- Update to 6.6.0

- Stage support

PR:		190508
Submitted by:	Muhammad Moinur Rahman

biology/emboss/Makefile

@@ -2,17 +2,17 @@
 # $FreeBSD$
 
 PORTNAME=	emboss
-PORTVERSION=	6.2.0
-RELEASE=	${PORTNAME:tu}-${PORTVERSION}
-PORTREVISION=	3
+PORTVERSION=	6.6.0
 CATEGORIES=	biology
 MASTER_SITES=	ftp://emboss.open-bio.org/pub/EMBOSS/
-DISTNAME=	${RELEASE}
+DISTNAME=	${PORTNAME:tu}-${PORTVERSION}
 DIST_SUBDIR=	${PORTNAME}
 
 MAINTAINER=	wen@FreeBSD.org
 COMMENT=	A collection of open source tools for genetic sequence analysis
 
+LICENSE=	GPLv2
+
 BUILD_DEPENDS=	clustalw:${PORTSDIR}/biology/clustalw \
 		primer3:${PORTSDIR}/biology/primer3
 LIB_DEPENDS=	libgd.so:${PORTSDIR}/graphics/gd \
@@ -22,37 +22,37 @@ CONFLICTS=	qmail-ldap-[0-9]* digest-[0-9]*
 
 PREFIX?=	${LOCALBASE}/emboss
 NO_MTREE=	yes
-USES=		gmake
+USES=		gmake libtool iconv
 USE_SUBMAKE=	yes
 GNU_CONFIGURE=	yes
-USE_AUTOTOOLS=	libtool
 USE_LDCONFIG=	yes
 SUB_FILES=	pkg-message
 SUB_LIST=	PREFIX=${PREFIX} DATADIR=${DATADIR}
+LDFLAGS+=	-L${LOCALBASE}/lib
+CONFIGURE_ARGS+=${ICONV_CONFIGURE_ARG}
 
 DOCSDIR=	${PREFIX}/share/${PORTNAME:tu}/doc
 DATADIR=	${PREFIX}/share/${PORTNAME:tu}
 
-CONFIGURE_ARGS+= --with-docroot=${DOCSDIR}
-
-.if !defined(WITHOUT_X11)
-USE_XORG=	x11
-USES+=		motif
-LIB_DEPENDS+=	libgd.so:${PORTSDIR}/graphics/gd \
+OPTIONS_DEFINE=	DOCS X11
+OPTIONS_DEFAULT=	X11
+DOCS_CONFIGURE_ON=	--with-docroot=${DOCSDIR}
+X11_USE=	XORG=x11
+X11_USES=	motif
+X11_LIB_DEPENDS=	libgd.so:${PORTSDIR}/graphics/gd \
 		libpng15.so:${PORTSDIR}/graphics/png
-.else
-CONFIGURE_ARGS+= --without-x
-.endif
+X11_CONFIGURE_OFF=	--without-x
 
-DOC_DIRS=	doc/manuals doc/tutorials doc/programs/text doc/programs/html
 CONFIG_FILE=	${WRKSRC}/emboss/emboss.default.template
 
-NO_STAGE=	yes
+post-patch:
+	@${REINPLACE_CMD} -e 's/-liconv/${ICONV_LIB}/' ${WRKSRC}/configure
+
 pre-install:
-	@ ${REINPLACE_CMD} -e 's#%%DATADIR%%#${DATADIR}#' ${CONFIG_FILE}
+	@ ${REINPLACE_CMD} -e 's#%%DATADIR%%#${PREFIX}/share/${PORTNAME:tu}#' ${CONFIG_FILE}
 
 post-install:
-	${CHOWN} ${SHAREOWN}:${SHAREGRP} ${DATADIR}/emboss.default.template
-	@ ${CAT} ${PKGMESSAGE}
+	${INSTALL_DATA} ${CONFIG_FILE} ${STAGEDIR}${DATADIR}
+	${CHOWN} ${SHAREOWN}:${SHAREGRP} ${STAGEDIR}${DATADIR}/emboss.default.template
 
 .include <bsd.port.mk>

biology/emboss/distinfo

@@ -1,2 +1,2 @@
-SHA256 (emboss/EMBOSS-6.2.0.tar.gz) = 4726371c0bcf3e232a5ee6b334e74b8c284dcbdcb176a475e77699515f8d122b
-SIZE (emboss/EMBOSS-6.2.0.tar.gz) = 23430911
+SHA256 (emboss/EMBOSS-6.6.0.tar.gz) = 7184a763d39ad96bb598bfd531628a34aa53e474db9e7cac4416c2a40ab10c6e
+SIZE (emboss/EMBOSS-6.6.0.tar.gz) = 117962028

biology/emboss/files/patch-Makefile.in

@@ -0,0 +1,30 @@
+--- Makefile.in.orig	2014-05-29 03:27:28.070199330 +0600
++++ Makefile.in	2014-05-29 03:28:00.167196553 +0600
+@@ -756,7 +756,7 @@
+ 
+ install-exec-am:
+ 	@$(NORMAL_INSTALL)
+-	$(MAKE) $(AM_MAKEFLAGS) install-exec-hook
++	$(MAKE) $(AM_MAKEFLAGS)
+ install-html: install-html-recursive
+ 
+ install-html-am:
+@@ -810,7 +810,7 @@
+ 	distclean-libtool distclean-tags distcleancheck distdir \
+ 	distuninstallcheck dvi dvi-am html html-am info info-am \
+ 	install install-am install-data install-data-am install-dvi \
+-	install-dvi-am install-exec install-exec-am install-exec-hook \
++	install-dvi-am install-exec install-exec-am \
+ 	install-html install-html-am install-info install-info-am \
+ 	install-man install-pdf install-pdf-am install-ps \
+ 	install-ps-am install-strip installcheck installcheck-am \
+@@ -832,9 +832,6 @@
+ 	tar cBf - doc | ( cd $(distdir); tar xBf - ; find doc -name CVS | xargs rm -rf; )
+ 	tar cBf - jemboss | ( cd $(distdir); tar xBf - ; find jemboss -name CVS | xargs rm -rf; find jemboss -name Makefile | xargs rm -rf; find jemboss -name .cvsignore | xargs rm -rf )
+ 
+-install-exec-hook:
+-	$(bindir)/embossupdate
+-
+ # Tell versions [3.59,3.63) of GNU make to not export all variables.
+ # Otherwise a system limit (for SysV at least) may be exceeded.
+ .NOEXPORT:

biology/emboss/files/patch-emboss-Makefile.in

@@ -0,0 +1,10 @@
+--- emboss/Makefile.in.orig	2014-05-29 14:42:20.540406535 +0600
++++ emboss/Makefile.in	2014-05-29 14:42:42.364404204 +0600
+@@ -3216,7 +3216,6 @@
+ 	$(am__append_3) ../ajax/pcre/libepcre.la \
+ 	../plplot/libeplplot.la $(XLIB)
+ dist_pkgdata_DATA = \
+-emboss.default.template \
+ emboss.standard \
+ server.biomart \
+ server.dasregistry \