modified CoverageRDD and FeatureRDD to extend MultisampleGenomicDataset #2051
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Dependent on bigdatagenomics/bdg-formats#167 |
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Test FAILed. Build result: FAILURE[...truncated 3 lines...]Building remotely on amp-jenkins-worker-05 (centos spark-test) in workspace /home/jenkins/workspace/ADAM-prbWiping out workspace first.Cloning the remote Git repositoryCloning repository https://github.com/bigdatagenomics/adam.git > git init /home/jenkins/workspace/ADAM-prb # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/heads/:refs/remotes/origin/ # timeout=15 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10 > git config --add remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=10 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > git rev-parse origin/pr/2051/merge^{commit} # timeout=10 > git branch -a -v --no-abbrev --contains e73cc8d # timeout=10Checking out Revision e73cc8d (origin/pr/2051/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f e73cc8d4279f57c70a932080afc0361b1b31e9c2First time build. Skipping changelog.Triggering ADAM-prb ? 2.7.3,2.11,2.2.2,ubuntuTriggering ADAM-prb ? 2.6.2,2.11,2.2.2,ubuntuADAM-prb ? 2.7.3,2.11,2.2.2,ubuntu completed with result FAILUREADAM-prb ? 2.6.2,2.11,2.2.2,ubuntu completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'Test FAILed. |
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Test FAILed. Build result: FAILURE[...truncated 3 lines...]Building remotely on amp-jenkins-worker-05 (centos spark-test) in workspace /home/jenkins/workspace/ADAM-prbWiping out workspace first.Cloning the remote Git repositoryCloning repository https://github.com/bigdatagenomics/adam.git > git init /home/jenkins/workspace/ADAM-prb # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/heads/:refs/remotes/origin/ # timeout=15 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10 > git config --add remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=10 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > git rev-parse origin/pr/2051/merge^{commit} # timeout=10 > git branch -a -v --no-abbrev --contains 502ccf3 # timeout=10Checking out Revision 502ccf3 (origin/pr/2051/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 502ccf3568d15c219c86e4af5acd861cda45d08aFirst time build. Skipping changelog.Triggering ADAM-prb ? 2.7.3,2.11,2.2.2,ubuntuTriggering ADAM-prb ? 2.6.2,2.11,2.2.2,ubuntuADAM-prb ? 2.7.3,2.11,2.2.2,ubuntu completed with result FAILUREADAM-prb ? 2.6.2,2.11,2.2.2,ubuntu completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'Test FAILed. |
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See #1498. |
akmorrow13
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This was tested on the yarn cluster for loading/converting multiple alignments to multisample coverage and reloading them from parquet. |
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Test FAILed. Build result: FAILURE[...truncated 3 lines...]Building remotely on amp-jenkins-worker-05 (centos spark-test) in workspace /home/jenkins/workspace/ADAM-prbWiping out workspace first.Cloning the remote Git repositoryCloning repository https://github.com/bigdatagenomics/adam.git > git init /home/jenkins/workspace/ADAM-prb # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/heads/:refs/remotes/origin/ # timeout=15 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10 > git config --add remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=10 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > git rev-parse origin/pr/2051/merge^{commit} # timeout=10 > git branch -a -v --no-abbrev --contains a6ecb14 # timeout=10Checking out Revision a6ecb14 (origin/pr/2051/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f a6ecb14d9f420c98b9395c256b26cc670df6cfd6First time build. Skipping changelog.Triggering ADAM-prb ? 2.7.3,2.11,2.2.2,ubuntuTriggering ADAM-prb ? 2.6.2,2.11,2.2.2,ubuntuADAM-prb ? 2.7.3,2.11,2.2.2,ubuntu completed with result FAILUREADAM-prb ? 2.6.2,2.11,2.2.2,ubuntu completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'Test FAILed. |
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bdg-formats version 0.11.4 has been released, this pull request should be updated when it hits Maven Central. |
akmorrow13
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Test FAILed. Build result: FAILUREGitHub pull request #2051 of commit d7a76f8 automatically merged.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos spark-test) in workspace /home/jenkins/workspace/ADAM-prbWiping out workspace first.Cloning the remote Git repositoryCloning repository https://github.com/bigdatagenomics/adam.git > git init /home/jenkins/workspace/ADAM-prb # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/heads/:refs/remotes/origin/ # timeout=15 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10 > git config --add remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=10 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > git rev-parse origin/pr/2051/merge^{commit} # timeout=10 > git branch -a -v --no-abbrev --contains fdeff57 # timeout=10Checking out Revision fdeff57 (origin/pr/2051/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f fdeff57d3b8c6eb6596daa0b48313382bcd36033First time build. Skipping changelog.Triggering ADAM-prb ? 2.7.5,2.11,2.2.2,ubuntuADAM-prb ? 2.7.5,2.11,2.2.2,ubuntu completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'Test FAILed. |
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Test FAILed. Build result: FAILUREGitHub pull request #2051 of commit 7423cd5 automatically merged.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos spark-test) in workspace /home/jenkins/workspace/ADAM-prbWiping out workspace first.Cloning the remote Git repositoryCloning repository https://github.com/bigdatagenomics/adam.git > git init /home/jenkins/workspace/ADAM-prb # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/heads/:refs/remotes/origin/ # timeout=15 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10 > git config --add remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=10 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > git rev-parse origin/pr/2051/merge^{commit} # timeout=10 > git branch -a -v --no-abbrev --contains cb60d93 # timeout=10Checking out Revision cb60d93 (origin/pr/2051/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f cb60d93b667aea4ed645884aaaed39b635c4664aFirst time build. Skipping changelog.Triggering ADAM-prb ? 2.7.5,2.11,2.2.2,ubuntuADAM-prb ? 2.7.5,2.11,2.2.2,ubuntu completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'Test FAILed. |
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Jenkins, retest this please |
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Test FAILed. Build result: FAILUREGitHub pull request #2051 of commit 7423cd5 automatically merged.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos spark-test) in workspace /home/jenkins/workspace/ADAM-prbWiping out workspace first.Cloning the remote Git repositoryCloning repository https://github.com/bigdatagenomics/adam.git > git init /home/jenkins/workspace/ADAM-prb # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/heads/:refs/remotes/origin/ # timeout=15 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10 > git config --add remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=10 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > git rev-parse origin/pr/2051/merge^{commit} # timeout=10 > git branch -a -v --no-abbrev --contains cb60d93 # timeout=10Checking out Revision cb60d93 (origin/pr/2051/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f cb60d93 > git rev-list cb60d93 # timeout=10Triggering ADAM-prb ? 2.7.5,2.11,2.2.2,ubuntuADAM-prb ? 2.7.5,2.11,2.2.2,ubuntu completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'Test FAILed. |
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Jenkins, retest this please. |
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Test FAILed. Build result: FAILUREGitHub pull request #2051 of commit 7423cd5 automatically merged.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos spark-test) in workspace /home/jenkins/workspace/ADAM-prbWiping out workspace first.Cloning the remote Git repositoryCloning repository https://github.com/bigdatagenomics/adam.git > git init /home/jenkins/workspace/ADAM-prb # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/heads/:refs/remotes/origin/ # timeout=15 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10 > git config --add remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=10 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > git rev-parse origin/pr/2051/merge^{commit} # timeout=10 > git branch -a -v --no-abbrev --contains cb60d93 # timeout=10Checking out Revision cb60d93 (origin/pr/2051/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f cb60d93 > git rev-list cb60d93 # timeout=10Triggering ADAM-prb ? 2.7.5,2.11,2.2.2,ubuntuADAM-prb ? 2.7.5,2.11,2.2.2,ubuntu completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'Test FAILed. |
akmorrow13
