R News

Changes in R-devel:

  Significant User-Visible Changes:

    • read.dcf() and write.dcf() now treat DCF files (such as package
      DESCRIPTION and repository PACKAGES files) as UTF-8, as required
      by the Debian control file format.  read.dcf() returns values in
      UTF-8 and write.dcf() always writes UTF-8 regardless of the
      session locale; bytes which are not valid UTF-8 are preserved by
      escaping them as <xx> rather than being re-encoded via a Encoding
      field.  As a consequence, the useBytes argument of write.dcf() is
      ignored, and non-UTF-8 DESCRIPTION files (e.g. those declaring
      Encoding: latin1) are no longer re-encoded on reading.

    • Fixing rbinom(), see PR#19049 below, to reproduce old results
      needs RNGkind() to get a new binom.kind argument and, e.g.
      RNGversion("4.6") keeps previous behaviour.

  New Features:

    • boxplot(): when notch=TRUE, new option warnN=FALSE suppresses
      warnings about “notches outside hinges”.

    • New function cumvar() to calculate cumulative variances.

    • The print() method for rle() now passes ...  to str().

    • rmultinom() now uses Kahan's arithmetic instead of LDOUBLE to
      avoid platform dependency, thanks to Mauricio Vargas' proposal in
      PR#18693.

    • _Object not found_ errors now signal error conditions of class
      objectNotFoundError. _Function not found_ errors signal
      conditions of the subclass functionNotFoundError.

    • Condition classes used internally for signaling some errors are
      now documented in ?conditions.

    • The as.data.frame() methods for atomic vector classes get an
      optional switch validRN, with default true to fix PR#19059 and
      false for some back compatibility, still allowing data frames in
      construction to contain NAs in row names.

    • tools::Rd2txt() now replaces --- and -- by Unicode dashes when
      the output encoding is UTF-8.

    • fisher.test() gains a new option pval.only = TRUE for the 2x2
      exact case, with substantial speed gains in the case of large
      counts.

    • binom.test() and poisson.test() can now at least optionally
      compute central two-sided p-values which match the confidence
      intervals.  Same for fisher.test() in the 2 by 2 case and
      mantelhaen.test() in the 2 by 2 by K case if an exact conditional
      test is performed.

    • New low-level function .OBJSXP() enables deparsing of non-S4
      "object" type objects.

    • use() gets an argument pos with a help example showing how to
      attach a “chain” of packages to search().

    • New higher-order functions Compose(), Funcall() and Partial().

    • New functions find_calls(), find_calls_in_package_code(),
      gsub_with_transformed_matches() and system_with_capture() in
      package tools.

  Installation on a Unix-Alike:

    • Installing R (creating libR.pc) no longer fails with a sed error
      when the new --package-metadata linker flag is involved; an
      s-command delimiter other than : was needed (PR#19060, thanks to
      Jeroen Ooms and Dirk Eddelbuettel).

  Package Installation:

    • .

  C-Level Facilities:

    • .

  Utilities:

    • tools::texi2pdf() now reports BibTeX warnings; in particular,
      missing references are now noted by R CMD check when re-building
      PDF vignettes.

    • R CMD build now excludes an obsolete data/datalist file when the
      package uses LazyData.

  Deprecated and Defunct:

    • structure() now deprecates the old “special” substitute
      attributes' names ".Dim", ".Dimnames", ".Names", ".Tsp", ".Label"
      in favour of the respective "dim", "dimnames", "names", "tsp",
      "levels" names.

  Bug Fixes:

    • For x <- <large-POSIXlt>, for some boundary cases with x$sec -
      floor(x$sec) close to 1, c(x) could become one second ahead of x
      in R 4.6.0; subassignments such as x[i] <- val have improved,
      thanks to suggestions by Suharto Anggono in PR#18989.

    • In an R installation without NLS, e.g., from --disable-nls
      configuration, the C ngettext() replacement now also keeps plural
      for “0 things”, thanks to Michael Chirico's PR#19065.

    • as.data.frame.vector(<row.names_w/_NA>) now signals the same
      error as data.frame(), fixing Hervé Pagès' PR#19059.  From
      Suharto Anggono's comment #c4, it gives the same error also when
      row.names = RN explicitly, where RN has NAs.

    • .leap.seconds again has no "tzone" attribute, as in earlier R
      versions, fixing PR#19072 thanks to Suharto Anggono.

    • as.POSIXct(x) for POSIXlt object x with .Machine$integer.max -
      x$year < 1900 no longer suffers from C level integer overflow,
      thanks to Suharto Anggono's patch for PR#19038.  Currently, this
      does not apply when the "internal" code for date-time conversion
      and printing is in use, as e.g., on Windows and macOS.

    • wilcox.test() gains new optional argument digits.zap, _and_ the
      default for argument digits.rank is changed from Inf to 7,
      addressing bugs PR#18035 and PR#19071, in order to deal with both
      ties of almost equal numbers and almost zeros of differences.

    • Exclude patterns from .Rbuildignore are now processed _before_
      preparing the package directory for the tarball, avoiding
      redundant file copies from the source directory (PR#17549).  In
      particular, when a source package foo/ folder contains broken
      symlinks matching an exclude pattern, R CMD build foo now
      succeeds, omitting these, thus fixing PR#18186.  (Thanks to Ivan
      Krylov and others, notably Jenny Bryan and R Dev Day @ useR! 2025
      contributors.)

    • strat_ratio != 1 in rfree1way did not work as advertised.

    • Zeros in the prob argument to power.free1way.test triggered an
      error and are now handled correctly.

    • Fix for PR#18874; "null" widths/heights in grid layouts are zero
      if widths/heights to allocate are zero. (Thanks to Maciej
      Nasinski and Trevor Davis.)

    • Fix for PR#19055; additional documentation for embedFonts().
      (Thanks to Chris Danek and Ivan Krylov.)

    • merge.data.frame now returns the correct column names when at
      least one of the merged data frames has zero rows and at least
      one of the merged data frames has only one column, fixing
      PR#18930. Thanks to David Molnar and Gabriel Becker.

    • trace() now works for functions whose S3 class attribute has more
      than one string, e.g., S7 generics and methods. Thanks to Hadley
      Wickham for the patch.

    • as(object, to) <- value no longer treats to as a class union when
      it was registered via setOldClass().

    • In methods, setOldClass(..., S4Class = ) no longer warns about
      undefined subclasses when the supplied S4 class inherits from a
      class union.

    • Fix for PR#19094; fill/stroke path based on text with col=NA.
      Thanks to Trevor Davis.

    • Fix for PR#18842; better documentation and warnings when specify
      inappropriate col to filled.contour().  Thanks to Darakhshan
      Nehal.

    • cor(*, method="kendall") and cov() now use the fast N*log(N)
      algorithm suggested in PR#18934 and offered by David Simcha on
      R-devel in 2010.  With thanks to the R Dev Day @ Nantes 2026
      contributors, notably Charles Bordet and Alexis Derumigny.

    • In nls, follow suggestion by Ben Bolker to reorder named vectors
      for lower and upper arguments to match names of the starting
      values (PR#18415). This has been extended so that you can now
      specify _only_ the parameters that you wish to constrain, and
      also so that it works when parameters are in the form of named
      lists.

    • summary(<aov>) for an almost perfect fit now warns analogously to
      summary(<lm>), using the same check.  Fixes fixes PR#18341 thanks
      to ‘R Dev Day @ useR! 2026’ participants Deepansh Khurana, Stefan
      Linner and Oscar de Leon.

    • Package methods provides a method for implicit generic function
      rcond with signature c(x="ANY", norm="missing") so that rcond(x)
      does not break after setGeneric("rcond").

    • rbinom()'s BTPE algorithm is fixed thanks to Kate Hudson's
      findings and report in PR#19049.  To ensure reproducibility,
      RNGkind() gets new argument binom.kind.

    • Fix segfault in postscript() and pdf() if set papersize option to
      very long string (PR#19108).  Thanks to Kevin Ushey.

    • Fix segfault in grid::gpar() if set fontfamily longer than 200
      characters (PR#19107).  Thanks to Kevin Ushey.

    • Fix cases where M and X matrices could be spanning the same
      subspace in mauchly.test(), anova.mlm, anova.mlmlist. (PR#16166,
      originally reported in 2015 by Florent Aubry, essentially
      analyzed Feb. 2020 just before the corona crisis, triaged 2026 by
      Michael Chirico)

Changes in R 4.6.1 patched:

  Bug Fixes:

    • In plain-text help (Rd2txt), paragraphs are again recognized even
      when started with a non-indented Rd comment, fixing a regression
      in R 4.4.0.

    • rhyper(N, m, n, k) now switches to the “large” scenario when m +
      n is larger than .Machine$integer.max, preventing integer
      overflow, thanks to Jonathan Blood's report on R-devel.

    • Fix long standing (Fortran compiler optimization related) bug in
      nlminb with constraints, thanks to Kasper Kristensen's PR#19086
      report and patch.

    • Fix for PR#19100: seq.int was not handling non-vector along.width
      arguments properly. Thanks to Mitchell O'Hara-Wild.

    • Wrapper objects make sure data pointers remain once obtained
      remain valid as long as a wrapper object is reachable. Reported
      by Ivan Krylov.

    • dummy.coef() becomes more robust to non-syntactic variable names,
      fixing PR#18468.  Thanks to Bill Dunlap and ‘R Dev Day’
      participants Vincent Arel-Bundock, Cynthia Huang, Tina Rozsos and
      Marina Marinelli.

    • Now PROTECT() in SubassignTypeFix, fixing PR#19110 thanks to
      Kevin Ushey.

    • writeChar() in a multibyte locale counts characters and bytes
      consistently and no longer overflows, thanks to Kevin Ushey's
      report and patch in PR#19112.

    • dim(a) <- vec now checks for too large prod(vec), thanks to Kevin
      Ushey's report and patch in PR#19109.

    • Tweaks (including to the parsers) for the C23 behaviour
      (preserving const) of strchr, strrchr and strstr.  (By Brian
      Ripley and Duncan Murdoch.)

    • make check-devel now works without recommended packages.

    • <matrix>[[i, j]] with negative i occasionally gives no error but
      accesses previous content; thanks to Kevin Ushey's report and
      very simple fix in PR#19116.

Changes in R 4.6.1:

  New Features:

    • The LaTeX class jss bundled in share/texmf/tex/latex/jss.cls has
      been updated to work with hyperref version 7.01q (2026/04/24).

    • Plain-text (and legacy HTML) conversion for a simple Rd \eqn{}
      now handles \geq, \leq, \neq and \ne in addition to \ge and \le
      (PR#19070).

  Bug Fixes:

    • abbreviate(<non-ASCII>) now works better, using iswlower() and
      *upper() to treat “wide” characters, thanks to Kevin's PR#19058.

    • cut(1:11, {}) now signals an error for the invalid breaks, fixing
      PR#19057, thanks to Kevin Ushey.

    • all(<symbol>) signals an error now, as some similar coercions;
      previously, the coercion of the symbol resulted in NULL
      internally, raised a warning, and could access illegal memory;
      thanks to Kevin Ushey's PR#19054.

    • stl() now checks its 3 x 3 tuning parameters on the R level;
      stl(*, s.window = 0) now “works” instead dumping core, stl(*,
      s.window = 1) “works” correctly, too.  Also, the summary() method
      mentions the robustness weights only if any robustness iterations
      happened.

      Further, stl() is now based on C code, translated from previous
      Fortran, triggered by a flang 22 compiler optimization bug (-O2).

    • The border case zapsmall(x, digits=Inf) where x contains an Inf
      entry no longer returns all NaN but rather x.  The improved help
      page now has more non-default examples.

    • wilcox.test(x, exact=FALSE, correct = k)'s p-value computation
      got a missing dnorm(z) factor, and so did the 2-sample case, in
      addition to more fixes.

    • The data part of getGenerics() listed package names for generic
      functions defined in more than one package.  Now it lists generic
      function names, as intended.  Thanks to Michael Chirico for
      report and patch proposal (PR#19080).

    • Overly long dyn.load() error messages (C level dlerror()), should
      no longer corrupt its state, thanks to Ivan Krylov's PR#19029
      report and patch.

    • as.matrix(<POSIXlt>) again produces a _numeric_ matrix, and the
      c() and subassignment methods for POSIXlt objects work correctly
      more often, e.g., without a "tzone" attribute, back porting a few
      of the PR#18989 fixes from R-devel, both thanks to Suharto
      Anggono.

    • In methods, as() now correctly coerces S4 objects to S4
      superclasses extending old-style classes, instead of returning
      only the S3 part.

Changes in R 4.6.0:

  Significant User-Visible Changes:

    • The R citation now provides a DOI (10.32614/R.manuals): please
      update your bibliographies accordingly.

    • The default C++ standard has been changed to C++20 where
      available (which it is on all known platforms from 2021 on): if
      not C++17 is used if available otherwise C++ is not supported (as
      before).

      (GCC 16 has also switched to C++20 as its default.)

      Packages can request C++17 if essential.

    • The Sweave driver Rtangle no longer puts empty lines at the end
      of tangled scripts.

  New Features:

    • The default AIC and BIC methods now check whether the methods
      namespace is loaded rather than stats4. They still use
      stats4::logLik (and stats4::nobs), but packages no longer need to
      load stats4 explicitly.

    • confint.default() now also works on S4 objects, as long as
      suitable coef() and vcov() methods exist.

    • binomial(identity) and quasibinomial(identity) now work without
      having to quote the argument.

    • str() now shows more via format() for external pointers.

    • terms(<formula>, specials = *) now treats non-syntactic specials
      more gracefully, thanks to Mikael Jagan's PR#18568.

    • help.start() gets a lib.loc option and its default for
      make.packages.html() is enhanced to allow, e.g., fast access to
      .Library when that contains only base and recommended packages.

    • In *.Rd help files, the \linkS4class macro now also works for
      links to other packages via \linkS4class[<pkg>]{<myClass>}, much
      nicer than the “workaround”
      \link[<pkg>:<myClass>-class]{<myClass>} necessary in earlier
      versions of R.

      Packages with the new syntax need to formally depend on R >=
      4.6.0.

    • tools::analyze_license() now also computes SPDX license
      identifiers, thanks to Thierry Onkelinx and LLuís Revilla.

    • read.dcf() now recognizes lines starting with # as comment lines.
      By Dirk Eddelbuettel, Laurent Gatto and Hugo Gruson.

    • tcltk::tclVersion() now only optionally includes the ‘patch
      level’, as Tcl full versions can be of the form 8.7a5 or 9.0b1
      without three clear components.

    • untar(tar = "internal") supports extras = "-P" to use unchanged
      the recorded file paths (as many external tar programs do).

    • extSoftVersion()[["zstd"]] now reports the version of the zstd
      compression library if available, thanks to Trevor Davis' patch
      proposal in PR#18914.

    • New logical option() quiet, defaulting to false, set to TRUE by
      R's command-line option --quiet (and similar), now can be
      switched during an R session.  Prompted by Dirk Eddelbuettel's
      proposal in PR#18913.

    • Credentials for basic HTTP authentication with download method
      "libcurl" can now be provided in a netrc file.  The path to the
      file can be specified in options("netrc").

    • tools::deparseLatex() gains a math argument, now used by the
      default bibstyle to format bibentry() fields with $...$ syntax
      via Rd \eqn markup.

    • gzcon() can now decompress a concatenation of compressed streams
      PR#18887.

    • Bibliographic citations and references in Rd files can now be
      auto-generated from bibentries in bibliographic databases in R or
      BibTeX formats.  See
      RShowDoc("R-exts#Bibliographic-citations-and-references") for
      more information.

    • Arguments to loadNamespace() which will be ignored because the
      namespace is already loaded are now noted.

    • chkDots()' optional argument allowed has been implemented thanks
      to Trevor Davis' proposal in PR#18936.

    • New function messageCondition() to create structured "message"
      objects analogous to warningCondition() and errorCondition()
      (PR#18940, by Trevor Davis).

    • wilcox.test() can now perform exact (conditional) inference in
      case of ties.  Based on contributions by Torsten Hothorn.

    • wilcox.test() can now optionally compute improved asymptotic
      p-values by including up to 3 correction terms of the Edgeworth
      series for the normal approximation.

    • barplot(.., orderH = *) for stacked bar plots allows to sort the
      stacks each according to size.

    • New argument panel.first for hist() (via plot.histogram()),
      barplot(), bxp(), and hence implicitly boxplot().  All except the
      former also gain a new panel.last.  Suggested by Marieke Stolte
      and Julian Welz.

    • plot.default() gets a new switch lim2 to indicate that the
      default xlim and ylim range computations only use _jointly_
      finite x- and y-values; indirectly suggested in PR#7986 by Jincai
      Jiang.

    • Rman.css, the stylesheet for the texi2any-generated HTML versions
      of the R manuals, was improved following joint efforts at the ‘R
      Dev Days’ of useR! 2024 and RSECon25.

    • New system Rd macro \manual{<name>}{<node>} to refer to a
      specific section _etc_ (possibly empty, for Top) of one of the R
      manuals (e.g., R-exts).

    • list.files() now has optional argument fixed to allow literal
      pattern matching.  Suggested and implemented by Duncan Murdoch in
      PR#18925.

    • substring(txt, i1, i2), substr(..) and their replacement versions
      now accept i2 = NULL to mean “to the end_of_string”, thus
      fulfilling Kevin Ushey (and others') suggestions in PR#18851.

    • The default method for pretty() gets a new switch bounds for
      completeness, corresponding to .pretty().  Also, it now catches
      typos such as eps.corrected = 2, noted in PR#18521 by Mikko
      Korpela.

    • Plain-text help now renders Rd \describe lists using line breaks
      after item labels.  Set tools::Rd2txt_options(descStyle=NULL) to
      get the old behaviour with a simple space; a "colon" variant is
      also available.

    • x %notin% table newly in base is an idiom for !(x %in% table) and
      provided almost entirely for convenience and code readability,
      from an R-devel suggestion, after many years of private
      definitions mostly hidden in packages, including in R's tools
      package.

    • The default method of sequence() gets a new option recycle to
      swap between current (not fully recycling) and future behaviour
      where all three of (nvec, from, by) are jointly recycled.

    • ftable()s default method and the as.table() method for "ftable"s
      get a perm argument with back compatible default.  The as.table()
      method also gets a named.dim = FALSE switch, no longer creating a
      named dim(<result>) by default.

    • match.arg() gets a new option several.ok = "all", fulfilling the
      wish of Jim Hester in PR#16659.

    • provideDimnames() gets new switch use.names, as proposed
      including patch by Mikael Jagan, in PR#18975.

    • The default summary() is more informative for character vectors,
      optionally resorting to the factor method via the new argument
      character.method = "factor", e.g., when summarizing a data frame
      (PR#16750).

      It also provides more useful summaries for complex vectors, with
      polar determining if polar or cartesian coordinates are more
      relevant; mostly based on a proposal by Mikael Jagan.

    • Error messages from failed Rd \Sexpr code now include the call
      from the original condition (if available).  Warning messages now
      include Rd source locations.

    • When the environment variable R_WARN_BOUNDS_OPT is set to "yes",
      options(warn = val) will check if val is inside -1:2; this may
      happen unconditionally in the future.

    • weighted.residuals() now returns weighted working residuals for
      "glm" objects. It used to return deviance residuals, but these do
      not give the one-step approximated dfbeta values, as pointed out
      by Ravi Varadhan. influence.glm() has been amended so that it now
      returns an object with both a "wt.res" and a "dev.res" element.

    • Several influence measures for "glm" objects have been updated to
      use Pearson residuals rather than deviance residuals (the latter
      are not unbiased) and to not use leave-one-out estimates of
      dispersion in models with fixed dispersion. Thanks to Ravi
      Varadhan for discussions and testing of these updates.

    • R now supports custom binary types which are of the form
      "<system>.binary.<build>" where <system> is lower-case name
      (letters only) of the system and <build> is the name of the build
      (alphanumeric and dashes). The corresponding paths returned by
      contrib.url (which govern the repository layout) with the above
      type= have the form bin/<system>/<build>/contrib/<x.y> where
      <x.y> is the R version without patch level. This is a
      generalisation of the binary types previously supported on macOS.
      In addition, binary packages can have the extensions .tar.bz2,
      .tar.xz, .tar.zst and .tar.zstd with the corresponding
      compression support.

    • The value of .Platform$pkgType which defines the native binary
      type for the current build of R can be overridden with
      R_PLATFORM_PKGTYPE environment variable (previously this was only
      set by the macOS builds of R). This should be typically only done
      by the author of a binary R distribution to define the type of
      binaries supported by that build of R.

    • If R uses custom binary type in its .Platform$pkgType then R CMD
      INSTALL --build will produce
      <package>_<ver>_R_<system>-<build>.tar.xz binary files. Please
      note that future versions may use .zstd compression by default so
      package tooling should support any of the above mentioned
      extensions.

    • New facilities have been introduced for package integrity
      verification and package signing. The optional file SHA256 in a
      package contains SHA-256 hashes, lengths and paths of files
      provided in the package allowing for more reliable integrity
      verification (relative to MD5). This file is now generated by
      default in R CMD INSTALL --build and optionally via R CMD build
      --sha256. A package can be signed by creating a detached GnuPG
      signature file SHA256.sig signing the entirety of the SHA256
      file. Upon installation, the signature is verified using GnuPG,
      thus ensuring the integrity of the SHA256 file and by induction
      all files in the package.  Both source and binary packages can be
      signed. Currently, this only applies to tar-based packages, and
      the command-line GnuPG gpg tool (or equivalent tool named in the
      GPG environment variable) has to be available for signing and
      verification to work. R CMD INSTALL --sign can be used to sign
      binary packages, including its use with --build.  System-wide
      GnuPG keyrings for the R installation can be placed in
      <R_HOME>/etc/keyrings as files with .gpg extensions and will be
      checked first before consulting user's GnuPG keyring (if
      present).

    • Experimentally, several math library (math.h) functions, such as
      exp(.), log1p(), sin(), atanh(), when called from R, are now
      ensured to give fully accurate results in a small neighbourhood
      of special values, such as exp(0) == 1, log1p(0) == 0, etc.  This
      makes R slightly less platform dependent for these functions,
      notably on platforms with less accurate system math libraries,
      see also
      <https://blog.r-project.org/2026/01/30/debugging-sensitivity-to-c-math-library-on-linux/>.

    • Function free1way() implementing semiparametrically efficient
      inference procedures (likelihood- and permutation-based) in
      distribution-free stratified K-sample one-way layouts was added
      to the stats package.  Approximate (via power.free1way.test())
      and simulation-based (utilising rfree1way() for random number
      generation) power-assessment and sample-size planning as well as
      model diagnostics (available from a plot method and
      probability-probability plots in ppplot()) complement the
      functionality.  Provided by Torsten Hothorn.

    • plot.data.frame() now supports a formula argument.

    • New Rd macro \linkS4methods{}, e.g., for easier linking to method
      docs in other packages, proposed and coded by Mikael Jagan in
      PR#18998.

    • Class "difftime" is now also among the S4 "OldClasses".

    • New function bitstring() as a user-friendly wrapper around
      intToBits(), etc.

    • plot.lm() now omits the smoother in the residuals vs leverage
      plot. This never made much sense, but if you really want it, you
      can force the old behaviour by setting panel.raw=panel.smooth.

    • hatvalues() now has a method for nls (nonlinear model) results,
      prompted by the proposal of Patrice Kiener and Heather Turner in
      PR#18897.

