[R] Oddities upgrading from 2.4.1 to 2.5.0

Gabor Grothendieck ggrothendieck at gmail.com
Sun May 13 18:24:00 CEST 2007

Using movedir.bat or copydir.bat from batchfiles:


you can move or copy your old packages over to the new R tree.
It won't overwrite any so you can do that even after you have
installed some by some other method such as that you describe
below.  Once you have moved or copied them over you can do
an update just to be sure.  See the README file for details.

On 5/13/07, Chris Evans <chris at psyctc.org> wrote:
> I'm working on Windoze XP and have for some time installed R in D:\R and
>  upgraded my packages after installing the new version of R with a bit
> of code I think I got from the list:
> ip <- installed.packages(lib.loc = "d:\\R\\R-2.4.1\\library")
> ip <- ip[ip[,1]!="base" ,1]
> install.packages(ip)
> This time around that's produced some warning grumbles:
> Warning messages:
> 1: packages 'dynamicGraph', 'ggplot', 'grid', 'Qtoolbox', 'ref',
> 'splines', 'stats4', 'tapiR', 'tcltk', 'tools' are not available
> 2: dependencies 'Design', 'graph', 'RBGL' are not available
> Sure enough, those in warning 1 were all in the 2.4.1 library directory
> tree and those in warning 2 weren't.  Now I'm trying to work out how
> these failures have happened.
> I think some of this could be because of a problem with the mirrors
> (though I've tried both UK(London) and Switzerland(Zurich)).  I have
> seen the posting saying that there are problems.  I also think some
> could be because I may have installed some packages under 2.4.1 which
> didn't come from CRAN but I didn't keep careful records stupidly.
> Anyway, looking at http://cran.r-project.org/ packages I think that:
> 'dynamicGraph', 'ggplot', 'ref', 'stats4' and 'Design' should all be
> there for me to install with install.packages() but they're definitely
> not at UK(London) or Switzerland(Zurich).
> Searching a bit I can see that Qtoolbox was a non-CRAN package I
> installed directly.
> However, I still seem to have created some warnings here that searching
> the R site search isn't answering for me.
> Two questions/suggestions:
> 1) is there a list somewhere of packages/libraries that were once in R
> but aren't now?
> 2) is there a way of checking for missing dependencies that will
> identify both what's missing (clearly something like this is producing
> warning 2 following my call of "install.packages(ip)") but might also
> produce a list of the origins of the dependencies?
> Sorry if these are trivial issues.
> TIA,
> Chris
> --
> Chris Evans <chris at psyctc.org> Skype: chris-psyctc
> Professor of Psychotherapy, Nottingham University;
> Consultant Psychiatrist in Psychotherapy, Notts PDD network;
> Research Programmes Director, Nottinghamshire NHS Trust;
> Hon. SL Institute of Psychiatry, Hon. Con., Tavistock & Portman Trust
> *If I am writing from one of those roles, it will be clear. Otherwise*
> *my views are my own and not representative of those institutions    *
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