pbdagcon →
0.3+git20161121.0000000+ds-1.1 →
armhf → 2019-02-14 23:04:56
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-04
+==============================================================================+
| pbdagcon 0.3+git20161121.0000000+ds-1.1 (armhf) Thu, 14 Feb 2019 22:40:35 +0000 |
+==============================================================================+
Package: pbdagcon
Version: 0.3+git20161121.0000000+ds-1.1
Source Version: 0.3+git20161121.0000000+ds-1.1
Distribution: buster-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/buster-staging-armhf-sbuild-04677564-61bd-4387-8ebd-4634b21c4c24' 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 [11.4 MB]
Get:3 http://172.17.0.1/private buster-staging/main armhf Packages [13.1 MB]
Fetched 24.4 MB in 27s (905 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: 'pbdagcon' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/pbdagcon.git
Please use:
git clone https://salsa.debian.org/med-team/pbdagcon.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 265 kB of source archives.
Get:1 http://172.17.0.1/private buster-staging/main pbdagcon 0.3+git20161121.0000000+ds-1.1 (dsc) [2209 B]
Get:2 http://172.17.0.1/private buster-staging/main pbdagcon 0.3+git20161121.0000000+ds-1.1 (tar) [256 kB]
Get:3 http://172.17.0.1/private buster-staging/main pbdagcon 0.3+git20161121.0000000+ds-1.1 (diff) [5956 B]
Fetched 265 kB in 0s (1808 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/pbdagcon-9qUQIQ/pbdagcon-0.3+git20161121.0000000+ds' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/pbdagcon-9qUQIQ' 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-RUyyaz/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-RUyyaz/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-RUyyaz/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-RUyyaz/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-RUyyaz/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-RUyyaz/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-RUyyaz/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-RUyyaz/apt_archive ./ Packages [432 B]
Fetched 2108 B in 1s (2754 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
ca-certificates dbus dbus-user-session krb5-locales libexpat1
libgpg-error-l10n libgssapi-krb5-2 libk5crypto3 libkeyutils1 libkrb5-3
libkrb5support0 libnss-systemd libpam-systemd libssl1.1 openssl systemd-sysv
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 60 not upgraded.
Need to get 852 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-RUyyaz/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 852 B in 0s (0 B/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 14049 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper (>= 12~), python, zlib1g-dev, libhdf5-dev, libboost-dev, libtclap-dev, libpbseq-dev, libpbbam-dev (>= 0.18.0+dfsg-1~), libpbdata-dev, googletest
Filtered Build-Depends: debhelper (>= 12~), python, zlib1g-dev, libhdf5-dev, libboost-dev, libtclap-dev, libpbseq-dev, libpbbam-dev (>= 0.18.0+dfsg-1~), libpbdata-dev, googletest
dpkg-deb: building package 'sbuild-build-depends-pbdagcon-dummy' in '/<<BUILDDIR>>/resolver-RUyyaz/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-RUyyaz/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-RUyyaz/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-RUyyaz/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-RUyyaz/apt_archive ./ Sources [559 B]
Get:5 copy:/<<BUILDDIR>>/resolver-RUyyaz/apt_archive ./ Packages [644 B]
Fetched 2536 B in 1s (3624 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install pbdagcon build dependencies (apt-based resolver)
--------------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
ca-certificates dbus dbus-user-session krb5-locales libgpg-error-l10n
libnss-systemd libpam-systemd openssl systemd-sysv
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils cpp-8 debhelper
dh-autoreconf dh-strip-nondeterminism dwz file g++-8 gcc-8 gcc-8-base
gettext gettext-base googletest groff-base hdf5-helpers intltool-debian
libaec-dev libaec0 libarchive-zip-perl libasan5 libatomic1 libblasr
libblasr-dev libboost-dev libboost1.67-dev libbsd0 libcc1-0 libcroco3
libcurl3-gnutls libelf1 libfile-stripnondeterminism-perl libgcc-8-dev
libgcc1 libgfortran5 libglib2.0-0 libgnutls30 libgomp1 libhdf5-103
libhdf5-cpp-103 libhdf5-dev libhts-dev libhts2 libicu63 libjpeg-dev
libjpeg62-turbo libjpeg62-turbo-dev liblzma-dev liblzma5 libmagic-mgc
libmagic1 libnghttp2-14 libpbbam-dev libpbbam0.19.0 libpbdata libpbdata-dev
libpbihdf libpbihdf-dev libpbseq-dev libpipeline1 libpsl5 libpython-stdlib
libpython2-stdlib libpython2.7-minimal libpython2.7-stdlib librtmp1
libsigsegv2 libssh2-1 libssl-dev libstdc++-8-dev libstdc++6 libsz2
libtclap-dev libtool libubsan1 libuchardet0 libxml2 m4 man-db mime-support
po-debconf python python-minimal python2 python2-minimal python2.7
python2.7-minimal zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
vacation gcc-8-locales dh-make gcc-8-doc libstdc++6-8-dbg libgcc1-dbg
libgomp1-dbg libitm1-dbg libatomic1-dbg libasan5-dbg liblsan0-dbg
libtsan0-dbg libubsan1-dbg libmpx2-dbg libquadmath0-dbg gettext-doc
libasprintf-dev libgettextpo-dev groff libboost-doc libboost1.67-doc
libboost-atomic1.67-dev libboost-chrono1.67-dev libboost-container1.67-dev
libboost-context1.67-dev libboost-coroutine1.67-dev
libboost-date-time1.67-dev libboost-exception1.67-dev libboost-fiber1.67-dev
libboost-filesystem1.67-dev libboost-graph1.67-dev
libboost-graph-parallel1.67-dev libboost-iostreams1.67-dev
libboost-locale1.67-dev libboost-log1.67-dev libboost-math1.67-dev
libboost-mpi1.67-dev libboost-mpi-python1.67-dev libboost-numpy1.67-dev
libboost-program-options1.67-dev libboost-python1.67-dev
libboost-random1.67-dev libboost-regex1.67-dev
libboost-serialization1.67-dev libboost-signals1.67-dev
libboost-stacktrace1.67-dev libboost-system1.67-dev libboost-test1.67-dev
libboost-thread1.67-dev libboost-timer1.67-dev libboost-type-erasure1.67-dev
libboost-wave1.67-dev libboost1.67-tools-dev libmpfrc++-dev libntl-dev
gnutls-bin libhdf5-doc liblzma-doc libssl-doc libstdc++-8-doc libtool-doc
gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser
libmail-box-perl python-doc python-tk python2-doc python2.7-doc
binfmt-support
Recommended packages:
curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info
xdg-user-dirs publicsuffix libltdl-dev libmail-sendmail-perl
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils debhelper
dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base
googletest groff-base hdf5-helpers intltool-debian libaec-dev libaec0
libarchive-zip-perl libblasr libblasr-dev libboost-dev libboost1.67-dev
libbsd0 libcroco3 libcurl3-gnutls libelf1 libfile-stripnondeterminism-perl
libgfortran5 libglib2.0-0 libhdf5-103 libhdf5-cpp-103 libhdf5-dev libhts-dev
libhts2 libicu63 libjpeg-dev libjpeg62-turbo libjpeg62-turbo-dev liblzma-dev
libmagic-mgc libmagic1 libnghttp2-14 libpbbam-dev libpbbam0.19.0 libpbdata
libpbdata-dev libpbihdf libpbihdf-dev libpbseq-dev libpipeline1 libpsl5
libpython-stdlib libpython2-stdlib libpython2.7-minimal libpython2.7-stdlib
librtmp1 libsigsegv2 libssh2-1 libssl-dev libsz2 libtclap-dev libtool
libuchardet0 libxml2 m4 man-db mime-support po-debconf python python-minimal
python2 python2-minimal python2.7 python2.7-minimal
sbuild-build-depends-pbdagcon-dummy zlib1g-dev
The following packages will be upgraded:
cpp-8 g++-8 gcc-8 gcc-8-base libasan5 libatomic1 libcc1-0 libgcc-8-dev
libgcc1 libgnutls30 libgomp1 liblzma5 libstdc++-8-dev libstdc++6 libubsan1
15 upgraded, 77 newly installed, 0 to remove and 45 not upgraded.
