math/R: maintainer rework

See PR for signficant changes to math/R port including options,
build defaults, and patch updates.

PR:		211393
Submitted by:	Joseph Mingrone (maintainer)

6 files changed, 59 insertions, 259 deletions

diff --git a/math/R/Makefile b/math/R/Makefile
index 5527d88a7541..09dbad9e7133 100644
--- a/math/R/Makefile
+++ b/math/R/Makefile
@@ -3,7 +3,7 @@
 
 PORTNAME?=		R
 PORTVERSION=		3.3.1
-PORTREVISION=		2
+PORTREVISION=		3
 CATEGORIES=		math lang
 MASTER_SITES=		http://cran.r-project.org/%SUBDIR%/ \
 			ftp://cran.r-project.org/pub/R/%SUBDIR%/ \
@@ -29,16 +29,19 @@ LICENSE=		GPLv2
 LIB_DEPENDS=		libcurl.so:ftp/curl \
 			libpcre.so:devel/pcre
 
+CONFIGURE_ARGS=		--disable-java \
+			--with-readline \
+			rdocdir=${DOCSDIR}
 GNU_CONFIGURE=		yes
-USES=			fortran iconv objc:compiler perl5
-USE_PERL5=		build
-USE_LDCONFIG=		${PREFIX}/lib/R/lib
-CONFIGURE_ARGS=		--disable-java --enable-memory-profiling rdocdir=${DOCSDIR}
 INSTALL_TARGET=		install-strip
+ONLY_FOR_ARCHS=		i386 amd64
+USES=			fortran iconv libtool localbase objc:compiler perl5 \
+			readline
+USE_PERL5=		build
 
-OPTIONS_DEFINE=		DOCS ICU INFO LETTER LIBR LDOUBLE LTO MISSING NLS \
-			OPENMP THREADS X11
-OPTIONS_GROUP=		NEEDX11
+OPTIONS_DEFINE=		DOCS ICU INFO LDOUBLE LETTER LIBR MEMPROF NLS RPROF X11
+OPTIONS_GROUP=		NEEDGCC NEEDX11
+OPTIONS_GROUP_NEEDGCC=	LTO OPENMP
 OPTIONS_GROUP_NEEDX11=	GHOSTSCRIPT JPEG CAIROPANGO PDF PNG TCLTK TIFF
 OPTIONS_SINGLE=		BLAS
 OPTIONS_SINGLE_BLAS=	ATLAS OPENBLAS NETLIB RBLAS
@@ -46,109 +49,83 @@ OPTIONS_SINGLE_BLAS=	ATLAS OPENBLAS NETLIB RBLAS
 OPTIONS_SUB=		YES
 
 ATLAS_DESC=		ATLAS BLAS implementation
-GHOSTSCRIPT_DESC=	Graphics Device for Bitmap Files via Ghostscript
+GHOSTSCRIPT_DESC=	Graphics device for bitmap files via Ghostscript
 CAIROPANGO_DESC=	Cairo graphics device and Pango multi-language text
 INFO_DESC=		GNU info manuals
 JPEG_DESC=		JPEG graphics device
-LDOUBLE_DESC=		Enable long double data type
-LETTER_DESC=		US Letter paper
-LIBR_DESC=		Build dynamic (shared) R library
-LTO_DESC=		Try to produce faster code through LTO
-MISSING_DESC=		Use libmissing rather than libquadmath
-NEEDX11_DESC=		X11-Implying Options
+LDOUBLE_DESC=		Long double data type
+LETTER_DESC=		US letter paper
+LIBR_DESC=		Shared R library
+LTO_DESC=		Use Link Time Optimization
+MEMPROF_DESC=		Memory profiling via Rprofmem() and tracemem()
+NEEDGCC_DESC=		Require GCC
+NEEDX11_DESC=		Require X11
 NETLIB_DESC=		Netlib BLAS implementation
 OPENBLAS_DESC=		OpenBLAS BLAS implementation
 PDF_DESC=		PDF manuals (requires TeX)
 PNG_DESC=		PNG graphics device
 RBLAS_DESC=		Use R-bundled BLAS implementation
+RPROF_DESC=		R profiling via Rprof()
 X11_DESC=		X11 graphics device
 
