(D'oh. Forgot to change the Subject: line...) I've rolled up R-2.10.0.tar.gz some hours ago. This is a development release which contains a number of new features, notably a brand new HTML based dynamic help system. Also, a number of mostly minor bugs have been fixed. See the full list of changes below. You can get it from http://cran.r-project.org/src/base/R-2/R-2.10.0.tar.gz or wait for it to be mirrored at a CRAN site nearer to you. Binaries for various platforms will appear in due course. For the R Core Team Peter Dalgaard These are the md5sums for the freshly created files, in case you wish to check that they are uncorrupted: 70447ae7f2c35233d3065b004aa4f331 INSTALL 433182754c05c2cf7a04ad0da474a1d0 README 4f004de59e24a52d0f500063b4603bcb OONEWS ff4bd9073ef440b1eb43b1428ce96872 ONEWS b80eafe743ef130e129c6d004793492f NEWS 7abcbbc7480df75a11a00bb09783db90 THANKS 070cca21d9f8a6af15f992edb47a24d5 AUTHORS a6f89e2100d9b6cdffcea4f398e37343 COPYING.LIB eb723b61539feef013de476e68b5c50a COPYING 020479f381d5f9038dcb18708997f5da RESOURCES 9ec5df24a0d6ecb04a9817275b825027 FAQ 4486934883b1dbcd5400135e22b26a75 R-2.10.0.tar.gz 4486934883b1dbcd5400135e22b26a75 R-latest.tar.gz This is the relevant part of the NEWS file: CHANGES IN R VERSION 2.10.0 SIGNIFICANT USER-VISIBLE CHANGES o Package help is now converted from Rd by the R-based converters that were first introduced in 2.9.0. This means - Packages that were installed by R-devel after 2009-08-09 should not be used with earlier versions of R, and most aspects of package help (including the runnable examples) will be missing if they are so used. - Text, HTML and latex help and examples for packages installed under the new system are converted on-demand from stored parsed Rd files. (Conversions stored in packages installed under R < 2.10.0 are used if no parsed Rd files are found. It is recommended that such packages be re-installed.) o HTML help is now generated dynamically using an HTTP server running in the R process and listening on the loopback interface. - Those worried about security implications of such a server can disable it by setting the environment variable R_DISABLE_HTTPD to a non-empty value. This disables help.start() and HTML help (so text help is shown instead). - The Java/Javascript search engine has been replaced by an HTML interface to help.search(). help.start() no longer has an argument 'searchEngine' as it is no longer needed. - The HTML help can now locate cross-references of the form \link[pkg]{foo} and \link[pkg:foo]{bar} where 'foo' is an alias in the package, rather than the documented (basename of a) filename (since the documentation has been much ignored). NEW FEATURES o polygon(), pdf() and postscript() now have a parameter 'fillOddEven' (default FALSE), which controls the mode used for polygon fills of self-intersecting shapes. o New debugonce() function; further, getOption("deparse.max.lines") is now observed when debugging, from a code suggestion by John Brzustowski. (PR#13647/8) o plot() methods for "stepfun" and hence "ecdf" no longer plot points by default for n >= 1000. o [g]sub(*, perl=TRUE) now also supports '\E' in order to *end* \U and \L case changes, thanks to a patch from Bill Dunlap. o factor(), `levels<-`(), etc, now ensure that the resulting factor levels are unique (as was always the implied intention). Factors with duplicated levels are still constructible by low-level means, but are now declared illegal. o New print() (S3) method for class "function", also used for auto-printing. Further, .Primitive functions now print and auto-print identically. The new method is based on code suggestions by Romain Fran?ois. o The print() and toLatex() methods for class "sessionInfo" now show the locale in a nicer format and have arguments to suppress locale information. o In addition to previously only round(), there are other 'Math' group (S3) methods for 'difftime', such as floor(), signif(), abs(), etc. o For completeness, old.packages() and available.packages() allow 'type' to be specified (you could always specify 'available' or 'contriburl'). o available.packages() by default only returns information on the latest versions of packages whose version requirements are satisified by the currently running R. o tools::write_PACKAGES() has a new argument 'latestOnly', which defaults to TRUE when only the latest versions in the repository will be listed in the index. o getOption() has a new argument 'default' that is returned if the specified option is not set. This simplifies querying a value and checking whether it is NULL or not. o parse() now warns if the requested encoding is not supported. o The "table" method of as.data.frame() gains a 'stringsAsFactors' argument to allow the classifying factors to be returned as character vectors rather than the default factor type. o If model.frame.default() encounters a character variable where 'xlev' indicates a factor, it now converts the variable to a factor (with a warning). o curve() now returns a list containing the points that were drawn. o spineplot() now accepts axes = FALSE, for consistency with other functions called by plot.factor(). o The Kendall and Spearman methods of cor.test() can optionally use continuity correction when not computing exact p-values. (The Kendall case is the wish of PR#13691.) o R now keeps track of line numbers during execution for code sourced with options(keep.source = TRUE). The source reference is displayed by debugging functions such as traceback(), browser(), recover(), and dump.frames(), and is stored as an attribute on each element returned by sys.calls(). [Experimental] o More functions now have an implicit (S4) generic definition. o quantile.default() now disallows factors (wish of PR#13631) and its help documents what numeric-like properties its input need to have to work correctly. o weighted.mean() is now generic and has "Date", "POSIXct" and "POSIXlt" methods. o Naming subscripts (e.g. x[i=1, j=2]) in data.frame methods for [ and [[ now gives a warning. (Names are ignored in the default method, but could have odd semantics for other methods, and do for the data.frame ones.) o as.data.frame() has an "aovproj" method. (Wish of PR#13505) o as.character(x) for numeric x no longer produces strings such as "0.30", i.e., with trailing zeros. This change also renders levels construction in factor() more consistent. o codocClasses(), which checks consistency of the documentation of S4 class slots, now does so in considerably more cases. The documentation of inherited slots (from superclasses) is now optional. This affects 'R CMD check <pkg>' when the package defines S4 classes. o codoc() now also checks S4 methods for code/documentation mismatches. o for(), while(), and repeat() loops now always return NULL as their (invisible) value. This change was needed to address a reference counting bug without creating performance penalties for some common use cases. o The print() method for ls.str() results now obeys an optional 'digits' argument. o The 'method' argument of glm() now allows user-contributed methods. o More general reorder.default() replaces functionality of reorder.factor() and reorder.character(). o The function aspell() has been added to provide an interface to the Aspell spell-checker. o Filters RdTextFilter() and SweaveTeXFilter() have been added to the tools package to provide support for aspell() or other spell checkers. o xtabs() with the new option 'sparse = TRUE' now returns a sparse Matrix, using package 'Matrix'. o contr.sum() etc gain an argument 'sparse' which allows sparse matrices to be returned. contrasts() also gains a 'sparse' argument which it passes to the actual contrast function if that has a formal argument 'sparse'. 'contrasts(f, .) <- val' now also works when 'val' is a sparse Matrix. It is planned that model.matrix() will work with such factors 'f' in the future. o readNEWS() will recognize a UTF-8 byte-order mark (BOM) in the NEWS file. However, it is safer to use only ASCII code there because not all editors recognize BOMs. o New utility function inheritedSlotNames() for S4 class programming. o tabulate() now allows NAs to pass through (and be ignored). o If debug() is called on an S3 generic function then all methods are debugged as well. o Outlier symbols drawn by boxplot() now obey the 'outlwd' argument. Reported by Jurgen Kluge. o svd(x) and eigen(x) now behave analogously to qr(x) in accepting logical matrices x. o File NEWS is now in UTF-8, and has a BOM (often invisible) on the first line, and Emacs local variables set for UTF-8 at the end. RShowDoc("NEWS") should display this correctly, given suitable fonts. o terms.formula(simplify = TRUE) now does not deparse the LHS and so preserves non-standard responses such as `a: b` (requested by Sundar Dorai-Raj). o New function news() for building and querying R or package news information. o z^n for integer n and complex z is more accurate now if |n| <= 65536. o factor(NULL) now returns the same as factor(character(0)) instead of an error, and table(NULL) consequently does analogously. o as.data.frame.vector() (and its copies) is slightly faster by avoiding a copy if there are no names (following a suggestion of Tim Hesterberg). o writeLines(), writeBin() and writeChar() have a new argument 'useBytes'. If false, character strings with marked encodings are translated to the current locale (as before) but if true they are written byte-by-byte. o iconv() has a new argument 'mark' which can be used (by experts) to suppress the declaration of encodings. o DESCRIPTION 'LinkingTo' specs are now recognized as installation dependencies, and included in package management computations. o Standardized DESCRIPTION 'License' specs are now available for package management computations. o "\uxxxx" and "\Uxxxxxxxx" escapes can now be parsed to a UTF-8 encoded string even in non-UTF-8 locales (this has been implemented on Windows since R 2.7.0). The semantics have been changed slightly: a string containing such escapes is always stored in UTF-8 (and hence is suitable for portably including Unicode text in packages). o New as.raw() method for "tclObj" objects (wish of PR#13578). o Rd.sty now makes a better job of setting email addresses, including using a monospaced font. o textConnection() gains an 'encoding' argument to determine how input