pbdagcon →
0~20151114+git1d12e13+ds-2 →
armhf → 2016-01-28 11:04:21
sbuild (Debian sbuild) 0.65.2 (24 Mar 2015) on bm-wb-04
╔══════════════════════════════════════════════════════════════════════════════╗
║ pbdagcon 0~20151114+git1d12e13+ds-2 (armhf) 28 Jan 2016 10:51 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: pbdagcon
Version: 0~20151114+git1d12e13+ds-2
Source Version: 0~20151114+git1d12e13+ds-2
Distribution: stretch-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'build/pbdagcon-yNHIJc/pbdagcon-0~20151114+git1d12e13+ds' with '«PKGBUILDDIR»'
I: NOTICE: Log filtering will replace 'build/pbdagcon-yNHIJc' with '«BUILDDIR»'
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/stretch-staging-armhf-sbuild-aba28019-d504-4fb6-b9f3-ca752abce556' 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 [8644 kB]
Get:3 http://172.17.0.1/private stretch-staging/main armhf Packages [10.7 MB]
Fetched 19.4 MB in 21s (901 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...
Building dependency tree...
Reading state information...
NOTICE: 'pbdagcon' packaging is maintained in the 'Git' version control system at:
git://anonscm.debian.org/debian-med/pbdagcon.git
Please use:
git clone git://anonscm.debian.org/debian-med/pbdagcon.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 110 kB of source archives.
Get:1 http://172.17.0.1/private stretch-staging/main pbdagcon 0~20151114+git1d12e13+ds-2 (dsc) [2139 B]
Get:2 http://172.17.0.1/private stretch-staging/main pbdagcon 0~20151114+git1d12e13+ds-2 (tar) [103 kB]
Get:3 http://172.17.0.1/private stretch-staging/main pbdagcon 0~20151114+git1d12e13+ds-2 (diff) [5224 B]
Fetched 110 kB in 0s (4286 kB/s)
Download complete and in download only mode
Check architectures
───────────────────
Check dependencies
──────────────────
Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/«BUILDDIR»/resolver-ZAzkn0/apt_archive/sbuild-build-depends-core-dummy.deb'.
OK
Get:1 file:/«BUILDDIR»/resolver-ZAzkn0/apt_archive ./ InRelease
Ign:1 file:/«BUILDDIR»/resolver-ZAzkn0/apt_archive ./ InRelease
Get:2 file:/«BUILDDIR»/resolver-ZAzkn0/apt_archive ./ Release [2119 B]
Get:2 file:/«BUILDDIR»/resolver-ZAzkn0/apt_archive ./ Release [2119 B]
Get:3 file:/«BUILDDIR»/resolver-ZAzkn0/apt_archive ./ Release.gpg [299 B]
Get:3 file:/«BUILDDIR»/resolver-ZAzkn0/apt_archive ./ Release.gpg [299 B]
Get:4 file:/«BUILDDIR»/resolver-ZAzkn0/apt_archive ./ Sources [208 B]
Get:5 file:/«BUILDDIR»/resolver-ZAzkn0/apt_archive ./ Packages [526 B]
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 NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 7 not upgraded.
Need to get 0 B/768 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 file:/«BUILDDIR»/resolver-ZAzkn0/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [768 B]
debconf: delaying package configuration, since apt-utils is not installed
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ...
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 13613 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy.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
Merged Build-Depends: libc6-dev | libc-dev, gcc (>= 4:4.9.1), g++ (>= 4:4.9.1), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), libboost-dev, libtclap-dev, libpbdata-dev, libblasr-dev, libpbihdf-dev, libgtest-dev
Filtered Build-Depends: libc6-dev, gcc (>= 4:4.9.1), g++ (>= 4:4.9.1), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), libboost-dev, libtclap-dev, libpbdata-dev, libblasr-dev, libpbihdf-dev, libgtest-dev
dpkg-deb: building package 'sbuild-build-depends-pbdagcon-dummy' in '/«BUILDDIR»/resolver-LqmS5h/apt_archive/sbuild-build-depends-pbdagcon-dummy.deb'.
OK
Get:1 file:/«BUILDDIR»/resolver-LqmS5h/apt_archive ./ InRelease
Ign:1 file:/«BUILDDIR»/resolver-LqmS5h/apt_archive ./ InRelease
Get:2 file:/«BUILDDIR»/resolver-LqmS5h/apt_archive ./ Release [2119 B]
Get:2 file:/«BUILDDIR»/resolver-LqmS5h/apt_archive ./ Release [2119 B]
Get:3 file:/«BUILDDIR»/resolver-LqmS5h/apt_archive ./ Release.gpg [299 B]
Get:3 file:/«BUILDDIR»/resolver-LqmS5h/apt_archive ./ Release.gpg [299 B]
Get:4 file:/«BUILDDIR»/resolver-LqmS5h/apt_archive ./ Sources [346 B]
Get:5 file:/«BUILDDIR»/resolver-LqmS5h/apt_archive ./ Packages [603 B]
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 additional packages will be installed:
autotools-dev bsdmainutils debhelper dh-strip-nondeterminism file gettext
gettext-base groff-base intltool-debian libarchive-zip-perl libblasr
libblasr-dev libboost-dev libboost1.58-dev libcroco3 libffi6
libfile-stripnondeterminism-perl libgfortran3 libglib2.0-0 libgtest-dev
libhdf5-10 libhdf5-cpp-11 libicu55 libmagic1 libpbdata libpbdata-dev
libpbihdf libpbihdf-dev libpipeline1 libtclap-dev libunistring0 libxml2
man-db po-debconf
Suggested packages:
wamerican | wordlist whois vacation dh-make gettext-doc autopoint
libasprintf-dev libgettextpo-dev groff libboost-doc libboost1.58-doc
libboost-atomic1.58-dev libboost-chrono1.58-dev libboost-context1.58-dev
libboost-coroutine1.58-dev libboost-date-time1.58-dev
libboost-exception1.58-dev libboost-filesystem1.58-dev
libboost-graph1.58-dev libboost-graph-parallel1.58-dev
libboost-iostreams1.58-dev libboost-locale1.58-dev libboost-log1.58-dev
libboost-math1.58-dev libboost-mpi1.58-dev libboost-mpi-python1.58-dev
libboost-program-options1.58-dev libboost-python1.58-dev
libboost-random1.58-dev libboost-regex1.58-dev
libboost-serialization1.58-dev libboost-signals1.58-dev
libboost-system1.58-dev libboost-test1.58-dev libboost-thread1.58-dev
libboost-timer1.58-dev libboost-wave1.58-dev libboost1.58-tools-dev
libmpfrc++-dev libntl-dev less www-browser libmail-box-perl
Recommended packages:
curl | wget | lynx-cur libglib2.0-data shared-mime-info xdg-user-dirs
xml-core libmail-sendmail-perl
The following NEW packages will be installed:
autotools-dev bsdmainutils debhelper dh-strip-nondeterminism file gettext
gettext-base groff-base intltool-debian libarchive-zip-perl libblasr
libblasr-dev libboost-dev libboost1.58-dev libcroco3 libffi6
libfile-stripnondeterminism-perl libgfortran3 libglib2.0-0 libgtest-dev
libhdf5-10 libhdf5-cpp-11 libicu55 libmagic1 libpbdata libpbdata-dev
libpbihdf libpbihdf-dev libpipeline1 libtclap-dev libunistring0 libxml2
man-db po-debconf sbuild-build-depends-pbdagcon-dummy
0 upgraded, 35 newly installed, 0 to remove and 7 not upgraded.
Need to get 27.8 MB/27.8 MB of archives.
After this operation, 185 MB of additional disk space will be used.
Get:1 file:/«BUILDDIR»/resolver-LqmS5h/apt_archive ./ sbuild-build-depends-pbdagcon-dummy 0.invalid.0 [846 B]
Get:2 http://172.17.0.1/private stretch-staging/main armhf groff-base armhf 1.22.3-5 [1083 kB]
Get:3 http://172.17.0.1/private stretch-staging/main armhf bsdmainutils armhf 9.0.6 [177 kB]
Get:4 http://172.17.0.1/private stretch-staging/main armhf libpipeline1 armhf 1.4.1-2 [23.7 kB]
Get:5 http://172.17.0.1/private stretch-staging/main armhf man-db armhf 2.7.5-1 [975 kB]
Get:6 http://172.17.0.1/private stretch-staging/main armhf libunistring0 armhf 0.9.3-5.2 [253 kB]
Get:7 http://172.17.0.1/private stretch-staging/main armhf libmagic1 armhf 1:5.25-2 [250 kB]
Get:8 http://172.17.0.1/private stretch-staging/main armhf file armhf 1:5.25-2 [61.2 kB]
Get:9 http://172.17.0.1/private stretch-staging/main armhf gettext-base armhf 0.19.7-2 [111 kB]
Get:10 http://172.17.0.1/private stretch-staging/main armhf libicu55 armhf 55.1-7 [7380 kB]
Get:11 http://172.17.0.1/private stretch-staging/main armhf libxml2 armhf 2.9.3+dfsg1-1 [800 kB]
Get:12 http://172.17.0.1/private stretch-staging/main armhf autotools-dev all 20150820.1 [71.7 kB]
Get:13 http://172.17.0.1/private stretch-staging/main armhf libffi6 armhf 3.2.1-4 [18.5 kB]
Get:14 http://172.17.0.1/private stretch-staging/main armhf libglib2.0-0 armhf 2.46.2-3 [2482 kB]
Get:15 http://172.17.0.1/private stretch-staging/main armhf libcroco3 armhf 0.6.11-1 [131 kB]
Get:16 http://172.17.0.1/private stretch-staging/main armhf gettext armhf 0.19.7-2 [1400 kB]
Get:17 http://172.17.0.1/private stretch-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:18 http://172.17.0.1/private stretch-staging/main armhf po-debconf all 1.0.19 [249 kB]
Get:19 http://172.17.0.1/private stretch-staging/main armhf libarchive-zip-perl all 1.56-2 [94.9 kB]
Get:20 http://172.17.0.1/private stretch-staging/main armhf libfile-stripnondeterminism-perl all 0.014-1 [10.6 kB]
Get:21 http://172.17.0.1/private stretch-staging/main armhf dh-strip-nondeterminism all 0.014-1 [7472 B]
Get:22 http://172.17.0.1/private stretch-staging/main armhf debhelper all 9.20160115 [827 kB]
Get:23 http://172.17.0.1/private stretch-staging/main armhf libpbdata armhf 0~20151014+gitbe5d1bf-2 [91.1 kB]
Get:24 http://172.17.0.1/private stretch-staging/main armhf libgfortran3 armhf 5.3.1-5+rpi1 [153 kB]
Get:25 http://172.17.0.1/private stretch-staging/main armhf libhdf5-10 armhf 1.8.16+docs-1 [977 kB]
Get:26 http://172.17.0.1/private stretch-staging/main armhf libhdf5-cpp-11 armhf 1.8.16+docs-1 [115 kB]
Get:27 http://172.17.0.1/private stretch-staging/main armhf libpbihdf armhf 0~20151014+gitbe5d1bf-2 [102 kB]
Get:28 http://172.17.0.1/private stretch-staging/main armhf libblasr armhf 0~20151014+gitbe5d1bf-2 [786 kB]
Get:29 http://172.17.0.1/private stretch-staging/main armhf libblasr-dev armhf 0~20151014+gitbe5d1bf-2 [1614 kB]
Get:30 http://172.17.0.1/private stretch-staging/main armhf libboost1.58-dev armhf 1.58.0+dfsg-4.1 [6234 kB]
Get:31 http://172.17.0.1/private stretch-staging/main armhf libboost-dev armhf 1.58.0.1 [3472 B]
Get:32 http://172.17.0.1/private stretch-staging/main armhf libgtest-dev armhf 1.7.0-4 [200 kB]
Get:33 http://172.17.0.1/private stretch-staging/main armhf libpbdata-dev armhf 0~20151014+gitbe5d1bf-2 [151 kB]
Get:34 http://172.17.0.1/private stretch-staging/main armhf libpbihdf-dev armhf 0~20151014+gitbe5d1bf-2 [194 kB]
Get:35 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 27.8 MB in 3s (7262 kB/s)
Selecting previously unselected package groff-base.
(Reading database ...
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 13613 files and directories currently installed.)
Preparing to unpack .../groff-base_1.22.3-5_armhf.deb ...
Unpacking groff-base (1.22.3-5) ...
Selecting previously unselected package bsdmainutils.
Preparing to unpack .../bsdmainutils_9.0.6_armhf.deb ...
Unpacking bsdmainutils (9.0.6) ...
Selecting previously unselected package libpipeline1:armhf.
Preparing to unpack .../libpipeline1_1.4.1-2_armhf.deb ...
Unpacking libpipeline1:armhf (1.4.1-2) ...
Selecting previously unselected package man-db.
Preparing to unpack .../man-db_2.7.5-1_armhf.deb ...
Unpacking man-db (2.7.5-1) ...
Selecting previously unselected package libunistring0:armhf.
Preparing to unpack .../libunistring0_0.9.3-5.2_armhf.deb ...
Unpacking libunistring0:armhf (0.9.3-5.2) ...
Selecting previously unselected package libmagic1:armhf.
Preparing to unpack .../libmagic1_1%3a5.25-2_armhf.deb ...
Unpacking libmagic1:armhf (1:5.25-2) ...
Selecting previously unselected package file.
Preparing to unpack .../file_1%3a5.25-2_armhf.deb ...
Unpacking file (1:5.25-2) ...
Selecting previously unselected package gettext-base.
Preparing to unpack .../gettext-base_0.19.7-2_armhf.deb ...
Unpacking gettext-base (0.19.7-2) ...
Selecting previously unselected package libicu55:armhf.
Preparing to unpack .../libicu55_55.1-7_armhf.deb ...
Unpacking libicu55:armhf (55.1-7) ...
Selecting previously unselected package libxml2:armhf.
Preparing to unpack .../libxml2_2.9.3+dfsg1-1_armhf.deb ...
Unpacking libxml2:armhf (2.9.3+dfsg1-1) ...
Selecting previously unselected package autotools-dev.
Preparing to unpack .../autotools-dev_20150820.1_all.deb ...
Unpacking autotools-dev (20150820.1) ...
Selecting previously unselected package libffi6:armhf.
Preparing to unpack .../libffi6_3.2.1-4_armhf.deb ...
Unpacking libffi6:armhf (3.2.1-4) ...
Selecting previously unselected package libglib2.0-0:armhf.
Preparing to unpack .../libglib2.0-0_2.46.2-3_armhf.deb ...
Unpacking libglib2.0-0:armhf (2.46.2-3) ...
Selecting previously unselected package libcroco3:armhf.
Preparing to unpack .../libcroco3_0.6.11-1_armhf.deb ...
Unpacking libcroco3:armhf (0.6.11-1) ...
Selecting previously unselected package gettext.
Preparing to unpack .../gettext_0.19.7-2_armhf.deb ...
Unpacking gettext (0.19.7-2) ...
Selecting previously unselected package intltool-debian.
Preparing to unpack .../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 .../po-debconf_1.0.19_all.deb ...
Unpacking po-debconf (1.0.19) ...
Selecting previously unselected package libarchive-zip-perl.
Preparing to unpack .../libarchive-zip-perl_1.56-2_all.deb ...
Unpacking libarchive-zip-perl (1.56-2) ...
Selecting previously unselected package libfile-stripnondeterminism-perl.
Preparing to unpack .../libfile-stripnondeterminism-perl_0.014-1_all.deb ...
Unpacking libfile-stripnondeterminism-perl (0.014-1) ...
Selecting previously unselected package dh-strip-nondeterminism.
Preparing to unpack .../dh-strip-nondeterminism_0.014-1_all.deb ...
Unpacking dh-strip-nondeterminism (0.014-1) ...
Selecting previously unselected package debhelper.
Preparing to unpack .../debhelper_9.20160115_all.deb ...
Unpacking debhelper (9.20160115) ...
Selecting previously unselected package libpbdata:armhf.
Preparing to unpack .../libpbdata_0~20151014+gitbe5d1bf-2_armhf.deb ...
Unpacking libpbdata:armhf (0~20151014+gitbe5d1bf-2) ...
Selecting previously unselected package libgfortran3:armhf.
Preparing to unpack .../libgfortran3_5.3.1-5+rpi1_armhf.deb ...
Unpacking libgfortran3:armhf (5.3.1-5+rpi1) ...
Selecting previously unselected package libhdf5-10:armhf.
Preparing to unpack .../libhdf5-10_1.8.16+docs-1_armhf.deb ...
Unpacking libhdf5-10:armhf (1.8.16+docs-1) ...
Selecting previously unselected package libhdf5-cpp-11:armhf.
Preparing to unpack .../libhdf5-cpp-11_1.8.16+docs-1_armhf.deb ...
Unpacking libhdf5-cpp-11:armhf (1.8.16+docs-1) ...
Selecting previously unselected package libpbihdf:armhf.
Preparing to unpack .../libpbihdf_0~20151014+gitbe5d1bf-2_armhf.deb ...
Unpacking libpbihdf:armhf (0~20151014+gitbe5d1bf-2) ...
Selecting previously unselected package libblasr:armhf.
Preparing to unpack .../libblasr_0~20151014+gitbe5d1bf-2_armhf.deb ...
Unpacking libblasr:armhf (0~20151014+gitbe5d1bf-2) ...
Selecting previously unselected package libblasr-dev:armhf.
Preparing to unpack .../libblasr-dev_0~20151014+gitbe5d1bf-2_armhf.deb ...
Unpacking libblasr-dev:armhf (0~20151014+gitbe5d1bf-2) ...
Selecting previously unselected package libboost1.58-dev:armhf.
Preparing to unpack .../libboost1.58-dev_1.58.0+dfsg-4.1_armhf.deb ...
Unpacking libboost1.58-dev:armhf (1.58.0+dfsg-4.1) ...
Selecting previously unselected package libboost-dev:armhf.
Preparing to unpack .../libboost-dev_1.58.0.1_armhf.deb ...
Unpacking libboost-dev:armhf (1.58.0.1) ...
Selecting previously unselected package libgtest-dev:armhf.
Preparing to unpack .../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 .../libpbdata-dev_0~20151014+gitbe5d1bf-2_armhf.deb ...
Unpacking libpbdata-dev:armhf (0~20151014+gitbe5d1bf-2) ...
Selecting previously unselected package libpbihdf-dev:armhf.
Preparing to unpack .../libpbihdf-dev_0~20151014+gitbe5d1bf-2_armhf.deb ...
Unpacking libpbihdf-dev:armhf (0~20151014+gitbe5d1bf-2) ...
Selecting previously unselected package libtclap-dev.
Preparing to unpack .../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 .../sbuild-build-depends-pbdagcon-dummy.deb ...
Unpacking sbuild-build-depends-pbdagcon-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.21-6) ...
Setting up groff-base (1.22.3-5) ...
Setting up bsdmainutils (9.0.6) ...
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 libpipeline1:armhf (1.4.1-2) ...
Setting up man-db (2.7.5-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libunistring0:armhf (0.9.3-5.2) ...
Setting up libmagic1:armhf (1:5.25-2) ...
Setting up file (1:5.25-2) ...
Setting up gettext-base (0.19.7-2) ...
Setting up libicu55:armhf (55.1-7) ...
Setting up libxml2:armhf (2.9.3+dfsg1-1) ...
Setting up autotools-dev (20150820.1) ...
Setting up libffi6:armhf (3.2.1-4) ...
Setting up libglib2.0-0:armhf (2.46.2-3) ...
No schema files found: doing nothing.
Setting up libcroco3:armhf (0.6.11-1) ...
Setting up gettext (0.19.7-2) ...
Setting up intltool-debian (0.35.0+20060710.4) ...
Setting up po-debconf (1.0.19) ...
Setting up libarchive-zip-perl (1.56-2) ...
Setting up libfile-stripnondeterminism-perl (0.014-1) ...
Setting up libpbdata:armhf (0~20151014+gitbe5d1bf-2) ...
Setting up libgfortran3:armhf (5.3.1-5+rpi1) ...
Setting up libhdf5-10:armhf (1.8.16+docs-1) ...
Setting up libhdf5-cpp-11:armhf (1.8.16+docs-1) ...
Setting up libpbihdf:armhf (0~20151014+gitbe5d1bf-2) ...
Setting up libblasr:armhf (0~20151014+gitbe5d1bf-2) ...
Setting up libblasr-dev:armhf (0~20151014+gitbe5d1bf-2) ...
Setting up libboost1.58-dev:armhf (1.58.0+dfsg-4.1) ...
Setting up libboost-dev:armhf (1.58.0.1) ...
Setting up libgtest-dev:armhf (1.7.0-4) ...
Setting up libpbdata-dev:armhf (0~20151014+gitbe5d1bf-2) ...
Setting up libpbihdf-dev:armhf (0~20151014+gitbe5d1bf-2) ...
Setting up libtclap-dev (1.2.1-1) ...
Setting up debhelper (9.20160115) ...
Setting up sbuild-build-depends-pbdagcon-dummy (0.invalid.0) ...
Setting up dh-strip-nondeterminism (0.014-1) ...
Processing triggers for libc-bin (2.21-6) ...
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_2.25.90.20160101-2 dpkg-dev_1.18.4 g++-5_5.3.1-5+rpi1 gcc-5_5.3.1-5+rpi1 libc6-dev_2.21-6 libstdc++-4.9-dev_4.9.3-10 libstdc++-5-dev_5.3.1-5+rpi1 libstdc++6_5.3.1-5+rpi1 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch
Package versions: acl_2.2.52-2 adduser_3.113+nmu3 apt_1.2 autotools-dev_20150820.1 base-files_9.5+rpi1 base-passwd_3.5.39 bash_4.3-14 binutils_2.25.90.20160101-2 bsdmainutils_9.0.6 bsdutils_1:2.27.1-1 build-essential_11.7 bzip2_1.0.6-8 coreutils_8.23-4 cpio_2.11+dfsg-4.1 cpp_4:5.3.1-1+rpi1 cpp-5_5.3.1-5+rpi1 dash_0.5.7-4 debconf_1.5.58 debfoster_2.7-2 debhelper_9.20160115 debianutils_4.5.1 dh-strip-nondeterminism_0.014-1 diffutils_1:3.3-3 dmsetup_2:1.02.114-1 dpkg_1.18.4 dpkg-dev_1.18.4 e2fslibs_1.42.13-1 e2fsprogs_1.42.13-1 fakeroot_1.20.2-1 file_1:5.25-2 findutils_4.6.0-2 g++_4:5.3.1-1+rpi1 g++-5_5.3.1-5+rpi1 gcc_4:5.3.1-1+rpi1 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8-base_4.8.5-3 gcc-4.9-base_4.9.3-10 gcc-5_5.3.1-5+rpi1 gcc-5-base_5.3.1-5+rpi1 gettext_0.19.7-2 gettext-base_0.19.7-2 gnupg_1.4.20-1 gpgv_1.4.20-1 grep_2.22-1 groff-base_1.22.3-5 gzip_1.6-4 hostname_3.16 init_1.24 init-system-helpers_1.24 initramfs-tools_0.120 initscripts_2.88dsf-59.2 insserv_1.14.0-5 intltool-debian_0.35.0+20060710.4 klibc-utils_2.0.4-6+rpi1 kmod_21-1 libacl1_2.2.52-2 libapparmor1_2.10-2+b3 libapt-pkg4.12_1.0.9.10 libapt-pkg5.0_1.2 libarchive-zip-perl_1.56-2 libasan1_4.9.3-10 libasan2_5.3.1-5+rpi1 libatomic1_5.3.1-5+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.4.5-1 libaudit1_1:2.4.5-1 libblasr_0~20151014+gitbe5d1bf-2 libblasr-dev_0~20151014+gitbe5d1bf-2 libblkid1_2.27.1-1 libboost-dev_1.58.0.1 libboost1.58-dev_1.58.0+dfsg-4.1 libbz2-1.0_1.0.6-8 libc-bin_2.21-6 libc-dev-bin_2.21-6 libc6_2.21-6 libc6-dev_2.21-6 libcap2_1:2.24-12 libcap2-bin_1:2.24-12 libcc1-0_5.3.1-5+rpi1 libcomerr2_1.42.13-1 libcroco3_0.6.11-1 libcryptsetup4_2:1.7.0-2 libdb5.3_5.3.28-11 libdbus-1-3_1.10.6-1 libdebconfclient0_0.201 libdevmapper1.02.1_2:1.02.114-1 libdpkg-perl_1.18.4 libdrm2_2.4.66-2 libfakeroot_1.20.2-1 libfdisk1_2.27.1-1 libffi6_3.2.1-4 libfile-stripnondeterminism-perl_0.014-1 libgc1c2_1:7.4.2-7.3 libgcc-4.9-dev_4.9.3-10 libgcc-5-dev_5.3.1-5+rpi1 libgcc1_1:5.3.1-5+rpi1 libgcrypt20_1.6.4-4 libgdbm3_1.8.3-13.1 libgfortran3_5.3.1-5+rpi1 libglib2.0-0_2.46.2-3 libgmp10_2:6.1.0+dfsg-2 libgomp1_5.3.1-5+rpi1 libgpg-error0_1.21-1 libgtest-dev_1.7.0-4 libhdf5-10_1.8.16+docs-1 libhdf5-cpp-11_1.8.16+docs-1 libicu55_55.1-7 libisl15_0.15-3 libklibc_2.0.4-6+rpi1 libkmod2_21-1 liblz4-1_0.0~r131-1 liblzma5_5.1.1alpha+20120614-2.1 libmagic1_1:5.25-2 libmount1_2.27.1-1 libmpc3_1.0.3-1 libmpfr4_3.1.3-2 libncurses5_6.0+20151024-2 libncursesw5_6.0+20151024-2 libpam-modules_1.1.8-3.2 libpam-modules-bin_1.1.8-3.2 libpam-runtime_1.1.8-3.2 libpam0g_1.1.8-3.2 libpbdata_0~20151014+gitbe5d1bf-2 libpbdata-dev_0~20151014+gitbe5d1bf-2 libpbihdf_0~20151014+gitbe5d1bf-2 libpbihdf-dev_0~20151014+gitbe5d1bf-2 libpcre3_2:8.38-1 libperl5.22_5.22.1-4 libpipeline1_1.4.1-2 libpng12-0_1.2.54-1 libprocps3_2:3.3.9-9 libprocps5_2:3.3.11-3 libreadline6_6.3-8+b3 libseccomp2_2.2.3-2 libselinux1_2.4-3 libsemanage-common_2.4-3 libsemanage1_2.4-3 libsepol1_2.4-2 libslang2_2.3.0-2+b1 libsmartcols1_2.27.1-1 libss2_1.42.13-1 libstdc++-4.9-dev_4.9.3-10 libstdc++-5-dev_5.3.1-5+rpi1 libstdc++6_5.3.1-5+rpi1 