pbdagcon →
0.3+20161121+ds-1+b1 →
armhf → 2017-08-01 06:43:23
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-01
+==============================================================================+
| pbdagcon 0.3+20161121+ds-1+b1 (armhf) Tue, 01 Aug 2017 06:20:13 +0000 |
+==============================================================================+
Package: pbdagcon
Version: 0.3+20161121+ds-1+b1
Source Version: 0.3+20161121+ds-1
Distribution: buster-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/run/schroot/mount/buster-staging-armhf-sbuild-06792f72-16b2-4cab-a8c9-6b56f6d0adef' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private buster-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private buster-staging/main Sources [10.0 MB]
Get:3 http://172.17.0.1/private buster-staging/main armhf Packages [11.9 MB]
Fetched 22.0 MB in 25s (878 kB/s)
Reading package lists...
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: 'pbdagcon' packaging is maintained in the 'Git' version control system at:
https://anonscm.debian.org/git/debian-med/pbdagcon.git
Please use:
git clone https://anonscm.debian.org/git/debian-med/pbdagcon.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 263 kB of source archives.
Get:1 http://172.17.0.1/private buster-staging/main pbdagcon 0.3+20161121+ds-1 (dsc) [2097 B]
Get:2 http://172.17.0.1/private buster-staging/main pbdagcon 0.3+20161121+ds-1 (tar) [256 kB]
Get:3 http://172.17.0.1/private buster-staging/main pbdagcon 0.3+20161121+ds-1 (diff) [4872 B]
Fetched 263 kB in 0s (2317 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/pbdagcon-SiHx5v/pbdagcon-0.3+20161121+ds' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/pbdagcon-SiHx5v' with '<<BUILDDIR>>'
+------------------------------------------------------------------------------+
| Install build-essential |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<<BUILDDIR>>/resolver-hcpNtq/apt_archive/sbuild-build-depends-core-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy
dpkg-scanpackages: info: Wrote 1 entries to output Packages file.
gpg: keybox '/<<BUILDDIR>>/resolver-hcpNtq/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-hcpNtq/gpg/trustdb.gpg: trustdb created
gpg: key 35506D9A48F77B2E: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg: imported: 1
gpg: key 35506D9A48F77B2E: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 35506D9A48F77B2E: secret key imported
gpg: Total number processed: 1
gpg: unchanged: 1
gpg: secret keys read: 1
gpg: secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-hcpNtq/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-hcpNtq/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-hcpNtq/apt_archive ./ Release.gpg [370 B]
Ign:3 copy:/<<BUILDDIR>>/resolver-hcpNtq/apt_archive ./ Release.gpg
Get:4 copy:/<<BUILDDIR>>/resolver-hcpNtq/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-hcpNtq/apt_archive ./ Packages [432 B]
Fetched 2108 B in 0s (2770 B/s)
Reading package lists...
W: copy:///<<BUILDDIR>>/resolver-hcpNtq/apt_archive/./Release.gpg: The key(s) in the keyring /etc/apt/trusted.gpg.d/sbuild-build-depends-archive.gpg are ignored as the file is not readable by user '_apt' executing apt-key.
W: GPG error: copy:/<<BUILDDIR>>/resolver-hcpNtq/apt_archive ./ Release: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY 35506D9A48F77B2E
Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
ca-certificates libssl1.1 openssl
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 15 not upgraded.
Need to get 774 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-hcpNtq/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [774 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 774 B in 0s (0 B/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 14837 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper (>= 10), python, zlib1g-dev, libhdf5-dev, libboost-dev, libtclap-dev, libpbseq-dev, libpbbam-dev, googletest
Filtered Build-Depends: debhelper (>= 10), python, zlib1g-dev, libhdf5-dev, libboost-dev, libtclap-dev, libpbseq-dev, libpbbam-dev, googletest
dpkg-deb: building package 'sbuild-build-depends-pbdagcon-dummy' in '/<<BUILDDIR>>/resolver-hcpNtq/apt_archive/sbuild-build-depends-pbdagcon-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-pbdagcon-dummy
dpkg-scanpackages: info: Wrote 2 entries to output Packages file.
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-hcpNtq/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-hcpNtq/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-hcpNtq/apt_archive ./ Release.gpg [370 B]
Ign:3 copy:/<<BUILDDIR>>/resolver-hcpNtq/apt_archive ./ Release.gpg
Get:4 copy:/<<BUILDDIR>>/resolver-hcpNtq/apt_archive ./ Sources [537 B]
Get:5 copy:/<<BUILDDIR>>/resolver-hcpNtq/apt_archive ./ Packages [619 B]
Fetched 2489 B in 0s (3444 B/s)
Reading package lists...
W: copy:///<<BUILDDIR>>/resolver-hcpNtq/apt_archive/./Release.gpg: The key(s) in the keyring /etc/apt/trusted.gpg.d/sbuild-build-depends-archive.gpg are ignored as the file is not readable by user '_apt' executing apt-key.
W: GPG error: copy:/<<BUILDDIR>>/resolver-hcpNtq/apt_archive ./ Release: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY 35506D9A48F77B2E
Reading package lists...
Install pbdagcon build dependencies (apt-based resolver)
--------------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
ca-certificates openssl
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils debhelper
dh-autoreconf dh-strip-nondeterminism file gettext gettext-base googletest
groff-base hdf5-helpers intltool-debian libaec-dev libaec0
libarchive-zip-perl libblasr libblasr-dev libboost-dev libboost1.62-dev
libbsd0 libcroco3 libcurl3-gnutls libexpat1 libfile-stripnondeterminism-perl
libgfortran3 libglib2.0-0 libgssapi-krb5-2 libhdf5-100 libhdf5-cpp-100
libhdf5-dev libhts-dev libhts2 libicu57 libjpeg-dev libjpeg62-turbo
libjpeg62-turbo-dev libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0
libldap-2.4-2 libldap-common libmagic-mgc libmagic1 libnghttp2-14 libpbbam
libpbbam-dev libpbdata libpbdata-dev libpbihdf libpbihdf-dev libpbseq-dev
libpipeline1 libpsl5 libpython-stdlib libpython2.7-minimal
libpython2.7-stdlib librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2
libssh2-1 libssl-dev libsz2 libtclap-dev libtimedate-perl libtool libxml2 m4
man-db mime-support po-debconf python python-minimal python2.7
python2.7-minimal zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
vacation dh-make gettext-doc libasprintf-dev libgettextpo-dev groff
libboost-doc libboost1.62-doc libboost-atomic1.62-dev
libboost-chrono1.62-dev libboost-context1.62-dev libboost-coroutine1.62-dev
libboost-date-time1.62-dev libboost-exception1.62-dev libboost-fiber1.62-dev
libboost-filesystem1.62-dev libboost-graph1.62-dev
libboost-graph-parallel1.62-dev libboost-iostreams1.62-dev
libboost-locale1.62-dev libboost-log1.62-dev libboost-math1.62-dev
libboost-mpi1.62-dev libboost-mpi-python1.62-dev
libboost-program-options1.62-dev libboost-python1.62-dev
libboost-random1.62-dev libboost-regex1.62-dev
libboost-serialization1.62-dev libboost-signals1.62-dev
libboost-system1.62-dev libboost-test1.62-dev libboost-thread1.62-dev
libboost-timer1.62-dev libboost-type-erasure1.62-dev libboost-wave1.62-dev
libboost1.62-tools-dev libmpfrc++-dev libntl-dev krb5-doc krb5-user
libhdf5-doc libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc less
www-browser libmail-box-perl python-doc python-tk python2.7-doc
binfmt-support
Recommended packages:
curl | wget | lynx-cur libarchive-cpio-perl libglib2.0-data shared-mime-info
xdg-user-dirs krb5-locales publicsuffix libsasl2-modules libssl-doc
libltdl-dev xml-core libmail-sendmail-perl
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils debhelper
dh-autoreconf dh-strip-nondeterminism file gettext gettext-base googletest
groff-base hdf5-helpers intltool-debian libaec-dev libaec0
libarchive-zip-perl libblasr libblasr-dev libboost-dev libboost1.62-dev
libbsd0 libcroco3 libcurl3-gnutls libexpat1 libfile-stripnondeterminism-perl
libgfortran3 libglib2.0-0 libgssapi-krb5-2 libhdf5-100 libhdf5-cpp-100
libhdf5-dev libhts-dev libhts2 libicu57 libjpeg-dev libjpeg62-turbo
libjpeg62-turbo-dev libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0
libldap-2.4-2 libldap-common libmagic-mgc libmagic1 libnghttp2-14 libpbbam
libpbbam-dev libpbdata libpbdata-dev libpbihdf libpbihdf-dev libpbseq-dev
libpipeline1 libpsl5 libpython-stdlib libpython2.7-minimal
libpython2.7-stdlib librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2
libssh2-1 libssl-dev libsz2 libtclap-dev libtimedate-perl libtool libxml2 m4
man-db mime-support po-debconf python python-minimal python2.7
python2.7-minimal sbuild-build-depends-pbdagcon-dummy zlib1g-dev
0 upgraded, 81 newly installed, 0 to remove and 15 not upgraded.
Need to get 42.3 MB of archives.
After this operation, 249 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-hcpNtq/apt_archive ./ sbuild-build-depends-pbdagcon-dummy 0.invalid.0 [822 B]
Get:2 http://172.17.0.1/private buster-staging/main armhf groff-base armhf 1.22.3-9 [1005 kB]
Get:3 http://172.17.0.1/private buster-staging/main armhf libbsd0 armhf 0.8.6-1 [95.7 kB]
Get:4 http://172.17.0.1/private buster-staging/main armhf bsdmainutils armhf 9.0.12+nmu1 [178 kB]
Get:5 http://172.17.0.1/private buster-staging/main armhf libpipeline1 armhf 1.4.2-1 [24.2 kB]
Get:6 http://172.17.0.1/private buster-staging/main armhf man-db armhf 2.7.6.1-2 [1014 kB]
Get:7 http://172.17.0.1/private buster-staging/main armhf libpython2.7-minimal armhf 2.7.13-2 [389 kB]
Get:8 http://172.17.0.1/private buster-staging/main armhf python2.7-minimal armhf 2.7.13-2 [1178 kB]
Get:9 http://172.17.0.1/private buster-staging/main armhf python-minimal armhf 2.7.13-2 [40.5 kB]
Get:10 http://172.17.0.1/private buster-staging/main armhf mime-support all 3.60 [36.7 kB]
Get:11 http://172.17.0.1/private buster-staging/main armhf libexpat1 armhf 2.2.2-2 [66.3 kB]
Get:12 http://172.17.0.1/private buster-staging/main armhf libpython2.7-stdlib armhf 2.7.13-2 [1827 kB]
Get:13 http://172.17.0.1/private buster-staging/main armhf python2.7 armhf 2.7.13-2 [285 kB]
Get:14 http://172.17.0.1/private buster-staging/main armhf libpython-stdlib armhf 2.7.13-2 [20.0 kB]
Get:15 http://172.17.0.1/private buster-staging/main armhf python armhf 2.7.13-2 [154 kB]
Get:16 http://172.17.0.1/private buster-staging/main armhf libmagic-mgc armhf 1:5.30-1 [222 kB]
Get:17 http://172.17.0.1/private buster-staging/main armhf libmagic1 armhf 1:5.30-1 [105 kB]
Get:18 http://172.17.0.1/private buster-staging/main armhf file armhf 1:5.30-1 [63.4 kB]
Get:19 http://172.17.0.1/private buster-staging/main armhf gettext-base armhf 0.19.8.1-2+b1 [117 kB]
Get:20 http://172.17.0.1/private buster-staging/main armhf libkeyutils1 armhf 1.5.9-9 [11.9 kB]
Get:21 http://172.17.0.1/private buster-staging/main armhf libkrb5support0 armhf 1.15.1-2 [58.4 kB]
Get:22 http://172.17.0.1/private buster-staging/main armhf libk5crypto3 armhf 1.15.1-2 [115 kB]
Get:23 http://172.17.0.1/private buster-staging/main armhf libkrb5-3 armhf 1.15.1-2 [265 kB]
Get:24 http://172.17.0.1/private buster-staging/main armhf libgssapi-krb5-2 armhf 1.15.1-2 [132 kB]
Get:25 http://172.17.0.1/private buster-staging/main armhf libsasl2-modules-db armhf 2.1.27~101-g0780600+dfsg-3 [66.9 kB]
Get:26 http://172.17.0.1/private buster-staging/main armhf libsasl2-2 armhf 2.1.27~101-g0780600+dfsg-3 [98.1 kB]
Get:27 http://172.17.0.1/private buster-staging/main armhf libldap-common all 2.4.45+dfsg-1 [87.0 kB]
Get:28 http://172.17.0.1/private buster-staging/main armhf libldap-2.4-2 armhf 2.4.45+dfsg-1 [197 kB]
Get:29 http://172.17.0.1/private buster-staging/main armhf libicu57 armhf 57.1-6 [7427 kB]
Get:30 http://172.17.0.1/private buster-staging/main armhf libxml2 armhf 2.9.4+dfsg1-3 [601 kB]
Get:31 http://172.17.0.1/private buster-staging/main armhf libsigsegv2 armhf 2.11-1 [29.3 kB]
Get:32 http://172.17.0.1/private buster-staging/main armhf m4 armhf 1.4.18-1 [185 kB]
Get:33 http://172.17.0.1/private buster-staging/main armhf autoconf all 2.69-10 [338 kB]
Get:34 http://172.17.0.1/private buster-staging/main armhf autotools-dev all 20161112.1 [73.4 kB]
Get:35 http://172.17.0.1/private buster-staging/main armhf automake all 1:1.15.1-2 [736 kB]
Get:36 http://172.17.0.1/private buster-staging/main armhf autopoint all 0.19.8.1-2 [433 kB]
Get:37 http://172.17.0.1/private buster-staging/main armhf libtool all 2.4.6-2 [545 kB]
Get:38 http://172.17.0.1/private buster-staging/main armhf dh-autoreconf all 14 [15.9 kB]
Get:39 http://172.17.0.1/private buster-staging/main armhf libarchive-zip-perl all 1.59-1 [95.5 kB]
Get:40 http://172.17.0.1/private buster-staging/main armhf libfile-stripnondeterminism-perl all 0.038-1 [17.6 kB]
Get:41 http://172.17.0.1/private buster-staging/main armhf libtimedate-perl all 2.3000-2 [42.2 kB]
Get:42 http://172.17.0.1/private buster-staging/main armhf dh-strip-nondeterminism all 0.038-1 [11.1 kB]
Get:43 http://172.17.0.1/private buster-staging/main armhf libglib2.0-0 armhf 2.52.3-1 [2576 kB]
Get:44 http://172.17.0.1/private buster-staging/main armhf libcroco3 armhf 0.6.12-1 [132 kB]
Get:45 http://172.17.0.1/private buster-staging/main armhf gettext armhf 0.19.8.1-2+b1 [1220 kB]
Get:46 http://172.17.0.1/private buster-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:47 http://172.17.0.1/private buster-staging/main armhf po-debconf all 1.0.20 [247 kB]
Get:48 http://172.17.0.1/private buster-staging/main armhf debhelper all 10.6.4 [970 kB]
Get:49 http://172.17.0.1/private buster-staging/main armhf googletest armhf 1.8.0-6 [653 kB]
Get:50 http://172.17.0.1/private buster-staging/main armhf hdf5-helpers armhf 1.10.0-patch1+docs-3 [35.9 kB]
Get:51 http://172.17.0.1/private buster-staging/main armhf libaec0 armhf 0.3.2-1 [19.4 kB]
Get:52 http://172.17.0.1/private buster-staging/main armhf libnghttp2-14 armhf 1.24.0-1 [70.4 kB]
Get:53 http://172.17.0.1/private buster-staging/main armhf libpsl5 armhf 0.17.0-5 [42.0 kB]
Get:54 http://172.17.0.1/private buster-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-1 [54.2 kB]
Get:55 http://172.17.0.1/private buster-staging/main armhf libssh2-1 armhf 1.8.0-1 [126 kB]
Get:56 http://172.17.0.1/private buster-staging/main armhf libcurl3-gnutls armhf 7.52.1-5 [259 kB]
Get:57 http://172.17.0.1/private buster-staging/main armhf libhts2 armhf 1.4.1-5 [247 kB]
Get:58 http://172.17.0.1/private buster-staging/main armhf libpbbam armhf 0.7.4+ds-1+rpi1+b1 [395 kB]
Get:59 http://172.17.0.1/private buster-staging/main armhf libpbdata armhf 0~20161219-1 [106 kB]
Get:60 http://172.17.0.1/private buster-staging/main armhf libgfortran3 armhf 6.4.0-1+rpi1 [166 kB]
Get:61 http://172.17.0.1/private buster-staging/main armhf libsz2 armhf 0.3.2-1 [5836 B]
Get:62 http://172.17.0.1/private buster-staging/main armhf libhdf5-100 armhf 1.10.0-patch1+docs-3 [1203 kB]
Get:63 http://172.17.0.1/private buster-staging/main armhf libhdf5-cpp-100 armhf 1.10.0-patch1+docs-3 [118 kB]
Get:64 http://172.17.0.1/private buster-staging/main armhf libpbihdf armhf 0~20161219-1 [141 kB]
Get:65 http://172.17.0.1/private buster-staging/main armhf libblasr armhf 0~20161219-1 [828 kB]
Get:66 http://172.17.0.1/private buster-staging/main armhf libblasr-dev armhf 0~20161219-1 [1672 kB]
Get:67 http://172.17.0.1/private buster-staging/main armhf libboost1.62-dev armhf 1.62.0+dfsg-4 [7009 kB]
Get:68 http://172.17.0.1/private buster-staging/main armhf libboost-dev armhf 1.62.0.1+b6 [3916 B]
Get:69 http://172.17.0.1/private buster-staging/main armhf zlib1g-dev armhf 1:1.2.8.dfsg-5 [198 kB]
Get:70 http://172.17.0.1/private buster-staging/main armhf libjpeg62-turbo armhf 1:1.5.1-2 [109 kB]
Get:71 http://172.17.0.1/private buster-staging/main armhf libjpeg62-turbo-dev armhf 1:1.5.1-2 [181 kB]
