[BioC] Windows binary for GEOquery (R 2.10.0)
James W. MacDonald
jmacdon at med.umich.edu
Tue Dec 8 19:23:12 CET 2009
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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