[BioC] MacOS Package installation problems

Wed May 30 20:57:22 CEST 2012

Hi Michael,

On Wed, May 30, 2012 at 11:49 AM, Michael Salbaum
<Michael.Salbaum at pbrc.edu> wrote:
> Hi Dan,
>
> I tried setting BioC as well as CRAN mirror as suggested.

>

It looks like there is a problem with the CRAN mirrors.
I tried installing DESeq on my own Mac and got the same problem as
you. I got it even if I tried the master mirror in Switzerland
(http://stat.ethz.ch/CRAN).

I will report this to the CRAN people and let you know what I hear from them.

In the meantime, you might try
biocLite("DESeq", type="source")
If you have the right development tools installed, that should work.
The "tedious" solution you came up with will also work until this is
resolved.

Dan

> Using
>
>
>
> source("http://bioconductor.org/biocLite.R")
> biocLite("DESeq")
>
> still directed to the resources listed below, with access problems, and
> single packages listed as missing.
>
> So, I set the BioC mirror to Seattle, the CRAN mirror to TX1 (assuming that
> it's close to Louisiana),
> and used the R package installer to fetch the 'missing' packages one by one
> (things like: xtable, genefilter, geneplotter and a few more).
>
> I apologize for my clumsiness in the ways of R, but I'm originally a
> wetbench person...
>
>
> Cheers, michael
>
>
>
>
> -----Original Message-----
> From: Dan Tenenbaum [mailto:dtenenba at fhcrc.org]
> Sent: Wed 5/30/2012 1:21 PM
> To: Michael Salbaum
> Cc: Sean Davis; bioconductor at r-project.org
> Subject: Re: [BioC] MacOS Package installation problems
>
> 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]]
>>>>>
>>>>> _______________________________________________
>>>>> Bioconductor mailing list
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>>>>
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>>
>