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Test FAILed. Build result: FAILUREGitHub pull request #2051 of commit 12db759 automatically merged.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos spark-test) in workspace /home/jenkins/workspace/ADAM-prbWiping out workspace first.Cloning the remote Git repositoryCloning repository https://github.com/bigdatagenomics/adam.git > git init /home/jenkins/workspace/ADAM-prb # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/heads/:refs/remotes/origin/ # timeout=15 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10 > git config --add remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=10 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > git rev-parse origin/pr/2051/merge^{commit} # timeout=10 > git branch -a -v --no-abbrev --contains 998f0f1 # timeout=10Checking out Revision 998f0f1 (origin/pr/2051/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 998f0f1 > git rev-list cb60d93 # timeout=10Triggering ADAM-prb ? 2.7.5,2.11,2.2.2,ubuntuADAM-prb ? 2.7.5,2.11,2.2.2,ubuntu completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'Test FAILed. |
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Jenkins, retest this please. |
akmorrow13
commented
Nov 11, 2018
adam-cli/src/test/scala/org/bdgenomics/adam/cli/TransformFeaturesSuite.scala
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Test FAILed. Build result: FAILUREGitHub pull request #2051 of commit 12db759 automatically merged.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos spark-test) in workspace /home/jenkins/workspace/ADAM-prbWiping out workspace first.Cloning the remote Git repositoryCloning repository https://github.com/bigdatagenomics/adam.git > git init /home/jenkins/workspace/ADAM-prb # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/heads/:refs/remotes/origin/ # timeout=15 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10 > git config --add remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=10 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > git rev-parse origin/pr/2051/merge^{commit} # timeout=10 > git branch -a -v --no-abbrev --contains 998f0f1 # timeout=10Checking out Revision 998f0f1 (origin/pr/2051/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 998f0f1 > git rev-list 998f0f1 # timeout=10Triggering ADAM-prb ? 2.7.5,2.11,2.2.2,ubuntuADAM-prb ? 2.7.5,2.11,2.2.2,ubuntu completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'Test FAILed. |
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Jenkins, retest this please. |
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Test FAILed. Build result: FAILUREGitHub pull request #2051 of commit 12db759 automatically merged.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos spark-test) in workspace /home/jenkins/workspace/ADAM-prbWiping out workspace first.Cloning the remote Git repositoryCloning repository https://github.com/bigdatagenomics/adam.git > git init /home/jenkins/workspace/ADAM-prb # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/heads/:refs/remotes/origin/ # timeout=15 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10 > git config --add remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=10 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > git rev-parse origin/pr/2051/merge^{commit} # timeout=10 > git branch -a -v --no-abbrev --contains 998f0f1 # timeout=10Checking out Revision 998f0f1 (origin/pr/2051/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 998f0f1 > git rev-list 998f0f1 # timeout=10Triggering ADAM-prb ? 2.7.5,2.11,2.2.2,ubuntuADAM-prb ? 2.7.5,2.11,2.2.2,ubuntu completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'Test FAILed. |
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Test FAILed. Build result: FAILUREGitHub pull request #2051 of commit 022888f automatically merged.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos spark-test) in workspace /home/jenkins/workspace/ADAM-prbWiping out workspace first.Cloning the remote Git repositoryCloning repository https://github.com/bigdatagenomics/adam.git > git init /home/jenkins/workspace/ADAM-prb # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/heads/:refs/remotes/origin/ # timeout=15 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10 > git config --add remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=10 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > git rev-parse origin/pr/2051/merge^{commit} # timeout=10 > git branch -a -v --no-abbrev --contains cc811de # timeout=10Checking out Revision cc811de (origin/pr/2051/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f cc811de > git rev-list 998f0f1 # timeout=10Triggering ADAM-prb ? 2.7.5,2.11,2.2.2,ubuntuADAM-prb ? 2.7.5,2.11,2.2.2,ubuntu completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'Test FAILed. |
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Jenkins, retest this please. |
