clonalframe →
1.2-5 →
armhf → 2016-07-27 10:47:42
sbuild (Debian sbuild) 0.66.0 (04 Oct 2015) on testwandboard
+==============================================================================+
| clonalframe 1.2-5 (armhf) 27 Jul 2016 10:35 |
+==============================================================================+
Package: clonalframe
Version: 1.2-5
Source Version: 1.2-5
Distribution: stretch-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'build/clonalframe-mjCzOq/clonalframe-1.2' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/clonalframe-mjCzOq' with '<<BUILDDIR>>'
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/stretch-staging-armhf-sbuild-a96a7894-c327-4ca1-b6c1-4db65fcaeb4d' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private stretch-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private stretch-staging/main Sources [9191 kB]
Get:3 http://172.17.0.1/private stretch-staging/main armhf Packages [11.1 MB]
Fetched 20.3 MB in 1min 18s (258 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: 'clonalframe' packaging is maintained in the 'Svn' version control system at:
svn://anonscm.debian.org/debian-med/trunk/packages/clonalframe/trunk
Need to get 51.6 kB of source archives.
Get:1 http://172.17.0.1/private stretch-staging/main clonalframe 1.2-5 (dsc) [2014 B]
Get:2 http://172.17.0.1/private stretch-staging/main clonalframe 1.2-5 (tar) [45.5 kB]
Get:3 http://172.17.0.1/private stretch-staging/main clonalframe 1.2-5 (diff) [4092 B]
Fetched 51.6 kB in 0s (250 kB/s)
Download complete and in download only mode
Check architectures
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Check dependencies
------------------
Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<<BUILDDIR>>/resolver-48gjgA/apt_archive/sbuild-build-depends-core-dummy.deb'.
Warning: apt-key output should not be parsed (stdout is not a terminal)
OK
Get:1 file:/<<BUILDDIR>>/resolver-48gjgA/apt_archive ./ InRelease
Ign:1 file:/<<BUILDDIR>>/resolver-48gjgA/apt_archive ./ InRelease
Get:2 file:/<<BUILDDIR>>/resolver-48gjgA/apt_archive ./ Release [2119 B]
Get:2 file:/<<BUILDDIR>>/resolver-48gjgA/apt_archive ./ Release [2119 B]
Get:3 file:/<<BUILDDIR>>/resolver-48gjgA/apt_archive ./ Release.gpg [299 B]
Get:3 file:/<<BUILDDIR>>/resolver-48gjgA/apt_archive ./ Release.gpg [299 B]
Get:4 file:/<<BUILDDIR>>/resolver-48gjgA/apt_archive ./ Sources [194 B]
Get:5 file:/<<BUILDDIR>>/resolver-48gjgA/apt_archive ./ Packages [504 B]
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
W: file:///<<BUILDDIR>>/resolver-48gjgA/apt_archive/./Release.gpg: Signature by key 3493EC2B8E6DC280C121C60435506D9A48F77B2E uses weak digest algorithm (SHA1)
Reading package lists...
+------------------------------------------------------------------------------+
| Install core build dependencies (apt-based resolver) |
+------------------------------------------------------------------------------+
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 42 not upgraded.
Need to get 0 B/768 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 file:/<<BUILDDIR>>/resolver-48gjgA/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [768 B]
debconf: delaying package configuration, since apt-utils is not installed
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(Reading database ... 13893 files and directories currently installed.)
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W: No sandbox user '_apt' on the system, can not drop privileges
Merged Build-Depends: debhelper (>= 9), qt4-qmake, libgsl-dev, libqt4-dev
Filtered Build-Depends: debhelper (>= 9), qt4-qmake, libgsl-dev, libqt4-dev
dpkg-deb: building package 'sbuild-build-depends-clonalframe-dummy' in '/<<BUILDDIR>>/resolver-_4k6_W/apt_archive/sbuild-build-depends-clonalframe-dummy.deb'.
Warning: apt-key output should not be parsed (stdout is not a terminal)
OK
Get:1 file:/<<BUILDDIR>>/resolver-_4k6_W/apt_archive ./ InRelease
Ign:1 file:/<<BUILDDIR>>/resolver-_4k6_W/apt_archive ./ InRelease
Get:2 file:/<<BUILDDIR>>/resolver-_4k6_W/apt_archive ./ Release [2119 B]
Get:2 file:/<<BUILDDIR>>/resolver-_4k6_W/apt_archive ./ Release [2119 B]
Get:3 file:/<<BUILDDIR>>/resolver-_4k6_W/apt_archive ./ Release.gpg [299 B]
Get:3 file:/<<BUILDDIR>>/resolver-_4k6_W/apt_archive ./ Release.gpg [299 B]
Get:4 file:/<<BUILDDIR>>/resolver-_4k6_W/apt_archive ./ Sources [215 B]
Get:5 file:/<<BUILDDIR>>/resolver-_4k6_W/apt_archive ./ Packages [531 B]
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
W: file:///<<BUILDDIR>>/resolver-_4k6_W/apt_archive/./Release.gpg: Signature by key 3493EC2B8E6DC280C121C60435506D9A48F77B2E uses weak digest algorithm (SHA1)
Reading package lists...
+------------------------------------------------------------------------------+
| Install clonalframe build dependencies (apt-based resolver) |
+------------------------------------------------------------------------------+
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils debhelper
dh-autoreconf dh-strip-nondeterminism file fontconfig fontconfig-config
fonts-dejavu-core gettext gettext-base groff-base intltool-debian
libarchive-zip-perl libaudio2 libbsd0 libcroco3 libexpat1 libffi6
libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libglib2.0-0
libgsl-dev libgsl2 libice6 libicu55 libjbig0 libjpeg62-turbo libjpeg8
liblcms2-2 libmagic1 libmng1 libpipeline1 libpng16-16 libqt4-dbus
libqt4-declarative libqt4-designer libqt4-dev libqt4-dev-bin libqt4-help
libqt4-network libqt4-qt3support libqt4-script libqt4-scripttools libqt4-sql
libqt4-svg libqt4-test libqt4-xml libqt4-xmlpatterns libqtcore4 libqtdbus4
libqtgui4 libsigsegv2 libsm6 libtiff5 libtimedate-perl libtool libunistring0
libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxml2 libxrender1
libxt6 m4 man-db po-debconf qdbus qt4-linguist-tools qt4-qmake qtchooser
qtcore4-l10n ucf x11-common
Suggested packages:
autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
vacation dh-make gettext-doc libasprintf-dev libgettextpo-dev groff nas
gsl-ref-psdoc | gsl-doc-pdf | gsl-doc-info | gsl-ref-html liblcms2-utils
libqt4-declarative-folderlistmodel libqt4-declarative-gestures
libqt4-declarative-particles libqt4-declarative-shaders qt4-qmlviewer
firebird-dev libmysqlclient-dev libpq-dev libsqlite0-dev libsqlite3-dev
qt4-dev-tools qt4-doc unixodbc-dev libthai0 qt4-qtconfig libtool-doc
gfortran | fortran95-compiler gcj-jdk less www-browser libmail-box-perl
Recommended packages:
curl | wget | lynx-cur libglib2.0-data shared-mime-info xdg-user-dirs
libqt4-opengl-dev ca-certificates libqt4-sql-mysql | libqt4-sql-odbc
| libqt4-sql-psql | libqt4-sql-sqlite | libqt4-sql-sqlite2 libcups2
qt-at-spi 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 fontconfig fontconfig-config
fonts-dejavu-core gettext gettext-base groff-base intltool-debian
libarchive-zip-perl libaudio2 libbsd0 libcroco3 libexpat1 libffi6
libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libglib2.0-0
libgsl-dev libgsl2 libice6 libicu55 libjbig0 libjpeg62-turbo libjpeg8
liblcms2-2 libmagic1 libmng1 libpipeline1 libpng16-16 libqt4-dbus
libqt4-declarative libqt4-designer libqt4-dev libqt4-dev-bin libqt4-help
libqt4-network libqt4-qt3support libqt4-script libqt4-scripttools libqt4-sql
libqt4-svg libqt4-test libqt4-xml libqt4-xmlpatterns libqtcore4 libqtdbus4
libqtgui4 libsigsegv2 libsm6 libtiff5 libtimedate-perl libtool libunistring0
libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxml2 libxrender1
libxt6 m4 man-db po-debconf qdbus qt4-linguist-tools qt4-qmake qtchooser
qtcore4-l10n sbuild-build-depends-clonalframe-dummy ucf x11-common
0 upgraded, 82 newly installed, 0 to remove and 42 not upgraded.
Need to get 36.0 MB/43.4 MB of archives.
After this operation, 157 MB of additional disk space will be used.
Get:1 file:/<<BUILDDIR>>/resolver-_4k6_W/apt_archive ./ sbuild-build-depends-clonalframe-dummy 0.invalid.0 [796 B]
Get:2 http://172.17.0.1/private stretch-staging/main armhf groff-base armhf 1.22.3-8 [1087 kB]
Get:3 http://172.17.0.1/private stretch-staging/main armhf libbsd0 armhf 0.8.3-1 [89.0 kB]
Get:4 http://172.17.0.1/private stretch-staging/main armhf bsdmainutils armhf 9.0.10 [177 kB]
Get:5 http://172.17.0.1/private stretch-staging/main armhf libpipeline1 armhf 1.4.1-2 [23.7 kB]
Get:6 http://172.17.0.1/private stretch-staging/main armhf man-db armhf 2.7.5-1 [975 kB]
Get:7 http://172.17.0.1/private stretch-staging/main armhf libexpat1 armhf 2.2.0-1 [61.7 kB]
Get:8 http://172.17.0.1/private stretch-staging/main armhf libpng16-16 armhf 1.6.23-1 [260 kB]
Get:9 http://172.17.0.1/private stretch-staging/main armhf libfreetype6 armhf 2.6.3-3+b1 [385 kB]
Get:10 http://172.17.0.1/private stretch-staging/main armhf ucf all 3.0036 [70.2 kB]
Get:11 http://172.17.0.1/private stretch-staging/main armhf fonts-dejavu-core all 2.36-1 [1068 kB]
Get:12 http://172.17.0.1/private stretch-staging/main armhf fontconfig-config all 2.11.0-6.4 [271 kB]
Get:13 http://172.17.0.1/private stretch-staging/main armhf libfontconfig1 armhf 2.11.0-6.4 [313 kB]
Get:14 http://172.17.0.1/private stretch-staging/main armhf fontconfig armhf 2.11.0-6.4 [401 kB]
Get:15 http://172.17.0.1/private stretch-staging/main armhf libxau6 armhf 1:1.0.8-1 [19.9 kB]
Get:16 http://172.17.0.1/private stretch-staging/main armhf x11-common all 1:7.7+16 [251 kB]
Get:17 http://172.17.0.1/private stretch-staging/main armhf libice6 armhf 2:1.0.9-1+b1 [51.9 kB]
Get:18 http://172.17.0.1/private stretch-staging/main armhf libsm6 armhf 2:1.2.2-1+b1 [31.2 kB]
Get:19 http://172.17.0.1/private stretch-staging/main armhf libxdmcp6 armhf 1:1.1.2-1.1 [24.9 kB]
Get:20 http://172.17.0.1/private stretch-staging/main armhf libxcb1 armhf 1.11.1-1 [40.9 kB]
Get:21 http://172.17.0.1/private stretch-staging/main armhf libx11-data all 2:1.6.3-1 [128 kB]
Get:22 http://172.17.0.1/private stretch-staging/main armhf libx11-6 armhf 2:1.6.3-1 [678 kB]
Get:23 http://172.17.0.1/private stretch-staging/main armhf libxt6 armhf 1:1.1.5-1 [155 kB]
Get:24 http://172.17.0.1/private stretch-staging/main armhf libaudio2 armhf 1.9.4-4 [72.5 kB]
Get:25 http://172.17.0.1/private stretch-staging/main armhf libjbig0 armhf 2.1-3.1 [27.5 kB]
Get:26 http://172.17.0.1/private stretch-staging/main armhf libjpeg8 armhf 8d1-2 [108 kB]
Get:27 http://172.17.0.1/private stretch-staging/main armhf liblcms2-2 armhf 2.7-1 [116 kB]
Get:28 http://172.17.0.1/private stretch-staging/main armhf libmng1 armhf 1.0.10+dfsg-3.1 [164 kB]
Get:29 http://172.17.0.1/private stretch-staging/main armhf libxext6 armhf 2:1.3.3-1 [48.1 kB]
Get:30 http://172.17.0.1/private stretch-staging/main armhf libmagic1 armhf 1:5.28-2 [269 kB]
Get:31 http://172.17.0.1/private stretch-staging/main armhf file armhf 1:5.28-2 [62.4 kB]
Get:32 http://172.17.0.1/private stretch-staging/main armhf gettext-base armhf 0.19.8.1-1 [117 kB]
Get:33 http://172.17.0.1/private stretch-staging/main armhf libxml2 armhf 2.9.4+dfsg1-1 [804 kB]
Get:34 http://172.17.0.1/private stretch-staging/main armhf libsigsegv2 armhf 2.10-5 [28.4 kB]
Get:35 http://172.17.0.1/private stretch-staging/main armhf m4 armhf 1.4.17-5 [239 kB]
Get:36 http://172.17.0.1/private stretch-staging/main armhf autoconf all 2.69-10 [338 kB]
Get:37 http://172.17.0.1/private stretch-staging/main armhf autotools-dev all 20160430.1 [72.6 kB]
Get:38 http://172.17.0.1/private stretch-staging/main armhf automake all 1:1.15-4 [735 kB]
Get:39 http://172.17.0.1/private stretch-staging/main armhf autopoint all 0.19.8.1-1 [433 kB]
Get:40 http://172.17.0.1/private stretch-staging/main armhf libglib2.0-0 armhf 2.48.1-2 [2546 kB]
Get:41 http://172.17.0.1/private stretch-staging/main armhf libcroco3 armhf 0.6.11-1 [131 kB]
Get:42 http://172.17.0.1/private stretch-staging/main armhf libunistring0 armhf 0.9.6+really0.9.3-0.1 [252 kB]
Get:43 http://172.17.0.1/private stretch-staging/main armhf gettext armhf 0.19.8.1-1 [1433 kB]
Get:44 http://172.17.0.1/private stretch-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:45 http://172.17.0.1/private stretch-staging/main armhf po-debconf all 1.0.19 [249 kB]
Get:46 http://172.17.0.1/private stretch-staging/main armhf libarchive-zip-perl all 1.57-1 [95.1 kB]
Get:47 http://172.17.0.1/private stretch-staging/main armhf libfile-stripnondeterminism-perl all 0.019-1 [12.2 kB]
Get:48 http://172.17.0.1/private stretch-staging/main armhf libtimedate-perl all 2.3000-2 [42.2 kB]
Get:49 http://172.17.0.1/private stretch-staging/main armhf dh-strip-nondeterminism all 0.019-1 [7352 B]
Get:50 http://172.17.0.1/private stretch-staging/main armhf libtool all 2.4.6-0.1 [200 kB]
Get:51 http://172.17.0.1/private stretch-staging/main armhf dh-autoreconf all 12 [15.8 kB]
Get:52 http://172.17.0.1/private stretch-staging/main armhf debhelper all 9.20160709 [799 kB]
Get:53 http://172.17.0.1/private stretch-staging/main armhf libgsl2 armhf 2.1+dfsg-2 [697 kB]
Get:54 http://172.17.0.1/private stretch-staging/main armhf libgsl-dev armhf 2.1+dfsg-2 [812 kB]
Get:55 http://172.17.0.1/private stretch-staging/main armhf libjpeg62-turbo armhf 1:1.5.0-1 [109 kB]
Get:56 http://172.17.0.1/private stretch-staging/main armhf qtcore4-l10n all 4:4.8.7+dfsg-8+rpi1 [660 kB]
Get:57 http://172.17.0.1/private stretch-staging/main armhf libqtcore4 armhf 4:4.8.7+dfsg-8+rpi1 [1363 kB]
Get:58 http://172.17.0.1/private stretch-staging/main armhf libqt4-xml armhf 4:4.8.7+dfsg-8+rpi1 [125 kB]
Get:59 http://172.17.0.1/private stretch-staging/main armhf libqtdbus4 armhf 4:4.8.7+dfsg-8+rpi1 [193 kB]
Get:60 http://172.17.0.1/private stretch-staging/main armhf qtchooser armhf 58-gfab25f1-1 [20.3 kB]
Get:61 http://172.17.0.1/private stretch-staging/main armhf qdbus armhf 4:4.8.7+dfsg-8+rpi1 [71.9 kB]
Get:62 http://172.17.0.1/private stretch-staging/main armhf libqt4-dbus armhf 4:4.8.7+dfsg-8+rpi1 [52.5 kB]
Get:63 http://172.17.0.1/private stretch-staging/main armhf libqt4-network armhf 4:4.8.7+dfsg-8+rpi1 [496 kB]
Get:64 http://172.17.0.1/private stretch-staging/main armhf libqt4-script armhf 4:4.8.7+dfsg-8+rpi1 [678 kB]
Get:65 http://172.17.0.1/private stretch-staging/main armhf libqt4-sql armhf 4:4.8.7+dfsg-8+rpi1 [128 kB]
Get:66 http://172.17.0.1/private stretch-staging/main armhf libqt4-xmlpatterns armhf 4:4.8.7+dfsg-8+rpi1 [877 kB]
Get:67 http://172.17.0.1/private stretch-staging/main armhf libtiff5 armhf 4.0.6-2 [203 kB]
Get:68 http://172.17.0.1/private stretch-staging/main armhf libxrender1 armhf 1:0.9.9-2 [28.9 kB]
Get:69 http://172.17.0.1/private stretch-staging/main armhf libqtgui4 armhf 4:4.8.7+dfsg-8+rpi1 [3422 kB]
Get:70 http://172.17.0.1/private stretch-staging/main armhf libqt4-declarative armhf 4:4.8.7+dfsg-8+rpi1 [895 kB]
Get:71 http://172.17.0.1/private stretch-staging/main armhf libqt4-designer armhf 4:4.8.7+dfsg-8+rpi1 [3355 kB]
Get:72 http://172.17.0.1/private stretch-staging/main armhf libqt4-qt3support armhf 4:4.8.7+dfsg-8+rpi1 [895 kB]
Get:73 http://172.17.0.1/private stretch-staging/main armhf libqt4-dev-bin armhf 4:4.8.7+dfsg-8+rpi1 [1432 kB]
Get:74 http://172.17.0.1/private stretch-staging/main armhf libqt4-help armhf 4:4.8.7+dfsg-8+rpi1 [219 kB]
Get:75 http://172.17.0.1/private stretch-staging/main armhf libqt4-scripttools armhf 4:4.8.7+dfsg-8+rpi1 [228 kB]
Get:76 http://172.17.0.1/private stretch-staging/main armhf libqt4-svg armhf 4:4.8.7+dfsg-8+rpi1 [156 kB]
Get:77 http://172.17.0.1/private stretch-staging/main armhf libqt4-test armhf 4:4.8.7+dfsg-8+rpi1 [97.1 kB]
Get:78 http://172.17.0.1/private stretch-staging/main armhf qt4-linguist-tools armhf 4:4.8.7+dfsg-8+rpi1 [753 kB]
Get:79 http://172.17.0.1/private stretch-staging/main armhf qt4-qmake armhf 4:4.8.7+dfsg-8+rpi1 [1136 kB]
Get:80 http://172.17.0.1/private stretch-staging/main armhf libqt4-dev armhf 4:4.8.7+dfsg-8+rpi1 [883 kB]
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update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
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update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults
Running in chroot, ignoring request.
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No schema files found: doing nothing.
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Setting up libaudio2:armhf (1.9.4-4) ...
Setting up fontconfig (2.11.0-6.4) ...
Regenerating fonts cache... done.
Setting up libxext6:armhf (2:1.3.3-1) ...
Setting up po-debconf (1.0.19) ...
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Setting up sbuild-build-depends-clonalframe-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.23-1+rpi1) ...
Processing triggers for systemd (230-5) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.5.0-1-armmp armhf (armv7l)
Toolchain package versions: binutils_2.26.1-1 dpkg-dev_1.18.7 g++-5_5.4.0-4 gcc-5_5.4.0-4 libc6-dev_2.23-1+rpi1 libstdc++-5-dev_5.4.0-4 libstdc++6_6.1.1-1+rpi1 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch
Package versions: adduser_3.115 apt_1.3~pre2 autoconf_2.69-10 automake_1:1.15-4 autopoint_0.19.8.1-1 autotools-dev_20160430.1 base-files_9.6+rpi1 base-passwd_3.5.39 bash_4.3-15 binutils_2.26.1-1 bsdmainutils_9.0.10 bsdutils_1:2.28-5 build-essential_11.7 bzip2_1.0.6-8 console-setup_1.146 console-setup-linux_1.146 coreutils_8.25-2 cpio_2.11+dfsg-5 cpp_4:5.3.1-3 cpp-5_5.4.0-4 dash_0.5.8-2.3 debconf_1.5.59 debfoster_2.7-2 debhelper_9.20160709 debianutils_4.8 dh-autoreconf_12 dh-strip-nondeterminism_0.019-1 diffutils_1:3.3-3 dmsetup_2:1.02.127-1 dpkg_1.18.7 dpkg-dev_1.18.7 e2fslibs_1.43.1-1 e2fsprogs_1.43.1-1 fakeroot_1.21-1 file_1:5.28-2 findutils_4.6.0+git+20160517-5 fontconfig_2.11.0-6.4 fontconfig-config_2.11.0-6.4 fonts-dejavu-core_2.36-1 fuse2fs_1.43.1-1 g++_4:5.3.1-3 g++-5_5.4.0-4 gcc_4:5.3.1-3 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_5.4.0-4 gcc-5-base_5.4.0-4 gcc-6-base_6.1.1-1+rpi1 gettext_0.19.8.1-1 gettext-base_0.19.8.1-1 gnupg_1.4.20-6 gpgv_1.4.20-6 grep_2.25-6 groff-base_1.22.3-8 gzip_1.6-5 hostname_3.18 ifupdown_0.8.13 init_1.36 init-system-helpers_1.36 initscripts_2.88dsf-59.7 insserv_1.14.0-5.3 intltool-debian_0.35.0+20060710.4 iproute2_4.3.0-1 kbd_2.0.3-2 keyboard-configuration_1.146 klibc-utils_2.0.4-9+rpi1 kmod_22-1.1 libacl1_2.2.52-3 libapparmor1_2.10.95-4 libapt-pkg5.0_1.3~pre2 libarchive-zip-perl_1.57-1 libasan2_5.4.0-4 libatm1_1:2.5.1-1.6 libatomic1_6.1.1-1+rpi1 libattr1_1:2.4.47-2 libaudio2_1.9.4-4 libaudit-common_1:2.5.2-1+rpi1 libaudit1_1:2.5.2-1+rpi1 libblkid1_2.28-5 libbsd0_0.8.3-1 libbz2-1.0_1.0.6-8 libc-bin_2.23-1+rpi1 libc-dev-bin_2.23-1+rpi1 libc6_2.23-1+rpi1 libc6-dev_2.23-1+rpi1 libcap2_1:2.25-1 libcap2-bin_1:2.25-1 libcc1-0_6.1.1-1+rpi1 libcomerr2_1.43.1-1 libcroco3_0.6.11-1 libcryptsetup4_2:1.7.0-2 libdb5.3_5.3.28-11 libdbus-1-3_1.10.8-1 libdebconfclient0_0.213 libdevmapper1.02.1_2:1.02.127-1 libdpkg-perl_1.18.7 libdrm2_2.4.68-1 libexpat1_2.2.0-1 libfakeroot_1.21-1 libfdisk1_2.28-5 libffi6_3.2.1-4 libfile-stripnondeterminism-perl_0.019-1 libfontconfig1_2.11.0-6.4 libfreetype6_2.6.3-3+b1 libfuse2_2.9.7-1 libgc1c2_1:7.4.2-8 libgcc-5-dev_5.4.0-4 libgcc1_1:6.1.1-1+rpi1 libgcrypt20_1.7.1-2 libgdbm3_1.8.3-14 libglib2.0-0_2.48.1-2 libgmp10_2:6.1.1+dfsg-1 libgomp1_6.1.1-1+rpi1 libgpg-error0_1.23-1 libgsl-dev_2.1+dfsg-2 libgsl2_2.1+dfsg-2 libice6_2:1.0.9-1+b1 libicu55_55.1-7 libidn11_1.32-3.1 libisl15_0.17.1-1 libjbig0_2.1-3.1 libjpeg62-turbo_1:1.5.0-1 libjpeg8_8d1-2 libklibc_2.0.4-9+rpi1 libkmod2_22-1.1 liblcms2-2_2.7-1 liblocale-gettext-perl_1.07-3 liblz4-1_0.0~r131-2 liblzma5_5.1.1alpha+20120614-2.1 libmagic1_1:5.28-2 libmng1_1.0.10+dfsg-3.1 libmount1_2.28-5 libmpc3_1.0.3-1 libmpfr4_3.1.4-2 libncurses5_6.0+20160319-2 libncursesw5_6.0+20160319-2 libpam-modules_1.1.8-3.3 libpam-modules-bin_1.1.8-3.3 libpam-runtime_1.1.8-3.3 libpam0g_1.1.8-3.3 libpcre3_2:8.38-3.1 libperl5.22_5.22.2-2 libpipeline1_1.4.1-2 libplymouth4_0.9.2-3 libpng12-0_1.2.54-6 libpng16-16_1.6.23-1 libprocps5_2:3.3.11-3 libqt4-dbus_4:4.8.7+dfsg-8+rpi1 libqt4-declarative_4:4.8.7+dfsg-8+rpi1 libqt4-designer_4:4.8.7+dfsg-8+rpi1 libqt4-dev_4:4.8.7+dfsg-8+rpi1 libqt4-dev-bin_4:4.8.7+dfsg-8+rpi1 libqt4-help_4:4.8.7+dfsg-8+rpi1 libqt4-network_4:4.8.7+dfsg-8+rpi1 libqt4-qt3support_4:4.8.7+dfsg-8+rpi1 libqt4-script_4:4.8.7+dfsg-8+rpi1 libqt4-scripttools_4:4.8.7+dfsg-8+rpi1 libqt4-sql_4:4.8.7+dfsg-8+rpi1 libqt4-svg_4:4.8.7+dfsg-8+rpi1 libqt4-test_4:4.8.7+dfsg-8+rpi1 libqt4-xml_4:4.8.7+dfsg-8+rpi1 libqt4-xmlpatterns_4:4.8.7+dfsg-8+rpi1 libqtcore4_4:4.8.7+dfsg-8+rpi1 libqtdbus4_4:4.8.7+dfsg-8+rpi1 libqtgui4_4:4.8.7+dfsg-8+rpi1 libreadline6_6.3-8+b3 libseccomp2_2.3.1-2 libselinux1_2.5-3 libsemanage-common_2.5-1 libsemanage1_2.5-1 libsepol1_2.5-1 libsigsegv2_2.10-5 libsm6_2:1.2.2-1+b1 libsmartcols1_2.28-5 libss2_1.43.1-1 libstdc++-5-dev_5.4.0-4 libstdc++6_6.1.1-1+rpi1 libsystemd0_230-5 libtext-charwidth-perl_0.04-7+b6 libtext-iconv-perl_1.7-5+b7 libtext-wrapi18n-perl_0.06-7.1 libtiff5_4.0.6-2 libtimedate-perl_2.3000-2 libtinfo5_6.0+20160319-2 libtool_2.4.6-0.1 libubsan0_6.1.1-1+rpi1 libudev1_230-5 libunistring0_0.9.6+really0.9.3-0.1 libusb-0.1-4_2:0.1.12-30 libustr-1.0-1_1.0.4-5 libuuid1_2.28-5 libx11-6_2:1.6.3-1 libx11-data_2:1.6.3-1 libxau6_1:1.0.8-1 libxcb1_1.11.1-1 libxdmcp6_1:1.1.2-1.1 libxext6_2:1.3.3-1 libxml2_2.9.4+dfsg1-1 libxrender1_1:0.9.9-2 libxt6_1:1.1.5-1 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch login_1:4.2-3.1 lsb-base_9.20160629+rpi1 m4_1.4.17-5 make_4.1-9 makedev_2.3.1-93 man-db_2.7.5-1 manpages_4.06-1 mawk_1.3.3-17 mount_2.28-5 multiarch-support_2.23-1+rpi1 ncurses-base_6.0+20160319-2 ncurses-bin_6.0+20160319-2 netbase_5.3 passwd_1:4.2-3.1 patch_2.7.5-1 perl_5.22.2-2 perl-base_5.22.2-2 perl-modules-5.22_5.22.2-2 po-debconf_1.0.19 procps_2:3.3.11-3 psmisc_22.21-2.1 qdbus_4:4.8.7+dfsg-8+rpi1 qt4-linguist-tools_4:4.8.7+dfsg-8+rpi1 qt4-qmake_4:4.8.7+dfsg-8+rpi1 qtchooser_58-gfab25f1-1 qtcore4-l10n_4:4.8.7+dfsg-8+rpi1 raspbian-archive-keyring_20120528.2 readline-common_6.3-8 sbuild-build-depends-clonalframe-dummy_0.invalid.0 sbuild-build-depends-core-dummy_0.invalid.0 sed_4.2.2-7.1 sensible-utils_0.0.9 startpar_0.59-3 systemd_230-5 systemd-sysv_230-5 sysv-rc_2.88dsf-59.7 sysvinit-utils_2.88dsf-59.7 tar_1.29-1+rpi1 tzdata_2016f-1 ucf_3.0036 udev_230-5 util-linux_2.28-5 x11-common_1:7.7+16 xkb-data_2.17-1 xz-utils_5.1.1alpha+20120614-2.1 zlib1g_1:1.2.8.dfsg-2+b1
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error
gpgv: Signature made Thu Jul 21 15:40:02 2016 UTC using RSA key ID D1C646D1
gpgv: Can't check signature: public key not found
dpkg-source: warning: failed to verify signature on ./clonalframe_1.2-5.dsc
dpkg-source: info: extracting clonalframe in clonalframe-1.2
dpkg-source: info: unpacking clonalframe_1.2.orig.tar.gz
dpkg-source: info: unpacking clonalframe_1.2-5.debian.tar.xz
dpkg-source: info: applying 01_gcc-4.6.patch
Check disc space
----------------
Sufficient free space for build
User Environment
----------------
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=stretch-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=stretch-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=stretch-staging-armhf-sbuild-a96a7894-c327-4ca1-b6c1-4db65fcaeb4d
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package clonalframe
dpkg-buildpackage: info: source version 1.2-5
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build clonalframe-1.2
dpkg-buildpackage: info: host architecture armhf
fakeroot debian/rules clean
dh clean
dh_testdir
dh_auto_clean
debian/rules override_dh_clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_clean
rm -rf bin build Makefile
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
debian/rules build-arch
dh build-arch
dh_testdir -a
dh_update_autotools_config -a
dh_auto_configure -a
qmake -makefile -nocache "QMAKE_CFLAGS_RELEASE=-g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2" "QMAKE_CFLAGS_DEBUG=-g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2" "QMAKE_CXXFLAGS_RELEASE=-g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2" "QMAKE_CXXFLAGS_DEBUG=-g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2" "QMAKE_LFLAGS_RELEASE=-fPIE -pie -Wl,-z,relro -Wl,-z,now" "QMAKE_LFLAGS_DEBUG=-fPIE -pie -Wl,-z,relro -Wl,-z,now" QMAKE_STRIP=: PREFIX=/usr
debian/rules override_dh_auto_build
make[1]: Entering directory '/<<PKGBUILDDIR>>'
qmake
# did not found a better way to push hardening flags into Makefile
sed -i -e "s:CFLAGS *= .*:& -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security:" \
-e "s:CXXFLAGS *= .*:& -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security:" \
-e "s:LFLAGS *= .*:& -fPIE -pie -Wl,-z,relro -Wl,-z,now:" Makefile
/usr/bin/make
make[2]: Entering directory '/<<PKGBUILDDIR>>'
g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -O2 -Wall -W -D_REENTRANT -DQT_NO_DEBUG -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4 -Ibuild -o build/alignment_xmfa.o src/alignment_xmfa.cpp
src/alignment_xmfa.cpp: In constructor 'wb::Alignment_xmfa::Alignment_xmfa(char*, bool, int)':
src/alignment_xmfa.cpp:129:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (j=0;j<strlen(bufin[i]);j++) {
^
g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -O2 -Wall -W -D_REENTRANT -DQT_NO_DEBUG -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4 -Ibuild -o build/alignment_structure.o src/alignment_structure.cpp
src/alignment_structure.cpp: In constructor 'wb::Alignment_structure::Alignment_structure(char*, int)':
src/alignment_structure.cpp:45:19: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
if (ch>='0' & ch<='9')
^
g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -O2 -Wall -W -D_REENTRANT -DQT_NO_DEBUG -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4 -Ibuild -o build/alignment.o src/alignment.cpp
src/alignment.cpp: In member function 'void wb::Alignment::writeToFile(char*)':
src/alignment.cpp:236:21: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
char * lets="ATCG";
^
src/alignment.cpp:241:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (unsigned int i=0;i<getB();i++) {
^
src/alignment.cpp:243:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (unsigned int j=0;j<getN();j++) {
^
src/alignment.cpp:244:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (unsigned int k=beg;k<end;k++)
^
src/alignment.cpp:246:41: warning: embedded '\0' in format [-Wformat-contains-nul]
sprintf(buf+end-beg,"\0");
^
g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -O2 -Wall -W -D_REENTRANT -DQT_NO_DEBUG -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4 -Ibuild -o build/boot.o src/boot.cpp
g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -O2 -Wall -W -D_REENTRANT -DQT_NO_DEBUG -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4 -Ibuild -o build/burst.o src/burst.cpp
src/burst.cpp: In member function 'void wb::Burst::burst(wb::Param*)':
src/burst.cpp:188:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (k=1;k<rid->size();k++)
^
src/burst.cpp:190:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (k>=rid->size()) continue;
^
src/burst.cpp: In member function 'void wb::Burst::optimiseFathers(gsl_vector_int*, std::vector<std::vector<int> >*, int)':
