhf 7.52.1-1 [258 kB]
Get:77 http://172.17.0.1/private stretch-staging/main armhf libhts1 armhf 1.3.2-2+rpi1 [215 kB]
Get:78 http://172.17.0.1/private stretch-staging/main armhf libpbbam armhf 0.7.0-1+rpi1 [392 kB]
Get:79 http://172.17.0.1/private stretch-staging/main armhf libpbdata armhf 0~20161219-1 [106 kB]
Get:80 http://172.17.0.1/private stretch-staging/main armhf libgfortran3 armhf 6.3.0-5+rpi1 [166 kB]
Get:81 http://172.17.0.1/private stretch-staging/main armhf libsz2 armhf 0.3.2-1 [5836 B]
Get:82 http://172.17.0.1/private stretch-staging/main armhf libhdf5-100 armhf 1.10.0-patch1+docs-3 [1203 kB]
Get:83 http://172.17.0.1/private stretch-staging/main armhf libhdf5-cpp-100 armhf 1.10.0-patch1+docs-3 [118 kB]
Get:84 http://172.17.0.1/private stretch-staging/main armhf libpbihdf armhf 0~20161219-1 [141 kB]
Get:85 http://172.17.0.1/private stretch-staging/main armhf libblasr armhf 0~20161219-1 [828 kB]
Get:86 http://172.17.0.1/private stretch-staging/main armhf libblasr-dev armhf 0~20161219-1 [1672 kB]
Get:87 http://172.17.0.1/private stretch-staging/main armhf libboost1.62-dev armhf 1.62.0+dfsg-4 [7009 kB]
Get:88 http://172.17.0.1/private stretch-staging/main armhf libboost-dev armhf 1.62.0.1+b1 [3918 B]
Get:89 http://172.17.0.1/private stretch-staging/main armhf zlib1g-dev armhf 1:1.2.8.dfsg-4 [198 kB]
Get:90 http://172.17.0.1/private stretch-staging/main armhf libjpeg62-turbo armhf 1:1.5.1-2 [109 kB]
Get:91 http://172.17.0.1/private stretch-staging/main armhf libjpeg62-turbo-dev armhf 1:1.5.1-2 [181 kB]
Get:92 http://172.17.0.1/private stretch-staging/main armhf libjpeg-dev all 1:1.5.1-2 [56.1 kB]
Get:93 http://172.17.0.1/private stretch-staging/main armhf libaec-dev armhf 0.3.2-1 [17.6 kB]
Get:94 http://172.17.0.1/private stretch-staging/main armhf libhdf5-dev armhf 1.10.0-patch1+docs-3 [2093 kB]
Get:95 http://172.17.0.1/private stretch-staging/main armhf libhts-dev armhf 1.3.2-2+rpi1 [270 kB]
Get:96 http://172.17.0.1/private stretch-staging/main armhf libpbbam-dev armhf 0.7.0-1+rpi1 [88.5 kB]
Get:97 http://172.17.0.1/private stretch-staging/main armhf libpbdata-dev armhf 0~20161219-1 [178 kB]
Get:98 http://172.17.0.1/private stretch-staging/main armhf libpbihdf-dev armhf 0~20161219-1 [249 kB]
Get:99 http://172.17.0.1/private stretch-staging/main armhf libpbseq-dev all 0~20161219-1 [3902 B]
Get:100 http://172.17.0.1/private stretch-staging/main armhf libtclap-dev armhf 1.2.1-1 [727 kB]
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Setting up libcc1-0:armhf (6.3.0-5+rpi1) ...
Setting up libasan3:armhf (6.3.0-5+rpi1) ...
Setting up libjpeg62-turbo:armhf (1:1.5.1-2) ...
Setting up libarchive-zip-perl (1.59-1) ...
Setting up libnghttp2-14:armhf (1.18.1-1) ...
Setting up mime-support (3.60) ...
Setting up libboost1.62-dev:armhf (1.62.0+dfsg-4) ...
Setting up libsigsegv2:armhf (2.10-5) ...
Setting up libldap-common (2.4.44+dfsg-3) ...
Setting up libubsan0:armhf (6.3.0-5+rpi1) ...
Setting up libgfortran3:armhf (6.3.0-5+rpi1) ...
Setting up groff-base (1.22.3-9) ...
Setting up libsasl2-modules-db:armhf (2.1.27~101-g0780600+dfsg-2) ...
Setting up libsasl2-2:armhf (2.1.27~101-g0780600+dfsg-2) ...
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 (1.4.18-1) ...
Setting up libicu57:armhf (57.1-5) ...
Setting up libbsd0:armhf (0.8.3-1) ...
Setting up libxml2:armhf (2.9.4+dfsg1-2.1) ...
Setting up libtasn1-6:armhf (4.10-1) ...
Setting up libmagic-mgc (1:5.29-2) ...
Setting up libmagic1:armhf (1:5.29-2) ...
Setting up libhogweed4:armhf (3.3-1) ...
Setting up libssh2-1:armhf (1.7.0-1) ...
Processing triggers for libc-bin (2.24-7+rpi1) ...
Setting up autotools-dev (20161112.1) ...
Setting up libunistring0:armhf (0.9.6+really0.9.3-0.1) ...
Setting up libssl1.1:armhf (1.1.0c-2) ...
Setting up binutils (2.27.90.20170124-2) ...
Setting up libffi6:armhf (3.2.1-6) ...
Setting up cpp-6 (6.3.0-5+rpi1) ...
Setting up libboost-dev:armhf (1.62.0.1+b1) ...
Setting up libjpeg62-turbo-dev:armhf (1:1.5.1-2) ...
Setting up libkeyutils1:armhf (1.5.9-9) ...
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 hdf5-helpers (1.10.0-patch1+docs-3) ...
Setting up libpython2.7-stdlib:armhf (2.7.13-1) ...
Setting up autopoint (0.19.8.1-1) ...
Setting up libsz2:armhf (0.3.2-1) ...
