From Uwe.Ligges at r-project.org Wed Jan 30 12:08:04 2008 From: Uwe.Ligges at r-project.org (Uwe Ligges) Date: Wed, 30 Jan 2008 12:08:04 +0100 Subject: useR! 2008: submission & registration started! Message-ID: <47A05A94.8010406@R-Project.org> We are happy to inform you that the online abstract submission and registration for `useR! 2008' is now available online from http://www.R-project.org/useR-2008/ This meeting of the R user community will take place at the Technische Universit?t Dortmund, Dortmund, Germany, August 12 to 14, 2008. The conference schedule comprises invited lectures and user-contributed sessions as well as half-day tutorials presented by R experts on August 11, 2008, prior to the conference. Invited speakers will include Peter B?hlmann, John Fox, Andrew Gelman, Kurt Hornik, Gary King, Duncan Murdoch, Jean Thioulouse, and Graham J. Williams. The spectrum of user-contributed sessions will depend on your submissions. Hence, we invite you to submit abstracts on topics presenting innovations or exciting applications of R. The call for papers along with the link to the online abstract submission is available at http://www.R-project.org/useR-2008/#Call Before the start of the official program, half-day tutorials will be offered on Monday, August 11. A list of topics and speakers can be found at http://www.R-project.org/useR-2008/tutorials/ Early birds fly until March 31st 2008, so now is the perfect time to write and submit an abstract, register as a participant and plan your trip to Dortmund. The conference web page http://www.R-project.org/useR-2008/ has a link to a local hotel booking service and much more news. We hope to meet you in Dortmund! The conference committee, Uwe Ligges (conference), Achim Zeileis (program), Claus Weihs, Gerd Kopp (local organization), Friedrich Leisch, Torsten Hothorn From P.Dalgaard at biostat.ku.dk Fri Feb 8 12:18:00 2008 From: P.Dalgaard at biostat.ku.dk (Peter Dalgaard) Date: Fri, 08 Feb 2008 12:18:00 +0100 Subject: R 2.6.2 is released Message-ID: <47AC3A68.4070807@biostat.ku.dk> I've rolled up R-2.6.2.tar.gz a short while ago. This is a maintenance release and fixes a number of mostly minor bugs. See the full list of changes below. You can get it (in a short while) from http://cran.r-project.org/src/base/R-2/R-2.6.2.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: 070cca21d9f8a6af15f992edb47a24d5 AUTHORS eb723b61539feef013de476e68b5c50a COPYING a6f89e2100d9b6cdffcea4f398e37343 COPYING.LIB 91f7aee4dda919e6503c46c2c31f8c15 FAQ 22607d0bc2ea0832ce62544715ad7885 NEWS 1099cbf02c624ceb459d9bbc4d0d1448 R-2.6.2.tar.gz 020479f381d5f9038dcb18708997f5da RESOURCES 1ad28cbc84485ccdf4ce5721b34ed645 THANKS Here is the relevant bit of the NEWS file: CHANGES IN R VERSION 2.6.2 NEW FEATURES o colnames(DF) is now also fast for large dataframes DF with automatic row.names. Note that the correct usage is names(DF). (PR#10470) o tools::texi2dvi() works around the failure of 'texi2dvi --quiet' to be quiet in texinfo 4.11. o On Linux, parallel 32/64-bit installations are supported using multilib. BUG FIXES o A compilation problem on one system where glob was not found has been corrected. (PR#10468) o The "profile.nls" method of plot() was losing the x axis labels. o array() computed the total number of entries in the array before coercing the dimensions to integer. (Reported by Allen McIntosh.) o persp() misreported errors in the y parameter. (Reported by Allen McIntosh.) o source("clipboard", echo=TRUE) and file("clipboard", open="rt") gave spurious errors. (Reported by Fernando Saldanha.) o attributes<-() stripped any existing attributes before checking that all elements of the right-hand side had names. o rbinom(n, size, *) gave NaN when 'size > .Machine$integer.max'. o print.summary.lm() is now consistent in the capitalization of "R-squared". o confint() misreported on some rank-deficient lm() models. (PR#10496) This could also occur in the default method. o \code{\var{}} was not rendered correctly to latex in Rd files for non-alphabetic arguments . o In 2.6.1, curve(*, add=TRUE) used a wrong default 'xlim' when x coordinates were logged. o The Java-based search in help.start() now only requires a JVM >= 1.4 (2.6.1 accidentally required >= 1.5). o The default method for range() was omitting 'na.rm' for non-numeric objects such as those of class "Date". (PR#10508) o cut(x, breaks=) misbehaved on a constant vector of negative values. o bxp(), the plotting engine of boxplot(), no longer plots staple ticks multiple times. (PR#10499) o The automatic detection of the domain for message translation was not working correctly for messages in message(), warning() and stop() in packages other than 'base'. o The profile.nls() function misbehaved when encountering non-convergence of the "port" algorithm. o Under certain rare circumstances in R 2.6.x, log(), round() and trunc() could alter their arguments in the caller. This involved passing of empty '...' arguments, and was spotted when using apply(x, 2, log). o par() no longer warns unnecessarily when asked to set new=FALSE on an unused graphics device. o plot.formula() was not passing on '...' when used with a one-sided formula. plot.formula() was not accepting expressions for annotations passed to title(). (PR#10525) o pchisq(x, df=0, ncp=L) now returns the correct limit exp(-L/2) for x=0 and is no longer returning NaN for x > 0, L < 80. (PR#10551) o Non-ASCII characters were only working correctly in Hershey fonts if these were specified by the 'vfont' argument to text() and not if specified as a font family. o There were several errors in Hershey$allowed, but the help page listed the allowed combinations correctly. o text() no longer attempts to use 'vfont' with an expression for 'labels' (it was documented not to work). o fisher.test(simulate.p.value = TRUE) gave incorrect answers in some extremely degenerate problems. (PR#10558) o src/extra/pcre has been updated to PCRE 7.5 (bugfix release). o capture.output() completes an incomplete final line of output when file = NULL. (PR#10534) o capture.output() now returns invisibly if output is written to a file/connection. o format.AsIs() did not remove the "AsIs" class and so could go into an infinite loop. o summary.mlm() lost the names of the coefficients when there was only one. o Rdconv was not marking examples files with an encoding if this was known from the package's DESCRIPTION file. o readChar() from a raw vector was reading a number of bytes, not characters. o slotNames() was erroneously treating classes that extend "character" as strings. o R no longer ignores SIGPIPE signals even in processes launched by system(). Instead PR#1959 is handled by a simple error handler which will give an error message in circumstances where none was given before. o The AIC() S4 generic in package stats4 no longer disables dispatch of S3 methods for AIC(). o The conflicts check in library() excluded all S4 generics, even where they were unrelated to the function masked. It is now more selective (although still too generous to S4 generics). o proc.time() was missing a protect and could misbehave if provoked by gctorture(). (PR#10600) o The cut() and hist() methods for dates and datetimes are now more accurate for intervals of "months" and "years", thanks to Marc Schwarz. o url()/download.file() could segfault if the HTTP interaction involved a redirect to an address starting with '/' on the same server. o Memory allocations used in format() and in an internal utility function could be off by one byte. (PR#10635) o isoreg(x, y) no longer segfaults when y has NAs. o split(x, g) always returns a list as documented. (It used to return NULL for a zero-length 'x'.) o tapply(x, g, ...) misbehaved if the args were of zero length. (PR#10644) o hist.POSIXt(*, xaxt = "n") no longer suppresses the y-axis. o strptime() crashed under certain locales on Mac OS X. o gregexpr() no longer segfaults when "" is given as the search pattern. Thanks to Herve Pages for the bug report. o matplot(x, *) with default 'pch' did not plot columns from column number 37 on (because the default pch was NA for those). (PR#10676) o print.htest() lost output when used within sink(file, split=TRUE). o Setting par(col.main=) also set par("col") to the same colour. o Anonymous fifos were broken (again). -- 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 From P.Dalgaard at biostat.ku.dk Tue Apr 22 10:16:54 2008 From: P.Dalgaard at biostat.ku.dk (Peter Dalgaard) Date: Tue, 22 Apr 2008 10:16:54 +0200 Subject: R 2.7.0 is released Message-ID: <480D9EF6.7040909@biostat.ku.dk> I've rolled up R-2.7.0.tar.gz a short while ago. This is a development release which contains a number of new features. Also, a number of mostly minor bugs have been fixed. See the full list of changes below. You can get it (later today) from http://cran.r-project.org/src/base/R-2/R-2.7.0.tar.gz or wait for it to be mirrored at a CRAN site nearer to you. In case of impatience, try http://www.biostat.ku.dk/~pd/R-release 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: 9eaee3eceec1d5f72cea5640ca90768c R-latest.tar.gz 9eaee3eceec1d5f72cea5640ca90768c R-2.7.0.tar.gz 3f4331cd3d66c36b9e350b0576fa8f42 FAQ 020479f381d5f9038dcb18708997f5da RESOURCES eb723b61539feef013de476e68b5c50a COPYING a6f89e2100d9b6cdffcea4f398e37343 COPYING.LIB 070cca21d9f8a6af15f992edb47a24d5 AUTHORS 1ad28cbc84485ccdf4ce5721b34ed645 THANKS f7a51a08be0aab537123b0fc66cd0e79 NEWS ff4bd9073ef440b1eb43b1428ce96872 ONEWS 4f004de59e24a52d0f500063b4603bcb OONEWS 433182754c05c2cf7a04ad0da474a1d0 README 70447ae7f2c35233d3065b004aa4f331 INSTALL This is the relevant part of the NEWS file: CHANGES IN R VERSION 2.7.0 SIGNIFICANT USER-VISIBLE CHANGES o The default graphics device in non-interactive use is now pdf() rather than postscript(). [PDF viewers are now more widely available than PostScript viewers.] The default width and height for pdf() and bitmap() have been changed to 7 (inches) to match the screen devices. o Most users of the X11() device will see a new device that has different fonts, anti-aliasing of lines and fonts and supports semi-transparent colours. o Considerable efforts have been made to make the default output from graphics devices as similar as possible (and in particular close to that from postscript/pdf). Many devices were misinterpreting 'pointsize' in some way, for example as being in device units (pixels) rather than in points. o Packages which include graphics devices need to be re-installed for this version of R, with recently updated versions. NEW FEATURES o The apse code used by agrep() has been updated to version 0.16, with various bug fixes. agrep() now supports multibyte character sets. o any() and all() avoid coercing zero-length arguments (which used a surprising amount of memory) since they cannot affect the answer. Coercion of other than integer arguments now gives a warning as this is often a mistake (e.g. writing all(pr) > 0 instead of all(pr > 0) ). o as.Date(), as.POSIXct() and as.POSIXlt() now convert numeric arguments (days or seconds since some epoch) provided the 'origin' argument is specified. o New function as.octmode() to create objects such as file permissions. o as.POSIXlt() is now generic, and it and as.POSIXct() gain a '...' argument. The character/factor methods now accept a 'format' argument (analogous to that for as.Date). o New function browseVignettes() lists available vignettes in an HTML browser with links to PDF, Rnw, and R files. o There are new capabilities "aqua" (for the AQUA GUI and quartz() device on Mac OS X) and "cairo" (for cairo-based graphics devices). o New function checkNEWS() in package 'tools' that detects common errors in NEWS file formatting. o deparse() gains a new argument 'nlines' to limit the number of lines of output, and this is used internally to make several functions more efficient. o deriv() now knows the derivatives of digamma(x), trigamma(x) and psigamma(x, deriv) (wrt to x). o dir.create() has a new argument 'mode', used on Unix-alikes (only) to set the permissions on the created directory. o Where an array is dropped to a length-one vector by drop() or [, drop = TRUE], the result now has names if exactly one of the dimensions was named. (This is compatible with S.) Previously there were no names. o The 'incomparables' argument to duplicated(), unique() and match() is now implemented, and passed to match() from merge(). o dyn.load() gains a 'DLLpath' argument to specify the path for dependent DLLs: currently only used on Windows. o The spreadsheet edit() methods (and used by fix()) for data frames and matrices now warn when classes are discarded. When editing a data frame, columns of unknown type (that is not numeric, logical, character or factor) are now converted to character (instead of numeric). o file.create() has a new argument 'showWarnings' (default TRUE) to show an informative warning when creation fails, and dir.create() warns under more error conditions. o New higher-order functions Find(), Negate() and Position(). o [dpqr]gamma(*, shape = 0) now work as limits of 'shape -> 0', corresponding to the point distribution with all mass at 0. o An informative warning (in addition to the error message) will be given when the basic, extended or perl mode of grep(), strsplit() and friends fails to compile the pattern. o More study is done of perl=TRUE patterns in grep() and friends when length(x) > 10: this should improve performance on long vectors. o grep(), strsplit() and friends with fixed=TRUE or perl=TRUE work in UTF-8 and preserve the UTF-8 encoding for UTF-8 inputs where supported. o help.search() now builds the database about 3x times faster. o iconv() now accepts "UTF8" on all platforms (many did, but not e.g. libiconv as used on Windows). o identity() convenience function to be used for programming. o In addition to warning when 'pkgs' is not found, install.packages() now reports if it finds a valid package with only a case mismatch in the name. o intToUtf8() now marks the Encoding of its output. o The function is() now works with S3 inheritance; that is, with objects having multiple strings in the class attribute. o Extensions to condition number computation for matrices, notably complex ones are provided, both in kappa() and the new rcond(). o list.file() gains a 'ignore.case' argument, to allow case-insensitive matching on some Windows/MacOS file systems. o ls.str() and lsf.str() have slightly changed arguments and defaults such that ls.str() {no arguments} works when debugging. o Under Unix, utils::make.packages.html() can now be used directly to set up linked HTML help pages, optionally without creating the package listing and search database (which can be much faster). o new.packages() now knows about the front-end package gnomeGUI (which does not install into a library). o optim(*, control = list(...)) now warns when '...' contains unexpected names, instead of silently ignoring them. o The options "browser" and "editor" may now be set to functions, just as "pager" already could. o packageDescription() makes use of installed metadata where available (for speed, e.g. in make.packages.html()). o pairwise.t.test() and pairwise.wilcox.test() now more explicitly allow paired tests. In the former case it is now flagged as an error if both 'paired' and 'pool.SD' are set TRUE (formerly, 'paired' was silently ignored), and one-sided tests are generated according to 'alternative' also if 'pool.SD' is TRUE. o paste() and file.path() are now completely internal, for speed. (This speeds up make.packages.html(packages=FALSE) severalfold, for example.) o paste() now sets the encoding on the result under some circumstances (see ?paste). o predict.loess() now works when loess() was fitted with transformed explanatory variables, e.g, loess(y ~ log(x) + log(z)). o print()'s new argument 'row.names' allows to suppress printing rownames. o print() and str() now also "work" for 'logLik' vectors longer than one. o Progress-bar functions txtProgressBar(), tkProgressBar() in package tcltk and winProgressBar() (Windows only). o readChar() gains an argument 'useBytes' to allow it to read a fixed number of bytes in an MBCS locale. o readNEWS() has been moved to the tools package. o round() and signif() now do internal argument matching if supplied with two arguments and at least one is named. o New function showNonASCII() in package tools to aid detection of non-ASCII characters in .R and .Rd files. o The [dpq]signrank() functions now typically use considerably less memory than previously, thanks to a patch from Ivo Ugrina. o spec.ar() now uses frequency(x) when calculating the frequencies of the estimated spectrum, so that for monthly series the frequencies are now per year (as for spec.pgram) rather than per month as before. o spline() gets an 'xout' argument, analogously to approx(). o sprintf() now does all the conversions needed in a first pass if length(fmt) == 1, and so can be many times faster if called with long vector arguments. o [g]sub(useBytes = FALSE) now sets the encoding on changed elements of the result when working on an element of known encoding. (This was previously done only for perl = TRUE.) o New function Sys.chmod(), a wrapper for 'chmod' on platforms which support it. (On Windows it handles only the read-only bit.) o New function Sys.umask(), a wrapper for 'umask' on platforms which support it. o New bindings ttk*() in package tcltk for the 'themed widgets' of Tk 8.5. The tcltk demos make use of these widgets where available. o write.table(d, row.names=FALSE) is faster when 'd' has millions of rows; in particular for a data frame with automatic row names. (Suggestion from Martin Morgan.) o The parser limit on string size has been removed. o If a NEWS file is present in the root of a source package, it is installed (analogously to LICENSE, LICENCE and COPYING). o Rd conversion to 'example' now quotes aliases which contain spaces. o The handling of DST on dates outside the range 1902-2037 has been improved. Dates after 2037 are assumed to have the same DST rules as currently predicted for the 2030's (rather than the 1970s), and dates prior to 1902 are assumed to have no DST and the same offset as in 1902 (if known, otherwise as in the 1970s). o On platforms where we can detect that mktime sets errno (e.g. Solaris and the code used on Windows but not Linux nor Mac OS X), 1969-12-31 23:59:59 GMT is converted from POSIXlt to POSIXct as -1 and not NA. o The definition of 'whitespace' used by the parser is slightly wider: it includes Unicode space characters on Windows and in UTF-8 locales on machines which use Unicode wide characters. o The src/extra/intl sources have been updated to those from gettext 0.17. o New flag --interactive on Unix-alikes forces the session to be interactive (as --ess does on Windows). o x[] <- NULL is always a no-op: previously type-checking was done on the replacement value and so this failed, whereas we now assume NULL can be promoted to any zero-length vector-like object. Other cases of a zero-length index are done more efficiently. o There is a new option in Rd markup of \donttest{} to mark example code that should be run by example() but not tested (e.g. because it might fail in some locales). o The error handler in the parser now reports line numbers for more syntax errors (MBCS and Unicode encoding errors, line length and context stack overflows, and mis-specified argument lists to functions). o The "MethodsList" objects originally used for method selection are being phased out. New utilities provide simpler alternatives (see ?findMethods), and direct use of the mangled names for the objects is now deprecated. o Creating new S4 class and method definitions in an environment that could not be identified (as package, namespace or global) previously generated an error. It now results in creating and using an artificial package name from the current date/time, with a warning. See ?getPackageName. o Unix-alikes now give a warning on startup if locale settings fail. (The Windows port has long done so.) o Parsing and scanning of numerical constants is now done by R's own C code. This ensures cross-platform consistency, and mitigates the effects of setting LC_NUMERIC (within base R it only applies to output -- packages may differ). The format accepted is more general than before and includes binary exponents in hexadecimal constants: see ?NumericConstants for details. o Dependence specifications for R or packages in the Depends field in a DESCRIPTION file can now make use of operators < > == and != (in addition to <= and >=): such packages will not be installable nor loadable in R < 2.7.0. There can be multiple mentions of R or a package in the Depends field in a DESCRIPTION file: only the first mention will be used in R < 2.7.0. GRAPHICS CHANGES o The default graphics devices in interactive and non-interactive sessions are now configurable via environment variables R_INTERACTIVE_DEVICE and R_DEFAULT_DEVICE respectively. o New function dev.new() to launch a new copy of the default graphics device (and taking care if it is "pdf" or "postscript" not to trample on the file of an already running copy). o dev.copy2eps() uses dev.displaylist() to detect screen devices, rather than list them in the function. o New function dev.copy2pdf(), the analogue of dev.copy2eps(). o dev.interactive() no longer treats a graphics device as interactive if it has a display list (but devices can still register themselves on the list of interactive devices). o The X11() and windows() graphics devices have a new argument 'title' to set the window title. o X11() now has the defaults for all of its arguments set by the new function X11.options(), inter alia replacing options "gamma", "colortype" and "X11fonts". o ps.options() now warns on unused option 'append'. xfig() no longer takes default arguments from ps.options(). (This was not documented prior to 2.6.1 patched.) pdf() now takes defaults from the new function pdf.options() rather that from ps.options() (and the latter was not documented prior to 2.6.1 patched). The defaults for all arguments other than 'file' in postscript() and pdf() can now be set by ps.options() or pdf.options() o New functions setEPS() and setPS() as wrappers to ps.options() to set appropriate defaults for figures for inclusion in other documents and for spooling to a printer respectively. o The meaning of numeric 'pch' has been extended where MBCSes are supported. Now negative integer values indicate Unicode points, integer values in 32-127 represent ASCII characters, and 128-255 are valid only in single-byte locales. (Previously what happened with negative pch values was undocumented: they were replaced by the current setting of par("pch").) o Graphics devices can say if they can rotate text well (e.g. postscript() and pdf() can) and if so the device's native text becomes the default for contour labels rather than using Hershey fonts. o The setting of the line spacing (par("cra")[2]) on the X11() and windows() devices is now comparable with postscript() etc, and roughly 20% smaller than before (it used to depend on the locale for X11). (So is the pictex() device, now 20% larger.) This affects the margin size in plots, and should result in better-looking plots. o There is a per-device setting for whether new frames need confirmation. This is controlled by either par("ask") or grid.prompt() and affects all subsequent plots on the device using base or grid graphics. o There is a new version of the X11() device based on cairo graphics which is selected by type "cairo" or "nbcairo", and is available on machines with cairo installed and preferably pango (which most machines with gtk+ >= 2.8 will have). This version supports translucent colours and normally does a better job of font selection so it has been possible to display (e.g.) English, Polish, Russian and Japanese text on a single X11() window. It is the default where available. There is a companion function, savePlot(), to save the current plot to a PNG file. On Unix-alikes, devices jpeg() and png() also accept type = "cairo", and with that option do not need a running X server. The meaning of capabilities("jpeg") and capabilities("png") has changed to reflect this. On MacOS X, there is a further type = "quartz". The default type is selected by the new option "bitmapType", and is "quartz" or "cairo" where available. Where cairo 1.2 or later is supported, there is a svg() device to write SVG files, and cairo_pdf() and cairo_ps() devices to write (possibly bitmap) PDF and postscript files via cairo. Some features require cairo >= 1.2, and some which are nominally supported under 1.2 seem to need 1.4 to work well. o There are new bmp() and tiff() devices. o New function devSize() to report the size of the current graphics device surface (in inches or device units). This gives the same information as par("din"), but independent of the graphics subsystem. o New base graphics function clip() to set the clipping region (in user coordinates). o New functions grconvertX() and grconvertY() to convert between coordinate systems in base graphics. o identify() recycles its 'labels' argument if necessary. o stripchart() is now a generic function, with default and formula methods defined. Additional graphics parameters may be included in the call. Formula handling is now similar to boxplot(). o strwidth() and strheight() gain 'font' and 'vfont' arguments and accept in-line pars such as 'family' in the same way as text() does. (Longstanding wish of PR#776) o example(ask=TRUE) now applies to grid graphics (e.g. from lattice) as well as to base graphics. o Option "device.ask.default" replaces "par.ask.default" now it applies also to grid.prompt(). o plot.formula() only prompts between plots for interactive devices (it used to prompt for all devices). o When plot.default() is called with y=NULL it now calls Axis() with the 'y' it constructs rather than use the default axis. DEPRECATED & DEFUNCT o In package installation, SaveImage: yes is defunct and lazyloading is attempted instead. o $ on an atomic vector or S4 object is now defunct. o Partial matching in [[ is now only performed if explicitly requested (by exact=FALSE or exact=NA). o Command-line completion has been moved from package 'rcompgen' to package 'utils': the former no longer exists as a separate package in the R distribution. o The S4 pseudo-classes "single" and double have been removed. (The S4 class for a REALSXP is "numeric": for back-compatibility as(x, "double") coerces to "numeric".) o gpar(gamma=) in the grid package is now defunct. o Several S4 class definition utilities, get*(), have been said to be deprecated since R 1.8.0; these are now formally deprecated. Ditto for removeMethodsObject(). o Use of the graphics headers Rgraphics.h and Rdevices.h is deprecated, and these will be unavailable in R 2.8.0. (They are hardly used except in graphics devices, for which there is an updated API in this version of R.) o options("par.ask.default") is deprecated in favour of "device.ask.default". o The 'device-independent' family "symbol" is deprecated as it was highly locale- and device-dependent (it only did something useful in single-byte locales on most devices) and font=5 (base) or fontface=5 (grid) did the job it was intended to do more reliably. o gammaCody() is now formally deprecated. o Two low-level functions using MethodsList metadata objects (mlistMetaName() and getAllMethods()) are deprecated. o Setting par(gamma=) is now deprecated, and the windows() device (the only known example) no longer allows it. o The C macro 'allocString' will be removed in 2.8.0 -- use 'mkChar', or 'allocVector' directly if really necessary. INSTALLATION o Tcl/Tk >= 8.3 (released in 2000) is now required to build package tcltk. o configure first tries TCL_INCLUDE_SPEC and TK_INCLUDE_SPEC when looking for Tcl/Tk headers. (The existing scheme did not work for the ActiveTcl package on Mac OS X.) o The Windows build only supports Windows 2000 or later (XP, Vista, Server 2003 and Server 2008). o New option --enable-R-static-lib installs libR.a which can be linked to a front-end via 'R CMD config --ldflags'. The tests/Embedding examples now work with a static R library. o Netscape (which was discontinued in Feb 2008) is no longer considered when selecting a browser. o xdg-open (the freedesktop.org interface to kfmclient/gnome-open/...) is considered as a possible browser, after real browsers such as firefox, mozilla and opera. o The search for tclConfig.sh and tkConfig.sh now only looks in directories with names containing $(LIBnn) in the hope of finding the version for the appropriate architecture (e.g. x86_64 or i386). o libtool has been updated to version 2.2. o Use of --with-system-zlib, --with-system-bzlib or --with-system-pcre now requires version >= 1.2.3, 1.0.5, 7.6 respectively, for security. UTILITIES o Rdconv now removes empty sections including alias and keyword entries, with a note. o Keyword entries are no longer mandatory in Rd files. o R CMD INSTALL now also installs tangled versions of all vignettes. o R CMD check now warns if spaces or non-ASCII characters are used in file paths, since these are not in general portable. o R CMD check (via massage-examples.pl) now checks all examples with a 7 inch square device region on A4 paper, for locale-independence and to be similar to viewing examples on an on-screen device. If a package declares an encoding in the DESCRIPTION file, the examples are assumed to be in that encoding when running the tests. (This avoids errors in running latin1 examples in a UTF-8 locale.) o R CMD check uses pdflatex (if available) to check the typeset version of the manual, producing PDF rather than DVI. (This is a better check since the package reference manuals on CRAN are in PDF.) o R CMD Rd2dvi gains a --encoding argument to be passed to R CMD Rdconv, to set the default encoding for conversions. If this is not supplied and the files are package sources and the DESCRIPTION file contains an Encoding field, that is used for the default encoding. o available.packages() (and hence install.packages() etc) now supports subdirectories in a repository, and tools::write_PACKAGES() can now produce PACKAGES files including subdirectories. o The default for 'stylepath' in Sweave's (default) RweaveLatex driver can be set by the environment variable SWEAVE_STYLEPATH_DEFAULT: see ?RweaveLatex. C-LEVEL FACILITIES o Both the Unix and Windows interfaces for embedding now make use of 'const char *' declarations where appropriate. o Rprintf() and REprintf() now use 'const char *' for their format argument -- this should reduce warnings when called from C++. o There is a new description of the interface for graphics devices in the 'R Internals' manual, and several new entry points. The API has been updated to version R_GE_version = 5, and graphics devices will need to be updated accordingly. o Graphics devices can now select to be sent text in UTF-8, even if the current locale is not UTF-8 (and so enable text entered in UTF-8 to be plotted). This is used by postscript(), pdf() and the windows() family of devices, as well as the new cairo-based devices. o More Lapack routines are available (and declared in R_Ext/Lapack.h), notably for (reciprocal) condition number estimation of complex matrices. o Experimental utility R_has_slot supplementing R_do_slot. o There is a new public interface to the encoding info stored on CHARSXPs, getCharCE and mkCharCE using the enumeration type cetype_t. o A new header 'R_ext/Visibility.h' contains some definitions for controlling the visibility of entry points, and how to control visibility is now documented in 'Writing R Extensions'. BUG FIXES o pt(x, df) is now even more accurate in some cases (e.g. 12 instead of 8 significant digits), when x^2 << df, thanks to a remark from Ian Smith, related to PR#9945. o co[rv](use = "complete.obs") now always gives an error if there are no complete cases: they used to give NA if method = "pearson" but an error for the other two methods. (Note that this is pretty arbitrary, but zero-length vectors always give an error so it is at least consistent.) cor(use="pair") used to give diagonal 1 even if the variable was completely missing for the rank methods but NA for the Pearson method: it now gives NA in all cases. cor(use="pair") for the rank methods gave a matrix result with dimensions > 0 even if one of the inputs had 0 columns. o Supplying edit.row.names = TRUE when editing a matrix without row names is now an error and not a segfault. (PR#10500) o The error handler in the parser reported unexpected & as && and | as ||. o ps.options(reset = TRUE) had not reset for a long time. o paste() and file.path() no longer allow NA_character_ for their 'sep' and 'collapse' arguments. o by() failed for 1-column matrices and dataframes. (PR#10506) However, to preserve the old behaviour, the default method when operating on a vector still passes subsets of the vector to FUN, and this is now documented. o Better behaviour of str.default() for non-default 'strict.width' (it was calling str() rather than str.default() internally); also, more useful handling of options("str"). o wilcox.test(exact=FALSE, conf.int=TRUE) could fail in some extreme two-sample problems. (Reported by Wolfgang Huber.) o par(pch=) would accept a multi-byte string but only use the first byte. This would lead to incorrect results in an MBCS locale if a non-ASCII character was supplied. o There are some checks for valid C-style formats in, e.g. png(filename=). (PR#10571) o vector() was misinterpreting some double 'length' values, e.g, NaN and NA_real_ were interpreted as zero. Also, invalid types of 'length' were interpreted as -1 and hence reported as negative. (length<- shared the code and hence the same misinterpretations.) o A basic class "S4" was added to correspond to the "S4" object type, so that objects with this type will print, etc. The class is VIRTUAL, since all actual S4 objects must have a real class. o Classes with no slots that contain only VIRTUAL classes are now VIRTUAL, as was intended but confused by having an empty S4 object as prototype. ## backed out temporarily ## o format.AsIs() discarded dimnames, causing dataframes with matrix variables to be printed without using the column names, unlike what happens in S-PLUS (Tim Hesterberg, PR#10730). o xspline() and grid::grid.xspline() work in device coordinates and now correct for anisotropy in the device coordinate system. o grid.locator() now indicates to the graphics device that it is is in 'graphics input' mode (as locator() and identify() always have). This means that devices can now indicate the 'graphics input' mode by e.g. a change of cursor. o Locales without encoding specification and non-UTF-8 locales now work properly on Mac OS X. Note that locales without encoding specification always use UTF-8 encoding in Mac OS X (except for specials "POSIX" and "C") - this is different from other operating systems. o iconv() now correctly handles to="" and from="" on Mac OS X. o In diag()'s argument list, drop the explicit default (' = n') for 'ncol' which is ugly when making diag() generic. o S4 classes with the same name from different packages were not recognized because of a bug in caching the new definition. o jpeg() and png() no longer maintain a display list, as they are not interactive devices. o Using attr(x, "names") <- value (instead of the correct names<-) with 'value' a pairlist (instead of the correct character vector) worked incorrectly. (PR#10807) o Using [<- to add a column to a data frame dropped other attributes whereas [[<- and $<- did not: now all preserve attributes. (PR#10873) o File access functions such as file.exists(), file.info(), dirname() and unlink() now treat an NA filename as a non-existent file and not the file "NA". o r(), the random number generators, are now more consistent in warning when NA's (specifically NaN's) are generated. o rnorm(n, mu = Inf) now returns rep(Inf, n) instead of NaN; similar changes are applied to rlnorm(), rexp(), etc. o [l]choose() now warns when rounding non-integer 'k' instead of doing so silently. (May help confused users such as PR#10766.) o gamma() was warning incorrectly for most negative values as being too near a negative integer. This also affected other functions making use of its C-level implementation. o dumpMethod() and dumpMethods() now work again. o package.skeleton() now also works for code_files with only metadata (e.g. S4 setClass) definitions; it handles S4 classes and methods, producing documentation and NAMESPACE exports if requested. o Some methods package utilities (implicitGeneric(), makeGeneric()) will be more robust in dealing with primitive functions (not a useful idea to call them with primitives, though) o Making a MethodsList from a function with no methods table will return an empty list, rather than cause an error (questionably a bug, but caused some obscure failures). o setAs() now catches 2 arguments in the method definition, if they do not match the arguments of coerce(). o S4 methods with missing arguments in the definition are handled correctly when non-signature arguments