Get:72 http://172.17.0.1/private buster-staging/main armhf libjpeg-dev all 1:1.5.1-2 [56.1 kB]
Get:73 http://172.17.0.1/private buster-staging/main armhf libaec-dev armhf 0.3.2-1 [17.6 kB]
Get:74 http://172.17.0.1/private buster-staging/main armhf libhdf5-dev armhf 1.10.0-patch1+docs-3 [2093 kB]
Get:75 http://172.17.0.1/private buster-staging/main armhf libhts-dev armhf 1.4.1-5 [338 kB]
Get:76 http://172.17.0.1/private buster-staging/main armhf libssl-dev armhf 1.1.0f-3 [1369 kB]
Get:77 http://172.17.0.1/private buster-staging/main armhf libpbbam-dev armhf 0.7.4+ds-1+rpi1+b1 [90.2 kB]
Get:78 http://172.17.0.1/private buster-staging/main armhf libpbdata-dev armhf 0~20161219-1 [178 kB]
Get:79 http://172.17.0.1/private buster-staging/main armhf libpbihdf-dev armhf 0~20161219-1 [249 kB]
Get:80 http://172.17.0.1/private buster-staging/main armhf libpbseq-dev all 0~20161219-1 [3902 B]
Get:81 http://172.17.0.1/private buster-staging/main armhf libtclap-dev armhf 1.2.1-1 [727 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Selecting previously unselected package groff-base.
(Reading database ... 14837 files and directories currently installed.)
Preparing to unpack .../00-groff-base_1.22.3-9_armhf.deb ...
Unpacking groff-base (1.22.3-9) ...
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Unpacking libbsd0:armhf (0.8.6-1) ...
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+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.9.0-0.bpo.1-armmp armhf (armv7l)
Toolchain package versions: binutils_2.28-6 dpkg-dev_1.18.24 g++-6_6.4.0-1+rpi1 gcc-6_6.4.0-1+rpi1 libc6-dev_2.24-12 libstdc++-6-dev_6.4.0-1+rpi1 libstdc++6_7.1.0-9+rpi1 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch
Package versions: adduser_3.115 apt_1.5~beta1+b3 autoconf_2.69-10 automake_1:1.15.1-2 autopoint_0.19.8.1-2 autotools-dev_20161112.1 base-files_10+rpi1 base-passwd_3.5.43 bash_4.4-5 binutils_2.28-6 bsdmainutils_9.0.12+nmu1 bsdutils_1:2.29.2-2+rpi1 build-essential_12.3 bzip2_1.0.6-8.1 ca-certificates_20161130+nmu1 coreutils_8.26-3 cpio_2.11+dfsg-6 cpp_4:6.3.0-4d1 cpp-6_6.4.0-1+rpi1 dash_0.5.8-2.5 debconf_1.5.63 debhelper_10.6.4 debianutils_4.8.1.1 dh-autoreconf_14 dh-strip-nondeterminism_0.038-1 diffutils_1:3.5-3 dmsetup_2:1.02.137-2 dpkg_1.18.24 dpkg-dev_1.18.24 e2fslibs_1.43.4-2 e2fsprogs_1.43.4-2 fakeroot_1.21-3.1 file_1:5.30-1 findutils_4.6.0+git+20170606-3 g++_4:6.3.0-4d1 g++-6_6.4.0-1+rpi1 gcc_4:6.3.0-4d1 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8-base_4.8.5-4 gcc-4.9-base_4.9.3-14 gcc-5-base_5.4.1-4 gcc-6_6.4.0-1+rpi1 gcc-6-base_6.4.0-1+rpi1 gcc-7-base_7.1.0-9+rpi1 gettext_0.19.8.1-2+b1 gettext-base_0.19.8.1-2+b1 gnupg_2.1.18-8 gnupg-agent_2.1.18-8 googletest_1.8.0-6 gpgv_2.1.18-8 grep_3.1-2 groff-base_1.22.3-9 gzip_1.6-5 hdf5-helpers_1.10.0-patch1+docs-3 hostname_3.18 init-system-helpers_1.48 initramfs-tools_0.130 initramfs-tools-core_0.130 intltool-debian_0.35.0+20060710.4 klibc-utils_2.0.4-9+rpi1 kmod_24-1 libacl1_2.2.52-3 libaec-dev_0.3.2-1 libaec0_0.3.2-1 libapparmor1_2.11.0-6 libapt-pkg5.0_1.5~beta1+b3 libarchive-zip-perl_1.59-1 libasan3_6.4.0-1+rpi1 libassuan0_2.4.3-2 libatomic1_7.1.0-9+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.7.7-1 libaudit1_1:2.7.7-1 libblasr_0~20161219-1 libblasr-dev_0~20161219-1 libblkid1_2.29.2-2+rpi1 libboost-dev_1.62.0.1+b6 libboost1.62-dev_1.62.0+dfsg-4 libbsd0_0.8.6-1 libbz2-1.0_1.0.6-8.1 libc-bin_2.24-12 libc-dev-bin_2.24-12 libc6_2.24-12 libc6-dev_2.24-12 libcap-ng0_0.7.7-3 libcap2_1:2.25-1 libcc1-0_7.1.0-9+rpi1 libcomerr2_1.43.4-2 libcroco3_0.6.12-1 libcryptsetup4_2:1.7.3-4 libcurl3-gnutls_7.52.1-5 libdb5.3_5.3.28-12 libdbus-1-3_1.10.20-1 libdebconfclient0_0.229 libdevmapper1.02.1_2:1.02.137-2 libdpkg-perl_1.18.24 libdrm2_2.4.81-2+rpi1 libexpat1_2.2.2-2 libfakeroot_1.21-3.1 libfdisk1_2.29.2-2+rpi1 libffi6_3.2.1-6 libfile-stripnondeterminism-perl_0.038-1 libgcc-6-dev_6.4.0-1+rpi1 libgcc1_1:7.1.0-9+rpi1 libgcrypt20_1.7.8-2 libgdbm3_1.8.3-14 libgfortran3_6.4.0-1+rpi1 libglib2.0-0_2.52.3-1 libgmp10_2:6.1.2+dfsg-1 libgnutls30_3.5.14-2 libgomp1_7.1.0-9+rpi1 libgpg-error0_1.27-3 libgssapi-krb5-2_1.15.1-2 libhdf5-100_1.10.0-patch1+docs-3 libhdf5-cpp-100_1.10.0-patch1+docs-3 libhdf5-dev_1.10.0-patch1+docs-3 libhogweed4_3.3-1 libhts-dev_1.4.1-5 libhts2_1.4.1-5 libicu57_57.1-6 libidn11_1.33-1 libidn2-0_2.0.2-1 libip4tc0_1.6.1-2 libisl15_0.18-1 libjpeg-dev_1:1.5.1-2 libjpeg62-turbo_1:1.5.1-2 libjpeg62-turbo-dev_1:1.5.1-2 libk5crypto3_1.15.1-2 libkeyutils1_1.5.9-9 libklibc_2.0.4-9+rpi1 libkmod2_24-1 libkrb5-3_1.15.1-2 libkrb5support0_1.15.1-2 libksba8_1.3.5-2 libldap-2.4-2_2.4.45+dfsg-1 libldap-common_2.4.45+dfsg-1 liblz4-1_0.0~r131-2 liblzma5_5.2.2-1.3 libmagic-mgc_1:5.30-1 libmagic1_1:5.30-1 libmount1_2.29.2-2+rpi1 libmpc3_1.0.3-1 libmpfr4_3.1.5-1 libncurses5_6.0+20170715-2 libncursesw5_6.0+20170715-2 libnettle6_3.3-1 libnghttp2-14_1.24.0-1 libnih-dbus1_1.0.3-8 libnih1_1.0.3-8 libnpth0_1.5-2 libp11-kit0_0.23.7-3 libpam-modules_1.1.8-3.6 libpam-modules-bin_1.1.8-3.6 libpam-runtime_1.1.8-3.6 libpam0g_1.1.8-3.6 libpbbam_0.7.4+ds-1+rpi1+b1 libpbbam-dev_0.7.4+ds-1+rpi1+b1 libpbdata_0~20161219-1 libpbdata-dev_0~20161219-1 libpbihdf_0~20161219-1 libpbihdf-dev_0~20161219-1 libpbseq-dev_0~20161219-1 libpcre3_2:8.39-3 libperl5.24_5.24.1-7 libperl5.26_5.26.0-4 libpipeline1_1.4.2-1 libplymouth4_0.9.2-4 libpng16-16_1.6.30-2 libprocps6_2:3.3.12-3 libpsl5_0.17.0-5 libpython-stdlib_2.7.13-2 libpython2.7-minimal_2.7.13-2 libpython2.7-stdlib_2.7.13-2 libreadline5_5.2+dfsg-3 libreadline7_7.0-3 librtmp1_2.4+20151223.gitfa8646d.1-1 libsasl2-2_2.1.27~101-g0780600+dfsg-3 libsasl2-modules-db_2.1.27~101-g0780600+dfsg-3 libseccomp2_2.3.1-2.1 libselinux1_2.6-3 libsemanage-common_2.6-2 libsemanage1_2.6-2 libsepol1_2.6-2 libsigsegv2_2.11-1 libsmartcols1_2.29.2-2+rpi1 libsqlite3-0_3.19.3-3 libss2_1.43.4-2 libssh2-1_1.8.0-1 libssl-dev_1.1.0f-3 libssl1.1_1.1.0f-3 libstdc++-6-dev_6.4.0-1+rpi1 libstdc++6_7.1.0-9+rpi1 libsystemd0_233-10 libsz2_0.3.2-1 libtasn1-6_4.12-2 libtclap-dev_1.2.1-1 libtimedate-perl_2.3000-2 libtinfo5_6.0+20170715-2 libtool_2.4.6-2 libubsan0_7.1.0-9+rpi1 libudev1_233-10 libunistring2_0.9.7-2 libustr-1.0-1_1.0.4-6 libuuid1_2.29.2-2+rpi1 libxml2_2.9.4+dfsg1-3 linux-base_4.5 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch login_1:4.4-4.1 lsb-base_9.20161125+rpi1 m4_1.4.18-1 make_4.1-9.1 makedev_2.3.1-93 man-db_2.7.6.1-2 mawk_1.3.3-17 mime-support_3.60 mount_2.29.2-2+rpi1 mountall_2.54 multiarch-support_2.24-12 ncurses-base_6.0+20170715-2 ncurses-bin_6.0+20170715-2 openssl_1.1.0f-3 passwd_1:4.4-4.1 patch_2.7.5-1 perl_5.26.0-4 perl-base_5.26.0-4 perl-modules-5.24_5.24.1-7 perl-modules-5.26_5.26.0-4 pinentry-curses_1.0.0-2 plymouth_0.9.2-4 po-debconf_1.0.20 procps_2:3.3.12-3 python_2.7.13-2 python-minimal_2.7.13-2 python2.7_2.7.13-2 python2.7-minimal_2.7.13-2 raspbian-archive-keyring_20120528.2 readline-common_7.0-3 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-pbdagcon-dummy_0.invalid.0 sed_4.4-1 sensible-utils_0.0.9+nmu1 systemd_233-10 sysvinit-utils_2.88dsf-59.9 tar_1.29b-2 tzdata_2017b-2 udev_233-10 util-linux_2.29.2-2+rpi1 xz-utils_5.2.2-1.3 zlib1g_1:1.2.8.dfsg-5 zlib1g-dev_1:1.2.8.dfsg-5
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Wed Dec 21 09:25:57 2016 UTC
gpgv: using RSA key 59B2306F3AF9DDC1
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./pbdagcon_0.3+20161121+ds-1.dsc
dpkg-source: info: extracting pbdagcon in /<<BUILDDIR>>/pbdagcon-0.3+20161121+ds
dpkg-source: info: unpacking pbdagcon_0.3+20161121+ds.orig.tar.gz
dpkg-source: info: unpacking pbdagcon_0.3+20161121+ds-1.debian.tar.xz
dpkg-source: info: applying compiler-flags.patch
Check disc space
----------------
Sufficient free space for build
Hack binNMU version
-------------------
Created changelog entry for binNMU version 0.3+20161121+ds-1+b1
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=root
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=buster-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=buster-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=buster-staging-armhf-sbuild-06792f72-16b2-4cab-a8c9-6b56f6d0adef
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=xterm
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package pbdagcon
dpkg-buildpackage: info: source version 0.3+20161121+ds-1+b1
dpkg-buildpackage: info: source distribution buster-staging
dpkg-source --before-build pbdagcon-0.3+20161121+ds
dpkg-buildpackage: info: host architecture armhf
fakeroot debian/rules clean
dh clean
dh_testdir
dh_auto_clean
make -j4 clean
make[1]: Entering directory '/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds'
make -C src/cpp clean
make[2]: Entering directory '/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/src/cpp'
rm -f *.d
rm -f *.o
rm -f pbdagcon
rm -f dazcon
make[2]: Leaving directory '/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/src/cpp'
make -C test/cpp clean
make[2]: Entering directory '/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/test/cpp'
rm -f .//*.o
rm -f *.o
rm -f test_*
make[2]: Leaving directory '/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/test/cpp'
make[1]: Leaving directory '/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds'
dh_autoreconf_clean
dh_clean
debian/rules build-arch
dh build-arch
dh_testdir -a
dh_update_autotools_config -a
dh_autoreconf -a
debian/rules override_dh_auto_configure
make[1]: Entering directory '/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds'
./configure.py --shared
uname -s
uname='Linux'
writing to '/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/defines.mk'
"""
DALIGNER_INCLUDE ?= ${DALIGNER_SRC}
DALIGNER_SRC ?= /<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DALIGNER
DAZZ_DB_INCLUDE ?= ${DAZZ_DB_SRC}
DAZZ_DB_SRC ?= /<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DAZZ_DB
GTEST_INCLUDE ?= /usr/src/googletest/googletest/include
GTEST_SRC ?= /usr/src/googletest/googletest/src
HDF5_LIB ?= /usr/lib/arm-linux-gnueabihf/hdf5/serial
HDF5_LIBFLAGS ?= -lhdf5_cpp -lhdf5
HTSLIB_LIBFLAGS ?= -lhts
LIBBLASR_INCLUDE ?= /usr/include/pbseq/alignment
LIBBLASR_LIBFLAGS ?= -lblasr
LIBPBDATA_INCLUDE ?= /usr/include/pbseq/pbdata
LIBPBDATA_LIBFLAGS ?= -lpbdata
LIBPBIHDF_INCLUDE ?= /usr/include/pbseq/hdf
LIBPBIHDF_LIBFLAGS ?= -lpbihdf
PBBAM_LIBFLAGS ?= -lpbbam
PTHREAD_LIBFLAGS ?= -lpthread
ZLIB_LIBFLAGS ?= -lz
LDLIBS+=-lrt
"""
make[1]: Leaving directory '/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds'
dh_auto_build -a
make -j4
make[1]: Entering directory '/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds'
make -C src/cpp
make[2]: Entering directory '/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/src/cpp'
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -Wall -Wuninitialized -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -I/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DAZZ_DB -I/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DALIGNER -I/usr/include/pbseq/alignment -I/usr/include/pbseq/pbdata -I/usr/include/pbseq/hdf -isystem.//third-party -c -o Alignment.o Alignment.cpp
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -Wall -Wuninitialized -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -I/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DAZZ_DB -I/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DALIGNER -I/usr/include/pbseq/alignment -I/usr/include/pbseq/pbdata -I/usr/include/pbseq/hdf -isystem.//third-party -c -o AlnGraphBoost.o AlnGraphBoost.cpp
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -Wall -Wuninitialized -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -I/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DAZZ_DB -I/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DALIGNER -I/usr/include/pbseq/alignment -I/usr/include/pbseq/pbdata -I/usr/include/pbseq/hdf -isystem.//third-party -c -o BlasrM5AlnProvider.o BlasrM5AlnProvider.cpp
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -Wall -Wuninitialized -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -I/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DAZZ_DB -I/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DALIGNER -I/usr/include/pbseq/alignment -I/usr/include/pbseq/pbdata -I/usr/include/pbseq/hdf -isystem.//third-party -c -o main.o main.cpp
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -Wall -Wuninitialized -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -I/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DAZZ_DB -I/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DALIGNER -I/usr/include/pbseq/alignment -I/usr/include/pbseq/pbdata -I/usr/include/pbseq/hdf -isystem.//third-party -c -o SimpleAligner.o SimpleAligner.cpp
cc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wextra -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -I/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DAZZ_DB -I/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DALIGNER -I/usr/include/pbseq/alignment -I/usr/include/pbseq/pbdata -I/usr/include/pbseq/hdf -isystem.//third-party -c -o DB.o /<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DAZZ_DB/DB.c
/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DAZZ_DB/DB.c: In function 'Load_QVs':
/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DAZZ_DB/DB.c:888:9: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(istub,DB_NFILE,&nfiles);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DAZZ_DB/DB.c:892:13: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
{ fscanf(istub,DB_FDATA,&last,fname,prolog);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DAZZ_DB/DB.c:897:13: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
{ fscanf(istub,DB_FDATA,&last,fname,prolog);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wextra -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -I/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DAZZ_DB -I/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DALIGNER -I/usr/include/pbseq/alignment -I/usr/include/pbseq/pbdata -I/usr/include/pbseq/hdf -isystem.//third-party -c -o QV.o /<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DAZZ_DB/QV.c
/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DAZZ_DB/QV.c: In function 'Build_Table':
/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DAZZ_DB/QV.c:127:23: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
{ uint64 symbol = (uint64) (node->lft);
^
/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DAZZ_DB/QV.c: In function 'Huffman':
/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DAZZ_DB/QV.c:174:33: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
node[value].lft = (HTree *) (uint64) i;
^
cc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wextra -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -I/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DAZZ_DB -I/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DALIGNER -I/usr/include/pbseq/alignment -I/usr/include/pbseq/pbdata -I/usr/include/pbseq/hdf -isystem.//third-party -c -o align.o /<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DALIGNER/align.c
In file included from /usr/include/c++/6/algorithm:62:0,
from SimpleAligner.cpp:6:
/usr/include/c++/6/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/6/bits/stl_algo.h:1837:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' will change in GCC 7.1
__insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_algo.h:1837:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:1837:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h: In function 'void std::__move_median_to_first(_Iterator, _Iterator, _Iterator, _Iterator, _Compare) [with _Iterator = __gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/6/bits/stl_algo.h:78:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' will change in GCC 7.1
__move_median_to_first(_Iterator __result,_Iterator __a, _Iterator __b,
^~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_algo.h:78:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:78:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:78:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:78:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:78:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' will change in GCC 7.1
In file included from /usr/include/c++/6/bits/stl_algo.h:61:0,
from /usr/include/c++/6/algorithm:62,
from SimpleAligner.cpp:6:
/usr/include/c++/6/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >; _Distance = int; _Tp = PositionDNATuple; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/6/bits/stl_heap.h:209:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' will change in GCC 7.1
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
In file included from /usr/include/c++/6/algorithm:62:0,
from SimpleAligner.cpp:6:
/usr/include/c++/6/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/6/bits/stl_algo.h:1937:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' will change in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_algo.h:1937:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:1918:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' will change in GCC 7.1
std::__move_median_to_first(__first, __first + 1, __mid, __last - 1,
^~~
/usr/include/c++/6/bits/stl_algo.h:1918:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:1918:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:1918:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:1951:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' will change in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
^~~
/usr/include/c++/6/bits/stl_algo.h: In function '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>]':
/usr/include/c++/6/bits/stl_algo.h:1965:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' will change in GCC 7.1
std::__introsort_loop(__first, __last,
^~~
/usr/include/c++/6/bits/stl_algo.h:1882:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' will change in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
^~~
/usr/include/c++/6/bits/stl_algo.h:1887:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' will change in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
^~~
/usr/include/c++/6/bits/stl_algo.h:1965:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' will change in GCC 7.1
std::__introsort_loop(__first, __last,
^~~
/usr/include/c++/6/bits/stl_algo.h:1882:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' will change in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
^~~
/usr/include/c++/6/bits/stl_algo.h:1887:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' will change in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
^~~
/usr/include/c++/6/bits/stl_algo.h:1965:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' will change in GCC 7.1
std::__introsort_loop(__first, __last,
^~~
/usr/include/c++/6/bits/stl_algo.h:1882:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' will change in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
^~~
/usr/include/c++/6/bits/stl_algo.h:1887:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' will change in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
^~~
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -Wall -Wuninitialized -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -I/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DAZZ_DB -I/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DALIGNER -I/usr/include/pbseq/alignment -I/usr/include/pbseq/pbdata -I/usr/include/pbseq/hdf -isystem.//third-party -c -o DazAlnProvider.o DazAlnProvider.cpp
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -Wall -Wuninitialized -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -I/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DAZZ_DB -I/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DALIGNER -I/usr/include/pbseq/alignment -I/usr/include/pbseq/pbdata -I/usr/include/pbseq/hdf -isystem.//third-party -c -o dazcon.o dazcon.cpp
g++ -o pbdagcon Alignment.o AlnGraphBoost.o BlasrM5AlnProvider.o main.o SimpleAligner.o -Wl,-z,relro -L /usr/lib/arm-linux-gnueabihf/hdf5/serial -lrt -lblasr -lpbdata -lpbihdf -lpbbam -lhdf5_cpp -lhdf5 -lhts -lz -lpthread
g++ -o dazcon Alignment.o AlnGraphBoost.o DB.o QV.o align.o DazAlnProvider.o dazcon.o -Wl,-z,relro -L /usr/lib/arm-linux-gnueabihf/hdf5/serial -lrt -lblasr -lpbdata -lpbihdf -lpbbam -lhdf5_cpp -lhdf5 -lhts -lz -lpthread
make[2]: Leaving directory '/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/src/cpp'
make[1]: Leaving directory '/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds'
dh_auto_test -a
make -j4 check
make[1]: Entering directory '/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds'
make -C src/cpp
make[2]: Entering directory '/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/src/cpp'
make[2]: Nothing to be done for 'all'.
