Sun Oct 11 15:22:56 2020 UTC ()
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.
(wen)
diff -r1.217 -r1.218 pkgsrc/math/R/Makefile
diff -r1.86 -r1.87 pkgsrc/math/R/distinfo
--- pkgsrc/math/R/Makefile 2020/08/31 18:10:10 1.217
+++ pkgsrc/math/R/Makefile 2020/10/11 15:22:56 1.218
| @@ -1,17 +1,16 @@ | | | @@ -1,17 +1,16 @@ |
1 | # $NetBSD: Makefile,v 1.217 2020/08/31 18:10:10 wiz Exp $ | | 1 | # $NetBSD: Makefile,v 1.218 2020/10/11 15:22:56 wen Exp $ |
2 | | | 2 | |
3 | DISTNAME= R-4.0.2 | | 3 | DISTNAME= R-4.0.3 |
4 | PKGREVISION= 2 | | | |
5 | CATEGORIES= math | | 4 | CATEGORIES= math |
6 | MASTER_SITES= ${MASTER_SITE_R_CRAN:=base/R-4/} | | 5 | MASTER_SITES= ${MASTER_SITE_R_CRAN:=base/R-4/} |
7 | | | 6 | |
8 | MAINTAINER= pkgsrc-users@NetBSD.org | | 7 | MAINTAINER= pkgsrc-users@NetBSD.org |
9 | HOMEPAGE= https://www.R-project.org/ | | 8 | HOMEPAGE= https://www.R-project.org/ |
10 | COMMENT= Statistical language for data analysis and graphics | | 9 | COMMENT= Statistical language for data analysis and graphics |
11 | LICENSE= gnu-gpl-v2 | | 10 | LICENSE= gnu-gpl-v2 |
12 | | | 11 | |
13 | USE_GCC_RUNTIME= yes | | 12 | USE_GCC_RUNTIME= yes |
14 | | | 13 | |
15 | BUILD_TARGET= all info | | 14 | BUILD_TARGET= all info |
16 | INSTALL_TARGET= install install-info | | 15 | INSTALL_TARGET= install install-info |
17 | TEST_TARGET= check | | 16 | TEST_TARGET= check |
--- pkgsrc/math/R/distinfo 2020/07/16 02:22:55 1.86
+++ pkgsrc/math/R/distinfo 2020/10/11 15:22:56 1.87
| @@ -1,11 +1,11 @@ | | | @@ -1,11 +1,11 @@ |
1 | $NetBSD: distinfo,v 1.86 2020/07/16 02:22:55 markd Exp $ | | 1 | $NetBSD: distinfo,v 1.87 2020/10/11 15:22:56 wen Exp $ |
2 | | | 2 | |
3 | SHA1 (R-4.0.2.tar.gz) = ee79a57730ed4786c0d6a05bd050d52a5d0290c1 | | 3 | SHA1 (R-4.0.3.tar.gz) = 5daba2d63e07a9f39d9b69b68f0642d71213ec5c |
4 | RMD160 (R-4.0.2.tar.gz) = a323d61573a6fc46a7ce80135348578f0e7b347d | | 4 | RMD160 (R-4.0.3.tar.gz) = dd6fac10033746e5e0dd4fb0200b9008695e58e5 |
5 | SHA512 (R-4.0.2.tar.gz) = b7330613ee9795f54cde3dd9f7509be83d9156fb8577c17179727ee01450db27704249f68bd48e0331e2df09c2d9833d8bb019c4f9ce9ba669df74650ff2e842 | | 5 | SHA512 (R-4.0.3.tar.gz) = 2493295f3052d077a4820c0f84ca1c37df262b8b357f62f2ea99dbfffea065861735a08fa2098421078e58e917c540e680a668546d450af734722b421669e058 |
6 | Size (R-4.0.2.tar.gz) = 33191186 bytes | | 6 | Size (R-4.0.3.tar.gz) = 33497010 bytes |
7 | SHA1 (patch-configure.ac) = 2732e3e0a39ee64ae4cba5c476f4754ecbd14942 | | 7 | SHA1 (patch-configure.ac) = 2732e3e0a39ee64ae4cba5c476f4754ecbd14942 |
8 | SHA1 (patch-m4_R.m4) = 704d5514e10adf0b5217bb71b06f44a612eca6e0 | | 8 | SHA1 (patch-m4_R.m4) = 704d5514e10adf0b5217bb71b06f44a612eca6e0 |
9 | SHA1 (patch-m4_cairo.m4) = a0c4ec68d7d6d3a73a2a24481d0dee8c192bf154 | | 9 | SHA1 (patch-m4_cairo.m4) = a0c4ec68d7d6d3a73a2a24481d0dee8c192bf154 |
10 | SHA1 (patch-src_library_stats_src_Makefile.in) = 4eb93292858392792c37a706399e2cef91821bbe | | 10 | SHA1 (patch-src_library_stats_src_Makefile.in) = 4eb93292858392792c37a706399e2cef91821bbe |
11 | SHA1 (patch-src_main_character.c) = 08d0096cd7a90131ec252342756499036a609c1c | | 11 | SHA1 (patch-src_main_character.c) = 08d0096cd7a90131ec252342756499036a609c1c |