[BioC] issue in arrayQuality package
Jean Yee Hwa Yang
jean at biostat.ucsf.edu
Thu Dec 30 01:39:09 CET 2004
There is a bug in the marray package. The path problem should be fixed in
marray version 1.5.27 which you can download from
On Wed, 29 Dec 2004, Longsi Ran wrote:
> I am using R 2.0.1 with Bioconductor Release 1.5 Packages (including
> arrayQuality 1.0.7 and hexbin 1.0.10) in Windows XP Professional.
> When I ran arrayQuality, I got following message:
> > library(arrayQuality)
> Loading required package: convert
> Loading required package: Biobase
> Welcome to Bioconductor
> Vignettes contain introductory material. To view,
> simply type: openVignette()
> For details on reading vignettes, see
> the openVignette help page.
>  "arrayQuality"
>  "Checking for missing packages"
> Garbage collection 397 = 333+42+22 (level 2) ...
> 384342 cons cells free (51%)
> 8.6 Mbytes of heap free (76%)
>  "Loading required packages"
> Attaching package 'mclust':
> The following object(s) are masked from package:stats :
> > maQualityPlots(mraw)
> Loading required package: hexbin
> NOTA BENE: This is is an outdated version of the 'hexbin' package.
> It is known to have bugs ``by design''.
> *Strongly* consider using the new 'hexbin' version instead!!
> Error in devga(paste("png:", filename, sep = ""), width, height, pointsize,
> unable to start device devga
> In addition: Warning message:
> Unable to open file
> `diagPlot.C:PROGRA~1/R/rw2001/library/marray/swirldata/swirl.1.png' for
> > maQualityPlots(mraw, headerInfo = "", save = TRUE, dev = "png", col=NULL,
> > badspotfunction=NULL, controlId = c("ID", "Name"), DEBUG=TRUE)
>  "function starting"
>  8448 4
>  "Re-evaluate Weight"
> Error in "[<-"(`*tmp*`, !test & !nas, value = NULL) :
> incompatible types
> How to debug it?
> Longsi Ran, M.D.
> Informatics Programming Specialist
> Division of Experimental Therapeutics
> Toronto General Research Institute, TGH
> Room 5R425, Max Bell Research Centre
> 200 Elizabeth St, Toronto, ON
> Canada M5G 2C4
> lran at uhnres.utoronto.ca
> Tel: 416-340-4800 x6965
> Fax: 416-340-3619
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
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