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Bugfix update to R-2.15.3.

Browse Source 
Until someone understand what is wrong with R-3.0.x and we can move
to the R-3 branch...
This commit is contained in:
dcoppa 2013-06-03 10:46:45 +00:00
parent 6f4c70e7bd
commit c7d96ee94d
8 changed files with 101 additions and 40 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

20
math/R/Makefile
View File

@ -1,11 +1,11 @@
# $OpenBSD: Makefile,v 1.55 2013/03/11 11:23:54 espie Exp $
# $OpenBSD: Makefile,v 1.56 2013/06/03 10:46:45 dcoppa Exp $
SHARED_ONLY= Yes
COMMENT= powerful math/statistics/graphics language
DISTNAME= R-2.15.2
DISTNAME= R-2.15.3
SHARED_LIBS= R 1.0 \
SHARED_LIBS= R 1.1 \
Rlapack 31.0 \
Rblas 31.0
@ -17,13 +17,11 @@ MAINTAINER= Rafael Sadowski <rafael@sizeofvoid.org>
# GPL
PERMIT_PACKAGE_CDROM= Yes
WANTLIB= GL ICE SM X11 Xext Xmu Xrender Xss Xt \
bz2 c cairo expat fontconfig freetype glib-2.0 \
gobject-2.0 icui18n icuuc jpeg lzma m ncurses \
pango-1.0 pangocairo-1.0 pangoft2-1.0 pcre \
pixman-1 png pthread-stubs readline tiff \
xcb xcb-render xcb-shm z \
${MODFORTRAN_WANTLIB} ${MODTK_WANTLIB}
WANTLIB= ICE SM X11 Xext Xmu Xss Xt bz2 c cairo \
fontconfig freetype glib-2.0 gobject-2.0 \
icui18n icuuc jpeg lzma m ncurses pango-1.0 \
pangocairo-1.0 pangoft2-1.0 pcre png readline \
tiff z ${MODFORTRAN_WANTLIB} ${MODTK_WANTLIB}
MASTER_SITES= http://cran.r-project.org/src/base/R-2/ \
ftp://cran.r-project.org/pub/R/src/base/R-2/ \
@ -59,6 +57,8 @@ LIB_DEPENDS= ${MODFORTRAN_LIB_DEPENDS} \
graphics/tiff \
textproc/icu4c
RUN_DEPENDS= archivers/gtar \
archivers/unzip \
archivers/zip \
devel/xdg-utils
CONFIGURE_STYLE=gnu

4
math/R/distinfo
View File

@ -1,2 +1,2 @@
SHA256 (R-2.15.2.tar.gz) = KSg3riWbdmhQm4pdTsi+CqUMMnz+elNLrEGbTKdm1m0=
SIZE (R-2.15.2.tar.gz) = 24338934
SHA256 (R-2.15.3.tar.gz) = xYOjj42tO8ASwIEW9LoeshgsrfrUsPjXvTzbokvCVdY=
SIZE (R-2.15.3.tar.gz) = 25409925

22
math/R/patches/patch-configure
View File

@ -1,4 +1,4 @@
$OpenBSD: patch-configure,v 1.15 2012/10/29 11:07:29 dcoppa Exp $
$OpenBSD: patch-configure,v 1.16 2013/06/03 10:46:45 dcoppa Exp $
Unbreak build on powerpc (relocation truncated to fit: R_PPC_GOT16...)
@ -6,9 +6,9 @@ Fix "--export-dynamic" linker flag
Fix linking with external libintl
--- configure.orig Fri Oct 19 00:05:56 2012
+++ configure Fri Oct 26 10:05:45 2012
@@ -26063,7 +26063,7 @@ if test "${GCC}" = yes; then
--- configure.orig Sat Feb 23 00:06:28 2013
+++ configure Mon Jun 3 09:06:33 2013
@@ -26069,7 +26069,7 @@ if test "${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
@ -17,7 +17,7 @@ Fix linking with external libintl
cpicflags="-fPIC"
;;
*)
@@ -26074,7 +26074,7 @@ if test "${GCC}" = yes; then
@@ -26080,7 +26080,7 @@ if test "${GCC}" = yes; then
fi
if test "${G77}" = yes; then
case "${host_cpu}" in
@ -26,7 +26,7 @@ Fix linking with external libintl
fpicflags="-fPIC"
;;
*)
@@ -26084,7 +26084,7 @@ if test "${G77}" = yes; then
@@ -26090,7 +26090,7 @@ if test "${G77}" = yes; then
fi
if test "${GXX}" = yes; then
case "${host_cpu}" in
@ -35,7 +35,7 @@ Fix linking with external libintl
cxxpicflags="-fPIC"
;;
*)
@@ -26337,7 +26337,7 @@ $as_echo "$as_me: WARNING: Use of flat namespace is re
@@ -26343,7 +26343,7 @@ $as_echo "$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__ | $CC -E - | grep __ELF__`"; then
@ -44,7 +44,7 @@ Fix linking with external libintl
shlib_ldflags="-shared -fPIC"
fi
;;
@@ -26528,13 +26528,6 @@ case "${host_os}" in
@@ -26534,13 +26534,6 @@ case "${host_os}" in
LAPACK_LDFLAGS="+s"
fi
;;
@ -58,7 +58,7 @@ Fix linking with external libintl
esac
if test -z "${DYLIB_LD}"; then
@@ -38391,7 +38384,7 @@ fi
@@ -38424,7 +38417,7 @@ 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
@ -67,7 +67,7 @@ Fix linking with external libintl
fcpicflags="-fPIC"
;;
*)
@@ -42499,7 +42492,7 @@ else
@@ -42533,7 +42526,7 @@ else
gt_save_CPPFLAGS="$CPPFLAGS"
CPPFLAGS="$CPPFLAGS $INCINTL"
gt_save_LIBS="$LIBS"
@ -76,7 +76,7 @@ Fix linking with external libintl
cat confdefs.h - <<_ACEOF >conftest.$ac_ext
/* end confdefs.h. */
#include <libintl.h>
@@ -42656,8 +42649,8 @@ $as_echo "$gt_source" >&6; }
@@ -42690,8 +42683,8 @@ $as_echo "$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_appl_Makefile_in
View File

@ -1,7 +1,7 @@
$OpenBSD: patch-src_appl_Makefile_in,v 1.1 2012/07/04 12:38:06 dcoppa Exp $
--- src/appl/Makefile.in.orig Thu Jun 28 12:57:43 2012
+++ src/appl/Makefile.in Thu Jun 28 12:58:09 2012
@@ -50,7 +50,7 @@ DISTFILES = COPYRIGHT COPYRIGHT.ftn README \
$OpenBSD: patch-src_appl_Makefile_in,v 1.2 2013/06/03 10:46:45 dcoppa Exp $
--- src/appl/Makefile.in.orig Tue Feb 5 00:05:10 2013
+++ src/appl/Makefile.in Mon Jun 3 09:06:33 2013
@@ -50,7 +50,7 @@ DISTFILES = \
@WANT_R_SHLIB_TRUE@ALL_CFLAGS = $(ALL_CFLAGS_LO)
@WANT_R_SHLIB_TRUE@ALL_FFLAGS = $(ALL_FFLAGS_LO)

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

@ -1,7 +1,7 @@
$OpenBSD: patch-src_main_connections_c,v 1.10 2012/10/29 11:07:29 dcoppa Exp $
--- src/main/connections.c.orig Tue Aug 14 00:05:06 2012
+++ src/main/connections.c Fri Oct 26 10:05:45 2012
@@ -2644,7 +2644,7 @@ static int text_vfprintf(Rconnection con, const char *
$OpenBSD: patch-src_main_connections_c,v 1.11 2013/06/03 10:46:45 dcoppa Exp $
--- src/main/connections.c.orig Sat Feb 16 00:05:03 2013
+++ src/main/connections.c Mon Jun 3 09:06:33 2013
@@ -2652,7 +2652,7 @@ 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 1.10 2012/10/29 11:07:29 dcoppa Exp $
} else if(res < 0) { /* just a failure indication */
#define NBUFSIZE (already + 100*BUFSIZE)
usedRalloc = TRUE;
@@ -4872,7 +4872,8 @@ static Rboolean gzcon_open(Rconnection con)
@@ -4880,7 +4880,8 @@ 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 1.5 2012/10/29 11:07:29 dcoppa Exp $
$OpenBSD: patch-src_main_platform_c,v 1.6 2013/06/03 10:46:45 dcoppa Exp $
Allow building with USE_SYSTRACE=Yes
--- src/main/platform.c.orig Thu Aug 16 00:05:05 2012
+++ src/main/platform.c Fri Oct 26 10:10:18 2012
@@ -2196,18 +2196,24 @@ SEXP attribute_hidden do_dircreate(SEXP call, SEXP op,
--- src/main/platform.c.orig Mon Dec 10 13:48:44 2012
+++ src/main/platform.c Mon Jun 3 09:06:33 2013
@@ -2197,18 +2197,24 @@ SEXP attribute_hidden do_dircreate(SEXP call, SEXP op,
res = mkdir(dir, (mode_t) mode);
/* Solaris 10 returns ENOSYS on automount, PR#13834
EROFS is allowed by POSIX, so we skip that too */

