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

[M. Edward (Ed) Borasky]

Duncan Murdoch wrote:
> 1.  Don't use 2.4.0, version 2.4.1 will be released on Monday.
Ah ... OK. I just notified the good folks at Gentoo about that. I've 
been off the mailing lists.
> 2.  There will not be a lot of change from 2.4.1 to 2.5.0.  R changes 
> slowly.
IIRC the R releases usually happen in April and October. My 0.99 release 
will probably be in March, so I may need to work with 2.4.1 unless I 
want to wait and sync up with 2.5. I think I'll try R-devel first just 
to get used to the new Sweave behavior.
> 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.)
I don't have any personal preferences, but in general more options are 
welcome in this area. I think I'll start with R-devel and see how it works.
> 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.
The core idea is that reproducible research should be easy. And R 
already does most of what I want to do -- what I want to add is a 
collection of workflow management and project automation tools built in 
Ruby. I also want to add symbolic computation capabilities, but right 
now I'm leaning towards just integrating Axiom rather than using a 
library, because Axiom also has literate programming tools built in.

-- 
M. Edward (Ed) Borasky, FBG, AB, PTA, PGS, MS, MNLP, NST, ACMC(P)
http://borasky-research.blogspot.com/

If God had meant for carrots to be eaten cooked, He would have given rabbits fire.