[BioC] R crashes when calling readCelFile in Starr package

[Koh, Fong Ming]

Thanks! Installing affxparser from the Aroma project solved the problem. (I'm on OS X 10.8.3 and running R v2.15.3.)

Cheers,
Fong

On Mar 16, 2013, at 12:36 AM, Henrik Bengtsson <hb at biostat.ucsf.edu> wrote:

> Workaround here:
> 
> http://aroma-project.org/install
> 
> Henrik
> 
> On Mar 15, 2013 11:18 PM, "Koh, Fong Ming" <Fongming.Koh at ucsf.edu> wrote:
> >
> > Hi all,
> >
> > I am trying to run the sample code found in the vignette for the Starr package, but my R crashes upon calling the readCelFile function. This problem seemed to have appeared previously (Nov 2011), but there was no solution listed. I've appended my session below. R crashes on the very last line. I'll be happy to take any suggestions on what I may be doing wrong.
> >
> > Thanks!
> > Fong Koh
> >
> > ================
> >
> > Package vignette: http://www.bioconductor.org/packages/2.11/bioc/vignettes/Starr/inst/doc/Starr.pdf
> > Previous mention of problem: https://stat.ethz.ch/pipermail/bioconductor/2011-November/042165.html
> >
> > ================
> >
> > > sessionInfo()
> > R version 2.15.3 (2013-03-01)
> > 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] stats     graphics  grDevices utils     datasets  methods   base
> > > source("http://bioconductor.org/biocLite.R")
> > Bioconductor version 2.11 (BiocInstaller 1.8.3), ?biocLite for help
> > > biocLite("Starr")
> > BioC_mirror: http://bioconductor.org
> > Using Bioconductor version 2.11 (BiocInstaller 1.8.3), R version 2.15.
> > Installing package(s) 'Starr'
> > trying URL 'http://bioconductor.org/packages/2.11/bioc/bin/macosx/leopard/contrib/2.15/Starr_1.14.1.tgz'
> > Content type 'application/x-gzip' length 1814289 bytes (1.7 Mb)
> > opened URL
> > ==================================================
> > downloaded 1.7 Mb
> >
> >
> > The downloaded binary packages are in
> >         /var/folders/tl/dm9b5srj1bqfqwx7fk4bllpc0000gn/T//Rtmp1VFAMD/downloaded_packages
> > > library(Starr)
> > Loading required package: Ringo
> > Loading required package: Biobase
> > Loading required package: BiocGenerics
> >
> > Attaching package: ‘BiocGenerics’
> >
> > The following object(s) are masked from ‘package:stats’:
> >
> >     xtabs
> >
> > The following object(s) are masked from ‘package:base’:
> >
> >     anyDuplicated, cbind, colnames, duplicated, eval, Filter, Find, get, intersect, lapply, Map,
> >     mapply, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rbind, Reduce, rep.int,
> >     rownames, sapply, setdiff, table, tapply, union, unique
> >
> > Welcome to Bioconductor
> >
> >     Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor,
> >     see 'citation("Biobase")', and for packages 'citation("pkgname")'.
> >
> > Loading required package: RColorBrewer
> > Loading required package: limma
> > Loading required package: Matrix
> > Loading required package: lattice
> > Loading required package: grid
> > Loading required package: affy
> >
> > Attaching package: ‘affy’
> >
> > The following object(s) are masked from ‘package:Ringo’:
> >
> >     probes
> >
> > Loading required package: affxparser
> >
> > Attaching package: ‘Starr’
> >
> > The following object(s) are masked from ‘package:affy’:
> >
> >     plotDensity
> >
> > The following object(s) are masked from ‘package:limma’:
> >
> >     plotMA
> >
> > > dataPath <- system.file("extdata", package="Starr")
> > > 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")
> >
> > ==== everything looks ok up to here, but crashes with the next line =======
> >
> > > rpb3Chr1 <- readCelFile(bpmapChr1, cels, names, type, featureData=T, log.it=T)
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