Saxon

I am running Saxon HE as a Groovy task as part of a Gradle build. I am frequently encountering an exception in Saxon HE which seems to involve a Stream closed exception while reading the built-in categories.xml file. Some facts:

• It is an intermittent error; the exact same code sometimes works and sometimes doesn't.
• I've made the code serial so I don't think it is a parallel execution issue.
• It seems to occur more often on Windows than on Linux but I've seen it on both.
• It happens usually on around the 3rd or 4th call to doTransform. It doesn't matter if it's on a new Transform() object or a re-used one.

I've included the stack trace below. If you look near the end it's eventually a Stream closed exception which seems to happen while processing categories.xml so I don't think it's related to my code or my files? If you think it does relate to my code then I can try to produce a minimal example that triggers it. I've seen this same exception with Saxon HE 9.9.1-8 and 11.4. Do you have any clues as to how to fix this?

08:12:14 Caused by: java.lang.ExceptionInInitializerError
08:12:14 	at net.sf.saxon.regex.RECompiler.escape(RECompiler.java:352)
08:12:14 	at net.sf.saxon.regex.RECompiler.parseAtom(RECompiler.java:789)
08:12:14 	at net.sf.saxon.regex.RECompiler.parseTerminal(RECompiler.java:990)
08:12:14 	at net.sf.saxon.regex.RECompiler.piece(RECompiler.java:1007)
08:12:14 	at net.sf.saxon.regex.RECompiler.parseBranch(RECompiler.java:1129)
08:12:14 	at net.sf.saxon.regex.RECompiler.parseExpr(RECompiler.java:1179)
08:12:14 	at net.sf.saxon.regex.RECompiler.compile(RECompiler.java:1302)
08:12:14 	at net.sf.saxon.regex.ARegularExpression.<init>(ARegularExpression.java:55)
08:12:14 	at net.sf.saxon.java.JavaPlatform.compileRegularExpression(JavaPlatform.java:482)
08:12:14 	at net.sf.saxon.Configuration.compileRegularExpression(Configuration.java:1871)
08:12:14 	at net.sf.saxon.functions.RegexFunction.tryToBindRegularExpression(RegexFunction.java:49)
08:12:14 	at net.sf.saxon.functions.RegexFunction.makeFunctionCall(RegexFunction.java:87)
08:12:14 	at net.sf.saxon.functions.Replace.makeFunctionCall(Replace.java:63)
08:12:14 	at net.sf.saxon.functions.RegexFunctionSansFlags.makeFunctionCall(RegexFunctionSansFlags.java:47)
08:12:14 	at net.sf.saxon.functions.registry.BuiltInFunctionSet.bind(BuiltInFunctionSet.java:219)
08:12:14 	at net.sf.saxon.functions.FunctionLibraryList.bind(FunctionLibraryList.java:127)
08:12:14 	at net.sf.saxon.expr.parser.XPathParser.parseFunctionCall(XPathParser.java:3685)
08:12:14 	at net.sf.saxon.expr.parser.XPathParser.parseBasicStep(XPathParser.java:2559)
08:12:14 	at net.sf.saxon.expr.parser.XPathParser.parseStepExpression(XPathParser.java:2434)
08:12:14 	at net.sf.saxon.expr.parser.XPathParser.parseRelativePath(XPathParser.java:2353)
08:12:14 	at net.sf.saxon.expr.parser.XPathParser.parsePathExpression(XPathParser.java:2315)
08:12:14 	at net.sf.saxon.expr.parser.XPathParser.parseSimpleMappingExpression(XPathParser.java:2329)
08:12:14 	at net.sf.saxon.expr.parser.XPathParser.parseUnaryExpression(XPathParser.java:2181)
08:12:14 	at net.sf.saxon.expr.parser.XPathParser.parseExprSingle(XPathParser.java:777)
08:12:14 	at net.sf.saxon.expr.parser.XPathParser.parseExpression(XPathParser.java:679)
08:12:14 	at net.sf.saxon.expr.parser.XPathParser.parse(XPathParser.java:535)
08:12:14 	at net.sf.saxon.expr.parser.ExpressionTool.make(ExpressionTool.java:89)
08:12:14 	at net.sf.saxon.style.StyleElement.makeExpression(StyleElement.java:709)
08:12:14 	at net.sf.saxon.style.XSLAnalyzeString.prepareAttributes(XSLAnalyzeString.java:77)
08:12:14 	at net.sf.saxon.style.StyleElement.processAttributes(StyleElement.java:604)
08:12:14 	at net.sf.saxon.style.StyleElement.processAllAttributes(StyleElement.java:541)
08:12:14 	at net.sf.saxon.style.StyleElement.processAllAttributes(StyleElement.java:544)
08:12:14 	at net.sf.saxon.style.XSLTemplate.processAllAttributes(XSLTemplate.java:428)
08:12:14 	at net.sf.saxon.style.PrincipalStylesheetModule.processAllAttributes(PrincipalStylesheetModule.java:587)
08:12:14 	at net.sf.saxon.style.PrincipalStylesheetModule.preprocess(PrincipalStylesheetModule.java:366)
08:12:14 	at net.sf.saxon.style.Compilation.compilePackage(Compilation.java:290)
08:12:14 	at net.sf.saxon.style.StylesheetModule.loadStylesheet(StylesheetModule.java:249)
08:12:14 	at net.sf.saxon.style.Compilation.compileSingletonPackage(Compilation.java:113)
08:12:14 	at net.sf.saxon.s9api.XsltCompiler.compile(XsltCompiler.java:936)
08:12:14 	at net.sf.saxon.Transform.doTransform(Transform.java:769)
08:12:14 	at net.sf.saxon.Transform.doTransform(Transform.java:916)
08:12:14 	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
08:12:14 	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
08:12:14 	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
08:12:14 	at XsltTransformation.execute(XsltTransformation.groovy:41)
08:12:14 	at org.gradle.workers.internal.DefaultWorkerServer.execute(DefaultWorkerServer.java:63)
08:12:14 	at org.gradle.workers.internal.AbstractClassLoaderWorker$1.create(AbstractClassLoaderWorker.java:49)
08:12:14 	at org.gradle.workers.internal.AbstractClassLoaderWorker$1.create(AbstractClassLoaderWorker.java:43)
08:12:14 	at org.gradle.internal.classloader.ClassLoaderUtils.executeInClassloader(ClassLoaderUtils.java:97)
08:12:14 	at org.gradle.workers.internal.AbstractClassLoaderWorker.executeInClassLoader(AbstractClassLoaderWorker.java:43)
08:12:14 	at org.gradle.workers.internal.IsolatedClassloaderWorker.run(IsolatedClassloaderWorker.java:49)
08:12:14 	at org.gradle.workers.internal.IsolatedClassloaderWorker.run(IsolatedClassloaderWorker.java:30)
08:12:14 	at org.gradle.workers.internal.IsolatedClassloaderWorkerFactory$1.lambda$execute$0(IsolatedClassloaderWorkerFactory.java:57)
08:12:14 	at org.gradle.workers.internal.AbstractWorker$1.call(AbstractWorker.java:44)
08:12:14 	at org.gradle.workers.internal.AbstractWorker$1.call(AbstractWorker.java:41)
08:12:14 	at org.gradle.internal.operations.DefaultBuildOperationRunner$CallableBuildOperationWorker.execute(DefaultBuildOperationRunner.java:204)
08:12:14 	at org.gradle.internal.operations.DefaultBuildOperationRunner$CallableBuildOperationWorker.execute(DefaultBuildOperationRunner.java:199)
08:12:14 	at org.gradle.internal.operations.DefaultBuildOperationRunner$2.execute(DefaultBuildOperationRunner.java:66)
08:12:14 	at org.gradle.internal.operations.DefaultBuildOperationRunner$2.execute(DefaultBuildOperationRunner.java:59)
08:12:14 	at org.gradle.internal.operations.DefaultBuildOperationRunner.execute(DefaultBuildOperationRunner.java:157)
08:12:14 	at org.gradle.internal.operations.DefaultBuildOperationRunner.execute(DefaultBuildOperationRunner.java:59)
08:12:14 	at org.gradle.internal.operations.DefaultBuildOperationRunner.call(DefaultBuildOperationRunner.java:53)
08:12:14 	at org.gradle.internal.operations.DefaultBuildOperationExecutor.call(DefaultBuildOperationExecutor.java:73)
08:12:14 	at org.gradle.workers.internal.AbstractWorker.executeWrappedInBuildOperation(AbstractWorker.java:41)
08:12:14 	at org.gradle.workers.internal.IsolatedClassloaderWorkerFactory$1.execute(IsolatedClassloaderWorkerFactory.java:49)
08:12:14 	at org.gradle.workers.internal.DefaultWorkerExecutor.lambda$submitWork$2(DefaultWorkerExecutor.java:205)
08:12:14 	at org.gradle.internal.work.DefaultConditionalExecutionQueue$ExecutionRunner.runExecution(DefaultConditionalExecutionQueue.java:187)
08:12:14 	at org.gradle.internal.work.DefaultConditionalExecutionQueue$ExecutionRunner.access$700(DefaultConditionalExecutionQueue.java:120)
08:12:14 	at org.gradle.internal.work.DefaultConditionalExecutionQueue$ExecutionRunner$1.run(DefaultConditionalExecutionQueue.java:162)
08:12:14 	at org.gradle.internal.Factories$1.create(Factories.java:31)
08:12:14 	at org.gradle.internal.work.DefaultWorkerLeaseService.withLocks(DefaultWorkerLeaseService.java:270)
08:12:14 	at org.gradle.internal.work.DefaultWorkerLeaseService.runAsWorkerThread(DefaultWorkerLeaseService.java:119)
08:12:14 	at org.gradle.internal.work.DefaultWorkerLeaseService.runAsWorkerThread(DefaultWorkerLeaseService.java:124)
08:12:14 	at org.gradle.internal.work.DefaultConditionalExecutionQueue$ExecutionRunner.runBatch(DefaultConditionalExecutionQueue.java:157)
08:12:14 	at org.gradle.internal.work.DefaultConditionalExecutionQueue$ExecutionRunner.run(DefaultConditionalExecutionQueue.java:126)
08:12:14 	... 2 more
08:12:14 Caused by: java.lang.RuntimeException: Failed to build categories.xml
08:12:14 	at net.sf.saxon.regex.charclass.Categories.build(Categories.java:126)
08:12:14 	at net.sf.saxon.regex.charclass.Categories.getCategory(Categories.java:198)
08:12:14 	at net.sf.saxon.regex.charclass.Categories.<clinit>(Categories.java:175)
08:12:14 	... 77 more
08:12:14 Caused by: net.sf.saxon.trans.XPathException: I/O error reported by XML parser processing categories.xml
08:12:14 	at net.sf.saxon.resource.ActiveSAXSource.deliver(ActiveSAXSource.java:231)
08:12:14 	at net.sf.saxon.resource.ActiveStreamSource.deliver(ActiveStreamSource.java:65)
08:12:14 	at net.sf.saxon.event.Sender.send(Sender.java:105)
08:12:14 	at net.sf.saxon.Configuration.buildDocumentTree(Configuration.java:4134)
08:12:14 	at net.sf.saxon.regex.charclass.Categories.build(Categories.java:124)
08:12:14 	... 79 more
08:12:14 Caused by: java.io.IOException: Stream closed
08:12:14 	at java.xml/com.sun.org.apache.xerces.internal.impl.XMLEntityManager$RewindableInputStream.readAndBuffer(XMLEntityManager.java:3024)
08:12:14 	at java.xml/com.sun.org.apache.xerces.internal.impl.XMLEntityManager$RewindableInputStream.read(XMLEntityManager.java:3064)
08:12:14 	at java.xml/com.sun.org.apache.xerces.internal.impl.io.UTF8Reader.read(UTF8Reader.java:303)
08:12:14 	at java.xml/com.sun.org.apache.xerces.internal.impl.XMLEntityScanner.load(XMLEntityScanner.java:1699)
08:12:14 	at java.xml/com.sun.org.apache.xerces.internal.impl.XMLEntityScanner.scanLiteral(XMLEntityScanner.java:1137)
08:12:14 	at java.xml/com.sun.org.apache.xerces.internal.impl.XMLScanner.scanPseudoAttribute(XMLScanner.java:644)
08:12:14 	at java.xml/com.sun.org.apache.xerces.internal.impl.XMLScanner.scanXMLDeclOrTextDecl(XMLScanner.java:457)
08:12:14 	at java.xml/com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanXMLDeclOrTextDecl(XMLDocumentFragmentScannerImpl.java:982)
08:12:14 	at java.xml/com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl$XMLDeclDriver.next(XMLDocumentScannerImpl.java:752)
08:12:14 	at java.xml/com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.next(XMLDocumentScannerImpl.java:605)
08:12:14 	at java.xml/com.sun.org.apache.xerces.internal.impl.XMLNSDocumentScannerImpl.next(XMLNSDocumentScannerImpl.java:112)
08:12:14 	at java.xml/com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanDocument(XMLDocumentFragmentScannerImpl.java:465)
08:12:14 	at java.xml/com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:888)
08:12:14 	at java.xml/com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:824)
08:12:14 	at java.xml/com.sun.org.apache.xerces.internal.parsers.XMLParser.parse(XMLParser.java:141)
08:12:14 	at java.xml/com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.parse(AbstractSAXParser.java:1216)
08:12:14 	at java.xml/com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl$JAXPSAXParser.parse(SAXParserImpl.java:635)
08:12:14 	at net.sf.saxon.resource.ActiveSAXSource.deliver(ActiveSAXSource.java:190)
08:12:14 	... 83 more