[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.
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Apr 26 2003: limma - imported version 1.0. GKS

Apr 25 2003: data packages - new data packages (1.2.1) constructed with 
        several changes:
        1. Any occurrence of AFFY has been replaced by PROBE to make the 
           term generic.
        2. Mappings to GO ids become a named vector with the name(s) being 
           the evidence code(s) provided by NCBI.
        3. Values of GOXXPARENTS in GO package also become named vectors 
           with the names being either isa or partof to indicate the 
           relations of GO ids to their parents.
        4. GO package includes GOXXCHILDREN to allow for search for direct 
           children and GOCATEGORY for grouping (to MF, BP, and CC)
        5. Dependance of Biobase removed. JZ
  
Apr 25 2003: reposTools - pathed the release 1.1 branch version of 
        reposTools to account for the bug fixes and updates to the
        package from the development branch over the last month.  JG

Apr 24 2003: Iyer517 -- new package 0.1 ... time course experiment from
	Science 1999 paper of Iyer in Eisen lab.  Includes vignette.
	May be ready for release VJC

Apr 24 2003: affy - The default background adjustment given by the rma() 
	function has been changed so that it agrees with the results of 
	expresso. If you wish to enable the previous behaviour use 
	bgversion=1 in your rma() call. The function just.rma() has 
	also been adjusted accordingly.  BMB

Apr 25 2003: limma 0.9.7 - new package - Linear Models for Microarray Data.
     Data analysis, linear models and differential expression for spotted
	 and oligonucleotide microarrays. GKS

Apr 24 2003: reposTools - Fixed several bugs, primarily one in which
     the system was not always checking that the version of the package
     available was newer than the current installation of a package. JG

Apr 23 2003: reposTools - Fixed a bug in the dependency checking routines,
     which would appear if a user maintained multiple libraries of R
     packages.  The system would only check for dependency resolution
     in the same library directory that the package was being installed to.
     It now checks .libPaths().  JG

Apr 22 2003: Rgraphviz - Graphs can be plotted w/ twopi layout method
     even if not fully connected. JG

Apr 22 2003: tkWidgets - a new function - DPExplorer - added. The function 
     allow users to explore a Bioconductor data package using an 
     interactive widget. JZ

Apr 22 2003: Rgraphviz - set up Rgraphviz to use stored images for generic
     and method code via install.R much like the Ruuid package.  JG

Apr 22 2003: reposTools - The default action when one specifies repositories
     manually is to no longer attach any repositories from the R options.
     This can be forced via 'searchOptions=TRUE'.  Furthermore, when
     repositories are manually specified, the system will *not* honor
     previous repository information during updates.  JG

Apr 20 2003: ROC no longer requires Biobase