FIXED BUGS LIST
I.  FIXED BUGS
II. ENHANCEMENTS
=================================================================

I.  FIXED BUGS

AUTOMATION EXTENSIONS
   If you have S-PLUS running and you try to use 
   automation to start up the S-PLUS OEM kit edition,
   it will not start because it detects the 
   presence of another S-PLUS instance.  (31749)

BIGDATA LIBRARY
   In S-PLUS big data, the data.dump() function 
   failed to dump bdFrames returned from the 
   bd.aggregate() function.  (41037)

   S-PLUS big data could not add a scalar 
   timeSpan to a big data timeDate vector.  (31615)

   Calling table() with the returned value from 
   cut(<<bdVector>>) created a bdNumeric vector 
   that caused an error.  (40978)

   The hist() function was unable to plot a big 
   data vector containing the same value for each 
   element.  (41104)

   Merging bdTimeSeries objects did not work 
   correctly with a small block size.  (41669)

   The cut() function did not handle NA values 
   in big data objects.  (41670)

   The bd.join() function did not correctly 
   return the column names after a join was 
   perfomed.  (41707)

   The bd.unstack() function became confused 
   when a group column value was same as key column 
   name.  (42165)

   Getting min/max of a timeDate column in a 
   bdFrame was slower than getting min/max of a 
   numeric column.  (42330)

   In S-PLUS big data, print.rows and print.cols 
   arguments have been added to the bdSeries 
   print method. For the bdVector print method, 
   a print.elements argument that defaults to
   bd.options("print.bdVector.elements")[[1]] 
   has been added.  (31607)

   Previously, setting bd.options(max.block.mb = 100) 
   and then running bd.by.group() on a large dataset 
   resulted in a java.lang.OutOfMemoryError.  The 
   default value of java heap size has increased, and
   error messages now appear if bd.options block size 
   is not set high enough. See Release Notes for 
   more information.   (31326)

   Some operations on bdFrame objects caused the 
   loss of column names.  (42310)

   Using cut() on a bdVector and specifying -Inf 
   or Inf as part of breaks argument resulted in an 
   error. (43398)

   bdTimeDate() and timeDate() returned inconsistent 
   default years. (44927)

   The Big Data predict methods erroneously required 
   the response variable to be present. (44763)


CONNECT/JAVA
   The S-PLUS exception classes (SplusBadDataException, 
   SplusEngineBusyException, SplusIncompleteExpressionException, 
   and SplusLicenseException) each now give a meaningful message. 
   (44517)

   SplusSessionImpl can issue an exception in two cases: 
   if the S-PLUS engine is currently busy, or if the 
   query times out. You now see a message describing the 
   type of exception occurring in these cases. (44518)

   SplusSessionImpl can issue an exception in two 
   cases: if the previous S-PLUS engine query was not 
   completed, or if the query timed out waiting for the 
   previous query to complete. You now see a message 
   describing the type of exception occurring in these 
   cases. (44519)

EXPRESSION LANGUAGE
   When converting text to Double with the 
   Expression Language's asDouble() function, 
   negative signs were recognized but positive 
   signs were not. For example, "-21" became 21, 
   but "+42" became NA.  (41020)

GRAPHICS
   The following message was generated in the 
   GUI if you ran Statistics-->Tree-->Tree Tools
   -->Histogram: "Warning messages: Retrieving 
   data from kyphosis".  (20593)

   When you drew a trellis plot with as.table=T, 
   the bottom x-axis was not drawn if the layout 
   caused the last panel not to be at the bottom 
   of the page. This resulted in the x-axis not being 
   drawn. (44723)

   Setting the graphical parameter par(mar) would break 
   graphical coordinates. (44730)

   Specifying xlim or ylim when plotting small spans 
   of data on a log scale would not work. (29843)

   Running Splus -j on Linux/UNIX with the 
   DISPLAY variable set to an X server (such as 
   XWin32 or Cygwin) on a PC sometimes caused 
   java.graph() to position a window partially 
   off the screen. This has been fixed such that 
   java.graph() always positions windows within 
   the display area, and alternates their 
   position to prevent multiple windows from 
   overlapping.   (40979)

   After creating a horizontal bar graph through 
   the GUI with a dataset, upon closing the 
   graphsheet, S-PLUS could appear to be hung. 
   It was actually just taking a long time to 
   process a large number of data points.  (25013)

