[BioC] Recent changes to Bioconductor packages

[madman at jimmy.harvard.edu]

This is an automated message sent out weekly to report recent changes
to Bioconductor packages.  Please see the URL 
http://www.bioconductor.org/changelog.html for a complete history of 
changes.  Unless otherwise noted, these changes apply to the developmental
packages only.
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21 Dec 2003: graph  1.2.2.  LG
     new function 'write.tlp()' to save graphs in the Tulip software
     file format.

21 Dec 2003: affypdnn 0.3-1.  LG
     Recent bug in expression value computations (following a round
     of optimization, it was returning all NAs). Fixed
 
20 Dec 2003: limma 1.3.9.  GKS
     - new function getSpacing()
	 - upgrades to printorder() to accommodate spacing by rows or topbottom
	 - corrections and updates to try to pass R CMD check in R1090dev, but
	   cannot get around that package nlme seems to be broken.

22 Dec 2003: ontoTools 1.2.1 VJC
     - namedSparse class revised to reduce indirections -- indexing environments
           jettisoned for simpler vector-based calculations
     - data elements updated to include version tag, using GO 1.4
     - examples/ontoTools vignette updated to work with new data elements
     - ontoToolsArchiving.Rnw vignette added to illustrate how stored
           access mats, concept probabilities are computed