Buildfile: build.xml clean: [delete] Deleting directory /home/rguha/src/java/cdk-nightly/cdk/build [delete] Deleting directory /home/rguha/src/java/cdk-nightly/cdk/sourcedist [delete] Deleting directory /home/rguha/src/java/cdk-nightly/cdk/dist [delete] Deleting directory /home/rguha/src/java/cdk-nightly/cdk/reports dist-all: checkPlatforms: check: setupBuildDir: [mkdir] Created dir: /home/rguha/src/java/cdk-nightly/cdk/build [mkdir] Created dir: /home/rguha/src/java/cdk-nightly/cdk/sourcedist [mkdir] Created dir: /home/rguha/src/java/cdk-nightly/cdk/dist [mkdir] Created dir: /home/rguha/src/java/cdk-nightly/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/rguha/src/java/cdk-nightly/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. [jjtree] Java Compiler Compiler Version 3.2 (Tree Builder) [jjtree] (type "jjtree" with no arguments for help) [jjtree] Reading from file /home/rguha/src/java/cdk-nightly/cdk/src/main/org/openscience/cdk/smiles/smarts/parser/SMARTSParser.jjt . . . [jjtree] Annotated grammar generated successfully in /home/rguha/src/java/cdk-nightly/cdk/src/main/org/openscience/cdk/smiles/smarts/parser/SMARTSParser.jj [javacc] Java Compiler Compiler Version 3.2 (Parser Generator) [javacc] (type "javacc" with no arguments for help) [javacc] Reading from file /home/rguha/src/java/cdk-nightly/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. [replace] Replaced 10 occurrences in 0 files. customize: runDoclet: [echo] Not skipping doclet run... [javac] Compiling 1 source file to /home/rguha/src/java/cdk-nightly/cdk/build compile-init: checkPlatforms: check: dist.init: [mkdir] Created dir: /home/rguha/src/java/cdk-nightly/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/rguha/src/java/cdk-nightly/cdk/build/src/interfaces [mkdir] Created dir: /home/rguha/src/java/cdk-nightly/cdk/build/interfaces [copy] Copying 45 files to /home/rguha/src/java/cdk-nightly/cdk/build/src/interfaces [javac] Compiling 45 source files to /home/rguha/src/java/cdk-nightly/cdk/build/interfaces [jar] Building jar: /home/rguha/src/java/cdk-nightly/cdk/dist/jar/cdk-interfaces.jar [delete] Deleting directory /home/rguha/src/java/cdk-nightly/cdk/build/src/interfaces [delete] Deleting directory /home/rguha/src/java/cdk-nightly/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/rguha/src/java/cdk-nightly/cdk/build/src/core [mkdir] Created dir: /home/rguha/src/java/cdk-nightly/cdk/build/core [copy] Copying 28 files to /home/rguha/src/java/cdk-nightly/cdk/build/src/core [javac] Compiling 28 source files to /home/rguha/src/java/cdk-nightly/cdk/build/core [jar] Building jar: /home/rguha/src/java/cdk-nightly/cdk/dist/jar/cdk-core.jar [delete] Deleting directory /home/rguha/src/java/cdk-nightly/cdk/build/src/core [delete] Deleting directory /home/rguha/src/java/cdk-nightly/cdk/build/core 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/rguha/src/java/cdk-nightly/cdk/build/src/standard [mkdir] Created dir: /home/rguha/src/java/cdk-nightly/cdk/build/standard [copy] Copying 84 files to /home/rguha/src/java/cdk-nightly/cdk/build/src/standard [javac] Compiling 84 source files to /home/rguha/src/java/cdk-nightly/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/rguha/src/java/cdk-nightly/cdk/dist/jar/cdk-standard.jar [delete] Deleting directory /home/rguha/src/java/cdk-nightly/cdk/build/src/standard [delete] Deleting directory /home/rguha/src/java/cdk-nightly/cdk/build/standard checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's atomtype 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/rguha/src/java/cdk-nightly/cdk/build/src/atomtype [mkdir] Created dir: /home/rguha/src/java/cdk-nightly/cdk/build/atomtype [copy] Copying 4 files to /home/rguha/src/java/cdk-nightly/cdk/build/src/atomtype [javac] Compiling 4 source files to /home/rguha/src/java/cdk-nightly/cdk/build/atomtype [jar] Building jar: /home/rguha/src/java/cdk-nightly/cdk/dist/jar/cdk-atomtype.jar [delete] Deleting directory /home/rguha/src/java/cdk-nightly/cdk/build/src/atomtype [delete] Deleting directory /home/rguha/src/java/cdk-nightly/cdk/build/atomtype 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/rguha/src/java/cdk-nightly/cdk/build/src/dict [mkdir] Created dir: /home/rguha/src/java/cdk-nightly/cdk/build/dict [copy] Copying 8 files to /home/rguha/src/java/cdk-nightly/cdk/build/src/dict [javac] Compiling 8 source files to /home/rguha/src/java/cdk-nightly/cdk/build/dict [jar] Building jar: /home/rguha/src/java/cdk-nightly/cdk/dist/jar/cdk-dict.jar [delete] Deleting directory /home/rguha/src/java/cdk-nightly/cdk/build/src/dict [delete] Deleting directory /home/rguha/src/java/cdk-nightly/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/rguha/src/java/cdk-nightly/cdk/build/src/data [mkdir] Created dir: /home/rguha/src/java/cdk-nightly/cdk/build/data [copy] Copying 41 files to /home/rguha/src/java/cdk-nightly/cdk/build/src/data [javac] Compiling 41 source files to /home/rguha/src/java/cdk-nightly/cdk/build/data [javac] Note: /home/rguha/src/java/cdk-nightly/cdk/build/src/data/org/openscience/cdk/formula/AdductFormula.java uses unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [jar] Building jar: /home/rguha/src/java/cdk-nightly/cdk/dist/jar/cdk-data.jar [delete] Deleting directory /home/rguha/src/java/cdk-nightly/cdk/build/src/data [delete] Deleting directory /home/rguha/src/java/cdk-nightly/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/rguha/src/java/cdk-nightly/cdk/build/src/render [mkdir] Created dir: /home/rguha/src/java/cdk-nightly/cdk/build/render [copy] Copying 11 files to /home/rguha/src/java/cdk-nightly/cdk/build/src/render [javac] Compiling 11 source files to /home/rguha/src/java/cdk-nightly/cdk/build/render [jar] Building jar: /home/rguha/src/java/cdk-nightly/cdk/dist/jar/cdk-render.jar [delete] Deleting directory /home/rguha/src/java/cdk-nightly/cdk/build/src/render [delete] Deleting directory /home/rguha/src/java/cdk-nightly/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/rguha/src/java/cdk-nightly/cdk/build/src/io [mkdir] Created dir: /home/rguha/src/java/cdk-nightly/cdk/build/io [copy] Copying 167 files to /home/rguha/src/java/cdk-nightly/cdk/build/src/io [javac] Compiling 167 source files to /home/rguha/src/java/cdk-nightly/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/rguha/src/java/cdk-nightly/cdk/dist/jar/cdk-io.jar [delete] Deleting directory /home/rguha/src/java/cdk-nightly/cdk/build/src/io [delete] Deleting directory /home/rguha/src/java/cdk-nightly/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/rguha/src/java/cdk-nightly/cdk/build/src/valencycheck [mkdir] Created dir: /home/rguha/src/java/cdk-nightly/cdk/build/valencycheck [copy] Copying 6 files to /home/rguha/src/java/cdk-nightly/cdk/build/src/valencycheck [javac] Compiling 6 source files to /home/rguha/src/java/cdk-nightly/cdk/build/valencycheck [jar] Building jar: /home/rguha/src/java/cdk-nightly/cdk/dist/jar/cdk-valencycheck.jar [delete] Deleting directory /home/rguha/src/java/cdk-nightly/cdk/build/src/valencycheck [delete] Deleting directory /home/rguha/src/java/cdk-nightly/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/rguha/src/java/cdk-nightly/cdk/build/src/sdg [mkdir] Created dir: /home/rguha/src/java/cdk-nightly/cdk/build/sdg [copy] Copying 6 files to /home/rguha/src/java/cdk-nightly/cdk/build/src/sdg [javac] Compiling 6 source files to /home/rguha/src/java/cdk-nightly/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/rguha/src/java/cdk-nightly/cdk/dist/jar/cdk-sdg.jar [delete] Deleting directory /home/rguha/src/java/cdk-nightly/cdk/build/src/sdg [delete] Deleting directory /home/rguha/src/java/cdk-nightly/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/rguha/src/java/cdk-nightly/cdk/build/src/control [mkdir] Created dir: /home/rguha/src/java/cdk-nightly/cdk/build/control [copy] Copying 14 files to /home/rguha/src/java/cdk-nightly/cdk/build/src/control [javac] Compiling 14 source files to /home/rguha/src/java/cdk-nightly/cdk/build/control [jar] Building jar: /home/rguha/src/java/cdk-nightly/cdk/dist/jar/cdk-control.jar [delete] Deleting directory /home/rguha/src/java/cdk-nightly/cdk/build/src/control [delete] Deleting directory /home/rguha/src/java/cdk-nightly/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/rguha/src/java/cdk-nightly/cdk/build/src/datadebug [mkdir] Created dir: /home/rguha/src/java/cdk-nightly/cdk/build/datadebug [copy] Copying 39 files to /home/rguha/src/java/cdk-nightly/cdk/build/src/datadebug [javac] Compiling 39 source files to /home/rguha/src/java/cdk-nightly/cdk/build/datadebug [javac] /home/rguha/src/java/cdk-nightly/cdk/build/src/datadebug/org/openscience/cdk/debug/DebugAdductFormula.java:70: warning: [deprecation] setCharge(java.lang.Double) in org.openscience.cdk.formula.AdductFormula has been deprecated [javac] public void setCharge(Double charge) { [javac] ^ [javac] /home/rguha/src/java/cdk-nightly/cdk/build/src/datadebug/org/openscience/cdk/debug/DebugAdductFormula.java:72: warning: [deprecation] setCharge(java.lang.Double) in org.openscience.cdk.formula.AdductFormula has been deprecated [javac] super.setCharge(charge); [javac] ^ [javac] /home/rguha/src/java/cdk-nightly/cdk/build/src/datadebug/org/openscience/cdk/debug/DebugAminoAcid.java:255: 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/rguha/src/java/cdk-nightly/cdk/build/src/datadebug/org/openscience/cdk/debug/DebugAminoAcid.java:257: warning: [deprecation] getBondOrderSum(org.openscience.cdk.interfaces.IAtom) in org.openscience.cdk.AtomContainer has been deprecated [javac] return super.getBondOrderSum(atom); [javac] ^ [javac] /home/rguha/src/java/cdk-nightly/cdk/build/src/datadebug/org/openscience/cdk/debug/DebugAtomContainer.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/rguha/src/java/cdk-nightly/cdk/build/src/datadebug/org/openscience/cdk/debug/DebugAtomContainer.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/rguha/src/java/cdk-nightly/cdk/build/src/datadebug/org/openscience/cdk/debug/DebugBioPolymer.java:256: 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/rguha/src/java/cdk-nightly/cdk/build/src/datadebug/org/openscience/cdk/debug/DebugBioPolymer.java:258: warning: [deprecation] getBondOrderSum(org.openscience.cdk.interfaces.IAtom) in org.openscience.cdk.AtomContainer has been deprecated [javac] return super.getBondOrderSum(atom); [javac] ^ [javac] /home/rguha/src/java/cdk-nightly/cdk/build/src/datadebug/org/openscience/cdk/debug/DebugCrystal.java:266: 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/rguha/src/java/cdk-nightly/cdk/build/src/datadebug/org/openscience/cdk/debug/DebugCrystal.java:268: warning: [deprecation] getBondOrderSum(org.openscience.cdk.interfaces.IAtom) in org.openscience.cdk.AtomContainer has been deprecated [javac] return super.getBondOrderSum(atom); [javac] ^ [javac] /home/rguha/src/java/cdk-nightly/cdk/build/src/datadebug/org/openscience/cdk/debug/DebugMolecule.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/rguha/src/java/cdk-nightly/cdk/build/src/datadebug/org/openscience/cdk/debug/DebugMolecule.