Upgrade to bdg-formats-0.10.0 #1135

Merged
merged 2 commits into from Nov 15, 2016

Conversation

Projects
3 participants
@fnothaft
Member

fnothaft commented Aug 26, 2016

For tracking.

@fnothaft

This comment has been minimized.

Show comment
Hide comment
@fnothaft

fnothaft Aug 26, 2016

Member

-1, not yet ready to merge.

Member

fnothaft commented Aug 26, 2016

-1, not yet ready to merge.

@AmplabJenkins

This comment has been minimized.

Show comment
Hide comment
@AmplabJenkins

AmplabJenkins 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.

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.

@AmplabJenkins

This comment has been minimized.

Show comment
Hide comment
@AmplabJenkins

AmplabJenkins 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.

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.

@heuermh heuermh referenced this pull request Sep 7, 2016

Closed

Release ADAM version 0.20.0 #1048

47 of 61 tasks complete
@AmplabJenkins

This comment has been minimized.

Show comment
Hide comment
@AmplabJenkins

AmplabJenkins 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.

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

This comment has been minimized.

Show comment
Hide comment
@fnothaft

fnothaft Sep 29, 2016

Member

Rebased. CC @heuermh

Member

fnothaft commented Sep 29, 2016

Rebased. CC @heuermh

@AmplabJenkins

This comment has been minimized.

Show comment
Hide comment
@AmplabJenkins

AmplabJenkins 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.

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.

@heuermh

This comment has been minimized.

Show comment
Hide comment
@heuermh

heuermh Oct 24, 2016

Member

@fnothaft could you rebase this?

Member

heuermh commented Oct 24, 2016

@fnothaft could you rebase this?

@AmplabJenkins

This comment has been minimized.

Show comment
Hide comment
@AmplabJenkins

AmplabJenkins 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.

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.

@AmplabJenkins

This comment has been minimized.

Show comment
Hide comment
@AmplabJenkins

AmplabJenkins 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.

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 some commits Aug 24, 2016

Bump to bdg-formats 0.10.0.
* 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

This comment has been minimized.

Show comment
Hide comment
@fnothaft

fnothaft Nov 15, 2016

Member

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

Member

fnothaft commented Nov 15, 2016

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

@heuermh

This comment has been minimized.

Show comment
Hide comment
@heuermh

heuermh Nov 15, 2016

Member

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.

Member

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.

@fnothaft

This comment has been minimized.

Show comment
Hide comment
@fnothaft

fnothaft Nov 15, 2016

Member

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.

Member

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.

@AmplabJenkins

This comment has been minimized.

Show comment
Hide comment
@AmplabJenkins

AmplabJenkins 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.

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

1 check passed

default Merged build finished.
Details

@fnothaft fnothaft deleted the upgrade-to-bdg-formats-0.10.0 branch Nov 15, 2016

@fnothaft

This comment has been minimized.

Show comment
Hide comment
@fnothaft

fnothaft Nov 15, 2016

Member

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

Member

fnothaft commented Nov 15, 2016

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

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment