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....................................................................
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........................................................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@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

 


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