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asad/smsd-cdk compile

Created July 26, 2011 09:10
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smsd cdk doc errors
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smsd-cdk compile
asad:cdksmsdgithub Asad$ ant -Dmodule=smsd qa-module
Buildfile: /users/Asad/Software/GITROOT/cdksmsdgithub/build.xml
checkPlatforms:
check:
dist.init:
qa-module:
[echo] Running QA for CDK's smsd module
checkPlatforms:
check:
noJunit:
test-module:
[echo] Testing classes for CDK's smsd module.
[echo] CDK dependencies defined: true
[echo] Library dependencies defined: true
[echo] Developer Library dependencies defined: true
[junit] Running org.openscience.cdk.modulesuites.MsmsdTests
^Casad:cdksmsdgithub Asad$ ant -Dmodule=smsd qa-module
Buildfile: /users/Asad/Software/GITROOT/cdksmsdgithub/build.xml
checkPlatforms:
check:
dist.init:
qa-module:
[echo] Running QA for CDK's smsd module
checkPlatforms:
check:
noJunit:
test-module:
[echo] Testing classes for CDK's smsd module.
[echo] CDK dependencies defined: true
[echo] Library dependencies defined: true
[echo] Developer Library dependencies defined: true
[junit] Running org.openscience.cdk.modulesuites.MsmsdTests
[junit] Tests run: 222, Failures: 2, Errors: 0, Time elapsed: 8.328 sec
[junit] Test org.openscience.cdk.modulesuites.MsmsdTests FAILED
ojdcheck-module:
[mkdir] Created dir: /users/Asad/Software/GITROOT/cdksmsdgithub/reports/ojdcheck
[javadoc] Generating Javadoc
[javadoc] Javadoc execution
[javadoc] Loading source files for package org.openscience.cdk.normalize...
[javadoc] Loading source files for package org.openscience.cdk.smsd...
[javadoc] Loading source files for package org.openscience.cdk.smsd.algorithm.matchers...
[javadoc] Loading source files for package org.openscience.cdk.smsd.algorithm.mcgregor...
[javadoc] Loading source files for package org.openscience.cdk.smsd.algorithm.mcsplus...
[javadoc] Loading source files for package org.openscience.cdk.smsd.algorithm.rgraph...
[javadoc] Loading source files for package org.openscience.cdk.smsd.algorithm.single...
[javadoc] Loading source files for package org.openscience.cdk.smsd.algorithm.vflib...
[javadoc] Loading source files for package org.openscience.cdk.smsd.algorithm.vflib.builder...
[javadoc] Loading source files for package org.openscience.cdk.smsd.algorithm.vflib.interfaces...
[javadoc] Loading source files for package org.openscience.cdk.smsd.algorithm.vflib.map...
[javadoc] Loading source files for package org.openscience.cdk.smsd.algorithm.vflib.query...
[javadoc] Loading source files for package org.openscience.cdk.smsd.algorithm.vflib.substructure...
[javadoc] Loading source files for package org.openscience.cdk.smsd.filters...
[javadoc] Loading source files for package org.openscience.cdk.smsd.global...
[javadoc] Loading source files for package org.openscience.cdk.smsd.helper...
[javadoc] Loading source files for package org.openscience.cdk.smsd.interfaces...
[javadoc] Loading source files for package org.openscience.cdk.smsd.ring...
[javadoc] Loading source files for package org.openscience.cdk.smsd.tools...
[javadoc] Constructing Javadoc information...
[javadoc] /users/Asad/Software/GITROOT/cdksmsdgithub/build/src/smsd/org/openscience/cdk/normalize/SMSDNormalizer.java:33: cannot find symbol
[javadoc] symbol : class Atom
[javadoc] location: package org.openscience.cdk
[javadoc] import org.openscience.cdk.Atom;
[javadoc] ^
[javadoc] /users/Asad/Software/GITROOT/cdksmsdgithub/build/src/smsd/org/openscience/cdk/normalize/SMSDNormalizer.java:34: cannot find symbol
[javadoc] symbol : class Bond
[javadoc] location: package org.openscience.cdk
[javadoc] import org.openscience.cdk.Bond;
[javadoc] ^
[javadoc] /users/Asad/Software/GITROOT/cdksmsdgithub/build/src/smsd/org/openscience/cdk/normalize/SMSDNormalizer.java:36: cannot find symbol
[javadoc] symbol : class CDKConstants
[javadoc] location: package org.openscience.cdk
[javadoc] import org.openscience.cdk.CDKConstants;
[javadoc] ^
[javadoc] /users/Asad/Software/GITROOT/cdksmsdgithub/build/src/smsd/org/openscience/cdk/normalize/SMSDNormalizer.java:37: cannot find symbol
[javadoc] symbol : class DefaultChemObjectBuilder
[javadoc] location: package org.openscience.cdk
[javadoc] import org.openscience.cdk.DefaultChemObjectBuilder;
[javadoc] ^
[javadoc] /users/Asad/Software/GITROOT/cdksmsdgithub/build/src/smsd/org/openscience/cdk/normalize/SMSDNormalizer.java:38: cannot find symbol
[javadoc] symbol : class PseudoAtom
[javadoc] location: package org.openscience.cdk
[javadoc] import org.openscience.cdk.PseudoAtom;
[javadoc] ^
