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; <[email protected]> +files/fsl-5.0.8-setup.patch: + new pathc by François Bissey + 25 Mar 2015; <[email protected]> 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
