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commit: 9a7852ed945ad222d4969f29460c12a230ec8c1e |
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Author: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org> |
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AuthorDate: Sat Jan 15 15:59:34 2022 +0000 |
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Commit: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org> |
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CommitDate: Sat Jan 15 15:59:34 2022 +0000 |
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URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=9a7852ed |
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|
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sci-biology/fsl: drop old |
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|
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Closes: https://github.com/gentoo/sci/issues/974 |
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Package-Manager: Portage-3.0.30, Repoman-3.0.3 |
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Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org> |
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|
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sci-biology/fsl/fsl-6.0.2-r1.ebuild | 203 ------------------------------------ |
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sci-biology/fsl/fsl-6.0.2.ebuild | 167 ----------------------------- |
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2 files changed, 370 deletions(-) |
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|
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diff --git a/sci-biology/fsl/fsl-6.0.2-r1.ebuild b/sci-biology/fsl/fsl-6.0.2-r1.ebuild |
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deleted file mode 100644 |
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index e9918bbeb..000000000 |
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--- a/sci-biology/fsl/fsl-6.0.2-r1.ebuild |
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+++ /dev/null |
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@@ -1,203 +0,0 @@ |
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-# Copyright 1999-2021 Gentoo Authors |
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-# Distributed under the terms of the GNU General Public License v2 |
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- |
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-EAPI=7 |
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- |
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-inherit cuda toolchain-funcs prefix |
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- |
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-DESCRIPTION="Analysis of functional, structural, and diffusion MRI brain imaging data" |
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-HOMEPAGE="https://www.fmrib.ox.ac.uk/fsl" |
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-SRC_URI="https://fsl.fmrib.ox.ac.uk/fsldownloads/${P}-sources.tar.gz -> ${P}.tar.gz" |
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- |
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-LICENSE="FSL BSD-2 newmat" |
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-SLOT="0" |
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-KEYWORDS="~amd64" |
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-IUSE="cuda" |
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- |
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-DEPEND=" |
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- dev-libs/boost |
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- <dev-python/fslpy-3 |
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- media-gfx/graphviz |
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- media-libs/gd |
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- media-libs/glu |
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- media-libs/libpng:0= |
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- sci-libs/ciftilib |
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- sci-libs/nlopt |
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- sys-libs/zlib |
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- dev-lang/tcl:0= |
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- dev-lang/tk:0= |
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- >=virtual/lapack-3.8 |
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- >=virtual/blas-3.8 |
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- |
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- cuda? ( |
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- || ( |
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- ( =dev-util/nvidia-cuda-toolkit-10* =sys-devel/gcc-8*:* ) |
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- ( =dev-util/nvidia-cuda-toolkit-11* =sys-devel/gcc-9*:* ) |
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- ) |
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- ) |
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- " |
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-RDEPEND="${DEPEND}" |
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- |
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-S=${WORKDIR}/${PN} |
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-UPSTREAM_FSLDIR="/usr/share/fsl" |
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- |
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-PATCHES=( |
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- "${FILESDIR}/${PN}"-6.0.2-gcc10_include.patch |
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- "${FILESDIR}/${PN}"-6.0.2-setup.patch |
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- "${FILESDIR}/${PN}"-6.0.2-template.patch |
