clonalframe →
1.2-5+b1 →
armhf → 2017-08-17 00:55:51
sbuild (Debian sbuild) 0.72.0 (25 Oct 2016) on mb-lxc-01
+==============================================================================+
| clonalframe 1.2-5+b1 (armhf) Thu, 17 Aug 2017 00:51:02 +0000 |
+==============================================================================+
Package: clonalframe
Version: 1.2-5+b1
Source Version: 1.2-5
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-db6555d9-db32-4c4e-bdb8-7ef7092e0a01' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private buster-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private buster-staging/main Sources [10.1 MB]
Get:3 http://172.17.0.1/private buster-staging/main armhf Packages [12.0 MB]
Fetched 22.1 MB in 9s (2305 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 buster-staging/main clonalframe 1.2-5 (dsc) [2014 B]
Get:2 http://172.17.0.1/private buster-staging/main clonalframe 1.2-5 (tar) [45.5 kB]
Get:3 http://172.17.0.1/private buster-staging/main clonalframe 1.2-5 (diff) [4092 B]
Fetched 51.6 kB in 0s (195 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/clonalframe-4wiaAc/clonalframe-1.2' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/clonalframe-4wiaAc' 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-94DrBp/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-94DrBp/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-94DrBp/gpg/trustdb.gpg: trustdb created
gpg: key 37145E60F90AF620: 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 37145E60F90AF620: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 37145E60F90AF620: 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-94DrBp/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-94DrBp/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-94DrBp/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-94DrBp/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-94DrBp/apt_archive ./ Packages [431 B]
Fetched 2107 B in 0s (5774 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 libssl1.1 openssl
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 33 not upgraded.
Need to get 776 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-94DrBp/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [776 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 776 B in 0s (0 B/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 14837 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
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 (>= 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-94DrBp/apt_archive/sbuild-build-depends-clonalframe-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-clonalframe-dummy sbuild-build-depends-core-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-94DrBp/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-94DrBp/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-94DrBp/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-94DrBp/apt_archive ./ Sources [510 B]
Get:5 copy:/<<BUILDDIR>>/resolver-94DrBp/apt_archive ./ Packages [591 B]
Fetched 2434 B in 0s (6473 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install clonalframe build dependencies (apt-based resolver)
-----------------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
ca-certificates libssl1.1 openssl
Use 'apt autoremove' to remove them.
The following 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
libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libglib2.0-0
libgsl-dev libgsl23 libgslcblas0 libice6 libicu57 libjbig0 libjpeg62-turbo
libjpeg8 liblcms2-2 libmagic-mgc libmagic1 libmng1 libpipeline1 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 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 m4-doc less www-browser
libmail-box-perl
Recommended packages:
curl | wget | lynx-cur libarchive-cpio-perl libglib2.0-data shared-mime-info
xdg-user-dirs libqt4-opengl-dev 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
libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libglib2.0-0
libgsl-dev libgsl23 libgslcblas0 libice6 libicu57 libjbig0 libjpeg62-turbo
libjpeg8 liblcms2-2 libmagic-mgc libmagic1 libmng1 libpipeline1 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 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, 81 newly installed, 0 to remove and 33 not upgraded.
Need to get 43.5 MB of archives.
After this operation, 156 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-94DrBp/apt_archive ./ sbuild-build-depends-clonalframe-dummy 0.invalid.0 [800 B]
Get:2 http://172.17.0.1/private buster-staging/main armhf groff-base armhf 1.22.3-9 [1005 kB]
Get:3 http://172.17.0.1/private buster-staging/main armhf libbsd0 armhf 0.8.6-1 [95.7 kB]
Get:4 http://172.17.0.1/private buster-staging/main armhf bsdmainutils armhf 9.0.12+nmu1 [178 kB]
Get:5 http://172.17.0.1/private buster-staging/main armhf libpipeline1 armhf 1.4.2-1 [24.2 kB]
Get:6 http://172.17.0.1/private buster-staging/main armhf man-db armhf 2.7.6.1-2 [1014 kB]
Get:7 http://172.17.0.1/private buster-staging/main armhf libexpat1 armhf 2.2.3-1 [67.1 kB]
Get:8 http://172.17.0.1/private buster-staging/main armhf libfreetype6 armhf 2.8-0.2 [393 kB]
Get:9 http://172.17.0.1/private buster-staging/main armhf ucf all 3.0036 [70.2 kB]
Get:10 http://172.17.0.1/private buster-staging/main armhf fonts-dejavu-core all 2.37-1 [1068 kB]
Get:11 http://172.17.0.1/private buster-staging/main armhf fontconfig-config all 2.12.3-0.2 [304 kB]
Get:12 http://172.17.0.1/private buster-staging/main armhf libfontconfig1 armhf 2.12.3-0.2 [349 kB]
Get:13 http://172.17.0.1/private buster-staging/main armhf fontconfig armhf 2.12.3-0.2 [435 kB]
Get:14 http://172.17.0.1/private buster-staging/main armhf libjbig0 armhf 2.1-3.1 [27.5 kB]
Get:15 http://172.17.0.1/private buster-staging/main armhf libjpeg8 armhf 8d1-2 [108 kB]
Get:16 http://172.17.0.1/private buster-staging/main armhf liblcms2-2 armhf 2.8-4 [118 kB]
Get:17 http://172.17.0.1/private buster-staging/main armhf libmng1 armhf 1.0.10+dfsg-3.1 [164 kB]
Get:18 http://172.17.0.1/private buster-staging/main armhf libxau6 armhf 1:1.0.8-1 [19.9 kB]
Get:19 http://172.17.0.1/private buster-staging/main armhf libxdmcp6 armhf 1:1.1.2-3 [25.0 kB]
Get:20 http://172.17.0.1/private buster-staging/main armhf libxcb1 armhf 1.12-1 [129 kB]
Get:21 http://172.17.0.1/private buster-staging/main armhf libx11-data all 2:1.6.4-3 [290 kB]
Get:22 http://172.17.0.1/private buster-staging/main armhf libx11-6 armhf 2:1.6.4-3 [683 kB]
Get:23 http://172.17.0.1/private buster-staging/main armhf libxext6 armhf 2:1.3.3-1 [48.1 kB]
Get:24 http://172.17.0.1/private buster-staging/main armhf libmagic-mgc armhf 1:5.31-1 [223 kB]
Get:25 http://172.17.0.1/private buster-staging/main armhf libmagic1 armhf 1:5.31-1 [105 kB]
Get:26 http://172.17.0.1/private buster-staging/main armhf file armhf 1:5.31-1 [63.5 kB]
Get:27 http://172.17.0.1/private buster-staging/main armhf gettext-base armhf 0.19.8.1-2+b1 [117 kB]
Get:28 http://172.17.0.1/private buster-staging/main armhf libicu57 armhf 57.1-6 [7427 kB]
Get:29 http://172.17.0.1/private buster-staging/main armhf libxml2 armhf 2.9.4+dfsg1-3 [601 kB]
Get:30 http://172.17.0.1/private buster-staging/main armhf libsigsegv2 armhf 2.11-1 [29.3 kB]
Get:31 http://172.17.0.1/private buster-staging/main armhf m4 armhf 1.4.18-1 [185 kB]
Get:32 http://172.17.0.1/private buster-staging/main armhf autoconf all 2.69-10 [338 kB]
Get:33 http://172.17.0.1/private buster-staging/main armhf autotools-dev all 20161112.1 [73.4 kB]
Get:34 http://172.17.0.1/private buster-staging/main armhf automake all 1:1.15.1-2 [736 kB]
Get:35 http://172.17.0.1/private buster-staging/main armhf autopoint all 0.19.8.1-2 [433 kB]
Get:36 http://172.17.0.1/private buster-staging/main armhf libtool all 2.4.6-2 [545 kB]
