[BioC] Problems installing Bioconductor Affy on Windows 7

Tue Mar 16 03:29:36 CET 2010

Hi Marissa --

On 03/15/2010 09:32 AM, Marissa LaMadrid wrote:
> Hi,
> 
>  
> 
> I originally had problems installing Affy on R version 2.10.1 (while
> learning to use Limma), read various threads on Affy installation issues and
> potential version incompatibilities, and decided to reinstall R from
> scratch, after deleting all previous versions.
> 
>  
> 
> Now, when I follow Bioconductor installing instructions, I get the message
> below.
> 
>  
> 
>> source("http://bioconductor.org/biocLite.R")
> 
>> biocLite()
> 
> Using R version 2.10.1, biocinstall version 2.5.10.
> 
> Installing Bioconductor version 2.5 packages:
> 
>  [1] "affy"         "affydata"     "affyPLM"      "annaffy"      "annotate"
> 
> 
>  [6] "Biobase"      "biomaRt"      "Biostrings"   "DynDoc"       "gcrma"
> 
> 
> [11] "genefilter"   "geneplotter"  "hgu95av2.db"  "limma"        "marray"
> 
> 
> [16] "multtest"     "vsn"          "xtable"       "affyQCReport"
> 
> Please wait...
> 
>  
> 
> Error in read.dcf(file = tmpf) : 
> 
>   Line starting '<!DOCTYPE HTML PUBLI ...' is malformed!

Hmm. My guess is that this is a network problem, either transient (the
bioconductor web site not available when you tried biocLite()?) or due
to a firewall or other configuration on your (company) end. Can you try

  source('http://bioconductor.org/biocLite.R')
  biocLite('Biobase')

and if it fails provide

  traceback()

? The usual suggestion for firewall types of issues is to start R (e.g.,
from the DOS prompt) with Rgui --internet2, so you might try that, too.

Martin

> 
> ****
> 
>  
> 
> Now, even the Limma library is not installed. 
> 
>  
> 
> What is this problem and how do I fix it? 
> 
>  
> 
> Marissa LaMadrid
> 
> Sound Choice Pharmaceutical Institute
> 
> Seattle, WA
> 
> 
> 	[[alternative HTML version deleted]]
> 
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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M1 B861
Phone: (206) 667-2793