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Stores original position and original cigar during realignment. #417

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merged 1 commit into from Nov 2, 2014

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niranjan93 commented Oct 14, 2014

Stores original position and original cigar during realignment.
Addresses issue #348 in the adam project.

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Can one of the admins verify this patch?

AmplabJenkins commented Oct 14, 2014

Can one of the admins verify this patch?

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Jenkins, add to whitelist.

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fnothaft commented Oct 14, 2014

Jenkins, add to whitelist.

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Test FAILed.
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Build result: FAILURE

GitHub pull request #417 of commit ae38a31 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/417/merge^{commit} # timeout=10Checking out Revision 4f3e5b7 (detached) > git config core.sparsecheckout # timeout=10 > git checkout -f 4f3e5b7 > git rev-list fa32bbf # timeout=10First time build. Skipping changelog.Triggering 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 FAILURE
Test FAILed.

AmplabJenkins commented Oct 14, 2014

Test FAILed.
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Build result: FAILURE

GitHub pull request #417 of commit ae38a31 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/417/merge^{commit} # timeout=10Checking out Revision 4f3e5b7 (detached) > git config core.sparsecheckout # timeout=10 > git checkout -f 4f3e5b7 > git rev-list fa32bbf # timeout=10First time build. Skipping changelog.Triggering 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 FAILURE
Test FAILed.

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Jenkins, retest this please.

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fnothaft commented Oct 14, 2014

Jenkins, retest this please.

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Test FAILed.
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Build result: FAILURE

GitHub pull request #417 of commit ae38a31 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/417/merge^{commit} # timeout=10Checking out Revision 7406d00 (detached) > git config core.sparsecheckout # timeout=10 > git checkout -f 7406d00 > git rev-list db0f900 # timeout=10Triggering ADAM-prb » 2.3.0,centosTriggering ADAM-prb » 2.2.0,centosTriggering ADAM-prb » 1.0.4,centosADAM-prb » 2.3.0,centos completed with result FAILUREADAM-prb » 2.2.0,centos completed with result FAILUREADAM-prb » 1.0.4,centos completed with result FAILURE
Test FAILed.

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Build result: FAILURE

GitHub pull request #417 of commit ae38a31 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/417/merge^{commit} # timeout=10Checking out Revision 7406d00 (detached) > git config core.sparsecheckout # timeout=10 > git checkout -f 7406d00 > git rev-list db0f900 # timeout=10Triggering ADAM-prb » 2.3.0,centosTriggering ADAM-prb » 2.2.0,centosTriggering ADAM-prb » 1.0.4,centosADAM-prb » 2.3.0,centos completed with result FAILUREADAM-prb » 2.2.0,centos completed with result FAILUREADAM-prb » 1.0.4,centos completed with result FAILURE
Test FAILed.

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Build result: FAILURE

GitHub pull request #417 of commit 77ea367 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/417/merge^{commit} # timeout=10Checking out Revision 01b4a29 (detached) > git config core.sparsecheckout # timeout=10 > git checkout -f 01b4a29 > git rev-list db0f900 # timeout=10Triggering ADAM-prb » 1.0.4,centosTriggering ADAM-prb » 2.3.0,centosTriggering ADAM-prb » 2.2.0,centosADAM-prb » 1.0.4,centos completed with result FAILUREADAM-prb » 2.3.0,centos completed with result FAILUREADAM-prb » 2.2.0,centos completed with result FAILURE
Test FAILed.

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Build result: FAILURE

GitHub pull request #417 of commit 77ea367 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/417/merge^{commit} # timeout=10Checking out Revision 01b4a29 (detached) > git config core.sparsecheckout # timeout=10 > git checkout -f 01b4a29 > git rev-list db0f900 # timeout=10Triggering ADAM-prb » 1.0.4,centosTriggering ADAM-prb » 2.3.0,centosTriggering ADAM-prb » 2.2.0,centosADAM-prb » 1.0.4,centos completed with result FAILUREADAM-prb » 2.3.0,centos completed with result FAILUREADAM-prb » 2.2.0,centos completed with result FAILURE
Test FAILed.

