[R-gregmisc-users] SF.net SVN: r-gregmisc: [1008] trunk/gplots

[<wa...@us...>]

Revision: 1008
          http://svn.sourceforge.net/r-gregmisc/?rev=1008&view=rev
Author:   warnes
Date:     2006-11-14 10:07:31 -0800 (Tue, 14 Nov 2006)

Log Message:
-----------
Update ChangeLog and NEWS files for release 2.3.2.

Modified Paths:
--------------
    trunk/gplots/ChangeLog
    trunk/gplots/NEWS

Modified: trunk/gplots/ChangeLog
===================================================================
--- trunk/gplots/ChangeLog	2006-11-14 17:59:51 UTC (rev 1007)
+++ trunk/gplots/ChangeLog	2006-11-14 18:07:31 UTC (rev 1008)
@@ -1,200 +1,262 @@
+2006-11-14 17:56  warnes
+
+	* man/heatmap.2.Rd: Correct problem with labeled correlation matrix
+	  example. Thanks to Jean Vidal for reporting the error..
+
+2006-08-02 22:21  warnes
+
+	* trunk/BalloonPlotPaper/BalloonPlot.pdf,
+	  trunk/BalloonPlotPaper/BalloonPlot.tex,
+	  trunk/MSOfficeUtil/DESCRIPTION,
+	  trunk/PathwayModeling/thesispaper/slides.tex,
+	  trunk/RMCMC/DESCRIPTION, trunk/RMCMC/man/make.density.Rd,
+	  trunk/Rlsf/DESCRIPTION, trunk/Rlsf/man/lsf.numcpu.Rd,
+	  trunk/Rlsf/man/lsf.parRapply.Rd, trunk/Rlsf/man/scat.Rd,
+	  trunk/bwRF/DESCRIPTION, trunk/bwRF/man/RF.Rd,
+	  trunk/exp.ssize/inst/doc/ssize.pdf,
+	  trunk/exp.ssize/inst/doc/ssize.tex, trunk/fork/DESCRIPTION,
+	  trunk/fork/man/exit.Rd, trunk/fork/man/fork.Rd,
+	  trunk/fork/man/getpid.Rd, trunk/fork/man/kill.Rd,
+	  trunk/fork/man/signame.Rd, trunk/fork/man/wait.Rd,
+	  trunk/gdata/inst/doc/gregmisc.tex,
+	  trunk/gdata/man/ConvertMedUnits.Rd,
+	  trunk/gdata/man/aggregate.table.Rd, trunk/gdata/man/combine.Rd,
+	  trunk/gdata/man/interleave.Rd, trunk/gdata/man/matchcols.Rd,
+	  trunk/gdata/man/nobs.Rd, trunk/gdata/man/read.xls.Rd,
+	  trunk/gdata/man/rename.vars.Rd, trunk/gdata/man/reorder.Rd,
+	  trunk/gdata/man/trim.Rd, trunk/gdata/man/unmatrix.Rd,
+	  trunk/gdata/man/upperTriangle.Rd,
+	  trunk/gmodels/man/fast.prcomp.Rd,
+	  trunk/gmodels/man/fit.contrast.Rd, trunk/gmodels/man/glh.test.Rd,
+	  trunk/gmodels/man/make.contrasts.Rd, inst/doc/BalloonPlot.pdf,
+	  man/balloonplot.Rd, man/bandplot.Rd, man/boxplot.n.Rd,
+	  man/colorpanel.Rd, man/hist2d.Rd, man/ooplot.Rd, man/overplot.Rd,
+	  man/plot.lm2.Rd, man/plotCI.Rd, man/plotmeans.Rd,
+	  man/residplot.Rd, man/sinkplot.Rd, man/smartlegend.Rd,
+	  man/space.Rd, man/textplot.Rd, man/wapply.Rd,
+	  trunk/gregmisc/DESCRIPTION,
+	  trunk/gregmisc/gregmisc/DESCRIPTION.standalone,
+	  trunk/gregmisc/inst/doc/gregmisc.tex,
+	  trunk/gtools/man/addLast.Rd, trunk/gtools/man/assert.Rd,
+	  trunk/gtools/man/capture.Rd, trunk/gtools/man/combinations.Rd,
+	  trunk/gtools/man/defmacro.Rd, trunk/gtools/man/dirichlet.Rd,
+	  trunk/gtools/man/foldchange.Rd, trunk/gtools/man/invalid.Rd,
+	  trunk/gtools/man/logit.Rd, trunk/gtools/man/mixedsort.Rd,
+	  trunk/gtools/man/oddeven.Rd, trunk/gtools/man/permute.Rd,
+	  trunk/gtools/man/quantcut.Rd, trunk/gtools/man/running.Rd,
+	  trunk/gtools/man/scat.Rd, trunk/gtools/man/setTCPNoDelay.Rd,
+	  trunk/nws/DESCRIPTION, trunk/qvalue/DESCRIPTION,
+	  trunk/qvalue/man/print.qvalue.Rd, trunk/ssize/DESCRIPTION,
+	  trunk/ssize/man/pow.Rd: Update my email address
+
+2006-06-26 21:08  nj7w
+
+	* R/heatmap.2.R: Fixed a bug which displayed warnings when Rowv and
+	  Colv were specified as dendrograms
+
+2006-03-10 17:24  warnes
+
+	* tests/heatmap2Test.R: Remove code that added a local path
+
+2006-03-09 22:53  nj7w
+
+	* tests/heatmap2Test.R, tests/heatmap2Test.Rout.save: Added the
+	  correct library path where gplots is installed locally and
+	  corresponding .save file
+
+2006-03-09 22:40  nj7w
+
+	* tests/heatmap2Test.R: Updated the tests file
+
+2006-03-09 22:39  nj7w
+
+	* R/heatmap.2.R: Removed the condition Colv != Rowv as it has
+	  already been taken care of
+
+2006-03-09 22:17  nj7w
+
+	* rtPCR.rda: Deleted rtPCR.rda from the main directory
+
+2006-03-09 22:09  nj7w
+
+	* ChangeLog: Added ChangeLog
+
+2006-03-07 18:18  nj7w
+
+	* DESCRIPTION, NEWS: Updated ChangeLog and NEWS
+
+2006-03-07 18:10  nj7w
+
+	* tests, tests/heatmap2Test.R, tests/heatmap2Test.Rout.save: Added
+	  the tests and fixed corrupted files
+
 2006-03-07 16:22  nj7w
 
-	* trunk/gplots/data/rtPCR.rda: Replaced the corrupted rtPCR.rda
-	  file in data directory
+	* data/rtPCR.rda: Replaced the corrupted rtPCR.rda file in data
+	  directory
 
 2006-03-07 16:14  nj7w
 
-	* trunk/gplots/tests: Removed the corrputed tests directory
+	* tests: Removed the corrputed tests directory
 
 2006-03-07 16:12  nj7w
 
-	* trunk/gplots/data/rtPCR.rda, trunk/gplots/rtPCR.rda: Replaced
-	  the corrupted rtPCR.rda file in data directory
+	* data/rtPCR.rda, rtPCR.rda: Replaced the corrupted rtPCR.rda file
+	  in data directory
 
 2006-03-03 21:03  nj7w
 
-	* trunk/gplots/R/heatmap.2.R, trunk/gplots/man/heatmap.2.Rd:
-	  Updated the code and man page to make sure the Rowv and Colv
-	  values are properly handled
+	* R/heatmap.2.R, man/heatmap.2.Rd: Updated the code and man page to
+	  make sure the Rowv and Colv values are properly handled
 
 2006-03-02 21:43  warnes
 
-	* trunk/gplots/R/balloonplot.R: Adjust row total placement to
-	  adjust for width of the totals
+	* R/balloonplot.R: Adjust row total placement to adjust for width
+	  of the totals
 
 2006-03-02 21:26  warnes
 
-	* trunk/gplots/DESCRIPTION, trunk/gplots/R/balloonplot.R,
-	  trunk/gplots/man/1: Row totals in ballonplot were in reverse
-	  order. Fixed.
+	* DESCRIPTION, R/balloonplot.R, man/1: Row totals in ballonplot
+	  were in reverse order. Fixed.
 
 2006-02-23 22:00  nj7w
 
-	* trunk/gplots/R/heatmap.2.R, trunk/gplots/tests/heatmap2Test.R:
-	  Add ability to scale the color key using the new 'keysize'
-	  argument.
+	* R/heatmap.2.R, tests/heatmap2Test.R: Add ability to scale the
+	  color key using the new 'keysize' argument.
 
 2006-02-23 21:34  nj7w
 
-	* trunk/gplots/tests, trunk/gplots/tests/heatmap2Test.R,
-	  trunk/gplots/tests/heatmap2Test.Rout.save: Add tests for
-	  heatmap.2
+	* tests, tests/heatmap2Test.R, tests/heatmap2Test.Rout.save: Add
+	  tests for heatmap.2
 
 2006-02-23 21:25  nj7w
 
-	* trunk/gplots/inst/doc/Figure1.eps,
-	  trunk/gplots/inst/doc/Table.eps, trunk/gplots/inst/doc/bka.bst,
-	  trunk/gplots/inst/doc/heatmap2.R,
-	  trunk/gplots/inst/doc/heatmap2.tex,
-	  trunk/gplots/inst/doc/regression_rank_image.Rda,
-	  trunk/gplots/inst/doc/regression_rank_image_II.Rda: Move heatmap
-	  and ballonplot paper source materials to their respective cvs
-	  modules
+	* inst/doc/Figure1.eps, inst/doc/Table.eps, inst/doc/bka.bst,
+	  inst/doc/heatmap2.R, inst/doc/heatmap2.tex,
+	  inst/doc/regression_rank_image.Rda,
+	  inst/doc/regression_rank_image_II.Rda: Move heatmap and
+	  ballonplot paper source materials to their respective cvs modules
 
 2006-02-23 21:20  nj7w
 
-	* trunk/gplots/inst/doc/BalloonPlot.R,
-	  trunk/gplots/inst/doc/BalloonPlot.tex,
-	  trunk/gplots/inst/doc/Figure1.pdf,
-	  trunk/gplots/inst/doc/Figure2.pdf,
-	  trunk/gplots/inst/doc/Figure3.pdf,
-	  trunk/gplots/inst/doc/Figure4.pdf,
-	  trunk/gplots/inst/doc/Rnews.sty,
-	  trunk/gplots/inst/doc/SurvivedPop.pdf,
-	  trunk/gplots/inst/doc/SurvivedPopWhite.pdf,
-	  trunk/gplots/inst/doc/SurvivedProp.pdf,
-	  trunk/gplots/inst/doc/TotalPop.pdf: Moved balloonplot paper
-	  materials to BallonPlotPaper cvs module
+	* inst/doc/BalloonPlot.R, inst/doc/BalloonPlot.tex,
+	  inst/doc/Figure1.pdf, inst/doc/Figure2.pdf, inst/doc/Figure3.pdf,
+	  inst/doc/Figure4.pdf, inst/doc/Rnews.sty,
+	  inst/doc/SurvivedPop.pdf, inst/doc/SurvivedPopWhite.pdf,
+	  inst/doc/SurvivedProp.pdf, inst/doc/TotalPop.pdf: Moved
+	  balloonplot paper materials to BallonPlotPaper cvs module
 
