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commit 52a4af4cbf93867a5100c40352adcc3a6f2a5eef Author: Gert Wollny <[email protected]> Date: Mon Sep 7 00:38:47 2015 +0200 prepare new upstream package * bump so-version * remove patches that are now in upstream * las minute correct the build dependencies --- debian/changelog | 12 +++++ debian/control | 52 +++++++++++----------- .../{libmia-2.2-0.install => libmia-2.2-4.install} | 0 ...an-overrides => libmia-2.2-4.lintian-overrides} | 8 ++-- ...disable-treeview-for-jquery-compatibility.patch | 1 + debian/patches/02-manpage-correction.patch | 37 --------------- debian/patches/02_correct_build_dependencies.patch | 43 ++++++++++++++++++ ...tion_of_default_3Dvectorfield_constructor.patch | 20 --------- debian/patches/04_correct_flag_outstream.patch | 21 --------- .../05_remove_timestamp_from_doxygen_output.patch | 17 ------- debian/patches/series | 5 +-- debian/rules | 2 +- debian/run_strip | 2 +- doc/reference.dox.cmake | 3 -- src/fluid2d/CMakeLists.txt | 1 + src/fluid3d/CMakeLists.txt | 2 +- src/isosurface/CMakeLists.txt | 2 + 17 files changed, 94 insertions(+), 134 deletions(-) diff --git a/debian/changelog b/debian/changelog index 965f5dd..2167778 100644 --- a/debian/changelog +++ b/debian/changelog @@ -1,3 +1,15 @@ +mia (2.2.4-1) UNRELEASED; urgency=medium + + * new upstream + * d/patches/* remove patches since they are now included upstream: + 02-manpage-correction-patch, 03_correct_instanciation.. + 04_correct_flag_outstream, 05_remove_timestamp_from_doxygen + * d/patches/ add 02_correct_build_dependencies.patch to correct build + * d/* bump so-version of the library package because of ABI change. + This also takes care of the needed gcc-5 transition + + -- Gert Wollny <[email protected]> Mon, 07 Sep 2015 00:00:10 +0200 + mia (2.2.3-2) unstable; urgency=medium * Backport from experimental diff --git a/debian/control b/debian/control index e8600a6..67553d7 100644 --- a/debian/control +++ b/debian/control @@ -3,33 +3,34 @@ Maintainer: Debian Med Packaging Team <[email protected]. Uploaders: Gert Wollny <[email protected]> Section: science Priority: optional -Build-Depends: cmake (>= 2.8.8), +Build-Depends: cmake, debhelper (>= 9.0.0), docbook-xsl, doxygen, graphviz, libblas-dev, - libboost-filesystem-dev (>= 1.46.1), - libboost-regex-dev (>= 1.46.1), - libboost-serialization-dev (>= 1.46.1), - libboost-system-dev (>= 1.46.1), - libboost-test-dev (>= 1.46.1), + libboost-filesystem-dev, + libboost-regex-dev, + libboost-serialization-dev, + libboost-system-dev, + libboost-test-dev, libdcmtk2-dev, libeigen3-dev, libfftw3-dev, - libgsl0-dev (>= 1.14), + libgsl0-dev, libgts-dev, libhdf5-dev, - libitpp-dev (>= 4.2), + libitpp-dev, + libmaxflow-dev, libnifti-dev, - libnlopt-dev (>= 2.2.3), - libopenexr-dev (>= 1.6.1), + libnlopt-dev, + libopenexr-dev, libpng-dev, - libtbb-dev (>= 3.0), + libtbb-dev, libtiff-dev, libvtk6-dev, - libvistaio-dev (>=1.2.12), - libxml++2.6-dev (>= 2.34.1), + libvistaio-dev, + libxml++2.6-dev, python-lxml, xsltproc Standards-Version: 3.9.6 @@ -40,17 +41,13 @@ Homepage: http://mia.sourceforge.net Package: libmia-2.2-dev Architecture: any Section: libdevel -Depends: libmia-2.2-0 (= ${binary:Version}), - libxml++2.6-dev (>= 2.34.1), - libeigen3-dev, +Depends: libmia-2.2-4 (= ${binary:Version}), libitpp-dev (>= 4.2), libtbb-dev, libgsl0-dev, - libboost-filesystem-dev (>= 1.46.1), - libboost-regex-dev (>= 1.46.1), - libboost-serialization-dev (>= 