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Can one of the admins verify this patch?

AmplabJenkins commented Oct 21, 2014

Can one of the admins verify this patch?

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Jenkins, add to whitelist.

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fnothaft commented Oct 21, 2014

Jenkins, add to whitelist.

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Test FAILed.
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Build result: FAILURE

GitHub pull request #417 of commit 77ea367.[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 77ea367^{commit} # timeout=10Checking out Revision 77ea367 (detached) > git config core.sparsecheckout # timeout=10 > git checkout -f 77ea367 > git rev-list db0f900 # timeout=10Triggering ADAM-prb » 1.0.4,centosTriggering ADAM-prb » 2.3.0,centosTriggering ADAM-prb » 2.2.0,centosADAM-prb » 1.0.4,centos completed with result FAILUREADAM-prb » 2.3.0,centos completed with result FAILUREADAM-prb » 2.2.0,centos completed with result FAILURE
Test FAILed.

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Test FAILed.
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Build result: FAILURE

GitHub pull request #417 of commit 77ea367.[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 77ea367^{commit} # timeout=10Checking out Revision 77ea367 (detached) > git config core.sparsecheckout # timeout=10 > git checkout -f 77ea367 > git rev-list db0f900 # timeout=10Triggering ADAM-prb » 1.0.4,centosTriggering ADAM-prb » 2.3.0,centosTriggering ADAM-prb » 2.2.0,centosADAM-prb » 1.0.4,centos completed with result FAILUREADAM-prb » 2.3.0,centos completed with result FAILUREADAM-prb » 2.2.0,centos completed with result FAILURE
Test FAILed.

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Build result: FAILURE

GitHub pull request #417 of commit f3ef0c8 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/417/merge^{commit} # timeout=10Checking out Revision 2592f2c (detached) > git config core.sparsecheckout # timeout=10 > git checkout -f 2592f2c > git rev-list a9008c4 # 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 FAILURE
Test FAILed.

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Build result: FAILURE

GitHub pull request #417 of commit f3ef0c8 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/417/merge^{commit} # timeout=10Checking out Revision 2592f2c (detached) > git config core.sparsecheckout # timeout=10 > git checkout -f 2592f2c > git rev-list a9008c4 # 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 FAILURE
Test FAILed.

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Build result: FAILURE

GitHub pull request #417 of commit f0bc0f0 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/417/merge^{commit} # timeout=10Checking out Revision 7dc5bba (detached) > git config core.sparsecheckout # timeout=10 > git checkout -f 7dc5bba > git rev-list c12c117 # 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 FAILURE
Test FAILed.

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GitHub pull request #417 of commit f0bc0f0 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/417/merge^{commit} # timeout=10Checking out Revision 7dc5bba (detached) > git config core.sparsecheckout # timeout=10 > git checkout -f 7dc5bba > git rev-list c12c117 # 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 FAILURE
Test FAILed.

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Build result: FAILURE

GitHub pull request #417 of commit 4186c74 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/417/merge^{commit} # timeout=10Checking out Revision 905bb58d27ebdf9a7b4cebedee15265f3ddbfbba (detached) > git config core.sparsecheckout # timeout=10 > git checkout -f 905bb58d27ebdf9a7b4cebedee15265f3ddbfbba > git rev-list 7dc5bba # 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 SUCCESSADAM-prb » 2.3.0,centos completed with result FAILURE
Test FAILed.

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Build result: FAILURE

GitHub pull request #417 of commit 4186c74 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/417/merge^{commit} # timeout=10Checking out Revision 905bb58d27ebdf9a7b4cebedee15265f3ddbfbba (detached) > git config core.sparsecheckout # timeout=10 > git checkout -f 905bb58d27ebdf9a7b4cebedee15265f3ddbfbba > git rev-list 7dc5bba # 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 SUCCESSADAM-prb » 2.3.0,centos completed with result FAILURE
Test FAILed.

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Test PASSed.

