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NEWS.Rd
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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{USER-VISIBLE CHANGES}{
\itemize{
\item \R now builds by default against a PCRE2 library for Perl-like
regular expressions if available at build time on non-Windows
platforms (otherwise PCRE1 is used as in older versions of \R).
PCRE2 is stricter in some cases and 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).
Option \code{PCRE_study} is no longer used, and reported as
\code{FALSE}.
The version of PCRE used can be obtained via
\code{extSoftVersion()}, PCRE1 has versions < 10, PCRE2 versions
>= 10.
}
}
\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()}, fulfilling the wish of \PR{17580}, reported
(incl.\sspace{}patch proposal) 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 (Windows) \command{Rterm} now works also when invoked from
MSYS2 terminals. Line editing is possible when \command{winpty}
is installed.
\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 help document accessed by
\code{help("file path encoding")}
detailing how file paths with marked encodings are handled.
\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.
}
}
\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 in 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 PCRE >= 8.32 (Nov 2012) or PCRE2 is required: the
deprecated provision for 8.20--8.31 has 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{REprintf} if used with
a C++11 compiler.
}
}
\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: this is strongly recommended as
PCRE1 is no longer developed (it only receives bug fixes and has
outdated Unicode tables). \command{configure} will warn if PCRE2
is not found and fall back to PCRE1. \command{configure} options
\option{--without-pcre1} and \option{--without-pcre2} can be used
to exclude one or the other (but at least one of PCRE2 and PCRE1
is required).
\item The minimum required version of \code{libcurl} is now 7.28.0
(Oct 2012).
}
}
\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 \code{rbind.data.frame()} 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{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 produces corrupt PostScript,
thanks to Daisuko Ogawa's \PR{17607}.
\item \code{x \%\% L} for finite \code{x} no longer returns
\code{NaN} when \code{L} is infinite, nor suffers from cancellation
for large finite \code{L}, thanks to Long Qu's \PR{17611}.
Analogously, \code{x \%/\% L} and \code{L \%/\% x} suffer less from
cancellation and return values corresponding to limits for large
\code{L}.
\item Certain \code{Ops} (notably comparison such as \code{==}) now
also work for 0-length data frames, after reports by Hilmar Berger.
}
}
}
\section{\Rlogo CHANGES IN R 3.6.1 patched}{
\subsection{NEW FEATURES}{
\itemize{
\item \code{runmed(x, *)} gets new option \code{na.action}
determining \emph{how} to handle \code{NaN} or \code{NA} in \code{x}.
}
}
\subsection{INSTALLATION on a UNIX-ALIKE}{
\itemize{
\item Detection of the C stack direction has been moved from
run-time to \command{configure}: this is safer with LTO builds and
allows the detection to be overridden -- see file
\file{config.site}.
}
}
\subsection{C-LEVEL FACILITIES}{
\itemize{
\item \code{installTrChar} (which is nowadays is wrapped by
\code{installChar}) is defined in \file{Rinternals.h}. (Neither
are part of the API.)
}
}
\subsection{PACKAGE INSTALLATION}{
\itemize{
\item Header \file{Rconfig.h} contains the value of
\code{FC_LEN_T} deduced at installation which is used by the
prototypes in headers \file{R_ext/BLAS.h} and
\file{R_ext/Lapack.h} but to avoid extensive breakage this is
only exposed when \code{USE_FC_LEN_T} is defined.
If a package's C/C++ calls to BLAS/LAPACK allow for the
\sQuote{hidden} arguments used by most Fortran compilers to pass
the lengths of Fortran character arguments, define
\code{USE_FC_LEN_T} and include \file{Rconfig.h} (possibly
\emph{via} \file{R.h}) before including \file{R_ext/BLAS.h} or
\file{R_ext/Lapack.h}.
\item A package with Fortran source code and perhaps C (but not
C++) sources can request for its shared object/DLL to be linked by
the Fortran compiler by including a line \code{USE_FC_TO_LINK=} in
\file{src/Makevars[.win]}.
