pbdagcon →
0~20151114+git1d12e13+ds-3 →
armhf → 2016-08-14 23:43:31
sbuild (Debian sbuild) 0.66.0 (04 Oct 2015) on testwandboard
+==============================================================================+
| pbdagcon 0~20151114+git1d12e13+ds-3 (armhf) 14 Aug 2016 23:32 |
+==============================================================================+
Package: pbdagcon
Version: 0~20151114+git1d12e13+ds-3
Source Version: 0~20151114+git1d12e13+ds-3
Distribution: stretch-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'build/pbdagcon-6uojuS/pbdagcon-0~20151114+git1d12e13+ds' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/pbdagcon-6uojuS' with '<<BUILDDIR>>'
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/stretch-staging-armhf-sbuild-de934924-2b24-4585-af14-6c5f12d94a3d' 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 [9224 kB]
Get:3 http://172.17.0.1/private stretch-staging/main armhf Packages [11.2 MB]
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+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
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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 110 kB of source archives.
Get:1 http://172.17.0.1/private stretch-staging/main pbdagcon 0~20151114+git1d12e13+ds-3 (dsc) [2144 B]
Get:2 http://172.17.0.1/private stretch-staging/main pbdagcon 0~20151114+git1d12e13+ds-3 (tar) [103 kB]
Get:3 http://172.17.0.1/private stretch-staging/main pbdagcon 0~20151114+git1d12e13+ds-3 (diff) [5388 B]
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Download complete and in download only mode
Check architectures
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Check dependencies
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Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<<BUILDDIR>>/resolver-sIA2y6/apt_archive/sbuild-build-depends-core-dummy.deb'.
Warning: apt-key output should not be parsed (stdout is not a terminal)
OK
Get:1 file:/<<BUILDDIR>>/resolver-sIA2y6/apt_archive ./ InRelease
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Get:3 file:/<<BUILDDIR>>/resolver-sIA2y6/apt_archive ./ Release.gpg [299 B]
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Get:4 file:/<<BUILDDIR>>/resolver-sIA2y6/apt_archive ./ Sources [194 B]
Get:5 file:/<<BUILDDIR>>/resolver-sIA2y6/apt_archive ./ Packages [504 B]
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+------------------------------------------------------------------------------+
| Install core build dependencies (apt-based resolver) |
+------------------------------------------------------------------------------+
Installing build dependencies
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The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 1 not upgraded.
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Merged Build-Depends: debhelper (>= 9), libboost-dev, libtclap-dev, libpbdata-dev, libblasr-dev, libpbihdf-dev, libgtest-dev
Filtered Build-Depends: 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-WLO6nH/apt_archive/sbuild-build-depends-pbdagcon-dummy.deb'.
Warning: apt-key output should not be parsed (stdout is not a terminal)
OK
Get:1 file:/<<BUILDDIR>>/resolver-WLO6nH/apt_archive ./ InRelease
Ign:1 file:/<<BUILDDIR>>/resolver-WLO6nH/apt_archive ./ InRelease
Get:2 file:/<<BUILDDIR>>/resolver-WLO6nH/apt_archive ./ Release [2119 B]
Get:2 file:/<<BUILDDIR>>/resolver-WLO6nH/apt_archive ./ Release [2119 B]
Get:3 file:/<<BUILDDIR>>/resolver-WLO6nH/apt_archive ./ Release.gpg [299 B]
