science/gromacs: Update to version 4.6.4

- Update to version 4.6.4
- Allow staging

PR:		ports/184224
Submitted by:	KATO Tsuguru <tkato432 yahoo.com>

3 files changed, 111 insertions, 42 deletions

diff --git a/science/gromacs/Makefile b/science/gromacs/Makefile
index 9d4001cd1cc2..05651f5cf638 100644
--- a/science/gromacs/Makefile
+++ b/science/gromacs/Makefile
@@ -2,8 +2,7 @@
 # $FreeBSD$
 
 PORTNAME=	gromacs
-PORTVERSION=	4.6.3
-PORTREVISION=	2
+PORTVERSION=	4.6.4
 CATEGORIES=	science
 MASTER_SITES=	ftp://ftp.gromacs.org/pub/gromacs/
 
@@ -31,59 +30,32 @@ CMAKE_ARGS=	-DBLAS_LIBRARIES:FILEPATH="${BLAS_LIBS}" \
 		-DLAPACK_LIBRARIES:FILEPATH="${LAPACK_LIBS}"
 USE_LDCONFIG=	yes
 
-MAN1=		do_dssp.1 editconf.1 eneconv.1 g_anadock.1 \
-		g_anaeig.1 g_analyze.1 g_angle.1 g_bar.1 \
-		g_bond.1 g_bundle.1 g_chi.1 g_cluster.1 \
-		g_clustsize.1 g_confrms.1 g_covar.1 g_current.1 \
-		g_density.1 g_densmap.1 g_densorder.1 g_dielectric.1 \
-		g_dipoles.1 g_disre.1 g_dist.1 g_dos.1 \
-		g_dyecoupl.1 g_dyndom.1 g_enemat.1 g_energy.1 \
-		g_filter.1 g_gyrate.1 g_h2order.1 g_hbond.1 \
-		g_helix.1 g_helixorient.1 g_hydorder.1 g_kinetics.1 \
-		g_lie.1 g_mdmat.1 g_membed.1 g_mindist.1 \
-		g_morph.1 g_msd.1 g_nmeig.1 g_nmens.1 \
-		g_nmtraj.1 g_order.1 g_pme_error.1 g_polystat.1 \
-		g_potential.1 g_principal.1 g_protonate.1 g_rama.1 \
-		g_rdf.1 g_rms.1 g_rmsdist.1 g_rmsf.1 \
-		g_rotacf.1 g_rotmat.1 g_saltbr.1 g_sans.1 \
-		g_sas.1 g_select.1 g_sgangle.1 g_sham.1 \
-		g_sigeps.1 g_sorient.1 g_spatial.1 g_spol.1 \
-		g_tcaf.1 g_traj.1 g_tune_pme.1 g_vanhove.1 \
-		g_velacc.1 g_wham.1 g_wheel.1 g_x2top.1 \
-		genbox.1 genconf.1 genion.1 genrestr.1 \
-		gmxcheck.1 gmxdump.1 grompp.1 make_edi.1 \
-		make_ndx.1 mdrun.1 mk_angndx.1 pdb2gmx.1 \
-		tpbconv.1 trjcat.1 trjconv.1 trjorder.1 \
-		xpm2ps.1
-MAN7=		gromacs.7
-
-NO_STAGE=	yes
 .include <bsd.port.options.mk>
 
 .if ${PORT_OPTIONS:MATLAS}
-LIB_DEPENDS+=	alapack:${PORTSDIR}/math/atlas
+LIB_DEPENDS+=	libalapack.so:${PORTSDIR}/math/atlas
 BLAS_LIBS=	${LOCALBASE}/lib/libcblas.so;${LOCALBASE}/lib/libf77blas.so
 LAPACK_LIBS=	${LOCALBASE}/lib/libalapack.so
 .else
-LIB_DEPENDS+=	blas:${PORTSDIR}/math/blas \
-		lapack:${PORTSDIR}/math/lapack
+LIB_DEPENDS+=	libblas.so:${PORTSDIR}/math/blas \
+		liblapack.so:${PORTSDIR}/math/lapack
 BLAS_LIBS=	${LOCALBASE}/lib/libblas.so
 LAPACK_LIBS=	${LOCALBASE}/lib/liblapack.so
 .endif
 
