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

Robert Castelo robert.castelo at upf.edu
Tue Apr 17 15:00:09 CEST 2012

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 

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 


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