Description of problem: It happens only for Arduino projects and not for plain C++ projects. How reproducible: Everytime Steps to Reproduce: Create an arduino project
!ENTRY org.eclipse.cdt.core 1 0 2016-05-04 19:25:10.499 !MESSAGE Indexed 'ArduinoHelloWorld' (0 sources, 0 headers) in 0.018 sec: 0 declarations; 0 references; 0 unresolved inclusions; 0 syntax errors; 0 unresolved names (0%) !ENTRY org.eclipse.cdt.core 4 0 2016-05-04 19:25:11.388 !MESSAGE Error !STACK 0 java.lang.NullPointerException at org.eclipse.cdt.arduino.core.internal.build.ArduinoBuildConfiguration.calculateScannerInfo(ArduinoBuildConfiguration.java:586) at org.eclipse.cdt.arduino.core.internal.build.ArduinoBuildConfiguration.getScannerInfo(ArduinoBuildConfiguration.java:557) at org.eclipse.cdt.arduino.core.internal.ArduinoScannerInfoProvider.getScannerInformation(ArduinoScannerInfoProvider.java:23) at org.eclipse.cdt.internal.core.model.TranslationUnit.getScannerInfo(TranslationUnit.java:1057) at org.eclipse.cdt.internal.core.pdom.indexer.ProjectIndexerInputAdapter.getBuildConfiguration(ProjectIndexerInputAdapter.java:157) at org.eclipse.cdt.internal.core.pdom.AbstractIndexerTask.getScannerInfo(AbstractIndexerTask.java:1013) at org.eclipse.cdt.internal.core.pdom.AbstractIndexerTask.parseLinkage(AbstractIndexerTask.java:897) at org.eclipse.cdt.internal.core.pdom.AbstractIndexerTask.runTask(AbstractIndexerTask.java:554) at org.eclipse.cdt.internal.core.pdom.indexer.PDOMIndexerTask.run(PDOMIndexerTask.java:161) at org.eclipse.cdt.internal.core.pdom.PDOMIndexerJob.run(PDOMIndexerJob.java:149) at org.eclipse.core.internal.jobs.Worker.run(Worker.java:55) !ENTRY org.eclipse.core.jobs 4 2 2016-05-04 19:25:11.394 !MESSAGE An internal error occurred during: "C/C++ Indexer". !STACK 0 java.lang.NullPointerException at org.eclipse.cdt.arduino.core.internal.build.ArduinoBuildConfiguration.calculateScannerInfo(ArduinoBuildConfiguration.java:586) at org.eclipse.cdt.arduino.core.internal.build.ArduinoBuildConfiguration.getScannerInfo(ArduinoBuildConfiguration.java:557) at org.eclipse.cdt.arduino.core.internal.ArduinoScannerInfoProvider.getScannerInformation(ArduinoScannerInfoProvider.java:23) at org.eclipse.cdt.internal.core.model.TranslationUnit.getScannerInfo(TranslationUnit.java:1057) at org.eclipse.cdt.internal.core.pdom.indexer.ProjectIndexerInputAdapter.getBuildConfiguration(ProjectIndexerInputAdapter.java:157) at org.eclipse.cdt.internal.core.pdom.AbstractIndexerTask.getScannerInfo(AbstractIndexerTask.java:1013) at org.eclipse.cdt.internal.core.pdom.AbstractIndexerTask.parseLinkage(AbstractIndexerTask.java:897) at org.eclipse.cdt.internal.core.pdom.AbstractIndexerTask.runTask(AbstractIndexerTask.java:554) at org.eclipse.cdt.internal.core.pdom.indexer.PDOMIndexerTask.run(PDOMIndexerTask.java:161) at org.eclipse.cdt.internal.core.pdom.PDOMIndexerJob.run(PDOMIndexerJob.java:149) at org.eclipse.core.internal.jobs.Worker.run(Worker.java:55)
Updated to 1:9.0.0-0.3.git0b93e81.fc24, it works now :)