Merge pull request #26 from kiwifb/fsl6
sci-biology/fsl: Initial fix to fsl 6.0.2
This commit is contained in:
Horea Christian
GitHub
commit
f6101338c1
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@ -1,3 +1,7 @@
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07 Nov 2019; François Bissey <frp.bissey@gmail.com>
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+files/fsl-6.0.2-setup.patch, fsl-6.0.2.ebuild:
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sci-biology/fsl: Initial fix to fsl 6.0.2
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*fsl-6.0.2 (06 Nov 2019)
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06 Nov 2019; <chymera@gentoo.org> +files/99fsl,
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@ -0,0 +1,169 @@
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diff --git a/build b/build
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index 05dac06..d90e407 100755
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--- a/build
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+++ b/build
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@@ -3,7 +3,7 @@
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if [ $# -ge 1 ] ; then
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PROJECTS="$@";
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else
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- MASTERPROJECTS="CiftiLib-master utils znzlib NewNifti niftiio fslio giftiio miscmaths newimage libhfunc libvis first_lib \
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+ MASTERPROJECTS="utils znzlib NewNifti niftiio fslio giftiio miscmaths newimage libhfunc libvis first_lib \
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meshclass fslvtkio misc_tcl basisfield warpfns bint shapeModel MVdisc fslvtkconv fslsurface libmeshutils newmesh \
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DiscreteOpt FastPDlib MSMRegLib misc_c dpm topup \
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asl_mfree \
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@@ -80,8 +80,8 @@ xtract";
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done
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fi
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-echo "Building projects - see build.log file for progress..."
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-./config/common/buildproj $PROJECTS > ./build.log 2>&1
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+echo "Building projects"
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+./config/common/buildproj $PROJECTS
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finalStatus=$?
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if [ $finalStatus -eq 0 ]; then
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echo "Build completed successfully.";
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diff --git a/config/buildSettings.mk b/config/buildSettings.mk
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index b2e1f15..04532fc 100644
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--- a/config/buildSettings.mk
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+++ b/config/buildSettings.mk
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@@ -18,7 +18,7 @@ MV = /bin/mv
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CHMOD = /bin/chmod
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MKDIR = /bin/mkdir
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INSTALL = install -p
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-TCLSH = ${FSLDIR}/bin/fsltclsh
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+TCLSH = tclsh
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DEPENDFLAGS = -MM
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MACHDBGFLAGS = -g
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#####################################################################
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@@ -124,19 +124,19 @@ endif # if Darwin
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#####################################################################
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ifeq ($(SYSTYPE), Linux)
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############### System Vars #####################################
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-CC = gcc
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-CXX = c++
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-CXX11 = c++
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+CC = @@GENTOO_CC@@
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+CXX = @@GENTOO_CXX@@
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+CXX11 = @@GENTOO_CXX@@
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CSTATICFLAGS = -static
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CXXSTATICFLAGS = -static
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-ARCHFLAGS = -m64
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-ARCHLDFLAGS = -Wl,-rpath,'$$ORIGIN/../lib'
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+ARCHFLAGS =
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+ARCHLDFLAGS =
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PARALLELFLAGS = -fopenmp
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-OPTFLAGS = -g -O3 -fexpensive-optimizations ${ARCHFLAGS}
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+OPTFLAGS =
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GNU_ANSI_FLAGS = -Wall -ansi -pedantic -Wno-long-long
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SGI_ANSI_FLAGS = -ansi -fullwarn
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ANSI_FLAGS = ${GNU_ANSI_FLAGS}
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-RANLIB = echo
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+RANLIB = @@GENTOO_RANLIB@@
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FSLML = ${FSLDIR}/bin/fslml
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# CUDA development environment
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CUDAVER := $(or $(CUDAVER),9.1)
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@@ -148,8 +148,8 @@ INC_CUDA = ${CUDA_INSTALLATION}/include
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NVCC = ${CUDA_INSTALLATION}/bin/nvcc
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############### External Libs #####################################
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# ZLIB library
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-LIB_ZLIB = /lib64
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-INC_ZLIB = /usr/include
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+#LIB_ZLIB = /lib64
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+#INC_ZLIB = /usr/include
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# QT library
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QTDIR = /usr/lib/qt3
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LIB_QT = ${QTDIR}/lib
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diff --git a/config/common/buildproj b/config/common/buildproj
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index 2f0f2b8..48624a1 100755
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--- a/config/common/buildproj
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+++ b/config/common/buildproj
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@@ -11,10 +11,10 @@ if [ X$1 = X-strict ] ; then
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fi
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PROJECTS="$@" ; export PROJECTS ;
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-FSLDIR=`pwd`
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+#FSLDIR=`pwd`
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FSLDEVDIR=${FSLDIR}
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FSLCONFDIR=${FSLDIR}/config
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-FSLMACHTYPE=`${FSLDIR}/etc/fslconf/fslmachtype.sh`
