On Wed, 30 Aug 2006, Henrik Bengtsson wrote:
> [Cross-posting to BioC-devel to]
>
> Thank you for this.
>
> > The changes are internal but extensive. All packages that use S4
> > methods and classes need to be reinstalled from source to use the new
> > version.
>
> Is there an easy way to detect if a package is using S4 or not? If
Yes, look at the Depends field of the DESCRIPTION
a <- installed.packages()
aa <- as.vector(a[grep("methods", a[, "Depends"]), 1])
install.packages(aa)
If you want to install them in the same place as before, do this for each
library in turn.
I'd hold off for a few days if you can: some packages will not yet
reinstall.
> so, I could scan my already installed libraries and call
> install.packages() on its S4 subset of packages. The alternative is
> to do install.packages() an all libraries (sic!). Bioconductor: maybe
> biocLite() could have such an update mechanism built in internally?
>
> If I miss to reinstall one S4 package, what should I expect? I assume
> there will be an error, but I just want to confirm that there is no
> risk of getting weird "results" but still a running program?
>
> Reinstallation is also required for all package that comes as Windows
> binaries, correct?
Correct, and from source at that since Uwe is not yet building packages
under R-devel (and his '2.4' is really 2.3, as I understand it).
--
Brian D. Ripley, [EMAIL PROTECTED]
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
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