FailedChanges

Summary

  1. Bump slf4j dependency version to 1.7.30. (commit: b418f50) (details)
  2. [ADAM-2262] Update Spark dependency version to 2.4.6 (#2263) (commit: 0f39a47) (details)
  3. [ADAM-2221] Remove support for Python 2.7 (#2244) (commit: 50797dc) (details)
  4. add move to spark 2/3 scripts (commit: 6c9a321) (details)
  5. fixes for removed deprecated code (commit: 36a2199) (details)
  6. fixes for code removed in Spark 3 (commit: 3ad77c6) (details)
  7. add missing file (commit: 4fca88a) (details)
  8. -print_metrics was removed (commit: b2a54bf) (details)
  9. add -v to curl (commit: 198668b) (details)
  10. use lazy val for spark session (commit: d1bb350) (details)
  11. Update bdg-formats to 0.3.0, remove hadoop 2.6 from jenkins-test (commit: 270de8a) (details)
  12. move to Spark version 3.0.0 (commit: a5b4fff) (details)
Commit b418f50d97c920d325f8accf44fe2f5d2415a17d by heuermh
Bump slf4j dependency version to 1.7.30.
(commit: b418f50)
The file was modifiedpom.xml (diff)
Commit 0f39a47c367160029d36c5d648d6634ea399d307 by noreply
[ADAM-2262] Update Spark dependency version to 2.4.6 (#2263)
* Update Spark dependency version to 2.4.6.

* Use https URLs consistently in Jenkins script.

* Use Apache mirror URL for Hadoop tarball download.
(commit: 0f39a47)
The file was modifiedscripts/jenkins-test (diff)
The file was modifiedscripts/move_to_spark_2.sh (diff)
The file was modifiedpom.xml (diff)
Commit 50797dc359912b3de1130c0c7dfc2a211ad9453e by noreply
[ADAM-2221] Remove support for Python 2.7 (#2244)
* remove 2.7 support checks

* bump adam setup python to >3.0
(commit: 50797dc)
The file was modifiedadam-python/setup.py (diff)
The file was modifiedscripts/jenkins-test (diff)
Commit 6c9a321d61d61c5e4ce40963b0d796805ebfa0f6 by heuermh
add move to spark 2/3 scripts
(commit: 6c9a321)
The file was addedscripts/move_to_spark_3.sh
The file was modifiedscripts/move_to_spark_2.sh (diff)
Commit 36a2199e0409547f539b33701abd995a6a5b3448 by heuermh
fixes for removed deprecated code
(commit: 36a2199)
The file was modifiedadam-core/src/main/scala/org/bdgenomics/adam/rdd/read/recalibration/DinucCovariate.scala (diff)
The file was modifiedadam-core/src/main/scala/org/bdgenomics/adam/rdd/TreeRegionJoin.scala (diff)
The file was modifiedadam-core/src/main/scala/org/bdgenomics/adam/rdd/variant/VariantContextDataset.scala (diff)
The file was modifiedadam-core/src/main/scala/org/bdgenomics/adam/rdd/read/recalibration/Recalibrator.scala (diff)
The file was modifiedadam-core/src/main/scala/org/bdgenomics/adam/rdd/ADAMContext.scala (diff)
The file was modifiedadam-core/src/main/scala/org/bdgenomics/adam/rdd/read/realignment/IndelRealignmentTarget.scala (diff)
The file was modifiedadam-core/src/main/scala/org/bdgenomics/adam/rdd/sequence/SequenceDataset.scala (diff)
The file was modifiedadam-core/src/main/scala/org/bdgenomics/adam/util/ParquetFileTraversable.scala (diff)
The file was modifiedadam-core/src/main/scala/org/bdgenomics/adam/models/SnpTable.scala (diff)
The file was modifiedadam-cli/pom.xml (diff)
The file was addedadam-core/src/main/scala/org/bdgenomics/adam/util/TextAlignment.scala
The file was modifiedadam-core/src/main/scala/org/bdgenomics/adam/rdd/fragment/FragmentDataset.scala (diff)
The file was modifiedadam-core/src/main/scala/org/bdgenomics/adam/rdd/read/realignment/RealignmentTargetFinder.scala (diff)
The file was modifiedadam-core/src/main/scala/org/bdgenomics/adam/rdd/GenomicDataset.scala (diff)
The file was modifiedadam-core/src/main/scala/org/bdgenomics/adam/converters/VariantContextConverter.scala (diff)
The file was modifiedadam-core/src/main/scala/org/bdgenomics/adam/rdd/read/ADAMSAMOutputFormat.scala (diff)
The file was modifiedadam-core/src/main/scala/org/bdgenomics/adam/rdd/read/MarkDuplicates.scala (diff)
The file was modifiedadam-core/src/main/scala/org/bdgenomics/adam/rdd/sequence/SliceDataset.scala (diff)
The file was modifiedpom.xml (diff)
The file was modifiedadam-core/src/main/scala/org/bdgenomics/adam/rdd/feature/FeatureDataset.scala (diff)
The file was modifiedadam-core/src/main/scala/org/bdgenomics/adam/converters/AlignmentConverter.scala (diff)
The file was modifiedadam-core/src/main/scala/org/bdgenomics/adam/rdd/read/ADAMCRAMOutputFormat.scala (diff)
The file was modifiedadam-core/src/main/scala/org/bdgenomics/adam/rdd/read/AlignmentDataset.scala (diff)
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/instrumentation/Timers.scala
The file was modifiedadam-core/src/main/scala/org/bdgenomics/adam/util/ADAMShell.scala (diff)
The file was modifiedadam-core/src/main/scala/org/bdgenomics/adam/rdd/read/recalibration/BaseQualityRecalibration.scala (diff)
The file was modifiedadam-core/pom.xml (diff)
The file was modifiedadam-core/src/main/scala/org/bdgenomics/adam/rdd/read/recalibration/RecalibrationTable.scala (diff)
The file was modifiedadam-core/src/main/scala/org/bdgenomics/adam/rdd/read/recalibration/CycleCovariate.scala (diff)
The file was modifiedadam-core/src/main/scala/org/bdgenomics/adam/rdd/read/ADAMBAMOutputFormat.scala (diff)
The file was modifiedadam-core/src/main/scala/org/bdgenomics/adam/rdd/read/ReferencePositionPair.scala (diff)
The file was modifiedadam-core/src/main/scala/org/bdgenomics/adam/rdd/read/realignment/RealignIndels.scala (diff)
The file was modifiedadam-cli/src/main/scala/org/bdgenomics/adam/cli/TransformAlignments.scala (diff)
Commit 3ad77c66266943cd53b2e378e4d988d142c75178 by heuermh
fixes for code removed in Spark 3
(commit: 3ad77c6)
The file was modifiedadam-core/src/main/scala/org/bdgenomics/adam/rdd/read/ReadDataset.scala (diff)
The file was modifiedadam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/VariantDatasetSuite.scala (diff)
The file was modifiedadam-core/src/main/scala/org/bdgenomics/adam/rdd/sequence/SliceDataset.scala (diff)
The file was modifiedadam-core/src/main/scala/org/bdgenomics/adam/rdd/variant/VariantDataset.scala (diff)
The file was modifiedadam-core/src/main/scala/org/bdgenomics/adam/rdd/variant/GenotypeDataset.scala (diff)
The file was modifiedadam-core/src/main/scala/org/bdgenomics/adam/rdd/sequence/SequenceDataset.scala (diff)
The file was modifiedadam-core/src/main/scala/org/bdgenomics/adam/rdd/ADAMContext.scala (diff)
The file was modifiedadam-core/src/test/scala/org/bdgenomics/adam/rdd/fragment/FragmentDatasetSuite.scala (diff)
The file was modifiedadam-core/src/main/scala/org/bdgenomics/adam/rdd/feature/CoverageDataset.scala (diff)
The file was modifiedadam-core/src/test/scala/org/bdgenomics/adam/rdd/ADAMContextSuite.scala (diff)
The file was modifiedadam-core/src/main/scala/org/bdgenomics/adam/rdd/read/MDTagging.scala (diff)
The file was modifiedadam-core/src/test/scala/org/bdgenomics/adam/rdd/read/AlignmentDatasetSuite.scala (diff)
The file was modifiedadam-core/src/main/scala/org/bdgenomics/adam/rdd/GenomicDataset.scala (diff)
The file was modifiedadam-core/src/main/scala/org/bdgenomics/adam/rdd/fragment/FragmentDataset.scala (diff)
The file was modifiedadam-core/src/main/scala/org/bdgenomics/adam/rdd/read/AlignmentDataset.scala (diff)
The file was modifiedadam-core/src/test/scala/org/bdgenomics/adam/rdd/feature/FeatureDatasetSuite.scala (diff)
The file was modifiedadam-core/src/main/scala/org/bdgenomics/adam/rdd/feature/FeatureDataset.scala (diff)
The file was modifiedadam-core/src/main/scala/org/bdgenomics/adam/rdd/variant/VariantContextDataset.scala (diff)
The file was modifiedadam-core/src/test/scala/org/bdgenomics/adam/rdd/feature/CoverageDatasetSuite.scala (diff)
The file was modifiedadam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/GenotypeDatasetSuite.scala (diff)
The file was addedadam-core/src/main/scala/org/bdgenomics/adam/util/ASCIITable.scala
The file was modifiedscripts/jenkins-test (diff)
The file was modifiedscripts/jenkins-test (diff)
Commit d1bb350d3da2c0390be42ab025709ecc219f5848 by heuermh
use lazy val for spark session
(commit: d1bb350)
The file was modifiedadam-core/src/main/scala/org/bdgenomics/adam/rdd/ADAMContext.scala (diff)
The file was modifiedadam-core/src/main/scala/org/bdgenomics/adam/rdd/GenomicDataset.scala (diff)
Commit 270de8abcc6fd63ff27e3a6e8d46410a2240e777 by heuermh
Update bdg-formats to 0.3.0, remove hadoop 2.6 from jenkins-test
(commit: 270de8a)
The file was modifiedscripts/jenkins-test (diff)
Commit a5b4fff2cc1a1922c098c66b5a730c5501ce7a19 by heuermh
move to Spark version 3.0.0
(commit: a5b4fff)
The file was modifiedscripts/move_to_spark_3.sh (diff)