Date: Mon, 25 Nov 2013 02:52:33 +0900 From: KATO Tsuguru <tkato432@yahoo.com> To: FreeBSD-gnats-submit@FreeBSD.org Subject: ports/184224: science/gromacs: Update to version 4.6.4 Message-ID: <20131125025233.369cf7f05cb19b1049a6afed@yahoo.com> Resent-Message-ID: <201311241810.rAOIA2vR046782@freefall.freebsd.org>
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>Number: 184224 >Category: ports >Synopsis: science/gromacs: Update to version 4.6.4 >Confidential: no >Severity: non-critical >Priority: low >Responsible: freebsd-ports-bugs >State: open >Quarter: >Keywords: >Date-Required: >Class: change-request >Submitter-Id: current-users >Arrival-Date: Sun Nov 24 18:10:01 UTC 2013 >Closed-Date: >Last-Modified: >Originator: KATO Tsuguru >Release: FreeBSD 8.4-RELEASE-p4 i386 >Organization: >Environment: >Description: - Update to version 4.6.4 >How-To-Repeat: >Fix: diff -urN /usr/ports/science/gromacs/Makefile science/gromacs/Makefile --- /usr/ports/science/gromacs/Makefile 2013-11-06 22:05:52.000000000 +0900 +++ science/gromacs/Makefile 2013-11-25 00:00:00.000000000 +0900 @@ -2,8 +2,7 @@ # $FreeBSD: head/science/gromacs/Makefile 331644 2013-10-26 00:52:33Z gerald $ 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 @@ -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 @@ 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 -urN /usr/ports/science/gromacs/distinfo science/gromacs/distinfo --- /usr/ports/science/gromacs/distinfo 2013-11-06 22:05:52.000000000 +0900 +++ science/gromacs/distinfo 2013-11-25 00:00:00.000000000 +0900 @@ -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 -urN /usr/ports/science/gromacs/pkg-plist science/gromacs/pkg-plist --- /usr/ports/science/gromacs/pkg-plist 2013-11-06 22:05:52.000000000 +0900 +++ science/gromacs/pkg-plist 2013-11-25 00:00:00.000000000 +0900 @@ -159,7 +159,13 @@ 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_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/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 @@ %%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 >Release-Note: >Audit-Trail: >Unformatted:
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