 2006-02-23 21:18  nj7w
 
-	* trunk/gplots/inst/doc/colSeparator.pdf,
-	  trunk/gplots/inst/doc/logData.pdf,
-	  trunk/gplots/inst/doc/logDataColDendrogram.pdf,
-	  trunk/gplots/inst/doc/logDataColOrd.pdf,
-	  trunk/gplots/inst/doc/logDataColOrdNo.pdf,
-	  trunk/gplots/inst/doc/logDataRowDendrogram.pdf,
-	  trunk/gplots/inst/doc/origScale.pdf,
-	  trunk/gplots/inst/doc/rowSeparator.pdf,
-	  trunk/gplots/inst/doc/scaled.pdf: Remove heatmap paper files and
-	  move them to the HeatmapPaper cvs module.
+	* inst/doc/colSeparator.pdf, inst/doc/logData.pdf,
+	  inst/doc/logDataColDendrogram.pdf, inst/doc/logDataColOrd.pdf,
+	  inst/doc/logDataColOrdNo.pdf, inst/doc/logDataRowDendrogram.pdf,
+	  inst/doc/origScale.pdf, inst/doc/rowSeparator.pdf,
+	  inst/doc/scaled.pdf: Remove heatmap paper files and move them to
+	  the HeatmapPaper cvs module.
 
 2006-02-23 19:57  nj7w
 
-	* trunk/gplots/inst/doc/colSeparator.pdf,
-	  trunk/gplots/inst/doc/logData.pdf,
-	  trunk/gplots/inst/doc/logDataColDendrogram.pdf,
-	  trunk/gplots/inst/doc/logDataColOrd.pdf,
-	  trunk/gplots/inst/doc/logDataColOrdNo.pdf,
-	  trunk/gplots/inst/doc/logDataRowDendrogram.pdf,
-	  trunk/gplots/inst/doc/origScale.pdf,
-	  trunk/gplots/inst/doc/rowSeparator.pdf,
-	  trunk/gplots/inst/doc/scaled.pdf: Added figures for heatmap2
-	  paper
+	* inst/doc/colSeparator.pdf, inst/doc/logData.pdf,
+	  inst/doc/logDataColDendrogram.pdf, inst/doc/logDataColOrd.pdf,
+	  inst/doc/logDataColOrdNo.pdf, inst/doc/logDataRowDendrogram.pdf,
+	  inst/doc/origScale.pdf, inst/doc/rowSeparator.pdf,
+	  inst/doc/scaled.pdf: Added figures for heatmap2 paper
 
 2006-02-23 19:54  nj7w
 
-	* trunk/gplots/inst/doc/regression_rank_image.Rda,
-	  trunk/gplots/inst/doc/regression_rank_image_II.Rda: Added the
-	  .Rda files for the heatmap2 paper
+	* inst/doc/regression_rank_image.Rda,
+	  inst/doc/regression_rank_image_II.Rda: Added the .Rda files for
+	  the heatmap2 paper
 
 2006-02-23 19:52  nj7w
 
-	* trunk/gplots/inst/doc/heatmap2.tex: Added the source - (tex
-	  file) of the heatmap paper
+	* inst/doc/heatmap2.tex: Added the source - (tex file) of the
+	  heatmap paper
 
 2006-02-23 19:51  nj7w
 
-	* trunk/gplots/inst/doc/heatmap2.R: Added the code for the figures
-	  of heatmap paper
+	* inst/doc/heatmap2.R: Added the code for the figures of heatmap
+	  paper
 
 2006-02-21 22:19  nj7w
 
-	* trunk/gplots/R/heatmap.2.R, trunk/gplots/man/heatmap.2.Rd: Minor
-	  updates to heatmap.2 - fixed Rowv, Colv and dendrogram
-	  behaviour. Now Rowv=NULL or FALSE both imply no dendrogram
-	  computation.
+	* R/heatmap.2.R, man/heatmap.2.Rd: Minor updates to heatmap.2 -
+	  fixed Rowv, Colv and dendrogram behaviour. Now Rowv=NULL or FALSE
+	  both imply no dendrogram computation.
 
 2006-01-12 23:10  warnes
 
-	* trunk/gplots/inst/doc/BalloonPlot.R,
-	  trunk/gplots/inst/doc/BalloonPlot.pdf,
-	  trunk/gplots/inst/doc/BalloonPlot.tex,
-	  trunk/gplots/inst/doc/Figure1.pdf,
-	  trunk/gplots/inst/doc/Figure2.pdf,
-	  trunk/gplots/inst/doc/Figure3.pdf,
-	  trunk/gplots/inst/doc/Figure4.pdf: more updates
+	* inst/doc/BalloonPlot.R, inst/doc/BalloonPlot.pdf,
+	  inst/doc/BalloonPlot.tex, inst/doc/Figure1.pdf,
+	  inst/doc/Figure2.pdf, inst/doc/Figure3.pdf, inst/doc/Figure4.pdf:
+	  more updates
 
 2006-01-12 23:01  warnes
 
-	* trunk/gplots/inst/doc/bka.bst: Add Biometrica bibliography style
-	  file
+	* inst/doc/bka.bst: Add Biometrica bibliography style file
 
 2006-01-12 22:34  warnes
 
-	* trunk/gplots/inst/doc/BalloonPlot.tex: A little more.
+	* inst/doc/BalloonPlot.tex: A little more.
 
 2006-01-12 22:32  warnes
 
-	* trunk/gplots/inst/doc/BalloonPlot.tex: Updates to respond to
-	  referee.
+	* inst/doc/BalloonPlot.tex: Updates to respond to referee.
 
 2006-01-12 19:59  nj7w
 
-	* trunk/gplots/inst/doc/BalloonPlot.tex: Added references
+	* inst/doc/BalloonPlot.tex: Added references
 
 2005-12-13 17:01  nj7w
 
-	* trunk/gplots/inst/doc/BalloonPlot.tex: Fixed Nitin's company name
+	* inst/doc/BalloonPlot.tex: Fixed Nitin's company name
 
 2005-12-13 16:18  nj7w
 
-	* trunk/gplots/ChangeLog, trunk/gplots/NEWS, trunk/gtools/NEWS:
-	  Updated NEWS and removed ChangeLog
+	* ChangeLog, NEWS, trunk/gtools/NEWS: Updated NEWS and removed
+	  ChangeLog
 
 2005-12-12 22:20  nj7w
 
-	* trunk/gplots/R/plotmeans.R: Fixed bug in plotmeans - based on
-	  Stefano Calza's suggestion
+	* R/plotmeans.R: Fixed bug in plotmeans - based on Stefano Calza's
+	  suggestion
 
 2005-12-07 18:52  nj7w
 
-	* trunk/gplots/DESCRIPTION: Updated version number
+	* DESCRIPTION: Updated version number
 
 2005-12-07 18:50  nj7w
 
-	* trunk/gplots/NAMESPACE, trunk/gplots/R/plot.lm.R,
-	  trunk/gplots/man/plot.lm2.Rd: Added plot.lm
+	* NAMESPACE, R/plot.lm.R, man/plot.lm2.Rd: Added plot.lm
 
 2005-12-07 18:48  nj7w
 
-	* trunk/gplots/man/barplot2.Rd: Changed the default grey colors to
-	  heat colors, if height is matrix
-	* trunk/gplots/R/barplot2.R: Changed the default greay colors to
-	  heat colors, if height is matrix
+	* man/barplot2.Rd: Changed the default grey colors to heat colors,
+	  if height is matrix
 
+2005-12-07 18:48  nj7w
+
+	* R/barplot2.R: Changed the default greay colors to heat colors, if
+	  height is matrix
+
 2005-12-06 22:41  nj7w
 
-	* trunk/gplots/man/barplot2.Rd: Fixed minor error in documentation
-	  of barplot2
+	* man/barplot2.Rd: Fixed minor error in documentation of barplot2
 
 2005-12-02 21:11  warnes
 
-	* trunk/gplots/R/plot.lm.R: Remove .Alias calls, since .Alias is
-	  defunct.
+	* R/plot.lm.R: Remove .Alias calls, since .Alias is defunct.
 
 2005-12-01 16:54  nj7w
 
 	* trunk/gmodels/man/ci.Rd, trunk/gmodels/man/coefFrame.Rd,
 	  trunk/gmodels/man/estimable.Rd,
 	  trunk/gmodels/man/fit.contrast.Rd,
-	  trunk/gmodels/man/make.contrasts.Rd,
-	  trunk/gplots/man/balloonplot.Rd, trunk/gplots/man/bandplot.Rd,
-	  trunk/gplots/man/boxplot.n.Rd, trunk/gplots/man/colorpanel.Rd,
-	  trunk/gplots/man/overplot.Rd, trunk/gplots/man/plotmeans.Rd,
-	  trunk/gplots/man/textplot.Rd, trunk/gplots/man/wapply.Rd,
-	  trunk/gtools/man/combinations.Rd,
+	  trunk/gmodels/man/make.contrasts.Rd, man/balloonplot.Rd,
+	  man/bandplot.Rd, man/boxplot.n.Rd, man/colorpanel.Rd,
+	  man/overplot.Rd, man/plotmeans.Rd, man/textplot.Rd,
+	  man/wapply.Rd, trunk/gtools/man/combinations.Rd,
 	  trunk/gtools/man/foldchange.Rd, trunk/gtools/man/invalid.Rd,
 	  trunk/gtools/man/logit.Rd, trunk/gtools/man/mixedsort.Rd,
 	  trunk/gtools/man/oddeven.Rd, trunk/gtools/man/quantcut.Rd,
@@ -202,187 +264,179 @@
 
 2005-11-23 22:05  nj7w
 
-	* trunk/gplots/inst/doc/BalloonPlot.R,
-	  trunk/gplots/inst/doc/BalloonPlot.pdf,
-	  trunk/gplots/inst/doc/BalloonPlot.tex,
-	  trunk/gplots/inst/doc/Figure2.pdf: Updated Figure 2 colors
+	* inst/doc/BalloonPlot.R, inst/doc/BalloonPlot.pdf,
+	  inst/doc/BalloonPlot.tex, inst/doc/Figure2.pdf: Updated Figure 2
+	  colors
 
 2005-11-18 20:40  warnes
 
-	* trunk/gplots/inst/doc/BalloonPlot.pdf,
-	  trunk/gplots/inst/doc/Figure1.pdf,
-	  trunk/gplots/inst/doc/Figure2.pdf,
-	  trunk/gplots/inst/doc/Figure3.pdf,
-	  trunk/gplots/inst/doc/Figure4.pdf: Latest version of the pdf
-	  files
+	* inst/doc/BalloonPlot.pdf, inst/doc/Figure1.pdf,
+	  inst/doc/Figure2.pdf, inst/doc/Figure3.pdf, inst/doc/Figure4.pdf:
+	  Latest version of the pdf files
 
 2005-11-18 20:37  warnes
 
-	* trunk/gplots/inst/doc/BalloonPlot.tex: Nitin works for the
-	  Cambrige Group, not Pfizer.
+	* inst/doc/BalloonPlot.tex: Nitin works for the Cambrige Group, not
+	  Pfizer.
 
 2005-11-18 20:34  warnes
 
-	* trunk/gplots/inst/doc/BalloonPlot.tex: Minor text rewording.
+	* inst/doc/BalloonPlot.tex: Minor text rewording.
 
 2005-11-18 20:31  warnes
 
-	* trunk/gplots/inst/doc/BalloonPlot.R,
-	  trunk/gplots/inst/doc/BalloonPlot.tex: More edits.
+	* inst/doc/BalloonPlot.R, inst/doc/BalloonPlot.tex: More edits.
 
 2005-11-18 19:50  warnes
 
-	* trunk/gplots/R/balloonplot.R: Recent changes to align row totals
-	  with the overall total broke how
+	* R/balloonplot.R: Recent changes to align row totals with the
+	  overall total broke how
 	  the marginal cumulative fractions were displayed. This patch
 	  fixes
 	  the problem.
 
 2005-11-18 01:17  warnes
 
-	* trunk/gplots/DESCRIPTION, trunk/gplots/R/balloonplot.R,
-	  trunk/gplots/R/plot.lm.R, trunk/gplots/inst/doc/BalloonPlot.pdf,
-	  trunk/gplots/man/balloonplot.Rd: - Update documentation for
-	  balloonplot to match the latest code.
+	* DESCRIPTION, R/balloonplot.R, R/plot.lm.R,
+	  inst/doc/BalloonPlot.pdf, man/balloonplot.Rd: - Update
+	  documentation for balloonplot to match the latest code.
 	  - Correct spelling of 'show.zeroes' to 'show.zeros'
 
 2005-11-18 00:16  warnes
 
-	* trunk/gplots/R/colorpanel.R: More changes: colorpanel now allows
-	  only 2 colors to be specified if
+	* R/colorpanel.R: More changes: colorpanel now allows only 2 colors
+	  to be specified if
 	  no 'middle' color is desired.
 
 2005-11-17 22:08  warnes
 
-	* trunk/gplots/R/balloonplot.R: Allow user to control removal of
-	  duplicate entries in balloonplot.
+	* R/balloonplot.R: Allow user to control removal of duplicate
+	  entries in balloonplot.
 
 2005-11-17 22:06  warnes
 
-	* trunk/gplots/R/colorpanel.R, trunk/gplots/man/colorpanel.Rd:
-	  Extend colorpanel to handle just two-colors in addition to three.
+	* R/colorpanel.R, man/colorpanel.Rd: Extend colorpanel to handle
+	  just two-colors in addition to three.
 
 2005-11-09 22:39  nj7w
 
-	* trunk/gplots/inst/doc/BalloonPlot.pdf: Updated the pdf file
+	* inst/doc/BalloonPlot.pdf: Updated the pdf file
 
 2005-11-09 22:38  nj7w
 
-	* trunk/gplots/inst/doc/BalloonPlot.R,
-	  trunk/gplots/inst/doc/BalloonPlot.tex: Updated the changes
+	* inst/doc/BalloonPlot.R, inst/doc/BalloonPlot.tex: Updated the
+	  changes
 
 2005-11-09 22:29  nj7w
 
-	* trunk/gplots/inst/doc/Figure4.pdf: Modified figure 4
-	* trunk/gplots/inst/doc/BalloonPlot.R: Updated code
+	* inst/doc/Figure4.pdf: Modified figure 4
 
+2005-11-09 22:29  nj7w
+
+	* inst/doc/BalloonPlot.R: Updated code
+
 2005-11-09 22:20  nj7w
 
-	* trunk/gplots/inst/doc/Figure3.pdf: Modified figure 3
-	* trunk/gplots/inst/doc/Figure2.pdf: Modified figure 2
+	* inst/doc/Figure3.pdf: Modified figure 3
 
+2005-11-09 22:20  nj7w
+
+	* inst/doc/Figure2.pdf: Modified figure 2
+
 2005-11-09 22:19  nj7w
 
-	* trunk/gplots/inst/doc/Figure1.pdf: Modified figure 1
+	* inst/doc/Figure1.pdf: Modified figure 1
 
 2005-11-08 16:19  nj7w
 
-	* trunk/gplots/man/plotCI.Rd: Updated Greg's email
+	* man/plotCI.Rd: Updated Greg's email
 
 2005-11-07 16:58  nj7w
 
-	* trunk/gplots/inst/doc/BalloonPlot.pdf,
-	  trunk/gplots/inst/doc/BalloonPlot.tex: Minor modifications to
-	  fit the code properly on pdf
+	* inst/doc/BalloonPlot.pdf, inst/doc/BalloonPlot.tex: Minor
+	  modifications to fit the code properly on pdf
 
 2005-11-07 14:22  warnes
 
-	* trunk/gplots/inst/doc/BalloonPlot.R: Add R code that generates
-	  plots
+	* inst/doc/BalloonPlot.R: Add R code that generates plots
 
 2005-11-07 14:18  warnes
 
-	* trunk/gplots/inst/doc/Figure2.pdf,
-	  trunk/gplots/inst/doc/Figure3.pdf,
-	  trunk/gplots/inst/doc/Figure4.pdf: Add figures to CVS
-	* trunk/gplots/inst/doc/BalloonPlot.pdf,
-	  trunk/gplots/inst/doc/BalloonPlot.tex,
-	  trunk/gplots/inst/doc/Figure1.pdf: Text changes
+	* inst/doc/Figure2.pdf, inst/doc/Figure3.pdf, inst/doc/Figure4.pdf:
+	  Add figures to CVS
 
+2005-11-07 14:18  warnes
+
+	* inst/doc/BalloonPlot.pdf, inst/doc/BalloonPlot.tex,
+	  inst/doc/Figure1.pdf: Text changes
+
 2005-11-04 21:48  warnes
 
-	* trunk/gplots/R/balloonplot.R: Fix some alignment issues.
+	* R/balloonplot.R: Fix some alignment issues.
 
 2005-11-04 19:05  warnes
 
-	* trunk/gplots/inst/doc/BalloonPlot.pdf,
-	  trunk/gplots/inst/doc/Table.pdf: Remove Table.pdf since it is no
-	  longer needed
+	* inst/doc/BalloonPlot.pdf, inst/doc/Table.pdf: Remove Table.pdf
+	  since it is no longer needed
 
 2005-11-04 19:04  warnes
 
-	* trunk/gplots/inst/doc/BalloonPlot.pdf,
-	  trunk/gplots/inst/doc/BalloonPlot.tex,
-	  trunk/gplots/inst/doc/Figure1.pdf: Nitin's Changes
+	* inst/doc/BalloonPlot.pdf, inst/doc/BalloonPlot.tex,
+	  inst/doc/Figure1.pdf: Nitin's Changes
 
 2005-11-04 19:00  warnes
 
-	* trunk/gplots/inst/doc/SurvivedPop.pdf,
-	  trunk/gplots/inst/doc/SurvivedPopWhite.pdf,
-	  trunk/gplots/inst/doc/SurvivedProp.pdf,
-	  trunk/gplots/inst/doc/TotalPop.pdf: Add figure plots
+	* inst/doc/SurvivedPop.pdf, inst/doc/SurvivedPopWhite.pdf,
+	  inst/doc/SurvivedProp.pdf, inst/doc/TotalPop.pdf: Add figure
+	  plots
 
 2005-11-04 18:59  warnes
 
-	* trunk/gplots/inst/doc/BalloonPlot.pdf,
-	  trunk/gplots/inst/doc/BalloonPlot.tex: Fix paths
+	* inst/doc/BalloonPlot.pdf, inst/doc/BalloonPlot.tex: Fix paths
 
 2005-10-20 18:36  nj7w
 
-	* trunk/gplots/inst/doc/Figure1.eps,
-	  trunk/gplots/inst/doc/Table.eps: added the eps version of figures
+	* inst/doc/Figure1.eps, inst/doc/Table.eps: added the eps version
+	  of figures
 
 2005-10-20 18:35  nj7w
 
-	* trunk/gplots/inst/doc/BalloonPlot.pdf: Updated BallonPlot.pdf
+	* inst/doc/BalloonPlot.pdf: Updated BallonPlot.pdf
 
 2005-10-20 18:34  nj7w
 
-	* trunk/gplots/inst/doc/SurvivedPop.pdf,
-	  trunk/gplots/inst/doc/SurvivedPopWhite.pdf,
-	  trunk/gplots/inst/doc/SurvivedProp.pdf,
-	  trunk/gplots/inst/doc/TotalPop.pdf: Removed Old Figure
+	* inst/doc/SurvivedPop.pdf, inst/doc/SurvivedPopWhite.pdf,
+	  inst/doc/SurvivedProp.pdf, inst/doc/TotalPop.pdf: Removed Old
+	  Figure
 
 2005-10-20 18:31  nj7w
 
-	* trunk/gplots/inst/doc/Figure1.pdf,
-	  trunk/gplots/inst/doc/Table.pdf: Added the new figure - for
-	  total popluation - Balloonplot
+	* inst/doc/Figure1.pdf, inst/doc/Table.pdf: Added the new figure -
+	  for total popluation - Balloonplot
 
 2005-10-20 18:29  nj7w
 
-	* trunk/gplots/inst/doc/BalloonPlot.tex: Modified the BallonPlot
-	  article
+	* inst/doc/BalloonPlot.tex: Modified the BallonPlot article
 
 2005-10-20 14:12  nj7w
 
-	* trunk/gplots/inst/doc/BalloonPlot.tex: Added references
+	* inst/doc/BalloonPlot.tex: Added references
 
 2005-10-19 16:57  arnima
 
-	* trunk/gplots/man/rich.color.Rd: The last example now displays
-	  the correct heat.colors.
+	* man/rich.color.Rd: The last example now displays the correct
+	  heat.colors.
 	  Default 'palette' argument is now a single string, not a vector.
 
