From p.murrell at auckland.ac.nz Tue Jan 23 21:28:32 2007 From: p.murrell at auckland.ac.nz (Paul Murrell) Date: Wed, 24 Jan 2007 09:28:32 +1300 Subject: DSC 2007 Additional Funding Message-ID: <45B66FF0.7090408@stat.auckland.ac.nz> Hi DSC 2007, a conference on systems and environments for statistical computing, will take place in Auckland, New Zealand on February 15 & 16, 2007. *** Travel and Accommodation Support *** Additional NSF funding to provide partial support for travel and accommodation for graduate students and junior faculty at U.S. post-secondary institutions to attend DSC 2007 may be available. If you wish to apply for this support, please send an application to dsc2007 at stat.auckland.ac.nz. Your application should include a brief CV a statement that demonstrates your eligibility, your need for support, and an amount of support requested students should include a brief letter of support from their supervisor faculty or post-doc applicants should include a brief statement about other funding sources The allocation will be based on merit and need; women and minority candidates are encouraged to apply. Applications must be made by February 2 (2007-02-02) and successful applicants will be notified by email soon thereafter. Please visit the conference web page at http://www.stat.auckland.ac.nz/dsc-2007/ Paul (on behalf of the Organising Committee) -- Dr Paul Murrell Department of Statistics The University of Auckland Private Bag 92019 Auckland New Zealand 64 9 3737599 x85392 paul at stat.auckland.ac.nz http://www.stat.auckland.ac.nz/~paul/ From dicook at iastate.edu Sun Feb 11 14:00:48 2007 From: dicook at iastate.edu (Dianne Cook) Date: Sun, 11 Feb 2007 07:00:48 -0600 Subject: useR! 2007 Message-ID: R Users and Developers, Plans are being made to hold the first North American useR! will be held at Iowa State University, Ames, Iowa, August 8?10, 2007, which will be a week after JSM'07. This follows successful meetings in Vienna, Austria, in 2006 and 2004, and also Directions in Statistical Computing (DSC) meetings in Auckland, NZ (Feb 2007), Seattle (2005), and Vienna (1999, 2001, 2003). Information about the meeting can be found at http://www.user2007.org/ If you have suggestions for the meeting please email the program committee at user2007 at iastate.edu. Regards, useR! 2007 Program Committee Douglas Bates, Dianne Cook, Dave Henderson, Heike Hofmann, Luke Tierney From dicook at iastate.edu Fri Mar 9 22:26:24 2007 From: dicook at iastate.edu (Dianne Cook) Date: Fri, 9 Mar 2007 15:26:24 -0600 Subject: useR! 2007 --- Call for papers and posters Message-ID: <6FA60D2B-695D-4249-B546-AB2018BA71CB@iastate.edu> R Users and Developers, The first North American useR! will be held at Iowa State University, Ames, Iowa, August 8?10, 2007. Information about the meeting can be found at http://www.user2007.org/. We are now ready to accept paper and poster submissions. Papers are encouraged in all areas, but particular emphasis is given to work describing newly created or improved R packages. Papers will be refereed and a best paper/presentation award is likely. Your full paper needs to be submitted by April 23, 5:00PM CST, to be considered for the meeting. There will also be the opportunity to present your work as a poster instead of a paper. Poster submissions will be in the form of an abstract and needs to be submitted by June 30. Submit full papers, and poster abstracts, to submissions at user2007.org. useR! Program Committee user2007 at iastate.edu From luke at stat.uiowa.edu Fri Apr 13 20:21:07 2007 From: luke at stat.uiowa.edu (Luke Tierney) Date: Fri, 13 Apr 2007 13:21:07 -0500 Subject: Subject: useR! 2007 --- programming competition Message-ID: <461FCA13.2050107@stat.uiowa.edu> R Users and Developers, The first North American useR! to be held at Iowa State University, Ames, Iowa, August 8-10, 2007, will include a programming competition. The challenge: Develop a package useful for the analysis of large data sets. Your package could augment an existing package like biglm, for example, by providing graphical or numerical diagnostic tools, or by adding support methods for transparently handling data from a database. Alternatively, you could develop a package for fitting linear or generalized linear models to large data sets that takes an entirely different approach. The winning team will receive a cash prize. The submission deadline is June 30, 2007. Further details are available at the conference website at http://www.user2007.org/. As a reminder, we are also calling for papers for presentation at the meeting. Papers are encouraged in all areas, but particular emphasis is given to work describing newly created or improved R packages. Papers will be refereed and a best paper/presentation award is likely. Also, if you wish to apply for financial support, please send an application to user2007 at iastate.edu by April 23 (include a brief CV and a statement that demonstrates your eligibility, your need for support, and an amount of support required - students should include the name of their supervisor). useR! Program Committee user2007 at iastate.edu From dicook at iastate.edu Fri Apr 20 18:33:49 2007 From: dicook at iastate.edu (Dianne Cook) Date: Fri, 20 Apr 2007 11:33:49 -0500 Subject: useR! 2007 online registration is now available Message-ID: <32D84D23-9383-438D-92C8-86A7AFA6EA63@iastate.edu> R Users and Developers, Online registration for useR! 2007 is now available on the conference web site. The deadline for the early registration discount has been extended to May 15. We haven't had many contributed papers as yet, or requests for travel support from young researchers and graduate students. Please consider contributing a paper, and encouraging your students and young faculty to submit a paper and request travel support. The deadline for these has also been extended to May 15. Contributed papers will be refereed. Please also note that we have negotiated airline discounts with both Northwest and United airlines. They are excellent discounts, there is some reduction in even the cheapest fares. So do keep this in mind when you plane your travel. Details are on the web page. The deadline to submit an abstract for a poster is June 30. These abstracts will not be refereed. All poster submissions will be accepted. Information about the meeting can be found at http://www.user2007.org/ If you have suggestions for the meeting please email the program committee at user2007 at iastate.edu. Douglas Bates, Dianne Cook, Dave Henderson, Heike Hofmann, Olivia Lau, Michael Lawrence, Luke Tierney, Hadley Wickham --------------------------- Di Cook dicook at iastate.edu From P.Dalgaard at biostat.ku.dk Tue Apr 24 12:34:31 2007 From: P.Dalgaard at biostat.ku.dk (Peter Dalgaard) Date: Tue, 24 Apr 2007 12:34:31 +0200 Subject: R 2.5.0 is released Message-ID: <462DDD37.4070700@biostat.ku.dk> I've rolled up R-2.5.0.tar.gz a short while ago. This is a development release which contains a number of new features. In particular: - Object name completion by integration of package 'rcompletion' by Deepayan Sarkar - New recommended package 'codetools' by Luke Tierney - New Rscript front-end, which enables shell-like R scripting also, a number of mostly minor bugs have been fixed. See the full list of changes below. You can get it (some time this evening) from http://cran.r-project.org/src/base/R-2/R-2.5.0.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: a8efde35b940278de19730d326f58449 AUTHORS eb723b61539feef013de476e68b5c50a COPYING a6f89e2100d9b6cdffcea4f398e37343 COPYING.LIB aa6d06dd154bbde39b4d35f26068675d FAQ 70447ae7f2c35233d3065b004aa4f331 INSTALL b12ff4c900a49f0d7786d80e249934c9 NEWS 88bbd6781faedc788a1cbd434194480c ONEWS 4f004de59e24a52d0f500063b4603bcb OONEWS b9088663fc539c059acfaf19d6d90a69 R-2.5.0.tar.gz b9088663fc539c059acfaf19d6d90a69 R-latest.tar.gz 433182754c05c2cf7a04ad0da474a1d0 README 020479f381d5f9038dcb18708997f5da RESOURCES 4eaf8a3e428694523edc16feb0140206 THANKS This is the relevant part of the NEWS file: CHANGES IN R VERSION 2.5.0 USER-VISIBLE CHANGES o apropos(x) and find(x) now both only work for character 'x', and hence drop all non-standard evaluation behaviour. o Data frames can have 'automatic' row names which are not converted to dimnames by as.matrix(). (Consequently, e.g., t(.) for such data frames has NULL column names.) This change leads to memory reductions in several places, but can break code which assumes character dimnames for data frames derived from matrices. No existing R object is regarded as having 'automatic' row names, and it may be beneficial to recreate such objects via read.table() or data.frame(). o Using $ on an atomic vector now raises a warning, as does use on an S4 class for which a method has not been defined. o The Unix-alike readline terminal interface now does command-completion for R objects, incorporating the functionality formerly in package 'rcompletion' by Deepayan Sarkar. This can be disabled by setting the environment variable R_COMPLETION=FALSE when starting R (e.g. in ~/.Renviron). (Note that when this is enabled, filename completion no longer works for file paths containing R operators such as '+' and '-'.) NEW FEATURES o abbreviate() no longer has an 8191 byte limit on the size of strings it can handle. o abs(x) now returns integer for integer or logical arguments. o apropos() has a new argument 'ignore.case' which defaults to TRUE, potentially matching more than previously, thanks to a suggestion by Seth Falcon. o args(), str() and print() now give the argument lists of primitive functions. o as.matrix() gains the '...' argument that several packages have assumed it always had (and S-PLUS has). o Manipulation of integers as roman numerals via as.roman() in package utils. o attr() no longer treats name = NA_character_ as meaning name = "NA". o binom.test() now allows a 'fuzz' for calculated integer values in its x and n arguments. o boxplot(*, notch = TRUE) now warns when notches are outside hinges; related to PR#7690. o New function callCC() providing a downward-only version of Scheme's call with current continuation. o capabilities() now has a "profmem" entry indicating whether R has been compiled with memory profiling. o colnames<-() and rownames<-() now handle data frames explicitly, so calling colnames<- on a data frame no longer alters the representation of the row names. o commandArgs() has a new 'trailingOnly' argument to be used in conjunction with --args. o contour() now passes graphical parameters in '...' to axis() and box(). o New data set 'crimtab' on Student(1908)'s 3000 criminals. o cut.default() has a new argument 'ordered_result'. o .deparseOpts() has two new options: "keepNA" to ensure that different types (logical, integer, double, character and complex) of NAs are distinguished, and "S_compatible" to suppress the use of R-specific features such as 