commit: 3713fffdc80a085c8de112f19a60000f0bd68810 Author: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org> AuthorDate: Thu Sep 15 11:16:22 2022 +0000 Commit: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org> CommitDate: Thu Sep 15 11:16:22 2022 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=3713fffd
sci-biology/ants: fix compile with itk-5.2 Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org> .../{ants-2.4.1.ebuild => ants-2.4.1-r1.ebuild} | 17 +-- .../ants/files/ants-2.3.1_p20191013-logic.patch | 37 ------- .../ants/files/ants-2.3.1_p20191013-paths.patch | 40 ------- sci-biology/ants/files/ants-2.3.4-libdir.patch | 117 --------------------- sci-biology/ants/files/ants-2.3.4-version.patch | 17 --- .../ants/files/ants-2.4.1-fix-compile.patch | 13 +++ 6 files changed, 23 insertions(+), 218 deletions(-) diff --git a/sci-biology/ants/ants-2.4.1.ebuild b/sci-biology/ants/ants-2.4.1-r1.ebuild similarity index 75% rename from sci-biology/ants/ants-2.4.1.ebuild rename to sci-biology/ants/ants-2.4.1-r1.ebuild index feba81d2c..70d5d8873 100644 --- a/sci-biology/ants/ants-2.4.1.ebuild +++ b/sci-biology/ants/ants-2.4.1-r1.ebuild @@ -10,9 +10,7 @@ MY_PN="ANTs" DESCRIPTION="Advanced Normalitazion Tools for neuroimaging" HOMEPAGE="https://stnava.github.io/ANTs/" -SRC_URI=" - https://github.com/ANTsX/ANTs/archive/v${PV}.tar.gz -> ${P}.tar.gz -" +SRC_URI="https://github.com/ANTsX/ANTs/archive/v${PV}.tar.gz -> ${P}.tar.gz" S="${WORKDIR}/${MY_PN}-${PV}" SLOT="0" @@ -22,22 +20,27 @@ IUSE="test vtk" RESTRICT="test" DEPEND=" - =sci-libs/itk-5.2* + !vtk? ( =sci-libs/itk-5.2*[fftw,-vtkglue] ) vtk? ( - =sci-libs/itk-5.2*[vtkglue] + =sci-libs/itk-5.2*[fftw,vtkglue] =sci-libs/vtk-9.1* ) " RDEPEND="${DEPEND}" +PATCHES=( + "${FILESDIR}/${P}-fix-compile.patch" +) + src_configure() { local mycmakeargs=( + -DBUILD_EXAMPLES=OFF -DUSE_SYSTEM_ITK=ON + -DITK_USE_SYSTEM_FFTW=ON -DITK_DIR="${EPREFIX}/usr/include/ITK-5.2/" -DBUILD_TESTING="$(usex test ON OFF)" -DUSE_VTK=$(usex vtk ON OFF) -DUSE_SYSTEM_VTK=$(usex vtk ON OFF) - -DANTS_SNAPSHOT_VERSION:STRING=${PV} ) use vtk && mycmakeargs+=( -DVTK_DIR="${EPREFIX}/usr/include/vtk-9.1/" @@ -46,7 +49,7 @@ src_configure() { } src_install() { - BUILD_DIR="${WORKDIR}/${P}_build/ANTS-build" + BUILD_DIR="${WORKDIR}/${MY_PN}-${PV}_build/ANTS-build" cmake_src_install cd "${S}/Scripts" || die "scripts dir not found" dobin *.sh diff --git a/sci-biology/ants/files/ants-2.3.1_p20191013-logic.patch b/sci-biology/ants/files/ants-2.3.1_p20191013-logic.patch deleted file mode 100644 index 932da9954..000000000 --- a/sci-biology/ants/files/ants-2.3.1_p20191013-logic.patch +++ /dev/null @@ -1,37 +0,0 @@ -From b2c828ff8e5ce537d7096af04b086e965fede9e8 Mon Sep 17 00:00:00 2001 -From: "Gabriel A. Devenyi" <gdeve...