[BioC] Hostname bug?

[Seth Falcon]

Hi Taejoon,

Taejoon Kwon <tk320 at cam.ac.uk> writes:
> Hi all, 
>
> When I tried to re-install bioconductor package in my new linux laptop, I 
> found that http://bioconductor.org and http://www.bioconductor.org were 
> used inconsistently. I guess that two sites are slightly differently 
> configured, so some scripts (such as biocLite.R) are not working properly.
>
> Could you check this?

Thanks for the report.  We are tracking this issue and trying to find
a fix.  For now, please use http://www.bioconductor.org.

>> install.packages("affy", 
>> repos="http://www.bioconductor.org/packages/1.8/bioc/", 
>> dependencies=TRUE)

This will only work for packages that do not have dependencies outside
of the BioC software package repository.  A more complete version of
this idea is:

install.packages("somePackage",
                 repos=c("http://www.bioconductor.org/packages/1.8/bioc/", 
                         "http://www.bioconductor.org/packages/1.8/omegahat/", 
                         "http://www.bioconductor.org/packages/1.8/data/annotation/", 
                         "http://www.bioconductor.org/packages/1.8/data/experiment/", 
                         "http://cran.fhcrc.org"),   ## or other CRAN mirror
                 dependencies=TRUE)

Sorry for the inconvenience.  We appreciate the reports and are
working to smooth out these website/hosting wrinkles as soon as
possible.

Best,

+ seth