Attachment #103508 for bug #143437

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Lines 6-14 Link Here

(-)biology/migrate/Makefile (-8 / +13 lines)
6	#	6	#
7		7
8	PORTNAME= migrate	8	PORTNAME= migrate
9	PORTVERSION= 3.0.3	9	PORTVERSION= 3.1.1
10	CATEGORIES= biology	10	CATEGORIES= biology
11	MASTER_SITES= http://people.scs.fsu.edu/~beerli/popgen/currentversion/	11	MASTER_SITES= http://people.sc.fsu.edu/~beerli/popgen/currentversion/
12	DISTNAME= ${PORTNAME}-${PORTVERSION}.src	12	DISTNAME= ${PORTNAME}-${PORTVERSION}.src
13		13
14	MAINTAINER= ports@FreeBSD.org	14	MAINTAINER= ports@FreeBSD.org
Lines 20-27 Link Here
20	CONFIGURE_ENV= ac_cv_prog_GMAKE="${MAKE}"	20	CONFIGURE_ENV= ac_cv_prog_GMAKE="${MAKE}"
21	MAKE_ARGS= PRETTYCFLAGS="${CFLAGS} -DNOJPEG -DNOZLIB -DNOPNG -Iharu -DPRETTY"	21	MAKE_ARGS= PRETTYCFLAGS="${CFLAGS} -DNOJPEG -DNOZLIB -DNOPNG -Iharu -DPRETTY"
22		22
23	MAN1= migrate.1	23	MAN1= ${PORTNAME}.1
24	MLINKS= migrate.1 migrate-n.1	24	MLINKS= ${PORTNAME}.1 ${PORTNAME}-n.1
		25	PORTDOCS= *
		26	PORTEXAMPLES= *
		27	PLIST_FILES= bin/${PORTNAME} bin/${PORTNAME}-n
25		28
26	.include <bsd.port.pre.mk>	29	.include <bsd.port.pre.mk>
27		30
Lines 41-54 Link Here
41	post-patch:	44	post-patch:
42	@${REINPLACE_CMD} -e 's\|="-O "\|="$$CFLAGS"\|g ; \	45	@${REINPLACE_CMD} -e 's\|="-O "\|="$$CFLAGS"\|g ; \
43	s\|-lpthread\|${PTHREAD_LIBS}\|g' ${WRKSRC}/configure	46	s\|-lpthread\|${PTHREAD_LIBS}\|g' ${WRKSRC}/configure
		47	@${REINPLACE_CMD} -e '/PRETTY$$/d' ${WRKSRC}/definitions.h
		48	@${REINPLACE_CMD} -e 's\|-O3\|\|g' ${WRKSRC}/haru/makefile.gcc
44		49
45	do-install:	50	do-install:
46	${INSTALL_PROGRAM} ${WRKSRC}/migrate-n ${PREFIX}/bin	51	${INSTALL_PROGRAM} ${WRKSRC}/${PORTNAME}-n ${PREFIX}/bin
47	${LN} -sf migrate-n ${PREFIX}/bin/migrate	52	${LN} -sf ${PORTNAME}-n ${PREFIX}/bin/${PORTNAME}
48	${INSTALL_MAN} ${WRKSRC}/migrate.1 ${MAN1PREFIX}/man/man1	53	${INSTALL_MAN} ${WRKSRC}/${PORTNAME}.1 ${MAN1PREFIX}/man/man1
49	.if !defined(NOPORTDOCS)	54	.if !defined(NOPORTDOCS)
50	@${MKDIR} ${DOCSDIR}	55	@${MKDIR} ${DOCSDIR}
51	.for i in HISTORY HOWTO-PARALLEL README migrate.html	56	.for i in HISTORY HOWTO-PARALLEL README ${PORTNAME}.html
52	${INSTALL_DATA} ${WRKSRC}/../${i} ${DOCSDIR}	57	${INSTALL_DATA} ${WRKSRC}/../${i} ${DOCSDIR}
53	.endfor	58	.endfor
54	@${MKDIR} ${DOCSDIR}/graphics	59	@${MKDIR} ${DOCSDIR}/graphics

Lines 1-3 Link Here

(-)biology/migrate/distinfo (-3 / +3 lines)
1	MD5 (migrate-3.0.3.src.tar.gz) = ea4a67a6320300a4df554f74a272581e	1	MD5 (migrate-3.1.1.src.tar.gz) = 5870d5e980a4bb9b34e4ea50d86ef98a
2	SHA256 (migrate-3.0.3.src.tar.gz) = d00c1999e7af055aca9f30565dfb610b03e42c2dcc60838c9c4367be87d0edd1	2	SHA256 (migrate-3.1.1.src.tar.gz) = 2149dadb91b164aea77759b4757aa8cc6269fc50743664bef05dc32239a9ad58
3	SIZE (migrate-3.0.3.src.tar.gz) = 5660159	3	SIZE (migrate-3.1.1.src.tar.gz) = 3874625




--- main.c.orig	2010-01-20 23:47:41.000000000 +0900
+++ main.c	2010-02-01 23:02:52.000000000 +0900
@@ -630,7 +630,9 @@
 	      {
 		fprintf(EARTH->outfile,"%5li %10.5f\n",locus+1,universe[locus]->averageheat);
 	      }
+#ifdef PRETTY
 	    pdf_print_averageheat(universe,options);
+#endif
 	  }
 #ifdef PRETTY
 	pdf_print_end_time(&page_height);
@@ -2443,8 +2445,10 @@
     {
       fprintf(file,"\n\nLocus      Raw Thermodynamic score(1a)  Bezier approximated score(1b)     Harmonic mean(2)\n");
       fprintf(file,"------------------------------------------------------------------------------------------\n");
+#ifdef PRETTY
       if(file==EARTH->outfile)
 	pdf_bayes_factor_rawscores_header(EARTH,options);
+#endif
     }
   if(options->heating)//-----------------------heating
     {

Lines 3-6 Link Here

(-)biology/migrate/pkg-descr (-1 / +1 lines)
3	migration rates and different subpopulation sizes. The n-population migrate	3	migration rates and different subpopulation sizes. The n-population migrate
4	can use sequence data, microsatellite data or electrophoretic data.	4	can use sequence data, microsatellite data or electrophoretic data.
5		5
6	WWW: http://popgen.csit.fsu.edu/Migrate-n.html	6	WWW: http://popgen.sc.fsu.edu/Migrate-n.html




bin/migrate
bin/migrate-n
%%PORTDOCS%%%%DOCSDIR%%/HISTORY
%%PORTDOCS%%%%DOCSDIR%%/HOWTO-PARALLEL
%%PORTDOCS%%%%DOCSDIR%%/README
%%PORTDOCS%%%%DOCSDIR%%/graphics/librarian.gif
%%PORTDOCS%%%%DOCSDIR%%/graphics/mail.gif
%%PORTDOCS%%%%DOCSDIR%%/graphics/migrate.gif
%%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%%

Return to bug 143437

Line 0 Link Here

(-)biology/migrate/files/patch-main.c (+23 lines)
	1	--- main.c.orig 2010-01-20 23:47:41.000000000 +0900
	2	+++ main.c 2010-02-01 23:02:52.000000000 +0900
	3	@@ -630,7 +630,9 @@
	4	{
	5	fprintf(EARTH->outfile,"%5li %10.5f\n",locus+1,universe[locus]->averageheat);
	6	}
	7	+#ifdef PRETTY
	8	pdf_print_averageheat(universe,options);
	9	+#endif
	10	}
	11	#ifdef PRETTY
	12	pdf_print_end_time(&page_height);
	13	@@ -2443,8 +2445,10 @@
	14	{
	15	fprintf(file,"\n\nLocus Raw Thermodynamic score(1a) Bezier approximated score(1b) Harmonic mean(2)\n");
	16	fprintf(file,"------------------------------------------------------------------------------------------\n");
	17	+#ifdef PRETTY
	18	if(file==EARTH->outfile)
	19	pdf_bayes_factor_rawscores_header(EARTH,options);
	20	+#endif
	21	}
	22	if(options->heating)//-----------------------heating
	23	{

Lines 1-76 Link Here

(-)biology/migrate/pkg-plist (-76 lines)
1	bin/migrate
2	bin/migrate-n
3	%%PORTDOCS%%%%DOCSDIR%%/HISTORY
4	%%PORTDOCS%%%%DOCSDIR%%/HOWTO-PARALLEL
5	%%PORTDOCS%%%%DOCSDIR%%/README
6	%%PORTDOCS%%%%DOCSDIR%%/graphics/librarian.gif
7	%%PORTDOCS%%%%DOCSDIR%%/graphics/mail.gif
8	%%PORTDOCS%%%%DOCSDIR%%/graphics/migrate.gif
9	%%PORTDOCS%%%%DOCSDIR%%/graphics/packet.gif
10	%%PORTDOCS%%%%DOCSDIR%%/migrate.html
11	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/README
12	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/aicfile
13	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/bayesallfile
14	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/bayesallfile.dated
15	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/bayesfile
16	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/bayesfile.dated
17	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/datefile.dated
18	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/infile
19	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/infile.benchmark
20	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/infile.dated
21	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/infile.ep
22	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/infile.msat
23	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/infile.seq
24	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mighistfile.dated
25	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/outfile
26	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/outfile-1
27	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/outfile-2
28	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/outfile-bayes
29	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/outfile-bayes-brown
30	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/outfile-bayes-multi0.5
31	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/outfile-bayes-multi0.5-0.5
32	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/outfile-bayes-saved
33	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/outfile-bayes-step
34	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/outfile-dated.pdf
35	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/outfile-ml
36	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/outfile-ml-3
37	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/outfile-ml-3.pdf
38	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/outfile-ml-paral2
39	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/outfile-ml-saved
40	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/outfile-ml-single
41	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/outfile-ml-watkins-0.5-0.5
42	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/outfile-ml.pdf
43	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/outfile.benchmark
44	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/outfile.benchmark_double
45	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/outfile.benchmark_float
46	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/outfile.dated
47	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/outfile.pdf
48	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/outifle-ml-3
49	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/parmfile
50	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/parmfile-testbayes.txt
51	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/parmfile.benchmark
52	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/parmfile.dated
53	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/parmfile.ep
54	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/parmfile.gugus
55	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/parmfile.msat
56	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/parmfile.seq
57	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/parmfile.testbayes
58	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/parmfile.testml
59	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/parmfile.testml-save
60	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/pretty
61	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/skylinefile.dated
62	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sumfile
63	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sumfile-1
64	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sumfile-2
65	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sumfile-3
66	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sumfile-mpi-ml
67	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sumfile-single
68	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sumfile1
69	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/treefile
70	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/treefile-1
71	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/treefile-2
72	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/treefile-3
73	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/treefile.dated
74	%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%
75	%%PORTDOCS%%@dirrm %%DOCSDIR%%/graphics
76	%%PORTDOCS%%@dirrm %%DOCSDIR%%