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- Update to 5.10.2

Browse Source 
PR:		192198
Submitted by:	tkato432@yahoo.com
This commit is contained in:
Wen Heping 2014-08-10 06:21:53 +00:00
parent 38541e7abb
commit f6912d8c17
Notes: svn2git 2021-03-31 03:12:20 +00:00 
svn path=/head/; revision=364504
4 changed files with 231 additions and 269 deletions
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64
biology/libsbml/Makefile
View File

@ -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
USES= gmake libtool
GNU_CONFIGURE= yes
USE_LDCONFIG= yes
WRKSRC= ${WRKDIR}/${PORTNAME}-${PORTVERSION}
.include <bsd.port.options.mk>
USES= cmake:outsource iconv
USE_GNOME= libxml2
USE_LDCONFIG= yes
.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}-${PYTHON_VERSION:S/thon//}.egg-info
.else
PLIST_SUB+= WITH_PYTHON="@comment "
.endif
CFLAGS+= -I${ICONV_PREFIX}/include
LDFLAGS+= -L${ICONV_PREFIX}/lib
.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>

4
biology/libsbml/distinfo
View File

@ -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

34
biology/libsbml/files/patch-Makefile.in
View File

@ -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;

398
biology/libsbml/pkg-plist
View File

@ -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