Need to get 71.7 MB/72.1 MB of archives.
After this operation, 253 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-RUyyaz/apt_archive ./ sbuild-build-depends-pbdagcon-dummy 0.invalid.0 [928 B]
Get:2 http://172.17.0.1/private buster-staging/main armhf libbsd0 armhf 0.9.1-1 [104 kB]
Get:3 http://172.17.0.1/private buster-staging/main armhf bsdmainutils armhf 11.1.2 [182 kB]
Get:4 http://172.17.0.1/private buster-staging/main armhf libcc1-0 armhf 8.2.0-16+rpi1 [37.9 kB]
Get:5 http://172.17.0.1/private buster-staging/main armhf gcc-8-base armhf 8.2.0-16+rpi1 [189 kB]
Get:6 http://172.17.0.1/private buster-staging/main armhf libgcc1 armhf 1:8.2.0-16+rpi1 [36.6 kB]
Get:7 http://172.17.0.1/private buster-staging/main armhf libgomp1 armhf 8.2.0-16+rpi1 [63.9 kB]
Get:8 http://172.17.0.1/private buster-staging/main armhf libatomic1 armhf 8.2.0-16+rpi1 [8104 B]
Get:9 http://172.17.0.1/private buster-staging/main armhf libasan5 armhf 8.2.0-16+rpi1 [318 kB]
Get:10 http://172.17.0.1/private buster-staging/main armhf libubsan1 armhf 8.2.0-16+rpi1 [104 kB]
Get:11 http://172.17.0.1/private buster-staging/main armhf g++-8 armhf 8.2.0-16+rpi1 [7467 kB]
Get:12 http://172.17.0.1/private buster-staging/main armhf libstdc++-8-dev armhf 8.2.0-16+rpi1 [1539 kB]
Get:13 http://172.17.0.1/private buster-staging/main armhf libgcc-8-dev armhf 8.2.0-16+rpi1 [597 kB]
Get:14 http://172.17.0.1/private buster-staging/main armhf gcc-8 armhf 8.2.0-16+rpi1 [7216 kB]
Get:15 http://172.17.0.1/private buster-staging/main armhf cpp-8 armhf 8.2.0-16+rpi1 [6789 kB]
Get:16 http://172.17.0.1/private buster-staging/main armhf libstdc++6 armhf 8.2.0-16+rpi1 [324 kB]
Get:17 http://172.17.0.1/private buster-staging/main armhf libuchardet0 armhf 0.0.6-3 [62.2 kB]
Get:18 http://172.17.0.1/private buster-staging/main armhf groff-base armhf 1.22.4-2 [782 kB]
Get:19 http://172.17.0.1/private buster-staging/main armhf libpipeline1 armhf 1.5.1-1 [26.6 kB]
Get:20 http://172.17.0.1/private buster-staging/main armhf man-db armhf 2.8.5-1 [1231 kB]
Get:21 http://172.17.0.1/private buster-staging/main armhf libpython2.7-minimal armhf 2.7.15-8 [394 kB]
Get:22 http://172.17.0.1/private buster-staging/main armhf python2.7-minimal armhf 2.7.15-8 [1089 kB]
Get:23 http://172.17.0.1/private buster-staging/main armhf python2-minimal armhf 2.7.15-4 [41.4 kB]
Get:24 http://172.17.0.1/private buster-staging/main armhf python-minimal armhf 2.7.15-4 [21.0 kB]
Get:25 http://172.17.0.1/private buster-staging/main armhf mime-support all 3.61 [37.1 kB]
Get:26 http://172.17.0.1/private buster-staging/main armhf libpython2.7-stdlib armhf 2.7.15-8 [1844 kB]
Get:27 http://172.17.0.1/private buster-staging/main armhf python2.7 armhf 2.7.15-8 [299 kB]
Get:28 http://172.17.0.1/private buster-staging/main armhf libpython2-stdlib armhf 2.7.15-4 [20.8 kB]
Get:29 http://172.17.0.1/private buster-staging/main armhf libpython-stdlib armhf 2.7.15-4 [20.8 kB]
Get:30 http://172.17.0.1/private buster-staging/main armhf python2 armhf 2.7.15-4 [41.6 kB]
Get:31 http://172.17.0.1/private buster-staging/main armhf python armhf 2.7.15-4 [22.8 kB]
Get:32 http://172.17.0.1/private buster-staging/main armhf libgnutls30 armhf 3.6.6-2 [1035 kB]
Get:33 http://172.17.0.1/private buster-staging/main armhf liblzma5 armhf 5.2.4-1 [144 kB]
Get:34 http://172.17.0.1/private buster-staging/main armhf libmagic-mgc armhf 1:5.35-2 [242 kB]
Get:35 http://172.17.0.1/private buster-staging/main armhf libmagic1 armhf 1:5.35-2 [109 kB]
Get:36 http://172.17.0.1/private buster-staging/main armhf file armhf 1:5.35-2 [65.1 kB]
Get:37 http://172.17.0.1/private buster-staging/main armhf gettext-base armhf 0.19.8.1-9 [117 kB]
Get:38 http://172.17.0.1/private buster-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:39 http://172.17.0.1/private buster-staging/main armhf m4 armhf 1.4.18-2 [185 kB]
Get:40 http://172.17.0.1/private buster-staging/main armhf autoconf all 2.69-11 [341 kB]
Get:41 http://172.17.0.1/private buster-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:42 http://172.17.0.1/private buster-staging/main armhf automake all 1:1.16.1-4 [771 kB]
Get:43 http://172.17.0.1/private buster-staging/main armhf autopoint all 0.19.8.1-9 [434 kB]
Get:44 http://172.17.0.1/private buster-staging/main armhf libtool all 2.4.6-9 [547 kB]
Get:45 http://172.17.0.1/private buster-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:46 http://172.17.0.1/private buster-staging/main armhf libarchive-zip-perl all 1.64-1 [96.8 kB]
Get:47 http://172.17.0.1/private buster-staging/main armhf libfile-stripnondeterminism-perl all 1.1.0-1 [19.5 kB]
Get:48 http://172.17.0.1/private buster-staging/main armhf dh-strip-nondeterminism all 1.1.0-1 [12.6 kB]
Get:49 http://172.17.0.1/private buster-staging/main armhf libelf1 armhf 0.175-2 [157 kB]
Get:50 http://172.17.0.1/private buster-staging/main armhf dwz armhf 0.12-3 [66.0 kB]
Get:51 http://172.17.0.1/private buster-staging/main armhf libglib2.0-0 armhf 2.58.3-1 [1077 kB]
Get:52 http://172.17.0.1/private buster-staging/main armhf libicu63 armhf 63.1-6 [7973 kB]
