[BioC] installing BioConductor

michael watson (IAH-C) michael.watson at bbsrc.ac.uk
Tue Sep 16 12:02:48 MEST 2003


I think what you need to do is start R thus:

Rgui.exe --internet2

Or something similar.  If you change your shortcut to point to:

"C:\path\to\R\Rgui.exe" --internet2

Then R should be able to access the internet (NOTE the location of the " marks is important)


-----Original Message-----
From: Nunez-Garcia, Javier [mailto:j.nunez at vla.defra.gsi.gov.uk]
Sent: 16 September 2003 10:53
To: 'bioconductor at stat.math.ethz.ch'
Subject: [BioC] installing BioConductor

Dear Sir/Madam,
I have recently started using R software on a windows 2000 system. I'm
trying to install BioConductor but I got the following error message when
running getBioC  
> getBioC()
Running getBioC version 1.2.41....
If you encounter problems, first make sure that
you are running the latest version of getBioC()
which can be found at: www.bioconductor.org/getBioC.R
Please direct any concerns or questions to bioconductor at stat.math.ethz.ch.
Error in getBioC() : Your R can not connect to the Bioconductor website,
which is required for getBioc to work properly.  The most likely cause of
this is the internet configuration of R
I have also tried to install it from the RGui menu packages but it didn't
work neither:
> local({a<- CRAN.packages(CRAN=getOption("BIOC"))
+ install.packages(select.list(a[,1],,TRUE), .libPaths()[1], available=a,
trying URL `http://www.bioconductor.org/bin/windows/contrib/1.7/PACKAGES'
unable to resolve 'www.bioconductor.org'.
Error in download.file(url = paste(contriburl, "PACKAGES", sep = "/"),  : 
        cannot open URL
My internet connection is working fine and I can access to the web sites
that R is trying to connect.
I have downloaded the packages and tried to install it using the packages
menu again but using the option: packages from local zip files,
> install.packages(choose.files('',filters=Filters[c('zip','All'),]),
.libPaths()[1], CRAN = NULL)
Error in file(file, "r") : unable to open connection
In addition: Warning messages: 
1: error -1 in extracting from zip file 
2: cannot open file `Bioconductor/DESCRIPTION' 
As well, I can unzip the packages using software such as winzip. Could you
please tell me if I'm missing something or if I'm doing something wrong?
Many thanks

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