Upgrade to bdg-formats-0.10.0 #1135
Merged
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
|
-1, not yet ready to merge. |
|
Test PASSed. |
fnothaft
force-pushed
the
upgrade-to-bdg-formats-0.10.0
branch
from
65adcf6
to
97d9290
Compare
|
Test FAILed. Build result: FAILUREGitHub 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
force-pushed
the
upgrade-to-bdg-formats-0.10.0
branch
from
97d9290
to
bd1c3de
Compare
|
Test PASSed. |
fnothaft
force-pushed
the
upgrade-to-bdg-formats-0.10.0
branch
from
bd1c3de
to
40b4b9b
Compare
|
Rebased. CC @heuermh |
|
Test FAILed. Build result: FAILUREGitHub 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. |
|
@fnothaft could you rebase this? |
fnothaft
force-pushed
the
upgrade-to-bdg-formats-0.10.0
branch
from
40b4b9b
to
12f245c
Compare
|
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 > /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
force-pushed
the
upgrade-to-bdg-formats-0.10.0
branch
from
12f245c
to
c06143b
Compare
|
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 > /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. |
* 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
force-pushed
the
upgrade-to-bdg-formats-0.10.0
branch
from
c06143b
to
c21401f
Compare
|
Had to update some test collateral. This should pass on this build. |
|
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. |
|
Test PASSed. |
|
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
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
For tracking.