Henrik Bengtsson | 16 Mar 08:36 2013
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Re: R crashes when calling readCelFile in Starr package

Workaround here:

http://aroma-project.org/install

Henrik

On Mar 15, 2013 11:18 PM, "Koh, Fong Ming" <Fongming.Koh@...> 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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