R News

CHANGES IN R 4.1.3:

  NEW FEATURES:

    • The default version of Bioconductor has been changed to 3.14.
      (This is used by setRepositories and the menus in GUIs.)

  UTILITIES:

    • 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.

  C-LEVEL FACILITIES:

    • 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.

  BUG FIXES:

    • 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).

CHANGES IN R 4.1.2:

  C-LEVEL FACILITIES:

    • 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.

  DEPRECATED AND DEFUNCT:

    • 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.

  BUG FIXES:

    • .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).

CHANGES IN R 4.1.1:

  NEW FEATURES:

    • require(pkg, quietly = TRUE) is quieter and in particular does
      not warn if the package is not found.

  DEPRECATED AND DEFUNCT:

    • 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.

  INSTALLATION:

    • make check now works also without a LaTeX installation.  (Thanks
      to Sebastian Meyer's PR#18103.)

  BUG FIXES:

    • 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.)

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 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
      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.

  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’ §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.

  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’ §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.

  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.  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.

  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.

    • 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).

CHANGES IN R 4.0.5:

  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).

CHANGES IN R 4.0.4:

  NEW FEATURES:

    • 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.

CHANGES IN R 4.0.3:

  NEW FEATURES:

    • 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.

CHANGES IN R 4.0.2:

  UTILITIES:

    • 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.

CHANGES IN R 4.0.1:

  NEW FEATURES:

    • 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.

CHANGES IN R 4.0.0:

  SIGNIFICANT USER-VISIBLE CHANGES:

    • 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:

    • 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.

  MIGRATION TO PCRE2:

    • 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.

  NEW FEATURES:

    • 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 calls 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 endian-ness 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.

  Windows:

    • 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).

  DEPRECATED AND DEFUNCT:

    • 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.

  C-LEVEL FACILITIES:

    • 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.

  INSTALLATION on a UNIX-ALIKE:

    • 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.

  UTILITIES:

    • 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.

  PACKAGE INSTALLATION:

    • 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.

  BUG FIXES:

    • 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

  BUG FIXES (Windows):

    • 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 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).

CHANGES in previous versions:

  • Older news can be found in text format in files NEWS.0, NEWS.1,
    NEWS.2 and NEWS.3 in the doc directory.  News in HTML format for R
    versions 3.x and from 2.10.0 to 2.15.3 is available at
    doc/html/NEWS.3.html and doc/html/NEWS.2.html.