@gmail.com> -Date: Mon, 7 Oct 2019 22:01:51 -0400 -Subject: [PATCH] Fix install logic - ---- - ANTS.cmake | 3 ++- - SuperBuild.cmake | 2 ++ - 2 files changed, 4 insertions(+), 1 deletion(-) - -diff --git a/ANTS.cmake b/ANTS.cmake -index a1baf845..95ffdc74 100644 ---- a/ANTS.cmake -+++ b/ANTS.cmake -@@ -172,7 +172,8 @@ install(PROGRAMS Scripts/ANTSpexec.sh - COMPONENT SCRIPTS - ) - --if(BUILD_SHARED_LIBS AND NOT (USE_SYSTEM_ITK AND USE_SYSTEM_VTK)) -+#Only install ITK/VTK libraries if shared build and superbuild is used -+if(BUILD_SHARED_LIBS AND ((NOT USE_SYSTEM_ITK) OR ((NOT USE_SYSTEM_VTK) AND USE_VTK))) - install(DIRECTORY ${CMAKE_BINARY_DIR}/../staging/lib/ - DESTINATION lib) - endif() -diff --git a/SuperBuild.cmake b/SuperBuild.cmake -index f4630e64..32b930c2 100644 ---- a/SuperBuild.cmake -+++ b/SuperBuild.cmake -@@ -207,6 +207,8 @@ list(APPEND ${CMAKE_PROJECT_NAME}_SUPERBUILD_EP_VARS - CMAKE_C_COMPILER_LAUNCHER:STRING - CMAKE_CXX_COMPILER_LAUNCHER:STRING - CMAKE_CUDA_COMPILER_LAUNCHER:STRING -+ USE_SYSTEM_ITK:BOOL -+ USE_SYSTEM_VTK:BOOL - ) - - _expand_external_project_vars() diff --git a/sci-biology/ants/files/ants-2.3.1_p20191013-paths.patch b/sci-biology/ants/files/ants-2.3.1_p20191013-paths.patch deleted file mode 100644 index aaea92808..000000000 --- a/sci-biology/ants/files/ants-2.3.1_p20191013-paths.patch +++ /dev/null @@ -1,40 +0,0 @@ -diff --git a/Examples/CMakeLists.txt b/Examples/CMakeLists.txt ---- a/Examples/CMakeLists.txt -+++ b/Examples/CMakeLists.txt -@@ -16,8 +16,9 @@ -+include(GNUInstallDirs) - install(TARGETS antsUtilities -- RUNTIME DESTINATION bin -+ RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR} - COMPONENT RUNTIME_antsUtilities -- LIBRARY DESTINATION lib -+ LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} - COMPONENT RUNTIME_antsUtilities -- ARCHIVE DESTINATION lib -+ ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR} - COMPONENT DEVELOPMENT_antsUtilities - ) -@@ -38,8 +38,8 @@ - install(TARGETS l_${ANTS_FUNCTION_NAME} ${ANTS_FUNCTION_NAME} -- RUNTIME DESTINATION bin -+ RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR} - COMPONENT RUNTIME_${ANTS_FUNCTION_NAME} -- LIBRARY DESTINATION lib -+ LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} - COMPONENT RUNTIME_${ANTS_FUNCTION_NAME} -- ARCHIVE DESTINATION lib -+ ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR} - COMPONENT DEVELOPMENT_${ANTS_FUNCTION_NAME} - ) -@@ -61,8 +61,8 @@ - install(TARGETS l_${ANTS_FUNCTION_NAME} ${ANTS_FUNCTION_NAME} -- RUNTIME DESTINATION bin -+ RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR} - COMPONENT RUNTIME_${ANTS_FUNCTION_NAME} -- LIBRARY DESTINATION lib -+ LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} - COMPONENT RUNTIME_${ANTS_FUNCTION_NAME} -- ARCHIVE DESTINATION lib -+ ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR} - COMPONENT DEVELOPMENT_${ANTS_FUNCTION_NAME} - ) diff --git a/sci-biology/ants/files/ants-2.3.4-libdir.patch b/sci-biology/ants/files/ants-2.3.4-libdir.patch deleted file mode 100644 index b593c2778..000000000 --- a/sci-biology/ants/files/ants-2.3.4-libdir.patch +++ /dev/null @@ -1,117 +0,0 @@ -From 329a7be631b33294d9cf3d58e8cdeb62e0aa993c Mon Sep 17 00:00:00 2001 -From: Philip A Cook <coo...