(math/R) Updated 4.3.1 to 4.3.2, Add TODO for strtoi issue

To: pkgsrc-wip-changes%NetBSD.org@localhost
Subject: (math/R) Updated 4.3.1 to 4.3.2, Add TODO for strtoi issue
From: Makoto Fujiwara <makoto%ki.nu@localhost>
Date: Fri, 05 Jan 2024 03:27:30 +0000
Module Name:	pkgsrc-wip
Committed By:	Makoto Fujiwara <makoto%ki.nu@localhost>
Pushed By:	mef
Date:		Fri Jan 5 12:27:30 2024 +0900
Changeset:	a8b48fa148acd3105cbf3fe66374d69c75fc84d9

Modified Files:
	R/Makefile
	R/PLIST
	R/distinfo
Added Files:
	R/TODO

Log Message:
(math/R) Updated 4.3.1 to 4.3.2, Add TODO for strtoi issue

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=a8b48fa148acd3105cbf3fe66374d69c75fc84d9

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

diffstat:
 R/Makefile |  5 +++-
 R/PLIST    | 12 +++++---
 R/TODO     | 95 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 R/distinfo |  8 ++++--
 4 files changed, 112 insertions(+), 8 deletions(-)

diffs:
diff --git a/R/Makefile b/R/Makefile
index 77a54bf1a0..6e7968bfff 100644
--- a/R/Makefile
+++ b/R/Makefile
@@ -4,7 +4,7 @@
 # If updating this package, please try to ensure PLIST.Darwin is kept in sync
 # to avoid unnecessarily breaking macOS users.
 #
-DISTNAME=	R-4.3.1
+DISTNAME=	R-4.3.2
 CATEGORIES=	math
 MASTER_SITES=	${MASTER_SITE_R_CRAN:=base/R-4/}
 
