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Port details
libsbml API Library for Working with SBML File
5.18.0 biology on this many watch lists=0 search for ports that depend on this port Find issues related to this port Report an issue related to this port 5.18.0Version of this port present on the latest quarterly branch.
Maintainer: sunpoet@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2009-05-28 23:36:42
Last Update: 2019-06-22 22:48:14
SVN Revision: 504890
Also Listed In: devel
License: LGPL21
Description:
SVNWeb : Homepage
pkg-plist: as obtained via: make generate-plist
Expand this list (539 items)
  1. /usr/local/share/licenses/libsbml-5.18.0/catalog.mk
  2. /usr/local/share/licenses/libsbml-5.18.0/LICENSE
  3. /usr/local/share/licenses/libsbml-5.18.0/LGPL21
  4. include/sbml/AlgebraicRule.h
  5. include/sbml/AssignmentRule.h
  6. include/sbml/Compartment.h
  7. include/sbml/CompartmentType.h
  8. include/sbml/Constraint.h
  9. include/sbml/Delay.h
  10. include/sbml/Event.h
  11. include/sbml/EventAssignment.h
  12. include/sbml/ExpectedAttributes.h
  13. include/sbml/FunctionDefinition.h
  14. include/sbml/InitialAssignment.h
  15. include/sbml/KineticLaw.h
  16. include/sbml/ListOf.h
  17. include/sbml/LocalParameter.h
  18. include/sbml/Model.h
  19. include/sbml/ModifierSpeciesReference.h
  20. include/sbml/Parameter.h
  21. include/sbml/Priority.h
  22. include/sbml/RateRule.h
  23. include/sbml/Reaction.h
  24. include/sbml/Rule.h
  25. include/sbml/SBMLConstructorException.h
  26. include/sbml/SBMLDocument.h
  27. include/sbml/SBMLError.h
  28. include/sbml/SBMLErrorLog.h
  29. include/sbml/SBMLErrorTable.h
  30. include/sbml/SBMLNamespaces.h
  31. include/sbml/SBMLReader.h
  32. include/sbml/SBMLTransforms.h
  33. include/sbml/SBMLTypeCodes.h
  34. include/sbml/SBMLTypes.h
  35. include/sbml/SBMLVisitor.h
  36. include/sbml/SBMLWriter.h
  37. include/sbml/SBO.h
  38. include/sbml/SBase.h
  39. include/sbml/SimpleSpeciesReference.h
  40. include/sbml/Species.h
  41. include/sbml/SpeciesReference.h
  42. include/sbml/SpeciesType.h
  43. include/sbml/StoichiometryMath.h
  44. include/sbml/SyntaxChecker.h
  45. include/sbml/Trigger.h
  46. include/sbml/Unit.h
  47. include/sbml/UnitDefinition.h
  48. include/sbml/UnitKind.h
  49. include/sbml/annotation/CVTerm.h
  50. include/sbml/annotation/Date.h
  51. include/sbml/annotation/ModelCreator.h
  52. include/sbml/annotation/ModelHistory.h
  53. include/sbml/annotation/RDFAnnotation.h
  54. include/sbml/annotation/RDFAnnotationParser.h
  55. include/sbml/common/common-documentation.h
  56. include/sbml/common/common-sbmlerror-codes.h
  57. include/sbml/common/common.h
  58. include/sbml/common/extern.h
  59. include/sbml/common/libsbml-config-common.h
  60. include/sbml/common/libsbml-config-packages.h
  61. include/sbml/common/libsbml-config.h
  62. include/sbml/common/libsbml-namespace.h
  63. include/sbml/common/libsbml-package.h
  64. include/sbml/common/libsbml-version.h
  65. include/sbml/common/operationReturnValues.h
  66. include/sbml/common/sbmlfwd.h
  67. include/sbml/compress/CompressCommon.h
  68. include/sbml/compress/InputDecompressor.h
  69. include/sbml/compress/OutputCompressor.h
  70. include/sbml/compress/bzfstream.h
  71. include/sbml/compress/crypt.h
  72. include/sbml/compress/ioapi.h
  73. include/sbml/compress/ioapi_mem.h
  74. include/sbml/compress/iowin32.h
  75. include/sbml/compress/unzip.h
  76. include/sbml/compress/zfstream.h
  77. include/sbml/compress/zip.h
  78. include/sbml/compress/zipfstream.h
  79. include/sbml/conversion/ConversionOption.h
  80. include/sbml/conversion/ConversionProperties.h
  81. include/sbml/conversion/SBMLConverter.h
  82. include/sbml/conversion/SBMLConverterRegister.h
  83. include/sbml/conversion/SBMLConverterRegistry.h
  84. include/sbml/conversion/SBMLConverterTypes.h
  85. include/sbml/conversion/SBMLFunctionDefinitionConverter.h
  86. include/sbml/conversion/SBMLIdConverter.h
  87. include/sbml/conversion/SBMLInferUnitsConverter.h
  88. include/sbml/conversion/SBMLInitialAssignmentConverter.h
  89. include/sbml/conversion/SBMLLevel1Version1Converter.h
  90. include/sbml/conversion/SBMLLevelVersionConverter.h
  91. include/sbml/conversion/SBMLLocalParameterConverter.h
  92. include/sbml/conversion/SBMLRateOfConverter.h
  93. include/sbml/conversion/SBMLReactionConverter.h
  94. include/sbml/conversion/SBMLRuleConverter.h
  95. include/sbml/conversion/SBMLStripPackageConverter.h
  96. include/sbml/conversion/SBMLUnitsConverter.h
  97. include/sbml/extension/ASTBasePlugin.h
  98. include/sbml/extension/ISBMLExtensionNamespaces.h
  99. include/sbml/extension/RegisterExtensions.h
  100. include/sbml/extension/SBMLDocumentPlugin.h
  101. include/sbml/extension/SBMLDocumentPluginNotRequired.h
  102. include/sbml/extension/SBMLExtension.h
  103. include/sbml/extension/SBMLExtensionException.h
  104. include/sbml/extension/SBMLExtensionNamespaces.h
  105. include/sbml/extension/SBMLExtensionRegister.h
  106. include/sbml/extension/SBMLExtensionRegistry.h
  107. include/sbml/extension/SBaseExtensionPoint.h
  108. include/sbml/extension/SBasePlugin.h
  109. include/sbml/extension/SBasePluginCreator.h
  110. include/sbml/extension/SBasePluginCreatorBase.h
  111. include/sbml/math/ASTNode.h
  112. include/sbml/math/ASTNodeType.h
  113. include/sbml/math/DefinitionURLRegistry.h
  114. include/sbml/math/FormulaFormatter.h
  115. include/sbml/math/FormulaParser.h
  116. include/sbml/math/FormulaTokenizer.h
  117. include/sbml/math/L3FormulaFormatter.h
  118. include/sbml/math/L3Parser.h
  119. include/sbml/math/L3ParserSettings.h
  120. include/sbml/math/MathML.h
  121. include/sbml/packages/l3v2extendedmath/common/L3v2extendedmathExtensionTypes.h
