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% -*- coding: utf-8 -*-
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\newcommand{\Rlogo}{\if{html}{\figure{../../html/Rlogo.svg}{options: class="toplogo" alt="[R logo]"}}\if{latex}{\figure{Rlogo.pdf}{options: width=0.5in}}}
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\name{NEWS}
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\title{R News}
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\encoding{UTF-8}
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\section{\Rlogo CHANGES IN R 3.6.0}{

   \subsection{SIGNIFICANT USER-VISIBLE CHANGES}{
     \itemize{
       \item Serialization format version 3 becomes the default for
       serialization and saving of the workspace (\code{save()},
       \code{serialize()}, \code{saveRDS()}, \code{compiler::cmpfile()}).
       Serialized data in format 3 cannot be read by versions of \R prior
       to version 3.5.0.  Serialization format version 2 is still
       supported and can be selected by \code{version = 2} in the
       save/serialization functions.  The default can be changed back for
       the whole \R session by setting environment variables
       \env{R_DEFAULT_SAVE_VERSION} and \env{R_DEFAULT_SERIALIZE_VERSION}
       to \code{2}.  For maximal back-compatibility, files
       \file{vignette.rds} and \file{partial.rdb} generated by \command{R
	 CMD build} are in serialization format version 2, and resave by
       default produces files in serialization format version 2 (unless
       the original is already in format version 3).

       \item The default method for generating from a discrete uniform
       distribution (used in \code{sample()}, for instance) has been
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       changed.  This addresses the fact, pointed out by Ottoboni and
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       Stark, that the previous method made \code{sample()} noticeably
       non-uniform on large populations.  See \PR{17494} for a
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       discussion.  The previous method can be requested using
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       \code{RNGkind()} or \code{RNGversion()} if necessary for
       reproduction of old results.  Thanks to Duncan Murdoch for
       contributing the patch and Gabe Becker for further assistance.
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       The output of \code{RNGkind()} has been changed to also return the
       \sQuote{kind} used by \code{sample()}.
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     }
  }

   \subsection{NEW FEATURES}{
    \itemize{
      \item \code{Sys.setFileTime()} has been vectorized so arguments
      \code{path} and \code{time} of length greater than one are now
      supported.

      \item \code{axis()} gets new option \code{gap.axis = NA} for
      specifying a multiplication factor for the minimal \dQuote{gap}
      (distance) between axis labels drawn.   Its default is \code{1}
      for labels \emph{parallel} to the axis, and \code{0.25} for
      perpendicular ones.

      Perpendicular labels no longer overlap, fixing bug \PR{17384}.

      \item The default method of \code{plot()} gains new arguments
      \code{xgap.axis = NA} and \code{ygap.axis = NA} to be passed to
      the x-- and y-- \code{axis(.., gap.axis=*)} calls.

      \item \code{removeSource()} now works not only for functions but
      also for some language objects.

      \item \code{as.call()}, \code{rep.int()}, \code{rep_len()} and
      \code{nchar()} dispatch internally.

      \item \code{is(object, class2)} looks for \code{class2} in the
      calling namespace after looking in the namespace of
      \code{class(object)}.

      \item \code{extendrange(.., f)} with a length-2 \code{f} now
      extends separately to the left and the right.

      \item \code{lengths()} dispatches internally to S4 methods.

      \item \code{download.file()} on Windows now uses \code{URLdecode()}
      to determine the file extension, and uses binary transfer
      (\code{mode = "wb"}) also for file extension \file{.rds}.

      The help page for \code{download.file()} now contains the same
      information on all platforms.

      \item Setting \samp{C} locale for collation \emph{via} environment
      variables \env{LC_ALL} and \env{LC_COLLATE} and \emph{via} a call
      to \code{Sys.setlocale()} now takes precedence over environment
      variable \env{R_ICU_LOCALE}.

      \item There is a new function, \code{nullfile()}, to give the file
      name of the null system device (e.g., \file{/dev/null}) on the
      current platform. % not the null graphics device.

      \item There are two new options, \code{keep.parse.data} and
      \code{keep.parse.data.pkgs}, which control whether parse data are
      included into sources when \code{keep.source} or
      \code{keep.source.pkgs} is \code{TRUE}.  By default,
      \code{keep.parse.data.pkgs} is now \code{FALSE}, which changes
      previous behavior and significantly reduces space and time overhead
      when sources are kept when installing packages.

      \item In \code{rapply(x, ..)}, \code{x} can also be
      \dQuote{list-like} and of length \eqn{\ge 2^{31}}{>= 2^{31}}.

      \item \code{trimws()} gets new optional \code{whitespace}
      argument, allowing more extensive definitions of \dQuote{space},
      such as including Unicode spaces (as wished in \PR{17431}).

      \item \code{weighted.mean()} no longer coerces the weights to a
      double/numeric vector, since \code{sum()} now handles integer
      overflow. This makes \code{weighted.mean()} more polymorphic and
      endomorphic, but be aware that the results are no longer
      guaranteed to be a vector of type \samp{double}.

      \item When loading namespaces, S3 method registrations which
      overwrite previous registrations are now noted by default (using
      \code{packageStartupMessage()}).

      \item \code{compiler::cmpfile()} gains a \code{version} argument, for
      use when the output file should be saved in serialization format 2.

      \item The axis labeling in the default method of \code{pairs()}
      may now be toggled by new options \code{horOdd} and \code{verOdd}.

      \item (Not Windows nor macOS.) Package \pkg{tcltk} now supports an
      environment variable \env{R_DONT_USE_TK} which if set disables Tk
      initialization.  This is intended for use to circumvent errors in
      loading the package, e.g.\sspace{}with recent Linux running under
      an address sanitizer.

      \item The \code{numeric} method of \code{all.equal()} gets
      optional arguments \code{countEQ} and \code{formatFUN}.  If
      \code{countEQ} is true, the mean error is more sensible when many
      entries are \bold{eq}ual.

      \item \code{outer(x,y, FUN = "*")} is more efficient using
      \code{tcrossprod(u,v)} instead of \code{u \%*\% t(v)}.

      \item \code{vcov(<mlm>)} is more efficient via new optional
      arguments in \code{summary.mlm()}.

      \item The default method of \code{summary()} gets an option to
      choose the \emph{kind} of \code{quantile()}s to use; wish of
      \PR{17438}.

      \item Fitting multiple linear models \emph{via} \code{lm()} does
      work with \emph{matrix} offsets, as suggested in \PR{17407}.

      \item The new functions \code{mem.maxVSize()} and
      \code{mem.maxMSize()} allow the maximal size of the vector heap
      and the maximal number of nodes allowed in the current \command{R}
      process to be queried and set.

      \item \code{news()} gains support for \file{NEWS.md} files.

      \item An effort has been started to have our reference manuals,
      i.e., all help pages. show platform-independent information (rather
      than Windows or Unix-alike specifics visible only on that platform).
      Consequently, the Windows version of \code{X11()} / \code{x11()}
      got identical formal arguments to the Unix one.

      \item \code{sessionInfo()$running} has been factored out in a new
      variable \code{osVersion}. % precomputed at utils namespace load time

      \item \code{slice.index()} now also works for multi-dimensional
      margins.

      \item \code{untar()} used with an external \command{tar} command
      assumes this supports decompression including \command{xz} and
      automagically detecting the compression type.  This has been true
      of all mainstream implementations since 2009 (for GNU
      \command{tar}, since version 1.22): older implementations are
      still supported \emph{via} the new argument
      \code{support_old_tars} whose default is controlled by environment
      variable \env{R_SUPPORT_OLD_TARS}.  (It looks like NetBSD and
      OpenBSD have \sQuote{older} \command{tar} commands for this
      purpose.)

      \item The new function \code{asplit()} allow splitting an array or
      matrix by its margins.

      \item New functions \code{errorCondition()} and
      \code{warningCondition()} provide a convenient way to create
      structured error and warning objects.

      \code{.Deprecated()} now signals a warning of class
      \code{"deprecatedWarning"}, and \code{.Defunct()} now signals an
      error of class \code{"defunctError"}.

      \item Many \sQuote{package not found} errors are now signaled as
      errors of class \code{"packageNotFoundError"}.

      \item As an experimental feature, when \code{loadNamespace()} fails
      because the requested package is not available the error is
      initially signaled with a \code{retry_loadNamespace} restart
      available.  This allows a calling handler to try to install the
      package and continue.

      \item \code{S3method()} directives in \file{NAMESPACE} can now
      also be used to perform \emph{delayed} S3 method registration.

      \item Experimentally, setting environment variable
      \env{_R_CHECK_LENGTH_1_LOGIC2_} will lead to warnings (or errors
      if the variable is set to a \sQuote{true} value) when \code{&&} or
      \code{||} encounter and use arguments of length more than one.

      \item Added \code{"lines"} and \code{"chars"} coordinate systems
      to \code{grconvertX()} and \code{grconvertY()}.

      \item \code{getOption()} is more efficient notably for the rare
      case when called with two arguments, from several contributors in
      \PR{17394}.

      \item In \code{.col(dim)} and \code{.row(dim)}, \code{dim} now may
      also be an integer-valued \code{"double"}.

      \item \code{sQuote()} and \code{dQuote()} get an explicit \code{q}
      argument with obvious default instead of using
      \code{getOption("fancyQuotes")} implicitly and unconditionally.

      \item \code{unzip()} can list archives with comments and with
      spaces in file names even using an external \command{unzip} command.

      \item Command line completion has a new setting
      \code{rc.settings(dots = FALSE)} to remove \code{...} from the
      list of possible function arguments.

      \item \code{library()} no longer checks packages with compiled
      code match \samp{R.version$platform}.  \code{loadNamespace()}
      never has, and increasingly the \sQuote{canonical name} does not
      reflect the important characteristics of compiled code.
      %% E.g. 32/64-bit compiler settings

      \item The primitive functions \code{drop()} and \code{unclass()}
      now avoid duplicating their data for atomic vectors that are large
      enough, by returning \code{ALTREP} wrapper objects with adjusted
      attributes.  \R{}-level assignments to change attributes will also
      use wrapper objects to avoid duplicating data for larger atomic
      vectors. \R functions like \code{structure()} and \code{unname()}
      will therefore not duplicate data in these settings.  Generic
      vectors as produced by \code{list()} are not yet covered by this
      optimization but may be in due course.

      \item In \code{formals()}, \code{envir} becomes an optional
      argument instead of being hardwired.

      \item Instead of signalling an error for an invalid S4 object
      \code{x}, \code{str(x)} now gives a warning and subsequently still
      shows most parts of \code{x}, e.g., when slots are missing.

      \item \code{gamma(x)} and \code{lgamma(x)} no longer warn when
      correctly returning \code{Inf} or underflowing to zero.  This
      helps maximum likelihood and similar computations.

      \item \code{convertColor()} is now vectorized, so a lot faster for
      converting many colours at once.  The new argument
      \code{vectorized} to \code{colorConverter()} ensures that
      non-vectorized colour converters still work.  (Thanks to Brodie
      Gaslam.)

      \item \code{download.file()} and \code{url()} get new argument
      \code{headers} for custom HTTP headers, e.g., allowing to perform
      basic http authentication, thanks to a patch contributed by Gábor
      Csárdi.

      \item File-based connection functions \code{file()},
      \code{gzfile()}, \code{bzfile()} and \code{xzfile()} now signal an
      error when used on a directory.

      \item For \code{approx()}, \code{splinefun()} \emph{etc}, a new
      setting \code{ties = c("ordered", <fun>)} allows skipping the
      sorting and still treat ties.

      \item \code{format(x)} gives a more user friendly error message in
      the case where no method is defined.  A minimal method is provided
      in \code{format.default(x)} when \code{isS4(x)} is true.

      \item \code{which(x)} now also works when \code{x} is a long
      vector, thanks to Suharto Anggono's \PR{17201}.  \strong{NB}: this
      may return a double result, breaking the previous guarantee of an
      integer result.

      \item \code{seq.default()} is more careful to return an
      \code{integer} (as opposed to \code{double}) result when its
      arguments are large and/or classed objects; see comment #9 of
      Suharto Anggono's \PR{17497}.

      \item The \code{plot()} method for \code{lm} and \code{glm} fits,
      \code{plot.lm()}, gains a new option \code{iter.smooth} with a
      default of \code{0} for binomial fits, no longer down-weighting
      when smoothing the residuals.

      \item \code{zip()} passes its list of files \emph{via} standard
      input to the external command when too long for the command line
      (on some platforms).

      \item \code{data()} gains an \code{overwrite} argument.

      \item \code{t.test()} now also returns the standard error (in
      list component \code{stderr}).

      \item \code{model.matrix(*, contrasts.arg = CC)} now warns about
      invalid \code{contrasts.arg}s.

      \item Performance of \code{substr()} and \code{substring()} has been
      improved.

      \item \code{stopifnot()} has been simplified thanks to Suharto
      Anggono's proposals to become considerably faster for cheap
      expressions.

      \item The default \sQuote{user agent} has been changed when
      accessing \samp{http://} and \samp{https://} sites using
      \samp{libcurl}.  (A site was found which caused \samp{libcurl} to
      infinite-loop with the previous default.)

      \item \code{sessionInfo()} now also contains \code{RNGkind()} and
      prints it when it differs from the default; based on a proposal and
      patch by Gabe Becker in \PR{17535}.
      Also, \code{RNGversion(getRversion())} works directly.

      \item \code{library()} and \code{require()} now allow more control
      over handling search path conflicts when packages are
      attached. The policy is controlled by the new
      \code{conflicts.policy} option.

      \item \code{barplot()} gets a formula method, thanks to a patch
      proposal by Arni Magnusson in \PR{17521}.

      \item \code{pmax()} and \code{pmin(x)} now also work for long
      vectors, thanks to Suharto Anggono's \PR{17533}.

      \item \code{bxp()} now warns when omitting duplicated arguments.

      \item New \code{hcl.colors()} function to provide wide range of
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      HCL-based colour palettes with much better perceptual properties
      than the existing RGB/HSV-based palettes like \code{rainbow()}.
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      Also a new \code{hcl.pals()} function to list available palette
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      names for \code{hcl.colors()}.

      Contributed by Achim Zeileis.

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      \item The default colours for \code{image()} and
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      \code{filled.contour()} are now based on \code{hcl.colors()}.

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      \item The palette-generating functions \code{rainbow()},
      \code{gray.colors()}, etc.\sspace{}get a new \code{rev} argument
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      to facilitate reversing the order of colors.
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      \item New \code{str2lang()} and \code{str2expression()} as streamlined
      versions of \code{parse(text=., keep.source=FALSE)} allow to abstract
      typical call constructions, e.g., in \code{formula} manipulations.
      (Somewhat experimental) % << TO DO

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      \item Add \code{update_PACKAGES()} for incrementally updating a
      package repository index, instead of rebuilding the index from
      scratch. Thanks to Gabe Becker in \PR{17544} for the patch, based
      on part of his \pkg{switchr} package.
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    }
  }

  \subsection{INSTALLATION on a UNIX-ALIKE}{
    \itemize{
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      \item The options selected for the C++ compiler default to the
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      C++11 standard if supported, otherwise to the C++98 standard.

      \item Visibility macros such as \samp{C_VISIBILITY} can now be
      user-set (including to empty), e.g.\sspace{}in \file{config.site}.

      \item Macro \samp{FCLIBS}, which has sometimes been needed on
      Solaris, has been renamed to \samp{FCLIBS_XTRA}.

      \item Macro \samp{F77} is always set to the value of \samp{FC}, so
      the latter should be set to user-select the Fortran compiler for
      both fixed-form and free-form Fortran.  In particular,
      \command{gfortran} is now the first choice for \samp{F77}, not
      \command{f95}.

      Macros \samp{FFLAGS} and \samp{FCFLAGS} remain distinct to allow
      for a compiler which needs a flag to select free- or fixed-form
      Fortran (most use the source-file extension to choose: \file{.f}
      is fixed-form and \file{.f90} and \file{.f95} are free-form).

      If only one of them is set, its value is used for both.

      \item The special-casing of \samp{CFLAGS}, \samp{CXXFLAGS} and
      \samp{FFLAGS} for Intel compilers on Linux has been removed: we do
      not have recent experience but the generic defaults now chosen are
      the same as those previously special-cased for \samp{x86_64}.

      If necessary, override the defaults on the \command{configure}
      command line or in file \file{config.site}.

      \item Long-untested \command{configure} support for HP-UX and very
      old versions of Linux has been removed.

      \item \command{configure --with-blas} (without specifying a value)
      includes OpenBLAS in its search (before ATLAS and a generic
      BLAS).  This follows recent versions of the \samp{ax_blas}
      autoconf macro.

      \item The \command{configure} macro \samp{MAKEINFO} has been
      updated to \samp{TEXI2ANY}.

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      \item Support for \command{make install-strip} has been enhanced.
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    }
  }

  \subsection{PACKAGE INSTALLATION}{
    \itemize{
      \item Source package installation is by default \sQuote{staged}:
      the package is installed into a temporary location under the final
      library directory and moved into place once the installation is
      complete.  The benefit is that partially-installed packages are
      hidden from other \R sessions.

      The overall default is set by environment variable
      \env{R_INSTALL_STAGED}.  \command{R CMD INSTALL} has new options
      \option{--staged-install} and \option{--no-staged-install}, and
      packages can use the \samp{StagedInstall} field in their
      \file{DESCRIPTION} file to opt out.  (That opt-out is a temporary
      measure which may be withdrawn in future.)

      Staged installation requires either \option{--pkglock} or
      \option{--lock}, one of which is used by default.

      \item The interpretation of source code with extension \file{.f}
      is changing.  Previously this denoted FORTRAN 77 code, but current
      compilers no longer have a FORTRAN 77 mode and interpret it as
      \sQuote{fixed-form} Fortran 90 (or later where supported) code.
      Extensions \file{.f90} and \file{.f95} continue to indicate
      \sQuote{free-form} Fortran code.

      Legal FORTRAN 77 code is also legal fixed-form Fortran 9x; however
      this change legitimizes the use of later features, in particular
      to replace features marked \sQuote{obsolescent} in Fortran 90 and
      \sQuote{deleted} in Fortran 2018 which \command{gfortran} 8.x and
      later warn about.

      \item Packages containing files in the \file{src} directory with
      extensions \file{.f90} or \file{.f95} are now linked using the C
      or C++ compiler rather than the Fortran 9x compiler.  This is
      consistent with fixed-form Fortran code and allows mixing of C++
      and free-form Fortran on most platforms.

      Consequentially, a package which includes free-form Fortran 9x
      code which uses OpenMP should include \samp{SHLIB_OPENMP_CFLAGS}
      (or the \samp{CXXFLAGS} version if they also include C++ code) in
      \samp{PKG_LIBS} rather than \samp{SHLIB_OPENMP_FCFLAGS} ---
      fortunately on almost all current platforms they are the same
      flag.

      \item Macro \samp{PKG_FFLAGS} will be used for the compilation of
      both fixed-form and free-form Fortran code unless
      \samp{PKG_FCFLAGS} is also set (in \file{src/Makevars} or
      \file{src/Makevars.win}).

      \item The make macro \samp{F_VISIBILITY} is now preferred for
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      both fixed-form and free-form Fortran, for use in
      \file{src/Makevars} and similar.
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      \item \command{R CMD INSTALL} gains a new option \option{--strip}
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      which (where supported) strips installed shared object(s): this
      can also be achieved by setting the environment variable
      \env{_R_SHLIB_STRIP_} to a true value.

      The new option \option{--strip-lib} attempts stripping of
      static and shared libraries installed under \file{lib}.

      These are most useful on platforms using GNU \code{binutils} (such
      as Linux) and compiling with \option{-g} flags.

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      \item There is more support for installing UTF-8-encoded packages
      in a strict Latin-1 locale (and probably for other Latin locales):
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      non-ASCII comments in \R code (and \file{NAMESPACE} files) are
      worked around better.
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    }
  }

  \subsection{UTILITIES}{
    \itemize{
      \item \command{R CMD check} now optionally checks makefiles for
      correct and portable use of the \samp{SHLIB_OPENMP_*FLAGS} macros.

      \item \command{R CMD check} now evaluates \code{\\Sexpr{}}
      expressions (including those in macros) before checking the
      contents of \file{Rd} files and so detects issues both in
      evaluating the expressions and in the expanded contents.

      \item \command{R CMD check} now lists missing packages separated
      by commas and with regular quotes such as to be useful as argument
      in calling \code{install.packages(c(..))}; from a suggestion by
      Marcel Ramos.

      \item \code{tools::Rd2latex()} now uses UTF-8 as its default
      output encoding.

      \item \command{R CMD check} now checks line endings of files with
      extension \file{.hpp} and those under \file{inst/include}.  The
      check now includes that a non-empty file is terminated with a
      newline.

      \command{R CMD build} will correct line endings in such files.

      \item \command{R CMD check} now tries re-building all vignettes
      rather than stopping at the first error: whilst doing so it adds
      \sQuote{bookmarks} to the log.  By default (see the \sQuote{R
      Internals} manual) it re-builds each vignette in a separate
      process.

      It now checks for duplicated vignette titles (also known as
      \sQuote{index entries}): they are used as hyperlinks on
      \acronym{CRAN} package pages and so do need to be unique.

      \item \command{R CMD check} has more comprehensive checks on the
      \file{data} directory and the functioning of \code{data()} in a
      package.

      \item \command{R CMD check} now checks
      \command{autoconf}-generated \file{configure} files have their
      corresponding source files, including optionally attempting to
      regenerate them on platforms with \command{autoreconf}.

      \item \command{R CMD build} has a new option
      \option{--compression} to select the compression used for the tarball.

      \item \command{R CMD build} now removes \file{src/*.mod} files on
      all platforms.
    }
  }

  \subsection{C-LEVEL FACILITIES}{
    \itemize{
      \item New pointer protection C functions \code{R_PreserveInMSet} and
      \code{R_ReleaseFromMSet} have been introduced to replace
      \code{UNPROTECT_PTR}, which is not safe to mix with \code{UNPROTECT}
      (and with \code{PROTECT_WITH_INDEX}). Intended for use in parsers
      only.

      \item \code{NAMEDMAX} has been raised to 7 to allow further
      protection of intermediate results from (usually ill-advised)
      assignments in arguments to \code{BUILTIN} functions. Properly
      written package code should not be affected.

      \item \code{R_unif_index} is now considered to be part of the C API.
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      \item \code{R_GetCurrentEnv()} allows C code to retrieve the current
      environment.
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    }
  }

  \subsection{DEPRECATED AND DEFUNCT}{
    \itemize{
      \item Argument \code{compressed} of \code{untar()} is
      deprecated --- it is only used for external \code{tar} commands
      which increasingly for extraction auto-detect compression and
      ignore their \option{zjJ} flags.

      \item \code{var(f)} and hence \code{sd(f)} now give an error for
      \code{factor} arguments; they gave a deprecation warning since \R
      3.2.3, \PR{16564}.

      \item Package \pkg{tools}' \code{vignetteDepends()} has been
      deprecated (it called a function deprecated since Feb 2016), being
      partly replaced by newly exported \code{vignetteInfo()}.

      \item The \command{f77_f2c} script has been removed: it
      no longer sufficed to compile the \file{.f} files in \R.

      \item The deprecated legacy support of \command{make} macros such
      as \samp{CXX1X} has been removed: use the \samp{CXX11} forms
      instead.

      \item Make macro \samp{F77_VISIBILITY} is deprecated in favour of
      \samp{F_VISIBILITY}.

      \item Make macros \samp{F77}, \samp{FCPIFCPLAGS} and
      \samp{SHLIB_OPENMP_FCFLAGS} are deprecated in favour of \samp{FC},
      \samp{FPICFLAGS} and \samp{SHLIB_OPENMP_FFLAGS} respectively.

      \item \code{$.data.frame} had become an expensive version of
      the default method, so has been removed. (Thanks to Radford Neal
      for picking this up and to Duncan Murdoch for providing a patch.)
    }
  }

  \subsection{BUG FIXES}{
    \itemize{
      \item \code{replayPlot(r)} now also works in the same \R session
      when \code{r} has been \dQuote{reproduced} from serialization,
      typically after saving to and reading from an RDS file.

      \item \code{substr()} and \code{substring()} now signal an error
      when the input is invalid UTF-8.

      \item \code{file.copy()} now works also when its argument \code{to}
      is of length greater than one.

      \item \code{mantelhaen.test()} no longer suffers from integer
      overflow in largish cases, thanks to Ben Bolker's \PR{17383}.

      \item Calling \code{setGeneric("foo")} in a package no longer
      fails when the enclosing environment of the implicit generic
      \code{foo()} is \code{.GlobalEnv}.

      \item \code{untar(file("<some>.tar.gz"), *)} now gives a better
      error message, suggesting to use \code{gzfile()} instead.

      \item Method dispatch uses more relevant environments when looking
      up class definitions.

      \item The documentation for \code{identify()} incorrectly claimed
      that the indices of identified points were returned in the order
      that the points were selected.  \code{identify()} now has a new
      argument \code{order} to allow the return value to include the
      order in which points were identified; the documentation has been
      updated.  Reported by Richard Rowe and Samuel Granjeaud.

      \item \code{order(...., decreasing=c(TRUE, FALSE))} could fail in
      some cases. Reported from StackOverflow via Karl Nordström.

      \item User macros in Rd files now accept empty and multi-line
      arguments.

      \item Changes in \code{print.*()}, thanks to Lionel Henry's
      patches in \PR{17398}:
      \itemize{
	\item Printing lists, pairlists or attributes containing calls
	with S3 class no longer evaluate those.

	\item Printing S4 objects within lists and pairlists dispatches
	with \code{show()} rather than \code{print()}, as with
	auto-printing.

	\item The indexing tags (names or \code{[[<n>]]}) of recursive
	data structures are now printed correctly in complex cases.

	\item Arguments supplied to \code{print()} are now properly
	forwarded to methods when printing lists, pairlists or
	attributes containing S3 objects.

	\item The print parameters are now preserved when printing S3
	objects or deparsing symbols and calls.  Previously, printing
	lists containing S3 objects or expressions would reset these
	parameters.

	\item Printing lists, pairlists or attributes containing
	functions now uses \code{srcref} attributes if present.
      }

      \item Calling \code{install.packages()} with a length zero
      \code{pkgs} argument now is a no-op (\PR{17422}).

      \item \code{unlist(x)} now returns a correct \code{factor} when
      \code{x} is a nested list with factor leaves, fixing \PR{12572}
      and \PR{17419}.

      \item The documentation \code{help(family)} gives more details
      about the \code{aic} component, thanks to Ben Bolker's prompting.

      \item The documentation for \code{attributes} and
      \code{`attributes<-`} now gives \code{x} as name of the first and
      main argument which the implementation has been requiring, fixing
      \PR{17434}.  For consistency, the first argument name is also
      changed from \code{obj} to \code{x} for \code{`mostattributes<-`}.

      \item \code{strwidth()} now uses \code{par("font")} as default
      font face (\PR{17352}).

      \item \code{plot(<table>, log="x")} no longer warns about \code{log}.

      \item The \code{print()} method for \code{"htest"} objects now
      formats the test statistic and parameter directly and hence no
      longer rounds to units \emph{before} the decimal point.  Consequently,
      printing of \code{t.test()} results with a small number of digits
      now shows non-large \code{df}'s to the full precision (\PR{17444}).

      \item \code{kruskal.test()} and \code{fligner.test()} no longer
      erroneously insist on numeric \code{g} group arguments (\PR{16719}).

      \item Printing a news db via the browser now does a much better
      job (\PR{17433}).

      \item \code{print.aov()} missed column names in the multivariate case
      due to misspelling (reported by Chris Andrews).

      \item \code{axis()} now creates valid \code{at} locations also for
      small subnormal number ranges in log scale plots.

      \item \code{format.POSIXlt()} now also recycles the \code{zone}
      and \code{gmtoff} list components to full length when needed,
      and its internal C code detects \code{have_zone} in more cases.
      In some cases, this changes its output to become compatible with
      \code{format.POSIXct()}.

      \item On Windows, \code{detectCores()} in package \pkg{parallel}
      now detects processors in all processor groups, not just the group
      \R is running in (impacts particularly systems with more than 64
      logical processors).  Reported by Arunkumar Srinivasan.

      \item On Windows, \code{socketSelect()} would hang with more than
      64 sockets, and hence \code{parallel::clusterApplyLB()} would hang
      with more than 64 workers.  Reported by Arunkumar Srinivasan.

      \item \code{as(1L, "double")} now does coerce (\PR{17457}).

      \item \code{lm.influence()}, \code{influence.measures()},
      \code{rstudent()} etc now work (more) correctly for multivariate
      models (\code{"mlm"}), thanks to (anonymous) stackoverflow remarks.

      \item \code{sample.int(2.9, *, replace=TRUE)} again behaves as
      documented and as in R < 3.0.0, namely identically to
      \code{sample.int(2, ..)}.% consider back porting to 3.5.x !

      \item Fixes to \code{convertColor()} for chromatic adaptation;
      thanks to Brodie Gaslam \PR{17473}.

