Kemia kemia → 0.9 backlog

(imported from github, reported by rwest) When I run ant build-docs I get:

Buildfile: build.xml



build-docs:

 [exec] js: Couldn't open file "/path/to/kemia/third-party/jsdoc-toolkit/templates/kemia/publish.js".

BUILD FAILED
/path/to/kemia/build.xml:148: exec returned: 4



Total time: 23 seconds

My jsdoc.log file has a great many warnings, the most relevant of which appears to be the last:

>> WARNING: The symbol 'kemia' is documented more than once.
>> WARNING: Overwriting symbol documentation for: kemia.
>> WARNING: Overwriting symbol documentation for: button.updateFromValue.
>> WARNING: Overwriting symbol documentation for: button.updateFromValue.
>> WARNING: Overwriting symbol documentation for: button.updateFromValue.
>> WARNING: Overwriting symbol documentation for: button.updateFromValue.
>> WARNING: The symbol 'kemia.controller.plugins.MoleculeEdit#logger' is documented more than once.
>> WARNING: Overwriting symbol documentation for: kemia.controller.plugins.MoleculeEdit#logger.
>> WARNING: Overwriting symbol documentation for: kemia.controller.ReactionEditor#handleMouseUp_.
>> WARNING: The symbol 'kemia.controller.ReactionEditor#isLoaded' is documented more than once.
>> WARNING: Overwriting symbol documentation for: kemia.controller.ReactionEditor#isLoaded.
>> WARNING: The symbol 'kemia.io.mdl.TRIPLE_BOND' is documented more than once.
>> WARNING: Overwriting symbol documentation for: kemia.io.mdl.TRIPLE_BOND.
>> WARNING: Can't document kemia.layout.Vector2D without first documenting kemia.layout.
>> WARNING: Can't document kemia.layout.Vector2D without first documenting kemia.layout.
>> WARNING: The symbol 'kemia.layout.Vector2D#negate' is documented more than once.
>> WARNING: Overwriting symbol documentation for: kemia.layout.Vector2D#negate.
>> WARNING: Can't document kemia.ring.PathGraph without first documenting kemia.ring.
>> WARNING: Can't document kemia.ring.PathGraph without first documenting kemia.ring.
>> WARNING: Can't document kemia.ring.PathEdge without first documenting kemia.ring.
>> WARNING: Can't document ArrowController as a member of undocumented symbol kemia.controller.
>> WARNING: Can't document AtomController as a member of undocumented symbol kemia.controller.
>> WARNING: Can't document BondController as a member of undocumented symbol kemia.controller.
>> WARNING: Can't document Command as a member of undocumented symbol kemia.controller.
>> WARNING: Can't document makeDefaultToolbar as a member of undocumented symbol kemia.controller.DefaultToolbar.
>> WARNING: Can't document makeToolbar as a member of undocumented symbol kemia.controller.DefaultToolbar.
>> WARNING: Can't document makeBuiltInToolbarButton as a member of undocumented symbol kemia.controller.DefaultToolbar.
>> WARNING: Can't document DEFAULT_BUTTONS as a member of undocumented symbol kemia.controller.DefaultToolbar.
>> WARNING: Can't document DEFAULT_BUTTONS_RTL as a member of undocumented symbol kemia.controller.DefaultToolbar.
>> WARNING: Can't document updateFromValue as a member of undocumented symbol button.
>> WARNING: Can't document updateFromValue as a member of undocumented symbol button.
>> WARNING: Can't document updateFromValue as a member of undocumented symbol button.
>> WARNING: Can't document updateFromValue as a member of undocumented symbol button.
>> WARNING: Can't document MSG_FORMAT_BLOCK_TITLE as a member of undocumented symbol kemia.controller.DefaultToolbar.
>> WARNING: Can't document MSG_FORMAT_BLOCK_CAPTION as a member of undocumented symbol kemia.controller.DefaultToolbar.
>> WARNING: Can't document MSG_UNDO_TITLE as a member of undocumented symbol kemia.controller.DefaultToolbar.
>> WARNING: Can't document MSG_REDO_TITLE as a member of undocumented symbol kemia.controller.DefaultToolbar.
>> WARNING: Can't document MSG_FONT_FACE_TITLE as a member of undocumented symbol kemia.controller.DefaultToolbar.
>> WARNING: Can't document MSG_FONT_SIZE_TITLE as a member of undocumented symbol kemia.controller.DefaultToolbar.
>> WARNING: Can't document MSG_FONT_COLOR_TITLE as a member of undocumented symbol kemia.controller.DefaultToolbar.
>> WARNING: Can't document MSG_BOLD_TITLE as a member of undocumented symbol kemia.controller.DefaultToolbar.
>> WARNING: Can't document MSG_ITALIC_TITLE as a member of undocumented symbol kemia.controller.DefaultToolbar.
>> WARNING: Can't document MSG_UNDERLINE_TITLE as a member of undocumented symbol kemia.controller.DefaultToolbar.
>> WARNING: Can't document MSG_BACKGROUND_COLOR_TITLE as a member of undocumented symbol kemia.controller.DefaultToolbar.
>> WARNING: Can't document MSG_LINK_TITLE as a member of undocumented symbol kemia.controller.DefaultToolbar.
>> WARNING: Can't document MSG_ORDERED_LIST_TITLE as a member of undocumented symbol kemia.controller.DefaultToolbar.
>> WARNING: Can't document MSG_UNORDERED_LIST_TITLE as a member of undocumented symbol kemia.controller.DefaultToolbar.
>> WARNING: Can't document MSG_OUTDENT_TITLE as a member of undocumented symbol kemia.controller.DefaultToolbar.
>> WARNING: Can't document MSG_INDENT_TITLE as a member of undocumented symbol kemia.controller.DefaultToolbar.
>> WARNING: Can't document MSG_ALIGN_LEFT_TITLE as a member of undocumented symbol kemia.controller.DefaultToolbar.
>> WARNING: Can't document MSG_ALIGN_CENTER_TITLE as a member of undocumented symbol kemia.controller.DefaultToolbar.
>> WARNING: Can't document MSG_ALIGN_RIGHT_TITLE as a member of undocumented symbol kemia.controller.DefaultToolbar.
>> WARNING: Can't document MSG_JUSTIFY_TITLE as a member of undocumented symbol kemia.controller.DefaultToolbar.
>> WARNING: Can't document MSG_REMOVE_FORMAT_TITLE as a member of undocumented symbol kemia.controller.DefaultToolbar.
>> WARNING: Can't document MSG_IMAGE_TITLE as a member of undocumented symbol kemia.controller.DefaultToolbar.
>> WARNING: Can't document MSG_STRIKE_THROUGH_TITLE as a member of undocumented symbol kemia.controller.DefaultToolbar.
>> WARNING: Can't document MSG_DIR_LTR_TITLE as a member of undocumented symbol kemia.controller.DefaultToolbar.
>> WARNING: Can't document MSG_DIR_RTL_TITLE as a member of undocumented symbol kemia.controller.DefaultToolbar.
>> WARNING: Can't document MSG_BLOCKQUOTE_TITLE as a member of undocumented symbol kemia.controller.DefaultToolbar.
>> WARNING: Can't document MSG_EDIT_HTML_TITLE as a member of undocumented symbol kemia.controller.DefaultToolbar.
>> WARNING: Can't document MSG_LINK_CAPTION as a member of undocumented symbol kemia.controller.DefaultToolbar.
>> WARNING: Can't document MSG_SUBSCRIPT as a member of undocumented symbol kemia.controller.DefaultToolbar.
>> WARNING: Can't document MSG_SUPERSCRIPT as a member of undocumented symbol kemia.controller.DefaultToolbar.
>> WARNING: Can't document MSG_EDIT_HTML_CAPTION as a member of undocumented symbol kemia.controller.DefaultToolbar.
>> WARNING: Can't document ButtonDescriptor as a member of undocumented symbol kemia.controller.DefaultToolbar.
>> WARNING: Can't document MoleculeController as a member of undocumented symbol kemia.controller.
>> WARNING: Can't document Plugin as a member of undocumented symbol kemia.controller.
>> WARNING: Can't document AbstractDialog as a member of undocumented symbol kemia.controller.plugins.
>> WARNING: Can't document AbstractDialogPlugin as a member of undocumented symbol kemia.controller.plugins.
>> WARNING: Can't document ArrowPlusEdit as a member of undocumented symbol kemia.controller.plugins.
>> WARNING: Can't document AtomEdit as a member of undocumented symbol kemia.controller.plugins.
>> WARNING: Can't document BondEdit as a member of undocumented symbol kemia.controller.plugins.
>> WARNING: Can't document Cleanup as a member of undocumented symbol kemia.controller.plugins.
>> WARNING: Can't document ClearEditor as a member of undocumented symbol kemia.controller.plugins.
>> WARNING: Can't document Erase as a member of undocumented symbol kemia.controller.plugins.
