This blog is updated daily.
A general description is here.
Mathlib function ‘lgammacor(x)’ no longer warns about underflow to zero
for large ‘x’.
Text widths and heights were incorrectly reported by the Quartz device
if the drawing context didn't exist yet (typically when drawing
off-screen to a window that is yet to appear, see PR#18591).
The Quartz device could segfault in cases where paths with spaces are
used in the new glyph drawing API. Thanks to Tomek Gieorgijewski
(PR#18758).
Functions ‘R_atof’ and ‘R_strtod’ declared in header ‘R_ext/Utils.h’
are now documented in ‘Writing R Extensions’ and so formally part of
the API.
The non-API entry points ‘Rf_setSVector’, ‘Rf_StringFalse’,
‘Rf_StringTrue’ and ‘Rf_isBlankString’ have been added to those
reported by ‘R CMD check’.
The new function ‘Rf_allocLang’ is now available. This provides an
alternative to the idiom of calling ‘Rf_allocList’ followed by
‘SET_TYPEOF’.
‘R CMD check’ now reports as warnings what ‘gfortran’ calls ‘Fortran
2018 deleted features’, all of which have long been marked as
‘obsolescent’ and some of which were deleted in Fortran 2008 or
earlier. Fortran compilers are no longer required to support these.
‘as.numeric()’, ‘scan()’, ‘type.convert()’ and other places which use
the internal C function ‘R_strtod’ now require a _non-empty_ digit
sequence in a decimal or binary exponent. This aligns with the C/POSIX
standard for ‘strtod’ and with ‘?NumericConstants’.
‘as.data.frame(m, make.names=NA)’ now works correctly for a matrix ‘m’
with ‘NA’'s in row names.
The error message from ‘<POSIXlt>[["hour"]]’ and similar now mentions
‘*[[, "hour"]]’, as wished for in PR#17409 and proposed by Michael
Chirico.
‘qbinom()’ and potentially ‘qpois()’, ‘qnbinom()’, no longer sometimes
fail accurate inversion (of ‘pbinom()’, etc), thanks to Christopher
Chang's report and patch in PR#18711.
The internal help server on Windows can again serve requests sent in
quick succession, fixing a regression in R 4.4.0.
‘debugcall(<S3Generic>())’ now also works when a corresponding
S4-generic version is in the ‘methods’ cache (PR#18143).
Package ‘tools’' ‘toTitleCase(ch0)’ now returns ‘character(0)’ when
‘ch0’ is of zero length; fixing PR#18724, reported by David Hugh Jones.
‘R CMD check’ is no longer broken (without a check result and no
explanation in ‘00check.log’) for a package which declares an invalid
‘VignetteBuilder’ in ‘DESCRIPTION’ but has no vignettes.
Startup banners, ‘R --version’, ‘sessionInfo()’ and ‘R CMD check’ no
longer report ‘(64-bit)’ as part of the platform as this is almost
universal - the increasingly rare 32-bit platforms will still report
‘(32-bit)’.
On Windows, ditto for window titles.
‘is.atomic(NULL)’ now returns ‘FALSE’, as ‘NULL’ is not an atomic
vector. Strict back-compatibility would replace ‘is.atomic(foo)’ by
‘(is.null(foo) || is.atomic(foo))’ but should happen only sparingly.
The ‘confint()’ methods for ‘"glm"’ and ‘"nls"’ objects have been
copied to the ‘stats’ package. Previously, they were stubs which
called versions in package ‘MASS’. The ‘MASS’ namespace is no longer
loaded if you invoke (say) ‘confint(glmfit)’. Further, the ‘"glm"’
method for ‘profile()’ and the ‘plot()’ and ‘pairs()’ methods for class
‘"profile"’ have been copied from ‘MASS’ to ‘stats’. (‘profile.nls()’
and ‘plot.profile.nls()’ were already in ‘stats’.)
The ‘confint()’ and ‘profile’ methods for ‘"glm"’ objects have gained a
possibility to do profiling based on the Rao Score statistic in
addition to the default Likelihood Ratio. This is controlled by a new
‘test =’ argument.
The ‘pairs()’ method for ‘"profile"’ objects has been extended with a
‘which =’ argument to allow plotting only a subset of the parameters.
The ‘"glm"’ method for ‘anova()’ computes test statistics and p-values
by default, using a chi-squared test or an F test depending on whether
the dispersion is fixed or free. Test statistics can be suppressed by
giving argument ‘test’ a false logical value.
In ‘setRepositories()’ the repositories can be set using their names
via ‘name =’ instead of index ‘ind =’.
‘methods()’ and ‘.S3methods()’ gain a ‘all.names’ option for the (rare)
case where functions starting with a ‘.’ should be included.
Serializations can now be interrupted (e.g., by ‘Ctrl-C’ on a
Unix-alike) if they take too long, e.g., from ‘save.image()’, thanks to
suggestions by Ivan Krylov and others on R-devel.
New startup option ‘--max-connections’ to set the maximum number of
simultaneous connections for the session. Defaults to 128 as before:
allowed values up to 4096 (but resource limits may in practice restrict
to smaller values).
R on Windows (since Windows 10 2004) now uses the new Segment Heap
allocator. This may improve performance of some memory-intensive
applications.
When R packages are built, typically by ‘R CMD build <pkg>’, the new
‘--user=<build_user>’ option overrides the (internally determined) user
name, currently ‘Sys.info()["user"]’ or ‘LOGNAME’. This is a
(modified) fulfillment of Will Landau's suggestion in PR#17530.
‘tools::testInstalledBasic()’ gets new optional arguments ‘outDir’ and
‘testSrcdir’, e.g., allowing to use it in a ‘<builddir> != <srcdir>’
setup, and in standard “binary” Windows installation *if* a source
‘tests/’ folder is present.
‘range(<DT_with_Inf>, finite = TRUE)’ now work for objects of class
‘"Date"’, ‘"POSIXct"’, and ‘"POSIXlt"’ with infinite entries,
analogously to ‘range.default()’, as proposed by Davis Vaughan on
R-devel. Other ‘range()’-methods can make use of new function
‘.rangeNum()’.
New ‘.internalGenerics’ object complementing ‘.S3PrimitiveGenerics’,
for documentation and low-level book-keeping.
‘grid()’ now invisibly returns the x- and y- coordinates at which the
grid-lines were drawn.
‘norm(., type)’ now also works for complex matrices.
‘kappa(., exact = TRUE, norm = *)’ now works for all norms and also for
complex matrices. In symmetric / triangular cases, the new argument
‘uplo = "U" | "L"’ allows the upper or lower triangular part to be
specified.
‘memDecompress(type = "unknown")’ recognizes compression in the default
‘zlib’ format as used by ‘memCompress(type = "gzip")’.
‘memCompress()’ and ‘memDecompress()’ will use the ‘libdeflate’ library
(<https://github.com/ebiggers/libdeflate>) if installed. This uses the
same type of compression for ‘type = "gzip"’ but is 1.5-2x faster than
the system ‘libz’ library on some common platforms: the speed-up may
depend on the library version.
‘diff()’ for objects of class ‘"Date"’, ‘"POSIXct"’, and ‘"POSIXlt"’
accepts a ‘units’ argument passed via ‘...’.
Dynamic help now does a much better job of rendering package
‘DESCRIPTION’ metadata.
‘Rprof()’ gains an ‘event’ argument and support for elapsed (real) time
profiling on Unix (PR#18076).
‘filled.contour()’ gains a ‘key.border’ argument.
‘tools::update_pkg_po()’ gets arguments ‘pot_make’ and ‘mo_make’ for
_not_ re-making the corresponding files, and additionally a ‘verbose’
argument.
Hexadecimal string colour specifications are now accepted in short
form, so, for example, we can use ‘"#123"’, which is equivalent to
‘"#112233"’.
Thanks to MikeFC for the original idea and Ella Kaye, Malcolm Barrett, George Stagg, and Hanne Oberman for the patch.
Plain-text help shows \var markup by angle brackets.
The new experimental primitive function ‘declare()’ is intended to
eventually allow information about R code to be communicated to the
interpreter, compiler, and code analysis tools. The syntax for
declarations is still being developed.
Functions ‘psmirnov()’, ‘qsmirnov()’ and ‘rsmirnov()’ in package
‘stats’ have had argument ‘two.sided’ renamed to ‘alternative’, to take
into account that the permutation distributions of the one-sided
statistics can be different in the case of ties. Consequence of
PR#18582.
‘sort()’ is now an implicit S4 generic in ‘methods’.
Formatting and printing, ‘format(z), print(z)’, of complex vectors ‘z’
no longer zap relatively small real or imaginary parts to zero, fixing
PR#16752. This is an API change, as it was documented previously to
round real and imaginary parts together on purpose, producing nicer
looking output. As mentioned, e.g. in the PR, this change is
compatible with many other “R-like” programming environments.
We have simplified the internal code and now basically format the real and imaginary parts independently of each other.
New experimental functions ‘Tailcall()’ and ‘Exec()’ to support writing
stack-space-efficient recursive functions.
Where characters are attempted to be plotted by ‘pdf()’, ‘postscript()’
and ‘xfig()’ which are not in the selected 8-bit character set (most
often Latin-1) and the R session is using a UTF-8 locale, the warning
messages will show the UTF-8 character rather than its bytes and one
dot will be substituted per character rather than per byte. (Platforms
whose ‘iconv()’ does transliteration silently plot the
transliteration.)
In a UTF-8 locale some transliterations are now done with a warning (e.g., dashes and Unicode minus to hyphen, ligatures are expanded, permille (‘‰’) is replaced by ‘o/oo’), although the OS may have got there first. These are warnings as they will continue to be replaced by dots in earlier versions of R.
The matrix multiplication functions ‘crossprod()’ and ‘tcrossprod()’
are now also primitive and S3 generic, as ‘%*%’ had become in R 4.3.0.
‘source()’ and ‘example()’ have a new optional argument ‘catch.aborts’
which allows continued evaluation of the R code after an error.
The non-Quartz ‘tiff()’ devices allow additional types of compression
if supported by the platform's ‘libtiff’ library.
The list of base and recommended package names is now provided by
‘tools::standard_package_names()’.
‘cairo_pdf()’ and ‘cairo_ps()’ default to ‘onefile = TRUE’ to closer
match ‘pdf()’ and ‘postscript()’.
New option ‘catch.script.errors’ provides a documented way to catch
errors and then continue in non-interactive use.
‘L %||% R’ newly in ‘base’ is an expressive idiom for the phrases
‘if(!is.null(L)) L else R’ or ‘if(is.null(L)) R else L’.
The return value from ‘warnings()’ now always inherits from
‘"warnings"’ as documented, now also in the case of no warnings where
it previously returned ‘NULL’.
‘as.complex("1i")’ now returns ‘0 + 1i’ instead of ‘NA’ with a warning.
‘z <- c(NA, 1i)’ now keeps the imaginary part ‘Im(z[1]) == 0’, no
longer coercing to ‘NA_complex_’. Similarly, ‘cumsum(z)’ correctly
sums real and imaginary parts separately, i.e., without “crosstalk” in
case of ‘NA’s.
On Alpine Linux ‘iconv()’ now maps ‘"latin2"’, ‘"latin-2"’, ‘"latin9"’
and ‘"latin-9"’ to encoding names the OS knows about
(case-insensitively).
‘iconv(sub = "Unicode")’ now always zero-pads to four (hex) digits,
rather than to 4 or 8. (This seems to have become the convention once
Unicode restricted the number of Unicode points to 2^21 - 1 and so will
never need more than 6 digits.)
‘NCOL(NULL)’ now returns 0 instead of 1, for consistency with
‘cbind()’.
The information for the Euro glyph missing from the Adobe ‘.afm’ files
for the Courier, Helvetica and Times families has been copied from
their URW equivalents - this will improve vertical centring in the
‘pdf()’ and ‘postscript()’ devices.
The included BLAS sources have been updated to those shipped with
LAPACK version 3.12.0. The changes are almost entirely cosmetic.
The included LAPACK sources have been updated to version 3.12.0 and
some further double-complex routines added.
There are new font families for the 2014-5 URW 2.0 fonts (see ‘?pdf’)
which are included in recent versions of Ghostscript. These have font
widths for most Greek glyphs and a few others which were missing from
the original versions (whose font families remain available for
reproducibility, although Ghostscript-based viewers will render using
the 2.0 versions).
Improve the large-n efficiency of ‘as.matrix(<dist>)’, thanks an R
contributors effort, notably by Tim Taylor and Heather Turner, see
PR#18660.
The default and ‘numeric’ methods of ‘all.equal()’ get a ‘check.class’
option.
‘zapsmall()’ gets new optional arguments, function ‘mFUN’ and ‘min.d’,
for extra flexibility; fulfills a wish in PR#18199. Also, it is now an
implicit S4 generic in package ‘methods’.
The Rd filter for ‘aspell()’ gains an ‘ignore’ argument.
New generic function ‘sort_by()’, primarily useful for the ‘data.frame’
method which can be used to sort rows of a data frame by one or more
columns.
The licence headers for the RPC code in ‘src/extra/xdr’ have been
updated to use the GPL-compatible licence published by Oracle America
in 2010.
New function ‘pkg2HTML()’ in ‘tools’ to create single-page HTML
reference manuals for R packages.
The byte code evaluator now uses less C stack space for recursive calls
to byte-compiled functions. It also makes more of an effort to avoid
allocations for scalar return values.
New completion option ‘backtick’ (disabled by default) allows
non-syntactic completions to be wrapped in backquotes. This is
currently only useful for Jupyter notebooks via the ‘IRkernel’ package,
and may cause problems for other backends.
The numeric version creators now stop on invalid non-character version
specifications.
The parser has been updated to work with ‘bison’ 3.8.2, which is now
used for the pre-generated parsers in ‘gram.c’, ‘file.c’, and
‘gramRd.c’. A few parser error messages have changed, which may affect
code that relies on exact messages.
System valgrind headers are now required to use ‘configure’ option
‘--with-valgrind-instrumentation’ with value ‘1’ or ‘2’.
‘configure’ will warn if it encounters a 32-bit build, as that is
nowadays almost untested.
Environment variable ‘R_SYSTEM_ABI’ is no longer used and so no longer
recorded in ‘etc/Renviron’ (it was not on Windows and was only ever
used when preparing package ‘tools’).
If the ‘libdeflate’ library and headers are available, ‘libdeflate’
rather than ‘libz’ is used to (de)compress R objects in lazy-load
databases. Typically tasks spend up to 5% of their time on such
operations, although creating lazy-data databases is one of the
exceptions.
This can be suppressed if the library is available by the ‘configure’ option ‘--without-libdeflate-compression’.
‘configure’ option ‘--enable-lto=check’ has not worked reliably since
2019 and has been removed.
The minimum ‘autoconf’ requirement for a maintainer build has been
increased to ‘autoconf’ 2.71.
It is intended to increase this to 2.72 for R 4.5.0: the distributed ‘configure’ file was generated using 2.72.
The minimum version requirement for an external LAPACK has been reduced
to 3.9.0.
No default C++ compiler is set if no C++17 compiler is detected: there
is no longer an automatic fallback to C++14 or C++11.
Compilers from the last five years should have sufficient support: for others macros ‘CXX’ and ‘CXXSTD’ can be set in file ‘config.site’ to provide a fallback if needed.
The Objective-C++ compiler now by default uses the standard selected by R for C++ (currently C++17) rather than the default standard for the C++ compiler (which on macOS is still C++98).
A new ‘configure’ option ‘--with-newAccelerate’ makes use of Apple's
‘new’ BLAS / LAPACK interfaces in their Accelerate framework. Those
interfaces are only available in macOS 13.3 or later, and building
requires SDK 13.3 or later (from the Command Line Tools or Xcode 14.3
or later).
By default the option uses new Accelerate for BLAS calls: to also use it for LAPACK use option ‘--with-newAccelerate=lapack’. The later interfaces provide LAPACK 3.9.1 rather than 3.2.1: 3.9.1 is from 2021-04 and does not include the improved algorithms introduced in LAPACK 3.10.0 (including for BLAS calls).
The makefiles and installer scripts for Windows have been tailored to
Rtools44, an update of the Rtools43 toolchain. It is based on GCC 13
and newer versions of MinGW-W64, binutils and libraries (targeting
64-bit Intel CPUs). R-devel can no longer be built using Rtools43
without changes.
Rtools44 has experimental support for 64-bit ARM (‘aarch64’) CPUs _via_
the LLVM 17 toolchain using ‘lld’, ‘clang’/‘flang-new’ and ‘libc++’.
‘R CMD check’ notes when S4-style exports are used without declaring a
strong dependence on package ‘methods’.
‘tools::checkRd()’ (used by ‘R CMD check’) detects more problems with
\Sexpr-based dynamic content, including bad nesting of \Sexprs and
invalid arguments.
‘tools::checkRd()’ now reports Rd titles and section names ending in a
period; this is ignored by ‘R CMD check’ unless environment variable
‘_R_CHECK_RD_CHECKRD_MINLEVEL_’ is set to -5 or smaller.
‘R CMD check’ now notes Rd files without an \alias, as long documented
in ‘Writing R Extensions’ §1.3.1. The check for a missing \description
has been moved from ‘tools::checkRd()’ to ‘tools::checkRdContents()’.
‘R CMD check’ now visits ‘inst/NEWS.Rd’ and OS-specific ‘man’
subdirectories when checking Rd files.
‘tools::checkDocFiles()’ and ‘tools::checkRdContents()’ now also check
internal Rd files by default, but “specially” (ignoring missing
documentation of arguments).
‘R CMD Rdiff’ gets option ‘--useEx’.
‘R CMD check’ now warns on non-portable uses of Fortran ‘KIND’ such as
‘INTEGER(KIND=4)’ and ‘REAL(KIND=8)’.
To see the failing lines set environment variable ‘_R_CHECK_FORTRAN_KIND_DETAILS_’ to a true value.
When checking Rd files, ‘R CMD check’ now notes some of the “lost
braces” that ‘tools::checkRd()’ finds. Typical problems are Rd macros
missing the initial backslash (e.g., ‘code{...}’), in-text set notation
(e.g., ‘{1, 2}’, where the braces need escaping), and \itemize lists
with \describe-style entries of the form \item{label}{description}.
‘R CMD INSTALL’ (and hence ‘check’) will compile C++ code with
‘-DR_NO_REMAP’ if environment variable ‘_R_CXX_USE_NO_REMAP_’ is set to
a true value. It is planned that this will in future become the
default for compiling C++.
The new built-in Rd macro \dontdiff{} can be used to mark example code
whose output should be ignored when comparing check output to reference
output (‘tests/Examples/<pkg>-Ex.Rout.save’). The \dontdiff tag, like
\donttest, is _not_ shown on the rendered help page, so provides a
clean alternative to ‘## IGNORE_RDIFF_(BEGIN|END)’ comments.
‘R CMD build’ when there is no ‘NAMESPACE’, now uses the recommended
‘exportPattern("^[^.]")’, instead of exporting everything.
‘R CMD check’ now warns about non-ASCII characters in the ‘NAMESPACE’
file (in addition to R files). Such packages are not portable and may
fail to install on some platforms.
Headers ‘R_ext/Applic.h’ and ‘R-ext/Linpack.h’ used to include
‘R_ext/BLAS.h’ although this was undocumented and unneeded by their
documented entry points. They no longer do so.
New function ‘R_missing()’, factored out from ‘do_missing()’, used to
fix PR#18579.
‘SEXP’ type ‘S4SXP’ has been renamed to ‘OBJSXP’ to support
experimenting with alternative object systems. The ‘S4SXP’ value can
still be used in ‘C’ code but is now deprecated. Based on
contributions from the R Consortium's Object-Oriented Programming
Working Group.
New function ‘pow1p(x,y)’ for accurate ‘(1+x)^y’.
‘mkCharLenCE’ was incorrectly documented to take a ‘size_t’ length but
was implemented with ‘int’ (and character strings in R are limited to
2^31 - 1 bytes).
‘data()’ no longer handles zipped data from long-defunct (since R
2.13.0) ‘--use-zip-data’ installations.
The legacy graphics devices ‘pictex()’ and ‘xfig()’ are now deprecated.
They do not support recent graphics enhancements and their font
handling is rudimentary. The intention is to retain them for historical
interest as long as they remain somewhat functional.
Support for ‘encoding = "MacRoman"’ has been removed from the ‘pdf()’
and ‘postscript()’ devices - this was a legacy encoding supporting
classic macOS up to 2001 and no longer has universal ‘libiconv’
support.
‘is.R()’ is deprecated as no other S dialect is known to be in use (and
this could only identify historical dialects, not future ones).
Further information on calls can be obtained by setting the environment variable ‘_R_DEPRECATED_IS_R_’ to ‘error’ which turns the deprecation warning into an error and so by default gives a traceback. (This is done by ‘R CMD check --as-cran’.)
