Dear Emacs, please make this -*-Text-*- mode! ************************************************** * * * 1.2 SERIES NEWS * * * ************************************************** CHANGES IN R VERSION 1.2.0 NEW FEATURES o hclust() takes new argument `members' allowing dissimilarity matrices both for singletons (as until now) and clusters. o hist() now returns a "histogram" object and calls the new function plot.histogram() for plotting. It now also allows character labels. o The more recent GNU regex from grep-2.4.2 is used. o `where' command added to debug. o inherits() is now an internal function and compatible with S. o R CMD build and check have been completely re-written in perl. In addition to running examples, check now also checks the directory structure and control files, makes a temporary installation and runs LaTeX on the help pages. Build has been reduced to cleaning, rewriting indices and creating tar files. The same files of Perl code are now also used under Windows. o Add-ons for utilities like perl or LaTeX have now a central place in $R_HOME/share. Migration of existing files might take a while, though. o --nsize up to 50M (2Gb on 64-bit Solaris) allowed. o The commands history can be loaded with loadhistory(), saved with savehistory() and displayed with history(), under Windows and under Unix using the readline or GNOME interfaces. o if(*) now gives a more intelligible error message when "*" cannot be coerced to logical. o New function Rprof() for profiling R expressions under Unix. Configure with --enable-R-profiling to make this operational. o New functions file.access() and file.info() for information on files on the user's file systems. o New convenience function file.copy(). o New function Sys.info() for platform, host and user information. o New function Sys.sleep() to suspend execution for a while. o Sys.getenv() becomes the preferred name for getenv(), which is now deprecated. o New function Sys.putenv() to set environment variables. o Formerly deprecated function provide() is now defunct. o New command-line option --no-restore-history implied by --vanilla. o Command-line option --restore is now --no-restore-data and --no-restore implies --no-restory-* (currently `data' and `history'). o The `mode' argument of exists() and get() is interpreted as mode(x) rather than typeof(x), following S. o Configure/build variables MAINLD and MAINLDFLAGS are renamed to MAIN_LD and MAIN_LDFLAGS for consistency with other MAIN_* vars, simlarly for SHLIBLD and SHLIBLDFLAGS. o Much improved support for C++ code in add-on packages under Unix. New configure/build variables SHLIB_CXXLD and SHLIB_CXXLDFLAGS for specifying the command and flags needed for building shared libraries containing objects from a C++ compiler. Configure tries to get these right in typical cases (GNU tools and/or common platforms). C++ source suffixes `.cpp' and `.C' are now recognized in adddition to `.cc'. o .Platform has new component "endian", useful for binary file manipulations. BUG FIXES o Postscript driver nolonger uses the initclip operator, which was against the EPSF specifications and broke inclusion of graphics in some documents. ************************************************** * * * 1.1 SERIES NEWS * * * ************************************************** CHANGES IN R VERSION 1.1.1 NEW FEATURES o data(), example() and help() now search the loaded packages, then in their .lib.loc argument, the latter as pre-0.99.0. See their help pages for the precise details. o help() has a new argument `try.all.packages' set by the option "help.try.all.packages". If help is not found in the normal path and this is TRUE then a search is made of all packages for possible matches. BUG FIXES o data() now works correctly with data-only packages. o Standalone Mathlib can now be made if builddir = srcdir (working around an undocumented autoconf `feature'). o Check for pre-1.1.0 saved object .Postscript.options in postscript(). o More stringent checks on the arguments to dataentry(). o Specifying xlab as an expression now works again. o dev2bitmap() works again. o Numerous uses of `F' and `T' replaced by `FALSE' and `TRUE'. o bxp() now extends `ylim' properly when notch=TRUE (and a notch is more extreme than other stats). Also, varwidth is okay again, see example(split). o Making manuals without making R first now works. o princomp() now works when some eigenvalues are tiny negative values (which are treated as zero). o SearchEngine.html was not installed when builddir != srcdir. o lm.{w}fit(x,y,..) now work when x has no column names. These functions no longer add and subtract n zeros when there's no offset. They are now documented somewhat. o Some HTML files used src="R.css" instead of href="R.css" causing some browsers to ignore the style sheet. R.css now passes the w3c CSS validator and gives the intended results with Internet Explorer. o The data editor no longer crashes when entries contain more than 45 characters, and works correctly if the field width is larger than the window width. o Recording plots used to ignore graphics events before the last replay. o plot(), points(), etc now give warnings and error for invalid `type' arguments. o matplot() now allows the same `type's as plot(). o dev.print() and dev.copy2eps() now work when called from a function. o anova.glmlist works correctly with decreasing models and test="F" now gets the correct residual df. o Functions created (not just edited) with fix() now get environment .GlobalEnv not the body of fix. o Rdconv was ignoring OS-specific parts of the files with some Perl versions. (This did not affect installing packages.) o R CMD check did not run more than one specific test. o keyword2html omitted items when changing up a level, so the HTML search engine keyword list was missing `data' and `utilities', for example. o aov() with multiple strata was setting some spurious options. CHANGES IN R VERSION 1.1.0 NEW FEATURES o There are several changes to the compile and link flags, and an attempt is made to use /usr/local/include and /usr/local/lib on all platforms. Please read config.site and INSTALL if you have set flags for previous versions. o New package tcltk, providing interface and language bindings for the Tcl/Tk graphical interface toolkit. This makes it possible to do some rather nifty things with buttons and entry fields and so forth in very few lines of code. It is still somewhat experimental so don't go churning out thousands of lines of GUI code and then blame us for changing the API later on. It does not currently work with GNOME because of event loop differences. See demo(tkttest) and demo(tkdensity). o Internally using global R_Expressions [getOption("expressions")] dramatically speeds up eval.c. o The X11 support code is now in a separate shared library, and flag --gui=none will run R without X11 support (and so x11() and data.entry() will not be available). R BATCH sets --gui=none. o Configuring without X (e.g. --without-x) does work (at last). configure will report if X11 support has been included. If R has been built without X11 the default GUI is "none". o GNOME support files have moved from src/gnome to src/unix/gnome and the code is now in a separate shared library. Both --gui=GNOME and --gui=gnome are allowed. The main graphics device for use with GNOME is now called gtk(); the x11() device from the X11 support can also be used. (The gnome() device remains unreliable, and is by default unavailable.) All GNOME support now installs in R_HOME/gnome to make it easier to package separately. o Command line option `-g' can now be used as short version of `--gui'. o The "keep.source" option now defaults to interactive() instead of TRUE. o Many interface enhancements to the data editor, which now uses (by default) variable-width columns and much less redrawing. See ?dataentry for a description of the current user interface. o R under Unix can be sent SIGUSR1 to quit and save or SIGUSR2 to quit and save without running .Last and on.exit expressions. o Added ability to use the graphics device driver to perform horizontal justification of strings. This is used in the x11(), windows(), postscript() and xfig() drivers and will lead to more accurate placing of centred or right-justified strings. o Formulas created with the tilde operator now contain the environment in which they were created. The environment of a formula can be accessed with the environment() function. This facility is still experimental; it is intended to help simplify writing modeling functions. o $ and $<- are now generic functions. o add1.glm() and drop1.glm() now allow test="F", which is appropriate for models with estimated dispersion. o approx() and approxfun() have an extra argument ties= to control handling of tied x values o New function as.symbol(), identical to as.name(). is.symbol and is.name() are now identical by definition; before, they were equivalent by implementation. o attach() now works for R data files. o axis() now has additional arguments. The argument "tick" turns tick drawing on and off (on by default). Additional arguments line, pos, and outer; allow more flexible placement of axes. o New device bitmap(), like dev2bitmap() but a stand-alone device. o boxplot() returns (and bxp() accepts) a list containing the summary statistics for the boxes (changed from a list of elements one for each box). o file="|cmd" is allowed (to pipe output to `cmd'), under cat() and postscript() and functions that use them (for example, write()). o New functions chartr() for general-purpose character translation in character vectors, and tolower() and toupper() for converting alphabetic characters to lower-case and upper-case, respectively. o coplot() has new option subscripts=TRUE to pass the indices to the panel function. o cor.test(method="spearman") might give slightly better P values, since it now relies on pnorm() (with proper tail) instead of alnorm. o dbinom() works for size=0 (where appropriate). o New trivial function det() for determinant computation (the example in ?qr did not seem to be sufficient). o If present in the package, a function .Last.lib will be called when a package is detached. o New function dev.copy2eps() copies the current device to an eps file, taking the size from that of the device. o dev.print() now prints if possible, and takes the size from the device being copied. o edit() or fix() applied to a numeric or character matrix now uses the data editor, if available. o edit.data.frame() edits factors in character mode by default, and will allow the row names to be edited, by default if they are not 1:nrow(name). o expand.model.frame() for adding variables to a model frame. o The handling of estimating the dispersion in glm() fits has been changed for consistency across methods. For `binomial' and `poisson' families the dispersion is always taken as one. For `quasibinomial' and `quasipoisson' families it is always estimated (by residual chisq/residual