Fixed patching

1 files changed, 0 insertions, 126 deletions

diff --git a/001-use_distribution_environment.patch b/001-use_distribution_environment.patch
index ef84b6e115d8..a42a432527ba 100644
--- a/001-use_distribution_environment.patch
+++ b/001-use_distribution_environment.patch
@@ -104,129 +104,3 @@
 +			${LIBRT}
  
  HDRS = common/gibbsshapemodel.h common/mrfshapemodel.h common/mvnshapemodel.h common/plotting.h common/profilefilters.h common/profilemixtures.h common/profilemodel.h common/profilepriors.h common/serialisation.h common/shape.h common/shapemodel.h common/stats.h common/transformation.h mist/builddate.h
- 
---- a/fsl/config/_FSLMACHTYPE/externallibs.mk	2018-10-10 13:12:48.000000000 +0200
-+++ b/fsl/config/_FSLMACHTYPE/externallibs.mk	2018-11-25 11:26:48.363038307 +0100
-@@ -7,26 +7,27 @@
- FSLEXTBIN=${FSLDIR}/extras/bin
- 
- # GD library
--LIB_GD = ${FSLEXTLIB}
--INC_GD = ${FSLEXTINC}
-+LIB_GD = /usr/lib
-+INC_GD = /usr/include
- 
- # GDC library
- LIB_GDC = ${FSLEXTLIB}
- INC_GDC = ${FSLEXTINC}/libgdc
- 
- # LIBXML2 library
--INC_XML2 = ${FSLEXTINC}/libxml2
-+INC_XML2 = /usr/include/libxml2
- 
- # LIBXML++ library
--INC_XML++ = ${FSLEXTINC}/libxml++-2.6
--INC_XML++CONF = ${FSLEXTLIB}/libxml++-2.6/include
-+INC_XML++ = /usr/include/libxml++-2.6
-+INC_XML++CONF = /usr/lib/libxml++-2.6/include
-+
- # GSL library
--LIB_GSL = ${FSLEXTLIB}
--INC_GSL = ${FSLEXTINC}/gsl
-+LIB_GSL = /usr/lib
-+INC_GSL = /usr/include/gsl
- 
- # PNG library
--LIB_PNG = ${FSLEXTLIB}
--INC_PNG = ${FSLEXTINC}
-+LIB_PNG = /usr/lib
-+INC_PNG = /usr/include/libpng1.6
- 
- # PROB library
- LIB_PROB = ${FSLEXTLIB}
-@@ -38,7 +39,9 @@
- 
- # NEWMAT library
- #LIB_NEWMAT = ${FSLEXTLIB} -llapack -lblas or just -lopenblas
--LIB_NEWMAT = ${FSLEXTLIB} -lopenblas
-+#LIB_NEWMAT = /usr/lib/newmat
-+#INC_NEWMAT = /usr/include/newmat
-+LIB_NEWMAT = ${FSLEXTLIB} -llapack -lblas
- INC_NEWMAT = ${FSLEXTINC}/armawrap/armawrap -DARMA_USE_LAPACK -DARMA_USE_BLAS -DARMA_64BIT_WORD
- 
- # NEWRAN library
-@@ -46,29 +49,29 @@
- INC_NEWRAN = ${FSLEXTINC}/newran
- 
- # ZLIB library
--LIB_ZLIB = /lib64
-+LIB_ZLIB = /usr/lib
- INC_ZLIB = /usr/include
- 
- # BOOST library
--BOOSTDIR = ${FSLEXTINC}/boost
--LIB_BOOST = ${BOOSTDIR}
--INC_BOOST = ${BOOSTDIR}
-+#BOOSTDIR = ${FSLEXTINC}/boost
-+LIB_BOOST = /usr/lib
-+INC_BOOST = /usr/include/boost
- 
- # QT library
--QTDIR = /usr/lib/qt3
--LIB_QT = ${QTDIR}/lib
--INC_QT = ${QTDIR}/include
-+#QTDIR = /usr/lib/qt5
-+LIB_QT = /usr/lib
-+INC_QT = ${QTDIR}/include/qt
- 
- # QWT library
--QWTDIR = /usr/local/qwt
--LIB_QWT = ${QWTDIR}/lib
--INC_QWT = ${QWTDIR}/include
-+#QWTDIR = /usr/local/qwt
-+LIB_QWT = /usr/lib
-+INC_QWT = /usr/include/qwt
- 
- # FFTW3 library
--LIB_FFTW3 = ${FSLEXTLIB}
--INC_FFTW3 = ${FSLEXTINC}/fftw3
-+LIB_FFTW3 = /usr/lib
-+INC_FFTW3 = /usr/include
- 
- # VTK library
--VTKDIR_INC = /home/fs0/cowboy/var/caper_linux_64-gcc4.4/VTK7/include/vtk-7.0
--VTKDIR_LIB = /home/fs0/cowboy/var/caper_linux_64-gcc4.4/VTK7/lib
--VTKSUFFIX = -7.0
-\ No newline at end of file
-+VTKDIR_INC = /usr/include/vtk
-+VTKDIR_LIB = /usr/lib
-+VTKSUFFIX =
---- a/fsl/config/_FSLMACHTYPE/systemvars.mk	2017-09-04 14:09:26.000000000 +0200
-+++ b/fsl/config/_FSLMACHTYPE/systemvars.mk	2018-11-25 11:26:48.363038307 +0100
-@@ -8,7 +8,7 @@
- CP = /bin/cp
- MV = /bin/mv
- INSTALL = install -p
--TCLSH = ${FSLDIR}/bin/fsltclsh
-+TCLSH = /usr/bin/tclsh
- RANLIB = echo
- 
- FSLML = ${FSLDIR}/bin/fslml
-@@ -30,14 +30,14 @@
- 
- DEPENDFLAGS = -MM
- 
--OPTFLAGS = -g -O3 -fexpensive-optimizations ${ARCHFLAGS}
-+OPTFLAGS = -march=native -g -O3 -fexpensive-optimizations ${ARCHFLAGS}
- MACHDBGFLAGS = -g
--GNU_ANSI_FLAGS = -Wall -ansi -pedantic -Wno-long-long
-+GNU_ANSI_FLAGS = -Wall -ansi -pedantic -std=c++11 -Wno-long-long
- SGI_ANSI_FLAGS = -ansi -fullwarn
- ANSI_FLAGS = ${GNU_ANSI_FLAGS}
- 
- # CUDA development environment
--CUDA_INSTALLATION = /opt/cuda-7.5
-+CUDA_INSTALLATION = /opt/cuda
- GENCODE_FLAGS = $(shell ${FSLDIR}/config/common/supportedGencodes.sh ${CUDA_INSTALLATION})
- LIB_CUDA = ${CUDA_INSTALLATION}/lib64
- INC_CUDA = ${CUDA_INSTALLATION}/include