@pennmedicine.upenn.edu> -Date: Fri, 26 Jun 2020 18:23:08 +0000 -Subject: [PATCH] ENH: Use GNUInstallDirs CMake module - -Trying to enable installation to the correct lib dir for each platform ---- - Common.cmake | 7 +++++-- - Examples/CMakeLists.txt | 32 ++++++++++++++++---------------- - 2 files changed, 21 insertions(+), 18 deletions(-) - -diff --git a/Common.cmake b/Common.cmake -index 5e52d7f1..1e604113 100644 ---- a/Common.cmake -+++ b/Common.cmake -@@ -103,8 +103,6 @@ if(PLATFORM_CHECK) - endif() - endif() - -- -- - #------------------------------------------------------------------------- - # Augment compiler flags - #------------------------------------------------------------------------- -@@ -124,3 +122,8 @@ if(NOT CMAKE_POSITION_INDEPENDENT_CODE) - set(CMAKE_POSITION_INDEPENDENT_CODE ON) - endif() - endif() -+ -+#------------------------------------------------------------------------- -+# Define install dirs for different platforms -+#------------------------------------------------------------------------- -+include(GNUInstallDirs) -diff --git a/Examples/CMakeLists.txt b/Examples/CMakeLists.txt -index 61781f56..cb352748 100644 ---- a/Examples/CMakeLists.txt -+++ b/Examples/CMakeLists.txt -@@ -1,4 +1,4 @@ --SET(CMAKE_INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/lib") -+SET(CMAKE_INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_LIBDIR}") - ## Note that the antsUtilities can always be built static. It will then be linked - ## Directly into the other libraries. - add_library(antsUtilities antsUtilities.cxx -@@ -14,11 +14,11 @@ add_library(antsUtilities antsUtilities.cxx - ) - target_link_libraries(antsUtilities ${ITK_LIBRARIES} ) - install(TARGETS antsUtilities -- RUNTIME DESTINATION bin -+ RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR} - COMPONENT RUNTIME_antsUtilities -- LIBRARY DESTINATION lib -+ LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} - COMPONENT RUNTIME_antsUtilities -- ARCHIVE DESTINATION lib -+ ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR} - COMPONENT DEVELOPMENT_antsUtilities - ) - -@@ -34,22 +34,22 @@ macro(STATIC_ANTS_BUILD ANTS_FUNCTION_NAME EXTRA_LIBS) - - if (ANTS_INSTALL_LIBS_ONLY) - install(TARGETS l_${ANTS_FUNCTION_NAME} -- # RUNTIME DESTINATION bin -+ # RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR} - # COMPONENT RUNTIME_${ANTS_FUNCTION_NAME} -- LIBRARY DESTINATION lib -+ LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} - COMPONENT RUNTIME_${ANTS_FUNCTION_NAME} -- ARCHIVE DESTINATION lib -+ ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR} - COMPONENT DEVELOPMENT_${ANTS_FUNCTION_NAME} - ) - else() - add_executable( ${ANTS_FUNCTION_NAME} cli_${ANTS_FUNCTION_NAME}.cxx ) - target_link_libraries( ${ANTS_FUNCTION_NAME} l_${ANTS_FUNCTION_NAME} ) - install(TARGETS l_${ANTS_FUNCTION_NAME} ${ANTS_FUNCTION_NAME} -- RUNTIME DESTINATION bin -+ RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR} - COMPONENT RUNTIME_${ANTS_FUNCTION_NAME} -- LIBRARY DESTINATION lib -+ LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} - COMPONENT