[med-svn] r13705 - in trunk/packages/gofigure2/trunk/debian: . patches
Mathieu Malaterre
malat at alioth.debian.org
Fri May 24 15:58:18 UTC 2013
Author: malat
Date: 2013-05-24 15:58:18 +0000 (Fri, 24 May 2013)
New Revision: 13705
Added:
trunk/packages/gofigure2/trunk/debian/gofigure.1
trunk/packages/gofigure2/trunk/debian/gofigure.1.in
trunk/packages/gofigure2/trunk/debian/gofigure2.manpages
trunk/packages/gofigure2/trunk/debian/patches/fiximagecomp.patch
trunk/packages/gofigure2/trunk/debian/patches/removedocfromall.patch
Removed:
trunk/packages/gofigure2/trunk/debian/gofigure.1
trunk/packages/gofigure2/trunk/debian/gofigure.1.in
Modified:
trunk/packages/gofigure2/trunk/debian/changelog
trunk/packages/gofigure2/trunk/debian/compat
trunk/packages/gofigure2/trunk/debian/control
trunk/packages/gofigure2/trunk/debian/copyright
trunk/packages/gofigure2/trunk/debian/patches/series
trunk/packages/gofigure2/trunk/debian/rules
Log:
Prepare next upload
Modified: trunk/packages/gofigure2/trunk/debian/changelog
===================================================================
--- trunk/packages/gofigure2/trunk/debian/changelog 2013-05-24 13:12:57 UTC (rev 13704)
+++ trunk/packages/gofigure2/trunk/debian/changelog 2013-05-24 15:58:18 UTC (rev 13705)
@@ -1,13 +1,14 @@
-gofigure2 (0.9.0-2) UNRELEASED; urgency=low
+gofigure2 (0.9.0-2) unstable; urgency=low
* Remove explicit B-D to libgdcm since not needed anymore
* Remove DMUA flag, use my @d.o alias
- * Bump Std-Vers to 3.9.3
+ * Bump Std-Vers to 3.9.4, no changes needed
* Fix building against newer VTK:
- debian/patches/missingx11link.patch
- * Use hardening flags
+ * Use hardening flags thanks to dh/9
+ * Fix lintian about d/copyright empty lines
- -- Mathieu Malaterre <malat at debian.org> Sun, 22 Apr 2012 17:41:49 +0200
+ -- Mathieu Malaterre <malat at debian.org> Fri, 24 May 2013 16:31:50 +0200
gofigure2 (0.9.0-1) unstable; urgency=low
Modified: trunk/packages/gofigure2/trunk/debian/compat
===================================================================
--- trunk/packages/gofigure2/trunk/debian/compat 2013-05-24 13:12:57 UTC (rev 13704)
+++ trunk/packages/gofigure2/trunk/debian/compat 2013-05-24 15:58:18 UTC (rev 13705)
@@ -1 +1 @@
-8
+9
Modified: trunk/packages/gofigure2/trunk/debian/control
===================================================================
--- trunk/packages/gofigure2/trunk/debian/control 2013-05-24 13:12:57 UTC (rev 13704)
+++ trunk/packages/gofigure2/trunk/debian/control 2013-05-24 15:58:18 UTC (rev 13705)
@@ -4,10 +4,11 @@
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Uploaders: Mathieu Malaterre <malat at debian.org>,
Andreas Tille <tille at debian.org>
-Build-Depends: debhelper (>= 8), cmake (>= 2.8.2), libboost-all-dev, libqt4-dev,
+Build-Depends: debhelper (>= 9), cmake (>= 2.8.2), libboost-all-dev, libqt4-dev,
libinsighttoolkit3-dev (>= 3.20), libvtk5-qt4-dev (>= 5.6), libfftw3-dev,
libqtwebkit-dev | libqt4-dev (<< 4.7)
-Standards-Version: 3.9.3
+Build-Depends-Indep: qt4-doc-html, doxygen (>= 1.7.4) , graphviz, vtk-doc
+Standards-Version: 3.9.4
Homepage: http://gofigure2.sourceforge.net
Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/gofigure2/trunk/
Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/gofigure2/trunk/
@@ -26,6 +27,7 @@
* generating and visualizing cell-lineage.