[javadoc] /users/Asad/Software/GITROOT/cdksmsdgithub/build/src/smsd/org/openscience/cdk/normalize/SMSDNormalizer.java:39: package org.openscience.cdk.annotations does not exist
[javadoc] import org.openscience.cdk.annotations.TestClass;
[javadoc] ^
[javadoc] /users/Asad/Software/GITROOT/cdksmsdgithub/build/src/smsd/org/openscience/cdk/normalize/SMSDNormalizer.java:40: package org.openscience.cdk.annotations does not exist
[javadoc] import org.openscience.cdk.annotations.TestMethod;
[javadoc] ^
[javadoc] /users/Asad/Software/GITROOT/cdksmsdgithub/build/src/smsd/org/openscience/cdk/normalize/SMSDNormalizer.java:41: package org.openscience.cdk.aromaticity does not exist
[javadoc] import org.openscience.cdk.aromaticity.CDKHueckelAromaticityDetector;
[javadoc] ^
[javadoc] /users/Asad/Software/GITROOT/cdksmsdgithub/build/src/smsd/org/openscience/cdk/normalize/SMSDNormalizer.java:42: package org.openscience.cdk.atomtype does not exist
[javadoc] import org.openscience.cdk.atomtype.CDKAtomTypeMatcher;
[javadoc] ^
[javadoc] /users/Asad/Software/GITROOT/cdksmsdgithub/build/src/smsd/org/openscience/cdk/normalize/SMSDNormalizer.java:43: package org.openscience.cdk.exception does not exist
[javadoc] import org.openscience.cdk.exception.CDKException;
[javadoc] ^
[javadoc] /users/Asad/Software/GITROOT/cdksmsdgithub/build/src/smsd/org/openscience/cdk/normalize/SMSDNormalizer.java:44: package org.openscience.cdk.interfaces does not exist
[javadoc] import org.openscience.cdk.interfaces.IAtom;
[javadoc] ^
[javadoc] /users/Asad/Software/GITROOT/cdksmsdgithub/build/src/smsd/org/openscience/cdk/normalize/SMSDNormalizer.java:45: package org.openscience.cdk.interfaces does not exist
[javadoc] import org.openscience.cdk.interfaces.IAtomContainer;
[javadoc] ^
[javadoc] /users/Asad/Software/GITROOT/cdksmsdgithub/build/src/smsd/org/openscience/cdk/normalize/SMSDNormalizer.java:46: package org.openscience.cdk.interfaces does not exist
[javadoc] import org.openscience.cdk.interfaces.IAtomParity;
[javadoc] ^
[javadoc] /users/Asad/Software/GITROOT/cdksmsdgithub/build/src/smsd/org/openscience/cdk/normalize/SMSDNormalizer.java:47: package org.openscience.cdk.interfaces does not exist
[javadoc] import org.openscience.cdk.interfaces.IAtomType;
[javadoc] ^
[javadoc] /users/Asad/Software/GITROOT/cdksmsdgithub/build/src/smsd/org/openscience/cdk/normalize/SMSDNormalizer.java:48: package org.openscience.cdk.interfaces does not exist
[javadoc] import org.openscience.cdk.interfaces.IBond;
[javadoc] ^
[javadoc] /users/Asad/Software/GITROOT/cdksmsdgithub/build/src/smsd/org/openscience/cdk/normalize/SMSDNormalizer.java:49: package org.openscience.cdk.interfaces does not exist
[javadoc] import org.openscience.cdk.interfaces.ILonePair;
[javadoc] ^
[javadoc] /users/Asad/Software/GITROOT/cdksmsdgithub/build/src/smsd/org/openscience/cdk/normalize/SMSDNormalizer.java:50: package org.openscience.cdk.interfaces does not exist
[javadoc] import org.openscience.cdk.interfaces.IMolecule;
[javadoc] ^
[javadoc] /users/Asad/Software/GITROOT/cdksmsdgithub/build/src/smsd/org/openscience/cdk/normalize/SMSDNormalizer.java:51: package org.openscience.cdk.interfaces does not exist
[javadoc] import org.openscience.cdk.interfaces.IRing;
[javadoc] ^
[javadoc] /users/Asad/Software/GITROOT/cdksmsdgithub/build/src/smsd/org/openscience/cdk/normalize/SMSDNormalizer.java:52: package org.openscience.cdk.interfaces does not exist
[javadoc] import org.openscience.cdk.interfaces.IRingSet;
[javadoc] ^
[javadoc] /users/Asad/Software/GITROOT/cdksmsdgithub/build/src/smsd/org/openscience/cdk/normalize/SMSDNormalizer.java:53: package org.openscience.cdk.interfaces does not exist
[javadoc] import org.openscience.cdk.interfaces.ISingleElectron;
[javadoc] ^
[javadoc] /users/Asad/Software/GITROOT/cdksmsdgithub/build/src/smsd/org/openscience/cdk/normalize/SMSDNormalizer.java:54: package org.openscience.cdk.interfaces.IBond does not exist
[javadoc] import org.openscience.cdk.interfaces.IBond.Order;
[javadoc] ^
[javadoc] /users/Asad/Software/GITROOT/cdksmsdgithub/build/src/smsd/org/openscience/cdk/normalize/SMSDNormalizer.java:55: package org.openscience.cdk.interfaces does not exist
[javadoc] import org.openscience.cdk.interfaces.IPseudoAtom;
[javadoc] ^
[javadoc] /users/Asad/Software/GITROOT/cdksmsdgithub/build/src/smsd/org/openscience/cdk/normalize/SMSDNormalizer.java:56: package org.openscience.cdk.ringsearch does not exist
[javadoc] import org.openscience.cdk.ringsearch.AllRingsFinder;
[javadoc] ^
[javadoc] /users/Asad/Software/GITROOT/cdksmsdgithub/build/src/smsd/org/openscience/cdk/normalize/SMSDNormalizer.java:57: package org.openscience.cdk.tools.manipulator does not exist
[javadoc] import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;
[javadoc] ^
[javadoc] /users/Asad/Software/GITROOT/cdksmsdgithub/build/src/smsd/org/openscience/cdk/normalize/SMSDNormalizer.java:58: package org.openscience.cdk.tools.manipulator does not exist
[javadoc] import org.openscience.cdk.tools.manipulator.AtomTypeManipulator;
[javadoc] ^
[javadoc] /users/Asad/Software/GITROOT/cdksmsdgithub/build/src/smsd/org/openscience/cdk/normalize/SMSDNormalizer.java:59: package org.openscience.cdk.tools.manipulator does not exist
[javadoc] import org.openscience.cdk.tools.manipulator.RingSetManipulator;
[javadoc] ^
[javadoc] /users/Asad/Software/GITROOT/cdksmsdgithub/build/src/smsd/org/openscience/cdk/normalize/SMSDNormalizer.java:69: cannot find symbol
[javadoc] symbol: class AtomContainerManipulator
[javadoc] public class SMSDNormalizer extends AtomContainerManipulator {
[javadoc] ^
[javadoc] /users/Asad/Software/GITROOT/cdksmsdgithub/build/src/smsd/org/openscience/cdk/normalize/SMSDNormalizer.java:68: cannot find symbol
[javadoc] symbol: class TestClass
[javadoc] @TestClass("org.openscience.cdk.normalize.SMSDNormalizerTest")
[javadoc] ^
[javadoc] /users/Asad/Software/GITROOT/cdksmsdgithub/build/src/smsd/org/openscience/cdk/normalize/SMSDNormalizer.java:77: cannot find symbol
[javadoc] symbol : class IAtomContainer
[javadoc] location: class org.openscience.cdk.normalize.SMSDNormalizer
[javadoc] public static IMolecule makeDeepCopy(IAtomContainer container) {
[javadoc] ^
[javadoc] /users/Asad/Software/GITROOT/cdksmsdgithub/build/src/smsd/org/openscience/cdk/normalize/SMSDNormalizer.java:77: cannot find symbol
[javadoc] symbol : class IMolecule
[javadoc] location: class org.openscience.cdk.normalize.SMSDNormalizer
[javadoc] public static IMolecule makeDeepCopy(IAtomContainer container) {
[javadoc] ^
[javadoc] /users/Asad/Software/GITROOT/cdksmsdgithub/build/src/smsd/org/openscience/cdk/normalize/SMSDNormalizer.java:125: cannot find symbol
[javadoc] symbol : class IAtomContainer
[javadoc] location: class org.openscience.cdk.normalize.SMSDNormalizer
[javadoc] public static void aromatizeMolecule(IAtomContainer mol) {
[javadoc] ^
[javadoc] /users/Asad/Software/GITROOT/cdksmsdgithub/build/src/smsd/org/openscience/cdk/normalize/SMSDNormalizer.java:191: cannot find symbol
[javadoc] symbol : class IAtomContainer
[javadoc] location: class org.openscience.cdk.normalize.SMSDNormalizer
[javadoc] public static int getExplicitHydrogenCount(IAtomContainer atomContainer, IAtom atom) {
[javadoc] ^
[javadoc] /users/Asad/Software/GITROOT/cdksmsdgithub/build/src/smsd/org/openscience/cdk/normalize/SMSDNormalizer.java:191: cannot find symbol
[javadoc] symbol : class IAtom
[javadoc] location: class org.openscience.cdk.normalize.SMSDNormalizer
[javadoc] public static int getExplicitHydrogenCount(IAtomContainer atomContainer, IAtom atom) {
[javadoc] ^
[javadoc] /users/Asad/Software/GITROOT/cdksmsdgithub/build/src/smsd/org/openscience/cdk/normalize/SMSDNormalizer.java:209: cannot find symbol
[javadoc] symbol : class IAtomContainer
[javadoc] location: class org.openscience.cdk.normalize.SMSDNormalizer
[javadoc] public static int getImplicitHydrogenCount(IAtomContainer atomContainer, IAtom atom) {
[javadoc] ^
[javadoc] /users/Asad/Software/GITROOT/cdksmsdgithub/build/src/smsd/org/openscience/cdk/normalize/SMSDNormalizer.java:209: cannot find symbol
[javadoc] symbol : class IAtom
[javadoc] location: class org.openscience.cdk.normalize.SMSDNormalizer
[javadoc] public static int getImplicitHydrogenCount(IAtomContainer atomContainer, IAtom atom) {
[javadoc] ^
[javadoc] /users/Asad/Software/GITROOT/cdksmsdgithub/build/src/smsd/org/openscience/cdk/normalize/SMSDNormalizer.java:220: cannot find symbol
[javadoc] symbol : class IAtomContainer
[javadoc] location: class org.openscience.cdk.normalize.SMSDNormalizer
[javadoc] public static int getHydrogenCount(IAtomContainer atomContainer, IAtom atom) {
[javadoc] ^
[javadoc] /users/Asad/Software/GITROOT/cdksmsdgithub/build/src/smsd/org/openscience/cdk/normalize/SMSDNormalizer.java:220: cannot find symbol
[javadoc] symbol : class IAtom
[javadoc] location: class org.openscience.cdk.normalize.SMSDNormalizer
[javadoc] public static int getHydrogenCount(IAtomContainer atomContainer, IAtom atom) {
[javadoc] ^
[javadoc] /users/Asad/Software/GITROOT/cdksmsdgithub/build/src/smsd/org/openscience/cdk/normalize/SMSDNormalizer.java:232: cannot find symbol
[javadoc] symbol : class IAtomContainer
[javadoc] location: class org.openscience.cdk.normalize.SMSDNormalizer
[javadoc] public static IAtomContainer removeHydrogensAndPreserveAtomID(IAtomContainer atomContainer) {
[javadoc] ^
[javadoc] /users/Asad/Software/GITROOT/cdksmsdgithub/build/src/smsd/org/openscience/cdk/normalize/SMSDNormalizer.java:232: cannot find symbol
[javadoc] symbol : class IAtomContainer
[javadoc] location: class org.openscience.cdk.normalize.SMSDNormalizer
[javadoc] public static IAtomContainer removeHydrogensAndPreserveAtomID(IAtomContainer atomContainer) {
[javadoc] ^
[javadoc] /users/Asad/Software/GITROOT/cdksmsdgithub/build/src/smsd/org/openscience/cdk/normalize/SMSDNormalizer.java:295: cannot find symbol
[javadoc] symbol : class IAtomContainer
[javadoc] location: class org.openscience.cdk.normalize.SMSDNormalizer
[javadoc] public static IAtomContainer convertExplicitToImplicitHydrogens(IAtomContainer atomContainer) {
[javadoc] ^
[javadoc] /users/Asad/Software/GITROOT/cdksmsdgithub/build/src/smsd/org/openscience/cdk/normalize/SMSDNormalizer.java:295: cannot find symbol
[javadoc] symbol : class IAtomContainer
[javadoc] location: class org.openscience.cdk.normalize.SMSDNormalizer
[javadoc] public static IAtomContainer convertExplicitToImplicitHydrogens(IAtomContainer atomContainer) {
[javadoc] ^
[javadoc] /users/Asad/Software/GITROOT/cdksmsdgithub/build/src/smsd/org/openscience/cdk/normalize/SMSDNormalizer.java:321: cannot find symbol
[javadoc] symbol : class IAtomContainer
[javadoc] location: class org.openscience.cdk.normalize.SMSDNormalizer
[javadoc] public static void percieveAtomTypesAndConfigureAtoms(IAtomContainer container) throws CDKException {
[javadoc] ^
[javadoc] /users/Asad/Software/GITROOT/cdksmsdgithub/build/src/smsd/org/openscience/cdk/normalize/SMSDNormalizer.java:321: cannot find symbol
[javadoc] symbol : class CDKException
[javadoc] location: class org.openscience.cdk.normalize.SMSDNormalizer
[javadoc] public static void percieveAtomTypesAndConfigureAtoms(IAtomContainer container) throws CDKException {
[javadoc] ^
[javadoc] /users/Asad/Software/GITROOT/cdksmsdgithub/build/src/smsd/org/openscience/cdk/normalize/SMSDNormalizer.java:335: cannot find symbol
[javadoc] symbol : class IAtomContainer
[javadoc] location: class org.openscience.cdk.normalize.SMSDNormalizer
[javadoc] private static IAtom[] copyAtoms(IAtomContainer container, IMolecule newAtomContainer) {
[javadoc] ^
[javadoc] /users/Asad/Software/GITROOT/cdksmsdgithub/build/src/smsd/org/openscience/cdk/normalize/SMSDNormalizer.java:335: cannot find symbol
[javadoc] symbol : class IMolecule
[javadoc] location: class org.openscience.cdk.normalize.SMSDNormalizer
[javadoc] private static IAtom[] copyAtoms(IAtomContainer container, IMolecule newAtomContainer) {
[javadoc] ^
[javadoc] /users/Asad/Software/GITROOT/cdksmsdgithub/build/src/smsd/org/openscience/cdk/normalize/SMSDNormalizer.java:335: cannot find symbol
[javadoc] symbol : class IAtom
[javadoc] location: class org.openscience.cdk.normalize.SMSDNormalizer
[javadoc] private static IAtom[] copyAtoms(IAtomContainer container, IMolecule newAtomContainer) {
[javadoc] ^
[javadoc] /users/Asad/Software/GITROOT/cdksmsdgithub/build/src/smsd/org/openscience/cdk/normalize/SMSDNormalizer.java:361: cannot find symbol
[javadoc] symbol : class IAtom
[javadoc] location: class org.openscience.cdk.normalize.SMSDNormalizer
[javadoc] private static void copyBonds(IAtom[] atoms, IAtomContainer container, IMolecule newAtomContainer) {
[javadoc] ^
[javadoc] /users/Asad/Software/GITROOT/cdksmsdgithub/build/src/smsd/org/openscience/cdk/normalize/SMSDNormalizer.java:361: cannot find symbol
[javadoc] symbol : class IAtomContainer
[javadoc] location: class org.openscience.cdk.normalize.SMSDNormalizer
[javadoc] private static void copyBonds(IAtom[] atoms, IAtomContainer container, IMolecule newAtomContainer) {
[javadoc] ^
[javadoc] /users/Asad/Software/GITROOT/cdksmsdgithub/build/src/smsd/org/openscience/cdk/normalize/SMSDNormalizer.java:361: cannot find symbol
[javadoc] symbol : class IMolecule
[javadoc] location: class org.openscience.cdk.normalize.SMSDNormalizer
[javadoc] private static void copyBonds(IAtom[] atoms, IAtomContainer container, IMolecule newAtomContainer) {
[javadoc] ^
[javadoc] /users/Asad/Software/GITROOT/cdksmsdgithub/build/src/smsd/org/openscience/cdk/normalize/SMSDNormalizer.java:396: cannot find symbol
[javadoc] symbol : class IMolecule
[javadoc] location: class org.openscience.cdk.normalize.SMSDNormalizer
[javadoc] IMolecule mol,
[javadoc] ^
[javadoc] /users/Asad/Software/GITROOT/cdksmsdgithub/build/src/smsd/org/openscience/cdk/normalize/SMSDNormalizer.java:397: cannot find symbol
[javadoc] symbol : class IAtomContainer
[javadoc] location: class org.openscience.cdk.normalize.SMSDNormalizer
[javadoc] IAtomContainer atomContainer,
[javadoc] ^
[javadoc] /users/Asad/Software/GITROOT/cdksmsdgithub/build/src/smsd/org/openscience/cdk/normalize/SMSDNormalizer.java:398: cannot find symbol
[javadoc] symbol : class IAtom
[javadoc] location: class org.openscience.cdk.normalize.SMSDNormalizer
[javadoc] List<IAtom> remove,
[javadoc] ^
[javadoc] /users/Asad/Software/GITROOT/cdksmsdgithub/build/src/smsd/org/openscience/cdk/normalize/SMSDNormalizer.java:399: cannot find symbol
[javadoc] symbol : class IAtom
[javadoc] location: class org.openscience.cdk.normalize.SMSDNormalizer
[javadoc] Map<IAtom, IAtom> map) {
[javadoc] ^
[javadoc] /users/Asad/Software/GITROOT/cdksmsdgithub/build/src/smsd/org/openscience/cdk/normalize/SMSDNormalizer.java:399: cannot find symbol
[javadoc] symbol : class IAtom
[javadoc] location: class org.openscience.cdk.normalize.SMSDNormalizer
[javadoc] Map<IAtom, IAtom> map) {
[javadoc] ^
[javadoc] /users/Asad/Software/GITROOT/cdksmsdgithub/build/src/smsd/org/openscience/cdk/normalize/SMSDNormalizer.java:395: cannot find symbol
[javadoc] symbol : class IMolecule
[javadoc] location: class org.openscience.cdk.normalize.SMSDNormalizer
[javadoc] private static IMolecule reComputeHydrogens(
[javadoc] ^
[javadoc] /users/Asad/Software/GITROOT/cdksmsdgithub/build/src/smsd/org/openscience/cdk/normalize/SMSDNormalizer.java:427: cannot find symbol
[javadoc] symbol : class IMolecule
[javadoc] location: class org.openscience.cdk.normalize.SMSDNormalizer
[javadoc] IMolecule mol,
[javadoc] ^
[javadoc] /users/Asad/Software/GITROOT/cdksmsdgithub/build/src/smsd/org/openscience/cdk/normalize/SMSDNormalizer.java:428: cannot find symbol
[javadoc] symbol : class IAtomContainer
[javadoc] location: class org.openscience.cdk.normalize.SMSDNormalizer
[javadoc] IAtomContainer atomContainer,
[javadoc] ^
[javadoc] /users/Asad/Software/GITROOT/cdksmsdgithub/build/src/smsd/org/openscience/cdk/normalize/SMSDNormalizer.java:429: cannot find symbol
[javadoc] symbol : class IAtom
[javadoc] location: class org.openscience.cdk.normalize.SMSDNormalizer
[javadoc] List<IAtom> remove,
[javadoc] ^
[javadoc] /users/Asad/Software/GITROOT/cdksmsdgithub/build/src/smsd/org/openscience/cdk/normalize/SMSDNormalizer.java:430: cannot find symbol
[javadoc] symbol : class IAtom
[javadoc] location: class org.openscience.cdk.normalize.SMSDNormalizer
[javadoc] Map<IAtom, IAtom> map) {
[javadoc] ^
[javadoc] /users/Asad/Software/GITROOT/cdksmsdgithub/build/src/smsd/org/openscience/cdk/normalize/SMSDNormalizer.java:430: cannot find symbol
[javadoc] symbol : class IAtom
[javadoc] location: class org.openscience.cdk.normalize.SMSDNormalizer
[javadoc] Map<IAtom, IAtom> map) {
[javadoc] ^
[javadoc] /users/Asad/Software/GITROOT/cdksmsdgithub/build/src/smsd/org/openscience/cdk/normalize/SMSDNormalizer.java:426: cannot find symbol
[javadoc] symbol : class IMolecule
[javadoc] location: class org.openscience.cdk.normalize.SMSDNormalizer
[javadoc] private static IMolecule cloneAndMarkNonHBonds(
[javadoc] ^
[javadoc] /users/Asad/Software/GITROOT/cdksmsdgithub/build/src/smsd/org/openscience/cdk/normalize/SMSDNormalizer.java:466: cannot find symbol
[javadoc] symbol : class IAtomContainer
[javadoc] location: class org.openscience.cdk.normalize.SMSDNormalizer
[javadoc] private static void set2D(IAtomContainer container, int index, IAtom[] atoms) {
[javadoc] ^
[javadoc] /users/Asad/Software/GITROOT/cdksmsdgithub/build/src/smsd/org/openscience/cdk/normalize/SMSDNormalizer.java:466: cannot find symbol
[javadoc] symbol : class IAtom
[javadoc] location: class org.openscience.cdk.normalize.SMSDNormalizer
[javadoc] private static void set2D(IAtomContainer container, int index, IAtom[] atoms) {
[javadoc] ^
[javadoc] /users/Asad/Software/GITROOT/cdksmsdgithub/build/src/smsd/org/openscience/cdk/normalize/SMSDNormalizer.java:472: cannot find symbol
[javadoc] symbol : class IAtomContainer
[javadoc] location: class org.openscience.cdk.normalize.SMSDNormalizer
[javadoc] private static void set3D(IAtomContainer container, int index, IAtom[] atoms) {
[javadoc] ^
[javadoc] /users/Asad/Software/GITROOT/cdksmsdgithub/build/src/smsd/org/openscience/cdk/normalize/SMSDNormalizer.java:472: cannot find symbol
[javadoc] symbol : class IAtom
[javadoc] location: class org.openscience.cdk.normalize.SMSDNormalizer
[javadoc] private static void set3D(IAtomContainer container, int index, IAtom[] atoms) {
[javadoc] ^
[javadoc] /users/Asad/Software/GITROOT/cdksmsdgithub/build/src/smsd/org/openscience/cdk/normalize/SMSDNormalizer.java:478: cannot find symbol
[javadoc] symbol : class IAtomContainer
[javadoc] location: class org.openscience.cdk.normalize.SMSDNormalizer
[javadoc] private static void setFractionalPoint3d(IAtomContainer container, int index, IAtom[] atoms) {
[javadoc] ^
[javadoc] /users/Asad/Software/GITROOT/cdksmsdgithub/build/src/smsd/org/openscience/cdk/normalize/SMSDNormalizer.java:478: cannot find symbol