>> WARNING: Can't document Highlight as a member of undocumented symbol kemia.controller.plugins.
>> WARNING: Can't document MoleculeEdit as a member of undocumented symbol kemia.controller.plugins.
>> WARNING: Can't document SelectorRectangle as a member of undocumented symbol kemia.controller.plugins.
>> WARNING: Can't document Smiles as a member of undocumented symbol kemia.controller.plugins.
>> WARNING: Can't document SmilesDialog as a member of undocumented symbol kemia.controller.plugins.
>> WARNING: Can't document MSG_EXAMPLE_DIALOG_PROMPT as a member of undocumented symbol kemia.controller.plugins.SmilesDialog#createContent_.
>> WARNING: Can't document UndoRedo as a member of undocumented symbol kemia.controller.plugins.
>> WARNING: Can't document Zoom as a member of undocumented symbol kemia.controller.plugins.
>> WARNING: Can't document PlusController as a member of undocumented symbol kemia.controller.
>> WARNING: Can't document ReactionController as a member of undocumented symbol kemia.controller.
>> WARNING: Can't document ReactionEditor as a member of undocumented symbol kemia.controller.
>> WARNING: Can't document TemplateMenuButtonRenderer as a member of undocumented symbol kemia.controller.
>> WARNING: Can't document ToolbarController as a member of undocumented symbol kemia.controller.
>> WARNING: Can't document commands as a member of undocumented symbol e.
>> WARNING: Can't document makeToolbar as a member of undocumented symbol kemia.controller.ToolbarFactory.
>> WARNING: Can't document makeButton as a member of undocumented symbol kemia.controller.ToolbarFactory.
>> WARNING: Can't document makeToggleButton as a member of undocumented symbol kemia.controller.ToolbarFactory.
>> WARNING: Can't document makeMenuButton as a member of undocumented symbol kemia.controller.ToolbarFactory.
>> WARNING: Can't document makeSelectButton as a member of undocumented symbol kemia.controller.ToolbarFactory.
>> WARNING: Can't document makeColorMenuButton as a member of undocumented symbol kemia.controller.ToolbarFactory.
>> WARNING: Can't document AffineTransform as a member of undocumented symbol kemia.graphics.
>> WARNING: Can't document BondType as a member of undocumented symbol kemia.io.json.
>> WARNING: Can't document StereoType as a member of undocumented symbol kemia.io.json.
>> WARNING: Can't document getTypeCode as a member of undocumented symbol kemia.io.json.
>> WARNING: Can't document getStereoCode as a member of undocumented symbol kemia.io.json.
>> WARNING: Can't document createBond as a member of undocumented symbol kemia.io.json.
>> WARNING: Can't document readMolecule as a member of undocumented symbol kemia.io.json.
>> WARNING: Can't document moleculeToJson as a member of undocumented symbol kemia.io.json.
>> WARNING: Can't document readReaction as a member of undocumented symbol kemia.io.json.
>> WARNING: Can't document reactionToJson as a member of undocumented symbol kemia.io.json.
>> WARNING: Can't document SINGLE_BOND as a member of undocumented symbol kemia.io.mdl.
>> WARNING: Can't document DOUBLE_BOND as a member of undocumented symbol kemia.io.mdl.
>> WARNING: Can't document TRIPLE_BOND as a member of undocumented symbol kemia.io.mdl.
>> WARNING: Can't document AROMATIC_BOND as a member of undocumented symbol kemia.io.mdl.
>> WARNING: Can't document SINGLE_OR_DOUBLE as a member of undocumented symbol kemia.io.mdl.
>> WARNING: Can't document SINGLE_OR_AROMATIC as a member of undocumented symbol kemia.io.mdl.
>> WARNING: Can't document DOUBLE_OR_AROMATIC as a member of undocumented symbol kemia.io.mdl.
>> WARNING: Can't document ANY as a member of undocumented symbol kemia.io.mdl.
>> WARNING: Can't document TRIPLE_BOND as a member of undocumented symbol kemia.io.mdl.
>> WARNING: Can't document NOT_STEREO as a member of undocumented symbol kemia.io.mdl.
>> WARNING: Can't document SINGLE_BOND_UP as a member of undocumented symbol kemia.io.mdl.
>> WARNING: Can't document SINGLE_BOND_UP_OR_DOWN as a member of undocumented symbol kemia.io.mdl.
>> WARNING: Can't document SINGLE_BOND_DOWN as a member of undocumented symbol kemia.io.mdl.
>> WARNING: Can't document getTypeCode as a member of undocumented symbol kemia.io.mdl.
