Update to 2.99.1 and unbreak.

Feature safe:	yes

4 files changed, 48 insertions, 26 deletions

diff --git a/science/libghemical/Makefile b/science/libghemical/Makefile
index 52bcfb7b7a8d..36873f19fc98 100644
--- a/science/libghemical/Makefile
+++ b/science/libghemical/Makefile
@@ -5,10 +5,9 @@
 # $FreeBSD$
 
 PORTNAME=	libghemical
-PORTVERSION=	2.98
-PORTREVISION=	3
+PORTVERSION=	2.99.1
 CATEGORIES=	science
-MASTER_SITES=	http://www.uku.fi/~thassine/projects/download/release20080731/ \
+MASTER_SITES=	http://www.uku.fi/~thassine/projects/download/release20090911/ \
 		http://bioinformatics.org/ghemical/download/
 DISTNAME=	${PORTNAME}-${PORTVERSION}
 
@@ -16,7 +15,9 @@ MAINTAINER=	maho@FreeBSD.org
 COMMENT=	Support libraries of science/ghemical port
 
 BUILD_DEPENDS=	openbabel:${PORTSDIR}/science/openbabel \
-		mopac7:${PORTSDIR}/biology/mopac
+		mopac7:${PORTSDIR}/biology/mopac \
+		intltool-update:${PORTSDIR}/textproc/intltool \
+		ld:${PORTSDIR}/devel/binutils
 LIB_DEPENDS+=	mpqc:${PORTSDIR}/science/mpqc \
 		f2c:${PORTSDIR}/lang/f2c
 
@@ -26,16 +27,15 @@ USE_GL=		gl
 GNU_CONFIGURE=	yes
 USE_LDCONFIG=   yes
 
-.include <bsd.port.pre.mk>
-
 USE_FORTRAN=	yes
-USE_AUTOTOOLS=	autoconf:262
-CONFIGURE_ARGS+=	--enable-mpqc --enable-openbabel --enable-mopac7 
-
+USE_AUTOTOOLS=	autoconf:262 libtool:22 automake:110
+CONFIGURE_ARGS+=	--enable-mpqc
 PLIST_SUB=	LIBGHEMICAL_VERSION="${PORTVERSION}"
 
-.if ${OSVERSION} >= 700000
-BROKEN=		does not configure
-.endif
+.include <bsd.port.pre.mk>
+
+pre-build:
+	${RM} -f ${WRKSRC}/libtool
+	${LN} -sf ${LIBTOOL} ${WRKSRC}/libtool
 
 .include <bsd.port.post.mk>
diff --git a/science/libghemical/distinfo b/science/libghemical/distinfo
index c55a9920b849..383c61fb57e7 100644
--- a/science/libghemical/distinfo
+++ b/science/libghemical/distinfo
@@ -1,3 +1,3 @@
-MD5 (libghemical-2.98.tar.gz) = 9ca4a60ba9b98f3c5003ee2e1a0ffeb0
-SHA256 (libghemical-2.98.tar.gz) = b4b0f037ed6632c84c6074badeb65cf52d04cbc5580e258275295b7520bd8bf6
-SIZE (libghemical-2.98.tar.gz) = 716300
+MD5 (libghemical-2.99.1.tar.gz) = d2dae2d7d786d3cba335cb29d85033ea
+SHA256 (libghemical-2.99.1.tar.gz) = f9b6df3c1e98a524f90644ebaaebb804792f391ca383c0f92b609060dc485d9f
+SIZE (libghemical-2.99.1.tar.gz) = 778812
diff --git a/science/libghemical/files/patch-configure.ac b/science/libghemical/files/patch-configure.ac
index be873d184dd0..bede93672d67 100644
--- a/science/libghemical/files/patch-configure.ac
+++ b/science/libghemical/files/patch-configure.ac
@@ -1,13 +1,30 @@
---- configure.ac~	2008-07-31 19:22:53.000000000 +0900
-+++ configure.ac	2008-08-23 06:17:58.000000000 +0900
-@@ -89,8 +89,8 @@
- AC_CHECK_LIB(m,acos,,[AC_MSG_ERROR([math library missing])])
+--- configure.ac	2009-09-11 21:24:01.000000000 +0900
++++ configure.ac	2009-10-09 10:13:23.000000000 +0900
+@@ -121,15 +121,15 @@
+ AC_CHECK_LIB([m], [acos],, AC_MSG_ERROR([math library missing]))
  
- if test $WITH_MPQC = yes; then
--	AC_CHECK_LIB([blas], [main], , AC_MSG_ERROR([Cannot find blas library needed for MPQC support]))
--	AC_CHECK_LIB([lapack], [main], , AC_MSG_ERROR([Cannot find lapack library needed for MPQC support]))
-+#	AC_CHECK_LIB([blas], [main], , AC_MSG_ERROR([Cannot find blas library needed for MPQC support]))
-+#	AC_CHECK_LIB([lapack], [main], , AC_MSG_ERROR([Cannot find lapack library needed for MPQC support]))
+ if test $enable_mpqc = yes; then
+-	AC_CHECK_LIB([blas], [main],, AC_MSG_ERROR([Cannot find blas library needed for MPQC support]))
+-	AC_CHECK_LIB([lapack], [main],, AC_MSG_ERROR([Cannot find lapack library needed for MPQC support]))
++	#AC_CHECK_LIB([blas], [main],, AC_MSG_ERROR([Cannot find blas library needed for MPQC support]))
++	#AC_CHECK_LIB([lapack], [main],, AC_MSG_ERROR([Cannot find lapack library needed for MPQC support]))
  	AM_PATH_SC(1.2.5, HAVE_MPQC="yes", HAVE_MPQC="no")
  	if test "${HAVE_MPQC}" = "yes"; then
- 		AC_DEFINE([ENABLE_MPQC], [], [Define if you are building a version that interfaces directly with MPQC])
+ 		AC_DEFINE([ENABLE_MPQC],, [Define if you are building a version that interfaces directly with MPQC])
+ 		AC_DEFINE_UNQUOTED([SC_MAJOR_VERSION], [$SC_MAJOR_VERSION], [This is the major version of SC (MPQC's underlying library) found by configure])
+ 		AC_DEFINE_UNQUOTED([SC_MINOR_VERSION], [$SC_MINOR_VERSION], [This is the minor version of SC (MPQC's underlying library) found by configure])
+ 		AC_DEFINE_UNQUOTED([SC_MICRO_VERSION], [$SC_MICRO_VERSION], [This is the micro version of SC (MPQC's underlying library) found by configure])
+-		CPPFLAGS="$CPPFLAGS $SC_CPPFLAGS"
++		CXXFLAGS="$CXXFLAGS $SC_CPPFLAGS"
+ 		LIBS="$LIBS $SC_LIBS"
+ 	else AC_MSG_ERROR([Cannot find proper SC version])
+ 	fi
+@@ -142,7 +142,7 @@
+ 	##alt	MOPAC7_CFLAGS=`$PKG_CONFIG --cflags libmopac7`
+ 	##alt	MOPAC7_LIBS=`$PKG_CONFIG --libs libmopac7`
+ 	
+-	CPPFLAGS="$CPPFLAGS $MOPAC7_CFLAGS"
++	CXXFLAGS="$CXXLAGS $MOPAC7_CFLAGS"
+ 	LIBS="$LIBS $MOPAC7_LIBS"
+ 	
+ 	REQUISITIONS="$REQUISITIONS libmopac7"
diff --git a/science/libghemical/pkg-plist b/science/libghemical/pkg-plist
index b0d626939960..e40537460cd1 100644
--- a/science/libghemical/pkg-plist
+++ b/science/libghemical/pkg-plist
@@ -19,6 +19,7 @@ include/ghemical/geomopt.h
 include/ghemical/intcrd.h
 include/ghemical/libghemicaldefine.h
 include/ghemical/libghemical-features.h
+include/ghemical/local_i18n.h
 include/ghemical/mfinder.h
 include/ghemical/model.h
 include/ghemical/moldyn.h
@@ -36,7 +37,7 @@ include/ghemical/typerule.h
 include/ghemical/utility.h
 include/ghemical/v3d.h
 @dirrm include/ghemical
-lib/libghemical.so.4
+lib/libghemical.so.5
 lib/libghemical.so
 lib/libghemical.la
 lib/libghemical.a
@@ -68,6 +69,10 @@ share/libghemical/%%LIBGHEMICAL_VERSION%%/param_mm/tripos52/parameters5.txt
 share/libghemical/%%LIBGHEMICAL_VERSION%%/param_sf/default/loopdip.txt
 share/libghemical/%%LIBGHEMICAL_VERSION%%/param_sf/default/looptor.txt
 share/libghemical/%%LIBGHEMICAL_VERSION%%/param_sf/default/nonbonded.txt
+share/locale/fi/LC_MESSAGES/libghemical.mo
+share/locale/mk/LC_MESSAGES/libghemical.mo
+share/locale/pt_BR/LC_MESSAGES/libghemical.mo
+share/locale/sq/LC_MESSAGES/libghemical.mo
 @dirrm share/libghemical/%%LIBGHEMICAL_VERSION%%/param_sf/default
 @dirrm share/libghemical/%%LIBGHEMICAL_VERSION%%/param_sf
 @dirrm share/libghemical/%%LIBGHEMICAL_VERSION%%/param_mm/tripos52