R help - Apr 2006 - Packages reappear for installation each time update.packages() is run

Hi,

Whenever I run update.packages() certain packages reappear over and over
again as packages to be updated. Specifically, the problems appear with
the packages gregmisc and gap:
> update.packages()
gregmisc :
 Version 2.0.7 installed in /usr/local/lib/R/library 
 Version 2.0.8 available at http://cran.dk.r-project.org
Update (y/N/c)?  n
gap :
 Version 1.0-3 installed in /usr/local/lib/R/library 
 Version 1.0-6 available at http://cran.dk.r-project.org
Update (y/N/c)?  n
XML :
 Version 0.97-8 installed in /usr/local/lib/R/library 
 Version 0.99-6 available at http://cran.dk.r-project.org
Update (y/N/c)?  n

Ignore the XML part. XML cannot be updated due to an old version of
libxml2.

Updates of gregmisc and gap complete succesfully. On the next
update.packages() they are update again...

I have no clue what causes this.

The system is a Red Hat Linux 9.0 system fully updated.

The R version is:

R : Copyright 2006, The R Foundation for Statistical Computing
Version 2.2.1 Patched (2006-03-13 r37533)
ISBN 3-900051-07-0

The problem has occurred consistently with a number of recent versions
of R, that I've had installed. The problem has been around with gregmisc
for a while but started to occur with gap fairly recently.

Uninstalling and reinstalling the packages does not remove the problem.

Best regards,

Bernt Guldbrandtsen
----------------------------------------------------------------------
Senior Researcher, Danish Institute of Agricultural Sciences
http://www.agrsci.dk, (45) 89 99 12 27

Both gregmisc and gap have been converted to package bundles and back 
again to single packages.  You need to remove them and all their 
constituent packages, and then reinstall gap (gregmisc is an empty shell 
now).  The problem is caused by the packages which the bundles once 
contained.

You should be able to fix gregmisc by

install.packages(c("gdata", "gtools", "gmodels",
gplots"))

(after which you no longer need gregmisc), but for gap you need to remove 
the former sub-packages and I not longer know what those are.


On Tue, 4 Apr 2006, Bernt Guldbrandtsen wrote:
> Hi,
>
> Whenever I run update.packages() certain packages reappear over and over
> again as packages to be updated. Specifically, the problems appear with
> the packages gregmisc and gap:
>
>> update.packages()
> gregmisc :
> Version 2.0.7 installed in /usr/local/lib/R/library
> Version 2.0.8 available at http://cran.dk.r-project.org
> Update (y/N/c)?  n
> gap :
> Version 1.0-3 installed in /usr/local/lib/R/library
> Version 1.0-6 available at http://cran.dk.r-project.org
> Update (y/N/c)?  n
> XML :
> Version 0.97-8 installed in /usr/local/lib/R/library
> Version 0.99-6 available at http://cran.dk.r-project.org
> Update (y/N/c)?  n
>
> Ignore the XML part. XML cannot be updated due to an old version of
> libxml2.
>
> Updates of gregmisc and gap complete succesfully. On the next
> update.packages() they are update again...
>
> I have no clue what causes this.
>
> The system is a Red Hat Linux 9.0 system fully updated.
>
> The R version is:
>
> R : Copyright 2006, The R Foundation for Statistical Computing
> Version 2.2.1 Patched (2006-03-13 r37533)
> ISBN 3-900051-07-0
>
> The problem has occurred consistently with a number of recent versions
> of R, that I've had installed. The problem has been around with
gregmisc
> for a while but started to occur with gap fairly recently.
>
> Uninstalling and reinstalling the packages does not remove the problem.
>
> Best regards,
>
> Bernt Guldbrandtsen
> ----------------------------------------------------------------------
> Senior Researcher, Danish Institute of Agricultural Sciences
> http://www.agrsci.dk, (45) 89 99 12 27
>
> ______________________________________________
> R-help at stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide!
http://www.R-project.org/posting-guide.html
>
-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595