123L and to deparse integer values of a double vector with a trailing decimal point. The 'keepInteger' option now uses the suffix 'L' rather than as.integer() where possible (unless all entries are NA or "S_compatible" is also set). Other deparse options can now be added to "all" (which has not for some time actually switched on all options). Integer sequences m:n are now deparsed in that form. o deparse() and dput() now include "keepInteger" and "keepNA" in their defaults for the 'control' argument. o detach() now takes another argument, unload, which indicates whether or not to unload the package and then only cleans up the S4 methods if the package successfully unloads. o There are new constants NA_integer_, NA_real_, NA_complex_ and NA_character_ to denote NAs of those types, and they will be used in deparsing in place of as.integer(NA) etc unless .deparseOpts() includes "S_compatible". o dev.print() now recognizes 'screen devices' as all those with an enabled display list, rather than a hard-coded set. o Objects of class "difftime" are now handled more flexibly. The units of such objects can now be accessed via a units() function, which also has a replacement form, and there are conversion methods to and from numeric, which also allow the specification of units. Objects of this class can also be stored in data frames now. A format() method has been added, and the print method was revised. o New function environmentName() to give the print name of environments such as "namespace:base". This is now used by str(). o New function env.profile() provides R level access to summary statistics on environments. In a related patch, new.env() now allows the user to specify an initial size for a hashed environment. o file() can read the X11 clipboard selection as "X11_clipboard" on suitable X11-using systems. o file("stdin") is now recognized, and refers to the process's 'stdin' file stream whereas stdin() refers to the console. These may differ, for example for a GUI console, an embedded application of R or if --file= has been used. o file_test() is now also available in package utils. (It is now private in package tools.) o file.show() gains an 'encoding' argument. o New functions formatUL() and formatOL() in package utils for formatting unordered (itemize) and ordered (enumerate) lists. o The statistics reported when gcinfo(TRUE) are now of the amounts used (in Mb) and not of the amounts free (which are not really relevant when there are no hard limits, only gc trigger points). o New function get_all_vars() to retrieve all the (untransformed) variables that the default method of model.frame() would use to create the model frame. o interaction() has a new argument 'lex.order'. o initialize() (in methods) now tries to be smarter about updating the new instance in place, thereby reducing copying. o install.packages(dependencies = NA) is a new default, which is to install essential dependencies when installing from repositories to a single library. As a result of this change, update.packages() will install any new dependencies of the packages it is updating (alongside the package in the same library tree). If 'lib' is not specified or is specified of length one and the chosen location is not a writable directory, install.packages() offers to create a personal library directory for you if one does not already exist, and to install there. o is.atomic, is.call, is.character, is.complex, is.double (== is.real), is.environment, is.expression, is.function, is.integer, is.list, is.logical, is.null, is.object, is.pairlist, is.recursive, is.single and is.symbol (== is.name) are no longer internally S3 generic, nor can S4 methods be written for them. The "factor" methods of is.integer and is.numeric have been replaced by internal code. o Added is.raw() for completeness. o l10n_info() also reports if the current locale is Latin-1. o levels<-(), names() and names<-() now dispatch internally for efficiency and so no longer have S3 default methods. o .libPaths() now does both tilde and glob expansion. o Functions lm(), glm() loess(), xtabs() and the default method of model.frame() coerce their 'formula' argument (if supplied) to a formula. o max(), min() and range() now work with character vectors. o message() has a new argument 'appendLF' to handle messages with and without newlines. There is a new message class packageStartupMessage() that can be suppressed separately. o A new function, method.skeleton() writes a skeleton version of a call to setMethod() to a file, with correct arguments and format, given the name of the function and the method signature. o mode<- and storage.mode<- do slightly less copying. o nls.control(* , printEval = FALSE, warnOnly = FALSE) are two new options to help better analyze (non-)convergence of nls(), thanks to Kate Mullen. nls() and summary(nls()) now contain more information and also print information about convergence. o options(device = ) now accepts a function object as well as the name of a function. o pdf() supports new values for 'paper' of "US" (same as "letter"), "a4r" and "USr" (the latter two meaning rotated to landscape). postscript() also accepts paper = "US". o persp() now respects the graphical pars 'cex.axis', 'cex.lab', 'font.axis' and 'font.lab'. o New faster internal functions pmax.int() and pmin.int() for inputs which are atomic vectors without classes (called by pmax/pmin where applicable). pmin/pmax are now more likely to work with classed objects: they work with POSIXlt datetimes, for example. o postscript() now by default writes grey colors (including black and white) via 'setgray', which gives more widely acceptable output. There are options to write pure RGB, CMYK or gray via the new argument 'colormodel'. o rbind.data.frame() now ignores all zero-row inputs, as well as zero-column inputs (which it used to do, undocumented). This is because read.table() can create zero-row data frames with NULL columns, and those cannot be extended. o readChar() and writeChar() can now work with a raw vector. o read.table(), write.table() and allies have been moved to package utils. o rgb() now accepts the red, green and blue components in a single matrix or data frame. o New utility function RShowDoc() in package 'utils' to find and display manuals and other documentation files. o New .row_names_info() utility function finds the number of rows efficiently for data frames; consequently, dim.data.frame() has become very fast for large data frames with 'automatic' row names. o RSiteSearch() now also allows to search postings of the 'R-devel' mailing list. o screeplot() is now (S3) generic with a default method, thanks to a patch from Gavin Simpson. o Experimental 'verbose' argument for selectMethod(). Might be replaced later by a better interface for method selection inspection. o Added links to source files to the parsing routines, so that source() can now echo the original source and comments (rather than deparsing). This affects example() and Sweave() as well. o stack() and unstack() have been moved to package utils. o strptime() now sets the "tzone" attribute on the result if tz != "". o str.default() typically prints fewer entries of logical vectors. o The RweaveLatex driver for Sweave() now supports two new options: expand=FALSE, to show chunk references in the output, and concordance=TRUE, to output the concordance between input and output lines. o system() now takes the same set of arguments on all platforms, with those which are not applicable being ignored with a warning. Unix-alikes gain 'input' and 'wait', and Windows gains 'ignore.stderr'. o system.time() and proc.time() now return an object of class "proc_time" with a print() method that returns a POSIX-like format with names. o Sys.getenv() has a new argument 'unset' to allow unset and set to "" to be distinguished (if the OS does). The results of Sys.getenv() are now sorted (by name). o New function Sys.glob(), a wrapper for the POSIX.2 function glob(3) to do wildcard expansion (on systems which have it, plus an emulation on Windows). o Sys.setenv() is a new (and preferred) synonym for Sys.putenv(). The internal C code uses the POSIX-preferred 'setenv' rather than 'putenv' where the former is available. o New function Sys.unsetenv() to remove environment variables (on systems where unsetenv is implemented or putenv can remove variables, such as on Windows). o text(), mtext(), strheight(), strwidth(), legend(), axis(), title(), pie(), grid.text() and textGrob() all attempt to coerce non-language annotation objects (in the sense of is.object) to character vectors. This is principally intended to cover factors and POSIXt and Date objects, and is done via the new utility function as.graphicsAnnot() in package grDevices. o tcltk:tk_select.list() now chooses the width to fit the widest item. o {re,un}tracemem() are now primitives for efficiency and so migrate from 'utils' to 'base'. o union(), interect(), setdiff() and setequal() now coerce their arguments to be vectors (and they were documented only to apply to vectors). o uniroot() now works if the zero occurs at one of the ends of the interval (suggestion of Tamas Papp). o There is a new function View() for viewing matrix-like objects in a spreadsheet, which can be left up whilst R is running. o New function withVisible() allows R level access to the visibility flag. o zip.file.extract() has been moved to package utils. o A few more cases of subassignment work, e.g. [] <- and [] <- , with suitable coercion of the LHS. o There is a warning if \ is used unnecessarily in a string when being parsed, e.g. "\." where probably "\\." was intended. ("\." is valid, but the same as ".".) Thanks to Bill Dunlap for the suggestion. o Introduced the suffix L for integer literals to create integer rather than numeric values, e.g. 100L, 0x10L, 1e2L. o Set the parser to give verbose error messages in case of syntax errors. o The class "LinearMethodsList" has been extended and will be used to create list versions of methods, derived from the methods tables (environments). The older recursive "MethodsList" class will be deprecated (by the release of 2.5.0 if possible). o There are more flexible ways to specify the default library search path. In addition to R_LIBS and .Library, there are .Library.site (defaults to R_HOME/site-library) and R_LIBS_USER (defaults to a platform- and version-specific directory in ~/R). See ?.libPaths for details. o LAPACK has been updated to version 3.1.0. This should cause only small changes to the output, but do remember that the sign of eigenvectors (and principal components) is indeterminate. o PCRE has been updated to version 7.0. o Several functions handle row names more efficiently: - read.table() and read.DIF() make use of integer row names where appropriate, and avoid at least one copy in assigning them. - data.frame() and the standard as.data.frame() methods avoid