[med-svn] [mia] 04/06: remove all patches and correct install files
Gert Wollny
gert-guest at moszumanska.debian.org
Sat Jul 23 14:52:58 UTC 2016
This is an automated email from the git hooks/post-receive script.
gert-guest pushed a commit to branch master
in repository mia.
commit 13908a9cf4def3f486429746856477c7f5907c05
Author: Gert Wollny <gw.fossdev at gmail.com>
Date: Sat Jul 23 14:35:19 2016 +0000
remove all patches and correct install files
---
debian/libmia-2.4-0.install | 2 +-
debian/libmia-2.4-0.lintian-overrides | 8 +-
debian/libmia-2.4-dev.install | 2 +-
debian/libmia-2.4-dev.lintian-overrides | 2 +-
debian/libmia-2.4-doc.doc-base | 4 +-
debian/libmia-2.4-doc.install | 2 +-
debian/libmia-2.4-doc.lintian-overrides | 2 +-
debian/mia-tools-doc.doc-base | 4 +-
debian/mia-tools-doc.install | 2 +-
debian/patches/01_spellcheck_corrections.patch | 73 ------------
.../02_accumulate-not-declared-mia-2.2.7.patch | 118 --------------------
debian/patches/03_fix-boost1.60_mia-2.2.7.patch | 123 ---------------------
debian/patches/04_add_userdoc_flag.patch | 51 ---------
debian/patches/series | 4 -
debian/run_strip | 2 +-
15 files changed, 15 insertions(+), 384 deletions(-)
diff --git a/debian/libmia-2.4-0.install b/debian/libmia-2.4-0.install
index 8f445d7..2561890 100644
--- a/debian/libmia-2.4-0.install
+++ b/debian/libmia-2.4-0.install
@@ -1,2 +1,2 @@
usr/lib/*/lib*.so.*
-usr/lib/*/mia-2.2/plugins/*
+usr/lib/*/mia-2.4/plugins/*
diff --git a/debian/libmia-2.4-0.lintian-overrides b/debian/libmia-2.4-0.lintian-overrides
index 9beabe0..ce6cf83 100644
--- a/debian/libmia-2.4-0.lintian-overrides
+++ b/debian/libmia-2.4-0.lintian-overrides
@@ -1,22 +1,22 @@
#
#The package provides multiple libraries, which means no unique soname can be given
#
-libmia-2.2-4 binary: package-name-doesnt-match-sonames
+libmia-2.4-0 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-2.2-4 binary: hardening-no-fortify-functions
+libmia-2.4-0 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-2.2-4 binary: no-symbols-control-file
+libmia-2.4-0 binary: no-symbols-control-file
#
# The libray command line parser is designed to call exit if a help
# option was given.
#
-libmia-2.2-4 binary: shlib-calls-exit
+libmia-2.4-0 binary: shlib-calls-exit
diff --git a/debian/libmia-2.4-dev.install b/debian/libmia-2.4-dev.install
index 7b9cf62..fd7d648 100644
--- a/debian/libmia-2.4-dev.install
+++ b/debian/libmia-2.4-dev.install
@@ -1,5 +1,5 @@
usr/include/*
usr/lib/*/lib*.so
-usr/lib/*/mia-2.2/include/*
+usr/lib/*/mia-2.4/include/*
usr/lib/*/pkgconfig/*
usr/share/mia-doctools/*
diff --git a/debian/libmia-2.4-dev.lintian-overrides b/debian/libmia-2.4-dev.lintian-overrides
