mirror of
https://git.FreeBSD.org/ports.git
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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)
This commit is contained in:
parent
e82895bb9b
commit
b95421020d
Notes:
svn2git
2021-03-31 03:12:20 +00:00
svn path=/head/; revision=419666
192
math/R/Makefile
192
math/R/Makefile
@ -3,7 +3,7 @@
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PORTNAME?= R
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PORTVERSION= 3.3.1
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PORTREVISION= 2
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PORTREVISION= 3
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CATEGORIES= math lang
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MASTER_SITES= http://cran.r-project.org/%SUBDIR%/ \
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ftp://cran.r-project.org/pub/R/%SUBDIR%/ \
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@ -29,16 +29,19 @@ LICENSE= GPLv2
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LIB_DEPENDS= libcurl.so:ftp/curl \
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libpcre.so:devel/pcre
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CONFIGURE_ARGS= --disable-java \
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--with-readline \
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rdocdir=${DOCSDIR}
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GNU_CONFIGURE= yes
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USES= fortran iconv objc:compiler perl5
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USE_PERL5= build
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USE_LDCONFIG= ${PREFIX}/lib/R/lib
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CONFIGURE_ARGS= --disable-java --enable-memory-profiling rdocdir=${DOCSDIR}
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INSTALL_TARGET= install-strip
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ONLY_FOR_ARCHS= i386 amd64
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USES= fortran iconv libtool localbase objc:compiler perl5 \
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readline
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USE_PERL5= build
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OPTIONS_DEFINE= DOCS ICU INFO LETTER LIBR LDOUBLE LTO MISSING NLS \
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OPENMP THREADS X11
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OPTIONS_GROUP= NEEDX11
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OPTIONS_DEFINE= DOCS ICU INFO LDOUBLE LETTER LIBR MEMPROF NLS RPROF X11
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OPTIONS_GROUP= NEEDGCC NEEDX11
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OPTIONS_GROUP_NEEDGCC= LTO OPENMP
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OPTIONS_GROUP_NEEDX11= GHOSTSCRIPT JPEG CAIROPANGO PDF PNG TCLTK TIFF
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OPTIONS_SINGLE= BLAS
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OPTIONS_SINGLE_BLAS= ATLAS OPENBLAS NETLIB RBLAS
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@ -46,109 +49,83 @@ OPTIONS_SINGLE_BLAS= ATLAS OPENBLAS NETLIB RBLAS
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OPTIONS_SUB= YES
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ATLAS_DESC= ATLAS BLAS implementation
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GHOSTSCRIPT_DESC= Graphics Device for Bitmap Files via Ghostscript
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GHOSTSCRIPT_DESC= Graphics device for bitmap files via Ghostscript
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CAIROPANGO_DESC= Cairo graphics device and Pango multi-language text
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INFO_DESC= GNU info manuals
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JPEG_DESC= JPEG graphics device
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LDOUBLE_DESC= Enable long double data type
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LETTER_DESC= US Letter paper
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LIBR_DESC= Build dynamic (shared) R library
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LTO_DESC= Try to produce faster code through LTO
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MISSING_DESC= Use libmissing rather than libquadmath
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NEEDX11_DESC= X11-Implying Options
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LDOUBLE_DESC= Long double data type
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LETTER_DESC= US letter paper
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LIBR_DESC= Shared R library
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LTO_DESC= Use Link Time Optimization
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MEMPROF_DESC= Memory profiling via Rprofmem() and tracemem()
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NEEDGCC_DESC= Require GCC
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NEEDX11_DESC= Require X11
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NETLIB_DESC= Netlib BLAS implementation
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OPENBLAS_DESC= OpenBLAS BLAS implementation
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PDF_DESC= PDF manuals (requires TeX)
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PNG_DESC= PNG graphics device
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RBLAS_DESC= Use R-bundled BLAS implementation
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RPROF_DESC= R profiling via Rprof()
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X11_DESC= X11 graphics device
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OPTIONS_DEFAULT= GHOSTSCRIPT ICU INFO JPEG LTO LIBR OPENBLAS OPENMP \
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CAIROPANGO PNG TCLTK TIFF THREADS X11
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OPTIONS_DEFAULT_armv6+= MISSING
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OPTIONS_DEFAULT_powerpc+= MISSING
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OPTIONS_DEFAULT_powerpc64+= MISSING
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OPTIONS_DEFAULT_sparc64+= MISSING
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OPTIONS_DEFAULT= CAIROPANGO GHOSTSCRIPT ICU INFO JPEG LDOUBLE LIBR PNG \
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RBLAS RPROF TCLTK TIFF X11
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ATLAS_USES= blaslapack:atlas
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.if defined(BATCH) || defined(PACKAGE_BUILDING)
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ATLAS_IGNORE= Choose a BLAS option other than ATLAS for package building.
