[gentoo-commits] proj/sci:master commit in: sci-biology/fsl/
commit: 33466f24f8ed105f0fd89626bff2604db2639a78
Author: Horea Christian mail ru>
AuthorDate: Wed Mar 25 12:51:09 2015 +
Commit: Francois Bissey massey ac nz>
CommitDate: Wed Mar 25 12:51:09 2015 +
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; fsl-5.0.4.ebuild, fsl-5.0.5.ebuild,
+ fsl-5.0.8.ebuild:
+ added licences to all versions
+
25 Mar 2015; 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=""
[gentoo-commits] proj/sci:master commit in: sci-biology/fsl/
commit: e4ec84ddd3e8f02d3d5c5824e7708de25147cc6c Author: Horea Christian mail ru> AuthorDate: Sat Mar 28 18:01:48 2015 + Commit: Francois Bissey massey ac nz> CommitDate: Sat Mar 28 18:01:48 2015 + 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; fsl-5.0.8.ebuild: + 28 Mar 2015; fsl-5.0.8.ebuild: using new setup patch file for new ebuild - 28 Mar 2015; +files/fsl-5.0.8-setup.patch: + 28 Mar 2015; +files/fsl-5.0.8-setup.patch: new pathc by François Bissey - 25 Mar 2015; fsl-5.0.4.ebuild, fsl-5.0.5.ebuild, + 25 Mar 2015; fsl-5.0.4.ebuild, fsl-5.0.5.ebuild, fsl-5.0.8.ebuild: added licences to all versions - 25 Mar 2015; fsl-5.0.6.ebuild: + 25 Mar 2015; fsl-5.0.6.ebuild: added license for included gdchart - 25 Mar 2015; fsl-5.0.6.ebuild: + 25 Mar 2015; fsl-5.0.6.ebuild: set the correct licences - 11 Mar 2015; fsl-5.0.6.ebuild: + 11 Mar 2015; fsl-5.0.6.ebuild: installing fslversion - 11 Mar 2015; fsl-5.0.6.ebuild: + 11 Mar 2015; fsl-5.0.6.ebuild: sed-ing before installing - 10 Mar 2015; fsl-5.0.6.ebuild: + 10 Mar 2015; fsl-5.0.6.ebuild: changed grep wrapper - 10 Mar 2015; fsl-5.0.6.ebuild: + 10 Mar 2015; fsl-5.0.6.ebuild: reformatted tcl sed calls - 10 Mar 2015; fsl-5.0.6.ebuild: + 10 Mar 2015; fsl-5.0.6.ebuild: fixed tcl location according to instructions by kiwifb - 10 Mar 2015; fsl-5.0.6.ebuild: + 10 Mar 2015; fsl-5.0.6.ebuild: installing fsl.sh - 05 Mar 2015; fsl-5.0.6.ebuild: + 05 Mar 2015; fsl-5.0.6.ebuild: removing faulty check - 04 Mar 2015; files/99fsl: + 04 Mar 2015; files/99fsl: added FSLPATH *fsl-5.0.8 (20 Feb 2015) - 20 Feb 2015; +fsl-5.0.8.ebuild: + 20 Feb 2015; +fsl-5.0.8.ebuild: bumped version 18 Oct 2013; François Bissey
[gentoo-commits] proj/sci:master commit in: sci-biology/fsl/
commit: 17d1701d267f7c6beb268b4dd661f042ec4b4f0b
Author: Horea Christian mail ru>
AuthorDate: Tue Apr 7 11:09:05 2015 +
Commit: Francois Bissey massey ac nz>
CommitDate: Tue Apr 7 11:09:05 2015 +
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; -fsl-5.0.4.ebuild, -fsl-5.0.5.ebuild:
+ removed ebuilds with unavailable sources
+
07 Apr 2015; 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..000
--- 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_fl
[gentoo-commits] proj/sci:master commit in: sci-biology/fsl/
commit: 68fe87b054ec542364e640086872e5e4b31f86b9
Author: Horea Christian mail ru>
AuthorDate: Wed Mar 25 10:53:29 2015 +
Commit: Francois Bissey massey ac nz>
CommitDate: Wed Mar 25 10:53:29 2015 +
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; fsl-5.0.6.ebuild:
+ added license for included gdchart
+
+ 25 Mar 2015; fsl-5.0.6.ebuild:
set the correct licences
11 Mar 2015; 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=""
[gentoo-commits] proj/sci:master commit in: sci-biology/fsl/, sci-biology/fsl/files/
commit: bdd5cc6f1d8eb2a7a07574df2632cc2381a7b9bc Author: Horea Christian mail ru> AuthorDate: Wed Mar 4 12:45:42 2015 + Commit: Francois Bissey massey ac nz> CommitDate: Wed Mar 4 12:45:42 2015 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=bdd5cc6f added FSLPATH Package-Manager: portage-2.2.17 sci-biology/fsl/ChangeLog | 3 +++ sci-biology/fsl/files/99fsl | 1 + 2 files changed, 4 insertions(+) diff --git a/sci-biology/fsl/ChangeLog b/sci-biology/fsl/ChangeLog index 979ce44..fac3cce 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: $ + 04 Mar 2015; files/99fsl: + added FSLPATH + *fsl-5.0.8 (20 Feb 2015) 20 Feb 2015; +fsl-5.0.8.ebuild: diff --git a/sci-biology/fsl/files/99fsl b/sci-biology/fsl/files/99fsl index b86b4cf..ca37941 100644 --- a/sci-biology/fsl/files/99fsl +++ b/sci-biology/fsl/files/99fsl @@ -2,3 +2,4 @@ FSLOUTPUTTYPE=NIFTI_GZ FSLMULTIFILEQUIT=TRUE FSLTCLSH=tclsh FSLWISH=wish +FSLDIR=/usr
[gentoo-commits] proj/sci:master commit in: sci-biology/fsl/
commit: fae6537014d7c03aeefc9c7d7c3ca23e841130e8
Author: Horea Christian mail ru>
AuthorDate: Sat Mar 28 17:56:30 2015 +
Commit: Francois Bissey massey ac nz>
CommitDate: Sat Mar 28 17:56:30 2015 +
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; fsl-5.0.8.ebuild:
+ using new setup patch file for new ebuild
+
28 Mar 2015; +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
[gentoo-commits] proj/sci:master commit in: sci-biology/fsl/, sci-biology/fsl/files/
commit: c936a53ac9ac5f4e923326f9dfbfac3739b2dde2
Author: Horea Christian mail ru>
AuthorDate: Thu Apr 9 02:07:29 2015 +
Commit: Francois Bissey massey ac nz>
CommitDate: Thu Apr 9 02:07:29 2015 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=c936a53a
removed 5.0.4 redux patch
Package-Manager: portage-2.2.18
sci-biology/fsl/ChangeLog | 3 +
sci-biology/fsl/files/fsl-5.0.4-fsldir_redux.patch | 467 -
2 files changed, 3 insertions(+), 467 deletions(-)
diff --git a/sci-biology/fsl/ChangeLog b/sci-biology/fsl/ChangeLog
index e509710..f97b5da 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: $
+ 09 Apr 2015; -files/fsl-5.0.4-fsldir_redux.patch:
+ removed 5.0.4 redux patch
+
07 Apr 2015; -fsl-5.0.4.ebuild, -fsl-5.0.5.ebuild:
removed ebuilds with unavailable sources
diff --git a/sci-biology/fsl/files/fsl-5.0.4-fsldir_redux.patch
b/sci-biology/fsl/files/fsl-5.0.4-fsldir_redux.patch
deleted file mode 100644
index 06f6445..000
--- a/sci-biology/fsl/files/fsl-5.0.4-fsldir_redux.patch
+++ /dev/null
@@ -1,467 +0,0 @@
src/fast4/fast_two.cc.orig 2013-10-19 23:45:02.636971888 +1300
-+++ src/fast4/fast_two.cc 2013-10-19 23:46:45.436138299 +1300
-@@ -166,7 +166,7 @@
- string csfPriorName, grayPriorName, whitePriorName;
- if(alternatePriors.unset())
- {
--string priorRootName=string(getenv("FSLDIR")) +
"/data/standard/tissuepriors/avg152T1_";
-+string