Setting up zlib1g-dev:armhf (1:1.2.8.dfsg-4) ...
Setting up libfile-stripnondeterminism-perl (0.029-2) ...
Setting up libgcc-6-dev:armhf (6.3.0-5+rpi1) ...
Setting up libidn2-0:armhf (0.16-1) ...
Setting up libstdc++-6-dev:armhf (6.3.0-5+rpi1) ...
Setting up libhdf5-100:armhf (1.10.0-patch1+docs-3) ...
Setting up libpsl5:armhf (0.16.1-1) ...
Setting up libglib2.0-0:armhf (2.50.2-2) ...
No schema files found: doing nothing.
Setting up libaec-dev:armhf (0.3.2-1) ...
Setting up python2.7 (2.7.13-1) ...
Setting up autoconf (2.69-10) ...
Setting up file (1:5.29-2) ...
Setting up libkrb5support0:armhf (1.15-1) ...
Setting up gcc-6 (6.3.0-5+rpi1) ...
Setting up libcroco3:armhf (0.6.11-2) ...
Setting up g++-6 (6.3.0-5+rpi1) ...
Setting up libpython-stdlib:armhf (2.7.13-1) ...
Setting up libjpeg-dev (1:1.5.1-2) ...
Setting up libp11-kit0:armhf (0.23.3-2) ...
Setting up automake (1:1.15-5) ...
update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode
Setting up man-db (2.7.6.1-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up python (2.7.13-1) ...
Setting up libtool (2.4.6-2) ...
Setting up libk5crypto3:armhf (1.15-1) ...
Setting up libhdf5-cpp-100:armhf (1.10.0-patch1+docs-3) ...
Setting up gettext (0.19.8.1-1) ...
Setting up libgnutls30:armhf (3.5.8-1) ...
Setting up libhdf5-dev (1.10.0-patch1+docs-3) ...
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 librtmp1:armhf (2.4+20151223.gitfa8646d.1-1) ...
Setting up intltool-debian (0.35.0+20060710.4) ...
Setting up googletest:armhf (1.8.0-5) ...
Setting up libldap-2.4-2:armhf (2.4.44+dfsg-3) ...
Setting up libkrb5-3:armhf (1.15-1) ...
Setting up po-debconf (1.0.20) ...
Setting up libgssapi-krb5-2:armhf (1.15-1) ...
Setting up libcurl3-gnutls:armhf (7.52.1-1) ...
Setting up libhts1:armhf (1.3.2-2+rpi1) ...
Setting up libhts-dev:armhf (1.3.2-2+rpi1) ...
Setting up libpbbam:armhf (0.7.0-1+rpi1) ...
Setting up libpbbam-dev (0.7.0-1+rpi1) ...
Setting up libpbdata:armhf (0~20161219-1) ...
Setting up libpbihdf:armhf (0~20161219-1) ...
Setting up libblasr:armhf (0~20161219-1) ...
Setting up libpbihdf-dev:armhf (0~20161219-1) ...
Setting up libpbdata-dev:armhf (0~20161219-1) ...
Setting up libblasr-dev:armhf (0~20161219-1) ...
Setting up libpbseq-dev (0~20161219-1) ...
Setting up dh-autoreconf (13) ...
Setting up debhelper (10.2.3) ...
Setting up sbuild-build-depends-pbdagcon-dummy (0.invalid.0) ...
Setting up dh-strip-nondeterminism (0.029-2) ...
Processing triggers for libc-bin (2.24-7+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 3.19.0-trunk-armmp armhf (armv7l)
Toolchain package versions: binutils_2.27.90.20170124-2 dpkg-dev_1.18.15 g++-6_6.3.0-5+rpi1 gcc-6_6.3.0-5+rpi1 libc6-dev_2.24-7+rpi1 libstdc++-4.9-dev_4.9.3-14 libstdc++-6-dev_6.3.0-5+rpi1 libstdc++6_6.3.0-5+rpi1 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch
Package versions: acl_2.2.52-3 adduser_3.115 apt_1.4~beta1 autoconf_2.69-10 automake_1:1.15-5 autopoint_0.19.8.1-1 autotools-dev_20161112.1 base-files_9.7+rpi1 base-passwd_3.5.41 bash_4.4-2 binutils_2.27.90.20170124-2 bsdmainutils_9.0.12 bsdutils_1:2.29-1 build-essential_12.2 bzip2_1.0.6-8 coreutils_8.25-2 cpio_2.11+dfsg-6 cpp_4:6.1.1-1 cpp-6_6.3.0-5+rpi1 dash_0.5.8-2.3 debconf_1.5.59 debfoster_2.7-2.1 debhelper_10.2.3 debianutils_4.8.1 dh-autoreconf_13 dh-strip-nondeterminism_0.029-2 diffutils_1:3.5-1 dmsetup_2:1.02.136-1 dpkg_1.18.15 dpkg-dev_1.18.15 e2fslibs_1.43.3-1 e2fsprogs_1.43.3-1 fakeroot_1.21-2 file_1:5.29-2 findutils_4.6.0+git+20161106-1 fuse2fs_1.43.3-1 g++_4:6.1.1-1 g++-6_6.3.0-5+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_6.3.0-5+rpi1 gcc-6-base_6.3.0-5+rpi1 gettext_0.19.8.1-1 gettext-base_0.19.8.1-1 gnupg_2.1.16-2 gnupg-agent_2.1.16-2 gnupg-l10n_2.1.16-2 googletest_1.8.0-5 gpgv_2.1.16-2 grep_2.26-1 groff-base_1.22.3-9 gzip_1.6-5 hdf5-helpers_1.10.0-patch1+docs-3 hostname_3.18 init_1.46 init-system-helpers_1.46 initscripts_2.88dsf-59.8 insserv_1.14.0-5.4 intltool-debian_0.35.0+20060710.4 klibc-utils_2.0.4-9+rpi1 kmod_23-1 libacl1_2.2.52-3 libaec-dev_0.3.2-1 libaec0_0.3.2-1 libapparmor1_2.10.95-6 libapt-pkg4.12_1.0.9.10 libapt-pkg5.0_1.4~beta1 libarchive-zip-perl_1.59-1 libasan1_4.9.3-14 libasan3_6.3.0-5+rpi1 libassuan0_2.4.3-2 libatomic1_6.3.0-5+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.6.7-1 libaudit1_1:2.6.7-1 libblasr_0~20161219-1 libblasr-dev_0~20161219-1 libblkid1_2.29-1 libboost-dev_1.62.0.1+b1 libboost1.62-dev_1.62.0+dfsg-4 libbsd0_0.8.3-1 libbz2-1.0_1.0.6-8 libc-bin_2.24-7+rpi1 libc-dev-bin_2.24-7+rpi1 libc6_2.24-7+rpi1 libc6-dev_2.24-7+rpi1 libcap-ng0_0.7.7-3 libcap2_1:2.25-1 libcap2-bin_1:2.25-1 libcc1-0_6.3.0-5+rpi1 libcomerr2_1.43.3-1 libcroco3_0.6.11-2 libcryptsetup4_2:1.7.3-2 libcurl3-gnutls_7.52.1-1 libdb5.3_5.3.28-12 libdbus-1-3_1.10.14-1 libdebconfclient0_0.218 libdevmapper1.02.1_2:1.02.136-1 libdpkg-perl_1.18.15 libdrm2_2.4.74-1 libexpat1_2.2.0-2 libfakeroot_1.21-2 libfdisk1_2.29-1 libffi6_3.2.1-6 libfile-stripnondeterminism-perl_0.029-2 libfuse2_2.9.7-1 libgc1c2_1:7.4.2-8 libgcc-4.9-dev_4.9.3-14 libgcc-6-dev_6.3.0-5+rpi1 libgcc1_1:6.3.0-5+rpi1 libgcrypt20_1.7.3-2 libgdbm3_1.8.3-14 libgfortran3_6.3.0-5+rpi1 