Date: Thu, 25 Aug 2011 03:35:04 +0900 From: KATO Tsuguru <tkato432@yahoo.com> To: FreeBSD-gnats-submit@FreeBSD.org Subject: ports/160083: Update port: biology/fastdnaml Message-ID: <20110825033504.adc84765.tkato432@yahoo.com> Resent-Message-ID: <201108241850.p7OIoFGI011293@freefall.freebsd.org>
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>Number: 160083 >Category: ports >Synopsis: Update port: biology/fastdnaml >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: Wed Aug 24 18:50:15 UTC 2011 >Closed-Date: >Last-Modified: >Originator: KATO Tsuguru >Release: FreeBSD 7.4-RELEASE-p2 i386 >Organization: >Environment: >Description: - Fix MASTER_SITES and WWW: line - Add LICENSE - Support CC/CFLAGS properly >How-To-Repeat: >Fix: diff -urN /usr/ports/biology/fastdnaml/Makefile biology/fastdnaml/Makefile --- /usr/ports/biology/fastdnaml/Makefile 2011-08-02 15:46:34.000000000 +0900 +++ biology/fastdnaml/Makefile 2011-08-25 00:12:15.000000000 +0900 @@ -7,30 +7,28 @@ PORTNAME= fastdnaml PORTVERSION= 1.2.2 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= biology -MASTER_SITES= http://geta.life.uiuc.edu:80/~gary/programs/fastDNAml/ +MASTER_SITES= http://www.life.illinois.edu/gary/programs/fastDNAml/ DISTNAME= fastDNAml_${PORTVERSION} MAINTAINER= ports@FreeBSD.org COMMENT= Faster DNAML, makes phylogenetic trees using maximum likelihood -DEPRECATED= No more public distfiles -EXPIRATION_DATE= 2011-09-01 +LICENSE= GPLv2 # (or later) +LICENSE_FILE= ${WRKSRC}/GNU_GENERAL_PUBLIC_LICENSE -USE_GMAKE= yes -do-build: - @(cd ${WRKSRC}/source; ${SETENV} ${MAKE_ENV} ${GMAKE} ${MAKE_FLAGS} ${MAKEFILE} ${MAKE_ARGS} ${ALL_TARGET}) +BUILD_WRKSRC= ${WRKSRC}/source + +MAKE_ARGS= CC="${CC}" CFLAGS="${CFLAGS}" do-install: - ${INSTALL_PROGRAM} ${WRKSRC}/source/fastDNAml ${PREFIX}/bin - ${MKDIR} ${PREFIX}/bin/${PORTNAME} + ${INSTALL_PROGRAM} ${BUILD_WRKSRC}/fastDNAml ${PREFIX}/bin + @${MKDIR} ${PREFIX}/bin/${PORTNAME} ${INSTALL_SCRIPT} ${WRKSRC}/scripts/* ${PREFIX}/bin/${PORTNAME} - -post-install: .if !defined(NOPORTDOCS) - ${MKDIR} ${PREFIX}/share/doc/${PORTNAME} - ${INSTALL_DATA} ${WRKSRC}/docs/*.txt ${PREFIX}/share/doc/${PORTNAME} + @${MKDIR} ${DOCSDIR} + ${INSTALL_DATA} ${WRKSRC}/docs/*.txt ${DOCSDIR} .endif .include <bsd.port.mk> diff -urN /usr/ports/biology/fastdnaml/pkg-descr biology/fastdnaml/pkg-descr --- /usr/ports/biology/fastdnaml/pkg-descr 2000-10-12 21:31:13.000000000 +0900 +++ biology/fastdnaml/pkg-descr 2011-08-16 19:13:56.000000000 +0900 @@ -1,22 +1,10 @@ -fastDNAml is a program for estimating maximum likelihood phylogenetic trees -from nucleotide sequences. +fastDNAml is a program derived from Joseph Felsenstein's version 3.3 DNAML +(part of his PHYLIP package). Users should consult the documentation for +DNAML before using this program. + +fastDNAml is an attempt to solve the same problem as DNAML, but to do so +faster and using less memory, so that larger trees and/or more bootstrap +replicates become tractable. Much of fastDNAml is merely a recoding of the +PHYLIP 3.3 DNAML program from PASCAL to C. -WWW: http://geta.life.uiuc.edu/~gary/programs/fastDNAml.html - -fastDNAml is an attempt to solve the same problem as Joseph Felsenstein's -DNAML, but to do so faster and using less memory, so that larger trees and/or -more bootstrap replicates become tractable. Much of fastDNAml is merely a -recoding of the PHYLIP 3.3 DNAML program from PASCAL to C. - -For Felsenstein's phylogenetic analysis softwares, including the latest -versions of DNAML, visit the PHYLIP Home Page: - http://evolution.genetics.washington.edu/phylip.html - -When publishing work that based on results from fastDNAml please cite: - - Felsenstein, J. 1981. Evolutionary trees from DNA sequences: - A maximum likelihood approach. J. Mol. Evol. 17: 368-376. - - Olsen, G. J., Matsuda, H., Hagstrom, R., and Overbeek, R. 1994. - fastDNAml: A tool for construction of phylogenetic trees of DNA - sequences using maximum likelihood. Comput. Appl. Biosci. 10: 41-48. +WWW: http://www.life.illinois.edu/gary/programs/fastDNAml.html >Release-Note: >Audit-Trail: >Unformatted:
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