--- extras/build.orig	2013-10-18 21:37:53.533939550 +1300
+++ extras/build	2013-10-18 21:40:42.283158471 +1300
@@ -41,7 +41,7 @@
 
 errorprojs="" ; export errorprojs ;
 
-PROJECTS="tcl tk zlib libpng libiconv libgd libgdc libprob libcprob newmat cprob newran cephes fftw"
+PROJECTS="libgdc libprob libcprob newmat cprob newran cephes"
 
 for projname in $PROJECTS; do
 
--- build.orig	2013-10-18 22:24:22.312777248 +1300
+++ build	2013-10-18 22:24:59.161835107 +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"
 
--- config/common/buildproj.orig	2013-10-18 22:28:40.683182435 +1300
+++ config/common/buildproj	2013-10-18 22:29:09.612227825 +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 ;
--- config/generic/systemvars.mk.orig	2007-07-13 23:00:20.000000000 +1200
+++ config/generic/systemvars.mk	2013-10-18 23:13:06.472693414 +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
--- config/common/vars.mk.orig	2013-10-18 23:39:26.384029157 +1300
+++ config/common/vars.mk	2013-10-18 23:40:49.489145387 +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} ${DBGFLAGS} ${USEDCSTATICFLAGS} ${USRCFLAGS} ${ARCHFLAGS} ${OPTFLAGS}  \
-	${AccumulatedIncFlags}
+	${AccumulatedIncFlags} ${USERCFLAGS}
 
 CXXFLAGS = ${ANSI_FLAGS} ${DBGFLAGS} ${USEDCXXSTATICFLAGS} ${USRCXXFLAGS} ${ARCHFLAGS} ${OPTFLAGS}  \
-	${AccumulatedIncFlags}
+	${AccumulatedIncFlags} ${USERCXXFLAGS}
 
 HFILES = *.h
 AFILES = *.a
--- config/common/buildproj.orig	2013-10-19 23:27:10.477238469 +1300
+++ config/common/buildproj	2013-10-19 23:28:32.207370622 +1300
@@ -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