 .if ${PORT_OPTIONS:MFLOAT}
 BUILD_DEPENDS+=	fftw3>0:${PORTSDIR}/math/fftw3
-LIB_DEPENDS+=	fftw3f:${PORTSDIR}/math/fftw3-float
+LIB_DEPENDS+=	libfftw3f.so:${PORTSDIR}/math/fftw3-float
 CMAKE_ARGS+=	-DGMX_DOUBLE:BOOL=OFF
 PLIST_SUB+=	SUFFIX_D=""
 .else
-LIB_DEPENDS+=	fftw3:${PORTSDIR}/math/fftw3
+LIB_DEPENDS+=	libfftw3.so:${PORTSDIR}/math/fftw3
 CMAKE_ARGS+=	-DGMX_DOUBLE:BOOL=ON
 PLIST_SUB+=	SUFFIX_D="_d"
 .endif
 
 .if ${PORT_OPTIONS:MGSL}
-LIB_DEPENDS+=	gsl:${PORTSDIR}/math/gsl
+LIB_DEPENDS+=	libgsl.so:${PORTSDIR}/math/gsl
 CMAKE_ARGS+=	-DGMX_GSL:BOOL=ON
 .else
 CMAKE_ARGS+=	-DGMX_GSL:BOOL=OFF
@@ -97,7 +69,6 @@ CMAKE_ARGS+=	-DGMX_CPU_ACCELERATION:STRING="None"
 USE_XORG=	xext x11
 CMAKE_ARGS+=	-DGMX_X11:BOOL=ON
 PLIST_SUB+=	X11=""
-MAN1+=		g_xrama.1 ngmx.1
 .else
 CMAKE_ARGS+=	-DGMX_X11:BOOL=OFF
 PLIST_SUB+=	X11="@comment "
diff --git a/science/gromacs/distinfo b/science/gromacs/distinfo
index 80e599e6bfe4..0b5360675957 100644
--- a/science/gromacs/distinfo
+++ b/science/gromacs/distinfo
@@ -1,2 +1,2 @@
-SHA256 (gromacs-4.6.3.tar.gz) = b748f912b606032471e7da2db349db44f53d717b2490ad9316eb962bd75eccd4
-SIZE (gromacs-4.6.3.tar.gz) = 10985615
+SHA256 (gromacs-4.6.4.tar.gz) = 4d4f15e6d10e97aff7a21d3bb5536283cf8ba669589310c456c1bb22bdfe7d8e
+SIZE (gromacs-4.6.4.tar.gz) = 10990996
diff --git a/science/gromacs/pkg-plist b/science/gromacs/pkg-plist
index 19f42e3b81fd..94182c12f5de 100644
--- a/science/gromacs/pkg-plist
+++ b/science/gromacs/pkg-plist
@@ -159,7 +159,13 @@ include/gromacs/gmx_omp.h
 include/gromacs/gmx_omp_nthreads.h
 include/gromacs/gmx_parallel_3dfft.h
 include/gromacs/gmx_random.h
+include/gromacs/gmx_simd4_macros.h
+include/gromacs/gmx_simd4_ref.h
 include/gromacs/gmx_simd_macros.h
+include/gromacs/gmx_simd_math_double.h
+include/gromacs/gmx_simd_math_single.h
+include/gromacs/gmx_simd_ref.h
+include/gromacs/gmx_simd_vec.h
 include/gromacs/gmx_sort.h
 include/gromacs/gmx_statistics.h
 include/gromacs/gmx_system_xdr.h
@@ -167,8 +173,6 @@ include/gromacs/gmx_thread_affinity.h
 include/gromacs/gmx_wallcycle.h
 include/gromacs/gmx_x86_avx_128_fma.h
 include/gromacs/gmx_x86_avx_256.h
-include/gromacs/gmx_x86_simd_double.h
-include/gromacs/gmx_x86_simd_single.h
 include/gromacs/gmx_x86_sse2.h
 include/gromacs/gmx_x86_sse4_1.h
 include/gromacs/gmxcomplex.h
@@ -356,11 +360,106 @@ libdata/pkgconfig/libgmx%%SUFFIX_MPI%%%%SUFFIX_D%%.pc
 libdata/pkgconfig/libgmxana%%SUFFIX_MPI%%%%SUFFIX_D%%.pc
 libdata/pkgconfig/libgmxpreprocess%%SUFFIX_MPI%%%%SUFFIX_D%%.pc
 libdata/pkgconfig/libmd%%SUFFIX_MPI%%%%SUFFIX_D%%.pc
+man/man1/do_dssp.1.gz
+man/man1/editconf.1.gz
+man/man1/eneconv.1.gz
+man/man1/g_anadock.1.gz
+man/man1/g_anaeig.1.gz
+man/man1/g_analyze.1.gz
+man/man1/g_angle.1.gz
+man/man1/g_bar.1.gz
+man/man1/g_bond.1.gz
+man/man1/g_bundle.1.gz
+man/man1/g_chi.1.gz
+man/man1/g_cluster.1.gz
+man/man1/g_clustsize.1.gz
+man/man1/g_confrms.1.gz
+man/man1/g_covar.1.gz
+man/man1/g_current.1.gz
+man/man1/g_density.1.gz
+man/man1/g_densmap.1.gz
+man/man1/g_densorder.1.gz
+man/man1/g_dielectric.1.gz
+man/man1/g_dipoles.1.gz
+man/man1/g_disre.1.gz
+man/man1/g_dist.1.gz
+man/man1/g_dos.1.gz
+man/man1/g_dyecoupl.1.gz
+man/man1/g_dyndom.1.gz
+man/man1/g_enemat.1.gz
+man/man1/g_energy.1.gz
+man/man1/g_filter.1.gz
+man/man1/g_gyrate.1.gz
+man/man1/g_h2order.1.gz
+man/man1/g_hbond.1.gz
+man/man1/g_helix.1.gz
+man/man1/g_helixorient.1.gz
+man/man1/g_hydorder.1.gz
+man/man1/g_kinetics.1.gz
+man/man1/g_lie.1.gz
+man/man1/g_mdmat.1.gz
+man/man1/g_membed.1.gz
+man/man1/g_mindist.1.gz
+man/man1/g_morph.1.gz
+man/man1/g_msd.1.gz
+man/man1/g_nmeig.1.gz
+man/man1/g_nmens.1.gz
+man/man1/g_nmtraj.1.gz
+man/man1/g_order.1.gz
+man/man1/g_pme_error.1.gz
+man/man1/g_polystat.1.gz
+man/man1/g_potential.1.gz
+man/man1/g_principal.1.gz
+man/man1/g_protonate.1.gz
+man/man1/g_rama.1.gz
+man/man1/g_rdf.1.gz
+man/man1/g_rms.1.gz
+man/man1/g_rmsdist.1.gz
+man/man1/g_rmsf.1.gz
+man/man1/g_rotacf.1.gz
+man/man1/g_rotmat.1.gz
+man/man1/g_saltbr.1.gz
+man/man1/g_sans.1.gz
+man/man1/g_sas.1.gz
+man/man1/g_select.1.gz
+man/man1/g_sgangle.1.gz
+man/man1/g_sham.1.gz
+man/man1/g_sigeps.1.gz
+man/man1/g_sorient.1.gz
+man/man1/g_spatial.1.gz
+man/man1/g_spol.1.gz
+man/man1/g_tcaf.1.gz
+man/man1/g_traj.1.gz
+man/man1/g_tune_pme.1.gz
+man/man1/g_vanhove.1.gz
+man/man1/g_velacc.1.gz
+man/man1/g_wham.1.gz
+man/man1/g_wheel.1.gz
+man/man1/g_x2top.1.gz
+%%X11%%man/man1/g_xrama.1.gz
+man/man1/genbox.1.gz
+man/man1/genconf.1.gz
+man/man1/genion.1.gz
+man/man1/genrestr.1.gz
+man/man1/gmxcheck.1.gz
+man/man1/gmxdump.1.gz
+man/man1/grompp.1.gz
+man/man1/make_edi.1.gz
+man/man1/make_ndx.1.gz
+man/man1/mdrun.1.gz
+man/man1/mk_angndx.1.gz
+%%X11%%man/man1/ngmx.1.gz
+man/man1/pdb2gmx.1.gz
+man/man1/tpbconv.1.gz
+man/man1/trjcat.1.gz
+man/man1/trjconv.1.gz
+man/man1/trjorder.1.gz
+man/man1/xpm2ps.1.gz
+man/man7/gromacs.7.gz
 %%DATADIR%%/COPYING
 %%DATADIR%%/CTestTestfile.cmake
 %%DATADIR%%/README.tutor
 %%DATADIR%%/README_FreeEnergyModifications.txt
-%%DATADIR%%/html/gmxfaq.html
 %%DATADIR%%/html/images/1ctf-0.2.jpg
 %%DATADIR%%/html/images/1ctf-0.5.jpg
 %%DATADIR%%/html/images/1ctf-0.jpg
@@ -547,7 +646,6 @@ libdata/pkgconfig/libmd%%SUFFIX_MPI%%%%SUFFIX_D%%.pc
 %%DATADIR%%/html/online/xtc.html
 %%DATADIR%%/html/online/xvg.html
 %%DATADIR%%/html/online/yourown.html
-%%DATADIR%%/html/online.html
 %%DATADIR%%/template/CMakeLists.txt
 %%DATADIR%%/template/Makefile.pkg
 %%DATADIR%%/template/README