46
math/R/patches/patch-src_scripts_javareconf Normal file
View File

@ -0,0 +1,46 @@
$OpenBSD: patch-src_scripts_javareconf,v 1.1 2013/06/03 10:46:45 dcoppa Exp $
--- src/scripts/javareconf.orig Sat Feb 23 00:05:04 2013
+++ src/scripts/javareconf Mon Jun 3 11:56:10 2013
@@ -3,7 +3,7 @@ if test -z "${R_HOME}"; then
exit 1
fi
-DYLIB_EXT=`${R_HOME}/bin/R CMD config DYLIB_EXT`
+SHLIB_EXT=`${R_HOME}/bin/R CMD config SHLIB_EXT`
tools_classpath=${R_SHARE_DIR}/java
revision='$Rev: 62021 $'
@@ -212,30 +212,17 @@ case "$hostos" in
LD_LIBRARY_PATH=
export LD_LIBRARY_PATH
# remove trailing/leading : (if any)
- java_library_path=`"$JAVA" -classpath "${tools_classpath}" getsp java.library.path| ${SED-sed} -e 's/:$//' -e 's/^://'`
- ## see if libjvm is on this path: it is not for recent Oracle Java
+ boot_path=`"$JAVA" -classpath "${tools_classpath}" getsp sun.boot.library.path| ${SED-sed} -e 's/:$//' -e 's/^://'`
has_libjvm=no
save_IFS=$IFS; IFS=:
- for dir in ${java_library_path}; do
- if test -f "$dir/libjvm${DYLIB_EXT}"; then
- has_libjvm=yes
- break
- fi
- done
- # Then try some heuristics using sun.boot.library.path
- if test ${has_libjvm} = no; then
- echo "NOTE: Your JVM has a bogus java.library.path system property!" >&2
- echo " Trying a heuristic via sun.boot.library.path to find jvm library..." >&2
- boot_path=`"$JAVA" -classpath "${tools_classpath}" getsp sun.boot.library.path| ${SED-sed} -e 's/:$//' -e 's/^://'`
- if test -n "${boot_path}"; then
+ if test -n "${boot_path}"; then
for dir in "${boot_path}" "${boot_path}/client" "${boot_path}/server"; do
- if test -f "$dir/libjvm${DYLIB_EXT}"; then
+ if test -f "$dir/libjvm${SHLIB_EXT}"; then
has_libjvm=yes
java_library_path="${dir}"
break
fi
done
- fi
fi
IFS=${save_IFS}
# replace occurrences of JAVA_HOME with $(JAVA_HOME)