The known reason for doing so is a package which uses Fortran
(only) OpenMP on a platform where the Fortran OpenMP runtime is
incompatible with the C one (e.g.\sspace{}\command{gfortran} 9.x
with \command{clang}).
}
}
\subsection{UTILITIES}{
\itemize{
\item \command{R CMD check} has a new option to mitigate checks
leaving files/directories in \file{/tmp}. See the \sQuote{R
Internals} manual -- this is part of \code{--as-cran}.
}
}
\subsection{DEPRECATED AND DEFUNCT}{
\itemize{
\item Support for specifying C++98 in package installation is
deprecated.
\item Support in \command{R CMD config} for \samp{F77},
\samp{FCPIFCPLAGS}, \samp{CPP}, \samp{CXXCPP} and \samp{CXX98} and
similar is deprecated. (\samp{CPP} is found from the system
\command{make} and may well not be set.)
Use \samp{$CC -E} and \samp{$CXX -E} instead of \samp{CPP} and
\samp{CXXCPP}.
}
}
\subsection{BUG FIXES}{
\itemize{
\item \code{runmed(x, *)} when \code{x} contains missing values
now works consistently for both \code{algorithm="Stuetzle"} and
\code{"Turlach"}, and no longer segfaults for \code{"Turlach"}, as
reported by Hilmar Berger.
\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{apply(diag(3), 2:3, mean)} now gives a helpful error message.
\item \code{dgamma(x, shape, log=TRUE)} now longer overflows
to \code{Inf} for shape < 1 and very small \code{x}, fixing
\PR{17577}, reported by Jonathan Rougier.
\item Buffer overflow in building error messages fixed. Reported
by Benjamin Tremblay.
\item \code{options(str = .)} is correctly initialized at
package \pkg{utils} load time, now. A consequence is that
\code{str()} in scripts now is more consistent to interactive use,
e.g., when displaying function(**) argument lists.
\item \code{as.numeric(<call>)} now gives correct error message.
\item Printing \code{ls.str()} no longer wrongly shows
\code{"<missing>"} in rare cases.
\item Auto-printing S4 objects no longer duplicates the object,
for faster speed and reduced memory consumption. Reported by Aaron
Lun.
\item \code{pchisq(<LRG>, <LRG>, ncp=100)} no longer takes
practically forever in some cases. Hence ditto for corresponding
\code{qchisq()} calls.
}
}
}
\section{\Rlogo CHANGES IN R 3.6.1}{
\subsection{INSTALLATION on a UNIX-ALIKE}{
\itemize{
\item The default detection of the shell variable \code{libNN} is
overridden for derivatives of Debian Linux, some of which have
started to have a \file{/usr/lib64} directory.
(E.g.\sspace{}Ubuntu 19.04.) As before, it can be specified in
\file{config.site}.
}
}
\subsection{UTILITIES}{
\itemize{
\item \command{R CMD config} knows the values of \code{AR} and
\code{RANLIB}, often set for LTO builds.
}
}
\subsection{DEPRECATED AND DEFUNCT}{
\itemize{
\item The use of a character vector with \code{.Fortran()} is
formally deprecated and gives a non-portability warning. (It has
long been strongly discouraged in \sQuote{Writing R Extensions}.)
}
}
\subsection{BUG FIXES}{
\itemize{
\item On Windows, GUI package installation via \code{menuInstallPkgs()}
works again, thanks to Len Weil's and Duncan Murdoch's \PR{17556}.
\item \command{R CMD check} on \code{data()} fixing \PR{17558}
thanks to Duncan Murdoch.
\item \code{quasi(*, variance = list(..))} now works more
efficiently, and should work in all cases fixing \PR{17560}.
Further, \code{quasi(var = mu(1-mu))} and \code{quasi(var = "mu ^ 3")}
now work, and \code{quasi(variance = "log(mu)")} now gives a correct
error message.
\item Creation of lazy loading database during package installation is
again robust to Rprofile changing the current working directory
(\PR{17559}).
\item \code{boxplot(y ~ f, horizontal=TRUE)} now produces correct x-
and y-labels.
\item \code{rbind.data.frame()} allows to keep \code{<NA>} levels
from factor columns (\PR{17562}) via new option \code{factor.exclude}.
Additionally, it works in one more case with matrix-columns which
had been reported on 2017-01-16 by Krzysztof Banas.
\item Correct messaging in C++ pragma checks in \pkg{tools} code for
\command{R CMD check}, fixing \PR{17566} thanks to Xavier Robin.
\item{print()}ing and auto-printing no longer differs for
\code{function}s with a user defined \code{print.function}, thanks to
Bill Dunlap's report.
\item On Windows, \code{writeClipboard(.., format = <n>)} now
does correctly pass \code{format} to the underlying C code, thanks to
a bug report (with patch) by Jenny Bryan.
\item \code{as.data.frame()} treats 1D arrays the same as vectors,
\PR{17570}.
\item Improvements in \code{smoothEnds(x, *)} working with
\code{NA}s (towards \code{runmed()} working in that case, in the next
version of R).
\item \code{vcov(glm(<quasi>), dispersion = *)} works correctly
again, fixing \PR{17571} thanks to Pavel Krivitsky.
\item \command{R CMD INSTALL} of binary packages on Windows now
works also with per-directory locking.
\item \command{R CMD INSTALL} and \code{install.packages()} on Windows
are now more robust against a locked file in an earlier installation
of the package to be installed. The default value of option
\code{install.lock} on Windows has been changed to \code{TRUE}.
\item On Unix alikes (when \command{readline} is active), only
expand tilde (\code{~}) file names starting with a tilde, instead of
almost all tildes.
\item In R documentation (\file{*.Rd}) files, \samp{\item [..]} is no
longer treated specially when rendered in LaTeX and hence pdf, but
rather shows the brackets in all cases.
}
}
}
\section{\Rlogo CHANGES IN R 3.6.0}{
\subsection{SIGNIFICANT USER-VISIBLE CHANGES}{
\itemize{
\item Serialization format version 3 becomes the default for
serialization and saving of the workspace (\code{save()},
\code{serialize()}, \code{saveRDS()}, \code{compiler::cmpfile()}).
Serialized data in format 3 cannot be read by versions of \R prior
to version 3.5.0. Serialization format version 2 is still
supported and can be selected by \code{version = 2} in the
save/serialization functions. The default can be changed back for
the whole \R session by setting environment variables
\env{R_DEFAULT_SAVE_VERSION} and \env{R_DEFAULT_SERIALIZE_VERSION}
to \code{2}. For maximal back-compatibility, files
\file{vignette.rds} and \file{partial.rdb} generated by \command{R
CMD build} are in serialization format version 2, and resave by
default produces files in serialization format version 2 (unless
the original is already in format version 3).
\item The default method for generating from a discrete uniform
distribution (used in \code{sample()}, for instance) has been
changed. This addresses the fact, pointed out by Ottoboni and
Stark, that the previous method made \code{sample()} noticeably
non-uniform on large populations. See \PR{17494} for a
discussion. The previous method can be requested using
\code{RNGkind()} or \code{RNGversion()} if necessary for
reproduction of old results. Thanks to Duncan Murdoch for
contributing the patch and Gabe Becker for further assistance.
The output of \code{RNGkind()} has been changed to also return the
\sQuote{kind} used by \code{sample()}.
}
}
\subsection{NEW FEATURES}{
\itemize{
\item \code{Sys.setFileTime()} has been vectorized so arguments
\code{path} and \code{time} of length greater than one are now
supported.
\item \code{axis()} gets new option \code{gap.axis = NA} for
specifying a multiplication factor for the minimal \dQuote{gap}
(distance) between axis labels drawn. Its default is \code{1}
for labels \emph{parallel} to the axis, and \code{0.25} for
perpendicular ones.
Perpendicular labels no longer overlap, fixing bug \PR{17384}.
\item The default method of \code{plot()} gains new arguments
\code{xgap.axis = NA} and \code{ygap.axis = NA} to be passed to
the x-- and y-- \code{axis(.., gap.axis=*)} calls.
\item \code{removeSource()} now works not only for functions but
also for some language objects.
\item \code{as.call()}, \code{rep.int()}, \code{rep_len()} and
\code{nchar()} dispatch internally.