[javadoc] symbol : class IAtom
[javadoc] location: class org.openscience.cdk.normalize.SMSDNormalizer
[javadoc] private static void setFractionalPoint3d(IAtomContainer container, int index, IAtom[] atoms) {
[javadoc] ^
[javadoc] /users/Asad/Software/GITROOT/cdksmsdgithub/build/src/smsd/org/openscience/cdk/normalize/SMSDNormalizer.java:484: cannot find symbol
[javadoc] symbol : class IAtomContainer
[javadoc] location: class org.openscience.cdk.normalize.SMSDNormalizer
[javadoc] private static void setID(IAtomContainer container, int index, IAtom[] atoms) {
[javadoc] ^
[javadoc] /users/Asad/Software/GITROOT/cdksmsdgithub/build/src/smsd/org/openscience/cdk/normalize/SMSDNormalizer.java:484: cannot find symbol
[javadoc] symbol : class IAtom
[javadoc] location: class org.openscience.cdk.normalize.SMSDNormalizer
[javadoc] private static void setID(IAtomContainer container, int index, IAtom[] atoms) {
[javadoc] ^
[javadoc] /users/Asad/Software/GITROOT/cdksmsdgithub/build/src/smsd/org/openscience/cdk/normalize/SMSDNormalizer.java:491: cannot find symbol
[javadoc] symbol : class IAtomContainer
[javadoc] location: class org.openscience.cdk.normalize.SMSDNormalizer
[javadoc] private static void setHydrogenCount(IAtomContainer container, int index, IAtom[] atoms) {
[javadoc] ^
[javadoc] /users/Asad/Software/GITROOT/cdksmsdgithub/build/src/smsd/org/openscience/cdk/normalize/SMSDNormalizer.java:491: cannot find symbol
[javadoc] symbol : class IAtom
[javadoc] location: class org.openscience.cdk.normalize.SMSDNormalizer
[javadoc] private static void setHydrogenCount(IAtomContainer container, int index, IAtom[] atoms) {
[javadoc] ^
[javadoc] /users/Asad/Software/GITROOT/cdksmsdgithub/build/src/smsd/org/openscience/cdk/normalize/SMSDNormalizer.java:497: cannot find symbol
[javadoc] symbol : class IAtomContainer
[javadoc] location: class org.openscience.cdk.normalize.SMSDNormalizer
[javadoc] private static void setCharge(IAtomContainer container, int index, IAtom[] atoms) {
[javadoc] ^
[javadoc] /users/Asad/Software/GITROOT/cdksmsdgithub/build/src/smsd/org/openscience/cdk/normalize/SMSDNormalizer.java:497: cannot find symbol
[javadoc] symbol : class IAtom
[javadoc] location: class org.openscience.cdk.normalize.SMSDNormalizer
[javadoc] private static void setCharge(IAtomContainer container, int index, IAtom[] atoms) {
[javadoc] ^
[javadoc] /users/Asad/Software/GITROOT/cdksmsdgithub/build/src/smsd/org/openscience/cdk/normalize/SMSDNormalizer.java:503: cannot find symbol
[javadoc] symbol : class IAtomContainer
[javadoc] location: class org.openscience.cdk.normalize.SMSDNormalizer
[javadoc] private static void setStereoParity(IAtomContainer container, int index, IAtom[] atoms) {
[javadoc] ^
[javadoc] /users/Asad/Software/GITROOT/cdksmsdgithub/build/src/smsd/org/openscience/cdk/normalize/SMSDNormalizer.java:503: cannot find symbol
[javadoc] symbol : class IAtom
[javadoc] location: class org.openscience.cdk.normalize.SMSDNormalizer
[javadoc] private static void setStereoParity(IAtomContainer container, int index, IAtom[] atoms) {
[javadoc] ^
[javadoc] /users/Asad/Software/GITROOT/cdksmsdgithub/build/src/smsd/org/openscience/cdk/normalize/SMSDNormalizer.java:509: cannot find symbol
[javadoc] symbol : class IAtomContainer
[javadoc] location: class org.openscience.cdk.normalize.SMSDNormalizer
[javadoc] private static void setAtomParity(IAtomContainer container, int index, IAtomContainer newAtomContainer) {
[javadoc] ^
[javadoc] /users/Asad/Software/GITROOT/cdksmsdgithub/build/src/smsd/org/openscience/cdk/normalize/SMSDNormalizer.java:509: cannot find symbol
[javadoc] symbol : class IAtomContainer
[javadoc] location: class org.openscience.cdk.normalize.SMSDNormalizer
[javadoc] private static void setAtomParity(IAtomContainer container, int index, IAtomContainer newAtomContainer) {
[javadoc] ^
[javadoc] /users/Asad/Software/GITROOT/cdksmsdgithub/build/src/smsd/org/openscience/cdk/smsd/AtomAtomMapping.java:34: package org.openscience.cdk.interfaces does not exist
[javadoc] import org.openscience.cdk.interfaces.IAtom;
[javadoc] ^
[javadoc] /users/Asad/Software/GITROOT/cdksmsdgithub/build/src/smsd/org/openscience/cdk/smsd/AtomAtomMapping.java:35: package org.openscience.cdk.interfaces does not exist
[javadoc] import org.openscience.cdk.interfaces.IAtomContainer;
[javadoc] ^
[javadoc] /users/Asad/Software/GITROOT/cdksmsdgithub/build/src/smsd/org/openscience/cdk/smsd/AtomAtomMapping.java:46: cannot find symbol
[javadoc] symbol : class IAtomContainer
[javadoc] location: class org.openscience.cdk.smsd.AtomAtomMapping
[javadoc] private final IAtomContainer query;
