Dear Emacs, please make this -*-Text-*- mode! ************************************************** * * * 2.1 SERIES NEWS * * * ************************************************** CHANGES IN R VERSION 2.1.1 patched BUG FIXES o runmed(x, k = -1) now gives an error instead of a seg.fault. o File creation errors in pdf(), postscript(), xfig() resulted in a pointer being freed twice. (Reported by Matt McCall) o model.matrix(~ .^2, data=foo) now works as most people would expect (it used to expand '.' after using the a^2 = a rule). o ftable() and xtabs() had a check for interactions that would not work correctly with '.' in the formula. o The formula method for pairs() was ignoring the na.action argument. o scan() with the default separator (only) was stripping backslashes inside quoted string inputs even if allowEscapes = FALSE. o The "col" parameter to pairs() is now treated consistently with plot(): it affects the data, not the axes. (Patch submitted by Olaf Mersmann) o Sweave failed for \Sexpr{character(0)}. Sweave-test-1.Rnw contained a print() statement that is no longer needed. o Typo meant that R_alloc was limited to 2^31 not 2^34 on 64-bit builds of R. o pgamma(Inf, shape) did not terminate for shape = 1.1 and some other values (but not all) (PR#8001). This affected pchisq(Inf, df1) and pf(Inf, df1, Inf) for some values of df1. o regexpr("[a-z]", ...) could cause a buffer overrun with multi-byte character sets, leading to random errors later. o Installing a package with a 'data' directory which contains files but those files generate no objects (e.g. the BioC package makecdfenv) created an incorrectly formatted data index that data(package="pkg") could not read. o density(1/(0:2)) now works again (PR#8033). o make.names() was not respecting the allow_=FALSE argument. o Arg(-1) now gives pi, not 0; Arg(0i + -1) always worked. o --enable-linux-lfs had been broken at 2.1.0. o Printing was not allowing for double-width characters in its layout. o axTicks() is now also correct for reverse axis. (PR#7973) o signif() rounded some numnbers near 1e-308 to the wrong number of places (this showed up in the print-tests.R), and made unnecessary rounding errors on some platforms on e.g. signif(18000, 3). o window() was sometimes failing incorrectly due to representation errors when the new and old deltat were not both integers (e.g. multiples of 0.1). o The 'lm' methods for add1() and drop1() ignored offsets (which were added for lm() after they written). (PR#8049) o atan2(0+1i, 0+0i) was incorrectly NA (from a typo in complex.c). o The POSIXct method for as.Date() was rounding part days before 1970-01-01 upwards rather than discarding them. o qpois() was using an incorrect starting point and so could be unnecessarily slow for large lambda. (PR#8058) o Formatting of complex numbers with nsmall > 0 could be incorrect (and was in print-tests.Rout) because of a typo. o The test for new levels when predicting using model.frame() sometimes reported levels that were not actually used. o order(c("5","6",NA,"4",NA), na.last=FALSE) was incorrect. o Coercion to raw could give spurious messages about discarding imaginary parts. Coercion of a list to raw was behaving inconsistently for out-of-range values (and not warning). o cor.test(method = "spearman") gave NA p-values for _very_ long vectors. (PR#8087) o Switching to the Mersenne-Twister RNG could cause a segfault on first use. A user-supplied RNG without user_unif_{nseed,seedloc} was being re-initialized at each call. o Reading very short tables from stdin() with read.table would fail because of a typo. CHANGES IN R VERSION 2.1.1 NEW FEATURES o bug.report() now reports the locale in use. o upgrade.packageStatus() allows user input "c" to cancel the upgrade, just as update.packages() does. o glm() now accepts 1D arrays (e.g. tables) as a response, dropping them to a vector whilst preserving names. o df() with one infinite df now works (to match pf()). o Added tclServiceMode() function to the tcltk package to allow updating to be suspended. o The Encoding: field of a DESCRIPTION file is now documented, and used by packageDescription() and library(help=). o There has been progress on translations: existing translations have been revised and expanded, and French and Korean have been added. The Windows installer supports a wide range of languages for installation. BUG FIXES o lm(qr=FALSE) now works. o predict.glm() not longer loses names for "response" predictions. (PR#7792) o Typo in menu(graphics=TRUE) meant it failed on Unix if tcltk was not available. o When names.dist() was removed, the result of cmdscale() lost its rownames. The example also lost the labels. o R CMD check assumed 'tar' was GNU tar and so supported -z. o read.table() was not handing escaped quotes inside quoted fields in the first five lines of the file. (PR#7789) It was also not handling correctly EOF in the first five lines when reading from stdin(). (PR#7772) o 'make uninstall' was incomplete. o make.packages.html() called by help.start() was failing if there were installed packages with help titles invalid in the current locale. o printCoefmat(signif.legend = FALSE) was non-functional. (PR#7802) o Some as.date.frame() methods failed because the expression deparsed into multiple lines. (PR#7808) o setRepositories() had a typo. (PR#7810) o Printing arrays/data frames with multibyte characters in the column labels was sometimes misaligned or using excessive space. (PR#7803) o The Tcl/Tk console did not support multibyte characters. o as.POSIXlt() could give infinite recursion if passed a corrupt "POSIXct" object (generated by an incorrect call to c.POSIXct, PR#7826). o update.packages() was not passing 'type' correctly to install.packages(). o Printing the result of an unbalanced model.tables() call sometimes got confused if terms() had rearranged interaction terms. (PR#7829) o .Platform$pkgType was wrong on the CRAN MacOS X build, and .install.macbinary() was missing. o as.personList() as used by citation() got confused by names containing "and". (PR#7797) o Subscripting an array by a matrix containing zero or negative values or the wrong number of columns was not handled consistently. (PR#7824) o select.list(multiple=TRUE) now detects and tries again for invalid text input. o add1.