[Bioc-devel] error message upon installing easyRNASeq PLUS OTHER QUESTION

[Dan Tenenbaum]

On Wed, Nov 14, 2012 at 2:14 PM, Dan Tenenbaum <dtenenba at fhcrc.org> wrote:
> On Wed, Nov 14, 2012 at 2:03 PM, Richard Friedman
> <friedman at cancercenter.columbia.edu> wrote:
>> Steve,
>>
>>         Rswitch is no longer on the server.
>
> I'm not sure where you're looking for Rswitch but it's here:
> http://r.research.att.com/
>

Whoops, you're right that the Rswitch link there is dead.
Here is what I do to switch between release and devel. I put the
following in my ~/.bash_profile:

alias release="rm /Library/Frameworks/R.framework/Versions/Current &&
ln -s /Library/Frameworks/R.framework/Versions/2.15
/Library/Frameworks/R.framework/Versions/Current"

alias devel="rm /Library/Frameworks/R.framework/Versions/Current && ln
-s /Library/Frameworks/R.framework/Versions/2.16
/Library/Frameworks/R.framework/Versions/Current"

This means when I type "release", I'm using R 2.15, and when I type
"devel", I'm using R 2.16. I can only use one version at any given
time.

This accomplishes the same thing as RSwitch.
Dan


>> I  will try renaming the app and reload R15.2.
>
> If you are suggesting renaming R.app, I don't think that will
> accomplish what you want. Try Rswitch.
>
> Incidentaly, all RSwitch does is create a symbolic link from the
> version you selected to "Current" in
> /Library/Frameworks/R.framework/Versions.
> If you are more comfortable using the command line to do this, you can.
>
> Dan
>
>
>> In the meantime I am installing new packages in
>> the development version so I can get things done.
>>
>> Thanks and best wishes,
>> Rich
>>
>>
>> On Nov 14, 2012, at 4:52 PM, Steve Lianoglou wrote:
>>
>>> Hi,
>>>
>>> On Wed, Nov 14, 2012 at 1:13 PM, Richard Friedman
>>> <friedman at cancercenter.columbia.edu> wrote:
>>> [snip]
>>>> I am keeping 2.16 and 2.15 separate as far as libraries go.
>>>> However the RGUI boots with 2.16. Is there a way that I can switch back and
>>>> forth
>>>> to get it to Boot with 2.15?
>>>> When I click on the R terminals in 2.15 and 2.16 I get windows but I really
>>>> like the GUI.
>>>
>>> If you are using the builds from r.research.att.com, you will need
>>> RSwitch, which you can get from here:
>>>
>>> http://r.research.att.com/#other
>>>
>>> It's a small app which lets you select which version of R you want to
>>> be "active" -- it simply shuffles the `Current` alias in
>>> `/Library/Frameworks/R.framework/Versions` to point to the right place
>>> (among other things, I guess).
>>>
>>> I'm not sure what will happen if you want to run an R-2.15 GUI and an
>>> R-2.16 GUI simultaneously -- I suspect this isn't easy to do, so ... I
>>> mean, I'm not sure what would happen if RSwitch has 2.15 set as
>>> current, and you launch R via the GUI. Then you tell RSwitch to set
>>> R-2.16 as the current, then launch R form the terminal ... I suspect
>>> this bad things will happen to your GUI session.
>>>
>>> Anyway, that's one easy way (if a bit limited in flexibility) to do
>>> what you want.
>>>
>>> There are other ways to have R-2.15 and R-2.16 running side by side,
>>> if you are comfortable compiling R-devel by source.
>>>
>>> There's also lots of good info on this R-sig-mac thread:
>>> http://thread.gmane.org/gmane.comp.lang.r.mac/6521
>>>
>>> HTH,
>>> -steve
>>>
>>> --
>>> Steve Lianoglou
>>> Graduate Student: Computational Systems Biology
>>> | Memorial Sloan-Kettering Cancer Center
>>> | Weill Medical College of Cornell University
>>> Contact Info: http://cbio.mskcc.org/~lianos/contact
>>
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