[BioC] ReadAffy crashes R-devel on mac

Helen Zhou zhou.helen at yahoo.com
Wed Feb 13 11:07:21 CET 2008

Dear list,

oddly enough, whenever I try to read in affymetrix
files my R-session crashes. This includes when I try
to re-run old scripts. I've never had this issue
before, but updated from 2.6.1 to 2.7.0 recently.

Any help/comments would be much appreciated! The full
list of commands + sessionInfo is shown below. I've
tried with other cel files as well (affy mouse
arrays), but the result is always the same.

> setwd("~/Desktop")
> library(affy)
Loading required package: Biobase
Loading required package: tools

Welcome to Bioconductor

  Vignettes contain introductory material. To view,
  'openVignette()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages

Loading required package: affyio
Loading required package: preprocessCore
> sessionInfo()
R version 2.7.0 Under development (unstable)
(2007-12-22 r43762) 


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

other attached packages:
[1] affy_1.17.3          preprocessCore_1.1.5
affyio_1.5.11        Biobase_1.17.8      
> raw <- ReadAffy("GSM172068.CEL")

 *** caught bus error ***
address 0xc, cause 'non-existent physical address'

 1: .Call("ReadHeader", as.character(filenames[[1]]),
PACKAGE = "affyio")
 2: read.affybatch(filenames = l$filenames, phenoData
= l$phenoData,     description = l$description, notes
= notes, compress = compress,     rm.mask = rm.mask,
rm.outliers = rm.outliers, rm.extra = rm.extra,    
verbose = verbose, sd = sd, cdfname = cdfname)
 3: ReadAffy("GSM172068.CEL")

Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace

- Helen

Be a better friend, newshound, and

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