src/burst.cpp:259:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (slvs->at(prop).size()>current && !descended(prop,i,fathers)) {
^
src/burst.cpp: At global scope:
src/burst.cpp:252:89: warning: unused parameter 'f' [-Wunused-parameter]
void Burst::optimiseFathers(gsl_vector_int * fathers,vector<vector<int> > *slvs,int f) {
^
g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -O2 -Wall -W -D_REENTRANT -DQT_NO_DEBUG -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4 -Ibuild -o build/consensus.o src/consensus.cpp
g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -O2 -Wall -W -D_REENTRANT -DQT_NO_DEBUG -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4 -Ibuild -o build/genes.o src/genes.cpp
g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -O2 -Wall -W -D_REENTRANT -DQT_NO_DEBUG -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4 -Ibuild -o build/hashcell.o src/hashcell.cpp
src/hashcell.cpp: In member function 'void wb::HashCell::addNode(wb::Tree*)':
src/hashcell.cpp:51:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (l>=t->recMap->size) break;
^
g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -O2 -Wall -W -D_REENTRANT -DQT_NO_DEBUG -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4 -Ibuild -o build/move_ages.o src/move_ages.cpp
src/move_ages.cpp: In member function 'virtual void wb::Move_ages::move(wb::Param*)':
src/move_ages.cpp:60:21: warning: suggest braces around empty body in an 'else' statement [-Wempty-body]
} else ;//printf("Age change rejected because out of range\n");
^
g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -O2 -Wall -W -D_REENTRANT -DQT_NO_DEBUG -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4 -Ibuild -o build/move_delta.o src/move_delta.cpp
src/move_delta.cpp:24:50: warning: unused parameter 'p' [-Wunused-parameter]
Move_delta::Move_delta(gsl_rng * rng,Param * p):Move(rng) {
^
g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -O2 -Wall -W -D_REENTRANT -DQT_NO_DEBUG -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4 -Ibuild -o build/move_gap.o src/move_gap.cpp
src/move_gap.cpp:24:46: warning: unused parameter 'p' [-Wunused-parameter]
Move_gap::Move_gap(gsl_rng * rng,Param * p) : Move(rng) {}
^
g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -O2 -Wall -W -D_REENTRANT -DQT_NO_DEBUG -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4 -Ibuild -o build/move_hidden.o src/move_hidden.cpp
src/move_hidden.cpp:25:52: warning: unused parameter 'p' [-Wunused-parameter]
Move_hidden::Move_hidden(gsl_rng * rng,Param * p) : Move(rng)
^
src/move_hidden.cpp: In member function 'void wb::Move_hidden::forwardfast(wb::Param*, wb::Tree*)':
src/move_hidden.cpp:127:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (unsigned int i=0;i<L;i++)
^
src/move_hidden.cpp:133:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (unsigned int j=0;j<nbstates;j++) gsl_vector_set(probas,j,gsl_vector_get(pbeg,j));
^
src/move_hidden.cpp:137:44: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (unsigned int j=0;j<nbstates;j++) gsl_vector_set(probas,j,gsl_vector_get(probas,j)*gsl_matrix_get(a,j,j)*gsl_matrix_get(e,j,msgs[k]));
^
src/move_hidden.cpp:132:21: warning: unused variable 'top' [-Wunused-variable]
int top=0,left=0,right=0;
^
src/move_hidden.cpp:132:27: warning: unused variable 'left' [-Wunused-variable]
int top=0,left=0,right=0;
^
src/move_hidden.cpp:132:34: warning: unused variable 'right' [-Wunused-variable]
int top=0,left=0,right=0;
^
src/move_hidden.cpp: In member function 'void wb::Move_hidden::backward(wb::Param*, gsl_matrix*, wb::Tree*)':
src/move_hidden.cpp:203:17: warning: unused variable 'd' [-Wunused-variable]
int d=gsl_vector_int_get(p->a->polySites,old)- gsl_vector_int_get(p->a->polySites,old-1);
^
src/move_hidden.cpp: In member function 'int wb::Move_hidden::setState(wb::Tree*, wb::Param*, int, gsl_vector*)':
src/move_hidden.cpp:271:64: warning: 'r' may be used uninitialized in this function [-Wmaybe-uninitialized]
gsl_vector_char_get(t->father->ancSeq,site));
^
g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -O2 -Wall -W -D_REENTRANT -DQT_NO_DEBUG -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4 -Ibuild -o build/move_hidden2.o src/move_hidden2.cpp
g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -O2 -Wall -W -D_REENTRANT -DQT_NO_DEBUG -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4 -Ibuild -o build/move_mu.o src/move_mu.cpp
src/move_mu.cpp:24:44: warning: unused parameter 'p' [-Wunused-parameter]
Move_mu::Move_mu(gsl_rng * rng,Param * p):Move(rng) {}
^
g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -O2 -Wall -W -D_REENTRANT -DQT_NO_DEBUG -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4 -Ibuild -o build/move_nu.o src/move_nu.cpp
src/move_nu.cpp:24:44: warning: unused parameter 'p' [-Wunused-parameter]
Move_nu::Move_nu(gsl_rng * rng,Param * p):Move(rng) {}
^
src/move_nu.cpp: In member function 'virtual void wb::Move_nu::move(wb::Param*)':
src/move_nu.cpp:56:16: warning: suggest explicit braces to avoid ambiguous 'else' [-Wparentheses]
if (gsl_vector_char_get(t->recMap,j)==1)
^
g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -O2 -Wall -W -D_REENTRANT -DQT_NO_DEBUG -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4 -Ibuild -o build/move_rho.o src/move_rho.cpp
src/move_rho.cpp:24:46: warning: unused parameter 'p' [-Wunused-parameter]
Move_rho::Move_rho(gsl_rng * rng,Param * p):Move(rng)
^
