(math/R) format COMMIT_MSG

[Makoto Fujiwara <makoto%if.t.u-tokyo.ac.jp@localhost>]

Module Name:	pkgsrc-wip
Committed By:	Makoto Fujiwara <makoto%if.t.u-tokyo.ac.jp@localhost>
Pushed By:	mef
Date:		Mon Apr 29 10:59:13 2024 +0900
Changeset:	ece5d2178b61b776feefe6b0fc1917e7da65466b

Modified Files:
	R/COMMIT_MSG

Log Message:
(math/R) format COMMIT_MSG

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=ece5d2178b61b776feefe6b0fc1917e7da65466b

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

diffstat:
 R/COMMIT_MSG | 331 ++++++++++++++++++++++++++++++++++++++---------------------
 1 file changed, 213 insertions(+), 118 deletions(-)

diffs:
diff --git a/R/COMMIT_MSG b/R/COMMIT_MSG
index 2a53efd516..393528174d 100644
--- a/R/COMMIT_MSG
+++ b/R/COMMIT_MSG
@@ -8,141 +8,236 @@ R News
 CHANGES IN R 4.4.0
 SIGNIFICANT USER-VISIBLE CHANGES:
 *   Startup banners, R --version, sessionInfo() and R CMD check no longer report
-(64-bit) as part of the platform as this is almost universal – the increasingly rare
-32-bit platforms will still report (32-bit).
-On Windows, ditto for window titles.
+    (64-bit) as part of the platform as this is almost universal – the increasingly rare
+    32-bit platforms will still report (32-bit).
+    On Windows, ditto for window titles.
+
 *   is.atomic(NULL) now returns FALSE, as NULL is not an atomic vector.
-Strict back-compatibility would replace is.atomic(foo) by (is.null(foo) ||
-is.atomic(foo)) but should happen only sparingly.
-NEW FEATURES:
+    Strict back-compatibility would replace is.atomic(foo) by (is.null(foo) ||
+    is.atomic(foo)) but should happen only sparingly.
+    NEW FEATURES:
+
 *   The confint() methods for "glm" and "nls" objects have been copied to the
-stats package. Previously, they were stubs which called versions in package MASS.
-The MASS namespace is no longer loaded if you invoke (say) confint(glmfit).
-Further, the "glm" method for profile() and the plot() and pairs() methods
-for class "profile" have been copied from MASS to stats. (profile.nls() and
-plot.profile.nls() were already in stats.)
+    stats package. Previously, they were stubs which called versions in package MASS.
+    The MASS namespace is no longer loaded if you invoke (say) confint(glmfit).
+    Further, the "glm" method for profile() and the plot() and pairs() methods
+    for class "profile" have been copied from MASS to stats. (profile.nls() and
+    plot.profile.nls() were already in stats.)
+
 *   The confint() and profile methods for "glm" objects have gained a possibility to
-do profiling based on the Rao Score statistic in addition to the default Likelihood
-Ratio. This is controlled by a new test = argument.
-*   The pairs() method for "profile" objects has been extended with a which = argument to allow plotting only a subset of the parameters.
-*   The "glm" method for anova() computes test statistics and p-values by default, using
-a chi-squared test or an F test depending on whether the dispersion is fixed or free.
-Test statistics can be suppressed by giving argument test a false logical value.
-*   In setRepositories() the repositories can be set using their names via name = instead of index ind =.
-*   methods() and .S3methods() gain a all.names option for the (rare) case where
-functions starting with a ‘.’ should be included.
-*   Serializations can now be interrupted (e.g., by Ctrl-C on a Unix-alike) if they take
-too long, e.g., from save.image(), thanks to suggestions by Ivan Krylov and others
-on R-devel.
-
-*   New startup option ‘--max-connections’ to set the maximum number of simultaneous connections for the session. Defaults to 128 as before: allowed values up to 4096
-(but resource limits may in practice restrict to smaller values).
