From f4bfd3bf46d55975fdbe111c05933b79cc347fdb Mon Sep 17 00:00:00 2001 From: Horea Christian Date: Mon, 10 Jan 2022 02:43:19 -0500 Subject: [PATCH] Fix merged in ::science https://gitweb.gentoo.org/proj/sci.git/commit/?id=3b227d5588eaac724032273e19541ee81aa53034 --- sci-libs/itk/ChangeLog | 12 -- sci-libs/itk/Manifest | 6 - ...nsformFileReader-TransformFileWriter.patch | 50 ----- ...asiNewtonOptimizerv4-wrapping-warnin.patch | 28 --- ...adientDescentOptimizerv4-wrapping-wa.patch | 73 ------- ...izerParameterScalesEstimatorTemplate.patch | 30 --- ...0005-make-gdcm-helper-library-static.patch | 11 - sci-libs/itk/files/ITKModuleRemote.patch | 45 ----- sci-libs/itk/files/itk-5.1.0-downloads.patch | 20 -- .../itk/files/itk-5.1.0-include_limits.patch | 10 - sci-libs/itk/files/nrrdio-linking.patch | 15 -- sci-libs/itk/files/tests.patch | 41 ---- sci-libs/itk/itk-5.1.0.ebuild | 191 ------------------ sci-libs/itk/metadata.xml | 24 --- 14 files changed, 556 deletions(-) delete mode 100644 sci-libs/itk/ChangeLog delete mode 100644 sci-libs/itk/Manifest delete mode 100644 sci-libs/itk/files/0001-BUG-Wrap-TransformFileReader-TransformFileWriter.patch delete mode 100644 sci-libs/itk/files/0002-COMP-Fixed-itkQuasiNewtonOptimizerv4-wrapping-warnin.patch delete mode 100644 sci-libs/itk/files/0003-COMP-Fixed-itkGradientDescentOptimizerv4-wrapping-wa.patch delete mode 100644 sci-libs/itk/files/0004-COMP-Warp-OptimizerParameterScalesEstimatorTemplate.patch delete mode 100644 sci-libs/itk/files/0005-make-gdcm-helper-library-static.patch delete mode 100644 sci-libs/itk/files/ITKModuleRemote.patch delete mode 100644 sci-libs/itk/files/itk-5.1.0-downloads.patch delete mode 100644 sci-libs/itk/files/itk-5.1.0-include_limits.patch delete mode 100644 sci-libs/itk/files/nrrdio-linking.patch delete mode 100644 sci-libs/itk/files/tests.patch delete mode 100644 sci-libs/itk/itk-5.1.0.ebuild delete mode 100644 sci-libs/itk/metadata.xml diff --git a/sci-libs/itk/ChangeLog b/sci-libs/itk/ChangeLog deleted file mode 100644 index 8f9907f..0000000 --- a/sci-libs/itk/ChangeLog +++ /dev/null @@ -1,12 +0,0 @@ -*itk-5.1.0 (09 Jan 2022) - - 09 Jan 2022; - +files/0001-BUG-Wrap-TransformFileReader-TransformFileWriter.patch, - +files/0002-COMP-Fixed-itkQuasiNewtonOptimizerv4-wrapping-warnin.patch, - +files/0003-COMP-Fixed-itkGradientDescentOptimizerv4-wrapping-wa.patch, - +files/0004-COMP-Warp-OptimizerParameterScalesEstimatorTemplate.patch, - +files/0005-make-gdcm-helper-library-static.patch, - +files/ITKModuleRemote.patch, +files/itk-5.1.0-downloads.patch, - +files/itk-5.1.0-include_limits.patch, +files/nrrdio-linking.patch, - +files/tests.patch, +itk-5.1.0.ebuild, +metadata.xml: - sci-libs/itk: trying to solve limits issue diff --git a/sci-libs/itk/Manifest b/sci-libs/itk/Manifest deleted file mode 100644 index 74570b6..0000000 --- a/sci-libs/itk/Manifest +++ /dev/null @@ -1,6 +0,0 @@ -DIST ITKGenericLabelInterpolator-5.1.0.tar.gz 140286 SHA256 84a045540f95a00e07df2123e9b9a7825ad0acece83a929639109a77e95435a1 SHA512 7bf6310e8b0ea2356ae8ce0ddd0bc3a1516aa6bb5e3e8df9ed0114f1bb2b299d2edd046f27dbae364082afc63e225a3691c794c93d347ee564db617ea3fbf489 WHIRLPOOL 0cd7bfde3d18dfbef7a798c4cbb17bf444bfab93b5b4887cdc0d244e2aef07ebe1b1af796f5f49c768af3568d3f96aed6aaaf5d23fb5553cb83b4fc6474b54fe -DIST InsightData-5.1.0.tar.gz 292322103 SHA256 777f587c587b47d76157a0ee87a5942b944742f334b801abe0e6dc1ad1d8424f SHA512 458c2959ba5e0745eee23e16ff7178230a7bae94d7dff065b3b38136e238becff96554693e3b2149d2307949c23a6c695c92676f8d44e6f7305dbb8bed48c9fa WHIRLPOOL d5785f862c627cabc97c469ac9fb84d1493e1827fd993c68ed5019e7062adc7fe68efe6ab2471c7c6b2a9d542cbfdb1a00c6633fa7be498cbc9e09fa12d3710a -DIST InsightToolkit-5.1.0.tar.gz 20694338 SHA256 121020a1611508cec8123eb5226215598cec07be627d843a2e6b6da891e61d13 