diff --git a/pom.xml b/pom.xml
index fb40634eb3d..288effc0b21 100644
--- a/pom.xml
+++ b/pom.xml
@@ -34,7 +34,7 @@
     <dependency>
       <groupId>org.eclipse.jdt</groupId>
       <artifactId>org.eclipse.jdt.core</artifactId>
-      <version>3.38.0</version>
+      <version>3.39.0</version>
       <exclusions>
         <exclusion>
           <groupId>org.eclipse.platform</groupId>
diff --git a/spoon-control-flow/src/test/java/fr/inria/controlflow/AllBranchesReturnTest.java b/spoon-control-flow/src/test/java/fr/inria/controlflow/AllBranchesReturnTest.java
index ef1ea725f6b..04daa5eb769 100644
--- a/spoon-control-flow/src/test/java/fr/inria/controlflow/AllBranchesReturnTest.java
+++ b/spoon-control-flow/src/test/java/fr/inria/controlflow/AllBranchesReturnTest.java
@@ -121,7 +121,7 @@ public void testSegment(AbstractProcessor processor) throws Exception {
 		//        "nestedIfSomeNotReturning", false);
 
 		Factory factory = new SpoonMetaFactory().buildNewFactory(
-				this.getClass().getResource("/control-flow").toURI().getPath(), 7);
+				this.getClass().getResource("/control-flow").toURI().getPath(), 11);
 		ProcessingManager pm = new QueueProcessingManager(factory);
 		pm.addProcessor(processor);
 		pm.process(factory.getModel().getRootPackage());
diff --git a/spoon-control-flow/src/test/java/fr/inria/controlflow/ForwardFlowBuilderVisitorTest.java b/spoon-control-flow/src/test/java/fr/inria/controlflow/ForwardFlowBuilderVisitorTest.java
index 9c94d18b7ce..57d1ee19a0e 100644
--- a/spoon-control-flow/src/test/java/fr/inria/controlflow/ForwardFlowBuilderVisitorTest.java
+++ b/spoon-control-flow/src/test/java/fr/inria/controlflow/ForwardFlowBuilderVisitorTest.java
@@ -46,7 +46,7 @@ public static ControlFlowGraph buildGraph(String folder, final String methodName
 			throws Exception {
 		final ControlFlowBuilder visitor = new ControlFlowBuilder();
 
-		Factory factory = new SpoonMetaFactory().buildNewFactory(folder, 5);
+		Factory factory = new SpoonMetaFactory().buildNewFactory(folder, 11);
 		ProcessingManager pm = new QueueProcessingManager(factory);
 		pm.addProcessor(new AbstractProcessor<CtMethod>() {
 			@Override
diff --git a/src/test/java/spoon/test/api/NoClasspathTest.java b/src/test/java/spoon/test/api/NoClasspathTest.java
index daf0d98eef4..06974d0cc18 100644
--- a/src/test/java/spoon/test/api/NoClasspathTest.java
+++ b/src/test/java/spoon/test/api/NoClasspathTest.java
@@ -42,6 +42,7 @@
 import spoon.support.visitor.SignaturePrinter;
 import spoon.test.api.testclasses.Bar;
 import spoon.testing.assertions.SpoonAssertions;
+import spoon.testing.utils.GitHubIssue;
 import spoon.testing.utils.ModelTest;
 
 import static java.util.function.Predicate.not;
@@ -209,6 +210,7 @@ public void testInheritanceInNoClassPathWithClasses() {
 		assertTrue(field.getType().isSubtypeOf(myInterfaceReference));
 	}
 
+	@GitHubIssue(issueNumber = 5977, fixed = false)
 	@ModelTest("src/test/resources/noclasspath/issue5591/DiamondConstructorCallTypeInference.java")
 	void testJdtFactoryMethodsForDiamond(CtModel model) {
 		// contract: Leftover <factory> methods from JDT's diamond constructor type inference are handled in
diff --git a/src/test/java/spoon/test/reference/ElasticsearchStackoverflowTest.java b/src/test/java/spoon/test/reference/ElasticsearchStackoverflowTest.java
index b57617c9f56..ad07a7120ab 100644
--- a/src/test/java/spoon/test/reference/ElasticsearchStackoverflowTest.java
+++ b/src/test/java/spoon/test/reference/ElasticsearchStackoverflowTest.java
@@ -28,6 +28,7 @@
 import spoon.reflect.reference.CtTypeReference;
 import spoon.reflect.visitor.CtScanner;
 import spoon.reflect.visitor.filter.TypeFilter;
+import spoon.testing.utils.GitHubIssue;
 
 import static org.junit.jupiter.api.Assertions.assertEquals;
 import static org.junit.jupiter.api.Assertions.assertFalse;
@@ -45,6 +46,7 @@ public <T> void visitCtExecutableReference(
 		}
 	}
 
+	@GitHubIssue(issueNumber = 5977, fixed = false)
 	@Test
 	public void testStackOverflow() {
 		Launcher launcher = new Launcher();