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upgradeable R layout

5 messages · Steven McKinney, David Winsemius, Steve Lianoglou +1 more

Original
Steven McKinney
# 
Greetings Alexy,
There are quite a few changes between R 2.7.2 and R 2.8.0

I abandoned my R 2.7.2 and have no regrets so far (but you
don't have to - you can have different versions and Simon Urbanek
provides a small RSwitch gui app that lets you switch back and forth).
This website is out of date because of the changes 
in place for R 2.8.0

For R 2.8.0 if you look into one of a package's library
directories, e.g. 
/MacintoshHD/Library/Frameworks/R.framework/Versions/2.8/Resources/libra
ry/Matrix

you will see a subdirectory 
/libs
which will contain further subdirectories (once you've installed for the
arch involved), e.g.
/ppc
/pp64
which hold the architecture-specific files.  So you don't have to keep a
64 bit version somewhere separate from your 32 bit version.  Nice.

I installed R from Simon Urbanek's website - always up to date - 
http://r.research.att.com/
using the method

Leopard builds can be installed as follows - paste in Terminal (for R
2.8.x):
curl -s http://r.research.att.com/R-2.8-branch-leopard-universal.tar.gz
| sudo tar fvxz - -C /

after setting up the various compilers and other software discussed
in the "Tools for R Development" and "Other binaries and tools"
sections.

Now you have R installed and it has all architectures ready.
(I've wrestled through 64 bit configure / make / install for
prior R versions, this is much better!  Thank you Simon Urbanek
and others!)

I then installed the 32 bit R-Gui and renamed it to R32.app.
I installed the 64 bit R-Gui and renamed it to R64.app,
so I can fire up either 32 bit or 64 bit (or both!) and
use the excellent package manager and package installer.
The package installer installs the package using the
architecture of the R-Gui it is invoked from, so architecture
is handled automagically.
With the R-Gui apps in place, you can install packages easily, they
are installed in their standard place and I've had no problems with
this.
Yes - one way is described above.
The only hiccup I encountered was a TCL/TK issue (now resolved)
but otherwise getting 32 bit and 64 bit R up and running
has been very smooth.  (Now the issue is that ppc64 is going
extinct in the not too distant future - time to put in a
request for an Intel Mac!)
Once you get set up as I have, you won't be missing anything!

Good luck
Steven McKinney

Statistician
Molecular Oncology and Breast Cancer Program
British Columbia Cancer Research Centre

email: smckinney at bccrc.ca
tel: 604-675-8000 x7561

BCCRC
Molecular Oncology
675 West 10th Ave, Floor 4
Vancouver B.C. 
V5Z 1L3

Canada
David Winsemius
# 
I am attempting to follow this set of directions and am hung up. I  
will trim the original message and describe what I have done so far:
On Nov 13, 2008, at 8:48 PM, Steven McKinney wrote:
The installation of the Tools is the sticking point:

I am attemptng to follow the directions at http://r.research.att.com/tools/

Checked Xcode and finding that it was 3.0 and seeing that 3.1.1 was  
available, download and installed  a 1GB file. Checked to see that  
Xcode.app had been updated.

Downloaded and installed the gfortran package from the ATT website.

copied "export PATH=$PATH:/usr/local/bin" to Terminal line.

Followed "Tools on CRAN" link:

devpack4-darwin8-bin4.tar.gz was download via Firefox to /Users/ 
Downloads/ and automatically expanded to a folder with Library and usr  
descendants within /Downloads/ which I think is not the correct  
location. The contents of Library were apparently destined for / 
Applications/Frameworks/R.framework/Resources/ so I dragged the  
fontconfig file there.

Viewing the world through the Mac Finder it is unclear where the /usr/ 
local folder contents are supposed to go. There is probably a Unix  
command that will safely copy the contents of the /usr/ folder  
currently residing in /Downlaods to where the "true" /usr/ folder  
resides. So I opened a Terminal window and typed:

cp  /usr/local/

Can I now just type:
cp /Users/davidwinsemius/Downloads/devpack4-darwin8-bin4/usr/local/* .

... and get all those new files put in the corresponding descendant  
folders?
Steve Lianoglou
# 
Hi David,
That looks wrong to me. After having d/l'd the devpack to see what was  
going on, it looks like the archive is destined to be expanded at the  
root level of your system, meaning the Library folder in there should  
really expand into:

/Library/Frameworks/R.framework ...

Same goes for the usr/local/blah/blah stuffs: this should be in /usr/ 
local/blah/blah.

I'm not sure if there's any undoing that needs to be done on your side  
(doesn't seem so(?)). So, assuming we're starting from scratch: in  
order to properly install the devpack that is d/l'd in your downloads  
folder, you can type this in the terminal and all files will expand  
into their correct place:

$ sudo tar fvxz /Users/davidwinsemius/Downloads/devpack4-darwin8- 
bin4.tar.gz -C /
You can't see that folder, by default, via the Finder as its hidden.  
You can force the Finder to open it in a window a few different ways,  
though. One way is to open a new finder window, hit Cmd-Shift-G to  
drop down the "Go to folder" dialog (Also available via the Go menu),  
and then type /usr/local.

Another way would be to fire up Terminal.app and type:
$ open /usr/local
This isn't really a valid command, as cp takes two arguments. Maybe  
you meant `cd`?
If you meant `cd` above, this command wouldn't successfully copy all  
of the stuff over to your directory, since you'll need the -R command  
to copy the directories over  ...

So, to re-iterate, all you have to do to get the devpack items  
installed in the right place is to fire off the `tar xvfz ... `  
command I listed above, don't do any more cp'ing or whatever else you  
tried after that.

Honestly, though, I'm tempted to provide a word of caution since it  
seems you might not be very comfortable using the command line (sorry  
if I'm making an incorrect assumption). You'll have to use `sudo` to  
get this to work, and may unintentionally blow out something in the  
process that could your system (the command I gave you is safe, tho (I  
just ran it on my system and I'm doing OK :-)).

Anyway, hope this helps.

-steve

--
Steve Lianoglou
Graduate Student: Physiology, Biophysics and Systems Biology
Weill Medical College of Cornell University

http://cbio.mskcc.org/~lianos
David Winsemius
# 
Thanks, Steve.

You are perfectly within rights to question how comfortable I am using  
the Unix command line. I started on CP/M and PC-DOS and twenty yaers  
ago did my stats homework and thesis work on a VAX but have not really  
used CLI Unix to the point where I am comfortable with it.  I had  
gotten to the point where I thought I needed to ask a question. You  
are also correct that I was using cd rather than cp to navigate the  
directory tree.  I suspected that there was a flag or switch for the  
cp command and you offered one.  Your sudo tar <....> solution appears  
to have worked as hoped. Thank you very much.
Simon Urbanek
#
On Nov 14, 2008, at 10:05 , David Winsemius wrote:

            

      
      
      
    

        
NOTE: Most users don't need to even look at the tools page! It is  
there mainly to allow experienced users to pick and choose some  
optional tools they may like. If you are not sure that you need any of  
it, the answer is you don't. The first two items (gfortran and tcltk)  
come bundled with R so you likely have them already and the devpack is  
only for people that want to build their own R and re-create the  
environment that the CRAN build machine is using.

            

      
      
      
    

        
No, use the same procedure you used for the R installation:
curl -s http://cran.r-project.org/bin/macosx/tools/devpack4-darwin8-bin4.tar.gz 
  \
sudo tar fvxz - -C /

Cheers,
S