priorRootName="@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/data/standard/tissuepriors/avg152T1_";
- csfPriorName = priorRootName+"csf";
- grayPriorName = priorRootName+"gray";
- whitePriorName = priorRootName+"white";
-@@ -215,15 +215,15 @@
- if(bapused>0)
- {
- char reg[1024];
-- sprintf(reg, "%s/bin/flirt -ref %s -in %s -out %s -applyxfm -init %s",
getenv("FSLDIR"), inname.c_str(), csfPriorName.c_str(),
(main_prior_vol+"_csf_stdspace").c_str(), bapriori.value().c_str());
-+ sprintf(reg, "flirt -ref %s -in %s -out %s -applyxfm -init %s",
inname.c_str(), csfPriorName.c_str(), (main_prior_vol+"_csf_stdspace").c_str(),
bapriori.value().c_str());
- if(verbose.value())
- cout< normalisedContrasts, model, triggers;
-- string fmriFileName, fslPath, featdir, vType, indexText;
-+ string fmriFileName, featdir, vType, indexText;
- ColumnVector NewimageVoxCoord(4),NiftiVoxCoord(4);
- bool outputText(true), useCoordinate(false), prewhiten(false),
useTriggers(false), customMask(false), modelFree(false), isHigherLevel(false),
outputDataOnly(false);
- bool zWeightClusters(true);
-@@ -307,7 +307,6 @@
- if (argc<2) usage("");
- featdir=string(argv[1]);
- fmriFileName=featdir+"/filtered_func_data";
-- fslPath=string(getenv("FSLDIR"));
-
- string outputName(featdir);
-
-@@ -725,7 +724,7 @@
- cerr << "Can't open output report file " << outputName << endl;
- exit(1);
- }
-- outputFile << "\n"<< statType << num2str(i)
<<"\n\n\nFEAT Time Series Report - "<<
statType << num2str(i) <<"\n\nFull plots\n"<<
graphText;
-+ outputFile << "\n"<< statType << num2str(i)
<<"\n\n\nFEAT
Time Series Report - "<< statType << num2str(i)
<<"\n\nFull plots\n"<< graphText;
- if (useTriggers) outputFile << "\nPeristimulus plots\n"<<
peristimulusText <<"\n\n\n";
- else outputFile << "\n\n\n";
- outputFile.close();
-@@ -740,7 +739,7 @@
- cerr << "Can't open output report file " << outputName << endl;
- exit(1);
- }
-- outputFile << "\nFEAT Time Series Report\n\n\nFEAT Time Series
Report\n\n" << indexText << "" << endl <<
endl;
-+ outputFile << "\nFEAT Time Series Report\n\n\nFEAT
Time Series Report\n\n" << indexText << ""
<< endl << endl;
- outputFile.close();
-
- /* now output same thing without start and end, for inclusion in feat
report */
src/feat5/feat_model.cc.orig 2013-10-19 23:52:13.456668655 +1300
-+++ src/feat5/feat_model.cc2013-10-19 23:53:31.655795065 +1300
-@@ -734,7 +734,6 @@
- vector G;
- vector titles;
- float tr, mult, trmult, nltffwhm=0, maxconvwin=0;
-- char fl[1], *FSLDIR;
- string fn, filename;
- FONT_DATA *font_data = new FONT_DATA[1];
-
-@@ -753,8 +752,6 @@
- if (argc==3)
- motionparams=remmean(read_ascii_matrix(arg
[gentoo-commits] proj/sci:master commit in: sci-biology/fsl/
commit: 894067c2f8dd681a3a1a7219ee90f70cdf4e0f33
Author: Horea Christian mail ru>
AuthorDate: Sat Mar 28 21:31:00 2015 +
Commit: Francois Bissey massey ac nz>
CommitDate: Sat Mar 28 21:31:00 2015 +
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; fsl-5.0.8.ebuild:
+ ported changes from 5.0.6 regarding FSLDIR
+
28 Mar 2015; 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
[gentoo-commits] proj/sci:master commit in: sci-biology/fsl/, sci-biology/fsl/files/
commit: c9252c4925cba26273c9aa67193d9dc1ffad7806 Author: Horea Christian mail ru> AuthorDate: Sat Mar 28 21:07:35 2015 + Commit: Francois Bissey massey ac nz> CommitDate: Sat Mar 28 21:07:35 2015 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=c9252c49 hunk implemented by upstream Package-Manager: portage-2.2.18 sci-biology/fsl/ChangeLog | 3 +++ sci-biology/fsl/files/fsl-5.0.4-headers.patch | 11 --- 2 files changed, 3 insertions(+), 11 deletions(-) diff --git a/sci-biology/fsl/ChangeLog b/sci-biology/fsl/ChangeLog index ea0bd2a..19478e2 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; files/fsl-5.0.4-headers.patch: + hunk implemented by upstream + 28 Mar 2015; fsl-5.0.8.ebuild: using new setup patch file for new ebuild diff --git a/sci-biology/fsl/files/fsl-5.0.4-headers.patch b/sci-biology/fsl/files/fsl-5.0.4-headers.patch index 803151b..ab2ab3d 100644 --- a/sci-biology/fsl/files/fsl-5.0.4-headers.patch +++ b/sci-biology/fsl/files/fsl-5.0.4-headers.patch @@ -1,14 +1,3 @@ src/avwutils/fslmaths.cc.orig 2013-10-19 00:17:44.765129309 +1300 -+++ src/avwutils/fslmaths.cc 2013-10-19 00:18:02.975157728 +1300 -@@ -71,7 +71,7 @@ - #include "newimage/newimageall.h" - #include "miscmaths/miscmaths.h" - #include "utils/fsl_isfinite.h" --#include "libprob/libprob.h" -+#include "libprob.h" - - using namespace MISCMATHS; - using namespace NEWIMAGE; --- src/miscvis/writepng.c.orig2013-10-19 00:18:32.415203592 +1300 +++ src/miscvis/writepng.c 2013-10-19 00:19:05.414255132 +1300 @@ -32,6 +32,7 @@
[gentoo-commits] proj/sci:master commit in: sci-biology/fsl/, sci-biology/fsl/files/
commit: 98eb215e0d2c9c3e42a9aac7e39a0f5d983f0cde
Author: Horea Christian mail ru>
AuthorDate: Sat Mar 28 17:55:57 2015 +
Commit: Francois Bissey massey ac nz>
CommitDate: Sat Mar 28 17:55:57 2015 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=98eb215e
new pathc by François Bissey
Package-Manager: portage-2.2.18
sci-biology/fsl/ChangeLog | 3 +
sci-biology/fsl/files/fsl-5.0.8-setup.patch | 113
2 files changed, 116 insertions(+)
diff --git a/sci-biology/fsl/ChangeLog b/sci-biology/fsl/ChangeLog
index 2b12763..3ac363f 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; +files/fsl-5.0.8-setup.patch:
+ new pathc by François Bissey
+
25 Mar 2015; fsl-5.0.4.ebuild, fsl-5.0.5.ebuild,
fsl-5.0.8.ebuild:
added licences to all versions
diff --git a/sci-biology/fsl/files/fsl-5.0.8-setup.patch
b/sci-biology/fsl/files/fsl-5.0.8-setup.patch
new file mode 100644
index 000..0cbda5d
--- /dev/null
+++ b/sci-biology/fsl/files/fsl-5.0.8-setup.patch
@@ -0,0 +1,113 @@
+diff -Naur fsl.orig/build fsl/build
+--- fsl.orig/build 2015-03-29 00:10:39.845936000 +1300
fsl/build 2015-03-29 00:12:37.160487000 +1300
+@@ -11,8 +11,7 @@
+ ifit load_varian load_dicom misc_scripts fdt first possum sgeutils flameo
oxford_asl relax qboot topup ptx2 lesions eddy dwssfp";
+ fi
+
+-echo "Building projects - see build.log file for progress..."
+-./config/common/buildproj $PROJECTS > ./build.log 2>&1
+-echo "Finished build : end of log file shows ..."