df). o Using "~" when specifying lib.loc (for example to help() or library()) is now supported. o image() has a new argument "breaks" and divides the zlim range into equal-length intervals. o install.packages() and update.packages() have a new `destdir' argument for the directory to which to download the packages. o New function interaction.plot(). o Internal cleanup of lapply()'s C code. o library(), require(), and sys.source() have a new argument ` keep.source = getOption("keep.source.pkgs") '. This defaults to false, but can be set (also for base) to true by setting the environment variable R_KEEP_PKG_SOURCE to "yes" o Par `lty' in lines() now defaults to par("lty") not "solid", for consistency with plot(). o list.files() [aka dir()]: path argument has now default = "." o locator() allows inline graphics parameters (for the plotting it does with type !="n"). o New function max.col() from MASS, thanks to V&R. o nlm() can now take additional arguments in ... to be passed to f. o par() returns elements in alphabetical order, and "ann" as a logical (not integer). o .Platform has a new component GUI specifying the GUI in use (which might be "unknown"). o plot.formula() searches for a plot method for the left-side of the formula before searching for a plot method for the right-side of the formula. o New bitmap devices png() and jpeg() on Unix/X11. (They were already available on Windows.) o postscript(print.it=TRUE) now does print the plot file. postscript(onefile=FALSE) now produces multiple separate files. o provide() is now deprecated. o New function quade.test() in package ctest for the Quade test for unreplicated blocked data. o quantile(x, probs) now propagates NA/NaN in probs. o Option for user-supplied normal random generator in RNGkind(). o read.fwf() is no longer dependent on Perl. o New arguments check.names and strip.white to read.table() and friends. o Functions recordPlot() and replayPlot() save a plot to an R variable and replay it. o residuals.lm() also allows types "partial" and "response" as residuals.glm(). o Added col option to rug(). o scale() is now generic with scale.default method. o New "call. = TRUE" argument for stop(), and new function stopifnot(.) -- to be used in "make check". o str(.) has a new optional argument "nchar.max = 128" and truncates strings longer than that. Also eliminated a few minor glitches. o The symbols() function is now implemented. o New function termplot() with similar functionality to plot.gam() in S. o The parameters to title() which specify the labels may now be specified as a list containing the parameter together with additional modifying par values (cex, col, font) which affect just that label. title() also has new line and outer arguments which provide functionality which matches that in axis(). o New functions which.min() amd which.max(). o The Wilcoxon and Ansari-Bradley tests now optionally return confidence intervals for the location or scale parameter of interest. o New argument `extend' to window() (and updated documentation). o write.table() can now write CSV files in the format Excel expects. o New device xfig() to produce XFig files. o New xyz.coords() utility function to be used for 3D highlevel plots. o R CMD build now also works for package bundles. o Rdconv allows an output file to be specified. o Initial support for C++ source code in add-on packages under Unix. o Mathlib can be built as a standalone library: see directory src/nmath/standalone. BUG FIXES o The Mathlib functions now use exactly the same values for +/-Inf, NaN and NA as the rest of R in all cases. o Improved automatic remaking. o option keep.source was not set correctly before the base package was loaded: some functions in the base package had the source kept. The memory usage should now be reduced by ca 1Mb. o The base file is no longer closed twice in case of a syntax error (caused segfault on Linux). o The X11 data editor scrolls cells and so allows more than ca 10 characters to be entered. Several interface/redraw errors have been corrected. o Using `destroy' or `close' on the X11 data editor window killed R. o Multiple `destroy' events or X11 errors killed R (PR#400). o Warnings from .Last or closing devices are printed where sensible (e.g. not on GNOME nor Windows console). o add1.glm() and drop1.glm gave() incorrect results in the "Chisq" test option when the scale was estimated. o aggregate() applied to multiple time series lost the series names. o as.hclust.twins() in package mva sets method=NA (PR#538) o ave(1:3) now works (as when is.null(list()) was TRUE years ago). o barplot(c(0.1, 0.5, 1), ylim = c(0, 1)) now works: [xy]axs="i" and exact limits now labels the limits. o by() works when embedded in a function. o The xlab and ylab in coplot() now set the x and y axis labels, as in S. Supply a second component to label the conditioning variables. o count.fields() and read.table() now have the same default quote = "\"'". o guard against segfault in dataentry(x<-1, Modes = plot), and the like. o dev.print() now checks if the current device is replayable (and not all devices were, despite the documentation). o The gtk() device (formerly x11() under GNOME) was incorrectly returning character information, so in particular `*' was wrongly centred as a plotting symbol. o is.qr() checks not only for $qr, but also for $rank & $qraux, PR#482. o library() will not leave the package on the search path if loading fails (including if .First.lib fails). o