Get:53 http://172.17.0.1/private buster-staging/main armhf libxml2 armhf 2.9.4+dfsg1-7+b1 [570 kB]
Get:54 http://172.17.0.1/private buster-staging/main armhf libcroco3 armhf 0.6.12-3 [132 kB]
Get:55 http://172.17.0.1/private buster-staging/main armhf gettext armhf 0.19.8.1-9 [1219 kB]
Get:56 http://172.17.0.1/private buster-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:57 http://172.17.0.1/private buster-staging/main armhf po-debconf all 1.0.21 [248 kB]
Get:58 http://172.17.0.1/private buster-staging/main armhf debhelper all 12 [1002 kB]
Get:59 http://172.17.0.1/private buster-staging/main armhf googletest armhf 1.8.1-3 [903 kB]
Get:60 http://172.17.0.1/private buster-staging/main armhf hdf5-helpers armhf 1.10.4+repack-10 [35.2 kB]
Get:61 http://172.17.0.1/private buster-staging/main armhf libaec-dev armhf 1.0.2-1 [19.1 kB]
Get:62 http://172.17.0.1/private buster-staging/main armhf libnghttp2-14 armhf 1.36.0-2 [73.6 kB]
Get:63 http://172.17.0.1/private buster-staging/main armhf libpsl5 armhf 0.20.2-2 [52.6 kB]
Get:64 http://172.17.0.1/private buster-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2 [54.0 kB]
Get:65 http://172.17.0.1/private buster-staging/main armhf libssh2-1 armhf 1.8.0-2 [125 kB]
Get:66 http://172.17.0.1/private buster-staging/main armhf libcurl3-gnutls armhf 7.64.0-1 [291 kB]
Get:67 http://172.17.0.1/private buster-staging/main armhf libhts2 armhf 1.9-8 [254 kB]
Get:68 http://172.17.0.1/private buster-staging/main armhf libpbbam0.19.0 armhf 0.19.0+dfsg-4+rpi1 [455 kB]
Get:69 http://172.17.0.1/private buster-staging/main armhf libpbdata armhf 5.3.1+dfsg-2.1 [106 kB]
Get:70 http://172.17.0.1/private buster-staging/main armhf libgfortran5 armhf 8.2.0-16+rpi1 [207 kB]
Get:71 http://172.17.0.1/private buster-staging/main armhf libhdf5-103 armhf 1.10.4+repack-10 [1259 kB]
Get:72 http://172.17.0.1/private buster-staging/main armhf libhdf5-cpp-103 armhf 1.10.4+repack-10 [121 kB]
Get:73 http://172.17.0.1/private buster-staging/main armhf libpbihdf armhf 5.3.1+dfsg-2.1 [138 kB]
Get:74 http://172.17.0.1/private buster-staging/main armhf libblasr armhf 5.3.1+dfsg-2.1 [832 kB]
Get:75 http://172.17.0.1/private buster-staging/main armhf libpbdata-dev armhf 5.3.1+dfsg-2.1 [175 kB]
Get:76 http://172.17.0.1/private buster-staging/main armhf libblasr-dev armhf 5.3.1+dfsg-2.1 [1664 kB]
Get:77 http://172.17.0.1/private buster-staging/main armhf libboost1.67-dev armhf 1.67.0-13 [8386 kB]
Get:78 http://172.17.0.1/private buster-staging/main armhf libboost-dev armhf 1.67.0.1+b1 [4140 B]
Get:79 http://172.17.0.1/private buster-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-1 [206 kB]
Get:80 http://172.17.0.1/private buster-staging/main armhf libhdf5-dev armhf 1.10.4+repack-10 [2221 kB]
Get:81 http://172.17.0.1/private buster-staging/main armhf liblzma-dev armhf 5.2.4-1 [203 kB]
Get:82 http://172.17.0.1/private buster-staging/main armhf libhts-dev armhf 1.9-8 [4280 kB]
Get:83 http://172.17.0.1/private buster-staging/main armhf libssl-dev armhf 1.1.1a-1 [1556 kB]
Get:84 http://172.17.0.1/private buster-staging/main armhf libpbbam-dev armhf 0.19.0+dfsg-4+rpi1 [93.4 kB]
Get:85 http://172.17.0.1/private buster-staging/main armhf libpbihdf-dev armhf 5.3.1+dfsg-2.1 [243 kB]
Get:86 http://172.17.0.1/private buster-staging/main armhf libpbseq-dev all 5.3.1+dfsg-2.1 [4612 B]
Get:87 http://172.17.0.1/private buster-staging/main armhf libtclap-dev armhf 1.2.2-1 [139 kB]
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Not building database; man-db/auto-update is not 'true'.
Created symlink /etc/systemd/system/timers.target.wants/man-db.timer -> /lib/systemd/system/man-db.timer.
Setting up libpython2-stdlib:armhf (2.7.15-4) ...
Setting up libgcc-8-dev:armhf (8.2.0-16+rpi1) ...
Setting up libhts2:armhf (1.9-8) ...
Setting up libtool (2.4.6-9) ...
Setting up libstdc++-8-dev:armhf (8.2.0-16+rpi1) ...
Setting up po-debconf (1.0.21) ...
Setting up libhts-dev:armhf (1.9-8) ...
Setting up libhdf5-cpp-103:armhf (1.10.4+repack-10) ...
Setting up libhdf5-dev (1.10.4+repack-10) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/pkgconfig/hdf5-serial.pc to provide /usr/lib/arm-linux-gnueabihf/pkgconfig/hdf5.pc (hdf5.pc) in auto mode
Setting up libpbbam0.19.0:armhf (0.19.0+dfsg-4+rpi1) ...
Setting up python2 (2.7.15-4) ...
Setting up gcc-8 (8.2.0-16+rpi1) ...
Setting up g++-8 (8.2.0-16+rpi1) ...
Setting up libpython-stdlib:armhf (2.7.15-4) ...
Setting up libboost1.67-dev:armhf (1.67.0-13) ...
Setting up libpbdata:armhf (5.3.1+dfsg-2.1) ...
Setting up libpbihdf:armhf (5.3.1+dfsg-2.1) ...
Setting up libboost-dev:armhf (1.67.0.1+b1) ...
Setting up python (2.7.15-4) ...
Setting up libblasr:armhf (5.3.1+dfsg-2.1) ...
Setting up libpbbam-dev (0.19.0+dfsg-4+rpi1) ...
Setting up libpbihdf-dev:armhf (5.3.1+dfsg-2.1) ...
Setting up libpbdata-dev:armhf (5.3.1+dfsg-2.1) ...
Setting up libblasr-dev:armhf (5.3.1+dfsg-2.1) ...
Setting up libpbseq-dev (5.3.1+dfsg-2.1) ...
Setting up dh-autoreconf (19) ...
Setting up debhelper (12) ...
Setting up sbuild-build-depends-pbdagcon-dummy (0.invalid.0) ...
Setting up dh-strip-nondeterminism (1.1.0-1) ...
