Eclipse (Juno) CDT indexer: "Error while parsing..." a Makefile project

Question

I am working on a clone of this Github project in Eclipse CDT and I haven't managed to create an error-free index of it (an example of the error log is given below for AncSplit.cpp). All the CPU resources (Intel® Core™ i7 CPU X 940 @ 2.13GHz × 8 with 8Gb RAM) are taken up for a while and parsing errors are generated for every .cpp and .h file in the project.

In order to reproduce/identify the problem I only kept the source files and the the customized project Makefile in a single folder. I also removed Eclipse (and workspace preferences...) and reinstalled it from scratch.
N.B. I also made the following changes -Xms1G, -Xmx2G and -XX:MaxPermSize=1G in the eclipse.ini file in order to bypass insufficient heap space related problems.
I am using Eclipse :
Version: Juno Service Release 1
Build id: 20121004-1855

Thanks in advance.

!SESSION 2012-12-12 23:44:47.084 -----------------------------------------------
eclipse.buildId=M20120914-1800
java.version=1.7.0_10
java.vendor=Oracle Corporation
BootLoader constants: OS=linux, ARCH=x86_64, WS=gtk, NL=en_US
Framework arguments:  -product org.eclipse.epp.package.cpp.product
Command-line arguments:  -os linux -ws gtk -arch x86_64 -product org.eclipse.epp.package.cpp.product

!ENTRY org.eclipse.cdt.core 4 0 2012-12-13 00:07:02.918
!MESSAGE Error while parsing /lagrange/AncSplit.cpp.
!STACK 0
java.lang.NullPointerException
    at org.eclipse.cdt.internal.core.dom.parser.Value.isDependentValue(Value.java:373)
    at org.eclipse.cdt.internal.core.dom.parser.cpp.semantics.CPPTemplates.isDependentArgument(CPPTemplates.java:2323)
    at org.eclipse.cdt.internal.core.dom.parser.cpp.semantics.CPPTemplates.hasDependentArgument(CPPTemplates.java:2313)
    at org.eclipse.cdt.internal.core.dom.parser.cpp.semantics.CPPTemplates.instantiate(CPPTemplates.java:181)
    at org.eclipse.cdt.internal.core.dom.parser.cpp.semantics.CPPTemplates.instantiate(CPPTemplates.java:166)
    at org.eclipse.cdt.internal.core.dom.parser.cpp.semantics.CPPTemplates.resolveDeferredClassInstance(CPPTemplates.java:2468)
    at org.eclipse.cdt.internal.core.dom.parser.cpp.semantics.CPPTemplates.resolveUnknown(CPPTemplates.java:2393)
    at org.eclipse.cdt.internal.core.dom.parser.cpp.semantics.CPPTemplates.instantiateType(CPPTemplates.java:1173)
    at org.eclipse.cdt.internal.core.dom.parser.cpp.semantics.CPPTemplates.resolveUnknown(CPPTemplates.java:2401)
    at org.eclipse.cdt.internal.core.dom.parser.cpp.semantics.CPPTemplates.instantiateType(CPPTemplates.java:1173)
    at org.eclipse.cdt.internal.core.dom.parser.cpp.AbstractCPPClassSpecializationScope.getBases(AbstractCPPClassSpecializationScope.java:158)
    at org.eclipse.cdt.internal.core.dom.parser.cpp.CPPClassSpecialization.getBases(CPPClassSpecialization.java:219)
    at org.eclipse.cdt.internal.core.dom.parser.cpp.ClassTypeHelper.getBases(ClassTypeHelper.java:243)
    at org.eclipse.cdt.internal.core.dom.parser.cpp.semantics.BaseClassLookup.lookupInBaseClass(BaseClassLookup.java:192)
    at org.eclipse.cdt.internal.core.dom.parser.cpp.semantics.BaseClassLookup.lookupInBaseClass(BaseClassLookup.java:235)
    at org.eclipse.cdt.internal.core.dom.parser.cpp.semantics.BaseClassLookup.lookupInBaseClasses(BaseClassLookup.java:54)
    at org.eclipse.cdt.internal.core.dom.parser.cpp.semantics.CPPSemantics.lookup(CPPSemantics.java:983)
    at org.eclipse.cdt.internal.core.dom.parser.cpp.semantics.CPPSemantics.resolveUnknownName(CPPSemantics.java:3679)
    at org.eclipse.cdt.internal.core.dom.parser.cpp.semantics.CPPTemplates.resolveUnknown(CPPTemplates.java:2425)
    at org.eclipse.cdt.internal.core.dom.parser.cpp.semantics.CPPTemplates.instantiateType(CPPTemplates.java:1173)
    at org.eclipse.cdt.internal.core.dom.parser.cpp.semantics.CPPTemplates.instantiateType(CPPTemplates.java:1223)
    at org.eclipse.cdt.internal.core.dom.parser.cpp.semantics.TemplateArgumentDeduction.deduceFromFunctionArgs(TemplateArgumentDeduction.java:125)
    at org.eclipse.cdt.internal.core.dom.parser.cpp.semantics.TemplateArgumentDeduction.deduceForFunctionCall(TemplateArgumentDeduction.java:88)
    at org.eclipse.cdt.internal.core.dom.parser.cpp.semantics.CPPTemplates.instantiateForFunctionCall(CPPTemplates.java:1749)
    at org.eclipse.cdt.internal.core.dom.parser.cpp.semantics.CPPTemplates.instantiateForFunctionCall(CPPTemplates.java:1728)
    at org.eclipse.cdt.internal.core.dom.parser.cpp.semantics.CPPSemantics.resolveFunction(CPPSemantics.java:2363)
    at org.eclipse.cdt.internal.core.dom.parser.cpp.semantics.EvalFunctionSet.resolveFunction(EvalFunctionSet.java:187)
    at org.eclipse.cdt.internal.core.dom.parser.cpp.semantics.EvalFunctionCall.instantiate(EvalFunctionCall.java:202)
    at org.eclipse.cdt.internal.core.dom.parser.cpp.semantics.EvalUnary.instantiate(EvalUnary.java:281)
    at org.eclipse.cdt.internal.core.dom.parser.cpp.semantics.EvalBinary.instantiate(EvalBinary.java:343)
    at org.eclipse.cdt.internal.core.dom.parser.cpp.semantics.CPPTemplates.instantiateValue(CPPTemplates.java:866)
