Remove file collisions

sci-biology/afni/afni-9999.ebuild

@@ -1,7 +1,7 @@
 # Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=7
+EAPI=8
 
 #CMAKE_MAKEFILE_GENERATOR="emake"
 PYTHON_COMPAT=( python3_{10..11} )
@@ -11,18 +11,20 @@ inherit cmake distutils-r1 git-r3 ninja-utils
 #inherit cmake distutils-r1 git-r3 multilib ninja-utils
 
 GTS_HASH="962155a01f5a1b87bd64e3e3d880b4dbc2347ac7"
-NIFTI_HASH="65f801b9c2f1f15f4de4a19d45e6595c25765632"
-GIFTI_HASH="5eae81ba1e87ef3553df3b6ba585f12dc81a0030"
+#NIFTI_HASH="65f801b9c2f1f15f4de4a19d45e6595c25765632"
+NIFTI_HASH="da476fd27f46098f37f5c9c4c1baee01e559572c"
+#GIFTI_HASH="5eae81ba1e87ef3553df3b6ba585f12dc81a0030"
+GIFTI_HASH="d3e873d8539d9b469daf7db04093da1d7e73d4f7"
 
 DESCRIPTION="Advanced Normalitazion Tools for neuroimaging"
 HOMEPAGE="http://stnava.github.io/ANTs/"
 SRC_URI="
-	https://github.com/leej3/gts/archive/${GTS_HASH}.tar.gz
 	https://github.com/NIFTI-Imaging/nifti_clib/archive/${NIFTI_HASH}.tar.gz
 	https://github.com/NIFTI-Imaging/gifti_clib/archive/${GIFTI_HASH}.tar.gz
 	"
-EGIT_REPO_URI="https://github.com/leej3/afni.git"
-EGIT_BRANCH="make_some_build_fixes_for_gentoo_packaging"
+	#https://github.com/leej3/gts/archive/${GTS_HASH}.tar.gz
+EGIT_REPO_URI="https://github.com/TheChymera/afni.git"
+EGIT_BRANCH="packaging"
 
 SLOT="0"
 LICENSE="GPL-3+"
@@ -41,6 +43,7 @@ RDEPEND="
 	media-libs/qhull
 	media-video/mpeg-tools
 	sci-libs/gsl
+	sci-libs/gts
 	sys-devel/llvm:*
 	sys-libs/libomp
 	dev-libs/libpthread-stubs
@@ -58,12 +61,11 @@ DEPEND="
 	app-shells/tcsh
 	"
 # Prospectively:
-#sci-libs/gts
 #Update jpeg-compat to virtual/jpeg:0
 # look for xmhtlm
 
+	#tar xf "${DISTDIR}/${GTS_HASH}.tar.gz" || die
 src_prepare() {
-	tar xf "${DISTDIR}/${GTS_HASH}.tar.gz" || die
 	tar xf "${DISTDIR}/${NIFTI_HASH}.tar.gz" || die
 	tar xf "${DISTDIR}/${GIFTI_HASH}.tar.gz" || die
 	cmake_src_prepare
@@ -76,19 +78,21 @@ src_configure() {
 	export GIT_REPO_VERSION=3.0.1.1
 	#export LDFLAGS="-lpthread ${LDFLAGS}"
 	#-CC="$(tc-getCC)"
+		#-DFETCHCONTENT_SOURCE_DIR_GTS="${WORKDIR}/${P}/gts-${GTS_HASH}"
+		#-DUSE_SYSTEM_GTS=OFF
 	local mycmakeargs=(
 		-GNinja
 		-DLIBDIR=/usr/$(get_libdir)
 		-DNIFTI_INSTALL_LIBRARY_DIR=/usr/$(get_libdir)
 		-DGIFTI_INSTALL_LIBRARY_DIR=/usr/$(get_libdir)
+		-DGIFTI_INSTALL_LIB_DIR=/usr/$(get_libdir)
 		-DAFNI_INSTALL_LIBRARY_DIR=/usr/$(get_libdir)
 		-DCMAKE_INSTALL_LIBDIR=/usr/$(get_libdir)
 		-DCOMP_COREBINARIES=ON
 		-DUSE_SYSTEM_NIFTI=OFF
 		-DUSE_SYSTEM_GIFTI=OFF
 		-DUSE_SYSTEM_XMHTML=OFF
-		-DUSE_SYSTEM_GTS=OFF
-		-DFETCHCONTENT_SOURCE_DIR_GTS="${WORKDIR}/${P}/gts-${GTS_HASH}"
+		-DUSE_SYSTEM_GTS=ON
 		-DFETCHCONTENT_SOURCE_DIR_NIFTI_CLIB="${WORKDIR}/${P}/nifti_clib-${NIFTI_HASH}"
 		-DFETCHCONTENT_SOURCE_DIR_GIFTI_CLIB="${WORKDIR}/${P}/gifti_clib-${GIFTI_HASH}"
 		-DCOMP_GUI=ON
@@ -98,14 +102,13 @@ src_configure() {
 		-DPython_FIND_VIRTUALENV=STANDARD
 		-DPython_FIND_STRATEGY=LOCATION
 	)
+		#-DBUILD_SHARED_LIBS=OFF
 	tc-export CC
 	cmake_src_configure
 }
 
 src_compile() {
 	cd ../afni-9999_build
-	pwd
-	ls -la
 	eninja || die
 }
 
@@ -113,6 +116,18 @@ src_compile() {
 
 src_install() {
 	cd ../afni-9999_build
+	# File collision, upstream confirmation here:
+	# https://github.com/afni/afni/issues/558#issuecomment-1887693900
+	#pwd
+	#ls -lah
+	#addpredict targets_built/libf2c.so
+	#rm targets_built/libf2c.so
+	#addpredict /usr/lib64/libf2c.so
+	#addpredict /usr/bin/whirlgif
+	#addpredict /usr/bin/mpeg_encode
+	#exit
+	rm targets_built/whirlgif
+	rm targets_built/mpeg_encode
 	DESTDIR=${D} eninja install
 	# This is old example ants stuff.
 	#BUILD_DIR="${WORKDIR}/${P}_build/ANTS-build"