[BioC] issue in arrayQuality package

[Jean Yee Hwa Yang]

Hi Longsi,

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 
http://www.bioconductor.org/repository/devel/package/html/marray.html

Jean


On Wed, 29 Dec 2004, Longsi Ran wrote:

> Hi,
> 
> 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.
> [1] "arrayQuality"
> [1] "Checking for missing packages"
> Garbage collection 397 = 333+42+22 (level 2) ...
> 384342 cons cells free (51%)
> 8.6 Mbytes of heap free (76%)
> [1] "Loading required packages"
> 
> Attaching package 'mclust':
> 
> 
>         The following object(s) are masked from package:stats :
> 
>          density
> 
> > 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 NOTA BENE: This is is an outdated version of the 'hexbin' package.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 
> writing
> > maQualityPlots(mraw, headerInfo = "", save = TRUE, dev = "png", col=NULL, 
> > badspotfunction=NULL, controlId = c("ID", "Name"), DEBUG=TRUE)
> [1] "function starting"
> [1] 8448    4
> [1] "Re-evaluate Weight"
> Error in "[<-"(`*tmp*`, !test & !nas, value = NULL) :
>         incompatible types
> 
> How to debug it?
> 
> Thanks!
> 
> 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
> 
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