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Test FAILed. Build result: FAILUREGitHub pull request #2051 of commit 022888f automatically merged.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos spark-test) in workspace /home/jenkins/workspace/ADAM-prbWiping out workspace first.Cloning the remote Git repositoryCloning repository https://github.com/bigdatagenomics/adam.git > git init /home/jenkins/workspace/ADAM-prb # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/heads/:refs/remotes/origin/ # timeout=15 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10 > git config --add remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=10 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > git rev-parse origin/pr/2051/merge^{commit} # timeout=10 > git branch -a -v --no-abbrev --contains cc811de # timeout=10Checking out Revision cc811de (origin/pr/2051/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f cc811de > git rev-list cc811de # timeout=10Triggering ADAM-prb ? 2.7.5,2.11,2.2.2,ubuntuADAM-prb ? 2.7.5,2.11,2.2.2,ubuntu completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'Test FAILed. |
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@shaneknapp Sorry for the out-of-the-blue mention -- is there anything out of the ordinary going on with the Jenkins failures in this pull request? I've also noticed that the nightly ADAM build has been failing often lately because it hits the 45 minute timeout. |
heuermh
requested changes
Nov 12, 2018
adam-cli/src/test/scala/org/bdgenomics/adam/cli/TransformFeaturesSuite.scala
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| @@ -31,10 +31,11 @@ private[adam] object Coverage { | |||
| * | |||
| * @param region ReferenceRegion in which Coverage spans | |||
| * @param count Coverage count for each base pair in region | |||
| * @param sampleId Option of sampleId for this Coverage record | |||
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sampleId → optSampleId; Option of sampleId → Optional sampleId
| @@ -79,29 +81,36 @@ private[adam] object Coverage { | |||
| * observed. | |||
| * @param end The end coordinate of the region where this coverage value was | |||
| * observed. | |||
| * @param sampleId Option of sampleId for this Coverage record | |||
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sampleId → optSampleId; Option of sampleId → Optional sampleId
adam-core/src/main/scala/org/bdgenomics/adam/rdd/feature/CoverageRDD.scala
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adam-core/src/main/scala/org/bdgenomics/adam/rdd/feature/CoverageRDD.scala
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| @@ -302,35 +318,37 @@ case class DatasetBoundFeatureRDD private[rdd] ( | |||
| lazy val rdd = dataset.rdd.map(_.toAvro) | |||
| protected lazy val optPartitionMap = None | |||
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| override def saveAsParquet(filePath: String, | |||
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By moving this to FeatureRDD, we're always converting to DF even in the RDD path, is that intentional?
| * | ||
| * @param newSequences The new sequence dictionary to attach. | ||
| * @return Returns a new DatasetBoundFeatureRDD with the sequences replaced. | ||
| */ | ||
| def replaceSequences(newSequences: SequenceDictionary): FeatureRDD = { |
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This method is defined with scaladoc in GenomicDataset, could we use override def instead?
| * @param newSamples The new sample metadata to attach. | ||
| * @return A DatasetBoundFeatureRDD with new sample metadata. | ||
| */ | ||
| def replaceSamples(newSamples: Iterable[Sample]): FeatureRDD = { |
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This method is defined with scaladoc in MultisampleGenomicDataset, could we use override def instead?
| * | ||
| * @param newSequences The new sequence dictionary to attach. | ||
| * @return Returns a new RDDBoundFeatureRDD with the sequences replaced. | ||
| */ | ||
| def replaceSequences(newSequences: SequenceDictionary): FeatureRDD = { |
There was a problem hiding this comment.
This method is defined with scaladoc in GenomicDataset, could we use override def instead?
| * @param newSamples The new sample metadata to attach. | ||
| * @return A RDDBoundFeatureRDD with new sample metadata. | ||
| */ | ||
| def replaceSamples(newSamples: Iterable[Sample]): FeatureRDD = { |
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This method is defined with scaladoc in MultisampleGenomicDataset, could we use override def instead?
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Test PASSed. |
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these are random, and literally undiagnoseable github timeouts and have
nothing to do w/jenkins.
i've had lengthy emails w/some folks @ github about this and we've
effectively ruled out this being something wrong w/our build system.
regarding ADAM builds timing out: you know you can just log in to jenkins
and up the timeout?
…On Mon, Nov 12, 2018 at 7:33 AM Michael L Heuer ***@***.***> wrote:
@shaneknapp <https://github.com/shaneknapp> Sorry for the out-of-the-blue
mention -- is there anything out of the ordinary going on with the Jenkins
failures in this pull request? I've also noticed that the nightly ADAM
build has been failing often lately because it hits the 45 minute timeout.
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<#2051 (comment)>,
or mute the thread
<https://github.com/notifications/unsubscribe-auth/ABiDrPniOytFyOXeHHutwD_Kvd_IoIE4ks5uuZTFgaJpZM4Ws9Ji>
.
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Thanks, @shaneknapp! I'll up the timeout on the nightly build. |
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Test FAILed. Build result: FAILUREGitHub pull request #2051 of commit 8f30775 automatically merged.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos spark-test) in workspace /home/jenkins/workspace/ADAM-prbWiping out workspace first.Cloning the remote Git repositoryCloning repository https://github.com/bigdatagenomics/adam.git > git init /home/jenkins/workspace/ADAM-prb # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/heads/:refs/remotes/origin/ # timeout=15 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10 > git config --add remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=10 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > git rev-parse origin/pr/2051/merge^{commit} # timeout=10 > git branch -a -v --no-abbrev --contains 79015dc # timeout=10Checking out Revision 79015dc (origin/pr/2051/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 79015dc > git rev-list d40b89a # timeout=10Triggering ADAM-prb ? 2.7.5,2.11,2.2.2,ubuntuADAM-prb ? 2.7.5,2.11,2.2.2,ubuntu completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'Test FAILed. |
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did someone force push to master?
…On Mon, Nov 12, 2018 at 12:00 PM UCB AMPLab ***@***.***> wrote:
Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/2874/
Build result: FAILUREGitHub pull request #2051
<#2051> of commit 8f30775
<8f30775>
automatically merged.Notifying endpoint 'HTTP:
https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading
node environment variables.Building remotely on amp-jenkins-worker-05
(centos spark-test) in workspace /home/jenkins/workspace/ADAM-prbWiping out
workspace first.Cloning the remote Git repositoryCloning repository
https://github.com/bigdatagenomics/adam.git > git init
/home/jenkins/workspace/ADAM-prb # timeout=10Fetching upstream changes from
https://github.com/bigdatagenomics/adam.git > git --version # timeout=10
> git fetch --tags --progress https://github.com/bigdatagenomics/adam.git
+refs/heads/*:refs/remotes/origin/* # timeout=15 > git config
remote.origin.url https://github.com/bigdatagenomics/adam.git #
timeout=10 > git config --add remote.origin.fetch +refs/heads/
*:refs/remotes/origin/* # timeout=10 > git config remote.origin.url
https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream
changes from https://github.com/bigdatagenomics/adam.git > git fetch
--tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/
*:refs/remotes/origin/pr/* # timeout=15 > git rev-parse
origin/pr/2051/merge^{commit} # timeout=10 > git branch -a -v --no-abbrev
--contains 79015dc
<79015dc>
# timeout=10Checking out Revision 79015dc
<79015dc>
(origin/pr/2051/merge) > git config core.sparsecheckout # timeout=10 > git
checkout -f 79015dc
<79015dc>
> git rev-list d40b89a
<d40b89a>
# timeout=10Triggering ADAM-prb ? 2.7.5,2.11,2.2.2,ubuntuADAM-prb ?
2.7.5,2.11,2.2.2,ubuntu completed with result FAILURENotifying endpoint
'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.
—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub
<#2051 (comment)>,
or mute the thread
<https://github.com/notifications/unsubscribe-auth/ABiDrJlsXsro5-pGz8MH3IqO05QjW2ZKks5uudNJgaJpZM4Ws9Ji>
.
