[BioC] MacOS Package installation problems

Wed May 30 18:35:41 CEST 2012

On Wed, May 30, 2012 at 9:33 AM, Sean Davis <sdavis2 at mail.nih.gov> wrote:
> On Wed, May 30, 2012 at 12:19 PM, Dan Tenenbaum <dtenenba at fhcrc.org> wrote:
>> On Wed, May 30, 2012 at 9:14 AM, Michael Salbaum
>> <Michael.Salbaum at pbrc.edu> wrote:
>>> Hi everyone,
>>>
>>> Newbie question:
>>>
>>> I'm having trouble with package installation on a Mac (OS 10.6.8)
>>>
>>>>  source("http://bioconductor.org/biocLite.R")
>>>>     biocLite("DESeq")
>>> BioC_mirror: http://bioconductor.org
>>> Using R version 2.15, BiocInstaller version 1.4.4.
>>> Warning: unable to access index for repository http://brainarray.mbni.med.umich.edu/bioc/bin/macosx/leopard/contrib/2.15
>>> Installing package(s) 'DESeq'
>>> Warning: unable to access index for repository http://cran.sixsigmaonline.org/bin/macosx/leopard/contrib/2.15
>>> Error: Line starting '<!DOCTYPE html PUBLI ...' is malformed!
>>>
>>> Dialing into http://cran.sixsigmaonline.org/bin/ only lists a linux directory, but no macosx
>>>
>>> Advice  is greatly appreciated - thanks!
>>
>> I would suggest using bioconductor.org as your repository.
>> Try:
>> chooseBioCmirror()
>> And choose the "Seattle" option.
>
> Dan, did you mean CRAN mirror?
>
> chooseCRANmirror()
>
> It looks like the CRAN mirror was the issue.

You are correct, my mistake.
Dan

>
> Sean
>
>> Dan
>>
>>
>>>
>>> J. Michael Salbaum, Ph.D.
>>> Associate Professor
>>> Pennington Biomedical Research Center
>>> Louisiana State University System
>>> 6400 Perkins Road
>>> Baton Rouge, LA 70808
>>>
>>> (225) 763-2782
>>>
>>>
>>>        [[alternative HTML version deleted]]
>>>
>>> _______________________________________________
>>> Bioconductor mailing list
>>> Bioconductor at r-project.org
>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at r-project.org
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor