Entering edit mode
Koh, Fong Ming
▴
20
@koh-fong-ming-5832
Last seen 10.3 years ago
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/vigne
ttes/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/leop
ard/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/d
ownloaded_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)