SHA512 413b6ef549b59d8f507038130446ccb704794c6d0980d8ab631d1b1051cb91f399e77c26b69fab6a1e9b9bb4cc233d49996c3ee735cd4de065993d4379b4ed4c WHIRLPOOL bbe7368cc46dc1a0869d8ab47218d0777e689be17114048653a537fbe792dfc0eb0e687b06fa894218cc35ef95143df75a46c17ffd6b072233e9f72a3c811825 -DIST itk-5.1.0-test-a5e11ea71164ff78c65fcf259db01ea5db981a9d868e60045ff2bffca92984df1174bf984a1076e450f0d5d69b4f0191ed1a61465c220e2c91a893b5df150c0a 1017 SHA256 d5e1b340676b07c4d08dd8938280c8ec490620a88ae8b3d3798975ed83506985 SHA512 e69c77894cab5b295ec5edbecdf693525ec9a4673810b87cbc28646ea40888b7792b5707840069e277905c8b0014bd84ecea036836f87c3b16f388f544e34341 WHIRLPOOL 2908b4ea8ec516bbe9fd290cd5aa03262418c0028128c0d575e1b855e9dc1af2c818d6c59c879c153f5f02e67ff8cbf902a5e3076dca6dc6d7de3dce28d318bc -DIST itk-5.1.0-test-bcdbb347f3704262d1f00be7179d6a0a6e68aed56c0653e8072ee5a94985c713bd229c935b1226a658af84fb7f1fffc2458c98364fc35303a2303b12f9f7ce2f 1018 SHA256 339345972050e6fabad649438852811612b80f35626d1b88dd6361296a21b036 SHA512 27952af5d6243aa31c187280ea9ba82c434db3614b3db3b406fe8e5c7e4b7e333bc179d5d9956d5a17aa670a7aa7cfce037d37c4225125e703602e322d8ec68b WHIRLPOOL 47f28fdb11ce0444763f91f7c295f2574da04d11bc6b8fdb65fb0ac35ee97f8d8706e7a20259030bcef517c07c8e6312825ea500d2396c3547836169cdde5491 -DIST itk-5.1.0-testingdata.tar.gz 2409232372 SHA256 bac8365cb56a6c5f68e565445e00012f31453b06e8f7879bc7c3238796a67948 SHA512 8b451608cb3f75d3ba6a78fd23e79495948c2792a98d831e0f0c93745595df84d3c2a8d76389976f67ac7e7e1f5a44a18d201e51d2ee659cdb708ae28536df8f WHIRLPOOL 4c9f65bb51a0714a24db6c1e739fff32b454e0289135cd190146df0fd6dece736ff348d9aeae388dff8ce9ccc9010c979f1a6051065f92bbb0bc98c8628aab4e diff --git a/sci-libs/itk/files/0001-BUG-Wrap-TransformFileReader-TransformFileWriter.patch b/sci-libs/itk/files/0001-BUG-Wrap-TransformFileReader-TransformFileWriter.patch deleted file mode 100644 index 094ee32..0000000 --- a/sci-libs/itk/files/0001-BUG-Wrap-TransformFileReader-TransformFileWriter.patch +++ /dev/null @@ -1,50 +0,0 @@ -From d069b7b94287dae15fcaf707775f5dd2bbebcc38 Mon Sep 17 00:00:00 2001 -From: Matt McCormick -Date: Wed, 5 Feb 2014 15:52:34 -0500 -Subject: [PATCH 1/3] BUG: Wrap TransformFileReader, TransformFileWriter. - -Missing CMakeLists.txt in the wrapping directory. Need to explicitly include -the headers after "Template" was appended to the class name. - -Suggested-by: Sami Koho - -Change-Id: I6f994bb18f37d5adf1d0f0311fa73506c41239a7 ---- - Modules/IO/TransformBase/wrapping/CMakeLists.txt | 3 +++ - Modules/IO/TransformBase/wrapping/itkTransformFileReader.wrap | 2 ++ - Modules/IO/TransformBase/wrapping/itkTransformFileWriter.wrap | 2 ++ - 3 files changed, 7 insertions(+) - create mode 100644 Modules/IO/TransformBase/wrapping/CMakeLists.txt - -diff --git a/Modules/IO/TransformBase/wrapping/CMakeLists.txt b/Modules/IO/TransformBase/wrapping/CMakeLists.txt -new file mode 100644 -index 0000000..6072567 ---- /dev/null -+++ b/Modules/IO/TransformBase/wrapping/CMakeLists.txt -@@ -0,0 +1,3 @@ -+itk_wrap_module(ITKIOTransformBase) -+itk_auto_load_submodules() -+itk_end_wrap_module() -diff --git a/Modules/IO/TransformBase/wrapping/itkTransformFileReader.wrap b/Modules/IO/TransformBase/wrapping/itkTransformFileReader.wrap -index 9b52fbc..662df9e 100644 ---- a/Modules/IO/TransformBase/wrapping/itkTransformFileReader.wrap -+++ b/Modules/IO/TransformBase/wrapping/itkTransformFileReader.wrap -@@ -1,3 +1,5 @@ -+set(WRAPPER_AUTO_INCLUDE_HEADERS OFF) -+itk_wrap_include("itkTransformFileReader.h") - itk_wrap_class("itk::TransformFileReaderTemplate" POINTER) - foreach(t ${WRAP_ITK_REAL}) - itk_wrap_template("${ITKM_${t}}" "${ITKT_${t}}") -diff --git a/Modules/IO/TransformBase/wrapping/itkTransformFileWriter.wrap b/Modules/IO/TransformBase/wrapping/itkTransformFileWriter.wrap -index 