Package: libgofigure0
+Section: libs
Architecture: any
Depends: ${shlibs:Depends}, ${misc:Depends}
Description: Tool for visualizing, processing and analysing of bioimages
@@ -53,3 +55,18 @@
* generating and visualizing cell-lineage.
.
The development libraries
+
+Package: gofigure2-doc
+Architecture: all
+Section: doc
+Depends: ${misc:Depends}, vtk-doc, doc-base
+Description: Tool for visualizing, processing and analysing of bioimages - doc
+ Main objectives of GoFigure2 are to provide
+ * interaction/visualization/navigation into 4D multichannels bio-images;
+ * save/retrieve information related to the imaging process, analysis results;
+ * extracting objects from bio-images (e.g. nucleii, cell-membranes...);
+ * tracking sub-cellular structure, cells;
+ * detecting and tracking cell-division through time;
+ * generating and visualizing cell-lineage.
+ .
+ This is the documentation for gofigure2
Modified: trunk/packages/gofigure2/trunk/debian/copyright
===================================================================
--- trunk/packages/gofigure2/trunk/debian/copyright 2013-05-24 13:12:57 UTC (rev 13704)
+++ trunk/packages/gofigure2/trunk/debian/copyright 2013-05-24 15:58:18 UTC (rev 13705)
@@ -7,7 +7,7 @@
License: BSD
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
-
+ .
Redistributions of source code must retain the above copyright notice,
this list of conditions and the following disclaimer.
Redistributions in binary form must reproduce the above copyright notice,
@@ -17,7 +17,7 @@
nor the names of its contributors may be used to endorse or promote
products derived from this software without specific prior written
permission.
-
+ .
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
@@ -58,25 +58,25 @@
License: BSD
Copyright (c) 1999-2008 Insight Software Consortium
All rights reserved.
-
+ .
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
-
+ .
* Redistributions of source code must retain the above copyright notice,
this list of conditions and the following disclaimer.
-
+ .
* Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution.
-
+ .
* The name of the Insight Software Consortium, or the names of any
consortium members, or of any contributors, may not be used to endorse or
promote products derived from this software without specific prior written
permission.
-
+ .
* Modified source versions must be plainly marked as such, and must not be
misrepresented as being the original software.
-
+ .
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDER AND CONTRIBUTORS ``AS IS''
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
@@ -94,21 +94,21 @@
License: BSD
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
-
+ .
* Redistributions of source code must retain the above copyright notice,
this list of conditions and the following disclaimer.
-
+ .
* Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution.
-
+ .
* Neither the name of INRIA or ASCLEPIOS, nor the names of any contributors
may be used to endorse or promote products derived from this software
without specific prior written permission.
-
+ .
* Modified source versions must be plainly marked as such, and must not be
misrepresented as being the original software.
-
+ .
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDER AND CONTRIBUTORS ``AS IS''
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
@@ -126,7 +126,7 @@
License: BSD
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
-
+ .
Redistributions of source code must retain the above copyright notice,
this list of conditions and the following disclaimer.
Redistributions in binary form must reproduce the above copyright notice,
@@ -135,7 +135,7 @@
Neither the name of the Johns Hopkins University nor the names of its
contributors may be used to endorse or promote products derived from this
software without specific prior written permission.
-
+ .
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
@@ -147,20 +147,20 @@
WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-
+ .
This code has been modified and wrapped to VTK.
Here is the corresponding license:
-
+ .
Authors: David Doria at Rensselaer Polytechnic Institute and
Arnaud Gelas at Harvard Medical School
-
+ .
Copyright (c) 2010, David Doria at Rensselaer Polytechnic Institute and
Arnaud Gelas at Harvard Medical School,
All rights reserved.
-
+ .
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
-
+ .
Redistributions of source code must retain the above copyright notice,
this list of conditions and the following disclaimer.
Redistributions in binary form must reproduce the above copyright notice,
@@ -170,7 +170,7 @@
Medical School nor the names of its contributors may be used to endorse
or promote products derived from this software without specific prior
written permission.
-
+ .