generating long dummy row names and then discarding them. - expand.grid() and merge() generate compact 'automatic' row names. - data.matrix() and as.matrix.data.frame() have a new argument 'rownames.force' that by default drops 'automatic' row names. o [i, j] is substantially more memory-efficient when only a small part of the data frame is selected, especially when (part of) a single column is selected. o Command-line R (and Rterm.exe under Windows) accepts the options '-f filename', '--file=filename' and '-e expression' to follow other script interpreters. These imply --no-save unless --save is specified. o Invalid bytes in character strings in an MBCS now deparse/print in the form "\xc1" rather than "", which means they can be parsed/scanned. o Printing functions (without source attributes) and expressions now preserves integers (using the L suffix) and NAs (using NA_real_ etc where necessary). o The 'internal' objects .helpForCall, .tryHelp and topicName are no longer exported from 'utils'. o The internal regex code has been upgraded to glibc 2.5 (from 2.3.6). o Text help now attempts to display files which have an \encoding section in the specified encoding via file.show(). o R now attempts to keep track of character strings which are known to be in Latin-1 or UTF-8 and print or plot them appropriately in other locales. This is primarily intended to make it possible to use data in Western European languages in both Latin-1 and UTF-8 locales. Currently scan(), read.table(), readLines(), parse() and source() allow encodings to be declared, and console input in suitable locales is also recognized. New function Encoding() can read or set the declared encodings for a character vector. o There have been numerous performance improvements to the data editor on both Windows and X11. In particular, resizing the window works much better on X11. DEPRECATED & DEFUNCT o symbol.C() and symbol.For() are defunct, and have been replaced by wrappers that give a warning. o Calling a builtin function with an empty argument is now always an error. o The autoloading of ts() is defunct. o The undocumented reserved word GLOBAL.ENV has been removed. (It was yet another way to get the value of the symbol .GlobalEnv.) o The deprecated behaviour of structure() in adding a class when specifying with "tsp" or "levels" attributes is now defunct. o unix() is now finally defunct, having been deprecated for at least seven years. o Sys.putenv() is now deprecated in favour of Sys.setenv(), following the POSIX recommendation. o Building R with --without-iconv is deprecated. o Using $ on an atomic vector is deprecated (it was previously valid and documented to return NULL). o The use of storage.mode<- for other than standard types (and in particular for value "single") is deprecated: use mode<- instead. INSTALLATION o A suitable iconv (e.g. from glibc or GNU libiconv) is required. For 2.5.x only you can build R without it by configuring using --without-iconv. o There is support again for building on AIX (tested on 5.2 and 5.3) thanks to Ei-ji Nakama. o Autoconf 2.60 or later is used to create 'configure'. This makes a number of small changes, and incorporates the changes to the detection of a C99-compliant C compiler backported for 2.4.1. o Detection of a Java development environment was added such that packages don't need to provide their own Java detection. Newly added make variables are JAVAC, JAVAH, JAR and JAVA_CPPFLAGS. R CMD javareconf was updated to look for the corresponding Java tools as well. In addition, Java detection honors user-supplied environment variables JAVA_CPPFLAGS, JAVA_LIBS and JAVA_LD_LIBRARY_PATH. o Added workaround for reported non-POSIX sh on OSF1. (PR#9375) o 'make install-strip' now works, stripping the executables and also the shared libraries and modules on platforms where 'libtool' knows how to do so. o Building R as a shared library and standalone nmath now installs pkg-config files 'libR.pc' and 'libRmath.pc' respectively. o Added test for insufficiently complete implementation of sigaction. C-LEVEL FACILITIES o Functions str2type, type2char and type2str are now available in Rinternals.h. o Added support for Objective C in R and packages (if available). o R_ParseVector() has a new 4th argument 'SEXP srcfile' allowing source references to be attached to the returned expression list. o Added ptr_R_WriteConsoleEx callback which allows consoles to distinguish between regular output and errors/warnings. To ensure backward compatibility it is only used if ptr_R_WriteConsole is set to NULL. UTILITIES o Additional Sweave() internal functions are exported to help writing new drivers, and RweaveLatexRuncode() is now created using a helper function (all from a patch submitted by Seth Falcon). o The following additional flags are accessible from R CMD config: OBJC, OBJCFLAGS, JAR, JAVA, JAVAC, JAVAH, JAVA_HOME, JAVA_LIBS and JAVA_CPPFLAGS. o R CMD build now takes the package name from the DESCRIPTION file and not from the directory. (PR#9266) o checkS3methods() (and hence R CMD check) now checks agreement with primitive internal generics, and checks for additional arguments in methods where the generic does not have a '...' argument. codoc() now knows the argument lists of primitive functions. o R CMD INSTALL and R CMD REMOVE now use as the default library (if -l is not specified) the first library that would be used if R were run in the current environment (and they run R to find it). o There is a new front-end Rscript which can be used for #! scripts and similar tasks. See help("Rscript") and 'An Introduction to R' for further details. o R CMD BATCH (not Windows) no longer prepends 'invisible(options(echo = TRUE))' to the input script. This was the default unless --slave is specified and the latter is no longer overridden. On all OSes it makes use of the -f argument to R, so file("stdin") can be used from BATCH scripts. On all OSes it reports proc.time() at the end of the script unless q() is called with options to inhibit this. o R CMD INSTALL now prepends the installation directory (if specified) to the library search path. o Package installation now re-encodes R files and the NAMESPACE file if the DESCRIPTION file specifies an encoding, and sets the encoding used for reading files in preparing for LazyData. This will help if a package needs to be used in (say) both latin1 and UTF-8 locales on different systems. o R CMD check now reports on non-ASCII strings in datasets. (These are a portability issue, which can be alleviated by marking their encoding: see 'Writing R Extensions'.) o Rdiff now converts CRLF endings in the target file, and converts UTF-8 single quotes in either to ASCII quotes. o New recommended package 'codetools' by Luke Tierney provides code-analysis tools. This can optionally be used by 'R CMD check' to detect problems, especially symbols which are not visible. o R CMD config now knows about LIBnn . o New recommended package 'rcompgen' by Deepayan Sarkar provides support for command-line completion under the Unix terminal interface (provided readline is enabled) and the Windows Rgui and Rterm front ends. BUG FIXES o gc() can now report quantities of 'Vcells' in excess of 16Gb on 64-bit systems (rather than reporting NA). o Assigning class "factor" to an object now requires it has integer (and not say double) codes. o structure() ensures that objects with added class "factor" have integer codes. o The "formula" and "outer" attributes of datasets 'ChickWeight', 'CO2', 'DNase', 'Indometh', 'Loblolly', 'Orange' and 'Theoph' now have an empty environment and not the environment used to dump the datasets in the package. o Dataset 'Seatbelts' now correctly has class c("mts", "ts"). o str() now labels classes on data frames more coherently. o Several 'special' primitives and .Internals could return invisibly if the evaluation of an argument led to the visibility flag being turned off. These included as.character(), as.vector(), call(), dim(), dimnames(), lapply(), rep(), seq() and seq_along(). Others (e.g. dput() and print.default()) could return visibly when this was not intended. o Several primitives such as dim() were not checking the number of arguments supplied before method dispatch. o Tracing of primitive functions has been corrected. It should now be the case that tracing either works or is not allowed for all primitive functions. (Problems remain if you make a primitive into a generic when it is being traced. To be fixed later.) o max.col() now omits infinite values in determining the relative tolerance. o R CMD Sweave and R CMD Stangle now respond to --help and --version like other utilities. o .libPaths() adds only existing directories (as it was documented to, but could add non-directories). o setIs() and setClassUnion() failed to find some existing subclasses and produced spurious warnings, now fixed. o data.frame() ignored 'row.names' for 0-column data frames, and no longer treats an explicit row.names=NULL differently from the default value. o identical() looked at the internal structure of the 'row.names' attribute, and not the value visible at R level. o abline(reg) now also correctly works with intercept-only lm models, and abline() warns more when it's called illogically. o warning() was truncating messages at getOption("warning.length") - 1 (not as documented), with no indication. It now appends '[... truncated]'. o Stangle/Sweave were throwing spurious warnings if options 'result' or 'strip.white' were unset. o all.equal() was ignoring 'check.attributes' for list and expression targets, and checking only attributes on raw vectors. Logical vectors were being compared as if they were numeric, (with a mean difference being quoted). o Calculating the number of significant digits in a number was itself subject to rounding errors for digits >= 16. The calculation has been changed to err on the side of slightly too few significant digits (but still at least 15) rather than far too many. (An example is print(1.001, digits=16).) o unlink() on Unix-alikes failed for paths containing spaces. o substr() and friends treated NA 'start' or 'stop' incorrectly. o merge(x, y, all.y = TRUE) would sometimes incorrectly return logical columns for columns only in y when there were no common rows. o read.table(fn, col.names=) on an empty file returned NULL columns, rather than logical(0) columns (which is what results from reading a file with just a header). o grid.[xy]axis(label=logical(0)) failed. o expression() was unnecessarily duplicating arguments. o as.expression() returned a single-element expression vector, which was not compatible with S: it now copies lists element-by-element. o supsmu(periodic = TRUE) could segfault. (PR#9502, detection and patch by Bill Dunlap.) o pmax/pmin called with only logical arguments did not coerce to numeric, although they were documented to do so (as max/min do). o methods() did not know that cbind() and rbind() are internally generic. o dim(x) <- NULL removed the names of x, but this was always undocumented. It is not clear that it is desirable but it is S-compatible and relied on, so is now documented. o which(x, arr.ind = TRUE) did not return a matrix (as documented) if 'x' was an array of length 0. o C-level duplicate() truncated CHARSXPs with embedded nuls. o Partial matching of attributes was not working as documented in some cases if there were more than two partial matches or if "names" was involved. o data(package=character(0)) was not looking in ./data as documented. o summary.mlm() failed if some response names were "" (as can easily happen if cbind() is used). o The postscript() and pdf() drivers shared an encoding list but used slightly different formats. This caused problems if both were used with the same non-default encoding in the same session. (PR#9517) o The data editor was not allowing Inf, NA and NaN to be entered in numerical columns. It was intended to differentiate between empty cells and NAs, but did not do so: it now does so for strings. o supsmu() could segfault if all cases had non-finite values. (PR#9519) o plnorm(x, lower.tail=FALSE) was returning the wrong tail for x <= 0. (PR#9520) o which.min() would not report a minimum of +Inf, and analogously for which.max(). (PR#9522) o 'R CMD check' could fail with an unhelpful error when checking Rd files for errors if there was only one file and that had a serious error. (PR#9459) o try() has been reimplemented using tryCatch() to solve two problems with the original implementation: (i) try() would run non-NULL options("error") expressions for errors within a try, and (ii) try() would catch user interrupts. o str(obj) could fail when obj contained a dendrogram. o Using [, ] <- NULL failed (PR#9565) o choose(n, k) could return non-integer values for integer n and small k on some platforms. o nclass.scott(x) and nclass.FD(x) no longer return NaN when var(x) or IQR(x) (respectively) is zero. hist() now allows breaks = 1 (which the above patch will return), but not breaks = Inf (which gave an obscure error). o strptime("%j") now also works for the first days of Feb-Dec. (PR#9577) o write.table() now recovers better if 'file' is an unopened connection. (It used to open it for both the column names and the data.) o Fixed bug in mosaicplot(sort=) introduced by undocumented change in R 2.4.1 (changeset r39655). o contr.treatment(n=0) failed with a spurious error message. (It remains an error.) o as.numeric() was incorrectly documented: it is identical to as.double. o jitter(rep(-1, 3)) gave NaNs. (PR#9580) o max.col() was not random for a row of zeroes. (PR#9542) o ansari.test(conf.int=TRUE, exact=FALSE) failed. o trace() now works on S3 registered methods, by modifying the version in the S3 methods table. o rep(length=1, each=0) segfaulted. o postscript() could overflow a buffer if used with a long 'command' argument. o The internal computations to copy complete attribute lists did not copy the flag marking S4 objects, so the copies no longer behaved like S4 objects. o The C code of nlminb() was altering a variable without duplicating it. (This did not affect nlminb() but would have if the code was called from a different wrapper.) o smooth(kind = "3RS3R") (the current default) used .C(DUP = FALSE) but altered its input argument. (This was masked by duplication in as.double.) o The signature for the predefined S4 method for as.character() was missing '...' . o readBin() could read beyond the end of the vector when size-changing was involved. o The C entry point PrintValue (designed to emulate auto-printing) would not find show() for use on S4 objects, and did not have the same search path (for show(), print() and print() methods) as auto-printing. Also, auto-printing and print() of S4 objects would fail to find 'show' if the methods namespace was loaded but the package was not attached (or otherwise not in the search path). o print() (and auto-printing) now recognize S4 objects even when 'methods' is not loaded, and print a short summary rather than dump the internal structure. o Sweave and Stangle had problems due to partial matching of code chunk names when run with split=TRUE. o install.packages() on a source package now ensures that R CMD INSTALL sees the same library search path as install.packages() did when computing dependencies. o density() now ensures its 'y' values are non-negative. (PR#8876) o is.finite() and is.infinite() (and many other primitives) are not internally generic and so do not support S4 methods, which can no longer be set. (PR#7951) o nls(algorithm = "port") now accepts a list 'start' argument, as for the other methods (and as documented). o Standard errors from the "ar" method of predict() could be wrong for the last p predictions for models near non-stationarity. (PR#9614) -- 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 hothorn at hothorn.de Wed Apr 25 12:56:40 2007 From: hothorn at hothorn.de (Torsten Hothorn) Date: Wed, 25 Apr 2007 12:56:40 +0200 (CEST) Subject: R News, volume 7, issue 1 is now available Message-ID: Hi The October 2006 issue of R News is now available on CRAN under the Documentation/Newsletter link. Torsten (on behalf of the R News Editorial Board) From P.Dalgaard at biostat.ku.dk Thu Jun 28 13:43:56 2007 From: P.Dalgaard at biostat.ku.dk (Peter Dalgaard) Date: Thu, 28 Jun 2007 13:43:56 +0200 Subject: R 2.5.1 is released Message-ID: <46839EFC.8070806@biostat.ku.dk> I've rolled up R-2.5.1.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-2.5.1.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: a8efde35b940278de19730d326f58449 AUTHORS eb723b61539feef013de476e68b5c50a COPYING a6f89e2100d9b6cdffcea4f398e37343 COPYING.LIB 24ad9647e525609bce11f6f6ff9eac2d FAQ 70447ae7f2c35233d3065b004aa4f331 INSTALL f04bdfaf8b021d046b8040c8d21dad41 NEWS 88bbd6781faedc788a1cbd434194480c ONEWS 4f004de59e24a52d0f500063b4603bcb OONEWS 162f6d5a1bd7c60fd652145e050f3f3c R-2.5.1.tar.gz 162f6d5a1bd7c60fd652145e050f3f3c R-latest.tar.gz 433182754c05c2cf7a04ad0da474a1d0 README 020479f381d5f9038dcb18708997f5da RESOURCES 4eaf8a3e428694523edc16feb0140206 THANKS Here is the relevant bit of the NEWS file: CHANGES IN R VERSION 2.5.1 NEW FEATURES o density(1:20, bw = "SJ") now works as bw.SJ() now tries a larger search interval than the default (lower, upper) if it does not find a solution within the latter. o The output of library() (no arguments) is now sorted by library trees in the order of .libPaths() and not alphabetically. o R_LIBS_USER and R_LIBS_SITE feature possible expansion of specifiers for R version specific information as part of the startup process. o C-level warning calls now print a more informative context, as C-level errors have for a while. o There is a new option "rl_word_breaks" to control the way the input line is tokenized in the readline-based terminal interface for object- and file-name completion. This allows it to be tuned for people who use their space bar vs those who do not. The default now allows filename-completion with +-* in the filenames. o If the srcfile argument to parse() is not NULL, it will be added to the result as a "srcfile" attribute. o It is no longer possible to interrupt lazy-loading (which was only at all likely when lazy-loading environments), which would leave the object being loaded in an unusable state. This is a temporary measure: error-recovery when evaluating promises will be tackled more comprehensively in 2.6.0. INSTALLATION o 'make check' will work with --without-iconv, to accommodate building on AIX where the system iconv conflicts with libiconv and is not compatible with R's requirements. o There is support for 'DESTDIR': see the R-admin manual. o The texinfo manuals are now converted to HTML with a style sheet: in recent versions of makeinfo the markup such as @file was being lost in the HTML rendering. o The use of inlining has been tweaked to avoid warnings from gcc >= 4.2.0 when compiling in C99 mode (which is the default from configure). BUG FIXES o as.dendrogram() failed on objects of class "dendrogram". o plot(type ="s") (or "S") with many (hundreds of thousands) of points could overflow the stack. (PR#9629) o Coercing an S4 classed object to "matrix" (or other basic class) failed to unset the S4 bit. o The 'useS4' argument of print.default() had been broken by an unrelated change prior to 2.4.1. This allowed print() and show() to bounce badly constructed S4 objects between themselves indefinitely. o Prediction of the seasonal component in HoltWinters() was one step out at one point in the calculations. decompose() incorrectly computed the 'random' component for a multiplicative fit. o Wildcards work again in unlink() on Unix-alikes (they did not in 2.5.0). o When qr() used pivoting, the coefficient names in qr.coef() were not pivoted to match. (PR#9623) o UseMethod() could crash R if the first argument was not a character string. o R and Rscript on Unix-alikes were not accepting spaces in -e arguments (even if quoted). o Hexadecimal integer constants (e.g. 0x10L) were not being parsed correctly on platforms where the C function atof did not accept hexadecimal prefixes (as required by C99, but not implemented in MinGW as used by R on Windows). (PR#9648) o libRlapack.dylib on Mac OS X had no version information and sometimes an invalid identification name. o Rd conversion of \usage treated '\\' as a single backslash in all but latex: it now acts consistently with the other verbatim-like environments (it was never 'verbatim' despite the documentation). \code{\.