CVS commit: pkgsrc/math/R

To: pkgsrc-changes%NetBSD.org@localhost
Subject: CVS commit: pkgsrc/math/R
From: "Makoto Fujiwara" <mef%netbsd.org@localhost>
Date: Sun, 14 Jul 2024 08:51:29 +0000

Module Name:    pkgsrc
Committed By:   mef
Date:           Sun Jul 14 08:51:29 UTC 2024

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

Log Message:
(math/R) Updated 4.4.0 to 4.4.1

 R CMD Rdconv --type=txt /tmp/math/R/work/R-4.4.1/doc/NEWS.Rd | head -70
CHANGES IN R 4.4.1:

  C-LEVEL FACILITIES:

         * Functions 'R_atof' and 'R_strtod' declared in header
           'R_ext/Utils.h' are now documented in 'Writing R Extensions'
           and so formally part of the API.

         * The non-API entry points 'Rf_setSVector', 'Rf_StringFalse',
           'Rf_StringTrue' and 'Rf_isBlankString' have been added to
           those reported by 'R CMD check'.

         * The new function 'Rf_allocLang' is now available. This
           provides an alternative to the idiom of calling
           'Rf_allocList' followed by 'SET_TYPEOF'.

  UTILITIES:

         * 'R CMD check' now reports as warnings what 'gfortran' calls
           'Fortran 2018 deleted features', all of which have long been
           marked as 'obsolescent' and some of which were deleted in
           Fortran 2008 or earlier.  Fortran compilers are no longer
           required to support these.

  BUG FIXES:

         * 'as.numeric()', 'scan()', 'type.convert()' and other places
           which use the internal C function 'R_strtod' now require a
           _non-empty_ digit sequence in a decimal or binary exponent.
           This aligns with the C/POSIX standard for 'strtod' and with
           '?NumericConstants'.

         * 'as.data.frame(m, make.names=NA)' now works correctly for a
           matrix 'm' with 'NA''s in row names.

         * The error message from '<POSIXlt>[["hour"]]' and similar now
           mentions '*[[, "hour"]]', as wished for in PR#17409 and
           proposed by Michael Chirico.

         * 'qbinom()' and potentially 'qpois()', 'qnbinom()', no longer
           sometimes fail accurate inversion (of 'pbinom()', etc),
           thanks to Christopher Chang's report and patch in PR#18711.

         * The internal help server on Windows can again serve requests
           sent in quick succession, fixing a regression in R 4.4.0.

         * 'debugcall(<S3Generic>())' now also works when a
           corresponding S4-generic version is in the 'methods' cache
           (PR#18143).

         * Package 'tools'' 'toTitleCase(ch0)' now returns
           'character(0)' when 'ch0' is of zero length; fixing
           PR#18724, reported by David Hugh Jones.

         * 'R CMD check' is no longer broken (without a check result
           and no explanation in '00check.log') for a package which
           declares an invalid 'VignetteBuilder' in 'DESCRIPTION' but
           has no vignettes.


To generate a diff of this commit:
cvs rdiff -u -r1.256 -r1.257 pkgsrc/math/R/Makefile
cvs rdiff -u -r1.40 -r1.41 pkgsrc/math/R/PLIST
cvs rdiff -u -r1.106 -r1.107 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:1.256 pkgsrc/math/R/Makefile:1.257
--- pkgsrc/math/R/Makefile:1.256        Wed May 29 16:33:25 2024
+++ pkgsrc/math/R/Makefile      Sun Jul 14 08:51:29 2024
@@ -1,11 +1,10 @@
-# $NetBSD: Makefile,v 1.256 2024/05/29 16:33:25 adam Exp $
+# $NetBSD: Makefile,v 1.257 2024/07/14 08:51:29 mef Exp $
 
 #
 # If updating this package, please try to ensure PLIST.Darwin is kept in sync
 # to avoid unnecessarily breaking macOS users.
 #
-DISTNAME=      R-4.4.0
-PKGREVISION=   1
+DISTNAME=      R-4.4.1
 CATEGORIES=    math
 MASTER_SITES=  ${MASTER_SITE_R_CRAN:=base/R-4/}
 
@@ -150,11 +149,6 @@ INSTALL_SCRIPT=            ${INSTALL} ${COPY} -m $
 #TOOL_DEPENDS+=                tex-mptopdf-[0-9]*:../../graphics/tex-mptopdf
 #TOOL_DEPENDS+=                tex-pdftex-def-[0-9]*:../../print/tex-pdftex
 
-#SUBST_CLASSES+=               rpath
-#SUBST_STAGE.rpath=    pre-configure
-#SUBST_FILES.rpath=    configure.ac
-#SUBST_VARS.rpath=     COMPILER_RPATH_FLAG
-
 SUBST_CLASSES+=                fixwrap
 SUBST_STAGE.fixwrap=   post-build
 SUBST_FILES.fixwrap=   libtool
@@ -185,7 +179,7 @@ fix-darwin-install-name:
 
 # remove orig version left out
 post-install:
-       ${RM}   ${DESTDIR}${PREFIX}/lib/R/library/survival/NEWS.Rd.orig
+       ${RM}   -f ${DESTDIR}${PREFIX}/lib/R/library/survival/NEWS.Rd.orig
 
 .include "../../archivers/bzip2/buildlink3.mk"
 .include "../../archivers/xz/buildlink3.mk"

Index: pkgsrc/math/R/PLIST
diff -u pkgsrc/math/R/PLIST:1.40 pkgsrc/math/R/PLIST:1.41
--- pkgsrc/math/R/PLIST:1.40    Fri May 31 04:41:09 2024
+++ pkgsrc/math/R/PLIST Sun Jul 14 08:51:29 2024
@@ -1,4 +1,4 @@
-@comment $NetBSD: PLIST,v 1.40 2024/05/31 04:41:09 mef Exp $
+@comment $NetBSD: PLIST,v 1.41 2024/07/14 08:51:29 mef Exp $
 bin/R
 bin/Rscript
 info/R-FAQ.info.gz
@@ -202,7 +202,6 @@ lib/R/include/Rinternals.h
 lib/R/include/Rmath.h
 lib/R/include/Rversion.h
 lib/R/lib/libR.so
-lib/R/library/grDevices/libs/cairo.so
 lib/R/library/KernSmooth/DESCRIPTION
 lib/R/library/KernSmooth/INDEX
 lib/R/library/KernSmooth/Meta/Rd.rds
@@ -776,6 +775,7 @@ lib/R/library/grDevices/html/00Index.htm
 lib/R/library/grDevices/html/R.css
 lib/R/library/grDevices/icc/srgb
 lib/R/library/grDevices/icc/srgb.flate
+lib/R/library/grDevices/libs/cairo.so
 lib/R/library/grDevices/libs/grDevices.so
 lib/R/library/graphics/DESCRIPTION
 lib/R/library/graphics/INDEX
@@ -1235,13 +1235,13 @@ 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/discrim.R
-lib/R/library/survival/doc/discrim.Rnw
-lib/R/library/survival/doc/discrim.pdf
 lib/R/library/survival/doc/index.html
 lib/R/library/survival/doc/matrix.R
 lib/R/library/survival/doc/matrix.Rnw
 lib/R/library/survival/doc/matrix.pdf
+lib/R/library/survival/doc/methods.R
+lib/R/library/survival/doc/methods.Rnw
+lib/R/library/survival/doc/methods.pdf
 lib/R/library/survival/doc/multi.Rnw
 lib/R/library/survival/doc/multi.pdf
 lib/R/library/survival/doc/other.Rnw

Index: pkgsrc/math/R/distinfo
diff -u pkgsrc/math/R/distinfo:1.106 pkgsrc/math/R/distinfo:1.107
--- pkgsrc/math/R/distinfo:1.106        Mon May 27 20:45:14 2024
+++ pkgsrc/math/R/distinfo      Sun Jul 14 08:51:29 2024
@@ -1,8 +1,8 @@
-$NetBSD: distinfo,v 1.106 2024/05/27 20:45:14 mef Exp $
+$NetBSD: distinfo,v 1.107 2024/07/14 08:51:29 mef Exp $
 
-BLAKE2s (R-4.4.0.tar.gz) = 31efebb6f183d6e754b82dfb14b4715659a01d5ee95b86048d6127f884d42d6a
-SHA512 (R-4.4.0.tar.gz) = 8f44eac49c58db7f161732135be4d1757f65b18545f3f15c463d499794735d02f4a4cb9bacff90d16e80b624ead8aa0af16899cf7654b6cb91a46868e405bd17
-Size (R-4.4.0.tar.gz) = 37335563 bytes
+BLAKE2s (R-4.4.1.tar.gz) = 3bd218962b3d7df6f89dd533979aa4feeb69e0a13a82e79d60b74d155a89636b
+SHA512 (R-4.4.1.tar.gz) = cc30172227b7d89a9d6e9d65c8622b2042bcbbf3f1b5e36c7460f60958a1a0589980a1867ec9989df2589c1618233f3382d4732700b147361ace3be6680b5643
+Size (R-4.4.1.tar.gz) = 37353459 bytes
 SHA1 (patch-configure.ac) = 91bed37afc2ee2f68695f8496c56ae23aaf42b43
 SHA1 (patch-m4_R.m4) = 3e1d390d8aa9895aee7cb479ddab371d82562b88
 SHA1 (patch-src_include_R__ext_Error.h) = bc55a8bba6bf931e3f6794577e63bfafdfc740cf

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