hey @ports, Update to latest R, all regress pass, Ok?
Index: Makefile =================================================================== RCS file: /cvs/ports/math/R/Makefile,v retrieving revision 1.62 diff -u -p -u -r1.62 Makefile --- Makefile 20 May 2014 11:02:12 -0000 1.62 +++ Makefile 14 Jul 2014 19:38:30 -0000 @@ -3,11 +3,11 @@ SHARED_ONLY= Yes COMMENT= powerful math/statistics/graphics language -DISTNAME= R-3.1.0 +DISTNAME= R-3.1.1 -SHARED_LIBS= R 2.1 # 2.0 -SHARED_LIBS+= Rlapack 31.2 # 31.1 -SHARED_LIBS+= Rblas 31.1 # 31.0 +SHARED_LIBS= R 2.1 # 2.1 +SHARED_LIBS+= Rlapack 31.2 # 31.2 +SHARED_LIBS+= Rblas 31.1 # 31.1 CATEGORIES= math HOMEPAGE= http://www.r-project.org/ Index: distinfo =================================================================== RCS file: /cvs/ports/math/R/distinfo,v retrieving revision 1.20 diff -u -p -u -r1.20 distinfo --- distinfo 20 May 2014 11:02:12 -0000 1.20 +++ distinfo 14 Jul 2014 19:38:30 -0000 @@ -1,2 +1,2 @@ -SHA256 (R-3.1.0.tar.gz) = imgDkPhMWMAdze/Wguqg6QOJ8J5tLy4JDHGvQAZfX+I= -SIZE (R-3.1.0.tar.gz) = 28469975 +SHA256 (R-3.1.1.tar.gz) = zlxNXjRBTOjx7C1WQoYUNfod3EzYm9M2Fyu+JaYsehk= +SIZE (R-3.1.1.tar.gz) = 28606569 Index: patches/patch-Makefile_in =================================================================== RCS file: /cvs/ports/math/R/patches/patch-Makefile_in,v retrieving revision 1.4 diff -u -p -u -r1.4 patch-Makefile_in --- patches/patch-Makefile_in 20 May 2014 11:02:12 -0000 1.4 +++ patches/patch-Makefile_in 14 Jul 2014 19:38:30 -0000 @@ -2,18 +2,18 @@ $OpenBSD: patch-Makefile_in,v 1.4 2014/0 Do not build PDF versions of the R manuals ---- Makefile.in.orig Thu Mar 13 00:02:06 2014 -+++ Makefile.in Tue May 20 10:42:46 2014 +--- Makefile.in.orig Wed May 21 00:15:03 2014 ++++ Makefile.in Sat Jun 14 16:18:50 2014 @@ -121,7 +121,7 @@ svnonly: fi \ fi --libR_la = lib/libR$(DYLIB_EXT) -+libR_la = lib/libR.so.$(LIBR_VERSION) +-@WANT_R_STATIC_FALSE@libR_la = libR$(DYLIB_EXT) ++@WANT_R_STATIC_FALSE@libR_la = libR.so.$(LIBR_VERSION) + @WANT_R_STATIC_TRUE@libR_la = libR.a install-libR: - @if test -f $(libR_la); then $(MAKE) install-libR-exists; fi - install-libR-exists: -@@ -213,13 +213,6 @@ distdir: $(DISTFILES) vignettes + @if test -f lib$(R_ARCH)/$(libR_la); then $(MAKE) install-libR-exists; fi +@@ -216,13 +216,6 @@ distdir: $(DISTFILES) vignettes cp library/$${d}/doc/*.pdf $(distdir)/src/library/$${d}/inst/doc; \ done @(cd $(distdir); tools/link-recommended) Index: patches/patch-configure =================================================================== RCS file: /cvs/ports/math/R/patches/patch-configure,v retrieving revision 1.19 diff -u -p -u -r1.19 patch-configure --- patches/patch-configure 20 May 2014 11:02:12 -0000 1.19 +++ patches/patch-configure 14 Jul 2014 19:38:30 -0000 @@ -8,9 +8,9 @@ Fix "--export-dynamic" linker flag Fix linking with external libintl ---- configure.orig Fri May 2 11:10:27 2014 -+++ configure Fri May 2 11:20:00 2014 -@@ -20899,12 +20899,12 @@ done +--- configure.orig Sat Jun 14 00:16:52 2014 ++++ configure Sat Jun 14 16:14:57 2014 +@@ -20900,12 +20900,12 @@ 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.