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synchronization the branche-miguelrojasch-IP with trunk

by Miguel Rojas Cherto-3 :: Rate this Message:

Hi all,

I finish branch /branches/miguelrojasch-IP which was supposed to close
the bug predicting the necessary energy to ionize orbitals localized
principally in heteroatoms and double bonds. The improvements has been:
- Model to predict ionizatio potential based on weka software with the
function LeastMedSq
- Divided the classification in different models according with which
group they belong
- Removed bug 1860497 which Descriptors are not anymore dependents
between them
- Create new Interface for IChargeCalculator which makes clean the code
grouping blablaCharges methods. IChargeCalculator is a extension of
IElectronicPropertyCalculator
- Added method in StructureResonanceGenerator which extracts container
in resonance given an IAtom object
- etc..

Here I also attached the junit-test-results comparing with trunk.

It would be very nice if you could take at look before to submit to
trunk and replay suggestions.

Thanks in advance,
Miquel

[branch.ant.log]

checkPlatforms: check: noJunit: dist-all: checkPlatforms: check: setupBuildDir: [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/sourcedist [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/dist [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/reports init: javacc: [echo] Compiling Ant 1.6 depending classes. [javacc] Java Compiler Compiler Version 3.2 (Parser Generator) [javacc] (type "javacc" with no arguments for help) [javacc] Reading from file /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/src/main/org/openscience/cdk/iupac/parser/NomParser.jj . . . [javacc] File "TokenMgrError.java" does not exist. Will create one. [javacc] File "ParseException.java" does not exist. Will create one. [javacc] File "Token.java" does not exist. Will create one. [javacc] File "SimpleCharStream.java" does not exist. Will create one. [javacc] Parser generated successfully. [javacc] Java Compiler Compiler Version 3.2 (Parser Generator) [javacc] (type "javacc" with no arguments for help) [javacc] Reading from file /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/src/main/org/openscience/cdk/smiles/smarts/parser/SMARTSParser.jj . . . [javacc] File "TokenMgrError.java" does not exist. Will create one. [javacc] File "ParseException.java" does not exist. Will create one. [javacc] File "Token.java" does not exist. Will create one. [javacc] File "SimpleCharStream.java" does not exist. Will create one. [javacc] Parser generated successfully. customize: runDoclet: [echo] Not skipping doclet run... [javac] Compiling 1 source file to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build compile-init: checkPlatforms: check: dist.init: [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/dist/jar compile-needed-test: compile-module: [echo] Compiling classes for CDK's interfaces module from src/main... [echo] Datafiles defined: ${module.datafiles.present} [echo] Extra files defined: ${module.extrafiles.present} [echo] CDK dependencies defined: ${module.cdkdepends.present} [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: ${module.devellibdepends.present} [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/interfaces [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/interfaces [copy] Copying 46 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/interfaces [javac] Compiling 46 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/interfaces [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/dist/jar/cdk-interfaces.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/interfaces [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/interfaces checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's core module from src/main... [echo] Datafiles defined: true [echo] Extra files defined: ${module.extrafiles.present} [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: ${module.devellibdepends.present} [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/core [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/core [copy] Copying 19 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/core [javac] Compiling 19 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/core [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/dist/jar/cdk-core.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/core [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/core checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's atomtype module from src/main... [echo] Datafiles defined: ${module.datafiles.present} [echo] Extra files defined: ${module.extrafiles.present} [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: ${module.devellibdepends.present} [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/atomtype [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/atomtype [copy] Copying 5 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/atomtype [javac] Compiling 5 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/atomtype [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/dist/jar/cdk-atomtype.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/atomtype [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/atomtype checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's standard module from src/main... [echo] Datafiles defined: ${module.datafiles.present} [echo] Extra files defined: ${module.extrafiles.present} [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: ${module.devellibdepends.present} [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/standard [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/standard [copy] Copying 80 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/standard [javac] Compiling 80 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/standard [javac] Note: Some input files use unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/dist/jar/cdk-standard.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/standard [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/standard checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's dict module from src/main... [echo] Datafiles defined: ${module.datafiles.present} [echo] Extra files defined: ${module.extrafiles.present} [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: ${module.devellibdepends.present} [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/dict [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/dict [copy] Copying 8 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/dict [javac] Compiling 8 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/dict [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/dist/jar/cdk-dict.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/dict [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/dict checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's data module from src/main... [echo] Datafiles defined: ${module.datafiles.present} [echo] Extra files defined: ${module.extrafiles.present} [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: ${module.devellibdepends.present} [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/data [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/data [copy] Copying 38 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/data [javac] Compiling 38 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/data [javac] Note: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/data/org/openscience/cdk/protein/data/PDBPolymer.java uses unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/dist/jar/cdk-data.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/data [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/data checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's render module from src/main... [echo] Datafiles defined: ${module.datafiles.present} [echo] Extra files defined: ${module.extrafiles.present} [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: ${module.devellibdepends.present} [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/render [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/render [copy] Copying 17 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/render [javac] Compiling 17 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/render [javac] Note: Some input files use unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/dist/jar/cdk-render.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/render [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/render checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's io module from src/main... [echo] Datafiles defined: true [echo] Extra files defined: ${module.extrafiles.present} [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: ${module.devellibdepends.present} [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/io [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/io [copy] Copying 168 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/io [javac] Compiling 168 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/io [javac] Note: Some input files use unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/dist/jar/cdk-io.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/io [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/io checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's valencycheck module from src/main... [echo] Datafiles defined: ${module.datafiles.present} [echo] Extra files defined: ${module.extrafiles.present} [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: ${module.devellibdepends.present} [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/valencycheck [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/valencycheck [copy] Copying 8 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/valencycheck [javac] Compiling 8 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/valencycheck [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/dist/jar/cdk-valencycheck.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/valencycheck [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/valencycheck checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's sdg module from src/main... [echo] Datafiles defined: ${module.datafiles.present} [echo] Extra files defined: ${module.extrafiles.present} [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: ${module.devellibdepends.present} [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/sdg [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/sdg [copy] Copying 6 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/sdg [javac] Compiling 6 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/sdg [javac] Note: Some input files use unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/dist/jar/cdk-sdg.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/sdg [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/sdg checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's control module from src/main... [echo] Datafiles defined: ${module.datafiles.present} [echo] Extra files defined: ${module.extrafiles.present} [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: ${module.devellibdepends.present} [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/control [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/control [copy] Copying 14 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/control [javac] Compiling 14 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/control [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/dist/jar/cdk-control.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/control [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/control checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's datadebug module from src/main... [echo] Datafiles defined: ${module.datafiles.present} [echo] Extra files defined: ${module.extrafiles.present} [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: ${module.devellibdepends.present} [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/datadebug [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/datadebug [copy] Copying 36 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/datadebug [javac] Compiling 36 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/datadebug [javac] /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/datadebug/org/openscience/cdk/debug/DebugAminoAcid.java:265: warning: [deprecation] getBondOrderSum(org.openscience.cdk.interfaces.IAtom) in org.openscience.cdk.AtomContainer has been deprecated [javac] public double getBondOrderSum(IAtom atom) { [javac] ^ [javac] /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/datadebug/org/openscience/cdk/debug/DebugAminoAcid.java:267: warning: [deprecation] getBondOrderSum(org.openscience.cdk.interfaces.IAtom) in org.openscience.cdk.AtomContainer has been deprecated [javac] return super.getBondOrderSum(atom); [javac] ^ [javac] /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/datadebug/org/openscience/cdk/debug/DebugAtomContainer.java:276: warning: [deprecation] getBondOrderSum(org.openscience.cdk.interfaces.IAtom) in org.openscience.cdk.AtomContainer has been deprecated [javac] public double getBondOrderSum(IAtom atom) { [javac] ^ [javac] /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/datadebug/org/openscience/cdk/debug/DebugAtomContainer.java:278: warning: [deprecation] getBondOrderSum(org.openscience.cdk.interfaces.IAtom) in org.openscience.cdk.AtomContainer has been deprecated [javac] return super.getBondOrderSum(atom); [javac] ^ [javac] /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/datadebug/org/openscience/cdk/debug/DebugBioPolymer.java:268: warning: [deprecation] getBondOrderSum(org.openscience.cdk.interfaces.IAtom) in org.openscience.cdk.AtomContainer has been deprecated [javac] public double getBondOrderSum(IAtom atom) { [javac] ^ [javac] /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/datadebug/org/openscience/cdk/debug/DebugBioPolymer.java:270: warning: [deprecation] getBondOrderSum(org.openscience.cdk.interfaces.IAtom) in org.openscience.cdk.AtomContainer has been deprecated [javac] return super.getBondOrderSum(atom); [javac] ^ [javac] /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/datadebug/org/openscience/cdk/debug/DebugCrystal.java:277: warning: [deprecation] getBondOrderSum(org.openscience.cdk.interfaces.IAtom) in org.openscience.cdk.AtomContainer has been deprecated [javac] public double getBondOrderSum(IAtom atom) { [javac] ^ [javac] /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/datadebug/org/openscience/cdk/debug/DebugCrystal.java:279: warning: [deprecation] getBondOrderSum(org.openscience.cdk.interfaces.IAtom) in org.openscience.cdk.AtomContainer has been deprecated [javac] return super.getBondOrderSum(atom); [javac] ^ [javac] /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/datadebug/org/openscience/cdk/debug/DebugMolecule.java:277: warning: [deprecation] getBondOrderSum(org.openscience.cdk.interfaces.IAtom) in org.openscience.cdk.AtomContainer has been deprecated [javac] public double getBondOrderSum(IAtom atom) { [javac] ^ [javac] /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/datadebug/org/openscience/cdk/debug/DebugMolecule.java:279: warning: [deprecation] getBondOrderSum(org.openscience.cdk.interfaces.IAtom) in org.openscience.cdk.AtomContainer has been deprecated [javac] return super.getBondOrderSum(atom); [javac] ^ [javac] /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/datadebug/org/openscience/cdk/debug/DebugMonomer.java:265: warning: [deprecation] getBondOrderSum(org.openscience.cdk.interfaces.IAtom) in org.openscience.cdk.AtomContainer has been deprecated [javac] public double getBondOrderSum(IAtom atom) { [javac] ^ [javac] /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/datadebug/org/openscience/cdk/debug/DebugMonomer.java:267: warning: [deprecation] getBondOrderSum(org.openscience.cdk.interfaces.IAtom) in org.openscience.cdk.AtomContainer has been deprecated [javac] return super.getBondOrderSum(atom); [javac] ^ [javac] /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/datadebug/org/openscience/cdk/debug/DebugPolymer.java:267: warning: [deprecation] getBondOrderSum(org.openscience.cdk.interfaces.IAtom) in org.openscience.cdk.AtomContainer has been deprecated [javac] public double getBondOrderSum(IAtom atom) { [javac] ^ [javac] /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/datadebug/org/openscience/cdk/debug/DebugPolymer.java:269: warning: [deprecation] getBondOrderSum(org.openscience.cdk.interfaces.IAtom) in org.openscience.cdk.AtomContainer has been deprecated [javac] return super.getBondOrderSum(atom); [javac] ^ [javac] /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/datadebug/org/openscience/cdk/debug/DebugRing.java:290: warning: [deprecation] getBondOrderSum(org.openscience.cdk.interfaces.IAtom) in org.openscience.cdk.AtomContainer has been deprecated [javac] public double getBondOrderSum(IAtom atom) { [javac] ^ [javac] /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/datadebug/org/openscience/cdk/debug/DebugRing.java:292: warning: [deprecation] getBondOrderSum(org.openscience.cdk.interfaces.IAtom) in org.openscience.cdk.AtomContainer has been deprecated [javac] return super.getBondOrderSum(atom); [javac] ^ [javac] /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/datadebug/org/openscience/cdk/debug/DebugStrand.java:268: warning: [deprecation] getBondOrderSum(org.openscience.cdk.interfaces.IAtom) in org.openscience.cdk.AtomContainer has been deprecated [javac] public double getBondOrderSum(IAtom atom) { [javac] ^ [javac] /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/datadebug/org/openscience/cdk/debug/DebugStrand.java:270: warning: [deprecation] getBondOrderSum(org.openscience.cdk.interfaces.IAtom) in org.openscience.cdk.AtomContainer has been deprecated [javac] return super.getBondOrderSum(atom); [javac] ^ [javac] Note: Some input files use unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [javac] 18 warnings [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/dist/jar/cdk-datadebug.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/datadebug [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/datadebug checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's nonotify module from src/main... [echo] Datafiles defined: ${module.datafiles.present} [echo] Extra files defined: ${module.extrafiles.present} [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: ${module.devellibdepends.present} [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/nonotify [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/nonotify [copy] Copying 36 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/nonotify [javac] Compiling 36 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/nonotify [javac] Note: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/nonotify/org/openscience/cdk/nonotify/NNPDBPolymer.java uses unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/dist/jar/cdk-nonotify.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/nonotify [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/nonotify checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's formula module from src/main... [echo] Datafiles defined: ${module.datafiles.present} [echo] Extra files defined: ${module.extrafiles.present} [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: ${module.devellibdepends.present} [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/formula [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/formula [copy] Copying 16 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/formula [javac] Compiling 16 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/formula [javac] Note: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/formula/org/openscience/cdk/formula/rules/IsotopePatternRule.java uses unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/dist/jar/cdk-formula.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/formula [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/formula checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's structgen module from src/main... [echo] Datafiles defined: ${module.datafiles.present} [echo] Extra files defined: ${module.extrafiles.present} [echo] CDK dependencies defined: true [echo] Library dependencies defined: ${module.libdepends.present} [echo] Developer Library dependencies defined: ${module.devellibdepends.present} [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/structgen [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/structgen [copy] Copying 11 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/structgen [javac] Compiling 11 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/structgen [javac] Note: Some input files use unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/dist/jar/cdk-structgen.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/structgen [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/structgen checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's pdb module from src/main... [echo] Datafiles defined: ${module.datafiles.present} [echo] Extra files defined: true [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: ${module.devellibdepends.present} [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/pdb [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/pdb [copy] Copying 4 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/pdb [javac] Compiling 4 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/pdb [javac] Note: Some input files use unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/dist/jar/cdk-pdb.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/pdb [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/pdb checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's isomorphism module from src/main... [echo] Datafiles defined: ${module.datafiles.present} [echo] Extra files defined: ${module.extrafiles.present} [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: ${module.devellibdepends.present} [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/isomorphism [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/isomorphism [copy] Copying 15 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/isomorphism [javac] Compiling 15 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/isomorphism [javac] Note: Some input files use unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/dist/jar/cdk-isomorphism.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/isomorphism [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/isomorphism checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's extra module from src/main... [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} [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/extra [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/extra [copy] Copying 118 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/extra [javac] Compiling 118 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/extra [javac] /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/extra/org/openscience/cdk/applications/swing/JExternalFrame.java:87: warning: [deprecation] show() in java.awt.Window has been deprecated [javac] super.show(); [javac] ^ [javac] /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/extra/org/openscience/cdk/validate/BasicValidator.java:318: warning: [deprecation] getBondOrderSum(org.openscience.cdk.interfaces.IAtom) in org.openscience.cdk.AtomContainer has been deprecated [javac] int bos = (int)molecule.getBondOrderSum(atom); [javac] ^ [javac] Note: Some input files use unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [javac] 2 warnings [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/dist/jar/cdk-extra.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/extra [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/extra checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's smiles module from src/main... [echo] Datafiles defined: ${module.datafiles.present} [echo] Extra files defined: ${module.extrafiles.present} [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: ${module.devellibdepends.present} [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/smiles [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/smiles [copy] Copying 7 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/smiles [javac] Compiling 7 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/smiles [javac] Note: Some input files use unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/dist/jar/cdk-smiles.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/smiles [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/smiles checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's libiocml module from src/main... [echo] Datafiles defined: ${module.datafiles.present} [echo] Extra files defined: ${module.extrafiles.present} [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: ${module.devellibdepends.present} [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/libiocml [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/libiocml [copy] Copying 3 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/libiocml [javac] Compiling 3 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/libiocml [javac] Note: Some input files use unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/dist/jar/cdk-libiocml.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/libiocml [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/libiocml checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's libiomd module from src/main... [echo] Datafiles defined: ${module.datafiles.present} [echo] Extra files defined: ${module.extrafiles.present} [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: ${module.devellibdepends.present} [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/libiomd [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/libiomd [copy] Copying 5 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/libiomd [javac] Compiling 5 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/libiomd [javac] Note: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/libiomd/org/openscience/cdk/libio/md/MDMolecule.java uses unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/dist/jar/cdk-libiomd.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/libiomd [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/libiomd checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's pdb-cml module from src/main... [echo] Datafiles defined: ${module.datafiles.present} [echo] Extra files defined: ${module.extrafiles.present} [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: ${module.devellibdepends.present} [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/pdb-cml [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/pdb-cml [copy] Copying 1 file to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/pdb-cml [javac] Compiling 1 source file to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/pdb-cml [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/dist/jar/cdk-pdb-cml.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/pdb-cml [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/pdb-cml checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's reaction module from src/main... [echo] Datafiles defined: ${module.datafiles.present} [echo] Extra files defined: ${module.extrafiles.present} [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: ${module.devellibdepends.present} [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/reaction [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/reaction [copy] Copying 50 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/reaction [javac] Compiling 50 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/reaction [javac] Note: Some input files use unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/dist/jar/cdk-reaction.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/reaction [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/reaction checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's charges module from src/main... [echo] Datafiles defined: ${module.datafiles.present} [echo] Extra files defined: ${module.extrafiles.present} [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: ${module.devellibdepends.present} [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/charges [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/charges [copy] Copying 9 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/charges [javac] Compiling 9 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/charges [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/dist/jar/cdk-charges.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/charges [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/charges checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's ionpot module from src/main... [echo] Datafiles defined: ${module.datafiles.present} [echo] Extra files defined: ${module.extrafiles.present} [echo] CDK dependencies defined: true [echo] Library dependencies defined: ${module.libdepends.present} [echo] Developer Library dependencies defined: ${module.devellibdepends.present} [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/ionpot [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/ionpot [copy] Copying 1 file to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/ionpot [javac] Compiling 1 source file to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/ionpot [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/dist/jar/cdk-ionpot.