[javadoc] ^
[javadoc] /users/Asad/Software/GITROOT/cdksmsdgithub/build/src/smsd/org/openscience/cdk/smsd/AtomAtomMapping.java:47: cannot find symbol
[javadoc] symbol : class IAtomContainer
[javadoc] location: class org.openscience.cdk.smsd.AtomAtomMapping
[javadoc] private final IAtomContainer target;
[javadoc] ^
[javadoc] /users/Asad/Software/GITROOT/cdksmsdgithub/build/src/smsd/org/openscience/cdk/smsd/AtomAtomMapping.java:48: cannot find symbol
[javadoc] symbol : class IAtom
[javadoc] location: class org.openscience.cdk.smsd.AtomAtomMapping
[javadoc] private final Map<IAtom, IAtom> mapping;
[javadoc] ^
[javadoc] /users/Asad/Software/GITROOT/cdksmsdgithub/build/src/smsd/org/openscience/cdk/smsd/AtomAtomMapping.java:48: cannot find symbol
[javadoc] symbol : class IAtom
[javadoc] location: class org.openscience.cdk.smsd.AtomAtomMapping
[javadoc] private final Map<IAtom, IAtom> mapping;
[javadoc] ^
[javadoc] /users/Asad/Software/GITROOT/cdksmsdgithub/build/src/smsd/org/openscience/cdk/smsd/AtomAtomMapping.java:55: cannot find symbol
[javadoc] symbol : class IAtomContainer
[javadoc] location: class org.openscience.cdk.smsd.AtomAtomMapping
[javadoc] public AtomAtomMapping(IAtomContainer query, IAtomContainer target) {
[javadoc] ^
[javadoc] /users/Asad/Software/GITROOT/cdksmsdgithub/build/src/smsd/org/openscience/cdk/smsd/AtomAtomMapping.java:55: cannot find symbol
[javadoc] symbol : class IAtomContainer
[javadoc] location: class org.openscience.cdk.smsd.AtomAtomMapping
[javadoc] public AtomAtomMapping(IAtomContainer query, IAtomContainer target) {
[javadoc] ^
[javadoc] /users/Asad/Software/GITROOT/cdksmsdgithub/build/src/smsd/org/openscience/cdk/smsd/AtomAtomMapping.java:66: cannot find symbol
[javadoc] symbol : class IAtom
[javadoc] location: class org.openscience.cdk.smsd.AtomAtomMapping
[javadoc] public synchronized void put(IAtom atom1, IAtom atom2) {
[javadoc] ^
[javadoc] /users/Asad/Software/GITROOT/cdksmsdgithub/build/src/smsd/org/openscience/cdk/smsd/AtomAtomMapping.java:66: cannot find symbol
[javadoc] symbol : class IAtom
[javadoc] location: class org.openscience.cdk.smsd.AtomAtomMapping
[javadoc] public synchronized void put(IAtom atom1, IAtom atom2) {
[javadoc] ^
[javadoc] /users/Asad/Software/GITROOT/cdksmsdgithub/build/src/smsd/org/openscience/cdk/smsd/AtomAtomMapping.java:110: cannot find symbol
[javadoc] symbol : class IAtom
[javadoc] location: class org.openscience.cdk.smsd.AtomAtomMapping
[javadoc] public synchronized Map<IAtom, IAtom> getMappings() {
[javadoc] ^
[javadoc] /users/Asad/Software/GITROOT/cdksmsdgithub/build/src/smsd/org/openscience/cdk/smsd/AtomAtomMapping.java:110: cannot find symbol
[javadoc] symbol : class IAtom
[javadoc] location: class org.openscience.cdk.smsd.AtomAtomMapping
[javadoc] public synchronized Map<IAtom, IAtom> getMappings() {
[javadoc] ^
[javadoc] /users/Asad/Software/GITROOT/cdksmsdgithub/build/src/smsd/org/openscience/cdk/smsd/AtomAtomMapping.java:120: cannot find symbol
[javadoc] symbol : class IAtom
[javadoc] location: class org.openscience.cdk.smsd.AtomAtomMapping
[javadoc] public synchronized int getQueryIndex(IAtom atom) {
[javadoc] ^
[javadoc] /users/Asad/Software/GITROOT/cdksmsdgithub/build/src/smsd/org/openscience/cdk/smsd/AtomAtomMapping.java:130: cannot find symbol
[javadoc] symbol : class IAtom
[javadoc] location: class org.openscience.cdk.smsd.AtomAtomMapping
[javadoc] public synchronized int getTargetIndex(IAtom atom) {
[javadoc] ^
[javadoc] /users/Asad/Software/GITROOT/cdksmsdgithub/build/src/smsd/org/openscience/cdk/smsd/AtomAtomMapping.java:137: cannot find symbol
[javadoc] symbol : class IAtomContainer
[javadoc] location: class org.openscience.cdk.smsd.AtomAtomMapping
[javadoc] public synchronized IAtomContainer getQuery() {
[javadoc] ^
[javadoc] /users/Asad/Software/GITROOT/cdksmsdgithub/build/src/smsd/org/openscience/cdk/smsd/AtomAtomMapping.java:144: cannot find symbol
[javadoc] symbol : class IAtomContainer
[javadoc] location: class org.openscience.cdk.smsd.AtomAtomMapping
[javadoc] public synchronized IAtomContainer getTarget() {
[javadoc] ^
[javadoc] /users/Asad/Software/GITROOT/cdksmsdgithub/build/src/smsd/org/openscience/cdk/smsd/BaseMapping.java:31: package org.openscience.cdk.annotations does not exist
[javadoc] import org.openscience.cdk.annotations.TestMethod;
[javadoc] ^
[javadoc] /users/Asad/Software/GITROOT/cdksmsdgithub/build/src/smsd/org/openscience/cdk/smsd/BaseMapping.java:32: package org.openscience.cdk.exception does not exist
[javadoc] import org.openscience.cdk.exception.CDKException;
[javadoc] ^
[javadoc] /users/Asad/Software/GITROOT/cdksmsdgithub/build/src/smsd/org/openscience/cdk/smsd/BaseMapping.java:33: package org.openscience.cdk.interfaces does not exist