exist, and check for conflicting local names in the method definition. o qgamma() and qchisq() could be inaccurate for small p, e.g. qgamma(1.2e-10, shape = 19) was 2.52 rather than 2.73. o dbeta(.., ncp) is now more accurate for large ncp, and typically no longer underflows for give.log = TRUE. o coerce() is now a proper S4 object and so prints correctly. o @ now checks it is being applied to an S4 object, and if not gives a warning (which will become an error in 2.8.0). o dump() and friends now warn that all S4 objects (even those based on vectors) are not source()able, with a stronger wording. o read.dcf(all = TRUE) was leaking connections. o scan() with a non-default separator could skip nul bytes, including those entered as \0 with allowEscapes=TRUE. This was different from the default separator. o determinant(matrix(,0,0)) now returns a correct "det" result; also value 1 or 0 depending on 'logarithm', rather than numeric(0). o Name space 'grDevices' was not unloading its DLL when the name space was unloaded. o getNativeSymbolInfo() was unaware of non-registered Fortran names, because one of the C support routines ignored them. o load() again reads correctly character strings with embedded nuls. (This was broken in 2.6.x, but worked in earlier versions.) CHANGES IN R VERSION 2.6.2 patched BUG FIXES o src/extra/pcre has been updated to PCRE 7.6 (bugfix release). o unlink(..., recursive=TRUE) no longer crashes on some platforms if a directory cannot be opened. o Loading in 2.6.2 a saved workspace could give an unimportant warning in a non-UTF-8 multibyte locale (in particular a CJK locale on Windows) which is now suppressed. o print() methods are more consistent in returning the original argument invisibly. o Using the X11 data editor (e.g. via edit(), fix() or View()) could crash if the 'End' key was used and all the columns would have fitted into the window. o Creating a new page on an X11() device (by plot.new() or grid.newpage()) did not flush out the XClearWindow call, so the X11 window might not be refreshed immediately. o libtool has been updated to version 1.5.26, which avoids many spurious configure warnings on Darwin/Mac OS X. o l10n_info() now recognizes how Darwin/Mac OS X reports Latin-1 locales (as charset ISO8859-1 rather than ISO-8859-1). o Checking examples which used grid (e.g. via lattice) without attaching grid no longer give errors from grid_plot_hook(). o kappa(m, exact=TRUE) no longer wrongly uses 'exact=FALSE' when m is an 'lm' or 'qr' object because the kappa.tri(x, exact=TRUE) now works correctly. o help(topic, offline=TRUE) misbehaved when there were multiple matches to 'topic'. (PR#10859) o The 'multilib' changes on Linux broke the use of sub-architectures without a main architecture. o source(echo=TRUE) would skip lines consisting entirely of the letter t. (PR#10923) o bzip2 has been updated to 1.0.5 (security fix). -- 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 From jfox at mcmaster.ca Wed May 28 05:02:14 2008 From: jfox at mcmaster.ca (John Fox) Date: Tue, 27 May 2008 23:02:14 -0400 Subject: R News, volume 8, issue 1 is now available Message-ID: <64D6F100-FFE1-4557-8D0A-5BBA99909CD8@mcmaster.ca> Dear R users, The May 2008 issue of `R News' is now available on CRAN under the Documentation/Newsletter link. John (on behalf of the R News Editorial Board) -------------------------------------------- John Fox, Professor Department of Sociology McMaster University Hamilton ON Canada L8S 4M4 web: socserv.mcmaster.ca/jfox From P.Dalgaard at biostat.ku.dk Mon Jun 23 10:01:43 2008 From: P.Dalgaard at biostat.ku.dk (Peter Dalgaard) Date: Mon, 23 Jun 2008 10:01:43 +0200 Subject: R 2.7.1 is released Message-ID: <485F5867.4020108@biostat.ku.dk> I've rolled up R-2.7.1.tar.gz a short while ago. This is a maintenance release and fixes a number of mostly minor bugs and platform issues. Notably, the numeric interpretation of "-", "+", and "." has reverted to pre-2.7.0 behaviour See the full list of changes below. You can get it (in a short while) from http://cran.r-project.org/src/base/R-2/R-2.7.1.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 1cff51aab2e4f3ce66200a700ede143b NEWS 1ad28cbc84485ccdf4ce5721b34ed645 THANKS 070cca21d9f8a6af15f992edb47a24d5 AUTHORS a6f89e2100d9b6cdffcea4f398e37343 COPYING.LIB eb723b61539feef013de476e68b5c50a COPYING 020479f381d5f9038dcb18708997f5da RESOURCES a04d059fa76b105566aad359d38864a0 FAQ b1ca7e499b7a0ea8ec4eb95a2231e97b R-2.7.1.tar.gz b1ca7e499b7a0ea8ec4eb95a2231e97b R-latest.tar.gz Here is the relevant bit of the NEWS file: CHANGES IN R VERSION 2.7.1 NEW FEATURES o tools::texi2dvi() has a new argument 'texinputs' to allow the TeX and bibtex input paths to be specified (even on MiKTeX). o dev.copy2pdf() gains an 'out.type' argument to allow it to be used with cairo_pdf() or quartz(type = "pdf"). o poly() has additional checks against user error (as in PR#11243). o The Mac OS quartz() device draws contiguous lines much faster. o A field containing just a sign is no longer regarded as numeric (it was on all platforms in 2.7.0, but not on most in earlier versions of R). Similarly, '.' is now always non-numeric. o CITATION files are now read in Latin-1: quite a few were failing if used in a multibyte locale such as UTF-8. o The DESCRIPTION file of a package can specify an 'OS_type' field as either 'unix' or 'windows' to confine installation to that OS type. o HoltWinters() now uses optimize() rather than optim for one-parameter problems which should be more reliable (PR#11469). o axis() now respects the setting of par("xpd") when clipping. o The 'factor' method of format() now preserves names, dims and dimnames in the same way as for character and numeric inputs. (PR#11512) o read.DIF(*, transpose=TRUE) now allows to correctly read DIF files produced by some versions of Excel. DEPRECATED & DEFUNCT o The use of unserialize() on character strings is deprecated: that was a format used in R < 2.4.0. o The use of embedded nuls in character strings is deprecated: They will no longer be allowed in R 2.8.0. UTILITIES o R CMD check checks for possible check directories in the sources -- in mid-2008 there were about 20 examples on CRAN. o R CMD build tries harder to clean up the inst/doc directory from the remnants of earlier builds. It also removes any directories with extension .Rcheck, and files .DS_Store and ._* (created by tar on Mac OS X under some circumstances: it now sets environment variables to ask for such files not to be created by that tar.) BUG FIXES o Encoding<- on NA_character_ converted it to "NA". o Adobe Symbol was missing from the encodings in tools::charset_to_Unicode. o diag(matrix(x, 0, 0)) now returns a 0-length vector of the correct mode, instead of always numeric. o The parser sometimes accepted invalid quoted strings in a UTF-8 locale. o plot.default(x, y) now dispatches to Axis() methods whether y is NULL or not. o On Mac OS X, the Cocoa Quartz window could close without warning under certain circumstances (specific autorelease pool flush). o Plotting symbols with separate border and fill colours (e.g., plot(pch = 21)) now works with transparent 'col', but opaque or semi-transparent 'bg'. Previously, if 'col' was transparent then 'bg' was ignored and nothing was drawn. o file.path() did not work correctly in 2.7.0 if the components had different encodings. o merge() failed if there were no common columns and one of the inputs had zero rows. o expand.grid() failed if an input had length 0. o match() does again truncate strings at embedded nuls (as newly documented in 2.7.0). o Because of a typo, 'pointsize' in png(type="cairo") (and jpeg, bmp, tiff) devices was being interpreted in pixels not bigpoints. o is() was wrong for some S3 class objects with class of length greater than one. o undoc() / codoc() were not checking all S4 methods in some cases. o Use of textConnection(NULL, mode="w") could segfault. o Use of strwidth/height(units="user") (the default) is again an error before a user coordinate system has been set on the device, rather than giving nonsensical values (the effect of r31367). o Rare string width calculations in package grid were not interpreting the string encoding correctly. o hasMethods(f, env) {without specified 'package'} now works better. o A missing PROTECT could cause segfaults on string comparisons. (PR#11421) o str(structure(1, classID = "Pooh")) now works fine. o A missing PROTECT could cause segfaults in if() if coercion of the condition was required or a warning was to be given. o plot() now uses a sensible default main title. o validObject() called with complete=TRUE did not use inherited validity methods for slot classes. o Several bugs fixed in as(): the initial method lookup was not using the table with inherited methods (so inheritance had to be recomputed each time); coerce() should not be called directly--it can insert invalid inherited methods; the constructed as() methods were not retaining the function's environment. o influence.measures() now computes the same Cook's distance approximations as cooks.distance(). o plot(, which=5) uses more correct Cook's distance contours; (fix to fix to PR#9316). o pdf() and postscript() were not working correctly in 2.7.0 with UTF-8 encoded data in a non-UTF-8 MBCS (e.g. EUC-JP on Unix, CJK locales on Windows). o conformMethod(), called by setMethod(), now checks better about argument names in wrong order. Whereas it only warns currently, it is planned to become an error in the future. o The predict() method for prcomp() had an incorrect check for the number of columns of 'newdata' if the columns were not named. o The axis() function now distinguishes between setting "at" to NULL or a zero-length vector, treating the latter as a request for no ticks. This corrects the handling of the "x" parameter to rug(). o glob2rx("*[*") now produces a correct regular expression. o The canvas is no longer painted on copy or save in Cocoa Quartz. o identify() in Quartz can now be terminated by either using popup menu equivalent (Ctrl-click or second mouse button) or by pressing the key. The latter was documented but did not work. o tools:::.check_package_depends() {called from 'R CMD check'} now also works correctly when directory-name != package-name. o Source references were sometimes off by a line. o The quartz() parameter 'antialias' is no longer ignored. o The Quartz device is now trying hard to remove anti-aliasing effects for rasterized backends in plots that use adjacent, borderless rectangles such as image(). o The srcfilecopy() function now adds a timestamp to the object it creates. o parse() would lose a token when run on stdin(). o socketConnection() was using internally the class "socket" and not "sockconn", which caused a conflict with make.socket(). (PR#11515) o Quartz is now trying harder to find the proper font for a given family which resolves font issues on Mac OS X 10.4. Full font names and PostScript names can be used interchangeably. (Note, however that italic/oblique font faces of Helvetica are not included in the Mac OS X 10.4 system). o qf() no longer gives NaN when one of df1 and df2 is large and the other is infinite (including if both are infinite); it is more accurate e.g. for qf(1e-18, 2,4). o qbeta(-1e10, 50, 40, log.p=TRUE) no longer hangs. o Cocoa Quartz backend autodetection of display DPI was not correct for screens rotated by 90 or 270 degrees. o selectMethod("coerce", .) now uses a correct default for 'useInherited', and hence no longer may mess up the method cache. o show() now also works on "unregistered" S3 class objects. o formatC(*, format="fg", flag="#") is no longer dropping trailing zeros. o read.table(file = stdin()) with invalid input could leave the connection in an invalid state and hence cause a later segfault. (PR#11627) o read.DIF() did not obey the default 'stringsAsFactors = TRUE'. o The 'noquote' method for c() now works correctly with three or more arguments. o symbol() in plotmath expressions works again with non-ASCII input on devices that use UTF-8 for the symbol font. -- 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 From P.Dalgaard at biostat.ku.dk Mon Jun 23 12:07:36 2008 From: P.Dalgaard at biostat.ku.dk (Peter Dalgaard) Date: Mon, 23 Jun 2008 12:07:36 +0200 Subject: R 2.7.1 re-released Message-ID: <485F75E8.7070504@biostat.ku.dk> There was a minor problem with the date in the previously