+-tail -10 build.log
++echo "Building projects"
++./config/common/buildproj $PROJECTS
++echo "Finished build"
+
+diff -Naur fsl.orig/config/common/buildproj fsl/config/common/buildproj
+--- fsl.orig/config/common/buildproj 2015-03-29 00:11:47.130998000 +1300
fsl/config/common/buildproj2015-03-29 00:12:37.164319000 +1300
+@@ -11,10 +11,10 @@
+ fi
+ PROJECTS="$@" ; export PROJECTS ;
+
+-FSLDIR=`pwd`
++#FSLDIR=`pwd`
+ FSLDEVDIR=${FSLDIR}
+ FSLCONFDIR=${FSLDIR}/config
+-FSLMACHTYPE=`${FSLDIR}/etc/fslconf/fslmachtype.sh`
++#FSLMACHTYPE=`${FSLDIR}/etc/fslconf/fslmachtype.sh`
+ export FSLDIR FSLDEVDIR FSLCONFDIR FSLMACHTYPE
+
+ buildmessages="" ; export buildmessages ;
+@@ -66,7 +66,7 @@
+ if [ -x fslconfig ] ; then
+ ./fslconfig ;
+ fi
+-if ${MAKE} -k ${MAKEOPTIONS} ; then
++if ${MAKE} ${MAKEOPTIONS} ${MAKEOPTS} ; then
+ if ${MAKE} install ; then
+ installok=true;
+ # Clean up after ourselves
+diff -Naur fsl.orig/config/common/vars.mk fsl/config/common/vars.mk
+--- fsl.orig/config/common/vars.mk 2015-03-29 00:11:47.18352 +1300
fsl/config/common/vars.mk 2015-03-29 00:18:53.151222000 +1300
+@@ -24,15 +24,15 @@
+ USRCFLAGS =
+ USRCXXFLAGS =
+
+-LDFLAGS = ${ARCHLDFLAGS} ${USRLDFLAGS} -L. -L${DEVLIBDIR} -L${LIBDIR}
++LDFLAGS = ${ARCHLDFLAGS} ${USRLDFLAGS} -L. -L${DEVLIBDIR} -L${LIBDIR}
${USERLDFLAGS}
+
+-AccumulatedIncFlags = ${USRINCFLAGS} -I. -I${DEVINCDIR} -I${INCDIR}
++AccumulatedIncFlags = ${USRINCFLAGS} -I. -I${DEVINCDIR} -I${INCDIR}
${CPPFLAGS}
+
+ CFLAGS = ${ANSI_FLAGS} ${ANSI_CFLAGS} ${DBGFLAGS} ${USEDCSTATICFLAGS}
${USRCFLAGS} ${ARCHFLAGS} ${OPTFLAGS} \
+- ${AccumulatedIncFlags}
++ ${AccumulatedIncFlags} ${USERCFLAGS}
+
+ CXXFLAGS = ${ANSI_FLAGS} ${ANSI_CXXFLAGS} ${DBGFLAGS} ${USEDCXXSTATICFLAGS}
${USRCXXFLAGS} ${ARCHFLAGS} ${OPTFLAGS} \
+- ${AccumulatedIncFlags}
++ ${AccumulatedIncFlags} ${USERCXXFLAGS}
+
+ HFILES = *.h
+ AFILES = *.a
+diff -Naur fsl.orig/config/generic/systemvars.mk
fsl/config/generic/systemvars.mk
+--- fsl.orig/config/generic/systemvars.mk 2015-03-29 00:11:47.534246000
+1300
fsl/config/generic/systemvars.mk 2015-03-29 00:12:37.162129000 +1300
+@@ -4,20 +4,20 @@
+
+ # System dependent commands (NB: the first two are the most platform
dependent)
+
+-INSTALL = ginstall -p
+-RANLIB = ranlib
++INSTALL = install -p
++RANLIB = @@GENTOO_RANLIB@@
+
+ RM = /bin/rm
+ CP = /bin/cp
+ MV = /bin/mv
+ CHMOD = /bin/chmod
+ MKDIR = /bin/mkdir
+-TCLSH = ${FSLDIR}/bin/fsltclsh
++TCLSH = tclsh
+
+ # Compiler dependent variables
+
+-CC = gcc
+-CXX = c++
++CC = @@GENTOO_CC@@
++CXX = @@GENTOO_CXX@@
+ CSTATICFLAGS = -static
+ CXXSTATICFLAGS = -static
+
+@@ -25,7 +25,7 @@
+
+ DEPENDFLAGS = -MM
+
+-OPTFLAGS = -O3 -fexpensive-optimizations ${ARCHFLAGS}
++OPTFLAGS =
+ MACHDBGFLAGS =
+ GNU_ANSI_FLAGS = -Wall -ansi -pedantic
+ SGI_ANSI_FLAGS = -ansi -fullwarn
+diff -Naur fsl.orig/extras/build fsl/extras/build
+--- fsl.orig/extras/build 2015-03-29 00:11:15.080236000 +1300
fsl/extras/build 2015-03-29 00:15:53.170496000 +1300
+@@ -60,7 +60,7 @@
+ if [ ${BUILDICONV} -eq 1 ]; then
+ PROJECTS="$
[gentoo-commits] proj/sci:master commit in: /
commit: 936bdadea119ee5e11e1a0760b97d3689fee0d2f
Author: François Bissey canterbury ac nz>
AuthorDate: Mon Apr 20 01:10:05 2015 +
Commit: Francois Bissey massey ac nz>
CommitDate: Mon Apr 20 01:10:05 2015 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=936bdade
Merge pull request #118 from TheChymera/fsl
FSL is in good enough condition to get in the overlay in my opinion. There is
still some work to do (splitting some dependencies not currently in the tree)
but this can be managed from the overlay.
sci-biology/fsl/ChangeLog | 82
sci-biology/fsl/Manifest | 2 +
sci-biology/fsl/files/99fsl| 5 +
sci-biology/fsl/files/fsl-5.0.4-headers.patch | 32 ++
sci-biology/fsl/files/fsl-5.0.4-setup.patch| 110 +
sci-biology/fsl/files/fsl-5.0.6-fsldir_redux.patch | 456 +
sci-biology/fsl/files/fsl-5.0.8-fsldir_redux.patch | 452
sci-biology/fsl/files/fsl-5.0.8-headers.patch | 21 +
sci-biology/fsl/files/fsl-5.0.8-setup.patch| 113 +
sci-biology/fsl/fsl-5.0.6.ebuild | 130 ++
sci-biology/fsl/fsl-5.0.8.ebuild | 130 ++
sci-biology/{OBO-Edit => fsl}/metadata.xml | 7 +-
12 files changed, 1536 insertions(+), 4 deletions(-)
[gentoo-commits] proj/sci:master commit in: sci-biology/fsl/
commit: 787b1ce2e28f44f17757f39e028442b37af1e0fa
Author: Horea Christian mail ru>
AuthorDate: Wed Mar 25 10:06:31 2015 +
Commit: Francois Bissey massey ac nz>
CommitDate: Wed Mar 25 10:06:31 2015 +
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; fsl-5.0.6.ebuild:
+ set the correct licences
+
11 Mar 2015; 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=""
[gentoo-commits] proj/sci:master commit in: sci-biology/fsl/files/, sci-biology/fsl/
commit: 5d5c08d1c7bca1b5ae4278cac0b9d5536b345ccb
Author: Horea Christian mail ru>
AuthorDate: Mon Mar 30 16:14:41 2015 +
Commit: Francois Bissey massey ac nz>
CommitDate: Mon Mar 30 16:14:41 2015 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=5d5c08d1
5.0.8 redux patch by François Bissey
Package-Manager: portage-2.2.18
sci-biology/fsl/ChangeLog | 3 +
sci-biology/fsl/files/fsl-5.0.8-redux.patch | 452
2 files changed, 455 insertions(+)
diff --git a/sci-biology/fsl/ChangeLog b/sci-biology/fsl/ChangeLog
index a8447db..9157f64 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: $
+ 30 Mar 2015; +files/fsl-5.0.8-redux.patch:
+ 5.0.8 redux patch by François Bissey
+
29 Mar 2015; fsl-5.0.8.ebuild:
using the 5.0.8 headers patch
diff --git a/sci-biology/fsl/files/fsl-5.0.8-redux.patch
b/sci-biology/fsl/files/fsl-5.0.8-redux.patch
new file mode 100644
index 000..593c1c8
--- /dev/null
+++ b/sci-biology/fsl/files/fsl-5.0.8-redux.patch
@@ -0,0 +1,452 @@
+diff -Naur src.orig/fast4/fast_two.cc src/fast4/fast_two.cc
+--- src.orig/fast4/fast_two.cc 2015-03-30 11:54:10.522550233 +1300
src/fast4/fast_two.cc 2015-03-30 11:54:18.412569892 +1300
+@@ -166,7 +166,7 @@
+ string csfPriorName, grayPriorName, whitePriorName;
+ if(alternatePriors.unset())
+ {
+-string priorRootName=string(getenv("FSLDIR")) +
"/data/standard/tissuepriors/avg152T1_";
++string
priorRootName="@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/data/standard/tissuepriors/avg152T1_";
+ csfPriorName = priorRootName+"csf";
+ grayPriorName = priorRootName+"gray";
+ whitePriorName = priorRootName+"white";
+@@ -215,15 +215,15 @@
+ if(bapused>0)
+ {
+ char reg[1024];
+- sprintf(reg, "%s/bin/flirt -ref %s -in %s -out %s -applyxfm -init %s",
getenv("FSLDIR"), inname.c_str(), csfPriorName.c_str(),
(main_prior_vol+"_csf_stdspace").c_str(), bapriori.value().c_str());
++ sprintf(reg, "flirt -ref %s -in %s -out %s -applyxfm -init %s",
inname.c_str(), csfPriorName.c_str(), (main_prior_vol+"_csf_stdspace").c_str(),
bapriori.value().c_str());
