Date: Tue, 13 Jan 2009 03:00:39 +0900 From: KATO Tsuguru <tkato432@yahoo.com> To: FreeBSD-gnats-submit@FreeBSD.org Subject: ports/130459: Update port: biology/migrate to 3.0.3 Message-ID: <20090113030039.3b8063f9.tkato432@yahoo.com> Resent-Message-ID: <200901121840.n0CIe4XO036772@freefall.freebsd.org>
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>Number: 130459 >Category: ports >Synopsis: Update port: biology/migrate to 3.0.3 >Confidential: no >Severity: non-critical >Priority: low >Responsible: freebsd-ports-bugs >State: open >Quarter: >Keywords: >Date-Required: >Class: change-request >Submitter-Id: current-users >Arrival-Date: Mon Jan 12 18:40:04 UTC 2009 >Closed-Date: >Last-Modified: >Originator: KATO Tsuguru >Release: FreeBSD 7.1-RELEASE-p1 i386 >Organization: >Environment: >Description: - Update to version 3.0.3 Remove file: files/patch-src-pretty-win32.cpp >How-To-Repeat: >Fix: 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%% >Release-Note: >Audit-Trail: >Unformatted:
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