make[2]: Leaving directory '/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/src/cpp'
make -C test/cpp
make[2]: Entering directory '/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/test/cpp'
g++ -O3 -std=c++11 -g -Wall -Wextra -pthread -Wdate-time -D_FORTIFY_SOURCE=2 -I. -I./ -I.//../../src/cpp -I/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DAZZ_DB -I/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DALIGNER -I/usr/include/pbseq/alignment -I/usr/include/pbseq/pbdata -I/usr/include/pbseq/hdf -I/usr/src/googletest/googletest/include -Ithird-party -isystem /usr/src/googletest/googletest/include -isystem /usr/src/googletest/googletest/src/.. -c -o gtest-all.o /usr/src/googletest/googletest/src/gtest-all.cc
g++ -O3 -std=c++11 -g -Wall -Wextra -pthread -Wdate-time -D_FORTIFY_SOURCE=2 -I. -I./ -I.//../../src/cpp -I/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DAZZ_DB -I/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DALIGNER -I/usr/include/pbseq/alignment -I/usr/include/pbseq/pbdata -I/usr/include/pbseq/hdf -I/usr/src/googletest/googletest/include -Ithird-party -isystem /usr/src/googletest/googletest/include -isystem /usr/src/googletest/googletest/src/.. -c -o gtest_main.o /usr/src/googletest/googletest/src/gtest_main.cc
g++ -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I. -I./ -I.//../../src/cpp -I/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DAZZ_DB -I/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DALIGNER -I/usr/include/pbseq/alignment -I/usr/include/pbseq/pbdata -I/usr/include/pbseq/hdf -I/usr/src/googletest/googletest/include -Ithird-party -c -o AlnGraphBoost.o .//../../src/cpp/AlnGraphBoost.cpp
g++ -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I. -I./ -I.//../../src/cpp -I/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DAZZ_DB -I/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DALIGNER -I/usr/include/pbseq/alignment -I/usr/include/pbseq/pbdata -I/usr/include/pbseq/hdf -I/usr/src/googletest/googletest/include -Ithird-party -c -o Alignment.o .//../../src/cpp/Alignment.cpp
g++ -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I. -I./ -I.//../../src/cpp -I/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DAZZ_DB -I/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DALIGNER -I/usr/include/pbseq/alignment -I/usr/include/pbseq/pbdata -I/usr/include/pbseq/hdf -I/usr/src/googletest/googletest/include -Ithird-party -c -o SimpleAligner.o .//../../src/cpp/SimpleAligner.cpp
g++ -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I. -I./ -I.//../../src/cpp -I/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DAZZ_DB -I/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DALIGNER -I/usr/include/pbseq/alignment -I/usr/include/pbseq/pbdata -I/usr/include/pbseq/hdf -I/usr/src/googletest/googletest/include -Ithird-party -c -o AlnGraphBoostTest.o AlnGraphBoostTest.cpp
mkdir xml
g++ -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I. -I./ -I.//../../src/cpp -I/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DAZZ_DB -I/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DALIGNER -I/usr/include/pbseq/alignment -I/usr/include/pbseq/pbdata -I/usr/include/pbseq/hdf -I/usr/src/googletest/googletest/include -Ithird-party -c -o AlignmentTest.o AlignmentTest.cpp
In file included from /usr/include/c++/6/algorithm:62:0,
from .//../../src/cpp/SimpleAligner.cpp:6:
/usr/include/c++/6/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/6/bits/stl_algo.h:1837:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' will change in GCC 7.1
__insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_algo.h:1837:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:1837:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h: In function 'void std::__move_median_to_first(_Iterator, _Iterator, _Iterator, _Iterator, _Compare) [with _Iterator = __gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/6/bits/stl_algo.h:78:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' will change in GCC 7.1
__move_median_to_first(_Iterator __result,_Iterator __a, _Iterator __b,
^~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_algo.h:78:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:78:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:78:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:78:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:78:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' will change in GCC 7.1
In file included from /usr/include/c++/6/bits/stl_algo.h:61:0,
from /usr/include/c++/6/algorithm:62,
from .//../../src/cpp/SimpleAligner.cpp:6:
/usr/include/c++/6/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >; _Distance = int; _Tp = PositionDNATuple; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/6/bits/stl_heap.h:209:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' will change in GCC 7.1
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
In file included from /usr/include/c++/6/algorithm:62:0,
from .//../../src/cpp/SimpleAligner.cpp:6:
/usr/include/c++/6/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/6/bits/stl_algo.h:1937:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' will change in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_algo.h:1937:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:1918:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' will change in GCC 7.1
std::__move_median_to_first(__first, __first + 1, __mid, __last - 1,
^~~
/usr/include/c++/6/bits/stl_algo.h:1918:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:1918:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:1918:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:1951:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' will change in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
^~~
/usr/include/c++/6/bits/stl_algo.h: In function '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>]':
/usr/include/c++/6/bits/stl_algo.h:1965:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' will change in GCC 7.1
std::__introsort_loop(__first, __last,
^~~
/usr/include/c++/6/bits/stl_algo.h:1882:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' will change in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
^~~
/usr/include/c++/6/bits/stl_algo.h:1887:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' will change in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
^~~
/usr/include/c++/6/bits/stl_algo.h:1965:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' will change in GCC 7.1
std::__introsort_loop(__first, __last,
^~~
/usr/include/c++/6/bits/stl_algo.h:1882:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' will change in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
^~~
/usr/include/c++/6/bits/stl_algo.h:1887:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' will change in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
^~~
/usr/include/c++/6/bits/stl_algo.h:1965:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' will change in GCC 7.1
std::__introsort_loop(__first, __last,
^~~
/usr/include/c++/6/bits/stl_algo.h:1882:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' will change in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
^~~
/usr/include/c++/6/bits/stl_algo.h:1887:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' will change in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
^~~
g++ -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I. -I./ -I.//../../src/cpp -I/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DAZZ_DB -I/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DALIGNER -I/usr/include/pbseq/alignment -I/usr/include/pbseq/pbdata -I/usr/include/pbseq/hdf -I/usr/src/googletest/googletest/include -Ithird-party -c -o SimpleAlignerTest.o SimpleAlignerTest.cpp
cc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I. -I./ -I.//../../src/cpp -I/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DAZZ_DB -I/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DALIGNER -I/usr/include/pbseq/alignment -I/usr/include/pbseq/pbdata -I/usr/include/pbseq/hdf -I/usr/src/googletest/googletest/include -Ithird-party -c -o DB.o /<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DAZZ_DB/DB.c
/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DAZZ_DB/DB.c: In function 'Load_QVs':
/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DAZZ_DB/DB.c:888:9: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf(istub,DB_NFILE,&nfiles);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DAZZ_DB/DB.c:892:13: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
{ fscanf(istub,DB_FDATA,&last,fname,prolog);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DAZZ_DB/DB.c:897:13: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
{ fscanf(istub,DB_FDATA,&last,fname,prolog);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I. -I./ -I.//../../src/cpp -I/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DAZZ_DB -I/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DALIGNER -I/usr/include/pbseq/alignment -I/usr/include/pbseq/pbdata -I/usr/include/pbseq/hdf -I/usr/src/googletest/googletest/include -Ithird-party -c -o QV.o /<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DAZZ_DB/QV.c
/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DAZZ_DB/QV.c: In function 'Build_Table':
/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DAZZ_DB/QV.c:127:23: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
{ uint64 symbol = (uint64) (node->lft);
^
/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DAZZ_DB/QV.c: In function 'Huffman':
/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DAZZ_DB/QV.c:174:33: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
node[value].lft = (HTree *) (uint64) i;
^
cc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I. -I./ -I.//../../src/cpp -I/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DAZZ_DB -I/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DALIGNER -I/usr/include/pbseq/alignment -I/usr/include/pbseq/pbdata -I/usr/include/pbseq/hdf -I/usr/src/googletest/googletest/include -Ithird-party -c -o align.o /<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DALIGNER/align.c
g++ -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I. -I./ -I.//../../src/cpp -I/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DAZZ_DB -I/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DALIGNER -I/usr/include/pbseq/alignment -I/usr/include/pbseq/pbdata -I/usr/include/pbseq/hdf -I/usr/src/googletest/googletest/include -Ithird-party -c -o DazAlnProvider.o .//../../src/cpp/DazAlnProvider.cpp
g++ -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I. -I./ -I.//../../src/cpp -I/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DAZZ_DB -I/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/DALIGNER -I/usr/include/pbseq/alignment -I/usr/include/pbseq/pbdata -I/usr/include/pbseq/hdf -I/usr/src/googletest/googletest/include -Ithird-party -c -o TargetHitTest.o TargetHitTest.cpp
g++ -o test-alngraph gtest-all.o gtest_main.o AlnGraphBoost.o Alignment.o SimpleAligner.o AlnGraphBoostTest.o -Wl,-z,relro -L /usr/lib/arm-linux-gnueabihf/hdf5/serial -lrt -lblasr -lpbdata -lpbihdf -lpbbam -lhdf5_cpp -lhdf5 -lhts -lz -lpthread
g++ -o test-alignment gtest-all.o gtest_main.o AlnGraphBoost.o Alignment.o SimpleAligner.o AlignmentTest.o -Wl,-z,relro -L /usr/lib/arm-linux-gnueabihf/hdf5/serial -lrt -lblasr -lpbdata -lpbihdf -lpbbam -lhdf5_cpp -lhdf5 -lhts -lz -lpthread
g++ -o test-simple_aligner gtest-all.o gtest_main.o AlnGraphBoost.o Alignment.o SimpleAligner.o SimpleAlignerTest.o -Wl,-z,relro -L /usr/lib/arm-linux-gnueabihf/hdf5/serial -lrt -lblasr -lpbdata -lpbihdf -lpbbam -lhdf5_cpp -lhdf5 -lhts -lz -lpthread
LD_LIBRARY_PATH=::::/usr/lib/arm-linux-gnueabihf/hdf5/serial:::: PBDAGCON_TEST_DATA_DIR=./ ./test-alngraph --gtest_output=xml:xml/test-alngraph.xml
Running main() from gtest_main.cc
[==========] Running 2 tests from 1 test case.
