Update hadoop-bam dependency version to 7.5.0 #989

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merged 1 commit into from May 18, 2016

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heuermh commented Apr 4, 2016

Will update to version 7.5.0 as appropriate on its release.

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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 #989 of commit ce04cb8 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/989/merge^{commit} # timeout=10 > git branch -a --contains bcaea16 # timeout=10 > git rev-parse remotes/origin/pr/989/merge^{commit} # timeout=10Checking out Revision bcaea16 (origin/pr/989/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f bcaea161e5ddf6ddc6b229db81461a82290906d0First 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/1129/

Build result: FAILURE

GitHub pull request #989 of commit ce04cb8 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/989/merge^{commit} # timeout=10 > git branch -a --contains bcaea16 # timeout=10 > git rev-parse remotes/origin/pr/989/merge^{commit} # timeout=10Checking out Revision bcaea16 (origin/pr/989/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f bcaea161e5ddf6ddc6b229db81461a82290906d0First 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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[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-parent_2.10 ---
[WARNING] Rule 1: org.apache.maven.plugins.enforcer.RequireJavaVersion failed with message:
ADAM requires Java 1.8 or greater

Looks like we'll need to update the JDK on our Jenkins box.

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heuermh commented Apr 4, 2016

[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-parent_2.10 ---
[WARNING] Rule 1: org.apache.maven.plugins.enforcer.RequireJavaVersion failed with message:
ADAM requires Java 1.8 or greater

Looks like we'll need to update the JDK on our Jenkins box.

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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/1135/

Build result: FAILURE

GitHub pull request #989 of commit f12cbd2 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/989/merge^{commit} # timeout=10 > git branch -a --contains 331a704 # timeout=10 > git rev-parse remotes/origin/pr/989/merge^{commit} # timeout=10Checking out Revision 331a704 (origin/pr/989/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 331a70448836aef00d5c3a2dfe0b0c57a193846bFirst 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/1135/

Build result: FAILURE

GitHub pull request #989 of commit f12cbd2 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/989/merge^{commit} # timeout=10 > git branch -a --contains 331a704 # timeout=10 > git rev-parse remotes/origin/pr/989/merge^{commit} # timeout=10Checking out Revision 331a704 (origin/pr/989/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 331a70448836aef00d5c3a2dfe0b0c57a193846bFirst 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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Jenkins, test this please.

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fnothaft commented Apr 20, 2016

Jenkins, test this please.

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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/1159/

Build result: FAILURE

GitHub pull request #989 of commit f12cbd2 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/989/merge^{commit} # timeout=10 > git branch -a --contains 3ae6a84 # timeout=10 > git rev-parse remotes/origin/pr/989/merge^{commit} # timeout=10Checking out Revision 3ae6a84 (origin/pr/989/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 3ae6a84bf49de57aa768aa7f6fbaeb4fa4808611First time build. Skipping changelog.Triggering ADAM-prb ? 2.6.0,2.10,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.11,1.5.2,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/1159/

Build result: FAILURE

GitHub pull request #989 of commit f12cbd2 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/989/merge^{commit} # timeout=10 > git branch -a --contains 3ae6a84 # timeout=10 > git rev-parse remotes/origin/pr/989/merge^{commit} # timeout=10Checking out Revision 3ae6a84 (origin/pr/989/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 3ae6a84bf49de57aa768aa7f6fbaeb4fa4808611First time build. Skipping changelog.Triggering ADAM-prb ? 2.6.0,2.10,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.11,1.5.2,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

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Jenkins, test this please.

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fnothaft commented Apr 21, 2016

Jenkins, test this please.

