FreeBSD Bugzilla – Attachment 145085 Details for
Bug 192198
biology/libsbml: Update to version 5.10.2
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[patch]
biology_libsbml.diff
biology_libsbml.diff (text/plain), 35.02 KB, created by
tkato432
on 2014-07-28 18:31:13 UTC
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Description:
biology_libsbml.diff
Filename:
MIME Type:
Creator:
tkato432
Created:
2014-07-28 18:31:13 UTC
Size:
35.02 KB
patch
obsolete
>diff -urN /usr/ports/biology/libsbml/Makefile biology/libsbml/Makefile >--- /usr/ports/biology/libsbml/Makefile 2014-06-21 17:47:35.000000000 +0900 >+++ biology/libsbml/Makefile 2014-07-29 00:00:00.000000000 +0900 >@@ -2,10 +2,9 @@ > # $FreeBSD: head/biology/libsbml/Makefile 353921 2014-05-13 07:04:17Z wen $ > > 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-${PORTVERSION}-core-src > > MAINTAINER= ports@FreeBSD.org >@@ -13,46 +12,38 @@ > > LICENSE= LGPL21 > >-LIB_DEPENDS= libxml2.so:${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} >-.include "../../Mk/bsd.python.mk" >-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} >-.include "../../Mk/bsd.ruby.mk" >-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 >+ @${MKDIR} ${STAGEDIR}${EXAMPLESDIR} >+ @${TAR} -C ${WRKSRC}/examples --exclude "*Makefile*" -cf - . | \ >+ ${TAR} -C ${STAGEDIR}${EXAMPLESDIR} --unlink -xf - >+ @${CHMOD} -R a+rX ${STAGEDIR}${EXAMPLESDIR} >+ > .include <bsd.port.mk> >diff -urN /usr/ports/biology/libsbml/distinfo biology/libsbml/distinfo >--- /usr/ports/biology/libsbml/distinfo 2014-06-21 17:47:35.000000000 +0900 >+++ biology/libsbml/distinfo 2014-07-29 00:00:00.000000000 +0900 >@@ -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 -urN /usr/ports/biology/libsbml/files/patch-Makefile.in biology/libsbml/files/patch-Makefile.in >--- /usr/ports/biology/libsbml/files/patch-Makefile.in 2014-06-21 17:47:35.000000000 +0900 >+++ biology/libsbml/files/patch-Makefile.in 1970-01-01 09:00:00.000000000 +0900 >@@ -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 -urN /usr/ports/biology/libsbml/pkg-plist biology/libsbml/pkg-plist >--- /usr/ports/biology/libsbml/pkg-plist 2014-06-21 17:47:35.000000000 +0900 >+++ biology/libsbml/pkg-plist 2014-07-29 00:00:00.000000000 +0900 >@@ -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/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/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/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/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/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/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 @@ > %%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 @@ > %%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 @@ > %%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 @@ > %%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 @@ > %%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 @@ > %%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 @@ > %%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 @@ > %%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 @@ > %%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 @@ > %%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 @@ > %%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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