   The trellis.settings data sets caused problems when
   the lists of the elements were different lengths.
   All of elements of the inner lists now have the  
   same length.  This avoids problems when calling  
   trellis.par.set to change values in one of the  
   inner lists. (21963)

GRAPHICS APPEARANCE
   On Windows, there were inconsistencies 
   between histograms generated from the GUI and 
   histograms generated from the command line.   
   (17704)

GRAPHICS COMMAND_LINE
   The menuXyplot() function failed if the 
   "groups" argument was specified and the 
   grouping column had missing values.  (25253)

GRAPHICS DEVICE
   Plots on the java.graph device were limited 
   to a maximum symbol size determined by 
   cex=2.7 and csi=0.29.  (31397)

GRAPHICS DISPLAY
   The maxiumum text size in java.graph was 
   approximately cex=2.7 or 2.8.  (41097)

GRAPHICS EXPORT
   On Windows, fill patterns such as 
   crosshatching did not replicate correctly 
   when the associated graphsheet was exported 
   to a file in WMF format. The resulting WMF 
   had more lines in hatching or diagonal than 
   it should.  (13075)

   On Windows, java.graph(file="abc") failed 
   without generating an error message if "abc" 
   already existed and was read-only. An error 
   message is now generated in this situation.  (41067)

   On Windows, the winjava library support for 
   saving non-interactive Scalable Vector 
   Graphics (SVG) files did not save an SVG file 
   and did not generate an error message. Saving 
   SVG files is now supported.  (41803)

GRAPHICS SCRIPT GENERATION
   The guiCreate("Legend"...) command did not 
   appear in the history file after choosing 
   "Insert" -> "Legend", but clicking the "Auto 
   Legend" button did result in a guiCreate call.
   (20707)

   The "Horizontal Grouped Box" button in the 
   ExtraPlots palette did not record its plot 
   type in the History Log. The command 
   'guiPlot(PlotType = "", ....)' was recorded 
   instead.  (21188)

GUI
   In wide multi-select list boxes, items 
   sometimes appeared to become deselected when 
   the user took no action to deselect them. For 
   example, in a list box with a long list of 
   options, all selected by default, an item 
   could appear to become deselected if the user 
   took another action such as selecting a check box.  
   (40062)

   on Windows, With the Options-->General 
   Settings-->Startup "Prompt for project folder"
   feature enabled, upon startup S-PLUS prompted 
   with a default of  C:/Documents and Settings/
   <username> regardless of the setting last 
   time the program was exited. Also, when that 
   startup feature was disabled, S-PLUS still 
   prompted upon startup but did not include a 
   drop-down list of recent directories.  (31680)

   The file path displayed in the Open S-PLUS 
   Project window did not allow you to scroll to 
   the end of a long path.  (41182)

   Selecting the S-PLUS Options-->General 
   Settings-->Startup option "Set Region-
   specific defaults" could cause an error in 
   the output date.  (41385)

   In some cases, items in the Help -> Online 
   Manuals menu in the Windows GUI would be 
   disabled (greyed out) after upgrading to 
   Adobe Reader 7.0.  (43708)

GUI DATA EDITOR
   The S-PLUS Big Data Viewer showed incorrect 
   min and max values in the Date tab.  (41571)

GUI DIALOGS
   On Windows, the File-->Import Data-->From 
   Database dialog generated an error and failed 
   if you entered a SQL query containing line 
   breaks.  (41331)

   The Nonlinear Regression dialog saved fitted 
   values as read-only. This has been changed to 
   save as writable by default.  (41558)

   In the S-PLUS GUI, Data-->Recode returned the 
   wrong "Current Value" for factors that have 
   numbers as levels (e.g., "1,2,3").  (41597)

GUI GRAPHICS
   On Windows, a pie chart generated from the 
   GUI using factors containing NA values 
   displayed abnormal dots and slashes around 
   the first slice drawn. If you resized the 
   graph, the first slice sometimes changed 
   colors and then disappeared.  (21008)

   On Windows, line/Scatter plots created from 
   large data sets that have a dashed line with 
   a thickness of 2 or greater did not produce a 
   smooth line.  (22499)