+ if(verbose.value())
+ cout< G;
+ vector titles;
+ float tr, mult, trmult, nltffwhm=0, maxconvwin=0;
+- char fl[1], *FSLDIR;
++ char fl[1];
+ string fn, filename;
+ FONT_DATA *font_data = new FONT_DATA[1];
+
+@@ -760,8 +760,6 @@
+ if (argc==3)
+ motionparams=remmean(read_ascii_matrix(argv[2]));
+
+- FSLDIR=getenv("FSLDIR");
+-
+ fn = string(argv[1])+".fsf";
+
+ level = atoi(find_line(fn, "fmri(level)", fl));
+@@ -1491,7 +1489,7 @@
+ writeCovarianceImage(string(argv[1])+"_cov.ppm", contrasts, F, nftests,
realDesign, level, evs.eigenvals, font_data, contrasts.RE);
+ writeImagePreview(string(argv[1])+".ppm", contrasts, F, nftests,
realDesign, level, evs, font_data, titles, tr, nltffwhm, nTimepoints, G);
+
+- filename=string(getenv("FSLDIR"))+"/bin/wpng -q -overwrite
"+string(argv[1])+".ppm ";
++ filename="wpng -q -overwrite "+string(argv[1])+".ppm ";
+ system(filename.c_str());
+
+ return(0);
+@@ -2134,6 +2132,6 @@
+
+ fclose(outputfile);
+
+-filename=string(getenv("FSLDIR")) + "/bin/wpng -q -overwrite " +
filename;
++filename="wpng -q -overwrite " + filename;
+ system(filename.c_str());
+ }
+diff -Naur src.orig/feat5/tsplot.cc src/feat5/tsplot.cc
+--- src.orig/feat5/tsplot.cc 2015-03-30 11:54:10.502550183 +1300
src/feat5/tsplot.cc2015-03-30 11:54:18.412569892 +1300
+@@ -293,7 +293,7 @@
+ ofstream outputFile;
+ int numEVs, npts, numContrasts=1, nftests=0, GRPHSIZE(600),
PSSIZE(600);
+ vector normalisedContrasts, model, triggers;
+- string fmriFileName, fslPath, featdir, vType, indexText;
++ string fmriFileName, featdir, vType, indexText;
+ ColumnVector NewimageVoxCoord(4),NiftiVoxCoord(4);
+ bool outputText(true), useCoordinate(false), prewhiten(false),
useTriggers(false), customMask(false), modelFree(false), isHigherLevel(false),
outputDataOnly(false);
+ bool zWeightClusters(true);
+@@ -307,7 +307,6 @@
+ if (argc<2) usage("");
+ featdir=string(argv[1]);
+ fmriFileName=featdir+"/filtered_func_data";
+- fslPath=string(getenv("FSLDIR"));
+
+ string outputName(featdir);
+
+@@ -725,7 +724,7 @@
+ cerr << "Can't open output report file " << outputName << endl;
+ exit(1);
+ }
+- outputFile << "\n"<< statType << num2str(i)
<<"\n\n\nFE
[gentoo-commits] proj/sci:master commit in: sci-biology/fsl/
commit: fdcd3e55349c5c26f32f911ec8b7d950386f3660
Author: Horea Christian mail ru>
AuthorDate: Sun Mar 29 23:53:26 2015 +
Commit: Francois Bissey massey ac nz>
CommitDate: Sun Mar 29 23:53:26 2015 +
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; fsl-5.0.8.ebuild:
+ using the 5.0.8 headers patch
+
29 Mar 2015; +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 \
[gentoo-commits] proj/sci:master commit in: sci-biology/fsl/
commit: 79f0c9f5b19678ffa18b0ca2e9fb393a5e1b7ae8
Author: Horea Christian mail ru>
AuthorDate: Tue Apr 7 11:08:26 2015 +
Commit: Francois Bissey massey ac nz>
CommitDate: Tue Apr 7 11:08:26 2015 +
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; fsl-5.0.6.ebuild:
+ added new gentoo fsl-5.0.6 source location
+
30 Mar 2015; +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"
[gentoo-commits] proj/sci:master commit in: sci-biology/fsl/
commit: f2b9e88047ac0f76bcdbf050d61685a2519b0426
Author: Horea Christian mail ru>
AuthorDate: Wed Mar 11 19:48:59 2015 +
Commit: Francois Bissey massey ac nz>
CommitDate: Wed Mar 11 19:48:59 2015 +
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; fsl-5.0.6.ebuild:
+ installing fslversion
+
+ 11 Mar 2015; fsl-5.0.6.ebuild:
sed-ing before installing
10 Mar 2015; 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
[gentoo-commits] proj/sci:master commit in: sci-biology/fsl/files/, sci-biology/fsl/
commit: 76a864a1f60bcf110e205e279086ab0c4ddd32c1
Author: Horea Christian mail ru>
AuthorDate: Mon Mar 30 16:16:51 2015 +
Commit: Francois Bissey massey ac nz>
CommitDate: Mon Mar 30 16:16:51 2015 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=76a864a1
implemented 5.0.8 fsldir redux patch
Package-Manager: portage-2.2.18
sci-biology/fsl/ChangeLog | 4
.../fsl/files/{fsl-5.0.8-redux.patch => fsl-5.0.8-fsldir_redux.patch} | 0
sci-biology/fsl/fsl-5.0.8.ebuild | 2 +-
3 files changed, 5 insertions(+), 1 deletion(-)
diff --git a/sci-biology/fsl/ChangeLog b/sci-biology/fsl/ChangeLog
index 9157f64..822c9b9 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: $
+ 30 Mar 2015; +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
+
30 Mar 2015; +files/fsl-5.0.8-redux.patch:
5.0.8 redux patch by François Bissey
diff --git a/sci-biology/fsl/files/fsl-5.0.8-redux.patch
b/sci-biology/fsl/files/fsl-5.0.8-fsldir_redux.patch
similarity index 100%
rename from sci-biology/fsl/files/fsl-5.0.8-redux.patch
rename to sci-biology/fsl/files/fsl-5.0.8-fsldir_redux.patch
diff --git a/sci-biology/fsl/fsl-5.0.8.ebuild b/sci-biology/fsl/fsl-5.0.8.ebuild
index 8583a3e..af486a9 100644
--- a/sci-biology/fsl/fsl-5.0.8.ebuild
+++ b/sci-biology/fsl/fsl-5.0.8.ebuild
@@ -33,7 +33,7 @@ S=${WORKDIR}/${PN}
src_prepare(){
epatch "${FILESDIR}/${PN}"-5.0.8-setup.patch
epatch "${FILESDIR}/${PN}"-5.0.8-headers.patch
- epatch "${FILESDIR}/${PN}"-5.0.6-fsldir_redux.patch
+ epatch "${FILESDIR}/${PN}"-5.0.8-fsldir_redux.patch
sed -i \
-e "s:@@GENTOO_RANLIB@@:$(tc-getRANLIB):" \
[gentoo-commits] proj/sci:master commit in: sci-biology/fsl/
commit: fd6c1087b199b9cd35e86ee8fb861ec1e6312f6e
Author: Horea Christian mail ru>
AuthorDate: Tue Mar 10 10:48:10 2015 +
Commit: Francois Bissey massey ac nz>
CommitDate: Tue Mar 10 10:48:10 2015 +
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; fsl-5.0.6.ebuild:
+ fixed tcl location according to instructions by kiwifb
+
+ 10 Mar 2015; fsl-5.0.6.ebuild:
installing fsl.sh
05 Mar 2015; 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
[gentoo-commits] proj/sci:master commit in: sci-biology/fsl/
commit: 0a6acd8e277e8b1bb63af24829e76852f2182056
Author: Horea Christian mail ru>
AuthorDate: Wed Mar 11 17:21:02 2015 +
Commit: Francois Bissey massey ac nz>
CommitDate: Wed Mar 11 17:21:02 2015 +
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; fsl-5.0.6.ebuild:
+ sed-ing before installing
+
10 Mar 2015; 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/*
[gentoo-commits] proj/sci:master commit in: sci-biology/fsl/files/, sci-biology/fsl/
commit: bc9caf8627d0ae109d4d294f9b20ca1affd15c45
Author: Horea Christian mail ru>
AuthorDate: Sun Mar 29 23:52:57 2015 +
Commit: Francois Bissey massey ac nz>
CommitDate: Sun Mar 29 23:52:57 2015 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=bc9caf86
reimplmented pathc fsl-5.0.4-headers
Package-Manager: portage-2.2.18
sci-biology/fsl/ChangeLog | 4
sci-biology/fsl/files/fsl-5.0.4-headers.patch | 11 +++
.../{fsl-5.0.4-headers.patch => fsl-5.0.8-headers.patch} | 0
3 files changed, 15 insertions(+)