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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/1160/

Build result: ABORTED

GitHub pull request #989 of commit f12cbd2 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/989/merge^{commit} # timeout=10 > git branch -a --contains 3ae6a84 # timeout=10 > git rev-parse remotes/origin/pr/989/merge^{commit} # timeout=10Checking out Revision 3ae6a84 (origin/pr/989/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 3ae6a84bf49de57aa768aa7f6fbaeb4fa4808611First time build. Skipping changelog.Triggering ADAM-prb ? 2.6.0,2.10,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.11,1.5.2,centosAbortedAborted by fnothaftInterrupting #1160Interrupting #1160Notifying 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/1160/

Build result: ABORTED

GitHub pull request #989 of commit f12cbd2 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/989/merge^{commit} # timeout=10 > git branch -a --contains 3ae6a84 # timeout=10 > git rev-parse remotes/origin/pr/989/merge^{commit} # timeout=10Checking out Revision 3ae6a84 (origin/pr/989/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 3ae6a84bf49de57aa768aa7f6fbaeb4fa4808611First time build. Skipping changelog.Triggering ADAM-prb ? 2.6.0,2.10,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.11,1.5.2,centosAbortedAborted by fnothaftInterrupting #1160Interrupting #1160Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

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Jenkins, test this please.

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fnothaft commented Apr 21, 2016

Jenkins, test this please.

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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/1161/

Build result: ABORTED

GitHub pull request #989 of commit f12cbd2 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/989/merge^{commit} # timeout=10 > git branch -a --contains 3ae6a84 # timeout=10 > git rev-parse remotes/origin/pr/989/merge^{commit} # timeout=10Checking out Revision 3ae6a84 (origin/pr/989/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 3ae6a84bf49de57aa768aa7f6fbaeb4fa4808611First time build. Skipping changelog.Triggering ADAM-prb ? 2.6.0,2.10,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.11,1.5.2,centosAbortedAborted by fnothaftInterrupting #1161Interrupting #1161Notifying 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/1161/

Build result: ABORTED

GitHub pull request #989 of commit f12cbd2 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/989/merge^{commit} # timeout=10 > git branch -a --contains 3ae6a84 # timeout=10 > git rev-parse remotes/origin/pr/989/merge^{commit} # timeout=10Checking out Revision 3ae6a84 (origin/pr/989/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 3ae6a84bf49de57aa768aa7f6fbaeb4fa4808611First time build. Skipping changelog.Triggering ADAM-prb ? 2.6.0,2.10,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.11,1.5.2,centosAbortedAborted by fnothaftInterrupting #1161Interrupting #1161Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

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Jenkins, test this please.

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fnothaft commented Apr 21, 2016

Jenkins, test this please.

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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/1162/

Build result: FAILURE

GitHub pull request #989 of commit f12cbd2 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/989/merge^{commit} # timeout=10 > git branch -a --contains 3ae6a84 # timeout=10 > git rev-parse remotes/origin/pr/989/merge^{commit} # timeout=10Checking out Revision 3ae6a84 (origin/pr/989/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 3ae6a84bf49de57aa768aa7f6fbaeb4fa4808611First time build. Skipping changelog.Triggering ADAM-prb ? 2.6.0,2.10,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.11,1.5.2,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/1162/

Build result: FAILURE

GitHub pull request #989 of commit f12cbd2 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/989/merge^{commit} # timeout=10 > git branch -a --contains 3ae6a84 # timeout=10 > git rev-parse remotes/origin/pr/989/merge^{commit} # timeout=10Checking out Revision 3ae6a84 (origin/pr/989/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 3ae6a84bf49de57aa768aa7f6fbaeb4fa4808611First time build. Skipping changelog.Triggering ADAM-prb ? 2.6.0,2.10,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.11,1.5.2,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

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Jenkins, test this please.

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fnothaft commented Apr 21, 2016

Jenkins, test this please.

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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/1163/

Build result: ABORTED

GitHub pull request #989 of commit f12cbd2 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/989/merge^{commit} # timeout=10 > git branch -a --contains 3ae6a84 # timeout=10 > git rev-parse remotes/origin/pr/989/merge^{commit} # timeout=10Checking out Revision 3ae6a84 (origin/pr/989/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 3ae6a84bf49de57aa768aa7f6fbaeb4fa4808611First time build. Skipping changelog.Triggering ADAM-prb ? 2.6.0,2.10,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.11,1.5.2,centosAbortedAborted by fnothaftInterrupting #1163Interrupting #1163Notifying 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/1163/

Build result: ABORTED

GitHub pull request #989 of commit f12cbd2 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/989/merge^{commit} # timeout=10 > git branch -a --contains 3ae6a84 # timeout=10 > git rev-parse remotes/origin/pr/989/merge^{commit} # timeout=10Checking out Revision 3ae6a84 (origin/pr/989/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 3ae6a84bf49de57aa768aa7f6fbaeb4fa4808611First time build. Skipping changelog.Triggering ADAM-prb ? 2.6.0,2.10,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.11,1.5.2,centosAbortedAborted by fnothaftInterrupting #1163Interrupting #1163Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

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Jenkins, test this please.

