[BioC] Problems installing Bioconductor Affy on Windows 7
Martin Morgan
mtmorgan at fhcrc.org
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
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