[----------] Global test environment set-up.
[----------] 2 tests from AlnGraphBoostTest
[ RUN ] AlnGraphBoostTest.RawConsensus
[ OK ] AlnGraphBoostTest.RawConsensus (1 ms)
[ RUN ] AlnGraphBoostTest.DanglingNodes
[ OK ] AlnGraphBoostTest.DanglingNodes (0 ms)
[----------] 2 tests from AlnGraphBoostTest (1 ms total)
[----------] Global test environment tear-down
[==========] 2 tests from 1 test case ran. (3 ms total)
[ PASSED ] 2 tests.
LD_LIBRARY_PATH=::::/usr/lib/arm-linux-gnueabihf/hdf5/serial:::: PBDAGCON_TEST_DATA_DIR=./ ./test-alignment --gtest_output=xml:xml/test-alignment.xml
Running main() from gtest_main.cc
[==========] Running 4 tests from 1 test case.
[----------] Global test environment set-up.
[----------] 4 tests from Alignment
[ RUN ] Alignment.Normalize
[ OK ] Alignment.Normalize (1 ms)
[ RUN ] Alignment.ParseBasic
[ OK ] Alignment.ParseBasic (1 ms)
[ RUN ] Alignment.ParseQuery
[ OK ] Alignment.ParseQuery (10 ms)
[ RUN ] Alignment.Trim
[ OK ] Alignment.Trim (0 ms)
[----------] 4 tests from Alignment (14 ms total)
[----------] Global test environment tear-down
[==========] 4 tests from 1 test case ran. (17 ms total)
[ PASSED ] 4 tests.
LD_LIBRARY_PATH=::::/usr/lib/arm-linux-gnueabihf/hdf5/serial:::: PBDAGCON_TEST_DATA_DIR=./ ./test-simple_aligner --gtest_output=xml:xml/test-simple_aligner.xml
Running main() from gtest_main.cc
[==========] Running 1 test from 1 test case.
[----------] Global test environment set-up.
[----------] 1 test from SimpleAligner
[ RUN ] SimpleAligner.align
[ OK ] SimpleAligner.align (2 ms)
[----------] 1 test from SimpleAligner (3 ms total)
[----------] Global test environment tear-down
[==========] 1 test from 1 test case ran. (8 ms total)
[ PASSED ] 1 test.
g++ -o test-target_hit gtest-all.o gtest_main.o DB.o QV.o align.o Alignment.o DazAlnProvider.o TargetHitTest.o -Wl,-z,relro -L /usr/lib/arm-linux-gnueabihf/hdf5/serial -lrt -lblasr -lpbdata -lpbihdf -lpbbam -lhdf5_cpp -lhdf5 -lhts -lz -lpthread
LD_LIBRARY_PATH=::::/usr/lib/arm-linux-gnueabihf/hdf5/serial:::: PBDAGCON_TEST_DATA_DIR=./ ./test-target_hit --gtest_output=xml:xml/test-target_hit.xml
Running main() from gtest_main.cc
[==========] Running 3 tests from 1 test case.
[----------] Global test environment set-up.
[----------] 3 tests from TargetHitTest
[ RUN ] TargetHitTest.single_overlap_perfect
[ OK ] TargetHitTest.single_overlap_perfect (1 ms)
[ RUN ] TargetHitTest.single_overlap_inaccurate
[ OK ] TargetHitTest.single_overlap_inaccurate (0 ms)
[ RUN ] TargetHitTest.multi_overlap_inaccurate
[ OK ] TargetHitTest.multi_overlap_inaccurate (0 ms)
[----------] 3 tests from TargetHitTest (2 ms total)
[----------] Global test environment tear-down
[==========] 3 tests from 1 test case ran. (3 ms total)
[ PASSED ] 3 tests.
make[2]: Leaving directory '/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds/test/cpp'
make[1]: Leaving directory '/<<BUILDDIR>>/pbdagcon-0.3+20161121+ds'
create-stamp debian/debhelper-build-stamp
fakeroot debian/rules binary-arch
dh binary-arch
dh_testroot -a
dh_prep -a
dh_auto_install -a
dh_install -a
dh_installdocs -a
dh_installchangelogs -a
dh_installexamples -a
dh_installman -a
dh_perl -a
dh_link -a
dh_strip_nondeterminism -a
dh_compress -a
dh_fixperms -a
dh_missing -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dpkg-shlibdeps: warning: can't extract name and version from library name 'libblasr.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libblasr.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbdata.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbdata.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbihdf.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbihdf.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbbam.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbbam.so'
dpkg-shlibdeps: warning: debian/pbdagcon/usr/bin/dazcon contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: can't extract name and version from library name 'libblasr.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libblasr.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbdata.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbdata.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbihdf.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbihdf.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbbam.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbbam.so'
dpkg-shlibdeps: warning: debian/pbdagcon/usr/bin/pbdagcon contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/pbdagcon/usr/bin/dazcon debian/pbdagcon/usr/bin/pbdagcon were not linked against libz.so.1 (they use none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/pbdagcon/usr/bin/dazcon debian/pbdagcon/usr/bin/pbdagcon were not linked against ld-linux-armhf.so.3 (they use none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/pbdagcon/usr/bin/dazcon debian/pbdagcon/usr/bin/pbdagcon were not linked against libpbbam.so (they use none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/pbdagcon/usr/bin/dazcon debian/pbdagcon/usr/bin/pbdagcon were not linked against libhdf5_serial.so.100 (they use none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/pbdagcon/usr/bin/dazcon debian/pbdagcon/usr/bin/pbdagcon were not linked against libpbihdf.so (they use none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/pbdagcon/usr/bin/dazcon debian/pbdagcon/usr/bin/pbdagcon were not linked against librt.so.1 (they use none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/pbdagcon/usr/bin/dazcon debian/pbdagcon/usr/bin/pbdagcon were not linked against libhdf5_cpp.so.100 (they use none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/pbdagcon/usr/bin/dazcon debian/pbdagcon/usr/bin/pbdagcon were not linked against libhts.so.2 (they use none of the library's symbols)
dh_installdeb -a
dh_gencontrol -a
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package 'pbdagcon' in '../pbdagcon_0.3+20161121+ds-1+b1_armhf.deb'.
dpkg-deb: building package 'pbdagcon-dbgsym' in '../pbdagcon-dbgsym_0.3+20161121+ds-1+b1_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../pbdagcon_0.3+20161121+ds-1+b1_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build pbdagcon-0.3+20161121+ds
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2017-08-01T06:39:34Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
pbdagcon_0.3+20161121+ds-1+b1_armhf.changes:
--------------------------------------------
Format: 1.8
Date: Wed, 21 Dec 2016 01:18:19 -0800
Source: pbdagcon (0.3+20161121+ds-1)
Binary: pbdagcon
Binary-Only: yes
Architecture: armhf
Version: 0.3+20161121+ds-1+b1
Distribution: buster-staging
Urgency: low
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Raspbian wandboard test autobuilder <root@raspbian.org>
Description:
pbdagcon - sequence consensus using directed acyclic graphs
Changes:
pbdagcon (0.3+20161121+ds-1+b1) buster-staging; urgency=low, binary-only=yes
.
