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mac question

3 messages · Steve Lianoglou, Antje

Antje
# 
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?

Can anybody give me a hint?

Antje
Steve Lianoglou
# 
Hi,
On Nov 3, 2009, at 2:41 AM, Antje wrote:

            

      
      
      
    

        
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.

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"

-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

  
  


  


      

    

    

      
      

        


  

        

      Antje
    

    

      
      #
    

  


  

      
Hi Steve,

        
Steve Lianoglou wrote:

            

      
      
      
    

        
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?

            

      
      
      
    

        
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...

            

      
      
      
    

        
Ciao,
Antje