index ac0530f..e7383c5 100644
--- a/debian/libmia-2.4-dev.lintian-overrides
+++ b/debian/libmia-2.4-dev.lintian-overrides
@@ -5,5 +5,5 @@
# use the package.
# python-lxml is suggested instead.
#
-libmia-2.2-dev binary: python-script-but-no-python-dep
+libmia-2.4-dev binary: python-script-but-no-python-dep
diff --git a/debian/libmia-2.4-doc.doc-base b/debian/libmia-2.4-doc.doc-base
index 9a38d7a..febf755 100644
--- a/debian/libmia-2.4-doc.doc-base
+++ b/debian/libmia-2.4-doc.doc-base
@@ -5,5 +5,5 @@ Abstract: This is the Doxygen reference of the MIA libraries
Section: Programming/libraries
Format: HTML
-Index: /usr/share/doc/mia-2.2/libdoc/index.html
-Files: /usr/share/doc/mia-2.2/libdoc/*.html
+Index: /usr/share/doc/mia-2.4/libdoc/index.html
+Files: /usr/share/doc/mia-2.4/libdoc/*.html
diff --git a/debian/libmia-2.4-doc.install b/debian/libmia-2.4-doc.install
index 8814815..d7248d5 100644
--- a/debian/libmia-2.4-doc.install
+++ b/debian/libmia-2.4-doc.install
@@ -1,2 +1,2 @@
-usr/share/doc/mia-2.2/libdoc/*
+usr/share/doc/mia-2.4/libdoc/*
diff --git a/debian/libmia-2.4-doc.lintian-overrides b/debian/libmia-2.4-doc.lintian-overrides
index 78a643f..8bde424 100644
--- a/debian/libmia-2.4-doc.lintian-overrides
+++ b/debian/libmia-2.4-doc.lintian-overrides
@@ -2,4 +2,4 @@
# by the one provided by libjs-jquery.
# For a rationale please see src::Doxygen/debian/README.jquery.
-libmia-2.2-doc binary: embedded-javascript-library
+libmia-2.4-doc binary: embedded-javascript-library
diff --git a/debian/mia-tools-doc.doc-base b/debian/mia-tools-doc.doc-base
index cd7f723..88ce366 100644
--- a/debian/mia-tools-doc.doc-base
+++ b/debian/mia-tools-doc.doc-base
@@ -5,5 +5,5 @@ Abstract: This is the reference for the MIA command line tools and plug-ins
Section: Science/Medicine
Format: HTML
-Index: /usr/share/doc/mia-2.2/userref/index.html
-Files: /usr/share/doc/mia-2.2/userref/*.html
+Index: /usr/share/doc/mia-2.4/userref/index.html
+Files: /usr/share/doc/mia-2.4/userref/*.html
diff --git a/debian/mia-tools-doc.install b/debian/mia-tools-doc.install
index 01f80e3..0e9ddd1 100644
--- a/debian/mia-tools-doc.install
+++ b/debian/mia-tools-doc.install
@@ -1 +1 @@
-usr/share/doc/mia-2.2/userref/*
+usr/share/doc/mia-2.4/userref/*
diff --git a/debian/patches/01_spellcheck_corrections.patch b/debian/patches/01_spellcheck_corrections.patch
deleted file mode 100644
index 9e7c7a2..0000000
--- a/debian/patches/01_spellcheck_corrections.patch
+++ /dev/null
@@ -1,73 +0,0 @@
-Description: Correct some spellings
-Author: Gert Wollny <gw.fossdev at gmail.com>
-
-Origin: upstream
-Forwarded: not-needed
-Last-Update: 2015-11-24
-
---- a/mia/2d/filter/thresh.cc
-+++ b/mia/2d/filter/thresh.cc
-@@ -70,7 +70,7 @@ C2DThreshNImageFilterFactory::C2DThreshNImageFilterFactory():
- m_thresh(5.0)
- {
- add_parameter("shape", make_param(m_shape, "4n", false, "neighborhood shape to take into account"));
-- add_parameter("thresh", make_param(m_thresh, false, "The threshhold value"));
-+ add_parameter("thresh", make_param(m_thresh, false, "The threshold value"));
- }
-
- C2DFilter *C2DThreshNImageFilterFactory::do_create()const
