Add R and Python into distribution artifacts #1765

fnothaft · 2017-10-17T18:38:48Z

AmplabJenkins · 2017-10-17T19:20:06Z

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.

AmplabJenkins · 2017-10-18T00:09:52Z

Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/2433/
Test PASSed.

heuermh · 2017-10-24T20:36:34Z

adam-r/pom.xml

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


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.

heuermh · 2017-10-24T20:37:15Z

This builds ok for me.

heuermh · 2017-10-25T16:32:05Z

adam-r/bdgenomics.adam/DESCRIPTION

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


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

heuermh · 2017-10-31T15:27:55Z

Created pull request fnothaft#22 to address review comments.

AmplabJenkins · 2017-10-31T16:18:51Z

Test PASSed.
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Test PASSed.

heuermh · 2017-10-31T16:42:28Z

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

AmplabJenkins · 2017-11-06T20:05:19Z

Merged build finished. Test FAILed.

AmplabJenkins · 2017-11-06T20:05:19Z

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.

Resolves bigdatagenomics#1668, bigdatagenomics#1672.

Resolves bigdatagenomics#1667.

AmplabJenkins · 2017-11-07T17:49:39Z

Merged build finished. Test FAILed.

AmplabJenkins · 2017-11-07T17:49:40Z

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 · 2017-11-07T17:50:48Z

Jenkins, retest this please.

AmplabJenkins · 2017-11-07T18:15:54Z

Merged build finished. Test FAILed.

AmplabJenkins · 2017-11-07T18:15:55Z

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 · 2017-11-07T18:18:31Z

Thank you, @fnothaft

fnothaft added this to the 0.23.0 milestone Oct 17, 2017

fnothaft mentioned this pull request Oct 17, 2017

[ADAM-1655] Move R package to bdgenomics.adam. #1764

Merged

heuermh requested changes Oct 24, 2017

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heuermh requested changes Oct 25, 2017

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fnothaft force-pushed the issues/1667-1668-1672-r-python-distribution branch from f336d39 to b9d2eed Compare November 6, 2017 19:40

fnothaft added 2 commits November 7, 2017 09:42

[ADAM-1668] Include R tarball in distribution, and build docs.

acaaea3

Resolves bigdatagenomics#1668, bigdatagenomics#1672.

[ADAM-1667] Package python into distribution.

e8934fc

Resolves bigdatagenomics#1667.

fnothaft force-pushed the issues/1667-1668-1672-r-python-distribution branch from b9d2eed to e8934fc Compare November 7, 2017 17:42

heuermh approved these changes Nov 7, 2017

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heuermh merged commit 17519ed into bigdatagenomics:master Nov 7, 2017

heuermh mentioned this pull request Nov 7, 2017

Generate docs from R API for distribution #1672

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Add R and Python into distribution artifacts #1765

Add R and Python into distribution artifacts #1765

fnothaft commented Oct 17, 2017

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heuermh Oct 24, 2017

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heuermh commented Nov 7, 2017

Add R and Python into distribution artifacts #1765

Add R and Python into distribution artifacts #1765

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fnothaft commented Oct 17, 2017

AmplabJenkins commented Oct 17, 2017

Build result: FAILURE

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Build result: FAILURE

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Build result: FAILURE

heuermh commented Nov 7, 2017

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AmplabJenkins commented Nov 7, 2017

Build result: FAILURE

heuermh commented Nov 7, 2017