Log Message:
Update to 4.1.0

Upstream changes:
CHANGES IN R 4.1.0:

  FUTURE DIRECTIONS:

    * 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 stringsAsFactor) 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 well as 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.

  GRAPHICS:

    * 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.

  C-LEVEL FACILITIES:

    * The _standalone_ libRmath math library and R's C API now provide
      log1pexp() again as documented, and gain log1mexp().

  INSTALLATION on a UNIX-ALIKE:

    * 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.

  LINK-TIME OPTIMIZATION on a UNIX-ALIKE:

    * 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.)

  BUILDING R on Windows:

    * 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).

  PACKAGE INSTALLATION:

    * 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)

  PACKAGE INSTALLATION on Windows:

    * 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' SS4.5.)

      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.

  PACKAGE INSTALLATION on macOS:

    * 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.

  UTILITIES:

    * 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' SS1.1.6 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.

  ENCODING-RELATED CHANGES:

    * 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.

    * 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.

  DEPRECATED AND DEFUNCT:

    * 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.

  BUG FIXES:

    * 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 calls 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 lists with a class and
      "irregular" method definitions such that e.g. lapply(*) will
      necessarily fail, as currently for different igraph objects.

    * 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).