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Update to R-3.1.2

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From maintainer Rafael Sadowski, with some tweaks by me
This commit is contained in:
dcoppa 2015-01-08 14:14:11 +00:00
parent 35ba509e50
commit f440b3b0f2
8 changed files with 116 additions and 88 deletions
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27
math/R/Makefile
View File

@ -1,13 +1,13 @@
# $OpenBSD: Makefile,v 1.63 2014/09/02 14:55:37 dcoppa Exp $
# $OpenBSD: Makefile,v 1.64 2015/01/08 14:14:11 dcoppa Exp $
SHARED_ONLY= Yes
COMMENT= powerful math/statistics/graphics language
DISTNAME= R-3.1.1
DISTNAME= R-3.1.2
SHARED_LIBS= R 2.1 # 2.1
SHARED_LIBS= R 3.0
SHARED_LIBS+= Rlapack 31.2 # 31.2
SHARED_LIBS+= Rblas 31.1 # 31.1
SHARED_LIBS+= Rblas 31.2 # 31.2
CATEGORIES= math
HOMEPAGE= http://www.r-project.org/
@ -26,19 +26,19 @@ WANTLIB= ICE SM X11 Xext Xmu Xss Xt bz2 c cairo \
MASTER_SITES= http://cran.r-project.org/src/base/R-3/ \
ftp://cran.r-project.org/pub/R/src/base/R-3/ \
ftp://ftp.u-aizu.ac.jp/pub/lang/R/CRAN/src/base/R-3/ \
http://cran.at.r-project.org/src/base/R-3/ \
http://cran.au.r-project.org/src/base/R-3/ \
http://cran.br.r-project.org/src/base/R-3/ \
http://cran.ch.r-project.org/src/base/R-3/ \
http://cran.es.r-project.org/src/base/R-3/ \
http://cran.dk.r-project.org/src/base/R-3/ \
http://cran.es.r-project.org/src/base/R-3/ \
http://cran.hu.r-project.org/src/base/R-3/ \
http://cran.stat.ucla.edu/src/base/R-3/ \
http://cran.uk.r-project.org/src/base/R-3/ \
http://cran.us.r-project.org/src/base/R-3/ \
http://cran.za.r-project.org/src/base/R-3/ \
ftp://ftp.u-aizu.ac.jp/pub/lang/R/CRAN/src/base/R-3/ \
http://lib.stat.cmu.edu/R/CRAN/src/base/R-3/ \
http://cran.stat.ucla.edu/src/base/R-3/ \
http://probability.ca/cran/src/base/R-3/
MODULES= fortran \
@ -52,6 +52,7 @@ BUILD_DEPENDS= ${MODFORTRAN_BUILD_DEPENDS} \
archivers/unzip \
archivers/zip \
devel/xdg-utils
LIB_DEPENDS= ${MODFORTRAN_LIB_DEPENDS} \
${MODTK_LIB_DEPENDS} \
archivers/bzip2 \
@ -64,14 +65,18 @@ LIB_DEPENDS= ${MODFORTRAN_LIB_DEPENDS} \
graphics/png \
graphics/tiff \
textproc/icu4c
RUN_DEPENDS= archivers/gtar \
archivers/unzip \
archivers/zip \
devel/gmake \
devel/xdg-utils
devel/xdg-utils \
print/texlive/base
CONFIGURE_STYLE=gnu
MODGNU_CONFIG_GUESS_DIRS=${WRKSRC}/tools
CONFIGURE_ARGS= ${CONFIGURE_SHARED} \
--enable-BLAS-shlib \
--enable-R-shlib \
@ -85,14 +90,16 @@ CONFIGURE_ARGS= ${CONFIGURE_SHARED} \
--with-system-bzlib \
--with-system-pcre \
--with-system-xz \
--with-tcltk \
--with-tcl-config=${MODTCL_CONFIG} \
--with-tcltk \
--with-tk-config=${MODTK_CONFIG}
CONFIGURE_ENV= FFLAGS="${FFLAGS}" \
CPPFLAGS="-I${LOCALBASE}/include/ereadline -I${LOCALBASE}/include" \
LDFLAGS="-L${LOCALBASE}/lib -Wl,-R${LOCALBASE}/lib/R/lib" \
ac_cv_path_TAR="${LOCALBASE}/bin/gtar"
LIBnn=lib \
ac_cv_path_TAR="${LOCALBASE}/bin/gtar" \
rdocdir="${PREFIX}/share/doc/R"
MAKE_FLAGS= INSTALL_DATA='install -c -m 644' \
INSTALL_PROGRAM='install -c -s -m 555' \