Processing triggers for libc-bin (2.28-5+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.9.0-0.bpo.4-armmp armhf (armv7l)
Toolchain package versions: binutils_2.31.1-11+rpi1 dpkg-dev_1.19.2 g++-8_8.2.0-16+rpi1 gcc-8_8.2.0-16+rpi1 libc6-dev_2.28-5+rpi1 libstdc++-8-dev_8.2.0-16+rpi1 libstdc++6_8.2.0-16+rpi1 linux-libc-dev_4.18.20-2+rpi1
Package versions: adduser_3.118 apt_1.8.0~beta1 autoconf_2.69-11 automake_1:1.16.1-4 autopoint_0.19.8.1-9 autotools-dev_20180224.1 base-files_10.1+rpi1 base-passwd_3.5.45 bash_5.0-2 binutils_2.31.1-11+rpi1 binutils-arm-linux-gnueabihf_2.31.1-11+rpi1 binutils-common_2.31.1-11+rpi1 bsdmainutils_11.1.2 bsdutils_1:2.33.1-0.1 build-essential_12.5 bzip2_1.0.6-9 ca-certificates_20170717 coreutils_8.30-1 cpio_2.12+dfsg-6 cpp_4:8.2.0-2+rpi1 cpp-8_8.2.0-16+rpi1 dash_0.5.10.2-5 dbus_1.12.12-1 dbus-user-session_1.12.12-1 debconf_1.5.70 debhelper_12 debianutils_4.8.6.1 dh-autoreconf_19 dh-strip-nondeterminism_1.1.0-1 diffutils_1:3.6-1 dirmngr_2.2.12-1+rpi1 dmsetup_2:1.02.155-1 dpkg_1.19.2 dpkg-dev_1.19.2 dwz_0.12-3 e2fslibs_1.44.5-1 e2fsprogs_1.44.5-1 fakeroot_1.23-1 fdisk_2.33.1-0.1 file_1:5.35-2 findutils_4.6.0+git+20190105-2 g++_4:8.2.0-2+rpi1 g++-8_8.2.0-16+rpi1 gcc_4:8.2.0-2+rpi1 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8-base_4.8.5-4 gcc-4.9-base_4.9.4-2+rpi1+b19 gcc-5-base_5.5.0-8 gcc-6-base_6.5.0-1+rpi1 gcc-8_8.2.0-16+rpi1 gcc-8-base_8.2.0-16+rpi1 gettext_0.19.8.1-9 gettext-base_0.19.8.1-9 gnupg_2.2.12-1+rpi1 gnupg-l10n_2.2.12-1+rpi1 gnupg-utils_2.2.12-1+rpi1 googletest_1.8.1-3 gpg_2.2.12-1+rpi1 gpg-agent_2.2.12-1+rpi1 gpg-wks-client_2.2.12-1+rpi1 gpg-wks-server_2.2.12-1+rpi1 gpgconf_2.2.12-1+rpi1 gpgsm_2.2.12-1+rpi1 gpgv_2.2.12-1+rpi1 grep_3.3-1 groff-base_1.22.4-2 gzip_1.9-3 hdf5-helpers_1.10.4+repack-10 hostname_3.21 inetutils-ping_2:1.9.4-5 init-system-helpers_1.56+nmu1 initramfs-tools_0.132 initramfs-tools-core_0.132 intltool-debian_0.35.0+20060710.5 klibc-utils_2.0.4-15+rpi1 kmod_25-2 krb5-locales_1.17-1 libacl1_2.2.52-3 libaec-dev_1.0.2-1 libaec0_1.0.2-1 libapparmor1_2.13.2-3 libapt-pkg5.0_1.8.0~beta1 libarchive-zip-perl_1.64-1 libargon2-1_0~20171227-0.1 libasan5_8.2.0-16+rpi1 libassuan0_2.5.2-1 libatomic1_8.2.0-16+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.8.4-2 libaudit1_1:2.8.4-2+b1 libbinutils_2.31.1-11+rpi1 libblasr_5.3.1+dfsg-2.1 libblasr-dev_5.3.1+dfsg-2.1 libblkid1_2.33.1-0.1 libboost-dev_1.67.0.1+b1 libboost1.67-dev_1.67.0-13 libbsd0_0.9.1-1 libbz2-1.0_1.0.6-9 libc-bin_2.28-5+rpi1 libc-dev-bin_2.28-5+rpi1 libc6_2.28-5+rpi1 libc6-dev_2.28-5+rpi1 libcap-ng0_0.7.9-2 libcap2_1:2.25-1.2 libcc1-0_8.2.0-16+rpi1 libcom-err2_1.44.5-1 libcroco3_0.6.12-3 libcryptsetup12_2:2.0.6-1 libcryptsetup4_2:1.7.5-1 libcurl3-gnutls_7.64.0-1 libdb5.3_5.3.28+dfsg1-0.2 libdbus-1-3_1.12.12-1 libdebconfclient0_0.246 libdevmapper1.02.1_2:1.02.155-1 libdpkg-perl_1.19.2 libdrm-common_2.4.95-1+rpi1 libdrm2_2.4.95-1+rpi1 libelf1_0.175-2 libexpat1_2.2.6-1 libext2fs2_1.44.5-1 libfakeroot_1.23-1 libfdisk1_2.33.1-0.1 libffi6_3.2.1-9 libfile-stripnondeterminism-perl_1.1.0-1 libgcc-8-dev_8.2.0-16+rpi1 libgcc1_1:8.2.0-16+rpi1 libgcrypt20_1.8.4-4 libgdbm-compat4_1.18.1-2 libgdbm3_1.8.3-14 libgdbm6_1.18.1-2 libgfortran5_8.2.0-16+rpi1 libglib2.0-0_2.58.3-1 libgmp10_2:6.1.2+dfsg-4 libgnutls30_3.6.6-2 libgomp1_8.2.0-16+rpi1 libgpg-error-l10n_1.33-3 libgpg-error0_1.33-3 libgssapi-krb5-2_1.17-1 libhdf5-103_1.10.4+repack-10 libhdf5-cpp-103_1.10.4+repack-10 libhdf5-dev_1.10.4+repack-10 libhogweed4_3.4.1~rc1-1 libhts-dev_1.9-8 libhts2_1.9-8 libicu63_63.1-6 libidn11_1.33-2.2 libidn2-0_2.0.5-1 libip4tc0_1.8.2-3 libisl19_0.20-2 libjpeg-dev_1:1.5.2-2 libjpeg62-turbo_1:1.5.2-2+b1 libjpeg62-turbo-dev_1:1.5.2-2+b1 libjson-c3_0.12.1-1.3 libk5crypto3_1.17-1 libkeyutils1_1.5.9-9.3 libklibc_2.0.4-15+rpi1 libkmod2_25-2 libkrb5-3_1.17-1 libkrb5support0_1.17-1 libksba8_1.3.5-2 libldap-2.4-2_2.4.47+dfsg-2 libldap-common_2.4.47+dfsg-2 liblz4-1_1.8.3-1 liblzma-dev_5.2.4-1 liblzma5_5.2.4-1 libmagic-mgc_1:5.35-2 libmagic1_1:5.35-2 libmount1_2.33.1-0.1 libmpc3_1.1.0-1 libmpfr6_4.0.2~rc1-1 libncurses5_6.1+20181013-1 libncurses6_6.1+20181013-1 libncursesw5_6.1+20181013-1 libncursesw6_6.1+20181013-1 libnettle6_3.4.1~rc1-1 libnghttp2-14_1.36.0-2 libnpth0_1.6-1 libnss-systemd_240-4+rpi1 libp11-kit0_0.23.14-2 libpam-modules_1.1.8-4 libpam-modules-bin_1.1.8-4 libpam-runtime_1.1.8-4 libpam-systemd_240-4+rpi1 libpam0g_1.1.8-4 libpbbam-dev_0.19.0+dfsg-4+rpi1 libpbbam0.19.0_0.19.0+dfsg-4+rpi1 libpbdata_5.3.1+dfsg-2.1 libpbdata-dev_5.3.1+dfsg-2.1 libpbihdf_5.3.1+dfsg-2.1 libpbihdf-dev_5.3.1+dfsg-2.1 libpbseq-dev_5.3.1+dfsg-2.1 libpcre3_2:8.39-11+rpi1 libperl5.28_5.28.1-3 libpipeline1_1.5.1-1 libplymouth4_0.9.4-1 libpng16-16_1.6.36-2 libprocps7_2:3.3.15-2 libpsl5_0.20.2-2 libpython-stdlib_2.7.15-4 libpython2-stdlib_2.7.15-4 libpython2.7-minimal_2.7.15-8 libpython2.7-stdlib_2.7.15-8 libreadline7_7.0-5 librtmp1_2.4+20151223.gitfa8646d.1-2 libsasl2-2_2.1.27+dfsg-1 libsasl2-modules-db_2.1.27+dfsg-1 libseccomp2_2.3.3-3+b1 libselinux1_2.8-1+b1 libsemanage-common_2.8-2 libsemanage1_2.8-2 libsepol1_2.8-1 libsigsegv2_2.12-2 libsmartcols1_2.33.1-0.1 libsqlite3-0_3.26.0+fossilbc891ac6b-1 libss2_1.44.5-1 libssh2-1_1.8.0-2 libssl-dev_1.1.1a-1 libssl1.1_1.1.1a-1 libstdc++-8-dev_8.2.0-16+rpi1 libstdc++6_8.2.0-16+rpi1 libsystemd0_240-4+rpi1 libsz2_1.0.2-1 libtasn1-6_4.13-3 libtclap-dev_1.2.2-1 libtinfo5_6.1+20181013-1 libtinfo6_6.1+20181013-1 libtool_2.4.6-9 libubsan1_8.2.0-16+rpi1 libuchardet0_0.0.6-3 libudev1_240-4+rpi1 libunistring2_0.9.10-1 libuuid1_2.33.1-0.1 libxml2_2.9.4+dfsg1-7+b1 libzstd1_1.3.8+dfsg-3+rpi1 linux-base_4.5 linux-libc-dev_4.18.20-2+rpi1 login_1:4.5-1.1 lsb-base_10.2018112800+rpi1 m4_1.4.18-2 make_4.2.1-1.2 makedev_2.3.1-94 man-db_2.8.5-1 mawk_1.3.3-17 mime-support_3.61 mount_2.33.1-0.1 multiarch-support_2.28-5+rpi1 nano_3.2-1 ncurses-base_6.1+20181013-1 ncurses-bin_6.1+20181013-1 netbase_5.5 openssl_1.1.1a-1 passwd_1:4.5-1.1 patch_2.7.6-3 perl_5.28.1-3 perl-base_5.28.1-3 perl-modules-5.28_5.28.1-3 pinentry-curses_1.1.0-1 plymouth_0.9.4-1 po-debconf_1.0.21 procps_2:3.3.15-2 python_2.7.15-4 python-minimal_2.7.15-4 python2_2.7.15-4 python2-minimal_2.7.15-4 python2.7_2.7.15-8 python2.7-minimal_2.7.15-8 raspbian-archive-keyring_20120528.2 readline-common_7.0-5 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-pbdagcon-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12 systemd_240-4+rpi1 systemd-sysv_240-4+rpi1 sysvinit-utils_2.93-5 tar_1.30+dfsg-4 tzdata_2018i-1 udev_240-4+rpi1 util-linux_2.33.1-0.1 xz-utils_5.2.2-1.3 zlib1g_1:1.2.11.dfsg-1 zlib1g-dev_1:1.2.11.dfsg-1
+------------------------------------------------------------------------------+
| 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 Feb 6 07:23:22 2019 UTC
