Hi, This diff fixes R's problem with pthread undefined symbols, as reported here:
http://marc.info/?l=openbsd-ports&m=132196919327917 and here: http://marc.info/?l=openbsd-ports&m=132187529729922 It also fixes libpthread linkage (-lpthread -> -pthread) and an incorrect usage of the "--export-dynamic" linker flag (it's '-Wl,--export-dynamic', not '-Wl,-export-dynamic'. Tested on sparc64 and amd64. Ok? ciao, David Index: Makefile =================================================================== RCS file: /cvs/ports/math/R/Makefile,v retrieving revision 1.44 diff -u -p -r1.44 Makefile --- Makefile 3 Nov 2011 20:28:09 -0000 1.44 +++ Makefile 19 Jan 2012 16:10:45 -0000 @@ -4,7 +4,7 @@ SHARED_ONLY= Yes COMMENT= clone of S, a powerful math/statistics/graphics language DISTNAME= R-2.8.1 -REVISION= 6 +REVISION= 7 SHARED_LIBS= Rlapack 29.0 \ Rblas 29.0 @@ -20,8 +20,8 @@ PERMIT_DISTFILES_FTP= Yes WANTLIB= GL ICE SM X11 Xext Xmu Xrender Xss Xt \ bz2 c cairo expat fontconfig freetype glib-2.0 \ gmodule-2.0 gobject-2.0 gthread-2.0 jpeg 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 \ + pangocairo-1.0 pangoft2-1.0 pcre pixman-1 png pthread \ + pthread-stubs readline tiff xcb xcb-render xcb-shm z \ ${MODFORTRAN_WANTLIB} ${MODTK_WANTLIB} MASTER_SITES= http://cran.r-project.org/src/base/R-2/ \ Index: patches/patch-configure =================================================================== RCS file: /cvs/ports/math/R/patches/patch-configure,v retrieving revision 1.10 diff -u -p -r1.10 patch-configure --- patches/patch-configure 11 Mar 2009 08:21:33 -0000 1.10 +++ patches/patch-configure 19 Jan 2012 16:10:45 -0000 @@ -1,6 +1,69 @@ $OpenBSD: patch-configure,v 1.10 2009/03/11 08:21:33 sthen Exp $ ---- configure.orig Thu Dec 18 14:03:48 2008 -+++ configure Wed Mar 11 00:21:36 2009 +--- configure.orig Thu Dec 18 15:03:48 2008 ++++ configure Thu Jan 19 14:38:44 2012 +@@ -31142,7 +31142,7 @@ echo "$as_me: WARNING: Use of flat namespace is reques + openbsd*) + ## looks like ${wl} is not defined here. Perhaps in libtool code? + if test -z "`echo __ELF__ | $CC -E - | grep __ELF__`"; then +- main_ldflags="${wl}-export-dynamic" ++ main_ldflags="${wl}--export-dynamic" + shlib_ldflags="-shared -fPIC" + fi + ;; +@@ -52736,13 +52736,13 @@ rm -f core conftest.err conftest.$ac_objext conftest_i + if test -n "$gl_have_pthread"; then + # The program links fine without libpthread. But it may actually + # need to link with libpthread in order to create multiple threads. +- { echo "$as_me:$LINENO: checking for pthread_kill in -lpthread" >&5 +-echo $ECHO_N "checking for pthread_kill in -lpthread... $ECHO_C" >&6; } ++ { echo "$as_me:$LINENO: checking for pthread_kill in -pthread" >&5 ++echo $ECHO_N "checking for pthread_kill in -pthread... $ECHO_C" >&6; } + if test "${ac_cv_lib_pthread_pthread_kill+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 + else + ac_check_lib_save_LIBS=$LIBS +-LIBS="-lpthread $LIBS" ++LIBS="-pthread $LIBS" + cat >conftest.