ports/130459: Update port: biology/migrate to 3.0.3
KATO Tsuguru
tkato432 at yahoo.com
Mon Jan 12 18:40:13 UTC 2009
>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 at 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 at 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:
More information about the freebsd-ports-bugs
mailing list