git: 16c89d12ec5c - main - math/R: Fix build with clang/openmp 13

[Joseph Mingrone]

The branch main has been updated by jrm:

URL: https://cgit.FreeBSD.org/ports/commit/?id=16c89d12ec5c03f824e4925d18b8849c4ab1e86b

commit 16c89d12ec5c03f824e4925d18b8849c4ab1e86b
Author:     Joseph Mingrone <jrm at FreeBSD.org>
AuthorDate: 2021-10-03 14:20:38 +0000
Commit:     Joseph Mingrone <jrm at FreeBSD.org>
CommitDate: 2021-10-03 20:28:52 +0000

    math/R: Fix build with clang/openmp 13
    
    The mgcv package is one of the recommended packages to be installed with
    R.  A problem with mgcv and clang/openmp 13 is that mgcv versions prior
    to 1.8-37 place 'include <omp.h>' after 'include <R.h>'.  This causes a
    conflict between '#define match' and an openmp pragma line, which uses
    match().  This problem was fixed in mgcv 1.8-37, so replace mgcv 1.8-36
    with this newer version.
    
    While here, incorporate formatting changes suggested by portclippy and
    portfmt.
    
    PR:             258887
    Approved by:    dim
    Differential Revision:  https://reviews.freebsd.org/D32280
---
 math/R/Makefile  | 18 ++++++++++++------
 math/R/distinfo  |  4 +++-
 math/R/pkg-plist |  2 --
 3 files changed, 15 insertions(+), 9 deletions(-)

diff --git a/math/R/Makefile b/math/R/Makefile
index f11b5efacc03..b7fb5c45083c 100644
--- a/math/R/Makefile
+++ b/math/R/Makefile
@@ -2,9 +2,13 @@
 
 PORTNAME=	R
 DISTVERSION=	4.1.1
-PORTREVISION=	1
+PORTREVISION=	2
 CATEGORIES=	math lang
-MASTER_SITES=	CRAN/src/base/R-${PORTVERSION:C|\..*||}
+MASTER_SITES=	CRAN/src/base/R-${PORTVERSION:C|\..*||} \
+		CRAN/src/contrib/:packages
+DISTFILES=	${DISTNAME}${EXTRACT_SUFX} \
+		mgcv_1.8-37${EXTRACT_SUFX}:packages
+EXTRACT_ONLY=	${DISTNAME}${EXTRACT_SUFX}
 
 MAINTAINER=	jrm at FreeBSD.org
 COMMENT=	Language for statistical computing and graphics
@@ -25,13 +29,12 @@ RUN_DEPENDS=	gmake:devel/gmake
 # - Create ports for each of the recommended packages
 # - Create a meta-port for the recommended packages
 
-USES=		compiler:c++11-lang cpe gmake iconv libtool localbase pathfix perl5 \
-		readline
+USES=		compiler:c++11-lang cpe gmake iconv libtool localbase pathfix \
+		perl5 readline
+CPE_VENDOR=	r-project
 USE_LDCONFIG=	${PREFIX}/lib/R/lib
 USE_PERL5=	build
 
-CPE_VENDOR=	r-project
-
 GNU_CONFIGURE=	yes
 CONFIGURE_ARGS=	--disable-java \
 		--enable-R-shlib \
@@ -141,6 +144,9 @@ USES+=		fortran
 .endif
 
 post-patch:
+	@${CP} ${DISTDIR}/mgcv_1.8-37${EXTRACT_SUFX} ${WRKSRC}/src/library/Recommended/
+	@${RM} ${WRKSRC}/src/library/Recommended/mgcv.tgz ${WRKSRC}/src/library/Recommended/mgcv_1.8-36.tar.gz
+	@${LN} -s ${WRKSRC}/src/library/Recommended/mgcv_1.8-37${EXTRACT_SUFX} ${WRKSRC}/src/library/Recommended/mgcv.tgz
 	@${REINPLACE_CMD} -e "s|/usr/local|${LOCALBASE}|g" ${WRKSRC}/configure
 	@${REINPLACE_CMD} \
 		-e "s|%%FULLVER%%|${DISTVERSION}|" \
diff --git a/math/R/distinfo b/math/R/distinfo
index 0bcc12e0d42c..354ed6a705f0 100644
--- a/math/R/distinfo
+++ b/math/R/distinfo
@@ -1,3 +1,5 @@
-TIMESTAMP = 1628692945
+TIMESTAMP = 1633269011
 SHA256 (R-4.1.1.tar.gz) = 515e03265752257d0b7036f380f82e42b46ed8473f54f25c7b67ed25bbbdd364
 SIZE (R-4.1.1.tar.gz) = 33719965
+SHA256 (mgcv_1.8-37.tar.gz) = 8823f6da39e65cf44da3fe9d17c08904e98f3669beca28d5ca6f7bd64938fc91
+SIZE (mgcv_1.8-37.tar.gz) = 1175506
diff --git a/math/R/pkg-plist b/math/R/pkg-plist
index 0cec80adca88..17dad47bc893 100644
--- a/math/R/pkg-plist
+++ b/math/R/pkg-plist
@@ -786,8 +786,6 @@ lib/R/library/mgcv/libs/mgcv.so
 %%NLS%%lib/R/library/mgcv/po/en at quot/LC_MESSAGES/mgcv.mo
 %%NLS%%lib/R/library/mgcv/po/fr/LC_MESSAGES/R-mgcv.mo
 %%NLS%%lib/R/library/mgcv/po/fr/LC_MESSAGES/mgcv.mo
-%%NLS%%lib/R/library/mgcv/po/it/LC_MESSAGES/R-mgcv.mo
-%%NLS%%lib/R/library/mgcv/po/it/LC_MESSAGES/mgcv.mo
 %%NLS%%lib/R/library/mgcv/po/ko/LC_MESSAGES/R-mgcv.mo
 %%NLS%%lib/R/library/mgcv/po/ko/LC_MESSAGES/mgcv.mo
 %%NLS%%lib/R/library/mgcv/po/pl/LC_MESSAGES/R-mgcv.mo