g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -O2 -Wall -W -D_REENTRANT -DQT_NO_DEBUG -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4 -Ibuild -o build/move_wb.o src/move_wb.cpp
src/move_wb.cpp: In member function 'virtual void wb::Move_wb::move(wb::Param*)':
src/move_wb.cpp:127:17: warning: unused variable 'sizeys2' [-Wunused-variable]
int sizeys2=propLocs(ys,probys,x,p);
^
g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -O2 -Wall -W -D_REENTRANT -DQT_NO_DEBUG -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4 -Ibuild -o build/move.o src/move.cpp
g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -O2 -Wall -W -D_REENTRANT -DQT_NO_DEBUG -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4 -Ibuild -o build/param.o src/param.cpp
g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -O2 -Wall -W -D_REENTRANT -DQT_NO_DEBUG -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4 -Ibuild -o build/recorder.o src/recorder.cpp
g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -O2 -Wall -W -D_REENTRANT -DQT_NO_DEBUG -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4 -Ibuild -o build/tree_coal.o src/tree_coal.cpp
g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -O2 -Wall -W -D_REENTRANT -DQT_NO_DEBUG -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4 -Ibuild -o build/tree_simple.o src/tree_simple.cpp
g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -O2 -Wall -W -D_REENTRANT -DQT_NO_DEBUG -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4 -Ibuild -o build/tree_upgma.o src/tree_upgma.cpp
g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -O2 -Wall -W -D_REENTRANT -DQT_NO_DEBUG -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4 -Ibuild -o build/tree_newick.o src/tree_newick.cpp
g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -O2 -Wall -W -D_REENTRANT -DQT_NO_DEBUG -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4 -Ibuild -o build/tree.o src/tree.cpp
src/tree.cpp: In static member function 'static wb::Tree* wb::Tree::move(wb::Tree*, wb::Tree*, double, gsl_vector_char*, gsl_vector_char*, wb::Param*)':
src/tree.cpp:99:12: warning: suggest explicit braces to avoid ambiguous 'else' [-Wparentheses]
if (z!=NULL)
^
src/tree.cpp: In member function 'double wb::Tree::llhoodb(wb::Param*)':
src/tree.cpp:229:96: warning: 'vals[9]' may be used uninitialized in this function [-Wmaybe-uninitialized]
} else if (gsl_vector_char_get(recMap,i)==0) {ret+=vals[8];} else {ret+=vals[9];p->rec++;}
^
src/tree.cpp:223:38: warning: 'vals[5]' may be used uninitialized in this function [-Wmaybe-uninitialized]
{ret+=vals[5];p->rec++;}
^
g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -O2 -Wall -W -D_REENTRANT -DQT_NO_DEBUG -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4 -Ibuild -o build/util.o src/util.cpp
src/util.cpp: In static member function 'static void wb::Util::normalize(double*, int)':
src/util.cpp:83:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (unsigned int i=0;i<size;i++) sum+=v[i];
^
src/util.cpp:85:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (unsigned int i=0;i<size;i++) v[i]/=sum;
^
g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -O2 -Wall -W -D_REENTRANT -DQT_NO_DEBUG -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4 -Ibuild -o build/ClonalFrame.o src/ClonalFrame.cpp
src/ClonalFrame.cpp: In function 'gsl_rng* makerng()':
src/ClonalFrame.cpp:83:14: warning: variable 'rng_seed' set but not used [-Wunused-but-set-variable]
long int rng_seed;
^
src/ClonalFrame.cpp: In function 'int main(int, char**)':
src/ClonalFrame.cpp:263:68: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
if (cleanup==true) {a->cleanUp();a->writeToFile("/tmp/out.xmfa");}
^
src/ClonalFrame.cpp:341:51: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long unsigned int' [-Wformat=]
printf("Time spent in MH in seconds:%d\n",t2-t);
^
g++ -Wl,-O1 -fPIE -pie -Wl,-z,relro -Wl,-z,now -o bin/ClonalFrame build/alignment_xmfa.o build/alignment_structure.o build/alignment.o build/boot.o build/burst.o build/consensus.o build/genes.o build/hashcell.o build/move_ages.o build/move_delta.o build/move_gap.o build/move_hidden.o build/move_hidden2.o build/move_mu.o build/move_nu.o build/move_rho.o build/move_wb.o build/move.o build/param.o build/recorder.o build/tree_coal.o build/tree_simple.o build/tree_upgma.o build/tree_newick.o build/tree.o build/util.o build/ClonalFrame.o -L/usr/lib/arm-linux-gnueabihf -lgsl -lgslcblas -lQtGui -lQtCore -lpthread
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_test -a
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_installman -a
dh_perl -a
dh_link -a
dh_strip_nondeterminism -a
dh_compress -a
dh_fixperms -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/clonalframe/usr/bin/ClonalFrame was not linked against libgslcblas.so.0 (it uses none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/clonalframe/usr/bin/ClonalFrame was not linked against libQtCore.so.4 (it uses none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/clonalframe/usr/bin/ClonalFrame was not linked against libpthread.so.0 (it uses none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/clonalframe/usr/bin/ClonalFrame was not linked against libQtGui.so.4 (it uses none of the library's symbols)
dh_installdeb -a
dh_gencontrol -a
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package 'clonalframe-dbgsym' in '../clonalframe-dbgsym_1.2-5_armhf.deb'.
dpkg-deb: building package 'clonalframe' in '../clonalframe_1.2-5_armhf.deb'.
