[BioC] R crashes after image array plots hgu133plus2 in R2.6.0

[Richard Friedman]

Dear Martin and Everybody,

	Here is a record of the session:

 > Data<-ReadAffy()
 > sessionInfo()
R version 2.6.0 (2007-10-03)
i386-apple-darwin8.10.1

locale:
en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] tools     stats     graphics  grDevices utils     datasets   
methods   base

other attached packages:
[1] affy_1.16.0          preprocessCore_1.0.0 affyio_1.6.1
[4] Biobase_1.16.1

loaded via a namespace (and not attached):
[1] simpleaffy_2.14.05
 > image(Data[,1])
#produced image which I closed
 > image(Data[,2])
#produced image, which I closed
 > image(Data[,3])

# R disappears and I get an error message that states

The application R quit unexpectedly

Are you interested in what I see when I click "Report". it is long.

THANKS!
Rich





On Oct 31, 2007, at 2:03 PM, Martin Morgan wrote:

> Hi Richard --
>
> what does sessionInfo() say? My guess (in a bit of rut on this!) is
> that you need to update packages so that Bioconductor and R agree. See
>
> http://www.bioconductor.org/docs/install-howto.html
>
> Please report back to the list, and if you do not have success include
> the output of sessionInfo(). Also provide additional detail about what
> 'crash' means (R error message? windows error dialog box?)
>
> Martin
>
> Richard Friedman <friedman at cancercenter.columbia.edu> writes:
>
>> correction to post below:
>>
>> I tried
>>
>> image(Data[,1])
>>
>> where data was an affybatch object
>>
>> Rich
>> On Oct 31, 2007, at 12:31 PM, Richard Friedman wrote:
>>
>>> Dear Bioconductor Users.
>>>
>>> 	I am trying to do Image array plots of hgu133plus2 chips with the
>>> new release of Bioconductor (includiong affy 1.16.0)
>>> under R 2.60 on a Mac (10.4) .  I am using the command
>>>
>>>> image(eset[,1])
>>>
>>> and I get an image array. But R crashes after the second image.
>>>
>>> I then tried it with the latest  version of R and Bioconductor on
>>> my PC,
>>> this time with AffylmGUI ( I have not yet got the GUI to work on the
>>> Mac, but
>>> that is not the problem I am writing about now).
>>>
>>> R didn't crash but again after  2 images I couldn't get another  
>>> image.
>>>
>>> I seemed to remember this operation working properly with earlier
>>> versions
>>> of R and Bioconductor on the same chip. So I tried it with AffylmGUI
>>> 1.5.4
>>> using Limma 2.7.6  unde R 2.31 on the PC. I was just able to get 3
>>> chip
>>> images in a row without mishap.
>>>
>>> So it seems that I am doing something that once worked and now
>>> no longer does.
>>>
>>> Any suggestions would be appreciated.
>>>
>>> Thanks and best wishes,
>>> Rich
>>> --------------------------------------------------------
>>> Richard A. Friedman, PhD
>>> Biomedical Informatics Shared Resource
>>> Lecturer
>>> Department of Biomedical Informatics
>>> Educational Coordinator
>>> Center for Computational Biology and Bioinformatics
>>> National Center for Multiscale Analysis of Genomic Networks
>>> Box 95, Room 130BB or P&S 1-420C
>>> Columbia University Medical Center
>>> 630 W. 168th St.
>>> New York, NY 10032
>>> (212)305-6901 (5-6901) (voice)
>>> friedman at cancercenter.columbia.edu
>>> http://cancercenter.columbia.edu/~friedman/
>>>
>>> "The last 250 pages of the last Harry Potter
>>> book took place in one day because alot
>>> happened in that day. All of Ulysses takes
>>> place in one day and nothing happened in that day."
>>> -Rose Friedman, age 11
>>>
>>> _______________________________________________
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>>
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