math/R: Update to version 3.5.0

Upstream changes: https://cran.r-project.org/doc/manuals/r-devel/NEWS.html

5 files changed, 54 insertions, 55 deletions

diff --git a/math/R/Makefile b/math/R/Makefile
index 64e200cf5142..0cc70123c98d 100644
--- a/math/R/Makefile
+++ b/math/R/Makefile
@@ -1,24 +1,23 @@
 # Created by: Maurice Castro <maurice@serc.rmit.edu.au>
 # $FreeBSD$
 
-PORTNAME=		R
-DISTVERSION=		3.4.4
-PORTREVISION=	1
-CATEGORIES=		math lang
-MASTER_SITES=		CRAN/src/base/R-${PORTVERSION:C|\..*||}
+PORTNAME=	R
+DISTVERSION=	3.5.0
+CATEGORIES=	math lang
+MASTER_SITES=	CRAN/src/base/R-${PORTVERSION:C|\..*||}
 
-MAINTAINER=		jrm@FreeBSD.org
-COMMENT=		Language for statistical computing and graphics
+MAINTAINER=	jrm@FreeBSD.org
+COMMENT=	Language for statistical computing and graphics
 
-LICENSE=		GPLv2
+LICENSE=	GPLv2
 
 BROKEN_FreeBSD_10_armv6=	Fails to build
-ONLY_FOR_ARCHS=		aarch64 amd64 armv6 armv7 i386
+ONLY_FOR_ARCHS=	aarch64 amd64 armv6 armv7 i386
 
-LIB_DEPENDS=		libcurl.so:ftp/curl \
-			libpcre.so:devel/pcre
-BUILD_DEPENDS=		texi2any:print/texinfo
-RUN_DEPENDS=		gmake:devel/gmake # R packages may require GNU make
+LIB_DEPENDS=	libcurl.so:ftp/curl \
+		libpcre.so:devel/pcre
+BUILD_DEPENDS=	texi2any:print/texinfo
+RUN_DEPENDS=	gmake:devel/gmake # R packages may require GNU make
 
 # possible TODO
 # - Use --with-recommended-packages=no by default
@@ -26,19 +25,19 @@ RUN_DEPENDS=		gmake:devel/gmake # R packages may require GNU make
 # - Create ports for each of the recommended packages
 # - Create a meta-port for the recommended packages
 
-CONFIGURE_ARGS=		--disable-java \
-			--enable-R-shlib \
-			--with-readline \
-			rdocdir=${DOCSDIR}
-GNU_CONFIGURE=		yes
-INSTALL_TARGET=		install-strip
-USES=			gmake iconv libtool localbase \
-			pathfix perl5 readline:port
-USE_PERL5=		build
-USE_LDCONFIG=		${PREFIX}/lib/R/lib
-
-OPTIONS_DEFINE=		FLANG ICU INFO LDOUBLE LETTER MEMPROF NLS OPENMP RPROF \
-			X11
+USES=		gmake iconv libtool localbase pathfix perl5 readline:port
+USE_LDCONFIG=	${PREFIX}/lib/R/lib
+USE_PERL5=	build
+
+CONFIGURE_ARGS=	--disable-java \
+		--enable-R-shlib \
+		--with-readline \
+		rdocdir=${DOCSDIR}
+GNU_CONFIGURE=	yes
+INSTALL_TARGET=	install-strip
+PLIST_SUB=	LIBVER=${LIBVER}
+
+OPTIONS_DEFINE=		FLANG ICU INFO LDOUBLE LETTER MEMPROF NLS OPENMP RPROF X11
 OPTIONS_EXCLUDE_aarch64=	FLANG OPENMP
 OPTIONS_EXCLUDE_armv6=	FLANG OPENMP
 OPTIONS_EXCLUDE_armv7=	FLANG OPENMP
@@ -47,7 +46,8 @@ OPTIONS_GROUP=		NEEDX11
 OPTIONS_GROUP_NEEDX11=	GHOSTSCRIPT JPEG CAIROPANGO PNG TCLTK TEXDOCS TIFF
 OPTIONS_SINGLE=		BLAS
 OPTIONS_SINGLE_BLAS=	ATLAS OPENBLAS NETLIB RBLAS
-
+OPTIONS_DEFAULT=	CAIROPANGO GHOSTSCRIPT ICU INFO JPEG LDOUBLE OPENMP PNG \
+			RBLAS RPROF TCLTK TIFF X11
 OPTIONS_SUB=		YES
 
 ATLAS_DESC=		ATLAS BLAS implementation
@@ -68,9 +68,6 @@ RPROF_DESC=		R profiling via Rprof()
 TEXDOCS_DESC=		Build/Install TeX-dependent documentation files
 X11_DESC=		X11 graphics device
 
-OPTIONS_DEFAULT=	CAIROPANGO GHOSTSCRIPT ICU INFO JPEG LDOUBLE OPENMP \
-			PNG RBLAS RPROF TCLTK TIFF X11
-
 ATLAS_USES=		blaslapack:atlas
 ATLAS_CONFIGURE_ON=	--disable-BLAS-shlib
 ATLAS_VARS=		MANUAL_PACKAGE_BUILD=\
@@ -128,13 +125,12 @@ X11_CONFIGURE_WITH=	x
 X11_USE=		xorg=ice,sm,x11,xext,xmu,xscrnsaver,xt
 
 LIBVER=		${PORTVERSION:R}
-PLIST_SUB=	LIBVER=${LIBVER}
 
 .include <bsd.port.options.mk>
 .include "compiler.mk"
 
 # LLVM, which gets pulled in with FLANG, provides libomp.  So, only depend on
-# devel/openmp, when GFORTRAN and OPENMP are on.
+# devel/openmp when GFORTRAN and OPENMP are on.
 .if ! ${PORT_OPTIONS:MFLANG} && ${PORT_OPTIONS:MOPENMP}
 LIB_DEPENDS+=	libomp.so:devel/openmp
 .endif
diff --git a/math/R/distinfo b/math/R/distinfo
index 0cb104503394..058376480939 100644
--- a/math/R/distinfo
+++ b/math/R/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1521122202
-SHA256 (R-3.4.4.tar.gz) = b3e97d2fab7256d1c655c4075934725ba1cd7cb9237240a11bb22ccdad960337
-SIZE (R-3.4.4.tar.gz) = 30474612
+TIMESTAMP = 1524567506
+SHA256 (R-3.5.0.tar.gz) = fd1725535e21797d3d9fea8963d99be0ba4c3aecadcf081b43e261458b416870
+SIZE (R-3.5.0.tar.gz) = 30675040
diff --git a/math/R/files/extra-patch-src_extra_blas_Makefile.in b/math/R/files/extra-patch-src_extra_blas_Makefile.in
index a2c5e19b4eed..44f76531aa3b 100644
--- a/math/R/files/extra-patch-src_extra_blas_Makefile.in
+++ b/math/R/files/extra-patch-src_extra_blas_Makefile.in
@@ -1,4 +1,4 @@
---- src/extra/blas/Makefile.in.orig	2017-07-16 08:46:49 UTC
+--- src/extra/blas/Makefile.in.orig	2018-04-24 11:01:59 UTC
 +++ src/extra/blas/Makefile.in
 @@ -19,7 +19,7 @@ SOURCES = blas00.c blas.f cmplxblas.f
  Rblas_la = libRblas$(R_DYLIB_EXT)
@@ -10,13 +10,13 @@
  Rblas_la_LIBADD0 = @RBLAS_LDFLAGS@
  