-OPTIONS_DEFAULT=	GHOSTSCRIPT ICU INFO JPEG LTO LIBR OPENBLAS OPENMP \
-			CAIROPANGO PNG TCLTK TIFF THREADS X11
-
-OPTIONS_DEFAULT_armv6+=		MISSING
-OPTIONS_DEFAULT_powerpc+=	MISSING
-OPTIONS_DEFAULT_powerpc64+=	MISSING
-OPTIONS_DEFAULT_sparc64+=	MISSING
+OPTIONS_DEFAULT=	CAIROPANGO GHOSTSCRIPT ICU INFO JPEG LDOUBLE LIBR PNG \
+			RBLAS RPROF TCLTK TIFF X11
 
 ATLAS_USES=		blaslapack:atlas
-.if defined(BATCH) || defined(PACKAGE_BUILDING)
-ATLAS_IGNORE=		Choose a BLAS option other than ATLAS for package building.
-.endif
-
+ALTAS_CONFIGURE_ON=	--disable-BLAS-shlib
+ATLAS_VARS=		MANUAL_PACKAGE_BUILD=\
+"Choose a BLAS option other than ATLAS for package building."
+CAIROPANGO_IMPLIES=	X11
+CAIROPANGO_CONFIGURE_WITH=cairo
+CAIROPANGO_USES=	gettext jpeg pkgconfig
+CAIROPANGO_USE=		gnome=pango,cairo
 DOCS_BUILD_DEPENDS=	texi2any:print/texinfo
-
 GHOSTSCRIPT_IMPLIES=	X11
 GHOSTSCRIPT_USES=	ghostscript
-
 ICU_CONFIGURE_WITH=	ICU
 ICU_LIB_DEPENDS=	libicui18n.so:devel/icu
-
 INFO_IMPLIES=		DOCS
 INFO_INSTALL_TARGET=	install-info
 INFO_INFO=		R-FAQ R-admin R-data R-exts R-ints R-intro R-lang
-
 JPEG_IMPLIES=		X11
 JPEG_CONFIGURE_WITH=	jpeglib
-
+JPEG_CONFIGURE_ENV=	r_cv_header_jpeglib_h=yes
+JPEG_USES=		jpeg
+LDOUBLE_CONFIGURE_ENABLE=long-double
 LETTER_CONFIGURE_ENV=	R_PAPERSIZE=letter
-
 LIBR_CONFIGURE_ENABLE=	R-shlib
-
-LDOUBLE_CONFIGURE_ENABLE=long-double
-
 LTO_CONFIGURE_ENABLE=	lto
-
-.for i in acos asin atan cos cosh exp log pow sin sinh tan tanh
-MISSING_CONFIGURE_ENV+=	ac_cv_have_decl_c${i}=yes
-.endfor
-MISSING_LIB_DEPENDS=	libmissing.so:math/libmissing
