Jackson was bumped from 2.10.x to 2.12.x, which could well explain it if you're exposed to the Spark classpath and have your own different Jackson dep.
On Sun, Aug 22, 2021 at 1:21 PM Michael Heuer <heue...@gmail.com> wrote: > 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 > > $ 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 > 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> 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/ >> >> The tag to be voted on is v3.2.0-rc1 (commit >> 6bb3523d8e838bd2082fb90d7f3741339245c044): >> 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/ >> >> Signatures used for Spark RCs can be found in this file: >> 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 >> >> The documentation corresponding to this release can be found at: >> 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 >> >> 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 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. >> >> >