[javadoc] import org.openscience.cdk.interfaces.IAtom;
[javadoc] ^
[javadoc] /users/Asad/Software/GITROOT/cdksmsdgithub/build/src/smsd/org/openscience/cdk/smsd/BaseMapping.java:34: package org.openscience.cdk.interfaces does not exist
[javadoc] import org.openscience.cdk.interfaces.IAtomContainer;
[javadoc] ^
[javadoc] /users/Asad/Software/GITROOT/cdksmsdgithub/build/src/smsd/org/openscience/cdk/smsd/BaseMapping.java:35: package org.openscience.cdk.interfaces does not exist
[javadoc] import org.openscience.cdk.interfaces.IBond;
[javadoc] ^
[javadoc] /users/Asad/Software/GITROOT/cdksmsdgithub/build/src/smsd/org/openscience/cdk/smsd/BaseMapping.java:36: package org.openscience.cdk.isomorphism.matchers does not exist
[javadoc] import org.openscience.cdk.isomorphism.matchers.IQueryAtomContainer;
[javadoc] ^
[javadoc] /users/Asad/Software/GITROOT/cdksmsdgithub/build/src/smsd/org/openscience/cdk/smsd/BaseMapping.java:37: package org.openscience.cdk.tools does not exist
[javadoc] import org.openscience.cdk.tools.ILoggingTool;
[javadoc] ^
[javadoc] Could not load class 'net.sf.cdk.tools.checkdoctest.MissingGithashTagletTest': net.sf.cdk.tools.checkdoctest.MissingGithashTagletTest
[javadoc] Could not load class 'net.sf.cdk.tools.checkdoctest.MissingModuleTagletTest': net.sf.cdk.tools.checkdoctest.MissingModuleTagletTest
[javadoc] Could not load class 'net.sf.cdk.tools.checkdoctest.IncorrectBugNumberTagletTest': net.sf.cdk.tools.checkdoctest.IncorrectBugNumberTagletTest
[javadoc] /users/Asad/Software/GITROOT/cdksmsdgithub/build/src/smsd/org/openscience/cdk/smsd/AtomAtomMapping.java:120: warning - @return tag has no arguments.
[javadoc] /users/Asad/Software/GITROOT/cdksmsdgithub/build/src/smsd/org/openscience/cdk/smsd/AtomAtomMapping.java:130: warning - @return tag has no arguments.
[javadoc] /users/Asad/Software/GITROOT/cdksmsdgithub/build/src/smsd/org/openscience/cdk/smsd/algorithm/matchers/DefaultVFAtomMatcher.java:159: warning - @return tag has no arguments.
[javadoc] /users/Asad/Software/GITROOT/cdksmsdgithub/build/src/smsd/org/openscience/cdk/smsd/algorithm/matchers/DefaultRGraphAtomMatcher.java:124: warning - @return tag has no arguments.
[javadoc] /users/Asad/Software/GITROOT/cdksmsdgithub/build/src/smsd/org/openscience/cdk/smsd/algorithm/matchers/DefaultMCSPlusAtomMatcher.java:181: warning - @return tag has no arguments.
[javadoc] /users/Asad/Software/GITROOT/cdksmsdgithub/build/src/smsd/org/openscience/cdk/smsd/algorithm/mcsplus/ExactMapping.java:78: warning - @return tag has no arguments.
[javadoc] /users/Asad/Software/GITROOT/cdksmsdgithub/build/src/smsd/org/openscience/cdk/smsd/algorithm/mcsplus/ExactMapping.java:98: warning - @return tag has no arguments.
[javadoc] /users/Asad/Software/GITROOT/cdksmsdgithub/build/src/smsd/org/openscience/cdk/smsd/algorithm/mcsplus/BKKCKCF.java:341: warning - @return tag has no arguments.
[javadoc] /users/Asad/Software/GITROOT/cdksmsdgithub/build/src/smsd/org/openscience/cdk/smsd/algorithm/vflib/substructure/VF2.java:86: warning - @return tag has no arguments.
[javadoc] /users/Asad/Software/GITROOT/cdksmsdgithub/build/src/smsd/org/openscience/cdk/smsd/algorithm/vflib/substructure/VF2.java:113: warning - @return tag has no arguments.
[javadoc] /users/Asad/Software/GITROOT/cdksmsdgithub/build/src/smsd/org/openscience/cdk/smsd/algorithm/vflib/substructure/VF2.java:132: warning - @return tag has no arguments.
[javadoc] /users/Asad/Software/GITROOT/cdksmsdgithub/build/src/smsd/org/openscience/cdk/smsd/filters/StereoFilter.java:270: warning - @return tag has no arguments.
[javadoc] /users/Asad/Software/GITROOT/cdksmsdgithub/build/src/smsd/org/openscience/cdk/smsd/filters/StereoFilter.java:270: warning - @return tag has no arguments.
[javadoc] /users/Asad/Software/GITROOT/cdksmsdgithub/build/src/smsd/org/openscience/cdk/smsd/filters/StereoFilter.java:305: warning - @return tag has no arguments.
[javadoc] /users/Asad/Software/GITROOT/cdksmsdgithub/build/src/smsd/org/openscience/cdk/smsd/filters/IChemicalFilter.java:51: warning - @return tag has no arguments.
[javadoc] 114 warnings
test-module:
[echo] Running PMD checks for CDK's smsd module.
[mkdir] Created dir: /users/Asad/Software/GITROOT/cdksmsdgithub/reports/pmd
test-module:
[echo] Checking for unused code in CDK's smsd module.
[mkdir] Created dir: /users/Asad/Software/GITROOT/cdksmsdgithub/reports/pmd-unused
test-module:
[echo] Checking for migrating code updates in CDK's smsd module.
[mkdir] Created dir: /users/Asad/Software/GITROOT/cdksmsdgithub/reports/pmd-migrating
BUILD SUCCESSFUL
Total time: 32 seconds
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