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

[Dan Tenenbaum]

On Tue, Apr 17, 2012 at 9:55 AM, Kasper Daniel Hansen
<kasperdanielhansen at gmail.com> wrote:
> On Tue, Apr 17, 2012 at 12:52 PM, Dan Tenenbaum <dtenenba at fhcrc.org> wrote:
>> 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).
>
> Just to be completely clear: you do recommend 2.15 patched, right?



Our build machines are currently running R 2.15.0. Our build machines
always use point releases, never patched. You can use patched if you
want as long as you are aware of this.



> Will the final version for Bioc 2.11 be the latest minor release of
> R-2.15, released before Bioc 2.11.



Yes. We will update all of our build machines when there is a point
release of R-2.15. So both release and devel (2.10 and 2.11) will be
building on the
same point release of R 2.15.


Dan

>
> Kasper
>
>
>>>
>>> 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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>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>
>>
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