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../clonalframe_1.2-5_armhf.changes
dpkg-genchanges: warning: package clonalframe-dbgsym listed in files list but not in control info
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build clonalframe-1.2
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 20160727-1047
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
clonalframe_1.2-5_armhf.changes:
--------------------------------
Format: 1.8
Date: Thu, 21 Jul 2016 17:33:28 +0200
Source: clonalframe
Binary: clonalframe
Architecture: armhf
Version: 1.2-5
Distribution: stretch-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
clonalframe - inference of bacterial microevolution using multilocus sequence d
Closes: 832012
Changes:
clonalframe (1.2-5) unstable; urgency=medium
.
* cme fix dpkg-control
* delete unused debian/get-orig-source
* Enable build with -fdebug-prefix-map
Closes: #832012
* hardening=+all
Checksums-Sha1:
422d47715df85ff3a42a821221a37d7626dd8254 229472 clonalframe-dbgsym_1.2-5_armhf.deb
13ee0a41b25ec197649c4c8ef103c3d4eb97c5bc 41556 clonalframe_1.2-5_armhf.deb
Checksums-Sha256:
a052361096fe9de0fea22ff454a9116ff7dce8ae59a2f1386d3608bf898ec342 229472 clonalframe-dbgsym_1.2-5_armhf.deb
c1373fce649244dd73c68583e7a90863f549bc8128399fb4f66eabf7fe2d4405 41556 clonalframe_1.2-5_armhf.deb
Files:
ffbb8baa25118e7cf1945a590061a76d 229472 debug extra clonalframe-dbgsym_1.2-5_armhf.deb
5aceff1fbf25b77e1f9eb28bad621ae3 41556 science optional clonalframe_1.2-5_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
clonalframe-dbgsym_1.2-5_armhf.deb
----------------------------------
new debian package, version 2.0.
size 229472 bytes: control archive=504 bytes.
445 bytes, 13 lines control
106 bytes, 1 lines md5sums
Package: clonalframe-dbgsym
Source: clonalframe
Version: 1.2-5
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 260
Depends: clonalframe (= 1.2-5)
Section: debug
Priority: extra
Homepage: http://www.xavierdidelot.xtreemhost.com/clonalframe.htm
Description: Debug symbols for clonalframe
Auto-Built-Package: debug-symbols
Build-Ids: 3a95312c18d2567c3db9406037acaa44cd7640d1
drwxr-xr-x root/root 0 2016-07-27 10:47 ./
drwxr-xr-x root/root 0 2016-07-27 10:47 ./usr/
drwxr-xr-x root/root 0 2016-07-27 10:47 ./usr/lib/
drwxr-xr-x root/root 0 2016-07-27 10:47 ./usr/lib/debug/
drwxr-xr-x root/root 0 2016-07-27 10:47 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2016-07-27 10:47 ./usr/lib/debug/.build-id/3a/
-rw-r--r-- root/root 255440 2016-07-27 10:47 ./usr/lib/debug/.build-id/3a/95312c18d2567c3db9406037acaa44cd7640d1.debug
drwxr-xr-x root/root 0 2016-07-27 10:47 ./usr/share/
drwxr-xr-x root/root 0 2016-07-27 10:47 ./usr/share/doc/
lrwxrwxrwx root/root 0 2016-07-27 10:47 ./usr/share/doc/clonalframe-dbgsym -> clonalframe
clonalframe_1.2-5_armhf.deb
---------------------------
new debian package, version 2.0.
size 41556 bytes: control archive=1023 bytes.
1242 bytes, 22 lines control
274 bytes, 4 lines md5sums
Package: clonalframe
Version: 1.2-5
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 100
Depends: libc6 (>= 2.4), libgcc1 (>= 1:3.5), libgsl2, libqtcore4 (>= 4:4.5.3), libqtgui4 (>= 4:4.5.3), libstdc++6 (>= 5.2)
Section: science
Priority: optional
Homepage: http://www.xavierdidelot.xtreemhost.com/clonalframe.htm
Description: inference of bacterial microevolution using multilocus sequence data
ClonalFrame identifies the clonal relationships between the members of
a sample, while also estimating the chromosomal position of homologous
recombination events that have disrupted the clonal inheritance.
.
ClonalFrame can be applied to any kind of sequence data, from a single
fragment of DNA to whole genomes. It is well suited for the analysis of
MLST data, where 7 gene fragments have been sequenced, but becomes
progressively more powerful as the sequenced regions increase in length
and number up to whole genomes. However, it requires the sequences to be
aligned. If you have genomic data that is not aligned, it is recommend to
use Mauve which produces alignment of whole bacterial genomes in
exactly the format required for analysis with ClonalFrame.
drwxr-xr-x root/root 0 2016-07-27 10:47 ./
drwxr-xr-x root/root 0 2016-07-27 10:46 ./usr/
drwxr-xr-x root/root 0 2016-07-27 10:47 ./usr/bin/
-rwxr-xr-x root/root 87604 2016-07-27 10:47 ./usr/bin/ClonalFrame
drwxr-xr-x root/root 0 2016-07-27 10:46 ./usr/share/
drwxr-xr-x root/root 0 2016-07-27 10:46 ./usr/share/doc/
drwxr-xr-x root/root 0 2016-07-27 10:47 ./usr/share/doc/clonalframe/
-rw-r--r-- root/root 734 2016-07-21 15:39 ./usr/share/doc/clonalframe/changelog.Debian.gz
-rw-r--r-- root/root 1268 2013-09-12 08:58 ./usr/share/doc/clonalframe/copyright
drwxr-xr-x root/root 0 2016-07-27 10:46 ./usr/share/man/
drwxr-xr-x root/root 0 2016-07-27 10:47 ./usr/share/man/man1/
-rw-r--r-- root/root 1055 2016-07-27 10:46 ./usr/share/man/man1/ClonalFrame.1.gz
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 3124
Build-Time: 155
Distribution: stretch-staging
Host Architecture: armhf
Install-Time: 487
Job: clonalframe_1.2-5
Machine Architecture: armhf
Package: clonalframe
Package-Time: 743
Source-Version: 1.2-5
Space: 3124
Status: successful
Version: 1.2-5
--------------------------------------------------------------------------------
Finished at 20160727-1047
Build needed 00:12:23, 3124k disc space