 @@ -43,6 +43,7 @@ Rblas_install: $(Rblas_la)
- 	@$(MKINSTALLDIRS) $(DESTDIR)$(Rexeclibdir)
+ 	@$(MKINSTALLDIRS) "$(DESTDIR)$(Rexeclibdir)"
  	@$(SHELL) $(top_srcdir)/tools/copy-if-change $(Rblas_la) \
- 	  $(DESTDIR)$(Rexeclibdir)/$(Rblas_la)
+ 	  "$(DESTDIR)$(Rexeclibdir)/$(Rblas_la)"
 +	@cd $(DESTDIR)$(Rexeclibdir) && ln -s $(Rblas_la) $(Rblas_la).%%LIBVER%%
  
  Rblas_install-strip: $(Rblas_la)
- 	@$(MKINSTALLDIRS) $(DESTDIR)$(Rexeclibdir)
+ 	@$(MKINSTALLDIRS) "$(DESTDIR)$(Rexeclibdir)"
 @@ -50,6 +51,7 @@ Rblas_install-strip: $(Rblas_la)
  	@if test -n "$(STRIP_LIBS)"; then \
  	  $(STRIP_LIBS) "$(DESTDIR)$(Rexeclibdir)/$(Rblas_la)" ;\
diff --git a/math/R/files/extra-patch-src_modules_lapack_Makefile.in b/math/R/files/extra-patch-src_modules_lapack_Makefile.in
index 73a9fcf1d2e2..c35cbd1ab0b3 100644
--- a/math/R/files/extra-patch-src_modules_lapack_Makefile.in
+++ b/math/R/files/extra-patch-src_modules_lapack_Makefile.in
@@ -1,6 +1,6 @@
---- src/modules/lapack/Makefile.in.orig	2017-07-16 08:46:49 UTC
+--- src/modules/lapack/Makefile.in.orig	2018-04-24 11:09:56 UTC
 +++ src/modules/lapack/Makefile.in
-@@ -82,16 +82,17 @@ $(lapack_la): $(lapack_la_OBJECTS)
+@@ -83,16 +83,18 @@ $(lapack_la): $(lapack_la_OBJECTS)
  ## Include BLAS here, as with (static) ATLAS that pulls all the
  ## BLAS routines into one place.
  $(Rlapack_la): $(LIBOBJECTS)
@@ -10,17 +10,18 @@
  Rlapack_install: $(Rlapack_la) 
  	@$(MKINSTALLDIRS) "$(DESTDIR)$(Rexeclibdir)"
  	@$(SHELL) $(top_srcdir)/tools/copy-if-change $(Rlapack_la) \
- 	  $(Rexeclibdir)/$(Rlapack_la)
--
+ 	  "$(Rexeclibdir)/$(Rlapack_la)"
 +	@cd $(Rexeclibdir) && ln -s $(Rlapack_la) $(Rlapack_la).%%LIBVER%%
+ 
  install: installdirs
  	@$(SHELL) $(top_srcdir)/tools/copy-if-change $(lapack_la) "$(DESTDIR)$(Rexecmodulesdir)/$(lapack_la)"
- @USE_EXTERNAL_LAPACK_FALSE@	@$(SHELL) $(top_srcdir)/tools/copy-if-change $(Rlapack_la) "$(DESTDIR)$(Rexeclibdir)/$(Rlapack_la)"
+-@USE_EXTERNAL_LAPACK_FALSE@	@$(SHELL) $(top_srcdir)/tools/copy-if-change $(Rlapack_la) "$(DESTDIR)$(Rexeclibdir)/$(Rlapack_la)"
 +@USE_EXTERNAL_LAPACK_FALSE@	@cd "$(DESTDIR)$(Rexeclibdir)" && ln -sf $(Rlapack_la) $(Rlapack_la).%%LIBVER%%
++
  installdirs:
  	@$(MKINSTALLDIRS) "$(DESTDIR)$(Rexecmodulesdir)"
  install-strip-Rlapack:
-@@ -104,6 +105,7 @@ install-strip: @USE_EXTERNAL_LAPACK_FALSE@ install-str
+@@ -105,6 +107,7 @@ install-strip: @USE_EXTERNAL_LAPACK_FALS
  	@if test -n "$(STRIP_LIBS)"; then \
  	  $(STRIP_LIBS) "$(DESTDIR)$(Rexecmodulesdir)/$(lapack_la)"; \
  	fi
diff --git a/math/R/pkg-plist b/math/R/pkg-plist
index 3ff8a1b4ef90..fef2b1dd6835 100644
--- a/math/R/pkg-plist
+++ b/math/R/pkg-plist
@@ -25,6 +25,10 @@
 %%DOCSDIR%%/html/up.jpg
 bin/R
 bin/Rscript
+%%RBLAS%%lib/R/lib/libRblas.so
+%%RBLAS%%lib/R/lib/libRblas.so.%%LIBVER%%
+%%RBLAS%%lib/R/lib/libRlapack.so
+%%RBLAS%%lib/R/lib/libRlapack.so.%%LIBVER%%
 lib/R/COPYING
 lib/R/SVN-REVISION
 lib/R/bin/BATCH
@@ -57,9 +61,8 @@ lib/R/etc/Renviron
 lib/R/etc/javaconf
 lib/R/etc/ldpaths
 lib/R/etc/repositories
-lib/R/include/Rconfig.h
-lib/R/include/Rdefines.h
-lib/R/include/Rembedded.h
+lib/R/include/R.h
+lib/R/include/R_ext/Altrep.h
 lib/R/include/R_ext/Applic.h
 lib/R/include/R_ext/Arith.h
 lib/R/include/R_ext/BLAS.h
@@ -81,12 +84,12 @@ lib/R/include/R_ext/Parse.h
 lib/R/include/R_ext/Print.h
 lib/R/include/R_ext/PrtUtil.h
 lib/R/include/R_ext/QuartzDevice.h
+lib/R/include/R_ext/R-ftp-http.h
 lib/R/include/R_ext/RS.h
 lib/R/include/R_ext/RStartup.h
 lib/R/include/R_ext/Rallocators.h
 lib/R/include/R_ext/Random.h
 lib/R/include/R_ext/Rdynload.h
-lib/R/include/R_ext/R-ftp-http.h
 lib/R/include/R_ext/Riconv.h
 lib/R/include/R_ext/Utils.h
 lib/R/include/R_ext/Visibility.h
@@ -94,22 +97,21 @@ lib/R/include/R_ext/eventloop.h
 lib/R/include/R_ext/libextern.h
 lib/R/include/R_ext/stats_package.h
 lib/R/include/R_ext/stats_stubs.h
-lib/R/include/R.h
+lib/R/include/Rconfig.h
+lib/R/include/Rdefines.h
+lib/R/include/Rembedded.h
 lib/R/include/Rinterface.h
 lib/R/include/Rinternals.h
 lib/R/include/Rmath.h
 lib/R/include/Rversion.h
 lib/R/include/S.h
-%%RBLAS%%lib/R/lib/libRblas.so
-%%RBLAS%%lib/R/lib/libRblas.so.%%LIBVER%%
-%%RBLAS%%lib/R/lib/libRlapack.so
-%%RBLAS%%lib/R/lib/libRlapack.so.%%LIBVER%%
 lib/R/lib/libR.so
 lib/R/lib/libR.so.%%LIBVER%%
+lib/R/library/cluster/test-tools.R
 lib/R/library/KernSmooth/DESCRIPTION
 lib/R/library/KernSmooth/INDEX
-lib/R/library/KernSmooth/Meta/features.rds
 lib/R/library/KernSmooth/Meta/Rd.rds
+lib/R/library/KernSmooth/Meta/features.rds
 lib/R/library/KernSmooth/Meta/hsearch.rds
 lib/R/library/KernSmooth/Meta/links.rds
 lib/R/library/KernSmooth/Meta/nsInfo.rds