[BioC] ReadAffy crashes R-devel on mac

[Ben Bolstad]

Looking at your sessionInfo() almost certainly your affyio is out of
date (both for R-2.6.1 and R-2.7.0),

Current Release version: 1.6.1
Current Devel version: 1.7.11

Your error is likely due to mismatched versions of the packages.

Best,

Ben





On Wed, 2008-02-13 at 02:07 -0800, Helen Zhou wrote:
> 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,
> type
>   'openVignette()'. To cite Bioconductor, see
>   'citation("Biobase")' and for packages
> 'citation(pkgname)'.
> 
> Loading required package: affyio
> Loading required package: preprocessCore
> > sessionInfo()
> R version 2.7.0 Under development (unstable)
> (2007-12-22 r43762) 
> i386-apple-darwin8.10.1 
> 
> locale:
> en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
> 
> 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'
> 
> Traceback:
>  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
> Selection: 
> 
> Regards
> - Helen
> 
> 
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