-*   R on Windows (since Windows 10 2004) now uses the new Segment Heap allocator.
-This may improve performance of some memory-intensive applications.
-*   When R packages are built, typically by R CMD build <pkg>, the new
---user=<build_user> option overrides the (internally determined) user name, currently Sys.info()["user"] or LOGNAME. This is a (modified) fulfillment of Will Landau’s suggestion in PR#17530.
-*   tools::testInstalledBasic() gets new optional arguments outDir and
-testSrcdir, e.g., allowing to use it in a builddir != srcdir setup, and in standard “binary” Windows installation if a source ‘tests/’ folder is present.
-*   range(<DT_with_Inf>, finite = TRUE) now work for objects of class "Date",
-"POSIXct", and "POSIXlt" with infinite entries, analogously to range.default(),
-as proposed by Davis Vaughan on R-devel. Other range()-methods can make use of
-new function .rangeNum().
-*   New .internalGenerics object complementing .S3PrimitiveGenerics, for documentation and low-level book-keeping.
-*   grid() now invisibly returns the x- and y- coordinates at which the grid-lines were
-drawn.
+    do profiling based on the Rao Score statistic in addition to the default Likelihood
+    Ratio. This is controlled by a new test = argument.
+
+* The pairs() method for "profile" objects has been extended with a
+    which = argument to allow plotting only a subset of the
+    parameters.
+
+* The "glm" method for anova() computes test statistics and p-values
+  by default, using a chi-squared test or an F test depending on whether
+  the dispersion is fixed or free.  Test statistics can be suppressed by
+  giving argument test a false logical value.
+
+* In setRepositories() the repositories can be set using their names
+    via name = instead of index ind =.
+
+* methods() and .S3methods() gain a all.names option for the (rare)
+  case where functions starting with a ‘.’ should be included.
+
+* Serializations can now be interrupted (e.g., by Ctrl-C on a
+  Unix-alike) if they take too long, e.g., from save.image(), thanks to
+  suggestions by Ivan Krylov and others on R-devel.
+
+* New startup option ‘--max-connections’ to set the maximum number of
+  simultaneous connections for the session. Defaults to 128 as before:
+  allowed values up to 4096 (but resource limits may in practice
+  restrict to smaller values).
+
+* R on Windows (since Windows 10 2004) now uses the new Segment Heap
+  allocator.  This may improve performance of some memory-intensive
+  applications.
+
+* When R packages are built, typically by R CMD build <pkg>, the new
+  --user=<build_user> option overrides the (internally determined) user
+  name, currently Sys.info()["user"] or LOGNAME. This is a (modified)
+  fulfillment of Will Landau’s suggestion in PR#17530.
+
+* tools::testInstalledBasic() gets new optional arguments outDir and
+  testSrcdir, e.g., allowing to use it in a builddir != srcdir setup,
+  and in standard “binary” Windows installation if a source ‘tests/’
+  folder is present.
+
+* range(<DT_with_Inf>, finite = TRUE) now work for objects of class
+  "Date", "POSIXct", and "POSIXlt" with infinite entries, analogously to
+  range.default(), as proposed by Davis Vaughan on R-devel. Other
+  range()-methods can make use of new function .rangeNum().
+
+* New .internalGenerics object complementing .S3PrimitiveGenerics, for
+    documentation and low-level book-keeping.
+
+* grid() now invisibly returns the x- and y- coordinates at which the
+  grid-lines were drawn.
+
 *   norm(., type) now also works for complex matrices.
-*   kappa(., exact = TRUE, norm = *) now works for all norms and also for complex
-matrices. In symmetric / triangular cases, the new argument uplo = "U" | "L" allows