} is now rendered as '\.' in all formats, as documented (it was not the case for latex conversion). codoc() (and checkDocStyle() and checkDocUsage()) now apply the same transformations to \usage as Rd conversion does, so {, % and \\ in strings in usages will now be related correctly to the help files. o rbind() failed if the only data frame had 0 rows. (PR#9657) o [i, j] could sometimes select the wrong column when j is numeric if there are duplicate column names. o sample(x, size, replace=TRUE, prob) had a memory leak if 10000 < size <= 100000. o x <- cbind(1:2); rownames(x) <- factor(c("A",NA)) now longer segfaults. o R CMD BATCH no longer assumes Sys.unsetenv() is supported (it is not on older Solaris systems). o median() returned a logical result when it was 'NA': it now returns an NA of appropriate type (e.g. integer or double). o grep(fixed = TRUE, perl = TRUE) ignored 'fixed', although it was documented to ignore 'perl' Same for [g]regexpr and [g]sub. o getNamespaceExports("base") works again. o runmed(c(), 1) no longer segfaults. o qr.coef(QR, b) failed for an LAPACK-produced QR if b was integer or for an over-determined system. qr.solve() for an under-determined system produces a solution with 0 and not NA for columns which are unused. o segments() was not handling full transparency correctly in PDF. (PR#9694) Nor was arrows(). o callGeneric() inside a method with extra arguments {and hence currently defined via .local()} now works. o [g]sub(fixed=TRUE, useBytes=FALSE) could substitute in the wrong place in an MBCS locale. gregexpr() could give incorrect answers in MBCS locales for perl = TRUE or fixed = TRUE (unless useBytes = TRUE). o The legacy quartz() device no longer crashes in locator() if the user attempts to close the window. o "CGGStackRestore: gstack underflow" warning is no longer shown in legacy quartz() device. o formatC() now limits 'digits' to 50 to avoid problems in C-level sprintf in some OSes. o seq.int(x, y, by=z) gave 'x' (and not an error) if 0 > (y-x)/z > -1. o promptClass() now lists methods, including those for generics in other attached packages. o Connection-related functions such as readBin() no longer crash when supplied with a non-connection object. o as.character.srcref() didn't handle bad srcref objects cleanly. o predict.nls() no longer requires 'newdata' to contain exactly the variable names needed to fit the model: variables used on the LHS only are no longer required and further variables are allowed. o plot.hclust() had a 'out by one' error, and ignored the last object when computing the window region (and could overrun arrays). o deriv() was creating results with double (and not integer) dims. o The unserialize code (e.g. as called by load()) looked for a function findPackageEnv() to set a saved package environment. This was missing, but is now supplied. o [cr]bind could segfault when creating a list matrix result. (Reported by Martin Morgan.) o besselI(x, nu, exp=TRUE) and besselY(x, nu) could give wrong answers for nu < 0. (Reported by Hiroyuki Kawakatsu.) o [g]sub could confuse a trailing byte '\' for a backreference in MBCSs where '\' can occur as a trailing byte (not UTF-8 nor EUC-JP, but SJIS and the CJK character sets used on Windows). (PR#9751) -- 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 Uwe.Ligges at r-project.org Fri Aug 3 14:48:47 2007 From: Uwe.Ligges at r-project.org (Uwe Ligges) Date: Fri, 03 Aug 2007 14:48:47 +0200 Subject: useR! 2008 Message-ID: <46B3242F.4060909@R-Project.org> We are happy to announce that the R user conference useR! 2008 is scheduled for August 12-14, 2008, and will take place at the University of Dortmund. As for the predecessor conferences, the program will consist of two parts: invited lectures and user-contributed sessions (abstract submission will be available online starting from December 2007). Prior to the conference, there will be tutorials on R (proposals for tutorials should be sent before 2007-10-31). INVITED LECTURES Invited speakers will include Peter B?hlmann, John Fox, Kurt Hornik, Gary King, Duncan Murdoch, Jean Thioulouse, Graham J. Williams, and Keith Worsley. USER-CONTRIBUTED SESSIONS The sessions will be a platform to bring together R users, contributors, package maintainers and developers in the S spirit that `users are developers'. People from different fields will show us how they solve problems with R in fascinating applications. The sessions are organized by members of the program committee, including Micah Altman, Roger Bivand, Peter Dalgaard, Jan de Leeuw, Ram?n D?az-Uriarte, Spencer Graves, Leonhard Held, Torsten Hothorn, Fran?ois Husson, Christian Kleiber, Friedrich Leisch, Andy Liaw, Martin M?chler, Kate Mullen, Ei-ji Nakama, Thomas Petzold, Martin Theus, and Heather Turner. The program will cover topics such as * Applied Statistics & Biostatistics * Bayesian Statistics * Bioinformatics * Chemometrics and Computational Physics * Data Mining * Econometrics & Finance * Environmetrics & Ecological Modeling * High Performance Computing * Machine Learning * Marketing & Business Analytics * Psychometrics * Robust Statistics * Sensometrics * Spatial Statistics * Statistics in the Social and Political Sciences * Teaching * Visualization & Graphics * and many more. PRE-CONFERENCE TUTORIALS Before the official program, half-day tutorials will be offered on Monday, August 11th. We invite R users to submit proposals for three hour tutorials on special topics on R. The proposals should give a brief description of the tutorial, including goals, detailed outline, justification why the tutorial is important, background knowledge required and potential attendees. The proposals should be sent before 2007-10-31 to useR-2008 at R-project.org. A web page offering more information on the `useR!' conference is available at http://www.R-project.org/useR-2008 ABOUT DORTMUND In the past, Dortmund was famous for coal, steel and the beer industry - quite typical for a city in the Ruhrgebiet. Today, Dortmund evolves to a city with high tech industry, exhibitions and service companies. Dortmund's football (i.e. soccer) club is world famous and attracts roughly 80000 people on a regular basis. IMPORTANT DATES 2007-10-31: submission deadline of tutorial proposals 2007-12-01: start of registration 2007-12-01: start of online abstract submission 2008-03-31: early registration deadline: 2008-03-31: submission deadline of abstracts 2008-05-15: notification of acceptance 2008-05-31: regular registration deadline 2008-07-25: registration deadline 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 Wed Oct 3 11:28:15 2007 From: P.Dalgaard at biostat.ku.dk (Peter Dalgaard) Date: Wed, 03 Oct 2007 11:28:15 +0200 Subject: R-2.6.0 is released Message-ID: <470360AF.8050701@biostat.ku.dk> I've rolled up R-2.6.0.tar.gz a short while ago. This is a development release which contains a number of new features. In particular, the handling of data with a large number of identical strings should be more memory-efficient. 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-2.5.0.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: 070cca21d9f8a6af15f992edb47a24d5 AUTHORS eb723b61539feef013de476e68b5c50a COPYING a6f89e2100d9b6cdffcea4f398e37343 COPYING.LIB 635d810c9c3dd14d14e98ab22cb08be2 FAQ 70447ae7f2c35233d3065b004aa4f331 INSTALL 68eb0e9747156cb793b61da6c39c0829 NEWS 88bbd6781faedc788a1cbd434194480c ONEWS 4f004de59e24a52d0f500063b4603bcb OONEWS 97e5d2542349925962b7469456d45731 R-2.6.0.tar.gz 97e5d2542349925962b7469456d45731 R-latest.tar.gz 433182754c05c2cf7a04ad0da474a1d0 README 020479f381d5f9038dcb18708997f5da RESOURCES 1ad28cbc84485ccdf4ce5721b34ed645 THANKS This is the relevant part of the NEWS file: CHANGES IN R VERSION 2.6.0 SIGNIFICANT USER-VISIBLE CHANGES o integrate(), nlm(), nlminb(), optim(), optimize() and uniroot() now have '...' much earlier in their argument list. This reduces the chances of unintentional partial matching but means that the later arguments must be named in full. o The default type for nchar() is now "chars". This is almost always what was intended, and differs from the previous default only for non-ASCII strings in a MBCS locale. There is a new argument 'allowNA', and the default behaviour is now to throw an error on an invalid multibyte string if type="chars" or type="width". o Connections will be closed if there is no R object referring to them. A warning is issued if this is done, either at garbage collection or if all the connection slots are in use. NEW FEATURES o abs(), sign(), sqrt(), floor(), ceiling(), exp() and the gamma, trig and hyperbolic trig functions now only accept one argument even when dispatching to a Math group method (which may accept more than one argument for other group members). o abbreviate() gains a 'method' argument with a new option "both.sides" which can make shorter abbreviations. o aggregate.data.frame() no longer changes the group variables into factors, and leaves alone the levels of those which are factors. (Inter alia grants the wish of PR#9666.) o The default 'max.names' in all.names() and all.vars() is now -1 which means unlimited. This fixes PR#9873. o as.vector() and the default methods of as.character(), as.complex(), as.double(), as.expression(), as.integer(), as.logical() and as.raw() no longer duplicate in most cases where the object is unchanged. (Beware: some code has been written that invalidly assumes that they do duplicate, often when using .C/.Fortran(DUP=FALSE).) o as.complex(), as.double(), as.integer(), as.logical() and as.raw() are now primitive and internally generic for efficiency. They no longer dispatch on S3 methods for as.vector() (which was never documented). as.real() and as.numeric() remain as alternative names for as.double(). expm1(), log(), log1p(), log2(), log10(), gamma(), lgamma(), digamma() and trigamma() are now primitive. (Note that logb() is not.) The Math2 and Summary groups (round, signif, all, any, max, min, summ, prod, range) are now primitive. See under METHODS PACKAGE below for some consquences for S4 methods. o apropos() now sorts by name and not by position on the search path. o attr() gains an 'exact = TRUE' argument to disable partial matching. o bxp() now allows 'xlim' to be specified. (PR#9754) o C(f, SAS) now works in the same way as C(f, treatment), etc. o chol() is now generic. o dev2bitmap() has a new option to go via PDF and so allow semi-transparent colours to be used. o dev.interactive() regards devices with the displaylist enabled as interactive, and packages can register the names of their devices as interactive via deviceIsInteractive(). o download.packages() and available.packages() (and functions which use them) now support in 'repos' or 'contriburl' either file: plus a general path (including drives on a UNC path on Windows) or a file:/// URL in the same way as url(). o dQuote() and sQuote() are more flexible, with rendering controlled by the new option 'useFancyQuotes'. This includes the ability to have TeX-style rendering and directional quotes (the so-called 'smart quotes') on Windows. The default is to use directional quotes in UTF-8 locales (as before) and in the Rgui console on Windows (new). o duplicated() and unique() and their methods in base gain an additional argument 'fromLast'. o fifo() no longer has a default 'description' argument. fifo("") is now implemented, and works in the same way as file(""). o file.edit() and file.show() now tilde-expand file paths on all interfaces (they used to on some and not others). o The find() argument is now named 'numeric' and not 'numeric.': the latter was needed to avoid warnings about name clashes many years ago, but partial matching was used. o stats:::.getXlevels() confines attention to factors since some users expected R to treat unclass() as a numeric vector. o grep(), strsplit() and friends now warn if incompatible sets of options are used, instead of silently using the documented priority. o gsub()/sub() with perl = TRUE now preserves attributes from the argument x on the result. o is.finite() and is.infinite() are now S3 and S4 generic. o jpeg(), png(), bmp() (Windows), dev2bitmap() and bitmap() have a new argument 'units' to