From 3d7eff6d6976c822ee5ba1fc146d80d3d865c77e Mon Sep 17 00:00:00 2001 From: Horea Christian Date: Tue, 4 Aug 2020 03:36:59 -0400 Subject: [PATCH] sci-biology/ants: version bump 2.3.4 ahead of Gentoo Science Package-Manager: Portage-3.0.0, Repoman-2.3.23 Signed-off-by: Horea Christian --- sci-biology/ants/ChangeLog | 8 ++ sci-biology/ants/Manifest | 4 +- ...3.1_p20191013.ebuild => ants-2.3.4.ebuild} | 25 ++-- .../files/ants-2.3.1_p20191013-logic.patch | 37 ------ .../files/ants-2.3.1_p20191013-paths.patch | 40 ------ .../ants/files/ants-2.3.4-libdir.patch | 117 ++++++++++++++++++ .../ants/files/ants-2.3.4-version.patch | 17 +++ 7 files changed, 156 insertions(+), 92 deletions(-) rename sci-biology/ants/{ants-2.3.1_p20191013.ebuild => ants-2.3.4.ebuild} (69%) delete mode 100644 sci-biology/ants/files/ants-2.3.1_p20191013-logic.patch delete mode 100644 sci-biology/ants/files/ants-2.3.1_p20191013-paths.patch create mode 100644 sci-biology/ants/files/ants-2.3.4-libdir.patch create mode 100644 sci-biology/ants/files/ants-2.3.4-version.patch diff --git a/sci-biology/ants/ChangeLog b/sci-biology/ants/ChangeLog index 664210a..f8e3a05 100644 --- a/sci-biology/ants/ChangeLog +++ b/sci-biology/ants/ChangeLog @@ -1,3 +1,11 @@ +*ants-2.3.4 (04 Aug 2020) + + 04 Aug 2020; +ants-2.3.4.ebuild, + +files/ants-2.3.4-libdir.patch, +files/ants-2.3.4-version.patch, + -ants-2.3.1_p20191013.ebuild, -files/ants-2.3.1_p20191013-logic.patch, + -files/ants-2.3.1_p20191013-paths.patch: + sci-biology/ants: version bump 2.3.4 ahead of Gentoo Science + 16 May 2020; ants-2.3.1_p20191013.ebuild: sci-biology/ants: building from tarball, failing diff --git a/sci-biology/ants/Manifest b/sci-biology/ants/Manifest index 22cf812..95766db 100644 --- a/sci-biology/ants/Manifest +++ b/sci-biology/ants/Manifest @@ -1,2 +1,2 @@ -DIST 2.3.1_p20191013.tar.gz 2445357 SHA256 819e60c215e61abff2990eac20520b85083fba78598a49a5a6ff915d7206a0c4 SHA512 3de360f58de63662be7db7704a1e4b74ccba03c656ee68dde7e82f4231cbeb6e9d6c7f20a01dab57d0e54740f1f33acd40d07fbe67673993230c08d8aecd9359 WHIRLPOOL 0338d27a73f0b01a079f80129727d413833771fce306d7e839c5a2d23a6c9da71c8ee751e67928d07791cb927b746039d8c5ae6396d7baa06e6ee3217347198b -DIST ants_testdata-2.3.1_p20191013.tar.xz 25056428 SHA256 df2396d453a37674945612b2248d4ca818fce6a0b2d97beb88ab3bc59d040657 SHA512 0f86b967cd5e6c7481804c5b1dfb8d638a0560fbb08f86f04d9a3dc508a64e3181d056c2c9cdc26cbcf8eae9e45ecb29fa58580a1377ed8733b87b1b04b15ab2 WHIRLPOOL 08a5adb931b4606a0b03e32effc218d4940395472f7c2b62098472fe999cc0f0a452454619eba2bb2da775a0d5e5eb7baa966bdccf087da1d57d781061006422 +DIST ants-2.3.4.tar.gz 2455843 SHA256 590b678f6fcbfa2f7bca4ae6059f49d5cf64ad07b2ed5088fb9226cb0f28ffec SHA512 084161505671a19530bec40c8209a67510d7de6e9d5afd151b806755ca703dadbea17c0a8d5c6472c7a81185821e17213ebf1488bc0325bfe858af783e8e6575 WHIRLPOOL bbdd587645580d5e47d5d276fdeba4d76330ab9ad10e7fecc6ebebb1c83f681db1d678bbfbb9bb36775606a2cfdc89dd38a759da0cb8e4a5d8e4a3967e8634c9 +DIST ants_testdata-2.3.4.tar.xz 25056552 SHA256 75fa0ada62533aa1636fa4db9b677564723622e4b25348a0e8b3a366b6d00e82 SHA512 a266fbf2de0003ee689a9369c424c97c92cdf7e4d08ba713623948276d96c9f0f02ab14480c329f462db0059217138680bfe39654f9ec4ac99bf947f51da853d