Attachment 173018 Details for Bug 211393 – svn diff to improve math/R

[patch] svn diff to improve math/R

R-3.3.1_2.diff (text/plain), 13.73 KB, created by Joseph Mingrone on 2016-07-26 20:00:44 UTC

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Creator: Joseph Mingrone

Created: 2016-07-26 20:00:44 UTC

Size: 13.73 KB

patch

obsolete

>Index: Makefile
>===================================================================
>--- Makefile	(revision 419125)
>+++ Makefile	(working copy)
>@@ -29,33 +29,35 @@
> LIB_DEPENDS=		libcurl.so:ftp/curl \
> 			libpcre.so:devel/pcre
> 
>+CONFIGURE_ARGS=		--disable-java \
>+			--enable-R-shlib \
>+			rdocdir=${DOCSDIR}
> GNU_CONFIGURE=		yes
>-USES=			fortran iconv objc:compiler perl5
>+INSTALL_TARGET=		install-strip
>+ONLY_FOR_ARCHS= 	i386 amd64
>+USES=			fortran iconv localbase 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
> 
>-OPTIONS_DEFINE=		DOCS ICU INFO LETTER LIBR LDOUBLE LTO MISSING NLS \
>-			OPENMP THREADS X11
>-OPTIONS_GROUP=		NEEDX11
>+OPTIONS_DEFINE=		DOCS ICU INFO LETTER LDOUBLE NLS 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
>+OPTIONS_RADIO=		BLAS
>+OPTIONS_RADIO_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
>+LETTER_DESC=		US letter paper
>+LTO_DESC=		Use Link Time Optimization
>+NEEDGCC_DESC=		Require GCC
>+NEEDX11_DESC=		Require X11
> NETLIB_DESC=		Netlib BLAS implementation
> OPENBLAS_DESC=		OpenBLAS BLAS implementation
> PDF_DESC=		PDF manuals (requires TeX)
>@@ -63,19 +65,18 @@
> RBLAS_DESC=		Use R-bundled BLAS implementation
> X11_DESC=		X11 graphics device
> 
>-OPTIONS_DEFAULT=	GHOSTSCRIPT ICU INFO JPEG LTO LIBR OPENBLAS OPENMP \
>-			CAIROPANGO PNG TCLTK TIFF THREADS X11
>+OPTIONS_DEFAULT=	CAIROPANGO GHOSTSCRIPT ICU INFO JPEG LDOUBLE PNG RBLAS \
>+			TCLTK TIFF X11
> 
>-OPTIONS_DEFAULT_armv6+=		MISSING
>-OPTIONS_DEFAULT_powerpc+=	MISSING
>-OPTIONS_DEFAULT_powerpc64+=	MISSING
>-OPTIONS_DEFAULT_sparc64+=	MISSING
>-
> ATLAS_USES=		blaslapack:atlas
>-.if defined(BATCH) || defined(PACKAGE_BUILDING)
>-ATLAS_IGNORE=		Choose a BLAS option other than ATLAS for package building.
>-.endif
>+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
>@@ -90,24 +91,16 @@
> 
> JPEG_IMPLIES=		X11
> JPEG_CONFIGURE_WITH=	jpeglib
>+JPEG_CONFIGURE_ENV=	r_cv_header_jpeglib_h=yes
>+JPEG_USES=		jpeg
> 
> LETTER_CONFIGURE_ENV=	R_PAPERSIZE=letter
> 
>-LIBR_CONFIGURE_ENABLE=	R-shlib
>-
> LDOUBLE_CONFIGURE_ENABLE=long-double
> 
> LTO_CONFIGURE_ENABLE=	lto
>+LTO_USE=		GCC
> 
>-.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>
>-
> NETLIB_USES=		blaslapack:netlib
> 
> NLS_CONFIGURE_OFF=	--disable-nls
>@@ -116,12 +109,8 @@
> OPENBLAS_USES=		blaslapack:openblas
> 
> OPENMP_CONFIGURE_ENABLE=openmp
>+OPENMP_USES=		compiler:openmp
> 
>-CAIROPANGO_IMPLIES=	X11
>-CAIROPANGO_CONFIGURE_WITH=cairo
>-CAIROPANGO_USES=	gettext jpeg pkgconfig
>-CAIROPANGO_USE=		gnome=pango,cairo
>-
> PDF_IMPLIES=		DOCS X11
> PDF_USE=		tex=dvipsk:build,kpathsea:build,pdftex:build
> PDF_INSTALL_TARGET=	install-pdf
>@@ -136,15 +125,14 @@
> RBLAS_CONFIGURE_ON=	--without-blas \
> 			--without-lapack
> RBLAS_CONFIGURE_OFF=	--with-blas="-L${LOCALBASE}/lib ${BLASLIB}" \
>-			--with-lapack="${LAPACKLIB}"
>+			--with-lapack="${LAPACKLIB}" \
>+			--enable-BLAS-shlib \
>+			--enable-memory-profiling
> 
