[BioC] readCelFile function in Starr is crashing R

[Noah Dowell [guest]]

Hello All,

I could find any solutions searching the archives so I throw this out there.  I think my packages are all updated.  

I have been trying to analyze some old data using the excellent Starr package.  Everything in my old Starr workflow was working fine several months ago but now when I try to read in cel files using the readCelFile function my R session crashes.  I went to the running the examples provides in the vignette and the same thing is happening.

Hopefully someone can help with this.

Best,

Noah


Here is my code from the vignette (I typed sessionInfo() before the readCelFile line so it is provided before my session crashes):

> dataPath <- system.file("extdata", package="Starr")

> dataPath
[1] "/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Starr/extdata"
> bpmapChr1 <- readBpmap(file.path(dataPath, "Scerevisiae_tlg_chr1.bpmap"))
> cels <- c(file.path(dataPath,"Rpb3_IP_chr1.cel"), file.path(dataPath,"wt_IP_chr1.cel"), 
+ 	file.path(dataPath,"Rpb3_IP2_chr1.cel"))
> names <- c("rpb3_1", "wt_1","rpb3_2")
> type <- c("IP", "CONTROL", "IP")
> sessionInfo()
R version 2.14.0 (2011-10-31)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-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] grid      stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] Starr_1.10.0       affxparser_1.26.1  affy_1.32.0        Ringo_1.18.0       Matrix_1.0-1       lattice_0.20-0    
[7] limma_3.10.0       RColorBrewer_1.0-5 Biobase_2.14.0    

loaded via a namespace (and not attached):
 [1] affyio_1.22.0         annotate_1.32.0       AnnotationDbi_1.16.2  BiocInstaller_1.2.1   DBI_0.2-5            
 [6] genefilter_1.36.0     IRanges_1.12.1        MASS_7.3-16           preprocessCore_1.16.0 pspline_1.0-14       
[11] RSQLite_0.10.0        splines_2.14.0        survival_2.36-10      xtable_1.6-0          zlibbioc_1.0.0       
> rpb3Chr1 <- readCelFile(bpmapChr1, cels, names, type, featureData=T, log.it=T)

 -- output of sessionInfo(): 

> sessionInfo()
R version 2.14.0 (2011-10-31)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-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] grid      stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] Starr_1.10.0       affxparser_1.26.1  affy_1.32.0        Ringo_1.18.0       Matrix_1.0-1       lattice_0.20-0    
[7] limma_3.10.0       RColorBrewer_1.0-5 Biobase_2.14.0    

loaded via a namespace (and not attached):
 [1] affyio_1.22.0         annotate_1.32.0       AnnotationDbi_1.16.2  BiocInstaller_1.2.1   DBI_0.2-5            
 [6] genefilter_1.36.0     IRanges_1.12.1        MASS_7.3-16           preprocessCore_1.16.0 pspline_1.0-14       
[11] RSQLite_0.10.0        splines_2.14.0        survival_2.36-10      xtable_1.6-0          zlibbioc_1.0.0

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