sci-biology/afni: version bump 19.3.12 (non-masked version)

Package-Manager: Portage-2.3.79, Repoman-2.3.18
Signed-off-by: Horea Christian <chr@chymera.eu>

2 files changed, 73 insertions, 0 deletions

diff --git a/sci-biology/afni/Manifest b/sci-biology/afni/Manifest
index 7a32c9376..18e3dcb87 100644
--- a/sci-biology/afni/Manifest
+++ b/sci-biology/afni/Manifest
@@ -1,2 +1,3 @@
 DIST afni-18.1.04.tar.gz 196776384 BLAKE2B 389c2dcf11bf3e3d067cbe1cce772a299b6f9096e21936616893041f72b2d3f490b3bed6ef10d94dd5f7c08436206379339a05384ac005349f55d40bb241e695 SHA512 16151d2512d115a2e4531932cbfd50cb1cf6c2e5c809d91fb439495d7d62f2d50f05f5f411395af0cc24e9a34bf8e98efd389b9e50bc75f783e051e7ab3db121
 DIST afni-19.0.21.tar.gz 38228297 BLAKE2B 2d04b1d27c39bfbdfe9319a464920604b21f646e0f68d3d06d9ffffd7415e7c299fff983316834b84417a303229731abd2799a6f20e1edab56188726124ed436 SHA512 fbc01ca2acb5f6d64f539942661e9500407ccf5f6d583c7685eac85b81326414e3d9959372c49ed6f6b95f5b0fca2e936207a47313b753ffd3190dc8c474b78a
+DIST afni-19.3.12.tar.gz 42337320 BLAKE2B f8f3347e38b7c4b3d720c3c49d5bc50f1057b1d3945e6a33b8415e84e7e539577e5eb351cfc61c53269b6a465619f900b9edcb25830ea056a53f54beb683b0ad SHA512 c4f9303312a89a6e87285646f58223df40b07329cf155bf251a48e8e63302988f103a97363d0666ddd8e9f62f762cf0c219bfc995265b4fe1f1ff5f782025371
diff --git a/sci-biology/afni/afni-19.3.12.ebuild b/sci-biology/afni/afni-19.3.12.ebuild
new file mode 100644
index 000000000..c60a87138
--- /dev/null
+++ b/sci-biology/afni/afni-19.3.12.ebuild
@@ -0,0 +1,72 @@
+# Copyright 1999-2019 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit eutils multilib pax-utils toolchain-funcs
+
+DESCRIPTION="An open-source environment for processing and displaying functional MRI data"
+HOMEPAGE="http://afni.nimh.nih.gov/"
+SRC_URI="https://github.com/afni/afni/archive/AFNI_${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="GPL-3+"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+RDEPEND="dev-libs/expat
+	media-libs/glu
+	media-libs/netpbm
+	media-libs/qhull
+	media-video/mpeg-tools
+	sci-libs/gsl
+	sys-devel/llvm:*
+	virtual/jpeg:0
+	x11-libs/libGLw
+	x11-libs/libXft
+	x11-libs/libXi
+	x11-libs/libXpm
+	x11-libs/motif[-static-libs]"
+
+# x11-libs/motif[static-libs] breaks the build.
+# See upstream discussion
+# http://afni.nimh.nih.gov/afni/community/board/read.php?1,85348,85348#msg-85348
+
+DEPEND="${RDEPEND}
+	app-shells/tcsh"
+
+S="${WORKDIR}/${PN}-AFNI_${PV}/src"
+BUILD="linux_fedora_19_64"
+BIN_CONFLICTS=(qdelaunay whirlgif djpeg cjpeg qhull rbox count mpeg_encode)
+
+src_prepare() {
+	find -type f -exec sed -i -e "s/-lXp //g" {} +
+	cp other_builds/Makefile.${BUILD} Makefile || die "Could not copy Makefile"
+	# Unbundle imcat
+	sed -e "s/ imcat / /g" \
+		-i Makefile.INCLUDE || die "Could not edit includes files."
+	sed -e "s~CC     = /usr/bin/gcc -O2 -m64~CC     = $(tc-getCC) \$(CFLAGS)~" \
+		-e "s~CCMIN  = /usr/bin/gcc -m64~CCMIN  = $(tc-getCC) \$(CFLAGS)~" \
+		-e "s~LD     = /usr/bin/gcc~LD     = $(tc-getCC)~" \
+		-e "s~AR     = /usr/bin/ar~AR     = $(tc-getAR)~" \
+		-e "s~RANLIB = /usr/bin/ranlib~RANLIB = $(tc-getRANLIB)~" \
+		-i Makefile || die "Could not edit Makefile"
+		# they provide somewhat problematic makefiles :(
+	sed -e "s~ifeq ($(CC),gcc)~ifeq (1,1)~"\
+		-i SUMA/SUMA_Makefile || die "Could not edit SUMA/SUMA_Makefile"
+		# upstream checks if $CC is EXACTLY gcc, else sets variables for Mac
+	find "${S}" -iname "*Makefile*" | xargs sed -e "s~/usr/~${EROOT}/usr/~g;" -i
+	eapply_user
+}
+
+src_compile() {
+	emake -j1 all plugins suma_exec
+}
+
+src_install() {
+	emake INSTALLDIR="${ED}/usr/bin" -j1 install install_plugins
+	emake INSTALLDIR="${ED}/usr/$(get_libdir)" -j1 install_lib
+	for CONFLICT in ${BIN_CONFLICTS[@]}; do
+		rm "${ED}/usr/bin/${CONFLICT}"
+	done
+}