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- "${FILESDIR}/${PN}"-6.0.2-no_xmlpp.patch |
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- "${FILESDIR}/${PN}"-5.0.11-niftiio_var_fix.patch |
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- "${FILESDIR}/${PN}"-5.0.11-ifstream_use.patch |
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- "${FILESDIR}/${PN}"-5.0.11-fslsurface_parallel_make.patch |
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- "${FILESDIR}/${PN}"-6.0.2-qstring_compat.patch |
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- "${FILESDIR}/${PN}"-5.0.9-headers.patch |
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- "${FILESDIR}/${PN}"-6.0.2-fsldir_redux-p1.patch |
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- "${FILESDIR}/${PN}"-6.0.2-fsldir_redux-p2.patch |
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-) |
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- |
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-src_prepare() { |
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- default |
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- |
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- sed -i \ |
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- -e "s:@@GENTOO_RANLIB@@:$(tc-getRANLIB):" \ |
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- -e "s:@@GENTOO_CC@@:$(tc-getCC):" \ |
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- -e "s:@@GENTOO_CXX@@:$(tc-getCXX):" \ |
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- config/buildSettings.mk || die |
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- |
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- eprefixify $(grep -rl GENTOO_PORTAGE_EPREFIX src/*) \ |
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- etc/js/label-div.html |
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- |
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- # Disable mist-clean the hard way for now. |
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- rm -rf src/mist-clean |
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- |
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- makefilelist=$(find src/ -name Makefile) |
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- |
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- sed -i \ |
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- -e "s:-I\${INC_BOOST}::" \ |
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- -e "s:-I\${INC_ZLIB}::" \ |
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- -e "s:-I\${INC_GD}::" \ |
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- -e "s:-I\${INC_PNG}::" \ |
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- -e "s:-L\${LIB_GD}::" \ |
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- -e "s:-L\${LIB_PNG}::" \ |
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- -e "s:-L\${LIB_ZLIB}::" \ |
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- ${makefilelist} || die |
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- |
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- sed -e "s:\${FSLDIR}/bin/::g" \ |
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- -e "s:\$FSLDIR/bin/::g" \ |
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- -i $(grep -rl "\${FSLDIR}/bin" src/*) \ |
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- -i $(grep -rl "\$FSLDIR/bin" src/*) \ |
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- $(grep -rl "\${FSLDIR}/bin" etc/matlab/*)\ |
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- $(grep -rl "\$FSLDIR/bin" etc/matlab/*) || die |
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- |
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- sed -e "s:\$FSLDIR/data:${EPREFIX}/usr/share/fsl/data:g" \ |
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- -e "s:\${FSLDIR}/data:${EPREFIX}/usr/share/fsl/data:g" \ |
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- -i $(grep -rl "\$FSLDIR/data" src/*) \ |
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- $(grep -rl "\${FSLDIR}/data" src/*) || die |
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- |
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- sed -e "s:\$FSLDIR/doc:${EPREFIX}/usr/share/fsl/doc:g" \ |
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- -e "s:\${FSLDIR}/doc:${EPREFIX}/usr/share/fsl/doc:g" \ |
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- -i $(grep -rl "\$FSLDIR/doc" src/*) \ |
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- $(grep -rl "\${FSLDIR}/doc" src/*) || die |
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- |
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- sed -e "s:/usr/share/fsl/doc:${EPREFIX}/usr/share/fsl/doc:g" \ |
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- -i $(grep -rl "/usr/share/fsl/doc" src/*) || die |
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- |
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- sed -e "s:\$FSLDIR/etc:${EPREFIX}/etc:g" \ |
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- -e "s:\${FSLDIR}/etc:${EPREFIX}/etc:g" \ |
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- -i $(grep -rlI "\$FSLDIR/etc" *) \ |
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- -i $(grep -rlI "\${FSLDIR}/etc" *) || die |
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- |
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- # Use generic blas/lapack rather than openblas |
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- sed -e "s:-lopenblas:-llapack -lblas:g" \ |
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- -i $(grep -rlI lopenblas *) || die |
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- |
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- # script wanting to have access to flsversion at buildtime |
