Hi Stefan,
I tried the dist-all target but it still gives me the same errors.
How/where should I run the javac command?
Thanks,
Luke
On Wed, 31 Jan 2007, Stefan Kuhn wrote:
> 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
> >
> > -------------------------------------------------------------------------
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> > _______________________________________________
> > Cdk-user mailing list
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>
> --
> 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
>
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