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% -*- coding: utf-8 -*-
\newcommand{\Rlogo}{\if{html}{\figure{../../html/Rlogo.svg}{options: class="toplogo" alt="[R logo]"}}\if{latex}{\figure{Rlogo.pdf}{options: width=0.5in}}}
\name{NEWS}
\title{R News}
\encoding{UTF-8}
\section{\Rlogo CHANGES IN R-devel}{
\subsection{SIGNIFICANT USER-VISIBLE CHANGES}{
\itemize{
\item Calling \code{&&} or \code{||} with either argument of
length greater than one is now an error.
[Scheduled for May 2.]
}
}
\subsection{NEW FEATURES}{
\itemize{
\item Placeholder.
}
}
\subsection{INSTALLATION on a UNIX-ALIKE}{
\itemize{
\item A system installation of generic LAPACK 3.10.0 or later will
be preferred to the version in the \R sources.
\command{configure} option \option{--with-lapack=no} (equivalently
\option{--without-lapack}) forces compilation of the internal
LAPACK sources.
If \option{--with-lapack} is not specified, a system
\code{liblapack} is looked for and used if it reports version
3.10.0 or later and does not contain BLAS routines.
Using 3.10.0 may give some different signs in SVDs (seen in the
\file{lapack.R} test).
Packages using LAPACK will need to be reinstalled if this changes
to using an external library.
}
}
\subsection{PACKAGE INSTALLATION}{
\itemize{
\item \code{USE_FC_LEN_T} is the default: this uses the
correct prototypes for Fortran BLAS/LAPACK routines called from
C/C++, and requires adjustment of most such calls -- see
\sQuote{Writing R Extensions} §6.6.1.
[In progress: scheduled for May 5 if enough packages are
corrected before then.
Setting environment variable \env{_R_INSTALL_USE_FC_LEN_T_} to a
true value enables this \emph{pro tem}. This is set by \command{R
CMD check --as-cran} when it installs a package.]
}
}
\subsection{C-LEVEL FACILITIES}{
\itemize{
\item The deprecated S-compatibility macros \code{DOUBLE_*} in
\file{R_ext/Constants.h} (included by \file{R.h}) have been
removed.
[Scheduled for Apr 23.]
}
}
\subsection{BUG FIXES}{
\itemize{
\item Hashed \code{environment}s with sizes less than 5 now can grow,
too. (Reported to R-devel by Duncan Garmonsway.)
}
}
}
\section{\Rlogo CHANGES IN R 4.2.0}{
\subsection{SIGNIFICANT USER-VISIBLE CHANGES}{
\itemize{
\item The \code{formula} method of \code{aggregate()} now matches
the generic in naming its first argument \code{x} (resolving
\PR{18299} by Thomas Soeiro).
This means that calling \code{aggregate()} with a formula as a
named first argument requires name \code{formula} in earlier
versions of \R and name \code{x} now, so portable code should not
name the argument (code in many packages did).
\item Calling \code{&&} or \code{||} with either argument of
length greater than one now gives a warning (which it is intended
will become an error).
\item Calling \code{if()} or \code{while()} with a condition of
length greater than one gives an error rather than a warning.
Consequently, environment variable
\env{_R_CHECK_LENGTH_1_CONDITION_} no longer has any effect.
\item Windows users should consult the WINDOWS section below for
some profound changes including
\itemize{
\item Support for 32-bit builds has been dropped.
\item UTF-8 locales are used where available.
\item The default locations for the \R installation and personal
library folder have been changed.
}
Thanks to Tomas Kalibera for months of work on the Windows port
for this release.
}
}
\subsection{NEW FEATURES}{
\itemize{
\item \code{matrix(x, n, m)} now warns in more cases where
\code{length(x)} differs from \code{n * m}, as suggested by Abby
Spurdle and Wolfgang Huber in Feb 2021 on the R-devel mailing
list.
This warning can be turned into an error by setting environment
variable \env{_R_CHECK_MATRIX_DATA_} to \samp{TRUE}: \command{R
CMD check --as-cran} does so unless it is already set.
\item Function \code{file_test()} in package \pkg{utils} gains
tests for symlinks, readability and writability.
\item \code{capabilities("libxml")} is now false.
The description of \code{capabilities("http/ftp")} now reflects
that it refers to the default method, no longer the internal one.
\item \code{simplify2array()} gains an \code{except} argument for
controlling the exceptions used by \code{sapply()}.
\item Environment variables \env{R_LIBS_USER} and
\env{R_LIBS_SITE} are both now set to the \R system default if
unset or empty, and can be set to \code{NULL} to indicate an empty
list of user or site library directories.
\item The warning for \code{axis()}(-like) calls in cases of relatively
small ranges (typically in log-scale situations) is slightly improved
\emph{and} suppressed from explicit calls to \code{.axisPars()} as
has always been the intention.
\item The \code{contrasts} setter function \code{`contrasts<-`}
gains an explicit default \code{how.many = NULL} rather than just
using \code{missing(how.many)}.
\item \code{grid.pretty()} gains a new optional argument \code{n = 5}.
\item There is a new function \code{.pretty()} with option
\code{bounds} as a technical-utility version of \code{pretty()}. It
and \code{pretty()} gain a new argument \code{f.min} with a better
than back-compatible default.
\item Function \code{grDevices::axisTicks()} and related functions
such as \code{graphics::axis()} work better, notably for the log
scale; partly because of the \code{pretty()} improvements, but also
because care is taken e.g., when \code{ylim} is finite but
\code{diff(ylim)} is infinite.
\item \code{nclass.FD()} gains a \code{digits} option.
\item The R Mathlib internal C function \code{bd0()} (called
indirectly from a dozen probability density and distribution
functions such as \code{dpois()}, \code{dbinom()},
\code{dgamma()}, \code{pgamma()} \emph{etc}) has been complemented
by a more sophisticated and (mostly) more accurate C function
\code{ebd0()}, currently called only by internal
\code{dpois_raw()} improving accuracy for \R level \code{dpois()}
and potentially others calling it such as \code{dnbinom()},
\code{dgamma()} or \code{pgamma()}. (Thanks to Morten Welinder's
\PR{15628}.)
\item \code{write.ftable()} gains \code{sep = " "} argument as
suggested by Thomas Soeiro.
\item The names of the locale categories supported by \R's
\code{Sys.getlocale()} and \code{Sys.setlocale()} are now provided
by variable \code{.LC.categories} in the \code{base} namespace.
\item The \code{Date} and \code{POSIXt} methods for \code{hist()}
and the \code{histogram} method for \code{plot()} now also use the
new default \code{col = "lightgray"} in consistency with the
corresponding change to \code{hist()}'s default for \R 4.0.0.
\item \code{hist.default()} gains new \code{fuzz} argument, and the
histogram \code{plot} method no longer uses fractional axis ticks
when displaying counts (\code{"Frequency"}).
\item \code{mapply()} and hence \code{Map()} now also obey the
\dQuote{max-or-0-if-any} recycling rule, such that, e.g.,
\code{Map(`+`, 1:3, 1[0])} is valid now.
\item \code{as.character(<obj>)} for \code{"hexmode"} or
\code{"octmode"} objects now fulfils the important basic rule
\code{as.character(x)[j] === as.character(x[j])}.
\item The set utility functions, notably \code{intersect()} have been
tweaked to be more consistent and symmetric in their two set
arguments, also preserving a common \code{mode}, see \code{?sets}.
\item \code{substr(ch, start,end) <- new} now e.g., preserves
\code{names(ch)}; ditto for \code{substring()}, thanks to a patch
from Brodie Gaslam.
\item \code{plot(<lm>)} gains a \code{extend.ylim.f} argument, in
partial response to \PR{15285}; further \PR{17784} is fixed thanks to
several contributors and a patch by Elin Waring.
The Cook's dist contours get customizable via \code{cook.col} and
\code{cook.lty} with a different default color and their legend is
nicer by default and customizable via \code{cook.legendChanges}.
\item Attempting to subset an object that is not subsettable now
signals an error of class \code{notSubsettableError}. The
non-subsettable object is contained in the \code{object} field of
the error condition.
\item Subscript-out-of-bounds errors are now signaled as errors of
class \code{subscriptOutOfBoundsError}.
\item Stack-overflow errors are now signaled as errors inheriting
from class \code{stackOverflowError}. See
\code{?stackOverflowError} for more details.
\item New partly experimental \code{Sys.setLanguage()} utility,
solving the main problem of \PR{18055}.
\item \code{gettext()} and \code{gettextf()} get a new option
\code{trim = TRUE} which when set to false allows translations for
strings such as \code{"Execution halted\n"} typical for C code.
\item An experimental implementation of hash tables is now
available. See \code{?hashtab} for more details.
\item \code{identical()} gains a \code{extptr.as.ref} argument for
requesting that external pointer objects be compared as reference
objects.
\item \code{reorder()} gets an argument \code{decreasing} which it
passes to \code{sort()} for level creation; based on the wish and
patch by Thomas Soeiro in \PR{18243}.
\item \code{as.vector()} gains a \code{data.frame} method which
returns a simple named list, also clearing a long standing
\sQuote{FIXME} to enable \code{as.vector(<data.frame>,
mode="list")}. This breaks code relying on
\code{as.vector(<data.frame>)} to return the unchanged data frame.
\item \code{legend()} is now vectorized for arguments \code{cex},
\code{x.intersp}, and \code{text.width}.
The latter can now also be specified as a vector (one element for
each column of the legend) or as \code{NA} for computing a proper
column wise maximum value of \code{strwidth(legend)}.
The argument \code{y.intersp} can be specified as a vector with
one entry for each row of the legend.
\code{legend()} also gains new arguments \code{title.cex} and
\code{title.font}. Thanks to Swetlana Herbrandt.
\item Deparsing no longer remaps attribute names \code{dim},
\code{dimnames}, \code{levels}, \code{names} and \code{tsp} to
historical S-compatible names (which \code{structure()} maps back).
\item \code{sample()} and \code{sample.int()} have additional
sanity checks on their \code{size} and \code{n} arguments.
\code{all.equal.numeric()} gains a sanity check on its
\code{tolerance} argument -- calling \code{all.equal(a, b, c)} for
three numeric vectors is a surprisingly common error.
\code{mean(na.rm =)}, \code{rank(na.last =)},
\code{barplot(legend.text =)}, \code{boxplot()},
\code{contour(drawlabels =)}, \code{polygon(border =)} and
\code{methods::is(class2 =)} have more robust sanity checks on
their arguments.
\command{R CMD Rd2pdf} (used by \command{R CMD check}) has a more
robust sanity check on the format of \code{\\alias{}} commands.
\item \code{psigamma(x, deriv)} for negative \code{x} now also works
for \code{deriv = 4} and \code{5}; their underlying C level
\code{dpsifn()} is documented in \sQuote{Writing R Extensions}.
\item The HTML help system now uses HTML5 (wish of \PR{18149}).
\item \code{ks.test()} now provides exact p-values also with ties
and MC p-values in the two-sample (Smirnov) case. By Torsten
Hothorn.
\item \code{ks.test()} gains a formula interface, with \code{y ~ 1}
for the one-sample (Kolmogorov) test and \code{y ~ group} for the
two-sample (Smirnov) test. Contributed by Torsten Hothorn.
\item The return value from \code{ks.test()} now has class
\code{c("ks.test", "htest")} -- packages using \code{try()} need
to take care to use \code{inherits()} and not \code{==} on the class.
\item New functions \code{psmirnov()}, \code{qsmirnov()} and
\code{rsmirnov()} in package \pkg{stats} implementing the
asymptotic and exact distributions of the two-sample Smirnov statistic.
\item \code{iconv()} now allows \code{sub = "c99"} to use C99-style
escapes for UTF-8 inputs which cannot be converted to encoding \code{to}.
\item In a forward pipe \code{|>} expression it is now possible to
use a named argument with the placeholder \code{_} in
the \code{rhs} call to specify where the \code{lhs} is to be
inserted. The placeholder can only appear once on the \code{rhs}.
\item The included LAPACK sources have been updated to version 3.10.0,
except for the four Fortran 77 routines which 3.10.0 has
re-implemented in Fortran 90 (where the older versions have been
retained as the \R build process does not support Fortran 90).
\item \code{path.expand()} and most other uses of tilde expansion now
warn if a path would be too long if expanded. (An exception is
\code{file.exists()}, which silently returns false.)
\item \code{trunc(<Date>, *)} now supports \code{units = "months"}
or \code{"years"} for consistency with the \code{POSIXt} method,
thanks to Dirk Eddelbuettel's proposal in \PR{18099}.
\item The HTML help system has several new features: LaTeX-like
math can be typeset using either \href{https://katex.org/}{KaTeX}
or \href{https://www.mathjax.org/}{MathJax}, usage and example
code is highlighted using \href{https://prismjs.com}{Prism}, and
for dynamic help the output of examples and demos can be shown
within the browser if the \CRANpkg{knitr} package is
installed. These features can be disabled by setting the
environment variable \code{_R_HELP_ENABLE_ENHANCED_HTML_} to a
false value.
}
}
\subsection{GRAPHICS}{
\itemize{
\item The graphics engine version, \code{R_GE_version}, has been
bumped to \code{15} and so packages that provide graphics devices
should be reinstalled.
\item The \pkg{grid} package now allows the user to specify a
\dQuote{vector} of pattern fills. The \code{fill} argument
to \code{gpar()} accepts a list of gradients and/or patterns and
the functions \code{linearGradient()}, \code{radialGradient()},
and \code{pattern()} have a new \code{group} argument.
Points grobs (data symbols) can now also have a pattern fill.
The \code{grobCoords()} function now returns a more informative
and complex result.
\item The \pkg{grid} package has new functions for drawing
isolated groups: \code{grid.group()}, \code{grid.define()}, and
\code{grid.use()}. These functions add compositing operators and
affine transformations to R's graphics capabilities.
The \pkg{grid} package also has new functions for stroking
and filling paths: \code{grid.stroke()}, \code{grid.fill()},
and \code{grid.fillStroke()}.