‘UseMethod()’ no longer forwards local variables assigned in the
generic function into method call environments before evaluating the
method body. This makes method calls behave more like standard function
calls and makes method code easier to analyze correctly.
The twelve ‘as.data.frame.<class>()’ methods which were deprecated only
via ‘_R_CHECK_AS_DATA_FRAME_EXPLICIT_METHOD_’ and in ‘R CMD check
--as-cran’ are formally deprecated now in favour of calling
‘as.data.frame()’ or ‘as.data.frame.vector()’. The deprecation “check”
now works also when ‘as.data.frame()’ is S4 generic thanks to Ivan
Krylov.
The default method for the directional comparison operators ‘<’, ‘>’,
‘<=’, and ‘>=’ now signals an error when one of the operands is a
language object, i.e. a symbol or a call.
For ‘terms.formula()’, deprecate ‘abb’ and ‘neg.out’ arguments
_formally_ in addition to just documenting it.
The ‘methods’ package is more robust to not being attached to the
search path. More work needs to be done.
‘pairwise.t.test()’ misbehaved when subgroups had 0 DF for variance,
even with ‘pool.sd = TRUE’. (PR#18594 by Jack Berry).
Probability distribution functions ‘[dpq]<distrib>(x, *)’, but also
‘bessel[IKJY](x, .)’ now consistently preserve ‘attributes(x)’ when
‘length(x) == 0’, e.g., for a 2 x 0 matrix, thanks to Karolis
Koncevičius' report PR#18509.
Group “Summary” computations such as ‘sum(1:3, 4, na.rm = 5, NA, 7,
na.rm = LL)’ now give an error instead of either ‘17’ or ‘NN’ for ‘LL’
true or false, as proposed by Ivan Krylov on the R-devel mailing list.
(This also means it is now an error to specify ‘na.rm’ more than once.)
‘as.complex(x)’ now returns ‘complex(real = x, imaginary = 0)’ for
_all_ numerical and logical ‘x’, notably also for ‘NA’ or
‘NA_integer_’.
Directories are now omitted by ‘file.copy(, recursive = FALSE)’ and in
‘file.append()’ (PR#17337).
‘gsub()’ and ‘sub()’ are now more robust to integer overflow when
reporting errors caused by too large input strings (PR#18346).
Top-level handlers are now more robust to attempts to remove a handler
whilst handlers are running (PR#18508).
The handling of ‘Alt+F4’ in dialogs created on Windows using GraphApp
has been fixed (PR#13870).
‘density()’ more consistently computes grid values for the FFT-based
convolution, following Robert Schlicht's analysis and proposal in
PR#18337, correcting density values typically by a factor of about
0.999. Argument ‘old.coords = TRUE’ provides back compatibility.
‘palette.colors()’ gains a ‘name’ argument that defaults to ‘FALSE’
controlling whether the vector of colours that is returned has names
(where possible). PR#18529.
‘tools::xgettext()’ no longer extracts the (non-translatable) class
names from ‘warningCondition’ and ‘errorCondition’ calls.
‘S3method(<gen>, <class>, <func>)’ in the ‘NAMESPACE’ file now works
(again) when ‘<func>’ is visible from the namespace, e.g., imported, or
in base.
‘getParseData(f)’ now also works for a function defined in the first of
several ‘<pkg>/R/*.R’ source files, thanks to Kirill Müller's report
and Duncan Murdoch's patch in PR#16756.
Rd \Sexpr macros with nested #ifdef conditionals were not processed.
A non-blocking connection with non-default encoding (such as a socket)
now correctly returns from ‘readLines()’ after new data has arrived
also when its EOF had been reached previously. Thanks to Peter
Meilstrup's report on R-devel and Ivan Krylov's report and patch
proposal in PR#18555.
‘tools::checkRdContents()’ failed to detect empty argument descriptions
when they spanned multiple lines, including those generated by
‘prompt()’. These cases are now noted by ‘R CMD check’.
Plain-text help no longer outputs spurious colons in the arguments list
(for multi-line \item labels in the Rd source).
‘kappa()’ and ‘rcond()’ work correctly in more cases; ‘kappa(., norm =
"2")’ now warns that it computes the 1-norm with (default) ‘exact =
FALSE’; prompted by Mikael Jagan's quite comprehensive PR#18543.
Rd skeletons generated by ‘prompt()’ or ‘promptData()’ now use a dummy
title (so ‘R CMD build’ works). ‘tools::checkRdContents()’ has been
updated to detect such template leftovers, including from
‘promptPackage()’.
When S4 method dispatch fails because no method was found, the error
message now includes the signature argument names; thanks to Michael
Chirico's proposal on the R-devel list.
‘withAutoprint({ .. })’ now preserves ‘srcref’s previously lost, thanks
to Andrew Simmons' report plus fix in PR#18572.
‘transform.data.frame()’ no longer adjusts names; in particular,
untransformed variables are kept as-is, including those with
syntactically invalid names (PR#17890).
The ‘keep.source’ option for Rd \Sexpr blocks is no longer ignored.
The ‘formula’ methods for ‘t.test()’ and ‘wilcox.test()’ now catch when
‘paired’ is passed, addressing PR#14359; use ‘Pair(x1, x2) ~ 1’ for a
paired test.
The level reported in the ‘browser’ prompt was often too large. It now
shows the number of browser contexts on the stack.
For ‘cbind()’ and ‘rbind()’, the optional ‘deparse.level’ argument is
now properly passed to methods, thanks to Mikael Jagan's PR#18579 and
comments there.
Some error and warning messages for large (‘long vector’) ‘matrix(v,
nr, nc)’ and ‘dim(m) <- d’ are now correct about sizes, using ‘long
long’ formatting, fixing PR#18612 (and more) reported by Mikael Jagan.
‘readChar(useBytes = TRUE)’ now terminates strings even when the
underlying connection uses extra spaces in the input buffer. This
fixes problems with extra garbage seen with ‘gzip’ connections,
PR#18605.
Named capture in PCRE regular expressions now works also with more than
127 named groups (PR#18588).
Datetime functions are now robust against long jumps when dealing with
internal time zone changes. This avoids confusing warnings about an
invalid time zone, previously triggered by turning warnings into errors
or handling them via ‘tryCatch’ (PR#17966, PR#17780).
Datetime functions now restore even an empty ‘TZ’ environment variable
after internal time zone changes (PR#17724). This makes results of
datetime functions with this (typically unintentional) setting more
predictable.
‘drop.terms(*)’ now drops response as by default, ‘keep.response =
FALSE’, fixing PR#18564 thanks to Mikael Jagan.
‘dummy.coef(.)’ now also works for ‘lm()’-models with ‘character’
categorical predictor variables rather than ‘factor’ ones, fixing
PR#18635 reported by Jinsong Zhao.
‘formals(f) <- formals(f)’ now also works for a function w/o arguments
and atomic _constant_ ‘body(f)’.
Correct ‘as.function(<invalid list>, .)’'s error message.
‘removeSource()’ is yet more thorough in finding and removing
‘"srcref"’ and the other source references from parsed R language
chunks, fixing PR#18638 thanks to Andrew Simmons.
‘dgeom()’ is more accurate now, notably when its result is very small,
fixing PR#18642 thanks to the proposal of Morten Welinder, also
improving other instances where C level ‘binom_raw(x, n, ..)’ has ‘x ==
0’ or ‘x== n’.
‘warning()’ with ‘options(warn = 1)’ has improved output for multi-line
messages.
‘axis.Date()’ and ‘axis.POSIXct()’ now respect the ‘par("lab")’ setting
for the number of ‘pretty()’ intervals.
Comparisons for language objects (which are based on deparsing) are now
more careful about using accurate deparsed results (PR#18676).
Plain-text help (‘Rd2txt’) now correctly preserves blank lines
following single-line \dontrun code.
‘<POSIXlt>[*]’ no longer sets wrong ‘"balanced"’ attribute, fixing
PR#18681 thanks to Mikael Jagan.
‘str(<classed-call>)’ now deparses the call as expected, fixing
PR#18684, reported by Dave Slager.
In Rd examples, code following the closing brace of a \dontrun,
\dontshow or \donttest tag on the same line is no longer skipped when
‘R CMD check’ runs the examples.
‘as.data.frame(matrix(*, ncol=0))’ now gets valid ‘names()’ and
‘colnames()’; reported by Davis Vaughan on the R-devel list.
Internal Mathlib function ‘stirlerr(n)’ is now almost fully (52-bit)
accurate for all n >= ~5.9 and more accurate also in the range 1 --
5.9. This entails small (“after 12th decimal”) changes in density
functions, e.g., ‘dgamma()’ in _some_ regions of their support. The
fix was partly prompted by Morten Welinder's PR#18640.
Numbers like ‘9876543.2’ are now considered non-integer by Mathlib
internal ‘R_nonint()’, amending original fix of PR#15734.
Rd comment lines no longer cause broken paragraphs in the rendered PDF
and plain-text help. In code blocks, pure comment lines (starting with
‘%’) no longer produce an empty line.
‘xtabs(Freq ~ .)’ now consistently defaults to ‘na.action = na.pass’,
using ‘na.rm = FALSE’ (added as an argument) when summing over ‘Freq’
(PR#17770).
‘tools::testInstalledPackage()’ is no longer silent about failures from
running examples or tests and its return code no longer ignores
failures from checking vignettes.
‘iconv()’ now fixes up variant encoding names such as ‘"utf8"’
case-insensitively.
The legacy ‘encoding = "MacRoman"’ is deprecated in ‘pdf()’ and
‘postscript()’: support was incomplete in earlier versions of R.
Arguments are now properly forwarded to methods on S4 generics with ...
in the middle of their formal arguments. This was broken for the case
when a method introduced an argument but did not include ... in its own
formals. Thanks to Hervé Pagès for the report PR#18538.
Some invalid ‘file’ arguments to ‘pictex()’, ‘postscript()’ and
‘xfig()’ opened a file called ‘NA’ rather than throw an error. These
included ‘postscript(NULL)’ (which some people expected to work like
‘pdf(NULL)’).
Passing ‘filename = NA’ to ‘svg()’, ‘cairo_pdf()’, ‘cairo_ps()’ or the
Cairo-based bitmap devices opened a file called ‘NA’: it now throws an
error.
‘quartz(file = NA)’ opened a file called ‘NA’, including when used as a
Quartz-based bitmap device. It now gives an error.
‘rank(<long vector>)’ now works, fixing PR#18617, thanks to Ilia Kats.
‘seq.int()’ did not adequately check its ‘length.out’ argument.
‘match(<POSIXct>, .)’ is correct again for differing time zones, ditto
for ‘"POSIXlt"’, fixing PR#18618 reported by Bastian Klein.
‘drop.terms(*, dropx = <0-length>)’ now works, fixing PR#18563 as
proposed by Mikael Jagan.
‘drop.terms(*)’ keeps ‘ + offset(.)’ terms when it should, PR#18565,
and ‘drop.terms()’ no longer makes up a response, PR#18566, fixing both
bugs thanks to Mikael Jagan.
‘getS3method("t", "test")’ no longer finds the ‘t.test()’ function,
fixing PR#18627.
‘pdf()’ and ‘postscript()’ support for the documented Adobe encodings
‘"Greek"’ and ‘"Cyrilllic"’ was missing (although the corresponding
Windows' codepages could be used).
Computations of glyph metric information for ‘pdf()’ and ‘postscript()’
did not take into account that transliteration could replace one
character by two or more (only seen on macOS 14) and typically warned
that the information was not known.
‘rank(x)’ no longer overflows during integer addition, when computing
rank average for largish but not-yet long vector ‘x’, fixing PR#18630,
thanks to Ilia Kats.
‘list.files()’ on Windows now returns also files with names longer that
260 bytes (the Windows limit is 260 characters). Previously, some file
names particularly with ‘East Asian’ characters were omitted.
‘cov2cor(<0 x 0>)’ now works, fixing PR#18423 thanks to Mikael Jagan
and Elin Waring.
‘cov2cor(<negative diagonal>)’ and similar now give one warning instead
of two, with better wording, fixing PR#18424 thanks to Mikael Jagan.
‘tools’‘:: startDynamicHelp()’ now ensures ‘port’ is in proper range,
fixing PR#18645.
‘pbeta(x, a,b)’ is correct now for ‘x’=0 or 1 in the boundary cases
where ‘a’ or ‘b’ or both are 0, fixing PR#18672 thanks to Michael Fay.
‘pmatch(x, table)’ for large ‘table’, also called for data frame row
selection, ‘dfrm[nm, ]’, is now interruptible, fixing PR#18656.
‘predict(<rank-deficient lm>, newdata=*)’ fix computing of ‘nbasis’,
see Russ Lenth's comment 29 in PR#16158.
Added a work-around for a bug in macOS 14.3.1 and higher which prevents
R plots in the Quartz Cocoa device from updating on screen.
The default initialization of the ‘"repos"’ option from the
‘repositories’ file at startup can be skipped by setting environment
variable ‘R_REPOSITORIES’ to ‘NULL’ such that ‘getOption("repos")’ is
empty if not set elsewhere.
‘qr.X()’ is now an implicit S4 generic in ‘methods’.
‘iconv(to = "ASCII//TRANSLIT")’ is emulated using substitution on
platforms which do not support it (notably Alpine Linux). This should
give a human-readable conversion in ASCII on all platforms (rather than
‘NA_character_’).
‘trans3d()’ gains options ‘continuous’ and ‘verbose’ addressing the
problem of possible “wrap around” when projecting too long curves, as
reported by Achim Zeileis in PR#18537.
‘tools::showNonASCII()’ has been rewritten to work better on macOS 14
(which has a changed implementation of ‘iconv()’).
‘tiff(type = "quartz")’ (the default on macOS) now warns if
‘compression’ is specified: it continues to be ignored.
There is some support for building with Intel's LLVM-based compilers on
‘x86_64’ Linux, such as (C) ‘icx’, (C++) ‘ipcx’ and (Fortran) ‘ifx’
from oneAPI 2023.x.y.
There is support for using LLVM's ‘flang-new’ as the Fortran compiler
from LLVM 16.0.x (preferably 17.0.0 or later).
‘R CMD check’ reports the use of the Fortran 90 random number generator
‘RANDOM_NUMBER()’ and the subroutines to initialize it.
‘Writing R Extensions’ has example code to use R's RNGs from Fortran.
‘substr(x, n, L) <- cc’ now works (more) correctly for multibyte UTF-8
strings ‘x’ when ‘L > nchar(x)’, thanks to a report and patch by
‘Architect 95’.
‘contrib.url(character())’ now returns 0-length ‘character()’ as
documented, which also avoids spurious warnings from
‘available.packages()’ et al. in the edge case of an empty vector of
repository URLs.
‘readChar(., 4e8)’ no longer fails, thanks to Kodi Arfer's report
(PR#18557).
‘lapply(<list>, as.data.frame)’ no longer warns falsely for some base
vector components.
Communication between parent and child processes in the ‘multicore’
part of ‘parallel’ could fail on platforms that do not support an
arbitrarily large payload in system functions ‘read()’/‘write()’ on
pipes (seen on macOS where a restriction to ‘INT_MAX’ bytes is
documented, without doing a partial read unlike Linux). The payload is
now split into 1Gb chunks to avoid that problem. (PR#18571)
‘qqplot(x,y, conf.level=.)’ gives better confidence bounds when
‘length(x) != length(y)’, thanks to Alexander Ploner's report and patch
proposal (PR#18557).
‘norm(<0-length>, "2")’ now gives zero instead of an error, as all the
other norm types, thanks to Mikael Jagan's PR#18542.
Build-stage Rd macros \packageAuthor and \packageMaintainer now process
‘Authors@R’, fixing ‘NA’ results when the package ‘DESCRIPTION’ omits
‘Author’ and ‘Maintainer’ fields.
Formatting and printing complex numbers could give things like
‘0.1683-0i’ because of rounding error: ‘-0i’ is now replaced by ‘+0i’.
‘postscript()’ refused to accept a ‘title’ comment containing the
letter “W” (PR#18599).
‘isoreg(c(1,Inf))’ signals an error instead of segfaulting, fixing
PR#18603.
‘tiff(type = "Xlib")’ was only outputting the last page of multi-page
plots.
‘tools::latexToUtf8()’ again knows about ‘\~{n}’ and other letters with
tilde, fixing a regression in R 4.3.0, and about ‘\^{i}’ as an
alternative to ‘\^{\i}’ (similarly with other accents). Furthermore,
LaTeX codes for accented I letters are now correctly converted, also
fixing related mistakes in ‘tools::encoded_text_to_latex()’.
‘tar(*, tar = "internal")’ no longer creates out-of-spec tar files in
the very rare case of user or group names longer than 32 bytes, fixing
PR#17871 with thanks to Ivan Krylov.
When using the “internal” timezone datetime code, adding a fraction of
a second no longer adds one second, fixing PR#16856 from a patch by
Ivan Krylov.
‘tools::checkRd()’ no longer produces spurious notes about “unnecessary
braces” from multi-line Rd results of \Sexpr macros.
The C-level API version of R's ‘integrate()’, ‘Rdqags()’ in ‘Applic.h’,
now returns the correct number of integrand evaluations ‘neval’, fixing
PR#18515 reported and diagnosed by Stephen Wade.
The C prototypes for LAPACK calls ‘dspgv’ and ‘dtptrs’ in
‘R_ext/Lapack.h’ had one too many and one too few character length
arguments - but this has not caused any known issues. To get the
corrected prototypes, include
#include <Rconfig.h> // for PR18534fixed #ifdef PR18534fixed # define usePR18534fix 1 #endif #include <R_ext/Lapack.h>
in your C/C++ code (PR#18534).
Many of the checks of esoteric Internet operations and those using
unreliable external sites have been moved to a new target that is not
run by default and primarily intended for the core developers. To run
them use
cd tests; make test-Internet-dev
‘.S3methods()’, typically called from ‘methods()’, again marks methods
from package ‘base’ as ‘visible’.
Also, the visibility of non-‘base’ methods is again determined by the method's presence in ‘search()’.
‘tools::Rdiff()’ is now more robust against invalid strings, fixing
installation tests on Windows without Rtools installed (PR#18530).
Fix (new) bug in ‘hcl.colors(2, *)’, by Achim Zeileis (PR#18523).
‘head(., <illegal>)’ and ‘tail(..)’ now produce more useful ‘"Error in
...."’ error messages, fixing PR#18362.
Package code syntax on Windows is checked in UTF-8 when UTF-8 is the
native encoding.
‘na.contiguous(x)’ now also returns the first run, when it is at the
beginning and there is a later one of the same length; reported to
R-devel, including a fix, by Georgi Boshnakov. Further, by default, it
modifies only an existing ‘attr(*,"tsp")’ but otherwise no longer sets
one.
‘chol(<not pos.def>, pivot = <T|F>)’ now gives a correct error or
warning message (depending on ‘pivot’), thanks to Mikael Jagan's
(PR#18541).
Calling ‘&&’ or ‘||’ with LHS or (if evaluated) RHS of length greater
than one is now always an error, with a report of the form
'length = 4' in coercion to 'logical(1)'
Environment variable ‘_R_CHECK_LENGTH_1_LOGIC2_’ no longer has any effect.
The included BLAS sources have been updated to those shipped with
LAPACK version 3.10.1. (This caused some platform-dependent changes to
package check output.) And then to the sources from LAPACK version
3.11.0 (with changes only to double complex subroutines).
The included LAPACK sources have been updated to include the four
Fortran 90 routines rather than their Fortran 77 predecessors. This
may give some different signs in SVDs or eigendecompositions.. (This
completes the transition to LAPACK 3.10.x begun in R 4.2.0.)
The LAPACK sources have been updated to version 3.11.0. (No new
subroutines have been added, so this almost entirely bug fixes: Those
fixes do affect some computations with ‘NaN’s, including R's ‘NA’.)
The parser now signals _classed_ errors, notably in case of the pipe
operator ‘|>’. The error object and message now give line and column
numbers, mostly as proposed and provided by Duncan Murdoch in PR#18328.
‘toeplitz()’ is now generalized for asymmetric cases, with a
‘toeplitz2()’ variant.
‘xy.coords()’ and ‘xyz.coords()’ and consequently, e.g., ‘plot(x,y, log
= "y")’ now signal a _classed_ warning about negative values of y
(where ‘log(.)’ is ‘NA’). Such a warning can be specifically
suppressed or caught otherwise.
Regular expression functions now check more thoroughly whether their
inputs are valid strings (in their encoding, e.g. in UTF-8).
The performance of ‘grep()’, ‘sub()’, ‘gsub()’ and ‘strsplit()’ has
been improved, particularly with ‘perl = TRUE’ and ‘fixed = TRUE’. Use
of ‘useBytes = TRUE’ for performance reasons should no longer be needed
and is discouraged: it may lead to incorrect results.
‘apropos()’ gains an argument ‘dot_internals’ which is used by the
completion (‘help(rcompgen)’) engine to also see ‘base’ internals such
as ‘.POSIXct()’.
Support in ‘tools::Rdiff()’ for comparing uncompressed PDF files is
further reduced - see its help page.
‘qqplot(x, y, ...)’ gains ‘conf.level’ and ‘conf.args’ arguments for
computing and plotting a confidence band for the treatment function
transforming the distribution of ‘x’ into the distribution of ‘y ’
(Switzer, 1976, _Biometrika_). Contributed by Torsten Hothorn.
Performance of ‘package_dependencies()’ has been improved for cases
when the number of dependencies is large.
Strings newly created by ‘gsub()’, ‘sub()’ and ‘strsplit()’, when any
of the inputs is marked as ‘"bytes"’, are also marked as ‘"bytes"’.
This reduces the risk of creating invalid strings and accidental
substitution of bytes deemed invalid.
Support for ‘readLines(encoding = "bytes")’ has been added to allow
processing special text files byte-by-byte, without creating invalid
strings.
‘iconv(from = "")’ now takes into account any declared encoding of the
input elements and uses it in preference to the native encoding. This
reduces the risk of accidental creation of invalid strings,
particularly when different elements of the input have different
encoding (including ‘"bytes"’).
Package repositories in ‘getOption("repos")’ are now initialized from
the ‘repositories’ file when ‘utils’ is loaded (if not already set,
e.g., in ‘.Rprofile’). (From a report and patch proposal by Gabriel
Becker in PR#18405.)
‘compactPDF()’ gets a ‘verbose’ option.
‘type.convert()’ and hence ‘read.table()’ get new option ‘tryLogical =
TRUE’ with back compatible default. When set to false, converts ‘"F"’
or ‘"T"’ columns to character.
Added new unit prefixes ‘"R"’ and ‘"Q"’ for abbreviating
(unrealistically large) sizes beyond 10^{27} in ‘standard = "SI"’,
thanks to Henrik Bengtsson's PR#18435.
‘as.data.frame()’'s default method now also works fine with atomic
objects inheriting from classes such as ‘"roman"’, ‘"octmode"’ and
‘"hexmode"’, thus fulfilling the wish of PR#18421, by Benjamin Feakins.
The ‘as.data.frame.vector()’ utility now errors for wrong-length
‘row.names’. It warned for almost six years, with “Will be an error!”.
‘sessionInfo()’ now also contains ‘La_version()’ and reports codepage
and timezone when relevant, in both ‘print()’ and ‘toLatex()’ methods
which also get new option ‘tzone’ for displaying timezone information
when ‘locale = FALSE’.
New function ‘R_compiled_by()’ reports the C and Fortran compilers used
to build R, if known.
‘predict(<lm>, newdata = *)’ no longer unnecessarily creates an
‘offset’ of all ‘0’s.
‘solve()’ for complex inputs now uses argument ‘tol’ and by default
checks for ‘computational singularity’ (as it long has done for numeric
inputs).
‘predict(<rank-deficient lm>, newdata=*)’ now obeys a new argument
‘rankdeficient’, with new default ‘"warnif"’, warning only if there are
non-estimable cases in ‘newdata’. Other options include ‘rankdeficient
= "NA"’, predicting ‘NA’ for non-estimable ‘newdata’ cases. This
addresses PR#15072 by Russ Lenth and is based on his original proposal
and discussions in PR#16158 also by David Firth and Elin Waring. Still
somewhat experimental.
‘Rgui’ console implementation now works better with the ‘NVDA’ screen
reader when the full blinking cursor is selected. The underlying
improvements in cursor handling may help also other screen readers on
Windows.
The drop-field control in GraphApp can now be left with the TAB key and
all controls can be navigated in the reverse order using the Shift+TAB
key, improving accessibility of the ‘Rgui’ configuration editor.
‘qnorm(<very large negative>, log.p=TRUE)’ is now fully accurate
(instead of to “only” minimally five digits).
‘demo(error.catching)’ now also shows off ‘withWarnings()’ and
‘tryCatchWEMs()’.
As an experimental feature the placeholder ‘_’ can now also be used in
the ‘rhs’ of a forward pipe ‘|>’ expression as the first argument in an
extraction call, such as ‘_$coef’. More generally, it can be used as
the head of a chain of extractions, such as ‘_$coef[[2]]’.
Spaces in the environment variable used to choose the R session's
temporary directory (‘TMPDIR’, ‘TMP’ and ‘TEMP’ are tried in turn) are
now fatal. (On Windows the ‘short path’ version of the path is tried
and used if that does not contain a space.)
‘all.equal.numeric()’ gets a new optional switch ‘giveErr’ to return
the numeric error as attribute. Relatedly,
‘stopifnot(all.equal<some>(a, b, ..))’ is as “smart” now, as
‘stopifnot(all.equal(....))’ has been already, thus allowing customized
‘all.equal<Some>()’ wrappers.
R on Windows is now able to work with path names longer than 260
characters when these are enabled in the system (requires at least
Windows 10 version 1607). Packages should be updated to work with long
paths as well, instead of assuming ‘PATH_MAX’ to be the maximum length.
Custom front-ends and applications embedding R need to update their
manifests if they wish to allow this feature. See
<https://blog.r-project.org/2023/03/07/path-length-limit-on-windows>
for more information.
‘Object not found’ and ‘Missing argument’ errors now give a more
accurate error context. Patch provided by Lionel Henry in PR#18241.
The ‘@’ operator is now an S3 generic. Based on contributions by Tomasz
Kalinowski in PR#18482.
New generic ‘chooseOpsMethod()’ provides a mechanism for objects to
resolve cases where two suitable methods are found for an Ops Group
Generic. This supports experimenting with alternative object systems.
Based on contributions by Tomasz Kalinowski in PR#18484.
‘inherits(x, what)’ now accepts values other than a simple character
vector for argument ‘what’. A new generic, ‘nameOfClass()’, is called
to resolve the class name from ‘what’. This supports experimenting with
alternative object systems. Based on contributions by Tomasz
Kalinowski in PR#18485.
Detection of BLAS/LAPACK in use (‘sessionInfo()’) with FlexiBLAS now
reports the current backend.
The ‘"data.frame"’ method for ‘subset()’ now warns about extraneous
arguments, typically catching the use of ‘=’ instead of ‘==’ in the
‘subset’ expression.
Calling ‘a:b’ when numeric ‘a’ or ‘b’ is longer than one may now be
made into an error by setting environment variable
‘_R_CHECK_LENGTH_COLON_’ to a true value, along the proposal in
PR#18419 by Henrik Bengtsson.
‘density(x, weights = *)’ now warns if automatic bandwidth selection
happens without using ‘weights’; new optional ‘warnWbw’ may suppress
the warning. Prompted by Christoph Dalitz' PR#18490 and its
discussants.
‘rm(list = *)’ is faster and more readable thanks to Kevin Ushey's
PR#18492.
The ‘plot.lm()’ function no longer produces a normal Q-Q plot for GLMs.
Instead it plots a half-normal Q-Q plot of the absolute value of the
standardized deviance residuals.
The ‘print()’ method for class ‘"summary.glm"’ no longer shows summary
statistics for the deviance residuals by default. Its optional
argument ‘show.residuals’ can be used to show them if required.
The ‘tapply()’ function now accepts a data frame as its ‘X’ argument,
and allows ‘INDEX’ to be a formula in that case. ‘by.data.frame()’
similarly allows ‘INDICES’ to be a formula.
The performance of ‘df[j] <- value’ (including for missing ‘j’) and
‘write.table(df)’ has been improved for data frames ‘df’ with a large
number of columns. (Thanks to Gabriel Becker's PR#18500, PR#18503 and
discussants, prompted by a report from Toby Dylan Hocking on the
R-devel mailing list.)
The matrix multiply operator ‘%*%’ is now an S3 generic, belonging to
new group generic ‘matrixOps’. From Tomasz Kalinowski's contribution
in PR#18483.
New function ‘array2DF()’ to convert arrays to data frames,
particularly useful for the list arrays created by ‘tapply()’.
On platforms where (non-UTC) datetimes before 1902 (or before 1900 as
with system functions on recent macOS) are guessed by extrapolating
time zones from 1902-2037, there is a warning at the first use of
extrapolation in a session. (As all time zones post 2037 are
extrapolation, we do not warn on those.)
(Platforms using ‘--with-internal-tzone’, including Windows and by
default macOS). How years are printed in dates or date-times can be
controlled by environment variable ‘R_PAD_YEARS_BY_ZERO’. The default
remains to pad to 4 digits by zeroes, but setting value ‘no’ gives no
padding (as used by default by ‘glibc’).
‘strftime()’ tries harder to determine the offset for the ‘"%z"’
format, and succeeds on the mainstream R platforms.
‘strftime()’ has a limit of 2048 bytes on the string produced -
attempting to exceed this is an error. (Previously it silently
truncated at 255 bytes.)
‘sessionInfo()’ records (and by default prints) the system time zone as
part of the locale information. Also, the source (system/internal) of
the date-time conversion and printing functions.
Objects of class ‘"POSIXlt"’ created in this version of R always have
11 components: component ‘zone’ is always set, and component ‘gmtoff’
is set for times in UTC and usually set on the (almost all) platforms
which have C-level support, otherwise is ‘NA’.
There are comprehensive validity checks on the structure of objects of
class ‘"POSIXlt"’ when converting (including formatting and printing).
(This avoids mis-conversions of hand-crafted objects.)
There is some support for using the native date-time routines on macOS:
this is only viable on recent versions (e.g. 12.6 and 13) and does get
wrong some historical changes (before 1900, during WWII). Use of
‘--with-internal-tzone’ remains the default.
‘as.POSIXct(<numeric>)’ and ‘as.POSIXlt(.)’ (without specifying
‘origin’) now work. So does ‘as.Date(<numeric>)’.
‘as.Date.POSIXct(., tz)’ now treats several ‘tz’ values, notably
‘"GMT"’ as equivalent to ‘"UTC"’, proposed and improved by Michael
Chirico and Joshua Ulrich in PR#17674.
Experimental ‘balancePOSIXlt()’ utility allows using “ragged” and or
out-of-range ‘"POSIXlt"’ objects more correctly, e.g., in subsetting
and subassignments. Such objects are now documented. Complemented by
the low-level ‘unCfillPOSIXlt()’ utility.
More experimentally, a ‘"POSIXlt"’ object may have an attribute ‘"balanced"’ indicating if it is known to be filled or fully balanced.
Functions ‘axis.Date()’ and ‘axis.POSIXct()’ are rewritten to gain
better default tick locations and better default formats via the
corresponding ‘pretty()’ methods. Thanks to Swetlana Herbrandt.
The mapping of Windows' names for time zones to IANA's ‘Olson’ names
has been updated. When ICU is available (it is by default), it is used
to get a mapping for the current region set in Windows. This can be
overridden by setting environment variable ‘TZ’ to the desired Olson
name - see ‘OlsonNames()’ for those currently available.
The graphics engine version, ‘R_GE_version’, has been bumped to ‘16’
and so packages that provide graphics devices should be reinstalled.
The ‘grDevices’ and ‘grid’ packages have new functions for rendering
typeset glyphs, primarily: ‘grDevices::glyphInfo()’ and
‘grid::grid.glyph()’.
Rendering of typeset glyphs is only supported so far on the Cairo-based graphics devices and on the ‘pdf()’ and ‘quartz()’ devices.
The defined behaviour for ‘"clear"’ and ‘"source"’ compositing
operators (via ‘grid::grid.group()’) has been changed (to align better
with simple interpretation of original Porter-Duff definitions).
Support for gradients, patterns, clipping paths, masks, groups,
compositing operators, and affine transformations has been added to the
‘quartz()’ device.
A system installation of generic LAPACK 3.10.0 or later will be
preferred to the version in the R sources.
‘configure’ option ‘--with-lapack=no’ (equivalently ‘--without-lapack’) forces compilation of the internal LAPACK sources.
If ‘--with-lapack’ is not specified, a system ‘liblapack’ is looked for and used if it reports version 3.10.0 or later and does not contain BLAS routines.
Packages using LAPACK will need to be reinstalled if this changes to using an external library.
On ‘aarch64’ Linux platforms using GCC, ‘configure’ now defaults to
‘-fPIC’ (instead of ‘-fpic’), as desired in PR#18326.
‘configure’ now checks conversion of datetimes between ‘POSIXlt’ and
‘POSIXct’ around year 2020. Failure (which has been seen on platforms
missing ‘tzdata’) is fatal.
If ‘configure’ option ‘--with-valgrind-instrumentation’ is given value
‘1’ or ‘2’, option ‘--with-system-valgrind-headers’ is now the default
and ignored (with a warning). It is highly recommended that the system
headers are installed alongside ‘valgrind’: they are part of its
packaging on some Linux distributions and packaged separately (e.g. in
the ‘valgrind-devel’ RPM) on others. ‘configure’ will give a warning
if they are not found.
The system headers will be required in a future release of R to build with ‘valgrind’ instrumentation.
‘libcurl’ 8.x is now accepted by ‘configure’: despite a change in major
version number it changes neither API nor ABI.
The makefiles and installer scripts for Windows have been tailored to
Rtools43, an update of the Rtools42 toolchain. It is based on GCC 12
and newer versions of MinGW-W64, binutils and libraries. At this time
R-devel can still be built using Rtools42 without changes, but when
R-devel is installed via the installer, it will by default look for
Rtools43.
Old make targets ‘rsync-extsoft’ and 32-bit ones that are no longer
needed have been removed.
Default builds (including for packages) no longer select C99. Thus the
C standard used is the default for the compiler, which for the
toolchain in ‘Rtools43’ is C17. (This is consistent with Unix builds.)
The default C++ standard has been changed to C++17 where available
(which it is on all currently checked platforms): if not C++14 or C++11
is used if available otherwise C++ is not supported.
‘USE_FC_LEN_T’ is the default: this uses the correct
(compiler-dependent) prototypes for Fortran BLAS/LAPACK routines called
from C/C++, and requires adjustment of many such calls - see ‘Writing R
Extensions’ §6.6.1.
There is initial support for C++23 as several compilers are now
supporting ‘-std=c++23’ or ‘-std=c++2b’ or similar. As for C++20,
there no additional ‘configure’ checks for C++23 features beyond a
check that the compiler reports a ‘__cplusplus’ value greater than that
in the C++20 standard. C++ feature tests should be used.
There is support for a package to indicate the version of the C
standard which should be used to compile it, and for the installing
user to specify this. In most cases R defaults to the C compiler's
default standard which is C17 (a `bug-fix' of C11) - earlier versions
of R or compilers may have defaulted to C99.
Current options are:
USE_C17 Use a standard that is at most C17. The intention is to allow legacy packages to still be installed when later C standards become the default, including packages using new keywords as identifiers or with K&R-style function declarations. This will use C17 if available, falling back to C11.
USE_C90 Use the C90 (aka C89) standard. (As that standard did not require compilers to identify that version, all we can verify is that the compiler does not claim to be using a later standard. It may accept C99 features - for example ‘clang’ accepts // to make comments.)
USE_C99 Use the C99 standard. This should be rarely needed - it avoids the few new features of C11/C17 which can be useful if a package assumes them if C17 is specified and they are not implemented.
USE_C23 Use C23 (or in future, later). Compiler/library support for C23 is still being implemented, but LLVM clang from 15.0.0 and GCC from 13 have quite extensive support.
These can be specified as part of the ‘SystemRequirements’ field in the package's ‘DESCRIPTION’ file or _via_ options ‘--use-C17’ and so on of ‘R CMD INSTALL’ and ‘R CMD SHLIB’.
For further details see “Writing R Extensions” §1.2.5.
(Windows) A ‘src/Makefile.ucrt’ or ‘src/Makefile.win’ file is now
included after ‘<R_HOME>/etc<R_ARCH>/Makeconf’ and so no longer needs
to include that file itself. Installation of a package with such a
file now uses a site ‘Makevars’ file in the same way as a package with
a ‘src/Makevars.win’ file would.
‘configure’ is now passed crucial variables such as ‘CC’ and ‘CFLAGS’
in its environment, as many packages were not setting them (as
documented in ‘Writing R Extensions’ §1.2).
This has most effect where ‘configure’ is used to compile parts of the package - most often by ‘cmake’ or ‘libtool’ which obfuscate the actual compile commands used.
Also used for ‘configure.win’ and ‘configure.ucrt’ on Windows.
The flag ‘-fno-optimize-sibling-calls’ is no longer forced for
‘gfortran’ 7 and later. It should no longer be needed now using
‘hidden’ character-length arguments when calling BLAS/LAPACK routines
from C/C++ is the default even for packages. (Unless perhaps packages
call Fortran code from C/C++ without using R's headers and without
allowing for these arguments.)
The deprecated S-compatibility macros ‘DOUBLE_*’ in ‘R_ext/Constants.h’
(included by ‘R.h’) have been removed.
The deprecated legacy typedefs of ‘Sint’ and ‘Sfloat’ in header ‘R.h’
are no longer defined, and that header no longer includes header
‘limits.h’ from C nor ‘climits’ from C++.
New macro ‘CAD5R()’ is provided in ‘Rinternals.h’ and used in a few
places in the R sources.
ALTREP now supports ‘VECSXP’ vectors. Contributed by Gabor Csardi in
PR#17620.
The ‘Rcomplex’ definition (in header ‘R_ext/Complex.h’) has been
extended to prevent possible mis-compilation when interfacing with
Fortran (PR#18430). The new definition causes compiler warnings with
static initializers such as ‘{1, 2}’, which can be changed to ‘{.r=1,
.i=2}’.
Using the new definition from C++ depends on compiler extensions supporting C features that have not been incorporated into the C++ standards but are available in ‘g++’ and ‘clang++’: this may result in C++ compiler warnings but these have been worked around for recent versions of common compilers (GCC, Apple/LLVM clang, Intel).
It is intended to change the inclusion of header ‘R_ext/Complex.h’ by other R headers, so C/C++ code files which make use of ‘Rcomplex’ should include that header explicitly.
‘R CMD check’ does more checking of package ‘.Rd’ files, warning about
invalid email addresses and (some) invalid URIs and noting empty
‘\item’ labels in description lists.
‘R CMD check’ now also reports problems when reading package news in md
(file ‘NEWS.md’) and (optionally) plain text (file ‘NEWS’) formats.
‘_R_CHECK_TIMINGS_’ defaults to a value from the environment even for
‘R CMD check --as-cran’; this allows for exceptionally fast or slow
platforms.
It now applies to checking PDF and HTML versions of the manuals, and ‘checking CRAN incoming feasibility’.
‘R CMD check’ can optionally (but included in ‘--as-cran’) check
whether HTML math rendering _via_ KaTeX works for the package ‘.Rd’
files.
Non-interactive debugger invocations can be trapped by setting the
environment variable ‘_R_CHECK_BROWSER_NONINTERACTIVE_’ to a true
value. This is enabled by ‘R CMD check --as-cran’ to detect the use of
leftover ‘browser()’ statements in the package.
The use of ‘sprintf’ and ‘vsprintf’ from C/C++ has been deprecated in
macOS 13 and is a known security risk. ‘R CMD check’ now reports (on
all platforms) if their use is found in compiled code: replace by
‘snprintf’ or ‘vsnprintf’ respectively. [*NB:* whether such calls get
compiled into the package is platform-dependent.]
Where recorded at installation, ‘R CMD check’ reports the C and Fortran
compilers used to build R.
It reports the OS in use (if known, as given by ‘osVersion’) as well as that R was built for.
It notes if a C++ standard was specified which is older than the current default: many packages have used C++11 to mean ‘not C++98’ - as C++11 is the minimum supported since R 4.0.0, that specification can probably be removed.
‘R CMD INSTALL’ reports the compilers (and on macOS, the SDK) used, and
this is copied to the output of ‘R CMD check’.
Where a C++ standard is specified, it is reported.
‘R CMD check’'s ‘checking compilation flags in Makevars’ has been
relaxed to accept the use of flags such as ‘-std=f2008’ in
‘PKG_FFLAGS’.
‘tools::buildVignettes()’ has a new argument ‘skip’, which is used by
‘R CMD check’ to skip (and note) vignettes with unavailable
‘\VignetteDepends’ (PR#18318).
New generic ‘.AtNames()’ added to enable class-specific completions
after ‘@’. The formerly internal function ‘findMatches()’ is now
exported, mainly for use in methods for ‘.DollarNames()’ and
‘.AtNames()’.
‘default.stringsAsFactors()’ is defunct.
Calling ‘as.data.frame.<class>()’ directly (for 12 atomic classes) is
going to be formally deprecated, currently activated by setting the
environment variable ‘_R_CHECK_AS_DATA_FRAME_EXPLICIT_METHOD_’ to
non-empty, which also happens in ‘R CMD check --as-cran’.
Hashed ‘environment’s with sizes less than 5 can now grow. (Reported
to R-devel by Duncan Garmonsway.)
‘as.character(<Rd>, deparse = TRUE)’ failed to re-escape curly braces
in LaTeX-like text. (Reported by Hadley Wickham in PR#18324.)
