svn commit: r369236 - in head/science: ghemical libghemical libint mpqc

Thu Sep 25 11:04:05 UTC 2014

Author: marino
Date: Thu Sep 25 11:04:02 2014
New Revision: 369236
URL: http://svnweb.freebsd.org/changeset/ports/369236
QAT: https://qat.redports.org/buildarchive/r369236/

Log:
  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

Modified:
  head/science/ghemical/Makefile
  head/science/ghemical/pkg-plist
  head/science/libghemical/Makefile
  head/science/libghemical/pkg-plist
  head/science/libint/Makefile
  head/science/libint/pkg-plist
  head/science/mpqc/Makefile
  head/science/mpqc/pkg-plist

Modified: head/science/ghemical/Makefile
==============================================================================

--- head/science/ghemical/Makefile	Thu Sep 25 11:03:20 2014	(r369235)
+++ head/science/ghemical/Makefile	Thu Sep 25 11:04:02 2014	(r369236)
@@ -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

Modified: head/science/ghemical/pkg-plist
==============================================================================
--- head/science/ghemical/pkg-plist	Thu Sep 25 11:03:20 2014	(r369235)
+++ head/science/ghemical/pkg-plist	Thu Sep 25 11:04:02 2014	(r369236)
@@ -151,18 +151,3 @@ share/ghemical/%%GHEMICAL_VERSION%%/pixm
 %%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
- at dirrm share/ghemical/%%GHEMICAL_VERSION%%/pixmaps
- at dirrm share/ghemical/%%GHEMICAL_VERSION%%/user-docs/images
- at dirrm share/ghemical/%%GHEMICAL_VERSION%%/user-docs
- at dirrm share/ghemical/%%GHEMICAL_VERSION%%/glade
- at dirrm share/ghemical/%%GHEMICAL_VERSION%%/examples/transition_state_search/tautomeric_shift_keto_enol
- at dirrm share/ghemical/%%GHEMICAL_VERSION%%/examples/transition_state_search/sigmatropic_rearrangement_Cope
- at dirrm share/ghemical/%%GHEMICAL_VERSION%%/examples/transition_state_search/cycloaddition_Diels-Alder
- at dirrm share/ghemical/%%GHEMICAL_VERSION%%/examples/transition_state_search/carbocation_rearrangement_methide_shift
- at dirrm share/ghemical/%%GHEMICAL_VERSION%%/examples/transition_state_search/carbocation_rearrangement_hydride_shift
- at dirrm share/ghemical/%%GHEMICAL_VERSION%%/examples/transition_state_search/SN2-reaction
- at dirrm share/ghemical/%%GHEMICAL_VERSION%%/examples/transition_state_search/E2-reaction
- at dirrm share/ghemical/%%GHEMICAL_VERSION%%/examples/transition_state_search
- at dirrm share/ghemical/%%GHEMICAL_VERSION%%/examples
- at dirrm share/ghemical/%%GHEMICAL_VERSION%%
- at dirrm share/ghemical

Modified: head/science/libghemical/Makefile
==============================================================================
--- head/science/libghemical/Makefile	Thu Sep 25 11:03:20 2014	(r369235)
+++ head/science/libghemical/Makefile	Thu Sep 25 11:04:02 2014	(r369236)
@@ -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/
 MAINTAINER=	ports at 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
 

Modified: head/science/libghemical/pkg-plist
==============================================================================
--- head/science/libghemical/pkg-plist	Thu Sep 25 11:03:20 2014	(r369235)
+++ head/science/libghemical/pkg-plist	Thu Sep 25 11:04:02 2014	(r369236)
@@ -36,7 +36,6 @@ include/ghemical/typedef.h
 include/ghemical/typerule.h
 include/ghemical/utility.h
 include/ghemical/v3d.h
- at 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.
 share/locale/pt_BR/LC_MESSAGES/libghemical.mo
 share/locale/ru/LC_MESSAGES/libghemical.mo
 share/locale/sq/LC_MESSAGES/libghemical.mo
- at dirrm share/libghemical/%%LIBGHEMICAL_VERSION%%/param_sf/default
- at dirrm share/libghemical/%%LIBGHEMICAL_VERSION%%/param_sf
- at dirrm share/libghemical/%%LIBGHEMICAL_VERSION%%/param_mm/tripos52
- at dirrm share/libghemical/%%LIBGHEMICAL_VERSION%%/param_mm/prmfit
- at dirrm share/libghemical/%%LIBGHEMICAL_VERSION%%/param_mm/default
- at dirrm share/libghemical/%%LIBGHEMICAL_VERSION%%/param_mm
- at dirrm share/libghemical/%%LIBGHEMICAL_VERSION%%/amber
- at dirrm share/libghemical/%%LIBGHEMICAL_VERSION%%/builder
- at dirrm share/libghemical/%%LIBGHEMICAL_VERSION%%
- at dirrm share/libghemical

Modified: head/science/libint/Makefile
==============================================================================
--- head/science/libint/Makefile	Thu Sep 25 11:03:20 2014	(r369235)
+++ head/science/libint/Makefile	Thu Sep 25 11:04:02 2014	(r369236)
@@ -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 at 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

Modified: head/science/libint/pkg-plist
==============================================================================
--- head/science/libint/pkg-plist	Thu Sep 25 11:03:20 2014	(r369235)
+++ head/science/libint/pkg-plist	Thu Sep 25 11:04:02 2014	(r369236)
@@ -15,6 +15,3 @@ lib/libr12-stable.so.1
 lib/libr12-stable.so.1.0.0
 lib/libr12.a
 lib/libr12.so
- at dirrm include/libderiv
- at dirrm include/libint
- at dirrm include/libr12

Modified: head/science/mpqc/Makefile
==============================================================================
--- head/science/mpqc/Makefile	Thu Sep 25 11:03:20 2014	(r369235)
+++ head/science/mpqc/Makefile	Thu Sep 25 11:04:02 2014	(r369236)
@@ -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}

Modified: head/science/mpqc/pkg-plist
==============================================================================
--- head/science/mpqc/pkg-plist	Thu Sep 25 11:03:20 2014	(r369235)
+++ head/science/mpqc/pkg-plist	Thu Sep 25 11:04:02 2014	(r369236)
@@ -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