A new function \code{as.path()} allows the user to specify the
fill rule for a path that is to be used for clipping, stroking, or
filling; available options are \code{"winding"} and
\code{"evenodd"}. A new function \code{as.mask()} allows the user
to specify the type of a mask; available options are
\code{"alpha"} and \code{"luminance"}.
These new features are only supported so far (at most) on the
Cairo-based graphics devices and on the \code{pdf()} device.
\item \code{dev.capabilities()} reports on device support
for the new features.
\item \code{par()} now warns about unnamed non-character arguments
to prevent misuse such as \code{{usr <- par("usr"); par(usr)}}.
}
}
\subsection{WINDOWS}{
\itemize{
\item \R uses UTF-8 as the native encoding on recent Windows
systems (at least Windows 10 version 1903, Windows Server 2022 or
Windows Server 1903). As a part of this change, R uses UCRT as
the C runtime. UCRT should be installed manually on systems older
than Windows 10 or Windows Server 2016 before installing \R.
\item The default personal library on Windows, folder
\file{R\\win-library\\x.y} where \file{x.y} stands for \R release
\file{x.y.z}, is now a subdirectory of Local Application Data
directory (usually a hidden directory
\file{C:\\Users\\username\\AppData\\Local}). Use
\code{shell.exec(.libPaths()[1])} from \R to open the personal
library in Explorer when it is first in the list (\PR{17842}).
\item \R uses a new 64-bit Tcl/Tk bundle. The previous
32-bit/64-bit bundle had a different layout and can no longer be
used.
\item Make files and installer scripts for Windows have been
tailored to \file{Rtools42}, the newly recommended 64-bit
\command{gcc} 10.3 MinGW-W64 UCRT toolchain.
\item \file{Rtools42} by default uses the Windows security
features ASLR and DEP; hence CRAN builds of \R and packages also
do.
\item \R now supports files \file{Makevars.ucrt},
\file{Makefile.ucrt}, \file{configure.ucrt} and
\file{cleanup.ucrt} in packages, which are used in preference to
the \file{.win} variants. This allows keeping the \file{.win}
files around to support older versions of \R. This feature will
be removed in the future once support for older versions of \R
would no longer be needed.
\item \code{R.version} gains a new field \code{crt} (only on
Windows) to denote the C runtime. The value is \code{"ucrt"}.
\item On Windows, \code{download.file(method = "auto")} and
\code{url(method = "default")} now follow Unix in using
\code{"libcurl"} for all except \samp{file://} URIs.
\item \file{Rtools42} includes an unpatched Msys2 build of GNU
\command{tar}. Paths including drive letters can be made to work
by adding \option{--force-local} to environment variable
\env{TAR_OPTIONS}. (\file{Rtools40} and earlier included a
patched version which defaulted to this option.)
\item Installer builds of \R automatically find the
\file{Rtools42} software collection as well as the compiler
toolchain. No \env{PATH} setting is required from the user.
\item The default installation directory of R for a user-only
installation has been changed to the User Program Files directory
(usually a hidden directory
\file{C:\\Users\\username\\AppData\\Local\\Programs}) to follow
Windows conventions. Use \code{shell.exec(R.home())} from \R{} to
open the \R installation directory in Explorer (\PR{17842}).
\item \R now supports installation-time patching of packages.
Patches may be installed from a supplied URL or a local directory
or disabled. Patches are included into the installed packages for
reference. This experimental feature may be removed in the
future.
\item \code{libcurl} is now required for building from source.
\item The clipboard connection now works also with text in other
than the current native encoding (\PR{18267}, with Hiroaki
Yutani). Text is always pasted to the clipboard in UTF16-LE and
the \code{encoding} argument is ignored.
\item The internal case-changing functions are now used by default
on Windows -- this circumvents problems (for example with E acute)
of the UCRT Windows' runtime.
\item \R on Windows now uses the system memory allocator. Doug
Lea's allocator was used since \R 1.2.0 to mitigate performance
limitations seen with system allocators on earlier versions of
Windows.
\item \code{memory.limit()} and \code{memory.size()} are now stubs on
Windows (as on Unix-alikes).
\item Applications embedding \R on Windows can now use additional
callbacks, which have so far only been available only on Unix
(\PR{18286}).
}
}
\subsection{INSTALLATION}{
\itemize{
\item Facilities for accessing \samp{ftp://} sites are no longer
tested (except \emph{pro tem} for \code{curlGetHeaders()}) as modern
browsers have removed support.
%% Chrome and Firefox did in early 2021: Safari and Edge never had it.
\item \R can now be built with \samp{DEFS = -DSTRICT_R_HEADERS} .
}
}
\subsection{PACKAGE INSTALLATION}{
\itemize{
\item \command{R CMD INSTALL} no longer tangles vignettes. This
completes an \command{R CMD build} change in \R 3.0.0 and affects
packages built before \R 3.0.2. Such packages should be re-made
with \command{R CMD build} to have the tangled \R code of vignettes
shipped with the tarball.
\item \code{USE_FC_LEN_T} will become the default: this uses the
correct prototypes for Fortran BLAS/LAPACK routines called from
C/C++, and requires adjustment of most such calls -- see
\sQuote{Writing R Extensions} §6.6.2. (This has been supported
since \R 3.6.2.)
\item Package installation speed for packages installed with
\code{keep.source} has been improved. This resolve the issue
reported by Ofek Shilon in \PR{18236}.
}
}
\subsection{UTILITIES}{
\itemize{
\item \command{R CMD check} can optionally report
files/directories left behind in home, \file{/tmp} (even though
\env{TMPDIR} is set) and other directories. See the \dQuote{R
Internals} manual for details.
\item \command{R CMD check} now reports byte-compilation errors
during installation. These are not usually fatal but may result
in parts of the package not being byte-compiled.
\item \env{_R_CHECK_DEPENDS_ONLY_} can be applied selectively to
examples, tests and/or vignettes in \command{R CMD check}: see the
\dQuote{R Internals} manual.
\item \env{_R_CHECK_SRC_MINUS_W_IMPLICIT_} now defaults to true:
recent versions of Apple \command{clang} on macOS have made
implicit function declarations in C into a compilation error.
\item \command{R CMD check --as-cran} makes use of the
environment variable \env{AUTORECONF}. See the
\dQuote{R Internals} manual §8 for further details.
\item \command{R CMD check --use-valgrind} also uses
\command{valgrind} when re-building vignettes as some non-Sweave
vignettes unhelpfully comment out all their code when
\command{R CMD check} runs vignettes.
\item Errors in re-building vignettes (unless there are LaTeX
errors) are reported by \command{R CMD check} as \samp{ERROR} rather
than \samp{WARNING} when running vignettes has been skipped (as it
frequently is in \acronym{CRAN} checks and by \option{--as-cran}).
\item \command{R CMD Rd2pdf} gains a \option{--quiet} option that is
used by \command{R CMD build} when building the PDF package manual.
\item \command{R CMD Rd2pdf} now always runs LaTeX in batch mode,
consistent with Texinfo \eqn{\ge}{>=} 6.7. The \option{--batch}
option is ignored.
\item \command{R CMD build} and \command{R CMD check} now include
the Rd file name and line numbers in the error message of an
\verb{\Sexpr} evaluation failure.
\item For packages using the \verb{\doi} Rd macro (now an
install-time \verb{\Sexpr}) but no other dynamic Rd content,
\command{R CMD build} now produces a smaller tarball and is
considerably faster -- skipping temporary package installation.
}
}
\subsection{C-LEVEL FACILITIES}{
\itemize{
\item The non-API header \file{R_ext/R-ftp-http.h} is no longer
provided, as the entry points it covered are now all defunct.
\item A number of non-API declarations and macro definitions have
been moved from the installed header \file{Rinternals.h} to the
internal header \file{Defn.h}. Packages that only use entry points
and definitions documented to be part of the API as specified in
\sQuote{Writing R Extensions} §6 should not be affected.
\item The macro \code{USE_RINTERNALS} no longer has any effect
when compiling package code. Packages which also use
\code{R_NO_REMAP} will need to ensure that the remapped names are
used for calls to API functions that were formerly also made
available as macros.
\item The deprecated legacy S-compatibility macros \code{PROBLEM},
\code{MESSAGE}, \code{ERROR}, \code{WARN}, \code{WARNING},
\code{RECOVER}, \dots{} are no longer defined in
\file{R_exts/RS.h} (included by \file{R.h}). Replace these by
calls to \code{Rf_error} and \code{Rf_warning} (defined in header
\file{R_ext/Error.h} included by \file{R.h}).
Header \file{R_ext/RS.h} no longer includes \file{R_ext/Error.h}.
\item Header \file{R_ext/Constants.h} (included by \file{R.h})
when included from C++ now includes the C++ header \file{cfloat}
rather than the C header \file{float.h} (now possible as C++11 is
required).
\item The legacy S-compatibility macros \code{DOUBLE_*} in
\file{R_ext/Constants.h} (included by \file{R.h}) are deprecated.
\item The deprecated S-compatibility macros \code{SINGLE_*} in
\file{R_ext/Constants.h} (included by \file{R.h}) have been
removed.
\item \code{R_Calloc}, \code{R_Free} and \code{R_Realloc} are
preferred to their unprefixed forms and error messages now use the
prefix. These forms were introduced in \R 3.4.0 and are available
even when \code{STRICT_R_HEADERS} is defined.
\item \code{rmultinom} has been documented in \sQuote{Writing R
Extensions} §6 so is now part of the \R API.
\item Similarly, \code{Rtanpi}, called from \R level \code{tanpi()}
is now part of the \R API.
\item The long-deprecated, undocumented and non-API entry point
\code{call_R} is no longer declared in \file{R_ext/RS.h} (included
by \file{R.h}).
\item The header \file{S.h} which has been unsupported since Jan
2016 has been removed. Use \file{R.h} instead.
}
}
\subsection{DEPRECATED AND DEFUNCT}{
\itemize{
\item The (non-default and deprecated) \code{method = "internal"}
for \code{download.file()} and \code{url()} no longer supports
\samp{http://} nor \samp{ftp://} URIs. (It is used only for
\samp{file://} URIs.)
On Windows, \code{download.file(method = "wininet")} no longer
supports \samp{ftp://} URIs. (It is no longer the default method,
which is \code{"libcurl"} and does.)
On Windows, the deprecated \code{method = "wininet"} now gives a
warning for \samp{http://} and \samp{https://} URIs for both
\code{download.file()} and \code{url()}. (It is no longer the default
method.)
\item On Windows, the command-line option \option{--max-mem-size}
and environment variable \env{R_MAX_MEM_SIZE} are defunct. The
memory allocation limit was important for 32-bit builds,
but these are no longer supported.
\item \code{default.stringsAsFactors()} is now formally deprecated,
where that was only mentioned on its regular help page,
previously. So it now gives a warning if called.
\item \code{unix.time()} is defunct now; it had been deprecated since
\R 3.4.0.
}
}
\subsection{BUG FIXES}{
\itemize{
\item Setting \code{digits = 0} in \code{format()},
\code{print.default()} (and hence typically \code{print()}) or
\code{options()} is again invalid. Its behaviour was
platform-dependent, and it is unclear what \dQuote{zero
significant digits} should mean (\PR{18098}).
\item Messages from C code in the \file{cairo} section of package
\pkg{grDevices} are now also offered for translation, thanks to
Michael Chirico's \PR{18123}.
\item \code{mean(x)} with finite \code{x} now is finite also without
"long.double" capability.
\item \command{R CMD Rd2pdf} no longer leaves an empty build
directory behind when it aborts due to an already existing output
file. (Thanks to Sebastian Meyer's \PR{18141}.)
\item \code{density(x, weights = w, na.rm = TRUE)} when \code{anyNA(x)}
is true, now removes weights \dQuote{in parallel} to \code{x}, fixing
\PR{18151}, reported by Matthias Gondan.
Additionally, it gets a \code{subdensity} option.
\item Conversion of \verb{\Sexpr[]{<expR>}} to LaTeX or HTML no longer
produces long blocks of empty lines when \code{<expR>} itself
contains several lines all producing empty output. Thanks to a
report and patch by Ivan Krylov posted to R-devel.
\item \command{R CMD build} no longer fails if a package vignette
uses child documents and \file{inst/doc} exists. (Thanks to
Sebastian Meyer's \PR{18156}.)
\item When an R documentation (\sQuote{help} source) file
\file{man/foo.Rd} in a package has \verb{\donttest{..}} examples
with a syntax error, it is now signalled as ERROR and with correct
line numbers relating to the \file{*-Ex.R} file, thanks to Duncan
Murdoch and Sebastian Meyer's reports and patch proposals in
\PR{17501}.
\item Improved determination of the correct translation domain in
non-base packages, addressing the combination of \PR{18092} and
\PR{17998} (\code{#c6}) with reports and \emph{augmented} patch
#2904 by Suharto Anggono.
Note that \code{"R-base"} is no longer the default domain e.g.,
for top-level calls to \code{gettext()}; rather translation needs
explicit \code{domain = *} specification in such cases.
\item \code{identical(attrib.as.set=FALSE)} now works correctly with
data frames with default row names (Thanks to Charlie Gao's
\PR{18179}).
\item \code{txtProgressBar()} now enforces a non-zero width for
argument \code{char}, without which no progress can be visible.
\item \code{dimnames(table(d))} is more consistent in the case where
\code{d} is a list with a single component, thanks to Thomas Soeiro's
report to R-devel.
Further, \code{table(d1, d2)} now gives an error when \code{d1} and
\code{d2} are data frames as suggested by Thomas in \PR{18224}.
\item Fix for drawing semi-transparent lines and fills on the
native Windows graphics device (\PR{18219} and \PR{16694}).
Thanks to Nick Ray for helpful diagnosis on Bugzilla.
\item The deparser now wraps sub-expressions such as \code{if(A) .. }
with parentheses when needed; thanks to Duncan Murdoch's \PR{18232}
and Lionel Henry's patches there.
\item \code{remove.packages()} no longer tries to uninstall
\code{Priority: base} packages, thanks to a report and suggestions
by Colin Fay in \PR{18227}.
\item \code{win.metafile()} now has \code{xpinch} and
\code{ypinch} arguments so that the user can override Windows'
(potentially wrong) guess at device dimensions.
\item \code{x[i]} and \code{x[[i]]} for non-integer \code{i}
should now behave in all cases as always documented: the index used is
equivalent to \code{as.integer(i)} unless that would overflow where
\code{trunc(i)} is used instead; thanks to Suharto Anggono's report
and patch proposals in \PR{17977}.
\item \code{asOneSidedFormula()} now associates the resulting
formula with the global environment rather than the evaluation
environment created for the call.
\item \code{<bibentry>$name} now matches the field name
case-insensitively, consistent with \code{bibentry()} creation and
the replacement method.
\item \code{cbind()} failed to detect some length mismatches with
a mixture of time-series and non-time-series inputs.
\item The default LaTeX style file \file{Sweave.sty} used by the
\code{RweaveLatex} driver no longer loads the obsolete \samp{ae}
package; thanks to a report by Thomas Soeiro in \PR{18271}.
Furthermore, it now skips \samp{\\usepackage[T1]{fontenc}} for
engines other than pdfTeX (if detected) or if the new
\samp{[nofontenc]} option is used.
\item \code{smooth.spline()} now stores its logical \code{cv}
argument more safely, fixing a rare bug when printing, and also
stores \code{n}.
\item \code{smooth.spline(x,y,*)} now computes the \code{cv.crit}
statistic correctly, also when \code{is.unsorted(x)}, fixing
\PR{18294}.
\item The \code{data.frame} method of \code{rbind()} now warns
when binding not-wholly-recycling vectors, by analogy to the default
method (for matrices).
\item \code{setAs()} finds the correct class for name \code{to}
when multiple packages define a class with that name. Thanks to
Gabor Csardi for the report.
\item Fix for detaching a package when two classes of the same name
are present in method signatures for the same generic. Thanks to
Gabor Csardi for the report.
\item \code{match.arg("", c("", "a", "B"))} gives a better error
message, in part from \PR{17959}, thanks to Elin Waring.
\item \command{R CMD Sweave --clean} no longer removes
pre-existing files or subdirectories (\PR{18242}).
\item The \code{quartz()} device no longer splits polylines into
subpaths. That has caused narrowly-spaced lines with many points
to always look solid even when dashed line type was used due to
dash phase restarts.
\item Deparsing constructs such as \code{quote(1 + `!`(2) + 3)} works
again as before R 3.5.0, thanks to the report and patch in \PR{18284}
by Suharto Anggono.
\item \code{as.list(f)} for a \code{factor} \code{f} now keeps
\code{names(f)}, fixing \PR{18309}.
\item \code{qbeta(.001, .9, .009)} and analogous \code{qf()} calls now
return a correct value instead of \code{NaN} or wrongly \code{1}, all
with a warning; thanks to the report by Ludger Goeminne in \PR{18302}.
\item \code{plot.lm()} failed to produce the plot of residuals vs.
factor levels (i.e., \code{which=5} when leverages are constant)
for models with character predictors (\PR{17840}).
\item \code{interaction.plot(..., xtick = TRUE)} misplaced the
x-axis line (\PR{18305}).
\item Not strictly fixing a bug, \code{format()}ing and
\code{print()}ing of non-finite \code{Date} and \code{POSIXt}
values \code{NaN} and \eqn{\pm}{+/-}\code{Inf} no longer show as
\code{NA} but the respective string, e.g., \code{Inf}, for
consistency with numeric vector's behaviour, fulfilling the wish
of \PR{18308}.
\item \command{R CMD check} no longer runs test scripts generated
from corresponding \file{.Rin} files twice and now signals an
ERROR if processing an \file{.Rin} script fails.
\item \code{tools::Rd2txt()} used for plain-text help pages now renders
\verb{\href}s (if \code{tools::Rd2txt_options(showURLs = TRUE)})
and \verb{\url}s with percent-encoding and standards-compliant
delimiting style (angle brackets and no \samp{URL: } prefix).
\verb{\email} is now rendered with a \samp{mailto:} prefix.
}
}
}
\section{\Rlogo CHANGES IN R 4.1.3}{
\subsection{NEW FEATURES}{
\itemize{
\item The default version of Bioconductor has been changed to
3.14. (This is used by \code{setRepositories} and the menus in
GUIs.)
}
}
\subsection{UTILITIES}{
\itemize{
\item \command{R CMD check --as-cran} has a workaround for a bug
in versions of \command{file} up to at least 5.41 which
mis-identify DBF files last changed in 2022 as executables.
}
}
\subsection{C-LEVEL FACILITIES}{
\itemize{
\item The legacy S-compatibility macros \code{SINGLE_*} in
\file{R_ext/Constants.h} (included by \file{R.h}) are deprecated
and will be removed in \R 4.2.0.
}
}
\subsection{BUG FIXES}{
\itemize{
\item Initialization of self-starting \code{nls()} models with
initialization functions following the pre-R-4.1.0 API
(without the \code{...} argument) works again for now, with a
deprecation warning.
\item Fixed quoting of \code{~autodetect~} in Java setting defaults
to avoid inadvertent user lookup due to leading \code{~}, reported
in \PR{18231} by Harold Gutch.
\item \code{substr(., start, stop) <- v} now treats \emph{negative}
\code{stop} values correctly. Reported with a patch in \PR{18228} by
Brodie Gaslam.
\item Subscripting an array \code{x} without dimnames by a
\code{length(dim(x))}-column character matrix gave "random"
non-sense, now an error; reported in \PR{18244} by Mikael Jagan.
\item \code{...names()} now matches \code{names(list(...))} closely,
fixing \PR{18247}.
\item \code{all.equal(*, scale = s)} now works as intended when
\code{length(s) > 1}, partly thanks to Michael Chirico's \PR{18272}.
\item \code{print(x)} for long vectors \code{x} now also works for
named atomic vectors or lists and prints the correct number when
reaching the \code{getOption("max.print")} limit; partly thanks to a
report and proposal by Hugh Parsonage to the R-devel list.
\item \code{all.equal(<selfStart>, *)} no longer signals a deprecation
warning.
\item \code{reformulate(*, response=r)} gives a helpful error message
now when \code{length(r) > 1}, thanks to Bill Dunlap's \PR{18281}.
\item Modifying \code{globalCallingHandlers} inside
\code{withCallingHandlers()} now works or fails correctly, thanks to
Henrik Bengtsson's \PR{18257}.
\item \code{hist(<Date>, breaks = "days")} and
\code{hist(<POSIXt>, breaks = "secs")}
no longer fail for inputs of length 1.
\item \code{qbeta(.001, .9, .009)} and similar cases now converge
correctly thanks to Ben Bolker's report in \PR{17746}.
\item \code{window(x, start, end)} no longer wrongly signals
\dQuote{'start' cannot be after 'end'}, fixing \PR{17527} and
\PR{18291}.
\item \code{data()} now checks that its (rarely used) \code{list}
argument is a character vector -- a couple of packages passed other
types and gave incorrect results.
\item \code{which()} now checks its \code{arr.ind} argument is
TRUE rather coercing to logical and taking the first element --
which gave incorrect results in package code.
\item \code{model.weights()} and \code{model.offset()} more carefully
extract their model components, thanks to Ben Bolker and Tim Taylor's
R-devel post.
\item \code{list.files(recursive = TRUE)} now shows all broken
symlinks (previously, some of them may have been omitted, \PR{18296}).
}
}
}
\section{\Rlogo CHANGES IN R 4.1.2}{
\subsection{C-LEVEL FACILITIES}{
\itemize{
\item The workaround in headers \file{R.h} and \file{Rmath.h}
(\code{using namespace std;}) for the Oracle Developer Studio
compiler is no longer needed now C++11 is required so has been
removed. A couple more usages of \code{log()} (which should have
been \code{std::log()}) with an \code{int} argument are reported on
Solaris.
\item The undocumented limit of 4095 bytes on messages from the
S-compatibility macros \code{PROBLEM} and \code{MESSAGE} is now
documented and longer messages will be silently truncated rather
than potentially causing segfaults.
\item If the \code{R_NO_SEGV_HANDLER} environment variable is
non-empty, the signal handler for SEGV/ILL/BUS signals (which
offers recovery user interface) is not set. This allows more
reliable debugging of crashes that involve the console.
}
}
\subsection{DEPRECATED AND DEFUNCT}{
\itemize{
\item The legacy S-compatibility macros \code{PROBLEM},
\code{MESSAGE}, \code{ERROR}, \code{WARN}, \code{WARNING},
\code{RECOVER}, \dots{} are deprecated and will be hidden in \R
4.2.0. \R{}'s native interface of \code{Rf_error} and
\code{Rf_warning} has long been preferred.
}
}
\subsection{BUG FIXES}{
\itemize{
\item \code{.mapply(F, dots, .)} no longer segfaults when
\code{dots} is not a \code{list} and uses \code{match.fun(F)} as
always documented; reported by Andrew Simmons in \PR{18164}.
\item \code{hist(<Date>, ...)} and \code{hist(<POSIXt>, ...)}
no longer pass arguments for \code{rect()} (such as \code{col} and
\code{density}) to \code{axis()}. (Thanks to Sebastian Meyer's
\PR{18171}.)
\item \verb{\Sexpr{ch}} now preserves \code{Encoding(ch)}. (Thanks to
report and patch by Jeroen Ooms in \PR{18152}.)
\item Setting the RNG to \code{"Marsaglia-Multicarry"} e.g., by
\code{RNGkind()}, now warns in more places, thanks to
André Gillibert's report and patch in \PR{18168}.
\item \code{gray(numeric(), alpha=1/2)} no longer segfaults, fixing
\PR{18183}, reported by Till Krenz.
\item Fixed \code{dnbinom(x, size=<very_small>, .., log=TRUE)}
regression, reported by Martin Morgan.
\item \code{as.Date.POSIXlt(x)} now keeps \code{names(x)}, thanks to
Davis Vaughan's report and patch in \PR{18188}.
\item \code{model.response()} now strips an \code{"AsIs"} class typically,
thanks to Duncan Murdoch's report and other discussants in \PR{18190}.
\item \code{try()} is considerably faster in case of an error and
long call, as e.g., from some \code{do.call()}. Thanks to
Alexander Kaever's suggestion posted to R-devel.
\item \code{qqline(y = <object>)} such as \code{y=I(.)}, now works,
see also \PR{18190}.
\item Non-integer \code{mgp} \code{par()} settings are now handled
correctly in \code{axis()} and \code{mtext()}, thanks to Mikael
Jagan and Duncan Murdoch's report and suggestion in \PR{18194}.
\item \code{formatC(x)} returns length zero \code{character()} now,
rather than \code{""} when \code{x} is of length zero, as documented,
thanks to Davis Vaughan's post to R-devel.
\item \code{removeSource(fn)} now retains (other) \code{attributes(fn)}.
}
}
}
\section{\Rlogo CHANGES IN R 4.1.1}{
\subsection{NEW FEATURES}{
\itemize{
\item \code{require(\var{pkg}, quietly = TRUE)} is quieter and in
particular does not warn if the package is not found.
}
}
\subsection{DEPRECATED AND DEFUNCT}{
\itemize{
\item Use of \samp{ftp://} URIs should be regarded as
deprecated, with on-going support confined to \code{method =
"libcurl"} and not routinely tested. (Nowadays no major browser
supports them.)
\item The non-default \code{method = "internal"} is deprecated for
\samp{http://} and \samp{ftp://} URIs for both
\code{download.file} and \code{url}.
\item On Windows, \code{method = "wininet"} is deprecated for
\samp{http://}, \samp{https://} and \samp{ftp://} URIs for both
\code{download.file} and \code{url}. (A warning is only given for
\samp{ftp://}.)
For \samp{ftp://} URIs the default method is now \code{"libcurl"}
if available (which it is on \acronym{CRAN} builds).
\code{method = "wininet"} remains the default for \samp{http://}
and \samp{https://} URIs but if \code{libcurl} is available, using
\code{method = "libcurl"} is preferred.
}
}
\subsection{INSTALLATION}{
\itemize{
\item \command{make check} now works also without a LaTeX
installation. (Thanks to Sebastian Meyer's \PR{18103}.)
}
}
\subsection{BUG FIXES}{
\itemize{
\item \command{make check-devel} works again in an \R build
configured with \option{--without-recommended-packages}.
\item \code{qnbinom(p, size, mu)} for large \code{size/mu} is correct
now in a range of cases (\PR{18095}); similarly for the \code{(size,
prob)} parametrization of the negative binomial. Also \code{qpois()}
and \code{qbinom()} are better and or faster for extreme cases. The
underlying C code has been modularized and is common to all four cases
of discrete distributions.
\item \code{gap.axis} is now part of the \code{axis()} arguments which
are passed from \code{bxp()}, and hence \code{boxplot()}. (Thanks to
Martin Smith's report and suggestions in \PR{18109}.)
\item \code{.First} and \code{.Last} can again be set from the site
profile.
\item \code{seq.int(from, to, *)} and \code{seq.default(..)} now work
better in large range cases where \code{from-to} is infinite where
the two boundaries are finite.
\item \code{all.equal(x,y)} now returns \code{TRUE} correctly also
when several entries of \code{abs(x)} and \code{abs(y)} are close to
\code{.Machine$double.xmax}, the largest finite \code{numeric}.
\item \code{model.frame()} now clears the object bit when removing the
\code{class} attribute of a value via \code{na.action} (\PR{18100}).
\item \code{charClass()} now works with multi-character
strings on Windows (\PR{18104}, fixed by Bill Dunlap).
\item \code{encodeString()} on Solaris now works again in Latin-1
encoding on characters represented differently in UTF-8. Support for
surrogate pairs on Solaris has been improved.
\item \code{file.show()} on Windows now works with non-ASCII path
names representable in the current native encoding (\PR{18132}).
\item Embedded \R on Windows can now find \R home directory via the
registry even when installed only for the current user (\PR{18135}).
\item \code{pretty(x)} with finite \code{x} now returns finite values
also in the case where the extreme \code{x} values are close in size
to the maximal representable number \code{.Machine$double.xmax}.
Also, it's been tweaked for very small ranges and when a boundary is
close (or equal) to zero; e.g., \code{pretty(c(0,1e-317))} no longer
has negative numbers, currently still warning about a very small
range, and \code{pretty(2^-(1024 - 2^-1/(c(24,10))))} is more accurate.
\item The error message for not finding vignette files when weaving
has correct file sizes now. (Thanks to Sebastian Meyer's \PR{18154}.)
\item \code{dnbinom(20, <large>, 1)} now correctly gives 0, and
similar cases are more accurate with underflow precaution.
(Reported by Francisco Vera Alcivar in \PR{18072}.)
}
}
}
\section{\Rlogo CHANGES IN R 4.1.0}{
\subsection{FUTURE DIRECTIONS}{
\itemize{
\item It is planned that the 4.1.x series will be the last to
support 32-bit Windows, with production of binary packages for
that series continuing until early 2023.
}
}
\subsection{SIGNIFICANT USER-VISIBLE CHANGES}{
\itemize{
\item Data set \code{esoph} in package \pkg{datasets} now provides
the correct numbers of controls; previously it had the numbers of
cases added to these. (Reported by Alexander Fowler in \PR{17964}.)
}
}
\subsection{NEW FEATURES}{
\itemize{
\item \samp{www.omegahat.net} is no longer one of the repositories
known by default to \code{setRepositories()}. (Nowadays it only
provides source packages and is often unavailable.)
%% it had one Windows binary package for 4.0, none for 3.6.
\item Function \code{package_dependencies()} (in package
\pkg{tools}) can now use different dependency types for direct and
recursive dependencies.
\item The checking of the size of tarball in
\command{R CMD check --as-cran <pkg>} may be tweaked via the new
environment variable
\env{_R_CHECK_CRAN_INCOMING_TARBALL_THRESHOLD_}, as suggested in
\PR{17777} by Jan Gorecki.
\item Using \code{c()} to combine a factor with other factors now
gives a factor, an ordered factor when combining ordered factors
with identical levels.
\item \code{apply()} gains a \code{simplify} argument to allow
disabling of simplification of results.
\item The \code{format()} method for class \code{"ftable"} gets a
new option \code{justify}. (Suggested by Thomas Soeiro.)
\item New \code{...names()} utility. (Proposed by Neal Fultz in
\PR{17705}.)
\item \code{type.convert()} now warns when its \code{as.is} argument
is not specified, as the help file always said it \emph{should}. In
that case, the default is changed to \code{TRUE} in line with its
change in \code{read.table()} (related to \code{stringsAsFactors}) in
\R 4.0.0.
\item When printing list arrays, classed objects are now shown
\emph{via} their \code{format()} value if this is a short enough
character string, or by giving the first elements of their class
vector and their length.
\item \code{capabilities()} gets new entry \code{"Rprof"} which is
\code{TRUE} when \R has been configured with the equivalent of
\command{--enable-R-profiling} (as it is by default). (Related to
Michael Orlitzky's report \PR{17836}.)
\item \code{str(xS4)} now also shows extraneous attributes of an
S4 object \code{xS4}.
\item Rudimentary support for vi-style tags in \code{rtags()} and
\code{R CMD rtags} has been added. (Based on a patch from Neal
Fultz in \PR{17214}.)
\item \code{checkRdContents()} is now exported from \pkg{tools}; it
and also \code{checkDocFiles()} have a new option \code{chkInternal}
allowing to check Rd files marked with keyword \code{"internal"} as
well. The latter can be activated for \command{R CMD check} via
environment variable \env{_R_CHECK_RD_INTERNAL_TOO_}.
\item New functions \code{numToBits()} and \code{numToInts()}
extend the \code{raw} conversion utilities to (double precision)
\code{numeric}.
\item Functions \code{URLencode()} and \code{URLdecode()} in
package \pkg{utils} now work on vectors of URIs.
(Based on patch from Bob Rudis submitted with \PR{17873}.)
\item \code{path.expand()} can expand \samp{~user} on most
Unix-alikes even when \code{readline} is not in use. It tries
harder to expand \samp{~}, for example should environment variable
\env{HOME} be unset.
\item For HTML help (both dynamic and static), Rd file links to
help pages in external packages are now treated as references to
topics rather than file names, and fall back to a file link only
if the topic is not found in the target package. The earlier rule
which prioritized file names over topics can be restored by
setting the environment variable \env{_R_HELP_LINKS_TO_TOPICS_} to
a false value.
\item \code{c()} now removes \code{NULL} arguments before
dispatching to methods, thus simplifying the implementation of
\code{c()} methods, \emph{but} for back compatibility keeps
\code{NULL} when it is the first argument. (From a report and
patch proposal by Lionel Henry in \PR{17900}.)
\item \code{Vectorize()}'s result function's environment no longer
keeps unneeded objects.
\item Function \code{...elt()} now propagates visibility
consistently with \code{..n}. (Thanks to Lionel Henry's
\PR{17905}.)
\item \code{capture.output()} no longer uses non-standard
evaluation to evaluate its arguments. This makes evaluation of
functions like \code{parent.frame()} more consistent. (Thanks to
Lionel Henry's \PR{17907}.)
\item \code{packBits(bits, type="double")} now works as inverse of
\code{numToBits()}. (Thanks to Bill Dunlap's proposal in
\PR{17914}.)
\item \code{curlGetHeaders()} has two new arguments,
\code{timeout} to specify the timeout for that call (overriding
\code{getOption("timeout")}) and \code{TLS} to specify the minimum
TLS protocol version to be used for \code{https://} URIs
(\emph{inter alia} providing a means to check for sites using
deprecated TLS versions 1.0 and 1.1).
\item For \code{nls()}, an optional constant \code{scaleOffset}
may be added to the denominator of the relative offset convergence
test for cases where the fit of a model is expected to be exact,
thanks to a proposal by John Nash. \code{nls(*, trace=TRUE)} now
also shows the convergence criterion.
\item Numeric differentiation \emph{via} \code{numericDeriv()}
gets new optional arguments \code{eps} and \code{central}, the
latter for taking central divided differences. The latter can be
activated for \code{nls()} via \code{nls.control(nDcentral =
TRUE)}.
\item \code{nls()} now passes the \code{trace} and \code{control}
arguments to \code{getInitial()}, notably for all self-starting models,
so these can also be fit in zero-noise situations via a
\code{scaleOffset}. For this reason, the \code{initial} function of a
\code{selfStart} model must now have \code{...} in its argument list.
\item \code{bquote(splice = TRUE)} can now splice expression
vectors with attributes: this makes it possible to splice the
result of \code{parse(keep.source = TRUE)}. (Report and patch
provided by Lionel Henry in \PR{17869}.)
\item \code{textConnection()} gets an optional \code{name} argument.
\item \code{get()}, \code{exists()}, and \code{get0()} now signal
an error if the first argument has length greater than 1.
Previously additional elements were silently ignored. (Suggested
by Antoine Fabri on R-devel.)
\item \R{} now provides a shorthand notation for creating functions,
e.g. \code{\(x) x + 1} is parsed as \code{function(x) x + 1}.
\item \R{} now provides a simple native forward pipe syntax
\code{|>}. The simple form of the forward pipe inserts the
left-hand side as the first argument in the right-hand side call.
The pipe implementation as a syntax transformation was motivated
by suggestions from Jim Hester and Lionel Henry.
\item \code{all.equal(f, g)} for \code{function}s now by default also
compares their \code{environment(.)}s, notably via new
\code{all.equal} method for class \code{function}. Comparison of
\code{nls()} fits, e.g., may now need \code{all.equal(m1, m2,
check.environment = FALSE)}.
\item \code{.libPaths()} gets a new option \code{include.site},
allowing to \emph{not} include the site library. (Thanks to Dario
Strbenac's suggestion and Gabe Becker's \PR{18016}.)
\item Lithuanian translations are now available. (Thanks to
Rimantas Žakauskas.)
\item \code{names()} now works for \code{DOTSXP} objects. On the
other hand, in \file{R-lang}, the R language manual, we now warn
against relying on the structure or even existence of such
dot-dot-dot objects.
\item \code{all.equal()} no longer gives an error on \code{DOTSXP}
objects.
%% The Homebrew arm64 libs have cairo but not cairo-xlib
\item \code{capabilities("cairo")} now applies only to the
file-based devices as it is now possible (if very unusual) to
build \R with Cairo support for those but not for \code{X11()}.
\item There is optional support for tracing the progress of
\code{loadNamespace()} --- see its help.
\item (Not Windows.)
\code{l10n_info()} reports an additional element, the name of the
encoding as reported by the OS (which may differ from the
encoding part (if any) of the result from
\code{Sys.getlocale("LC_CTYPE")}).
\item New function \code{gregexec()} which generalizes \code{regexec()}
to find \emph{all} disjoint matches and all substrings
corresponding to parenthesized subexpressions of the given regular
expression. (Contributed by Brodie Gaslam.)
\item New function \code{charClass()} in package \pkg{utils} to
query the wide-character classification functions in use (such as
\code{iswprint}).
\item The names of \code{quantile()}'s result no longer depend on the
global \code{getOption("digits")}, but \code{quantile()} gets a new
optional argument \code{digits = 7} instead.
\item \code{grep()}, \code{sub()}, \code{regexp} and variants work
considerably faster for long factors with few levels. (Thanks to
Michael Chirico's \PR{18063}.)
\item Provide grouping of \code{x11()} graphics windows within
a window manager such as \code{Gnome} or \code{Unity}; thanks to a
patch by Ivan Krylov posted to R-devel.
\item The \code{split()} method for class \code{data.frame} now
allows the \code{f} argument to be specified as a formula.
\item \code{sprintf} now warns on arguments unused by the format
string.
\item New palettes \code{"Rocket"} and \code{"Mako"} for
\code{hcl.colors()} (approximating palettes of the same name
from the \pkg{viridisLite} package).
Contributed by Achim Zeileis.
\item The base environment and its namespace are now locked (so
one can no longer add bindings to these or remove from these).
\item \command{Rterm} handling of multi-byte characters has been
improved, allowing use of such characters when supported by the
current locale.
\item \command{Rterm} now accepts \code{ALT+ +xxxxxxxx} sequences to
enter Unicode characters as hex digits.
\item Environment variable \env{LC_ALL} on Windows now takes
precedence over \env{LC_CTYPE} and variables for other supported
categories, matching the POSIX behaviour.
\item \code{duplicated()} and \code{anyDuplicated()} are now
optimized for integer and real vectors that are known to be sorted
via the ALTREP framework. Contributed by Gabriel Becker via \PR{17993}.
}
}
\subsection{GRAPHICS}{
\itemize{
\item The graphics engine version, \code{R_GE_version}, has been
bumped to \code{14} and so packages that provide graphics devices
should be reinstalled.
\item Graphics devices should now specify \code{deviceVersion} to
indicate what version of the graphics engine they support.
\item Graphics devices can now specify \code{deviceClip}. If
\code{TRUE}, the graphics engine will never perform any clipping
of output itself.
The clipping that the graphics engine does perform (for both
\code{canClip = TRUE} and \code{canClip = FALSE}) has been
improved to avoid producing unnecessary artifacts in clipped
output.
\item The \pkg{grid} package now allows \code{gpar(fill)} to be
a \code{linearGradient()}, a \code{radialGradient()}, or a
\code{pattern()}. The \code{viewport(clip)} can now also be
a grob, which defines a clipping path, and there is a new
\code{viewport(mask)} that can also be a grob, which defines
a mask.
These new features are only supported so far on the Cairo-based
graphics devices and on the \code{pdf()} device.
\item (Not Windows.)
A warning is given when a Cairo-based type is specified for a
\code{png()}, \code{jpeg()}, \code{tiff()} or \code{bmp()}
device but Cairo is unsupported (so \code{type = "Xlib"}
is tried instead).
\item \code{grSoftVersion()} now reports the versions of FreeType
and FontConfig if they are used directly (not \emph{via} Pango),
as is most commonly done on macOS.
}
}
\subsection{C-LEVEL FACILITIES}{
\itemize{
\item The \emph{standalone} \file{libRmath} math library and \R's C
API now provide \code{log1pexp()} again as documented, and gain
\code{log1mexp()}.
}
}
\subsection{INSTALLATION on a UNIX-ALIKE}{
\itemize{
\item \command{configure} checks for a program \command{pkgconf}
if program \command{pkg-config} is not found. These are now only
looked for on the path (like almost all other programs) so if needed
specify a full path to the command in \code{PKG_CONFIG}, for example
in file \file{config.site}.
\item C99 function \code{iswblank} is required -- it was last seen
missing ca 2003 so the workaround has been removed.
\item There are new \command{configure} options
\option{--with-internal-iswxxxxx},
\option{--with-internal-towlower} and
\option{--with-internal-wcwidth} which allows the system functions
for wide-character classification, case-switching and width
(\code{wcwidth} and \code{wcswidth}) to be replaced by internal
ones. The first has long been used on macOS, AIX (and Windows)
but this enables it to be unselected there and selected for other
platforms (it is the new default on Solaris). The second is new
in this version of \R and is selected by default on macOS and
Solaris. The third has long been the default and remains so as it
contains customizations for East Asian languages.
System versions of these functions are often minimally implemented
(sometimes only for ASCII characters) and may not cover the full
range of Unicode points: for example Solaris (and Windows) only
cover the Basic Multilingual Plane.
\item Cairo installations without X11 are more likely to be
detected by \command{configure}, when the file-based Cairo
graphics devices will be available but not \code{X11(type =
"cairo")}.
\item There is a new \command{configure} option
\option{--with-static-cairo} which is the default on macOS. This
should be used when only static cairo (and where relevant, Pango)
libraries are available.
\item Cairo-based graphics devices on platforms without Pango but
with FreeType/FontConfig will make use of the latter for font selection.
