[BioC] Sweave update

[Friedrich.Leisch@ci.tuwien.ac.at]

I have committed an Sweave update to the devel version of R (also
avaliable form the usual place at
http://www.ci.tuwien.ac.at/~leisch/Sweave) which should fulfill all
pending feature requests:

*) The major change is that the syntax is no longer hard-wirded, but
 can be specified by the user (OK, there is almost no docu for that,
 but the code is in place). I provide (in addition to noweb) a
 latex-style syntax which looks like

  \begin{Scode}{fig=TRUE}
  plot(1:10)
  \end{Scode}

 and is used if the input file has extension .[RS]tex, or if

  \SweaveSyntax{SweaveSyntaxLatex} 

 appears in the document (one can also use the command line or an
 option() to specify the default syntax). There is an example .Stex on
 the web page.

*) Code chunks can be reused, i.e.

 <<a>>=
 ...
 @

 <<c>>=
 ...
 <<a>>
 ...
 @

 works.

*) Hooks are now more compatible with the load hooks used by library() in
 the sense that they now should be stored in option("SweaveHooks"),
 which is a list of functions. A more general framework for handling
 hooks in R would of course help.

*) The user can define arbitrary options with the sole purpose of
 running the hooks associated with them. E.g., cleaning the workspace
 before running each code chunk could be done by defining a hook for
 option `clean' and having \SweaveOpts{clean=TRUE}. Probably we should
 start collecting useful hooks and include them in the standard
 distribution.

The only thing that is really missing is proper testing (due to lack
of time)... so please don't kill me if I have introduced a number of
serious bugs. Bioconductor has the largest collection of .Rnw files
not written by me ... so package checking there will probably soon
put the code under test :-)

Best,
Fritz