[R] Profiling code with lots of 'apply' calls?

David Reiss dreiss at systemsbiology.org
Wed Jan 21 22:05:25 CET 2009


Hi,
I have some code with a bunch of apply/sapply/lapply calls to
different functions. I am trying to profile it using Rprof, however
the resulting summary looks like this (output from 'R CMD Rprof'):

   %       total       %       self
 total    seconds     self    seconds    name
100.00     14.52      0.32      0.05     "source"
 99.99     14.52      0.24      0.04     "eval.with.vis"
 88.21     12.81     12.21      1.77     "FUN"
 86.04     12.49      4.08      0.59     "lapply"
 82.90     12.03      0.05      0.01     "sapply"
 25.80      3.75      2.72      0.39     "apply"

All of the functions called by the apply/sapply/lapply calls seem to
be getting munged into a single "FUN" reference. Is there a way to get
Rprof() and/or summaryRprof() to independently report the different
functions being 'apply'-ed?

Thanks.
-David




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