libglib2.0-0_2.50.2-2 libgmp10_2:6.1.1+dfsg-1 libgnutls30_3.5.8-1 libgomp1_6.3.0-5+rpi1 libgpg-error0_1.25-1 libgssapi-krb5-2_1.15-1 libhdf5-100_1.10.0-patch1+docs-3 libhdf5-cpp-100_1.10.0-patch1+docs-3 libhdf5-dev_1.10.0-patch1+docs-3 libhogweed4_3.3-1 libhts-dev_1.3.2-2+rpi1 libhts1_1.3.2-2+rpi1 libicu57_57.1-5 libidn11_1.33-1 libidn2-0_0.16-1 libip4tc0_1.6.0-4 libisl15_0.17.1-1 libjpeg-dev_1:1.5.1-2 libjpeg62-turbo_1:1.5.1-2 libjpeg62-turbo-dev_1:1.5.1-2 libk5crypto3_1.15-1 libkeyutils1_1.5.9-9 libklibc_2.0.4-9+rpi1 libkmod2_23-1 libkrb5-3_1.15-1 libkrb5support0_1.15-1 libksba8_1.3.5-2 libldap-2.4-2_2.4.44+dfsg-3 libldap-common_2.4.44+dfsg-3 liblz4-1_0.0~r131-2 liblzma5_5.2.2-1.2 libmagic-mgc_1:5.29-2 libmagic1_1:5.29-2 libmount1_2.29-1 libmpc3_1.0.3-1 libmpfr4_3.1.5-1 libncurses5_6.0+20160917-1 libncursesw5_6.0+20160917-1 libnettle6_3.3-1 libnghttp2-14_1.18.1-1 libnpth0_1.3-1 libp11-kit0_0.23.3-2 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 libpbbam_0.7.0-1+rpi1 libpbbam-dev_0.7.0-1+rpi1 libpbdata_0~20161219-1 libpbdata-dev_0~20161219-1 libpbihdf_0~20161219-1 libpbihdf-dev_0~20161219-1 libpbseq-dev_0~20161219-1 libpcre3_2:8.39-2 libperl5.24_5.24.1~rc4-1 libpipeline1_1.4.1-2 libpng12-0_1.2.54-6 libprocps3_2:3.3.9-9 libprocps6_2:3.3.12-3 libpsl5_0.16.1-1 libpython-stdlib_2.7.13-1 libpython2.7-minimal_2.7.13-1 libpython2.7-stdlib_2.7.13-1 libreadline7_7.0-1 librtmp1_2.4+20151223.gitfa8646d.1-1 libsasl2-2_2.1.27~101-g0780600+dfsg-2 libsasl2-modules-db_2.1.27~101-g0780600+dfsg-2 libseccomp2_2.3.1-2.1 libselinux1_2.6-3 libsemanage-common_2.6-1 libsemanage1_2.6-1 libsepol1_2.6-1 libsigsegv2_2.10-5 libslang2_2.3.1-5 libsmartcols1_2.29-1 libsqlite3-0_3.15.2-1 libss2_1.43.3-1 libssh2-1_1.7.0-1 libssl1.1_1.1.0c-2 libstdc++-4.9-dev_4.9.3-14 libstdc++-6-dev_6.3.0-5+rpi1 libstdc++6_6.3.0-5+rpi1 libsystemd0_232-6 libsz2_0.3.2-1 libtasn1-6_4.10-1 libtclap-dev_1.2.1-1 libtimedate-perl_2.3000-2 libtinfo5_6.0+20160917-1 libtool_2.4.6-2 libubsan0_6.3.0-5+rpi1 libudev1_232-6 libunistring0_0.9.6+really0.9.3-0.1 libusb-0.1-4_2:0.1.12-30 libustr-1.0-1_1.0.4-6 libuuid1_2.29-1 libxml2_2.9.4+dfsg1-2.1 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch login_1:4.2-3.3 lsb-base_9.20161125+rpi1 m4_1.4.18-1 make_4.1-9 makedev_2.3.1-93 man-db_2.7.6.1-2 manpages_4.08-1 mawk_1.3.3-17 mime-support_3.60 mount_2.29-1 multiarch-support_2.24-7+rpi1 nano_2.7.1-1 ncurses-base_6.0+20160917-1 ncurses-bin_6.0+20160917-1 passwd_1:4.2-3.3 patch_2.7.5-1 perl_5.24.1~rc4-1 perl-base_5.24.1~rc4-1 perl-modules-5.24_5.24.1~rc4-1 pinentry-curses_0.9.7-9 po-debconf_1.0.20 procps_2:3.3.12-3 python_2.7.13-1 python-minimal_2.7.13-1 python2.7_2.7.13-1 python2.7-minimal_2.7.13-1 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_232-6 systemd-sysv_232-6 sysv-rc_2.88dsf-59.8 sysvinit-utils_2.88dsf-59.8 tar_1.29b-1.1 tzdata_2016j-2 udev_232-6 util-linux_2.29-1 xz-utils_5.2.2-1.2 zlib1g_1:1.2.8.dfsg-4 zlib1g-dev_1:1.2.8.dfsg-4
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Wed Dec 21 09:25:57 2016 UTC
gpgv: using RSA key 59B2306F3AF9DDC1
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./pbdagcon_0.3+20161121+ds-1.dsc
dpkg-source: info: extracting pbdagcon in /<<BUILDDIR>>/pbdagcon-0.3+20161121+ds
dpkg-source: info: unpacking pbdagcon_0.3+20161121+ds.orig.tar.gz
dpkg-source: info: unpacking pbdagcon_0.3+20161121+ds-1.debian.tar.xz
dpkg-source: info: applying compiler-flags.patch
Check disc space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=stretch-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=stretch-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=stretch-staging-armhf-sbuild-440d0824-4156-47e3-8442-8357b9e5213e
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 0.3+20161121+ds-1
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build pbdagcon-0.3+20161121+ds
dpkg-buildpackage: info: host architecture armhf
fakeroot debian/rules clean
dh clean
dh_testdir
dh_auto_clean
make -j4 clean
make[1]: Entering directory '/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds'
make -C src/cpp clean
make[2]: Entering directory '/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/src/cpp'
rm -f *.d
rm -f *.o
rm -f pbdagcon
rm -f dazcon
make[2]: Leaving directory '/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/src/cpp'
make -C test/cpp clean
make[2]: Entering directory '/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/test/cpp'
rm -f .//*.o
rm -f *.o
rm -f test_*
make[2]: Leaving directory '/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/test/cpp'
make[1]: Leaving directory '/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds'
dh_autoreconf_clean
dh_clean
debian/rules build-arch
dh build-arch
dh_testdir -a
dh_update_autotools_config -a
dh_autoreconf -a
debian/rules override_dh_auto_configure
make[1]: Entering directory '/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds'
./configure.py --shared
uname -s
uname='Linux'
writing to '/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/defines.mk'
"""
DALIGNER_INCLUDE ?= ${DALIGNER_SRC}
DALIGNER_SRC ?= /<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DALIGNER