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/ionpot [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/ionpot checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's qsar module from src/main... [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} [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/qsar [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/qsar [copy] Copying 31 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/qsar [javac] Compiling 31 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/qsar [javac] /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/qsar/org/openscience/cdk/qsar/model/R/CNNRegressionModel.java:442: warning: [deprecation] org.openscience.cdk.qsar.model.R.CNNRegressionModelSummary in org.openscience.cdk.qsar.model.R has been deprecated [javac] public CNNRegressionModelSummary summary() throws QSARModelException { [javac] ^ [javac] /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/qsar/org/openscience/cdk/qsar/model/R/LinearRegressionModel.java:381: warning: [deprecation] org.openscience.cdk.qsar.model.R.LinearRegressionModelSummary in org.openscience.cdk.qsar.model.R has been deprecated [javac] public LinearRegressionModelSummary summary() throws QSARModelException { [javac] ^ [javac] /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/qsar/org/openscience/cdk/qsar/descriptors/atompair/PiContactDetectionDescriptor.java:177: warning: [deprecation] DescriptorValue(org.openscience.cdk.qsar.DescriptorSpecification,java.lang.String[],java.lang.Object[],org.openscience.cdk.qsar.result.IDescriptorResult) in org.openscience.cdk.qsar.DescriptorValue has been deprecated [javac] return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(), new BooleanResult(piContact)); [javac] ^ [javac] /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/qsar/org/openscience/cdk/qsar/model/R/PLSRegressionModelFit.java:111: warning: [deprecation] org.openscience.cdk.qsar.model.R.V2M in org.openscience.cdk.qsar.model.R has been deprecated [javac] this.rms = V2M.VectorToMatrix(rms, ncase, npvar); [javac] ^ [javac] /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/qsar/org/openscience/cdk/qsar/model/R/PLSRegressionModelFit.java:112: warning: [deprecation] org.openscience.cdk.qsar.model.R.V2M in org.openscience.cdk.qsar.model.R has been deprecated [javac] this.xscores = V2M.VectorToMatrix(xscores, nobs, maxncomp); [javac] ^ [javac] /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/qsar/org/openscience/cdk/qsar/model/R/PLSRegressionModelFit.java:113: warning: [deprecation] org.openscience.cdk.qsar.model.R.V2M in org.openscience.cdk.qsar.model.R has been deprecated [javac] this.yscores = V2M.VectorToMatrix(yscores, nobs, maxncomp); [javac] ^ [javac] /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/qsar/org/openscience/cdk/qsar/model/R/PLSRegressionModelFit.java:114: warning: [deprecation] org.openscience.cdk.qsar.model.R.V2M in org.openscience.cdk.qsar.model.R has been deprecated [javac] this.yload = V2M.VectorToMatrix(yload, npvar, maxncomp); [javac] ^ [javac] /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/qsar/org/openscience/cdk/qsar/model/R/PLSRegressionModelFit.java:115: warning: [deprecation] org.openscience.cdk.qsar.model.R.V2M in org.openscience.cdk.qsar.model.R has been deprecated [javac] this.xload = V2M.VectorToMatrix(xload, nvar, maxncomp); [javac] ^ [javac] /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/qsar/org/openscience/cdk/qsar/model/R/PLSRegressionModelFit.java:116: warning: [deprecation] org.openscience.cdk.qsar.model.R.V2M in org.openscience.cdk.qsar.model.R has been deprecated [javac] this.ypred = V2M.VectorToCube(ypred, ncase, nobs, npvar); [javac] ^ [javac] /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/qsar/org/openscience/cdk/qsar/model/R/PLSRegressionModelFit.java:117: warning: [deprecation] org.openscience.cdk.qsar.model.R.V2M in org.openscience.cdk.qsar.model.R has been deprecated [javac] this.B = V2M.VectorToCube(B, ncase, nvar, npvar); [javac] ^ [javac] /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/qsar/org/openscience/cdk/qsar/model/R/PLSRegressionModelFit.java:143: warning: [deprecation] org.openscience.cdk.qsar.model.R.V2M in org.openscience.cdk.qsar.model.R has been deprecated [javac] this.rms = V2M.VectorToMatrix(rms, ncase, npvar); [javac] ^ [javac] /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/qsar/org/openscience/cdk/qsar/model/R/PLSRegressionModelFit.java:144: warning: [deprecation] org.openscience.cdk.qsar.model.R.V2M in org.openscience.cdk.qsar.model.R has been deprecated [javac] this.rmssd = V2M.VectorToMatrix(rmssd, ncase, npvar); [javac] ^ [javac] /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/qsar/org/openscience/cdk/qsar/model/R/PLSRegressionModelFit.java:145: warning: [deprecation] org.openscience.cdk.qsar.model.R.V2M in org.openscience.cdk.qsar.model.R has been deprecated [javac] this.r2 = V2M.VectorToMatrix(r2, ncase, npvar);; [javac] ^ [javac] /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/qsar/org/openscience/cdk/qsar/model/R/PLSRegressionModelFit.java:146: warning: [deprecation] org.openscience.cdk.qsar.model.R.V2M in org.openscience.cdk.qsar.model.R has been deprecated [javac] this.ypred = V2M.VectorToCube(ypred, ncase, nobs, npvar); [javac] ^ [javac] Note: Some input files use unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [javac] 14 warnings [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/dist/jar/cdk-qsar.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/qsar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/qsar checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's qsaratomic module from src/main... [echo] Datafiles defined: ${module.datafiles.present} [echo] Extra files defined: ${module.extrafiles.present} [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: ${module.devellibdepends.present} [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/qsaratomic [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/qsaratomic [copy] Copying 29 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/qsaratomic [javac] Compiling 29 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/qsaratomic [javac] /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/qsaratomic/org/openscience/cdk/qsar/descriptors/atomic/AtomHybridizationVSEPRDescriptor.java:196: warning: [deprecation] DescriptorValue(org.openscience.cdk.qsar.DescriptorSpecification,java.lang.String[],java.lang.Object[],org.openscience.cdk.qsar.result.IDescriptorResult) in org.openscience.cdk.qsar.DescriptorValue has been deprecated [javac] return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(), new IntegerResult(hybridizationCDK)); [javac] ^ [javac] /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/qsaratomic/org/openscience/cdk/qsar/descriptors/atomic/BondsToAtomDescriptor.java:149: warning: [deprecation] DescriptorValue(org.openscience.cdk.qsar.DescriptorSpecification,java.lang.String[],java.lang.Object[],org.openscience.cdk.qsar.result.IDescriptorResult) in org.openscience.cdk.qsar.DescriptorValue has been deprecated [javac] return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(), new IntegerResult(bondsToAtom)); [javac] ^ [javac] /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/qsaratomic/org/openscience/cdk/qsar/descriptors/atomic/CovalentRadiusDescriptor.java:155: warning: [deprecation] DescriptorValue(org.openscience.cdk.qsar.DescriptorSpecification,java.lang.String[],java.lang.Object[],org.openscience.cdk.qsar.result.IDescriptorResult) in org.openscience.cdk.qsar.DescriptorValue has been deprecated [javac] return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(), new DoubleResult(covalentradius)); [javac] ^ [javac] /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/qsaratomic/org/openscience/cdk/qsar/descriptors/atomic/DistanceToAtomDescriptor.java:141: warning: [deprecation] DescriptorValue(org.openscience.cdk.qsar.DescriptorSpecification,java.lang.String[],java.lang.Object[],org.openscience.cdk.qsar.result.IDescriptorResult) in org.openscience.cdk.qsar.DescriptorValue has been deprecated [javac] return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(), new DoubleResult(distanceToAtom)); [javac] ^ [javac] /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/qsaratomic/org/openscience/cdk/qsar/descriptors/atomic/EffectiveAtomPolarizabilityDescriptor.java:128: warning: [deprecation] DescriptorValue(org.openscience.cdk.qsar.DescriptorSpecification,java.lang.String[],java.lang.Object[],org.openscience.cdk.qsar.result.IDescriptorResult) in org.openscience.cdk.qsar.DescriptorValue has been deprecated [javac] return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(), new DoubleResult(polarizability)); [javac] ^ [javac] /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/qsaratomic/org/openscience/cdk/qsar/descriptors/atomic/InductiveAtomicHardnessDescriptor.java:216: warning: [deprecation] DescriptorValue(org.openscience.cdk.qsar.DescriptorSpecification,java.lang.String[],java.lang.Object[],org.openscience.cdk.qsar.result.IDescriptorResult) in org.openscience.cdk.qsar.DescriptorValue has been deprecated [javac] return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(), new DoubleResult(atomicHardness)); [javac] ^ [javac] /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/qsaratomic/org/openscience/cdk/qsar/descriptors/atomic/InductiveAtomicSoftnessDescriptor.java:214: warning: [deprecation] DescriptorValue(org.openscience.cdk.qsar.DescriptorSpecification,java.lang.String[],java.lang.Object[],org.openscience.cdk.qsar.result.IDescriptorResult) in org.openscience.cdk.qsar.DescriptorValue has been deprecated [javac] return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(), new DoubleResult(atomicSoftness)); [javac] ^ [javac] /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/qsaratomic/org/openscience/cdk/qsar/descriptors/atomic/IsProtonInAromaticSystemDescriptor.java:177: warning: [deprecation] DescriptorValue(org.openscience.cdk.qsar.DescriptorSpecification,java.lang.String[],java.lang.Object[],org.openscience.cdk.qsar.result.IDescriptorResult) in org.openscience.cdk.qsar.DescriptorValue has been deprecated [javac] return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(), new IntegerResult(isProtonInAromaticSystem)); [javac] ^ [javac] /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/qsaratomic/org/openscience/cdk/qsar/descriptors/atomic/IsProtonInConjugatedPiSystemDescriptor.java:171: warning: [deprecation] DescriptorValue(org.openscience.cdk.qsar.DescriptorSpecification,java.lang.String[],java.lang.Object[],org.openscience.cdk.qsar.result.IDescriptorResult) in org.openscience.cdk.qsar.DescriptorValue has been deprecated [javac] return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(), new BooleanResult(isProtonInPiSystem)); [javac] ^ [javac] /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/qsaratomic/org/openscience/cdk/qsar/descriptors/atomic/PartialSigmaChargeDescriptor.java:159: warning: [deprecation] DescriptorValue(org.openscience.cdk.qsar.DescriptorSpecification,java.lang.String[],java.lang.Object[],org.openscience.cdk.qsar.result.IDescriptorResult) in org.openscience.cdk.qsar.DescriptorValue has been deprecated [javac] ? new DescriptorValue(getSpecification(), getParameterNames(), getParameters(), getCachedDescriptorValue(atom)) [javac] ^ [javac] /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/qsaratomic/org/openscience/cdk/qsar/descriptors/atomic/PeriodicTablePositionDescriptor.java:167: warning: [deprecation] DescriptorValue(org.openscience.cdk.qsar.DescriptorSpecification,java.lang.String[],java.lang.Object[],org.openscience.cdk.qsar.result.IDescriptorResult) in org.openscience.cdk.qsar.DescriptorValue has been deprecated [javac] return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(), new IntegerResult(period)); [javac] ^ [javac] /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/qsaratomic/org/openscience/cdk/qsar/descriptors/atomic/ProtonTotalPartialChargeDescriptor.java:144: warning: [deprecation] DescriptorValue(org.openscience.cdk.qsar.DescriptorSpecification,java.lang.String[],java.lang.Object[],org.openscience.cdk.qsar.result.IDescriptorResult) in org.openscience.cdk.qsar.DescriptorValue has been deprecated [javac] return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(), protonPartialCharge); [javac] ^ [javac] /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/qsaratomic/org/openscience/cdk/qsar/descriptors/atomic/VdWRadiusDescriptor.java:153: warning: [deprecation] DescriptorValue(org.openscience.cdk.qsar.DescriptorSpecification,java.lang.String[],java.lang.Object[],org.openscience.cdk.qsar.result.IDescriptorResult) in org.openscience.cdk.qsar.DescriptorValue has been deprecated [javac] return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(), new DoubleResult(vdwradius)); [javac] ^ [javac] Note: Some input files use unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [javac] 13 warnings [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/dist/jar/cdk-qsaratomic.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/qsaratomic [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/qsaratomic checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's qsarbond module from src/main... [echo] Datafiles defined: ${module.datafiles.present} [echo] Extra files defined: ${module.extrafiles.present} [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: ${module.devellibdepends.present} [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/qsarbond [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/qsarbond [copy] Copying 6 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/qsarbond [javac] Compiling 6 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/qsarbond [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/dist/jar/cdk-qsarbond.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/qsarbond [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/qsarbond checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's qsarmolecular module from src/main... [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} [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/qsarmolecular [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/qsarmolecular [copy] Copying 43 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/qsarmolecular [javac] Compiling 43 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/qsarmolecular [javac] Note: Some input files use unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/dist/jar/cdk-qsarmolecular.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/qsarmolecular [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/qsarmolecular checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's qsarprotein module from src/main... [echo] Datafiles defined: ${module.datafiles.present} [echo] Extra files defined: ${module.extrafiles.present} [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: ${module.devellibdepends.present} [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/qsarprotein [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/qsarprotein [copy] Copying 2 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/qsarprotein [javac] Compiling 2 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/qsarprotein [javac] /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/qsarprotein/org/openscience/cdk/qsar/descriptors/protein/TaeAminoAcidDescriptor.java:300: warning: [deprecation] DescriptorValue(org.openscience.cdk.qsar.DescriptorSpecification,java.lang.String[],java.lang.Object[],org.openscience.cdk.qsar.result.IDescriptorResult) in org.openscience.cdk.qsar.DescriptorValue has been deprecated [javac] return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(), retval); [javac] ^ [javac] Note: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/qsarprotein/org/openscience/cdk/qsar/descriptors/protein/TaeAminoAcidDescriptor.java uses unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [javac] 1 warning [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/dist/jar/cdk-qsarprotein.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/qsarprotein [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/qsarprotein checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's qsar-cml module from src/main... [echo] Datafiles defined: ${module.datafiles.present} [echo] Extra files defined: ${module.extrafiles.present} [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: ${module.devellibdepends.present} [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/qsar-cml [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/qsar-cml [copy] Copying 1 file to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/qsar-cml [javac] Compiling 1 source file to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/qsar-cml [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/dist/jar/cdk-qsar-cml.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/qsar-cml [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/qsar-cml checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's forcefield module from src/main... [echo] Datafiles defined: true [echo] Extra files defined: ${module.extrafiles.present} [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: ${module.devellibdepends.present} [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/forcefield [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/forcefield [copy] Copying 23 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/forcefield [javac] Compiling 23 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/forcefield [javac] Note: Some input files use unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/dist/jar/cdk-forcefield.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/forcefield [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/forcefield checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's builder3d module from src/main... [echo] Datafiles defined: true [echo] Extra files defined: ${module.extrafiles.present} [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: ${module.devellibdepends.present} [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/builder3d [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/builder3d [copy] Copying 5 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/builder3d [javac] Compiling 5 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/builder3d [javac] /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/builder3d/org/openscience/cdk/qsar/descriptors/atomic/PartialTChargeMMFF94Descriptor.java:130: warning: [deprecation] DescriptorValue(org.openscience.cdk.qsar.DescriptorSpecification,java.lang.String[],java.lang.Object[],org.openscience.cdk.qsar.result.IDescriptorResult) in org.openscience.cdk.qsar.DescriptorValue has been deprecated [javac] return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(), aphaPartialCharge); [javac] ^ [javac] Note: Some input files use unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [javac] 1 warning [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/dist/jar/cdk-builder3d.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/builder3d [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/builder3d checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's builder3dtools module from src/main... [echo] Datafiles defined: ${module.datafiles.present} [echo] Extra files defined: ${module.extrafiles.present} [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: ${module.devellibdepends.present} [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/builder3dtools [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/builder3dtools [copy] Copying 1 file to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/builder3dtools [javac] Compiling 1 source file to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/builder3dtools [javac] Note: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/builder3dtools/org/openscience/cdk/modeling/builder3d/TemplateExtractor.java uses unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/dist/jar/cdk-builder3dtools.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/builder3dtools [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/builder3dtools checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's smarts module from src/main... [echo] Datafiles defined: ${module.datafiles.present} [echo] Extra files defined: ${module.extrafiles.present} [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: ${module.devellibdepends.present} [echo] Autogenerated files specified: true [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/smarts [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/smarts [copy] Copying 52 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/smarts [javac] Compiling 52 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/smarts [javac] Note: Some input files use unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [copy] Copying 1 file to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/dist/jar/cdk-smarts.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/smarts [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/smarts checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's experimental module from src/main... [echo] Datafiles defined: ${module.datafiles.present} [echo] Extra files defined: ${module.extrafiles.present} [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: ${module.devellibdepends.present} [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/experimental [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/experimental [copy] Copying 22 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/experimental [javac] Compiling 22 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/experimental [javac] Note: Some input files use unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/dist/jar/cdk-experimental.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/experimental [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/experimental checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's pcore module from src/main... [echo] Datafiles defined: ${module.datafiles.present} [echo] Extra files defined: ${module.extrafiles.present} [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: ${module.devellibdepends.present} [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/pcore [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/pcore [copy] Copying 6 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/pcore [javac] Compiling 6 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/pcore [javac] Note: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/pcore/org/openscience/cdk/pharmacophore/PharmacophoreMatcher.java uses unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/dist/jar/cdk-pcore.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/pcore [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/pcore checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's applications module from src/main... [echo] Datafiles defined: true [echo] Extra files defined: ${module.extrafiles.present} [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: ${module.devellibdepends.present} [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/applications [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/applications [copy] Copying 26 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/applications [javac] Compiling 26 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/applications [javac] Note: Some input files use unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/dist/jar/cdk-applications.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/applications [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/applications checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's inchi module from src/main... [echo] Datafiles defined: ${module.datafiles.present} [echo] Extra files defined: ${module.extrafiles.present} [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: ${module.devellibdepends.present} [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/inchi [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/inchi [copy] Copying 3 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/inchi [javac] Compiling 3 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/inchi [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/dist/jar/cdk-inchi.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/inchi [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/inchi test-dist-all: checkPlatforms: check: setupBuildDir: init: javacc: customize: runDoclet: [echo] Not skipping doclet run... compile-init: checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's test module from src/test... [echo] Datafiles defined: ${module.datafiles.present} [echo] Extra files defined: ${module.extrafiles.present} [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: true [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/test [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/test [copy] Copying 4 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/test [javac] Compiling 4 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/test [javac] Note: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/test/org/openscience/cdk/CoverageAnnotationTest.java uses unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/dist/jar/cdk-test.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/test [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/test checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's test-core module from src/test... [echo] Datafiles defined: ${module.datafiles.present} [echo] Extra files defined: true [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: true [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/test-core [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/test-core [copy] Copying 16 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/test-core [javac] Compiling 16 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/test-core [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/dist/jar/cdk-test-core.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/test-core [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/test-core checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's test-atomtype module from src/test... [echo] Datafiles defined: ${module.datafiles.present} [echo] Extra files defined: true [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: true [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/test-atomtype [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/test-atomtype [copy] Copying 8 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/test-atomtype [javac] Compiling 8 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/test-atomtype [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/dist/jar/cdk-test-atomtype.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/test-atomtype [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/test-atomtype checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's test-standard module from src/test... [echo] Datafiles defined: ${module.datafiles.present} [echo] Extra files defined: true [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: true [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/test-standard [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/test-standard [copy] Copying 75 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/test-standard [javac] Compiling 75 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/test-standard [javac] /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/test-standard/org/openscience/cdk/qsar/DescriptorValueTest.java:62: warning: [deprecation] DescriptorValue(org.openscience.cdk.qsar.DescriptorSpecification,java.lang.String[],java.lang.Object[],org.openscience.cdk.qsar.result.IDescriptorResult) in org.openscience.cdk.qsar.DescriptorValue has been deprecated [javac] DescriptorValue value = new DescriptorValue( [javac] ^ [javac] Note: Some input files use unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [javac] 1 warning [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/dist/jar/cdk-test-standard.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/test-standard [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/test-standard checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's test-data module from src/test... [echo] Datafiles defined: ${module.datafiles.present} [echo] Extra files defined: ${module.extrafiles.present} [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: true [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/test-data [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/test-data [copy] Copying 41 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/test-data [javac] Compiling 41 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/test-data [javac] Note: Some input files use unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/dist/jar/cdk-test-data.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/test-data [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/test-data checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's test-dict module from src/test... [echo] Datafiles defined: ${module.datafiles.present} [echo] Extra files defined: ${module.extrafiles.present} [echo] CDK dependencies defined: true [echo] Library dependencies defined: ${module.libdepends.present} [echo] Developer Library dependencies defined: true [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/test-dict [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/test-dict [copy] Copying 2 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/test-dict [javac] Compiling 2 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/test-dict [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/dist/jar/cdk-test-dict.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/test-dict [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/test-dict checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's test-datadebug module from src/test... [echo] Datafiles defined: ${module.datafiles.present} [echo] Extra files defined: ${module.extrafiles.present} [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: true [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/test-datadebug [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/test-datadebug [copy] Copying 36 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/test-datadebug [javac] Compiling 36 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/test-datadebug [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/dist/jar/cdk-test-datadebug.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/test-datadebug [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/test-datadebug checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's test-nonotify module from src/test... [echo] Datafiles defined: ${module.datafiles.present} [echo] Extra files defined: ${module.extrafiles.present} [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: true [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/test-nonotify [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/test-nonotify [copy] Copying 35 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/test-nonotify [javac] Compiling 35 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/test-nonotify [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/dist/jar/cdk-test-nonotify.