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 <chr@chymera.eu>
This commit is contained in:
Horea Christian
parent
4124c531d9
commit
3d7eff6d69
@ -1,3 +1,11 @@
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*ants-2.3.4 (04 Aug 2020)
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04 Aug 2020; <chymera@gentoo.org> +ants-2.3.4.ebuild,
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+files/ants-2.3.4-libdir.patch, +files/ants-2.3.4-version.patch,
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-ants-2.3.1_p20191013.ebuild, -files/ants-2.3.1_p20191013-logic.patch,
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-files/ants-2.3.1_p20191013-paths.patch:
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sci-biology/ants: version bump 2.3.4 ahead of Gentoo Science
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16 May 2020; <chymera@gentoo.org> ants-2.3.1_p20191013.ebuild:
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sci-biology/ants: building from tarball, failing
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@ -1,2 +1,2 @@
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DIST 2.3.1_p20191013.tar.gz 2445357 SHA256 819e60c215e61abff2990eac20520b85083fba78598a49a5a6ff915d7206a0c4 SHA512 3de360f58de63662be7db7704a1e4b74ccba03c656ee68dde7e82f4231cbeb6e9d6c7f20a01dab57d0e54740f1f33acd40d07fbe67673993230c08d8aecd9359 WHIRLPOOL 0338d27a73f0b01a079f80129727d413833771fce306d7e839c5a2d23a6c9da71c8ee751e67928d07791cb927b746039d8c5ae6396d7baa06e6ee3217347198b
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DIST ants_testdata-2.3.1_p20191013.tar.xz 25056428 SHA256 df2396d453a37674945612b2248d4ca818fce6a0b2d97beb88ab3bc59d040657 SHA512 0f86b967cd5e6c7481804c5b1dfb8d638a0560fbb08f86f04d9a3dc508a64e3181d056c2c9cdc26cbcf8eae9e45ecb29fa58580a1377ed8733b87b1b04b15ab2 WHIRLPOOL 08a5adb931b4606a0b03e32effc218d4940395472f7c2b62098472fe999cc0f0a452454619eba2bb2da775a0d5e5eb7baa966bdccf087da1d57d781061006422
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DIST ants-2.3.4.tar.gz 2455843 SHA256 590b678f6fcbfa2f7bca4ae6059f49d5cf64ad07b2ed5088fb9226cb0f28ffec SHA512 084161505671a19530bec40c8209a67510d7de6e9d5afd151b806755ca703dadbea17c0a8d5c6472c7a81185821e17213ebf1488bc0325bfe858af783e8e6575 WHIRLPOOL bbdd587645580d5e47d5d276fdeba4d76330ab9ad10e7fecc6ebebb1c83f681db1d678bbfbb9bb36775606a2cfdc89dd38a759da0cb8e4a5d8e4a3967e8634c9
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DIST ants_testdata-2.3.4.tar.xz 25056552 SHA256 75fa0ada62533aa1636fa4db9b677564723622e4b25348a0e8b3a366b6d00e82 SHA512 a266fbf2de0003ee689a9369c424c97c92cdf7e4d08ba713623948276d96c9f0f02ab14480c329f462db0059217138680bfe39654f9ec4ac99bf947f51da853d WHIRLPOOL 3d269afa1d7d9b7426000c48c3773c09bc92d3f4c790dfd71ccb6f6fc98db7e8c16534f4e852f7b5eb793819ec40b7054ff7371eb07b9219fe3787b15c118783
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@ -5,15 +5,14 @@ EAPI=7
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CMAKE_MAKEFILE_GENERATOR="emake"
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inherit cmake-utils multilib
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inherit cmake multilib
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MY_COMMIT="f78b2d4a382d3090230641b5ade5da28962dad04"
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MY_PN="ANTs"
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DESCRIPTION="Advanced Normalitazion Tools for neuroimaging"
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HOMEPAGE="http://stnava.github.io/ANTs/"
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SRC_URI="
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https://github.com/ANTsX/ANTs/archive/${MY_COMMIT}.tar.gz -> ${PV}.tar.gz
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https://github.com/ANTsX/ANTs/archive/v${PV}.tar.gz -> ${P}.tar.gz
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test? (
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http://chymera.eu/distfiles/ants_testdata-${PV}.tar.xz
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)
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@ -26,19 +25,19 @@ IUSE="test vtk"
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DEPEND="
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vtk? (
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~sci-libs/itk-5.0.1[vtkglue]
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~sci-libs/itk-5.1.0[vtkglue]
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sci-libs/vtk
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)
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!vtk? ( ~sci-libs/itk-5.0.1 )
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!vtk? ( ~sci-libs/itk-5.1.0 )
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"
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RDEPEND="${DEPEND}"
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PATCHES=(
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"${FILESDIR}/${P}-logic.patch"
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"${FILESDIR}/${P}-paths.patch"
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"${FILESDIR}/${P}-version.patch"
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"${FILESDIR}/${P}-libdir.patch"
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)
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S="${WORKDIR}/${MY_PN}-${MY_COMMIT}"
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S="${WORKDIR}/${MY_PN}-${PV}"
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src_unpack() {
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default
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@ -51,10 +50,11 @@ src_unpack() {
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src_configure() {
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local mycmakeargs=(
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-DUSE_SYSTEM_ITK=ON
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-DITK_DIR="${EROOT}/usr/include/ITK-5.0/"
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-DITK_DIR="${EROOT}/usr/include/ITK-5.1/"
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-DBUILD_TESTING="$(usex test ON OFF)"
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-DUSE_VTK=$(usex vtk ON OFF)
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-DUSE_SYSTEM_VTK=$(usex vtk ON OFF)
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-DANTS_SNAPSHOT_VERSION:STRING=${PV}
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)
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use vtk && mycmakeargs+=(
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-DVTK_DIR="${EROOT}/usr/include/vtk-8.1/"
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@ -62,17 +62,16 @@ src_configure() {
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use test && mycmakeargs+=(
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-DExternalData_OBJECT_STORES="${S}/.ExternalData/MD5"
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)
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cmake-utils_src_configure
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cmake_src_configure
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}
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src_install() {
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BUILD_DIR="${WORKDIR}/${P}_build/ANTS-build"
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cmake-utils_src_install
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cd "${WORKDIR}/${P}/Scripts" || die "scripts dir not found"
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cmake_src_install
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cd "${S}/Scripts" || die "scripts dir not found"
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dobin *.sh
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dodir /usr/$(get_libdir)/ants
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insinto "/usr/$(get_libdir)/ants"
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doins *
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#install -t "${D}"/"${EROOT%/}"/usr/$(get_libdir)/ants * || die
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doenvd "${FILESDIR}"/99ants
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}
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@ -1,37 +0,0 @@
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From b2c828ff8e5ce537d7096af04b086e965fede9e8 Mon Sep 17 00:00:00 2001
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From: "Gabriel A. Devenyi" <gdevenyi@gmail.com>
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Date: Mon, 7 Oct 2019 22:01:51 -0400
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Subject: [PATCH] Fix install logic
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---
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ANTS.cmake | 3 ++-
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SuperBuild.cmake | 2 ++
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2 files changed, 4 insertions(+), 1 deletion(-)
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diff --git a/ANTS.cmake b/ANTS.cmake
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index a1baf845..95ffdc74 100644
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--- a/ANTS.cmake
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+++ b/ANTS.cmake
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@@ -172,7 +172,8 @@ install(PROGRAMS Scripts/ANTSpexec.sh
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COMPONENT SCRIPTS
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)
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-if(BUILD_SHARED_LIBS AND NOT (USE_SYSTEM_ITK AND USE_SYSTEM_VTK))
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+#Only install ITK/VTK libraries if shared build and superbuild is used
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+if(BUILD_SHARED_LIBS AND ((NOT USE_SYSTEM_ITK) OR ((NOT USE_SYSTEM_VTK) AND USE_VTK)))
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install(DIRECTORY ${CMAKE_BINARY_DIR}/../staging/lib/
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DESTINATION lib)
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endif()
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diff --git a/SuperBuild.cmake b/SuperBuild.cmake
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index f4630e64..32b930c2 100644
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--- a/SuperBuild.cmake
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+++ b/SuperBuild.cmake
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@@ -207,6 +207,8 @@ list(APPEND ${CMAKE_PROJECT_NAME}_SUPERBUILD_EP_VARS
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CMAKE_C_COMPILER_LAUNCHER:STRING
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CMAKE_CXX_COMPILER_LAUNCHER:STRING
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CMAKE_CUDA_COMPILER_LAUNCHER:STRING
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+ USE_SYSTEM_ITK:BOOL
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+ USE_SYSTEM_VTK:BOOL
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)
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_expand_external_project_vars()
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@ -1,40 +0,0 @@
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diff --git a/Examples/CMakeLists.txt b/Examples/CMakeLists.txt
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--- a/Examples/CMakeLists.txt
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+++ b/Examples/CMakeLists.txt
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@@ -16,8 +16,9 @@
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+include(GNUInstallDirs)
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install(TARGETS antsUtilities
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- RUNTIME DESTINATION bin
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+ RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}
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COMPONENT RUNTIME_antsUtilities
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- LIBRARY DESTINATION lib
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+ LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
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COMPONENT RUNTIME_antsUtilities
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- ARCHIVE DESTINATION lib
