[Rcpp-devel] Interfacing Rcpp with a C library: memory allocation

Alessandro Mammana mammana at molgen.mpg.de
Wed Nov 20 18:27:40 CET 2013

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:

|-- 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

      @(cd samtools-0.1.19 && $(MAKE) libbam.a \
          CC="$(CC)" CFLAGS="$(CFLAGS) $(CPICFLAGS)" AR="$(AR)"

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

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