@@ -171,6 +171,9 @@ fix-darwin-install-name:
 	done
 .endif
 
+post-install:
+	${RM}	${DESTDIR}${PREFIX}/lib/R/library/survival/NEWS.Rd.orig
+
 .include "../../archivers/bzip2/buildlink3.mk"
 .include "../../archivers/xz/buildlink3.mk"
 .include "../../converters/libiconv/buildlink3.mk"
diff --git a/R/PLIST b/R/PLIST
index 9fc905e1e9..c17e01ed87 100644
--- a/R/PLIST
+++ b/R/PLIST
@@ -274,9 +274,7 @@ lib/R/library/MASS/scripts/ch13.R
 lib/R/library/MASS/scripts/ch14.R
 lib/R/library/MASS/scripts/ch15.R
 lib/R/library/MASS/scripts/ch16.R
-lib/R/library/Matrix/Copyrights
 lib/R/library/Matrix/DESCRIPTION
-lib/R/library/Matrix/Doxyfile
 lib/R/library/Matrix/INDEX
 lib/R/library/Matrix/LICENCE
 lib/R/library/Matrix/Meta/Rd.rds
@@ -297,7 +295,6 @@ lib/R/library/Matrix/data/KNex.R
 lib/R/library/Matrix/data/USCounties.R
 lib/R/library/Matrix/data/datalist
 lib/R/library/Matrix/data/wrld_1deg.R
-lib/R/library/Matrix/doc/Announce.txt
 lib/R/library/Matrix/doc/Comparisons.R
 lib/R/library/Matrix/doc/Comparisons.Rnw
 lib/R/library/Matrix/doc/Comparisons.pdf
@@ -315,7 +312,6 @@ lib/R/library/Matrix/doc/SuiteSparse/CHOLMOD.txt
 lib/R/library/Matrix/doc/SuiteSparse/COLAMD.txt
 lib/R/library/Matrix/doc/SuiteSparse/SPQR.txt
 lib/R/library/Matrix/doc/SuiteSparse/SuiteSparse_config.txt
-lib/R/library/Matrix/doc/SuiteSparse/UserGuides.txt
 lib/R/library/Matrix/doc/index.html
 lib/R/library/Matrix/doc/sparseModels.R
 lib/R/library/Matrix/doc/sparseModels.Rnw
@@ -883,6 +879,8 @@ lib/R/library/mgcv/po/en@quot/LC_MESSAGES/R-mgcv.mo
 lib/R/library/mgcv/po/en@quot/LC_MESSAGES/mgcv.mo
 lib/R/library/mgcv/po/fr/LC_MESSAGES/R-mgcv.mo
 lib/R/library/mgcv/po/fr/LC_MESSAGES/mgcv.mo
+lib/R/library/mgcv/po/it/LC_MESSAGES/R-mgcv.mo
+lib/R/library/mgcv/po/it/LC_MESSAGES/mgcv.mo
 lib/R/library/mgcv/po/ko/LC_MESSAGES/R-mgcv.mo
 lib/R/library/mgcv/po/ko/LC_MESSAGES/mgcv.mo
 lib/R/library/mgcv/po/pl/LC_MESSAGES/R-mgcv.mo
@@ -1184,6 +1182,9 @@ 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/multi.Rnw
 lib/R/library/survival/doc/multi.pdf
 lib/R/library/survival/doc/other.Rnw
@@ -1191,6 +1192,9 @@ 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/redistribute.R
+lib/R/library/survival/doc/redistribute.Rnw
+lib/R/library/survival/doc/redistribute.pdf
 lib/R/library/survival/doc/splines.R
 lib/R/library/survival/doc/splines.Rnw
 lib/R/library/survival/doc/splines.pdf
diff --git a/R/TODO b/R/TODO
new file mode 100644
index 0000000000..18bdef0011
--- /dev/null
+++ b/R/TODO
@@ -0,0 +1,95 @@
+strtoi issue
+It seems strtoi in NetBSD  and R became inconsistent.
+FreeBSD does not have strtoi defined yet.
+
+
+gcc -I../../src/extra  -I. -I../../src/include -I../../src/include -I/usr/pkg/include -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/glib-2.0 -I/usr/pkg/include/gio-unix-2.0 -I/usr/pkg/lib/glib-2.0/include -I/usr/X11R7/include -I/usr/pkg/include/freetype2 -I/usr/pkg/include/harfbuzz -I/usr/include/krb5 -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -pthread -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/glib-2.0 -I/usr/pkg/include/gio-unix-2.0 -I/usr/pkg/lib/glib-2.0/include -I/usr/X11R7/include -I/usr/pkg/include/freetype2 -I/usr/pkg/include/harfbuzz -I/usr/include/krb5  -c character.c -o character.o
+character.c:1752:12: error: conflicting types for 'strtoi'
+ 1752 | static int strtoi(SEXP s, int base)
+      |            ^~~~~~
+In file included from ../../src/include/Defn.h:907,
+                 from character.c:85:
+/usr/include/inttypes.h:81:10: note: previous declaration of 'strtoi' was here
+   81 | intmax_t strtoi(const char * __restrict, char ** __restrict, int,
+      |          ^~~~~~
+
+
+For the test, 
+if the NetBSD definition of following changed (which can not be
+done anyway), R-4.3.2 is packaged fine
+
+--- /usr/include/inttypes.h.orig	2023-10-06 23:48:08.000000000 +0900
++++ /usr/include/inttypes.h	2024-01-05 10:28:39.954745456 +0900
+@@ -78,8 +78,10 @@
+ 
+ 
+ #if defined(_NETBSD_SOURCE)
++/*
+ intmax_t	strtoi(const char * __restrict, char ** __restrict, int,
+ 	               intmax_t, intmax_t, int *);
++*/
+ uintmax_t	strtou(const char * __restrict, char ** __restrict, int,
+ 	               uintmax_t, uintmax_t, int *);
+ 
+
+Shall we rename strtoi in R to strtoiR  for the moment ?
+
+
+h97@makoto 11:10:52/240105(..wip/R)% (cd /tmp/wip/R/work/R-4.3.2/; find .  -exec grep strtoi '{}' /dev/null \;)
+./tests/reg-tests-1d.R:## strtoi("") :
+./tests/reg-tests-1d.R:stopifnot(is.na(strtoi("")),
+./tests/reg-tests-1d.R:          is.na(strtoi("", 2L)))
+./doc/NEWS.3:    • strtoi("", base) now gives NA on all platforms, following its
+./doc/html/NEWS.2.html:<li><p> New function <code>strtoi()</code>, a wrapper for the C function
+./doc/html/NEWS.3.html:<li> <p><code>strtoi("", base)</code> now gives <code>NA</code> on all platforms,
+./doc/NEWS.2:    • New function strtoi(), a wrapper for the C function strtol.
+./doc/NEWS.3.Rd:      \item \code{strtoi("", base)} now gives \code{NA} on all platforms,
+./doc/NEWS.2.Rd:      \item New function \code{strtoi()}, a wrapper for the C function
+./src/include/Internal.h:SEXP do_strtoi(SEXP,SEXP,SEXP,SEXP);
+./src/library/base/man/hexmode.Rd:  converting integers to hex, \code{\link{strtoi}} to convert hex
+./src/library/base/man/octmode.Rd:  converting integers to octal, \code{\link{strtoi}} to convert octal
+./src/library/base/man/strtoi.Rd:% File src/library/base/man/strtoi.Rd
+./src/library/base/man/strtoi.Rd:\name{strtoi}
+./src/library/base/man/strtoi.Rd:\alias{strtoi}
+./src/library/base/man/strtoi.Rd:\usage{strtoi(x, base = 0L)}
+./src/library/base/man/strtoi.Rd:strtoi(c("0xff", "077", "123"))
+./src/library/base/man/strtoi.Rd:strtoi(c("ffff", "FFFF"), 16L)
+./src/library/base/man/strtoi.Rd:strtoi(c("177", "377"), 8L)
+./src/library/base/R/octhex.R:        z <- strtoi(x, 8L)
+./src/library/base/R/octhex.R:        z <- strtoi(x, 16L)
+./src/library/base/R/version.R:        strtoi(substring(elt, first, last), 8L)
+./src/library/base/R/character.R:strtoi <-
+./src/library/base/R/character.R:    .Internal(strtoi(as.character(x), as.integer(base)))
+./src/gnuwin32/Rdll.hide: do_strtoi
+./src/main/names.c:{"strtoi",   do_strtoi,      0,      11,     2,      {PP_FUNCALL, PREC_FN,   0}},
+./src/main/character.c.orig:static int strtoi(SEXP s, int base)
+./src/main/character.c.orig:attribute_hidden SEXP do_strtoi(SEXP call, SEXP op, SEXP args, SEXP env)
+./src/main/character.c.orig:    INTEGER(ans)[i] = strtoi(STRING_ELT(x, i), base);
+./src/main/character.c:static int strtoi(SEXP s, int base)
+./src/main/character.c:attribute_hidden SEXP do_strtoi(SEXP call, SEXP op, SEXP args, SEXP env)
+./src/main/character.c: INTEGER(ans)[i] = strtoi(STRING_ELT(x, i), base);
+h97@makoto 11:11:02/240105(..wip/R)% 
+
+
+
+h97@makoto 12:19:10/240105(..wip/R)%  (cd /tmp/wip/R/work/R-4.3.2/; grep -lr strtoi  .)                         
+./tests/reg-tests-1d.R
+./doc/NEWS.3
+./doc/html/NEWS.2.html
+./doc/html/NEWS.3.html
+./doc/NEWS.2
+./doc/NEWS.3.Rd
+./doc/NEWS.2.Rd
+./src/include/Internal.h
+./src/library/base/man/hexmode.Rd
+./src/library/base/man/octmode.Rd
+./src/library/base/man/strtoi.Rd
+./src/library/base/R/octhex.R
+./src/library/base/R/version.R
+./src/library/base/R/character.R
+./src/gnuwin32/Rdll.hide
+./src/main/names.c
+./src/main/character.c.orig
+./src/main/character.c
+
+But this way ask all of R application/plug-in's to rename strtoi to strtoiR
diff --git a/R/distinfo b/R/distinfo
index f2ebd760a3..fe90516775 100644
--- a/R/distinfo
+++ b/R/distinfo
@@ -1,7 +1,9 @@
 $NetBSD: distinfo,v 1.97 2023/03/22 13:53:29 wiz Exp $
 