    at org.eclipse.cdt.internal.core.dom.parser.cpp.semantics.CPPTemplates.createSpecialization(CPPTemplates.java:786)
    at org.eclipse.cdt.internal.core.dom.parser.cpp.CPPClassSpecialization.specializeMember(CPPClassSpecialization.java:176)
    at org.eclipse.cdt.internal.core.dom.parser.cpp.AbstractCPPClassSpecializationScope.getBindings(AbstractCPPClassSpecializationScope.java:116)
    at org.eclipse.cdt.internal.core.dom.parser.cpp.semantics.CPPSemantics.getBindingsFromScope(CPPSemantics.java:1205)
    at org.eclipse.cdt.internal.core.dom.parser.cpp.semantics.CPPSemantics.lookup(CPPSemantics.java:953)
    at org.eclipse.cdt.internal.core.dom.parser.cpp.semantics.EvalID.resolveName(EvalID.java:320)
    at org.eclipse.cdt.internal.core.dom.parser.cpp.semantics.EvalID.instantiate(EvalID.java:307)
    at org.eclipse.cdt.internal.core.dom.parser.cpp.semantics.EvalBinary.instantiate(EvalBinary.java:343)
    at org.eclipse.cdt.internal.core.dom.parser.cpp.semantics.EvalBinary.instantiate(EvalBinary.java:343)
    at org.eclipse.cdt.internal.core.dom.parser.cpp.semantics.CPPTemplates.instantiateValue(CPPTemplates.java:866)
    at org.eclipse.cdt.internal.core.dom.parser.cpp.semantics.CPPTemplates.createSpecialization(CPPTemplates.java:786)
    at org.eclipse.cdt.internal.core.dom.parser.cpp.CPPClassSpecialization.specializeMember(CPPClassSpecialization.java:176)
    at org.eclipse.cdt.internal.core.dom.parser.cpp.AbstractCPPClassSpecializationScope.getBindings(AbstractCPPClassSpecializationScope.java:116)
    at org.eclipse.cdt.internal.core.dom.parser.cpp.semantics.CPPSemantics.getBindingsFromScope(CPPSemantics.java:1205)
    at org.eclipse.cdt.internal.core.dom.parser.cpp.semantics.CPPSemantics.lookup(CPPSemantics.java:953)
    at org.eclipse.cdt.internal.core.dom.parser.cpp.semantics.EvalID.resolveName(EvalID.java:320)
    at org.eclipse.cdt.internal.core.dom.parser.cpp.semantics.EvalID.instantiate(EvalID.java:307)
    at org.eclipse.cdt.internal.core.dom.parser.cpp.semantics.CPPTemplates.instantiateValue(CPPTemplates.java:866)
    at org.eclipse.cdt.internal.core.dom.parser.cpp.semantics.CPPTemplates.instantiateArgument(CPPTemplates.java:1079)
    at org.eclipse.cdt.internal.core.dom.parser.cpp.semantics.CPPTemplates.instantiateArguments(CPPTemplates.java:1053)
    at org.eclipse.cdt.internal.core.dom.parser.cpp.semantics.CPPTemplates.resolveDeferredClassInstance(CPPTemplates.java:2447)
    at org.eclipse.cdt.internal.core.dom.parser.cpp.semantics.CPPTemplates.resolveUnknown(CPPTemplates.java:2393)
    at org.eclipse.cdt.internal.core.dom.parser.cpp.semantics.CPPTemplates.instantiateType(CPPTemplates.java:1173)
    at org.eclipse.cdt.internal.core.dom.parser.cpp.semantics.CPPTemplates.resolveUnknown(CPPTemplates.java:2401)
    at org.eclipse.cdt.internal.core.dom.parser.cpp.semantics.CPPTemplates.instantiateType(CPPTemplates.java:1173)
    at org.eclipse.cdt.internal.core.dom.parser.cpp.AbstractCPPClassSpecializationScope.getBases(AbstractCPPClassSpecializationScope.java:158)
    at org.eclipse.cdt.internal.core.dom.parser.cpp.CPPClassSpecialization.getBases(CPPClassSpecialization.java:219)
    at org.eclipse.cdt.internal.core.dom.parser.cpp.ClassTypeHelper.getBases(ClassTypeHelper.java:243)
    at org.eclipse.cdt.internal.core.dom.parser.cpp.semantics.SemanticUtil.inheritanceClosure(SemanticUtil.java:153)
    at org.eclipse.cdt.internal.core.dom.parser.cpp.semantics.SemanticUtil.getConversionOperators(SemanticUtil.java:129)
    at org.eclipse.cdt.internal.core.dom.parser.cpp.semantics.BuiltinOperators.getClassConversionTypes(BuiltinOperators.java:669)
    at org.eclipse.cdt.internal.core.dom.parser.cpp.semantics.BuiltinOperators.arithmeticAssignement(BuiltinOperators.java:487)
    at org.eclipse.cdt.internal.core.dom.parser.cpp.semantics.BuiltinOperators.create(BuiltinOperators.java:195)
