Date: Tue, 9 Oct 2012 02:55:57 +0900 From: KATO Tsuguru <tkato432@yahoo.com> To: FreeBSD-gnats-submit@FreeBSD.org Subject: ports/172498: biology/seaview: Update to version 4.4.0 Message-ID: <20121009025557.81dae3f4115c3dec1bf99cdb@yahoo.com> Resent-Message-ID: <201210081810.q98IAEwn086318@freefall.freebsd.org>
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>Number: 172498 >Category: ports >Synopsis: biology/seaview: Update to version 4.4.0 >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: Mon Oct 08 18:10:14 UTC 2012 >Closed-Date: >Last-Modified: >Originator: KATO Tsuguru >Release: FreeBSD 7.4-RELEASE-p10 i386 >Organization: >Environment: >Description: - Update to version 4.4.0 New file: files/patch-Makefile files/patch-use_mase_files.cxx Remove file: pkg-plist >How-To-Repeat: >Fix: diff -urN /usr/ports/biology/seaview/Makefile biology/seaview/Makefile --- /usr/ports/biology/seaview/Makefile 2012-10-01 23:45:16.000000000 +0900 +++ biology/seaview/Makefile 2012-10-04 23:36:29.000000000 +0900 @@ -2,31 +2,59 @@ # $FreeBSD: ports/biology/seaview/Makefile,v 1.47 2012/10/01 14:45:16 tabthorpe Exp $ PORTNAME= seaview -PORTVERSION= 2006.02.13 -PORTREVISION= 9 +PORTVERSION= 4.4.0 +PORTEPOCH= 1 CATEGORIES= biology -MASTER_SITES= ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview/archive/ -DISTNAME= ${PORTNAME}${PORTVERSION:S/.//g} -EXTRACT_SUFX= .tar +MASTER_SITES= http://pbil.univ-lyon1.fr/software/seaview_data/archive/ +DISTNAME= ${PORTNAME}_${PORTVERSION} MAINTAINER= ports@FreeBSD.org COMMENT= Multiple DNA/protein sequence alignment editor -LIB_DEPENDS= fltk.1:${PORTSDIR}/x11-toolkits/fltk \ - pdf.6:${PORTSDIR}/print/pdflib +LIB_DEPENDS= fltk:${PORTSDIR}/x11-toolkits/fltk -NO_WRKSUBDIR= yes -EXTRACT_CMD= ${CAT} -EXTRACT_BEFORE_ARGS= # +OPTIONS_DEFINE= PDFLIB +OPTIONS_DEFAULT=PDFLIB +PDFLIB_DESC= PDFlib support + +WRKSRC= ${WRKDIR}/${PORTNAME} + +USE_XORG= xext xft xinerama +USE_GMAKE= yes +MAKE_ENV= HELPFILE='-DDEFAULT_HELPFILE=\"${DATADIR}/seaview.html\"' \ + PHYMLNAME='-DPHYMLNAME=\"phyml\"' \ + IFLTK='-I${LOCALBASE}/include' \ + LFLTK='-L${LOCALBASE}/lib' \ + USE_XFT='-DUSE_XFT' \ + OPT="${CFLAGS}" ALL_TARGET= ${PORTNAME} +MAKE_JOBS_SAFE= yes -CFLAGS+= -D HAVE_DIRENT_H \ - -D DEFAULT_HELPFILE=${PREFIX}/lib/X11/${PORTNAME}/seaview.help +PLIST_FILES= bin/seaview %%DATADIR%%/seaview.html +PLIST_DIRS= %%DATADIR%% + +.include <bsd.port.options.mk> + +.if ${PORT_OPTIONS:MPDFLIB} +LIB_DEPENDS+= pdf:${PORTSDIR}/print/pdflib +MAKE_ENV+= LPDF='-L${LOCALBASE}/lib -lpdf' +.else +MAKE_ENV+= PDF_PS_FLAGS='-DNO_PDF' +.endif + +post-patch: + @${REINPLACE_CMD} -e \ + 's|^PDF_PS_FLAGS |#PDF_PS_FLAGS | ; \ + s|^FLTK |#FLTK | ; \ + s|^USE_XFT |#USE_XFT | ; \ + s|^CC |#CC | ; \ + s|^CXX |#CXX | ; \ + s|^OPT |#OPT | ; \ + s|-lpthread|${PTHREAD_LIBS}|' ${WRKSRC}/Makefile do-install: - ${INSTALL_PROGRAM} ${WRKDIR}/${PORTNAME} ${PREFIX}/bin - ${INSTALL_SCRIPT} ${WRKDIR}/seaview_align.sh ${PREFIX}/bin - @${MKDIR} ${PREFIX}/lib/X11/${PORTNAME} - ${INSTALL_DATA} ${WRKDIR}/seaview.help ${PREFIX}/lib/X11/${PORTNAME} + ${INSTALL_PROGRAM} ${WRKSRC}/${PORTNAME} ${PREFIX}/bin + @${MKDIR} ${DATADIR} + ${INSTALL_DATA} ${WRKSRC}/seaview.html ${DATADIR} .include <bsd.port.mk> diff -urN /usr/ports/biology/seaview/distinfo biology/seaview/distinfo --- /usr/ports/biology/seaview/distinfo 2011-03-19 21:29:38.000000000 +0900 +++ biology/seaview/distinfo 2012-10-04 22:35:55.000000000 +0900 @@ -1,2 +1,2 @@ -SHA256 (seaview20060213.tar) = 3b6cd132a8c9c2d29881e3bcb14a85b9a52524a5974317a9df09d9e15ffc7776 -SIZE (seaview20060213.tar) = 573952 +SHA256 (seaview_4.4.0.tar.gz) = e1dcaef67cb93da63bfa6fa102042340297c18055928645f03defb6547e9ede3 +SIZE (seaview_4.4.0.tar.gz) = 309611 diff -urN /usr/ports/biology/seaview/files/patch-Makefile biology/seaview/files/patch-Makefile --- /usr/ports/biology/seaview/files/patch-Makefile 2010-03-24 06:14:31.000000000 +0900 +++ biology/seaview/files/patch-Makefile 1970-01-01 09:00:00.000000000 +0900 @@ -1,25 +0,0 @@ ---- Makefile.orig 2010-01-08 13:42:25.000000000 +0100 -+++ Makefile 2010-01-08 13:42:24.000000000 +0100 -@@ -1,18 +1,15 @@ --FLTK = ../fltk --PDF = ../PDFlib-Lite-6.0.1/libs/pdflib --X11 = /usr/X11R6 - CXX = g++ - --CFLAGS = -Dunix -U__APPLE__ -c $(OPT) -I$(FLTK) -I$(PDF) -I$(X11)/include -+CFLAGS+= -Dunix -U__APPLE__ -c $(OPT) `fltk-config --cflags` - - - OBJECTS = seaview.o pdf.o custom.o use_mase_files.o regions.o load_seq.o align.o xfmatpt.o comlines.o chooser_plus.o resource.o nexus.o - - - seaview : $(OBJECTS) -- $(CXX) -o $@ $(OBJECTS) -L$(FLTK)/lib -lfltk \ -- -Xlinker -Bstatic -L$(PDF)/.libs -lpdf -Xlinker -Bdynamic \ -- -L$(X11)/lib -lX11 -lm -+ $(CXX) -o $@ $(OBJECTS) `fltk-config --ldflags` \ -+ -Xlinker -Bstatic -lpdf -Xlinker -Bdynamic \ -+ -L$(LOCALBASE)/lib -lX11 -lm - strip $@ - - diff -urN /usr/ports/biology/seaview/files/patch-use_mase_files.cxx biology/seaview/files/patch-use_mase_files.cxx --- /usr/ports/biology/seaview/files/patch-use_mase_files.cxx 2011-11-17 22:22:29.000000000 +0900 +++ biology/seaview/files/patch-use_mase_files.cxx 1970-01-01 09:00:00.000000000 +0900 @@ -1,29 +0,0 @@ ---- use_mase_files.cxx.orig 2011-11-17 14:20:13.000000000 +0100 -+++ use_mase_files.cxx 2011-11-17 14:20:01.000000000 +0100 -@@ -1457,8 +1457,6 @@ - - #else - --extern "C" { int stat(char *, void *); } -- - int check_path(char *fname) - /* to check for presence of file fname - searching for it through all path directories -@@ -1468,7 +1466,7 @@ - #define Mxdir 200 - char dir[Mxdir+1], *path, *deb, *fin; - int lf, ltot; -- static char stat_struct[250]; /* bigger than necessary */ -+ struct stat sb; - path=getenv("PATH"); /* get the list of path directories, - separated by : - */ -@@ -1488,7 +1486,7 @@ - dir[ltot]='/'; - strcpy(dir+ltot+1,fname); - /* now dir is appended with filename */ -- if( stat(dir, stat_struct) == 0) return 0; -+ if( stat(dir, &sb) == 0) return 0; - } - deb=fin+1; - } diff -urN /usr/ports/biology/seaview/pkg-plist biology/seaview/pkg-plist --- /usr/ports/biology/seaview/pkg-plist 2002-11-20 23:03:25.000000000 +0900 +++ biology/seaview/pkg-plist 1970-01-01 09:00:00.000000000 +0900 @@ -1,4 +0,0 @@ -bin/seaview -bin/seaview_align.sh -lib/X11/seaview/seaview.help -@dirrm lib/X11/seaview >Release-Note: >Audit-Trail: >Unformatted:
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