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massie Nov 1, 2014

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Aside from relaxing the Maven version requirement, this code looks ready to merge to me.

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massie commented Nov 1, 2014

Aside from relaxing the Maven version requirement, this code looks ready to merge to me.

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Should I change it to 3.1.1? What is the preferred Maven version?

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niranjan93 commented Nov 1, 2014

Should I change it to 3.1.1? What is the preferred Maven version?

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Yes. 3.1.1 please.

-Matt
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On Nov 1, 2014 1:39 PM, "niranjan93" notifications@github.com wrote:

Should I change it to 3.1.1? What is the preferred Maven version?


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#417 (comment).

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massie commented Nov 1, 2014

Yes. 3.1.1 please.

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On Nov 1, 2014 1:39 PM, "niranjan93" notifications@github.com wrote:

Should I change it to 3.1.1? What is the preferred Maven version?


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Unfortunately, changing the version from 3.0.4 to 3.1.1 causes the build to fail:

niranjan93@crick:~/adam$ mvn test
[INFO] Scanning for projects...
[WARNING]
[WARNING] Some problems were encountered while building the effective model for org.bdgenomics.adam:adam-core:jar:0.14.1-SNAPSHOT
[WARNING] 'dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '' does not match a valid id pattern. @ org.bdgenomics.adam:adam-parent:0.14.1-SNAPSHOT, /home/niranjan93/adam/pom.xml, line 364, column 25
[WARNING] 'dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '
' does not match a valid id pattern. @ org.bdgenomics.adam:adam-parent:0.14.1-SNAPSHOT, /home/niranjan93/adam/pom.xml, line 368, column 25
[WARNING] 'dependencyManagement.dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '' does not match a valid id pattern. @ org.bdgenomics.adam:adam-parent:0.14.1-SNAPSHOT, /home/niranjan93/adam/pom.xml, line 364, column 25
[WARNING] 'dependencyManagement.dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '
' does not match a valid id pattern. @ org.bdgenomics.adam:adam-parent:0.14.1-SNAPSHOT, /home/niranjan93/adam/pom.xml, line 368, column 25
[WARNING]
[WARNING] Some problems were encountered while building the effective model for org.bdgenomics.adam:adam-apis:jar:0.14.1-SNAPSHOT
[WARNING] 'dependencyManagement.dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '' does not match a valid id pattern. @ org.bdgenomics.adam:adam-parent:0.14.1-SNAPSHOT, /home/niranjan93/adam/pom.xml, line 364, column 25
[WARNING] 'dependencyManagement.dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '
' does not match a valid id pattern. @ org.bdgenomics.adam:adam-parent:0.14.1-SNAPSHOT, /home/niranjan93/adam/pom.xml, line 368, column 25
[WARNING]
[WARNING] Some problems were encountered while building the effective model for org.bdgenomics.adam:adam-cli:jar:0.14.1-SNAPSHOT
[WARNING] 'dependencyManagement.dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '' does not match a valid id pattern. @ org.bdgenomics.adam:adam-parent:0.14.1-SNAPSHOT, /home/niranjan93/adam/pom.xml, line 364, column 25
[WARNING] 'dependencyManagement.dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '
' does not match a valid id pattern. @ org.bdgenomics.adam:adam-parent:0.14.1-SNAPSHOT, /home/niranjan93/adam/pom.xml, line 368, column 25
[WARNING]
[WARNING] Some problems were encountered while building the effective model for org.bdgenomics.adam:adam-parent:pom:0.14.1-SNAPSHOT
[WARNING] 'dependencyManagement.dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '' does not match a valid id pattern. @ line 364, column 25
[WARNING] 'dependencyManagement.dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '
' does not match a valid id pattern. @ line 368, column 25
[WARNING]
[WARNING] It is highly recommended to fix these problems because they threaten the stability of your build.
[WARNING]
[WARNING] For this reason, future Maven versions might no longer support building such malformed projects.
[WARNING]
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Build Order:
[INFO]
[INFO] ADAM
[INFO] ADAM: Core
[INFO] ADAM: APIs for Java
[INFO] ADAM: CLI
[INFO]
[INFO] ------------------------------------------------------------------------
[INFO] Building ADAM 0.14.1-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO]
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-parent ---
[WARNING] Rule 0: org.apache.maven.plugins.enforcer.RequireMavenVersion failed with message:
ADAM requires Maven 3.1.1 or greater
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO]
[INFO] ADAM .............................................. FAILURE [0.631s]
[INFO] ADAM: Core ........................................ SKIPPED
[INFO] ADAM: APIs for Java ............................... SKIPPED
[INFO] ADAM: CLI ......................................... SKIPPED
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 0.981s
[INFO] Finished at: Sat Nov 01 14:25:47 PDT 2014
[INFO] Final Memory: 21M/1963M
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal org.apache.maven.plugins:maven-enforcer-plugin:1.0:enforce (enforce-versions) on project adam-parent: Some Enforcer rules have failed. Look above for specific messages explaining why the rule failed. -> [Help 1]
[ERROR]
[ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch.
[ERROR] Re-run Maven using the -X switch to enable full debug logging.
[ERROR]
[ERROR] For more information about the errors and possible solutions, please read the following articles:
[ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/MojoExecutionException

