[BioC] MacOS Package installation problems

Wed May 30 20:21:08 CEST 2012

Hi Michael,

On Wed, May 30, 2012 at 11:16 AM, Michael Salbaum
<Michael.Salbaum at pbrc.edu> wrote:
> Got it to work.
> A bit tedious, loading single packages by hand, but nevertheless.

What do you mean by this? You should not have to *install* single
packages by hand.
The following should install DESeq and all its dependencies in one
step (assuming you set your CRAN mirror to a working mirror as
discussed earlier):

source("http://bioconductor.org/biocLite.R")
biocLite("DESeq")

Then, to *load* DESeq, the following should load it and all its dependencies:

library(DESeq)

What was the tedious part?
Dan

> Thanks for the help,
>
> Cheers, michael
>
>
>
>
>
> -----Original Message-----
> From: Dan Tenenbaum [mailto:dtenenba at fhcrc.org]
> Sent: Wed 5/30/2012 11:35 AM
> To: Sean Davis
> Cc: Michael Salbaum; bioconductor at r-project.org
> Subject: Re: [BioC] MacOS Package installation problems
>
> 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]]
>>>>
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>