diff --git a/science/plumed/Makefile b/science/plumed/Makefile index cf0ec9948065..0e8a83c8fcfe 100644 --- a/science/plumed/Makefile +++ b/science/plumed/Makefile @@ -1,49 +1,50 @@ PORTNAME= plumed -DISTVERSION= 2.8.0 -PORTREVISION= 2 +DISTVERSION= 2.9.3 CATEGORIES= science graphics MASTER_SITES= https://github.com/${PORTNAME}/${PORTNAME}2/releases/download/v${DISTVERSION}/ MAINTAINER= yuri@FreeBSD.org COMMENT= PLUgin for MolEcular Dynamics WWW= https://www.plumed.org/ LICENSE= LGPL3 LICENSE_FILE= ${WRKSRC}/COPYING.LESSER BROKEN_i386= undefined reference to `__atomic_load' BUILD_DEPENDS= bash:shells/bash LIB_DEPENDS= libblas.so:math/blas \ libfftw3.so:math/fftw3 \ libgsl.so:math/gsl \ liblapack.so:math/lapack RUN_DEPENDS= bash:shells/bash TEST_DEPENDS= gawk:lang/gawk USES= autoreconf compiler:c++11-lang gmake localbase pkgconfig shebangfix tar:tgz USE_LDCONFIG= yes SHEBANG_GLOB= *.sh SHEBANG_FILES= src/maketools/makecmd \ src/maketools/xxd \ regtest/scripts/check \ regtest/scripts/run \ regtest/scripts/what GNU_CONFIGURE= yes CONFIGURE_ARGS= --enable-shared --disable-python TEST_TARGET= check # the 'installcheck' target checks installed version # 1 test is known to fail: https://github.com/plumed/plumed2/issues/782 BINARY_ALIAS= make=${GMAKE} # only needed for tests post-patch: @${REINPLACE_CMD} -e 's|#! /bin/bash|#! ${LOCALBASE}/bin/bash|' ${WRKSRC}/src/lib/Makefile post-install: @${RMDIR} ${STAGEDIR}${PREFIX}/lib/plumed/obj @cd ${STAGEDIR}${PREFIX} && ${STRIP_CMD} bin/plumed lib/plumed/plumed-runtime lib/libplumed.so lib/libplumedKernel.so +# tests as of 2.9.3: 277 tests performed, 352 tests not applicable + .include diff --git a/science/plumed/distinfo b/science/plumed/distinfo index 7f199b706e8b..578262619f8a 100644 --- a/science/plumed/distinfo +++ b/science/plumed/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1652729274 -SHA256 (plumed-2.8.0.tgz) = 24b243c531fa83752be5e54f5f0b677164855da539bc2b2c5b00dcc9f192aa82 -SIZE (plumed-2.8.0.tgz) = 107630231 +TIMESTAMP = 1737474140 +SHA256 (plumed-2.9.3.tgz) = 2ba5095bc7c7cfde1ca95780c1240d852b7dc1b00c9de5b31e607120449ff827 +SIZE (plumed-2.9.3.tgz) = 118993592 diff --git a/science/plumed/pkg-plist b/science/plumed/pkg-plist index ce031e5ccc6b..5e12bcbf2910 100644 --- a/science/plumed/pkg-plist +++ b/science/plumed/pkg-plist @@ -1,528 +1,623 @@ bin/plumed bin/plumed-config bin/plumed-patch include/plumed/analysis/AnalysisBase.h include/plumed/analysis/AverageVessel.h include/plumed/analysis/DataCollectionObject.h include/plumed/analysis/LandmarkSelectionBase.h include/plumed/analysis/ReadAnalysisFrames.h include/plumed/asmjit/arch.h include/plumed/asmjit/arm.h include/plumed/asmjit/asmjit.h include/plumed/asmjit/asmjit_apibegin.h include/plumed/asmjit/asmjit_apiend.h include/plumed/asmjit/asmjit_build.h include/plumed/asmjit/assembler.h include/plumed/asmjit/base.h include/plumed/asmjit/codebuilder.h include/plumed/asmjit/codecompiler.h include/plumed/asmjit/codeemitter.h include/plumed/asmjit/codeholder.h include/plumed/asmjit/constpool.h include/plumed/asmjit/cpuinfo.h include/plumed/asmjit/func.h include/plumed/asmjit/globals.h include/plumed/asmjit/inst.h include/plumed/asmjit/logging.h include/plumed/asmjit/misc_p.h include/plumed/asmjit/moved_string.h include/plumed/asmjit/operand.h include/plumed/asmjit/osutils.h include/plumed/asmjit/regalloc_p.h include/plumed/asmjit/runtime.h include/plumed/asmjit/simdtypes.h include/plumed/asmjit/utils.h include/plumed/asmjit/vmem.h include/plumed/asmjit/x86.h include/plumed/asmjit/x86assembler.h include/plumed/asmjit/x86builder.h include/plumed/asmjit/x86compiler.h include/plumed/asmjit/x86emitter.h include/plumed/asmjit/x86globals.h include/plumed/asmjit/x86inst.h include/plumed/asmjit/x86instimpl_p.h include/plumed/asmjit/x86internal_p.h include/plumed/asmjit/x86logging_p.h include/plumed/asmjit/x86misc.h include/plumed/asmjit/x86operand.h include/plumed/asmjit/x86regalloc_p.h include/plumed/asmjit/zone.h include/plumed/bias/ActionRegister.h include/plumed/bias/Bias.h include/plumed/bias/ReweightBase.h include/plumed/blas/blas.h include/plumed/blas/def_external.h include/plumed/blas/def_internal.h include/plumed/blas/real.h include/plumed/cltools/CLTool.h include/plumed/cltools/CLToolRegister.h include/plumed/colvar/ActionRegister.h include/plumed/colvar/Colvar.h include/plumed/colvar/CoordinationBase.h include/plumed/colvar/PathMSDBase.h include/plumed/config/Config.h include/plumed/config/version.h include/plumed/core/Action.h include/plumed/core/ActionAnyorder.h include/plumed/core/ActionAtomistic.h include/plumed/core/ActionPilot.h include/plumed/core/ActionRegister.h include/plumed/core/ActionSet.h include/plumed/core/ActionSetup.h include/plumed/core/ActionShortcut.h include/plumed/core/ActionWithArguments.h include/plumed/core/ActionWithValue.h include/plumed/core/ActionWithVirtualAtom.h include/plumed/core/Atoms.h include/plumed/core/CLTool.h include/plumed/core/CLToolMain.h include/plumed/core/CLToolRegister.h include/plumed/core/Colvar.h include/plumed/core/DataFetchingObject.h include/plumed/core/ExchangePatterns.h include/plumed/core/FlexibleBin.h include/plumed/core/GREX.h include/plumed/core/GenericMolInfo.h include/plumed/core/MDAtoms.h +include/plumed/core/ModuleMap.h include/plumed/core/PlumedMain.h include/plumed/core/PlumedMainInitializer.h include/plumed/core/TargetDist.h include/plumed/core/Value.h include/plumed/core/WithCmd.h include/plumed/function/ActionRegister.h include/plumed/function/Function.h include/plumed/gridtools/ActionWithGrid.h include/plumed/gridtools/ActionWithInputGrid.h include/plumed/gridtools/ActionWithIntegral.h include/plumed/gridtools/AverageOnGrid.h include/plumed/gridtools/ContourFindingBase.h include/plumed/gridtools/GridPrintingBase.h include/plumed/gridtools/GridSearch.h include/plumed/gridtools/GridVessel.h include/plumed/gridtools/HistogramOnGrid.h include/plumed/isdb/MetainferenceBase.h include/plumed/lapack/def_external.h include/plumed/lapack/def_internal.h include/plumed/lapack/lapack.h include/plumed/lapack/lapack_limits.h include/plumed/lapack/real.h include/plumed/lepton/CompiledExpression.h include/plumed/lepton/CustomFunction.h include/plumed/lepton/Exception.h include/plumed/lepton/ExpressionProgram.h include/plumed/lepton/ExpressionTreeNode.h include/plumed/lepton/Lepton.h include/plumed/lepton/MSVC_erfc.h include/plumed/lepton/Operation.h include/plumed/lepton/ParsedExpression.h include/plumed/lepton/Parser.h include/plumed/lepton/windowsIncludes.h include/plumed/mapping/Mapping.h include/plumed/mapping/PathBase.h include/plumed/mapping/PathReparameterization.h include/plumed/mapping/TrigonometricPathVessel.h include/plumed/molfile/Gromacs.h include/plumed/molfile/endianswap.h include/plumed/molfile/fastio.h include/plumed/molfile/largefiles.h include/plumed/molfile/libmolfile_plugin.h include/plumed/molfile/molfile_plugin.h include/plumed/molfile/periodic_table.h include/plumed/molfile/readpdb.h include/plumed/molfile/vmdplugin.h include/plumed/multicolvar/ActionVolume.h include/plumed/multicolvar/AtomValuePack.h include/plumed/multicolvar/BridgedMultiColvarFunction.h include/plumed/multicolvar/CatomPack.h include/plumed/multicolvar/MultiColvarBase.h include/plumed/multicolvar/MultiColvarFilter.h include/plumed/multicolvar/VolumeGradientBase.h include/plumed/reference/ArgumentOnlyDistance.h include/plumed/reference/DRMSD.h include/plumed/reference/Direction.h include/plumed/reference/FakeFrame.h include/plumed/reference/MetricRegister.h include/plumed/reference/MultiDomainRMSD.h include/plumed/reference/RMSDBase.h include/plumed/reference/ReferenceArguments.h include/plumed/reference/ReferenceAtoms.h include/plumed/reference/ReferenceConfiguration.h include/plumed/reference/ReferenceValuePack.h include/plumed/reference/SingleDomainRMSD.h include/plumed/secondarystructure/SecondaryStructureRMSD.h include/plumed/setup/ActionSetup.h include/plumed/tools/Angle.h include/plumed/tools/AtomNumber.h include/plumed/tools/BiasRepresentation.h include/plumed/tools/Brent1DRootSearch.h include/plumed/tools/Citations.h include/plumed/tools/Communicator.h include/plumed/tools/ConjugateGradient.h include/plumed/tools/DLLoader.h include/plumed/tools/DynamicList.h include/plumed/tools/ERMSD.h include/plumed/tools/Exception.h include/plumed/tools/File.h include/plumed/tools/FileBase.h include/plumed/tools/ForwardDecl.h include/plumed/tools/Grid.h include/plumed/tools/HistogramBead.h include/plumed/tools/IFile.h include/plumed/tools/KernelFunctions.h include/plumed/tools/Keywords.h include/plumed/tools/LatticeReduction.h include/plumed/tools/LinkCells.h include/plumed/tools/Log.h include/plumed/tools/LoopUnroller.h include/plumed/tools/Matrix.h include/plumed/tools/MatrixSquareBracketsAccess.h include/plumed/tools/Minimise1DBrent.h include/plumed/tools/MinimiseBase.h include/plumed/tools/MolDataClass.h include/plumed/tools/MultiValue.h include/plumed/tools/NeighborList.h include/plumed/tools/OFile.h include/plumed/tools/OpenMP.h include/plumed/tools/PDB.h include/plumed/tools/Pbc.h include/plumed/tools/PlumedHandle.h include/plumed/tools/RMSD.h include/plumed/tools/Random.h include/plumed/tools/RootFindingBase.h include/plumed/tools/Stopwatch.h include/plumed/tools/Subprocess.h include/plumed/tools/SwitchingFunction.h