    • The Sweave driver RweaveLatex now allows the value of logical and
      numerical chunk options (only) to be the name of an object
      defined in earlier, evaluated code chunks. This is useful to pass
      computed values to options. For options set this way for weaving
      purposes, the Rtangle driver rather uses their default values,
      with a warning.  By Vincent Goulet.

    • The Sweave driver RweaveLatex gains an option to include
      unparsable R code or arbitrary text in code chunks. Chunks marked
      as ignore.on.weave = TRUE are completely ignored on weaving,
      i.e., not even parsed. The chunks however remain written out
      verbatim on tangling.

      Similarly, the driver Rtangle gains an option to control the
      extraction of code chunks. Chunks marked as ignore.on.tangle=TRUE
      are processed as usual on weaving, but left out of the tangled
      scripts (or thrown away when split=TRUE).

      The drivers also support the shorter aliases weave for
      !ignore.on.weave, and tangle for !ignore.on.tangle. A further
      option ignore, available for both drivers, sets ignore.on.weave
      and ignore.on.tangle at once.

      By Vincent Goulet.

    • The Sweave driver Rtangle now provides an option chunk.sep to
      control the separator between code chunks in tangled scripts
      (with an unchanged default of \n\n).  Using check.sep=FALSE omits
      the separator (between two chunks when used as a chunk option).
      By Vincent Goulet.

    • The Sweave driver Rtangle now provides an option extension to
      specify the extension, without the leading dot, for the file name
      of a tangled code chunk when splitting is selected (the option
      has no effect with split=FALSE). If TRUE, the default extension
      of Rtangle (usually .R) is used; if FALSE, no extension is added
      to the file name.  By Vincent Goulet.

    • New function SweaveGetSourceName in package utils to obtain the
      name of the file being woven by an Sweave process launched from
      the command line.  By Vincent Goulet.

  Graphics:

    • The graphics engine version, R_GE_version, has been bumped to 17
      and so packages that provide graphics devices should be
      reinstalled.

      The glyphFont() function gains a variations argument, which
      allows variable font axes to be specified, e.g., c(wght = 100).

      Only the quartz() device and Cairo-based graphics devices (but
      not cairo_pdf()) support variable font axes so far.

  Installation on a Unix-Alike:

    • configure appends bsdtar to the list of command names it tries
      when finding a default for TAR.

    • Failures in building the documentation for the base packages,
      including from parsing their Rd files, are no longer ignored by
      make docs.

    • Building the R manuals now requires Texinfo 6.8 or later.

    • A new LIBR_LDFLAGS defaulting to LDFLAGS allows more flexibility,
      e.g., for distributions such as Gentoo, Debian or Ubuntu, fixing
      PR#18992; additionally a make failure to create libR.pc should no
      longer be ignored, fixing PR#18993; both thanks to Benjamin
      Drung.

  Checking an Installation:

    • There is a new directory tests/C++Standards which contains small
      packages which can be test-installed to check support for various
      C++ standards.  This is principally for use on Windows as on a
      Unix-alike this partially duplicates tests done by configure —
      although it can also be used to test the behaviour of R CMD
      INSTALL on unsupported standards.

  Package Installation:

    • Specifying C++11 or C++14 in src/Makevars has long given a note:
      in 99% of CRAN packages the specification was unnecessary as the
      default C++17 sufficed (in a few cases with a deprecation warning
      from some compilers).

      Support for these standards has been removed: the default C++
      standard will be used.

      R CMD config variables CXX11, CXX14 and their associated
      CXXxxFLAGS, CXXxxPICFLAGS CXXxxSTD, SHLIBCXXxxLD and
      SHLIBCXXxxLDFLAGS variables are no longer supported and reported
      as ‘defunct’.

    • When installing binary packages the time stamp in the "Built"
      field is considered even if the package version is identical to
      allow binary package repositories to update binaries without the
      need to increase the package version.

    • The "Built" column returned by installed.packages() and
      old.packages() now contains the full value of the "Built" entry
      from the (installed) DESCRIPTION file. Previously, only the R
      version from the "Built" entry was returned.

    • If the timestamp passed as --built-timestamp to R CMD INSTALL is
      in RFC-2822 form (with time-zone offset) it will be converted to
      ISO UTC form to conform to the format used by R for purposes
      described above. (PR#19037, thanks to Dirk Eddelbuettel)

  C-Level Facilities:

    • New functions GEcreateDD() and GEfreeDD() for allocating (and
      initialising) DevDesc structures.  Can be used by external
      graphics devices.  Satisfies PR#18292.

    • New function R_eval_with_gd() designed to “lock” a graphics
      device during call to eval() within device drawing routines.
      External _on-screen_ graphics devices should consider using this
      function to avoid crashes from the device being closed by the
      user (e.g., a mouse click) during drawing.

    • Declarations for non-API functions LOGICAL0, INTEGER0, REAL0,
      COMPLEX0, and RAW0 have been removed from installed header files.

    • Non-API entry points Rf_acopy_string and Rf_lazy_duplicate have
      been added to those reported by R CMD check.

    • Packages using the non-API functions ATTRIB and SET_ATTRIB will
      now receive check NOTEs.  See ‘Writing R Extensions’ for
      alternatives to use.

    • R CMD check NOTEs on the use of these non-API entry points have
      been upgraded to WARNINGs in preparation for removing
      declarations and, where possible, hiding these entry points:
      R_nchar, R_tryWrap, Rf_GetOption, R_lsInternal, BODY, FORMALS,
      CLOENV, SET_TYPEOF, STRING_PTR, R_duplicate_attr, getConnection,
      R_data_class, STRING_PTR, SET_OBJECT, ATTRIB, SET_ATTRIB,
      Rf_findVarInFrame3.

    • The deprecated macros CHARACTER_DATA and CHARACTER_POINTER now
      return const pointers since using writable pointers in packages
      is not safe.

    • New function DATAPTR_RW() for use in implementing ALTREP Dataptr
      methods. This function should not be used in any other contexts.

    • New function R_class() as the C equivalent of class() in R.

    • New function Rf_isScalarString.

    • The R_ObjectTable type definitions formerly in R_ext/Callbacks.h
      are now available in the new header file R_ext/ObjectTable.h.
      This new header file should be used in packages instead of
      R_ext/Callbacks.h.

    • Task callback support declared in R_ext/Callbacks.h has been
      enabled again. It was disabled for R 4.5.0.

    • The non-API header file R_ext/PrtUtil.h is no longer copied to
      the installed include directory.

    • New function R_mapAttrib for iterating over the attributes of an
      object.

    • New functions R_altrep_class_name and R_altrep_class_package for
      retrieving the class name symbol and package name symbol of an
      ALTREP object. These should be used instead of ALTREP_CLASS.

    • New function R_getAttributes returns the same result as the R
      function attributes. New functions R_getAttribCount,
      R_getAttribNames, R_hasAttrib, R_nrow, and R_ncol.

    • The function Rf_isFrame has been removed; use Rf_isDataFrame
      instead.

    • The function VECTOR_PTR has been removed.

      The non-API function DATAPTR is no longer declared in an
      installed header file.

    • These entry points are now marked as hidden and no longer have
      declarations in installed header files: ENVFLAGS, EXTPTR_PROT,
      FRAME, ENCLOS, EXTPTR_PTR, EXTPTR_TAG, HASHTAB, IS_S4_OBJECT,
      LEVELS, NAMED, OBJECT, R_shallow_duplicate_attr,
      Rf_isValidString, Rf_lazy_duplicate, Rf_NonNullStringMatch,
      SETLENGTH, SETLEVELS, SET_BODY, SET_CLOENV, SET_ENCLOS,
      SET_FORMALS, SET_ENVFLAGS, SET_FRAME, SET_GROWABLE_BIT,
      SET_HASHTAB, SET_NAMED, SET_S4_OBJECT, SET_TRUELENGTH,
      STDVEC_DATAPTR, TRUELENGTH, UNSET_S4_OBJECT, XTRUELENGTH.

    • New experimental API for working with variable bindings in
      environments. The function R_GetBindingType identifies the
      binding type without forcing a delayed or active binding.  New
      bindings care created by R_MakeDelayedBinding,
      R_MakeForcedBinding and R_MakeMissingBinding.  Delayed and forced
      bindings can be inspected with R_ForcedBindingExpression,
      R_DelayedBindingExpression, and R_DelayedBindingEnvironment.
      Bindings for ... in function call environments can be examined
      with R_findDotsEnv, R_DotsExist, R_DotsLength, R_DotsNames,
      R_DotsElt, R_GetDotType, R_DotDelayedExpression,
      R_DotDelayedEnvironment, and R_DotForcedExpression. Contributed
      by Lionel Henry, Davis Vaughan, and Charlie Gao in PR#18928.

    • New function R_envSymbols returns a vector of the symbols for
      which an environment contains bindings (PR#18928).

    • R CMD check NOTEs on the use of the non-API entry points PRCODE,
      SET_PRCODE, PRENV, SET_PRENV, PRVALUE, SET_PRVALUE,
      R_PromiseExpr, and Rf_allocSExp have been upgraded to WARNINGs in
      preparation for removing declarations and, where possible, hiding
      these entry points.

    • New functions R_getVar and R_getVarEx. In most cases these can be
      used instead of the non-API functions Rf_findVar and
      Rf_findVarInFrame.  Other cases can be handled by the new API for
      working with variable bindings.

    • Packages using any non-API variables will now receive check
      NOTEs.

    • New function R_getRegisteredNamespace finds and returns the
      namespace environment registered for a name, or R_NilValue if
      none is found.

  Utilities:

    • R CMD check now reports further clang warnings including
      -Wkeyword-macro.  This is most commonly seen for the C23 keywords
      bool, true and false, but is also seen for nullptr (C23 and
      C++11). Masking these by macros _may_ generate correct code (but
      not always) and always results in confusing-to-read code.

    • The cascaded stylesheet R.css now adds less vertical white space
      when rendering Rd files' \itemize, \enumerate, and \describe list
      \items to HTML.

      Where R is used via extensive IDEs such as RStudio, their
      maintainers may need to adapt R.css files accordingly.

    • R CMD check when passed a tarball looks at its contents and so no
      longer derives the package name from the tarball name (which can
      now be arbitrary).

    • Package README.md files are now installed and featured in HTML
      help.

    • package.skeleton() now invisibly returns the path of the created
      directory, similar to prompt() et al., and allows creating blank
      skeletons without any R objects.

  Deprecated and Defunct:

    • structure(NULL, <name> = <val>) is now defunct.

    • Three tk*.slaves() functions were deprecated in favor of
      tk*.child() which do need Tcl/Tk version 8.6 or higher.

  Bug Fixes:

    • chol(x, pivot=TRUE) now zeroes the trailing submatrix when the
      algorithm stops early. Following the help page instructions on
      how to reconstruct the matrix in positive semidefinite cases gave
      incorrect results if the rank was 2 or more less than the
      dimension (PR#15853).

    • Profiling "mle" objects (stats4 package) could fail because
      profile MLE used starting value from full MLE. Now starts from
      profile MLE from previous step.

    • Setting attributes on primitive functions is now an error;
      previously it modified without copying (as noticed by Henrik
      Bengtsson on the R-devel mailing list).

      Relatedly, changing the environment() of a primitive function
      does no longer happen and gives a warning (to become an error,
      later).

    • Dataset LifeCycleSavings had a misspelled row name: "Guatamala"
      was corrected to "Guatemala".

    • The Pair(x,y) construction in the formula interface to paired
      tests did not work with the subset argument, due to the absence
      of a [.Pair method, which has now been added (PR#18898).

    • Subsetting "table" objects keeps S3 classes more consistently,
      fixing PR#18845.

    • When browser() is active or when otherwise debugging, R code such
      as if(TRUE) no longer triggers a new browser level, fixing
      PR#18885 (differently than the fix for PR#15770), with thanks to
      Ivan Krylov.

    • text() now truncates labels to maximum length of x and y (if it
      is longer), fixing PR#7084.  Thanks to Heather Turner, Ella Kaye,
      and Philippe Grosjean.

    • <Date> %in% set is again as fast as it was before R 4.3.0, _via_
      a new S3 method mtfrm.Date.

      <character> %in% <Date> and vice versa are now documented to work
      in concordance with == and as an exception to the typical match()
      behaviour which relies on “univariate” mtfrm() alone.

    • It is now possible to convert _to_ "snpc" units via, e.g.,
      grid::convertWidth(), fixing PR#18915. Thanks to Trevor Davis.

    • The precip dataset had typos in the names "Bismarck" and
      "Pittsburgh" (PR#18895).

    • tools::checkReplaceFuns() now deals better with replacement
      methods _not_ available as regular functions in the namespace.

    • length(xpr) <- n now also works for expression vectors, the same
      as for lists, i.e., padding with NULL entries if the length is
      increased.  Thanks to Mikael Jagan's PR#18917.

    • <complex>[i] <- NA now only sets the _real_ part to NA,
      consistently with the as.complex(NA) behaviour since R 4.4.0;
      thanks to Mikael Jagan's PR#18918.

    • format(<list>) calling format.default() now calls generic
      format() on each list element (rather than format.default()).

    • tools::Rd2HTML() detects paragraphs in more cases of
      \Sexpr-generated Rd code, fixing a regression in R 3.6.0
      originally reported by Georgi Boshnakov and later also in
      PR#18470.  An inactive #ifdef block no longer breaks the
      paragraph.

    • Parsing a multi-line string from Rd \Sexpr code no longer doubles
      the newlines.

    • requireNamespace(.., versionCheck = *) now shows an error and
      returns FALSE when the package version check is not fulfilled,
      thanks to Iris Simmons and Trevor Davis's PR#18255.
      Additionally, the versionCheck argument is checked and when
      invalid, an error is signalled to avoid subsequent confusing
      error messages.

    • requireNamespace() now throws an error even if the name space is
      already loaded if it is called with an unmatched argument such as
      quitely = TRUE or quiet = TRUE (argument quietly cannot be
      abbreviated as it follows ...).

    • rep() signals more specific error messages, notably when using
      both times and each optional arguments.  Fixes PR#18926, thanks
      to Ella Kaye and collaborators at useR! 2025's ‘R Dev Day’.

    • jitter(x, amount, factor) becomes more robust for non-finite x or
      also negative amount, factor.  help(jitter) is easier to read,
      fixing PR#17279, thanks to its contributors.

    • Plain-text help (Rd2txt) lacked markup for \cited titles, which
      are now wrapped in single quotes.

    • Default column labels are now correctly aligned when printing a
      matrix with right alignment (PR#18943, thanks to Mikael Jagan).

    • poly(fct, n) signals an error again, for a non-ordered factor
      fct, thanks to Roland Fuss' notice on R-devel.

    • terms(<formula>, simplify=TRUE) now works correctly also in the
      cases where the formula has more than one term with NAs such as
      f(u, b=NA) or g(NA), finally fixing PR#15275 thanks to Mikael
      Jagan's patch.

    • The help page example(matplot) now correctly labels Sepal vs
      Petal dimensions in its first iris data plot, thanks to Jeff
      Dick's post on R-devel.

    • diff(m, lag, dif) for matrix m now still returns matrices, also
      when lag * dif > nrow(m) (PR#18972, thanks to Mikael Jagan and
      Suharto Anggono).  diff(<ts-matrix>) remains matrix, even when it
      has length zero.

    • Values returned by active binding functions are now marked as not
      mutable to prevent unintended mutation in complex assignment
      operations.

    • The default method of sequence() now allows to fully recycle all
      three of (nvec, from, by) as always documented; with thanks to
      Mikael Jagan's report and patch in PR#18304.  Its behaviour
      remains back compatible for now, but can be switched to future
      behaviour via environment variable R_sequence_recycle, or
      explicit recycle = TRUE.

    • Subassignment, x[ind] <- val, to 1-dimensional arrays no longer
      “drops” them to simple vectors when ind is a name, fixing
      PR#18973, reported by Thomas Soeiro.

    • The implicitGeneric definition for toeplitz() produced a default
      method that failed when toeplitz(x, r) was called with more than
      the first argument.  Simple fix from Mikael Jagan.

    • The error message for array(dim = c()) now uses "'dim'", thanks
      to Hugo Gruson.

    • Some legal but strange nested complex assignments are handled a
      bit more robustly in interpreted code.

    • cacheMetaData() does not to mangle primitive generics.

    • The S4 method norm(<ANY>, type = <missing>) for the implicit
      generic norm() now uses type = "O" as has been the intention for
      more than ten years, fixing PR#18979 thanks to Mikael Jagan.

    • On Windows terminals Ctrl-C now breaks out of waiting for
      keyboard input, fixing PR#18982.

    • The default summary() and its factor method now label missing
      values NAs rather than NA's, fixing a decades-old grammatical
      faux pas inherited from S (PR#16348 and PR#18948).

    • Asymmetric toeplitz(x, r) is type consistent now, even when r of
      length 0 or 1 is not used directly.  Fixes PR#18996, thanks to
      Mikael Jagan's patch and test.

    • format(r) now keeps names(r) also for raw objects r.

    • rep.int() and rep_len() again drop names also for factors, fixing
      a regression in R 4.0.0.  (Thanks to a report by Rui Barradas and
      PR#18999 by Suharto Anggono.)

    • str(x) with a list-like x of a class having an str() S3 method
      using NextMethod(), now no longer outputs "List of <...>" in the
      default method, thanks to Ian Farm's report and fix proposal in
      PR#19001.

    • as.POSIXlt(ch), as.Date(ch) etc now also work correctly when ch
      contains "Inf", via strptime(.), fixing PR#19006.

    • c(<POSIXlt>, ..) now fully preserves sub-second accuracy,
      fulfilling a part of Suharto Anggono's wishlist PR#18989.

    • When subassigning "POSIXlt", e.g., <dat>[i] <- v, v is now
      converted to the time zone of dat, before being assigned, see
      PR#18919.

    • The "tzone" attribute of "POSIXlt" objects should no longer
      depend on earlier calls, fixing PR#19005 thanks to Ivan Krylov, a
      patch by Suharto Anggono and reports of “Non-deterministic
      POSIXlt tzone in Europe/London ..” on R-devel.

    • In intervals with very low density cdplot() was unreliable,
      returning probabilities that are greater than one or NaN
      (PR#19011).  Fix from Christoph Dalitz and Achim Zeileis.

    • R CMD build now installs packages providing their own vignette
      engine (PR#18191).  Patch by Paul Smith.

    • ar.burg(), ar.yw() and ar.ols() deal better with non finite AIC
      values thanks to Simone Giannerini's remarks on R-devel.

    • Parsing deeply nested expressions no longer should segfault in
      certain circumstances, fixing five different checks on context
      stack size, thanks to Kevin Ushey's report and Michael Chirico's
      patch in PR#18994.

    • The internal cwilcox function used in computations for the
      Wilcoxon distribution is now based on an implementation of a
      formula by Andreas Löffler provided by Andreas Löffler, Aidan
      Lakshman, and Ivan Krylov, substantially reducing the memory
      complexity of the original implementation (PR#18655).

    • When Ops group methods for matrix-"ts" return a zero-extent
      matrix, its type is correct now.  E.g., <int> + <dbl> now returns
      type "double", see also PR#18972.

    • intToUtf8(<negative>) now returns NA and no longer accesses
      invalid memory, thanks to Kevin Ushey's report with patch in
      PR#19052.

    • When file.choose() is terminated with an EOF, it now signals an
      error rather than returning garbage, thanks to Kevin Ushey's
      report and patch in PR#19053,

Changes in R 4.5.3:

  Utilities:

    • tools/fetch-recommended can be used instead of
      tools/rsync-recommended to fetch recommended packages into R
      sources using curl on systems without rsync or behind firewalls.

  Package Installation:

    • C++ standard specifications (CXX_STD = in src/Makevars* and in
      the SystemRequirements field of the DESCRIPTION file) are now
      checked more thoroughly.  Invalid values are still ignored but
      now give a warning, as do contradictory specifications.

    • (Preliminary) support for C++26 has been extended to Windows.

    • A non-zero exit status from cleanup, cleanup.win or cleanup.ucrt,
      if requested via options --clean or --preclean, is now reported
      with a warning.

  Bug Fixes:

    • all.equal(obj, simple, check.class=FALSE) now is true, also when
      simple is a bare atomic vector and obj has a simple class, fixing
      the first part of PR#18971 thanks to Jan Gorecki.

    • str(x, give.attr=FALSE) no longer shows attributes when x is a
      zero length "Date" or "POSIXt" object.

    • Tweaks to binning for bw.SJ() and bw.ucv() in the very rare case
      of data which have an extremely small range compared to their
      absolute values, e.g., x <- 6e9 + 6:9.

    • Formatting book-type bibentry objects now converts LaTeX accents
      also in the publisher and series fields.

    • model.frame(~1, list(), na.action=na.pass) and similar
      “border-line” uses no longer produce invalid data frames, fixing
      PR#18977, reported with patch by Mikael Jagan.

    • length(<POSIXlt>) <- v is more careful about balancing, notably
      when v is not integer, thanks to Suharto Anggono's remarks on the
      mailing list R-devel.

    • approx(<x_with_ties>, <y_with_NA>, na.rm = FALSE) now should
      always call the ties() function, fixing PR#17604 reported by Bill
      Dunlap.

    • besselJ(1, 1e-15) and similar now give correct results, thanks to
      Leo Mada and other “R-help”ers.

    • vignette(<pkg>::<topic>) is now a documented usage variant and
      confines vignette retrieval to the specified package.

    • pretty(ch) again correctly works with ch a character vector of
      numbers.

    • persp() labels the three axes correctly also when C level
      atan2pi() is available, fixing PR#19007 by Klaus Schliep.

    • Large (tall) subscripts in plotmath expressions are now
      positioned correctly.  They were being positioned too high.

    • Ops group (Arith, Compare, ...) methods for matrix-"ts" now do
      return (zero length) matrices even when the two series do not
      overlap; a very partial fix of PR#18972, which is to be fully
      addressed later.

Changes in R 4.5.2:

  Utilities:

    • R CMD check now handles archives with extension .tar or .tar.zstd
      (where zstd compression is supported by the R build).

  Bug Fixes:

    • t.test(c(1:3, Inf)) and similar no longer produce an error but
      return a (still not so useful) "htest" result, fixing PR#18901,
      thanks to Jesse Alderliesten.

    • attr(., "tsp") <- val now uses getOption("ts.eps") instead of
      hardwired 1e-5; consequently, ts(.., ts.eps=*) now passes ts.eps
      to the "tsp" setting C code; both fixing a long-standing ‘FIXME’.

    • insertSource() now ignores the internal .packageName object,
      avoiding a superfluous message.

    • In static HTML help, links to vignette files from the default
      doc/index.html page now also work for packages not installed in
      the default .Library, thanks to a report by Patrice Kiener.

    • fixInNamespace("<S3method>") failed to update the S3 methods
      table when the generic was not on the search path.

    • In plain-text help (Rd2txt), an initial newline from an Rd inline
      \eqn no longer breaks the paragraph.

    • hist(*, log = "x") now works without a warning, thanks to Martin
      Smith's PR#18921.

    • Subassigning "POSIXlt", i.e., <tdat>[i] <- val and <tdat>[[i]] <-
      val now rebalance as they should; thanks mostly to Mikael Jagan's
      PR#18919.

    • <POSIXlt>[*] (re-)setting "balanced", fixing PR#18681 comment #7,
      thanks to Mikael Jagan.

    • All four of {col,row}{Sums,Means}(Z, na.rm=TRUE) now correctly
      work with complex Z where is.na(Re(Z)) differs from is.na(Im(Z)),
      fixing PR#18942, unearthed by Dirk Eddelbuettel.

    • Fix for glyph rendering on the quartz() device when there is
      other (“normal”) text drawn on the device.  The problem was that
      the text transformation matrix was not reset so glyphs would be
      rendered incorrectly (often completely outside the device, i.e.,
      not visible).

    • Functions install.packages() and download.packages() again
      consult option download.file.method when the download method is
      unspecified.

    • Tanguy Barthelemy and colleagues at the ‘R Dev Day’ following
      Rencontres R in May 2025 extended the help page of lm(), fixing
      PR#18058.  As suggested by Thomas Soeiro, such notes were also
      added to the glm(), poly() and splines::bs() and ns() pages.

    • lbeta(1i, 1) now signals an error, as lbeta() is not implemented
      for complex, fixing PR#18946 from Ben Bolker and Kasper
      Kristensen.

    • The Cairo-based SVG device uses pt as the default document unit
      also with Cairo >= 1.17.8 (PR#18912).

    • pretty(*, eps.correct = 2) has been fixed, e.g., to avoid over 1
      million length result for pretty(c(0, 1e-322), eps.correct = 2).

    • When "POSIXlt" date-time objects are NA-padded from subsetting or
      increasing length in the `[` or `length<-` methods, the
      "balanced" attribute is set to NA, now; noted in PR#18681, thanks
      to Mikael Jagan.

Changes in R 4.5.1:

  New Features:

    • The internal method of unzip() now follows unzip 6.00 in how it
      handles extracted file paths which contain "../".  With thanks to
      Ivan Krylov.

  Installation:

    • Standalone nmath can be built with early-2025 versions of
      clang-based compilers such as LLVM clang 20, Apple clang 17 and
      Intel icx 2025.0.

    • Tcl/Tk 9 can be used to build package tcltk: this has become the
      default in some Linux distributions.

  Bug Fixes:

    • Java detection in javareconf could not detect libjvm.* in the
      zero variant of the JDK (PR#18884).  All valid variants as of JDK
      24u are now supported.

    • factanal(.., rotation=*) now correctly updates rotmat, fixing
      PR#18886.

    • dnbinom(<large>, <muchlarger>, ..) now is 0 correctly, instead of
      NaN or Inf sometimes.

    • dbinom(<large>, n=Inf, ..) is 0 now correctly, instead of NaN
      which also fixes many dnbinom() cases, notably those mentioned in
      PR#16727 comment #5.

    • Fixing C level “binomial deviance” bd0() for extreme arguments
      (preventing under-/overflow) solves more PR#16727 cases and also
      prevents some full accuracy loss in such cases for dbinom(),
      dnbinom(), and via dbinom_raw() potentially dgeom(), dhyper(),
      dbeta(), and df().

    • signif(1.**e308, digits) no longer truncates unnecessarily (but
      still to prevent overflow to Inf), fixing PR#18889.

    • prettyNum(*, zero.print={>=1-char}, replace.zero=TRUE) now works
      as documented, thanks to Marttila Mikko and Ivan Krylov's
      messages on R-devel.

    • pbeta(x, a,b, ..) for very large a,b no longer returns NaN but
      the correct values (0 or 1, or their logs for log.p = TRUE).
      This improves Mathlib's C level bratio() and hence also
      pnbinom(), etc..

Changes in R 4.5.0:

  New Features:

    • as.integer(rl) and hence as.raw(rl) now work for a list of raw(1)
      elements, as proposed by Michael Chirico's PR#18696.

    • graphics' grid() gains optional argument nintLog.

    • New functions check_package_urls() and check_package_dois() in
      package tools for checking URLs and DOIs in package sources.

    • New head() and tail() methods for class "ts" time series,
      proposed by Spencer Graves on R-devel.

    • New qr.influence() function, a “bare bones” interface to the
      lm.influence() leave-one-out diagnostics computations; wished for
      in PR#18739.

    • Package citation() results auto-generated from the package
      metadata now also provide package DOIs for CRAN and Bioconductor
      packages.

    • New function grepv() identical to grep() except for the default
      value = TRUE.

    • methods(<pkg>:::<genfun>) now does report methods when neither
      the generic nor the methods have been exported.

    • pdf() gains an author argument to set the corresponding metadata
      field, and logical arguments timestamp and producer to optionally
      omit the respective metadata.  (Thanks to Edzer Pebesma.)

    • grDevices::glyphInfo() gains a rot argument to allow per-glyph
      rotation.  (Thanks to Daniel Sabanes Bove.)

    • Package tools now exports functions CRAN_current_db(),
      CRAN_aliases_db(), CRAN_rdxrefs_db(), CRAN_archive_db(), and
      CRAN_authors_db().

    • Package tools now exports functions R() and
      parse_URI_reference().

    • Package tools now exports functions base_aliases_db() and
      base_rdxrefs_db().

    • It is now possible to set the background color for row and column
      names in the data editor on Windows (Rgui).

    • Rterm on Windows now accepts input lines of unlimited length.

    • file.info() on Windows now provides file owner name and domain.

    • Sys.info() on Windows now provides current user domain.

    • findInterval() gets new arguments checkSorted and checkNA which
      allow skipping relatively costly checks; related to PR#16567.

    • pnorm(x) underflows more gracefully.

    • get(nam, env) now signals a _classed_ error, "getMissingError",
      as “subclass” of "missingArgError" where the latter is used also
      in similar situations, e.g., f <- function(x) exp(x); try(f()) .

    • The set operations now avoid the as.vector() transformation for
      same-kind apparently vector-like operands.

    • md5sum() can be used to compute an MD5 hash of a raw vector of
      bytes by using the bytes= argument instead of files=. The two
      arguments are mutually exclusive.

    • Added function sha256sum() in package tools analogous to md5sum()
      implementing the SHA-256 hashing algorithm.

    • The xtfrm() method for class "AsIs" is now considerably faster
      thanks to a patch provided by Ivan Krylov.

    • The merge() method for data frames will no longer convert row
      names used for indexing using I(), which will lead to faster
      execution in cases where sort = TRUE and all.x and/or all.y are
      set to TRUE.

    • The methods package internal function .requirePackage() now calls
      requireNamespace(p) instead of require(p), hence no longer adding
      packages to the search() path in cases methods or class
      definitions are needed.  Consequently, previous workflows relying
      on the old behaviour will have to be amended by adding
      corresponding library(p) calls.

    • More R-level messages use a common format containing "character
      string" for more consistency and less translation work.

    • available.packages() and install.packages() get an optional
      switch cache_user_dir, somewhat experimentally.

    • The sunspot.month data have been updated to Oct 2024; because of
      recalibration also historical numbers are changed, and we keep
      the previous data as sunspot.m2014 for reproducibility.

    • The quartz() device now supports alpha masks.  Thanks to George
      Stagg, Gwynn Gebeyhu, Heather Turner, and Tomek Gieorgijewski.

    • The print() method for date-time objects (POSIX.t) gets an
      optional digits argument for _fractional_ seconds, passed to
      improved format.POSIXlt(); consequently, print(<date.time>,
      digits = n) allows to print fractions of seconds.

    • install.packages() and download.packages() download packages
      simultaneously using libcurl, significantly reducing download
      times when installing or downloading multiple packages.

    • Status reporting in download.file() has been extended to report
      the outcome for individual files in simultaneous downloads.

    • The Rd \link macro now allows markup in the link text when the
      topic is given by the optional argument, e.g.,
      \link[=gamma]{\eqn{\Gamma(x)}}.

    • If La_library() is empty, sessionInfo() still reports
      La_version() when available.

    • seq.int(from, to, by, ....) when |by| = 1 now behaves as if by
      was omitted, and hence returns from:to, possibly integer.

    • seq.Date(from, to, by, ....) and seq.POSIXt(..)  now also work
      when from is missing and sufficient further arguments are
      provided, thanks to Michael Chirico's report, patch proposal in
      PR#17672 and ‘R Dev Day’ contributions.

      The Date method also works for seq(from, to), when by is missing
      and now defaults to "1 days".

      It is now documented (and tested) that the by string may be
      _abbreviated_ in both seq methods.

      Both methods return or keep internal type "integer" more
      consistently now.  Also, as.POSIXct({}) is internally integer.

    • duplicated(), unique(), and anyDuplicated() now also work for
      class expression vectors.

    • New function use() to use packages in R scripts with full control
      over what gets added to the search path.  (Actually already
      available since R 4.4.0.)

    • New connection type zstdfile for files compressed by zstd if R
      was built with such support.  file() and gzfile() can
      automagically read such files.

    • memCompress() and memDecompress() have options to use zstd
      compression if R was built with support for it.

    • There is some support for zstd compression of tarballs in tar()
      and untar().  (This depends on OS support of libzstd or by tar.)

    • print(summary(<numbers>)) gets new optional argument zdigits to
      allow more flexible and consistent (double) rounding.  The
      current default zdigits = 4L is somewhat experimental.
      Specifying both digits = *, zdigits = * allows behaviour
      independent of the global digits option.

    • The format() method for "difftime" objects gets a new back
      compatible option with.units.

    • A summary() method for "difftime" objects which prints nicely,
      similar to those for "Date" and "POSIXct".

    • unique()'s default method now also deals with "difftime" objects.

    • optimize(f, *) when f(x) is not finite says more about the value
      in its warning message.  It no longer replaces -Inf by the
      largest _positive_ finite number.

    • The documentation of gamma() and is.numeric() is more specific,
      thanks to the contributors of PR#18677.

    • New dataset gait thanks to Heather Turner and Ella Kaye, used in
      examples.

    • New datasets penguins and penguins_raw thanks to Ella Kaye,
      Heather Turner, and Kristen Gorman.

    • isSymmetric(<matrix>) gains a new option trans = "C"; when set to
      non-default, it tests for “simple” symmetry of complex matrices.

    • model.frame() produces more informative error messages in some
      cases when variables in the formula are not found, thanks to Ben
      Bolker's PR#18860.

    • selectMethod(f, ..) now keeps the function name if the function
      belongs to a group generic and the method is for the generic.

  BLAS and LAPACK:

    • The bundled BLAS and LAPACK sources have been updated to those
      shipped as part of January 2025's LAPACK 3.12.1.

    • It is intended that this will be the last update to BLAS and
      LAPACK in the R sources.  Those building R from source are
      encouraged to use external BLAS and LAPACK and this will be
      required in future.

    • This update was mainly bug fixes but contained a barely
      documented major change.  The set of BLAS routines had been
      unchanged since 1988, so throughout R's history.  This update
      introduced new BLAS routines dgemmtr and zgemmtr which are now
      used by LAPACK routines.  This means that BLAS implementations
      are no longer interchangeable.

    • To work around this, R can be configured with option
      --with-2025blas which arranges for the 2025 BLAS additions to be
      compiled into libRlapack (the internal LAPACK, not built if an
      external LAPACK is used).

      This option allows the continuation of the practice of swapping
      the BLAS in use by symlinking lib/libRblas.*.  It has the
      disadvantage of using the reference BLAS version of the 2025
      routines whereas an enhanced BLAS might have an optimized version
      (OpenBLAS does as from version 0.3.29).

    • Windows builds currently use the internal LAPACK and by default
      the internal BLAS: notes on how to swap the latter _via_
      Rblas.dll are in file src/extra/blas/Makefile.win.

  Installation on a Unix-Alike:

    • A C23 compiler (if available) is now selected by default for
      compilation of R and packages.  R builds can opt out _via_ the
      configure flag --without-C23, unless the specified or default
      (usually gcc) compiler defaults to C23: gcc 15 does.

      A C23 compiler is known to be selected with gcc 13–15, LLVM clang
      18–20 (and 15 should), Apple clang 15–17 and Intel 2024.2–2025.0
      (and 2022.2 should).

      Current binary distributions on macOS use Apple clang 14 and so
      do not use C23.

    • The minimum autoconf requirement for a maintainer build has been
      increased to autoconf 2.72.

    • Building the HTML and Info versions of the R manuals now requires
      texi2any from Texinfo 6.1 or later.

    • Failures in building the manuals under doc now abort the
      installation, removing any file which caused the failure.

    • Control of symbol visibility is now supported on macOS (the
      previous check only worked on ELF platforms).

    • There is now support for installing the debug symbols for
      recommended packages on macOS: see REC_INSTALL_OPT in file
      config.site.

    • configure is now able to find an external libintl on macOS (the
      code from an older GNU gettext distribution failed to try linking
      with the macOS Core Foundation framework).

  Installation on Windows:

    • Both building R and installing packages use the C compiler in C23
      mode.

    • R on Windows by default uses pkg-config for linking against
      external libraries.  This makes it easier to test R and packages
      with alternative toolchains (such as from Msys2, e.g., testing
      with LLVM and possibly with sanitizers). It also allows more
      significant Rtools updates within a single R minor release.

    • The installer scripts for Windows have been tailored to Rtools45,
      an update of the Rtools44 toolchain.  It is based on GCC 14.  The
      experimental support for 64-bit ARM (aarch64) CPUs is based on
      LLVM 19.  R-devel and R 4.5.x are no longer maintained to be
      buildable using Rtools44 and it is advised to switch to Rtools45.

  Deprecated and Defunct:

    • is.R() is defunct.  Environment variable _R_DEPRECATED_IS_R_ no
      longer has any effect.

    • Deprecated (for more than 9 years!) functions linearizeMlist,
      listFromMlist, and showMlist and the "MethodsList" class for S4
      method handling were removed from package methods.  Deprecated
      functions balanceMethodsList, emptyMethodsList, insertMethod,
      makeMethodsList, mergeMethods, MethodsList, MethodsListSelect,
      and SignatureMethod were made defunct, as were the "MethodsList"
      branches of functions assignMethodsMetaData, finalDefaultMethod,
      and MethodAddCoerce.

    • getMethods(*, table = TRUE) is deprecated.

    • Building with the bundled (and old) version of libintl is
      deprecated and now gives a configure warning.  This should be
      selected only if neither the OS's libc (as on GNU Linux) nor an
      external libintl library provide suitable functions.

      Instead install libintl from a recent version of GNU gettext
      (available for macOS) or use configure option --disable-nls.

      The ability to use the bundled version may be removed as soon as
      R 4.5.1.

    • The deprecated xfig() graphics device has been removed.

  Package Installation:

    • Packages are now installed using C23 where supported by the OS
      and R build.

      Packages using R's compiler settings can ask *not* to use C23
      _via_ including USE_C17 in SystemRequirements or can be installed
      by R CMD INSTALL --use-C17.  (Some packages ignore these settings
      in their configure script or when compiling in sub-directories of
      src, as will those using a src/Makefile.)

    • Source installs now report the package version in the log.

    • There is preliminary support for C++26 with GCC >= 14, Apple
      clang++ >= 16 and LLVM clang++ >= 17.

  C-Level Facilities:

    • The non-API and hidden entry points Rf_setIVector, Rf_setRVector
      and Rf_setSVector have been removed.

    • The internal code for changing the parent of an environment now
      signals an error if the new parent is not an environment or if
      the change would create a cycle in the parent chain.

    • SET_TYPEOF now signals an error unless the old and new types have
      compatible memory structure and content. Use of SET_TYPE in
      package C code should be avoided and may be deprecated in the
      near future. It is better to allocate an object of the desired
      type in the first place.

    • The set of LAPACK (double and complex) routines declared in the
      headers R_ext/Lapack.h and R_ext/Applic.h has been extended,
      mostly to routines actually in use by packages.

    • Memory allocation messages now use the (non-SI notation) "Mb",
      "Gb" , ..., and "Mbytes" strings as _arguments_ instead of as
      part of the (translatable format) string.  This is one step for
      PR#18297; from Henrik Bengtsson.

    • Header R_ext/Constants.h (included by R.h) now always includes
      header float.h or cfloat for constants such as DBL_MAX.

    • Strict R headers are now the default.  This removes the legacy
      definitions of PI, Calloc, Realloc and Free: use M_PI, R_Calloc,
      R_Realloc or R_Free instead.

    • The deprecated and seemingly never-used S-compatibility macros
      F77_COM and F77_COMDECL have been removed from header R_ext/RS.h.

    • The enum Rboolean defined in header R_ext/Boolean.h now has a
      fixed underlying type of int on platforms whose C compiler
      supports this.

      This is a C23 feature (taken from C++11) and also supported in
      all C standards by some versions of clang (from LLVM and Apple)
      and (with a warning when using -pedantic) by GCC when in C17
      mode.

      A fair amount of code has assumed this: it may be changed to a
      smaller type in future.  In particular, as standard compilers do
      not check the validity of assignment to an enum, it has been
      possible to assign NA_INTEGER to an Rboolean variable, coerce it
      to int and recover the value.

      If there were a platform which used an underlying type of a
      different size this would be an ABI-breaking change (but we are
      unaware of any such platform).

    • Header R_ext/Boolean.h now ensures that a bool type is available
      either as a keyword (C23 and C++) or by including the C99 header
      stdbool.h.  This is being used internally in R to replace
      Rboolean by bool.

    • There are new functions asRboolean and asBool, variants of
      asLogical more suited to converting logical arguments to Rboolean
      or to bool. They require a length-one input and throw an error if
      that evaluates to NA.

    • Header R_exts/Error.h now ensures that Rf_error and similar are
      given a noreturn attribute when used from C++ under all
      compilers.

    • Header R_exts/Utils.h no longer contains a declaration for
      F77_SUB(interv).  This is intended to be called from Fortran and
      was wrongly declared: LOGICAL in Fortran corresponds to int * not
      Rboolean *.

    • Defining R_INCLUDE_BOOLEAN_H to 0 before including headers R.h or
      Rinternals.h (or any other header which includes R_ext/Boolean.h)
      stops the inclusion of header R_ext/Boolean.h which `defines'
      constants TRUE, FALSE, true, false and the type bool which some
      package maintainers wish to avoid.

      Note that the last three are keywords in C23 and C++11 so cannot
      be avoided entirely.  However, with commonly-used compilers they
      can be masked by a macro of the same name, often with a warning.

  C-Level API:

    • The ‘Writing R Extensions’ Texinfo source now contains very
      experimental annotations for more clearly identifying the API
      status of C entry points. These annotations are used to produce
      indices for API, experimental API, and embedded API entry points
      in the rendered versions.  This is very preliminary and may be
      dropped if a better approach emerges.

      Also for Fortran-callable entry points which are part of the API.

    • ‘Writing R Extensions’ has a new section ‘Moving into C API
      compliance’ to help package authors move away from using non-API
      endpoints. This section will continue to be updated as work on
      clarifying and tightening the C API continues.

    • New API function R_mkClosure. This checks that its arguments are
      valid and should be used instead of allocSExp(CLOSXP followed by
      SET_FORMALS, SET_BODY, and SET_CLOENV.

    • New API functions R_ClosureFormals, R_ClosureBody, and
      R_ClosureEnv for extracting closure components.  The existing
      functions R_ClosureExpr and R_BytecodeExpr have also been added
      to the API.

    • New API function R_ParentEnv corresponding to R's parent.env().

    • Further non-API entry points have been added to those reported by
      R CMD check: COMPLEX0, ddfind, DDVAL, ENSURE_NAMEDMAX, ENVFLAGS,
      FRAME, HASHTAB, INTERNAL, IS_ASCII, IS_UTF8, LEVELS, NAMED,
      PRSEEN, RDEBUG, REAL0, Rf_findVarInFrame3, SET_BODY, SET_CLOENV,
      SET_FORMALS, SET_PRSEEN, SET_RDEBUG, STRING_PTR, SYMVALUE, and
      VECTOR_PTR. Any declarations for these in public header files
      will be removed in the near future, and they will be hidden where
      possible.

    • Some R CMD check NOTEs on the use of non-API entry points have
      been upgraded to WARNINGs in preparation for removing
      declarations and, where possible, hiding these entry points.

    • Additional non-API entry points have been added to those reported
      by R CMD check: IS_LONG_VEC, PRCODE, PRENV, PRVALUE, R_nchar,
      Rf_NonNullStringMatch, R_shallow_duplicate_attr, Rf_StringBlank,
      SET_TYPEOF, TRUELENGTH, XLENGTH_EX, and XTRUELENGTH.

    • Enable defining R_NO_REMAP_RMATH and calling Rf_*() as has been
      documented in ‘Writing R Extensions’ for a while, fixing PR#18800
      thanks to Mikael Jagan and Suharto Anggono.

    • R_GetCurrentSrcref(skip) now skips calls rather than srcrefs,
      consistent with counting items in the traceback() display.  If
      skip == NA_INTEGER, it searches for the first srcref, starting at
      the current evaluation state and proceeding through the call
      stack; otherwise, it returns the srcref of the requested entry
      from the call stack.

  Utilities:

    • R CMD INSTALL (and hence check) now compile C++ code with
      -DR_NO_REMAP.

      ‘Writing R Extensions’ has been revised to describe the remapped
      entry points, for with the Rf_ prefix remains optional when used
      from C code (but is recommended for new C code).

    • R CMD check --as-cran notes bad parts in the DESCRIPTION file's
      URL fields.

    • R CMD check now reports more warnings on long-deprecated/obsolete
      Fortran features reported by gfortran -Wall.  For hints on how to
      modernize these, see
      <https://fortranwiki.org/fortran/show/Modernizing+Old+Fortran>.

    • Since almost all supported R versions now use UTF-8, R CMD check
      no longer by default reports on marked UTF-8 or Latin-1 strings
      in character data.  Set environment variable
      _R_CHECK_PACKAGE_DATASETS_SUPPRESS_NOTES_ to a false value for
      the previous behaviour.

    • tools::checkDocFiles() notes more cases of usage documentation
      without corresponding \alias.

    • R CMD check with a true value for environment variable
      _R_CHECK_BASHISMS_ checks more thoroughly, including for bash
      scripts and bashisms in components of autoconf-generated
      configure scripts.

    • R CMD check gains option --run-demo to check demo scripts
      analogously to tests.  This includes a check for undeclared
      package dependencies: it can also be enabled separately by
      setting the environment variable _R_CHECK_PACKAGES_USED_IN_DEMO_
      to a true value (as done by R CMD check --as-cran).

    • R CMD build now supports --compression=zstd on platforms with
      sufficient support for zstd.

    • tools::texi2pdf(..., texinputs=<paths>) now _pre_pends the
      specified <paths> to TEXINPUTS.  When building R itself
      (doc/NEWS.pdf and base vignettes) or package manuals using R CMD
      Rd2pdf, it is ensured that this R's Rd.sty takes precedence over
      any other (incompatible) versions in default “texmf trees”.

    • tools::Rd2latex() no longer outputs an \inputencoding{utf8} line
      by default; such a declaration is obsolete since LaTeX
      2018-04-01.

  Bug Fixes:

    • update_pkg_po() now copies .mo files to the translation package
      even if a DESCRIPTION file exists, thanks to Michael Chirico
      fixing PR#18694.

    • Auto-generated citation() entries no longer include (additional)
      URLs in the note field (PR#18547).

    • as.data.frame.list() gets a new option new.names and now
      preserves NA names, thus fixing the format() method for data
      frames, and also bug PR#18745.  Relatedly, the format() method
      gets an option cut.names.

    • stem() formats correctly also in cases where rounding up, e.g.,
      from 9.96 to 10 needs more digits; thanks to Ella Kaye and Kelly
      Bodwin, fixing PR#8934 during ‘R Dev Day’ at useR!2024.

      Additionally, stem(x) now works normally also when length(x) ==
      1.

    • tools' toTitleCase() now works better, fixing PR#18674, thanks to
      Shannon Pileggi, Sarah Zeller, Reiko Okamoto, and Hugo Gruson's
      ‘R Dev Day’ effort.

