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.
--
David Winsemius
On Nov 14, 2008, at 11:09 AM, Steve Lianoglou wrote:
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/
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 /
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
--
Steve Lianoglou
Graduate Student: Physiology, Biophysics and Systems Biology
Weill Medical College of Cornell University
http://cbio.mskcc.org/~lianos
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