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* [gentoo-commits] proj/sci:master commit in: sci-biology/fsl/
@ 2015-09-21 17:44 Justin Lecher
  0 siblings, 0 replies; 27+ messages in thread
From: Justin Lecher @ 2015-09-21 17:44 UTC (permalink / raw
  To: gentoo-commits

commit:     65da06ae6c6b80c958e4179df93c350c279968cc
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Sep 21 17:21:47 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Sep 21 17:21:47 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=65da06ae

sci-biology/fsl: Add subslot operators

Package-Manager: portage-2.2.20.1
Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

 sci-biology/fsl/fsl-5.0.6.ebuild | 130 ---------------------------------------
 sci-biology/fsl/fsl-5.0.8.ebuild |  32 +++++-----
 2 files changed, 17 insertions(+), 145 deletions(-)

diff --git a/sci-biology/fsl/fsl-5.0.6.ebuild b/sci-biology/fsl/fsl-5.0.6.ebuild
deleted file mode 100644
index ed0ae88..0000000
--- a/sci-biology/fsl/fsl-5.0.6.ebuild
+++ /dev/null
@@ -1,130 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-inherit eutils toolchain-funcs prefix
-
-DESCRIPTION="Analysis of functional, structural, and diffusion MRI brain imaging data"
-HOMEPAGE="http://www.fmrib.ox.ac.uk/fsl"
-SRC_URI="http://dev.gentoo.org/~jlec/distfiles/${P}-sources.tar.gz"
-
-LICENSE="FSL BSD-2 newmat"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-COMMON_DEPEND="media-libs/glu
-	media-libs/libpng
-	media-libs/gd
-	sys-libs/zlib
-	dev-libs/boost
-	media-gfx/graphviz
-	"
-DEPEND="${COMMON_DEPEND}"
-RDEPEND="${COMMON_DEPEND}
-	dev-lang/tcl
-	dev-lang/tk
-	"
-
-S=${WORKDIR}/${PN}
-
-src_prepare(){
-	epatch "${FILESDIR}/${PN}"-5.0.4-setup.patch
-	epatch "${FILESDIR}/${PN}"-5.0.4-headers.patch
-	epatch "${FILESDIR}/${PN}"-5.0.6-fsldir_redux.patch
-
-	sed -i \
-		-e "s:@@GENTOO_RANLIB@@:$(tc-getRANLIB):" \
-		-e "s:@@GENTOO_CC@@:$(tc-getCC):" \
-		-e "s:@@GENTOO_CXX@@:$(tc-getCXX):" \
-		config/generic/systemvars.mk || die
-
-	eprefixify $(grep -rl GENTOO_PORTAGE_EPREFIX src/*) \
-		etc/js/label-div.html
-
-	makefilelist=$(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 -i "s:\${FSLDIR}/bin/::g" \
-		$(grep -rl "\${FSLDIR}/bin" src/*) \
-		$(grep -rl "\${FSLDIR}/bin" etc/matlab/*)
-	sed -i "s:\$FSLDIR/bin/::g" \
-		$(grep -rl "\$FSLDIR/bin" src/*) \
-		$(grep -rl "\$FSLDIR/bin" etc/matlab/*)
-
-	sed -i "s:\$FSLDIR/data:${EPREFIX}/usr/share/fsl/data:g" \
-		$(grep -rl "\$FSLDIR/data" src/*)
-
-	sed -i "s:\${FSLDIR}/data:${EPREFIX}/usr/share/fsl/data:g" \
-		$(grep -rl "\${FSLDIR}/data" src/*)
-
-	sed -i "s:\$FSLDIR/etc:${EPREFIX}/etc:g" \
-		$(grep -rl "\$FSLDIR/etc" src/*)
-
-	sed -i "s:\${FSLDIR}/etc:${EPREFIX}/etc:g" \
-		$(grep -rl "\${FSLDIR}/etc" src/*)
-
-	sed -i "s:\$FSLDIR/doc:${EPREFIX}/usr/share/fsl/doc:g" \
-		$(grep -rl "\$FSLDIR/doc" src/*)
-
-	sed -i "s:\${FSLDIR}/doc:${EPREFIX}/usr/share/fsl/doc:g" \
-		$(grep -rl "\${FSLDIR}/doc" src/*)
-
-	sed -i "s:\'\${FSLDIR}\'/doc:${EPREFIX}/usr/share/fsl/doc:g" \
-		$(grep -rl "\'\${FSLDIR}\'/doc" src/*)
-
-	sed -i -e "s:\$FSLDIR/etc:/etc:g" `grep -rlI \$FSLDIR/etc *`
-}
-
-src_compile() {
-	export FSLDIR=${WORKDIR}/${PN}
-	export FSLCONDIR=${WORKDIR}/${PN}/config
-	export FSLMACHTYPE=generic
-
-	export USERLDFLAGS="${LDFLAGS}"
-	export USERCFLAGS="${CFLAGS}"
-	export USERCXXFLAGS="${CXXFLAGS}"
-
-	./build || die
-}
-
-src_install() {
-	sed -i "s:\${FSLDIR}/tcl:/usr/libexec/fsl:g" \
-		$(grep -lI "\${FSLDIR}/tcl" bin/*) \
-		$(grep -l "\${FSLDIR}/tcl"  tcl/*)
-	sed -i "s:\$FSLDIR/tcl:/usr/libexec/fsl:g" \
-		$(grep -l "\$FSLDIR/tcl" tcl/*)
-
-	exeinto /usr/bin
-	doexe bin/*
-
-	insinto /usr/share/${PN}
-	doins -r doc data 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
-	#if use matlab; then
-	#	doins etc/matlab
-	#fi
-
-	doenvd "${FILESDIR}"/99fsl
-	rm "${D}"/usr/bin/cluster
-}

diff --git a/sci-biology/fsl/fsl-5.0.8.ebuild b/sci-biology/fsl/fsl-5.0.8.ebuild
index 4bf38ff..f82d5fe 100644
--- a/sci-biology/fsl/fsl-5.0.8.ebuild
+++ b/sci-biology/fsl/fsl-5.0.8.ebuild
@@ -15,25 +15,27 @@ SLOT="0"
 KEYWORDS="~amd64"
 IUSE=""
 
-COMMON_DEPEND="media-libs/glu
-	media-libs/libpng
-	media-libs/gd
-	sys-libs/zlib
+COMMON_DEPEND="
 	dev-libs/boost
 	media-gfx/graphviz
+	media-libs/gd
+	media-libs/glu
+	media-libs/libpng:0=
+	sys-libs/zlib
 	"
 DEPEND="${COMMON_DEPEND}"
 RDEPEND="${COMMON_DEPEND}
-	dev-lang/tcl
-	dev-lang/tk
+	dev-lang/tcl:0=
+	dev-lang/tk:0=
 	"
 
 S=${WORKDIR}/${PN}
 
 src_prepare(){
-	epatch "${FILESDIR}/${PN}"-5.0.8-setup.patch
-	epatch "${FILESDIR}/${PN}"-5.0.8-headers.patch
-	epatch "${FILESDIR}/${PN}"-5.0.8-fsldir_redux.patch
+	epatch \
+		"${FILESDIR}/${PN}"-5.0.8-setup.patch \
+		"${FILESDIR}/${PN}"-5.0.8-headers.patch \
+		"${FILESDIR}/${PN}"-5.0.8-fsldir_redux.patch
 
 	sed -i \
 		-e "s:@@GENTOO_RANLIB@@:$(tc-getRANLIB):" \
@@ -102,15 +104,15 @@ src_compile() {
 src_install() {
 	sed -i "s:\${FSLDIR}/tcl:/usr/libexec/fsl:g" \
 		$(grep -lI "\${FSLDIR}/tcl" bin/*) \
-		$(grep -l "\${FSLDIR}/tcl"  tcl/*)
+		$(grep -l "\${FSLDIR}/tcl"  tcl/*) || die
 	sed -i "s:\$FSLDIR/tcl:/usr/libexec/fsl:g" \
-		$(grep -l "\$FSLDIR/tcl" tcl/*)
+		$(grep -l "\$FSLDIR/tcl" tcl/*) || die
 
-	exeinto /usr/bin
-	doexe bin/*
+	dobin bin/*
 
 	insinto /usr/share/${PN}
-	doins -r doc data refdoc
+	doins -r data
+	dodoc -r doc/. refdoc
 
 	insinto /usr/libexec/fsl
 	doins -r tcl/*
@@ -126,5 +128,5 @@ src_install() {
 	#fi
 
 	doenvd "${FILESDIR}"/99fsl
-	rm "${D}"/usr/bin/cluster
+	rm "${ED}"/usr/bin/cluster || die
 }


^ permalink raw reply related	[flat|nested] 27+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/fsl/
@ 2024-02-29 21:15 Horea Christian
  0 siblings, 0 replies; 27+ messages in thread
From: Horea Christian @ 2024-02-29 21:15 UTC (permalink / raw
  To: gentoo-commits

commit:     a28423309bc3562113676a5009af778a18447267
Author:     Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Thu Feb 29 21:10:29 2024 +0000
Commit:     Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Thu Feb 29 21:10:29 2024 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=a2842330

sci-biology/fsl: updated C++ version

Signed-off-by: Horea Christian <chr <AT> chymera.eu>

 sci-biology/fsl/fsl-6.0.4.ebuild | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/sci-biology/fsl/fsl-6.0.4.ebuild b/sci-biology/fsl/fsl-6.0.4.ebuild
index cd91cf192..6e5d6e779 100644
--- a/sci-biology/fsl/fsl-6.0.4.ebuild
+++ b/sci-biology/fsl/fsl-6.0.4.ebuild
@@ -151,8 +151,8 @@ src_compile() {
 
 	# define the default build system to match upstream official standard
 	#  -> individual projects may overwrite the '-std=' flag
-	export ANSI_CFLAGS="-std=c99"
-	export ANSI_CXXFLAGS="-std=c++98"
+	export ANSI_CFLAGS="-std=c11"
+	export ANSI_CXXFLAGS="-std=c++11"
 
 	export USERLDFLAGS="${LDFLAGS}"
 	export USERCFLAGS="${CFLAGS}"


