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Dear Emacs, please make this -*-Text-*- mode!
This file covers NEWS from the release of 2.0.0 up to the
release of R-2.10.0. See 'NEWS' (or doc/html/NEWS.html or
doc/NEWS.Rd) for subsequent changes.
**************************************************
* *
* 2.9 SERIES NEWS *
* *
**************************************************
CHANGES IN R VERSION 2.9.2 patched
NEW FEATURES
o On systems using ICU for collation (including Mac OS X), using
Sys.setlocale() to change the LC_COLLATE setting is more
likely to change the collation provided by ICU.
BUG FIXES
o On systems using zipped data and help (Windows) the names of
datasets could clash with temporary filenames used when
running examples, causing errors.
o as.complex() sometimes warned about NAs on coercions and
sometimes not (when the C function asComplex was used, e.g. on
list elements). (PR#13942)
o cat() on an unopened connection could close it twice, and
with file() connections segfaulted on some systems.
o Printing a list could segfault if the elements are nested too
deeply.
CHANGES IN R VERSION 2.9.2
NEW FEATURES
o install.packages(NULL) now lists packages only once even if they
occur in more than one repository (as the latest compatible
version of those available will always be downloaded).
o approxfun() and approx() now accept a 'rule' of length two, for
easy specification of different interpolation rules on left and
right.
They no longer segfault for invalid zero-length specification
of 'yleft, 'yright', or 'f'.
o seq_along(x) is now equivalent to seq_len(length(x)) even where
length() has an S3/S4 method; previously it (intentionally)
always used the default method for length().
o PCRE has been updated to version 7.9 (for bug fixes).
o agrep() uses 64-bit ints where available on 32-bit platforms
and so may do a better job with complex matches.
(E.g. PR#13789, which failed only on 32-bit systems.)
DEPRECATED & DEFUNCT
o R CMD Rd2txt is deprecated. (It is just a wrapper for
R CMD Rdconv -t txt.)
o tools::Rd_parse() is deprecated and will be removed in 2.10.0
(which will use only Rd version 2).
BUG FIXES
o parse_Rd() still did not handle source reference encodings
properly.
o The C utility function PrintValue no longer attempts to print
attributes for CHARSXPs as those attributes are used
internally for the CHARSXP cache. This fixes a segfault when
calling it on a CHARSXP from C code.
o PDF graphics output was producing two instances of anything
drawn with the symbol font face. (Report from Baptiste Auguie.)
o length(x) <- newval and grep() could cause memory corruption.
(PR#13837)
o If model.matrix() was given too large a model, it could crash
R. (PR#13838, fix found by Olaf Mersmann.)
o gzcon() (used by load()) would re-open an open connection,
leaking a file descriptor each time. (PR#13841)
o The checks for inconsistent inheritance reported by setClass()
now detect inconsistent superclasses and give better warning
messages.
o print.anova() failed to recognize the column labelled
P(>|Chi|) from a Poisson/binomial GLM anova as a p-value
column in order to format it appropriately (and as a
consequence it gave no significance stars).
o A missing PROTECT caused rare segfaults during calls to
load(). (PR#13880, fix found by Bill Dunlap.)
o gsub() in a non-UTF-8 locale with a marked UTF-8 input
could in rare circumstances overrun a buffer and so segfault.
o R CMD Rdconv --version was not working correctly.
o Missing PROTECTs in nlm() caused "random" errors. (PR#13381 by
Adam D.I. Kramer, analysis and suggested fix by Bill Dunlap.)
o Some extreme cases of pbeta(log.p = TRUE) are more accurate
(finite values < -700 rather than -Inf). (PR#13786)
pbeta() now reports on more cases where the asymptotic
expansions lose accuracy (the underlying TOMS708 C code was
ignoring some of these, including the PR#13786 example).
o new.env(hash = TRUE, size = NA) now works the way it has been
documented to for a long time.
o tcltk::tk_choose.files(multi = TRUE) produces better-formatted
output with filenames containing spaces. (PR#13875)
o R CMD check --use-valgrind did not run valgrind on the package tests.
o The tclvalue() and the print() and as.xxx methods for class
"tclObj" crashed R with an invalid object -- seen with an
object saved from an earlier session.
o R CMD BATCH garbled options -d <debugger> (useful for
valgrind, although --debugger=valgrind always worked)
o INSTALL with LazyData and Encoding declared in DESCRIPTION
might have left options("encoding") set for the rest of the
package installation.
CHANGES IN R VERSION 2.9.1
NEW FEATURES
o New function anyDuplicated(x) returns 0 (= FALSE) or the index
of the first duplicated entry of x.
o matplot(), matlines() and matpoints() now also obey a 'lend'
argument, determining line end styles. (Wish of PR#13619).
o bw.SJ(), bw.bcv() and bw.ucv() now gain an optional 'tol'
argument allowing more accurate estimates.
o new.packages() no longer regards packages with the same name
as a member of an installed bundle as 'new' (this is now
consistent with the dependency checks in install.packages()).
It no longer reports on partially installed bundles (since
members can be updated individually if a bundle is unbundled).
o old.packages() and hence updates.packages() will look for
updates to members of package bundles before updates to the
whole bundle: this allow bundles to be split and installations
updated.
o nlminb() gives better non-convergence messages in some cases.
o S3 method dispatch will support S4 class inheritance for S3
methods, for primitives and via UseMethod(), if the argument
S3methods=TRUE is given to setClass(). S4 method dispatch
will use S3 per-object inheritance if S3Class() is set on the
object. See ?Methods and the paper referenced there.
o R CMD INSTALL is more tolerant of (malformed) packages with a
'man' directory but no validly named .Rd files.
o R CMD check now reports where options are used that cause some
of the checks to be skipped.
o RSiteSearch has been updated to be consistent with the new
layout of the search site itself, which now includes separate
options for vignettes, views, and r-sig-mixed-models, as well
as changed names for r-help. (Contributed by Jonathan Baron.)
o That R CMD check makes use of a
<pkg>/tests/Examples/<pkg>-Ex.Rout.save file as a reference
result is now documented in 'Writing R Extensions'.
DEPRECATED & DEFUNCT
o print.atomic() (defunct since 1.9.0) has been removed since it
caused confusion for an S4 class union "atomic".
o png(type="cairo1") is deprecated -- it was only needed for
platforms with 1.0 <= cairo < 1.2.
BUG FIXES
o The ... argument was not handled properly when ... was found
in the enclosure of the current function, rather than in the
function header itself. (This caused integrate() to fail in
certain cases.)
o col2rgb("#00000080", TRUE) would return the background colour.
(Reported by Hadley Wickham.)
o interaction() now ensures that the levels of the result are unique.
o packageDescription() and hence sessionInfo() now report the correct
package version also for a non-attached loaded namespace of
a version different from the default lib.loc.
o smoothScatter() now also works when e.g. xlim[2] < xlim[1].
o Invalid use of sprintf() such as sprintf("%S%") now give an error
instead of a segmentation fault, as do very unusual cases such as
sprintf("%s", tryCatch(stop(), error=identity)). (It was
always documented that misuse could crash R in
platform-dependent ways.)
o parse_Rd() would mishandle braces when they occurred at
the start of a line within an R string in an Rd file (reported
by Alex Couture-Beil) or when they occurred in an R comment
(reported by Mark Bravington).
o readNEWS() missed version numbers with more than one digit.
o building R --without-x no longer fails (PR#13665)
o printCoefmat(cbind(0,1)) now works too (PR#13677)
o bw.SJ(c(1:99, 1e6)) now works too.
o Rd2txt() could not handle empty descriptions of items in an Rd
file (reported by Mark Bravington), and did not wrap long lists
of arguments if they were given in a single item.
o stars() would do a partial plot when called with plot = FALSE;
it now consistently returns the locations of the stars.
o Rd2latex() could not handle empty sections.
o old.packages() and hence update.packages() would fail on a
repository which contained only one package but with multiple
versions of that package.
o as.character.Rd() added extra braces when displaying two-argument
macros. (Report and fix by Manuel Eugster.)
o unsplit() was misbehaving in the case of single-column data
frames. (Reported by Will Gray.)
o as(I(1), "vector") and similar coercions from objects of
"unregistered" S3 classes now work.
o srcref records produced by parse() and parse_Rd() did not record
the encoding of the source file. (Reported by Romain Francois.)
o The X11 version of View() was misbehaving in MBCS locales, and
PgUp/PgDn now behave better, thanks to a patch from Ei-ji Nakama.
o R CMD check looked at the environment variable PDFLATEX, but
as from R 2.8.1 R CMD Rd2dvi used R_PDFLATEXCMD in
preference, and that was set by R CMD (and not PDFLATEX). Now
R CMD check looks at R_PDFLATEXCMD.
o sprintf() now signals an error when the result of single format
specification would be longer than the limit (8192 bytes); it would
return "somewhat random" results or segfault previously. (PR#13667)
Further, arguments of type "language" or "symbol" are no longer
allowed, as these, e.g., sprintf("%s", quote(list())), typically
lead to unexpected results or hard to understand error messages.
o The new (in 2.9.0) 'stringsAsFactors' argument to expand.grid()
was not working: it now does work but has default TRUE for
backwards compatibility.
o tcrossprod(<1d-array>, <matrix>) now does work when the arguments
are of compatible dimensions.
o qbinom() now is accurate also in (large size, small prob)
cases. (PR#13711)
o The calculation of the Spearman p-value in cor.test() is
slightly more accurate in some cases. (PR#13574)
o The digamma(), trigamma() and psigamma() functions could be
inaccurate for values of x around 1e-15 due to cancellation.
(PR#13714).
o median.default() was altered in 2.8.1 to use sum() rather
than mean(), although it was still documented to use mean().
This caused problems for POSIXt objects, for which mean() but
not sum() makes sense, so the change has been reverted.
o Assigning an extra 0-length column to a data frame by
DF$foo <- value gave a corrupt data frame rather than failing.
(PR#13724) This also happened for DF[["foo"]] <- value.
o R CMD INSTALL no longer gives a spurious warning about old R
versions ignoring multiple dependencies, if the conditions are
known to be satisfied.
o The test for setting dim() allowed a value with two or more
NAs to be set on a 0-length object. (PR#13729) Also, it
allowed an even number of negative values.
o xtfrm(), rank(), sort() and order() did not always make use of
custom comparison methods specific to the class of elements
being sorted.
o Increase NAMED value on 'seq' value in for() loop so loop code
cannot modify 'seq' value.
o Prevent rectangles of size < 0.5 pixel from disappearing in
Quartz when using rastered backend. (PR#13744)
o Printing _NA_complex_ had a low-level thinko; patch thanks to
Bill Dunlap.
o CP1257 encoding for postscript/PDF has been corrected. (PR#13736)
o aov() with an error term was evaluating the ... arguments in
2.9.0 whilst checking their names, so could fail by evaluating
them in the wrong place. (PR#13733)
o The print() method for arima() failed if all coefs were fixed.
o R CMD INSTALL --no-latex was not implemented in 2.9.0 (only).
o Added a needed PROTECT call in RunFinalizers to handle cases where
the routine is called recursively from a GC in a finalizer.
o Constructing error messages about unused arguments in calls to
closures no longer evaluates the arguments.
o qr(x, LAPACK=TRUE) did not coerce integer x to numeric.
o qr.coef() misbehaved in the LAPACK case with a matrix RHS, so
that solve(qr(x, LAPACK=TRUE)) gave wrong results. (Found by
Avraham Adler, PR#13762 by Ravi Varadhan.)
CHANGES IN R VERSION 2.9.0
NEW FEATURES
o Package 'Matrix' is now a recommended package contained in the
basic R distribution. It provides S4 classes and methods for
dense and sparse matrices, often by using the numerical
libraries Lapack and from the SuiteSparse collection CHOLMOD,
CSparse, and SPQR among others.
o pdf() and postscript() gain a 'useKerning' argument to place
strings using kerning (which had previously been ignored in
display but not in strwidth), based in part on an idea and
code from Ei-ji Nakama. The default is TRUE.
Kerning involving spaces is now ignored (it was previously
only used in the computation of string widths).
o seq.default() and seq.int() ensure that the result is within the
interval [from, to] even when the last value would previously
have been slightly out of range because of the allowance for
rounding error in computing the number of elements.
o boxplot() gains a simple 'matrix' method, enabling boxplot(mat)
instead of boxplot(data.frame(mat)).
o zip.file.extract() gains an optional 'dir' argument (but use
unzip() instead).
o source() with 'encoding' specified (and not as "unknown") marks
the encoding of character strings in Latin-1 and UTF-8
locales.
o parse(text=z) now marks the encoding of character strings in
Latin-1 and UTF-8 locales if 'z' is of known encoding (that is
all elements are either ASCII or marked as Latin-1 or UTF-8).
o sprintf() does stricter error checking on input formats to
avoid passing invalid formats to the OS (which have a tendency
to crash under such inputs).
o expand.grid() gains a 'stringsAsFactors' argument to ask for
automatic conversion of character vectors to factors (which
happened for many years but was not previously documented).
