[BioC] Windows binary for GEOquery (R 2.10.0)

[Keith Satterley]

Hi Scott,

Sean Davis responded to me on Bioc-devel about this problem. However the 
Bioc-devel archives report his email as "

  "An embedded and charset-unspecified text was scrubbed..."

so I guess that is why google doesn't find it. His response on Nov-25-2009 was:

On Mon, Nov 23, 2009 at 6:33 PM, Keith Satterley <keith at wehi.edu.au <mailto:keith at wehi.edu.au>> wrote:

    Hi Sean,

    I was reading your response to Amit Mandal's query re normalization
    of affy data and it prompted me to check my installation of GEOquery
    on R-2.10.0 on my Windows box and of course you know that it is not
    available at the moment.

    Wondering if it maybe come available soon as I generally work on
    Windows and have used your package very successfully on R-2.9.2,


I've made some changes to the vignette in the hopes that it will build 
fast enough to become available again.  I don't have any idea why the 
Windows build is slower than that on Linux or MacOS, but that appears to 
be the case, resulting in a timeout in the vignette build process.  In 
the meantime, the package can almost certainly be installed from source 
on Windows IF you have the capability of doing that.

Sean

Hope that helps,

cheers,

Keith

========================
Keith Satterley
Bioinformatics Division
The Walter and Eliza Hall Institute of Medical Research
Parkville, Melbourne,
Victoria, Australia
email:keith at wehi.edu.au
=======================



Scott Markel wrote:
> I attempted to use GEOquery in R 2.10.0 today.  I'm running Windows XP.
>
> ======================
>   
>> source("http://bioconductor.org/biocLite.R")
>> biocLite("GEOquery")
>>     
> Using R version 2.10.0, biocinstall version 2.5.8.
> Installing Bioconductor version 2.5 packages:
> [1] "GEOquery"
> Please wait...
>
> Warning message:
> In getDependencies(pkgs, dependencies, available, lib) :
>   package 'GEOquery' is not available
> ======================
>
> Checking the GEOquery package page
> (http://bioconductor.org/packages/2.5/bioc/html/GEOquery.html)
> I see that the Windows binary is indeed listed as "Not available".
> Checking the vignette, mailing list, and a Google search didn't
> provide any 2.10.0-specific information that I saw.
>
> Are there plans for releasing a new Windows binary for GEOquery?
>
> Scott
>
>   
>> sessionInfo()
>>     
> R version 2.10.0 (2009-10-26) 
> i386-pc-mingw32 
>
> locale:
> [1] LC_COLLATE=English_United States.1252 
> [2] LC_CTYPE=English_United States.1252   
> [3] LC_MONETARY=English_United States.1252
> [4] LC_NUMERIC=C                          
> [5] LC_TIME=English_United States.1252    
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base     
>
> loaded via a namespace (and not attached):
> [1] tools_2.10.0
>
>
> Scott Markel, Ph.D.
> Principal Bioinformatics Architect  email:  smarkel at accelrys.com
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>
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>
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>   

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