R SIG Debian - Aug 2012 - segfault in gplots::heatmap.2

Hi all,

I am taking this over from r-help (see
http://permalink.gmane.org/gmane.comp.lang.r.general/273985).

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.

Regards,
Andreas

Andreas Leha <andreas.leha at med.uni-goettingen.de> writes:

> Hi all,
>
> I am taking this over from r-help (see
> http://permalink.gmane.org/gmane.comp.lang.r.general/273985).
>
> 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.
>
> Regards,
> Andreas

Hi all,

this issue has been taken to R-devel and is discussed there now (see
http://permalink.gmane.org/gmane.comp.lang.r.devel/31667).

Regards,
Andreas