[pkgsrc/trunk]: pkgsrc/math/R Update to 3.3.3

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

details:   https://anonhg.NetBSD.org/pkgsrc/rev/2aebf81b958e
branches:  trunk
changeset: 359437:2aebf81b958e
user:      wen <wen%pkgsrc.org@localhost>
date:      Sat Mar 11 09:50:34 2017 +0000

description:
Update to 3.3.3

Upstream changes:
CHANGES IN R 3.3.3
NEW FEATURES

    Changes when redirection of a http:// URL to a https:// URL is encountered:

        The internal methods of download.file() and url() now report that they cannot follow this (rather than failing silently).

        (Unix-alike) download.file(method = "auto") (the default) re-tries with method = "libcurl".

        (Unix-alike) url(method = "default") with an explicit open argument re-tries with method = "libcurl". This covers many of the usages, e.g. readLines() with a URL argument.

INSTALLATION on a UNIX-ALIKE

    The configure check for the zlib version is now robust to versions longer than 5 characters, including 1.2.11.

UTILITIES

    Environmental variable _R_CHECK_TESTS_NLINES_ controls how R CMD check reports failing tests (see ?8 of the ?R Internals? manual).

DEPRECATED AND DEFUNCT

    (C-level Native routine registration.) The undocumented styles field of the components of R_CMethodDef and R_FortranMethodDef is deprecated.

BUG FIXES

    vapply(x, *) now works with long vectors x. (PR#17174)

    isS3method("is.na.data.frame") and similar are correct now. (PR#17171)

    grepRaw(<long>, <short>, fixed = TRUE) now works, thanks to a patch by Mikko Korpela. (PR#17132)

    Package installation into a library where the package exists via symbolic link now should work wherever Sys.readlink() works, resolving PR#16725.

    "Cincinnati" was missing an "n" in the precip dataset.

    Fix buffer overflow vulnerability in pdf() when loading an encoding file. Reported by Talos (TALOS-2016-0227).

    getDLLRegisteredRoutines() now produces its warning correctly when multiple DLLs match, thanks to Matt Dowle's PR#17184.

    Sys.timezone() now returns non-NA also on platforms such as Ubuntu 14.04.5 LTS, thanks to Mikko Korpela's PR#17186.

    format(x) for an illegal "POSIXlt" object x no longer segfaults.

    methods(f) now also works for f "(" or "{".

    (Windows only) dir.create() did not check the length of the path to create, and so could overflow a buffer and crash R. (PR#17206)

    On some systems, very small hexadecimal numbers in hex notation would underflow to zero. (PR#17199)

    pmin() and pmax() now work again for ordered factors and 0-length S3 classed objects, thanks to Suharto Anggono's PR#17195 and PR#17200.

    bug.report() did not do any validity checking on a package's BugReports field. It now ignores an empty field, removes leading whitespace and only attempts to open http:// and https:// URLs, 
falling back to emailing the maintainer.

    Bandwidth selectors bw.ucv() and bw.SJ() gave incorrect answers or incorrectly reported an error (because of integer overflow) for inputs longer than 46341. Similarly for bw.bcv() at length 5793.

    Another possible integer overflow is checked and may result in an error report (rather than an incorrect result) for much longer inputs (millions for a smooth distribution).

    findMethod() failed if the active signature had expanded beyond what a particular package used. (Example with packages XR and XRJulia on CRAN.)

    qbeta() underflowed too early in some very asymmetric cases. (PR#17178)

    R CMD Rd2pdf had problems with packages with non-ASCII titles in ?.Rd? files (usually the titles were omitted).

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 3bc7bb1089a7 -r 2aebf81b958e math/R/Makefile
--- a/math/R/Makefile   Sat Mar 11 07:37:00 2017 +0000
+++ b/math/R/Makefile   Sat Mar 11 09:50:34 2017 +0000
@@ -1,7 +1,6 @@
-# $NetBSD: Makefile,v 1.171 2017/01/01 16:06:26 adam Exp $
+# $NetBSD: Makefile,v 1.172 2017/03/11 09:50:34 wen Exp $
 
-DISTNAME=              R-3.3.2
-PKGREVISION=           1
+DISTNAME=              R-3.3.3
 CATEGORIES=            math
 MASTER_SITES=          ${MASTER_SITE_R_CRAN:=base/R-3/}
 
diff -r 3bc7bb1089a7 -r 2aebf81b958e math/R/PLIST
--- a/math/R/PLIST      Sat Mar 11 07:37:00 2017 +0000
+++ b/math/R/PLIST      Sat Mar 11 09:50:34 2017 +0000
@@ -1,4 +1,4 @@
-@comment $NetBSD: PLIST,v 1.25 2016/07/26 04:53:33 wen Exp $
+@comment $NetBSD: PLIST,v 1.26 2017/03/11 09:50:34 wen Exp $
 bin/R
 bin/Rscript
 info/R-FAQ.info.gz
@@ -1044,6 +1044,9 @@
 lib/R/library/survival/doc/compete.Rnw
 lib/R/library/survival/doc/compete.pdf
 lib/R/library/survival/doc/index.html
+lib/R/library/survival/doc/multi.R
+lib/R/library/survival/doc/multi.Rnw
+lib/R/library/survival/doc/multi.pdf
 lib/R/library/survival/doc/splines.R
 lib/R/library/survival/doc/splines.Rnw
 lib/R/library/survival/doc/splines.pdf
diff -r 3bc7bb1089a7 -r 2aebf81b958e math/R/distinfo
--- a/math/R/distinfo   Sat Mar 11 07:37:00 2017 +0000
+++ b/math/R/distinfo   Sat Mar 11 09:50:34 2017 +0000
@@ -1,9 +1,9 @@
-$NetBSD: distinfo,v 1.74 2016/11/06 02:08:16 wen Exp $
+$NetBSD: distinfo,v 1.75 2017/03/11 09:50:34 wen Exp $
 
-SHA1 (R-3.3.2.tar.gz) = 0e39e9c2d28fe6bab9c55ca23e08ba8727fd2fca
-RMD160 (R-3.3.2.tar.gz) = 99eb136e8ffb6f4a09943565af08f3dd4a5a7491
-SHA512 (R-3.3.2.tar.gz) = 06a98687c0b180cb0bfd57440ea26088212d9f48948d503136475bf54b42d72cfec5bea7e333c0cedd60733bd614dd0f8c2eced7e24478b6c89f48e8d0c43482
-Size (R-3.3.2.tar.gz) = 29440670 bytes
+SHA1 (R-3.3.3.tar.gz) = 9e205a817970578ecd80384f397bae35b46f13b9
+RMD160 (R-3.3.3.tar.gz) = 5f0d3aa3cf26132ac8774d2589083a12493c18ad
+SHA512 (R-3.3.3.tar.gz) = bcb0d92fc0b22c13e345a2f660e3b3cc5810f6a07c8f2e37949c81308c2b8a5edc322df0394ece563888645442b6c01a3e1e7005aa60bd9beacc718200829e75
+Size (R-3.3.3.tar.gz) = 29804326 bytes
 SHA1 (patch-ac) = 68c1943a352e6f8b2842331578ed746b1ac27bea
 SHA1 (patch-ad) = a43b4875a2ee4677b5f762abf3f9a623fd12cbb5
 SHA1 (patch-src_include_GraphicsBase.h) = eed25eaca982ca76bf75d199dd8bf48be2a99ac5