require kryo registration in tests

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1180/Build result: FAILUREGitHub pull request #1020 of commit be48ef698313f66741997362a4121bb45caf56d4 automatically merged.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos spark-test) 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/1020/merge^{commit} # timeout=10 > git branch -a --contains 800261e6bc1cccf11b4eb5690bd08352e3c09dc9 # timeout=10 > git rev-parse remotes/origin/pr/1020/merge^{commit} # timeout=10Checking out Revision 800261e6bc1cccf11b4eb5690bd08352e3c09dc9 (origin/pr/1020/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 800261e6bc1cccf11b4eb5690bd08352e3c09dc9First time build. Skipping changelog.Triggering ADAM-prb ? 2.6.0,2.10,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.11,1.5.2,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

jenkins, retest this please

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1182/Build result: FAILUREGitHub pull request #1020 of commit 9f102aa09cfa638f80c2f469d19b00e1c898d5c9 automatically merged.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos spark-test) 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/1020/merge^{commit} # timeout=10 > git branch -a --contains 394bc9ca51e1b910613e4e88680b6e9ae1cbe58b # timeout=10 > git rev-parse remotes/origin/pr/1020/merge^{commit} # timeout=10Checking out Revision 394bc9ca51e1b910613e4e88680b6e9ae1cbe58b (origin/pr/1020/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 394bc9ca51e1b910613e4e88680b6e9ae1cbe58bFirst time build. Skipping changelog.Triggering ADAM-prb ? 2.6.0,2.10,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.11,1.5.2,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1183/Build result: FAILUREGitHub pull request #1020 of commit 4047c3b3056c3f984a1fe868906edf2daac0e7b5 automatically merged.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos spark-test) 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/1020/merge^{commit} # timeout=10 > git branch -a --contains 394bc9ca51e1b910613e4e88680b6e9ae1cbe58b # timeout=10 > git rev-parse remotes/origin/pr/1020/merge^{commit} # timeout=10Checking out Revision 394bc9ca51e1b910613e4e88680b6e9ae1cbe58b (origin/pr/1020/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 394bc9ca51e1b910613e4e88680b6e9ae1cbe58bFirst time build. Skipping changelog.Triggering ADAM-prb ? 2.6.0,2.10,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.11,1.5.2,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1184/Build result: FAILUREGitHub pull request #1020 of commit 76a0fc55c91918f4d1d52af0f34433ff8d90c9ea automatically merged.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos spark-test) 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/1020/merge^{commit} # timeout=10 > git branch -a --contains 394bc9ca51e1b910613e4e88680b6e9ae1cbe58b # timeout=10 > git rev-parse remotes/origin/pr/1020/merge^{commit} # timeout=10Checking out Revision 394bc9ca51e1b910613e4e88680b6e9ae1cbe58b (origin/pr/1020/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 394bc9ca51e1b910613e4e88680b6e9ae1cbe58bFirst time build. Skipping changelog.Triggering ADAM-prb ? 2.6.0,2.10,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.11,1.5.2,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1186/Build result: FAILUREGitHub pull request #1020 of commit c24aae5619621fe18acc46e7a870301f94e130e9 automatically merged.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos spark-test) 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/1020/merge^{commit} # timeout=10 > git branch -a --contains c637cf7fe857fdd53e6c25513cb059723e4e7c11 # timeout=10 > git rev-parse remotes/origin/pr/1020/merge^{commit} # timeout=10Checking out Revision c637cf7fe857fdd53e6c25513cb059723e4e7c11 (origin/pr/1020/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f c637cf7fe857fdd53e6c25513cb059723e4e7c11 > git rev-list 394bc9ca51e1b910613e4e88680b6e9ae1cbe58b # timeout=10Triggering ADAM-prb ? 2.6.0,2.10,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.11,1.5.2,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