   On 2D conditioned plots created from the GUI, 
   changing the x Column from the Plot Summary 
   dialog box (right-click-->Plot Summary) 
   changed the x-axis label but the plot 
   remained the same; it was not redrawn with the 
   new data.  (25547)

   On Windows, on 3D plots from the GUI, using 
   factor variable for one of the axes caused 
   axis labels to be displayed as numeric 
   representation, not as the factor's text 
   representation.  (27575)

   On Windows, lines in plots created from the 
   GUI were not smooth. This was especially 
   apparent with horizontal lines.  (27596)

   On Windows, Trellis (conditioned) GUI charts 
   using the Robust LTS plot type failed. The 
   plots were incorrect and fit line was missing.  
   (28802)

   On Windows, generating a Contour Plot from 
   the GUI caused a warning and the plot was not 
   generated if you specified a subset in the 
   “Subset Rows with" field.  (28810)

   On Windows, when creating a trellis 
   multipanel plot from the GUI, if you changed 
   the strip fill color (by selecting Fills from 
   the right-click menu and then selecting 'Save 
   Panel Strips as default' from the right-click 
   menu) and then created another multipanel plot.
   the strips had the old fill color.  (29696)

   On Windows, when creating a conditioned bar 
   plot from the GUI, if you had multiple bars 
   with the same value, changing the bar color 
   for the first one changed the color of all 
   bars with that value.  (30603)

   On Windows, on the first attempt to scroll to 
   the bottom of a data set viewer in the GUI, 
   the scroll bar did not reach the last line in 
   the data set.  (40327)

   On Windows,in a GUI scatter plot with symbols 
   varied by color, the 'Select data points' 
   tool did not highlight points in red.  (40364)

   On Windows, in multi-page graphsheet, if you  
   'Convert to Objects' any page except the last.
   it moved to the last page and disappeared 
   from the original.  (40499)

   On Windows, modifying GUI boxplot 
   WhiskerCalcStyle via command line resulted in 
   'bp.trunc' error and corrupt session.  (40507)

   On Windows, plot borders were sometimes 
   missing when printing multi-page GUI 
   conditioned plots.  (40545)

   On Windows, importing data via the GUI with 
   attached .csv file produced the following 
   error: "Syntax error: illegal "if" on input line 3".  
   (40722)

   Immediately after starting S-PLUS, an error 
   would be generated by a call to guiModify() 
   with the argument VaryAxisRange=T to change a 
   gui plot.  (41352)

   On Windows, guiPlot("Bubble", DataSetValues=mydata)
   generated the following error message when 
   subsequent calls to guiPlot(), attach() or 
   detach() were made: 'Problem: Syntax error: 
   illegal "[" on input line 1' . Interferes 
   with detaching a data.frame.  (28620)

GUI OPTIONS
   Importing data via File-->Import Data-->From 
   File caused the following error if you 
   clicked the Show Columns button on the 
   Columns tab: Syntax error illegal name 
   ("guiOpenView") on input line 2 error.  (41272)

IMPORT/EXPORT
   On Linux, importData(type="DIRECT-*") caused 
   the following error: "Cannot load library: 
   libstsyb.so.1". However, no reason was given.
   (31631)

   An error was generated when the startRow 
   argument was used in openData().  (40489)

   Upper-case letters in the column names of 
   data frames were converted to lower-case by 
   exportData(type="SPLUS").  (40568)

   On Unix, exportData type="SPLUS" did not 
   output data.dump format.  (40572)

   On Windows, when you imported data from an 
   Excel file that contained NAs in a numeric 
   column, the column would be imported as 
   character, rather than numeric, and values 
   might be truncated. (43350)

   On Windows, in the importData dialog, the 
   Show Columns view on the columns tab displayed 
   unwanted columns if the imported Excel data file 
   contained a column offset. (44769)

IMPORT/EXPORT ASCII
   On Windows, opening two files at once with 
   openData() could lead to incorrect results 
   from readNextDataRows or writeNextDataRows.  
   (41438)

   The following parameters did not restrict the 
   imported results to one row: importData:startRow=1, 
   endRow=1. They returned the complete table.  (31722)

IMPORT/EXPORT DATABASE
   Native database connections did not work with 
   SQL Server 2005 client.  (40977)

IMPORT/EXPORT FILE_IMPORT)
   S-PLUS now allows long column names of up to 
   256 characters. (28518)