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niranjan93 commented Nov 1, 2014

Unfortunately, changing the version from 3.0.4 to 3.1.1 causes the build to fail:

niranjan93@crick:~/adam$ mvn test
[INFO] Scanning for projects...
[WARNING]
[WARNING] Some problems were encountered while building the effective model for org.bdgenomics.adam:adam-core:jar:0.14.1-SNAPSHOT
[WARNING] 'dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '' does not match a valid id pattern. @ org.bdgenomics.adam:adam-parent:0.14.1-SNAPSHOT, /home/niranjan93/adam/pom.xml, line 364, column 25
[WARNING] 'dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '
' does not match a valid id pattern. @ org.bdgenomics.adam:adam-parent:0.14.1-SNAPSHOT, /home/niranjan93/adam/pom.xml, line 368, column 25
[WARNING] 'dependencyManagement.dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '' does not match a valid id pattern. @ org.bdgenomics.adam:adam-parent:0.14.1-SNAPSHOT, /home/niranjan93/adam/pom.xml, line 364, column 25
[WARNING] 'dependencyManagement.dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '
' does not match a valid id pattern. @ org.bdgenomics.adam:adam-parent:0.14.1-SNAPSHOT, /home/niranjan93/adam/pom.xml, line 368, column 25
[WARNING]
[WARNING] Some problems were encountered while building the effective model for org.bdgenomics.adam:adam-apis:jar:0.14.1-SNAPSHOT
[WARNING] 'dependencyManagement.dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '' does not match a valid id pattern. @ org.bdgenomics.adam:adam-parent:0.14.1-SNAPSHOT, /home/niranjan93/adam/pom.xml, line 364, column 25
[WARNING] 'dependencyManagement.dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '
' does not match a valid id pattern. @ org.bdgenomics.adam:adam-parent:0.14.1-SNAPSHOT, /home/niranjan93/adam/pom.xml, line 368, column 25
[WARNING]
[WARNING] Some problems were encountered while building the effective model for org.bdgenomics.adam:adam-cli:jar:0.14.1-SNAPSHOT
[WARNING] 'dependencyManagement.dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '' does not match a valid id pattern. @ org.bdgenomics.adam:adam-parent:0.14.1-SNAPSHOT, /home/niranjan93/adam/pom.xml, line 364, column 25
[WARNING] 'dependencyManagement.dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '
' does not match a valid id pattern. @ org.bdgenomics.adam:adam-parent:0.14.1-SNAPSHOT, /home/niranjan93/adam/pom.xml, line 368, column 25
[WARNING]
[WARNING] Some problems were encountered while building the effective model for org.bdgenomics.adam:adam-parent:pom:0.14.1-SNAPSHOT
[WARNING] 'dependencyManagement.dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '' does not match a valid id pattern. @ line 364, column 25
[WARNING] 'dependencyManagement.dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '
' does not match a valid id pattern. @ line 368, column 25
[WARNING]
[WARNING] It is highly recommended to fix these problems because they threaten the stability of your build.
[WARNING]
[WARNING] For this reason, future Maven versions might no longer support building such malformed projects.
[WARNING]
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Build Order:
[INFO]
[INFO] ADAM
[INFO] ADAM: Core
[INFO] ADAM: APIs for Java
[INFO] ADAM: CLI
[INFO]
[INFO] ------------------------------------------------------------------------
[INFO] Building ADAM 0.14.1-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO]
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-parent ---
[WARNING] Rule 0: org.apache.maven.plugins.enforcer.RequireMavenVersion failed with message:
ADAM requires Maven 3.1.1 or greater
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO]
[INFO] ADAM .............................................. FAILURE [0.631s]
[INFO] ADAM: Core ........................................ SKIPPED
[INFO] ADAM: APIs for Java ............................... SKIPPED
[INFO] ADAM: CLI ......................................... SKIPPED
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 0.981s
[INFO] Finished at: Sat Nov 01 14:25:47 PDT 2014
[INFO] Final Memory: 21M/1963M
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal org.apache.maven.plugins:maven-enforcer-plugin:1.0:enforce (enforce-versions) on project adam-parent: Some Enforcer rules have failed. Look above for specific messages explaining why the rule failed. -> [Help 1]
[ERROR]
[ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch.
[ERROR] Re-run Maven using the -X switch to enable full debug logging.
[ERROR]
[ERROR] For more information about the errors and possible solutions, please read the following articles:
[ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/MojoExecutionException

