Attachment 92746 Details for Bug 130459 – file.diff

[patch] file.diff

file.diff (text/plain), 11.30 KB, created by tkato432 on 2009-01-12 18:40:04 UTC

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Creator: tkato432

Created: 2009-01-12 18:40:04 UTC

Size: 11.30 KB

patch

obsolete

>diff -urN /usr/ports/biology/migrate/Makefile biology/migrate/Makefile
>--- /usr/ports/biology/migrate/Makefile	2008-02-28 00:38:21.000000000 +0900
>+++ biology/migrate/Makefile	2008-12-10 00:54:08.000000000 +0900
>@@ -6,11 +6,9 @@
> #
> 
> PORTNAME=	migrate
>-PORTVERSION=	2.4.3
>-PORTREVISION=	1
>+PORTVERSION=	3.0.3
> CATEGORIES=	biology
>-MASTER_SITES=	http://popgen.csit.fsu.edu/%SUBDIR%/
>-MASTER_SITE_SUBDIR=	currentversion oldversions/${PORTVERSION}
>+MASTER_SITES=	http://people.scs.fsu.edu/~beerli/popgen/currentversion/
> DISTNAME=	${PORTNAME}-${PORTVERSION}.src
> 
> MAINTAINER=	ports@FreeBSD.org
>@@ -18,10 +16,9 @@
> 
> WRKSRC=		${WRKDIR}/${PORTNAME}-${PORTVERSION}/src
> 
>-USE_GNOME=	gnometarget
> GNU_CONFIGURE=	yes
>-MAKE_ARGS=	HARDWARECFLAGS="${CFLAGS}" \
>-		MYCPPFLAGS="${CFLAGS} -DNOJPEG -DNOPNG -DNOZLIB"
>+CONFIGURE_ENV=	ac_cv_prog_GMAKE="${MAKE}"
>+MAKE_ARGS=	PRETTYCFLAGS="${CFLAGS} -DNOJPEG -DNOZLIB -DNOPNG -Iharu -DPRETTY"
> 
> MAN1=		migrate.1
> MLINKS=		migrate.1 migrate-n.1
>@@ -42,8 +39,8 @@
> .endif
> 
> post-patch:
>-	@${REINPLACE_CMD} -e \
>-		's|-lpthread|${PTHREAD_LIBS}|g' ${WRKSRC}/configure
>+	@${REINPLACE_CMD} -e 's|="-O "|="$$CFLAGS"|g ; \
>+		 s|-lpthread|${PTHREAD_LIBS}|g' ${WRKSRC}/configure
> 
> do-install:
> 	${INSTALL_PROGRAM} ${WRKSRC}/migrate-n ${PREFIX}/bin
>@@ -59,7 +56,7 @@
> .endif
> .if !defined(NOPORTEXAMPLES)
> 	@${MKDIR} ${EXAMPLESDIR}
>-	${INSTALL_DATA} ${WRKSRC}/../example/* ${EXAMPLESDIR}
>+	${INSTALL_DATA} ${WRKSRC}/../example/[A-Za-z]* ${EXAMPLESDIR}
> .endif
> 
> .include <bsd.port.post.mk>
>diff -urN /usr/ports/biology/migrate/distinfo biology/migrate/distinfo
>--- /usr/ports/biology/migrate/distinfo	2008-02-28 00:38:21.000000000 +0900
>+++ biology/migrate/distinfo	2008-12-09 13:45:56.000000000 +0900
>@@ -1,3 +1,3 @@
>-MD5 (migrate-2.4.3.src.tar.gz) = 3cf0e169191826c657fc1fbcedecb32d
>-SHA256 (migrate-2.4.3.src.tar.gz) = 6732fc8c97373e6f08b9e43a78902a9a313fc37841e58752dbd9c7a924a708d4
>-SIZE (migrate-2.4.3.src.tar.gz) = 1958543
>+MD5 (migrate-3.0.3.src.tar.gz) = ea4a67a6320300a4df554f74a272581e
>+SHA256 (migrate-3.0.3.src.tar.gz) = d00c1999e7af055aca9f30565dfb610b03e42c2dcc60838c9c4367be87d0edd1
>+SIZE (migrate-3.0.3.src.tar.gz) = 5660159
>diff -urN /usr/ports/biology/migrate/files/patch-Makefile.in biology/migrate/files/patch-Makefile.in
>--- /usr/ports/biology/migrate/files/patch-Makefile.in	2008-01-21 06:56:24.000000000 +0900
>+++ biology/migrate/files/patch-Makefile.in	2008-12-09 15:17:19.000000000 +0900
>@@ -1,40 +1,66 @@
>---- Makefile.in.orig	Thu Jan 10 10:33:23 2008
>-+++ Makefile.in	Sun Jan 13 04:43:42 2008
>-@@ -56,11 +56,11 @@
>- # machines or ./configure --enable-altivec on PowerPC architectures, this will then set the option 
>- # correctly
>- HARDWARECFLAGS    = @HARDWARECFLAGS@
>--COMMONFLAGS       = $(ARCH) -DHIGHBITS -DHAVE_CONFIG_H -DHAVE_MALLOCWRAP $(CFLAGS_MT) $(HARDWARECFLAGS)
>-+COMMONFLAGS       = -DHIGHBITS -DHAVE_CONFIG_H -DHAVE_MALLOCWRAP $(CFLAGS_MT) $(HARDWARECFLAGS)
>+--- 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 @@
>+ # -DNEXUSTREE print nexus tree instead of plain newick trees
>+ # -UEP calculates unique event polymorphism
>+ NEWSTUFF          = -DNEWVERSION -DBFDEBUG
>+-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)\\\"\" 
>--CFLAGS            = @CFLAGS@ $(COMMONVFLAGS) -DMIGRATEVERSION=\"\\\"$(MIGRATEVERSION)\\\"\" 