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fnothaft commented Apr 21, 2016

Jenkins, test this please.

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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/1164/

Build result: FAILURE

GitHub pull request #989 of commit f12cbd2 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/989/merge^{commit} # timeout=10 > git branch -a --contains 3ae6a84 # timeout=10 > git rev-parse remotes/origin/pr/989/merge^{commit} # timeout=10Checking out Revision 3ae6a84 (origin/pr/989/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 3ae6a84bf49de57aa768aa7f6fbaeb4fa4808611First time build. Skipping changelog.Triggering ADAM-prb ? 2.6.0,2.10,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.11,1.5.2,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/1164/

Build result: FAILURE

GitHub pull request #989 of commit f12cbd2 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/989/merge^{commit} # timeout=10 > git branch -a --contains 3ae6a84 # timeout=10 > git rev-parse remotes/origin/pr/989/merge^{commit} # timeout=10Checking out Revision 3ae6a84 (origin/pr/989/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 3ae6a84bf49de57aa768aa7f6fbaeb4fa4808611First time build. Skipping changelog.Triggering ADAM-prb ? 2.6.0,2.10,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.11,1.5.2,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

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Jenkins, test this please.

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fnothaft commented Apr 21, 2016

Jenkins, test this please.

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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/1165/

Build result: FAILURE

GitHub pull request #989 of commit f12cbd2 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/989/merge^{commit} # timeout=10 > git branch -a --contains 3ae6a84 # timeout=10 > git rev-parse remotes/origin/pr/989/merge^{commit} # timeout=10Checking out Revision 3ae6a84 (origin/pr/989/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 3ae6a84bf49de57aa768aa7f6fbaeb4fa4808611First time build. Skipping changelog.Triggering ADAM-prb ? 2.6.0,2.10,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.11,1.5.2,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/1165/

Build result: FAILURE

GitHub pull request #989 of commit f12cbd2 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/989/merge^{commit} # timeout=10 > git branch -a --contains 3ae6a84 # timeout=10 > git rev-parse remotes/origin/pr/989/merge^{commit} # timeout=10Checking out Revision 3ae6a84 (origin/pr/989/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 3ae6a84bf49de57aa768aa7f6fbaeb4fa4808611First time build. Skipping changelog.Triggering ADAM-prb ? 2.6.0,2.10,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.11,1.5.2,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

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Jenkins, test this please.

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fnothaft commented Apr 21, 2016

Jenkins, test this please.

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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/1166/

Build result: FAILURE

GitHub pull request #989 of commit f12cbd2 automatically merged.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.[EnvInject] - Preparing an environment for the build.[EnvInject] - Keeping Jenkins build variables.[EnvInject] - Injecting contributions.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/989/merge^{commit} # timeout=10 > git branch -a --contains 3ae6a84 # timeout=10 > git rev-parse remotes/origin/pr/989/merge^{commit} # timeout=10Checking out Revision 3ae6a84 (origin/pr/989/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 3ae6a84bf49de57aa768aa7f6fbaeb4fa4808611First time build. Skipping changelog.Triggering ADAM-prb ? 2.6.0,2.10,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.11,1.5.2,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/1166/

Build result: FAILURE

GitHub pull request #989 of commit f12cbd2 automatically merged.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.[EnvInject] - Preparing an environment for the build.[EnvInject] - Keeping Jenkins build variables.[EnvInject] - Injecting contributions.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/989/merge^{commit} # timeout=10 > git branch -a --contains 3ae6a84 # timeout=10 > git rev-parse remotes/origin/pr/989/merge^{commit} # timeout=10Checking out Revision 3ae6a84 (origin/pr/989/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 3ae6a84bf49de57aa768aa7f6fbaeb4fa4808611First time build. Skipping changelog.Triggering ADAM-prb ? 2.6.0,2.10,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.11,1.5.2,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

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Well, this is strange.

...
[EnvInject] - Injecting as environment variables the properties content 
JAVA_HOME=/usr/java/jdk1.8.0_60
PATH=/usr/java/jdk1.8.0_60/bin/:/home/anaconda/bin:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.1.1/bin/:/home/android-sdk/:/usr/local/bin:/bin:/usr/bin

[EnvInject] - Variables injected successfully.
[centos] $ /bin/bash /tmp/hudson1618264243236400584.sh
/usr/java/jdk1.8.0_60
/home/jenkins/tools/hudson.model.JDK/JDK_7u60/bin:/usr/java/jdk1.8.0_60/bin/:/home/anaconda/bin:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.1.1/bin/:/home/android-sdk/:/usr/local/bin:/bin:/usr/bin
java version "1.7.0_60"
Java(TM) SE Runtime Environment (build 1.7.0_60-b19)
Java HotSpot(TM) 64-Bit Server VM (build 24.60-b09, mixed mode)
/home/jenkins/tools/hudson.model.JDK/JDK_7u60/bin/java
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heuermh commented Apr 21, 2016

Well, this is strange.

...
[EnvInject] - Injecting as environment variables the properties content 
JAVA_HOME=/usr/java/jdk1.8.0_60
PATH=/usr/java/jdk1.8.0_60/bin/:/home/anaconda/bin:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.1.1/bin/:/home/android-sdk/:/usr/local/bin:/bin:/usr/bin

[EnvInject] - Variables injected successfully.
[centos] $ /bin/bash /tmp/hudson1618264243236400584.sh
/usr/java/jdk1.8.0_60
/home/jenkins/tools/hudson.model.JDK/JDK_7u60/bin:/usr/java/jdk1.8.0_60/bin/:/home/anaconda/bin:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.1.1/bin/:/home/android-sdk/:/usr/local/bin:/bin:/usr/bin
java version "1.7.0_60"
Java(TM) SE Runtime Environment (build 1.7.0_60-b19)
Java HotSpot(TM) 64-Bit Server VM (build 24.60-b09, mixed mode)
/home/jenkins/tools/hudson.model.JDK/JDK_7u60/bin/java
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That's me going through and testing. The TL;DR from my tests is that Jenkins prepends $JAVA_HOME to $PATH when running Maven, which is all sorts of a hassle.

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fnothaft commented Apr 21, 2016

That's me going through and testing. The TL;DR from my tests is that Jenkins prepends $JAVA_HOME to $PATH when running Maven, which is all sorts of a hassle.

@heuermh heuermh added the needs work label Apr 21, 2016

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Jenkins, test this please.

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fnothaft commented Apr 21, 2016

Jenkins, test this please.

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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/1167/

Build result: FAILURE

GitHub pull request #989 of commit f12cbd2 automatically merged.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.[EnvInject] - Preparing an environment for the build.[EnvInject] - Injecting contributions.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/989/merge^{commit} # timeout=10 > git branch -a --contains 6c91112 # timeout=10 > git rev-parse remotes/origin/pr/989/merge^{commit} # timeout=10Checking out Revision 6c91112 (origin/pr/989/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 6c911123ec6683d5b444683d290ff23db8eb466fFirst time build. Skipping changelog.Triggering ADAM-prb ? 2.6.0,2.10,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.11,1.5.2,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/1167/

Build result: FAILURE

GitHub pull request #989 of commit f12cbd2 automatically merged.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.[EnvInject] - Preparing an environment for the build.[EnvInject] - Injecting contributions.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/989/merge^{commit} # timeout=10 > git branch -a --contains 6c91112 # timeout=10 > git rev-parse remotes/origin/pr/989/merge^{commit} # timeout=10Checking out Revision 6c91112 (origin/pr/989/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 6c911123ec6683d5b444683d290ff23db8eb466fFirst time build. Skipping changelog.Triggering ADAM-prb ? 2.6.0,2.10,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.11,1.5.2,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

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Jenkins, test this please.