4f1ac4a..356aaf3 100644 ---- a/Modules/IO/TransformBase/wrapping/itkTransformFileWriter.wrap -+++ b/Modules/IO/TransformBase/wrapping/itkTransformFileWriter.wrap -@@ -1,3 +1,5 @@ -+set(WRAPPER_AUTO_INCLUDE_HEADERS OFF) -+itk_wrap_include("itkTransformFileWriter.h") - itk_wrap_class("itk::TransformFileWriterTemplate" POINTER) - foreach(t ${WRAP_ITK_REAL}) - itk_wrap_template("${ITKM_${t}}" "${ITKT_${t}}") --- -1.8.5.3 - diff --git a/sci-libs/itk/files/0002-COMP-Fixed-itkQuasiNewtonOptimizerv4-wrapping-warnin.patch b/sci-libs/itk/files/0002-COMP-Fixed-itkQuasiNewtonOptimizerv4-wrapping-warnin.patch deleted file mode 100644 index 4c74d54..0000000 --- a/sci-libs/itk/files/0002-COMP-Fixed-itkQuasiNewtonOptimizerv4-wrapping-warnin.patch +++ /dev/null @@ -1,28 +0,0 @@ -From 66d2955fbe5528d9df216c639277d1d2686447e5 Mon Sep 17 00:00:00 2001 -From: Michka Popoff -Date: Fri, 7 Feb 2014 19:24:49 +0100 -Subject: [PATCH 2/3] COMP: Fixed itkQuasiNewtonOptimizerv4 wrapping warnings - -The warning : -/scratch/dashboards/Linux-x86_64-gcc4.4-WrapITK/ITK-build/Wrapping/Modules/ITKOptimizersv4/itkQuasiNewtonOptimizerv4.xml: warning(5): Unknown type type: itk::QuasiNewtonOptimizerv4 [typedef] -/scratch/dashboards/Linux-x86_64-gcc4.4-WrapITK/ITK-build/Wrapping/Modules/ITKOptimizersv4/itkQuasiNewtonOptimizerv4.xml: warning(4): ITK type not wrapped, or currently not known: itk::QuasiNewtonOptimizerv4Template< double > ---- - .../Numerics/Optimizersv4/wrapping/itkQuasiNewtonOptimizerv4.wrap | 8 +++++++- - 1 file changed, 7 insertions(+), 1 deletion(-) - -diff --git a/Modules/Numerics/Optimizersv4/wrapping/itkQuasiNewtonOptimizerv4.wrap b/Modules/Numerics/Optimizersv4/wrapping/itkQuasiNewtonOptimizerv4.wrap -index 4a43dd4..7eed11c 100644 ---- a/Modules/Numerics/Optimizersv4/wrapping/itkQuasiNewtonOptimizerv4.wrap -+++ b/Modules/Numerics/Optimizersv4/wrapping/itkQuasiNewtonOptimizerv4.wrap -@@ -1 +1,7 @@ --itk_wrap_simple_class("itk::QuasiNewtonOptimizerv4" POINTER) -+set(WRAPPER_AUTO_INCLUDE_HEADERS OFF) -+itk_wrap_include("itkQuasiNewtonOptimizerv4.h") -+itk_wrap_class("itk::QuasiNewtonOptimizerv4Template" POINTER) -+ foreach(t ${WRAP_ITK_REAL}) -+ itk_wrap_template("${ITKM_${t}}" "${ITKT_${t}}") -+ endforeach(t) -+itk_end_wrap_class() --- -1.8.5.3 - diff --git a/sci-libs/itk/files/0003-COMP-Fixed-itkGradientDescentOptimizerv4-wrapping-wa.patch b/sci-libs/itk/files/0003-COMP-Fixed-itkGradientDescentOptimizerv4-wrapping-wa.patch deleted file mode 100644 index d77345e..0000000 --- a/sci-libs/itk/files/0003-COMP-Fixed-itkGradientDescentOptimizerv4-wrapping-wa.patch +++ /dev/null @@ -1,73 +0,0 @@ -From fced46ce8769b4edc7971ea0928045390b5c3f84 Mon Sep 17 00:00:00 2001 -From: Michka Popoff -Date: Mon, 10 Feb 2014 09:41:42 +0100 -Subject: [PATCH 3/3] COMP: Fixed itkGradientDescentOptimizerv4 wrapping - warnings - -I splitted the 3 wrapping calls in 3 separate files and fixed the wrapping. - -The warnings : -/home/kevin/kitware/ITK_Build/Wrapping/Modules/ITKOptimizersv4/itkGradientDescentOptimizerv4.xml: warning(5): Unknown type type: itk::GradientDescentOptimizerBasev4 [typedef] -/home/kevin/kitware/ITK_Build/Wrapping/Modules/ITKOptimizersv4/itkGradientDescentOptimizerv4.xml: warning(5): Unknown type type: itk::GradientDescentOptimizerv4 [typedef] -/home/kevin/kitware/ITK_Build/Wrapping/Modules/ITKOptimizersv4/itkGradientDescentOptimizerv4.xml: warning(5): Unknown type type: itk::ObjectToObjectOptimizerBase [typedef] -/home/kevin/kitware/ITK_Build/Wrapping/Modules/ITKOptimizersv4/itkGradientDescentOptimizerv4.xml: warning(4): ITK type not wrapped, or currently not known: itk::GradientDescentOptimizerBasev4Template< double > -/home/kevin/kitware/ITK_Build/Wrapping/Modules/ITKOptimizersv4/itkGradientDescentOptimizerv4.xml: warning(4): ITK type not wrapped, or currently not known: itk::GradientDescentOptimizerv4Template< double > -/home/kevin/kitware/ITK_Build/Wrapping/Modules/ITKOptimizersv4/itkGradientDescentOptimizerv4.xml: warning(4): ITK type not wrapped, or currently not known: itk::ObjectToObjectOptimizerBaseTemplate< double > - -Should also hopefully fix the new error on the dashboard I introduced by fixing the itkQuasiNewtonOptimizerv4 warnings (http://review.source.kitware.com/#/c/14317/) -/home/kevin/kitware/ITK_Build/Wrapping/Typedefs/itkQuasiNewtonOptimizerv4.i:87: Warning 401: Nothing known about base class 'itk::GradientDescentOptimizerv4Template< float >'. Ignored. -/home/kevin/kitware/ITK_Build/Wrapping/Typedefs/itkQuasiNewtonOptimizerv4.i:87: Warning 401: Maybe you forgot to instantiate 'itk::GradientDescentOptimizerv4Template< float >' using %template. - -Change-Id: I15b6af11690ed6efeaced68f73af5212ab5dc364 ---- - .../wrapping/itkGradientDescentOptimizerBasev4.wrap | 7 +++++++ - .../Optimizersv4/wrapping/itkGradientDescentOptimizerv4.wrap | 10 +++++++--- - .../Optimizersv4/wrapping/itkObjectToObjectOptimizerBase.wrap | 7 +++++++ - 3 files changed, 21 insertions(+), 3 deletions(-) - create mode 100644 Modules/Numerics/Optimizersv4/wrapping/itkGradientDescentOptimizerBasev4.wrap - create mode 100644 Modules/Numerics/Optimizersv4/wrapping/itkObjectToObjectOptimizerBase.wrap - -diff --git a/Modules/Numerics/Optimizersv4/wrapping/itkGradientDescentOptimizerBasev4.wrap b/Modules/Numerics/Optimizersv4/wrapping/itkGradientDescentOptimizerBasev4.wrap -new file mode 100644 -index 0000000..74f5a6c ---- /dev/null -+++ b/Modules/Numerics/Optimizersv4/wrapping/itkGradientDescentOptimizerBasev4.wrap -@@ -0,0 +1,7 @@ -+set(WRAPPER_AUTO_INCLUDE_HEADERS OFF) -+itk_wrap_include("itkGradientDescentOptimizerBasev4.h") -+itk_wrap_class("itk::GradientDescentOptimizerBasev4Template" POINTER) -+ foreach(t ${WRAP_ITK_REAL}) -+ itk_wrap_template("${ITKM_${t}}" "${ITKT_${t}}") -+ endforeach(t) -+itk_end_wrap_class() -diff --git a/Modules/Numerics/Optimizersv4/wrapping/itkGradientDescentOptimizerv4.wrap b/Modules/Numerics/Optimizersv4/wrapping/itkGradientDescentOptimizerv4.wrap -index d53a176..3236448 100644 ---- a/Modules/Numerics/Optimizersv4/wrapping/itkGradientDescentOptimizerv4.wrap -+++ b/Modules/Numerics/Optimizersv4/wrapping/itkGradientDescentOptimizerv4.wrap -@@ -1,3 +1,7 @@ --itk_wrap_simple_class("itk::ObjectToObjectOptimizerBase" POINTER) --itk_wrap_simple_class("itk::GradientDescentOptimizerBasev4" POINTER) --itk_wrap_simple_class("itk::GradientDescentOptimizerv4" POINTER) -+set(WRAPPER_AUTO_INCLUDE_HEADERS OFF) -+itk_wrap_include("itkGradientDescentOptimizerv4.h") -+itk_wrap_class("itk::GradientDescentOptimizerv4Template" POINTER) -+ foreach(t ${WRAP_ITK_REAL}) -+ itk_wrap_template("${ITKM_${t}}" "${ITKT_${t}}") -+ endforeach(t) -+itk_end_wrap_class() -diff --git a/Modules/Numerics/Optimizersv4/wrapping/itkObjectToObjectOptimizerBase.wrap b/Modules/Numerics/Optimizersv4/wrapping/itkObjectToObjectOptimizerBase.wrap -new file mode 100644 -index 0000000..61b2c44 ---- /dev/null -+++ b/Modules/Numerics/Optimizersv4/wrapping/itkObjectToObjectOptimizerBase.wrap -@@ -0,0 +1,7 @@ -+set(WRAPPER_AUTO_INCLUDE_HEADERS OFF) -+itk_wrap_include("itkObjectToObjectOptimizerBase.h") -+itk_wrap_class("itk::ObjectToObjectOptimizerBaseTemplate" POINTER) -+ foreach(t ${WRAP_ITK_REAL}) -+ itk_wrap_template("${ITKM_${t}}" "${ITKT_${t}}") -+ endforeach(t) -+itk_end_wrap_class() --- -1.8.5.3 - diff --git a/sci-libs/itk/files/0004-COMP-Warp-OptimizerParameterScalesEstimatorTemplate.patch b/sci-libs/itk/files/0004-COMP-Warp-OptimizerParameterScalesEstimatorTemplate.patch deleted file mode 100644 index 83b3956..0000000 --- a/sci-libs/itk/files/0004-COMP-Warp-OptimizerParameterScalesEstimatorTemplate.patch +++ /dev/null @@ -1,30 +0,0 @@ -Author: Matt McCormick -Date: Thu Feb 6 10:26:49 2014 -0500 - - COMP: Wrap OptimizerParameterScalesEstimatorTemplate. - - The class name changed and it became templated. Fixes: - - /playpen/blowekamp/MacOSX-WrapITK/ITK-build/Wrapping/Modules/ITKOptimizersv4/itkOptimizerParameterScalesEstimator.xml: - warning(5): Unknown type type: itk::OptimizerParameterScalesEstimator - [typedef] - /playpen/blowekamp/MacOSX-WrapITK/ITK-build/Wrapping/Modules/ITKOptimizersv4/itkOptimizerParameterScalesEstimator.xml: - warning(4): ITK type not wrapped, or currently not known: - itk::OptimizerParameterScalesEstimatorTemplate< double > - - Change-Id: Ic6b4d6fba10d5d6c7b58de8d842bad6511e1ae7b - -diff --git a/Modules/Numerics/Optimizersv4/wrapping/itkOptimizerParameterScalesEstimator.wrap b/Modules/Numerics/Optimizersv4/wrapping/itkOptim -index efd6a8c..a647ee4 100644 ---- a/Modules/Numerics/Optimizersv4/wrapping/itkOptimizerParameterScalesEstimator.wrap -+++ b/Modules/Numerics/Optimizersv4/wrapping/itkOptimizerParameterScalesEstimator.wrap -@@ -1 +1,7 @@ --itk_wrap_simple_class("itk::OptimizerParameterScalesEstimator" POINTER) -+set(WRAPPER_AUTO_INCLUDE_HEADERS OFF) -+itk_wrap_include("itkOptimizerParameterScalesEstimator.h") -+itk_wrap_class("itk::OptimizerParameterScalesEstimatorTemplate" POINTER) -+ foreach(t ${WRAP_ITK_REAL}) -+ itk_wrap_template("${ITKM_${t}}" "${ITKT_${t}}") -+ endforeach(t) -+itk_end_wrap_class() - diff --git a/sci-libs/itk/files/0005-make-gdcm-helper-library-static.patch b/sci-libs/itk/files/0005-make-gdcm-helper-library-static.patch deleted file mode 100644 index d760ac7..0000000 --- a/sci-libs/itk/files/0005-make-gdcm-helper-library-static.patch +++ /dev/null @@ -1,11 +0,0 @@ -diff --git a/Modules/ThirdParty/GDCM/src/CMakeLists.txt b/Modules/ThirdParty/GDCM/src/CMakeLists.txt -index e98077c..70f4286 100644 ---- a/Modules/ThirdParty/GDCM/src/CMakeLists.txt -+++ b/Modules/ThirdParty/GDCM/src/CMakeLists.txt -@@ -1,5 +1,5 @@ - if(ITK_USE_SYSTEM_GDCM) -- add_library(ITKGDCM ITK-GDCM.cxx) -+ add_library(ITKGDCM STATIC ITK-GDCM.cxx) - target_link_libraries(ITKGDCM gdcmDICT gdcmMSFF) - itk_module_target(ITKGDCM) - return() diff --git a/sci-libs/itk/files/ITKModuleRemote.patch b/sci-libs/itk/files/ITKModuleRemote.patch deleted file mode 100644 index eb13015..0000000 --- a/sci-libs/itk/files/ITKModuleRemote.patch +++ /dev/null @@ -1,45 +0,0 @@ -Disable automatic git clone attempt for modules: -https://github.com/InsightSoftwareConsortium/ITK/issues/1157 - ---- a/CMake/ITKModuleRemote.cmake 2019-08-13 18:10:33.385472767 +0200 -+++ b/CMake/ITKModuleRemote.cmake 2019-08-13 18:12:04.020198966 +0200 -@@ -165,39 +165,4 @@ - set(Module_${_name} ON CACHE FORCE "${_description}") - endif() - -- if(Module_${_name}) -- itk_download_attempt_check(Module_${_name}) -- include(CMakeParseArguments) -- cmake_parse_arguments(_fetch_options "" "GIT_REPOSITORY;GIT_TAG" "" ${ARGN}) -- find_package(Git) -- if(NOT GIT_EXECUTABLE) -- message(FATAL_ERROR "error: could not find git for clone of ${_name}") -- endif() -- execute_process( -- COMMAND "${GIT_EXECUTABLE}" --version -- OUTPUT_VARIABLE ov -- OUTPUT_STRIP_TRAILING_WHITESPACE -- ) -- string(REGEX REPLACE "^git version (.+)$" "\\1" _version "${ov}") -- if("${_version}" VERSION_LESS 1.6.6) -- message(FATAL_ERROR "Git version 1.6.6 or later is required.") -- endif() -- -- set(REMOTE_GIT_TAG "${_fetch_options_GIT_TAG}") -- -- if( DEFINED REMOTE_GIT_TAG_${_name} AND NOT "${REMOTE_GIT_TAG_${_name}}" STREQUAL "${_fetch_options_GIT_TAG}") -- set(REMOTE_GIT_TAG "${REMOTE_GIT_TAG_${_name}}") -- message(STATUS "NOTE: Using override 'REMOTE_GIT_TAG_${_name}=${REMOTE_GIT_TAG}'\n" -- " instead of value 'GIT_TAG=${_fetch_options_GIT_TAG}'\n" -- " specified in file ${ITK_SOURCE_DIR}/Modules/Remote/${_name}.remote.cmake'") -- endif() -- set(REMOTE_GIT_TAG_${_name} "${REMOTE_GIT_TAG}" CACHE STRING "Override default GIT_TAG value for remote module ${_name}") -- mark_as_advanced(REMOTE_GIT_TAG_${_name}) -- -- _fetch_with_git("${GIT_EXECUTABLE}" -- "${_fetch_options_GIT_REPOSITORY}" -- "${REMOTE_GIT_TAG}" -- "${ITK_SOURCE_DIR}/Modules/Remote/${_name}" -- ) -- endif() - endfunction() diff --git a/sci-libs/itk/files/itk-5.1.0-downloads.patch b/sci-libs/itk/files/itk-5.1.0-downloads.patch deleted file mode 100644 index 34fdb76..0000000 --- a/sci-libs/itk/files/itk-5.1.0-downloads.patch +++ /dev/null @@ -1,20 +0,0 @@ ---- a/CMake/ITKDownloadSetup.cmake 2020-07-30 19:03:10.330325423 -0400 -+++ b/CMake/ITKDownloadSetup.cmake 2020-07-30 19:03:10.330325423 -0400 -@@ -11,7 +11,7 @@ - - macro(itk_download_attempt_check _name) - if(ITK_FORBID_DOWNLOADS) -- message(SEND_ERROR "Attempted to download ${_name} when ITK_FORBID_DOWNLOADS is ON") -+ message(WARNING "Attempted to download ${_name} when ITK_FORBID_DOWNLOADS is ON") - endif() - endmacro() - ---- a/Modules/Remote/GenericLabelInterpolator.remote.cmake 2020-04-25 14:30:53.000000000 -0400 -+++ b/Modules/Remote/GenericLabelInterpolator.remote.cmake 2020-04-25 14:30:53.000000000 -0400 -@@ -44,6 +44,4 @@ - itk_fetch_module(GenericLabelInterpolator - "A generic interpolator for multi-label images." - MODULE_COMPLIANCE_LEVEL 2 -- GIT_REPOSITORY ${git_protocol}://github.com/InsightSoftwareConsortium/ITKGenericLabelInterpolator.git -- GIT_TAG b95fe46c7f4fe8002af67c67e6fe4e1f087bf6b7 - ) diff --git a/sci-libs/itk/files/itk-5.1.0-include_limits.patch b/sci-libs/itk/files/itk-5.1.0-include_limits.patch deleted file mode 100644 index a1e3cb4..0000000 --- a/sci-libs/itk/files/itk-5.1.0-include_limits.patch +++ /dev/null @@ -1,10 +0,0 @@ ---- a/Modules/ThirdParty/GDCM/src/gdcm/Source/MediaStorageAndFileFormat/gdcmImageChangePhotometricInterpretation.h -+++ a/Modules/ThirdParty/GDCM/src/gdcm/Source/MediaStorageAndFileFormat/gdcmImageChangePhotometricInterpretation.h -@@ -16,6 +16,7 @@ - - #include "gdcmImageToImageFilter.h" - #include "gdcmPhotometricInterpretation.h" -+#include - - namespace gdcm - { diff --git a/sci-libs/itk/files/nrrdio-linking.patch b/sci-libs/itk/files/nrrdio-linking.patch deleted file mode 100644 index a549650..0000000 --- a/sci-libs/itk/files/nrrdio-linking.patch +++ /dev/null @@ -1,15 +0,0 @@ -Description: Link libITKNrrdIO with -lm (needed for sqrt) -Author: Steve Robbins -Forwarded: no - ---- insighttoolkit4-4.5.0.orig/Modules/ThirdParty/NrrdIO/src/NrrdIO/CMakeLists.txt -+++ insighttoolkit4-4.5.0/Modules/ThirdParty/NrrdIO/src/NrrdIO/CMakeLists.txt -@@ -64,7 +64,7 @@ - ADD_DEFINITIONS(-DTEEM_ZLIB=1) - - ADD_LIBRARY(ITKNrrdIO ${nrrdio_SRCS} ) --TARGET_LINK_LIBRARIES(ITKNrrdIO ${ITKZLIB_LIBRARIES}) -+TARGET_LINK_LIBRARIES(ITKNrrdIO ${ITKZLIB_LIBRARIES} -lm) - - IF(ITK_LIBRARY_PROPERTIES) - SET_TARGET_PROPERTIES(ITKNrrdIO PROPERTIES ${ITK_LIBRARY_PROPERTIES}) diff --git a/sci-libs/itk/files/tests.patch b/sci-libs/itk/files/tests.patch deleted file mode 100644 index c24714e..0000000 --- a/sci-libs/itk/files/tests.patch +++ /dev/null @@ -1,41 +0,0 @@ -Known to fail by upstream: -https://github.com/InsightSoftwareConsortium/ITK/issues/1212#issuecomment-527998115 - ---- a/Modules/Bridge/VtkGlue/test/CMakeLists.txt 2019-09-09 00:45:14.736032139 +0200 -+++ b/Modules/Bridge/VtkGlue/test/CMakeLists.txt 2019-09-09 00:49:42.183935497 +0200 -@@ -7,8 +7,6 @@ - if(NOT VTK_RENDERING_BACKEND STREQUAL "None") - list(APPEND ITKVtkGlueTests - itkVtkMedianFilterTest.cxx -- itkVtkConnectedComponentImageFilterTest.cxx -- QuickViewTest.cxx - # ### runViewImage ### - # No test generated. Use it for view images (2D or 3D) with: - # ITKVtkGlueTestDriver runViewImage image_file -@@ -40,26 +38,3 @@ - NAME