Jenkins, retest this please

Last build failure mentions c24aae5619621fe18acc46e7a870301f94e130e9 but seems to check out and test 394bc9ca51e1b910613e4e88680b6e9ae1cbe58b, which I can't even find in my local checkout of ADAM, so I'm not sure what happened there but am hoping a retest will pick up my HEAD commit here, https://github.com/bigdatagenomics/adam/pull/1020/commits/c24aae5619621fe18acc46e7a870301f94e130e9

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1188/Build result: FAILUREGitHub pull request #1020 of commit c24aae5619621fe18acc46e7a870301f94e130e9 automatically merged.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos spark-test) 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/1020/merge^{commit} # timeout=10 > git branch -a --contains c637cf7fe857fdd53e6c25513cb059723e4e7c11 # timeout=10 > git rev-parse remotes/origin/pr/1020/merge^{commit} # timeout=10Checking out Revision c637cf7fe857fdd53e6c25513cb059723e4e7c11 (origin/pr/1020/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f c637cf7fe857fdd53e6c25513cb059723e4e7c11 > git rev-list c637cf7fe857fdd53e6c25513cb059723e4e7c11 # timeout=10Triggering ADAM-prb ? 2.6.0,2.10,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.11,1.5.2,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

OK, that picked up my last commit, and apparently there's more that I need to register.
What I don't understand is that only two builds in the matrix have been failing this whole time, and I can't reproduce those failures locally.
Jenkins runs:
mvn clean package -Dhadoop.version=2.6.0 -Dspark.version=1.5.2

and the FlattenSuite in adam-cli fails.
When I run locally:
mvn clean test -Dsuites='*FlattenSuite*' -pl adam-cli -Dhadoop.version=2.6.0 -Dspark.version=1.5.2

the test passes.
Also only the Spark 1.5.2, Hadoop 2.6.0 builds fail.

Also only the Spark 1.5.2, Hadoop 2.6.0 builds fail.

We only run all of the other build configurations if the Spark 1.5.2/Hadoop 2.6.0 builds pass. If they fail, we don't run the other builds.

What I don't understand is that only two builds in the matrix have been failing this whole time

They are set to be the default build configuration, in that if they fail, the rest are not run.  Unfortunately the Jenkins matrix chart shows green for the rest of the build configurations, even though those were not run.
$ HADOOP_VERSION=2.6.0 SPARK_VERSION=1.5.2 ./scripts/jenkins-test

should replicate what you see in Jenkins.

Test FAILed.
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https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1189/Build result: FAILUREGitHub pull request #1020 of commit b527f1887de27b66dc17df5c0ab02def84f71a15 automatically merged.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos spark-test) 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/1020/merge^{commit} # timeout=10 > git branch -a --contains 2ba4ee6518f25684e384bb40f90a9ade10f83eec # timeout=10 > git rev-parse remotes/origin/pr/1020/merge^{commit} # timeout=10Checking out Revision 2ba4ee6518f25684e384bb40f90a9ade10f83eec (origin/pr/1020/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 2ba4ee6518f25684e384bb40f90a9ade10f83eec > git rev-list c637cf7fe857fdd53e6c25513cb059723e4e7c11 # timeout=10Triggering ADAM-prb ? 2.6.0,2.10,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.11,1.5.2,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

Thanks for the info about the 1.5.2/2.6.0 builds!

[EnvInject] - Loading node environment variables.
Building remotely on amp-jenkins-worker-04 (centos spark-test) in workspace /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.5.2/label/centos
 > git rev-parse --is-inside-work-tree # timeout=10
Fetching changes from the remote Git repository
 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10
Fetching 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/*
Checking out Revision c637cf7fe857fdd53e6c25513cb059723e4e7c11 (origin/pr/1020/merge)
 > git config core.sparsecheckout # timeout=10
 > git checkout -f c637cf7fe857fdd53e6c25513cb059723e4e7c11

It prints b527f1887de27b66dc17df5c0ab02def84f71a15 at first, but then checks out c637cf7fe857fdd53e6c25513cb059723e4e7c11, which again I can't find anywhere.

