ports/172498: biology/seaview: Update to version 4.4.0
KATO Tsuguru
tkato432 at yahoo.com
Mon Oct 8 18:10:17 UTC 2012
>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 at 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
- at dirrm lib/X11/seaview
>Release-Note:
>Audit-Trail:
>Unformatted:
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