Most likely a damaged file. Check all the file sizes (I'd go to the terminal and run "du -hsc *.CEL" (without quotes). My guess is that most of them will be about the size size and one will show a strange (usual smaller) value, and this one is a strong candidate for being the problematic file.


Sent from a mobile device. Please apologise for brevity, spelling and punctuation.

Robert Scharpf <rscharpf@jhsph.edu> wrote:
Jianhong,

This could be a corrupt file.  try reading the cel headers directly:

library(affxparser)
file.exists(celfiles)
for(i in seq_along(celfiles)) readCelHeader(celfiles[i])

Rob


On Sep 25, 2012, at 4:21 PM, "Ou, Jianhong" <Jianhong.Ou@umassmed.edu> wrote:

> Hi all,
>
> When I run oligo to analysis the data of http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE7822 at Mac OS X (10.6.8), the R always crash. How could I figure out this? Here is my codes and sessionInfo.
>
>> library(oligo)
> Loading required package: oligoClasses
> Loading package bit 1.1-8
> package:bit (c) 2008/2009 Jens Oehlschlaegel (GPL-2)
> creators: bit bitwhich
> coercion: as.logical as.integer as.bit as.bitwhich which
> operator: ! & | xor != ==
> querying: print length any all min max range sum summary
> bit access: length<- [ [<- [[ [[<-
> for more help type ?bit
> Loading package ff2.2-7
> - getOption("fftempdir")=="/var/folders/Dj/Dj+bWjS7HxiNJ0kYFeKdTE+++TI/-Tmp-//RtmpPa6Fh5"
>
> - getOption("ffextension")=="ff"
>
> - getOption("ffdrop")==TRUE
>
> - getOption("fffinonexit")==TRUE
>
> - getOption("ffpagesize")==65536
>
> - getOption("ffcaching")=="mmnoflush"  -- consider "ffeachflush" if your system stalls on large writes
>
> - getOption("ffbatchbytes")==16777216 -- consider a different value for tuning your system
>
> - getOption("ffmaxbytes")==536870912 -- consider a different value for tuning your system
>
> Welcome to oligoClasses version 1.18.0
> ===========================================================================================================================================================================
> Welcome to oligo version 1.20.4
> ===========================================================================================================================================================================
>> celfiles <- c(paste("GSM1879", 38:49, ".CEL", sep=""), paste("GSM1881", 16:22, ".CEL", sep=""))
>> library("pd.mapping50k.hind240")
> Loading required package: RSQLite
> Loading required package: DBI
>> crlmm(celfiles, "hindIIout")
>
> *** caught segfault ***
> address 0xfffffffc, cause 'memory not mapped'
>
> Traceback:
> 1: .Call("R_affx_get_cel_file_header", filename, PACKAGE = "affxparser")
> 2: readCelHeader(filenames[1])
> 3: tolower(x)
> 4: paste("pd.", tolower(x), sep = "")
> 5: gsub("[_-]", ".", paste("pd.", tolower(x), sep = ""))
> 6: cleanPlatformName(readCelHeader(filenames[1])$chiptype)
> 7: crlmm(celfiles, "hindIIout")
>
> Possible actions:
> 1: abort (with core dump, if enabled)
> 2: normal R exit
> 3: exit R without saving workspace
> 4: exit R saving workspace
>
>> sessionInfo()
> R version 2.15.1 (2012-06-22)
> Platform: i386-apple-darwin9.8.0/i386 (32-bit)
>
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] pd.mapping50k.hind240_1.6.0 RSQLite_0.11.2              DBI_0.2-5                   oligo_1.20.4                oligoClasses_1.18.0
>
> loaded via a namespace (and not attached):
> [1] affxparser_1.28.1     affyio_1.24.0         Biobase_2.16.0        BiocGenerics_0.2.0    BiocInstaller_1.4.7   Biostrings_2.25.8     bit_1.1-8
> [8] codetools_0.2-8       ff_2.2-7              foreach_1.4.0         IRanges_1.15.24       iterators_1.0.6       preprocessCore_1.18.0 splines_2.15.1
> [15] stats4_2.15.1         zlibbioc_1.2.0
>
>
> Yours sincerely,
>
> Jianhong Ou
>
> jianhong.ou@umassmed.edu<mailto:jianhong.ou@umassmed.edu>
>
>
>
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>
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