Dependency version bump + BroadcastRegionJoin fix #1440

fnothaft · 2017-03-16T21:55:14Z

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

fnothaft · 2017-03-16T21:56:11Z

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

AmplabJenkins · 2017-03-16T21:58:58Z

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 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.

heuermh · 2017-03-16T22:14:45Z

Thanks for putting this together

devin-petersohn · 2017-03-19T09:04:06Z

Locally built #1324 on this and it builds correctly.

fnothaft · 2017-03-20T04:43:00Z

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.

coveralls · 2017-03-20T04:50:14Z

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

AmplabJenkins · 2017-03-20T04:52:55Z

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 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.

fnothaft · 2017-03-20T05:04:37Z

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.

fnothaft · 2017-03-20T05:19:09Z

Jenkins, retest this please.

coveralls · 2017-03-20T05:30:36Z

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

AmplabJenkins · 2017-03-20T05:33:59Z

Test PASSed.
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Test PASSed.

fnothaft · 2017-03-21T17:27:25Z

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

devin-petersohn · 2017-03-21T17:27:54Z

Thanks @fnothaft!

heuermh · 2017-03-21T20:27:54Z

utils 0.2.13 is up, e.g. http://repo1.maven.org/maven2/org/bdgenomics/utils/utils-parent_2.10/0.2.13/

fnothaft · 2017-03-21T22:17:53Z

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

coveralls · 2017-03-21T22:28:31Z

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

AmplabJenkins · 2017-03-21T22:33:24Z

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.

heuermh · 2017-03-21T23:04:12Z

Jenkins, retest this please.

coveralls · 2017-03-21T23:16:06Z

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

AmplabJenkins · 2017-03-21T23:20:27Z

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.

Includes a fix for bad broadcast joins due to thread unsafe variable being shared.

Resolves bigdatagenomics#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.

fnothaft · 2017-03-27T22:49:56Z

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

coveralls · 2017-03-27T23:01:01Z

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

AmplabJenkins · 2017-03-27T23:03:54Z

Test PASSed.
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Test PASSed.

heuermh · 2017-03-27T23:04:59Z

Thank you, @fnothaft!

heuermh mentioned this pull request Mar 17, 2017

[UTILS-114] Add abstract duplicate method to IntervalArray. bigdatagenomics/utils#116

Merged

fnothaft force-pushed the heuermh-dep-versions branch from 041b4f2 to 5f5fbbc Compare March 20, 2017 04:42

fnothaft requested review from heuermh and devin-petersohn March 20, 2017 04:43

fnothaft added this to the 0.22.0 milestone Mar 20, 2017

heuermh approved these changes Mar 20, 2017

View reviewed changes

devin-petersohn approved these changes Mar 21, 2017

View reviewed changes

fnothaft force-pushed the heuermh-dep-versions branch from 5f5fbbc to 791dc90 Compare March 21, 2017 22:17

heuermh mentioned this pull request Mar 22, 2017

[CANNOLI-10] Attach record groups and sequence dictionary to BWA output. bigdatagenomics/cannoli#11

Merged

fnothaft mentioned this pull request Mar 23, 2017

Update to Hadoop-BAM 7.8.0 #1455

Closed

heuermh and others added 2 commits March 27, 2017 13:55

Update bdg-utils dependency version to 0.2.13.

d5ee95a

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

d533097

Resolves bigdatagenomics#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.

fnothaft force-pushed the heuermh-dep-versions branch from 791dc90 to d533097 Compare March 27, 2017 22:49

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

fnothaft deleted the heuermh-dep-versions branch March 28, 2017 00:38

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Dependency version bump + BroadcastRegionJoin fix #1440

Dependency version bump + BroadcastRegionJoin fix #1440

fnothaft commented Mar 16, 2017

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Dependency version bump + BroadcastRegionJoin fix #1440

Dependency version bump + BroadcastRegionJoin fix #1440

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Build result: FAILURE

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