    • Printing matrices (typically with many rows and or columns) now
      also omits columns when desirable according to option max.print,
      or argument max, respectively.  This is primarily the work of
      Lorena Abad, Ekaterina Akimova, Hanne Oberman, Abhishek Ulayil,
      and Lionel Henry at the ‘R Dev Day’, thus fixing PR#15027.

    • Sys.setLanguage() now warns about _some_ failures to change the
      language.

    • Printing ls.str() now shows "<missing>" even when R's language
      setting is not English.

    • xyTable() now handles and reports NAs fixing PR#18654.  Thanks to
      Heather Turner and Zhian Kamvar for report and patch.

    • as(*, "raw") now works as documented, thanks to Mikael Jagan's
      PR#18795.

    • Informational messages of e.g., print(1:1e4, max=1000), now
      correctly mention max in addition to getOption("max.print").

    • rowSums(A, dims = dd), colMeans(..), etc, give a more helpful
      error message when dd is not of length one, thanks to Michael
      Chirico's PR#18811.

    • seq.Date() no longer explicitly coerces results from integer to
      double, analogously with seq.default(), seq.int() and
      seq.POSIXt(), resolving a _modified_ PR#18782.

    • axisTicks(usr, ...) documentation clarification for log = TRUE,
      fixing bug PR#18821 thanks to Duncan Murdoch.

    • debug() and debugonce(fun) now also accept a string fun when it
      names an S4 generic, fixing PR#18822 thanks to Mikael Jagan.

    • debugonce(<S4-simple-body>, signature=*) now works correctly when
      “called twice”, fixing PR#18824 thanks to Mikael Jagan.

    • format(dtime, digits=* / format=*) is more consistent when the
      POSIXt date-time object dtime has fractional (non integer)
      seconds.  Fixes PR#17350, thanks to new contributions by LatinR's
      ‘R Dev Day’ participants, Heather Turner and Dirk Eddelbuettel;
      also fixes more cases, notably when format contains %OS<nodigit>.

    • options(scipen = NULL) and other invalid values now signal an
      error instead of invalidating ops relying on a finite integer
      value.  Values outside the range -9 .. 9999 are now warned about
      and set to a boundary or to the default 0, e.g., in case of an
      NA.  This also fixes PR#16322.

    • cbind() could segfault with NULL inputs.  (Seen when R was built
      with gcc-14, LTO and C99 inlining semantics.)

    • Fix segfault on quartz() from grid.glyph() call with glyphInfo()
      that describes non-existent font (PR#18784).  Thanks to Tomek
      Gieorgijewski.

    • format() etc, using decimal.mark = s, by default getting s <-
      getOption("OutDec"), signals a warning (to become an error in the
      future) when s is not a string with exactly one character.

    • When s <- getOption("OutDec") is not a string of one character, a
      warning is signalled now whenever it is used in internal C code,
      notably when calling the default methods of format().

    • pwilcox() and qwilcox() now check for user interrupt less
      frequently.

    • summary(<stl>) (which prints directly) finally gets the same
      digits default as the formatting printing of default summary()
      method results, and it is documented explicitly.

    • options(show.error.locations = TRUE) once again shows the most
      recent known location when an error is reported.  Setting its
      value to "bottom" is no longer supported.  Numerical values are
      converted to logical.

    • C API function R_GetCurrentSrcref(skip) now returns srcref
      entries correctly.  (Note that there is also a change to the
      interpretation of skip; see the C-Level API entry above.)

    • tools::Rd2latex() now removes leading and trailing spaces from
      \alias entries as documented, fixing indexing and linking hiccups
      in some PDF manuals.

    • R CMD Rd2pdf can now render the package manual from a --latex
      installation also when the help contains figures.

    • The argument of as.environment() is now named x, not object, as
      was always documented and shown when printing it; thanks to Gael
      Millot's PR#18849.

    • When R CMD check aims at getting the time+date from a world
      clock, it is more robust against unexpected non-error results,
      thanks to Michael Chirico's PR#18852.

    • The tools::parseLatex() parser made several parsing errors
      (PR#18855).

    • Error messages produced by tools::parseLatex() are now more
      readable (PR#18855).

    • R CMD build <pkg> excludes more file patterns when it tars the
      <pkg> directory, fixing both PR#18432 and PR#18434, for vim and
      GNU Global emacs users, thanks to Dirk Eddelbuettel's patch.

    • quantile()'s default method gets an option fuzz to protect
      against floating point inaccuracy before rounding, thus fixing
      PR#15811 and, en passant, PR#17683.

    • Printing arrays now also omits columns, rows and slices when
      desirable according to option max.print, or argument max,
      respectively, addressing most of the remaining part of PR#15027,
      thanks to Sherry Zhang's patch.

    • drop.terms(y ~ w, 1) and similar now work, thanks to Benjamin
      Sommer's report in PR#18861 and collaboration with Heather Turner
      improving reformulate().

    • Many arguments which should be length-1 logical are checked more
      thoroughly.  The most commonly seen errors are in unlink(,
      recursive), tempdir() and the na.rm arguments of max(), min(),
      sum(), ....

      grep(), strsplit() and similar took non-TRUE/FALSE values of
      their logical arguments as FALSE, but these were almost always
      mismatches to unnamed arguments and are now reported as NA.

    • vignette("reshape") is now also available on Windows.

    • trace(coerce, ..) now works correctly, fixing PR#18823 thanks to
      Mikael Jagan.

    • R CMD check now also reports bad symbols in package shared
      objects linked in from local static libraries (PR#18789).

    • factanal() now works correctly also, e.g., for GPArotation,
      oblimin() rotations, fixing PR#18417, thanks to Coen Bernaards
      and others.

    • Setting attributes on primitive functions is deprecated now and
      already an error in the development version of R.  Changing the
      environment of a primitive does no longer happen and signals a
      warning.

Changes in R 4.4.3:

  Installation:

    • R can be installed using C23 (for example with -std=gnu23 or
      -std=gnu2x) with recent compilers including gcc 12–14, Apple
      clang 15–16, LLVM clang 17–20 and Intel icx 2024.2.

      It can be installed with the upcoming (at the time of writing)
      gcc 15, which defaults to C23.

  C-Level Facilities:

    • The functions R_strtod and R_atof now allow hexadecimal constants
      without an exponent, for compatibility with their C99 versions
      (PR#18805).

  Utilities:

    • R CMD build and R CMD check now allow reference output for demo
      scripts (demo/<demo>.Rout.save files) to be shipped with the
      package, as proposed by Torsten Hothorn in PR#18816.

  Bug Fixes:

    • kappa(A, exact=TRUE) for singular A returns Inf more generally,
      fixing PR#18817 reported by Mikael Jagan.

    • Fixed URLs of the sun spots (sunspot.month etc) data sets and
      mention future changes due to recalibration.

    • The parser now accepts hexadecimal constants with a decimal point
      without an exponent (taken as p0) as documented in
      ?NumericConstants (PR#18819).

    • rbind() now works correctly when inputs include a raw vector and
      a logical, integer or double vector – previously the inclusion of
      the latter was garbled.

    • smooth.spline() checks validity of its arguments df.offset and
      penalty: it could segfault if they were NULL.

    • isGeneric(<primitive>, fdef=*, getName=TRUE) now also returns the
      name instead of just TRUE, fixing PR#18829 reported by Mikael
      Jagan.

    • isGeneric(fdef = print) now works, fixing PR#18369 thanks to
      Mikael Jagan.

    • sort(x, method = "qsort") made illegal accesses when x has length
      0.

    • dir.create() is protected against being passed an empty string as
      its path argument.

    • Silent integer overflow could occur in the ‘exact’ computations
      for fisher.test() for unrealistic inputs: this is now an error.

    • Some invalid C-level memory accesses are avoided for loglin(,
      margin = NULL).

      loglin(, param = TRUE) no longer gives an error in corner cases
      such as a one-dimensional input.

    • dev.capabilities() $ events now reports "Idle" if the device
      provides it, fixing PR#18836, thanks to Trevor Davis.

    • arima(.., seasonal = <wrong-vector>) correctly errors now, ditto
      for arima0(), thanks to Norbert Kuder's report on the R-devel
      list.

    • binomial(<link>)$linkinv(eta) and .. $mu.eta(eta) now also work
      for "logit" link when is.integer(eta).

    • as.roman(x) now should work platform independently, also for,
      e.g., x = "IIIII" (= V) and x = "IIIIII" (= VI).

    • R CMD Rd2pdf works again on an installed package directory
      containing LaTeX help (from option --latex), thanks to a report
      by Peter Ruckdeschel.

Changes in R 4.4.2:

  C-Level Facilities:

    • The S-compatibility macros F77_COM and F77_COMDECL defined in
      header R_ext/RS.h are deprecated and will be removed shortly.  We
      could find no record of their use.

  Bug Fixes:

    • Mathlib function lgammacor(x) no longer warns about underflow to
      zero for large x.

    • Text widths and heights were incorrectly reported by the Quartz
      device if the drawing context didn't exist yet (typically when
      drawing off-screen to a window that is yet to appear, see
      PR#18591).

    • The Quartz device could segfault in cases where paths with spaces
      are used in the new glyph drawing API.  Thanks to Tomek
      Gieorgijewski (PR#18758).

    • On macOS in R CRAN builds, it is again possible to read
      little-endian UTF-16 text with a BOM from a connection using
      encoding="UTF-16".  Users building R from source should avoid
      using the system libiconv in macOS 14.1 and later.

    • methods' internal .requirePackage() now re-enables primitive
      method dispatch when needed; thanks to Ivan Krylov for
      demystifying CRAN package check failures on the R-devel mailing
      list.

Changes in R 4.4.1:

  C-Level Facilities:

    • Functions R_atof and R_strtod declared in header R_ext/Utils.h
      are now documented in ‘Writing R Extensions’ and so formally part
      of the API.

    • The non-API entry points Rf_setSVector, Rf_StringFalse,
      Rf_StringTrue and Rf_isBlankString have been added to those
      reported by R CMD check.

    • The new function Rf_allocLang is now available. This provides an
      alternative to the idiom of calling Rf_allocList followed by
      SET_TYPEOF.

  Utilities:

    • R CMD check now reports as warnings what gfortran calls ‘Fortran
      2018 deleted features’, all of which have long been marked as
      ‘obsolescent’ and some of which were deleted in Fortran 2008 or
      earlier.  Fortran compilers are no longer required to support
      these.

  Bug Fixes:

    • as.numeric(), scan(), type.convert() and other places which use
      the internal C function R_strtod now require a _non-empty_ digit
      sequence in a decimal or binary exponent.  This aligns with the
      C/POSIX standard for strtod and with ?NumericConstants.

    • as.data.frame(m, make.names=NA) now works correctly for a matrix
      m with NA's in row names.

    • The error message from <POSIXlt>[["hour"]] and similar now
      mentions *[[, "hour"]], as wished for in PR#17409 and proposed by
      Michael Chirico.

    • qbinom() and potentially qpois(), qnbinom(), no longer sometimes
      fail accurate inversion (of pbinom(), etc), thanks to Christopher
      Chang's report and patch in PR#18711.

    • The internal help server on Windows can again serve requests sent
      in quick succession, fixing a regression in R 4.4.0.

    • debugcall(<S3Generic>()) now also works when a corresponding
      S4-generic version is in the methods cache (PR#18143).

    • Package tools' toTitleCase(ch0) now returns character(0) when ch0
      is of zero length; fixing PR#18724, reported by David Hugh Jones.

    • R CMD check is no longer broken (without a check result and no
      explanation in 00check.log) for a package which declares an
      invalid VignetteBuilder in DESCRIPTION but has no vignettes.

Changes in R 4.4.0:

  Significant User-Visible Changes:

    • Startup banners, R --version, sessionInfo() and R CMD check no
      longer report (64-bit) as part of the platform as this is almost
      universal – the increasingly rare 32-bit platforms will still
      report (32-bit).

      On Windows, ditto for window titles.

    • is.atomic(NULL) now returns FALSE, as NULL is not an atomic
      vector.  Strict back-compatibility would replace is.atomic(foo)
      by (is.null(foo) || is.atomic(foo)) but should happen only
      sparingly.

  New Features:

    • The confint() methods for "glm" and "nls" objects have been
      copied to the stats package.  Previously, they were stubs which
      called versions in package MASS. The MASS namespace is no longer
      loaded if you invoke (say) confint(glmfit).  Further, the "glm"
      method for profile() and the plot() and pairs() methods for class
      "profile" have been copied from MASS to stats.  (profile.nls()
      and plot.profile.nls() were already in stats.)

    • The confint() and profile methods for "glm" objects have gained a
      possibility to do profiling based on the Rao Score statistic in
      addition to the default Likelihood Ratio. This is controlled by a
      new test = argument.

    • The pairs() method for "profile" objects has been extended with a
      which = argument to allow plotting only a subset of the
      parameters.

    • The "glm" method for anova() computes test statistics and
      p-values by default, using a chi-squared test or an F test
      depending on whether the dispersion is fixed or free.  Test
      statistics can be suppressed by giving argument test a false
      logical value.

    • In setRepositories() the repositories can be set using their
      names via name = instead of index ind =.

    • methods() and .S3methods() gain a all.names option for the (rare)
      case where functions starting with a . should be included.

    • Serializations can now be interrupted (e.g., by Ctrl-C on a
      Unix-alike) if they take too long, e.g., from save.image(),
      thanks to suggestions by Ivan Krylov and others on R-devel.

    • New startup option --max-connections to set the maximum number of
      simultaneous connections for the session.  Defaults to 128 as
      before: allowed values up to 4096 (but resource limits may in
      practice restrict to smaller values).

    • R on Windows (since Windows 10 2004) now uses the new Segment
      Heap allocator. This may improve performance of some
      memory-intensive applications.

    • When R packages are built, typically by R CMD build <pkg>, the
      new --user=<build_user> option overrides the (internally
      determined) user name, currently Sys.info()["user"] or LOGNAME.
      This is a (modified) fulfillment of Will Landau's suggestion in
      PR#17530.

    • tools::testInstalledBasic() gets new optional arguments outDir
      and testSrcdir, e.g., allowing to use it in a <builddir> !=
      <srcdir> setup, and in standard “binary” Windows installation
      *if* a source tests/ folder is present.

    • range(<DT_with_Inf>, finite = TRUE) now work for objects of class
      "Date", "POSIXct", and "POSIXlt" with infinite entries,
      analogously to range.default(), as proposed by Davis Vaughan on
      R-devel.  Other range()-methods can make use of new function
      .rangeNum().

    • New .internalGenerics object complementing .S3PrimitiveGenerics,
      for documentation and low-level book-keeping.

    • grid() now invisibly returns the x- and y- coordinates at which
      the grid-lines were drawn.

    • norm(., type) now also works for complex matrices.

    • kappa(., exact = TRUE, norm = *) now works for all norms and also
      for complex matrices.  In symmetric / triangular cases, the new
      argument uplo = "U" | "L" allows the upper or lower triangular
      part to be specified.

    • memDecompress(type = "unknown") recognizes compression in the
      default ‘zlib’ format as used by memCompress(type = "gzip").

    • memCompress() and memDecompress() will use the libdeflate library
      (<https://github.com/ebiggers/libdeflate>) if installed.  This
      uses the same type of compression for type = "gzip" but is 1.5-2x
      faster than the system libz library on some common platforms: the
      speed-up may depend on the library version.

    • diff() for objects of class "Date", "POSIXct", and "POSIXlt"
      accepts a units argument passed via ....

    • Dynamic help now does a much better job of rendering package
      DESCRIPTION metadata.

    • Rprof() gains an event argument and support for elapsed (real)
      time profiling on Unix (PR#18076).

    • filled.contour() gains a key.border argument.

    • tools::update_pkg_po() gets arguments pot_make and mo_make for
      _not_ re-making the corresponding files, and additionally a
      verbose argument.

    • Hexadecimal string colour specifications are now accepted in
      short form, so, for example, we can use "#123", which is
      equivalent to "#112233".

      Thanks to MikeFC for the original idea and Ella Kaye, Malcolm
      Barrett, George Stagg, and Hanne Oberman for the patch.

    • Plain-text help shows \var markup by angle brackets.

    • The new experimental primitive function declare() is intended to
      eventually allow information about R code to be communicated to
      the interpreter, compiler, and code analysis tools. The syntax
      for declarations is still being developed.

    • Functions psmirnov(), qsmirnov() and rsmirnov() in package stats
      have had argument two.sided renamed to alternative, to take into
      account that the permutation distributions of the one-sided
      statistics can be different in the case of ties.  Consequence of
      PR#18582.

    • sort() is now an implicit S4 generic in methods.

    • Formatting and printing, format(z), print(z), of complex vectors
      z no longer zap relatively small real or imaginary parts to zero,
      fixing PR#16752.  This is an API change, as it was documented
      previously to round real and imaginary parts together on purpose,
      producing nicer looking output.  As mentioned, e.g. in the PR,
      this change is compatible with many other “R-like” programming
      environments.

      We have simplified the internal code and now basically format the
      real and imaginary parts independently of each other.

    • New experimental functions Tailcall() and Exec() to support
      writing stack-space-efficient recursive functions.

    • Where characters are attempted to be plotted by pdf(),
      postscript() and xfig() which are not in the selected 8-bit
      character set (most often Latin-1) and the R session is using a
      UTF-8 locale, the warning messages will show the UTF-8 character
      rather than its bytes and one dot will be substituted per
      character rather than per byte.  (Platforms whose iconv() does
      transliteration silently plot the transliteration.)

      In a UTF-8 locale some transliterations are now done with a
      warning (e.g., dashes and Unicode minus to hyphen, ligatures are
      expanded, permille (‰) is replaced by o/oo), although the OS may
      have got there first.  These are warnings as they will continue
      to be replaced by dots in earlier versions of R.

    • The matrix multiplication functions crossprod() and tcrossprod()
      are now also primitive and S3 generic, as %*% had become in R
      4.3.0.

    • source() and example() have a new optional argument catch.aborts
      which allows continued evaluation of the R code after an error.

    • The non-Quartz tiff() devices allow additional types of
      compression if supported by the platform's libtiff library.

    • The list of base and recommended package names is now provided by
      tools::standard_package_names().

    • cairo_pdf() and cairo_ps() default to onefile = TRUE to closer
      match pdf() and postscript().

    • New option catch.script.errors provides a documented way to catch
      errors and then continue in non-interactive use.

    • L %||% R newly in base is an expressive idiom for the phrases
      if(!is.null(L)) L else R or if(is.null(L)) R else L.

    • The return value from warnings() now always inherits from
      "warnings" as documented, now also in the case of no warnings
      where it previously returned NULL.

    • as.complex("1i") now returns 0 + 1i instead of NA with a warning.

    • z <- c(NA, 1i) now keeps the imaginary part Im(z[1]) == 0, no
      longer coercing to NA_complex_.  Similarly, cumsum(z) correctly
      sums real and imaginary parts separately, i.e., without
      “crosstalk” in case of NAs.

    • On Alpine Linux iconv() now maps "latin2", "latin-2", "latin9"
      and "latin-9" to encoding names the OS knows about
      (case-insensitively).

    • iconv(sub = "Unicode") now always zero-pads to four (hex) digits,
      rather than to 4 or 8.  (This seems to have become the convention
      once Unicode restricted the number of Unicode points to 2^21 - 1
      and so will never need more than 6 digits.)

    • NCOL(NULL) now returns 0 instead of 1, for consistency with
      cbind().

    • The information for the Euro glyph missing from the Adobe .afm
      files for the Courier, Helvetica and Times families has been
      copied from their URW equivalents – this will improve vertical
      centring in the pdf() and postscript() devices.

    • The included BLAS sources have been updated to those shipped with
      LAPACK version 3.12.0.  The changes are almost entirely cosmetic.

    • The included LAPACK sources have been updated to version 3.12.0
      and some further double-complex routines added.

    • There are new font families for the 2014–5 URW 2.0 fonts (see
      ?pdf) which are included in recent versions of Ghostscript.
      These have font widths for most Greek glyphs and a few others
      which were missing from the original versions (whose font
      families remain available for reproducibility, although
      Ghostscript-based viewers will render using the 2.0 versions).

    • Improve the large-n efficiency of as.matrix(<dist>), thanks an R
      contributors effort, notably by Tim Taylor and Heather Turner,
      see PR#18660.

    • The default and numeric methods of all.equal() get a check.class
      option.

    • zapsmall() gets new optional arguments, function mFUN and min.d,
      for extra flexibility; fulfills a wish in PR#18199.  Also, it is
      now an implicit S4 generic in package methods.

    • The Rd filter for aspell() gains an ignore argument.

    • New generic function sort_by(), primarily useful for the
      data.frame method which can be used to sort rows of a data frame
      by one or more columns.

    • The licence headers for the RPC code in src/extra/xdr have been
      updated to use the GPL-compatible licence published by Oracle
      America in 2010.

    • New function pkg2HTML() in tools to create single-page HTML
      reference manuals for R packages.

    • The byte code evaluator now uses less C stack space for recursive
      calls to byte-compiled functions. It also makes more of an effort
      to avoid allocations for scalar return values.

    • New completion option backtick (disabled by default) allows
      non-syntactic completions to be wrapped in backquotes. This is
      currently only useful for Jupyter notebooks via the IRkernel
      package, and may cause problems for other backends.

    • The numeric version creators now stop on invalid non-character
      version specifications.

  Installation:

    • The parser has been updated to work with bison 3.8.2, which is
      now used for the pre-generated parsers in gram.c, file.c, and
      gramRd.c. A few parser error messages have changed, which may
      affect code that relies on exact messages.

  Installation on a Unix-Alike:

    • System valgrind headers are now required to use configure option
      --with-valgrind-instrumentation with value 1 or 2.

    • configure will warn if it encounters a 32-bit build, as that is
      nowadays almost untested.

    • Environment variable R_SYSTEM_ABI is no longer used and so no
      longer recorded in etc/Renviron (it was not on Windows and was
      only ever used when preparing package tools).

    • If the libdeflate library and headers are available, libdeflate
      rather than libz is used to (de)compress R objects in lazy-load
      databases.  Typically tasks spend up to 5% of their time on such
      operations, although creating lazy-data databases is one of the
      exceptions.

      This can be suppressed if the library is available by the
      configure option --without-libdeflate-compression.

    • configure option --enable-lto=check has not worked reliably since
      2019 and has been removed.

    • The minimum autoconf requirement for a maintainer build has been
      increased to autoconf 2.71.

      It is intended to increase this to 2.72 for R 4.5.0: the
      distributed configure file was generated using 2.72.

    • The minimum version requirement for an external LAPACK has been
      reduced to 3.9.0.

    • No default C++ compiler is set if no C++17 compiler is detected:
      there is no longer an automatic fallback to C++14 or C++11.

      Compilers from the last five years should have sufficient
      support: for others macros CXX and CXXSTD can be set in file
      config.site to provide a fallback if needed.

      The Objective-C++ compiler now by default uses the standard
      selected by R for C++ (currently C++17) rather than the default
      standard for the C++ compiler (which on macOS is still C++98).

  Installation on macOS:

    • A new configure option --with-newAccelerate makes use of Apple's
      ‘new’ BLAS / LAPACK interfaces in their Accelerate framework.
      Those interfaces are only available in macOS 13.3 or later, and
      building requires SDK 13.3 or later (from the Command Line Tools
      or Xcode 14.3 or later).

      By default the option uses new Accelerate for BLAS calls: to also
      use it for LAPACK use option --with-newAccelerate=lapack.  The
      later interfaces provide LAPACK 3.9.1 rather than 3.2.1: 3.9.1 is
      from 2021-04 and does not include the improved algorithms
      introduced in LAPACK 3.10.0 (including for BLAS calls).

