[Bioc-devel] running devel and release versions of R and bioc on mac os?

Steve Lianoglou mailinglist.honeypot at gmail.com
Wed Jul 20 21:37:40 CEST 2011

Ahh .. thanks for sharing!

I've always jut had the "official" releases installed and use them to
run the latest (official) version of R, and have been relying on
compiling R-devel into /usr/local/whatever to run R-devel.

I made symlinks for R-devel to point to the R script in my devel's bin
directory and just worked with things this way.

I'll try to give your way a shot, thanks!

Also -- this is way OT (sorry!), but I'm not sure where to ask this
question and it seems that you and Paul run R in a similar way as I

In particular I run emacs/ess through the terminal (iTerm2 actually).
I can sometimes get emacs to freeze up (while running in terminal) if
I'm scrolling up/down in a buffer (using the arrows), and if the
cursor hits, say "the ceiling" of the buffer, it will sometimes get
stuck there and the whole terminal just locks up. (I'm also typically
using gnu/screen).

Other times I find that R somehow just "force quites" when I'm running
it through ess.

Do you guys run a somehow-similar setup? And does this ever happen to
you guys at all?

Currently on osx.6.8, ess 5.13 and emacs 23.3 (from emacsforosx.com)


On Wed, Jul 20, 2011 at 12:14 PM, Kasper Daniel Hansen
<kasperdanielhansen at gmail.com> wrote:
> Yes.
> A full install on OS X installs R into
> # ls -l /Library/Frameworks/R.framework/Versions/
> total 8
> drwxrwxr-x  7 root  admin   238B Jul 10 13:06 2.13
> drwxrwxr-x  6 root  admin   204B Jul 10 12:56 2.14
> lrwxr-xr-x  1 root  admin    45B Jul 10 13:06 Current ->
> /Library/Frameworks/R.framework/Versions/2.13
> As you can see on my system there are version directories and then a
> symlink from "Current" to whatever version is current (under some
> definition).  The Rswitch utility essentially switches this symlink
> around.
> If you grab the nighties (the tar.gz and _not_ the pkg) from
> r.research it looks to be compiled code that simply adds a new
> directory under /Library/Framework/R.framework (you should check
> this).  But it also overwrites the "Current" link so that "Current"
> points to 2.14. Using an installer tends to create a new directory,
> but remove the old ones; this is why people complain about missing old
> versions.
> Now, assuming you have two (full) directories under OS X you need the following
>  (1) decide which version should be "R" (in my script below that is
> always latest stable release)
>  (2) make some simple scripts/symlinks that start the other versions of R
>  (3) (this is the tricky part) Make sure that the R scripts installed
> inside /bin directories deep in the Framework dirs are modified
> because (unfortunately) on mac certain paths are hardcorded.
> This script does all of it, and it needs to be run with sudo post
> installation (and you need to run it every time you re-install a
> nightie).  Based on what I see in the current tarball
> (R-devel-leopard-universal.tar.gz), this script should work with the
> nighties tarball.
> #!/bin/bash
> sudo ln -f -s /Library/Frameworks/R.framework/Versions/2.13/Resources/R
> /usr/bin/R-2.13
> sudo ln -f -s /Library/Frameworks/R.framework/Versions/2.13/Resources/Rscript
> /usr/bin/Rscript-2.13
> sudo ln -f -s /Library/Frameworks/R.framework/Versions/2.14/Resources/R
> /usr/bin/R-devel
> sudo ln -f -s /Library/Frameworks/R.framework/Versions/2.14/Resources/Rscript
> /usr/bin/Rscript-devel
> sudo ln -f -s /Library/Frameworks/R.framework/Versions/2.13/Resources/R
> /usr/bin/R
> sudo ln -f -s /Library/Frameworks/R.framework/Versions/2.13/Resources/Rscript
> /usr/bin/Rscript
> sudo rm /Library/Frameworks/R.framework/Versions/Current
> sudo ln -f -s /Library/Frameworks/R.framework/Versions/2.13
> /Library/Frameworks/R.framework/Versions/Current
> sudo sed -i tmp
> "s|R.framework/Resources|R.framework/Versions/2.13/Resources|"
> /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R
> sudo sed -i tmp
> "s|R.framework/Resources|R.framework/Versions/2.14/Resources|"
> /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R
> The first 6 lines just sets up symlinks in /usr/bin  (R (pointing to
> 2.13), R-2.13 and R-devel, expand as needed for more versions).  That
> is, they solve (1) above
> The next two lines makes sure that Current links to 2.13, solving (2) above
> The last line fixes the hard-coded path in the scripts, solving (3) above.
> Kasper
> On Wed, Jul 20, 2011 at 11:57 AM, Paul Shannon
> <pshannon at systemsbiology.org> wrote:
>> Thanks, Kasper.
>> I, too, run R from emacs using ESS, and my hope is to run (with or without ESS) the two versions in separate buffers, making for easy comparisons in a familiar environment.
>> Rather than building from source, I am inclined to get the latest build from
>>  http://r.research.att.com/#nightly
>> Any further suggestions?
>> Thanks!
>>  - Paul
>> On Jul 20, 2011, at 8:34 AM, Kasper Daniel Hansen wrote:
>>> I do this routinely, but I access R from the terminal or from within
>>> Emacs, using ESS.  I also compile R myself.
>>> It is possible to do this using the Rgui by using the Rswitch
>>> application, but that depends quite a bit on how you install R-devel
>>> (installer (is that possible?), compile or untar compiled code).
>>> However, using Rswitch you will only ever have a single R running.  If
>>> you want to run them side by side I think you need to modify stuff
>>> (which I do and which is not that hard).
>>> This seems like a reasonable request so I wonder what other people do
>>> (although I predict most people will say compile from source).
>>> Kasper
>>> On Wed, Jul 20, 2011 at 11:16 AM, Paul Shannon
>>> <pshannon at systemsbiology.org> wrote:
>>>> Are there any special techniques you can advise me of, for installing and running two concurrent R/bioc versions installed on Mac OS?
>>>> I wish to have the latest build of the devel version without sacrificing the current release as well.
>>>> Thanks,
>>>>  - Paul
>>>> _______________________________________________
>>>> Bioc-devel at r-project.org mailing list
>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> _______________________________________________
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> https://stat.ethz.ch/mailman/listinfo/bioc-devel

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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