Adding CI scripts #12

fnothaft · 2017-02-03T08:24:22Z

Resolves #10. Don't merge until @AmplabJenkins runs and passes.

AmplabJenkins · 2017-02-03T08:25:35Z

Merged build finished. Test FAILed.

AmplabJenkins · 2017-02-03T08:25:35Z

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/gnocchi-prb/1/

Build result: FAILURE

GitHub pull request #12 of commit d71db19 automatically merged.[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-06 (centos spark-test) in workspace /home/jenkins/workspace/gnocchi-prbCloning the remote Git repositoryCloning repository https://github.com/bigdatagenomics/gnocchi.git > git init /home/jenkins/workspace/gnocchi-prb # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/gnocchi.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/gnocchi.git +refs/heads/:refs/remotes/origin/ > git config remote.origin.url https://github.com/bigdatagenomics/gnocchi.git # timeout=10 > git config --add remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=10 > git config remote.origin.url https://github.com/bigdatagenomics/gnocchi.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/gnocchi.git > git fetch --tags --progress https://github.com/bigdatagenomics/gnocchi.git +refs/pull/:refs/remotes/origin/pr/ > git rev-parse origin/pr/12/merge^{commit} # timeout=10 > git branch -a --contains d455086b5d66d05a3eef4c5dbc5598d79302fad4 # timeout=10 > git rev-parse remotes/origin/pr/12/merge^{commit} # timeout=10Checking out Revision d455086b5d66d05a3eef4c5dbc5598d79302fad4 (origin/pr/12/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f d455086b5d66d05a3eef4c5dbc5598d79302fad4First time build. Skipping changelog.Triggering gnocchi-prb ? 2.6.0,2.11,1.5.2,centosTriggering gnocchi-prb ? 2.6.0,2.10,1.5.2,centosTouchstone configurations resulted in FAILURE, so aborting...
Test FAILed.

heuermh · 2017-02-03T13:39:26Z

Also fixes #6, thank you!

AmplabJenkins · 2017-02-03T16:21:25Z

Merged build finished. Test FAILed.

AmplabJenkins · 2017-02-03T16:21:26Z

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/gnocchi-prb/2/

Build result: FAILURE

GitHub pull request #12 of commit 50f72f0 automatically merged.[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-06 (centos spark-test) in workspace /home/jenkins/workspace/gnocchi-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/gnocchi.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/gnocchi.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/gnocchi.git +refs/pull/:refs/remotes/origin/pr/ > git rev-parse origin/pr/12/merge^{commit} # timeout=10 > git branch -a --contains d420f6079864ba3f01f3ce69a8a2f349ebcbaa23 # timeout=10 > git rev-parse remotes/origin/pr/12/merge^{commit} # timeout=10Checking out Revision d420f6079864ba3f01f3ce69a8a2f349ebcbaa23 (origin/pr/12/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f d420f6079864ba3f01f3ce69a8a2f349ebcbaa23First time build. Skipping changelog.Triggering gnocchi-prb ? 2.6.0,2.11,1.5.2,centosTriggering gnocchi-prb ? 2.6.0,2.10,1.5.2,centosTouchstone configurations resulted in FAILURE, so aborting...
Test FAILed.

AmplabJenkins · 2017-02-03T16:34:15Z

Merged build finished. Test FAILed.

AmplabJenkins · 2017-02-03T16:34:15Z

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/gnocchi-prb/3/

Build result: FAILURE

GitHub pull request #12 of commit 65d94bc automatically merged.[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-06 (centos spark-test) in workspace /home/jenkins/workspace/gnocchi-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/gnocchi.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/gnocchi.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/gnocchi.git +refs/pull/:refs/remotes/origin/pr/ > git rev-parse origin/pr/12/merge^{commit} # timeout=10 > git branch -a --contains f8d8a33ce71b92aa11c4a6c37b6724893a8dbac8 # timeout=10 > git rev-parse remotes/origin/pr/12/merge^{commit} # timeout=10Checking out Revision f8d8a33ce71b92aa11c4a6c37b6724893a8dbac8 (origin/pr/12/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f f8d8a33ce71b92aa11c4a6c37b6724893a8dbac8First time build. Skipping changelog.Triggering gnocchi-prb ? 2.6.0,2.11,1.5.2,centosTriggering gnocchi-prb ? 2.6.0,2.10,1.5.2,centosTouchstone configurations resulted in FAILURE, so aborting...
Test FAILed.