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.endif
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DOCS_BUILD_DEPENDS= texi2any:print/texinfo
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GHOSTSCRIPT_IMPLIES= X11
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GHOSTSCRIPT_USES= ghostscript
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ICU_CONFIGURE_WITH= ICU
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ICU_LIB_DEPENDS= libicui18n.so:devel/icu
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INFO_IMPLIES= DOCS
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INFO_INSTALL_TARGET= install-info
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INFO_INFO= R-FAQ R-admin R-data R-exts R-ints R-intro R-lang
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JPEG_IMPLIES= X11
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JPEG_CONFIGURE_WITH= jpeglib
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LETTER_CONFIGURE_ENV= R_PAPERSIZE=letter
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LIBR_CONFIGURE_ENABLE= R-shlib
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LDOUBLE_CONFIGURE_ENABLE=long-double
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LTO_CONFIGURE_ENABLE= lto
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.for i in acos asin atan cos cosh exp log pow sin sinh tan tanh
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MISSING_CONFIGURE_ENV+= ac_cv_have_decl_c${i}=yes
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.endfor
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MISSING_LIB_DEPENDS= libmissing.so:math/libmissing
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MISSING_VARS= LIBM="-L${LOCALBASE}/lib -lmissing -lm" \
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LIBMH=<missing_math.h>
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MISSING_VARS_OFF= LIBM='-lquadmath -lm' \
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LIBMH=<quadmath.h>
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NETLIB_USES= blaslapack:netlib
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NLS_CONFIGURE_OFF= --disable-nls
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NLS_USES= gettext
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OPENBLAS_USES= blaslapack:openblas
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OPENMP_CONFIGURE_ENABLE=openmp
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ALTAS_CONFIGURE_ON= --disable-BLAS-shlib
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ATLAS_VARS= MANUAL_PACKAGE_BUILD=\
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"Choose a BLAS option other than ATLAS for package building."
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CAIROPANGO_IMPLIES= X11
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CAIROPANGO_CONFIGURE_WITH=cairo
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CAIROPANGO_USES= gettext jpeg pkgconfig
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CAIROPANGO_USE= gnome=pango,cairo
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DOCS_BUILD_DEPENDS= texi2any:print/texinfo
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GHOSTSCRIPT_IMPLIES= X11
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GHOSTSCRIPT_USES= ghostscript
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ICU_CONFIGURE_WITH= ICU
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ICU_LIB_DEPENDS= libicui18n.so:devel/icu
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INFO_IMPLIES= DOCS
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INFO_INSTALL_TARGET= install-info
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INFO_INFO= R-FAQ R-admin R-data R-exts R-ints R-intro R-lang
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JPEG_IMPLIES= X11
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JPEG_CONFIGURE_WITH= jpeglib
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JPEG_CONFIGURE_ENV= r_cv_header_jpeglib_h=yes
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JPEG_USES= jpeg
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LDOUBLE_CONFIGURE_ENABLE=long-double
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LETTER_CONFIGURE_ENV= R_PAPERSIZE=letter
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LIBR_CONFIGURE_ENABLE= R-shlib
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LTO_CONFIGURE_ENABLE= lto
