base R packages conflicting with CRAN packages

[Brook Milligan <brook%nmsu.edu@localhost>]

I have identified a case in which the math/R package installs a recommended package (in this case survival v2.39.5) that is not a new enough version to satisfy the needs of another package, which needs survival v2.40.1.  Because survival is installed with the base R package it is impossible to replace it with a newer R-survival package because they would inevitably conflict.  This is not a case of R being old, as pkgsrc installs the most recent release.  Instead, it is a case of the version of survival recommended by base R being older than the most recent survival package available from CRAN.

How should this be handled?  Must we turn all the packages otherwise installed by base R into individual packages so that they can be upgraded as needed independently of base R?  If so, how do we prevent pkgsrc from installing the recommended set of packages along with R?What other options are there?

Thanks for your input.

Cheers,
Brook