[R-gui] GUI for require(package)!

[James Wettenhall]

Hi John,

Great work!

Yes I agree that it's not too difficult to provide a PACKAGES
file on a CD.  On the other hand, I do still like the idea
of having a GUI option to install a missing R package from an
aribtrary place on your hard disk, e.g. your desktop (without
necessarily having a PACKAGES file).  I'll look at your code
and think about this.  (Maybe this is coming from a Windows
point of view - unlike Mac, it's easy to have multiple R
installations, e.g. C:\rw1090\ and C:\rw1091\ , so you could
download an R package and install it within your R 1.9.0
installation but not your R 1.9.1 installation, and then later
decide that you want it in R 1.9.1)

In my R packages, I'm not sure if .onLoad() is the right place
to install _all_ missing R packages, because some of the
R packages are really only 'recommended' rather than
'required', i.e. a complete microarray analysis can be
performed using my GUI(s), without the 'recommended'
packages, as long as you don't choose the 'advanced' or
'extra-memory-hungry' normalization options.

So I would still like users to be able to run my GUIs without
some of the 'recommended' packages, but there are certainly
some packages which are critically required, so maybe they
could be installed in .onLoad() or .First.lib() if missing.
For the 'recommended' packages, .onLoad() should not fail if
they are unavailable, but it could give a warning.

Another thing which could be incorporated into this is
the new reposTools / install.packages2() / getBioC() methods of
installation for the case of Bioconductor packages.  This may
not be of general interest to people on this list, but obviously
I am interested in Bioconductor.  The advantage of the
Bioconductor package-installation methods, is that they try
to take care of dependencies automatically.  I would assume that
the "Install package(s) from Bioconductor" menu item in Rgui for
Windows, doesn't yet use this, i.e. it probably uses the
original install.packages() and a PACKAGES file.

For an example of dependencies, if my limmaGUI package depends
on limma, but I forget that limma depends on statmod, then if
limma is missing, install.packages2() in Bioconductor's
reposTools packages should automatically see that statmod is
required for limma, and find it on CRAN.

But the reposTools / install.packages2() method can be slow
sometimes, because it searches multiple repositories for an R
package.  This may be fixed now, but in the past, I found that
(using the default options), it often searched the wrong
repository first, e.g. CRAN instead of Bioconductor.

Jeff Gentry is the expert on reposTools, install.packages2(),
and getBioC().  He also has a widgetInvoke package on
Bioconductor which could be of interest to Gtk fans on this
mailing list.

Regards,
James