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LTO_USE= gcc=yes
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MEMPROF_CONFIGURE_ENABLE=memory-profiling
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NETLIB_USES= blaslapack:netlib
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NETLIB_CONFIGURE_ON= --disable-BLAS-shlib
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NLS_CONFIGURE_OFF= --disable-nls
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NLS_USES= gettext
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OPENBLAS_USES= blaslapack:openblas
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OPENBLAS_CONFIGURE_ON= --disable-BLAS-shlib
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OPENMP_CONFIGURE_ENABLE=openmp
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OPENMP_USE= compiler:openmp
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PDF_IMPLIES= DOCS X11
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PDF_USE= tex=dvipsk:build,kpathsea:build,pdftex:build
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PDF_INSTALL_TARGET= install-pdf
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.for i in KPSEWHICH MAKEINDEX PDFLATEX PDFTEX TEX TEXI2DVI
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PDF_CONFIGURE_ENV_OFF+= ac_cv_path_${i}=""
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.endfor
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PNG_IMPLIES= X11
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PNG_LIB_DEPENDS= libpng.so:graphics/png
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PNG_CONFIGURE_WITH= libpng
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RBLAS_CONFIGURE_ON= --without-blas \
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--without-lapack
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--without-lapack \
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--enable-BLAS-shlib
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RBLAS_CONFIGURE_OFF= --with-blas="-L${LOCALBASE}/lib ${BLASLIB}" \
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--with-lapack="${LAPACKLIB}"
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RPROF_CONFIGURE_ENABLE= R-profiling
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TCLTK_IMPLIES= X11
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TCLTK_USES= tcl tk:84+
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TCLTK_CONFIGURE_WITH= tcltk
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THREADS_CONFIGURE_ON= --enable-threads=posix
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THREADS_CONFIGURE_OFF= --disable-threads
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TIFF_IMPLIES= X11
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TIFF_LIB_DEPENDS= libtiff.so:graphics/tiff
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TIFF_CONFIGURE_WITH= libtiff
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X11_CONFIGURE_WITH= x
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X11_USE= xorg=ice,sm,x11,xext,xmu,xscrnsaver,xt
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@ -160,70 +137,21 @@ PLIST_SUB= R_SOVERSION="${R_SOVERSION}" \
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RBLAS_SOVERSION="${RBLAS_SOVERSION}" \
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RLAPACK_SOVERSION="${RLAPACK_SOVERSION}"
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.include "compiler.mk"
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.include <bsd.port.options.mk>
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.include "compiler.mk"
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.if ${OPSYS} == FreeBSD && ${OSVERSION} > 1000052 && \
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(${ARCH} == amd64 || ${ARCH} == i386 || ${ARCH} == ia64 || ${ARCH} == pc98 || \
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${ARCH} == sparc64)
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.for i in coshl erfcl erfl lgammal powl sinhl tanhl tgammal
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CFLAGS+= -fno-builtin-${i}
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LDFLAGS+= -fno-builtin-${i}
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.endfor
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# OPT_USE= ldconfig=${PREFIX}/lib/R/lib is broken.
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# It adds /lib/R/lib (without PREFIX) to ${PREFIX}/libdata/R.
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.if ${PORT_OPTIONS:MLIBR} || ${PORT_OPTIONS:MRBLAS}
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USE_LDCONFIG= ${PREFIX}/lib/R/lib
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.endif
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post-patch:
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.if ${OPSYS} == FreeBSD
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.if !${PORT_OPTIONS:MMISSING}
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.if ${OSVERSION} < 1000016
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@${REINPLACE_CMD} -e \
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's/# define EXP expl/# define EXP(x) (long double)expq((__float128)(x))/' \
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${WRKSRC}/src/nmath/pnchisq.c \
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${WRKSRC}/src/nmath/pgamma.c
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@${REINPLACE_CMD} -e \
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's/# define LOG logl/# define LOG(x) (long double)logq((__float128)(x))/' \
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${WRKSRC}/src/nmath/pnchisq.c \
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${WRKSRC}/src/nmath/pgamma.c
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.endif
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.if ${OSVERSION} < 1000034
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@${REINPLACE_CMD} -Ee 's/(log)(1p)?l\(/(long double)\1\2q((__float128)/'\
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${WRKSRC}/src/nmath/dnbeta.c \
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${WRKSRC}/src/nmath/pnbeta.c
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.endif
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@${REINPLACE_CMD} -Ee \
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's/powl\((.*)(long double)/(long double)powq((__float128)\1__float128/' \
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${WRKSRC}/src/main/format.c
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.else # !PORT_OPTIONS:MMISSING
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.if ${OSVERSION} > 1000052 && \
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(${ARCH} == amd64 || ${ARCH} == i386 || ${ARCH} == ia64 || ${ARCH} == pc98 || \
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${ARCH} == sparc64)
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@${REINPLACE_CMD} -e '\|^FLIBS="$$ac_cv_f77_libs"|s|"|&${LIBM} |' \
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${WRKSRC}/configure
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.endif
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@${REINPLACE_CMD} -e \
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'\|#[[:blank:]]*include[[:blank:]]*<complex.h>|{x;s|^.*$$|#include "missing_complex.h"|;H;x;}' \
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${WRKSRC}/src/main/complex.c
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.endif # !PORT_OPTIONS:MMISSING
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.endif # ${OPSYS} == FreeBSD
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@${REINPLACE_CMD} -e \
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'\|#[[:blank:]]*include[[:blank:]]*<math.h>|{x;s|^.*$$|#include ${LIBMH}|;H;x;}'\
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${WRKSRC}/src/nmath/nmath.h \
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${WRKSRC}/src/include/Rmath.h0.in
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@${REINPLACE_CMD} -e 's|(libdir)/pkgconfig|(prefix)/libdata/pkgconfig|g'\
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${WRKSRC}/src/nmath/standalone/Makefile.in \
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${WRKSRC}/src/unix/Makefile.in
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@${REINPLACE_CMD} -e "s|/usr/local|${LOCALBASE}|g" \
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${WRKSRC}/configure \
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${WRKSRC}/src/library/profile/Rprofile.unix \
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${WRKSRC}/src/scripts/javareconf.in
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.if !${PORT_OPTIONS:MMISSING}
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pre-configure:
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@if [ ! -f ${_GCC_RUNTIME}/libquadmath.a ] ; then \
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IGNORE="\n\n\n%s\n\n\n" "libquadmath is not available for your\
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compiler and architecture: please enable the MISSING option."; \
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fi
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.endif
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${WRKSRC}/configure
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post-install:
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.for L in R Rblas Rlapack
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|
@ -1,2 +1,10 @@
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# Compiler settings required for R and the R-cran ports.
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.if ${OPSYS} == FreeBSD
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. if ${OSVERSION} < 1000015
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USE_GCC= yes
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. endif
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.else
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. if ${OPSYS} == DragonFly
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USE_GCC= 6
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. endif
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.endif
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@ -1,3 +1,3 @@
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TIMESTAMP = 1467276607
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TIMESTAMP = 1470250856
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SHA256 (R-3.3.1.tar.gz) = 3dc59ae5831f5380f83c169bac2103ad052efe0ecec4ffa74bde4d85a0fda9e2
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SIZE (R-3.3.1.tar.gz) = 29848329
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@ -1,113 +0,0 @@
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--- configure.orig 2016-04-25 22:17:08 UTC
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+++ configure
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@@ -22470,13 +22470,13 @@ if test "x$ac_cv_lib_mw__mwvalidcheckl"
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LIBM=-lmw
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fi
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- { $as_echo "$as_me:${as_lineno-$LINENO}: checking for cos in -lm" >&5
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-$as_echo_n "checking for cos in -lm... " >&6; }
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+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for cos in -lquadmath -lquadmath -lm" >&5
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+$as_echo_n "checking for cos in -lquadmath -lquadmath -lm... " >&6; }