-the upper or lower triangular part to be specified.
-*   memDecompress(type = "unknown") recognizes compression in the default ‘zlib’ format as used by memCompress(type = "gzip").
-*   memCompress() and memDecompress() will use the libdeflate library (https:
-//github.com/ebiggers/libdeflate) if installed. This uses the same type of compression for type = "gzip" but is 1.5-2x faster than the system libz library on some
-common platforms: the speed-up may depend on the library version.
-*   diff() for objects of class "Date", "POSIXct", and "POSIXlt" accepts a units argument passed via ....
-*   Dynamic help now does a much better job of rendering package ‘DESCRIPTION’ metadata.
-*   Rprof() gains an event argument and support for elapsed (real) time profiling on
-Unix (PR#18076).
+
+* kappa(., exact = TRUE, norm = *) now works for all norms and also
+  for complex matrices. In symmetric / triangular cases, the new
+  argument uplo = "U" | "L" allows the upper or lower triangular part to
+  be specified.
+
+* memDecompress(type = "unknown") recognizes compression in the
+    default ‘zlib’ format as used by memCompress(type = "gzip").
+
+* memCompress() and memDecompress() will use the libdeflate library
+  (https: //github.com/ebiggers/libdeflate) if installed. This uses the
+  same type of compression for type = "gzip" but is 1.5-2x faster than
+  the system libz library on some common platforms: the speed-up may
+  depend on the library version.
+
+* diff() for objects of class "Date", "POSIXct", and "POSIXlt" accepts
+    a units argument passed via ....
+
+* Dynamic help now does a much better job of rendering package
+    ‘DESCRIPTION’ metadata.
+
+* Rprof() gains an event argument and support for elapsed (real) time
+profiling on Unix (PR#18076).
+
 *   filled.contour() gains a key.border argument.
-*   tools::update_pkg_po() gets arguments pot_make and mo_make for not re-making
-the corresponding files, and additionally a verbose argument.
-*   Hexadecimal string colour specifications are now accepted in short form, so, for example, we can use "#123", which is equivalent to "#112233".
-Thanks to MikeFC for the original idea and Ella Kaye, Malcolm Barrett, George
-Stagg, and Hanne Oberman for the patch.
+
+* tools::update_pkg_po() gets arguments pot_make and mo_make for not
+  re-making the corresponding files, and additionally a verbose
+  argument.
+
+* Hexadecimal string colour specifications are now accepted in short
+  form, so, for example, we can use "#123", which is equivalent to
+  "#112233".  Thanks to MikeFC for the original idea and Ella Kaye,
+  Malcolm Barrett, George Stagg, and Hanne Oberman for the patch.
+
 *   Plain-text help shows \var markup by angle brackets.
-*   The new experimental primitive function declare() is intended to eventually allow
-information about R code to be communicated to the interpreter, compiler, and code
-analysis tools. The syntax for declarations is still being developed.
-*   Functions psmirnov(), qsmirnov() and rsmirnov() in package stats have had argument two.sided renamed to alternative, to take into account that the permutation
-distributions of the one-sided statistics can be different in the case of ties. Consequence of PR#18582.
+
+* The new experimental primitive function declare() is intended to
+  eventually allow information about R code to be communicated to the
+  interpreter, compiler, and code analysis tools. The syntax for
+  declarations is still being developed.
+
+* Functions psmirnov(), qsmirnov() and rsmirnov() in package stats
+  have had argument two.sided renamed to alternative, to take into
+  account that the permutation distributions of the one-sided statistics
+  can be different in the case of ties. Consequence of PR#18582.
 
 *   sort() is now an implicit S4 generic in methods.
-*   Formatting and printing, format(z), print(z), of complex vectors z no longer zap
-relatively small real or imaginary parts to zero, fixing PR#16752. This is an API
-change, as it was documented previously to round real and imaginary parts together
-on purpose, producing nicer looking output. As mentioned, e.g. in the PR, this change
-is compatible with many other “R-like” programming environments.
-We have simplified the internal code and now basically format the real and imaginary
-parts independently of each other.
-*   New experimental functions Tailcall() and Exec() to support writing stack-spaceefficient recursive functions.
-*   Where characters are attempted to be plotted by pdf(), postscript() and xfig()
-which are not in the selected 8-bit character set (most often Latin-1) and the R session
-is using a UTF-8 locale, the warning messages will show the UTF-8 character rather
-than its bytes and one dot will be substituted per character rather than per byte.
-(Platforms whose iconv() does transliteration silently plot the transliteration.)
-In a UTF-8 locale some transliterations are now done with a warning (e.g., dashes
-and Unicode minus to hyphen, ligatures are expanded, permille (‘‰’) is replaced by
-‘o/oo’), although the OS may have got there first. These are warnings as they will
-continue to be replaced by dots in earlier versions of R.
-*   The matrix multiplication functions crossprod() and tcrossprod() are now also
-primitive and S3 generic, as %*% had become in R 4.3.0.
-*   source() and example() have a new optional argument catch.aborts which allows
-continued evaluation of the R code after an error.
-*   The non-Quartz tiff() devices allow additional types of compression if supported
-by the platform’s ‘libtiff’ library.
+
+* Formatting and printing, format(z), print(z), of complex vectors z
+  no longer zap relatively small real or imaginary parts to zero, fixing
+  PR#16752. This is an API change, as it was documented previously to
+  round real and imaginary parts together on purpose, producing nicer
+  looking output. As mentioned, e.g. in the PR, this change is
+  compatible with many other “R-like” programming environments.  We have
+  simplified the internal code and now basically format the real and
+  imaginary parts independently of each other.
+
+* New experimental functions Tailcall() and Exec() to support writing
+    stack-spaceefficient recursive functions.
+
+* Where characters are attempted to be plotted by pdf(), postscript()
+  and xfig() which are not in the selected 8-bit character set (most
+  often Latin-1) and the R session is using a UTF-8 locale, the warning
+  messages will show the UTF-8 character rather than its bytes and one
+  dot will be substituted per character rather than per byte.
+  (Platforms whose iconv() does transliteration silently plot the
+  transliteration.)  In a UTF-8 locale some transliterations are now
+  done with a warning (e.g., dashes and Unicode minus to hyphen,
+  ligatures are expanded, permille (‘‰’) is replaced by ‘o/oo’),
+  although the OS may have got there first. These are warnings as they
+  will continue to be replaced by dots in earlier versions of R.
+
+* The matrix multiplication functions crossprod() and tcrossprod() are
+  now also primitive and S3 generic, as %*% had become in R 4.3.0.
+
+* source() and example() have a new optional argument catch.aborts
+  which allows continued evaluation of the R code after an error.
+
+* The non-Quartz tiff() devices allow additional types of compression
+  if supported by the platform’s ‘libtiff’ library.
+
 *   The list of base and recommended package names is now provided by
-tools::standard_package_names().
-*   cairo_pdf() and cairo_ps() default to onefile = TRUE to closer match pdf() and
-postscript().
-*   New option catch.script.errors provides a documented way to catch errors and
-then continue in non-interactive use.
-*   L %||% R newly in base is an expressive idiom for the phrases if(!is.null(L)) L
-else R or if(is.null(L)) R else L.
-*   The return value from warnings() now always inherits from "warnings" as documented, now also in the case of no warnings where it previously returned NULL.
+    tools::standard_package_names().
+
+* cairo_pdf() and cairo_ps() default to onefile = TRUE to closer match
+  pdf() and postscript().
+
+* New option catch.script.errors provides a documented way to catch
+  errors and then continue in non-interactive use.
+
+* L %||% R newly in base is an expressive idiom for the phrases
+  if(!is.null(L)) L else R or if(is.null(L)) R else L.
+
+* The return value from warnings() now always inherits from "warnings"
+    as documented, now also in the case of no warnings where it
+    previously returned NULL.
+
 *   as.complex("1i") now returns 0 + 1i instead of NA with a warning.
-*   z <- c(NA, 1i) now keeps the imaginary part Im(z[1]) == 0, no longer coercing to
-NA_complex_. Similarly, cumsum(z) correctly sums real and imaginary parts separately, i.e., without “crosstalk” in case of NAs.
+
+* z <- c(NA, 1i) now keeps the imaginary part Im(z[1]) == 0, no longer
+  coercing to NA_complex_. Similarly, cumsum(z) correctly sums real and
+  imaginary parts separately, i.e., without “crosstalk” in case of NAs.
+
 *   On Alpine Linux iconv() now maps "latin2", "latin-2", "latin9" and "latin-9"
-to encoding names the OS knows about (case-insensitively).
-*   iconv(sub = "Unicode") now always zero-pads to four (hex) digits, rather than to 4
-or 8. (This seems to have become the convention once Unicode restricted the number
-of Unicode points to 221 − 1 and so will never need more than 6 digits.)
+    to encoding names the OS knows about (case-insensitively).
+
+* iconv(sub = "Unicode") now always zero-pads to four (hex) digits,
+  rather than to 4 or 8. (This seems to have become the convention
+  once Unicode restricted the number of Unicode points to 221 − 1
+  and so will never need more than 6 digits.)
+
 *   NCOL(NULL) now returns 0 instead of 1, for consistency with cbind().
-*   The information for the Euro glyph missing from the Adobe ‘.afm’ files for the
-Courier, Helvetica and Times families has been copied from their URW equivalents –
-this will improve vertical centring in the pdf() and postscript() devices.
-*   The included BLAS sources have been updated to those shipped with LAPACK version 3.12.0. The changes are almost entirely cosmetic.
+
+* The information for the Euro glyph missing from the Adobe ‘.afm’
+  files for the Courier, Helvetica and Times families has been copied
+  from their URW equivalents – this will improve vertical centring in
+  the pdf() and postscript() devices.
+
+* The included BLAS sources have been updated to those shipped with
+  LAPACK version 3.12.0. The changes are almost entirely cosmetic.
 
 
 *   The included LAPACK sources have been updated to version 3.12.0 and some further
 double-complex routines added.
-*   There are new font families for the 2014–5 URW 2.0 fonts (see ?pdf) which are
-included in recent versions of Ghostscript. These have font widths for most Greek
-glyphs and a few others which were missing from the original versions (whose font
-families remain available for reproducibility, although Ghostscript-based viewers will
-render using the 2.0 versions).
-*   Improve the large-n efficiency of as.matrix(<dist>), thanks an R contributors effort,
-notably by Tim Taylor and Heather Turner, see PR#18660.
+
+* There are new font families for the 2014–5 URW 2.0 fonts (see ?pdf)
+  which are included in recent versions of Ghostscript. These have font
+  widths for most Greek glyphs and a few others which were missing from
+  the original versions (whose font families remain available for
+  reproducibility, although Ghostscript-based viewers will render using
+  the 2.0 versions).
+
+* Improve the large-n efficiency of as.matrix(<dist>), thanks an R
+  contributors effort, notably by Tim Taylor and Heather Turner, see
+  PR#18660.
+
 *   The default and numeric methods of all.equal() get a check.class option.
-*   zapsmall() gets new optional arguments, function mFUN and min.d, for extra flexibility; fulfills a wish in PR#18199. Also, it is now an implicit S4 generic in package
-methods.
+
+* zapsmall() gets new optional arguments, function mFUN and min.d, for
+  extra flexibility; fulfills a wish in PR#18199. Also, it is now an
+  implicit S4 generic in package methods.
+
 *   The Rd filter for aspell() gains an ignore argument.
-*   New generic function sort_by(), primarily useful for the data.frame method which
-can be used to sort rows of a data frame by one or more columns.
+
+* New generic function sort_by(), primarily useful for the data.frame
+  method which can be used to sort rows of a data frame by one or more
+  columns.
+
 *   The icence headers for the RPC code in ‘src/extra/xdr’ have been updated to use
-the GPL-compatible licence published by Oracle America in 2010.
+    the GPL-compatible licence published by Oracle America in 2010.
+
 *   New function pkg2HTML() in tools to create single-page HTML reference manuals for
-R packages.
-*   The byte code evaluator now uses less C stack space for recursive calls to bytecompiled functions. It also makes more of an effort to avoid allocations for scalar
-return values.
-*   New completion option backtick (disabled by default) allows non-syntactic completions to be wrapped in backquotes. This is currently only useful for Jupyter notebooks
-via the IRkernel package, and may cause problems for other backends.
+    R packages.
+
+* The byte code evaluator now uses less C stack space for recursive
+  calls to bytecompiled functions. It also makes more of an effort to
+  avoid allocations for scalar return values.
+
+* New completion option backtick (disabled by default) allows
+  non-syntactic completions to be wrapped in backquotes. This is
+  currently only useful for Jupyter notebooks via the IRkernel package,
+  and may cause problems for other backends.