DAZZ_DB_INCLUDE ?= ${DAZZ_DB_SRC}
DAZZ_DB_SRC ?= /<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DAZZ_DB
GTEST_INCLUDE ?= /usr/src/googletest/googletest/include
GTEST_SRC ?= /usr/src/googletest/googletest/src
HDF5_LIB ?= /usr/lib/arm-linux-gnueabihf/hdf5/serial
HDF5_LIBFLAGS ?= -lhdf5_cpp -lhdf5
HTSLIB_LIBFLAGS ?= -lhts
LIBBLASR_INCLUDE ?= /usr/include/pbseq/alignment
LIBBLASR_LIBFLAGS ?= -lblasr
LIBPBDATA_INCLUDE ?= /usr/include/pbseq/pbdata
LIBPBDATA_LIBFLAGS ?= -lpbdata
LIBPBIHDF_INCLUDE ?= /usr/include/pbseq/hdf
LIBPBIHDF_LIBFLAGS ?= -lpbihdf
PBBAM_LIBFLAGS ?= -lpbbam
PTHREAD_LIBFLAGS ?= -lpthread
ZLIB_LIBFLAGS ?= -lz
LDLIBS+=-lrt
"""
make[1]: Leaving directory '/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds'
dh_auto_build -a
make -j4
make[1]: Entering directory '/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds'
make -C src/cpp
make[2]: Entering directory '/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/src/cpp'
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -Wall -Wuninitialized -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -I/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DAZZ_DB -I/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DALIGNER -I/usr/include/pbseq/alignment -I/usr/include/pbseq/pbdata -I/usr/include/pbseq/hdf -isystem.//third-party -c -o Alignment.o Alignment.cpp
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -Wall -Wuninitialized -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -I/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DAZZ_DB -I/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DALIGNER -I/usr/include/pbseq/alignment -I/usr/include/pbseq/pbdata -I/usr/include/pbseq/hdf -isystem.//third-party -c -o AlnGraphBoost.o AlnGraphBoost.cpp
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -Wall -Wuninitialized -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -I/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DAZZ_DB -I/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DALIGNER -I/usr/include/pbseq/alignment -I/usr/include/pbseq/pbdata -I/usr/include/pbseq/hdf -isystem.//third-party -c -o BlasrM5AlnProvider.o BlasrM5AlnProvider.cpp
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -Wall -Wuninitialized -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -I/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DAZZ_DB -I/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DALIGNER -I/usr/include/pbseq/alignment -I/usr/include/pbseq/pbdata -I/usr/include/pbseq/hdf -isystem.//third-party -c -o main.o main.cpp
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -Wall -Wuninitialized -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -I/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DAZZ_DB -I/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DALIGNER -I/usr/include/pbseq/alignment -I/usr/include/pbseq/pbdata -I/usr/include/pbseq/hdf -isystem.//third-party -c -o SimpleAligner.o SimpleAligner.cpp
cc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wextra -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -I/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DAZZ_DB -I/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DALIGNER -I/usr/include/pbseq/alignment -I/usr/include/pbseq/pbdata -I/usr/include/pbseq/hdf -isystem.//third-party -c -o DB.o /<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DAZZ_DB/DB.c
/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DAZZ_DB/DB.c: In function 'Load_QVs':
/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DAZZ_DB/DB.c:888:9: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(istub,DB_NFILE,&nfiles);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DAZZ_DB/DB.c:892:13: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
{ fscanf(istub,DB_FDATA,&last,fname,prolog);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DAZZ_DB/DB.c:897:13: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
{ fscanf(istub,DB_FDATA,&last,fname,prolog);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wextra -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -I/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DAZZ_DB -I/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DALIGNER -I/usr/include/pbseq/alignment -I/usr/include/pbseq/pbdata -I/usr/include/pbseq/hdf -isystem.//third-party -c -o QV.o /<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DAZZ_DB/QV.c
/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DAZZ_DB/QV.c: In function 'Build_Table':
/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DAZZ_DB/QV.c:127:23: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
{ uint64 symbol = (uint64) (node->lft);
^
/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DAZZ_DB/QV.c: In function 'Huffman':
/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DAZZ_DB/QV.c:174:33: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
node[value].lft = (HTree *) (uint64) i;
^