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/test-nonotify [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/test-nonotify checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's test-io module from src/test... [echo] Datafiles defined: ${module.datafiles.present} [echo] Extra files defined: true [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: true [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/test-io [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/test-io [copy] Copying 47 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/test-io [javac] Compiling 47 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/test-io [javac] Note: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/test-io/org/openscience/cdk/io/ChemObjectIOInstantionTests.java uses unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/dist/jar/cdk-test-io.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/test-io [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/test-io checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's test-structgen module from src/test... [echo] Datafiles defined: ${module.datafiles.present} [echo] Extra files defined: ${module.extrafiles.present} [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: true [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/test-structgen [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/test-structgen [copy] Copying 12 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/test-structgen [javac] Compiling 12 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/test-structgen [javac] /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/test-structgen/org/openscience/cdk/structgen/SingleStructureRandomGeneratorTest.java:95: warning: [deprecation] getBondOrderSum(org.openscience.cdk.interfaces.IAtom) in org.openscience.cdk.AtomContainer has been deprecated [javac] bondCount = mol.getBondOrderSum(atom); [javac] ^ [javac] /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/test-structgen/org/openscience/cdk/structgen/deterministic/EquivalentClassesDeterministicGeneratorTest.java:77: warning: [deprecation] getBondOrderSum(org.openscience.cdk.interfaces.IAtom) in org.openscience.cdk.AtomContainer has been deprecated [javac] bondCount = mol.getBondOrderSum(atom); [javac] ^ [javac] Note: Some input files use unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [javac] 2 warnings [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/dist/jar/cdk-test-structgen.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/test-structgen [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/test-structgen checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's test-isomorphism module from src/test... [echo] Datafiles defined: ${module.datafiles.present} [echo] Extra files defined: ${module.extrafiles.present} [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: true [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/test-isomorphism [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/test-isomorphism [copy] Copying 2 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/test-isomorphism [javac] Compiling 2 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/test-isomorphism [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/dist/jar/cdk-test-isomorphism.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/test-isomorphism [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/test-isomorphism checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's test-extra module from src/test... [echo] Datafiles defined: ${module.datafiles.present} [echo] Extra files defined: true [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: true [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/test-extra [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/test-extra [copy] Copying 43 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/test-extra [javac] Compiling 43 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/test-extra [javac] Note: Some input files use unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/dist/jar/cdk-test-extra.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/test-extra [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/test-extra checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's test-smiles module from src/test... [echo] Datafiles defined: ${module.datafiles.present} [echo] Extra files defined: true [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: true [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/test-smiles [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/test-smiles [copy] Copying 7 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/test-smiles [javac] Compiling 7 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/test-smiles [javac] /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/test-smiles/org/openscience/cdk/smiles/SmilesGeneratorTest.java:555: warning: [deprecation] getBondOrderSum(org.openscience.cdk.interfaces.IAtom) in org.openscience.cdk.AtomContainer has been deprecated [javac] bondCount = mol.getBondOrderSum(atom); [javac] ^ [javac] 1 warning [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/dist/jar/cdk-test-smiles.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/test-smiles [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/test-smiles checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's test-reaction module from src/test... [echo] Datafiles defined: ${module.datafiles.present} [echo] Extra files defined: true [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: true [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/test-reaction [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/test-reaction [copy] Copying 55 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/test-reaction [javac] Compiling 55 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/test-reaction [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/dist/jar/cdk-test-reaction.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/test-reaction [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/test-reaction checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's test-builder3d module from src/test... [echo] Datafiles defined: ${module.datafiles.present} [echo] Extra files defined: true [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: true [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/test-builder3d [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/test-builder3d [copy] Copying 3 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/test-builder3d [javac] Compiling 3 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/test-builder3d [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/dist/jar/cdk-test-builder3d.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/test-builder3d [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/test-builder3d checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's test-forcefield module from src/test... [echo] Datafiles defined: ${module.datafiles.present} [echo] Extra files defined: true [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: true [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/test-forcefield [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/test-forcefield [copy] Copying 4 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/test-forcefield [javac] Compiling 4 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/test-forcefield [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/dist/jar/cdk-test-forcefield.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/test-forcefield [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/test-forcefield checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's test-valencycheck module from src/test... [echo] Datafiles defined: ${module.datafiles.present} [echo] Extra files defined: true [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: true [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/test-valencycheck [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/test-valencycheck [copy] Copying 9 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/test-valencycheck [javac] Compiling 9 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/test-valencycheck [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/dist/jar/cdk-test-valencycheck.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/test-valencycheck [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/test-valencycheck checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's test-charges module from src/test... [echo] Datafiles defined: ${module.datafiles.present} [echo] Extra files defined: ${module.extrafiles.present} [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: true [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/test-charges [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/test-charges [copy] Copying 10 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/test-charges [javac] Compiling 10 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/test-charges [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/dist/jar/cdk-test-charges.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/test-charges [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/test-charges checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's test-ionpot module from src/test... [echo] Datafiles defined: ${module.datafiles.present} [echo] Extra files defined: ${module.extrafiles.present} [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: true [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/test-ionpot [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/test-ionpot [copy] Copying 3 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/test-ionpot [javac] Compiling 3 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/test-ionpot [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/dist/jar/cdk-test-ionpot.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/test-ionpot [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/test-ionpot checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's test-qsar module from src/test... [echo] Datafiles defined: ${module.datafiles.present} [echo] Extra files defined: true [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: true [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/test-qsar [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/test-qsar [copy] Copying 6 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/test-qsar [javac] Compiling 6 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/test-qsar [javac] Note: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/test-qsar/org/openscience/cdk/qsar/model/R2/QSARRModelTests.java uses unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/dist/jar/cdk-test-qsar.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/test-qsar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/test-qsar checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's test-qsaratomic module from src/test... [echo] Datafiles defined: ${module.datafiles.present} [echo] Extra files defined: true [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: true [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/test-qsaratomic [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/test-qsaratomic [copy] Copying 33 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/test-qsaratomic [javac] Compiling 33 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/test-qsaratomic [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/dist/jar/cdk-test-qsaratomic.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/test-qsaratomic [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/test-qsaratomic checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's test-qsarbond module from src/test... [echo] Datafiles defined: ${module.datafiles.present} [echo] Extra files defined: true [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: true [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/test-qsarbond [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/test-qsarbond [copy] Copying 9 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/test-qsarbond [javac] Compiling 9 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/test-qsarbond [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/dist/jar/cdk-test-qsarbond.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/test-qsarbond [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/test-qsarbond checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's test-qsarmolecular module from src/test... [echo] Datafiles defined: ${module.datafiles.present} [echo] Extra files defined: true [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: true [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/test-qsarmolecular [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/test-qsarmolecular [copy] Copying 46 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/test-qsarmolecular [javac] Compiling 46 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/test-qsarmolecular [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/dist/jar/cdk-test-qsarmolecular.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/test-qsarmolecular [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/test-qsarmolecular checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's test-experimental module from src/test... [echo] Datafiles defined: ${module.datafiles.present} [echo] Extra files defined: true [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: true [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/test-experimental [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/test-experimental [copy] Copying 7 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/test-experimental [javac] Compiling 7 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/test-experimental [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/dist/jar/cdk-test-experimental.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/test-experimental [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/test-experimental checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's test-qsarprotein module from src/test... [echo] Datafiles defined: ${module.datafiles.present} [echo] Extra files defined: true [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: true [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/test-qsarprotein [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/test-qsarprotein [copy] Copying 3 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/test-qsarprotein [javac] Compiling 3 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/test-qsarprotein [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/dist/jar/cdk-test-qsarprotein.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/test-qsarprotein [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/test-qsarprotein checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's test-pdb module from src/test... [echo] Datafiles defined: ${module.datafiles.present} [echo] Extra files defined: true [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: true [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/test-pdb [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/test-pdb [copy] Copying 4 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/test-pdb [javac] Compiling 4 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/test-pdb [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/dist/jar/cdk-test-pdb.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/test-pdb [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/test-pdb checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's test-inchi module from src/test... [echo] Datafiles defined: ${module.datafiles.present} [echo] Extra files defined: ${module.extrafiles.present} [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: true [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/test-inchi [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/test-inchi [copy] Copying 2 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/test-inchi [javac] Compiling 2 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/test-inchi [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/dist/jar/cdk-test-inchi.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/test-inchi [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/test-inchi checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's test-libiomd module from src/test... [echo] Datafiles defined: ${module.datafiles.present} [echo] Extra files defined: ${module.extrafiles.present} [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: true [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/test-libiomd [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/test-libiomd [copy] Copying 2 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/test-libiomd [javac] Compiling 2 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/test-libiomd [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/dist/jar/cdk-test-libiomd.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/test-libiomd [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/test-libiomd checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's test-libiocml module from src/test... [echo] Datafiles defined: ${module.datafiles.present} [echo] Extra files defined: true [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: true [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/test-libiocml [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/test-libiocml [copy] Copying 5 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/test-libiocml [javac] Compiling 5 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/test-libiocml [javac] Note: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/test-libiocml/org/openscience/cdk/modulesuites/MlibiocmlTests.java uses unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/dist/jar/cdk-test-libiocml.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/test-libiocml [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/test-libiocml checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's test-smarts module from src/test... [echo] Datafiles defined: ${module.datafiles.present} [echo] Extra files defined: true [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: true [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/test-smarts [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/test-smarts [copy] Copying 9 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/test-smarts [javac] Compiling 9 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/test-smarts [javac] Note: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/test-smarts/org/openscience/cdk/modulesuites/MsmartsTests.java uses unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/dist/jar/cdk-test-smarts.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/test-smarts [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/test-smarts checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's test-pcore module from src/test... [echo] Datafiles defined: ${module.datafiles.present} [echo] Extra files defined: true [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: true [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/test-pcore [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/test-pcore [copy] Copying 8 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/test-pcore [javac] Compiling 8 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/test-pcore [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/dist/jar/cdk-test-pcore.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/test-pcore [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/test-pcore checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's test-formula module from src/test... [echo] Datafiles defined: ${module.datafiles.present} [echo] Extra files defined: ${module.extrafiles.present} [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: true [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/test-formula [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/test-formula [copy] Copying 18 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/test-formula [javac] Compiling 18 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/test-formula [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/dist/jar/cdk-test-formula.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/src/test-formula [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/branches/cdk-miguelrojasch-IP/build/test-formula test-all: checkPlatforms: check: noJunit: test-module: [echo] Testing classes for CDK's core module. [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: true [junit] Running org.openscience.cdk.modulesuites.McoreTests [junit] Tests run: 113, Failures: 0, Errors: 0, Time elapsed: 5.567 sec checkPlatforms: check: noJunit: test-module: [echo] Testing classes for CDK's data module. [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: true [junit] Running org.openscience.cdk.modulesuites.MdataTests [junit] Tests run: 700, Failures: 0, Errors: 0, Time elapsed: 1.741 sec checkPlatforms: check: noJunit: test-module: [echo] Testing classes for CDK's datadebug module. [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: true [junit] Running org.openscience.cdk.modulesuites.MdatadebugTests [junit] Tests run: 663, Failures: 0, Errors: 0, Time elapsed: 1.67 sec checkPlatforms: check: noJunit: test-module: [echo] Testing classes for CDK's nonotify module. [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: true [junit] Running org.openscience.cdk.modulesuites.MnonotifyTests [junit] Tests run: 663, Failures: 0, Errors: 0, Time elapsed: 1.778 sec checkPlatforms: check: noJunit: test-module: [echo] Testing classes for CDK's atomtype module. [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: true [junit] Running org.openscience.cdk.modulesuites.MatomtypeTests [junit] Tests run: 183, Failures: 0, Errors: 3, Time elapsed: 2.885 sec [junit] Test org.openscience.cdk.modulesuites.MatomtypeTests FAILED checkPlatforms: check: noJunit: test-module: [echo] Testing classes for CDK's standard module. [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: true [junit] Running org.openscience.cdk.modulesuites.MstandardTests [junit] Tests run: 426, Failures: 2, Errors: 2, Time elapsed: 27.462 sec [junit] Test org.openscience.cdk.modulesuites.MstandardTests FAILED checkPlatforms: check: noJunit: test-module: [echo] Testing classes for CDK's io module. [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: true [junit] Running org.openscience.cdk.modulesuites.MioTests [junit] Tests run: 211, Failures: 1, Errors: 0, Time elapsed: 10.855 sec [junit] Test org.openscience.cdk.modulesuites.MioTests FAILED checkPlatforms: check: noJunit: test-module: [echo] Testing classes for CDK's extra module. [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: true [junit] Running org.openscience.cdk.modulesuites.MextraTests [junit] Tests run: 126, Failures: 1, Errors: 3, Time elapsed: 8.525 sec [junit] Test org.openscience.cdk.modulesuites.MextraTests FAILED checkPlatforms: check: noJunit: test-module: [echo] Testing classes for CDK's builder3d module. [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: true [junit] Running org.openscience.cdk.modulesuites.Mbuilder3dTests [junit] Tests run: 12, Failures: 0, Errors: 11, Time elapsed: 12.398 sec [junit] Test org.openscience.cdk.modulesuites.Mbuilder3dTests FAILED checkPlatforms: check: noJunit: test-module: [echo] Testing classes for CDK's forcefield module. [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: true [junit] Running org.openscience.cdk.modulesuites.MforcefieldTests [junit] Tests run: 15, Failures: 0, Errors: 2, Time elapsed: 14.542 sec [junit] Test org.openscience.cdk.modulesuites.MforcefieldTests FAILED checkPlatforms: check: noJunit: test-module: [echo] Testing classes for CDK's valencycheck module. [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: true [junit] Running org.openscience.cdk.modulesuites.MvalencycheckTests [junit] Tests run: 74, Failures: 0, Errors: 9, Time elapsed: 0.886 sec [junit] Test org.openscience.cdk.modulesuites.MvalencycheckTests FAILED checkPlatforms: check: noJunit: test-module: [echo] Testing classes for CDK's charges module. [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: true [junit] Running org.openscience.cdk.modulesuites.MchargesTests [junit] Tests run: 29, Failures: 0, Errors: 7, Time elapsed: 0.972 sec [junit] Test org.openscience.cdk.modulesuites.MchargesTests FAILED checkPlatforms: check: noJunit: test-module: [echo] Testing classes for CDK's reaction module. [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: true [junit] Running org.openscience.cdk.modulesuites.MreactionTests [junit] Tests run: 639, Failures: 0, Errors: 0, Time elapsed: 13.803 sec checkPlatforms: check: noJunit: test-module: [echo] Testing classes for CDK's smarts module. [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: true [junit] Running org.openscience.cdk.modulesuites.MsmartsTests [junit] Tests run: 817, Failures: 16, Errors: 1, Time elapsed: 8.663 sec [junit] Test org.openscience.cdk.modulesuites.MsmartsTests FAILED checkPlatforms: check: noJunit: test-module: [echo] Testing classes for CDK's smiles module. [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: true [junit] Running org.openscience.cdk.modulesuites.MsmilesTests [junit] Tests run: 136, Failures: 1, Errors: 8, Time elapsed: 6.398 sec [junit] Test org.openscience.cdk.modulesuites.MsmilesTests FAILED checkPlatforms: check: noJunit: test-module: [echo] Testing classes for CDK's experimental module. [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: true [junit] Running org.openscience.cdk.modulesuites.MexperimentalTests [junit] Tests run: 51, Failures: 5, Errors: 6, Time elapsed: 18.21 sec [junit] Test org.openscience.cdk.modulesuites.MexperimentalTests FAILED checkPlatforms: check: noJunit: test-module: [echo] Testing classes for CDK's qsar module. [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: true [junit] Running org.openscience.cdk.modulesuites.MqsarTests [junit] Tests run: 0, Failures: 0, Errors: 0, Time elapsed: 0.005 sec checkPlatforms: check: noJunit: test-module: [echo] Testing classes for CDK's qsaratomic module. [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: true [junit] Running org.openscience.cdk.modulesuites.MqsaratomicTests [junit] Tests run: 396, Failures: 3, Errors: 7, Time elapsed: 40.405 sec [junit] Test org.openscience.cdk.modulesuites.MqsaratomicTests FAILED checkPlatforms: check: noJunit: test-module: [echo] Testing classes for CDK's qsarbond module. [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: true [junit] Running org.openscience.cdk.modulesuites.MqsarbondTests [junit] Tests run: 87, Failures: 0, Errors: 0, Time elapsed: 16.757 sec checkPlatforms: check: noJunit: test-module: [echo] Testing classes for CDK's qsarmolecular module. [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: true [junit] Running org.openscience.cdk.modulesuites.MqsarmolecularTests [junit] Tests run: 533, Failures: 27, Errors: 3, Time elapsed: 12.463 sec [junit] Test org.openscience.cdk.modulesuites.MqsarmolecularTests FAILED checkPlatforms: check: noJunit: test-module: [echo] Testing classes for CDK's qsarprotein module. [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: true [junit] Running org.openscience.cdk.modulesuites.MqsarproteinTests [junit] Tests run: 4, Failures: 0, Errors: 0, Time elapsed: 1.976 sec checkPlatforms: check: noJunit: test-module: [echo] Testing classes for CDK's pdb module. [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: true [junit] Running org.openscience.cdk.modulesuites.MpdbTests [junit] Tests run: 14, Failures: 0, Errors: 0, Time elapsed: 4.345 sec checkPlatforms: check: noJunit: test-module: [echo] Testing classes for CDK's pcore module. [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: true [junit] Running org.openscience.cdk.modulesuites.MpcoreTests [junit] Tests run: 9, Failures: 0, Errors: 1, Time elapsed: 3.056 sec [junit] Test org.openscience.cdk.modulesuites.MpcoreTests FAILED checkPlatforms: check: noJunit: test-module: [echo] Testing classes for CDK's inchi module. [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: true [junit] Running org.openscience.cdk.modulesuites.MinchiTests [junit] Tests run: 10, Failures: 0, Errors: 0, Time elapsed: 1.304 sec checkPlatforms: check: noJunit: test-module: [echo] Testing classes for CDK's structgen module. [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: true [junit] Running org.openscience.cdk.modulesuites.MstructgenTests [junit] Tests run: 48, Failures: 10, Errors: 0, Time elapsed: 9.792 sec [junit] Test org.openscience.cdk.modulesuites.MstructgenTests FAILED checkPlatforms: check: noJunit: test-module: [echo] Testing classes for CDK's libiomd module. [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: true [junit] Running org.openscience.cdk.modulesuites.MlibiomdTests [junit] Tests run: 3, Failures: 0, Errors: 0, Time elapsed: 0.894 sec checkPlatforms: check: noJunit: test-module: [echo] Testing classes for CDK's libiocml module. [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: true [junit] Running org.openscience.cdk.modulesuites.MlibiocmlTests [junit] Tests run: 63, Failures: 2, Errors: 1, Time elapsed: 2.135 sec [junit] Test org.openscience.cdk.modulesuites.MlibiocmlTests FAILED checkPlatforms: check: noJunit: test-module: [echo] Testing classes for CDK's formula module. [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: true [junit] Running org.openscience.cdk.modulesuites.MformulaTests [junit] Tests run: 156, Failures: 0, Errors: 1, Time elapsed: 3.359 sec [junit] Test org.openscience.cdk.modulesuites.MformulaTests FAILED BUILD SUCCESSFUL Total time: 6 minutes 57 seconds

