R: update to 4.0.2

CHANGES IN R 4.0.0:

  SIGNIFICANT USER-VISIBLE CHANGES:

    * Packages need to be (re-)installed under this version (4.0.0) of
      R.

    * matrix objects now also inherit from class "array", so e.g.,
      class(diag(1)) is c("matrix", "array").  This invalidates code
      incorrectly assuming that class(matrix_obj)) has length one.

      S3 methods for class "array" are now dispatched for matrix
      objects.

    * There is a new syntax for specifying _raw_ character constants
      similar to the one used in C++: r"(...)" with ... any character
      sequence not containing the sequence )".  This makes it easier to
      write strings that contain backslashes or both single and double
      quotes.  For more details see ?Quotes.

    * R now uses a stringsAsFactors = FALSE default, and hence by
      default no longer converts strings to factors in calls to
      data.frame() and read.table().

      A large number of packages relied on the previous behaviour and
      so have needed/will need updating.

    * The plot() S3 generic function is now in package base rather than
      package graphics, as it is reasonable to have methods that do not
      use the graphics package.  The generic is currently re-exported
      from the graphics namespace to allow packages importing it from
      there to continue working, but this may change in future.

      Packages which define S4 generics for plot() should be
      re-installed and package code using such generics from other
      packages needs to ensure that they are imported rather than rely
      on their being looked for on the search path (as in a namespace,
      the base namespace has precedence over the search path).


See ${PREFIX}/lib/R/doc/NEWS for full changes.

3 files changed, 30 insertions, 18 deletions

diff --git a/math/R/Makefile b/math/R/Makefile
index 9416876d8f6..23c3bb0ed3e 100644
--- a/math/R/Makefile
+++ b/math/R/Makefile
@@ -1,9 +1,8 @@
-# $NetBSD: Makefile,v 1.214 2020/05/22 10:56:20 adam Exp $
+# $NetBSD: Makefile,v 1.215 2020/07/16 02:22:55 markd Exp $
 
-DISTNAME=	R-3.6.1
-PKGREVISION=	7
+DISTNAME=	R-4.0.2
 CATEGORIES=	math
-MASTER_SITES=	${MASTER_SITE_R_CRAN:=base/R-3/}
+MASTER_SITES=	${MASTER_SITE_R_CRAN:=base/R-4/}
 