23
math/R/pkg/PLIST
View File

@ -1,4 +1,4 @@
@comment $OpenBSD: PLIST,v 1.18 2012/10/29 11:07:29 dcoppa Exp $
@comment $OpenBSD: PLIST,v 1.19 2013/06/03 10:46:45 dcoppa Exp $
bin/R
@bin bin/Rscript
lib/R/
@ -419,7 +419,6 @@ lib/R/library/Matrix/doc/Intro2Matrix.pdf
lib/R/library/Matrix/doc/Introduction.R
lib/R/library/Matrix/doc/Introduction.Rnw
lib/R/library/Matrix/doc/Introduction.pdf
lib/R/library/Matrix/doc/Matrix.bib
lib/R/library/Matrix/doc/SuiteSparse/
lib/R/library/Matrix/doc/SuiteSparse/AMD.txt
lib/R/library/Matrix/doc/SuiteSparse/CHOLMOD.txt
@ -514,7 +513,9 @@ lib/R/library/Matrix/html/formatSparseM.html
lib/R/library/Matrix/html/generalMatrix-class.html
lib/R/library/Matrix/html/image-methods.html
lib/R/library/Matrix/html/index-class.html
lib/R/library/Matrix/html/invPerm.html
lib/R/library/Matrix/html/is.na-methods.html
lib/R/library/Matrix/html/is.null.DN.html
lib/R/library/Matrix/html/isSymmetric-methods.html
lib/R/library/Matrix/html/kronecker-methods.html
lib/R/library/Matrix/html/ldenseMatrix-class.html
@ -919,7 +920,6 @@ lib/R/library/base/html/readLines.html
lib/R/library/base/html/readRDS.html
lib/R/library/base/html/readRenviron.html
lib/R/library/base/html/readline.html
lib/R/library/base/html/real.html
lib/R/library/base/html/reg.finalizer.html
lib/R/library/base/html/regex.html
lib/R/library/base/html/regmatches.html
@ -1540,6 +1540,7 @@ lib/R/library/datasets/html/warpbreaks.html
lib/R/library/datasets/html/women.html
lib/R/library/datasets/html/zCO2.html
lib/R/library/foreign/
lib/R/library/foreign/COPYRIGHTS
lib/R/library/foreign/DESCRIPTION
lib/R/library/foreign/INDEX
lib/R/library/foreign/LICENCE
@ -3023,7 +3024,9 @@ lib/R/library/rpart/Meta/hsearch.rds
lib/R/library/rpart/Meta/links.rds
lib/R/library/rpart/Meta/nsInfo.rds
lib/R/library/rpart/Meta/package.rds
lib/R/library/rpart/Meta/vignette.rds
lib/R/library/rpart/NAMESPACE
lib/R/library/rpart/NEWS.Rd
lib/R/library/rpart/R/
lib/R/library/rpart/R/rpart
lib/R/library/rpart/R/rpart.rdb
@ -3032,6 +3035,14 @@ lib/R/library/rpart/data/
lib/R/library/rpart/data/Rdata.rdb
lib/R/library/rpart/data/Rdata.rds
lib/R/library/rpart/data/Rdata.rdx
lib/R/library/rpart/doc/
lib/R/library/rpart/doc/index.html
lib/R/library/rpart/doc/longintro.R
lib/R/library/rpart/doc/longintro.Rnw
lib/R/library/rpart/doc/longintro.pdf
lib/R/library/rpart/doc/usercode.R
lib/R/library/rpart/doc/usercode.Rnw
lib/R/library/rpart/doc/usercode.pdf
lib/R/library/rpart/help/
lib/R/library/rpart/help/AnIndex
lib/R/library/rpart/help/aliases.rds
@ -3042,6 +3053,7 @@ lib/R/library/rpart/html/
lib/R/library/rpart/html/00Index.html
lib/R/library/rpart/html/R.css
lib/R/library/rpart/html/car.test.frame.html
lib/R/library/rpart/html/car90.html
lib/R/library/rpart/html/cu.summary.html
lib/R/library/rpart/html/kyphosis.html
lib/R/library/rpart/html/labels.rpart.html
@ -3058,12 +3070,13 @@ lib/R/library/rpart/html/prune.rpart.html
lib/R/library/rpart/html/residuals.rpart.html
lib/R/library/rpart/html/rpart-internal.html
lib/R/library/rpart/html/rpart.control.html
lib/R/library/rpart/html/rpart.exp.html
lib/R/library/rpart/html/rpart.html
lib/R/library/rpart/html/rpart.object.html
lib/R/library/rpart/html/rpconvert.html
lib/R/library/rpart/html/rsq.rpart.html
lib/R/library/rpart/html/snip.rpart.html
lib/R/library/rpart/html/solder.html
lib/R/library/rpart/html/stagec.html
lib/R/library/rpart/html/summary.rpart.html
lib/R/library/rpart/html/text.rpart.html
lib/R/library/rpart/html/xpred.rpart.html
@ -3745,6 +3758,7 @@ lib/R/library/survival/data/Rdata.rds
lib/R/library/survival/data/Rdata.rdx
lib/R/library/survival/doc/
lib/R/library/survival/doc/index.html
lib/R/library/survival/doc/sourcecode.pdf
lib/R/library/survival/doc/timedep.R
lib/R/library/survival/doc/timedep.Rnw
lib/R/library/survival/doc/timedep.pdf
@ -3806,6 +3820,7 @@ lib/R/library/survival/html/quantile.survfit.html
lib/R/library/survival/html/ratetable.html
lib/R/library/survival/html/ratetableDate.html
lib/R/library/survival/html/rats.html
lib/R/library/survival/html/rats2.html
lib/R/library/survival/html/residuals.coxph.html
lib/R/library/survival/html/residuals.survreg.html
lib/R/library/survival/html/ridge.html