itkVTKImageToImageFilterTest - COMMAND ITKVtkGlueTestDriver - itkVTKImageToImageFilterTest) -- --if(NOT VTK_RENDERING_BACKEND STREQUAL "None") -- itk_add_test( -- NAME itkVtkMedianImageFilterTest -- COMMAND ITKVtkGlueTestDriver -- itkVtkMedianFilterTest DATA{${ITK_DATA_ROOT}/Input/cthead1.png} 2) -- set_property(TEST itkVtkMedianImageFilterTest APPEND PROPERTY LABELS REQUIRES_DISPLAY) -- -- itk_add_test( -- NAME QuickViewTest -- COMMAND ITKVtkGlueTestDriver -- --compare DATA{Baseline/QuickViewTest.png,:} -- ${ITK_TEST_OUTPUT_DIR}/QuickViewTest0.png -- --compareNumberOfPixelsTolerance 1500 -- QuickViewTest DATA{${ITK_DATA_ROOT}/Input/peppers.png} ${ITK_TEST_OUTPUT_DIR}) -- set_property(TEST QuickViewTest APPEND PROPERTY LABELS REQUIRES_DISPLAY) -- -- itk_add_test( -- NAME itkVtkConnectedComponentImageFilterTest -- COMMAND ITKVtkGlueTestDriver -- itkVtkConnectedComponentImageFilterTest DATA{${ITK_DATA_ROOT}/Input/cthead1.png}) -- set_property(TEST itkVtkConnectedComponentImageFilterTest APPEND PROPERTY LABELS REQUIRES_DISPLAY) --endif() diff --git a/sci-libs/itk/itk-5.1.0.ebuild b/sci-libs/itk/itk-5.1.0.ebuild deleted file mode 100644 index 0f46dc4..0000000 --- a/sci-libs/itk/itk-5.1.0.ebuild +++ /dev/null @@ -1,191 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python3_{7,8,9} ) - -inherit cmake python-single-r1 - -MY_PN="InsightToolkit" -MY_P="${MY_PN}-${PV}" -GLI_HASH="a02cbeaf28cb3d28ac66b9ac651073530eb6ab78" -TEST_HASH="0eb202e23ae81be123b1b26cf31a9ba743824700" -declare -a GLI_TEST_HASHES=( - "a5e11ea71164ff78c65fcf259db01ea5db981a9d868e60045ff2bffca92984df1174bf984a1076e450f0d5d69b4f0191ed1a61465c220e2c91a893b5df150c0a" - "bcdbb347f3704262d1f00be7179d6a0a6e68aed56c0653e8072ee5a94985c713bd229c935b1226a658af84fb7f1fffc2458c98364fc35303a2303b12f9f7ce2f" -) - -GLI_TEST_SRC="" -for i in "${GLI_TEST_HASHES[@]}"; do - GLI_TEST_SRC+="https://data.kitware.com/api/v1/file/hashsum/sha512/${i} -> ${P}-test-${i} " -done - -DESCRIPTION="NLM Insight Segmentation and Registration Toolkit" -HOMEPAGE="http://www.itk.org" -SRC_URI=" - https://github.com/InsightSoftwareConsortium/ITK/releases/download/v${PV}/${MY_P}.tar.gz - https://github.com/InsightSoftwareConsortium/ITKGenericLabelInterpolator/archive/${GLI_HASH}.tar.gz -> ITKGenericLabelInterpolator-${PV}.tar.gz - test? ( - https://github.com/InsightSoftwareConsortium/ITK/releases/download/v${PV}/InsightData-${PV}.tar.gz - https://github.com/InsightSoftwareConsortium/ITKTestingData/archive/${TEST_HASH}.tar.gz -> ${P}-testingdata.tar.gz - ${GLI_TEST_SRC} - ) - " - -LICENSE="Apache-2.0" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="debug doc examples fftw itkv4-compat python review test vtkglue" -RESTRICT="!test? ( test )" -# python will not work, this is a know issue upstream: -# https://github.com/InsightSoftwareConsortium/ITK/issues/2005 -# https://github.com/InsightSoftwareConsortium/ITK/issues/1229 -# https://github.com/InsightSoftwareConsortium/ITKGenericLabelInterpolator/issues/10 - -RDEPEND=" - dev-libs/double-conversion:0= - media-libs/openjpeg:2 - media-libs/libpng:0= - media-libs/tiff:0=[jpeg] - sci-libs/dcmtk:0= - sci-libs/hdf5:0=[cxx] - sys-libs/zlib:0= - virtual/jpeg:0= - fftw? ( sci-libs/fftw:3.0= ) - vtkglue? ( sci-libs/vtk:0=[rendering,python?] ) - python? ( ${PYTHON_DEPS} ) -" -DEPEND="${RDEPEND} - sys-apps/coreutils - python? ( - >=dev-lang/swig-2.0:0 - dev-cpp/castxml - ) - doc? ( app-doc/doxygen ) -" - -REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )" - -S="${WORKDIR}/${MY_P}" - -PATCHES=( - "${FILESDIR}"/tests.patch - "${FILESDIR}"/${P}-downloads.patch - "${FILESDIR}"/${P}-include_limits.patch -) - -pkg_pretend() { - if [[ -z ${ITK_COMPUTER_MEMORY_SIZE} ]]; then - elog "To tune ITK to make the best use of working memory you can set" - elog " ITK_COMPUTER_MEMORY_SIZE=XX" - elog "in make.conf, default is 1 (unit is GB)" - fi - if use python && [[ -z ${ITK_WRAP_DIMS} ]]; then - elog "For Python language bindings, you can define the dimensions" - elog "you want to create bindings for by setting" - elog " ITK_WRAP_DIMS=X;Y;Z..." - elog "in make.conf, default is 2;3 for 2D and 3D data" - fi -} - -src_prepare() { - sed -i -e "s/find_package(OpenJPEG 2.0.0/find_package(OpenJPEG/g"\ - Modules/ThirdParty/GDCM/src/gdcm/CMakeLists.txt - ln -sr ../ITKGenericLabelInterpolator-* Modules/External/ITKGenericLabelInterpolator || die - cmake_src_prepare - if use test; then - cp -rf "../ITKTestingData-${TEST_HASH}/"* ".ExternalData/" || die - mv "../ITKTestingData-${TEST_HASH}" "${BUILD_DIR}/.ExternalData" || die - for i in "${GLI_TEST_HASHES[@]}"; do - cp "${DISTDIR}/${i}" ".ExternalData/SHA512/" || die - cp "${DISTDIR}/${i}" "${BUILD_DIR}/.ExternalData/SHA512/" || die - done - fi -} - -src_configure() { - local mycmakeargs=( - -DITK_BUILD_DOCUMENTATION="$(usex doc ON OFF)" - -DBUILD_EXAMPLES="$(usex examples ON OFF)" - -DBUILD_SHARED_LIBS=ON - -DBUILD_TESTING="$(usex test ON OFF)" - -Ddouble-conversion_INCLUDE_DIRS="${EPREFIX}/usr/include/double-conversion" - -DExternalData_OBJECT_STORES="${WORKDIR}/InsightToolkit-${PV}/.ExternalData" - -DGDCM_USE_SYSTEM_OPENJPEG=ON - -DITK_FORBID_DOWNLOADS:BOOL=ON - -DITK_INSTALL_LIBRARY_DIR=$(get_libdir) - -DITK_USE_REVIEW="$(usex review ON OFF)" - -DITK_USE_SYSTEM_DCMTK=ON - -DITK_USE_SYSTEM_DOUBLECONVERSION=ON - -DITK_USE_SYSTEM_CASTXML=ON - -DITK_USE_SYSTEM_HDF5=ON - -DITK_USE_SYSTEM_JPEG=ON - -DITK_USE_SYSTEM_PNG=ON - -DITK_USE_SYSTEM_SWIG=ON - -DITK_USE_SYSTEM_TIFF=ON - -DITK_USE_SYSTEM_ZLIB=ON - -DITK_USE_KWSTYLE=OFF - -DITK_BUILD_DEFAULT_MODULES=ON - -DITK_COMPUTER_MEMORY_SIZE="${ITK_COMPUTER_MEMORY_SIZE:-1}" - -DModule_GenericLabelInterpolator:BOOL=ON - -DModule_ITKReview:BOOL=ON - -DWRAP_ITK_JAVA=OFF - -DWRAP_ITK_TCL=OFF - -DITKV4_COMPATIBILITY:BOOL=$(usex itkv4-compat) - ) - if use fftw; then - mycmakeargs+=( - -DUSE_FFTWD=ON - -DUSE_FFTWF=ON - -DUSE_SYSTEM_FFTW=ON - -DITK_WRAP_double=ON - -DITK_WRAP_vector_double=ON - -DITK_WRAP_covariant_vector_double=ON - -DITK_WRAP_complex_double=ON - ) - fi - if use vtkglue; then - mycmakeargs+=( - -DModule_ITKVtkGlue=ON - ) - fi - if use python; then - mycmakeargs+=( - -DITK_WRAP_PYTHON=ON - -DITK_WRAP_DIMS="${ITK_WRAP_DIMS:-2;3}" - ) - else - mycmakeargs+=( - -DITK_WRAP_PYTHON=OFF - ) - fi - cmake_src_configure -} - -src_install() { - cmake_src_install - - if use examples; then - docinto examples - docompress -x /usr/share/doc/${PF}/examples - dodoc -r "${S}"/Examples/* - fi - - echo "ITK_DATA_ROOT=${EROOT}/usr/share/${PN}/data" > ${T}/40${PN} - local ldpath="${EROOT}/usr/$(get_libdir)/InsightToolkit" - if use python; then - echo "PYTHONPATH=${EROOT}/usr/$(get_libdir)/InsightToolkit/WrapITK/Python" >> "${T}"/40${PN} - ldpath="${ldpath}:${EROOT}/usr/$(get_libdir)/InsightToolkit/WrapITK/lib" - fi - echo "LDPATH=${ldpath}" >> "${T}"/40${PN} - doenvd "${T}"/40${PN} - - if use doc; then - cd "${WORKDIR}"/html || die - rm *.md5 || die "Failed to remove superfluous hashes" - einfo "Installing API docs. This may take some time." - docinto api-docs - dodoc -r * - fi -} diff --git a/sci-libs/itk/metadata.xml b/sci-libs/itk/metadata.xml deleted file mode 100644 index c41202e..0000000 --- a/sci-libs/itk/metadata.xml +++ /dev/null @@ -1,24 +0,0 @@ - - - - - maintainer-wanted@gentoo.org - - - sci-biology@gentoo.org - Gentoo Biology Project - - - Insight Segmentation and Registration Toolkit (ITK) is a library - that provides developers with an extensive suite of tools for image - analysis. - - - Compatibility for applications using ITKv4 API - Enable compilation of methods under review - PLEASE FIX MY DESCRIPTION - - - itk - -