-BLAKE2s (R-4.3.1.tar.gz) = ec3d8b86a707169e2fb65d8bf455f6f57e13385a4c4712d08a5053e13c9a4f7c
-SHA512 (R-4.3.1.tar.gz) = f571c378dbdd675e267ef4419bb1141198924dadc08297c93c8dff58504994604918b3e045bb7139ba473972a063a68ed1c7426f37d4e8208b79358561d34d77
-Size (R-4.3.1.tar.gz) = 34899964 bytes
+BLAKE2s (R-4.3.2.tar.gz) = a79080d65222ec6698175c037390e666385567b1e123acf6ce1e33ee3f122005
+SHA512 (R-4.3.2.tar.gz) = 125114357f20d4a3248aee86727768d1dc15e07e44353f8a68fe2ef1fedae508e85d944301d00c0edd61e8b012b0b3cdcde53ac60be903713f96542d83ad5b1d
+Size (R-4.3.2.tar.gz) = 35039225 bytes
 SHA1 (patch-configure.ac) = 56a92d2d75ecdad45c06ca05ebc260af83a5a0ea
 SHA1 (patch-m4_R.m4) = 76a280dc2aeea2eb0e473ae770f636d00314d68a
+SHA1 (patch-src_extr_tre_tre-internal.h) = 476807e45f82e350ae30d91fe7a7ad94b1a555b3
+SHA1 (patch-src_main_character.c) = e5edd0ec0686a98c7792103e7a7ac5166bf8d5d4
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