[ADAM-1006] Split überjar out to adam-assembly submodule. #1072

fnothaft · 2016-07-06T19:06:59Z

Resolves #1006.

heuermh · 2016-07-06T19:11:42Z

adam-assembly/pom.xml

+    </dependency>
+  </dependencies>
+  <profiles>
+    <profile>


this can be removed

AmplabJenkins · 2016-07-06T19:11:51Z

Test FAILed.
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Build result: FAILURE

GitHub pull request #1072 of commit 2b8b12b 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/1072/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains ec68563af086f51e3ee289e9f645153c0b557b30 # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/1072/merge^{commit} # timeout=10Checking out Revision ec68563af086f51e3ee289e9f645153c0b557b30 (origin/pr/1072/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f ec68563af086f51e3ee289e9f645153c0b557b30First 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.

AmplabJenkins · 2016-07-06T19:16:46Z

Test FAILed.
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Build result: FAILURE

GitHub pull request #1072 of commit 96e31c2 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/1072/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains 6ac9206 # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/1072/merge^{commit} # timeout=10Checking out Revision 6ac9206 (origin/pr/1072/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 6ac9206c42d241aeed4cb66c8b64da62fe97633aFirst 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.

AmplabJenkins · 2016-07-06T20:02:29Z

Test FAILed.
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Build result: FAILURE

GitHub pull request #1072 of commit f1f502f.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 f1f502f^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains f1f502f # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/1072/head^{commit} # timeout=10Checking out Revision f1f502f (origin/pr/1072/head) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f f1f502f484c72e89b59e738d216648981954e423First 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.

AmplabJenkins · 2016-07-06T20:12:50Z

Test FAILed.
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Build result: FAILURE

GitHub pull request #1072 of commit 911f1bd 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/1072/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains 4719ef49d194aab7b40067fabbb61f67c5071fb7 # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/1072/merge^{commit} # timeout=10Checking out Revision 4719ef49d194aab7b40067fabbb61f67c5071fb7 (origin/pr/1072/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 4719ef49d194aab7b40067fabbb61f67c5071fb7First 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.

AmplabJenkins · 2016-07-06T20:42:42Z

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 #1072 of commit de1e4ea 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/1072/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains 21c5be163baf13c96f7ee8474d9467adf4f8ef31 # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/1072/merge^{commit} # timeout=10Checking out Revision 21c5be163baf13c96f7ee8474d9467adf4f8ef31 (origin/pr/1072/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 21c5be163baf13c96f7ee8474d9467adf4f8ef31 > /home/jenkins/git2/bin/git rev-list 4719ef49d194aab7b40067fabbb61f67c5071fb7 # timeout=10Triggering 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 · 2016-07-06T21:27:21Z

Jenkins, retest this please.

AmplabJenkins · 2016-07-06T21:43:30Z

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1313/

Build result: FAILURE

[...truncated 24 lines...]Triggering ADAM-prb ? 2.6.0,2.11,1.4.1,centosTriggering ADAM-prb ? 2.6.0,2.10,1.4.1,centosTriggering ADAM-prb ? 2.3.0,2.11,1.4.1,centosTriggering ADAM-prb ? 2.3.0,2.10,1.6.1,centosTriggering ADAM-prb ? 2.3.0,2.10,1.5.2,centosTriggering ADAM-prb ? 2.3.0,2.11,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.11,1.3.1,centosTriggering ADAM-prb ? 2.6.0,2.11,1.6.1,centosTriggering ADAM-prb ? 2.3.0,2.11,1.3.1,centosADAM-prb ? 2.6.0,2.10,1.3.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.10,1.3.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.10,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.10,1.4.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.11,1.5.2,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.11,1.4.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.10,1.4.1,centos completed with result FAILUREADAM-prb ? 2.3.0,2.11,1.4.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.10,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.10,1.5.2,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.11,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.11,1.3.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.11,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.11,1.3.1,centos completed with result SUCCESSNotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

fnothaft · 2016-07-06T21:48:29Z

Jenkins, retest this please.

fnothaft · 2016-07-06T21:56:56Z

Jenkins, retest this please.

