Attachment 141677 Details for Bug 188554 – libsbml-5.9.0.patch

[patch] libsbml-5.9.0.patch

libsbml-5.9.0.patch (text/plain), 19.83 KB, created by Muhammad Moinur Rahman on 2014-04-13 13:30:00 UTC

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Creator: Muhammad Moinur Rahman

Created: 2014-04-13 13:30:00 UTC

Size: 19.83 KB

patch

obsolete

>diff -ruN /usr/ports//biology/libsbml/Makefile ./Makefile
>--- /usr/ports//biology/libsbml/Makefile	2014-03-07 21:52:40.000000000 +0600
>+++ ./Makefile	2014-04-13 18:18:28.850648524 +0600
>@@ -2,27 +2,26 @@
> # $FreeBSD: head/biology/libsbml/Makefile 347402 2014-03-07 15:52:40Z bapt $
> 
> PORTNAME=	libsbml
>-PORTVERSION=	4.2.0
>+PORTVERSION=	5.9.0
> CATEGORIES=	biology devel
> MASTER_SITES=	SF
>-MASTER_SITE_SUBDIR=	sbml/${PORTNAME}/${PORTVERSION}
>-DISTNAME=	${PORTNAME}-${PORTVERSION}-src
>+MASTER_SITE_SUBDIR=	sbml/${PORTNAME}/${PORTVERSION}/stable
>+DISTNAME=	libSBML-${PORTVERSION}-core-src
> 
> MAINTAINER=	wen@FreeBSD.org
> COMMENT=	API Library for Working with SBML File
> 
>+LICENSE=	LGPL21
>+
> LIB_DEPENDS=	libxml2.so:${PORTSDIR}/textproc/libxml2
> 
>-OPTIONS_DEFINE=	PYTHON RUBY
>+OPTIONS_DEFINE=	PYTHON RUBY EXAMPLES
> 
>-USES=		gmake zip
>-USE_GCC=	any
>+USES=	gmake
> GNU_CONFIGURE=	yes
> USE_LDCONFIG=	yes
> WRKSRC=		${WRKDIR}/${PORTNAME}-${PORTVERSION}
>-MAKE_JOBS_UNSAFE=	yes
> 
>-NO_STAGE=	yes
> .include <bsd.port.options.mk>
> 
> .if ${PORT_OPTIONS:MPYTHON}
>@@ -45,14 +44,15 @@
> .endif
> 
> post-patch:
>-	${REINPLACE_CMD} -e 's#%%PREFIX%%#${PREFIX}#' \
>+	${REINPLACE_CMD} -e 's#%%PREFIX%%#${STAGEDIR}${PREFIX}#' \
> 		${WRKSRC}/Makefile.in
> 
> post-install:
> .if ${PORT_OPTIONS:MEXAMPLES}
>-	${MKDIR} ${EXAMPLESDIR}
>+	${MKDIR} ${STAGEDIR}${EXAMPLESDIR}
> 	cd ${WRKSRC}/examples \
>-		&& ${FIND} . -type d -exec ${MKDIR} ${EXAMPLESDIR}/\{} \; \
>-		&& ${FIND} . -type f -exec ${INSTALL_DATA} \{} ${EXAMPLESDIR}/\{} \;
>+		&& ${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
> .include <bsd.port.mk>
>diff -ruN /usr/ports//biology/libsbml/distinfo ./distinfo
>--- /usr/ports//biology/libsbml/distinfo	2014-01-22 21:30:13.000000000 +0600
>+++ ./distinfo	2014-04-10 01:28:57.412678100 +0600
>@@ -1,2 +1,2 @@
>-SHA256 (libsbml-4.2.0-src.zip) = 31f4c63adc2bdd2ef7093dc206b4eb940a0c9cc0b98366f27316635fc44472ba
>-SIZE (libsbml-4.2.0-src.zip) = 9469890
>+SHA256 (libSBML-5.9.0-core-src.tar.gz) = 8991e4a6876721999433495b747b790af7981ae57b485e6c92b7fbb105bd7e96
>+SIZE (libSBML-5.9.0-core-src.tar.gz) = 11478158
>diff -ruN /usr/ports//biology/libsbml/pkg-plist ./pkg-plist
>--- /usr/ports//biology/libsbml/pkg-plist	2014-01-22 21:16:56.000000000 +0600
>+++ ./pkg-plist	2014-04-13 17:41:12.416799772 +0600
>@@ -42,8 +42,6 @@
> include/sbml/annotation/RDFAnnotation.h
> include/sbml/common/common.h
> include/sbml/common/extern.h
>-include/sbml/common/libsbml-config-unix.h
>-include/sbml/common/libsbml-config-win.h
> include/sbml/common/libsbml-config.h
> include/sbml/common/libsbml-namespace.h
> include/sbml/common/libsbml-version.h
>@@ -91,7 +89,6 @@
> include/sbml/validator/VConstraint.h
> include/sbml/validator/Validator.h
> include/sbml/validator/constraints/IdBase.h
>-include/sbml/validator/constraints/IdList.h
> include/sbml/validator/constraints/MathMLBase.h
> include/sbml/validator/constraints/OverDeterminedCheck.h
> include/sbml/validator/constraints/UniqueIdBase.h
>@@ -118,27 +115,68 @@
> include/sbml/xml/XMLToken.h
> include/sbml/xml/XMLTokenizer.h
> include/sbml/xml/XMLTriple.h
>-lib/libsbml.so.6
>+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/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.14
> lib/libsbml.so
> lib/libsbml.la
> lib/libsbml.a
>-@dirrm include/sbml/annotation
>-@dirrm include/sbml/common
>-@dirrm include/sbml/compress
>-@dirrm include/sbml/math
>-@dirrm include/sbml/units
>-@dirrm include/sbml/util
>-@dirrm include/sbml/validator/constraints
>-@dirrm include/sbml/validator
>-@dirrm include/sbml/xml
>-@dirrm include/sbml/
> %%WITH_PYTHON%%%%PYTHON_SITELIBDIR%%/libsbml/_libsbml.so
>-%%WITH_PYTHON%%%%PYTHON_SITELIBDIR%%/libsbml/libsbml.py
>-%%WITH_PYTHON%%%%PYTHON_SITELIBDIR%%/libsbml/libsbml.pyc
> %%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_SITEARCHLIBDIR%%/libSBML.so
>+%%WITH_RUBY%%%%RUBY_SITELIBDIR%%/%%RUBY_ARCH%%/libSBML.so
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/CMakeLists.txt
> %%PORTEXAMPLES%%%%EXAMPLESDIR%%/README.txt
> %%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/FormulaGraphvizFormatter.h
> %%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/Makefile
>@@ -153,6 +191,23 @@
> %%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/translateMath.c
> %%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/util.c
> %%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/util.h
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/CMakeLists.txt
>+%%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/createExampleSBML.c
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/printAnnotation.c
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/printNotes.c
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/printRegisteredPackages.c
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/printSupported.c
