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modified CoverageRDD and FeatureRDD to extend MultisampleGenomicDataset #2051

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merged 1 commit into from Nov 13, 2018

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akmorrow13 commented Sep 18, 2018

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@akmorrow13 akmorrow13 referenced this pull request Sep 18, 2018

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Multi-sample coverage #2050

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akmorrow13 commented Sep 18, 2018

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AmplabJenkins commented Sep 18, 2018

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/2812/

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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AmplabJenkins commented Sep 18, 2018

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/2814/

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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heuermh commented Sep 21, 2018

See #1498.

@akmorrow13 akmorrow13 force-pushed the akmorrow13:multisampleRDD branch from c4a0f1b to 57f97d5 Oct 17, 2018

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akmorrow13 commented Oct 17, 2018

This was tested on the yarn cluster for loading/converting multiple alignments to multisample coverage and reloading them from parquet.

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AmplabJenkins commented Oct 17, 2018

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/2835/

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.

@heuermh heuermh added this to the 0.25.0 milestone Nov 7, 2018

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heuermh commented Nov 7, 2018

bdg-formats version 0.11.4 has been released, this pull request should be updated when it hits Maven Central.

@akmorrow13 akmorrow13 force-pushed the akmorrow13:multisampleRDD branch 2 times, most recently from d7a76f8 to 7423cd5 Nov 8, 2018

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AmplabJenkins commented Nov 8, 2018

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
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Build result: FAILURE

GitHub 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.
Refer to this link for build results (access rights to CI server needed):
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Build result: FAILURE

GitHub 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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heuermh commented Nov 8, 2018

Jenkins, retest this please

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AmplabJenkins commented Nov 8, 2018

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/2863/

Build result: FAILURE

GitHub 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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akmorrow13 commented Nov 8, 2018

Jenkins, retest this please.

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AmplabJenkins commented Nov 8, 2018

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
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Build result: FAILURE

GitHub 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 akmorrow13 force-pushed the akmorrow13:multisampleRDD branch from 7423cd5 to 12db759 Nov 11, 2018

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Test FAILed.
Refer to this link for build results (access rights to CI server needed):
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Build result: FAILURE

GitHub 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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akmorrow13 commented Nov 11, 2018

Jenkins, retest this please.

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coveralls commented Nov 11, 2018

Coverage Status

Coverage increased (+0.1%) to 79.179% when pulling 5a57421 on akmorrow13:multisampleRDD into de21474 on bigdatagenomics:master.

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Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/2866/

Build result: FAILURE

GitHub 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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akmorrow13 commented Nov 11, 2018

Jenkins, retest this please.

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AmplabJenkins commented Nov 11, 2018

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/2867/

Build result: FAILURE

GitHub 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.
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Build result: FAILURE

GitHub 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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akmorrow13 commented Nov 11, 2018

Jenkins, retest this please.

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AmplabJenkins commented Nov 11, 2018

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/2869/

Build result: FAILURE

GitHub 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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Looks good! A few style and doc changes requested.

Show resolved Hide resolved ...-cli/src/test/scala/org/bdgenomics/adam/cli/TransformFeaturesSuite.scala
@@ -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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sampleIdoptSampleId; 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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sampleIdoptSampleId; Option of sampleId → Optional sampleId

Show resolved Hide resolved adam-core/src/main/scala/org/bdgenomics/adam/rdd/feature/CoverageRDD.scala
Show resolved Hide resolved adam-core/src/main/scala/org/bdgenomics/adam/rdd/feature/CoverageRDD.scala
@@ -302,35 +318,37 @@ case class DatasetBoundFeatureRDD private[rdd] (
lazy val rdd = dataset.rdd.map(_.toAvro)
protected lazy val optPartitionMap = None

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 = {

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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 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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Test PASSed.

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shaneknapp commented Nov 12, 2018

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heuermh commented Nov 12, 2018

Thanks, @shaneknapp! I'll up the timeout on the nightly build.

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Test FAILed.
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Build result: FAILURE

GitHub 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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shaneknapp commented Nov 12, 2018

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heuermh commented Nov 12, 2018

did someone force push to master?

No, not to master. We do allow force pushes on pull request branches to squash commits. This pull request is on branch akmorrow13:multisampleRDD.

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heuermh commented Nov 12, 2018

Jenkins, retest this please

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Test PASSed.
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Test FAILed.
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Build result: FAILURE

GitHub 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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akmorrow13 commented Nov 12, 2018

Jenkins, retest this please.

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heuermh commented Nov 12, 2018

Jenkins, retest this please

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heuermh commented Nov 12, 2018

Oops, don't cross the streams!

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Test FAILed.
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Build result: FAILURE

GitHub 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.
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Build result: FAILURE

GitHub 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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akmorrow13 commented Nov 13, 2018

Jenkins, retest this please.

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Test PASSed.
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Test PASSed.

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heuermh commented Nov 13, 2018

Squash and merge now, or do you have more commits to add?

@akmorrow13 akmorrow13 force-pushed the akmorrow13:multisampleRDD branch from 87bd373 to 5a57421 Nov 13, 2018

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akmorrow13 commented Nov 13, 2018

Squashed!

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Build result: FAILURE

GitHub 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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heuermh commented Nov 13, 2018

Sweet! I'll merge when Jenkins passes, and then start on the 0.25.0 release.

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akmorrow13 commented Nov 13, 2018

Jenkins, retest this please.

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AmplabJenkins commented Nov 13, 2018

Test PASSed.
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Test PASSed.

@heuermh heuermh merged commit 833ab8a into bigdatagenomics:master Nov 13, 2018

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heuermh commented Nov 13, 2018

Thank you, @akmorrow13!

@heuermh heuermh referenced this pull request Dec 5, 2018

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Compute coverage by sample #1498

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