[R-SIG-Mac] Consistency of information about installed packages

[Simon Urbanek]

On Apr 28, 2005, at 4:44 PM, Rob J Goedman wrote:

> On Apr 28, 2005, at 1:00 PM, Simon Urbanek wrote:
>
>> It's ok to install over previous version, no problem, but if you  
>> use your own private R packages, you cannot share them across R  
>> versions (that's why personally I recommend to avoid that practice  
>> unless you have no admin access). The safest thing is to delete ~/ 
>> Library/R after upgrade. We don't want the installer to be  
>> destructive, that's why don't do it by default.
>>
>
> I know, but if you install R-2.1.0 on top of an existing install,  
> except the default libraries, doesn't it leave
> all other libraries in the system library folder intact as well?

It does, but they are in let's say
/Library/Frameworks/R.framework/Versions/2.0.1/Resources/library
so they won't bother your most recent R which will look in
/Library/Frameworks/R.framework/Versions/2.1.0/Resources/library

In fact each R (unless you use R_HOME or patch the R script) will  
look into
/Library/Frameworks/R.framework/Resources/library
which symlinks to
/Library/Frameworks/R.framework/Versions/Current/Resources/library
and "Current" is the symlink that the installer changes to point to  
2.1.0

The bottom line is that each new version of R framework doesn't care  
about any other installed version and won't touch it(*).

> I've not seen many problems with packages in this upgrade (from  
> R-2.0.1 to R-2.1.0), but isn't it a good idea to pick up a fresh  
> set of packages?

Yes, but the fact that the paths are different will force you to re- 
install system-wide packages anyway.(**)

> If Don has a copy of deldir in the system library, could this  
> behaviour be the result?

It should not, because install.packages won't touch any other  
locations than the one it is told to install the package into. It  
doesn't care if there are other versions around, either (AFAIK).

>> I remember that sometimes the script tries to change permissions  
>> of the .css file, which fails depending on your setup, but that's  
>> irrelevat for the package), but if a package is retained after  
>> installation it usaully indicates that the installation was  
>> successful, regardles of the exit status.
>>
>
> Indeed, I typically change the permissions of the R.css file
> ( /Library/Frameworks/R.framework/Resources/library/R.css ) to  
> allow Read & Write
> permissions by myself.

I may be wrong, but I think that the script actually tries to change  
the permissions to g-w, which it's not allowed to as non-root. In a  
sense it's good that the system prevents it from doing so :P

BTW: I think there may an unrelated bug indeed - for some strange  
reason my R.app adds ~/library/R to the library paths even if the  
preferences tell it to not do so - I'll investigate that...

Cheers,
Simon

(*) - technically the latest installer will actually touch all  
versions inside R.framework, namely setting the permissions to g+w.  
This is consistent with Apple's permissions concept and allows admin  
users to install system-wide package w/o root authentication. It  
won't change any content, though.
(**) - in order to allow retention of packages across patch-levels,  
there is in fact a symlink 2.1 in Versions in the CRAN release, but  
it's not used (yet).
(***) - I like those footnotes, don't you? ;)