 MAINTAINER=	pkgsrc-users@NetBSD.org
 HOMEPAGE=	https://www.R-project.org/
@@ -160,7 +159,7 @@ fix-darwin-install-name:
 .include "../../devel/gettext-lib/buildlink3.mk"
 .include "../../devel/glib2/buildlink3.mk"
 .include "../../devel/pango/buildlink3.mk"
-.include "../../devel/pcre/buildlink3.mk"
+.include "../../devel/pcre2/buildlink3.mk"
 # uses callback interface
 .include "../../devel/readline/buildlink3.mk"
 .include "../../devel/zlib/buildlink3.mk"
diff --git a/math/R/PLIST b/math/R/PLIST
index 597bb84c116..55250153162 100644
--- a/math/R/PLIST
+++ b/math/R/PLIST
@@ -1,4 +1,4 @@
-@comment $NetBSD: PLIST,v 1.32 2019/06/09 13:39:12 wen Exp $
+@comment $NetBSD: PLIST,v 1.33 2020/07/16 02:22:55 markd Exp $
 bin/R
 bin/Rscript
 info/R-FAQ.info.gz
@@ -46,11 +46,15 @@ lib/R/doc/NEWS
 lib/R/doc/NEWS.0
 lib/R/doc/NEWS.1
 lib/R/doc/NEWS.2
+lib/R/doc/NEWS.2.rds
+lib/R/doc/NEWS.3
+lib/R/doc/NEWS.3.rds
 lib/R/doc/NEWS.pdf
 lib/R/doc/NEWS.rds
 lib/R/doc/RESOURCES
 lib/R/doc/THANKS
 lib/R/doc/html/NEWS.2.html
+lib/R/doc/html/NEWS.3.html
 lib/R/doc/html/NEWS.html
 lib/R/doc/html/R.css
 lib/R/doc/html/Rlogo.pdf
@@ -152,6 +156,7 @@ lib/R/library/KernSmooth/libs/KernSmooth.so
 lib/R/library/KernSmooth/po/de/LC_MESSAGES/R-KernSmooth.mo
 lib/R/library/KernSmooth/po/en@quot/LC_MESSAGES/R-KernSmooth.mo
 lib/R/library/KernSmooth/po/fr/LC_MESSAGES/R-KernSmooth.mo
+lib/R/library/KernSmooth/po/it/LC_MESSAGES/R-KernSmooth.mo
 lib/R/library/KernSmooth/po/ko/LC_MESSAGES/R-KernSmooth.mo
 lib/R/library/KernSmooth/po/pl/LC_MESSAGES/R-KernSmooth.mo
 lib/R/library/MASS/CITATION
@@ -183,6 +188,7 @@ lib/R/library/MASS/libs/MASS.so
 lib/R/library/MASS/po/de/LC_MESSAGES/R-MASS.mo
 lib/R/library/MASS/po/en@quot/LC_MESSAGES/R-MASS.mo
 lib/R/library/MASS/po/fr/LC_MESSAGES/R-MASS.mo
+lib/R/library/MASS/po/it/LC_MESSAGES/R-MASS.mo
 lib/R/library/MASS/po/ko/LC_MESSAGES/R-MASS.mo
 lib/R/library/MASS/po/pl/LC_MESSAGES/R-MASS.mo
 lib/R/library/MASS/scripts/ch01.R
@@ -331,6 +337,7 @@ lib/R/library/boot/html/R.css
 lib/R/library/boot/po/de/LC_MESSAGES/R-boot.mo
 lib/R/library/boot/po/en@quot/LC_MESSAGES/R-boot.mo
 lib/R/library/boot/po/fr/LC_MESSAGES/R-boot.mo
+lib/R/library/boot/po/it/LC_MESSAGES/R-boot.mo
 lib/R/library/boot/po/ko/LC_MESSAGES/R-boot.mo
 lib/R/library/boot/po/pl/LC_MESSAGES/R-boot.mo
 lib/R/library/boot/po/ru/LC_MESSAGES/R-boot.mo
@@ -359,6 +366,7 @@ lib/R/library/class/libs/class.so
 lib/R/library/class/po/de/LC_MESSAGES/R-class.mo
 lib/R/library/class/po/en@quot/LC_MESSAGES/R-class.mo
 lib/R/library/class/po/fr/LC_MESSAGES/R-class.mo
+lib/R/library/class/po/it/LC_MESSAGES/R-class.mo
 lib/R/library/class/po/ko/LC_MESSAGES/R-class.mo
 lib/R/library/class/po/pl/LC_MESSAGES/R-class.mo
 lib/R/library/cluster/CITATION
@@ -487,6 +495,8 @@ lib/R/library/foreign/po/en@quot/LC_MESSAGES/R-foreign.mo
 lib/R/library/foreign/po/en@quot/LC_MESSAGES/foreign.mo
 lib/R/library/foreign/po/fr/LC_MESSAGES/R-foreign.mo
 lib/R/library/foreign/po/fr/LC_MESSAGES/foreign.mo
+lib/R/library/foreign/po/it/LC_MESSAGES/R-foreign.mo
