Without seeing your code, this is a lot like playing 20 questions, but if your C code is correct, you might get memory-related segfaults by misunderstanding the lifetime of the R objects Rcpp references.
Krzysztof On Wed, Nov 20, 2013 at 12:27 PM, Alessandro Mammana <mamm...@molgen.mpg.de> wrote: > Dear all, > I'm trying to write some efficient code for analyzing sequencing data > in R. To do this I would like to use the C library samtools. I've > created a package where the src directory looks like this: > > src > |-- Makevars > |-- RcppExports.cpp > |-- mysourcecode.cpp > `-- samtools > |-- all *.c and *.h files as well as an independent Makefile > > My Makevars file looks like this: > > PKG_CPPFLAGS = -Isamtools > PKG_LIBS = `$(R_HOME)/bin/Rscript -e "Rcpp:::LdFlags()"` > PKG_LIBS += -Lsamtools -lbam -lz -lpthread > > $(SHLIB): samtools/libbam.a > > samtools/libbam.a: > @(cd samtools-0.1.19 && $(MAKE) libbam.a \ > CC="$(CC)" CFLAGS="$(CFLAGS) $(CPICFLAGS)" AR="$(AR)" > RANLIB="$(RANLIB)") > > Everything compiles and I get my cpp functions in R, however I am > getting some weird segfaults, I think they are due to memory > allocation, but it's hard for me to track them. Especially now, these > errors are showing up not immediately, but at the second time that I > call a Rcpp function. > > I wanted to ask the following: > 1. Is it the right way of using external C libraries? I couldn't find > much documentation around > 2. The C library uses malloc and free, and so do I (as little as > possible, just to interface with the library), is this mechanism > clashing against Rcpp/R memory management? Could it happen, for > instance, that R tries to free allocated memory that I already > manually freed myself? > > In general I didn't understand much about memory allocation in Rcpp > and I couldn't find many resources talking about it. Is there anything > R- or Rcpp-specific that I have to keep in mind or should I program as > if I were programming in C/C++? > > Thanks a lot! > > > -- > Alessandro Mammana, PhD Student > Max Planck Institute for Molecular Genetics > Ihnestraße 63-73 > D-14195 Berlin, Germany > _______________________________________________ > Rcpp-devel mailing list > Rcpp-devel@lists.r-forge.r-project.org > https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel -- Krzysztof Sakrejda Organismic and Evolutionary Biology University of Massachusetts, Amherst 319 Morrill Science Center South 611 N. Pleasant Street Amherst, MA 01003 work #: 413-325-6555 email: sakre...@cns.umass.edu ----------------------------------------------- _______________________________________________ Rcpp-devel mailing list Rcpp-devel@lists.r-forge.r-project.org https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel
