We're seeing runtime classpath issues with Avro 1.10.2, Parquet 1.12.0, and Spark 3.2.0 RC1.
Our dependency tree is deep though, and will require further investigation. https://github.com/bigdatagenomics/adam/pull/2289 <https://github.com/bigdatagenomics/adam/pull/2289> $ mvn test ... *** RUN ABORTED *** java.lang.NoClassDefFoundError: com/fasterxml/jackson/annotation/JsonKey at com.fasterxml.jackson.databind.introspect.JacksonAnnotationIntrospector.hasAsKey(JacksonAnnotationIntrospector.java:1080) at com.fasterxml.jackson.databind.introspect.AnnotationIntrospectorPair.hasAsKey(AnnotationIntrospectorPair.java:611) at com.fasterxml.jackson.databind.introspect.AnnotationIntrospectorPair.hasAsKey(AnnotationIntrospectorPair.java:611) at com.fasterxml.jackson.databind.introspect.POJOPropertiesCollector._addFields(POJOPropertiesCollector.java:495) at com.fasterxml.jackson.databind.introspect.POJOPropertiesCollector.collectAll(POJOPropertiesCollector.java:421) at com.fasterxml.jackson.databind.introspect.POJOPropertiesCollector.getJsonValueAccessor(POJOPropertiesCollector.java:270) at com.fasterxml.jackson.databind.introspect.BasicBeanDescription.findJsonValueAccessor(BasicBeanDescription.java:258) at com.fasterxml.jackson.databind.ser.BasicSerializerFactory.findSerializerByAnnotations(BasicSerializerFactory.java:391) at com.fasterxml.jackson.databind.ser.BeanSerializerFactory._createSerializer2(BeanSerializerFactory.java:220) at com.fasterxml.jackson.databind.ser.BeanSerializerFactory.createSerializer(BeanSerializerFactory.java:169) at com.fasterxml.jackson.databind.SerializerProvider._createUntypedSerializer(SerializerProvider.java:1473) at com.fasterxml.jackson.databind.SerializerProvider._createAndCacheUntypedSerializer(SerializerProvider.java:1421) at com.fasterxml.jackson.databind.SerializerProvider.findValueSerializer(SerializerProvider.java:520) at com.fasterxml.jackson.databind.SerializerProvider.findTypedValueSerializer(SerializerProvider.java:798) at com.fasterxml.jackson.databind.ser.DefaultSerializerProvider.serializeValue(DefaultSerializerProvider.java:308) at com.fasterxml.jackson.databind.ObjectMapper._writeValueAndClose(ObjectMapper.java:4487) at com.fasterxml.jackson.databind.ObjectMapper.writeValueAsString(ObjectMapper.java:3742) at org.apache.spark.rdd.RDDOperationScope.toJson(RDDOperationScope.scala:52) at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:145) at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:112) at org.apache.spark.SparkContext.withScope(SparkContext.scala:789) at org.apache.spark.SparkContext.newAPIHadoopFile(SparkContext.scala:1239) at org.bdgenomics.adam.ds.ADAMContext.readVcfRecords(ADAMContext.scala:2668) at org.bdgenomics.adam.ds.ADAMContext.loadVcf(ADAMContext.scala:2686) at org.bdgenomics.adam.ds.ADAMContext.loadVariants(ADAMContext.scala:3608) at org.bdgenomics.adam.ds.variant.VariantDatasetSuite.$anonfun$new$1(VariantDatasetSuite.scala:128) at org.bdgenomics.utils.misc.SparkFunSuite.$anonfun$sparkTest$1(SparkFunSuite.scala:111) > On Aug 22, 2021, at 10:58 AM, Sean Owen <sro...@gmail.com> wrote: > > So far, I've tested Java 8 + Scala 2.12, Scala 2.13 and the results look good > per usual. > Good to see Scala 2.13 artifacts!! Unless I've forgotten something we're OK > for Scala 2.13 now, and Java 11 (and, IIRC, Java 14 works fine minus some > very minor corners of the project's deps) > > I think we're going to have to have this fix, which just missed the 3.2 RC: > https://github.com/apache/spark/commit/c441c7e365cdbed4bae55e9bfdf94fa4a118fb21 > > <https://github.com/apache/spark/commit/c441c7e365cdbed4bae55e9bfdf94fa4a118fb21> > I think that means we shouldn't release this RC, but, of course let's test. > > > > On Fri, Aug 20, 2021 at 12:05 PM Gengliang Wang <ltn...@gmail.com > <mailto:ltn...@gmail.com>> wrote: > Please vote on releasing the following candidate as Apache Spark version > 3.2.0. > > The vote is open until 11:59pm Pacific time Aug 25 and passes if a majority > +1 PMC votes are cast, with a minimum of 3 +1 votes. > > [ ] +1 Release this package as Apache Spark 3.2.0 > [ ] -1 Do not release this package because ... > > To learn more about Apache Spark, please see http://spark.apache.org/ > <http://spark.apache.org/> > > The tag to be voted on is v3.2.0-rc1 (commit > 6bb3523d8e838bd2082fb90d7f3741339245c044): > https://github.com/apache/spark/tree/v3.2.0-rc1 > <https://github.com/apache/spark/tree/v3.2.0-rc1> > > The release files, including signatures, digests, etc. can be found at: > https://dist.apache.org/repos/dist/dev/spark/v3.2.0-rc1-bin/ > <https://dist.apache.org/repos/dist/dev/spark/v3.2.0-rc1-bin/> > > Signatures used for Spark RCs can be found in this file: > https://dist.apache.org/repos/dist/dev/spark/KEYS > <https://dist.apache.org/repos/dist/dev/spark/KEYS> > > The staging repository for this release can be found at: > https://repository.apache.org/content/repositories/orgapachespark-1388 > <https://repository.apache.org/content/repositories/orgapachespark-1388> > > The documentation corresponding to this release can be found at: > https://dist.apache.org/repos/dist/dev/spark/v3.2.0-rc1-docs/ > <https://dist.apache.org/repos/dist/dev/spark/v3.2.0-rc1-docs/> > > The list of bug fixes going into 3.2.0 can be found at the following URL: > https://issues.apache.org/jira/projects/SPARK/versions/12349407 > <https://issues.apache.org/jira/projects/SPARK/versions/12349407> > > This release is using the release script of the tag v3.2.0-rc1. > > > FAQ > > ========================= > How can I help test this release? > ========================= > If you are a Spark user, you can help us test this release by taking > an existing Spark workload and running on this release candidate, then > reporting any regressions. > > If you're working in PySpark you can set up a virtual env and install > the current RC and see if anything important breaks, in the Java/Scala > you can add the staging repository to your projects resolvers and test > with the RC (make sure to clean up the artifact cache before/after so > you don't end up building with a out of date RC going forward). > > =========================================== > What should happen to JIRA tickets still targeting 3.2.0? > =========================================== > The current list of open tickets targeted at 3.2.0 can be found at: > https://issues.apache.org/jira/projects/SPARK > <https://issues.apache.org/jira/projects/SPARK> and search for "Target > Version/s" = 3.2.0 > > Committers should look at those and triage. Extremely important bug > fixes, documentation, and API tweaks that impact compatibility should > be worked on immediately. Everything else please retarget to an > appropriate release. > > ================== > But my bug isn't fixed? > ================== > In order to make timely releases, we will typically not hold the > release unless the bug in question is a regression from the previous > release. That being said, if there is something which is a regression > that has not been correctly targeted please ping me or a committer to > help target the issue. >
