[BioC] Installing Bioconductor in a multi-platform R installation

[Atro Tossavainen]

Hello Seth,

> > How can I force "getBioC()" to recreate the .so's for every platform?
> 
> One possibility is to not use getBioC().  Instead download the package 
> tarballs and install them with R CMD INSTALL.  This should force a 
> compile even if the package is already installed.

Will try, thanks.

> You might also try specifying the destdir parameter.  Given an empty 
> destdir, I'm hoping you'll get the behavior you want.

I'm sorry, but I can't see where there would be an empty destdir I
could use.

> > If I can avoid installing R and Bioconductor separately for each 
> > platform, I would very much like to do that.
> 
> Eh?  Haven't you already had to do this?  Given that the platforms are 
> not all binary compatible, I don't think there's any way to avoid this.

In a way, yes.  I've compiled everything separately on all the platforms
we use, then installed everything in the same place with just one copy
of the files that are identical across platforms and separate copies for
those that aren't, with AFS magic taking care of picking the right copy
of non-identical files on each platform.  (On AFS, you can use the @sys
macro that the client will expand to its own platform name at runtime
in file names.  Therefore, if "file" is a symlink to "file. at sys", the
client will look for, say, "file.i386_linux24", or "file.alpha_dux40",
or... you get the picture.)

> If it were me, I would go for the "disk space is cheap" notion and 
> spend time automating install scripts to make admin'ing all those 
> installs easier.

Disk space is cheap, but making sure that all of the separate installs
are up to the same level with add-on packages could potentially become
a major pain, which is why I try to do the same with anything I install
on AFS for multiple platforms.

-- 
Atro Tossavainen (Mr.)               / The Institute of Biotechnology at
Systems Analyst, Techno-Amish &     / the University of Helsinki, Finland,
+358-9-19158939  UNIX Dinosaur     / employs me, but my opinions are my own.
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