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...efore_ starting the compilation, as I don't really see any cleanup process (eg. making a target clean) - but this may very well be due to my limited understanding of these scripts. Any help/hints on how to proceed? Especially if I want it to be portable? Kasper The full Makevars file: MYCXXFLAGS=-O0 %.o: %.cpp $(CXX) $(ALL_CPPFLAGS) $(ALL_CXXFLAGS) $(MYCXXFLAGS) -c $< -o $@ PKG_CPPFLAGS=\ -imacros R_affx_constants.h\ -Ifusion_sdk/calvin_files/array/src\ -Ifusion_sdk/calvin_files/data/src\ -Ifusion_sdk/calvin_files/exception/src\ -Ifusion_sdk/calvin_files/fusion/src\ -Ifusion_sdk/cal...

Why is it that R places CFLAGS after PKG_CFLAGS and not before when compiling a package (e.g. through R CMD build pkg)? This can be problematic if, for instance, you want to use -O3, but -O2 is in R_HOME/etc/Makeconf. If -O2 (in CFLAGS) appears after -O3 (in PKG_CFLAGS), you are left with what you didn't want: -O2. In R-exts, it says that "Flags which are set in file etc/Makeconf

Hi. I am writing some code in C that I would like to link into R. My Makevars file is: PKG_CPPFLAGS=-I/usr/local/include PKG_LIBS=-L/usr/local/lib -lgsl PKG_CFLAGS = -Wall -O0 -g -p -pg The source file is core.c,. and I am compiling using R CMD SHLIB core.c The output is gcc -arch x86_64 -O3 -g -p -std=gnu99 -I/Library/Frameworks/ R.framework/Resources/include