Pulling biosimulations fatal: repository 'http://git.bioshell.pl/biosimulations/' not found commit fca6c0ab250f19592fa7ec4e6fa4c4093b0d48c1 (HEAD, origin/master, origin/HEAD, master) Author: Dominik Gront Date: Fri May 16 14:10:55 2014 +0200 newer version of pdb2cabs writes cabs-bb files tests/scientific/jcabs/pdb2cabs.py | 47 +++++++++++++++++++++++++++++++++++++- 1 file changed, 46 insertions(+), 1 deletion(-) sh: 1: source: not found Buildfile: build.xml clean: [delete] Deleting directory /home/git/src.git/biosimulations/classes setup-mac: setup-linux: [echo] Building for Linux jar: [mkdir] Created dir: /home/git/src.git/biosimulations/classes [javac] Compiling 277 source files to /home/git/src.git/biosimulations/classes [javac] warning: [options] bootstrap class path not set in conjunction with -source 1.6 [javac] /home/git/src.git/biosimulations/jbcl/external/rosetta/fragments/RosettaFragment.java:9: error: package jbcl.calc.structural.properties does not exist [javac] import jbcl.calc.structural.properties.TorsionBin; [javac] ^ [javac] /home/git/src.git/biosimulations/jbcl/external/rosetta/fragments/RosettaFragment.java:10: error: package jbcl.data.dict does not exist [javac] import jbcl.data.dict.Monomer; [javac] ^ [javac] /home/git/src.git/biosimulations/jbcl/external/rosetta/fragments/RosettaFragment.java:11: error: package jbcl.data.dict does not exist [javac] import jbcl.data.dict.MonomersFactory; [javac] ^ [javac] /home/git/src.git/biosimulations/jbcl/external/rosetta/fragments/RosettaFragment.java:12: error: package jbcl.data.types does not exist [javac] import jbcl.data.types.Sequence; [javac] ^ [javac] /home/git/src.git/biosimulations/jbcl/external/rosetta/fragments/RosettaFragment.java:13: error: cannot find symbol [javac] import jbcl.util.GZipAwareBufferedReader; [javac] ^ [javac] symbol: class GZipAwareBufferedReader [javac] location: package jbcl.util [javac] /home/git/src.git/biosimulations/jbcl/external/rosetta/fragments/RosettaFragment.java:14: error: package jbcl.util.exceptions does not exist [javac] import jbcl.util.exceptions.NoDataAcquiredException; [javac] ^ [javac] /home/git/src.git/biosimulations/jbcl/external/rosetta/fragments/RosettaFragment.java:34: error: cannot find symbol [javac] Monomer[] seq, final String ss, final double[][] phiPsisOmega) { [javac] ^ [javac] symbol: class Monomer [javac] location: class RosettaFragment [javac] /home/git/src.git/biosimulations/jbcl/external/rosetta/fragments/RosettaFragment.java:60: error: cannot find symbol [javac] public Monomer getResidueType(final int pos) { [javac] ^ [javac] symbol: class Monomer [javac] location: class RosettaFragment [javac] /home/git/src.git/biosimulations/jbcl/external/rosetta/fragments/RosettaFragment.java:288: error: cannot find symbol [javac] private final Monomer[] sequence; [javac] ^ [javac] symbol: class Monomer [javac] location: class RosettaFragment [javac] /home/git/src.git/biosimulations/jbcl/external/rosetta/outfile/FrameLinesIterator.java:3: error: cannot find symbol [javac] import static jbcl.util.StringUtils.whiteSpaceSplitter; [javac] ^ [javac] symbol: class StringUtils [javac] location: package jbcl.util [javac] /home/git/src.git/biosimulations/jbcl/external/rosetta/outfile/FrameLinesIterator.java:3: error: static import only from classes and interfaces [javac] import static jbcl.util.StringUtils.whiteSpaceSplitter; [javac] ^ [javac] /home/git/src.git/biosimulations/jbcl/external/rosetta/outfile/FrameLinesIterator.java:13: error: cannot find symbol [javac] import jbcl.util.GZipAwareBufferedReader; [javac] ^ [javac] symbol: class GZipAwareBufferedReader [javac] location: package jbcl.util [javac] /home/git/src.git/biosimulations/jbcl/external/rosetta/outfile/OutFileDataFrame.java:3: error: cannot find symbol [javac] import static jbcl.util.StringUtils.whiteSpaceSplitter; [javac] ^ [javac] symbol: class StringUtils [javac] location: package jbcl.util [javac] /home/git/src.git/biosimulations/jbcl/external/rosetta/outfile/OutFileDataFrame.java:3: error: static import only from classes and interfaces [javac] import static jbcl.util.StringUtils.whiteSpaceSplitter; [javac] ^ [javac] /home/git/src.git/biosimulations/jbcl/external/rosetta/outfile/OutFileDataFrame.java:9: error: cannot find symbol [javac] import jbcl.util.StringUtils; [javac] ^ [javac] symbol: class StringUtils [javac] location: package jbcl.util [javac] /home/git/src.git/biosimulations/jbcl/external/rosetta/outfile/OutFileDataFrame.java:10: error: package jbcl.util.exceptions does not exist [javac] import jbcl.util.exceptions.NoDataAcquiredException; [javac] ^ [javac] /home/git/src.git/biosimulations/jbcl/external/rosetta/outfile/OutFileIO.java:9: error: package jbcl.data.types does not exist [javac] import jbcl.data.types.Vector3D; [javac] ^ [javac] /home/git/src.git/biosimulations/jbcl/external/rosetta/outfile/ScoreFileIO.java:7: error: package jbcl.data.basic does not exist [javac] import jbcl.data.basic.DataTable; [javac] ^ [javac] /home/git/src.git/biosimulations/jbcl/external/rosetta/outfile/ScoreFileIO.java:8: error: cannot find symbol [javac] import jbcl.util.GZipAwareBufferedReader; [javac] ^ [javac] symbol: class GZipAwareBufferedReader [javac] location: package jbcl.util [javac] /home/git/src.git/biosimulations/jbcl/external/rosetta/outfile/ScoreFileIO.java:22: error: cannot find symbol [javac] public static final DataTable read(BufferedReader in) throws IOException { [javac] ^ [javac] symbol: class DataTable [javac] location: class ScoreFileIO [javac] /home/git/src.git/biosimulations/jbcl/external/rosetta/outfile/ScoreFileIO.java:44: error: cannot find symbol [javac] public static final DataTable read(String fileName) throws IOException { [javac] ^ [javac] symbol: class DataTable [javac] location: class ScoreFileIO [javac] /home/git/src.git/biosimulations/jbcl/simulations/bbq2/LambdaLibrary.java:9: error: package jbcl.calc.structural.properties does not exist [javac] import jbcl.calc.structural.properties.PlanarAngle; [javac] ^ [javac] /home/git/src.git/biosimulations/jbcl/simulations/bbq2/LambdaLibrary.java:10: error: package jbcl.calc.structural.properties does not exist [javac] import jbcl.calc.structural.properties.TorsionalAngle; [javac] ^ [javac] /home/git/src.git/biosimulations/jbcl/simulations/bbq2/LambdaLibrary.java:11: error: package jbcl.data.types does not exist [javac] import jbcl.data.types.Vector3D; [javac] ^ [javac] /home/git/src.git/biosimulations/jbcl/simulations/bbq2/LambdaLibrary.java:12: error: cannot find symbol [javac] import jbcl.util.StringUtils; [javac] ^ [javac] symbol: class StringUtils [javac] location: package jbcl.util [javac] /home/git/src.git/biosimulations/jbcl/simulations/bbq2/LambdaLibrary.java:18: error: cannot find symbol [javac] public static final double[] lambda(final Vector3D prevCA, final Vector3D theCA, final Vector3D nextCA, [javac] ^ [javac] symbol: class Vector3D [javac] location: class LambdaLibrary [javac] /home/git/src.git/biosimulations/jbcl/simulations/bbq2/LambdaLibrary.java:18: error: cannot find