released version. It has been replaced with a new file. The updated md5sums are 565b06a1f3f11020399934cc7b47a59d R-2.7.1.tar.gz 565b06a1f3f11020399934cc7b47a59d R-latest.tar.gz -- 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 From p.dalgaard at biostat.ku.dk Sun Aug 10 21:48:58 2008 From: p.dalgaard at biostat.ku.dk (Peter Dalgaard) Date: Sun, 10 Aug 2008 21:48:58 +0200 Subject: R 2,7.2 is scheduled for August 25 Message-ID: <489F462A.6050408@biostat.ku.dk> This is to announce that we plan to release R version 2.7.2 on Monday, August 25, 2008. Release procedures start Friday August 15 (when we get back from useR). The source tarballs will be made available daily (barring build troubles) and the tarballs can be picked up at http://cran.r-project.org/src/base-prerelease/ a little later. Binary builds are expected to appear starting Monday 18 at the latest. For the Core Team Peter Dalgaard -- 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 From Friedrich.Leisch at R-project.org Fri Aug 22 11:32:30 2008 From: Friedrich.Leisch at R-project.org (Friedrich.Leisch at R-project.org) Date: Fri, 22 Aug 2008 11:32:30 +0200 Subject: Forthcoming R Conferences Message-ID: <18606.34734.358781.844169@lxh5.stat.uni-muenchen.de> Dear useRs and developeRs, I hope all attending useR! in Dortmund last week had as much a good time as I had and a safe trip home. This email is to announce our plans for forthcoming conferences. In 2009 there will be a useR! in Rennes, France (July 8-10), directly followed by a DSC in Copenhagen, Denmark (July 13-14). We would like to have a useR! 2010 in North America, and 2011 in Europe. Locations for 2010 and 2011 have not been fixed yet, but there are already some plans. Proposals to host a conference are of course more than welcome. There have also been questions why 2009 is again in Europe. The main reasons were: a) we had a very good offer from Rennes, and (and at least almost one year ago, when planning started) none from outside Europe b) Having European useR!s in odd years will make it easier to set a date: in even years there are the biannual Compstat conferences, which together with all their satellite meetings block mid-August to the beginning of September. In odd years on the other hand, there is no regular big conference on computational statistics in Europe. So the basic plan is to be in Europe in odd years, and North America in even years from now on. Either continent could of course be replaced by one of the other 5 continents if we get a good offer. Antarctica may be hard to get to, though ;-) On behalf of the R Foundation, Fritz Leisch -- ----------------------------------------------------------------------- Prof. Dr. Friedrich Leisch Institut f?r Statistik Tel: (+49 89) 2180 3165 Ludwig-Maximilians-Universit?t Fax: (+49 89) 2180 5308 Ludwigstra?e 33 D-80539 M?nchen http://www.statistik.lmu.de/~leisch ----------------------------------------------------------------------- Journal Computational Statistics --- http://www.springer.com/180 M?nchner R Kurse --- http://www.statistik.lmu.de/R From p.dalgaard at biostat.ku.dk Mon Aug 25 11:57:29 2008 From: p.dalgaard at biostat.ku.dk (Peter Dalgaard) Date: Mon, 25 Aug 2008 11:57:29 +0200 Subject: R 2.7.2 is released Message-ID: <48B28209.6040106@biostat.ku.dk> I've rolled up R-2.7.2.tar.gz a short while ago. This is intended as a wrap-up release containing all known fixes to issues with the 2.7.x series. See the full list of changes below. You can get it (in a short while) from http://cran.r-project.org/src/base/R-2/R-2.7.2.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 2335719fbb03eb98954abf14b340e46f NEWS 1ad28cbc84485ccdf4ce5721b34ed645 THANKS 070cca21d9f8a6af15f992edb47a24d5 AUTHORS a6f89e2100d9b6cdffcea4f398e37343 COPYING.LIB eb723b61539feef013de476e68b5c50a COPYING 020479f381d5f9038dcb18708997f5da RESOURCES 620f0b60f7f14bcb3f8adcbecd590768 FAQ 6122945e9301825b97a506151b3cefde R-2.7.2.tar.gz 6122945e9301825b97a506151b3cefde R-latest.tar.gz Here is the relevant bit of the NEWS file: CHANGES IN R VERSION 2.7.2 NEW FEATURES o sprintf() returns elements of the result in UTF-8 when the format or any character input has a corresponding element declared as UTF-8. Similarly for paste(), elements of the result are in UTF-8 when any input to that element is declared as UTF-8. o axis() has new arguments 'col.ticks' and 'lwd.ticks' to allow the colour and line width of ticks to be set separately from that of the line (e.g. to set one or the other to transparent or zero width). o legend() has a new argument 'box.col' to set the colour of the enclosing box. o legend() gains a 'xpd' argument to make it easier to place a legend in the margins or outer margins. o stripchart() now passes '...' to title() (as well as to plot.default() and axis()). (Wish of PR#12202) o help.search() has new argument 'searchEngine' to go directly to the search form: this is needed by users of Firefox 3 to workaround a bug in interpreting the search results pages. BUG FIXES o Plotmath computed the glyph metrics for the wrong character (and perhaps for a non-existent one) if this was a single-byte character with the top bit set. An example was symbol("\300"). o sink() and cat() could divert output to a non-writable connection. o phyper(x, 0,0,0) no longer hangs for huge x and gives 1 for x >= 0. (PR#11813) o plnorm(x, ..., log.p=TRUE) is now correct for x <= 0. (PR#11867) o [, ch] gives an error (again!) when ch is a string not exactly matching the column names, thanks to an oral bug report by Matthew Dowle. o data.frame(x=1:2, y=3:4, row.names=c("a","NA"))[c(2,NA),] has correct row names c("NA,"NA.1") again. o The GUI data editor for dataframes did not handle escape characters in entries properly. (PR#11897) o PCRE has been updated to 7.7 (bugfix release). o package.skeleton() wrongly warned about invalid code_files names when these were not in the current directory. o shapiro.test(c(0,0,1)) now has P value >= 0 (instead of barely negative). o assign() now warns if given a character vector of length > 1, rather than silently taking the first element. o rcond() now gives 0 instead of an error. o There was a memory leak in C function ucstoutf8 used by some graphics devices. o Plots of profile.mle() objects (package 'stats4') were misbehaving when the 'which' argument had been used in their calculation. o dnbinom(x, size, mu=*, ..) is now more accurate for very large 'size'. The same applies to pnbinom() and rnbinom(). o axis() was ignoring par() mgp[3] if mgp was set in-line. o Closing an X11 View() or dataentry window via its frame's close control now works better on some window managers. o Calling lapply() was not handling method dispatch correctly for is.numeric(), is.matrix(), is.array(), log() and the Math2 group. This affected data.matrix() which incorrectly regarded "Date" and "POSIXct" objects as numeric, and has been adjusted to do so as exceptions. o package.skeleton() was not looking for non-function objects in its 'environment' argument. o nls() was only finding its 'weights' argument in the case when all the variables in the formula were of the same length and hence that model.frame() could be used. It was silently ignoring 'subset' and 'na.action' except in that case. Now they are ignored only if 'data' is a list and variables taken from 'data' are not all of the same length, in which case a warning is given. o The 'mle' confint() method now takes 'level' into account when setting 'alpha' for the profile. o within() was not handling correctly expressions that produced NULL columns. (PR#11131) o dev.print() and dev.copy2{eps,pdf}() now ensure that the current device is restored as the active device even if an error occurs. (PR#9801) o as.Date() could fail to convert character strings representing days on which midnight did not exist in the current timezone (as happened in parts of Africa on 1960-01-01). o The automatic placement of legend() with 'title' and a reversed 'x' axis was incorrect. (PR#12019) o The use of multiple packages in 'LinkingTo' works again, and now works when the dependent packages are in the library to be installed to (but not in the library path seen by R --vanilla). o bxp() (and hence boxplot) now respects in-line graphical parameters 'xaxp'/'yaxp' as appropriate. (PR#11463) o barplot(log = "y") failed if there were NAs in the 'height' argument. (PR#11585) o pbeta() is more accurate in some cases with extreme values of 'ncp'. (PR#11277). o edit.data.frame() no longer fails if called on a 0-column data frame and no column is created. o pchisq(x, df=0) was always one even for x < 0; similarly for pgamma(x, alpha=0). o add1() and drop1() now return a P-value of NaN in cases with df=0 for test="Chisq" (they gave NaN until pchisq was altered in R 2.6.2). o The default methods of drop1() and add1() now re-evaluate in the object's formula environment, rather than simply in the parent (informal bug report by Werner Stahel). o The undocumented limit of 8191 bytes on comments (from # to the end of the line) in R code has been removed. o qgamma() warns if used with shape < 1e-10, when it may be unreliable. (PR#12324) o Installing a source package was not using the package's declared encoding (if any) as a default encoding for the help.search() database in Meta/hsearch.rds. This could cause packages with a default encoding to have some of their entries rejected by help.search() in a multi-byte locale (such as a UTF-8 locale). o duplicated() and unique() now handle 'incomparables' better, and avoid occasional segfaults (PR#12551). o data.frame(row.names=NULL) once again behaves differently from the default (as documented). o plot(isoreg(x,y)) now plots the points correctly, also when 'x' is not sorted. -- 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 From P.Dalgaard at biostat.ku.dk Wed Sep 17 19:30:36 2008 From: P.Dalgaard at biostat.ku.dk (Peter Dalgaard) Date: Wed, 17 Sep 2008 19:30:36 +0200 Subject: R 2.8.0 is scheduled for October 20 Message-ID: <48D13EBC.3000700@biostat.ku.dk> This is to announce that we plan to release R version 2.8.0 on Monday, October 20, 2008. Release procedures start Friday, September 19. The detailed schedule can be found on http://developer.r-project.org The source tarballs will be made available daily (barring build troubles) and the tarballs can be picked up at http://cran.r-project.org/src/base-prerelease/ a little later. Binary builds are expected to appear starting Monday, September 22. For the Core Team Peter Dalgaard -- 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 From maechler at stat.math.ethz.ch Thu Sep 25 22:57:40 2008 From: maechler at stat.math.ethz.ch (Martin Maechler) Date: Thu, 25 Sep 2008 22:57:40 +0200 Subject: R Foundation adopts Certification/Validation document In-Reply-To: <48DB90DD.70908@fhcrc.org> References: <48D930FD.6040401@fhcrc.org> <3f1d2410809240833t5fe6ca53w309a98ce23223cc2@mail.gmail.com> <48DACC04.8080502@fhcrc.org> <18651.24665.485342.595935@stat.math.ethz.ch> <48DB90DD.70908@fhcrc.org> Message-ID: <18651.64324.600568.842290@stat.math.ethz.ch> The Board of the R Foundation would like to announce the unanimous adoption of the document entitled: "R: Regulatory Compliance and Validation Issues. A Guidance Document for the Use of R in Regulated Clinical Trial Environments" The updated version of the document, dated August 17, 2008, is available from the main R web page (http://www.r-project.org/) via the Certification link, listed under Documentation. The document provides extensive background and detailed guidance for the use of R within the regulated framework of human clinical trials, covering GxP and 21 CFR Part 11 issues. This document should serve R users as a key reference for their internal regulatory activities relating to the use of statistical software for clinical trials. We would like to thank all of those whose hard work has resulted in this finished document! - - - - - For The R Foundation for Statistical Computing, Martin Maechler ETH Zurich Note: As an exception, we are announcing this through R-announce. From P.Dalgaard at biostat.ku.dk Mon Oct 20 11:33:08 2008 From: P.Dalgaard at biostat.ku.dk (Peter Dalgaard) Date: Mon, 20 Oct 2008 11:33:08 +0200 Subject: R 2.8.0 is released Message-ID: <48FC5054.5030307@biostat.ku.dk> I've rolled up R-2.8.0.tar.gz a short while ago. This is a development release which contains a number of new features. Also, a number of mostly minor bugs have been fixed. See the full list of changes below. You can get it (later today) from http://cran.r-project.org/src/base/R-2/R-2.8.0.tar.gz or wait for it to be mirrored at a CRAN site nearer to you. In case of impatience, try http://www.biostat.ku.dk/~pd/R-release 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 2e66a7217f24f1d7961275438243adc7 NEWS 1ad28cbc84485ccdf4ce5721b34ed645 THANKS 070cca21d9f8a6af15f992edb47a24d5 AUTHORS a6f89e2100d9b6cdffcea4f398e37343 COPYING.LIB eb723b61539feef013de476e68b5c50a COPYING 020479f381d5f9038dcb18708997f5da RESOURCES 5717a4e29823dd379e4a6cf82e820eb2 FAQ 5213c9644aec984278b669df1a63a2ce R-2.8.0.tar.gz 5213c9644aec984278b669df1a63a2ce R-latest.tar.gz This is the relevant part of the NEWS file: CHANGES IN R VERSION 2.8.0 SIGNIFICANT USER-VISIBLE CHANGES o var(), cov(), cor(), sd() etc now by default (when 'use' is not specified) return NA in many cases where they signalled an error before. NEW FEATURES o abbreviate() gains an optional argument 'strict' allowing cheap and fast strict abbrevation. o The "lm" methods of add1(), anova() and drop1() warn if they are mis-used on an essentially exact fit. o as.array() is now generic, gains a '...' argument. o New function as.hexmode() for converting integers in hex format. format.hexmode() and as.character.hexmode() gain an 'upper.case' argument. o bitmap() and dev2bitmap() gain support for anti-aliasing. The default type has been changed to 'png16m', which supports anti-aliasing. o Box.test() gains a 'fitdf' argument to adjust the degrees of freedom if applied to residuals. o browseURL() has a new argument 'encodeIfNeeded' to use URLencode() in cases where it seems likely that would be helpful. (Unfortunately, those are hard to guess.) o by() gains a 'simplify' argument, passed to tapply(). o capabilities() gains a new argument "tiff" to report if tiff() is operational. o chol2inv() now treats as a [1 x 1]-matrix. o cov() and cor() have the option 'use = "everything"' as default, and so does var() with its default 'na.rm = FALSE'. This returns NA instead of signalling an error for NA observations. Another new option is 'use = "na.or.complete"' which is the default for var(*, na.rm=FALSE). var(double(0), na.rm= L) now returns NA instead of signalling an error, for both L = TRUE or FALSE, as one consequence of these changes. o data.matrix() now tries harder to convert non-numeric columns, via as.numeric() or as(, "numeric"). o dev.interactive() is able to recognize the standard screen devices if getOption("device") is a function (as well as by name). o dev.new() gains a '...' argument which can be used to pass named arguments which will be used if appropriate to the device selected. o dimnames(x) <- value extends 'value' if it a list and too short, and 'x' is an array. This allows constructions such as dimnames(x)[[1]] <- 1:3 to work whether or not 'x' already has dimnames. o format(), formatC() and prettyNum() gain a new argument 'drop0trailing' which can be used to suppress trailing "0"s. o format() now works for environments; also print(env) and str(env) share the same code for environments. o It is now possible to create and open a text-mode gzfile() connection by explicitly using e.g. open="rt". o New help.request() function for compiling an e-mail to R-help according to "the rules". It is built on the new utility, create.post() on which also bug.report() is based now; both thanks to a contribution by Heather Turner. o help.search() now assumes that non-ASCII items are in latin1 if that makes sense (all known examples on CRAN are). o HoltWinters() and decompose() use a (statistically) more efficient computation for seasonal fits (they used to waste one period). o intToUtf8() and intToBits() now accept numeric vectors, truncating them to integers. o is.unsorted() gains an argument 'strictly'. It now works for classed objects with a >= or > method (as incorrectly documented earlier). o library() no longer warns about the masking objects that are identical(.,.) to those they mask. o lockBinding(), unlockBinding(), lockEnvironment() and makeActiveBinding() now all return invisibly (they always return NULL). o mood.test() now behaves better in the presence of ties. o na.action() now works on fits of classes "lm", "glm", .... o optim(.., method="SANN", .., trace=TRUE) is now customizable via the 'REPORT' control argument, thanks to code proposals by Thomas Petzoldt. o The 'factory-fresh' defaults for options("device") have been changed to refer to the devices as functions in the grDevices namespace and not as names. This makes it more likely that the incorrect (since R 2.5.0) assumption in packages that get(getOption("device"))() will work will catch users of those packages. o pch=16 now has no border (for consistency with 15, 17, 18) and hence is now different from pch=19. o pdf() has new arguments 'useDingbats' (set this to FALSE for use with broken viewers) and 'colormodel'. It now only references the ZapfDingbats font if it is used (for small opaque circles). The default PDF version is now 1.4, since viewers that do not accept that are now rare. Different viewers were rendering consecutive text() calls on a pdf() device in different ways where translucency was involved. The PDF generated has been changed to force each call to be rendered separately (which is the way xpdf or ghostscript was rendering, but Acrobat was forming a transparency group), which is consistent with other graphics devices supporting semi-transparency. o plot.dendrogram() has new arguments (xlim, ylim) which allows zooming into a hiearchical clustering dendrogram. o plot.histogram() gains an 'ann' argument. (Wish from Ben Bolker.) o plot() now warns when it omits points with leverage one from a plot. o Plotmath now recognizes 'aleph' and 'nabla' (the Adobe Symbol 'gradient' glyph) as symbol names. o polyroot() no longer has a maximum degree. o The alpha/alphamax argument of the 'nls' and 'mle' profile() methods is used to compute confidence limits for univariate t-statistics rather than a confidence region for all the parameters (and not just those being profiled). o quantile.default() allows 'probs' to stray just beyond [0, 1], to allow for computed values. o New functions rawConnection() and rawConnectionValue() allow raw vectors to be treated as connections. o read.dcf() now consistently gives an error for malformed DCF. o read.fwf() no longer passes its default for 'as.is' to read.table(): this allows the latter's default to be used. o readBin(), writeBin(), readChar() and writeChar() now open a connection which was not already open in an appropriate binary mode rather than the default mode. readLines(), cat() and sink() now open a connection which was not already open in an appropriate text mode rather than the default mode. o readCitationFile() (and hence citation) now reads a package's CITATION file in the package's declared encoding (if there is one). o The behaviour of readLines() for incomplete final lines on binary-mode connections has been changed to be like blocking rather than non-blocking text-mode connections. o A new reorder.character() method has been added. This allows use of 'reorder(x, ...)' as a shorthand for 'reorder(factor(x), ...)' when 'x' is a character vector. o round() now computes in long doubles where possible so the results are more likely to be correct to representation error. o rug() now uses axis()'s new arguments from 2.7.2, hence no longer draws an axis line. o save() (optionally, but by default) checks for the existence of objects before opening the file/connections (wish of PR#12543). o segments(), arrows() and rect() allow zero-length coordinates. (Wish of PR#11192) o set.seed(kind=NULL) now takes 'kind' from a saved seed if the workspace has been restored or .Random.seed has been set in some other way. Previously it took the 'currently used' value, which was "default" unless random numbers had been used in the current session. Similarly for the values reported by RNGkind(). (Related to PR#12567.) set.seed() gains a 'normal.kind' argument. o setEPS() and setPS() gain '...' to allow other arguments to be passed to ps.options(), including overriding 'width' and 'height'. o setTimeLimit() function to set limits on the CPU and/or elapsed time for each top-level computation, and setSessionLimit() to set limits for the rest of the session. o splinefun() has a new method = "monoH.FC" for monotone Hermite spline interpolation. o sprintf() optionally supports the %a/%A notation of C99 (if the platform does, including under Windows). o str()'s default method gains a 'formatNum' function argument which is used for formatting numeric vectors. Note that this is very slightly not backward compatible, and that its default may change before release. o The summary() method for class "ecdf" now uses a print() method rather than printing directly. o summary.manova() uses a stabler computation of the test statistics, and gains a 'tol' argument to allow highly correlated responses to be explored (with probable loss of accuracy). Similar changes have been made to anova.mlm() and anova.mlmlist(). o Sweave() now writes concordance information inside a \Sconcordance LaTeX macro, which allows it to be inserted into PDF output. o system.time() now uses lazy evaluation rather than eval/substitute, which results in more natural scoping. (PR#11169) o In table(), 'exclude=NULL' now does something also for factor arguments. A new 'useNA' argument allows you to control whether to add NA levels unconditionally or only when present in data. A new convenience function addNA() gives similar functionality by adding NA levels to individual factors. o unlink() tries the literal pattern if it does not match with wildcards interpreted -- this helps with e.g. unlink("a[b") which previously needed to be unlink("a\\[b"). o update.packages() gains an argument 'oldPkgs', where new.packages() and old.packages() get 'instPkgs'. These allow to consider only subsets of packages instead of all installed ones. o which(b) is somewhat faster now, notably for named vectors, thanks to a suggestion by Henrik Bengtsson. o New generic function xtfrm() as an auxiliary helper for sort(), order() and rank(). This should return a numeric vector that sorts in the same way as its input. The default method supports any class with ==, > and is.na() methods but specific methods can be much faster. As a side-effect, rank() will now work better on classed objects, although possibly rather slowly. o X11() and capabilities("X11") now catch some X11 I/O errors that previously terminated R. These were rare and have only be seen with a misconfigured X11 setup on some versions of X11. o The handling of nuls in character strings has been changed -- they are no longer allowed, and attempting to create such a string now gives a truncation warning (unless options("warnEscapes") is false). o The user environment and profile files can now be specified via environment variables 'R_ENVIRON_USER' and 'R_PROFILE_USER', respectively. o ?pkg::topic and ?pkg:::topic now find help on 'topic' from package 'pkg' (and not help on :: or :::). o ??topic now does help.search("topic"); variations such as ??pkg::topic or field??topic are also supported. o There is support for using ICU (International Components for Unicode) for collation, enabled by configure option --with-ICU on a Unix-alike and by a setting in MkRules on Windows. Function icuSetCollate() allows the collation rules (including the locale) to be tuned. [Experimental] o If S4 method dispatch is on and S4 objects are found as attributes, show() rather than print() is used to print the S4 attributes. o Starting package tcltk without access to Tk (e.g. no available display) is now a warning rather than an error, as Tcl will still be usable. (On most platforms it was possible to inhibit Tk by not having DISPLAY set, but not on Windows nor Mac OS X builds with --with-aqua.) o Using $ on a non-subsettable object (such as a function) is now an error (rather than returning NULL). o Hexadecimal numerical constants (such as 0xab.cdp+12) may now contain a decimal point. o PCRE has been updated to version 7.8 (mainly bug fixes). o plot.ecdf() now defaults to pch=19 so as to better convey the left-closed line segments. NEW FEATURES IN PACKAGE 'methods' o S3 classes that are registered by a call