Added an optimisation to spare not required shuffle of unpaired reads

[benraha]

trafficstars

This PR adds an option to avoid shuffling the entire alignment dataset when transforming to FragmentDataset.

This adds a boolean parameter to the function toFragments() that, when specified, the FragmentDataset is created with one read per Fragment record.

This resolved issue #2281 .

[benraha]

Jenkins, test this please

[AmplabJenkins]

Test FAILed. Refer to this link for build results (access rights to CI server needed): https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/3131/

Build result: FAILURE

[...truncated 5 lines...]Cloning the remote Git repositoryCloning repository https://github.com/bigdatagenomics/adam.git > git init /home/jenkins/workspace/ADAM-prb # 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/heads/:refs/remotes/origin/ # timeout=15 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10 > git config --add remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=10 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > git rev-parse origin/pr/2282/merge^{commit} # timeout=10 > git branch -a -v --no-abbrev --contains 1654f4582adc31c44bbf7eae908934548ba29afd # timeout=10Checking out Revision 1654f4582adc31c44bbf7eae908934548ba29afd (origin/pr/2282/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 1654f4582adc31c44bbf7eae908934548ba29afdFirst time build. Skipping changelog.Triggering ADAM-prb ? 2.7.5,2.12,3.0.1,ubuntuTriggering ADAM-prb ? 2.7.5,2.11,2.4.7,ubuntuTriggering ADAM-prb ? 2.7.5,2.12,2.4.7,ubuntuADAM-prb ? 2.7.5,2.12,3.0.1,ubuntu completed with result FAILUREADAM-prb ? 2.7.5,2.11,2.4.7,ubuntu completed with result FAILUREADAM-prb ? 2.7.5,2.12,2.4.7,ubuntu completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8' Test FAILed.

[heuermh]

The Jenkins failure logs are a bit much to go through, this is the relevant part

...
[INFO] ------------< org.bdgenomics.adam:adam-python-spark2_2.11 >-------------
[INFO] Building ADAM_2.11: Python APIs 0.33.0-SNAPSHOT                    [8/9]
[INFO] --------------------------------[ jar ]---------------------------------
...
=================================== FAILURES ===================================
____________________ AlignmentDatasetTest.test_to_fragments ____________________

self = <bdgenomics.adam.test.alignmentDataset_test.AlignmentDatasetTest testMethod=test_to_fragments>

    def test_to_fragments(self):
    
        readsPath = self.resourceFile("unsorted.sam")
        ac = ADAMContext(self.ss)
    
        reads = ac.loadAlignments(readsPath)
    
>       fragments = reads.toFragments()

bdgenomics/adam/test/alignmentDataset_test.py:169: 
...
E                   py4j.protocol.Py4JError: An error occurred while calling o1728.toFragments. Trace:
E                   py4j.Py4JException: Method toFragments([]) does not exist
E                   	at py4j.reflection.ReflectionEngine.getMethod(ReflectionEngine.java:318)
E                   	at py4j.reflection.ReflectionEngine.getMethod(ReflectionEngine.java:326)
E                   	at py4j.Gateway.invoke(Gateway.java:274)
E                   	at py4j.commands.AbstractCommand.invokeMethod(AbstractCommand.java:132)
E                   	at py4j.commands.CallCommand.execute(CallCommand.java:79)
E                   	at py4j.GatewayConnection.run(GatewayConnection.java:238)
E                   	at java.lang.Thread.run(Thread.java:748)

[benraha]

@heuermh Thanks! The tests should pass now, I'm ready to review and merge :)

[AmplabJenkins]

Test FAILed. Refer to this link for build results (access rights to CI server needed): https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/3132/

Build result: FAILURE

[...truncated 5 lines...]Cloning the remote Git repositoryCloning repository https://github.com/bigdatagenomics/adam.git > git init /home/jenkins/workspace/ADAM-prb # 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/heads/:refs/remotes/origin/ # timeout=15 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10 > git config --add remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=10 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > git rev-parse origin/pr/2282/merge^{commit} # timeout=10 > git branch -a -v --no-abbrev --contains f142e4c93b3a8733c1f790ac4c73fb6d138ee442 # timeout=10Checking out Revision f142e4c93b3a8733c1f790ac4c73fb6d138ee442 (origin/pr/2282/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f f142e4c93b3a8733c1f790ac4c73fb6d138ee442First time build. Skipping changelog.Triggering ADAM-prb ? 2.7.5,2.12,3.0.1,ubuntuTriggering ADAM-prb ? 2.7.5,2.11,2.4.7,ubuntuTriggering ADAM-prb ? 2.7.5,2.12,2.4.7,ubuntuADAM-prb ? 2.7.5,2.12,3.0.1,ubuntu completed with result FAILUREADAM-prb ? 2.7.5,2.11,2.4.7,ubuntu completed with result FAILUREADAM-prb ? 2.7.5,2.12,2.4.7,ubuntu completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8' Test FAILed.

[benraha]

Jenkins, test this please

[AmplabJenkins]

Test FAILed. Refer to this link for build results (access rights to CI server needed): https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/3133/

Build result: FAILURE

[...truncated 5 lines...]Cloning the remote Git repositoryCloning repository https://github.com/bigdatagenomics/adam.git > git init /home/jenkins/workspace/ADAM-prb # 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/heads/:refs/remotes/origin/ # timeout=15 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10 > git config --add remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=10 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > git rev-parse origin/pr/2282/merge^{commit} # timeout=10 > git branch -a -v --no-abbrev --contains f142e4c93b3a8733c1f790ac4c73fb6d138ee442 # timeout=10Checking out Revision f142e4c93b3a8733c1f790ac4c73fb6d138ee442 (origin/pr/2282/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f f142e4c93b3a8733c1f790ac4c73fb6d138ee442First time build. Skipping changelog.Triggering ADAM-prb ? 2.7.5,2.12,3.0.1,ubuntuTriggering ADAM-prb ? 2.7.5,2.11,2.4.7,ubuntuTriggering ADAM-prb ? 2.7.5,2.12,2.4.7,ubuntuADAM-prb ? 2.7.5,2.12,3.0.1,ubuntu completed with result FAILUREADAM-prb ? 2.7.5,2.11,2.4.7,ubuntu completed with result FAILUREADAM-prb ? 2.7.5,2.12,2.4.7,ubuntu completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8' Test FAILed.

[benraha]

Jenkins, test this please

[AmplabJenkins]

Test FAILed. Refer to this link for build results (access rights to CI server needed): https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/3134/

Build result: FAILURE

[...truncated 5 lines...]Cloning the remote Git repositoryCloning repository https://github.com/bigdatagenomics/adam.git > git init /home/jenkins/workspace/ADAM-prb # 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/heads/:refs/remotes/origin/ # timeout=15 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10 > git config --add remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=10 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > git rev-parse origin/pr/2282/merge^{commit} # timeout=10 > git branch -a -v --no-abbrev --contains f142e4c93b3a8733c1f790ac4c73fb6d138ee442 # timeout=10Checking out Revision f142e4c93b3a8733c1f790ac4c73fb6d138ee442 (origin/pr/2282/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f f142e4c93b3a8733c1f790ac4c73fb6d138ee442First time build. Skipping changelog.Triggering ADAM-prb ? 2.7.5,2.12,3.0.1,ubuntuTriggering ADAM-prb ? 2.7.5,2.11,2.4.7,ubuntuTriggering ADAM-prb ? 2.7.5,2.12,2.4.7,ubuntuADAM-prb ? 2.7.5,2.12,3.0.1,ubuntu completed with result FAILUREADAM-prb ? 2.7.5,2.11,2.4.7,ubuntu completed with result FAILUREADAM-prb ? 2.7.5,2.12,2.4.7,ubuntu completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8' Test FAILed.