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+#FSLMACHTYPE=`${FSLDIR}/etc/fslconf/fslmachtype.sh`
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FSLMASTERBUILD=1
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export FSLDIR FSLDEVDIR FSLCONFDIR FSLMACHTYPE FSLMASTERBUILD
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@@ -67,7 +67,7 @@ for projname in $PROJECTS; do
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if [ -x ./fslconfig ] ; then
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. ./fslconfig ;
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fi
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- if ${MAKE} -k ${MAKEOPTIONS} ; then
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+ if ${MAKE} ${MAKEOPTIONS} ; then
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if ${MAKE} ${MAKEOPTIONS} install ; then
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installok=true;
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# Clean up after ourselves
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@@ -82,6 +82,7 @@ for projname in $PROJECTS; do
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if [ $installok = false ] ; then
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echo " "
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echo "ERROR::Could not install $projname successfully" ;
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+ exit 1
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fi
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else
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echo " "
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@@ -90,6 +91,7 @@ for projname in $PROJECTS; do
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echo " "
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echo " "
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errorprojs="$errorprojs $projname" ; export errorprojs ;
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+ exit 1
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fi
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fi
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done
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diff --git a/config/common/vars.mk b/config/common/vars.mk
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index b027b01..aeeae67 100755
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--- a/config/common/vars.mk
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+++ b/config/common/vars.mk
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@@ -24,15 +24,15 @@ USRINCFLAGS =
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USRCFLAGS =
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USRCXXFLAGS =
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-LDFLAGS = ${ARCHLDFLAGS} ${USRLDFLAGS} -L. -L${DEVLIBDIR} -L${LIBDIR}
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+LDFLAGS = ${ARCHLDFLAGS} ${USRLDFLAGS} -L. -L${DEVLIBDIR} -L${LIBDIR} ${USERLDFLAGS}
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-AccumulatedIncFlags = -I${INC_BOOST} ${USRINCFLAGS} -I. -I${DEVINCDIR} -I${INCDIR}
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+AccumulatedIncFlags = ${USRINCFLAGS} -I. -I${DEVINCDIR} -I${INCDIR} ${CPPFLAGS}
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CFLAGS = ${ANSI_FLAGS} ${ANSI_CFLAGS} ${DBGFLAGS} ${USEDCSTATICFLAGS} ${USRCFLAGS} ${ARCHFLAGS} ${OPTFLAGS} \
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- ${AccumulatedIncFlags}
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+ ${AccumulatedIncFlags} ${USERCFLAGS}
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-CXXFLAGS = ${ANSI_FLAGS} ${ANSI_CXXFLAGS} ${DBGFLAGS} ${USEDCXXSTATICFLAGS} ${USRCXXFLAGS} ${ARCHFLAGS} ${OPTFLAGS} \
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- ${AccumulatedIncFlags}
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+CXXFLAGS = ${ANSI_CXXFLAGS} ${DBGFLAGS} ${USEDCXXSTATICFLAGS} ${USRCXXFLAGS} ${ARCHFLAGS} ${OPTFLAGS} \
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+ ${AccumulatedIncFlags} ${USERCXXFLAGS}
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HFILES = *.h
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AFILES = *.a
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diff --git a/extras/build b/extras/build
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index 59e7a2e..2cead09 100755
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--- a/extras/build
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+++ b/extras/build
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@@ -104,8 +104,8 @@ PROJECTS="${PROJECTS} libpng"
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if [ ${BUILDICONV} -eq 1 ]; then
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PROJECTS="${PROJECTS} libiconv"
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fi
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-PROJECTS="${PROJECTS} libgd libgdc libprob libcprob newmat cprob newran fftw"
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-PROJECTS="${PROJECTS} boost libxml2-2.9.2 libxmlpp libsqlite libnlopt ../include/armawrap/dummy_newmat"
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+PROJECTS="${PROJECTS} libgdc libprob libcprob newmat cprob newran"
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+PROJECTS="${PROJECTS} ../include/armawrap/dummy_newmat"
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for projname in $PROJECTS; do
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if [ -d $FSLESRCDIR/$projname ] ; then
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buildIt $FSLESRCDIR $projname 1
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diff --git a/src/mist-clean/Makefile b/src/mist-clean/Makefile
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index 20402cc..6918bee 100755
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--- a/src/mist-clean/Makefile
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+++ b/src/mist-clean/Makefile
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@@ -52,6 +52,6 @@ installpython:
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cp -r python/* ${DESTDIR}/python/mist
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clean:
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- rm -f ${OBJS} mist/mist.o mist/mist
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+ rm -f ${OBJS} mist/mist.o mist/mist || echo "CLEAN could not locate some files scheduled for deletion."
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.PHONY: all clean installdata
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@ -34,7 +34,7 @@ S=${WORKDIR}/${PN}
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UPSTREAM_FSLDIR="/usr/share/fsl"
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PATCHES=(
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#"${FILESDIR}/${PN}"-5.0.11-setup.patch
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"${FILESDIR}/${PN}"-6.0.2-setup.patch
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#"${FILESDIR}/${PN}"-5.0.11-no_xmlpp.patch
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"${FILESDIR}/${PN}"-5.0.11-niftiio_var_fix.patch
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"${FILESDIR}/${PN}"-5.0.11-ifstream_use.patch
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@ -51,7 +51,7 @@ src_prepare(){
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-e "s:@@GENTOO_RANLIB@@:$(tc-getRANLIB):" \
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-e "s:@@GENTOO_CC@@:$(tc-getCC):" \
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-e "s:@@GENTOO_CXX@@:$(tc-getCXX):" \
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config/generic/systemvars.mk || die
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config/buildSettings.mk || die
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eprefixify $(grep -rl GENTOO_PORTAGE_EPREFIX src/*) \
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etc/js/label-div.html
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