-MISSING_VARS=		LIBM="-L${LOCALBASE}/lib -lmissing -lm" \
-			LIBMH=<missing_math.h>
-MISSING_VARS_OFF=	LIBM='-lquadmath -lm' \
-			LIBMH=<quadmath.h>
-
+LTO_USE=		gcc=yes
+MEMPROF_CONFIGURE_ENABLE=memory-profiling
 NETLIB_USES=		blaslapack:netlib
-
+NETLIB_CONFIGURE_ON=	--disable-BLAS-shlib
 NLS_CONFIGURE_OFF=	--disable-nls
 NLS_USES=		gettext
-
 OPENBLAS_USES=		blaslapack:openblas
-
+OPENBLAS_CONFIGURE_ON=	--disable-BLAS-shlib
 OPENMP_CONFIGURE_ENABLE=openmp
-
-CAIROPANGO_IMPLIES=	X11
-CAIROPANGO_CONFIGURE_WITH=cairo
-CAIROPANGO_USES=	gettext jpeg pkgconfig
-CAIROPANGO_USE=		gnome=pango,cairo
-
+OPENMP_USE=		compiler:openmp
 PDF_IMPLIES=		DOCS X11
 PDF_USE=		tex=dvipsk:build,kpathsea:build,pdftex:build
 PDF_INSTALL_TARGET=	install-pdf
 .for i in KPSEWHICH MAKEINDEX PDFLATEX PDFTEX TEX TEXI2DVI
 PDF_CONFIGURE_ENV_OFF+=	ac_cv_path_${i}=""
 .endfor
-
 PNG_IMPLIES=		X11
 PNG_LIB_DEPENDS=	libpng.so:graphics/png
 PNG_CONFIGURE_WITH=	libpng
-
 RBLAS_CONFIGURE_ON=	--without-blas \
-			--without-lapack
+			--without-lapack \
+			--enable-BLAS-shlib
 RBLAS_CONFIGURE_OFF=	--with-blas="-L${LOCALBASE}/lib ${BLASLIB}" \
 			--with-lapack="${LAPACKLIB}"
-
+RPROF_CONFIGURE_ENABLE=	R-profiling
 TCLTK_IMPLIES=		X11
 TCLTK_USES=		tcl tk:84+
 TCLTK_CONFIGURE_WITH=	tcltk
-
-THREADS_CONFIGURE_ON=	--enable-threads=posix
-THREADS_CONFIGURE_OFF=	--disable-threads
-
 TIFF_IMPLIES=		X11
 TIFF_LIB_DEPENDS=	libtiff.so:graphics/tiff
 TIFF_CONFIGURE_WITH=	libtiff
-
 X11_CONFIGURE_WITH=	x
 X11_USE=		xorg=ice,sm,x11,xext,xmu,xscrnsaver,xt
 