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fnothaft commented Apr 21, 2016

Jenkins, test this please.

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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/1168/

Build result: FAILURE

GitHub pull request #989 of commit f12cbd2 automatically merged.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.[EnvInject] - Preparing an environment for the build.[EnvInject] - Injecting contributions.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/989/merge^{commit} # timeout=10 > git branch -a --contains 6c91112 # timeout=10 > git rev-parse remotes/origin/pr/989/merge^{commit} # timeout=10Checking out Revision 6c91112 (origin/pr/989/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 6c911123ec6683d5b444683d290ff23db8eb466fFirst time build. Skipping changelog.Triggering ADAM-prb ? 2.6.0,2.10,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.11,1.5.2,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/1168/

Build result: FAILURE

GitHub pull request #989 of commit f12cbd2 automatically merged.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.[EnvInject] - Preparing an environment for the build.[EnvInject] - Injecting contributions.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/989/merge^{commit} # timeout=10 > git branch -a --contains 6c91112 # timeout=10 > git rev-parse remotes/origin/pr/989/merge^{commit} # timeout=10Checking out Revision 6c91112 (origin/pr/989/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 6c911123ec6683d5b444683d290ff23db8eb466fFirst time build. Skipping changelog.Triggering ADAM-prb ? 2.6.0,2.10,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.11,1.5.2,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

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Jenkins, test this please.

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fnothaft commented Apr 21, 2016

Jenkins, test this please.

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Test FAILed.
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https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1169/

Build result: FAILURE

GitHub pull request #989 of commit f12cbd2 automatically merged.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.[EnvInject] - Preparing an environment for the build.[EnvInject] - Injecting contributions.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/989/merge^{commit} # timeout=10 > git branch -a --contains 6c91112 # timeout=10 > git rev-parse remotes/origin/pr/989/merge^{commit} # timeout=10Checking out Revision 6c91112 (origin/pr/989/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 6c911123ec6683d5b444683d290ff23db8eb466fFirst time build. Skipping changelog.Triggering ADAM-prb ? 2.6.0,2.10,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.11,1.5.2,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/1169/

Build result: FAILURE

GitHub pull request #989 of commit f12cbd2 automatically merged.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.[EnvInject] - Preparing an environment for the build.[EnvInject] - Injecting contributions.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/989/merge^{commit} # timeout=10 > git branch -a --contains 6c91112 # timeout=10 > git rev-parse remotes/origin/pr/989/merge^{commit} # timeout=10Checking out Revision 6c91112 (origin/pr/989/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 6c911123ec6683d5b444683d290ff23db8eb466fFirst time build. Skipping changelog.Triggering ADAM-prb ? 2.6.0,2.10,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.11,1.5.2,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

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Jenkins, test this please.

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fnothaft commented Apr 21, 2016

Jenkins, test this please.

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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/1170/

Build result: FAILURE

[...truncated 6 lines...][EnvInject] - Injecting as environment variables the properties content JAVA_HOME=/usr/java/jdk1.8.0_60PATH=/usr/java/jdk1.8.0_60/bin/:/home/anaconda/bin:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.1.1/bin/:/home/android-sdk/:/home/anaconda/bin:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.1.1/bin/:/home/android-sdk/:/usr/local/bin:/bin:/usr/bin[EnvInject] - Variables injected successfully.[EnvInject] - Injecting contributions.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/989/merge^{commit} # timeout=10 > git branch -a --contains 6c91112 # timeout=10 > git rev-parse remotes/origin/pr/989/merge^{commit} # timeout=10Checking out Revision 6c91112 (origin/pr/989/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 6c911123ec6683d5b444683d290ff23db8eb466fFirst time build. Skipping changelog.Triggering ADAM-prb ? 2.6.0,2.10,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.11,1.5.2,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

Test FAILed.
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Build result: FAILURE

