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

[Nicolas Delhomme]

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.
> 
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