Date: Sun, 10 Aug 2014 06:21:54 +0000 (UTC) From: Wen Heping <wen@FreeBSD.org> To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r364504 - in head/biology/libsbml: . files Message-ID: <53e70f82.2c5f.1169fb26@svn.freebsd.org>
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Author: wen Date: Sun Aug 10 06:21:53 2014 New Revision: 364504 URL: http://svnweb.freebsd.org/changeset/ports/364504 QAT: https://qat.redports.org/buildarchive/r364504/ Log: - Update to 5.10.2 PR: 192198 Submitted by: tkato432@yahoo.com Deleted: head/biology/libsbml/files/ Modified: head/biology/libsbml/Makefile head/biology/libsbml/distinfo head/biology/libsbml/pkg-plist Modified: head/biology/libsbml/Makefile ============================================================================== --- head/biology/libsbml/Makefile Sun Aug 10 06:06:12 2014 (r364503) +++ head/biology/libsbml/Makefile Sun Aug 10 06:21:53 2014 (r364504) @@ -2,10 +2,9 @@ # $FreeBSD$ PORTNAME= libsbml -PORTVERSION= 5.10.0 +PORTVERSION= 5.10.2 CATEGORIES= biology devel -MASTER_SITES= SF -MASTER_SITE_SUBDIR= sbml/${PORTNAME}/${PORTVERSION}/stable +MASTER_SITES= SF/sbml/${PORTNAME}/${PORTVERSION}/stable DISTNAME= libSBML-${PORTVERSION}-core-src MAINTAINER= ports@FreeBSD.org @@ -13,46 +12,39 @@ COMMENT= API Library for Working with SB LICENSE= LGPL21 -LIB_DEPENDS= libxml2.so:${PORTSDIR}/textproc/libxml2 - -OPTIONS_DEFINE= PYTHON RUBY EXAMPLES +WRKSRC= ${WRKDIR}/${PORTNAME}-${PORTVERSION} -USES= gmake libtool -GNU_CONFIGURE= yes +USES= cmake:outsource iconv +USE_GNOME= libxml2 USE_LDCONFIG= yes -WRKSRC= ${WRKDIR}/${PORTNAME}-${PORTVERSION} -.include <bsd.port.options.mk> +CFLAGS+= -I${ICONV_PREFIX}/include +LDFLAGS+= -L${ICONV_PREFIX}/lib -.if ${PORT_OPTIONS:MPYTHON} -USE_PYTHON= yes -BUILD_DEPENDS+= ${LOCALBASE}/bin/python:${PORTSDIR}/lang/python -CONFIGURE_ARGS+= --with-python -PLIST_SUB+= WITH_PYTHON="" \ - SBML_EGGINFO=${PORTNAME}-${PORTVERSION}-${PYTHON_VERSION:S/thon//}.egg-info -.else -PLIST_SUB+= WITH_PYTHON="@comment " -.endif - -.if ${PORT_OPTIONS:MRUBY} -USE_RUBY= yes -BUILD_DEPENDS+= ${LOCALBASE}/bin/ruby:${PORTSDIR}/lang/ruby19 -CONFIGURE_ARGS+= --with-ruby -PLIST_SUB+= WITH_RUBY="" -.else -PLIST_SUB+= WITH_RUBY="@comment " -.endif +OPTIONS_DEFINE= EXAMPLES PYTHON RUBY +OPTIONS_SUB= yes + +PYTHON_BUILD_DEPENDS= swig2.0:${PORTSDIR}/devel/swig20 +PYTHON_USE= python=yes +PYTHON_CMAKE_ON= -DWITH_PYTHON:BOOL=ON \ + -DPYTHON_INCLUDE_DIR:STRING="${PYTHON_INCLUDEDIR}" \ + -DPYTHON_LIBRARY:STRING="${PYTHONBASE}/lib/lib${PYTHON_VERSION}.so" \ + -DPYTHON_EXECUTABLE:STRING="${PYTHON_CMD}" + +RUBY_BUILD_DEPENDS= swig2.0:${PORTSDIR}/devel/swig20 +RUBY_USE= ruby=yes +RUBY_CMAKE_ON= -DWITH_RUBY:BOOL=ON post-patch: - ${REINPLACE_CMD} -e 's#%%PREFIX%%#${STAGEDIR}${PREFIX}#' \ - ${WRKSRC}/Makefile.in + @${REINPLACE_CMD} -e \ + 's|/usr/local/include|${LOCALBASE}/include| ; \ + s|/usr/local/lib|${LOCALBASE}/lib| ; \ + /$${DOCUMENTATION_FILES}/s|^|#|' ${WRKSRC}/CMakeLists.txt post-install: -.if ${PORT_OPTIONS:MEXAMPLES} ${MKDIR} ${STAGEDIR}${EXAMPLESDIR} - cd ${WRKSRC}/examples \ - && ${FIND} . -type f -name "._Makefile.in" -exec ${RM} -f {} \; \ - && ${FIND} . -type d -exec ${MKDIR} ${STAGEDIR}${EXAMPLESDIR}/\{} \; \ - && ${FIND} . -type f -exec ${INSTALL_DATA} \{} ${STAGEDIR}${EXAMPLESDIR}/\{} \; -.endif + @${TAR} -C ${WRKSRC}/examples --exclude "*Makefile*" -cf - . | \ + ${TAR} -C ${STAGEDIR}${EXAMPLESDIR} --unlink -xf - + @${CHMOD} -R a+rX ${STAGEDIR}${EXAMPLESDIR} + .include <bsd.port.mk> Modified: head/biology/libsbml/distinfo ============================================================================== --- head/biology/libsbml/distinfo Sun Aug 10 06:06:12 2014 (r364503) +++ head/biology/libsbml/distinfo Sun Aug 10 06:21:53 2014 (r364504) @@ -1,2 +1,2 @@ -SHA256 (libSBML-5.10.0-core-src.tar.gz) = c7e733443caaf4615e90a29111ff988b89b1c9a679de0a9737fc2a86840df1e0 -SIZE (libSBML-5.10.0-core-src.tar.gz) = 11577010 +SHA256 (libSBML-5.10.2-core-src.tar.gz) = 2e8f1af4e90abfe0ee641a9b0d005ca8adf71b977f88e030a513729d3bb80538 +SIZE (libSBML-5.10.2-core-src.tar.gz) = 11858327 Modified: head/biology/libsbml/pkg-plist ============================================================================== --- head/biology/libsbml/pkg-plist Sun Aug 10 06:06:12 2014 (r364503) +++ head/biology/libsbml/pkg-plist Sun Aug 10 06:21:53 2014 (r364504) @@ -1,20 +1,25 @@ -libdata/pkgconfig/libsbml.pc +include/sbml/AlgebraicRule.h +include/sbml/AssignmentRule.h include/sbml/Compartment.h include/sbml/CompartmentType.h include/sbml/Constraint.h include/sbml/Delay.h include/sbml/Event.h include/sbml/EventAssignment.h +include/sbml/ExpectedAttributes.h include/sbml/FunctionDefinition.h include/sbml/InitialAssignment.h include/sbml/KineticLaw.h include/sbml/ListOf.h include/sbml/LocalParameter.h include/sbml/Model.h +include/sbml/ModifierSpeciesReference.h include/sbml/Parameter.h include/sbml/Priority.h +include/sbml/RateRule.h include/sbml/Reaction.h include/sbml/Rule.h +include/sbml/SBMLConstructorException.h include/sbml/SBMLDocument.h include/sbml/SBMLError.h include/sbml/SBMLErrorLog.h @@ -28,6 +33,7 @@ include/sbml/SBMLVisitor.h include/sbml/SBMLWriter.h include/sbml/SBO.h include/sbml/SBase.h +include/sbml/SimpleSpeciesReference.h include/sbml/Species.h include/sbml/SpeciesReference.h include/sbml/SpeciesType.h @@ -38,12 +44,20 @@ include/sbml/Unit.h include/sbml/UnitDefinition.h include/sbml/UnitKind.h include/sbml/annotation/CVTerm.h +include/sbml/annotation/Date.h +include/sbml/annotation/ModelCreator.h include/sbml/annotation/ModelHistory.h include/sbml/annotation/RDFAnnotation.h +include/sbml/annotation/RDFAnnotationParser.h +include/sbml/common/common-documentation.h +include/sbml/common/common-sbmlerror-codes.h include/sbml/common/common.h include/sbml/common/extern.h +include/sbml/common/libsbml-config-common.h +include/sbml/common/libsbml-config-packages.h include/sbml/common/libsbml-config.h include/sbml/common/libsbml-namespace.h +include/sbml/common/libsbml-package.h include/sbml/common/libsbml-version.h include/sbml/common/operationReturnValues.h include/sbml/common/sbmlfwd.h @@ -58,15 +72,77 @@ include/sbml/compress/unzip.h include/sbml/compress/zfstream.h include/sbml/compress/zip.h include/sbml/compress/zipfstream.h +include/sbml/conversion/ConversionOption.h +include/sbml/conversion/ConversionProperties.h +include/sbml/conversion/SBMLConverter.h +include/sbml/conversion/SBMLConverterRegister.h +include/sbml/conversion/SBMLConverterRegistry.h +include/sbml/conversion/SBMLFunctionDefinitionConverter.h +include/sbml/conversion/SBMLIdConverter.h +include/sbml/conversion/SBMLInferUnitsConverter.h +include/sbml/conversion/SBMLInitialAssignmentConverter.h +include/sbml/conversion/SBMLLevelVersionConverter.h +include/sbml/conversion/SBMLLocalParameterConverter.h +include/sbml/conversion/SBMLReactionConverter.h +include/sbml/conversion/SBMLRuleConverter.h +include/sbml/conversion/SBMLStripPackageConverter.h +include/sbml/conversion/SBMLUnitsConverter.h +include/sbml/extension/ASTBasePlugin.h +include/sbml/extension/ISBMLExtensionNamespaces.h +include/sbml/extension/RegisterExtensions.h +include/sbml/extension/SBMLDocumentPlugin.h +include/sbml/extension/SBMLDocumentPluginNotRequired.h +include/sbml/extension/SBMLExtension.h +include/sbml/extension/SBMLExtensionException.h +include/sbml/extension/SBMLExtensionNamespaces.h +include/sbml/extension/SBMLExtensionRegister.h +include/sbml/extension/SBMLExtensionRegistry.h +include/sbml/extension/SBaseExtensionPoint.h +include/sbml/extension/SBasePlugin.h +include/sbml/extension/SBasePluginCreator.h +include/sbml/extension/SBasePluginCreatorBase.h +include/sbml/math/ASTBase.h +include/sbml/math/ASTBinaryFunctionNode.h +include/sbml/math/ASTCSymbol.h +include/sbml/math/ASTCSymbolAvogadroNode.h +include/sbml/math/ASTCSymbolDelayNode.h +include/sbml/math/ASTCSymbolTimeNode.h +include/sbml/math/ASTCiFunctionNode.h +include/sbml/math/ASTCiNumberNode.h +include/sbml/math/ASTCnBase.h +include/sbml/math/ASTCnExponentialNode.h +include/sbml/math/ASTCnIntegerNode.h +include/sbml/math/ASTCnRationalNode.h +include/sbml/math/ASTCnRealNode.h +include/sbml/math/ASTConstantNumberNode.h +include/sbml/math/ASTFunction.h +include/sbml/math/ASTFunctionBase.h +include/sbml/math/ASTLambdaFunctionNode.h +include/sbml/math/ASTNaryFunctionNode.h include/sbml/math/ASTNode.h +include/sbml/math/ASTNumber.h +include/sbml/math/ASTPiecewiseFunctionNode.h +include/sbml/math/ASTQualifierNode.h +include/sbml/math/ASTSemanticsNode.h +include/sbml/math/ASTTypes.h +include/sbml/math/ASTUnaryFunctionNode.h include/sbml/math/FormulaFormatter.h include/sbml/math/FormulaParser.h include/sbml/math/FormulaTokenizer.h +include/sbml/math/L3FormulaFormatter.h +include/sbml/math/L3Parser.h +include/sbml/math/L3ParserSettings.h include/sbml/math/MathML.h include/sbml/units/FormulaUnitsData.h include/sbml/units/UnitFormulaFormatter.h include/sbml/units/UnitKindList.h +include/sbml/util/ElementFilter.h +include/sbml/util/IdFilter.h +include/sbml/util/IdList.h +include/sbml/util/IdentifierTransformer.h include/sbml/util/List.h +include/sbml/util/MetaIdFilter.h +include/sbml/util/PrefixTransformer.h include/sbml/util/Stack.h include/sbml/util/StringBuffer.h include/sbml/util/memory.h @@ -84,16 +160,16 @@ include/sbml/validator/L3v1Compatibility include/sbml/validator/MathMLConsistencyValidator.h include/sbml/validator/ModelingPracticeValidator.h include/sbml/validator/OverdeterminedValidator.h +include/sbml/validator/SBMLExternalValidator.h +include/sbml/validator/SBMLInternalValidator.h +include/sbml/validator/SBMLValidator.h include/sbml/validator/SBOConsistencyValidator.h include/sbml/validator/UnitConsistencyValidator.h include/sbml/validator/VConstraint.h include/sbml/validator/Validator.h -include/sbml/validator/constraints/IdBase.h -include/sbml/validator/constraints/MathMLBase.h -include/sbml/validator/constraints/OverDeterminedCheck.h -include/sbml/validator/constraints/UniqueIdBase.h -include/sbml/validator/constraints/UniqueMetaId.h -include/sbml/validator/constraints/UnitsBase.h +include/sbml/xml/ExpatAttributes.h +include/sbml/xml/ExpatHandler.h +include/sbml/xml/ExpatParser.h include/sbml/xml/LibXMLAttributes.h