@@ -160,70 +137,21 @@ PLIST_SUB=		R_SOVERSION="${R_SOVERSION}" \
 			RBLAS_SOVERSION="${RBLAS_SOVERSION}" \
 			RLAPACK_SOVERSION="${RLAPACK_SOVERSION}"
 
-.include "compiler.mk"
 .include <bsd.port.options.mk>
+.include "compiler.mk"
 
-.if ${OPSYS} == FreeBSD && ${OSVERSION} > 1000052 && \
-(${ARCH} == amd64 || ${ARCH} == i386 || ${ARCH} == ia64 || ${ARCH} == pc98 || \
-${ARCH} == sparc64)
-.for i in coshl erfcl erfl lgammal powl sinhl tanhl tgammal
-CFLAGS+=		-fno-builtin-${i}
-LDFLAGS+=		-fno-builtin-${i}
-.endfor
+# OPT_USE= ldconfig=${PREFIX}/lib/R/lib is broken.
+# It adds /lib/R/lib (without PREFIX) to ${PREFIX}/libdata/R.
+.if ${PORT_OPTIONS:MLIBR} || ${PORT_OPTIONS:MRBLAS}
+USE_LDCONFIG=		${PREFIX}/lib/R/lib
 .endif
 
 post-patch:
-.if ${OPSYS} == FreeBSD
-.if !${PORT_OPTIONS:MMISSING}
-.if ${OSVERSION} < 1000016
-	@${REINPLACE_CMD} -e \
-'s/# define EXP expl/# define EXP(x) (long double)expq((__float128)(x))/' \
-		${WRKSRC}/src/nmath/pnchisq.c \
-		${WRKSRC}/src/nmath/pgamma.c
-	@${REINPLACE_CMD} -e \
-'s/# define LOG logl/# define LOG(x) (long double)logq((__float128)(x))/' \
-		${WRKSRC}/src/nmath/pnchisq.c \
-		${WRKSRC}/src/nmath/pgamma.c
-.endif
-.if ${OSVERSION} < 1000034
-	@${REINPLACE_CMD} -Ee 's/(log)(1p)?l\(/(long double)\1\2q((__float128)/'\
-		${WRKSRC}/src/nmath/dnbeta.c \
-		${WRKSRC}/src/nmath/pnbeta.c
-.endif
-	@${REINPLACE_CMD} -Ee \
-'s/powl\((.*)(long double)/(long double)powq((__float128)\1__float128/' \
-		${WRKSRC}/src/main/format.c
-.else # !PORT_OPTIONS:MMISSING
-.if ${OSVERSION} > 1000052 && \
-(${ARCH} == amd64 || ${ARCH} == i386 || ${ARCH} == ia64 || ${ARCH} == pc98 || \
-${ARCH} == sparc64)
-	@${REINPLACE_CMD} -e '\|^FLIBS="$$ac_cv_f77_libs"|s|"|&${LIBM} |' \
-		${WRKSRC}/configure
-.endif
-	@${REINPLACE_CMD} -e \
-'\|#[[:blank:]]*include[[:blank:]]*<complex.h>|{x;s|^.*$$|#include "missing_complex.h"|;H;x;}' \
-		${WRKSRC}/src/main/complex.c
-.endif # !PORT_OPTIONS:MMISSING
-.endif  # ${OPSYS} == FreeBSD
-	@${REINPLACE_CMD} -e \
-'\|#[[:blank:]]*include[[:blank:]]*<math.h>|{x;s|^.*$$|#include ${LIBMH}|;H;x;}'\
-		${WRKSRC}/src/nmath/nmath.h \
-		${WRKSRC}/src/include/Rmath.h0.in
 	@${REINPLACE_CMD} -e 's|(libdir)/pkgconfig|(prefix)/libdata/pkgconfig|g'\
 		${WRKSRC}/src/nmath/standalone/Makefile.in \
 		${WRKSRC}/src/unix/Makefile.in
 	@${REINPLACE_CMD} -e "s|/usr/local|${LOCALBASE}|g" \
-		${WRKSRC}/configure \
-		${WRKSRC}/src/library/profile/Rprofile.unix \
-		${WRKSRC}/src/scripts/javareconf.in
-
-.if !${PORT_OPTIONS:MMISSING}
-pre-configure:
-	@if [ ! -f ${_GCC_RUNTIME}/libquadmath.a ] ; then \
-		IGNORE="\n\n\n%s\n\n\n" "libquadmath is not available for your\
-		compiler and architecture: please enable the MISSING option."; \
-	fi
-.endif
+		${WRKSRC}/configure
 