+lib/R/library/foreign/po/it/LC_MESSAGES/foreign.mo
 lib/R/library/foreign/po/pl/LC_MESSAGES/R-foreign.mo
 lib/R/library/foreign/po/pl/LC_MESSAGES/foreign.mo
 lib/R/library/grDevices/DESCRIPTION
@@ -858,6 +868,7 @@ lib/R/library/nnet/libs/nnet.so
 lib/R/library/nnet/po/de/LC_MESSAGES/R-nnet.mo
 lib/R/library/nnet/po/en@quot/LC_MESSAGES/R-nnet.mo
 lib/R/library/nnet/po/fr/LC_MESSAGES/R-nnet.mo
+lib/R/library/nnet/po/it/LC_MESSAGES/R-nnet.mo
 lib/R/library/nnet/po/ko/LC_MESSAGES/R-nnet.mo
 lib/R/library/nnet/po/pl/LC_MESSAGES/R-nnet.mo
 lib/R/library/parallel/DESCRIPTION
@@ -953,6 +964,7 @@ lib/R/library/spatial/libs/spatial.so
 lib/R/library/spatial/po/de/LC_MESSAGES/R-spatial.mo
 lib/R/library/spatial/po/en@quot/LC_MESSAGES/R-spatial.mo
 lib/R/library/spatial/po/fr/LC_MESSAGES/R-spatial.mo
+lib/R/library/spatial/po/it/LC_MESSAGES/R-spatial.mo
 lib/R/library/spatial/po/ko/LC_MESSAGES/R-spatial.mo
 lib/R/library/spatial/po/pl/LC_MESSAGES/R-spatial.mo
 lib/R/library/spatial/ppdata/agter.dat
@@ -1068,6 +1080,9 @@ lib/R/library/survival/data/Rdata.rdx
 lib/R/library/survival/doc/adjcurve.R
 lib/R/library/survival/doc/adjcurve.Rnw
 lib/R/library/survival/doc/adjcurve.pdf
+lib/R/library/survival/doc/approximate.R
+lib/R/library/survival/doc/approximate.Rnw
+lib/R/library/survival/doc/approximate.pdf
 lib/R/library/survival/doc/compete.R
 lib/R/library/survival/doc/compete.Rnw
 lib/R/library/survival/doc/compete.pdf
@@ -1075,21 +1090,19 @@ 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
 lib/R/library/survival/doc/multi.pdf
+lib/R/library/survival/doc/other.Rnw
+lib/R/library/survival/doc/other.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/survival.R
-lib/R/library/survival/doc/survival.Rnw
-lib/R/library/survival/doc/survival.pdf
 lib/R/library/survival/doc/splines.R
 lib/R/library/survival/doc/splines.Rnw
 lib/R/library/survival/doc/splines.pdf
-lib/R/library/survival/doc/tests.R
-lib/R/library/survival/doc/tests.Rnw
-lib/R/library/survival/doc/tests.pdf
+lib/R/library/survival/doc/survival.R
+lib/R/library/survival/doc/survival.Rnw
+lib/R/library/survival/doc/survival.pdf
 lib/R/library/survival/doc/tiedtimes.R
 lib/R/library/survival/doc/tiedtimes.Rnw
 lib/R/library/survival/doc/tiedtimes.pdf
diff --git a/math/R/distinfo b/math/R/distinfo
index b8bbc5db377..af6ec1fee00 100644
--- a/math/R/distinfo
+++ b/math/R/distinfo
@@ -1,9 +1,9 @@
-$NetBSD: distinfo,v 1.85 2019/08/14 14:36:59 wen Exp $
+$NetBSD: distinfo,v 1.86 2020/07/16 02:22:55 markd Exp $
 
-SHA1 (R-3.6.1.tar.gz) = 0041c025561b5622e3dc88cdedf82334620cd3c2
-RMD160 (R-3.6.1.tar.gz) = 0944f67117372acf342251c988d83b83839deccf
-SHA512 (R-3.6.1.tar.gz) = fae7d114437c4b5d10fcb2a4265acd707ad2a4810eeb7c11e25caca1d85093a1495c2e13457b4894c1508830ec1b2be95379b7d54007cf3e574c2a9eea28ef80
-Size (R-3.6.1.tar.gz) = 30463021 bytes
+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 (patch-configure.ac) = 2732e3e0a39ee64ae4cba5c476f4754ecbd14942
 SHA1 (patch-m4_R.m4) = 704d5514e10adf0b5217bb71b06f44a612eca6e0
 SHA1 (patch-m4_cairo.m4) = a0c4ec68d7d6d3a73a2a24481d0dee8c192bf154