IMPORT/EXPORT FILE_EXPORT
   When exporting data with bigdata=TRUE, the 
   maximum length of na.string was 8 characters. 
   This has been increased to 11 characters 
   (same as the maximum number of characters 
   when exporting standard data).   (31596)

IMPORT/EXPORT ODBC
   On Windows, an error was generated when 
   importing via ODBC with an umlaut character 
   in the table name and bigdata=T.  (41241)

INSTALLATION
   On Windows, after an S-PLUS Windows 
   installation was removed, the Windows Add/Remove 
   Programs tool still listed entries for the 
   S-PLUS modules, although the modules had been 
   removed.  (41028)


LICENSE
   Running an S-PLUS 7 script named "server" via 
   the command "Splus LICENSE server start" 
   produced an error when there were multiple 
   license files.  (40701)

   Running S-PLUS from Java caused a FLEXlm 
   License Finder dialog to appear.  (40737)

LICENSE EXTENSIONS
   On Linux, S-PLUS did not check out 00 license.
   although module() does check out a module 
   license. This was due to a bug in S-PLUS 
   LICENSE users; as flexlm server log file 
   showed Linux licenses being checked in and out.
   (31715)

MULTIVARIATE_ANALYSIS STATS/MODELS
   The summary.discrim() function failed with 
   the following error if the group variable had 
   level names that were not valid S-PLUS object 
   names: Problem in "[.data.frame"(x, ..1, ..2):
   undefined columns selected.  (23870)

PACKAGES
   Previous messages for running library(pkgutils) 
   and install.pkgutils() were unclear. (44715)

PERFORMANCE
   In Windows, the Commands window did not 
   scroll up or down when using the mouse 
   wheel. (41982)

   In Windows, resizing the Commands window, 
   and then saving the window size as the default 
   resulted in a History Display error. (44742)

   In Windows, the state.vbm map files erroneously 
   went missing in the S-PLUS distribution. They 
   are back now. (24251)

REGRESSION STATS/MODELS
   The multicomp function does not handle 
   objects with class aovlist. The following 
   error was generated: Problem in multicomp: 
   argument adjust= not matched. This now returns 
   a more informative error message.  (28413)

S LANGUAGE
   A problem with the assign() and get() 
   functions caused S-PLUS to become unstable 
   and generate the following error: "Problem in 
   rbind.data.frame: Missing value where logical 
   needed... Error during wrapup: No data to 
   interpret as logical value"  (31660)

   The merge() function did not handle the case 
   where a vector was merged with a data.frame.  
   (40524)

   The word "return" is not a reserved word in R.
   although it is the name of a function. In
   S-PLUS, it was reserved by the parser.  (40774)

   Creating a class with an undefined class 
   caused Workbench to crash.  (40782)

   "The rm() function accepted only unquoted 
   names, even if you used the backquote syntax 
   to specify a non-syntactic name.  (41119)

   The ymin argument to the plot.survfit() 
   function did not work correctly.  (15675)

   For scripts that generated the error: "Problem:
   internal error: trying to free an overwritten 
   block of S storage, probably in frame 1" 
   executing the code a second time caused 
   S-PLUS to close.  (30975)

   A call to if(expr || expr) failed if the 
   left expr was NULL.   (41254)

   If the number of milliseconds in timeSpan() 
   was equivalent to less than 24 hours, result 
   was not converted to days (for example, 
   timeSpan(ms=86400000)).  (43511)

   The function deriv() did not handle atan, 
   asin, or acos. (10249)

   Running the function supsmu() in a while 
   loop would cause S-PLUS to crash. (44817)

   complete.cases() did not provide expected 
   results. (44716)

   Subscript replacement for a data frame now 
   uses the current version of 
         "[<-.data.frame", 
   rather than an outdated version. 
   Also, Subscript replacement for a data frame 
   now handles replacement for zero rows correctly; 
   e.g. this will now work when all values of 
   z are  
       < 3:x[ which(z>3), 1:2] <- x[ which(z>3), 3:4] 
   (44855)

   The method file.copy omitted null bytes from 
   the resulting copy. (44462)

S LANGUAGE METHODS/CLASSES
   functionArgs<- replacement did not coerce a 
   return back to a function.  (41187)

