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