[pkgsrc/trunk]: pkgsrc/math/R Update to 3.5.2

[wen <wen%pkgsrc.org@localhost>]

details:   https://anonhg.NetBSD.org/pkgsrc/rev/e770b234fe7c
branches:  trunk
changeset: 316845:e770b234fe7c
user:      wen <wen%pkgsrc.org@localhost>
date:      Fri Dec 21 02:55:06 2018 +0000

description:
Update to 3.5.2

Upstream changes:
CHANGES IN R 3.5.2:

  PACKAGE INSTALLATION:

    * New macro CXX_VISIBILITY analogous to C_VISIBILITY (which several
      packages have been misusing for C++ code) for the default C++
      compiler (but not necessarily one used for non-default C++
      dialects like C++14).

  TESTING:

    * The random number generator tests in tests/p-r-random-tests.R no
      longer fail occasionally as they now randomly sample from
      "certified" random seeds.

  BUG FIXES:

    * The "glm" method of drop1() miscalculated the score test
      (test="Rao") when the model contained an offset.

    * Linear multiple empty models such as lm(y ~ 0) now have a
      correctly dimensioned empty coefficient matrix; reported by Brett
      Presnell.

    * vcov(<empty mlm>) and hence confint() now work (via a consistency
      change in summary.lm()).

    * confint(<multiple lm()>) now works correctly; reported on R-devel
      by Steven Pav.

    * quade.test() now also works correctly when its arguments are not
      yet sorted along groups, fixing PR#15842.

    * Installation on a Unix-alike tries harder to link to the pthread
      library where required (rather than relying on OpenMP to provide
      it: configuring with --disable-openmp was failing on some Linux
      systems).

    * The data.frame method for print(x) is fast now also for large
      data frames x and got an optional argument max, thanks to
      suggestions by Juan Telleria.

    * hist() no longer integer overflows in very rare cases, fixing
      PR#17450.

    * untar() ignored a character compressed argument: however many
      external tar programs ignore the flags which should have been set
      and automagically choose the compression type, and if appropriate
      gzip or bzip2 compression would have been chosen from the magic
      header of the tarball.

    * zapsmall(x) now works for more "number-like" objects.

    * The tools-internal function called from R CMD INSTALL now gets a
      warnOption = 1 argument and only sets options(warn = warnOption)
      when that increases the warning level (PR#17453).

    * Analogously, the tools-internal function called from R CMD check
      gets a warnOption = 1 argument and uses the larger of that and
      getOption("warn"), also allowing to be run with increased warning
      level.

    * Parse data now have deterministic parent nodes (PR#16041).

    * Calling match() with length one x and POSIXlt table gave a
      segfault (PR#17459).

    * Fork clusters could hang due to a race condition in cluster
      initialization (makeCluster()).

    * nextn(n) now also works for larger n and no longer loops
      infinitely for e.g, n <- 214e7.

    * cooks.distance() and rstandard() now work correctly for multiple
      linear models ("mlm").

    * polym() and corresponding lm() prediction now also work for a
      boundary "vector" case fixing PR#17474, reported by Alexandre
      Courtiol.

    * With a very large number of variables terms() could segfault
      (PR#17480).

    * cut(rep(0, 7)) now works, thanks to Joey Reid and Benjamin Tyner
      (PR#16802).

    * download.file(*, method = "curl", cacheOK = FALSE) should work
      now on Windows, thanks to Kevin Ushey's patch in PR#17323.

    * duplicated(<dataframe with 'f'>) now works, too, thanks to
      Andreas Kersting's PR#17485; ditto for anyDuplicated().

    * legend(*, cex = 1:2) now works less badly.

    * The print() method for POSIXct and POSIXlt now correctly obeys
      getOption("max.print"), fixing a long-standing typo, and it also
      gets a corresponding optional max argument.

    * Unserialization of raw vectors serialized in ASCII representation
      now works correctly.

    * <data frame>[TRUE, <new>] <- list(c1, c2) now works correctly,
      thanks to Suharto Anggono's PR#15362 and Emil Bode's patch in
      PR#17504.

    * seq.int(*, by=by, length=n) no longer wrongly "drops fractional
      parts" when by is integer, thanks to Suharto Anggono's report
      PR#17506.

    * Buffering is disabled for file() connections to non-regular files
      (like sockets), as well as fifo() and pipe() connections.  Fixes
      PR#17470, reported by Chris Culnane.

diffstat:

 math/R/Makefile |   5 ++---
 math/R/PLIST    |   5 ++++-
 math/R/distinfo |  10 +++++-----
 3 files changed, 11 insertions(+), 9 deletions(-)

diffs (50 lines):

diff -r 8707f20bfcc3 -r e770b234fe7c math/R/Makefile
--- a/math/R/Makefile   Thu Dec 20 23:55:34 2018 +0000
+++ b/math/R/Makefile   Fri Dec 21 02:55:06 2018 +0000
@@ -1,7 +1,6 @@
-# $NetBSD: Makefile,v 1.193 2018/12/13 19:52:08 adam Exp $
+# $NetBSD: Makefile,v 1.194 2018/12/21 02:55:06 wen Exp $
 
-DISTNAME=      R-3.5.1
-PKGREVISION=   5
+DISTNAME=      R-3.5.2
 CATEGORIES=    math
 MASTER_SITES=  ${MASTER_SITE_R_CRAN:=base/R-3/}
 
diff -r 8707f20bfcc3 -r e770b234fe7c math/R/PLIST
--- a/math/R/PLIST      Thu Dec 20 23:55:34 2018 +0000
+++ b/math/R/PLIST      Fri Dec 21 02:55:06 2018 +0000
@@ -1,4 +1,4 @@
-@comment $NetBSD: PLIST,v 1.30 2018/07/04 07:27:13 wen Exp $
+@comment $NetBSD: PLIST,v 1.31 2018/12/21 02:55:06 wen Exp $
 bin/R
 bin/Rscript
 info/R-FAQ.info.gz
@@ -1071,6 +1071,9 @@
 lib/R/library/survival/doc/compete.R
 lib/R/library/survival/doc/compete.Rnw
 lib/R/library/survival/doc/compete.pdf
+lib/R/library/survival/doc/concordance.R
+lib/R/library/survival/doc/concordance.Rnw
+lib/R/library/survival/doc/concordance.pdf
 lib/R/library/survival/doc/index.html
 lib/R/library/survival/doc/multi.R
 lib/R/library/survival/doc/multi.Rnw
diff -r 8707f20bfcc3 -r e770b234fe7c math/R/distinfo
--- a/math/R/distinfo   Thu Dec 20 23:55:34 2018 +0000
+++ b/math/R/distinfo   Fri Dec 21 02:55:06 2018 +0000
@@ -1,9 +1,9 @@
-$NetBSD: distinfo,v 1.81 2018/07/04 07:27:13 wen Exp $
+$NetBSD: distinfo,v 1.82 2018/12/21 02:55:06 wen Exp $
 
-SHA1 (R-3.5.1.tar.gz) = 9314d3d372b05546a33791fbc8dd579c92ebd16b
-RMD160 (R-3.5.1.tar.gz) = 394b122f4477b0c8e87c48fcc8cf4a1f8282a9bc
-SHA512 (R-3.5.1.tar.gz) = 382cc6e200469dd168799948edcf3a0b869d7ef3b3176fdfc60752f3f37e6ba356323c47d8815a4d9ab6ad3a21cd045d26ef5e75107c8685328e0ffcfd172f7f
-Size (R-3.5.1.tar.gz) = 29812849 bytes
+SHA1 (R-3.5.2.tar.gz) = 057ea91daed3e68a12b2a473ee1283cf26f360e2
+RMD160 (R-3.5.2.tar.gz) = c1cee244f1ae0cf7466b2af69a70bb7eee1321ed
+SHA512 (R-3.5.2.tar.gz) = 53e94f01ecee6c90cecfa07ee9950d62130a331010c0b23baaf88ab5009007856c9352ce97916404ff35d19632495902d41cb655a5fd116a7d2f5d6767d7b447
+Size (R-3.5.2.tar.gz) = 30186438 bytes
 SHA1 (patch-ad) = a43b4875a2ee4677b5f762abf3f9a623fd12cbb5
 SHA1 (patch-configure.ac) = f4829c37304e81485e13b4ed8beaeac7edd16189
 SHA1 (patch-m4_R.m4) = 704d5514e10adf0b5217bb71b06f44a612eca6e0