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Test PASSed.
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Test PASSed.

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Test PASSed.
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Test PASSed.

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I believe that someone fixed this. I just checked and the Maven version for
ADAM and ADAM pull request builder are 3.1.1. All your tests passed! Looks
good.

-Matt

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Test PASSed.
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Test PASSed.


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#417 (comment).

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massie commented Nov 1, 2014

I believe that someone fixed this. I just checked and the Maven version for
ADAM and ADAM pull request builder are 3.1.1. All your tests passed! Looks
good.

-Matt

On Sat, Nov 1, 2014 at 2:39 PM, UCB AMPLab notifications@github.com wrote:

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#417 (comment).

@@ -305,7 +305,7 @@
<dependency>
<groupId>org.bdgenomics.bdg-formats</groupId>
<artifactId>bdg-formats</artifactId>
<version>0.3.1</version>
<version>0.3.2</version>

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Is the bump to bdg-formats intentional?

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Is the bump to bdg-formats intentional?

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I'm not actually sure why it's 0.3.2. Should I change it to 0.3.1?

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niranjan93 commented Nov 1, 2014

I'm not actually sure why it's 0.3.2. Should I change it to 0.3.1?

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Yes, please. Once you change it to 0.3.1, I'll be happy to merge this code.
Thanks for the contribution!

-Matt

On Sat, Nov 1, 2014 at 3:31 PM, niranjan93 notifications@github.com wrote:

I'm not actually sure why it's 0.3.2. Should I change it to 0.3.1?


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massie commented Nov 1, 2014

Yes, please. Once you change it to 0.3.1, I'll be happy to merge this code.
Thanks for the contribution!

-Matt

On Sat, Nov 1, 2014 at 3:31 PM, niranjan93 notifications@github.com wrote:

I'm not actually sure why it's 0.3.2. Should I change it to 0.3.1?


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#417 (comment).

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Test FAILed.
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Build result: FAILURE

GitHub pull request #417 of commit ccc640b 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/417/merge^{commit} # timeout=10Checking out Revision 5a3a8ea90533d65453d705fda97b9408ec65e730 (detached) > git config core.sparsecheckout # timeout=10 > git checkout -f 5a3a8ea90533d65453d705fda97b9408ec65e730 > git rev-list c648a6f2090c2b8df001dfef497bea6c70f02df4 # 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 FAILURE
Test FAILed.