lqs(, method="S") rounded k0 on passing to C. o na.omit() now handles vectors and matrices as well as data frames. o plot.lm(*, which=4) now works thanks to Marcel Wolbers. o postscript() now uses the options "papersize" and "printcmd" rather than the values of R_PAPERSIZE in the environment and R_PRINTCMD found at build time. o postscript() now makes use of kerning information in computing string widths. o M <- 2 ; print(ppr(.., nterms = M)) now works. o ppr(, sm.method="spline") had an internal limit of 250 rows: this is now 2500 and is now checked. o predict.lm(,type="terms",se.fit=T) gives correct standard errors (thanks to John Maindonald) o print.ftable() now returns its argument. o proj.aovlist() now gives a non-zero result for strata with no fitted effects. o qnorm() is now based on AS 241 instead of AS 111, and should give precise results up to 16 digits precision. o rgeom(, prob=1) gives 0 rather than NA o rpois(*, lambda) now works when lambda > .Machine$integer.max o strheight("X") with no active device would segfault. o system() is now (partially) functional on systems without popen. o Fixed bug in undoc() - requiring new `chdir' argument for sys.source() o Fixed problem in usemethod() where CAR(call) could be non-symbol. o The x11() device no longer crashes R if a font is not found, and will warn if there is a size mismatch of more than 10%. o R CMD Rd2dvi now sorts files alphabetically. o Rdconv now reports if an invalid type is specified (rather than using latex). o Support for Rd conversion to Sd has been reinstated (it was unintentionally removed along with nroff-based conversion to text). o \deqn{} fix in R-exts.texi, PR#523. o Linpack.h now makes clear which routines are actually in R. o Entry-point "pythag" is now loaded even though it is not necessarily used in R. Where "hypot" is available pythag just calls hypot after checking for special values. o call_R will now correctly handle character vector arguments. o The alphabet links on top of HTML function indices with more than 100 entries now contain only the letters which are really first letters of at least one entry. CHANGES IN R VERSION 1.0.1 BUG FIXES o pgamma(Inf, 1, Inf) gives NaN instead of an infinite loop, PR#462. o Inline xaxt and yaxt parameters were ignored. o Setting the normal RNG was not always recorded in .Random.seed. o \link[pkg]{foo} links were wrongly translated to HTML. o Direct use of show.data() with no args was incorrect. o print.coefmat does sensible things if options show.signif.stars and show.coef.Pvalues are not set correctly. o x <- list(a=1, b=2) ; x["c"] <- 3 now (again) stretches the list rather than give a "subscript out of bounds" error. o Models with response appearing on rhs could cause segfault. o as.data.frame.matrix will now ensure the columns added have non-empty names. o Some (strange?) model formulas could cause memory corruption (thanks to John Fox for digging this up). o Matrix multiplication in cases such as 1:3 %*% t(1:2) is accepted. o Options --nsize and --vsize to R CMD check gave warning messages and only one was accepted. o The autoload()s during startup are "wrapped" such that conflicting objects don't break startup. o cor.test(*, meth="spear") {pkg ctest} now works (again) for n <= 6 o scale = 0 in biplot.princomp() now works. o The scores given by princomp(, cor = TRUE) and the rotated values given by prcomp(, scale = TRUE) are now computed from the scaled data. o barplot now works okay when length(col) < length(legend.txt), thanks to Ben Bolker, PR#494. o legend has new args `ncol' and `horiz' thanks to Ben Bolker. o kernel("dirichlet", m=10, r=1) in package ts now works. o save/restore of environments containing "..." object should work now. o qhyper should work better for large N. o qbinom(1-1e-16, n, p) , qpois() and qnbinom(*) looped for ever. o as.matrix.data.frame no longer escapes quotes in character vectors. o R would try to save the readline history at the end of non-interactive sessions, causing crashes on some systems. o Subtle roundoff problems caused arrays to be allocated short in loess.c in some cases, leading to segfaults. o Document that postscript(file="") sends the output directly to the default printer. o ts.union(, dframe=TRUE) had a long-standing typo, now works. o save(, ascii=TRUE) had problem with octal escapes in strings when there was a digit following, should work now. o matpoints() and matlines() now also have a "type =" argument with defaults "p" and "l", respectively; PR#506. o The new Perl 5.6 broke our version-detection mechanism. A better one has been inserted. o X11(colortype="gray") failed to work on 8-bit screens, and more generally when colour allocation failed X11() did not revert to monochrome correctly (and did not say it was doing so). It was not documented in the help that to change the X11 colortype one needs to close all open X11 devices. o loessf.f in modreg defined DSIGN unecessarily and this caused a conflict on AIX. o plot.lm will now work with rlm objects. o start and end behave better when the frequency is not an integer. o aggregate.ts is closer to S-PLUS's aggregate.rts. o quantile(x) now works when x contains several +/- Inf's. o guard against segfault in dataentry(0,0) (or, more realistically, when mistyping data.entry(x,y) as dataentry(x,y)) ********************************************************* * * * News of 1.0.0 and earlier is in file `ONEWS' * * * *********************************************************