-
Notifications
You must be signed in to change notification settings - Fork 10
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Adding CI scripts #12
Conversation
Merged build finished. Test FAILed. |
Test FAILed. Build result: FAILUREGitHub 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. |
Also fixes #6, thank you! |
Merged build finished. Test FAILed. |
Test FAILed. Build result: FAILUREGitHub 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. |
50f72f0
to
65d94bc
Compare
Merged build finished. Test FAILed. |
Test FAILed. Build result: FAILUREGitHub 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. |
Merged build finished. Test FAILed. |
Test FAILed. Build result: FAILUREGitHub 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. |
Merged build finished. Test FAILed. |
Test FAILed. Build result: FAILUREGitHub 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. |
Merged build finished. Test FAILed. |
Test FAILed. Build result: FAILUREGitHub 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. |
a05b85a
to
f5ee6ba
Compare
Merged build finished. Test FAILed. |
Test FAILed. 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 FAILURETest FAILed. |
Changes Unknown when pulling 2451ba2 on fnothaft:issues/10-add-ci into ** on bigdatagenomics:master**. |
Merged build finished. Test FAILed. |
Test FAILed. 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 FAILURETest FAILed. |
Am I reading it right that we are still on ADAM 0.19.0? That release is over a year old. |
Changes Unknown when pulling 7111420 on fnothaft:issues/10-add-ci into ** on bigdatagenomics:master**. |
1 similar comment
Changes Unknown when pulling 7111420 on fnothaft:issues/10-add-ci into ** on bigdatagenomics:master**. |
Merged build finished. Test PASSed. |
Test PASSed. |
* 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. | ||
*/ |
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
I believe the copyright statement below also needs to go
* 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. | ||
*/ |
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
...and here
* 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. | ||
*/ | ||
|
||
/** |
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
...and here
With ADAM 0.19.0 the Spark 2.x build will most likely fail at runtime due to the |
tkdagdelen/gnocchi_old#36 has George's updates for spark and stuff |
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. |
Cleaned up the headers. Will squash this on passing tests. |
Changes Unknown when pulling b2f5349 on fnothaft:issues/10-add-ci into ** on bigdatagenomics:master**. |
Merged build finished. Test PASSed. |
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.
b2f5349
to
eed5afc
Compare
Changes Unknown when pulling eed5afc on fnothaft:issues/10-add-ci into ** on bigdatagenomics:master**. |
Merged build finished. Test PASSed. |
Test PASSed. |
Thank you, @fnothaft! |
* v1 * resolved import issues, fixed JavaGnocchiSession, corrected BetterPhenotype
* v1 * resolved import issues, fixed JavaGnocchiSession, corrected BetterPhenotype
* 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
Resolves #10. Don't merge until @AmplabJenkins runs and passes.