}
}
\subsection{LINK-TIME OPTIMIZATION on a UNIX-ALIKE}{
\itemize{
\item Configuring with flag \option{--enable-lto=R} now also uses
LTO when installing the recommended packages.
\item \command{R CMD INSTALL} and \command{R CMD SHLIB} have a new
flag \option{--use-LTO} to use LTO when compiling code, for use
with \R configured with \option{--enable-lto=R}. For \R
configured with \option{--enable-lto}, they have the new flag
\option{--no-use-LTO}.
Packages can opt in or out of LTO compilation \emph{via} a
\samp{UseLTO} field in the \file{DESCRIPTION} file. (As usual this
can be overridden by the command-line flags.)
}
}
\subsection{BUILDING R on Windows}{
\itemize{
\item for GCC \eqn{\ge}{>=} 8, \code{FC_LEN_T} is defined in
\file{config.h} and hence character lengths are passed from C to
Fortran in \emph{inter alia} BLAS and LAPACK calls.
\item There is a new text file
\file{src/gnuwin32/README.compilation}, which outlines how C/Fortran
code compilation is organized and documents new features:
\itemize{
\item \R can be built with Link-Time Optimization with a
suitable compiler -- doing so with GCC 9.2 showed several
inconsistencies which have been corrected.
\item There is support for cross-compiling the C and Fortran
code in \R and standard packages on suitable (Linux) platforms.
This is mainly intended to allow developers to test later
versions of compilers -- for example using GCC 9.2 or 10.x has
detected issues that GCC 8.3 in Rtools40 does not.
\item There is experimental support for cross-building \R
packages with C, C++ and/or Fortran code.
}
\item The R installer can now be optionally built to support a single
architecture (only 64-bit or only 32-bit).
}
}
\subsection{PACKAGE INSTALLATION}{
\itemize{
\item The default C++ standard has been changed to C++14 where
available (which it is on all currently checked platforms): if not
(as before) C++11 is used if available otherwise C++ is not
supported.
Packages which specify C++11 will still be installed using C++11.
C++14 compilers may give deprecation warnings, most often for
\code{std::random_shuffle} (deprecated in C++14 and removed in
C++17). Either specify C++11 (see \sQuote{Writing R Extensions})
or modernize the code and if needed specify C++14. The latter has
been supported since \R 3.4.0 so the package's \file{DESCRIPTION}
would need to include something like
\preformatted{
Depends: R (>= 3.4)
}
}
}
\subsection{PACKAGE INSTALLATION on Windows}{
\itemize{
\item \command{R CMD INSTALL} and \command{R CMD SHLIB} make use
of their flag \option{--use-LTO} when the \samp{LTO_OPT} make
macro is set in file \file{etc/$\{R_ARCH\}/Makeconf} or in a
personal/site \file{Makevars} file. (For details see
\sQuote{Writing R Extensions} §4.5.)
This provides a valuable check on code consistency. It does work
with GCC 8.3 as in Rtools40, but that does not detect everything
the \acronym{CRAN} checks with current GCC do.
}
}
\subsection{PACKAGE INSTALLATION on macOS}{
\itemize{
\item The default personal library directory on builds with
\option{--enable-aqua} (including \acronym{CRAN} builds) now
differs by CPU type, one of
\preformatted{
~/Library/R/x86_64/x.y/library
~/Library/R/arm64/x.y/library
}
This uses the CPU type \R (and hence the packages) were built for,
so when a \samp{x86_64} build of R is run under Rosetta emulation on
an \samp{arm64} Mac, the first is used.
}
}
\subsection{UTILITIES}{
\itemize{
\item \command{R CMD check} can now scan package functions for
bogus \code{return} statements, which were possibly intended as
\code{return()} calls (wish of \PR{17180}, patch by Sebastian
Meyer). This check can be activated via the new environment
variable \env{_R_CHECK_BOGUS_RETURN_}, true for \code{--as-cran}.
\item \command{R CMD build} omits tarballs and binaries of
previous builds from the top-level package directory.
(\PR{17828}, patch by Sebastian Meyer.)
\item \command{R CMD check} now runs sanity checks on the use of
\samp{LazyData}, for example that a \file{data} directory is
present and that \samp{LazyDataCompression} is not specified
without \samp{LazyData} and has a documented value. For packages
with large LazyData databases without specifying
\samp{LazyDataCompression}, there is a reference to the code given
in \sQuote{Writing R Extensions} §1.1.6 to test the choice of
compression (as in all the \acronym{CRAN} packages tested a
non-default method was preferred).
\item \command{R CMD build} removes \samp{LazyData} and
\samp{LazyDataCompression} fields from the \file{DESCRIPTION} file
of packages without a \file{data} directory.
}
}
\subsection{ENCODING-RELATED CHANGES}{
\itemize{
\item The parser now treats \samp{\\Unnnnnnnn} escapes larger than
the upper limit for Unicode points (\samp{\\U10FFFF}) as an error
as they cannot be represented by valid UTF-8.
Where such escapes are used for outputting non-printable
(including unassigned) characters, 6 hex digits are used (rather
than 8 with leading zeros). For clarity, braces are used, for
example \samp{\\U\{0effff\}}.
\item The parser now looks for non-ASCII spaces on Solaris (as
previously on most other OSes).
\item There are warnings (including from the parser) on the use of
unpaired surrogate Unicode points such as \samp{\\uD834}. (These
cannot be converted to valid UTF-8.)
\item Functions \code{nchar()}, \code{tolower()}, \code{toupper()}
and \code{chartr()} and those using regular expressions have more
support for inputs with a marked Latin-1 encoding.
\item The character-classification functions used (by default) to
replace the system \code{iswxxxxx} functions on Windows, macOS and
AIX have been updated to Unicode 13.0.0.
The character-width tables have been updated to include new
assignments in Unicode 13.0.0. This included treating all control
characters as having zero width.
\item The code for evaluating default (extended) regular
expressions now uses the same character-classification functions
as the rest of \R (previously they differed on Windows, macOS and
AIX).
\item There is a build-time option to replace the system's
wide-character \code{wctrans} C function by tables shipped with
\R: use \command{configure} option
\option{--with-internal-towlower} or (on Windows)
\samp{-DUSE_RI18N_CASE} in \samp{CFLAGS} when building \R. This
may be needed to allow \code{tolower()} and \code{toupper()} to
work with Unicode characters beyond the Basic Multilingual Plane
where not supported by system functions (e.g. on Solaris where it
is the new default).
\item R is more careful when truncating UTF-8 and other multi-byte
strings that are too long to be printed, passed to the system or
libraries or placed into an internal buffer. Truncation will no
longer produce incomplete multibyte characters.
}
}
\subsection{DEPRECATED AND DEFUNCT}{
\itemize{
\item Function \code{plclust()} from the package \pkg{stats} and
\code{package.dependencies()}, \code{pkgDepends()},
\code{getDepList()}, \code{installFoundDepends()}, and
\code{vignetteDepends()} from package \pkg{tools} are defunct.
\item Defunct functions \code{checkNEWS()} and \code{readNEWS()} from
package \pkg{tools} and \code{CRAN.packages()} from \pkg{utils} have
been removed.
\item \command{R CMD config CXXCPP} is defunct (it was deprecated
in \R{} 3.6.2).
\item \code{parallel::detectCores()} drops support for Irix
(retired in 2013).
\item The \code{LINPACK} argument to \code{chol.default()},
\code{chol2inv()}, \code{solve.default()} and \code{svd()} has
been defunct since \R 3.1.0. It was silently ignored up to \R
4.0.3 but now gives an error.
\item Subsetting/indexing, such as \code{ddd[*]} or \code{ddd$x}
on a \code{DOTSXP} (dot-dot-dot) object \code{ddd} has been
disabled; it worked by accident only and was undocumented.
}
}
\subsection{BUG FIXES}{
\itemize{
\item Many more C-level allocations (mainly by \code{malloc} and
\code{strdup}) are checked for success with suitable alternative
actions.
\item Bug fix for \code{replayPlot()}; this was turning off
graphics engine display list recording if a recorded plot was
replayed in the same session. The impact of the bug became
visible if resize the device after replay OR if attempted another
\code{savePlot()} after replay (empty display list means empty
screen on resize or empty saved plot).
\item \command{R CMD check} etc now warn when a package exports
non-existing S4 classes or methods, also in case of no
\dQuote{methods} presence. (Reported by Alex Bertram;
reproducible example and patch by Sebastian Meyer in \PR{16662}.)
\item \code{boxplot()} now also accepts \code{call}s for labels such
as \code{ylab}, the same as \code{plot()}. (Reported by Marius Hofert.)
\item The help page for \code{xtabs()} now correctly states that
\code{addNA} is setting \code{na.action = na.pass} among others.
(Reported as \PR{17770} by Thomas Soeiro.)
\item The \command{R CMD check <pkg>} gives a longer and more
comprehensible message when \file{DESCRIPTION} misses dependencies,
e.g., in \code{Imports:}. (Thanks to the contributors of \PR{17179}.)
\item \code{update.default()} now calls the generic \code{update()}
on the formula to work correctly for models with extended formulas.
(As reported and suggested by Neal Fultz in \PR{17865}.)
\item The horizontal position of leaves in a dendrogram is now
correct also with \code{center = FALSE}. (\PR{14938}, patch from
Sebastian Meyer.)
\item \code{all.equal.POSIXt()} no longer warns about and
subsequently ignores inconsistent \code{"tzone"} attributes, but
describes the difference in its return value (\PR{17277}).
This check can be disabled \emph{via} the new argument
\code{check.tzone = FALSE} as suggested by Sebastian Meyer.
\item \code{as.POSIXct()} now populates the \code{"tzone"}
attribute from its \code{tz} argument when \code{x} is a logical
vector consisting entirely of \code{NA} values.
\item \code{x[[2^31]] <- v} now works. (Thanks to the report and
patch by Suharto Anggono in \PR{17330}.)
\item In log-scale graphics, \code{axis()} ticks and label positions
are now computed more carefully and symmetrically in their range,
typically providing \emph{more} ticks, fulfilling wishes
in \PR{17936}. The change really corresponds to an improved
\code{axisTicks()} (package \pkg{grDevices}), potentially influencing
\pkg{grid} and \pkg{lattice}, for example.
\item \code{qnorm(<very large negative>, log.p=TRUE)} is now correct
to at least five digits where it was catastrophically wrong,
previously.
\item \code{sum(df)} and similar \code{"Summary"}- and
\code{"Math"}-group member functions now work for data frames
\code{df} with \code{\link{logical}} columns, notably also of zero
rows. (Reported to R-devel by Martin \dQuote{b706}.)
\item \code{unsplit()} had trouble with tibbles due to unsound use of
\code{rep(NA, len)}-indexing, which should use \code{NA_integer_}
(Reported to R-devel by Mario Annau.)
\item \code{pnorm(x, log.p = TRUE)} underflows to \code{-Inf} slightly
later.
\item \code{show(<hidden S4 generic>)} prints better and without
quotes for non-hidden S4 generics.
\item \code{read.table()} and relatives treated an "NA" column name as
missing when \code{check.names = FALSE} \PR{18007}.
\item Parsing strings containing UTF-16 surrogate pairs such as
\code{"\uD834\uDD1E"} works better on some (uncommon) platforms.
\code{sprintf("\%X", utf8ToInt("\uD834\uDD1E"))} should now give
\code{"1D11E"} on all platforms.
%% failed on Solaris
\item \code{identical(x,y)} is no longer true for differing
\code{DOTSXP} objects, fixing \PR{18032}.
\item \code{str()} now works correctly for \code{DOTSXP} and related
exotics, even when these are doomed.
Additionally, it no longer fails for \code{list}s with a \code{class} and
\dQuote{irregular} method definitions such that e.g. \code{lapply(*)} will
necessarily fail, as currently for different \CRANpkg{igraph} objects.
\item Message translation domains, e.g., for errors and warnings, are
now correctly determined also when e.g., a \pkg{base} function is
called from \dQuote{top-level} function (i.e., defined in \code{globalenv()}),
thanks to a patch from Joris Goosen fixing \PR{17998}.
\item Too long lines in environment files (e.g., \file{Renviron}) no
longer crash \R. This limit has been increased to 100,000 bytes.
(\PR{18001}.)
\item There is a further workaround for FreeType giving
incorrect italic font faces with cairo-based graphics devices on
macOS.
\item \code{add_datalist(*, force = TRUE)} (from package
\pkg{tools}) now actually updates an existing \file{data/datalist}
file for new content. (Thanks to a report and patch by Sebastian
Meyer in \PR{18048}.)
\item \code{cut.Date()} and \code{cut.POSIXt()} could produce an
empty last interval for \code{breaks = "months"} or \code{breaks =
"years"}. (Reported as \PR{18053} by Christopher Carbone.)
\item Detection of the encoding of \sQuote{regular} macOS locales
such as \samp{en_US} (which is UTF-8) had been broken by a macOS
change: fortunately these are now rarely used with
\samp{en_US.UTF-8} being preferred.
\item \code{sub()} and \code{gsub(pattern, repl, x, *)} now keep
attributes of \code{x} such as \code{names()} also when
\code{pattern} is \code{NA} (\PR{18079}).
\item Time differences (\code{"difftime"} objects) get a replacement
and a \code{rep()} method to keep \code{"units"} consistent.
(Thanks to a report and patch by Nicolas Bennett in \PR{18066}.)
\item The \verb{\RdOpts} macro, setting defaults for \verb{\Sexpr}
options in an Rd file, had been ineffective since \R 2.12.0: it
now works again.
(Thanks to a report and patch by Sebastian Meyer in \PR{18073}.)
\item \code{mclapply} and \code{pvec} no longer accidentally terminate
parallel processes started before by \code{mcparallel} or related
calls in package \pkg{parallel} (\PR{18078}).
\item \code{grep} and other functions for evaluating (extended)
regular expressions handle in Unicode also strings not explicitly
flagged UTF-8, but flagged native when running in UTF-8 locale.
\item Fixed a crash in \code{fifo} implementation on Windows
(\PR{18031}).