4
math/R/distinfo
View File

@ -1,2 +1,2 @@
SHA256 (R-3.1.1.tar.gz) = zlxNXjRBTOjx7C1WQoYUNfod3EzYm9M2Fyu+JaYsehk=
SIZE (R-3.1.1.tar.gz) = 28606569
SHA256 (R-3.1.2.tar.gz) = vNFQr8rg4C9u+181pqtyQyvoLoSexSzgu4nYw0Ko+no=
SIZE (R-3.1.2.tar.gz) = 28655941

30
math/R/patches/patch-configure
View File

@ -1,4 +1,4 @@
$OpenBSD: patch-configure,v 1.20 2014/09/02 14:55:37 dcoppa Exp $
$OpenBSD: patch-configure,v 1.21 2015/01/08 14:14:11 dcoppa Exp $
Use GNU readline instead of our base readline
@ -8,9 +8,9 @@ Fix "--export-dynamic" linker flag
Fix linking with external libintl
--- configure.orig Sat Jun 14 00:16:52 2014
+++ configure Sat Jun 14 16:14:57 2014
@@ -20900,12 +20900,12 @@ done
--- configure.orig Thu Oct 23 17:16:36 2014
+++ configure Thu Jan 8 05:51:05 2015
@@ -20903,12 +20903,12 @@ done
## don't use the cached value as we need to rebuild LIBS
unset ac_cv_lib_readline_rl_callback_read_char
{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for rl_callback_read_char in -lreadline" >&5
@ -25,7 +25,7 @@ Fix linking with external libintl
cat confdefs.h - <<_ACEOF >conftest.$ac_ext
/* end confdefs.h. */
@@ -20940,7 +20940,7 @@ if test "x$ac_cv_lib_readline_rl_callback_read_char" =
@@ -20943,7 +20943,7 @@ if test "x$ac_cv_lib_readline_rl_callback_read_char" =
#define HAVE_LIBREADLINE 1
_ACEOF
@ -34,7 +34,7 @@ Fix linking with external libintl
fi
@@ -21067,13 +21067,13 @@ fi
@@ -21070,13 +21070,13 @@ fi
fi
@ -51,7 +51,7 @@ Fix linking with external libintl
cat confdefs.h - <<_ACEOF >conftest.$ac_ext
/* end confdefs.h. */
@@ -21108,7 +21108,7 @@ if test "x$ac_cv_lib_readline_rl_callback_read_char" =
@@ -21111,7 +21111,7 @@ if test "x$ac_cv_lib_readline_rl_callback_read_char" =
#define HAVE_LIBREADLINE 1
_ACEOF
@ -60,7 +60,7 @@ Fix linking with external libintl
fi
@@ -26241,7 +26241,7 @@ if test "${GCC}" = yes; then
@@ -26244,7 +26244,7 @@ if test "${GCC}" = yes; then
## has 32k and so can use -fpic.
## However, although the gcc docs do not mention it, it seems s390/s390x
## also supports and needs -fPIC
@ -69,7 +69,7 @@ Fix linking with external libintl
cpicflags="-fPIC"
;;
*)
@@ -26252,7 +26252,7 @@ if test "${GCC}" = yes; then
@@ -26255,7 +26255,7 @@ if test "${GCC}" = yes; then
fi
if test "${G77}" = yes; then
case "${host_cpu}" in
@ -78,7 +78,7 @@ Fix linking with external libintl
fpicflags="-fPIC"
;;
*)
@@ -26262,7 +26262,7 @@ if test "${G77}" = yes; then
@@ -26265,7 +26265,7 @@ if test "${G77}" = yes; then
fi
if test "${GXX}" = yes; then
case "${host_cpu}" in
@ -87,7 +87,7 @@ Fix linking with external libintl
cxxpicflags="-fPIC"
;;
*)
@@ -26518,7 +26518,7 @@ $as_echo "$as_me: WARNING: Use of flat namespace is re
@@ -26521,7 +26521,7 @@ $as_echo "$as_me: WARNING: Use of flat namespace is re
openbsd*)
## looks like ${wl} is not defined here. Perhaps in libtool code?
if test -z "`echo __ELF__ | $CC -E - | grep __ELF__`"; then
@ -96,7 +96,7 @@ Fix linking with external libintl
shlib_ldflags="-shared -fPIC"
fi
;;
@@ -26721,13 +26721,6 @@ case "${host_os}" in
@@ -26724,13 +26724,6 @@ case "${host_os}" in
LAPACK_LDFLAGS="+s"
fi
;;
@ -110,7 +110,7 @@ Fix linking with external libintl
esac
if test -z "${DYLIB_LD}"; then
@@ -38736,7 +38729,7 @@ fi
@@ -38743,7 +38736,7 @@ fi
## use this to pick out gfortran (even though it is unreliable).
if test "${ac_cv_fc_compiler_gnu}" = yes; then
case "${host_cpu}" in
@ -119,7 +119,7 @@ Fix linking with external libintl
fcpicflags="-fPIC"
;;
*)
@@ -42490,7 +42483,7 @@ else
@@ -42497,7 +42490,7 @@ else
gt_save_CPPFLAGS="$CPPFLAGS"
CPPFLAGS="$CPPFLAGS $INCINTL"
gt_save_LIBS="$LIBS"
@ -128,7 +128,7 @@ Fix linking with external libintl
cat confdefs.h - <<_ACEOF >conftest.$ac_ext
/* end confdefs.h. */
#include <libintl.h>
@@ -42647,8 +42640,8 @@ $as_echo "$gt_source" >&6; }
@@ -42654,8 +42647,8 @@ $as_echo "$gt_source" >&6; }
if { eval "gt_val=\$$gt_func_gnugettext_libintl"; test "$gt_val" = "yes"; }; then
{ $as_echo "$as_me:${as_lineno-$LINENO}: checking how to link with libintl" >&5
$as_echo_n "checking how to link with libintl... " >&6; }

