math/R: Update to version 3.4.1

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

Port changes:
- Add aarch64 to ONLY_FOR_ARCHS [1]
- Add off-by-default option for experimental fortran support via flang [2]

Submitted by:	[1] andrew, [2] yuri@rawbw.com

math/R/Makefile

@@ -2,8 +2,8 @@
 # $FreeBSD$
 
 PORTNAME=		R
-PORTVERSION=		3.4.0
-PORTREVISION=		2
+PORTVERSION=		3.4.1
+PORTREVISION=		0
 CATEGORIES=		math lang
 MASTER_SITES=		CRAN/src/base/R-${PORTVERSION:C|\..*||}
 
@@ -22,9 +22,9 @@ CONFIGURE_ARGS=		--disable-java \
 			rdocdir=${DOCSDIR}
 GNU_CONFIGURE=		yes
 INSTALL_TARGET=		install-strip
-ONLY_FOR_ARCHS=		amd64 i386
-USES=			fortran gmake iconv libtool localbase objc:compiler \
-			pathfix perl5 readline
+ONLY_FOR_ARCHS=		aarch64 amd64 i386
+USES=			gmake iconv libtool localbase objc:compiler \
+			pathfix perl5 readline:port
 
 USE_PERL5=		build
 
@@ -32,14 +32,20 @@ OPTIONS_DEFINE=		ICU INFO LDOUBLE LETTER LIBR MEMPROF NLS RPROF X11
 OPTIONS_GROUP=		NEEDGCC NEEDX11
 OPTIONS_GROUP_NEEDGCC=	LTO OPENMP
 OPTIONS_GROUP_NEEDX11=	GHOSTSCRIPT JPEG CAIROPANGO PNG TCLTK TEXDOCS TIFF
-OPTIONS_SINGLE=		BLAS
+OPTIONS_SINGLE=		BLAS FORTRAN
 OPTIONS_SINGLE_BLAS=	ATLAS OPENBLAS NETLIB RBLAS
+OPTIONS_SINGLE_FORTRAN=	${OPTIONS_SINGLE_FORTRAN_${MACHINE_ARCH}}
+OPTIONS_SINGLE_FORTRAN_i386=	GFORTRAN
+OPTIONS_SINGLE_FORTRAN_armv6=	GFORTRAN
+OPTIONS_SINGLE_FORTRAN_amd64=	GFORTRAN FLANG
 
 OPTIONS_SUB=		YES
 
 ATLAS_DESC=		ATLAS BLAS implementation
+FLANG_DESC=		Experimental Fortan support via flang
 GHOSTSCRIPT_DESC=	Graphics device for bitmap files via Ghostscript
 CAIROPANGO_DESC=	Cairo graphics device and Pango multi-language text
+GFORTRAN_DESC=		Fortan support via gfortran
 INFO_DESC=		GNU info manuals
 JPEG_DESC=		JPEG graphics device
 LDOUBLE_DESC=		Long double data type
@@ -57,8 +63,8 @@ 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 LIBR PNG \
-			RBLAS RPROF TCLTK TIFF X11
+OPTIONS_DEFAULT=	CAIROPANGO GFORTRAN GHOSTSCRIPT ICU INFO JPEG LDOUBLE \
+			LIBR PNG RBLAS RPROF TCLTK TIFF X11
 
