[Bioc-devel] C++ code performance issues

[Peter Glaus]

Hi,
I am working on BitSeq package, which has both command line C++ version 
and Bioconductor version in which R calls the same C++ code with .C 
function. While testing the development version of package on R 3.0.0 I 
noticed that the "R version" runs much slower: 2-3 TIMES slower than the 
pure C++ implementation.
Interestingly, the stable release of the "R version" seems to be as fast 
as C++ version. (The underlying code has changed slightly but there 
shouldn't be much difference)
Is there any reason for such behavior? Has anyone encountered similar 
issue? Is there a way to make the C++ code called from R faster?

More details:
I compiled the C++ code with same g++ flags (... -O3 -pipe -fpic -g... ) 
and removed OpenMP support from both.
The functions take exactly the same input (input is read from a file), 
and produce exactly same output (using same seed). A specific 
computation that took the C++ version 12minutes, took the R(C++) version 
47minutes. There is no IO during that part of the code and there was 
just one R_CheckUserInterrupt() call during this time (I changed the 
code, so that there would not be many of these calls.).
There are just few differences in the last stable release and that seems 
to run even faster than current C++ (10m). (The stable release uses -O2 
while compiling the c++ code.)

Thanks,
Peter.