   If you set options(warn=2), the message "Engine 
   connection failure" was returned when a defining 
   function with assignment was the last expression.
   Now, it returns more useful message. (41024)

S-PLUS
   The crosstabs() function's na.action=na.include
   argument was ignored if the variable in the 
   formula was numeric.  (40757)

   The format() function on an NA numeric matrix 
   with a justify argument did not keep 
   dimension settings.  (41185)

   trace(plot,browser) caused problems with F2 
   key (expand plot window to entire screen) and 
   command echoing.  (40052)

   The dumpClass() and dumpInterface() functions 
   failed because they used cat(fill=2), which 
   is only in SV4 (not in Splus or R).  (40913)

   Calls to help and find.doc failed if the 
   attached directory included the word "Data" 
   (for example, FunctionalData). (40415)

   World map has been updated and errors 
   fixed. (40928)

   The sconnect source code would not compile 
   under Microsoft Visual Studio 2005. (42384)

SPXML
   Using xml2pdf() to convert an XML file 
   produced from a matrix by the createXMLFile() 
   function resulted a PDF that contained only 
   the header.  (40066)

   The createXMLFile() function failed if 
   winjava library was not loaded.  (40421)

   An XML file larger than 35 MB could be 
   processed by a command-line SAX xsl 
   transformer but not by SPXML.  (40881)

   The SPXML library example summaryReport 
   produced errors because of white space
   in the fo:table-cell. (44775)

STATS/MODELS
   The glme() function failed if the 
   observations for one of the levels of a fixed 
   effect factor variable were missing.  (40818)

   The cmdscale() function failed if the 
   optional k argument (desired dimensionality 
   of the output space) was k=1.  (41000)

   The results of cor.test() are now printed 
   even if the correlation is greater than 
   0.999999.  (41010)

   The nls() function did not return derivatives 
   as expected.  (41671)

   The plot.lmRob() function failed with the 
   following error if final.alg="Adaptive":Problem
   in test.lmRob(object[[i]]): Tests for bias 
   are only available for MM-estimates.  (41731)

   The fix for the lmRob.fit.compute() function 
   specified in the book "Robust Statistics: 
   Theory and Methods" has been implemented (for 
   details, refer to 
   http://www.insightful.com/support/splusbooks/robstats/).
   (42062)

   The print.summary.survfit() function returns 
   an error if the summary.survfit object is 
   created using the design library.  (41253)

   The R-squared value was not included in the 
   summary of an mlm object.  (40834)

   predict.gls might fail when passed newdata, 
   and resulted in an array subscript out-of-bounds 
   error.  (41082)

   In the Robust library, if you called plot.lmfm, 
   the plot was not correct when there was a single 
   covariate in the model.

   print.aov displayed the wrong Residual Sum of 
   Squares if the model had weights. (44645)

WORKBENCH
   When you copy code from the Console View or 
   the Output View, you now have the option of 
   copying the prompts. See the help for S-PLUS 
   preferences for more information.  (31006)

   The S-PLUS Workbench now has a "Stop" button 
   in the Console and other views  (41494)

   Previously, the S-PLUS engine was not 
   initialized until the Console Tab is activated 
   Now, the S-PLUS engine is initialized when 
   you start the Workbench.  (41890)

   Previously, the Variables view default 
   displayed all values of all variables. This 
   could create problems for code that contained 
   hundreds or thousands of variables. Now, the 
   default limit is 100; however, the user can 
   change this default.  (41933)

   In the S-PLUS Workbench, the function 
   .on.attach containing library(libname, T) did 
   not load the library after toggling to project.
   This has been corrected.  (41962)

   When you create an S-PLUS project in the 
   Workbench, now, it is automatically set to be 
   the working project, and a .Data directory is 
   created, where the project's data objects are 
   stored. The user can change this option to 
   set the working directory to the workspace 
   (and its .Data directory).  (42002)

   Sometimes, formatting code in the S-PLUS 
   Script Editor changed the color unexpectedly. 
   This no longer occurs.  (42028)

   The S-PLUS Workbench now automatically saves 
   a script file before sourcing.  (42035)

   The browser no longer displays an extra line 
   prompt.  (42059)

   The S-PLUS Workbench now uses the default 
   Eclipse text editor sections; therefore, many 
   options and preferences previously not 
   available in the S-PLUS Script Editor now 
   work as expected..  (41640)