 post-install:
 .for L in R Rblas Rlapack
diff --git a/math/R/compiler.mk b/math/R/compiler.mk
index 6a3352b0d345..51ce77479d6f 100644
--- a/math/R/compiler.mk
+++ b/math/R/compiler.mk
@@ -1,2 +1,10 @@
 # Compiler settings required for R and the R-cran ports.
+.if ${OPSYS} == FreeBSD
+.  if ${OSVERSION} < 1000015
 USE_GCC=	yes
+.  endif
+.else
+.  if ${OPSYS} == DragonFly
+USE_GCC=	6
+.  endif
+.endif
diff --git a/math/R/distinfo b/math/R/distinfo
index 882438c3fe0f..f63322597f89 100644
--- a/math/R/distinfo
+++ b/math/R/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1467276607
+TIMESTAMP = 1470250856
 SHA256 (R-3.3.1.tar.gz) = 3dc59ae5831f5380f83c169bac2103ad052efe0ecec4ffa74bde4d85a0fda9e2
 SIZE (R-3.3.1.tar.gz) = 29848329
diff --git a/math/R/files/patch-configure b/math/R/files/patch-configure
deleted file mode 100644
index da96c4789130..000000000000
--- a/math/R/files/patch-configure
+++ /dev/null
@@ -1,113 +0,0 @@
---- configure.orig	2016-04-25 22:17:08 UTC
-+++ configure
-@@ -22470,13 +22470,13 @@ if test "x$ac_cv_lib_mw__mwvalidcheckl" 
-   LIBM=-lmw
- fi
- 
--  { $as_echo "$as_me:${as_lineno-$LINENO}: checking for cos in -lm" >&5
--$as_echo_n "checking for cos in -lm... " >&6; }
-+  { $as_echo "$as_me:${as_lineno-$LINENO}: checking for cos in -lquadmath -lquadmath -lm" >&5
-+$as_echo_n "checking for cos in -lquadmath -lquadmath -lm... " >&6; }
- if ${ac_cv_lib_m_cos+:} false; then :
-   $as_echo_n "(cached) " >&6
- else
-   ac_check_lib_save_LIBS=$LIBS
--LIBS="-lm  $LIBS"
-+LIBS="-lquadmath -lquadmath -lm  $LIBS"
- cat confdefs.h - <<_ACEOF >conftest.$ac_ext
- /* end confdefs.h.  */
- 
-@@ -22507,18 +22507,18 @@ fi
- { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_m_cos" >&5
- $as_echo "$ac_cv_lib_m_cos" >&6; }
- if test "x$ac_cv_lib_m_cos" = xyes; then :
--  LIBM="$LIBM -lm"
-+  LIBM="$LIBM -lquadmath -lquadmath -lm"
- fi
- 
-   ;;
- *)
--  { $as_echo "$as_me:${as_lineno-$LINENO}: checking for cos in -lm" >&5
--$as_echo_n "checking for cos in -lm... " >&6; }
-+  { $as_echo "$as_me:${as_lineno-$LINENO}: checking for cos in -lquadmath -lquadmath -lm" >&5
-+$as_echo_n "checking for cos in -lquadmath  -lquadmath -lm... " >&6; }
- if ${ac_cv_lib_m_cos+:} false; then :
-   $as_echo_n "(cached) " >&6
- else
-   ac_check_lib_save_LIBS=$LIBS
--LIBS="-lm  $LIBS"
-+LIBS="-lquadmath -lquadmath -lm  $LIBS"
- cat confdefs.h - <<_ACEOF >conftest.$ac_ext
- /* end confdefs.h.  */
- 
-@@ -22549,7 +22549,7 @@ fi
- { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_m_cos" >&5
- $as_echo "$ac_cv_lib_m_cos" >&6; }
- if test "x$ac_cv_lib_m_cos" = xyes; then :
--  LIBM=-lm
-+  LIBM="-lquadmath -lquadmath -lm"
- fi
- 
-   ;;
-@@ -22560,13 +22560,13 @@ esac
- ## </NOTE>
- ## AC_CHECK_LIBM computes LIBM but does not add to LIBS, hence we do
- ## the following as well.
--{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for sin in -lm" >&5
--$as_echo_n "checking for sin in -lm... " >&6; }
-+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for sin in -lquadmath -lquadmath -lm" >&5
-+$as_echo_n "checking for sin in -lquadmath -lquadmath -lm... " >&6; }
- if ${ac_cv_lib_m_sin+:} false; then :
-   $as_echo_n "(cached) " >&6
- else
-   ac_check_lib_save_LIBS=$LIBS
--LIBS="-lm  $LIBS"