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/rguha/src/java/cdk-nightly/cdk/build/src/datadebug/org/openscience/cdk/debug/DebugMonomer.java:255: 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/rguha/src/java/cdk-nightly/cdk/build/src/datadebug/org/openscience/cdk/debug/DebugMonomer.java:257: warning: [deprecation] getBondOrderSum(org.openscience.cdk.interfaces.IAtom) in org.openscience.cdk.AtomContainer has been deprecated [javac] return super.getBondOrderSum(atom); [javac] ^ [javac] /home/rguha/src/java/cdk-nightly/cdk/build/src/datadebug/org/openscience/cdk/debug/DebugPolymer.java:256: 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/rguha/src/java/cdk-nightly/cdk/build/src/datadebug/org/openscience/cdk/debug/DebugPolymer.java:258: warning: [deprecation] getBondOrderSum(org.openscience.cdk.interfaces.IAtom) in org.openscience.cdk.AtomContainer has been deprecated [javac] return super.getBondOrderSum(atom); [javac] ^ [javac] /home/rguha/src/java/cdk-nightly/cdk/build/src/datadebug/org/openscience/cdk/debug/DebugRing.java:280: 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/rguha/src/java/cdk-nightly/cdk/build/src/datadebug/org/openscience/cdk/debug/DebugRing.java:282: warning: [deprecation] getBondOrderSum(org.openscience.cdk.interfaces.IAtom) in org.openscience.cdk.AtomContainer has been deprecated [javac] return super.getBondOrderSum(atom); [javac] ^ [javac] /home/rguha/src/java/cdk-nightly/cdk/build/src/datadebug/org/openscience/cdk/debug/DebugStrand.java:256: 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/rguha/src/java/cdk-nightly/cdk/build/src/datadebug/org/openscience/cdk/debug/DebugStrand.java:258: 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] 20 warnings [jar] Building jar: /home/rguha/src/java/cdk-nightly/cdk/dist/jar/cdk-datadebug.jar [delete] Deleting directory /home/rguha/src/java/cdk-nightly/cdk/build/src/datadebug [delete] Deleting directory /home/rguha/src/java/cdk-nightly/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/rguha/src/java/cdk-nightly/cdk/build/src/nonotify [mkdir] Created dir: /home/rguha/src/java/cdk-nightly/cdk/build/nonotify [copy] Copying 39 files to /home/rguha/src/java/cdk-nightly/cdk/build/src/nonotify [javac] Compiling 39 source files to /home/rguha/src/java/cdk-nightly/cdk/build/nonotify [jar] Building jar: /home/rguha/src/java/cdk-nightly/cdk/dist/jar/cdk-nonotify.jar [delete] Deleting directory /home/rguha/src/java/cdk-nightly/cdk/build/src/nonotify [delete] Deleting directory /home/rguha/src/java/cdk-nightly/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/rguha/src/java/cdk-nightly/cdk/build/src/formula [mkdir] Created dir: /home/rguha/src/java/cdk-nightly/cdk/build/formula [copy] Copying 15 files to /home/rguha/src/java/cdk-nightly/cdk/build/src/formula [javac] Compiling 15 source files to /home/rguha/src/java/cdk-nightly/cdk/build/formula [javac] Note: /home/rguha/src/java/cdk-nightly/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/rguha/src/java/cdk-nightly/cdk/dist/jar/cdk-formula.jar [delete] Deleting directory /home/rguha/src/java/cdk-nightly/cdk/build/src/formula [delete] Deleting directory /home/rguha/src/java/cdk-nightly/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/rguha/src/java/cdk-nightly/cdk/build/src/structgen [mkdir] Created dir: /home/rguha/src/java/cdk-nightly/cdk/build/structgen [copy] Copying 8 files to /home/rguha/src/java/cdk-nightly/cdk/build/src/structgen [javac] Compiling 8 source files to /home/rguha/src/java/cdk-nightly/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/rguha/src/java/cdk-nightly/cdk/dist/jar/cdk-structgen.jar [delete] Deleting directory /home/rguha/src/java/cdk-nightly/cdk/build/src/structgen [delete] Deleting directory /home/rguha/src/java/cdk-nightly/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: 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/rguha/src/java/cdk-nightly/cdk/build/src/pdb [mkdir] Created dir: /home/rguha/src/java/cdk-nightly/cdk/build/pdb [copy] Copying 4 files to /home/rguha/src/java/cdk-nightly/cdk/build/src/pdb [javac] Compiling 4 source files to /home/rguha/src/java/cdk-nightly/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/rguha/src/java/cdk-nightly/cdk/dist/jar/cdk-pdb.jar [delete] Deleting directory /home/rguha/src/java/cdk-nightly/cdk/build/src/pdb [delete] Deleting directory /home/rguha/src/java/cdk-nightly/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/rguha/src/java/cdk-nightly/cdk/build/src/isomorphism [mkdir] Created dir: /home/rguha/src/java/cdk-nightly/cdk/build/isomorphism [copy] Copying 15 files to /home/rguha/src/java/cdk-nightly/cdk/build/src/isomorphism [javac] Compiling 15 source files to /home/rguha/src/java/cdk-nightly/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/rguha/src/java/cdk-nightly/cdk/dist/jar/cdk-isomorphism.jar [delete] Deleting directory /home/rguha/src/java/cdk-nightly/cdk/build/src/isomorphism [delete] Deleting directory /home/rguha/src/java/cdk-nightly/cdk/build/isomorphism 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/rguha/src/java/cdk-nightly/cdk/build/src/smarts [mkdir] Created dir: /home/rguha/src/java/cdk-nightly/cdk/build/smarts [copy] Copying 78 files to /home/rguha/src/java/cdk-nightly/cdk/build/src/smarts [javac] Compiling 78 source files to /home/rguha/src/java/cdk-nightly/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/rguha/src/java/cdk-nightly/cdk/build [jar] Building jar: /home/rguha/src/java/cdk-nightly/cdk/dist/jar/cdk-smarts.jar [delete] Deleting directory /home/rguha/src/java/cdk-nightly/cdk/build/src/smarts [delete] Deleting directory /home/rguha/src/java/cdk-nightly/cdk/build/smarts checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's fingerprint module from src/main... [echo] Datafiles defined: true [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/rguha/src/java/cdk-nightly/cdk/build/src/fingerprint [mkdir] Created dir: /home/rguha/src/java/cdk-nightly/cdk/build/fingerprint [copy] Copying 5 files to /home/rguha/src/java/cdk-nightly/cdk/build/src/fingerprint [javac] Compiling 5 source files to /home/rguha/src/java/cdk-nightly/cdk/build/fingerprint [jar] Building jar: /home/rguha/src/java/cdk-nightly/cdk/dist/jar/cdk-fingerprint.jar [delete] Deleting directory /home/rguha/src/java/cdk-nightly/cdk/build/src/fingerprint [delete] Deleting directory /home/rguha/src/java/cdk-nightly/cdk/build/fingerprint 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/rguha/src/java/cdk-nightly/cdk/build/src/smiles [mkdir] Created dir: /home/rguha/src/java/cdk-nightly/cdk/build/smiles [copy] Copying 7 files to /home/rguha/src/java/cdk-nightly/cdk/build/src/smiles [javac] Compiling 7 