[Bioc-devel] Tips for using R-2.15 with BioC 2.10 and 2.11

[Steve Lianoglou]

FWIW, I have a very similar (but much more kindergarden like) script
as Nico. So far I think it's working out OK, although I don't hop
around between devel and release too often, I have once or twice.

-steve


On Tue, Apr 17, 2012 at 9:12 AM, Nicolas Delhomme <delhomme at embl.de> wrote:
> Dear Robert,
>
> I have made myself a small shell script that sets the environment variable R_LIBS and then start R.:
>
> #!/bin/bash
>
> ## the profile
> export R_PROFILE=/Users/delhomme/etc/R-profile-for-R-2.16.site
>
> ## the R libs
> if test -z $R_LIBS
>     then
>    export R_LIBS=/Users/delhomme/opt/R-libs-for-R-2.16
> else
>     export R_LIBS=$R_LIBS:/Users/delhomme/opt/R-libs-for-R-2.16
> fi
> echo $R_LIBS
>
> ## start R
> exec /Users/delhomme/opt/R-2.16.0/bin/R $@
>
> HTH,
>
> Nico
>
> ---------------------------------------------------------------
> Nicolas Delhomme
>
> Genome Biology Computational Support
>
> European Molecular Biology Laboratory
>
> Tel: +49 6221 387 8310
> Email: nicolas.delhomme at embl.de
> Meyerhofstrasse 1 - Postfach 10.2209
> 69102 Heidelberg, Germany
> ---------------------------------------------------------------
>
>
>
>
>
> On 17 Apr 2012, at 15:00, Robert Castelo wrote:
>
>> Dear Dan, and specially those using mac osx for developing packages,
>>
>> i've tried to follow the instructions below for Mac OSX, concretely
>>
>> On 04/03/2012 01:04 AM, Dan Tenenbaum wrote:
>>> Hello BioC Developers,
>>>
>> [...]
>>
>>> On Linux and Mac OS X, You can create bash aliases (called e.g. Rdevel
>>> and Rrelease) that will invoke the command line above. (Note that the
>>> "devel" in "Rdevel" refers not to the development version of R, but to
>>> that of Bioconductor; slightly confusing). Put the following in
>>> ~/.bash_profile:
>>>
>>> # Mac OS X
>>> alias Rdevel='R_LIBS_USER=~/Library/R/2.15-bioc-devel/library R'
>>> alias Rrelease='R_LIBS_USER=~/Library/R/2.15-bioc-release/library R'
>>
>> i've created this ~/.bash_profile in my laptop running Mac OSX 10.6.8 and when i start with
>>
>> $ Rdevel
>>
>> my .libPaths() always reports the release directory and never the devel directory, i.e.,
>>
>> > .libPaths()
>> [1] "/Users/rcastelo/Library/R/2.15-bioc-release/library"
>> [2] "/Library/Frameworks/R.framework/Versions/2.15/Resources/library"
>>
>> if i rename '~/Library/R/2.15-bioc-release' to 'tmp' or i comment the alias line about the release in the .bash_profile (i.e., trying to force the system to see only ~/Library/R/2.15-bioc-devel/library) i only get the default path, i.e.,
>>
>> > .libPaths()
>> [1] "/Library/Frameworks/R.framework/Versions/2.15/Resources/library"
>>
>> i've checked permissions and both directories ~/Library/R/2.15-bioc-release/library and ~/Library/R/2.15-bioc-devel/library are exactly the same in this regard (drwxr-xr-x).
>>
>> can any Mac OSX user replicate this problem?
>>
>> if not, i guess i must be doing something wrong, but i have no clue what it could be, any hint to a possible diagnostic/QC will be very much appreciated.
>>
>> thanks,
>> robert.
>>
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
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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