‘library()’ now passes its ‘lib.loc’ argument when requiring ‘Depends’
packages; reported (with fix) in PR#18331 by Mikael Jagan.
‘R CMD Stangle’: improved message about ‘Output’ files.
‘head(x, n)’ and ‘tail(x, n)’ now signal an error if ‘n’ is not
numeric, instead of incidentally “working” sometimes returning all of
‘x’. Reported and discussed by Colin Fay, in PR#18357.
The ‘"lm"’ method for ‘summary()’ now gives the correct F-statistic
when the model contains an offset. Reported in PR#18008.
‘C()’ and ‘`contrasts<-`()’ now preserve factor level names when given
a function object (as opposed a function name which did preserve
names). Reported in PR#17616.
‘c(a = 1, 2)[[]]’ no longer matches ‘2’ but rather signals a _classed_
error. Reported and analysed by Davis Vaughan in PR#18367, a duplicate
of PR#18004, by Jan Meis et al. For consistency, ‘NULL[[]]’ is also
erroneous now. ‘x[[]] <- v’ gives an error of the same class
‘"MissingSubscriptError"’.
The ‘relist()’ function of ‘utils’ now supports ‘NULL’ elements in the
skeleton (PR#15854).
‘ordered(levels = *)’ (missing ‘x’) now works analogously to ‘factor(,
ordered=TRUE)’; reported (with fix) by Achim Zeileis in PR#18389.
User-defined Rd macro definitions can now span multiple lines, thanks
to a patch from Duncan Murdoch. Previously, the Rd parser silently
ignored everything after the first line.
Plain-text help (‘tools::Rd2txt()’) now preserves an initial blank line
for text following description list items.
‘tools::Rd2HTML()’ and ‘tools::Rd2latex()’ no longer split \arguments
and \value lists at Rd comments.
‘tools::Rd2latex()’ now correctly handles optional text outside \items
of argument lists as well as bracketed text at the beginning of
sections, e.g., \value{[NULL]}.
‘as.character(<POSIXt>)’ now behaves more in line with the methods for
atomic vectors such as numbers, and is no longer influenced by
‘options()’. Ditto for ‘as.character(<Date>)’. The ‘as.character()’
method gets arguments ‘digits’ and ‘OutDec’ with defaults _not_
depending on ‘options()’. Use of ‘as.character(*, format = .)’ now
warns.
Similarly, the ‘as.character.hexmode()’ and ‘*.octmode()’ methods also
behave as ‘good citizen’ methods and back compatibility option ‘keepStr
= TRUE’.
The ‘as.POSIXlt(<POSIXlt>)’ and ‘as.POSIXct(<POSIXct>)’ default methods
now do obey their ‘tz’ argument, also in this case.
‘as.POSIXlt(<Date>)’ now does apply a ‘tz’ (time zone) argument, as
does ‘as.POSIXct()’; partly suggested by Roland Fuß on the R-devel
mailing list.
‘as.Date.POSIXlt(x)’ now also works when the list components are of
unequal length, aka “partially filled” or “ragged”.
‘expand.model.frame()’ looked up variables in the wrong environment
when applied to models fitted without ‘data’. Reported in PR#18414.
‘time()’ now (also) uses the ‘ts.eps = getOption("ts.eps")’ argument
and thus by default rounds values very close to the start (or end) of a
year. Based on a proposal by Andreï V. Kostyrka on R-help.
Printing of a ‘factanal()’ result with just one factor and ‘sort =
TRUE’ now works regularly, fixing PR#17863 by Timothy Bates, thanks to
the ‘R Contributors’ working group.
Printing 0-length objects of class ‘"factor"’, ‘"roman"’, ‘"hexmode"’,
‘"octmode"’, ‘"person"’, ‘"bibentry"’, or ‘"citation"’ now prints
something better, one of which fixes PR#18422, reported by Benjamin
Feakins.
‘Sys.timezone()’ queries ‘timedatectl’ only if ‘systemd’ is loaded;
addressing a report by Jan Gorecki in PR#17421.
The formula method of ‘cor.test()’ had scoping problems when
‘environment(formula)’ was not the calling environment; reported with a
patch proposal by Mao Kobayashi in PR#18439.
‘attach()’ of an environment with active bindings now preserves the
active bindings. Reported by Kevin Ushey in PR#18425.
BLAS detection now works also with system-provided libraries not
available as regular files. This fixes detection of the Accelerate
framework on macOS since Big Sur. Reported by David Novgorodsky.
‘download.file()’ gives a helpful error message in case of an invalid
‘download.file.method’ option, thanks to Colin Fay's report in
PR#18455.
Sporadic crashes of ‘Rterm’ when using completion have been fixed.
‘Rprof()’ is now more reliable. A livelock in thread initialization
with too short sampling interval has been fixed on macOS. A deadlock
in using the C runtime has been fixed on Windows. A potential deadlock
has been prevented on Unix.
Cursor placement in ‘Rgui’ now works even after a fixed-width font is
selected.
Mandatory options (‘options()’) are now set on startup so that saving
and restoring them always works (PR#18372).
Package installation, ‘R CMD INSTALL’ or ‘install.packages(*)’, now
parses each of the ‘<pkg>/R/*.R’ files individually instead of first
concatenating and then ‘parse()’ing the large resulting file. This
allows parser or syntax errors to be diagnosed with correct file names
and line numbers, thanks to Simon Dedman's report and Bill Dunlap's
patch in PR#17859.
This _does_ require syntactically self contained R source files now, fixing another inadvertent bug.
‘predict.lm(<model with offset>)’ now finds the offset in the correct
environment, thanks to André Gillibert's report and patch in PR#18456.
‘getInitial(<formula>)’ now finds the ‘selfStart’ model in the correct
environment. (Reported by Ivan Krylov in PR#18368.)
Fix for possible segfault when using recently-added graphics features,
such as gradients, clipping paths, masks, and groups with
‘pdf(file=NULL)’.
‘class(m) <- class(m)’ no longer changes a matrix ‘m’ by adding a class
_attribute_.
‘packageDate(pkg)’ now only warns once if there is no ‘pkg’.
When ‘ts()’ creates a multivariate time series, ‘"mts"’, it also
inherits from ‘"array"’ now, and ‘is.mts()’ is documented _and_
stricter.
‘Rd2txt()’ now preserves line breaks of \verb Rd content and from
duplicated \cr. The former also fixes the rendering of verbatim output
from Rd \Sexpr in plain-text help.
‘uniroot(f, interval)’ should no longer wrongly converge _outside_ the
interval in some cases where ‘abs(f(x)) == Inf’ for an ‘x’ at the
interval boundary, thanks to posts by Ben Bolker and Serguei Sokol on
R-devel.
Vectorized alpha handling in palette functions such as in ‘gray()’,
‘rainbow()’, or ‘hcl.colors()’ works correctly now, thanks to Achim
Zeileis' report and patch in PR#18476.
Formatting and ‘print()’ing of ‘bibentry’ objects has dropped the
deprecated ‘citation.bibtex.max’ argument, such that the ‘bibtex’
argument's default for ‘print.bibentry()’ depends directly on the
‘citation.bibtex.max’ option, whereas in ‘format.bibentry()’ the option
no longer applies.
Attempting to use a character string naming a foreign function entry
point in a foreign function call in a package will now signal an error
if the packages has called ‘R_forceSymbols’ to specify that symbols
must be used.
An error in ‘table()’ could permanently set ‘options(warn=2)’ promoting
all subsequent warnings to errors.
The ‘sigma()’ function gave misleading results for binary GLMs. A new
method for objects of class ‘"glm"’ returns the square root of the
estimate of the dispersion parameter using the same calculation as
‘summary.glm()’.
‘bs()’ and ‘ns()’ in the (typical) case of automatic knot construction,
when some of the supposedly inner knots coincide with boundary knots,
now moves them inside (with a warning), building on PR#18442 by Ben
Bolker.
‘R CMD’ on Windows now skips the site profile with ‘--no-site-file’ and
‘--vanilla’ even when ‘R_PROFILE’ is set (PR#18512, from Kevin Ushey).
The definition of ‘DL_FUNC’ in ‘R_ext/Rdynload.h’ has been changed to
be fully C-compliant. This means that functions loaded _via_ for
example ‘R_GetCCallable’ need to be cast to an appropriate type if they
have any arguments.
‘.Machine’ has a new element ‘sizeof.time_t’ to identify old systems
with a 32-bit type and hence a limited range of date-times (and limited
support for dates millions of years from present).
(Windows) The default C++ standard had accidentally been left at C++11
when it was changed to C++14 on Unix.
As ‘"POSIXlt"’ objects may be “partially filled” and their list
components meant to be recycled, ‘length()’ now is the length of the
longest component.
‘as.POSIXlt.Date()’ could underflow for dates in the far past (more
than half a million years BCE).
‘as.Date.POSIXlt(x)’ would return ‘"1970-01-01"’ instead of ‘NA’ in R
4.2.2, e.g., for
x <- as.POSIXlt(c("2019-01-30","2001-1-1")) x$mon <- c(0L, NA); as.Date(x)
‘R CMD check’ failed to apply enabled ‘_R_CHECK_SUGGESTS_ONLY_’ to
examples and vignettes (regression in R 4.2.0).
‘R CMD check’ did not re-build vignettes in separate processes by
default (regression in R 4.2.0).
Running examples from HTML documentation now restores previous ‘knitr’
settings and options (PR#18420).
Quartz: fonts are now located using Core Graphics API instead of
deprecated ATS which is no longer supported in the macOS 13 SDK
(PR#18426). This also addresses an issue where the currently used font
in the Quartz device context was not correctly retained.
(Windows) Math symbols in text drawing functions are again rendered
correctly (PR#18440). This fixes a regression in R 4.2.1 caused by a
fix in PR#18382 which uncovered an issue in GraphApp due to which the
symbol charset was not used with TT Symbol font face.
(Windows) Installing a package with a ‘src/Makefile.{win,ucrt}’ file
includes ‘~/.R/Makevars.win64’ in the search for user makevars, as
documented in “R Installation and Administration” and done for packages
with a ‘src/Makevars.{win,ucrt}’ file.
‘format(<POSIXlt_w/_unbalanced_sec>, "....%OS<n>")’ with n > 0 no
longer accidentally uses the unbalanced seconds, thanks to Suharto
Anggono's report (including patch) in PR#18448.
‘solve.default(a, b)’ works around issues with some versions of LAPACK
when ‘a’ contains ‘NA’ or ‘NaN’ values.
When ‘UseMethod()’ cannot dispatch, it no longer segfaults producing
the error message in case of a long ‘class()’, thanks to Joris
Vankerschaver's report (including patch) in PR#18447.
When ‘example(foo, ..)’ produces graphics on an interactive device it
needs to open itself, it now leaves ‘devAskNewPage()’ unchanged even
when it was ‘FALSE’, thus fixing a 14 years old ‘FIXME’.
‘packageDescription()’ again catches errors from encoding conversions.
This also fixes broken ‘packageVersion()’ in C locale on systems where
‘iconv’ does not support transliteration.
‘tools::Rdiff(useDiff = TRUE)’ checks for the presence of an external
‘diff’ command and switches to ‘useDiff = FALSE’ if none is found.
This allows ‘R CMD Rdiff’ to always work.
On Windows, environment variable ‘R_LIBCURL_SSL_REVOKE_BEST_EFFORT’ can
be used to switch to only ‘best-effort’ SSL certificate revocation
checks with the default ‘"libcurl"’ download method. This reduces
security, but may be needed for downloads to work with MITM proxies
(PR#18379).
(macOS) The run-time check for libraries from XQuartz for X11 and
Tcl/Tk no longer uses ‘otool’ from the Apple Developer Tools
(PR#18400).
The LaTeX style for producing the PDF manuals, ‘Rd.sty’, now loads the
standard ‘amsmath’, ‘amsfonts’ and ‘amssymb’ packages for greater
coverage of math commands in the Rd \eqn and \deqn macros. The
\mathscr LaTeX command is also provided (via the ‘mathrsfs’ package, if
available, or the ‘amsfonts’ bundle otherwise), fulfilling the wish of
PR#18398.
(Windows) The default format of ‘readClipboard()’ and
‘writeClipboard()’ has been changed to ‘13’ (‘CF_UNICODETEXT’).
The PDF manuals (if built) can be compacted by the new target ‘make
compact-pdf’ (at the top level or in directory ‘doc/manual’).
There is now ‘configure’ support for LLVM clang 15 on Linux, which
defaults to position-independent (PIE) executables whereas ‘gfortran’
does not.
Many small changes to ease compilation (and suppress warnings) with
LLVM ‘clang’ 15.
‘Rscript -e’ would fail if ‘stdin’ were closed (Reported by Henrik
Bengtsson.)
‘qt(*, log.p=TRUE)’ in outer tails no longer produces ‘NaN’ in its
final steps, thus fixing PR#18360.
‘tools::Rd2latex()’ now escapes hashes and ampersands when writing
URLs, fixing LaTeX errors with such URLs in \tabular.
When ‘isGeneric(f, fdef=*)’ is used with mismatching names, the warning
is better understandable; reported (with fix) in PR#18370 by Gabe
Becker.
‘poly(x, n)’ now works again (and is now documented) when ‘x’ is a
‘"Date"’ or ‘"POSIXct"’ object, or of another class while fulfilling
‘mode(x) == "numeric"’. This also enables ‘poly(x, *, raw=TRUE)’ for
such variables. Reported by Michael Chirico to R-devel.
‘write.table()’, ‘write.csv()’ and ‘write.csv2()’ restore their
numerical precision (internal equivalent of ‘digits = 15’) after an
interrupt (PR#18384).
One can now read also byte ‘FF’ from a clipboard connection (PR#18385).
‘source("")’ and ‘source(character())’ now give more helpful error
messages.
‘R CMD check --as-cran’ set ‘_R_CHECK_TIMINGS_’ too late to have the
intended effect.
‘as.POSIXlt(x)’ now also works with very large dates ‘x’, fixing
PR#18401 reported by Hannes Mühleisen.
Files can now be extracted even from very large zip archives (PR#18390,
thanks to Martin Jakt).
Non-finite objects of class ‘"POSIXlt"’ are now correctly coerced to
classes ‘"Date"’ and ‘"POSIXct"’; following up on the extension to
‘format()’ them correctly.
Added methods for ‘is.finite()’, ‘is.infinite()’ and ‘is.nan()’ for
‘"POSIXlt"’ date-time objects.
Non-ASCII characters are now properly displayed on Windows in windows
created using GraphApp via e.g. ‘winDialogString’ thanks to a
workaround for an at least surprising Windows behavior with UTF-8 as
the system encoding (PR#18382).
Find and replace operations work again in the script editor in ‘Rgui’
on Windows.
Computation of window size based on requested client size in GraphApp
when running in a multi-byte locale on Windows has been fixed
(regression in R 4.2.0 for users of systems where R 4.1 used a
single-byte locale). ‘Rgui’ again respects the number of console rows
and columns given in ‘Rconsole’ file.
‘Rterm’ support for ‘Alt+xxx’ sequences has been fixed to produce the
corresponding character (only) once. This fixes pasting text with tilde
on Italian keyboard (PR#18391).
New function ‘utils::findCRANmirror()’ to find out if a CRAN mirror has
been selected, otherwise fallback to the main site. This behaves in
the same way as ‘tools::CRAN_package_db()’ and is intended for packages
wishing to access CRAN for purposes other than installing packages.
The need for this was shown by a day when the main CRAN website was offline and a dozen or so packages which had its URL hardcoded failed their checks.
The libraries searched for by ‘--with-blas’ (without a value) now
include BLIS (after OpenBLAS but before ATLAS). And on macOS, the
Accelerate framework (after ATLAS). (This is patterned after the
‘AX_BLAS’ macro from the Autoconf Archive.)
The included LAPACK sources have been updated to 3.10.1.
The (full path to) the command ‘tidy’ to be used for HTML validation
can be set by environment variable ‘R_TIDYCMD’.
Setting environment variable ‘_R_CHECK_RD_VALIDATE_RD2HTML_’ to a false
value will override ‘R CMD check --as-cran’ and turn off HTML
validation. This provides a way to circumvent a problematic ‘tidy’.
The 2006 version that ships with macOS is always skipped.
The undocumented legacy declarations of ‘Sint’, ‘Sfloat’, ‘SINT_MAX’
and ‘SINT_MIN’ in header ‘R.h’ are deprecated.
‘fisher.test(d)’ no longer segfaults for “large” ‘d’; fixing PR#18336
by preventing/detecting an integer overflow reliably.
‘tar(., files=*)’ now produces correctly the warning about invalid UID
or GID of files, fixing PR#18344, reported by Martin Morgan.
‘tk_choose.files()’ with ‘multi = FALSE’ misbehaved on paths containing
spaces (PR#18334) (regression introduced in R 4.0.0).
‘sort(x, partial = ind, *)’ now works correctly notably for the
non-default ‘na.last = FALSE’ or ‘TRUE’, fixing PR#18335 reported by
James Edwards.
Environment variable ‘_R_CHECK_XREFS_REPOSITORIES_’ is only used for
checking ‘.Rd’ cross-references in ‘R CMD check’ (as documented) and
not for other uses looking for a CRAN mirror.
The search for a CRAN mirror when checking packages now uses
‘getOption("repos")’ if that specifies a CRAN mirror, even when it does
not also specify all three Bioconductor repositories (as was previously
required).
The HTML code generated by ‘tools::Rd2HTML()’ has been improved to pass
‘tidy’ 5.8.0.
Writing to a clipboard connection works again, fixing a regression in R
4.2.0 (PR#18332). Re-using a closed clipboard connection no longer
issues a spurious warning about an ignored encoding argument.
C function ‘getlocale’ no longer attempts to query an unsupported
category from the OS, even when requested at R level, which may cause
crashes when R 4.2.0 (which uses UCRT) is embedded (reported by Kevin
Ushey).
Accent keys now work in GraphApp Unicode windows, which are used by
‘Rgui’ whenever running in a multibyte locale (so also in UTF-8, hence
fixing a regression in R 4.2.0 for users of systems where R 4.1 used a
single-byte locale).
Completion in ‘Rgui’ now works also with non-ASCII characters.
‘Rgui’ no longer truncates usage information with ‘--help’.
Text injection from external applications via ‘SendInput’ now works in
GraphApp Unicode windows, fixing a regression in R 4.2.0 for ‘Rgui’
users of systems where R 4.1 used a single-byte locale but R 4.2.0 uses
UTF-8.
Performance of ‘txtProgressBar()’ in ‘Rgui’ when running in a
multi-byte locale has been improved (fixing a performance regression in
R 4.2.0 for users of systems where R 4.1 used a single-byte locale).
The script editor in ‘Rgui’ now works also on systems using UTF-8 as
the native encoding. Users of the script editor have to convert their
scripts with non-ASCII characters to UTF-8 before reading them in R
4.2.1 or newer (on recent Windows where UTF-8 is used). This fixes a
regression in R 4.2.0, which prevented some operations with scripts
when they contained non-ASCII characters.
The ‘formula’ method of ‘aggregate()’ now matches the generic in naming
its first argument ‘x’ (resolving PR#18299 by Thomas Soeiro).
This means that calling ‘aggregate()’ with a formula as a named first argument requires name ‘formula’ in earlier versions of R and name ‘x’ now, so portable code should not name the argument (code in many packages did).
Calling ‘&&’ or ‘||’ with either argument of length greater than one
now gives a warning (which it is intended will become an error).
Calling ‘if()’ or ‘while()’ with a condition of length greater than one
gives an error rather than a warning. Consequently, environment
variable ‘_R_CHECK_LENGTH_1_CONDITION_’ no longer has any effect.
Windows users should consult the WINDOWS section below for some
profound changes including
• Support for 32-bit builds has been dropped.
• UTF-8 locales are used where available.
• 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.
‘matrix(x, n, m)’ now warns in more cases where ‘length(x)’ differs
from ‘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 ‘_R_CHECK_MATRIX_DATA_’ to ‘TRUE’: ‘R CMD check --as-cran’ does so unless it is already set.
Function ‘file_test()’ in package ‘utils’ gains tests for symlinks,
readability and writability.
‘capabilities("libxml")’ is now false.
The description of ‘capabilities("http/ftp")’ now reflects that it refers to the default method, no longer the internal one.
‘simplify2array()’ gains an ‘except’ argument for controlling the
exceptions used by ‘sapply()’.
Environment variables ‘R_LIBS_USER’ and ‘R_LIBS_SITE’ are both now set
to the R system default if unset or empty, and can be set to ‘NULL’ to
indicate an empty list of user or site library directories.
The warning for ‘axis()’(-like) calls in cases of relatively small
ranges (typically in log-scale situations) is slightly improved _and_
suppressed from explicit calls to ‘.axisPars()’ as has always been the
intention.
