From b73fad9d8cfa065767980199980c1206d650e348 Mon Sep 17 00:00:00 2001 From: markd Date: Tue, 13 Jun 2006 12:28:09 +0000 Subject: Update to R 2.3.1 This version contains several minor fixups and removes a couple of bad bugs such as NA-handling of mean() for integer vectors. Changes 2.3.0 This version contains several changes and additions, mostly incremental. --- math/R/Makefile | 5 +-- math/R/distinfo | 16 ++++---- math/R/patches/patch-aa | 16 ++++---- math/R/patches/patch-ac | 100 +++++++++++++++++++++++++----------------------- math/R/patches/patch-ad | 20 +++++----- math/R/patches/patch-ae | 24 ------------ math/R/patches/patch-at | 8 ---- 7 files changed, 80 insertions(+), 109 deletions(-) delete mode 100644 math/R/patches/patch-ae delete mode 100644 math/R/patches/patch-at diff --git a/math/R/Makefile b/math/R/Makefile index 40c1b612df5..9aefd7167fc 100644 --- a/math/R/Makefile +++ b/math/R/Makefile @@ -1,7 +1,6 @@ -# $NetBSD: Makefile,v 1.84 2006/06/09 11:15:32 rillig Exp $ +# $NetBSD: Makefile,v 1.85 2006/06/13 12:28:09 markd Exp $ -DISTNAME= R-2.2.1 -PKGREVISION= 3 +DISTNAME= R-2.3.1 CATEGORIES= math MASTER_SITES= ${MASTER_SITE_R_CRAN:=base/R-2/} diff --git a/math/R/distinfo b/math/R/distinfo index 92733f17cfb..9e93bda7a48 100644 --- a/math/R/distinfo +++ b/math/R/distinfo @@ -1,11 +1,9 @@ -$NetBSD: distinfo,v 1.31 2006/02/26 11:58:25 markd Exp $ +$NetBSD: distinfo,v 1.32 2006/06/13 12:28:09 markd Exp $ -SHA1 (R-2.2.1.tar.gz) = 537e0b89b8de55c1156474c76c19c1fcc210f756 -RMD160 (R-2.2.1.tar.gz) = b63b6c5ef1db27a879783460b0ecb6de0d4bba18 -Size (R-2.2.1.tar.gz) = 13665367 bytes -SHA1 (patch-aa) = 52f7ca0159087a6a5f319dd5476223785fe75a7a +SHA1 (R-2.3.1.tar.gz) = 62cf87f4a273f17d5a55a5ffaf0bfcdfdae3c03d +RMD160 (R-2.3.1.tar.gz) = 061a77f25d3b1144aecdce479aa707e7bea21a82 +Size (R-2.3.1.tar.gz) = 14285120 bytes +SHA1 (patch-aa) = 4041b32f8cc54d6428b47dfac82ceb275bc0ffdf SHA1 (patch-ab) = b724b549cd9920865c4d4ae60c71dff48c4c0c06 -SHA1 (patch-ac) = 95888e1a7bbd17a7c258973281adf9c702305673 -SHA1 (patch-ad) = 83c9b046822b1d350daec8739ca4ee2a6b7e1978 -SHA1 (patch-ae) = 4193b3f975bd55ce1d8f720878db31b67ba2d02c -SHA1 (patch-at) = d972e1072a7f6a30b5fbc2e5fa076bc5bdec5952 +SHA1 (patch-ac) = acf4d4bf230c5128571d19462efd50330eb66812 +SHA1 (patch-ad) = c081d45bdcea860584354b9b35427f70a94f3984 diff --git a/math/R/patches/patch-aa b/math/R/patches/patch-aa index 0960f1a4a7f..ca6f83f5c41 100644 --- a/math/R/patches/patch-aa +++ b/math/R/patches/patch-aa @@ -1,17 +1,17 @@ -$NetBSD: patch-aa,v 1.15 2005/05/02 16:57:19 drochner Exp $ +$NetBSD: patch-aa,v 1.16 2006/06/13 12:28:09 markd Exp $ ---- configure.ac.orig 2005-04-18 23:30:54.000000000 +0200 +--- configure.ac.orig 2006-05-18 21:13:59.000000000 +1200 +++ configure.ac -@@ -306,7 +306,7 @@ AC_ARG_WITH([pcre], +@@ -361,7 +361,7 @@ AC_ARG_WITH([valgrind-instrumentation], ## needs to come after GNOME AM_CONDITIONAL(WANT_R_SHLIB, [test "x${want_R_shlib}" = xyes]) if test "${want_R_shlib}" = yes; then -- LIBR="-L\$(R_HOME)/lib -lR" -+ LIBR="-Wl,-R${prefix}/lib/R/lib -L\$(R_HOME)/lib -lR" +- LIBR="-L\$(R_HOME)/lib\$(R_ARCH) -lR" ++ LIBR="-Wl,-R${prefix}/lib/R/lib\$(R_ARCH) -L\$(R_HOME)/lib\$(R_ARCH) -lR" else LIBR= fi -@@ -536,9 +536,9 @@ if test "${use_readline}" = yes; then +@@ -628,9 +628,9 @@ if test "${use_readline}" = yes; then if test "${use_readline}" = no; then ## only need ncurses if libreadline is not statically linked against it unset ac_cv_lib_readline_rl_callback_read_char @@ -24,7 +24,7 @@ $NetBSD: patch-aa,v 1.15 2005/05/02 16:57:19 drochner Exp $ AC_CHECK_LIB(readline, rl_callback_read_char) use_readline="${ac_cv_lib_readline_rl_callback_read_char}" fi -@@ -681,13 +681,6 @@ case "${host_cpu}" in +@@ -779,13 +779,6 @@ case "${host_cpu}" in R_PROG_CC_FLAG([-ieee_with_inexact], R_SH_VAR_ADD(R_XTRA_CFLAGS, [-ieee_with_inexact])) fi @@ -38,7 +38,7 @@ $NetBSD: patch-aa,v 1.15 2005/05/02 16:57:19 drochner Exp $ if test "${GXX}" = yes; then R_PROG_CXX_FLAG([-mieee], R_SH_VAR_ADD(R_XTRA_CXXFLAGS, [-mieee])) -@@ -986,6 +979,7 @@ case "${host_os}" in +@@ -1244,6 +1237,7 @@ case "${host_os}" in fpicflags= ;; netbsd*) diff --git a/math/R/patches/patch-ac b/math/R/patches/patch-ac index 3cac6ae4175..b12b23ea15f 100644 --- a/math/R/patches/patch-ac +++ b/math/R/patches/patch-ac @@ -1,38 +1,17 @@ -$NetBSD: patch-ac,v 1.16 2006/02/04 22:25:06 markd Exp $ +$NetBSD: patch-ac,v 1.17 2006/06/13 12:28:09 markd Exp $ ---- configure.orig 2005-12-16 16:07:00.000000000 +1300 +--- configure.orig 2006-06-01 20:12:54.000000000 +1200 +++ configure -@@ -1910,17 +1910,17 @@ fi - - ## R installation directories - --if test -z ${rdocdir}; then -+if test -z "${rdocdir}"; then - rdocdir='${rhome}/doc' - fi - - --if test -z ${rincludedir}; then -+if test -z "${rincludedir}"; then - rincludedir='${rhome}/include' - fi - - --if test -z ${rsharedir}; then -+if test -z "${rsharedir}"; then - rsharedir='${rhome}/share' - fi - -@@ -2246,7 +2246,7 @@ else +@@ -2272,7 +2272,7 @@ else fi if test "${want_R_shlib}" = yes; then -- LIBR="-L\$(R_HOME)/lib -lR" -+ LIBR="-Wl,-R${prefix}/lib/R/lib -L\$(R_HOME)/lib -lR" +- LIBR="-L\$(R_HOME)/lib\$(R_ARCH) -lR" ++ LIBR="-Wl,-R${prefix}/lib/R/lib\$(R_ARCH) -L\$(R_HOME)/lib\$(R_ARCH) -lR" else LIBR= fi -@@ -6438,7 +6438,7 @@ darwin* | rhapsody*) +@@ -6580,7 +6580,7 @@ darwin* | rhapsody*) lt_cv_deplibs_check_method=pass_all ;; @@ -41,7 +20,7 @@ $NetBSD: patch-ac,v 1.16 2006/02/04 22:25:06 markd Exp $ if echo __ELF__ | $CC -E - | grep __ELF__ > /dev/null; then case $host_cpu in i*86 ) -@@ -8963,7 +8963,7 @@ if test -z "$aix_libpath"; then aix_libp +@@ -9101,7 +9101,7 @@ if test -z "$aix_libpath"; then aix_libp ;; # FreeBSD 3 and greater uses gcc -shared to do shared libraries. @@ -50,7 +29,7 @@ $NetBSD: patch-ac,v 1.16 2006/02/04 22:25:06 markd Exp $ archive_cmds='$CC -shared -o $lib $libobjs $deplibs $compiler_flags' hardcode_libdir_flag_spec='-R$libdir' hardcode_direct=yes -@@ -9541,7 +9541,7 @@ kfreebsd*-gnu) +@@ -9679,7 +9679,7 @@ kfreebsd*-gnu) dynamic_linker='GNU ld.so' ;; @@ -59,7 +38,7 @@ $NetBSD: patch-ac,v 1.16 2006/02/04 22:25:06 markd Exp $ objformat=`test -x /usr/bin/objformat && /usr/bin/objformat || echo aout` version_type=freebsd-$objformat case $version_type in -@@ -11921,7 +11921,7 @@ if test -z "$aix_libpath"; then aix_libp +@@ -12060,7 +12060,7 @@ if test -z "$aix_libpath"; then aix_libp freebsd-elf*) archive_cmds_need_lc_CXX=no ;; @@ -68,7 +47,7 @@ $NetBSD: patch-ac,v 1.16 2006/02/04 22:25:06 markd Exp $ # FreeBSD 3 and later use GNU C++ and GNU ld with standard ELF # conventions ld_shlibs_CXX=yes -@@ -12632,7 +12632,7 @@ echo $ECHO_N "checking for $compiler opt +@@ -12767,7 +12767,7 @@ echo $ECHO_N "checking for $compiler opt ;; esac ;; @@ -77,7 +56,7 @@ $NetBSD: patch-ac,v 1.16 2006/02/04 22:25:06 markd Exp $ # FreeBSD uses GNU C++ ;; hpux9* | hpux10* | hpux11*) -@@ -13243,7 +13243,7 @@ kfreebsd*-gnu) +@@ -13378,7 +13378,7 @@ kfreebsd*-gnu) dynamic_linker='GNU ld.so' ;; @@ -86,7 +65,7 @@ $NetBSD: patch-ac,v 1.16 2006/02/04 22:25:06 markd Exp $ objformat=`test -x /usr/bin/objformat && /usr/bin/objformat || echo aout` version_type=freebsd-$objformat case $version_type in -@@ -15814,7 +15814,7 @@ if test -z "$aix_libpath"; then aix_libp +@@ -15949,7 +15949,7 @@ if test -z "$aix_libpath"; then aix_libp ;; # FreeBSD 3 and greater uses gcc -shared to do shared libraries. @@ -95,7 +74,7 @@ $NetBSD: patch-ac,v 1.16 2006/02/04 22:25:06 markd Exp $ archive_cmds_F77='$CC -shared -o $lib $libobjs $deplibs $compiler_flags' hardcode_libdir_flag_spec_F77='-R$libdir' hardcode_direct_F77=yes -@@ -16392,7 +16392,7 @@ kfreebsd*-gnu) +@@ -16527,7 +16527,7 @@ kfreebsd*-gnu) dynamic_linker='GNU ld.so' ;; @@ -104,7 +83,7 @@ $NetBSD: patch-ac,v 1.16 2006/02/04 22:25:06 markd Exp $ objformat=`test -x /usr/bin/objformat && /usr/bin/objformat || echo aout` version_type=freebsd-$objformat case $version_type in -@@ -18165,7 +18165,7 @@ if test -z "$aix_libpath"; then aix_libp +@@ -18296,7 +18296,7 @@ if test -z "$aix_libpath"; then aix_libp ;; # FreeBSD 3 and greater uses gcc -shared to do shared libraries. @@ -113,7 +92,7 @@ $NetBSD: patch-ac,v 1.16 2006/02/04 22:25:06 markd Exp $ archive_cmds_GCJ='$CC -shared -o $lib $libobjs $deplibs $compiler_flags' hardcode_libdir_flag_spec_GCJ='-R$libdir' hardcode_direct_GCJ=yes -@@ -18743,7 +18743,7 @@ kfreebsd*-gnu) +@@ -18874,7 +18874,7 @@ kfreebsd*-gnu) dynamic_linker='GNU ld.so' ;; @@ -122,7 +101,7 @@ $NetBSD: patch-ac,v 1.16 2006/02/04 22:25:06 markd Exp $ objformat=`test -x /usr/bin/objformat && /usr/bin/objformat || echo aout` version_type=freebsd-$objformat case $version_type in -@@ -21746,13 +21746,13 @@ fi +@@ -21901,13 +21901,13 @@ fi ## only need ncurses if libreadline is not statically linked against it unset ac_cv_lib_readline_rl_callback_read_char @@ -131,7 +110,7 @@ $NetBSD: patch-ac,v 1.16 2006/02/04 22:25:06 markd Exp $ -if test "${ac_cv_lib_ncurses_main+set}" = set; then +echo "$as_me:$LINENO: checking for main in -ltermcap" >&5 +echo $ECHO_N "checking for main in -ltermcap... $ECHO_C" >&6 -+if test "${ac_cv_lib_termcap_main+set}" = set; then ++if test "${ac_cv_lib_termcap+set}" = set; then echo $ECHO_N "(cached) $ECHO_C" >&6 else ac_check_lib_save_LIBS=$LIBS @@ -140,7 +119,7 @@ $NetBSD: patch-ac,v 1.16 2006/02/04 22:25:06 markd Exp $ cat >conftest.