[BioC] New version of annaffy

[Colin A. Smith]

After languishing for about 9 months, I have finished a new version of 
annaffy. It represents almost a complete rewrite including:

- separation of data retrieval and HTML/text generation
- better options for interfacing with web databases from the R console
- more powerful ways of including user data
- a vignette (annaffy is now fully Bioconductor compliant)
- updated for use with the version 1.2.6 affy data packages
- more robust and expandable data structures
- pervasive use of S4 classes and methods
- stronger typing (no more NULL or NA, empty objects or vectors are 
used instead)

I'm calling this version 0.8. My tentative release schedule consists of 
a feature freeze at 0.9 in about 2-3 weeks and 1.0 shortly thereafter, 
following a short but hopefully rigorous QA period.

Package download:
http://genome.nasa.gov/downloads/annaffy_0.8.tar.gz
(Make sure to install the GO and KEGG data packages as well)

A rough version of the vignette:
http://genome.nasa.gov/downloads/annaffy.pdf

Sample output from the vignette:
http://genome.nasa.gov/downloads/example2.html

I would appreciate any and all positive or negative comments, feature 
requests, and bug reports regarding the package itself, the 
documentation, or coding.

Thanks.

-Colin