specify the units of 'width' and 'height'. o levels() is now generic (levels<- has been for a long time). o Loading serialized raw objects with load() is now considerably faster. o New primitive nzchar() as a faster alternative to nchar(x) > 0 (and avoids having to convert to wide chars in a MBCS locale and hence consider validity). o The way old.packages() and hence update.packages() handle packages with different versions in multiple package repositories has been changed. The first package encountered was selected, now the one with highest version number. o optim(method = "L-BFGS-B") now accepts zero-length parameters, like the other methods. Also, method = "SANN" no longer attempts to optimize in this case. o New options 'showWarnCalls' and 'showErrorCalls' to give a concise traceback on warnings and errors. showErrorCalls=TRUE is the default for non-interactive sessions. Option 'showNCalls' controls how abbreviated the call sequence is. o New options 'warnPartialMatchDollar', 'warnPartialMatchArgs' and 'warnPartialMatchAttr' to help detect the unintended use of partial matching in $, argument matching and attr() respectively. o A device named as a character string in options(device =) is now looked for in the grDevices name space if it is not visible from the global environment. o pmatch(x, y, duplicates.ok = TRUE) now uses hashing and so is much faster for large x and y when most matches are exact. o qr() is now generic. o It is now a warning to have an non-integer object for .Random.seed: this indicates a user had been playing with it, and it has always been documented that users should only save and restore it. o New higher-order functions Reduce(), Filter() and Map(). o [g]regexpr() gain an 'ignore.case' argument for consistency with grep(). (This does change the positional matching of arguments, but no instances of positional matching beyond the second were found.) o relist() utility, an S3 generic with several methods, providing an 'inverse' for unlist(); thanks to a code proposal from Andrew Clausen. o require() now returns invisibly. o The interface to reshape() has been revised, allowing some simplified forms that did not work before, and somewhat improved error handling. A new argument 'sep' has been introduced to replace simple usages of 'split' (the old features are retained). o rmultinom() uses a high-precision accumulator where available, and so is more likely to give the same result on different platforms (although it is still possible to get different results, and the result may differ from previous versions of R). o row() and col() now work on matrix-like objects such as data frames, not just matrices. o Rprof() allows smaller values of 'interval' on machines that support it: for example modern Linux systems support interval = 0.001. o sample() now requires its first argument 'x' to be numeric (in the sense of is.numeric()) as well as of length 1 and >= 1 before it is regarded as shorthand for 1:x. o sessionInfo() now provides details about package name spaces that are loaded but not attached. The output of sessionInfo has been improved to make it easier to read when it is inadvertently wrapped after being pasted into an email message. o setRepositories() has a new argument 'ind' to allow selections to be made programmatically. o showMethods() has a "smart" default for 'inherited' such that showMethods(, incl = TRUE) becomes a useful short cut. o sprintf() no longer has a output string length limit. o storage.mode<- is now primitive, and hence makes fewer copies of an object (none if the mode is unchanged). It is a little less general than mode<-, which remains available. (See also the entry under DEFUNCT below.) o sweep() gains an argument 'check.margin = TRUE' which warns about mismatched dimensions. o The mathematical annotation facility (plotmath) now recognises a symbol() function which forces the font to be a symbol font. This allows access to all characters in the Adobe Symbol encoding within plotmath expressions. o For OSes that cannot unset environment variables, Sys.unsetenv() sets the value to "", with a warning. o New function Sys.which(), an interface to 'which' on Unix-alikes and an emulation on Windows. o On Unix-alikes, system(, intern = TRUE) reports on very long lines that may be truncated, giving the line number of the content being read. o termplot() has a default for 'ask' that uses dev.interactive(). It allows 'ylim' to be set, or computed to cover all the plots to be made (the new default) or computed for each plot (the previous default). o uniroot(f, *) is slightly faster for non-trivial f() because it computes f(lower) and f(upper) only once, and it has new optional arguments 'f.lower' and 'f.upper' by which the caller can pass these. o unlink() is now internal, using common POSIX code on all platforms. o unsplit() now works with lists of dataframes. o The vcov() methods for classes "gls" and "nlme" have migrated to package 'nlme'. o vignette() has a new argument 'all' to choose between showing vignettes in attached packages or in all installed packages. o New function within(), which is like with(), except that it returns modified versions back of lists and data frames. o X11(), postscript() (and hence bitmap()), xfig(), jpeg(), png() and the Windows devices win.print(), win.metafile() and bmp() now warn (once at first use) if semi-transparent colours are used (rather than silently treating them as fully transparent). o New function xspline() to provide base graphics support of X-splines (cf grid.xspline). o New function xyTable() does the 2D gridding "computations" used by sunflowerplot(). o Rd conversion to HTML and CHM now makes use of classes, which are set in the stylesheets. Editing R.css will change the styles used for \env, \option, \pkg etc. (CHM styles are set at compilation time.) o The documented arguments of '%*%' have been changed to be x and y, to match S and the implicit S4 generic. o If members of the Ops group (the arithmetic, logical and comparison operators) and '%*%' are called as functions, e.g. '>'(x, y), positional matching is always used. (It used to be the case that positional matching was used for the default methods, but names would be matched for S3 and S4 methods and in the case of '!' the argument name differed between S3 and S4 methods.) o Imports environments of name spaces are named (as "imports:foo"), and so are known e.g. to environmentName(). o Package 'stats4' uses lazy-loading not SaveImage (which is now deprecated). o Installing help for a package now parses the .Rd file only once, rather than once for each type. o PCRE has been updated to version 7.2. o bzip2 has been updated to version 1.0.4. o gettext has been updated to version 0.16.1. o There is now a global CHARSXP cache, R_StringHash. CHARSXPs are no longer duplicated and must not be modified in place. Developers should strive to only use mkChar (and mkString) for creating new CHARSXPs and avoid use of allocString. A new macro, CallocCharBuf, can be used to obtain a temporary char buffer for manipulating character data. This patch was written by Seth Falcon. o The internal equivalents of as.complex, as.double, as.integer and as.logical used to handle length-1 arguments now accept character strings (rather than report that this is 'unimplemented'). o Lazy-loading a package is now substantially more efficient (in memory saved and load time). o Various performance improvements lead to a 45% reduction in the startup time without 'methods' (and one-sixth with - 'methods' now takes 75% of the startup time of a default session). o The [[ subsetting operator now has an argument 'exact' that allows programmers to disable partial matching (which will in due course become the default). The default value is exact=NA which causes a warning to be issued when partial matching occurs. When exact = TRUE, no partial matching will be performed. When exact = FALSE, partial matching can occur and no warning will be issued. This patch was written by Seth Falcon. o Many of the C-level warning / error messages (e.g. from subscripting) have been re-worked to give more detailed information on either the location or the cause of the problem. o The S3 and S4 Math groups have been harmonized. Functions log1p(), expm1(), log10() and log2() are members of the S3 group, and sign(), log1p(), expm1(), log2(), cummax(), cummin(), digamma(), trigamma() and trunk() are members of the S4 group. gammaCody() is no longer in the S3 Math group. They are now all primitive. o The initialization of the random-number stream makes use of the sub-second part of the current time where available. Initialization of the 1997 Knuth TAOCP generator is now done in R code, avoiding some C code whose licence status has been questioned. o The reporting of syntax errors has been made more user- friendly. METHODS PACKAGE o Packages using 'methods' have to have been installed in R 2.4.0 or later (when various internal representations were changed). o Internally generic primitives no longer dispatch S4 methods on S3 objects. o load() and restoring a workspace attempt to detect and warn on the loading of pre-2.4.0 S4 objects. o Making functions primitive changes the semantics of S4 dispatch: these no longer dispatch on classes based on types but do dispatch whenever the function in the base name space is called. This applies to as.complex(), as.integer(), as.logical(), as.numeric(), as.raw(), expm1(), log(), log1p(), log2(), log10(), gamma(), lgamma(), digamma() and trigamma(), as well as the Math2 and Summary groups. Because all members of the group generics are now primitive, they are all S4 generic and setting an S4 group generic does at last apply to all members and not just those already made S4 generic. as.double() and as.real() are identical to as.numeric(), and now remain so even if S4 methods are set on any of them. Since 'as.numeric' is the traditional name used in S4, currently methods must be exported from a NAMESPACE for 'as.numeric' only. o The S4 generic for '!' has been changed to have signature (x) (was (e1)) to match the documentation and the S3 generic. setMethod() will fix up methods defined for (e1), with a warning. o The "structure" S4 class now has methods that implement the concept of structures as described in the Blue Book--that element-by-element functions and operators leave structure intact unless they change the length. The informal behavior of R for vectors with attributes was inconsistent. o The implicitGeneric() function and relatives have been added to specify how a function in a package should look when methods are defined for it. This will be used to ensure that generic versions of functions in R core are consistent. See ?implicitGeneric. o Error messages generated by some of the functions in the methods package provide the name of the generic to provide more contextual information. o It is now