symbol [javac] public static final double[] lambda(final Vector3D prevCA, final Vector3D theCA, final Vector3D nextCA, [javac] ^ [javac] symbol: class Vector3D [javac] location: class LambdaLibrary [javac] /home/git/src.git/biosimulations/jbcl/simulations/bbq2/LambdaLibrary.java:18: error: cannot find symbol [javac] public static final double[] lambda(final Vector3D prevCA, final Vector3D theCA, final Vector3D nextCA, [javac] ^ [javac] symbol: class Vector3D [javac] location: class LambdaLibrary [javac] /home/git/src.git/biosimulations/jbcl/simulations/bbq2/LambdaLibrary.java:19: error: cannot find symbol [javac] final Vector3D nnextCA) { [javac] ^ [javac] symbol: class Vector3D [javac] location: class LambdaLibrary [javac] /home/git/src.git/biosimulations/jbcl/simulations/bbq2/LambdaLibrary.java:43: error: cannot find symbol [javac] public static final int index(final Vector3D prevCA, final Vector3D theCA, final Vector3D nextCA, [javac] ^ [javac] symbol: class Vector3D [javac] location: class LambdaLibrary [javac] /home/git/src.git/biosimulations/jbcl/simulations/bbq2/LambdaLibrary.java:43: error: cannot find symbol [javac] public static final int index(final Vector3D prevCA, final Vector3D theCA, final Vector3D nextCA, [javac] ^ [javac] symbol: class Vector3D [javac] location: class LambdaLibrary [javac] /home/git/src.git/biosimulations/jbcl/simulations/bbq2/LambdaLibrary.java:43: error: cannot find symbol [javac] public static final int index(final Vector3D prevCA, final Vector3D theCA, final Vector3D nextCA, [javac] ^ [javac] symbol: class Vector3D [javac] location: class LambdaLibrary [javac] /home/git/src.git/biosimulations/jbcl/simulations/bbq2/LambdaLibrary.java:44: error: cannot find symbol [javac] final Vector3D nnextCA) { [javac] ^ [javac] symbol: class Vector3D [javac] location: class LambdaLibrary [javac] /home/git/src.git/biosimulations/jbcl/simulations/bbq2/PhiPsiEntry.java:5: error: package jbcl.calc.structural.properties does not exist [javac] import jbcl.calc.structural.properties.PhiAngle; [javac] ^ [javac] /home/git/src.git/biosimulations/jbcl/simulations/bbq2/PhiPsiEntry.java:6: error: package jbcl.calc.structural.properties does not exist [javac] import jbcl.calc.structural.properties.PsiAngle; [javac] ^ [javac] /home/git/src.git/biosimulations/jbcl/simulations/bbq2/PhiPsiEntry.java:7: error: package jbcl.data.types does not exist [javac] import jbcl.data.types.AAResidue; [javac] ^ [javac] /home/git/src.git/biosimulations/jbcl/simulations/bbq2/PhiPsiEntry.java:30: error: cannot find symbol [javac] public static PhiPsiEntry create(final AAResidue prevResidue, final AAResidue theResidue, AAResidue nextResidue) { [javac] ^ [javac] symbol: class AAResidue [javac] location: class PhiPsiEntry [javac] /home/git/src.git/biosimulations/jbcl/simulations/bbq2/PhiPsiEntry.java:30: error: cannot find symbol [javac] public static PhiPsiEntry create(final AAResidue prevResidue, final AAResidue theResidue, AAResidue nextResidue) { [javac] ^ [javac] symbol: class AAResidue [javac] location: class PhiPsiEntry [javac] /home/git/src.git/biosimulations/jbcl/simulations/bbq2/PhiPsiEntry.java:30: error: cannot find symbol [javac] public static PhiPsiEntry create(final AAResidue prevResidue, final AAResidue theResidue, AAResidue nextResidue) { [javac] ^ [javac] symbol: class AAResidue [javac] location: class PhiPsiEntry [javac] /home/git/src.git/biosimulations/jbcl/simulations/bbq2/PhiPsiLibrary.java:3: error: cannot find symbol [javac] import static