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Add R and Python into distribution artifacts #1765

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@fnothaft
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@fnothaft fnothaft commented Oct 17, 2017

Resolves #1667, #1668, #1672.

@fnothaft fnothaft added this to the 0.23.0 milestone Oct 17, 2017
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@AmplabJenkins AmplabJenkins commented Oct 17, 2017

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/2430/

Build result: FAILURE

[...truncated 15 lines...] > /home/jenkins/git2/bin/git 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/1765/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a -v --no-abbrev --contains 16c533b # timeout=10Checking out Revision 16c533b (origin/pr/1765/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 16c533b586512aac399ab69313dc527fdde5a8b6First time build. Skipping changelog.Triggering ADAM-prb ? 2.6.2,2.11,1.6.3,centosTriggering ADAM-prb ? 2.7.3,2.11,1.6.3,centosTriggering ADAM-prb ? 2.7.3,2.11,2.2.0,centosTriggering ADAM-prb ? 2.7.3,2.10,1.6.3,centosTriggering ADAM-prb ? 2.6.2,2.10,1.6.3,centosTriggering ADAM-prb ? 2.6.2,2.10,2.2.0,centosTriggering ADAM-prb ? 2.7.3,2.10,2.2.0,centosTriggering ADAM-prb ? 2.6.2,2.11,2.2.0,centosADAM-prb ? 2.6.2,2.11,1.6.3,centos completed with result SUCCESSADAM-prb ? 2.7.3,2.11,1.6.3,centos completed with result SUCCESSADAM-prb ? 2.7.3,2.11,2.2.0,centos completed with result FAILUREADAM-prb ? 2.7.3,2.10,1.6.3,centos completed with result SUCCESSADAM-prb ? 2.6.2,2.10,1.6.3,centos completed with result SUCCESSADAM-prb ? 2.6.2,2.10,2.2.0,centos completed with result SUCCESSADAM-prb ? 2.7.3,2.10,2.2.0,centos completed with result SUCCESSADAM-prb ? 2.6.2,2.11,2.2.0,centos completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

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@AmplabJenkins AmplabJenkins commented Oct 18, 2017

Test PASSed.
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Test PASSed.

<executable>R</executable>
<arguments>
<argument>-e</argument>
<argument>"library(devtools);devtools::document()"</argument>

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@heuermh

heuermh Oct 24, 2017
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This should require a mention in https://github.com/bigdatagenomics/adam/blob/master/docs/source/02_installation.md#building-for-r-r-build of additional preparation steps necessary, i.e. installing testthat, devtools and roxygen2 packages. See #1672 (comment) and thread for details.

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@heuermh heuermh commented Oct 24, 2017

This builds ok for me.

@@ -1,4 +1,4 @@
Package: bdg.adam
Package: bdgenomics.adam
Type: Package
Version: 0.23.0
Title: R Frontend for Big Data Genomics/ADAM

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@heuermh

heuermh Oct 25, 2017
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Sorry, missed this before, the Description line below needs updating, it refers to SparkR.

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@heuermh heuermh commented Oct 31, 2017

Created pull request fnothaft#22 to address review comments.

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@AmplabJenkins AmplabJenkins commented Oct 31, 2017

Test PASSed.
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https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/2457/
Test PASSed.

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@heuermh heuermh commented Oct 31, 2017

Github thinks there is a conflict, could you rebase and squash f336d39 into bbfe98f?

@fnothaft fnothaft force-pushed the fnothaft:issues/1667-1668-1672-r-python-distribution branch from f336d39 to b9d2eed Nov 6, 2017
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@AmplabJenkins AmplabJenkins commented Nov 6, 2017

Merged build finished. Test FAILed.

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@AmplabJenkins AmplabJenkins commented Nov 6, 2017

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/2461/

Build result: FAILURE

[...truncated 15 lines...] > /home/jenkins/git2/bin/git 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/1765/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a -v --no-abbrev --contains 3bebe43 # timeout=10Checking out Revision 3bebe43 (origin/pr/1765/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 3bebe43c677610d2cea93d574e1545791fd9cce1First time build. Skipping changelog.Triggering ADAM-prb ? 2.6.2,2.11,1.6.3,centosTriggering ADAM-prb ? 2.6.2,2.11,2.2.0,centosTriggering ADAM-prb ? 2.6.2,2.10,1.6.3,centosTriggering ADAM-prb ? 2.6.2,2.10,2.2.0,centosTriggering ADAM-prb ? 2.7.3,2.10,2.2.0,centosTriggering ADAM-prb ? 2.7.3,2.10,1.6.3,centosTriggering ADAM-prb ? 2.7.3,2.11,1.6.3,centosTriggering ADAM-prb ? 2.7.3,2.11,2.2.0,centosADAM-prb ? 2.6.2,2.11,1.6.3,centos completed with result FAILUREADAM-prb ? 2.6.2,2.11,2.2.0,centos completed with result FAILUREADAM-prb ? 2.6.2,2.10,1.6.3,centos completed with result FAILUREADAM-prb ? 2.6.2,2.10,2.2.0,centos completed with result FAILUREADAM-prb ? 2.7.3,2.10,2.2.0,centos completed with result FAILUREADAM-prb ? 2.7.3,2.10,1.6.3,centos completed with result FAILUREADAM-prb ? 2.7.3,2.11,1.6.3,centos completed with result FAILUREADAM-prb ? 2.7.3,2.11,2.2.0,centos completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

@fnothaft fnothaft force-pushed the fnothaft:issues/1667-1668-1672-r-python-distribution branch from b9d2eed to e8934fc Nov 7, 2017
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@AmplabJenkins AmplabJenkins commented Nov 7, 2017

Merged build finished. Test FAILed.

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@AmplabJenkins AmplabJenkins commented Nov 7, 2017

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/2470/

Build result: FAILURE

[...truncated 15 lines...] > /home/jenkins/git2/bin/git 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/1765/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a -v --no-abbrev --contains dcc68c64d5c1c73d8afa7351f0f90022492c563b # timeout=10Checking out Revision dcc68c64d5c1c73d8afa7351f0f90022492c563b (origin/pr/1765/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f dcc68c64d5c1c73d8afa7351f0f90022492c563b > /home/jenkins/git2/bin/git rev-list 3bebe43 # timeout=10Triggering ADAM-prb ? 2.6.2,2.11,1.6.3,centosTriggering ADAM-prb ? 2.6.2,2.11,2.2.0,centosTriggering ADAM-prb ? 2.6.2,2.10,1.6.3,centosTriggering ADAM-prb ? 2.6.2,2.10,2.2.0,centosTriggering ADAM-prb ? 2.7.3,2.10,2.2.0,centosTriggering ADAM-prb ? 2.7.3,2.10,1.6.3,centosTriggering ADAM-prb ? 2.7.3,2.11,1.6.3,centosTriggering ADAM-prb ? 2.7.3,2.11,2.2.0,centosADAM-prb ? 2.6.2,2.11,1.6.3,centos completed with result FAILUREADAM-prb ? 2.6.2,2.11,2.2.0,centos completed with result FAILUREADAM-prb ? 2.6.2,2.10,1.6.3,centos completed with result FAILUREADAM-prb ? 2.6.2,2.10,2.2.0,centos completed with result FAILUREADAM-prb ? 2.7.3,2.10,2.2.0,centos completed with result FAILUREADAM-prb ? 2.7.3,2.10,1.6.3,centos completed with result FAILUREADAM-prb ? 2.7.3,2.11,1.6.3,centos completed with result FAILUREADAM-prb ? 2.7.3,2.11,2.2.0,centos completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

@heuermh
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@heuermh heuermh commented Nov 7, 2017

Jenkins, retest this please.

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@AmplabJenkins AmplabJenkins commented Nov 7, 2017

Merged build finished. Test FAILed.

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@AmplabJenkins AmplabJenkins commented Nov 7, 2017

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/2471/

Build result: FAILURE

[...truncated 15 lines...] > /home/jenkins/git2/bin/git 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/1765/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a -v --no-abbrev --contains dcc68c64d5c1c73d8afa7351f0f90022492c563b # timeout=10Checking out Revision dcc68c64d5c1c73d8afa7351f0f90022492c563b (origin/pr/1765/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f dcc68c64d5c1c73d8afa7351f0f90022492c563b > /home/jenkins/git2/bin/git rev-list dcc68c64d5c1c73d8afa7351f0f90022492c563b # timeout=10Triggering ADAM-prb ? 2.6.2,2.11,1.6.3,centosTriggering ADAM-prb ? 2.6.2,2.11,2.2.0,centosTriggering ADAM-prb ? 2.6.2,2.10,1.6.3,centosTriggering ADAM-prb ? 2.6.2,2.10,2.2.0,centosTriggering ADAM-prb ? 2.7.3,2.10,2.2.0,centosTriggering ADAM-prb ? 2.7.3,2.10,1.6.3,centosTriggering ADAM-prb ? 2.7.3,2.11,1.6.3,centosTriggering ADAM-prb ? 2.7.3,2.11,2.2.0,centosADAM-prb ? 2.6.2,2.11,1.6.3,centos completed with result FAILUREADAM-prb ? 2.6.2,2.11,2.2.0,centos completed with result FAILUREADAM-prb ? 2.6.2,2.10,1.6.3,centos completed with result FAILUREADAM-prb ? 2.6.2,2.10,2.2.0,centos completed with result FAILUREADAM-prb ? 2.7.3,2.10,2.2.0,centos completed with result FAILUREADAM-prb ? 2.7.3,2.10,1.6.3,centos completed with result FAILUREADAM-prb ? 2.7.3,2.11,1.6.3,centos completed with result FAILUREADAM-prb ? 2.7.3,2.11,2.2.0,centos completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

@heuermh
heuermh approved these changes Nov 7, 2017
@heuermh heuermh merged commit 17519ed into bigdatagenomics:master Nov 7, 2017
1 of 2 checks passed
1 of 2 checks passed
default Merged build finished.
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codacy/pr Good work! A positive pull request.
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@heuermh
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@heuermh heuermh commented Nov 7, 2017

Thank you, @fnothaft

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