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- sed -e "s:/etc/fslversion:${S}/etc/fslversion:g" \ |
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- -i ${makefilelist} || die |
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- |
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- if use cuda; then |
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- einfo |
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- |
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- gcc_ver=`gcc-fullversion` |
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- einfo "GCC version: ${gcc_ver}" |
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- |
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- cuda_gcc=`cuda_gccdir` |
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- cuda_NVCC_flags=`cuda_gccdir -f` |
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- einfo "CUDA GCC path: ${cuda_gcc}" |
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- einfo " ${cuda_NVCC_flags}" |
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- |
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- CUDA_INSTALLATION="/opt/cuda" |
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- CUDAVER=`cuda_toolkit_version` |
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- |
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- eapply "${FILESDIR}/${PN}-6.0.2-eddy_cuda.patch" |
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- eapply "${FILESDIR}/${PN}-6.0.2-cuda_buildsettings.patch" |
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- |
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- sed -i \ |
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- -e "s:@@GENTOO_NVCC_FLAGS@@:${cuda_NVCC_flags}:" \ |
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- src/eddy/Makefile || die |
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- |
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- cuda_sanitize |
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- fi |
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-} |
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- |
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-src_compile() { |
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- export FSLDIR=${WORKDIR}/${PN} |
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- export FSLCONDIR=${WORKDIR}/${PN}/config |
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- export FSLMACHTYPE=generic |
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- |
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- export USERLDFLAGS="${LDFLAGS}" |
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- export USERCFLAGS="${CFLAGS}" |
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- export USERCXXFLAGS="${CXXFLAGS}" |
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- |
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- export CIFTICFLAGS="$($(tc-getPKG_CONFIG) --cflags CiftiLib)" |
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- export CIFTILIBS="$($(tc-getPKG_CONFIG) --libs-only-l CiftiLib)" |
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- |
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- if use cuda; then |
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- einfo "CUDA_INSTALLATION: ${CUDA_INSTALLATION}" |
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- einfo "CUDAVER: ${CUDAVER}" |
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- fi |
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- |
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- ./build || die |
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-} |
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- |
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-src_install() { |
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- sed -i "s:\${FSLDIR}/tcl:/usr/libexec/fsl:g" \ |
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- $(grep -lI "\${FSLDIR}/tcl" bin/*) \ |
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- $(grep -l "\${FSLDIR}/tcl" tcl/*) || die |
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- sed -i "s:\$FSLDIR/tcl:/usr/libexec/fsl:g" \ |
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- $(grep -l "\$FSLDIR/tcl" tcl/*) || die |
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- |
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- dobin bin/* |
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- |
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- insinto /usr/share/${PN} |
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- doins -r data |
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- dodoc -r doc/. refdoc |
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- |
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- insinto /usr/libexec/fsl |
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- doins -r tcl/* |
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- |
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- insinto /etc/fslconf |
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- doins etc/fslconf/fsl.sh |
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- |
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- insinto /etc |
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- doins etc/fslversion |
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- doins -r etc/default_flobs.flobs etc/flirtsch etc/js etc/luts |
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- |
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- #the following is needed for FSL and depending programs to be able |
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- #to find its files, since FSL uses an uncommon installation path: |
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- #https://github.com/gentoo-science/sci/pull/612#r60289295 |
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- dosym ../../../etc ${UPSTREAM_FSLDIR}/etc |
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- dosym ../doc/${PF} ${UPSTREAM_FSLDIR}/doc |
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- dosym ../../bin ${UPSTREAM_FSLDIR}/bin |
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- |
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- doenvd "$(prefixify_ro "${FILESDIR}"/99fsl)" |
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- mv "${ED}"/usr/bin/{,fsl_}cluster || die |
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-} |
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- |
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-pkg_postinst() { |
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- echo |
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- einfo "Please run the following commands if you" |
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- einfo "intend to use fsl from an existing shell:" |
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- einfo "env-update && source /etc/profile" |
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- echo |
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-} |
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|
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diff --git a/sci-biology/fsl/fsl-6.0.2.ebuild b/sci-biology/fsl/fsl-6.0.2.ebuild |
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deleted file mode 100644 |
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index f7b0e9b73..000000000 |
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--- a/sci-biology/fsl/fsl-6.0.2.ebuild |
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+++ /dev/null |
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@@ -1,167 +0,0 @@ |
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-# Copyright 1999-2021 Gentoo Authors |
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-# Distributed under the terms of the GNU General Public License v2 |
236 |
- |
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-EAPI=7 |
238 |
- |
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-inherit toolchain-funcs prefix |
240 |
- |
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-DESCRIPTION="Analysis of functional, structural, and diffusion MRI brain imaging data" |
242 |
-HOMEPAGE="https://www.fmrib.ox.ac.uk/fsl" |
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-SRC_URI="https://fsl.fmrib.ox.ac.uk/fsldownloads/${P}-sources.tar.gz -> ${P}.tar.gz" |
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- |
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-LICENSE="FSL BSD-2 newmat" |
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-SLOT="0" |
247 |
-KEYWORDS="~amd64" |
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-IUSE="" |
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- |
250 |
-DEPEND=" |
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- dev-libs/boost |
252 |
- <dev-python/fslpy-3 |
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- media-gfx/graphviz |
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- media-libs/gd |
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- media-libs/glu |
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- media-libs/libpng:0= |
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- sci-libs/ciftilib |
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- sci-libs/nlopt |
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- sys-libs/zlib |
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- dev-lang/tcl:0= |
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- dev-lang/tk:0= |
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- >=virtual/lapack-3.8 |
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- >=virtual/blas-3.8 |
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- " |
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-RDEPEND="${DEPEND}" |
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- |
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-S=${WORKDIR}/${PN} |
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-UPSTREAM_FSLDIR="/usr/share/fsl" |
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- |
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-PATCHES=( |
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- "${FILESDIR}/${PN}"-6.0.2-gcc10_include.patch |
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- "${FILESDIR}/${PN}"-6.0.2-setup.patch |
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- "${FILESDIR}/${PN}"-6.0.2-template.patch |
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- "${FILESDIR}/${PN}"-6.0.2-no_xmlpp.patch |
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- "${FILESDIR}/${PN}"-5.0.11-niftiio_var_fix.patch |
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- "${FILESDIR}/${PN}"-5.0.11-ifstream_use.patch |
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- "${FILESDIR}/${PN}"-5.0.11-fslsurface_parallel_make.patch |
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- "${FILESDIR}/${PN}"-6.0.2-qstring_compat.patch |
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- "${FILESDIR}/${PN}"-5.0.9-headers.patch |
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- "${FILESDIR}/${PN}"-6.0.2-fsldir_redux-p1.patch |
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- "${FILESDIR}/${PN}"-6.0.2-fsldir_redux-p2.patch |
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-) |
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- |
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-src_prepare(){ |
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- default |
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- |
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- sed -i \ |
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- -e "s:@@GENTOO_RANLIB@@:$(tc-getRANLIB):" \ |