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Build result: FAILURE

GitHub pull request #417 of commit ccc640b 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/417/merge^{commit} # timeout=10Checking out Revision 5a3a8ea90533d65453d705fda97b9408ec65e730 (detached) > git config core.sparsecheckout # timeout=10 > git checkout -f 5a3a8ea90533d65453d705fda97b9408ec65e730 > git rev-list c648a6f2090c2b8df001dfef497bea6c70f02df4 # 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 FAILURE
Test FAILed.

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@massie the bdg-formats dependency needs to be 0.3.2; we added the originalCigar and originalPosition fields in 0.3.2.

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fnothaft commented Nov 1, 2014

@massie the bdg-formats dependency needs to be 0.3.2; we added the originalCigar and originalPosition fields in 0.3.2.

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Build result: FAILURE

GitHub pull request #417 of commit fef9713 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/417/merge^{commit} # timeout=10Checking out Revision a7a2569f68f2981425bb14e2fffc1bdbd8024b8c (detached) > git config core.sparsecheckout # timeout=10 > git checkout -f a7a2569f68f2981425bb14e2fffc1bdbd8024b8c > git rev-list 5a3a8ea90533d65453d705fda97b9408ec65e730 # 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 FAILURE
Test FAILed.

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Build result: FAILURE

GitHub pull request #417 of commit fef9713 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/417/merge^{commit} # timeout=10Checking out Revision a7a2569f68f2981425bb14e2fffc1bdbd8024b8c (detached) > git config core.sparsecheckout # timeout=10 > git checkout -f a7a2569f68f2981425bb14e2fffc1bdbd8024b8c > git rev-list 5a3a8ea90533d65453d705fda97b9408ec65e730 # 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 FAILURE
Test FAILed.

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I changed 0.3.1 back to 0.3.2, but the build still fails. I made sure that I didn't change anything else. I also did another rebase before pushing, but Git notified me that everything is up to date.

niranjan93@crick:/adam$ git fetch upstream
niranjan93@crick:
/adam$ git status

On branch NK_schema_tags

nothing to commit (working directory clean)
niranjan93@crick:/adam$ git rebase upstream/master
Current branch NK_schema_tags is up to date.
niranjan93@crick:
/adam$

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niranjan93 commented Nov 1, 2014

I changed 0.3.1 back to 0.3.2, but the build still fails. I made sure that I didn't change anything else. I also did another rebase before pushing, but Git notified me that everything is up to date.

niranjan93@crick:/adam$ git fetch upstream
niranjan93@crick:
/adam$ git status

On branch NK_schema_tags

nothing to commit (working directory clean)
niranjan93@crick:/adam$ git rebase upstream/master
Current branch NK_schema_tags is up to date.
niranjan93@crick:
/adam$

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I have no idea why the font became so big. I had just pasted the command line output from crick. Sorry.

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niranjan93 commented Nov 1, 2014

I have no idea why the font became so big. I had just pasted the command line output from crick. Sorry.

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Jenkins, retest this please.

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massie commented Nov 2, 2014

Jenkins, retest this please.

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There is no need to be sorry. Hopefully the tests will pass now.

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massie commented Nov 2, 2014

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There is no need to be sorry. Hopefully the tests will pass now.

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Big fonts are back in vogue; it's like hair in the 80's. ;)

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fnothaft commented Nov 2, 2014

Big fonts are back in vogue; it's like hair in the 80's. ;)

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Test PASSed.
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Test PASSed.

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Test PASSed.

massie added a commit that referenced this pull request Nov 2, 2014

Merge pull request #417 from niranjan93/NK_schema_tags
Stores original position and original cigar during realignment.

@massie massie merged commit c4e8e23 into bigdatagenomics:master Nov 2, 2014

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default Merged build finished.
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I see it passes now. Thanks Matt! Thanks Frank!

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niranjan93 commented Nov 2, 2014

I see it passes now. Thanks Matt! Thanks Frank!

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Thanks, @niranjan93 !

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massie commented Nov 2, 2014

Thanks, @niranjan93 !

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