Index: head/biology/migrate/Makefile =================================================================== --- head/biology/migrate/Makefile (revision 254017) +++ head/biology/migrate/Makefile (revision 254018) @@ -1,67 +1,67 @@ # New ports collection makefile for: migrate # Date created: 6 August 2001 # Whom: Johann Visagie # # $FreeBSD$ # PORTNAME= migrate -PORTVERSION= 3.1.3 +PORTVERSION= 3.1.4 CATEGORIES= biology MASTER_SITES= http://people.sc.fsu.edu/~beerli/popgen/currentversion/ DISTNAME= ${PORTNAME}-${PORTVERSION}.src MAINTAINER= glen.j.barber@gmail.com COMMENT= A program to estimate population sizes and migration rates WRKSRC= ${WRKDIR}/${PORTNAME}-${PORTVERSION}/src GNU_CONFIGURE= yes CONFIGURE_ENV= ac_cv_prog_GMAKE="${MAKE}" MAKE_ARGS= PRETTYCFLAGS="${CFLAGS} -DNOJPEG -DNOZLIB -DNOPNG -Iharu -DPRETTY" MAN1= ${PORTNAME}.1 MLINKS= ${PORTNAME}.1 ${PORTNAME}-n.1 PORTDOCS= * PORTEXAMPLES= * PLIST_FILES= bin/${PORTNAME} bin/${PORTNAME}-n .include NOT_FOR_ARCHS= alpha ONLY_FOR_ARCHS_REASON= Does not compile .if defined(WITH_THREAD_PRETTY) ALL_TARGET= thread-pretty .elif defined(WITH_PRETTY) ALL_TARGET= pretty .elif defined(WITH_THREAD) ALL_TARGET= thread .else ALL_TARGET= all .endif post-patch: @${REINPLACE_CMD} -e 's|="-O "|="$$CFLAGS"|g ; \ s|-lpthread|${PTHREAD_LIBS}|g' ${WRKSRC}/configure @${REINPLACE_CMD} -e '/PRETTY$$/d' ${WRKSRC}/definitions.h @${REINPLACE_CMD} -e 's|-O3||g' ${WRKSRC}/haru/makefile.gcc do-install: ${INSTALL_PROGRAM} ${WRKSRC}/${PORTNAME}-n ${PREFIX}/bin ${LN} -sf ${PORTNAME}-n ${PREFIX}/bin/${PORTNAME} ${INSTALL_MAN} ${WRKSRC}/${PORTNAME}.1 ${MAN1PREFIX}/man/man1 .if !defined(NOPORTDOCS) @${MKDIR} ${DOCSDIR} .for i in HISTORY HOWTO-PARALLEL README ${PORTNAME}.html ${INSTALL_DATA} ${WRKSRC}/../${i} ${DOCSDIR} .endfor @${MKDIR} ${DOCSDIR}/graphics ${INSTALL_DATA} ${WRKSRC}/../graphics/* ${DOCSDIR}/graphics .endif .if !defined(NOPORTEXAMPLES) @${MKDIR} ${EXAMPLESDIR} ${INSTALL_DATA} ${WRKSRC}/../example/[A-Za-z]* ${EXAMPLESDIR} .endif .include Property changes on: head/biology/migrate/Makefile ___________________________________________________________________ Modified: cvs2svn:cvs-rev ## -1 +1 ## -1.21 \ No newline at end of property +1.22 \ No newline at end of property Index: head/biology/migrate/distinfo =================================================================== --- head/biology/migrate/distinfo (revision 254017) +++ head/biology/migrate/distinfo (revision 254018) @@ -1,3 +1,3 @@ -MD5 (migrate-3.1.3.src.tar.gz) = 20b07feaeb3624769d6befec640a30e2 -SHA256 (migrate-3.1.3.src.tar.gz) = 176f516c8dec12b5370230e91dbc454b2ab6740656fdbb1a2475a5377fee630d -SIZE (migrate-3.1.3.src.tar.gz) = 2021127 +MD5 (migrate-3.1.4.src.tar.gz) = a1ffa3baa8a78b17b2dcb387de7801ee +SHA256 (migrate-3.1.4.src.tar.gz) = f09d35f544865f1cde3677b9b347b8a5de9e907f81d4f509e8f15c2fd28ea110 +SIZE (migrate-3.1.4.src.tar.gz) = 2227530 Property changes on: head/biology/migrate/distinfo ___________________________________________________________________ Modified: cvs2svn:cvs-rev ## -1 +1 ## -1.16 \ No newline at end of property +1.17 \ No newline at end of property Index: head/biology/migrate/files/patch-Makefile.in =================================================================== --- head/biology/migrate/files/patch-Makefile.in (revision 254017) +++ head/biology/migrate/files/patch-Makefile.in (revision 254018) @@ -1,66 +1,73 @@ ---- Makefile.in.orig 2008-12-06 03:19:25.000000000 +0900 -+++ Makefile.in 2008-12-09 15:17:10.000000000 +0900 -@@ -79,7 +79,7 @@ +--- Makefile.in.orig 2010-05-01 16:14:26.000000000 -0400 ++++ Makefile.in 2010-05-08 16:08:49.000000000 -0400 +@@ -80,7 +80,7 @@ # -DNEXUSTREE print nexus tree instead of plain newick trees # -UEP calculates unique event polymorphism - NEWSTUFF = -DNEWVERSION -DBFDEBUG + NEWSTUFF = -COMMONFLAGS = $(ARCH) $(MACOSVERSION) $(NEWSTUFF) -DHIGHBITS -DHAVE_CONFIG_H -DHAVE_MALLOCWRAP $(CFLAGS_MT) $(HARDWARECFLAGS) +COMMONFLAGS = $(MACOSVERSION) $(NEWSTUFF) -DHIGHBITS -DHAVE_CONFIG_H -DHAVE_MALLOCWRAP $(CFLAGS_MT) $(HARDWARECFLAGS) # # combine the common flags with the version number and subversion number COMMONVFLAGS = $(COMMONFLAGS) -DMIGRATESUBVERSION=\"\\\"$(MIGRATESUBVERSION)\\\"\" -@@ -195,22 +195,21 @@ - @echo ' make install (installs the executables and man page)' +@@ -202,22 +202,21 @@ + @echo ' make install (installs the executables and man page [out of date])' @echo ' [there are other targets for debugging purposes, check the Makefile]' -all:: haru - $(MAKE) $(NAME) "CFLAGS = $(CFLAGS) $(PRETTYCFLAGS)" "LIBS = $(PDFLIB) $(LIBS)" "LDFLAGS = $(LDFLAGS) $(EXCEPTIONS)" +all:: + $(MAKE) $(NAME) "CFLAGS = $(CFLAGS)" "LIBS = $(LIBS)" "LDFLAGS = $(LDFLAGS) $(EXCEPTIONS)" pretty:: haru $(MAKE) $(NAME) "CFLAGS = $(CFLAGS) $(PRETTYCFLAGS)" "LIBS = $(PDFLIB) $(LIBS)" "LDFLAGS = $(LDFLAGS) $(EXCEPTIONS)" -thread:: haru +thread-pretty:: haru $(MAKE) $(NAME) "CFLAGS = $(CFLAGS) $(PRETTYCFLAGS) $(THREADCFLAGS)" "LIBS = $(OTHERLIBS) $(PDFLIB) $(LIBS)" "LDFLAGS = $(LDFLAGS) $(EXCEPTIONS)" debug:: haru $(MAKE) $(NAME) "CFLAGS = $(DEBUGCFLAGS) $(PRETTYCFLAGS)" "LIBS = $(PDFLIB) $(LIBS)" "LDFLAGS =$(LDFLAGS) $(EXCEPTIONS)" thread:: - $(MAKE) $(NAME) "CFLAGS = $(CFLAGS) $(THREADCFLAGS)" "LIBS = $(OTHERLIBS) $(LIBS)";\ - strip $(NAME) + $(MAKE) $(NAME) "CFLAGS = $(CFLAGS) $(THREADCFLAGS)" "LIBS = $(OTHERLIBS) $(LIBS)" mpis-thread:: haru $(MAKE) $(NAME) "CC=$(MPICC)" "CFLAGS = $(CFLAGS) $(PRETTYCFLAGS) $(THREADCFLAGS) -DMPI -DSLOWNET -DNEWREPLICANT -DMPIREPLICANT" "LIBS = $(OTHERLIBS) $(PDFLIB) $(LIBS)" -@@ -398,22 +397,22 @@ +@@ -405,22 +404,22 @@ else echo Must define $@; exit 1; fi $(NAME): $(PRODUCT_DEPENDS) - $(CC) $(CFLAGS) $(LDFLAGS) -o $@ $(OFILES) $(LIBS) ; + $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ $(OFILES) $(LIBS) ; $(WINNAME): $(PRODUCT_DEPENDS) - $(CC) $(CFLAGS) $(LDFLAGS) -o $@ $(OFILES) $(OTHERLIBS) $(WINLIBS) ; + $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ $(OFILES) $(OTHERLIBS) $(WINLIBS) ; $(EFENCENAME): $(PRODUCT_DEPENDS) - $(CC) $(CFLAGS) $(LDFLAGS) -o $@ $(OFILES) $(EFENCELIBS) $(LIBS) ; + $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ $(OFILES) $(EFENCELIBS) $(LIBS) ; $(MEMDEBUGNAME): $(PRODUCT_DEPENDS) - $(CC) $(CFLAGS) $(LDFLAGS) -o $@ $(OFILES) $(MEMDEBUGLIBS) $(LIBS) ; + $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ $(OFILES) $(MEMDEBUGLIBS) $(LIBS) ; $(DMALLOCNAME): $(PRODUCT_DEPENDS) - $(CC) $(CFLAGS) $(LDFLAGS) -o $@ $(OFILES) $(DMALLOCLIBS) $(LIBS) ; + $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ $(OFILES) $(DMALLOCLIBS) $(LIBS) ; #---------------------------------------------------------------- +@@ -473,4 +472,4 @@ + #---------------------------------------------------------------- + # BEAGLE + beagle: +- $(MAKE) $(NAME) "CFLAGS = $(DEBUGCFLAGS) $(BEAGLEFLAGS) $(PRETTYCFLAGS)" "LIBS = $(PDFLIB) $(LIBS)" "LDFLAGS =$(LDFLAGS) $(EXCEPTIONS) `pkg-config /Users/beerli/src/beagle-lib/hmsbeagle-1.0.pc --cflags --libs` -framework OpenCL" +\ No newline at end of file ++ $(MAKE) $(NAME) "CFLAGS = $(DEBUGCFLAGS) $(BEAGLEFLAGS) $(PRETTYCFLAGS)" "LIBS = $(PDFLIB) $(LIBS)" "LDFLAGS =$(LDFLAGS) $(EXCEPTIONS) `pkg-config /Users/beerli/src/beagle-lib/hmsbeagle-1.0.pc --cflags --libs` -framework OpenCL" Property changes on: head/biology/migrate/files/patch-Makefile.in ___________________________________________________________________ Modified: cvs2svn:cvs-rev ## -1 +1 ## -1.5 \ No newline at end of property +1.6 \ No newline at end of property