[pkgsrc/trunk]: pkgsrc/math/R Update to 3.5.1

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

details:   https://anonhg.NetBSD.org/pkgsrc/rev/598041659ac8
branches:  trunk
changeset: 310037:598041659ac8
user:      wen <wen%pkgsrc.org@localhost>
date:      Wed Jul 04 07:27:13 2018 +0000

description:
Update to 3.5.1

Upstream changes:
CHANGES IN R 3.5.1
BUG FIXES

    file("stdin") is no longer considered seekable.

    dput() and dump() are no longer truncating when options(deparse.max.lines = *) is set.

    Calls with an S3 class are no longer evaluated when printed, fixing part of PR#17398, thanks to a patch from Lionel Henry.

    Allow file argument of Rscript to include space even when it is first on the command line.

    callNextMethod() uses the generic from the environment of the calling method. Reported by Herv? Pag?s with well documented examples.

    Compressed file connections are marked as blocking.

    optim(*, lower = c(-Inf, -Inf)) no longer warns (and switches the method), thanks to a suggestion by John Nash.

    predict(fm, newdata) is now correct also for models where the formula has terms such as splines::ns(..) or stats::poly(..), fixing PR#17414, based on a patch from Duncan Murdoch.

    simulate.lm(glm(*, gaussian(link = <non-default>))) has been corrected, fixing PR#17415 thanks to Alex Courtiol.

    unlist(x) no longer fails in some cases of nested empty lists. Reported by Steven Nydick.

    qr.coef(qr(<all 0, w/ colnames>)) now works. Reported by Kun Ren.

    The radix sort is robust to vectors with >1 billion elements (but long vectors are still unsupported). Thanks to Matt Dowle for the fix.

    Terminal connections (e.g., stdin) are no longer buffered. Fixes PR#17432.

    deparse(x), dput(x) and dump() now respect c()'s argument names recursive and use.names, e.g., for x <- setNames(0, "recursive"), thanks to Suharto Anggono's PR#17427.

    Unbuffered connections now work with encoding conversion. Reported by Stephen Berman.

    ?.Renviron? on Windows with Rgui is again by default searched for in user documents directory when invoked via the launcher icon. Reported by Jeroen Ooms.

    printCoefmat() now also works with explicit right=TRUE.

    print.noquote() now also works with explicit quote=FALSE.

    The default method for pairs(.., horInd=*, verInd=*) now gets the correct order, thanks to reports by Chris Andrews and Gerrit Eichner. Additionally, when horInd or verInd contain only a subset 
of variables, all the axes are labeled correctly now.

    agrep("..|..", .., fixed=FALSE) now matches when it should, thanks to a reminder by Andreas Kolter.

    str(ch) now works for more invalid multibyte strings.

diffstat:

 math/R/Makefile |   4 ++--
 math/R/PLIST    |   6 ++++--
 math/R/distinfo |  10 +++++-----
 3 files changed, 11 insertions(+), 9 deletions(-)

diffs (57 lines):

diff -r 1b21d38614c6 -r 598041659ac8 math/R/Makefile
--- a/math/R/Makefile   Wed Jul 04 06:50:04 2018 +0000
+++ b/math/R/Makefile   Wed Jul 04 07:27:13 2018 +0000
@@ -1,6 +1,6 @@
-# $NetBSD: Makefile,v 1.185 2018/05/31 10:23:02 wen Exp $
+# $NetBSD: Makefile,v 1.186 2018/07/04 07:27:13 wen Exp $
 
-DISTNAME=      R-3.5.0
+DISTNAME=      R-3.5.1
 CATEGORIES=    math
 MASTER_SITES=  ${MASTER_SITE_R_CRAN:=base/R-3/}
 
diff -r 1b21d38614c6 -r 598041659ac8 math/R/PLIST
--- a/math/R/PLIST      Wed Jul 04 06:50:04 2018 +0000
+++ b/math/R/PLIST      Wed Jul 04 07:27:13 2018 +0000
@@ -1,4 +1,4 @@
-@comment $NetBSD: PLIST,v 1.29 2018/05/31 10:23:02 wen Exp $
+@comment $NetBSD: PLIST,v 1.30 2018/07/04 07:27:13 wen Exp $
 bin/R
 bin/Rscript
 info/R-FAQ.info.gz
@@ -1065,7 +1065,6 @@
 lib/R/library/survival/data/Rdata.rdb
 lib/R/library/survival/data/Rdata.rds
 lib/R/library/survival/data/Rdata.rdx
-lib/R/library/survival/data/datalist
 lib/R/library/survival/doc/adjcurve.R
 lib/R/library/survival/doc/adjcurve.Rnw
 lib/R/library/survival/doc/adjcurve.pdf
@@ -1076,6 +1075,9 @@
 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/population.R
+lib/R/library/survival/doc/population.Rnw
+lib/R/library/survival/doc/population.pdf
 lib/R/library/survival/doc/splines.R
 lib/R/library/survival/doc/splines.Rnw
 lib/R/library/survival/doc/splines.pdf
diff -r 1b21d38614c6 -r 598041659ac8 math/R/distinfo
--- a/math/R/distinfo   Wed Jul 04 06:50:04 2018 +0000
+++ b/math/R/distinfo   Wed Jul 04 07:27:13 2018 +0000
@@ -1,9 +1,9 @@
-$NetBSD: distinfo,v 1.80 2018/05/31 10:23:02 wen Exp $
+$NetBSD: distinfo,v 1.81 2018/07/04 07:27:13 wen Exp $
 
-SHA1 (R-3.5.0.tar.gz) = 69f9ff4ecc78057095aedc145eb33f66f48b27ed
-RMD160 (R-3.5.0.tar.gz) = 404a2795ddeb2539422b636a95670d31a54ee0a6
-SHA512 (R-3.5.0.tar.gz) = c2703e892eb6f12ec7b536540b823d4ef011dddcbdca06c12d438bc1f07debae9dbd0f72abb6f0d4c577a3c74b155452ef527489cf023ed892109dd86c23bc37
-Size (R-3.5.0.tar.gz) = 30675040 bytes
+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 (patch-ad) = a43b4875a2ee4677b5f762abf3f9a623fd12cbb5
 SHA1 (patch-configure.ac) = f4829c37304e81485e13b4ed8beaeac7edd16189
 SHA1 (patch-m4_R.m4) = 704d5514e10adf0b5217bb71b06f44a612eca6e0