$ac_ext <<_ACEOF /* confdefs.h. */ _ACEOF -@@ -21791,35 +21791,35 @@ if { (eval echo "$as_me:$LINENO: \"$ac_l +@@ -21946,35 +21946,35 @@ if { (eval echo "$as_me:$LINENO: \"$ac_l ac_status=$? echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); }; }; then @@ -187,7 +166,7 @@ $NetBSD: patch-ac,v 1.16 2006/02/04 22:25:06 markd Exp $ cat >conftest.$ac_ext <<_ACEOF /* confdefs.h. */ _ACEOF -@@ -21858,35 +21858,35 @@ if { (eval echo "$as_me:$LINENO: \"$ac_l +@@ -22013,35 +22013,35 @@ if { (eval echo "$as_me:$LINENO: \"$ac_l ac_status=$? echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); }; }; then @@ -234,7 +213,7 @@ $NetBSD: patch-ac,v 1.16 2006/02/04 22:25:06 markd Exp $ cat >conftest.$ac_ext <<_ACEOF /* confdefs.h. */ _ACEOF -@@ -21925,25 +21925,25 @@ if { (eval echo "$as_me:$LINENO: \"$ac_l +@@ -22080,25 +22080,25 @@ if { (eval echo "$as_me:$LINENO: \"$ac_l ac_status=$? echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); }; }; then @@ -267,7 +246,7 @@ $NetBSD: patch-ac,v 1.16 2006/02/04 22:25:06 markd Exp $ fi -@@ -27173,6 +27173,7 @@ cat > conftest.c < conftest.c < conftest.c < conftest.c <&6 +@@ -28277,157 +28284,6 @@ echo "${ECHO_T}no" >&6 fi fi @@ -453,7 +432,16 @@ $NetBSD: patch-ac,v 1.16 2006/02/04 22:25:06 markd Exp $ if test "${GXX}" = yes; then ac_safe=_mieee echo "$as_me:$LINENO: checking whether ${CXX-c++} accepts -mieee" >&5 -@@ -29210,7 +29066,7 @@ fi ;; +@@ -28762,7 +28618,7 @@ _ACEOF + if test "${GCC}" = yes; then + ## only Apple build of gcc supports (and needs?) -no-cpp-precomp + ${CC} --version|grep Apple >/dev/null 2>/dev/null +- if test $? == 0; then ++ if test $? = 0; then + separator="" + test -z "${separator}" && separator=" " + if test -z "${R_XTRA_CPPFLAGS}"; then +@@ -29726,7 +29582,7 @@ fi ;; SHLIB_LIBADD="-lcc_dynamic" fi ;; @@ -462,7 +450,7 @@ $NetBSD: patch-ac,v 1.16 2006/02/04 22:25:06 markd Exp $ ## Only sure for FreeBSD 3 and above. main_ldflags="-export-dynamic" shlib_ldflags="-shared" -@@ -29458,6 +29314,7 @@ fi +@@ -29814,6 +29670,7 @@ fi ;; fpicflags= ;; netbsd*) @@ -470,3 +458,21 @@ $NetBSD: patch-ac,v 1.16 2006/02/04 22:25:06 markd Exp $ if ${CPP} - -dM < /dev/null | grep __ELF__ >/dev/null ; then main_ldflags="-export-dynamic" shlib_ldflags="-shared" +@@ -29912,7 +29769,7 @@ fi + : ${FPICFLAGS="${fpicflags}"} + if test -z "${FPICFLAGS}"; then + case "${host_os}" in +- aix*|irix*|mingw*|osf*) ++ aix*|irix*|mingw*|osf*|darwin*) + ;; + *) + { echo "$as_me:$LINENO: WARNING: I could not determine FPICFLAGS." >&5 +@@ -38863,7 +38720,7 @@ cat >>confdefs.h <<\_ACEOF + _ACEOF + + r_save_LIBS=${LIBS} +- if test "$want_utf8_support" == yes ; then ++ if test "$want_utf8_support" = yes ; then + LIBS="${LIBS} ${X_LIBS}" + + diff --git a/math/R/patches/patch-ad b/math/R/patches/patch-ad index bdff1143661..9a6f7eda800 100644 --- a/math/R/patches/patch-ad +++ b/math/R/patches/patch-ad @@ -1,13 +1,13 @@ -$NetBSD: patch-ad,v 1.9 2005/05/02 16:57:19 drochner Exp $ +$NetBSD: patch-ad,v 1.10 2006/06/13 12:28:09 markd Exp $ ---- src/main/Makefile.in.orig 2005-04-18 23:29:59.000000000 +0200 +--- src/main/Makefile.in.orig 2006-04-10 10:19:51.000000000 +1200 +++ src/main/Makefile.in -@@ -144,7 +144,7 @@ R: Makefile +@@ -103,7 +103,7 @@ COMMON_DEPENDENCIES = \ + R_binary = R.bin + R_bin_OBJECTS = Rmain.o @WANT_R_SHLIB_FALSE@$(OBJECTS) + @WANT_R_SHLIB_FALSE@R_bin_LDADD = $(RLIBS) $(EXTRA_LIBS) +-@WANT_R_SHLIB_TRUE@R_bin_LDADD = -L../../lib@R_ARCH@ -lR ++@WANT_R_SHLIB_TRUE@R_bin_LDADD = -L../../lib@R_ARCH@ ${COMPILER_RPATH_FLAG}$(Rexeclibdir) -lR + R_bin_DEPENDENCIES =@WANT_R_SHLIB_FALSE@ $(RLIBS) $(COMMON_DEPENDENCIES) - $(R_binary): $(R_bin_OBJECTS) $(R_bin_DEPENDENCIES) - @WANT_R_SHLIB_FALSE@ $(MAIN_LINK) -o $@ $(R_bin_LDFLAGS) $(R_bin_OBJECTS) $(R_bin_LDADD) $(READLINE_LIBS) $(LIBS) --@WANT_R_SHLIB_TRUE@ $(MAIN_LINK) -o $@ $(R_bin_LDFLAGS) $(R_bin_OBJECTS) -L../../lib -lR -+@WANT_R_SHLIB_TRUE@ $(MAIN_LINK) -o $@ $(R_bin_LDFLAGS) $(R_bin_OBJECTS) -L../../lib ${COMPILER_RPATH_FLAG}$(Rexeclibdir) -lR - - install-bin-local: $(R_binary) - @$(MAKE) rhome="$(abs_top_builddir)" install-bin + libR_la = libR$(DYLIB_EXT) diff --git a/math/R/patches/patch-ae b/math/R/patches/patch-ae deleted file mode 100644 index 2be9e1bc9c4..00000000000 --- a/math/R/patches/patch-ae +++ /dev/null @@ -1,24 +0,0 @@ -$NetBSD: patch-ae,v 1.13 2006/02/26 11:58:25 markd Exp $ - ---- src/nmath/log1p.c.orig 2005-12-06 12:00:17.000000000 +1300 -+++ src/nmath/log1p.c -@@ -98,16 +98,18 @@ double log1p(double x) - -.33410026677731010351377066666666e-30, - +.63533936180236187354180266666666e-31, - }; -- const static double xmin = -1 + sqrt(DBL_EPSILON);/*was sqrt(d1mach(4)); */ - - #ifdef NOMORE_FOR_THREADS - static int nlnrel = 0; -+ static double xmin = 0.0; - -+ if (xmin == 0.0) xmin = -1 + sqrt(DBL_EPSILON);/*was sqrt(d1mach(4)); */ - if (nlnrel == 0) {/* initialize chebychev coefficients */ - nlnrel = chebyshev_init(alnrcs, 43, DBL_EPSILON/20);/*was .1*d1mach(3)*/ - } - #else - # define nlnrel 22 -+ const static double xmin = -0.999999985; - /* 22: for IEEE double precision where DBL_EPSILON = 2.22044604925031e-16 */ - #endif - diff --git a/math/R/patches/patch-at b/math/R/patches/patch-at deleted file mode 100644 index d924dd4b33b..00000000000 --- a/math/R/patches/patch-at +++ /dev/null @@ -1,8 +0,0 @@ -$NetBSD: patch-at,v 1.1 2004/03/30 16:49:32 jwise Exp $ - ---- src/modules/X11/dataentry.c.orig -+++ src/modules/X11/dataentry.c -32c32 -< #define NeedFunctionPrototypes 0 ---- -> /* #define NeedFunctionPrototypes 0 */ -- cgit v1.2.3