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- -e "s:@@GENTOO_CC@@:$(tc-getCC):" \ |
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- -e "s:@@GENTOO_CXX@@:$(tc-getCXX):" \ |
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- config/buildSettings.mk || die |
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- |
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- eprefixify $(grep -rl GENTOO_PORTAGE_EPREFIX src/*) \ |
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- etc/js/label-div.html |
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- |
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- # Disable mist-clean the hard way for now. |
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- rm -rf src/mist-clean |
298 |
- |
299 |
- makefilelist=$(find src/ -name Makefile) |
300 |
- |
301 |
- sed -i \ |
302 |
- -e "s:-I\${INC_BOOST}::" \ |
303 |
- -e "s:-I\${INC_ZLIB}::" \ |
304 |
- -e "s:-I\${INC_GD}::" \ |
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- -e "s:-I\${INC_PNG}::" \ |
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- -e "s:-L\${LIB_GD}::" \ |
307 |
- -e "s:-L\${LIB_PNG}::" \ |
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- -e "s:-L\${LIB_ZLIB}::" \ |
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- ${makefilelist} || die |
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- |
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- sed -e "s:\${FSLDIR}/bin/::g" \ |
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- -e "s:\$FSLDIR/bin/::g" \ |
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- -i $(grep -rl "\${FSLDIR}/bin" src/*) \ |
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- -i $(grep -rl "\$FSLDIR/bin" src/*) \ |
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- $(grep -rl "\${FSLDIR}/bin" etc/matlab/*)\ |
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- $(grep -rl "\$FSLDIR/bin" etc/matlab/*) || die |
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- |
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- sed -e "s:\$FSLDIR/data:${EPREFIX}/usr/share/fsl/data:g" \ |
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- -e "s:\${FSLDIR}/data:${EPREFIX}/usr/share/fsl/data:g" \ |
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- -i $(grep -rl "\$FSLDIR/data" src/*) \ |
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- $(grep -rl "\${FSLDIR}/data" src/*) || die |
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- |
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- sed -e "s:\$FSLDIR/doc:${EPREFIX}/usr/share/fsl/doc:g" \ |
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- -e "s:\${FSLDIR}/doc:${EPREFIX}/usr/share/fsl/doc:g" \ |
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- -i $(grep -rl "\$FSLDIR/doc" src/*) \ |
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- $(grep -rl "\${FSLDIR}/doc" src/*) || die |
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- |
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- sed -e "s:/usr/share/fsl/doc:${EPREFIX}/usr/share/fsl/doc:g" \ |
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- -i $(grep -rl "/usr/share/fsl/doc" src/*) || die |
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- |
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- sed -e "s:\$FSLDIR/etc:${EPREFIX}/etc:g" \ |
332 |
- -e "s:\${FSLDIR}/etc:${EPREFIX}/etc:g" \ |
333 |
- -i $(grep -rlI "\$FSLDIR/etc" *) \ |
334 |
- -i $(grep -rlI "\${FSLDIR}/etc" *) || die |
335 |
- |
336 |
- # Use generic blas/lapack rather than openblas |
337 |
- sed -e "s:-lopenblas:-llapack -lblas:g" \ |
338 |
- -i $(grep -rlI lopenblas *) || die |
339 |
- |
340 |
- # script wanting to have access to flsversion at buildtime |
341 |
- sed -e "s:/etc/fslversion:${S}/etc/fslversion:g" \ |
342 |
- -i ${makefilelist} || die |
343 |
-} |
344 |
- |
345 |
-src_compile() { |
346 |
- export FSLDIR=${WORKDIR}/${PN} |
347 |
- export FSLCONDIR=${WORKDIR}/${PN}/config |
348 |
- export FSLMACHTYPE=generic |
349 |
- |
350 |
- export USERLDFLAGS="${LDFLAGS}" |
351 |
- export USERCFLAGS="${CFLAGS}" |
352 |
- export USERCXXFLAGS="${CXXFLAGS}" |
353 |
- |
354 |
- export CIFTICFLAGS="$($(tc-getPKG_CONFIG) --cflags CiftiLib)" |
355 |
- export CIFTILIBS="$($(tc-getPKG_CONFIG) --libs-only-l CiftiLib)" |
356 |
- |
357 |
- ./build || die |
358 |
-} |
359 |
- |
360 |
-src_install() { |
361 |
- sed -i "s:\${FSLDIR}/tcl:/usr/libexec/fsl:g" \ |
362 |
- $(grep -lI "\${FSLDIR}/tcl" bin/*) \ |
363 |
- $(grep -l "\${FSLDIR}/tcl" tcl/*) || die |
364 |
- sed -i "s:\$FSLDIR/tcl:/usr/libexec/fsl:g" \ |
365 |
- $(grep -l "\$FSLDIR/tcl" tcl/*) || die |
366 |
- |
367 |
- dobin bin/* |
368 |
- |
369 |
- insinto /usr/share/${PN} |
370 |
- doins -r data |
371 |
- dodoc -r doc/. refdoc |
372 |
- |
373 |
- insinto /usr/libexec/fsl |
374 |
- doins -r tcl/* |
375 |
- |
376 |
- insinto /etc/fslconf |
377 |
- doins etc/fslconf/fsl.sh |
378 |
- |
379 |
- insinto /etc |
380 |
- doins etc/fslversion |
381 |
- doins -r etc/default_flobs.flobs etc/flirtsch etc/js etc/luts |
382 |
- |
383 |
- #the following is needed for FSL and depending programs to be able |
384 |
- #to find its files, since FSL uses an uncommon installation path: |
385 |
- #https://github.com/gentoo-science/sci/pull/612#r60289295 |
386 |
- dosym ../../../etc ${UPSTREAM_FSLDIR}/etc |
387 |
- dosym ../doc/${PF} ${UPSTREAM_FSLDIR}/doc |
388 |
- dosym ../../bin ${UPSTREAM_FSLDIR}/bin |
389 |
- |
390 |
- doenvd "$(prefixify_ro "${FILESDIR}"/99fsl)" |
391 |
- mv "${ED}"/usr/bin/{,fsl_}cluster || die |
392 |
-} |
393 |
- |
394 |
-pkg_postinst() { |
395 |
- echo |
396 |
- einfo "Please run the following commands if you" |
397 |
- einfo "intend to use fsl from an existing shell:" |
398 |
- einfo "env-update && source /etc/profile" |
399 |
- echo |
400 |
-} |