sci-biology/ants: pushed to Gentoo Science
https://gitweb.gentoo.org/proj/sci.git/commit/?id=40022cd56f21a7152d812b6435734aafa032c7f8 Signed-off-by: Horea Christian <chr@chymera.eu>
This commit is contained in:
Horea Christian
parent
5a99fee6e2
commit
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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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*ants-2.3.1_p20191013 (14 Dec 2019)
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14 Dec 2019; <chymera@gentoo.org> +ants-2.3.1_p20191013.ebuild,
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-ants-9999.ebuild, metadata.xml:
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sci-biology/ants: prefix fix ahead of Gentoo Science
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25 Nov 2019; <chymera@gentoo.org> -ants-2.3.1_p20191013.ebuild:
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sci-biology/ants: migrated version bump to Gentoo Scinece https://gitweb.gent
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oo.org/proj/sci.git/commit/?id=402183f38c721910fe038ed4ce04e0a98a37c584
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17 Oct 2019; <chymera@gentoo.org> ants-9999.ebuild:
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sci-biology/ants: patch merged by ANTs upstream
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13 Oct 2019; <chymera@gentoo.org> +files/ants-2.3.1_p20191013-logic.patch,
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+files/ants-2.3.1_p20191013-paths.patch, ants-2.3.1_p20191013.ebuild,
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ants-9999.ebuild:
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sci-biology/ants: updated ebuild style
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23 Sep 2019; <chymera@gentoo.org> ants-2.3.1_p20190704.ebuild:
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sci-biology/ants: improved testing support
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*ants-2.3.1_p20190704 (21 Sep 2019)
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21 Sep 2019; <chymera@gentoo.org> +ants-2.3.1_p20190704.ebuild,
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-ants-2.3.1-r1.ebuild, -ants-2.3.1.ebuild, ants-9999.ebuild:
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sci-biology/ants: version bump 2.3.1_p20190704
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*ants-2.3.1 (18 May 2019)
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18 May 2019; <chymera@gentoo.org> +ants-2.3.1.ebuild:
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sci-biology/ants: unsandboxed fix fro bundling Do not include in Gentoo
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Science, work on unbundled revbump
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*ants-2.3.1-r1 (25 Mar 2019)
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*ants-9999 (25 Mar 2019)
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25 Mar 2019; <chymera@gentoo.org> +ants-2.3.1-r1.ebuild, +ants-9999.ebuild,
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+files/99ants, +metadata.xml:
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sci-biology/ants: fixes ahead of Gentoo Science
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@ -1,2 +0,0 @@
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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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@ -1,77 +0,0 @@
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# Copyright 1999-2020 Gentoo Authors
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# Distributed under the terms of the GNU General Public License v2
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EAPI=7
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CMAKE_MAKEFILE_GENERATOR="emake"
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inherit cmake multilib
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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/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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"
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SLOT="0"
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LICENSE="BSD"
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KEYWORDS="~amd64 ~x86"
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IUSE="test vtk"
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DEPEND="
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vtk? (
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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-5.1.0 )
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"
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RDEPEND="${DEPEND}"
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PATCHES=(
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"${FILESDIR}/${P}-version.patch"
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"${FILESDIR}/${P}-libdir.patch"
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)
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S="${WORKDIR}/${MY_PN}-${PV}"
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src_unpack() {
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default
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if use test; then
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mkdir -p "${S}/.ExternalData/MD5" || die "Could not create test data directory."
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tar xvf "${DISTDIR}/ants_testdata-${PV}.tar.xz" -C "${S}/.ExternalData/MD5/" > /dev/null || die "Could not unpack test data."
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fi
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}
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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="${EROOT}/usr/include/ITK-5.1/"
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-DBUILD_TESTING="$(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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)
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use test && mycmakeargs+=(
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-DExternalData_OBJECT_STORES="${S}/.ExternalData/MD5"
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)
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cmake_src_configure
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}
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src_install() {
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BUILD_DIR="${WORKDIR}/${P}_build/ANTS-build"
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cmake_src_install
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cd "${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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doenvd "${FILESDIR}"/99ants
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}
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@ -1 +0,0 @@
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ANTSPATH=/usr/bin/
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@ -1,117 +0,0 @@
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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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@ -1,17 +0,0 @@
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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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@ -1,24 +0,0 @@
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<?xml version="1.0" encoding="UTF-8"?>
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<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
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<pkgmetadata>
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<maintainer type="person">
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<email>chr@chymera.eu</email>
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<name>Horea Christian</name>
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</maintainer>
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<maintainer type="project">
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<email>sci@gentoo.org</email>
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<name>Gentoo Science Project</name>
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</maintainer>
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<longdescription>
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ANTs extracts information from complex datasets that include imaging
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(Word Cloud). Paired with ANTsR (answer), ANTs is useful for managing,
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interpreting and visualizing multidimensional data. ANTs is popularly
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considered a state-of-the-art medical image registration and segmentation
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toolkit. ANTsR is an emerging tool supporting standardized multimodality
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image analysis. ANTs depends on the Insight ToolKit (ITK), a widely used
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medical image processing library to which ANTs developers contribute.
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</longdescription>
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<use>
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<flag name="vtk">Optional support for a number of surface enabled tools (via sci-libs/vtk).</flag>
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</use>
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</pkgmetadata>
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