1.46.1), - libboost-system-dev (>= 1.46.1), - libboost-test-dev (>= 1.46.1), + libboost-regex-dev, + libboost-serialization-dev, + libboost-test-dev, libfftw3-dev, libblas-dev, ${misc:Depends} @@ -78,24 +75,29 @@ Description: library for 2D and 3D gray scale image processing, documentation algorithms, that can be specialized by specifying the apropriate plug-ins. This package provides the Doxygen generated API reference. -Package: libmia-2.2-0 +Package: libmia-2.2-4 Architecture: any Section: libs Depends: ${shlibs:Depends}, ${misc:Depends} Pre-Depends: ${misc:Pre-Depends} +Replaces: libmia-2.2-0 +Breaks: libmia-2.2-0, + libmia-2.2-0-dbg Description: library for 2D and 3D gray scale image processing libmia comprises a set of libraries and plug-ins for general purpose 2D and 3D gray scale image processing and basic handling of triangular meshes. The libraries provide a basic infrastructure and generic algorithms, that can be specialized by specifying the apropriate plug-ins. -Package: libmia-2.2-0-dbg +Package: libmia-2.2-4-dbg Architecture: any Section: debug Priority: extra -Depends: libmia-2.2-0 (= ${binary:Version}), +Depends: libmia-2.2-4 (= ${binary:Version}), ${misc:Depends} +Replaces: libmia-2.2-0-dbg +Breaks: libmia-2.2-0-dbg Description: Debug information for the MIA library libmia comprises a set of libraries and plug.ins for general purpose 2D and 3D gray scale image processing and basic handling of triangular @@ -106,7 +108,7 @@ Description: Debug information for the MIA library Package: mia-tools Architecture: any -Depends: libmia-2.2-0 (= ${binary:Version}), +Depends: libmia-2.2-4 (= ${binary:Version}), ${shlibs:Depends}, ${misc:Depends} Recommends: mia-tools-doc diff --git a/debian/libmia-2.2-0.install b/debian/libmia-2.2-4.install similarity index 100% rename from debian/libmia-2.2-0.install rename to debian/libmia-2.2-4.install diff --git a/debian/libmia-2.2-0.lintian-overrides b/debian/libmia-2.2-4.lintian-overrides similarity index 70% rename from debian/libmia-2.2-0.lintian-overrides rename to debian/libmia-2.2-4.lintian-overrides index afe279c..9beabe0 100644 --- a/debian/libmia-2.2-0.lintian-overrides +++ b/debian/libmia-2.2-4.lintian-overrides @@ -1,22 +1,22 @@ # #The package provides multiple libraries, which means no unique soname can be given # -libmia-2.2-0 binary: package-name-doesnt-match-sonames +libmia-2.2-4 binary: package-name-doesnt-match-sonames # # The SOURCE_FORTIFY=2 flag is used, but in many cases the compiler is just good enough # to detect that fortification is not needed # -libmia-2.2-0 binary: hardening-no-fortify-functions +libmia-2.2-4 binary: hardening-no-fortify-functions # # Since the symbols will differ greatly between 32 bit and 64 bit builds a symbols file # would have to be provided for each arch # -libmia-2.2-0 binary: no-symbols-control-file +libmia-2.2-4 binary: no-symbols-control-file # # The libray command line parser is designed to call exit if a help # option was given. # -libmia-2.2-0 binary: shlib-calls-exit +libmia-2.2-4 binary: shlib-calls-exit diff --git a/debian/patches/01_disable-treeview-for-jquery-compatibility.patch b/debian/patches/01_disable-treeview-for-jquery-compatibility.patch index a899b21..d5231ba 100644 --- a/debian/patches/01_disable-treeview-for-jquery-compatibility.patch +++ b/debian/patches/01_disable-treeview-for-jquery-compatibility.patch @@ -24,3 +24,4 @@ Last-Update: 2012-12-11 TREEVIEW_WIDTH = 250 GENERATE_LATEX = NO LATEX_OUTPUT = + diff --git