  Installation on Windows:

    • The makefiles and installer scripts for Windows have been
      tailored to Rtools44, an update of the Rtools43 toolchain.  It is
      based on GCC 13 and newer versions of MinGW-W64, binutils and
      libraries (targeting 64-bit Intel CPUs).  R-devel can no longer
      be built using Rtools43 without changes.

    • Rtools44 has experimental support for 64-bit ARM (aarch64) CPUs
      _via_ the LLVM 17 toolchain using lld, clang/flang-new and
      libc++.

  Utilities:

    • R CMD check notes when S4-style exports are used without
      declaring a strong dependence on package methods.

    • tools::checkRd() (used by R CMD check) detects more problems with
      \Sexpr-based dynamic content, including bad nesting of \Sexprs
      and invalid arguments.

    • tools::checkRd() now reports Rd titles and section names ending
      in a period; this is ignored by R CMD check unless environment
      variable _R_CHECK_RD_CHECKRD_MINLEVEL_ is set to -5 or smaller.

    • R CMD check now notes Rd files without an \alias, as long
      documented in ‘Writing R Extensions’ §1.3.1.  The check for a
      missing \description has been moved from tools::checkRd() to
      tools::checkRdContents().

    • R CMD check now visits inst/NEWS.Rd and OS-specific man
      subdirectories when checking Rd files.

    • tools::checkDocFiles() and tools::checkRdContents() now also
      check internal Rd files by default, but “specially” (ignoring
      missing documentation of arguments).

    • R CMD Rdiff gets option --useEx.

    • R CMD check now warns on non-portable uses of Fortran KIND such
      as INTEGER(KIND=4) and REAL(KIND=8).

      To see the failing lines set environment variable
      _R_CHECK_FORTRAN_KIND_DETAILS_ to a true value.

    • When checking Rd files, R CMD check now notes some of the “lost
      braces” that tools::checkRd() finds.  Typical problems are Rd
      macros missing the initial backslash (e.g., code{...}), in-text
      set notation (e.g., {1, 2}, where the braces need escaping), and
      \itemize lists with \describe-style entries of the form
      \item{label}{description}.

    • R CMD INSTALL (and hence check) will compile C++ code with
      -DR_NO_REMAP if environment variable _R_CXX_USE_NO_REMAP_ is set
      to a true value.  It is planned that this will in future become
      the default for compiling C++.

    • The new built-in Rd macro \dontdiff{} can be used to mark example
      code whose output should be ignored when comparing check output
      to reference output (tests/Examples/<pkg>-Ex.Rout.save).  The
      \dontdiff tag, like \donttest, is _not_ shown on the rendered
      help page, so provides a clean alternative to ##
      IGNORE_RDIFF_(BEGIN|END) comments.

    • R CMD build when there is no NAMESPACE, now uses the recommended
      exportPattern("^[^.]"), instead of exporting everything.

    • R CMD check now warns about non-ASCII characters in the NAMESPACE
      file (in addition to R files). Such packages are not portable and
      may fail to install on some platforms.

  C-Level Facilities:

    • Headers R_ext/Applic.h and R-ext/Linpack.h used to include
      R_ext/BLAS.h although this was undocumented and unneeded by their
      documented entry points.  They no longer do so.

    • New function R_missing(), factored out from do_missing(), used to
      fix PR#18579.

    • SEXP type S4SXP has been renamed to OBJSXP to support
      experimenting with alternative object systems.  The S4SXP value
      can still be used in C code but is now deprecated.  Based on
      contributions from the R Consortium's Object-Oriented Programming
      Working Group.

    • New function pow1p(x,y) for accurate (1+x)^y.

    • mkCharLenCE was incorrectly documented to take a size_t length
      but was implemented with int (and character strings in R are
      limited to 2^31 - 1 bytes).

  Deprecated and Defunct:

    • data() no longer handles zipped data from long-defunct (since R
      2.13.0) --use-zip-data installations.

    • The legacy graphics devices pictex() and xfig() are now
      deprecated.  They do not support recent graphics enhancements and
      their font handling is rudimentary. The intention is to retain
      them for historical interest as long as they remain somewhat
      functional.

    • Support for encoding = "MacRoman" has been removed from the pdf()
      and postscript() devices – this was a legacy encoding supporting
      classic macOS up to 2001 and no longer has universal libiconv
      support.

    • is.R() is deprecated as no other S dialect is known to be in use
      (and this could only identify historical dialects, not future
      ones).

      Further information on calls can be obtained by setting the
      environment variable _R_DEPRECATED_IS_R_ to error which turns the
      deprecation warning into an error and so by default gives a
      traceback.  (This is done by R CMD check --as-cran.)

    • UseMethod() no longer forwards local variables assigned in the
      generic function into method call environments before evaluating
      the method body. This makes method calls behave more like
      standard function calls and makes method code easier to analyze
      correctly.

    • The twelve as.data.frame.<class>() methods which were deprecated
      only via _R_CHECK_AS_DATA_FRAME_EXPLICIT_METHOD_ and in R CMD
      check --as-cran are formally deprecated now in favour of calling
      as.data.frame() or as.data.frame.vector().  The deprecation
      “check” now works also when as.data.frame() is S4 generic thanks
      to Ivan Krylov.

    • The default method for the directional comparison operators <, >,
      <=, and >= now signals an error when one of the operands is a
      language object, i.e. a symbol or a call.

    • For terms.formula(), deprecate abb and neg.out arguments
      _formally_ in addition to just documenting it.

  Bug Fixes:

    • The methods package is more robust to not being attached to the
      search path.  More work needs to be done.

    • pairwise.t.test() misbehaved when subgroups had 0 DF for
      variance, even with pool.sd = TRUE.  (PR#18594 by Jack Berry.)

    • Probability distribution functions [dpq]<distrib>(x, *), but also
      bessel[IKJY](x, .) now consistently preserve attributes(x) when
      length(x) == 0, e.g., for a 2 x 0 matrix, thanks to Karolis
      Koncevičius' report PR#18509.

    • Group “Summary” computations such as sum(1:3, 4, na.rm = 5, NA,
      7, na.rm = LL) now give an error instead of either 17 or NN for
      LL true or false, as proposed by Ivan Krylov on the R-devel
      mailing list.  (This also means it is now an error to specify
      na.rm more than once.)

    • as.complex(x) now returns complex(real = x, imaginary = 0) for
      _all_ numerical and logical x, notably also for NA or
      NA_integer_.

    • Directories are now omitted by file.copy(, recursive = FALSE) and
      in file.append() (PR#17337).

    • gsub() and sub() are now more robust to integer overflow when
      reporting errors caused by too large input strings (PR#18346).

    • Top-level handlers are now more robust to attempts to remove a
      handler whilst handlers are running (PR#18508).

    • The handling of Alt+F4 in dialogs created on Windows using
      GraphApp has been fixed (PR#13870).

    • density() more consistently computes grid values for the
      FFT-based convolution, following Robert Schlicht's analysis and
      proposal in PR#18337, correcting density values typically by a
      factor of about 0.999.  Argument old.coords = TRUE provides back
      compatibility.

    • palette.colors() gains a name argument that defaults to FALSE
      controlling whether the vector of colours that is returned has
      names (where possible).  PR#18529.

    • tools::xgettext() no longer extracts the (non-translatable) class
      names from warningCondition and errorCondition calls.

    • S3method(<gen>, <class>, <func>) in the NAMESPACE file now works
      (again) when <func> is visible from the namespace, e.g.,
      imported, or in base.

    • getParseData(f) now also works for a function defined in the
      first of several <pkg>/R/*.R source files, thanks to Kirill
      Müller's report and Duncan Murdoch's patch in PR#16756.

    • Rd \Sexpr macros with nested #ifdef conditionals were not
      processed.

    • A non-blocking connection with non-default encoding (such as a
      socket) now correctly returns from readLines() after new data has
      arrived also when its EOF had been reached previously.  Thanks to
      Peter Meilstrup's report on R-devel and Ivan Krylov's report and
      patch proposal in PR#18555.

    • tools::checkRdContents() failed to detect empty argument
      descriptions when they spanned multiple lines, including those
      generated by prompt().  These cases are now noted by R CMD check.

    • Plain-text help no longer outputs spurious colons in the
      arguments list (for multi-line \item labels in the Rd source).

    • kappa() and rcond() work correctly in more cases; kappa(., norm =
      "2") now warns that it computes the 1-norm with (default) exact =
      FALSE; prompted by Mikael Jagan's quite comprehensive PR#18543.

    • Rd skeletons generated by prompt() or promptData() now use a
      dummy title (so R CMD build works).  tools::checkRdContents() has
      been updated to detect such template leftovers, including from
      promptPackage().

    • When S4 method dispatch fails because no method was found, the
      error message now includes the signature argument names; thanks
      to Michael Chirico's proposal on the R-devel list.

    • withAutoprint({ .. }) now preserves srcrefs previously lost,
      thanks to Andrew Simmons' report plus fix in PR#18572.

    • transform.data.frame() no longer adjusts names; in particular,
      untransformed variables are kept as-is, including those with
      syntactically invalid names (PR#17890).

    • The keep.source option for Rd \Sexpr blocks is no longer ignored.

    • The formula methods for t.test() and wilcox.test() now catch when
      paired is passed, addressing PR#14359; use Pair(x1, x2) ~ 1 for a
      paired test.

    • The level reported in the browser prompt was often too large. It
      now shows the number of browser contexts on the stack.

    • For cbind() and rbind(), the optional deparse.level argument is
      now properly passed to methods, thanks to Mikael Jagan's PR#18579
      and comments there.

    • Some error and warning messages for large (‘long vector’)
      matrix(v, nr, nc) and dim(m) <- d are now correct about sizes,
      using long long formatting, fixing PR#18612 (and more) reported
      by Mikael Jagan.

    • readChar(useBytes = TRUE) now terminates strings even when the
      underlying connection uses extra spaces in the input buffer.
      This fixes problems with extra garbage seen with gzip
      connections, PR#18605.

    • Named capture in PCRE regular expressions now works also with
      more than 127 named groups (PR#18588).

    • Datetime functions are now robust against long jumps when dealing
      with internal time zone changes.  This avoids confusing warnings
      about an invalid time zone, previously triggered by turning
      warnings into errors or handling them via tryCatch (PR#17966,
      PR#17780).

    • Datetime functions now restore even an empty TZ environment
      variable after internal time zone changes (PR#17724).  This makes
      results of datetime functions with this (typically unintentional)
      setting more predictable.

    • drop.terms(*) now drops response as by default, keep.response =
      FALSE, fixing PR#18564 thanks to Mikael Jagan.

    • dummy.coef(.) now also works for lm()-models with character
      categorical predictor variables rather than factor ones, fixing
      PR#18635 reported by Jinsong Zhao.

    • formals(f) <- formals(f) now also works for a function w/o
      arguments and atomic _constant_ body(f).

    • Correct as.function(<invalid list>, .)'s error message.

    • removeSource() is yet more thorough in finding and removing
      "srcref" and the other source references from parsed R language
      chunks, fixing PR#18638 thanks to Andrew Simmons.

    • dgeom() is more accurate now, notably when its result is very
      small, fixing PR#18642 thanks to the proposal of Morten Welinder,
      also improving other instances where C level binom_raw(x, n, ..)
      has x == 0 or x== n.

    • warning() with options(warn = 1) has improved output for
      multi-line messages.

    • axis.Date() and axis.POSIXct() now respect the par("lab") setting
      for the number of pretty() intervals.

    • Comparisons for language objects (which are based on deparsing)
      are now more careful about using accurate deparsed results
      (PR#18676).

    • Plain-text help (Rd2txt) now correctly preserves blank lines
      following single-line \dontrun code.

    • <POSIXlt>[*] no longer sets wrong "balanced" attribute, fixing
      PR#18681 thanks to Mikael Jagan.

    • str(<classed-call>) now deparses the call as expected, fixing
      PR#18684, reported by Dave Slager.

    • In Rd examples, code following the closing brace of a \dontrun,
      \dontshow or \donttest tag on the same line is no longer skipped
      when R CMD check runs the examples.

    • as.data.frame(matrix(*, ncol=0)) now gets valid names() and
      colnames(); reported by Davis Vaughan on the R-devel list.

    • Internal Mathlib function stirlerr(n) is now almost fully
      (52-bit) accurate for all n >= ~5.9 and more accurate also in the
      range 1 -- 5.9.  This entails small (“after 12th decimal”)
      changes in density functions, e.g., dgamma() in _some_ regions of
      their support.  The fix was partly prompted by Morten Welinder's
      PR#18640.

    • Numbers like 9876543.2 are now considered non-integer by Mathlib
      internal R_nonint(), amending original fix of PR#15734.

    • Rd comment lines no longer cause broken paragraphs in the
      rendered PDF and plain-text help. In code blocks, pure comment
      lines (starting with %) no longer produce an empty line.

    • xtabs(Freq ~ .) now consistently defaults to na.action = na.pass,
      using na.rm = FALSE (added as an argument) when summing over Freq
      (PR#17770).

    • tools::testInstalledPackage() is no longer silent about failures
      from running examples or tests and its return code no longer
      ignores failures from checking vignettes.

Changes in R 4.3.3:

  New Features:

    • iconv() now fixes up variant encoding names such as "utf8"
      case-insensitively.

  Deprecated and Defunct:

    • The legacy encoding = "MacRoman" is deprecated in pdf() and
      postscript(): support was incomplete in earlier versions of R.

  Bug Fixes:

    • Arguments are now properly forwarded to methods on S4 generics
      with ... in the middle of their formal arguments. This was broken
      for the case when a method introduced an argument but did not
      include ... in its own formals. Thanks to Hervé Pagès for the
      report PR#18538.

    • Some invalid file arguments to pictex(), postscript() and xfig()
      opened a file called NA rather than throw an error.  These
      included postscript(NULL) (which some people expected to work
      like pdf(NULL)).

    • Passing filename = NA to svg(), cairo_pdf(), cairo_ps() or the
      Cairo-based bitmap devices opened a file called NA: it now throws
      an error.

    • quartz(file = NA) opened a file called NA, including when used as
      a Quartz-based bitmap device.  It now gives an error.

    • rank(<long vector>) now works, fixing PR#18617, thanks to Ilia
      Kats.

    • seq.int() did not adequately check its length.out argument.

    • match(<POSIXct>, .) is correct again for differing time zones,
      ditto for "POSIXlt", fixing PR#18618 reported by Bastian Klein.

    • drop.terms(*, dropx = <0-length>) now works, fixing PR#18563 as
      proposed by Mikael Jagan.

    • drop.terms(*) keeps + offset(.) terms when it should, PR#18565,
      and drop.terms() no longer makes up a response, PR#18566, fixing
      both bugs thanks to Mikael Jagan.

    • getS3method("t", "test") no longer finds the t.test() function,
      fixing PR#18627.

    • pdf() and postscript() support for the documented Adobe encodings
      "Greek" and "Cyrilllic" was missing (although the corresponding
      Windows' codepages could be used).

    • Computations of glyph metric information for pdf() and
      postscript() did not take into account that transliteration could
      replace one character by two or more (only seen on macOS 14) and
      typically warned that the information was not known.

    • rank(x) no longer overflows during integer addition, when
      computing rank average for largish but not-yet long vector x,
      fixing PR#18630, thanks to Ilia Kats.

    • list.files() on Windows now returns also files with names longer
      that 260 bytes (the Windows limit is 260 characters).
      Previously, some file names particularly with ‘East Asian’
      characters were omitted.

    • cov2cor(<0 x 0>) now works, fixing PR#18423 thanks to Mikael
      Jagan and Elin Waring.

    • cov2cor(<negative diagonal>) and similar now give one warning
      instead of two, with better wording, fixing PR#18424 thanks to
      Mikael Jagan.

    • tools:: startDynamicHelp() now ensures port is in proper range,
      fixing PR#18645.

    • pbeta(x, a,b) is correct now for x=0 or 1 in the boundary cases
      where a or b or both are 0, fixing PR#18672 thanks to Michael
      Fay.

    • pmatch(x, table) for large table, also called for data frame row
      selection, dfrm[nm, ], is now interruptible, fixing PR#18656.

    • predict(<rank-deficient lm>, newdata=*) fix computing of nbasis,
      see Russ Lenth's comment 29 in PR#16158.

    • Added a work-around for a bug in macOS 14.3.1 and higher which
      prevents R plots in the Quartz Cocoa device from updating on
      screen.

Changes in R 4.3.2:

  New Features:

    • The default initialization of the "repos" option from the
      repositories file at startup can be skipped by setting
      environment variable R_REPOSITORIES to NULL such that
      getOption("repos") is empty if not set elsewhere.

    • qr.X() is now an implicit S4 generic in methods.

    • iconv(to = "ASCII//TRANSLIT") is emulated using substitution on
      platforms which do not support it (notably Alpine Linux).  This
      should give a human-readable conversion in ASCII on all platforms
      (rather than NA_character_).

    • trans3d() gains options continuous and verbose addressing the
      problem of possible “wrap around” when projecting too long
      curves, as reported by Achim Zeileis in PR#18537.

    • tools::showNonASCII() has been rewritten to work better on macOS
      14 (which has a changed implementation of iconv()).

    • tiff(type = "quartz") (the default on macOS) now warns if
      compression is specified: it continues to be ignored.

  Installation on a Unix-Alike:

    • There is some support for building with Intel's LLVM-based
      compilers on x86_64 Linux, such as (C) icx, (C++) ipcx and
      (Fortran) ifx from oneAPI 2023.x.y.

    • There is support for using LLVM's flang-new as the Fortran
      compiler from LLVM 16.0.x (preferably 17.0.0 or later).

  Utilities:

    • R CMD check reports the use of the Fortran 90 random number
      generator RANDOM_NUMBER() and the subroutines to initialize it.

      ‘Writing R Extensions’ has example code to use R's RNGs from
      Fortran.

  Bug Fixes:

    • substr(x, n, L) <- cc now works (more) correctly for multibyte
      UTF-8 strings x when L > nchar(x), thanks to a report and patch
      by ‘Architect 95’.

    • contrib.url(character()) now returns 0-length character() as
      documented, which also avoids spurious warnings from
      available.packages() et al. in the edge case of an empty vector
      of repository URLs.

    • readChar(., 4e8) no longer fails, thanks to Kodi Arfer's report
      (PR#18557).

    • lapply(<list>, as.data.frame) no longer warns falsely for some
      base vector components.

    • Communication between parent and child processes in the multicore
      part of parallel could fail on platforms that do not support an
      arbitrarily large payload in system functions read()/write() on
      pipes (seen on macOS where a restriction to INT_MAX bytes is
      documented, without doing a partial read unlike Linux). The
      payload is now split into 1Gb chunks to avoid that problem.
      (PR#18571)

    • qqplot(x,y, conf.level=.) gives better confidence bounds when
      length(x) != length(y), thanks to Alexander Ploner's report and
      patch proposal (PR#18557).

    • norm(<0-length>, "2") now gives zero instead of an error, as all
      the other norm types, thanks to Mikael Jagan's PR#18542.

    • Build-stage Rd macros \packageAuthor and \packageMaintainer now
      process Authors@R, fixing NA results when the package DESCRIPTION
      omits Author and Maintainer fields.

    • Formatting and printing complex numbers could give things like
      0.1683-0i because of rounding error: -0i is now replaced by +0i.

    • postscript() refused to accept a title comment containing the
      letter “W” (PR#18599).

    • isoreg(c(1,Inf)) signals an error instead of segfaulting, fixing
      PR#18603.

    • tiff(type = "Xlib") was only outputting the last page of
      multi-page plots.

    • tools::latexToUtf8() again knows about \~{n} and other letters
      with tilde, fixing a regression in R 4.3.0, and about \^{i} as an
      alternative to \^{\i} (similarly with other accents).
      Furthermore, LaTeX codes for accented I letters are now correctly
      converted, also fixing related mistakes in
      tools::encoded_text_to_latex().

    • tar(*, tar = "internal") no longer creates out-of-spec tar files
      in the very rare case of user or group names longer than 32
      bytes, fixing PR#17871 with thanks to Ivan Krylov.

    • When using the “internal” timezone datetime code, adding a
      fraction of a second no longer adds one second, fixing PR#16856
      from a patch by Ivan Krylov.

    • tools::checkRd() no longer produces spurious notes about
      “unnecessary braces” from multi-line Rd results of \Sexpr macros.

Changes in R 4.3.1:

  C-Level Facilities:

    • The C-level API version of R's integrate(), Rdqags() in Applic.h,
      now returns the correct number of integrand evaluations neval,
      fixing PR#18515 reported and diagnosed by Stephen Wade.

    • The C prototypes for LAPACK calls dspgv and dtptrs in
      R_ext/Lapack.h had one too many and one too few character length
      arguments — but this has not caused any known issues. To get the
      corrected prototypes, include

              #include <Rconfig.h> // for PR18534fixed
              #ifdef PR18534fixed
              # define usePR18534fix 1
              #endif
              #include <R_ext/Lapack.h>
      
      in your C/C++ code (PR#18534).

  Installation:

    • Many of the checks of esoteric Internet operations and those
      using unreliable external sites have been moved to a new target
      that is not run by default and primarily intended for the core
      developers.  To run them use

              cd tests; make test-Internet-dev
      
  Bug Fixes:

    • .S3methods(), typically called from methods(), again marks
      methods from package base as visible.

      Also, the visibility of non-base methods is again determined by
      the method's presence in search().

    • tools::Rdiff() is now more robust against invalid strings, fixing
      installation tests on Windows without Rtools installed
      (PR#18530).

    • Fix (new) bug in hcl.colors(2, *), by Achim Zeileis (PR#18523).

    • head(., <illegal>) and tail(..) now produce more useful "Error in
      ...." error messages, fixing PR#18362.

    • Package code syntax on Windows is checked in UTF-8 when UTF-8 is
      the native encoding.

    • na.contiguous(x) now also returns the first run, when it is at
      the beginning and there is a later one of the same length;
      reported to R-devel, including a fix, by Georgi Boshnakov.
      Further, by default, it modifies only an existing attr(*,"tsp")
      but otherwise no longer sets one.

    • chol(<not pos.def>, pivot = <T|F>) now gives a correct error or
      warning message (depending on pivot), thanks to Mikael Jagan's
      (PR#18541).

Changes in R 4.3.0:

  Significant User-Visible Changes:

    • Calling && or || with LHS or (if evaluated) RHS of length greater
      than one is now always an error, with a report of the form

          'length = 4' in coercion to 'logical(1)'
      
      Environment variable _R_CHECK_LENGTH_1_LOGIC2_ no longer has any
      effect.

  New Features:

    • The included BLAS sources have been updated to those shipped with
      LAPACK version 3.10.1.  (This caused some platform-dependent
      changes to package check output.)  And then to the sources from
      LAPACK version 3.11.0 (with changes only to double complex
      subroutines).

    • The included LAPACK sources have been updated to include the four
      Fortran 90 routines rather than their Fortran 77 predecessors.
      This may give some different signs in SVDs or
      eigendecompositions..  (This completes the transition to LAPACK
      3.10.x begun in R 4.2.0.)

    • The LAPACK sources have been updated to version 3.11.0.  (No new
      subroutines have been added, so this almost entirely bug fixes:
      Those fixes do affect some computations with NaNs, including R's
      NA.)

    • The parser now signals _classed_ errors, notably in case of the
      pipe operator |>.  The error object and message now give line and
      column numbers, mostly as proposed and provided by Duncan Murdoch
      in PR#18328.

    • toeplitz() is now generalized for asymmetric cases, with a
      toeplitz2() variant.

    • xy.coords() and xyz.coords() and consequently, e.g., plot(x,y,
      log = "y") now signal a _classed_ warning about negative values
      of y (where log(.) is NA).  Such a warning can be specifically
      suppressed or caught otherwise.

    • Regular expression functions now check more thoroughly whether
      their inputs are valid strings (in their encoding, e.g. in
      UTF-8).

    • The performance of grep(), sub(), gsub() and strsplit() has been
      improved, particularly with perl = TRUE and fixed = TRUE.  Use of
      useBytes = TRUE for performance reasons should no longer be
      needed and is discouraged: it may lead to incorrect results.

    • apropos() gains an argument dot_internals which is used by the
      completion (help(rcompgen)) engine to also see base internals
      such as .POSIXct().

    • Support in tools::Rdiff() for comparing uncompressed PDF files is
      further reduced – see its help page.

    • qqplot(x, y, ...) gains conf.level and conf.args arguments for
      computing and plotting a confidence band for the treatment
      function transforming the distribution of x into the distribution
      of y (Switzer, 1976, _Biometrika_). Contributed by Torsten
      Hothorn.

    • Performance of package_dependencies() has been improved for cases
      when the number of dependencies is large.

    • Strings newly created by gsub(), sub() and strsplit(), when any
      of the inputs is marked as "bytes", are also marked as "bytes".
      This reduces the risk of creating invalid strings and accidental
      substitution of bytes deemed invalid.

    • Support for readLines(encoding = "bytes") has been added to allow
      processing special text files byte-by-byte, without creating
      invalid strings.

    • iconv(from = "") now takes into account any declared encoding of
      the input elements and uses it in preference to the native
      encoding.  This reduces the risk of accidental creation of
      invalid strings, particularly when different elements of the
      input have different encoding (including "bytes").

    • Package repositories in getOption("repos") are now initialized
      from the repositories file when utils is loaded (if not already
      set, e.g., in .Rprofile).  (From a report and patch proposal by
      Gabriel Becker in PR#18405.)

    • compactPDF() gets a verbose option.

    • type.convert() and hence read.table() get new option tryLogical =
      TRUE with back compatible default.  When set to false, converts
      "F" or "T" columns to character.

    • Added new unit prefixes "R" and "Q" for abbreviating
      (unrealistically large) sizes beyond 10^{27} in standard = "SI",
      thanks to Henrik Bengtsson's PR#18435.

    • as.data.frame()'s default method now also works fine with atomic
      objects inheriting from classes such as "roman", "octmode" and
      "hexmode", thus fulfilling the wish of PR#18421, by Benjamin
      Feakins.

    • The as.data.frame.vector() utility now errors for wrong-length
      row.names.  It warned for almost six years, with “Will be an
      error!”.

    • sessionInfo() now also contains La_version() and reports codepage
      and timezone when relevant, in both print() and toLatex() methods
      which also get new option tzone for displaying timezone
      information when locale = FALSE.

    • New function R_compiled_by() reports the C and Fortran compilers
      used to build R, if known.

    • predict(<lm>, newdata = *) no longer unnecessarily creates an
      offset of all 0s.

    • solve() for complex inputs now uses argument tol and by default
      checks for ‘computational singularity’ (as it long has done for
      numeric inputs).

    • predict(<rank-deficient lm>, newdata=*) now obeys a new argument
      rankdeficient, with new default "warnif", warning only if there
      are non-estimable cases in newdata.  Other options include
      rankdeficient = "NA", predicting NA for non-estimable newdata
      cases.  This addresses PR#15072 by Russ Lenth and is based on his
      original proposal and discussions in PR#16158 also by David Firth
      and Elin Waring.  Still somewhat experimental.

    • Rgui console implementation now works better with the NVDA screen
      reader when the full blinking cursor is selected.  The underlying
      improvements in cursor handling may help also other screen
      readers on Windows.

    • The drop-field control in GraphApp can now be left with the TAB
      key and all controls can be navigated in the reverse order using
      the Shift+TAB key, improving accessibility of the Rgui
      configuration editor.

    • qnorm(<very large negative>, log.p=TRUE) is now fully accurate
      (instead of to “only” minimally five digits).

    • demo(error.catching) now also shows off withWarnings() and
      tryCatchWEMs().

    • As an experimental feature the placeholder _ can now also be used
      in the rhs of a forward pipe |> expression as the first argument
      in an extraction call, such as _$coef. More generally, it can be
      used as the head of a chain of extractions, such as _$coef[[2]].

    • Spaces in the environment variable used to choose the R session's
      temporary directory (TMPDIR, TMP and TEMP are tried in turn) are
      now fatal.  (On Windows the ‘short path’ version of the path is
      tried and used if that does not contain a space.)

    • all.equal.numeric() gets a new optional switch giveErr to return
      the numeric error as attribute.  Relatedly,
      stopifnot(all.equal<some>(a, b, ..)) is as “smart” now, as
      stopifnot(all.equal(....)) has been already, thus allowing
      customized all.equal<Some>() wrappers.

    • R on Windows is now able to work with path names longer than 260
      characters when these are enabled in the system (requires at
      least Windows 10 version 1607).  Packages should be updated to
      work with long paths as well, instead of assuming PATH_MAX to be
      the maximum length.  Custom front-ends and applications embedding
      R need to update their manifests if they wish to allow this
      feature.  See
      <https://blog.r-project.org/2023/03/07/path-length-limit-on-windows>
      for more information.

    • ‘Object not found’ and ‘Missing argument’ errors now give a more
      accurate error context. Patch provided by Lionel Henry in
      PR#18241.

    • The @ operator is now an S3 generic. Based on contributions by
      Tomasz Kalinowski in PR#18482.

    • New generic chooseOpsMethod() provides a mechanism for objects to
      resolve cases where two suitable methods are found for an Ops
      Group Generic. This supports experimenting with alternative
      object systems.  Based on contributions by Tomasz Kalinowski in
      PR#18484.

    • inherits(x, what) now accepts values other than a simple
      character vector for argument what. A new generic, nameOfClass(),
      is called to resolve the class name from what. This supports
      experimenting with alternative object systems.  Based on
      contributions by Tomasz Kalinowski in PR#18485.

    • Detection of BLAS/LAPACK in use (sessionInfo()) with FlexiBLAS
      now reports the current backend.

    • The "data.frame" method for subset() now warns about extraneous
      arguments, typically catching the use of = instead of == in the
      subset expression.

    • Calling a:b when numeric a or b is longer than one may now be
      made into an error by setting environment variable
      _R_CHECK_LENGTH_COLON_ to a true value, along the proposal in
      PR#18419 by Henrik Bengtsson.

    • density(x, weights = *) now warns if automatic bandwidth
      selection happens without using weights; new optional warnWbw may
      suppress the warning.  Prompted by Christoph Dalitz' PR#18490 and
      its discussants.

    • rm(list = *) is faster and more readable thanks to Kevin Ushey's
      PR#18492.

    • The plot.lm() function no longer produces a normal Q-Q plot for
      GLMs. Instead it plots a half-normal Q-Q plot of the absolute
      value of the standardized deviance residuals.

    • The print() method for class "summary.glm" no longer shows
      summary statistics for the deviance residuals by default.  Its
      optional argument show.residuals can be used to show them if
      required.

    • The tapply() function now accepts a data frame as its X argument,
      and allows INDEX to be a formula in that case. by.data.frame()
      similarly allows INDICES to be a formula.

    • The performance of df[j] <- value (including for missing j) and
      write.table(df) has been improved for data frames df with a large
      number of columns.  (Thanks to Gabriel Becker's PR#18500,
      PR#18503 and discussants, prompted by a report from Toby Dylan
      Hocking on the R-devel mailing list.)

    • The matrix multiply operator %*% is now an S3 generic, belonging
      to new group generic matrixOps.  From Tomasz Kalinowski's
      contribution in PR#18483.

    • New function array2DF() to convert arrays to data frames,
      particularly useful for the list arrays created by tapply().

  Dates and Times:

    • On platforms where (non-UTC) datetimes before 1902 (or before
      1900 as with system functions on recent macOS) are guessed by
      extrapolating time zones from 1902-2037, there is a warning at
      the first use of extrapolation in a session.  (As all time zones
      post 2037 are extrapolation, we do not warn on those.)

    • (Platforms using --with-internal-tzone, including Windows and by
      default macOS). How years are printed in dates or date-times can
      be controlled by environment variable R_PAD_YEARS_BY_ZERO.  The
      default remains to pad to 4 digits by zeroes, but setting value
      no gives no padding (as used by default by glibc).

    • strftime() tries harder to determine the offset for the "%z"
      format, and succeeds on the mainstream R platforms.

    • strftime() has a limit of 2048 bytes on the string produced –
      attempting to exceed this is an error.  (Previously it silently
      truncated at 255 bytes.)

    • sessionInfo() records (and by default prints) the system time
      zone as part of the locale information.  Also, the source
      (system/internal) of the date-time conversion and printing
      functions.

    • Objects of class "POSIXlt" created in this version of R always
      have 11 components: component zone is always set, and component
      gmtoff is set for times in UTC and usually set on the (almost
      all) platforms which have C-level support, otherwise is NA.

    • There are comprehensive validity checks on the structure of
      objects of class "POSIXlt" when converting (including formatting
      and printing).  (This avoids mis-conversions of hand-crafted
      objects.)

    • There is some support for using the native date-time routines on
      macOS: this is only viable on recent versions (e.g. 12.6 and 13)
      and does get wrong some historical changes (before 1900, during
      WWII).  Use of --with-internal-tzone remains the default.

    • as.POSIXct(<numeric>) and as.POSIXlt(.) (without specifying
      origin) now work.  So does as.Date(<numeric>).

    • as.Date.POSIXct(., tz) now treats several tz values, notably
      "GMT" as equivalent to "UTC", proposed and improved by Michael
      Chirico and Joshua Ulrich in PR#17674.

    • Experimental balancePOSIXlt() utility allows using “ragged” and
      or out-of-range "POSIXlt" objects more correctly, e.g., in
      subsetting and subassignments.  Such objects are now documented.
      Complemented by the low-level unCfillPOSIXlt() utility.

      More experimentally, a "POSIXlt" object may have an attribute
      "balanced" indicating if it is known to be filled or fully
      balanced.

    • Functions axis.Date() and axis.POSIXct() are rewritten to gain
      better default tick locations and better default formats via the
      corresponding pretty() methods.  Thanks to Swetlana Herbrandt.

    • The mapping of Windows' names for time zones to IANA's ‘Olson’
      names has been updated.  When ICU is available (it is by
      default), it is used to get a mapping for the current region set
      in Windows.  This can be overridden by setting environment
      variable TZ to the desired Olson name — see OlsonNames() for
      those currently available.

  Graphics:

    • The graphics engine version, R_GE_version, has been bumped to 16
      and so packages that provide graphics devices should be
      reinstalled.

    • The grDevices and grid packages have new functions for rendering
      typeset glyphs, primarily: grDevices::glyphInfo() and
      grid::grid.glyph().

      Rendering of typeset glyphs is only supported so far on the
      Cairo-based graphics devices and on the pdf() and quartz()
      devices.

    • The defined behaviour for "clear" and "source" compositing
      operators (via grid::grid.group()) has been changed (to align
      better with simple interpretation of original Porter-Duff
      definitions).

    • Support for gradients, patterns, clipping paths, masks, groups,
      compositing operators, and affine transformations has been added
      to the quartz() device.

  Installation on a Unix-Alike:

    • A system installation of generic LAPACK 3.10.0 or later will be
      preferred to the version in the R sources.

      configure option --with-lapack=no (equivalently --without-lapack)
      forces compilation of the internal LAPACK sources.

      If --with-lapack is not specified, a system liblapack is looked
      for and used if it reports version 3.10.0 or later and does not
      contain BLAS routines.

      Packages using LAPACK will need to be reinstalled if this changes
      to using an external library.

    • On aarch64 Linux platforms using GCC, configure now defaults to
      -fPIC (instead of -fpic), as desired in PR#18326.

    • configure now checks conversion of datetimes between POSIXlt and
      POSIXct around year 2020.  Failure (which has been seen on
      platforms missing tzdata) is fatal.

    • If configure option --with-valgrind-instrumentation is given
      value 1 or 2, option --with-system-valgrind-headers is now the
      default and ignored (with a warning).  It is highly recommended
      that the system headers are installed alongside valgrind: they
      are part of its packaging on some Linux distributions and
      packaged separately (e.g. in the valgrind-devel RPM) on others.
      configure will give a warning if they are not found.

      The system headers will be required in a future release of R to
      build with valgrind instrumentation.

    • libcurl 8.x is now accepted by configure: despite a change in
      major version number it changes neither API nor ABI.

  Installation on Windows:

    • The makefiles and installer scripts for Windows have been
      tailored to Rtools43, an update of the Rtools42 toolchain.  It is
      based on GCC 12 and newer versions of MinGW-W64, binutils and
      libraries.  At this time R-devel can still be built using
      Rtools42 without changes, but when R-devel is installed via the
      installer, it will by default look for Rtools43.

    • Old make targets rsync-extsoft and 32-bit ones that are no longer
      needed have been removed.

    • Default builds (including for packages) no longer select C99.
      Thus the C standard used is the default for the compiler, which
      for the toolchain in Rtools43 is C17.  (This is consistent with
      Unix builds.)

  Package Installation:

    • The default C++ standard has been changed to C++17 where
      available (which it is on all currently checked platforms): if
      not C++14 or C++11 is used if available otherwise C++ is not
      supported.

    • USE_FC_LEN_T is the default: this uses the correct
      (compiler-dependent) prototypes for Fortran BLAS/LAPACK routines
      called from C/C++, and requires adjustment of many such calls –
      see ‘Writing R Extensions’ §6.6.1.

    • There is initial support for C++23 as several compilers are now
      supporting -std=c++23 or -std=c++2b or similar.  As for C++20,
      there no additional configure checks for C++23 features beyond a
      check that the compiler reports a __cplusplus value greater than
      that in the C++20 standard.  C++ feature tests should be used.

    • There is support for a package to indicate the version of the C
      standard which should be used to compile it, and for the
      installing user to specify this.  In most cases R defaults to the
      C compiler's default standard which is C17 (a `bug-fix' of C11) –
      earlier versions of R or compilers may have defaulted to C99.

      Current options are:

      USE_C17
          Use a standard that is at most C17.  The intention is to
          allow legacy packages to still be installed when later C
          standards become the default, including packages using new
          keywords as identifiers or with K&R-style function
          declarations.  This will use C17 if available, falling back
          to C11.

      USE_C90
          Use the C90 (aka C89) standard.  (As that standard did not
          require compilers to identify that version, all we can verify
          is that the compiler does not claim to be using a later
          standard.  It may accept C99 features – for example clang
          accepts // to make comments.)

      USE_C99
          Use the C99 standard. This should be rarely needed – it
          avoids the few new features of C11/C17 which can be useful if
          a package assumes them if C17 is specified and they are not
          implemented.

      USE_C23
          Use C23 (or in future, later).  Compiler/library support for
          C23 is still being implemented, but LLVM clang from 15.0.0
          and GCC from 13 have quite extensive support.

      These can be specified as part of the SystemRequirements field in
      the package's DESCRIPTION file or _via_ options --use-C17 and so
      on of R CMD INSTALL and R CMD SHLIB.

      For further details see “Writing R Extensions” §1.2.5.

    • (Windows) A src/Makefile.ucrt or src/Makefile.win file is now
      included after <R_HOME>/etc<R_ARCH>/Makeconf and so no longer
      needs to include that file itself.  Installation of a package
      with such a file now uses a site Makevars file in the same way as
      a package with a src/Makevars.win file would.

    • configure is now passed crucial variables such as CC and CFLAGS
      in its environment, as many packages were not setting them (as
      documented in ‘Writing R Extensions’ §1.2).

      This has most effect where configure is used to compile parts of
      the package – most often by cmake or libtool which obfuscate the
      actual compile commands used.

      Also used for configure.win and configure.ucrt on Windows.

  FORTRAN Flags:

    • The flag -fno-optimize-sibling-calls is no longer forced for
      gfortran 7 and later.  It should no longer be needed now using
      ‘hidden’ character-length arguments when calling BLAS/LAPACK
      routines from C/C++ is the default even for packages.  (Unless
      perhaps packages call Fortran code from C/C++ without using R's
      headers and without allowing for these arguments.)

  C-Level Facilities:

    • The deprecated S-compatibility macros DOUBLE_* in
      R_ext/Constants.h (included by R.h) have been removed.

    • The deprecated legacy typedefs of Sint and Sfloat in header R.h
      are no longer defined, and that header no longer includes header
      limits.h from C nor climits from C++.

    • New macro CAD5R() is provided in Rinternals.h and used in a few
      places in the R sources.

    • ALTREP now supports VECSXP vectors. Contributed by Gabor Csardi
      in PR#17620.

    • The Rcomplex definition (in header R_ext/Complex.h) has been
      extended to prevent possible mis-compilation when interfacing
      with Fortran (PR#18430).  The new definition causes compiler
      warnings with static initializers such as {1, 2}, which can be
      changed to {.r=1, .i=2}.

      Using the new definition from C++ depends on compiler extensions
      supporting C features that have not been incorporated into the
      C++ standards but are available in g++ and clang++: this may
      result in C++ compiler warnings but these have been worked around
      for recent versions of common compilers (GCC, Apple/LLVM clang,
      Intel).

      It is intended to change the inclusion of header R_ext/Complex.h
      by other R headers, so C/C++ code files which make use of
      Rcomplex should include that header explicitly.

  Utilities:

    • R CMD check does more checking of package .Rd files, warning
      about invalid email addresses and (some) invalid URIs and noting
      empty \item labels in description lists.

    • R CMD check now also reports problems when reading package news
      in md (file NEWS.md) and (optionally) plain text (file NEWS)
      formats.

    • _R_CHECK_TIMINGS_ defaults to a value from the environment even
      for R CMD check --as-cran; this allows for exceptionally fast or
      slow platforms.

      It now applies to checking PDF and HTML versions of the manuals,
      and ‘checking CRAN incoming feasibility’.

    • R CMD check can optionally (but included in --as-cran) check
      whether HTML math rendering _via_ KaTeX works for the package .Rd
      files.

    • Non-interactive debugger invocations can be trapped by setting
      the environment variable _R_CHECK_BROWSER_NONINTERACTIVE_ to a
      true value.  This is enabled by R CMD check --as-cran to detect
      the use of leftover browser() statements in the package.

    • The use of sprintf and vsprintf from C/C++ has been deprecated in
      macOS 13 and is a known security risk.  R CMD check now reports
      (on all platforms) if their use is found in compiled code:
      replace by snprintf or vsnprintf respectively. [*NB:* whether
      such calls get compiled into the package is platform-dependent.]

    • Where recorded at installation, R CMD check reports the C and
      Fortran compilers used to build R.

      It reports the OS in use (if known, as given by osVersion) as
      well as that R was built for.

      It notes if a C++ standard was specified which is older than the
      current default: many packages have used C++11 to mean ‘not
      C++98’ — as C++11 is the minimum supported since R 4.0.0, that
      specification can probably be removed.

    • R CMD INSTALL reports the compilers (and on macOS, the SDK) used,
      and this is copied to the output of R CMD check.

      Where a C++ standard is specified, it is reported.

    • R CMD check's ‘checking compilation flags in Makevars’ has been
      relaxed to accept the use of flags such as -std=f2008 in
      PKG_FFLAGS.

    • tools::buildVignettes() has a new argument skip, which is used by
      R CMD check to skip (and note) vignettes with unavailable
      \VignetteDepends (PR#18318).

    • New generic .AtNames() added to enable class-specific completions
      after @. The formerly internal function findMatches() is now
      exported, mainly for use in methods for .DollarNames() and
      .AtNames().

  Deprecated and Defunct:

    • default.stringsAsFactors() is defunct.

    • Calling as.data.frame.<class>() directly (for 12 atomic classes)
      is going to be formally deprecated, currently activated by
      setting the environment variable
      _R_CHECK_AS_DATA_FRAME_EXPLICIT_METHOD_ to non-empty, which also
      happens in R CMD check --as-cran.

  Bug Fixes:

    • Hashed environments with sizes less than 5 can now grow.
      (Reported to R-devel by Duncan Garmonsway.)

    • as.character(<Rd>, deparse = TRUE) failed to re-escape curly
      braces in LaTeX-like text.  (Reported by Hadley Wickham in
      PR#18324.)

    • library() now passes its lib.loc argument when requiring Depends
      packages; reported (with fix) in PR#18331 by Mikael Jagan.

    • R CMD Stangle: improved message about ‘Output’ files.

    • head(x, n) and tail(x, n) now signal an error if n is not
      numeric, instead of incidentally “working” sometimes returning
      all of x.  Reported and discussed by Colin Fay, in PR#18357.

    • The "lm" method for summary() now gives the correct F-statistic
      when the model contains an offset.  Reported in PR#18008.

    • C() and `contrasts<-`() now preserve factor level names when
      given a function object (as opposed a function name which did
      preserve names). Reported in PR#17616.

    • c(a = 1, 2)[[]] no longer matches 2 but rather signals a
      _classed_ error.  Reported and analysed by Davis Vaughan in
      PR#18367, a duplicate of PR#18004, by Jan Meis et al.  For
      consistency, NULL[[]] is also erroneous now.  x[[]] <- v gives an
      error of the same class "MissingSubscriptError".

    • The relist() function of utils now supports NULL elements in the
      skeleton (PR#15854).

    • ordered(levels = *) (missing x) now works analogously to factor(,
      ordered=TRUE); reported (with fix) by Achim Zeileis in PR#18389.

    • User-defined Rd macro definitions can now span multiple lines,
      thanks to a patch from Duncan Murdoch. Previously, the Rd parser
      silently ignored everything after the first line.

    • Plain-text help (tools::Rd2txt()) now preserves an initial blank
      line for text following description list items.

    • tools::Rd2HTML() and tools::Rd2latex() no longer split \arguments
      and \value lists at Rd comments.

    • tools::Rd2latex() now correctly handles optional text outside
      \items of argument lists as well as bracketed text at the
      beginning of sections, e.g., \value{[NULL]}.

    • as.character(<POSIXt>) now behaves more in line with the methods
      for atomic vectors such as numbers, and is no longer influenced
      by options().  Ditto for as.character(<Date>).  The
      as.character() method gets arguments digits and OutDec with
      defaults _not_ depending on options().  Use of as.character(*,
      format = .) now warns.

    • Similarly, the as.character.hexmode() and *.octmode() methods
      also behave as good citizen methods and back compatibility option
      keepStr = TRUE.

    • The as.POSIXlt(<POSIXlt>) and as.POSIXct(<POSIXct>) default
      methods now do obey their tz argument, also in this case.

    • as.POSIXlt(<Date>) now does apply a tz (time zone) argument, as
      does as.POSIXct(); partly suggested by Roland Fuß on the R-devel
      mailing list.

    • as.Date.POSIXlt(x) now also works when the list components are of
      unequal length, aka “partially filled” or “ragged”.

    • expand.model.frame() looked up variables in the wrong environment
      when applied to models fitted without data.  Reported in
      PR#18414.

    • time() now (also) uses the ts.eps = getOption("ts.eps") argument
      and thus by default rounds values very close to the start (or
      end) of a year.  Based on a proposal by Andreï V. Kostyrka on
      R-help.

