Attachment #83841 for bug #119719

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#

PORTNAME=	migrate
PORTVERSION=	2.4.1
CATEGORIES=	biology
MASTER_SITES=	http://popgen.csit.fsu.edu/%SUBDIR%/
MASTER_SITE_SUBDIR=	currentversion oldversions/${PORTVERSION}
DISTNAME=	${PORTNAME}-${PORTVERSION}.src

MAINTAINER=	ports@FreeBSD.org

post-patch:
	@${REINPLACE_CMD} -e \
		's|-lpthread|${PTHREAD_LIBS}|g' ${WRKSRC}/configure
	@${REINPLACE_CMD} -e 's|@CFLAGS@||g ; \
		 s|make -f|$$(MAKE) -f|g' ${WRKSRC}/Makefile.in

do-install:
	${INSTALL_PROGRAM} ${WRKSRC}/migrate-n ${PREFIX}/bin

Lines 1-3 Link Here

(-)biology/migrate/distinfo (-3 / +3 lines)
1	MD5 (migrate-2.3.src.tar.gz) = 12dbf7bd9d69b6ba87a9ba16b68ff7e5	1	MD5 (migrate-2.4.1.src.tar.gz) = cd0e1d2bb551d09b553d833bb90a5df5
2	SHA256 (migrate-2.3.src.tar.gz) = 3407a92b41f23d036a6ef5fd11f77e6d1aa8ee39fa4f61c65b0f71670b8b8f62	2	SHA256 (migrate-2.4.1.src.tar.gz) = 09cb370f6911794d94b721e0f2a1a26c5f3bde5b2e55256f52ad57e9a0c0cdee
3	SIZE (migrate-2.3.src.tar.gz) = 1952466	3	SIZE (migrate-2.4.1.src.tar.gz) = 1950793




--- 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)
 #
 # 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
 
-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)
 
 distrib::
 	$(MAKE) srcdistrib;




%%PORTDOCS%%%%DOCSDIR%%/graphics/packet.gif
%%PORTDOCS%%%%DOCSDIR%%/migrate.html
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/README
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/bayesfile
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/infile.benchmark
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/infile.ep
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/infile.msat
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/infile.seq
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/outfile-bayes
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/outfile-bayes-saved
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/outfile-ml-saved
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/outfile.pdf
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/parmfile
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/parmfile.benchmark
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/parmfile.ep
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/parmfile.msat
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/parmfile.seq
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/parmfile.testbayes
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/parmfile.testml
%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%

Return to bug 119719

Lines 6-14 Link Here

(-)biology/migrate/Makefile (-4 / +3 lines)
6	#	6	#
7		7
8	PORTNAME= migrate	8	PORTNAME= migrate
9	PORTVERSION= 2.3	9	PORTVERSION= 2.4.1
10	CATEGORIES= biology	10	CATEGORIES= biology
11	MASTER_SITES= http://popgen.csit.fsu.edu/currentversion/	11	MASTER_SITES= http://popgen.csit.fsu.edu/%SUBDIR%/
		12	MASTER_SITE_SUBDIR= currentversion oldversions/${PORTVERSION}
12	DISTNAME= ${PORTNAME}-${PORTVERSION}.src	13	DISTNAME= ${PORTNAME}-${PORTVERSION}.src
13		14
14	MAINTAINER= ports@FreeBSD.org	15	MAINTAINER= ports@FreeBSD.org
Lines 42-49 Link Here
42	post-patch:	43	post-patch:
43	@${REINPLACE_CMD} -e \	44	@${REINPLACE_CMD} -e \
44	's\|-lpthread\|${PTHREAD_LIBS}\|g' ${WRKSRC}/configure	45	's\|-lpthread\|${PTHREAD_LIBS}\|g' ${WRKSRC}/configure
45	@${REINPLACE_CMD} -e 's\|@CFLAGS@\|\|g ; \
46	s\|make -f\|$$(MAKE) -f\|g' ${WRKSRC}/Makefile.in
47		46
48	do-install:	47	do-install:
49	${INSTALL_PROGRAM} ${WRKSRC}/migrate-n ${PREFIX}/bin	48	${INSTALL_PROGRAM} ${WRKSRC}/migrate-n ${PREFIX}/bin

Line 0 Link Here

(-)biology/migrate/files/patch-Makefile.in (+40 lines)
	1	--- Makefile.in.orig Thu Jan 10 10:33:23 2008
	2	+++ Makefile.in Sun Jan 13 04:43:42 2008
	3	@@ -56,11 +56,11 @@
	4	# machines or ./configure --enable-altivec on PowerPC architectures, this will then set the option
	5	# correctly
	6	HARDWARECFLAGS = @HARDWARECFLAGS@
	7	-COMMONFLAGS = $(ARCH) -DHIGHBITS -DHAVE_CONFIG_H -DHAVE_MALLOCWRAP $(CFLAGS_MT) $(HARDWARECFLAGS)
	8	+COMMONFLAGS = -DHIGHBITS -DHAVE_CONFIG_H -DHAVE_MALLOCWRAP $(CFLAGS_MT) $(HARDWARECFLAGS)
	9	#
	10	# combine the common flags with the version number and subversion number
	11	COMMONVFLAGS = $(COMMONFLAGS) -DMIGRATESUBVERSION=\"\\\"$(MIGRATESUBVERSION)\\\"\"
	12	-CFLAGS = @CFLAGS@ $(COMMONVFLAGS) -DMIGRATEVERSION=\"\\\"$(MIGRATEVERSION)\\\"\"
	13	+CFLAGS = $(COMMONVFLAGS) -DMIGRATEVERSION=\"\\\"$(MIGRATEVERSION)\\\"\"
	14	# IBM xlc compiler
	15	# CC = xlc
	16	# CFLAGS_XLC = -O3 -Q -qunroll -qalloca -qhot -qipa -qthreaded
	17	@@ -151,8 +151,8 @@
	18	@echo "----------------------------------------------------"
	19	$(MAKE) all
	20
	21	-all:: haru
	22	- $(MAKE) $(NAME) "CFLAGS = $(CFLAGS) $(PRETTYCFLAGS)" "LIBS = $(PDFLIB) $(LIBS)" "LDFLAGS = $(LDFLAGS) -fexceptions"
	23	+all::
	24	+ $(MAKE) $(NAME) "CFLAGS = $(CFLAGS)" "LIBS = $(LIBS)" "LDFLAGS = $(LDFLAGS) -fexceptions"
	25
	26	debug::
	27	$(MAKE) $(NAME) "CFLAGS = $(DEBUGCFLAGS)"
	28	@@ -274,10 +274,10 @@
	29	-/bin/chmod +x $(CONFIGUREEXEC)
	30
	31	haru::
	32	- (cd ./haru ; make -f makefile.osx "CC=$(CC)" "CPP=$(CC)" "ARCH=$(ARCH)")
	33	+ (cd ./haru ; $(MAKE) -f makefile.osx "CC=$(CC)" "CPP=$(CC)" "ARCH=")
	34
	35	haru-clean::
	36	- (cd ./haru ; make -f makefile.osx clean)
	37	+ (cd ./haru ; $(MAKE) -f makefile.osx clean)
	38
	39	distrib::
	40	$(MAKE) srcdistrib;

Lines 9-28 Link Here

(-)biology/migrate/pkg-plist (-8 lines)
9	%%PORTDOCS%%%%DOCSDIR%%/graphics/packet.gif	9	%%PORTDOCS%%%%DOCSDIR%%/graphics/packet.gif
10	%%PORTDOCS%%%%DOCSDIR%%/migrate.html	10	%%PORTDOCS%%%%DOCSDIR%%/migrate.html
11	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/README	11	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/README
12	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/bayesfile
13	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/infile.benchmark
14	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/infile.ep	12	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/infile.ep
15	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/infile.msat	13	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/infile.msat
16	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/infile.seq	14	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/infile.seq
17	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/outfile-bayes
18	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/outfile-bayes-saved	15	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/outfile-bayes-saved
19	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/outfile-ml-saved	16	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/outfile-ml-saved
20	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/outfile.pdf
21	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/parmfile	17	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/parmfile
22	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/parmfile.benchmark
23	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/parmfile.ep
24	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/parmfile.msat
25	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/parmfile.seq
26	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/parmfile.testbayes	18	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/parmfile.testbayes
27	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/parmfile.testml	19	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/parmfile.testml
28	%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%	20	%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%