a/debian/patches/02-manpage-correction.patch b/debian/patches/02-manpage-correction.patch deleted file mode 100644 index b5af0e3..0000000 --- a/debian/patches/02-manpage-correction.patch +++ /dev/null @@ -1,37 +0,0 @@ -Description: Correct the lintian warnings abut man page problems - Correct some help examples to silence manpage warnings that are - reported by lintian. - . -Author: Gert Wollny <[email protected]> - ---- -The information above should follow the Patch Tagging Guidelines, please -checkout http://dep.debian.net/deps/dep3/ to learn about the format. Here -are templates for supplementary fields that you might want to add: - -Origin: upstream -Forwarded: not-needed -Last-Update: 2015-01-08 - ---- mia-2.2.3.orig/src/2dmulti-force.cc -+++ mia-2.2.3/src/2dmulti-force.cc -@@ -38,7 +38,7 @@ const SProgramDescription g_description - "The input images must be of the same dimensions and gray scale (whatever bit-depth)."}, - {pdi_example_descr, "Evaluate the force normimage weighted sum of costs SSD and NGF of " - "image1.v and image2.v. and store the result to force.v."}, -- {pdi_example_code, "-o force.v image:cost=ssd,src=image1.v,ref=image2.v,weight=0.1 " -+ {pdi_example_code, "-o force.v \n image:cost=ssd,src=image1.v,ref=image2.v,weight=0.1\n " - "image:cost=ngf,src=image1.v,ref=image2.v,weight=2.0"} - }; - ---- mia-2.2.3.orig/src/2dmultiimageregistration.cc -+++ mia-2.2.3/src/2dmultiimageregistration.cc -@@ -47,7 +47,7 @@ const SProgramDescription g_description - "Use two multiresolution levels, ssd as image cost function and divcurl weighted by 10.0 " - "as transformation smoothness penalty. The resulting transformation is saved in reg.vf."}, - -- {pdi_example_code, "-o reg.vf -l 2 -f spline:rate=3,penalty=divcurl image:cost=ssd,src=test.v,ref=ref.v"} -+ {pdi_example_code, "-o reg.vf -l 2\n -f spline:rate=3,penalty=divcurl\n image:cost=ssd,src=test.v,ref=ref.v"} - }; - - diff --git a/debian/patches/02_correct_build_dependencies.patch b/debian/patches/02_correct_build_dependencies.patch new file mode 100644 index 0000000..72c3b38 --- /dev/null +++ b/debian/patches/02_correct_build_dependencies.patch @@ -0,0 +1,43 @@ +diff --git a/src/fluid2d/CMakeLists.txt b/src/fluid2d/CMakeLists.txt +index e4962d8..99f345a 100644 +--- a/src/fluid2d/CMakeLists.txt ++++ b/src/fluid2d/CMakeLists.txt +@@ -20,6 +20,7 @@ SET(fluid2d_SOURCES main.cc vfluid.cc elast.cc helpers.cc) + + ADD_EXECUTABLE(mia-2dfluid ${fluid2d_SOURCES}) + TARGET_LINK_LIBRARIES(mia-2dfluid mia2d) ++ADD_DEPENDENCIES(mia-2dfluid plugin_test_links) + MIA_EXE_CREATE_DOCU_AND_INTERFACE(mia 2dfluid) + + INSTALL(TARGETS mia-2dfluid RUNTIME DESTINATION "bin") +diff --git a/src/fluid3d/CMakeLists.txt b/src/fluid3d/CMakeLists.txt +index cfee179..45bac96 100644 +--- a/src/fluid3d/CMakeLists.txt ++++ b/src/fluid3d/CMakeLists.txt +@@ -27,7 +27,7 @@ ADD_DEFINITIONS(-DVSTREAM_DOMAIN=\"fluid3d\") + ADD_EXECUTABLE(mia-3dfluid ${fluid3d_SOURCES}) + TARGET_LINK_LIBRARIES(mia-3dfluid mia3d) + INSTALL(TARGETS mia-3dfluid RUNTIME DESTINATION "bin") +- ++ADD_DEPENDENCIES(mia-2dfluid plugin_test_links) + MIA_EXE_CREATE_DOCU_AND_INTERFACE(mia 3dfluid) + + +diff --git a/src/isosurface/CMakeLists.txt b/src/isosurface/CMakeLists.txt +index de416b2..1ed6682 100644 +--- a/src/isosurface/CMakeLists.txt ++++ b/src/isosurface/CMakeLists.txt +@@ -38,11 +38,13 @@ IF(GTS_FOUND) + + # add the ISO-surface programs + ADD_EXECUTABLE(mia-3disosurface-from-volume iso.cc) ++ ADD_DEPENDENCIES(mia-3disosurface-from-volume