gpgv: using RSA key 3AFA757FAC6EA11D2FF45DF088D24287A2D898B1
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./pbdagcon_0.3+git20161121.0000000+ds-1.1.dsc
dpkg-source: info: extracting pbdagcon in /<<BUILDDIR>>/pbdagcon-0.3+git20161121.0000000+ds
dpkg-source: info: unpacking pbdagcon_0.3+git20161121.0000000+ds.orig.tar.gz
dpkg-source: info: unpacking pbdagcon_0.3+git20161121.0000000+ds-1.1.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying compiler-flags.patch
Check disc space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=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-04677564-61bd-4387-8ebd-4634b21c4c24
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package pbdagcon
dpkg-buildpackage: info: source version 0.3+git20161121.0000000+ds-1.1
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
fakeroot debian/rules clean
dh clean
dh_auto_clean
make -j4 clean
make[1]: Entering directory '/<<BUILDDIR>>/pbdagcon-0.3+git20161121.0000000+ds'
make -C src/cpp clean
make[2]: Entering directory '/<<BUILDDIR>>/pbdagcon-0.3+git20161121.0000000+ds/src/cpp'
rm -f *.d
rm -f *.o
rm -f pbdagcon
rm -f dazcon
make[2]: Leaving directory '/<<BUILDDIR>>/pbdagcon-0.3+git20161121.0000000+ds/src/cpp'
make -C test/cpp clean
make[2]: Entering directory '/<<BUILDDIR>>/pbdagcon-0.3+git20161121.0000000+ds/test/cpp'
rm -f .//*.o
rm -f *.o
rm -f test_*
make[2]: Leaving directory '/<<BUILDDIR>>/pbdagcon-0.3+git20161121.0000000+ds/test/cpp'
make[1]: Leaving directory '/<<BUILDDIR>>/pbdagcon-0.3+git20161121.0000000+ds'
dh_clean
debian/rules build-arch
dh build-arch
dh_update_autotools_config -a
dh_autoreconf -a
debian/rules override_dh_auto_configure
make[1]: Entering directory '/<<BUILDDIR>>/pbdagcon-0.3+git20161121.0000000+ds'
./configure.py --shared
uname -s
uname='Linux'
writing to '/<<BUILDDIR>>/pbdagcon-0.3+git20161121.0000000+ds/defines.mk'
"""
DALIGNER_INCLUDE ?= ${DALIGNER_SRC}
DALIGNER_SRC ?= /<<BUILDDIR>>/pbdagcon-0.3+git20161121.0000000+ds/DALIGNER
DAZZ_DB_INCLUDE ?= ${DAZZ_DB_SRC}
DAZZ_DB_SRC ?= /<<BUILDDIR>>/pbdagcon-0.3+git20161121.0000000+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_INCLUDE ?= /usr/include/pbseq
PBBAM_LIBFLAGS ?= -lpbbam
PTHREAD_LIBFLAGS ?= -lpthread
ZLIB_LIBFLAGS ?= -lz
LDLIBS+=-lrt
"""
make[1]: Leaving directory '/<<BUILDDIR>>/pbdagcon-0.3+git20161121.0000000+ds'
dh_auto_build -a
make -j4 "INSTALL=install --strip-program=true"
make[1]: Entering directory '/<<BUILDDIR>>/pbdagcon-0.3+git20161121.0000000+ds'
make -C src/cpp
make[2]: Entering directory '/<<BUILDDIR>>/pbdagcon-0.3+git20161121.0000000+ds/src/cpp'
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbdagcon-0.3+git20161121.0000000+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+git20161121.0000000+ds/DAZZ_DB -I/<<BUILDDIR>>/pbdagcon-0.3+git20161121.0000000+ds/DALIGNER -I/usr/include/pbseq/alignment -I/usr/include/pbseq/pbdata -I/usr/include/pbseq/hdf -I/usr/include/pbseq -isystem.//third-party -c -o Alignment.o Alignment.cpp
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbdagcon-0.3+git20161121.0000000+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+git20161121.0000000+ds/DAZZ_DB -I/<<BUILDDIR>>/pbdagcon-0.3+git20161121.0000000+ds/DALIGNER -I/usr/include/pbseq/alignment -I/usr/include/pbseq/pbdata -I/usr/include/pbseq/hdf -I/usr/include/pbseq -isystem.//third-party -c -o AlnGraphBoost.o AlnGraphBoost.cpp
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbdagcon-0.3+git20161121.0000000+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+git20161121.0000000+ds/DAZZ_DB -I/<<BUILDDIR>>/pbdagcon-0.3+git20161121.0000000+ds/DALIGNER -I/usr/include/pbseq/alignment -I/usr/include/pbseq/pbdata -I/usr/include/pbseq/hdf -I/usr/include/pbseq -isystem.//third-party -c -o BlasrM5AlnProvider.o BlasrM5AlnProvider.cpp
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbdagcon-0.3+git20161121.0000000+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+git20161121.0000000+ds/DAZZ_DB -I/<<BUILDDIR>>/pbdagcon-0.3+git20161121.0000000+ds/DALIGNER -I/usr/include/pbseq/alignment -I/usr/include/pbseq/pbdata -I/usr/include/pbseq/hdf -I/usr/include/pbseq -isystem.//third-party -c -o main.o main.cpp
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbdagcon-0.3+git20161121.0000000+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+git20161121.0000000+ds/DAZZ_DB -I/<<BUILDDIR>>/pbdagcon-0.3+git20161121.0000000+ds/DALIGNER -I/usr/include/pbseq/alignment -I/usr/include/pbseq/pbdata -I/usr/include/pbseq/hdf -I/usr/include/pbseq -isystem.//third-party -c -o SimpleAligner.o SimpleAligner.cpp
cc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbdagcon-0.3+git20161121.0000000+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+git20161121.0000000+ds/DAZZ_DB -I/<<BUILDDIR>>/pbdagcon-0.3+git20161121.0000000+ds/DALIGNER -I/usr/include/pbseq/alignment -I/usr/include/pbseq/pbdata -I/usr/include/pbseq/hdf -I/usr/include/pbseq -isystem.//third-party -c -o DB.o /<<BUILDDIR>>/pbdagcon-0.3+git20161121.0000000+ds/DAZZ_DB/DB.c
/<<BUILDDIR>>/pbdagcon-0.3+git20161121.0000000+ds/DAZZ_DB/DB.c: In function 'Load_QVs':
/<<BUILDDIR>>/pbdagcon-0.3+git20161121.0000000+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+git20161121.0000000+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+git20161121.0000000+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+git20161121.0000000+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+git20161121.0000000+ds/DAZZ_DB -I/<<BUILDDIR>>/pbdagcon-0.3+git20161121.0000000+ds/DALIGNER -I/usr/include/pbseq/alignment -I/usr/include/pbseq/pbdata -I/usr/include/pbseq/hdf -I/usr/include/pbseq -isystem.//third-party -c -o QV.o /<<BUILDDIR>>/pbdagcon-0.3+git20161121.0000000+ds/DAZZ_DB/QV.c
/<<BUILDDIR>>/pbdagcon-0.3+git20161121.0000000+ds/DAZZ_DB/QV.c: In function 'Build_Table':
/<<BUILDDIR>>/pbdagcon-0.3+git20161121.0000000+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+git20161121.0000000+ds/DAZZ_DB/QV.c: In function 'Huffman':
/<<BUILDDIR>>/pbdagcon-0.3+git20161121.0000000+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+git20161121.0000000+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+git20161121.0000000+ds/DAZZ_DB -I/<<BUILDDIR>>/pbdagcon-0.3+git20161121.0000000+ds/DALIGNER -I/usr/include/pbseq/alignment -I/usr/include/pbseq/pbdata -I/usr/include/pbseq/hdf -I/usr/include/pbseq -isystem.//third-party -c -o align.o /<<BUILDDIR>>/pbdagcon-0.3+git20161121.0000000+ds/DALIGNER/align.c
In file included from /usr/include/c++/8/bits/stl_algo.h:61,
from /usr/include/c++/8/algorithm:62,
from SimpleAligner.cpp:6:
/usr/include/c++/8/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++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' changed in GCC 7.1
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