    • Printing of a factanal() result with just one factor and sort =
      TRUE now works regularly, fixing PR#17863 by Timothy Bates,
      thanks to the ‘R Contributors’ working group.

    • Printing 0-length objects of class "factor", "roman", "hexmode",
      "octmode", "person", "bibentry", or "citation" now prints
      something better, one of which fixes PR#18422, reported by
      Benjamin Feakins.

    • Sys.timezone() queries timedatectl only if systemd is loaded;
      addressing a report by Jan Gorecki in PR#17421.

    • The formula method of cor.test() had scoping problems when
      environment(formula) was not the calling environment; reported
      with a patch proposal by Mao Kobayashi in PR#18439.

    • attach() of an environment with active bindings now preserves the
      active bindings.  Reported by Kevin Ushey in PR#18425.

    • BLAS detection now works also with system-provided libraries not
      available as regular files.  This fixes detection of the
      Accelerate framework on macOS since Big Sur.  Reported by David
      Novgorodsky.

    • download.file() gives a helpful error message in case of an
      invalid download.file.method option, thanks to Colin Fay's report
      in PR#18455.

    • Sporadic crashes of Rterm when using completion have been fixed.

    • Rprof() is now more reliable.  A livelock in thread
      initialization with too short sampling interval has been fixed on
      macOS.  A deadlock in using the C runtime has been fixed on
      Windows.  A potential deadlock has been prevented on Unix.

    • Cursor placement in Rgui now works even after a fixed-width font
      is selected.

    • Mandatory options (options()) are now set on startup so that
      saving and restoring them always works (PR#18372).

    • Package installation, R CMD INSTALL or install.packages(*), now
      parses each of the <pkg>/R/*.R files individually instead of
      first concatenating and then parse()ing the large resulting file.
      This allows parser or syntax errors to be diagnosed with correct
      file names and line numbers, thanks to Simon Dedman's report and
      Bill Dunlap's patch in PR#17859.

      This _does_ require syntactically self contained R source files
      now, fixing another inadvertent bug.

    • predict.lm(<model with offset>) now finds the offset in the
      correct environment, thanks to André Gillibert's report and patch
      in PR#18456.

    • getInitial(<formula>) now finds the selfStart model in the
      correct environment.  (Reported by Ivan Krylov in PR#18368.)

    • Fix for possible segfault when using recently-added graphics
      features, such as gradients, clipping paths, masks, and groups
      with pdf(file=NULL).

    • class(m) <- class(m) no longer changes a matrix m by adding a
      class _attribute_.

    • packageDate(pkg) now only warns once if there is no pkg.

    • When ts() creates a multivariate time series, "mts", it also
      inherits from "array" now, and is.mts() is documented _and_
      stricter.

    • Rd2txt() now preserves line breaks of \verb Rd content and from
      duplicated \cr.  The former also fixes the rendering of verbatim
      output from Rd \Sexpr in plain-text help.

    • uniroot(f, interval) should no longer wrongly converge _outside_
      the interval in some cases where abs(f(x)) == Inf for an x at the
      interval boundary, thanks to posts by Ben Bolker and Serguei
      Sokol on R-devel.

    • Vectorized alpha handling in palette functions such as in gray(),
      rainbow(), or hcl.colors() works correctly now, thanks to Achim
      Zeileis' report and patch in PR#18476.

    • Formatting and print()ing of bibentry objects has dropped the
      deprecated citation.bibtex.max argument, such that the bibtex
      argument's default for print.bibentry() depends directly on the
      citation.bibtex.max option, whereas in format.bibentry() the
      option no longer applies.

    • Attempting to use a character string naming a foreign function
      entry point in a foreign function call in a package will now
      signal an error if the packages has called R_forceSymbols to
      specify that symbols must be used.

    • An error in table() could permanently set options(warn=2)
      promoting all subsequent warnings to errors.

    • The sigma() function gave misleading results for binary GLMs.  A
      new method for objects of class "glm" returns the square root of
      the estimate of the dispersion parameter using the same
      calculation as summary.glm().

    • bs() and ns() in the (typical) case of automatic knot
      construction, when some of the supposedly inner knots coincide
      with boundary knots, now moves them inside (with a warning),
      building on PR#18442 by Ben Bolker.

    • R CMD on Windows now skips the site profile with --no-site-file
      and --vanilla even when R_PROFILE is set (PR#18512, from Kevin
      Ushey).

Changes in R 4.2.3:

  C-Level Facilities:

    • The definition of DL_FUNC in R_ext/Rdynload.h has been changed to
      be fully C-compliant.  This means that functions loaded _via_ for
      example R_GetCCallable need to be cast to an appropriate type if
      they have any arguments.

    • .Machine has a new element sizeof.time_t to identify old systems
      with a 32-bit type and hence a limited range of date-times (and
      limited support for dates millions of years from present).

  Package Installation:

    • (Windows) The default C++ standard had accidentally been left at
      C++11 when it was changed to C++14 on Unix.

  Bug Fixes:

    • As "POSIXlt" objects may be “partially filled” and their list
      components meant to be recycled, length() now is the length of
      the longest component.

    • as.POSIXlt.Date() could underflow for dates in the far past (more
      than half a million years BCE).

    • as.Date.POSIXlt(x) would return "1970-01-01" instead of NA in R
      4.2.2, e.g., for

              x <- as.POSIXlt(c("2019-01-30","2001-1-1"))
              x$mon <- c(0L, NA); as.Date(x)
      
    • R CMD check failed to apply enabled _R_CHECK_SUGGESTS_ONLY_ to
      examples and vignettes (regression in R 4.2.0).

    • R CMD check did not re-build vignettes in separate processes by
      default (regression in R 4.2.0).

    • Running examples from HTML documentation now restores previous
      knitr settings and options (PR#18420).

    • Quartz: fonts are now located using Core Graphics API instead of
      deprecated ATS which is no longer supported in the macOS 13 SDK
      (PR#18426).  This also addresses an issue where the currently
      used font in the Quartz device context was not correctly
      retained.

    • (Windows) Math symbols in text drawing functions are again
      rendered correctly (PR#18440).  This fixes a regression in R
      4.2.1 caused by a fix in PR#18382 which uncovered an issue in
      GraphApp due to which the symbol charset was not used with TT
      Symbol font face.

    • (Windows) Installing a package with a src/Makefile.{win,ucrt}
      file includes ~/.R/Makevars.win64 in the search for user
      makevars, as documented in “R Installation and Administration”
      and done for packages with a src/Makevars.{win,ucrt} file.

    • format(<POSIXlt_w/_unbalanced_sec>, "....%OS<n>") with n > 0 no
      longer accidentally uses the unbalanced seconds, thanks to
      Suharto Anggono's report (including patch) in PR#18448.

    • solve.default(a, b) works around issues with some versions of
      LAPACK when a contains NA or NaN values.

    • When UseMethod() cannot dispatch, it no longer segfaults
      producing the error message in case of a long class(), thanks to
      Joris Vankerschaver's report (including patch) in PR#18447.

    • When example(foo, ..) produces graphics on an interactive device
      it needs to open itself, it now leaves devAskNewPage() unchanged
      even when it was FALSE, thus fixing a 14 years old ‘FIXME’.

    • packageDescription() again catches errors from encoding
      conversions. This also fixes broken packageVersion() in C locale
      on systems where iconv does not support transliteration.

Changes in R 4.2.2:

  New Features:

    • tools::Rdiff(useDiff = TRUE) checks for the presence of an
      external diff command and switches to useDiff = FALSE if none is
      found.  This allows R CMD Rdiff to always work.

    • On Windows, environment variable R_LIBCURL_SSL_REVOKE_BEST_EFFORT
      can be used to switch to only ‘best-effort’ SSL certificate
      revocation checks with the default "libcurl" download method.
      This reduces security, but may be needed for downloads to work
      with MITM proxies (PR#18379).

    • (macOS) The run-time check for libraries from XQuartz for X11 and
      Tcl/Tk no longer uses otool from the Apple Developer Tools
      (PR#18400).

    • The LaTeX style for producing the PDF manuals, Rd.sty, now loads
      the standard amsmath, amsfonts and amssymb packages for greater
      coverage of math commands in the Rd \eqn and \deqn macros.  The
      \mathscr LaTeX command is also provided (via the mathrsfs
      package, if available, or the amsfonts bundle otherwise),
      fulfilling the wish of PR#18398.

    • (Windows) The default format of readClipboard() and
      writeClipboard() has been changed to 13 (CF_UNICODETEXT).

  Installation on a Unix-Alike:

    • The PDF manuals (if built) can be compacted by the new target
      make compact-pdf (at the top level or in directory doc/manual).

    • There is now configure support for LLVM clang 15 on Linux, which
      defaults to position-independent (PIE) executables whereas
      gfortran does not.

    • Many small changes to ease compilation (and suppress warnings)
      with LLVM clang 15.

  Bug Fixes:

    • Rscript -e would fail if stdin were closed (Reported by Henrik
      Bengtsson.)

    • qt(*, log.p=TRUE) in outer tails no longer produces NaN in its
      final steps, thus fixing PR#18360.

    • tools::Rd2latex() now escapes hashes and ampersands when writing
      URLs, fixing LaTeX errors with such URLs in \tabular.

    • When isGeneric(f, fdef=*) is used with mismatching names, the
      warning is better understandable; reported (with fix) in PR#18370
      by Gabe Becker.

    • poly(x, n) now works again (and is now documented) when x is a
      "Date" or "POSIXct" object, or of another class while fulfilling
      mode(x) == "numeric".  This also enables poly(x, *, raw=TRUE) for
      such variables.  Reported by Michael Chirico to R-devel.

    • write.table(), write.csv() and write.csv2() restore their
      numerical precision (internal equivalent of digits = 15) after an
      interrupt (PR#18384).

    • One can now read also byte FF from a clipboard connection
      (PR#18385).

    • source("") and source(character()) now give more helpful error
      messages.

    • R CMD check --as-cran set _R_CHECK_TIMINGS_ too late to have the
      intended effect.

    • as.POSIXlt(x) now also works with very large dates x, fixing
      PR#18401 reported by Hannes Mühleisen.

    • Files can now be extracted even from very large zip archives
      (PR#18390, thanks to Martin Jakt).

    • Non-finite objects of class "POSIXlt" are now correctly coerced
      to classes "Date" and "POSIXct"; following up on the extension to
      format() them correctly.

    • Added methods for is.finite(), is.infinite() and is.nan() for
      "POSIXlt" date-time objects.

  Bug Fixes (Windows):

    • Non-ASCII characters are now properly displayed on Windows in
      windows created using GraphApp via e.g. winDialogString thanks to
      a workaround for an at least surprising Windows behavior with
      UTF-8 as the system encoding (PR#18382).

    • Find and replace operations work again in the script editor in
      Rgui on Windows.

    • Computation of window size based on requested client size in
      GraphApp when running in a multi-byte locale on Windows has been
      fixed (regression in R 4.2.0 for users of systems where R 4.1
      used a single-byte locale).  Rgui again respects the number of
      console rows and columns given in Rconsole file.

    • Rterm support for Alt+xxx sequences has been fixed to produce the
      corresponding character (only) once. This fixes pasting text with
      tilde on Italian keyboard (PR#18391).

Changes in R 4.2.1:

  New Features:

    • New function utils::findCRANmirror() to find out if a CRAN mirror
      has been selected, otherwise fallback to the main site.  This
      behaves in the same way as tools::CRAN_package_db() and is
      intended for packages wishing to access CRAN for purposes other
      than installing packages.

      The need for this was shown by a day when the main CRAN website
      was offline and a dozen or so packages which had its URL
      hardcoded failed their checks.

  Installation on a Unix-Alike:

    • The libraries searched for by --with-blas (without a value) now
      include BLIS (after OpenBLAS but before ATLAS).  And on macOS,
      the Accelerate framework (after ATLAS).  (This is patterned after
      the AX_BLAS macro from the Autoconf Archive.)

    • The included LAPACK sources have been updated to 3.10.1.

  Utilities:

    • The (full path to) the command tidy to be used for HTML
      validation can be set by environment variable R_TIDYCMD.

    • Setting environment variable _R_CHECK_RD_VALIDATE_RD2HTML_ to a
      false value will override R CMD check --as-cran and turn off HTML
      validation.  This provides a way to circumvent a problematic
      tidy.

      The 2006 version that ships with macOS is always skipped.

  C-Level Facilities:

    • The undocumented legacy declarations of Sint, Sfloat, SINT_MAX
      and SINT_MIN in header R.h are deprecated.

  Bug Fixes:

    • fisher.test(d) no longer segfaults for “large” d; fixing PR#18336
      by preventing/detecting an integer overflow reliably.

    • tar(., files=*) now produces correctly the warning about invalid
      UID or GID of files, fixing PR#18344, reported by Martin Morgan.

    • tk_choose.files() with multi = FALSE misbehaved on paths
      containing spaces (PR#18334) (regression introduced in R 4.0.0).

    • sort(x, partial = ind, *) now works correctly notably for the
      non-default na.last = FALSE or TRUE, fixing PR#18335 reported by
      James Edwards.

    • Environment variable _R_CHECK_XREFS_REPOSITORIES_ is only used
      for checking .Rd cross-references in R CMD check (as documented)
      and not for other uses looking for a CRAN mirror.

    • The search for a CRAN mirror when checking packages now uses
      getOption("repos") if that specifies a CRAN mirror, even when it
      does not also specify all three Bioconductor repositories (as was
      previously required).

    • The HTML code generated by tools::Rd2HTML() has been improved to
      pass tidy 5.8.0.

  Bug Fixes (Windows):

    • Writing to a clipboard connection works again, fixing a
      regression in R 4.2.0 (PR#18332).  Re-using a closed clipboard
      connection no longer issues a spurious warning about an ignored
      encoding argument.

    • C function getlocale no longer attempts to query an unsupported
      category from the OS, even when requested at R level, which may
      cause crashes when R 4.2.0 (which uses UCRT) is embedded
      (reported by Kevin Ushey).

    • Accent keys now work in GraphApp Unicode windows, which are used
      by Rgui whenever running in a multibyte locale (so also in UTF-8,
      hence fixing a regression in R 4.2.0 for users of systems where R
      4.1 used a single-byte locale).

    • Completion in Rgui now works also with non-ASCII characters.

    • Rgui no longer truncates usage information with --help.

    • Text injection from external applications via SendInput now works
      in GraphApp Unicode windows, fixing a regression in R 4.2.0 for
      Rgui users of systems where R 4.1 used a single-byte locale but R
      4.2.0 uses UTF-8.

    • Performance of txtProgressBar() in Rgui when running in a
      multi-byte locale has been improved (fixing a performance
      regression in R 4.2.0 for users of systems where R 4.1 used a
      single-byte locale).

    • The script editor in Rgui now works also on systems using UTF-8
      as the native encoding.  Users of the script editor have to
      convert their scripts with non-ASCII characters to UTF-8 before
      reading them in R 4.2.1 or newer (on recent Windows where UTF-8
      is used).  This fixes a regression in R 4.2.0, which prevented
      some operations with scripts when they contained non-ASCII
      characters.

Changes in R 4.2.0:

  Significant User-Visible Changes:

    • The formula method of aggregate() now matches the generic in
      naming its first argument x (resolving PR#18299 by Thomas
      Soeiro).

      This means that calling aggregate() with a formula as a named
      first argument requires name formula in earlier versions of R and
      name x now, so portable code should not name the argument (code
      in many packages did).

    • Calling && or || with either argument of length greater than one
      now gives a warning (which it is intended will become an error).

    • Calling if() or while() with a condition of length greater than
      one gives an error rather than a warning.  Consequently,
      environment variable _R_CHECK_LENGTH_1_CONDITION_ no longer has
      any effect.

    • Windows users should consult the Windows section below for some
      profound changes including

        • Support for 32-bit builds has been dropped.

        • UTF-8 locales are used where available.

        • The default locations for the R installation and personal
          library folder have been changed.

      Thanks to Tomas Kalibera for months of work on the Windows port
      for this release.

  New Features:

    • matrix(x, n, m) now warns in more cases where length(x) differs
      from n * m, as suggested by Abby Spurdle and Wolfgang Huber in
      Feb 2021 on the R-devel mailing list.

      This warning can be turned into an error by setting environment
      variable _R_CHECK_MATRIX_DATA_ to TRUE: R CMD check --as-cran
      does so unless it is already set.

    • Function file_test() in package utils gains tests for symlinks,
      readability and writability.

    • capabilities("libxml") is now false.

      The description of capabilities("http/ftp") now reflects that it
      refers to the default method, no longer the internal one.

    • simplify2array() gains an except argument for controlling the
      exceptions used by sapply().

    • Environment variables R_LIBS_USER and R_LIBS_SITE are both now
      set to the R system default if unset or empty, and can be set to
      NULL to indicate an empty list of user or site library
      directories.

    • The warning for axis()(-like) calls in cases of relatively small
      ranges (typically in log-scale situations) is slightly improved
      _and_ suppressed from explicit calls to .axisPars() as has always
      been the intention.

    • The contrasts setter function `contrasts<-` gains an explicit
      default how.many = NULL rather than just using missing(how.many).

    • grid.pretty() gains a new optional argument n = 5.

    • There is a new function .pretty() with option bounds as a
      technical-utility version of pretty().  It and pretty() gain a
      new argument f.min with a better than back-compatible default.

    • Function grDevices::axisTicks() and related functions such as
      graphics::axis() work better, notably for the log scale; partly
      because of the pretty() improvements, but also because care is
      taken e.g., when ylim is finite but diff(ylim) is infinite.

    • nclass.FD() gains a digits option.

    • The R Mathlib internal C function bd0() (called indirectly from a
      dozen probability density and distribution functions such as
      dpois(), dbinom(), dgamma(), pgamma() _etc_) has been
      complemented by a more sophisticated and (mostly) more accurate C
      function ebd0(), currently called only by internal dpois_raw()
      improving accuracy for R level dpois() and potentially others
      calling it such as dnbinom(), dgamma() or pgamma().  (Thanks to
      Morten Welinder's PR#15628.)

    • write.ftable() gains sep = " " argument as suggested by Thomas
      Soeiro.

    • The names of the locale categories supported by R's
      Sys.getlocale() and Sys.setlocale() are now provided by variable
      .LC.categories in the base namespace.

    • The Date and POSIXt methods for hist() and the histogram method
      for plot() now also use the new default col = "lightgray" in
      consistency with the corresponding change to hist()'s default for
      R 4.0.0.

    • hist.default() gains new fuzz argument, and the histogram plot
      method no longer uses fractional axis ticks when displaying
      counts ("Frequency").

    • mapply() and hence Map() now also obey the “max-or-0-if-any”
      recycling rule, such that, e.g., Map(`+`, 1:3, 1[0]) is valid
      now.

    • as.character(<obj>) for "hexmode" or "octmode" objects now
      fulfils the important basic rule as.character(x)[j] ===
      as.character(x[j]).

    • The set utility functions, notably intersect() have been tweaked
      to be more consistent and symmetric in their two set arguments,
      also preserving a common mode.

    • substr(ch, start,end) <- new now e.g., preserves names(ch); ditto
      for substring(), thanks to a patch from Brodie Gaslam.

    • plot(<lm>) gains a extend.ylim.f argument, in partial response to
      PR#15285; further PR#17784 is fixed thanks to several
      contributors and a patch by Elin Waring.  The Cook's dist
      contours get customizable via cook.col and cook.lty with a
      different default color and their legend is nicer by default and
      customizable via cook.legendChanges.

    • Attempting to subset an object that is not subsettable now
      signals an error of class notSubsettableError. The
      non-subsettable object is contained in the object field of the
      error condition.

    • Subscript-out-of-bounds errors are now signaled as errors of
      class subscriptOutOfBoundsError.

    • Stack-overflow errors are now signaled as errors inheriting from
      class stackOverflowError. See ?stackOverflowError for more
      details.

    • New partly experimental Sys.setLanguage() utility, solving the
      main problem of PR#18055.

    • gettext() and gettextf() get a new option trim = TRUE which when
      set to false allows translations for strings such as "Execution
      halted\n" typical for C code.

    • An experimental implementation of hash tables is now available.
      See ?hashtab for more details.

    • identical() gains a extptr.as.ref argument for requesting that
      external pointer objects be compared as reference objects.

    • reorder() gets an argument decreasing which it passes to sort()
      for level creation; based on the wish and patch by Thomas Soeiro
      in PR#18243.

    • as.vector() gains a data.frame method which returns a simple
      named list, also clearing a long-standing ‘FIXME’ to enable
      as.vector(<data.frame>, mode="list").  This breaks code relying
      on as.vector(<data.frame>) to return the unchanged data frame.

    • legend() is now vectorized for arguments cex, x.intersp, and
      text.width.  The latter can now also be specified as a vector
      (one element for each column of the legend) or as NA for
      computing a proper column wise maximum value of strwidth(legend).
      The argument y.intersp can be specified as a vector with one
      entry for each row of the legend.

      legend() also gains new arguments title.cex and title.font.
      Thanks to Swetlana Herbrandt.

    • Deparsing no longer remaps attribute names dim, dimnames, levels,
      names and tsp to historical S-compatible names (which structure()
      maps back).

    • sample() and sample.int() have additional sanity checks on their
      size and n arguments.

      all.equal.numeric() gains a sanity check on its tolerance
      argument – calling all.equal(a, b, c) for three numeric vectors
      is a surprisingly common error.

      mean(na.rm =), rank(na.last =), barplot(legend.text =),
      boxplot(), contour(drawlabels =), polygon(border =) and
      methods::is(class2 =) have more robust sanity checks on their
      arguments.

      R CMD Rd2pdf (used by R CMD check) has a more robust sanity check
      on the format of \alias{} commands.

    • psigamma(x, deriv) for negative x now also works for deriv = 4
      and 5; their underlying C level dpsifn() is documented in
      ‘Writing R Extensions’.

    • The HTML help system now uses HTML5 (wish of PR#18149).

    • ks.test() now provides exact p-values also with ties and MC
      p-values in the two-sample (Smirnov) case.  By Torsten Hothorn.

    • ks.test() gains a formula interface, with y ~ 1 for the
      one-sample (Kolmogorov) test and y ~ group for the two-sample
      (Smirnov) test.  Contributed by Torsten Hothorn.

    • The return value from ks.test() now has class c("ks.test",
      "htest") – packages using try() need to take care to use
      inherits() and not == on the class.

    • New functions psmirnov(), qsmirnov() and rsmirnov() in package
      stats implementing the asymptotic and exact distributions of the
      two-sample Smirnov statistic.

    • iconv() now allows sub = "c99" to use C99-style escapes for UTF-8
      inputs which cannot be converted to encoding to.

    • In a forward pipe |> expression it is now possible to use a named
      argument with the placeholder _ in the rhs call to specify where
      the lhs is to be inserted.  The placeholder can only appear once
      on the rhs.

    • The included LAPACK sources have been updated to version 3.10.0,
      except for the four Fortran 77 routines which 3.10.0 has
      re-implemented in Fortran 90 (where the older versions have been
      retained as the R build process does not support Fortran 90).

    • path.expand() and most other uses of tilde expansion now warn if
      a path would be too long if expanded.  (An exception is
      file.exists(), which silently returns false.)

    • trunc(<Date>, *) now supports units = "months" or "years" for
      consistency with the POSIXt method, thanks to Dirk Eddelbuettel's
      proposal in PR#18099.

    • list2DF() now checks that its arguments are of the same length,
      rather than use recycling.