to setOldClass() now have the S3 class as a special slot, and therefore so do any S4 classes that contain them. This mechanism is used to support S4 classes that extend S3 classes, to the extent possible. See ?Classes, ?setOldClass, and ?S3Class. The treatment of special pseudo-classes "matrix", "array", and "ts" as S4 classes has also been modified to be more consistent and, within limitations imposed by special treatment of these objects in the base code, to allow other classes to contain them. See class?ts. A general feature added to implement "ts" and also "data.frame" as S4 classes is that an S4 class definition can be supplied to setOldClass() when the S3 class has known attributes of known class. setOldClass() now saves all the S3 inheritance, allowing the calls to be built up in stages, rather than including all the S3 classes in each call. Also allows as(x,"S3") to generate valid S3 inheritance from the stored definition. See ?S3. o S4 methods may now be defined corresponding to "...", by creating a generic function that has "..." as its signature. A method will be selected and called if all the arguments matching "..." are from this class or a subclass. See ?dotsMethods. o New functions S3Part() and S3Class() provide access to the corresponding S3 object and class for S4 classes that extend either an S3 class or a basic R object type. o show() now also shows the class name. INSTALLATION o If sub-architectures are used, a copy of Rscript is installed in ${R_HOME}/bin/exec${R_ARCH} (since that in ${R_HOME}/bin and /usr/bin might be overwritten in a subsequent installation). PACKAGE INSTALLATION o LazyLoad: yes is now the default, so packages wanting to avoid lazy loading must set 'LazyLoad: no' (or an equivalent value) in the DESCRIPTION file. o R CMD INSTALL will now fail if it finds a non-executable 'configure' script in the package -- this usually indicates a file system with insufficient permissions. If a non-executable 'cleanup' script is found and either --clean or --preclean is used, a warning is given. DEPRECATED & DEFUNCT o Use in packages of the graphics headers Rdevices.h and Rgraphics.h is defunct: they are no longer installed. o options("par.ask.default") is defunct in favour of "device.ask.default". o The 'device-independent' family "symbol" is defunct: use font=5 (base) or fontface=5 (grid) instead. o gammaCody() is defunct. o par("gamma") is defunct. o 'methods' package functions getAccess(), getAllMethods(), getClassName(), getClassPackage(), getExtends(), getProperties(), getPrototype(), getSubclasses, getVirtual(), mlistMetaName(), removeMethodsObject() and seemsS4Object() are defunct. o Use of a non-integer .Random.seed is now an error. (R itself has never generated such values, but user code has, and R >= 2.6.0 has given a warning.) o methods::allGenerics() is deprecated. o In package installation, SaveImage: yes is now ignored, and any use of the field will give a warning. o unserialize() no longer accepts character strings as input. o The C macro 'allocString' has been removed -- use 'mkChar' and variants. o Use of allocVector(CHARSXP ...) is deprecated and gives a warning. UTILITIES o The default for 'stylepath' in Sweave's (default) RweaveLatex driver is now FALSE rather than TRUE if SWEAVE_STYLEPATH_DEFAULT is unset : see ?RweaveLatex. To support this, tools::texi2dvi adds the R 'texmf' directory to the input search path. o R CMD Rd2dvi now previews PDF output (as was documented) if R_PDFVIEWER is set (as it will normally be on a Unix-alike but not on Windows, where the file association is used by default). o R CMD check checks for binary executable files (which should not appear in a source package), using a suitable 'file' if available, else by name. o R CMD check now also uses codetools' checks on the body of S4 methods. C-LEVEL FACILITIES o R_ReadConsole will now be called with a buffer size of 4096 bytes (rather than 1024): maintainers of alternative front-ends should check that they do not have a smaller limit. o Graphics structure NewDevDesc has been renamed to DevDesc. For now there is a compatibility define in GraphicsDevice.h, but it will be removed in R 2.9.0. o PROTECT and UNPROTECT macros now work even with R_NO_REMAP. BUG FIXES o @ now gives an error (and not just a warning) if it is being applied to a non-S4 object. o R CMD appends (not prepends) R's texmf path to TEXINPUTS. o Objects generated by new() from S4 classes should now all satisfy isS4(object). Previously, prototypes not of object type S4 would not be S4 objects. new() applied to basic, non-S4 classes still will (and should) return non-S4 objects. o Functions writing to connections such as writeLines(), writeBin(), writeChar(), save(), dput() and dump() now check more carefully that the connections are opened for writing, including connections that they open themselves. Similarly functions which read such as readLines(), scan(), dcf() and parse() check connections for being open for reading. o Equality comparison of factors with levels now works correctly again. o Repainting of open X11 View() windows is now done whilst an X11 dataentry window is in use. o Indexing of data frames with NA column names and a numeric or logical column index works again even if columns with NA names are selected. o on.exit() has been fixed to use lexical scope in determining where to evaluate the exit action when the on.exit expression appears in a function argument. o rank() now consistently returns a double result for ties.method = "average" and an integer result otherwise. Previously the storage mode depended on 'na.last' and if any NAs were present. o The "lm" methods of add1(), and drop1() now also work on a model fit with na.action = na.exclude. o median(c(x = NA_real_)) no longer has spurious names(). o isoreg(x, y) now returns the correct result also when x has ties, in all cases. o What na.action() does is now correctly documented. o source() with echo=TRUE now behaves like ordinary automatic printing, by using methods::show() for S4 objects. o Several bugs fixed in `?` with topics: it previously died trying to construct some error messages; for S4 methods, class "ANY" should be used for omitted arguments and default methods. o trace() should create missing traceable classes in the global environment, not in baseenv() where other classes will not be found. o Class inheritance using explicit coerce= methods via setIs() failed to coerce the argument in method dispatch. With this fixed, a mechanism was needed to prohibit such inheritance when it would break the generic function (e.g., initialize). See ?setIs and ?setGeneric. o RSiteSearch() encodes its query (it seems this is occasionally needed on some platforms, but encoding other fields is harmful). o 'incomparables' in match() was looking up indices in the wrong table. o write.dcf() did not escape "." according to Debian policy (PR#12816). o col2rgb() sometimes opened a graphics device unnecessarily, and col2rgb(NA) did not return a transparent color, as documented. o pdf(family="Japan") [and other CIDfonts] no longer seg.faults when writing "western" text strings. o as.list() applied to an environment now forces promises and returns values. o Promises capturing calls to sys.parent() and friends did not work properly when evaluated via method dispatch for internal S3 generics. o The default pkgType option for non-CRAN builds of R on Mac OS X is now correctly "source" as documented. o The default R_LIBS_USER path in AQUA builds now matches the Mac-specifc path used by the Mac GUI: ~/Library/R/x.y/library o splinefun() with natural splines incorrectly evaluated derivatives to the left of the first knot. (PR#13132, fix thanks to Berwin Turlach) o anova(glm(..., y=FALSE)) now works. (PR#13098) o cut.Date(x, "weeks") could fail if x has only one unique value which fell on a week boundary. (PR#13159) -- 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 From P.Dalgaard at biostat.ku.dk Fri Oct 24 13:24:01 2008 From: P.Dalgaard at biostat.ku.dk (Peter Dalgaard) Date: Fri, 24 Oct 2008 13:24:01 +0200 Subject: DSC 2009 First announcement Message-ID: <4901B051.6010802@biostat.ku.dk> The sixth international workshop on 'Distributed Statistical Computing' (DSC 2009) will take place at the the University of Copenhagen, Denmark, 13th-14th of July 2009. This conference follows on from the successful DSC 1999, 2001, and 2003 conferences at the Vienna University of Technology, DSC 2005 at the University of Washington in Seattle, and DSC 2007 at the University of Auckland. The workshop will focus on, but is not limited to, open source statistical computing and aims to provide a platform for exchanging ideas about developments in statistical computing (rather than 'only' the usage of statistical software for applications). It is expected that a large proportion of participants will bring a presentation. We particularly welcome contributions advancing statistical computing as an independent topic. Home page: http://www.r-project.org/dsc-2009 Organizing committee: Peter Dalgaard, Claus Ekstr?m, Klaus K. Holst, S?ren H?jsgaard Programme committee: Roger Bivand, G?ran Brostr?m, Jari Oksanen, Balasubramanian Narasimhan (Naras), Peter Dalgaard Important dates: March 15: Submission deadline April 15: Notification of accept/reject May 1: Early registration ends Fee structure (EUR, Academic/Non-Academic/Student) Early: 170/270/90 Full: 200/300/100 On the Day: 220/330/110 ("Students" not including Ph.D. students.) -- 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 From jfox at mcmaster.ca Tue Nov 4 13:35:20 2008 From: jfox at mcmaster.ca (John Fox) Date: Tue, 4 Nov 2008 07:35:20 -0500 Subject: R News, volume 8, issue 2 is now available Message-ID: <000a01c93e79$cd13ed90$673bc8b0$@ca> Dear R users, The October 2008 issue of 'R News' is now available on CRAN under the Documentation/Newsletter link. John (on behalf of the R News Editorial Board) ------------------------------ John Fox, Professor Department of Sociology McMaster University Hamilton, Ontario, Canada web: socserv.mcmaster.ca/jfox From francois.husson at agrocampus-ouest.fr Wed Dec 3 18:12:48 2008 From: francois.husson at agrocampus-ouest.fr (Francois Husson) Date: Wed, 03 Dec 2008 17:12:48 +0000 Subject: useR!2009 conference announcement Message-ID: <4936BE10.3010206@agrocampus-ouest.fr> We are happy to inform you that the online abstract submission and registration for `useR! 2009' is now available online from http://www.R-project.org/useR-2009/ This meeting of the R user community will take place at Agrocampus, Rennes, France, July 8 to 10, 2000. The conference schedule comprises invited lectures and user-contributed sessions as well as half-day tutorials presented by R experts on July 7, 2009, prior to the conference. Invited speakers will include Adele Cutler, Peter Dalgaard, Jerome H. Friedman, Michael Greenacre, Trevor Hastie, John Storey, Martin Theus. The spectrum of user-contributed sessions will depend on your submissions. Hence, we invite you to submit abstracts for a talk or a poster on topics presenting innovations or exciting applications of R. The call for papers along with the link to the online abstract submission is available at http://www.R-project.org/useR-2009/#Call Before the start of the official program, half-day tutorials will be offered on Tuesday, July 7. A list of topics and speakers can be found at http://www.R-project.org/useR-2009/tutorials/ The deadline for early registration and to submit an abstract is February 27th 2009, so now is the perfect time to write and submit an abstract, register as a participant and plan your trip to Rennes (Rennes will be busy at the conference time because the cultural event `Festival Les tomb?es de la nuit' will take place at the same time, so we recommend to book as soon as possible). The conference web page http://www.agrocampus-ouest.fr/math/useR-2009/accomodation.html gives a list of hotels and some student rooms (200) are also available on the campus. We hope to meet you in Rennes! The conference committee, Julie Josse, Fran?ois Husson, David Causeur, Maela Kloareg, S?bastien L?, Aline Legrand, Eric Matzner-Lober & J?r?me Pag?s From p.dalgaard at biostat.ku.dk Mon Dec 8 18:31:02 2008 From: p.dalgaard at biostat.ku.dk (Peter Dalgaard) Date: Mon, 08 Dec 2008 18:31:02 +0100 Subject: [R] R 2.8.1 is scheduled for December 22 Message-ID: <493D59D6.10203@biostat.ku.dk> This is to announce that we plan to release R version 2.8.1 on Monday, December 22, 2008. Release procedures start Friday, December 12. Those directly involved should review the generic schedule at http://developer.r-project.org/release-checklist.html The source tarballs will be made available daily (barring build troubles) and the tarballs can be picked up at http://cran.r-project.org/src/base-prerelease/ a little later. Binary builds are expected to appear starting Monday 15 at the latest. For the Core Team Peter Dalgaard -- 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 ______________________________________________ R-help at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. From P.Dalgaard at biostat.ku.dk Fri Dec 12 16:07:04 2008 From: P.Dalgaard at biostat.ku.dk (Peter Dalgaard) Date: Fri, 12 Dec 2008 16:07:04 +0100 Subject: DSC 2009: Now open for registration and abstract submission Message-ID: <49427E18.8030003@biostat.ku.dk> Re. Workshop on Directions in Statistical Computing, Copenhagen 13-14 July 2009. http://www.r-project.org/dsc-2009 The web interface for registration and submission of abstracts is now open. (The site is still under construction in a number of respects. In particular, we haven't negotiated discounts with any of the hotels yet.) -- 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 From edd at debian.org Fri Dec 19 20:52:28 2008 From: edd at debian.org (Dirk Eddelbuettel) Date: Fri, 19 Dec 2008 13:52:28 -0600 Subject: R/Finance 2009: Applied Finance with R -- Call for Papers Message-ID: <18763.64380.278257.890026@ron.nulle.part> Call for Papers The Finance Department of the University of Illinois at Chicago (UIC), the International Center for Futures and Derivatives at UIC, and members of the R finance community are pleased to announce R/Finance 2009: Applied Finance with R on April 24 and 25, 2009, in Chicago, IL, USA Confirmed keynote speakers include: Patrick Burns (Burns Statistics) David Kane (Kane Capital) Roger Koenker (U of Illinois at Urbana/Champaign) David Ruppert (Cornell) Diethelm Wuertz (ETH Z?rich) Eric Zivot (U of Washington) We invite all users of R in Finance to submit one-page abstracts or complete papers (in txt/pdf/doc format). We encourage papers both on academic research topics and related to use of R by Finance practitioners. Presenters are strongly encouraged to provide working R code to accompany the presentation/paper. Datasets need not be made public. Please send submissions to committee at RinFinance.com. The submission deadline is January 31st, 2009. Submissions will be evaluated and submitters notified via email on a rolling basis. Additional details about the conference will be announced as available. For the program committee: Gib Bassett, Peter Carl, Dirk Eddelbuettel, John Miller, Brian Peterson, Dale Rosenthal, Jeffrey Ryan From p.dalgaard at biostat.ku.dk Mon Dec 22 10:24:27 2008 From: p.dalgaard at biostat.ku.dk (Peter Dalgaard) Date: Mon, 22 Dec 2008 10:24:27 +0100 Subject: R 2.8.1 is released Message-ID: <494F5CCB.90203@biostat.ku.dk> I've rolled up R-2.8.1.tar.gz a short while ago. This is a maintenance release and fixes a number of mostly minor bugs and platform issues. See the full list of changes below. You can get it (in a short while) from http://cran.r-project.org/src/base/R-2/R-2.8.1.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 4eff8b4937a55a2c3ece8b0a31772b62 NEWS 1ad28cbc84485ccdf4ce5721b34ed645 THANKS 070cca21d9f8a6af15f992edb47a24d5 AUTHORS a6f89e2100d9b6cdffcea4f398e37343 COPYING.LIB eb723b61539feef013de476e68b5c50a COPYING 020479f381d5f9038dcb18708997f5da RESOURCES 5d443029346cbad2f2df7c62a0ea8e0f FAQ acd40621b8942a2464daa2f9cef3273d R-2.8.1.tar.gz acd40621b8942a2464daa2f9cef3273d R-latest.tar.gz Here is the relevant part of the NEWS file: CHANGES IN R VERSION 2.8.1 NEW FEATURES o sum() now has a method for "difftime" objects (via the Summary group). max(), min() and range() applied to "difftime" object(s) now return a result in the common units of the objects, if there is one. o installed.packages() is now tolerant of malformed DESCRIPTION files in installed packages (it ignores them, with a warning). o qt() now works for 0 < df < 1. o For consistency with matrix() and array(), dimnames(x) <- list() removes the dimnames (as assigning NULL would do). It was previously an error. o nlminb() copies names from 'start' to the parameter vector used (for consistency with optim()). o legend() gains a 'title.col' argument: the title colour was previously set from the first element of 'text.col' (which remains the default). o In an Rd file, use of top-level \itemize{} inside a \value{} block is unnecessary and almost always gave a faulty conversion. Most cases are now detected and corrected, but give a warning as such code will not work correctly in earlier versins of R. Also, use of \code{} inside a code block such as \examples{} will give a erroneous conversion that is now detected and warned against. o Autoflushing of stdout is turned on when Rd processing, so warnings/error are likely to appear in the right place in redirected output (such as that from R CMD check). UTILITIES o R_PDFLATEXCMD is added to the environment variables set by 'R CMD' and is used by R CMD Rd2dvi. R_LATEXCMD, R_PDFLATEXCMD, R_MAKEINDEXCMD and R_DVIPSCMD default to 'latex', 'pdflatex', 'makeindex' and 'dvips' respectively if no suitable executable was found at configure time (since they might well be available at run time, particularly for binary installations of R). This affects R CMD Rd2dvi and help(offline=TRUE). R CMD Rd2dvi now gives an explicit error message if latex (or pdflatex) fails. R CMD Rd2dvi gains a --no-index argument: processing some special characters on PDF indices gave errors which used to be ignored. DEPRECATED & DEFUNCT o R CMD INSTALL --with-package-versions is deprecated (and support has always been incomplete on Windows). So is install.packages(installWithVers = TRUE). o Rd conversion to Sd and Ssgm is now deprecated as we no longer have any means to check the results (and Sd is long obsolete). BUG FIXES o add1.glm() no longer warns if applied to a binomial glm with a factor response. o aggregate.data.frame() now does something sensible with a zero-column 'x' rather than failing with an obscure error message. It gives an explicit error message if called with a zero-row 'x'. o integrate() now accepts integer results from f(): as documented, but only double was accepted. o contrib.url() produced an incorrect URL for the type "mac.binary". o pairwise.wilcox.test() did not pass on the 'paired' argument (caught by Matthias Kohl) o bmp(), jpeg(), and png() on unix with type="cairo" would segfault on closure if the output file could not be opened. o tiff() on unix would not write the output file for the first page when multiple pages were plotted. o str(1 + structure(1, class = "test")) no longer recurses indefinitely. o pf(x, .., ncp, lower.tail=FALSE, log=TRUE) is much more accurate for large x now. o dev2bitmap() failed in 2.8.0 if 'taa' and 'gaa' were both NA. o Under rare circumstances equality tests for character strings could fail to report equality in 2.8.0 in the same way as 2.7.2. (This needed a current encoding of Latin-1 or UTF-8, one string whose encoding was marked as that encoding and one that was marked as "unknown". In that circumstance the two strings are not actually known to be equal, but earlier versions of R assumed that "unknown" meant the current encoding, and this is done once again.) o R CMD config could echo messages from GNU make if called from within a Makefile (as e.g. package Rcpp did), especially from within a parallel make run. o Rounding error could affect window(extend=TRUE) when applied to monthly series. (PR#13272) o Offline help on a Unix-alike now works even if options "latexcmd" and "dvipscmd" contain spaces (e.g. "dvips -Pmy_printer"). Informative error messages are given if running latex or dvips fail. o Using plot.lm() on a "glm" object since 2.7.1 with which=5 caused the Pearson rather than deviance residuals to be used in which=2 or 3 (including in the default case). (Thanks to Effie Greathouse and Greg Snow.) plot.lm() did not report on omitting observations with leverage one if they also had residual exactly zero. This was seen in example(occupationalStatus). o deparse(nlines=) no longer pads short results with blank lines. (PR#13299) o legend(xpd=) now restores 'xpd' correctly. (PR#12756) o The "formula" method for lines() now works if 'subset' is supplied and no 'data' argument (as that for points() did). o Sweave() now takes the defaults for the options 'pdf.version' and 'pdf.encoding' of its RweaveLatex driver from pdf.options(). o prettyNum(x, drop0trailing=TRUE) treated "1.1e20" as "1.1e2" and hence str() did as well, in 2.8.0 only. o dchisq(x, df, ncp) no longer hangs for large x and ncp > 0, and is more accurate in some cases (PR#13309). o installed.packages(lib.loc = D, priority="NA") now also works when D contains a single package. (PR#13332) o legend(...., merge=TRUE) now warns and has no effect in the case where no line segments are drawn. (PR#13340) o transform.data.frame() works better when two or more columns are added. o Deparsing argument lists with non-syntactic names (e.g. that for transform()) now uses backticks rather than double quotes to produce syntactically valid output. o matrix() failed to check for 0-length 'dimnames': it now treats them as NULL (as array did). (PR#13361) o 0^NA is now NA, not Inf, consistent with x^NA, x != 1. o anova.mlm() did not work if T had only one row (including e.g. the case M = ~1). o axis.POSIXct() mislabelled for some time ranges of a few hours (reported by Martin Becker). o mantelhaen.test() with 'exact=FALSE' was not respecting 'alternative'. It now does one-sided tests similarly to prop.test(). o anova.mlm() had trouble with some designs where near-zero rows of the tranformation matrix were not removed (caught by Nils Skutara). o Rd conversion was handling expressions like '\item{foo}{see \eqn{x}}' (with one argument to \eqn immediately followed by a right brace) incorrectly, sometimes giving a spurious warning about 'missing text'. o R CMD INSTALL used the C locale to install the DESCRIPTION file, and so escaped non-ASCII characters in packages with a declared encoding of "latin1" or "UTF-8". (However, the installed DESCRIPTION file was rarely used since the dumped metadata are available.) o xspline() now respects inline par settings. It and grid.xspline() now handle the special case of only two control points, and splines with control points that are located well outside the device (e.g., a zoomed view of a larger curve). (Both cases were giving the error "reached MAXNUMPTS"). o In setClass("C", contains="list"); x <- new("C", 1:3), x[2:3] now remains of class "C". So does rep(x, 2) or rep.int(x, 3). o median.default() now also works for "numeric"-like vectors. o The pdf() device can now handle the case where an image uses a very large number of colours with different levels of semi-transparency (alpha-values). It used to segfault. (Also PR#13264.) o window() failed to apply a fuzz to 'start' or 'end' and so sometimes warned incorrectly for time series with 'freq' not a power of two (e.g. 12 or 24). o unique.default() now preserves the "tzone" attribute on "POSIXct" objects. o If all the packages had dependency lists of equal lengths, occasionally install.packages() would compute an incorrect sort order. o col(x, as.factor=TRUE) and row(x, as.factor=TRUE) would fail if x had no column (row) names. It was documented incorrectly, and now returns a matrix factor. o setRepositories() failed if "pkgType" was set to "mac.binary.leopard". o formals<-() changed the body of the function if this was a length-one list. o body<-() failed if the function had no arguments. It now warns if discarding elements from a 'value' of type "expression". o qr.coef() failed in the complex case for non-square systems. (PR#13305) o plot.dendrogram(horizontal=TRUE) did not not plot 'edgetext' at the correct locations. (PR#13313) o The starting point for plot.acf(ci.type="ma") was lag 0 when it should have been lag 1. (PR#13071) o There was an obscure bug with srcrefs, which could put the parser into a condition giving "Error: bad value" on any input -- 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