   History view now displays the correct 
   information in the tip box.  (41916)

   Default font for Console/Output has changed 
   from Tahoma 8pt Courier 10pt.   (42825)

   The data viewer in the S-PLUS Workbench displayed 
   incorrect matrix dimensions. (44550)

   The Workbench debugger did not always catch a 
   breakpoint because of an error in array handling 
   in an internal Eclipse function. (44617)

   Preference selections caused incorrect formatting 
   of inline functions. (44719)

   Using the browser() function within the Workbench  
   caused it to crash. (44759)

   When you specified a PDF viewer using S-PLUS Workbench  
   preferences, the specified viewer opened in a modal 
   dialog. (44760)

   In the Workbench, The S-PLUS Editor Syntax Highlighting 
   (color) did not match what was displayed. (44870)


WORKBENCH DEBUGGER
   Graphics now appear as expected when you work 
   in the Debugger mode.  (41886)

   Using the debugger and profiler can slow down 
   computing time and consume a lot of memory. 
   This problem has been partially addressed. 
   (44754)


===================================================
II.  ENHANCEMENTS. 

JAVA
   You can now automatically load the JVM from within 
   S-PLUS by calling a function (such as java.graph) 
   that requires it. This change means that you do not 
   need to accommodate the overhead of the JVM until you  
   need it.

WORKBENCH
   The right-click menu for the S-PLUS Script Editor has  
   been enhanced.

   You can now source multiple files in the Workbench

   The .r file extenstion is now associated with S-PLUS color 
   layout in the Workbench.

   Using the Find References menu item, you can now easily  
   find all of the locations in a project where a certain  
   function is called.

   Graph devices are now embedded in the Workspace view.  
   They appear to the right of the Console/Output view: by  
   default in the lower right corner. 
  
   You can now format script blocks using the text editor  
   preferences in the Workbench. 
  
   You can now clear the Workbench Console View input line  
   by pressing ESC. 

   You can now enter multiple keywords at a time in the 
   Workbench. 

   The Search Path View now automatically refreshes when you  
   select to toggle Working S-PLUS Project.

   The project name now is displayed in the Search Path view  
   instead of the entire path to the project.

   You can now switch between views (for example, from  Console  
   view to Output view) at any time, even when you are running 
   a command.

   In the Outline view, the view no longer collapses when you sort 
   alphabetically.

   You can now access all manuals from the Help>S-PLUS Manuals 
   menu option.

   The Workbench now includes a progress bar.

   The Workbench now features better visual cues to show when the  
   Console or Output views are busy.

   In the Workbench, you can now copy prompts from the console.

   You can now set the working S-PLUS Project from the File menu.

   You can create packages in the Workbench.

GRAPHICS
   The Line/Scatter Plot dialog now includes an option to vary line  
   color.

   If you set the current graphics device with dev.set(), it now also  
   sets guiSetCurrMetaDoc("GraphSheet", Name="x"), where "x" is the  
   graphics device you just set with dev.set(). Then dev.cur() and  
   guiGetCurrMetaDoc("GraphSheet") return the same graph sheet. 
  
   The Data to Plot page of the Line/Scatter Plot dialog now includes  
   a "Create Subset" button.

   trellis.par.get() now returns all possible arguments and parameters,  
   fully expanded.

   You can now plot an empty graphsheet by calling the plot function 
   and specifying no x and y length values. To set up the tick mark 
   parameters, specify xlim and ylim. For example, 
   plot(xlim=c(0,10), ylim = c(-1, 1)). The resulting plot has axes, 
   but the default xlab and ylab will be "".

S LANGUAGE

   The jitter() function now has an amount argument with a default 
   value of 0.

   The dhyper() and dwilcox functions now each have a log argument. 
   dhyper() sets log to FALSE by default; dwilcox() just uses the 
   log of what it computes.

   S-PLUS now includes the function lfactorial().

STATS/MODELLING
   Default contrastshave changed from "helmert" to "treatment"
 
   In summary.lm, the correlation argument is now False by default.
 
   In plot.lmRob, the argument for which.plots is now "all" by default.

OTHER
   On Linux. S-PLUS no longer links against library names with fixed  
   version numbers.

   You can now increase the default java max heap size using the -Xmx  
   option.

   The default time zone list now includes Western Europe Daylight 
   Time (WED)