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Dependency version bump + BroadcastRegionJoin fix #1440

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merged 2 commits into from Mar 27, 2017

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fnothaft commented Mar 16, 2017

On top of #1360. Potential fix for the flagging unit test issues in #1324 and #1360. See bigdatagenomics/utils#116. CC @heuermh @devin-petersohn

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This will fail because the bigdatagenomics/utils#116 patch isn't in the 0.2.13-SNAPSHOT yet, but, it conceptually should work.

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fnothaft commented Mar 16, 2017

This will fail because the bigdatagenomics/utils#116 patch isn't in the 0.2.13-SNAPSHOT yet, but, it conceptually should work.

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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/1883/

Build result: FAILURE

[...truncated 16 lines...] > /home/jenkins/git2/bin/git rev-parse origin/pr/1440/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains 9526db8db491833a21096adedcabc8abf87050f2 # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/1440/merge^{commit} # timeout=10Checking out Revision 9526db8db491833a21096adedcabc8abf87050f2 (origin/pr/1440/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 9526db8db491833a21096adedcabc8abf87050f2First time build. Skipping changelog.Triggering ADAM-prb ? 2.3.0,2.11,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.10,1.6.1,centosTriggering ADAM-prb ? 2.3.0,2.11,2.0.0,centosTriggering ADAM-prb ? 2.3.0,2.10,2.0.0,centosTriggering ADAM-prb ? 2.6.0,2.11,2.0.0,centosTriggering ADAM-prb ? 2.6.0,2.10,2.0.0,centosTriggering ADAM-prb ? 2.3.0,2.10,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.11,1.6.1,centosADAM-prb ? 2.3.0,2.11,1.6.1,centos completed with result FAILUREADAM-prb ? 2.6.0,2.10,1.6.1,centos completed with result FAILUREADAM-prb ? 2.3.0,2.11,2.0.0,centos completed with result FAILUREADAM-prb ? 2.3.0,2.10,2.0.0,centos completed with result FAILUREADAM-prb ? 2.6.0,2.11,2.0.0,centos completed with result FAILUREADAM-prb ? 2.6.0,2.10,2.0.0,centos completed with result FAILUREADAM-prb ? 2.3.0,2.10,1.6.1,centos completed with result FAILUREADAM-prb ? 2.6.0,2.11,1.6.1,centos completed with result FAILURENotifying 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 16 lines...] > /home/jenkins/git2/bin/git rev-parse origin/pr/1440/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains 9526db8db491833a21096adedcabc8abf87050f2 # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/1440/merge^{commit} # timeout=10Checking out Revision 9526db8db491833a21096adedcabc8abf87050f2 (origin/pr/1440/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 9526db8db491833a21096adedcabc8abf87050f2First time build. Skipping changelog.Triggering ADAM-prb ? 2.3.0,2.11,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.10,1.6.1,centosTriggering ADAM-prb ? 2.3.0,2.11,2.0.0,centosTriggering ADAM-prb ? 2.3.0,2.10,2.0.0,centosTriggering ADAM-prb ? 2.6.0,2.11,2.0.0,centosTriggering ADAM-prb ? 2.6.0,2.10,2.0.0,centosTriggering ADAM-prb ? 2.3.0,2.10,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.11,1.6.1,centosADAM-prb ? 2.3.0,2.11,1.6.1,centos completed with result FAILUREADAM-prb ? 2.6.0,2.10,1.6.1,centos completed with result FAILUREADAM-prb ? 2.3.0,2.11,2.0.0,centos completed with result FAILUREADAM-prb ? 2.3.0,2.10,2.0.0,centos completed with result FAILUREADAM-prb ? 2.6.0,2.11,2.0.0,centos completed with result FAILUREADAM-prb ? 2.6.0,2.10,2.0.0,centos completed with result FAILUREADAM-prb ? 2.3.0,2.10,1.6.1,centos completed with result FAILUREADAM-prb ? 2.6.0,2.11,1.6.1,centos completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

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Thanks for putting this together

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heuermh commented Mar 16, 2017

Thanks for putting this together

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Locally built #1324 on this and it builds correctly.