[trunk.ant.log]

checkPlatforms: check: noJunit: dist-all: checkPlatforms: check: setupBuildDir: [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/sourcedist [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/dist [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/reports init: javacc: [echo] Compiling Ant 1.6 depending classes. [javacc] Java Compiler Compiler Version 3.2 (Parser Generator) [javacc] (type "javacc" with no arguments for help) [javacc] Reading from file /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/src/main/org/openscience/cdk/iupac/parser/NomParser.jj . . . [javacc] File "TokenMgrError.java" does not exist. Will create one. [javacc] File "ParseException.java" does not exist. Will create one. [javacc] File "Token.java" does not exist. Will create one. [javacc] File "SimpleCharStream.java" does not exist. Will create one. [javacc] Parser generated successfully. [javacc] Java Compiler Compiler Version 3.2 (Parser Generator) [javacc] (type "javacc" with no arguments for help) [javacc] Reading from file /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/src/main/org/openscience/cdk/smiles/smarts/parser/SMARTSParser.jj . . . [javacc] File "TokenMgrError.java" does not exist. Will create one. [javacc] File "ParseException.java" does not exist. Will create one. [javacc] File "Token.java" does not exist. Will create one. [javacc] File "SimpleCharStream.java" does not exist. Will create one. [javacc] Parser generated successfully. customize: runDoclet: [echo] Not skipping doclet run... [javac] Compiling 1 source file to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build compile-init: checkPlatforms: check: dist.init: [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/dist/jar compile-needed-test: compile-module: [echo] Compiling classes for CDK's interfaces module from src/main... [echo] Datafiles defined: ${module.datafiles.present} [echo] Extra files defined: ${module.extrafiles.present} [echo] CDK dependencies defined: ${module.cdkdepends.present} [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: ${module.devellibdepends.present} [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/interfaces [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/interfaces [copy] Copying 46 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/interfaces [javac] Compiling 46 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/interfaces [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/dist/jar/cdk-interfaces.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/interfaces [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/interfaces checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's core module from src/main... [echo] Datafiles defined: true [echo] Extra files defined: ${module.extrafiles.present} [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: ${module.devellibdepends.present} [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/core [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/core [copy] Copying 19 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/core [javac] Compiling 19 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/core [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/dist/jar/cdk-core.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/core [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/core checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's atomtype module from src/main... [echo] Datafiles defined: ${module.datafiles.present} [echo] Extra files defined: ${module.extrafiles.present} [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: ${module.devellibdepends.present} [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/atomtype [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/atomtype [copy] Copying 5 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/atomtype [javac] Compiling 5 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/atomtype [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/dist/jar/cdk-atomtype.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/atomtype [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/atomtype checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's standard module from src/main... [echo] Datafiles defined: ${module.datafiles.present} [echo] Extra files defined: ${module.extrafiles.present} [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: ${module.devellibdepends.present} [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/standard [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/standard [copy] Copying 80 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/standard [javac] Compiling 80 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/standard [javac] Note: Some input files use unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/dist/jar/cdk-standard.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/standard [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/standard checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's dict module from src/main... [echo] Datafiles defined: ${module.datafiles.present} [echo] Extra files defined: ${module.extrafiles.present} [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: ${module.devellibdepends.present} [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/dict [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/dict [copy] Copying 8 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/dict [javac] Compiling 8 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/dict [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/dist/jar/cdk-dict.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/dict [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/dict checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's data module from src/main... [echo] Datafiles defined: ${module.datafiles.present} [echo] Extra files defined: ${module.extrafiles.present} [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: ${module.devellibdepends.present} [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/data [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/data [copy] Copying 38 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/data [javac] Compiling 38 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/data [javac] Note: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/data/org/openscience/cdk/protein/data/PDBPolymer.java uses unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/dist/jar/cdk-data.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/data [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/data checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's render module from src/main... [echo] Datafiles defined: ${module.datafiles.present} [echo] Extra files defined: ${module.extrafiles.present} [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: ${module.devellibdepends.present} [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/render [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/render [copy] Copying 17 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/render [javac] Compiling 17 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/render [javac] Note: Some input files use unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/dist/jar/cdk-render.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/render [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/render checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's io module from src/main... [echo] Datafiles defined: true [echo] Extra files defined: ${module.extrafiles.present} [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: ${module.devellibdepends.present} [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/io [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/io [copy] Copying 168 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/io [javac] Compiling 168 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/io [javac] Note: Some input files use unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/dist/jar/cdk-io.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/io [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/io checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's valencycheck module from src/main... [echo] Datafiles defined: ${module.datafiles.present} [echo] Extra files defined: ${module.extrafiles.present} [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: ${module.devellibdepends.present} [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/valencycheck [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/valencycheck [copy] Copying 8 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/valencycheck [javac] Compiling 8 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/valencycheck [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/dist/jar/cdk-valencycheck.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/valencycheck [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/valencycheck checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's sdg module from src/main... [echo] Datafiles defined: ${module.datafiles.present} [echo] Extra files defined: ${module.extrafiles.present} [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: ${module.devellibdepends.present} [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/sdg [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/sdg [copy] Copying 6 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/sdg [javac] Compiling 6 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/sdg [javac] Note: Some input files use unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/dist/jar/cdk-sdg.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/sdg [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/sdg checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's control module from src/main... [echo] Datafiles defined: ${module.datafiles.present} [echo] Extra files defined: ${module.extrafiles.present} [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: ${module.devellibdepends.present} [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/control [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/control [copy] Copying 14 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/control [javac] Compiling 14 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/control [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/dist/jar/cdk-control.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/control [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/control checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's datadebug module from src/main... [echo] Datafiles defined: ${module.datafiles.present} [echo] Extra files defined: ${module.extrafiles.present} [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: ${module.devellibdepends.present} [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/datadebug [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/datadebug [copy] Copying 36 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/datadebug [javac] Compiling 36 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/datadebug [javac] /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/datadebug/org/openscience/cdk/debug/DebugAminoAcid.java:265: warning: [deprecation] getBondOrderSum(org.openscience.cdk.interfaces.IAtom) in org.openscience.cdk.AtomContainer has been deprecated [javac] public double getBondOrderSum(IAtom atom) { [javac] ^ [javac] /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/datadebug/org/openscience/cdk/debug/DebugAminoAcid.java:267: warning: [deprecation] getBondOrderSum(org.openscience.cdk.interfaces.IAtom) in org.openscience.cdk.AtomContainer has been deprecated [javac] return super.getBondOrderSum(atom); [javac] ^ [javac] /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/datadebug/org/openscience/cdk/debug/DebugAtomContainer.java:276: warning: [deprecation] getBondOrderSum(org.openscience.cdk.interfaces.IAtom) in org.openscience.cdk.AtomContainer has been deprecated [javac] public double getBondOrderSum(IAtom atom) { [javac] ^ [javac] /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/datadebug/org/openscience/cdk/debug/DebugAtomContainer.java:278: warning: [deprecation] getBondOrderSum(org.openscience.cdk.interfaces.IAtom) in org.openscience.cdk.AtomContainer has been deprecated [javac] return super.getBondOrderSum(atom); [javac] ^ [javac] /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/datadebug/org/openscience/cdk/debug/DebugBioPolymer.java:268: warning: [deprecation] getBondOrderSum(org.openscience.cdk.interfaces.IAtom) in org.openscience.cdk.AtomContainer has been deprecated [javac] public double getBondOrderSum(IAtom atom) { [javac] ^ [javac] /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/datadebug/org/openscience/cdk/debug/DebugBioPolymer.java:270: warning: [deprecation] getBondOrderSum(org.openscience.cdk.interfaces.IAtom) in org.openscience.cdk.AtomContainer has been deprecated [javac] return super.getBondOrderSum(atom); [javac] ^ [javac] /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/datadebug/org/openscience/cdk/debug/DebugCrystal.java:277: warning: [deprecation] getBondOrderSum(org.openscience.cdk.interfaces.IAtom) in org.openscience.cdk.AtomContainer has been deprecated [javac] public double getBondOrderSum(IAtom atom) { [javac] ^ [javac] /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/datadebug/org/openscience/cdk/debug/DebugCrystal.java:279: warning: [deprecation] getBondOrderSum(org.openscience.cdk.interfaces.IAtom) in org.openscience.cdk.AtomContainer has been deprecated [javac] return super.getBondOrderSum(atom); [javac] ^ [javac] /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/datadebug/org/openscience/cdk/debug/DebugMolecule.java:277: warning: [deprecation] getBondOrderSum(org.openscience.cdk.interfaces.IAtom) in org.openscience.cdk.AtomContainer has been deprecated [javac] public double getBondOrderSum(IAtom atom) { [javac] ^ [javac] /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/datadebug/org/openscience/cdk/debug/DebugMolecule.java:279: warning: [deprecation] getBondOrderSum(org.openscience.cdk.interfaces.IAtom) in org.openscience.cdk.AtomContainer has been deprecated [javac] return super.getBondOrderSum(atom); [javac] ^ [javac] /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/datadebug/org/openscience/cdk/debug/DebugMonomer.java:265: warning: [deprecation] getBondOrderSum(org.openscience.cdk.interfaces.IAtom) in org.openscience.cdk.AtomContainer has been deprecated [javac] public double getBondOrderSum(IAtom atom) { [javac] ^ [javac] /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/datadebug/org/openscience/cdk/debug/DebugMonomer.java:267: warning: [deprecation] getBondOrderSum(org.openscience.cdk.interfaces.IAtom) in org.openscience.cdk.AtomContainer has been deprecated [javac] return super.getBondOrderSum(atom); [javac] ^ [javac] /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/datadebug/org/openscience/cdk/debug/DebugPolymer.java:267: warning: [deprecation] getBondOrderSum(org.openscience.cdk.interfaces.IAtom) in org.openscience.cdk.AtomContainer has been deprecated [javac] public double getBondOrderSum(IAtom atom) { [javac] ^ [javac] /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/datadebug/org/openscience/cdk/debug/DebugPolymer.java:269: warning: [deprecation] getBondOrderSum(org.openscience.cdk.interfaces.IAtom) in org.openscience.cdk.AtomContainer has been deprecated [javac] return super.getBondOrderSum(atom); [javac] ^ [javac] /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/datadebug/org/openscience/cdk/debug/DebugRing.java:290: warning: [deprecation] getBondOrderSum(org.openscience.cdk.interfaces.IAtom) in org.openscience.cdk.AtomContainer has been deprecated [javac] public double getBondOrderSum(IAtom atom) { [javac] ^ [javac] /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/datadebug/org/openscience/cdk/debug/DebugRing.java:292: warning: [deprecation] getBondOrderSum(org.openscience.cdk.interfaces.IAtom) in org.openscience.cdk.AtomContainer has been deprecated [javac] return super.getBondOrderSum(atom); [javac] ^ [javac] /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/datadebug/org/openscience/cdk/debug/DebugStrand.java:268: warning: [deprecation] getBondOrderSum(org.openscience.cdk.interfaces.IAtom) in org.openscience.cdk.AtomContainer has been deprecated [javac] public double getBondOrderSum(IAtom atom) { [javac] ^ [javac] /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/datadebug/org/openscience/cdk/debug/DebugStrand.java:270: warning: [deprecation] getBondOrderSum(org.openscience.cdk.interfaces.IAtom) in org.openscience.cdk.AtomContainer has been deprecated [javac] return super.getBondOrderSum(atom); [javac] ^ [javac] Note: Some input files use unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [javac] 18 warnings [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/dist/jar/cdk-datadebug.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/datadebug [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/datadebug checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's nonotify module from src/main... [echo] Datafiles defined: ${module.datafiles.present} [echo] Extra files defined: ${module.extrafiles.present} [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: ${module.devellibdepends.present} [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/nonotify [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/nonotify [copy] Copying 36 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/nonotify [javac] Compiling 36 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/nonotify [javac] Note: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/nonotify/org/openscience/cdk/nonotify/NNPDBPolymer.java uses unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/dist/jar/cdk-nonotify.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/nonotify [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/nonotify checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's formula module from src/main... [echo] Datafiles defined: ${module.datafiles.present} [echo] Extra files defined: ${module.extrafiles.present} [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: ${module.devellibdepends.present} [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/formula [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/formula [copy] Copying 16 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/formula [javac] Compiling 16 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/formula [javac] Note: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/formula/org/openscience/cdk/formula/rules/IsotopePatternRule.java uses unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/dist/jar/cdk-formula.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/formula [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/formula checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's structgen module from src/main... [echo] Datafiles defined: ${module.datafiles.present} [echo] Extra files defined: ${module.extrafiles.present} [echo] CDK dependencies defined: true [echo] Library dependencies defined: ${module.libdepends.present} [echo] Developer Library dependencies defined: ${module.devellibdepends.present} [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/structgen [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/structgen [copy] Copying 11 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/structgen [javac] Compiling 11 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/structgen [javac] Note: Some input files use unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/dist/jar/cdk-structgen.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/structgen [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/structgen checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's pdb module from src/main... [echo] Datafiles defined: ${module.datafiles.present} [echo] Extra files defined: true [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: ${module.devellibdepends.present} [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/pdb [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/pdb [copy] Copying 4 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/pdb [javac] Compiling 4 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/pdb [javac] Note: Some input files use unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/dist/jar/cdk-pdb.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/pdb [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/pdb checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's isomorphism module from src/main... [echo] Datafiles defined: ${module.datafiles.present} [echo] Extra files defined: ${module.extrafiles.present} [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: ${module.devellibdepends.present} [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/isomorphism [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/isomorphism [copy] Copying 15 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/isomorphism [javac] Compiling 15 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/isomorphism [javac] Note: Some input files use unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/dist/jar/cdk-isomorphism.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/isomorphism [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/isomorphism checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's extra module from src/main... [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} [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/extra [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/extra [copy] Copying 118 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/extra [javac] Compiling 118 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/extra [javac] /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/extra/org/openscience/cdk/applications/swing/JExternalFrame.java:87: warning: [deprecation] show() in java.awt.Window has been deprecated [javac] super.show(); [javac] ^ [javac] /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/extra/org/openscience/cdk/validate/BasicValidator.java:318: warning: [deprecation] getBondOrderSum(org.openscience.cdk.interfaces.IAtom) in org.openscience.cdk.AtomContainer has been deprecated [javac] int bos = (int)molecule.getBondOrderSum(atom); [javac] ^ [javac] Note: Some input files use unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [javac] 2 warnings [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/dist/jar/cdk-extra.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/extra [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/extra checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's smiles module from src/main... [echo] Datafiles defined: ${module.datafiles.present} [echo] Extra files defined: ${module.extrafiles.present} [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: ${module.devellibdepends.present} [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/smiles [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/smiles [copy] Copying 7 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/smiles [javac] Compiling 7 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/smiles [javac] Note: Some input files use unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/dist/jar/cdk-smiles.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/smiles [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/smiles checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's libiocml module from src/main... [echo] Datafiles defined: ${module.datafiles.present} [echo] Extra files defined: ${module.extrafiles.present} [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: ${module.devellibdepends.present} [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/libiocml [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/libiocml [copy] Copying 3 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/libiocml [javac] Compiling 3 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/libiocml [javac] Note: Some input files use unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/dist/jar/cdk-libiocml.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/libiocml [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/libiocml checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's libiomd module from src/main... [echo] Datafiles defined: ${module.datafiles.present} [echo] Extra files defined: ${module.extrafiles.present} [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: ${module.devellibdepends.present} [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/libiomd [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/libiomd [copy] Copying 5 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/libiomd [javac] Compiling 5 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/libiomd [javac] Note: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/libiomd/org/openscience/cdk/libio/md/MDMolecule.java uses unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/dist/jar/cdk-libiomd.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/libiomd [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/libiomd checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's pdb-cml module from src/main... [echo] Datafiles defined: ${module.datafiles.present} [echo] Extra files defined: ${module.extrafiles.present} [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: ${module.devellibdepends.present} [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/pdb-cml [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/pdb-cml [copy] Copying 1 file to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/pdb-cml [javac] Compiling 1 source file to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/pdb-cml [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/dist/jar/cdk-pdb-cml.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/pdb-cml [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/pdb-cml checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's reaction module from src/main... [echo] Datafiles defined: ${module.datafiles.present} [echo] Extra files defined: ${module.extrafiles.present} [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: ${module.devellibdepends.present} [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/reaction [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/reaction [copy] Copying 50 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/reaction [javac] Compiling 50 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/reaction [javac] Note: Some input files use unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/dist/jar/cdk-reaction.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/reaction [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/reaction checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's charges module from src/main... [echo] Datafiles defined: ${module.datafiles.present} [echo] Extra files defined: ${module.extrafiles.present} [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: ${module.devellibdepends.present} [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/charges [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/charges [copy] Copying 6 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/charges [javac] Compiling 6 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/charges [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/dist/jar/cdk-charges.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/charges [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/charges checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's qsar module from src/main... [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} [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/qsar [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/qsar [copy] Copying 30 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/qsar [javac] Compiling 30 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/qsar [javac] /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/qsar/org/openscience/cdk/qsar/model/R/CNNRegressionModel.java:442: warning: [deprecation] org.openscience.cdk.qsar.model.R.CNNRegressionModelSummary in org.openscience.cdk.qsar.model.R has been deprecated [javac] public CNNRegressionModelSummary summary() throws QSARModelException { [javac] ^ [javac] /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/qsar/org/openscience/cdk/qsar/model/R/LinearRegressionModel.java:381: warning: [deprecation] org.openscience.cdk.qsar.model.R.LinearRegressionModelSummary in org.openscience.cdk.qsar.model.R has been deprecated [javac] public LinearRegressionModelSummary summary() throws QSARModelException { [javac] ^ [javac] /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/qsar/org/openscience/cdk/qsar/descriptors/atompair/PiContactDetectionDescriptor.java:177: warning: [deprecation] DescriptorValue(org.openscience.cdk.qsar.DescriptorSpecification,java.lang.String[],java.lang.Object[],org.openscience.cdk.qsar.result.IDescriptorResult) in org.openscience.cdk.qsar.DescriptorValue has been deprecated [javac] return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(), new BooleanResult(piContact)); [javac] ^ [javac] /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/qsar/org/openscience/cdk/qsar/model/R/PLSRegressionModelFit.java:111: warning: [deprecation] org.openscience.cdk.qsar.model.R.V2M in org.openscience.cdk.qsar.model.R has been deprecated [javac] this.rms = V2M.VectorToMatrix(rms, ncase, npvar); [javac] ^ [javac] /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/qsar/org/openscience/cdk/qsar/model/R/PLSRegressionModelFit.java:112: warning: [deprecation] org.openscience.cdk.qsar.model.R.V2M in org.openscience.cdk.qsar.model.R has been deprecated [javac] this.xscores = V2M.VectorToMatrix(xscores, nobs, maxncomp); [javac] ^ [javac] /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/qsar/org/openscience/cdk/qsar/model/R/PLSRegressionModelFit.java:113: warning: [deprecation] org.openscience.cdk.qsar.model.R.V2M in org.openscience.cdk.qsar.model.R has been deprecated [javac] this.yscores = V2M.VectorToMatrix(yscores, nobs, maxncomp); [javac] ^ [javac] /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/qsar/org/openscience/cdk/qsar/model/R/PLSRegressionModelFit.java:114: warning: [deprecation] org.openscience.cdk.qsar.model.R.V2M in org.openscience.cdk.qsar.model.R has been deprecated [javac] this.yload = V2M.VectorToMatrix(yload, npvar, maxncomp); [javac] ^ [javac] /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/qsar/org/openscience/cdk/qsar/model/R/PLSRegressionModelFit.java:115: warning: [deprecation] org.openscience.cdk.qsar.model.R.V2M in org.openscience.cdk.qsar.model.R has been deprecated [javac] this.xload = V2M.VectorToMatrix(xload, nvar, maxncomp); [javac] ^ [javac] /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/qsar/org/openscience/cdk/qsar/model/R/PLSRegressionModelFit.java:116: warning: [deprecation] org.openscience.cdk.qsar.model.R.V2M in org.openscience.cdk.qsar.model.R has been deprecated [javac] this.ypred = V2M.VectorToCube(ypred, ncase, nobs, npvar); [javac] ^ [javac] /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/qsar/org/openscience/cdk/qsar/model/R/PLSRegressionModelFit.java:117: warning: [deprecation] org.openscience.cdk.qsar.model.R.V2M in org.openscience.cdk.qsar.model.R has been deprecated [javac] this.B = V2M.VectorToCube(B, ncase, nvar, npvar); [javac] ^ [javac] /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/qsar/org/openscience/cdk/qsar/model/R/PLSRegressionModelFit.java:143: warning: [deprecation] org.openscience.cdk.qsar.model.R.V2M in org.openscience.cdk.qsar.model.R has been deprecated [javac] this.rms = V2M.VectorToMatrix(rms, ncase, npvar); [javac] ^ [javac] /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/qsar/org/openscience/cdk/qsar/model/R/PLSRegressionModelFit.java:144: warning: [deprecation] org.openscience.cdk.qsar.model.R.V2M in org.openscience.cdk.qsar.model.R has been deprecated [javac] this.rmssd = V2M.VectorToMatrix(rmssd, ncase, npvar); [javac] ^ [javac] /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/qsar/org/openscience/cdk/qsar/model/R/PLSRegressionModelFit.java:145: warning: [deprecation] org.openscience.cdk.qsar.model.R.V2M in org.openscience.cdk.qsar.model.R has been deprecated [javac] this.r2 = V2M.VectorToMatrix(r2, ncase, npvar);; [javac] ^ [javac] /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/qsar/org/openscience/cdk/qsar/model/R/PLSRegressionModelFit.java:146: warning: [deprecation] org.openscience.cdk.qsar.model.R.V2M in org.openscience.cdk.qsar.model.R has been deprecated [javac] this.ypred = V2M.VectorToCube(ypred, ncase, nobs, npvar); [javac] ^ [javac] Note: Some input files use unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [javac] 14 warnings [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/dist/jar/cdk-qsar.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/qsar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/qsar checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's qsaratomic module from src/main... [echo] Datafiles defined: ${module.datafiles.present} [echo] Extra files defined: ${module.extrafiles.present} [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: ${module.devellibdepends.present} [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/qsaratomic [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/qsaratomic [copy] Copying 26 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/qsaratomic [javac] Compiling 26 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/qsaratomic [javac] /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/qsaratomic/org/openscience/cdk/qsar/descriptors/atomic/AtomHybridizationVSEPRDescriptor.java:196: warning: [deprecation] DescriptorValue(org.openscience.cdk.qsar.DescriptorSpecification,java.lang.String[],java.lang.Object[],org.openscience.cdk.qsar.result.IDescriptorResult) in org.openscience.cdk.qsar.DescriptorValue has been deprecated [javac] return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(), new IntegerResult(hybridizationCDK)); [javac] ^ [javac] /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/qsaratomic/org/openscience/cdk/qsar/descriptors/atomic/AtomValenceDescriptor.java:167: warning: [deprecation] DescriptorValue(org.openscience.cdk.qsar.DescriptorSpecification,java.lang.String[],java.lang.Object[],org.openscience.cdk.qsar.result.IDescriptorResult) in org.openscience.cdk.qsar.DescriptorValue has been deprecated [javac] return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(), new IntegerResult(atomValence)); [javac] ^ [javac] /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/qsaratomic/org/openscience/cdk/qsar/descriptors/atomic/BondsToAtomDescriptor.java:149: warning: [deprecation] DescriptorValue(org.openscience.cdk.qsar.DescriptorSpecification,java.lang.String[],java.lang.Object[],org.openscience.cdk.qsar.result.IDescriptorResult) in org.openscience.cdk.qsar.DescriptorValue has been deprecated [javac] return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(), new IntegerResult(bondsToAtom)); [javac] ^ [javac] /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/qsaratomic/org/openscience/cdk/qsar/descriptors/atomic/CovalentRadiusDescriptor.java:155: warning: [deprecation] DescriptorValue(org.openscience.cdk.qsar.DescriptorSpecification,java.lang.String[],java.lang.Object[],org.openscience.cdk.qsar.result.IDescriptorResult) in org.openscience.cdk.qsar.DescriptorValue has been deprecated [javac] return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(), new DoubleResult(covalentradius)); [javac] ^ [javac] /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/qsaratomic/org/openscience/cdk/qsar/descriptors/atomic/DistanceToAtomDescriptor.java:141: warning: [deprecation] DescriptorValue(org.openscience.cdk.qsar.DescriptorSpecification,java.lang.String[],java.lang.Object[],org.openscience.cdk.qsar.result.IDescriptorResult) in org.openscience.cdk.qsar.DescriptorValue has been deprecated [javac] return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(), new DoubleResult(distanceToAtom)); [javac] ^ [javac] /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/qsaratomic/org/openscience/cdk/qsar/descriptors/atomic/EffectiveAtomPolarizabilityDescriptor.java:128: warning: [deprecation] DescriptorValue(org.openscience.cdk.qsar.DescriptorSpecification,java.lang.String[],java.lang.Object[],org.openscience.cdk.qsar.result.IDescriptorResult) in org.openscience.cdk.qsar.DescriptorValue has been deprecated [javac] return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(), new DoubleResult(polarizability)); [javac] ^ [javac] /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/qsaratomic/org/openscience/cdk/qsar/descriptors/atomic/InductiveAtomicHardnessDescriptor.java:216: warning: [deprecation] DescriptorValue(org.openscience.cdk.qsar.DescriptorSpecification,java.lang.String[],java.lang.Object[],org.openscience.cdk.qsar.result.IDescriptorResult) in org.openscience.cdk.qsar.DescriptorValue has been deprecated [javac] return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(), new DoubleResult(atomicHardness)); [javac] ^ [javac] /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/qsaratomic/org/openscience/cdk/qsar/descriptors/atomic/InductiveAtomicSoftnessDescriptor.java:214: warning: [deprecation] DescriptorValue(org.openscience.cdk.qsar.DescriptorSpecification,java.lang.String[],java.lang.Object[],org.openscience.cdk.qsar.result.IDescriptorResult) in org.openscience.cdk.qsar.DescriptorValue has been deprecated [javac] return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(), new DoubleResult(atomicSoftness)); [javac] ^ [javac] /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/qsaratomic/org/openscience/cdk/qsar/descriptors/atomic/IsProtonInAromaticSystemDescriptor.java:177: warning: [deprecation] DescriptorValue(org.openscience.cdk.qsar.DescriptorSpecification,java.lang.String[],java.lang.Object[],org.openscience.cdk.qsar.result.IDescriptorResult) in org.openscience.cdk.qsar.DescriptorValue has been deprecated [javac] return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(), new IntegerResult(isProtonInAromaticSystem)); [javac] ^ [javac] /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/qsaratomic/org/openscience/cdk/qsar/descriptors/atomic/IsProtonInConjugatedPiSystemDescriptor.java:171: warning: [deprecation] DescriptorValue(org.openscience.cdk.qsar.DescriptorSpecification,java.lang.String[],java.lang.Object[],org.openscience.cdk.qsar.result.IDescriptorResult) in org.openscience.cdk.qsar.DescriptorValue has been deprecated [javac] return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(), new BooleanResult(isProtonInPiSystem)); [javac] ^ [javac] /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/qsaratomic/org/openscience/cdk/qsar/descriptors/atomic/PartialSigmaChargeDescriptor.java:159: warning: [deprecation] DescriptorValue(org.openscience.cdk.qsar.DescriptorSpecification,java.lang.String[],java.lang.Object[],org.openscience.cdk.qsar.result.IDescriptorResult) in org.openscience.cdk.qsar.DescriptorValue has been deprecated [javac] ? new DescriptorValue(getSpecification(), getParameterNames(), getParameters(), getCachedDescriptorValue(atom)) [javac] ^ [javac] /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/qsaratomic/org/openscience/cdk/qsar/descriptors/atomic/PeriodicTablePositionDescriptor.java:167: warning: [deprecation] DescriptorValue(org.openscience.cdk.qsar.DescriptorSpecification,java.lang.String[],java.lang.Object[],org.openscience.cdk.qsar.result.IDescriptorResult) in org.openscience.cdk.qsar.DescriptorValue has been deprecated [javac] return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(), new IntegerResult(period)); [javac] ^ [javac] /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/qsaratomic/org/openscience/cdk/qsar/descriptors/atomic/ProtonTotalPartialChargeDescriptor.java:144: warning: [deprecation] DescriptorValue(org.openscience.cdk.qsar.DescriptorSpecification,java.lang.String[],java.lang.Object[],org.openscience.cdk.qsar.result.IDescriptorResult) in org.openscience.cdk.qsar.DescriptorValue has been deprecated [javac] return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(), protonPartialCharge); [javac] ^ [javac] /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/qsaratomic/org/openscience/cdk/qsar/descriptors/atomic/VdWRadiusDescriptor.java:153: warning: [deprecation] DescriptorValue(org.openscience.cdk.qsar.DescriptorSpecification,java.lang.String[],java.lang.Object[],org.openscience.cdk.qsar.result.IDescriptorResult) in org.openscience.cdk.qsar.DescriptorValue has been deprecated [javac] return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(), new DoubleResult(vdwradius)); [javac] ^ [javac] Note: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/qsaratomic/org/openscience/cdk/qsar/descriptors/atomic/AtomValenceDescriptor.java uses unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [javac] 14 warnings [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/dist/jar/cdk-qsaratomic.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/qsaratomic [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/qsaratomic checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's qsarbond module from src/main... [echo] Datafiles defined: ${module.datafiles.present} [echo] Extra files defined: ${module.extrafiles.present} [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: ${module.devellibdepends.present} [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/qsarbond [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/qsarbond [copy] Copying 5 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/qsarbond [javac] Compiling 5 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/qsarbond [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/dist/jar/cdk-qsarbond.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/qsarbond [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/qsarbond checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's qsarmolecular module from src/main... [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} [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/qsarmolecular [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/qsarmolecular [copy] Copying 45 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/qsarmolecular [javac] Compiling 45 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/qsarmolecular [javac] /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/qsarmolecular/org/openscience/cdk/qsar/descriptors/atomic/IPAtomicDescriptor.java:204: warning: [deprecation] DescriptorValue(org.openscience.cdk.qsar.DescriptorSpecification,java.lang.String[],java.lang.Object[],org.openscience.cdk.qsar.result.IDescriptorResult) in org.openscience.cdk.qsar.DescriptorValue has been deprecated [javac] return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(), new DoubleResult(resultD)); [javac] ^ [javac] Note: Some input files use unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [javac] 1 warning [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/dist/jar/cdk-qsarmolecular.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/qsarmolecular [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/qsarmolecular checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's qsarprotein module from src/main... [echo] Datafiles defined: ${module.datafiles.present} [echo] Extra files defined: ${module.extrafiles.present} [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: ${module.devellibdepends.present} [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/qsarprotein [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/qsarprotein [copy] Copying 2 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/qsarprotein [javac] Compiling 2 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/qsarprotein [javac] /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/qsarprotein/org/openscience/cdk/qsar/descriptors/protein/TaeAminoAcidDescriptor.java:300: warning: [deprecation] DescriptorValue(org.openscience.cdk.qsar.DescriptorSpecification,java.lang.String[],java.lang.Object[],org.openscience.cdk.qsar.result.IDescriptorResult) in org.openscience.cdk.qsar.DescriptorValue has been deprecated [javac] return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(), retval); [javac] ^ [javac] Note: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/qsarprotein/org/openscience/cdk/qsar/descriptors/protein/TaeAminoAcidDescriptor.java uses unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [javac] 1 warning [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/dist/jar/cdk-qsarprotein.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/qsarprotein [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/qsarprotein checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's qsar-cml module from src/main... [echo] Datafiles defined: ${module.datafiles.present} [echo] Extra files defined: ${module.extrafiles.present} [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: ${module.devellibdepends.present} [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/qsar-cml [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/qsar-cml [copy] Copying 1 file to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/qsar-cml [javac] Compiling 1 source file to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/qsar-cml [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/dist/jar/cdk-qsar-cml.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/qsar-cml [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/qsar-cml checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's forcefield module from src/main... [echo] Datafiles defined: true [echo] Extra files defined: ${module.extrafiles.present} [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: ${module.devellibdepends.present} [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/forcefield [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/forcefield [copy] Copying 23 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/forcefield [javac] Compiling 23 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/forcefield [javac] Note: Some input files use unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/dist/jar/cdk-forcefield.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/forcefield [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/forcefield checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's builder3d module from src/main... [echo] Datafiles defined: true [echo] Extra files defined: ${module.extrafiles.present} [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: ${module.devellibdepends.present} [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/builder3d [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/builder3d [copy] Copying 5 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/builder3d [javac] Compiling 5 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/builder3d [javac] /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/builder3d/org/openscience/cdk/qsar/descriptors/atomic/PartialTChargeMMFF94Descriptor.java:130: warning: [deprecation] DescriptorValue(org.openscience.cdk.qsar.DescriptorSpecification,java.lang.String[],java.lang.Object[],org.openscience.cdk.qsar.result.IDescriptorResult) in org.openscience.cdk.qsar.DescriptorValue has been deprecated [javac] return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(), aphaPartialCharge); [javac] ^ [javac] Note: Some input files use unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [javac] 1 warning [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/dist/jar/cdk-builder3d.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/builder3d [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/builder3d checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's builder3dtools module from src/main... [echo] Datafiles defined: ${module.datafiles.present} [echo] Extra files defined: ${module.extrafiles.present} [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: ${module.devellibdepends.present} [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/builder3dtools [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/builder3dtools [copy] Copying 1 file to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/builder3dtools [javac] Compiling 1 source file to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/builder3dtools [javac] Note: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/builder3dtools/org/openscience/cdk/modeling/builder3d/TemplateExtractor.java uses unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/dist/jar/cdk-builder3dtools.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/builder3dtools [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/builder3dtools checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's smarts module from src/main... [echo] Datafiles defined: ${module.datafiles.present} [echo] Extra files defined: ${module.extrafiles.present} [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: ${module.devellibdepends.present} [echo] Autogenerated files specified: true [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/smarts [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/smarts [copy] Copying 52 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/smarts [javac] Compiling 52 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/smarts [javac] Note: Some input files use unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [copy] Copying 1 file to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/dist/jar/cdk-smarts.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/smarts [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/smarts checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's experimental module from src/main... [echo] Datafiles defined: ${module.datafiles.present} [echo] Extra files defined: ${module.extrafiles.present} [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: ${module.devellibdepends.present} [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/experimental [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/experimental [copy] Copying 22 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/experimental [javac] Compiling 22 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/experimental [javac] Note: Some input files use unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/dist/jar/cdk-experimental.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/experimental [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/experimental checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's pcore module from src/main... [echo] Datafiles defined: ${module.datafiles.present} [echo] Extra files defined: ${module.extrafiles.present} [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: ${module.devellibdepends.present} [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/pcore [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/pcore [copy] Copying 6 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/pcore [javac] Compiling 6 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/pcore [javac] Note: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/pcore/org/openscience/cdk/pharmacophore/PharmacophoreMatcher.java uses unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/dist/jar/cdk-pcore.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/pcore [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/pcore checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's applications module from src/main... [echo] Datafiles defined: true [echo] Extra files defined: ${module.extrafiles.present} [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: ${module.devellibdepends.present} [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/applications [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/applications [copy] Copying 26 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/applications [javac] Compiling 26 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/applications [javac] Note: Some input files use unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/dist/jar/cdk-applications.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/applications [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/applications checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's inchi module from src/main... [echo] Datafiles defined: ${module.datafiles.present} [echo] Extra files defined: ${module.extrafiles.present} [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: ${module.devellibdepends.present} [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/inchi [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/inchi [copy] Copying 3 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/inchi [javac] Compiling 3 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/inchi [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/dist/jar/cdk-inchi.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/inchi [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/inchi test-dist-all: checkPlatforms: check: setupBuildDir: init: javacc: customize: runDoclet: [echo] Not skipping doclet run... compile-init: checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's test module from src/test... [echo] Datafiles defined: ${module.datafiles.present} [echo] Extra files defined: ${module.extrafiles.present} [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: true [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/test [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/test [copy] Copying 4 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/test [javac] Compiling 4 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/test [javac] Note: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/test/org/openscience/cdk/CoverageAnnotationTest.java uses unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/dist/jar/cdk-test.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/test [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/test checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's test-core module from src/test... [echo] Datafiles defined: ${module.datafiles.present} [echo] Extra files defined: true [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: true [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/test-core [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/test-core [copy] Copying 16 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/test-core [javac] Compiling 16 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/test-core [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/dist/jar/cdk-test-core.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/test-core [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/test-core checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's test-atomtype module from src/test... [echo] Datafiles defined: ${module.datafiles.present} [echo] Extra files defined: true [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: true [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/test-atomtype [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/test-atomtype [copy] Copying 8 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/test-atomtype [javac] Compiling 8 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/test-atomtype [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/dist/jar/cdk-test-atomtype.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/test-atomtype [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/test-atomtype checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's test-standard module from src/test... [echo] Datafiles defined: ${module.datafiles.present} [echo] Extra files defined: true [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: true [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/test-standard [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/test-standard [copy] Copying 75 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/test-standard [javac] Compiling 75 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/test-standard [javac] /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/test-standard/org/openscience/cdk/qsar/DescriptorValueTest.java:62: warning: [deprecation] DescriptorValue(org.openscience.cdk.qsar.DescriptorSpecification,java.lang.String[],java.lang.Object[],org.openscience.cdk.qsar.result.IDescriptorResult) in org.openscience.cdk.qsar.DescriptorValue has been deprecated [javac] DescriptorValue value = new DescriptorValue( [javac] ^ [javac] Note: Some input files use unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [javac] 1 warning [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/dist/jar/cdk-test-standard.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/test-standard [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/test-standard checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's test-data module from src/test... [echo] Datafiles defined: ${module.datafiles.present} [echo] Extra files defined: ${module.extrafiles.present} [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: true [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/test-data [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/test-data [copy] Copying 41 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/test-data [javac] Compiling 41 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/test-data [javac] Note: Some input files use unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/dist/jar/cdk-test-data.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/test-data [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/test-data checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's test-dict module from src/test... [echo] Datafiles defined: ${module.datafiles.present} [echo] Extra files defined: ${module.extrafiles.present} [echo] CDK dependencies defined: true [echo] Library dependencies defined: ${module.libdepends.present} [echo] Developer Library dependencies defined: true [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/test-dict [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/test-dict [copy] Copying 2 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/test-dict [javac] Compiling 2 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/test-dict [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/dist/jar/cdk-test-dict.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/test-dict [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/test-dict checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's test-datadebug module from src/test... [echo] Datafiles defined: ${module.datafiles.present} [echo] Extra files defined: ${module.extrafiles.present} [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: true [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/test-datadebug [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/test-datadebug [copy] Copying 36 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/test-datadebug [javac] Compiling 36 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/test-datadebug [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/dist/jar/cdk-test-datadebug.