diff --git a/sci-biology/fsl/ChangeLog b/sci-biology/fsl/ChangeLog
index e6857b2..fdcd6b1 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: $
+ 29 Mar 2015; +files/fsl-5.0.8-headers.patch,
+ files/fsl-5.0.4-headers.patch:
+ reimplmented pathc fsl-5.0.4-headers
+
28 Mar 2015; fsl-5.0.8.ebuild:
ported changes from 5.0.6 regarding FSLDIR
diff --git a/sci-biology/fsl/files/fsl-5.0.4-headers.patch
b/sci-biology/fsl/files/fsl-5.0.4-headers.patch
index ab2ab3d..803151b 100644
--- a/sci-biology/fsl/files/fsl-5.0.4-headers.patch
+++ b/sci-biology/fsl/files/fsl-5.0.4-headers.patch
@@ -1,3 +1,14 @@
+--- src/avwutils/fslmaths.cc.orig 2013-10-19 00:17:44.765129309 +1300
src/avwutils/fslmaths.cc 2013-10-19 00:18:02.975157728 +1300
+@@ -71,7 +71,7 @@
+ #include "newimage/newimageall.h"
+ #include "miscmaths/miscmaths.h"
+ #include "utils/fsl_isfinite.h"
+-#include "libprob/libprob.h"
++#include "libprob.h"
+
+ using namespace MISCMATHS;
+ using namespace NEWIMAGE;
--- src/miscvis/writepng.c.orig2013-10-19 00:18:32.415203592 +1300
+++ src/miscvis/writepng.c 2013-10-19 00:19:05.414255132 +1300
@@ -32,6 +32,7 @@
diff --git a/sci-biology/fsl/files/fsl-5.0.4-headers.patch
b/sci-biology/fsl/files/fsl-5.0.8-headers.patch
similarity index 100%
copy from sci-biology/fsl/files/fsl-5.0.4-headers.patch
copy to sci-biology/fsl/files/fsl-5.0.8-headers.patch
[gentoo-commits] proj/sci:master commit in: sci-biology/fsl/
commit: 3956c9c9482c4360acb377884903f0b09c7cd0a6
Author: Horea Christian mail ru>
AuthorDate: Tue Mar 10 23:19:18 2015 +
Commit: Francois Bissey massey ac nz>
CommitDate: Tue Mar 10 23:19:18 2015 +
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; fsl-5.0.6.ebuild:
+ changed grep wrapper
+
+ 10 Mar 2015; fsl-5.0.6.ebuild:
reformatted tcl sed calls
10 Mar 2015; 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/*
[gentoo-commits] proj/sci:master commit in: sci-biology/fsl/
commit: 24370907c9b2211dbfcc32e8a2f9de46eda62b20
Author: Horea Christian mail ru>
AuthorDate: Tue Mar 10 01:44:09 2015 +
Commit: Francois Bissey massey ac nz>
CommitDate: Tue Mar 10 01:44:09 2015 +
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; fsl-5.0.6.ebuild:
+ installing fsl.sh
+
05 Mar 2015; 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
[gentoo-commits] proj/sci:master commit in: sci-biology/fsl/
commit: 2520b2c4c4fcfabe5157aa3a90db2a40acf927cf
Author: Horea Christian mail ru>
AuthorDate: Thu Mar 5 12:14:10 2015 +
Commit: Francois Bissey massey ac nz>
CommitDate: Thu Mar 5 12:14:10 2015 +
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; fsl-5.0.6.ebuild:
+ removing faulty check
+
04 Mar 2015; 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() {
[gentoo-commits] proj/sci:master commit in: sci-biology/fsl/
commit: 4e242526131439aa84b88b301a16ea64479a9038
Author: Horea Christian mail ru>
AuthorDate: Tue Mar 10 12:10:36 2015 +
Commit: Francois Bissey massey ac nz>
CommitDate: Tue Mar 10 12:10:36 2015 +
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; fsl-5.0.6.ebuild:
+ reformatted tcl sed calls
+
+ 10 Mar 2015; fsl-5.0.6.ebuild:
fixed tcl location according to instructions by kiwifb
10 Mar 2015; 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/*
[gentoo-commits] proj/sci:master commit in: sci-libs/lapack-reference/
commit: 016ec1d0bdaa14b88e3556dffc692ba1de7969f5
Author: François Bissey canterbury ac nz>
AuthorDate: Mon Oct 13 09:17:07 2014 +
Commit: Francois Bissey massey ac nz>
CommitDate: Mon Oct 13 09:17:07 2014 +
URL:http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=016ec1d0
Fix support for xblas, it is only available for 32bit integers.
---
sci-libs/lapack-reference/lapack-reference-.ebuild | 16
1 file changed, 8 insertions(+), 8 deletions(-)
diff --git a/sci-libs/lapack-reference/lapack-reference-.ebuild
b/sci-libs/lapack-reference/lapack-reference-.ebuild
index 02e8871..18e5e7c 100644
--- a/sci-libs/lapack-reference/lapack-reference-.ebuild
+++ b/sci-libs/lapack-reference/lapack-reference-.ebuild
@@ -136,7 +136,7 @@ src_prepare() {
SRC/CMakeLists.txt || die
sed -i \
-e 's:-llapack:-l${LIBNAME}:g' \
- -e 's/Requires: blas/Requires:
${BLAS_PROFNAME}\nFflags=${LAPACK_PKGCONFIG_FFLAGS}/' \
+ -e 's/Requires: blas/Requires: ${BLAS_PROFNAME}
${XBLASPC}\nFflags=${LAPACK_PKGCONFIG_FFLAGS}/' \
lapack.pc.in || die
# some string does not get passed properly
sed -i \
@@ -146,12 +146,6 @@ src_prepare() {
sed -i \
-e '/lapack_install_library(tmglib)/d' \
TESTING/MATGEN/CMakeLists.txt || die
- # if xblas is used add it in the .pc file
- if use xblas ; then
- sed -i \
- -e '/Requires/s:blas:blas xblas:' \
- lapack.pc.in || die
- fi
}
src_configure() {
@@ -160,6 +154,7 @@ src_configure() {
local profname=$(get_profname)
local libname="${profname//-/_}"
local blas_profname=$(get_blas_profname)
+ local xblaspc=""
local mycmakeargs=(
-DPROFNAME="${profname}"
-DBLAS_PROFNAME="${blas_profname}"
@@ -167,18 +162,23 @@ src_configure() {
-DUSE_OPTIMIZED_BLAS=ON
-DBLAS_LIBRARIES="$($(tc-getPKG_CONFIG) --libs
${blas_profname})"
$(cmake-utils_use_build test TESTING)
- $(cmake-utils_use_use xblas XBLAS)
$@
)
+ # xblas is only available for 32bit integers
if [[ "${MULTIBUILD_ID}" =~ "_${INT64_SUFFIX}" ]]; then
mycmakeargs+=(
-DCMAKE_Fortran_FLAGS="$($(tc-getPKG_CONFIG)
--cflags ${blas_profname}) $(get_abi_CFLAGS) -fdefault-integer-8 ${FCFLAGS}"
-DLAPACK_PKGCONFIG_FFLAGS="-fdefault-integer-8"
+ -DXBLASPC=""
+ -DUSE_XBLAS=OFF
)
else
+ use xblas && xblaspc="xblas"
mycmakeargs+=(
-DCMAKE_Fortran_FLAGS="$($(tc-getPKG_CONFIG)
--cflags ${blas_profname}) $(get_abi_CFLAGS) ${FCFLAGS}"
-DLAPACK_PKGCONFIG_FFLAGS=""
+ -DXBLASPC="${xblaspc}"
+ $(cmake-utils_use_use xblas XBLAS)
)
fi
if [[ "${MULTIBUILD_ID}" =~ "_${STATIC_SUFFIX}" ]]; then
[gentoo-commits] proj/sci:master commit in: sci-libs/lapack-reference/
commit: 68dc06c382a117e2148005a58062afb831f23d15
Author: François Bissey canterbury ac nz>
AuthorDate: Thu Sep 25 21:21:26 2014 +
Commit: Francois Bissey massey ac nz>
CommitDate: Thu Sep 25 21:21:26 2014 +
URL:http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=68dc06c3
The dependency needs to be on xblas[fortran] otherwise libxblas won't have the
required fortran symbols.
Package-Manager: portage-2.2.10
---
sci-libs/lapack-reference/ChangeLog| 5 +
sci-libs/lapack-reference/lapack-reference-.ebuild | 2 +-
2 files changed, 6 insertions(+), 1 deletion(-)
diff --git a/sci-libs/lapack-reference/ChangeLog
b/sci-libs/lapack-reference/ChangeLog
index 57fcfa7..3c1104e 100644
--- a/sci-libs/lapack-reference/ChangeLog
+++ b/sci-libs/lapack-reference/ChangeLog
@@ -4,6 +4,11 @@
25 Sep 2014; François Bissey
lapack-reference-.ebuild:
+ The dependency needs to be on xblas[fortran] otherwise libxblas won't have
the
+ required fortran symbols.
+
+ 25 Sep 2014; François Bissey
+ lapack-reference-.ebuild:
Add xblas to the .pc file when it is in use see bug#523388
*lapack-reference-3.5.0 (08 Dec 2013)
diff --git a/sci-libs/lapack-reference/lapack-reference-.ebuild
b/sci-libs/lapack-reference/lapack-reference-.ebuild
index f9c9ca9..aca6ba0 100644
--- a/sci-libs/lapack-reference/lapack-reference-.ebuild
+++ b/sci-libs/lapack-reference/lapack-reference-.ebuild
@@ -26,7 +26,7 @@ IUSE="static-libs test xblas"
RDEPEND="
virtual/blas
- xblas? ( sci-libs/xblas )"
+ xblas? ( sci-libs/xblas[fortran] )"
DEPEND="${RDEPEND}
virtual/pkgconfig"
[gentoo-commits] proj/sci:master commit in: sci-libs/lapack-reference/
commit: 2448b0086ae46343357b04a54062f05f0d6d9cb3
Author: François Bissey canterbury ac nz>
AuthorDate: Thu Sep 25 10:44:36 2014 +
Commit: Francois Bissey massey ac nz>
CommitDate: Thu Sep 25 10:44:36 2014 +
URL:http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=2448b008
Add xblas to the .pc file when it is in use see bug#523388
Package-Manager: portage-2.2.10
---
sci-libs/lapack-reference/ChangeLog| 6 +-
sci-libs/lapack-reference/lapack-reference-.ebuild | 6 ++
2 files changed, 11 insertions(+), 1 deletion(-)
diff --git a/sci-libs/lapack-reference/ChangeLog
b/sci-libs/lapack-reference/ChangeLog
index 0e0a1b8..57fcfa7 100644
--- a/sci-libs/lapack-reference/ChangeLog
+++ b/sci-libs/lapack-reference/ChangeLog
@@ -1,7 +1,11 @@
# ChangeLog for sci-libs/lapack-reference
-# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
# $Header: /var/cvsroot/gentoo-x86/sci-libs/lapack-reference/ChangeLog,v 1.51
2010/10/02 20:49:51 grobian Exp $
+ 25 Sep 2014; François Bissey
+ lapack-reference-.ebuild:
+ Add xblas to the .pc file when it is in use see bug#523388
+
*lapack-reference-3.5.0 (08 Dec 2013)
08 Dec 2013; Sébastien Fabbro
diff --git a/sci-libs/lapack-reference/lapack-reference-.ebuild
b/sci-libs/lapack-reference/lapack-reference-.ebuild
index cdcbe65..f9c9ca9 100644
--- a/sci-libs/lapack-reference/lapack-reference-.ebuild
+++ b/sci-libs/lapack-reference/lapack-reference-.ebuild
@@ -55,6 +55,12 @@ src_prepare() {
sed -i \
-e '/lapack_install_library(tmglib)/d' \
TESTING/MATGEN/CMakeLists.txt || die
+ # if xblas is used add it in the .pc file
+ if use xblas ; then
+ sed -i \
+ -e '/Requires/s:blas:blas xblas:' \
+ lapack.pc.in || die
+ fi
}
src_configure() {
[gentoo-commits] proj/sci:master commit in: sci-libs/calculix-ccx/, sci-libs/calculix-ccx/files/
commit: dbbb91e76fa7c58458dd7e3e20827e2337f6bd26
Author: François Bissey canterbury ac nz>
AuthorDate: Mon Sep 8 10:06:52 2014 +
Commit: Francois Bissey massey ac nz>
CommitDate: Mon Sep 8 10:06:52 2014 +
URL:http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=dbbb91e7
Fixing issue #264 and giving it a serious look over and clean. Enabled
threading. More could be done.
Package-Manager: portage-2.2.10
---
sci-libs/calculix-ccx/ChangeLog| 6 +
sci-libs/calculix-ccx/calculix-ccx-2.7-r1.ebuild | 26 ++
...7_Makefile_custom_cc_flags_spooles_arpack.patch | 2 +-
3 files changed, 19 insertions(+), 15 deletions(-)
diff --git a/sci-libs/calculix-ccx/ChangeLog b/sci-libs/calculix-ccx/ChangeLog
index 7eccdea..9e1b1f5 100644
--- a/sci-libs/calculix-ccx/ChangeLog
+++ b/sci-libs/calculix-ccx/ChangeLog
@@ -2,6 +2,12 @@
# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 08 Sep 2014; François Bissey
+ calculix-ccx-2.7-r1.ebuild,
+ files/01_ccx_2.7_Makefile_custom_cc_flags_spooles_arpack.patch:
+ Fixing issue #264 and giving it a serious look over and clean. Enabled
+ threading. More could be done.
+
*calculix-ccx-2.7-r1 (07 Sep 2014)
07 Sep 2014; Rongcui Dong +calculix-ccx-2.7-r1.ebuild,
diff --git a/sci-libs/calculix-ccx/calculix-ccx-2.7-r1.ebuild
b/sci-libs/calculix-ccx/calculix-ccx-2.7-r1.ebuild
index 2394647..a511dc9 100644
--- a/sci-libs/calculix-ccx/calculix-ccx-2.7-r1.ebuild
+++ b/sci-libs/calculix-ccx/calculix-ccx-2.7-r1.ebuild
@@ -18,12 +18,12 @@ SRC_URI="
LICENSE="GPL-2"
SLOT="0"
KEYWORDS="~amd64 ~x86"
-IUSE="arpack doc examples lapack"
+IUSE="arpack doc examples threads"
RDEPEND="
- arpack? ( sci-libs/arpack )
- lapack? ( virtual/lapack )
- >=sci-libs/spooles-2.2
+ arpack? ( >=sci-libs/arpack-3.1.3 )
+ >=sci-libs/spooles-2.2[threads=]
+ virtual/lapack
virtual/blas"
DEPEND="${RDEPEND}
virtual/pkgconfig
@@ -32,25 +32,23 @@ DEPEND="${RDEPEND}
S=${WORKDIR}/CalculiX/${MY_P}/src
src_prepare() {
- #epatch "${FILESDIR}"/01_${MY_P}_Makefile_spooles_arpack.patch
epatch
"${FILESDIR}"/01_${MY_P}_Makefile_custom_cc_flags_spooles_arpack.patch
- use lapack && epatch "${FILESDIR}"/01_${MY_P}_lapack.patch
+ epatch "${FILESDIR}"/01_${MY_P}_lapack.patch
}
src_configure() {
- use lapack && export LAPACK=$($(tc-getPKG_CONFIG) --libs lapack)
+ # Technically we currently only need this when arpack is not used.
+ # Keeping things this way in case we change pkgconfig for arpack
+ export LAPACK=$($(tc-getPKG_CONFIG) --libs lapack)
- export BLAS=$($(tc-getPKG_CONFIG) --libs blas)
-
- #export SPOOLESINC="-I/usr/include/spooles -DSPOOLES"
append-cflags "-I/usr/include/spooles -DSPOOLES"
- #export SPOOLESLIB="-lspooles -lpthread"
- export USE_MT="-DUSE_MT"
+ if use threads; then
+ append-cflags "-DUSE_MT"
+ fi
if use arpack; then
- export ARPACK="-DARPACK"
export ARPACKLIB=$($(tc-getPKG_CONFIG) --libs arpack)
- append-cflags "${ARPACK}"
+ append-cflags "-DARPACK"
fi
export CC="$(tc-getCC)"
export FC="$(tc-getFC)"
diff --git
a/sci-libs/calculix-ccx/files/01_ccx_2.7_Makefile_custom_cc_flags_spooles_arpack.patch
b/sci-libs/calculix-ccx/files/01_ccx_2.7_Makefile_custom_cc_flags_spooles_arpack.patch
index db3b301..b042634 100644
---
a/sci-libs/calculix-ccx/files/01_ccx_2.7_Makefile_custom_cc_flags_spooles_arpack.patch
+++
b/sci-libs/calculix-ccx/files/01_ccx_2.7_Makefile_custom_cc_flags_spooles_arpack.patch
@@ -25,7 +25,7 @@ diff -rupN CalculiX/ccx_2.7/src/Makefile
CalculiX.patched/ccx_2.7/src/Makefile
- $(DIR)/spooles.a \
- ../../../ARPACK/libarpack_INTEL.a \
- -lpthread -lm -lc
-+LIBS = $(SPOOLESLIB) $(ARPACKLIB) $(BLAS) -lm -lc -lpthread -lspooles
++LIBS = $(ARPACKLIB) $(LAPACK) -lm -lc -lspooles -lpthread
ccx_2.7: $(OCCXMAIN) ccx_2.7.a $(LIBS)
./date.pl; $(CC) $(CFLAGS) -c ccx_2.7.c; $(FC) -Wall -O3 -o $@
$(OCCXMAIN) ccx_2.7.a $(LIBS)
[gentoo-commits] proj/sci:master commit in: sci-libs/m4ri/
commit: 6f1600029a9db4bfd1154451aad5dffb7f0e90a0
Author: François Bissey canterbury ac nz>
AuthorDate: Thu Sep 4 22:30:46 2014 +
Commit: Francois Bissey massey ac nz>
CommitDate: Thu Sep 4 22:30:46 2014 +
URL:http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=6f160002
Removing out of date m4ri. More up to date and maintained ebuilds in
sage-on-gentoo overlay
---
sci-libs/m4ri/ChangeLog| 24
sci-libs/m4ri/m4ri-20090512.ebuild | 18 --
sci-libs/m4ri/m4ri-20100221.ebuild | 38 --
sci-libs/m4ri/metadata.xml | 6 --
4 files changed, 86 deletions(-)
diff --git a/sci-libs/m4ri/ChangeLog b/sci-libs/m4ri/ChangeLog
deleted file mode 100644
index c2ef4c1..000
--- a/sci-libs/m4ri/ChangeLog
+++ /dev/null
@@ -1,24 +0,0 @@
-# ChangeLog for sci-libs/m4ri
-# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
-# $Header: $
-
- 18 Sep 2011; Andreas K. Huettel m4ri-20100221.ebuild:
- Add $(use_enable debug) on request from mgorny
-
-*m4ri-20100221 (20 Aug 2010)
-
- 20 Aug 2010; Christopher Schwan
- +m4ri-20100221.ebuild:
- Version bump - ebuild taken from sage-on-gentoo overlay without
- changes. New ebuild was migrated to autotools-utils and has an option
- for USE=openmp
-
-*m4ri-20090512 (03 Nov 2009)
-
- 03 Nov 2009; François Bissey
- -m4ri-20080624.ebuild, +m4ri-20090512.ebuild:
- version bump
-
- 16 Jul 2008; Francois Bissey ChangeLog:
- Initial import, see bug #230431
-
diff --git a/sci-libs/m4ri/m4ri-20090512.ebuild
b/sci-libs/m4ri/m4ri-20090512.ebuild
deleted file mode 100644
index 4adad1d..000
--- a/sci-libs/m4ri/m4ri-20090512.ebuild
+++ /dev/null
@@ -1,18 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-DESCRIPTION="Method of four russian for inversion (M4RI)"
-HOMEPAGE="http://m4ri.sagemath.org/";
-SRC_URI="http://m4ri.sagemath.org/downloads/${P}.tar.gz";
-
-LICENSE="GPL-2"
-SLOT="0"
-RESTRICT="mirror"
-KEYWORDS="~amd64 ~ppc ~ppc64 ~x86"
-IUSE=""
-
-src_install() {
- make DESTDIR="${D}" install || die "make install failed"
- dodoc README
-}
diff --git a/sci-libs/m4ri/m4ri-20100221.ebuild
b/sci-libs/m4ri/m4ri-20100221.ebuild
deleted file mode 100644
index c4da27a..000
--- a/sci-libs/m4ri/m4ri-20100221.ebuild
+++ /dev/null
@@ -1,38 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI="3"
-
-inherit autotools-utils
-
-MY_P="lib${P}"
-
-DESCRIPTION="Method of four russian for inversion (M4RI)"
-HOMEPAGE="http://m4ri.sagemath.org/";
-SRC_URI="mirror://sage/spkg/standard/${MY_P}.spkg -> ${P}.tar.bz2"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~ppc ~ppc64 ~x86"
-IUSE="debug openmp static-libs"
-
-RESTRICT="mirror"
-
-DEPEND="openmp? ( >=sys-devel/gcc-4.2[openmp] )"
-RDEPEND=""
-
-S="${WORKDIR}/${MY_P}/src"
-
-DOCS=( AUTHORS README )
-
-src_configure() {
- # cachetune option is not available, because it kills (at least my) X
when I
- # switch from yakuake to desktop
- myeconfargs=(
- $(use_with openmp)
- $(use_enable debug)
- )
-
- autotools-utils_src_configure
-}
diff --git a/sci-libs/m4ri/metadata.xml b/sci-libs/m4ri/metadata.xml
deleted file mode 100644
index c1959fd..000
--- a/sci-libs/m4ri/metadata.xml
+++ /dev/null
@@ -1,6 +0,0 @@
-
-http://www.gentoo.org/dtd/metadata.dtd";>
-
- sci
- M4RI is a library for fast arithmetic with dense
matrices over F2. The name M4RI comes from the first implemented algorithm: The
'Method of the Four Russians' inversion algorithm published by Gregory Bard.
This algorithm in turn is named after the 'Method of the Four Russians'
multiplication algorithm which is probably better referred to as Kronrod's
method.
-
[gentoo-commits] proj/sci:master commit in: dev-lang/julia/
commit: e04237a3380a5df2fbe4a71e4aee1f11588e3319 Author: François Bissey canterbury ac nz> AuthorDate: Wed Aug 27 04:32:39 2014 + Commit: Francois Bissey massey ac nz> CommitDate: Wed Aug 27 04:32:39 2014 + URL:http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=e04237a3 Bump dependency on llvm as in 0.3 Package-Manager: portage-2.2.10 --- dev-lang/julia/ChangeLog | 4 dev-lang/julia/julia-.ebuild | 2 +- 2 files changed, 5 insertions(+), 1 deletion(-) diff --git a/dev-lang/julia/ChangeLog b/dev-lang/julia/ChangeLog index 9a0ecfe..c53e175 100644 --- a/dev-lang/julia/ChangeLog +++ b/dev-lang/julia/ChangeLog @@ -4,6 +4,10 @@ 27 Aug 2014; François Bissey julia-.ebuild: + Bump dependency on llvm as in 0.3 + + 27 Aug 2014; François Bissey + julia-.ebuild: Few fixes: julia wants threaded fftw; multilib-strict install; Added USE_BLAS64=0 to Make.user, some proprietary blas/lapack may be suitable for the other setting but we cannot count on julia to recognize support just based diff --git a/dev-lang/julia/julia-.ebuild b/dev-lang/julia/julia-.ebuild index bac01db..69bff79 100644 --- a/dev-lang/julia/julia-.ebuild +++ b/dev-lang/julia/julia-.ebuild @@ -31,7 +31,7 @@ RDEPEND=" sci-libs/spqr:0= sci-libs/umfpack:0= sci-mathematics/glpk:0= - =sys-devel/llvm-3.3* + =sys-devel/llvm-3.4* >=sys-libs/libunwind-1.1:7= sys-libs/readline:0= sys-libs/zlib:0=
[gentoo-commits] proj/sci:master commit in: dev-lang/julia/
commit: d166beaefa32ee96bba9d3e4c3fca9c3e680d7ab
Author: François Bissey canterbury ac nz>
AuthorDate: Wed Aug 27 03:52:41 2014 +
Commit: Francois Bissey massey ac nz>
CommitDate: Wed Aug 27 03:52:41 2014 +
URL:http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=d166beae
Few fixes: julia wants threaded fftw; multilib-strict install; Added
USE_BLAS64=0 to Make.user, some proprietary blas/lapack may be
suitable for the other setting but we cannot count on julia to recognize
support just based on name.
Package-Manager: portage-2.2.10
---
dev-lang/julia/ChangeLog | 7 +++
dev-lang/julia/julia-.ebuild | 7 ---
2 files changed, 11 insertions(+), 3 deletions(-)
diff --git a/dev-lang/julia/ChangeLog b/dev-lang/julia/ChangeLog
index 3816f2c..9a0ecfe 100644
--- a/dev-lang/julia/ChangeLog
+++ b/dev-lang/julia/ChangeLog
@@ -2,6 +2,13 @@
# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 27 Aug 2014; François Bissey
+ julia-.ebuild:
+ Few fixes: julia wants threaded fftw; multilib-strict install; Added
+ USE_BLAS64=0 to Make.user, some proprietary blas/lapack may be suitable for
+ the other setting but we cannot count on julia to recognize support just
based
+ on name.
+
02 Apr 2014; Sebastien Fabbro julia-.ebuild,
metadata.xml:
various consistent fixes for main tree
diff --git a/dev-lang/julia/julia-.ebuild b/dev-lang/julia/julia-.ebuild
index ae77b70..bac01db 100644
--- a/dev-lang/julia/julia-.ebuild
+++ b/dev-lang/julia/julia-.ebuild
@@ -26,7 +26,7 @@ RDEPEND="
sci-libs/arpack:0=
sci-libs/camd:0=
sci-libs/cholmod:0=
- sci-libs/fftw:3.0=
+ sci-libs/fftw:3.0=[threads]
sci-libs/openlibm:0=
sci-libs/spqr:0=
sci-libs/umfpack:0=
@@ -58,7 +58,7 @@ src_prepare() {
sed -i \
-e "s|\(JULIA_EXECUTABLE = \)\(\$(JULIAHOME)/julia\)|\1
LD_LIBRARY_PATH=\$(BUILD)/$(get_libdir) \2|" \
-e "s|-O3|${CFLAGS}|g" \
- -e "s|LIBDIR = lib|LIBDIR = $(get_libdir)|" \
+ -e "s|libdir = \$(prefix)/lib|libdir =
\$(prefix)/$(get_libdir)|" \
-e "s|/usr/lib|${EPREFIX}/usr/$(get_libdir)|" \
-e "s|/usr/include|${EPREFIX}/usr/include|" \
-e "s|\$(BUILD)/lib|\$(BUILD)/$(get_libdir)|" \
@@ -83,6 +83,7 @@ src_configure() {
LIBBLASNAME=$($(tc-getPKG_CONFIG) --libs blas | sed -e
"s/-l\([a-z0-9]*\).*/lib\1/")
LIBLAPACK=$($(tc-getPKG_CONFIG) --libs lapack)
LIBLAPACKNAME=$($(tc-getPKG_CONFIG) --libs lapack | sed -e
"s/-l\([a-z0-9]*\).*/lib\1/")
+ USE_BLAS64=0
USE_LLVM_SHLIB=1
USE_SYSTEM_ARPACK=1
USE_SYSTEM_BLAS=1
@@ -125,7 +126,7 @@ src_test() {
}
src_install() {
- emake install PREFIX="${ED}/usr"
+ emake install prefix="${ED}/usr"
cat > 99julia <<-EOF
LDPATH=${EROOT%/}/usr/$(get_libdir)/julia
EOF
[gentoo-commits] proj/sci:master commit in: /
commit: 82c44a73de1b7eb9452360c199ee07175e1d2bab Author: François Bissey canterbury ac nz> AuthorDate: Wed Jul 2 22:12:00 2014 + Commit: Francois Bissey massey ac nz> CommitDate: Wed Jul 2 22:12:00 2014 + URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=82c44a73 Merge remote-tracking branch 'github/master' sci-visualization/visit/visit-2.7.3.ebuild | 1 + 1 file changed, 1 insertion(+)
[gentoo-commits] proj/sci:master commit in: /
commit: 6e46701e689734b1e8ee8357d60f6988568db76a Author: Sébastien Fabbro gmail com> AuthorDate: Wed Jul 2 16:29:54 2014 + Commit: Francois Bissey massey ac nz> CommitDate: Wed Jul 2 16:29:54 2014 + URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=6e46701e Merge pull request #235 from gentryx/master added lib path for VisIt's libsim and friends sci-visualization/visit/visit-2.7.3.ebuild | 1 + 1 file changed, 1 insertion(+)
[gentoo-commits] proj/sci:master commit in: sci-visualization/visit/
commit: b837d7c531f733564f654eb4b4334780440ae3bd
Author: Andreas Schäfer gmx de>
AuthorDate: Wed Jul 2 07:52:48 2014 +
Commit: Francois Bissey massey ac nz>
CommitDate: Wed Jul 2 07:52:48 2014 +
URL:
http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=b837d7c5
added lib path for VisIt's libsim and friends
---
sci-visualization/visit/visit-2.7.3.ebuild | 1 +
1 file changed, 1 insertion(+)
diff --git a/sci-visualization/visit/visit-2.7.3.ebuild
b/sci-visualization/visit/visit-2.7.3.ebuild
index 593318c..67442ed 100644
--- a/sci-visualization/visit/visit-2.7.3.ebuild
+++ b/sci-visualization/visit/visit-2.7.3.ebuild
@@ -77,6 +77,7 @@ src_install() {
cat > "${T}"/99visit <<- EOF
PATH=${EPREFIX}/opt/visit/bin
+ LDPATH=${EPREFIX}/opt/visit/${PV}/linux-$(arch)/lib/
EOF
doenvd "${T}"/99visit
}
[gentoo-commits] proj/sci:master commit in: sci-libs/cblas-reference/
commit: 53cb72c1ffc12d4192bbecc00b92c1fb983e4784
Author: François Bissey canterbury ac nz>
AuthorDate: Wed Jul 2 22:10:21 2014 +
Commit: Francois Bissey massey ac nz>
CommitDate: Wed Jul 2 22:10:52 2014 +
URL:
http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=53cb72c1
More fix for macos. We need to create the link for both linux and macos.
Package-Manager: portage-2.2.10
---
sci-libs/cblas-reference/ChangeLog | 4
sci-libs/cblas-reference/cblas-reference-20110218.ebuild | 2 +-
2 files changed, 5 insertions(+), 1 deletion(-)
diff --git a/sci-libs/cblas-reference/ChangeLog
b/sci-libs/cblas-reference/ChangeLog
index a48b811..b998a4a 100644
--- a/sci-libs/cblas-reference/ChangeLog
+++ b/sci-libs/cblas-reference/ChangeLog
@@ -2,6 +2,10 @@
# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
# $Header: /var/cvsroot/gentoo-x86/sci-libs/cblas-reference/ChangeLog,v 1.33
2010/03/07 19:14:51 jlec Exp $
+ 02 Jul 2014; François Bissey
+ cblas-reference-20110218.ebuild:
+ More fix for macos. We need to create the link for both linux and macos.
+
30 Jun 2014; François Bissey
cblas-reference-20110218.ebuild:
Tweak src_install for OS X support. Added documentation in the ebuild itself.
diff --git a/sci-libs/cblas-reference/cblas-reference-20110218.ebuild
b/sci-libs/cblas-reference/cblas-reference-20110218.ebuild
index 52fa8c8..cec9dae 100644
--- a/sci-libs/cblas-reference/cblas-reference-20110218.ebuild
+++ b/sci-libs/cblas-reference/cblas-reference-20110218.ebuild
@@ -46,8 +46,8 @@ static_to_shared() {
if [[ $(get_version_component_count) -gt 1 ]]; then
ln -s ${soname} ${libdir}/${libname}$(get_libname
$(get_major_version)) || die
fi
- ln -s ${soname} ${libdir}/${libname}$(get_libname) || die
fi
+ ln -s ${soname} ${libdir}/${libname}$(get_libname) || die
}
src_prepare() {
[gentoo-commits] proj/sci:master commit in: sci-libs/gsl/
commit: 4a1bb90c574ea27b61d9ff5d70ac4ec88763a0e2
Author: François Bissey canterbury ac nz>
AuthorDate: Wed Jul 2 00:09:01 2014 +
Commit: Francois Bissey massey ac nz>
CommitDate: Wed Jul 2 00:09:01 2014 +
URL:
http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=4a1bb90c
Tested on x64-macos, keywording.
Package-Manager: portage-2.2.10
---
sci-libs/gsl/ChangeLog | 6 +-
sci-libs/gsl/gsl-1.16-r1.ebuild | 2 +-
2 files changed, 6 insertions(+), 2 deletions(-)
diff --git a/sci-libs/gsl/ChangeLog b/sci-libs/gsl/ChangeLog
index f35223d..81ecb25 100644
--- a/sci-libs/gsl/ChangeLog
+++ b/sci-libs/gsl/ChangeLog
@@ -1,7 +1,11 @@
# ChangeLog for sci-libs/gsl
-# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
# $Header: /var/cvsroot/gentoo-x86/sci-libs/gsl/ChangeLog,v 1.77 2010/08/09
09:32:55 xarthisius Exp $
+ 02 Jul 2014; François Bissey
+ gsl-1.16-r1.ebuild:
+ Tested on x64-macos, keywording.
+
*gsl-1.16-r1 (19 Aug 2013)
19 Aug 2013; Sébastien Fabbro
diff --git a/sci-libs/gsl/gsl-1.16-r1.ebuild b/sci-libs/gsl/gsl-1.16-r1.ebuild
index c1fd0e5..f19bba1 100644
--- a/sci-libs/gsl/gsl-1.16-r1.ebuild
+++ b/sci-libs/gsl/gsl-1.16-r1.ebuild
@@ -14,7 +14,7 @@ SRC_URI="mirror://gnu/${PN}/${P}.tar.gz"
LICENSE="GPL-3"
SLOT="0"
-KEYWORDS="~alpha ~amd64 ~arm ~hppa ~ia64 ~mips ~ppc ~ppc64 ~s390 ~sh ~sparc
~x86 ~x86-fbsd ~x86-interix ~amd64-linux ~x86-linux ~x86-macos ~sparc-solaris
~x86-solaris"
+KEYWORDS="~alpha ~amd64 ~arm ~hppa ~ia64 ~mips ~ppc ~ppc64 ~s390 ~sh ~sparc
~x86 ~x86-fbsd ~x86-interix ~amd64-linux ~x86-linux ~x86-macos ~x64-macos
~sparc-solaris ~x86-solaris"
IUSE="cblas-external static-libs"
RDEPEND="cblas-external? ( virtual/cblas )"
[gentoo-commits] proj/sci:master commit in: sci-libs/cblas-reference/
commit: 0a2cfdaaf9f1845ed227642ab97a69403ca16047
Author: François Bissey canterbury ac nz>
AuthorDate: Tue Jul 1 00:28:05 2014 +
Commit: Francois Bissey massey ac nz>
CommitDate: Tue Jul 1 00:28:05 2014 +
URL:
http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=0a2cfdaa
Tweak src_install for OS X support. Added documentation in the ebuild itself.
Package-Manager: portage-2.2.10
---
sci-libs/cblas-reference/ChangeLog | 4
sci-libs/cblas-reference/cblas-reference-20110218.ebuild | 4 +++-
2 files changed, 7 insertions(+), 1 deletion(-)
diff --git a/sci-libs/cblas-reference/ChangeLog
b/sci-libs/cblas-reference/ChangeLog
index 47408ea..a48b811 100644
--- a/sci-libs/cblas-reference/ChangeLog
+++ b/sci-libs/cblas-reference/ChangeLog
@@ -2,6 +2,10 @@
# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
# $Header: /var/cvsroot/gentoo-x86/sci-libs/cblas-reference/ChangeLog,v 1.33
2010/03/07 19:14:51 jlec Exp $
+ 30 Jun 2014; François Bissey
+ cblas-reference-20110218.ebuild:
+ Tweak src_install for OS X support. Added documentation in the ebuild itself.
+
13 Jan 2014; Christoph Junghans
cblas-reference-20110218.ebuild:
fixed die mastery
diff --git a/sci-libs/cblas-reference/cblas-reference-20110218.ebuild
b/sci-libs/cblas-reference/cblas-reference-20110218.ebuild
index e6ebf28..52fa8c8 100644
--- a/sci-libs/cblas-reference/cblas-reference-20110218.ebuild
+++ b/sci-libs/cblas-reference/cblas-reference-20110218.ebuild
@@ -86,7 +86,9 @@ src_test() {
}
src_install() {
- dolib.so lib/lib${LIBNAME}$(get_libname)*
+ # On linux dynamic libraries are of the form .so.${someversion}
+ # On OS X dynamic libraries are of the form ${someversion}.dylib
+ dolib.so lib/lib${LIBNAME}*$(get_libname)*
use static-libs && dolib.a lib/lib${LIBNAME}.a
insinto /usr/include/cblas
doins include/cblas.h