$ac_ext /* end confdefs.h. */ -@@ -20939,7 +20939,7 @@ if test "x$ac_cv_lib_readline_rl_callback_read_char" = +@@ -20940,7 +20940,7 @@ if test "x$ac_cv_lib_readline_rl_callback_read_char" = #define HAVE_LIBREADLINE 1 _ACEOF @@ -34,7 +34,7 @@ Fix linking with external libintl fi -@@ -21066,13 +21066,13 @@ fi +@@ -21067,13 +21067,13 @@ fi fi @@ -51,7 +51,7 @@ Fix linking with external libintl cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ -@@ -21107,7 +21107,7 @@ if test "x$ac_cv_lib_readline_rl_callback_read_char" = +@@ -21108,7 +21108,7 @@ if test "x$ac_cv_lib_readline_rl_callback_read_char" = #define HAVE_LIBREADLINE 1 _ACEOF @@ -60,7 +60,7 @@ Fix linking with external libintl fi -@@ -26240,7 +26240,7 @@ if test "${GCC}" = yes; then +@@ -26241,7 +26241,7 @@ if test "${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" ;; *) -@@ -26251,7 +26251,7 @@ if test "${GCC}" = yes; then +@@ -26252,7 +26252,7 @@ if test "${GCC}" = yes; then fi if test "${G77}" = yes; then case "${host_cpu}" in @@ -78,7 +78,7 @@ Fix linking with external libintl fpicflags="-fPIC" ;; *) -@@ -26261,7 +26261,7 @@ if test "${G77}" = yes; then +@@ -26262,7 +26262,7 @@ if test "${G77}" = yes; then fi if test "${GXX}" = yes; then case "${host_cpu}" in @@ -87,7 +87,7 @@ Fix linking with external libintl cxxpicflags="-fPIC" ;; *) -@@ -26517,7 +26517,7 @@ $as_echo "$as_me: WARNING: Use of flat namespace is re +@@ -26518,7 +26518,7 @@ $as_echo "$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__ | $CC -E - | grep __ELF__`"; then @@ -96,7 +96,7 @@ Fix linking with external libintl shlib_ldflags="-shared -fPIC" fi ;; -@@ -26720,13 +26720,6 @@ case "${host_os}" in +@@ -26721,13 +26721,6 @@ case "${host_os}" in LAPACK_LDFLAGS="+s" fi ;; @@ -110,7 +110,7 @@ Fix linking with external libintl esac if test -z "${DYLIB_LD}"; then -@@ -38731,7 +38724,7 @@ fi +@@ -38736,7 +38729,7 @@ 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" ;; *) -@@ -42485,7 +42478,7 @@ else +@@ -42490,7 +42483,7 @@ 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> -@@ -42642,8 +42635,8 @@ $as_echo "$gt_source" >&6; } +@@ -42647,8 +42640,8 @@ $as_echo "$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; } Index: patches/patch-src_main_connections_c =================================================================== RCS file: /cvs/ports/math/R/patches/patch-src_main_connections_c,v retrieving revision 1.13 diff -u -p -u -r1.13 patch-src_main_connections_c --- patches/patch-src_main_connections_c 20 May 2014 11:02:12 -0000 1.13 +++ patches/patch-src_main_connections_c 14 Jul 2014 19:38:30 -0000 @@ -1,7 +1,7 @@ $OpenBSD: patch-src_main_connections_c,v 1.13 2014/05/20 11:02:12 dcoppa Exp $ ---- src/main/connections.c.orig Tue May 20 10:07:58 2014 -+++ src/main/connections.c Tue May 20 10:10:23 2014 -@@ -2902,7 +2902,7 @@ static int text_vfprintf(Rconnection con, const char * +--- 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 * 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 } else if(res < 0) { /* just a failure indication */ #define NBUFSIZE (already + 