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authorgabor <gabor@FreeBSD.org>2006-12-10 20:39:32 +0800
committergabor <gabor@FreeBSD.org>2006-12-10 20:39:32 +0800
commit6887a6589bd774034a51c8fe1739678f9c5ea47b (patch)
tree08ff10eaed1cb0678c6dbeb42b46872858660edb /biology/migrate
parent80cc04bc581053e77f1471eb4cf2d8d35284d06a (diff)
downloadfreebsd-ports-gnome-6887a6589bd774034a51c8fe1739678f9c5ea47b.tar.gz
freebsd-ports-gnome-6887a6589bd774034a51c8fe1739678f9c5ea47b.tar.zst
freebsd-ports-gnome-6887a6589bd774034a51c8fe1739678f9c5ea47b.zip
- Update to 2.1.3
- Fix fetching - Remove old patch and use MAKE_ARGS instead - portlint(1) and whitespace Approved by: erwin (mentor)
Diffstat (limited to 'biology/migrate')
-rw-r--r--biology/migrate/Makefile23
-rw-r--r--biology/migrate/distinfo6
-rw-r--r--biology/migrate/files/patch-Makefile.in14
-rw-r--r--biology/migrate/pkg-plist9
4 files changed, 19 insertions, 33 deletions
diff --git a/biology/migrate/Makefile b/biology/migrate/Makefile
index 351bc6e5966b..0be9c9a3be0e 100644
--- a/biology/migrate/Makefile
+++ b/biology/migrate/Makefile
@@ -6,9 +6,9 @@
#
PORTNAME= migrate
-PORTVERSION= 2.0.3
+PORTVERSION= 2.1.3
CATEGORIES= biology
-MASTER_SITES= ftp://evolution.genetics.washington.edu/pub/lamarc/migrate/
+MASTER_SITES= http://popgen.csit.fsu.edu/currentversion/
DISTNAME= ${PORTNAME}-${PORTVERSION}.src
MAINTAINER= ports@FreeBSD.org
@@ -17,17 +17,18 @@ COMMENT= A program to estimate population sizes and migration rates
WRKSRC= ${WRKDIR}/${PORTNAME}-${PORTVERSION}/src
GNU_CONFIGURE= yes
CONFIGURE_TARGET= --build=${MACHINE_ARCH}-portbld-freebsd${OSREL}
+MAKE_ARGS= CFLAGS="${CFLAGS}"
MAN1= migrate.1
MLINKS= migrate.1 migrate-n.1
DOCS= HISTORY HOWTO-PARALLEL README migrate.html
-EXAMPLES= README infile.benchmark infile.ep infile.msat infile.seq \
- parmfile parmfile.benchmark parmfile.ep parmfile.msat \
- parmfile.seq
+EXAMPLES= README infile.ep infile.msat infile.seq \
+ outfile-bayes-saved outfile-ml-saved \
+ parmfile parmfile.testbayes parmfile.testml
post-patch:
- @${REINPLACE_CMD} 's,-falign-loops=16,,g' ${WRKSRC}/configure
+ @${REINPLACE_CMD} 's,-falign-loops=16,,g' ${WRKSRC}/configure
do-install:
@ ${INSTALL_PROGRAM} ${WRKSRC}/migrate-n ${PREFIX}/bin
@@ -35,12 +36,12 @@ do-install:
@ ${INSTALL_MAN} ${WRKSRC}/migrate.1 ${MAN1PREFIX}/man/man1
.if !defined(NOPORTDOCS)
@ ${MKDIR} ${DOCSDIR}/graphics
-.for file in ${DOCS}
- @ ${INSTALL_DATA} ${WRKSRC}/../${file} ${DOCSDIR}
+.for i in ${DOCS}
+ @ ${INSTALL_DATA} ${WRKSRC}/../${i} ${DOCSDIR}
.endfor
@ ${MKDIR} ${EXAMPLESDIR}
-.for file in ${EXAMPLES}
- @ ${INSTALL_DATA} ${WRKSRC}/../example/${file} ${EXAMPLESDIR}
+.for i in ${EXAMPLES}
+ @ ${INSTALL_DATA} ${WRKSRC}/../example/${i} ${EXAMPLESDIR}
