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

Dan Tenenbaum dtenenba at fhcrc.org
Tue Apr 17 18:36:59 CEST 2012

On Tue, Apr 17, 2012 at 6:00 AM, Robert Castelo <robert.castelo at upf.edu> 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?

I was having a similar problem until I realized that I hadn't created
both directories (I had only created one of them). After I did that,
my aliases worked just fine.

Creating them in .bash_profile has also not been a problem for me.

Nico, thanks for sharing your script, but if you are working with
R-devel (2.16) I'm not sure you need it. R 2.16 will keep all its
packages in a separate directory from 2.15 automatically. The
R_LIBS_USER trick is intended for using R 2.15 with two different
versions of Bioconductor.


> 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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