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
@@ -183,25 +183,24 @@
OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-
Files: Code/ExternalCode/vtkLSM/*
Copyright: © 2004-2008 BioImageXD Development Team
License: BSD
All rights reserved.
-
+ .
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
-
+ .
* Redistributions of source code must retain the above copyright notice,
this list of conditions and the following disclaimer.
-
+ .
* Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution.
-
+ .
* Modified source versions must be plainly marked as such, and must not be
misrepresented as being the original software.
-
+ .
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS
IS'' AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
Deleted: trunk/packages/gofigure2/trunk/debian/gofigure.1
===================================================================
--- trunk/packages/gofigure2/trunk/debian/gofigure.1 2013-05-24 13:12:57 UTC (rev 13704)
+++ trunk/packages/gofigure2/trunk/debian/gofigure.1 2013-05-24 15:58:18 UTC (rev 13705)
@@ -1,35 +0,0 @@
-.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.38.2.
-.TH GOFIGURE "1" "December 2011" "gofigure GoFigure2-v0.9.0" "User Commands"
-.SH NAME
-gofigure \- Tool for visualizing, processing and analysing of bioimages
-.SH SYNOPSIS
-.B gofigure
-.RI [ options ] " files" ...
-.SH DESCRIPTION
-The prime goal of GoFigure2 is the automatic segmentation of nuclei and cell
-membranes and in temporally tracking them amidst cell division to create
-lineages.
-.SS "Usage:"
-.IP
-gofigure [options]:
-.SS "Generic Options:"
-.TP
-\fB\-h\fR [ \fB\-\-help\fR ]
-Display this information
-.TP
-\fB\-v\fR [ \fB\-\-version\fR ]
-Display GoFigure2 version information
-.TP
-\fB\-\-shortcuts\fR
-Display all shortcuts
-.SS "Configuration:"
-.TP
-\fB\-i\fR [ \fB\-\-input\fR ] arg
-input file (single file)
-.TP
-\fB\-\-max\-meshes\fR arg
-Maximum number of meshes to load in memory (default
-5000)
-.SH AUTHORS
-This manual page was written by Mathieu Malaterre <malat at debian.org>,
-for the Debian project (and may be used by others).
Added: trunk/packages/gofigure2/trunk/debian/gofigure.1
===================================================================
--- trunk/packages/gofigure2/trunk/debian/gofigure.1 (rev 0)
+++ trunk/packages/gofigure2/trunk/debian/gofigure.1 2013-05-24 15:58:18 UTC (rev 13705)
@@ -0,0 +1,35 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.38.2.
+.TH GOFIGURE "1" "December 2011" "gofigure GoFigure2-v0.9.0" "User Commands"
+.SH NAME
+gofigure \- Tool for visualizing, processing and analysing of bioimages
+.SH SYNOPSIS
+.B gofigure
+.RI [ options ] " files" ...
+.SH DESCRIPTION
+The prime goal of GoFigure2 is the automatic segmentation of nuclei and cell
+membranes and in temporally tracking them amidst cell division to create
+lineages.
+.SS "Usage:"
+.IP
+gofigure [options]:
+.SS "Generic Options:"
+.TP
+\fB\-h\fR [ \fB\-\-help\fR ]
+Display this information
+.TP
+\fB\-v\fR [ \fB\-\-version\fR ]
+Display GoFigure2 version information
+.TP
+\fB\-\-shortcuts\fR
+Display all shortcuts
+.SS "Configuration:"
+.TP
+\fB\-i\fR [ \fB\-\-input\fR ] arg
+input file (single file)
+.TP
+\fB\-\-max\-meshes\fR arg
+Maximum number of meshes to load in memory (default
+5000)
+.SH AUTHORS
+This manual page was written by Mathieu Malaterre <malat at debian.org>,
+for the Debian project (and may be used by others).
Deleted: trunk/packages/gofigure2/trunk/debian/gofigure.1.in
===================================================================
--- trunk/packages/gofigure2/trunk/debian/gofigure.1.in 2013-05-24 13:12:57 UTC (rev 13704)
+++ trunk/packages/gofigure2/trunk/debian/gofigure.1.in 2013-05-24 15:58:18 UTC (rev 13705)
@@ -1,15 +0,0 @@
-[NAME]
-gofigure \- Tool for visualizing, processing and analysing of bioimages
-
-[SYNOPSIS]
-.B gofigure
-.RI [ options ] " files" ...
