[BioC] Biobase/reposTools Dependency

[Colin A. Smith]

I am looking into using Bioconductor as a slave batch processor for 
other programs. (BASE, other web tools, etc.) I've found that when 
using Bioconductor for the statistical analysis, a majority of the CPU 
time gets spent just loading it and not on the actual computation, 
which seems like a waste. This added overhead makes providing 
reasonably interactive output to the user difficult. While it might be 
possible to set up some sort of persistent R session that gets used, 
I'd rather reduce the complexity and just run R anew for each analysis.

Breaking the dependency of Biobase on reposTools strikes me as a 
particularly effective way to optimize the load sequence. They both 
take a long time to load relative to the loading of R itself. (This 
seems to stem mostly from the use of methods. Profiling shows that 60% 
of CPU time gets spent in setMethod while loading reposTools.)

While it's nice to be able to automagically download and install R 
libraries, the overwhelming majority of R sessions probably don't use 
this. (Especially if the R library directory isn't owned by the current 
user. The warning that pops up when this happens is another 
annoyance...) Is there some other showstopping reason for Biobase 
depending on reposTools?