[BioC] Problem running summarizeOverlaps()

[Jessica Perry Hekman]

On 05/19/2014 09:32 PM, Martin Morgan wrote:
> On 05/19/2014 06:55 PM, Jessica Perry Hekman wrote:
>> I am working from
>>
>> http://bioconductor.org/packages/release/bioc/vignettes/gage/inst/doc/RNA-seqWorkflow.pdf

>> gnCnt <- summarizeOverlaps(exByGn, bamfls, mode="Union",
>>           ignore.strand=TRUE, single.end=TRUE, param=param)

> Hi Jessica --
>
> I think that summarizeOverlaps is trying to evaluate your counting
> algorithm in on several different cores, but an error occurs. Try
> running the commands above, and then immediately before
> summarizeOverlaps evaluate
>
>    options(mc.cores=1)
>    gnCnt <- summarizeOverlaps(exByGn, bamfls, mode="Union",
>        ignore.strand=TRUE, single.end=TRUE, param=param)
>
> Hopefully this will at least make the error apparent, even if it might
> still be cryptic.
>
> Please be sure to include the output of the command 'sessionInfo()'
> after you have a problem; here's mine

Ah yes! Very helpful! The error message after I added mc.cores=1 to my 
script is:

Error: C stack usage is too close to the limit

...which is indeed much less cryptic. I am still not sure how to fix the 
problem, though!

sessionInfo() output:

R version 3.0.2 (2013-09-25)
Platform: x86_64-redhat-linux-gnu (64-bit)

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

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

other attached packages:
  [1] leeBamViews_0.99.24
  [2] BSgenome_1.30.0
  [3] Rsamtools_1.14.3
  [4] Biostrings_2.30.1
  [5] TxDb.Hsapiens.UCSC.hg19.knownGene_2.10.1
  [6] GenomicFeatures_1.14.5
  [7] AnnotationDbi_1.24.0
  [8] Biobase_2.22.0
  [9] GenomicRanges_1.14.4
[10] XVector_0.2.0
[11] IRanges_1.20.7
[12] BiocGenerics_0.8.0

loaded via a namespace (and not attached):
  [1] biomaRt_2.18.0     bitops_1.0-6       DBI_0.2-7 
RCurl_1.95-4.1
  [5] RSQLite_0.11.4     rtracklayer_1.22.7 stats4_3.0.2 
tools_3.0.2
  [9] XML_3.98-1.1       zlibbioc_1.8.0

...and I should have remembered that I am using an older version of R. 
What I am running is the latest version that my package manager has on 
offer. Last time I installed a more recent version separately from yum, 
it was a huge annoyance to keep the two separate versions on the system. 
Do you think updating R and Bioconductor (which appears to depend on the 
most recent R in order to upgrade) will help?

Thanks very much,
Jessica