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/parser/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/applications/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/applications/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/applications/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/applications/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/applications/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/applications/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/applications/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/applications/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.getSetOfMolecules());
[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/parser/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/parser/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/parser/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/parser/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/parser/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/parser/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/parser/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/parser/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/parser/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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