R 2.5.0 is released

From: Peter Dalgaard <P.Dalgaard_at_biostat.ku.dk>
Date: Tue, 24 Apr 2007 12:34:31 +0200


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:

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. <raw>[] <- <list> and <vector>[] <- <expression>, 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 <data frame>[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 "<c1>", 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(<list>) 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 <data frame>[, <last column>] <- 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(<raw vector>) 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 Ă˜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 Received on Tue 24 Apr 2007 - 17:15:14 GMT

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