>> WARNING: Can't document getStereoCode as a member of undocumented symbol kemia.io.mdl.
>> WARNING: Can't document createBond as a member of undocumented symbol kemia.io.mdl.
>> WARNING: Can't document readMolfile as a member of undocumented symbol kemia.io.mdl.
>> WARNING: Can't document writeRxnfile as a member of undocumented symbol kemia.io.mdl.
>> WARNING: Can't document writeMolfile as a member of undocumented symbol kemia.io.mdl.
>> WARNING: Can't document readRxnfile as a member of undocumented symbol kemia.io.mdl.
>> WARNING: Can't document BondType as a member of undocumented symbol kemia.io.smiles.
>> WARNING: Can't document BondStereo as a member of undocumented symbol kemia.io.smiles.
>> WARNING: Can't document createBond as a member of undocumented symbol kemia.io.smiles.
>> WARNING: Can't document parse as a member of undocumented symbol kemia.io.smiles.SmilesParser.
>> WARNING: Can't document getSymbolForOrganicSubsetElement as a member of undocumented symbol kemia.io.smiles.SmilesParser.
>> WARNING: Can't document getInitialLongestChain as a member of undocumented symbol kemia.layout.AtomPlacer.
>> WARNING: Can't document computeFloydAPSP as a member of undocumented symbol kemia.layout.AtomPlacer.
>> WARNING: Can't document getLongestUnplacedChain as a member of undocumented symbol kemia.layout.AtomPlacer.
>> WARNING: Can't document getDegreeSum as a member of undocumented symbol kemia.layout.AtomPlacer.
>> WARNING: Can't document getConnectedBondsCount as a member of undocumented symbol kemia.layout.AtomPlacer.
>> WARNING: Can't document breadthFirstSearch as a member of undocumented symbol kemia.layout.AtomPlacer.
>> WARNING: Can't document placeLinearChain as a member of undocumented symbol kemia.layout.AtomPlacer.
>> WARNING: Can't document distributePartners as a member of undocumented symbol kemia.layout.AtomPlacer.
>> WARNING: Can't document sortBy2DDistance as a member of undocumented symbol kemia.layout.AtomPlacer.
>> WARNING: Can't document populatePolygonCorners as a member of undocumented symbol kemia.layout.AtomPlacer.
>> WARNING: Can't document partitionPartners as a member of undocumented symbol kemia.layout.AtomPlacer.
>> WARNING: Can't document BOND_LENGTH as a member of undocumented symbol kemia.layout.CoordinateGenerator.
>> WARNING: Can't document layoutRingSet as a member of undocumented symbol kemia.layout.CoordinateGenerator.
>> WARNING: Can't document placeFirstBond as a member of undocumented symbol kemia.layout.CoordinateGenerator.
>> WARNING: Can't document getNextAtomWithAliphaticUnplacedNeigbors as a member of undocumented symbol kemia.layout.CoordinateGenerator.
>> WARNING: Can't document handleAliphatics as a member of undocumented symbol kemia.layout.CoordinateGenerator.
>> WARNING: Can't document getRingCenterOfFirstRing as a member of undocumented symbol kemia.layout.RingPlacer.
>> WARNING: Can't document placeRing as a member of undocumented symbol kemia.layout.RingPlacer.
>> WARNING: Can't document placeBridgedRing as a member of undocumented symbol kemia.layout.RingPlacer.
>> WARNING: Can't document findDirection as a member of undocumented symbol kemia.layout.RingPlacer.
>> WARNING: Can't document getBridgeAtoms as a member of undocumented symbol kemia.layout.RingPlacer.
>> WARNING: Can't document placeFusedRing as a member of undocumented symbol kemia.layout.RingPlacer.
>> WARNING: Can't document placeSpiroRing as a member of undocumented symbol kemia.layout.RingPlacer.
>> WARNING: Can't document getNativeRingRadius as a member of undocumented symbol kemia.layout.RingPlacer.
>> WARNING: Can't document center as a member of undocumented symbol kemia.layout.RingPlacer.
>> WARNING: Can't document resetUnplacedRingAtoms as a member of undocumented symbol kemia.layout.RingPlacer.
>> WARNING: Can't document Vector2D as a member of undocumented symbol kemia.layout.
>> WARNING: Can't document Line as a member of undocumented symbol kemia.math.
>> WARNING: Can't document Atom as a member of undocumented symbol kemia.model.
>> WARNING: Can't document Bond as a member of undocumented symbol kemia.model.
>> WARNING: Can't document Molecule as a member of undocumented symbol kemia.model.
