* [gentoo-commits] proj/sci:master commit in: profiles/, sci-biology/afni/
@ 2018-06-25 1:22 Horea Christian
0 siblings, 0 replies; 2+ messages in thread
From: Horea Christian @ 2018-06-25 1:22 UTC (permalink / raw
To: gentoo-commits
commit: d361c9c4a2380e2f918740463206ca430fe60e24
Author: Horea Christian <horea.christ <AT> yandex <DOT> com>
AuthorDate: Mon Jun 25 01:10:25 2018 +0000
Commit: Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Mon Jun 25 01:22:05 2018 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=d361c9c4
sci-biology/afni: new package
Package-Manager: Portage-2.3.40, Repoman-2.3.9
profiles/package.mask | 7 ++++
sci-biology/afni/afni-18.1.04.ebuild | 68 +++++++++++++++++++++++++++++++++++
sci-biology/afni/afni-9999.ebuild | 69 ++++++++++++++++++++++++++++++++++++
sci-biology/afni/metadata.xml | 16 +++++++++
4 files changed, 160 insertions(+)
diff --git a/profiles/package.mask b/profiles/package.mask
index 73022d876..9ea56c307 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -30,6 +30,13 @@
#--- END OF EXAMPLES ---
+# Horea Christian <horea.christ@gmail.com> (10 Mar 2012)
+# Serious bundling issues, upstream does not support Gentoo
+# or more generally unbundling. Masked until unbundling
+# efforts ( https://github.com/afni/afni/pull/60 ) come to
+# fruition.
+=sci-biology/afni-18.1.04
+
# Sebasien Fabbro <bicatali@gentoo.org> (10 Mar 2012)
# incompatible API with previous versions of metis (4)
# masked until reverse depedencies are fixed
diff --git a/sci-biology/afni/afni-18.1.04.ebuild b/sci-biology/afni/afni-18.1.04.ebuild
new file mode 100644
index 000000000..3a646ffb7
--- /dev/null
+++ b/sci-biology/afni/afni-18.1.04.ebuild
@@ -0,0 +1,68 @@
+# Copyright 1999-2018 Gentoo Foundation
+# 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 -> ${P}.tar.gz"
+
+LICENSE="GPL-3+"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE=""
+
+RDEPEND="dev-libs/expat
+ media-libs/netpbm
+ media-libs/qhull
+ media-video/mpeg-tools
+ sci-libs/gsl
+ sys-devel/llvm:*
+ virtual/jpeg:0
+ x11-libs/libGLw
+ x11-libs/libXft
+ x11-libs/libXi
+ x11-libs/libXpm
+ x11-libs/motif[-static-libs]"
+
+# x11-libs/motif[static-libs] breaks the build.
+# See upstream discussion
+# http://afni.nimh.nih.gov/afni/community/board/read.php?1,85348,85348#msg-85348
+
+DEPEND="${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"
+ 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/${CONFLICT}"
+ done
+}
diff --git a/sci-biology/afni/afni-9999.ebuild b/sci-biology/afni/afni-9999.ebuild
new file mode 100644
index 000000000..e73bef8cc
--- /dev/null
+++ b/sci-biology/afni/afni-9999.ebuild
@@ -0,0 +1,69 @@
+# Copyright 1999-2018 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit eutils multilib pax-utils git-r3 toolchain-funcs
+
+DESCRIPTION="An open-source environment for processing and displaying functional MRI data"
+HOMEPAGE="http://afni.nimh.nih.gov/"
+SRC_URI=""
+EGIT_REPO_URI="https://github.com/AFNI/AFNI"
+
+LICENSE="GPL-3+"
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+RDEPEND="dev-libs/expat
+ media-libs/netpbm
+ media-libs/qhull
+ media-video/mpeg-tools
+ sci-libs/gsl
+ sys-devel/llvm:*
+ virtual/jpeg:0
+ x11-libs/libGLw
+ x11-libs/libXft
+ x11-libs/libXi
+ x11-libs/libXpm
+ x11-libs/motif[-static-libs]"
+
+# x11-libs/motif[static-libs] breaks the build.
+# See upstream discussion
+# http://afni.nimh.nih.gov/afni/community/board/read.php?1,85348,85348#msg-85348
+
+DEPEND="${RDEPEND}
+ app-shells/tcsh"
+
+S="${WORKDIR}/${P}/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"
+ 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
+}
diff --git a/sci-biology/afni/metadata.xml b/sci-biology/afni/metadata.xml
new file mode 100644
index 000000000..0923769c1
--- /dev/null
+++ b/sci-biology/afni/metadata.xml
@@ -0,0 +1,16 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="person">
+ <email>horea.christ@gmail.com</email>
+ <name>Horea Christian</name>
+ </maintainer>
+ <maintainer type="project">
+ <email>sci@gentoo.org</email>
+ <name>Gentoo Science Project</name>
+ </maintainer>
+ <longdescription>
+ Analysis of Functional NeuroImages (AFNI) is an open-source environment for processing and displaying
+ functional MRI data—a technique for mapping human brain activity.
+ </longdescription>
+</pkgmetadata>
^ permalink raw reply related [flat|nested] 2+ messages in thread
* [gentoo-commits] proj/sci:master commit in: profiles/, sci-biology/afni/
@ 2019-03-02 18:08 Horea Christian
0 siblings, 0 replies; 2+ messages in thread
From: Horea Christian @ 2019-03-02 18:08 UTC (permalink / raw
To: gentoo-commits
commit: 9c3493015edd58f073ee3d0493753721a04a7d6b
Author: Horea Christian <horea.christ <AT> yandex <DOT> com>
AuthorDate: Sat Mar 2 18:05:25 2019 +0000
Commit: Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Sat Mar 2 18:07:33 2019 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=9c349301
sci-biology/afni: version bump
Package-Manager: Portage-2.3.62, Repoman-2.3.12
Signed-off-by: Horea Christian <horea.christ <AT> yandex.com>
profiles/package.mask | 1 +
sci-biology/afni/afni-19.0.21.ebuild | 68 ++++++++++++++++++++++++++++++++++++
2 files changed, 69 insertions(+)
diff --git a/profiles/package.mask b/profiles/package.mask
index 25cd51884..9f3e2465b 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -39,6 +39,7 @@ sci-biology/samri
# or more generally unbundling. Masked until unbundling
# efforts ( https://github.com/afni/afni/pull/60 ) come to
# fruition.
+=sci-biology/afni-19.0.21
=sci-biology/afni-18.1.04
# Sebastien Fabbro <bicatali@gentoo.org> (23 Aug 2011)
diff --git a/sci-biology/afni/afni-19.0.21.ebuild b/sci-biology/afni/afni-19.0.21.ebuild
new file mode 100644
index 000000000..104015772
--- /dev/null
+++ b/sci-biology/afni/afni-19.0.21.ebuild
@@ -0,0 +1,68 @@
+# 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 -> ${P}.tar.gz"
+
+LICENSE="GPL-3+"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+RDEPEND="dev-libs/expat
+ media-libs/netpbm
+ media-libs/qhull
+ media-video/mpeg-tools
+ sci-libs/gsl
+ sys-devel/llvm:*
+ virtual/jpeg:0
+ x11-libs/libGLw
+ x11-libs/libXft
+ x11-libs/libXi
+ x11-libs/libXpm
+ x11-libs/motif[-static-libs]"
+
+# x11-libs/motif[static-libs] breaks the build.
+# See upstream discussion
+# http://afni.nimh.nih.gov/afni/community/board/read.php?1,85348,85348#msg-85348
+
+DEPEND="${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"
+ 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
+}
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