svn commit: r353913 - head/biology/libsbml
Wen Heping
wen at FreeBSD.org
Tue May 13 02:46:26 UTC 2014
Author: wen
Date: Tue May 13 02:46:25 2014
New Revision: 353913
URL: http://svnweb.freebsd.org/changeset/ports/353913
QAT: https://qat.redports.org/buildarchive/r353913/
Log:
- Update to 5.9.0 [1]
- Stage support [1]
- Add LICENSE [1]
- Reset maintainer to port@
PR: 188554 [1]
Submitted by: Muhammad Moinur Rahman <5u623l20 at gmail.com> [1]
Modified:
head/biology/libsbml/Makefile
head/biology/libsbml/distinfo
head/biology/libsbml/pkg-plist
Modified: head/biology/libsbml/Makefile
==============================================================================
--- head/biology/libsbml/Makefile Tue May 13 02:07:06 2014 (r353912)
+++ head/biology/libsbml/Makefile Tue May 13 02:46:25 2014 (r353913)
@@ -2,28 +2,26 @@
# $FreeBSD$
PORTNAME= libsbml
-PORTVERSION= 4.2.0
-PORTREVISION= 1
+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-${PORTVERSION}-core-src
-MAINTAINER= wen at FreeBSD.org
+MAINTAINER= ports at FreeBSD.org
COMMENT= API Library for Working with SBML File
+LICENSE= LGPL21
+
LIB_DEPENDS= libxml2.so:${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}
@@ -46,14 +44,15 @@ PLIST_SUB+= WITH_RUBY="@comment "
.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>
Modified: head/biology/libsbml/distinfo
==============================================================================
--- head/biology/libsbml/distinfo Tue May 13 02:07:06 2014 (r353912)
+++ head/biology/libsbml/distinfo Tue May 13 02:46:25 2014 (r353913)
@@ -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
Modified: head/biology/libsbml/pkg-plist
==============================================================================
--- head/biology/libsbml/pkg-plist Tue May 13 02:07:06 2014 (r353912)
+++ head/biology/libsbml/pkg-plist Tue May 13 02:46:25 2014 (r353913)
@@ -42,8 +42,6 @@ include/sbml/annotation/ModelHistory.h
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/UnitConsistencyVa
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/XMLParser.h
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
- at dirrm include/sbml/annotation
- at dirrm include/sbml/common
- at dirrm include/sbml/compress
- at dirrm include/sbml/math
- at dirrm include/sbml/units
- at dirrm include/sbml/util
- at dirrm include/sbml/validator/constraints
- at dirrm include/sbml/validator
- at dirrm include/sbml/xml
- at 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 @@ lib/libsbml.a
%%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 @@ lib/libsbml.a
%%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 @@ lib/libsbml.a
%%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 @@ lib/libsbml.a
%%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 @@ lib/libsbml.a
%%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%%
+ at dirrm include/sbml/annotation
+ at dirrm include/sbml/common
+ at dirrm include/sbml/compress
+ at dirrm include/sbml/conversion
+ at dirrm include/sbml/extension
+ at dirrm include/sbml/math
+ at dirrm include/sbml/units
+ at dirrm include/sbml/util
+ at dirrm include/sbml/validator/constraints
+ at dirrm include/sbml/validator
+ at dirrm include/sbml/xml
+ at dirrm include/sbml/
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