  122. include/sbml/packages/l3v2extendedmath/common/l3v2extendedmathfwd.h
  123. include/sbml/packages/l3v2extendedmath/extension/L3v2extendedmathASTPlugin.h
  124. include/sbml/packages/l3v2extendedmath/extension/L3v2extendedmathExtension.h
  125. include/sbml/packages/l3v2extendedmath/extension/L3v2extendedmathSBMLDocumentPlugin.h
  126. include/sbml/packages/l3v2extendedmath/validator/L3v2extendedmathMathMLConsistencyValidator.h
  127. include/sbml/packages/l3v2extendedmath/validator/L3v2extendedmathSBMLError.h
  128. include/sbml/packages/l3v2extendedmath/validator/L3v2extendedmathSBMLErrorTable.h
  129. include/sbml/packages/l3v2extendedmath/validator/L3v2extendedmathUnitConsistencyValidator.h
  130. include/sbml/packages/l3v2extendedmath/validator/L3v2extendedmathValidator.h
  131. include/sbml/packages/l3v2extendedmath/validator/constraints/L3v2EMArgumentsUnitsCheck.h
  132. include/sbml/packages/l3v2extendedmath/validator/constraints/L3v2EMNumberArgsMathCheck.h
  133. include/sbml/units/FormulaUnitsData.h
  134. include/sbml/units/UnitFormulaFormatter.h
  135. include/sbml/units/UnitKindList.h
  136. include/sbml/util/CallbackRegistry.h
  137. include/sbml/util/ElementFilter.h
  138. include/sbml/util/IdFilter.h
  139. include/sbml/util/IdList.h
  140. include/sbml/util/IdentifierTransformer.h
  141. include/sbml/util/List.h
  142. include/sbml/util/MathFilter.h
  143. include/sbml/util/MetaIdFilter.h
  144. include/sbml/util/PrefixTransformer.h
  145. include/sbml/util/Stack.h
  146. include/sbml/util/StringBuffer.h
  147. include/sbml/util/memory.h
  148. include/sbml/util/util.h
  149. include/sbml/validator/ConsistencyValidator.h
  150. include/sbml/validator/ConstraintMacros.h
  151. include/sbml/validator/IdentifierConsistencyValidator.h
  152. include/sbml/validator/InternalConsistencyValidator.h
  153. include/sbml/validator/L1CompatibilityValidator.h
  154. include/sbml/validator/L2v1CompatibilityValidator.h
  155. include/sbml/validator/L2v2CompatibilityValidator.h
  156. include/sbml/validator/L2v3CompatibilityValidator.h
  157. include/sbml/validator/L2v4CompatibilityValidator.h
  158. include/sbml/validator/L3v1CompatibilityValidator.h
  159. include/sbml/validator/L3v2CompatibilityValidator.h
  160. include/sbml/validator/MathMLConsistencyValidator.h
  161. include/sbml/validator/ModelingPracticeValidator.h
  162. include/sbml/validator/OverdeterminedValidator.h
  163. include/sbml/validator/SBMLExternalValidator.h
  164. include/sbml/validator/SBMLInternalValidator.h
  165. include/sbml/validator/SBMLValidator.h
  166. include/sbml/validator/SBOConsistencyValidator.h
  167. include/sbml/validator/StrictUnitConsistencyValidator.h
  168. include/sbml/validator/UnitConsistencyValidator.h
  169. include/sbml/validator/VConstraint.h
  170. include/sbml/validator/Validator.h
  171. include/sbml/xml/ExpatAttributes.h
  172. include/sbml/xml/ExpatHandler.h
  173. include/sbml/xml/ExpatParser.h
  174. include/sbml/xml/LibXMLAttributes.h
  175. include/sbml/xml/LibXMLHandler.h
  176. include/sbml/xml/LibXMLNamespaces.h
  177. include/sbml/xml/LibXMLParser.h
  178. include/sbml/xml/LibXMLTranscode.h
  179. include/sbml/xml/XMLAttributes.h
  180. include/sbml/xml/XMLBuffer.h
  181. include/sbml/xml/XMLConstructorException.h
  182. include/sbml/xml/XMLError.h
  183. include/sbml/xml/XMLErrorLog.h
  184. include/sbml/xml/XMLExtern.h
  185. include/sbml/xml/XMLFileBuffer.h
  186. include/sbml/xml/XMLHandler.h
  187. include/sbml/xml/XMLInputStream.h
  188. include/sbml/xml/XMLLogOverride.h
  189. include/sbml/xml/XMLMemoryBuffer.h
  190. include/sbml/xml/XMLNamespaces.h
  191. include/sbml/xml/XMLNode.h
  192. include/sbml/xml/XMLOutputStream.h
  193. include/sbml/xml/XMLParser.h
  194. include/sbml/xml/XMLToken.h
  195. include/sbml/xml/XMLTokenizer.h
  196. include/sbml/xml/XMLTriple.h
  197. include/sbml/xml/XercesAttributes.h
  198. include/sbml/xml/XercesHandler.h
  199. include/sbml/xml/XercesNamespaces.h
  200. include/sbml/xml/XercesParser.h
  201. include/sbml/xml/XercesTranscode.h
  202. lib/libsbml-static.a
  203. lib/libsbml.so
  204. lib/libsbml.so.5
  205. lib/libsbml.so.5.18.0
  206. libdata/pkgconfig/libsbml.pc
  207. lib/cmake/sbml-config-release.cmake
  208. lib/cmake/sbml-config-version.cmake
  209. lib/cmake/sbml-config.cmake
  210. lib/cmake/sbml-static-config-release.cmake
  211. lib/cmake/sbml-static-config-version.cmake
  212. lib/cmake/sbml-static-config.cmake
  213. @comment %%PYTHON_SITELIBDIR%%/libsbml.pth
  214. @comment %%PYTHON_SITELIBDIR%%/libsbml/_libsbml.so
  215. @comment %%PYTHON_SITELIBDIR%%/libsbml/libsbml.py
  216. @comment %%RUBY_SITEARCHLIBDIR%%/libSBML.so
  217. share/examples/libsbml/CMakeLists.txt
  218. share/examples/libsbml/README.txt
  219. share/examples/libsbml/c/CMakeLists.txt
  220. share/examples/libsbml/c/FormulaGraphvizFormatter.h
  221. share/examples/libsbml/c/addCVTerms.c
  222. share/examples/libsbml/c/addModelHistory.c
  223. share/examples/libsbml/c/addingEvidenceCodes_1.c
  224. share/examples/libsbml/c/addingEvidenceCodes_2.c
  225. share/examples/libsbml/c/appendAnnotation.c
  226. share/examples/libsbml/c/convertSBML.c
  227. share/examples/libsbml/c/createExampleSBML.c
  228. share/examples/libsbml/c/drawMath.c
  229. share/examples/libsbml/c/echoSBML.c
  230. share/examples/libsbml/c/evaluateMath.c
  231. share/examples/libsbml/c/printAnnotation.c
  232. share/examples/libsbml/c/printMath.c
  233. share/examples/libsbml/c/printNotes.c
  234. share/examples/libsbml/c/printRegisteredPackages.c
  235. share/examples/libsbml/c/printSBML.c
  236. share/examples/libsbml/c/printSupported.c
  237. share/examples/libsbml/c/printUnits.c
  238. share/examples/libsbml/c/promoteParameters.c
  239. share/examples/libsbml/c/readSBML.c
