[Bioc-devel] Sweave changes (keep.source = TRUE or FALSE?)

Duncan Murdoch murdoch at stats.uwo.ca
Sun Dec 17 03:56:12 CET 2006

On 12/16/2006 7:22 PM, M. Edward (Ed) Borasky wrote:
> As is my "tradition", I'm about to take a holiday break from my "day 
> job" and work on my own personal open source projects. Not entirely by 
> coincidence, this year's project involves literate programming, 
> reproducible research, R, Sweave, NoWeb, LyX, and some other tools, most 
> notably the Ruby "scripting language" and SWIG. It's a rather ambitious 
> project, given how little free time I have, but I'm hoping to at least 
> get the infrastructure in place by mid-March.
> As a result, I don't have an "existing code base" for changes to Sweave 
> to force changes in, but I very much want to be able to build code in 
> the next week or so that's going to work both with the current R 2.4.0  
> and future versions of R, with as much "agility" and "pragmatic project 
> automation", to use the concepts I'm picking up from the Ruby world, as 
> possible. So how should I proceed?
> Should I download the R-devel source and build around that, knowing that 
> between now and mid-March there will be a lot of change? Or should I 
> stick with R 2.4.0, knowing that one of the core areas of the project is 
> going to change in R? Or should I drop the whole idea and tackle a less 
> ambitious project? :)

1.  Don't use 2.4.0, version 2.4.1 will be released on Monday.

2.  There will not be a lot of change from 2.4.1 to 2.5.0.  R changes 

3.  If you want to maintain comments and formatting in your source code 
in Sweave, then use R-devel and turn on the option.  If you don't care, 
then it doesn't matter which version you use.  If you hate the idea of 
displaying your formatting and comments, then turn off the option. (This 
works in 2.4.0, which won't even blink when you turn off the 
non-existent option.)

4.  If you had some other "core idea of the project" in mind, then you 
should say more explicitly what it is.  I don't think the new Sweave 
capability changes a core idea of the project, but I think that's what 
you were talking about.

Duncan Murdoch

> To clarify (I hope) why I'm asking these questions, you can get an old 
> partial description of the project at the RubyForge repository. 
> Unfortunately, the web interface seems to be down, but the anonymous CVS 
> is working.
> $ cvs -d :pserver:anonymous at rubyforge.org:/var/cvs/cougar checkout 
> Rameau/Rameau.pdf

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