The ‘contrasts’ setter function ‘`contrasts<-`’ gains an explicit
default ‘how.many = NULL’ rather than just using ‘missing(how.many)’.
‘grid.pretty()’ gains a new optional argument ‘n = 5’.
There is a new function ‘.pretty()’ with option ‘bounds’ as a
technical-utility version of ‘pretty()’. It and ‘pretty()’ gain a new
argument ‘f.min’ with a better than back-compatible default.
Function ‘grDevices::axisTicks()’ and related functions such as
‘graphics::axis()’ work better, notably for the log scale; partly
because of the ‘pretty()’ improvements, but also because care is taken
e.g., when ‘ylim’ is finite but ‘diff(ylim)’ is infinite.
‘nclass.FD()’ gains a ‘digits’ option.
The R Mathlib internal C function ‘bd0()’ (called indirectly from a
dozen probability density and distribution functions such as ‘dpois()’,
‘dbinom()’, ‘dgamma()’, ‘pgamma()’ _etc_) has been complemented by a
more sophisticated and (mostly) more accurate C function ‘ebd0()’,
currently called only by internal ‘dpois_raw()’ improving accuracy for
R level ‘dpois()’ and potentially others calling it such as
‘dnbinom()’, ‘dgamma()’ or ‘pgamma()’. (Thanks to Morten Welinder's
PR#15628.)
‘write.ftable()’ gains ‘sep = " "’ argument as suggested by Thomas
Soeiro.
The names of the locale categories supported by R's ‘Sys.getlocale()’
and ‘Sys.setlocale()’ are now provided by variable ‘.LC.categories’ in
the ‘base’ namespace.
The ‘Date’ and ‘POSIXt’ methods for ‘hist()’ and the ‘histogram’ method
for ‘plot()’ now also use the new default ‘col = "lightgray"’ in
consistency with the corresponding change to ‘hist()’'s default for R
4.0.0.
‘hist.default()’ gains new ‘fuzz’ argument, and the histogram ‘plot’
method no longer uses fractional axis ticks when displaying counts
(‘"Frequency"’).
‘mapply()’ and hence ‘Map()’ now also obey the “max-or-0-if-any”
recycling rule, such that, e.g., ‘Map(`+`, 1:3, 1[0])’ is valid now.
‘as.character(<obj>)’ for ‘"hexmode"’ or ‘"octmode"’ objects now
fulfils the important basic rule ‘as.character(x)[j] ===
as.character(x[j])’.
The set utility functions, notably ‘intersect()’ have been tweaked to
be more consistent and symmetric in their two set arguments, also
preserving a common ‘mode’.
‘substr(ch, start,end) <- new’ now e.g., preserves ‘names(ch)’; ditto
for ‘substring()’, thanks to a patch from Brodie Gaslam.
‘plot(<lm>)’ gains a ‘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
‘cook.col’ and ‘cook.lty’ with a different default color and their
legend is nicer by default and customizable via ‘cook.legendChanges’.
Attempting to subset an object that is not subsettable now signals an
error of class ‘notSubsettableError’. The non-subsettable object is
contained in the ‘object’ field of the error condition.
Subscript-out-of-bounds errors are now signaled as errors of class
‘subscriptOutOfBoundsError’.
Stack-overflow errors are now signaled as errors inheriting from class
‘stackOverflowError’. See ‘?stackOverflowError’ for more details.
New partly experimental ‘Sys.setLanguage()’ utility, solving the main
problem of PR#18055.
‘gettext()’ and ‘gettextf()’ get a new option ‘trim = TRUE’ which when
set to false allows translations for strings such as ‘"Execution
halted\n"’ typical for C code.
An experimental implementation of hash tables is now available. See
‘?hashtab’ for more details.
‘identical()’ gains a ‘extptr.as.ref’ argument for requesting that
external pointer objects be compared as reference objects.
‘reorder()’ gets an argument ‘decreasing’ which it passes to ‘sort()’
for level creation; based on the wish and patch by Thomas Soeiro in
PR#18243.
‘as.vector()’ gains a ‘data.frame’ method which returns a simple named
list, also clearing a long standing ‘FIXME’ to enable
‘as.vector(<data.frame>, mode="list")’. This breaks code relying on
‘as.vector(<data.frame>)’ to return the unchanged data frame.
‘legend()’ is now vectorized for arguments ‘cex’, ‘x.intersp’, and
‘text.width’. The latter can now also be specified as a vector (one
element for each column of the legend) or as ‘NA’ for computing a
proper column wise maximum value of ‘strwidth(legend)’. The argument
‘y.intersp’ can be specified as a vector with one entry for each row of
the legend.
‘legend()’ also gains new arguments ‘title.cex’ and ‘title.font’. Thanks to Swetlana Herbrandt.
Deparsing no longer remaps attribute names ‘dim’, ‘dimnames’, ‘levels’,
‘names’ and ‘tsp’ to historical S-compatible names (which ‘structure()’
maps back).
‘sample()’ and ‘sample.int()’ have additional sanity checks on their
‘size’ and ‘n’ arguments.
‘all.equal.numeric()’ gains a sanity check on its ‘tolerance’ argument - calling ‘all.equal(a, b, c)’ for three numeric vectors is a surprisingly common error.
‘mean(na.rm =)’, ‘rank(na.last =)’, ‘barplot(legend.text =)’, ‘boxplot()’, ‘contour(drawlabels =)’, ‘polygon(border =)’ and ‘methods::is(class2 =)’ have more robust sanity checks on their arguments.
‘R CMD Rd2pdf’ (used by ‘R CMD check’) has a more robust sanity check on the format of ‘\alias{}’ commands.
‘psigamma(x, deriv)’ for negative ‘x’ now also works for ‘deriv = 4’
and ‘5’; their underlying C level ‘dpsifn()’ is documented in ‘Writing
R Extensions’.
The HTML help system now uses HTML5 (wish of PR#18149).
‘ks.test()’ now provides exact p-values also with ties and MC p-values
in the two-sample (Smirnov) case. By Torsten Hothorn.
‘ks.test()’ gains a formula interface, with ‘y ~ 1’ for the one-sample
(Kolmogorov) test and ‘y ~ group’ for the two-sample (Smirnov) test.
Contributed by Torsten Hothorn.
The return value from ‘ks.test()’ now has class ‘c("ks.test", "htest")’
- packages using ‘try()’ need to take care to use ‘inherits()’ and not
‘==’ on the class.
New functions ‘psmirnov()’, ‘qsmirnov()’ and ‘rsmirnov()’ in package
‘stats’ implementing the asymptotic and exact distributions of the
two-sample Smirnov statistic.
‘iconv()’ now allows ‘sub = "c99"’ to use C99-style escapes for UTF-8
inputs which cannot be converted to encoding ‘to’.
In a forward pipe ‘|>’ expression it is now possible to use a named
argument with the placeholder ‘_’ in the ‘rhs’ call to specify where
the ‘lhs’ is to be inserted. The placeholder can only appear once on
the ‘rhs’.
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).
‘path.expand()’ and most other uses of tilde expansion now warn if a
path would be too long if expanded. (An exception is ‘file.exists()’,
which silently returns false.)
‘trunc(<Date>, *)’ now supports ‘units = "months"’ or ‘"years"’ for
consistency with the ‘POSIXt’ method, thanks to Dirk Eddelbuettel's
proposal in PR#18099.
‘list2DF()’ now checks that its arguments are of the same length,
rather than use recycling.
The HTML help system has several new features: LaTeX-like math can be
typeset using either KaTeX or MathJax, usage and example code is
highlighted using Prism, and for dynamic help the output of examples
and demos can be shown within the browser if the ‘knitr’ package is
installed. These features can be disabled by setting the environment
variable ‘_R_HELP_ENABLE_ENHANCED_HTML_’ to a false value.
The graphics engine version, ‘R_GE_version’, has been bumped to ‘15’
and so packages that provide graphics devices should be reinstalled.
The ‘grid’ package now allows the user to specify a “vector” of pattern
fills. The ‘fill’ argument to ‘gpar()’ accepts a list of gradients
and/or patterns and the functions ‘linearGradient()’,
‘radialGradient()’, and ‘pattern()’ have a new ‘group’ argument.
Points grobs (data symbols) can now also have a pattern fill.
The ‘grobCoords()’ function now returns a more informative and complex result.
The ‘grid’ package has new functions for drawing isolated groups:
‘grid.group()’, ‘grid.define()’, and ‘grid.use()’. These functions add
compositing operators and affine transformations to R's graphics
capabilities.
The ‘grid’ package also has new functions for stroking and filling paths: ‘grid.stroke()’, ‘grid.fill()’, and ‘grid.fillStroke()’.
A new function ‘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 ‘"winding"’ and ‘"evenodd"’. A new function ‘as.mask()’ allows the user to specify the type of a mask; available options are ‘"alpha"’ and ‘"luminance"’.
These new features are only supported so far (at most) on the Cairo-based graphics devices and on the ‘pdf()’ device.
‘dev.capabilities()’ reports on device support for the new features.
‘par()’ now warns about unnamed non-character arguments to prevent
misuse such as ‘{usr <- par("usr"); par(usr)}’.
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.
The default personal library on Windows, folder ‘R\win-library\x.y’
where ‘x.y’ stands for R release ‘x.y.z’, is now a subdirectory of
Local Application Data directory (usually a hidden directory
‘C:\Users\username\AppData\Local’). Use ‘shell.exec(.libPaths()[1])’
from R to open the personal library in Explorer when it is first in the
list (PR#17842).
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.
Make files and installer scripts for Windows have been tailored to
‘Rtools42’, the newly recommended 64-bit ‘gcc’ 10.3 MinGW-W64 UCRT
toolchain.
‘Rtools42’ by default uses the Windows security features ASLR and DEP;
hence CRAN builds of R and packages also do.
R now supports files ‘Makevars.ucrt’, ‘Makefile.ucrt’, ‘configure.ucrt’
and ‘cleanup.ucrt’ in packages, which are used in preference to the
‘.win’ variants. This allows keeping the ‘.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.
‘R.version’ gains a new field ‘crt’ (only on Windows) to denote the C
runtime. The value is ‘"ucrt"’.
On Windows, ‘download.file(method = "auto")’ and ‘url(method =
"default")’ now follow Unix in using ‘"libcurl"’ for all except
‘file://’ URIs.
‘Rtools42’ includes an unpatched Msys2 build of GNU ‘tar’. Paths
including drive letters can be made to work by adding ‘--force-local’
to environment variable ‘TAR_OPTIONS’. (‘Rtools40’ and earlier
included a patched version which defaulted to this option.)
Installer builds of R automatically find the ‘Rtools42’ software
collection as well as the compiler toolchain. No ‘PATH’ setting is
required from the user.
The default installation directory of R for a user-only installation
has been changed to the User Program Files directory (usually a hidden
directory ‘C:\Users\username\AppData\Local\Programs’) to follow Windows
conventions. Use ‘shell.exec(R.home())’ from R to open the R
installation directory in Explorer (PR#17842).
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.
‘libcurl’ is now required for building from source.
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 ‘encoding’ argument
is ignored.
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.
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.
‘memory.limit()’ and ‘memory.size()’ are now stubs on Windows (as on
Unix-alikes).
Applications embedding R on Windows can now use additional callbacks,
which have so far only been available only on Unix (PR#18286).
Facilities for accessing ‘ftp://’ sites are no longer tested (except
_pro tem_ for ‘curlGetHeaders()’) as modern browsers have removed
support.
R can now be built with ‘DEFS = -DSTRICT_R_HEADERS’ .
‘R CMD INSTALL’ no longer tangles vignettes. This completes an ‘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 ‘R CMD build’ to have the tangled
R code of vignettes shipped with the tarball.
‘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 ‘Writing R Extensions’
§6.6.1. (This has been supported since R 3.6.2.)
Package installation speed for packages installed with ‘keep.source’
has been improved. This resolve the issue reported by Ofek Shilon in
PR#18236.
‘R CMD check’ can optionally report files/directories left behind in
home, ‘/tmp’ (even though ‘TMPDIR’ is set) and other directories. See
the “R Internals” manual for details.
‘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.
‘_R_CHECK_DEPENDS_ONLY_’ can be applied selectively to examples, tests
and/or vignettes in ‘R CMD check’: see the “R Internals” manual.
‘_R_CHECK_SRC_MINUS_W_IMPLICIT_’ now defaults to true: recent versions
of Apple ‘clang’ on macOS have made implicit function declarations in C
into a compilation error.
‘R CMD check --as-cran’ makes use of the environment variable
‘AUTORECONF’. See the “R Internals” manual §8 for further details.
‘R CMD check --use-valgrind’ also uses ‘valgrind’ when re-building
vignettes as some non-Sweave vignettes unhelpfully comment out all
their code when ‘R CMD check’ runs vignettes.
Errors in re-building vignettes (unless there are LaTeX errors) are
reported by ‘R CMD check’ as ‘ERROR’ rather than ‘WARNING’ when running
vignettes has been skipped (as it frequently is in CRAN checks and by
‘--as-cran’).
‘R CMD Rd2pdf’ gains a ‘--quiet’ option that is used by ‘R CMD build’
when building the PDF package manual.
‘R CMD Rd2pdf’ now always runs LaTeX in batch mode, consistent with
Texinfo >= 6.7. The ‘--batch’ option is ignored.
‘R CMD build’ and ‘R CMD check’ now include the Rd file name and line
numbers in the error message of an \Sexpr evaluation failure.
For packages using the \doi Rd macro (now an install-time \Sexpr) but
no other dynamic Rd content, ‘R CMD build’ now produces a smaller
tarball and is considerably faster - skipping temporary package
installation.
‘R CMD check’ can optionally (but included in ‘--as-cran’) validate the
HTML produced from the packages ‘.Rd’ files. See
<https://blog.r-project.org/2022/04/08/enhancements-to-html-documentation/>:
this needs a fairly recent version of HTML Tidy to be available.
The non-API header ‘R_ext/R-ftp-http.h’ is no longer provided, as the
entry points it covered are now all defunct.
A number of non-API declarations and macro definitions have been moved
from the installed header ‘Rinternals.h’ to the internal header
‘Defn.h’. Packages that only use entry points and definitions
documented to be part of the API as specified in ‘Writing R Extensions’
§6 should not be affected.
The macro ‘USE_RINTERNALS’ no longer has any effect when compiling
package code. Packages which also use ‘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.
The deprecated legacy S-compatibility macros ‘PROBLEM’, ‘MESSAGE’,
‘ERROR’, ‘WARN’, ‘WARNING’, ‘RECOVER’, ... are no longer defined in
‘R_ext/RS.h’ (included by ‘R.h’). Replace these by calls to ‘Rf_error’
and ‘Rf_warning’ (defined in header ‘R_ext/Error.h’ included by ‘R.h’).
Header ‘R_ext/RS.h’ no longer includes ‘R_ext/Error.h’.
Header ‘R_ext/Constants.h’ (included by ‘R.h’) when included from C++
now includes the C++ header ‘cfloat’ rather than the C header ‘float.h’
(now possible as C++11 is required).
The legacy S-compatibility macros ‘DOUBLE_*’ in ‘R_ext/Constants.h’
(included by ‘R.h’) are deprecated.
The deprecated S-compatibility macros ‘SINGLE_*’ in ‘R_ext/Constants.h’
(included by ‘R.h’) have been removed.
‘R_Calloc’, ‘R_Free’ and ‘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 ‘STRICT_R_HEADERS’ is
defined.
‘rmultinom’ has been documented in ‘Writing R Extensions’ §6 so is now
part of the R API.
Similarly, ‘Rtanpi’, called from R level ‘tanpi()’ is now part of the R
API.
The long-deprecated, undocumented and non-API entry point ‘call_R’ is
no longer declared in ‘R_ext/RS.h’ (included by ‘R.h’).
The header ‘S.h’ which has been unsupported since Jan 2016 has been
removed. Use ‘R.h’ instead.
The (non-default and deprecated) ‘method = "internal"’ for
‘download.file()’ and ‘url()’ no longer supports ‘http://’ nor ‘ftp://’
URIs. (It is used only for ‘file://’ URIs.)
On Windows, ‘download.file(method = "wininet")’ no longer supports ‘ftp://’ URIs. (It is no longer the default method, which is ‘"libcurl"’ and does.)
On Windows, the deprecated ‘method = "wininet"’ now gives a warning for ‘http://’ and ‘https://’ URIs for both ‘download.file()’ and ‘url()’. (It is no longer the default method.)
On Windows, the command-line option ‘--max-mem-size’ and environment
variable ‘R_MAX_MEM_SIZE’ are defunct. The memory allocation limit was
important for 32-bit builds, but these are no longer supported.
‘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.
‘unix.time()’ is defunct now; it had been deprecated since R 3.4.0.
Setting ‘digits = 0’ in ‘format()’, ‘print.default()’ (and hence
typically ‘print()’) or ‘options()’ is again invalid. Its behaviour
was platform-dependent, and it is unclear what “zero significant
digits” should mean (PR#18098).
Messages from C code in the ‘cairo’ section of package ‘grDevices’ are
now also offered for translation, thanks to Michael Chirico's PR#18123.
‘mean(x)’ with finite ‘x’ now is finite also without "long.double"
capability.
‘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.)
‘density(x, weights = w, na.rm = TRUE)’ when ‘anyNA(x)’ is true, now
removes weights “in parallel” to ‘x’, fixing PR#18151, reported by
Matthias Gondan. Additionally, it gets a ‘subdensity’ option.
Conversion of \Sexpr[]{<expR>} to LaTeX or HTML no longer produces long
blocks of empty lines when ‘<expR>’ itself contains several lines all
producing empty output. Thanks to a report and patch by Ivan Krylov
posted to R-devel.
‘R CMD build’ no longer fails if a package vignette uses child
documents and ‘inst/doc’ exists. (Thanks to Sebastian Meyer's
PR#18156.)
When an R documentation (‘help’ source) file ‘man/foo.Rd’ in a package
has \donttest{..} examples with a syntax error, it is now signalled as
ERROR and with correct line numbers relating to the ‘*-Ex.R’ file,
thanks to Duncan Murdoch and Sebastian Meyer's reports and patch
proposals in PR#17501.
Improved determination of the correct translation domain in non-base
packages, addressing the combination of PR#18092 and PR#17998 (‘#c6’)
with reports and _augmented_ patch #2904 by Suharto Anggono.
Note that ‘"R-base"’ is no longer the default domain e.g., for top-level calls to ‘gettext()’; rather translation needs explicit ‘domain = *’ specification in such cases.
‘identical(attrib.as.set=FALSE)’ now works correctly with data frames
with default row names (Thanks to Charlie Gao's PR#18179).
‘txtProgressBar()’ now enforces a non-zero width for argument ‘char’,
without which no progress can be visible.
‘dimnames(table(d))’ is more consistent in the case where ‘d’ is a list
with a single component, thanks to Thomas Soeiro's report to R-devel.
Further, ‘table(d1, d2)’ now gives an error when ‘d1’ and ‘d2’ are data frames as suggested by Thomas in PR#18224.
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.
The deparser now wraps sub-expressions such as ‘if(A) .. ’ with
parentheses when needed; thanks to Duncan Murdoch's PR#18232 and Lionel
Henry's patches there.
‘remove.packages()’ no longer tries to uninstall ‘Priority: base’
packages, thanks to a report and suggestions by Colin Fay in PR#18227.
‘win.metafile()’ now has ‘xpinch’ and ‘ypinch’ arguments so that the
user can override Windows' (potentially wrong) guess at device
dimensions.
‘x[i]’ and ‘x[[i]]’ for non-integer ‘i’ should now behave in all cases
as always documented: the index used is equivalent to ‘as.integer(i)’
unless that would overflow where ‘trunc(i)’ is used instead; thanks to
Suharto Anggono's report and patch proposals in PR#17977.
‘asOneSidedFormula()’ now associates the resulting formula with the
global environment rather than the evaluation environment created for
the call.
‘<bibentry>$name’ now matches the field name case-insensitively,
consistent with ‘bibentry()’ creation and the replacement method.
‘cbind()’ failed to detect some length mismatches with a mixture of
time-series and non-time-series inputs.
The default LaTeX style file ‘Sweave.sty’ used by the ‘RweaveLatex’
driver no longer loads the obsolete ‘ae’ package; thanks to a report by
Thomas Soeiro in PR#18271. Furthermore, it now skips
‘\usepackage[T1]{fontenc}’ for engines other than pdfTeX (if detected)
or if the new ‘[nofontenc]’ option is used.
‘smooth.spline()’ now stores its logical ‘cv’ argument more safely,
fixing a rare bug when printing, and also stores ‘n’.
‘smooth.spline(x,y,*)’ now computes the ‘cv.crit’ statistic correctly,
also when ‘is.unsorted(x)’, fixing PR#18294.
The ‘data.frame’ method of ‘rbind()’ now warns when binding
not-wholly-recycling vectors, by analogy to the default method (for
matrices).
