[BioC] issue in arrayQuality package

[Longsi Ran]

Hi, Jean,

Yes, it fixed.

Thank you, Jean!

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 8:57 PM
Subject: Re: [BioC] issue in arrayQuality package


> Hi Longsi,
>
> Sorry ... there was also an update in arrayQuality.
> You need arrayQuality 1.0.8  which can be downloaded on
> http://www.bioconductor.org/repository/devel/package/html/arrayQuality.html
>
> Cheers
>
> YH
>
> 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 NOTA BENE: This is is an outdated version of the 'hexbin' package.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
>>
>
>