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

M. Edward (Ed) Borasky znmeb at cesmail.net
Sun Dec 17 07:35:14 CET 2006

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)

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

More information about the Bioc-devel mailing list