WHIRLPOOL 3d269afa1d7d9b7426000c48c3773c09bc92d3f4c790dfd71ccb6f6fc98db7e8c16534f4e852f7b5eb793819ec40b7054ff7371eb07b9219fe3787b15c118783 diff --git a/sci-biology/ants/ants-2.3.1_p20191013.ebuild b/sci-biology/ants/ants-2.3.4.ebuild similarity index 69% rename from sci-biology/ants/ants-2.3.1_p20191013.ebuild rename to sci-biology/ants/ants-2.3.4.ebuild index e286a3d..e008651 100644 --- a/sci-biology/ants/ants-2.3.1_p20191013.ebuild +++ b/sci-biology/ants/ants-2.3.4.ebuild @@ -5,15 +5,14 @@ EAPI=7 CMAKE_MAKEFILE_GENERATOR="emake" -inherit cmake-utils multilib +inherit cmake multilib -MY_COMMIT="f78b2d4a382d3090230641b5ade5da28962dad04" MY_PN="ANTs" DESCRIPTION="Advanced Normalitazion Tools for neuroimaging" HOMEPAGE="http://stnava.github.io/ANTs/" SRC_URI=" - https://github.com/ANTsX/ANTs/archive/${MY_COMMIT}.tar.gz -> ${PV}.tar.gz + https://github.com/ANTsX/ANTs/archive/v${PV}.tar.gz -> ${P}.tar.gz test? ( http://chymera.eu/distfiles/ants_testdata-${PV}.tar.xz ) @@ -26,19 +25,19 @@ IUSE="test vtk" DEPEND=" vtk? ( - ~sci-libs/itk-5.0.1[vtkglue] + ~sci-libs/itk-5.1.0[vtkglue] sci-libs/vtk ) - !vtk? ( ~sci-libs/itk-5.0.1 ) + !vtk? ( ~sci-libs/itk-5.1.0 ) " RDEPEND="${DEPEND}" PATCHES=( - "${FILESDIR}/${P}-logic.patch" - "${FILESDIR}/${P}-paths.patch" + "${FILESDIR}/${P}-version.patch" + "${FILESDIR}/${P}-libdir.patch" ) -S="${WORKDIR}/${MY_PN}-${MY_COMMIT}" +S="${WORKDIR}/${MY_PN}-${PV}" src_unpack() { default @@ -51,10 +50,11 @@ src_unpack() { src_configure() { local mycmakeargs=( -DUSE_SYSTEM_ITK=ON - -DITK_DIR="${EROOT}/usr/include/ITK-5.0/" + -DITK_DIR="${EROOT}/usr/include/ITK-5.1/" -DBUILD_TESTING="$(usex test ON OFF)" -DUSE_VTK=$(usex vtk ON OFF) -DUSE_SYSTEM_VTK=$(usex vtk ON OFF) + -DANTS_SNAPSHOT_VERSION:STRING=${PV} ) use vtk && mycmakeargs+=( -DVTK_DIR="${EROOT}/usr/include/vtk-8.1/" @@ -62,17 +62,16 @@ src_configure() { use test && mycmakeargs+=( -DExternalData_OBJECT_STORES="${S}/.ExternalData/MD5" ) - cmake-utils_src_configure + cmake_src_configure } src_install() { BUILD_DIR="${WORKDIR}/${P}_build/ANTS-build" - cmake-utils_src_install - cd "${WORKDIR}/${P}/Scripts" || die "scripts dir not found" + cmake_src_install + cd "${S}/Scripts" || die "scripts dir not found" dobin *.sh dodir /usr/$(get_libdir)/ants insinto "/usr/$(get_libdir)/ants" doins * - #install -t "${D}"/"${EROOT%/}"/usr/$(get_libdir)/ants * || die doenvd "${FILESDIR}"/99ants } 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 932da99..0000000 --- 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" -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 aaea928..0000000 --- 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 new file mode 100644 index 0000000..b593c27 --- /dev/null +++ b/sci-biology/ants/files/ants-2.3.4-libdir.patch @@ -0,0 +1,117 @@ +From 329a7be631b33294d9cf3d58e8cdeb62e0aa993c Mon Sep 17 00:00:00 2001 +From: Philip A Cook +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 new file mode 100644 index 0000000..487151d --- /dev/null +++ b/sci-biology/ants/files/ants-2.3.4-version.patch @@ -0,0 +1,17 @@ +--- 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()