Date: Fri, 1 Mar 2013 02:43:03 +0900 From: KATO Tsuguru <tkato432@yahoo.com> To: FreeBSD-gnats-submit@FreeBSD.org Subject: ports/176552: biology/wise: Update to version 2.4.1 Message-ID: <20130301024303.b0176678c7790c5a0114b3b3@yahoo.com> Resent-Message-ID: <201302281810.r1SIA887023477@freefall.freebsd.org>
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>Number: 176552 >Category: ports >Synopsis: biology/wise: Update to version 2.4.1 >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: Thu Feb 28 18:10:08 UTC 2013 >Closed-Date: >Last-Modified: >Originator: KATO Tsuguru >Release: FreeBSD 7.4-RELEASE-p10 i386 >Organization: >Environment: >Description: - Update to version 2.4.1 Remove file: pkg-plist >How-To-Repeat: >Fix: diff -urN /usr/ports/biology/wise/Makefile biology/wise/Makefile --- /usr/ports/biology/wise/Makefile 2012-11-08 06:54:19.000000000 +0900 +++ biology/wise/Makefile 2013-02-19 03:24:19.000000000 +0900 @@ -1,24 +1,30 @@ -# New ports collection makefile for: wise -# Date created: 26 February 2002 -# Whom: Tony Maher <tonym@biolateral.com.au> -# +# Created by: Tony Maher <tonym@biolateral.com.au> # $FreeBSD: head/biology/wise/Makefile 300895 2012-07-14 12:56:14Z beat $ -# PORTNAME= wise -PORTVERSION= 2.2.0 +PORTVERSION= 2.4.1 CATEGORIES= biology -MASTER_SITES= ftp://ftp.ebi.ac.uk/pub/software/unix/wise2/ +MASTER_SITES= http://www.ebi.ac.uk/~birney/wise2/ DISTNAME= ${PORTNAME}${PORTVERSION} MAINTAINER= ports@FreeBSD.org COMMENT= Intelligent algorithms for DNA searches -WRKTOP= ${WRKDIR}/${DISTNAME} -WRKSRC= ${WRKTOP}/src +OPTIONS_DEFINE= DOCS EXAMPLES + +BUILD_WRKSRC= ${WRKSRC}/src + +USE_GNOME= glib20 MAKEFILE= makefile +MAKE_JOBS_SAFE= yes + SUB_FILES= pkg-message +PORTDOCS= * +PORTEXAMPLES= * +PLIST_FILES= ${BINFILES:S,^,bin/,} ${DATAFILES:S,^,%%DATADIR%%/,} +PLIST_DIRS= %%DATADIR%% + # # Actually want an 'ALL_TARGET = all perl' which then requires # 'USE_PERL5= yes' but the perl sub-build is currently broken. @@ -29,68 +35,44 @@ # something like '@cd ${WRKSRC}/perl/Wise2; ${MAKE} install' # -BINFILES= dba dnal estwise estwisedb genewise genewisedb \ - genomewise psw pswdb -DATAFILES= BLOSUM30.bla BLOSUM45.bla BLOSUM62.bla BLOSUM80.bla \ - aa.rnd blosum30.bla blosum62.bla cb.tmf codon.table \ - gene.stat gon120.bla gon160.bla gon200.bla gon250.bla \ - gon350.bla human.gf human.gp human.stats idenity.bla \ - methods pb.gf pombe.gf tm.pri wise.2 wise.per worm.gf -DOCFILES= README apiend.tex appendix.tex dynamite.tex \ - genewise21.eps genewise6.eps gettex.pl makefile \ - wise2.tex wise2api.tex wise3arch.tex -EXFILES= README db.hmm hn_est.fa human.genomic \ - keratin_intron.human keratin_intron.mouse pep.fa \ - road.pep rrm.HMM vav.dna xeno.cdna xeno.pep - -# -# Top level makefile does not respect CFLAGS. Fixing it means -# having to fix some of the sub-directory makefiles. -# Note: some makefiles are ok and know that '-c' does not belong -# in CFLAGS and are part of the rule. -# - -post-configure: - @${REINPLACE_CMD} \ - -e s'#^CFLAGS = -c -O#CFLAGS ?= -c -O#;' \ - -e s'#\tcsh welcome.csh##;' \ - ${WRKSRC}/${MAKEFILE} - @${REINPLACE_CMD} \ - -e s'#CFLAGS) $?#CFLAGS) -c $?#;' \ - ${WRKSRC}/base/${MAKEFILE} - @${REINPLACE_CMD} \ - -e s'#INCFLAGS) $?#INCFLAGS) -c $?#;' \ - ${WRKSRC}/dynlibsrc/${MAKEFILE} - @${REINPLACE_CMD} \ - -e s'#INCFLAGS) $?#INCFLAGS) -c $?#;' \ - -e s'#CFLAGS) estwise.c#CFLAGS) -c estwise.c#;' \ - -e s'#CFLAGS) estwiseb.c#CFLAGS) -c estwiseb.c#;' \ - -e s'#CFLAGS) estwisedb.c#CFLAGS) -c estwisedb.c#;' \ - -e s'#CFLAGS) genewise.c#CFLAGS) -c genewise.c#;' \ - -e s'#CFLAGS) genewisedb.c#CFLAGS) -c genewisedb.c#;' \ - ${WRKSRC}/models/${MAKEFILE} +BINFILES= dba dnal estwise estwisedb genewise genewisedb promoterwise \ + psw pswdb scanwise scanwise_server +DATAFILES= BLOSUM30.bla BLOSUM45.bla BLOSUM62.bla BLOSUM80.bla aa.rnd \ + cb.tmf codon.table gene.stat gon120.bla gon160.bla \ + gon200.bla gon250.bla gon350.bla human.gf human.gp \ + human.stats idenity.bla methods pb.gf pombe.gf tm.pri \ + wise.2 wise.per worm.gf + +.include <bsd.port.options.mk> + +post-patch: + @${FIND} ${BUILD_WRKSRC} -name "makefile" | ${XARGS} \ + ${REINPLACE_CMD} -e \ + 's|^CC =|CC ?=| ; \ + s|^CFLAGS =|CFLAGS +=| ; \ + s|-O[0-9] | | ; \ + s|-g | | ; \ + s|-g[0-9] | | ; \ + s|-lpthread|-pthread| ; \ + s|glib-config|pkg-config glib-2.0| ; \ + /welcome.csh/s|^|#|' do-install: -.for file in ${BINFILES} - @${INSTALL_PROGRAM} ${WRKSRC}/bin/${file} ${PREFIX}/bin +.for i in ${BINFILES} + (cd ${BUILD_WRKSRC}/bin && ${INSTALL_PROGRAM} ${i} ${PREFIX}/bin) .endfor @${MKDIR} ${DATADIR} -.for file in ${DATAFILES} - @${INSTALL_DATA} ${WRKTOP}/wisecfg/${file} ${DATADIR} +.for i in ${DATAFILES} + (cd ${WRKSRC}/wisecfg && ${INSTALL_DATA} ${i} ${DATADIR}) .endfor -.if !defined(NOPORTDOCS) +.if ${PORT_OPTIONS:MDOCS} @${MKDIR} ${DOCSDIR} -.for file in ${DOCFILES} - @${INSTALL_DATA} ${WRKTOP}/docs/${file} ${DOCSDIR} -.endfor + @(cd ${WRKSRC}/docs && ${COPYTREE_SHARE} . ${DOCSDIR}) +.endif +.if ${PORT_OPTIONS:MEXAMPLES} @${MKDIR} ${EXAMPLESDIR} -.for file in ${EXFILES} - @${INSTALL_DATA} ${WRKTOP}/test_data/${file} ${EXAMPLESDIR} -.endfor - + @(cd ${WRKSRC}/test_data && ${COPYTREE_SHARE} . ${EXAMPLESDIR}) .endif - -post-install: @${CAT} ${PKGMESSAGE} .include <bsd.port.mk> diff -urN /usr/ports/biology/wise/distinfo biology/wise/distinfo --- /usr/ports/biology/wise/distinfo 2012-11-08 06:54:19.000000000 +0900 +++ biology/wise/distinfo 2013-02-19 02:23:09.000000000 +0900 @@ -1,2 +1,2 @@ -SHA256 (wise2.2.0.tar.gz) = 192db34ffa76ef14a9804cc5a7ab72554498284c841f940f8951b4bfae96d780 -SIZE (wise2.2.0.tar.gz) = 2108151 +SHA256 (wise2.4.1.tar.gz) = 240e2b12d6cd899040e2efbcb85b0d3c10245c255f3d07c1db45d0af5a4d5fa1 +SIZE (wise2.4.1.tar.gz) = 3193910 diff -urN /usr/ports/biology/wise/pkg-plist biology/wise/pkg-plist --- /usr/ports/biology/wise/pkg-plist 2012-11-08 06:54:19.000000000 +0900 +++ biology/wise/pkg-plist 1970-01-01 09:00:00.000000000 +0900 @@ -1,61 +0,0 @@ -bin/genomewise -%%PORTDOCS%%%%DOCSDIR%%/README -%%PORTDOCS%%%%DOCSDIR%%/apiend.tex -%%PORTDOCS%%%%DOCSDIR%%/appendix.tex -%%PORTDOCS%%%%DOCSDIR%%/dynamite.tex -%%PORTDOCS%%%%DOCSDIR%%/genewise21.eps -%%PORTDOCS%%%%DOCSDIR%%/genewise6.eps -%%PORTDOCS%%%%DOCSDIR%%/gettex.pl -%%PORTDOCS%%%%DOCSDIR%%/makefile -%%PORTDOCS%%%%DOCSDIR%%/wise2.tex -%%PORTDOCS%%%%DOCSDIR%%/wise2api.tex -%%PORTDOCS%%%%DOCSDIR%%/wise3arch.tex -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/README -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/db.hmm -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/hn_est.fa -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/human.genomic -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/keratin_intron.human -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/keratin_intron.mouse -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/pep.fa -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/road.pep -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/rrm.HMM -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vav.dna -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/xeno.cdna -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/xeno.pep -%%DATADIR%%/BLOSUM30.bla -%%DATADIR%%/BLOSUM45.bla -%%DATADIR%%/BLOSUM62.bla -%%DATADIR%%/BLOSUM80.bla -%%DATADIR%%/aa.rnd -%%DATADIR%%/blosum30.bla -%%DATADIR%%/blosum62.bla -%%DATADIR%%/cb.tmf -%%DATADIR%%/codon.table -%%DATADIR%%/gene.stat -%%DATADIR%%/gon120.bla -%%DATADIR%%/gon160.bla -%%DATADIR%%/gon200.bla -%%DATADIR%%/gon250.bla -%%DATADIR%%/gon350.bla -%%DATADIR%%/human.gf -%%DATADIR%%/human.gp -%%DATADIR%%/human.stats -%%DATADIR%%/idenity.bla -%%DATADIR%%/methods -%%DATADIR%%/pb.gf -%%DATADIR%%/pombe.gf -%%DATADIR%%/tm.pri -%%DATADIR%%/wise.2 -%%DATADIR%%/wise.per -%%DATADIR%%/worm.gf -bin/dba -bin/dnal -bin/estwise -bin/estwisedb -bin/genewise -bin/genewisedb -bin/psw -bin/pswdb -%%PORTDOCS%%@dirrm %%DOCSDIR%% -%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%% -@dirrm %%DATADIR%% >Release-Note: >Audit-Trail: >Unformatted:
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