[AmplabJenkins]

Test FAILed. Refer to this link for build results (access rights to CI server needed): https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/3135/

Build result: FAILURE

[...truncated 5 lines...]Cloning the remote Git repositoryCloning repository https://github.com/bigdatagenomics/adam.git > git init /home/jenkins/workspace/ADAM-prb # 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/heads/:refs/remotes/origin/ # timeout=15 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10 > git config --add remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=10 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > git rev-parse origin/pr/2282/merge^{commit} # timeout=10 > git branch -a -v --no-abbrev --contains bb2f0780be008639963f08cff4fdddfaab8a37c4 # timeout=10Checking out Revision bb2f0780be008639963f08cff4fdddfaab8a37c4 (origin/pr/2282/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f bb2f0780be008639963f08cff4fdddfaab8a37c4First time build. Skipping changelog.Triggering ADAM-prb ? 2.7.5,2.12,3.0.1,ubuntuTriggering ADAM-prb ? 2.7.5,2.11,2.4.7,ubuntuTriggering ADAM-prb ? 2.7.5,2.12,2.4.7,ubuntuADAM-prb ? 2.7.5,2.12,3.0.1,ubuntu completed with result SUCCESSADAM-prb ? 2.7.5,2.11,2.4.7,ubuntu completed with result SUCCESSADAM-prb ? 2.7.5,2.12,2.4.7,ubuntu completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8' Test FAILed.

[benraha]

There seems to be some kind of issue unpacking the hadoop tar gz

https://amplab.cs.berkeley.edu/jenkins/job/ADAM-prb/3135/HADOOP_VERSION=2.7.5,SCALA_VERSION=2.12,SPARK_VERSION=2.4.7,label=ubuntu/console

[heuermh]

Sorry for all the trouble with Jenkins, I have seen something similar recently on another project

https://amplab.cs.berkeley.edu/jenkins/job/mango-prb/1002/HADOOP_VERSION=2.7.5,SCALAVER=2.12,SPARK_VERSION=2.4.7,label=amp-jenkins-staging-worker-02/console

That Apache mirror download link 404s, not sure what the actual issue is. Also odd that 2.7.7 doesn't match $HADOOP_VERSION . . . that will cause trouble when we add Hadoop 3.x to the build matrix (#2267).

[heuermh]

And a note from our admin staff:

i'm going to be upgrading jenkins to something more reasonable, and there will definitely be some downtime as i get things sorted.

we should be back up and building by monday.

[benraha]

Jenkins, test this please

[AmplabJenkins]

Refer to this link for build results (access rights to CI server needed): https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/3136/

Build result: FAILURE

[...truncated 717 B...][WARNING] Reference path does not exist: /home/jenkins/gitcaches/adam.referenceFetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=30 > git --version # 'git version 1.7.1' > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/heads/:refs/remotes/origin/ # timeout=15 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=30 > git config --add remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=30 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=30Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > git rev-parse e6332ef5bac0dc6ce37cb840631c62f3e67a8351^{commit} # timeout=30Checking out Revision e6332ef5bac0dc6ce37cb840631c62f3e67a8351 (detached) > git config core.sparsecheckout # timeout=30 > git checkout -f e6332ef5bac0dc6ce37cb840631c62f3e67a8351 # timeout=30Commit message: "code format fix"First time build. Skipping changelog.Triggering ADAM-prb » 2.7.5,2.12,2.4.7,ubuntuTriggering ADAM-prb » 2.7.5,2.11,2.4.7,ubuntuTriggering ADAM-prb » 2.7.5,2.12,3.0.1,ubuntuADAM-prb » 2.7.5,2.12,2.4.7,ubuntu completed with result FAILUREADAM-prb » 2.7.5,2.11,2.4.7,ubuntu completed with result SUCCESSADAM-prb » 2.7.5,2.12,3.0.1,ubuntu completed with result FAILURENotifying endpoint with url 'https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'Setting status of e6332ef5bac0dc6ce37cb840631c62f3e67a8351 to FAILURE with url https://amplab.cs.berkeley.edu/jenkins/job/ADAM-prb/3136/ and message: 'Build finished. '

[heuermh]

re: Jenkins, might want to follow these threads

http://apache-spark-developers-list.1001551.n3.nabble.com/jenkins-downtime-tomorrow-evening-weekend-td30405.html

http://apache-spark-developers-list.1001551.n3.nabble.com/build-system-IMPORTANT-UPDATE-td30430.html

[benraha]

Jenkins, test this please

[AmplabJenkins]

Refer to this link for build results (access rights to CI server needed): https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/3137/