AmplabJenkins · 2017-02-03T17:13:49Z

Merged build finished. Test FAILed.

AmplabJenkins · 2017-02-03T17:13:49Z

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/gnocchi-prb/4/

Build result: FAILURE

GitHub pull request #12 of commit 9a526b9 automatically merged.[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-06 (centos spark-test) in workspace /home/jenkins/workspace/gnocchi-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/gnocchi.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/gnocchi.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/gnocchi.git +refs/pull/:refs/remotes/origin/pr/ > git rev-parse origin/pr/12/merge^{commit} # timeout=10 > git branch -a --contains 40e1c559f5aa114bc2a8464f5c32f585f3be9e25 # timeout=10 > git rev-parse remotes/origin/pr/12/merge^{commit} # timeout=10Checking out Revision 40e1c559f5aa114bc2a8464f5c32f585f3be9e25 (origin/pr/12/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 40e1c559f5aa114bc2a8464f5c32f585f3be9e25First time build. Skipping changelog.Triggering gnocchi-prb ? 2.6.0,2.11,1.5.2,centosTriggering gnocchi-prb ? 2.6.0,2.10,1.5.2,centosTouchstone configurations resulted in FAILURE, so aborting...
Test FAILed.

AmplabJenkins · 2017-02-03T20:07:11Z

Merged build finished. Test FAILed.

AmplabJenkins · 2017-02-03T20:07:11Z

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/gnocchi-prb/5/

Build result: FAILURE

GitHub pull request #12 of commit b96e3c3 automatically merged.[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-06 (centos spark-test) in workspace /home/jenkins/workspace/gnocchi-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/gnocchi.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/gnocchi.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/gnocchi.git +refs/pull/:refs/remotes/origin/pr/ > git rev-parse origin/pr/12/merge^{commit} # timeout=10 > git branch -a --contains 0418a4a4f293318bd01d666b02dee676d31ba410 # timeout=10 > git rev-parse remotes/origin/pr/12/merge^{commit} # timeout=10Checking out Revision 0418a4a4f293318bd01d666b02dee676d31ba410 (origin/pr/12/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 0418a4a4f293318bd01d666b02dee676d31ba410First time build. Skipping changelog.Triggering gnocchi-prb ? 2.6.0,2.11,1.5.2,centosTriggering gnocchi-prb ? 2.6.0,2.10,1.5.2,centosTouchstone configurations resulted in FAILURE, so aborting...
Test FAILed.

AmplabJenkins · 2017-02-03T22:03:21Z

Merged build finished. Test FAILed.

AmplabJenkins · 2017-02-03T22:03:22Z

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/gnocchi-prb/6/

Build result: FAILURE

GitHub pull request #12 of commit a05b85a automatically merged.[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-06 (centos spark-test) in workspace /home/jenkins/workspace/gnocchi-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/gnocchi.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/gnocchi.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/gnocchi.git +refs/pull/:refs/remotes/origin/pr/ > git rev-parse origin/pr/12/merge^{commit} # timeout=10 > git branch -a --contains 0a21ab2 # timeout=10 > git rev-parse remotes/origin/pr/12/merge^{commit} # timeout=10Checking out Revision 0a21ab2 (origin/pr/12/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 0a21ab2583bad20ad00f6a7da657cf0e4d4c33b5First time build. Skipping changelog.Triggering gnocchi-prb ? 2.6.0,2.11,1.5.2,centosTriggering gnocchi-prb ? 2.6.0,2.10,1.5.2,centosTouchstone configurations resulted in FAILURE, so aborting...
Test FAILed.

AmplabJenkins · 2017-03-01T00:50:28Z

Merged build finished. Test FAILed.

