[gentoo-commits] proj/sci:master commit in: sci-biology/fsl/, sci-biology/fsl/files/

["Francois Bissey" <f.r.bissey@massey.ac.nz>]

commit:     98eb215e0d2c9c3e42a9aac7e39a0f5d983f0cde
Author:     Horea Christian <h.chr <AT> mail <DOT> ru>
AuthorDate: Sat Mar 28 17:55:57 2015 +0000
Commit:     Francois Bissey <f.r.bissey <AT> massey <DOT> ac <DOT> nz>
CommitDate: Sat Mar 28 17:55:57 2015 +0000
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;  <chymera@gentoo.org> +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,
   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 0000000..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 $PROJECTS
++echo "Finished build"
+ 
+diff -Naur fsl.orig/config/common/buildproj fsl/config/common/buildproj
+--- fsl.orig/config/common/buildproj	2015-03-29 00:11:47.130998000 +1300
++++ fsl/config/common/buildproj	2015-03-29 00:12:37.164319000 +1300
+@@ -11,10 +11,10 @@
+ fi
+ PROJECTS="$@" ; 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 00:11:47.183520000 +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 [ ${BUILDICONV} -eq 1 ]; then
+   PROJECTS="${PROJECTS} libiconv"
+ fi
+-PROJECTS="${PROJECTS} libgd libgdc libprob libcprob newmat cprob newran fftw"
++PROJECTS="libgdc libprob libcprob newmat cprob newran"
+ for projname in $PROJECTS; do
+ 
+     if [ -d $FSLESRCDIR/$projname ] ; then