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 <[email protected]> (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 <[email protected]> (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>[email protected]</email> + <name>Horea Christian</name> + </maintainer> + <maintainer type="project"> + <email>[email protected]</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>