AmplabJenkins · 2017-03-01T00:50:28Z

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/gnocchi-prb/7/

Build result: FAILURE

[...truncated 8 lines...] > git fetch --tags --progress https://github.com/bigdatagenomics/gnocchi.git +refs/pull/:refs/remotes/origin/pr/ > git rev-parse origin/pr/12/merge^{commit} # timeout=10 > git branch -a --contains f6408f09807326466868dc15ec0c0ad0561bf7d7 # timeout=10 > git rev-parse remotes/origin/pr/12/merge^{commit} # timeout=10Checking out Revision f6408f09807326466868dc15ec0c0ad0561bf7d7 (origin/pr/12/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f f6408f09807326466868dc15ec0c0ad0561bf7d7First time build. Skipping changelog.Triggering gnocchi-prb ? 2.6.0,2.11,1.6.1,centosTriggering gnocchi-prb ? 2.3.0,2.11,1.6.1,centosTriggering gnocchi-prb ? 2.3.0,2.11,2.0.0,centosTriggering gnocchi-prb ? 2.3.0,2.10,1.6.1,centosTriggering gnocchi-prb ? 2.6.0,2.10,2.0.0,centosTriggering gnocchi-prb ? 2.6.0,2.11,2.0.0,centosTriggering gnocchi-prb ? 2.6.0,2.10,1.6.1,centosTriggering gnocchi-prb ? 2.3.0,2.10,2.0.0,centosgnocchi-prb ? 2.6.0,2.11,1.6.1,centos completed with result FAILUREgnocchi-prb ? 2.3.0,2.11,1.6.1,centos completed with result FAILUREgnocchi-prb ? 2.3.0,2.11,2.0.0,centos completed with result FAILUREgnocchi-prb ? 2.3.0,2.10,1.6.1,centos completed with result FAILUREgnocchi-prb ? 2.6.0,2.10,2.0.0,centos completed with result FAILUREgnocchi-prb ? 2.6.0,2.11,2.0.0,centos completed with result FAILUREgnocchi-prb ? 2.6.0,2.10,1.6.1,centos completed with result FAILUREgnocchi-prb ? 2.3.0,2.10,2.0.0,centos completed with result FAILURE
Test FAILed.

coveralls · 2017-03-01T01:38:00Z

Changes Unknown when pulling 2451ba2 on fnothaft:issues/10-add-ci into ** on bigdatagenomics:master**.

AmplabJenkins · 2017-03-01T01:38:14Z

Merged build finished. Test FAILed.

AmplabJenkins · 2017-03-01T01:38:14Z

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/gnocchi-prb/8/

Build result: FAILURE

[...truncated 8 lines...] > git fetch --tags --progress https://github.com/bigdatagenomics/gnocchi.git +refs/pull/:refs/remotes/origin/pr/ > git rev-parse origin/pr/12/merge^{commit} # timeout=10 > git branch -a --contains 529ea812d26e613b4292e3186abf8a2b8157bf8d # timeout=10 > git rev-parse remotes/origin/pr/12/merge^{commit} # timeout=10Checking out Revision 529ea812d26e613b4292e3186abf8a2b8157bf8d (origin/pr/12/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 529ea812d26e613b4292e3186abf8a2b8157bf8dFirst time build. Skipping changelog.Triggering gnocchi-prb ? 2.6.0,2.11,1.6.1,centosTriggering gnocchi-prb ? 2.3.0,2.11,1.6.1,centosTriggering gnocchi-prb ? 2.3.0,2.11,2.0.0,centosTriggering gnocchi-prb ? 2.3.0,2.10,1.6.1,centosTriggering gnocchi-prb ? 2.6.0,2.10,2.0.0,centosTriggering gnocchi-prb ? 2.6.0,2.11,2.0.0,centosTriggering gnocchi-prb ? 2.6.0,2.10,1.6.1,centosTriggering gnocchi-prb ? 2.3.0,2.10,2.0.0,centosgnocchi-prb ? 2.6.0,2.11,1.6.1,centos completed with result FAILUREgnocchi-prb ? 2.3.0,2.11,1.6.1,centos completed with result FAILUREgnocchi-prb ? 2.3.0,2.11,2.0.0,centos completed with result FAILUREgnocchi-prb ? 2.3.0,2.10,1.6.1,centos completed with result SUCCESSgnocchi-prb ? 2.6.0,2.10,2.0.0,centos completed with result FAILUREgnocchi-prb ? 2.6.0,2.11,2.0.0,centos completed with result FAILUREgnocchi-prb ? 2.6.0,2.10,1.6.1,centos completed with result SUCCESSgnocchi-prb ? 2.3.0,2.10,2.0.0,centos completed with result FAILURE
Test FAILed.

