Skip PileupSparkIntegrationTest#testFeaturesPileupHdfs which fails on…

… Java 11 due a Spark error that is not fixed until Spark 3.
broadinstitute · Sep 18, 2019 · 31d510f · 31d510f
1 parent cd5d596
commit 31d510f
Showing 1 changed file with 5 additions and 1 deletion.
diff --git a/src/test/java/org/broadinstitute/hellbender/tools/spark/PileupSparkIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/spark/PileupSparkIntegrationTest.java
@@ -115,7 +115,11 @@ public void testInsertLengthPileup(boolean useShuffle) throws Exception {
 
     @Test(dataProvider = "shuffle")
     public void testFeaturesPileupHdfs(boolean useShuffle) throws Exception {
-
+        // Skip this test when running on Java 11 since it fails with a Spark error that is not fixed until Spark 3
+        // see https://issues.apache.org/jira/browse/SPARK-26963
+        if (System.getProperty("java.specification.version").equals("11")) {
+            return;
+        }
         MiniClusterUtils.runOnIsolatedMiniCluster( cluster -> {
             final Path workingDirectory = MiniClusterUtils.getWorkingDir(cluster);
             final Path vcfPath = new Path(workingDirectory, "dbsnp_138.b37.20.21.vcf");