>> WARNING: Can't document NeighborList as a member of undocumented symbol kemia.model.
>> WARNING: Can't document PseudoAtom as a member of undocumented symbol kemia.model.
>> WARNING: Can't document Reaction as a member of undocumented symbol kemia.model.
>> WARNING: Can't document Hanser as a member of undocumented symbol kemia.ring.
>> WARNING: Can't document Ring as a member of undocumented symbol kemia.ring.
>> WARNING: Can't document getPartitionedRings as a member of undocumented symbol kemia.ring.RingPartitioner.
>> WARNING: Can't document directConnectedRings as a member of undocumented symbol kemia.ring.RingPartitioner.
>> WARNING: Can't document isCandidateInSet as a member of undocumented symbol kemia.ring.SSSR.
>> WARNING: Can't document findRings as a member of undocumented symbol kemia.ring.SSSR.
>> WARNING: Can't document Orders as a member of undocumented symbol kemia.util.BondUtil.
>> WARNING: Can't document ArrowRenderer as a member of undocumented symbol kemia.view.
>> WARNING: Can't document AtomRenderer as a member of undocumented symbol kemia.view.
>> WARNING: Can't document BondRenderer as a member of undocumented symbol kemia.view.
>> WARNING: Can't document BondRendererFactory as a member of undocumented symbol kemia.view.
>> WARNING: Can't document DoubleBondRenderer as a member of undocumented symbol kemia.view.
>> WARNING: Can't document MoleculeRenderer as a member of undocumented symbol kemia.view.
>> WARNING: Can't document PlusRenderer as a member of undocumented symbol kemia.view.
>> WARNING: Can't document QuadrupleBondRenderer as a member of undocumented symbol kemia.view.
>> WARNING: Can't document ReactionRenderer as a member of undocumented symbol kemia.view.
>> WARNING: Can't document Renderer as a member of undocumented symbol kemia.view.
>> WARNING: Can't document SingleBondRenderer as a member of undocumented symbol kemia.view.
>> WARNING: Can't document SingleDownBondRenderer as a member of undocumented symbol kemia.view.
>> WARNING: Can't document SingleUpBondRenderer as a member of undocumented symbol kemia.view.
>> WARNING: Can't document SingleUpOrDownBondRenderer as a member of undocumented symbol kemia.view.
>> WARNING: Can't document TripleBondRenderer as a member of undocumented symbol kemia.view.
>> WARNING: Can't augment contributer: , not found.
>> WARNING: Can't augment contributer: , not found.
>> WARNING: Can't augment contributer: , not found.
>> WARNING: Can't augment contributer: , not found.
>> WARNING: Can't augment contributer: , not found.
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>> WARNING: Can't augment contributer: , not found.
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>> WARNING: Can't augment contributer: , not found.
>> WARNING: Can't augment contributer: , not found.
>> WARNING: Can't augment contributer: , not found.
>> WARNING: Can't augment contributer: , not found.
>> WARNING: Can't augment contributer: , not found.
>> WARNING: Can't augment contributer: , not found.
>> WARNING: Can't augment contributer: , not found.
>> WARNING: Can't augment contributer: , not found.
>> WARNING: Can't augment contributer: , not found.
>> WARNING: Can't augment contributer: , not found.
>> WARNING: Can't augment contributer: , not found.
>> WARNING: Can't augment contributer: , not found.
>> WARNING: Can't augment contributer: , not found.
>> WARNING: Can't augment contributer: , not found.
>> WARNING: Can't augment contributer: , not found.
>> WARNING: Can't augment contributer: , not found.
>> WARNING: Can't augment contributer: , not found.
>> WARNING: Can't augment contributer: , not found.
>> WARNING: Can't augment contributer: , not found.
>> WARNING: Can't augment contributer: , not found.
>> WARNING: Can't augment contributer: , not found.
>> WARNING: Can't augment contributer: , not found.
>> WARNING: Can't augment contributer: , not found.
>> WARNING: Can't augment contributer: , not found.
>> WARNING: Can't augment contributer: , not found.
>> WARNING: Can't augment contributer: , not found.
>> WARNING: Can't augment contributer: , not found.
>> WARNING: Can't augment contributer: , not found.
>> WARNING: Can't augment contributer: , not found.
>> WARNING: Can't augment contributer: , not found.
>> WARNING: Sorry, that doesn't seem to be a valid template: /path/to/kemia/third-party/jsdoc-toolkit/templates/kemia/publish.js : ReferenceError: "publish" is not defined.
225 warnings.