[BioC] Recent changes to Bioconductor packages

madman at jimmy.harvard.edu madman at jimmy.harvard.edu
Sat Mar 8 05:00:02 MET 2003

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.
March 06, 2003: annotate - Added function 'pmAbst2html' which will 
   take a list of pubMedAbst objects and create a simple web page. JG

March 06, 2003: annotate - added some functions to annotate to make getting 
   different identifiers more transparent. RG

March 06, 2003: modified graph -- fixed some bugs and made boundary, subGraph 
   and edges much faster. Added missing documentation. RG

Mar 05, 2003: Biobase - Added a function createpackage() for the 
       automatic creation of series of packages (e.g. cdf or ProbeTools 
       packages for Affymetrix chips) from a set of template R, src,
       and man files. These may contain @PLACEHOLDERS@ to be filled in
       at the runtime of createpackage(). - WH

Mar 05, 2003: tkWidgets/widgetTools - Put in a part in the first.lib 
              which if the user is using Windows and can not load 
              package 'tcltk', will point them to the R-Windows FAQ
              question 3.6 (on how to configure Tcl/Tk on their system),
              the  most common cause of the problem. (devel & release1.1) - JG

Mar 04, 2003: reposTools - Made the "versForce" option default to TRUE
              instead of FALSE.  This gets rid of the effect where it
              would not install .zip based packages on Windows if they
              were built under a diff version of R.  (devel & release1.1) - JG

Mar 04, 2003: annotate - added a 'pmid' slot to the pubMedAbst class - JG

Mar 04, 2003: Rgraphviz - added the 'neato' layout engine to the plots - JG

Mar 03, 2003: exprDB - some fixes to improve compiling under older (gcc 2.96)
        compilers. Under RH7.1 this appears to require <float.h> -- BE

Mar 01, 2003: affy - computeExprSet in Affybatch and expresso return
	an exprSet with an attribute 'pps.warnings'. method plot.ProbeSet.
	parameter 'scale' in barplot.ProbeSet... -- LG

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