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/test-datadebug [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/test-datadebug checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's test-nonotify module from src/test... [echo] Datafiles defined: ${module.datafiles.present} [echo] Extra files defined: ${module.extrafiles.present} [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: true [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/test-nonotify [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/test-nonotify [copy] Copying 35 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/test-nonotify [javac] Compiling 35 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/test-nonotify [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/dist/jar/cdk-test-nonotify.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/test-nonotify [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/test-nonotify checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's test-io module from src/test... [echo] Datafiles defined: ${module.datafiles.present} [echo] Extra files defined: true [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: true [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/test-io [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/test-io [copy] Copying 47 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/test-io [javac] Compiling 47 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/test-io [javac] Note: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/test-io/org/openscience/cdk/io/ChemObjectIOInstantionTests.java uses unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/dist/jar/cdk-test-io.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/test-io [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/test-io checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's test-structgen module from src/test... [echo] Datafiles defined: ${module.datafiles.present} [echo] Extra files defined: ${module.extrafiles.present} [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: true [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/test-structgen [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/test-structgen [copy] Copying 12 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/test-structgen [javac] Compiling 12 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/test-structgen [javac] /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/test-structgen/org/openscience/cdk/structgen/SingleStructureRandomGeneratorTest.java:95: warning: [deprecation] getBondOrderSum(org.openscience.cdk.interfaces.IAtom) in org.openscience.cdk.AtomContainer has been deprecated [javac] bondCount = mol.getBondOrderSum(atom); [javac] ^ [javac] /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/test-structgen/org/openscience/cdk/structgen/deterministic/EquivalentClassesDeterministicGeneratorTest.java:77: warning: [deprecation] getBondOrderSum(org.openscience.cdk.interfaces.IAtom) in org.openscience.cdk.AtomContainer has been deprecated [javac] bondCount = mol.getBondOrderSum(atom); [javac] ^ [javac] Note: Some input files use unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [javac] 2 warnings [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/dist/jar/cdk-test-structgen.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/test-structgen [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/test-structgen checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's test-isomorphism module from src/test... [echo] Datafiles defined: ${module.datafiles.present} [echo] Extra files defined: ${module.extrafiles.present} [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: true [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/test-isomorphism [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/test-isomorphism [copy] Copying 2 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/test-isomorphism [javac] Compiling 2 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/test-isomorphism [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/dist/jar/cdk-test-isomorphism.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/test-isomorphism [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/test-isomorphism checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's test-extra module from src/test... [echo] Datafiles defined: ${module.datafiles.present} [echo] Extra files defined: true [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: true [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/test-extra [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/test-extra [copy] Copying 43 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/test-extra [javac] Compiling 43 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/test-extra [javac] Note: Some input files use unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/dist/jar/cdk-test-extra.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/test-extra [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/test-extra checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's test-smiles module from src/test... [echo] Datafiles defined: ${module.datafiles.present} [echo] Extra files defined: true [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: true [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/test-smiles [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/test-smiles [copy] Copying 7 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/test-smiles [javac] Compiling 7 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/test-smiles [javac] /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/test-smiles/org/openscience/cdk/smiles/SmilesGeneratorTest.java:555: warning: [deprecation] getBondOrderSum(org.openscience.cdk.interfaces.IAtom) in org.openscience.cdk.AtomContainer has been deprecated [javac] bondCount = mol.getBondOrderSum(atom); [javac] ^ [javac] 1 warning [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/dist/jar/cdk-test-smiles.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/test-smiles [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/test-smiles checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's test-reaction module from src/test... [echo] Datafiles defined: ${module.datafiles.present} [echo] Extra files defined: true [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: true [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/test-reaction [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/test-reaction [copy] Copying 55 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/test-reaction [javac] Compiling 55 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/test-reaction [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/dist/jar/cdk-test-reaction.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/test-reaction [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/test-reaction checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's test-builder3d module from src/test... [echo] Datafiles defined: ${module.datafiles.present} [echo] Extra files defined: true [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: true [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/test-builder3d [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/test-builder3d [copy] Copying 3 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/test-builder3d [javac] Compiling 3 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/test-builder3d [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/dist/jar/cdk-test-builder3d.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/test-builder3d [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/test-builder3d checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's test-forcefield module from src/test... [echo] Datafiles defined: ${module.datafiles.present} [echo] Extra files defined: true [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: true [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/test-forcefield [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/test-forcefield [copy] Copying 4 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/test-forcefield [javac] Compiling 4 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/test-forcefield [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/dist/jar/cdk-test-forcefield.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/test-forcefield [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/test-forcefield checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's test-valencycheck module from src/test... [echo] Datafiles defined: ${module.datafiles.present} [echo] Extra files defined: true [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: true [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/test-valencycheck [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/test-valencycheck [copy] Copying 9 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/test-valencycheck [javac] Compiling 9 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/test-valencycheck [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/dist/jar/cdk-test-valencycheck.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/test-valencycheck [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/test-valencycheck checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's test-charges module from src/test... [echo] Datafiles defined: ${module.datafiles.present} [echo] Extra files defined: ${module.extrafiles.present} [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: true [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/test-charges [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/test-charges [copy] Copying 6 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/test-charges [javac] Compiling 6 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/test-charges [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/dist/jar/cdk-test-charges.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/test-charges [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/test-charges checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's test-qsar module from src/test... [echo] Datafiles defined: ${module.datafiles.present} [echo] Extra files defined: true [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: true [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/test-qsar [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/test-qsar [copy] Copying 6 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/test-qsar [javac] Compiling 6 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/test-qsar [javac] Note: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/test-qsar/org/openscience/cdk/qsar/model/R2/QSARRModelTests.java uses unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/dist/jar/cdk-test-qsar.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/test-qsar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/test-qsar checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's test-qsaratomic module from src/test... [echo] Datafiles defined: ${module.datafiles.present} [echo] Extra files defined: true [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: true [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/test-qsaratomic [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/test-qsaratomic [copy] Copying 30 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/test-qsaratomic [javac] Compiling 30 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/test-qsaratomic [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/dist/jar/cdk-test-qsaratomic.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/test-qsaratomic [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/test-qsaratomic checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's test-qsarbond module from src/test... [echo] Datafiles defined: ${module.datafiles.present} [echo] Extra files defined: true [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: true [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/test-qsarbond [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/test-qsarbond [copy] Copying 8 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/test-qsarbond [javac] Compiling 8 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/test-qsarbond [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/dist/jar/cdk-test-qsarbond.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/test-qsarbond [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/test-qsarbond checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's test-qsarmolecular module from src/test... [echo] Datafiles defined: ${module.datafiles.present} [echo] Extra files defined: true [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: true [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/test-qsarmolecular [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/test-qsarmolecular [copy] Copying 48 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/test-qsarmolecular [javac] Compiling 48 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/test-qsarmolecular [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/dist/jar/cdk-test-qsarmolecular.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/test-qsarmolecular [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/test-qsarmolecular checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's test-experimental module from src/test... [echo] Datafiles defined: ${module.datafiles.present} [echo] Extra files defined: true [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: true [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/test-experimental [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/test-experimental [copy] Copying 7 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/test-experimental [javac] Compiling 7 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/test-experimental [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/dist/jar/cdk-test-experimental.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/test-experimental [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/test-experimental checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's test-qsarprotein module from src/test... [echo] Datafiles defined: ${module.datafiles.present} [echo] Extra files defined: true [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: true [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/test-qsarprotein [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/test-qsarprotein [copy] Copying 3 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/test-qsarprotein [javac] Compiling 3 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/test-qsarprotein [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/dist/jar/cdk-test-qsarprotein.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/test-qsarprotein [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/test-qsarprotein checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's test-pdb module from src/test... [echo] Datafiles defined: ${module.datafiles.present} [echo] Extra files defined: true [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: true [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/test-pdb [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/test-pdb [copy] Copying 4 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/test-pdb [javac] Compiling 4 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/test-pdb [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/dist/jar/cdk-test-pdb.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/test-pdb [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/test-pdb checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's test-inchi module from src/test... [echo] Datafiles defined: ${module.datafiles.present} [echo] Extra files defined: ${module.extrafiles.present} [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: true [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/test-inchi [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/test-inchi [copy] Copying 2 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/test-inchi [javac] Compiling 2 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/test-inchi [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/dist/jar/cdk-test-inchi.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/test-inchi [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/test-inchi checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's test-libiomd module from src/test... [echo] Datafiles defined: ${module.datafiles.present} [echo] Extra files defined: ${module.extrafiles.present} [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: true [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/test-libiomd [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/test-libiomd [copy] Copying 2 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/test-libiomd [javac] Compiling 2 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/test-libiomd [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/dist/jar/cdk-test-libiomd.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/test-libiomd [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/test-libiomd checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's test-libiocml module from src/test... [echo] Datafiles defined: ${module.datafiles.present} [echo] Extra files defined: true [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: true [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/test-libiocml [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/test-libiocml [copy] Copying 5 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/test-libiocml [javac] Compiling 5 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/test-libiocml [javac] Note: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/test-libiocml/org/openscience/cdk/modulesuites/MlibiocmlTests.java uses unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/dist/jar/cdk-test-libiocml.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/test-libiocml [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/test-libiocml checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's test-smarts module from src/test... [echo] Datafiles defined: ${module.datafiles.present} [echo] Extra files defined: true [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: true [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/test-smarts [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/test-smarts [copy] Copying 9 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/test-smarts [javac] Compiling 9 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/test-smarts [javac] Note: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/test-smarts/org/openscience/cdk/modulesuites/MsmartsTests.java uses unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/dist/jar/cdk-test-smarts.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/test-smarts [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/test-smarts checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's test-pcore module from src/test... [echo] Datafiles defined: ${module.datafiles.present} [echo] Extra files defined: true [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: true [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/test-pcore [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/test-pcore [copy] Copying 8 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/test-pcore [javac] Compiling 8 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/test-pcore [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/dist/jar/cdk-test-pcore.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/test-pcore [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/test-pcore checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's test-formula module from src/test... [echo] Datafiles defined: ${module.datafiles.present} [echo] Extra files defined: ${module.extrafiles.present} [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: true [echo] Autogenerated files specified: ${module.autogenerated.present} [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/test-formula [mkdir] Created dir: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/test-formula [copy] Copying 18 files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/test-formula [javac] Compiling 18 source files to /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/test-formula [jar] Building jar: /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/dist/jar/cdk-test-formula.jar [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/src/test-formula [delete] Deleting directory /home/mrc/Development/Sourceforge/cdkDir/cdk/trunk/cdk/build/test-formula test-all: checkPlatforms: check: noJunit: test-module: [echo] Testing classes for CDK's core module. [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: true [junit] Running org.openscience.cdk.modulesuites.McoreTests [junit] Tests run: 113, Failures: 0, Errors: 0, Time elapsed: 8.288 sec checkPlatforms: check: noJunit: test-module: [echo] Testing classes for CDK's data module. [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: true [junit] Running org.openscience.cdk.modulesuites.MdataTests [junit] Tests run: 700, Failures: 0, Errors: 0, Time elapsed: 2.285 sec checkPlatforms: check: noJunit: test-module: [echo] Testing classes for CDK's datadebug module. [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: true [junit] Running org.openscience.cdk.modulesuites.MdatadebugTests [junit] Tests run: 663, Failures: 0, Errors: 0, Time elapsed: 2.179 sec checkPlatforms: check: noJunit: test-module: [echo] Testing classes for CDK's nonotify module. [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: true [junit] Running org.openscience.cdk.modulesuites.MnonotifyTests [junit] Tests run: 663, Failures: 0, Errors: 0, Time elapsed: 2.691 sec checkPlatforms: check: noJunit: test-module: [echo] Testing classes for CDK's atomtype module. [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: true [junit] Running org.openscience.cdk.modulesuites.MatomtypeTests [junit] Tests run: 180, Failures: 0, Errors: 3, Time elapsed: 3.354 sec [junit] Test org.openscience.cdk.modulesuites.MatomtypeTests FAILED checkPlatforms: check: noJunit: test-module: [echo] Testing classes for CDK's standard module. [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: true [junit] Running org.openscience.cdk.modulesuites.MstandardTests [junit] Tests run: 426, Failures: 2, Errors: 2, Time elapsed: 35.483 sec [junit] Test org.openscience.cdk.modulesuites.MstandardTests FAILED checkPlatforms: check: noJunit: test-module: [echo] Testing classes for CDK's io module. [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: true [junit] Running org.openscience.cdk.modulesuites.MioTests [junit] Tests run: 211, Failures: 1, Errors: 0, Time elapsed: 15.254 sec [junit] Test org.openscience.cdk.modulesuites.MioTests FAILED checkPlatforms: check: noJunit: test-module: [echo] Testing classes for CDK's extra module. [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: true [junit] Running org.openscience.cdk.modulesuites.MextraTests [junit] Tests run: 134, Failures: 1, Errors: 3, Time elapsed: 14.284 sec [junit] Test org.openscience.cdk.modulesuites.MextraTests FAILED checkPlatforms: check: noJunit: test-module: [echo] Testing classes for CDK's builder3d module. [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: true [junit] Running org.openscience.cdk.modulesuites.Mbuilder3dTests [junit] Tests run: 12, Failures: 0, Errors: 11, Time elapsed: 17.666 sec [junit] Test org.openscience.cdk.modulesuites.Mbuilder3dTests FAILED checkPlatforms: check: noJunit: test-module: [echo] Testing classes for CDK's forcefield module. [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: true [junit] Running org.openscience.cdk.modulesuites.MforcefieldTests [junit] Tests run: 15, Failures: 0, Errors: 2, Time elapsed: 18.617 sec [junit] Test org.openscience.cdk.modulesuites.MforcefieldTests FAILED checkPlatforms: check: noJunit: test-module: [echo] Testing classes for CDK's valencycheck module. [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: true [junit] Running org.openscience.cdk.modulesuites.MvalencycheckTests [junit] Tests run: 74, Failures: 0, Errors: 9, Time elapsed: 2.148 sec [junit] Test org.openscience.cdk.modulesuites.MvalencycheckTests FAILED checkPlatforms: check: noJunit: test-module: [echo] Testing classes for CDK's charges module. [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: true [junit] Running org.openscience.cdk.modulesuites.MchargesTests [junit] Tests run: 18, Failures: 0, Errors: 7, Time elapsed: 1.681 sec [junit] Test org.openscience.cdk.modulesuites.MchargesTests FAILED checkPlatforms: check: noJunit: test-module: [echo] Testing classes for CDK's reaction module. [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: true [junit] Running org.openscience.cdk.modulesuites.MreactionTests [junit] Tests run: 633, Failures: 0, Errors: 0, Time elapsed: 22.513 sec checkPlatforms: check: noJunit: test-module: [echo] Testing classes for CDK's smarts module. [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: true [junit] Running org.openscience.cdk.modulesuites.MsmartsTests [junit] Tests run: 817, Failures: 16, Errors: 1, Time elapsed: 13.666 sec [junit] Test org.openscience.cdk.modulesuites.MsmartsTests FAILED checkPlatforms: check: noJunit: test-module: [echo] Testing classes for CDK's smiles module. [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: true [junit] Running org.openscience.cdk.modulesuites.MsmilesTests [junit] Tests run: 136, Failures: 1, Errors: 7, Time elapsed: 9.616 sec [junit] Test org.openscience.cdk.modulesuites.MsmilesTests FAILED checkPlatforms: check: noJunit: test-module: [echo] Testing classes for CDK's experimental module. [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: true [junit] Running org.openscience.cdk.modulesuites.MexperimentalTests [junit] Tests run: 51, Failures: 5, Errors: 6, Time elapsed: 21.417 sec [junit] Test org.openscience.cdk.modulesuites.MexperimentalTests FAILED checkPlatforms: check: noJunit: test-module: [echo] Testing classes for CDK's qsar module. [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: true [junit] Running org.openscience.cdk.modulesuites.MqsarTests [junit] Tests run: 0, Failures: 0, Errors: 0, Time elapsed: 0.001 sec checkPlatforms: check: noJunit: test-module: [echo] Testing classes for CDK's qsaratomic module. [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: true [junit] Running org.openscience.cdk.modulesuites.MqsaratomicTests [junit] Tests run: 348, Failures: 3, Errors: 6, Time elapsed: 31.152 sec [junit] Test org.openscience.cdk.modulesuites.MqsaratomicTests FAILED checkPlatforms: check: noJunit: test-module: [echo] Testing classes for CDK's qsarbond module. [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: true [junit] Running org.openscience.cdk.modulesuites.MqsarbondTests [junit] Tests run: 68, Failures: 0, Errors: 0, Time elapsed: 8.799 sec checkPlatforms: check: noJunit: test-module: [echo] Testing classes for CDK's qsarmolecular module. [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: true [junit] Running org.openscience.cdk.modulesuites.MqsarmolecularTests [junit] Tests run: 578, Failures: 39, Errors: 13, Time elapsed: 29.302 sec [junit] Test org.openscience.cdk.modulesuites.MqsarmolecularTests FAILED checkPlatforms: check: noJunit: test-module: [echo] Testing classes for CDK's qsarprotein module. [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: true [junit] Running org.openscience.cdk.modulesuites.MqsarproteinTests [junit] Tests run: 4, Failures: 0, Errors: 0, Time elapsed: 1.817 sec checkPlatforms: check: noJunit: test-module: [echo] Testing classes for CDK's pdb module. [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: true [junit] Running org.openscience.cdk.modulesuites.MpdbTests [junit] Tests run: 14, Failures: 0, Errors: 0, Time elapsed: 3.629 sec checkPlatforms: check: noJunit: test-module: [echo] Testing classes for CDK's pcore module. [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: true [junit] Running org.openscience.cdk.modulesuites.MpcoreTests [junit] Tests run: 9, Failures: 0, Errors: 1, Time elapsed: 2.822 sec [junit] Test org.openscience.cdk.modulesuites.MpcoreTests FAILED checkPlatforms: check: noJunit: test-module: [echo] Testing classes for CDK's inchi module. [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: true [junit] Running org.openscience.cdk.modulesuites.MinchiTests [junit] Tests run: 10, Failures: 0, Errors: 0, Time elapsed: 0.854 sec checkPlatforms: check: noJunit: test-module: [echo] Testing classes for CDK's structgen module. [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: true [junit] Running org.openscience.cdk.modulesuites.MstructgenTests [junit] Tests run: 48, Failures: 10, Errors: 0, Time elapsed: 9.302 sec [junit] Test org.openscience.cdk.modulesuites.MstructgenTests FAILED checkPlatforms: check: noJunit: test-module: [echo] Testing classes for CDK's libiomd module. [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: true [junit] Running org.openscience.cdk.modulesuites.MlibiomdTests [junit] Tests run: 3, Failures: 0, Errors: 0, Time elapsed: 0.963 sec checkPlatforms: check: noJunit: test-module: [echo] Testing classes for CDK's libiocml module. [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: true [junit] Running org.openscience.cdk.modulesuites.MlibiocmlTests [junit] Tests run: 63, Failures: 2, Errors: 1, Time elapsed: 1.629 sec [junit] Test org.openscience.cdk.modulesuites.MlibiocmlTests FAILED checkPlatforms: check: noJunit: test-module: [echo] Testing classes for CDK's formula module. [echo] CDK dependencies defined: true [echo] Library dependencies defined: true [echo] Developer Library dependencies defined: true [junit] Running org.openscience.cdk.modulesuites.MformulaTests [junit] Tests run: 156, Failures: 0, Errors: 1, Time elapsed: 2.399 sec [junit] Test org.openscience.cdk.modulesuites.MformulaTests FAILED BUILD SUCCESSFUL Total time: 8 minutes 36 seconds