possible to use setGeneric(useAsDefault = FALSE) to define a new generic with the name of a primitive function (but having no connection with the primitive). DEPRECATED & DEFUNCT o $ on an atomic vector now gives a warning that it is 'invalid'. It remains deprecated, but may be removed in R >= 2.7.0. o storage.mode(x) <- "real" and storage.mode(x) <- "single" are defunct: use instead storage.mode(x) <- "double" and mode(x) <- "single". o In package installation, SaveImage: yes is deprecated in favour of LazyLoad: yes. o seemsS4Object (methods package) is deprecated in favour of isS4(). o It is planned that [[exact=TRUE]] will become the default in R 2.7.0. UTILITIES o checkS3methods() (invoked by R CMD check) now checks the arguments of methods for primitive members of the S3 group generics. o R CMD check now does a recursive copy on the 'tests' directory. o R CMD check now warns on non-ASCII .Rd files without an \encoding field, rather than just on ones that are definitely not from an ISO-8859 encoding. This agrees with the long-standing stipulation in 'Writing R Extensions', and catches some packages with UTF-8 man pages. o R CMD check now warns on DESCRIPTION files with a non-portable Encoding field, or with non-ASCII data and no Encoding field. o R CMD check now loads all the 'Suggests' and 'Enhances' dependencies to reduce warnings about non-visible objects, and also emulates standard functions (such as shell()) on alternative R platforms. o R CMD check now (by default) attempts to latex the vignettes rather than just weave and tangle them: this will give a NOTE if there are latex errors. o R CMD check computations no longer ignore Rd \usage entries for functions for extracting or replacing parts of an object, so S3 methods should use the appropriate \method{} markup. o R CMD check now checks for CR (as well as CRLF) line endings in C/C++/Fortran source files, and for non-LF line endings in Makefile[.in] and Makevars[.in] in the package 'src' directory. R CMD build will correct non-LF line endings in source files and in the make files mentioned. o Rdconv now warns about unmatched braces rather than silently omitting sections containing them. (Suggestion by Bill Dunlap, PR#9649) Rdconv now renders (rather than ignores) \var{} inside \code{} markup in latex conversion. R CMD Rdconv gains a --encoding argument to set the default encoding for conversions. o The list of CRAN mirrors now has a new (manually maintained) column "OK" which flags mirrors that seem to be OK, only those are used by chooseCRANmirror(). The now exported function getCRANmirrors() can be used to get all known mirrors or only the ones that are OK. o R CMD SHLIB gains arguments --clean and --preclean to clean up intermediate files after and before building. o R CMD config now knows about FC and FCFLAGS (used for F9x compilation). o R CMD Rdconv now does a better job of rendering quotes in titles in HTML, and \sQuote and \dQuote into text on Windows. C-LEVEL FACILITIES o New utility function alloc3DArray similar to allocMatrix. o The entry point R_seemsS4Object in Rinternals.h has not been needed since R 2.4.0 and has been removed. Use IS_S4_OBJECT instead. o Applications embedding R can use R_getEmbeddingDllInfo() to obtain DllInfo for registering symbols present in the application itself. o The instructions for making and using standalone libRmath have been moved to the R Installation and Administration manual. o CHAR() now returns (const char *) since CHARSXPs should no longer be modified in place. This change allows compilers to warn or error about improper modification. Thanks to Herve Pages for the suggestion. o acopy_string is a (provisional) new helper function that copies character data and returns a pointer to memory allocated using R_alloc. This can be used to create a copy of a string stored in a CHARSXP before passing the data on to a function that modifies its arguments. o asLogical, asInteger, asReal and asComplex now accept STRSXP and CHARSXP arguments, and asChar accepts CHARSXP. o New R_GE_str2col() exported via R_ext/GraphicsEngine.h for external device developers. o doKeybd and doMouseevent are now exported in GraphicsDevice.h. o R_alloc now has first argument of type 'size_t' to support 64-bit platforms (e.g. Win64) with a 32-bit 'long' type. o The type of the last two arguments of getMatrixDimnames (non-API but mentioned in R-exts.texi and in Rinternals.h) has been changed to 'const char **' (from char **). o R_FINITE now always resolves to the function call R_finite in packages (rather than sometimes substituting isfinite). This avoids some issues where R headers are called from C++ code using features tested on the C compiler. o The advice to include R headers from C++ inside extern "C" {} has been changed. It is nowadays better *not* to wrap the headers, as they include other headers which on some OSes should not be wrapped. o Rinternals.h no longer includes a substantial set of C headers. All but ctype.h and errno.h are included by R.h which is supposed to be used before Rinternals.h. o Including C system headers can be avoided by defining NO_C_HEADERS before including R headers. This is intended to be used from C++ code, and you will need to include C++ equivalents such as before the R headers. INSTALLATION o The 'test-Lapack' test is now part of 'make check'. o The 'stat' system call is now required, along with 'opendir' (which had long been used but not tested for). ('make check' would have failed in earlier versions without these calls.) o 'evince' is now considered as a possible PDF viewer. o 'make install-strip' now also strips the DLLs in the standard packages. o Perl 5.8.0 (released in July 2002) or later is now required. (R 2.4.0 and later have in fact required 5.6.1 or later.) o The C function 'finite' is no longer used: we expect a C99 compiler which will have 'isfinite'. (If that is missing, we test separately for NaN, Inf and -Inf.) o A script/executable 'texi2dvi' is now required on Unix-alikes: it is part of the texinfo distribution. o Files texinfo.tex and txi-en.tex are no longer supplied in doc/manual (as the latest versions have an incompatible licence). You will need to ensure that your texinfo and/or TeX installations supply them. o wcstod is now required for MBCS support. o There are some experimental provisions for building on Cygwin. PACKAGE INSTALLATION o The encoding declared in the DESCRIPTION file is now used as the default encoding for .Rd files. o A standard for specifying package license information in the DESCRIPTION License field was introduced, see 'Writing R Extensions'. In addition, files LICENSE or LICENCE in a package top-level source directory are now installed (so putting copies into the 'inst' subdirectory is no longer necessary). o install.packages() on a Unix-alike now updates doc/html/packages.html only if packages are installed to .Library (by that exact name). o R CMD INSTALL --clean now runs SHLIB --clean to do the clean up (unless there is a src/Makefile), and this will remove $(OBJECTS) (which might have been redefined in Makevars). R CMD INSTALL --preclean cleans up the sources after a previous installation (as if that had used --clean) before attempting to install. R CMD INSTALL will now run R CMD SHLIB in the 'src' directory if src/Makevars is present, even if there are no source files with known extensions. o If there is a file src/Makefile, src/Makevars is now ignored (it could be included by src/Makefile if desired), and it is preceded by etc/Makeconf rather than share/make/shlib.mk. Thus the makefiles read are R_HOME/etc/Makeconf, src/Makefile in the package and then any personal Makevars files. o R CMD SHLIB used to support the use of 'OBJS' in Makevars, but this was changed to 'OBJECTS' in 2001. The undocumented alternative of 'OBJS' has finally been removed. o R CMD check no longer issues a warning about no data sets being present if a lazyload db is found (as determined by the presence of Rdata.rdb, Rdata.rds, and Rdata.rdx in the 'data' subdirectory. BUG FIXES o charmatch() and pmatch() used to accept non-integer values for 'nomatch' even though the return value was documented to be integer. Now 'nomatch' is coerced to integer (rather than the result being coerced to the type of 'nomatch'). o match.call() no longer 'works' outside a function unless 'definition' is supplied. (Under some circumstances it used to 'work', matching itself.) o The formula methods of boxplot, cdplot, pairs and spineplot now attach 'stats' so that model.frame() is visible where they evaluate it. o Date-time objects are no longer regarded as numeric by is.numeric(). o methods("Math") did not work if 'methods' was not attached. o readChar() read an extra empty item (or more than one) beyond the end of the source; in some conditions it would terminate early when reading an item of length 0. o Added a promise evaluation stack so interrupted promise evaluations can be restarted. o R.version[1:10] now nicely prints. o In the methods package, prototypes are now inherited for the .Data "slot"; i.e., for classes that contain one of the basic data types. o [[i, j]] now works if 'i' is character. o write.dcf() no longer writes NA fields (PR#9796), and works correctly on empty descriptions. o pbeta(x, log.p = TRUE) now has improved accuracy in many cases, and so have functions depending on it such as pt(), pf() and pbinom(). o mle() had problems with the L-BFGS-B in the no-parameter case and consequentially also when profiling 1-parameter models (fix thanks to Ben Bolker). o Two bugs fixed in methods that in involve the "..." argument in the generic function: previously failed to catch methods that just dropped the "..."; and use of callGeneric() with no arguments failed in some circumstances when "..." was a formal argument. o sequence() now behaves more reasonably, although not back-compatibly for zero or negative input. o nls() now allows more peculiar but reasonable ways of being called, e.g., with data=list() or a model without variables. o match.arg() was not behaving as documented when several.ok=TRUE (PR#9859), gave spurious warnings when 'arg' had the wrong length and was incorrectly documented (exact matches are returned even when there is more than one partial match). o The data.frame method for split<-() was broken. o The test for -D__NO_MATH_INLINES was badly broken and returned true on all non-glibc platforms and false on all glibc ones (whether they were broken or not). o LF was missing after the last prompt when --quiet was used without --slave. Use --slave when no final LF is desired. o Fixed bug in initialisation code in 'grid' package for determining the boundaries of shapes. Problem reported by Hadley Wickham; symptom was error message: "Polygon edge not found". o str() is no longer slow for large POSIXct objects. Its output is also slightly more compact for such objects; implementation