-
-[DESCRIPTION]
-The prime goal of GoFigure2 is the automatic segmentation of nuclei and cell
-membranes and in temporally tracking them amidst cell division to create
-lineages.
-
-[AUTHORS]
-This manual page was written by Mathieu Malaterre <malat at debian.org>,
-for the Debian project (and may be used by others).
Added: trunk/packages/gofigure2/trunk/debian/gofigure.1.in
===================================================================
--- trunk/packages/gofigure2/trunk/debian/gofigure.1.in (rev 0)
+++ trunk/packages/gofigure2/trunk/debian/gofigure.1.in 2013-05-24 15:58:18 UTC (rev 13705)
@@ -0,0 +1,15 @@
+[NAME]
+gofigure \- Tool for visualizing, processing and analysing of bioimages
+
+[SYNOPSIS]
+.B gofigure
+.RI [ options ] " files" ...
+
+[DESCRIPTION]
+The prime goal of GoFigure2 is the automatic segmentation of nuclei and cell
+membranes and in temporally tracking them amidst cell division to create
+lineages.
+
+[AUTHORS]
+This manual page was written by Mathieu Malaterre <malat at debian.org>,
+for the Debian project (and may be used by others).
Added: trunk/packages/gofigure2/trunk/debian/gofigure2.manpages
===================================================================
--- trunk/packages/gofigure2/trunk/debian/gofigure2.manpages (rev 0)
+++ trunk/packages/gofigure2/trunk/debian/gofigure2.manpages 2013-05-24 15:58:18 UTC (rev 13705)
@@ -0,0 +1 @@
+debian/gofigure2.1
Added: trunk/packages/gofigure2/trunk/debian/patches/fiximagecomp.patch
===================================================================
--- trunk/packages/gofigure2/trunk/debian/patches/fiximagecomp.patch (rev 0)
+++ trunk/packages/gofigure2/trunk/debian/patches/fiximagecomp.patch 2013-05-24 15:58:18 UTC (rev 13705)
@@ -0,0 +1,22 @@
+Description: fix compilation
+Author: Mathieu Malaterre <malat at debian.org>
+Forwarded: no
+
+--- gofigure2-0.9.0.orig/Main/CMakeLists.txt
++++ gofigure2-0.9.0/Main/CMakeLists.txt
+@@ -31,11 +31,13 @@ IF( BUILD_COMPARETOOL )
+
+ SET( GOFIGURE_APPLICATION_SOURCE_LIST
+ ${GOFIGURE_APPLICATION_SOURCE_LIST}
+- ${QGoSynchronizedViewMainWindow.cxx}
++ QGoSynchronizedViewMainWindow.cxx
+ )
+ ENDIF( BUILD_COMPARETOOL )
+
+-INCLUDE_DIRECTORIES( ${GOFIGURE2_BINARY_DIR}/Main/ )
++INCLUDE_DIRECTORIES( ${GOFIGURE2_BINARY_DIR}/Main/
++ ${GOFIGURE2_SOURCE_DIR}/Code/GUI/lib/SynchronizedViews/
++)
+
+ QT4_WRAP_UI( QGoMainWindow_UI_H ${QGoMainWindow_UI} )
+
Added: trunk/packages/gofigure2/trunk/debian/patches/removedocfromall.patch
===================================================================
--- trunk/packages/gofigure2/trunk/debian/patches/removedocfromall.patch (rev 0)
+++ trunk/packages/gofigure2/trunk/debian/patches/removedocfromall.patch 2013-05-24 15:58:18 UTC (rev 13705)
@@ -0,0 +1,17 @@
+Description: remove doc from target all
+Author: Mathieu Malaterre <malat at debian.org>
+Forwarded: not-needed
+