‘setAs()’ finds the correct class for name ‘to’ when multiple packages
define a class with that name. Thanks to Gabor Csardi for the report.
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.
‘match.arg("", c("", "a", "B"))’ gives a better error message, in part
from PR#17959, thanks to Elin Waring.
‘R CMD Sweave --clean’ no longer removes pre-existing files or
subdirectories (PR#18242).
The ‘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.
Deparsing constructs such as ‘quote(1 + `!`(2) + 3)’ works again as
before R 3.5.0, thanks to the report and patch in PR#18284 by Suharto
Anggono.
‘as.list(f)’ for a ‘factor’ ‘f’ now keeps ‘names(f)’, fixing PR#18309.
‘qbeta(.001, .9, .009)’ and analogous ‘qf()’ calls now return a correct
value instead of ‘NaN’ or wrongly ‘1’, all with a warning; thanks to
the report by Ludger Goeminne in PR#18302.
‘plot.lm()’ failed to produce the plot of residuals vs. factor levels
(i.e., ‘which=5’ when leverages are constant) for models with character
predictors (PR#17840).
‘interaction.plot(..., xtick = TRUE)’ misplaced the x-axis line
(PR#18305).
Not strictly fixing a bug, ‘format()’ing and ‘print()’ing of non-finite
‘Date’ and ‘POSIXt’ values ‘NaN’ and +/-‘Inf’ no longer show as ‘NA’
but the respective string, e.g., ‘Inf’, for consistency with numeric
vector's behaviour, fulfilling the wish of PR#18308.
‘R CMD check’ no longer runs test scripts generated from corresponding
‘.Rin’ files twice and now signals an ERROR if processing an ‘.Rin’
script fails.
‘tools::Rd2txt()’ used for plain-text help pages now renders \hrefs (if
‘tools::Rd2txt_options(showURLs = TRUE)’) and \urls with
percent-encoding and standards-compliant delimiting style (angle
brackets and no ‘URL: ’ prefix). \email is now rendered with a
‘mailto:’ prefix.
The default version of Bioconductor has been changed to 3.14. (This is
used by ‘setRepositories’ and the menus in GUIs.)
‘R CMD check --as-cran’ has a workaround for a bug in versions of
‘file’ up to at least 5.41 which mis-identify DBF files last changed in
2022 as executables.
The legacy S-compatibility macros ‘SINGLE_*’ in ‘R_ext/Constants.h’
(included by ‘R.h’) are deprecated and will be removed in R 4.2.0.
Initialization of self-starting ‘nls()’ models with initialization
functions following the pre-R-4.1.0 API (without the ‘...’ argument)
works again for now, with a deprecation warning.
Fixed quoting of ‘~autodetect~’ in Java setting defaults to avoid
inadvertent user lookup due to leading ‘~’, reported in PR#18231 by
Harold Gutch.
‘substr(., start, stop) <- v’ now treats _negative_ ‘stop’ values
correctly. Reported with a patch in PR#18228 by Brodie Gaslam.
Subscripting an array ‘x’ without dimnames by a ‘length(dim(x))’-column
character matrix gave "random" non-sense, now an error; reported in
PR#18244 by Mikael Jagan.
‘...names()’ now matches ‘names(list(...))’ closely, fixing PR#18247.
‘all.equal(*, scale = s)’ now works as intended when ‘length(s) > 1’,
partly thanks to Michael Chirico's PR#18272.
‘print(x)’ for long vectors ‘x’ now also works for named atomic vectors
or lists and prints the correct number when reaching the
‘getOption("max.print")’ limit; partly thanks to a report and proposal
by Hugh Parsonage to the R-devel list.
‘all.equal(<selfStart>, *)’ no longer signals a deprecation warning.
‘reformulate(*, response=r)’ gives a helpful error message now when
‘length(r) > 1’, thanks to Bill Dunlap's PR#18281.
Modifying ‘globalCallingHandlers’ inside ‘withCallingHandlers()’ now
works or fails correctly, thanks to Henrik Bengtsson's PR#18257.
‘hist(<Date>, breaks = "days")’ and ‘hist(<POSIXt>, breaks = "secs")’
no longer fail for inputs of length 1.
‘qbeta(.001, .9, .009)’ and similar cases now converge correctly thanks
to Ben Bolker's report in PR#17746.
‘window(x, start, end)’ no longer wrongly signals “'start' cannot be
after 'end'”, fixing PR#17527 and PR#18291.
‘data()’ now checks that its (rarely used) ‘list’ argument is a
character vector - a couple of packages passed other types and gave
incorrect results.
‘which()’ now checks its ‘arr.ind’ argument is TRUE rather coercing to
logical and taking the first element - which gave incorrect results in
package code.
‘model.weights()’ and ‘model.offset()’ more carefully extract their
model components, thanks to Ben Bolker and Tim Taylor's R-devel post.
‘list.files(recursive = TRUE)’ now shows all broken symlinks
(previously, some of them may have been omitted, PR#18296).
The workaround in headers ‘R.h’ and ‘Rmath.h’ (‘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 ‘log()’
(which should have been ‘std::log()’) with an ‘int’ argument are
reported on Solaris.
The undocumented limit of 4095 bytes on messages from the
S-compatibility macros ‘PROBLEM’ and ‘MESSAGE’ is now documented and
longer messages will be silently truncated rather than potentially
causing segfaults.
If the ‘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.
The legacy S-compatibility macros ‘PROBLEM’, ‘MESSAGE’, ‘ERROR’,
‘WARN’, ‘WARNING’, ‘RECOVER’, ... are deprecated and will be hidden in
R 4.2.0. R's native interface of ‘Rf_error’ and ‘Rf_warning’ has long
been preferred.
‘.mapply(F, dots, .)’ no longer segfaults when ‘dots’ is not a ‘list’
and uses ‘match.fun(F)’ as always documented; reported by Andrew
Simmons in PR#18164.
‘hist(<Date>, ...)’ and ‘hist(<POSIXt>, ...)’ no longer pass arguments
for ‘rect()’ (such as ‘col’ and ‘density’) to ‘axis()’. (Thanks to
Sebastian Meyer's PR#18171.)
\Sexpr{ch} now preserves ‘Encoding(ch)’. (Thanks to report and patch by
Jeroen Ooms in PR#18152.)
Setting the RNG to ‘"Marsaglia-Multicarry"’ e.g., by ‘RNGkind()’, now
warns in more places, thanks to André Gillibert's report and patch in
PR#18168.
‘gray(numeric(), alpha=1/2)’ no longer segfaults, fixing PR#18183,
reported by Till Krenz.
Fixed ‘dnbinom(x, size=<very_small>, .., log=TRUE)’ regression,
reported by Martin Morgan.
‘as.Date.POSIXlt(x)’ now keeps ‘names(x)’, thanks to Davis Vaughan's
report and patch in PR#18188.
‘model.response()’ now strips an ‘"AsIs"’ class typically, thanks to
Duncan Murdoch's report and other discussants in PR#18190.
‘try()’ is considerably faster in case of an error and long call, as
e.g., from some ‘do.call()’. Thanks to Alexander Kaever's suggestion
posted to R-devel.
‘qqline(y = <object>)’ such as ‘y=I(.)’, now works, see also PR#18190.
Non-integer ‘mgp’ ‘par()’ settings are now handled correctly in
‘axis()’ and ‘mtext()’, thanks to Mikael Jagan and Duncan Murdoch's
report and suggestion in PR#18194.
‘formatC(x)’ returns length zero ‘character()’ now, rather than ‘""’
when ‘x’ is of length zero, as documented, thanks to Davis Vaughan's
post to R-devel.
‘removeSource(fn)’ now retains (other) ‘attributes(fn)’.
‘require(<pkg>, quietly = TRUE)’ is quieter and in particular does not
warn if the package is not found.
Use of ‘ftp://’ URIs should be regarded as deprecated, with on-going
support confined to ‘method = "libcurl"’ and not routinely tested.
(Nowadays no major browser supports them.)
The non-default ‘method = "internal"’ is deprecated for ‘http://’ and
‘ftp://’ URIs for both ‘download.file’ and ‘url’.
On Windows, ‘method = "wininet"’ is deprecated for ‘http://’,
‘https://’ and ‘ftp://’ URIs for both ‘download.file’ and ‘url’. (A
warning is only given for ‘ftp://’.)
For ‘ftp://’ URIs the default method is now ‘"libcurl"’ if available (which it is on CRAN builds).
‘method = "wininet"’ remains the default for ‘http://’ and ‘https://’ URIs but if ‘libcurl’ is available, using ‘method = "libcurl"’ is preferred.
‘make check’ now works also without a LaTeX installation. (Thanks to
Sebastian Meyer's PR#18103.)
‘make check-devel’ works again in an R build configured with
‘--without-recommended-packages’.
‘qnbinom(p, size, mu)’ for large ‘size/mu’ is correct now in a range of
cases (PR#18095); similarly for the ‘(size, prob)’ parametrization of
the negative binomial. Also ‘qpois()’ and ‘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.
‘gap.axis’ is now part of the ‘axis()’ arguments which are passed from
‘bxp()’, and hence ‘boxplot()’. (Thanks to Martin Smith's report and
suggestions in PR#18109.)
‘.First’ and ‘.Last’ can again be set from the site profile.
‘seq.int(from, to, *)’ and ‘seq.default(..)’ now work better in large
range cases where ‘from-to’ is infinite where the two boundaries are
finite.
‘all.equal(x,y)’ now returns ‘TRUE’ correctly also when several entries
of ‘abs(x)’ and ‘abs(y)’ are close to ‘.Machine$double.xmax’, the
largest finite ‘numeric’.
‘model.frame()’ now clears the object bit when removing the ‘class’
attribute of a value via ‘na.action’ (PR#18100).
‘charClass()’ now works with multi-character strings on Windows
(PR#18104, fixed by Bill Dunlap).
‘encodeString()’ on Solaris now works again in Latin-1 encoding on
characters represented differently in UTF-8. Support for surrogate
pairs on Solaris has been improved.
‘file.show()’ on Windows now works with non-ASCII path names
representable in the current native encoding (PR#18132).
Embedded R on Windows can now find R home directory via the registry
even when installed only for the current user (PR#18135).
‘pretty(x)’ with finite ‘x’ now returns finite values also in the case
where the extreme ‘x’ values are close in size to the maximal
representable number ‘.Machine$double.xmax’.
Also, it's been tweaked for very small ranges and when a boundary is close (or equal) to zero; e.g., ‘pretty(c(0,1e-317))’ no longer has negative numbers, currently still warning about a very small range, and ‘pretty(2^-(1024 - 2^-1/(c(24,10))))’ is more accurate.
The error message for not finding vignette files when weaving has
correct file sizes now. (Thanks to Sebastian Meyer's PR#18154.)
‘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.)
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.
Data set ‘esoph’ in package ‘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.)
‘www.omegahat.net’ is no longer one of the repositories known by
default to ‘setRepositories()’. (Nowadays it only provides source
packages and is often unavailable.)
Function ‘package_dependencies()’ (in package ‘tools’) can now use
different dependency types for direct and recursive dependencies.
The checking of the size of tarball in ‘R CMD check --as-cran <pkg>’
may be tweaked via the new environment variable
‘_R_CHECK_CRAN_INCOMING_TARBALL_THRESHOLD_’, as suggested in PR#17777
by Jan Gorecki.
Using ‘c()’ to combine a factor with other factors now gives a factor,
an ordered factor when combining ordered factors with identical levels.
‘apply()’ gains a ‘simplify’ argument to allow disabling of
simplification of results.
The ‘format()’ method for class ‘"ftable"’ gets a new option ‘justify’.
(Suggested by Thomas Soeiro.)
New ‘...names()’ utility. (Proposed by Neal Fultz in PR#17705.)
‘type.convert()’ now warns when its ‘as.is’ argument is not specified,
as the help file always said it _should_. In that case, the default is
changed to ‘TRUE’ in line with its change in ‘read.table()’ (related to
‘stringsAsFactors’) in R 4.0.0.
When printing list arrays, classed objects are now shown _via_ their
‘format()’ value if this is a short enough character string, or by
giving the first elements of their class vector and their length.
‘capabilities()’ gets new entry ‘"Rprof"’ which is ‘TRUE’ when R has
been configured with the equivalent of ‘--enable-R-profiling’ (as it is
by default). (Related to Michael Orlitzky's report PR#17836.)
‘str(xS4)’ now also shows extraneous attributes of an S4 object ‘xS4’.
Rudimentary support for vi-style tags in ‘rtags()’ and ‘R CMD rtags’
has been added. (Based on a patch from Neal Fultz in PR#17214.)
‘checkRdContents()’ is now exported from ‘tools’; it and also
‘checkDocFiles()’ have a new option ‘chkInternal’ allowing to check Rd
files marked with keyword ‘"internal"’ as well. The latter can be
activated for ‘R CMD check’ via environment variable
‘_R_CHECK_RD_INTERNAL_TOO_’.
New functions ‘numToBits()’ and ‘numToInts()’ extend the ‘raw’
conversion utilities to (double precision) ‘numeric’.
Functions ‘URLencode()’ and ‘URLdecode()’ in package ‘utils’ now work
on vectors of URIs. (Based on patch from Bob Rudis submitted with
PR#17873.)
‘path.expand()’ can expand ‘~user’ on most Unix-alikes even when
‘readline’ is not in use. It tries harder to expand ‘~’, for example
should environment variable ‘HOME’ be unset.
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
‘_R_HELP_LINKS_TO_TOPICS_’ to a false value.
‘c()’ now removes ‘NULL’ arguments before dispatching to methods, thus
simplifying the implementation of ‘c()’ methods, _but_ for back
compatibility keeps ‘NULL’ when it is the first argument. (From a
report and patch proposal by Lionel Henry in PR#17900.)
‘Vectorize()’'s result function's environment no longer keeps unneeded
objects.
Function ‘...elt()’ now propagates visibility consistently with ‘..n’.
(Thanks to Lionel Henry's PR#17905.)
‘capture.output()’ no longer uses non-standard evaluation to evaluate
its arguments. This makes evaluation of functions like
‘parent.frame()’ more consistent. (Thanks to Lionel Henry's PR#17907.)
‘packBits(bits, type="double")’ now works as inverse of ‘numToBits()’.
(Thanks to Bill Dunlap's proposal in PR#17914.)
‘curlGetHeaders()’ has two new arguments, ‘timeout’ to specify the
timeout for that call (overriding ‘getOption("timeout")’) and ‘TLS’ to
specify the minimum TLS protocol version to be used for ‘https://’ URIs
(_inter alia_ providing a means to check for sites using deprecated TLS
versions 1.0 and 1.1).
For ‘nls()’, an optional constant ‘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. ‘nls(*, trace=TRUE)’ now also shows the convergence criterion.
Numeric differentiation _via_ ‘numericDeriv()’ gets new optional
arguments ‘eps’ and ‘central’, the latter for taking central divided
differences. The latter can be activated for ‘nls()’ via
‘nls.control(nDcentral = TRUE)’.
‘nls()’ now passes the ‘trace’ and ‘control’ arguments to
‘getInitial()’, notably for all self-starting models, so these can also
be fit in zero-noise situations via a ‘scaleOffset’. For this reason,
the ‘initial’ function of a ‘selfStart’ model must now have ‘...’ in
its argument list.
‘bquote(splice = TRUE)’ can now splice expression vectors with
attributes: this makes it possible to splice the result of
‘parse(keep.source = TRUE)’. (Report and patch provided by Lionel
Henry in PR#17869.)
‘textConnection()’ gets an optional ‘name’ argument.
‘get()’, ‘exists()’, and ‘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.)
R now provides a shorthand notation for creating functions, e.g. ‘\(x)
x + 1’ is parsed as ‘function(x) x + 1’.
R now provides a simple native forward pipe syntax ‘|>’. 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.
‘all.equal(f, g)’ for ‘function’s now by default also compares their
‘environment(.)’s, notably via new ‘all.equal’ method for class
‘function’. Comparison of ‘nls()’ fits, e.g., may now need
‘all.equal(m1, m2, check.environment = FALSE)’.
‘.libPaths()’ gets a new option ‘include.site’, allowing to _not_
include the site library. (Thanks to Dario Strbenac's suggestion and
Gabe Becker's PR#18016.)
Lithuanian translations are now available. (Thanks to Rimantas
Žakauskas.)
‘names()’ now works for ‘DOTSXP’ objects. On the other hand, in
‘R-lang’, the R language manual, we now warn against relying on the
structure or even existence of such dot-dot-dot objects.
‘all.equal()’ no longer gives an error on ‘DOTSXP’ objects.
‘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 ‘X11()’.
There is optional support for tracing the progress of ‘loadNamespace()’
- see its help.
(Not Windows.) ‘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 ‘Sys.getlocale("LC_CTYPE")’).
New function ‘gregexec()’ which generalizes ‘regexec()’ to find _all_
disjoint matches and all substrings corresponding to parenthesized
subexpressions of the given regular expression. (Contributed by Brodie
Gaslam.)
New function ‘charClass()’ in package ‘utils’ to query the
wide-character classification functions in use (such as ‘iswprint’).
The names of ‘quantile()’'s result no longer depend on the global
‘getOption("digits")’, but ‘quantile()’ gets a new optional argument
‘digits = 7’ instead.
‘grep()’, ‘sub()’, ‘regexp’ and variants work considerably faster for
long factors with few levels. (Thanks to Michael Chirico's PR#18063.)
Provide grouping of ‘x11()’ graphics windows within a window manager
such as ‘Gnome’ or ‘Unity’; thanks to a patch by Ivan Krylov posted to
R-devel.
The ‘split()’ method for class ‘data.frame’ now allows the ‘f’ argument
to be specified as a formula.
‘sprintf’ now warns on arguments unused by the format string.
New palettes ‘"Rocket"’ and ‘"Mako"’ for ‘hcl.colors()’ (approximating
palettes of the same name from the ‘viridisLite’ package).
Contributed by Achim Zeileis.
The base environment and its namespace are now locked (so one can no
longer add bindings to these or remove from these).
‘Rterm’ handling of multi-byte characters has been improved, allowing
use of such characters when supported by the current locale.
‘Rterm’ now accepts ‘ALT+ +xxxxxxxx’ sequences to enter Unicode
characters as hex digits.
Environment variable ‘LC_ALL’ on Windows now takes precedence over
‘LC_CTYPE’ and variables for other supported categories, matching the
POSIX behaviour.
‘duplicated()’ and ‘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.
The graphics engine version, ‘R_GE_version’, has been bumped to ‘14’
and so packages that provide graphics devices should be reinstalled.
Graphics devices should now specify ‘deviceVersion’ to indicate what
version of the graphics engine they support.
Graphics devices can now specify ‘deviceClip’. If ‘TRUE’, the graphics
engine will never perform any clipping of output itself.
The clipping that the graphics engine does perform (for both ‘canClip = TRUE’ and ‘canClip = FALSE’) has been improved to avoid producing unnecessary artifacts in clipped output.
The ‘grid’ package now allows ‘gpar(fill)’ to be a ‘linearGradient()’,
a ‘radialGradient()’, or a ‘pattern()’. The ‘viewport(clip)’ can now
also be a grob, which defines a clipping path, and there is a new
‘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 ‘pdf()’ device.
(Not Windows.) A warning is given when a Cairo-based type is specified
for a ‘png()’, ‘jpeg()’, ‘tiff()’ or ‘bmp()’ device but Cairo is
unsupported (so ‘type = "Xlib"’ is tried instead).
‘grSoftVersion()’ now reports the versions of FreeType and FontConfig
if they are used directly (not _via_ Pango), as is most commonly done
on macOS.
The _standalone_ ‘libRmath’ math library and R's C API now provide
‘log1pexp()’ again as documented, and gain ‘log1mexp()’.
‘configure’ checks for a program ‘pkgconf’ if program ‘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
‘PKG_CONFIG’, for example in file ‘config.site’.
C99 function ‘iswblank’ is required - it was last seen missing ca 2003
so the workaround has been removed.
There are new ‘configure’ options ‘--with-internal-iswxxxxx’,
‘--with-internal-towlower’ and ‘--with-internal-wcwidth’ which allows
the system functions for wide-character classification, case-switching
and width (‘wcwidth’ and ‘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.
Cairo installations without X11 are more likely to be detected by
‘configure’, when the file-based Cairo graphics devices will be
available but not ‘X11(type = "cairo")’.
There is a new ‘configure’ 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.
Cairo-based graphics devices on platforms without Pango but with
FreeType/FontConfig will make use of the latter for font selection.
Configuring with flag ‘--enable-lto=R’ now also uses LTO when
installing the recommended packages.
‘R CMD INSTALL’ and ‘R CMD SHLIB’ have a new flag ‘--use-LTO’ to use
LTO when compiling code, for use with R configured with
‘--enable-lto=R’. For R configured with ‘--enable-lto’, they have the
new flag ‘--no-use-LTO’.