cc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wextra -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -I/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DAZZ_DB -I/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DALIGNER -I/usr/include/pbseq/alignment -I/usr/include/pbseq/pbdata -I/usr/include/pbseq/hdf -isystem.//third-party -c -o align.o /<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DALIGNER/align.c
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -Wall -Wuninitialized -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -I/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DAZZ_DB -I/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DALIGNER -I/usr/include/pbseq/alignment -I/usr/include/pbseq/pbdata -I/usr/include/pbseq/hdf -isystem.//third-party -c -o DazAlnProvider.o DazAlnProvider.cpp
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -Wall -Wuninitialized -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -I/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DAZZ_DB -I/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DALIGNER -I/usr/include/pbseq/alignment -I/usr/include/pbseq/pbdata -I/usr/include/pbseq/hdf -isystem.//third-party -c -o dazcon.o dazcon.cpp
g++ -o pbdagcon Alignment.o AlnGraphBoost.o BlasrM5AlnProvider.o main.o SimpleAligner.o -Wl,-z,relro -L /usr/lib/arm-linux-gnueabihf/hdf5/serial -lrt -lblasr -lpbdata -lpbihdf -lpbbam -lhdf5_cpp -lhdf5 -lhts -lz -lpthread
g++ -o dazcon Alignment.o AlnGraphBoost.o DB.o QV.o align.o DazAlnProvider.o dazcon.o -Wl,-z,relro -L /usr/lib/arm-linux-gnueabihf/hdf5/serial -lrt -lblasr -lpbdata -lpbihdf -lpbbam -lhdf5_cpp -lhdf5 -lhts -lz -lpthread
make[2]: Leaving directory '/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/src/cpp'
make[1]: Leaving directory '/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds'
dh_auto_test -a
make -j4 check
make[1]: Entering directory '/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds'
make -C src/cpp
make[2]: Entering directory '/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/src/cpp'
make[2]: Nothing to be done for 'all'.
make[2]: Leaving directory '/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/src/cpp'
make -C test/cpp
make[2]: Entering directory '/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/test/cpp'
g++ -O3 -std=c++11 -g -Wall -Wextra -pthread -Wdate-time -D_FORTIFY_SOURCE=2 -I. -I./ -I.//../../src/cpp -I/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DAZZ_DB -I/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DALIGNER -I/usr/include/pbseq/alignment -I/usr/include/pbseq/pbdata -I/usr/include/pbseq/hdf -I/usr/src/googletest/googletest/include -Ithird-party -isystem /usr/src/googletest/googletest/include -isystem /usr/src/googletest/googletest/src/.. -c -o gtest-all.o /usr/src/googletest/googletest/src/gtest-all.cc
g++ -O3 -std=c++11 -g -Wall -Wextra -pthread -Wdate-time -D_FORTIFY_SOURCE=2 -I. -I./ -I.//../../src/cpp -I/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DAZZ_DB -I/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DALIGNER -I/usr/include/pbseq/alignment -I/usr/include/pbseq/pbdata -I/usr/include/pbseq/hdf -I/usr/src/googletest/googletest/include -Ithird-party -isystem /usr/src/googletest/googletest/include -isystem /usr/src/googletest/googletest/src/.. -c -o gtest_main.o /usr/src/googletest/googletest/src/gtest_main.cc
g++ -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I. -I./ -I.//../../src/cpp -I/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DAZZ_DB -I/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DALIGNER -I/usr/include/pbseq/alignment -I/usr/include/pbseq/pbdata -I/usr/include/pbseq/hdf -I/usr/src/googletest/googletest/include -Ithird-party -c -o AlnGraphBoost.o .//../../src/cpp/AlnGraphBoost.cpp
g++ -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I. -I./ -I.//../../src/cpp -I/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DAZZ_DB -I/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DALIGNER -I/usr/include/pbseq/alignment -I/usr/include/pbseq/pbdata -I/usr/include/pbseq/hdf -I/usr/src/googletest/googletest/include -Ithird-party -c -o Alignment.o .//../../src/cpp/Alignment.cpp
g++ -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I. -I./ -I.//../../src/cpp -I/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DAZZ_DB -I/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DALIGNER -I/usr/include/pbseq/alignment -I/usr/include/pbseq/pbdata -I/usr/include/pbseq/hdf -I/usr/src/googletest/googletest/include -Ithird-party -c -o SimpleAligner.o .//../../src/cpp/SimpleAligner.cpp
g++ -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I. -I./ -I.//../../src/cpp -I/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DAZZ_DB -I/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DALIGNER -I/usr/include/pbseq/alignment -I/usr/include/pbseq/pbdata -I/usr/include/pbseq/hdf -I/usr/src/googletest/googletest/include -Ithird-party -c -o AlnGraphBoostTest.o AlnGraphBoostTest.cpp
mkdir xml
g++ -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I. -I./ -I.//../../src/cpp -I/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DAZZ_DB -I/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DALIGNER -I/usr/include/pbseq/alignment -I/usr/include/pbseq/pbdata -I/usr/include/pbseq/hdf -I/usr/src/googletest/googletest/include -Ithird-party -c -o AlignmentTest.o AlignmentTest.cpp