Get:3 file:/<<BUILDDIR>>/resolver-WLO6nH/apt_archive ./ Release.gpg [299 B]
Get:4 file:/<<BUILDDIR>>/resolver-WLO6nH/apt_archive ./ Sources [226 B]
Get:5 file:/<<BUILDDIR>>/resolver-WLO6nH/apt_archive ./ Packages [541 B]
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
W: file:///<<BUILDDIR>>/resolver-WLO6nH/apt_archive/./Release.gpg: Signature by key 3493EC2B8E6DC280C121C60435506D9A48F77B2E uses weak digest algorithm (SHA1)
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:
autoconf automake autopoint autotools-dev bsdmainutils debhelper
dh-autoreconf dh-strip-nondeterminism file gettext gettext-base groff-base
intltool-debian libaec0 libarchive-zip-perl libblasr libblasr-dev
libboost-dev libboost1.61-dev libbsd0 libcroco3 libffi6
libfile-stripnondeterminism-perl libgfortran3 libglib2.0-0 libgtest-dev
libhdf5-10 libhdf5-cpp-11 libicu57 libmagic-mgc libmagic1 libpbdata
libpbdata-dev libpbihdf libpbihdf-dev libpipeline1 libsigsegv2 libsz2
libtclap-dev libtimedate-perl libtool libunistring0 libxml2 m4 man-db
po-debconf
Suggested packages:
autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
vacation dh-make gettext-doc libasprintf-dev libgettextpo-dev groff
libboost-doc libboost1.61-doc libboost-atomic1.61-dev
libboost-chrono1.61-dev libboost-context1.61-dev libboost-coroutine1.61-dev
libboost-date-time1.61-dev libboost-exception1.61-dev
libboost-filesystem1.61-dev libboost-graph1.61-dev
libboost-graph-parallel1.61-dev libboost-iostreams1.61-dev
libboost-locale1.61-dev libboost-log1.61-dev libboost-math1.61-dev
libboost-mpi1.61-dev libboost-mpi-python1.61-dev
libboost-program-options1.61-dev libboost-python1.61-dev
libboost-random1.61-dev libboost-regex1.61-dev
libboost-serialization1.61-dev libboost-signals1.61-dev
libboost-system1.61-dev libboost-test1.61-dev libboost-thread1.61-dev
libboost-timer1.61-dev libboost-wave1.61-dev libboost1.61-tools-dev
libmpfrc++-dev libntl-dev libtool-doc gfortran | fortran95-compiler gcj-jdk
less www-browser libmail-box-perl
Recommended packages:
curl | wget | lynx-cur libglib2.0-data shared-mime-info xdg-user-dirs
libltdl-dev xml-core libmail-sendmail-perl
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils debhelper
dh-autoreconf dh-strip-nondeterminism file gettext gettext-base groff-base
intltool-debian libaec0 libarchive-zip-perl libblasr libblasr-dev
libboost-dev libboost1.61-dev libbsd0 libcroco3 libffi6
libfile-stripnondeterminism-perl libgfortran3 libglib2.0-0 libgtest-dev
libhdf5-10 libhdf5-cpp-11 libicu57 libmagic-mgc libmagic1 libpbdata
libpbdata-dev libpbihdf libpbihdf-dev libpipeline1 libsigsegv2 libsz2
libtclap-dev libtimedate-perl libtool libunistring0 libxml2 m4 man-db
po-debconf sbuild-build-depends-pbdagcon-dummy
0 upgraded, 47 newly installed, 0 to remove and 1 not upgraded.
Need to get 30.7 MB/30.7 MB of archives.
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Get:1 file:/<<BUILDDIR>>/resolver-WLO6nH/apt_archive ./ sbuild-build-depends-pbdagcon-dummy 0.invalid.0 [802 B]
Get:2 http://172.17.0.1/private stretch-staging/main armhf groff-base armhf 1.22.3-8 [1087 kB]
Get:3 http://172.17.0.1/private stretch-staging/main armhf libbsd0 armhf 0.8.3-1 [89.0 kB]
Get:4 http://172.17.0.1/private stretch-staging/main armhf bsdmainutils armhf 9.0.10 [177 kB]
Get:5 http://172.17.0.1/private stretch-staging/main armhf libpipeline1 armhf 1.4.1-2 [23.7 kB]
Get:6 http://172.17.0.1/private stretch-staging/main armhf man-db armhf 2.7.5-1 [975 kB]