Build result: FAILURE

[...truncated 717 B...][WARNING] Reference path does not exist: /home/jenkins/gitcaches/adam.referenceFetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=30 > git --version # 'git version 2.25.1' > git fetch --tags --force --progress -- https://github.com/bigdatagenomics/adam.git +refs/heads/:refs/remotes/origin/ # timeout=15 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=30 > git config --add remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=30 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=30Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git fetch --tags --force --progress -- https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > git rev-parse e6332ef5bac0dc6ce37cb840631c62f3e67a8351^{commit} # timeout=30Checking out Revision e6332ef5bac0dc6ce37cb840631c62f3e67a8351 (detached) > git config core.sparsecheckout # timeout=30 > git checkout -f e6332ef5bac0dc6ce37cb840631c62f3e67a8351 # timeout=30Commit message: "code format fix" > git rev-list --no-walk e6332ef5bac0dc6ce37cb840631c62f3e67a8351 # timeout=30Triggering ADAM-prb » 2.7.5,2.12,2.4.7,ubuntuTriggering ADAM-prb » 2.7.5,2.11,2.4.7,ubuntuTriggering ADAM-prb » 2.7.5,2.12,3.0.1,ubuntuADAM-prb » 2.7.5,2.12,2.4.7,ubuntu completed with result FAILUREADAM-prb » 2.7.5,2.11,2.4.7,ubuntu completed with result SUCCESSADAM-prb » 2.7.5,2.12,3.0.1,ubuntu completed with result SUCCESSNotifying endpoint with url 'https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'Setting status of e6332ef5bac0dc6ce37cb840631c62f3e67a8351 to FAILURE with url https://amplab.cs.berkeley.edu/jenkins/job/ADAM-prb/3137/ and message: 'Build finished. '

[heuermh]

Re

The JAVA_HOME environment variable is not defined correctly
This environment variable is needed to run this program
NB: JAVA_HOME should point to a JDK not a JRE
Build step 'Execute shell' marked build as failure

This in Jenkins Build: Execute shell is apparently no longer correct

export JAVA_HOME=/usr/lib/jvm/java-8-oracle
export CONDA_BIN=/home/anaconda/bin/
export PATH=${JAVA_HOME}/bin/:${CONDA_BIN}:${PATH}

[shaneknapp]

test this please

[shaneknapp]

Re

The JAVA_HOME environment variable is not defined correctly
This environment variable is needed to run this program
NB: JAVA_HOME should point to a JDK not a JRE
Build step 'Execute shell' marked build as failure

This in Jenkins Build: Execute shell is apparently no longer correct

export JAVA_HOME=/usr/lib/jvm/java-8-oracle
export CONDA_BIN=/home/anaconda/bin/
export PATH=${JAVA_HOME}/bin/:${CONDA_BIN}:${PATH}

i fixed JAVA_HOME to point to /usr/java/latest (java 8)

[AmplabJenkins]

Refer to this link for build results (access rights to CI server needed): https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/3138/

Build result: FAILURE

[...truncated 713 B...][WARNING] Reference path does not exist: /home/jenkins/gitcaches/adam.referenceFetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=30 > git --version # 'git version 2.25.1' > git fetch --tags --force --progress -- https://github.com/bigdatagenomics/adam.git +refs/heads/:refs/remotes/origin/ # timeout=15 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=30 > git config --add remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=30 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=30Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git fetch --tags --force --progress -- https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > git rev-parse e6332ef5bac0dc6ce37cb840631c62f3e67a8351^{commit} # timeout=30Checking out Revision e6332ef5bac0dc6ce37cb840631c62f3e67a8351 (detached) > git config core.sparsecheckout # timeout=30 > git checkout -f e6332ef5bac0dc6ce37cb840631c62f3e67a8351 # timeout=30Commit message: "code format fix" > git rev-list --no-walk e6332ef5bac0dc6ce37cb840631c62f3e67a8351 # timeout=30Triggering ADAM-prb » 2.7.5,2.12,2.4.7,ubuntuTriggering ADAM-prb » 2.7.5,2.11,2.4.7,ubuntuTriggering ADAM-prb » 2.7.5,2.12,3.0.1,ubuntuADAM-prb » 2.7.5,2.12,2.4.7,ubuntu completed with result FAILUREADAM-prb » 2.7.5,2.11,2.4.7,ubuntu completed with result SUCCESSADAM-prb » 2.7.5,2.12,3.0.1,ubuntu completed with result SUCCESSNotifying endpoint with url 'https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'Setting status of e6332ef5bac0dc6ce37cb840631c62f3e67a8351 to FAILURE with url https://amplab.cs.berkeley.edu/jenkins/job/ADAM-prb/3138/ and message: 'Build finished. '