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No, not to master. We do allow force pushes on pull request branches to squash commits. This pull request is on branch |
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Jenkins, retest this please |
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Test PASSed. |
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Test FAILed. Build result: FAILUREGitHub pull request #2051 of commit 04b56cc automatically merged.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos spark-test) in workspace /home/jenkins/workspace/ADAM-prbWiping out workspace first.Cloning the remote Git repositoryCloning repository https://github.com/bigdatagenomics/adam.git > git init /home/jenkins/workspace/ADAM-prb # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/heads/:refs/remotes/origin/ # timeout=15 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10 > git config --add remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=10 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > git rev-parse origin/pr/2051/merge^{commit} # timeout=10 > git branch -a -v --no-abbrev --contains 4c42606 # timeout=10Checking out Revision 4c42606 (origin/pr/2051/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 4c42606 > git rev-list 79015dc # timeout=10Triggering ADAM-prb ? 2.7.5,2.11,2.2.2,ubuntuADAM-prb ? 2.7.5,2.11,2.2.2,ubuntu completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'Test FAILed. |
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Jenkins, retest this please. |
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Jenkins, retest this please |
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Oops, don't cross the streams! |
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Test FAILed. Build result: FAILUREGitHub pull request #2051 of commit 04b56cc automatically merged.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos spark-test) in workspace /home/jenkins/workspace/ADAM-prbWiping out workspace first.Cloning the remote Git repositoryCloning repository https://github.com/bigdatagenomics/adam.git > git init /home/jenkins/workspace/ADAM-prb # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/heads/:refs/remotes/origin/ # timeout=15 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10 > git config --add remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=10 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > git rev-parse origin/pr/2051/merge^{commit} # timeout=10 > git branch -a -v --no-abbrev --contains 4c42606 # timeout=10Checking out Revision 4c42606 (origin/pr/2051/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 4c42606 > git rev-list 4c42606 # timeout=10Triggering ADAM-prb ? 2.7.5,2.11,2.2.2,ubuntuADAM-prb ? 2.7.5,2.11,2.2.2,ubuntu completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'Test FAILed. |
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Test FAILed. Build result: FAILUREGitHub pull request #2051 of commit 87bd373 automatically merged.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos spark-test) in workspace /home/jenkins/workspace/ADAM-prbWiping out workspace first.Cloning the remote Git repositoryCloning repository https://github.com/bigdatagenomics/adam.git > git init /home/jenkins/workspace/ADAM-prb # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/heads/:refs/remotes/origin/ # timeout=15 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10 > git config --add remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=10 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > git rev-parse origin/pr/2051/merge^{commit} # timeout=10 > git branch -a -v --no-abbrev --contains e3cb766 # timeout=10Checking out Revision e3cb766 (origin/pr/2051/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f e3cb766 > git rev-list 4c42606 # timeout=10Triggering ADAM-prb ? 2.7.5,2.11,2.2.2,ubuntuADAM-prb ? 2.7.5,2.11,2.2.2,ubuntu completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'Test FAILed. |
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Jenkins, retest this please. |
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Test PASSed. |
heuermh
approved these changes
Nov 13, 2018
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Squash and merge now, or do you have more commits to add? |
akmorrow13
force-pushed
the
multisampleRDD
branch
from
87bd373
to
5a57421
Compare
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Squashed! |
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Test FAILed. Build result: FAILUREGitHub pull request #2051 of commit 5a57421 automatically merged.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos spark-test) in workspace /home/jenkins/workspace/ADAM-prbWiping out workspace first.Cloning the remote Git repositoryCloning repository https://github.com/bigdatagenomics/adam.git > git init /home/jenkins/workspace/ADAM-prb # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/heads/:refs/remotes/origin/ # timeout=15 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10 > git config --add remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=10 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > git rev-parse origin/pr/2051/merge^{commit} # timeout=10 > git branch -a -v --no-abbrev --contains ff995ca # timeout=10Checking out Revision ff995ca (origin/pr/2051/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f ff995ca > git rev-list e3cb766 # timeout=10Triggering ADAM-prb ? 2.7.5,2.11,2.2.2,ubuntuADAM-prb ? 2.7.5,2.11,2.2.2,ubuntu completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'Test FAILed. |
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Sweet! I'll merge when Jenkins passes, and then start on the 0.25.0 release. |
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Jenkins, retest this please. |
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Test PASSed. |
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Thank you, @akmorrow13! |
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