\item Binary mode in \code{fifo} on Windows is now properly detected
from argument \code{open} (\PR{15600}, \PR{18031}).
}
}
}
\section{\Rlogo CHANGES IN R 4.0.5}{
\subsection{BUG FIXES}{
\itemize{
\item The change to the internal table in \R 4.0.4 for
\code{iswprint} has been reverted: it contained some errors in
printability of \sQuote{East Asian} characters.
\item For packages using \samp{LazyData}, \command{R CMD build}
ignored the \option{--resave-data} option and the
\samp{BuildResaveData} field of the \file{DESCRIPTION} file (in \R
versions 4.0.0 to 4.0.4).
}
}
}
\section{\Rlogo CHANGES IN R 4.0.4}{
\subsection{NEW FEATURES}{
\itemize{
\item File \file{share/texmf/tex/latex/jss.cls} has been updated
to work with LaTeX versions since Oct 2020.
\item Unicode character width tables (as used by
\code{nchar(, type = "w")}) have been updated to Unicode 12.1
by Brodie Gaslam (\PR{17781}), including many emoji.
\item The internal table for \code{iswprint} (used on Windows,
macOS and AIX) has been updated to include many recent Unicode
characters.
}
}
\subsection{INSTALLATION on a UNIX-ALIKE}{
\itemize{
\item If an external BLAS is specified by \option{--with-blas=foo}
or \emph{via} environment variable \env{BLAS_LIBS} is not found,
this is now a configuration error. The previous behaviour was not
clear from the documentation: it was to continue the search as if
\option{--with-blas=yes} was specified.
}
}
\subsection{BUG FIXES}{
\itemize{
\item \code{all.equal(x,y)} now \dQuote{sees} the two different
\code{NA}s in factors, thanks to Bill Dunlap and others in
\PR{17897}.
\item \code{(~ NULL)[1]} and similar formula subsetting now works,
thanks to a report and patch by Henrik Bengtsson in \PR{17935}.
Additionally, subsetting leaving an empty formula now works too,
thanks to suggestions by Suharto Anggono.
\item \code{.traceback(n)} keeps source references again, as before
\R 4.0.0, fixing a regression; introduced by the \PR{17580}, reported
including two patch proposals by Brodie Gaslam.
\item \code{unlist(plst, recursive=FALSE)} no longer drops content
for pairlists with list components, thanks to the report and patch
by Suharto Anggono in \PR{17950}.
\item \code{iconvlist()} now also works on MUSL based (Linux)
systems, from a report and patch suggestion by Wesley Chan in
\PR{17970}.
\item \code{round()} and \code{signif()} no longer tolerate wrong
argument names, notably in 1-argument calls; reported by Shane
Mueller on R-devel (mailing list); later reported as \PR{17976}.
\item \code{.Machine} has \code{longdouble.*} elements only if
\code{capabilities("long.double")} is true, as documented.
(Previously they were included if the platform had \code{long
double} identical to \code{double}, as ARM does.)
\item \code{p.adjust(numeric(), n=0)} now works, fixing \PR{18002}.
\item \code{identical(x,y)} no longer prints "Unknown Type .." for
\code{typeof(x) == "..."} objects.
\item Fix (auto-)\code{print()}ing of named complex vectors, see
\PR{17868} and \PR{18019}.
\item \code{all.equal(<language>, <...>)} now works, fixing \PR{18029}.
\item \code{as.data.frame.list(L, row.names=NULL)} now behaves in line
with \code{data.frame()}, disregarding names of components of
\code{L}, fixing \PR{18034}, reported by Kevin Tappe.
\item \code{checkRdaFiles(ff)$version} is now correct also when
\code{ff} contains files of different versions, thanks to a report
and patch from Sebastian Meyer in \PR{18041}.
\item macOS: Quartz device live drawing could fail (no plot is shown)
if the system changes the drawing context after view update (often
the case since macOS Big Sur). System log may show
"CGContextDelegateCreateForContext: invalid context" error.
}
}
}
\section{\Rlogo CHANGES IN R 4.0.3}{
\subsection{NEW FEATURES}{
\itemize{
\item On platforms using \command{configure} option
\option{--with-internal-tzcode}, additional values
\code{"internal"} and (on macOS only) \code{"macOS"} are accepted
for the environment variable \env{TZDIR}. (See \code{?TZDIR}.)
On macOS, \code{"macOS"} is used by default if the system timezone
database is a newer version than that in the \R installation.
\item When \code{install.packages(type = "source")} fails to find
a package in a repository it mentions package versions which are
excluded by their \R version requirement and links to hints on
why a package might not be found.
\item The default value for \code{options("timeout")} can be set
from environment variable \env{R_DEFAULT_INTERNET_TIMEOUT}, still
defaulting to 60 (seconds) if that is not set or invalid.
This may be needed when child \R processes are doing downloads,
for example during the installation of source packages which
download jars or other forms of data.
}
}
\subsection{LINK-TIME OPTIMIZATION on a UNIX-ALIKE}{
\itemize{
\item There is now support for parallelized Link-Time Optimization
(LTO) with GCC and for \sQuote{thin} LTO with
\command{clang} \emph{via} setting the \samp{LTO} macro.
\item There is support for setting a different LTO flag for the
Fortran compiler, including to empty when mixing \command{clang}
and \command{gfortran} (as on macOS). See file \file{config.site}.
\item There is a new \samp{LTO_LD} macro to set linker options for
LTO compilation, for example to select an alternative linker or
to parallelize thin LTO.
}
}
\subsection{DEPRECATED AND DEFUNCT}{
\itemize{
\item The \code{LINPACK} argument to \code{chol.default()},
\code{chol2inv()}, \code{solve.default()} and \code{svd()} has been
defunct since \R 3.1.0. Using it now gives a warning which will
become an error in \R 4.1.0.
}
}
\subsection{BUG FIXES}{
\itemize{
\item The code mitigating stack overflow with PCRE regexps on very
long strings is enabled for PCRE2 < 10.30 also when JIT is enabled,
since stack overflows have been seen in that case.
%% Ubuntu 16.04LTS has PCRE2 10.21
\item Fix to correctly show the group labels in \code{dotchart()}
(which where lost in the \code{ylab} improvement for \R 4.0.0).
\item \code{addmargins(*, ..)} now also works when \code{fn()} is a
local function, thanks to bug report and patch \PR{17124} from Alex
Bertram.
\item \code{rank(x)} and hence \code{sort(x)} now work when \code{x}
is an object (as per \code{is.object(x)}) of type \code{"raw"}
\emph{and} provides a valid \code{`[`} method, e.g., for
\code{gmp::as.bigz(.)} numbers.
\item \code{chisq.test(*, simulate.p.value=TRUE)} and
\code{r2dtable()} now work correctly for large table entries (in the
millions). Reported by Sebastian Meyer and investigated by more
helpers in \PR{16184}.
\item Low-level socket read/write operations have been fixed to
correctly signal communication errors. Previously, such errors could
lead to a segfault due to invalid memory access. Reported
and debugged by Dmitriy Selivanov in \PR{17850}.
\item \code{quantile(x, pr)} works more consistently for \code{pr}
values slightly outside [0,1], thanks to Suharto Anggono's \PR{17891}.
Further, \code{quantile(x, prN, names=FALSE)} now works even when
\code{prN} contains \code{NA}s, thanks to Anggono's \PR{17892}.
Ditto for ordered factors or \code{Date} objects
when \code{type = 1} or \code{3}, thanks to \PR{17899}.
\item Libcurl-based internet access, including
\code{curlGetHeaders()}, was not respecting the \code{"timeout"}
option. If this causes unanticipated timeouts, consider
increasing the default by setting \env{R_DEFAULT_INTERNET_TIMEOUT}.
\item \code{as.Date(<char>)} now also works with an initial
\code{""}, thanks to Michael Chirico's \PR{17909}.
\item \code{isS3stdGeneric(f)} now detects an S3 generic also when it
it is \code{trace()}d, thanks to Gabe Becker's \PR{17917}.
\item \code{R_allocLD()} has been fixed to return memory aligned for
long double type \PR{16534}.
\item \code{fisher.test()} no longer segfaults when called again after
its internal stack has been exceeded \PR{17904}.
\item Accessing a long vector represented by a compact integer
sequence no longer segfaults (reported and debugged by Hugh
Parsonage).
\item \code{duplicated()} now works also for strings with multiple
encodings inside a single vector \PR{17809}.
\item \code{phyper(11, 15, 0, 12, log.p=TRUE)} no longer gives
\code{NaN}; reported as \PR{17271} by Alexey Stukalov.
\item Fix incorrect calculation in \code{logLik.nls()} \PR{16100}, patch
from Sebastian Meyer.
\item A very old bug could cause a segfault in \code{model.matrix()}
when terms involved logical variables. Part of \PR{17879}.
\item \code{model.frame.default()} allowed \code{data = 1}, leading to
involuntary variable capture (rest of \PR{17879}).
\item \code{tar()} no longer skips non-directory files, thanks to a
patch by Sebastian Meyer, fixing the remaining part of \PR{16716}.
}
}
}
\section{\Rlogo CHANGES IN R 4.0.2}{
\subsection{UTILITIES}{
\itemize{
\item \command{R CMD check} skips vignette re-building (with a
warning) if the \samp{VignetteBuilder} package(s) are not available.
}
}
\subsection{BUG FIXES}{
\itemize{
\item Paths with non-ASCII characters caused problems for
package loading on Windows \PR{17833}.
\item Using \pkg{tcltk} widgets no longer crashes R on
Windows.
\item \code{source(*, echo=TRUE)} no longer fails in some cases with
empty lines; reported by Bill Dunlap in \PR{17769}.
\item \code{on.exit()} now correctly matches named arguments, thanks
to \PR{17815} (including patch) by Brodie Gaslam.
\item \code{regexpr(*, perl=TRUE)} no longer returns incorrect
positions into text containing characters outside of the Unicode
Basic Multilingual Plane on Windows.
}
}
}
\section{\Rlogo CHANGES IN R 4.0.1}{
\subsection{NEW FEATURES}{
\itemize{
\item \code{paste()} and \code{paste0()} gain a new optional
argument \code{recycle0}. When set to true, zero-length
arguments are recycled leading to \code{character(0)} after the
\code{sep}-concatenation, i.e., to the empty string \code{""} if
\code{collapse} is a string and to the zero-length value
\code{character(0)} when \code{collapse = NULL}.
A package whose code uses this should depend on \samp{R (>= 4.0.1)}.
\item The \code{summary(<warnings>)} method now maps the counts
correctly to the warning messages.
}
}
\subsection{BUG FIXES}{
\itemize{
\item \code{aov(frml, ...)} now also works where the \code{formula}
deparses to more than 500 characters, thanks to a report and patch
proposal by Jan Hauffa.
\item Fix a dozen places (code, examples) as \code{Sys.setlocale()}
returns the new rather than the previous setting.
\item Fix for adding two complex \pkg{grid} units via \code{sum()}.
Thanks to Gu Zuguang for the report and Thomas Lin Pedersen for
the patch.
\item Fix \code{parallel::mclapply(..., mc.preschedule=FALSE)}
to handle raw vector results correctly. \PR{17779}
\item Computing the \code{base} value, i.e., 2, \dQuote{everywhere},
now uses \code{FLT_RADIX}, as the original \file{machar} code looped
indefinitely on the ppc64 architecture for the \code{longdouble} case.
\item In \R 4.0.0, \code{sort.list(x)} when \code{is.object(x)} was
true, e.g., for \code{x <- I(letters)}, was accidentally using
\code{method = "radix"}. Consequently, e.g., \code{merge(<data.frame>)}
was much slower than previously; reported in \PR{17794}.
\item \code{plot(y ~ x, ylab = quote(y[i]))} now works, as e.g., for
\code{xlab}; related to \PR{10525}.
\item \code{parallel::detect.cores(all.tests = TRUE)} tries a
matching OS name before the other tests (which were intended only
for unknown OSes).
\item Parse data for raw strings is now recorded correctly. Reported
by Gabor Csardi.
}
}
}
\section{\Rlogo CHANGES IN R 4.0.0}{
\subsection{SIGNIFICANT USER-VISIBLE CHANGES}{
\itemize{
\item Packages need to be (re-)installed under this version
(4.0.0) of \R.
\item \code{matrix} objects now also inherit from class
\code{"array"}, so e.g., \code{class(diag(1))} is \code{c("matrix",
"array")}. This invalidates code incorrectly assuming that
\code{class(matrix_obj))} has length one.
S3 methods for class \code{"array"} are now dispatched for
\code{matrix} objects.
\item There is a new syntax for specifying \emph{raw} character
constants similar to the one used in C++: \code{r"(...)"} with
\code{...} any character sequence not containing the sequence
\samp{)"}. %}) \samp{*}: Rd-parser bug for \code{*}"
This makes it easier to write strings that contain backslashes or
both single and double quotes. For more details see \code{?Quotes}.
\item \R now uses a \samp{stringsAsFactors = FALSE} default, and
hence by default no longer converts strings to factors in calls
to \code{data.frame()} and \code{read.table()}.
A large number of packages relied on the previous behaviour and
so have needed/will need updating.
\item The \code{plot()} S3 generic function is now in package
\pkg{base} rather than package \pkg{graphics}, as it is
reasonable to have methods that do not use the \pkg{graphics}
package. The generic is currently re-exported from the
\pkg{graphics} namespace to allow packages importing it from
there to continue working, but this may change in future.
Packages which define S4 generics for \code{plot()} should be
re-installed and package code using such generics from other
packages needs to ensure that they are imported rather than rely
on their being looked for on the search path (as in a namespace,
the base namespace has precedence over the search path).
}
}
\subsection{REFERENCE COUNTING}{
\itemize{
\item Reference counting is now used instead of the \code{NAMED}
mechanism for determining when objects can be safely mutated in
base C code. This reduces the need for copying in some cases and
should allow further optimizations in the future. It should
help make the internal code easier to maintain.
This change is expected to have almost no impact on packages
using supported coding practices in their C/C++ code.
}
}
\subsection{MIGRATION TO PCRE2}{
\itemize{
\item This version of \R is built against the PCRE2 library for
Perl-like regular expressions, if available. (On non-Windows
platforms PCRE1 can optionally be used if PCRE2 is not available
at build time.) The version of PCRE in use can be obtained
\emph{via} \code{extSoftVersion()}: PCRE1 (formerly known as
\sQuote{PCRE}) has versions <= 8, PCRE2 versions >= 10.
\item Making PCRE2 available when building \R from source is
strongly recommended (preferably version 10.30 or later) as PCRE1
is no longer developed: version 8.44 is
\sQuote{likely to be the final release}.
% https://lists.exim.org/lurker/message/20200212.174850.6edd8277.en.html
\item PCRE2 reports errors for some regular expressions that were
accepted by PCRE1. A hyphen now has to be escaped in a character
class to be interpreted as a literal (unless first or last in the
class definition). \samp{\\R}, \samp{\\B} and \samp{\\X} are no
longer allowed in character classes (PCRE1 treated these as
literals).
\item Option \code{PCRE_study} is no longer used with PCRE2, and is
reported as \code{FALSE} when that is in use.
}
}
\subsection{NEW FEATURES}{
\itemize{
\item \code{assertError()} and \code{assertWarning()} (in package
\pkg{tools}) can now check for \emph{specific} error or warning
classes \emph{via} the new optional second argument \code{classes}
(which is not back compatible with previous use of an unnamed second
argument).
\item \code{DF2formula()}, the utility for the data frame method of
\code{formula()}, now works without parsing and explicit evaluation,
starting from Suharto Anggono's suggestion in \PR{17555}.
\item \code{approxfun()} and \code{approx()} gain a new argument
\code{na.rm} defaulting to true. If set to false, missing
\code{y} values now propagate into the interpolated values.
\item Long vectors are now supported as the \code{seq} argument of
a \code{for()} loop.
\item \code{str(x)} gets a new \code{deparse.lines} option with a
default to speed it up when \code{x} is a large \code{call} object.
\item The internal traceback object produced when an error is
signalled (\code{.Traceback}), now contains the \code{call}s
rather than the \emph{\code{deparse()}d} calls, deferring the
deparsing to the user-level functions \code{.traceback()} and
\code{traceback()}. This fulfils the wish of \PR{17580}, reported
including two patch proposals by Brodie Gaslam.
\item \code{data.matrix()} now converts character columns to
factors and from this to integers.
\item \code{package.skeleton()} now explicitly lists all exports
in the \file{NAMESPACE} file.
\item New function \code{.S3method()} to register S3 methods in R
scripts.
\item \code{file.path()} has some support for file paths not in
the session encoding, e.g.\sspace{}with UTF-8 inputs in a
non-UTF-8 locale the output is marked as UTF-8.
\item Most functions with file-path inputs will give an explicit
error if a file-path input in a marked encoding cannot be
translated (to the native encoding or in some cases on Windows to
UTF-8), rather than translate to a different file path using
escapes. Some (such as \code{dir.exists()}, \code{file.exists()},
\code{file.access()}, \code{file.info()}, \code{list.files()},
\code{normalizePath()} and \code{path.expand()}) treat this like
any other non-existent file, often with a warning.
\item There is a new help document accessed by
\code{help("file path encoding")} detailing how file paths with
marked encodings are handled.
\item New function \code{list2DF()} for creating data frames from
lists of variables.
\item \code{iconv()} has a new option \code{sub = "Unicode"} to
translate UTF-8 input invalid in the \samp{to} encoding using
\samp{<U+xxxx>} escapes.
\item There is a new function \code{infoRDS()} providing information
about the serialization format of a serialized object.
\item S3 method lookup now by default skips the elements of the
search path between the global and base environments.
\item Added an argument \code{add_datalist(*, small.size = 0)} to
allow the creation of a \file{data/datalist} file even when the
total size of the data sets is small.
\item The backquote function \code{bquote()} has a new argument
\code{splice} to enable splicing a computed list of values into an
expression, like \code{,@} in LISP's backquote.
\item The formula interface to \code{t.test()} and
\code{wilcox.test()} has been extended to handle one-sample and
paired tests.
\item The \code{palette()} function has a new default set of
colours (which are less saturated and have better accessibility
properties). There are also some new built-in palettes, which
are listed by the new \code{palette.pals()} function. These
include the old default palette under the name \code{"R3"}. Finally,
the new \code{palette.colors()} function allows a subset of
colours to be selected from any of the built-in palettes.
\item \code{n2mfrow()} gains an option \code{asp = 1} to specify the
aspect ratio, fulfilling the wish and extending the proposal of
Michael Chirico in \PR{17648}.
\item For \code{head(x, n)} and \code{tail()} the default and
other S3 methods notably for \emph{vector} \code{n}, e.g. to get a
\dQuote{corner} of a matrix, has been extended to \code{array}'s
of higher dimension thanks to the patch proposal by Gabe Becker in
\PR{17652}. Consequently, optional argument \code{addrownums} is
deprecated and replaced by the (more general) argument
\code{keepnums}. An invalid second argument \code{n} now leads
to typically more easily readable error messages.
\item New function \code{.class2()} provides the full character
vector of class names used for S3 method dispatch.
\item Printing \code{methods(..)} now uses a new \code{format()} method.
\item \code{sort.list(x)} now works for non-atomic objects
\code{x} and \code{method = "auto"} (the default) or
\code{"radix"} in cases \code{order(x)} works, typically via a
\code{xtfrm()} method.
\item Where they are available, \code{writeBin()} allows
long vectors.% (those of length \eqn{\ge 2^{31}}{>= 2^31}).
\item New function \code{deparse1()} produces one string, wrapping
\code{deparse()}, to be used typically in
\code{deparse1(substitute(*))}, e.g., to fix \PR{17671}.
\item \code{wilcox.test()} enhancements: In the (non-paired)
two-sample case, \code{Inf} values are treated as very large for
robustness consistency. If exact computations are used, the
result now has \code{"exact"} in the \code{method} element of its
return value. New arguments \code{tol.root} and
\code{digits.rank} where the latter may be used for stability to
treat very close numbers as ties.
\item \code{readBin()} and \code{writeBin()} now report an error
for an invalid \code{endian} value. The affected code needs to be
fixed with care as the old undocumented behavior was to swap
endian-ness in such cases.
\item \code{sequence()} is now an S3 generic with an internally
implemented default method, and gains arguments to generate more
complex sequences. Based on code from the \pkg{S4Vectors}
Bioconductor package and the advice of Hervé Pagès.
\item \code{print()}'s default method and many other methods (by
calling the default eventually and passing \code{...}) now make
use of a new optional \code{width} argument, avoiding the need for
the user to set and reset \code{options("width")}.
\item \code{memDecompress()} supports the RFC 1952 format
(e.g.\sspace{}in-memory copies of \command{gzip}-compressed files)
as well as RFC 1950.
\item \code{memCompress()} and \code{memDecompress()} support long
raw vectors for types \code{"gzip"} and \code{"zx"}.
\item \code{sweep()} and \code{slice.index()} can now use names
of dimnames for their \code{MARGIN} argument (\code{apply} has
had this for almost a decade).
\item New function \code{proportions()} and
\code{marginSums()}. These should replace the unfortunately named
\code{prop.table()} and \code{margin.table()}. They are drop-in
replacements, but also add named-margin functionality. The old
function names are retained as aliases for back-compatibility.
\item Functions \code{rbinom()}, \code{rgeom()}, \code{rhyper()},
\code{rpois()}, \code{rnbinom(),} \code{rsignrank()} and
\code{rwilcox()} which have returned integer since \R 3.0.0 and hence
\code{NA} when the numbers would have been outside the integer range,
now return double vectors (without NAs, typically) in these cases.
\item \code{matplot(x,y)} (and hence \code{matlines()} and
\code{matpoints()}) now call the corresponding methods of
\code{plot()} and \code{lines()}, e.g, when \code{x} is a
\code{"Date"} or \code{"POSIXct"} object; prompted by Spencer Graves'
suggestion.
\item \code{stopifnot()} now allows customizing error messages via
argument names, thanks to a patch proposal by Neal Fultz in \PR{17688}.
\item \code{unlink()} gains a new argument \code{expand} to disable
wildcard and tilde expansion. Elements of \code{x} of value
\code{"~"} are now ignored.
\item \code{mle()} in the \code{stats4} package has had its
interface extended so that arguments to the negative
log-likelihood function can be one or more vectors, with similar
conventions applying to bounds, start values, and parameter values
to be kept fixed. This required a minor extension to class
\code{"mle"}, so saved objects from earlier versions may need to
be recomputed.
\item The default for \code{pdf()} is now
\code{useDingbats = FALSE}.
\item The default fill colour for \code{hist()} and
\code{boxplot()} is now \code{col = "lightgray"}.
\item The default order of the levels on the y-axis for
\code{spineplot()} and \code{cdplot()} has been reversed.
\item If the \env{R_ALWAYS_INSTALL_TESTS} environment variable is
set to a true value, \command{R CMD INSTALL} behaves as if
the \option{--install-tests} option is always specified. Thanks to
Reinhold Koch for the suggestion.
\item New function \code{R_user_dir()} in package \pkg{tools}
suggests paths appropriate for storing \R-related user-specific
data, configuration and cache files.
\item \code{capabilities()} gains a new logical option \code{Xchk}
to avoid warnings about X11-related capabilities.
\item The internal implementation of \pkg{grid} units has changed,
but the only visible effects at user-level should be
\itemize{
\item a slightly different print format for some units
(especially unit arithmetic),
\item faster performance (for unit operations) and
\item two new functions \code{unitType()} and \code{unit.psum()}.
}
Based on code contributed by Thomas Lin Pedersen.
\item When internal dispatch for \code{rep.int()}
and \code{rep_len()} fails, there is an attempt to dispatch on the
equivalent call to \code{rep()}.
\item Object \code{.Machine} now contains new \code{longdouble.*}
entries (when \R uses long doubles internally).
\item \code{news()} has been enhanced to cover the news on \R 3.x
and 2.x.
\item For consistency, \code{N <- NULL; N[[1]] <- val} now turns
\code{N} into a \code{list} also when \code{val)} has length one.
This enables \code{dimnames(r1)[[1]] <- "R1"} for a 1-row matrix
\code{r1}, fixing \PR{17719} reported by Serguei Sokol.
\item \code{deparse(..)}, \code{dump(..)}, and \code{dput(x,
control = "all")} now include control option \code{"digits17"}
which typically ensures 1:1 invertibility. New option
\code{control = "exact"} ensures numeric exact invertibility
via \code{"hexNumeric"}.
\item When loading data sets via \code{read.table()},
\code{data()} now uses \samp{LC_COLLATE=C} to ensure
locale-independent results for possible string-to-factor
conversions.
\item A server socket connection, a new connection type
representing a listening server socket, is created via
\code{serverSocket()} and can accept multiple socket connections
via \code{socketAccept()}.
\item New function \code{socketTimeout()} changes the connection
timeout of a socket connection.
\item The time needed to start a homogeneous \samp{PSOCK} cluster on
\samp{localhost} with many nodes has been significantly reduced
(package \pkg{parallel}).
\item New \code{globalCallingHandlers()} function to establish
global condition handlers. This allows registering default
handlers for specific condition classes. Developed in
collaboration with Lionel Henry.
\item New function \code{tryInvokeRestart()} to invoke a specified
restart if one is available and return without signaling an error
if no such restart is found. Contributed by Lionel Henry in
\PR{17598}.
\item \code{str(x)} now shows the length of \code{attributes} in some
cases for a data frame \code{x}.
\item \code{Rprof()} gains a new argument \code{filter.callframes}
to request that intervening call frames due to lazy evaluation or
explicit \code{eval()} calls be omitted from the recorded profile
data. Contributed by Lionel Henry in \PR{17595}.
\item The handling of \code{$\{FOO-bar\}} and \code{$\{FOO:-bar\}}
in \file{Renviron} files now follows POSIX shells (at least on a
Unix-alike), so the first treats empty environment variables as
set and the second does not. Previously both ignored empty
variables. There are several uses of the first form in
\file{etc/Renviron}.
\item New \code{classes} argument for \code{suppressWarnings()}
and \code{suppressMessages()} to selectively suppress only
warnings or messages that inherit from particular classes.
Based on patch from Lionel Henry submitted with \PR{17619}.
\item New function \code{activeBindingFunction()} retrieves the
function of an active binding.
\item New \code{"cairoFT"} and \code{"pango"} components in the
output of \code{grSoftVersion()}.
\item New argument \code{symbolfamily} in cairo-based graphics
devices and new function \code{cairoSymbolFont()} that can be used
to provide the value for that argument.
}
}% end{ NEW FEATURES }
\subsection{Windows}{
\itemize{
\item \command{Rterm} now works also when invoked from MSYS2
terminals. Line editing is possible when command \command{winpty} is
installed.
\item \code{normalizePath()} now resolves symbolic links and
normalizes case of long names of path elements in case-insensitive
folders (\PR{17165}).
\item \code{md5sum()} supports UTF-8 file names with characters
that cannot be translated to the native encoding (\PR{17633}).
\item \command{Rterm} gains a new option \option{--workspace} to
specify the workspace to be restored. This allows equals to be
part of the name when opening \emph{via} Windows file associations
(reported by Christian Asseburg).
\item \command{Rterm} now accepts \code{ALT+xxx} sequences also
with NumLock on. Tilde can be pasted with an Italian keyboard
(\PR{17679}).
\item \R falls back to copying when junction creation fails during
package checking (patch from Duncan Murdoch).
}
}
\subsection{DEPRECATED AND DEFUNCT}{
\itemize{
\item Make macro \samp{F77_VISIBILITY} has been removed
and replaced by \samp{F_VISIBILITY}.
\item Make macros \samp{F77}, \samp{FCPIFCPLAGS} and
\samp{SHLIB_OPENMP_FCFLAGS} have been removed and replaced by
\samp{FC}, \samp{FPICFLAGS} and \samp{SHLIB_OPENMP_FFLAGS}
respectively. (Most \command{make} programs will set \samp{F77}
to the value of \samp{FC}, which is set for package compilation.
But portable code should not rely on this.)
\item The deprecated support for specifying C++98 for package
installation has been removed.
\item \command{R CMD config} no longer knows about the
unused settings \samp{F77} and \samp{FCPIFCPLAGS}, nor
\samp{CXX98} and similar.
\item Either PCRE2 or PCRE1 >= 8.32 (Nov 2012) is required: the
deprecated provision for 8.20--8.31 has been removed.
\item Defunct functions \code{mem.limits()}, \code{.readRDS()},
\code{.saveRDS()}, \code{.find.package()}, and \code{.path.package()}
from package \pkg{base}
and \code{allGenerics()}, \code{getAccess()}, \code{getAllMethods()},
\code{getClassName()}, \code{getClassPackage()}, \code{getExtends()},
\code{getProperties()}, \code{getPrototype()},
\code{getSubclasses()}, \code{getVirtual()}, \code{mlistMetaName()},
\code{removeMethodsObject()}, \code{seemsS4Object()},
\code{traceOff()}, and \code{traceOn()} from \pkg{methods} have been
removed.
}
}
\subsection{C-LEVEL FACILITIES}{
\itemize{
\item \code{installChar} is now remapped in \file{Rinternals.h} to
\code{installTrChar}, of which it has been a wrapper since
\R\sspace{}3.6.0. Neither are part of the API, but packages using
\code{installChar} can replace it if they depend on \samp{R >= 3.6.2}.
\item Header \file{R_ext/Print.h} defines \samp{R_USE_C99_IN_CXX}
and hence exposes \code{Rvprintf} and \code{REvprintf} if used
with a C++11 (or later) compiler.
\item There are new Fortran subroutines \code{dblepr1},
\code{realpr1} and \code{intpr1} to print a scalar variable
(\command{gfortran} 10 enforces the distinction between scalars
and length-one arrays). Also \code{labelpr} to print just a label.
\item \code{R_withCallingErrorHandler} is now available for
establishing a calling handler in C code for conditions inheriting
from class \code{error}.
}
}
\subsection{INSTALLATION on a UNIX-ALIKE}{
\itemize{
\item User-set \samp{DEFS} (e.g., in \file{config.site}) is now
used for compiling packages (including base packages).
\item There is a new variant option \option{--enable-lto=check}
for checking consistency of BLAS/LAPACK/LINPACK calls --- see
\sQuote{Writing R Extensions}.
\item A C++ compiler default is set only if the C++11 standard is
supported: it no longer falls back to C++98.
\item PCRE2 is used if available. To make use of PCRE1 if PCRE2
is unavailable, configure with option \option{--with-pcre1}.
\item The minimum required version of \code{libcurl} is now 7.28.0
(Oct 2012).
\item New make target \command{distcheck} checks
\itemize{
\item \R can be rebuilt from the tarball created by
\command{make dist},
\item the build from the tarball passes \command{make check-all},
\item the build installs and uninstalls,
\item the source files are properly cleaned by \command{make distclean}.
}
}
}
\subsection{UTILITIES}{
\itemize{
\item \command{R --help} now mentions the option \command{--no-echo}
(renamed from \command{--slave}) and its previously undocumented
short form \command{-s}.
\item \command{R CMD check} now optionally checks
\command{configure} and \command{cleanup} scripts for
non-Bourne-shell code (\sQuote{bashisms}).
\item \command{R CMD check --as-cran} now runs \code{\\donttest}
examples (which are run by \code{example()}) instead of
instructing the tester to do so. This can be temporarily
circumvented during development by setting environment variable
\env{_R_CHECK_DONTTEST_EXAMPLES_} to a false value.
}
}
\subsection{PACKAGE INSTALLATION}{
\itemize{
\item There is the beginnings of support for the recently approved
C++20 standard, specified analogously to C++14 and C++17. There is
currently only limited support for this in compilers, with flags
such as \option{-std=c++20} and \option{-std=c++2a}. For the time
being the \command{configure} test is of accepting one of these
flags and compiling C++17 code.
}
}
\subsection{BUG FIXES}{
\itemize{
\item \code{formula(x)} with \code{length(x) > 1} character vectors,
is deprecated now. Such use has been rare, and has \sQuote{worked}
as expected in some cases only. In other cases, wrong \code{x} have
silently been truncated, not detecting previous errors.
\item Long-standing issue where the X11 device could lose events
shortly after startup has been addressed (\PR{16702}).
\item The \code{data.frame} method for \code{rbind()} no longer
drops \code{<NA>} levels from factor columns by default
(\PR{17562}).
\item \code{available.packages()} and hence \code{install.packages()}
now pass their \code{...} argument to \code{download.file()},
fulfilling the wish of \PR{17532}; subsequently,
\code{available.packages()} gets new argument \code{quiet}, solving
\PR{17573}.
\item \code{stopifnot()} gets new argument \code{exprObject} to allow
an \R object of class \code{expression} (or other \sQuote{language})
to work more consistently, thanks to suggestions by Suharto Anggono.
\item \code{conformMethod()} now works correctly in cases containing
a \dQuote{\code{&&} logic} bug, reported by Henrik Bengtsson. It now
creates methods with \code{"missing"} entries in the signature.
Consequently, \code{rematchDefinition()} is amended to use
appropriate \code{.local()} calls with named arguments where needed.
\item \code{format.default(*, scientific = FALSE)} now corresponds to
a practically most extreme \code{options(scipen = n)} setting rather
than arbitrary \code{n = 100}.
\item \code{format(as.symbol("foo"))} now works (returning \code{"foo"}).
\item \code{postscript(.., title = *)} now signals an error when
the title string contains a character which would produce corrupt
PostScript, thanks to \PR{17607} by Daisuko Ogawa.
\item Certain \code{Ops} (notably comparison such as \code{==}) now
also work for 0-length data frames, after reports by Hilmar Berger.
\item \code{methods(class = class(glm(..)))} now warns more usefully
and only once.
\item \code{write.dcf()} no longer mangles field names (\PR{17589}).
\item Primitive replacement functions no longer mutate a
referenced first argument when used outside of a complex
assignment context.
\item A better error message for \code{contour(*, levels = Inf)}.
\item The return value of \code{contourLines()} is no longer
\code{invisible()}.
\item The Fortran code for calculating the \code{coefficients}
component in \code{lm.influence()} was very inefficient. It has
(for now) been replaced with much faster \R{} code (\PR{17624}).
\item \code{cm.colors(n)} \emph{etc} no longer append the code for
\code{alpha = 1}, \code{"FF"}, to all colors. Hence all eight
\code{*.colors()} functions and \code{rainbow()} behave
consistently and have the same non-explicit default (\PR{17659}).
\item \code{dnorm} had a problematic corner case with \code{sd ==
-Inf} or negative \code{sd} which was not flagged as an error in
all cases. Thanks to Stephen D. Weigand for reporting and Wang
Jiefei for analyzing this; similar change has been made in
\code{dlnorm()}.
\item The optional \code{iter.smooth} argument of
\code{plot.lm()}, (the \code{plot()} method for \code{lm} and
\code{glm} fits) now defaults to \code{0} for all \code{glm} fits.
Especially for binary observations with high or low fitted
probabilities, this effectively deleted all observations of 1 or
0. Also, the type of residuals used in the \code{glm} case has
been switched to \code{"pearson"} since deviance residuals do not
in general have approximately zero mean.
\item In \code{plot.lm}, Cook's distance was computed from unweighted
residuals, leading to inconsistencies. Replaced with usual weighted
version. (\PR{16056})
\item Time-series \code{ts(*, start, end, frequency)} with
fractional \code{frequency} are supported more consistently;
thanks to a report from Johann Kleinbub and analysis and patch by
Duncan Murdoch in \PR{17669}.
\item In case of errors \code{mcmapply()} now preserves attributes
of returned \code{"try-error"} objects and avoids simplification,
overriding \code{SIMPLIFY} to \code{FALSE}. (\PR{17653})
\item \code{as.difftime()} gets new optional \code{tz = "UTC"}
argument which should fix behaviour during
daylight-savings-changeover days, fixing \PR{16764}, thanks to
proposals and analysis by Johannes Ranke and Kirill Müller.
\item \code{round()} does a better job of rounding
\emph{\dQuote{to nearest}} by \emph{measuring} and
\emph{\dQuote{to even}}; thanks to a careful algorithm originally
prompted by the report from Adam Wheeler and then others, in
\PR{17668}. \cr \code{round(x, dig)} for \emph{negative} digits
is much more rational now, notably for large \eqn{|dig|}.
\item Inheritance information on S4 classes is maintained more
consistently, particularly in the case of class unions (in part
due to \PR{17596} and a report from Ezra Tucker).
\item \code{is()} behaves more robustly when its argument
\code{class2} is a \code{classRepresentation} object.
\item The warning message when attempting to export an nonexistent
class is now more readable; thanks to Thierry Onkelinx for
recognizing the problem.
\item \code{choose()} misbehaved in corner cases where it switched
\code{n - k} for \code{k} and \code{n} was only \emph{nearly} integer
(report from Erik Scott Wright).
\item \code{mle()} in the \code{stats4} package had problems
combining use of box constraints and fixed starting values (in
particular, confidence intervals were affected).
\item Operator \code{?} now has lower precedence than \code{=} to
work as documented, so \code{=} behaves like \code{<-} in help
expressions (\PR{16710}).
\item \code{smoothEnds(x)} now returns \code{integer} type in
\emph{both} cases when \code{x} is \code{integer}, thanks to a
report and proposal by Bill Dunlap \PR{17693}.
\item The \pkg{methods} package does a better job of tracking
inheritance relationships across packages.
\item \code{norm(diag(c(1, NA)), "2")} now works.
\item \code{subset()} had problems with 0-col dataframes (reported
by Bill Dunlap, \PR{17721}).
\item Several cases of integer overflow detected by the
\sQuote{undefined behaviour sanitizer} of \command{clang} 10 have
been circumvented. One in \code{rhyper()} may change the
generated value for large input values.
\item \code{dotchart()} now places the y-axis label (\code{ylab})
much better, not overplotting labels, thanks to a report and
suggestion by Alexey Shipunov.
%% detected by clang-ASAN in examples/tests of adehabitatHR.
\item A rare C-level array overflow in \code{chull()} has been
worked around.
\item Some invalid specifications of the day-of-the-year
(\emph{via} \code{\%j}, e.g.\sspace{}day 366 in 2017) or week
plus day-of-the-week are now detected by \code{strptime()}.
They now return \code{NA} but give a warning as they may have
given random results or corrupted memory in earlier versions of \R.
\item \code{socketConnection(server = FALSE)} now respects the
connection timeout also on Linux.
\item \code{socketConnection(server = FALSE)} no longer leaks a
connection that is available right away without waiting (e.g. on
\samp{localhost}).
\item Socket connections are now robust against spurious readability
and spurious availability of an incoming connection.
\item \code{blocking = FALSE} is now respected also on the server side
of a socket connection, allowing non-blocking read operations.
\item \code{anova.glm()} and \code{anova.glmlist()} computed
incorrect score (Rao) tests in no-intercept cases. (André
Gillibert, \PR{17735})
\item \code{summaryRprof()} now should work correctly for the
\code{Rprof(*, memory.profiling=TRUE)} case with small chunk size (and
\code{"tseries"} or similar) thanks to a patch proposal by Benjamin
Tyner, in \PR{15886}.
\item \code{xgettext()} ignores strings passed to
\code{ngettext()}, since the latter is handled by
\code{xngettext()}. Thanks to Daniele Medri for the report and all
the recent work he has done on the Italian translations.
\item \code{data(package = "P")} for \code{P} in \pkg{base} and
\pkg{stats} no longer reports the data sets from package
\pkg{datasets} (which it did for back compatibility for 16 years),
fixing \PR{17730}.
\item \code{x[[Inf]]} (returning \code{NULL}) no longer leads to
undefined behavior, thanks to a report by Kirill Müller in
\PR{17756}. Further, \code{x[[-Inf]]} and \code{x[[-n]]} now give
more helpful error messages.
\item \code{Gamma()} family sometimes had trouble storing
link name \PR{15891}
}
}
\subsection{BUG FIXES (Windows)}{
\itemize{
\item \code{Sys.glob()} now supports all characters
from the Unicode Basic Multilingual Plane, no longer corrupting
some (less commonly used) characters (\PR{17638}).
\item \command{Rterm} now correctly displays
multi-byte-coded characters representable in the current native
encoding (at least on Windows 10 they were sometimes omitted,
\PR{17632}).
\item \code{scan()} issues with UTF-8 data when running in a DBCS
locale have been resolved (\PR{16520}, \PR{16584}).
\item \command{Rterm} now accepts enhanced/arrow keys also with
ConPTY.
\item \R can can now be started \emph{via} the launcher icon in a
user documents directory whose path is not representable in the
system encoding.
\item \code{socketConnection(server = FALSE)} now returns instantly
also on Windows when connection failure is signalled.
\item Problems with UTF-16 surrogate pairs have been fixed in
several functions, including \command{tolower()} and
\command{toupper()} (\PR{17645}).
}
}
}
\section{CHANGES in previous versions}{
\itemize{
\item Older news can be found in text format in files
\ifelse{html}{\href{../NEWS.0}{NEWS.0}, \href{../NEWS.1}{NEWS.1},
\href{../NEWS.2}{NEWS.2} and
and \href{../NEWS.3}{NEWS.3}}{\file{NEWS.0}, \file{NEWS.1},
\file{NEWS.2} and \file{NEWS.3}}
in the \file{doc} directory. News in HTML format for
\R versions 3.x and from 2.10.0 to 2.15.3 is available at
\ifelse{html}{\url{NEWS.3.html}}{\file{doc/html/NEWS.3.html}}
and
\ifelse{html}{\url{NEWS.2.html}}{\file{doc/html/NEWS.2.html}}.
}
}