Packages can opt in or out of LTO compilation _via_ a ‘UseLTO’ field in the ‘DESCRIPTION’ file. (As usual this can be overridden by the command-line flags.)
for GCC >= 8, ‘FC_LEN_T’ is defined in ‘config.h’ and hence character
lengths are passed from C to Fortran in _inter alia_ BLAS and LAPACK
calls.
There is a new text file ‘src/gnuwin32/README.compilation’, which
outlines how C/Fortran code compilation is organized and documents new
features:
• 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.
• 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.
• There is experimental support for cross-building R packages with C, C++ and/or Fortran code.
The R installer can now be optionally built to support a single
architecture (only 64-bit or only 32-bit).
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 ‘std::random_shuffle’ (deprecated in C++14 and removed in C++17). Either specify C++11 (see ‘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 ‘DESCRIPTION’ would need to include something like
Depends: R (>= 3.4)
‘R CMD INSTALL’ and ‘R CMD SHLIB’ make use of their flag ‘--use-LTO’
when the ‘LTO_OPT’ make macro is set in file ‘etc/${R_ARCH}/Makeconf’
or in a personal/site ‘Makevars’ file. (For details see ‘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 CRAN checks with current GCC do.
The default personal library directory on builds with ‘--enable-aqua’
(including CRAN builds) now differs by CPU type, one of
~/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 ‘x86_64’ build of R is run under Rosetta emulation on an ‘arm64’ Mac, the first is used.
‘R CMD check’ can now scan package functions for bogus ‘return’
statements, which were possibly intended as ‘return()’ calls (wish of
PR#17180, patch by Sebastian Meyer). This check can be activated via
the new environment variable ‘_R_CHECK_BOGUS_RETURN_’, true for
‘--as-cran’.
‘R CMD build’ omits tarballs and binaries of previous builds from the
top-level package directory. (PR#17828, patch by Sebastian Meyer.)
‘R CMD check’ now runs sanity checks on the use of ‘LazyData’, for
example that a ‘data’ directory is present and that
‘LazyDataCompression’ is not specified without ‘LazyData’ and has a
documented value. For packages with large LazyData databases without
specifying ‘LazyDataCompression’, there is a reference to the code
given in ‘Writing R Extensions’ §1.1.6 to test the choice of
compression (as in all the CRAN packages tested a non-default method
was preferred).
‘R CMD build’ removes ‘LazyData’ and ‘LazyDataCompression’ fields from
the ‘DESCRIPTION’ file of packages without a ‘data’ directory.
The parser now treats ‘\Unnnnnnnn’ escapes larger than the upper limit
for Unicode points (‘\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 ‘\U{0effff}’.
The parser now looks for non-ASCII spaces on Solaris (as previously on
most other OSes).
There are warnings (including from the parser) on the use of unpaired
surrogate Unicode points such as ‘\uD834’. (These cannot be converted
to valid UTF-8.)
Functions ‘nchar()’, ‘tolower()’, ‘toupper()’ and ‘chartr()’ and those
using regular expressions have more support for inputs with a marked
Latin-1 encoding.
The character-classification functions used (by default) to replace the
system ‘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.
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).
There is a build-time option to replace the system's wide-character
‘wctrans’ C function by tables shipped with R: use ‘configure’ option
‘--with-internal-towlower’ or (on Windows) ‘-DUSE_RI18N_CASE’ in
‘CFLAGS’ when building R. This may be needed to allow ‘tolower()’ and
‘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).
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.
Function ‘plclust()’ from the package ‘stats’ and
‘package.dependencies()’, ‘pkgDepends()’, ‘getDepList()’,
‘installFoundDepends()’, and ‘vignetteDepends()’ from package ‘tools’
are defunct.
Defunct functions ‘checkNEWS()’ and ‘readNEWS()’ from package ‘tools’
and ‘CRAN.packages()’ from ‘utils’ have been removed.
‘R CMD config CXXCPP’ is defunct (it was deprecated in R 3.6.2).
‘parallel::detectCores()’ drops support for IRIX (retired in 2013).
The ‘LINPACK’ argument to ‘chol.default()’, ‘chol2inv()’,
‘solve.default()’ and ‘svd()’ has been defunct since R 3.1.0. It was
silently ignored up to R 4.0.3 but now gives an error.
Subsetting/indexing, such as ‘ddd[*]’ or ‘ddd$x’ on a ‘DOTSXP’
(dot-dot-dot) object ‘ddd’ has been disabled; it worked by accident
only and was undocumented.
Many more C-level allocations (mainly by ‘malloc’ and ‘strdup’) are
checked for success with suitable alternative actions.
Bug fix for ‘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 ‘savePlot()’ after replay (empty
display list means empty screen on resize or empty saved plot).
‘R CMD check’ etc now warn when a package exports non-existing S4
classes or methods, also in case of no “methods” presence. (Reported
by Alex Bertram; reproducible example and patch by Sebastian Meyer in
PR#16662.)
‘boxplot()’ now also accepts ‘call’s for labels such as ‘ylab’, the
same as ‘plot()’. (Reported by Marius Hofert.)
The help page for ‘xtabs()’ now correctly states that ‘addNA’ is
setting ‘na.action = na.pass’ among others. (Reported as PR#17770 by
Thomas Soeiro.)
The ‘R CMD check <pkg>’ gives a longer and more comprehensible message
when ‘DESCRIPTION’ misses dependencies, e.g., in ‘Imports:’. (Thanks
to the contributors of PR#17179.)
‘update.default()’ now calls the generic ‘update()’ on the formula to
work correctly for models with extended formulas. (As reported and
suggested by Neal Fultz in PR#17865.)
The horizontal position of leaves in a dendrogram is now correct also
with ‘center = FALSE’. (PR#14938, patch from Sebastian Meyer.)
‘all.equal.POSIXt()’ no longer warns about and subsequently ignores
inconsistent ‘"tzone"’ attributes, but describes the difference in its
return value (PR#17277). This check can be disabled _via_ the new
argument ‘check.tzone = FALSE’ as suggested by Sebastian Meyer.
‘as.POSIXct()’ now populates the ‘"tzone"’ attribute from its ‘tz’
argument when ‘x’ is a logical vector consisting entirely of ‘NA’
values.
‘x[[2^31]] <- v’ now works. (Thanks to the report and patch by Suharto
Anggono in PR#17330.)
In log-scale graphics, ‘axis()’ ticks and label positions are now
computed more carefully and symmetrically in their range, typically
providing _more_ ticks, fulfilling wishes in PR#17936. The change
really corresponds to an improved ‘axisTicks()’ (package ‘grDevices’),
potentially influencing ‘grid’ and ‘lattice’, for example.
‘qnorm(<very large negative>, log.p=TRUE)’ is now correct to at least
five digits where it was catastrophically wrong, previously.
‘sum(df)’ and similar ‘"Summary"’- and ‘"Math"’-group member functions
now work for data frames ‘df’ with ‘logical’ columns, notably also of
zero rows. (Reported to R-devel by Martin “b706”.)
‘unsplit()’ had trouble with tibbles due to unsound use of ‘rep(NA,
len)’-indexing, which should use ‘NA_integer_’ (Reported to R-devel by
Mario Annau.)
‘pnorm(x, log.p = TRUE)’ underflows to ‘-Inf’ slightly later.
‘show(<hidden S4 generic>)’ prints better and without quotes for
non-hidden S4 generics.
‘read.table()’ and relatives treated an "NA" column name as missing
when ‘check.names = FALSE’ PR#18007.
Parsing strings containing UTF-16 surrogate pairs such as
‘"\uD834\uDD1E"’ works better on some (uncommon) platforms.
‘sprintf("%X", utf8ToInt("\uD834\uDD1E"))’ should now give ‘"1D11E"’ on
all platforms.
‘identical(x,y)’ is no longer true for differing ‘DOTSXP’ objects,
fixing PR#18032.
‘str()’ now works correctly for ‘DOTSXP’ and related exotics, even when
these are doomed.
Additionally, it no longer fails for ‘list’s with a ‘class’ and “irregular” method definitions such that e.g. ‘lapply(*)’ will necessarily fail, as currently for different ‘igraph’ objects.
Message translation domains, e.g., for errors and warnings, are now
correctly determined also when e.g., a ‘base’ function is called from
“top-level” function (i.e., defined in ‘globalenv()’), thanks to a
patch from Joris Goosen fixing PR#17998.
Too long lines in environment files (e.g., ‘Renviron’) no longer crash
R. This limit has been increased to 100,000 bytes. (PR#18001.)
There is a further workaround for FreeType giving incorrect italic font
faces with cairo-based graphics devices on macOS.
‘add_datalist(*, force = TRUE)’ (from package ‘tools’) now actually
updates an existing ‘data/datalist’ file for new content. (Thanks to a
report and patch by Sebastian Meyer in PR#18048.)
‘cut.Date()’ and ‘cut.POSIXt()’ could produce an empty last interval
for ‘breaks = "months"’ or ‘breaks = "years"’. (Reported as PR#18053
by Christopher Carbone.)
Detection of the encoding of ‘regular’ macOS locales such as ‘en_US’
(which is UTF-8) had been broken by a macOS change: fortunately these
are now rarely used with ‘en_US.UTF-8’ being preferred.
‘sub()’ and ‘gsub(pattern, repl, x, *)’ now keep attributes of ‘x’ such
as ‘names()’ also when ‘pattern’ is ‘NA’ (PR#18079).
Time differences (‘"difftime"’ objects) get a replacement and a ‘rep()’
method to keep ‘"units"’ consistent. (Thanks to a report and patch by
Nicolas Bennett in PR#18066.)
The \RdOpts macro, setting defaults for \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.)
‘mclapply’ and ‘pvec’ no longer accidentally terminate parallel
processes started before by ‘mcparallel’ or related calls in package
‘parallel’ (PR#18078).
‘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.
Fixed a crash in ‘fifo’ implementation on Windows (PR#18031).
Binary mode in ‘fifo’ on Windows is now properly detected from argument
‘open’ (PR#15600, PR#18031).
The change to the internal table in R 4.0.4 for ‘iswprint’ has been
reverted: it contained some errors in printability of ‘East Asian’
characters.
For packages using ‘LazyData’, ‘R CMD build’ ignored the
‘--resave-data’ option and the ‘BuildResaveData’ field of the
‘DESCRIPTION’ file (in R versions 4.0.0 to 4.0.4).
File ‘share/texmf/tex/latex/jss.cls’ has been updated to work with
LaTeX versions since Oct 2020.
Unicode character width tables (as used by ‘nchar(, type = "w")’) have
been updated to Unicode 12.1 by Brodie Gaslam (PR#17781), including
many emoji.
The internal table for ‘iswprint’ (used on Windows, macOS and AIX) has
been updated to include many recent Unicode characters.
If an external BLAS is specified by ‘--with-blas=foo’ or _via_
environment variable ‘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 ‘--with-blas=yes’
was specified.
‘all.equal(x,y)’ now “sees” the two different ‘NA’s in factors, thanks
to Bill Dunlap and others in PR#17897.
‘(~ 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.
‘.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.
‘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.
‘iconvlist()’ now also works on MUSL based (Linux) systems, from a
report and patch suggestion by Wesley Chan in PR#17970.
‘round()’ and ‘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.
‘.Machine’ has ‘longdouble.*’ elements only if
‘capabilities("long.double")’ is true, as documented. (Previously they
were included if the platform had ‘long double’ identical to ‘double’,
as ARM does.)
‘p.adjust(numeric(), n=0)’ now works, fixing PR#18002.
‘identical(x,y)’ no longer prints "Unknown Type .." for ‘typeof(x) ==
"..."’ objects.
Fix (auto-)‘print()’ing of named complex vectors, see PR#17868 and
PR#18019.
‘all.equal(<language>, <...>)’ now works, fixing PR#18029.
‘as.data.frame.list(L, row.names=NULL)’ now behaves in line with
‘data.frame()’, disregarding names of components of ‘L’, fixing
PR#18034, reported by Kevin Tappe.
‘checkRdaFiles(ff)$version’ is now correct also when ‘ff’ contains
files of different versions, thanks to a report and patch from
Sebastian Meyer in PR#18041.
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.
On platforms using ‘configure’ option ‘--with-internal-tzcode’,
additional values ‘"internal"’ and (on macOS only) ‘"macOS"’ are
accepted for the environment variable ‘TZDIR’. (See ‘?TZDIR’.)
On macOS, ‘"macOS"’ is used by default if the system timezone database is a newer version than that in the R installation.
When ‘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.
The default value for ‘options("timeout")’ can be set from environment
variable ‘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.
There is now support for parallelized Link-Time Optimization (LTO) with
GCC and for ‘thin’ LTO with ‘clang’ _via_ setting the ‘LTO’ macro.
There is support for setting a different LTO flag for the Fortran
compiler, including to empty when mixing ‘clang’ and ‘gfortran’ (as on
macOS). See file ‘config.site’.
There is a new ‘LTO_LD’ macro to set linker options for LTO
compilation, for example to select an alternative linker or to
parallelize thin LTO.
The ‘LINPACK’ argument to ‘chol.default()’, ‘chol2inv()’,
‘solve.default()’ and ‘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.
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.
Fix to correctly show the group labels in ‘dotchart()’ (which where
lost in the ‘ylab’ improvement for R 4.0.0).
‘addmargins(*, ..)’ now also works when ‘fn()’ is a local function,
thanks to bug report and patch PR#17124 from Alex Bertram.
‘rank(x)’ and hence ‘sort(x)’ now work when ‘x’ is an object (as per
‘is.object(x)’) of type ‘"raw"’ _and_ provides a valid ‘`[`’ method,
e.g., for ‘gmp::as.bigz(.)’ numbers.
‘chisq.test(*, simulate.p.value=TRUE)’ and ‘r2dtable()’ now work
correctly for large table entries (in the millions). Reported by
Sebastian Meyer and investigated by more helpers in PR#16184.
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.
‘quantile(x, pr)’ works more consistently for ‘pr’ values slightly
outside [0,1], thanks to Suharto Anggono's PR#17891.
Further, ‘quantile(x, prN, names=FALSE)’ now works even when ‘prN’ contains ‘NA’s, thanks to Anggono's PR#17892. Ditto for ordered factors or ‘Date’ objects when ‘type = 1’ or ‘3’, thanks to PR#17899.
Internet access based on libcurl, including ‘curlGetHeaders()’, was not
respecting the ‘"timeout"’ option. If this causes unanticipated
timeouts, consider increasing the default by setting
‘R_DEFAULT_INTERNET_TIMEOUT’.
‘as.Date(<char>)’ now also works with an initial ‘""’, thanks to
Michael Chirico's PR#17909.
‘isS3stdGeneric(f)’ now detects an S3 generic also when it is
‘trace()’d, thanks to Gabe Becker's PR#17917.
‘R_allocLD()’ has been fixed to return memory aligned for long double
type PR#16534.
‘fisher.test()’ no longer segfaults when called again after its
internal stack has been exceeded PR#17904.
Accessing a long vector represented by a compact integer sequence no
longer segfaults (reported and debugged by Hugh Parsonage).
‘duplicated()’ now works also for strings with multiple encodings
inside a single vector PR#17809.
‘phyper(11, 15, 0, 12, log.p=TRUE)’ no longer gives ‘NaN’; reported as
PR#17271 by Alexey Stukalov.
Fix incorrect calculation in ‘logLik.nls()’ PR#16100, patch from
Sebastian Meyer.
A very old bug could cause a segfault in ‘model.matrix()’ when terms
involved logical variables. Part of PR#17879.
‘model.frame.default()’ allowed ‘data = 1’, leading to involuntary
variable capture (rest of PR#17879).
‘tar()’ no longer skips non-directory files, thanks to a patch by
Sebastian Meyer, fixing the remaining part of PR#16716.
‘R CMD check’ skips vignette re-building (with a warning) if the
‘VignetteBuilder’ package(s) are not available.
Paths with non-ASCII characters caused problems for package loading on
Windows PR#17833.
Using ‘tcltk’ widgets no longer crashes R on Windows.
‘source(*, echo=TRUE)’ no longer fails in some cases with empty lines;
reported by Bill Dunlap in PR#17769.
‘on.exit()’ now correctly matches named arguments, thanks to PR#17815
(including patch) by Brodie Gaslam.
‘regexpr(*, perl=TRUE)’ no longer returns incorrect positions into text
containing characters outside of the Unicode Basic Multilingual Plane
on Windows.
‘paste()’ and ‘paste0()’ gain a new optional argument ‘recycle0’. When
set to true, zero-length arguments are recycled leading to
‘character(0)’ after the ‘sep’-concatenation, i.e., to the empty string
‘""’ if ‘collapse’ is a string and to the zero-length value
‘character(0)’ when ‘collapse = NULL’.
A package whose code uses this should depend on ‘R (>= 4.0.1)’.
The ‘summary(<warnings>)’ method now maps the counts correctly to the
warning messages.
‘aov(frml, ...)’ now also works where the ‘formula’ deparses to more
than 500 characters, thanks to a report and patch proposal by Jan
Hauffa.
Fix a dozen places (code, examples) as ‘Sys.setlocale()’ returns the
new rather than the previous setting.
Fix for adding two complex ‘grid’ units via ‘sum()’. Thanks to Gu
Zuguang for the report and Thomas Lin Pedersen for the patch.
Fix ‘parallel::mclapply(..., mc.preschedule=FALSE)’ to handle raw
vector results correctly. PR#17779
Computing the ‘base’ value, i.e., 2, “everywhere”, now uses
‘FLT_RADIX’, as the original ‘machar’ code looped indefinitely on the
ppc64 architecture for the ‘longdouble’ case.
In R 4.0.0, ‘sort.list(x)’ when ‘is.object(x)’ was true, e.g., for ‘x
<- I(letters)’, was accidentally using ‘method = "radix"’.
Consequently, e.g., ‘merge(<data.frame>)’ was much slower than
previously; reported in PR#17794.
‘plot(y ~ x, ylab = quote(y[i]))’ now works, as e.g., for ‘xlab’;
related to PR#10525.
‘parallel::detect.cores(all.tests = TRUE)’ tries a matching OS name
before the other tests (which were intended only for unknown OSes).
Parse data for raw strings is now recorded correctly. Reported by Gabor
Csardi.
Packages need to be (re-)installed under this version (4.0.0) of R.
‘matrix’ objects now also inherit from class ‘"array"’, so e.g.,
‘class(diag(1))’ is ‘c("matrix", "array")’. This invalidates code
incorrectly assuming that ‘class(matrix_obj))’ has length one.
S3 methods for class ‘"array"’ are now dispatched for ‘matrix’ objects.
There is a new syntax for specifying _raw_ character constants similar
to the one used in C++: ‘r"(...)"’ with ‘...’ any character sequence
not containing the sequence ‘)"’. This makes it easier to write
strings that contain backslashes or both single and double quotes. For
more details see ‘?Quotes’.
R now uses a ‘stringsAsFactors = FALSE’ default, and hence by default
no longer converts strings to factors in calls to ‘data.frame()’ and
‘read.table()’.
A large number of packages relied on the previous behaviour and so have needed/will need updating.
The ‘plot()’ S3 generic function is now in package ‘base’ rather than
package ‘graphics’, as it is reasonable to have methods that do not use
the ‘graphics’ package. The generic is currently re-exported from the
‘graphics’ namespace to allow packages importing it from there to
continue working, but this may change in future.
Packages which define S4 generics for ‘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).
Reference counting is now used instead of the ‘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.
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 _via_ ‘extSoftVersion()’: PCRE1
(formerly known as ‘PCRE’) has versions <= 8, PCRE2 versions >= 10.
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 ‘likely to be the final release’.
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). ‘\R’, ‘\B’ and ‘\X’ are no longer allowed in character
classes (PCRE1 treated these as literals).
Option ‘PCRE_study’ is no longer used with PCRE2, and is reported as
‘FALSE’ when that is in use.
‘assertError()’ and ‘assertWarning()’ (in package ‘tools’) can now
check for _specific_ error or warning classes _via_ the new optional
second argument ‘classes’ (which is not back compatible with previous
use of an unnamed second argument).
‘DF2formula()’, the utility for the data frame method of ‘formula()’,
now works without parsing and explicit evaluation, starting from
Suharto Anggono's suggestion in PR#17555.
‘approxfun()’ and ‘approx()’ gain a new argument ‘na.rm’ defaulting to
true. If set to false, missing ‘y’ values now propagate into the
interpolated values.
Long vectors are now supported as the ‘seq’ argument of a ‘for()’ loop.
‘str(x)’ gets a new ‘deparse.lines’ option with a default to speed it
up when ‘x’ is a large ‘call’ object.
The internal traceback object produced when an error is signalled
(‘.Traceback’), now contains the ‘call’s rather than the _‘deparse()’d_
calls, deferring the deparsing to the user-level functions
‘.traceback()’ and ‘traceback()’. This fulfils the wish of PR#17580,
reported including two patch proposals by Brodie Gaslam.
‘data.matrix()’ now converts character columns to factors and from this
to integers.
