• 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.

SIGNIFICANT USER-VISIBLE CHANGES:

• 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.)

NEW FEATURES:

• 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 functions 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
  Zakauskas.)

• 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_CTYP...

BUG FIXES:

• 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.

INSTALLATION on a UNIX-ALIKE:

• 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.

BUG FIXES:

• all.equal(x,y) now "sees" the two different NAs 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.

LINK-TIME OPTIMIZATION on a UNIX-ALIKE:

• 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.

DEPRECATED AND DEFUNCT:

• 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.

BUG FIXES:

• 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 NAs, thanks to Anggono's PR#17892. Ditto for ordered
  factors or Date objects when type = 1 or 3, thanks to PR#17899.

• Libcurl-based internet access, 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 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.

BUG FIXES:

• 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.

BUG FIXES:

• 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.