Thanks for all the responses.
I have successfully put R-devel up on a machine, and then installed the
shortread package. To start, I was trying to have a local library with the
add-ons, working with the installed R base on a shared server. This was not a
straightforward exercise.
A suggestion: much of my confusion was due to the fact that there were not
any
manual pages for biocLite, bioinstall, etc; or at least no documentation that I
easily found. So I tried the standard R install (no luck), and various other
fruitless paths based on wrong guesses. Sean's explanation of why biocLite
does
what it does was helpful; I'd already guessed some of it by reading source
code.
Perhaps the standard install of biocLite could finish with a message pointing
one to a short 1-2 paragraph overview. When it works biocLite is nice, but
when it doesn't there isn't much hint of where to begin. It consistently
ignored my "lib" directive, for instance. And from my reading of the source
code it wouldn't have helped in the end if it had paid attention -- there is,
is
there not, an assumption that the "stubs" are in an include directory in the R
home tree, not the user's?
I anticipate that the Solexa, and the threat of a couple more coming in soon,
will accelerate my familiarity with bioconductor. The shortread package
already
has repaid with interest for these install nuisances.
Terry T.
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