CVS commit: pkgsrc/math/R

To: pkgsrc-changes%NetBSD.org@localhost
Subject: CVS commit: pkgsrc/math/R
From: "Mark Davies" <markd%netbsd.org@localhost>
Date: Thu, 16 Jul 2020 02:22:55 +0000

Module Name:    pkgsrc
Committed By:   markd
Date:           Thu Jul 16 02:22:55 UTC 2020

Modified Files:
        pkgsrc/math/R: Makefile PLIST distinfo

Log Message:
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.


To generate a diff of this commit:
cvs rdiff -u -r1.214 -r1.215 pkgsrc/math/R/Makefile
cvs rdiff -u -r1.32 -r1.33 pkgsrc/math/R/PLIST
cvs rdiff -u -r1.85 -r1.86 pkgsrc/math/R/distinfo

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

Modified files:

Index: pkgsrc/math/R/Makefile
diff -u pkgsrc/math/R/Makefile:1.214 pkgsrc/math/R/Makefile:1.215
--- pkgsrc/math/R/Makefile:1.214        Fri May 22 10:56:20 2020
+++ pkgsrc/math/R/Makefile      Thu Jul 16 02:22:55 2020
@@ -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@localhost
 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"

Index: pkgsrc/math/R/PLIST
diff -u pkgsrc/math/R/PLIST:1.32 pkgsrc/math/R/PLIST:1.33
--- pkgsrc/math/R/PLIST:1.32    Sun Jun  9 13:39:12 2019
+++ pkgsrc/math/R/PLIST Thu Jul 16 02:22:55 2020
@@ -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
 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_MESS
 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

Index: pkgsrc/math/R/distinfo
diff -u pkgsrc/math/R/distinfo:1.85 pkgsrc/math/R/distinfo:1.86
--- pkgsrc/math/R/distinfo:1.85 Wed Aug 14 14:36:59 2019
+++ pkgsrc/math/R/distinfo      Thu Jul 16 02:22:55 2020
@@ -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

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