g++ -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I. -I./ -I.//../../src/cpp -I/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DAZZ_DB -I/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DALIGNER -I/usr/include/pbseq/alignment -I/usr/include/pbseq/pbdata -I/usr/include/pbseq/hdf -I/usr/src/googletest/googletest/include -Ithird-party -c -o SimpleAlignerTest.o SimpleAlignerTest.cpp
cc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I. -I./ -I.//../../src/cpp -I/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DAZZ_DB -I/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DALIGNER -I/usr/include/pbseq/alignment -I/usr/include/pbseq/pbdata -I/usr/include/pbseq/hdf -I/usr/src/googletest/googletest/include -Ithird-party -c -o DB.o /<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DAZZ_DB/DB.c
/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DAZZ_DB/DB.c: In function 'Load_QVs':
/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DAZZ_DB/DB.c:888:9: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(istub,DB_NFILE,&nfiles);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DAZZ_DB/DB.c:892:13: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
{ fscanf(istub,DB_FDATA,&last,fname,prolog);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DAZZ_DB/DB.c:897:13: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
{ fscanf(istub,DB_FDATA,&last,fname,prolog);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I. -I./ -I.//../../src/cpp -I/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DAZZ_DB -I/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DALIGNER -I/usr/include/pbseq/alignment -I/usr/include/pbseq/pbdata -I/usr/include/pbseq/hdf -I/usr/src/googletest/googletest/include -Ithird-party -c -o QV.o /<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DAZZ_DB/QV.c
/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DAZZ_DB/QV.c: In function 'Build_Table':
/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DAZZ_DB/QV.c:127:23: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
{ uint64 symbol = (uint64) (node->lft);
^
/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DAZZ_DB/QV.c: In function 'Huffman':
/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DAZZ_DB/QV.c:174:33: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
node[value].lft = (HTree *) (uint64) i;
^
cc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I. -I./ -I.//../../src/cpp -I/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DAZZ_DB -I/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DALIGNER -I/usr/include/pbseq/alignment -I/usr/include/pbseq/pbdata -I/usr/include/pbseq/hdf -I/usr/src/googletest/googletest/include -Ithird-party -c -o align.o /<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DALIGNER/align.c
g++ -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I. -I./ -I.//../../src/cpp -I/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DAZZ_DB -I/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DALIGNER -I/usr/include/pbseq/alignment -I/usr/include/pbseq/pbdata -I/usr/include/pbseq/hdf -I/usr/src/googletest/googletest/include -Ithird-party -c -o DazAlnProvider.o .//../../src/cpp/DazAlnProvider.cpp
g++ -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I. -I./ -I.//../../src/cpp -I/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DAZZ_DB -I/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DALIGNER -I/usr/include/pbseq/alignment -I/usr/include/pbseq/pbdata -I/usr/include/pbseq/hdf -I/usr/src/googletest/googletest/include -Ithird-party -c -o TargetHitTest.o TargetHitTest.cpp
g++ -o test-alngraph gtest-all.o gtest_main.o AlnGraphBoost.o Alignment.o SimpleAligner.o AlnGraphBoostTest.o -Wl,-z,relro -L /usr/lib/arm-linux-gnueabihf/hdf5/serial -lrt -lblasr -lpbdata -lpbihdf -lpbbam -lhdf5_cpp -lhdf5 -lhts -lz -lpthread
g++ -o test-alignment gtest-all.o gtest_main.o AlnGraphBoost.o Alignment.o SimpleAligner.o AlignmentTest.o -Wl,-z,relro -L /usr/lib/arm-linux-gnueabihf/hdf5/serial -lrt -lblasr -lpbdata -lpbihdf -lpbbam -lhdf5_cpp -lhdf5 -lhts -lz -lpthread
g++ -o test-simple_aligner gtest-all.o gtest_main.o AlnGraphBoost.o Alignment.o SimpleAligner.o SimpleAlignerTest.o -Wl,-z,relro -L /usr/lib/arm-linux-gnueabihf/hdf5/serial -lrt -lblasr -lpbdata -lpbihdf -lpbbam -lhdf5_cpp -lhdf5 -lhts -lz -lpthread
LD_LIBRARY_PATH=::::/usr/lib/arm-linux-gnueabihf/hdf5/serial:::: PBDAGCON_TEST_DATA_DIR=./ ./test-alngraph --gtest_output=xml:xml/test-alngraph.xml
Running main() from gtest_main.cc
[==========] Running 2 tests from 1 test case.
[----------] Global test environment set-up.
[----------] 2 tests from AlnGraphBoostTest
[ RUN ] AlnGraphBoostTest.RawConsensus
[ OK ] AlnGraphBoostTest.RawConsensus (1 ms)
[ RUN ] AlnGraphBoostTest.DanglingNodes
[ OK ] AlnGraphBoostTest.DanglingNodes (0 ms)
[----------] 2 tests from AlnGraphBoostTest (3 ms total)
[----------] Global test environment tear-down
[==========] 2 tests from 1 test case ran. (7 ms total)
[ PASSED ] 2 tests.
