[ADAM-439] Fix ADAM to account for BDG-FORMATS-35: Avro uses Strings #440
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Test FAILed. Build result: FAILUREGitHub pull request #440 of commit 3ff93b3 automatically merged.[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-slave-01 (centos) 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/440/merge^{commit} # timeout=10Checking out Revision 88a1fcd (detached) > git config core.sparsecheckout # timeout=10 > git checkout -f 88a1fcd > git rev-list 77ea367 # timeout=10Triggering ADAM-prb » 2.2.0,centosTriggering ADAM-prb » 1.0.4,centosTriggering ADAM-prb » 2.3.0,centosADAM-prb » 2.2.0,centos completed with result FAILUREADAM-prb » 1.0.4,centos completed with result FAILUREADAM-prb » 2.3.0,centos completed with result FAILURETest FAILed. |
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Test FAILed. Build result: FAILUREGitHub pull request #440 of commit f0441ef automatically merged.[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-slave-01 (centos) 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/440/merge^{commit} # timeout=10Checking out Revision a16515a (detached) > git config core.sparsecheckout # timeout=10 > git checkout -f a16515a > git rev-list 77ea367 # timeout=10Triggering ADAM-prb » 2.2.0,centosTriggering ADAM-prb » 1.0.4,centosTriggering ADAM-prb » 2.3.0,centosADAM-prb » 2.2.0,centos completed with result FAILUREADAM-prb » 1.0.4,centos completed with result FAILUREADAM-prb » 2.3.0,centos completed with result FAILURETest FAILed. |
| @@ -31,8 +31,8 @@ object ImplicitJavaConversions { | |||
| seqAsJavaList(list.map(i => i: java.lang.Integer)) | |||
| } | |||
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| implicit def charSequenceToString(cs: CharSequence): String = cs.toString | |||
| // implicit def charSequenceToString(cs: CharSequence): String = cs.toString | |||
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Oh, yeah, that was exactly what I wanted to ask. Any objections?
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@fnothaft get a chance to look at the failure? |
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@laserson yeah, I'm still looking into it. I think I've figured it out, but haven't been able to fix it yet. |
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Just following up on this |
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@laserson just pushed a fix towards your fork. |
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Test FAILed. Build result: FAILUREGitHub pull request #440 of commit 65d18a9 automatically merged.[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-slave-01 (centos) 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/440/merge^{commit} # timeout=10Checking out Revision f214a4407bbbb2172945bc3fc4f411b44908b0f4 (detached) > git config core.sparsecheckout # timeout=10 > git checkout -f f214a4407bbbb2172945bc3fc4f411b44908b0f4 > git rev-list f211b54 # timeout=10Triggering ADAM-prb » 2.3.0,centosTriggering ADAM-prb » 1.0.4,centosTriggering ADAM-prb » 2.2.0,centosADAM-prb » 2.3.0,centos completed with result FAILUREADAM-prb » 1.0.4,centos completed with result FAILUREADAM-prb » 2.2.0,centos completed with result FAILURETest FAILed. |
laserson
changed the title
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Yikes, sorry about the ugly commit history. Let me know if you'd prefer me to squash this. |
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Test FAILed. Build result: ABORTEDGitHub pull request #440 of commit e12c48d automatically merged.[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-slave-01 (centos) 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/440/merge^{commit} # timeout=10Checking out Revision ba78b0d16b230b789f55674b67464908f626ca20 (detached) > git config core.sparsecheckout # timeout=10 > git checkout -f ba78b0d16b230b789f55674b67464908f626ca20 > git rev-list f211b54 # timeout=10Triggering ADAM-prb » 2.3.0,centosTriggering ADAM-prb » 1.0.4,centosTriggering ADAM-prb » 2.2.0,centosADAM-prb » 2.3.0,centos completed with result ABORTEDADAM-prb » 1.0.4,centos completed with result ABORTEDADAM-prb » 2.2.0,centos completed with result ABORTEDTest FAILed. |
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:-/ builds fine on my machine |
Includes commit by @fnothaft: Fixed flipped index in indel realigner. Fixes bigdatagenomics#439
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Building locally now... |
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Just did the same...passed for me |
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Test PASSed. |
fnothaft
added a commit
that referenced
this pull request
Nov 17, 2014
[ADAM-439] Fix ADAM to account for BDG-FORMATS-35: Avro uses Strings
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Just changed a bunch of
CharSequences toStrings.Some tests fail, though not sure why, as I'm not familiar with that part of the codebase.