[BioC] R hanging up on install of BioConductor

[Steve Lianoglou]

Sorry for not finishing that thought, but in short: try running R
through the terminal to see if it reports installation progress
better.

-steve

On Tue, Oct 5, 2010 at 3:14 PM, Steve Lianoglou
<mailinglist.honeypot at gmail.com> wrote:
> Also, if you are running R using the R.app GUI, I believe it just
> looks like it's doing nothing when all the install process is going
> on.
>
> It's actually been a long time since I used the GUI (I just run
> through terminal, or emacs), so I'm not sure if this is your problem,
> but I remember it doing that back when I was first using "it" (the
> GUI) and getting into R.
>
> -steve
>
> On Tue, Oct 5, 2010 at 2:36 PM, Hollis Wright <wrighth at ohsu.edu> wrote:
>> For what it's worth, the Fred Hutch mirror does seem to be agonizingly slow for me at the moment. I switched to the Bethesda mirror with chooseBioCMirror and setRepositories and it is installing at
>> normal speed. Could be worth a try.
>>
>> Hollis Wright, PhD
>> Oregon Clinical and Translational Research Institute
>> ________________________________________
>> From: bioconductor-bounces at stat.math.ethz.ch [bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Vincent Carey [stvjc at channing.harvard.edu]
>> Sent: Tuesday, October 05, 2010 11:01 AM
>> To: ANJAN PURKAYASTHA
>> Cc: bioconductor at stat.math.ethz.ch
>> Subject: Re: [BioC] R hanging up on install of BioConductor
>>
>> There is no evidence of a problem at the bioc server end, so you need
>> to consider your
>> network connectivity.  Try to work within R, using install.packages,
>> to acquire something small
>> like
>>
>> install.packages("ash")
>>
>> R "hanging" might indicate that you don't have sufficient connectivity
>> to complete the transaction;
>> it is not a bioconductor issue.  Various issues regarding the roles of
>> proxies are reviewed in the
>> documentation retrieved with ?download.file in R
>>
>> On Tue, Oct 5, 2010 at 12:14 PM, ANJAN PURKAYASTHA
>> <anjan.purkayastha at gmail.com> wrote:
>>> Hi,
>>> Am working on  Mac OS X 10.5.8. Just installed R 2.11.1.
>>> Tried to install the base packages of Bioconductor with :
>>>
>>> source("http://bioconductor.org/biocLite.R")
>>> biocLite()
>>>
>>>
>>> R hangs while downloading the various modules.   Have tried it multiple
>>> times (after multiple reinstalls of R) - no success.  Anybody else having
>>> this problem?
>>> Thanks,
>>> Anjan
>>>
>>>
>>>
>>>
>>> --
>>> ===================================
>>> anjan purkayastha, phd.
>>> research associate
>>> fas center for systems biology,
>>> harvard university
>>> 52 oxford street
>>> cambridge ma 02138
>>> phone-703.740.6939
>>> ===================================
>>>
>>>        [[alternative HTML version deleted]]
>>>
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>>
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>
>
>
> --
> Steve Lianoglou
> Graduate Student: Computational Systems Biology
>  | Memorial Sloan-Kettering Cancer Center
>  | Weill Medical College of Cornell University
> Contact Info: http://cbio.mskcc.org/~lianos/contact
>



-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact