[BioC] Bioconductor installation problem: unable to access repository

Patrick Aboyoun paboyoun at fhcrc.org
Wed Oct 22 19:48:02 CEST 2008

I appears that R 2.8 has changed the way it regulates Mac OS X binary packages for users running Mac OS X 10.5 (Leopard). We have just become aware of this change and will be adjusting the Bioconductor Mac OS X repositories accordingly over the next few days to adjust to these changes. The good news is that R 2.8 supports binary packages for both Mac OS X 10.4 (Tiger) and Mac OS X 10.5 (Leopard). I'll send out an e-mail to this group when the Mac OS X 10.5 (Leopard) packages are available for BioC 2.3.


Shinichiro Wachi wrote:
> I am installing Bioconductor on a new machine (Intel Mac running OSX 10.5.5), R
> version is 2.8.0.
> sudo R is used for this session.
> These are the error messages I get:
> source("http://bioconductor.org/biocLite.R")
> biocinstall()
> Running biocinstall version 2.3.8 with R version 2.8.0 (under development)
> Your version of R requires version 2.3 of Bioconductor.
> Warning: unable to access index for repository
> http://bioconductor.org/packages/2.3/bioc/bin/macosx//contrib/2.8
> Warning: unable to access index for repository
> http://bioconductor.org/packages/2.3/data/annotation/bin/macosx//contrib/2.8
> Warning: unable to access index for repository
> http://bioconductor.org/packages/2.3/data/experiment/bin/macosx//contrib/2.8
> Warning: unable to access index for repository
> http://bioconductor.org/packages/2.3/extra/bin/macosx//contrib/2.8
> Warning: unable to access index for repository
> http://cran.fhcrc.org/bin/macosx//contrib/2.8
> Warning message:
> package 'Biobase' is not available 
> http://bioconductor.org/packages/2.3/bioc/src/contrib/PACKAGES
> will produce a web page displaying packages. (I read a post that asked for this.
> I am assuming this was a quick server diagnostics).
> Is there a problem with the server, or is this a temporary glitch in the
> installer?  Is there a workaround?
> Much thanks.
> Shin
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