^ permalink raw reply related	[flat|nested] 27+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/fsl/
@ 2022-05-02 12:22 Andrew Ammerlaan
  0 siblings, 0 replies; 27+ messages in thread
From: Andrew Ammerlaan @ 2022-05-02 12:22 UTC (permalink / raw
  To: gentoo-commits

commit:     a533606704b86ace1e75de7786c3ca962e9687e5
Author:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Mon May  2 12:16:46 2022 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Mon May  2 12:16:46 2022 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=a5336067

sci-biology/fsl: drop dep on cuda-10

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>

 sci-biology/fsl/fsl-6.0.4.ebuild | 6 +-----
 sci-biology/fsl/fsl-6.0.5.ebuild | 4 +---
 2 files changed, 2 insertions(+), 8 deletions(-)

diff --git a/sci-biology/fsl/fsl-6.0.4.ebuild b/sci-biology/fsl/fsl-6.0.4.ebuild
index 4797c1298..cd91cf192 100644
--- a/sci-biology/fsl/fsl-6.0.4.ebuild
+++ b/sci-biology/fsl/fsl-6.0.4.ebuild
@@ -28,12 +28,8 @@ DEPEND="
 	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*:* )
-		   )
+		=dev-util/nvidia-cuda-toolkit-11* =sys-devel/gcc-9*:*
 	)
 	"
 RDEPEND="${DEPEND}"

diff --git a/sci-biology/fsl/fsl-6.0.5.ebuild b/sci-biology/fsl/fsl-6.0.5.ebuild
index c51a9d30e..d3ec1de1d 100644
--- a/sci-biology/fsl/fsl-6.0.5.ebuild
+++ b/sci-biology/fsl/fsl-6.0.5.ebuild
@@ -39,9 +39,7 @@ DEPEND="
 	>=virtual/lapack-3.8
 	>=virtual/blas-3.8
 	cuda? (
-		|| (
-			( =dev-util/nvidia-cuda-toolkit-11* =sys-devel/gcc-9*:* )
-		   )
+		=dev-util/nvidia-cuda-toolkit-11* =sys-devel/gcc-9*:*
 	)
 	"
 RDEPEND="${DEPEND}"


^ permalink raw reply related	[flat|nested] 27+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/fsl/
@ 2022-01-15 15:59 Andrew Ammerlaan
  0 siblings, 0 replies; 27+ messages in thread
From: Andrew Ammerlaan @ 2022-01-15 15:59 UTC (permalink / raw
  To: gentoo-commits

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
-}


^ permalink raw reply related	[flat|nested] 27+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/fsl/
@ 2022-01-14 20:36 Andrew Ammerlaan
  0 siblings, 0 replies; 27+ messages in thread
From: Andrew Ammerlaan @ 2022-01-14 20:36 UTC (permalink / raw
  To: gentoo-commits

commit:     ea391932cb773a0305bcb60273dca6b59dfc331f
Author:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Fri Jan 14 20:36:21 2022 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Fri Jan 14 20:36:21 2022 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=ea391932

sci-biology/fsl: add version 6.0.5

No keywords, compile fails, need patches

Package-Manager: Portage-3.0.30, Repoman-3.0.3
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>

 sci-biology/fsl/fsl-6.0.5.ebuild | 220 +++++++++++++++++++++++++++++++++++++++
 1 file changed, 220 insertions(+)

diff --git a/sci-biology/fsl/fsl-6.0.5.ebuild b/sci-biology/fsl/fsl-6.0.5.ebuild
new file mode 100644
index 000000000..c51a9d30e
--- /dev/null
+++ b/sci-biology/fsl/fsl-6.0.5.ebuild
@@ -0,0 +1,220 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+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 -> ${P}.tar.gz"
+S="${WORKDIR}/${PN}"
+
+LICENSE="FSL BSD-2 newmat"
+SLOT="0"
+KEYWORDS=""
+IUSE="cuda"
+
+DEPEND="
+	dev-cpp/libxmlpp:=
+	dev-cpp/tbb
+	dev-db/sqlite
+	dev-libs/boost
+	dev-libs/libfmt
+	dev-libs/libxml2
+	dev-libs/pugixml
+	>=dev-python/fslpy-3.7.0
+	media-gfx/graphviz
+	media-libs/gd
+	media-libs/glu
+	media-libs/libpng:0=
+	sci-libs/gsl
+	sci-libs/ciftilib
+	sci-libs/fftw
+	sci-libs/nlopt
+	sci-libs/vtk
+	sys-libs/zlib
+	dev-lang/tcl:0=
+	dev-lang/tk:0=
+	>=virtual/lapack-3.8
+	>=virtual/blas-3.8
+	cuda? (
+		|| (
+			( =dev-util/nvidia-cuda-toolkit-11* =sys-devel/gcc-9*:* )
+		   )
+	)
+	"
+RDEPEND="${DEPEND}"
+
+UPSTREAM_FSLDIR="/usr/share/fsl"
+
+PATCHES=(
+#	"${FILESDIR}/${PN}"-6.0.4-gcc10_include.patch
+	"${FILESDIR}/${PN}"-6.0.4-setup.patch
+# 	"${FILESDIR}/${PN}"-6.0.2-no_xmlpp.patch
+# 	"${FILESDIR}/${PN}"-5.0.11-niftiio_var_fix.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}"-6.0.4-flameo_std.patch
+	"${FILESDIR}/${PN}"-6.0.4-melodic_std.patch
+	"${FILESDIR}/${PN}"-6.0.4-remove_fslpy_collisions-p1.patch
+	"${FILESDIR}/${PN}"-6.0.4-remove_fslpy_collisions-p2.patch
+# 	"${FILESDIR}/${PN}"-6.0.4-fdt_cuda.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 $(grep -rl GENTOO_PORTAGE_EPREFIX src/*) \
+		etc/js/label-div.html
+
+# 	# Disable mist the hard way for now.
+# 	rm -r src/mist || die
+#
+# 	# Disable ptx2 for now
+# 	rm -r src/ptx2 || die
+#
+	makefilelist=$(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 $(grep -rlI lopenblas *) || die
+
+	# script wanting to have access to fslversion at buildtime
+	sed -e "s:/etc/fslversion:${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}/${PN}-6.0.4-eddy_cuda.patch"
+		eapply "${FILESDIR}/${PN}-6.0.4-cuda_buildsettings.patch"
+
+		sed -i \
+			-e "s:@@GENTOO_NVCC_FLAGS@@:${cuda_NVCC_flags}:" \
+			src/eddy/Makefile || die
+
+		cuda_sanitize
+	fi
+}
+
+src_compile() {
+	export FSLDIR=${WORKDIR}/${PN}
+	export FSLCONDIR=${WORKDIR}/${PN}/config
+	export FSLMACHTYPE=generic
+
+	# define the default build system to match upstream official standard
+	#  -> individual projects may overwrite the '-std=' flag
+	export ANSI_CFLAGS="-std=c99"
+	export ANSI_CXXFLAGS="-std=c++98"
+
+	export USERLDFLAGS="${LDFLAGS}"
+	export USERCFLAGS="${CFLAGS}"
+	export USERCPPFLAGS="${CPPFLAGS}"
+	export USERCXXFLAGS="${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
+}


^ permalink raw reply related	[flat|nested] 27+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/fsl/
@ 2021-06-01  9:24 Andrew Ammerlaan
  0 siblings, 0 replies; 27+ messages in thread
From: Andrew Ammerlaan @ 2021-06-01  9:24 UTC (permalink / raw
  To: gentoo-commits

commit:     755c8ee10ebd59213df38f1366b36def28320c99
Author:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Tue Jun  1 09:22:58 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Tue Jun  1 09:22:58 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=755c8ee1

sci-biology/fsl: fix dependency.missingslot

Package-Manager: Portage-3.0.19, Repoman-3.0.3
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>

 sci-biology/fsl/fsl-6.0.2-r1.ebuild | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/sci-biology/fsl/fsl-6.0.2-r1.ebuild b/sci-biology/fsl/fsl-6.0.2-r1.ebuild
index c9162fd0e..71314a8f8 100644
--- a/sci-biology/fsl/fsl-6.0.2-r1.ebuild
+++ b/sci-biology/fsl/fsl-6.0.2-r1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2020 Gentoo Authors
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=7
@@ -31,8 +31,8 @@ DEPEND="
 
 	cuda? (
 		|| (
-			( =dev-util/nvidia-cuda-toolkit-10* =sys-devel/gcc-8* )
-			( =dev-util/nvidia-cuda-toolkit-11* =sys-devel/gcc-9* )
+			( =dev-util/nvidia-cuda-toolkit-10* =sys-devel/gcc-8*:* )
+			( =dev-util/nvidia-cuda-toolkit-11* =sys-devel/gcc-9*:* )
 		   )
 	)
 	"


^ permalink raw reply related	[flat|nested] 27+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/fsl/
@ 2017-11-18 19:49 Justin Lecher
  0 siblings, 0 replies; 27+ messages in thread
From: Justin Lecher @ 2017-11-18 19:49 UTC (permalink / raw
  To: gentoo-commits

commit:     f22242259497a007fc4b36db8b2201cd72ab8d8b
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat Nov 18 18:55:26 2017 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Nov 18 19:49:18 2017 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=f2224225

sci-biology/fsl: Fix repoman warnings

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>
Package-Manager: Portage-2.3.14, Repoman-2.3.6

 sci-biology/fsl/fsl-5.0.8.ebuild | 4 ++--
 sci-biology/fsl/fsl-5.0.9.ebuild | 6 +++---
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/sci-biology/fsl/fsl-5.0.8.ebuild b/sci-biology/fsl/fsl-5.0.8.ebuild
index 7916c0811..d420bbacc 100644
--- a/sci-biology/fsl/fsl-5.0.8.ebuild
+++ b/sci-biology/fsl/fsl-5.0.8.ebuild
@@ -130,8 +130,8 @@ src_install() {
 	#the following is needed for FSL and depending programs to be able
 	#to find its files, since FSL uses an uncommon:
 	#https://github.com/gentoo-science/sci/pull/612#r60289295
-	dosym /etc /usr/share/fsl/etc
-	dosym /usr/share/doc/${P} /usr/share/fsl/doc
+	dosym ../../../etc /usr/share/fsl/etc
+	dosym ../doc/${P} /usr/share/fsl/doc
 
 	cp "${FILESDIR}"/99fsl "${TMPDIR}"/99fsl || die
 	eprefixify "${TMPDIR}"/99fsl

diff --git a/sci-biology/fsl/fsl-5.0.9.ebuild b/sci-biology/fsl/fsl-5.0.9.ebuild
index bc96cec06..6e9ff6233 100644
--- a/sci-biology/fsl/fsl-5.0.9.ebuild
+++ b/sci-biology/fsl/fsl-5.0.9.ebuild
@@ -125,9 +125,9 @@ src_install() {
 	#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 ${UPSTREAM_FSLDIR}/etc
-	dosym /usr/share/doc/${PF} ${UPSTREAM_FSLDIR}/doc
-	dosym /usr/bin ${UPSTREAM_FSLDIR}/bin
+	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