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devin-petersohn commented Mar 19, 2017

Locally built #1324 on this and it builds correctly.

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Updated to cut out the updates from #1360 that we don't want in 0.22.0. If this passes CI, I'll cut a 0.2.13 of utils tomorrow.

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fnothaft commented Mar 20, 2017

Updated to cut out the updates from #1360 that we don't want in 0.22.0. If this passes CI, I'll cut a 0.2.13 of utils tomorrow.

@fnothaft fnothaft requested review from heuermh and devin-petersohn Mar 20, 2017

@fnothaft fnothaft added this to the 0.22.0 milestone Mar 20, 2017

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Coverage Status

Coverage decreased (-0.01%) to 76.468% when pulling 5f5fbbc on fnothaft:heuermh-dep-versions into cf39e6c on bigdatagenomics:master.

coveralls commented Mar 20, 2017

Coverage Status

Coverage decreased (-0.01%) to 76.468% when pulling 5f5fbbc on fnothaft:heuermh-dep-versions into cf39e6c on bigdatagenomics:master.

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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

[...truncated 16 lines...] > /home/jenkins/git2/bin/git rev-parse origin/pr/1440/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains 1ae0225 # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/1440/merge^{commit} # timeout=10Checking out Revision 1ae0225 (origin/pr/1440/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 1ae0225d47097c607c229c755be6b0de9c6992b9First time build. Skipping changelog.Triggering ADAM-prb ? 2.3.0,2.11,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.10,1.6.1,centosTriggering ADAM-prb ? 2.3.0,2.11,2.0.0,centosTriggering ADAM-prb ? 2.3.0,2.10,2.0.0,centosTriggering ADAM-prb ? 2.6.0,2.11,2.0.0,centosTriggering ADAM-prb ? 2.6.0,2.10,2.0.0,centosTriggering ADAM-prb ? 2.3.0,2.10,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.11,1.6.1,centosADAM-prb ? 2.3.0,2.11,1.6.1,centos completed with result FAILUREADAM-prb ? 2.6.0,2.10,1.6.1,centos completed with result FAILUREADAM-prb ? 2.3.0,2.11,2.0.0,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.10,2.0.0,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.11,2.0.0,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.10,2.0.0,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.10,1.6.1,centos completed with result FAILUREADAM-prb ? 2.6.0,2.11,1.6.1,centos completed with result FAILURENotifying 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 16 lines...] > /home/jenkins/git2/bin/git rev-parse origin/pr/1440/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains 1ae0225 # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/1440/merge^{commit} # timeout=10Checking out Revision 1ae0225 (origin/pr/1440/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 1ae0225d47097c607c229c755be6b0de9c6992b9First time build. Skipping changelog.Triggering ADAM-prb ? 2.3.0,2.11,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.10,1.6.1,centosTriggering ADAM-prb ? 2.3.0,2.11,2.0.0,centosTriggering ADAM-prb ? 2.3.0,2.10,2.0.0,centosTriggering ADAM-prb ? 2.6.0,2.11,2.0.0,centosTriggering ADAM-prb ? 2.6.0,2.10,2.0.0,centosTriggering ADAM-prb ? 2.3.0,2.10,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.11,1.6.1,centosADAM-prb ? 2.3.0,2.11,1.6.1,centos completed with result FAILUREADAM-prb ? 2.6.0,2.10,1.6.1,centos completed with result FAILUREADAM-prb ? 2.3.0,2.11,2.0.0,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.10,2.0.0,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.11,2.0.0,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.10,2.0.0,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.10,1.6.1,centos completed with result FAILUREADAM-prb ? 2.6.0,2.11,1.6.1,centos completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

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Whoops! Messed up the CI build for utils and we weren't pushing snapshots for the Spark 1 builds. Fixed that and am kicking off a utils trunk build now.

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fnothaft commented Mar 20, 2017

Whoops! Messed up the CI build for utils and we weren't pushing snapshots for the Spark 1 builds. Fixed that and am kicking off a utils trunk build now.

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Jenkins, retest this please.

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fnothaft commented Mar 20, 2017

Jenkins, retest this please.

