Date: Sun, 13 Apr 2014 18:20:27 +0600 (BDT) From: Muhammad Moinur Rahman <5u623l20@gmail.com> To: FreeBSD-gnats-submit@freebsd.org Cc: wen@FreeBSD.org Subject: ports/188554: [PATCH] biology/libsbml: update to 5.9.0 Message-ID: <201404131220.s3DCKRqO081215@bofh.1asiacom.net> Resent-Message-ID: <201404131230.s3DCU0JO038094@freefall.freebsd.org>
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>Number: 188554 >Category: ports >Synopsis: [PATCH] biology/libsbml: update to 5.9.0 >Confidential: no >Severity: non-critical >Priority: low >Responsible: freebsd-ports-bugs >State: open >Quarter: >Keywords: >Date-Required: >Class: update >Submitter-Id: current-users >Arrival-Date: Sun Apr 13 12:30:00 UTC 2014 >Closed-Date: >Last-Modified: >Originator: Muhammad Moinur Rahman >Release: FreeBSD 11.0-CURRENT amd64 >Organization: >Environment: System: FreeBSD bofh.1asiacom.net 11.0-CURRENT FreeBSD 11.0-CURRENT #1 r263870: Fri Mar 28 16:37:49 BDT >Description: - Update to 5.9.0 For Committer's reference: http://pdr.s.ubze.ro/bulk/latest-per-pkg/libsbml/5.9.0/84i386-default.log http://pdr.s.ubze.ro/bulk/latest-per-pkg/libsbml/5.9.0/84amd64-default.log http://pdr.s.ubze.ro/bulk/latest-per-pkg/libsbml/5.9.0/92i386-default.log http://pdr.s.ubze.ro/bulk/latest-per-pkg/libsbml/5.9.0/92amd64-default.log http://pdr.s.ubze.ro/bulk/latest-per-pkg/libsbml/5.9.0/100i386-default.log http://pdr.s.ubze.ro/bulk/latest-per-pkg/libsbml/5.9.0/100amd64-default.log http://pdr.s.ubze.ro/bulk/latest-per-pkg/libsbml/5.9.0/110i386-default.log http://pdr.s.ubze.ro/bulk/latest-per-pkg/libsbml/5.9.0/100amd64-default.log Superseeds ports/167251. Port maintainer (wen@FreeBSD.org) is cc'd. Generated with FreeBSD Port Tools 1.00.2014.03.23 (mode: update, diff: ports) >How-To-Repeat: >Fix: --- libsbml-5.9.0.patch begins here --- 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/ --- libsbml-5.9.0.patch ends here --- >Release-Note: >Audit-Trail: >Unformatted:
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