In file included from /usr/include/c++/8/algorithm:62,
from SimpleAligner.cpp:6:
/usr/include/c++/8/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++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' changed in GCC 7.1
__insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' changed in GCC 7.1
In file included from /usr/include/c++/8/vector:69,
from SimpleAligner.cpp:1:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const PositionDNATuple&}; _Tp = PositionDNATuple; _Alloc = std::allocator<PositionDNATuple>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<PositionDNATuple, std::allocator<PositionDNATuple> >::iterator' {aka '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<PositionDNATuple, std::allocator<PositionDNATuple> >::iterator' {aka '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >'} changed in GCC 7.1
In file included from /usr/include/c++/8/vector:64,
from SimpleAligner.cpp:1:
/usr/include/c++/8/bits/stl_vector.h: In function 'int SequenceToTupleList(Sequence&, TupleMetrics&, TupleList<PositionDNATuple>&) [with Sequence = DNASequence]':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/algorithm:62,
from SimpleAligner.cpp:6:
/usr/include/c++/8/bits/stl_algo.h: In function 'void std::__heap_select(_RandomAccessIterator, _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++/8/bits/stl_algo.h:1668:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' changed in GCC 7.1
__heap_select(_RandomAccessIterator __first,
^~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1668:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1668:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1668:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' changed in GCC 7.1
/usr/include/c++/8/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++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' changed in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' changed in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1933:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' changed in GCC 7.1
std::__heap_select(__first, __middle, __last, __comp);
~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbdagcon-0.3+git20161121.0000000+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+git20161121.0000000+ds/DAZZ_DB -I/<<BUILDDIR>>/pbdagcon-0.3+git20161121.0000000+ds/DALIGNER -I/usr/include/pbseq/alignment -I/usr/include/pbseq/pbdata -I/usr/include/pbseq/hdf -I/usr/include/pbseq -isystem.//third-party -c -o DazAlnProvider.o DazAlnProvider.cpp
/usr/include/c++/8/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++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbdagcon-0.3+git20161121.0000000+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+git20161121.0000000+ds/DAZZ_DB -I/<<BUILDDIR>>/pbdagcon-0.3+git20161121.0000000+ds/DALIGNER -I/usr/include/pbseq/alignment -I/usr/include/pbseq/pbdata -I/usr/include/pbseq/hdf -I/usr/include/pbseq -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+git20161121.0000000+ds/src/cpp'
make[1]: Leaving directory '/<<BUILDDIR>>/pbdagcon-0.3+git20161121.0000000+ds'
dh_auto_test -a
make -j4 check
make[1]: Entering directory '/<<BUILDDIR>>/pbdagcon-0.3+git20161121.0000000+ds'
make -C src/cpp
make[2]: Entering directory '/<<BUILDDIR>>/pbdagcon-0.3+git20161121.0000000+ds/src/cpp'
make[2]: Nothing to be done for 'all'.
make[2]: Leaving directory '/<<BUILDDIR>>/pbdagcon-0.3+git20161121.0000000+ds/src/cpp'
make -C test/cpp
make[2]: Entering directory '/<<BUILDDIR>>/pbdagcon-0.3+git20161121.0000000+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+git20161121.0000000+ds/DAZZ_DB -I/<<BUILDDIR>>/pbdagcon-0.3+git20161121.0000000+ds/DALIGNER -I/usr/include/pbseq/alignment -I/usr/include/pbseq/pbdata -I/usr/include/pbseq/hdf -I/usr/include/pbseq -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+git20161121.0000000+ds/DAZZ_DB -I/<<BUILDDIR>>/pbdagcon-0.3+git20161121.0000000+ds/DALIGNER -I/usr/include/pbseq/alignment -I/usr/include/pbseq/pbdata -I/usr/include/pbseq/hdf -I/usr/include/pbseq -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+git20161121.0000000+ds/DAZZ_DB -I/<<BUILDDIR>>/pbdagcon-0.3+git20161121.0000000+ds/DALIGNER -I/usr/include/pbseq/alignment -I/usr/include/pbseq/pbdata -I/usr/include/pbseq/hdf -I/usr/include/pbseq -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+git20161121.0000000+ds/DAZZ_DB -I/<<BUILDDIR>>/pbdagcon-0.3+git20161121.0000000+ds/DALIGNER -I/usr/include/pbseq/alignment -I/usr/include/pbseq/pbdata -I/usr/include/pbseq/hdf -I/usr/include/pbseq -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+git20161121.0000000+ds/DAZZ_DB -I/<<BUILDDIR>>/pbdagcon-0.3+git20161121.0000000+ds/DALIGNER -I/usr/include/pbseq/alignment -I/usr/include/pbseq/pbdata -I/usr/include/pbseq/hdf -I/usr/include/pbseq -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+git20161121.0000000+ds/DAZZ_DB -I/<<BUILDDIR>>/pbdagcon-0.3+git20161121.0000000+ds/DALIGNER -I/usr/include/pbseq/alignment -I/usr/include/pbseq/pbdata -I/usr/include/pbseq/hdf -I/usr/include/pbseq -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+git20161121.0000000+ds/DAZZ_DB -I/<<BUILDDIR>>/pbdagcon-0.3+git20161121.0000000+ds/DALIGNER -I/usr/include/pbseq/alignment -I/usr/include/pbseq/pbdata -I/usr/include/pbseq/hdf -I/usr/include/pbseq -I/usr/src/googletest/googletest/include -Ithird-party -c -o AlignmentTest.o AlignmentTest.cpp
In file included from /usr/include/c++/8/bits/stl_algo.h:61,
from /usr/include/c++/8/algorithm:62,
from .//../../src/cpp/SimpleAligner.cpp:6:
/usr/include/c++/8/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++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' changed in GCC 7.1
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
In file included from /usr/include/c++/8/algorithm:62,
from .//../../src/cpp/SimpleAligner.cpp:6:
/usr/include/c++/8/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++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' changed in GCC 7.1
__insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' changed in GCC 7.1
g++ -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I. -I./ -I.//../../src/cpp -I/<<BUILDDIR>>/pbdagcon-0.3+git20161121.0000000+ds/DAZZ_DB -I/<<BUILDDIR>>/pbdagcon-0.3+git20161121.0000000+ds/DALIGNER -I/usr/include/pbseq/alignment -I/usr/include/pbseq/pbdata -I/usr/include/pbseq/hdf -I/usr/include/pbseq -I/usr/src/googletest/googletest/include -Ithird-party -c -o SimpleAlignerTest.o SimpleAlignerTest.cpp
In file included from /usr/include/c++/8/vector:69,