Get:7 http://172.17.0.1/private stretch-staging/main armhf libmagic-mgc armhf 1:5.28-4 [210 kB]
Get:8 http://172.17.0.1/private stretch-staging/main armhf libmagic1 armhf 1:5.28-4 [104 kB]
Get:9 http://172.17.0.1/private stretch-staging/main armhf file armhf 1:5.28-4 [62.7 kB]
Get:10 http://172.17.0.1/private stretch-staging/main armhf gettext-base armhf 0.19.8.1-1 [117 kB]
Get:11 http://172.17.0.1/private stretch-staging/main armhf libicu57 armhf 57.1-2 [7404 kB]
Get:12 http://172.17.0.1/private stretch-staging/main armhf libxml2 armhf 2.9.4+dfsg1-1+b1 [803 kB]
Get:13 http://172.17.0.1/private stretch-staging/main armhf libsigsegv2 armhf 2.10-5 [28.4 kB]
Get:14 http://172.17.0.1/private stretch-staging/main armhf m4 armhf 1.4.17-5 [239 kB]
Get:15 http://172.17.0.1/private stretch-staging/main armhf autoconf all 2.69-10 [338 kB]
Get:16 http://172.17.0.1/private stretch-staging/main armhf autotools-dev all 20160430.1 [72.6 kB]
Get:17 http://172.17.0.1/private stretch-staging/main armhf automake all 1:1.15-4 [735 kB]
Get:18 http://172.17.0.1/private stretch-staging/main armhf autopoint all 0.19.8.1-1 [433 kB]
Get:19 http://172.17.0.1/private stretch-staging/main armhf libglib2.0-0 armhf 2.48.1-2 [2546 kB]
Get:20 http://172.17.0.1/private stretch-staging/main armhf libcroco3 armhf 0.6.11-1 [131 kB]
Get:21 http://172.17.0.1/private stretch-staging/main armhf libunistring0 armhf 0.9.6+really0.9.3-0.1 [252 kB]
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Get:23 http://172.17.0.1/private stretch-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:24 http://172.17.0.1/private stretch-staging/main armhf po-debconf all 1.0.19 [249 kB]
Get:25 http://172.17.0.1/private stretch-staging/main armhf libarchive-zip-perl all 1.58-1 [95.5 kB]
Get:26 http://172.17.0.1/private stretch-staging/main armhf libfile-stripnondeterminism-perl all 0.022-1 [13.1 kB]
Get:27 http://172.17.0.1/private stretch-staging/main armhf libtimedate-perl all 2.3000-2 [42.2 kB]
Get:28 http://172.17.0.1/private stretch-staging/main armhf dh-strip-nondeterminism all 0.022-1 [7902 B]
Get:29 http://172.17.0.1/private stretch-staging/main armhf libtool all 2.4.6-0.1 [200 kB]
Get:30 http://172.17.0.1/private stretch-staging/main armhf dh-autoreconf all 12 [15.8 kB]
Get:31 http://172.17.0.1/private stretch-staging/main armhf debhelper all 9.20160709 [799 kB]
Get:32 http://172.17.0.1/private stretch-staging/main armhf libaec0 armhf 0.3.2-1 [19.4 kB]
Get:33 http://172.17.0.1/private stretch-staging/main armhf libpbdata armhf 0~20151014+gitbe5d1bf-2 [91.1 kB]
Get:34 http://172.17.0.1/private stretch-staging/main armhf libgfortran3 armhf 6.1.1-11+rpi1 [166 kB]
Get:35 http://172.17.0.1/private stretch-staging/main armhf libsz2 armhf 0.3.2-1 [5836 B]
Get:36 http://172.17.0.1/private stretch-staging/main armhf libhdf5-10 armhf 1.8.16+docs-8 [981 kB]
Get:37 http://172.17.0.1/private stretch-staging/main armhf libhdf5-cpp-11 armhf 1.8.16+docs-8 [115 kB]
Get:38 http://172.17.0.1/private stretch-staging/main armhf libpbihdf armhf 0~20151014+gitbe5d1bf-2 [102 kB]
Get:39 http://172.17.0.1/private stretch-staging/main armhf libblasr armhf 0~20151014+gitbe5d1bf-2 [786 kB]
Get:40 http://172.17.0.1/private stretch-staging/main armhf libblasr-dev armhf 0~20151014+gitbe5d1bf-2 [1614 kB]
Get:41 http://172.17.0.1/private stretch-staging/main armhf libboost1.61-dev armhf 1.61.0+dfsg-2.1 [6851 kB]
Get:42 http://172.17.0.1/private stretch-staging/main armhf libboost-dev armhf 1.61.0.2 [3758 B]