[g]lm could give strange results with interaction terms when the model and the upper scope had different orders for the main effects. (PR#7842) o A bug had sneaked into the anova.mlmlist() code, affecting the Greenhouse-Geisser epsilon. Code wrongly assumed a matrix to be symmetric. (Thanks to Bela Bauer.) o anova.mlmlist() and mauchley.test() are now more tolerant to rank deficiency in the M and X matrices (also when they are implicitly generated via model.matrix()). o anova.mlm had a scoping issue (PR#7898) o pf() with infinite df is allowed again. It is now more accurate for extreme ratios of dfs, especially when there is a non-centrality parameter. o df() was inaccurate for large df (1e16 or greater). o dt() was inaccurate for large df (1e9 or greater) with a non-centrality parameter. o runmed(*, algorithm="Turlach") seg.faulted in rare cases. o strwrap() now makes a reasonable job of text that is invalid in the current locale. o Reading with encoding "UCS-2LE" will remove any Byte Order Mark, as most implementations of iconv fail to handle BOMs (which are present in 'Windows Unicode' files). o unique() for a list was incorrectly reporting `unimplemented'. o The parser's contextstack was not protected against overflow, e.g. more than 50 unmatched '('. (PR#7859) o source(file, chdir = TRUE) was not checking that 'file' was a filepath (rather than a URL). For 2.1.0 only, it did not work even if 'file' was a filepath. o Hershey fonts were being sized based on pixels not points so came out too small on devices where pixels were noticeably different from points (e.g., win.printer() and high-resolution screens). Fix means that default size of Hershey fonts may be slightly different, for example, smaller by default on PostScript and PDF. o The branch cuts in the complex versions of the inverse trigonometric and hyperbolic functions were non-standard. (PR#7871) o truncate() on file() connections was limited to files < 2Gb. It now works for larger files at least on 64-bit OSes and others where ftruncate supports such files. (Related to PR#7879) o proj.aovlist() did not work correctly on objects fitted from a data frame with row names. o The coding standards recommendations had nuke-trailing-whitespace where newer versions of ESS need ess-nuke-trailing-whitespace. (PR#7888) o package.skeleton() missed the first newline in the DESCRIPTION file. o pbirthday() reported p = 1 too often when coincident > 2. o plot(1:3, exp(1:3), log = "y", ylim = c(30,1)) {reversed log-scale axis} now works, based on Uwe Ligges' suggestions. (PR#7894) o install.packages() was aborting when a package in a bundle was chosen from a menu. It failed if more than one package in a bundle was chosen from the command line. o qcauchy() suffered from underflow in the extreme tails. (PR#7902) o Printing of raw matrices/arrays was not implemented. (PR#7912) o getCallingDLL()'s default first argument did not correspond to its description and has been changed. The mismatch caused symbols in .C/.Call/.Fortran calls without a PACKAGE= argument to be potentially looked up in the wrong namespace. o Binary save() of raw vectors was not working correctly on big-endian platforms. (PR#7812) o as.Date.factor() now accepts a format argument. o Workaround added for FreeBSD which does not have alloca.h _and_ does not allow alloca() to be declared. o identify() now respects 'cex'. (PR#660) Warnings from identify() are now printed immediately even on consoles with delayed printing. CHANGES IN R VERSION 2.1.0 USER-VISIBLE CHANGES o box plots {by boxplot() or bxp()} now have the median line three times the normal line width in order to distinguish it from the quartile ones. o Unix-alike versions of R can now be used in UTF-8 locales on suitably equipped OSes. See the internationalization section below. o The meaning of 'encoding' for a connection has changed: See the internationalization section below. o There has been some rationalization of the format of warning/error messages, to make them easier to translate. Generally names of functions and arguments are single-quoted, and classes double-quoted. o Reading text files with embedded "\" (as in Windows file names) may now need to use scan(* , allowEscapes = FALSE), see also below. NEW FEATURES o %% now warns if its accuracy is likely to be affected by lack of precision (as in 1e18 %% 11, the unrealistic expectation of PR#7409), and tries harder to return a value in range when it is. o abbreviate() now warns if used with non-ASCII chars, as the algorithm is designed for English words. o The default methods for add1() and drop1() check for changes in the number of cases in use. The "lm" and "glm" methods for add1() quoted the model on the original fitted values when using (with a warning) a smaller set of cases for the expanded models. o Added alarm() function to generate a bell or beep or visual alert. o all/any() now attempt to coerce their arguments to logical, as documented in the Blue Book. This means e.g. any(list()) works. o New functions for multivariate linear models: anova.mlm(), SSD(), estVar(), mauchley.test() (for sphericity). vcov() now does something more sensible for "mlm" class objects. o as.data.frame.table() has a new argument 'responseName' (contributed by Bill Venables). o as.dist() and cophenetic() are now generic, and the latter has a new method for objects of class "dendrogram". o as.ts() is now generic. o binomial() has a new "cauchit" link (suggested by Roger Koenker). o chisq.test() has a new argument 'rescale.p'. It is now possible to simulate (slowly) the P value also in the 1D case (contributed by Rolf Turner). o choose(n,k) and lchoose(.) now also work for arbitrary (real) n in accordance with the general binomial theorem. choose(*,k) is more accurate (and faster) for small k. o Added colorRamp() and colorRampPalette() functions for color interpolation. o colSums()/rowSums() now allow arrays with a zero-length extent (requested by PR#7775). o confint() has stub methods for classes "glm" and "nls" that invoke those in package MASS. This avoids using the "lm" method for "glm" objects if MASS is not attached. confint() has a default method using asymptotic normality. o contr.SAS() has been moved from the 'nlme' package to the 'stats' package. o New function convertColors() maps between color spaces. colorRamp() uses it. o The cov() function in the non-Pearson cases now ranks data after removal of missing values, not before. The pairwise-complete method should now be consistent with cor.test. (Code contributed by Shigenobu Aoki.) o Added delayedAssign() function to replace delay(), which is now deprecated. o dir.create() has a new argument 'recursive' serving the same purpose as Unix's mkdir -p. o do.call() now takes either a function or a character string as its first argument. The supplied arguments can optionally be quoted. o duplicated() and unique() now accept "list" objects, but are fast only for simple list objects. o ecdf() now has jumps of the correct size (a multiple of 1/n) if there are ties. (Wished by PR#7292). o eff.aovlist() assumed orthogonal contrasts for any term with more than one degree of freedom: this is now documented and checked for. Where each term only occurs in only one stratum the efficiencies are all one: this is detected and orthogonal contrasts are not required. o New function encodeString() to encode character strings in the same way that printing does. o file("clipboard") now work for reading the primary selection on Unix-alikes with an active X11 display. (It has long worked for reading and writing under Windows.) The secondary selection can also be read: see ?file. file() now allows mode "w+b" as well as "w+". o file.append() has been tuned, including for the case of appending many files to a single file. o Functions flush.console() and select.list() are now available on all platforms. There is a Tcl/Tk-based version of select.list() called tk_select.list() in package tcltk. o gc() now reports maximum as well as current memory use. o A new function getGraphicsEvent() has been added which will allow mouse or keyboard input from a graphics device. (NB: currently only the Windows screen device supports this function. This should improve before the 2.1.0 release.) o New functions gray.colors()/grey.colors() for gray color palettes. o grep(), gsub(), sub() and regexpr() now always attempt to coerce their 'pattern', 'x', 'replacement' and 'text' arguments to character. Previously this was undocumented but done by [g]sub() and regexpr() for some values of their other arguments. (Wish of PR#7742.) o gsub/sub() have a new 'fixed' method. o New function hcl() for creating colors for a given hue, chroma and luminance (i.e. perceptual hsv). o isTRUE() convenience function to be used for programming. o kmeans() now returns an object of class "kmeans" which has a print() method. Two alternative algorithms have been implemented. If the number of centres is supplied, it has a new option of multiple random starts. o The limits on the grid size in layout() are now documented, and have been raised somewhat by using more efficient internal structures. o legend() now accepts positioning by keyword, e.g. "topleft", and can put a title within the legend. (Suggested by Elizabeth Purdom in PR#7400.) o mahalanobis() now has a '...' argument which is passed to solve() for computing the inverse of the covariance matrix, this replaces the former 'tol.inv' argument. o menu() uses a multi-column layout if possible for more than 10 choices. menu(graphics = TRUE) is implemented on most platforms via select.list() or tk_select.list(). o New function message() in 'base' for generating "simple" diagnostic messages, replacing such a function in the 'methods' package. o na.contiguous() is now (S3) generic with first argument renamed to 'object'. o New function normalizePath() to find canonical paths (and on Windows, canonical names of components). o The default in options("expressions") has been increased to 5000, and the maximal settable value to 500000. o p.adjust() has a new method "BY". o pbeta() now uses a different algorithm for large values of at least one of the shape parameters, which is much faster and is accurate and reliable for very large values. (This affects pbinom(), pf(), qbeta() and other functions using pbeta at C level.) o pch="." now by default produces a rectangle at least 0.01" per side on high-resolution devices. (It used to be one-pixel square even on high-resolution screens and Windows printers, but 1/72" on postscript() and pdf() devices.) Additionally, the size is now scalable by 'cex'; see ?points and note that the details are subject to change. o pdf() now responds to the 'paper' and 'pagecentre' arguments. The default value of 'paper' is "special" for backward-compatibility (this is different from the default for postscript()). o plot.data.frame() tries harder to produce sensible plots for non-numeric data frames with one or two columns. o The predict() methods for "prcomp" and "princomp" now match the columns of 'newdata' to the original fit using column names if these are available. o New function recordGraphics() to encapsulate calculations and graphics output together on graphics engine display list. To be used with care. o New function RSiteSearch() to query R-related resources on-line (contributed by Jonathan Baron and Andy Liaw). o scan() arranges to share storage of duplicated character strings read in: this can dramatically reduce the memory requirements for large character vectors which will subsequently be turned into factors with relatively few levels. For a million items this halved the time and reduced storage by a factor of 20. scan() has a new argument 'allowEscapes' (default TRUE) that controls when C-style escapes in the input are interpreted. Previously only \n and \r were interpreted, and then only within quoted strings when no separator was supplied. scan() used on an open connection now pushes back on the connection its private `ungetc' and so is safer to use to read partial lines. o scatter.smooth() and loess.smooth() now handle missing values in their inputs. o seq.Date() and seq.POSIXt() now allow 'to' to be before 'from' if 'by' is negative. o sprintf() has been enhanced to allow the POSIX/XSI specifiers like "%2$6d", and also accepts "%x" and "%X". sprintf() does limited coercion of its arguments. sprintf() accepts vector arguments and operates on them in parallel (after re-cycling if needed). o New function strtrim() to trim character vectors to a display width, allowing for double-width characters in multi-byte character sets. o subset() now has a method for matrices, similar to that for data frames. o Faster algorithm in summaryRprof(). o sunflowerplot() has new arguments 'col' and 'bg'. o sys.function() now has argument 'which' (as has long been presaged on its help page). o Sys.setlocale("LC_ALL", ) now only sets the locale categories which R uses, and Sys.setlocale("LC_NUMERIC", ) now gives a warning (as it can cause R to malfunction). o unclass() is no longer allowed for environments and external pointers (since these cannot be copied and so unclass() was destructive of its argument). You can still change the "class" attribute. o File-name matching is no longer case-insensitive with unz() connections, even on Windows. o New argument 'immediate.' to warning() to send an immediate warning. o New convenience wrappers write.csv() and write.csv2(). o There is a new version for write.table() which is implemented in C. For simple matrices and data frames this is several times faster than before, and uses negligible memory compared to the object size. The old version (which no longer coerces a matrix to a data frame and then back to a matrix) is available for now as write.table0(). o The functions xinch(), yinch(), and xyinch() have been moved from package 'grDevices' into package 'graphics'. o Plotmath now allows underline in expressions. (PR#7286, contributed by Uwe Ligges.) o BATCH on Unix no longer sets --gui="none" as the X11 module is only loaded if needed. o The X11 module (and the hence X11(), jpeg() and png() devices and the X-based dataentry editor) is now in principle available under all Unix GUIs except --gui="none", and this is reflected in capabilities(). capabilities("X11") determines if an X server can be accessed, and so is more likely to be accurate. o Printing of arrays now honours the 'right' argument if there are more than two dimensions. o Tabular printing of numbers now has headers right-justified, as they were prior to version 1.7.0 (spotted by Rob Baer). o Lazy-loading databases are now cached in memory at first use: this enables R to run much faster from slow file systems such as USB flash drives. There is a small (less than 2Mb) increase in default memory usage. o The implicit class structure for numeric vectors has been changed, so that integer/real vectors try first methods for class "integer"/"double" and then those for class "numeric". The implicit classes for matrices and arrays have been changed to be "matrix"/"array" followed by the class(es) of the underlying vector. o splines::splineDesign() now allows the evaluation of a B-spline basis everywhere instead of just inside the "inner" knots, by setting the new argument `outer.ok = TRUE'. o Hashing has been tweaked to use half as much memory as before. o Readline is not used for tilde expansion when R is run with --no-readline, nor from embedded applications. Then "~name" is no longer expanded, but "~" still is. o The regular expression code is now based on that in glibc 2.3.3. It has stricter conformance to POSIX, so metachars such as { } + * may need to be escaped where before they did not (but could have been). o New encoding 'TeXtext.enc' improves the way postscript() works with Computer Modern fonts. o Replacement in a non-existent column of a data frame tries harder to create a column of the correct length and so avoid a corrupt data frame. o For Windows and readline-based history, the saved file size is re-read from R_HISTSIZE immediately before saving. o Collected warnings during start-up are now printed before the initial prompt rather than after the first command. o Changes to package 'grid': - preDrawDetails(), drawDetails(), and postDrawDetails() methods are now recorded on the graphics engine display list. This means that calculations within these methods are now run when a device is resized or when output is copied from one device to another. - Fixed bug in grid.text() when 'rot' argument has length 0. (privately reported by Emmanuel Paradis) - New getNames() function to return just the names of all top-level grobs on the display list. - Recording on the grid display list is turned off within preDrawDetails(), drawDetails(), and postDrawDetails() methods. - Grid should recover better from errors or user-interrupts during drawing (i.e., not leave you in a strange viewport or with strange graphical parameter settings). - New function grid.refresh() to redraw the grid display list. - New function grid.record() to capture calculations with grid graphics output. - grobWidth and grobHeight ("grobwidth" and "grobheight" units) for primitives (text, rects, etc, ...) are now calculated based on a bounding box for the relevant grob. NOTE: this has changed the calculation of the size of a scalar rect (or circle or lines). - New arguments 'warn' and 'wrap' for function grid.grab() - New function grid.grabExpr() which captures the output from an expression (i.e., not from the current scene) without doing any drawing (i.e., no impact on the current scene). - upViewport() now (invisibly) returns the path that it goes up (suggested by Ross Ihaka). - The 'gamma' gpar has been deprecated (this is a device property not a property of graphical objects; suggested by Ross Ihaka). - New 'lex' gpar; a line width multiplier. - grid.text() now handles any language object as mathematical annotation (instead of just expressions). - plotViewport() has default value for 'margins' argument (that match the default value for par(mar)). - The 'extension' argument to dataViewport() can now be vector, in which case the first value is used to extend the xscale and the second value is used to extend the y scale. (suggested by Ross Ihaka). - All 'just' arguments (for viewports, layouts, rectangles, text) can now be numeric values (typically between 0 [left] and 1 [right]) as well as character values ("left", "right", ...). For rectangles and text, there are additional 'hjust' and 'vjust' arguments which allow numeric vectors of justification in each direction (e.g., so that several pieces of text can have different justifications). (suggested by Ross Ihaka) - New 'edits' argument for grid.xaxis() and grid.yaxis() to allow specification of on-the-fly edits to axis children. - applyEdit(x, edit) returns x if target of edit (i.e., child specified by a gPath) cannot be found. - Fix for calculation of length of max/min/sum unit. Length is now (correctly) reported as 1 (was reported as length of first arg). - Viewport names can now be any string (they used to have to be a valid R symbol). - The 'label' argument for grid.xaxis() and grid.yaxis() can now also be a language object or string vector, in which case it specifies custom labels for the tick marks. INTERNATIONALIZATION o Unix-alike versions of R can now be used in UTF-8 and other multi-byte locales on suitably equipped OSes if configured with option --enable-mbcs (which is the default). [The changes to font handling in the X11 module are based on the Japanization patches of Ei-ji Nakama.] Windows versions of R can be used in `East Asian' locales on suitable versions of Windows. See the 'Internationalization' chapter in the 'Installation and Administration' manual. o New command-line flag --encoding to specify the encoding to be assumed for stdin (but not for a console). o New function iconv() to convert character vectors between encodings, on those OSes which support this. See the new capabilities("iconv"). o The meaning of 'encoding' for a connection has changed: it now allows any charset encoding supported by iconv on the platform, and can re-encode output as well as input. As the new specification is a character string and the old was numeric, this should not cause incorrect operation. o New function localeToCharset() to find/guess encoding(s) from the locale name. o nchar() returns the true number of bytes stored (including any embedded nuls), this being 2 for missing values. It has an optional argument 'type' with possible non-default values "chars" and "width" to give the number of characters or the display width in columns. o Characters can be entered in hexadecimal as e.g. \x9c, and in UTF-8 and other multibyte locales as \uxxxx, \u{xxxx}, \Uxxxxxxxx or \U{xxxxxxxx}. Non-printable Unicode characters are displayed C-style as \uxxxx or \Uxxxxxxxx. o LC_MONETARY is set to the locale, which affects the result of Sys.localeconv(), but nothing else in R itself. (It could affect add-on packages.) o source() now has an 'encoding' argument which can be used to make it try out various possible encodings. This is made use of by example() which will convert (non-UTF-8) Latin-1 example files in a UTF-8 locale. o read/writeChar() work in units of characters, not bytes. o .C() now accepts an ENCODING= argument where re-encoding is supported by the OS. See `Writing R Extensions'. o delimMatch (tools) now reports match positions and lengths in units of characters, not bytes. The delimiters can be strings, not just single ASCII characters. o .Rd files can indicate via a \encoding{} argument the encoding that should be assumed for non-ASCII characters they contain. o Phrases in .Rd files can be marked by \enc{}{} to show a transliteration to ASCII for use in e.g. text help. o The use of 'pch' in points() now allows for multi-byte character sets: in such a locale a glyph can either be specified as a multi-byte single character or as a number, the Unicode point. o New function l10n_info() reports on aspects of the locale/charset currently in use. o scan() is now aware of double-byte locales such as Shift-JIS in which ASCII characters can occur as the second ('trail') byte. o Functions sQuote() and dQuote() use the Unicode directional quotes if in a UTF-8 locale. o The infrastructure is now in place for C-level error and warning messages to be translated and used on systems with Native Language Support. This has been used for the startup message in English and to translate Americanisms such as 'color' into English: translations to several other languages are under way, and some are included in this release. See 'Writing R Extensions' for how to make use of this in a package: all the standard packages have been set up to do translation, and the 'language' 'en@quot' is implemented to allow Unicode directional quotes in a UTF-8 locale. o R-level stop(), warning() and message() messages can be translated, as can other messages via the new function gettext(). Tools xgettext() and xgettext2pot() are provided in package tools to help manage error messages. gettextf() is a new wrapper to call sprintf() using gettext() on the format string. o Function ngettext() allows the management of singular and plural forms of messages. UTILITIES o New functions mirror2html() and checkCRAN(). o R CMD check has a new option '--use-valgrind'. o R CMD check now checks that Fortran and C++ files have LF line endings, as well as C files. It also checks Makevars[.in] files for portable compilation flags. o R CMD check will now work on a source tarball and prints out information about the version of R and the package. o tools:::.install_package_code_files() (used to collate R files when installing packages) ensures files are separated by a line feed. o vignette() now returns an object of class "vignette" whose print() method opens the corresponding PDF file. The edit() method can be used to open the code of the vignette in an editor. o R CMD INSTALL on Unix has a new option '--build' matching that on Windows, to package as tarball the installed package. o R CMD INSTALL on Unix can now install binary bundles. o R CMD build now changes src files to LF line endings if necessary. o R CMD build now behaves consistently between source and binary builds: in each case it prepares a source directory and then either packages that directory as a tarball or calls R CMD INSTALL --build on the prepared sources. This means that R CMD build --binary now respects .Rbuildignore and will rebuild vignettes (unless the option --no-vignettes is used). For the latter, it now installs the current sources into a temporary library and uses that version of the package/bundle to rebuild the vignettes. o R CMD build now reports empty directories in the source tree. o New function write_PACKAGES() in package 'tools' to help with preparing local package repositories. (Based on a contribution by Uwe Ligges.) How to prepare such repositories is documented in the 'R Installation and Administration' manual. o package.skeleton() adds a bit more to DESCRIPTION. o Sweave changes: - \usepackage[nogin]{Sweave} in the header of an Sweave file supresses auto-setting of the graphical parameter like width of graphics. - The new \SweaveInput{} command works similar to LaTeX's \input{} command. - Option value strip.white=all strips all blank lines from the output of a code chunk. - Code chunks with eval=false are commented out by Stangle() and hence no longer tested by R CMD check. DOCUMENTATION o File doc/html/faq.html no longer exists, and doc/manual/R-FAQ.html (which has active links to other manuals) is used instead. (If makeinfo >= 4.7 is not available, the version on CRAN is linked to.) o Manual 'Writing R Extensions' has further details on writing new front-ends for R using the new public header files. o There are no longer any restrictions on characters in the \name{} field of a .Rd file: in particular _ is supported. C-LEVEL FACILITIES o There are new public C/C++ header files Rinterface.h and R_ext/RStartup.h for use with external GUIs. o Added an onExit() function to graphics devices, to be executed upon user break if non-NULL. o ISNAN now works even in C++ code that undefines the 'isnan' macro. o R_alloc's limit on 64-bit systems has been raised from just under 2^31 bytes (2Gb) to just under 2^34 (16Gb), and is now checked. o New math utility functions log1pmx(x), lgamma1p(x), logspace_add(logx, logy), and logspace_sub(logx, logy). DEPRECATED & DEFUNCT o The aqua module for MacOS X has been removed: --with-aqua now refers to the unbundled Cocoa GUI. o Capabilities "bzip2", "GNOME, "libz" and "PCRE" are defunct. o The undocumented use of UseMethod() with no argument was deprecated in 2.0.1 and is now regarded as an error. o Capability "IEEE754" is deprecated. o The 'CRAN' argument to update.packages(), old.packages(), new.packages(), download.packages() and install.packages() is deprecated in favour of 'repos', which replaces it as a positional argument (so this is only relevant for calls with named args). o The S3 methods for getting and setting names of "dist" objects have been removed (as they provided names with a different length from the "dist" object itself). o Option "repositories" is no longer used and so not set. o loadURL() is deprecated in favour of load(url()). o delay() is deprecated. Use delayedAssign() instead. INSTALLATION CHANGES o New configure option --enable-mbcs to enable support for UTF-8 locales, on by default. o R_XTRA_[CF]FLAGS are now used during the configuration tests, and [CF]PICFLAGS if --enable-R-shlib was specified. This ensures that features such as inlining are only used if the compilation flags specified support them. (PR#7257) o Files FAQ, RESOURCES, doc/html/resources.html are no longer in the SVN sources but are made by 'make dist'. o The GNOME GUI is unbundled, now provided as a package on CRAN. o Configuring without having the recommended packages is now an error unless --with-recommended-packages=no (or equivalent) is used. o Configuring without having the X11 headers and libraries is now an error unless --with-x=no (or equivalent) is used. o Configure tries harder to find a minimal set of FLIBS. Under some circumstances this may remove from R_LD_LIBRARY_PATH path elements that ought to have specified in LDFLAGS (but were not). o The C code for most of the graphics device drivers and their afm files are now in package grDevices. o R is now linked against ncurses/termlib/termcap only if readline is specified (now the default) and that requires it. o Makeinfo 4.7 or later is now required for building the HTML and Info versions of the manuals. PACKAGE INSTALLATION CHANGES o There are new types of packages, identified by the Type field in the DESCRIPTION file. For example the GNOME console is now a separate package (on CRAN), and translations can be distributed as packages. o There is now support of installing from within R both source and binary packages on MacOS X and Windows. Most of the R functions now have a 'type' argument defaulting to getOption("pkgType") and with possible values "source", "win.binary" and "mac.binary". The default is "source" except under Windows and the CRAN GUI build for MacOS X. o install.packages() and friends now accept a vector of URLs for 'repos' or 'contriburl' and get the newest available version of a package from the first repository on the list in which it is found. The argument 'CRAN' is still accepted, but deprecated. install.packages() on Unix can now install from local .tar.gz files via repos = NULL (as has long been done on Windows). install.packages() no longer asks if downloaded packages should be deleted: they will be deleted at the end of the session anyway (and can be deleted by the user at any time). If the repository provides the information, install.packages() will now accept the name of a package in a bundle. If 'pkgs' is omitted install.packages() will use a listbox to display the available packages, on suitable systems. 'dependencies' can be a character vector to allow only some levels of dependencies (e.g. not "Suggests") to be requested. o There is a new possible value update.packages(ask="graphics") that uses a widget to (de)select packages, on suitable systems. o The option used is now getOption("repos") not getOption("CRAN") and it is initially set to a dummy value. Its value can be a character vector (preferably named) giving one or several repositories. A new function chooseCRANmirror() will select a CRAN mirror. This is called automatically if the contrib.url() encounters the initial dummy value of getOption("repos") A new function setRepositories() can be used to create getOption("repos") from a (platform-specific) list of known repositories. o New function new.packages() to report uninstalled packages available at the requested repositories. This also reports incomplete bundles. It will optionally install new packages. o New function available.packages(), similar to CRAN.packages() but for use with multiple repositories. Both now only report packages whose R version requirements are met. o update.packages() and old.packages() have a new option 'checkBuilt' to allow packages installed under earlier versions of R to be updated. o remove.packages() can now remove bundles. o The Contains: field of the DESCRIPTION file of package bundles is now installed, so later checks can find out if the bundle is complete. o packageStatus() is now built on top of *.packages, and gains a 'method' argument. It defaults to the same repositories as the other tools, those specified by getOption("repos"). BUG FIXES o Configuring for Tcl/Tk makes use of ${TK_LIB_SPEC} ${TK_LIBS} not ${TK_LIB_SPEC} ${TK_XLIBSW}, which is correct for recent versions of Tk, but conceivably not for old tkConfig.sh files. o detach() was not recomputing the S4 methods for primitives correctly. o Methods package now has class "expression" partly fixed in basic classes, so S4 classes can extend these (but "expression" is pretty broken as a vector class in R). o Collected warnings had messages with unneeded trailing space. o S4 methods for primitive functions must be exported from namespaces; this is now done automatically. Note that is.primitive() is now in "base", not "methods". o Package grid: - Fixed bug in grid.text() when "rot" argument has length 0. (reported by Emmanuel Paradis) o .install_package_vignette_index() created an index even in an empty 'doc' directory. o The print() method for factors now escapes characters in the levels in the same way as they are printed. o str() removed any class from environment objects. str() no longer interprets control characters in character strings and factor levels; also no longer truncates factor levels unless they are longer than 'nchar.max'. Truncation of such long strings is now indicated ''outside'' the string. str() was misleading for the case of a single slot. str() now also properly displays S4 class definitions (such as returned by getClass(). o print.factor(quote=TRUE) was not quoting levels, causing ambiguity when the levels contained spaces or quotes. o R CMD check was confused by a trailing / on a package name. o write.table() was writing incorrect column names if the data frame contained any matrix-like columns. o write.table() was not quoting row names for a 0-column x. o t(x)'s default method now also preserves names(dimnames(x)) for 1D arrays 'x'. o r <- a %*% b no longer produces names(dimnames(r)) == c("", "") unless one of a or b has named dimnames. o Some .Internal functions that were supposed to return invisibly did not. This was behind PR#7397 and PR#7466. o eval(expr, NULL, encl) now looks up variables in encl, as eval(expr, list(), encl) always did o Coercing as.data.frame(NULL) to a pairlist caused an error. o p.adjust(p, ..) now correctly works when `p' contains NAs (or when it is of length 0 or length 2 for method = "hommel"). o 'methods' initialization was calling a function intended for .Call() with .C(). o optim() needed a check that the objective function returns a value of length 1 (spotted by Ben Bolker). o X11() was only scaling its fonts to pointsize if the dpi was within 0.5 of 100dpi. o X11() font selection was looking for any symbol font, and sometimes got e.g. bold italic if the server has such a font. o dpois(*, lambda=Inf) now returns 0 (or -Inf for log). o Using pch="" gave a square (pch=0)! Now it is regarded as the same as NA, which was also undocumented but omits the point. o Base graphics now notices (ab)lines which have a zero coordinate on log scale, and omits them. (PR#7559) o stop() and warning() now accept NULL as they are documented to do (although this seems of little use and is equivalent to ""). o weighted.mean() now checks the length of the weight vector w. o getAnywhere() was confused by names with leading or trailing dots (spotted by Robert McGehee) o eval() was not handling values from return() correctly. o par(omd) is now of the form c(x1, x2, y1, y2) to match the documentation and for S-PLUS compatibility. [Previously, par(omd) was of the form c(bottom, left, top, right) like par(oma) and par(omi)] o formatC() did not check its 'flag' argument, and could segfault if it was incorrect. (PR#7686) o Contrasts needed to be coerced to numeric (e.g. from integer) inside model.matrix. (PR#7695) o socketSelect() did not check for buffered input. o Reads on a non-blocking socket with no available data were not handled properly and could result in a segfault. o The "aovlist" method for se.contrast() failed in some very simple cases that were effectively not multistratum designs, e.g. only one treatment occurring in only one stratum. o pgamma() uses completely re-written algorithms, and should work for all (even very extreme) arguments; this is based on Morten Welinder's contribution related to PR#7307. o dpois(10, 2e-308, log=TRUE) and similar cases gave -Inf. o x <- 2^(0:1000); plot(x, x^.9, type="l", log="xy")# and x <- 2^-(1070:170); plot(x, x^.9, type="l", log="xy")# now both work o summary.lm() asked for a report on a reasonable occurrence, but the check failed to take account of NAs. o lm() was miscalculating 'df.residual' for empty models with a matrix response. o summary.lm() now behaves more sensibly for empty models. o plot.window() was using the wrong sign when adjusting xlim/ylim for positive 'asp' and a reversed axis. o If malloc() fails when allocating a large object the allocator now does a gc and tries the malloc() again. o packageSlot() and getGroupMembers() are now exported from the 'methods' package as they should from documentation and the Green Book. o rhyper() was giving numbers slightly too small, due to a bug in the original algorithm. (PR#7314) o gsub() was sometimes incorrectly matching ^ inside a string, e.g. gsub("^12", "x", "1212") was "xx". o [g]sub(perl = TRUE) was giving random results for a 0-length initial match. (PR#7742) o [g]sub was ignoring most 0-length matches, including all initial ones. Note that substitutions such as gsub("[[:space:]]*", " ", ...) now work as they do in 'sed' (whereas the effect was previously the same as gsub("[[:space:]]+", " ", ...)). (In part PR#7742) o Promises are now evaluated when extracted from an environment using '$' or '[[ ]]'. o reshape(direction="wide") had some sorting problems when guessing time points (PR#7669) o par() set 'xaxp' before 'xlog' and 'yaxp' before 'ylog', causing PR#831. o The logic in tclRequire() to check the availability of a Tcl package turned out to be fallible. It now uses a try()-and-see mechanism instead. o Opening a unz() connection on a non-existent file left a file handle in use. o "dist" objects of length 0 failed to print. o INSTALL and the libR try harder to find a temporary directory (since there might be one left over with the same PID). o acf() could cause a segfault with some datasets. (PR#7771) o tan(1+LARGEi) now gives 0+1i rather than 0+NaNi (PR#7781) o summary(data.frame(mat = I(matrix(1:8, 4)))) does not go into infinite recursion anymore. o writeBin() performed byte-swapping incorrectly on complex vectors, also swapping real and imaginary parts. (PR#7778) o read.table() sometimes discarded as blank lines containing only white space, even if sep=",". ************************************************** * * * 2.0 SERIES NEWS * * * ************************************************** CHANGES IN R VERSION 2.0.1 patched NEW FEATURES o warnings() now looks only in the workspace for `last.warning' (suggested by PR#7363). o The search for browsers now starts with firefox, and has mozilla ahead of netscape. PACKAGE INSTALLATION CHANGES o A package DESCRIPTION file which contains a Built field (it should not!) is now worked around, with loud warnings. BUG FIXES o split() was accepting raw and list vectors as input, but not populating the output correctly. split() now handles vectors with names internally and so is almost as fast as on vectors without names (and maybe 100x faster than before). o subset() now throws an error if its 'subset' argument is not logical whereas it could appear to work and give wrong answers with e.g. a numeric 'subset' argument. o sum(), max(), min(), prod(), any() and all() were incorrectly using partial matching for their na.rm argument. o kmeans() now ensures that the initial cluster centers it chooses are distinct. o text()'s default method could segfault if passed 0-length coordinates. o R CMD INSTALL (Unix) was sometimes leaving a temporary dir behind. (PR#7230) o read.table() could fail when the row.names were looking like numbers. o seq(length= ) now always returns "integer" storage. o labels.lm was broken. (PR#7417) o The hashing used for character vectors in object.size() was inefficient for vectors with thousands of identical values not sharing the same storage (an unusual case). o data.matrix() now warns if applied to a data frame with classed columns. o Plotting histograms where the expression used to deparse to multiple lines now gives a sensible default title. (PR#7421) o The print method for getDLLRegisteredRoutines() was badly designed, and failed for all the standard packages' DLLs. o getDLLRegisteredRoutines.character() was broken. o write.table(x, row.names=FALSE) was incorrect for a 0-column x. o write.table() assumed dec = "," if it was not ".". o morley.tab used by R-intro was not installed on Unix since 2.0.0 (it was on Windows). o gsub(perl=TRUE) returned a string which printed with trailing garbage if there was a match at the beginning whose replacement was shorter. (PR#7479) Similarly, the result was truncated if a replacement at the beginning was longer. o Some PDF readers do not define PDFDocEncoding, so pdf()'s ISOLatin1 encoding is now derived from WinAnsi rather than PDFDocEncoding. o xfig() had not been updated for the 2.0.0 alpha changes. Using more than one plot with a non-white background and with onefile=FALSE could segfault. o sprintf() did not check for buffer overflow on character strings. (PR#7554) o The error message when evaluation depth was exceeded itself caused an error in deparsing and so was not shown. o The 'datalist' file was not being used during installation (2.0.1 only). o replications() was wrongly reporting lack of balance in designs with interactions (and had since unique() gained a matrix method). CHANGES IN R VERSION 2.0.1 NEW FEATURES o Platform equivalence in library() is tested by a new function testPlatformEquivalence() which ignores the 'vendor' field and can be customized by cognescenti. o The assignment form of split() allows recycling of vectors within the value list. In particular, things like split(x, g) <- lapply(split(x, g), mean) now work DOCUMENTATION o Manual `Writing R Extensions' has new sections on writing portable packages and on writing new front-ends for R -- the latter will be more comprehensive