8
math/R/patches/patch-src_main_Makefile_in
View File

@ -1,6 +1,6 @@
$OpenBSD: patch-src_main_Makefile_in,v 1.8 2014/05/20 11:02:12 dcoppa Exp $
--- src/main/Makefile.in.orig Thu Mar 13 00:03:13 2014
+++ src/main/Makefile.in Tue May 20 10:45:51 2014
$OpenBSD: patch-src_main_Makefile_in,v 1.9 2015/01/08 14:14:11 dcoppa Exp $
--- src/main/Makefile.in.orig Mon Jul 14 17:15:06 2014
+++ src/main/Makefile.in Thu Jan 8 05:51:05 2015
@@ -98,7 +98,7 @@ EXTRA_STATIC_LIBS = \
$(R_ZLIBS) $(R_BZLIBS) $(R_PCRE) $(R_TRE) $(R_XDR) $(R_XZ) $(R_LIBINTL) $(R_TZONE)
STATIC_LIBS = $(MAIN_LIBS) $(EXTRA_STATIC_LIBS)
@ -11,7 +11,7 @@ $OpenBSD: patch-src_main_Makefile_in,v 1.8 2014/05/20 11:02:12 dcoppa Exp $
R_binary = R.bin
R_bin_OBJECTS = Rmain.o @WANT_R_SHLIB_FALSE@$(OBJECTS)
@@ -107,7 +107,7 @@ R_bin_OBJECTS = Rmain.o @WANT_R_SHLIB_FALSE@$(OBJECTS)
@WANT_R_SHLIB_TRUE@R_bin_LDADD = -L../../lib@R_ARCH@ -lR @BLAS_SHLIB_TRUE@-lRblas
@WANT_R_SHLIB_TRUE@R_bin_LDADD = -lR @BLAS_SHLIB_TRUE@-lRblas
@BUILD_LTO_FALSE@R_bin_DEPENDENCIES =@WANT_R_SHLIB_FALSE@ libR.a @USE_EXPORTFILES_TRUE@ $(top_builddir)/etc/R.exp
-libR_la = libR$(DYLIB_EXT)