-@@ -80,8 +80,8 @@ C2DFilter *C2DThreshNImageFilterFactory::do_create()const
-
- const std::string C2DThreshNImageFilterFactory::do_get_descr() const
- {
-- return "This filter sets all pixels of an image to zero that fall below a certain threshhold and "
-- "whose neighbours in a given neighborhood shape also fall below a this threshhold";
-+ return "This filter sets all pixels of an image to zero that fall below a certain threshold and "
-+ "whose neighbours in a given neighborhood shape also fall below a this threshold";
- }
-
- extern "C" EXPORT CPluginBase *get_plugin_interface()
---- mia-2.2.7.orig/mia/template/watershed.hh
-+++ mia-2.2.7/mia/template/watershed.hh
-@@ -323,7 +323,7 @@ TWatershedFilterPlugin<dim>::TWatershedF
- this->add_parameter("n", make_param(m_neighborhood, "sphere:r=1", false, "Neighborhood for watershead region growing"));
- this->add_parameter("mark", new mia::CBoolParameter(m_with_borders, false, "Mark the segmented watersheds with a special gray scale value"));
- this->add_parameter("thresh", make_coi_param(m_thresh, 0, 1.0, false, "Relative gradient norm threshold. The actual value "
-- "threshhold value is thresh * (max_grad - min_grad) + min_grad. Bassins "
-+ "threshold value is thresh * (max_grad - min_grad) + min_grad. Bassins "
- "separated by gradients with a lower norm will be joined"));
- this->add_parameter("evalgrad", new mia::CBoolParameter(m_eval_grad, false, "Set to 1 if the input image does "
- "not represent a gradient norm image"));
---- mia-2.2.7.orig/src/2dgroundtruthreg.cc
-+++ mia-2.2.7/src/2dgroundtruthreg.cc
-@@ -166,7 +166,7 @@ int do_main( int argc, char *argv[] )
- options.add(make_opt( pgt_params.beta, "beta", 'B', "temporal second derivative penalty weight",
- CCmdOptionFlags::required));
- options.add(make_opt( pgt_params.rho_thresh, "rho_thresh", 'R',
-- "crorrelation threshhold for neighborhood analysis", CCmdOptionFlags::required));
-+ "correlation threshold for neighborhood analysis", CCmdOptionFlags::required));
-
-
-
---- mia-2.2.7.orig/src/2dmyoicapgt.cc
-+++ mia-2.2.7/src/2dmyoicapgt.cc
-@@ -480,7 +480,7 @@ int do_main( int argc, char *argv[] )
- options.add(make_opt( pgt_alpha, "alpha", 'A', "spacial neighborhood penalty weight"));
- options.add(make_opt( pgt_beta, "beta", 'B', "temporal second derivative penalty weight"));
- options.add(make_opt( pgt_rho_thresh, "rho-thresh", 'T',
-- "crorrelation threshhold for neighborhood analysis"));
-+ "correlation threshold for neighborhood analysis"));
-
-
-
---- mia-2.2.7.orig/src/2dmyopgt-nonrigid.cc
-+++ mia-2.2.7/src/2dmyopgt-nonrigid.cc
-@@ -147,7 +147,7 @@ int do_main( int argc, char *argv[] )
- options.add(make_opt( alpha, "alpha", 'A', "spacial neighborhood penalty weight"));
- options.add(make_opt( beta, "beta", 'B', "temporal second derivative penalty weight"));
- options.add(make_opt( rho_thresh, "rho-thresh", 'R',
-- "crorrelation threshhold for neighborhood analysis"));
-+ "correlation threshold for neighborhood analysis"));
- options.add(make_opt( skip_images, "skip", 'k', "skip images at the beginning of the series "