in R 2.1.0 which has new public header files. DEPRECATED & DEFUNCT o The aqua module in MacOS X is deprecated. o Capabilities "bzip2", "GNOME, "libz" and "PCRE" are deprecated. o The GNOME GUI on Unix-alikes is deprecated as part of R; it will be available in another form as from R 2.1.0. o The undocumented use of UseMethod() with no argument is now formally deprecated. INSTALLATION CHANGES o Building on Alpha OSF/1 no longer forces the C flag -std1, which appears to be no longer needed. (PR#7257) o The compiler flag -mieee-fp is no longer used on i386 Linux (these days it is only passed to the linker and was only invoked for compilation steps). o -D__NO_MATH_INLINES is only used on older ix86 glibc-based systems which need it (tested at configure time). This leads to small improvements in speed and accuracy on modern systems. o If makeinfo >= 4.5 is not available, warnings are given that some of the HTML manuals will be missing, and the index page given by help.start() will link to CRAN versions of those manuals. o Files aclocal.m4 and acinclude.m4 used in maintainer builds are not longer included in the distribution. C-LEVEL FACILITIES o It was not clear in 'Writing R Extensions' that some of the entry points in the 'Utilities' section were not declared in (they were in ). Now all the entry points in that section are declared in , included by . BUG FIXES o The grid.grab() function in package grid would throw an error if there were no viewports pushed (now returns NULL). o model.frame.default() takes row names from the response variable if that has suitable names and there is no 'data' argument. (This follows S but was not previously implemented in R.) o write.table() was not respecting the 'dec' argument for complex numbers. o write.table() printed a mixture of numeric and complex numbers as all complex. (PR#7260) o R CMD INSTALL failed with versioned installs on packages which save images (only). o dlogis() gave NaN not 0 for large negative arguments. o Importing from another namespace was broken for versioned installs, incorrectly reporting something like "package 'imported_from' does not have a name space". o The GNOME interface under Linux/Unix was broken. (PR#7276) o For the jpeg/png devices under Linux/Unix, under certain rare circumstances clipping needed to be cleared before starting a new page. (PR#7270, which has been the case since the devices were introduced in 1.1.0.) o First lattice plot (first grid.newpage() call) did not start a new page IF there had been a previous traditional graphics plot (on the same device). o Using install.packages() to install the same package to more than one library gave an incorrect warning message. (If there were two or more such packages it might give an error.) o .packages(all.available=TRUE) returned packages with an invalid version field in their DESCRIPTION whereas .find.packages() and packageDescription() did not. Now all do not. o packageDescription() now correctly reports that a package does not exist, rather than that its DESCRIPTION file is 'missing or broken'. o 'make dist' from builddir != sourcedir was copying not linking recommended packages to *.tgz. o Slots in prototype objects can inherit from locally defined classes (which were not being found correctly before). o Several fixes to the behavior of as() when there are either coerce= or replace= methods supplied in a call to setIs(). Related fixes to setIs() to handle correctly previous methods, if there were any. o splinefun(1[0], 1[0])(1) doesn't segfault anymore (PR#7290). spline() and splinefun() now also work with missing values by omiting them. o ecdf() was failing on inputs containing NAs. (Part of PR#7292) o tools:::.install_package_description was splitting the Built: field across lines on platforms with very long names. o capabilities() was wrong for the Aqua GUI on MacOS X. o Using Rprof() with a non-writable 'file' argument is now a non-fatal error and does not abort R. o binom.test() did not deparse its arguments early enough such that the reported data were ugly if x was a table. o Systems based on glibc, including those using R's substitute for strptime, were handling strptime("2001", "%Y") incorrectly, in some cases crashing. R's substitute code has been corrected (but problems may remain if glibc is used). See the ?strptime for what should happen (which is system-specific). o untrace() after trace() failed if package 'methods' was attached. (PR#7301) o summary.stepfun() was reporting for n > 6 summaries of the knots and levels as the actual values. Both print() and summary() methods called the constant values "step heights", although they were not the heights of the steps. o is.na/is.nan() were giving spurious warnings if applied to a raw vector. o is.atomic() gave incorrect result (false) for a raw vector. o rank() and order() accepted raw and list inputs, but did not give a sensible answer (always 1:n). Similarly, partial sorts of a raw vector were accepted but did nothing. o require() without a version argument tried for an unversioned load of a package even though a versioned install was already loaded. This often led to a message that a required package was being loaded when it was not actually being loaded. o str() made use of attributes() instead of slot(), and hence didn't properly print NULL slots. o contrib.url() now handles URLs ending in '/' correctly. o str() removed any class from externalptr objects. o logLik() and hence AIC() failed or gave incorrect answers on "lm" fits with na.action = na.exclude (and perhaps other na.actions's except na.omit and na.fail). o pmax() and pmin() sometimes used NAs in internal subassignments, and sometimes these failed. o Subassigning an expression, e.g. expr[2] <- 1, could leave an invalid object and so cause a segfault. (PR#7326) o download/install.packages() would misbehave if there was more than one version of a package in a repository. o sort(partial=) silently ignored some other arguments: using 'decreasing' or 'index.return' or supplying a factor are now errors. o The ave() function had trouble if the grouping contained unused levels. o read.fwf() got confused by skip > 0 and could infinite loop under some circumstances. (PR#7350) o upgrade(x, ask = FALSE) was broken for a "packageStatus" object. o Class "raw" had been omitted from the list of basic classes in the "methods" package and so could not be used in S4 classes. o Function getGroupMembers(), part of the definition of S4 classes, had been promised for release 2.0, but slipped through. o toLatex(sessionInfo()) produced incorrect LaTeX on some platforms due to special characters in the platform identifier. ********************************************************* * * * News of 1.x.y and 2.0.0 is in file `ONEWS' * * News of 1.0.0 and earlier is in file `OONEWS' * * * *********************************************************