10
math/R/patches/patch-src_main_connections_c
View File

@ -1,7 +1,7 @@
$OpenBSD: patch-src_main_connections_c,v 1.14 2014/09/02 14:55:37 dcoppa Exp $
--- src/main/connections.c.orig Sat Jun 14 00:15:13 2014
+++ src/main/connections.c Sat Jun 14 16:14:58 2014
@@ -2901,7 +2901,7 @@ static int text_vfprintf(Rconnection con, const char *
$OpenBSD: patch-src_main_connections_c,v 1.15 2015/01/08 14:14:11 dcoppa Exp $
--- src/main/connections.c.orig Wed Sep 24 17:15:13 2014
+++ src/main/connections.c Thu Jan 8 05:51:05 2015
@@ -2905,7 +2905,7 @@ static int text_vfprintf(Rconnection con, const char *
b = R_alloc(res + already + 1, sizeof(char));
strcpy(b, this->lastline);
p = b + already;
@ -10,7 +10,7 @@ $OpenBSD: patch-src_main_connections_c,v 1.14 2014/09/02 14:55:37 dcoppa Exp $
} else if(res < 0) { /* just a failure indication */
#define NBUFSIZE (already + 100*BUFSIZE)
vmax = vmaxget();
@@ -5162,7 +5162,8 @@ static Rboolean gzcon_open(Rconnection con)
@@ -5169,7 +5169,8 @@ static Rboolean gzcon_open(Rconnection con)
if(con->canread) {
/* read header */

8
math/R/patches/patch-src_main_platform_c
View File

@ -1,10 +1,10 @@
$OpenBSD: patch-src_main_platform_c,v 1.9 2014/09/02 14:55:37 dcoppa Exp $
$OpenBSD: patch-src_main_platform_c,v 1.10 2015/01/08 14:14:11 dcoppa Exp $
Allow building with USE_SYSTRACE=Yes
--- src/main/platform.c.orig Sat Jun 14 00:15:13 2014
+++ src/main/platform.c Sat Jun 14 16:14:58 2014
@@ -2159,17 +2159,22 @@ SEXP attribute_hidden do_dircreate(SEXP call, SEXP op,
--- src/main/platform.c.orig Wed Sep 24 17:15:13 2014
+++ src/main/platform.c Thu Jan 8 05:51:05 2015
@@ -2166,17 +2166,22 @@ SEXP attribute_hidden do_dircreate(SEXP call, SEXP op,
/* Solaris 10 returns ENOSYS on automount, PR#13834
EROFS is allowed by POSIX, so we skip that too */
serrno = errno;