LD_LIBRARY_PATH=::::/usr/lib/arm-linux-gnueabihf/hdf5/serial:::: PBDAGCON_TEST_DATA_DIR=./ ./test-alignment --gtest_output=xml:xml/test-alignment.xml
LD_LIBRARY_PATH=::::/usr/lib/arm-linux-gnueabihf/hdf5/serial:::: PBDAGCON_TEST_DATA_DIR=./ ./test-simple_aligner --gtest_output=xml:xml/test-simple_aligner.xml
Running main() from gtest_main.cc
[==========] Running 4 tests from 1 test case.
[----------] Global test environment set-up.
[----------] 4 tests from Alignment
[ RUN ] Alignment.Normalize
[ OK ] Alignment.Normalize (1 ms)
[ RUN ] Alignment.ParseBasic
[ OK ] Alignment.ParseBasic (1 ms)
[ RUN ] Alignment.ParseQuery
[ OK ] Alignment.ParseQuery (9 ms)
[ RUN ] Alignment.Trim
[ OK ] Alignment.Trim (0 ms)
[----------] 4 tests from Alignment (15 ms total)
[----------] Global test environment tear-down
[==========] 4 tests from 1 test case ran. (18 ms total)
[ PASSED ] 4 tests.
Running main() from gtest_main.cc
[==========] Running 1 test from 1 test case.
[----------] Global test environment set-up.
[----------] 1 test from SimpleAligner
[ RUN ] SimpleAligner.align
[ OK ] SimpleAligner.align (2 ms)
[----------] 1 test from SimpleAligner (3 ms total)
[----------] Global test environment tear-down
[==========] 1 test from 1 test case ran. (3 ms total)
[ PASSED ] 1 test.
g++ -o test-target_hit gtest-all.o gtest_main.o DB.o QV.o align.o Alignment.o DazAlnProvider.o TargetHitTest.o -Wl,-z,relro -L /usr/lib/arm-linux-gnueabihf/hdf5/serial -lrt -lblasr -lpbdata -lpbihdf -lpbbam -lhdf5_cpp -lhdf5 -lhts -lz -lpthread
LD_LIBRARY_PATH=::::/usr/lib/arm-linux-gnueabihf/hdf5/serial:::: PBDAGCON_TEST_DATA_DIR=./ ./test-target_hit --gtest_output=xml:xml/test-target_hit.xml
Running main() from gtest_main.cc
[==========] Running 3 tests from 1 test case.
[----------] Global test environment set-up.
[----------] 3 tests from TargetHitTest
[ RUN ] TargetHitTest.single_overlap_perfect
[ OK ] TargetHitTest.single_overlap_perfect (0 ms)
[ RUN ] TargetHitTest.single_overlap_inaccurate
[ OK ] TargetHitTest.single_overlap_inaccurate (0 ms)
[ RUN ] TargetHitTest.multi_overlap_inaccurate
[ OK ] TargetHitTest.multi_overlap_inaccurate (0 ms)
[----------] 3 tests from TargetHitTest (3 ms total)
[----------] Global test environment tear-down
[==========] 3 tests from 1 test case ran. (6 ms total)
[ PASSED ] 3 tests.
make[2]: Leaving directory '/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/test/cpp'
make[1]: Leaving directory '/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds'
fakeroot debian/rules binary-arch
dh binary-arch
dh_testroot -a
dh_prep -a
dh_auto_install -a
dh_install -a
dh_installdocs -a
dh_installchangelogs -a
dh_installexamples -a
dh_installman -a
dh_perl -a
dh_link -a
dh_strip_nondeterminism -a
dh_compress -a
dh_fixperms -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dpkg-shlibdeps: warning: 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: can't extract name and version from library name 'libpbbam.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbbam.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbihdf.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbihdf.so'
dpkg-shlibdeps: warning: debian/pbdagcon/usr/bin/dazcon contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
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: 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 'libpbihdf.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbihdf.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbbam.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbbam.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/dazcon debian/pbdagcon/usr/bin/pbdagcon were not linked against libhdf5_serial.so.100 (they use none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/pbdagcon/usr/bin/dazcon debian/pbdagcon/usr/bin/pbdagcon 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/pbdagcon/usr/bin/dazcon debian/pbdagcon/usr/bin/pbdagcon were not linked against libhdf5_cpp.so.100 (they use none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/pbdagcon/usr/bin/dazcon debian/pbdagcon/usr/bin/pbdagcon were not linked against librt.so.1 (they use none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/pbdagcon/usr/bin/dazcon debian/pbdagcon/usr/bin/pbdagcon were not linked against libhts.so.1 (they use none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/pbdagcon/usr/bin/dazcon debian/pbdagcon/usr/bin/pbdagcon were not linked against ld-linux-armhf.so.3 (they use none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/pbdagcon/usr/bin/dazcon debian/pbdagcon/usr/bin/pbdagcon were not linked against libpbihdf.so (they use none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/pbdagcon/usr/bin/dazcon debian/pbdagcon/usr/bin/pbdagcon were not linked against libpbbam.so (they use none of the library's symbols)
dh_installdeb -a
dh_gencontrol -a
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package 'pbdagcon-dbgsym' in '../pbdagcon-dbgsym_0.3+20161121+ds-1_armhf.deb'.
dpkg-deb: building package 'pbdagcon' in '../pbdagcon_0.3+20161121+ds-1_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genbuildinfo: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../pbdagcon_0.3+20161121+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-0.3+20161121+ds
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2017-02-01T00:42:45Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
pbdagcon_0.3+20161121+ds-1_armhf.changes:
-----------------------------------------
Format: 1.8
Date: Wed, 21 Dec 2016 01:18:19 -0800
Source: pbdagcon
Binary: pbdagcon
Architecture: armhf
Version: 0.3+20161121+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
Closes: 848755
Changes:
pbdagcon (0.3+20161121+ds-1) unstable; urgency=medium
.
