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Revisions of R-base

Detlef Steuer (dsteuer) committed about 2 years ago (revision 121)

- 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.

Detlef Steuer (dsteuer) committed over 2 years ago (revision 120)

- CHANGES IN R 4.1.2:
  C-LEVEL FACILITIES:
    * The workaround in headers R.h and Rmath.h (using namespace std;)
      for the Oracle Developer Studio compiler is no longer needed now
      C++11 is required so has been removed.  A couple more usages of
      log() (which should have been std::log()) with an int argument
      are reported on Solaris.
    * The undocumented limit of 4095 bytes on messages from the
      S-compatibility macros PROBLEM and MESSAGE is now documented and
      longer messages will be silently truncated rather than
      potentially causing segfaults.
    * If the R_NO_SEGV_HANDLER environment variable is non-empty, the
      signal handler for SEGV/ILL/BUS signals (which offers recovery
      user interface) is not set. This allows more reliable debugging
      of crashes that involve the console.
  DEPRECATED AND DEFUNCT:
    * The legacy S-compatibility macros PROBLEM, MESSAGE, ERROR, WARN,
      WARNING, RECOVER, ... are deprecated and will be hidden in R
      4.2.0. R's native interface of Rf_error and Rf_warning has long
      been preferred.
  BUG FIXES:
    * .mapply(F, dots, .) no longer segfaults when dots is not a list
      and uses match.fun(F) as always documented; reported by Andrew
      Simmons in PR#18164.
    * hist(<Date>, ...) and hist(<POSIXt>, ...)  no longer pass
      arguments for rect() (such as col and density) to axis().
      (Thanks to Sebastian Meyer's PR#18171.)
    * \Sexpr{ch} now preserves Encoding(ch). (Thanks to report and
      patch by Jeroen Ooms in PR#18152.)
    * Setting the RNG to "Marsaglia-Multicarry" e.g., by RNGkind(), now

Detlef Steuer (dsteuer) committed over 2 years ago (revision 119)

- repaired https://bugzilla.suse.com/show_bug.cgi?id=1191380
  (rpmacros now go to rpmmacrodir)
- minor clean-ups in spec file

Detlef Steuer (dsteuer) committed almost 3 years ago (revision 118)

- CHANGES IN R 4.1.1:
  NEW FEATURES:
    * require(pkg, quietly = TRUE) is quieter and in particular does
      not warn if the package is not found.
  DEPRECATED AND DEFUNCT:
    * Use of ftp:// URIs should be regarded as deprecated, with
      on-going support confined to method = "libcurl" and not routinely
      tested.  (Nowadays no major browser supports them.)
    * The non-default method = "internal" is deprecated for http:// and
      ftp:// URIs for both download.file and url.
    * On Windows, method = "wininet" is deprecated for http://,
      https:// and ftp:// URIs for both download.file and url.  (A
      warning is only given for ftp://.)
      For ftp:// URIs the default method is now "libcurl" if available
      (which it is on CRAN builds).
      method = "wininet" remains the default for http:// and https://
      URIs but if libcurl is available, using method = "libcurl" is
      preferred.
  INSTALLATION:
    * make check now works also without a LaTeX installation.  (Thanks
      to Sebastian Meyer's PR#18103.)
  BUG FIXES:
    * make check-devel works again in an R build configured with
      --without-recommended-packages.
    * qnbinom(p, size, mu) for large size/mu is correct now in a range
      of cases (PR#18095); similarly for the (size, prob)
      parametrization of the negative binomial.  Also qpois() and
      qbinom() are better and or faster for extreme cases.  The
      underlying C code has been modularized and is common to all four
      cases of discrete distributions.

buildservice-autocommit accepted request 899423 from

Factory Maintainer (factory-maintainer) almost 3 years ago (revision 117)

baserev update by copy to link target

Detlef Steuer (dsteuer) committed almost 3 years ago (revision 116)

- The line %{__install} -m 755 -d %{_infodir}
  no longer works in TW or Factory.
  But without that line it works everywhere. So this instruction
  was commented out of the spec file.

Detlef Steuer (dsteuer) accepted request 896932 from

Pierre Bonamy (flyos) almost 3 years ago (revision 115)

- Commenting out the following line:
  %{__install} -m 755 -d %{_infodir}
  which results in failure in Tumbleweed and doesn't seem to serve
  any purpose for other distributions.

buildservice-autocommit accepted request 894139 from

Detlef Steuer (dsteuer) about 3 years ago (revision 114)

baserev update by copy to link target

Detlef Steuer (dsteuer) committed about 3 years ago (revision 113)

- 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

Detlef Steuer (dsteuer) committed about 3 years ago (revision 112)

- improved spec file according to comments of dimstar in
  https://build.opensuse.org/request/show/892685

Detlef Steuer (dsteuer) committed about 3 years ago (revision 111)

- To get in sync with d:l:R:autoCRAN the Matrix package's split
  in -devel was reversed.

buildservice-autocommit accepted request 882498 from

Detlef Steuer (dsteuer) about 3 years ago (revision 110)

baserev update by copy to link target

Detlef Steuer (dsteuer) committed about 3 years ago (revision 109)

- 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).

buildservice-autocommit accepted request 872357 from

Detlef Steuer (dsteuer) about 3 years ago (revision 108)

baserev update by copy to link target

Detlef Steuer (dsteuer) committed over 3 years ago (revision 107)

- 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.

buildservice-autocommit accepted request 841472 from

Detlef Steuer (dsteuer) over 3 years ago (revision 106)

baserev update by copy to link target

Detlef Steuer (dsteuer) committed over 3 years ago (revision 105)

- 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

buildservice-autocommit accepted request 817664 from

Factory Maintainer (factory-maintainer) almost 4 years ago (revision 104)

baserev update by copy to link target

Detlef Steuer (dsteuer) committed almost 4 years ago (revision 103)

- CHANGES IN R 4.0.2:
  UTILITIES:
    * R CMD check skips vignette re-building (with a warning) if the
      VignetteBuilder package(s) are not available.
  BUG FIXES:
    * Paths with non-ASCII characters caused problems for package
      loading on Windows PR#17833.
    * Using tcltk widgets no longer crashes R on Windows.
    * source(*, echo=TRUE) no longer fails in some cases with empty
      lines; reported by Bill Dunlap in PR#17769.
    * on.exit() now correctly matches named arguments, thanks to
      PR#17815 (including patch) by Brodie Gaslam.
    * regexpr(*, perl=TRUE) no longer returns incorrect positions into
      text containing characters outside of the Unicode Basic
      Multilingual Plane on Windows.

buildservice-autocommit accepted request 812058 from

Detlef Steuer (dsteuer) almost 4 years ago (revision 102)

baserev update by copy to link target

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