from .//../../src/cpp/SimpleAligner.cpp:1:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const PositionDNATuple&}; _Tp = PositionDNATuple; _Alloc = std::allocator<PositionDNATuple>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<PositionDNATuple, std::allocator<PositionDNATuple> >::iterator' {aka '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<PositionDNATuple, std::allocator<PositionDNATuple> >::iterator' {aka '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >'} changed in GCC 7.1
In file included from /usr/include/c++/8/vector:64,
from .//../../src/cpp/SimpleAligner.cpp:1:
/usr/include/c++/8/bits/stl_vector.h: In function 'int SequenceToTupleList(Sequence&, TupleMetrics&, TupleList<PositionDNATuple>&) [with Sequence = DNASequence]':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/algorithm:62,
from .//../../src/cpp/SimpleAligner.cpp:6:
/usr/include/c++/8/bits/stl_algo.h: In function 'void std::__heap_select(_RandomAccessIterator, _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++/8/bits/stl_algo.h:1668:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' changed in GCC 7.1
__heap_select(_RandomAccessIterator __first,
^~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1668:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1668:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1668:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' changed in GCC 7.1
/usr/include/c++/8/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++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' changed in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' changed in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1933:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' changed in GCC 7.1
std::__heap_select(__first, __middle, __last, __comp);
~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/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++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
cc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbdagcon-0.3+git20161121.0000000+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I. -I./ -I.//../../src/cpp -I/<<BUILDDIR>>/pbdagcon-0.3+git20161121.0000000+ds/DAZZ_DB -I/<<BUILDDIR>>/pbdagcon-0.3+git20161121.0000000+ds/DALIGNER -I/usr/include/pbseq/alignment -I/usr/include/pbseq/pbdata -I/usr/include/pbseq/hdf -I/usr/include/pbseq -I/usr/src/googletest/googletest/include -Ithird-party -c -o DB.o /<<BUILDDIR>>/pbdagcon-0.3+git20161121.0000000+ds/DAZZ_DB/DB.c
/<<BUILDDIR>>/pbdagcon-0.3+git20161121.0000000+ds/DAZZ_DB/DB.c: In function 'Load_QVs':
/<<BUILDDIR>>/pbdagcon-0.3+git20161121.0000000+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+git20161121.0000000+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+git20161121.0000000+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+git20161121.0000000+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I. -I./ -I.//../../src/cpp -I/<<BUILDDIR>>/pbdagcon-0.3+git20161121.0000000+ds/DAZZ_DB -I/<<BUILDDIR>>/pbdagcon-0.3+git20161121.0000000+ds/DALIGNER -I/usr/include/pbseq/alignment -I/usr/include/pbseq/pbdata -I/usr/include/pbseq/hdf -I/usr/include/pbseq -I/usr/src/googletest/googletest/include -Ithird-party -c -o QV.o /<<BUILDDIR>>/pbdagcon-0.3+git20161121.0000000+ds/DAZZ_DB/QV.c
/<<BUILDDIR>>/pbdagcon-0.3+git20161121.0000000+ds/DAZZ_DB/QV.c: In function 'Build_Table':
/<<BUILDDIR>>/pbdagcon-0.3+git20161121.0000000+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+git20161121.0000000+ds/DAZZ_DB/QV.c: In function 'Huffman':
/<<BUILDDIR>>/pbdagcon-0.3+git20161121.0000000+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+git20161121.0000000+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I. -I./ -I.//../../src/cpp -I/<<BUILDDIR>>/pbdagcon-0.3+git20161121.0000000+ds/DAZZ_DB -I/<<BUILDDIR>>/pbdagcon-0.3+git20161121.0000000+ds/DALIGNER -I/usr/include/pbseq/alignment -I/usr/include/pbseq/pbdata -I/usr/include/pbseq/hdf -I/usr/include/pbseq -I/usr/src/googletest/googletest/include -Ithird-party -c -o align.o /<<BUILDDIR>>/pbdagcon-0.3+git20161121.0000000+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+git20161121.0000000+ds/DAZZ_DB -I/<<BUILDDIR>>/pbdagcon-0.3+git20161121.0000000+ds/DALIGNER -I/usr/include/pbseq/alignment -I/usr/include/pbseq/pbdata -I/usr/include/pbseq/hdf -I/usr/include/pbseq -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+git20161121.0000000+ds/DAZZ_DB -I/<<BUILDDIR>>/pbdagcon-0.3+git20161121.0000000+ds/DALIGNER -I/usr/include/pbseq/alignment -I/usr/include/pbseq/pbdata -I/usr/include/pbseq/hdf -I/usr/include/pbseq -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
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
LD_LIBRARY_PATH=::::/usr/lib/arm-linux-gnueabihf/hdf5/serial:::: PBDAGCON_TEST_DATA_DIR=./ ./test-alngraph --gtest_output=xml:xml/test-alngraph.xml
LD_LIBRARY_PATH=::::/usr/lib/arm-linux-gnueabihf/hdf5/serial:::: PBDAGCON_TEST_DATA_DIR=./ ./test-alignment --gtest_output=xml:xml/test-alignment.xml
LD_LIBRARY_PATH=::::/usr/lib/arm-linux-gnueabihf/hdf5/serial:::: PBDAGCON_TEST_DATA_DIR=./ ./test-simple_aligner --gtest_output=xml:xml/test-simple_aligner.xml
Running main() from /usr/src/googletest/googletest/src/gtest_main.cc
[==========] Running 2 tests from 1 test case.
Running main() from /usr/src/googletest/googletest/src/gtest_main.cc
[==========] Running 1 test from 1 test case.
Running main() from /usr/src/googletest/googletest/src/gtest_main.cc
[==========] Running 4 tests from 1 test case.
[----------] Global test environment set-up.
[----------] Global test environment set-up.
[----------] 1 test from SimpleAligner
[----------] 4 tests from Alignment
[ RUN ] SimpleAligner.align
[ RUN ] Alignment.Normalize
[ OK ] Alignment.Normalize (0 ms)
[ RUN ] Alignment.ParseBasic
[ OK ] Alignment.ParseBasic (1 ms)
[ OK ] SimpleAligner.align (1 ms)
[----------] 1 test from SimpleAligner (1 ms total)
[----------] Global test environment tear-down
Running main() from /usr/src/googletest/googletest/src/gtest_main.cc
[==========] Running 3 tests from 1 test case.
[----------] Global test environment set-up.
[----------] 3 tests from TargetHitTest
[ RUN ] TargetHitTest.single_overlap_perfect
[ OK ] TargetHitTest.single_overlap_perfect (0 ms)
[ RUN ] TargetHitTest.single_overlap_inaccurate
[ OK ] TargetHitTest.single_overlap_inaccurate (0 ms)
[ RUN ] TargetHitTest.multi_overlap_inaccurate
[ OK ] TargetHitTest.multi_overlap_inaccurate (0 ms)
[----------] 3 tests from TargetHitTest (0 ms total)
[----------] Global test environment tear-down
[ RUN ] Alignment.ParseQuery
[----------] Global test environment set-up.
[----------] 2 tests from AlnGraphBoostTest
[ RUN ] AlnGraphBoostTest.RawConsensus
[ OK ] AlnGraphBoostTest.RawConsensus (0 ms)
[ RUN ] AlnGraphBoostTest.DanglingNodes
[ OK ] AlnGraphBoostTest.DanglingNodes (0 ms)
[----------] 2 tests from AlnGraphBoostTest (1 ms total)
[----------] Global test environment tear-down
[==========] 1 test from 1 test case ran. (2 ms total)
[ PASSED ] 1 test.