fnothaft · 2017-03-01T02:42:09Z

Am I reading it right that we are still on ADAM 0.19.0? That release is over a year old.

coveralls · 2017-03-01T02:48:25Z

Changes Unknown when pulling 7111420 on fnothaft:issues/10-add-ci into ** on bigdatagenomics:master**.

coveralls · 2017-03-01T02:48:25Z

Changes Unknown when pulling 7111420 on fnothaft:issues/10-add-ci into ** on bigdatagenomics:master**.

AmplabJenkins · 2017-03-01T02:49:32Z

Merged build finished. Test PASSed.

AmplabJenkins · 2017-03-01T02:49:33Z

Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/gnocchi-prb/9/
Test PASSed.

heuermh · 2017-03-01T03:00:27Z

gnocchi-core/src/main/scala/net/fnothaft/gnocchi/association/LoadPhenotypes.scala

+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */


I believe the copyright statement below also needs to go

heuermh · 2017-03-01T03:01:07Z

gnocchi-core/src/main/scala/net/fnothaft/gnocchi/pmml/GnocchiPMMLExportable.scala

+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */


...and here

heuermh · 2017-03-01T03:01:33Z

gnocchi-core/src/main/scala/net/fnothaft/gnocchi/transformations/Gs2variant.scala

+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */

 /**


...and here

heuermh · 2017-03-01T03:07:45Z

With ADAM 0.19.0 the Spark 2.x build will most likely fail at runtime due to the Logging breaking change. Do you want to do that and a version bump for other dependencies (utils, parquet, avro, hadoop, scala, etc.) in this pull request or a separate one?

akmorrow13 · 2017-03-01T03:19:36Z

tkdagdelen/gnocchi_old#36 has George's updates for spark and stuff

fnothaft · 2017-03-01T06:44:02Z

With ADAM 0.19.0 the Spark 2.x build will most likely fail at runtime due to the Logging breaking change. Do you want to do that and a version bump for other dependencies (utils, parquet, avro, hadoop, scala, etc.) in this pull request or a separate one?

We didn't support 2.x in ADAM 0.19.0, so I've disabled that for now. We can probably plan to pull in the patch that @akmorrow13 pointed to.

fnothaft · 2017-03-01T06:48:43Z

Cleaned up the headers. Will squash this on passing tests.

coveralls · 2017-03-01T06:52:48Z

Changes Unknown when pulling b2f5349 on fnothaft:issues/10-add-ci into ** on bigdatagenomics:master**.

AmplabJenkins · 2017-03-01T06:54:03Z

Merged build finished. Test PASSed.

AmplabJenkins · 2017-03-01T06:54:04Z

Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/gnocchi-prb/10/
Test PASSed.

Resolves bigdatagenomics#10: * Run scalariform and fix license headers. * Deleting Gnocchi-test submodule. * Add coverage profile with support for pushing to coveralls. * Misc. pom.xml cleanup. * Scala 2.11 cannot have case classes without (). * Remove commented files.

coveralls · 2017-03-01T07:02:33Z

Changes Unknown when pulling eed5afc on fnothaft:issues/10-add-ci into ** on bigdatagenomics:master**.

AmplabJenkins · 2017-03-01T07:03:14Z

Merged build finished. Test PASSed.

AmplabJenkins · 2017-03-01T07:03:14Z

Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/gnocchi-prb/11/
Test PASSed.

heuermh · 2017-03-01T13:11:36Z

Thank you, @fnothaft!

