[R-SIG-Mac] upgradeable R layout

Steve Lianoglou mailinglist.honeypot at gmail.com
Fri Nov 14 17:09:27 CET 2008

Hi David,

> 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.

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/ 

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 /

> Viewing the world through the Mac Finder it is unclear where the / 
> usr/local folder contents are supposed to go.

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

> 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/

This isn't really a valid command, as cp takes two arguments. Maybe  
you meant `cd`?

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

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


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