[...truncated 6 lines...][EnvInject] - Injecting as environment variables the properties content JAVA_HOME=/usr/java/jdk1.8.0_60PATH=/usr/java/jdk1.8.0_60/bin/:/home/anaconda/bin:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.1.1/bin/:/home/android-sdk/:/home/anaconda/bin:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.1.1/bin/:/home/android-sdk/:/usr/local/bin:/bin:/usr/bin[EnvInject] - Variables injected successfully.[EnvInject] - Injecting contributions.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/989/merge^{commit} # timeout=10 > git branch -a --contains 6c91112 # timeout=10 > git rev-parse remotes/origin/pr/989/merge^{commit} # timeout=10Checking out Revision 6c91112 (origin/pr/989/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 6c911123ec6683d5b444683d290ff23db8eb466fFirst time build. Skipping changelog.Triggering ADAM-prb ? 2.6.0,2.10,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.11,1.5.2,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

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Jenkins, test this please.

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fnothaft commented Apr 21, 2016

Jenkins, test this please.

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Build result: FAILURE

[...truncated 6 lines...][EnvInject] - Injecting as environment variables the properties content JAVA_HOME=/usr/java/jdk1.8.0_60PATH=/usr/java/jdk1.8.0_60/bin/:/home/anaconda/bin:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.1.1/bin/:/home/android-sdk/:/home/anaconda/bin:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.1.1/bin/:/home/android-sdk/:/usr/local/bin:/bin:/usr/bin[EnvInject] - Variables injected successfully.[EnvInject] - Injecting contributions.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/989/merge^{commit} # timeout=10 > git branch -a --contains 6c91112 # timeout=10 > git rev-parse remotes/origin/pr/989/merge^{commit} # timeout=10Checking out Revision 6c91112 (origin/pr/989/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 6c911123ec6683d5b444683d290ff23db8eb466fFirst time build. Skipping changelog.Triggering ADAM-prb ? 2.6.0,2.10,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.11,1.5.2,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):
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Build result: FAILURE

[...truncated 6 lines...][EnvInject] - Injecting as environment variables the properties content JAVA_HOME=/usr/java/jdk1.8.0_60PATH=/usr/java/jdk1.8.0_60/bin/:/home/anaconda/bin:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.1.1/bin/:/home/android-sdk/:/home/anaconda/bin:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.1.1/bin/:/home/android-sdk/:/usr/local/bin:/bin:/usr/bin[EnvInject] - Variables injected successfully.[EnvInject] - Injecting contributions.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/989/merge^{commit} # timeout=10 > git branch -a --contains 6c91112 # timeout=10 > git rev-parse remotes/origin/pr/989/merge^{commit} # timeout=10Checking out Revision 6c91112 (origin/pr/989/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 6c911123ec6683d5b444683d290ff23db8eb466fFirst time build. Skipping changelog.Triggering ADAM-prb ? 2.6.0,2.10,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.11,1.5.2,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

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Jenkins, test this please.

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fnothaft commented Apr 21, 2016

Jenkins, test this please.

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Test PASSed.
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Woot!

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heuermh commented Apr 21, 2016

Woot!

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Great! H/T to @shaneknapp for help getting Java 8 working. I will have a follow up PR (see #1008) that pulls the workarounds into our repo.

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fnothaft commented Apr 21, 2016

Great! H/T to @shaneknapp for help getting Java 8 working. I will have a follow up PR (see #1008) that pulls the workarounds into our repo.

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The question then is whether to merge this with a snapshot dependency on Hadoop-BAM or wait until the next release is available. Reports on gitter are that this branch may not help the gzipped/bgzipped VCF problem (yet).

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heuermh commented Apr 21, 2016

The question then is whether to merge this with a snapshot dependency on Hadoop-BAM or wait until the next release is available. Reports on gitter are that this branch may not help the gzipped/bgzipped VCF problem (yet).

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@heuermh discussed the snapshot dependency and will reach out to @tomwhite & @AndreSchumacher to see when a new Hadoop-BAM release will be cut.

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fnothaft commented Apr 21, 2016

@heuermh discussed the snapshot dependency and will reach out to @tomwhite & @AndreSchumacher to see when a new Hadoop-BAM release will be cut.

