[BioC] MEDIPS

[Paolo Kunderfranco]

Dear All,
I am facing some problems with MEDIPS package,
I Think I'am running out of memory once I run the command MEDIPS.meth
................
Adjusting p.values for multiple testing...
Creating results table...
Adding differential coverage results...
Error: cannot allocate vector of size 207.9 Mb
Inoltre: Warning messages:
1: In unlist(vlist, recursive = FALSE, use.names = FALSE) :
  Reached total allocation of 24501Mb: see help(memory.size)
2: In unlist(vlist, recursive = FALSE, use.names = FALSE) :
  Reached total allocation of 24501Mb: see help(memory.size)
3: In unlist(vlist, recursive = FALSE, use.names = FALSE) :
  Reached total allocation of 24501Mb: see help(memory.size)
4: In unlist(vlist, recursive = FALSE, use.names = FALSE) :
  Reached total allocation of 24501Mb: see help(memory.size)

Is there a way to avoid this problem?

I have a 24 Gb RAM workstation I don't see why it fails...

Thanks,
Paolo


> sessionInfo()
R version 3.0.0 (2013-04-03)
Platform: x86_64-w64-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=Italian_Italy.1252  LC_CTYPE=Italian_Italy.1252
LC_MONETARY=Italian_Italy.1252 LC_NUMERIC=C
LC_TIME=Italian_Italy.1252

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

other attached packages:
[1] MEDIPS_1.10.0        BiocInstaller_1.10.3 gtools_3.1.0
DNAcopy_1.34.0       BSgenome_1.28.0      Biostrings_2.28.0
GenomicRanges_1.12.4 IRanges_1.18.1       BiocGenerics_0.6.0

loaded via a namespace (and not attached):
 [1] biomaRt_2.16.0   bitops_1.0-6     edgeR_3.2.4      limma_3.16.8
  RCurl_1.95-4.1   Rsamtools_1.12.4 stats4_3.0.0     tools_3.0.0
XML_3.98-1.1     zlibbioc_1.6.0