  240. share/examples/libsbml/c/stripPackage.c
  241. share/examples/libsbml/c/translateL3Math.c
  242. share/examples/libsbml/c/translateMath.c
  243. share/examples/libsbml/c/unsetAnnotation.c
  244. share/examples/libsbml/c/unsetNotes.c
  245. share/examples/libsbml/c/util.c
  246. share/examples/libsbml/c/util.h
  247. share/examples/libsbml/c/validateSBML.c
  248. share/examples/libsbml/c++/CMakeLists.txt
  249. share/examples/libsbml/c++/addCVTerms.cpp
  250. share/examples/libsbml/c++/addCustomValidator.cpp
  251. share/examples/libsbml/c++/addModelHistory.cpp
  252. share/examples/libsbml/c++/addingEvidenceCodes_1.cpp
  253. share/examples/libsbml/c++/addingEvidenceCodes_2.cpp
  254. share/examples/libsbml/c++/appendAnnotation.cpp
  255. share/examples/libsbml/c++/callExternalValidator.cpp
  256. share/examples/libsbml/c++/convertReactions.cpp
  257. share/examples/libsbml/c++/convertSBML.cpp
  258. share/examples/libsbml/c++/convertToL1V1.cpp
  259. share/examples/libsbml/c++/createExampleSBML.cpp
  260. share/examples/libsbml/c++/echoSBML.cpp
  261. share/examples/libsbml/c++/getAllElementsWithNotes.cpp
  262. share/examples/libsbml/c++/inferUnits.cpp
  263. share/examples/libsbml/c++/inlineFunctionDefintions.cpp
  264. share/examples/libsbml/c++/layout/CMakeLists.txt
  265. share/examples/libsbml/c++/layout/addLayout.cpp
  266. share/examples/libsbml/c++/layout/convertLayout.cpp
  267. share/examples/libsbml/c++/layout/example1-L3.cpp
  268. share/examples/libsbml/c++/layout/example1.cpp
  269. share/examples/libsbml/c++/layout/example2-L3.cpp
  270. share/examples/libsbml/c++/layout/example2.cpp
  271. share/examples/libsbml/c++/layout/example3-L3.cpp
  272. share/examples/libsbml/c++/layout/example3.cpp
  273. share/examples/libsbml/c++/printAnnotation.cpp
  274. share/examples/libsbml/c++/printMath.cpp
  275. share/examples/libsbml/c++/printNotes.cpp
  276. share/examples/libsbml/c++/printRegisteredPackages.cpp
  277. share/examples/libsbml/c++/printSBML.cpp
  278. share/examples/libsbml/c++/printSupported.cpp
  279. share/examples/libsbml/c++/printUnits.cpp
  280. share/examples/libsbml/c++/promoteParameters.cpp
  281. share/examples/libsbml/c++/readSBML.cpp
  282. share/examples/libsbml/c++/renameSId.cpp
  283. share/examples/libsbml/c++/rngvalidator.cpp
  284. share/examples/libsbml/c++/setIdFromNames.cpp
  285. share/examples/libsbml/c++/setNamesFromIds.cpp
  286. share/examples/libsbml/c++/stripPackage.cpp
  287. share/examples/libsbml/c++/translateL3Math.cpp
  288. share/examples/libsbml/c++/translateMath.cpp
  289. share/examples/libsbml/c++/unsetAnnotation.cpp
  290. share/examples/libsbml/c++/unsetNotes.cpp
  291. share/examples/libsbml/c++/util.c
  292. share/examples/libsbml/c++/util.h
  293. share/examples/libsbml/c++/validateSBML.cpp
  294. share/examples/libsbml/csharp/CMakeLists.txt
  295. share/examples/libsbml/csharp/GetAllElementsWithNotes.cs
  296. share/examples/libsbml/csharp/SetIdFromNames.cs
  297. share/examples/libsbml/csharp/addCVTerms.cs
  298. share/examples/libsbml/csharp/addCustomValidator.cs
  299. share/examples/libsbml/csharp/addModelHistory.cs
  300. share/examples/libsbml/csharp/addingEvidenceCodes_1.cs
  301. share/examples/libsbml/csharp/addingEvidenceCodes_2.cs
  302. share/examples/libsbml/csharp/appendAnnotation.cs
  303. share/examples/libsbml/csharp/callExternalValidator.cs
  304. share/examples/libsbml/csharp/convertSBML.cs
  305. share/examples/libsbml/csharp/createExampleSBML.cs
  306. share/examples/libsbml/csharp/echoSBML.cs
  307. share/examples/libsbml/csharp/evaluateCustomMath.cs
  308. share/examples/libsbml/csharp/inlineInitialAssignments.cs
  309. share/examples/libsbml/csharp/layout/CMakeLists.txt
  310. share/examples/libsbml/csharp/layout/example1-L3.cs
  311. share/examples/libsbml/csharp/printAnnotation.cs
  312. share/examples/libsbml/csharp/printMath.cs
  313. share/examples/libsbml/csharp/printNotes.cs
  314. share/examples/libsbml/csharp/printRegisteredPackages.cs
  315. share/examples/libsbml/csharp/printSBML.cs
  316. share/examples/libsbml/csharp/printUnits.cs
  317. share/examples/libsbml/csharp/printsupported.cs
  318. share/examples/libsbml/csharp/promoteParameters.cs
  319. share/examples/libsbml/csharp/readSBML.cs
  320. share/examples/libsbml/csharp/replaceOneFD.cs
  321. share/examples/libsbml/csharp/stripPackage.cs
  322. share/examples/libsbml/csharp/translateMath.cs
  323. share/examples/libsbml/csharp/unsetAnnotation.cs
  324. share/examples/libsbml/csharp/unsetNotes.cs
  325. share/examples/libsbml/csharp/validateSBML.cs
  326. share/examples/libsbml/java/CMakeLists.txt
  327. share/examples/libsbml/java/README.txt
  328. share/examples/libsbml/java/addCVTerms.java
  329. share/examples/libsbml/java/addCustomValidator.java
  330. share/examples/libsbml/java/addModelHistory.java
  331. share/examples/libsbml/java/addingEvidenceCodes_1.java
  332. share/examples/libsbml/java/addingEvidenceCodes_2.java
  333. share/examples/libsbml/java/appendAnnotation.java
  334. share/examples/libsbml/java/callExternalValidator.java
  335. share/examples/libsbml/java/convertSBML.java
  336. share/examples/libsbml/java/createExampleSBML.java
  337. share/examples/libsbml/java/echoSBML.java
  338. share/examples/libsbml/java/evaluateCustomMath.java
  339. share/examples/libsbml/java/evaluateMath.java
  340. share/examples/libsbml/java/getAllElementsWithNotes.java
  341. share/examples/libsbml/java/inlineInitialAssignments.java
  342. share/examples/libsbml/java/layout/CMakeLists.txt
  343. share/examples/libsbml/java/layout/SimpleLayoutConverter.java
  344. share/examples/libsbml/java/layout/layout_example1.java
  345. share/examples/libsbml/java/layout/layout_example1_L3.java
