[BioC] rGADEM crash

[Arnaud Droit]

Hi all, 

It looks like the problem was caused by some bad memory management in the C code. We made a small adjustment to deal with it. The corrected code will be available in rGADEM version 2.3.2.

Thank you very much for reporting this bug and for helping us fix it!

Best,

Arnaud.

Le 2012-01-04 à 15:55, Dan Tenenbaum a écrit :

> Hi all,
> 
> A user (Dave, CC'd) reported a crash with the rGADEM package on Linux
> and Martin and I have been able to reproduce it.
> 
> Using the attached file with R-2.14, these steps will reproduce the crash:
> library(rGADEM)
> seq <- read.DNAStringSet("small.txt", "fasta")
> GADEM(seq[1:220])
> 
> Martin ran this under gdb and determined that the problem is in the
> macros in evalue_meme.h. At some point a lookup into one of the log
> tables is made with a negative number. Since the tables are arrays,
> they expect positive indices.
> 
> Thanks,
> Dan
> <small.txt>