Get:37 http://172.17.0.1/private buster-staging/main armhf dh-autoreconf all 14 [15.9 kB]
Get:38 http://172.17.0.1/private buster-staging/main armhf libarchive-zip-perl all 1.59-1 [95.5 kB]
Get:39 http://172.17.0.1/private buster-staging/main armhf libfile-stripnondeterminism-perl all 0.038-1 [17.6 kB]
Get:40 http://172.17.0.1/private buster-staging/main armhf libtimedate-perl all 2.3000-2 [42.2 kB]
Get:41 http://172.17.0.1/private buster-staging/main armhf dh-strip-nondeterminism all 0.038-1 [11.1 kB]
Get:42 http://172.17.0.1/private buster-staging/main armhf libglib2.0-0 armhf 2.53.4-3 [2628 kB]
Get:43 http://172.17.0.1/private buster-staging/main armhf libcroco3 armhf 0.6.12-1 [132 kB]
Get:44 http://172.17.0.1/private buster-staging/main armhf gettext armhf 0.19.8.1-2+b1 [1220 kB]
Get:45 http://172.17.0.1/private buster-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:46 http://172.17.0.1/private buster-staging/main armhf po-debconf all 1.0.20 [247 kB]
Get:47 http://172.17.0.1/private buster-staging/main armhf debhelper all 10.7.2 [975 kB]
Get:48 http://172.17.0.1/private buster-staging/main armhf x11-common all 1:7.7+19 [251 kB]
Get:49 http://172.17.0.1/private buster-staging/main armhf libice6 armhf 2:1.0.9-2 [51.6 kB]
Get:50 http://172.17.0.1/private buster-staging/main armhf libsm6 armhf 2:1.2.2-1+b1 [31.2 kB]
Get:51 http://172.17.0.1/private buster-staging/main armhf libxt6 armhf 1:1.1.5-1 [155 kB]
Get:52 http://172.17.0.1/private buster-staging/main armhf libaudio2 armhf 1.9.4-6 [72.7 kB]
Get:53 http://172.17.0.1/private buster-staging/main armhf libgslcblas0 armhf 2.4+dfsg-6 [75.1 kB]
Get:54 http://172.17.0.1/private buster-staging/main armhf libgsl23 armhf 2.4+dfsg-6 [681 kB]
Get:55 http://172.17.0.1/private buster-staging/main armhf libgsl-dev armhf 2.4+dfsg-6 [863 kB]
Get:56 http://172.17.0.1/private buster-staging/main armhf libjpeg62-turbo armhf 1:1.5.1-2 [109 kB]
Get:57 http://172.17.0.1/private buster-staging/main armhf qtcore4-l10n all 4:4.8.7+dfsg-11+rpi1 [662 kB]
Get:58 http://172.17.0.1/private buster-staging/main armhf libqtcore4 armhf 4:4.8.7+dfsg-11+rpi1 [1366 kB]
Get:59 http://172.17.0.1/private buster-staging/main armhf libqt4-xml armhf 4:4.8.7+dfsg-11+rpi1 [126 kB]
Get:60 http://172.17.0.1/private buster-staging/main armhf libqtdbus4 armhf 4:4.8.7+dfsg-11+rpi1 [193 kB]
Get:61 http://172.17.0.1/private buster-staging/main armhf qtchooser armhf 63-g13a3d08-1 [21.9 kB]
Get:62 http://172.17.0.1/private buster-staging/main armhf qdbus armhf 4:4.8.7+dfsg-11+rpi1 [72.2 kB]
Get:63 http://172.17.0.1/private buster-staging/main armhf libqt4-dbus armhf 4:4.8.7+dfsg-11+rpi1 [52.8 kB]
Get:64 http://172.17.0.1/private buster-staging/main armhf libqt4-network armhf 4:4.8.7+dfsg-11+rpi1 [496 kB]
Get:65 http://172.17.0.1/private buster-staging/main armhf libqt4-script armhf 4:4.8.7+dfsg-11+rpi1 [684 kB]
Get:66 http://172.17.0.1/private buster-staging/main armhf libqt4-sql armhf 4:4.8.7+dfsg-11+rpi1 [128 kB]
Get:67 http://172.17.0.1/private buster-staging/main armhf libqt4-xmlpatterns armhf 4:4.8.7+dfsg-11+rpi1 [879 kB]
Get:68 http://172.17.0.1/private buster-staging/main armhf libtiff5 armhf 4.0.8-4 [219 kB]
Get:69 http://172.17.0.1/private buster-staging/main armhf libxrender1 armhf 1:0.9.10-1 [29.9 kB]
Get:70 http://172.17.0.1/private buster-staging/main armhf libqtgui4 armhf 4:4.8.7+dfsg-11+rpi1 [3426 kB]
Get:71 http://172.17.0.1/private buster-staging/main armhf libqt4-declarative armhf 4:4.8.7+dfsg-11+rpi1 [896 kB]
Get:72 http://172.17.0.1/private buster-staging/main armhf libqt4-designer armhf 4:4.8.7+dfsg-11+rpi1 [3355 kB]
Get:73 http://172.17.0.1/private buster-staging/main armhf libqt4-qt3support armhf 4:4.8.7+dfsg-11+rpi1 [895 kB]
Get:74 http://172.17.0.1/private buster-staging/main armhf libqt4-dev-bin armhf 4:4.8.7+dfsg-11+rpi1 [1430 kB]
Get:75 http://172.17.0.1/private buster-staging/main armhf libqt4-help armhf 4:4.8.7+dfsg-11+rpi1 [220 kB]
Get:76 http://172.17.0.1/private buster-staging/main armhf libqt4-scripttools armhf 4:4.8.7+dfsg-11+rpi1 [229 kB]
Get:77 http://172.17.0.1/private buster-staging/main armhf libqt4-svg armhf 4:4.8.7+dfsg-11+rpi1 [156 kB]
Get:78 http://172.17.0.1/private buster-staging/main armhf libqt4-test armhf 4:4.8.7+dfsg-11+rpi1 [97.7 kB]
Get:79 http://172.17.0.1/private buster-staging/main armhf qt4-linguist-tools armhf 4:4.8.7+dfsg-11+rpi1 [755 kB]
Get:80 http://172.17.0.1/private buster-staging/main armhf qt4-qmake armhf 4:4.8.7+dfsg-11+rpi1 [1061 kB]
Get:81 http://172.17.0.1/private buster-staging/main armhf libqt4-dev armhf 4:4.8.7+dfsg-11+rpi1 [882 kB]
debconf: delaying package configuration, since apt-utils is not installed
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update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults
invoke-rc.d: could not determine current runlevel
All runlevel operations denied by policy
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update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode
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Not building database; man-db/auto-update is not 'true'.
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Setting up libxrender1:armhf (1:0.9.10-1) ...
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Setting up libqt4-network:armhf (4:4.8.7+dfsg-11+rpi1) ...
Setting up libaudio2:armhf (1.9.4-6) ...
Setting up fontconfig (2.12.3-0.2) ...
Regenerating fonts cache... done.
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Setting up libqt4-xmlpatterns:armhf (4:4.8.7+dfsg-11+rpi1) ...
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Setting up sbuild-build-depends-clonalframe-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.24-12) ...
Processing triggers for systemd (233-10) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.4.0-79-generic armhf (armv8l)
Toolchain package versions: binutils_2.28-6 dpkg-dev_1.18.24 g++-6_6.4.0-1+rpi1 gcc-6_6.4.0-1+rpi1 libc6-dev_2.24-12 libstdc++-6-dev_6.4.0-1+rpi1 libstdc++6_7.1.0-9+rpi1 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch
Package versions: adduser_3.115 apt_1.5~beta1+b3 autoconf_2.69-10 automake_1:1.15.1-2 autopoint_0.19.8.1-2 autotools-dev_20161112.1 base-files_10+rpi1 base-passwd_3.5.43 bash_4.4-5 binutils_2.28-6 bsdmainutils_9.0.12+nmu1 bsdutils_1:2.29.2-2+rpi1 build-essential_12.3 bzip2_1.0.6-8.1 ca-certificates_20161130+nmu1 coreutils_8.26-3 cpio_2.11+dfsg-6 cpp_4:6.3.0-4d1 cpp-6_6.4.0-1+rpi1 dash_0.5.8-2.5 debconf_1.5.63 debhelper_10.7.2 debianutils_4.8.1.1 dh-autoreconf_14 dh-strip-nondeterminism_0.038-1 diffutils_1:3.5-3 dmsetup_2:1.02.137-2 dpkg_1.18.24 dpkg-dev_1.18.24 e2fslibs_1.43.4-2 e2fsprogs_1.43.4-2 fakeroot_1.21-3.1 file_1:5.31-1 findutils_4.6.0+git+20170606-3 fontconfig_2.12.3-0.2 fontconfig-config_2.12.3-0.2 