[shaneknapp]

test this please

[shaneknapp]

(i also updated the build config so that the main prb build runs on the workers, and not the primary node)

[AmplabJenkins]

Refer to this link for build results (access rights to CI server needed): https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/3139/

Build result: FAILURE

[...truncated 1.02 KB...]Using reference repository: /home/jenkins/gitcaches/adam.referenceFetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git --version # 'git version 2.25.1' > git fetch --tags --force --progress -- https://github.com/bigdatagenomics/adam.git +refs/heads/:refs/remotes/origin/ # timeout=15 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10 > git config --add remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=10 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git fetch --tags --force --progress -- https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > git rev-parse e6332ef5bac0dc6ce37cb840631c62f3e67a8351^{commit} # timeout=10Checking out Revision e6332ef5bac0dc6ce37cb840631c62f3e67a8351 (detached) > git config core.sparsecheckout # timeout=10 > git checkout -f e6332ef5bac0dc6ce37cb840631c62f3e67a8351 # timeout=10Commit message: "code format fix" > git rev-list --no-walk e6332ef5bac0dc6ce37cb840631c62f3e67a8351 # timeout=10Triggering ADAM-prb » 2.7.5,2.12,2.4.7,ubuntuTriggering ADAM-prb » 2.7.5,2.11,2.4.7,ubuntuTriggering ADAM-prb » 2.7.5,2.12,3.0.1,ubuntuADAM-prb » 2.7.5,2.12,2.4.7,ubuntu completed with result FAILUREADAM-prb » 2.7.5,2.11,2.4.7,ubuntu completed with result SUCCESSADAM-prb » 2.7.5,2.12,3.0.1,ubuntu completed with result SUCCESSNotifying endpoint with url 'https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'Setting status of e6332ef5bac0dc6ce37cb840631c62f3e67a8351 to FAILURE with url https://amplab.cs.berkeley.edu/jenkins/job/ADAM-prb/3139/ and message: 'Build finished. '

[benraha]

Jenkins, test this please

[AmplabJenkins]

Refer to this link for build results (access rights to CI server needed): https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/3157/

Build result: FAILURE

[...truncated 905 B...]Wiping out workspace first.Cloning the remote Git repositoryCloning repository https://github.com/bigdatagenomics/adam.git > git init /home/jenkins/workspace/ADAM-prb # timeout=10Using reference repository: /home/jenkins/gitcaches/adam.referenceFetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git --version # 'git version 2.25.1' > git fetch --tags --force --progress -- https://github.com/bigdatagenomics/adam.git +refs/heads/:refs/remotes/origin/ # timeout=15 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10 > git config --add remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=10 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git fetch --tags --force --progress -- https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > git rev-parse e6332ef5bac0dc6ce37cb840631c62f3e67a8351^{commit} # timeout=10Checking out Revision e6332ef5bac0dc6ce37cb840631c62f3e67a8351 (detached) > git config core.sparsecheckout # timeout=10 > git checkout -f e6332ef5bac0dc6ce37cb840631c62f3e67a8351 # timeout=10Commit message: "code format fix" > git rev-list --no-walk a895649d542ec33052f8626ea0be922d31f5ecb3 # timeout=10Triggering ADAM-prb » 3.2.1,2.12,3.0.2,ubuntuADAM-prb » 3.2.1,2.12,3.0.2,ubuntu completed with result FAILURENotifying endpoint with url 'https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'Setting status of e6332ef5bac0dc6ce37cb840631c62f3e67a8351 to FAILURE with url https://amplab.cs.berkeley.edu/jenkins/job/ADAM-prb/3157/ and message: 'Build finished. '