Hi Luke,
you should either use dist-all or run javacc before compilation.
Stefan
Am Wednesday 31 January 2007 18:07 schrieb Luke Yen:
> Hi,
>
> I am trying to build the CDK from source, and I tried both Sun's 1.4
> and 1.5 versions without success.
>
> Here's the Ant output from compiling with 1.4:
>
> compile-module:
> [echo] Compiling classes for CDK's extra module.
> [echo] Datafiles defined: true
> [echo] Extra files defined: true
> [echo] CDK dependencies defined: true
> [echo] Library dependencies defined: true
> [echo] Developer Library dependencies defined:
> ${module.devellibdepends.present}
> [delete] Deleting directory /scratch/luke/cdk-source-20060718/build
> [mkdir] Created dir: /scratch/luke/cdk-source-20060718/build
> [mkdir] Created dir: /scratch/luke/cdk-source-20060718/build/src
> [copy] Copying 165 files to
> /scratch/luke/cdk-source-20060718/build/src
> [javac] Compiling 165 source files to
> /scratch/luke/cdk-source-20060718/build
> [javac]
> /scratch/luke/cdk-source-20060718/build/src/org/openscience/cdk/iupac/parse
>r/NomParser.java:25: cannot resolve symbol
> [javac] symbol : class MoleculeBuilder
> [javac] location: package parser
> [javac] import org.openscience.cdk.iupac.parser.MoleculeBuilder;
> [javac] ^
> [javac]
> /scratch/luke/cdk-source-20060718/build/src/org/openscience/cdk/application
>s/undoredo/AddAtomsAndBondsEdit.java:70: warning:
> getAllInOneContainer(org.openscience.cdk.interfaces.IChemModel) in
> org.openscience.cdk.tools.manipulator.ChemModelManipulator has been
> deprecated
> [javac] IAtomContainer container =
> ChemModelManipulator.getAllInOneContainer(chemModel);
> [javac]
> ^
> [javac]
> /scratch/luke/cdk-source-20060718/build/src/org/openscience/cdk/application
>s/undoredo/AddAtomsAndBondsEdit.java:91: warning:
> getAllInOneContainer(org.openscience.cdk.interfaces.IChemModel) in
> org.openscience.cdk.tools.manipulator.ChemModelManipulator has been
> deprecated
> [javac] IAtomContainer container =
> ChemModelManipulator.getAllInOneContainer(chemModel);
> [javac]
> ^
> [javac]
> /scratch/luke/cdk-source-20060718/build/src/org/openscience/cdk/application
>s/undoredo/AddHydrogenEdit.java:146: warning:
> getAllInOneContainer(org.openscience.cdk.interfaces.IChemModel) in
> org.openscience.cdk.tools.manipulator.ChemModelManipulator has been
> deprecated
> [javac]
> .getAllInOneContainer(model);
> [javac] ^
> [javac]
> /scratch/luke/cdk-source-20060718/build/src/org/openscience/cdk/application
>s/undoredo/BondChangeEdit.java:67: warning:
> getAllInOneContainer(org.openscience.cdk.interfaces.IChemModel) in
> org.openscience.cdk.tools.manipulator.ChemModelManipulator has been
> deprecated
> [javac] IAtomContainer container =
> ChemModelManipulator.getAllInOneContainer(chemModel);
> [javac]
> ^
> [javac]
> /scratch/luke/cdk-source-20060718/build/src/org/openscience/cdk/application
>s/undoredo/BondChangeEdit.java:83: warning:
> getAllInOneContainer(org.openscience.cdk.interfaces.IChemModel) in
> org.openscience.cdk.tools.manipulator.ChemModelManipulator has been
> deprecated
> [javac] IAtomContainer container =
> ChemModelManipulator.getAllInOneContainer(chemModel);
> [javac]
> ^
> [javac]
> /scratch/luke/cdk-source-20060718/build/src/org/openscience/cdk/application
>s/undoredo/MergeMoleculesEdit.java:37: warning:
> getAllInOneContainer(org.openscience.cdk.interfaces.IChemModel) in
> org.openscience.cdk.tools.manipulator.ChemModelManipulator has been
> deprecated
> [javac] IAtomContainer container =
> ChemModelManipulator.getAllInOneContainer(chemModel);
> [javac]
> ^
> [javac]
> /scratch/luke/cdk-source-20060718/build/src/org/openscience/cdk/application
>s/undoredo/MergeMoleculesEdit.java:67: warning:
> getAllInOneContainer(org.openscience.cdk.interfaces.IChemModel) in
> org.openscience.cdk.tools.manipulator.ChemModelManipulator has been
> deprecated
> [javac] IAtomContainer container =
> ChemModelManipulator.getAllInOneContainer(chemModel);
> [javac]
> ^
> [javac]
> /scratch/luke/cdk-source-20060718/build/src/org/openscience/cdk/application
>s/undoredo/RemoveAtomsAndBondsEdit.java:55: warning:
> getAllInOneContainer(org.openscience.cdk.interfaces.IChemModel) in
> org.openscience.cdk.tools.manipulator.ChemModelManipulator has been
> deprecated
> [javac] this.container =