Jenkins, retest this please.

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1190/Build result: FAILUREGitHub pull request #1020 of commit b527f1887de27b66dc17df5c0ab02def84f71a15 automatically merged.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos spark-test) 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/1020/merge^{commit} # timeout=10 > git branch -a --contains 2ba4ee6518f25684e384bb40f90a9ade10f83eec # timeout=10 > git rev-parse remotes/origin/pr/1020/merge^{commit} # timeout=10Checking out Revision 2ba4ee6518f25684e384bb40f90a9ade10f83eec (origin/pr/1020/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 2ba4ee6518f25684e384bb40f90a9ade10f83eec > git rev-list 2ba4ee6518f25684e384bb40f90a9ade10f83eec # timeout=10Triggering ADAM-prb ? 2.6.0,2.10,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.11,1.5.2,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

I ran
HADOOP_VERSION=2.6.0 SPARK_VERSION=1.5.2 ./scripts/jenkins-test

and the failing test here (FlattenSuite) passed; still failing via Jenkins 😢

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1191/Build result: FAILUREGitHub pull request #1020 of commit fc60199492ebebd9e944295d82d811495b12371d automatically merged.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos spark-test) 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/1020/merge^{commit} # timeout=10 > git branch -a --contains 681e81a9c0bdc56f36ee4186e5ea09f86579d7cb # timeout=10 > git rev-parse remotes/origin/pr/1020/merge^{commit} # timeout=10Checking out Revision 681e81a9c0bdc56f36ee4186e5ea09f86579d7cb (origin/pr/1020/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 681e81a9c0bdc56f36ee4186e5ea09f86579d7cb > git rev-list 2ba4ee6518f25684e384bb40f90a9ade10f83eec # timeout=10Triggering ADAM-prb ? 2.6.0,2.10,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.11,1.5.2,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

Jenkins, retest this please.

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1192/Build result: FAILUREGitHub pull request #1020 of commit fc60199492ebebd9e944295d82d811495b12371d automatically merged.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos spark-test) 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/1020/merge^{commit} # timeout=10 > git branch -a --contains 681e81a9c0bdc56f36ee4186e5ea09f86579d7cb # timeout=10 > git rev-parse remotes/origin/pr/1020/merge^{commit} # timeout=10Checking out Revision 681e81a9c0bdc56f36ee4186e5ea09f86579d7cb (origin/pr/1020/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 681e81a9c0bdc56f36ee4186e5ea09f86579d7cb > git rev-list 681e81a9c0bdc56f36ee4186e5ea09f86579d7cb # timeout=10Triggering ADAM-prb ? 2.6.0,2.10,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.11,1.5.2,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1193/Build result: FAILUREGitHub pull request #1020 of commit 2ef52bb9f20975ebd53f43a4c0e68c784a1057b1 automatically merged.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos spark-test) 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/1020/merge^{commit} # timeout=10 > git branch -a --contains 9ab067f0c397f03cf2b792e1ccc7951dee35dea2 # timeout=10 > git rev-parse remotes/origin/pr/1020/merge^{commit} # timeout=10Checking out Revision 9ab067f0c397f03cf2b792e1ccc7951dee35dea2 (origin/pr/1020/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 9ab067f0c397f03cf2b792e1ccc7951dee35dea2 > git rev-list 681e81a9c0bdc56f36ee4186e5ea09f86579d7cb # timeout=10Triggering ADAM-prb ? 2.6.0,2.10,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.11,1.5.2,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

This looks like the usual "commit not found" issue that happens after a force-push; however, I specifically didn't force-push the commit that triggered this build, to try to see if that simplified my iterations here. ❓
Jenkins, retest this please.

Jenkins, retest this please.