AmplabJenkins · 2016-07-06T22:15:21Z

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
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Build result: FAILURE

[...truncated 24 lines...]Triggering ADAM-prb ? 2.6.0,2.11,1.4.1,centosTriggering ADAM-prb ? 2.6.0,2.10,1.4.1,centosTriggering ADAM-prb ? 2.3.0,2.11,1.4.1,centosTriggering ADAM-prb ? 2.3.0,2.10,1.6.1,centosTriggering ADAM-prb ? 2.3.0,2.10,1.5.2,centosTriggering ADAM-prb ? 2.3.0,2.11,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.11,1.3.1,centosTriggering ADAM-prb ? 2.6.0,2.11,1.6.1,centosTriggering ADAM-prb ? 2.3.0,2.11,1.3.1,centosADAM-prb ? 2.6.0,2.10,1.3.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.10,1.3.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.10,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.10,1.4.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.11,1.5.2,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.11,1.4.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.10,1.4.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.11,1.4.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.10,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.10,1.5.2,centos completed with result FAILUREADAM-prb ? 2.3.0,2.11,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.11,1.3.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.11,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.11,1.3.1,centos completed with result SUCCESSNotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

AmplabJenkins · 2016-07-06T22:40:35Z

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
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Build result: FAILURE

[...truncated 24 lines...]Triggering ADAM-prb ? 2.6.0,2.11,1.4.1,centosTriggering ADAM-prb ? 2.6.0,2.10,1.4.1,centosTriggering ADAM-prb ? 2.3.0,2.11,1.4.1,centosTriggering ADAM-prb ? 2.3.0,2.10,1.6.1,centosTriggering ADAM-prb ? 2.3.0,2.10,1.5.2,centosTriggering ADAM-prb ? 2.3.0,2.11,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.11,1.3.1,centosTriggering ADAM-prb ? 2.6.0,2.11,1.6.1,centosTriggering ADAM-prb ? 2.3.0,2.11,1.3.1,centosADAM-prb ? 2.6.0,2.10,1.3.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.10,1.3.1,centos completed with result FAILUREADAM-prb ? 2.6.0,2.10,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.10,1.4.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.11,1.5.2,centos completed with result FAILUREADAM-prb ? 2.6.0,2.11,1.4.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.10,1.4.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.11,1.4.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.10,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.10,1.5.2,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.11,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.11,1.3.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.11,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.11,1.3.1,centos completed with result SUCCESSNotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

fnothaft · 2016-07-07T01:13:44Z

Jenkins, retest this please.

AmplabJenkins · 2016-07-07T01:37:32Z

Test PASSed.
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Test PASSed.

fnothaft · 2016-07-07T03:17:34Z

@heuermh I believe this is good to go.

heuermh · 2016-07-07T13:28:31Z

bin/adam-submit

 if [ "$num_jars" -eq "0" ]; then
  echo "Failed to find ADAM cli assembly in $ASSEMBLY_DIR." 1>&2
  echo "You need to build ADAM before running this program." 1>&2
  exit 1
 fi

-ASSEMBLY_JARS="$(ls -1 "$ASSEMBLY_DIR" | grep "^adam-cli_[0-9A-Za-z\.-]*\.jar$" | grep -v javadoc || true)"
+ASSEMBLY_JARS="$(ls -1 "$ASSEMBLY_DIR" | grep "^adam-assembly_[0-9A-Za-z\.-]*\.jar$" | grep -v javadoc || true)"


I wonder if it might be preferable to use <finalName>adam_2.10</finalName> for the fat jar artifact?

I'm agnostic. LMK your preference.

AmplabJenkins · 2016-07-07T13:57:28Z

Test FAILed.
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Build result: FAILURE

[...truncated 24 lines...]Triggering ADAM-prb ? 2.6.0,2.11,1.4.1,centosTriggering ADAM-prb ? 2.6.0,2.10,1.4.1,centosTriggering ADAM-prb ? 2.3.0,2.11,1.4.1,centosTriggering ADAM-prb ? 2.3.0,2.10,1.6.1,centosTriggering ADAM-prb ? 2.3.0,2.10,1.5.2,centosTriggering ADAM-prb ? 2.3.0,2.11,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.11,1.3.1,centosTriggering ADAM-prb ? 2.6.0,2.11,1.6.1,centosTriggering ADAM-prb ? 2.3.0,2.11,1.3.1,centosADAM-prb ? 2.6.0,2.10,1.3.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.10,1.3.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.10,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.10,1.4.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.11,1.5.2,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.11,1.4.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.10,1.4.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.11,1.4.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.10,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.10,1.5.2,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.11,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.11,1.3.1,centos completed with result FAILUREADAM-prb ? 2.6.0,2.11,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.11,1.3.1,centos completed with result SUCCESSNotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

fnothaft · 2016-07-07T14:42:36Z

Got the finalName patch in.