    • The HTML help system has several new features: LaTeX-like math
      can be typeset using either KaTeX or MathJax, usage and example
      code is highlighted using Prism, and for dynamic help the output
      of examples and demos can be shown within the browser if the
      knitr package is installed. These features can be disabled by
      setting the environment variable _R_HELP_ENABLE_ENHANCED_HTML_ to
      a false value.

  Graphics:

    • The graphics engine version, R_GE_version, has been bumped to 15
      and so packages that provide graphics devices should be
      reinstalled.

    • The grid package now allows the user to specify a “vector” of
      pattern fills.  The fill argument to gpar() accepts a list of
      gradients and/or patterns and the functions linearGradient(),
      radialGradient(), and pattern() have a new group argument.

      Points grobs (data symbols) can now also have a pattern fill.

      The grobCoords() function now returns a more informative and
      complex result.

    • The grid package has new functions for drawing isolated groups:
      grid.group(), grid.define(), and grid.use().  These functions add
      compositing operators and affine transformations to R's graphics
      capabilities.

      The grid package also has new functions for stroking and filling
      paths: grid.stroke(), grid.fill(), and grid.fillStroke().

      A new function as.path() allows the user to specify the fill rule
      for a path that is to be used for clipping, stroking, or filling;
      available options are "winding" and "evenodd".  A new function
      as.mask() allows the user to specify the type of a mask;
      available options are "alpha" and "luminance".

      These new features are only supported so far (at most) on the
      Cairo-based graphics devices and on the pdf() device.

    • dev.capabilities() reports on device support for the new
      features.

    • par() now warns about unnamed non-character arguments to prevent
      misuse such as {usr <- par("usr"); par(usr)}.

  Windows:

    • R uses UTF-8 as the native encoding on recent Windows systems (at
      least Windows 10 version 1903, Windows Server 2022 or Windows
      Server 1903).  As a part of this change, R uses UCRT as the C
      runtime.  UCRT should be installed manually on systems older than
      Windows 10 or Windows Server 2016 before installing R.

    • The default personal library on Windows, folder R\win-library\x.y
      where x.y stands for R release x.y.z, is now a subdirectory of
      Local Application Data directory (usually a hidden directory
      C:\Users\username\AppData\Local).  Use shell.exec(.libPaths()[1])
      from R to open the personal library in Explorer when it is first
      in the list (PR#17842).

    • R uses a new 64-bit Tcl/Tk bundle.  The previous 32-bit/64-bit
      bundle had a different layout and can no longer be used.

    • Make files and installer scripts for Windows have been tailored
      to Rtools42, the newly recommended 64-bit gcc 10.3 MinGW-W64 UCRT
      toolchain.

    • Rtools42 by default uses the Windows security features ASLR and
      DEP; hence CRAN builds of R and packages also do.

    • R now supports files Makevars.ucrt, Makefile.ucrt, configure.ucrt
      and cleanup.ucrt in packages, which are used in preference to the
      .win variants.  This allows keeping the .win files around to
      support older versions of R.  This feature will be removed in the
      future once support for older versions of R would no longer be
      needed.

    • R.version gains a new field crt (only on Windows) to denote the C
      runtime.  The value is "ucrt".

    • On Windows, download.file(method = "auto") and url(method =
      "default") now follow Unix in using "libcurl" for all except
      file:// URIs.

    • Rtools42 includes an unpatched Msys2 build of GNU tar.  Paths
      including drive letters can be made to work by adding
      --force-local to environment variable TAR_OPTIONS.  (Rtools40 and
      earlier included a patched version which defaulted to this
      option.)

    • Installer builds of R automatically find the Rtools42 software
      collection as well as the compiler toolchain.  No PATH setting is
      required from the user.

    • The default installation directory of R for a user-only
      installation has been changed to the User Program Files directory
      (usually a hidden directory
      C:\Users\username\AppData\Local\Programs) to follow Windows
      conventions.  Use shell.exec(R.home()) from R to open the R
      installation directory in Explorer (PR#17842).

    • R now supports installation-time patching of packages.  Patches
      may be installed from a supplied URL or a local directory or
      disabled.  Patches are included into the installed packages for
      reference.  This experimental feature may be removed in the
      future.

    • libcurl is now required for building from source.

    • The clipboard connection now works also with text in other than
      the current native encoding (PR#18267, with Hiroaki Yutani).
      Text is always pasted to the clipboard in UTF16-LE and the
      encoding argument is ignored.

    • The internal case-changing functions are now used by default on
      Windows – this circumvents problems (for example with E acute) of
      the UCRT Windows' runtime.

    • R on Windows now uses the system memory allocator.  Doug Lea's
      allocator was used since R 1.2.0 to mitigate performance
      limitations seen with system allocators on earlier versions of
      Windows.

    • memory.limit() and memory.size() are now stubs on Windows (as on
      Unix-alikes).

    • Applications embedding R on Windows can now use additional
      callbacks, which have so far only been available only on Unix
      (PR#18286).

  Installation:

    • Facilities for accessing ftp:// sites are no longer tested
      (except _pro tem_ for curlGetHeaders()) as modern browsers have
      removed support.

    • R can now be built with DEFS = -DSTRICT_R_HEADERS .

  Package Installation:

    • R CMD INSTALL no longer tangles vignettes. This completes an R
      CMD build change in R 3.0.0 and affects packages built before R
      3.0.2. Such packages should be re-made with R CMD build to have
      the tangled R code of vignettes shipped with the tarball.

    • USE_FC_LEN_T will become the default: this uses the correct
      prototypes for Fortran BLAS/LAPACK routines called from C/C++,
      and requires adjustment of most such calls – see ‘Writing R
      Extensions’ §6.6.1.  (This has been supported since R 3.6.2.)

    • Package installation speed for packages installed with
      keep.source has been improved. This resolve the issue reported by
      Ofek Shilon in PR#18236.

  Utilities:

    • R CMD check can optionally report files/directories left behind
      in home, /tmp (even though TMPDIR is set) and other directories.
      See the “R Internals” manual for details.

    • R CMD check now reports byte-compilation errors during
      installation.  These are not usually fatal but may result in
      parts of the package not being byte-compiled.

    • _R_CHECK_DEPENDS_ONLY_ can be applied selectively to examples,
      tests and/or vignettes in R CMD check: see the “R Internals”
      manual.

    • _R_CHECK_SRC_MINUS_W_IMPLICIT_ now defaults to true: recent
      versions of Apple clang on macOS have made implicit function
      declarations in C into a compilation error.

    • R CMD check --as-cran makes use of the environment variable
      AUTORECONF.  See the “R Internals” manual §8 for further details.

    • R CMD check --use-valgrind also uses valgrind when re-building
      vignettes as some non-Sweave vignettes unhelpfully comment out
      all their code when R CMD check runs vignettes.

    • Errors in re-building vignettes (unless there are LaTeX errors)
      are reported by R CMD check as ERROR rather than WARNING when
      running vignettes has been skipped (as it frequently is in CRAN
      checks and by --as-cran).

    • R CMD Rd2pdf gains a --quiet option that is used by R CMD build
      when building the PDF package manual.

    • R CMD Rd2pdf now always runs LaTeX in batch mode, consistent with
      Texinfo >= 6.7. The --batch option is ignored.

    • R CMD build and R CMD check now include the Rd file name and line
      numbers in the error message of an \Sexpr evaluation failure.

    • For packages using the \doi Rd macro (now an install-time \Sexpr)
      but no other dynamic Rd content, R CMD build now produces a
      smaller tarball and is considerably faster – skipping temporary
      package installation.

    • R CMD check can optionally (but included in --as-cran) validate
      the HTML produced from the packages .Rd files.  See
      <https://blog.r-project.org/2022/04/08/enhancements-to-html-documentation/>:
      this needs a fairly recent version of HTML Tidy to be available.

  C-Level Facilities:

    • The non-API header R_ext/R-ftp-http.h is no longer provided, as
      the entry points it covered are now all defunct.

    • A number of non-API declarations and macro definitions have been
      moved from the installed header Rinternals.h to the internal
      header Defn.h. Packages that only use entry points and
      definitions documented to be part of the API as specified in
      ‘Writing R Extensions’ §6 should not be affected.

    • The macro USE_RINTERNALS no longer has any effect when compiling
      package code.  Packages which also use R_NO_REMAP will need to
      ensure that the remapped names are used for calls to API
      functions that were formerly also made available as macros.

    • The deprecated legacy S-compatibility macros PROBLEM, MESSAGE,
      ERROR, WARN, WARNING, RECOVER, ... are no longer defined in
      R_ext/RS.h (included by R.h).  Replace these by calls to Rf_error
      and Rf_warning (defined in header R_ext/Error.h included by R.h).

      Header R_ext/RS.h no longer includes R_ext/Error.h.

    • Header R_ext/Constants.h (included by R.h) when included from C++
      now includes the C++ header cfloat rather than the C header
      float.h (now possible as C++11 is required).

    • The legacy S-compatibility macros DOUBLE_* in R_ext/Constants.h
      (included by R.h) are deprecated.

    • The deprecated S-compatibility macros SINGLE_* in
      R_ext/Constants.h (included by R.h) have been removed.

    • R_Calloc, R_Free and R_Realloc are preferred to their unprefixed
      forms and error messages now use the prefix. These forms were
      introduced in R 3.4.0 and are available even when
      STRICT_R_HEADERS is defined.

    • rmultinom has been documented in ‘Writing R Extensions’ §6 so is
      now part of the R API.

    • Similarly, Rtanpi, called from R level tanpi() is now part of the
      R API.

    • The long-deprecated, undocumented and non-API entry point call_R
      is no longer declared in R_ext/RS.h (included by R.h).

    • The header S.h which has been unsupported since Jan 2016 has been
      removed.  Use R.h instead.

  Deprecated and Defunct:

    • The (non-default and deprecated) method = "internal" for
      download.file() and url() no longer supports http:// nor ftp://
      URIs.  (It is used only for file:// URIs.)

      On Windows, download.file(method = "wininet") no longer supports
      ftp:// URIs.  (It is no longer the default method, which is
      "libcurl" and does.)

      On Windows, the deprecated method = "wininet" now gives a warning
      for http:// and https:// URIs for both download.file() and url().
      (It is no longer the default method.)

    • On Windows, the command-line option --max-mem-size and
      environment variable R_MAX_MEM_SIZE are defunct.  The memory
      allocation limit was important for 32-bit builds, but these are
      no longer supported.

    • default.stringsAsFactors() is now formally deprecated, where that
      was only mentioned on its regular help page, previously.  So it
      now gives a warning if called.

    • unix.time() is defunct now; it had been deprecated since R 3.4.0.

  Bug Fixes:

    • Setting digits = 0 in format(), print.default() (and hence
      typically print()) or options() is again invalid.  Its behaviour
      was platform-dependent, and it is unclear what “zero significant
      digits” should mean (PR#18098).

    • Messages from C code in the cairo section of package grDevices
      are now also offered for translation, thanks to Michael Chirico's
      PR#18123.

    • mean(x) with finite x now is finite also without "long.double"
      capability.

    • R CMD Rd2pdf no longer leaves an empty build directory behind
      when it aborts due to an already existing output file.  (Thanks
      to Sebastian Meyer's PR#18141.)

    • density(x, weights = w, na.rm = TRUE) when anyNA(x) is true, now
      removes weights “in parallel” to x, fixing PR#18151, reported by
      Matthias Gondan.  Additionally, it gets a subdensity option.

    • Conversion of \Sexpr[]{<expR>} to LaTeX or HTML no longer
      produces long blocks of empty lines when <expR> itself contains
      several lines all producing empty output.  Thanks to a report and
      patch by Ivan Krylov posted to R-devel.

    • R CMD build no longer fails if a package vignette uses child
      documents and inst/doc exists.  (Thanks to Sebastian Meyer's
      PR#18156.)

    • When an R documentation (‘help’ source) file man/foo.Rd in a
      package has \donttest{..} examples with a syntax error, it is now
      signalled as ERROR and with correct line numbers relating to the
      *-Ex.R file, thanks to Duncan Murdoch and Sebastian Meyer's
      reports and patch proposals in PR#17501.

    • Improved determination of the correct translation domain in
      non-base packages, addressing the combination of PR#18092 and
      PR#17998 (#c6) with reports and _augmented_ patch #2904 by
      Suharto Anggono.

      Note that "R-base" is no longer the default domain e.g., for
      top-level calls to gettext(); rather translation needs explicit
      domain = * specification in such cases.

    • identical(attrib.as.set=FALSE) now works correctly with data
      frames with default row names.  (Thanks to Charlie Gao's
      PR#18179.)

    • txtProgressBar() now enforces a non-zero width for argument char,
      without which no progress can be visible.

    • dimnames(table(d)) is more consistent in the case where d is a
      list with a single component, thanks to Thomas Soeiro's report to
      R-devel.

      Further, table(d1, d2) now gives an error when d1 and d2 are data
      frames as suggested by Thomas in PR#18224.

    • Fix for drawing semi-transparent lines and fills on the native
      Windows graphics device (PR#18219 and PR#16694).  Thanks to Nick
      Ray for helpful diagnosis on Bugzilla.

    • The deparser now wraps sub-expressions such as if(A) ..  with
      parentheses when needed; thanks to Duncan Murdoch's PR#18232 and
      Lionel Henry's patches there.

    • remove.packages() no longer tries to uninstall Priority: base
      packages, thanks to a report and suggestions by Colin Fay in
      PR#18227.

    • win.metafile() now has xpinch and ypinch arguments so that the
      user can override Windows' (potentially wrong) guess at device
      dimensions.

    • x[i] and x[[i]] for non-integer i should now behave in all cases
      as always documented: the index used is equivalent to
      as.integer(i) unless that would overflow where trunc(i) is used
      instead; thanks to Suharto Anggono's report and patch proposals
      in PR#17977.

    • asOneSidedFormula() now associates the resulting formula with the
      global environment rather than the evaluation environment created
      for the call.

    • <bibentry>$name now matches the field name case-insensitively,
      consistent with bibentry() creation and the replacement method.

    • cbind() failed to detect some length mismatches with a mixture of
      time-series and non-time-series inputs.

    • The default LaTeX style file Sweave.sty used by the RweaveLatex
      driver no longer loads the obsolete ae package; thanks to a
      report by Thomas Soeiro in PR#18271.  Furthermore, it now skips
      \usepackage[T1]{fontenc} for engines other than pdfTeX (if
      detected) or if the new [nofontenc] option is used.

    • smooth.spline() now stores its logical cv argument more safely,
      fixing a rare bug when printing, and also stores n.

    • smooth.spline(x,y,*) now computes the cv.crit statistic
      correctly, also when is.unsorted(x), fixing PR#18294.

    • The data.frame method of rbind() now warns when binding
      not-wholly-recycling vectors, by analogy to the default method
      (for matrices).

    • setAs() finds the correct class for name to when multiple
      packages define a class with that name. Thanks to Gabor Csardi
      for the report.

    • Fix for detaching a package when two classes of the same name are
      present in method signatures for the same generic. Thanks to
      Gabor Csardi for the report.

    • match.arg("", c("", "a", "B")) gives a better error message, in
      part from PR#17959, thanks to Elin Waring.

    • R CMD Sweave --clean no longer removes pre-existing files or
      subdirectories (PR#18242).

    • The quartz() device no longer splits polylines into subpaths.
      That has caused narrowly-spaced lines with many points to always
      look solid even when dashed line type was used due to dash phase
      restarts.

    • Deparsing constructs such as quote(1 + `!`(2) + 3) works again as
      before R 3.5.0, thanks to the report and patch in PR#18284 by
      Suharto Anggono.

    • as.list(f) for a factor f now keeps names(f), fixing PR#18309.

    • qbeta(.001, .9, .009) and analogous qf() calls now return a
      correct value instead of NaN or wrongly 1, all with a warning;
      thanks to the report by Ludger Goeminne in PR#18302.

    • plot.lm() failed to produce the plot of residuals vs.  factor
      levels (i.e., which=5 when leverages are constant) for models
      with character predictors (PR#17840).

    • interaction.plot(..., xtick = TRUE) misplaced the x-axis line
      (PR#18305).

    • Not strictly fixing a bug, format()ing and print()ing of
      non-finite Date and POSIXt values NaN and +/-Inf no longer show
      as NA but the respective string, e.g., Inf, for consistency with
      numeric vector's behaviour, fulfilling the wish of PR#18308.

    • R CMD check no longer runs test scripts generated from
      corresponding .Rin files twice and now signals an ERROR if
      processing an .Rin script fails.

    • tools::Rd2txt() used for plain-text help pages now renders \hrefs
      (if tools::Rd2txt_options(showURLs = TRUE)) and \urls with
      percent-encoding and standards-compliant delimiting style (angle
      brackets and no URL: prefix).  \email is now rendered with a
      mailto: prefix.

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.

    • Internet access based on libcurl, including curlGetHeaders(), was
      not respecting the "timeout" option.  If this causes
      unanticipated timeouts, consider increasing the default by
      setting R_DEFAULT_INTERNET_TIMEOUT.

    • as.Date(<char>) now also works with an initial "", thanks to
      Michael Chirico's PR#17909.

    • isS3stdGeneric(f) now detects an S3 generic also when it is
      trace()d, thanks to Gabe Becker's PR#17917.

    • R_allocLD() has been fixed to return memory aligned for long
      double type PR#16534.

    • fisher.test() no longer segfaults when called again after its
      internal stack has been exceeded PR#17904.

    • Accessing a long vector represented by a compact integer sequence
      no longer segfaults (reported and debugged by Hugh Parsonage).

    • duplicated() now works also for strings with multiple encodings
      inside a single vector PR#17809.

    • phyper(11, 15, 0, 12, log.p=TRUE) no longer gives NaN; reported
      as PR#17271 by Alexey Stukalov.

    • Fix incorrect calculation in logLik.nls() PR#16100, patch from
      Sebastian Meyer.

    • A very old bug could cause a segfault in model.matrix() when
      terms involved logical variables.  Part of PR#17879.

    • model.frame.default() allowed data = 1, leading to involuntary
      variable capture (rest of PR#17879).

    • tar() no longer skips non-directory files, thanks to a patch by
      Sebastian Meyer, fixing the remaining part of PR#16716.

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 endianness in such
      cases.

    • sequence() is now an S3 generic with an internally implemented
      default method, and gains arguments to generate more complex
      sequences.  Based on code from the S4Vectors Bioconductor package
      and the advice of Hervé Pagès.

    • print()'s default method and many other methods (by calling the
      default eventually and passing ...) now make use of a new
      optional width argument, avoiding the need for the user to set
      and reset options("width").

    • memDecompress() supports the RFC 1952 format (e.g. in-memory
      copies of gzip-compressed files) as well as RFC 1950.

    • memCompress() and memDecompress() support long raw vectors for
      types "gzip" and "zx".

    • sweep() and slice.index() can now use names of dimnames for their
      MARGIN argument (apply has had this for almost a decade).

    • New function proportions() and marginSums(). These should replace
      the unfortunately named prop.table() and margin.table(). They are
      drop-in replacements, but also add named-margin functionality.
      The old function names are retained as aliases for
      back-compatibility.

    • Functions rbinom(), rgeom(), rhyper(), rpois(), rnbinom(),
      rsignrank() and rwilcox() which have returned integer since R
      3.0.0 and hence NA when the numbers would have been outside the
      integer range, now return double vectors (without NAs, typically)
      in these cases.

    • matplot(x,y) (and hence matlines() and matpoints()) now call the
      corresponding methods of plot() and lines(), e.g, when x is a
      "Date" or "POSIXct" object; prompted by Spencer Graves'
      suggestion.

    • stopifnot() now allows customizing error messages via argument
      names, thanks to a patch proposal by Neal Fultz in PR#17688.

    • unlink() gains a new argument expand to disable wildcard and
      tilde expansion.  Elements of x of value "~" are now ignored.

    • mle() in the stats4 package has had its interface extended so
      that arguments to the negative log-likelihood function can be one
      or more vectors, with similar conventions applying to bounds,
      start values, and parameter values to be kept fixed.  This
      required a minor extension to class "mle", so saved objects from
      earlier versions may need to be recomputed.

    • The default for pdf() is now useDingbats = FALSE.

    • The default fill colour for hist() and boxplot() is now col =
      "lightgray".

    • The default order of the levels on the y-axis for spineplot() and
      cdplot() has been reversed.

    • If the R_ALWAYS_INSTALL_TESTS environment variable is set to a
      true value, R CMD INSTALL behaves as if the --install-tests
      option is always specified. Thanks to Reinhold Koch for the
      suggestion.

    • New function R_user_dir() in package tools suggests paths
      appropriate for storing R-related user-specific data,
      configuration and cache files.

    • capabilities() gains a new logical option Xchk to avoid warnings
      about X11-related capabilities.

    • The internal implementation of grid units has changed, but the
      only visible effects at user-level should be

        • a slightly different print format for some units (especially
          unit arithmetic),

        • faster performance (for unit operations) and

        • two new functions unitType() and unit.psum().

      Based on code contributed by Thomas Lin Pedersen.

    • When internal dispatch for rep.int() and rep_len() fails, there
      is an attempt to dispatch on the equivalent call to rep().

    • Object .Machine now contains new longdouble.* entries (when R
      uses long doubles internally).

    • news() has been enhanced to cover the news on R 3.x and 2.x.

    • For consistency, N <- NULL; N[[1]] <- val now turns N into a list
      also when val) has length one.  This enables dimnames(r1)[[1]] <-
      "R1" for a 1-row matrix r1, fixing PR#17719 reported by Serguei
      Sokol.

    • deparse(..), dump(..), and dput(x, control = "all") now include
      control option "digits17" which typically ensures 1:1
      invertibility.  New option control = "exact" ensures numeric
      exact invertibility via "hexNumeric".

    • When loading data sets via read.table(), data() now uses
      LC_COLLATE=C to ensure locale-independent results for possible
      string-to-factor conversions.

    • A server socket connection, a new connection type representing a
      listening server socket, is created via serverSocket() and can
      accept multiple socket connections via socketAccept().

    • New function socketTimeout() changes the connection timeout of a
      socket connection.

    • The time needed to start a homogeneous PSOCK cluster on localhost
      with many nodes has been significantly reduced (package
      parallel).

    • New globalCallingHandlers() function to establish global
      condition handlers.  This allows registering default handlers for
      specific condition classes. Developed in collaboration with
      Lionel Henry.

    • New function tryInvokeRestart() to invoke a specified restart if
      one is available and return without signaling an error if no such
      restart is found.  Contributed by Lionel Henry in PR#17598.

    • str(x) now shows the length of attributes in some cases for a
      data frame x.

    • Rprof() gains a new argument filter.callframes to request that
      intervening call frames due to lazy evaluation or explicit eval()
      calls be omitted from the recorded profile data.  Contributed by
      Lionel Henry in PR#17595.

    • The handling of ${FOO-bar} and ${FOO:-bar} in Renviron files now
      follows POSIX shells (at least on a Unix-alike), so the first
      treats empty environment variables as set and the second does
      not.  Previously both ignored empty variables.  There are several
      uses of the first form in etc/Renviron.

    • New classes argument for suppressWarnings() and
      suppressMessages() to selectively suppress only warnings or
      messages that inherit from particular classes.  Based on patch
      from Lionel Henry submitted with PR#17619.

    • New function activeBindingFunction() retrieves the function of an
      active binding.

    • New "cairoFT" and "pango" components in the output of
      grSoftVersion().

    • New argument symbolfamily in cairo-based graphics devices and new
      function cairoSymbolFont() that can be used to provide the value
      for that argument.

  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 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 are available at
    doc/html/NEWS.3.html and doc/html/NEWS.2.html.