RUNTIME_${ANTS_FUNCTION_NAME} -- ARCHIVE DESTINATION lib -+ ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR} - COMPONENT DEVELOPMENT_${ANTS_FUNCTION_NAME} - ) - endif() -@@ -68,11 +68,11 @@ macro(DYNAMIC_ANTS_BUILD ANTS_FUNCTION_NAME EXTRA_LIBS) - - if (ANTS_INSTALL_LIBS_ONLY) - install(TARGETS l_${ANTS_FUNCTION_NAME} -- # RUNTIME DESTINATION bin -+ # RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR} - # COMPONENT RUNTIME_${ANTS_FUNCTION_NAME} -- LIBRARY DESTINATION lib -+ LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} - COMPONENT RUNTIME_${ANTS_FUNCTION_NAME} -- ARCHIVE DESTINATION lib -+ ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR} - COMPONENT DEVELOPMENT_${ANTS_FUNCTION_NAME} - ) - else() -@@ -80,11 +80,11 @@ macro(DYNAMIC_ANTS_BUILD ANTS_FUNCTION_NAME EXTRA_LIBS) - target_link_libraries( ${ANTS_FUNCTION_NAME} l_${ANTS_FUNCTION_NAME} ) - - install(TARGETS l_${ANTS_FUNCTION_NAME} ${ANTS_FUNCTION_NAME} -- RUNTIME DESTINATION bin -+ RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR} - COMPONENT RUNTIME_${ANTS_FUNCTION_NAME} -- LIBRARY DESTINATION lib -+ LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} - COMPONENT RUNTIME_${ANTS_FUNCTION_NAME} -- ARCHIVE DESTINATION lib -+ ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR} - COMPONENT DEVELOPMENT_${ANTS_FUNCTION_NAME} - ) - endif() diff --git a/sci-biology/ants/files/ants-2.3.4-version.patch b/sci-biology/ants/files/ants-2.3.4-version.patch deleted file mode 100644 index 487151d69..000000000 --- a/sci-biology/ants/files/ants-2.3.4-version.patch +++ /dev/null @@ -1,17 +0,0 @@ ---- a/ANTS.cmake 2020-06-08 12:11:14.000000000 -0400 -+++ b/ANTS.cmake 2020-08-03 16:44:00.826633506 -0400 -@@ -37,7 +37,6 @@ - set(${PROJECT_NAME}_VERSION_MAJOR 0) - set(${PROJECT_NAME}_VERSION_MINOR 0) - set(${PROJECT_NAME}_VERSION_PATCH 0) -- set(${PROJECT_NAME}_VERSION_TWEAK 0) - set(${PROJECT_NAME}_VERSION "snapshot-${ANTS_SNAPSHOT_VERSION}") - endif() - -@@ -46,7 +45,6 @@ - set(${PROJECT_NAME}_VERSION_MAJOR 0) - set(${PROJECT_NAME}_VERSION_MINOR 0) - set(${PROJECT_NAME}_VERSION_PATCH 0) -- set(${PROJECT_NAME}_VERSION_TWEAK 0) - set(${PROJECT_NAME}_VERSION "0.0.0.0") - endif() diff --git a/sci-biology/ants/files/ants-2.4.1-fix-compile.patch b/sci-biology/ants/files/ants-2.4.1-fix-compile.patch new file mode 100644 index 000000000..bd7eecbcf --- /dev/null +++ b/sci-biology/ants/files/ants-2.4.1-fix-compile.patch @@ -0,0 +1,13 @@ +diff --git a/Examples/PrintHeader.cxx b/Examples/PrintHeader.cxx +index d1e7586..048d934 100644 +--- a/Examples/PrintHeader.cxx ++++ b/Examples/PrintHeader.cxx +@@ -281,7 +281,7 @@ PrintHeader(int argc, char * argv[]) + // Get the metadata as a generic object + string key = itMeta->first, v_string; + itk::SpatialOrientation::ValidCoordinateOrientationFlags v_oflags = +- itk::SpatialOrientationEnums::ValidCoordinateOrientations::ITK_COORDINATE_ORIENTATION_INVALID; ++ itk::SpatialOrientation::ITK_COORDINATE_ORIENTATION_INVALID; + + if (itk::ExposeMetaData<string>(mdd, key, v_string)) + {