 ATLAS_USES=		blaslapack:atlas
 ATLAS_CONFIGURE_ON=	--disable-BLAS-shlib
@@ -68,6 +74,14 @@ CAIROPANGO_IMPLIES=	X11
 CAIROPANGO_CONFIGURE_WITH=cairo
 CAIROPANGO_USES=	gettext jpeg pkgconfig
 CAIROPANGO_USE=		GNOME=pango,cairo
+FLANG_USE=		binutils
+FLANG_BUILD_DEPENDS=	flang:devel/flang
+FLANG_RUN_DEPENDS=	flang:devel/flang
+FLANG_VARS=		F77=flang FC=flang
+FLANG_LDFLAGS=		-L${LOCALBASE}/flang/lib -lflang -lexecinfo
+FLANG_CONFIGURE_ENV=	F77="${F77}" FC="${FC}" FFLAGS="${FFLAGS}"
+FLANG_MAKE_ENV=		F77="${F77}" FC="${FC}" FFLAGS="${FFLAGS}"
+GFORTRAN_USES=		fortran
 GHOSTSCRIPT_IMPLIES=	X11
 GHOSTSCRIPT_USES=	ghostscript
 ICU_CONFIGURE_WITH=	ICU
@@ -84,6 +98,7 @@ LIBR_CONFIGURE_ENABLE=	R-shlib
 LTO_CONFIGURE_ENABLE=	lto
 LTO_CONFIGURE_ENV=	AR="${LOCALBASE}/bin/gcc-ar${GCC_DEFAULT:S/.//g}" \
 			RANLIB="${LOCALBASE}/bin/gcc-ranlib${GCC_DEFAULT:S/.//g}"
+LTO_PREVENTS=		FLANG
 LTO_USE=		GCC=yes
 LTO_VARS=		BINUTILS="ADDR2LINE AS CPPFILT GPROF LD NM OBJCOPY \
 			OBJDUMP READELF SIZE STRINGS"
@@ -95,6 +110,7 @@ NLS_USES=		gettext
 OPENBLAS_USES=		blaslapack:openblas
 OPENBLAS_CONFIGURE_ON=	--disable-BLAS-shlib
 OPENMP_CONFIGURE_ENABLE=openmp
+OPENMP_LIB_DEPENDS=	libomp.so:devel/openmp
 OPENMP_USES=		compiler:openmp
 PNG_IMPLIES=		X11
 PNG_LIB_DEPENDS=	libpng.so:graphics/png

math/R/distinfo

@@ -1,3 +1,3 @@
-TIMESTAMP = 1492859308
-SHA256 (R-3.4.0.tar.gz) = 288e9ed42457c47720780433b3d5c3c20983048b789291cc6a7baa11f9428b91
-SIZE (R-3.4.0.tar.gz) = 30175855
+TIMESTAMP = 1498946951
+SHA256 (R-3.4.1.tar.gz) = 02b1135d15ea969a3582caeb95594a05e830a6debcdb5b85ed2d5836a6a3fc78
+SIZE (R-3.4.1.tar.gz) = 30200109

math/R/files/patch-configure

@@ -0,0 +1,10 @@
+--- configure.orig	2017-04-19 21:38:22 UTC
++++ configure
+@@ -7528,6 +7528,7 @@ if test $ac_compiler_gnu = yes; then
+ else
+   G77=
+ fi
++G77=yes
+ ac_ext=c
+ ac_cpp='$CPP $CPPFLAGS'
+ ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'

math/R/files/patch-src_main_complex.c

@@ -0,0 +1,20 @@
+--- src/main/complex.c.orig	2017-03-27 22:15:12 UTC
++++ src/main/complex.c
+@@ -133,7 +133,7 @@ static double complex mycpow (double com
+     } else if (yi == 0.0 && yr == (k = (int) yr) && abs(k) <= 65536)
+ 	Z = R_cpow_n(X, k);
+     else
+-#ifdef HAVE_CPOW
++#if defined(HAVE_CPOW) && !defined(__FreeBSD__)
+ 	Z = cpow(X, Y);
+ #else
+     {
+@@ -365,7 +365,7 @@ void attribute_hidden z_prec_r(Rcomplex 
+    Currently (Feb 2011) they are used on FreeBSD.
+ */
+ 
+-#ifndef HAVE_CLOG
++#if !defined(HAVE_CLOG) || defined(__FreeBSD__)
+ #define clog R_clog
+ /* FIXME: maybe add full IEC60559 support */
+ static double complex clog(double complex x)

math/R/pkg-plist

@@ -443,7 +443,9 @@ lib/R/library/foreign/R/foreign.rdb
 lib/R/library/foreign/R/foreign.rdx
 lib/R/library/foreign/files/HillRace.SYD
 lib/R/library/foreign/files/Iris.syd
+lib/R/library/foreign/files/electric.sav
 lib/R/library/foreign/files/sids.dbf
+lib/R/library/foreign/files/testdata.sav
 lib/R/library/foreign/help/AnIndex
 lib/R/library/foreign/help/aliases.rds
 lib/R/library/foreign/help/foreign.rdb