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/printUnits.c
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/promoteParameters.c
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/stripPackage.c
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/translateL3Math.c
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/unsetAnnotation.c
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/unsetNotes.c
> %%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/validateSBML.c
> %%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/Makefile
> %%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/Makefile.in
>@@ -176,10 +231,60 @@
> %%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/addLayout.cpp
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/layout/convertLayout.cpp
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/layout/example1-L3.cpp
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/layout/example1.cpp
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/layout/example2-L3.cpp
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/layout/example2.cpp
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/layout/example3-L3.cpp
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/layout/example3.cpp
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/printRegisteredPackages.cpp
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/printSupported.cpp
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/promoteParameters.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%%/csharp/CMakeLists.txt
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/GetAllElementsWithNotes.cs
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/SetIdFromNames.cs
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/addCVTerms.cs
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/addCustomValidator.cs
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/addModelHistory.cs
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/addingEvidenceCodes_1.cs
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/addingEvidenceCodes_2.cs
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/appendAnnotation.cs
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/callExternalValidator.cs
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/convertSBML.cs
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/createExampleSBML.cs
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/layout/example1-L3.cs
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/printAnnotation.cs
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/printMath.cs
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/printNotes.cs
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/printRegisteredPackages.cs
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/printSBML.cs
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/printUnits.cs
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/printsupported.cs
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/promoteParameters.cs
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/readSBML.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%%/java/README.txt
>@@ -199,13 +304,21 @@
> %%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/unsetAnnotation.java
> %%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/unsetNotes.java
> %%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/validateSBML.java
>-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/layout/Makefile.in
>-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/layout/example1.cpp
>-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/layout/example1.java
>-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/layout/example1.py
>-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/layout/example2.cpp
>-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/layout/example3.cpp
>-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/layout/layout2svg.xsl
>+%%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/README.txt
> %%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/convertSBML.pl
> %%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/evaluateMath.pl
> %%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/extractReactionInfo.pl
>@@ -215,12 +328,101 @@
> %%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
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/addingEvidenceCodes_1.pl
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/addingEvidenceCodes_2.pl
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/appendAnnotation.pl
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/callExternalValidator.pl
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/createExampleSBML.pl
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/echoSBML.pl
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/layout/example1-L3.pl
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/printAnnotation.pl
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/printNotes.pl
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/printRegisteredPackages.pl
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/printUnits.pl
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/printsupported.pl