  346. share/examples/libsbml/java/printAnnotation.java
  347. share/examples/libsbml/java/printMath.java
  348. share/examples/libsbml/java/printNotes.java
  349. share/examples/libsbml/java/printRegisteredPackages.java
  350. share/examples/libsbml/java/printSBML.java
  351. share/examples/libsbml/java/printUnits.java
  352. share/examples/libsbml/java/printsupported.java
  353. share/examples/libsbml/java/promoteParameters.java
  354. share/examples/libsbml/java/readSBML.java
  355. share/examples/libsbml/java/replaceOneFD.java
  356. share/examples/libsbml/java/setIdFromNames.java
  357. share/examples/libsbml/java/stripPackage.java
  358. share/examples/libsbml/java/translateMath.java
  359. share/examples/libsbml/java/unsetAnnotation.java
  360. share/examples/libsbml/java/unsetNotes.java
  361. share/examples/libsbml/java/validateSBML.java
  362. share/examples/libsbml/javascript/addCVTerms.js
  363. share/examples/libsbml/javascript/addModelHistory.js
  364. share/examples/libsbml/javascript/addingEvidenceCodes_1.js
  365. share/examples/libsbml/javascript/addingEvidenceCodes_2.js
  366. share/examples/libsbml/javascript/appendAnnotation.js
  367. share/examples/libsbml/javascript/callExternalValidator.js
  368. share/examples/libsbml/javascript/convertSBML.js
  369. share/examples/libsbml/javascript/createExampleSBML.js
  370. share/examples/libsbml/javascript/echoSBML.js
  371. share/examples/libsbml/javascript/printAnnotation.js
  372. share/examples/libsbml/javascript/printMath.js
  373. share/examples/libsbml/javascript/printNotes.js
  374. share/examples/libsbml/javascript/printRegisteredPackages.js
  375. share/examples/libsbml/javascript/printSBML.js
  376. share/examples/libsbml/javascript/printUnits.js
  377. share/examples/libsbml/javascript/printsupported.js
  378. share/examples/libsbml/javascript/promoteParameters.js
  379. share/examples/libsbml/javascript/readSBML.js
  380. share/examples/libsbml/javascript/stripPackage.js
  381. share/examples/libsbml/javascript/translateMath.js
  382. share/examples/libsbml/javascript/unsetAnnotation.js
  383. share/examples/libsbml/javascript/unsetNotes.js
  384. share/examples/libsbml/javascript/validateSBML.js
  385. share/examples/libsbml/layout-package.cmake
  386. share/examples/libsbml/layout/README.txt
  387. share/examples/libsbml/perl/addCVTerms.pl
  388. share/examples/libsbml/perl/addCustomValidator.pl
  389. share/examples/libsbml/perl/addModelHistory.pl
  390. share/examples/libsbml/perl/addingEvidenceCodes_1.pl
  391. share/examples/libsbml/perl/addingEvidenceCodes_2.pl
  392. share/examples/libsbml/perl/appendAnnotation.pl
  393. share/examples/libsbml/perl/callExternalValidator.pl
  394. share/examples/libsbml/perl/convertSBML.pl
  395. share/examples/libsbml/perl/createExampleSBML.pl
  396. share/examples/libsbml/perl/echoSBML.pl
  397. share/examples/libsbml/perl/evaluateMath.pl
  398. share/examples/libsbml/perl/extractReactionInfo.pl
  399. share/examples/libsbml/perl/extractReactions.pl
  400. share/examples/libsbml/perl/layout/example1-L3.pl
  401. share/examples/libsbml/perl/printAnnotation.pl
  402. share/examples/libsbml/perl/printMath.pl
  403. share/examples/libsbml/perl/printNotes.pl
  404. share/examples/libsbml/perl/printRegisteredPackages.pl
  405. share/examples/libsbml/perl/printSBML.pl
  406. share/examples/libsbml/perl/printUnits.pl
  407. share/examples/libsbml/perl/printsupported.pl
  408. share/examples/libsbml/perl/promoteParameters.pl
  409. share/examples/libsbml/perl/readSBML.pl
  410. share/examples/libsbml/perl/renameSId.pl
  411. share/examples/libsbml/perl/stripPackage.pl
  412. share/examples/libsbml/perl/translateMath.pl
  413. share/examples/libsbml/perl/unsetAnnotation.pl
  414. share/examples/libsbml/perl/unsetNotes.pl
  415. share/examples/libsbml/perl/validateSBML.pl
  416. share/examples/libsbml/php/createExampleSBML.php
  417. share/examples/libsbml/php/echoSBML.php
  418. share/examples/libsbml/php/validateSBML.php
  419. share/examples/libsbml/python/addCVTerms.py
  420. share/examples/libsbml/python/addCustomValidator.py
  421. share/examples/libsbml/python/addModelHistory.py
  422. share/examples/libsbml/python/addingEvidenceCodes_1.py
  423. share/examples/libsbml/python/addingEvidenceCodes_2.py
  424. share/examples/libsbml/python/append_to_note.py
  425. share/examples/libsbml/python/appendAnnotation.py
  426. share/examples/libsbml/python/callExternalValidator.py
  427. share/examples/libsbml/python/convertSBML.py
  428. share/examples/libsbml/python/createExampleSBML.py
  429. share/examples/libsbml/python/createSimpleModel.py
  430. share/examples/libsbml/python/echoSBML.py
  431. share/examples/libsbml/python/evaluateCustomMath.py
  432. share/examples/libsbml/python/getAllElementsWithNotes.py
  433. share/examples/libsbml/python/inlineFunctionDefinitions.py
  434. share/examples/libsbml/python/inlineInitialAssignments.py
  435. share/examples/libsbml/python/layout/convertLayout.py
  436. share/examples/libsbml/python/layout/example1-L3.py
  437. share/examples/libsbml/python/layout/example1.py
  438. share/examples/libsbml/python/printAnnotation.py
  439. share/examples/libsbml/python/printMath.py
  440. share/examples/libsbml/python/printNotes.py
  441. share/examples/libsbml/python/printRegisteredPackages.py
  442. share/examples/libsbml/python/printSBML.py
  443. share/examples/libsbml/python/printUnits.py
  444. share/examples/libsbml/python/printsupported.py
  445. share/examples/libsbml/python/promoteParameters.py
  446. share/examples/libsbml/python/readSBML.py
  447. share/examples/libsbml/python/renameSId.py
  448. share/examples/libsbml/python/replaceOneFD.py
  449. share/examples/libsbml/python/setIdFromNames.py
  450. share/examples/libsbml/python/stringInput.py
  451. share/examples/libsbml/python/stripPackage.py
  452. share/examples/libsbml/python/translateMath.py
  453. share/examples/libsbml/python/unsetAnnotation.py
  454. share/examples/libsbml/python/unsetNotes.py
  455. share/examples/libsbml/python/validateSBML.py
  456. share/examples/libsbml/python/validateSBMLWithCallback.py
  457. share/examples/libsbml/r/addCVTerms.R
  458. share/examples/libsbml/r/addModelHistory.R
  459. share/examples/libsbml/r/addingEvidenceCodes_1.R
  460. share/examples/libsbml/r/addingEvidenceCodes_2.R
  461. share/examples/libsbml/r/appendAnnotation.R
  462. share/examples/libsbml/r/convertSBML.R
  463. share/examples/libsbml/r/createExampleSBML.R
  464. share/examples/libsbml/r/echoSBML.R
  465. share/examples/libsbml/r/evaluateMath.R
  466. share/examples/libsbml/r/printAnnotation.R
  467. share/examples/libsbml/r/printMath.R
  468. share/examples/libsbml/r/printNotes.R
  469. share/examples/libsbml/r/printRegisteredPackages.R
  470. share/examples/libsbml/r/printSBML.R
  471. share/examples/libsbml/r/printSupported.R
  472. share/examples/libsbml/r/printUnits.R
  473. share/examples/libsbml/r/promoteParameters.R
  474. share/examples/libsbml/r/readSBML.R
  475. share/examples/libsbml/r/stripPackage.R
  476. share/examples/libsbml/r/translateMath.R
  477. share/examples/libsbml/r/unsetAnnotation.R
  478. share/examples/libsbml/r/unsetNotes.R
  479. share/examples/libsbml/r/validateSBML.R
  480. share/examples/libsbml/ruby/addCVTerms.rb
  481. share/examples/libsbml/ruby/addCustomValidator.rb
  482. share/examples/libsbml/ruby/addModelHistory.rb
  483. share/examples/libsbml/ruby/addingEvidenceCodes_1.rb
  484. share/examples/libsbml/ruby/addingEvidenceCodes_2.rb
  485. share/examples/libsbml/ruby/appendAnnotation.rb
  486. share/examples/libsbml/ruby/callExternalValidator.rb
  487. share/examples/libsbml/ruby/convertSBML.rb
  488. share/examples/libsbml/ruby/createExampleSBML.rb
  489. share/examples/libsbml/ruby/echoSBML.rb
  490. share/examples/libsbml/ruby/layout/example1-L3.rb
  491. share/examples/libsbml/ruby/printAnnotation.rb
  492. share/examples/libsbml/ruby/printMath.rb
  493. share/examples/libsbml/ruby/printNotes.rb
  494. share/examples/libsbml/ruby/printRegisteredPackages.rb
  495. share/examples/libsbml/ruby/printSBML.rb
  496. share/examples/libsbml/ruby/printUnits.rb
  497. share/examples/libsbml/ruby/printsupported.rb
  498. share/examples/libsbml/ruby/promoteParameters.rb
  499. share/examples/libsbml/ruby/readSBML.rb
  500. share/examples/libsbml/ruby/stripPackage.rb
  501. share/examples/libsbml/ruby/translateMath.rb
  502. share/examples/libsbml/ruby/unsetAnnotation.rb
  503. share/examples/libsbml/ruby/unsetNotes.rb
  504. share/examples/libsbml/ruby/validateSBML.rb
  505. share/examples/libsbml/sample-models/README.txt
  506. share/examples/libsbml/sample-models/from-spec/level-2/README.txt
  507. share/examples/libsbml/sample-models/from-spec/level-2/algebraicrules.xml
  508. share/examples/libsbml/sample-models/from-spec/level-2/assignmentrules.xml
  509. share/examples/libsbml/sample-models/from-spec/level-2/boundarycondition.xml
  510. share/examples/libsbml/sample-models/from-spec/level-2/delay.xml
  511. share/examples/libsbml/sample-models/from-spec/level-2/dimerization.xml
  512. share/examples/libsbml/sample-models/from-spec/level-2/enzymekinetics.xml
  513. share/examples/libsbml/sample-models/from-spec/level-2/events.xml
  514. share/examples/libsbml/sample-models/from-spec/level-2/functiondef.xml
  515. share/examples/libsbml/sample-models/from-spec/level-2/multicomp.xml
  516. share/examples/libsbml/sample-models/from-spec/level-2/overdetermined.xml
  517. share/examples/libsbml/sample-models/from-spec/level-2/twodimensional.xml
  518. share/examples/libsbml/sample-models/from-spec/level-2/units.xml
  519. share/examples/libsbml/sample-models/from-spec/level-3/README.txt
  520. share/examples/libsbml/sample-models/from-spec/level-3/algebraicrules.xml
  521. share/examples/libsbml/sample-models/from-spec/level-3/assignmentrules.xml
  522. share/examples/libsbml/sample-models/from-spec/level-3/boundarycondition.xml
  523. share/examples/libsbml/sample-models/from-spec/level-3/conversionfactor1.xml
  524. share/examples/libsbml/sample-models/from-spec/level-3/conversionfactor2.xml
  525. share/examples/libsbml/sample-models/from-spec/level-3/delay.xml
  526. share/examples/libsbml/sample-models/from-spec/level-3/dimerization.xml
  527. share/examples/libsbml/sample-models/from-spec/level-3/enzymekineticext.xml
  528. share/examples/libsbml/sample-models/from-spec/level-3/enzymekinetics.xml
  529. share/examples/libsbml/sample-models/from-spec/level-3/events.xml
  530. share/examples/libsbml/sample-models/from-spec/level-3/fullydeterminedevent.xml
  531. share/examples/libsbml/sample-models/from-spec/level-3/functiondef.xml
  532. share/examples/libsbml/sample-models/from-spec/level-3/membrane.xml
  533. share/examples/libsbml/sample-models/from-spec/level-3/multicomp.xml
  534. share/examples/libsbml/sample-models/from-spec/level-3/overdetermined.xml
  535. share/examples/libsbml/sample-models/from-spec/level-3/twoalgebraicrules.xml
  536. share/examples/libsbml/sample-models/from-spec/level-3/twodimensional.xml
  537. share/examples/libsbml/xslt/layout/layout2svg.xsl
  538. @postexec /usr/sbin/service ldconfig restart > /dev/null
  539. @postunexec /usr/sbin/service ldconfig restart > /dev/null
Collapse this list.
Dependency lines:
  • libsbml>0:biology/libsbml
  • libsbml.so:biology/libsbml
To install the port: cd /usr/ports/biology/libsbml/ && make install clean
To add the package: pkg install libsbml
PKGNAME: libsbml
Flavors: there is no flavor information for this port.
distinfo:

Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. cmake : devel/cmake
  2. ninja : devel/ninja
  3. iconv : converters/libiconv
Library dependencies:
  1. libxml2.so : textproc/libxml2
This port is required by:
for Libraries

    Deleted ports which required this port:

    Expand this list of 1 deleted port
    1. science/MOOSE-neural-simulator*
    2. Collapse this list of deleted ports.
* - deleted ports are only shown under the This port is required by section. It was harder to do for the Required section. Perhaps later...

Configuration Options

USES:

Master Sites:
  1. http://cytranet.dl.sourceforge.net/project/sbml/libsbml/5.18.0/stable/
  2. http://downloads.sourceforge.net/project/sbml/libsbml/5.18.0/stable/
  3. http://excellmedia.dl.sourceforge.net/project/sbml/libsbml/5.18.0/stable/
  4. http://freefr.dl.sourceforge.net/project/sbml/libsbml/5.18.0/stable/
  5. http://jaist.dl.sourceforge.net/project/sbml/libsbml/5.18.0/stable/
  6. http://kent.dl.sourceforge.net/project/sbml/libsbml/5.18.0/stable/
  7. http://nchc.dl.sourceforge.net/project/sbml/libsbml/5.18.0/stable/
  8. http://netcologne.dl.sourceforge.net/project/sbml/libsbml/5.18.0/stable/
  9. http://netix.dl.sourceforge.net/project/sbml/libsbml/5.18.0/stable/
  10. http://superb-dca2.dl.sourceforge.net/project/sbml/libsbml/5.18.0/stable/
  11. http://superb-sea2.dl.sourceforge.net/project/sbml/libsbml/5.18.0/stable/
  12. http://ufpr.dl.sourceforge.net/project/sbml/libsbml/5.18.0/stable/
  13. http://vorboss.dl.sourceforge.net/project/sbml/libsbml/5.18.0/stable/
  14. https://cytranet.dl.sourceforge.net/project/sbml/libsbml/5.18.0/stable/
  15. https://downloads.sourceforge.net/project/sbml/libsbml/5.18.0/stable/
  16. https://excellmedia.dl.sourceforge.net/project/sbml/libsbml/5.18.0/stable/
  17. https://freefr.dl.sourceforge.net/project/sbml/libsbml/5.18.0/stable/
  18. https://jaist.dl.sourceforge.net/project/sbml/libsbml/5.18.0/stable/
  19. https://kent.dl.sourceforge.net/project/sbml/libsbml/5.18.0/stable/
  20. https://nchc.dl.sourceforge.net/project/sbml/libsbml/5.18.0/stable/
  21. https://netcologne.dl.sourceforge.net/project/sbml/libsbml/5.18.0/stable/
  22. https://netix.dl.sourceforge.net/project/sbml/libsbml/5.18.0/stable/
  23. https://superb-dca2.dl.sourceforge.net/project/sbml/libsbml/5.18.0/stable/
  24. https://superb-sea2.dl.sourceforge.net/project/sbml/libsbml/5.18.0/stable/
  25. https://ufpr.dl.sourceforge.net/project/sbml/libsbml/5.18.0/stable/
  26. https://vorboss.dl.sourceforge.net/project/sbml/libsbml/5.18.0/stable/

Number of commits found: 40

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
22 Jun 2019 21:48:14
Original commit files touched by this commit  5.18.0
Revision:504890
sunpoet search for other commits by this committer
Use USES=pathfix

- Add USES=gnome
- Use = instead of += for PLIST_SUB
- Use CMAKE_BOOL
- Cosmetic change
- Take maintainership
20 May 2019 09:12:42
Original commit files touched by this commit  5.18.0
Revision:502097
wen search for other commits by this committer
- Update to 5.18.0
25 Dec 2018 20:25:40
Original commit files touched by this commit  5.17.0
Revision:488341
tcberner search for other commits by this committer
Change cmake default behaviour to outsource.

Ports that build out of source now simply can use "USES=cmake"
instead of "USES=cmake:outsource". Ports that fail to build
out of source now need to specify "USES=cmake:insource".

I tried to only set insource where explictely needed.

PR:		232038
Exp-run by:	antoine
25 Aug 2018 03:31:43
Original commit files touched by this commit  5.17.0
Revision:477994
tobik search for other commits by this committer
biology/libsbml: Fix build with Clang 6

In file included from
/wrkdirs/usr/ports/biology/libsbml/work/libsbml-5.17.0/src/sbml/Model.cpp:41:
In file included from
/wrkdirs/usr/ports/biology/libsbml/work/libsbml-5.17.0/src/sbml/SBMLDocument.h:298:
In file included from
/wrkdirs/usr/ports/biology/libsbml/work/libsbml-5.17.0/src/sbml/SBMLTransforms.h:48:
In file included from
/wrkdirs/usr/ports/biology/libsbml/work/libsbml-5.17.0/src/sbml/FunctionDefinition.h:129:
In file included from
/wrkdirs/usr/ports/biology/libsbml/work/libsbml-5.17.0/src/sbml/SBO.h:207:
/usr/include/c++/v1/map:629:15: error: object of type
'std::__1::pair<std::__1::pair<const std::__1::basic_string<char>, int>,
FormulaUnitsData *>' cannot be assigned because its copy assignment operator is
implicitly deleted
        {__nc = __v.__cc; return *this;}
              ^

http://beefy11.nyi.freebsd.org/data/head-i386-default/p477696_s338122/logs/errors/libsbml-5.17.0.log
24 Aug 2018 06:24:31
Original commit files touched by this commit  5.17.0
Revision:477936
linimon search for other commits by this committer
Mark as broken with clang6 after r473289.
25 Jun 2018 01:37:52
Original commit files touched by this commit  5.17.0
Revision:473289
wen search for other commits by this committer
- Update to 5.17.0
01 Jan 2018 08:24:54
Original commit files touched by this commit  5.16.0
Revision:457754
wen search for other commits by this committer
- Update to 5.16.0
20 Dec 2017 19:34:12
Original commit files touched by this commit  5.15.0
Revision:456845
bapt search for other commits by this committer
Switch from swig 2.0 to swig 3.0
30 Nov 2017 15:50:34
Original commit files touched by this commit  5.15.0
Revision:455210  Sanity Test Failure
mat search for other commits by this committer
Convert Python ports to FLAVORS.

  Ports using USE_PYTHON=distutils are now flavored.  They will
  automatically get flavors (py27, py34, py35, py36) depending on what
  versions they support.

  There is also a USE_PYTHON=flavors for ports that do not use distutils
  but need FLAVORS to be set.  A USE_PYTHON=noflavors can be set if
  using distutils but flavors are not wanted.

  A new USE_PYTHON=optsuffix that will add PYTHON_PKGNAMESUFFIX has been
  added to cope with Python ports that did not have the Python
  PKGNAMEPREFIX but are flavored.

  USES=python now also exports a PY_FLAVOR variable that contains the
(Only the first 15 lines of the commit message are shown above View all of this commit message)
18 May 2017 02:22:18
Original commit files touched by this commit  5.15.0
Revision:441126
wen search for other commits by this committer
- Update to 5.15.0
02 Nov 2016 22:45:14
Original commit files touched by this commit  5.13.0
Revision:425174
mat search for other commits by this committer
Cleanup no longer needed CHMOD usage after r424898.

PR:		213743
Submitted by:	mat
Exp-run by:	antoine
Sponsored by:	Absolight
16 Apr 2016 01:54:15
Original commit files touched by this commit  5.13.0
Revision:413410
mi search for other commits by this committer
Upgrade from 5.12.0 to 5.13.0. Release-announcement available here:

	https://groups.google.com/forum/#!topic/sbml-discuss/OEq_49c_X78

Notified by:	portscout
01 Apr 2016 13:29:17
Original commit files touched by this commit  5.12.0
Revision:412344
mat search for other commits by this committer
Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.

With hat:	portmgr
Sponsored by:	Absolight
27 Mar 2016 07:09:34
Original commit files touched by this commit  5.12.0
Revision:411978
wen search for other commits by this committer
- Update to 5.12.0
14 Oct 2015 23:51:20
Original commit files touched by this commit  5.11.4_1
Revision:399316
amdmi3 search for other commits by this committer
- Add LICENSE_FILE
- Switch to options helpers
25 Aug 2015 13:15:17
Original commit files touched by this commit  5.11.4_1
Revision:395248
rakuco search for other commits by this committer
Switch to USES=iconv:build.