^ permalink raw reply related	[flat|nested] 27+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/fsl/
@ 2016-04-13 10:47 Marius Brehler
  0 siblings, 0 replies; 27+ messages in thread
From: Marius Brehler @ 2016-04-13 10:47 UTC (permalink / raw
  To: gentoo-commits

commit:     f20b269ef04b89aa34a817da04a2463351ab6567
Author:     Horea Christian <horea.christ <AT> yandex <DOT> com>
AuthorDate: Mon Apr  4 16:24:50 2016 +0000
Commit:     Marius Brehler <marbre <AT> linux <DOT> sungazer <DOT> de>
CommitDate: Mon Apr  4 16:24:50 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=f20b269e

cluster to fsl_cluster rename

* sci-biology/fsl: trying to resolve namespace conflict with graphviz

Package-Manager: portage-2.2.28

* sci-biology/fsl: corrected fix for naming collision

Package-Manager: portage-2.2.28

 sci-biology/fsl/fsl-5.0.8.ebuild | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sci-biology/fsl/fsl-5.0.8.ebuild b/sci-biology/fsl/fsl-5.0.8.ebuild
index 4bcb6a0..3e9dc99 100644
--- a/sci-biology/fsl/fsl-5.0.8.ebuild
+++ b/sci-biology/fsl/fsl-5.0.8.ebuild
@@ -128,7 +128,7 @@ src_install() {
 	#fi
 
 	doenvd "${FILESDIR}"/99fsl
-	rm "${ED}"/usr/bin/cluster || die
+	mv "${ED}"/usr/bin/{,fsl_}cluster || die
 }
 
 pkg_postinst() {


^ permalink raw reply related	[flat|nested] 27+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/fsl/
@ 2015-11-24  2:03 Christoph Junghans
  0 siblings, 0 replies; 27+ messages in thread
From: Christoph Junghans @ 2015-11-24  2:03 UTC (permalink / raw
  To: gentoo-commits

commit:     6d2fe5739e0bf0478db40c4429215e78110b3326
Author:     Horea Christian <h.chr <AT> mail <DOT> ru>
AuthorDate: Sat Nov 21 02:51:11 2015 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Sat Nov 21 02:51:11 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=6d2fe573

typo

 sci-biology/fsl/fsl-5.0.8.ebuild | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sci-biology/fsl/fsl-5.0.8.ebuild b/sci-biology/fsl/fsl-5.0.8.ebuild
index 406e35c..4bcb6a0 100644
--- a/sci-biology/fsl/fsl-5.0.8.ebuild
+++ b/sci-biology/fsl/fsl-5.0.8.ebuild
@@ -135,6 +135,6 @@ 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/porfile"
+	einfo "env-update && source /etc/profile"
 	echo
 }


^ permalink raw reply related	[flat|nested] 27+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/fsl/
@ 2015-11-17 15:46 Justin Lecher
  0 siblings, 0 replies; 27+ messages in thread
From: Justin Lecher @ 2015-11-17 15:46 UTC (permalink / raw
  To: gentoo-commits

commit:     062ff55d99a5f7c8e232aa453b49984917998ecc
Author:     Horea Christian <h.chr <AT> mail <DOT> ru>
AuthorDate: Sat Nov 14 03:13:00 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Nov 14 03:13:00 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=062ff55d

sci-biology/fsl: added info about updating environment

Package-Manager: portage-2.2.23

 sci-biology/fsl/ChangeLog        | 3 +++
 sci-biology/fsl/fsl-5.0.8.ebuild | 8 ++++++++
 2 files changed, 11 insertions(+)

diff --git a/sci-biology/fsl/ChangeLog b/sci-biology/fsl/ChangeLog
index ff2e8c5..f802c57 100644
--- a/sci-biology/fsl/ChangeLog
+++ b/sci-biology/fsl/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
 # $Id$
 
+  14 Nov 2015;  <chymera@gentoo.org> fsl-5.0.8.ebuild:
+  sci-biology/fsl: added info about updating environment
+
   04 Nov 2015; Horea Christian <h.chr@mail.ru> fsl-5.0.8.ebuild:
   sci-biology/fsl: new sources location (upstream removes old sources)
 

diff --git a/sci-biology/fsl/fsl-5.0.8.ebuild b/sci-biology/fsl/fsl-5.0.8.ebuild
index 6762267..406e35c 100644
--- a/sci-biology/fsl/fsl-5.0.8.ebuild
+++ b/sci-biology/fsl/fsl-5.0.8.ebuild
@@ -130,3 +130,11 @@ src_install() {
 	doenvd "${FILESDIR}"/99fsl
 	rm "${ED}"/usr/bin/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/porfile"
+	echo
+}


^ permalink raw reply related	[flat|nested] 27+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/fsl/
@ 2015-11-05 15:14 Marius Brehler
  0 siblings, 0 replies; 27+ messages in thread
From: Marius Brehler @ 2015-11-05 15:14 UTC (permalink / raw
  To: gentoo-commits

commit:     da112361823dcd1856a50268b4fe4954c279aada
Author:     Horea Christian <h.chr <AT> mail <DOT> ru>
AuthorDate: Wed Nov  4 21:55:34 2015 +0000
Commit:     Marius Brehler <marbre <AT> linux <DOT> sungazer <DOT> de>
CommitDate: Wed Nov  4 21:55:34 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=da112361

sci-biology/fsl: new sources location (upstream removes old sources)

Package-Manager: portage-2.2.23

 sci-biology/fsl/ChangeLog        | 3 +++
 sci-biology/fsl/fsl-5.0.8.ebuild | 2 +-
 2 files changed, 4 insertions(+), 1 deletion(-)

diff --git a/sci-biology/fsl/ChangeLog b/sci-biology/fsl/ChangeLog
index 44498f6..ff2e8c5 100644
--- a/sci-biology/fsl/ChangeLog
+++ b/sci-biology/fsl/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
 # $Id$
 
+  04 Nov 2015; Horea Christian <h.chr@mail.ru> fsl-5.0.8.ebuild:
+  sci-biology/fsl: new sources location (upstream removes old sources)
+
   09 Apr 2015; Horea Christian <h.chr@mail.ru>
   -files/fsl-5.0.4-fsldir_redux.patch:
   removed 5.0.4 redux patch

diff --git a/sci-biology/fsl/fsl-5.0.8.ebuild b/sci-biology/fsl/fsl-5.0.8.ebuild
index f82d5fe..6762267 100644
--- a/sci-biology/fsl/fsl-5.0.8.ebuild
+++ b/sci-biology/fsl/fsl-5.0.8.ebuild
@@ -8,7 +8,7 @@ inherit eutils toolchain-funcs prefix
 
 DESCRIPTION="Analysis of functional, structural, and diffusion MRI brain imaging data"
 HOMEPAGE="http://www.fmrib.ox.ac.uk/fsl"
-SRC_URI="http://fsl.fmrib.ox.ac.uk/fsldownloads/${P}-sources.tar.gz"
+SRC_URI="https://dev.gentoo.org/~jlec/distfiles/${P}-sources.tar.gz"
 
 LICENSE="FSL BSD-2 newmat"
 SLOT="0"


^ permalink raw reply related	[flat|nested] 27+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/fsl/
@ 2015-04-20  1:11 Francois Bissey
  0 siblings, 0 replies; 27+ messages in thread
From: Francois Bissey @ 2015-04-20  1:11 UTC (permalink / raw
  To: gentoo-commits

commit:     894067c2f8dd681a3a1a7219ee90f70cdf4e0f33
Author:     Horea Christian <h.chr <AT> mail <DOT> ru>
AuthorDate: Sat Mar 28 21:31:00 2015 +0000
Commit:     Francois Bissey <f.r.bissey <AT> massey <DOT> ac <DOT> nz>
CommitDate: Sat Mar 28 21:31:00 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=894067c2

ported changes from 5.0.6 regarding FSLDIR

Package-Manager: portage-2.2.18

 sci-biology/fsl/ChangeLog        |  3 +++
 sci-biology/fsl/fsl-5.0.8.ebuild | 14 +++++++++++++-
 2 files changed, 16 insertions(+), 1 deletion(-)

diff --git a/sci-biology/fsl/ChangeLog b/sci-biology/fsl/ChangeLog
index 19478e2..e6857b2 100644
--- a/sci-biology/fsl/ChangeLog
+++ b/sci-biology/fsl/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  28 Mar 2015;  <chymera@gentoo.org> fsl-5.0.8.ebuild:
+  ported changes from 5.0.6 regarding FSLDIR
+
   28 Mar 2015;  <chymera@gentoo.org> files/fsl-5.0.4-headers.patch:
   hunk implemented by upstream
 

diff --git a/sci-biology/fsl/fsl-5.0.8.ebuild b/sci-biology/fsl/fsl-5.0.8.ebuild
index e185863..c2f8a10 100644
--- a/sci-biology/fsl/fsl-5.0.8.ebuild
+++ b/sci-biology/fsl/fsl-5.0.8.ebuild
@@ -83,6 +83,8 @@ src_prepare(){
 
 	sed -i "s:\'\${FSLDIR}\'/doc:${EPREFIX}/usr/share/fsl/doc:g" \
 		$(grep -rl "\'\${FSLDIR}\'/doc" src/*)
+
+	sed -i -e "s:\$FSLDIR/etc:/etc:g" `grep -rlI \$FSLDIR/etc *`
 }
 
 src_compile() {
@@ -98,6 +100,12 @@ src_compile() {
 }
 
 src_install() {
+	sed -i "s:\${FSLDIR}/tcl:/usr/libexec/fsl:g" \
+		$(grep -lI "\${FSLDIR}/tcl" bin/*) \
+		$(grep -l "\${FSLDIR}/tcl"  tcl/*)
+	sed -i "s:\$FSLDIR/tcl:/usr/libexec/fsl:g" \
+		$(grep -l "\$FSLDIR/tcl" tcl/*)
+
 	exeinto /usr/bin
 	doexe bin/*
 