Get:43 http://172.17.0.1/private stretch-staging/main armhf libgtest-dev armhf 1.7.0-4 [200 kB]
Get:44 http://172.17.0.1/private stretch-staging/main armhf libpbdata-dev armhf 0~20151014+gitbe5d1bf-2 [151 kB]
Get:45 http://172.17.0.1/private stretch-staging/main armhf libpbihdf-dev armhf 0~20151014+gitbe5d1bf-2 [194 kB]
Get:46 http://172.17.0.1/private stretch-staging/main armhf libtclap-dev armhf 1.2.1-1 [727 kB]
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+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.5.0-1-armmp armhf (armv7l)
Toolchain package versions: binutils_2.26.1-1 dpkg-dev_1.18.10 g++-6_6.1.1-11+rpi1 gcc-6_6.1.1-11+rpi1 libc6-dev_2.23-4 libstdc++-6-dev_6.1.1-11+rpi1 libstdc++6_6.1.1-11+rpi1 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch
Package versions: adduser_3.115 apt_1.3~pre3 autoconf_2.69-10 automake_1:1.15-4 autopoint_0.19.8.1-1 autotools-dev_20160430.1 base-files_9.6+rpi1 base-passwd_3.5.39 bash_4.3-15 binutils_2.26.1-1 bsdmainutils_9.0.10 bsdutils_1:2.28-6 build-essential_12.2 bzip2_1.0.6-8 console-setup_1.147 console-setup-linux_1.147 coreutils_8.25-2 cpio_2.11+dfsg-5 cpp_4:6.1.1-1 cpp-6_6.1.1-11+rpi1 dash_0.5.8-2.3 debconf_1.5.59 debfoster_2.7-2.1 debhelper_9.20160709 debianutils_4.8 dh-autoreconf_12 dh-strip-nondeterminism_0.022-1 diffutils_1:3.3-3 dmsetup_2:1.02.130-1 dpkg_1.18.10 dpkg-dev_1.18.10 e2fslibs_1.43.1-1 e2fsprogs_1.43.1-1 fakeroot_1.21-1 file_1:5.28-4 findutils_4.6.0+git+20160703-2 fuse2fs_1.43.1-1 g++_4:6.1.1-1 g++-6_6.1.1-11+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-5-base_5.4.0-4 gcc-6_6.1.1-11+rpi1 gcc-6-base_6.1.1-11+rpi1 gettext_0.19.8.1-1 gettext-base_0.19.8.1-1 gnupg_1.4.20-6 gpgv_1.4.20-6 grep_2.25-6 groff-base_1.22.3-8 gzip_1.6-5 hostname_3.18 ifupdown_0.8.13 init_1.42 init-system-helpers_1.42 initscripts_2.88dsf-59.8 insserv_1.14.0-5.4 intltool-debian_0.35.0+20060710.4 iproute2_4.6.0-1 kbd_2.0.3-2 keyboard-configuration_1.147 klibc-utils_2.0.4-9+rpi1 kmod_22-1.1 libacl1_2.2.52-3 libaec0_0.3.2-1 libapparmor1_2.10.95-4 libapt-pkg5.0_1.3~pre3 libarchive-zip-perl_1.58-1 libasan3_6.1.1-11+rpi1 libatm1_1:2.5.1-1.6 libatomic1_6.1.1-11+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.6.5-1 libaudit1_1:2.6.5-1 libblasr_0~20151014+gitbe5d1bf-2 libblasr-dev_0~20151014+gitbe5d1bf-2 libblkid1_2.28-6 libboost-dev_1.61.0.2 libboost1.61-dev_1.61.0+dfsg-2.1 libbsd0_0.8.3-1 libbz2-1.0_1.0.6-8 libc-bin_2.23-4 libc-dev-bin_2.23-4 libc6_2.23-4 libc6-dev_2.23-4 libcap-ng0_0.7.7-3 libcap2_1:2.25-1 libcap2-bin_1:2.25-1 libcc1-0_6.1.1-11+rpi1 libcomerr2_1.43.1-1 libcroco3_0.6.11-1 libcryptsetup4_2:1.7.0-2 libdb5.3_5.3.28-12 libdbus-1-3_1.10.8-1 libdebconfclient0_0.215 libdevmapper1.02.1_2:1.02.130-1 libdpkg-perl_1.18.10 libdrm2_2.4.70-1 libfakeroot_1.21-1 libfdisk1_2.28-6 libffi6_3.2.1-4 libfile-stripnondeterminism-perl_0.022-1 libfuse2_2.9.7-1 libgc1c2_1:7.4.2-8 libgcc-6-dev_6.1.1-11+rpi1 libgcc1_1:6.1.1-11+rpi1 libgcrypt20_1.7.2-2 libgdbm3_1.8.3-14 libgfortran3_6.1.1-11+rpi1 libglib2.0-0_2.48.1-2 libgmp10_2:6.1.1+dfsg-1 libgomp1_6.1.1-11+rpi1 libgpg-error0_1.24-1 libgtest-dev_1.7.0-4 libhdf5-10_1.8.16+docs-8 libhdf5-cpp-11_1.8.16+docs-8 libicu57_57.1-2 libidn11_1.33-1 libisl15_0.17.1-1 libklibc_2.0.4-9+rpi1 libkmod2_22-1.1 liblocale-gettext-perl_1.07-3 liblz4-1_0.0~r131-2 liblzma5_5.1.1alpha+20120614-2.1 libmagic-mgc_1:5.28-4 libmagic1_1:5.28-4 libmount1_2.28-6 libmpc3_1.0.3-1 libmpfr4_3.1.4-2 libncurses5_6.0+20160625-1 libncursesw5_6.0+20160625-1 