configure

ITKRCMAKE=`${R_HOME}/bin/Rscript -e 'a<-ITKR:::itkIncludes(); cat(a)'`
ITKRLIB=`${R_HOME}/bin/Rscript -e 'a<-ITKR:::itkLibs(); cat(a)'`
compflags=`${R_HOME}/bin/Rscript -e 'a<-ITKR:::itkCompileFlags(); cat(a)'`
ITKDIR=`${R_HOME}/bin/Rscript -e 'a<-ITKR:::itkDir(); cat(a)'`

CMAKE_BUILD_TYPE=Release


str='options(timeout=200); download.file('
str=${str}'"https://ndownloader.figshare.com/files/27383972"'
str=${str}', destfile = "ROBEX.zip", mode = "wb")'
"${R_HOME}/bin/Rscript" -e "${str}"

"${R_HOME}/bin/Rscript" -e 'unzip("ROBEX.zip", exdir = ".")'
rm ROBEX.zip

mkdir -p inst/dat
mkdir -p inst/ref_vols/
cp -r ROBEX/dat/* inst/dat/
cp -r ROBEX/ref_vols/* inst/ref_vols/
cp ROBEX/runROBEX.sh inst/

mkdir -p src
cd src/

# make sure these are tabs
all_flags="-Wformat=0 -Wno-inconsistent-missing-override -Wno-parentheses -Wno-writable-strings  -Wno-unused-result"
echo "PKG_CXXFLAGS=${all_flags}" > Makefile
echo "CXXFLAGS=${all_flags}" >> Makefile
# echo "PKG_CFLAGS=${all_flags}" >> Makefile
echo "ROBEX: build"  >> Makefile
echo "	cd build && make && chmod +x ROBEX && cp ROBEX ../../inst/ && rm -rf ../build/*"  >> Makefile
echo "clean:" >> Makefile
echo "	rm -rf ROBEX/" >> Makefile

# echo "ROBEX: \$(MAKE) -j 2 &&  \$(MAKE) all install" > Makevars

mkdir -p build
cd build
#     -DCMAKE_INSTALL_PREFIX:PATH="${R_PACKAGE_DIR}/inst/"  \

cmake -DITK_DIR:PATH="${ITKDIR}" \
    -DCMAKE_CXX_FLAGS="${all_flags}" \
    -DCMAKE_EXE_LINKER_FLAGS:STRING=-lstdc++ \
    -DCMAKE_BUILD_TYPE:STRING="${CMAKE_BUILD_TYPE}" ../../ROBEX
cd ../../

# needed for warning
# rm -rf ROBEX