    at org.eclipse.cdt.internal.core.dom.parser.cpp.semantics.BuiltinOperators.create(BuiltinOperators.java:68)
    at org.eclipse.cdt.internal.core.dom.parser.cpp.semantics.CPPSemantics.findOverloadedOperator(CPPSemantics.java:3383)
    at org.eclipse.cdt.internal.core.dom.parser.cpp.semantics.CPPSemantics.findOverloadedBinaryOperator(CPPSemantics.java:2992)
    at org.eclipse.cdt.internal.core.dom.parser.cpp.semantics.EvalBinary.computeOverload(EvalBinary.java:242)
    at org.eclipse.cdt.internal.core.dom.parser.cpp.semantics.EvalBinary.getOverload(EvalBinary.java:224)
    at org.eclipse.cdt.internal.core.dom.parser.cpp.CPPASTBinaryExpression.getOverload(CPPASTBinaryExpression.java:262)
    at org.eclipse.cdt.internal.core.dom.parser.cpp.CPPASTBinaryExpression.getImplicitNames(CPPASTBinaryExpression.java:131)
    at org.eclipse.cdt.internal.core.dom.parser.cpp.CPPASTBinaryExpression.accept(CPPASTBinaryExpression.java:164)
    at org.eclipse.cdt.internal.core.dom.parser.cpp.CPPASTExpressionStatement.accept(CPPASTExpressionStatement.java:73)
    at org.eclipse.cdt.internal.core.dom.parser.cpp.CPPASTCompoundStatement.accept(CPPASTCompoundStatement.java:85)
    at org.eclipse.cdt.internal.core.dom.parser.cpp.CPPASTIfStatement.accept(CPPASTIfStatement.java:145)
    at org.eclipse.cdt.internal.core.dom.parser.cpp.CPPASTCompoundStatement.accept(CPPASTCompoundStatement.java:85)
    at org.eclipse.cdt.internal.core.dom.parser.cpp.CPPASTIfStatement.accept(CPPASTIfStatement.java:145)
    at org.eclipse.cdt.internal.core.dom.parser.cpp.CPPASTCompoundStatement.accept(CPPASTCompoundStatement.java:85)
    at org.eclipse.cdt.internal.core.dom.parser.cpp.CPPASTFunctionDefinition.accept(CPPASTFunctionDefinition.java:201)
    at org.eclipse.cdt.internal.core.dom.parser.cpp.CPPASTTemplateDeclaration.accept(CPPASTTemplateDeclaration.java:127)
    at org.eclipse.cdt.internal.core.dom.parser.cpp.CPPASTNamespaceDefinition.accept(CPPASTNamespaceDefinition.java:139)
    at org.eclipse.cdt.internal.core.dom.parser.ASTTranslationUnit.accept(ASTTranslationUnit.java:251)
    at org.eclipse.cdt.internal.core.pdom.PDOMWriter.extractSymbols(PDOMWriter.java:444)
    at org.eclipse.cdt.internal.core.pdom.PDOMWriter.addSymbols(PDOMWriter.java:225)
    at org.eclipse.cdt.internal.core.pdom.AbstractIndexerTask.writeToIndex(AbstractIndexerTask.java:1170)
    at org.eclipse.cdt.internal.core.pdom.AbstractIndexerTask.parseFile(AbstractIndexerTask.java:1007)
    at org.eclipse.cdt.internal.core.pdom.AbstractIndexerTask.parseLinkage(AbstractIndexerTask.java:828)
    at org.eclipse.cdt.internal.core.pdom.AbstractIndexerTask.runTask(AbstractIndexerTask.java:508)
    at org.eclipse.cdt.internal.core.pdom.indexer.PDOMIndexerTask.run(PDOMIndexerTask.java:139)
    at org.eclipse.cdt.internal.core.pdom.indexer.PDOMRebuildTask.run(PDOMRebuildTask.java:87)
    at org.eclipse.cdt.internal.core.pdom.PDOMIndexerJob.run(PDOMIndexerJob.java:137)
    at org.eclipse.core.internal.jobs.Worker.run(Worker.java:53)

Answer 1

Figured it out, it was indeed a bug (and I have filed one).
A colleague of mine managed to flawlessly index the Github project which resulted in :

Indexed 'src' (20 sources, 1,061 headers) in 43.46 sec: 86,471 declarations; 231,728 references; 0 unresolved inclusions; 12 syntax errors; 592 unresolved names (0.19%)

He was on a Fedora distribution with its default package of Eclipse Juno CDT. This meant that he was using :

Eclipse C/C++ Development Tools
Version: 8.1.0.201206111645

which is not quite the same as the standard Juno CDT download :

Eclipse C/C++ Development Tools
Version: 8.1.1.201209170703

I checked this workaround on my Ubuntu system (12.04 LTS) by installing Classic Juno along with CDT 8.1.0 and the indexing/parsing works all right now.