$ac_ext <<_ACEOF + /* confdefs.h. */ + _ACEOF +@@ -52806,7 +52806,7 @@ fi + { echo "$as_me:$LINENO: result: $ac_cv_lib_pthread_pthread_kill" >&5 + echo "${ECHO_T}$ac_cv_lib_pthread_pthread_kill" >&6; } + if test $ac_cv_lib_pthread_pthread_kill = yes; then +- LIBMULTITHREAD=-lpthread LTLIBMULTITHREAD=-lpthread ++ LIBMULTITHREAD=-pthread LTLIBMULTITHREAD=-pthread + # On Solaris and HP-UX, most pthread functions exist also in libc. + # Therefore pthread_in_use() needs to actually try to create a + # thread: pthread_create from libc will fail, whereas +@@ -52824,13 +52824,13 @@ fi + + else + # Some library is needed. Try libpthread and libc_r. +- { echo "$as_me:$LINENO: checking for pthread_kill in -lpthread" >&5 +-echo $ECHO_N "checking for pthread_kill in -lpthread... $ECHO_C" >&6; } ++ { echo "$as_me:$LINENO: checking for pthread_kill in -pthread" >&5 ++echo $ECHO_N "checking for pthread_kill in -pthread... $ECHO_C" >&6; } + if test "${ac_cv_lib_pthread_pthread_kill+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 + else + ac_check_lib_save_LIBS=$LIBS +-LIBS="-lpthread $LIBS" ++LIBS="-pthread $LIBS" + cat >conftest.$ac_ext <<_ACEOF + /* confdefs.h. */ + _ACEOF +@@ -52895,8 +52895,8 @@ fi + echo "${ECHO_T}$ac_cv_lib_pthread_pthread_kill" >&6; } + if test $ac_cv_lib_pthread_pthread_kill = yes; then + gl_have_pthread=yes +- LIBTHREAD=-lpthread LTLIBTHREAD=-lpthread +- LIBMULTITHREAD=-lpthread LTLIBMULTITHREAD=-lpthread ++ LIBTHREAD=-pthread LTLIBTHREAD=-pthread ++ LIBMULTITHREAD=-pthread LTLIBMULTITHREAD=-pthread + fi + + if test -z "$gl_have_pthread"; then @@ -60283,7 +60283,7 @@ LIBTHREAD!$LIBTHREAD$ac_delim LTLIBTHREAD!$LTLIBTHREAD$ac_delim LIBMULTITHREAD!$LIBMULTITHREAD$ac_delim Index: patches/patch-src_main_Makefile_in =================================================================== RCS file: patches/patch-src_main_Makefile_in diff -N patches/patch-src_main_Makefile_in --- /dev/null 1 Jan 1970 00:00:00 -0000 +++ patches/patch-src_main_Makefile_in 19 Jan 2012 16:10:45 -0000 @@ -0,0 +1,15 @@ +$OpenBSD$ + +Fix runtime errors due to libpthread undefined symbols + +--- src/main/Makefile.in.orig Thu Jan 19 12:12:26 2012 ++++ src/main/Makefile.in Thu Jan 19 12:13:35 2012 +@@ -91,7 +91,7 @@ MAIN_LIBS = ../unix/libunix.a ../appl/libappl.a ../nma + EXTRA_STATIC_LIBS = $(R_ZLIBS) $(R_BZLIBS) $(R_PCRE) $(R_XDR)$(R_LIBINTL) + STATIC_LIBS = $(MAIN_LIBS) $(EXTRA_STATIC_LIBS) + +-EXTRA_LIBS = $(BLAS_LIBS) $(FLIBS) $(R_XTRA_LIBS) @LIBINTL@ $(READLINE_LIBS) $(LIBS) ++EXTRA_LIBS = $(BLAS_LIBS) $(FLIBS) $(R_XTRA_LIBS) @LIBINTL@ $(READLINE_LIBS) $(LIBS) -pthread + + R_binary = R.bin + R_bin_OBJECTS = Rmain.o
