[BioC] issue in arrayQuality package

Longsi Ran longsi at sympatico.ca
Wed Dec 29 22:20:16 CET 2004


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 :


> 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NOTA BENE: This is is an outdated version of the 'hexbin' package.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)
[1] "function starting"
[1] 8448    4
[1] "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

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