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

[Dan Tenenbaum]

On Tue, Apr 17, 2012 at 9:46 AM, Nicolas Delhomme <delhomme at embl.de> wrote:
> Hi Dan,
>
> I, indeed, have a different setup, therefore the script. I just pasted it unchanged.
>
> Now I'm curious about what your recommendations are for the current development version (2.11). I have read your previous email about this topic, but I still need some clarifications. Is it important wether we use R-2.16 or R-2.15 for developing packages for Bioc 2.11? Or do we have to use R-2.15 for Bioc 2.11 and switch to R-2.16 for Bioc 2.12 in six months?

We recommend using R-2.15 for developing packages for BioC 2.11.
After BioC 2.11 is released, you can switch to using R 2.16 (R-devel)
for developing BioC 2.12 packages.

We don't recommend using R-2.16 before then because it could introduce
changes that will not be present in R-2.15, which is the R version
that BioC 2.11 is intended to run with, and is what our build machines
are running (for that matter, R-2.15 is also the R version that BioC
2.10 is intended to run with).

Thanks,
Dan



>
> Cheers,
>
> Nico
>
> On 17 Apr 2012, at 18:36, Dan Tenenbaum 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?
>>>
>>
>> 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.
>>
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>