TheChymera-overlay/sci-biology/fsl/files/fsl-5.0.11-setup.patch

diff --git a/build b/build
index 6827443..19b2002 100755
--- a/build
+++ b/build
@@ -3,7 +3,7 @@
 if [ $# -ge 1 ] ; then
   PROJECTS="$@";
 else
-  MASTERPROJECTS="CiftiLib-master utils znzlib NewNifti niftiio fslio giftiio miscmaths newimage libhfunc libvis first_lib \ 
+  MASTERPROJECTS="utils znzlib NewNifti niftiio fslio giftiio miscmaths newimage libhfunc libvis first_lib \ 
 meshclass fslvtkio misc_tcl basisfield warpfns bint shapeModel MVdisc fslvtkconv fslsurface libmeshutils newmesh \
 DiscreteOpt FastPDlib MSMRegLib \
 misc_c avwutils basil bet2 cluster dpm copain tissue fast4 feat5 film filmbabe flirt fabber baycest \
@@ -25,8 +25,8 @@ flameo oxford_asl relax qboot topup ptx2 lesions eddy dwssfp verbena MSM bianca
   done
 fi
 
-echo "Building projects - see build.log file for progress..."
-./config/common/buildproj $PROJECTS > ./build.log 2>&1
+echo "Building projects"
+./config/common/buildproj $PROJECTS
 finalStatus=$?
 if [ $finalStatus -eq 0 ]; then
     echo "Build completed successfully.";
diff --git a/config/common/buildproj b/config/common/buildproj
index 3450bda..ec3edc1 100755
--- a/config/common/buildproj
+++ b/config/common/buildproj
@@ -11,10 +11,10 @@ if [ X$1 = X-strict ] ; then
 fi
 PROJECTS="$@" ; 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 @@ for projname in $PROJECTS; do
 	  if [ -x ./fslconfig ] ; then
 	    . ./fslconfig ;
 	  fi
-	  if ${MAKE} -k ${MAKEOPTIONS} ; then 
+	  if ${MAKE} ${MAKEOPTIONS} ${MAKEOPTS} ; then 
 	    if ${MAKE} ${MAKEOPTIONS} install ; then
 	      installok=true;
 	      # Clean up after ourselves
@@ -81,6 +81,7 @@ for projname in $PROJECTS; do
 	    if [ $installok = false ]  ; then
 	      echo " "
 	      echo "ERROR::Could not install $projname successfully" ;
+	      exit 1
 	    fi
 	  else
 	    echo " "
@@ -89,6 +90,7 @@ for projname in $PROJECTS; do
 	    echo " "
 	    echo " "
 	    errorprojs="$errorprojs $projname" ; export errorprojs ;
+	    exit 1
 	  fi
     fi
 done
diff --git a/config/common/vars.mk b/config/common/vars.mk
index 53754be..ff7a117 100755
--- a/config/common/vars.mk
+++ b/config/common/vars.mk
@@ -24,15 +24,15 @@ USRINCFLAGS =
 USRCFLAGS = 
 USRCXXFLAGS =
 
-LDFLAGS = ${ARCHLDFLAGS} ${USRLDFLAGS} -L. -L${DEVLIBDIR} -L${LIBDIR}
+LDFLAGS = ${ARCHLDFLAGS} ${USRLDFLAGS} -L. -L${DEVLIBDIR} -L${LIBDIR} ${USERLDFLAGS}
 
-AccumulatedIncFlags = -I${INC_BOOST} ${USRINCFLAGS} -I. -I${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}
+CXXFLAGS = ${ANSI_CXXFLAGS} ${DBGFLAGS} ${USEDCXXSTATICFLAGS} ${USRCXXFLAGS} ${ARCHFLAGS} ${OPTFLAGS}  \
+	${AccumulatedIncFlags} ${USERCXXFLAGS}
 
 HFILES = *.h
 AFILES = *.a
diff --git a/config/generic/systemvars.mk b/config/generic/systemvars.mk
index e40e3d6..ddb5bfe 100755
--- a/config/generic/systemvars.mk
+++ b/config/generic/systemvars.mk
@@ -4,20 +4,20 @@ SHELL = /bin/sh
 
 # 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 @@ ARCHFLAGS =
 
 DEPENDFLAGS = -MM
 
-OPTFLAGS =  -O3 -fexpensive-optimizations ${ARCHFLAGS}
+OPTFLAGS =
 MACHDBGFLAGS =
 GNU_ANSI_FLAGS = -Wall -ansi -pedantic
 SGI_ANSI_FLAGS = -ansi -fullwarn
diff --git a/extras/build b/extras/build
index 6133a1b..caeae2d 100755
--- a/extras/build
+++ b/extras/build
@@ -104,8 +104,8 @@ PROJECTS="${PROJECTS} libpng"
 if [ ${BUILDICONV} -eq 1 ]; then
   PROJECTS="${PROJECTS} libiconv"
 fi
-PROJECTS="${PROJECTS} libgd libgdc libprob libcprob newmat cprob newran fftw"
-PROJECTS="${PROJECTS} boost libxml2-2.9.2 libxml++-2.34.0 libsqlite libnlopt ../include/armawrap/dummy_newmat"
+PROJECTS="libgdc libprob libcprob newmat cprob newran"
+PROJECTS="${PROJECTS} ../include/armawrap/dummy_newmat"
 for projname in $PROJECTS; do
     if [ -d $FSLESRCDIR/$projname ] ; then
        buildIt $FSLESRCDIR $projname 1 
diff --git a/src/mist-clean/Makefile b/src/mist-clean/Makefile
index b3a32fc..e949ba1 100755
--- a/src/mist-clean/Makefile
+++ b/src/mist-clean/Makefile
@@ -52,7 +52,7 @@ installpython:
 		cp -r python/* ${DESTDIR}/python/mist
 
 clean:
-			rm ${OBJS} mist/mist.o mist/mist
+			rm -f ${OBJS} mist/mist.o mist/mist || echo "CLEAN could not locate some files scheduled for deletion."
 
 .PHONY:		all clean installdata