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Upgrade to bdg-formats-0.10.0 #1135

Merged
merged 2 commits into from Nov 15, 2016
Merged

Upgrade to bdg-formats-0.10.0 #1135

merged 2 commits into from Nov 15, 2016

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@fnothaft
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fnothaft commented Aug 26, 2016

For tracking.

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fnothaft commented Aug 26, 2016

-1, not yet ready to merge.

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AmplabJenkins commented Aug 26, 2016

Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1429/
Test PASSed.

@fnothaft fnothaft force-pushed the upgrade-to-bdg-formats-0.10.0 branch from 65adcf6 to 97d9290 Aug 31, 2016
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AmplabJenkins commented Aug 31, 2016

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1446/

Build result: FAILURE

GitHub pull request #1135 of commit 97d9290 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-prb > /home/jenkins/git2/bin/git rev-parse --is-inside-work-tree # timeout=10Fetching changes from the remote Git repository > /home/jenkins/git2/bin/git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > /home/jenkins/git2/bin/git --version # timeout=10 > /home/jenkins/git2/bin/git -c core.askpass=true fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > /home/jenkins/git2/bin/git rev-parse origin/pr/1135/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains b6f5607 # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/1135/merge^{commit} # timeout=10Checking out Revision b6f5607 (origin/pr/1135/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f b6f56070e9959d8984b5f258da765e8c187df791First time build. Skipping changelog.Triggering ADAM-prb ? 2.6.0,2.11,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.10,1.5.2,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

@fnothaft fnothaft force-pushed the upgrade-to-bdg-formats-0.10.0 branch from 97d9290 to bd1c3de Sep 7, 2016
@heuermh heuermh mentioned this pull request Sep 7, 2016
47 of 61 tasks complete
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AmplabJenkins commented Sep 7, 2016

Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1465/
Test PASSed.

@fnothaft fnothaft force-pushed the upgrade-to-bdg-formats-0.10.0 branch from bd1c3de to 40b4b9b Sep 29, 2016
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fnothaft commented Sep 29, 2016

Rebased. CC @heuermh

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AmplabJenkins commented Sep 29, 2016

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1510/

Build result: FAILURE

GitHub pull request #1135 of commit 40b4b9b 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-prb > /home/jenkins/git2/bin/git rev-parse --is-inside-work-tree # timeout=10Fetching changes from the remote Git repository > /home/jenkins/git2/bin/git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > /home/jenkins/git2/bin/git --version # timeout=10 > /home/jenkins/git2/bin/git -c core.askpass=true fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > /home/jenkins/git2/bin/git rev-parse origin/pr/1135/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains 9d75e6c # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/1135/merge^{commit} # timeout=10Checking out Revision 9d75e6c (origin/pr/1135/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 9d75e6cd069f4d6dd49f9607bb8275e857708d0dFirst time build. Skipping changelog.Triggering ADAM-prb ? 2.6.0,2.11,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.10,1.5.2,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

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heuermh commented Oct 24, 2016

@fnothaft could you rebase this?

@fnothaft fnothaft force-pushed the upgrade-to-bdg-formats-0.10.0 branch from 40b4b9b to 12f245c Nov 3, 2016
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AmplabJenkins commented Nov 3, 2016

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1555/

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 > /home/jenkins/git2/bin/git init /home/jenkins/workspace/ADAM-prb # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > /home/jenkins/git2/bin/git --version # timeout=10 > /home/jenkins/git2/bin/git -c core.askpass=true fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/heads/:refs/remotes/origin/ # timeout=15 > /home/jenkins/git2/bin/git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10 > /home/jenkins/git2/bin/git config --add remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=10 > /home/jenkins/git2/bin/git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > /home/jenkins/git2/bin/git -c core.askpass=true fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > /home/jenkins/git2/bin/git rev-parse origin/pr/1135/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains 23c7434 # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/1135/merge^{commit} # timeout=10Checking out Revision 23c7434 (origin/pr/1135/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 23c743476d76e12130feb43292efaddca714a8a9First time build. Skipping changelog.Triggering ADAM-prb ? 2.6.0,2.11,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.10,1.5.2,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

@fnothaft fnothaft added this to the 0.21.0 milestone Nov 8, 2016
@fnothaft fnothaft force-pushed the upgrade-to-bdg-formats-0.10.0 branch from 12f245c to c06143b Nov 15, 2016
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AmplabJenkins commented Nov 15, 2016

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1604/

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 > /home/jenkins/git2/bin/git init /home/jenkins/workspace/ADAM-prb # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > /home/jenkins/git2/bin/git --version # timeout=10 > /home/jenkins/git2/bin/git -c core.askpass=true fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/heads/:refs/remotes/origin/ # timeout=15 > /home/jenkins/git2/bin/git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10 > /home/jenkins/git2/bin/git config --add remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=10 > /home/jenkins/git2/bin/git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > /home/jenkins/git2/bin/git -c core.askpass=true fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > /home/jenkins/git2/bin/git rev-parse origin/pr/1135/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains 315acf4 # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/1135/merge^{commit} # timeout=10Checking out Revision 315acf4 (origin/pr/1135/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 315acf406db133ac85ee3169ba287bc616928ecdFirst time build. Skipping changelog.Triggering ADAM-prb ? 2.6.0,2.11,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.10,1.5.2,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

heuermh added 2 commits Aug 24, 2016
* Update for bdg-formats code style changes (#1126)
* Remove StructuralVariant and StructuralVariantType, add names field to Variant
* Merge VariantAnnotation and DatabaseVariantAnnotation records
* Implement separate variant and genotype filters; rename VariantContext.databases field
@fnothaft fnothaft force-pushed the upgrade-to-bdg-formats-0.10.0 branch from c06143b to c21401f Nov 15, 2016
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fnothaft commented Nov 15, 2016

Had to update some test collateral. This should pass on this build.

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heuermh commented Nov 15, 2016

Right, the unit test failures here are due to filter-related changes. I'm not sure why I didn't run into these on #1250.

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fnothaft commented Nov 15, 2016

Right, the unit test failures here are due to filter-related changes. I'm not sure why I didn't run into these on #1250.

I was scratching my head there for a bit too, but then I realized it was because we had added said tests more recently than the last time we rebased this branch.

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AmplabJenkins commented Nov 15, 2016

Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1605/
Test PASSed.

@fnothaft fnothaft merged commit c21401f into master Nov 15, 2016
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@fnothaft fnothaft deleted the upgrade-to-bdg-formats-0.10.0 branch Nov 15, 2016
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fnothaft commented Nov 15, 2016

Merged! Huge tip of the hat to @heuermh for leading this refactor.

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