[BioC] issue in arrayQuality package

[Longsi Ran]

Hi, Jean,

I have installed marray 1.5.27.  The bug still existed:

> library(arrayQuality)
Loading required package: convert
Loading required package: Biobase
Loading required package: tools
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 85 = 58+13+14 (level 2) ...
225307 cons cells free (37%)
7.5 Mbytes of heap free (75%)
[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NOTA BENE: This is is an outdated version of the 'hexbin' package.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

The file of 'swirl.1.png' was unable to be created even I have the Full 
control rights for the folder.

Thanks for your attention.

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


----- Original Message ----- 
From: "Jean Yee Hwa Yang" <jean at biostat.ucsf.edu>
To: "Longsi Ran" <lran at UHNRES.UTORONTO.CA>
Cc: <bioconductor at stat.math.ethz.ch>
Sent: Wednesday, December 29, 2004 7:39 PM
Subject: Re: [BioC] issue in arrayQuality package


> 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
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at stat.math.ethz.ch
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>
>
>