Date: Mon, 3 Sep 2007 02:00:18 +0900 From: KATO Tsuguru <tkato432@yahoo.com> To: FreeBSD-gnats-submit@FreeBSD.org Subject: ports/116019: Update port: biology/migrate to 2.3 Message-ID: <20070903020018.64449522.tkato432@yahoo.com> Resent-Message-ID: <200709021710.l82HA6NQ009012@freefall.freebsd.org>
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>Number: 116019 >Category: ports >Synopsis: Update port: biology/migrate to 2.3 >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: Sun Sep 02 17:10:05 GMT 2007 >Closed-Date: >Last-Modified: >Originator: KATO Tsuguru >Release: FreeBSD 6.2-RELEASE-p7 i386 >Organization: >Environment: >Description: - Update to version 2.3 >How-To-Repeat: >Fix: diff -urN /usr/ports/biology/migrate/Makefile biology/migrate/Makefile --- /usr/ports/biology/migrate/Makefile Sun Dec 10 21:39:32 2006 +++ biology/migrate/Makefile Thu Aug 30 01:02:42 2007 @@ -6,7 +6,7 @@ # PORTNAME= migrate -PORTVERSION= 2.1.3 +PORTVERSION= 2.3 CATEGORIES= biology MASTER_SITES= http://popgen.csit.fsu.edu/currentversion/ DISTNAME= ${PORTNAME}-${PORTVERSION}.src @@ -15,41 +15,52 @@ COMMENT= A program to estimate population sizes and migration rates WRKSRC= ${WRKDIR}/${PORTNAME}-${PORTVERSION}/src + +USE_GNOME= gnometarget GNU_CONFIGURE= yes -CONFIGURE_TARGET= --build=${MACHINE_ARCH}-portbld-freebsd${OSREL} -MAKE_ARGS= CFLAGS="${CFLAGS}" +MAKE_ARGS= HARDWARECFLAGS="${CFLAGS}" \ + MYCPPFLAGS="${CFLAGS} -DNOJPEG -DNOPNG -DNOZLIB" MAN1= migrate.1 MLINKS= migrate.1 migrate-n.1 -DOCS= HISTORY HOWTO-PARALLEL README migrate.html -EXAMPLES= README infile.ep infile.msat infile.seq \ - outfile-bayes-saved outfile-ml-saved \ - parmfile parmfile.testbayes parmfile.testml +.include <bsd.port.pre.mk> + +.if ${ARCH} == "alpha" +BROKEN= Does not compile +.endif + +.if defined(WITH_THREAD_PRETTY) +ALL_TARGET= thread-pretty +.elif defined(WITH_PRETTY) +ALL_TARGET= pretty +.elif defined(WITH_THREAD) +ALL_TARGET= thread +.else +ALL_TARGET= all +.endif post-patch: - @${REINPLACE_CMD} 's,-falign-loops=16,,g' ${WRKSRC}/configure + @${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 - @ cd ${PREFIX}/bin && ${LN} -s migrate-n migrate - @ ${INSTALL_MAN} ${WRKSRC}/migrate.1 ${MAN1PREFIX}/man/man1 + ${INSTALL_PROGRAM} ${WRKSRC}/migrate-n ${PREFIX}/bin + ${LN} -sf migrate-n ${PREFIX}/bin/migrate + ${INSTALL_MAN} ${WRKSRC}/migrate.1 ${MAN1PREFIX}/man/man1 .if !defined(NOPORTDOCS) - @ ${MKDIR} ${DOCSDIR}/graphics -.for i in ${DOCS} - @ ${INSTALL_DATA} ${WRKSRC}/../${i} ${DOCSDIR} -.endfor - @ ${MKDIR} ${EXAMPLESDIR} -.for i in ${EXAMPLES} - @ ${INSTALL_DATA} ${WRKSRC}/../example/${i} ${EXAMPLESDIR} + @${MKDIR} ${DOCSDIR} +.for i in HISTORY HOWTO-PARALLEL README migrate.html + ${INSTALL_DATA} ${WRKSRC}/../${i} ${DOCSDIR} .endfor - @ ${INSTALL_DATA} ${WRKSRC}/../graphics/* ${DOCSDIR}/graphics + @${MKDIR} ${DOCSDIR}/graphics + ${INSTALL_DATA} ${WRKSRC}/../graphics/* ${DOCSDIR}/graphics .endif - -.include <bsd.port.pre.mk> - -.if ${ARCH} == "alpha" -BROKEN= Does not compile +.if !defined(NOPORTEXAMPLES) + @${MKDIR} ${EXAMPLESDIR} + ${INSTALL_DATA} ${WRKSRC}/../example/* ${EXAMPLESDIR} .endif .include <bsd.port.post.mk> diff -urN /usr/ports/biology/migrate/distinfo biology/migrate/distinfo --- /usr/ports/biology/migrate/distinfo Sun Dec 10 21:39:32 2006 +++ biology/migrate/distinfo Thu Aug 30 00:10:01 2007 @@ -1,3 +1,3 @@ -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 +MD5 (migrate-2.3.src.tar.gz) = 12dbf7bd9d69b6ba87a9ba16b68ff7e5 +SHA256 (migrate-2.3.src.tar.gz) = 3407a92b41f23d036a6ef5fd11f77e6d1aa8ee39fa4f61c65b0f71670b8b8f62 +SIZE (migrate-2.3.src.tar.gz) = 1952466 diff -urN /usr/ports/biology/migrate/pkg-descr biology/migrate/pkg-descr --- /usr/ports/biology/migrate/pkg-descr Mon Aug 6 23:26:51 2001 +++ biology/migrate/pkg-descr Wed Aug 29 23:57:31 2007 @@ -3,12 +3,5 @@ migration rates and different subpopulation sizes. The n-population migrate can use sequence data, microsatellite data or electrophoretic data. -Migrate forms part of the Lamarc (Likelihood Analysis with Metropolis -Algorithm using Random Coalescence) suite. See: - - http://evolution.genetics.washington.edu/lamarc.html - -Author: Peter Beerli <beerli@genetics.washington.edu> -WWW: http://evolution.genetics.washington.edu/lamarc/migrate.html - --- Johann Visagie <wjv@FreeBSD.org> +Author: Peter Beerli <beerli@scs.fsu.edu> +WWW: http://popgen.scs.fsu.edu/Migrate-n.html diff -urN /usr/ports/biology/migrate/pkg-plist biology/migrate/pkg-plist --- /usr/ports/biology/migrate/pkg-plist Sun Dec 10 21:39:32 2006 +++ biology/migrate/pkg-plist Thu Aug 30 01:06:06 2007 @@ -8,15 +8,23 @@ %%PORTDOCS%%%%DOCSDIR%%/graphics/migrate.gif %%PORTDOCS%%%%DOCSDIR%%/graphics/packet.gif %%PORTDOCS%%%%DOCSDIR%%/migrate.html -%%PORTDOCS%%%%EXAMPLESDIR%%/README -%%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.testbayes -%%PORTDOCS%%%%EXAMPLESDIR%%/parmfile.testml -%%PORTDOCS%%@dirrm %%EXAMPLESDIR%% +%%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%% %%PORTDOCS%%@dirrm %%DOCSDIR%%/graphics %%PORTDOCS%%@dirrm %%DOCSDIR%% >Release-Note: >Audit-Trail: >Unformatted:
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