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

stefano iacus stefano.iacus at unimi.it
Fri Apr 29 00:59:21 CEST 2005

It seems clear to be clear to Don, but probably other users will be 
interested to know this:  when upgrading to a major version of R like 
from 2.0.x to 2.1.0 it is not an option to re-install fresh packages as 
most of the package contain DLL's linked against libR.dylib, and entry 
points/symbols are stable (inside libR.dylib) only inside each major 
version of R (i.e. packages built for R 2.0.0 works with R 2.0.1, but 
not with R 2.1.x)

On 28/apr/05, at 23:04, Simon Urbanek wrote:

> 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? ;)
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