[R] Sweave Executes Package Functions Twice

From: Dario Strbenac <D.Strbenac_at_garvan.org.au>
Date: Fri, 15 Apr 2011 21:00:20 +1000 (EST)


I've got something strange going on. I'm trying to compile a vignette using Sweave("vignette.Rnw"), and in the first code chunk that illustrates an example, I noticed from the output text I have inside the function, that it is running it twice, because the sequence of message() statements is output on screen twice, and takes twice as long to do.

Processing sample 1
Processing sample 2
Processing sample 3
Processing sample 1

Processing sample 2
Processing sample 3

If I open up a new R session, and copy and paste the lines of code from the .Rnw one by one, the function isn't called twice - only one complete set of progress outputs show.

I tried using debug() to get more of an idea of what was happening. The function is called enrichmentPlot, so I did debug(enrichmentPlot), then Sweave("vignette.Rnw"). Execution pauses when it gets to the right code chunk, then I type in "n" at the Browse[2]> prompt, but I don't get any output from debug, like "debugging in:", but it runs for a while and I get all of the messages from within my function, then execution pauses again. But just before it pauses I get the debug output :

debugging in: enrichmentPlot(samples.list, 300) debug: standardGeneric("enrichmentPlot") Browse[2]>

Then I enter "n", and it runs the same code all over again.

... ... # Same progress outputs from inside my function. exiting from: enrichmentPlot(samples.list, 300)

I have the current 2.13.0 version of R. I'm sure I've done something wrong, I just can't figure out what. Thanks for any help.

Dario Strbenac
Research Assistant
Cancer Epigenetics
Garvan Institute of Medical Research
Darlinghurst NSW 2010

R-help_at_r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. Received on Fri 15 Apr 2011 - 12:26:19 GMT

Archive maintained by Robert King, hosted by the discipline of statistics at the University of Newcastle, Australia.
Archive generated by hypermail 2.2.0, at Fri 15 Apr 2011 - 12:50:30 GMT.

Mailing list information is available at https://stat.ethz.ch/mailman/listinfo/r-help. Please read the posting guide before posting to the list.

list of date sections of archive