+Index: gofigure2-0.9.0/Documentation/Doxygen/CMakeLists.txt
+===================================================================
+--- gofigure2-0.9.0.orig/Documentation/Doxygen/CMakeLists.txt 2011-12-07 21:48:18.000000000 +0000
++++ gofigure2-0.9.0/Documentation/Doxygen/CMakeLists.txt 2013-05-24 14:46:28.806681743 +0000
+@@ -77,7 +77,7 @@
+ ${GOFIGURE2_BINARY_DIR}/Doxyfile.txt
+ )
+
+-ADD_CUSTOM_TARGET(doc ALL
++ADD_CUSTOM_TARGET(doc
+ ${DOXYGEN_EXECUTABLE} ${GOFIGURE2_BINARY_DIR}/Doxyfile.txt
+ DEPENDS ${GOFIGURE2_BINARY_DIR}/Doxyfile.txt
+ )
Modified: trunk/packages/gofigure2/trunk/debian/patches/series
===================================================================
--- trunk/packages/gofigure2/trunk/debian/patches/series 2013-05-24 13:12:57 UTC (rev 13704)
+++ trunk/packages/gofigure2/trunk/debian/patches/series 2013-05-24 15:58:18 UTC (rev 13705)
@@ -1 +1,4 @@
missingx11link.patch
+removedocfromall.patch
+fiximagecomp.patch
+dotsvgoutput.patch
Modified: trunk/packages/gofigure2/trunk/debian/rules
===================================================================
--- trunk/packages/gofigure2/trunk/debian/rules 2013-05-24 13:12:57 UTC (rev 13704)
+++ trunk/packages/gofigure2/trunk/debian/rules 2013-05-24 15:58:18 UTC (rev 13705)
@@ -1,18 +1,48 @@
#!/usr/bin/make -f
#export DH_VERBOSE=1
-DPKG_EXPORT_BUILDFLAGS = 1
--include /usr/share/dpkg/buildflags.mk
+export DEB_LDFLAGS_MAINT_APPEND = -Wl,--as-needed
+DEB_HOST_MULTIARCH ?= $(shell dpkg-architecture -qDEB_HOST_MULTIARCH)
+# deduce documentation option (build-indep target)
+ifeq "" "$(filter %-doc,$(shell dh_listpackages))"
+ BUILDDOC=OFF
+else
+ BUILDDOC=ON
+endif
+
+CMAKE_EXTRA_FLAGS = \
+ -DCMAKE_INSTALL_PREFIX:PATH=/usr \
+ -DCMAKE_BUILD_TYPE:STRING=RelWithDebInfo \
+ -DCMAKE_SKIP_RPATH:BOOL=OFF \
+ -DBUILD_SHARED_LIBS:BOOL=ON \
+ -DGOFIGURE2_INSTALL_LIB_DIR:STRING=lib/$(DEB_HOST_MULTIARCH) \
+ -DBUILD_TESTING:BOOL=ON \
+ -DBUILD_DOCUMENTATION:BOOL=$(BUILDDOC) \
+ -DBUILD_PLUGINS:BOOL=ON \
+ -DENABLE_VIDEO_RECORD_FFMPEG:BOOL=ON \
+ -DBUILD_COMPARETOOL:BOOL=ON \
+ -DSUPERBUILD:BOOL=OFF \
+ -DLINK_EXTERNAL_DOC:BOOL=ON \
+ -DDOXYGEN_NIGHTLY_LINK:BOOL=OFF \
+ -DQT_DOC_DIR=/usr/share/qt4/doc/
+
%:
dh $@ --parallel
override_dh_auto_configure:
- dh_auto_configure -- -DGOFIGURE2_INSTALL_LIB_DIR:STRING=lib -DCMAKE_BUILD_TYPE:STRING=RelWithDebInfo
+ dh_auto_configure -- $(CMAKE_EXTRA_FLAGS)
-override_dh_shlibdeps:
- LD_LIBRARY_PATH=debian/gofigure2/usr/lib/gofigure2 dh_shlibdeps -l/usr/lib/gofigure2
+# Let's be smart with building doc
+override_dh_auto_build-indep:
+ $(MAKE) -C obj-* doc
+# No tests needed for docs
+override_dh_auto_test-indep:
+
+override_dh_install-arch:
+ dh_install --list-missing
+
debian/gofigure.1: debian/gofigure.1.in
help2man --include=debian/gofigure.1.in \
--output=debian/gofigure.1 --no-info gofigure
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