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math/R: maintainer rework

Browse Source 
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:
John Marino 2016-08-05 02:30:18 +00:00
parent e82895bb9b
commit b95421020d
Notes: svn2git 2021-03-31 03:12:20 +00:00 
svn path=/head/; revision=419666
6 changed files with 73 additions and 273 deletions
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192
math/R/Makefile
View File

@ -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
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
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>
NETLIB_USES= blaslapack:netlib
NLS_CONFIGURE_OFF= --disable-nls
NLS_USES= gettext
OPENBLAS_USES= blaslapack:openblas
OPENMP_CONFIGURE_ENABLE=openmp
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
LTO_CONFIGURE_ENABLE= lto
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
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

8
math/R/compiler.mk
View File

@ -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

2
math/R/distinfo
View File

@ -1,3 +1,3 @@
TIMESTAMP = 1467276607
TIMESTAMP = 1470250856
SHA256 (R-3.3.1.tar.gz) = 3dc59ae5831f5380f83c169bac2103ad052efe0ecec4ffa74bde4d85a0fda9e2
SIZE (R-3.3.1.tar.gz) = 29848329

113
math/R/files/patch-configure
View File

@ -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; }

11
math/R/files/patch-src__nmath__standalone__test.c
View File

@ -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;

20
math/R/files/patch-src_extra_tre_tre-internal.h
View File

@ -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