99
math/R/pkg/PLIST
View File

@ -1,4 +1,4 @@
@comment $OpenBSD: PLIST,v 1.23 2014/09/02 14:55:37 dcoppa Exp $
@comment $OpenBSD: PLIST,v 1.24 2015/01/08 14:14:11 dcoppa Exp $
bin/R
@bin bin/Rscript
lib/R/
@ -31,53 +31,6 @@ lib/R/bin/libtool
lib/R/bin/mkinstalldirs
lib/R/bin/pager
lib/R/bin/rtags
lib/R/doc/
lib/R/doc/AUTHORS
lib/R/doc/COPYING
lib/R/doc/COPYRIGHTS
lib/R/doc/CRAN_mirrors.csv
lib/R/doc/FAQ
lib/R/doc/KEYWORDS
lib/R/doc/KEYWORDS.db
lib/R/doc/NEWS
lib/R/doc/NEWS.0
lib/R/doc/NEWS.1
lib/R/doc/NEWS.2
lib/R/doc/NEWS.rds
lib/R/doc/RESOURCES
lib/R/doc/THANKS
lib/R/doc/html/
lib/R/doc/html/NEWS.2.html
lib/R/doc/html/NEWS.html
lib/R/doc/html/R.css
lib/R/doc/html/Search.html
lib/R/doc/html/SearchOn.html
lib/R/doc/html/about.html
lib/R/doc/html/favicon.ico
lib/R/doc/html/index.html
lib/R/doc/html/left.jpg
lib/R/doc/html/logo.jpg
lib/R/doc/html/logosm.jpg
lib/R/doc/html/packages-head-utf8.html
lib/R/doc/html/packages.html
lib/R/doc/html/resources.html
lib/R/doc/html/right.jpg
lib/R/doc/html/up.jpg
lib/R/doc/manual/
lib/R/doc/manual/R-FAQ.html
lib/R/doc/manual/R-admin.html
lib/R/doc/manual/R-data.html
lib/R/doc/manual/R-exts.html
lib/R/doc/manual/R-intro.html
lib/R/doc/manual/R-ints.html
lib/R/doc/manual/R-lang.html
lib/R/doc/manual/images/
lib/R/doc/manual/images/QQ.png
lib/R/doc/manual/images/ecdf.png
lib/R/doc/manual/images/fig11.png
lib/R/doc/manual/images/fig12.png
lib/R/doc/manual/images/hist.png
lib/R/doc/manual/images/ice.png
lib/R/etc/
lib/R/etc/Makeconf
lib/R/etc/Renviron
@ -2306,6 +2259,7 @@ lib/R/library/mgcv/html/gam.fit3.html
lib/R/library/mgcv/html/gam.html
lib/R/library/mgcv/html/gam.models.html
lib/R/library/mgcv/html/gam.outer.html
lib/R/library/mgcv/html/gam.scale.html
lib/R/library/mgcv/html/gam.selection.html
lib/R/library/mgcv/html/gam.side.html
lib/R/library/mgcv/html/gam.vcomp.html
@ -3216,6 +3170,7 @@ lib/R/library/stats/html/ksmooth.html
lib/R/library/stats/html/lag.html
lib/R/library/stats/html/lag.plot.html
lib/R/library/stats/html/line.html
lib/R/library/stats/html/listof.html
lib/R/library/stats/html/lm.html
lib/R/library/stats/html/lm.influence.html
lib/R/library/stats/html/lm.summaries.html
@ -4224,6 +4179,54 @@ lib/R/share/sh/echo.sh
lib/pkgconfig/libR.pc
@man man/man1/R.1
@man man/man1/Rscript.1
share/doc/R/
share/doc/R/AUTHORS
share/doc/R/COPYING
share/doc/R/COPYRIGHTS
share/doc/R/CRAN_mirrors.csv
share/doc/R/FAQ
share/doc/R/KEYWORDS
share/doc/R/KEYWORDS.db
share/doc/R/NEWS
share/doc/R/NEWS.0
share/doc/R/NEWS.1
share/doc/R/NEWS.2
share/doc/R/NEWS.rds
share/doc/R/RESOURCES
share/doc/R/THANKS
share/doc/R/html/
share/doc/R/html/NEWS.2.html
share/doc/R/html/NEWS.html
share/doc/R/html/R.css
share/doc/R/html/Search.html
share/doc/R/html/SearchOn.html
share/doc/R/html/about.html
share/doc/R/html/favicon.ico
share/doc/R/html/index.html
share/doc/R/html/left.jpg
share/doc/R/html/logo.jpg
share/doc/R/html/logosm.jpg
share/doc/R/html/packages-head-utf8.html
share/doc/R/html/packages.html
share/doc/R/html/resources.html
share/doc/R/html/right.jpg
share/doc/R/html/up.jpg
share/doc/R/manual/
share/doc/R/manual/R-FAQ.html
share/doc/R/manual/R-admin.html
share/doc/R/manual/R-data.html
share/doc/R/manual/R-exts.html
share/doc/R/manual/R-intro.html
share/doc/R/manual/R-ints.html
share/doc/R/manual/R-lang.html
share/doc/R/manual/images/
share/doc/R/manual/images/QQ.png
share/doc/R/manual/images/ecdf.png
share/doc/R/manual/images/fig11.png
share/doc/R/manual/images/fig12.png
share/doc/R/manual/images/hist.png
share/doc/R/manual/images/ice.png
share/doc/pkg-readmes/${FULLPKGNAME}
share/texmf-local/
share/texmf-local/bibtex/
share/texmf-local/bibtex/bib/

18
math/R/pkg/README Normal file
View File

@ -0,0 +1,18 @@
$OpenBSD: README,v 1.1 2015/01/08 14:14:11 dcoppa Exp $
+-----------------------------------------------------------------------
| Running ${FULLPKGNAME} on OpenBSD
+-----------------------------------------------------------------------
Configuring Java support
========================
To enable Java support, R needs to know where the JVM and the Java
libraries are located.
Running:
# export JAVA_HOME=${LOCALBASE}/jdk-1.7.0
# ${TRUEPREFIX}/bin/R CMD javareconf
as root, will update both ${TRUEPREFIX}/lib/R/etc/Makeconf and
${TRUEPREFIX}/lib/R/etc/ldpaths with the right settings.