plugin_test_links) + MIA_EXE_CREATE_DOCU_AND_INTERFACE(mia 3disosurface-from-volume) + TARGET_LINK_LIBRARIES(mia-3disosurface-from-volume miagts) + INSTALL(TARGETS mia-3disosurface-from-volume RUNTIME DESTINATION "bin") + + ADD_EXECUTABLE(mia-3disosurface-from-stack iso_from_slices.cc) ++ ADD_DEPENDENCIES(mia-3disosurface-from-stack plugin_test_links) + MIA_EXE_CREATE_DOCU_AND_INTERFACE(mia 3disosurface-from-stack) + TARGET_LINK_LIBRARIES(mia-3disosurface-from-stack miagts) + INSTALL(TARGETS mia-3disosurface-from-stack RUNTIME DESTINATION "bin") diff --git a/debian/patches/03_correct_instaciation_of_default_3Dvectorfield_constructor.patch b/debian/patches/03_correct_instaciation_of_default_3Dvectorfield_constructor.patch deleted file mode 100644 index cdb5ebe..0000000 --- a/debian/patches/03_correct_instaciation_of_default_3Dvectorfield_constructor.patch +++ /dev/null @@ -1,20 +0,0 @@ -Description: correct instanciation of 3DVectorfield constructor - It seems that the instanciation behaviour changed for defaulted - constructors in templates changed with the latest g++. This patch - now implements the constructor. -Author: Gert Wollny <[email protected]> -Origin: upstream -Forwarded: not-needed -Last-Update: 2015-05-29 - ---- mia-2.2.3.orig/mia/3d/vectorfield.hh -+++ mia-2.2.3/mia/3d/vectorfield.hh -@@ -39,7 +39,7 @@ extern template class EXPORT_3D T3DDataf - template <typename T> - class T3DVectorfield: public T3DDatafield<T>, public CAttributedData { - public: -- T3DVectorfield() = default; -+ T3DVectorfield(){}; - T3DVectorfield(const T3DVectorfield<T>& org): - T3DDatafield<T>(org), - CAttributedData(org) diff --git a/debian/patches/04_correct_flag_outstream.patch b/debian/patches/04_correct_flag_outstream.patch deleted file mode 100644 index c1813c1..0000000 --- a/debian/patches/04_correct_flag_outstream.patch +++ /dev/null @@ -1,21 +0,0 @@ -Description: Remove the os from the stream chain. - This was a bug anyway and with g++-5 it finally shows up as compile error -Author: Gert Wollny <[email protected]> -Origin: upstream -Forwarded: not-needed -Bug-Debian: http://bugs.debian.org/778005 -Last-Update: 2015-05-29 - -diff --git a/mia/core/cmdlineparser.cc b/mia/core/cmdlineparser.cc -index 452084c..33a6bcc 100644 ---- a/mia/core/cmdlineparser.cc -+++ b/mia/core/cmdlineparser.cc -@@ -854,7 +854,7 @@ void CCmdFlagOption::do_write_value(std::ostream& os) const - - void CCmdFlagOption::do_get_long_help(std::ostream& os) const - { -- os << " supported flags:(" <<m_map.get_flagnames() << os << ")"; -+ os << " supported flags:(" <<m_map.get_flagnames() << ")"; - } - - const std::string CCmdFlagOption::do_get_value_as_string() const diff --git a/debian/patches/05_remove_timestamp_from_doxygen_output.patch b/debian/patches/05_remove_timestamp_from_doxygen_output.patch deleted file mode 100644 index 05329c8..0000000 --- a/debian/patches/05_remove_timestamp_from_doxygen_output.patch +++ /dev/null @@ -1,17 +0,0 @@ -Description: Remove time stamp from Doxygen generated docu - This is needed for reproducible builds. -Author: Gert Wollny <[email protected]> -Origin: upstream -Forwarded: not-needed -Last-Update: 2015-05-29 - -diff --git a/doc/reference.dox.cmake b/doc/reference.dox.cmake -index 7a581bc..37da51c 100644 ---- a/doc/reference.dox.cmake -+++ b/doc/reference.dox.cmake -@@ -152,4 +152,4 @@ DOT_CLEANUP = YES - SEARCHENGINE = NO - SHOW_NAMESPACES = NO - DOT_GRAPH_MAX_NODES = 100 -- -+HTML_TIMESTAMP = NO diff --git a/debian/patches/series b/debian/patches/series index 9c64088..8f686eb 100644 --- a/debian/patches/series +++ b/debian/patches/series @@ -1,5 +1,2 @@ 01_disable-treeview-for-jquery-compatibility.patch -02-manpage-correction.patch -03_correct_instaciation_of_default_3Dvectorfield_constructor.patch -04_correct_flag_outstream.patch -05_remove_timestamp_from_doxygen_output.patch +02_correct_build_dependencies.patch diff --git a/debian/rules b/debian/rules index 2f632a9..3e17641 100755 --- a/debian/rules +++ b/debian/rules @@ -29,7 +29,7 @@ override_dh_strip: `pwd`/debian/run_strip override_dh_shlibdeps: - dh_shlibdeps -- $(shell find debian/libmia-2.2-0/ -name "*.mia") + dh_shlibdeps -- $(shell find debian/libmia-2.2-4/ -name "*.mia") override_dh_auto_test: dh_auto_test || \ diff --git a/debian/run_strip b/debian/run_strip index 9a26b1b..04edaaa 100755 --- a/debian/run_strip +++ b/debian/run_strip @@ -1,5 +1,5 @@ #!/bin/bash for f in $(find . -name "*.mia"); do chmod 755 $f; done -/usr/bin/dh_strip -plibmia-2.2-0 --dbg-package=libmia-2.2-0-dbg +/usr/bin/dh_strip -plibmia-2.2-4 --dbg-package=libmia-2.2-4-dbg /usr/bin/dh_strip -pmia-tools --dbg-package=mia-tools-dbg for f in $(find . -name "*.mia"); do chmod 644 $f; done diff --git a/doc/reference.dox.cmake b/doc/reference.dox.cmake index de00502..6b1f595 100644 --- a/doc/reference.dox.cmake +++ b/doc/reference.dox.cmake @@ -153,8 +153,5 @@ SEARCHENGINE = NO SHOW_NAMESPACES = NO DOT_GRAPH_MAX_NODES = 100 HTML_TIMESTAMP = NO -<<<<<<< HEAD -======= ->>>>>>> upstream/2.2.4 diff --git a/src/fluid2d/CMakeLists.txt b/src/fluid2d/CMakeLists.txt index e4962d8..99f345a 100644 --- a/src/fluid2d/CMakeLists.txt +++ b/src/fluid2d/CMakeLists.txt @@ -20,6 +20,7 @@ SET(fluid2d_SOURCES main.cc vfluid.cc elast.cc helpers.cc) ADD_EXECUTABLE(mia-2dfluid ${fluid2d_SOURCES}) TARGET_LINK_LIBRARIES(mia-2dfluid mia2d) +ADD_DEPENDENCIES(mia-2dfluid plugin_test_links) MIA_EXE_CREATE_DOCU_AND_INTERFACE(mia 2dfluid) INSTALL(TARGETS mia-2dfluid RUNTIME DESTINATION "bin") diff --git a/src/fluid3d/CMakeLists.txt b/src/fluid3d/CMakeLists.txt index cfee179..45bac96 100644 --- a/src/fluid3d/CMakeLists.txt +++ b/src/fluid3d/CMakeLists.txt @@ -27,7 +27,7 @@ ADD_DEFINITIONS(-DVSTREAM_DOMAIN=\"fluid3d\") ADD_EXECUTABLE(mia-3dfluid ${fluid3d_SOURCES}) TARGET_LINK_LIBRARIES(mia-3dfluid mia3d) INSTALL(TARGETS mia-3dfluid RUNTIME DESTINATION "bin") - +ADD_DEPENDENCIES(mia-2dfluid plugin_test_links) MIA_EXE_CREATE_DOCU_AND_INTERFACE(mia 3dfluid) diff --git a/src/isosurface/CMakeLists.txt b/src/isosurface/CMakeLists.txt index de416b2..1ed6682 100644 --- a/src/isosurface/CMakeLists.txt +++ b/src/isosurface/CMakeLists.txt @@ -38,11 +38,13 @@ IF(GTS_FOUND) # add the ISO-surface programs ADD_EXECUTABLE(mia-3disosurface-from-volume iso.cc) + ADD_DEPENDENCIES(mia-3disosurface-from-volume plugin_test_links) MIA_EXE_CREATE_DOCU_AND_INTERFACE(mia 3disosurface-from-volume) TARGET_LINK_LIBRARIES(mia-3disosurface-from-volume miagts) INSTALL(TARGETS mia-3disosurface-from-volume RUNTIME DESTINATION "bin") ADD_EXECUTABLE(mia-3disosurface-from-stack iso_from_slices.cc) + ADD_DEPENDENCIES(mia-3disosurface-from-stack plugin_test_links) MIA_EXE_CREATE_DOCU_AND_INTERFACE(mia 3disosurface-from-stack) TARGET_LINK_LIBRARIES(mia-3disosurface-from-stack miagts) INSTALL(TARGETS mia-3disosurface-from-stack RUNTIME DESTINATION "bin") -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/mia.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