AmplabJenkins · 2016-07-07T15:00:30Z

Test PASSed.
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Test PASSed.

heuermh · 2016-07-07T20:35:28Z

Merged commit 48302d9

Thank you, @fnothaft!

fnothaft force-pushed the issues/1006-separate-fat-jar branch from 2b8b12b to 96e31c2 Compare July 6, 2016 19:10

heuermh reviewed Jul 6, 2016
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adam-assembly/pom.xml

</dependency>

</dependencies>

<profiles>

<profile>

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this can be removed

fnothaft force-pushed the issues/1006-separate-fat-jar branch from 96e31c2 to f1f502f Compare July 6, 2016 19:57

fnothaft force-pushed the issues/1006-separate-fat-jar branch from f1f502f to 911f1bd Compare July 6, 2016 20:03

fnothaft force-pushed the issues/1006-separate-fat-jar branch from 911f1bd to de1e4ea Compare July 6, 2016 20:34

heuermh reviewed Jul 7, 2016
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fnothaft force-pushed the issues/1006-separate-fat-jar branch 2 times, most recently from 6d8dd3e to 397c113 Compare July 7, 2016 13:37

[ADAM-1006] Split uberjar out to adam-assembly submodule.

48302d9

fnothaft force-pushed the issues/1006-separate-fat-jar branch from 397c113 to 48302d9 Compare July 7, 2016 14:42

heuermh closed this Jul 7, 2016

heuermh mentioned this pull request Jul 7, 2016

Separate fat jar build from adam-cli to new maven module #1006

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[ADAM-1006] Split überjar out to adam-assembly submodule. #1072

[ADAM-1006] Split überjar out to adam-assembly submodule. #1072

fnothaft commented Jul 6, 2016

heuermh Jul 6, 2016

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fnothaft commented Jul 6, 2016

AmplabJenkins commented Jul 6, 2016

fnothaft commented Jul 6, 2016

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AmplabJenkins commented Jul 6, 2016

fnothaft commented Jul 7, 2016

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fnothaft commented Jul 7, 2016

heuermh Jul 7, 2016

fnothaft Jul 7, 2016

AmplabJenkins commented Jul 7, 2016

fnothaft commented Jul 7, 2016

AmplabJenkins commented Jul 7, 2016

heuermh commented Jul 7, 2016

[ADAM-1006] Split überjar out to adam-assembly submodule. #1072

[ADAM-1006] Split überjar out to adam-assembly submodule. #1072

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AmplabJenkins commented Jul 6, 2016

Build result: FAILURE

AmplabJenkins commented Jul 6, 2016

Build result: FAILURE

AmplabJenkins commented Jul 6, 2016

Build result: FAILURE

AmplabJenkins commented Jul 6, 2016

Build result: FAILURE

AmplabJenkins commented Jul 6, 2016

Build result: FAILURE

fnothaft commented Jul 6, 2016

AmplabJenkins commented Jul 6, 2016

Build result: FAILURE

fnothaft commented Jul 6, 2016

fnothaft commented Jul 6, 2016

AmplabJenkins commented Jul 6, 2016

Build result: FAILURE

AmplabJenkins commented Jul 6, 2016

Build result: FAILURE

fnothaft commented Jul 7, 2016

AmplabJenkins commented Jul 7, 2016

fnothaft commented Jul 7, 2016

heuermh Jul 7, 2016

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fnothaft Jul 7, 2016

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AmplabJenkins commented Jul 7, 2016

Build result: FAILURE

fnothaft commented Jul 7, 2016

AmplabJenkins commented Jul 7, 2016

heuermh commented Jul 7, 2016