Date: Sat, 8 May 2010 20:52:09 GMT From: Glen Barber <glen.j.barber@gmail.com> To: freebsd-gnats-submit@FreeBSD.org Subject: ports/146411: [patch][maintainer] biology/migrate: update to latest version Message-ID: <201005082052.o48Kq9ZW035877@www.freebsd.org> Resent-Message-ID: <201005082100.o48L0DaM042062@freefall.freebsd.org>
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>Number: 146411 >Category: ports >Synopsis: [patch][maintainer] biology/migrate: update to latest version >Confidential: no >Severity: non-critical >Priority: low >Responsible: freebsd-ports-bugs >State: open >Quarter: >Keywords: >Date-Required: >Class: maintainer-update >Submitter-Id: current-users >Arrival-Date: Sat May 08 21:00:13 UTC 2010 >Closed-Date: >Last-Modified: >Originator: Glen Barber >Release: 8.0-STABLE >Organization: >Environment: FreeBSD orion 8.0-STABLE FreeBSD 8.0-STABLE #89 r207326: Wed Apr 28 11:28:39 EDT 2010 root@orion:/usr/obj/usr/src/sys/ORION amd64 >Description: Update biology/migrate from 3.1.3 -> 3.1.4 >How-To-Repeat: >Fix: Patch attached with submission follows: diff -ruN /usr/ports/biology/migrate.orig/Makefile /usr/ports/biology/migrate/Makefile --- /usr/ports/biology/migrate.orig/Makefile 2010-03-24 02:46:44.000000000 -0400 +++ /usr/ports/biology/migrate/Makefile 2010-05-08 16:15:19.000000000 -0400 @@ -6,7 +6,7 @@ # PORTNAME= migrate -PORTVERSION= 3.1.3 +PORTVERSION= 3.1.4 CATEGORIES= biology MASTER_SITES= http://people.sc.fsu.edu/~beerli/popgen/currentversion/ DISTNAME= ${PORTNAME}-${PORTVERSION}.src diff -ruN /usr/ports/biology/migrate.orig/distinfo /usr/ports/biology/migrate/distinfo --- /usr/ports/biology/migrate.orig/distinfo 2010-03-24 02:46:44.000000000 -0400 +++ /usr/ports/biology/migrate/distinfo 2010-05-08 14:42:58.000000000 -0400 @@ -1,3 +1,3 @@ -MD5 (migrate-3.1.3.src.tar.gz) = 20b07feaeb3624769d6befec640a30e2 -SHA256 (migrate-3.1.3.src.tar.gz) = 176f516c8dec12b5370230e91dbc454b2ab6740656fdbb1a2475a5377fee630d -SIZE (migrate-3.1.3.src.tar.gz) = 2021127 +MD5 (migrate-3.1.4.src.tar.gz) = a1ffa3baa8a78b17b2dcb387de7801ee +SHA256 (migrate-3.1.4.src.tar.gz) = f09d35f544865f1cde3677b9b347b8a5de9e907f81d4f509e8f15c2fd28ea110 +SIZE (migrate-3.1.4.src.tar.gz) = 2227530 diff -ruN /usr/ports/biology/migrate.orig/files/patch-Makefile.in /usr/ports/biology/migrate/files/patch-Makefile.in --- /usr/ports/biology/migrate.orig/files/patch-Makefile.in 2009-01-14 11:00:34.000000000 -0500 +++ /usr/ports/biology/migrate/files/patch-Makefile.in 2010-05-08 16:10:34.000000000 -0400 @@ -1,16 +1,16 @@ ---- 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 @@ +--- Makefile.in.orig 2010-05-01 16:14:26.000000000 -0400 ++++ Makefile.in 2010-05-08 16:08:49.000000000 -0400 +@@ -80,7 +80,7 @@ # -DNEXUSTREE print nexus tree instead of plain newick trees # -UEP calculates unique event polymorphism - NEWSTUFF = -DNEWVERSION -DBFDEBUG + NEWSTUFF = -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)\\\"\" -@@ -195,22 +195,21 @@ - @echo ' make install (installs the executables and man page)' +@@ -202,22 +202,21 @@ + @echo ' make install (installs the executables and man page [out of date])' @echo ' [there are other targets for debugging purposes, check the Makefile]' -all:: haru @@ -36,7 +36,7 @@ mpis-thread:: haru $(MAKE) $(NAME) "CC=$(MPICC)" "CFLAGS = $(CFLAGS) $(PRETTYCFLAGS) $(THREADCFLAGS) -DMPI -DSLOWNET -DNEWREPLICANT -DMPIREPLICANT" "LIBS = $(OTHERLIBS) $(PDFLIB) $(LIBS)" -@@ -398,22 +397,22 @@ +@@ -405,22 +404,22 @@ else echo Must define $@; exit 1; fi $(NAME): $(PRODUCT_DEPENDS) @@ -64,3 +64,10 @@ #---------------------------------------------------------------- +@@ -473,4 +472,4 @@ + #---------------------------------------------------------------- + # BEAGLE + beagle: +- $(MAKE) $(NAME) "CFLAGS = $(DEBUGCFLAGS) $(BEAGLEFLAGS) $(PRETTYCFLAGS)" "LIBS = $(PDFLIB) $(LIBS)" "LDFLAGS =$(LDFLAGS) $(EXCEPTIONS) `pkg-config /Users/beerli/src/beagle-lib/hmsbeagle-1.0.pc --cflags --libs` -framework OpenCL" +\ No newline at end of file ++ $(MAKE) $(NAME) "CFLAGS = $(DEBUGCFLAGS) $(BEAGLEFLAGS) $(PRETTYCFLAGS)" "LIBS = $(PDFLIB) $(LIBS)" "LDFLAGS =$(LDFLAGS) $(EXCEPTIONS) `pkg-config /Users/beerli/src/beagle-lib/hmsbeagle-1.0.pc --cflags --libs` -framework OpenCL" >Release-Note: >Audit-Trail: >Unformatted:
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