 2005-10-19 16:56  arnima
 
-	* trunk/gplots/R/rich.color.R: Default 'palette' argument is now a
-	  single string, not a vector.
+	* R/rich.color.R: Default 'palette' argument is now a single
+	  string, not a vector.
 
 2005-10-14 19:13  warnes
 
-	* trunk/gplots/DESCRIPTION, trunk/gplots/R/balloonplot.R,
-	  trunk/gplots/man/balloonplot.Rd: Formatting fixes:
+	* DESCRIPTION, R/balloonplot.R, man/balloonplot.Rd: Formatting
+	  fixes:
 	  - Handle multiple row or column category variables
 	  - Separate rows/columns of category labels by lines
 	  - Fix handling of 'cumsum' plots on row/column labels
@@ -390,54 +444,50 @@
 
 2005-10-13 20:00  warnes
 
-	* trunk/gplots/man/balloonplot.Rd: Add example using Titanic data
-	  that exercises the multi-factor
+	* man/balloonplot.Rd: Add example using Titanic data that exercises
+	  the multi-factor
 	  display.
 
 2005-10-11 21:20  warnes
 
-	* trunk/gplots/R/balloonplot.R: Initial changes to allow multiple
-	  x and y factor variables. Yet to
+	* R/balloonplot.R: Initial changes to allow multiple x and y factor
+	  variables. Yet to
 	  be done: 1) remove extra 'boxes'. 2) omit duplicated values
 
 2005-10-04 19:39  warnes
 
-	* trunk/gplots/inst/doc/BalloonPlot.pdf,
-	  trunk/gplots/inst/doc/BalloonPlot.tex: more minor fixes
+	* inst/doc/BalloonPlot.pdf, inst/doc/BalloonPlot.tex: more minor
+	  fixes
 
 2005-10-04 19:29  warnes
 
-	* trunk/gplots/inst/doc/BalloonPlot.pdf,
-	  trunk/gplots/inst/doc/BalloonPlot.tex: fix spacing
+	* inst/doc/BalloonPlot.pdf, inst/doc/BalloonPlot.tex: fix spacing
 
 2005-10-04 19:08  warnes
 
-	* trunk/gplots/inst/doc/Rnews.sty: Inlcude Rnews.sty
+	* inst/doc/Rnews.sty: Inlcude Rnews.sty
 
 2005-10-04 19:07  warnes
 
-	* trunk/gplots/inst/doc/BalloonPlot.pdf,
-	  trunk/gplots/inst/doc/BalloonPlot.tex: Some textual edits.
+	* inst/doc/BalloonPlot.pdf, inst/doc/BalloonPlot.tex: Some textual
+	  edits.
 
 2005-10-03 16:23  nj7w
 
-	* trunk/gplots/inst/doc/SurvivedPop.pdf,
-	  trunk/gplots/inst/doc/SurvivedPopWhite.pdf,
-	  trunk/gplots/inst/doc/SurvivedProp.pdf,
-	  trunk/gplots/inst/doc/TotalPop.pdf: Added figures for the R-News
-	  Article
+	* inst/doc/SurvivedPop.pdf, inst/doc/SurvivedPopWhite.pdf,
+	  inst/doc/SurvivedProp.pdf, inst/doc/TotalPop.pdf: Added figures
+	  for the R-News Article
 
 2005-09-29 21:02  nj7w
 
-	* trunk/gplots/inst/doc/BalloonPlot.pdf,
-	  trunk/gplots/inst/doc/BalloonPlot.tex: Updated the documentation
-	  - added the name of the person who asked the question
+	* inst/doc/BalloonPlot.pdf, inst/doc/BalloonPlot.tex: Updated the
+	  documentation - added the name of the person who asked the
+	  question
 
 2005-09-29 20:29  nj7w
 
-	* trunk/gplots/inst, trunk/gplots/inst/doc,
-	  trunk/gplots/inst/doc/BalloonPlot.pdf,
-	  trunk/gplots/inst/doc/BalloonPlot.tex: Added R-news article
+	* inst, inst/doc, inst/doc/BalloonPlot.pdf,
+	  inst/doc/BalloonPlot.tex: Added R-news article
 
 2005-09-12 15:44  nj7w
 
@@ -446,47 +496,47 @@
 	  trunk/gdata/man/nobs.Rd, trunk/gdata/man/read.xls.Rd,
 	  trunk/gdata/man/rename.vars.Rd, trunk/gdata/man/trim.Rd,
 	  trunk/gdata/man/unmatrix.Rd, trunk/gmodels/man/fast.prcomp.Rd,
-	  trunk/gmodels/man/glh.test.Rd, trunk/gplots/man/hist2d.Rd,
-	  trunk/gplots/man/ooplot.Rd, trunk/gplots/man/residplot.Rd,
-	  trunk/gplots/man/sinkplot.Rd, trunk/gplots/man/smartlegend.Rd,
-	  trunk/gplots/man/space.Rd, trunk/gtools/man/assert.Rd,
+	  trunk/gmodels/man/glh.test.Rd, man/hist2d.Rd, man/ooplot.Rd,
+	  man/residplot.Rd, man/sinkplot.Rd, man/smartlegend.Rd,
+	  man/space.Rd, trunk/gtools/man/assert.Rd,
 	  trunk/gtools/man/dirichlet.Rd, trunk/gtools/man/permute.Rd,
 	  trunk/gtools/man/scat.Rd: Updated Greg's email
 
 2005-09-12 14:45  nj7w
 
-	* trunk/gplots/R/balloonplot.R: Updated version of balloonplot -
-	  by Romain Francois <fra...@fr...>
+	* R/balloonplot.R: Updated version of balloonplot - by Romain
+	  Francois <fra...@fr...>
 
 2005-09-09 20:34  nj7w
 
-	* trunk/gplots/ChangeLog, trunk/gplots/DESCRIPTION: Updated the
-	  version and ChangeLog
+	* ChangeLog, DESCRIPTION: Updated the version and ChangeLog
 
 2005-09-09 20:32  nj7w
 
-	* trunk/gplots/R/balloonplot.R, trunk/gplots/man/balloonplot.Rd:
-	  Changes in ballon plot based on Romain Francois
-	  (fra...@fr...) suggestions
+	* R/balloonplot.R, man/balloonplot.Rd: Changes in ballon plot based
+	  on Romain Francois (fra...@fr...) suggestions
 
 2005-09-06 21:41  nj7w
 
-	* trunk/gplots/DESCRIPTION: Updated package dependencies
-	* trunk/gplots/NEWS: Added NEWS
+	* DESCRIPTION: Updated package dependencies
 
+2005-09-06 21:41  nj7w
+
+	* NEWS: Added NEWS
+
 2005-09-02 23:10  nj7w
 
-	* trunk/gmodels/ChangeLog, trunk/gplots/ChangeLog: Added ChangeLog
+	* trunk/gmodels/ChangeLog, ChangeLog: Added ChangeLog
 
 2005-08-31 16:28  nj7w
 
-	* trunk/gdata/DESCRIPTION, trunk/gmodels/DESCRIPTION,
-	  trunk/gplots/DESCRIPTION: Added DESCRIPTION file
+	* trunk/gdata/DESCRIPTION, trunk/gmodels/DESCRIPTION, DESCRIPTION:
+	  Added DESCRIPTION file
 
 2005-08-31 16:27  nj7w
 
 	* trunk/gdata/DESCRIPTION.in, trunk/gmodels/DESCRIPTION.in,
-	  trunk/gplots/DESCRIPTION.in: removed DESCRIPTION.in
+	  DESCRIPTION.in: removed DESCRIPTION.in
 
 2005-06-09 14:20  nj7w
 
@@ -498,8 +548,7 @@
 	  trunk/gdata/R/matchcols.R, trunk/gdata/R/nobs.R,
 	  trunk/gdata/R/read.xls.R, trunk/gdata/R/rename.vars.R,
 	  trunk/gdata/R/reorder.R, trunk/gdata/R/trim.R,
-	  trunk/gdata/R/unmatrix.R,
-	  trunk/gdata/inst/perl/IO/AtomicFile.pm,
+	  trunk/gdata/R/unmatrix.R, trunk/gdata/inst/perl/IO/AtomicFile.pm,
 	  trunk/gdata/inst/perl/IO/InnerFile.pm,
 	  trunk/gdata/inst/perl/IO/Lines.pm,
 	  trunk/gdata/inst/perl/IO/Scalar.pm,
@@ -518,24 +567,15 @@
 	  trunk/gmodels/man/CrossTable.Rd, trunk/gmodels/man/ci.Rd,
 	  trunk/gmodels/man/coefFrame.Rd, trunk/gmodels/man/estimable.Rd,
 	  trunk/gmodels/man/fast.prcomp.Rd,
-	  trunk/gmodels/man/fit.contrast.Rd,
-	  trunk/gmodels/man/glh.test.Rd,
-	  trunk/gmodels/man/make.contrasts.Rd,
-	  trunk/gplots/R/balloonplot.R, trunk/gplots/R/bandplot.R,
-	  trunk/gplots/R/boxplot.n.R, trunk/gplots/R/colorpanel.R,
-	  trunk/gplots/R/heatmap.2.R, trunk/gplots/R/hist2d.R,
-	  trunk/gplots/R/lowess.R, trunk/gplots/R/ooplot.R,
-	  trunk/gplots/R/overplot.R, trunk/gplots/R/plotCI.R,
-	  trunk/gplots/R/plotmeans.R, trunk/gplots/R/qqnorm.aov.R,
-	  trunk/gplots/R/residplot.R, trunk/gplots/R/rich.color.R,
-	  trunk/gplots/R/sinkplot.R, trunk/gplots/R/smartlegend.R,
-	  trunk/gplots/R/space.R, trunk/gplots/R/textplot.R,
-	  trunk/gplots/R/wapply.R, trunk/gplots/man/1,
-	  trunk/gplots/man/bandplot.Rd, trunk/gplots/man/barplot2.Rd,
-	  trunk/gplots/man/boxplot.n.Rd, trunk/gplots/man/hist2d.Rd,
-	  trunk/gplots/man/lowess.Rd, trunk/gplots/man/plotCI.Rd,
-	  trunk/gplots/man/plotmeans.Rd, trunk/gplots/man/residplot.Rd,
-	  trunk/gplots/man/space.Rd, trunk/gplots/man/wapply.Rd,
+	  trunk/gmodels/man/fit.contrast.Rd, trunk/gmodels/man/glh.test.Rd,
+	  trunk/gmodels/man/make.contrasts.Rd, R/balloonplot.R,
+	  R/bandplot.R, R/boxplot.n.R, R/colorpanel.R, R/heatmap.2.R,
+	  R/hist2d.R, R/lowess.R, R/ooplot.R, R/overplot.R, R/plotCI.R,
+	  R/plotmeans.R, R/qqnorm.aov.R, R/residplot.R, R/rich.color.R,
+	  R/sinkplot.R, R/smartlegend.R, R/space.R, R/textplot.R,
+	  R/wapply.R, man/1, man/bandplot.Rd, man/barplot2.Rd,
+	  man/boxplot.n.Rd, man/hist2d.Rd, man/lowess.Rd, man/plotCI.Rd,
+	  man/plotmeans.Rd, man/residplot.Rd, man/space.Rd, man/wapply.Rd,
 	  trunk/gtools/R/RSCompat.S, trunk/gtools/R/combinations.R,
 	  trunk/gtools/R/dirichlet.R, trunk/gtools/R/foldchange.R,
 	  trunk/gtools/R/invalid.R, trunk/gtools/R/logit.R,
@@ -553,22 +593,21 @@
 
 2005-06-09 14:15  nj7w
 
-	* trunk/gplots/R/barplot2.R: Changes based on Marc Schwartz's
-	  suggestions to handel 0's and NA's appropriately.
+	* R/barplot2.R: Changes based on Marc Schwartz's suggestions to
+	  handel 0's and NA's appropriately.
 
 2005-05-13 18:59  nj7w
 
 	* trunk/gdata/R/read.xls.R, trunk/gmodels/man/CrossTable.Rd,
-	  trunk/gplots/man/heatmap.2.Rd: 1) Using dQuote.ascii function in
-	  read.xls as the new version of dQuote doesn't work proprly with
-	  UTF-8 locale.
+	  man/heatmap.2.Rd: 1) Using dQuote.ascii function in read.xls as
+	  the new version of dQuote doesn't work proprly with UTF-8 locale.
 	  2) Modified CrossTable.Rd usage in gmodels
 	  3) Modified heatmap.2 usage in gplots.
 
 2005-04-04 14:23  warnes
 
-	* trunk/gplots/R/overplot.R: Explicitly reference package
-	  containing lowess.formula in
+	* R/overplot.R: Explicitly reference package containing
+	  lowess.formula in
 	  panel.overplot(). This should fix the error reported by Troels
 	  Ring
 	  <tr...@gv...>.
@@ -577,57 +616,55 @@
 
 	* trunk/gdata/NAMESPACE, trunk/gdata/man/elem.Rd,
 	  trunk/gdata/man/env.Rd, trunk/gdata/man/ll.Rd,
-	  trunk/gdata/man/read.xls.Rd, trunk/gplots/R/heatmap.2.R,
-	  trunk/gplots/man/heatmap.2.Rd, trunk/gplots/man/rich.color.Rd,
-	  trunk/gplots/man/sinkplot.Rd, trunk/gplots/man/textplot.Rd: ***
-	  empty log message ***
+	  trunk/gdata/man/read.xls.Rd, R/heatmap.2.R, man/heatmap.2.Rd,
+	  man/rich.color.Rd, man/sinkplot.Rd, man/textplot.Rd: *** empty
+	  log message ***
 
 2005-02-25 23:22  warnes
 
 	* trunk/gdata/R/elem.R, trunk/gdata/R/env.R, trunk/gdata/R/ll.R,
 	  trunk/gdata/man/Args.Rd, trunk/gdata/man/env.Rd,
-	  trunk/gdata/man/ll.Rd, trunk/gplots/man/rich.color.Rd: Integrate
-	  changes submitted by Arni Magnusson
+	  trunk/gdata/man/ll.Rd, man/rich.color.Rd: Integrate changes
+	  submitted by Arni Magnusson
 
 2005-02-25 22:31  warnes
 
-	* trunk/gplots/NAMESPACE: Add dependency imports from 'stats'
-	  package.
+	* NAMESPACE: Add dependency imports from 'stats' package.
 
 2005-02-22 21:01  warnes
 
-	* trunk/gplots/R/bandplot.R: Fix problem in passing graphical
-	  parameters (xlim,etc).@
+	* R/bandplot.R: Fix problem in passing graphical parameters
+	  (xlim,etc).@
 
 2005-02-08 16:41  warnes
 
-	* trunk/gplots/DESCRIPTION.in: Improve package title.
+	* DESCRIPTION.in: Improve package title.
 
 2005-02-08 16:40  warnes
 
-	* trunk/gplots/R/heatmap.2.R: Ignore missing values when computing
-	  symmetric range.
+	* R/heatmap.2.R: Ignore missing values when computing symmetric
+	  range.
 
 2005-02-02 19:25  warnes
 
-	* trunk/gplots/man/plotmeans.Rd: Add more extensive example.
+	* man/plotmeans.Rd: Add more extensive example.
 
 2005-01-14 19:05  warnes
 
-	* trunk/gplots/R/textplot.R: Code can be simplified because R now
-	  supports selecting a fixed width font.
+	* R/textplot.R: Code can be simplified because R now supports
+	  selecting a fixed width font.
 
 2005-01-12 20:50  warnes
 
 	* trunk/gdata/DESCRIPTION.in, trunk/gmodels/DESCRIPTION.in,
-	  trunk/gplots/DESCRIPTION.in, trunk/gtools/DESCRIPTION.in: Add
-	  dependency on R 1.9.0+ to prevent poeple from installing on old
+	  DESCRIPTION.in, trunk/gtools/DESCRIPTION.in: Add dependency on R
+	  1.9.0+ to prevent poeple from installing on old
 	  versions of R which don't support namespaces.
 
 2004-11-30 01:06  warnes
 
-	* trunk/gplots/R/heatmap.2.R, trunk/gplots/man/heatmap.2.Rd: 1.
-	  Add new parameters for controlling color key:
+	* R/heatmap.2.R, man/heatmap.2.Rd: 1. Add new parameters for
+	  controlling color key:
 	  - If `symkey==TRUE', the color key will be made symmetric about
 	  0.
 	  - The `densadj' parameter can be used to modify the smoother
@@ -640,8 +677,7 @@
 	  
 	  3. Vector of length 2 giving the width (colsep) or height
 	  (rowsep) the separator box
-	  drawn by colsep and rowsep as a function of the width
-	  (colsep) or
+	  drawn by colsep and rowsep as a function of the width (colsep) or
 	  height (rowsep) of a cell.
 	  
 	  4. Appropriate changes to the corresponding help page, plus some
@@ -649,8 +685,8 @@
 
 2004-11-03 19:43  warnes
 
-	* trunk/gplots/R/heatmap.2.R: Fix bugs in layout of cell notes.
-	  They were being plotted top down
+	* R/heatmap.2.R: Fix bugs in layout of cell notes. They were being
+	  plotted top down
 	  rather than bottom up. Further reordering of the x matrix didn't
 	  also reorder the notes. Both issues should now be resolved.
 
@@ -659,18 +695,19 @@
 	* trunk/gdata/DESCRIPTION, trunk/gdata/DESCRIPTION.in,
 	  trunk/gdata/NAMESPACE, trunk/gdata/man/.Rhistory,
 	  trunk/gmodels/DESCRIPTION, trunk/gmodels/DESCRIPTION.in,
-	  trunk/gplots/DESCRIPTION, trunk/gplots/DESCRIPTION.in,
-	  trunk/gplots/man/sinkplot.Rd, trunk/gplots/man/textplot.Rd,
+	  DESCRIPTION, DESCRIPTION.in, man/sinkplot.Rd, man/textplot.Rd,
 	  trunk/gregmisc/.Rhistory, trunk/gregmisc/DESCRIPTION,
 	  trunk/gtools/DESCRIPTION, trunk/gtools/DESCRIPTION.in,
 	  trunk/gtools/man/running.Rd: Updated to pass R CMD check.
 
 2004-09-03 22:50  warneg
 
-	* trunk/gplots/man/textplot.Rd: Provide explicit package for call
-	  to nobs.
-	* trunk/gplots/man/heatmap.2.Rd: Fix typos.
+	* man/textplot.Rd: Provide explicit package for call to nobs.
 
+2004-09-03 22:50  warneg
+
+	* man/heatmap.2.Rd: Fix typos.
+
 2004-09-03 17:27  warneg
 
 	* trunk/gdata/DESCRIPTION, trunk/gdata/DESCRIPTION.in,
@@ -688,58 +725,49 @@
 	  trunk/gmodels/R/fast.prcomp.R, trunk/gmodels/R/fit.contrast.R,
 	  trunk/gmodels/R/glh.test.R, trunk/gmodels/R/make.contrasts.R,
 	  trunk/gmodels/man/estimable.Rd,
-	  trunk/gmodels/man/fit.contrast.Rd,
-	  trunk/gmodels/man/glh.test.Rd,
-	  trunk/gmodels/man/make.contrasts.Rd, trunk/gplots/DESCRIPTION,
-	  trunk/gplots/NAMESPACE, trunk/gplots/R/balloonplot.R,
-	  trunk/gplots/R/bandplot.R, trunk/gplots/R/barplot2.R,
-	  trunk/gplots/R/boxplot.n.R, trunk/gplots/R/colorpanel.R,
-	  trunk/gplots/R/heatmap.2.R, trunk/gplots/R/hist2d.R,
-	  trunk/gplots/R/lowess.R, trunk/gplots/R/ooplot.R,
-	  trunk/gplots/R/overplot.R, trunk/gplots/R/plotCI.R,
-	  trunk/gplots/R/plotmeans.R, trunk/gplots/R/qqnorm.aov.R,
-	  trunk/gplots/R/residplot.R, trunk/gplots/R/rich.color.R,
-	  trunk/gplots/R/sinkplot.R, trunk/gplots/R/smartlegend.R,
-	  trunk/gplots/R/space.R, trunk/gplots/R/textplot.R,
-	  trunk/gplots/R/wapply.R, trunk/gtools/DESCRIPTION,
-	  trunk/gtools/NAMESPACE, trunk/gtools/R/dirichlet.R,
-	  trunk/gtools/R/foldchange.R, trunk/gtools/R/invalid.R,
-	  trunk/gtools/R/mixedsort.R, trunk/gtools/R/oddeven.R,
-	  trunk/gtools/R/permute.R, trunk/gtools/R/quantcut.R,
-	  trunk/gtools/R/running.R, trunk/gtools/man/running.Rd: initial
-	  bundle checkin
+	  trunk/gmodels/man/fit.contrast.Rd, trunk/gmodels/man/glh.test.Rd,
+	  trunk/gmodels/man/make.contrasts.Rd, DESCRIPTION, NAMESPACE,
+	  R/balloonplot.R, R/bandplot.R, R/barplot2.R, R/boxplot.n.R,
+	  R/colorpanel.R, R/heatmap.2.R, R/hist2d.R, R/lowess.R,
+	  R/ooplot.R, R/overplot.R, R/plotCI.R, R/plotmeans.R,
+	  R/qqnorm.aov.R, R/residplot.R, R/rich.color.R, R/sinkplot.R,
+	  R/smartlegend.R, R/space.R, R/textplot.R, R/wapply.R,
+	  trunk/gtools/DESCRIPTION, trunk/gtools/NAMESPACE,
+	  trunk/gtools/R/dirichlet.R, trunk/gtools/R/foldchange.R,
+	  trunk/gtools/R/invalid.R, trunk/gtools/R/mixedsort.R,
+	  trunk/gtools/R/oddeven.R, trunk/gtools/R/permute.R,
+	  trunk/gtools/R/quantcut.R, trunk/gtools/R/running.R,
+	  trunk/gtools/man/running.Rd: initial bundle checkin
 
 2004-09-02 17:14  warneg
 
 	* trunk/gdata/DESCRIPTION, trunk/gdata/DESCRIPTION.in,
 	  trunk/gdata/NAMESPACE, trunk/gdata/man/.Rhistory,
 	  trunk/gmodels/DESCRIPTION, trunk/gmodels/DESCRIPTION.in,
-	  trunk/gmodels/NAMESPACE, trunk/gplots/DESCRIPTION,
-	  trunk/gplots/DESCRIPTION.in, trunk/gplots/NAMESPACE,
-	  trunk/gplots/man/1, trunk/gplots/man/residplot.Rd,
-	  trunk/gregmisc/.Rhistory, trunk/gtools/DESCRIPTION,
-	  trunk/gtools/DESCRIPTION.in, trunk/gtools/NAMESPACE: Initial
-	  revision
+	  trunk/gmodels/NAMESPACE, DESCRIPTION, DESCRIPTION.in, NAMESPACE,
+	  man/1, man/residplot.Rd, trunk/gregmisc/.Rhistory,
+	  trunk/gtools/DESCRIPTION, trunk/gtools/DESCRIPTION.in,
+	  trunk/gtools/NAMESPACE: Initial revision
 
 2004-07-29 14:49  warnes
 
-	* trunk/gplots/R/plotCI.R, trunk/gplots/man/plotCI.Rd: Integrate
-	  changes from the version of plotCI maintained by Martin Maechler.
+	* R/plotCI.R, man/plotCI.Rd: Integrate changes from the version of
+	  plotCI maintained by Martin Maechler.
 
 2004-06-30 19:32  warnes
 
-	* trunk/gplots/R/textplot.R: Remove commented-out code.
+	* R/textplot.R: Remove commented-out code.
 
 2004-06-30 19:26  warnes
 
-	* trunk/gplots/R/textplot.R: Fixed text size calculations
+	* R/textplot.R: Fixed text size calculations
 
 2004-06-28 20:16  warnes
 
-	* trunk/gplots/R/barplot2.R, trunk/gplots/man/barplot2.Rd: -
-	  Default 2-d color set to grey as in (v2.0.0) r-devel
-	  - The default (v1.9.1) barplot method now handles vectors and
-	  1-d arrays
+	* R/barplot2.R, man/barplot2.Rd: - Default 2-d color set to grey as
+	  in (v2.0.0) r-devel
+	  - The default (v1.9.1) barplot method now handles vectors and 1-d
+	  arrays
 	  (e.g., obtained by table()) the same, and uses grey instead of
 	  heat color palettes in these cases. (Also fixes PR#6776.)
 	  - Updated to reflect the addition of 'offset' argument in base
@@ -748,234 +776,223 @@
 
 2004-06-24 16:57  warnes
 
-	* trunk/gplots/R/heatmap.2.R, trunk/gplots/man/heatmap.2.Rd: Add
-	  ability to specify color of NA cells.
+	* R/heatmap.2.R, man/heatmap.2.Rd: Add ability to specify color of
+	  NA cells.
 
 2004-05-27 15:11  warnes
 
-	* trunk/gplots/man/plotCI.Rd: Fix spelling error.
+	* man/plotCI.Rd: Fix spelling error.
 
 2004-05-26 14:56  warnes
 
-	* trunk/gplots/R/overplot.R: One more fix to get it right.
+	* R/overplot.R: One more fix to get it right.
 
 2004-05-26 13:50  warnes
 
-	* trunk/gplots/R/overplot.R: Use triple-colon operator ':::' to
-	  access plot.formula from the graphics package.
+	* R/overplot.R: Use triple-colon operator ':::' to access
+	  plot.formula from the graphics package.
 
 2004-05-26 13:19  warnes
 
-	* trunk/gplots/man/rich.color.Rd: Replace 'F' by 'FALSE' to pass R
-	  CMD check.
+	* man/rich.color.Rd: Replace 'F' by 'FALSE' to pass R CMD check.
 
 2004-05-25 18:32  warnes
 
-	* trunk/gplots/R/overplot.R: Work around bug in R 1.9.X due to
-	  plot.formula() not having the same
+	* R/overplot.R: Work around bug in R 1.9.X due to plot.formula()
+	  not having the same
 	  arguments as plot().
 
 2004-05-25 17:33  warnes
 
-	* trunk/gplots/R/rich.color.R, trunk/gplots/man/rich.color.Rd: Add
-	  rich.colors() submitted by Arni Magnusson
-	  <arnima@u.washington.edu>.
+	* R/rich.color.R, man/rich.color.Rd: Add rich.colors() submitted by
+	  Arni Magnusson <arnima@u.washington.edu>.
 
 2004-05-25 02:58  warnes
 
-	* trunk/gplots/R/ooplot.R, trunk/gplots/man/ooplot.Rd: ??
+	* R/ooplot.R, man/ooplot.Rd: ??
 
 2004-05-24 23:43  warnes
 
-	* trunk/gplots/R/plotCI.R, trunk/gplots/R/plotmeans.R: Modified to
-	  use invalid() to check arguments instead of missing().
+	* R/plotCI.R, R/plotmeans.R: Modified to use invalid() to check
+	  arguments instead of missing().
 	  This fixes some build errors under R-1.9.0-Patched.
 
 2004-04-22 15:44  warnes
 
-	* trunk/gplots/R/ooplot.R, trunk/gplots/man/ooplot.Rd: Integrate
-	  changes from Lodewijk Bonebakker <bon...@co...>
+	* R/ooplot.R, man/ooplot.Rd: Integrate changes from Lodewijk
+	  Bonebakker <bon...@co...>
 
 2004-04-13 13:42  warnes
 
-	* trunk/gplots/R/space.R, trunk/gplots/man/space.Rd: Add ability
-	  to space points along 'y' direction.
+	* R/space.R, man/space.Rd: Add ability to space points along 'y'
+	  direction.
 
 2004-04-02 19:06  warnes
 
-	* trunk/gplots/R/smartlegend.R: Fixed smartlegend() positioning
-	  when x and/or y axis are log-scale.
+	* R/smartlegend.R: Fixed smartlegend() positioning when x and/or y
+	  axis are log-scale.
 
 2004-03-30 19:04  warnes
 
-	* trunk/gplots/R/textplot.R, trunk/gregmisc/DESCRIPTION: - Fix bug
-	  in textplot() reported by Wright, Kevin
-	  <kev...@pi...>.
+	* R/textplot.R, trunk/gregmisc/DESCRIPTION: - Fix bug in textplot()
+	  reported by Wright, Kevin <kev...@pi...>.
 
 2004-03-26 22:27  warnes
 
-	* trunk/gplots/man/textplot.Rd: Update to match changes in
-	  textplot() code.
+	* man/textplot.Rd: Update to match changes in textplot() code.
 
 2004-03-26 22:25  warnes
 
-	* trunk/gplots/man/ooplot.Rd: Remove Windows EOL characters.
+	* man/ooplot.Rd: Remove Windows EOL characters.
 
 2004-03-26 22:20  warnes
 
-	* trunk/gplots/man/barplot2.Rd: - Remove some commented-out code.
+	* man/barplot2.Rd: - Remove some commented-out code.
 	  - Remove cvs log tag.
 
 2004-03-26 22:16  warnes
 
-	* trunk/gplots/R/textplot.R: Misc changes.
+	* R/textplot.R: Misc changes.
 
 2004-02-17 22:22  warnes
 
-	* trunk/gplots/man/ooplot.Rd: Minor fix to ooplot documentation.
+	* man/ooplot.Rd: Minor fix to ooplot documentation.
 
 2004-02-17 22:21  warnes
 
-	* trunk/gplots/R/ooplot.R, trunk/gplots/man/ooplot.Rd: Integrate
-	  ooplot updates provided by Lodewijk Bonebakker
+	* R/ooplot.R, man/ooplot.Rd: Integrate ooplot updates provided by
+	  Lodewijk Bonebakker
 	  <bon...@co...>
 
 2004-02-02 16:26  warnes
 
-	* trunk/gplots/R/colorpanel.R, trunk/gplots/man/colorpanel.Rd: -
-	  Add colorpanel function, which generates a smoothly varying band
-	  of
+	* R/colorpanel.R, man/colorpanel.Rd: - Add colorpanel function,
+	  which generates a smoothly varying band of
 	  colors over a three color range (lo, mid, high).
 
 2004-01-21 12:07  warnes
 
-	* trunk/gplots/man/textplot.Rd: - Correct arguments to halign to
-	  match code.
+	* man/textplot.Rd: - Correct arguments to halign to match code.
 
 2004-01-21 05:17  warnes
 
-	* trunk/gplots/R/lowess.R: Track R 1.9.0's move of 'lowess' from
-	  the base package to the (new)
+	* R/lowess.R: Track R 1.9.0's move of 'lowess' from the base
+	  package to the (new)
 	  stats package.
 
 2004-01-21 04:44  warnes
 
-	* trunk/gplots/man/sinkplot.Rd: - Fix sinkplot() example by
-	  replacing 'T' with 'TRUE'.
+	* man/sinkplot.Rd: - Fix sinkplot() example by replacing 'T' with
+	  'TRUE'.
 
 2004-01-21 04:42  warnes
 
-	* trunk/gplots/man/ooplot.Rd: - Add some more details to the
-	  ooplot() documentation. The
+	* man/ooplot.Rd: - Add some more details to the ooplot()
+	  documentation. The
 	  documentation is *not* complete.
 