strings with marked encodings will be handled. o R CMD Rd2pdf is available as a shortcut for R CMD Rd2dvi --pdf. o R CMD check now checks links where a package is specified (\link[pkg]{file} or \link[pkg:file]{topic}), if the package is available. It notes if the package is not available, as in many cases this is an error in the link. o identical() gains three logical arguments, which allow for even more differentiation, notably '-0' and '0'. o legend() now can specify the 'border' color of filled boxes, thanks to a patch from Frederic Schutz. o Indexing with a vector index to [[]] has now been extended to all recursive types. o Pairlists may now be assigned as elements of lists. (Lists could always be created with pairlist elements, but [[<- didn't support assigning them.) o The parser now supports C-preprocessor-like #line directives, so error messages and source references may refer to the original file rather than an intermediate one. o New functions findLineNum() and setBreakpoint() work with the source references to find the location of source lines and set breakpoints (using trace()) at those lines. o Namespace importing is more careful about warning on masked generics, thanks to a patch by Yohan Chalabi. o detach() now has an argument 'character.only' with the same meaning as for library() or require(). o available.packages() gains a 'filters' argument for specifying the filtering operations performed on the packages found in the repositories. A new built-in 'license/FOSS' filter only retains packages for which installation can proceed solely based on packages which can be verified as Free or Open Source Software (FOSS) employing the available license specifications. o In registering an S3 class by a call to setOldClass(), the data part (e.g., the object type) required for the class can be included as one of the superclasses in the Classes argument. o The argument 'f' to showMethods() can be an expression evaluating to a generic function, allowing methods to be shown for non-exported generics and other nonstandard cases. o sprintf() now supports '%o' for octal conversions. o New function Sys.readlink() for information about symbolic links, including if a file is a symbolic link. o Package 'tools' has new functions checkRdaFiles() and resaveRdaFiles() to report on the format of .rda/.RData data files, and to re-save them in a different compressed format, including choosing the most compact format available. A new INSTALL option, --resave-data, makes use of this. o File ~/.R/config is used in preference to ~/.Rconfig, and these are now documented in 'R Installation and Administration'. o Logic operations with complex numbers now work, as they were always documented to, and as in S. o arrows() and segments() allow one of x1 or y1 to be omitted to simplify the specification of vertical or horizontal lines (suggestion of Tim Hesterberg). o approxfun() is faster by avoiding repeated NA checks (diagnosis and patch by Karline Soetaert & Thomas Petzoldt). o There are the beginnings of a Nynorsk translation by Karl Ove Hufthammer. o stripchart() allows par 'bg' to be passed in for the background colour for pch = 21 (wish of PR#13984). o New generic function .DollarNames() to enable class authors to customize completion after the $ extractor. o load(), save(), dput() and dump() now open a not-yet-open connection in the appropriate mode (as other functions using connections directly already did). REGULAR EXPRESSIONS o A different regular expression engine is used for basic and extended regexps and is also for approximate matching. This is based on the TRE library of Ville Laurikari, a modifed copy of which is included in the R sources. This is often faster, especially in a MBCS locale. Some known differences are that it is less tolerant of invalid inputs in MBCS locales, and in its interpretation of undefined (extended) regexps such as "^*". Also, the interpretation of ranges such as [W-z] in caseless matching is no longer to map the range to lower case. This engine may in future be used in 'literal' mode for fixed = TRUE, and there is a compile-time option in src/main/grep.c to do so. o The use of repeated boundary regexps in gsub() and gregexpr() as warned about in the help page does not work in this engine (it did in the previous one since 2005). o Extended (and basic) regexps now support same set of options as for fixed = TRUE and perl = TRUE, including 'useBytes' and support for UTF-8-encoded strings in non-UTF-8 locales. o agrep() now has full support for MBCS locales with a modest speed penalty. This enables help.search() to use approximate matching character-wise rather than byte-wise. o [g]sub use a single-pass algorithm instead of matching twice and so is usually faster. o The perl = TRUE versions now work correctly in a non-UTF-8 MBCS locale, by translating the inputs to UTF-8. o useBytes = TRUE now inhibits the translation of inputs with marked encodings. o strsplit() gains a 'useBytes' argument. o The algorithm used by strsplit() has been reordered to batch by elements of 'split': this can be much faster for fixed = FALSE (as multiple compilation of regexps is avoided). o The help pages, including ?regexp, have been updated and should be consulted for details of the new implementations. HELP & Rd FILE CHANGES o A new dynamic HTML help system is used by default, and may be controlled using tools::startDynamicHelp(). With this enabled, HTML help pages will be generated on request, resolving links by searching through the current .libPaths(). The user may set option("help.ports") to control which IP port is used by the server. o help.start() no longer sets options(htmlhelp = TRUE) (it used to on Unix but not on Windows). Nor does it on Unix reset the "browser" option if given an argument of that name. Arguments 'update' and 'remote' are now available on all platforms: the default is update = FALSE since the http server will update the package index at first use. o help() has a new argument 'help_type' (with default set by the option of that name) to supersede 'offline', 'htmlhelp' and 'chmhelp' (although for now they still work if 'help_type' is unset). There is a new type, "PDF" to allow offline PDF (rather than PostScript). A function offline_help_helper() will be used if this exists in the workspace or further down the search path, otherwise the function of that name in the 'utils' name space is used. o Plain text help is now used as the fallback for HTML help (as it always was for Compiled HTML help on Windows). o It is possible to ask for static HTML pages to be prebuilt via the configure option --enable-prebuilt-html. This may be useful for those who wish to make HTML help available outside R, e.g. on a local web site. o An experimental tag \Sexpr has been added to Rd files, to evaluate expressions at build, install, or render time. Currently install time and render time evaluation are supported. o Tags \if, \ifelse and \out have been added to allow format-specific (or more general, using \Sexpr) conditional text in man pages. o The parse_Rd() parser has been made more tolerant of coding errors in Rd files: now all syntax errors are reported as warnings, and an attempt is made to continue parsing. o parse_Rd() now has an argument 'fragment' (default FALSE) to accept small fragments of Rd files (so that \Sexpr can output Rd code which is then parsed). o parse_Rd() now always converts its input to UTF-8. The Rd2* rendering functions have a new parameter, 'outputEncoding', which controls how their output is encoded. o parse_Rd() no longer includes the newline as part of a "%"-style comment. o There have been various bug fixes and code reorganization in the Rd renderers Rd2HTML, Rd2latex, Rd2txt, and Rd2ex. All example files are now created with either ASCII or UTF-8 encoding, and the encoding is only marked in the file if there is any non-UTF-8 code (previously it was marked if the help file had non-ASCII contents, possibly in other sections). o print.Rd() now adds necessary escape characters so that printing and re-parsing an Rd object should produce an equivalent object. o parse_Rd() was incorrectly handling multiple backslashes in R code strings, converting 4n+3 backslashes to 2n+1 instead of 2n+2. o parse_Rd() now recognizes the \var tag within a quoted string in R-like text. o parse_Rd() now treats the argument of \command as LaTeX-like, rather than verbatim. COMPRESSION o New function untar() to list or unpack tar archives, possibly compressed. This uses either an external 'tar' command or an internal implementation. o New function tar() to create (possibly compressed) tar archives. o New functions memCompress() and memDecompress() for in-memory compression and decompression. o bzfile() has a 'compress' argument to select the amount of effort put into compression when writing. o New function xzfile() for use with xz-compressed files. (This can also read files compressed by some versions of 'lzma'.) o gzfile() looks at the file header and so can now also read bzip2-ed files and xz-compressed files. o There are the new options of save(compress = "bzip2") and "xz" to use bzip2 or xz compression (which will be slower, but can give substantially smaller files). Argument compression_level gives finer control over the space/time tradeoffs. load() can read such saves (but only as from this version of R). o R CMD INSTALL/check and tools::writePACKAGES accept a wider range of compressed tar archives. Precisely how wide depends on the capabilities of the host system's 'tar' command: they almost always include .tar.bz2 archives, and with modern versions of 'tar' other forms of compression such as lzma and xz, and arbitrary extensions. o R CMD INSTALL has a new option --data-compress to control the compression used when lazy-loading data. New possibilities are --data-compress=bzip2 which will give ca 15% better compression at the expense of slower installation times, and --data-compress=xz, often giving even better compression on large datasets at the expense of much longer installation times. (The latter is used for the recommended packages: it is particularly effective for 'survival'.) o file() for open = "", "r" or "rt" will automagically detect compressed files (from gzip, bzip2 or xz). This means that compressed files can be specified by file name (rather than via a gzfile() connection) to read.table(), readlines(), scan() and so on. o data() can handle compressed text files with extensions .