> TCLTK_IMPLIES=		X11
> TCLTK_USES=		tcl tk:84+
> TCLTK_CONFIGURE_WITH=	tcltk
> 
>-THREADS_CONFIGURE_ON=	--enable-threads=posix
>-THREADS_CONFIGURE_OFF=	--disable-threads
>-
> TIFF_IMPLIES=		X11
> TIFF_LIB_DEPENDS=	libtiff.so:graphics/tiff
> TIFF_CONFIGURE_WITH=	libtiff
>@@ -160,69 +148,19 @@
> 			RBLAS_SOVERSION="${RBLAS_SOVERSION}" \
> 			RLAPACK_SOVERSION="${RLAPACK_SOVERSION}"
> 
>-.include "compiler.mk"
> .include <bsd.port.options.mk>
> 
>-.if ${OSVERSION} > 1000052 && \
>-(${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
>+.if ${OSVERSION} < 1000015
>+USE_GCC=		yes
> .endif
> 
> post-patch:
>-.if !${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;}' \
>-		${WRKSRC}/src/main/complex.c
>-.endif # !PORT_OPTIONS:MMISSING
>-	@${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
>+		${WRKSRC}/configure
> 
>-.if !${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
>-
> post-install:
> .for L in R Rblas Rlapack
> 	@if [ -d ${STAGEDIR}${PREFIX}/lib/R/lib ] ; then \
>Index: compiler.mk
>===================================================================
>--- compiler.mk	(revision 419125)
>+++ compiler.mk	(working copy)
>@@ -1,2 +0,0 @@
>-# Compiler settings required for R and the R-cran ports.
>-USE_GCC=	yes
>Index: files/patch-configure
>===================================================================
>--- files/patch-configure	(revision 419125)
>+++ files/patch-configure	(working copy)
>@@ -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; }
>Index: files/patch-src__nmath__standalone__test.c
>===================================================================
>--- files/patch-src__nmath__standalone__test.c	(revision 419125)
>+++ files/patch-src__nmath__standalone__test.c	(working copy)
>@@ -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;
>Index: files/patch-src_extra_tre_tre-internal.h
>===================================================================
>--- files/patch-src_extra_tre_tre-internal.h	(revision 419125)
>+++ files/patch-src_extra_tre_tre-internal.h	(working copy)
>@@ -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
>Index: pkg-plist
>===================================================================
>--- pkg-plist	(revision 419125)
>+++ pkg-plist	(working copy)
>@@ -99,12 +99,12 @@
> 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.%%RBLAS_SOVERSION%%
>-%%RBLAS%%lib/R/lib/libRlapack.so
>-%%RBLAS%%lib/R/lib/libRlapack.so.%%RLAPACK_SOVERSION%%
>-%%LIBR%%lib/R/lib/libR.so
>-%%LIBR%%lib/R/lib/libR.so.%%R_SOVERSION%%
>+lib/R/lib/libRblas.so
>+lib/R/lib/libRblas.so.%%RBLAS_SOVERSION%%
>+lib/R/lib/libRlapack.so
>+lib/R/lib/libRlapack.so.%%RLAPACK_SOVERSION%%
>+lib/R/lib/libR.so
>+lib/R/lib/libR.so.%%R_SOVERSION%%
> lib/R/library/KernSmooth/DESCRIPTION
> lib/R/library/KernSmooth/INDEX
> lib/R/library/KernSmooth/Meta/Rd.rds
>@@ -1486,7 +1486,7 @@
> lib/R/share/texmf/tex/latex/omscmtt.fd
> lib/R/share/texmf/tex/latex/ts1aer.fd
> lib/R/share/texmf/tex/latex/ts1aett.fd
>-%%LIBR%%libdata/pkgconfig/libR.pc
>+libdata/pkgconfig/libR.pc
> man/man1/R.1.gz
> man/man1/Rscript.1.gz
> %%DOCSDIR%%/html/NEWS.2.html

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jrm: maintainer-approval+

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Attachments on bug 211393: 173018 | 173086 | 173182 | 173265