science: Fix mpqc, libint and unbreak ghemical, and libghemical atomically

science/ghemical would not link because libghemical.so (from science/
libghemical port) had never been properly linked.  Links to all mpqc "SC"
libraries were added to LDFLAGS to rectify this.  The configure breakage
and solution is described below.

After the version of lang/gcc was bumped from 4.7 to 4.8,
science/libghemical ceased to configure and it was marked broken.  After
recreating the conftest, it was discovered that two versions incompatible
versions of libgcc_s.so were getting pulled in by the realtime linker:
the base version and the gcc48 ports version.

The base version was getting pulled in by science/libint.  To unbreak
libghemical, libint is now built with lang/gcc.  It was necessary to
force libtool to link with LDFLAGS that Mk/bsd.gcc.mk sets so that
the runpaths match across libraries used by libghemical.

When science/mpqc was staged, it utilized libtool which renumbered all
the library versions from 8.0.1 to 7.1.0.  This was caused by the age
component being greater than 0.  By patching configure.in with a new
version, we can generate major SHLIB of 8 again.  While here, fix the
bin/sc-config tool to remove a bad include cflag.

With this fixes, science/ghemical builds successfully.  Bump all 4 of
these ports, remove any BROKEN designation and remove redundant
@dirrm in pkg-plist

8 files changed, 80 insertions, 92 deletions

diff --git a/science/ghemical/Makefile b/science/ghemical/Makefile
index 05f9bfda792..ce4032565c8 100644
--- a/science/ghemical/Makefile
+++ b/science/ghemical/Makefile
@@ -3,7 +3,7 @@
 
 PORTNAME=	ghemical
 PORTVERSION=	3.0.0
-PORTREVISION=	5
+PORTREVISION=	6
 CATEGORIES=	science
 MASTER_SITES=	http://bioinformatics.org/ghemical/download/release20111012/	\
 		http://bioinformatics.org/ghemical/download/current
@@ -25,7 +25,8 @@ USES=		fortran gettext gmake pkgconfig
 USE_GNOME=	glib20 gtk20 libglade2
 USE_GL=		glut
 GNU_CONFIGURE=	yes
-CONFIGURE_ARGS=	--enable-gamess --enable-mpqc --enable-openbabel --enable-gtk --enable-threads --enable-mopac7
+CONFIGURE_ARGS=	--enable-gamess --enable-mpqc --enable-openbabel --enable-gtk \
+		--enable-threads --enable-mopac7
 PLIST_SUB=	GHEMICAL_VERSION="${PORTVERSION}"
 
 CPPFLAGS=	-I${LOCALBASE}/include
diff --git a/science/ghemical/pkg-plist b/science/ghemical/pkg-plist
index 1f7cc40c7a9..2b35e04a38e 100644
--- a/science/ghemical/pkg-plist
+++ b/science/ghemical/pkg-plist
@@ -151,18 +151,3 @@ share/ghemical/%%GHEMICAL_VERSION%%/pixmaps/ghemical.png
 %%NLS%%share/locale/pt_BR/LC_MESSAGES/ghemical.mo
 %%NLS%%share/locale/ru/LC_MESSAGES/ghemical.mo
 %%NLS%%share/locale/sq/LC_MESSAGES/ghemical.mo
-@dirrm share/ghemical/%%GHEMICAL_VERSION%%/pixmaps
-@dirrm share/ghemical/%%GHEMICAL_VERSION%%/user-docs/images
-@dirrm share/ghemical/%%GHEMICAL_VERSION%%/user-docs
-@dirrm share/ghemical/%%GHEMICAL_VERSION%%/glade
-@dirrm share/ghemical/%%GHEMICAL_VERSION%%/examples/transition_state_search/tautomeric_shift_keto_enol
-@dirrm share/ghemical/%%GHEMICAL_VERSION%%/examples/transition_state_search/sigmatropic_rearrangement_Cope
-@dirrm share/ghemical/%%GHEMICAL_VERSION%%/examples/transition_state_search/cycloaddition_Diels-Alder
-@dirrm share/ghemical/%%GHEMICAL_VERSION%%/examples/transition_state_search/carbocation_rearrangement_methide_shift
-@dirrm share/ghemical/%%GHEMICAL_VERSION%%/examples/transition_state_search/carbocation_rearrangement_hydride_shift
-@dirrm share/ghemical/%%GHEMICAL_VERSION%%/examples/transition_state_search/SN2-reaction
-@dirrm share/ghemical/%%GHEMICAL_VERSION%%/examples/transition_state_search/E2-reaction
-@dirrm share/ghemical/%%GHEMICAL_VERSION%%/examples/transition_state_search
-@dirrm share/ghemical/%%GHEMICAL_VERSION%%/examples
-@dirrm share/ghemical/%%GHEMICAL_VERSION%%
-@dirrm share/ghemical
diff --git a/science/libghemical/Makefile b/science/libghemical/Makefile
index 19c715ccafb..f6ba58cbbe1 100644
--- a/science/libghemical/Makefile
+++ b/science/libghemical/Makefile
@@ -3,7 +3,7 @@
 
 PORTNAME=	libghemical
 PORTVERSION=	3.0.0
-PORTREVISION=	4
+PORTREVISION=	5
 CATEGORIES=	science
 MASTER_SITES=	http://bioinformatics.org/ghemical/download/release20111012/	\
 		http://bioinformatics.org/ghemical/download/current
@@ -11,8 +11,6 @@ MASTER_SITES=	http://bioinformatics.org/ghemical/download/release20111012/	\
 MAINTAINER=	ports@FreeBSD.org
 COMMENT=	Support libraries of science/ghemical port
 
-BROKEN=		Fails to configure
-
 BUILD_DEPENDS=	obabel:${PORTSDIR}/science/openbabel \
 		intltool-update:${PORTSDIR}/textproc/intltool \
 		ld:${PORTSDIR}/devel/binutils
@@ -26,7 +24,13 @@ USE_LDCONFIG=   yes
 
 CONFIGURE_ARGS+=	--enable-mpqc
 CPPFLAGS+=	-I${LOCALBASE}/include
-LDFLAGS+=	-L${LOCALBASE}/lib
+LDFLAGS=	-L${LOCALBASE}/lib -lSCbasis -lSCcints -lSCclass \
+		-lSCcontainer -lSCdft -lSCgroup -lSCintv3 -lSCisosurf \
+		-lSCkeyval -lSCmbpt -lSCmbptr12 -lSCmisc -lSCmolecule \
+		-lSCoint3 -lSCoptimize -lSCoptions -lSCpsi -lSCref \
+		-lSCrender -lSCscf -lSCscmat -lSCsolvent -lSCstate \
+		-lSCsymmetry -lSCwfn \
+		-lgfortran -lpthread -lblas -llapack
 PLIST_SUB=	LIBGHEMICAL_VERSION="${PORTVERSION}"
 INSTALL_TARGET=	install-strip
 
diff --git a/science/libghemical/pkg-plist b/science/libghemical/pkg-plist
index ea89ef59fc0..8239250ef4d 100644
--- a/science/libghemical/pkg-plist
+++ b/science/libghemical/pkg-plist
@@ -36,7 +36,6 @@ include/ghemical/typedef.h
 include/ghemical/typerule.h
 include/ghemical/utility.h
 include/ghemical/v3d.h
-@dirrm include/ghemical
 lib/libghemical.so.5.0.1
 lib/libghemical.so.5
 lib/libghemical.so
@@ -74,13 +73,3 @@ share/locale/mk/LC_MESSAGES/libghemical.mo
 share/locale/pt_BR/LC_MESSAGES/libghemical.mo
 share/locale/ru/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
-@dirrm share/libghemical/%%LIBGHEMICAL_VERSION%%/param_mm/prmfit
-@dirrm share/libghemical/%%LIBGHEMICAL_VERSION%%/param_mm/default
-@dirrm share/libghemical/%%LIBGHEMICAL_VERSION%%/param_mm
-@dirrm share/libghemical/%%LIBGHEMICAL_VERSION%%/amber
-@dirrm share/libghemical/%%LIBGHEMICAL_VERSION%%/builder
-@dirrm share/libghemical/%%LIBGHEMICAL_VERSION%%
-@dirrm share/libghemical
diff --git a/science/libint/Makefile b/science/libint/Makefile
index 95e56607fe8..5edc3d5a0e2 100644
--- a/science/libint/Makefile
+++ b/science/libint/Makefile
@@ -3,14 +3,21 @@
 
 PORTNAME=	libint
 PORTVERSION=	1.1.4
-PORTREVISION=	1
+PORTREVISION=	2
 CATEGORIES=	science
 MASTER_SITES=	http://www.files.chem.vt.edu/chem-dept/valeev/software/libint/src/
 
 MAINTAINER=	ports@FreeBSD.org
 COMMENT=	Evaluate the integrals in modern atomic and molecular theory
 
+# USE_GCC=yes is required because libint is used with mpqc which is built
+# by gfortran48 (from lang/gcc) and these two libraries each try to pull in
+# a different version of libgcc_s.so which fails.  Forcing this port to
+# build with lang/gcc as well resolves the conflict that manifests in
+# science/libghemical
+
 USES=		perl5 gmake libtool
+USE_GCC=	yes
 USE_LDCONFIG=	yes
 ALL_TARGET=	# empty
 