libpam-modules_1.1.8-3.3 libpam-modules-bin_1.1.8-3.3 libpam-runtime_1.1.8-3.3 libpam0g_1.1.8-3.3 libpbdata_0~20151014+gitbe5d1bf-2 libpbdata-dev_0~20151014+gitbe5d1bf-2 libpbihdf_0~20151014+gitbe5d1bf-2 libpbihdf-dev_0~20151014+gitbe5d1bf-2 libpcre3_2:8.39-1 libperl5.22_5.22.2-3 libpipeline1_1.4.1-2 libplymouth4_0.9.2-3 libpng12-0_1.2.54-6 libprocps6_2:3.3.12-2 libreadline6_6.3-8+b3 libseccomp2_2.3.1-2 libselinux1_2.5-3 libsemanage-common_2.5-1 libsemanage1_2.5-1 libsepol1_2.5-1 libsigsegv2_2.10-5 libsmartcols1_2.28-6 libss2_1.43.1-1 libstdc++-6-dev_6.1.1-11+rpi1 libstdc++6_6.1.1-11+rpi1 libsystemd0_230-7+b1 libsz2_0.3.2-1 libtclap-dev_1.2.1-1 libtext-charwidth-perl_0.04-7+b6 libtext-iconv-perl_1.7-5+b7 libtext-wrapi18n-perl_0.06-7.1 libtimedate-perl_2.3000-2 libtinfo5_6.0+20160625-1 libtool_2.4.6-0.1 libubsan0_6.1.1-11+rpi1 libudev1_230-7+b1 libunistring0_0.9.6+really0.9.3-0.1 libusb-0.1-4_2:0.1.12-30 libustr-1.0-1_1.0.4-5 libuuid1_2.28-6 libxml2_2.9.4+dfsg1-1+b1 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch login_1:4.2-3.1 lsb-base_9.20160629+rpi1 m4_1.4.17-5 make_4.1-9 makedev_2.3.1-93 man-db_2.7.5-1 manpages_4.07-1 mawk_1.3.3-17 mount_2.28-6 multiarch-support_2.23-4 ncurses-base_6.0+20160625-1 ncurses-bin_6.0+20160625-1 netbase_5.3 passwd_1:4.2-3.1 patch_2.7.5-1 perl_5.22.2-3 perl-base_5.22.2-3 perl-modules-5.22_5.22.2-3 po-debconf_1.0.19 procps_2:3.3.12-2 psmisc_22.21-2.1 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_4.2.2-7.1 sensible-utils_0.0.9 startpar_0.59-3.1 systemd_230-7+b1 systemd-sysv_230-7+b1 sysv-rc_2.88dsf-59.8 sysvinit-utils_2.88dsf-59.8 tar_1.29b-1 tzdata_2016f-1 udev_230-7+b1 util-linux_2.28-6 xkb-data_2.17-1 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 Thu Aug 4 07:44:37 2016 UTC using RSA key ID 3AF9DDC1
gpgv: Can't check signature: public key not found
dpkg-source: warning: failed to verify signature on ./pbdagcon_0~20151114+git1d12e13+ds-3.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-3.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-de934924-2b24-4585-af14-6c5f12d94a3d
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package pbdagcon
dpkg-buildpackage: info: source version 0~20151114+git1d12e13+ds-3
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build pbdagcon-0~20151114+git1d12e13+ds
dpkg-buildpackage: info: host architecture armhf
fakeroot debian/rules clean
dh clean --parallel
dh_testdir -O--parallel
dh_auto_clean -O--parallel
make -j4 clean
make[1]: Entering directory '/<<BUILDDIR>>/pbdagcon-0~20151114+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 -fdebug-prefix-map=/<<BUILDDIR>>/pbdagcon-0~20151114+git1d12e13+ds=. -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 -fdebug-prefix-map=/<<BUILDDIR>>/pbdagcon-0~20151114+git1d12e13+ds=. -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 -fdebug-prefix-map=/<<BUILDDIR>>/pbdagcon-0~20151114+git1d12e13+ds=. -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 -fdebug-prefix-map=/<<BUILDDIR>>/pbdagcon-0~20151114+git1d12e13+ds=. -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 -fdebug-prefix-map=/<<BUILDDIR>>/pbdagcon-0~20151114+git1d12e13+ds=. -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<T>&, 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<T>&, 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<T>&, 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<T>&, 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<T>&, 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<T>&, 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<T>&, 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<T>&, DNALength&, DNALength&, int) [with T_Point = Fragment]':