[trunk.branch.overview]

--- trunk.overview 2008-05-20 15:37:31.000000000 +0200 +++ branches.overview 2008-05-20 15:55:05.000000000 +0200 @@ -1,11 +1,11 @@ -atomtype: run=180 failed=0 error=3 +atomtype: run=183 failed=0 error=3 builder3d: run=12 failed=0 error=11 -charges: run=18 failed=0 error=7 +charges: run=29 failed=0 error=7 core: run=113 failed=0 error=0 datadebug: run=663 failed=0 error=0 data: run=700 failed=0 error=0 experimental: run=51 failed=5 error=6 -extra: run=134 failed=1 error=3 +extra: run=126 failed=1 error=3 forcefield: run=15 failed=0 error=2 formula: run=156 failed=0 error=1 inchi: run=10 failed=0 error=0 @@ -15,14 +15,14 @@ nonotify: run=663 failed=0 error=0 pcore: run=9 failed=0 error=1 pdb: run=14 failed=0 error=0 -qsaratomic: run=348 failed=3 error=6 -qsarbond: run=68 failed=0 error=0 -qsarmolecular: run=578 failed=39 error=13 +qsaratomic: run=396 failed=3 error=7 +qsarbond: run=87 failed=0 error=0 +qsarmolecular: run=533 failed=27 error=3 qsarprotein: run=4 failed=0 error=0 qsar: run=0 failed=0 error=0 -reaction: run=633 failed=0 error=0 +reaction: run=639 failed=0 error=0 smarts: run=817 failed=16 error=1 -smiles: run=136 failed=1 error=7 +smiles: run=136 failed=1 error=8 standard: run=426 failed=2 error=2 structgen: run=48 failed=10 error=0 valencycheck: run=74 failed=0 error=9

