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egonw / cdkbook

Groovy Cheminformatics with the Chemistry Development Kit
https://egonw.github.io/cdkbook/
Creative Commons Attribution Share Alike 4.0 International
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error in the build system #17

Closed egonw closed 4 years ago

egonw commented 4 years ago 
Processing  SimpleFingerprintDemo.groovyin
doing SimpleFingerprintDemo.out...
Caught: java.lang.NoClassDefFoundError: org/openscience/cdk/fingerprint/IFingerprinter
java.lang.NoClassDefFoundError: org/openscience/cdk/fingerprint/IFingerprinter
        at java.lang.ClassLoader.defineClass1(Native Method)
        at java.lang.ClassLoader.defineClass(ClassLoader.java:763)
        at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:142)
        at java.net.URLClassLoader.defineClass(URLClassLoader.java:468)
        at java.net.URLClassLoader.access$100(URLClassLoader.java:74)
        at java.net.URLClassLoader$1.run(URLClassLoader.java:369)
        at java.net.URLClassLoader$1.run(URLClassLoader.java:363)
        at java.security.AccessController.doPrivileged(Native Method)
        at java.net.URLClassLoader.findClass(URLClassLoader.java:362)
        at org.codehaus.groovy.tools.RootLoader.oldFindClass(RootLoader.java:175)
        at org.codehaus.groovy.tools.RootLoader.loadClass(RootLoader.java:147)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:411)
        at groovy.lang.GroovyClassLoader.loadClass(GroovyClassLoader.java:702)
        at groovy.lang.GroovyClassLoader.loadClass(GroovyClassLoader.java:570)
        at org.codehaus.groovy.control.ClassNodeResolver.tryAsLoaderClassOrScript(ClassNodeResolver.java:184)
        at org.codehaus.groovy.control.ClassNodeResolver.findClassNode(ClassNodeResolver.java:169)
        at org.codehaus.groovy.control.ClassNodeResolver.resolveName(ClassNodeResolver.java:125)
        at org.codehaus.groovy.control.ResolveVisitor.resolveToOuter(ResolveVisitor.java:740)
        at org.codehaus.groovy.control.ResolveVisitor.resolve(ResolveVisitor.java:377)
        at org.codehaus.groovy.control.ResolveVisitor.resolve(ResolveVisitor.java:340)
        at org.codehaus.groovy.control.ResolveVisitor.resolveOrFail(ResolveVisitor.java:324)
        at org.codehaus.groovy.control.ResolveVisitor.resolveOrFail(ResolveVisitor.java:336)
        at org.codehaus.groovy.control.ResolveVisitor.transformConstructorCallExpression(ResolveVisitor.java:1131)
        at org.codehaus.groovy.control.ResolveVisitor.transform(ResolveVisitor.java:770)
        at org.codehaus.groovy.control.ResolveVisitor.transformBinaryExpression(ResolveVisitor.java:1099)
        at org.codehaus.groovy.control.ResolveVisitor.transform(ResolveVisitor.java:764)
        at org.codehaus.groovy.ast.ClassCodeExpressionTransformer.visitExpressionStatement(ClassCodeExpressionTransformer.java:144)
        at org.codehaus.groovy.ast.stmt.ExpressionStatement.visit(ExpressionStatement.java:42)
        at org.codehaus.groovy.ast.CodeVisitorSupport.visitBlockStatement(CodeVisitorSupport.java:88)
        at org.codehaus.groovy.ast.ClassCodeVisitorSupport.visitBlockStatement(ClassCodeVisitorSupport.java:166)
        at org.codehaus.groovy.control.ResolveVisitor.visitBlockStatement(ResolveVisitor.java:1402)
        at org.codehaus.groovy.ast.stmt.BlockStatement.visit(BlockStatement.java:71)
        at org.codehaus.groovy.ast.ClassCodeVisitorSupport.visitClassCodeContainer(ClassCodeVisitorSupport.java:104)
        at org.codehaus.groovy.ast.ClassCodeVisitorSupport.visitConstructorOrMethod(ClassCodeVisitorSupport.java:115)
        at org.codehaus.groovy.ast.ClassCodeExpressionTransformer.visitConstructorOrMethod(ClassCodeExpressionTransformer.java:55)
        at org.codehaus.groovy.control.ResolveVisitor.visitConstructorOrMethod(ResolveVisitor.java:239)
        at org.codehaus.groovy.ast.ClassCodeVisitorSupport.visitMethod(ClassCodeVisitorSupport.java:126)
        at org.codehaus.groovy.ast.ClassNode.visitContents(ClassNode.java:1081)
        at org.codehaus.groovy.ast.ClassCodeVisitorSupport.visitClass(ClassCodeVisitorSupport.java:53)
        at org.codehaus.groovy.control.ResolveVisitor.visitClass(ResolveVisitor.java:1345)
        at org.codehaus.groovy.control.ResolveVisitor.startResolving(ResolveVisitor.java:214)
        at org.codehaus.groovy.control.CompilationUnit$12.call(CompilationUnit.java:684)
        at org.codehaus.groovy.control.CompilationUnit.applyToSourceUnits(CompilationUnit.java:966)
        at org.codehaus.groovy.control.CompilationUnit.doPhaseOperation(CompilationUnit.java:626)
        at org.codehaus.groovy.control.CompilationUnit.compile(CompilationUnit.java:575)
        at groovy.lang.GroovyClassLoader.doParseClass(GroovyClassLoader.java:323)
        at groovy.lang.GroovyClassLoader.parseClass(GroovyClassLoader.java:293)
        at groovy.lang.GroovyShell.parseClass(GroovyShell.java:677)
        at groovy.lang.GroovyShell.run(GroovyShell.java:506)
        at groovy.lang.GroovyShell.run(GroovyShell.java:496)
        at groovy.ui.GroovyMain.processOnce(GroovyMain.java:597)
        at groovy.ui.GroovyMain.run(GroovyMain.java:329)
        at groovy.ui.GroovyMain.process(GroovyMain.java:315)
        at groovy.ui.GroovyMain.processArgs(GroovyMain.java:134)
        at groovy.ui.GroovyMain.main(GroovyMain.java:114)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:498)
        at org.codehaus.groovy.tools.GroovyStarter.rootLoader(GroovyStarter.java:116)
        at org.codehaus.groovy.tools.GroovyStarter.main(GroovyStarter.java:138)
Caused by: java.lang.ClassNotFoundException: org.openscience.cdk.fingerprint.IFingerprinter
        at org.codehaus.groovy.tools.RootLoader.findClass(RootLoader.java:179)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
        at org.codehaus.groovy.tools.RootLoader.loadClass(RootLoader.java:151)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
        ... 61 more
egonw commented 4 years ago

