CVS commit: pkgsrc/math/R

["Wen Heping" <wen%netbsd.org@localhost>]

Module Name:    pkgsrc
Committed By:   wen
Date:           Fri Mar 11 10:27:29 UTC 2022

Modified Files:
        pkgsrc/math/R: Makefile distinfo

Log Message:
Update to 4.1.3

Upstream changes:
CHANGES IN R 4.1.3:

  NEW FEATURES:

    * The default version of Bioconductor has been changed to 3.14.
      (This is used by setRepositories and the menus in GUIs.)

  UTILITIES:

    * R CMD check --as-cran has a workaround for a bug in versions of
      file up to at least 5.41 which mis-identify DBF files last
      changed in 2022 as executables.

  C-LEVEL FACILITIES:

    * The legacy S-compatibility macros SINGLE_* in R_ext/Constants.h
      (included by R.h) are deprecated and will be removed in R 4.2.0.

  BUG FIXES:

    * Initialization of self-starting nls() models with initialization
      functions following the pre-R-4.1.0 API (without the ...
      argument) works again for now, with a deprecation warning.

    * Fixed quoting of ~autodetect~ in Java setting defaults to avoid
      inadvertent user lookup due to leading ~, reported in PR#18231 by
      Harold Gutch.

    * substr(., start, stop) <- v now treats _negative_ stop values
      correctly.  Reported with a patch in PR#18228 by Brodie Gaslam.

    * Subscripting an array x without dimnames by a
      length(dim(x))-column character matrix gave "random" non-sense,
      now an error; reported in PR#18244 by Mikael Jagan.

    * ...names() now matches names(list(...)) closely, fixing PR#18247.

    * all.equal(*, scale = s) now works as intended when length(s) > 1,
      partly thanks to Michael Chirico's PR#18272.

    * print(x) for long vectors x now also works for named atomic
      vectors or lists and prints the correct number when reaching the
      getOption("max.print") limit; partly thanks to a report and
      proposal by Hugh Parsonage to the R-devel list.

    * all.equal(<selfStart>, *) no longer signals a deprecation
      warning.

    * reformulate(*, response=r) gives a helpful error message now when
      length(r) > 1, thanks to Bill Dunlap's PR#18281.

    * Modifying globalCallingHandlers inside withCallingHandlers() now
      works or fails correctly, thanks to Henrik Bengtsson's PR#18257.

    * hist(<Date>, breaks = "days") and hist(<POSIXt>, breaks = "secs")
      no longer fail for inputs of length 1.

    * qbeta(.001, .9, .009) and similar cases now converge correctly
      thanks to Ben Bolker's report in PR#17746.

    * window(x, start, end) no longer wrongly signals "'start' cannot
      be after 'end'", fixing PR#17527 and PR#18291.

    * data() now checks that its (rarely used) list argument is a
      character vector - a couple of packages passed other types and
      gave incorrect results.

    * which() now checks its arr.ind argument is TRUE rather coercing
      to logical and taking the first element - which gave incorrect
      results in package code.

    * model.weights() and model.offset() more carefully extract their
      model components, thanks to Ben Bolker and Tim Taylor's R-devel
      post.

    * list.files(recursive = TRUE) now shows all broken symlinks
      (previously, some of them may have been omitted, PR#18296).


To generate a diff of this commit:
cvs rdiff -u -r1.229 -r1.230 pkgsrc/math/R/Makefile
cvs rdiff -u -r1.92 -r1.93 pkgsrc/math/R/distinfo

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

Modified files:

Index: pkgsrc/math/R/Makefile
diff -u pkgsrc/math/R/Makefile:1.229 pkgsrc/math/R/Makefile:1.230
--- pkgsrc/math/R/Makefile:1.229        Wed Dec  8 16:05:31 2021
+++ pkgsrc/math/R/Makefile      Fri Mar 11 10:27:29 2022
@@ -1,11 +1,10 @@
-# $NetBSD: Makefile,v 1.229 2021/12/08 16:05:31 adam Exp $
+# $NetBSD: Makefile,v 1.230 2022/03/11 10:27:29 wen Exp $
 
 #
 # If updating this package, please try to ensure PLIST.Darwin is kept in sync
 # to avoid unnecessarily breaking macOS users.
 #
-DISTNAME=      R-4.1.2
-PKGREVISION=   1
+DISTNAME=      R-4.1.3
 CATEGORIES=    math
 MASTER_SITES=  ${MASTER_SITE_R_CRAN:=base/R-4/}
 

Index: pkgsrc/math/R/distinfo
diff -u pkgsrc/math/R/distinfo:1.92 pkgsrc/math/R/distinfo:1.93
--- pkgsrc/math/R/distinfo:1.92 Thu Nov  4 14:38:47 2021
+++ pkgsrc/math/R/distinfo      Fri Mar 11 10:27:29 2022
@@ -1,8 +1,8 @@
-$NetBSD: distinfo,v 1.92 2021/11/04 14:38:47 wen Exp $
+$NetBSD: distinfo,v 1.93 2022/03/11 10:27:29 wen Exp $
 
-BLAKE2s (R-4.1.2.tar.gz) = 8ef0d0b0599eca38ff309edda9df7098476335a52d5f6e363b97855044414228
-SHA512 (R-4.1.2.tar.gz) = 657c7950a88f632f1bbb08dbd0b3fb485732a25d8bbcb8a7939a40b23c7a235fdb9b46c296acaa9f72eabebe96e270ecbdcd7970fc9d3a299e6687bea45f2d3f
-Size (R-4.1.2.tar.gz) = 34009074 bytes
+BLAKE2s (R-4.1.3.tar.gz) = bee2174be0be0102367553b25fbf38b1ed2324a9193310a3fe98babec69b7988
+SHA512 (R-4.1.3.tar.gz) = cb71cc6c9551cc9cef4819ed778a8d0ef40490ec2bed27669c8e93d464a93bef5e73c2a03a714db03c87112b291a752ec2d21194e5abef81d85cb6c62643127c
+Size (R-4.1.3.tar.gz) = 35026517 bytes
 SHA1 (patch-configure.ac) = 2732e3e0a39ee64ae4cba5c476f4754ecbd14942
 SHA1 (patch-m4_R.m4) = 704d5514e10adf0b5217bb71b06f44a612eca6e0
 SHA1 (patch-src_library_stats_src_Makefile.in) = 4eb93292858392792c37a706399e2cef91821bbe