[trunk.branch.results]

--- trunk.results 2008-05-20 09:21:28.000000000 +0200 +++ branch.results 2008-05-20 15:54:14.000000000 +0200 @@ -5,6 +5,7 @@ Testcase: test1810(org.openscience.cdk.qsar.descriptors.molecular.XLogPDescriptorTest) Testcase: test1822(org.openscience.cdk.qsar.descriptors.molecular.XLogPDescriptorTest) Testcase: test1844(org.openscience.cdk.qsar.descriptors.molecular.XLogPDescriptorTest) +Testcase: testAcyclicUreas(org.openscience.cdk.smiles.smarts.parser.SMARTSSearchTest) Testcase: testAprindine(org.openscience.cdk.qsar.descriptors.molecular.XLogPDescriptorTest) Testcase: testAtomProperty(org.openscience.cdk.io.cml.CMLRoundTripTest) Testcase: testBasicAmineOnDrugs(org.openscience.cdk.smiles.smarts.parser.RecursiveTest) @@ -13,7 +14,6 @@ Testcase: testBondStereo2(org.openscience.cdk.smiles.smarts.parser.ParserTest) Testcase: testBondStereo3(org.openscience.cdk.smiles.smarts.parser.ParserTest) Testcase: testBug1365547(org.openscience.cdk.tools.ValencyHybridCheckerTest) -Testcase: testCalculate_IAtomContainer(org.openscience.cdk.qsar.descriptors.atomic.IPAtomicDescriptorTest) Testcase: testCalculate_IAtomContainer(org.openscience.cdk.qsar.descriptors.atomic.PartialTChargeMMFF94DescriptorTest) Testcase: testcalculate_IAtomContainer(org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorChargeTest) Testcase: testcalculate_IAtomContainer(org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorMassTest) @@ -30,6 +30,7 @@ Testcase: testCoverage(org.openscience.cdk.ChargesCoverageTest) Testcase: testCoverage(org.openscience.cdk.IoCoverageTest) Testcase: testCoverage(org.openscience.cdk.PcoreCoverageTest) +Testcase: testCoverage(org.openscience.cdk.QsaratomicCoverageTest) Testcase: testCoverage(org.openscience.cdk.QsarmolecularCoverageTest) Testcase: testCoverage(org.openscience.cdk.SMARTSCoverageTest) Testcase: testCoverage(org.openscience.cdk.StandardCoverageTest) @@ -48,7 +49,6 @@ Testcase: testFindMatchingAtomType_IAtomContainer_IAtom_Chloromethane(org.openscience.cdk.atomtype.MMFF94AtomTypeMatcherTest) Testcase: testGenerateMurckoFragments13(org.openscience.cdk.tools.GenerateFragmentsTest) Testcase: testGenerateMurckoFragments14(org.openscience.cdk.tools.GenerateFragmentsTest) -Testcase: testGenerateMurckoFragments17(org.openscience.cdk.tools.GenerateFragmentsTest) Testcase: testGenerateMurckoFragments4(org.openscience.cdk.tools.GenerateFragmentsTest) Testcase: testGenerateMurckoFragments8(org.openscience.cdk.tools.GenerateFragmentsTest) Testcase: testGenerateMurckoFragments9(org.openscience.cdk.tools.GenerateFragmentsTest) @@ -56,32 +56,13 @@ Testcase: testGetDescriptorResultType(org.openscience.cdk.qsar.descriptors.molecular.LengthOverBreadthDescriptorTest) Testcase: testGetFunctionalGroupSubstructureSet(org.openscience.cdk.fingerprint.StandardSubstructureSetsTest) Testcase: testGetInstance(org.openscience.cdk.modeling.builder3d.TemplateHandler3DTest) -Testcase: testGetParameterNames(org.openscience.cdk.qsar.descriptors.atomic.IPAtomicDescriptorTest) -Testcase: testGetParameters(org.openscience.cdk.qsar.descriptors.atomic.IPAtomicDescriptorTest) -Testcase: testGetParameterType_String(org.openscience.cdk.qsar.descriptors.atomic.IPAtomicDescriptorTest) Testcase: testGetPath_IAtomContainer_IAtom_IAtom(org.openscience.cdk.graph.SpanningTreeTest) Testcase: testGetPrime(org.openscience.cdk.smiles.InvPairTest) -Testcase: testGetSpecification(org.openscience.cdk.qsar.descriptors.atomic.IPAtomicDescriptorTest) Testcase: testGetTotalNaturalAbundance_IMolecularFormula3(org.openscience.cdk.formula.MolecularFormulaManipulatorTest) -Testcase: testHasSetSuperDotDescriptor(org.openscience.cdk.qsar.descriptors.atomic.IPAtomicDescriptorTest) -Testcase: testIDescriptor5(org.openscience.cdk.qsar.descriptors.atomic.IPAtomicDescriptorTest) Testcase: testImidazole3(org.openscience.cdk.smiles.SmilesParserTest) Testcase: testImplicitHCountAtom(org.openscience.cdk.isomorphism.SMARTSTest) -Testcase: testIPConjugatedDescriptor1(org.openscience.cdk.qsar.descriptors.bond.IPBondDescriptorTest) -Testcase: testIPDescriptor_3(org.openscience.cdk.qsar.descriptors.molecular.IPMolecularDescriptorTest) -Testcase: testIPDescriptor_5(org.openscience.cdk.qsar.descriptors.atomic.IPAtomicDescriptorTest) -Testcase: testIPDescriptor_9(org.openscience.cdk.qsar.descriptors.atomic.IPAtomicDescriptorTest) -Testcase: testIPDescriptorReaction1(org.openscience.cdk.qsar.descriptors.bond.IPBondDescriptorTest) -Testcase: testIPDescriptorReaction3(org.openscience.cdk.qsar.descriptors.molecular.IPMolecularDescriptorTest) -Testcase: testIPDescriptorReaction4(org.openscience.cdk.qsar.descriptors.molecular.IPMolecularDescriptorTest) -Testcase: testIPDescriptorReaction(org.openscience.cdk.qsar.descriptors.atomic.IPAtomicDescriptorTest) -Testcase: testIPDescriptorReaction(org.openscience.cdk.qsar.descriptors.molecular.IPMolecularDescriptorTest) -Testcase: testIPPySystemReaction1(org.openscience.cdk.qsar.descriptors.bond.IPBondDescriptorTest) -Testcase: testIPPySystemWithHeteroatomDescriptor1(org.openscience.cdk.qsar.descriptors.atomic.IPAtomicDescriptorTest) -Testcase: testIPPySystemWithHeteroatomDescriptor2(org.openscience.cdk.qsar.descriptors.atomic.IPAtomicDescriptorTest) -Testcase: testIPPySystemWithHeteroatomDescriptor3(org.openscience.cdk.qsar.descriptors.atomic.IPAtomicDescriptorTest) +Testcase: testIPDescriptor_3(org.openscience.cdk.qsar.descriptors.molecular.IPMolecularLearningDescriptorTest) Testcase: testIsProtonInAromaticSystemDescriptor(org.openscience.cdk.qsar.descriptors.atomic.IsProtonInAromaticSystemDescriptorTest) -Testcase: testLabels(org.openscience.cdk.qsar.descriptors.atomic.IPAtomicDescriptorTest) Testcase: testLabels(org.openscience.cdk.qsar.descriptors.atomic.PartialTChargeMMFF94DescriptorTest) Testcase: testLabels(org.openscience.cdk.qsar.descriptors.atomic.ProtonTotalPartialChargeDescriptorTest) Testcase: testLabels(org.openscience.cdk.qsar.descriptors.molecular.LengthOverBreadthDescriptorTest) @@ -111,7 +92,6 @@ Testcase: testno990(org.openscience.cdk.qsar.descriptors.molecular.XLogPDescriptorTest) Testcase: testOar(org.openscience.cdk.atomtype.MM2AtomTypeMatcherTest) Testcase: testOar(org.openscience.cdk.atomtype.MMFF94AtomTypeMatcherTest) -Testcase: testParameterConsistency(org.openscience.cdk.qsar.descriptors.atomic.IPAtomicDescriptorTest) Testcase: testPartialTotalChargeDescriptor_Benzene(org.openscience.cdk.qsar.descriptors.atomic.PartialTChargeMMFF94DescriptorTest) Testcase: testPartialTotalChargeDescriptor_Chloromethane(org.openscience.cdk.qsar.descriptors.atomic.PartialTChargeMMFF94DescriptorTest) Testcase: testPartialTotalChargeDescriptor_Methylamine(org.openscience.cdk.qsar.descriptors.atomic.PartialTChargeMMFF94DescriptorTest) @@ -121,6 +101,7 @@ Testcase: testPropertyAromatic5(org.openscience.cdk.smiles.smarts.parser.SMARTSSearchTest) Testcase: testPyrrole3(org.openscience.cdk.smiles.SmilesParserTest) Testcase: testPyrroleAnion1(org.openscience.cdk.smiles.SmilesParserTest) +Testcase: testPyrroleAnion(org.openscience.cdk.atomtype.CDKAtomTypeMatcherTest) Testcase: testRecursive28(org.openscience.cdk.smiles.smarts.parser.RecursiveTest) Testcase: testRecursive29(org.openscience.cdk.smiles.smarts.parser.RecursiveTest) Testcase: testRecursiveSmarts25(org.openscience.cdk.smiles.smarts.parser.RecursiveTest) @@ -128,9 +109,9 @@ Testcase: testRecursiveSmarts27(org.openscience.cdk.smiles.smarts.parser.RecursiveTest) Testcase: testRecursiveSmarts33(org.openscience.cdk.smiles.smarts.parser.RecursiveTest) Testcase: testResolveOverlap1(org.openscience.cdk.layout.OverlapResolverTest) -Testcase: testSetParameters_arrayObject(org.openscience.cdk.qsar.descriptors.atomic.IPAtomicDescriptorTest) Testcase: testSFBug1085912_1(org.openscience.cdk.io.cml.CML2Test) Testcase: testSFBug1208740(org.openscience.cdk.isomorphism.UniversalIsomorphismTesterTest) +Testcase: testSmiles9(org.openscience.cdk.smiles.SmilesParserTest) Testcase: testSthi(org.openscience.cdk.atomtype.MM2AtomTypeMatcherTest) Testcase: testWHIM(org.openscience.cdk.qsar.descriptors.molecular.WHIMDescriptorTest) Testcase: warning(junit.framework.TestSuite$1)

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