[BioC] Running time for make.cdf.package

[Jiang, Zhen]

It's a custom Affy array.  Because of company confidentiality, I'm not
sure if I should reveal the name.
The probeset size is only 3.  So the number of probesets are huge
comparing to normal Affy arrays, which have probeset size about 9 to 11.
I have made three CDF packages before. The results almost came instantly
for those three.  
Now this time, it's has been running for more than 3 days and I haven't
got any output yet.  That's why I'm asking if it is normal or it
indicates something is wrong with my code or the file.

Thanks,

Zhen Jiang


-----Original Message-----
From: Kasper Daniel Hansen [mailto:khansen at stat.berkeley.edu] 
Sent: Monday, February 16, 2009 3:24 PM
To: Jiang, Zhen
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] Running time for make.cdf.package

Why don't you tell us the size of the chip, ie. number of probes and  
number of probesets. You might even want to reveal the actual name  
(!). Since it is human, I guess it is pretty big. Your main problem is  
probably memory or a faulty file. In general, making a CDF package is  
pretty quick. I would be shocked if it took more than 1 hour on a  
suitable computer.

Do you get any output, since you are running with verbose = TRUE.

Kasper

On Feb 16, 2009, at 9:57 , Jiang, Zhen wrote:

> Dear list,
>
> I have a CDF file of size 404,514KB.  I'm using the following code to
> build a package from it.
>
> library(affy)
> library(makecdfenv)
>
> ## CDF Package
> make.cdf.package("xxxx.CDF",
>                 species="Homo_sapiens",
>                 version="0.0.1",unlink=TRUE,
>                 verbose=TRUE)
>
> It has been running for two and half days.  Is it because the CDF is  
> too
> large for R to handle or something is wrong with my code?
> I have successfully build R packages for other much smaller CDF files
> using the same code, only with different CDF name.
>
> The sessionInfo() is listed below.
>
>> sessionInfo()
> R version 2.7.0 (2008-04-22)
> i386-pc-mingw32
>
> locale:
> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
> States.1252;LC_MONETARY=English_United
> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
>
> attached base packages:
> [1] tools     stats     graphics  grDevices utils     datasets   
> methods
>
> [8] base
>
> other attached packages:
> [1] makecdfenv_1.18.0    affy_1.18.2          preprocessCore_1.2.1
> [4] affyio_1.8.1         Biobase_2.0.1
>
> Thank you very much.
>
> Zhen Jiang
>
>
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