Hi Steve,
Steve Lianoglou wrote:
Hi,
On Nov 3, 2009, at 2:41 AM, Antje wrote:
Hi there,
currently, I've updated R on my Mac (OS X) to version 2.10. I was
wondering if I have to install all additional packages again???
In Windows, I just needed to copy the library folder of the old
installation but how does it work with Mac?
This isn't really a mac or windows thing, actually. Although this
method may have worked for you in the past, it's generally not
recommended to use libraries compiled from one R version in another.
Using the same libraries between 2.9.X to 2.9.X+n is fine, but doing
the same when going from 2.9 to 2.10 is not a good idea.
for Windows, the FAQ tells exactly this way when upgrading the R version
(http://cran.mirroring.de/bin/windows/base/rw-FAQ.html#What_0027s-the-best-way-to-upgrade_003f)
Or did I missunderstood anything?
So, in short, you should updated/reinstall your packages now that
you've updated R.
An easy way to do that would have been to save a file of all packages
installed from 2.9, then use that file to reinstall those packages
from within 2.10. Here's a recipe to do that now (assuming R 2.9 is
still installed on your system).
You can use RSwitch to switch which version of R is "active" at a
time, available here:
http://r.research.att.com/RSwitch-1.1.dmg
1. Fire up RSwitch and pick R 2.9
1.5. I have these two functions I use when I want to be lazy:
installedPackages <- function(to="~/R.packages.dump.txt") {
writeLines(installed.packages()[,1], con=to)
}
reloadPackages <- function(from="~/R.packages.dump.txt") {
source("http://bioconductor.org/biocLite.R";)
packages <- readLines(from)
biocLite(packages)
}
2. Call installedPackages() from within R 2.9 and quit
3. Use rswitch to make R 2.10 active
4. Open R 2.10 and run reloadPackages()
biocLite is a function to install bioconductor packages, but it also
installs "normal" cran packages. You can likely replace the call to
biocLite with a call to install.packages(packages) if you don't have
any bioc packages to install, if you like, although it shouldn't be
necessary.
It might take a while to d/l all your packages again, but it should
"just work"
Thanks a lot for this recommendation. I'm just afraid it won't help this
time. It seems to me that the old version was overwritten with the new
installation but I don't know how to find out...
Next time, I might do it this way...
-steve
--
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
Ciao,
Antje
______________________________________________
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
