[R] mac question

[Antje]

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