@@ -105,9 +113,13 @@ src_install() {
 	doins -r doc data refdoc
 
 	insinto /usr/libexec/fsl
-	doins -r tcl
+	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
 	#if use matlab; then
 	#	doins etc/matlab


^ permalink raw reply related	[flat|nested] 27+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/fsl/
@ 2015-04-20  1:11 Francois Bissey
  0 siblings, 0 replies; 27+ messages in thread
From: Francois Bissey @ 2015-04-20  1:11 UTC (permalink / raw
  To: gentoo-commits

commit:     fdcd3e55349c5c26f32f911ec8b7d950386f3660
Author:     Horea Christian <h.chr <AT> mail <DOT> ru>
AuthorDate: Sun Mar 29 23:53:26 2015 +0000
Commit:     Francois Bissey <f.r.bissey <AT> massey <DOT> ac <DOT> nz>
CommitDate: Sun Mar 29 23:53:26 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=fdcd3e55

using the 5.0.8 headers patch

Package-Manager: portage-2.2.18

 sci-biology/fsl/ChangeLog        | 3 +++
 sci-biology/fsl/fsl-5.0.8.ebuild | 2 +-
 2 files changed, 4 insertions(+), 1 deletion(-)

diff --git a/sci-biology/fsl/ChangeLog b/sci-biology/fsl/ChangeLog
index fdcd6b1..a8447db 100644
--- a/sci-biology/fsl/ChangeLog
+++ b/sci-biology/fsl/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  29 Mar 2015;  <chymera@gentoo.org> fsl-5.0.8.ebuild:
+  using the 5.0.8 headers patch
+
   29 Mar 2015;  <chymera@gentoo.org> +files/fsl-5.0.8-headers.patch,
   files/fsl-5.0.4-headers.patch:
   reimplmented pathc fsl-5.0.4-headers

diff --git a/sci-biology/fsl/fsl-5.0.8.ebuild b/sci-biology/fsl/fsl-5.0.8.ebuild
index c2f8a10..8583a3e 100644
--- a/sci-biology/fsl/fsl-5.0.8.ebuild
+++ b/sci-biology/fsl/fsl-5.0.8.ebuild
@@ -32,7 +32,7 @@ S=${WORKDIR}/${PN}
 
 src_prepare(){
 	epatch "${FILESDIR}/${PN}"-5.0.8-setup.patch
-	epatch "${FILESDIR}/${PN}"-5.0.4-headers.patch
+	epatch "${FILESDIR}/${PN}"-5.0.8-headers.patch
 	epatch "${FILESDIR}/${PN}"-5.0.6-fsldir_redux.patch
 
 	sed -i \


^ permalink raw reply related	[flat|nested] 27+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/fsl/
@ 2015-04-20  1:11 Francois Bissey
  0 siblings, 0 replies; 27+ messages in thread
From: Francois Bissey @ 2015-04-20  1:11 UTC (permalink / raw
  To: gentoo-commits

commit:     17d1701d267f7c6beb268b4dd661f042ec4b4f0b
Author:     Horea Christian <h.chr <AT> mail <DOT> ru>
AuthorDate: Tue Apr  7 11:09:05 2015 +0000
Commit:     Francois Bissey <f.r.bissey <AT> massey <DOT> ac <DOT> nz>
CommitDate: Tue Apr  7 11:09:05 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=17d1701d

removed ebuilds with unavailable sources

Package-Manager: portage-2.2.18

 sci-biology/fsl/ChangeLog        |   3 +
 sci-biology/fsl/fsl-5.0.4.ebuild | 115 ---------------------------------------
 sci-biology/fsl/fsl-5.0.5.ebuild | 115 ---------------------------------------
 3 files changed, 3 insertions(+), 230 deletions(-)

diff --git a/sci-biology/fsl/ChangeLog b/sci-biology/fsl/ChangeLog
index 48835a1..e509710 100644
--- a/sci-biology/fsl/ChangeLog
+++ b/sci-biology/fsl/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  07 Apr 2015;  <chymera@gentoo.org> -fsl-5.0.4.ebuild, -fsl-5.0.5.ebuild:
+  removed ebuilds with unavailable sources
+
   07 Apr 2015;  <chymera@gentoo.org> fsl-5.0.6.ebuild:
   added new gentoo fsl-5.0.6 source location
 

diff --git a/sci-biology/fsl/fsl-5.0.4.ebuild b/sci-biology/fsl/fsl-5.0.4.ebuild
deleted file mode 100644
index b036faf..0000000
--- a/sci-biology/fsl/fsl-5.0.4.ebuild
+++ /dev/null
@@ -1,115 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI=5
-
-inherit eutils toolchain-funcs prefix
-
-DESCRIPTION="Analysis of functional, structural, and diffusion MRI brain imaging data"
-HOMEPAGE="http://www.fmrib.ox.ac.uk/fsl"
-SRC_URI="http://fsl.fmrib.ox.ac.uk/fsldownloads/${P}-sources.tar.gz"
-
-LICENSE="FSL BSD-2 newmat"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-COMMON_DEPEND="media-libs/glu
-	media-libs/libpng
-	media-libs/gd
-	sys-libs/zlib
-	dev-libs/boost
-	"
-DEPEND="${COMMON_DEPEND}"
-RDEPEND="${COMMON_DEPEND}
-	dev-lang/tcl
-	dev-lang/tk
-	"
-
-S=${WORKDIR}/${PN}
-
-src_prepare(){
-	epatch "${FILESDIR}/${P}"-setup.patch
-	epatch "${FILESDIR}/${P}"-headers.patch
-	epatch "${FILESDIR}/${P}"-fsldir_redux.patch
-
-	sed -i \
-		-e "s:@@GENTOO_RANLIB@@:$(tc-getRANLIB):" \
-		-e "s:@@GENTOO_CC@@:$(tc-getCC):" \
-		-e "s:@@GENTOO_CXX@@:$(tc-getCXX):" \
-		config/generic/systemvars.mk || die
-
-	eprefixify $(grep -rl GENTOO_PORTAGE_EPREFIX src/*) \
-		etc/js/label-div.html
-
-	makefilelist=$(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 -i "s:\${FSLDIR}/bin/::g" \
-		$(grep -rl "\${FSLDIR}/bin" src/*) \
-		$(grep -rl "\${FSLDIR}/bin" etc/matlab/*)
-	sed -i "s:\$FSLDIR/bin/::g" \
-		$(grep -rl "\$FSLDIR/bin" src/*) \
-		$(grep -rl "\$FSLDIR/bin" etc/matlab/*)
-
-	sed -i "s:\$FSLDIR/data:${EPREFIX}/usr/share/fsl/data:g" \
-		$(grep -rl "\$FSLDIR/data" src/*)
-
-	sed -i "s:\${FSLDIR}/data:${EPREFIX}/usr/share/fsl/data:g" \
-		$(grep -rl "\${FSLDIR}/data" src/*)
-
-	sed -i "s:\$FSLDIR/etc:${EPREFIX}/etc:g" \
-		$(grep -rl "\$FSLDIR/etc" src/*)
-
-	sed -i "s:\${FSLDIR}/etc:${EPREFIX}/etc:g" \
-		$(grep -rl "\${FSLDIR}/etc" src/*)
-
-	sed -i "s:\$FSLDIR/doc:${EPREFIX}/usr/share/fsl/doc:g" \
-		$(grep -rl "\$FSLDIR/doc" src/*)
-
-	sed -i "s:\${FSLDIR}/doc:${EPREFIX}/usr/share/fsl/doc:g" \
-		$(grep -rl "\${FSLDIR}/doc" src/*)
-
-	sed -i "s:\'\${FSLDIR}\'/doc:${EPREFIX}/usr/share/fsl/doc:g" \
-		$(grep -rl "\'\${FSLDIR}\'/doc" src/*)
-}
-
-src_compile() {
-	export FSLDIR=${WORKDIR}/${PN}
-	export FSLCONDIR=${WORKDIR}/${PN}/config
-	export FSLMACHTYPE=generic
-
-	export USERLDFLAGS="${LDFLAGS}"
-	export USERCFLAGS="${CFLAGS}"
-	export USERCXXFLAGS="${CXXFLAGS}"
-
-	./build || die
-}
-
-src_install() {
-	doexe bin/*
-
-	insinto /usr/share/${PN}
-	doins -r doc data refdoc
-
-	insinto /usr/libexec/fsl
-	doins -r tcl
-
-	insinto /etc
-	doins -r etc/default_flobs.flobs etc/flirtsch etc/js etc/luts
-	#if use matlab; then
-	#	doins etc/matlab
-	#fi
-
-	doenvd "${FILESDIR}"/99fsl
-}

diff --git a/sci-biology/fsl/fsl-5.0.5.ebuild b/sci-biology/fsl/fsl-5.0.5.ebuild
deleted file mode 100644
index 5b13e77..0000000
--- a/sci-biology/fsl/fsl-5.0.5.ebuild
+++ /dev/null
@@ -1,115 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI=5
-
-inherit eutils toolchain-funcs prefix
-
-DESCRIPTION="Analysis of functional, structural, and diffusion MRI brain imaging data"
-HOMEPAGE="http://www.fmrib.ox.ac.uk/fsl"
-SRC_URI="http://fsl.fmrib.ox.ac.uk/fsldownloads/${P}-sources.tar.gz"
-
-LICENSE="FSL BSD-2 newmat"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-COMMON_DEPEND="media-libs/glu
-	media-libs/libpng
-	media-libs/gd
-	sys-libs/zlib
-	dev-libs/boost
-	"
-DEPEND="${COMMON_DEPEND}"
-RDEPEND="${COMMON_DEPEND}
-	dev-lang/tcl
-	dev-lang/tk
-	"
-
-S=${WORKDIR}/${PN}
-
-src_prepare(){
-	epatch "${FILESDIR}/${PN}"-5.0.4-setup.patch
-	epatch "${FILESDIR}/${PN}"-5.0.4-headers.patch
-	epatch "${FILESDIR}/${PN}"-5.0.4-fsldir_redux.patch
-
-	sed -i \
-		-e "s:@@GENTOO_RANLIB@@:$(tc-getRANLIB):" \
-		-e "s:@@GENTOO_CC@@:$(tc-getCC):" \
-		-e "s:@@GENTOO_CXX@@:$(tc-getCXX):" \
-		config/generic/systemvars.mk || die
-
-	eprefixify $(grep -rl GENTOO_PORTAGE_EPREFIX src/*) \
-		etc/js/label-div.html
-
-	makefilelist=$(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 -i "s:\${FSLDIR}/bin/::g" \
-		$(grep -rl "\${FSLDIR}/bin" src/*) \
-		$(grep -rl "\${FSLDIR}/bin" etc/matlab/*)
-	sed -i "s:\$FSLDIR/bin/::g" \
-		$(grep -rl "\$FSLDIR/bin" src/*) \
-		$(grep -rl "\$FSLDIR/bin" etc/matlab/*)
-
-	sed -i "s:\$FSLDIR/data:${EPREFIX}/usr/share/fsl/data:g" \
-		$(grep -rl "\$FSLDIR/data" src/*)
-
-	sed -i "s:\${FSLDIR}/data:${EPREFIX}/usr/share/fsl/data:g" \
-		$(grep -rl "\${FSLDIR}/data" src/*)
-
-	sed -i "s:\$FSLDIR/etc:${EPREFIX}/etc:g" \
-		$(grep -rl "\$FSLDIR/etc" src/*)
-
-	sed -i "s:\${FSLDIR}/etc:${EPREFIX}/etc:g" \
-		$(grep -rl "\${FSLDIR}/etc" src/*)
-
-	sed -i "s:\$FSLDIR/doc:${EPREFIX}/usr/share/fsl/doc:g" \
-		$(grep -rl "\$FSLDIR/doc" src/*)
-
-	sed -i "s:\${FSLDIR}/doc:${EPREFIX}/usr/share/fsl/doc:g" \
-		$(grep -rl "\${FSLDIR}/doc" src/*)
-
-	sed -i "s:\'\${FSLDIR}\'/doc:${EPREFIX}/usr/share/fsl/doc:g" \
-		$(grep -rl "\'\${FSLDIR}\'/doc" src/*)
-}
-
-src_compile() {
-	export FSLDIR=${WORKDIR}/${PN}
-	export FSLCONDIR=${WORKDIR}/${PN}/config
-	export FSLMACHTYPE=generic
-
-	export USERLDFLAGS="${LDFLAGS}"
-	export USERCFLAGS="${CFLAGS}"
-	export USERCXXFLAGS="${CXXFLAGS}"
-
-	./build || die
-}
-
-src_install() {
-	doexe bin/*
-
-	insinto /usr/share/${PN}
-	doins -r doc data refdoc
-
-	insinto /usr/libexec/fsl
-	doins -r tcl
-
-	insinto /etc
-	doins -r etc/default_flobs.flobs etc/flirtsch etc/js etc/luts
-	#if use matlab; then
-	#	doins etc/matlab
-	#fi
-
-	doenvd "${FILESDIR}"/99fsl
-}


^ permalink raw reply related	[flat|nested] 27+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/fsl/
@ 2015-04-20  1:11 Francois Bissey
  0 siblings, 0 replies; 27+ messages in thread
From: Francois Bissey @ 2015-04-20  1:11 UTC (permalink / raw
  To: gentoo-commits

commit:     79f0c9f5b19678ffa18b0ca2e9fb393a5e1b7ae8
Author:     Horea Christian <h.chr <AT> mail <DOT> ru>
AuthorDate: Tue Apr  7 11:08:26 2015 +0000
Commit:     Francois Bissey <f.r.bissey <AT> massey <DOT> ac <DOT> nz>
CommitDate: Tue Apr  7 11:08:26 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=79f0c9f5

added new gentoo fsl-5.0.6 source location

Package-Manager: portage-2.2.18

 sci-biology/fsl/ChangeLog        | 3 +++
 sci-biology/fsl/fsl-5.0.6.ebuild | 2 +-
 2 files changed, 4 insertions(+), 1 deletion(-)

diff --git a/sci-biology/fsl/ChangeLog b/sci-biology/fsl/ChangeLog
index 822c9b9..48835a1 100644
--- a/sci-biology/fsl/ChangeLog
+++ b/sci-biology/fsl/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  07 Apr 2015;  <chymera@gentoo.org> fsl-5.0.6.ebuild:
+  added new gentoo fsl-5.0.6 source location
+
   30 Mar 2015;  <chymera@gentoo.org> +files/fsl-5.0.8-fsldir_redux.patch,
   -files/fsl-5.0.8-redux.patch, fsl-5.0.8.ebuild:
   implemented 5.0.8 fsldir redux patch

diff --git a/sci-biology/fsl/fsl-5.0.6.ebuild b/sci-biology/fsl/fsl-5.0.6.ebuild
index 81c9faa..8e5874d 100644
--- a/sci-biology/fsl/fsl-5.0.6.ebuild
+++ b/sci-biology/fsl/fsl-5.0.6.ebuild
@@ -8,7 +8,7 @@ inherit eutils toolchain-funcs prefix
 
 DESCRIPTION="Analysis of functional, structural, and diffusion MRI brain imaging data"
 HOMEPAGE="http://www.fmrib.ox.ac.uk/fsl"
-SRC_URI="http://fsl.fmrib.ox.ac.uk/fsldownloads/${P}-sources.tar.gz"
+SRC_URI="http://dev.gentoo.org/~jlec/distfiles/${P}-sources.tar.gz"
 
 LICENSE="FSL BSD-2 newmat"
 SLOT="0"


^ permalink raw reply related	[flat|nested] 27+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/fsl/
@ 2015-04-20  1:11 Francois Bissey
  0 siblings, 0 replies; 27+ messages in thread
From: Francois Bissey @ 2015-04-20  1:11 UTC (permalink / raw
  To: gentoo-commits

commit:     e4ec84ddd3e8f02d3d5c5824e7708de25147cc6c
Author:     Horea Christian <h.chr <AT> mail <DOT> ru>
AuthorDate: Sat Mar 28 18:01:48 2015 +0000
Commit:     Francois Bissey <f.r.bissey <AT> massey <DOT> ac <DOT> nz>
CommitDate: Sat Mar 28 18:01:48 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=e4ec84dd

corrected the changelog

Package-Manager: portage-2.2.18

 sci-biology/fsl/ChangeLog | 28 ++++++++++++++--------------
 1 file changed, 14 insertions(+), 14 deletions(-)

diff --git a/sci-biology/fsl/ChangeLog b/sci-biology/fsl/ChangeLog
index fcf8b9f..ea0bd2a 100644
--- a/sci-biology/fsl/ChangeLog
+++ b/sci-biology/fsl/ChangeLog
@@ -2,49 +2,49 @@
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
-  28 Mar 2015;  <chymera@gentoo.org> fsl-5.0.8.ebuild:
+  28 Mar 2015;  <h.chr@mail.ru> fsl-5.0.8.ebuild:
   using new setup patch file for new ebuild
 
-  28 Mar 2015;  <chymera@gentoo.org> +files/fsl-5.0.8-setup.patch:
+  28 Mar 2015;  <h.chr@mail.ru> +files/fsl-5.0.8-setup.patch:
   new pathc by François Bissey
 
-  25 Mar 2015;  <chymera@gentoo.org> fsl-5.0.4.ebuild, fsl-5.0.5.ebuild,
+  25 Mar 2015;  <h.chr@mail.ru> fsl-5.0.4.ebuild, fsl-5.0.5.ebuild,
   fsl-5.0.8.ebuild:
   added licences to all versions
 
-  25 Mar 2015;  <chymera@gentoo.org> fsl-5.0.6.ebuild:
+  25 Mar 2015;  <h.chr@mail.ru> fsl-5.0.6.ebuild:
   added license for included gdchart
 
-  25 Mar 2015;  <chymera@gentoo.org> fsl-5.0.6.ebuild:
+  25 Mar 2015;  <h.chr@mail.ru> fsl-5.0.6.ebuild:
   set the correct licences
 
-  11 Mar 2015;  <chymera@gentoo.org> fsl-5.0.6.ebuild:
+  11 Mar 2015;  <h.chr@mail.ru> fsl-5.0.6.ebuild:
   installing fslversion
 
-  11 Mar 2015;  <chymera@gentoo.org> fsl-5.0.6.ebuild:
+  11 Mar 2015;  <h.chr@mail.ru> fsl-5.0.6.ebuild:
   sed-ing before installing
 
-  10 Mar 2015;  <chymera@gentoo.org> fsl-5.0.6.ebuild:
+  10 Mar 2015;  <h.chr@mail.ru> fsl-5.0.6.ebuild:
   changed grep wrapper
 
-  10 Mar 2015;  <chymera@gentoo.org> fsl-5.0.6.ebuild:
+  10 Mar 2015;  <h.chr@mail.ru> fsl-5.0.6.ebuild:
   reformatted tcl sed calls
 
-  10 Mar 2015;  <chymera@gentoo.org> fsl-5.0.6.ebuild:
+  10 Mar 2015;  <h.chr@mail.ru> fsl-5.0.6.ebuild:
   fixed tcl location according to instructions by kiwifb
 
-  10 Mar 2015;  <chymera@gentoo.org> fsl-5.0.6.ebuild:
+  10 Mar 2015;  <h.chr@mail.ru> fsl-5.0.6.ebuild:
   installing fsl.sh
 
-  05 Mar 2015;  <chymera@gentoo.org> fsl-5.0.6.ebuild:
+  05 Mar 2015;  <h.chr@mail.ru> fsl-5.0.6.ebuild:
   removing faulty check
 
-  04 Mar 2015;  <chymera@gentoo.org> files/99fsl:
+  04 Mar 2015;  <h.chr@mail.ru> files/99fsl:
   added FSLPATH
 
 *fsl-5.0.8 (20 Feb 2015)
 
-  20 Feb 2015;  <chymera@gentoo.org> +fsl-5.0.8.ebuild:
+  20 Feb 2015;  <h.chr@mail.ru> +fsl-5.0.8.ebuild:
   bumped version
 
   18 Oct 2013; François Bissey <francois.bissey@canterbury.ac.nz>


^ permalink raw reply related	[flat|nested] 27+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/fsl/
@ 2015-04-20  1:11 Francois Bissey
  0 siblings, 0 replies; 27+ messages in thread
From: Francois Bissey @ 2015-04-20  1:11 UTC (permalink / raw
  To: gentoo-commits

commit:     0a6acd8e277e8b1bb63af24829e76852f2182056
Author:     Horea Christian <h.chr <AT> mail <DOT> ru>
AuthorDate: Wed Mar 11 17:21:02 2015 +0000
Commit:     Francois Bissey <f.r.bissey <AT> massey <DOT> ac <DOT> nz>
CommitDate: Wed Mar 11 17:21:02 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=0a6acd8e

sed-ing before installing

Package-Manager: portage-2.2.18

 sci-biology/fsl/ChangeLog        |  3 +++
 sci-biology/fsl/fsl-5.0.6.ebuild | 12 ++++++------
 2 files changed, 9 insertions(+), 6 deletions(-)

diff --git a/sci-biology/fsl/ChangeLog b/sci-biology/fsl/ChangeLog
index 682727d..54d0251 100644
--- a/sci-biology/fsl/ChangeLog
+++ b/sci-biology/fsl/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  11 Mar 2015;  <chymera@gentoo.org> fsl-5.0.6.ebuild:
+  sed-ing before installing
+
   10 Mar 2015;  <chymera@gentoo.org> fsl-5.0.6.ebuild:
   changed grep wrapper
 

diff --git a/sci-biology/fsl/fsl-5.0.6.ebuild b/sci-biology/fsl/fsl-5.0.6.ebuild
index 6f9584f..b819813 100644
--- a/sci-biology/fsl/fsl-5.0.6.ebuild
+++ b/sci-biology/fsl/fsl-5.0.6.ebuild
@@ -100,18 +100,18 @@ src_compile() {
 }
 
 src_install() {
-	exeinto /usr/bin
-	doexe bin/*
-
-	insinto /usr/share/${PN}
-	doins -r doc data refdoc
-
 	sed -i "s:\${FSLDIR}/tcl:/usr/libexec/fsl:g" \
 		$(grep -lI "\${FSLDIR}/tcl" bin/*) \
 		$(grep -l "\${FSLDIR}/tcl"  tcl/*)
 	sed -i "s:\$FSLDIR/tcl:/usr/libexec/fsl:g" \
 		$(grep -l "\$FSLDIR/tcl" tcl/*)
 
+	exeinto /usr/bin
+	doexe bin/*
+
+	insinto /usr/share/${PN}
+	doins -r doc data refdoc
+
 	insinto /usr/libexec/fsl
 	doins -r tcl/*
 


^ permalink raw reply related	[flat|nested] 27+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/fsl/
@ 2015-04-20  1:11 Francois Bissey
  0 siblings, 0 replies; 27+ messages in thread
From: Francois Bissey @ 2015-04-20  1:11 UTC (permalink / raw
  To: gentoo-commits

commit:     33466f24f8ed105f0fd89626bff2604db2639a78
Author:     Horea Christian <h.chr <AT> mail <DOT> ru>
AuthorDate: Wed Mar 25 12:51:09 2015 +0000
Commit:     Francois Bissey <f.r.bissey <AT> massey <DOT> ac <DOT> nz>
CommitDate: Wed Mar 25 12:51:09 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=33466f24

added licences to all versions

Package-Manager: portage-2.2.18

 sci-biology/fsl/ChangeLog        | 4 ++++
 sci-biology/fsl/fsl-5.0.4.ebuild | 4 ++--
 sci-biology/fsl/fsl-5.0.5.ebuild | 4 ++--
 sci-biology/fsl/fsl-5.0.8.ebuild | 2 +-
 4 files changed, 9 insertions(+), 5 deletions(-)

diff --git a/sci-biology/fsl/ChangeLog b/sci-biology/fsl/ChangeLog
index 7dfe56a..2b12763 100644
--- a/sci-biology/fsl/ChangeLog
+++ b/sci-biology/fsl/ChangeLog
@@ -2,6 +2,10 @@
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  25 Mar 2015;  <chymera@gentoo.org> fsl-5.0.4.ebuild, fsl-5.0.5.ebuild,
+  fsl-5.0.8.ebuild:
+  added licences to all versions
+
   25 Mar 2015;  <chymera@gentoo.org> fsl-5.0.6.ebuild:
   added license for included gdchart
 

diff --git a/sci-biology/fsl/fsl-5.0.4.ebuild b/sci-biology/fsl/fsl-5.0.4.ebuild
index 18b2819..b036faf 100644
--- a/sci-biology/fsl/fsl-5.0.4.ebuild
+++ b/sci-biology/fsl/fsl-5.0.4.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2013 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 
@@ -10,7 +10,7 @@ DESCRIPTION="Analysis of functional, structural, and diffusion MRI brain imaging
 HOMEPAGE="http://www.fmrib.ox.ac.uk/fsl"
 SRC_URI="http://fsl.fmrib.ox.ac.uk/fsldownloads/${P}-sources.tar.gz"
 
-LICENSE="GPL-3+"
+LICENSE="FSL BSD-2 newmat"
 SLOT="0"
 KEYWORDS="~amd64"
 IUSE=""

diff --git a/sci-biology/fsl/fsl-5.0.5.ebuild b/sci-biology/fsl/fsl-5.0.5.ebuild
index 73df7b2..5b13e77 100644
--- a/sci-biology/fsl/fsl-5.0.5.ebuild
+++ b/sci-biology/fsl/fsl-5.0.5.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2013 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 
@@ -10,7 +10,7 @@ DESCRIPTION="Analysis of functional, structural, and diffusion MRI brain imaging
 HOMEPAGE="http://www.fmrib.ox.ac.uk/fsl"
 SRC_URI="http://fsl.fmrib.ox.ac.uk/fsldownloads/${P}-sources.tar.gz"
 
-LICENSE="GPL-3+"
+LICENSE="FSL BSD-2 newmat"
 SLOT="0"
 KEYWORDS="~amd64"
 IUSE=""

diff --git a/sci-biology/fsl/fsl-5.0.8.ebuild b/sci-biology/fsl/fsl-5.0.8.ebuild
index b927eec..2d358e5 100644
--- a/sci-biology/fsl/fsl-5.0.8.ebuild
+++ b/sci-biology/fsl/fsl-5.0.8.ebuild
@@ -10,7 +10,7 @@ DESCRIPTION="Analysis of functional, structural, and diffusion MRI brain imaging
 HOMEPAGE="http://www.fmrib.ox.ac.uk/fsl"
 SRC_URI="http://fsl.fmrib.ox.ac.uk/fsldownloads/${P}-sources.tar.gz"
 
-LICENSE="GPL-3+"
+LICENSE="FSL BSD-2 newmat"
 SLOT="0"
 KEYWORDS="~amd64"
 IUSE=""


^ permalink raw reply related	[flat|nested] 27+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/fsl/
@ 2015-04-20  1:11 Francois Bissey
  0 siblings, 0 replies; 27+ messages in thread
From: Francois Bissey @ 2015-04-20  1:11 UTC (permalink / raw
  To: gentoo-commits

commit:     f2b9e88047ac0f76bcdbf050d61685a2519b0426
Author:     Horea Christian <h.chr <AT> mail <DOT> ru>
AuthorDate: Wed Mar 11 19:48:59 2015 +0000
Commit:     Francois Bissey <f.r.bissey <AT> massey <DOT> ac <DOT> nz>
CommitDate: Wed Mar 11 19:48:59 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=f2b9e880

installing fslversion

Package-Manager: portage-2.2.18

 sci-biology/fsl/ChangeLog        | 3 +++
 sci-biology/fsl/fsl-5.0.6.ebuild | 1 +
 2 files changed, 4 insertions(+)

diff --git a/sci-biology/fsl/ChangeLog b/sci-biology/fsl/ChangeLog
index 54d0251..3d36590 100644
--- a/sci-biology/fsl/ChangeLog
+++ b/sci-biology/fsl/ChangeLog
@@ -3,6 +3,9 @@
 # $Header: $
 
   11 Mar 2015;  <chymera@gentoo.org> fsl-5.0.6.ebuild:
+  installing fslversion
+
+  11 Mar 2015;  <chymera@gentoo.org> fsl-5.0.6.ebuild:
   sed-ing before installing
 
   10 Mar 2015;  <chymera@gentoo.org> fsl-5.0.6.ebuild:

diff --git a/sci-biology/fsl/fsl-5.0.6.ebuild b/sci-biology/fsl/fsl-5.0.6.ebuild
index b819813..ae9722c 100644
--- a/sci-biology/fsl/fsl-5.0.6.ebuild
+++ b/sci-biology/fsl/fsl-5.0.6.ebuild
@@ -119,6 +119,7 @@ src_install() {
 	doins etc/fslconf/fsl.sh
 
 	insinto /etc
+	doins etc/fslversion
 	doins -r etc/default_flobs.flobs etc/flirtsch etc/js etc/luts
 	#if use matlab; then
 	#	doins etc/matlab


^ permalink raw reply related	[flat|nested] 27+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/fsl/
@ 2015-04-20  1:11 Francois Bissey
  0 siblings, 0 replies; 27+ messages in thread
From: Francois Bissey @ 2015-04-20  1:11 UTC (permalink / raw
  To: gentoo-commits

commit:     fae6537014d7c03aeefc9c7d7c3ca23e841130e8
Author:     Horea Christian <h.chr <AT> mail <DOT> ru>
AuthorDate: Sat Mar 28 17:56:30 2015 +0000
Commit:     Francois Bissey <f.r.bissey <AT> massey <DOT> ac <DOT> nz>
CommitDate: Sat Mar 28 17:56:30 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=fae65370

using new setup patch file for new ebuild

Package-Manager: portage-2.2.18

 sci-biology/fsl/ChangeLog        | 3 +++
 sci-biology/fsl/fsl-5.0.8.ebuild | 2 +-
 2 files changed, 4 insertions(+), 1 deletion(-)

diff --git a/sci-biology/fsl/ChangeLog b/sci-biology/fsl/ChangeLog
index 3ac363f..fcf8b9f 100644
--- a/sci-biology/fsl/ChangeLog
+++ b/sci-biology/fsl/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  28 Mar 2015;  <chymera@gentoo.org> fsl-5.0.8.ebuild:
+  using new setup patch file for new ebuild
+
   28 Mar 2015;  <chymera@gentoo.org> +files/fsl-5.0.8-setup.patch:
   new pathc by François Bissey
 

diff --git a/sci-biology/fsl/fsl-5.0.8.ebuild b/sci-biology/fsl/fsl-5.0.8.ebuild
index 2d358e5..e185863 100644
--- a/sci-biology/fsl/fsl-5.0.8.ebuild
+++ b/sci-biology/fsl/fsl-5.0.8.ebuild
@@ -31,7 +31,7 @@ RDEPEND="${COMMON_DEPEND}
 S=${WORKDIR}/${PN}
 
 src_prepare(){
-	epatch "${FILESDIR}/${PN}"-5.0.4-setup.patch
+	epatch "${FILESDIR}/${PN}"-5.0.8-setup.patch
 	epatch "${FILESDIR}/${PN}"-5.0.4-headers.patch
 	epatch "${FILESDIR}/${PN}"-5.0.6-fsldir_redux.patch
 


^ permalink raw reply related	[flat|nested] 27+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/fsl/
@ 2015-04-20  1:11 Francois Bissey
  0 siblings, 0 replies; 27+ messages in thread
From: Francois Bissey @ 2015-04-20  1:11 UTC (permalink / raw
  To: gentoo-commits

commit:     68fe87b054ec542364e640086872e5e4b31f86b9
Author:     Horea Christian <h.chr <AT> mail <DOT> ru>
AuthorDate: Wed Mar 25 10:53:29 2015 +0000
Commit:     Francois Bissey <f.r.bissey <AT> massey <DOT> ac <DOT> nz>
CommitDate: Wed Mar 25 10:53:29 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=68fe87b0

added license for included gdchart

Package-Manager: portage-2.2.18

 sci-biology/fsl/ChangeLog        | 3 +++
 sci-biology/fsl/fsl-5.0.6.ebuild | 2 +-
 2 files changed, 4 insertions(+), 1 deletion(-)

diff --git a/sci-biology/fsl/ChangeLog b/sci-biology/fsl/ChangeLog
index c5f5df0..7dfe56a 100644
--- a/sci-biology/fsl/ChangeLog
+++ b/sci-biology/fsl/ChangeLog
@@ -3,6 +3,9 @@
 # $Header: $
 
   25 Mar 2015;  <chymera@gentoo.org> fsl-5.0.6.ebuild:
+  added license for included gdchart
+
+  25 Mar 2015;  <chymera@gentoo.org> fsl-5.0.6.ebuild:
   set the correct licences
 
   11 Mar 2015;  <chymera@gentoo.org> fsl-5.0.6.ebuild:

diff --git a/sci-biology/fsl/fsl-5.0.6.ebuild b/sci-biology/fsl/fsl-5.0.6.ebuild
index d0fafe0..81c9faa 100644
--- a/sci-biology/fsl/fsl-5.0.6.ebuild
+++ b/sci-biology/fsl/fsl-5.0.6.ebuild
@@ -10,7 +10,7 @@ DESCRIPTION="Analysis of functional, structural, and diffusion MRI brain imaging
 HOMEPAGE="http://www.fmrib.ox.ac.uk/fsl"
 SRC_URI="http://fsl.fmrib.ox.ac.uk/fsldownloads/${P}-sources.tar.gz"
 
-LICENSE="FSL newmat"
+LICENSE="FSL BSD-2 newmat"
 SLOT="0"
 KEYWORDS="~amd64"
 IUSE=""


^ permalink raw reply related	[flat|nested] 27+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/fsl/
@ 2015-04-20  1:11 Francois Bissey
  0 siblings, 0 replies; 27+ messages in thread
From: Francois Bissey @ 2015-04-20  1:11 UTC (permalink / raw
  To: gentoo-commits

commit:     787b1ce2e28f44f17757f39e028442b37af1e0fa
Author:     Horea Christian <h.chr <AT> mail <DOT> ru>
AuthorDate: Wed Mar 25 10:06:31 2015 +0000
Commit:     Francois Bissey <f.r.bissey <AT> massey <DOT> ac <DOT> nz>
CommitDate: Wed Mar 25 10:06:31 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=787b1ce2

set the correct licences

Package-Manager: portage-2.2.18

 sci-biology/fsl/ChangeLog        | 3 +++
 sci-biology/fsl/fsl-5.0.6.ebuild | 2 +-
 2 files changed, 4 insertions(+), 1 deletion(-)

diff --git a/sci-biology/fsl/ChangeLog b/sci-biology/fsl/ChangeLog
index 3d36590..c5f5df0 100644
--- a/sci-biology/fsl/ChangeLog
+++ b/sci-biology/fsl/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  25 Mar 2015;  <chymera@gentoo.org> fsl-5.0.6.ebuild:
+  set the correct licences
+
   11 Mar 2015;  <chymera@gentoo.org> fsl-5.0.6.ebuild:
   installing fslversion
 

diff --git a/sci-biology/fsl/fsl-5.0.6.ebuild b/sci-biology/fsl/fsl-5.0.6.ebuild
index ae9722c..d0fafe0 100644
--- a/sci-biology/fsl/fsl-5.0.6.ebuild
+++ b/sci-biology/fsl/fsl-5.0.6.ebuild
@@ -10,7 +10,7 @@ DESCRIPTION="Analysis of functional, structural, and diffusion MRI brain imaging
 HOMEPAGE="http://www.fmrib.ox.ac.uk/fsl"
 SRC_URI="http://fsl.fmrib.ox.ac.uk/fsldownloads/${P}-sources.tar.gz"
 
-LICENSE="GPL-3+"
+LICENSE="FSL newmat"
 SLOT="0"
 KEYWORDS="~amd64"
 IUSE=""


^ permalink raw reply related	[flat|nested] 27+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/fsl/
@ 2015-04-20  1:11 Francois Bissey
  0 siblings, 0 replies; 27+ messages in thread
From: Francois Bissey @ 2015-04-20  1:11 UTC (permalink / raw
  To: gentoo-commits

commit:     2520b2c4c4fcfabe5157aa3a90db2a40acf927cf
Author:     Horea Christian <h.chr <AT> mail <DOT> ru>
AuthorDate: Thu Mar  5 12:14:10 2015 +0000
Commit:     Francois Bissey <f.r.bissey <AT> massey <DOT> ac <DOT> nz>
CommitDate: Thu Mar  5 12:14:10 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=2520b2c4

removing faulty check

Package-Manager: portage-2.2.17

 sci-biology/fsl/ChangeLog        | 3 +++
 sci-biology/fsl/fsl-5.0.6.ebuild | 4 +++-
 2 files changed, 6 insertions(+), 1 deletion(-)

diff --git a/sci-biology/fsl/ChangeLog b/sci-biology/fsl/ChangeLog
index fac3cce..4475d87 100644
--- a/sci-biology/fsl/ChangeLog
+++ b/sci-biology/fsl/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  05 Mar 2015;  <chymera@gentoo.org> fsl-5.0.6.ebuild:
+  removing faulty check
+
   04 Mar 2015;  <chymera@gentoo.org> files/99fsl:
   added FSLPATH
 

diff --git a/sci-biology/fsl/fsl-5.0.6.ebuild b/sci-biology/fsl/fsl-5.0.6.ebuild
index 84755e2..80e06e1 100644
--- a/sci-biology/fsl/fsl-5.0.6.ebuild
+++ b/sci-biology/fsl/fsl-5.0.6.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2013 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 
@@ -83,6 +83,8 @@ src_prepare(){
 
 	sed -i "s:\'\${FSLDIR}\'/doc:${EPREFIX}/usr/share/fsl/doc:g" \
 		$(grep -rl "\'\${FSLDIR}\'/doc" src/*)
+
+	sed -i -e "s:\$FSLDIR/etc:/etc:g" `grep -rlI \$FSLDIR/etc *`
 }
 
 src_compile() {


^ permalink raw reply related	[flat|nested] 27+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/fsl/
@ 2015-04-20  1:11 Francois Bissey
  0 siblings, 0 replies; 27+ messages in thread
From: Francois Bissey @ 2015-04-20  1:11 UTC (permalink / raw
  To: gentoo-commits

commit:     24370907c9b2211dbfcc32e8a2f9de46eda62b20
Author:     Horea Christian <h.chr <AT> mail <DOT> ru>
AuthorDate: Tue Mar 10 01:44:09 2015 +0000
Commit:     Francois Bissey <f.r.bissey <AT> massey <DOT> ac <DOT> nz>
CommitDate: Tue Mar 10 01:44:09 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=24370907

installing fsl.sh

Package-Manager: portage-2.2.18

 sci-biology/fsl/ChangeLog        | 3 +++
 sci-biology/fsl/fsl-5.0.6.ebuild | 3 +++
 2 files changed, 6 insertions(+)

diff --git a/sci-biology/fsl/ChangeLog b/sci-biology/fsl/ChangeLog
index 4475d87..815ad20 100644
--- a/sci-biology/fsl/ChangeLog
+++ b/sci-biology/fsl/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  10 Mar 2015;  <chymera@gentoo.org> fsl-5.0.6.ebuild:
+  installing fsl.sh
+
   05 Mar 2015;  <chymera@gentoo.org> fsl-5.0.6.ebuild:
   removing faulty check
 

diff --git a/sci-biology/fsl/fsl-5.0.6.ebuild b/sci-biology/fsl/fsl-5.0.6.ebuild
index 80e06e1..5f26672 100644
--- a/sci-biology/fsl/fsl-5.0.6.ebuild
+++ b/sci-biology/fsl/fsl-5.0.6.ebuild
@@ -109,6 +109,9 @@ src_install() {
 	insinto /usr/libexec/fsl
 	doins -r tcl
 
+	insinto /etc/fslconf
+	doins etc/fslconf/fsl.sh
+
 	insinto /etc
 	doins -r etc/default_flobs.flobs etc/flirtsch etc/js etc/luts
 	#if use matlab; then


^ permalink raw reply related	[flat|nested] 27+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/fsl/
@ 2015-04-20  1:11 Francois Bissey
  0 siblings, 0 replies; 27+ messages in thread
From: Francois Bissey @ 2015-04-20  1:11 UTC (permalink / raw
  To: gentoo-commits

commit:     4e242526131439aa84b88b301a16ea64479a9038
Author:     Horea Christian <h.chr <AT> mail <DOT> ru>
AuthorDate: Tue Mar 10 12:10:36 2015 +0000
Commit:     Francois Bissey <f.r.bissey <AT> massey <DOT> ac <DOT> nz>
CommitDate: Tue Mar 10 12:10:36 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=4e242526

reformatted tcl sed calls

Package-Manager: portage-2.2.18

 sci-biology/fsl/ChangeLog        | 3 +++
 sci-biology/fsl/fsl-5.0.6.ebuild | 9 +++++----
 2 files changed, 8 insertions(+), 4 deletions(-)

diff --git a/sci-biology/fsl/ChangeLog b/sci-biology/fsl/ChangeLog
index 915ff81..5c76f1e 100644
--- a/sci-biology/fsl/ChangeLog
+++ b/sci-biology/fsl/ChangeLog
@@ -3,6 +3,9 @@
 # $Header: $
 
   10 Mar 2015;  <chymera@gentoo.org> fsl-5.0.6.ebuild:
+  reformatted tcl sed calls
+
+  10 Mar 2015;  <chymera@gentoo.org> fsl-5.0.6.ebuild:
   fixed tcl location according to instructions by kiwifb
 
   10 Mar 2015;  <chymera@gentoo.org> fsl-5.0.6.ebuild:

diff --git a/sci-biology/fsl/fsl-5.0.6.ebuild b/sci-biology/fsl/fsl-5.0.6.ebuild
index 6de5ff7..e1b4ac6 100644
--- a/sci-biology/fsl/fsl-5.0.6.ebuild
+++ b/sci-biology/fsl/fsl-5.0.6.ebuild
@@ -85,10 +85,6 @@ src_prepare(){
 		$(grep -rl "\'\${FSLDIR}\'/doc" src/*)
 
 	sed -i -e "s:\$FSLDIR/etc:/etc:g" `grep -rlI \$FSLDIR/etc *`
-
-	sed -i "s:\${FSLDIR}/tcl:/usr/libexec/fsl:g" `grep -lI \${FSLDIR}/tcl bin/*` `grep -l 
-\${FSLDIR}/tcl  tcl/*`
-	sed -i "s:\$FSLDIR/tcl:/usr/libexec/fsl:g" `grep -l \$FSLDIR/tcl tcl/*`
 }
 
 src_compile() {
@@ -110,6 +106,11 @@ src_install() {
 	insinto /usr/share/${PN}
 	doins -r doc data refdoc
 
+	sed -i "s:\${FSLDIR}/tcl:/usr/libexec/fsl:g" \
+		`grep -lI \${FSLDIR}/tcl bin/*` \
+		`grep -l \${FSLDIR}/tcl  tcl/*`
+	sed -i "s:\$FSLDIR/tcl:/usr/libexec/fsl:g" `grep -l \$FSLDIR/tcl tcl/*`	
+
 	insinto /usr/libexec/fsl
 	doins -r tcl/*
 


^ permalink raw reply related	[flat|nested] 27+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/fsl/
@ 2015-04-20  1:11 Francois Bissey
  0 siblings, 0 replies; 27+ messages in thread
From: Francois Bissey @ 2015-04-20  1:11 UTC (permalink / raw
  To: gentoo-commits

commit:     3956c9c9482c4360acb377884903f0b09c7cd0a6
Author:     Horea Christian <h.chr <AT> mail <DOT> ru>
AuthorDate: Tue Mar 10 23:19:18 2015 +0000
Commit:     Francois Bissey <f.r.bissey <AT> massey <DOT> ac <DOT> nz>
CommitDate: Tue Mar 10 23:19:18 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=3956c9c9

changed grep wrapper

Package-Manager: portage-2.2.18

 sci-biology/fsl/ChangeLog        | 3 +++
 sci-biology/fsl/fsl-5.0.6.ebuild | 7 ++++---
 2 files changed, 7 insertions(+), 3 deletions(-)

diff --git a/sci-biology/fsl/ChangeLog b/sci-biology/fsl/ChangeLog
index 5c76f1e..682727d 100644
--- a/sci-biology/fsl/ChangeLog
+++ b/sci-biology/fsl/ChangeLog
@@ -3,6 +3,9 @@
 # $Header: $
 
   10 Mar 2015;  <chymera@gentoo.org> fsl-5.0.6.ebuild:
+  changed grep wrapper
+
+  10 Mar 2015;  <chymera@gentoo.org> fsl-5.0.6.ebuild:
   reformatted tcl sed calls
 
   10 Mar 2015;  <chymera@gentoo.org> fsl-5.0.6.ebuild:

diff --git a/sci-biology/fsl/fsl-5.0.6.ebuild b/sci-biology/fsl/fsl-5.0.6.ebuild
index e1b4ac6..6f9584f 100644
--- a/sci-biology/fsl/fsl-5.0.6.ebuild
+++ b/sci-biology/fsl/fsl-5.0.6.ebuild
@@ -107,9 +107,10 @@ src_install() {
 	doins -r doc data refdoc
 
 	sed -i "s:\${FSLDIR}/tcl:/usr/libexec/fsl:g" \
-		`grep -lI \${FSLDIR}/tcl bin/*` \
-		`grep -l \${FSLDIR}/tcl  tcl/*`
-	sed -i "s:\$FSLDIR/tcl:/usr/libexec/fsl:g" `grep -l \$FSLDIR/tcl tcl/*`	
+		$(grep -lI "\${FSLDIR}/tcl" bin/*) \
+		$(grep -l "\${FSLDIR}/tcl"  tcl/*)
+	sed -i "s:\$FSLDIR/tcl:/usr/libexec/fsl:g" \
+		$(grep -l "\$FSLDIR/tcl" tcl/*)
 
 	insinto /usr/libexec/fsl
 	doins -r tcl/*


^ permalink raw reply related	[flat|nested] 27+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/fsl/
@ 2015-04-20  1:11 Francois Bissey
  0 siblings, 0 replies; 27+ messages in thread
From: Francois Bissey @ 2015-04-20  1:11 UTC (permalink / raw
  To: gentoo-commits

commit:     fd6c1087b199b9cd35e86ee8fb861ec1e6312f6e
Author:     Horea Christian <h.chr <AT> mail <DOT> ru>
AuthorDate: Tue Mar 10 10:48:10 2015 +0000
Commit:     Francois Bissey <f.r.bissey <AT> massey <DOT> ac <DOT> nz>
CommitDate: Tue Mar 10 10:48:10 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=fd6c1087

fixed tcl location according to instructions by kiwifb

Package-Manager: portage-2.2.18

 sci-biology/fsl/ChangeLog        | 3 +++
 sci-biology/fsl/fsl-5.0.6.ebuild | 6 +++++-
 2 files changed, 8 insertions(+), 1 deletion(-)

diff --git a/sci-biology/fsl/ChangeLog b/sci-biology/fsl/ChangeLog
index 815ad20..915ff81 100644
--- a/sci-biology/fsl/ChangeLog
+++ b/sci-biology/fsl/ChangeLog
@@ -3,6 +3,9 @@
 # $Header: $
 
   10 Mar 2015;  <chymera@gentoo.org> fsl-5.0.6.ebuild:
+  fixed tcl location according to instructions by kiwifb
+
+  10 Mar 2015;  <chymera@gentoo.org> fsl-5.0.6.ebuild:
   installing fsl.sh
 
   05 Mar 2015;  <chymera@gentoo.org> fsl-5.0.6.ebuild:

diff --git a/sci-biology/fsl/fsl-5.0.6.ebuild b/sci-biology/fsl/fsl-5.0.6.ebuild
index 5f26672..6de5ff7 100644
--- a/sci-biology/fsl/fsl-5.0.6.ebuild
+++ b/sci-biology/fsl/fsl-5.0.6.ebuild
@@ -85,6 +85,10 @@ src_prepare(){
 		$(grep -rl "\'\${FSLDIR}\'/doc" src/*)
 
 	sed -i -e "s:\$FSLDIR/etc:/etc:g" `grep -rlI \$FSLDIR/etc *`
+
+	sed -i "s:\${FSLDIR}/tcl:/usr/libexec/fsl:g" `grep -lI \${FSLDIR}/tcl bin/*` `grep -l 
+\${FSLDIR}/tcl  tcl/*`
+	sed -i "s:\$FSLDIR/tcl:/usr/libexec/fsl:g" `grep -l \$FSLDIR/tcl tcl/*`
 }
 
 src_compile() {
@@ -107,7 +111,7 @@ src_install() {
 	doins -r doc data refdoc
 
 	insinto /usr/libexec/fsl
-	doins -r tcl
+	doins -r tcl/*
 
 	insinto /etc/fslconf
 	doins etc/fslconf/fsl.sh


^ permalink raw reply related	[flat|nested] 27+ messages in thread
end of thread, other threads:[~2024-02-29 21:15 UTC | newest]

Thread overview: 27+ messages (download: mbox.gz follow: Atom feed
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2015-09-21 17:44 [gentoo-commits] proj/sci:master commit in: sci-biology/fsl/ Justin Lecher
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2024-02-29 21:15 Horea Christian
2022-05-02 12:22 Andrew Ammerlaan
2022-01-15 15:59 Andrew Ammerlaan
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2021-06-01  9:24 Andrew Ammerlaan
2017-11-18 19:49 Justin Lecher
2016-04-13 10:47 Marius Brehler
2015-11-24  2:03 Christoph Junghans
2015-11-17 15:46 Justin Lecher
2015-11-05 15:14 Marius Brehler
2015-04-20  1:11 Francois Bissey
2015-04-20  1:11 Francois Bissey
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