[Bioc-devel] Recent changes to geneplotter in BioC 2.4 and R >= 2.9 RC

Patrick Aboyoun paboyoun at fhcrc.org
Thu Apr 16 20:36:09 CEST 2009

Hello fellow developers,
Three functions from geneplotter (smoothScatter, panel.smoothScatter, 
and densCols) have recently been promoted to "base" R starting with R 
2.9 RC due to their usage beyond the Bioconductor sphere. As such, these 
three functions were removed from geneplotter on 15 April and the 
following packages have been modified to use smoothScatter, 
panel.smoothScatter, and/or densCols from R 2.9 RC graphics, lattice, 
and grDevices respectively:

affy, affyPLM, affyQCReport, arrayQualityMetrics, beadarray, cellHTS, 
cellHTS2, flowCore, flowViz, GGBase, GGexplorer, GGtools, lumi, maDB, 
oligo, ppiStats, prada, Ringo, spkTools, tilingArray, vsn, XDE, yaqcaffy

Today's builds are in


and if you wish to use these new packages you must upgrade to R 2.9 RC 
or R-devel since geneplotter no longer contains the functions mentioned. 
For those interested in seeing package interdependence trimmed down, 
this change reduced the number of packages that Depends/Imports/Suggests 
geneplotter from 23 packages down to 9 packages.

Just as a reminder,  BioC 2.4 release is scheduled for release 21 April 
so check your check-ins using R 2.9 RC to ensure you haven't 
inadvertently introduced a problem.


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