\item \code{is(object, class2)} looks for \code{class2} in the
calling namespace after looking in the namespace of
\code{class(object)}.
\item \code{extendrange(.., f)} with a length-2 \code{f} now
extends separately to the left and the right.
\item \code{lengths()} dispatches internally to S4 methods.
\item \code{download.file()} on Windows now uses \code{URLdecode()}
to determine the file extension, and uses binary transfer
(\code{mode = "wb"}) also for file extension \file{.rds}.
The help page for \code{download.file()} now contains the same
information on all platforms.
\item Setting \samp{C} locale for collation \emph{via} environment
variables \env{LC_ALL} and \env{LC_COLLATE} and \emph{via} a call
to \code{Sys.setlocale()} now takes precedence over environment
variable \env{R_ICU_LOCALE}.
\item There is a new function, \code{nullfile()}, to give the file
name of the null system device (e.g., \file{/dev/null}) on the
current platform. % not the null graphics device.
\item There are two new options, \code{keep.parse.data} and
\code{keep.parse.data.pkgs}, which control whether parse data are
included into sources when \code{keep.source} or
\code{keep.source.pkgs} is \code{TRUE}. By default,
\code{keep.parse.data.pkgs} is now \code{FALSE}, which changes
previous behavior and significantly reduces space and time overhead
when sources are kept when installing packages.
\item In \code{rapply(x, ..)}, \code{x} can also be
\dQuote{list-like} and of length \eqn{\ge 2^{31}}{>= 2^{31}}.
\item \code{trimws()} gets new optional \code{whitespace}
argument, allowing more extensive definitions of \dQuote{space},
such as including Unicode spaces (as wished in \PR{17431}).
\item \code{weighted.mean()} no longer coerces the weights to a
double/numeric vector, since \code{sum()} now handles integer
overflow. This makes \code{weighted.mean()} more polymorphic and
endomorphic, but be aware that the results are no longer
guaranteed to be a vector of type \samp{double}.
\item When loading namespaces, S3 method registrations which
overwrite previous registrations are now noted by default (using
\code{packageStartupMessage()}).
\item \code{compiler::cmpfile()} gains a \code{version} argument, for
use when the output file should be saved in serialization format 2.
\item The axis labeling in the default method of \code{pairs()}
may now be toggled by new options \code{horOdd} and \code{verOdd}.
\item (Not Windows nor macOS.) Package \pkg{tcltk} now supports an
environment variable \env{R_DONT_USE_TK} which if set disables Tk
initialization. This is intended for use to circumvent errors in
loading the package, e.g.\sspace{}with recent Linux running under
an address sanitizer.
\item The \code{numeric} method of \code{all.equal()} gets
optional arguments \code{countEQ} and \code{formatFUN}. If
\code{countEQ} is true, the mean error is more sensible when many
entries are \bold{eq}ual.
\item \code{outer(x,y, FUN = "*")} is more efficient using
\code{tcrossprod(u,v)} instead of \code{u \%*\% t(v)}.
\item \code{vcov(<mlm>)} is more efficient via new optional
arguments in \code{summary.mlm()}.
\item The default method of \code{summary()} gets an option to
choose the \emph{kind} of \code{quantile()}s to use; wish of
\PR{17438}.
\item Fitting multiple linear models \emph{via} \code{lm()} does
work with \emph{matrix} offsets, as suggested in \PR{17407}.
\item The new functions \code{mem.maxVSize()} and
\code{mem.maxMSize()} allow the maximal size of the vector heap
and the maximal number of nodes allowed in the current \command{R}
process to be queried and set.
\item \code{news()} gains support for \file{NEWS.md} files.
\item An effort has been started to have our reference manuals,
i.e., all help pages. show platform-independent information (rather
than Windows or Unix-alike specifics visible only on that platform).
Consequently, the Windows version of \code{X11()} / \code{x11()}
got identical formal arguments to the Unix one.
\item \code{sessionInfo()$running} has been factored out in a new
variable \code{osVersion}. % precomputed at utils namespace load time
\item \code{slice.index()} now also works for multi-dimensional
margins.
\item \code{untar()} used with an external \command{tar} command
assumes this supports decompression including \command{xz} and
automagically detecting the compression type. This has been true
of all mainstream implementations since 2009 (for GNU
\command{tar}, since version 1.22): older implementations are
still supported \emph{via} the new argument
\code{support_old_tars} whose default is controlled by environment
variable \env{R_SUPPORT_OLD_TARS}. (It looks like NetBSD and
OpenBSD have \sQuote{older} \command{tar} commands for this
purpose.)
\item The new function \code{asplit()} allow splitting an array or
matrix by its margins.
\item New functions \code{errorCondition()} and
\code{warningCondition()} provide a convenient way to create
structured error and warning objects.
\code{.Deprecated()} now signals a warning of class
\code{"deprecatedWarning"}, and \code{.Defunct()} now signals an
error of class \code{"defunctError"}.
\item Many \sQuote{package not found} errors are now signaled as
errors of class \code{"packageNotFoundError"}.
\item As an experimental feature, when \code{loadNamespace()} fails
because the requested package is not available the error is
initially signaled with a \code{retry_loadNamespace} restart
available. This allows a calling handler to try to install the
package and continue.
\item \code{S3method()} directives in \file{NAMESPACE} can now
also be used to perform \emph{delayed} S3 method registration.
\item Experimentally, setting environment variable
\env{_R_CHECK_LENGTH_1_LOGIC2_} will lead to warnings (or errors
if the variable is set to a \sQuote{true} value) when \code{&&} or
\code{||} encounter and use arguments of length more than one.
\item Added \code{"lines"} and \code{"chars"} coordinate systems
to \code{grconvertX()} and \code{grconvertY()}.
\item \code{getOption()} is more efficient notably for the rare
case when called with two arguments, from several contributors in
\PR{17394}.
\item In \code{.col(dim)} and \code{.row(dim)}, \code{dim} now may
also be an integer-valued \code{"double"}.
\item \code{sQuote()} and \code{dQuote()} get an explicit \code{q}
argument with obvious default instead of using
\code{getOption("fancyQuotes")} implicitly and unconditionally.
\item \code{unzip()} can list archives with comments and with
spaces in file names even using an external \command{unzip} command.
\item Command line completion has a new setting
\code{rc.settings(dots = FALSE)} to remove \code{...} from the
list of possible function arguments.
\item \code{library()} no longer checks packages with compiled
code match \samp{R.version$platform}. \code{loadNamespace()}
never has, and increasingly the \sQuote{canonical name} does not
reflect the important characteristics of compiled code.
%% E.g. 32/64-bit compiler settings
\item The primitive functions \code{drop()} and \code{unclass()}
now avoid duplicating their data for atomic vectors that are large
enough, by returning \code{ALTREP} wrapper objects with adjusted
attributes. \R{}-level assignments to change attributes will also
use wrapper objects to avoid duplicating data for larger atomic
vectors. \R functions like \code{structure()} and \code{unname()}
will therefore not duplicate data in these settings. Generic
vectors as produced by \code{list()} are not yet covered by this
optimization but may be in due course.
\item In \code{formals()}, \code{envir} becomes an optional
argument instead of being hardwired.
\item Instead of signalling an error for an invalid S4 object
\code{x}, \code{str(x)} now gives a warning and subsequently still
shows most parts of \code{x}, e.g., when slots are missing.
\item \code{gamma(x)} and \code{lgamma(x)} no longer warn when
correctly returning \code{Inf} or underflowing to zero. This
helps maximum likelihood and similar computations.
\item \code{convertColor()} is now vectorized, so a lot faster for
converting many colours at once. The new argument
\code{vectorized} to \code{colorConverter()} ensures that
non-vectorized colour converters still work. (Thanks to Brodie
Gaslam.)
\item \code{download.file()} and \code{url()} get new argument
\code{headers} for custom HTTP headers, e.g., allowing to perform
basic http authentication, thanks to a patch contributed by Gábor
Csárdi.
\item File-based connection functions \code{file()},
\code{gzfile()}, \code{bzfile()} and \code{xzfile()} now signal an
error when used on a directory.
\item For \code{approx()}, \code{splinefun()} \emph{etc}, a new
setting \code{ties = c("ordered", <fun>)} allows skipping the
sorting and still treat ties.
\item \code{format(x)} gives a more user friendly error message in
the case where no method is defined. A minimal method is provided
in \code{format.default(x)} when \code{isS4(x)} is true.
\item \code{which(x)} now also works when \code{x} is a long
vector, thanks to Suharto Anggono's \PR{17201}. \strong{NB}: this
may return a double result, breaking the previous guarantee of an
integer result.
\item \code{seq.default()} is more careful to return an
\code{integer} (as opposed to \code{double}) result when its
arguments are large and/or classed objects; see comment #9 of
Suharto Anggono's \PR{17497}.
\item The \code{plot()} method for \code{lm} and \code{glm} fits,
\code{plot.lm()}, gains a new option \code{iter.smooth} with a
default of \code{0} for binomial fits, no longer down-weighting
when smoothing the residuals.
\item \code{zip()} passes its list of files \emph{via} standard
input to the external command when too long for the command line
(on some platforms).
\item \code{data()} gains an \code{overwrite} argument.
\item \code{t.test()} now also returns the standard error (in
list component \code{stderr}).
\item \code{model.matrix(*, contrasts.arg = CC)} now warns about
invalid \code{contrasts.arg}s.
\item Performance of \code{substr()} and \code{substring()} has been
improved.
\item \code{stopifnot()} has been simplified thanks to Suharto
Anggono's proposals to become considerably faster for cheap
expressions.
\item The default \sQuote{user agent} has been changed when
accessing \samp{http://} and \samp{https://} sites using
\samp{libcurl}. (A site was found which caused \samp{libcurl} to
infinite-loop with the previous default.)
\item \code{sessionInfo()} now also contains \code{RNGkind()} and
prints it when it differs from the default; based on a proposal and
patch by Gabe Becker in \PR{17535}.
Also, \code{RNGversion(getRversion())} works directly.
\item \code{library()} and \code{require()} now allow more control
over handling search path conflicts when packages are
attached. The policy is controlled by the new
\code{conflicts.policy} option.
\item \code{barplot()} gets a formula method, thanks to a patch
proposal by Arni Magnusson in \PR{17521}.
\item \code{pmax()} and \code{pmin(x)} now also work for long
vectors, thanks to Suharto Anggono's \PR{17533}.
\item \code{bxp()} now warns when omitting duplicated arguments.
\item New \code{hcl.colors()} function to provide wide range of
HCL-based colour palettes with much better perceptual properties
than the existing RGB/HSV-based palettes like \code{rainbow()}.
Also a new \code{hcl.pals()} function to list available palette
names for \code{hcl.colors()}.
Contributed by Achim Zeileis.
\item The default colours for \code{image()} and
\code{filled.contour()} are now based on \code{hcl.colors()}.
\item The palette-generating functions \code{rainbow()},
\code{gray.colors()}, etc.\sspace{}get a new \code{rev} argument
to facilitate reversing the order of colors.
\item New \code{str2lang()} and \code{str2expression()} as streamlined
versions of \code{parse(text=., keep.source=FALSE)} allow to abstract
typical call constructions, e.g., in \code{formula} manipulations.
(Somewhat experimental) % << TO DO
\item Add \code{update_PACKAGES()} for incrementally updating a
package repository index, instead of rebuilding the index from
scratch. Thanks to Gabe Becker in \PR{17544} for the patch, based
on part of his \pkg{switchr} package.
}
}
\subsection{INSTALLATION on a UNIX-ALIKE}{
\itemize{
\item The options selected for the C++ compiler default to the
C++11 standard if supported, otherwise to the C++98 standard.
\item Visibility macros such as \samp{C_VISIBILITY} can now be
user-set (including to empty), e.g.\sspace{}in \file{config.site}.
\item Macro \samp{FCLIBS}, which has sometimes been needed on
Solaris, has been renamed to \samp{FCLIBS_XTRA}.
\item Macro \samp{F77} is always set to the value of \samp{FC}, so
the latter should be set to user-select the Fortran compiler for
both fixed-form and free-form Fortran. In particular,
\command{gfortran} is now the first choice for \samp{F77}, not
\command{f95}.
Macros \samp{FFLAGS} and \samp{FCFLAGS} remain distinct to allow
for a compiler which needs a flag to select free- or fixed-form
Fortran (most use the source-file extension to choose: \file{.f}
is fixed-form and \file{.f90} and \file{.f95} are free-form).
If only one of them is set, its value is used for both.
\item The special-casing of \samp{CFLAGS}, \samp{CXXFLAGS} and
\samp{FFLAGS} for Intel compilers on Linux has been removed: we do
not have recent experience but the generic defaults now chosen are
the same as those previously special-cased for \samp{x86_64}.
If necessary, override the defaults on the \command{configure}
command line or in file \file{config.site}.
\item Long-untested \command{configure} support for HP-UX and very
old versions of Linux has been removed.
\item \command{configure --with-blas} (without specifying a value)
includes OpenBLAS in its search (before ATLAS and a generic
BLAS). This follows recent versions of the \samp{ax_blas}
autoconf macro.
\item The \command{configure} macro \samp{MAKEINFO} has been
updated to \samp{TEXI2ANY}.
\item Support for \command{make install-strip} has been enhanced.
}
}
\subsection{PACKAGE INSTALLATION}{
\itemize{
\item Source package installation is by default \sQuote{staged}:
the package is installed into a temporary location under the final
library directory and moved into place once the installation is
complete. The benefit is that partially-installed packages are
hidden from other \R sessions.
The overall default is set by environment variable
\env{R_INSTALL_STAGED}. \command{R CMD INSTALL} has new options
\option{--staged-install} and \option{--no-staged-install}, and
packages can use the \samp{StagedInstall} field in their
\file{DESCRIPTION} file to opt out. (That opt-out is a temporary
measure which may be withdrawn in future.)
Staged installation requires either \option{--pkglock} or
\option{--lock}, one of which is used by default.
\item The interpretation of source code with extension \file{.f}
is changing. Previously this denoted FORTRAN 77 code, but current
compilers no longer have a FORTRAN 77 mode and interpret it as
\sQuote{fixed-form} Fortran 90 (or later where supported) code.
Extensions \file{.f90} and \file{.f95} continue to indicate
\sQuote{free-form} Fortran code.
Legal FORTRAN 77 code is also legal fixed-form Fortran 9x; however
this change legitimizes the use of later features, in particular
to replace features marked \sQuote{obsolescent} in Fortran 90 and
\sQuote{deleted} in Fortran 2018 which \command{gfortran} 8.x and
later warn about.
\item Packages containing files in the \file{src} directory with
extensions \file{.f90} or \file{.f95} are now linked using the C
or C++ compiler rather than the Fortran 9x compiler. This is
consistent with fixed-form Fortran code and allows mixing of C++
and free-form Fortran on most platforms.
Consequentially, a package which includes free-form Fortran 9x
code which uses OpenMP should include \samp{SHLIB_OPENMP_CFLAGS}
(or the \samp{CXXFLAGS} version if they also include C++ code) in
\samp{PKG_LIBS} rather than \samp{SHLIB_OPENMP_FCFLAGS} ---
fortunately on almost all current platforms they are the same
flag.
\item Macro \samp{PKG_FFLAGS} will be used for the compilation of
both fixed-form and free-form Fortran code unless
\samp{PKG_FCFLAGS} is also set (in \file{src/Makevars} or
\file{src/Makevars.win}).
\item The make macro \samp{F_VISIBILITY} is now preferred for
both fixed-form and free-form Fortran, for use in
\file{src/Makevars} and similar.
\item \command{R CMD INSTALL} gains a new option \option{--strip}
which (where supported) strips installed shared object(s): this
can also be achieved by setting the environment variable
\env{_R_SHLIB_STRIP_} to a true value.
The new option \option{--strip-lib} attempts stripping of
static and shared libraries installed under \file{lib}.
These are most useful on platforms using GNU \code{binutils} (such
as Linux) and compiling with \option{-g} flags.
\item There is more support for installing UTF-8-encoded packages
in a strict Latin-1 locale (and probably for other Latin locales):
non-ASCII comments in \R code (and \file{NAMESPACE} files) are
worked around better.
}
}
\subsection{UTILITIES}{
\itemize{
\item \command{R CMD check} now optionally checks makefiles for
correct and portable use of the \samp{SHLIB_OPENMP_*FLAGS} macros.
\item \command{R CMD check} now evaluates \code{\\Sexpr{}}
expressions (including those in macros) before checking the
contents of \file{Rd} files and so detects issues both in
evaluating the expressions and in the expanded contents.
\item \command{R CMD check} now lists missing packages separated
by commas and with regular quotes such as to be useful as argument
in calling \code{install.packages(c(..))}; from a suggestion by
Marcel Ramos.
\item \code{tools::Rd2latex()} now uses UTF-8 as its default
output encoding.
\item \command{R CMD check} now checks line endings of files with
extension \file{.hpp} and those under \file{inst/include}. The
check now includes that a non-empty file is terminated with a
newline.
\command{R CMD build} will correct line endings in such files.
\item \command{R CMD check} now tries re-building all vignettes
rather than stopping at the first error: whilst doing so it adds
\sQuote{bookmarks} to the log. By default (see the \sQuote{R
Internals} manual) it re-builds each vignette in a separate
process.
It now checks for duplicated vignette titles (also known as
\sQuote{index entries}): they are used as hyperlinks on
\acronym{CRAN} package pages and so do need to be unique.
\item \command{R CMD check} has more comprehensive checks on the
\file{data} directory and the functioning of \code{data()} in a
package.
\item \command{R CMD check} now checks
\command{autoconf}-generated \file{configure} files have their
corresponding source files, including optionally attempting to
regenerate them on platforms with \command{autoreconf}.
\item \command{R CMD build} has a new option
\option{--compression} to select the compression used for the tarball.
\item \command{R CMD build} now removes \file{src/*.mod} files on
all platforms.
}
}
\subsection{C-LEVEL FACILITIES}{
\itemize{
\item New pointer protection C functions \code{R_PreserveInMSet} and
\code{R_ReleaseFromMSet} have been introduced to replace
\code{UNPROTECT_PTR}, which is not safe to mix with \code{UNPROTECT}
(and with \code{PROTECT_WITH_INDEX}). Intended for use in parsers
only.
\item \code{NAMEDMAX} has been raised to 7 to allow further
protection of intermediate results from (usually ill-advised)
assignments in arguments to \code{BUILTIN} functions. Properly
written package code should not be affected.
\item \code{R_unif_index} is now considered to be part of the C API.
\item \code{R_GetCurrentEnv()} allows C code to retrieve the current
environment.
}
}
\subsection{DEPRECATED AND DEFUNCT}{
\itemize{
\item Argument \code{compressed} of \code{untar()} is
deprecated --- it is only used for external \code{tar} commands
which increasingly for extraction auto-detect compression and
ignore their \option{zjJ} flags.
\item \code{var(f)} and hence \code{sd(f)} now give an error for
\code{factor} arguments; they gave a deprecation warning since \R
3.2.3, \PR{16564}.
\item Package \pkg{tools}' \code{vignetteDepends()} has been
deprecated (it called a function deprecated since Feb 2016), being
partly replaced by newly exported \code{vignetteInfo()}.
\item The \command{f77_f2c} script has been removed: it
no longer sufficed to compile the \file{.f} files in \R.
\item The deprecated legacy support of \command{make} macros such
as \samp{CXX1X} has been removed: use the \samp{CXX11} forms
instead.
\item Make macro \samp{F77_VISIBILITY} is deprecated in favour of
\samp{F_VISIBILITY}.
\item Make macros \samp{F77}, \samp{FCPIFCPLAGS} and
\samp{SHLIB_OPENMP_FCFLAGS} are deprecated in favour of \samp{FC},
\samp{FPICFLAGS} and \samp{SHLIB_OPENMP_FFLAGS} respectively.