* Binary-only non-maintainer upload for armhf; no source changes.
* rebuild due to debcheck failure
Checksums-Sha1:
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8e074ef009bc7837a3f5b56d944d50685459d654 243030 pbdagcon_0.3+20161121+ds-1+b1_armhf.deb
7ded70fbb083a6161f4db8271f5c2d6cc1a975fe 6640 pbdagcon_0.3+20161121+ds-1_armhf.buildinfo
Checksums-Sha256:
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85cac08a6f9ed36ecc7d8cebddba6e20d31cd310aefcafa28d2872269f9a0c06 243030 pbdagcon_0.3+20161121+ds-1+b1_armhf.deb
d5d8b3eac0cff33d6a53bcac759cada9afa322e600bbcdf8c27281fbba849fe8 6640 pbdagcon_0.3+20161121+ds-1_armhf.buildinfo
Files:
e8829ad528dbf51ed94544dc33d4dccd 4239184 debug extra pbdagcon-dbgsym_0.3+20161121+ds-1+b1_armhf.deb
45d9da4d4c2e00fb6e955c290d88b3c6 243030 science optional pbdagcon_0.3+20161121+ds-1+b1_armhf.deb
5eedca8dd90048403e763ef00de6101a 6640 science optional pbdagcon_0.3+20161121+ds-1_armhf.buildinfo
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
pbdagcon-dbgsym_0.3+20161121+ds-1+b1_armhf.deb
----------------------------------------------
new debian package, version 2.0.
size 4239184 bytes: control archive=531 bytes.
459 bytes, 12 lines control
212 bytes, 2 lines md5sums
Package: pbdagcon-dbgsym
Source: pbdagcon (0.3+20161121+ds-1)
Version: 0.3+20161121+ds-1+b1
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 4481
Depends: pbdagcon (= 0.3+20161121+ds-1+b1)
Section: debug
Priority: extra
Description: Debug symbols for pbdagcon
Build-Ids: 6b4d3765c7309802490052b3f7a39532167c0f7b c8cc17009a2e064d5029c40b58dff123f899bffc
drwxr-xr-x root/root 0 2016-12-21 09:18 ./
drwxr-xr-x root/root 0 2016-12-21 09:18 ./usr/
drwxr-xr-x root/root 0 2016-12-21 09:18 ./usr/lib/
drwxr-xr-x root/root 0 2016-12-21 09:18 ./usr/lib/debug/
drwxr-xr-x root/root 0 2016-12-21 09:18 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2016-12-21 09:18 ./usr/lib/debug/.build-id/6b/
-rw-r--r-- root/root 2207904 2016-12-21 09:18 ./usr/lib/debug/.build-id/6b/4d3765c7309802490052b3f7a39532167c0f7b.debug
drwxr-xr-x root/root 0 2016-12-21 09:18 ./usr/lib/debug/.build-id/c8/
-rw-r--r-- root/root 2368112 2016-12-21 09:18 ./usr/lib/debug/.build-id/c8/cc17009a2e064d5029c40b58dff123f899bffc.debug
drwxr-xr-x root/root 0 2016-12-21 09:18 ./usr/share/
drwxr-xr-x root/root 0 2016-12-21 09:18 ./usr/share/doc/
lrwxrwxrwx root/root 0 2016-12-21 09:18 ./usr/share/doc/pbdagcon-dbgsym -> pbdagcon
pbdagcon_0.3+20161121+ds-1+b1_armhf.deb
---------------------------------------
new debian package, version 2.0.
size 243030 bytes: control archive=1405 bytes.
1706 bytes, 31 lines control
783 bytes, 11 lines md5sums
Package: pbdagcon
Source: pbdagcon (0.3+20161121+ds-1)
Version: 0.3+20161121+ds-1+b1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 876
Depends: libc6 (>= 2.7), libgcc1 (>= 1:3.5), libhdf5-100, libhdf5-cpp-100 (>= 1.8.13), libhts2, libstdc++6 (>= 6), zlib1g (>= 1:1.1.4), libpbseq, libpbbam
Suggests: blasr
Section: science
Priority: optional
Homepage: https://github.com/PacificBiosciences/pbdagcon
Description: sequence consensus using directed acyclic graphs
pbdagcon is a tool that implements DAGCon (Directed Acyclic Graph Consensus)
which is a sequence consensus algorithm based on using directed acyclic
graphs to encode multiple sequence alignment.
.
It uses the alignment information from blasr to align sequence reads to a
"backbone" sequence. Based on the underlying alignment directed acyclic graph
(DAG), it will be able to use the new information from the reads to find the
discrepancies between the reads and the "backbone" sequences. A dynamic
programming process is then applied to the DAG to find the optimum sequence
of bases as the consensus. The new consensus can be used as a new backbone
sequence to iteratively improve the consensus quality.
.
While the code is developed for processing PacBio(TM) raw sequence data,
the algorithm can be used for general consensus purpose. Currently, it only
takes FASTA input. For shorter read sequences, one might need to adjust the
blasr alignment parameters to get the alignment string properly.
.
The code and the underlying graphical data structure have been used for some
algorithm development prototyping including phasing reads and pre-assembly.
drwxr-xr-x root/root 0 2016-12-21 09:18 ./
drwxr-xr-x root/root 0 2016-12-21 09:18 ./usr/
drwxr-xr-x root/root 0 2016-12-21 09:18 ./usr/bin/
-rwxr-xr-x root/root 457084 2016-12-21 09:18 ./usr/bin/dazcon
-rwxr-xr-x root/root 407920 2016-12-21 09:18 ./usr/bin/pbdagcon
drwxr-xr-x root/root 0 2016-12-21 09:18 ./usr/share/
drwxr-xr-x root/root 0 2016-12-21 09:18 ./usr/share/doc/
drwxr-xr-x root/root 0 2016-12-21 09:18 ./usr/share/doc/pbdagcon/
-rw-r--r-- root/root 2365 2016-12-21 05:55 ./usr/share/doc/pbdagcon/README.md.gz
-rw-r--r-- root/root 228 2016-12-21 09:18 ./usr/share/doc/pbdagcon/changelog.Debian.armhf.gz
-rw-r--r-- root/root 733 2016-12-21 09:18 ./usr/share/doc/pbdagcon/changelog.Debian.gz
-rw-r--r-- root/root 4729 2016-12-21 09:17 ./usr/share/doc/pbdagcon/copyright
drwxr-xr-x root/root 0 2016-12-21 09:18 ./usr/share/doc/pbdagcon/examples/
-rwxr-xr-x root/root 1588 2016-12-21 05:55 ./usr/share/doc/pbdagcon/examples/filterm4.py
-rw-r--r-- root/root 2224 2016-12-21 05:55 ./usr/share/doc/pbdagcon/examples/m4topre.py.gz
-rwxr-xr-x root/root 1145 2016-12-21 05:55 ./usr/share/doc/pbdagcon/examples/pbdagcon_wf.sh
-rw-r--r-- root/root 1771 2016-12-21 05:55 ./usr/share/doc/pbdagcon/examples/q-sense.py.gz
drwxr-xr-x root/root 0 2016-12-21 09:18 ./usr/share/man/
drwxr-xr-x root/root 0 2016-12-21 09:18 ./usr/share/man/man1/
-rw-r--r-- root/root 775 2016-12-21 09:18 ./usr/share/man/man1/pbdagcon.1.gz
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 61388
Build-Time: 497
Distribution: buster-staging
Host Architecture: armhf
Install-Time: 615
Job: pbdagcon_0.3+20161121+ds-1
Machine Architecture: armhf
Package: pbdagcon
Package-Time: 1161
Source-Version: 0.3+20161121+ds-1
Space: 61388
Status: successful
Version: 0.3+20161121+ds-1+b1
--------------------------------------------------------------------------------
Finished at 2017-08-01T06:39:34Z
Build needed 00:19:21, 61388k disc space