      \item Using \code{\\Sexpr[stage=install]{..}} to create an
      \file{Rd} section no longer gives a warning in \command{R CMD
	check}; problem originally posted by Gábor Csárdi, then reported
      as \PR{17479} with a partial patch by Duncan Murdoch.

      \item Parse data now include a special node for equal assignment.

      \item \code{split.default()} no longer relies on \code{[[<-()}, so
      it behaves as expected when splitting an object by a factor with
      the empty string as one of its levels.  Thanks to Brad Friedman for
      the report.

      \item Line numbers in messages about \file{.Rd} files are now more
      reliable, thanks to a patch from Duncan Murdoch.

      \item In the \code{numeric} method for \code{all.equal()}, a
      numeric \code{scale} argument is now checked to be positive and
      allowed to be of length > 1. (The latter worked originally and
      with a warning in recent years).

      \item Deferred string conversions now record the \code{OutDec}
      option setting when not equal to the default.  Reported by Michael
      Sannella.

      \item When \code{y} is numeric and \code{f} a \code{factor},
      \code{plot(y ~ f)} nicely uses "y" and "f" as y- and x-labels.
      The more direct \code{boxplot(y ~ f)} now does too.  The new
      argument \code{ann = FALSE} may be used to suppress these.

      \item Subassignment to no/empty rows of a data frame is more
      consistent and typically a no-op in all cases instead of sometimes
      an error; part of Emil Bode's \PR{17483}.

      \item Calls like \code{formatC(*, zero.print = "< 0.001")} no
      longer give an error and are further improved via new optional
      argument \code{replace.zero}.  Reported by David Hugh-Jones.

      \item \code{methods::formalArgs("<fn>")} now finds the same
      function as \code{formals("<fn>")}, fixing Emil Bode's \PR{17499}.

      \item The \pkg{methods} package better handles duplicated class
      names across packages.

      \item The default method of \code{seq()} now avoids integer
      overflow, thanks to the report and "cumsum" patch of Suharto
      Anggono's \PR{17497}.

      \item \code{sub()} no longer loses encodings for non-ASCII
      replacements (\PR{17509}).

      \item Fix for rotated raster image on X11 device.  (Partial
      fix for \PR{17148};  thanks to Mikko Korpela).

      \item \code{formula(model.frame(frml, ..))} now returns \code{frml}
      in all cases, thanks to Bill Dunlap.   The previous behavior is
      available as \code{DF2formula(<model.frame>)}.

      \item \code{ar.ols()} also returns scalar \code{var.pred} in
      univariate case (\PR{17517}).

      \item \code{normalizePath()} now treats \code{NA} path as non-existent
      and normalizes it to \code{NA}.  \code{file.access()} treats \code{NA}
      file name as non-existent.  \code{file.edit()} and connection
      functions such as \code{file()} now treat \code{NA} file names as
      errors.

      \item The internal \code{regularize.values()} auxiliary of
      \code{approx()}, \code{splinefun()} etc now warns again when there
      are ties and the caller did not specify \code{ties}.  Further, it no
      longer duplicates \code{x} and \code{y} unnecessarily when \code{x}
      is already sorted (\PR{17515}).

      \item \code{strtoi("", base)} now gives \code{NA} on all platforms,
      following its documentation.  Reported by Michael Chirico.

      \item In the definition of an S4 class, prototype elements are
      checked against the slots of the class, with giving a prototype
      for an undefined slot now being an error.  (Reported by Bill
      Dunlap.)

      \item From \code{setClassUnion()}, if environment variable
      \env{_R_METHODS_SHOW_CHECKSUBCLASSES} is set
      to true, the internal \code{.checkSubclasses()} utility prints
      debugging info to see where it is used.

      \item \code{max.col(m)} with an \code{m} of zero columns now
      returns integer \code{NA} (instead of \code{1}).

      \item \code{axTicks()} no longer returns small \dQuote{almost zero}
      numbers (in exponential format) instead of zero, fixing Ilario
      Gelmetti's \PR{17534}.

      \item \code{isSymmetric(matrix(0, dimnames=list("A","b")))} is
      \code{FALSE} again, as always documented.

      \item The \code{cairo_pdf} graphics device (and other Cairo-based
      devices) now clip correctly to the right and bottom border.

      There was an off-by-one-pixel bug, reported by Lee Kelvin.

      \item \code{as.roman(3) <= 2:4} and all other comparisons now work,
      as do group \code{"Summary"} function calls such as
      \code{max(as.roman(sample(20)))} and \code{as.roman(NA)}.
      (Partly reported by Bill Dunlap in \PR{17542}.)

      \item \code{reformulate("x", response = "sin(y)")} no longer produces
      extra back quotes, \PR{17359}, and gains new optional argument
      \code{env}.
824

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      \item When reading console input from \file{stdin} with re-encoding
      (\command{R --encoding=enc < input}) the code on a Unix-alike now
      ensures that each converted input line is terminated with a
      newline even if re-encoding fails.
829 830 831 832 833 834 835

      \item \code{as.matrix.data.frame()} now produces better strings from
      logicals, thanks to \PR{17548} from Gabe Becker.

      \item The S4 generic signature of \code{rowSums()},
      \code{rowMeans()}, \code{colSums()} and \code{colMeans()} is
      restricted to \code{"x"}.
836 837 838 839 840 841 842 843 844

      \item \code{match(x, tab)} now works for long \emph{character}
      vectors \code{x}, thanks to \PR{17552} by Andreas Kersting.

      \item Class unions are unloaded when their namespace is
      unloaded (\PR{17531}, adapted from a patch by Brodie Gaslam).

      \item \code{selectMethod()} is robust to ANY-truncation of method
      signatures (thanks to Herve Pages for the report).
845 846 847 848
    }
  }
}

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\section{\Rlogo CHANGES IN R 3.5.3}{

  \subsection{INSTALLATION on a UNIX-ALIKE}{
    \itemize{
      \item Detection of flags for C++98/11/14/17 has been improved: in
      particular if CXX??STD is set, it is tried first with no
      additional flags.
    }
  }

  \subsection{PACKAGE INSTALLATION}{
    \itemize{
      \item New macro \samp{F_VISIBILITY} as an alternative to
      \samp{F77_VISIBILITY}.  This will become the preferred form in
      \R 3.6.0.
    }
  }

  \subsection{BUG FIXES}{
    \itemize{
      \item \code{writeLines(readLines(fnam), fnam)} now works as expected,
      thanks to Peter Meissner's \PR{17528}.

      \item \code{setClassUnion()} no longer warns, but uses \code{message()}
      for now, when encountering \dQuote{non local} subclasses of class members.

      \item \code{stopifnot(exprs = T)} no longer fails.
    }
  }
}

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\section{\Rlogo CHANGES IN R 3.5.2}{

  \subsection{PACKAGE INSTALLATION}{
    \itemize{
      \item New macro \samp{CXX_VISIBILITY} analogous to
      \samp{C_VISIBILITY} (which several packages have been misusing for
      C++ code) for the default C++ compiler (but not necessarily one used
      for non-default C++ dialects like C++14).
    }
  }

  \subsection{TESTING}{
    \itemize{
      \item The random number generator tests in
      \file{tests/p-r-random-tests.R} no longer fail occasionally as
      they now randomly sample from \dQuote{certified} random seeds.
    }
  }

  \subsection{BUG FIXES}{
    \itemize{
      \item The \code{"glm"} method of \code{drop1()} miscalculated the
      score test (\code{test="Rao"}) when the model contained an offset.

      \item Linear multiple empty models such as \code{lm(y ~ 0)}
      now have a correctly dimensioned empty coefficient matrix;
      reported by Brett Presnell.

      \item \code{vcov(<empty mlm>)} and hence \code{confint()} now
      work (via a consistency change in \code{summary.lm()}).

      \item \code{confint(<multiple lm()>)} now works correctly;
      reported on R-devel by Steven Pav.

      \item \code{quade.test()} now also works correctly when its
      arguments are not yet sorted along \code{groups}, fixing \PR{15842}.

      \item Installation on a Unix-alike tries harder to link to the
      \samp{pthread} library where required (rather than relying on
      OpenMP to provide it: configuring with \option{--disable-openmp}
      was failing on some Linux systems).

      \item The \code{data.frame} method for \code{print(x)} is fast now
      also for large data frames \code{x} and got an optional argument
      \code{max}, thanks to suggestions by Juan Telleria.

      \item \code{hist()} no longer integer overflows in very rare
      cases, fixing \PR{17450}.

      \item \code{untar()} ignored a character \code{compressed}
      argument: however many external \command{tar} programs ignore
      the flags which should have been set and automagically choose the
      compression type, and if appropriate \command{gzip} or
      \command{bzip2} compression would have been chosen from the magic
      header of the tarball.

      \item \code{zapsmall(x)} now works for more \dQuote{number-like} objects.

      \item The tools-internal function called from \command{R CMD
	INSTALL} now gets a \code{warnOption = 1} argument and only sets
      \code{options(warn = warnOption)} when that increases the warning
      level (\PR{17453}).

      \item Analogously, the tools-internal function called from \command{R CMD
	check} gets a \code{warnOption = 1} argument and uses the larger
      of that and \code{getOption("warn")}, also allowing to be run with
      increased warning level.

      \item Parse data now have deterministic parent nodes (\PR{16041}).

      \item Calling \code{match()} with length one \code{x} and POSIXlt
      \code{table} gave a segfault (\PR{17459}).

      \item Fork clusters could hang due to a race condition in cluster
      initialization (\code{makeCluster()}).

      \item \code{nextn(n)} now also works for larger \code{n} and no
      longer loops infinitely for e.g, \code{n <- 214e7}.

      \item \code{cooks.distance()} and \code{rstandard()} now work
      correctly for multiple linear models (\code{"mlm"}).

      \item \code{polym()} and corresponding \code{lm()} prediction now
      also work for a boundary "vector" case fixing \PR{17474},
      reported by Alexandre Courtiol.

      \item With a very large number of variables \code{terms()} could
      segfault (\PR{17480}).

      \item \code{cut(rep(0, 7))} now works, thanks to Joey Reid and
      Benjamin Tyner (\PR{16802}).

      \item \code{download.file(*, method = "curl", cacheOK = FALSE)}
      should work now on Windows, thanks to Kevin Ushey's patch in
      \PR{17323}.

      \item \code{duplicated(<dataframe with 'f'>)} now works, too,
      thanks to Andreas Kersting's \PR{17485}; ditto for
      \code{anyDuplicated()}.

      \item \code{legend(*, cex = 1:2)} now works less badly.

      \item The \code{print()} method for \code{POSIXct} and
      \code{POSIXlt} now correctly obeys \code{getOption("max.print")},
      fixing a long-standing typo, and it also gets a corresponding
      optional \code{max} argument.

      \item Unserialization of raw vectors serialized in ASCII
      representation now works correctly.

      \item \code{<data frame>[TRUE, <new>] <- list(c1, c2)} now works
      correctly, thanks to Suharto Anggono's \PR{15362} and Emil Bode's
      patch in \PR{17504}.

      \item \code{seq.int(*, by=by, length=n)} no longer wrongly
      \dQuote{drops fractional parts} when \code{by} is integer, thanks
      to Suharto Anggono's report \PR{17506}.

      \item Buffering is disabled for \code{file()} connections to
      non-regular files (like sockets), as well as \code{fifo()} and
      \code{pipe()} connections.  Fixes \PR{17470}, reported by Chris
      Culnane.
    }
  }
}

\section{\Rlogo CHANGES IN R 3.5.1}{
1007 1008 1009 1010 1011 1012 1013 1014 1015 1016 1017 1018 1019 1020 1021 1022 1023 1024 1025 1026 1027 1028 1029 1030 1031 1032 1033 1034 1035 1036 1037 1038 1039 1040 1041 1042 1043 1044 1045 1046 1047 1048 1049 1050 1051 1052 1053 1054 1055 1056 1057 1058 1059 1060 1061 1062

  \subsection{BUG FIXES}{
    \itemize{
      \item \code{file("stdin")} is no longer considered seekable.

      \item \code{dput()} and \code{dump()} are no longer truncating
      when \code{options(deparse.max.lines = *)} is set.

      \item Calls with an S3 class are no longer evaluated when printed,
      fixing part of \PR{17398}, thanks to a patch from Lionel Henry.

      \item Allow \code{file} argument of \command{Rscript} to include space
      even when it is first on the command line.

      \item \code{callNextMethod()} uses the generic from the
      environment of the calling method. Reported by Hervé Pagès with
      well documented examples.

      \item Compressed file connections are marked as blocking.

      \item \code{optim(*, lower = c(-Inf, -Inf))} no longer warns (and
      switches the method), thanks to a suggestion by John Nash.

      \item \code{predict(fm, newdata)} is now correct also for models
      where the formula has terms such as \code{splines::ns(..)} or
      \code{stats::poly(..)}, fixing \PR{17414}, based on a patch from
      Duncan Murdoch.

      \item \code{simulate.lm(glm(*, gaussian(link = <non-default>)))}
      has been corrected, fixing \PR{17415} thanks to Alex Courtiol.

      \item \code{unlist(x)} no longer fails in some cases of nested
      empty lists.  Reported by Steven Nydick.

      \item \code{qr.coef(qr(<all 0, w/ colnames>))} now works.
      Reported by Kun Ren.

      \item The radix sort is robust to vectors with >1 billion elements
      (but long vectors are still unsupported). Thanks to Matt Dowle for
      the fix.

      \item Terminal connections (e.g., stdin) are no longer
      buffered. Fixes \PR{17432}.

      \item \code{deparse(x)}, \code{dput(x)} and \code{dump()} now
      respect \code{c()}'s argument names \code{recursive} and
      \code{use.names}, e.g., for \code{x <- setNames(0, "recursive")},
      thanks to Suharto Anggono's \PR{17427}.

      \item Unbuffered connections now work with encoding conversion.
      Reported by Stephen Berman.

      \item \file{.Renviron} on Windows with \command{Rgui} is again by
      default searched for in user documents directory when invoked
      \emph{via} the launcher icon.  Reported by Jeroen Ooms.

1063 1064
      \item \code{printCoefmat()} now also works with explicit
      \code{right=TRUE}.
1065

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      \item \code{print.noquote()} now also works with explicit
      \code{quote=FALSE}.
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      \item The default method for \code{pairs(.., horInd=*, verInd=*)}
      now gets the correct order, thanks to reports by Chris Andrews and
      Gerrit Eichner.  Additionally, when \code{horInd} or \code{verInd}
      contain only a subset of variables, all the axes are labeled
      correctly now.

      \item \code{agrep("..|..", .., fixed=FALSE)} now matches when it
      should, thanks to a reminder by Andreas Kolter.

      \item \code{str(ch)} now works for more invalid multibyte strings.
    }
  }
}

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\section{\Rlogo CHANGES IN R 3.5.0}{

  \subsection{SIGNIFICANT USER-VISIBLE CHANGES}{
    \itemize{
      \item All packages are by default byte-compiled on installation.
      This makes the installed packages larger (usually marginally so)
      and may affect the format of messages and tracebacks (which often
      exclude \code{.Call} and similar).
    }
  }

  \subsection{NEW FEATURES}{
    \itemize{
      \item \code{factor()} now uses \code{order()} to sort its levels,
      rather than \code{sort.list()}.  This allows \code{factor()} to
      support custom vector-like objects if methods for the appropriate
      generics are defined.  It has the side effect of making
      \code{factor()} succeed on empty or length-one non-atomic
      vector(-like) types (e.g., \code{"list"}), where it failed before.

      \item \code{diag()} gets an optional \code{names} argument: this
      may require updates to packages defining S4 methods for it.

      \item \code{chooseCRANmirror()} and \code{chooseBioCmirror()} no
      longer have a \code{useHTTPS} argument, not needed now all \R
      builds support \samp{https://} downloads.

      \item New \code{summary()} method for \code{warnings()} with a
      (somewhat experimental) \code{print()} method.

      \item (\pkg{methods} package.) \code{.self} is now automatically
      registered as a global variable when registering a reference class
      method.

      \item \code{tempdir(check = TRUE)} recreates the \code{tempdir()}
      directory if it is no longer valid (e.g.\sspace{}because some
      other process has cleaned up the \file{/tmp} directory).

      \item New \code{askYesNo()} function and \code{"askYesNo"} option
      to ask the user binary response questions in a customizable but
      consistent way.  (Suggestion of \PR{17242}.)

      \item New low level utilities \code{...elt(n)} and \code{...length()}
      for working with \code{...} parts inside a function.

      \item \code{isTRUE()} is more tolerant and now true
      in  \preformatted{   x <- rlnorm(99)
   isTRUE(median(x) == quantile(x)["50\%"])}
      New function \code{isFALSE()} defined analogously to \code{isTRUE()}.

      \item The default symbol table size has been increased from 4119
      to 49157; this may improve the performance of symbol resolution
      when many packages are loaded.  (Suggested by Jim Hester.)

      \item \code{line()} gets a new option \code{iter = 1}.

      \item Reading from connections in text mode is buffered,
      significantly improving the performance of \code{readLines()}, as
      well as \code{scan()} and \code{read.table()}, at least when
      specifying \code{colClasses}.

      \item \code{order()} is smarter about picking a default sort
      \code{method} when its arguments are objects.

      \item \code{available.packages()} has two new arguments which
      control if the values from the per-session repository cache are
      used (default true, as before) and if so how old cached values can
1150
      be used (default one hour).
1151 1152 1153 1154 1155 1156 1157 1158 1159 1160 1161 1162 1163 1164 1165 1166 1167 1168 1169 1170 1171 1172 1173 1174 1175 1176 1177 1178 1179 1180 1181 1182 1183 1184 1185 1186 1187 1188 1189 1190 1191 1192 1193 1194 1195 1196 1197 1198 1199 1200 1201 1202 1203 1204 1205 1206 1207 1208 1209 1210 1211 1212 1213 1214 1215 1216 1217 1218 1219 1220 1221 1222 1223 1224 1225 1226 1227 1228 1229 1230 1231 1232 1233 1234 1235 1236 1237 1238 1239 1240 1241 1242 1243 1244 1245 1246 1247 1248 1249 1250 1251 1252 1253 1254 1255 1256 1257 1258 1259 1260 1261 1262 1263 1264 1265 1266 1267 1268 1269 1270 1271 1272 1273 1274 1275 1276 1277 1278 1279 1280 1281 1282 1283 1284 1285 1286 1287 1288 1289 1290 1291 1292 1293 1294 1295 1296 1297 1298 1299 1300 1301 1302 1303 1304 1305 1306 1307 1308 1309 1310 1311 1312 1313 1314 1315 1316 1317 1318 1319 1320 1321 1322 1323 1324 1325 1326 1327 1328 1329

      These arguments can be passed from \code{install.packages()},
      \code{update.packages()} and functions calling that: to enable
      this \code{available.packages()}, \code{packageStatus()} and
      \code{download.file()} gain a \code{\dots} argument.

      \item \code{packageStatus()}'s \code{upgrade()} method no longer
      ignores its \code{\dots} argument but passes it to
      \code{install.packages()}.

      \item \code{installed.packages()} gains a \code{\dots} argument to
      allow arguments (including \code{noCache}) to be passed from
      \code{new.packages()}, \code{old.packages()},
      \code{update.packages()} and \code{packageStatus()}.

      \item \code{factor(x, levels, labels)} now allows duplicated
      \code{labels} (not duplicated \code{levels}!).  Hence you can map
      different values of \code{x} to the same level directly.

      \item Attempting to use \code{names<-()} on an S4 derivative of a
      basic type no longer emits a warning.

      \item The \code{list} method of \code{within()} gains an option
      \code{keepAttrs = FALSE} for some speed-up.

      \item \command{system()} and \command{system2()} now allow the
      specification of a maximum elapsed time (\sQuote{timeout}).

      \item \code{debug()} supports debugging of methods on any object
      of S4 class \code{"genericFunction"}, including group generics.

      \item Attempting to increase the length of a variable containing
      \code{NULL} using \code{length()<-} still has no effect on the
      target variable, but now triggers a warning.

      \item \code{type.convert()} becomes a generic function, with
      additional methods that operate recursively over list and
      \code{data.frame} objects. Courtesy of Arni Magnusson
      (\PR{17269}).

      \item \code{lower.tri(x)} and \code{upper.tri(x)} only needing
      \code{dim(x)} now work via new functions \code{.row()} and
      \code{.col()}, so no longer call \code{as.matrix()} by default in
      order to work efficiently for all kind of matrix-like objects.

      \item \code{print()} methods for \code{"xgettext"} and
      \code{"xngettext"} now use \code{encodeString()} which keeps,
      e.g.\sspace{}\code{"\n"}, visible.  (Wish of \PR{17298}.)

      \item \code{package.skeleton()} gains an optional \code{encoding}
      argument.

      \item \code{approx()}, \code{spline()}, \code{splinefun()} and
      \code{approxfun()} also work for long vectors.

      %% one item with several paragraphs
      \item \code{deparse()} and \code{dump()} are more useful for S4
      objects, \code{dput()} now using the same internal C code instead
      of its previous imperfect workaround R code.  S4 objects now
      typically deparse perfectly, i.e., can be recreated identically
      from deparsed code.

      \code{dput()}, \code{deparse()} and \code{dump()} now print the
      \code{names()} information only once, using the more readable
      \code{(tag = value)} syntax, notably for \code{list()}s, i.e.,
      including data frames.

      These functions gain a new control option \code{"niceNames"} (see
      \code{.deparseOpts()}), which when set (as by default) also uses
      the \code{(tag = value)} syntax for atomic vectors.  On the other
      hand, without deparse options \code{"showAttributes"} and
      \code{"niceNames"}, names are no longer shown also for lists.
      \code{as.character(list(  c (one = 1)))} now includes the name, as
      \code{as.character(list(list(one = 1)))} has always done.

      \code{m:n} now also deparses nicely when \eqn{m > n}.

      The \code{"quoteExpressions"} option, also part of \code{"all"},
      no longer \code{quote()}s formulas as that may not re-parse
      identically.  (\PR{17378})

      \item If the option \code{setWidthOnResize} is set and \code{TRUE},
      \R run in a terminal using a recent \code{readline} library will
      set the \code{width} option when the terminal is
      resized.  Suggested by Ralf Goertz.

      \item If multiple \code{on.exit()} expressions are set using
      \code{add = TRUE} then all expressions will now be run even if one
      signals an error.

      \item \code{mclapply()} gets an option \code{affinity.list} which
      allows more efficient execution with heterogeneous processors,
      thanks to Helena Kotthaus.

      \item The \code{character} methods for \code{as.Date()} and
      \code{as.POSIXlt()} are more flexible \emph{via} new arguments
      \code{tryFormats} and \code{optional}: see their help pages.

      \item \code{on.exit()} gains an optional argument \code{after}
      with default \code{TRUE}. Using \code{after = FALSE} with
      \code{add = TRUE} adds an exit expression before any
      existing ones. This way the expressions are run in a first-in
      last-out fashion. (From Lionel Henry.)

      \item On Windows, \code{file.rename()} internally retries the
      operation in case of error to attempt to recover from possible
      anti-virus interference.

      \item Command line completion on \samp{::} now also includes
      lazy-loaded data.

      \item If the \env{TZ} environment variable is set when date-time
      functions are first used, it is recorded as the session default
      and so will be used rather than the default deduced from the OS
      if \env{TZ} is subsequently unset.

      \item There is now a \code{[} method for class \code{"DLLInfoList"}.

      \item \code{glm()} and \code{glm.fit} get the same
      \code{singular.ok = TRUE} argument that \code{lm()} has had
      forever.  As a consequence, in \code{glm(*, method = <your_own>)},
      user specified methods need to accept a \code{singular.ok}
      argument as well.

      \item \code{aspell()} gains a filter for Markdown (\file{.md} and
      \file{.Rmd}) files.

      \item \code{intToUtf8(multiple = FALSE)} gains an argument to
      allow surrogate pairs to be interpreted.

      \item The maximum number of DLLs that can be loaded into R
      e.g.\sspace{}\emph{via} \code{dyn.load()} has been increased up to 614
      when the OS limit on the number of open files allows.

      \item \code{Sys.timezone()} on a Unix-alike caches the value at
      first use in a session: \emph{inter alia} this means that setting
      \env{TZ} later in the session affects only the \emph{current} time
      zone and not the \emph{system} one.

      \code{Sys.timezone()} is now used to find the system timezone to
      pass to the code used when \R is configured with
      \option{--with-internal-tzcode}.

      \item When \code{tar()} is used with an external command which is
      detected to be GNU \command{tar} or libarchive \command{tar} (aka
      \command{bsdtar}), a different command-line is generated to
      circumvent line-length limits in the shell.

      \item \code{system(*, intern = FALSE)}, \code{system2()} (when not
      capturing output), \code{file.edit()} and \code{file.show()} now
      issue a warning when the external command cannot be executed.

      \item The \dQuote{default} (\code{"lm"} etc) methods of
      \code{vcov()} have gained new optional argument \code{complete =
      TRUE} which makes the \code{vcov()} methods more consistent with
      the \code{coef()} methods in the case of singular designs.  The
      former (back-compatible) behavior is given by \code{vcov(*,
	complete = FALSE)}.

      \item \code{coef()} methods (for \code{lm} etc) also gain a
      \code{complete = TRUE} optional argument for consistency with
      \code{vcov()}. \cr
      For \code{"aov"}, both \code{coef()} and \code{vcov()} methods
      remain back-compatibly consistent, using the \emph{other} default,
      \code{complete = FALSE}.

      \item \code{attach(*, pos = 1)} is now an error instead of a
      warning.

      \item New function \code{getDefaultCluster()} in package
      \pkg{parallel} to get the default cluster set via
      \code{setDefaultCluster()}.

      \item \code{str(x)} for atomic objects \code{x} now treats both
      cases of \code{is.vector(x)} similarly, and hence much less often
      prints \code{"atomic"}.  This is a slight non-back-compatible
      change producing typically both more informative and shorter
      output.

1330 1331
      \item \code{gc()} gets new argument \code{full}.

1332 1333 1334 1335 1336 1337 1338 1339 1340 1341 1342 1343 1344 1345 1346 1347 1348 1349 1350 1351 1352 1353 1354 1355 1356 1357 1358 1359 1360 1361 1362 1363 1364 1365 1366 1367 1368 1369 1370 1371 1372 1373 1374 1375 1376
      \item \code{write.dcf()} gets optional argument \code{useBytes}.

      \item New, partly experimental \code{packageDate()} which tries to
      get a valid \code{"Date"} object from a package \file{DESCRIPTION}
      file, thanks to suggestions in \PR{17324}.

      \item \code{tools::resaveRdaFiles()} gains a \code{version}
      argument, for use when packages should remain compatible with
      earlier versions of \R.

      \item \code{ar.yw(x)} and hence by default \code{ar(x)} now work
      when \code{x} has \code{NA}s, mostly thanks to a patch by Pavel
      Krivitsky in \PR{17366}.   The \code{ar.yw.default()}'s AIC
      computations have become more efficient by using
      \code{determinant()}.

      \item New \code{warnErrList()} utility (from package \pkg{nlme},
      improved).

      \item By default the (arbitrary) signs of the loadings from
      \code{princomp()} are chosen so the first element is non-negative.

      \item If \option{--default-packages} is not used, then
      \command{Rscript} now checks the environment variable
      \env{R_SCRIPT_DEFAULT_PACKAGES}. If this is set, then it takes
      precedence over \env{R_DEFAULT_PACKAGES}. If default packages are
      not specified on the command line or by one of these environment
      variables, then \command{Rscript} now uses the same default
      packages as \command{R}. For now, the previous behavior of not
      including \pkg{methods} can be restored by setting the environment
      variable \env{R_SCRIPT_LEGACY} to \samp{yes}.

      \item When a package is found more than once, the warning from
      \code{find.package(*, verbose=TRUE)} lists all library locations.

      \item POSIXt objects can now also be rounded or truncated to month
      or year.

      \item \code{stopifnot()} can be used alternatively via new argument
      \code{exprs} which is nicer and useful when testing several
      expressions in one call.

      \item The environment variable \env{R_MAX_VSIZE} can now be used
      to specify the maximal vector heap size. On macOS, unless specified
      by this environment variable, the maximal vector heap size is set to
1377
      the maximum of 16GB and the available physical memory. This is to
1378 1379 1380
      avoid having the \command{R} process killed when macOS over-commits
      memory.

1381
      \item \code{sum(x)} and \code{sum(x1, x2, .., x<N>)} with many or
1382 1383 1384 1385 1386 1387 1388 1389 1390 1391 1392 1393 1394 1395 1396 1397 1398 1399 1400 1401 1402 1403 1404 1405 1406 1407 1408 1409 1410 1411 1412 1413 1414 1415 1416 1417 1418 1419 1420 1421
      long logical or integer vectors no longer overflows (and returns
      \code{NA} with a warning), but returns \code{double} numbers in
      such cases.

      \item Single components of \code{"POSIXlt"} objects can now be
      extracted and replaced via \code{[} indexing with 2 indices.

