[R] Oddities upgrading from 2.4.1 to 2.5.0

[Chris Evans]

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    *