CVS commit: pkgsrc/math/R

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

Module Name:    pkgsrc
Committed By:   wen
Date:           Sun Oct 11 15:22:56 UTC 2020

Modified Files:
        pkgsrc/math/R: Makefile distinfo

Log Message:
Update to 4.0.3

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
      it now gives a warning which will become an error in R 4.1.0.

  BUG FIXES:

    * The code mitigating stack overflow with PCRE regexps on very long
      strings is enabled for PCRE2 < 10.30 also when JIT is enabled,
      since stack overflows have been seen in that case.

    * Fix to correctly show the group labels in dotchart() (which where
      lost in the ylab improvement for R 4.0.0).

    * addmargins(*, ..) now also works when fn() is a local function,
      thanks to bug report and patch PR#17124 from Alex Bertram.

    * rank(x) and hence sort(x) now work when x is an object (as per
      is.object(x)) of type "raw" _and_ provides a valid `[` method,
      e.g., for gmp::as.bigz(.) numbers.

    * chisq.test(*, simulate.p.value=TRUE) and r2dtable() now work
      correctly for large table entries (in the millions).  Reported by
      Sebastian Meyer and investigated by more helpers in PR#16184.

    * Low-level socket read/write operations have been fixed to
      correctly signal communication errors. Previously, such errors
      could lead to a segfault due to invalid memory access. Reported
      and debugged by Dmitriy Selivanov in PR#17850.

    * quantile(x, pr) works more consistently for pr values slightly
      outside [0,1], thanks to Suharto Anggono's PR#17891.

      Further, quantile(x, prN, names=FALSE) now works even when prN
      contains NAs, thanks to Anggono's PR#17892.  Ditto for ordered
      factors or Date objects when type = 1 or 3, thanks to PR#17899.

    * Libcurl-based internet access, including curlGetHeaders(), was
      not respecting the "timeout" option.  If this causes
      unanticipated timeouts, consider increasing the default by
      setting R_DEFAULT_INTERNET_TIMEOUT.

    * as.Date(<char>) now also works with an initial "", thanks to
      Michael Chirico's PR#17909.

    * isS3stdGeneric(f) now detects an S3 generic also when it it is
      trace()d, thanks to Gabe Becker's PR#17917.

    * R_allocLD() has been fixed to return memory aligned for long
      double type PR#16534.

    * fisher.test() no longer segfaults when called again after its
      internal stack has been exceeded PR#17904.

    * Accessing a long vector represented by a compact integer sequence
      no longer segfaults (reported and debugged by Hugh Parsonage).

    * duplicated() now works also for strings with multiple encodings
      inside a single vector PR#17809.

    * phyper(11, 15, 0, 12, log.p=TRUE) no longer gives NaN; reported
      as PR#17271 by Alexey Stukalov.

    * Fix incorrect calculation in logLik.nls() PR#16100, patch from
      Sebastian Meyer.

    * A very old bug could cause a segfault in model.matrix() when
      terms involved logical variables.  Part of PR#17879.

    * model.frame.default() allowed data = 1, leading to involuntary
      variable capture (rest of PR#17879).

    * tar() no longer skips non-directory files, thanks to a patch by
      Sebastian Meyer, fixing the remaining part of PR#16716.


To generate a diff of this commit:
cvs rdiff -u -r1.217 -r1.218 pkgsrc/math/R/Makefile
cvs rdiff -u -r1.86 -r1.87 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:1.217 pkgsrc/math/R/Makefile:1.218
--- pkgsrc/math/R/Makefile:1.217        Mon Aug 31 18:10:10 2020
+++ pkgsrc/math/R/Makefile      Sun Oct 11 15:22:56 2020
@@ -1,7 +1,6 @@
-# $NetBSD: Makefile,v 1.217 2020/08/31 18:10:10 wiz Exp $
+# $NetBSD: Makefile,v 1.218 2020/10/11 15:22:56 wen Exp $
 
-DISTNAME=      R-4.0.2
-PKGREVISION=   2
+DISTNAME=      R-4.0.3
 CATEGORIES=    math
 MASTER_SITES=  ${MASTER_SITE_R_CRAN:=base/R-4/}
 

Index: pkgsrc/math/R/distinfo
diff -u pkgsrc/math/R/distinfo:1.86 pkgsrc/math/R/distinfo:1.87
--- pkgsrc/math/R/distinfo:1.86 Thu Jul 16 02:22:55 2020
+++ pkgsrc/math/R/distinfo      Sun Oct 11 15:22:56 2020
@@ -1,9 +1,9 @@
-$NetBSD: distinfo,v 1.86 2020/07/16 02:22:55 markd Exp $
+$NetBSD: distinfo,v 1.87 2020/10/11 15:22:56 wen Exp $
 
-SHA1 (R-4.0.2.tar.gz) = ee79a57730ed4786c0d6a05bd050d52a5d0290c1
-RMD160 (R-4.0.2.tar.gz) = a323d61573a6fc46a7ce80135348578f0e7b347d
-SHA512 (R-4.0.2.tar.gz) = b7330613ee9795f54cde3dd9f7509be83d9156fb8577c17179727ee01450db27704249f68bd48e0331e2df09c2d9833d8bb019c4f9ce9ba669df74650ff2e842
-Size (R-4.0.2.tar.gz) = 33191186 bytes
+SHA1 (R-4.0.3.tar.gz) = 5daba2d63e07a9f39d9b69b68f0642d71213ec5c
+RMD160 (R-4.0.3.tar.gz) = dd6fac10033746e5e0dd4fb0200b9008695e58e5
+SHA512 (R-4.0.3.tar.gz) = 2493295f3052d077a4820c0f84ca1c37df262b8b357f62f2ea99dbfffea065861735a08fa2098421078e58e917c540e680a668546d450af734722b421669e058
+Size (R-4.0.3.tar.gz) = 33497010 bytes
 SHA1 (patch-configure.ac) = 2732e3e0a39ee64ae4cba5c476f4754ecbd14942
 SHA1 (patch-m4_R.m4) = 704d5514e10adf0b5217bb71b06f44a612eca6e0
 SHA1 (patch-m4_cairo.m4) = a0c4ec68d7d6d3a73a2a24481d0dee8c192bf154