Revisions of R-base

Dominique Leuenberger's avatar Dominique Leuenberger (dimstar_suse) accepted request 1155848 from Factory Maintainer's avatar Factory Maintainer (factory-maintainer) (revision 91)
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Ana Guerrero's avatar Ana Guerrero (anag+factory) accepted request 1124841 from Factory Maintainer's avatar Factory Maintainer (factory-maintainer) (revision 90)
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Dominique Leuenberger's avatar Dominique Leuenberger (dimstar_suse) accepted request 1094852 from Factory Maintainer's avatar Factory Maintainer (factory-maintainer) (revision 89)
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Dominique Leuenberger's avatar Dominique Leuenberger (dimstar_suse) accepted request 1083568 from Factory Maintainer's avatar Factory Maintainer (factory-maintainer) (revision 88)
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Dominique Leuenberger's avatar Dominique Leuenberger (dimstar_suse) accepted request 1073781 from Factory Maintainer's avatar Factory Maintainer (factory-maintainer) (revision 87)
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Dominique Leuenberger's avatar Dominique Leuenberger (dimstar_suse) accepted request 1033874 from Detlef Steuer's avatar Detlef Steuer (dsteuer) (revision 86)
- 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:
Dominique Leuenberger's avatar Dominique Leuenberger (dimstar_suse) accepted request 986019 from Factory Maintainer's avatar Factory Maintainer (factory-maintainer) (revision 85)
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Dominique Leuenberger's avatar Dominique Leuenberger (dimstar_suse) accepted request 972315 from Detlef Steuer's avatar Detlef Steuer (dsteuer) (revision 84)
- 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.
Dominique Leuenberger's avatar Dominique Leuenberger (dimstar_suse) accepted request 962175 from Detlef Steuer's avatar Detlef Steuer (dsteuer) (revision 83)
- 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.
Dominique Leuenberger's avatar Dominique Leuenberger (dimstar_suse) accepted request 930112 from Factory Maintainer's avatar Factory Maintainer (factory-maintainer) (revision 82)
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Richard Brown's avatar Richard Brown (RBrownSUSE) accepted request 912679 from Factory Maintainer's avatar Factory Maintainer (factory-maintainer) (revision 81)
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Dominique Leuenberger's avatar Dominique Leuenberger (dimstar_suse) accepted request 899423 from Factory Maintainer's avatar Factory Maintainer (factory-maintainer) (revision 80)
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Dominique Leuenberger's avatar Dominique Leuenberger (dimstar_suse) accepted request 894139 from Detlef Steuer's avatar Detlef Steuer (dsteuer) (revision 79)
- 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
Richard Brown's avatar Richard Brown (RBrownSUSE) accepted request 882498 from Detlef Steuer's avatar Detlef Steuer (dsteuer) (revision 78)
- 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).
Dominique Leuenberger's avatar Dominique Leuenberger (dimstar_suse) accepted request 872357 from Detlef Steuer's avatar Detlef Steuer (dsteuer) (revision 77)
- 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.
Dominique Leuenberger's avatar Dominique Leuenberger (dimstar_suse) accepted request 841472 from Detlef Steuer's avatar Detlef Steuer (dsteuer) (revision 76)
- 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
      enviromnent 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
Dominique Leuenberger's avatar Dominique Leuenberger (dimstar_suse) accepted request 817664 from Factory Maintainer's avatar Factory Maintainer (factory-maintainer) (revision 75)
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Dominique Leuenberger's avatar Dominique Leuenberger (dimstar_suse) accepted request 812058 from Detlef Steuer's avatar Detlef Steuer (dsteuer) (revision 74)
- 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
Dominique Leuenberger's avatar Dominique Leuenberger (dimstar_suse) accepted request 797070 from Detlef Steuer's avatar Detlef Steuer (dsteuer) (revision 73)
- CHANGES IN 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:
Dominique Leuenberger's avatar Dominique Leuenberger (dimstar_suse) accepted request 780561 from Detlef Steuer's avatar Detlef Steuer (dsteuer) (revision 72)
- CHANGES IN R 3.6.3:
  NEW FEATURES:
    * The included LAPACK has been updated to version 3.9.0 (for the
      included routines, just bug fixes).
  BUG FIXES:
    * Fixed a C level integer overflow in rhyper(); reported by
      Benjamin Tyner in PR#17694.
    * Uses of url(gzcon(.)) needing to extend buffer size have failed
      (with HTTP/2 servers), reported by G'abor Cs'ardi.
    * predict(loess(..), se=TRUE) now errors out (instead of
      seg.faulting etc) for large sample sizes, thanks to a report and
      patch by Benjamin Tyner in PR#17121.
    * tools:assertCondition(., "error") and hence assertError() no
      longer return errors twice (invisibly).
    * update(form, new) in the case of a long new formula sometimes
      wrongly eliminated the intercept from form, or (more rarely)
      added a garbage term (or seg.faulted !); the fix happened by
      simplifying the C-level logic of terms.formula().  Reported by
      Mathias Amb"uhl in PR#16326.
    * The error message from stopifnot(.., <error producing call>)
      again contains the full "stopifnot(.......)" call: Its attempted
      suppression did not work consistently.
    * On Windows, download.file(., , "wininet", headers=character())
      would fail; reported with patch proposal by Kevin Ushey in
      PR#17710.
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