[BioC] Can Bioconductor be used offline?

[Wolfgang Huber]

Dear Fedor

it should be sufficient to install the 'probe' package associated with your microarray type.
http://www.bioconductor.org/packages/release/BiocViews.html#___AffymetrixChip

	Best wishes
	Wolfgang

Il giorno Dec 21, 2012, alle ore 10:06 PM, Fedor Syagin <fs2307 at c2b2.columbia.edu> ha scritto:

> Greetings. 
> 
> Sorry to bother you. 
> 
> My name is Fedor Syagin and I work for Columbia University - C2B2.
> 
> One of the users on our computational cluster keep getting following error
> 
> 
> Adjusting for optical
> effect....................................................................
> ..........................................................................
> ..........................................................................
> ..........................................................................
> ..........................................................................
> ..........................................................................
> ..........................................................................
> ..........................................................................
> ..........................................................................
> ..........................................................................
> ..........................................................................
> ........................................................Done.
> Computing affinitiesError in getProbePackage(probepackagename) :
> The current operation could not access the Bioconductor repository. Please
> check your internet connection, and report further problems to
> bioconductor at stat.math.ethz.ch
> Calls: gcrma ... bg.adjust.gcrma -> compute.affinities -> getProbePackage
> 
> 
> 
> 
> 
> after running following code:
> 
> 
> 
> library ("AnnotationDbi")
> 
> library("affy")
> 
> library("affyPLM")
> 
> library("simpleaffy")
> 
> library("yaqcaffy")
> 
> library("gcrma")
> 
> library("limma")
> 
> library("arrayQualityMetrics")
> 
> library("gplots")
> 
> 
> 
> AffyBatch = ReadAffy()
> 
> NormalizedEset_gcrma <- gcrma(AffyBatch,fast=FALSE)
> 
> 
> 
> 
> 
> When job are submitted on the cluster there is no internet connectivity -
> so question is does this error indicate that 
> 
> Bioconductor require active internet connection at all time (not only
> during package installation) or this is error in code / installation.
> 
> 
> 
> Is there a particular way how this can be avoided that comes to your mind.
> 
> I would appreciate your help in this matter.
> 
> Thank you and have great holidays.
> 
> 
> 
> 
> 
> Sincerely yours Fedor Syagin
> 
> 
> 
> (212) 851-4796
> 
> (917) 710-6664
> 
> 
> 
> 
> 	[[alternative HTML version deleted]]
> 
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