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/promoteParameters.pl
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/stripPackage.pl
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/unsetAnnotation.pl
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/unsetNotes.pl
> %%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/echoSBML.py
> %%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/validateSBML.py
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/addCVTerms.py
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/addCustomValidator.py
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/addModelHistory.py
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/addingEvidenceCodes_1.py
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/addingEvidenceCodes_2.py
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/appendAnnotation.py
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/callExternalValidator.py
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/convertSBML.py
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/createExampleSBML.py
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/getAllElementsWithNotes.py
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/layout/example1-L3.py
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/layout/example1.py
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/printAnnotation.py
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/printMath.py
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/printNotes.py
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/printRegisteredPackages.py
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/printSBML.py
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/printUnits.py
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/printsupported.py
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/promoteParameters.py
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/readSBML.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%%/r/addCVTerms.R
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/r/addModelHistory.R
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/r/addingEvidenceCodes_1.R
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/r/addingEvidenceCodes_2.R
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/r/appendAnnotation.R
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/r/convertSBML.R
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/r/createExampleSBML.R
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/r/echoSBML.R
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/r/evaluateMath.R
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/r/printAnnotation.R
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/r/printMath.R
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/r/printNotes.R
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/r/printRegisteredPackages.R
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/r/printSBML.R
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/r/printSupported.R
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/r/printUnits.R
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/r/promoteParameters.R
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/r/readSBML.R
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/r/stripPackage.R
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/r/translateMath.R
>+%%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
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ruby/addingEvidenceCodes_1.rb
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ruby/addingEvidenceCodes_2.rb
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ruby/appendAnnotation.rb
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ruby/callExternalValidator.rb
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ruby/createExampleSBML.rb
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ruby/printAnnotation.rb
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ruby/printNotes.rb
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ruby/printRegisteredPackages.rb
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ruby/printSBML.rb
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ruby/printUnits.rb
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ruby/printsupported.rb
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ruby/promoteParameters.rb
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ruby/readSBML.rb
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ruby/stripPackage.rb
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ruby/translateMath.rb
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ruby/unsetAnnotation.rb
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ruby/unsetNotes.rb
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ruby/layout/example1-L3.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
>@@ -252,16 +454,38 @@
> %%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%%/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%%
>+@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
>+@dirrm include/sbml/xml
>+@dirrm include/sbml/

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Attachments on bug 188554: 141677