 2004-01-21 04:31  warnes
 
-	* trunk/gplots/R/textplot.R, trunk/gtools/R/capture.R: - Mark
-	  sprint() as depreciated.
+	* R/textplot.R, trunk/gtools/R/capture.R: - Mark sprint() as
+	  depreciated.
 	  - Replace references to sprint with capture.output()
 	  - Use match.arg for halign and valign arguments to
 	  textplot.default.
 	  - Fix textplot.character so that a vector of characters is
 	  properly
-	  displayed. Previouslt, character vectors were plotted on top
-	  of each
+	  displayed. Previouslt, character vectors were plotted on top of
+	  each
 	  other.
 
 2004-01-19 23:43  warnes
 
-	* trunk/gplots/R/sinkplot.R, trunk/gplots/man/sinkplot.Rd: New
-	  function sinkplot(), as requested on R-devel by Kevin Wright
+	* R/sinkplot.R, man/sinkplot.Rd: New function sinkplot(), as
+	  requested on R-devel by Kevin Wright
 	  <kw...@es...> in
 	  https://www.stat.math.ethz.ch/pipermail/r-devel/2004-January/028483.html.
 
 2004-01-15 05:14  warnes
 
-	* trunk/gplots/R/ooplot.R, trunk/gplots/man/ooplot.Rd: Add initial
-	  code and docs for ooplot() function submitted by Lodewijk
+	* R/ooplot.R, man/ooplot.Rd: Add initial code and docs for ooplot()
+	  function submitted by Lodewijk
 	  Bonebakker <bon...@co...>.
 
 2003-12-03 02:46  warnes
 
-	* trunk/gdata/man/elem.Rd, trunk/gdata/man/ll.Rd,
-	  trunk/gplots/man/lowess.Rd, trunk/gplots/man/textplot.Rd,
-	  trunk/gplots/man/wapply.Rd, trunk/gtools/man/foldchange.Rd: -
+	* trunk/gdata/man/elem.Rd, trunk/gdata/man/ll.Rd, man/lowess.Rd,
+	  man/textplot.Rd, man/wapply.Rd, trunk/gtools/man/foldchange.Rd: -
 	  match function argument defaults with 'usage'
 
 2003-12-03 02:42  warnes
 
-	* trunk/gplots/R/heatmap.2.R, trunk/gplots/man/heatmap.2.Rd: - Fix
-	  buglets in heatmap function
+	* R/heatmap.2.R, man/heatmap.2.Rd: - Fix buglets in heatmap
+	  function
 	  - Make a slight enhancement to the example code.
 
 2003-12-02 22:49  warnes
 
-	* trunk/gplots/R/heatmap.2.R: Integrated some suggestions from
-	  Sean Davis <sd...@ma...>.
+	* R/heatmap.2.R: Integrated some suggestions from Sean Davis
+	  <sd...@ma...>.
 
 2003-12-02 18:22  warnes
 
-	* trunk/gplots/man/heatmap.2.Rd: - Make final example use 16
-	  colors instead of 8. This looks nicer.
+	* man/heatmap.2.Rd: - Make final example use 16 colors instead of
+	  8. This looks nicer.
 
 2003-12-02 16:58  warnes
 
-	* trunk/gplots/man/barplot2.Rd: - Remove '%' character from
-	  example code to avoid errors.
+	* man/barplot2.Rd: - Remove '%' character from example code to
+	  avoid errors.
 
 2003-12-02 16:54  warnes
 
-	* trunk/gplots/R/plotCI.R: - Add '...' parameter to call to text
-	  to allow user to control size/color/etc.
+	* R/plotCI.R: - Add '...' parameter to call to text to allow user
+	  to control size/color/etc.
 
 2003-12-01 16:00  warnes
 
-	* trunk/gplots/man/barplot2.Rd: - updated to match changes to
-	  barplot() in base.
+	* man/barplot2.Rd: - updated to match changes to barplot() in base.
 
 2003-12-01 15:59  warnes
 
-	* trunk/gplots/data, trunk/gplots/data/rtPCR.rda: - Renamed
-	  rtPCR.Rda to rtPCR.rda so that R will properly load the file
+	* data, data/rtPCR.rda: - Renamed rtPCR.Rda to rtPCR.rda so that R
+	  will properly load the file
 	  when data(rtPCR) is executed.
 
 2003-12-01 15:55  warnes
 
-	* trunk/gplots/R/barplot2.R: - Follow patches applied to barplot()
-	  in base.
+	* R/barplot2.R: - Follow patches applied to barplot() in base.
 
 2003-11-24 21:32  warnes
 
-	* trunk/gplots/man/heatmap.2.Rd: Fix unbalanced braces.
+	* man/heatmap.2.Rd: Fix unbalanced braces.
 
 2003-11-24 15:09  warnes
 
-	* trunk/gplots/R/overplot.R, trunk/gplots/man/overplot.Rd: Fix
-	  errors reported by R CMD check.
+	* R/overplot.R, man/overplot.Rd: Fix errors reported by R CMD
+	  check.
 
 2003-11-21 23:13  warnes
 
-	* trunk/gplots/man/overplot.Rd: Added missing closing brace.
+	* man/overplot.Rd: Added missing closing brace.
 
 2003-11-21 23:08  warnes
 
-	* trunk/gplots/man/rtPCR.Rd: Initial addition of these files.
-	  Used in examples of overplot().
+	* man/rtPCR.Rd: Initial addition of these files. Used in examples
+	  of overplot().
 
 2003-11-21 22:59  warnes
 
-	* trunk/gplots/R/heatmap.2.R, trunk/gplots/man/heatmap.2.Rd:
-	  Applied my enhancements to the heatmap() code from R 1.8.0, and
-	  added
+	* R/heatmap.2.R, man/heatmap.2.Rd: Applied my enhancements to the
+	  heatmap() code from R 1.8.0, and added
 	  documentation of these changes.
 
 2003-11-21 22:58  warnes
 
-	* trunk/gplots/R/overplot.R, trunk/gplots/man/overplot.Rd: -
-	  Discovered that axis(N) does the right thing without needing to
-	  be
-	  given location for tick marks. This allowed simplification of
-	  the code.
+	* R/overplot.R, man/overplot.Rd: - Discovered that axis(N) does the
+	  right thing without needing to be
+	  given location for tick marks. This allowed simplification of the
+	  code.
 	  
 	  - Minor other changes for distribution
 	  
@@ -983,30 +1000,29 @@
 
 2003-11-21 19:50  warnes
 
-	* trunk/gplots/R/heatmap.2.R, trunk/gplots/man/heatmap.2.Rd: -
-	  Integrated my extensions into the R 1.8.0 version of heatmap.
+	* R/heatmap.2.R, man/heatmap.2.Rd: - Integrated my extensions into
+	  the R 1.8.0 version of heatmap.
 	  - Add Rd documentation.
 
 2003-11-19 14:52  warnes
 
-	* trunk/gplots/man/bandplot.Rd: Remove extranious NULL that
-	  confused R CMD check.
+	* man/bandplot.Rd: Remove extranious NULL that confused R CMD
+	  check.
 
 2003-11-18 18:59  warnes
 
-	* trunk/gplots/man/barplot2.Rd: - Tiny fix to remove R CMD check
-	  error.
+	* man/barplot2.Rd: - Tiny fix to remove R CMD check error.
 
 2003-11-18 18:58  warnes
 
-	* trunk/gplots/man/smartlegend.Rd: - Added missing closing brace.
+	* man/smartlegend.Rd: - Added missing closing brace.
 
 2003-11-18 18:45  warnes
 
 	* trunk/gdata/R/elem.R, trunk/gdata/R/env.R,
 	  trunk/gdata/R/is.what.R, trunk/gdata/R/keep.R,
-	  trunk/gdata/R/ll.R, trunk/gplots/R/overplot.R: - Convert from
-	  MS-Dos to Unix line endings.
+	  trunk/gdata/R/ll.R, R/overplot.R: - Convert from MS-Dos to Unix
+	  line endings.
 	  - Reformat to 80 columns.
 
 2003-11-10 22:11  warnes
@@ -1015,61 +1031,56 @@
 	  trunk/gdata/R/is.what.R, trunk/gdata/R/keep.R,
 	  trunk/gdata/R/ll.R, trunk/gdata/man/elem.Rd,
 	  trunk/gdata/man/env.Rd, trunk/gdata/man/is.what.Rd,
-	  trunk/gdata/man/keep.Rd, trunk/gdata/man/ll.Rd,
-	  trunk/gplots/R/heatmap.2.R, trunk/gplots/R/overplot.R,
-	  trunk/gplots/R/plotmeans.R, trunk/gplots/R/space.R,
-	  trunk/gplots/R/wapply.R, trunk/gregmisc/DESCRIPTION,
-	  trunk/gtools/R/capture.R, trunk/gtools/man/capture.Rd: - Add
-	  files contributed by Arni Magnusson
+	  trunk/gdata/man/keep.Rd, trunk/gdata/man/ll.Rd, R/heatmap.2.R,
+	  R/overplot.R, R/plotmeans.R, R/space.R, R/wapply.R,
+	  trunk/gregmisc/DESCRIPTION, trunk/gtools/R/capture.R,
+	  trunk/gtools/man/capture.Rd: - Add files contributed by Arni
+	  Magnusson
 	  <arnima@u.washington.edu>. As well as some of my own.
 
 2003-08-19 14:58  warnes
 
-	* trunk/gplots/R/heatmap.2.R: - Copy of local changes.
+	* R/heatmap.2.R: - Copy of local changes.
 
 2003-08-19 14:57  warnes
 
-	* trunk/gplots/R/heatmap.2.R: - Checkin before re-integrating
-	  local changes.
+	* R/heatmap.2.R: - Checkin before re-integrating local changes.
 
 2003-06-19 21:23  warnes
 
-	* trunk/gplots/R/heatmap.2.R: - Added enhanced heatmap function.
+	* R/heatmap.2.R: - Added enhanced heatmap function.
 
 2003-06-09 15:10  warnes
 
-	* trunk/gplots/man/smartlegend.Rd: - Add help text for smartlegend.
+	* man/smartlegend.Rd: - Add help text for smartlegend.
 
 2003-06-09 14:57  warnes
 
-	* trunk/gplots/R/smartlegend.R: - New function smartlegend().
+	* R/smartlegend.R: - New function smartlegend().
 
 2003-04-22 17:28  warnes
 
-	* trunk/gplots/R/plotmeans.R: - Fixeed warning messing caused when
-	  'connect' is a vector.
+	* R/plotmeans.R: - Fixeed warning messing caused when 'connect' is
+	  a vector.
 
 2003-04-22 15:34  warnes
 
-	* trunk/gplots/R/barplot2.R: Update from Marc Schwartz, modified
-	  by Gregory Warnes:
+	* R/barplot2.R: Update from Marc Schwartz, modified by Gregory
+	  Warnes:
 	  
 	  - Modified dim() checks for 'ci.l' and 'ci.u' against 'height'
-	  to remove R v1.7.0 if() based error msgs for vector
-	  conditions.
+	  to remove R v1.7.0 if() based error msgs for vector conditions.
 
 2003-04-04 13:49  warnes
 
-	* trunk/gplots/R/balloonplot.R, trunk/gplots/man/qqnorm.aov.Rd,
-	  trunk/gtools/R/dirichlet.R: - Change occurences of 'T' to 'TRUE'
+	* R/balloonplot.R, man/qqnorm.aov.Rd, trunk/gtools/R/dirichlet.R: -
+	  Change occurences of 'T' to 'TRUE'
 
 2003-04-04 13:44  warnes
 
-	* trunk/gplots/man/textplot.Rd: - Updated to match changes in
-	  textplot function:
+	* man/textplot.Rd: - Updated to match changes in textplot function:
 	  - Added textplot.character
-	  - Renamed arguments "col.margin" and "row.margin" to "cmar",
-	  and
+	  - Renamed arguments "col.margin" and "row.margin" to "cmar", and
 	  "rmar" so that specifying "col='red'" is possible.
 	  - Fixed R CMD check errors
 	  - Improve comments in example
@@ -1077,65 +1088,62 @@
 
 2003-04-04 13:41  warnes
 
-	* trunk/gplots/R/textplot.R: - Added textplot.character to handle
-	  character strings.
+	* R/textplot.R: - Added textplot.character to handle character
+	  strings.
 	  - Moved test for vector and matrix arguments to textplot.default.
 	  - Renamed arguments "col.margin" and "row.margin" to "cmar", and
 	  "rmar" so that specifying "col='red'" is possible.
 
 2003-04-02 22:29  warnes
 
-	* trunk/gplots/R/textplot.R, trunk/gplots/man/textplot.Rd: - Added
-	  textplot function and friends, as well as documentation.
+	* R/textplot.R, man/textplot.Rd: - Added textplot function and
+	  friends, as well as documentation.
 
 2003-03-08 16:30  warnes
 
-	* trunk/gplots/man/balloonplot.Rd: - Forgot to update arglist in
-	  \usage section.
+	* man/balloonplot.Rd: - Forgot to update arglist in \usage section.
 
 2003-03-08 16:22  warnes
 
-	* trunk/gplots/R/balloonplot.R, trunk/gplots/man/balloonplot.Rd: -
-	  Added parameters for rotation of and amount of space allocated
-	  for
+	* R/balloonplot.R, man/balloonplot.Rd: - Added parameters for
+	  rotation of and amount of space allocated for
 	  the row and column labels.
 
 2003-03-07 15:48  warnes
 
-	* trunk/gmodels/R/fast.prcomp.R, trunk/gplots/R/hist2d.R,
-	  trunk/gplots/R/qqnorm.aov.R, trunk/gregmisc/DESCRIPTION,
-	  trunk/gtools/R/RSCompat.S: - Minor changes to code to allow the
-	  package to be provided as an
+	* trunk/gmodels/R/fast.prcomp.R, R/hist2d.R, R/qqnorm.aov.R,
+	  trunk/gregmisc/DESCRIPTION, trunk/gtools/R/RSCompat.S: - Minor
+	  changes to code to allow the package to be provided as an
 	  S-Plus chapter.
 
 2003-03-07 15:43  warnes
 
-	* trunk/gplots/R/lowess.R: - Add 'NULL' as the last element of if
-	  statement that defines
+	* R/lowess.R: - Add 'NULL' as the last element of if statement that
+	  defines
 	  lowess.default so that when the file is sourced, S-Plus doesn't
 	  display the function definition.
 
 2003-03-07 15:41  warnes
 
-	* trunk/gplots/R/lowess.R: - Specify where the defualt lowess
-	  function should be found.
+	* R/lowess.R: - Specify where the defualt lowess function should be
+	  found.
 	  - Use getFunction in S-Plus instead of 'get'
 
 2003-01-30 21:43  warnes
 
-	* trunk/gplots/R/barplot2.R, trunk/gplots/man/barplot2.Rd: - Added
-	  argument 'add' to allow for the addition of a barplot to an
+	* R/barplot2.R, man/barplot2.Rd: - Added argument 'add' to allow
+	  for the addition of a barplot to an
 	  existing graphic. Default is FALSE
 
 2003-01-20 18:35  warnes
 
-	* trunk/gplots/R/balloonplot.R, trunk/gplots/man/balloonplot.Rd: -
-	  Updated balloonplot help page.
+	* R/balloonplot.R, man/balloonplot.Rd: - Updated balloonplot help
+	  page.
 
 2003-01-20 17:13  warnes
 
-	* trunk/gplots/R/wapply.R, trunk/gplots/man/wapply.Rd: - Updated
-	  wapply.R to allow specification of evaluation points when
+	* R/wapply.R, man/wapply.Rd: - Updated wapply.R to allow
+	  specification of evaluation points when
 	  method is 'width' or 'range' using the 'pts' argument.
 	  - Updated wapply.Rd to add 'pts' argument
 	  - Fixed typos, spelling errors, gramatical errors and lack of
@@ -1144,62 +1152,58 @@
 
 2003-01-03 21:34  warnes
 
-	* trunk/gplots/R/balloonplot.R, trunk/gplots/man/balloonplot.Rd: -
-	  Initial checkin of balloonplot functions and documentation.
+	* R/balloonplot.R, man/balloonplot.Rd: - Initial checkin of
+	  balloonplot functions and documentation.
 
 2003-01-03 19:23  warnes
 
-	* trunk/gplots/man/space.Rd: - Added reference to and comparison
-	  example of sunflowerplot.
+	* man/space.Rd: - Added reference to and comparison example of
+	  sunflowerplot.
 	  - Added code to put example plots on same plot window using
 	  par(mfrow=...).
 
 2003-01-02 16:09  warnes
 
-	* trunk/gplots/R/barplot2.R: - Changed assignment statements that
-	  used "=" to "<-" to avoid syntax
+	* R/barplot2.R: - Changed assignment statements that used "=" to
+	  "<-" to avoid syntax
 	  errors in older versions of the S language.
 
 2003-01-02 16:07  warnes
 
-	* trunk/gplots/R/lowess.R: - Added wrapper code so that R-specific
-	  fiddling won't be executed
+	* R/lowess.R: - Added wrapper code so that R-specific fiddling
+	  won't be executed
 	  under S-Plus.
 
 2003-01-02 15:40  warnes
 
-	* trunk/gplots/R/qqnorm.aov.R, trunk/gplots/man/qqnorm.aov.Rd: -
-	  Renamed first parameter to match qqnorm generic.
+	* R/qqnorm.aov.R, man/qqnorm.aov.Rd: - Renamed first parameter to
+	  match qqnorm generic.
 
 2003-01-02 15:14  warnes
 
-	* trunk/gplots/man/qqnorm.aov.Rd: Added additional help text from
-	  Kjeitl.
+	* man/qqnorm.aov.Rd: Added additional help text from Kjeitl.
 
 2002-12-31 19:50  warnes
 
-	* trunk/gplots/R/qqnorm.aov.R, trunk/gplots/man/qqnorm.aov.Rd:
-	  Initial checkin of qqnorm.aov function and documentation
-	  submitted by
+	* R/qqnorm.aov.R, man/qqnorm.aov.Rd: Initial checkin of qqnorm.aov
+	  function and documentation submitted by
 	  Kjetil Halvorsen <kj...@ju...>.
 
 2002-11-04 14:21  warnes
 
-	* trunk/gplots/R/barplot2.R, trunk/gplots/man/barplot2.Rd: Updates
-	  from Marc Schwartz:
+	* R/barplot2.R, man/barplot2.Rd: Updates from Marc Schwartz:
 	  
-	  - Updated underlying code to be based upon the new barplot() in
-	  R v1.6.1
+	  - Updated underlying code to be based upon the new barplot() in R
+	  v1.6.1
 	  - This now uses the 'axis.lty' and 'border' arguments
 	  - In R v1.6.0, R Core introduced a new function called axTicks().
 	  This is an R equivalent of the C code for CreateAtVector in
 	  plot.c.
 	  This now enables me to get the axis tick mark positions
 	  consistently
-	  when the 'height' related axis is either linear or log. Thus,
-	  I can
-	  now have consistent tick marks and can plot grid lines in
-	  either
+	  when the 'height' related axis is either linear or log. Thus, I
+	  can
+	  now have consistent tick marks and can plot grid lines in either
 	  situation. If 'plot.grid = TRUE' and 'grid.inc' is specified,
 	  then
 	  I still use pretty() to determine the tick marks and lines.
@@ -1207,23 +1211,22 @@
 
 2002-10-30 02:21  warnes
 
-	* trunk/gplots/R/plot.lm.R: - Commented out plot.lm() code since
-	  recent changes in R have broken it.
+	* R/plot.lm.R: - Commented out plot.lm() code since recent changes
+	  in R have broken it.
 
 2002-10-11 18:02  warnes
 
-	* trunk/gplots/R/barplot2.R: - Fixed log scale errors in legend()
-	  call
+	* R/barplot2.R: - Fixed log scale errors in legend() call
 
 2002-10-01 18:16  warnes
 
-	* trunk/gplots/man/hist2d.Rd: - Added examples of using 'contour'
-	  and 'filled.contour' for display.
+	* man/hist2d.Rd: - Added examples of using 'contour' and
+	  'filled.contour' for display.
 
 2002-09-24 14:53  warnes
 
-	* trunk/gplots/R/plotmeans.R: - Changed digits=options("digits")
-	  which produces a list of length 1
+	* R/plotmeans.R: - Changed digits=options("digits") which produces
+	  a list of length 1
 	  to digits=getOption("digits") which returns a vector of length
 	  one.
 	  The former was causing an error when passed to round().
@@ -1231,10 +1234,10 @@
 2002-09-23 14:27  warnes
 
 	* trunk/gmodels/man/CrossTable.Rd, trunk/gmodels/man/glh.test.Rd,
-	  trunk/gplots/man/barplot2.Rd: - Fixed syntax errors in
-	  barplot2.Rd and CrossTable.Rd
-	  - Fixed incorrect translation of 'F' (distribution) to 'FALSE'
-	  in glh.test.Rd
+	  man/barplot2.Rd: - Fixed syntax errors in barplot2.Rd and
...
 
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