>-+CFLAGS            = $(COMMONVFLAGS) -DMIGRATEVERSION=\"\\\"$(MIGRATEVERSION)\\\"\" 
>- # IBM xlc compiler
>- # CC              = xlc
>- # CFLAGS_XLC      = -O3 -Q -qunroll -qalloca -qhot -qipa -qthreaded 
>-@@ -151,8 +151,8 @@
>- 	@echo "----------------------------------------------------"
>- 	$(MAKE) all
>+@@ -195,22 +195,21 @@
>+ 	@echo '  make install (installs the executables and man page)'
>+ 	@echo '  [there are other targets for debugging purposes, check the Makefile]'
>  
> -all::   haru
>--	$(MAKE) $(NAME) "CFLAGS = $(CFLAGS)  $(PRETTYCFLAGS)" "LIBS = $(PDFLIB) $(LIBS)" "LDFLAGS = $(LDFLAGS) -fexceptions" 
>-+all::   
>-+	$(MAKE) $(NAME) "CFLAGS = $(CFLAGS)" "LIBS = $(LIBS)" "LDFLAGS = $(LDFLAGS) -fexceptions" 
>- 
>- debug::   
>- 	$(MAKE) $(NAME) "CFLAGS = $(DEBUGCFLAGS)"
>-@@ -274,10 +274,10 @@
>- 	-/bin/chmod +x $(CONFIGUREEXEC) 	
>- 
>- haru::
>--	(cd ./haru ; make -f makefile.osx "CC=$(CC)" "CPP=$(CC)" "ARCH=$(ARCH)")
>-+	(cd ./haru ; $(MAKE) -f makefile.osx "CC=$(CC)" "CPP=$(CC)" "ARCH=")
>- 
>- haru-clean::
>--	(cd ./haru ; make -f makefile.osx clean)
>-+	(cd ./haru ; $(MAKE) -f makefile.osx clean)
>+-	$(MAKE) $(NAME) "CFLAGS = $(CFLAGS)  $(PRETTYCFLAGS)" "LIBS = $(PDFLIB) $(LIBS)" "LDFLAGS = $(LDFLAGS) $(EXCEPTIONS)" 
>++all::
>++	$(MAKE) $(NAME) "CFLAGS = $(CFLAGS)" "LIBS = $(LIBS)" "LDFLAGS = $(LDFLAGS) $(EXCEPTIONS)" 
>  
>- distrib::
>- 	$(MAKE) srcdistrib;
>+ 
>+ 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 @@
>+ 	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) ;
>+ 
>+ 
>+ #----------------------------------------------------------------
>diff -urN /usr/ports/biology/migrate/files/patch-src-pretty-win32.cpp biology/migrate/files/patch-src-pretty-win32.cpp
>--- /usr/ports/biology/migrate/files/patch-src-pretty-win32.cpp	2008-02-27 16:34:21.000000000 +0900
>+++ biology/migrate/files/patch-src-pretty-win32.cpp	1970-01-01 09:00:00.000000000 +0900
>@@ -1,12 +0,0 @@
>---- pretty-win32.cpp.orgi	2008-02-27 08:15:26.000000000 +0100
>-+++ pretty-win32.cpp	2008-02-27 08:16:07.000000000 +0100
>-@@ -13,9 +13,3 @@
>-   _set_new_handler(throw_new_handler);
>- }
>- #endif
>--
>--int dummy_function(int do_nothing)
>--{
>--  print("Some computer fail to compile MIGRATE with empty files\n");
>--  return 0;
>--}
>diff -urN /usr/ports/biology/migrate/pkg-descr biology/migrate/pkg-descr
>--- /usr/ports/biology/migrate/pkg-descr	2007-09-04 00:08:16.000000000 +0900
>+++ biology/migrate/pkg-descr	2008-12-09 13:52:06.000000000 +0900
>@@ -4,4 +4,4 @@
> can use sequence data, microsatellite data or electrophoretic data.
> 
> Author: Peter Beerli <beerli@scs.fsu.edu>
>-WWW:    http://popgen.scs.fsu.edu/Migrate-n.html
>+WWW:    http://popgen.csit.fsu.edu/Migrate-n.html
>diff -urN /usr/ports/biology/migrate/pkg-plist biology/migrate/pkg-plist
>--- /usr/ports/biology/migrate/pkg-plist	2008-01-21 17:12:55.000000000 +0900
>+++ biology/migrate/pkg-plist	2008-12-10 00:52:35.000000000 +0900
>@@ -9,14 +9,68 @@
> %%PORTDOCS%%%%DOCSDIR%%/graphics/packet.gif
> %%PORTDOCS%%%%DOCSDIR%%/migrate.html
> %%PORTEXAMPLES%%%%EXAMPLESDIR%%/README
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/aicfile
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/bayesallfile
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/bayesallfile.dated
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/bayesfile
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/bayesfile.dated
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/datefile.dated
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/infile
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/infile.benchmark
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/infile.dated
> %%PORTEXAMPLES%%%%EXAMPLESDIR%%/infile.ep
> %%PORTEXAMPLES%%%%EXAMPLESDIR%%/infile.msat
> %%PORTEXAMPLES%%%%EXAMPLESDIR%%/infile.seq
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mighistfile.dated
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/outfile
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/outfile-1
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/outfile-2
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/outfile-bayes
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/outfile-bayes-brown
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/outfile-bayes-multi0.5
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/outfile-bayes-multi0.5-0.5
> %%PORTEXAMPLES%%%%EXAMPLESDIR%%/outfile-bayes-saved
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/outfile-bayes-step
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/outfile-dated.pdf
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/outfile-ml
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/outfile-ml-3
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/outfile-ml-3.pdf
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/outfile-ml-paral2
> %%PORTEXAMPLES%%%%EXAMPLESDIR%%/outfile-ml-saved
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/outfile-ml-single
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/outfile-ml-watkins-0.5-0.5
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/outfile-ml.pdf
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/outfile.benchmark
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/outfile.benchmark_double
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/outfile.benchmark_float
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/outfile.dated
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/outfile.pdf
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/outifle-ml-3
> %%PORTEXAMPLES%%%%EXAMPLESDIR%%/parmfile
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/parmfile-testbayes.txt
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/parmfile.benchmark
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/parmfile.dated
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/parmfile.ep
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/parmfile.gugus
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/parmfile.msat
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/parmfile.seq
> %%PORTEXAMPLES%%%%EXAMPLESDIR%%/parmfile.testbayes
> %%PORTEXAMPLES%%%%EXAMPLESDIR%%/parmfile.testml
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/parmfile.testml-save
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/pretty
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/skylinefile.dated
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sumfile
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sumfile-1
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sumfile-2
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sumfile-3
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sumfile-mpi-ml
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sumfile-single
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sumfile1
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/treefile
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/treefile-1
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/treefile-2
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/treefile-3
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/treefile.dated
> %%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%
> %%PORTDOCS%%@dirrm %%DOCSDIR%%/graphics
> %%PORTDOCS%%@dirrm %%DOCSDIR%%

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Attachments on bug 130459: 92746