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+ ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}
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COMPONENT DEVELOPMENT_antsUtilities
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)
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@@ -38,8 +38,8 @@
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install(TARGETS l_${ANTS_FUNCTION_NAME} ${ANTS_FUNCTION_NAME}
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- RUNTIME DESTINATION bin
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+ RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}
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COMPONENT RUNTIME_${ANTS_FUNCTION_NAME}
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- LIBRARY DESTINATION lib
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+ LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
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COMPONENT RUNTIME_${ANTS_FUNCTION_NAME}
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- ARCHIVE DESTINATION lib
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+ ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}
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COMPONENT DEVELOPMENT_${ANTS_FUNCTION_NAME}
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)
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@@ -61,8 +61,8 @@
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install(TARGETS l_${ANTS_FUNCTION_NAME} ${ANTS_FUNCTION_NAME}
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- RUNTIME DESTINATION bin
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+ RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}
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COMPONENT RUNTIME_${ANTS_FUNCTION_NAME}
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- LIBRARY DESTINATION lib
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+ LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
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COMPONENT RUNTIME_${ANTS_FUNCTION_NAME}
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- ARCHIVE DESTINATION lib
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+ ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}
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COMPONENT DEVELOPMENT_${ANTS_FUNCTION_NAME}
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)
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117
sci-biology/ants/files/ants-2.3.4-libdir.patch
Normal file
117
sci-biology/ants/files/ants-2.3.4-libdir.patch
Normal file
@ -0,0 +1,117 @@
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From 329a7be631b33294d9cf3d58e8cdeb62e0aa993c Mon Sep 17 00:00:00 2001
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From: Philip A Cook <cookpa@pennmedicine.upenn.edu>
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Date: Fri, 26 Jun 2020 18:23:08 +0000
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Subject: [PATCH] ENH: Use GNUInstallDirs CMake module
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Trying to enable installation to the correct lib dir for each platform
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---
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Common.cmake | 7 +++++--
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Examples/CMakeLists.txt | 32 ++++++++++++++++----------------
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2 files changed, 21 insertions(+), 18 deletions(-)
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diff --git a/Common.cmake b/Common.cmake
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index 5e52d7f1..1e604113 100644
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--- a/Common.cmake
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+++ b/Common.cmake
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@@ -103,8 +103,6 @@ if(PLATFORM_CHECK)
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endif()
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endif()
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-
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-
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#-------------------------------------------------------------------------
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# Augment compiler flags
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#-------------------------------------------------------------------------
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@@ -124,3 +122,8 @@ if(NOT CMAKE_POSITION_INDEPENDENT_CODE)
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set(CMAKE_POSITION_INDEPENDENT_CODE ON)
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endif()
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endif()
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+
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+#-------------------------------------------------------------------------
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+# Define install dirs for different platforms
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+#-------------------------------------------------------------------------
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+include(GNUInstallDirs)
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diff --git a/Examples/CMakeLists.txt b/Examples/CMakeLists.txt
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index 61781f56..cb352748 100644
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--- a/Examples/CMakeLists.txt
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+++ b/Examples/CMakeLists.txt
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@@ -1,4 +1,4 @@
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-SET(CMAKE_INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/lib")
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+SET(CMAKE_INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_LIBDIR}")
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## Note that the antsUtilities can always be built static. It will then be linked
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## Directly into the other libraries.
