- Update to 5.10.2

PR:		192198
Submitted by:	tkato432@yahoo.com

4 files changed, 232 insertions, 270 deletions

diff --git a/biology/libsbml/Makefile b/biology/libsbml/Makefile
index 1f2b2753a337..970c2781be51 100644
--- a/biology/libsbml/Makefile
+++ b/biology/libsbml/Makefile
@@ -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 SBML File
 
 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>
-
-.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
+CFLAGS+=	-I${ICONV_PREFIX}/include
+LDFLAGS+=	-L${ICONV_PREFIX}/lib
+
+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>
diff --git a/biology/libsbml/distinfo b/biology/libsbml/distinfo
index f44159ea4470..619b27e6f35f 100644
--- a/biology/libsbml/distinfo
+++ b/biology/libsbml/distinfo
@@ -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
diff --git a/biology/libsbml/files/patch-Makefile.in b/biology/libsbml/files/patch-Makefile.in
deleted file mode 100644
index db9ad2cb6215..000000000000
--- a/biology/libsbml/files/patch-Makefile.in
+++ /dev/null
@@ -1,34 +0,0 @@
---- Makefile.in.orig	2009-05-27 23:09:33.000000000 +0800
-+++ Makefile.in	2009-05-27 23:33:47.000000000 +0800
-@@ -413,7 +413,7 @@
- endif
- 
- install-pc: libsbml.pc
--	$(INSTALL_SH) libsbml.pc -m 0644 "$(DESTDIR)$(LIBDIR)/pkgconfig/libsbml.pc"
-+	$(INSTALL_SH) libsbml.pc -m 0644 "%%PREFIX%%/libdata/pkgconfig/libsbml.pc"
- 
- install-la: libsbml.la
- ifeq "$(HOST_TYPE)" "cygwin"
-@@ -449,17 +449,17 @@
- 	$(warning $(uninstall-warning-msg))
- 
- uninstall-libsbml-pc:
--	@target="$(DESTDIR)$(LIBDIR)/pkgconfig/libsbml.pc"; \
-+	@target="%%PREFIX%%/libdata/pkgconfig/libsbml.pc"; \
- 	if test -f $$target ; then \
- 	  echo rm $$target; \
- 	  rm $$target; \
- 	fi; \
--	if test -d "$(DESTDIR)$(LIBDIR)/pkgconfig"; then \
-+	if test -d "%%PREFIX%%/libdata/pkgconfig"; then \
- 	  if test -n "`find $(DESTDIR)$(LIBDIR) -maxdepth 0 -empty`"; then \
--	    echo rmdir "$(DESTDIR)$(LIBDIR)/pkgconfig"; \
--	    rmdir "$(DESTDIR)$(LIBDIR)/pkgconfig"; \
-+	    echo rmdir "%%PREFIX%%/libdata/pkgconfig"; \
-+	    rmdir "%%PREFIX%%/libdata/pkgconfig"; \
- 	  else \
--	    echo "Directory $(DESTDIR)$(LIBDIR)/pkgconfig not empty; leaving it alone"; \
-+	    echo "Directory %%PREFIX%%/libdata/pkgconfig not empty; leaving it alone"; \
- 	  fi; \
- 	fi;
- 
diff --git a/biology/libsbml/pkg-plist b/biology/libsbml/pkg-plist
index cd9f9ff63e31..106b9d1da659 100644
--- a/biology/libsbml/pkg-plist
+++ b/biology/libsbml/pkg-plist
@@ -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/L3v1CompatibilityValidator.h
 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