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coveralls Mar 20, 2017

Coverage Status

Coverage increased (+0.08%) to 76.554% when pulling 5f5fbbc on fnothaft:heuermh-dep-versions into cf39e6c on bigdatagenomics:master.

coveralls commented Mar 20, 2017

Coverage Status

Coverage increased (+0.08%) to 76.554% when pulling 5f5fbbc on fnothaft:heuermh-dep-versions into cf39e6c on bigdatagenomics:master.

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Test PASSed.
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Test PASSed.

Test PASSed.
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Test PASSed.

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Just cut org.bdgenomics.utils 0.2.13; waiting for the push to Maven Central.

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fnothaft commented Mar 21, 2017

Just cut org.bdgenomics.utils 0.2.13; waiting for the push to Maven Central.

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devin-petersohn commented Mar 21, 2017

Thanks @fnothaft!

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Thanks for the ping, @heuermh! Just pushed an update.

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fnothaft commented Mar 21, 2017

Thanks for the ping, @heuermh! Just pushed an update.

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coveralls Mar 21, 2017

Coverage Status

Coverage decreased (-0.3%) to 80.315% when pulling 791dc90 on fnothaft:heuermh-dep-versions into fd0cb6e on bigdatagenomics:master.

Coverage Status

Coverage decreased (-0.3%) to 80.315% when pulling 791dc90 on fnothaft:heuermh-dep-versions into fd0cb6e on bigdatagenomics:master.

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Test FAILed.
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Build result: FAILURE

[...truncated 16 lines...] > /home/jenkins/git2/bin/git rev-parse origin/pr/1440/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains 15e9ae6 # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/1440/merge^{commit} # timeout=10Checking out Revision 15e9ae6 (origin/pr/1440/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 15e9ae6454eb9e6d98f78946199a7189468d2420First time build. Skipping changelog.Triggering ADAM-prb ? 2.3.0,2.11,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.10,1.6.1,centosTriggering ADAM-prb ? 2.3.0,2.11,2.0.0,centosTriggering ADAM-prb ? 2.3.0,2.10,2.0.0,centosTriggering ADAM-prb ? 2.6.0,2.11,2.0.0,centosTriggering ADAM-prb ? 2.6.0,2.10,2.0.0,centosTriggering ADAM-prb ? 2.3.0,2.10,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.11,1.6.1,centosADAM-prb ? 2.3.0,2.11,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.10,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.11,2.0.0,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.10,2.0.0,centos completed with result FAILUREADAM-prb ? 2.6.0,2.11,2.0.0,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.10,2.0.0,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.10,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.11,1.6.1,centos completed with result SUCCESSNotifying 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 16 lines...] > /home/jenkins/git2/bin/git rev-parse origin/pr/1440/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains 15e9ae6 # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/1440/merge^{commit} # timeout=10Checking out Revision 15e9ae6 (origin/pr/1440/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 15e9ae6454eb9e6d98f78946199a7189468d2420First time build. Skipping changelog.Triggering ADAM-prb ? 2.3.0,2.11,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.10,1.6.1,centosTriggering ADAM-prb ? 2.3.0,2.11,2.0.0,centosTriggering ADAM-prb ? 2.3.0,2.10,2.0.0,centosTriggering ADAM-prb ? 2.6.0,2.11,2.0.0,centosTriggering ADAM-prb ? 2.6.0,2.10,2.0.0,centosTriggering ADAM-prb ? 2.3.0,2.10,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.11,1.6.1,centosADAM-prb ? 2.3.0,2.11,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.10,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.11,2.0.0,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.10,2.0.0,centos completed with result FAILUREADAM-prb ? 2.6.0,2.11,2.0.0,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.10,2.0.0,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.10,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.11,1.6.1,centos completed with result SUCCESSNotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

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Jenkins, retest this please.

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heuermh commented Mar 21, 2017

Jenkins, retest this please.

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Coverage Status

Coverage decreased (-0.3%) to 80.315% when pulling 791dc90 on fnothaft:heuermh-dep-versions into fd0cb6e on bigdatagenomics:master.

coveralls commented Mar 21, 2017

Coverage Status

Coverage decreased (-0.3%) to 80.315% when pulling 791dc90 on fnothaft:heuermh-dep-versions into fd0cb6e on bigdatagenomics:master.

