1 files changed, 0 insertions, 198 deletions
diff --git a/sci-biology/fsl/files/fsl-6.0.2-setup.patch b/sci-biology/fsl/files/fsl-6.0.2-setup.patch
deleted file mode 100644
index 39737fd85..000000000
--- a/sci-biology/fsl/files/fsl-6.0.2-setup.patch
+++ /dev/null
@@ -1,198 +0,0 @@
-From baae97cc3c8d0cadcabb7ed16559f4e4de26ddbe Mon Sep 17 00:00:00 2001
-From: François Bissey <frp.bissey@gmail.com>
-Date: Mon, 20 Jan 2020 11:54:37 +1300
-Subject: [PATCH] Adjust the build system so it doesnt build packages
- externally provided by portage. Make the compilation flags more generic and
- easily adjustable. Make the build system stop at the first fault.
-
----
- build                   |  6 +++---
- config/buildSettings.mk | 20 ++++++++++----------
- config/common/buildproj |  8 +++++---
- config/common/vars.mk   | 10 +++++-----
- extras/build            |  8 ++++----
- src/mist-clean/Makefile |  2 +-
- 6 files changed, 28 insertions(+), 26 deletions(-)
-
-diff --git a/build b/build
-index 05dac06c..d90e407b 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 dpm topup \
- asl_mfree \
-@@ -80,8 +80,8 @@ xtract";
-   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/buildSettings.mk b/config/buildSettings.mk
-index b2e1f150..04532fc2 100644
---- a/config/buildSettings.mk
-+++ b/config/buildSettings.mk
-@@ -18,7 +18,7 @@ MV = /bin/mv
- CHMOD = /bin/chmod
- MKDIR = /bin/mkdir
- INSTALL = install -p 
--TCLSH = ${FSLDIR}/bin/fsltclsh
-+TCLSH = tclsh
- DEPENDFLAGS = -MM
- MACHDBGFLAGS = -g
- #####################################################################
-@@ -124,19 +124,19 @@ endif # if Darwin
- #####################################################################
- ifeq ($(SYSTYPE), Linux)
- ###############   System Vars   #####################################
--CC = gcc
--CXX = c++
--CXX11 = c++
-+CC = @@GENTOO_CC@@
-+CXX = @@GENTOO_CXX@@
-+CXX11 = @@GENTOO_CXX@@
- CSTATICFLAGS = -static
- CXXSTATICFLAGS = -static
--ARCHFLAGS = -m64
--ARCHLDFLAGS = -Wl,-rpath,'$$ORIGIN/../lib'
-+ARCHFLAGS =
-+ARCHLDFLAGS =
- PARALLELFLAGS = -fopenmp
--OPTFLAGS = -g -O3 -fexpensive-optimizations ${ARCHFLAGS}
-+OPTFLAGS =
- GNU_ANSI_FLAGS = -Wall -ansi -pedantic -Wno-long-long
- SGI_ANSI_FLAGS = -ansi -fullwarn
- ANSI_FLAGS = ${GNU_ANSI_FLAGS}
--RANLIB = echo
-+RANLIB = @@GENTOO_RANLIB@@
- FSLML = ${FSLDIR}/bin/fslml
- # CUDA development environment
- CUDAVER := $(or $(CUDAVER),9.1)
-@@ -148,8 +148,8 @@ INC_CUDA = ${CUDA_INSTALLATION}/include
- NVCC = ${CUDA_INSTALLATION}/bin/nvcc
- ###############   External Libs   #####################################
- # ZLIB library
--LIB_ZLIB = /lib64
--INC_ZLIB = /usr/include
-+#LIB_ZLIB = /lib64
-+#INC_ZLIB = /usr/include
- # QT library
- QTDIR = /usr/lib/qt3
- LIB_QT = ${QTDIR}/lib
-diff --git a/config/common/buildproj b/config/common/buildproj
-index 2f0f2b8f..48624a1f 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`
- FSLMASTERBUILD=1
- export FSLDIR FSLDEVDIR FSLCONFDIR FSLMACHTYPE FSLMASTERBUILD
- 
-@@ -67,7 +67,7 @@ for projname in $PROJECTS; do
- 	  if [ -x ./fslconfig ] ; then
- 	    . ./fslconfig ;
- 	  fi
--	  if ${MAKE} -k ${MAKEOPTIONS} ; then 
-+	  if ${MAKE} ${MAKEOPTIONS} ; then 
- 	    if ${MAKE} ${MAKEOPTIONS} install ; then
- 	      installok=true;
- 	      # Clean up after ourselves
-@@ -82,6 +82,7 @@ for projname in $PROJECTS; do
- 	    if [ $installok = false ]  ; then
- 	      echo " "
- 	      echo "ERROR::Could not install $projname successfully" ;
-+	      exit 1
- 	    fi
- 	  else
- 	    echo " "
-@@ -90,6 +91,7 @@ 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 b027b010..aeeae67c 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} ${USERCXXFLAGS}
- 
- HFILES = *.h
- AFILES = *.a
-diff --git a/extras/build b/extras/build
-index 59e7a2ed..0d68232e 100755
---- a/extras/build
-+++ b/extras/build
-@@ -96,16 +96,16 @@ if [ X"${OS}" = "XDarwin" ]; then
- 	BUILDICONV=1
-     fi
- fi
--PROJECTS="tcl tk"
-+#PROJECTS="tcl tk"
- if [ ${BUILDZLIB} -eq 1 ]; then
-   PROJECTS="${PROJECTS} zlib"
- fi
--PROJECTS="${PROJECTS} libpng"
-+#PROJECTS="${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 libxmlpp libsqlite libnlopt ../include/armawrap/dummy_newmat"
-+PROJECTS="${PROJECTS} libgdc libprob libcprob newmat cprob newran"
-+PROJECTS="${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 20402cca..6918bee4 100755
---- a/src/mist-clean/Makefile
-+++ b/src/mist-clean/Makefile
-@@ -52,6 +52,6 @@ installpython:
- 		cp -r python/* ${DESTDIR}/python/mist
- 
- clean:
--			rm -f ${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
--- 
-2.24.1
-