source files to /home/rguha/src/java/cdk-nightly/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/rguha/src/java/cdk-nightly/cdk/dist/jar/cdk-smiles.jar [delete] Deleting directory /home/rguha/src/java/cdk-nightly/cdk/build/src/smiles [delete] Deleting directory /home/rguha/src/java/cdk-nightly/cdk/build/smiles 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: ${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/rguha/src/java/cdk-nightly/cdk/build/src/extra [mkdir] Created dir: /home/rguha/src/java/cdk-nightly/cdk/build/extra [copy] Copying 85 files to /home/rguha/src/java/cdk-nightly/cdk/build/src/extra [javac] Compiling 85 source files to /home/rguha/src/java/cdk-nightly/cdk/build/extra [javac] /home/rguha/src/java/cdk-nightly/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] 1 warning [jar] Building jar: /home/rguha/src/java/cdk-nightly/cdk/dist/jar/cdk-extra.jar [delete] Deleting directory /home/rguha/src/java/cdk-nightly/cdk/build/src/extra [delete] Deleting directory /home/rguha/src/java/cdk-nightly/cdk/build/extra 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/rguha/src/java/cdk-nightly/cdk/build/src/libiocml [mkdir] Created dir: /home/rguha/src/java/cdk-nightly/cdk/build/libiocml [copy] Copying 3 files to /home/rguha/src/java/cdk-nightly/cdk/build/src/libiocml [javac] Compiling 3 source files to /home/rguha/src/java/cdk-nightly/cdk/build/libiocml [javac] Note: /home/rguha/src/java/cdk-nightly/cdk/build/src/libiocml/org/openscience/cdk/io/RssWriter.java uses unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [jar] Building jar: /home/rguha/src/java/cdk-nightly/cdk/dist/jar/cdk-libiocml.jar [delete] Deleting directory /home/rguha/src/java/cdk-nightly/cdk/build/src/libiocml [delete] Deleting directory /home/rguha/src/java/cdk-nightly/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/rguha/src/java/cdk-nightly/cdk/build/src/libiomd [mkdir] Created dir: /home/rguha/src/java/cdk-nightly/cdk/build/libiomd [copy] Copying 5 files to /home/rguha/src/java/cdk-nightly/cdk/build/src/libiomd [javac] Compiling 5 source files to /home/rguha/src/java/cdk-nightly/cdk/build/libiomd [javac] Note: /home/rguha/src/java/cdk-nightly/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/rguha/src/java/cdk-nightly/cdk/dist/jar/cdk-libiomd.jar [delete] Deleting directory /home/rguha/src/java/cdk-nightly/cdk/build/src/libiomd [delete] Deleting directory /home/rguha/src/java/cdk-nightly/cdk/build/libiomd checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's pdbcml 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/rguha/src/java/cdk-nightly/cdk/build/src/pdbcml [mkdir] Created dir: /home/rguha/src/java/cdk-nightly/cdk/build/pdbcml [copy] Copying 1 file to /home/rguha/src/java/cdk-nightly/cdk/build/src/pdbcml [javac] Compiling 1 source file to /home/rguha/src/java/cdk-nightly/cdk/build/pdbcml [jar] Building jar: /home/rguha/src/java/cdk-nightly/cdk/dist/jar/cdk-pdbcml.jar [delete] Deleting directory /home/rguha/src/java/cdk-nightly/cdk/build/src/pdbcml [delete] Deleting directory /home/rguha/src/java/cdk-nightly/cdk/build/pdbcml 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/rguha/src/java/cdk-nightly/cdk/build/src/reaction [mkdir] Created dir: /home/rguha/src/java/cdk-nightly/cdk/build/reaction [copy] Copying 51 files to /home/rguha/src/java/cdk-nightly/cdk/build/src/reaction [javac] Compiling 51 source files to /home/rguha/src/java/cdk-nightly/cdk/build/reaction [jar] Building jar: /home/rguha/src/java/cdk-nightly/cdk/dist/jar/cdk-reaction.jar [delete] Deleting directory /home/rguha/src/java/cdk-nightly/cdk/build/src/reaction [delete] Deleting directory /home/rguha/src/java/cdk-nightly/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/rguha/src/java/cdk-nightly/cdk/build/src/charges [mkdir] Created dir: /home/rguha/src/java/cdk-nightly/cdk/build/charges [copy] Copying 10 files to /home/rguha/src/java/cdk-nightly/cdk/build/src/charges [javac] Compiling 10 source files to /home/rguha/src/java/cdk-nightly/cdk/build/charges [jar] Building jar: /home/rguha/src/java/cdk-nightly/cdk/dist/jar/cdk-charges.jar [delete] Deleting directory /home/rguha/src/java/cdk-nightly/cdk/build/src/charges [delete] Deleting directory /home/rguha/src/java/cdk-nightly/cdk/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/rguha/src/java/cdk-nightly/cdk/build/src/ionpot [mkdir] Created dir: /home/rguha/src/java/cdk-nightly/cdk/build/ionpot [copy] Copying 1 file to /home/rguha/src/java/cdk-nightly/cdk/build/src/ionpot [javac] Compiling 1 source file to /home/rguha/src/java/cdk-nightly/cdk/build/ionpot [jar] Building jar: /home/rguha/src/java/cdk-nightly/cdk/dist/jar/cdk-ionpot.jar [delete] Deleting directory /home/rguha/src/java/cdk-nightly/cdk/build/src/ionpot [delete] Deleting directory /home/rguha/src/java/cdk-nightly/cdk/build/ionpot checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's qm 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/rguha/src/java/cdk-nightly/cdk/build/src/qm [mkdir] Created dir: /home/rguha/src/java/cdk-nightly/cdk/build/qm [copy] Copying 16 files to /home/rguha/src/java/cdk-nightly/cdk/build/src/qm [javac] Compiling 16 source files to /home/rguha/src/java/cdk-nightly/cdk/build/qm [javac] Note: /home/rguha/src/java/cdk-nightly/cdk/build/src/qm/org/openscience/cdk/renderer/GraphRendererModel.java uses unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [jar] Building jar: /home/rguha/src/java/cdk-nightly/cdk/dist/jar/cdk-qm.jar [delete] Deleting directory /home/rguha/src/java/cdk-nightly/cdk/build/src/qm [delete] Deleting directory /home/rguha/src/java/cdk-nightly/cdk/build/qm 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/rguha/src/java/cdk-nightly/cdk/build/src/qsar [mkdir] Created dir: /home/rguha/src/java/cdk-nightly/cdk/build/qsar [copy] Copying 30 files to /home/rguha/src/java/cdk-nightly/cdk/build/src/qsar [javac] Compiling 30 source files to /home/rguha/src/java/cdk-nightly/cdk/build/qsar [javac] /home/rguha/src/java/cdk-nightly/cdk/build/src/qsar/org/openscience/cdk/qsar/model/R/CNNRegressionModel.java:446: 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/rguha/src/java/cdk-nightly/cdk/build/src/qsar/org/openscience/cdk/qsar/model/R/LinearRegressionModel.java:385: 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/rguha/src/java/cdk-nightly/cdk/build/src/qsar/org/openscience/cdk/qsar/model/R/CNNClassificationModel.java:400: warning: [deprecation] org.openscience.cdk.qsar.model.R.CNNClassificationModelFit in org.openscience.cdk.qsar.model.R has been deprecated [javac] this.modelfit = (CNNClassificationModelFit)revaluator.call("buildCNNClass", [javac] ^ [javac] /home/rguha/src/java/cdk-nightly/cdk/build/src/qsar/org/openscience/cdk/qsar/model/R/CNNClassificationModel.java:428: warning: [deprecation] org.openscience.cdk.qsar.model.R.CNNClassificationModelPredict in org.openscience.cdk.qsar.model.R has been deprecated [javac] this.modelpredict = (CNNClassificationModelPredict)revaluator.call("predictCNNClass", [javac] ^ [javac] /home/rguha/src/java/cdk-nightly/cdk/build/src/qsar/org/openscience/cdk/qsar/model/R/CNNClassificationModel.java:449: warning: [deprecation] org.openscience.cdk.qsar.model.R.CNNClassificationModelFit in org.openscience.cdk.qsar.model.R has been deprecated [javac] this.modelfit = (CNNClassificationModelFit)model; [javac] ^ [javac] /home/rguha/src/java/cdk-nightly/cdk/build/src/qsar/org/openscience/cdk/qsar/model/R/CNNClassificationModel.java:469: warning: [deprecation] org.openscience.cdk.qsar.model.R.CNNClassificationModelFit in org.openscience.cdk.qsar.model.R has been deprecated [javac] this.modelfit =(CNNClassificationModelFit)model; [javac] ^ [javac] /home/rguha/src/java/cdk-nightly/cdk/build/src/qsar/org/openscience/cdk/qsar/model/R/CNNRegressionModel.java:176: warning: [deprecation] org.openscience.cdk.qsar.model.R.CNNClassificationModel in org.openscience.cdk.qsar.model.R has been deprecated [javac] this.currentID = CNNClassificationModel.globalID; [javac] ^ [javac] /home/rguha/src/java/cdk-nightly/cdk/build/src/qsar/org/openscience/cdk/qsar/model/R/CNNRegressionModel.java:177: warning: [deprecation] org.openscience.cdk.qsar.model.R.CNNClassificationModel in org.openscience.cdk.qsar.model.R has been deprecated [javac] CNNClassificationModel.globalID++; [javac] ^ [javac] /home/rguha/src/java/cdk-nightly/cdk/build/src/qsar/org/openscience/cdk/qsar/model/R/CNNRegressionModel.java:401: warning: [deprecation] org.openscience.cdk.qsar.model.R.CNNRegressionModelFit in org.openscience.cdk.qsar.model.R has been deprecated [javac] this.modelfit = (CNNRegressionModelFit)revaluator.call("buildCNN", [javac] ^ [javac] /home/rguha/src/java/cdk-nightly/cdk/build/src/qsar/org/openscience/cdk/qsar/model/R/CNNRegressionModel.java:428: warning: [deprecation] org.openscience.cdk.qsar.model.R.CNNRegressionModelPredict in org.openscience.cdk.qsar.model.R has been deprecated [javac] this.modelpredict = (CNNRegressionModelPredict)revaluator.call("predictCNN", [javac] ^ [javac] /home/rguha/src/java/cdk-nightly/cdk/build/src/qsar/org/openscience/cdk/qsar/model/R/CNNRegressionModel.java:450: warning: [deprecation] org.openscience.cdk.qsar.model.R.CNNRegressionModelSummary in org.openscience.cdk.qsar.model.R has been deprecated [javac] CNNRegressionModelSummary s = null; [javac] ^ [javac] /home/rguha/src/java/cdk-nightly/cdk/build/src/qsar/org/openscience/cdk/qsar/model/R/CNNRegressionModel.java:452: warning: [deprecation] org.openscience.cdk.qsar.model.R.CNNRegressionModelSummary in org.openscience.cdk.qsar.model.R has been deprecated [javac] s = (CNNRegressionModelSummary)revaluator.call("summaryModel", [javac] ^ [javac] /home/rguha/src/java/cdk-nightly/cdk/build/src/qsar/org/openscience/cdk/qsar/model/R/CNNRegressionModel.java:474: warning: [deprecation] org.openscience.cdk.qsar.model.R.CNNRegressionModelFit in org.openscience.cdk.qsar.model.R has been deprecated [javac] this.modelfit = (CNNRegressionModelFit)model; [javac] ^ [javac] /home/rguha/src/java/cdk-nightly/cdk/build/src/qsar/org/openscience/cdk/qsar/model/R/CNNRegressionModel.java:494: warning: [deprecation] org.openscience.cdk.qsar.model.R.CNNRegressionModelFit in org.openscience.cdk.qsar.model.R has been deprecated [javac] this.modelfit =(CNNRegressionModelFit)model; [javac] ^ [javac] /home/rguha/src/java/cdk-nightly/cdk/build/src/qsar/org/openscience/cdk/qsar/model/R/LinearRegressionModel.java:283: warning: [deprecation] org.openscience.cdk.qsar.model.R.LinearRegressionModelFit in org.openscience.cdk.qsar.model.R has been deprecated [javac] this.modelfit = (LinearRegressionModelFit)revaluator.call("buildLM", [javac] ^ [javac] /home/rguha/src/java/cdk-nightly/cdk/build/src/qsar/org/openscience/cdk/qsar/model/R/LinearRegressionModel.java:367: warning: [deprecation] org.openscience.cdk.qsar.model.R.LinearRegressionModelPredict in org.openscience.cdk.qsar.model.R has been deprecated [javac] this.modelpredict = (LinearRegressionModelPredict)revaluator.call("predictLM", [javac] ^ [javac] /home/rguha/src/java/cdk-nightly/cdk/build/src/qsar/org/openscience/cdk/qsar/model/R/LinearRegressionModel.java:389: warning: [deprecation] org.openscience.cdk.qsar.model.R.LinearRegressionModelSummary in org.openscience.cdk.qsar.model.R has been deprecated [javac] LinearRegressionModelSummary s = null; [javac] ^ [javac] /home/rguha/src/java/cdk-nightly/cdk/build/src/qsar/org/openscience/cdk/qsar/model/R/LinearRegressionModel.java:391: warning: [deprecation] org.openscience.cdk.qsar.model.R.LinearRegressionModelSummary in org.openscience.cdk.qsar.model.R has been deprecated [javac] s = (LinearRegressionModelSummary)revaluator.call("summaryModel", [javac] ^ [javac] /home/rguha/src/java/cdk-nightly/cdk/build/src/qsar/org/openscience/cdk/qsar/model/R/LinearRegressionModel.java:413: warning: [deprecation] org.openscience.cdk.qsar.model.R.LinearRegressionModelFit in org.openscience.cdk.qsar.model.R has been deprecated [javac] this.modelfit =(LinearRegressionModelFit)model; [javac] ^ [javac] /home/rguha/src/java/cdk-nightly/cdk/build/src/qsar/org/openscience/cdk/qsar/model/R/LinearRegressionModel.java:433: warning: [deprecation] org.openscience.cdk.qsar.model.R.LinearRegressionModelFit in org.openscience.cdk.qsar.model.R has been deprecated [javac] this.modelfit =(LinearRegressionModelFit)model; [javac] ^ [javac] /home/rguha/src/java/cdk-nightly/cdk/build/src/qsar/org/openscience/cdk/qsar/model/R/PLSRegressionModel.java:289: warning: [deprecation] org.openscience.cdk.qsar.model.R.PLSRegressionModelPredict in org.openscience.cdk.qsar.model.R has been deprecated [javac] this.modelpredict = (PLSRegressionModelPredict)revaluator.call("predictPLS", [javac] ^ [javac] /home/rguha/src/java/cdk-nightly/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.rms = V2M.VectorToMatrix(rms, ncase, npvar); [javac] ^ [javac] /home/rguha/src/java/cdk-nightly/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.xscores = V2M.VectorToMatrix(xscores, nobs, maxncomp); [javac] ^ [javac] /home/rguha/src/java/cdk-nightly/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.yscores = V2M.VectorToMatrix(yscores, nobs, maxncomp); [javac] ^ [javac] /home/rguha/src/java/cdk-nightly/cdk/build/src/qsar/org/openscience/cdk/qsar/model/R/PLSRegressionModelFit.java:118: 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/rguha/src/java/cdk-nightly/cdk/build/src/qsar/org/openscience/cdk/qsar/model/R/PLSRegressionModelFit.java:119: 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/rguha/src/java/cdk-nightly/cdk/build/src/qsar/org/openscience/cdk/qsar/model/R/PLSRegressionModelFit.java:120: 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/rguha/src/java/cdk-nightly/cdk/build/src/qsar/org/openscience/cdk/qsar/model/R/PLSRegressionModelFit.java:121: 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/rguha/src/java/cdk-nightly/cdk/build/src/qsar/org/openscience/cdk/qsar/model/R/PLSRegressionModelFit.java:147: 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/rguha/src/java/cdk-nightly/cdk/build/src/qsar/org/openscience/cdk/qsar/model/R/PLSRegressionModelFit.java:148: 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/rguha/src/java/cdk-nightly/cdk/build/src/qsar/org/openscience/cdk/qsar/model/R/PLSRegressionModelFit.java:149: 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/rguha/src/java/cdk-nightly/cdk/build/src/qsar/org/openscience/cdk/qsar/model/R/PLSRegressionModelFit.java:150: 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] 32 warnings [jar] Building jar: /home/rguha/src/java/cdk-nightly/cdk/dist/jar/cdk-qsar.jar [delete] Deleting directory /home/rguha/src/java/cdk-nightly/cdk/build/src/qsar [delete] Deleting directory /home/rguha/src/java/cdk-nightly/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: 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/rguha/src/java/cdk-nightly/cdk/build/src/qsaratomic [mkdir] Created dir: /home/rguha/src/java/cdk-nightly/cdk/build/qsaratomic [copy] Copying 28 files to /home/rguha/src/java/cdk-nightly/cdk/build/src/qsaratomic [javac] Compiling 28 source files to /home/rguha/src/java/cdk-nightly/cdk/build/qsaratomic [jar] Building jar: /home/rguha/src/java/cdk-nightly/cdk/dist/jar/cdk-qsaratomic.jar [delete] Deleting directory /home/rguha/src/java/cdk-nightly/cdk/build/src/qsaratomic [delete] Deleting directory /home/rguha/src/java/cdk-nightly/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/rguha/src/java/cdk-nightly/cdk/build/src/qsarbond [mkdir] Created dir: /home/rguha/src/java/cdk-nightly/cdk/build/qsarbond [copy] Copying 5 files to /home/rguha/src/java/cdk-nightly/cdk/build/src/qsarbond [javac] Compiling 5 source files to /home/rguha/src/java/cdk-nightly/cdk/build/qsarbond [jar] Building jar: /home/rguha/src/java/cdk-nightly/cdk/dist/jar/cdk-qsarbond.jar [delete] Deleting directory /home/rguha/src/java/cdk-nightly/cdk/build/src/qsarbond [delete] Deleting directory /home/rguha/src/java/cdk-nightly/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/rguha/src/java/cdk-nightly/cdk/build/src/qsarmolecular [mkdir] Created dir: /home/rguha/src/java/cdk-nightly/cdk/build/qsarmolecular [copy] Copying 44 files to /home/rguha/src/java/cdk-nightly/cdk/build/src/qsarmolecular [javac] Compiling 44 source files to /home/rguha/src/java/cdk-nightly/cdk/build/qsarmolecular [javac] Note: Some input files use unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [jar] Building jar: /home/rguha/src/java/cdk-nightly/cdk/dist/jar/cdk-qsarmolecular.jar [delete] Deleting directory /home/rguha/src/java/cdk-nightly/cdk/build/src/qsarmolecular [delete] Deleting directory /home/rguha/src/java/cdk-nightly/cdk/build/qsarmolecular checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's qsarionpot 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/rguha/src/java/cdk-nightly/cdk/build/src/qsarionpot [mkdir] Created dir: /home/rguha/src/java/cdk-nightly/cdk/build/qsarionpot [copy] Copying 3 files to /home/rguha/src/java/cdk-nightly/cdk/build/src/qsarionpot [javac] Compiling 3 source files to /home/rguha/src/java/cdk-nightly/cdk/build/qsarionpot [jar] Building jar: /home/rguha/src/java/cdk-nightly/cdk/dist/jar/cdk-qsarionpot.jar [delete] Deleting directory /home/rguha/src/java/cdk-nightly/cdk/build/src/qsarionpot [delete] Deleting directory /home/rguha/src/java/cdk-nightly/cdk/build/qsarionpot 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/rguha/src/java/cdk-nightly/cdk/build/src/qsarprotein [mkdir] Created dir: /home/rguha/src/java/cdk-nightly/cdk/build/qsarprotein [copy] Copying 2 files to /home/rguha/src/java/cdk-nightly/cdk/build/src/qsarprotein [javac] Compiling 2 source files to /home/rguha/src/java/cdk-nightly/cdk/build/qsarprotein [javac] Note: /home/rguha/src/java/cdk-nightly/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. [jar] Building jar: /home/rguha/src/java/cdk-nightly/cdk/dist/jar/cdk-qsarprotein.jar [delete] Deleting directory /home/rguha/src/java/cdk-nightly/cdk/build/src/qsarprotein [delete] Deleting directory /home/rguha/src/java/cdk-nightly/cdk/build/qsarprotein checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's qsarcml 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/rguha/src/java/cdk-nightly/cdk/build/src/qsarcml [mkdir] Created dir: /home/rguha/src/java/cdk-nightly/cdk/build/qsarcml [copy] Copying 1 file to /home/rguha/src/java/cdk-nightly/cdk/build/src/qsarcml [javac] Compiling 1 source file to /home/rguha/src/java/cdk-nightly/cdk/build/qsarcml [jar] Building jar: /home/rguha/src/java/cdk-nightly/cdk/dist/jar/cdk-qsarcml.jar [delete] Deleting directory /home/rguha/src/java/cdk-nightly/cdk/build/src/qsarcml [delete] Deleting directory /home/rguha/src/java/cdk-nightly/cdk/build/qsarcml 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/rguha/src/java/cdk-nightly/cdk/build/src/forcefield [mkdir] Created dir: /home/rguha/src/java/cdk-nightly/cdk/build/forcefield [copy] Copying 23 files to /home/rguha/src/java/cdk-nightly/cdk/build/src/forcefield [javac] Compiling 23 source files to /home/rguha/src/java/cdk-nightly/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/rguha/src/java/cdk-nightly/cdk/dist/jar/cdk-forcefield.jar [delete] Deleting directory /home/rguha/src/java/cdk-nightly/cdk/build/src/forcefield [delete] Deleting directory /home/rguha/src/java/cdk-nightly/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/rguha/src/java/cdk-nightly/cdk/build/src/builder3d [mkdir] Created dir: /home/rguha/src/java/cdk-nightly/cdk/build/builder3d [copy] Copying 5 files to /home/rguha/src/java/cdk-nightly/cdk/build/src/builder3d [javac] Compiling 5 source files to /home/rguha/src/java/cdk-nightly/cdk/build/builder3d [javac] Note: /home/rguha/src/java/cdk-nightly/cdk/build/src/builder3d/org/openscience/cdk/modeling/builder3d/AtomPlacer3D.java uses unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [jar] Building jar: /home/rguha/src/java/cdk-nightly/cdk/dist/jar/cdk-builder3d.jar [delete] Deleting directory /home/rguha/src/java/cdk-nightly/cdk/build/src/builder3d [delete] Deleting directory /home/rguha/src/java/cdk-nightly/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/rguha/src/java/cdk-nightly/cdk/build/src/builder3dtools [mkdir] Created dir: /home/rguha/src/java/cdk-nightly/cdk/build/builder3dtools [copy] Copying 1 file to /home/rguha/src/java/cdk-nightly/cdk/build/src/builder3dtools [javac] Compiling 1 source file to /home/rguha/src/java/cdk-nightly/cdk/build/builder3dtools [javac] Note: /home/rguha/src/java/cdk-nightly/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/rguha/src/java/cdk-nightly/cdk/dist/jar/cdk-builder3dtools.jar [delete] Deleting directory /home/rguha/src/java/cdk-nightly/cdk/build/src/builder3dtools [delete] Deleting directory /home/rguha/src/java/cdk-nightly/cdk/build/builder3dtools 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/rguha/src/java/cdk-nightly/cdk/build/src/pcore [mkdir] Created dir: /home/rguha/src/java/cdk-nightly/cdk/build/pcore [copy] Copying 8 files to /home/rguha/src/java/cdk-nightly/cdk/build/src/pcore [javac] Compiling 8 source files to /home/rguha/src/java/cdk-nightly/cdk/build/pcore [jar] Building jar: /home/rguha/src/java/cdk-nightly/cdk/dist/jar/cdk-pcore.jar [delete] Deleting directory /home/rguha/src/java/cdk-nightly/cdk/build/src/pcore [delete] Deleting directory /home/rguha/src/java/cdk-nightly/cdk/build/pcore 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/rguha/src/java/cdk-nightly/cdk/build/src/inchi [mkdir] Created dir: /home/rguha/src/java/cdk-nightly/cdk/build/inchi [copy] Copying 3 files to /home/rguha/src/java/cdk-nightly/cdk/build/src/inchi [javac] Compiling 3 source files to /home/rguha/src/java/cdk-nightly/cdk/build/inchi [jar] Building jar: /home/rguha/src/java/cdk-nightly/cdk/dist/jar/cdk-inchi.jar [delete] Deleting directory /home/rguha/src/java/cdk-nightly/cdk/build/src/inchi [delete] Deleting directory /home/rguha/src/java/cdk-nightly/cdk/build/inchi checkPlatforms: check: dist.init: compile-needed-test: compile-module: [echo] Compiling classes for CDK's diff 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/rguha/src/java/cdk-nightly/cdk/build/src/diff [mkdir] Created dir: /home/rguha/src/java/cdk-nightly/cdk/build/diff [copy] Copying 24 files to /home/rguha/src/java/cdk-nightly/cdk/build/src/diff [javac] Compiling 24 source files to /home/rguha/src/java/cdk-nightly/cdk/build/diff [jar] Building jar: /home/rguha/src/java/cdk-nightly/cdk/dist/jar/cdk-diff.jar [delete] Deleting directory /home/rguha/src/java/cdk-nightly/cdk/build/src/diff [delete] Deleting directory /home/rguha/src/java/cdk-nightly/cdk/build/diff dist-large: [mkdir] Created dir: /home/rguha/src/java/cdk-nightly/cdk/dist/appjars [unjar] Expanding: /home/rguha/src/java/cdk-nightly/cdk/jar/JRI.jar into /home/rguha/src/java/cdk-nightly/cdk/dist/appjars [unjar] Expanding: /home/rguha/src/java/cdk-nightly/cdk/jar/jama-1.0.2.jar into /home/rguha/src/java/cdk-nightly/cdk/dist/appjars [unjar] Expanding: /home/rguha/src/java/cdk-nightly/cdk/jar/jgrapht-0.6.0.jar into /home/rguha/src/java/cdk-nightly/cdk/dist/appjars [unjar] Expanding: /home/rguha/src/java/cdk-nightly/cdk/jar/jniinchi-0.4.jar into /home/rguha/src/java/cdk-nightly/cdk/dist/appjars [unjar] Expanding: /home/rguha/src/java/cdk-nightly/cdk/jar/jumbo-5.4.2-b2.jar into /home/rguha/src/java/cdk-nightly/cdk/dist/appjars [unjar] Expanding: /home/rguha/src/java/cdk-nightly/cdk/jar/log4j.jar into /home/rguha/src/java/cdk-nightly/cdk/dist/appjars [unjar] Expanding: /home/rguha/src/java/cdk-nightly/cdk/jar/sjava-0.68.jar into /home/rguha/src/java/cdk-nightly/cdk/dist/appjars [unjar] Expanding: /home/rguha/src/java/cdk-nightly/cdk/jar/vecmath1.2-1.14.jar