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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/1897/

Build result: FAILURE

[...truncated 16 lines...] > /home/jenkins/git2/bin/git rev-parse origin/pr/1440/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains 15e9ae6 # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/1440/merge^{commit} # timeout=10Checking out Revision 15e9ae6 (origin/pr/1440/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 15e9ae6454eb9e6d98f78946199a7189468d2420First time build. Skipping changelog.Triggering ADAM-prb ? 2.3.0,2.11,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.10,1.6.1,centosTriggering ADAM-prb ? 2.3.0,2.11,2.0.0,centosTriggering ADAM-prb ? 2.3.0,2.10,2.0.0,centosTriggering ADAM-prb ? 2.6.0,2.11,2.0.0,centosTriggering ADAM-prb ? 2.6.0,2.10,2.0.0,centosTriggering ADAM-prb ? 2.3.0,2.10,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.11,1.6.1,centosADAM-prb ? 2.3.0,2.11,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.10,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.11,2.0.0,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.10,2.0.0,centos completed with result FAILUREADAM-prb ? 2.6.0,2.11,2.0.0,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.10,2.0.0,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.10,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.11,1.6.1,centos completed with result SUCCESSNotifying 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 16 lines...] > /home/jenkins/git2/bin/git rev-parse origin/pr/1440/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains 15e9ae6 # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/1440/merge^{commit} # timeout=10Checking out Revision 15e9ae6 (origin/pr/1440/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 15e9ae6454eb9e6d98f78946199a7189468d2420First time build. Skipping changelog.Triggering ADAM-prb ? 2.3.0,2.11,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.10,1.6.1,centosTriggering ADAM-prb ? 2.3.0,2.11,2.0.0,centosTriggering ADAM-prb ? 2.3.0,2.10,2.0.0,centosTriggering ADAM-prb ? 2.6.0,2.11,2.0.0,centosTriggering ADAM-prb ? 2.6.0,2.10,2.0.0,centosTriggering ADAM-prb ? 2.3.0,2.10,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.11,1.6.1,centosADAM-prb ? 2.3.0,2.11,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.10,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.11,2.0.0,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.10,2.0.0,centos completed with result FAILUREADAM-prb ? 2.6.0,2.11,2.0.0,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.10,2.0.0,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.10,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.11,1.6.1,centos completed with result SUCCESSNotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

heuermh and others added some commits Mar 14, 2017

Update bdg-utils dependency version to 0.2.13.
Includes a fix for bad broadcast joins due to thread unsafe variable being shared.
[ADAM-1455] Upgrade to Hadoop-BAM 7.8.0 and htsjdk 2.9.1
Resolves #1455. Adds `org.bdgenomics.adam.rdd.read.RepairPartitions`, which
works around removed functionality from Hadoop-BAM for keeping read pairs from
a queryname sorted BAM file in a single partition.
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Resolves #1455 now. Ping @heuermh for re-review.

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fnothaft commented Mar 27, 2017

Resolves #1455 now. Ping @heuermh for re-review.

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coveralls Mar 27, 2017

Coverage Status

Coverage increased (+0.1%) to 80.705% when pulling d533097 on fnothaft:heuermh-dep-versions into a9a0039 on bigdatagenomics:master.

coveralls commented Mar 27, 2017

Coverage Status

Coverage increased (+0.1%) to 80.705% when pulling d533097 on fnothaft:heuermh-dep-versions into a9a0039 on bigdatagenomics:master.

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AmplabJenkins Mar 27, 2017

Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1914/
Test PASSed.

Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1914/
Test PASSed.

@heuermh heuermh merged commit 4a74482 into bigdatagenomics:master Mar 27, 2017

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codacy/pr Not so good... This pull request quality could be better.
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coverage/coveralls Coverage increased (+0.1%) to 80.705%
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default Merged build finished.
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Thank you, @fnothaft!

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heuermh commented Mar 27, 2017

Thank you, @fnothaft!

@fnothaft fnothaft deleted the fnothaft:heuermh-dep-versions branch Mar 28, 2017

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