/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<T>&, 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++ -I/usr/src/gtest -g -Wall -Wextra -pthread -c /usr/src/gtest/src/gtest-all.cc
g++ -I/usr/src/gtest -g -Wall -Wextra -pthread -c /usr/src/gtest/src/gtest_main.cc
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbdagcon-0~20151114+git1d12e13+ds=. -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 -fdebug-prefix-map=/<<BUILDDIR>>/pbdagcon-0~20151114+git1d12e13+ds=. -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 -fdebug-prefix-map=/<<BUILDDIR>>/pbdagcon-0~20151114+git1d12e13+ds=. -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_alngraph ===
=== Building test_simple_aligner ===
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
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
=== 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_alngraph
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 (0 ms)
[ RUN ] AlnGraphBoostTest.DanglingNodes
[ OK ] AlnGraphBoostTest.DanglingNodes (1 ms)
[----------] 2 tests from AlnGraphBoostTest (3 ms total)
[----------] Global test environment tear-down
[==========] 2 tests from 1 test case ran. (6 ms total)
[ PASSED ] 2 tests.
./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
[ OK ] SimpleAligner.align (36 ms)
[----------] 1 test from SimpleAligner (36 ms total)
[----------] Global test environment tear-down
[==========] 1 test from 1 test case ran. (38 ms total)
[ PASSED ] 1 test.
./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 (1 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. (3 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-3_armhf.deb'.
dpkg-deb: building package 'pbdagcon' in '../pbdagcon_0~20151114+git1d12e13+ds-3_armhf.deb'.
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../pbdagcon_0~20151114+git1d12e13+ds-3_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build pbdagcon-0~20151114+git1d12e13+ds
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 20160814-2343
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
pbdagcon_0~20151114+git1d12e13+ds-3_armhf.changes:
--------------------------------------------------
Format: 1.8
Date: Thu, 04 Aug 2016 00:42:55 -0700
Source: pbdagcon
Binary: pbdagcon
Architecture: armhf
Version: 0~20151114+git1d12e13+ds-3
Distribution: stretch-staging
Urgency: low
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Afif Elghraoui <afif@debian.org>
Description:
pbdagcon - sequence consensus using directed acyclic graphs
Closes: 831105
Changes:
pbdagcon (0~20151114+git1d12e13+ds-3) unstable; urgency=low
.
* Bump Standards-Version to 3.9.8
* Update email address and bump copyright year
* Use encrypted protocols for VCS URLs
* Do not use -isystem while building (Closes: #831105)
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Files:
a3e27539851028651f9d77c51af286c8 2144010 debug extra pbdagcon-dbgsym_0~20151114+git1d12e13+ds-3_armhf.deb
e864aaa607ed8c76008b8c2d03488540 153724 science optional pbdagcon_0~20151114+git1d12e13+ds-3_armhf.deb
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pbdagcon-dbgsym_0~20151114+git1d12e13+ds-3_armhf.deb
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new debian package, version 2.0.
size 2144010 bytes: control archive=510 bytes.