{txt,tab,csv}.{gz,bz2,xz} . DEPRECATED & DEFUNCT o png(type="cairo1") is defunct: the value is no longer recognized. o tools::Rd_parse() is defunct (as this version of R uses only Rd version 2). o Use of ~/.Rconf (which was deprecated in favour of ~/.Rconfig in 2004) has finally been removed. o Bundles of packages are deprecated. See 'Writing R Extensions' for the steps needed to unbundle a bundle. o help() arguments 'offline', 'htmlhelp' and 'chmhelp' are deprecated in favour of 'help_type'. o clearNames() ('stats') is deprecated for unname(). o Basic regular expressions (extended = FALSE) are deprecated in strsplit, grep and friends. There is a precise POSIX standard for them, but it is not what recent RE engines implement, and it seems that in almost all cases package authors intended fixed = TRUE when using extended = FALSE. o methods::trySilent() is deprecated for try(*, silent=TRUE) or - more efficiently and flexibly - something like tryCatch(*, error = function(e) e). o index.search() is deprecated: there are no longer directories of types other than 'help'. INSTALLATION o cairo >= 1.2 is now required (1.2.0 was released in July 2006) for cairo-based graphics devices (which remain optional). o A suitable iconv() is now required: support for configure option --without-iconv has been withdrawn (it was deprecated in R 2.5.0). o Perl is no longer 'essential'. R can be built without it, but scripts R CMD build, check, Rprof and Sd2d require it. o A system 'glob' function is now essential (a working Sys.glob() has been assumed since R 2.9.0 at least). o C99 support for MBCS is now required, and configure option --disable-mbcs has been withdrawn. o Having a version of 'tar' capable of automagically detecting compressed archives is useful for utils::untar(), and so 'gtar' (a common name for GNU tar) is preferred to 'tar': set environment variable TAR to specify a particular 'tar' command. INTERNATIONALIZATION o There is some makefile support for adding/updating translations in packages: see po/README and 'Writing R Extensions'. There is support for the use of 'dngettext' for C-level translations in packages: see 'Writing R Extensions'. BUG FIXES o Assigning an extra 0-length column to a data frame by DF[, "foo"] <- value now works in most cases (by filling with NAs) or fails. (It used to give a corrupt data frame.) o validObject() avoids an error during evaluation in the case of various incorrect slot definitions. o n:m now returns a result of type "integer" in a few more boundary cases. o The 'zap.ind' argument to printCoefmat() did not usually work as other code attempted to ensure that non-zero values had a non-zero representation. o printCoefmat() formatted groups of columns together, not just the cs.ind group but also the zap.ind group and a residual group. It now formats all columns except the cs.ind group separately (and zaps the zap.ind group column-by-column). The main effect will be see in the output from print.anova, as this grouped SS-like columns in the zap.ind group. o R_ReplDLLinit() initializes the top-level jump so that some embedded applications on Windows no longer crash on error. o identical() failed to take the encoding of character strings into account, so identical byte patterns are not necessarily identical strings, and similarly Latin-1 and UTF-8 versions of the same string differ in byte pattern. o methods(f) used to warn unnecessarily for an S4 generic 'f' which had been created based on an existing S3 generic. o The check for consistent ordering of superclasses was not ignoring all conditional relations (the symptom was usually spurious warnings for classes extending "array"). o Trying to assign into a raw vector with an index vector containing NAs could cause a segfault. Reported by Herv? Pag?s. o Rscript could segfault if (by user error) its filename argument was missing. Reported by Martin Morgan. o getAnywhere() (and functions that use it, including argument completion in the console) did not handle special built-in functions. Reported by Romain Francois. o order() was missing a PROTECT() call and so could segfault when called on character data under certain (rare) circumstances involving marked non-native encodings. o prettyNum(z, drop0trailing=TRUE) did not work correctly when z was a complex vector. Consequently, str(z, ...) also did not. (PR#13985) o 'make distclean' removed too many files in etc/ if builddir = srcdir. o R CMD replaced TEXINPUTS rather than appending to it (as documented and intended). o help.start() no longer fails on unix when "browser" is a function. o pbeta(x, *, log.p = TRUE) is sometimes more accurate, e.g., for very small x. o Unserializing a pre-2.8 workspace containing pure ASCII character objects with a LATIN1 or UTF-8 encoding would corrupt the CHARSXP cache. -- O__ ---- Peter Dalgaard ?ster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk) FAX: (+45) 35327907 _______________________________________________ R-announce at stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-announce