Also here:

Processing  GuessSMILES.groovyin
doing GuessSMILES.out...
Caught: java.lang.NoClassDefFoundError: org/openscience/cdk/io/formats/IChemFormatMatcher
java.lang.NoClassDefFoundError: org/openscience/cdk/io/formats/IChemFormatMatcher
        at java.lang.ClassLoader.defineClass1(Native Method)
        at java.lang.ClassLoader.defineClass(ClassLoader.java:763)
        at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:142)
        at java.net.URLClassLoader.defineClass(URLClassLoader.java:468)
        at java.net.URLClassLoader.access$100(URLClassLoader.java:74)
        at java.net.URLClassLoader$1.run(URLClassLoader.java:369)
        at java.net.URLClassLoader$1.run(URLClassLoader.java:363)
        at java.security.AccessController.doPrivileged(Native Method)
        at java.net.URLClassLoader.findClass(URLClassLoader.java:362)
        at org.codehaus.groovy.tools.RootLoader.oldFindClass(RootLoader.java:175)
        at org.codehaus.groovy.tools.RootLoader.loadClass(RootLoader.java:147)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:411)
        at groovy.lang.GroovyClassLoader.loadClass(GroovyClassLoader.java:702)
        at groovy.lang.GroovyClassLoader.loadClass(GroovyClassLoader.java:570)
        at org.codehaus.groovy.control.ClassNodeResolver.tryAsLoaderClassOrScript(ClassNodeResolver.java:184)
        at org.codehaus.groovy.control.ClassNodeResolver.findClassNode(ClassNodeResolver.java:169)
        at org.codehaus.groovy.control.ClassNodeResolver.resolveName(ClassNodeResolver.java:125)
        at org.codehaus.groovy.control.ResolveVisitor.resolveToOuter(ResolveVisitor.java:740)
        at org.codehaus.groovy.control.ResolveVisitor.resolve(ResolveVisitor.java:377)
        at org.codehaus.groovy.control.ResolveVisitor.resolve(ResolveVisitor.java:340)
        at org.codehaus.groovy.control.ResolveVisitor.transformVariableExpression(ResolveVisitor.java:1007)
        at org.codehaus.groovy.control.ResolveVisitor.transform(ResolveVisitor.java:758)
        at org.codehaus.groovy.control.ResolveVisitor.transformMethodCallExpression(ResolveVisitor.java:1147)
        at org.codehaus.groovy.control.ResolveVisitor.transform(ResolveVisitor.java:766)
        at org.codehaus.groovy.ast.expr.Expression.transformExpressions(Expression.java:51)
        at org.codehaus.groovy.ast.expr.ArgumentListExpression.transformExpression(ArgumentListExpression.java:69)
        at org.codehaus.groovy.control.ResolveVisitor.transform(ResolveVisitor.java:775)
        at org.codehaus.groovy.control.ResolveVisitor.transformMethodCallExpression(ResolveVisitor.java:1145)
        at org.codehaus.groovy.control.ResolveVisitor.transform(ResolveVisitor.java:766)
        at org.codehaus.groovy.ast.ClassCodeExpressionTransformer.visitExpressionStatement(ClassCodeExpressionTransformer.java:144)
        at org.codehaus.groovy.ast.stmt.ExpressionStatement.visit(ExpressionStatement.java:42)