467 bytes, 13 lines control
106 bytes, 1 lines md5sums
Package: pbdagcon-dbgsym
Source: pbdagcon
Version: 0~20151114+git1d12e13+ds-3
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 2266
Depends: pbdagcon (= 0~20151114+git1d12e13+ds-3)
Section: debug
Priority: extra
Homepage: https://github.com/PacificBiosciences/pbdagcon
Description: Debug symbols for pbdagcon
Auto-Built-Package: debug-symbols
Build-Ids: 7d64d4847903c35f7a9baf58825977fb4af1dd25
drwxr-xr-x root/root 0 2016-08-04 07:42 ./
drwxr-xr-x root/root 0 2016-08-04 07:42 ./usr/
drwxr-xr-x root/root 0 2016-08-04 07:42 ./usr/lib/
drwxr-xr-x root/root 0 2016-08-04 07:42 ./usr/lib/debug/
drwxr-xr-x root/root 0 2016-08-04 07:42 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2016-08-04 07:42 ./usr/lib/debug/.build-id/7d/
-rw-r--r-- root/root 2309928 2016-08-04 07:42 ./usr/lib/debug/.build-id/7d/64d4847903c35f7a9baf58825977fb4af1dd25.debug
drwxr-xr-x root/root 0 2016-08-04 07:42 ./usr/share/
drwxr-xr-x root/root 0 2016-08-04 07:42 ./usr/share/doc/
lrwxrwxrwx root/root 0 2016-08-04 07:42 ./usr/share/doc/pbdagcon-dbgsym -> pbdagcon
pbdagcon_0~20151114+git1d12e13+ds-3_armhf.deb
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new debian package, version 2.0.
size 153724 bytes: control archive=1339 bytes.
1604 bytes, 30 lines control
722 bytes, 10 lines md5sums
Package: pbdagcon
Version: 0~20151114+git1d12e13+ds-3
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 (>= 6), libpbdata, libblasr
Suggests: blasr
Section: science
Priority: optional
Homepage: https://github.com/PacificBiosciences/pbdagcon
Description: sequence consensus using directed acyclic graphs
pbdagcon is a tool that implements DAGCon (Directed Acyclic Graph Consensus)
which is a sequence consensus algorithm based on using directed acyclic
graphs to encode multiple sequence alignment.
.
It uses the alignment information from blasr to align sequence reads to a
"backbone" sequence. Based on the underlying alignment directed acyclic graph
(DAG), it will be able to use the new information from the reads to find the
discrepancies between the reads and the "backbone" sequences. A dynamic
programming process is then applied to the DAG to find the optimum sequence
of bases as the consensus. The new consensus can be used as a new backbone
sequence to iteratively improve the consensus quality.
.
While the code is developed for processing PacBio(TM) raw sequence data,
the algorithm can be used for general consensus purpose. Currently, it only
takes FASTA input. For shorter read sequences, one might need to adjust the
blasr alignment parameters to get the alignment string properly.
.
The code and the underlying graphical data structure have been used for some
algorithm development prototyping including phasing reads and pre-assembly.
drwxr-xr-x root/root 0 2016-08-04 07:42 ./
drwxr-xr-x root/root 0 2016-08-04 07:42 ./usr/
drwxr-xr-x root/root 0 2016-08-04 07:42 ./usr/bin/
-rwxr-xr-x root/root 399664 2016-08-04 07:42 ./usr/bin/pbdagcon
drwxr-xr-x root/root 0 2016-08-04 07:42 ./usr/share/
drwxr-xr-x root/root 0 2016-08-04 07:42 ./usr/share/doc/
drwxr-xr-x root/root 0 2016-08-04 07:42 ./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 396 2016-08-04 07:42 ./usr/share/doc/pbdagcon/changelog.Debian.gz
-rw-r--r-- root/root 4723 2016-08-04 07:11 ./usr/share/doc/pbdagcon/copyright
drwxr-xr-x root/root 0 2016-08-04 07:42 ./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 2016-08-04 07:42 ./usr/share/lintian/
drwxr-xr-x root/root 0 2016-08-04 07:42 ./usr/share/lintian/overrides/
-rw-r--r-- root/root 272 2016-01-22 15:17 ./usr/share/lintian/overrides/pbdagcon
drwxr-xr-x root/root 0 2016-08-04 07:42 ./usr/share/man/
drwxr-xr-x root/root 0 2016-08-04 07:42 ./usr/share/man/man1/
-rw-r--r-- root/root 775 2016-08-04 07:42 ./usr/share/man/man1/pbdagcon.1.gz
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| Cleanup |
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Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
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| Summary |
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Build Architecture: armhf
Build-Space: 51128
Build-Time: 292
Distribution: stretch-staging
Host Architecture: armhf
Install-Time: 293
Job: pbdagcon_0~20151114+git1d12e13+ds-3
Machine Architecture: armhf
Package: pbdagcon
Package-Time: 633
Source-Version: 0~20151114+git1d12e13+ds-3
Space: 51128
Status: successful
Version: 0~20151114+git1d12e13+ds-3
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Finished at 20160814-2343
Build needed 00:10:33, 51128k disc space