fonts-dejavu-core_2.37-1 g++_4:6.3.0-4d1 g++-6_6.4.0-1+rpi1 gcc_4:6.3.0-4d1 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8-base_4.8.5-4 gcc-4.9-base_4.9.3-14 gcc-5-base_5.4.1-4 gcc-6_6.4.0-1+rpi1 gcc-6-base_6.4.0-1+rpi1 gcc-7-base_7.1.0-9+rpi1 gettext_0.19.8.1-2+b1 gettext-base_0.19.8.1-2+b1 gnupg_2.1.18-8 gnupg-agent_2.1.18-8 gpgv_2.1.18-8 grep_3.1-2 groff-base_1.22.3-9 gzip_1.6-5 hostname_3.18 init-system-helpers_1.49 initramfs-tools_0.130 initramfs-tools-core_0.130 intltool-debian_0.35.0+20060710.4 klibc-utils_2.0.4-9+rpi1 kmod_24-1 libacl1_2.2.52-3 libapparmor1_2.11.0-6 libapt-pkg5.0_1.5~beta1+b3 libarchive-zip-perl_1.59-1 libasan3_6.4.0-1+rpi1 libassuan0_2.4.3-2 libatomic1_7.1.0-9+rpi1 libattr1_1:2.4.47-2 libaudio2_1.9.4-6 libaudit-common_1:2.7.7-1 libaudit1_1:2.7.7-1 libblkid1_2.29.2-2+rpi1 libbsd0_0.8.6-1 libbz2-1.0_1.0.6-8.1 libc-bin_2.24-12 libc-dev-bin_2.24-12 libc6_2.24-12 libc6-dev_2.24-12 libcap-ng0_0.7.7-3 libcap2_1:2.25-1 libcc1-0_7.1.0-9+rpi1 libcomerr2_1.43.4-2 libcroco3_0.6.12-1 libcryptsetup4_2:1.7.3-4 libdb5.3_5.3.28-12 libdbus-1-3_1.10.20-1 libdebconfclient0_0.229 libdevmapper1.02.1_2:1.02.137-2 libdpkg-perl_1.18.24 libdrm2_2.4.81-2+rpi1 libexpat1_2.2.3-1 libfakeroot_1.21-3.1 libfdisk1_2.29.2-2+rpi1 libffi6_3.2.1-6 libfile-stripnondeterminism-perl_0.038-1 libfontconfig1_2.12.3-0.2 libfreetype6_2.8-0.2 libgcc-6-dev_6.4.0-1+rpi1 libgcc1_1:7.1.0-9+rpi1 libgcrypt20_1.7.8-2 libgdbm3_1.8.3-14 libglib2.0-0_2.53.4-3 libgmp10_2:6.1.2+dfsg-1 libgnutls30_3.5.14-2 libgomp1_7.1.0-9+rpi1 libgpg-error0_1.27-3 libgsl-dev_2.4+dfsg-6 libgsl23_2.4+dfsg-6 libgslcblas0_2.4+dfsg-6 libhogweed4_3.3-1 libice6_2:1.0.9-2 libicu57_57.1-6 libidn11_1.33-1 libidn2-0_2.0.2-1 libip4tc0_1.6.1-2 libisl15_0.18-1 libjbig0_2.1-3.1 libjpeg62-turbo_1:1.5.1-2 libjpeg8_8d1-2 libklibc_2.0.4-9+rpi1 libkmod2_24-1 libksba8_1.3.5-2 liblcms2-2_2.8-4 liblz4-1_0.0~r131-2 liblzma5_5.2.2-1.3 libmagic-mgc_1:5.31-1 libmagic1_1:5.31-1 libmng1_1.0.10+dfsg-3.1 libmount1_2.29.2-2+rpi1 libmpc3_1.0.3-1 libmpfr4_3.1.5-1 libncurses5_6.0+20170715-2 libncursesw5_6.0+20170715-2 libnettle6_3.3-1 libnih-dbus1_1.0.3-8 libnih1_1.0.3-8 libnpth0_1.5-2 libp11-kit0_0.23.7-3 libpam-modules_1.1.8-3.6 libpam-modules-bin_1.1.8-3.6 libpam-runtime_1.1.8-3.6 libpam0g_1.1.8-3.6 libpcre3_2:8.39-3 libperl5.24_5.24.1-7 libperl5.26_5.26.0-4 libpipeline1_1.4.2-1 libplymouth4_0.9.2-4 libpng16-16_1.6.30-2 libprocps6_2:3.3.12-3 libqt4-dbus_4:4.8.7+dfsg-11+rpi1 libqt4-declarative_4:4.8.7+dfsg-11+rpi1 libqt4-designer_4:4.8.7+dfsg-11+rpi1 libqt4-dev_4:4.8.7+dfsg-11+rpi1 libqt4-dev-bin_4:4.8.7+dfsg-11+rpi1 libqt4-help_4:4.8.7+dfsg-11+rpi1 libqt4-network_4:4.8.7+dfsg-11+rpi1 libqt4-qt3support_4:4.8.7+dfsg-11+rpi1 libqt4-script_4:4.8.7+dfsg-11+rpi1 libqt4-scripttools_4:4.8.7+dfsg-11+rpi1 libqt4-sql_4:4.8.7+dfsg-11+rpi1 libqt4-svg_4:4.8.7+dfsg-11+rpi1 libqt4-test_4:4.8.7+dfsg-11+rpi1 libqt4-xml_4:4.8.7+dfsg-11+rpi1 libqt4-xmlpatterns_4:4.8.7+dfsg-11+rpi1 libqtcore4_4:4.8.7+dfsg-11+rpi1 libqtdbus4_4:4.8.7+dfsg-11+rpi1 libqtgui4_4:4.8.7+dfsg-11+rpi1 libreadline5_5.2+dfsg-3 libreadline7_7.0-3 libseccomp2_2.3.1-2.1 libselinux1_2.6-3 libsemanage-common_2.6-2 libsemanage1_2.6-2 libsepol1_2.6-2 libsigsegv2_2.11-1 libsm6_2:1.2.2-1+b1 libsmartcols1_2.29.2-2+rpi1 libsqlite3-0_3.19.3-3 libss2_1.43.4-2 libssl1.1_1.1.0f-3 libstdc++-6-dev_6.4.0-1+rpi1 libstdc++6_7.1.0-9+rpi1 libsystemd0_233-10 libtasn1-6_4.12-2 libtiff5_4.0.8-4 libtimedate-perl_2.3000-2 libtinfo5_6.0+20170715-2 libtool_2.4.6-2 libubsan0_7.1.0-9+rpi1 libudev1_233-10 libunistring2_0.9.7-2 libustr-1.0-1_1.0.4-6 libuuid1_2.29.2-2+rpi1 libx11-6_2:1.6.4-3 libx11-data_2:1.6.4-3 libxau6_1:1.0.8-1 libxcb1_1.12-1 libxdmcp6_1:1.1.2-3 libxext6_2:1.3.3-1 libxml2_2.9.4+dfsg1-3 libxrender1_1:0.9.10-1 libxt6_1:1.1.5-1 linux-base_4.5 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch login_1:4.4-4.1 lsb-base_9.20161125+rpi1 m4_1.4.18-1 make_4.1-9.1 makedev_2.3.1-93 man-db_2.7.6.1-2 mawk_1.3.3-17 mount_2.29.2-2+rpi1 mountall_2.54 multiarch-support_2.24-12 ncurses-base_6.0+20170715-2 ncurses-bin_6.0+20170715-2 openssl_1.1.0f-3 passwd_1:4.4-4.1 patch_2.7.5-1 perl_5.26.0-4 perl-base_5.26.0-4 perl-modules-5.24_5.24.1-7 perl-modules-5.26_5.26.0-4 pinentry-curses_1.0.0-2 plymouth_0.9.2-4 po-debconf_1.0.20 procps_2:3.3.12-3 qdbus_4:4.8.7+dfsg-11+rpi1 qt4-linguist-tools_4:4.8.7+dfsg-11+rpi1 qt4-qmake_4:4.8.7+dfsg-11+rpi1 qtchooser_63-g13a3d08-1 qtcore4-l10n_4:4.8.7+dfsg-11+rpi1 raspbian-archive-keyring_20120528.2 readline-common_7.0-3 sbuild-build-depends-clonalframe-dummy_0.invalid.0 sbuild-build-depends-core-dummy_0.invalid.0 sed_4.4-1 sensible-utils_0.0.9+nmu1 systemd_233-10 sysvinit-utils_2.88dsf-59.9 tar_1.29b-2 tzdata_2017b-2 ucf_3.0036 udev_233-10 util-linux_2.29.2-2+rpi1 x11-common_1:7.7+19 xz-utils_5.2.2-1.3 zlib1g_1:1.2.8.dfsg-5
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Thu Jul 21 15:40:02 2016 UTC
gpgv: using RSA key 578A0494D1C646D1
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./clonalframe_1.2-5.dsc
dpkg-source: info: extracting clonalframe in /<<PKGBUILDDIR>>
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 disk space
----------------
Sufficient free space for build
Hack binNMU version
-------------------
Created changelog entry for binNMU version 1.2-5+b1
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=112
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=buster-staging-armhf-sbuild-db6555d9-db32-4c4e-bdb8-7ef7092e0a01
SCHROOT_UID=107
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package clonalframe
dpkg-buildpackage: info: source version 1.2-5+b1
dpkg-buildpackage: info: source distribution buster-staging
dpkg-source --before-build clonalframe-1.2
dpkg-buildpackage: info: host architecture armhf
fakeroot debian/rules clean
dh clean
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_update_autotools_config -a
dh_auto_configure -a
qmake -makefile -nocache "QMAKE_CFLAGS_RELEASE=-g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2" "QMAKE_CFLAGS_DEBUG=-g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2" "QMAKE_CXXFLAGS_RELEASE=-g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2" "QMAKE_CXXFLAGS_DEBUG=-g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2" "QMAKE_LFLAGS_RELEASE=-Wl,-z,relro -Wl,-z,now" "QMAKE_LFLAGS_DEBUG=-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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security:" \
-e "s:CXXFLAGS *= .*:& -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security:" \
-e "s:LFLAGS *= .*:& -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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: ISO C++ forbids converting a 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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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: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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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: In constructor 'wb::Move_delta::Move_delta(gsl_rng*, wb::Param*)':
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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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: In constructor 'wb::Move_gap::Move_gap(gsl_rng*, wb::Param*)':
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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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: In constructor 'wb::Move_hidden::Move_hidden(gsl_rng*, wb::Param*)':
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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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: In constructor 'wb::Move_mu::Move_mu(gsl_rng*, wb::Param*)':
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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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: In constructor 'wb::Move_nu::Move_nu(gsl_rng*, wb::Param*)':
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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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: In constructor 'wb::Move_rho::Move_rho(gsl_rng*, wb::Param*)':
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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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:229:87: 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:223:29: 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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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: ISO C++ forbids converting a 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 -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_missing -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dpkg-shlibdeps: warning: debian/clonalframe/usr/bin/ClonalFrame 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/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 libQtGui.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 ld-linux-armhf.so.3 (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)
dh_installdeb -a
dh_gencontrol -a
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package 'clonalframe' in '../clonalframe_1.2-5+b1_armhf.deb'.
dpkg-deb: building package 'clonalframe-dbgsym' in '../clonalframe-dbgsym_1.2-5+b1_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian mythic lxc autobuilder 1 <root@raspbian.org> >../clonalframe_1.2-5+b1_armhf.changes
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 2017-08-17T00:55:45Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
clonalframe_1.2-5+b1_armhf.changes:
-----------------------------------
Format: 1.8
Date: Thu, 21 Jul 2016 17:33:28 +0200
Source: clonalframe (1.2-5)
Binary: clonalframe
Binary-Only: yes
Architecture: armhf
Version: 1.2-5+b1
Distribution: buster-staging
Urgency: low
Maintainer: Raspbian mythic lxc autobuilder 1 <root@raspbian.org>
Changed-By: Raspbian mythic lxc autobuilder 1 <root@raspbian.org>
Description:
clonalframe - inference of bacterial microevolution using multilocus sequence d
Changes:
clonalframe (1.2-5+b1) buster-staging; urgency=low, binary-only=yes
.
* Binary-only non-maintainer upload for armhf; no source changes.
* rebuild due to debcheck failure
Checksums-Sha1:
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a0ae41d39a7d013b4eddbd5470c1e8cb61194cd4 6464 clonalframe_1.2-5_armhf.buildinfo
Checksums-Sha256:
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3809379a80cfcca4f18b68122e7b8bae9988acd21e011fa1887928b4fcb0747e 40684 clonalframe_1.2-5+b1_armhf.deb
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Files:
67820081f46dd8797bf4cead02da19da 284064 debug extra clonalframe-dbgsym_1.2-5+b1_armhf.deb
6ec0da01fd9561c7831b204b8a1e5a89 40684 science optional clonalframe_1.2-5+b1_armhf.deb
95a0a7ddddb4779a2e1a980515a0e1fe 6464 science optional clonalframe_1.2-5_armhf.buildinfo
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
clonalframe-dbgsym_1.2-5+b1_armhf.deb
-------------------------------------
new debian package, version 2.0.
size 284064 bytes: control archive=464 bytes.
393 bytes, 12 lines control
106 bytes, 1 lines md5sums
Package: clonalframe-dbgsym
Source: clonalframe (1.2-5)
Version: 1.2-5+b1
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 317
Depends: clonalframe (= 1.2-5+b1)
Section: debug
Priority: extra
Description: Debug symbols for clonalframe
Build-Ids: 5a41294a9f9f8bb88b23bd3b6d648bf1a331666b
drwxr-xr-x root/root 0 2016-07-21 15:33 ./
drwxr-xr-x root/root 0 2016-07-21 15:33 ./usr/
drwxr-xr-x root/root 0 2016-07-21 15:33 ./usr/lib/
drwxr-xr-x root/root 0 2016-07-21 15:33 ./usr/lib/debug/
drwxr-xr-x root/root 0 2016-07-21 15:33 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2016-07-21 15:33 ./usr/lib/debug/.build-id/5a/
-rw-r--r-- root/root 313404 2016-07-21 15:33 ./usr/lib/debug/.build-id/5a/41294a9f9f8bb88b23bd3b6d648bf1a331666b.debug
drwxr-xr-x root/root 0 2016-07-21 15:33 ./usr/share/
drwxr-xr-x root/root 0 2016-07-21 15:33 ./usr/share/doc/
lrwxrwxrwx root/root 0 2016-07-21 15:33 ./usr/share/doc/clonalframe-dbgsym -> clonalframe
clonalframe_1.2-5+b1_armhf.deb
------------------------------
new debian package, version 2.0.
size 40684 bytes: control archive=1071 bytes.
1288 bytes, 23 lines control
360 bytes, 5 lines md5sums
Package: clonalframe
Source: clonalframe (1.2-5)
Version: 1.2-5+b1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 101
Depends: libc6 (>= 2.4), libgcc1 (>= 1:3.5), libgsl23, libgslcblas0, 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 2016-07-21 15:33 ./
drwxr-xr-x root/root 0 2016-07-21 15:33 ./usr/
drwxr-xr-x root/root 0 2016-07-21 15:33 ./usr/bin/
-rwxr-xr-x root/root 87604 2016-07-21 15:33 ./usr/bin/ClonalFrame
drwxr-xr-x root/root 0 2016-07-21 15:33 ./usr/share/
drwxr-xr-x root/root 0 2016-07-21 15:33 ./usr/share/doc/
drwxr-xr-x root/root 0 2016-07-21 15:33 ./usr/share/doc/clonalframe/
-rw-r--r-- root/root 221 2016-07-21 15:33 ./usr/share/doc/clonalframe/changelog.Debian.armhf.gz
-rw-r--r-- root/root 734 2016-07-21 15:33 ./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 2016-07-21 15:33 ./usr/share/man/
drwxr-xr-x root/root 0 2016-07-21 15:33 ./usr/share/man/man1/
-rw-r--r-- root/root 1055 2016-07-21 15:33 ./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: 3764
Build-Time: 64
Distribution: buster-staging
Host Architecture: armhf
Install-Time: 201
Job: clonalframe_1.2-5
Machine Architecture: armhf
Package: clonalframe
Package-Time: 283
Source-Version: 1.2-5
Space: 3764
Status: successful
Version: 1.2-5+b1
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Finished at 2017-08-17T00:55:45Z
Build needed 00:04:43, 3764k disk space