[This did not actually work prior to R 2.9.1.]
o bxp() now computes the 'ylim' including the outliers only if
'outline = TRUE'. (Wish of PR#13196)
o barplot() gains a 'args.legend' argument. (Wish of PR#13265).
o RweaveLatexSetup() now accepts all (and not just some) options
passed through from Sweave()
o cumsum(x) and cumprod(x) for double precision x now use a long
double accumulator where available and so more closely match
sum() and prod() in potentially being more accurate.
o plot() methods for "stepfun" (and hence "ecdf") gain an 'col'
argument, allowing to set all three colors simultaneously.
o Iterating over a factor in a for loop now coerces to a character
vector (rather than using the integer codes).
o data.frame() now recycles columns of list arguments, not just
vectors and factors.
o plot.ts(plot.type="multiple") now makes use of *.lab and
*.axis graphical parameters (wish of PR#13134 and 13135).
o Classes can be exported from a name space using the NAMESPACE
file directive 'exportClassPattern' which has the same syntax
as 'exportPattern'.
o strftime() now converts its first argument with as.POSIXlt()
and so is no longer an alias for format.POSIXLt.
o body<-() now treats list values consistently with other
types: they no longer need to be wrapped in a list() call.
o option("pdfbrowser") is now set on Windows as well as on Unix-alikes.
o object.size() now returns an object of class "object_size" and
has a print() method.
o [col/row]Sums(), *Means() now have an additional '...' argument,
so that they can more easily be turned into generic functions.
o Package 'tools' contains dependsOnPkgs() to compute reverse
dependencies.
o Strict type checking is now turned on: this catches more
internal corruptions, and some badly written contributed code.
o There are new functions in package 'tcltk', tk_choose.files(),
tk_choose.dir() and tk_messageBox(), analogues of functions
available on Windows (the last is an analogue of winDialog).
o Sys.glob() now does tilde expansion on all platforms.
o read.table() and friends gain a 'fileEncoding' argument to
make re-encoding of input just a little bit simpler.
o grep() gains an 'invert' argument mimicking 'grep -v/--invert'.
o strwrap() now allows a separate prefix for the first line.
o grep() has a more efficient sibling grepl() that returns a
logical vector.
o xfig() has new arguments 'defaultFont' and 'textSpecial'
contributed by Sebastian Fischmeister.
o parse() and parse_Rd() now point to syntax errors in the
reported error context, and include the filename and line and
column numbers so smart text editors can jump to the error
location.
o str(<1d-array>) now writes "[1:n(1d)]" instead of the previous
less clear "[, 1:n]".
o New function testInstalledPackage() in package 'tools' allows
the examples (and if they were installed) any package-specific
tests to be run on an installed package.
testInstalledPackages() can run all the examples and tests in
the standard and/or recommended packages. Also
testInstalledBasic() can run the basic tests (if installed).
o file.copy() now has a 'recursive' argument.
o Errors in setOldClass() will cause a previous definition to be restored.
o Ambiguities in class inheritance and method selection resulting
from duplicates in superclasses are now resolved by requiring
(if possible) consistency with all the superclass inheritance. The
rules for method selection have been revised to take advantage of
the improved ordering.
See ?Methods and the reference there related to inheritance.
o New function unzip() in package 'utils' to expand or list zip
archives.
o Replacement functions for class() and oldClass() will unset
the S4 bit when the replacement can't be an S4 object;
oldClass() will return the S3 class for S4 objects with slot
.S3Class.
o clip() takes extra steps to avoid the next graphics call
resetting the clip region.
o New function sample.int() to provide documented access to the
internal part of sample() (sampling from seq_len(n)).
o New version of withVisible() for better handling of cases like
withVisible(eval.parent(....)). Moved to package 'base' with a
view to replace .Internal(eval.with.vis) in source() later.
o showClass() which is also used to auto-print class definitions, now
mentions the package where the class comes from, if there is one.
o simulate(obj) now also works for "glm" objects and for weighted
fits, thanks in part to contributions from Ben Bolker and
Heather Turner. There is now a means to extend the methods
available for "glm" objects, as glm families can have an
optional 'simulate' component.
o S4 classes that inherit from any of the "structure" classes or
from "vector" will turn on methods for all the "Ops" group of
functions when the package containing the classes is
loaded. See class?structure.
o A mechanism now allows S4 classes to inherit from object types
"environment", "externalptr" and symbol ("name"). See ?setClass.
o demo() gains 'echo' and 'ask' arguments, with defaults similar
to example().
o library() no longer checks for the packages merged during the
re-organization of 1.9.0.
o New function poisson.test() in package 'stats' for exact test
of rates and rate ratios.
o New function isdebugged() indicates whether its argument has the
debug flag set or not.
o ls.str() [via print method] now also works when some objects in
the environment are missing().
o Subsetting S4-objects (without an explicit "[" method) no longer
preserves the class in cases like setClass("C",
contains="list"); This reverts a "bug fix" activated in R 2.8.0.
o .packages() and .find.packages() no longer check the package
info for installed packages with dumped metadata, since this
was checked when the package was installed. .packages() only
considers such packages to be validly installed (any others
were installed in a long-obsolete version of R). Both changes
speed up searches in libraries of thousands of packages.
o boxplot() uses butt line endings for its median line
(suggestion of Uwe Ligges, PR#13553).
o S4 objects passed to a non-default S3 method will be converted
to a valid S3 object with the S3 class. See the section on
inheriting from non-S4 classes in ?Classes.
o A new class "nonStructure" has been defined; classes that extend
a vector class but that should lose their slots under Math or
Ops functions should extend this class. See class?nonStructure.
o axis.POSIXct() now plots in the timezone marked for its inputs
(if any) rather than in the local time. The latter was a
deliberate choice, but is easy to select by removing the
'tzone' attribute. (Suggestion of Dan Kelley.)
o A new function classesToAM() returns an adjacency matrix
representing the inheritance of the classes specified. Allows
better human examination of the patterns, e.g. by using the
matrix as input to one of the graph packages (see the
documentation).
o X11options(antialias = "none") now works, for consistency with
X11().
o sprintf() now allows zero-length arguments (with a zero-length
result). (Suggestion of Bill Dunlap.)
o unlink() is now able to remove broken symbolic links on
Unix-alikes.
o New selectSuperClasses() utility in package 'methods'.
o HoltWinters() now allows parameters alpha and beta to be fixed
at 0 and hence beta = FALSE and gamma = FALSE are used to
specify restricted models.
o A new function smoothScatter() has been added to package
'graphics'. It is appropriate for very dense scatter plots
and uses density estimation and color to reflect density of
plotting.
DEPRECATED & DEFUNCT
o allGenerics() is defunct.
o Use of allocVector(CHARSXP ...) is defunct and gives an error.
o The compatibility define for graphics structure NewDevDesc in
GraphicsDevice.h has been removed.
o Support for versioned installs (R CMD INSTALL --with-package-versions
and install.packages(installWithVers = TRUE)) has been removed.
Packages installed with versioned names will be ignored.
o The numeric and power(0.5) forms of argument to make.link()
which were deprecated in 2.4.0 are now defunct: use power()
directly.
o Conversion to Sd and Ssgm by R CMD Rdconv is now defunct.
o Support for R --gui=gnome is now defunct (and package
gnomeGUI has been withdrwan as it used a long-obsolete version
of GNOME).
o R CMD SHLIB on Windows will call the first target (not 'all') in
Makevars[.win] in future versions: so make 'all' the first
target if you have any.
UTILITIES
o R CMD build now also uses a Makevars[.win] file for cleaning
up src/.
o R CMD Rd2dvi and R CMD check are now able to cope with Cyrillic
characters in UTF-8 if environment variable _R_CYRILLIC_TEX_
is set to a non-empty value and the latex system has suitable
fonts (thanks to a hint from Alexey Shipunov).
o New function rtags() in package 'utils' that provides etags-like
indexing capabilities for R code files.
New front-end script R CMD rtags provides an interface to the
rtags() function (see R CMD rtags --help for details).
o New environment variable R_TEXI2DVICMD to hold the path (if any)
to 'texi2dvi' found at configure time: this now provides the
default to option("texi2dvi").
o massage-Examples.pl has been replaced by the R function
tools:::massageExamples().
o R CMD REMOVE now uses remove.packages() and hence removes all
members of a bundle.
o R CMD SHLIB is now an R script and has a new option -n aka
--dry-run to show what commands would be run. The same code
is used on Unix and Windows.
o R CMD Rdconv has new options --package and --version to set the
corresponding fields in HTML conversion.
o R CMD check runs the package tests with a custom startup file,
currently containing 'options(useFancyQuotes = FALSE)'.
Those tests are run by an R script: using a tests/Makefile
(undocumented) no longer works.
o R CMD config now knows about DYLIB_EXT and SHLIB_EXT, for use
in configure files.
o R CMD BATCH has a new option --no-timing to suppress printing
out the session timing.
o R CMD Rd2dvi can now work on an installed package.
o R CMD check no longer loads package 'tcltk' when checking for
code problems, so more problems may be reported.
o For R CMD SHLIB on Windows the default 'all' target only makes
the DLL, and no longer call targets 'before' and 'after'.
Rd CONVERSION
o Rd files have an optional \Rdversion{} section, which if
missing defaults to 1.0. There is support for version 1.1, a
slightly modified version with the following changes:
- The warnings for \code{} inside example are suppressed.
- Whitespace between arguments in \item and \section is
accepted without a warning (see below).
- $ is treated literally in text, even for latex conversions.
- \ is only an escape before % { } \ .
- \R, \dots and \ldots can be followed by {}, and it is
recommended that they when not followed by whitespace.
- The obsolete interpretation of \Alpha etc is no longer done.
o Rd conversion now handles ^ ~ < > | correctly in non-code
environments (such as \samp), and # and _ even in latex
conversion (but $ still needs to be escaped in version 1.0).
o Whitespace between first and second arguments is now accepted
for \item and \section, e.g. \item{foo} {some value}.
Previously arguments after whitespace were silently ignored,
and a warning is given for version 1.0 files.
o The Rd files created by prompt() and friends are declared to be
version 1.1.
o \alias now supports the escaping of { as well as of %, and this
is recommended.
o parse_Rd(), an experimental parser for Rd files, and Rd2txt(),
Rd2HTML(), Rd2latex() and Rd2ex(), even more experimental
converters, have been added to package 'tools'.
o R CMD check runs the package's Rd files through parse_Rd() for a
stricter syntax check. This can be suppressed by setting
_R_CHECK_RD_PARSE_ to FALSE.
o Added markup \verb, which displays like \code, but parses as
verbatim text. Currently only supported by parse_Rd() and
Rd2HTML().
INSTALLATION
o The shell used by the 'R' script and other shell scripts
intended to be run directly can be specified at installation
time by setting the (precious) configure variable R_SHELL.
o libtool has been updated to 2.2.6a.
o --with-ICU is now the default: this means that ICU will be
used for collation on Mac OS >= 10.4.
o make install-tests can be used to install the test files,
to allowed an installed version of R to be tested -- see the
R-admin manual. This is also supported by the function
testInstalledPackages() in package 'tools'.
o 'make install' using a parallel make should now work.
o 'make check' now always re-makes and re-runs the package
examples, which are now collated in the locale's order (and
not ASCII order).
o configure will now set the default optimization level for
gfortran on x86_64 Linux to -O as -O2 has caused problems with
gfortran 4.3.x.
PACKAGE INSTALLATION
o install.packages() is able to infer that repos=NULL was
intended from the extension on the file name specified as 'pkgs'.
On Mac OS X it now supports local binary packages with .tar.gz
extension. Nonetheless .tgz remains the preferred extension
and is expected in repositories.
It now checks >= version dependencies for dependent packages,
and so will install a newer version of a dependency if needed
and available on the repositories.
The library being installed into is considered when looking
for installed packages if it is not already part of
.libPaths() (as INSTALL already does).
It has a new argument 'Ncpus' to support parallel installs of
source packages.
o HTML links will be resolved first to the standard packages: this
avoids other installed packages diverting help on e.g. qr()
and plot() to themselves. The HTML files are only "touched" if
they have changed.
o A check is done that the R files can be parsed: this both
prevents a broken package without lazy-loading from being
installed and gives better diagnostics.
o install.packages() gains a 'configure.vars' argument, and both
this and 'configure.args' get their defaults from options().
o There is a unified R script for INSTALL on both Unix-alike and
Windows that takes option names used by either in the past.
It adds --no-multiarch to disable building other than the main
sub-architecture, and allows multiple instances of
--configure-args and --configure-vars (which will be
concatenated).
New option --install-tests will install any package-specific
tests.
o Times in the Packaged: and Built: fields are now recorded in
UTC, and in most cases in ISO 8601 format.
C-LEVEL FACILITIES
o A helper function, asCharacterFactor, converts from factors to
character vectors.
BUG FIXES
o The postscript() output for setting text is faster and smaller.
o Subsetting a data frame with duplicate column names without
selecting columns (e.g. z[i,]) no longer makes the column
names unique. This was never documented, but some packages
have assumed it.
o data.frame() no longer ignores row names on objects if the
first name is empty. (PR#13230: this has been the behaviour
for a long time, but apparently undocumented.)
o deparse(control="S_compatible") now never uses backticks.
o X-spline drawing is improved for cases where the control
points are located well off the edges of the device.
The symptom of this problem is the error "reached MAXNUMPTS".
o exists() with mode= "any" will no longer run an active binding's
function.
o format(c(1 + 2i, NA)) no longer has extraneous space in " NA".
o mood.test() could fail in 2.8.x on large samples because of
integer overflow.
o heatmap() without a dendrogram could fail. (PR#13512)
o Checks for missing values will no longer occasionally result in
an infinite loop or stack overflow error, depending on the
compiler. Active bindings are now always considered to be
non-missing.
o Rd conversion was not accepting \p (as in \pkg} or (when using
Perl 5.10.x) \k (as in \kbd) in any preamble text in a
\value{} section, since those are nowadays interpreted by
Perl. (PR#13575)
o if(as.raw(1)) TRUE now works as expected. (PR#13630)
Also, c(as.raw(12), TRUE) or c(raw(3), pi) do.
o duplicated(<data frame>, incomparables = NA) now gives the
intended error message. (PR#13632)
o name handling of as.data.frame() has been sanitized somewhat
o Evaluating an assignment expression with a string on the left
hand side no longer destructively changes the string to a symbol
in the expression.
**************************************************
* *
* 2.8 SERIES NEWS *
* *
**************************************************
CHANGES IN R VERSION 2.8.1 patched
NEW FEATURES
o R CMD check has a new argument '--install-args' to pass
command-line arguments to INSTALL.
E.g. --install-args="--docs=normal" on Windows if the HTML
Help Workshop is not installed.
o R-Forge has been added to R_HOME/etc/repositories, so it will
be available interactively in setRepositories().
o The compiled loess() code has been updated to the current
version of dloess from Netlib. This includes patches from Ben
Tyner which correct some errors when degree = 0 and hence
solve PR#13570.
INSTALLATION
o --with-ICU is now supported (and recommended) on Mac OS X using
Apple's supplied port. Note however that the locale category
LC_COLLATE cannot be changed whilst R is running on Apple's
version of ICU.
Configure supports a wider range of ICU versions on other
OSes: version 3.0 should suffice, and 3.2, 3.8 and 4.0 have
been tested.
BUG FIXES
o grid-based plots no longer reset the base text size to the
default 96dpi in cairo-based bitmap devices.
o Rd conversion was incorrectly parsing \\\* and \\\{ (and other
cases with an odd number of backslashes greater than one).
Text conversion of \code{\ etc} was incorrect (a single
backslash stands for itself inside \code).
\code{} inside \examples{} is now fixed up (but the warning
remains, since it will be handled incorrectly in earlier
versions of R).
o as.matrix.data.frame() could fail if coercion changed the
dimension of one of the columns (as e.g. the coercion of a "Surv"
object to a character vector does).
o When extracting part of a complex list structure using [[]]
with a vector index, the extracted part was not marked for
duplication on change. (PR#13411)
o Assigning an additional element to a pairlist/language element
by x[["foo"]] <- value did not name the additional element.
o .Call() and .External() were not accepting "NativeSymbolInfo"
and "NativeSymbol" objects as claimed. (Patch from Olaf
Mersmann.)
o codoc() was missing some default value mismatches with
unescaped backslashes, e.g. final="\\" needs to be written as
final="\\\\" in the Rd file.
The reports on values now give strings in the original quoted
format (with \ and " escaped).
o The $<- method for pairlists (including language objects)
failed to duplicate if NAMED was 2.
o read.table(blank.lines.skip = FALSE) gave a final empty row on
files with less than 5 lines (PR#13433).
o Workaround for a bug in some versions of iconv that was seen
with output lines of more than 10,000 bytes and with
re-encoding requested on an output connection.
o The fullrefman.{dvi,pdf} duplicated part I in part II (at
least on some systems).
o cbind() could crash with a zero-length input and a list result.
o pdf(colormodel = "gray") was setting the stroke colour for fills.
o file.show() with multiple files would only show multiple
copies of the first one. (PR#13469)
o formatC(mode = "character") was documented to work, but
did not. (PR#13474)
o besselI(x,.., expon.scaled=TRUE) now gives accurate results for
x < 1e5 whereas it previously underflowed for x >~= 1500.
Further, besselJ(x,..) also computes up to 1e5 (instead of 1e4).
o str() was incorrectly warning about its option component
'formatNum' set by strOptions().
o nls(algorithm = "port") did not accept the [factor] notation.
(PR#13650)
o The relational (aka "comparison") operators are now binary, also in
a lower level sense, and an expression as "<"(1) is now erronous.
o The 'offset' argument for lm() and glm() is not longer
documented to be allowed to be of length 1: this has not been
true for a long time.
o format.info(x) is now also correct when x has no finite content.
o predict.lm() now works correctly when the fit had more than
one offset (possibly specified both in the formula and as an
argument). This function is called by predict.glm(), so the
same isses are corrected there.
o besselI(x, nu) with nu a negative integer (a singular case) is now
correct. (PR#13556)
CHANGES IN R VERSION 2.8.1
NEW FEATURES
o sum() now has a method for "difftime" objects (via the Summary
group).
max(), min() and range() applied to "difftime" object(s) now
return a result in the common units of the objects, if there
is one.
o installed.packages() is now tolerant of malformed DESCRIPTION
files in installed packages (it ignores them, with a warning).
o qt() now works for 0 < df < 1.
o For consistency with matrix() and array(), dimnames(x) <-
list() removes the dimnames (as assigning NULL would do).
It was previously an error.
o nlminb() copies names from 'start' to the parameter vector
used (for consistency with optim()).
o legend() gains a 'title.col' argument: the title colour was
previously set from the first element of 'text.col' (which
remains the default).
o In an Rd file, use of top-level \itemize{} inside a \value{}
block is unnecessary and almost always gave a faulty
conversion. Most cases are now detected and corrected, but
give a warning as such code will not work correctly in earlier
versins of R.
Also, use of \code{} inside a code block such as \examples{}
will give a erroneous conversion that is now detected and
warned against.
o Autoflushing of stdout is turned on when Rd processing, so
warnings/error are likely to appear in the right place in
redirected output (such as that from R CMD check).
UTILITIES
o R_PDFLATEXCMD is added to the environment variables set by
'R CMD' and is used by R CMD Rd2dvi.
R_LATEXCMD, R_PDFLATEXCMD, R_MAKEINDEXCMD and R_DVIPSCMD
default to 'latex', 'pdflatex', 'makeindex' and 'dvips'
respectively if no suitable executable was found at configure
time (since they might well be available at run time,
particularly for binary installations of R). This affects
R CMD Rd2dvi and help(offline=TRUE).
R CMD Rd2dvi now gives an explicit error message if latex (or
pdflatex) fails.
R CMD Rd2dvi gains a --no-index argument: processing some
special characters on PDF indices gave errors which used to be
ignored.
DEPRECATED & DEFUNCT
o R CMD INSTALL --with-package-versions is deprecated (and
support has always been incomplete on Windows).
So is install.packages(installWithVers = TRUE).
o Rd conversion to Sd and Ssgm is now deprecated as we no longer
have any means to check the results (and Sd is long obsolete).
BUG FIXES
o add1.glm() no longer warns if applied to a binomial glm with a
factor response.
o aggregate.data.frame() now does something sensible with a
zero-column 'x' rather than failing with an obscure error
message. It gives an explicit error message if called with a
zero-row 'x'.
o integrate() now accepts integer results from f(): as documented,
but only double was accepted.
o contrib.url() produced an incorrect URL for the type
"mac.binary".
o pairwise.wilcox.test() did not pass on the 'paired' argument
(caught by Matthias Kohl)
o bmp(), jpeg(), and png() on unix with type="cairo" would segfault
on closure if the output file could not be opened.
o tiff() on unix would not write the output file for the first page
when multiple pages were plotted.
o str(1 + structure(1, class = "test")) no longer recurses indefinitely.
o pf(x, .., ncp, lower.tail=FALSE, log=TRUE) is much more accurate
for large x now.
o dev2bitmap() failed in 2.8.0 if 'taa' and 'gaa' were both NA.
o Under rare circumstances equality tests for character strings
could fail to report equality in 2.8.0 in the same way as
2.7.2. (This needed a current encoding of Latin-1 or UTF-8,
one string whose encoding was marked as that encoding and one
that was marked as "unknown". In that circumstance the two
strings are not actually known to be equal, but earlier
versions of R assumed that "unknown" meant the current
encoding, and this is done once again.)
o R CMD config could echo messages from GNU make if called from
within a Makefile (as e.g. package Rcpp did), especially from
within a parallel make run.
o Rounding error could affect window(extend=TRUE) when applied
to monthly series. (PR#13272)
o Offline help on a Unix-alike now works even if options
"latexcmd" and "dvipscmd" contain spaces
(e.g. "dvips -Pmy_printer").
Informative error messages are given if running latex or dvips
fail.
o Using plot.lm() on a "glm" object since 2.7.1 with which=5
caused the Pearson rather than deviance residuals to be used
in which=2 or 3 (including in the default case). (Thanks to
Effie Greathouse and Greg Snow.)
plot.lm() did not report on omitting observations with
leverage one if they also had residual exactly zero. This was
seen in example(occupationalStatus).
o deparse(nlines=) no longer pads short results with blank
lines. (PR#13299)
o legend(xpd=) now restores 'xpd' correctly. (PR#12756)
o The "formula" method for lines() now works if 'subset' is
supplied and no 'data' argument (as that for points() did).
o Sweave() now takes the defaults for the options 'pdf.version'
and 'pdf.encoding' of its RweaveLatex driver from pdf.options().
o prettyNum(x, drop0trailing=TRUE) treated "1.1e20" as "1.1e2"
and hence str() did as well, in 2.8.0 only.
o dchisq(x, df, ncp) no longer hangs for large x and ncp > 0,
and is more accurate in some cases (PR#13309).
o installed.packages(lib.loc = D, priority="NA") now also works when
D contains a single package. (PR#13332)
o legend(...., merge=TRUE) now warns and has no effect in the
case where no line segments are drawn. (PR#13340)
o transform.data.frame() works better when two or more columns are
added.
o Deparsing argument lists with non-syntactic names (e.g. that for
transform()) now uses backticks rather than double quotes to
produce syntactically valid output.
o matrix() failed to check for 0-length 'dimnames': it now
treats them as NULL (as array did). (PR#13361)
o 0^NA is now NA, not Inf, consistent with x^NA, x != 1.
o anova.mlm() did not work if T had only one row (including
e.g. the case M = ~1).
o axis.POSIXct() mislabelled for some time ranges of a few hours
(reported by Martin Becker).
o mantelhaen.test() with 'exact=FALSE' was not respecting
'alternative'. It now does one-sided tests similarly to
prop.test().
o anova.mlm() had trouble with some designs where near-zero rows of
the tranformation matrix were not removed (caught by Nils Skutara).
o Rd conversion was handling expressions like
'\item{foo}{see \eqn{x}}' (with one argument to \eqn
immediately followed by a right brace) incorrectly, sometimes
giving a spurious warning about 'missing text'.
o R CMD INSTALL used the C locale to install the DESCRIPTION
file, and so escaped non-ASCII characters in packages with a
declared encoding of "latin1" or "UTF-8". (However, the
installed DESCRIPTION file was rarely used since the dumped
metadata are available.)
o xspline() now respects inline par settings.
It and grid.xspline() now handle the special case of only two
control points, and splines with control points that are
located well outside the device (e.g., a zoomed view of a
larger curve). (Both cases were giving the error "reached
MAXNUMPTS").
o In setClass("C", contains="list"); x <- new("C", 1:3), x[2:3] now
remains of class "C". So does rep(x, 2) or rep.int(x, 3).
[NOTE: This "feature" has been reverted for R 2.9.0, see above]
o median.default() now also works for "numeric"-like vectors.
o The pdf() device can now handle the case where an image uses a
very large number of colours with different levels of
semi-transparency (alpha-values). It used to segfault.
(Also PR#13264.)
o window() failed to apply a fuzz to 'start' or 'end' and so
sometimes warned incorrectly for time series with 'freq' not a
power of two (e.g. 12 or 24).
o unique.default() now preserves the "tzone" attribute on
"POSIXct" objects.
o If all the packages had dependency lists of equal lengths,
occasionally install.packages() would compute an incorrect
sort order.
o col(x, as.factor=TRUE) and row(x, as.factor=TRUE) would fail
if x had no column (row) names. It was documented
incorrectly, and now returns a matrix factor.
o setRepositories() failed if "pkgType" was set to
"mac.binary.leopard".
o formals<-() changed the body of the function if this was a
length-one list.
o body<-() failed if the function had no arguments. It now
warns if discarding elements from a 'value' of type "expression".
o qr.coef() failed in the complex case for non-square systems.
(PR#13305)
o plot.dendrogram(horizontal=TRUE) did not not plot 'edgetext'
at the correct locations. (PR#13313)
o The starting point for plot.acf(ci.type="ma") was lag 0 when it
should have been lag 1. (PR#13071)
o There was an obscure bug with srcrefs, which could put the
parser into a condition giving "Error: bad value" on any input
CHANGES IN R VERSION 2.8.0
SIGNIFICANT USER-VISIBLE CHANGES
o var(), cov(), cor(), sd() etc now by default (when 'use' is not
specified) return NA in many cases where they signalled an
error before.
NEW FEATURES
o abbreviate() gains an optional argument 'strict' allowing cheap
and fast strict abbrevation.
o The "lm" methods of add1(), anova() and drop1() warn if they are
mis-used on an essentially exact fit.
o as.array() is now generic, gains a '...' argument.
o New function as.hexmode() for converting integers in hex format.
format.hexmode() and as.character.hexmode() gain an 'upper.case'
argument.
o bitmap() and dev2bitmap() gain support for anti-aliasing.
The default type has been changed to 'png16m', which supports
anti-aliasing.
o Box.test() gains a 'fitdf' argument to adjust the degrees of
freedom if applied to residuals.
o browseURL() has a new argument 'encodeIfNeeded' to use
URLencode() in cases where it seems likely that would be
helpful. (Unfortunately, those are hard to guess.)
o by() gains a 'simplify' argument, passed to tapply().
o capabilities() gains a new argument "tiff" to report if tiff()
is operational.
o chol2inv() now treats <numeric(1)> as a [1 x 1]-matrix.
o cov() and cor() have the option 'use = "everything"' as default,
and so does var() with its default 'na.rm = FALSE'. This
returns NA instead of signalling an error for NA observations.
Another new option is 'use = "na.or.complete"' which is the default
for var(*, na.rm=FALSE).
var(double(0), na.rm= L) now returns NA instead of signalling an error,
for both L = TRUE or FALSE, as one consequence of these changes.
o data.matrix() now tries harder to convert non-numeric columns,
via as.numeric() or as(, "numeric").
o dev.interactive() is able to recognize the standard screen
devices if getOption("device") is a function (as well as by name).
o dev.new() gains a '...' argument which can be used to pass
named arguments which will be used if appropriate to the
device selected.
o dimnames(x) <- value extends 'value' if it a list and too
short, and 'x' is an array. This allows constructions such as
dimnames(x)[[1]] <- 1:3 to work whether or not 'x' already has
dimnames.
o format(), formatC() and prettyNum() gain a new argument
'drop0trailing' which can be used to suppress trailing "0"s.
o format() now works for environments; also print(env) and str(env)
share the same code for environments.
o It is now possible to create and open a text-mode gzfile()
connection by explicitly using e.g. open="rt".
o New help.request() function for compiling an e-mail to R-help
according to "the rules". It is built on the new utility,
create.post() on which also bug.report() is based now; both
thanks to a contribution by Heather Turner.
o help.search() now assumes that non-ASCII items are in latin1
if that makes sense (all known examples on CRAN are).
o HoltWinters() and decompose() use a (statistically) more
efficient computation for seasonal fits (they used to waste
one period).
o intToUtf8() and intToBits() now accept numeric vectors,
truncating them to integers.
o is.unsorted() gains an argument 'strictly'. It now works for
classed objects with a >= or > method (as incorrectly
documented earlier).
o library() no longer warns about the masking objects that are
identical(.,.) to those they mask.
o lockBinding(), unlockBinding(), lockEnvironment() and
makeActiveBinding() now all return invisibly (they always
return NULL).
o mood.test() now behaves better in the presence of ties.
o na.action() now works on fits of classes "lm", "glm", ....
o optim(.., method="SANN", .., trace=TRUE) is now customizable via
the 'REPORT' control argument, thanks to code proposals by
Thomas Petzoldt.
o The 'factory-fresh' defaults for options("device") have been
changed to refer to the devices as functions in the grDevices
namespace and not as names. This makes it more likely that
the incorrect (since R 2.5.0) assumption in packages that
get(getOption("device"))() will work will catch users of those
packages.
o pch=16 now has no border (for consistency with 15, 17, 18) and
hence is now different from pch=19.
o pdf() has new arguments 'useDingbats' (set this to FALSE for use
with broken viewers) and 'colormodel'. It now only references
the ZapfDingbats font if it is used (for small opaque circles).
The default PDF version is now 1.4, since viewers that do not
accept that are now rare.
Different viewers were rendering consecutive text() calls on a
pdf() device in different ways where translucency was
involved. The PDF generated has been changed to force each
call to be rendered separately (which is the way xpdf or
ghostscript was rendering, but Acrobat was forming a
transparency group), which is consistent with other graphics
devices supporting semi-transparency.
o plot.dendrogram() has new arguments (xlim, ylim) which allows
zooming into a hiearchical clustering dendrogram.
o plot.ecdf() now defaults to pch=19 so as to better convey the
left-closed line segments.
o plot.histogram() gains an 'ann' argument. (Wish from Ben Bolker.)
o plot(<lm_obj>) now warns when it omits points with leverage one
from a plot.
o Plotmath now recognizes 'aleph' and 'nabla' (the Adobe Symbol
'gradient' glyph) as symbol names.
o polyroot() no longer has a maximum degree.
o The alpha/alphamax argument of the 'nls' and 'mle' profile()
methods is used to compute confidence limits for univariate
t-statistics rather than a confidence region for all the
parameters (and not just those being profiled).
o quantile.default() allows 'probs' to stray just beyond [0, 1],
to allow for computed values.
o New functions rawConnection() and rawConnectionValue() allow
raw vectors to be treated as connections.
o read.dcf() now consistently gives an error for malformed DCF.
o read.fwf() no longer passes its default for 'as.is' to
read.table(): this allows the latter's default to be used.
o readBin(), writeBin(), readChar() and writeChar() now open a
connection which was not already open in an appropriate binary
mode rather than the default mode.
readLines(), cat() and sink() now open a connection which was
not already open in an appropriate text mode rather than the
default mode.
o readCitationFile() (and hence citation) now reads a package's
CITATION file in the package's declared encoding (if there is one).
o The behaviour of readLines() for incomplete final lines on
binary-mode connections has been changed to be like blocking
rather than non-blocking text-mode connections.
o A new reorder.character() method has been added. This allows
use of 'reorder(x, ...)' as a shorthand for
'reorder(factor(x), ...)' when 'x' is a character vector.
o round() now computes in long doubles where possible so the
results are more likely to be correct to representation error.
o rug() now uses axis()'s new arguments from 2.7.2, hence no
longer draws an axis line.
o save() (optionally, but by default) checks for the existence
of objects before opening the file/connection (wish of
PR#12543).
o segments(), arrows() and rect() allow zero-length
coordinates. (Wish of PR#11192)
o set.seed(kind=NULL) now takes 'kind' from a saved seed if the
workspace has been restored or .Random.seed has been set in
some other way. Previously it took the 'currently used' value,
which was "default" unless random numbers had been used in
the current session. Similarly for the values reported by
RNGkind(). (Related to PR#12567.)
set.seed() gains a 'normal.kind' argument.
o setEPS() and setPS() gain '...' to allow other arguments to be
passed to ps.options(), including overriding 'width' and 'height'.
o setTimeLimit() function to set limits on the CPU
and/or elapsed time for each top-level computation, and
setSessionLimit() to set limits for the rest of the session.
o splinefun() has a new method = "monoH.FC" for monotone Hermite
spline interpolation.
o sprintf() optionally supports the %a/%A notation of C99 (if the
platform does, including under Windows).
o str()'s default method gains a 'formatNum' function argument which
is used for formatting numeric vectors. Note that this is very
slightly not backward compatible.
o The summary() method for class "ecdf" now uses a print()
method rather than printing directly.
o summary.manova() uses a stabler computation of the test
statistics, and gains a 'tol' argument to allow highly
correlated responses to be explored (with probable loss of
accuracy). Similar changes have been made to anova.mlm() and
anova.mlmlist().
o Sweave() now writes concordance information inside a
\Sconcordance LaTeX macro, which allows it to be inserted into
PDF output.
o system.time() now uses lazy evaluation rather than
eval/substitute, which results in more natural scoping. (PR#11169)
o In table(), 'exclude=NULL' now does something also for factor
arguments. A new 'useNA' argument allows you to control
whether to add NA levels unconditionally or only when present
in data. A new convenience function addNA() gives similar
functionality by adding NA levels to individual factors.
o unlink() tries the literal pattern if it does not match with
wildcards interpreted -- this helps with e.g. unlink("a[b")
which previously needed to be unlink("a\\[b").
o update.packages() gains an argument 'oldPkgs', where
new.packages() and old.packages() get 'instPkgs'. These allow
consideration of only subsets of packages instead of all
installed ones.
o which(b) is somewhat faster now, notably for named vectors, thanks
to a suggestion by Henrik Bengtsson.
o New generic function xtfrm() as an auxiliary helper for
sort(), order() and rank(). This should return a numeric
vector that sorts in the same way as its input. The default
method supports any class with ==, > and is.na() methods but
specific methods can be much faster.
As a side-effect, rank() will now work better on classed
objects, although possibly rather slowly.
o X11() and capabilities("X11") now catch some X11 I/O errors that
previously terminated R. These were rare and have only be
seen with a misconfigured X11 setup on some versions of X11.
o The handling of nuls in character strings has been changed --
they are no longer allowed, and attempting to create such a
string now gives a truncation warning (unless
options("warnEscapes") is false).
o The user environment and profile files can now be specified via
environment variables 'R_ENVIRON_USER' and 'R_PROFILE_USER',
respectively.
o ?pkg::topic and ?pkg:::topic now find help on 'topic' from
package 'pkg' (and not help on :: or :::).
o ??topic now does help.search("topic"); variations such as
??pkg::topic or field??topic are also supported.
o There is support for using ICU (International Components for
Unicode) for collation, enabled by configure option --with-ICU
on a Unix-alike and by a setting in MkRules on Windows.
Function icuSetCollate() allows the collation rules (including
the locale) to be tuned.
o If S4 method dispatch is on and S4 objects are found as
attributes, show() rather than print() is used to print the
S4 attributes.
o Starting package tcltk without access to Tk (e.g. no available
display) is now a warning rather than an error, as Tcl
will still be usable. (On most platforms it was possible to
inhibit Tk by not having DISPLAY set, but not on Windows nor
Mac OS X builds with --with-aqua.)
o Using $ on a non-subsettable object (such as a function) is
now an error (rather than returning NULL).
o Hexadecimal numerical constants (such as 0xab.cdp+12) may now
contain a decimal point.
o PCRE has been updated to version 7.8 (mainly bug fixes).
NEW FEATURES IN PACKAGE 'methods'
o S3 classes that are registered by a call to setOldClass() now
have the S3 class as a special slot, and therefore so do
any S4 classes that contain them. This mechanism is used to
support S4 classes that extend S3 classes, to the extent
possible. See ?Classes, ?setOldClass, and ?S3Class.
The treatment of special pseudo-classes "matrix", "array", and
"ts" as S4 classes has also been modified to be more
consistent and, within limitations imposed by special
treatment of these objects in the base code, to allow other
classes to contain them. See class?ts.
A general feature added to implement "ts" and also
"data.frame" as S4 classes is that an S4 class definition can
be supplied to setOldClass() when the S3 class has known
attributes of known class.
setOldClass() now saves all the S3 inheritance, allowing the
calls to be built up in stages, rather than including all the
S3 classes in each call. Also allows as(x,"S3") to generate
valid S3 inheritance from the stored definition. See ?S3.
o S4 methods may now be defined corresponding to "...", by
creating a generic function that has "..." as its signature.
A method will be selected and called if all the arguments
matching "..." are from this class or a subclass. See ?dotsMethods.
o New functions S3Part() and S3Class() provide access to the
corresponding S3 object and class for S4 classes that extend
either an S3 class or a basic R object type.
o show(<class definition>) now also shows the class name.
INSTALLATION
o If sub-architectures are used, a copy of Rscript is installed
in ${R_HOME}/bin/exec${R_ARCH} (since that in ${R_HOME}/bin
and /usr/bin might be overwritten in a subsequent installation).
PACKAGE INSTALLATION
o LazyLoad: yes is now the default, so packages wanting to avoid
lazy loading must set 'LazyLoad: no' (or an equivalent value) in
the DESCRIPTION file.
o R CMD INSTALL will now fail if it finds a non-executable
'configure' script in the package -- this usually indicates a
file system with insufficient permissions. If a
non-executable 'cleanup' script is found and either
--clean or --preclean is used, a warning is given.
DEPRECATED & DEFUNCT
o Use in packages of the graphics headers Rdevices.h and
Rgraphics.h is defunct: they are no longer installed.
o options("par.ask.default") is defunct in favour of
"device.ask.default".
o The 'device-independent' family "symbol" is defunct: use
font=5 (base) or fontface=5 (grid) instead.
o gammaCody() is defunct.
o par("gamma") is defunct.
o 'methods' package functions getAccess(), getAllMethods(),
getClassName(), getClassPackage(), getExtends(),
getProperties(), getPrototype(), getSubclasses, getVirtual(),
mlistMetaName(), removeMethodsObject() and seemsS4Object() are
defunct.
o Use of a non-integer .Random.seed is now an error. (R itself
has never generated such values, but user code has, and
R >= 2.6.0 has given a warning.)
o methods::allGenerics() is deprecated.
o In package installation, SaveImage: yes is now ignored, and
any use of the field will give a warning.
o unserialize() no longer accepts character strings as input.
o The C macro 'allocString' has been removed -- use 'mkChar' and
variants.
o Use of allocVector(CHARSXP ...) is deprecated and gives a warning.
UTILITIES
o The default for 'stylepath' in Sweave's (default) RweaveLatex
driver is now FALSE rather than TRUE if
SWEAVE_STYLEPATH_DEFAULT is unset : see ?RweaveLatex.
To support this, tools::texi2dvi adds the R 'texmf' directory
to the input search path.
o R CMD Rd2dvi now previews PDF output (as was documented) if
R_PDFVIEWER is set (as it will normally be on a Unix-alike but
not on Windows, where the file association is used by default).
o R CMD check checks for binary executable files (which should not
appear in a source package), using a suitable 'file' if
available, else by name.
o R CMD check now also uses codetools' checks on the body of S4
methods.
C-LEVEL FACILITIES
o R_ReadConsole will now be called with a buffer size of 4096
bytes (rather than 1024): maintainers of alternative
front-ends should check that they do not have a smaller limit.
o Graphics structure NewDevDesc has been renamed to DevDesc.
For now there is a compatibility define in GraphicsDevice.h,
but it will be removed in R 2.9.0.
o PROTECT and UNPROTECT macros now work even with R_NO_REMAP.
BUG FIXES
o @ now gives an error (and not just a warning) if it is being
applied to a non-S4 object.
o R CMD appends (not prepends) R's texmf path to TEXINPUTS.
o Objects generated by new() from S4 classes should now all
satisfy isS4(object). Previously, prototypes not of object
type S4 would not be S4 objects. new() applied to basic,
non-S4 classes still will (and should) return non-S4 objects.
o Functions writing to connections such as writeLines(),
writeBin(), writeChar(), save(), dput() and dump() now check
more carefully that the connections are opened for writing,
including connections that they open themselves.
Similarly functions which read such as readLines(), scan(),
dcf() and parse() check connections for being open for reading.
o Equality comparison of factors with <NA> levels now works
correctly again.
o Repainting of open X11 View() windows is now done whilst an
X11 dataentry window is in use.
o Indexing of data frames with NA column names and a numeric or
logical column index works again even if columns with NA names
are selected.
o on.exit() has been fixed to use lexical scope in determining
where to evaluate the exit action when the on.exit expression
appears in a function argument.
o rank() now consistently returns a double result for
ties.method = "average" and an integer result otherwise.
Previously the storage mode depended on 'na.last' and if any
NAs were present.
o The "lm" methods of add1(), and drop1() now also work on a model
fit with na.action = na.exclude.
o median(c(x = NA_real_)) no longer has spurious names().
o isoreg(x, y) now returns the correct result also when x has ties,
in all cases.
o What na.action() does is now correctly documented.
o source() with echo=TRUE now behaves like ordinary automatic
printing, by using methods::show() for S4 objects.
o Several bugs fixed in `?` with topics: it previously died trying
to construct some error messages; for S4 methods, class "ANY"
should be used for omitted arguments and default methods.
o trace() should create missing traceable classes in the global
environment, not in baseenv() where other classes will not be
found.
o Class inheritance using explicit coerce= methods via setIs()
failed to coerce the argument in method dispatch. With this
fixed, a mechanism was needed to prohibit such inheritance
when it would break the generic function (e.g.,
initialize). See ?setIs and ?setGeneric.
o RSiteSearch() encodes its query (it seems this is occasionally
needed on some platforms, but encoding other fields is harmful).
o 'incomparables' in match() was looking up indices in the wrong
table.
o write.dcf() did not escape "." according to Debian policy
(PR#12816).
o col2rgb() sometimes opened a graphics device unnecessarily, and
col2rgb(NA) did not return a transparent color, as documented.
o pdf(family="Japan") [and other CIDfonts] no longer seg.faults
when writing "western" text strings.
o as.list() applied to an environment now forces promises and
returns values.
o Promises capturing calls to sys.parent() and friends did not
work properly when evaluated via method dispatch for internal
S3 generics.
o The default "pkgType" option for non-CRAN builds of R on Mac OS X
is now correctly "source" as documented.
o The default R_LIBS_USER path in AQUA builds now matches the
Mac-specifc path used by the Mac GUI: ~/Library/R/x.y/library
o splinefun() with natural splines incorrectly evaluated derivatives
to the left of the first knot. (PR#13132, fix thanks to
Berwin Turlach)
o anova(glm(..., y=FALSE)) now works. (PR#13098)
o cut.Date(x, "weeks") could fail if x has only one unique value
which fell on a week boundary. (PR#13159)
**************************************************
* *
* 2.7 SERIES NEWS *
* *
**************************************************
CHANGES IN R VERSION 2.7.2 patched
BUG FIXES
o within(<dataframe>, { ... }) now also works when '...' removes
more than one column.
o Attempting to open an X11() device on a non-existent display
when one is already open on another display now gives a
warning rather than terminating R via a fatal X11 error.
(PR#12628)
o source() did not respect the setting of options("keep.source")
when setting source references.
o seek() now clears the pushback on a text-mode connection if
used to set a new position. (PR#12640)
o quartz() would segfault if asked to create a file for bitmap
output which could not be created. This applied also to the
type="quartz" versions of bmp(), jpeg(), png() and tiff().
o dnbinom(0, size, mu = <large>) suffered from cancellation in 2.7.2
only.
CHANGES IN R VERSION 2.7.2
NEW FEATURES
o sprintf() returns elements of the result in UTF-8 when the
format or any character input has a corresponding element
declared as UTF-8. Similarly for paste(), elements of the
result are in UTF-8 when any input to that element is declared
as UTF-8.
o axis() has new arguments 'col.ticks' and 'lwd.ticks' to allow
the colour and line width of ticks to be set separately from
that of the line (e.g. to set one or the other to transparent
or zero width).
o legend() has a new argument 'box.col' to set the colour of the
enclosing box.
o legend() gains a 'xpd' argument to make it easier to place a
legend in the margins or outer margins.
o stripchart() now passes '...' to title() (as well as to
plot.default() and axis()). (Wish of PR#12202)
o help.search() has new argument 'searchEngine' to go directly
to the search form: this is needed by users of Firefox 3.0.x,
for x <= 6, to workaround a bug in interpreting the search
results pages.
BUG FIXES
o Plotmath computed the glyph metrics for the wrong character (and
perhaps for a non-existent one) if this was a single-byte
character with the top bit set. An example was symbol("\300").
o sink() and cat() could divert output to a non-writable connection.
o phyper(x, 0,0,0) no longer hangs for huge x and gives 1 for x >= 0.
(PR#11813)
o plnorm(x, ..., log.p=TRUE) is now correct for x <= 0. (PR#11867)
o <data.frame>[, ch] gives an error (again!) when ch is a string not
exactly matching the column names, thanks to an oral bug report by
Matthew Dowle.
o data.frame(x=1:2, y=3:4, row.names=c("a","NA"))[c(2,NA),] has
correct row names c("NA","NA.1") again.
o The GUI data editor for dataframes did not handle escape
characters in entries properly. (PR#11897)
o PCRE has been updated to 7.7 (bugfix release).
o package.skeleton() wrongly warned about invalid code_files names
when these were not in the current directory.
o shapiro.test(c(0,0,1)) now has P value >= 0 (instead of barely
negative).
o assign() now warns if given a character vector of length > 1,
rather than silently taking the first element.
o rcond(<exactly singular matrix>) now gives 0 instead of an error.
o There was a memory leak in C function ucstoutf8 used by some
graphics devices.
o Plots of profile.mle() objects (package 'stats4') were
misbehaving when the 'which' argument had been used in their
calculation.
o dnbinom(x, size, mu=*, ..) is now more accurate for very large
'size'. The same applies to pnbinom() and rnbinom().
o axis() was ignoring par() mgp[3] if mgp was set in-line.
o Closing an X11 View() or dataentry window via its frame's
close control now works better on some window managers.
o Calling lapply() was not handling method dispatch correctly for
is.numeric(), is.matrix(), is.array(), log() and the Math2
group. This affected data.matrix() which incorrectly regarded
"Date" and "POSIXct" objects as numeric, and has been adjusted
to do so as exceptions.
o package.skeleton() was not looking for non-function objects in
its 'environment' argument.
o nls() was only finding its 'weights' argument in the case when
all the variables in the formula were of the same length and
hence that model.frame() could be used.
It was silently ignoring 'subset' and 'na.action' except in
that case. Now they are ignored only if 'data' is a list and
variables taken from 'data' are not all of the same length,
in which case a warning is given.
o The 'mle' confint() method now takes 'level' into account when
setting 'alpha' for the profile.
o within() was not handling correctly expressions that produced
NULL columns. (PR#11131)
o dev.print() and dev.copy2{eps,pdf}() now ensure that the current
device is restored as the active device even if an error
occurs. (PR#9801)
o as.Date() could fail to convert character strings representing
days on which midnight did not exist in the current timezone
(as happened in parts of Africa on 1960-01-01).
o The automatic placement of legend() with 'title' and a
reversed 'x' axis was incorrect. (PR#12019)
o The use of multiple packages in 'LinkingTo' works again, and
now works when the dependent packages are in the library to be
installed to (but not in the library path seen by R --vanilla).
o bxp() (and hence boxplot) now respects in-line graphical
parameters 'xaxp'/'yaxp' as appropriate. (PR#11463)
o barplot(log = "y") failed if there were NAs in the 'height'
argument. (PR#11585)
o pbeta() is more accurate in some cases with extreme values of
'ncp'. (PR#11277).
o edit.data.frame() no longer fails if called on a 0-column
data frame and no column is created.
o pchisq(x, df=0) was always one even for x < 0; similarly for
pgamma(x, alpha=0).
o add1() and drop1() now return a P-value of NaN in cases with
df=0 for test="Chisq" (they gave NaN until pchisq was altered
in R 2.6.2).
o The default methods of drop1() and add1() now re-evaluate in the
object's formula environment, rather than simply in the parent
(informal bug report by Werner Stahel).
o The undocumented limit of 8191 bytes on comments (from # to
the end of the line) in R code has been removed.
o qgamma() warns if used with shape < 1e-10, when it may be
unreliable. (PR#12324)
o Installing a source package was not using the package's declared
encoding (if any) as a default encoding for the help.search()
database in Meta/hsearch.rds. This could cause packages with
a default encoding to have some of their entries rejected by
help.search() in a multi-byte locale (such as a UTF-8 locale).
o duplicated() and unique() now handle 'incomparables' better,
and avoid occasional segfaults (PR#12551).
o plot(isoreg(x, y)) now plots the points correctly when 'x'
is unssorted.
o data.frame(row.names=NULL) once again behaves differently from
the default (as documented).
CHANGES IN R VERSION 2.7.1
NEW FEATURES
o tools::texi2dvi() has a new argument 'texinputs' to allow the
TeX and bibtex input paths to be specified (even on MiKTeX).
o dev.copy2pdf() gains an 'out.type' argument to allow it to be
used with cairo_pdf() or quartz(type = "pdf").
o poly() has additional checks against user error (as in PR#11243).
o The Mac OS quartz() device draws contiguous lines much faster.
o A field containing just a sign is no longer regarded as numeric
(it was on all platforms in 2.7.0, but not on most in earlier
versions of R). Similarly, '.' is now always non-numeric.
o CITATION files are now read in Latin-1: quite a few were
failing if used in a multibyte locale such as UTF-8.
o The DESCRIPTION file of a package can specify an 'OS_type' field
as either 'unix' or 'windows' to confine installation to that
OS type.
o HoltWinters() now uses optimize() rather than optim for
one-parameter problems which should be more reliable (PR#11469).
o axis() now respects the setting of par("xpd") when clipping.
o The 'factor' method of format() now preserves names, dims and
dimnames in the same way as for character and numeric inputs.
(PR#11512)
o read.DIF(*, transpose=TRUE) now allows to correctly read DIF files
produced by some versions of Excel.
DEPRECATED & DEFUNCT
o The use of unserialize() on character strings is deprecated:
that was a format used in R < 2.4.0.
o The use of embedded nuls in character strings is deprecated:
They will no longer be allowed in R 2.8.0.
UTILITIES
o R CMD check checks for possible check directories in the
sources -- in mid-2008 there were about 20 examples on CRAN.
o R CMD build tries harder to clean up the inst/doc directory
from the remnants of earlier builds.
It also removes any directories with extension .Rcheck, and
files .DS_Store and ._* (created by tar on Mac OS X under some
circumstances: it now sets environment variables to ask for
such files not to be created by that tar.)
BUG FIXES
o Encoding<- on NA_character_ converted it to "NA".
o Adobe Symbol was missing from the encodings in
tools::charset_to_Unicode.
o diag(matrix(x, 0, 0)) now returns a 0-length vector of the
correct mode, instead of always numeric.
o The parser sometimes accepted invalid quoted strings in a UTF-8
locale.
o plot.default(x, y) now dispatches to Axis() methods whether
y is NULL or not.
o On Mac OS X, the Cocoa Quartz window could close without warning
under certain circumstances (specific autorelease pool flush).
o Plotting symbols with separate border and fill colours (e.g.,
plot(pch = 21)) now works with transparent 'col', but opaque
or semi-transparent 'bg'. Previously, if 'col' was
transparent then 'bg' was ignored and nothing was drawn.
o file.path() did not work correctly in 2.7.0 if the components
had different encodings.
o merge() failed if there were no common columns and one of the
inputs had zero rows.
o expand.grid() failed if an input had length 0.
o match() does again truncate strings at embedded nuls (as newly
documented in 2.7.0).
o Because of a typo, 'pointsize' in png(type="cairo") (and jpeg,
bmp, tiff) devices was being interpreted in pixels not bigpoints.
o is() was wrong for some S3 class objects with class of length
greater than one.
o undoc() / codoc() were not checking all S4 methods in some cases.
o Use of textConnection(NULL, mode="w") could segfault.
o Use of strwidth/height(units="user") (the default) is again an
error before a user coordinate system has been set on the
device, rather than giving nonsensical values (the effect of
r31367).
o Rare string width calculations in package grid were not
interpreting the string encoding correctly.
o hasMethods(f, env) {without specified 'package'} now works better.
o A missing PROTECT could cause segfaults on string
comparisons. (PR#11421)
o str(structure(1, classID = "Pooh")) now works fine.
o A missing PROTECT could cause segfaults in if() if coercion of
the condition was required or a warning was to be given.
o plot(<table>) now uses a sensible default main title.
o validObject() called with complete=TRUE did not use inherited
validity methods for slot classes.
o Several bugs fixed in as(): the initial method lookup was not
using the table with inherited methods (so inheritance had to
be recomputed each time); coerce() should not be called
directly--it can insert invalid inherited methods; the
constructed as() methods were not retaining the function's
environment.
o influence.measures(<glm-object>) now computes the same
Cook's distance approximations as cooks.distance().
o plot(<glm>, which=5) uses more correct Cook's distance contours;
(fix to fix to PR#9316).
o pdf() and postscript() were not working correctly in 2.7.0 with
UTF-8 encoded data in a non-UTF-8 MBCS (e.g. EUC-JP on Unix,
CJK locales on Windows).
o conformMethod(), called by setMethod(), now checks better about
argument names in wrong order. Whereas it only warns currently,
it is planned to become an error in the future.
o The predict() method for prcomp() had an incorrect check for
the number of columns of 'newdata' if the columns were not named.
o The axis() function now distinguishes between setting "at" to
NULL or a zero-length vector, treating the latter as a request
for no ticks. This corrects the handling of the "x" parameter
to rug().
o glob2rx("*[*") now produces a correct regular expression.
o The canvas is no longer painted on copy or save in Cocoa Quartz.
o identify() in Quartz can now be terminated by either using popup
menu equivalent (Ctrl-click or second mouse button) or by pressing
the <Esc> key. The latter was documented but did not work.
o tools:::.check_package_depends() {called from 'R CMD check'} now
also works correctly when directory-name != package-name.
o Source references were sometimes off by a line.
o The quartz() parameter 'antialias' is no longer ignored.
o The Quartz device is now trying hard to remove anti-aliasing
effects for rasterized backends in plots that use adjacent,
borderless rectangles such as image().
o The srcfilecopy() function now adds a timestamp to the object it
creates.
o parse() would lose a token when run on stdin().
o socketConnection() was using internally the class "socket"
and not "sockconn", which caused a conflict with make.socket().
(PR#11515)
o Quartz is now trying harder to find the proper font for a given
family which resolves font issues on Mac OS X 10.4. Full font
names and PostScript names can be used interchangeably. (Note,
however that italic/oblique font faces of Helvetica are not
included in the Mac OS X 10.4 system).
o qf() no longer gives NaN when one of df1 and df2 is large and
the other is infinite (including if both are infinite); it is more
accurate e.g. for qf(1e-18, 2,4).
o qbeta(-1e10, 50, 40, log.p=TRUE) no longer hangs.
o Cocoa Quartz backend autodetection of display DPI was not
correct for screens rotated by 90 or 270 degrees.
o selectMethod("coerce", .) now uses a correct default for
'useInherited', and hence no longer may mess up the method cache.
o show() now also works on "unregistered" S3 class objects.
o formatC(*, format="fg", flag="#") is no longer dropping trailing
zeros.
o read.table(file = stdin()) with invalid input could leave the
connection in an invalid state and hence cause a later
segfault. (PR#11627)
o read.DIF() did not obey the default 'stringsAsFactors = TRUE'.
o The 'noquote' method for c() now works correctly with three or
more arguments.
o symbol() in plotmath expressions works again with non-ASCII
input on devices that use UTF-8 for the symbol font.
CHANGES IN R VERSION 2.7.0
SIGNIFICANT USER-VISIBLE CHANGES
o The default graphics device in non-interactive use is now
pdf() rather than postscript(). [PDF viewers are now
more widely available than PostScript viewers.]
The default width and height for pdf() and bitmap() have been
changed to 7 (inches) to match the screen devices.
o Most users of the X11() device will see a new device that has
different fonts, anti-aliasing of lines and fonts and
supports semi-transparent colours.
o Considerable efforts have been made to make the default output
from graphics devices as similar as possible (and in
particular close to that from postscript/pdf). Many devices
were misinterpreting 'pointsize' in some way, for example as
being in device units (pixels) rather than in points.
o Packages which include graphics devices need to be re-installed
for this version of R, with recently updated versions.
NEW FEATURES
o The apse code used by agrep() has been updated to version
0.16, with various bug fixes.
agrep() now supports multibyte character sets.
o any() and all() avoid coercing zero-length arguments (which
used a surprising amount of memory) since they cannot affect
the answer.
Coercion of other than integer arguments now gives a warning
as this is often a mistake (e.g. writing all(pr) > 0 instead
of all(pr > 0) ).
o as.Date(), as.POSIXct() and as.POSIXlt() now convert numeric
arguments (days or seconds since some epoch) provided the
'origin' argument is specified.
o New function as.octmode() to create objects such as file
permissions.
o as.POSIXlt() is now generic, and it and as.POSIXct() gain a
'...' argument. The character/factor methods now accept a
'format' argument (analogous to that for as.Date).
o New function browseVignettes() lists available vignettes in an
HTML browser with links to PDF, Rnw, and R files.
o There are new capabilities "aqua" (for the AQUA GUI and quartz()
device on Mac OS X) and "cairo" (for cairo-based graphics
devices).
o New function checkNEWS() in package 'tools' that detects common
errors in NEWS file formatting.
o deparse() gains a new argument 'nlines' to limit the number of
lines of output, and this is used internally to make several
functions more efficient.
o deriv() now knows the derivatives of digamma(x), trigamma(x)
and psigamma(x, deriv) (wrt to x).
o dir.create() has a new argument 'mode', used on Unix-alikes
(only) to set the permissions on the created directory.
o Where an array is dropped to a length-one vector by drop() or
[, drop = TRUE], the result now has names if exactly one of
the dimensions was named. (This is compatible with S.)
Previously there were no names.
o The 'incomparables' argument to duplicated(), unique() and
match() is now implemented, and passed to match() from merge().
o dyn.load() gains a 'DLLpath' argument to specify the path for
dependent DLLs: currently only used on Windows.
o The spreadsheet edit() methods (and used by fix()) for data
frames and matrices now warn when classes are discarded.
When editing a data frame, columns of unknown type (that is
not numeric, logical, character or factor) are now converted
to character (instead of numeric).
o file.create() has a new argument 'showWarnings' (default TRUE)
to show an informative warning when creation fails, and
dir.create() warns under more error conditions.
o New higher-order functions Find(), Negate() and Position().
o [dpqr]gamma(*, shape = 0) now work as limits of 'shape -> 0',
corresponding to the point distribution with all mass at 0.
o An informative warning (in addition to the error message) will
be given when the basic, extended or perl mode of grep(),
strsplit() and friends fails to compile the pattern.
o More study is done of perl=TRUE patterns in grep() and friends
when length(x) > 10: this should improve performance on long
vectors.
o grep(), strsplit() and friends with fixed=TRUE or perl=TRUE
work in UTF-8 and preserve the UTF-8 encoding for UTF-8 inputs
where supported.
o help.search() now builds the database about 3x times faster.
o iconv() now accepts "UTF8" on all platforms (many did, but not
e.g. libiconv as used on Windows).
o identity() convenience function to be used for programming.
o In addition to warning when 'pkgs' is not found,
install.packages() now reports if it finds a valid package
with only a case mismatch in the name.
o intToUtf8() now marks the Encoding of its output.
o The function is() now works with S3 inheritance; that is, with
objects having multiple strings in the class attribute.
o Extensions to condition number computation for matrices, notably
complex ones are provided, both in kappa() and the new rcond().
o list.files() gains a 'ignore.case' argument, to allow
case-insensitive matching on some Windows/MacOS file systems.
o ls.str() and lsf.str() have slightly changed arguments and
defaults such that ls.str() {no arguments} works when debugging.
o Under Unix, utils::make.packages.html() can now be used directly
to set up linked HTML help pages, optionally without creating
the package listing and search database (which can be much
faster).
o new.packages() now knows about the front-end package gnomeGUI
(which does not install into a library).
o optim(*, control = list(...)) now warns when '...' contains
unexpected names, instead of silently ignoring them.
o The options "browser" and "editor" may now be set to functions,
just as "pager" already could.
o packageDescription() makes use of installed metadata where
available (for speed, e.g. in make.packages.html()).
o pairwise.t.test() and pairwise.wilcox.test() now more explicitly
allow paired tests. In the former case it is now flagged as an
error if both 'paired' and 'pool.SD' are set TRUE (formerly,
'paired' was silently ignored), and one-sided tests are generated
according to 'alternative' also if 'pool.SD' is TRUE.
o paste() and file.path() are now completely internal, for speed.
(This speeds up make.packages.html(packages=FALSE)
severalfold, for example.)
o paste() now sets the encoding on the result under some
circumstances (see ?paste).
o predict.loess() now works when loess() was fitted with
transformed explanatory variables, e.g, loess(y ~ log(x) + log(z)).
o print(<data.frame>)'s new argument 'row.names' allows to suppress
printing rownames.
o print() and str() now also "work" for 'logLik' vectors longer than
one.
o Progress-bar functions txtProgressBar(), tkProgressBar() in
package tcltk and winProgressBar() (Windows only).
o readChar() gains an argument 'useBytes' to allow it to read a
fixed number of bytes in an MBCS locale.
o readNEWS() has been moved to the tools package.
o round() and signif() now do internal argument matching if
supplied with two arguments and at least one is named.
o New function showNonASCII() in package tools to aid detection
of non-ASCII characters in .R and .Rd files.
o The [dpq]signrank() functions now typically use considerably
less memory than previously, thanks to a patch from Ivo
Ugrina.
o spec.ar() now uses frequency(x) when calculating the
frequencies of the estimated spectrum, so that for monthly
series the frequencies are now per year (as for spec.pgram)
rather than per month as before.
o spline() gets an 'xout' argument, analogously to approx().
o sprintf() now does all the conversions needed in a first pass if
length(fmt) == 1, and so can be many times faster if called
with long vector arguments.
o [g]sub(useBytes = FALSE) now sets the encoding on changed
elements of the result when working on an element of known
encoding. (This was previously done only for perl = TRUE.)
o New function Sys.chmod(), a wrapper for 'chmod' on platforms
which support it. (On Windows it handles only the read-only
bit.)
o New function Sys.umask(), a wrapper for 'umask' on platforms
which support it.
o New bindings ttk*() in package tcltk for the 'themed widgets'
of Tk 8.5. The tcltk demos make use of these widgets where
available.
o write.table(d, row.names=FALSE) is faster when 'd' has millions of
rows; in particular for a data frame with automatic row names.
(Suggestion from Martin Morgan.)
o The parser limit on string size has been removed.
o If a NEWS file is present in the root of a source package, it
is installed (analogously to LICENSE, LICENCE and COPYING).
o Rd conversion to 'example' now quotes aliases which contain
spaces.
o The handling of DST on dates outside the range 1902-2037 has
been improved. Dates after 2037 are assumed to have the same
DST rules as currently predicted for the 2030's (rather than
the 1970s), and dates prior to 1902 are assumed to have no DST
and the same offset as in 1902 (if known, otherwise as in the
1970s).
o On platforms where we can detect that mktime sets errno
(e.g. Solaris and the code used on Windows but not Linux nor
Mac OS X), 1969-12-31 23:59:59 GMT is converted from POSIXlt
to POSIXct as -1 and not NA.
o The definition of 'whitespace' used by the parser is slightly
wider: it includes Unicode space characters on Windows and in
UTF-8 locales on machines which use Unicode wide characters.
o The src/extra/intl sources have been updated to those from
gettext 0.17.
o New flag --interactive on Unix-alikes forces the session to be
interactive (as --ess does on Windows).
o x[<zero-length>] <- NULL is always a no-op: previously
type-checking was done on the replacement value and so this
failed, whereas we now assume NULL can be promoted to any
zero-length vector-like object.
Other cases of a zero-length index are done more efficiently.
o There is a new option in Rd markup of \donttest{} to mark
example code that should be run by example() but not tested
(e.g. because it might fail in some locales).
o The error handler in the parser now reports line numbers for
more syntax errors (MBCS and Unicode encoding errors, line
length and context stack overflows, and mis-specified argument
lists to functions).
o The "MethodsList" objects originally used for method selection
are being phased out. New utilities provide simpler
alternatives (see ?findMethods), and direct use of the mangled
names for the objects is now deprecated.
o Creating new S4 class and method definitions in an environment
that could not be identified (as package, namespace or global)
previously generated an error. It now results in creating and
using an artificial package name from the current date/time,
with a warning. See ?getPackageName.
o Unix-alikes now give a warning on startup if locale settings
fail. (The Windows port has long done so.)
o Parsing and scanning of numerical constants is now done by R's
own C code. This ensures cross-platform consistency, and
mitigates the effects of setting LC_NUMERIC (within base R it
only applies to output -- packages may differ).
The format accepted is more general than before and includes
binary exponents in hexadecimal constants: see
?NumericConstants for details.
o Dependence specifications for R or packages in the Depends
field in a DESCRIPTION file can now make use of operators
< > == and != (in addition to <= and >=): such packages will
not be installable nor loadable in R < 2.7.0.
There can be multiple mentions of R or a package in the Depends
field in a DESCRIPTION file: only the first mention will be
used in R < 2.7.0.
GRAPHICS CHANGES
o The default graphics devices in interactive and
non-interactive sessions are now configurable via environment
variables R_INTERACTIVE_DEVICE and R_DEFAULT_DEVICE
respectively.
o New function dev.new() to launch a new copy of the default
graphics device (and taking care if it is "pdf" or
"postscript" not to trample on the file of an already running
copy).
o dev.copy2eps() uses dev.displaylist() to detect screen
devices, rather than list them in the function.
o New function dev.copy2pdf(), the analogue of dev.copy2eps().
o dev.interactive() no longer treats a graphics device as
interactive if it has a display list (but devices can still
register themselves on the list of interactive devices).
o The X11() and windows() graphics devices have a new argument
'title' to set the window title.
o X11() now has the defaults for all of its arguments set by the
new function X11.options(), inter alia replacing options
"gamma", "colortype" and "X11fonts".
o ps.options() now warns on unused option 'append'.
xfig() no longer takes default arguments from ps.options().
(This was not documented prior to 2.6.1 patched.)
pdf() now takes defaults from the new function pdf.options()
rather that from ps.options() (and the latter was not
documented prior to 2.6.1 patched).
The defaults for all arguments other than 'file' in
postscript() and pdf() can now be set by ps.options() or
pdf.options()
o New functions setEPS() and setPS() as wrappers to ps.options()
to set appropriate defaults for figures for inclusion in other
documents and for spooling to a printer respectively.
o The meaning of numeric 'pch' has been extended where MBCSes are
supported. Now negative integer values indicate Unicode
points, integer values in 32-127 represent ASCII characters,
and 128-255 are valid only in single-byte locales.
(Previously what happened with negative pch values was
undocumented: they were replaced by the current setting of
par("pch").)
o Graphics devices can say if they can rotate text well
(e.g. postscript() and pdf() can) and if so the device's
native text becomes the default for contour labels rather than
using Hershey fonts.
o The setting of the line spacing (par("cra")[2]) on the X11() and
windows() devices is now comparable with postscript() etc, and
roughly 20% smaller than before (it used to depend on the
locale for X11). (So is the pictex() device, now 20% larger.)
This affects the margin size in plots, and should result in
better-looking plots.
o There is a per-device setting for whether new frames need
confirmation. This is controlled by either par("ask") or
grid.prompt() and affects all subsequent plots on the device
using base or grid graphics.
o There is a new version of the X11() device based on cairo
graphics which is selected by type "cairo" or "nbcairo", and
is available on machines with cairo installed and preferably
pango (which most machines with gtk+ >= 2.8 will have). This
version supports translucent colours and normally does a
better job of font selection so it has been possible to
display (e.g.) English, Polish, Russian and Japanese text on
a single X11() window. It is the default where available.
There is a companion function, savePlot(), to save the current
plot to a PNG file.
On Unix-alikes, devices jpeg() and png() also accept
type = "cairo", and with that option do not need a running
X server. The meaning of capabilities("jpeg") and
capabilities("png") has changed to reflect this. On MacOS X,
there is a further type = "quartz". The default type is
selected by the new option "bitmapType", and is "quartz" or
"cairo" where available.
Where cairo 1.2 or later is supported, there is a svg() device
to write SVG files, and cairo_pdf() and cairo_ps() devices to
write (possibly bitmap) PDF and postscript files via cairo.
Some features require cairo >= 1.2, and some which are
nominally supported under 1.2 seem to need 1.4 to work well.
o There are new bmp() and tiff() devices.
o New function devSize() to report the size of the current
graphics device surface (in inches or device units). This
gives the same information as par("din"), but independent of
the graphics subsystem.
o New base graphics function clip() to set the clipping region (in
user coordinates).
o New functions grconvertX() and grconvertY() to convert between
coordinate systems in base graphics.
o identify() recycles its 'labels' argument if necessary.
o stripchart() is now a generic function, with default and
formula methods defined. Additional graphics parameters may
be included in the call. Formula handling is now
similar to boxplot().
o strwidth() and strheight() gain 'font' and 'vfont' arguments and
accept in-line pars such as 'family' in the same way as text()
does. (Longstanding wish of PR#776)
o example(ask=TRUE) now applies to grid graphics (e.g. from
lattice) as well as to base graphics.
o Option "device.ask.default" replaces "par.ask.default" now it
applies also to grid.prompt().
o plot.formula() only prompts between plots for interactive
devices (it used to prompt for all devices).
o When plot.default() is called with y=NULL it now calls Axis()
with the 'y' it constructs rather than use the default axis.
DEPRECATED & DEFUNCT
o In package installation, SaveImage: yes is defunct and
lazyloading is attempted instead.
o $ on an atomic vector or S4 object is now defunct.
o Partial matching in [[ is now only performed if explicitly
requested (by exact=FALSE or exact=NA).
o Command-line completion has been moved from package 'rcompgen'
to package 'utils': the former no longer exists as a separate
package in the R distribution.
o The S4 pseudo-classes "single" and double have been removed.
(The S4 class for a REALSXP is "numeric": for back-compatibility
as(x, "double") coerces to "numeric".)
o gpar(gamma=) in the grid package is now defunct.
o Several S4 class definition utilities, get*(), have been said
to be deprecated since R 1.8.0; these are now formally deprecated.
Ditto for removeMethodsObject().
o Use of the graphics headers Rgraphics.h and Rdevices.h is
deprecated, and these will be unavailable in R 2.8.0.
(They are hardly used except in graphics devices, for which
there is an updated API in this version of R.)
o options("par.ask.default") is deprecated in favour of
"device.ask.default".
o The 'device-independent' family "symbol" is deprecated as it was
highly locale- and device-dependent (it only did something
useful in single-byte locales on most devices) and font=5
(base) or fontface=5 (grid) did the job it was intended to do
more reliably.
o gammaCody() is now formally deprecated.
o Two low-level functions using MethodsList metadata objects
(mlistMetaName() and getAllMethods()) are deprecated.
o Setting par(gamma=) is now deprecated, and the windows()
device (the only known example) no longer allows it.
o The C macro 'allocString' will be removed in 2.8.0 -- use
'mkChar', or 'allocVector' directly if really necessary.
INSTALLATION
o Tcl/Tk >= 8.3 (released in 2000) is now required to build
package tcltk.
o configure first tries TCL_INCLUDE_SPEC and TK_INCLUDE_SPEC
when looking for Tcl/Tk headers. (The existing scheme did
not work for the ActiveTcl package on Mac OS X.)
o The Windows build only supports Windows 2000 or later (XP,
Vista, Server 2003 and Server 2008).
o New option --enable-R-static-lib installs libR.a which can
be linked to a front-end via 'R CMD config --ldflags'.
The tests/Embedding examples now work with a static R
library.
o Netscape (which was discontinued in Feb 2008) is no longer
considered when selecting a browser.
o xdg-open (the freedesktop.org interface to
kfmclient/gnome-open/...) is considered as a possible browser,
after real browsers such as firefox, mozilla and opera.
o The search for tclConfig.sh and tkConfig.sh now only looks in
directories with names containing $(LIBnn) in the hope of
finding the version for the appropriate architecture
(e.g. x86_64 or i386).
o libtool has been updated to version 2.2.
o Use of --with-system-zlib, --with-system-bzlib or
--with-system-pcre now requires version >= 1.2.3, 1.0.5, 7.6
respectively, for security.
UTILITIES
o Rdconv now removes empty sections including alias and keyword
entries, with a note.
o Keyword entries are no longer mandatory in Rd files.
o R CMD INSTALL now also installs tangled versions of all vignettes.
o R CMD check now warns if spaces or non-ASCII characters are
used in file paths, since these are not in general portable.
o R CMD check (via massage-Examples.pl) now checks all examples
with a 7 inch square device region on A4 paper, for
locale-independence and to be similar to viewing examples on
an on-screen device.
If a package declares an encoding in the DESCRIPTION file,
the examples are assumed to be in that encoding when running
the tests. (This avoids errors in running latin1 examples in a
UTF-8 locale.)
o R CMD check uses pdflatex (if available) to check the typeset
version of the manual, producing PDF rather than DVI. (This
is a better check since the package reference manuals on CRAN
are in PDF.)
o R CMD Rd2dvi gains a --encoding argument to be passed to
R CMD Rdconv, to set the default encoding for conversions.
If this is not supplied and the files are package sources and
the DESCRIPTION file contains an Encoding field, that is used
for the default encoding.
o available.packages() (and hence install.packages() etc) now
supports subdirectories in a repository, and
tools::write_PACKAGES() can now produce PACKAGES files
including subdirectories.
o The default for 'stylepath' in Sweave's (default) RweaveLatex
driver can be set by the environment variable
SWEAVE_STYLEPATH_DEFAULT: see ?RweaveLatex.
C-LEVEL FACILITIES
o Both the Unix and Windows interfaces for embedding now make
use of 'const char *' declarations where appropriate.
o Rprintf() and REprintf() now use 'const char *' for their format
argument -- this should reduce warnings when called from C++.
o There is a new description of the interface for graphics
devices in the 'R Internals' manual, and several new entry
points. The API has been updated to version R_GE_version = 5,
and graphics devices will need to be updated accordingly.
o Graphics devices can now select to be sent text in UTF-8, even
if the current locale is not UTF-8 (and so enable text entered
in UTF-8 to be plotted). This is used by postscript(), pdf()
and the windows() family of devices, as well as the new
cairo-based devices.
o More Lapack routines are available (and declared in R_Ext/Lapack.h),
notably for (reciprocal) condition number estimation of complex
matrices.
o Experimental utility R_has_slot supplementing R_do_slot.
o There is a new public interface to the encoding info stored on
CHARSXPs, getCharCE and mkCharCE using the enumeration type
cetype_t.
o A new header 'R_ext/Visibility.h' contains some definitions for
controlling the visibility of entry points, and how to control
visibility is now documented in 'Writing R Extensions'.
BUG FIXES
o pt(x, df) is now even more accurate in some cases (e.g. 12 instead
of 8 significant digits), when x^2 << df, thanks to a remark from
Ian Smith, related to PR#9945.
o co[rv](use = "complete.obs") now always gives an error if there
are no complete cases: they used to give NA if
method = "pearson" but an error for the other two methods.
(Note that this is pretty arbitrary, but zero-length vectors
always give an error so it is at least consistent.)