100*BUFSIZE) vmax = vmaxget(); -@@ -5163,7 +5163,8 @@ static Rboolean gzcon_open(Rconnection con) +@@ -5162,7 +5162,8 @@ static Rboolean gzcon_open(Rconnection con) if(con->canread) { /* read header */ Index: patches/patch-src_main_main_c =================================================================== RCS file: /cvs/ports/math/R/patches/patch-src_main_main_c,v retrieving revision 1.7 diff -u -p -u -r1.7 patch-src_main_main_c --- patches/patch-src_main_main_c 20 May 2014 11:02:12 -0000 1.7 +++ patches/patch-src_main_main_c 14 Jul 2014 19:38:30 -0000 @@ -2,8 +2,8 @@ $OpenBSD: patch-src_main_main_c,v 1.7 20 OpenBSD always returns EINVAL when trying to disable an active stack ---- src/main/main.c.orig Thu Mar 13 00:03:16 2014 -+++ src/main/main.c Tue May 20 10:14:48 2014 +--- src/main/main.c.orig Sat Jun 14 00:15:13 2014 ++++ src/main/main.c Sat Jun 14 16:14:58 2014 @@ -28,6 +28,8 @@ #include <ctype.h> #include <stdlib.h> @@ -13,7 +13,7 @@ OpenBSD always returns EINVAL when tryin #define __MAIN__ #define R_USE_SIGNALS 1 -@@ -618,7 +620,8 @@ static void init_signal_handlers(void) +@@ -622,7 +624,8 @@ static void init_signal_handlers(void) sigstk.ss_size = SIGSTKSZ + R_USAGE; sigstk.ss_flags = 0; if(sigaltstack(&sigstk, NULL) < 0) Index: patches/patch-src_main_platform_c =================================================================== RCS file: /cvs/ports/math/R/patches/patch-src_main_platform_c,v retrieving revision 1.8 diff -u -p -u -r1.8 patch-src_main_platform_c --- patches/patch-src_main_platform_c 20 May 2014 11:02:12 -0000 1.8 +++ patches/patch-src_main_platform_c 14 Jul 2014 19:38:30 -0000 @@ -2,9 +2,9 @@ $OpenBSD: patch-src_main_platform_c,v 1. Allow building with USE_SYSTRACE=Yes ---- src/main/platform.c.orig Fri May 2 11:47:39 2014 -+++ src/main/platform.c Fri May 2 11:50:07 2014 -@@ -2147,17 +2147,22 @@ SEXP attribute_hidden do_dircreate(SEXP call, SEXP op, +--- 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, /* Solaris 10 returns ENOSYS on automount, PR#13834 EROFS is allowed by POSIX, so we skip that too */ serrno = errno; Index: patches/patch-src_scripts_javareconf_in =================================================================== RCS file: /cvs/ports/math/R/patches/patch-src_scripts_javareconf_in,v retrieving revision 1.2 diff -u -p -u -r1.2 patch-src_scripts_javareconf_in --- patches/patch-src_scripts_javareconf_in 20 May 2014 11:02:12 -0000 1.2 +++ patches/patch-src_scripts_javareconf_in 14 Jul 2014 19:38:30 -0000 @@ -1,6 +1,6 @@ $OpenBSD: patch-src_scripts_javareconf_in,v 1.2 2014/05/20 11:02:12 dcoppa Exp $ ---- src/scripts/javareconf.in.orig Fri May 2 11:53:06 2014 -+++ src/scripts/javareconf.in Fri May 2 11:55:35 2014 +--- src/scripts/javareconf.in.orig Mon May 19 00:15:04 2014 ++++ src/scripts/javareconf.in Sat Jun 14 16:14:58 2014 @@ -6,7 +6,7 @@ fi ## pick up configure-time settings . "${R_HOME}/etc${R_ARCH}/javaconf" @@ -9,7 +9,7 @@ $OpenBSD: patch-src_scripts_javareconf_i +SHLIB_EXT=`${R_HOME}/bin/R CMD config SHLIB_EXT` tools_classpath=${R_SHARE_DIR}/java - revision='$Rev: 63871 $' + revision='$Rev: 65645 $' @@ -218,30 +218,18 @@ if test "${JAVA_LIBS}" = "~autodetect~"; then LD_LIBRARY_PATH= export LD_LIBRARY_PATH Index: pkg/PLIST =================================================================== RCS file: /cvs/ports/math/R/pkg/PLIST,v retrieving revision 1.22 diff -u -p -u -r1.22 PLIST --- pkg/PLIST 20 May 2014 11:02:12 -0000 1.22 +++ pkg/PLIST 14 Jul 2014 19:38:30 -0000 @@ -570,6 +570,7 @@ lib/R/library/Matrix/html/rcond.html lib/R/library/Matrix/html/rep2abI.html lib/R/library/Matrix/html/replValue-class.html lib/R/library/Matrix/html/rleDiff-class.html +lib/R/library/Matrix/html/rsparsematrix.html lib/R/library/Matrix/html/solve-methods.html lib/R/library/Matrix/html/spMatrix.html lib/R/library/Matrix/html/sparse.model.matrix.html @@ -2273,6 +2274,7 @@ lib/R/library/mgcv/help/mgcv.rdx lib/R/library/mgcv/help/paths.rds lib/R/library/mgcv/html/ lib/R/library/mgcv/html/00Index.html +lib/R/library/mgcv/html/Beta.html lib/R/library/mgcv/html/Predict.matrix.cr.smooth.html lib/R/library/mgcv/html/Predict.matrix.html lib/R/library/mgcv/html/Predict.matrix.soap.film.html @@ -2286,8 +2288,10 @@ lib/R/library/mgcv/html/cSplineDes.html lib/R/library/mgcv/html/choose.k.html lib/R/library/mgcv/html/columb.html lib/R/library/mgcv/html/concurvity.html +lib/R/library/mgcv/html/coxph.html lib/R/library/mgcv/html/exclude.too.far.html lib/R/library/mgcv/html/extract.lme.cov.html +lib/R/library/mgcv/html/family.mgcv.html lib/R/library/mgcv/html/fix.family.link.html lib/R/library/mgcv/html/fixDependence.html lib/R/library/mgcv/html/formXtViX.html @@ -2309,6 +2313,7 @@ lib/R/library/mgcv/html/gam2objective.ht lib/R/library/mgcv/html/gamObject.html lib/R/library/mgcv/html/gamSim.html lib/R/library/mgcv/html/gamm.html +lib/R/library/mgcv/html/gaulss.html lib/R/library/mgcv/html/get.var.html lib/R/library/mgcv/html/in.out.html lib/R/library/mgcv/html/inSide.html @@ -2327,11 +2332,13 @@ lib/R/library/mgcv/html/mgcv-parallel.ht lib/R/library/mgcv/html/model.matrix.gam.html lib/R/library/mgcv/html/mono.con.html lib/R/library/mgcv/html/mroot.html +lib/R/library/mgcv/html/mvn.html lib/R/library/mgcv/html/negbin.html lib/R/library/mgcv/html/new.name.html lib/R/library/mgcv/html/notExp.html lib/R/library/mgcv/html/notExp2.html lib/R/library/mgcv/html/null.space.dimension.html +lib/R/library/mgcv/html/ocat.html lib/R/library/mgcv/html/pcls.html lib/R/library/mgcv/html/pdIdnot.html lib/R/library/mgcv/html/pdTens.html @@ -2348,6 +2355,7 @@ lib/R/library/mgcv/html/random.effects.h lib/R/library/mgcv/html/residuals.gam.html lib/R/library/mgcv/html/rig.html lib/R/library/mgcv/html/s.html +lib/R/library/mgcv/html/scat.html lib/R/library/mgcv/html/slanczos.html lib/R/library/mgcv/html/smooth.construct.ad.smooth.spec.html lib/R/library/mgcv/html/smooth.construct.cr.smooth.spec.html @@ -2374,6 +2382,8 @@ lib/R/library/mgcv/html/tensor.prod.mode lib/R/library/mgcv/html/uniquecombs.html lib/R/library/mgcv/html/vcov.gam.html lib/R/library/mgcv/html/vis.gam.html +lib/R/library/mgcv/html/ziP.html +lib/R/library/mgcv/html/ziplss.html lib/R/library/mgcv/libs/ lib/R/library/mgcv/libs/mgcv.so lib/R/library/nlme/
