diff options
Diffstat (limited to '001-use_distribution_environment.patch')
| -rw-r--r-- | 001-use_distribution_environment.patch | 154 |
1 files changed, 12 insertions, 142 deletions
diff --git a/001-use_distribution_environment.patch b/001-use_distribution_environment.patch index ef84b6e115d8..65bc781bfee2 100644 --- a/001-use_distribution_environment.patch +++ b/001-use_distribution_environment.patch @@ -37,38 +37,34 @@ export FSLTCLSH FSLWISH ---- a/fsl/extras/build 2016-11-15 15:30:21.000000000 +0100 -+++ b/fsl/extras/build 2018-11-25 14:10:48.382885194 +0100 -@@ -96,21 +96,20 @@ - BUILDICONV=1 +--- a/fsl/extras/build 2019-09-29 14:50:57.966635464 +0200 ++++ b/fsl/extras/build 2019-09-29 14:53:48.906589517 +0200 +@@ -96,21 +96,12 @@ + BUILDICONV=1 fi fi -PROJECTS="tcl tk" -+PROJECTS="" - if [ ${BUILDZLIB} -eq 1 ]; then +-if [ ${BUILDZLIB} -eq 1 ]; then - PROJECTS="${PROJECTS} zlib" -+ PROJECTS="${PROJECTS}" - fi +-fi -PROJECTS="${PROJECTS} libpng" -+PROJECTS="${PROJECTS}" - if [ ${BUILDICONV} -eq 1 ]; then +-if [ ${BUILDICONV} -eq 1 ]; then - PROJECTS="${PROJECTS} libiconv" -+ PROJECTS="${PROJECTS}" - fi +-fi -PROJECTS="${PROJECTS} libgd libgdc libprob libcprob newmat cprob newran fftw" --PROJECTS="${PROJECTS} boost libxml2-2.9.2 libxml++-2.34.0 libsqlite libnlopt ../include/armawrap/dummy_newmat" +-PROJECTS="${PROJECTS} boost libxml2-2.9.2 libxmlpp libsqlite libnlopt ../include/armawrap/dummy_newmat" +PROJECTS="${PROJECTS} libgdc libprob libcprob cprob newran ../include/armawrap/dummy_newmat" for projname in $PROJECTS; do if [ -d $FSLESRCDIR/$projname ] ; then - buildIt $FSLESRCDIR $projname 1 + buildIt $FSLESRCDIR $projname 1 elif [ "$projname" = "boost" -a -d ${FSLEXTINC}/boost/boost ]; then - buildIt $FSLEXTINC boost 0 + buildIt $FSLEXTINC 0 fi done ---- a/fsl/src/mist-clean/Makefile 2018-10-17 13:00:28.000000000 +0200 -+++ b/fsl/src/mist-clean/Makefile 2018-11-25 11:26:42.643047048 +0100 +--- a/fsl/src/mist/Makefile 2018-10-17 13:00:28.000000000 +0200 ++++ b/fsl/src/mist/Makefile 2018-11-25 11:26:42.643047048 +0100 @@ -2,15 +2,15 @@ NLOPT_INC = ${FSLEXTINC} @@ -104,129 +100,3 @@ + ${LIBRT} HDRS = common/gibbsshapemodel.h common/mrfshapemodel.h common/mvnshapemodel.h common/plotting.h common/profilefilters.h common/profilemixtures.h common/profilemodel.h common/profilepriors.h common/serialisation.h common/shape.h common/shapemodel.h common/stats.h common/transformation.h mist/builddate.h - ---- a/fsl/config/_FSLMACHTYPE/externallibs.mk 2018-10-10 13:12:48.000000000 +0200 -+++ b/fsl/config/_FSLMACHTYPE/externallibs.mk 2018-11-25 11:26:48.363038307 +0100 -@@ -7,26 +7,27 @@ - FSLEXTBIN=${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 |