jbcl.util.StringUtils.whiteSpaceSplitter; [javac] ^ [javac] symbol: class StringUtils [javac] location: package jbcl.util [javac] /home/git/src.git/biosimulations/jbcl/simulations/bbq2/PhiPsiLibrary.java:3: error: static import only from classes and interfaces [javac] import static jbcl.util.StringUtils.whiteSpaceSplitter; [javac] ^ [javac] /home/git/src.git/biosimulations/jbcl/simulations/bbq2/PhiPsiLibrary.java:12: error: package jbcl.calc.bbq does not exist [javac] import jbcl.calc.bbq.DistanceIndex; [javac] ^ [javac] /home/git/src.git/biosimulations/jbcl/simulations/bbq2/PhiPsiLibrary.java:13: error: package jbcl.calc.bbq does not exist [javac] import jbcl.calc.bbq.QuadrilateralIndex; [javac] ^ [javac] /home/git/src.git/biosimulations/jbcl/simulations/bbq2/PhiPsiLibrary.java:14: error: package jbcl.calc.bbq does not exist [javac] import jbcl.calc.bbq.QuadrilateralsLibrary; [javac] ^ [javac] /home/git/src.git/biosimulations/jbcl/simulations/bbq2/PhiPsiLibrary.java:15: error: package jbcl.data.formats does not exist [javac] import jbcl.data.formats.PDB; [javac] ^ [javac] /home/git/src.git/biosimulations/jbcl/simulations/bbq2/PhiPsiLibrary.java:16: error: package jbcl.data.types does not exist [javac] import jbcl.data.types.AAResidue; [javac] ^ [javac] /home/git/src.git/biosimulations/jbcl/simulations/bbq2/PhiPsiLibrary.java:17: error: package jbcl.data.types does not exist [javac] import jbcl.data.types.ProteinChain; [javac] ^ [javac] /home/git/src.git/biosimulations/jbcl/simulations/bbq2/PhiPsiLibrary.java:18: error: package jbcl.data.types does not exist [javac] import jbcl.data.types.Structure; [javac] ^ [javac] /home/git/src.git/biosimulations/jbcl/simulations/bbq2/PhiPsiLibrary.java:27: error: cannot find symbol [javac] public class PhiPsiLibrary extends QuadrilateralsLibrary { [javac] ^ [javac] symbol: class QuadrilateralsLibrary [javac] /home/git/src.git/biosimulations/jbcl/simulations/bbq2/PhiPsiLibrary.java:34: error: cannot find symbol [javac] public PhiPsiLibrary(QuadrilateralIndex indexingMethod) { [javac] ^ [javac] symbol: class QuadrilateralIndex [javac] location: class PhiPsiLibrary [javac] /home/git/src.git/biosimulations/jbcl/simulations/bbq2/PhiPsiLibrary.java:48: error: cannot find symbol [javac] public static PhiPsiLibrary createLibrary(QuadrilateralIndex indexingMethod, String[] trainingSet) { [javac] ^ [javac] symbol: class QuadrilateralIndex [javac] location: class PhiPsiLibrary [javac] /home/git/src.git/biosimulations/jbcl/simulations/bbq2/PhiPsiLibrary.java:67: error: cannot find symbol [javac] public static HashMap> createObservations(QuadrilateralIndex indexingMethod, [javac] ^ [javac] symbol: class QuadrilateralIndex [javac] location: class PhiPsiLibrary [javac] /home/git/src.git/biosimulations/jbcl/simulations/bbq2/PhiPsiLibrary.java:156: error: cannot find symbol [javac] protected QuadrilateralIndex indexType; ///< Object used to index the BBQ grid [javac] ^ [javac] symbol: class QuadrilateralIndex [javac] location: class PhiPsiLibrary [javac] /home/git/src.git/biosimulations/jbcl/simulations/cartesian/BoundaryConditions.java:3: error: package jbcl.data.basic does not exist [javac] import jbcl.data.basic.IntList; [javac] ^ [javac] /home/git/src.git/biosimulations/jbcl/simulations/cartesian/BoundaryConditions.java:54: error: cannot find symbol [javac] public abstract void apply(IntList whichParticles); [javac] ^ [javac] symbol: class IntList [javac] location: class BoundaryConditions [javac] /home/git/src.git/biosimulations/jbcl/simulations/cartesian/CubicPeriodicBoundaryConditions.java:3: error: package jbcl.data.basic does not exist [javac] import jbcl.data.basic.IntList; [javac] ^ [javac] /home/git/src.git/biosimulations/jbcl/simulations/cartesian/CubicPeriodicBoundaryConditions.java:153: error: cannot find symbol [javac] public void apply(IntList whichParticle) { [javac] ^ [javac] symbol: class IntList [javac] location: class CubicPeriodicBoundaryConditions [javac] /home/git/src.git/biosimulations/jbcl/simulations/cartesian/CubicReflectiveConditions.java:3: error: package jbcl.data.basic does not exist [javac] import jbcl.data.basic.IntList; [javac] ^ [javac] /home/git/src.git/biosimulations/jbcl/simulations/cartesian/CubicReflectiveConditions.java:84: error: cannot find symbol [javac] public void apply(IntList whichParticle) { [javac] ^ [javac] symbol: class IntList [javac] location: class CubicReflectiveConditions [javac] /home/git/src.git/biosimulations/jbcl/simulations/cartesian/MappedCartesianCoordinates.java:5: error: package jbcl.data.types does not exist [javac] import jbcl.data.types.Sequence; [javac] ^ [javac] /home/git/src.git/biosimulations/jbcl/simulations/core/SequenceMapping.java:3: error: package jbcl.data.basic does not exist [javac] import jbcl.data.basic.ThreeTuple; [javac] ^ [javac] /home/git/src.git/biosimulations/jbcl/simulations/core/SequenceMapping.java:4: error: package jbcl.data.dict does not exist [javac] import jbcl.data.dict.AtomType; [javac] ^ [javac] /home/git/src.git/biosimulations/jbcl/simulations/core/SequenceMapping.java:5: error: package jbcl.data.dict does not exist [javac] import jbcl.data.dict.Monomer; [javac] ^ [javac] /home/git/src.git/biosimulations/jbcl/simulations/cartesian/MappedCartesianCoordinates.java:53: error: cannot find symbol [javac] public abstract Sequence getChainSequence(final int whichChain); [javac] ^ [javac] symbol: class Sequence [javac] location: class MappedCartesianCoordinates [javac] /home/git/src.git/biosimulations/jbcl/simulations/core/SequenceMapping.java:31: error: cannot find symbol [javac] public AtomType getMappedAtomType(final int atomIndex); [javac] ^ [javac] symbol: class AtomType [javac] location: interface SequenceMapping [javac] /home/git/src.git/biosimulations/jbcl/simulations/core/SequenceMapping.java:37: error: cannot find symbol [javac] public AtomType[] getMappedAtomTypes(); [javac] ^ [javac] symbol: class AtomType [javac] location: interface SequenceMapping [javac] /home/git/src.git/biosimulations/jbcl/simulations/core/SequenceMapping.java:43: error: cannot find symbol [javac] public int getMappedAtomIndex(final ThreeTuple atomLocator); [javac] ^ [javac] symbol: class ThreeTuple [javac] location: interface SequenceMapping [javac] /home/git/src.git/biosimulations/jbcl/simulations/core/SequenceMapping.java:88: error: cannot find symbol [javac] public Monomer getMappedResidueType(final int atomIndex); [javac] ^ [javac] symbol: class Monomer [javac] location: interface SequenceMapping [javac] /home/git/src.git/biosimulations/jbcl/simulations/cartesian/PDBCartesianSystem.java:8: error: package jbcl.data.basic does not exist [javac] import jbcl.data.basic.ThreeTuple; [javac] ^ [javac] /home/git/src.git/biosimulations/jbcl/simulations/cartesian/PDBCartesianSystem.java:9: error: package jbcl.data.dict does not exist [javac] import jbcl.data.dict.AtomType; [javac] ^ [javac] /home/git/src.git/biosimulations/jbcl/simulations/cartesian/PDBCartesianSystem.java:10: error: package jbcl.data.dict does not exist [javac] import jbcl.data.dict.Monomer; [javac] ^ [javac] /home/git/src.git/biosimulations/jbcl/simulations/cartesian/PDBCartesianSystem.java:11: error: package jbcl.data.formats does not exist [javac] import jbcl.data.formats.PDB; [javac] ^ [javac] /home/git/src.git/biosimulations/jbcl/simulations/cartesian/PDBCartesianSystem.java:12: error: package jbcl.data.types does not exist [javac] import jbcl.data.types.AAResidue; [javac] ^ [javac] /home/git/src.git/biosimulations/jbcl/simulations/cartesian/PDBCartesianSystem.java:13: error: package jbcl.data.types does not exist [javac] import jbcl.data.types.Chain; [javac] ^ [javac] /home/git/src.git/biosimulations/jbcl/simulations/cartesian/PDBCartesianSystem.java:14: error: package jbcl.data.types does not exist [javac] import jbcl.data.types.Ligand; [javac] ^ [javac] /home/git/src.git/biosimulations/jbcl/simulations/cartesian/PDBCartesianSystem.java:15: error: package jbcl.data.types does not exist [javac] import jbcl.data.types.LigandsChain; [javac] ^ [javac] /home/git/src.git/biosimulations/jbcl/simulations/cartesian/PDBCartesianSystem.java:16: error: package jbcl.data.types does not exist [javac] import jbcl.data.types.NResidue; [javac] ^ [javac] /home/git/src.git/biosimulations/jbcl/simulations/cartesian/PDBCartesianSystem.java:17: error: package jbcl.data.types does not exist [javac] import jbcl.data.types.NucleicChain; [javac] ^ [javac] /home/git/src.git/biosimulations/jbcl/simulations/cartesian/PDBCartesianSystem.java:18: error: package jbcl.data.types does not exist [javac] import jbcl.data.types.PdbAtom; [javac] ^ [javac] /home/git/src.git/biosimulations/jbcl/simulations/cartesian/PDBCartesianSystem.java:19: error: package jbcl.data.types does not exist [javac] import jbcl.data.types.ProteinChain; [javac] ^ [javac] /home/git/src.git/biosimulations/jbcl/simulations/cartesian/PDBCartesianSystem.java:20: error: package jbcl.data.types does not exist [javac] import jbcl.data.types.Residue; [javac] ^ [javac] /home/git/src.git/biosimulations/jbcl/simulations/cartesian/PDBCartesianSystem.java:21: error: package jbcl.data.types does not exist [javac] import jbcl.data.types.Sequence; [javac] ^ [javac] /home/git/src.git/biosimulations/jbcl/simulations/cartesian/PDBCartesianSystem.java:22: error: package jbcl.data.types does not exist [javac] import jbcl.data.types.Structure; [javac] ^ [javac] /home/git/src.git/biosimulations/jbcl/simulations/cartesian/PDBCartesianSystem.java:51: error: cannot find symbol [javac] public PDBCartesianSystem(final Structure object) { [javac] ^ [javac] symbol: class Structure [javac] location: class PDBCartesianSystem [javac] /home/git/src.git/biosimulations/jbcl/simulations/cartesian/PDBCartesianSystem.java:114: error: cannot find symbol [javac] public PDBCartesianSystem(final Residue[] residues) { [javac] ^ [javac] symbol: class Residue [javac] location: class PDBCartesianSystem [javac] /home/git/src.git/biosimulations/jbcl/simulations/cartesian/PDBCartesianSystem.java:229: error: cannot find symbol [javac] public final AtomType getMappedAtomType(final int atomIndex) { [javac] ^ [javac] symbol: class AtomType [javac] location: class PDBCartesianSystem [javac] /home/git/src.git/biosimulations/jbcl/simulations/cartesian/PDBCartesianSystem.java:235: error: cannot find symbol [javac] public final AtomType[] getMappedAtomTypes() { [javac] ^ [javac] symbol: class AtomType [javac] location: class PDBCartesianSystem [javac] /home/git/src.git/biosimulations/jbcl/simulations/cartesian/PDBCartesianSystem.java:256: error: cannot find symbol [javac] public int getMappedAtomIndex(final ThreeTuple atomLocator) { [javac] ^ [javac] symbol: class ThreeTuple [javac] location: class PDBCartesianSystem [javac] /home/git/src.git/biosimulations/jbcl/simulations/cartesian/PDBCartesianSystem.java:308: error: cannot find symbol [javac] public Monomer getMappedResidueType(final int atomIndex) { [javac] ^ [javac] symbol: class Monomer [javac] location: class PDBCartesianSystem [javac] /home/git/src.git/biosimulations/jbcl/simulations/cartesian/PDBCartesianSystem.java:343: error: cannot find symbol [javac] public Sequence getChainSequence(final int whichChain) { [javac] ^ [javac] symbol: class Sequence [javac] location: class PDBCartesianSystem [javac] /home/git/src.git/biosimulations/jbcl/simulations/cartesian/PDBCartesianSystem.java:361: error: cannot find symbol [javac] public final void coordinatesFromStructure(final Structure source) { [javac] ^ [javac] symbol: class Structure [javac] location: class PDBCartesianSystem [javac] /home/git/src.git/biosimulations/jbcl/simulations/cartesian/PDBCartesianSystem.java:400: error: cannot find symbol [javac] public final void coordinatesToStructure(final Structure destination) { [javac] ^ [javac] symbol: class Structure [javac] location: class PDBCartesianSystem [javac] /home/git/src.git/biosimulations/jbcl/simulations/cartesian/PDBCartesianSystem.java:439: error: cannot find symbol [javac] public final Structure createStructure(final String code) { [javac] ^ [javac] symbol: class Structure [javac] location: class PDBCartesianSystem [javac] /home/git/src.git/biosimulations/jbcl/simulations/cartesian/PDBCartesianSystem.java:496: error: cannot find symbol [javac] protected AtomType[] atomTypes; [javac] ^ [javac] symbol: class AtomType [javac] location: class PDBCartesianSystem [javac] /home/git/src.git/biosimulations/jbcl/simulations/cartesian/PDBCartesianSystem.java:497: error: cannot find symbol [javac] protected final Sequence[] aaSequences; [javac] ^ [javac] symbol: class Sequence [javac] location: class PDBCartesianSystem [javac] /home/git/src.git/biosimulations/jbcl/simulations/cartesian/PDBCartesianSystem.java:506: error: cannot find symbol [javac] private static final int countAtoms(final Residue[] residues) { [javac] ^ [javac] symbol: class Residue [javac] location: class PDBCartesianSystem [javac] /home/git/src.git/biosimulations/jbcl/simulations/cartesian/SimpleAtomicSystem.java:7: error: package jbcl.calc.statistics does not exist [javac] import jbcl.calc.statistics.RandGenerator; [javac] ^ [javac] /home/git/src.git/biosimulations/jbcl/simulations/cartesian/SimpleAtomicSystem.java:8: error: package jbcl.data.basic does not exist [javac] import jbcl.data.basic.IntList; [javac] ^ [javac] /home/git/src.git/biosimulations/jbcl/simulations/cartesian/SimpleAtomicSystem.java:9: error: package jbcl.data.basic does not exist [javac] import jbcl.data.basic.ThreeTuple; [javac] ^ [javac] /home/git/src.git/biosimulations/jbcl/simulations/cartesian/SimpleAtomicSystem.java:10: error: package jbcl.data.dict does not exist [javac] import jbcl.data.dict.AtomType; [javac] ^ [javac] Note: /home/git/src.git/biosimulations/jbcl/simulations/interactions/methods/NBList.java uses unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [javac] 100 errors [javac] 1 warning BUILD FAILED /home/git/src.git/biosimulations/build.xml:95: Compile failed; see the compiler error output for details. Total time: 3 seconds Deploying bioshell.biosimulations-0.9-tests.jar Deploying bioshell.biosimulations-0.9-ff.jar