via new optional argument 'give.head'. o strsplit(*, fixed=TRUE), potentially iconv() and internal string formatting is now faster for large strings, thanks to report PR#9902 by John Brzustowski. o de.restore() gave a spurious warning for matrices (Ben Bolker) o plot(fn, xlim=c(a,b)) would not set "from" and "to" properly when plotting a function. The argument lists to curve() and plot.function() have been modified slightly as part of the fix. o julian() was documented to work with POSIXt origins, but did not work with POSIXlt ones. (PR#9908) o Dataset HairEyeColor has been corrected to agree with Friendly (2000): the change involves the breakdown of the Brown hair / Brown eye cell by Sex, and only totals over Sex are given in the original source. o Trailing spaces are now consistently stripped from \alias{} entries in .Rd files, and this is now documented. (PR#9915) o .find.packages(), packageDescription() and sessionInfo() assumed that attached environments named "package:foo" were package environments, although misguided users could use such a name in attach(). o spline() and splinefun() with method = "periodic" could return incorrect results when length(x) was 2 or 3. o getS3method() could fail if the method name contained a regexp metacharacter such as "+". o help() now uses the name and not the value of the vector unless it has length exactly one, so e.g. help(letters) now gives help on 'letters'. (Related to PR#9927) o Ranges in chartr() now work better in CJK locales, thanks to Ei-ji Nakama. -- 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 Oct 3 12:02:42 2007 From: P.Dalgaard at biostat.ku.dk (Peter Dalgaard) Date: Wed, 03 Oct 2007 12:02:42 +0200 Subject: [R] R-2.6.0 is released In-Reply-To: <470360AF.8050701@biostat.ku.dk> References: <470360AF.8050701@biostat.ku.dk> Message-ID: <470368C2.5040200@biostat.ku.dk> Peter Dalgaard wrote: > I've rolled up R-2.6.0.tar.gz a short while ago. This is a development > release which contains a number of new features. In particular, the handling > of data with a large number of identical strings should be more memory-efficient. > > 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-2.5.0.tar.gz > > OK, OK, make that http://cran.r-project.org/src/base/R-2/R-2.6.0.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 Thomas.Petzoldt at tu-dresden.de Fri Oct 5 13:29:32 2007 From: Thomas.Petzoldt at tu-dresden.de (Thomas Petzoldt) Date: Fri, 05 Oct 2007 13:29:32 +0200 Subject: JSS: Special volume about R in ecology and ecological modelling Message-ID: <4706201C.2040406@tu-dresden.de> Dear useRs, the new special volume of JSS about "R in Ecology and Ecological Modelling" is now online. The scope of the papers ranges from theoretical ecology and ecological modelling to statistical methodology relevant for data analyses in ecological applications. JSS, the Journal of Statistical Software, is an OpenAccess journal. All articles and the accompanying software are freely available online: http://www.jstatsoft.org Select "Browse", "Vol. 22" Enjoy reading and get new experiences while using the published examples yourself! Thomas Petzoldt + Thomas Kneib, guest editors Selected KEYWORDS: analogue matching, palaeoecology, environmental prediction, multivariate analysis, ade4, graphical user interface, habitat selection, radiotracking, Mantel test, spatial pattern, qualitative validation criteria, individual-based model, demography, human ecology, model life tables, matrix population model unified neutral theory, biodiversity, R From Torsten.Hothorn at stat.uni-muenchen.de Tue Oct 30 14:04:51 2007 From: Torsten.Hothorn at stat.uni-muenchen.de (Torsten Hothorn) Date: Tue, 30 Oct 2007 14:04:51 +0100 (CET) Subject: R News, volume 7, issue 2 is now available (fwd) Message-ID: Dear useRs, The October 2007 issue of R News is now available on CRAN under the Documentation/Newsletter link. Torsten (on behalf of the R News Editorial Board) From ligges at statistik.uni-dortmund.de Thu Nov 1 18:48:26 2007 From: ligges at statistik.uni-dortmund.de (Uwe Ligges) Date: Thu, 01 Nov 2007 18:48:26 +0100 Subject: useR! 2008 - last call for tutorial proposals Message-ID: <472A116A.9080106@statistik.uni-dortmund.de> As most of you already know from a previous announcement, the R user conference useR! 2008 is scheduled for August 12-14, 2008, and will take place at the University of Dortmund. PRE-CONFERENCE TUTORIALS Before the official program, half-day tutorials will be offered on Monday, August 11th. We invite R users to submit proposals for three hour tutorials on special topics on R. The proposals should give a brief description of the tutorial, including goals, detailed outline, justification why the tutorial is important, background knowledge required and potential attendees. This is the last call for submitting proposals for pre-conference tutorials to useR-2008 at R-project.org. The proposals should be sent before 2007-11-09. A web page offering more information on the `useR!' conference is available at http://www.R-project.org/useR-2008 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 Mon Nov 26 15:38:54 2007 From: P.Dalgaard at biostat.ku.dk (Peter Dalgaard) Date: Mon, 26 Nov 2007 15:38:54 +0100 Subject: R-2.6.1 is released Message-ID: <474ADA7E.7030209@biostat.ku.dk> I've rolled up R-2.6.1.tar.gz a short while ago. This is a maintenance release and fixes a number of mostly minor bugs and platform issues, as well as a couple of major problems. Probably, the most important issues were - save-to-postscript on Windows - tcltk event loop with X11 - build issue on recent MacOSX 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-2.6.1.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: 070cca21d9f8a6af15f992edb47a24d5 AUTHORS eb723b61539feef013de476e68b5c50a COPYING a6f89e2100d9b6cdffcea4f398e37343 COPYING.LIB 619aa712a6032fdbffd4f0c69d962859 FAQ 70447ae7f2c35233d3065b004aa4f331 INSTALL b6ed12e20f627a466378fc28006dc9c9 NEWS 88bbd6781faedc788a1cbd434194480c ONEWS 4f004de59e24a52d0f500063b4603bcb OONEWS 19c35a69e1afa73f5f70f91ff9939233 R-2.6.1.tar.gz 19c35a69e1afa73f5f70f91ff9939233 R-latest.tar.gz 433182754c05c2cf7a04ad0da474a1d0 README 020479f381d5f9038dcb18708997f5da RESOURCES 1ad28cbc84485ccdf4ce5721b34ed645 THANKS Here is the relevant bit of the NEWS file: CHANGES IN R VERSION 2.6.1 NEW FEATURES o The "data.frame" and "factor" methods for [[ now support the 'exact' argument introduced in 2.6.0. o plot.lm() gains a new argument 'cex.caption' to allow the size of the captions to be controlled. o A series of changes make the CHARSXP cache introduced in 2.6.0 faster (and in some cases many times faster) in sessions with a large number (e.g. a million) of unique character strings, and also if there are many empty strings. o embedFonts(), bitmap() and dev2bitmap() explicitly turn off auto-rotation in Ghostscript when generating PDF. o The canonical architecture is no longer checked when loading packages using a non-empty sub-architecture, since it is possible to (e.g.) build packages for i386-pc-linux-gnu on both that architecture and on x86_64-unknown-linux-gnu. o Deparsing will (if option warnIncomplete is set) warn on strings longer than the parser limit (8192 bytes). o url() now uses the UserAgent header in http transactions in the same way as download.file() (making use of option "HTTPUserAgent"). BUG FIXES o iconv() is again able to translate character strings with embedded nuls (such as those in UCS-2). o new.packages() and update.packages() failed when called on an empty library, since old.packages() threw an error. old.packages() now returns NULL (as documented) in that case. o Builds on Mac OS X 10.4 or higher now allocate enough space in the binary headers to relocate dependent libraries into the framework. o R CMD build now computes the exclusion list on the copy it makes: this avoids problems if the original sources contain symbolic links (which are resolved in the copy). Thanks to Michael Lawrence for diagnosis and patch. o object.size() had slightly too low a size for objects of type "S4". o symbol() in plotmath expressions was only accepting valid character strings, which made it impossible to specify symbols such as aleph (obtained by symbol("\300")) in a UTF-8 locale. o An event handling issue caused autorepeat functions to misbehave with tcltk (notably scrollbars). o plot(sin, -5, 5) gives ylab 'sin(x)' again, where it resulted in 'x(x)' in 2.6.0. Further, plot(sin) again plots from [0,1] also in cases where a previously used coordinate system differs. o curve() with unspecified 'from', 'to' and 'xlim' now reuses the previous x limits, and not slightly larger ones. o It was intended that R code filenames in packages should start with an ASCII letter or digits (and R CMD INSTALL uses that), but the test used in R CMD build ([A-Za-z0-9]) was locale-specific (and excluded t to y in Estonian, for example). (PR#10351) o 'R CMD build' could misbehave when faced with files with CRLF line endings *and* no line ending on the final line of the file, removing the last byte of the file. o DF[i, j] failed in 2.6.0 if j was a logical vector selecting a single column. o Unix x11() would fail if a valid 'display' was specified but DISPLAY was unset. (PR#10379) o postscript() was not always ignoring .Postscript.Options in the workspace (where it should not have occurred). o help.search() would give an error if it found a badly installed package, even if 'package' was not specified. o tclServiceMode() (package tcltk) now works under Unix-alikes. (Although documented, it used only to work under Windows.) o As Mac OS X 10.5.0 comes with incompatible /bin/sh shell, we force SHELL=/bin/bash (which is ok) in that case. [Only for 2.6.x: another solution is used in 2.7.0.] o Deliberately using malformed source attributes no longer causes deparsing/printing of functions to crash R. (PR#10437) o R CMD check and R CMD INSTALL now work with (some) directory names containing spaces. o choose(n, k) gave incorrect values for negative n and small k. o plot.ts(x,y) could use wrong default labels; fixed thanks to Antonio, Fabio di Narzo. o reshape() got column names out of sync with contents in some cases; found by Antonio, Fabio Di Narzo. o ar(x) for short 'x' (i.e. length <= 10) could fail because the default 'order.max' was >= length(x) which is non-sensical. o Keyboard events in getGraphicsEvent() could cause stack imbalance errors (PR#10453) -- 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 Torsten.Hothorn at stat.uni-muenchen.de Wed Dec 19 09:07:51 2007 From: Torsten.Hothorn at stat.uni-muenchen.de (Torsten Hothorn) Date: Wed, 19 Dec 2007 09:07:51 +0100 (CET) Subject: R News, volume 7, issue 3 is now available Message-ID: Dear useRs, The December 2007 issue of `R News' is now available on CRAN under the Documentation/Newsletter link. Torsten (on behalf of the R News Editorial Board)