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add_library(antsUtilities antsUtilities.cxx
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@@ -14,11 +14,11 @@ add_library(antsUtilities antsUtilities.cxx
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)
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target_link_libraries(antsUtilities ${ITK_LIBRARIES} )
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install(TARGETS antsUtilities
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- RUNTIME DESTINATION bin
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+ RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}
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COMPONENT RUNTIME_antsUtilities
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- LIBRARY DESTINATION lib
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+ LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
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COMPONENT RUNTIME_antsUtilities
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- ARCHIVE DESTINATION lib
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+ ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}
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COMPONENT DEVELOPMENT_antsUtilities
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)
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@@ -34,22 +34,22 @@ macro(STATIC_ANTS_BUILD ANTS_FUNCTION_NAME EXTRA_LIBS)
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if (ANTS_INSTALL_LIBS_ONLY)
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install(TARGETS l_${ANTS_FUNCTION_NAME}
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- # RUNTIME DESTINATION bin
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+ # RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}
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# COMPONENT RUNTIME_${ANTS_FUNCTION_NAME}
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- LIBRARY DESTINATION lib
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+ LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
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COMPONENT RUNTIME_${ANTS_FUNCTION_NAME}
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- ARCHIVE DESTINATION lib
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+ ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}
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COMPONENT DEVELOPMENT_${ANTS_FUNCTION_NAME}
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)
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else()
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add_executable( ${ANTS_FUNCTION_NAME} cli_${ANTS_FUNCTION_NAME}.cxx )
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target_link_libraries( ${ANTS_FUNCTION_NAME} l_${ANTS_FUNCTION_NAME} )
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install(TARGETS l_${ANTS_FUNCTION_NAME} ${ANTS_FUNCTION_NAME}
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- RUNTIME DESTINATION bin
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+ RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}
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COMPONENT RUNTIME_${ANTS_FUNCTION_NAME}
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- LIBRARY DESTINATION lib
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+ LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
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COMPONENT RUNTIME_${ANTS_FUNCTION_NAME}
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- ARCHIVE DESTINATION lib
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+ ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}
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COMPONENT DEVELOPMENT_${ANTS_FUNCTION_NAME}
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)
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endif()
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@@ -68,11 +68,11 @@ macro(DYNAMIC_ANTS_BUILD ANTS_FUNCTION_NAME EXTRA_LIBS)
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if (ANTS_INSTALL_LIBS_ONLY)
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install(TARGETS l_${ANTS_FUNCTION_NAME}
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- # RUNTIME DESTINATION bin
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+ # RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}
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# COMPONENT RUNTIME_${ANTS_FUNCTION_NAME}
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- LIBRARY DESTINATION lib
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+ LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
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COMPONENT RUNTIME_${ANTS_FUNCTION_NAME}
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- ARCHIVE DESTINATION lib
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+ ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}
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COMPONENT DEVELOPMENT_${ANTS_FUNCTION_NAME}
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)
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else()
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@@ -80,11 +80,11 @@ macro(DYNAMIC_ANTS_BUILD ANTS_FUNCTION_NAME EXTRA_LIBS)
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target_link_libraries( ${ANTS_FUNCTION_NAME} l_${ANTS_FUNCTION_NAME} )
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install(TARGETS l_${ANTS_FUNCTION_NAME} ${ANTS_FUNCTION_NAME}
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- RUNTIME DESTINATION bin
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+ RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}
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COMPONENT RUNTIME_${ANTS_FUNCTION_NAME}
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- LIBRARY DESTINATION lib
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+ LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
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COMPONENT RUNTIME_${ANTS_FUNCTION_NAME}
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- ARCHIVE DESTINATION lib
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+ ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}
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COMPONENT DEVELOPMENT_${ANTS_FUNCTION_NAME}
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)
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endif()
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17
sci-biology/ants/files/ants-2.3.4-version.patch
Normal file
17
sci-biology/ants/files/ants-2.3.4-version.patch
Normal file
@ -0,0 +1,17 @@
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--- a/ANTS.cmake 2020-06-08 12:11:14.000000000 -0400
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+++ b/ANTS.cmake 2020-08-03 16:44:00.826633506 -0400
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@@ -37,7 +37,6 @@
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set(${PROJECT_NAME}_VERSION_MAJOR 0)
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set(${PROJECT_NAME}_VERSION_MINOR 0)
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set(${PROJECT_NAME}_VERSION_PATCH 0)
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- set(${PROJECT_NAME}_VERSION_TWEAK 0)
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set(${PROJECT_NAME}_VERSION "snapshot-${ANTS_SNAPSHOT_VERSION}")
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endif()
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@@ -46,7 +45,6 @@
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set(${PROJECT_NAME}_VERSION_MAJOR 0)
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set(${PROJECT_NAME}_VERSION_MINOR 0)
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set(${PROJECT_NAME}_VERSION_PATCH 0)
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- set(${PROJECT_NAME}_VERSION_TWEAK 0)
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set(${PROJECT_NAME}_VERSION "0.0.0.0")
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endif()
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