[Bioc-devel] rGADEM crash

[Gustavo Fernández Bayón]

Hi everybody.

I am experiencing problems with rGADEM. Say I have the following script, 
which I have written trying to replicate the error:

library(FDb.InfiniumMethylation.hg19)
library(BSgenome.Hsapiens.UCSC.hg19)
library(rGADEM)
annot <- get450k()
rois <- keepSeqlevels(annot[1:10], paste0('chr', c(1:22, 'X', 'Y')))
rois <- resize(rois, 300, fix='center')
seqs <- getSeq(BSgenome.Hsapiens.UCSC.hg19, rois)
gad <- GADEM(seqs, verbose=1)

Approximately, a third of the the times I execute the previous code from 
the command line by using either R or Rscript, it crashes with a core 
dumped. It is not always the same error. For example, this is the last 
error message I have seen:

*** Running an unseeded analysis ***
GADEM cycle  1: enumerate and count k-mers... top 3  4, 5-mers: 2 2 2
Done.
Initializing GA... Done.
*** glibc detected *** /usr/lib/R/bin/exec/R: double free or corruption 
(!prev): 0x00007fee0c135da0 ***
======= Backtrace: =========
/lib/x86_64-linux-gnu/libc.so.6(+0x7eb96)[0x7fee5b3ffb96]
/lib/x86_64-linux-gnu/libc.so.6(+0x81cc0)[0x7fee5b402cc0]
/lib/x86_64-linux-gnu/libc.so.6(realloc+0xee)[0x7fee5b40476e]
/usr/local/lib/R/site-library/rGADEM/libs/rGADEM.so(get_llr_pv+0xc1)[0x7fee4da65eb1]
/usr/local/lib/R/site-library/rGADEM/libs/rGADEM.so(E_value+0x180)[0x7fee4da66c90]
/usr/local/lib/R/site-library/rGADEM/libs/rGADEM.so(populationCalculation+0x47b)[0x7fee4da5674b]
/usr/local/lib/R/site-library/rGADEM/libs/rGADEM.so(+0x4a67)[0x7fee4da56a67]
/usr/local/lib/R/site-library/rGADEM/libs/rGADEM.so(GADEM_Analysis+0xf6e)[0x7fee4da57f1e]
/usr/lib/R/lib/libR.so(+0xb8b87)[0x7fee5ba15b87]
/usr/lib/R/lib/libR.so(Rf_eval+0x73d)[0x7fee5ba50b1d]
/usr/lib/R/lib/libR.so(+0xf56b0)[0x7fee5ba526b0]
/usr/lib/R/lib/libR.so(Rf_eval+0x51f)[0x7fee5ba508ff]
/usr/lib/R/lib/libR.so(+0xf5830)[0x7fee5ba52830]
/usr/lib/R/lib/libR.so(Rf_eval+0x51f)[0x7fee5ba508ff]
/usr/lib/R/lib/libR.so(Rf_applyClosure+0x34d)[0x7fee5ba53d1d]
/usr/lib/R/lib/libR.so(Rf_eval+0x400)[0x7fee5ba507e0]
/usr/lib/R/lib/libR.so(+0xf56b0)[0x7fee5ba526b0]
/usr/lib/R/lib/libR.so(Rf_eval+0x51f)[0x7fee5ba508ff]
/usr/lib/R/lib/libR.so(Rf_ReplIteration+0x1e3)[0x7fee5ba8ce63]
/usr/lib/R/lib/libR.so(+0x1300f0)[0x7fee5ba8d0f0]
/usr/lib/R/lib/libR.so(run_Rmainloop+0x5a)[0x7fee5ba8d18a]
/usr/lib/R/bin/exec/R(main+0x1b)[0x40078b]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xed)[0x7fee5b3a276d]
/usr/lib/R/bin/exec/R[0x4007bd]

Sometimes it also gives a 'memory not mapped' error.

My current guess is that the error is related to some bad memory 
allocation in the C code, but I am not able to spot where. I have tried 
to run it with valgrind, and it complains about memory leaks, but I have 
to admit that I have no idea of how I could solve this. Hope somebody 
can help or give a hint.

Output from my sessionInfo():

 > sessionInfo()
R version 2.15.2 (2012-10-26)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
  [1] LC_CTYPE=es_ES.UTF-8       LC_NUMERIC=C
  [3] LC_TIME=es_ES.UTF-8        LC_COLLATE=es_ES.UTF-8
  [5] LC_MONETARY=es_ES.UTF-8    LC_MESSAGES=es_ES.UTF-8
  [7] LC_PAPER=C                 LC_NAME=C
  [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=es_ES.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods base

other attached packages:
[1] BiocInstaller_1.8.3

loaded via a namespace (and not attached):
[1] tcltk_2.15.2 tools_2.15.2

Regards,
Gus