[BioC] R crashes when calling readCelFile in Starr package

Koh, Fong Ming Fongming.Koh at ucsf.edu
Sat Mar 16 00:42:35 CET 2013

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.

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)

[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
> 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’:


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’:


Loading required package: affxparser

Attaching package: ‘Starr’

The following object(s) are masked from ‘package:affy’:


The following object(s) are masked from ‘package:limma’:


> 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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