[Bioc-devel] biocLite.R has been modified (BiocInstaller package)

[Kasper Daniel Hansen]

Dan et al.

I have not looked at the new package, but since you seem to be
actively working on it, I want to shoot of an old suggestion of mine:
I think we need a function called something like
  checkBiocVersion
or whatever.  It would do the following
1) identify which version of Bioc a given R version should be using
2) go through either all installed packages or all loaded packages and
check the installed package version against the version of
Bioconductor.  It should both report packages that are old as well as
packages that are too new (in case the user has installed package not
from biocLite).

Such a function would be invaluable in helping people on the email
list I think.  We have had many cases where package versions are
either too new or too old compared to "what they should be".

Sorry I am not providing an alpha version, but I wanted to put in my
wishlist when you are actively working on it as opposed to weeks from
now.

And this functionality might exists in the new package; as I said I
have suggested it before and I have not looked at the new code.

Kasper

On Sat, Aug 20, 2011 at 4:38 PM, Dan Tenenbaum <dtenenba at fhcrc.org> wrote:
> Hi all,
>
> Our new package for installing packages, BiocInstaller, is now used by
> default (in recent versions of R-devel) when you:
>
> source("http://bioconductor.org/biocLite.R")
>
> As mentioned below, a major difference is that now, the biocLite()
> function will attempt to update out-of-date packages. You can control
> this behavior; see the documentation:
>
> ?biocLite
>
> for more information.
>
> Please let us know on this list if you have questions, concerns, or issues.
>
> Thanks,
> Dan
>
>
>
> ---------- Forwarded message ----------
> From: Martin Morgan <mtmorgan at fhcrc.org>
> Date: Tue, Jun 14, 2011 at 3:21 PM
> Subject: [Bioc-devel] Updated biocLite -- please try!
> To: "bioc-devel at stat.math.ethz.ch" <bioc-devel at stat.math.ethz.ch>
>
>
> Hi BiocDevelopers --
>
> As mentioned previously, we have revised how biocLite works. Please try
>
>   source("http://bioconductor.org/scratch-repos/biocLite.R")
>
> and then installing your favorite package
>
>  biocLite("MyFavoritePackage")
>
> The 'source()' command will download, install (first time only!) and
> load the 'BiocInstaller' package.
>
> biocLite does behave differently. It'll check for out-of-date packages
> and ask, after installing MyFavoritePackage, whether you'd like to
> update them. With no arguments, biocLite() installs just Biobase,
> IRanges, and AnnotationDbi. biocLite(character()) will look for
> out-of-date packages to update. And ?biocLite will provide a help
> page(!).
>
> The revised behavior should only occur in the 'devel' version of R,
> R-2.13 should behave as before.
>
> Any feedback most welcome.
>
> Martin
> --
> Computational Biology
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109
>
> Location: M1-B861
> Telephone: 206 667-2793
>
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