      \item S3 method lookup now searches the namespace registry after
      the top level environment of the calling environment.

      \item Arithmetic sequences created by \code{1:n},
      \code{seq_along}, and the like now use compact internal
      representations via the \code{ALTREP} framework.  Coercing integer
      and numeric vectors to character also now uses the \code{ALTREP}
      framework to defer the actual conversion until first use.

      \item Finalizers are now run with interrupts suspended.

      \item \code{merge()} gains new option \code{no.dups} and by
      default suffixes the second of two duplicated column names,
      thanks to a proposal by Scott Ritchie (and Gabe Becker).

      \item \code{scale.default(x, center, scale)} now also allows
      \code{center} or \code{scale} to be \dQuote{numeric-alike}, i.e.,
      such that \code{as.numeric(.)} coerces them correctly.  This also
      eliminates a wrong error message in such cases.

      \item \code{par*apply} and \code{par*applyLB} gain an optional
      argument \code{chunk.size} which allows to specify the granularity of
      scheduling.

      \item Some \code{as.data.frame()} methods, notably the
      \code{matrix} one, are now more careful in not accepting
      duplicated or \code{NA} row names, and by default produce unique
      non-NA row names.  This is based on new function
      \code{.rowNamesDF(x, make.names = *) <- rNms} where the logical
      argument \code{make.names} allows to specify \emph{how} invalid
      row names \code{rNms} are handled.  \code{.rowNamesDF()} is a
      \dQuote{workaround} compatible default.

1422 1423 1424 1425 1426 1427 1428 1429 1430 1431 1432 1433
      \item R has new serialization format (version 3) which supports
      custom serialization of \code{ALTREP} framework objects.  These
      objects can still be serialized in format 2, but less efficiently.
      Serialization format 3 also records the current native encoding of
      unflagged strings and converts them when de-serialized in R
      running under different native encoding.  Format 3 comes with new
      serialization magic numbers (RDA3, RDB3, RDX3).  Format 3 can be
      selected by \code{version = 3} in \code{save()},
      \code{serialize()} and \code{saveRDS()}, but format 2 remains the
      default for all serialization and saving of the workspace.
      Serialized data in format 3 cannot be read by versions of \R prior
      to version 3.5.0.
1434 1435 1436

      \item The \code{"Date"} and \dQuote{date-time} classes
      \code{"POSIXlt"} and \code{"POSIXct"} now have a working
1437
      \code{length<-()} method, as wished in \PR{17387}.
1438 1439 1440 1441

      \item \code{optim(*, control = list(warn.1d.NelderMead = FALSE))}
      allows to turn off the warning when applying the default
      \code{"Nelder-Mead"} method to 1-dimensional problems.
1442 1443 1444 1445

      \item \code{matplot(.., panel.first = .)} etc now work, as
      \code{log} becomes explicit argument and \code{...} is passed to
      \code{plot()} unevaluated, as suggested by Sebastian Meyer in \PR{17386}.
1446 1447 1448 1449 1450 1451 1452 1453 1454 1455 1456 1457 1458

      \item Interrupts can be suspended while evaluating an expression
      using \code{suspendInterrupts}.  Subexpression can be evaluated
      with interrupts enabled using \code{allowInterrupts}.  These
      functions can be used to make sure cleanup handlers cannot be
      interrupted.

      \item \R 3.5.0 includes a framework that allows packages to
      provide alternate representations of basic \R objects
      (\code{ALTREP}).  The framework is still experimental and may
      undergo changes in future \R releases as more experience is
      gained. For now, documentation is provided in
      \url{https://svn.r-project.org/R/branches/ALTREP/ALTREP.html}.
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    }
  }

  \subsection{UTILITIES}{
    \itemize{
      \item \code{install.packages()} for source packages now has the
      possibility to set a \sQuote{timeout} (elapsed-time limit).  For
      serial installs this uses the \code{timeout} argument of
      \code{system2()}: for parallel installs it requires the
      \command{timeout} utility command from GNU \pkg{coreutils}.

      \item It is now possible to set \sQuote{timeouts} (elapsed-time
      limits) for most parts of \command{R CMD check} \emph{via}
      environment variables documented in the \sQuote{R Internals}
      manual.

      \item The \sQuote{BioC extra} repository which was dropped from
      Bioconductor 3.6 and later has been removed from
      \code{setRepositories()}.  This changes the mapping for 6--8 used
      by \code{setRepositories(ind=)}.

      \item \command{R CMD check} now also applies the settings of
      environment variables \env{_R_CHECK_SUGGESTS_ONLY_} and
      \env{_R_CHECK_DEPENDS_ONLY_} to the re-building of vignettes.

      \item \command{R CMD check} with environment variable
      \env{_R_CHECK_DEPENDS_ONLY_} set to a true value makes
      test-suite-management packages available and (for the time being)
      works around a common omission of \CRANpkg{rmarkdown} from the
      \samp{VignetteBuilder} field.
    }
  }

  \subsection{INSTALLATION on a UNIX-ALIKE}{
    \itemize{
      \item Support for a system Java on macOS has been
      removed --- install a fairly recent Oracle Java (see \sQuote{R
	Installation and Administration} §C.3.2).

      \item \command{configure} works harder to set additional flags in
      \samp{SAFE_FFLAGS} only where necessary, and to use flags which
      have little or no effect on performance.

      In rare circumstances it may be necessary to override the
      setting of \samp{SAFE_FFLAGS}.

      \item C99 functions \code{expm1}, \code{hypot}, \code{log1p} and
      \code{nearbyint} are now required.

1508
      \item \command{configure} sets a \option{-std} flag for the C++
1509
      compiler for all supported C++ standards (e.g., \option{-std=gnu++11}
1510 1511 1512
      for the C++11 compiler).   Previously this was not done in a few
      cases where the default standard passed the tests made
      (e.g.\sspace\command{clang 6.0.0} for C++11).
1513 1514 1515 1516 1517 1518 1519 1520 1521 1522 1523 1524 1525 1526 1527 1528 1529 1530 1531 1532 1533 1534 1535 1536 1537 1538 1539 1540 1541 1542 1543 1544 1545 1546 1547 1548 1549 1550 1551 1552 1553 1554 1555 1556 1557 1558 1559 1560 1561 1562 1563 1564 1565 1566 1567 1568 1569 1570 1571 1572 1573 1574 1575 1576 1577 1578 1579 1580 1581 1582 1583 1584 1585 1586 1587 1588 1589 1590 1591 1592 1593 1594 1595 1596 1597 1598 1599 1600 1601 1602 1603 1604 1605 1606 1607 1608 1609 1610 1611 1612 1613 1614 1615 1616 1617 1618 1619 1620 1621 1622 1623 1624 1625 1626 1627 1628 1629 1630 1631 1632 1633 1634 1635 1636 1637 1638 1639 1640 1641 1642 1643 1644 1645 1646 1647 1648 1649 1650 1651 1652 1653 1654 1655 1656 1657 1658 1659 1660 1661 1662 1663 1664 1665 1666 1667 1668 1669 1670 1671 1672 1673 1674 1675 1676 1677 1678 1679 1680 1681 1682 1683 1684 1685 1686 1687 1688 1689 1690 1691 1692 1693 1694 1695 1696 1697 1698 1699 1700 1701 1702 1703 1704 1705 1706 1707 1708 1709 1710 1711 1712 1713 1714
    }
  }

  \subsection{C-LEVEL FACILITIES}{
    \itemize{
      \item \sQuote{Writing R Extensions} documents macros
      \code{MAYBE_REFERENCED}, \code{MAYBE_SHARED} and
      \code{MARK_NOT_MUTABLE} that should be used by package \code{C}
      code instead \code{NAMED} or \code{SET_NAMED}.

      \item The object header layout has been changed to support merging
      the \code{ALTREP} branch. This requires re-installing packages
      that use compiled code.

      \item \sQuote{Writing R Extensions} now documents the
      \code{R_tryCatch}, \code{R_tryCatchError}, and
      \code{R_UnwindProtect} functions.

      \item \code{NAMEDMAX} has been raised to 3 to allow protection of
      intermediate results from (usually ill-advised) assignments in
      arguments to \code{BUILTIN} functions. Package \code{C} code using
      \code{SET_NAMED} may need to be revised.
    }
  }

  \subsection{DEPRECATED AND DEFUNCT}{
    \itemize{
      \item \code{Sys.timezone(location = FALSE)} is defunct, and is
      ignored (with a warning).

      \item \code{methods:::bind_activation()} is defunct now; it
      typically has been unneeded for years.

      The undocumented \sQuote{hidden} objects \code{.__H__.cbind} and
      \code{.__H__.rbind} in package \pkg{base} are deprecated (in
      favour of \code{cbind} and \code{rbind}).

      \item The declaration of \code{pythag()} in \file{Rmath.h} has
      been removed --- the entry point has not been provided since \R
      2.14.0.
    }
  }

  \subsection{BUG FIXES}{
    \itemize{
      \item \code{printCoefmat()} now also works without column names.

      \item The S4 methods on \code{Ops()} for the \code{"structure"} class no
      longer cause infinite recursion when the structure is not an S4 object.

      \item \code{nlm(f, ..)} for the case where \code{f()} has a
      \code{"hessian"} attribute now computes
      \eqn{LL' = H + \mu I}{LL' = H + µI} correctly.  (\PR{17249}).

      \item An S4 method that \dQuote{rematches} to its generic and
      overrides the default value of a generic formal argument to
      \code{NULL} no longer drops the argument from its formals.

      \item \code{Rscript} can now accept more than one argument given on
      the \samp{#!} line of a script. Previously, one could only pass a
      single argument on the \samp{#!} line in Linux.

      \item Connections are now written correctly with encoding
      \code{"UTF-16LE"}.  (\PR{16737}).

      \item Evaluation of \code{..0} now signals an error.  When
      \code{..1} is used and \code{...} is empty, the error message is
      more appropriate.