The port does not use iconv on its own, the only dependency comes via
libxml2, which has one header that includes iconv.h.
12 May 2015 08:58:14
Original commit files touched by this commit  5.11.4
Revision:386129
wen search for other commits by this committer
- Update to 5.11.4
04 Jan 2015 08:23:24
Original commit files touched by this commit  5.11.0
Revision:376179
mva search for other commits by this committer
- Convert USE_PYTHON -> USES leftovers missed in the previous commits

Spotted by:	antoine
With hat:	python
30 Dec 2014 12:57:54
Original commit files touched by this commit  5.11.0
Revision:375831
wen search for other commits by this committer
- Update to 5.11.0

PR:		196377
Submitted by:	koue@chaosophia.net
20 Oct 2014 07:10:48
Original commit files touched by this commit  5.10.2
Revision:371237
bapt search for other commits by this committer
Cleanup plist
10 Aug 2014 06:21:54
Original commit files touched by this commit  5.10.2
Revision:364504
wen search for other commits by this committer
- Update to 5.10.2

PR:		192198
Submitted by:	tkato432@yahoo.com
09 Aug 2014 15:44:28
Original commit files touched by this commit  5.10.0
Revision:364450
mva search for other commits by this committer
Convert the Python framework bits to USES=python.

Please use USES=python instead of USE_PYTHON.

  USE_PYTHON=yes becomes USES=python
  USE_PYTHON=2.7+ becomes USES=python:2.7+
  USE_PYTHON_BUILD=3.3 becomes USES=python:3.3,build
  ...

A new PYTHON_FEATURES variable was added, which enables certain features for a
port and replaces some knobs at the same time;

  PYTHON_FEATURES=distutils replaces USE_PYDISTUTILS
  PYTHON_FEATURES=autoplist replaces PYDISTUTILS_AUTOPLIST
  PYTHON_FEATURES=py3kplist replaces PYTHON_PY3K_PLIST_HACK
(Only the first 15 lines of the commit message are shown above View all of this commit message)
13 May 2014 07:04:17
Original commit files touched by this commit  5.10.0
Revision:353921
wen search for other commits by this committer
- Update to 5.10.0
13 May 2014 02:46:25
Original commit files touched by this commit  5.9.0
Revision:353913
wen search for other commits by this committer
- 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@gmail.com> [1]
16 Apr 2014 18:28:50
Original commit files touched by this commit  4.2.0_1
Revision:351411
zeising search for other commits by this committer
The FreeBSD x11@ and graphics team proudly presents
a zeising, kwm production, with help from dumbbell, bdrewery:

NEW XORG ON FREEBSD 9-STABLE AND 10-STABLE

This update switches over to use the new xorg stack by default on FreeBSD 9
and 10 stable, on osversions where vt(9) is available.
It is still possible to use the old stack by specifying WITHOUT_NEW_XORG in
/etc/make.conf .
FreeBSD 8-STABLE and released versions of FreeBSD still use
the old version.
A package repository with binary packages for new xorg will
be available soon.

This patch also contains updates of libxcb and related ports, pixman, as well
(Only the first 15 lines of the commit message are shown above View all of this commit message)
07 Mar 2014 15:52:40
Original commit files touched by this commit  4.2.0
Revision:347402
bapt search for other commits by this committer
Convert b* to USES=zip
15 Jan 2014 22:50:51
Original commit files touched by this commit  4.2.0
Revision:339844
bapt search for other commits by this committer
Reduce over inclusion of bsd.port.mk
11 Dec 2013 14:43:51
Original commit files touched by this commit  4.2.0
Revision:336171
bapt search for other commits by this committer
In preparation for making libtool generate libraries with a sane name, fix all
LIB_DEPENDS in biology
01 Dec 2013 01:58:32
Original commit files touched by this commit  4.2.0
Revision:335360
wen search for other commits by this committer
- Fix build on head
10 Oct 2013 18:08:34
Original commit files touched by this commit  4.2.0
Revision:330025
tabthorpe search for other commits by this committer
- Switch to build with lang/ruby19
- No PORTREVISION bump, option is off by default

With hat:	portmgr
20 Sep 2013 15:55:44
Original commit files touched by this commit  4.2.0
Revision:327709
bapt search for other commits by this committer
Add NO_STAGE all over the place in preparation for the staging support (cat:
biology)
18 Mar 2013 06:50:13
Original commit files touched by this commit  4.2.0
Revision:314530
jgh search for other commits by this committer
- adoption of optionsNG
- trim historical header
- tighten COMMENT

Approved by:	portmgr (miwi)
19 Mar 2011 12:38:54
Original commit files touched by this commit  4.2.0

miwi search for other commits by this committer
- Get Rid MD5 support
08 Oct 2010 02:06:53
Original commit files touched by this commit  4.2.0

wen search for other commits by this committer
- Update to 4.2.0
16 Sep 2010 03:31:29
Original commit files touched by this commit  4.1.0

wen search for other commits by this committer
- Update to 4.1.0
24 May 2010 07:19:35
Original commit files touched by this commit  4.0.1

wen search for other commits by this committer
- Update to 4.0.1
20 Nov 2009 22:53:09
Original commit files touched by this commit  4.0.0

pav search for other commits by this committer
- Mark MAKE_JOBS_UNSAFE

Reported by:    pointyhat
23 Sep 2009 01:06:29
Original commit files touched by this commit  4.0.0

wen search for other commits by this committer
- Update to 4.0.0
- Update my mail address to FreeBSD

PR:             ports/137652
Submitted by:   wenheping@gmail.com(myself)
Approved by:    miwi(mentor)
Feature safe:   yes
22 Aug 2009 00:15:15
Original commit files touched by this commit  3.3.2

amdmi3 search for other commits by this committer
- Switch SourceForge ports to the new File Release System: categories starting
with B,C
28 May 2009 23:36:10
Original commit files touched by this commit  3.3.2

miwi search for other commits by this committer
LibSBML is an open-source programming library to help you read, write,
manipulate, translate, and validate SBML files and data streams. It is
not an application itself (though it does come with example programs),
but rather a library you can embed in your own applications.

LibSBML understands all Levels and Versions of SBML, as well as the
SBML Layout proposal by Gauges, Rost, Sahle and Wegner. It's written in
ISO C and C++ but can be used from all the languages listed in the
right-hand box.

WWW: http://www.sbml.org/

PR:             ports/135022
Submitted by:   Wen Heping <wenheping at gmail.com>

Number of commits found: 40

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8 vulnerabilities affecting 177 ports have been reported in the past 14 days

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