Since sd(na.rm=TRUE) and var(na.rm=TRUE) both call cov(use =
"complete.obs"), this applies also to them.
cor(use="pair") used to give diagonal 1 even if the variable
was completely missing for the rank methods but NA for the
Pearson method: it now gives NA in all cases.
cor(use="pair") for the rank methods gave a matrix result with
dimensions > 0 even if one of the inputs had 0 columns.
o Supplying edit.row.names = TRUE when editing a matrix without
row names is now an error and not a segfault. (PR#10500)
o The error handler in the parser reported unexpected
& as && and | as ||.
o ps.options(reset = TRUE) had not reset for a long time.
o paste() and file.path() no longer allow NA_character_ for
their 'sep' and 'collapse' arguments.
o by() failed for 1-column matrices and dataframes. (PR#10506)
However, to preserve the old behaviour, the default method
when operating on a vector still passes subsets of the vector
to FUN, and this is now documented.
o Better behaviour of str.default() for non-default
'strict.width' (it was calling str() rather than str.default()
internally); also, more useful handling of options("str").
o wilcox.test(exact=FALSE, conf.int=TRUE) could fail in some
extreme two-sample problems. (Reported by Wolfgang Huber.)
o par(pch=) would accept a multi-byte string but only use the
first byte. This would lead to incorrect results in an MBCS
locale if a non-ASCII character was supplied.
o There are some checks for valid C-style formats in, e.g.
png(filename=). (PR#10571)
o vector() was misinterpreting some double 'length' values, e.g,
NaN and NA_real_ were interpreted as zero. Also, invalid
types of 'length' were interpreted as -1 and hence reported as
negative. (length<- shared the code and hence the same
misinterpretations.)
o A basic class "S4" was added to correspond to the "S4" object
type, so that objects with this type will print, etc. The
class is VIRTUAL, since all actual S4 objects must have a real
class.
o Classes with no slots that contain only VIRTUAL classes are now
VIRTUAL, as was intended but confused by having an empty S4
object as prototype. ## backed out temporarily ##
o format.AsIs() discarded dimnames, causing dataframes with matrix
variables to be printed without using the column names, unlike
what happens in S-PLUS (Tim Hesterberg, PR#10730).
o xspline() and grid::grid.xspline() work in device coordinates
and now correct for anisotropy in the device coordinate
system.
o grid.locator() now indicates to the graphics device that it is
is in 'graphics input' mode (as locator() and identify()
always have). This means that devices can now indicate the
'graphics input' mode by e.g. a change of cursor.
o Locales without encoding specification and non-UTF-8 locales
now work properly on Mac OS X. Note that locales without
encoding specification always use UTF-8 encoding in Mac OS X
(except for specials "POSIX" and "C") - this is different from
other operating systems.
o iconv() now correctly handles to="" and from="" on Mac OS X.
o In diag()'s argument list, drop the explicit default (' = n')
for 'ncol' which is ugly when making diag() generic.
o S4 classes with the same name from different packages were not
recognized because of a bug in caching the new definition.
o jpeg() and png() no longer maintain a display list, as they
are not interactive devices.
o Using attr(x, "names") <- value (instead of the correct
names<-) with 'value' a pairlist (instead of the correct
character vector) worked incorrectly. (PR#10807)
o Using [<- to add a column to a data frame dropped other
attributes whereas [[<- and $<- did not: now all preserve
attributes. (PR#10873)
o File access functions such as file.exists(), file.info(),
dirname() and unlink() now treat an NA filename as a
non-existent file and not the file "NA".
o r<foo>(), the random number generators, are now more consistent
in warning when NA's (specifically NaN's) are generated.
o rnorm(n, mu = Inf) now returns rep(Inf, n) instead of NaN;
similar changes are applied to rlnorm(), rexp(), etc.
o [l]choose() now warns when rounding non-integer 'k' instead of
doing so silently. (May help confused users such as PR#10766.)
o gamma() was warning incorrectly for most negative values as being
too near a negative integer. This also affected other
functions making use of its C-level implementation.
o dumpMethod() and dumpMethods() now work again.
o package.skeleton() now also works for code_files with only
metadata (e.g. S4 setClass) definitions; it handles S4 classes and
methods, producing documentation and NAMESPACE exports if requested.
o Some methods package utilities (implicitGeneric(), makeGeneric())
will be more robust in dealing with primitive functions (not a
useful idea to call them with primitives, though)
o Making a MethodsList from a function with no methods table will
return an empty list, rather than cause an error (questionably
a bug, but caused some obscure failures).
o setAs() now catches 2 arguments in the method definition, if
they do not match the arguments of coerce().
o S4 methods with missing arguments in the definition are handled
correctly when non-signature arguments exist, and check for
conflicting local names in the method definition.
o qgamma() and qchisq() could be inaccurate for small p,
e.g. qgamma(1.2e-10, shape = 19) was 2.52 rather than 2.73.
o dbeta(.., ncp) is now more accurate for large ncp, and typically no
longer underflows for give.log = TRUE.
o coerce() is now a proper S4 object and so prints correctly.
o @ now checks it is being applied to an S4 object, and if not
gives a warning (which will become an error in 2.8.0).
o dump() and friends now warn that all S4 objects (even those
based on vectors) are not source()able, with a stronger wording.
o read.dcf(all = TRUE) was leaking connections.
o scan() with a non-default separator could skip nul bytes,
including those entered as \0 with allowEscapes=TRUE. This
was different from the default separator.
o determinant(matrix(,0,0)) now returns a correct "det" result;
also value 1 or 0 depending on 'logarithm', rather than numeric(0).
o Name space 'grDevices' was not unloading its DLL when the
name space was unloaded.
o getNativeSymbolInfo() was unaware of non-registered Fortran
names, because one of the C support routines ignored them.
o load() again reads correctly character strings with embedded nuls.
(This was broken in 2.6.x, but worked in earlier versions.)
**************************************************
* *
* 2.6 SERIES NEWS *
* *
**************************************************
CHANGES IN R VERSION 2.6.2 patched
BUG FIXES
o src/extra/pcre has been updated to PCRE 7.6 (bugfix release).
o unlink(..., recursive=TRUE) no longer crashes on some platforms
if a directory cannot be opened.
o Loading in 2.6.2 a saved workspace could give an unimportant
warning in a non-UTF-8 multibyte locale (in particular a CJK
locale on Windows) which is now suppressed.
o print() methods are more consistent in returning the original
argument invisibly.
o Using the X11 data editor (e.g. via edit(), fix() or View())
could crash if the 'End' key was used and all the columns
would have fitted into the window.
o Creating a new page on an X11() device (by plot.new() or
grid.newpage()) did not flush out the XClearWindow call, so
the X11 window might not be refreshed immediately.
o libtool has been updated to version 1.5.26, which avoids
many spurious configure warnings on Darwin/Mac OS X.
o l10n_info() now recognizes how Darwin/Mac OS X reports
Latin-1 locales (as charset ISO8859-1 rather than ISO-8859-1).
o Checking examples which used grid (e.g. via lattice) without
attaching grid no longer give errors from grid_plot_hook().
o kappa(m, exact=TRUE) no longer wrongly uses 'exact=FALSE' when m
is an 'lm' or 'qr' object because the kappa.tri(x, exact=TRUE)
now works correctly.
o help(topic, offline=TRUE) misbehaved when there were multiple
matches to 'topic'. (PR#10859)
o The 'multilib' changes on Linux broke the use of
sub-architectures without a main architecture.
o source(echo=TRUE) would skip lines consisting entirely of the
letter t. (PR#10923)
o bzip2 has been updated to 1.0.5 (security fix).
CHANGES IN R VERSION 2.6.2
NEW FEATURES
o colnames(DF) is now also fast for large dataframes DF with
automatic row.names. Note that the correct usage is
names(DF). (PR#10470)
o tools::texi2dvi() works around the failure of 'texi2dvi --quiet'
to be quiet in texinfo 4.11.
o On Linux, parallel 32/64-bit installations are supported using
multilib.
BUG FIXES
o A compilation problem on one system where glob was not found
has been corrected. (PR#10468)
o The "profile.nls" method of plot() was losing the x axis labels.
o array() computed the total number of entries in the array before
coercing the dimensions to integer. (Reported by Allen McIntosh.)
o persp() misreported errors in the y parameter. (Reported by Allen
McIntosh.)
o source("clipboard", echo=TRUE) and file("clipboard", open="rt")
gave spurious errors. (Reported by Fernando Saldanha.)
o attributes<-() stripped any existing attributes before checking
that all elements of the right-hand side had names.
o rbinom(n, size, *) gave NaN when 'size > .Machine$integer.max'.
o print.summary.lm() is now consistent in the capitalization of
"R-squared".
o confint() misreported on some rank-deficient lm() models.
(PR#10496) This could also occur in the default method.
o \code{\var{<name>}} was not rendered correctly to latex in Rd
files for non-alphabetic arguments <name>.
o In 2.6.1, curve(*, add=TRUE) used a wrong default 'xlim' when x
coordinates were logged.
o The Java-based search in help.start() now only requires a
JVM >= 1.4 (2.6.1 accidentally required >= 1.5).
o The default method for range() was omitting 'na.rm' for
non-numeric objects such as those of class "Date". (PR#10508)
o cut(x, breaks=<n>) misbehaved on a constant vector of negative
values.
o bxp(), the plotting engine of boxplot(), no longer plots staple
ticks multiple times. (PR#10499)
o The automatic detection of the domain for message translation
was not working correctly for messages in message(), warning()
and stop() in packages other than 'base'.
o The profile.nls() function misbehaved when encountering
non-convergence of the "port" algorithm.
o Under certain rare circumstances in R 2.6.x, log(), round()
and trunc() could alter their arguments in the caller. This
involved passing of empty '...' arguments, and was spotted
when using apply(x, 2, log).
o par() no longer warns unnecessarily when asked to set new=FALSE
on an unused graphics device.
o plot.formula() was not passing on '...' when used with a
one-sided formula.
plot.formula() was not accepting expressions for annotations
passed to title(). (PR#10525)
o pchisq(x, df=0, ncp=L) now returns the correct limit exp(-L/2) for
x=0 and is no longer returning NaN for x > 0, L < 80. (PR#10551)
o Non-ASCII characters were only working correctly in Hershey
fonts if these were specified by the 'vfont' argument to
text() and not if specified as a font family.
o There were several errors in Hershey$allowed, but the help
page listed the allowed combinations correctly.
o text() no longer attempts to use 'vfont' with an expression
for 'labels' (it was documented not to work).
o fisher.test(simulate.p.value = TRUE) gave incorrect answers
in some extremely degenerate problems. (PR#10558)
o src/extra/pcre has been updated to PCRE 7.5 (bugfix release).
o capture.output() completes an incomplete final line of
output when file = NULL. (PR#10534)
o capture.output() now returns invisibly if output is written to
a file/connection.
o format.AsIs() did not remove the "AsIs" class and so could go
into an infinite loop.
o summary.mlm() lost the names of the coefficients when there
was only one.
o Rdconv was not marking examples files with an encoding if
this was known from the package's DESCRIPTION file.
o readChar() from a raw vector was reading a number of bytes,
not characters.
o slotNames() was erroneously treating classes that extend
"character" as strings.
o R no longer ignores SIGPIPE signals even in processes launched
by system(). Instead PR#1959 is handled by a simple error
handler which will give an error message in circumstances
where none was given before.
o The AIC() S4 generic in package stats4 no longer disables
dispatch of S3 methods for AIC().
o The conflicts check in library() excluded all S4 generics, even
where they were unrelated to the function masked. It is now
more selective (although still too generous to S4 generics).
o proc.time() was missing a protect and could misbehave if
provoked by gctorture(). (PR#10600)
o The cut() and hist() methods for dates and datetimes are now
more accurate for intervals of "months" and "years", thanks to
Marc Schwarz.
o url()/download.file() could segfault if the HTTP interaction
involved a redirect to an address starting with '/' on the
same server.
o Memory allocations used in format() and in an internal utility
function could be off by one byte. (PR#10635)
o isoreg(x, y) no longer segfaults when y has NAs.
o split(x, g) always returns a list as documented. (It used to
return NULL for a zero-length 'x'.)
o tapply(x, g, ...) misbehaved if the args were of zero length.
(PR#10644)
o hist.POSIXt(*, xaxt = "n") no longer suppresses the y-axis.
o strptime() crashed under certain locales on Mac OS X.
o gregexpr() no longer segfaults when "" is given as the search
pattern. Thanks to Hervé Pagès for the bug report.
o matplot(x, *) with default 'pch' did not plot columns from column
number 37 on (because the default pch was NA for those). (PR#10676)
o print.htest() lost output when used within sink(file, split=TRUE).
o Setting par(col.main=) also set par("col") to the same colour.
o Anonymous fifos were broken (again).
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.x 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)
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,
sum, prod, range) are now primitive.
See under METHODS PACKAGE below for some consequences 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(<a factor>) 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 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).
o showMethods() has a "smart" default for 'inherited' such that
showMethods(<genfun>, incl = TRUE) becomes a useful short cut.
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 Hervé
Pagès 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 entry point R_GE_str2col listed in R_ext/GraphicsEngine.h
for external graphics 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.