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if ${ac_cv_lib_m_cos+:} false; then :
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$as_echo_n "(cached) " >&6
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else
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ac_check_lib_save_LIBS=$LIBS
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-LIBS="-lm $LIBS"
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+LIBS="-lquadmath -lquadmath -lm $LIBS"
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cat confdefs.h - <<_ACEOF >conftest.$ac_ext
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/* end confdefs.h. */
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@@ -22507,18 +22507,18 @@ fi
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{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_m_cos" >&5
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$as_echo "$ac_cv_lib_m_cos" >&6; }
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if test "x$ac_cv_lib_m_cos" = xyes; then :
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- LIBM="$LIBM -lm"
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+ LIBM="$LIBM -lquadmath -lquadmath -lm"
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fi
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;;
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*)
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- { $as_echo "$as_me:${as_lineno-$LINENO}: checking for cos in -lm" >&5
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-$as_echo_n "checking for cos in -lm... " >&6; }
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+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for cos in -lquadmath -lquadmath -lm" >&5
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+$as_echo_n "checking for cos in -lquadmath -lquadmath -lm... " >&6; }
|
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if ${ac_cv_lib_m_cos+:} false; then :
|
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$as_echo_n "(cached) " >&6
|
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else
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ac_check_lib_save_LIBS=$LIBS
|
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-LIBS="-lm $LIBS"
|
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+LIBS="-lquadmath -lquadmath -lm $LIBS"
|
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cat confdefs.h - <<_ACEOF >conftest.$ac_ext
|
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/* end confdefs.h. */
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@@ -22549,7 +22549,7 @@ fi
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{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_m_cos" >&5
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$as_echo "$ac_cv_lib_m_cos" >&6; }
|
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if test "x$ac_cv_lib_m_cos" = xyes; then :
|
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- LIBM=-lm
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+ LIBM="-lquadmath -lquadmath -lm"
|
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fi
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|
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;;
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@@ -22560,13 +22560,13 @@ esac
|
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## </NOTE>
|
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## AC_CHECK_LIBM computes LIBM but does not add to LIBS, hence we do
|
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## the following as well.
|
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-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for sin in -lm" >&5
|
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-$as_echo_n "checking for sin in -lm... " >&6; }
|
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+{ $as_echo "$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 ${ac_cv_lib_m_sin+:} false; then :
|
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$as_echo_n "(cached) " >&6
|
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else
|
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ac_check_lib_save_LIBS=$LIBS
|
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-LIBS="-lm $LIBS"
|
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+LIBS="-lquadmath -lquadmath -lm $LIBS"
|
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cat confdefs.h - <<_ACEOF >conftest.$ac_ext
|
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/* end confdefs.h. */
|
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|
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@@ -22601,7 +22601,7 @@ if test "x$ac_cv_lib_m_sin" = xyes; then
|
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#define HAVE_LIBM 1
|
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_ACEOF
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|
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- LIBS="-lm $LIBS"
|
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+ LIBS="-lquadmath -lquadmath -lm $LIBS"
|
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|
||||
fi
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@@ -27958,7 +27958,7 @@ fi
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## if nothing was obtained for SHLIB_CXXLDFLAGS.
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##
|
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## Note also that some systems (formerly AIX) do not allow for unresolved
|
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-## symbols at link time. For such systems, we link against -lm (in case
|
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+## symbols at link time. For such systems, we link against -lquadmath -lm (in case
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## it exists) when building a shlib module via SHLIB_LIBADD.
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|
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main_ld="${CC}"
|
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@@ -30147,7 +30147,7 @@ if ${ac_cv_lib_rt_clock_gettime+:} false
|
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$as_echo_n "(cached) " >&6
|
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else
|
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ac_check_lib_save_LIBS=$LIBS
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-LIBS="-lrt $LIBS"
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+LIBS="$LIBS"
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cat confdefs.h - <<_ACEOF >conftest.$ac_ext
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/* end confdefs.h. */
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@@ -30190,7 +30190,7 @@ if test "x$ac_cv_lib_rt_clock_gettime" =
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#define HAVE_LIBRT 1
|
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_ACEOF
|
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|
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- LIBS="-lrt $LIBS"
|
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+ LIBS="$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; }
|
@ -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;
|
@ -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
|
||||
|
Loading…
Reference in New Issue
Block a user