Update to 2.98.

5 files changed, 21 insertions, 94 deletions

diff --git a/science/libghemical/Makefile b/science/libghemical/Makefile
index d4f5e9713f0c..b2cc267df2f3 100644
--- a/science/libghemical/Makefile
+++ b/science/libghemical/Makefile
@@ -5,10 +5,9 @@
 # $FreeBSD$
 
 PORTNAME=	libghemical
-PORTVERSION=	2.10
-PORTREVISION=	4
+PORTVERSION=	2.98
 CATEGORIES=	science
-MASTER_SITES=	http://www.uku.fi/~thassine/projects/download/ \
+MASTER_SITES=	http://www.uku.fi/~thassine/projects/download/release20080731/ \
 		http://bioinformatics.org/ghemical/download/
 DISTNAME=	${PORTNAME}-${PORTVERSION}
 
@@ -28,25 +27,10 @@ USE_LDCONFIG=   yes
 .include <bsd.port.pre.mk>
 
 USE_FORTRAN=	yes
+USE_AUTOTOOLS=	autoconf:262
+CONFIGURE_ARGS+=	--enable-mpqc --enable-openbabel --enable-mopac7 
 CONFIGURE_ENV+=	FC="${FC}" F77="${F77}" FFLAGS="${FFLAGS}"
 
-.if exists(${LOCALBASE}/lib/libatlas_r.so) && !defined(WITH_BLAS)
-WITH_ATLAS=	yes
-.endif
-.if defined(WITH_ATLAS)
-LIB_DEPENDS+=	atlas.2:${PORTSDIR}/math/atlas
-BLAS=		-lf77blas -latlas
-LAPACK=		-lalapack
-.else
-LIB_DEPENDS+=	blas.2:${PORTSDIR}/math/blas
-LIB_DEPENDS+=	lapack.4:${PORTSDIR}/math/lapack
-BLAS=		-lblas
-LAPACK=		-llapack
-.endif
-
-CONFIGURE_ARGS+=	--enable-mopac7 --enable-mpqc --enable-openbabel --with-blas="-L${LOCALBASE}/lib ${BLAS}" -with-lapack="-L${LOCALBASE}/lib ${LAPACK}"
-
-USE_AUTOTOOLS=	autoconf:262
 PLIST_SUB=	LIBGHEMICAL_VERSION="${PORTVERSION}"
 
 .include <bsd.port.post.mk>
diff --git a/science/libghemical/distinfo b/science/libghemical/distinfo
index c23da640d46f..c55a9920b849 100644
--- a/science/libghemical/distinfo
+++ b/science/libghemical/distinfo
@@ -1,3 +1,3 @@
-MD5 (libghemical-2.10.tar.gz) = a248fc3aebf26582367326716f208594
-SHA256 (libghemical-2.10.tar.gz) = b0d6639d3b79f865cffb8cf4c2721f6bc7e81c562240a10441766358f4576a7e
-SIZE (libghemical-2.10.tar.gz) = 690680
+MD5 (libghemical-2.98.tar.gz) = 9ca4a60ba9b98f3c5003ee2e1a0ffeb0
+SHA256 (libghemical-2.98.tar.gz) = b4b0f037ed6632c84c6074badeb65cf52d04cbc5580e258275295b7520bd8bf6
+SIZE (libghemical-2.98.tar.gz) = 716300
diff --git a/science/libghemical/files/patch-configure.ac b/science/libghemical/files/patch-configure.ac
index 9487ccf730d7..be873d184dd0 100644
--- a/science/libghemical/files/patch-configure.ac
+++ b/science/libghemical/files/patch-configure.ac
@@ -1,48 +1,13 @@
---- configure.ac.orig	Mon Apr 24 19:58:14 2006
-+++ configure.ac	Mon Jul  3 10:54:47 2006
-@@ -46,6 +46,16 @@
- 		;;
- esac
- 
-+AC_ARG_WITH(blas,
-+[  --with-blas             Gives BLAS name you use(e.g., -lblas).],
-+BLAS=$withval
-+)
-+
-+AC_ARG_WITH(lapack,
-+[  --with-lapack           Gives LAPACK name you use(e.g., -llapack).],
-+LAPACK=$withval
-+)
-+
- AC_ARG_ENABLE(mpqc,[  --enable-mpqc           compile with MPQC support],WITH_MPQC="$enableval",WITH_MPQC="no")
- AC_ARG_ENABLE(mopac7,[  --enable-mopac7         compile with MOPAC7 support],WITH_MOPAC7="$enableval",WITH_MOPAC7="no")
- ##removed20060208##AC_ARG_ENABLE(openbabel,[  --enable-openbabel      compile with OpenBabel support],WITH_OPENBABEL="$enableval",WITH_OPENBABEL="no")
-@@ -69,8 +79,26 @@
- AC_CHECK_LIB([m], [acos])
+--- 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])])
  
  if test $WITH_MPQC = yes; then
 -	AC_CHECK_LIB([blas], [main], , AC_MSG_ERROR([Cannot find blas library needed for MPQC support]))
 -	AC_CHECK_LIB([lapack], [main], , AC_MSG_ERROR([Cannot find lapack library needed for MPQC support]))
-+
-+#Blas and lapack ...actually not checked...
-+BLAS=""
-+ if test "$BLASNAME" = NONE; then
-+   AC_MSG_ERROR([BLAS is required to complete the build])
-+ else
-+   HAVE_BLAS="yes"
-+   BLAS="$BLASNAME"
-+ fi
-+ 
-+ AC_SUBST(HAVE_BLAS)
-+
-+LAPACK=""
-+if test "$LAPACKNAME" = NONE; then
-+  AC_MSG_ERROR([LAPACK is required to complete the build])
-+else
-+  HAVE_LAPACK="yes"
-+  LAPACK="$LAPACKNAME"
-+fi
-+
++#	AC_CHECK_LIB([blas], [main], , AC_MSG_ERROR([Cannot find blas library needed for MPQC support]))
++#	AC_CHECK_LIB([lapack], [main], , AC_MSG_ERROR([Cannot find lapack library needed for MPQC support]))
  	AM_PATH_SC(1.2.5, HAVE_MPQC="yes", HAVE_MPQC="no")
  	if test "${HAVE_MPQC}" = "yes"; then
  		AC_DEFINE([ENABLE_MPQC], [], [Define if you are building a version that interfaces directly with MPQC])
diff --git a/science/libghemical/files/patch-f2c b/science/libghemical/files/patch-f2c
deleted file mode 100644
index be95ed1790cd..000000000000
--- a/science/libghemical/files/patch-f2c
+++ /dev/null
@@ -1,23 +0,0 @@
-We need -lf2c here... we will never depend on g2c.
---- Makefile.in~	Wed Jan 17 12:08:54 2007
-+++ Makefile.in	Wed Jan 17 12:39:20 2007
-@@ -128,7 +128,7 @@
- LTLIBOBJS = @LTLIBOBJS@
- MAKEINFO = @MAKEINFO@
- MOPAC7_CFLAGS = @MOPAC7_CFLAGS@
--MOPAC7_LIBS = @MOPAC7_LIBS@
-+MOPAC7_LIBS = @MOPAC7_LIBS@ -lf2c
- OBJEXT = @OBJEXT@
- PACKAGE = @PACKAGE@
- PACKAGE_BUGREPORT = @PACKAGE_BUGREPORT@
-
-why we need it here again?
---- libghemical.pc.in~	Tue Aug  1 19:46:49 2006
-+++ libghemical.pc.in	Wed Jan 17 13:15:00 2007
-@@ -6,5 +6,5 @@
- Name: libghemical
- Description: A library that contains molecular modelling functionality.
- Version: @LIBVERSION@
--Libs: -L${libdir} -lghemical @SC_LIBS@ @MOPAC7_LIBS@
-+Libs: -L${libdir} -lghemical @SC_LIBS@ @MOPAC7_LIBS@ -lf2c
- Cflags: -I${includedir}/ghemical @SC_CPPFLAGS@ @MOPAC7_CFLAGS@
diff --git a/science/libghemical/pkg-plist b/science/libghemical/pkg-plist
index eff439800d91..b0d626939960 100644
--- a/science/libghemical/pkg-plist
+++ b/science/libghemical/pkg-plist
@@ -17,14 +17,15 @@ include/ghemical/eng2_qm_mm.h
 include/ghemical/engine.h
 include/ghemical/geomopt.h
 include/ghemical/intcrd.h
-include/ghemical/libghemicalconfig2.h
 include/ghemical/libghemicaldefine.h
+include/ghemical/libghemical-features.h
 include/ghemical/mfinder.h
 include/ghemical/model.h
 include/ghemical/moldyn.h
 include/ghemical/notice.h
 include/ghemical/pop_ana.h
 include/ghemical/resonance.h
+include/ghemical/sasaeval.h
 include/ghemical/search.h
 include/ghemical/seqbuild.h
 include/ghemical/tab_mm_default.h
@@ -35,17 +36,17 @@ include/ghemical/typerule.h
 include/ghemical/utility.h
 include/ghemical/v3d.h
 @dirrm include/ghemical
-lib/libghemical.so.0
+lib/libghemical.so.4
 lib/libghemical.so
 lib/libghemical.la
 lib/libghemical.a
 lib/pkgconfig/libghemical.pc
 @dirrm lib/pkgconfig
-share/libghemical/%%LIBGHEMICAL_VERSION%%/amber/all_amino02.in
-share/libghemical/%%LIBGHEMICAL_VERSION%%/amber/all_aminoct02.in
-share/libghemical/%%LIBGHEMICAL_VERSION%%/amber/all_aminont02.in
-share/libghemical/%%LIBGHEMICAL_VERSION%%/amber/all_nuc02.in
-share/libghemical/%%LIBGHEMICAL_VERSION%%/amber/parm99.dat
+share/libghemical/%%LIBGHEMICAL_VERSION%%/amber/all_amino94_MOD.in
+share/libghemical/%%LIBGHEMICAL_VERSION%%/amber/all_aminoct94.in
+share/libghemical/%%LIBGHEMICAL_VERSION%%/amber/all_aminont94.in
+share/libghemical/%%LIBGHEMICAL_VERSION%%/amber/all_nuc94_MOD.in
+share/libghemical/%%LIBGHEMICAL_VERSION%%/amber/parm99_frcmod_ff99SB.dat
 share/libghemical/%%LIBGHEMICAL_VERSION%%/builder/amino.txt
 share/libghemical/%%LIBGHEMICAL_VERSION%%/builder/nucleic.txt
 share/libghemical/%%LIBGHEMICAL_VERSION%%/param_mm/default/atomtypes.txt