* v1 * resolved import issues, fixed JavaGnocchiSession, corrected BetterPhenotype

…omics#32) * Added python binding boilerplate * more boilerplate for bindings * adding todo file for java wrapper * laying out more skeleton code * Implemented gnocchiSession python object * Working on Java Wrapper for Bindings adgirish: * adding todo file for java wrapper * laying out more skeleton code * added empty interfaces * todo add method comments * added empty interfaces * todo add method comments * Bindings (#7) * adding todo file for java wrapper * laying out more skeleton code * added empty interfaces * todo add method comments * added empty interfaces * todo add method comments * added pom.xml * Fix Project Modules and pom files * adding todo file for java wrapper * laying out more skeleton code * added empty interfaces * todo add method comments * added empty interfaces * todo add method comments * added pom.xml * changing reference in pom.xml * changing reference in pom.xml v2 * added python pointer wrappers * Created and Modified pom files * Updated JavaGnocchiSession and Refactor * make file for gnocchi-python * Added assembly and packaging * Bindingsv3 (#12) * v1 * resolved import issues, fixed JavaGnocchiSession, corrected BetterPhenotype * Bindingsv3 (#13) * v1 * resolved import issues, fixed JavaGnocchiSession, corrected BetterPhenotype * added test to verify java wrappers * added test to verify java wrappers * resolve conflicts - 2 * remove redundant makefile * updated packing and dependencies * fixes maven build * fixed issues with assembly build * updated load genotypes method * SparkSession Creation fix for compatibility with pySpark (bigdatagenomics#21) * rebasing onto nate's branch and moving remaining packages to org.bdgenomics * resolve dependency issues caused by refactor * Documentation for JVM and Python Gnocchi Session * cleaning unused dependencies * adding JavaGnocchiSession tests (bigdatagenomics#22) * remove unused dependencies * resolved nates comments

fnothaft force-pushed the issues/10-add-ci branch from 50f72f0 to 65d94bc Compare February 3, 2017 16:26

heuermh mentioned this pull request Feb 18, 2017

Instrumentation for RegressPhenotypes #18

Closed

fnothaft force-pushed the issues/10-add-ci branch from a05b85a to f5ee6ba Compare March 1, 2017 00:41

heuermh requested changes Mar 1, 2017

View reviewed changes

fnothaft force-pushed the issues/10-add-ci branch from b2f5349 to eed5afc Compare March 1, 2017 06:57

heuermh approved these changes Mar 1, 2017

View reviewed changes

heuermh merged commit 804a415 into bigdatagenomics:master Mar 1, 2017

This was referenced Mar 1, 2017

Add LICENSE_header.txt and update source file headers #6

Closed

Repository cleanup #5

Closed

adgirish referenced this pull request in adgirish/gnocchi Oct 3, 2017

Bindingsv3 (#12)

f7df635

* v1 * resolved import issues, fixed JavaGnocchiSession, corrected BetterPhenotype

adgirish referenced this pull request in adgirish/gnocchi Oct 6, 2017

Bindingsv3 (#12)

2b486a0

* v1 * resolved import issues, fixed JavaGnocchiSession, corrected BetterPhenotype

adgirish referenced this pull request in adgirish/gnocchi Oct 25, 2017

Bindingsv3 (#12)

6b7f8da

* v1 * resolved import issues, fixed JavaGnocchiSession, corrected BetterPhenotype

Adding CI scripts #12

Adding CI scripts #12

Conversation

fnothaft commented Feb 3, 2017

AmplabJenkins commented Feb 3, 2017

AmplabJenkins commented Feb 3, 2017

Build result: FAILURE

heuermh commented Feb 3, 2017

AmplabJenkins commented Feb 3, 2017

AmplabJenkins commented Feb 3, 2017

Build result: FAILURE

AmplabJenkins commented Feb 3, 2017

AmplabJenkins commented Feb 3, 2017

Build result: FAILURE

AmplabJenkins commented Feb 3, 2017

AmplabJenkins commented Feb 3, 2017

Build result: FAILURE

AmplabJenkins commented Feb 3, 2017

AmplabJenkins commented Feb 3, 2017

Build result: FAILURE

AmplabJenkins commented Feb 3, 2017

AmplabJenkins commented Feb 3, 2017

Build result: FAILURE

AmplabJenkins commented Mar 1, 2017

AmplabJenkins commented Mar 1, 2017

Build result: FAILURE

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AmplabJenkins commented Mar 1, 2017

Build result: FAILURE

fnothaft commented Mar 1, 2017

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