- "e.g. because as they are of other modalities"));
-
diff --git a/debian/patches/02_accumulate-not-declared-mia-2.2.7.patch b/debian/patches/02_accumulate-not-declared-mia-2.2.7.patch
deleted file mode 100644
index 2dd6d9c..0000000
--- a/debian/patches/02_accumulate-not-declared-mia-2.2.7.patch
+++ /dev/null
@@ -1,118 +0,0 @@
-Description: Correct includes because of stricter handling by g++
-Author: Gert Wollny <gw.fossdev at gmail.com>
-
-Origin: upstream
-Forwarded: not-needed
-Last-Update: 2016-04-25
-
---- a/mia/core/waveletslopeclassifier.cc
-+++ b/mia/core/waveletslopeclassifier.cc
-@@ -20,6 +20,7 @@
-
- #include <map>
- #include <algorithm>
-+#include <numeric>
- #include <stdexcept>
- #include <cmath>
-
---- a/mia/3d/cost/ngf.cc
-+++ b/mia/3d/cost/ngf.cc
-@@ -21,6 +21,7 @@
- #include <mia/3d/cost/ngf.hh>
- #include <mia/3d/nfg.hh>
-
-+#include <numeric>
-
- NS_BEGIN(ngf_3dimage_cost)
-
---- a/mia/3d/ppmatrix.cc
-+++ b/mia/3d/ppmatrix.cc
-@@ -32,6 +32,8 @@
- #include <emmintrin.h>
- #endif
-
-+#include <numeric>
-+
- using namespace tbb;
- using namespace std;
-
---- a/mia/core/test_sparse_solver.cc
-+++ b/mia/core/test_sparse_solver.cc
-@@ -22,6 +22,7 @@
-
- #include <mia/internal/autotest.hh>
- #include <mia/core/sparse_solver.hh>
-+#include <numeric>
-
- /**
- This test only tests the general idea of the unified solver class, and
---- a/src/2dmyocard-segment.cc
-+++ b/src/2dmyocard-segment.cc
-@@ -43,6 +43,8 @@
- #include <mia/2d/transformfactory.hh>
- #include <mia/2d/datafield.cxx>
-
-+#include <numeric>
-+
- NS_MIA_USE;
- using namespace std;
-
---- a/src/2dsegment-fuzzyw.cc
-+++ b/src/2dsegment-fuzzyw.cc
-@@ -29,6 +29,7 @@
-
- #include <memory>
- #include <vector>
-+#include <numeric>
-
- using namespace mia;
- using namespace std;
---- a/src/2dseries-segdistance.cc
-+++ b/src/2dseries-segdistance.cc
-@@ -37,6 +37,8 @@
- #include <mia/2d/imageio.hh>
- #include <mia/2d/filter.hh>
-
-+#include <numeric>
-+
- using namespace std;
- using namespace mia;
- using xmlpp::DomParser;
---- a/src/wavelettrans.cc
-+++ b/src/wavelettrans.cc
-@@ -20,6 +20,7 @@
-
- #define VSTREAM_DOMAIN "wavelet"
-
-+#include <cmath>
- #include <fstream>
- #include <sstream>
- #include <iostream>
---- a/mia/core/test_slopestatistics.cc
-+++ b/mia/core/test_slopestatistics.cc
-@@ -19,12 +19,11 @@
- */
-
- #include <mia/internal/autotest.hh>
-+#include <mia/core/slopestatistics.hh>
-
- #include <stdexcept>
- #include <cmath>
--
--#include <mia/core/slopestatistics.hh>
--
-+#include <numeric>
-
- using namespace std;
- NS_MIA_USE
---- a/test/test_minimizer.cc
-+++ b/test/test_minimizer.cc
-@@ -27,7 +27,7 @@
- #include <mia/core/minimizer.hh>
- #include <mia/core/cmdlineparser.hh>
- #include <mia/core/msgstream.hh>
--
-+#include <numeric>
-
-
- using namespace std;
diff --git a/debian/patches/03_fix-boost1.60_mia-2.2.7.patch b/debian/patches/03_fix-boost1.60_mia-2.2.7.patch
deleted file mode 100644
index dfb6369..0000000
--- a/debian/patches/03_fix-boost1.60_mia-2.2.7.patch
+++ /dev/null
@@ -1,123 +0,0 @@
-Description: BOOST_MESSAGE has been renamed in BOOST_TEST_MESSAGE now.
-Author: Gianfranco Costamagna <locutusofborg at debian.org>
-
---- a/mia/3d/test_nonrigidregister.cc
-+++ b/mia/3d/test_nonrigidregister.cc
-@@ -36,7 +36,7 @@
-
- BOOST_AUTO_TEST_CASE ( test_nothing )
- {
-- BOOST_MESSAGE("This is a placeholder");
-+ BOOST_TEST_MESSAGE("This is a placeholder");
- }
-
- #if 0
---- a/mia/3d/test_vector.cc
-+++ b/mia/3d/test_vector.cc
-@@ -119,7 +119,7 @@
- BOOST_FAIL("error value not detected");
- }
- catch (invalid_argument& x) {
-- BOOST_MESSAGE(string("Caught:") + string(x.what()));
-+ BOOST_TEST_MESSAGE(string("Caught:") + string(x.what()));
- }
- }
-
-@@ -144,7 +144,7 @@
- BOOST_FAIL("error value not detected");
- }
- catch (invalid_argument& x) {
-- BOOST_MESSAGE(string("Caught:") + string(x.what()));
-+ BOOST_TEST_MESSAGE(string("Caught:") + string(x.what()));
- }
- }
-
---- a/mia/core/test_cmdlineparser.cc
-+++ b/mia/core/test_cmdlineparser.cc
-@@ -77,7 +77,7 @@
- BOOST_FAIL("error value not detected");
- }
- catch (invalid_argument& x) {
-- BOOST_MESSAGE(string("Caught:") + string(x.what()));
-+ BOOST_TEST_MESSAGE(string("Caught:") + string(x.what()));
- }
- }
-
-@@ -161,7 +161,7 @@
- BOOST_FAIL("error value not detected");
- }
- catch (invalid_argument& x) {
-- BOOST_MESSAGE(string("Caught:") + string(x.what()));
-+ BOOST_TEST_MESSAGE(string("Caught:") + string(x.what()));
- }
- }
-
-@@ -187,7 +187,7 @@
- BOOST_FAIL("error value not detected");
- }
- catch (invalid_argument& x) {
-- BOOST_MESSAGE(string("Caught:") + string(x.what()));
-+ BOOST_TEST_MESSAGE(string("Caught:") + string(x.what()));
- }
- }
-
-@@ -295,7 +295,7 @@
- BOOST_CHECK_EQUAL(olist.parse(options.size(), (const char**)&options[0], "remaining"), CCmdOptionList::hr_no);
-
- for(auto i = olist.get_remaining().begin(); i != olist.get_remaining().end(); ++i)
-- BOOST_MESSAGE(*i);
-+ BOOST_TEST_MESSAGE(*i);
-
- BOOST_CHECK_EQUAL(int_value1,12);
- BOOST_CHECK_EQUAL(int_value2,13);
---- a/mia/core/test_core.cc
-+++ b/mia/core/test_core.cc
-@@ -64,7 +64,7 @@
- BOOST_FAIL("'this-file-should-not-exist.11111' was opened for reading");
- }
- catch (runtime_error& x) {
-- BOOST_MESSAGE(string("caught an expected exception:") + x.what());
-+ BOOST_TEST_MESSAGE(string("caught an expected exception:") + x.what());
- }
-
- try {
-@@ -73,7 +73,7 @@
- }
-
- catch (runtime_error& x) {
-- BOOST_MESSAGE(string("caught an expected exception:") + x.what());
-+ BOOST_TEST_MESSAGE(string("caught an expected exception:") + x.what());
- }
- }
-
---- a/mia/core/test_optparam.cc
-+++ b/mia/core/test_optparam.cc
-@@ -125,7 +125,7 @@
- }
- catch (invalid_argument& x) {
- // it should throw ...
-- BOOST_MESSAGE(x.what());
-+ BOOST_TEST_MESSAGE(x.what());
- }
-
- }
-@@ -140,7 +140,7 @@
- }
- catch (invalid_argument& x) {
- // it should throw ...