.endfor
@ ${INSTALL_DATA} ${WRKSRC}/../graphics/* ${DOCSDIR}/graphics
.endif
@@ -48,7 +49,7 @@ do-install:
.include <bsd.port.pre.mk>
.if ${ARCH} == "alpha"
-BROKEN= "Does not compile"
+BROKEN= Does not compile
.endif
.include <bsd.port.post.mk>
diff --git a/biology/migrate/distinfo b/biology/migrate/distinfo
index 5de258062d1f..915a48e0a13f 100644
--- a/biology/migrate/distinfo
+++ b/biology/migrate/distinfo
@@ -1,3 +1,3 @@
-MD5 (migrate-2.0.3.src.tar.gz) = 8e8e93790cb66093ad5297dcbfc83439
-SHA256 (migrate-2.0.3.src.tar.gz) = f1210cf94e6b67cd762eae5949f97316b082b9f052b4188cf024afc7d8c1db56
-SIZE (migrate-2.0.3.src.tar.gz) = 467274
+MD5 (migrate-2.1.3.src.tar.gz) = fdff82f3dd509811fa4780287a554931
+SHA256 (migrate-2.1.3.src.tar.gz) = 91c8636c5b7a189fd693ddb9a863ff5995abf7157f10bf005e8e3e2497d56023
+SIZE (migrate-2.1.3.src.tar.gz) = 1637715
diff --git a/biology/migrate/files/patch-Makefile.in b/biology/migrate/files/patch-Makefile.in
deleted file mode 100644
index 67bb12994344..000000000000
--- a/biology/migrate/files/patch-Makefile.in
+++ /dev/null
@@ -1,14 +0,0 @@
-
-$FreeBSD$
-
---- Makefile.in.orig
-+++ Makefile.in
-@@ -40,7 +40,7 @@
- COMMONFLAGS = -DHIGHBITS -DHAVE_CONFIG_H -DHAVE_MALLOCWRAP -DBAYESUPDATE
- #COMMONFLAGS = -DHIGHBITS -DHAVE_CONFIG_H -DHAVE_MALLOCWRAP -DMERSENNE_TWISTER
- COMMONVFLAGS = $(COMMONFLAGS)
--CFLAGS = @CFLAGS@ $(COMMONVFLAGS) -DMIGRATEVERSION=\"\\\" $(MIGRATEVERSION)\\\"\"
-+CFLAGS += @CFLAGS@ $(COMMONVFLAGS) -DMIGRATEVERSION=\"\\\" $(MIGRATEVERSION)\\\"\"
- # IBM PowerPC compiler on macosx needs also CC=xlc
- #CFLAGS = -O3 -Q -qunroll -qalloca -qhot -qipa -qthreaded -Dpowerpc $(COMMONVFLAGS) -DMIGRATEVERSION=\"\\\" $(MIGRATEVERSION)\\\"\"
- THREADCFLAGS= @THREADCFLAGS@
diff --git a/biology/migrate/pkg-plist b/biology/migrate/pkg-plist
index 62135c58c177..66649c66e5f1 100644
--- a/biology/migrate/pkg-plist
+++ b/biology/migrate/pkg-plist
@@ -9,15 +9,14 @@ bin/migrate-n
%%PORTDOCS%%%%DOCSDIR%%/graphics/packet.gif
%%PORTDOCS%%%%DOCSDIR%%/migrate.html
%%PORTDOCS%%%%EXAMPLESDIR%%/README
-%%PORTDOCS%%%%EXAMPLESDIR%%/infile.benchmark
%%PORTDOCS%%%%EXAMPLESDIR%%/infile.ep
%%PORTDOCS%%%%EXAMPLESDIR%%/infile.msat
%%PORTDOCS%%%%EXAMPLESDIR%%/infile.seq
+%%PORTDOCS%%%%EXAMPLESDIR%%/outfile-bayes-saved
+%%PORTDOCS%%%%EXAMPLESDIR%%/outfile-ml-saved
%%PORTDOCS%%%%EXAMPLESDIR%%/parmfile
-%%PORTDOCS%%%%EXAMPLESDIR%%/parmfile.benchmark
-%%PORTDOCS%%%%EXAMPLESDIR%%/parmfile.ep
-%%PORTDOCS%%%%EXAMPLESDIR%%/parmfile.msat
-%%PORTDOCS%%%%EXAMPLESDIR%%/parmfile.seq
+%%PORTDOCS%%%%EXAMPLESDIR%%/parmfile.testbayes
+%%PORTDOCS%%%%EXAMPLESDIR%%/parmfile.testml
%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%
%%PORTDOCS%%@dirrm %%DOCSDIR%%/graphics
%%PORTDOCS%%@dirrm %%DOCSDIR%%