into /home/rguha/src/java/cdk-nightly/cdk/dist/appjars [unjar] Expanding: /home/rguha/src/java/cdk-nightly/cdk/jar/xom-1.1.jar into /home/rguha/src/java/cdk-nightly/cdk/dist/appjars [unjar] Expanding: /home/rguha/src/java/cdk-nightly/cdk/jar/xpp3-1.1.4c.jar into /home/rguha/src/java/cdk-nightly/cdk/dist/appjars [unjar] Expanding: /home/rguha/src/java/cdk-nightly/cdk/dist/jar/cdk-atomtype.jar into /home/rguha/src/java/cdk-nightly/cdk/dist/appjars [unjar] Expanding: /home/rguha/src/java/cdk-nightly/cdk/dist/jar/cdk-builder3d.jar into /home/rguha/src/java/cdk-nightly/cdk/dist/appjars [unjar] Expanding: /home/rguha/src/java/cdk-nightly/cdk/dist/jar/cdk-builder3dtools.jar into /home/rguha/src/java/cdk-nightly/cdk/dist/appjars [unjar] Expanding: /home/rguha/src/java/cdk-nightly/cdk/dist/jar/cdk-charges.jar into /home/rguha/src/java/cdk-nightly/cdk/dist/appjars [unjar] Expanding: /home/rguha/src/java/cdk-nightly/cdk/dist/jar/cdk-control.jar into /home/rguha/src/java/cdk-nightly/cdk/dist/appjars [unjar] Expanding: /home/rguha/src/java/cdk-nightly/cdk/dist/jar/cdk-core.jar into /home/rguha/src/java/cdk-nightly/cdk/dist/appjars [unjar] Expanding: /home/rguha/src/java/cdk-nightly/cdk/dist/jar/cdk-data.jar into /home/rguha/src/java/cdk-nightly/cdk/dist/appjars [unjar] Expanding: /home/rguha/src/java/cdk-nightly/cdk/dist/jar/cdk-datadebug.jar into /home/rguha/src/java/cdk-nightly/cdk/dist/appjars [unjar] Expanding: /home/rguha/src/java/cdk-nightly/cdk/dist/jar/cdk-dict.jar into /home/rguha/src/java/cdk-nightly/cdk/dist/appjars [unjar] Expanding: /home/rguha/src/java/cdk-nightly/cdk/dist/jar/cdk-diff.jar into /home/rguha/src/java/cdk-nightly/cdk/dist/appjars [unjar] Expanding: /home/rguha/src/java/cdk-nightly/cdk/dist/jar/cdk-extra.jar into /home/rguha/src/java/cdk-nightly/cdk/dist/appjars [unjar] Expanding: /home/rguha/src/java/cdk-nightly/cdk/dist/jar/cdk-fingerprint.jar into /home/rguha/src/java/cdk-nightly/cdk/dist/appjars [unjar] Expanding: /home/rguha/src/java/cdk-nightly/cdk/dist/jar/cdk-forcefield.jar into /home/rguha/src/java/cdk-nightly/cdk/dist/appjars [unjar] Expanding: /home/rguha/src/java/cdk-nightly/cdk/dist/jar/cdk-formula.jar into /home/rguha/src/java/cdk-nightly/cdk/dist/appjars [unjar] Expanding: /home/rguha/src/java/cdk-nightly/cdk/dist/jar/cdk-inchi.jar into /home/rguha/src/java/cdk-nightly/cdk/dist/appjars [unjar] Expanding: /home/rguha/src/java/cdk-nightly/cdk/dist/jar/cdk-interfaces.jar into /home/rguha/src/java/cdk-nightly/cdk/dist/appjars [unjar] Expanding: /home/rguha/src/java/cdk-nightly/cdk/dist/jar/cdk-io.jar into /home/rguha/src/java/cdk-nightly/cdk/dist/appjars [unjar] Expanding: /home/rguha/src/java/cdk-nightly/cdk/dist/jar/cdk-ionpot.jar into /home/rguha/src/java/cdk-nightly/cdk/dist/appjars [unjar] Expanding: /home/rguha/src/java/cdk-nightly/cdk/dist/jar/cdk-isomorphism.jar into /home/rguha/src/java/cdk-nightly/cdk/dist/appjars [unjar] Expanding: /home/rguha/src/java/cdk-nightly/cdk/dist/jar/cdk-libiocml.jar into /home/rguha/src/java/cdk-nightly/cdk/dist/appjars [unjar] Expanding: /home/rguha/src/java/cdk-nightly/cdk/dist/jar/cdk-libiomd.jar into /home/rguha/src/java/cdk-nightly/cdk/dist/appjars [unjar] Expanding: /home/rguha/src/java/cdk-nightly/cdk/dist/jar/cdk-nonotify.jar into /home/rguha/src/java/cdk-nightly/cdk/dist/appjars [unjar] Expanding: /home/rguha/src/java/cdk-nightly/cdk/dist/jar/cdk-pcore.jar into /home/rguha/src/java/cdk-nightly/cdk/dist/appjars [unjar] Expanding: /home/rguha/src/java/cdk-nightly/cdk/dist/jar/cdk-pdb.jar into /home/rguha/src/java/cdk-nightly/cdk/dist/appjars [unjar] Expanding: /home/rguha/src/java/cdk-nightly/cdk/dist/jar/cdk-pdbcml.jar into /home/rguha/src/java/cdk-nightly/cdk/dist/appjars [unjar] Expanding: /home/rguha/src/java/cdk-nightly/cdk/dist/jar/cdk-qsar.jar into /home/rguha/src/java/cdk-nightly/cdk/dist/appjars [unjar] Expanding: /home/rguha/src/java/cdk-nightly/cdk/dist/jar/cdk-qsaratomic.jar into /home/rguha/src/java/cdk-nightly/cdk/dist/appjars [unjar] Expanding: /home/rguha/src/java/cdk-nightly/cdk/dist/jar/cdk-qsarbond.jar into /home/rguha/src/java/cdk-nightly/cdk/dist/appjars [unjar] Expanding: /home/rguha/src/java/cdk-nightly/cdk/dist/jar/cdk-qsarcml.jar into /home/rguha/src/java/cdk-nightly/cdk/dist/appjars [unjar] Expanding: /home/rguha/src/java/cdk-nightly/cdk/dist/jar/cdk-qsarionpot.jar into /home/rguha/src/java/cdk-nightly/cdk/dist/appjars [unjar] Expanding: /home/rguha/src/java/cdk-nightly/cdk/dist/jar/cdk-qsarmolecular.jar into /home/rguha/src/java/cdk-nightly/cdk/dist/appjars [unjar] Expanding: /home/rguha/src/java/cdk-nightly/cdk/dist/jar/cdk-qsarprotein.jar into /home/rguha/src/java/cdk-nightly/cdk/dist/appjars [unjar] Expanding: /home/rguha/src/java/cdk-nightly/cdk/dist/jar/cdk-reaction.jar into /home/rguha/src/java/cdk-nightly/cdk/dist/appjars [unjar] Expanding: /home/rguha/src/java/cdk-nightly/cdk/dist/jar/cdk-render.jar into /home/rguha/src/java/cdk-nightly/cdk/dist/appjars [unjar] Expanding: /home/rguha/src/java/cdk-nightly/cdk/dist/jar/cdk-sdg.jar into /home/rguha/src/java/cdk-nightly/cdk/dist/appjars [unjar] Expanding: /home/rguha/src/java/cdk-nightly/cdk/dist/jar/cdk-smarts.jar into /home/rguha/src/java/cdk-nightly/cdk/dist/appjars [unjar] Expanding: /home/rguha/src/java/cdk-nightly/cdk/dist/jar/cdk-smiles.jar into /home/rguha/src/java/cdk-nightly/cdk/dist/appjars [unjar] Expanding: /home/rguha/src/java/cdk-nightly/cdk/dist/jar/cdk-standard.jar into /home/rguha/src/java/cdk-nightly/cdk/dist/appjars [unjar] Expanding: /home/rguha/src/java/cdk-nightly/cdk/dist/jar/cdk-structgen.jar into /home/rguha/src/java/cdk-nightly/cdk/dist/appjars [unjar] Expanding: /home/rguha/src/java/cdk-nightly/cdk/dist/jar/cdk-valencycheck.jar into /home/rguha/src/java/cdk-nightly/cdk/dist/appjars [jar] Building jar: /home/rguha/src/java/cdk-nightly/cdk/dist/jar/cdk-svn-20081121.jar BUILD SUCCESSFUL Total time: 3 minutes 26 seconds