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Posted to issues@spark.apache.org by "Michael Heuer (JIRA)" <ji...@apache.org> on 2017/02/22 17:19:44 UTC
[jira] [Updated] (SPARK-19697) NoSuchMethodError:
org.apache.avro.Schema.getLogicalType()
[ https://issues.apache.org/jira/browse/SPARK-19697?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ]
Michael Heuer updated SPARK-19697:
----------------------------------
Environment: Apache Spark 2.1.0, Scala version 2.11.8, Java HotSpot(TM) 64-Bit Server VM, 1.8.0_60 (was: {{
$ spark-submit --version
Welcome to
____ __
/ __/__ ___ _____/ /__
_\ \/ _ \/ _ `/ __/ '_/
/___/ .__/\_,_/_/ /_/\_\ version 2.1.0
/_/
Using Scala version 2.11.8, Java HotSpot(TM) 64-Bit Server VM, 1.8.0_60
Branch
Compiled by user jenkins on 2016-12-16T02:04:48Z
Revision
Url
Type --help for more information.
}}
)
> NoSuchMethodError: org.apache.avro.Schema.getLogicalType()
> ----------------------------------------------------------
>
> Key: SPARK-19697
> URL: https://issues.apache.org/jira/browse/SPARK-19697
> Project: Spark
> Issue Type: Bug
> Components: Build, Spark Core
> Affects Versions: 2.1.0
> Environment: Apache Spark 2.1.0, Scala version 2.11.8, Java HotSpot(TM) 64-Bit Server VM, 1.8.0_60
> Reporter: Michael Heuer
>
> In a downstream project (https://github.com/bigdatagenomics/adam), adding a dependency on `parquet-avro` version 1.8.2 results in `NoSuchMethodException`s at runtime on various Spark versions, including 2.1.0.
> pom.xml:
> {{
> <dependencyManagement>
> <dependencies>
> <dependency>
> <groupId>org.apache.parquet</groupId>
> <artifactId>parquet-avro</artifactId>
> <version>${parquet.version}</version>
> </dependency>
> <dependency>
> <groupId>org.apache.parquet</groupId>
> <!-- This library has no Scala 2.11 version, but using the 2.10 version seems to work. -->
> <artifactId>parquet-scala_2.10</artifactId>
> <version>${parquet.version}</version>
> <exclusions>
> <exclusion>
> <groupId>org.scala-lang</groupId>
> <artifactId>scala-library</artifactId>
> </exclusion>
> </exclusions>
> </dependency>
> }}
> Example using `spark-submit` (called via `adam-submit` below)
> {{
> $ ./bin/adam-submit vcf2adam \
> adam-core/src/test/resources/small.vcf \
> small.adam
> ...
> java.lang.NoSuchMethodError: org.apache.avro.Schema.getLogicalType()Lorg/apache/avro/LogicalType;
> at org.apache.parquet.avro.AvroSchemaConverter.convertField(AvroSchemaConverter.java:178)
> at org.apache.parquet.avro.AvroSchemaConverter.convertUnion(AvroSchemaConverter.java:214)
> at org.apache.parquet.avro.AvroSchemaConverter.convertField(AvroSchemaConverter.java:171)
> at org.apache.parquet.avro.AvroSchemaConverter.convertField(AvroSchemaConverter.java:130)
> at org.apache.parquet.avro.AvroSchemaConverter.convertField(AvroSchemaConverter.java:227)
> at org.apache.parquet.avro.AvroSchemaConverter.convertFields(AvroSchemaConverter.java:124)
> at org.apache.parquet.avro.AvroSchemaConverter.convertField(AvroSchemaConverter.java:152)
> at org.apache.parquet.avro.AvroSchemaConverter.convertUnion(AvroSchemaConverter.java:214)
> at org.apache.parquet.avro.AvroSchemaConverter.convertField(AvroSchemaConverter.java:171)
> at org.apache.parquet.avro.AvroSchemaConverter.convertField(AvroSchemaConverter.java:130)
> at org.apache.parquet.avro.AvroSchemaConverter.convertField(AvroSchemaConverter.java:227)
> at org.apache.parquet.avro.AvroSchemaConverter.convertFields(AvroSchemaConverter.java:124)
> at org.apache.parquet.avro.AvroSchemaConverter.convert(AvroSchemaConverter.java:115)
> at org.apache.parquet.avro.AvroWriteSupport.init(AvroWriteSupport.java:117)
> at org.apache.parquet.hadoop.ParquetOutputFormat.getRecordWriter(ParquetOutputFormat.java:311)
> at org.apache.parquet.hadoop.ParquetOutputFormat.getRecordWriter(ParquetOutputFormat.java:283)
> at org.apache.spark.rdd.InstrumentedOutputFormat.getRecordWriter(InstrumentedOutputFormat.scala:35)
> at org.apache.spark.rdd.PairRDDFunctions$$anonfun$saveAsNewAPIHadoopDataset$1$$anonfun$12.apply(PairRDDFunctions.scala:1119)
> at org.apache.spark.rdd.PairRDDFunctions$$anonfun$saveAsNewAPIHadoopDataset$1$$anonfun$12.apply(PairRDDFunctions.scala:1102)
> at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:87)
> at org.apache.spark.scheduler.Task.run(Task.scala:99)
> at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:282)
> at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
> at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
> at java.lang.Thread.run(Thread.java:745)
> }}
> The issue can be reproduced from this pull request
> https://github.com/bigdatagenomics/adam/pull/1360
> and is reported as Jenkins CI test failures
> https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1810
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