@@ -18,7 +25,8 @@ GNU_CONFIGURE=	yes
 CONFIGURE_ARGS=	--enable-shared
 
 post-patch:
-	@${REINPLACE_CMD} -e 's|echo aout|echo elf|' ${WRKSRC}/configure
+	@${REINPLACE_CMD} -e 's| -rpath|${LDFLAGS} -rpath|g' \
+		${WRKSRC}/src/lib/MakeVars.in
 
 post-install:
 	${STRIP_CMD} ${STAGEDIR}${PREFIX}/lib/*.so
diff --git a/science/libint/pkg-plist b/science/libint/pkg-plist
index e366e807a2f..d633a2e0005 100644
--- a/science/libint/pkg-plist
+++ b/science/libint/pkg-plist
@@ -15,6 +15,3 @@ lib/libr12-stable.so.1
 lib/libr12-stable.so.1.0.0
 lib/libr12.a
 lib/libr12.so
-@dirrm include/libderiv
-@dirrm include/libint
-@dirrm include/libr12
diff --git a/science/mpqc/Makefile b/science/mpqc/Makefile
index 6929448be3e..fd4a122a1ff 100644
--- a/science/mpqc/Makefile
+++ b/science/mpqc/Makefile
@@ -3,7 +3,7 @@
 
 PORTNAME=	mpqc
 PORTVERSION=	2.3.1
-PORTREVISION=	23
+PORTREVISION=	24
 CATEGORIES=	science parallel
 MASTER_SITES=	SF
 
@@ -16,12 +16,11 @@ GNU_CONFIGURE=	yes
 USES=		fortran gmake libtool perl5 tar:bzip2
 USE_AUTOTOOLS=	autoconf
 USE_LDCONFIG=	yes
-MPQC_COMMAND=	${PREFIX}/bin/mpqc
 
 CONFIGURE_ARGS+=--with-cc=${CC} \
 		--with-cxx=${CXX} \
 		--with-f77=${FC} \
-		--with-include="-I${WRKDIR} -I${LOCALBASE}/include" \
+		--with-include="-I${LOCALBASE}/include" \
 		--with-libdirs="-L${LOCALBASE}/lib ${LDFLAGS}" \
 		--with-blas="${BLAS}" \
 		--with-lapack="${LAPACK}" \
@@ -84,6 +83,11 @@ CFLAGS+=	-O2 -ffast-math
 CXXFLAGS+=	-O2 -ffast-math
 .endif
 
+post-patch:
+	# To get so.8.0.1, we need to -version-info to show 8.1.0
+	# <current>:<rev>:<age> => so.(current-age).(age).(rev)
+	${REINPLACE_CMD} -e 's|\[8:0:1\]|\[8:1:0\]|' ${WRKSRC}/configure.in
+
 do-build:
 	(cd ${WRKSRC} && ${MAKE_CMD})
 .if ${PORT_OPTIONS:MDOCS}
diff --git a/science/mpqc/pkg-plist b/science/mpqc/pkg-plist
index db911e95fa2..3aadea1f174 100644
--- a/science/mpqc/pkg-plist
+++ b/science/mpqc/pkg-plist
@@ -353,108 +353,108 @@ include/scdirlist.h
 @dirrm include/chemistry
 lib/libSCbasis.a
 lib/libSCbasis.so
-lib/libSCbasis.so.7
-lib/libSCbasis.so.7.1.0
+lib/libSCbasis.so.8
+lib/libSCbasis.so.8.0.1
 lib/libSCcints.so
-lib/libSCcints.so.7
-lib/libSCcints.so.7.1.0
+lib/libSCcints.so.8
+lib/libSCcints.so.8.0.1
 lib/libSCcints.a
 lib/libSCclass.a
 lib/libSCclass.so
-lib/libSCclass.so.7
-lib/libSCclass.so.7.1.0
+lib/libSCclass.so.8
+lib/libSCclass.so.8.0.1
 lib/libSCcontainer.a
 lib/libSCcontainer.so
-lib/libSCcontainer.so.7
-lib/libSCcontainer.so.7.1.0
+lib/libSCcontainer.so.8
+lib/libSCcontainer.so.8.0.1
 lib/libSCdft.a
 lib/libSCdft.so
-lib/libSCdft.so.7
-lib/libSCdft.so.7.1.0
+lib/libSCdft.so.8
+lib/libSCdft.so.8.0.1
 lib/libSCgroup.a
 lib/libSCgroup.so
-lib/libSCgroup.so.7
-lib/libSCgroup.so.7.1.0
+lib/libSCgroup.so.8
+lib/libSCgroup.so.8.0.1
 lib/libSCintv3.a
 lib/libSCintv3.so
-lib/libSCintv3.so.7
-lib/libSCintv3.so.7.1.0
+lib/libSCintv3.so.8
+lib/libSCintv3.so.8.0.1
 lib/libSCisosurf.a
 lib/libSCisosurf.so
-lib/libSCisosurf.so.7
-lib/libSCisosurf.so.7.1.0
+lib/libSCisosurf.so.8
+lib/libSCisosurf.so.8.0.1
 lib/libSCkeyval.a
 lib/libSCkeyval.so
-lib/libSCkeyval.so.7
-lib/libSCkeyval.so.7.1.0
+lib/libSCkeyval.so.8
+lib/libSCkeyval.so.8.0.1
 lib/libSCmbpt.a
 lib/libSCmbpt.so
-lib/libSCmbpt.so.7
-lib/libSCmbpt.so.7.1.0
+lib/libSCmbpt.so.8
+lib/libSCmbpt.so.8.0.1
 lib/libSCmbptr12.so
-lib/libSCmbptr12.so.7
-lib/libSCmbptr12.so.7.1.0
+lib/libSCmbptr12.so.8
+lib/libSCmbptr12.so.8.0.1
 lib/libSCmbptr12.a
 lib/libSCmisc.a
 lib/libSCmisc.so
-lib/libSCmisc.so.7
-lib/libSCmisc.so.7.1.0
+lib/libSCmisc.so.8
+lib/libSCmisc.so.8.0.1
 lib/libSCmolecule.a
 lib/libSCmolecule.so
-lib/libSCmolecule.so.7
-lib/libSCmolecule.so.7.1.0
+lib/libSCmolecule.so.8
+lib/libSCmolecule.so.8.0.1
 lib/libSCoint3.a
 lib/libSCoint3.so
-lib/libSCoint3.so.7
-lib/libSCoint3.so.7.1.0
+lib/libSCoint3.so.8
+lib/libSCoint3.so.8.0.1
 lib/libSCoptimize.a
 lib/libSCoptimize.so
-lib/libSCoptimize.so.7
-lib/libSCoptimize.so.7.1.0
+lib/libSCoptimize.so.8
+lib/libSCoptimize.so.8.0.1
 lib/libSCoptions.a
 lib/libSCoptions.so
-lib/libSCoptions.so.7
-lib/libSCoptions.so.7.1.0
+lib/libSCoptions.so.8
+lib/libSCoptions.so.8.0.1
 lib/libSCpsi.a
 lib/libSCpsi.so
-lib/libSCpsi.so.7
-lib/libSCpsi.so.7.1.0
+lib/libSCpsi.so.8
+lib/libSCpsi.so.8.0.1
 lib/libSCref.a
 lib/libSCref.so
-lib/libSCref.so.7
-lib/libSCref.so.7.1.0
+lib/libSCref.so.8
+lib/libSCref.so.8.0.1
 lib/libSCrender.a
 lib/libSCrender.so
-lib/libSCrender.so.7
-lib/libSCrender.so.7.1.0
+lib/libSCrender.so.8
+lib/libSCrender.so.8.0.1
 lib/libSCscf.a
 lib/libSCscf.so
-lib/libSCscf.so.7
-lib/libSCscf.so.7.1.0
+lib/libSCscf.so.8
+lib/libSCscf.so.8.0.1
 lib/libSCscmat.a
 lib/libSCscmat.so
-lib/libSCscmat.so.7
-lib/libSCscmat.so.7.1.0
+lib/libSCscmat.so.8
+lib/libSCscmat.so.8.0.1
 lib/libSCsolvent.a
 lib/libSCsolvent.so
-lib/libSCsolvent.so.7
-lib/libSCsolvent.so.7.1.0
+lib/libSCsolvent.so.8
+lib/libSCsolvent.so.8.0.1
 lib/libSCstate.a
 lib/libSCstate.so
-lib/libSCstate.so.7
-lib/libSCstate.so.7.1.0
+lib/libSCstate.so.8
+lib/libSCstate.so.8.0.1
 lib/libSCsymmetry.a
 lib/libSCsymmetry.so
-lib/libSCsymmetry.so.7
-lib/libSCsymmetry.so.7.1.0
+lib/libSCsymmetry.so.8
+lib/libSCsymmetry.so.8.0.1
 lib/libSCwfn.a
 lib/libSCwfn.so
-lib/libSCwfn.so.7
-lib/libSCwfn.so.7.1.0
+lib/libSCwfn.so.8
+lib/libSCwfn.so.8.0.1
 lib/libmpqc.a
 lib/libmpqc.so
-lib/libmpqc.so.7
-lib/libmpqc.so.7.1.0
+lib/libmpqc.so.8
+lib/libmpqc.so.8.0.1
 %%DOCS%%man/man1/mpqc.1.gz
 %%DOCS%%man/man1/mpqcrun.1.gz
 %%DOCS%%man/man1/scls.1.gz