-+LIBS="-lquadmath -lquadmath -lm  $LIBS"
- cat confdefs.h - <<_ACEOF >conftest.$ac_ext
- /* end confdefs.h.  */
- 
-@@ -22601,7 +22601,7 @@ if test "x$ac_cv_lib_m_sin" = xyes; then
- #define HAVE_LIBM 1
- _ACEOF
- 
--  LIBS="-lm $LIBS"
-+  LIBS="-lquadmath -lquadmath -lm $LIBS"
- 
- fi
- 
-@@ -27958,7 +27958,7 @@ fi
- ## if nothing was obtained for SHLIB_CXXLDFLAGS.
- ##
- ## Note also that some systems (formerly AIX) do not allow for unresolved
--## symbols at link time.  For such systems, we link against -lm (in case
-+## symbols at link time.  For such systems, we link against -lquadmath -lm (in case
- ## it exists) when building a shlib module via SHLIB_LIBADD.
- 
- main_ld="${CC}"
-@@ -30147,7 +30147,7 @@ if ${ac_cv_lib_rt_clock_gettime+:} false
-   $as_echo_n "(cached) " >&6
- else
-   ac_check_lib_save_LIBS=$LIBS
--LIBS="-lrt  $LIBS"
-+LIBS="$LIBS"
- cat confdefs.h - <<_ACEOF >conftest.$ac_ext
- /* end confdefs.h.  */
- 
-@@ -30190,7 +30190,7 @@ if test "x$ac_cv_lib_rt_clock_gettime" =
- #define HAVE_LIBRT 1
- _ACEOF
- 
--  LIBS="-lrt $LIBS"
-+  LIBS="$LIBS"
- 
- fi
- 
-@@ -35109,7 +35109,7 @@ fi
-     ## Part 2.  Try finding the tk library.
-     if test -n "${TK_CONFIG}"; then
-       . ${TK_CONFIG}
--      TCLTK_LIBS="${TCLTK_LIBS} ${TK_LIB_SPEC} ${TK_XLIBSW}"
-+      TCLTK_LIBS="${TCLTK_LIBS} ${TK_LIB_SPEC} ${TK_XLIBSW} ${TCL_LD_FLAGS}"
-     else
-       { $as_echo "$as_me:${as_lineno-$LINENO}: checking for Tk_Init in -ltk" >&5
- $as_echo_n "checking for Tk_Init in -ltk... " >&6; }
diff --git a/math/R/files/patch-src__nmath__standalone__test.c b/math/R/files/patch-src__nmath__standalone__test.c
deleted file mode 100644
index 0aefc4bf9fc6..000000000000
--- a/math/R/files/patch-src__nmath__standalone__test.c
+++ /dev/null
@@ -1,11 +0,0 @@
---- src/nmath/standalone/test.c.orig	2015-08-25 22:18:53 UTC
-+++ src/nmath/standalone/test.c
-@@ -38,7 +38,7 @@ main(int argc, char** argv)
-     qnorm(0.7, 0.0, 1.0, 0, 0);
-     printf("*** loaded '%s'\n", argv[0]);
-     set_seed(123, 456);
--    N01_kind = AHRENS_DIETER;
-+    N01type N01_kind = AHRENS_DIETER;
-     printf("one normal %f\n", norm_rand());
-     set_seed(123, 456);
-     N01_kind = BOX_MULLER;
diff --git a/math/R/files/patch-src_extra_tre_tre-internal.h b/math/R/files/patch-src_extra_tre_tre-internal.h
index 9648c7b240ce..1f059c45942e 100644
--- a/math/R/files/patch-src_extra_tre_tre-internal.h
+++ b/math/R/files/patch-src_extra_tre_tre-internal.h
@@ -1,22 +1,10 @@
---- src/extra/tre/tre-internal.h.orig	2016-05-05 10:54:54 UTC
+--- src/extra/tre/tre-internal.h.orig	2016-07-23 16:50:17 UTC
 +++ src/extra/tre/tre-internal.h
-@@ -17,6 +17,7 @@
- #include <wctype.h>
+@@ -18,6 +18,7 @@
  #endif /* !HAVE_WCTYPE_H */
  
-+#include <limits.h>
  #include <ctype.h>
++#include <stdint.h>
  #include "tre.h"
  
-@@ -47,7 +48,11 @@
- #ifdef TRE_WCHAR
- 
- /* Wide characters. */
-+#if WCHAR_MAX <= INT_MAX
- typedef wint_t tre_cint_t;
-+#else /* WCHAR_MAX > INT_MAX */
-+#define TRE_CHAR_MAX INT_MAX
-+#endif
- /* Workaround problem seen on AIX, (2010 & 2015), e.g.,
-     https://stat.ethz.ch/pipermail/r-devel/2015-October/071902.html
-   WCHAR_MAX = UINT32_MAX on AIX and that is "not possible to work"
+ #ifdef TRE_DEBUG