-- BOOST_MESSAGE(x.what());
-+ BOOST_TEST_MESSAGE(x.what());
- }
- }
-
---- a/cmake/macros.cmake
-+++ b/cmake/macros.cmake
-@@ -210,7 +210,7 @@
-
- MIA_EXE_CREATE_DOCU_AND_INTERFACE(mia ${name})
- ADD_DEPENDENCIES(mia-${name} plugin_test_links)
-- ADD_TEST(${name} mia-${name} --selftest)
-+ ADD_TEST(${name} mia-${name} -- --selftest)
- ENDMACRO(DEFCHKEXE)
-
-
diff --git a/debian/patches/04_add_userdoc_flag.patch b/debian/patches/04_add_userdoc_flag.patch
deleted file mode 100644
index 4ac0b7d..0000000
--- a/debian/patches/04_add_userdoc_flag.patch
+++ /dev/null
@@ -1,51 +0,0 @@
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -78,6 +78,7 @@
- OPTION(ALWAYS_CREATE_DOC "Create all documentation during the normal build process (normally you need to run 'make doc')" TRUE)
- OPTION(BUILD_EXAMPLES "Build example plug-ins and programs" FALSE)
- OPTION(ENABLE_DEBUG_MESSAGES "Enable debug and trace outputs" TRUE)
-+OPTION(MIA_CREATE_USERDOC "Enable creation of html user documentation" TRUE)
-
- INCLUDE(GNUInstallDirs)
-
-@@ -451,13 +452,18 @@
- #
- # python is needed for creating end-user documentation
- #
--SET(CREATE_USERDOC FALSE)
-+
-
- FIND_PACKAGE(PythonInterp)
- IF(PYTHONINTERP_FOUND)
- EXECUTE_PROCESS(COMMAND ${PYTHON_EXECUTABLE} -c "import lxml" RESULT_VARIABLE LXML_ERR)
- IF(LXML_ERR)
-- MESSAGE(python found, but no lxml, no user documantation will be created)
-+ IF(STRICT_DEPENDECIES)
-+ MESSAGE(ERROR ": requested user Html documentation creation, but python-lxml not found")
-+ ELSE(STRICT_DEPENDECIES)
-+ MESSAGE(python found, but no lxml, no user documantation will be created)
-+ SET(MIA_CREATE_USERDOC FALSE)
-+ ENDIF(STRICT_DEPENDECIES)
- ELSE(LXML_ERR)
- SET(CREATE_USERDOC TRUE)
- ENDIF(LXML_ERR)
---- a/doc/CMakeLists.txt
-+++ b/doc/CMakeLists.txt
-@@ -41,7 +41,7 @@
- INSTALL(PROGRAMS ${MIADOCTOOLS_PYTHON_EXE} DESTINATION ${MIA_DOCTOOLS_INSTALL_ROOT})
-
-
--IF(CREATE_USERDOC)
-+IF(MIA_CREATE_USERDOC)
-
- ##################################################################
- # for html userref xsltproc and the style sheet is needed
-@@ -107,7 +107,7 @@
- ENDIF(ALWAYS_CREATE_DOC)
- ENDIF(HTML_CHUNK_FILEPATH)
-
--ENDIF(CREATE_USERDOC)
-+ENDIF(MIA_CREATE_USERDOC)
-
- IF (DOXYGEN_FOUND)
- ADD_CUSTOM_TARGET(LibraryDoc echo "creating user library documentation")
diff --git a/debian/patches/series b/debian/patches/series
deleted file mode 100644
index d3384fa..0000000
--- a/debian/patches/series
+++ /dev/null
@@ -1,4 +0,0 @@
-01_spellcheck_corrections.patch
-02_accumulate-not-declared-mia-2.2.7.patch
-03_fix-boost1.60_mia-2.2.7.patch
-04_add_userdoc_flag.patch
diff --git a/debian/run_strip b/debian/run_strip
index af4480c..4d918f0 100755
--- a/debian/run_strip
+++ b/debian/run_strip
@@ -1,4 +1,4 @@
#!/bin/bash
for f in $(find . -name "*.mia"); do chmod 755 $f; done
-dh_strip --dbgsym-migration='libmia-2.2-4-dbg (<< 2.2.7-6), mia-tools-dbg (<< 2.2.7-6)'
+dh_strip
for f in $(find . -name "*.mia"); do chmod 644 $f; done
--
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