Updating build dependency versions to latest minor versions #847
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
|
Test FAILed. Build result: FAILUREGitHub pull request #847 of commit 19f3bad 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 > git rev-parse --is-inside-work-tree # timeout=10Fetching changes from the remote Git repository > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # 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/pull/:refs/remotes/origin/pr/ > git rev-parse origin/pr/847/merge^{commit} # timeout=10 > git branch -a --contains 5430ce6e0320aa56c3bf939d0f15318b10ba8bb1 # timeout=10 > git rev-parse remotes/origin/pr/847/merge^{commit} # timeout=10Checking out Revision 5430ce6e0320aa56c3bf939d0f15318b10ba8bb1 (origin/pr/847/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 5430ce6e0320aa56c3bf939d0f15318b10ba8bb1First time build. Skipping changelog.Triggering ADAM-prb ? 2.6.0,2.11,1.4.1,centosTriggering ADAM-prb ? 2.6.0,2.10,1.4.1,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'Test FAILed. |
|
Those are just header version issues because the htsjdk version changed. If you update the unittest collateral, this should go away. |
|
Ah right, I assume since those were handcrafted .sam files, there'd be no harm in manually updating the version number? Running them through |
|
Yeah, I would just manually update them. |
|
ok, then I get farther Looks like I jumped too far ahead with args4j. |
heuermh
force-pushed
the
dependency-versions
branch
from
19f3bad
to
e6ce184
Compare
heuermh
changed the title
|
Test FAILed. Build result: FAILUREGitHub pull request #847 of commit e6ce184 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 > git rev-parse --is-inside-work-tree # timeout=10Fetching changes from the remote Git repository > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # 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/pull/:refs/remotes/origin/pr/ > git rev-parse origin/pr/847/merge^{commit} # timeout=10 > git branch -a --contains 22a204a627fd75fe7919955210074aa84eabbc0d # timeout=10 > git rev-parse remotes/origin/pr/847/merge^{commit} # timeout=10Checking out Revision 22a204a627fd75fe7919955210074aa84eabbc0d (origin/pr/847/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 22a204a627fd75fe7919955210074aa84eabbc0dFirst time build. Skipping changelog.Triggering ADAM-prb ? 2.6.0,2.11,1.4.1,centosTriggering ADAM-prb ? 2.6.0,2.10,1.4.1,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'Test FAILed. |
|
Bugger, |
heuermh
force-pushed
the
dependency-versions
branch
from
e6ce184
to
21901e7
Compare
|
Test FAILed. Build result: FAILUREGitHub pull request #847 of commit 21901e7 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 > git rev-parse --is-inside-work-tree # timeout=10Fetching changes from the remote Git repository > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # 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/pull/:refs/remotes/origin/pr/ > git rev-parse origin/pr/847/merge^{commit} # timeout=10 > git branch -a --contains 9ff0c01 # timeout=10 > git rev-parse remotes/origin/pr/847/merge^{commit} # timeout=10Checking out Revision 9ff0c01 (origin/pr/847/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 9ff0c01e1ffa7f03be73a32db12aa38a4ad74542First time build. Skipping changelog.Triggering ADAM-prb ? 2.6.0,2.11,1.4.1,centosTriggering ADAM-prb ? 2.6.0,2.10,1.4.1,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'Test FAILed. |
|
Grrr. Guava version mismatch |
heuermh
force-pushed
the
dependency-versions
branch
from
21901e7
to
a21a02f
Compare
|
Upgrading guava past version |
heuermh
force-pushed
the
dependency-versions
branch
from
a21a02f
to
a446b0b
Compare
|
Test FAILed. Build result: FAILUREGitHub pull request #847 of commit a21a02f 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 > git rev-parse --is-inside-work-tree # timeout=10Fetching changes from the remote Git repository > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # 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/pull/:refs/remotes/origin/pr/ > git rev-parse origin/pr/847/merge^{commit} # timeout=10 > git branch -a --contains a5c1468 # timeout=10 > git rev-parse remotes/origin/pr/847/merge^{commit} # timeout=10Checking out Revision a5c1468 (origin/pr/847/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f a5c1468950f2b5abf11e24e53b4b4516d81dc9a5First time build. Skipping changelog.Triggering ADAM-prb ? 2.6.0,2.11,1.4.1,centosTriggering ADAM-prb ? 2.6.0,2.10,1.4.1,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'Test FAILed. |
|
Test FAILed. Build result: FAILUREGitHub pull request #847 of commit a446b0b 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 > git rev-parse --is-inside-work-tree # timeout=10Fetching changes from the remote Git repository > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # 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/pull/:refs/remotes/origin/pr/ > git rev-parse origin/pr/847/merge^{commit} # timeout=10 > git branch -a --contains c99a355 # timeout=10 > git rev-parse remotes/origin/pr/847/merge^{commit} # timeout=10Checking out Revision c99a355 (origin/pr/847/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f c99a3555ee8cd60a142d6bc4e52f012a4cf0eeffFirst time build. Skipping changelog.Triggering ADAM-prb ? 2.6.0,2.11,1.4.1,centosTriggering ADAM-prb ? 2.6.0,2.10,1.4.1,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'Test FAILed. |
|
Jenkins, retest this please. |
|
Test PASSed. |
|
This change looks good, but let's hold on merging it until after 0.18.0. |
|
I agree. |
heuermh
force-pushed
the
dependency-versions
branch
from
a446b0b
to
0f621e7
Compare
|
Test FAILed. Build result: FAILURE[...truncated 16 lines...] > git rev-list c99a355 # timeout=10Triggering ADAM-prb ? 2.6.0,2.11,1.4.1,centosTriggering ADAM-prb ? 2.6.0,2.10,1.4.1,centosTriggering ADAM-prb ? 2.3.0,2.11,1.2.1,centosTriggering ADAM-prb ? 2.6.0,2.10,1.3.1,centosTriggering ADAM-prb ? 1.0.4,2.10,1.2.1,centosTriggering ADAM-prb ? 2.3.0,2.11,1.3.1,centosTriggering ADAM-prb ? 2.3.0,2.10,1.2.1,centosTriggering ADAM-prb ? 2.6.0,2.11,1.3.1,centosTriggering ADAM-prb ? 1.0.4,2.11,1.2.1,centosTriggering ADAM-prb ? 2.3.0,2.10,1.3.1,centosTriggering ADAM-prb ? 2.3.0,2.10,1.4.1,centosTriggering ADAM-prb ? 2.3.0,2.11,1.4.1,centosADAM-prb ? 2.3.0,2.11,1.2.1,centos completed with result FAILUREADAM-prb ? 2.6.0,2.10,1.3.1,centos completed with result FAILUREADAM-prb ? 1.0.4,2.10,1.2.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.11,1.3.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.10,1.2.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.11,1.3.1,centos completed with result SUCCESSADAM-prb ? 1.0.4,2.11,1.2.1,centos completed with result FAILUREADAM-prb ? 2.3.0,2.10,1.3.1,centos completed with result FAILUREADAM-prb ? 2.3.0,2.10,1.4.1,centos completed with result FAILUREADAM-prb ? 2.3.0,2.11,1.4.1,centos completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'Test FAILed. |
|
Jenkins, test this please. |
|
Test FAILed. Build result: FAILUREGitHub pull request #847 of commit 0f621e7 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 > git rev-parse --is-inside-work-tree # timeout=10Fetching changes from the remote Git repository > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # 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/pull/:refs/remotes/origin/pr/ > git rev-parse origin/pr/847/merge^{commit} # timeout=10 > git branch -a --contains d53322c # timeout=10 > git rev-parse remotes/origin/pr/847/merge^{commit} # timeout=10Checking out Revision d53322c (origin/pr/847/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f d53322c > git rev-list 9413aea # timeout=10Triggering ADAM-prb ? 2.6.0,2.11,1.4.1,centosTriggering ADAM-prb ? 2.6.0,2.10,1.4.1,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'Test FAILed. |
|
Jenkins, test this please. |
|
Test PASSed. |
heuermh
force-pushed
the
dependency-versions
branch
from
0f621e7
to
f31cfa3
Compare
|
Test FAILed. Build result: FAILUREGitHub pull request #847 of commit f31cfa3 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 > git rev-parse --is-inside-work-tree # timeout=10Fetching changes from the remote Git repository > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # 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/pull/:refs/remotes/origin/pr/ > git rev-parse origin/pr/847/merge^{commit} # timeout=10 > git branch -a --contains 90bd871 # timeout=10 > git rev-parse remotes/origin/pr/847/merge^{commit} # timeout=10Checking out Revision 90bd871 (origin/pr/847/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 90bd871 > git rev-list d53322c # timeout=10Triggering ADAM-prb ? 2.6.0,2.11,1.4.1,centosTriggering ADAM-prb ? 2.6.0,2.10,1.4.1,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'Test FAILed. |
|
Jenkins, retest this please. |
|
Test PASSed. |
heuermh
force-pushed
the
dependency-versions
branch
from
f31cfa3
to
4b71d0e
Compare
|
Test FAILed. Build result: FAILUREGitHub pull request #847 of commit 4b71d0e 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 > git rev-parse --is-inside-work-tree # timeout=10Fetching changes from the remote Git repository > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # 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/pull/:refs/remotes/origin/pr/ > git rev-parse origin/pr/847/merge^{commit} # timeout=10 > git branch -a --contains d982a8a9d36f1d6c221846988e12f05b0494c4e6 # timeout=10 > git rev-parse remotes/origin/pr/847/merge^{commit} # timeout=10Checking out Revision d982a8a9d36f1d6c221846988e12f05b0494c4e6 (origin/pr/847/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f d982a8a9d36f1d6c221846988e12f05b0494c4e6 > git rev-list 90bd871 # timeout=10Triggering ADAM-prb ? 2.6.0,2.11,1.4.1,centosTriggering ADAM-prb ? 2.6.0,2.10,1.4.1,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'Test FAILed. |
|
Jenkins, retest this please. |
|
Test PASSed. |
|
Thanks! |
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.
I updated several dependency versions to the latest minor version (and guava from 14.0.1 --> 18.0) hoping that the build would still be ok. Three unit tests fail: