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

[Dan Tenenbaum]

On Tue, Apr 17, 2012 at 9:36 AM, Dan Tenenbaum <dtenenba at fhcrc.org> wrote:
> 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?
>>
>
One more thing to check--after modifying .bash_profile, you have to
either source it or open a new terminal window, before the changes you
made will be active. Could that be the problem?
Dan




> 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.
>
> Thanks,
> Dan
>
>
>> 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.