libsystemd0_228-4 libtclap-dev_1.2.1-1 libtimedate-perl_2.3000-2 libtinfo5_6.0+20151024-2 libubsan0_5.3.1-5+rpi1 libudev1_228-4 libunistring0_0.9.3-5.2 libusb-0.1-4_2:0.1.12-28 libustr-1.0-1_1.0.4-5 libuuid1_2.27.1-1 libxml2_2.9.3+dfsg1-1 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch login_1:4.2-3.1 lsb-base_4.1+Debian13+rpi1+nmu1 make_4.0-8.2 makedev_2.3.1-93 man-db_2.7.5-1 manpages_4.04-0.1 mawk_1.3.3-17 mount_2.27.1-1 multiarch-support_2.21-6 nano_2.4.3-1 ncurses-base_6.0+20151024-2 ncurses-bin_6.0+20151024-2 passwd_1:4.2-3.1 patch_2.7.5-1 perl_5.22.1-4 perl-base_5.22.1-4 perl-modules-5.22_5.22.1-4 po-debconf_1.0.19 procps_2:3.3.11-3 raspbian-archive-keyring_20120528.2 readline-common_6.3-8 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-pbdagcon-dummy_0.invalid.0 sed_4.2.2-6.1 sensible-utils_0.0.9 startpar_0.59-3 systemd_228-4 systemd-sysv_228-4 sysv-rc_2.88dsf-59.2 sysvinit-utils_2.88dsf-59.2 tar_1.28-2.1 tzdata_2015g-1 udev_228-4 util-linux_2.27.1-1 xz-utils_5.1.1alpha+20120614-2.1 zlib1g_1:1.2.8.dfsg-2+b1
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
└──────────────────────────────────────────────────────────────────────────────┘
Unpack source
─────────────
gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error
gpgv: Signature made Fri Jan 22 18:40:21 2016 UTC using RSA key ID D1C646D1
gpgv: Can't check signature: public key not found
dpkg-source: warning: failed to verify signature on ./pbdagcon_0~20151114+git1d12e13+ds-2.dsc
dpkg-source: info: extracting pbdagcon in pbdagcon-0~20151114+git1d12e13+ds
dpkg-source: info: unpacking pbdagcon_0~20151114+git1d12e13+ds.orig.tar.xz
dpkg-source: info: unpacking pbdagcon_0~20151114+git1d12e13+ds-2.debian.tar.xz
dpkg-source: info: applying external-libs.patch
dpkg-source: info: applying compiler-flags.patch
dpkg-source: info: applying gtest-directory.patch
dpkg-source: info: applying disable-dazcon-tests.patch
Check disc space
────────────────
Sufficient free space for build
User Environment
────────────────
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
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-aba28019-d504-4fb6-b9f3-ca752abce556
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd
dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package pbdagcon
dpkg-buildpackage: source version 0~20151114+git1d12e13+ds-2
dpkg-buildpackage: source distribution unstable
dpkg-source --before-build pbdagcon-0~20151114+git1d12e13+ds
dpkg-buildpackage: 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-0~20151114+git1d12e13+ds'
make -C src/cpp clean
make[2]: Entering directory '/«BUILDDIR»/pbdagcon-0~20151114+git1d12e13+ds/src/cpp'
rm -f *.d
rm -f *.o
rm -f pbdagcon
rm -f dazcon
make[2]: Leaving directory '/«BUILDDIR»/pbdagcon-0~20151114+git1d12e13+ds/src/cpp'
make -C test/cpp clean
make[2]: Entering directory '/«BUILDDIR»/pbdagcon-0~20151114+git1d12e13+ds/test/cpp'
rm -f ../../src/cpp/*.o
rm -f *.o
rm -f test_*
rm -f gtest_main.a
make[2]: Leaving directory '/«BUILDDIR»/pbdagcon-0~20151114+git1d12e13+ds/test/cpp'
make[1]: Leaving directory '/«BUILDDIR»/pbdagcon-0~20151114+git1d12e13+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
dh_auto_configure -a -O--parallel
dh_auto_build -a -O--parallel
make -j4
make[1]: Entering directory '/«BUILDDIR»/pbdagcon-0~20151114+git1d12e13+ds'
make -C src/cpp
make[2]: Entering directory '/«BUILDDIR»/pbdagcon-0~20151114+git1d12e13+ds/src/cpp'
g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -Wall -Wuninitialized -pedantic -I third-party -I /usr/include/boost -I/usr/include/pbdata -I/usr/include/blasr -Wdate-time -D_FORTIFY_SOURCE=2 -c -o Alignment.o Alignment.cpp
g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -Wall -Wuninitialized -pedantic -I third-party -I /usr/include/boost -I/usr/include/pbdata -I/usr/include/blasr -Wdate-time -D_FORTIFY_SOURCE=2 -c -o AlnGraphBoost.o AlnGraphBoost.cpp
g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -Wall -Wuninitialized -pedantic -I third-party -I /usr/include/boost -I/usr/include/pbdata -I/usr/include/blasr -Wdate-time -D_FORTIFY_SOURCE=2 -c -o BlasrM5AlnProvider.o BlasrM5AlnProvider.cpp
g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -Wall -Wuninitialized -pedantic -I third-party -I /usr/include/boost -I/usr/include/pbdata -I/usr/include/blasr -Wdate-time -D_FORTIFY_SOURCE=2 -c -o main.o main.cpp
g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -Wall -Wuninitialized -pedantic -I third-party -I /usr/include/boost -I/usr/include/pbdata -I/usr/include/blasr -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SimpleAligner.o SimpleAligner.cpp
In file included from /usr/include/blasr/algorithms/alignment/GuidedAlign.hpp:15:0,
from SimpleAligner.hpp:45,
from SimpleAligner.cpp:44:
/usr/include/blasr/datastructures/anchoring/MatchPos.hpp: In constructor 'MatchPos::MatchPos(DNALength, DNALength, DNALength, int)':
/usr/include/blasr/datastructures/anchoring/MatchPos.hpp:15:9: warning: 'MatchPos::m' will be initialized after [-Wreorder]
int m; // multiplicity
^
/usr/include/blasr/datastructures/anchoring/MatchPos.hpp:13:17: warning: 'MatchWeight MatchPos::w' [-Wreorder]
MatchWeight w;
^
/usr/include/blasr/datastructures/anchoring/MatchPos.hpp:46:8: warning: when initialized here [-Wreorder]
inline MatchPos::MatchPos(DNALength pt, DNALength pq, DNALength pl, int pm) :
^
In file included from /usr/include/blasr/algorithms/alignment/SDPAlign.hpp:62:0,
from SimpleAligner.hpp:44,
from SimpleAligner.cpp:44:
/usr/include/blasr/algorithms/alignment/SDPAlignImpl.hpp: In instantiation of 'int SDPAlign(T_QuerySequence&, T_TargetSequence&, T_ScoreFn&, int, int, int, float, blasr::Alignment&, std::vector<Fragment>&, std::vector<Fragment>&, std::vector<Fragment>&, T_TupleList&, T_TupleList&, T_TupleList&, std::vector<int>&, AlignmentType, bool, bool, DNALength, bool, unsigned int) [with T_QuerySequence = FASTQSequence; T_TargetSequence = DNASequence; T_ScoreFn = DistanceMatrixScoreFunction<DNASequence, FASTQSequence>; T_TupleList = TupleList<PositionDNATuple>; DNALength = unsigned int]':
/usr/include/blasr/algorithms/alignment/SDPAlignImpl.hpp:45:20: required from 'int SDPAlign(T_QuerySequence&, T_TargetSequence&, T_ScoreFn&, int, int, int, float, blasr::Alignment&, AlignmentType, bool, bool, DNALength, bool, unsigned int) [with T_QuerySequence = FASTQSequence; T_TargetSequence = DNASequence; T_ScoreFn = DistanceMatrixScoreFunction<DNASequence, FASTQSequence>; DNALength = unsigned int]'
SimpleAligner.cpp:73:31: required from here
/usr/include/blasr/algorithms/alignment/SDPAlignImpl.hpp:241:13: warning: unused variable 'prev' [-Wunused-variable]
int prev = fragmentSet.size();
^
In file included from /usr/include/blasr/algorithms/alignment/SDPAlign.hpp:62:0,
from SimpleAligner.hpp:44,
