[BioC] Windows binary for GEOquery (R 2.10.0)

[James W. MacDonald]

Keith Satterley wrote:
> 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.

And having the capability to build packages on Windows is now almost 
trivial. See

http://cran.r-project.org/bin/windows/base/rw-FAQ.html#Can-I-install-packages-into-libraries-in-this-version_003f

for more information.

Best,

Jim


> 
> 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
>> Accelrys (SciTegic R&D)             mobile: +1 858 205 3653
>> 10188 Telesis Court, Suite 100      voice:  +1 858 799 5603
>> San Diego, CA 92121                 fax:    +1 858 799 5222
>> USA                                 web:    http://www.accelrys.com
>>
>> http://www.linkedin.com/in/smarkel
>> Vice President, Board of Directors:
>>     International Society for Computational Biology
>> Chair: ISCB Publications Committee
>> Associate Editor: PLoS Computational Biology
>> Editorial Board: Briefings in Bioinformatics
>>
>> _______________________________________________
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>>   
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826
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