[R] segfault in gplots::heatmap.2

[R. Michael Weylandt]

On Thu, Aug 30, 2012 at 2:30 AM, Andreas Leha
<andreas.leha at med.uni-goettingen.de> wrote:
> Hi all,
>
> I experience a segfault when calling gplots::heatmap.2(), but only when
> certain other packages are loaded.
>
> I am not sure for the correct place to send this bug report.  Should I send
> it to the package maintainers directly?  If R-help is the wrong place,
> please feel free to direct me to the correct one.
>
> I am on debian (testing) linux 64 with the binary R distribution
> from the repositories (version 2.15.1).
>
> Below follows a simple reproducible example causing the segfault on my
> machine.
> The offending dataset is quite big, so instead of posting it here I put
> it here: https://gist.github.com/3523761.  Please put it into offending.txt to
> make the code below working.
>
> This is the example.  Note, that without loading 'XLConnect' this works
> nicely.
> #+begin_src R
>   library("gplots")
>   library("XLConnect") # any of XLConnect, venneuler, xlsx case a segfault
>
>   offending <- dget("offending.txt")
>   heatmap.2(x=offending)
> #+end_src
>
> Interestingly, I get a segfault when loading any of c("XLConnect",
> "venneuler", "xlsx"), which all depend on rJava.  But loading rJava on
> its own did not produce a segfault.

Hi Andreas,

Thanks for the nicely reproducible example. Unfortunately, I can't
reproduce the segfault on my Mac OS X 10.6 running R 2.15.0. I could
only test with rJava + venneuler because xlsx and XLConnect fall
victim to Mac's Java "infelicities." It's something of a formality,
but are you sure you are up-to-date with your packages as well as with
R itself. Something like

update.packages(checkBuilt = TRUE)

will ensure you've got the most current release of all your packages.
(Note that I'm not sure that's the right way to do it on Debian)

Do you happen to know if this happens with other versions of R? e.g.,
2.15.0 or the not-yet-released R-devel or R-patched (maintenance
branch of 2.15.z which will become 2.15.2 eventually)

Consequently, I'd suspect that there's something going on in the
intersection of Java + R + Deb Testing, so three places you might seek
more advanced help, as this is likely deeper than the day-to-day of
this list. i) The rJava mailing list
(http://mailman.rz.uni-augsburg.de/mailman/listinfo/stats-rosuda-devel);
ii) the R-SIG-Debian list; iii) the R Devel list.

I'm not sure which one makes the most sense to try, but I'd think the
third should be of last resort, because it seems least likely to be a
problem in base-R if it requires rJava being around to reproduce. The
R-SIG-Debian list most likely has someone who can reproduce your exact
config.

Cheers,
Michael

>
> Regards,
> Andreas
>
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