> ChemModelManipulator.getAllInOneContainer(chemModel);
> [javac] ^
> [javac]
> /scratch/luke/cdk-source-20060718/build/src/org/openscience/cdk/controller/
>AbstractController2D.java:946: warning:
> getAllInOneContainer(org.openscience.cdk.interfaces.IChemModel) in
> org.openscience.cdk.tools.manipulator.ChemModelManipulator has been
> deprecated
> [javac] IAtomContainer container =
> ChemModelManipulator.getAllInOneContainer(chemModel);
> [javac]
> ^
> [javac]
> /scratch/luke/cdk-source-20060718/build/src/org/openscience/cdk/controller/
>AbstractController2D.java:960: warning:
> getAllInOneContainer(org.openscience.cdk.interfaces.IChemModel) in
> org.openscience.cdk.tools.manipulator.ChemModelManipulator has been
> deprecated
> [javac] container =
> ChemModelManipulator.getAllInOneContainer(chemModel);
> [javac] ^
> [javac]
> /scratch/luke/cdk-source-20060718/build/src/org/openscience/cdk/controller/
>AbstractController2D.java:996: warning:
> getAllInOneContainer(org.openscience.cdk.interfaces.IChemModel) in
> org.openscience.cdk.tools.manipulator.ChemModelManipulator has been
> deprecated
> [javac] IAtomContainer container =
> ChemModelManipulator.getAllInOneContainer(chemModel);
> [javac]
> ^
> [javac]
> /scratch/luke/cdk-source-20060718/build/src/org/openscience/cdk/controller/
>AbstractController2D.java:1139: warning:
> getAllInOneContainer(org.openscience.cdk.interfaces.IChemModel) in
> org.openscience.cdk.tools.manipulator.ChemModelManipulator has been
> deprecated
> [javac] IAtomContainer atomCon =
> ChemModelManipulator.getAllInOneContainer(chemModel);
> [javac]
> ^
> [javac]
> /scratch/luke/cdk-source-20060718/build/src/org/openscience/cdk/controller/
>AbstractController2D.java:1709: warning:
> getAllInOneContainer(org.openscience.cdk.interfaces.IChemModel) in
> org.openscience.cdk.tools.manipulator.ChemModelManipulator has been
> deprecated
> [javac] IAtomContainer atomCon =
> ChemModelManipulator.getAllInOneContainer(chemModel);
> [javac] ^
> [javac]
> /scratch/luke/cdk-source-20060718/build/src/org/openscience/cdk/controller/
>AbstractController2D.java:1807: warning:
> getAllInOneContainer(org.openscience.cdk.interfaces.IChemModel) in
> org.openscience.cdk.tools.manipulator.ChemModelManipulator has been
> deprecated
> [javac] IAtomContainer atomCon =
> ChemModelManipulator.getAllInOneContainer(chemModel);
> [javac] ^
> [javac]
> /scratch/luke/cdk-source-20060718/build/src/org/openscience/cdk/controller/
>AbstractController2D.java:1834: warning:
> getAllInOneContainer(org.openscience.cdk.interfaces.IChemModel) in
> org.openscience.cdk.tools.manipulator.ChemModelManipulator has been
> deprecated
> [javac] IAtomContainer atomCon =
> ChemModelManipulator.getAllInOneContainer(chemModel);
> [javac] ^
> [javac]
> /scratch/luke/cdk-source-20060718/build/src/org/openscience/cdk/controller/
>AbstractController2D.java:2060: warning:
> getAllInOneContainer(org.openscience.cdk.interfaces.IChemModel) in
> org.openscience.cdk.tools.manipulator.ChemModelManipulator has been
> deprecated
> [javac] IAtomContainer atomCon =
> ChemModelManipulator.getAllInOneContainer(chemModel);
> [javac]
> ^
> [javac]
> /scratch/luke/cdk-source-20060718/build/src/org/openscience/cdk/controller/
>AbstractController2D.java:2126: warning:
> getAllInOneContainer(org.openscience.cdk.interfaces.ISetOfMolecules) in
> org.openscience.cdk.tools.manipulator.SetOfMoleculesManipulator has been
> deprecated
> [javac] IAtomContainer
> allinone=SetOfMoleculesManipulator.getAllInOneContainer(chemModel.getSetOfM
>olecules()); [javac]
> ^
> [javac]
> /scratch/luke/cdk-source-20060718/build/src/org/openscience/cdk/controller/
>Controller2D.java:97: warning:
> getAllInOneContainer(org.openscience.cdk.interfaces.IChemModel) in
> org.openscience.cdk.tools.manipulator.ChemModelManipulator has been
> deprecated
> [javac] return
> ChemModelManipulator.getAllInOneContainer(chemModel);
> [javac] ^
> [javac]
> /scratch/luke/cdk-source-20060718/build/src/org/openscience/cdk/controller/
>Controller2D.java:115: warning:
> getAllInOneContainer(org.openscience.cdk.interfaces.IReaction) in
> org.openscience.cdk.tools.manipulator.ReactionManipulator has been
> deprecated
> [javac] IAtomContainer atomContainer =
> ReactionManipulator.getAllInOneContainer(reactions[i]);
> [javac]
> ^
> [javac]
> /scratch/luke/cdk-source-20060718/build/src/org/openscience/cdk/iupac/parse
>r/NomParser.java:87: cannot resolve symbol
> [javac] symbol : class MoleculeBuilder
> [javac] location: class org.openscience.cdk.iupac.parser.NomParser
> [javac] MoleculeBuilder moleculeBuilder = new
> MoleculeBuilder();
> [javac] ^
> [javac]
> /scratch/luke/cdk-source-20060718/build/src/org/openscience/cdk/iupac/parse
>r/NomParser.java:87: cannot resolve symbol
> [javac] symbol : class MoleculeBuilder
> [javac] location: class org.openscience.cdk.iupac.parser.NomParser
> [javac] MoleculeBuilder moleculeBuilder = new
> MoleculeBuilder();
> [javac] ^
> [javac]
> /scratch/luke/cdk-source-20060718/build/src/org/openscience/cdk/iupac/parse
>r/NomParser.java:105: cannot resolve symbol
> [javac] symbol : class AttachedGroup
> [javac] location: class org.openscience.cdk.iupac.parser.NomParser
> [javac] AttachedGroup ag = (AttachedGroup)
> vectorIterator.next();
> [javac] ^
> [javac]
> /scratch/luke/cdk-source-20060718/build/src/org/openscience/cdk/iupac/parse
>r/NomParser.java:105: cannot resolve symbol
> [javac] symbol : class AttachedGroup
> [javac] location: class org.openscience.cdk.iupac.parser.NomParser
> [javac] AttachedGroup ag = (AttachedGroup)
> vectorIterator.next();
>
> And 1.5's output (it fails in the same spot in compilation):
>
> [javac]
> /scratch/luke/cdk-source-20060718/build/src/org/openscience/cdk/iupac/parse
>r/NomParser.java:87: cannot find symbol
> [javac] symbol : class MoleculeBuilder
> [javac] location: class org.openscience.cdk.iupac.parser.NomParser
> [javac] MoleculeBuilder moleculeBuilder = new
> MoleculeBuilder();
> [javac] ^
> [javac]
> /scratch/luke/cdk-source-20060718/build/src/org/openscience/cdk/iupac/parse
>r/NomParser.java:87: cannot find symbol
> [javac] symbol : class MoleculeBuilder
> [javac] location: class org.openscience.cdk.iupac.parser.NomParser
> [javac] MoleculeBuilder moleculeBuilder = new
> MoleculeBuilder();
> [javac] ^
> [javac]
> /scratch/luke/cdk-source-20060718/build/src/org/openscience/cdk/iupac/parse
>r/NomParser.java:105: cannot find symbol
> [javac] symbol : class AttachedGroup
> [javac] location: class org.openscience.cdk.iupac.parser.NomParser
> [javac] AttachedGroup ag = (AttachedGroup)
> vectorIterator.next();
> [javac] ^
> [javac]
> /scratch/luke/cdk-source-20060718/build/src/org/openscience/cdk/iupac/parse
>r/NomParser.java:105: cannot find symbol
> [javac] symbol : class AttachedGroup
> [javac] location: class org.openscience.cdk.iupac.parser.NomParser
> [javac] AttachedGroup ag = (AttachedGroup)
> vectorIterator.next();
> [javac] ^
> [javac]
> /scratch/luke/cdk-source-20060718/build/src/org/openscience/cdk/iupac/parse
>r/NomParser.java:143: cannot find symbol
> [javac] symbol : class AttachedGroup
> [javac] location: class org.openscience.cdk.iupac.parser.NomParser
> [javac] attachedSubstituents.add (new AttachedGroup (tempLocation,
> currentNumber) );
>
> Any suggestions on how to fix this problem would be greatly
> appreciated.
>
> Luke
>
> -------------------------------------------------------------------------
> Take Surveys. Earn Cash. Influence the Future of IT
> Join SourceForge.net's Techsay panel and you'll get the chance to share
> your opinions on IT & business topics through brief surveys - and earn cash
> http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV
> _______________________________________________
> Cdk-user mailing list
> [email protected]
> https://lists.sourceforge.net/lists/listinfo/cdk-user
--
Stefan Kuhn B. Sc. M. A.
Cologne University BioInformatics Center (http://www.cubic.uni-koeln.de)
Zülpicher Str. 47, 50674 Cologne
Tel: +49(0)221-470-7428 Fax: +49 (0) 221-470-7786
My public PGP key is available at http://pgp.mit.edu
-------------------------------------------------------------------------
Take Surveys. Earn Cash. Influence the Future of IT
Join SourceForge.net's Techsay panel and you'll get the chance to share your
opinions on IT & business topics through brief surveys - and earn cash
http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV
_______________________________________________
Cdk-user mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/cdk-user