[==========] 3 tests from 1 test case ran. (1 ms total)
[ PASSED ] 3 tests.
[==========] 2 tests from 1 test case ran. (8 ms total)
[ PASSED ] 2 tests.
[ OK ] Alignment.ParseQuery (15 ms)
[ RUN ] Alignment.Trim
[ OK ] Alignment.Trim (0 ms)
[----------] 4 tests from Alignment (21 ms total)
[----------] Global test environment tear-down
[==========] 4 tests from 1 test case ran. (22 ms total)
[ PASSED ] 4 tests.
make[2]: Leaving directory '/<<BUILDDIR>>/pbdagcon-0.3+git20161121.0000000+ds/test/cpp'
make[1]: Leaving directory '/<<BUILDDIR>>/pbdagcon-0.3+git20161121.0000000+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_dwz -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: 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: 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 libpbbam.so.0.19.0 (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.103 (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 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 librt.so.1 (they use none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/pbdagcon/usr/bin/dazcon debian/pbdagcon/usr/bin/pbdagcon were not linked against libhts.so.2 (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.103 (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-dbgsym' in '../pbdagcon-dbgsym_0.3+git20161121.0000000+ds-1.1_armhf.deb'.
dpkg-deb: building package 'pbdagcon' in '../pbdagcon_0.3+git20161121.0000000+ds-1.1_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../pbdagcon_0.3+git20161121.0000000+ds-1.1_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2019-02-14T23:04:48Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
pbdagcon_0.3+git20161121.0000000+ds-1.1_armhf.changes:
------------------------------------------------------
Format: 1.8
Date: Wed, 06 Feb 2019 09:20:03 +0200
Source: pbdagcon
Binary: pbdagcon
Architecture: armhf
Version: 0.3+git20161121.0000000+ds-1.1
Distribution: buster-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Adrian Bunk <bunk@debian.org>
Description:
pbdagcon - sequence consensus using directed acyclic graphs
Changes:
pbdagcon (0.3+git20161121.0000000+ds-1.1) unstable; urgency=medium
.
* Non-maintainer upload.
* Remove manual dependencies on libpbbam, version build
dependency on libpbbam-dev to ensure a proper dependency
is generated.
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Files:
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6c37818246091fd96b7db9d202c48e26 6640 science optional pbdagcon_0.3+git20161121.0000000+ds-1.1_armhf.buildinfo
046e282a726d363a2ddd2ad8505bd560 238856 science optional pbdagcon_0.3+git20161121.0000000+ds-1.1_armhf.deb
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pbdagcon-dbgsym_0.3+git20161121.0000000+ds-1.1_armhf.deb
--------------------------------------------------------
new Debian package, version 2.0.
size 5295884 bytes: control archive=656 bytes.
462 bytes, 12 lines control
300 bytes, 3 lines md5sums
Package: pbdagcon-dbgsym
Source: pbdagcon
Version: 0.3+git20161121.0000000+ds-1.1
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 5548
Depends: pbdagcon (= 0.3+git20161121.0000000+ds-1.1)
Section: debug
Priority: optional
Description: debug symbols for pbdagcon
Build-Ids: 15f9d3e91df535ac97b8bec0d62282281c6ea6cf 1d3b271b646372c28a19e663174b0b3e0f1a0b6b
drwxr-xr-x root/root 0 2019-02-06 07:20 ./
drwxr-xr-x root/root 0 2019-02-06 07:20 ./usr/
drwxr-xr-x root/root 0 2019-02-06 07:20 ./usr/lib/
drwxr-xr-x root/root 0 2019-02-06 07:20 ./usr/lib/debug/
drwxr-xr-x root/root 0 2019-02-06 07:20 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2019-02-06 07:20 ./usr/lib/debug/.build-id/15/
-rw-r--r-- root/root 2680616 2019-02-06 07:20 ./usr/lib/debug/.build-id/15/f9d3e91df535ac97b8bec0d62282281c6ea6cf.debug
drwxr-xr-x root/root 0 2019-02-06 07:20 ./usr/lib/debug/.build-id/1d/
-rw-r--r-- root/root 2311908 2019-02-06 07:20 ./usr/lib/debug/.build-id/1d/3b271b646372c28a19e663174b0b3e0f1a0b6b.debug
drwxr-xr-x root/root 0 2019-02-06 07:20 ./usr/lib/debug/.dwz/
drwxr-xr-x root/root 0 2019-02-06 07:20 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/
-rw-r--r-- root/root 674788 2019-02-06 07:20 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/pbdagcon.debug
drwxr-xr-x root/root 0 2019-02-06 07:20 ./usr/share/
drwxr-xr-x root/root 0 2019-02-06 07:20 ./usr/share/doc/
lrwxrwxrwx root/root 0 2019-02-06 07:20 ./usr/share/doc/pbdagcon-dbgsym -> pbdagcon
pbdagcon_0.3+git20161121.0000000+ds-1.1_armhf.deb
-------------------------------------------------
new Debian package, version 2.0.
size 238856 bytes: control archive=1460 bytes.
1711 bytes, 30 lines control
694 bytes, 10 lines md5sums
Package: pbdagcon
Version: 0.3+git20161121.0000000+ds-1.1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 864
Depends: libc6 (>= 2.7), libgcc1 (>= 1:3.5), libhdf5-103, libhdf5-cpp-103 (>= 1.8.13), libhts2 (>= 1.0), libpbbam0.19.0 (>= 0.19.0+dfsg), libstdc++6 (>= 6), zlib1g (>= 1:1.1.4), libpbseq
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 2019-02-06 07:20 ./
drwxr-xr-x root/root 0 2019-02-06 07:20 ./usr/
drwxr-xr-x root/root 0 2019-02-06 07:20 ./usr/bin/
-rwxr-xr-x root/root 440788 2019-02-06 07:20 ./usr/bin/dazcon
-rwxr-xr-x root/root 403936 2019-02-06 07:20 ./usr/bin/pbdagcon
drwxr-xr-x root/root 0 2019-02-06 07:20 ./usr/share/
drwxr-xr-x root/root 0 2019-02-06 07:20 ./usr/share/doc/
drwxr-xr-x root/root 0 2019-02-06 07:20 ./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 1122 2019-02-06 07:20 ./usr/share/doc/pbdagcon/changelog.Debian.gz
-rw-r--r-- root/root 4761 2019-02-04 14:36 ./usr/share/doc/pbdagcon/copyright
drwxr-xr-x root/root 0 2019-02-06 07:20 ./usr/share/doc/pbdagcon/examples/
-rwxr-xr-x root/root 1588 2016-12-21 05:55 ./usr/share/doc/pbdagcon/examples/filterm4.py
-rwxr-xr-x root/root 5948 2016-12-21 05:55 ./usr/share/doc/pbdagcon/examples/m4topre.py
-rwxr-xr-x root/root 1145 2016-12-21 05:55 ./usr/share/doc/pbdagcon/examples/pbdagcon_wf.sh
-rwxr-xr-x root/root 7025 2016-12-21 05:55 ./usr/share/doc/pbdagcon/examples/q-sense.py
drwxr-xr-x root/root 0 2019-02-06 07:20 ./usr/share/man/
drwxr-xr-x root/root 0 2019-02-06 07:20 ./usr/share/man/man1/
-rw-r--r-- root/root 775 2019-02-06 07:20 ./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 |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 85740
Build-Time: 563
Distribution: buster-staging
Host Architecture: armhf
Install-Time: 841
Job: pbdagcon_0.3+git20161121.0000000+ds-1.1
Machine Architecture: armhf
Package: pbdagcon
Package-Time: 1453
Source-Version: 0.3+git20161121.0000000+ds-1.1
Space: 85740
Status: successful
Version: 0.3+git20161121.0000000+ds-1.1
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Finished at 2019-02-14T23:04:48Z
Build needed 00:24:13, 85740k disc space