* New upstream revision (upstream git 87f393f)
* Include repository's submodules
* Base package versioning on program versions indicated in the source code
* Build with pbbam (Closes: #848755)
* Use pbseqlib metapackages as dependencies
* Build dazcon
* Activate build-time tests
* Use debhelper compat 10
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Checksums-Sha256:
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c4c77e144c1a177b4daf577d9998b45fd90f3fb639519464b0237102325059b2 6378 pbdagcon_0.3+20161121+ds-1_armhf.buildinfo
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Files:
abaeb477c0ab85ed764d5cba66f5ab06 4234098 debug extra pbdagcon-dbgsym_0.3+20161121+ds-1_armhf.deb
b47078ce0a110ee3f3d25d60ae7303cf 6378 science optional pbdagcon_0.3+20161121+ds-1_armhf.buildinfo
3fc193cb4f6c7ec049c1d2efe2b457de 243424 science optional pbdagcon_0.3+20161121+ds-1_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
pbdagcon-dbgsym_0.3+20161121+ds-1_armhf.deb
-------------------------------------------
new debian package, version 2.0.
size 4234098 bytes: control archive=558 bytes.
490 bytes, 13 lines control
212 bytes, 2 lines md5sums
Package: pbdagcon-dbgsym
Source: pbdagcon
Version: 0.3+20161121+ds-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 4475
Depends: pbdagcon (= 0.3+20161121+ds-1)
Section: debug
Priority: extra
Homepage: https://github.com/PacificBiosciences/pbdagcon
Description: Debug symbols for pbdagcon
Auto-Built-Package: debug-symbols
Build-Ids: 221ff40d74a1f485a045dc8e2411f46bddc80e80 55ace28ee36e2c77d64cee3f2d767c28c8a53dfa
drwxr-xr-x root/root 0 2016-12-21 09:18 ./
drwxr-xr-x root/root 0 2016-12-21 09:18 ./usr/
drwxr-xr-x root/root 0 2016-12-21 09:18 ./usr/lib/
drwxr-xr-x root/root 0 2016-12-21 09:18 ./usr/lib/debug/
drwxr-xr-x root/root 0 2016-12-21 09:18 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2016-12-21 09:18 ./usr/lib/debug/.build-id/22/
-rw-r--r-- root/root 2206112 2016-12-21 09:18 ./usr/lib/debug/.build-id/22/1ff40d74a1f485a045dc8e2411f46bddc80e80.debug
drwxr-xr-x root/root 0 2016-12-21 09:18 ./usr/lib/debug/.build-id/55/
-rw-r--r-- root/root 2363440 2016-12-21 09:18 ./usr/lib/debug/.build-id/55/ace28ee36e2c77d64cee3f2d767c28c8a53dfa.debug
drwxr-xr-x root/root 0 2016-12-21 09:18 ./usr/share/
drwxr-xr-x root/root 0 2016-12-21 09:18 ./usr/share/doc/
lrwxrwxrwx root/root 0 2016-12-21 09:18 ./usr/share/doc/pbdagcon-dbgsym -> pbdagcon
pbdagcon_0.3+20161121+ds-1_armhf.deb
------------------------------------
new debian package, version 2.0.
size 243424 bytes: control archive=1367 bytes.
1675 bytes, 30 lines control
700 bytes, 10 lines md5sums
Package: pbdagcon
Version: 0.3+20161121+ds-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 875
Depends: libc6 (>= 2.7), libgcc1 (>= 1:3.5), libhdf5-100, libhdf5-cpp-100 (>= 1.8.13), libhts1 (>= 1.0), libstdc++6 (>= 6), zlib1g (>= 1:1.1.4), libpbseq, libpbbam
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 2016-12-21 09:18 ./
drwxr-xr-x root/root 0 2016-12-21 09:18 ./usr/
drwxr-xr-x root/root 0 2016-12-21 09:18 ./usr/bin/
-rwxr-xr-x root/root 457084 2016-12-21 09:18 ./usr/bin/dazcon
-rwxr-xr-x root/root 407920 2016-12-21 09:18 ./usr/bin/pbdagcon
drwxr-xr-x root/root 0 2016-12-21 09:18 ./usr/share/
drwxr-xr-x root/root 0 2016-12-21 09:18 ./usr/share/doc/
drwxr-xr-x root/root 0 2016-12-21 09:18 ./usr/share/doc/pbdagcon/
-rw-r--r-- root/root 2365 2016-12-21 05:55 ./usr/share/doc/pbdagcon/README.md.gz
-rw-r--r-- root/root 733 2016-12-21 09:18 ./usr/share/doc/pbdagcon/changelog.Debian.gz
-rw-r--r-- root/root 4729 2016-12-21 09:17 ./usr/share/doc/pbdagcon/copyright
drwxr-xr-x root/root 0 2016-12-21 09:18 ./usr/share/doc/pbdagcon/examples/
-rwxr-xr-x root/root 1588 2016-12-21 05:55 ./usr/share/doc/pbdagcon/examples/filterm4.py
-rw-r--r-- root/root 2224 2016-12-21 05:55 ./usr/share/doc/pbdagcon/examples/m4topre.py.gz
-rwxr-xr-x root/root 1145 2016-12-21 05:55 ./usr/share/doc/pbdagcon/examples/pbdagcon_wf.sh
-rw-r--r-- root/root 1771 2016-12-21 05:55 ./usr/share/doc/pbdagcon/examples/q-sense.py.gz
drwxr-xr-x root/root 0 2016-12-21 09:18 ./usr/share/man/
drwxr-xr-x root/root 0 2016-12-21 09:18 ./usr/share/man/man1/
-rw-r--r-- root/root 775 2016-12-21 09:18 ./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: 61300
Build-Time: 496
Distribution: stretch-staging
Host Architecture: armhf
Install-Time: 615
Job: pbdagcon_0.3+20161121+ds-1
Machine Architecture: armhf
Package: pbdagcon
Package-Time: 1158
Source-Version: 0.3+20161121+ds-1
Space: 61300
Status: successful
Version: 0.3+20161121+ds-1
--------------------------------------------------------------------------------
Finished at 2017-02-01T00:42:45Z
Build needed 00:19:18, 61300k disc space