include/plumed/tools/Tensor.h include/plumed/tools/Tools.h include/plumed/tools/Torsion.h include/plumed/tools/Tree.h include/plumed/tools/TypesafePtr.h include/plumed/tools/Units.h include/plumed/tools/Vector.h include/plumed/tools/h36.h include/plumed/vatom/ActionRegister.h include/plumed/vatom/ActionWithVirtualAtom.h include/plumed/vesselbase/ActionWithAveraging.h include/plumed/vesselbase/ActionWithInputVessel.h include/plumed/vesselbase/ActionWithVessel.h include/plumed/vesselbase/AveragingVessel.h include/plumed/vesselbase/Between.h include/plumed/vesselbase/BridgeVessel.h include/plumed/vesselbase/FunctionVessel.h include/plumed/vesselbase/LessThan.h include/plumed/vesselbase/OrderingVessel.h include/plumed/vesselbase/ShortcutVessel.h include/plumed/vesselbase/StoreDataVessel.h include/plumed/vesselbase/ValueVessel.h include/plumed/vesselbase/Vessel.h include/plumed/vesselbase/VesselRegister.h include/plumed/wrapper/Plumed.h include/plumed/xdrfile/xdrfile.h include/plumed/xdrfile/xdrfile_trr.h include/plumed/xdrfile/xdrfile_xtc.h lib/libplumed.a lib/libplumed.so lib/libplumedKernel.so lib/libplumedWrapper.a lib/plumed/fortran/plumed.f90 lib/plumed/fortran/plumed_f08.f90 +lib/plumed/json/syntax.json lib/plumed/modulefile -lib/plumed/patches/gromacs-2019.6.config -lib/plumed/patches/gromacs-2019.6.diff/src/gromacs/CMakeLists.txt -lib/plumed/patches/gromacs-2019.6.diff/src/gromacs/CMakeLists.txt.preplumed -lib/plumed/patches/gromacs-2019.6.diff/src/gromacs/mdlib/force.cpp 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lib/plumed/vim/help/REWEIGHT_BIAS.txt lib/plumed/vim/help/REWEIGHT_METAD.txt lib/plumed/vim/help/REWEIGHT_TEMP_PRESS.txt lib/plumed/vim/help/REWEIGHT_WHAM.txt lib/plumed/vim/help/RMSD.txt +lib/plumed/vim/help/SANS.txt lib/plumed/vim/help/SAXS.txt lib/plumed/vim/help/SELECT.txt lib/plumed/vim/help/SELECTOR.txt lib/plumed/vim/help/SORT.txt lib/plumed/vim/help/STATS.txt lib/plumed/vim/help/TARGET.txt lib/plumed/vim/help/TEMPLATE.txt lib/plumed/vim/help/TETRAHEDRALPORE.txt lib/plumed/vim/help/TIME.txt lib/plumed/vim/help/TORSION.txt lib/plumed/vim/help/TORSIONS.txt lib/plumed/vim/help/UNITS.txt lib/plumed/vim/help/UPDATE_IF.txt lib/plumed/vim/help/UPPER_WALLS.txt lib/plumed/vim/help/VOLUME.txt lib/plumed/vim/help/WHAM_HISTOGRAM.txt lib/plumed/vim/help/WHAM_WEIGHTS.txt lib/plumed/vim/help/WHOLEMOLECULES.txt lib/plumed/vim/help/WRAPAROUND.txt lib/plumed/vim/help/XANGLES.txt lib/plumed/vim/help/XDISTANCES.txt lib/plumed/vim/help/XYDISTANCES.txt lib/plumed/vim/help/XYTORSIONS.txt lib/plumed/vim/help/XZDISTANCES.txt lib/plumed/vim/help/XZTORSIONS.txt lib/plumed/vim/help/YANGLES.txt lib/plumed/vim/help/YDISTANCES.txt lib/plumed/vim/help/YXTORSIONS.txt lib/plumed/vim/help/YZDISTANCES.txt lib/plumed/vim/help/YZTORSIONS.txt lib/plumed/vim/help/ZANGLES.txt lib/plumed/vim/help/ZDISTANCES.txt lib/plumed/vim/help/ZXTORSIONS.txt lib/plumed/vim/help/ZYTORSIONS.txt lib/plumed/vim/scripts.vim lib/plumed/vim/syntax/plumed.vim lib/plumed/vim/syntax/plumedf.vim libdata/pkgconfig/plumed.pc libdata/pkgconfig/plumedInternals.pc libdata/pkgconfig/plumedWrapper.pc