‘package.skeleton()’ now explicitly lists all exports in the
‘NAMESPACE’ file.
New function ‘.S3method()’ to register S3 methods in R scripts.
‘file.path()’ has some support for file paths not in the session
encoding, e.g. with UTF-8 inputs in a non-UTF-8 locale the output is
marked as UTF-8.
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
‘dir.exists()’, ‘file.exists()’, ‘file.access()’, ‘file.info()’,
‘list.files()’, ‘normalizePath()’ and ‘path.expand()’) treat this like
any other non-existent file, often with a warning.
There is a new help document accessed by ‘help("file path encoding")’
detailing how file paths with marked encodings are handled.
New function ‘list2DF()’ for creating data frames from lists of
variables.
‘iconv()’ has a new option ‘sub = "Unicode"’ to translate UTF-8 input
invalid in the ‘to’ encoding using ‘<U+xxxx>’ escapes.
There is a new function ‘infoRDS()’ providing information about the
serialization format of a serialized object.
S3 method lookup now by default skips the elements of the search path
between the global and base environments.
Added an argument ‘add_datalist(*, small.size = 0)’ to allow the
creation of a ‘data/datalist’ file even when the total size of the data
sets is small.
The backquote function ‘bquote()’ has a new argument ‘splice’ to enable
splicing a computed list of values into an expression, like ‘,@’ in
LISP's backquote.
The formula interface to ‘t.test()’ and ‘wilcox.test()’ has been
extended to handle one-sample and paired tests.
The ‘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
‘palette.pals()’ function. These include the old default palette under
the name ‘"R3"’. Finally, the new ‘palette.colors()’ function allows a
subset of colours to be selected from any of the built-in palettes.
‘n2mfrow()’ gains an option ‘asp = 1’ to specify the aspect ratio,
fulfilling the wish and extending the proposal of Michael Chirico in
PR#17648.
For ‘head(x, n)’ and ‘tail()’ the default and other S3 methods notably
for _vector_ ‘n’, e.g. to get a “corner” of a matrix, has been extended
to ‘array’'s of higher dimension thanks to the patch proposal by Gabe
Becker in PR#17652. Consequently, optional argument ‘addrownums’ is
deprecated and replaced by the (more general) argument ‘keepnums’. An
invalid second argument ‘n’ now leads to typically more easily readable
error messages.
New function ‘.class2()’ provides the full character vector of class
names used for S3 method dispatch.
Printing ‘methods(..)’ now uses a new ‘format()’ method.
‘sort.list(x)’ now works for non-atomic objects ‘x’ and ‘method =
"auto"’ (the default) or ‘"radix"’ in cases ‘order(x)’ works, typically
via a ‘xtfrm()’ method.
Where they are available, ‘writeBin()’ allows long vectors.
New function ‘deparse1()’ produces one string, wrapping ‘deparse()’, to
be used typically in ‘deparse1(substitute(*))’, e.g., to fix PR#17671.
‘wilcox.test()’ enhancements: In the (non-paired) two-sample case,
‘Inf’ values are treated as very large for robustness consistency. If
exact computations are used, the result now has ‘"exact"’ in the
‘method’ element of its return value. New arguments ‘tol.root’ and
‘digits.rank’ where the latter may be used for stability to treat very
close numbers as ties.
‘readBin()’ and ‘writeBin()’ now report an error for an invalid
‘endian’ value. The affected code needs to be fixed with care as the
old undocumented behavior was to swap endianness in such cases.
‘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 ‘S4Vectors’ Bioconductor package and the advice
of Hervé Pagès.
‘print()’'s default method and many other methods (by calling the
default eventually and passing ‘...’) now make use of a new optional
‘width’ argument, avoiding the need for the user to set and reset
‘options("width")’.
‘memDecompress()’ supports the RFC 1952 format (e.g. in-memory copies
of ‘gzip’-compressed files) as well as RFC 1950.
‘memCompress()’ and ‘memDecompress()’ support long raw vectors for
types ‘"gzip"’ and ‘"zx"’.
‘sweep()’ and ‘slice.index()’ can now use names of dimnames for their
‘MARGIN’ argument (‘apply’ has had this for almost a decade).
New function ‘proportions()’ and ‘marginSums()’. These should replace
the unfortunately named ‘prop.table()’ and ‘margin.table()’. They are
drop-in replacements, but also add named-margin functionality. The old
function names are retained as aliases for back-compatibility.
Functions ‘rbinom()’, ‘rgeom()’, ‘rhyper()’, ‘rpois()’, ‘rnbinom(),’
‘rsignrank()’ and ‘rwilcox()’ which have returned integer since R 3.0.0
and hence ‘NA’ when the numbers would have been outside the integer
range, now return double vectors (without NAs, typically) in these
cases.
‘matplot(x,y)’ (and hence ‘matlines()’ and ‘matpoints()’) now call the
corresponding methods of ‘plot()’ and ‘lines()’, e.g, when ‘x’ is a
‘"Date"’ or ‘"POSIXct"’ object; prompted by Spencer Graves' suggestion.
‘stopifnot()’ now allows customizing error messages via argument names,
thanks to a patch proposal by Neal Fultz in PR#17688.
‘unlink()’ gains a new argument ‘expand’ to disable wildcard and tilde
expansion. Elements of ‘x’ of value ‘"~"’ are now ignored.
‘mle()’ in the ‘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 ‘"mle"’, so saved objects from earlier versions may need to be
recomputed.
The default for ‘pdf()’ is now ‘useDingbats = FALSE’.
The default fill colour for ‘hist()’ and ‘boxplot()’ is now ‘col =
"lightgray"’.
The default order of the levels on the y-axis for ‘spineplot()’ and
‘cdplot()’ has been reversed.
If the ‘R_ALWAYS_INSTALL_TESTS’ environment variable is set to a true
value, ‘R CMD INSTALL’ behaves as if the ‘--install-tests’ option is
always specified. Thanks to Reinhold Koch for the suggestion.
New function ‘R_user_dir()’ in package ‘tools’ suggests paths
appropriate for storing R-related user-specific data, configuration and
cache files.
‘capabilities()’ gains a new logical option ‘Xchk’ to avoid warnings
about X11-related capabilities.
The internal implementation of ‘grid’ units has changed, but the only
visible effects at user-level should be
• a slightly different print format for some units (especially unit arithmetic),
• faster performance (for unit operations) and
• two new functions ‘unitType()’ and ‘unit.psum()’.
Based on code contributed by Thomas Lin Pedersen.
When internal dispatch for ‘rep.int()’ and ‘rep_len()’ fails, there is
an attempt to dispatch on the equivalent call to ‘rep()’.
Object ‘.Machine’ now contains new ‘longdouble.*’ entries (when R uses
long doubles internally).
‘news()’ has been enhanced to cover the news on R 3.x and 2.x.
For consistency, ‘N <- NULL; N[[1]] <- val’ now turns ‘N’ into a ‘list’
also when ‘val)’ has length one. This enables ‘dimnames(r1)[[1]] <-
"R1"’ for a 1-row matrix ‘r1’, fixing PR#17719 reported by Serguei
Sokol.
‘deparse(..)’, ‘dump(..)’, and ‘dput(x, control = "all")’ now include
control option ‘"digits17"’ which typically ensures 1:1 invertibility.
New option ‘control = "exact"’ ensures numeric exact invertibility via
‘"hexNumeric"’.
When loading data sets via ‘read.table()’, ‘data()’ now uses
‘LC_COLLATE=C’ to ensure locale-independent results for possible
string-to-factor conversions.
A server socket connection, a new connection type representing a
listening server socket, is created via ‘serverSocket()’ and can accept
multiple socket connections via ‘socketAccept()’.
New function ‘socketTimeout()’ changes the connection timeout of a
socket connection.
The time needed to start a homogeneous ‘PSOCK’ cluster on ‘localhost’
with many nodes has been significantly reduced (package ‘parallel’).
New ‘globalCallingHandlers()’ function to establish global condition
handlers. This allows registering default handlers for specific
condition classes. Developed in collaboration with Lionel Henry.
New function ‘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.
‘str(x)’ now shows the length of ‘attributes’ in some cases for a data
frame ‘x’.
‘Rprof()’ gains a new argument ‘filter.callframes’ to request that
intervening call frames due to lazy evaluation or explicit ‘eval()’
calls be omitted from the recorded profile data. Contributed by Lionel
Henry in PR#17595.
The handling of ‘${FOO-bar}’ and ‘${FOO:-bar}’ in ‘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 ‘etc/Renviron’.
New ‘classes’ argument for ‘suppressWarnings()’ and
‘suppressMessages()’ to selectively suppress only warnings or messages
that inherit from particular classes. Based on patch from Lionel Henry
submitted with PR#17619.
New function ‘activeBindingFunction()’ retrieves the function of an
active binding.
New ‘"cairoFT"’ and ‘"pango"’ components in the output of
‘grSoftVersion()’.
New argument ‘symbolfamily’ in cairo-based graphics devices and new
function ‘cairoSymbolFont()’ that can be used to provide the value for
that argument.
‘Rterm’ now works also when invoked from MSYS2 terminals. Line editing
is possible when command ‘winpty’ is installed.
‘normalizePath()’ now resolves symbolic links and normalizes case of
long names of path elements in case-insensitive folders (PR#17165).
‘md5sum()’ supports UTF-8 file names with characters that cannot be
translated to the native encoding (PR#17633).
‘Rterm’ gains a new option ‘--workspace’ to specify the workspace to be
restored. This allows equals to be part of the name when opening _via_
Windows file associations (reported by Christian Asseburg).
‘Rterm’ now accepts ‘ALT+xxx’ sequences also with NumLock on. Tilde
can be pasted with an Italian keyboard (PR#17679).
R falls back to copying when junction creation fails during package
checking (patch from Duncan Murdoch).
Make macro ‘F77_VISIBILITY’ has been removed and replaced by
‘F_VISIBILITY’.
Make macros ‘F77’, ‘FCPIFCPLAGS’ and ‘SHLIB_OPENMP_FCFLAGS’ have been
removed and replaced by ‘FC’, ‘FPICFLAGS’ and ‘SHLIB_OPENMP_FFLAGS’
respectively. (Most ‘make’ programs will set ‘F77’ to the value of
‘FC’, which is set for package compilation. But portable code should
not rely on this.)
The deprecated support for specifying C++98 for package installation
has been removed.
‘R CMD config’ no longer knows about the unused settings ‘F77’ and
‘FCPIFCPLAGS’, nor ‘CXX98’ and similar.
Either PCRE2 or PCRE1 >= 8.32 (Nov 2012) is required: the deprecated
provision for 8.20-8.31 has been removed.
Defunct functions ‘mem.limits()’, ‘.readRDS()’, ‘.saveRDS()’,
‘.find.package()’, and ‘.path.package()’ from package ‘base’ and
‘allGenerics()’, ‘getAccess()’, ‘getAllMethods()’, ‘getClassName()’,
‘getClassPackage()’, ‘getExtends()’, ‘getProperties()’,
‘getPrototype()’, ‘getSubclasses()’, ‘getVirtual()’, ‘mlistMetaName()’,
‘removeMethodsObject()’, ‘seemsS4Object()’, ‘traceOff()’, and
‘traceOn()’ from ‘methods’ have been removed.
‘installChar’ is now remapped in ‘Rinternals.h’ to ‘installTrChar’, of
which it has been a wrapper since R 3.6.0. Neither are part of the
API, but packages using ‘installChar’ can replace it if they depend on
‘R >= 3.6.2’.
Header ‘R_ext/Print.h’ defines ‘R_USE_C99_IN_CXX’ and hence exposes
‘Rvprintf’ and ‘REvprintf’ if used with a C++11 (or later) compiler.
There are new Fortran subroutines ‘dblepr1’, ‘realpr1’ and ‘intpr1’ to
print a scalar variable (‘gfortran’ 10 enforces the distinction between
scalars and length-one arrays). Also ‘labelpr’ to print just a label.
‘R_withCallingErrorHandler’ is now available for establishing a calling
handler in C code for conditions inheriting from class ‘error’.
User-set ‘DEFS’ (e.g., in ‘config.site’) is now used for compiling
packages (including base packages).
There is a new variant option ‘--enable-lto=check’ for checking
consistency of BLAS/LAPACK/LINPACK calls - see ‘Writing R Extensions’.
A C++ compiler default is set only if the C++11 standard is supported:
it no longer falls back to C++98.
PCRE2 is used if available. To make use of PCRE1 if PCRE2 is
unavailable, configure with option ‘--with-pcre1’.
The minimum required version of ‘libcurl’ is now 7.28.0 (Oct 2012).
New make target ‘distcheck’ checks
• R can be rebuilt from the tarball created by ‘make dist’,
• the build from the tarball passes ‘make check-all’,
• the build installs and uninstalls,
• the source files are properly cleaned by ‘make distclean’.
‘R --help’ now mentions the option ‘--no-echo’ (renamed from ‘--slave’)
and its previously undocumented short form ‘-s’.
‘R CMD check’ now optionally checks ‘configure’ and ‘cleanup’ scripts
for non-Bourne-shell code (‘bashisms’).
‘R CMD check --as-cran’ now runs \donttest examples (which are run by
‘example()’) instead of instructing the tester to do so. This can be
temporarily circumvented during development by setting environment
variable ‘_R_CHECK_DONTTEST_EXAMPLES_’ to a false value.
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
‘-std=c++20’ and ‘-std=c++2a’. For the time being the ‘configure’ test
is of accepting one of these flags and compiling C++17 code.
‘formula(x)’ with ‘length(x) > 1’ character vectors, is deprecated now.
Such use has been rare, and has ‘worked’ as expected in some cases
only. In other cases, wrong ‘x’ have silently been truncated, not
detecting previous errors.
Long-standing issue where the X11 device could lose events shortly
after startup has been addressed (PR#16702).
The ‘data.frame’ method for ‘rbind()’ no longer drops ‘<NA>’ levels
from factor columns by default (PR#17562).
‘available.packages()’ and hence ‘install.packages()’ now pass their
‘...’ argument to ‘download.file()’, fulfilling the wish of PR#17532;
subsequently, ‘available.packages()’ gets new argument ‘quiet’, solving
PR#17573.
‘stopifnot()’ gets new argument ‘exprObject’ to allow an R object of
class ‘expression’ (or other ‘language’) to work more consistently,
thanks to suggestions by Suharto Anggono.
‘conformMethod()’ now works correctly in cases containing a “‘&&’
logic” bug, reported by Henrik Bengtsson. It now creates methods with
‘"missing"’ entries in the signature. Consequently,
‘rematchDefinition()’ is amended to use appropriate ‘.local()’ calls
with named arguments where needed.
‘format.default(*, scientific = FALSE)’ now corresponds to a
practically most extreme ‘options(scipen = n)’ setting rather than
arbitrary ‘n = 100’.
‘format(as.symbol("foo"))’ now works (returning ‘"foo"’).
‘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.
Certain ‘Ops’ (notably comparison such as ‘==’) now also work for
0-length data frames, after reports by Hilmar Berger.
‘methods(class = class(glm(..)))’ now warns more usefully and only
once.
‘write.dcf()’ no longer mangles field names (PR#17589).
Primitive replacement functions no longer mutate a referenced first
argument when used outside of a complex assignment context.
A better error message for ‘contour(*, levels = Inf)’.
The return value of ‘contourLines()’ is no longer ‘invisible()’.
The Fortran code for calculating the ‘coefficients’ component in
‘lm.influence()’ was very inefficient. It has (for now) been replaced
with much faster R code (PR#17624).
‘cm.colors(n)’ _etc_ no longer append the code for ‘alpha = 1’, ‘"FF"’,
to all colors. Hence all eight ‘*.colors()’ functions and ‘rainbow()’
behave consistently and have the same non-explicit default (PR#17659).
‘dnorm’ had a problematic corner case with ‘sd == -Inf’ or negative
‘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 ‘dlnorm()’.
The optional ‘iter.smooth’ argument of ‘plot.lm()’, (the ‘plot()’
method for ‘lm’ and ‘glm’ fits) now defaults to ‘0’ for all ‘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 ‘glm’ case has been switched to
‘"pearson"’ since deviance residuals do not in general have
approximately zero mean.
In ‘plot.lm’, Cook's distance was computed from unweighted residuals,
leading to inconsistencies. Replaced with usual weighted version.
(PR#16056)
Time-series ‘ts(*, start, end, frequency)’ with fractional ‘frequency’
are supported more consistently; thanks to a report from Johann
Kleinbub and analysis and patch by Duncan Murdoch in PR#17669.
In case of errors ‘mcmapply()’ now preserves attributes of returned
‘"try-error"’ objects and avoids simplification, overriding ‘SIMPLIFY’
to ‘FALSE’. (PR#17653)
‘as.difftime()’ gets new optional ‘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.
‘round()’ does a better job of rounding _“to nearest”_ by _measuring_
and _“to even”_; thanks to a careful algorithm originally prompted by
the report from Adam Wheeler and then others, in PR#17668.
‘round(x, dig)’ for _negative_ digits is much more rational now,
notably for large |dig|.
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).
‘is()’ behaves more robustly when its argument ‘class2’ is a
‘classRepresentation’ object.
The warning message when attempting to export an nonexistent class is
now more readable; thanks to Thierry Onkelinx for recognizing the
problem.
‘choose()’ misbehaved in corner cases where it switched ‘n - k’ for ‘k’
and ‘n’ was only _nearly_ integer (report from Erik Scott Wright).
‘mle()’ in the ‘stats4’ package had problems combining use of box
constraints and fixed starting values (in particular, confidence
intervals were affected).
Operator ‘?’ now has lower precedence than ‘=’ to work as documented,
so ‘=’ behaves like ‘<-’ in help expressions (PR#16710).
‘smoothEnds(x)’ now returns ‘integer’ type in _both_ cases when ‘x’ is
‘integer’, thanks to a report and proposal by Bill Dunlap PR#17693.
The ‘methods’ package does a better job of tracking inheritance
relationships across packages.
‘norm(diag(c(1, NA)), "2")’ now works.
‘subset()’ had problems with 0-col dataframes (reported by Bill Dunlap,
PR#17721).
Several cases of integer overflow detected by the ‘undefined behaviour
sanitizer’ of ‘clang’ 10 have been circumvented. One in ‘rhyper()’ may
change the generated value for large input values.
‘dotchart()’ now places the y-axis label (‘ylab’) much better, not
overplotting labels, thanks to a report and suggestion by Alexey
Shipunov.
A rare C-level array overflow in ‘chull()’ has been worked around.
Some invalid specifications of the day-of-the-year (_via_ ‘%j’, e.g.
day 366 in 2017) or week plus day-of-the-week are now detected by
‘strptime()’. They now return ‘NA’ but give a warning as they may have
given random results or corrupted memory in earlier versions of R.
‘socketConnection(server = FALSE)’ now respects the connection timeout
also on Linux.
‘socketConnection(server = FALSE)’ no longer leaks a connection that is
available right away without waiting (e.g. on ‘localhost’).
Socket connections are now robust against spurious readability and
spurious availability of an incoming connection.
‘blocking = FALSE’ is now respected also on the server side of a socket
connection, allowing non-blocking read operations.
‘anova.glm()’ and ‘anova.glmlist()’ computed incorrect score (Rao)
tests in no-intercept cases. (André Gillibert, PR#17735)
‘summaryRprof()’ now should work correctly for the ‘Rprof(*,
memory.profiling=TRUE)’ case with small chunk size (and ‘"tseries"’ or
similar) thanks to a patch proposal by Benjamin Tyner, in PR#15886.
‘xgettext()’ ignores strings passed to ‘ngettext()’, since the latter
is handled by ‘xngettext()’. Thanks to Daniele Medri for the report and
all the recent work he has done on the Italian translations.
‘data(package = "P")’ for ‘P’ in ‘base’ and ‘stats’ no longer reports
the data sets from package ‘datasets’ (which it did for back
compatibility for 16 years), fixing PR#17730.
‘x[[Inf]]’ (returning ‘NULL’) no longer leads to undefined behavior,
thanks to a report by Kirill Müller in PR#17756. Further, ‘x[[-Inf]]’
and ‘x[[-n]]’ now give more helpful error messages.
‘Gamma()’ family sometimes had trouble storing link name PR#15891
‘Sys.glob()’ now supports all characters from the Unicode Basic
Multilingual Plane, no longer corrupting some (less commonly used)
characters (PR#17638).
‘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).
‘scan()’ issues with UTF-8 data when running in a DBCS locale have been
resolved (PR#16520, PR#16584).
‘Rterm’ now accepts enhanced/arrow keys also with ConPTY.
R can now be started _via_ the launcher icon in a user documents
directory whose path is not representable in the system encoding.
‘socketConnection(server = FALSE)’ now returns instantly also on
Windows when connection failure is signalled.
Problems with UTF-16 surrogate pairs have been fixed in several
functions, including ‘tolower()’ and ‘toupper()’ (PR#17645).