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@heuermh heuermh changed the title from Update hadoop-bam dependency version to 7.4.1-SNAPSHOT to Update hadoop-bam dependency version to 7.5.0-SNAPSHOT Apr 27, 2016

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The BCF-related unit tests will fail due to samtools/htsjdk#507.

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heuermh commented Apr 27, 2016

The BCF-related unit tests will fail due to samtools/htsjdk#507.

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Build result: FAILURE

GitHub pull request #989 of commit 760270c 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/989/merge^{commit} # timeout=10 > git branch -a --contains 8f02a89 # timeout=10 > git rev-parse remotes/origin/pr/989/merge^{commit} # timeout=10Checking out Revision 8f02a89 (origin/pr/989/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 8f02a89031e3dc8697a45610462a7d7f83dffbc3First time build. Skipping changelog.Triggering ADAM-prb ? 2.6.0,2.10,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.11,1.5.2,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

Test FAILed.
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Build result: FAILURE

GitHub pull request #989 of commit 760270c 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/989/merge^{commit} # timeout=10 > git branch -a --contains 8f02a89 # timeout=10 > git rev-parse remotes/origin/pr/989/merge^{commit} # timeout=10Checking out Revision 8f02a89 (origin/pr/989/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 8f02a89031e3dc8697a45610462a7d7f83dffbc3First time build. Skipping changelog.Triggering ADAM-prb ? 2.6.0,2.10,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.11,1.5.2,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

@heuermh heuermh referenced this pull request in HadoopGenomics/Hadoop-BAM Apr 28, 2016

Merged

Improve block/gzip compressed VCF format detection #90

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Build result: FAILURE

GitHub pull request #989 of commit 065f6d7 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/989/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains 99b4657 # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/989/merge^{commit} # timeout=10Checking out Revision 99b4657 (origin/pr/989/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 99b465746e97cfc1779d58c9adba0f48623cf017First time build. Skipping changelog.Triggering ADAM-prb ? 2.6.0,2.10,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.11,1.5.2,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

Test FAILed.
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Build result: FAILURE

GitHub pull request #989 of commit 065f6d7 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/989/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains 99b4657 # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/989/merge^{commit} # timeout=10Checking out Revision 99b4657 (origin/pr/989/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 99b465746e97cfc1779d58c9adba0f48623cf017First time build. Skipping changelog.Triggering ADAM-prb ? 2.6.0,2.10,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.11,1.5.2,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

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Build result: FAILURE

GitHub pull request #989 of commit ec9aca4 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/989/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains e99f621 # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/989/merge^{commit} # timeout=10Checking out Revision e99f621 (origin/pr/989/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f e99f6215c863734d993e1c869b27f793cd9ff217First time build. Skipping changelog.Triggering ADAM-prb ? 2.6.0,2.10,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.11,1.5.2,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

Test FAILed.
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Build result: FAILURE

GitHub pull request #989 of commit ec9aca4 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/989/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains e99f621 # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/989/merge^{commit} # timeout=10Checking out Revision e99f621 (origin/pr/989/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f e99f6215c863734d993e1c869b27f793cd9ff217First time build. Skipping changelog.Triggering ADAM-prb ? 2.6.0,2.10,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.11,1.5.2,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

@heuermh heuermh changed the title from Update hadoop-bam dependency version to 7.5.0-SNAPSHOT to Update hadoop-bam dependency version to 7.5.0 May 18, 2016

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@heuermh heuermh added ready to merge and removed needs work labels May 18, 2016

@fnothaft fnothaft merged commit e8fc206 into bigdatagenomics:master May 18, 2016

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Merged. Thanks @heuermh!

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fnothaft commented May 18, 2016

Merged. Thanks @heuermh!

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Thank you, sir

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heuermh commented May 18, 2016

Thank you, sir

@heuermh heuermh deleted the heuermh:hadoop-bam-741-snapshot branch May 18, 2016

@heuermh heuermh referenced this pull request Jun 7, 2016

Closed

Release ADAM version 0.20.0 #1048

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