from SimpleAligner.cpp:44:
/usr/include/blasr/algorithms/alignment/SDPAlignImpl.hpp:421:21: warning: variable 'frontAlignmentScore' set but not used [-Wunused-but-set-variable]
int frontAlignmentScore;
^
/usr/include/blasr/algorithms/alignment/SDPAlignImpl.hpp:472:17: warning: variable 'alignScore' set but not used [-Wunused-but-set-variable]
int alignScore;
^
In file included from /usr/include/blasr/algorithms/alignment/SDPAlign.hpp:62:0,
from SimpleAligner.hpp:44,
from SimpleAligner.cpp:44:
/usr/include/blasr/algorithms/alignment/SDPAlignImpl.hpp:137:51: warning: variable 'middlePos' set but not used [-Wunused-but-set-variable]
int prefixLength, middleLength, suffixLength, middlePos, suffixPos; // prefix pos is 0
^
/usr/include/blasr/algorithms/alignment/SDPAlignImpl.hpp:160:54: warning: variable 'qMiddlePos' set but not used [-Wunused-but-set-variable]
int qPrefixLength, qMiddleLength, qSuffixLength, qMiddlePos, qSuffixPos; // prefix pos is 0
^
/usr/include/blasr/algorithms/alignment/SDPAlignImpl.hpp:234:9: warning: variable 'nOnOpt' set but not used [-Wunused-but-set-variable]
int nOnOpt = fragmentSet.size();
^
In file included from /usr/include/blasr/algorithms/alignment/SDPAlign.hpp:62:0,
from SimpleAligner.hpp:44,
from SimpleAligner.cpp:44:
/usr/include/blasr/algorithms/alignment/SDPAlignImpl.hpp:357:10: warning: unused variable 'badBlock' [-Wunused-variable]
bool badBlock;
^
In file included from /usr/include/blasr/algorithms/alignment/GraphPaper.hpp:29:0,
from /usr/include/blasr/algorithms/alignment/SDPAlignImpl.hpp:17,
from /usr/include/blasr/algorithms/alignment/SDPAlign.hpp:62,
from SimpleAligner.hpp:44,
from SimpleAligner.cpp:44:
/usr/include/blasr/algorithms/alignment/GraphPaperImpl.hpp: In instantiation of 'int GraphPaper(std::vector<_RealType>&, int, int, FlatMatrix2D<int>&, FlatMatrix2D<int>&, FlatMatrix2D<Arrow>&, std::vector<bool>&) [with T_Point = Fragment]':
/usr/include/blasr/algorithms/alignment/SDPAlignImpl.hpp:238:38: required from 'int SDPAlign(T_QuerySequence&, T_TargetSequence&, T_ScoreFn&, int, int, int, float, blasr::Alignment&, std::vector<Fragment>&, std::vector<Fragment>&, std::vector<Fragment>&, T_TupleList&, T_TupleList&, T_TupleList&, std::vector<int>&, AlignmentType, bool, bool, DNALength, bool, unsigned int) [with T_QuerySequence = FASTQSequence; T_TargetSequence = DNASequence; T_ScoreFn = DistanceMatrixScoreFunction<DNASequence, FASTQSequence>; T_TupleList = TupleList<PositionDNATuple>; DNALength = unsigned int]'
/usr/include/blasr/algorithms/alignment/SDPAlignImpl.hpp:45:20: required from 'int SDPAlign(T_QuerySequence&, T_TargetSequence&, T_ScoreFn&, int, int, int, float, blasr::Alignment&, AlignmentType, bool, bool, DNALength, bool, unsigned int) [with T_QuerySequence = FASTQSequence; T_TargetSequence = DNASequence; T_ScoreFn = DistanceMatrixScoreFunction<DNASequence, FASTQSequence>; DNALength = unsigned int]'
SimpleAligner.cpp:73:31: required from here
/usr/include/blasr/algorithms/alignment/GraphPaperImpl.hpp:73:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (i = 0; i < points.size(); i++) {
^
/usr/include/blasr/algorithms/alignment/GraphPaperImpl.hpp:137:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (i = 0; i < points.size(); i++) {
^
/usr/include/blasr/algorithms/alignment/GraphPaperImpl.hpp: In instantiation of 'void RemoveOffOpt(std::vector<_RealType>&, std::vector<bool>&) [with T_Point = Fragment]':
/usr/include/blasr/algorithms/alignment/SDPAlignImpl.hpp:242:21: required from 'int SDPAlign(T_QuerySequence&, T_TargetSequence&, T_ScoreFn&, int, int, int, float, blasr::Alignment&, std::vector<Fragment>&, std::vector<Fragment>&, std::vector<Fragment>&, T_TupleList&, T_TupleList&, T_TupleList&, std::vector<int>&, AlignmentType, bool, bool, DNALength, bool, unsigned int) [with T_QuerySequence = FASTQSequence; T_TargetSequence = DNASequence; T_ScoreFn = DistanceMatrixScoreFunction<DNASequence, FASTQSequence>; T_TupleList = TupleList<PositionDNATuple>; DNALength = unsigned int]'
/usr/include/blasr/algorithms/alignment/SDPAlignImpl.hpp:45:20: required from 'int SDPAlign(T_QuerySequence&, T_TargetSequence&, T_ScoreFn&, int, int, int, float, blasr::Alignment&, AlignmentType, bool, bool, DNALength, bool, unsigned int) [with T_QuerySequence = FASTQSequence; T_TargetSequence = DNASequence; T_ScoreFn = DistanceMatrixScoreFunction<DNASequence, FASTQSequence>; DNALength = unsigned int]'
SimpleAligner.cpp:73:31: required from here
/usr/include/blasr/algorithms/alignment/GraphPaperImpl.hpp:166:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (i = 0, c = 0; i < points.size(); i++) {
^
In file included from /usr/include/blasr/algorithms/alignment/sdp/SparseDynamicProgramming.hpp:35:0,
from /usr/include/blasr/algorithms/alignment/SDPAlignImpl.hpp:20,
from /usr/include/blasr/algorithms/alignment/SDPAlign.hpp:62,
from SimpleAligner.hpp:44,
from SimpleAligner.cpp:44:
/usr/include/blasr/algorithms/alignment/sdp/SparseDynamicProgrammingImpl.hpp: In instantiation of 'int SDPLongestCommonSubsequence(DNALength, std::vector<_RealType>&, DNALength, int, int, int, std::vector<int>&, AlignmentType) [with T_Fragment = Fragment; DNALength = unsigned int]':
/usr/include/blasr/algorithms/alignment/SDPAlignImpl.hpp:275:32: required from 'int SDPAlign(T_QuerySequence&, T_TargetSequence&, T_ScoreFn&, int, int, int, float, blasr::Alignment&, std::vector<Fragment>&, std::vector<Fragment>&, std::vector<Fragment>&, T_TupleList&, T_TupleList&, T_TupleList&, std::vector<int>&, AlignmentType, bool, bool, DNALength, bool, unsigned int) [with T_QuerySequence = FASTQSequence; T_TargetSequence = DNASequence; T_ScoreFn = DistanceMatrixScoreFunction<DNASequence, FASTQSequence>; T_TupleList = TupleList<PositionDNATuple>; DNALength = unsigned int]'
/usr/include/blasr/algorithms/alignment/SDPAlignImpl.hpp:45:20: required from 'int SDPAlign(T_QuerySequence&, T_TargetSequence&, T_ScoreFn&, int, int, int, float, blasr::Alignment&, AlignmentType, bool, bool, DNALength, bool, unsigned int) [with T_QuerySequence = FASTQSequence; T_TargetSequence = DNASequence; T_ScoreFn = DistanceMatrixScoreFunction<DNASequence, FASTQSequence>; DNALength = unsigned int]'
SimpleAligner.cpp:73:31: required from here
/usr/include/blasr/algorithms/alignment/sdp/SparseDynamicProgrammingImpl.hpp:71:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
while (fSweep < fragmentSetSize and
^
/usr/include/blasr/algorithms/alignment/sdp/SparseDynamicProgrammingImpl.hpp:86:17: warning: unused variable 'drift' [-Wunused-variable]
int drift, driftPenalty;
^
/usr/include/blasr/algorithms/alignment/sdp/SparseDynamicProgrammingImpl.hpp:184:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
while (fSweep < fragmentSetSize and
^
/usr/include/blasr/algorithms/alignment/sdp/SparseDynamicProgrammingImpl.hpp:194:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
while (fTrail < fragmentSetSize and
^
In file included from /usr/include/blasr/algorithms/alignment/AlignmentUtils.hpp:137:0,
from SimpleAligner.hpp:43,
from SimpleAligner.cpp:44:
/usr/include/blasr/algorithms/alignment/AlignmentUtilsImpl.hpp: In instantiation of 'int ComputeAlignmentScore(blasr::Alignment&, T_QuerySequence&, T_TargetSequence&, T_ScoreFn&, bool) [with T_QuerySequence = FASTQSequence; T_TargetSequence = DNASequence; T_ScoreFn = DistanceMatrixScoreFunction<DNASequence, FASTQSequence>]':
/usr/include/blasr/algorithms/alignment/SDPAlignImpl.hpp:610:43: required from 'int SDPAlign(T_QuerySequence&, T_TargetSequence&, T_ScoreFn&, int, int, int, float, blasr::Alignment&, std::vector<Fragment>&, std::vector<Fragment>&, std::vector<Fragment>&, T_TupleList&, T_TupleList&, T_TupleList&, std::vector<int>&, AlignmentType, bool, bool, DNALength, bool, unsigned int) [with T_QuerySequence = FASTQSequence; T_TargetSequence = DNASequence; T_ScoreFn = DistanceMatrixScoreFunction<DNASequence, FASTQSequence>; T_TupleList = TupleList<PositionDNATuple>; DNALength = unsigned int]'
/usr/include/blasr/algorithms/alignment/SDPAlignImpl.hpp:45:20: required from 'int SDPAlign(T_QuerySequence&, T_TargetSequence&, T_ScoreFn&, int, int, int, float, blasr::Alignment&, AlignmentType, bool, bool, DNALength, bool, unsigned int) [with T_QuerySequence = FASTQSequence; T_TargetSequence = DNASequence; T_ScoreFn = DistanceMatrixScoreFunction<DNASequence, FASTQSequence>; DNALength = unsigned int]'
SimpleAligner.cpp:73:31: required from here
/usr/include/blasr/algorithms/alignment/AlignmentUtilsImpl.hpp:14:27: warning: unused variable 'bi' [-Wunused-variable]
VectorIndex b, q, t, l, bi, gi;
^
In file included from /usr/include/blasr/algorithms/alignment/GraphPaper.hpp:29:0,
from /usr/include/blasr/algorithms/alignment/SDPAlignImpl.hpp:17,
from /usr/include/blasr/algorithms/alignment/SDPAlign.hpp:62,
from SimpleAligner.hpp:44,
from SimpleAligner.cpp:44:
/usr/include/blasr/algorithms/alignment/GraphPaperImpl.hpp: In instantiation of 'bool SetBounds(std::vector<_RealType>&, DNALength&, DNALength&, int) [with T_Point = Fragment; DNALength = unsigned int]':
/usr/include/blasr/algorithms/alignment/GraphPaperImpl.hpp:64:12: required from 'int GraphPaper(std::vector<_RealType>&, int, int, FlatMatrix2D<int>&, FlatMatrix2D<int>&, FlatMatrix2D<Arrow>&, std::vector<bool>&) [with T_Point = Fragment]'
/usr/include/blasr/algorithms/alignment/SDPAlignImpl.hpp:238:38: required from 'int SDPAlign(T_QuerySequence&, T_TargetSequence&, T_ScoreFn&, int, int, int, float, blasr::Alignment&, std::vector<Fragment>&, std::vector<Fragment>&, std::vector<Fragment>&, T_TupleList&, T_TupleList&, T_TupleList&, std::vector<int>&, AlignmentType, bool, bool, DNALength, bool, unsigned int) [with T_QuerySequence = FASTQSequence; T_TargetSequence = DNASequence; T_ScoreFn = DistanceMatrixScoreFunction<DNASequence, FASTQSequence>; T_TupleList = TupleList<PositionDNATuple>; DNALength = unsigned int]'
/usr/include/blasr/algorithms/alignment/SDPAlignImpl.hpp:45:20: required from 'int SDPAlign(T_QuerySequence&, T_TargetSequence&, T_ScoreFn&, int, int, int, float, blasr::Alignment&, AlignmentType, bool, bool, DNALength, bool, unsigned int) [with T_QuerySequence = FASTQSequence; T_TargetSequence = DNASequence; T_ScoreFn = DistanceMatrixScoreFunction<DNASequence, FASTQSequence>; DNALength = unsigned int]'
SimpleAligner.cpp:73:31: required from here
/usr/include/blasr/algorithms/alignment/GraphPaperImpl.hpp:19:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (i = 1; i < points.size(); i++) {
^
/usr/include/blasr/algorithms/alignment/GraphPaperImpl.hpp:7:13: warning: unused variable 'maxRow' [-Wunused-variable]
DNALength maxRow = 0;
^
In file included from /usr/include/blasr/algorithms/alignment/sdp/SparseDynamicProgramming.hpp:35:0,
from /usr/include/blasr/algorithms/alignment/SDPAlignImpl.hpp:20,
from /usr/include/blasr/algorithms/alignment/SDPAlign.hpp:62,
from SimpleAligner.hpp:44,
from SimpleAligner.cpp:44:
/usr/include/blasr/algorithms/alignment/sdp/SparseDynamicProgrammingImpl.hpp: In instantiation of 'void StoreAbove(std::vector<_RealType>&, DNALength) [with T_Fragment = Fragment; DNALength = unsigned int]':
/usr/include/blasr/algorithms/alignment/sdp/SparseDynamicProgrammingImpl.hpp:55:15: required from 'int SDPLongestCommonSubsequence(DNALength, std::vector<_RealType>&, DNALength, int, int, int, std::vector<int>&, AlignmentType) [with T_Fragment = Fragment; DNALength = unsigned int]'
/usr/include/blasr/algorithms/alignment/SDPAlignImpl.hpp:275:32: required from 'int SDPAlign(T_QuerySequence&, T_TargetSequence&, T_ScoreFn&, int, int, int, float, blasr::Alignment&, std::vector<Fragment>&, std::vector<Fragment>&, std::vector<Fragment>&, T_TupleList&, T_TupleList&, T_TupleList&, std::vector<int>&, AlignmentType, bool, bool, DNALength, bool, unsigned int) [with T_QuerySequence = FASTQSequence; T_TargetSequence = DNASequence; T_ScoreFn = DistanceMatrixScoreFunction<DNASequence, FASTQSequence>; T_TupleList = TupleList<PositionDNATuple>; DNALength = unsigned int]'
/usr/include/blasr/algorithms/alignment/SDPAlignImpl.hpp:45:20: required from 'int SDPAlign(T_QuerySequence&, T_TargetSequence&, T_ScoreFn&, int, int, int, float, blasr::Alignment&, AlignmentType, bool, bool, DNALength, bool, unsigned int) [with T_QuerySequence = FASTQSequence; T_TargetSequence = DNASequence; T_ScoreFn = DistanceMatrixScoreFunction<DNASequence, FASTQSequence>; DNALength = unsigned int]'
SimpleAligner.cpp:73:31: required from here
/usr/include/blasr/algorithms/alignment/sdp/SparseDynamicProgrammingImpl.hpp:20:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (i = 1; i < fragmentSet.size(); i++) {
^
In file included from /usr/include/blasr/algorithms/alignment/GraphPaper.hpp:29:0,
from /usr/include/blasr/algorithms/alignment/SDPAlignImpl.hpp:17,
from /usr/include/blasr/algorithms/alignment/SDPAlign.hpp:62,
from SimpleAligner.hpp:44,
from SimpleAligner.cpp:44:
/usr/include/blasr/algorithms/alignment/GraphPaperImpl.hpp: In function 'bool SetBounds(std::vector<_RealType>&, DNALength&, DNALength&, int) [with T_Point = Fragment; DNALength = unsigned int]':
/usr/include/blasr/algorithms/alignment/GraphPaperImpl.hpp:34:1: warning: control reaches end of non-void function [-Wreturn-type]
}
^
/usr/include/blasr/algorithms/alignment/GraphPaperImpl.hpp: In function 'int GraphPaper(std::vector<_RealType>&, int, int, FlatMatrix2D<int>&, FlatMatrix2D<int>&, FlatMatrix2D<Arrow>&, std::vector<bool>&) [with T_Point = Fragment]':
/usr/include/blasr/algorithms/alignment/GraphPaperImpl.hpp:65:3: warning: 'xMax' may be used uninitialized in this function [-Wmaybe-uninitialized]
xMax++; // make half-open interval.
^
/usr/include/blasr/algorithms/alignment/GraphPaperImpl.hpp:67:3: warning: 'yMax' may be used uninitialized in this function [-Wmaybe-uninitialized]
yMax++; // ditto.
^
In file included from /usr/include/blasr/algorithms/alignment/GuidedAlign.hpp:15:0,
from SimpleAligner.hpp:45,
from main.cpp:60:
/usr/include/blasr/datastructures/anchoring/MatchPos.hpp: In constructor 'MatchPos::MatchPos(DNALength, DNALength, DNALength, int)':
/usr/include/blasr/datastructures/anchoring/MatchPos.hpp:15:9: warning: 'MatchPos::m' will be initialized after [-Wreorder]
int m; // multiplicity
^
/usr/include/blasr/datastructures/anchoring/MatchPos.hpp:13:17: warning: 'MatchWeight MatchPos::w' [-Wreorder]
MatchWeight w;
^
/usr/include/blasr/datastructures/anchoring/MatchPos.hpp:46:8: warning: when initialized here [-Wreorder]
inline MatchPos::MatchPos(DNALength pt, DNALength pq, DNALength pl, int pm) :
^
In file included from main.cpp:58:0:
BoundedBuffer.hpp: In instantiation of 'BoundedBuffer<T>::push(T)::<lambda()> [with T = std::vector<dagcon::Alignment>]':
BoundedBuffer.hpp:63:31: required from 'struct BoundedBuffer<T>::push(T) [with T = std::vector<dagcon::Alignment>]::<lambda()>'
BoundedBuffer.hpp:63:9: required from 'void BoundedBuffer<T>::push(T) [with T = std::vector<dagcon::Alignment>]'
main.cpp:112:35: required from here
BoundedBuffer.hpp:63:61: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
not_full_.wait(lock, [this](){return buffer_.size() != max_;});
^
BoundedBuffer.hpp: In instantiation of 'BoundedBuffer<T>::push(T)::<lambda()> [with T = std::__cxx11::basic_string<char>]':
BoundedBuffer.hpp:63:31: required from 'struct BoundedBuffer<T>::push(T) [with T = std::__cxx11::basic_string<char>]::<lambda()>'
BoundedBuffer.hpp:63:9: required from 'void BoundedBuffer<T>::push(T) [with T = std::__cxx11::basic_string<char>]'
main.cpp:180:42: required from here
BoundedBuffer.hpp:63:61: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -Wl,--no-as-needed -o pbdagcon Alignment.o AlnGraphBoost.o BlasrM5AlnProvider.o main.o SimpleAligner.o -Wl,-z,relro -L/usr/lib/arm-linux-gnueabihf/blasr -L/usr/lib/arm-linux-gnueabihf/pbdata -L/usr/include/pbdata -L/usr/include/blasr -lpbdata -lblasr -lpthread
make[2]: Leaving directory '/«BUILDDIR»/pbdagcon-0~20151114+git1d12e13+ds/src/cpp'
make[1]: Leaving directory '/«BUILDDIR»/pbdagcon-0~20151114+git1d12e13+ds'
dh_auto_test -a -O--parallel
make -j4 check
make[1]: Entering directory '/«BUILDDIR»/pbdagcon-0~20151114+git1d12e13+ds'
make -C test/cpp
make[2]: Entering directory '/«BUILDDIR»/pbdagcon-0~20151114+git1d12e13+ds/test/cpp'
g++ -isystem /usr/include -I/usr/src/gtest -g -Wall -Wextra -pthread -c /usr/src/gtest/src/gtest-all.cc
g++ -isystem /usr/include -I/usr/src/gtest -g -Wall -Wextra -pthread -c /usr/src/gtest/src/gtest_main.cc
g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -I/usr/include/pbdata -I/usr/include/blasr -I/usr/include/boost -I/usr/src/gtest -I../../src/cpp -Wdate-time -D_FORTIFY_SOURCE=2 -c -o AlnGraphBoostTest.o AlnGraphBoostTest.cpp
g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -I/usr/include/pbdata -I/usr/include/blasr -I/usr/include/boost -I/usr/src/gtest -I../../src/cpp -Wdate-time -D_FORTIFY_SOURCE=2 -c -o AlignmentTest.o AlignmentTest.cpp
g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -I/usr/include/pbdata -I/usr/include/blasr -I/usr/include/boost -I/usr/src/gtest -I../../src/cpp -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SimpleAlignerTest.o SimpleAlignerTest.cpp
ar rv gtest_main.a gtest-all.o gtest_main.o
ar: creating gtest_main.a
a - gtest-all.o
a - gtest_main.o
=== Building test_simple_aligner ===
=== Building test_alngraph ===
g++ gtest_main.a ../../src/cpp/AlnGraphBoost.o ../../src/cpp/Alignment.o ../../src/cpp/SimpleAligner.o AlnGraphBoostTest.o -o test_alngraph -Wl,-z,relro -L/usr/lib/arm-linux-gnueabihf/blasr -L/usr/lib/arm-linux-gnueabihf/pbdata -L/usr/include/pbdata -L/usr/include/blasr -lpbdata -lblasr -lpthread
g++ gtest_main.a ../../src/cpp/AlnGraphBoost.o ../../src/cpp/Alignment.o ../../src/cpp/SimpleAligner.o SimpleAlignerTest.o -o test_simple_aligner -Wl,-z,relro -L/usr/lib/arm-linux-gnueabihf/blasr -L/usr/lib/arm-linux-gnueabihf/pbdata -L/usr/include/pbdata -L/usr/include/blasr -lpbdata -lblasr -lpthread
./test_alngraph
./test_simple_aligner
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
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 ] SimpleAligner.align (32 ms)
[ OK ] AlnGraphBoostTest.RawConsensus (9 ms)
[ RUN ] AlnGraphBoostTest.DanglingNodes
[ OK ] AlnGraphBoostTest.DanglingNodes (0 ms)
[----------] 2 tests from AlnGraphBoostTest (11 ms total)
[----------] Global test environment tear-down
[==========] 2 tests from 1 test case ran. (12 ms total)
[ PASSED ] 2 tests.
[----------] 1 test from SimpleAligner (35 ms total)
[----------] Global test environment tear-down
[==========] 1 test from 1 test case ran. (38 ms total)
[ PASSED ] 1 test.
=== Building test_alignment ===
g++ gtest_main.a ../../src/cpp/AlnGraphBoost.o ../../src/cpp/Alignment.o ../../src/cpp/SimpleAligner.o AlignmentTest.o -o test_alignment -Wl,-z,relro -L/usr/lib/arm-linux-gnueabihf/blasr -L/usr/lib/arm-linux-gnueabihf/pbdata -L/usr/include/pbdata -L/usr/include/blasr -lpbdata -lblasr -lpthread
./test_alignment
Running main() from gtest_main.cc
[==========] Running 4 tests from 2 test cases.
[----------] Global test environment set-up.
[----------] 3 tests from Alignment
[ RUN ] Alignment.Normalize
[ OK ] Alignment.Normalize (0 ms)
[ RUN ] Alignment.ParseBasic
[ OK ] Alignment.ParseBasic (1 ms)
[ RUN ] Alignment.ParseQuery
[ OK ] Alignment.ParseQuery (0 ms)
[----------] 3 tests from Alignment (2 ms total)
[----------] 1 test from AlnGraphBoostTest
[ RUN ] AlnGraphBoostTest.Trim
[ OK ] AlnGraphBoostTest.Trim (0 ms)
[----------] 1 test from AlnGraphBoostTest (0 ms total)
[----------] Global test environment tear-down
[==========] 4 tests from 2 test cases ran. (4 ms total)
[ PASSED ] 4 tests.
make[2]: Leaving directory '/«BUILDDIR»/pbdagcon-0~20151114+git1d12e13+ds/test/cpp'
make[1]: Leaving directory '/«BUILDDIR»/pbdagcon-0~20151114+git1d12e13+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_lintian -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 '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: 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 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_0~20151114+git1d12e13+ds-2_armhf.deb'.
dpkg-deb: building package 'pbdagcon' in '../pbdagcon_0~20151114+git1d12e13+ds-2_armhf.deb'.
dpkg-genchanges -B -mRaspbian wandboard test autobuilder <root@raspbian.org> >../pbdagcon_0~20151114+git1d12e13+ds-2_armhf.changes
dpkg-genchanges: warning: package pbdagcon-dbgsym listed in files list but not in control info
dpkg-genchanges: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build pbdagcon-0~20151114+git1d12e13+ds
dpkg-buildpackage: binary-only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
Build finished at 20160128-1101
Finished
────────
I: Built successfully
┌──────────────────────────────────────────────────────────────────────────────┐
│ Post Build Chroot │
└──────────────────────────────────────────────────────────────────────────────┘
┌──────────────────────────────────────────────────────────────────────────────┐
│ Changes │
└──────────────────────────────────────────────────────────────────────────────┘
pbdagcon_0~20151114+git1d12e13+ds-2_armhf.changes:
──────────────────────────────────────────────────
Format: 1.8
Date: Fri, 22 Jan 2016 07:43:17 -0800
Source: pbdagcon
Binary: pbdagcon
Architecture: armhf
Version: 0~20151114+git1d12e13+ds-2
Distribution: stretch-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Afif Elghraoui <afif@ghraoui.name>
Description:
pbdagcon - sequence consensus using directed acyclic graphs
Changes:
pbdagcon (0~20151114+git1d12e13+ds-2) unstable; urgency=medium
.
* Adjust packaging for differences in pbseqlib organization.
Checksums-Sha1:
9d65b0a2bf08ffff3241d8f3210200c6ff155b46 2145382 pbdagcon-dbgsym_0~20151114+git1d12e13+ds-2_armhf.deb
b6db7d9fd27ce63fdc15ba013a270bd42e187828 153474 pbdagcon_0~20151114+git1d12e13+ds-2_armhf.deb
Checksums-Sha256:
0b553daa0d9c6715b4dfa00cbd593118c14c23d4c342c3b5dbb04312fef1000e 2145382 pbdagcon-dbgsym_0~20151114+git1d12e13+ds-2_armhf.deb
3d66753ff7a930afb423eaf9b37afec9ad3818a50d458237ec0dd50d89fbc16a 153474 pbdagcon_0~20151114+git1d12e13+ds-2_armhf.deb
Files:
c0e0c8d83f95e35eddd26a2d3a940947 2145382 debug extra pbdagcon-dbgsym_0~20151114+git1d12e13+ds-2_armhf.deb
19bec27e61ed86208ed0ebe0e5ac414a 153474 science optional pbdagcon_0~20151114+git1d12e13+ds-2_armhf.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
pbdagcon-dbgsym_0~20151114+git1d12e13+ds-2_armhf.deb
────────────────────────────────────────────────────
new debian package, version 2.0.
size 2145382 bytes: control archive=514 bytes.
467 bytes, 13 lines control
106 bytes, 1 lines md5sums
Package: pbdagcon-dbgsym
Source: pbdagcon
Version: 0~20151114+git1d12e13+ds-2
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 2275
Depends: pbdagcon (= 0~20151114+git1d12e13+ds-2)
Section: debug
Priority: extra
Homepage: https://github.com/PacificBiosciences/pbdagcon
Description: Debug symbols for pbdagcon
Auto-Built-Package: debug-symbols
Build-Ids: 572bc11d64fc7fe6bc55577b8ab7573abc51b455
drwxr-xr-x root/root 0 2016-01-28 11:01 ./
drwxr-xr-x root/root 0 2016-01-28 11:01 ./usr/
drwxr-xr-x root/root 0 2016-01-28 11:01 ./usr/lib/
drwxr-xr-x root/root 0 2016-01-28 11:01 ./usr/lib/debug/
drwxr-xr-x root/root 0 2016-01-28 11:01 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2016-01-28 11:01 ./usr/lib/debug/.build-id/57/
-rw-r--r-- root/root 2318352 2016-01-28 11:01 ./usr/lib/debug/.build-id/57/2bc11d64fc7fe6bc55577b8ab7573abc51b455.debug
drwxr-xr-x root/root 0 2016-01-28 11:01 ./usr/share/
drwxr-xr-x root/root 0 2016-01-28 11:01 ./usr/share/doc/
lrwxrwxrwx root/root 0 2016-01-28 11:01 ./usr/share/doc/pbdagcon-dbgsym -> pbdagcon
pbdagcon_0~20151114+git1d12e13+ds-2_armhf.deb
─────────────────────────────────────────────
new debian package, version 2.0.
size 153474 bytes: control archive=1341 bytes.
1606 bytes, 30 lines control
722 bytes, 10 lines md5sums
Package: pbdagcon
Version: 0~20151114+git1d12e13+ds-2
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 425
Depends: libc6 (>= 2.4), libgcc1 (>= 1:3.5), libstdc++6 (>= 5.2), 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 2016-01-28 11:01 ./
drwxr-xr-x root/root 0 2016-01-28 11:00 ./usr/
drwxr-xr-x root/root 0 2016-01-28 11:01 ./usr/bin/
-rwxr-xr-x root/root 399652 2016-01-28 11:01 ./usr/bin/pbdagcon
drwxr-xr-x root/root 0 2016-01-28 11:00 ./usr/share/
drwxr-xr-x root/root 0 2016-01-28 11:00 ./usr/share/doc/
drwxr-xr-x root/root 0 2016-01-28 11:00 ./usr/share/doc/pbdagcon/
-rw-r--r-- root/root 2346 2015-07-01 23:46 ./usr/share/doc/pbdagcon/README.md.gz
-rw-r--r-- root/root 244 2016-01-22 18:38 ./usr/share/doc/pbdagcon/changelog.Debian.gz
-rw-r--r-- root/root 4720 2016-01-22 18:38 ./usr/share/doc/pbdagcon/copyright
drwxr-xr-x root/root 0 2016-01-28 11:00 ./usr/share/doc/pbdagcon/examples/
-rwxr-xr-x root/root 1588 2015-07-01 23:46 ./usr/share/doc/pbdagcon/examples/filterm4.py
-rw-r--r-- root/root 2224 2015-07-01 23:46 ./usr/share/doc/pbdagcon/examples/m4topre.py.gz
-rwxr-xr-x root/root 3046 2015-07-01 23:46 ./usr/share/doc/pbdagcon/examples/pbdagcon_wf.sh
-rw-r--r-- root/root 2682 2015-07-01 23:46 ./usr/share/doc/pbdagcon/examples/q-sense.py.gz
drwxr-xr-x root/root 0 2016-01-28 11:00 ./usr/share/lintian/
drwxr-xr-x root/root 0 2016-01-28 11:00 ./usr/share/lintian/overrides/
-rw-r--r-- root/root 272 2016-01-22 18:38 ./usr/share/lintian/overrides/pbdagcon
drwxr-xr-x root/root 0 2016-01-28 11:00 ./usr/share/man/
drwxr-xr-x root/root 0 2016-01-28 11:00 ./usr/share/man/man1/
-rw-r--r-- root/root 775 2016-01-28 11:00 ./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: 50928
Build-Time: 250
Distribution: stretch-staging
Host Architecture: armhf
Install-Time: 279
Job: pbdagcon_0~20151114+git1d12e13+ds-2
Machine Architecture: armhf
Package: pbdagcon
Package-Time: 577
Source-Version: 0~20151114+git1d12e13+ds-2
Space: 50928
Status: successful
Version: 0~20151114+git1d12e13+ds-2
────────────────────────────────────────────────────────────────────────────────
Finished at 20160128-1101
Build needed 00:09:37, 50928k disc space