        at org.codehaus.groovy.ast.CodeVisitorSupport.visitBlockStatement(CodeVisitorSupport.java:88)
        at org.codehaus.groovy.ast.ClassCodeVisitorSupport.visitBlockStatement(ClassCodeVisitorSupport.java:166)
        at org.codehaus.groovy.control.ResolveVisitor.visitBlockStatement(ResolveVisitor.java:1402)
        at org.codehaus.groovy.ast.stmt.BlockStatement.visit(BlockStatement.java:71)
        at org.codehaus.groovy.ast.ClassCodeVisitorSupport.visitClassCodeContainer(ClassCodeVisitorSupport.java:104)
        at org.codehaus.groovy.ast.ClassCodeVisitorSupport.visitConstructorOrMethod(ClassCodeVisitorSupport.java:115)
        at org.codehaus.groovy.ast.ClassCodeExpressionTransformer.visitConstructorOrMethod(ClassCodeExpressionTransformer.java:55)
        at org.codehaus.groovy.control.ResolveVisitor.visitConstructorOrMethod(ResolveVisitor.java:239)
        at org.codehaus.groovy.ast.ClassCodeVisitorSupport.visitMethod(ClassCodeVisitorSupport.java:126)
        at org.codehaus.groovy.ast.ClassNode.visitContents(ClassNode.java:1081)
        at org.codehaus.groovy.ast.ClassCodeVisitorSupport.visitClass(ClassCodeVisitorSupport.java:53)
        at org.codehaus.groovy.control.ResolveVisitor.visitClass(ResolveVisitor.java:1345)
        at org.codehaus.groovy.control.ResolveVisitor.startResolving(ResolveVisitor.java:214)
        at org.codehaus.groovy.control.CompilationUnit$12.call(CompilationUnit.java:684)
        at org.codehaus.groovy.control.CompilationUnit.applyToSourceUnits(CompilationUnit.java:966)
        at org.codehaus.groovy.control.CompilationUnit.doPhaseOperation(CompilationUnit.java:626)
        at org.codehaus.groovy.control.CompilationUnit.compile(CompilationUnit.java:575)
        at groovy.lang.GroovyClassLoader.doParseClass(GroovyClassLoader.java:323)
        at groovy.lang.GroovyClassLoader.parseClass(GroovyClassLoader.java:293)
        at groovy.lang.GroovyShell.parseClass(GroovyShell.java:677)
        at groovy.lang.GroovyShell.run(GroovyShell.java:506)
        at groovy.lang.GroovyShell.run(GroovyShell.java:496)
        at groovy.ui.GroovyMain.processOnce(GroovyMain.java:597)
        at groovy.ui.GroovyMain.run(GroovyMain.java:329)
        at groovy.ui.GroovyMain.process(GroovyMain.java:315)
        at groovy.ui.GroovyMain.processArgs(GroovyMain.java:134)
        at groovy.ui.GroovyMain.main(GroovyMain.java:114)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:498)
        at org.codehaus.groovy.tools.GroovyStarter.rootLoader(GroovyStarter.java:116)
        at org.codehaus.groovy.tools.GroovyStarter.main(GroovyStarter.java:138)
Caused by: java.lang.ClassNotFoundException: org.openscience.cdk.io.formats.IChemFormatMatcher
        at org.codehaus.groovy.tools.RootLoader.findClass(RootLoader.java:179)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
        at org.codehaus.groovy.tools.RootLoader.loadClass(RootLoader.java:151)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
        ... 64 more
egonw commented 4 years ago

Solved.