On Aug 28, 2008, at 6:35 AM, James Milks wrote:
So, what it boils down to is that I'm installing my packages at too
high of a level (I'm an administrator for my system) and should
save them in places other than the R framework folder.
Exactly, and your situation is similar to mine. To answer Rolf's
question about R_LIBS not being seen when you click R.app from the
Finder, the answer is that any application run through the GUI does
not at all read your shell login files, like .bash_profile or
whatever else you are using. It inherits the Finder's environment
instead of the shell's environment. There are two solutions:
1) Set R_LIBS in a file like .bash_profile, which is then read
whenever a terminal window opens, and then every time start R.app
from the terminal window via the command:
"open -a R". Then this R process will be inheriting the shell's
environment.
2) Create a file ~/.MacOSX/environment.plist containing this R_LIBS
definition, as specified in http://developer.apple.com/qa/qa2001/
qa1067.html. This file is respected by all GUI apps as well. Requires
a system restart. If you go with this option, I would try to keep
this file as minimal as possible.
Thanks too all for the tips and links.
Jim Milks
Haris Skiadas
Department of Mathematics and Computer Science
Hanover College
On Aug 28, 2008, at 5:08 AM, Prof Brian Ripley wrote:
The standard R mechanisms for installing packages into a different
library
apply on Mac OS X just as anywhere else. It was not said that R
was being run from the R.app GUI, but I'll assume that is the case.
The rw-FAQ provides detailed advice for Windows users: see
http://cran.r-project.org/bin/windows/base/rw-FAQ.html#What_0027s-
the-best-way-to-upgrade_003f
http://cran.r-project.org/bin/windows/base/rw-FAQ.html#I-don_0027t-
have-permission-to-write-to-the-R_002d2_002e7_002e2_005clibrary-
directory
The differences for Mac OS users are small -- some of the names
and how to set the library path via R_LIBS.
We arrange not to install packages within .Library on any of our
systems -- and for most users they do not have permission to do so.
On Wed, 27 Aug 2008, William Revelle wrote:
This is actually an R-sig-mac question so I am responding there.
In general, if you want to install a new version without losing
the previous packages, using the finder, go to Library/Receipts
and remove the R.app and R.Gui receipts. Then install the new
version. That will keep the previous packages. This is not
mysterious, this is R.
Thanks to Simon et al. for the upgrade.
Bill
At 11:00 PM -0400 8/27/08, Charilaos Skiadas wrote:
On Aug 27, 2008, at 10:40 PM, Rolf Turner wrote:
On 28/08/2008, at 2:02 PM, James Milks wrote:
The title says it all. Does anyone know of a way to save your
packages when you upgrade to a new version of R? This may
seem petty, but I'm accumulating enough packages that having
to download and install each of them anew every time I install
a new version of R is rather of a pain. Ideally, I would like
the new version of R to recognize the packages I've installed
on the previous version without needing to reinstall the
packages. Is that possible?
My system: Mac OS 10.5.4.
Current R version: 2.7.1
Mac OS moves in mysterious ways, but apparently your
installation moves in more mysterious
ways than most.
I also (by necessity, not by choice) run Mac OS. But I
certainly don't lose my
packages when I update R. The new version of R certainly
``recognizes'' the packages
that I have installed. No action required.
There may be something funny about *where* you have your
packages installed, and
what environment variables you have set.
To answer your question ``Is that possible?'' --- Yes. Not
just possible,
but universal. Except, it would seem, in your case. What have
you done
to offend the gods? :-)
Actually have had the same problem as James. By default, unless
I'm mistaken, R will save installed packages within the
"R.framework" framework (system-wide installation). This
framework gets completely replaced when a new version is
installed. In my system, the location of these packages is:
/Library/Frameworks/R.framework/Resources/library
So unless I am mistaken you have to take some action to prevent
packages from being installed there. I do hope I am wrong.
cheers,
Rolf Turner
Haris Skiadas
Department of Mathematics and Computer Science
Hanover College
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