Update hadoop-bam dependency version to 7.5.0 #989

heuermh · 2016-04-04T23:40:18Z

Will update to version 7.5.0 as appropriate on its release.

AmplabJenkins · 2016-04-04T23:44:29Z

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.

heuermh · 2016-04-04T23:52:27Z

[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.

AmplabJenkins · 2016-04-06T21:47:02Z

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.

fnothaft · 2016-04-20T22:33:00Z

Jenkins, test this please.

AmplabJenkins · 2016-04-20T22:34:53Z

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.

fnothaft · 2016-04-21T00:50:48Z

Jenkins, test this please.

AmplabJenkins · 2016-04-21T00:53:59Z

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.

fnothaft · 2016-04-21T00:54:27Z

Jenkins, test this please.

AmplabJenkins · 2016-04-21T00:59:04Z

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.

fnothaft · 2016-04-21T01:01:49Z

Jenkins, test this please.

AmplabJenkins · 2016-04-21T01:03:51Z

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.

fnothaft · 2016-04-21T01:05:33Z

Jenkins, test this please.

AmplabJenkins · 2016-04-21T01:09:06Z

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.

fnothaft · 2016-04-21T01:09:32Z

Jenkins, test this please.

AmplabJenkins · 2016-04-21T01:15:15Z

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.

fnothaft · 2016-04-21T01:21:59Z

Jenkins, test this please.

AmplabJenkins · 2016-04-21T01:24:19Z

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.

fnothaft · 2016-04-21T01:57:48Z

Jenkins, test this please.

AmplabJenkins · 2016-04-21T01:59:16Z

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.

heuermh · 2016-04-21T02:45:48Z

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

fnothaft · 2016-04-21T03:03:56Z

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.

fnothaft · 2016-04-21T16:38:22Z

Jenkins, test this please.

AmplabJenkins · 2016-04-21T16:44:52Z

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.

fnothaft · 2016-04-21T17:02:01Z

Jenkins, test this please.

AmplabJenkins · 2016-04-21T17:04:42Z

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.

fnothaft · 2016-04-21T17:07:17Z

Jenkins, test this please.

AmplabJenkins · 2016-04-21T17:09:52Z

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.

fnothaft · 2016-04-21T18:01:10Z

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.

heuermh · 2016-04-21T18:01:40Z

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).

fnothaft · 2016-04-21T20:17:45Z

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

AmplabJenkins · 2016-04-22T20:31:11Z

Test PASSed.
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Test PASSed.

AmplabJenkins · 2016-04-22T20:56:27Z

Test PASSed.
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Test PASSed.

heuermh · 2016-04-27T16:26:15Z

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

AmplabJenkins · 2016-04-27T16:31:02Z

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.

AmplabJenkins · 2016-05-02T19:01:06Z

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.

AmplabJenkins · 2016-05-12T22:10:45Z

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.

…nimum JDK to JDK8

AmplabJenkins · 2016-05-18T15:24:52Z

Test PASSed.
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Test PASSed.

fnothaft · 2016-05-18T15:41:04Z

Merged. Thanks @heuermh!

heuermh · 2016-05-18T15:42:27Z

Thank you, sir

heuermh force-pushed the hadoop-bam-741-snapshot branch from ce04cb8 to f12cbd2 Compare April 6, 2016 21:36

heuermh mentioned this pull request Apr 7, 2016

error: no reads in first split: bad BAM file or tiny split size? #896

Closed

heuermh added the needs work label Apr 21, 2016

fnothaft mentioned this pull request Apr 21, 2016

Roll Jenkins JDK 8 changes into ./scripts/jenkins-test #1008

Closed

heuermh force-pushed the hadoop-bam-741-snapshot branch from f12cbd2 to bc6f3db Compare April 22, 2016 20:17

heuermh force-pushed the hadoop-bam-741-snapshot branch from bc6f3db to 0c59a41 Compare April 22, 2016 20:41

heuermh force-pushed the hadoop-bam-741-snapshot branch from 0c59a41 to 760270c Compare April 27, 2016 16:24

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

heuermh mentioned this pull request Apr 28, 2016

Improve block/gzip compressed VCF format detection HadoopGenomics/Hadoop-BAM#90

Merged

heuermh force-pushed the hadoop-bam-741-snapshot branch from 760270c to 065f6d7 Compare May 2, 2016 18:56

heuermh force-pushed the hadoop-bam-741-snapshot branch from 065f6d7 to ec9aca4 Compare May 12, 2016 22:06

Update hadoop-bam dependency version to 7.5.0, htsjdk to 2.3.0 and mi…

e8fc206

…nimum JDK to JDK8

heuermh force-pushed the hadoop-bam-741-snapshot branch from ec9aca4 to e8fc206 Compare May 18, 2016 15:11

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

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

heuermh mentioned this pull request May 18, 2016

[ADAM-1008] Modify jenkins-test script to support Java 8 build. #1026

Merged

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

heuermh deleted the hadoop-bam-741-snapshot branch May 18, 2016 15:42

fnothaft mentioned this pull request May 18, 2016

Remove code workarounds necessary for Spark 1.2.1/Hadoop 1.0.x support #959

Closed

heuermh mentioned this pull request Jun 7, 2016

Release ADAM version 0.20.0 #1048

Closed

61 tasks

Update hadoop-bam dependency version to 7.5.0 #989

Update hadoop-bam dependency version to 7.5.0 #989

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heuermh commented Apr 4, 2016 • edited Loading

AmplabJenkins commented Apr 4, 2016

Build result: FAILURE

heuermh commented Apr 4, 2016

AmplabJenkins commented Apr 6, 2016

Build result: FAILURE

fnothaft commented Apr 20, 2016

AmplabJenkins commented Apr 20, 2016

Build result: FAILURE

fnothaft commented Apr 21, 2016

AmplabJenkins commented Apr 21, 2016

Build result: ABORTED

fnothaft commented Apr 21, 2016

AmplabJenkins commented Apr 21, 2016

Build result: ABORTED

fnothaft commented Apr 21, 2016

AmplabJenkins commented Apr 21, 2016

Build result: FAILURE

fnothaft commented Apr 21, 2016

AmplabJenkins commented Apr 21, 2016

Build result: ABORTED

fnothaft commented Apr 21, 2016

AmplabJenkins commented Apr 21, 2016

Build result: FAILURE

fnothaft commented Apr 21, 2016

AmplabJenkins commented Apr 21, 2016

Build result: FAILURE

fnothaft commented Apr 21, 2016

AmplabJenkins commented Apr 21, 2016

Build result: FAILURE

heuermh commented Apr 21, 2016

fnothaft commented Apr 21, 2016

fnothaft commented Apr 21, 2016

AmplabJenkins commented Apr 21, 2016

Build result: FAILURE

fnothaft commented Apr 21, 2016

AmplabJenkins commented Apr 21, 2016

Build result: FAILURE

fnothaft commented Apr 21, 2016

AmplabJenkins commented Apr 21, 2016

Build result: FAILURE

fnothaft commented Apr 21, 2016

heuermh commented Apr 21, 2016

fnothaft commented Apr 21, 2016

AmplabJenkins commented Apr 22, 2016

AmplabJenkins commented Apr 22, 2016

heuermh commented Apr 27, 2016

AmplabJenkins commented Apr 27, 2016

Build result: FAILURE

AmplabJenkins commented May 2, 2016

Build result: FAILURE

AmplabJenkins commented May 12, 2016

Build result: FAILURE

AmplabJenkins commented May 18, 2016

fnothaft commented May 18, 2016

heuermh commented May 18, 2016

heuermh commented Apr 4, 2016 •

edited

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