include/sbml/xml/LibXMLHandler.h include/sbml/xml/LibXMLNamespaces.h @@ -101,12 +177,14 @@ include/sbml/xml/LibXMLParser.h include/sbml/xml/LibXMLTranscode.h include/sbml/xml/XMLAttributes.h include/sbml/xml/XMLBuffer.h +include/sbml/xml/XMLConstructorException.h include/sbml/xml/XMLError.h include/sbml/xml/XMLErrorLog.h include/sbml/xml/XMLExtern.h include/sbml/xml/XMLFileBuffer.h include/sbml/xml/XMLHandler.h include/sbml/xml/XMLInputStream.h +include/sbml/xml/XMLLogOverride.h include/sbml/xml/XMLMemoryBuffer.h include/sbml/xml/XMLNamespaces.h include/sbml/xml/XMLNode.h @@ -115,130 +193,66 @@ include/sbml/xml/XMLParser.h include/sbml/xml/XMLToken.h include/sbml/xml/XMLTokenizer.h include/sbml/xml/XMLTriple.h -include/sbml/AlgebraicRule.h -include/sbml/AssignmentRule.h -include/sbml/ExpectedAttributes.h -include/sbml/ModifierSpeciesReference.h -include/sbml/RateRule.h -include/sbml/SBMLConstructorException.h -include/sbml/SimpleSpeciesReference.h -include/sbml/annotation/Date.h -include/sbml/annotation/ModelCreator.h -include/sbml/annotation/RDFAnnotationParser.h -include/sbml/common/libsbml-config-common.h -include/sbml/conversion/ConversionOption.h -include/sbml/conversion/ConversionProperties.h -include/sbml/conversion/SBMLConverter.h -include/sbml/conversion/SBMLConverterRegister.h -include/sbml/conversion/SBMLConverterRegistry.h -include/sbml/conversion/SBMLFunctionDefinitionConverter.h -include/sbml/conversion/SBMLIdConverter.h -include/sbml/conversion/SBMLInferUnitsConverter.h -include/sbml/conversion/SBMLInitialAssignmentConverter.h -include/sbml/conversion/SBMLLevelVersionConverter.h -include/sbml/conversion/SBMLLocalParameterConverter.h -include/sbml/conversion/SBMLReactionConverter.h -include/sbml/conversion/SBMLRuleConverter.h -include/sbml/conversion/SBMLStripPackageConverter.h -include/sbml/conversion/SBMLUnitsConverter.h -include/sbml/extension/ISBMLExtensionNamespaces.h -include/sbml/extension/SBMLDocumentPlugin.h -include/sbml/extension/SBMLDocumentPluginNotRequired.h -include/sbml/extension/SBMLExtension.h -include/sbml/extension/SBMLExtensionException.h -include/sbml/extension/SBMLExtensionNamespaces.h -include/sbml/extension/SBMLExtensionRegister.h -include/sbml/extension/SBMLExtensionRegistry.h -include/sbml/extension/SBaseExtensionPoint.h -include/sbml/extension/SBasePlugin.h -include/sbml/extension/SBasePluginCreator.h -include/sbml/extension/SBasePluginCreatorBase.h -include/sbml/math/L3FormulaFormatter.h -include/sbml/math/L3Parser.h -include/sbml/math/L3ParserSettings.h -include/sbml/util/ElementFilter.h -include/sbml/util/IdFilter.h -include/sbml/util/IdList.h -include/sbml/util/IdentifierTransformer.h -include/sbml/util/MetaIdFilter.h -include/sbml/validator/SBMLExternalValidator.h -include/sbml/validator/SBMLInternalValidator.h -include/sbml/validator/SBMLValidator.h -include/sbml/xml/XMLConstructorException.h -include/sbml/xml/XMLLogOverride.h -lib/libsbml.so.5.10.0 -lib/libsbml.so.5 +include/sbml/xml/XercesAttributes.h +include/sbml/xml/XercesHandler.h +include/sbml/xml/XercesNamespaces.h +include/sbml/xml/XercesParser.h +include/sbml/xml/XercesTranscode.h +lib/libsbml-static.a lib/libsbml.so -lib/libsbml.a -%%WITH_PYTHON%%%%PYTHON_SITELIBDIR%%/libsbml/_libsbml.so -%%WITH_PYTHON%%%%PYTHON_SITELIBDIR%%/libsbml.pth -%%WITH_PYTHON%%%%PYTHON_SITELIBDIR%%/%%SBML_EGGINFO%% -%%WITH_PYTHON%%%%PYTHON_SITELIBDIR%%/libsbml/__init__.py -%%WITH_PYTHON%%%%PYTHON_SITELIBDIR%%/libsbml/__init__.pyc -%%WITH_PYTHON%%@dirrm %%PYTHON_SITELIBDIR%%/libsbml -%%WITH_RUBY%%%%RUBY_SITELIBDIR%%/%%RUBY_ARCH%%/libSBML.so +lib/libsbml.so.5 +lib/libsbml.so.5.10.2 +%%PYTHON%%%%PYTHON_SITELIBDIR%%/libsbml.pth +%%PYTHON%%%%PYTHON_SITELIBDIR%%/libsbml/_libsbml.so +%%PYTHON%%%%PYTHON_SITELIBDIR%%/libsbml/libsbml.py +%%RUBY%%%%RUBY_SITEARCHLIBDIR%%/libSBML.so %%PORTEXAMPLES%%%%EXAMPLESDIR%%/CMakeLists.txt %%PORTEXAMPLES%%%%EXAMPLESDIR%%/README.txt -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/FormulaGraphvizFormatter.h -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/Makefile -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/Makefile.in -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/convertSBML.c -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/drawMath.c -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/echoSBML.c -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/evaluateMath.c -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/printMath.c -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/printSBML.c -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/readSBML.c -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/translateMath.c -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/util.c -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/util.h %%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/CMakeLists.txt +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/FormulaGraphvizFormatter.h %%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/addCVTerms.c %%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/addModelHistory.c %%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/addingEvidenceCodes_1.c %%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/addingEvidenceCodes_2.c %%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/appendAnnotation.c +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/convertSBML.c %%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/createExampleSBML.c +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/drawMath.c +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/echoSBML.c +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/evaluateMath.c %%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/printAnnotation.c +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/printMath.c %%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/printNotes.c %%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/printRegisteredPackages.c +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/printSBML.c %%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/printSupported.c %%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/printUnits.c %%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/promoteParameters.c +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/readSBML.c %%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/stripPackage.c %%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/translateL3Math.c +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/translateMath.c %%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/unsetAnnotation.c %%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/unsetNotes.c +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/util.c +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/util.h %%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/validateSBML.c -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/Makefile -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/Makefile.in +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/CMakeLists.txt %%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/addCVTerms.cpp +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/addCustomValidator.cpp +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/addModelHistory.cpp %%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/addingEvidenceCodes_1.cpp %%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/addingEvidenceCodes_2.cpp -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/addModelHistory.cpp %%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/appendAnnotation.cpp +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/callExternalValidator.cpp +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/convertReactions.cpp %%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/convertSBML.cpp %%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/createExampleSBML.cpp %%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/echoSBML.cpp -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/printAnnotation.cpp -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/printMath.cpp -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/printNotes.cpp -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/printSBML.cpp -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/printUnits.cpp -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/readSBML.cpp -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/translateMath.cpp -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/unsetAnnotation.cpp -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/unsetNotes.cpp -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/util.c -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/util.h -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/validateSBML.cpp -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/CMakeLists.txt -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/addCustomValidator.cpp -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/callExternalValidator.cpp %%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/getAllElementsWithNotes.cpp %%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/inferUnits.cpp %%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/inlineFunctionDefintions.cpp -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/layout/Makefile.in +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/layout/CMakeLists.txt %%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/layout/addLayout.cpp %%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/layout/convertLayout.cpp %%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/layout/example1-L3.cpp @@ -247,19 +261,27 @@ lib/libsbml.a %%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/layout/example2.cpp %%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/layout/example3-L3.cpp %%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/layout/example3.cpp +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/printAnnotation.cpp +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/printMath.cpp +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/printNotes.cpp %%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/printRegisteredPackages.cpp +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/printSBML.cpp %%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/printSupported.cpp +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/printUnits.cpp %%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/promoteParameters.cpp +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/readSBML.cpp %%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/renameSId.cpp %%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/rngvalidator.cpp %%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/setIdFromNames.cpp %%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/setNamesFromIds.cpp %%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/stripPackage.cpp %%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/translateL3Math.cpp -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/Makefile -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/Makefile.in -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/echoSBML.cs -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/validateSBML.cs +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/translateMath.cpp +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/unsetAnnotation.cpp +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/unsetNotes.cpp +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/util.c +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/util.h +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/validateSBML.cpp %%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/CMakeLists.txt %%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/GetAllElementsWithNotes.cs %%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/SetIdFromNames.cs @@ -272,6 +294,10 @@ lib/libsbml.a %%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/callExternalValidator.cs %%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/convertSBML.cs %%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/createExampleSBML.cs +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/echoSBML.cs +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/evaluateCustomMath.cs +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/inlineInitialAssignments.cs +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/layout/CMakeLists.txt %%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/layout/example1-L3.cs %%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/printAnnotation.cs %%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/printMath.cs @@ -282,53 +308,49 @@ lib/libsbml.a %%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/printsupported.cs %%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/promoteParameters.cs %%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/readSBML.cs +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/replaceOneFD.cs %%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/stripPackage.cs %%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/translateMath.cs %%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/unsetAnnotation.cs %%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/unsetNotes.cs -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/Makefile -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/Makefile.in +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/validateSBML.cs +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/CMakeLists.txt %%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/README.txt %%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/addCVTerms.java +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/addCustomValidator.java %%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/addModelHistory.java +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/addingEvidenceCodes_1.java +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/addingEvidenceCodes_2.java %%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/appendAnnotation.java +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/callExternalValidator.java %%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/convertSBML.java +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/createExampleSBML.java %%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/echoSBML.java +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/evaluateCustomMath.java %%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/evaluateMath.java +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/getAllElementsWithNotes.java +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/inlineInitialAssignments.java +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/layout/CMakeLists.txt +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/layout/layout_example1.java +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/layout/layout_example1_L3.java %%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/printAnnotation.java %%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/printMath.java %%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/printNotes.java +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/printRegisteredPackages.java %%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/printSBML.java %%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/printUnits.java +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/printsupported.java +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/promoteParameters.java %%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/readSBML.java +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/replaceOneFD.java +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/setIdFromNames.java +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/stripPackage.java %%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/translateMath.java %%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/unsetAnnotation.java %%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/unsetNotes.java %%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/validateSBML.java -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/CMakeLists.txt -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/addCustomValidator.java -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/addingEvidenceCodes_1.java -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/addingEvidenceCodes_2.java -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/callExternalValidator.java -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/createExampleSBML.java -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/getAllElementsWithNotes.java -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/layout/layout_example1.java -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/layout/layout_example1_L3.java -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/printRegisteredPackages.java -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/printsupported.java -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/promoteParameters.java -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/setIdFromNames.java -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/stripPackage.java +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/layout-package.cmake %%PORTEXAMPLES%%%%EXAMPLESDIR%%/layout/README.txt -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/convertSBML.pl -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/evaluateMath.pl -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/extractReactionInfo.pl -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/extractReactions.pl -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/printMath.pl -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/printSBML.pl -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/readSBML.pl -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/translateMath.pl -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/validateSBML.pl %%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/addCVTerms.pl %%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/addCustomValidator.pl %%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/addModelHistory.pl @@ -336,20 +358,27 @@ lib/libsbml.a %%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/addingEvidenceCodes_2.pl %%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/appendAnnotation.pl %%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/callExternalValidator.pl +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/convertSBML.pl %%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/createExampleSBML.pl %%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/echoSBML.pl +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/evaluateMath.pl +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/extractReactionInfo.pl +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/extractReactions.pl %%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/layout/example1-L3.pl %%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/printAnnotation.pl +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/printMath.pl %%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/printNotes.pl %%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/printRegisteredPackages.pl +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/printSBML.pl %%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/printUnits.pl %%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/printsupported.pl %%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/promoteParameters.pl +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/readSBML.pl %%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/stripPackage.pl +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/translateMath.pl %%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/unsetAnnotation.pl %%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/unsetNotes.pl -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/echoSBML.py -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/validateSBML.py +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/validateSBML.pl %%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/addCVTerms.py %%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/addCustomValidator.py %%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/addModelHistory.py @@ -359,7 +388,12 @@ lib/libsbml.a %%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/callExternalValidator.py %%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/convertSBML.py %%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/createExampleSBML.py +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/createSimpleModel.py +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/echoSBML.py +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/evaluateCustomMath.py %%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/getAllElementsWithNotes.py +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/inlineInitialAssignments.py +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/layout/convertLayout.py %%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/layout/example1-L3.py %%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/layout/example1.py %%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/printAnnotation.py @@ -371,11 +405,13 @@ lib/libsbml.a %%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/printsupported.py %%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/promoteParameters.py %%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/readSBML.py +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/replaceOneFD.py %%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/setIdFromNames.py %%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/stripPackage.py %%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/translateMath.py %%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/unsetAnnotation.py %%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/unsetNotes.py +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/validateSBML.py %%PORTEXAMPLES%%%%EXAMPLESDIR%%/r/addCVTerms.R %%PORTEXAMPLES%%%%EXAMPLESDIR%%/r/addModelHistory.R %%PORTEXAMPLES%%%%EXAMPLESDIR%%/r/addingEvidenceCodes_1.R @@ -399,10 +435,6 @@ lib/libsbml.a %%PORTEXAMPLES%%%%EXAMPLESDIR%%/r/unsetAnnotation.R %%PORTEXAMPLES%%%%EXAMPLESDIR%%/r/unsetNotes.R %%PORTEXAMPLES%%%%EXAMPLESDIR%%/r/validateSBML.R -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ruby/convertSBML.rb -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ruby/echoSBML.rb -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ruby/printMath.rb -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ruby/validateSBML.rb %%PORTEXAMPLES%%%%EXAMPLESDIR%%/ruby/addCVTerms.rb %%PORTEXAMPLES%%%%EXAMPLESDIR%%/ruby/addCustomValidator.rb %%PORTEXAMPLES%%%%EXAMPLESDIR%%/ruby/addModelHistory.rb @@ -410,8 +442,12 @@ lib/libsbml.a %%PORTEXAMPLES%%%%EXAMPLESDIR%%/ruby/addingEvidenceCodes_2.rb %%PORTEXAMPLES%%%%EXAMPLESDIR%%/ruby/appendAnnotation.rb %%PORTEXAMPLES%%%%EXAMPLESDIR%%/ruby/callExternalValidator.rb +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ruby/convertSBML.rb %%PORTEXAMPLES%%%%EXAMPLESDIR%%/ruby/createExampleSBML.rb +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ruby/echoSBML.rb +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ruby/layout/example1-L3.rb %%PORTEXAMPLES%%%%EXAMPLESDIR%%/ruby/printAnnotation.rb +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ruby/printMath.rb %%PORTEXAMPLES%%%%EXAMPLESDIR%%/ruby/printNotes.rb %%PORTEXAMPLES%%%%EXAMPLESDIR%%/ruby/printRegisteredPackages.rb %%PORTEXAMPLES%%%%EXAMPLESDIR%%/ruby/printSBML.rb @@ -423,7 +459,7 @@ lib/libsbml.a %%PORTEXAMPLES%%%%EXAMPLESDIR%%/ruby/translateMath.rb %%PORTEXAMPLES%%%%EXAMPLESDIR%%/ruby/unsetAnnotation.rb %%PORTEXAMPLES%%%%EXAMPLESDIR%%/ruby/unsetNotes.rb -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ruby/layout/example1-L3.rb +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ruby/validateSBML.rb %%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample-models/README.txt %%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample-models/from-spec/level-2/README.txt %%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample-models/from-spec/level-2/algebraicrules.xml @@ -438,6 +474,7 @@ lib/libsbml.a %%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample-models/from-spec/level-2/overdetermined.xml %%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample-models/from-spec/level-2/twodimensional.xml %%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample-models/from-spec/level-2/units.xml +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample-models/from-spec/level-3/README.txt %%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample-models/from-spec/level-3/algebraicrules.xml %%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample-models/from-spec/level-3/assignmentrules.xml %%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample-models/from-spec/level-3/boundarycondition.xml @@ -452,73 +489,40 @@ lib/libsbml.a %%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample-models/from-spec/level-3/membrane.xml %%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample-models/from-spec/level-3/multicomp.xml %%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample-models/from-spec/level-3/overdetermined.xml -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample-models/from-spec/level-3/README.txt %%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample-models/from-spec/level-3/twoalgebraicrules.xml %%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample-models/from-spec/level-3/twodimensional.xml %%PORTEXAMPLES%%%%EXAMPLESDIR%%/xslt/layout/layout2svg.xsl -%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/c -%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/c++/layout -%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/c++ -%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/csharp/layout -%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/csharp -%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/java/layout -%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/java -%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/perl/layout -%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/layout -%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/perl -%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/python/layout -%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/python -%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/r -%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/ruby/layout -%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/ruby +%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/xslt/layout +%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/xslt %%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/sample-models/from-spec/level-3 %%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/sample-models/from-spec/level-2 %%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/sample-models/from-spec %%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/sample-models -%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/xslt/layout -%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/xslt +%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/ruby/layout +%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/ruby +%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/r +%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/python/layout +%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/python +%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/perl/layout +%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/perl +%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/layout +%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/java/layout +%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/java +%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/csharp/layout +%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/csharp +%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/c++/layout +%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/c++ +%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/c %%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%% -@dirrm include/sbml/annotation -@dirrm include/sbml/common -@dirrm include/sbml/compress -@dirrm include/sbml/conversion -@dirrm include/sbml/extension -@dirrm include/sbml/math -@dirrm include/sbml/units -@dirrm include/sbml/util -@dirrm include/sbml/validator/constraints -@dirrm include/sbml/validator +%%PYTHON%%@dirrm %%PYTHON_SITELIBDIR%%/libsbml @dirrm include/sbml/xml -@dirrm include/sbml/ -include/sbml/extension/ASTBasePlugin.h -include/sbml/math/ASTBase.h -include/sbml/math/ASTBinaryFunctionNode.h -include/sbml/math/ASTCSymbol.h -include/sbml/math/ASTCSymbolAvogadroNode.h -include/sbml/math/ASTCSymbolDelayNode.h -include/sbml/math/ASTCSymbolTimeNode.h -include/sbml/math/ASTCiFunctionNode.h -include/sbml/math/ASTCiNumberNode.h -include/sbml/math/ASTCnBase.h -include/sbml/math/ASTCnExponentialNode.h -include/sbml/math/ASTCnIntegerNode.h -include/sbml/math/ASTCnRationalNode.h -include/sbml/math/ASTCnRealNode.h -include/sbml/math/ASTConstantNumberNode.h -include/sbml/math/ASTFunction.h -include/sbml/math/ASTFunctionBase.h -include/sbml/math/ASTLambdaFunctionNode.h -include/sbml/math/ASTNaryFunctionNode.h -include/sbml/math/ASTNumber.h -include/sbml/math/ASTPiecewiseFunctionNode.h -include/sbml/math/ASTQualifierNode.h -include/sbml/math/ASTSemanticsNode.h -include/sbml/math/ASTTypes.h -include/sbml/math/ASTUnaryFunctionNode.h -include/sbml/util/PrefixTransformer.h -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/convertReactions.cpp -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/layout/CMakeLists.txt -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/layout/CMakeLists.txt -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/layout/CMakeLists.txt -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/layout-package.cmake -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/layout/convertLayout.py +@dirrm include/sbml/validator +@dirrm include/sbml/util +@dirrm include/sbml/units +@dirrm include/sbml/math +@dirrm include/sbml/extension +@dirrm include/sbml/conversion +@dirrm include/sbml/compress +@dirrm include/sbml/common +@dirrm include/sbml/annotation +@dirrm include/sbml
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