      \item (Windows mainly.)  Unicode code points which require
      surrogate pairs in UTF-16 are now handled.  All systems should
      properly handle surrogate pairs, even those systems that do not
      need to make use of them.  (\PR{16098})

      \item \code{stopifnot(e, e2, ...)} now evaluates the
      expressions sequentially and in case of an error or warning shows
      the relevant expression instead of the full \code{stopifnot(..)}
      call.

      \item \code{path.expand()} on Windows now accepts paths specified as
      UTF-8-encoded character strings even if not representable in the
      current locale.  (\PR{17120})

      \item \code{line(x, y)} now correctly computes the medians of the
      left and right group's x-values and in all cases reproduces
      straight lines.

      \item Extending S4 classes with slots corresponding to special
      attributes like \code{dim} and \code{dimnames} now works.

      \item Fix for \code{legend()} when \code{fill} has multiple values
      the first of which is \code{NA} (all colours used to default to
      \code{par(fg)}).  (\PR{17288})

      \item \code{installed.packages()} did not remove the cached value
      for a library tree that had been emptied (but would not use the
      old value, just waste time checking it).

      \item The documentation for \code{installed.packages(noCache = TRUE)}
      incorrectly claimed it would refresh the cache.

      \item \code{aggregate(<data.frame>)} no longer uses spurious names
      in some cases.  (\PR{17283})

      \item \code{object.size()} now also works for long vectors.

      \item \code{packageDescription()} tries harder to solve
      re-encoding issues, notably seen in some Windows locales.  This
      fixes the \code{citation()} issue in \PR{17291}.

      \item \code{poly(<matrix>, 3)} now works, thanks to prompting by
      Marc Schwartz.

      \item \code{readLines()} no longer segfaults on very large files
      with embedded \code{'\0'} (aka \sQuote{nul}) characters.
      (\PR{17311})

      \item \code{ns()} (package \pkg{splines}) now also works for a
      single observation.  \code{interpSpline()} gives a more friendly
      error message when the number of points is less than four.

      \item \code{dist(x, method = "canberra")} now uses the correct
      definition; the result may only differ when \code{x} contains
      values of differing signs, e.g.\sspace{}not for 0-1 data.

      \item \code{methods:::cbind()} and \code{methods:::rbind()} avoid
      deep recursion, thanks to Suharto Anggono via \PR{17300}.

      \item Arithmetic with zero-column data frames now works more
      consistently; issue raised by Bill Dunlap.

      Arithmetic with data frames gives a data frame for \code{^} (which
      previously gave a numeric matrix).

      \item \code{pretty(x, n)} for large \code{n} or large
      \code{diff(range(x))} now works better (though
      it was never meant for large \code{n}); internally it uses the
      same rounding fuzz (1e-10) as \code{seq.default()} --- as it did up
      to 2010-02-03 when both were 1e-7.

      \item Internal C-level \code{R_check_class_and_super()} and hence
      \code{R_check_class_etc()} now also consider non-direct super
      classes and hence return a match in more cases.  This e.g., fixes
      behaviour of derived classes in package \CRANpkg{Matrix}.

      \item Reverted unintended change in behavior of \code{return}
      calls in \code{on.exit} expressions introduced by stack unwinding
      changes in \R 3.3.0.

      \item Attributes on symbols are now detected and prevented; attempt
      to add an attribute to a symbol results in an error.

      \item \code{fisher.test(*, workspace = <n>)} now may also increase
      the internal stack size which allows larger problem to be solved,
      fixing \PR{1662}.

      \item The \pkg{methods} package no longer directly copies slots
      (attributes) into a prototype that is of an \dQuote{abnormal}
      (reference) type, like a symbol.

      \item The \pkg{methods} package no longer attempts to call
      \code{length<-()} on \code{NULL} (during the bootstrap process).

      \item The \pkg{methods} package correctly shows methods when there
      are multiple methods with the same signature for the same generic
      (still not fully supported, but at least the user can see them).

      \item \code{sys.on.exit()} is now always evaluated in the right
      frame. (From Lionel Henry.)

      \item \code{seq.POSIXt(*, by = "<n> DSTdays")} now should work
      correctly in all cases and is faster.  (\PR{17342})

      \item \code{.C()} when returning a logical vector now always maps
      values other than FALSE and NA to TRUE (as documented).

      \item Subassignment with zero length vectors now coerces as
      documented (\PR{17344}).\cr
      Further, \code{x <- numeric(); x[1] <- character()} now signals
      an error \sQuote{\verb{replacement has length zero}} (or a
      translation of that) instead of doing nothing.

      \item (Package \pkg{parallel}.)  \code{mclapply()}, \code{pvec()}
      and \code{mcparallel()} (when \code{mccollect()} is used to
      collect results) no longer leave zombie processes behind.

      \item \code{R CMD INSTALL <pkg>} now produces the intended error
      message when, e.g., the \code{LazyData} field is invalid.

      \item \code{as.matrix(dd)} now works when the data frame \code{dd}
      contains a column which is a data frame or matrix, including a
      0-column matrix/d.f. .

      \item \code{mclapply(X, mc.cores)} now follows its documentation
      and calls \code{lapply()} in case \code{mc.cores = 1} also in the
      case \code{mc.preschedule} is false.  (\PR{17373})

      \item \code{aggregate(<data.frame>, drop=FALSE)} no longer calls
      the function on <empty> parts but sets corresponding results to
      \code{NA}.  (Thanks to Suharto Anggono's patches in \PR{17280}).

      \item The \code{duplicated()} method for data frames is now based
1715
      on the \code{list} method (instead of string coercion).  Consequently
1716 1717 1718 1719 1720 1721 1722 1723 1724 1725 1726 1727 1728 1729 1730 1731 1732 1733 1734 1735 1736 1737 1738 1739
      \code{unique()} is better distinguishing data frame rows, fixing
      \PR{17369} and \PR{17381}.  The methods for matrices and arrays
      are changed accordingly.

      \item Calling \code{names()} on an S4 object derived from
      \code{"environment"} behaves (by default) like calling
      \code{names()} on an ordinary environment.

      \item \code{read.table()} with a non-default separator now
      supports quotes following a non-whitespace character, matching the
      behavior of \code{scan()}.

      \item \code{parLapplyLB} and \code{parSapplyLB} have been fixed to do
      load balancing (dynamic scheduling).  This also means that results of
      computations depending on random number generators will now really be
      non-reproducible, as documented.

      \item Indexing a list using dollar and empty string (\code{l$""})
      returns NULL.

      \item Using \code{ \\usage\{ data(<name>, package="<pkg>") \} }
      no longer produces \command{R CMD check} warnings.

      \item \code{match.arg()} more carefully chooses the environment
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      for constructing default \code{choices}, fixing \PR{17401} as
1741
      proposed by Duncan Murdoch.
1742 1743 1744 1745 1746 1747

      \item Deparsing of consecutive \code{!} calls is now consistent
      with deparsing unary \code{-} and \code{+} calls and creates code
      that can be reparsed exactly; thanks to a patch by Lionel Henry in
      \PR{17397}.  (As a side effect, this uses fewer parentheses in
      some other deparsing involving \code{!} calls.)
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    }
  }
}

\section{\Rlogo CHANGES IN R 3.4.4}{

  \subsection{NEW FEATURES}{
    \itemize{
      \item \code{Sys.timezone()} tries more heuristics on Unix-alikes and so
      is more likely to succeed (especially on Linux).  For the slowest
      method, a warning is given recommending that \env{TZ} is set to
      avoid the search.

      \item The version of LAPACK included in the sources has been
      updated to 3.8.0 (for the routines used by \R, a very minor bug-fix
      change).

      \item \code{parallel::detectCores(logical = FALSE)} is ignored on
      Linux systems, since the information is not available with
      virtualized OSes.
    }
  }

  \subsection{INSTALLATION on a UNIX-ALIKE}{
    \itemize{
      \item \command{configure} will use \command{pkg-config} to find the
      flags to link to \code{jpeg} if available (as it should be for the
      recently-released \code{jpeg-9c} and \code{libjpeg-turbo}).  (This
      amends the code added in \R 3.3.0 as the module name in
      \code{jpeg-9c} is not what that tested for.)
    }
  }

  \subsection{DEPRECATED AND DEFUNCT}{
    \itemize{
      \item \code{Sys.timezone(location = FALSE)} (which was a stop-gap
      measure for Windows long ago) is deprecated.  It no longer returns
      the value of environment variable \env{TZ} (usually a location).

      \item Legacy support of \command{make} macros such as \samp{CXX1X}
      is formally deprecated: use the \samp{CXX11} forms instead.
    }
  }

  \subsection{BUG FIXES}{
    \itemize{
      \item \code{power.prop.test()} now warns when it cannot solve the
      problem, typically because of impossible constraints. (\PR{17345})

      \item \code{removeSource()} no longer erroneously removes
      \code{NULL} in certain cases, thanks to Dénes Tóth.

      \item \code{nls(`NO [mol/l]` ~ f(t))} and \code{nls(y ~ a)} now
      work.  (Partly from \PR{17367})

      \item \command{R CMD build} checks for GNU \command{cp} rather
      than assuming Linux has it.  (\PR{17370} says \sQuote{Alpine
	Linux} does not.)

      \item Non-UTF-8 multibyte character handling fixed more
      permanently (\PR{16732}).

      \item \code{sum(<large ints>, <stuff>)} is more consistent.
      (\PR{17372})

      \item \code{rf()} and \code{rbeta()} now also work correctly when
      \code{ncp} is not scalar, notably when (partly) \code{NA}.
      (\PR{17375})

      \item \code{is.na(NULL)} no longer warns.  (\PR{16107})

      \item \command{R CMD INSTALL} now correctly sets C++ compiler flags
      when all source files are in sub-directories of \file{src}.
    }
  }