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1194/Build result: FAILUREGitHub pull request #1020 of commit 2ef52bb9f20975ebd53f43a4c0e68c784a1057b1 automatically merged.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos spark-test) 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/1020/merge^{commit} # timeout=10 > git branch -a --contains 9ab067f0c397f03cf2b792e1ccc7951dee35dea2 # timeout=10 > git rev-parse remotes/origin/pr/1020/merge^{commit} # timeout=10Checking out Revision 9ab067f0c397f03cf2b792e1ccc7951dee35dea2 (origin/pr/1020/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 9ab067f0c397f03cf2b792e1ccc7951dee35dea2 > git rev-list 9ab067f0c397f03cf2b792e1ccc7951dee35dea2 # timeout=10Triggering ADAM-prb ? 2.6.0,2.10,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.11,1.5.2,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1195/Build result: FAILUREGitHub pull request #1020 of commit 92c87a766e9d5e76a376b8675c3a2a2b1f1c726b automatically merged.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos spark-test) 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/1020/merge^{commit} # timeout=10 > git branch -a --contains 22c9b054830cabe68dc80f6dfda686b08dedc7ef # timeout=10 > git rev-parse remotes/origin/pr/1020/merge^{commit} # timeout=10Checking out Revision 22c9b054830cabe68dc80f6dfda686b08dedc7ef (origin/pr/1020/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 22c9b054830cabe68dc80f6dfda686b08dedc7ef > git rev-list 9ab067f0c397f03cf2b792e1ccc7951dee35dea2 # timeout=10Triggering ADAM-prb ? 2.6.0,2.10,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.11,1.5.2,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

Jenkins, retest this please.

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1196/Build result: FAILUREGitHub pull request #1020 of commit 92c87a766e9d5e76a376b8675c3a2a2b1f1c726b automatically merged.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos spark-test) 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/1020/merge^{commit} # timeout=10 > git branch -a --contains 22c9b054830cabe68dc80f6dfda686b08dedc7ef # timeout=10 > git rev-parse remotes/origin/pr/1020/merge^{commit} # timeout=10Checking out Revision 22c9b054830cabe68dc80f6dfda686b08dedc7ef (origin/pr/1020/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 22c9b054830cabe68dc80f6dfda686b08dedc7ef > git rev-list 22c9b054830cabe68dc80f6dfda686b08dedc7ef # timeout=10Triggering ADAM-prb ? 2.6.0,2.10,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.11,1.5.2,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

@fnothaft @massie @shaneknapp It is possible there is something else at play here?  I had a similar amount of trouble with Jenkins builds on #979.  I don't think it is right to force dealing with all these failed builds on external collaborators.  Not everyone has as much patience as @ryan-williams (and thank you for it!).
What do folks think about dropping Jenkins for pull request builds and using Travis instead?

Test FAILed.
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https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1197/Build result: FAILUREGitHub pull request #1020 of commit 34932cdc7044648cb6e54ed84d7a544c0ef5ed3f automatically merged.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos spark-test) 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/1020/merge^{commit} # timeout=10 > git branch -a --contains af7a4f98ddcb4aa2035464dada0c214580c18ee6 # timeout=10 > git rev-parse remotes/origin/pr/1020/merge^{commit} # timeout=10Checking out Revision af7a4f98ddcb4aa2035464dada0c214580c18ee6 (origin/pr/1020/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f af7a4f98ddcb4aa2035464dada0c214580c18ee6 > git rev-list 22c9b054830cabe68dc80f6dfda686b08dedc7ef # timeout=10Triggering ADAM-prb ? 2.6.0,2.10,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.11,1.5.2,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

TBH, without any real background in this right now, i'd be really hesitant to ditch jenkins for an entirely new build system setup.  i'll talk to @fnothaft right now and get his input/feelings.

Jenkins, retest this please.

Test FAILed.
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https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1198/Build result: FAILUREGitHub pull request #1020 of commit 34932cdc7044648cb6e54ed84d7a544c0ef5ed3f automatically merged.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos spark-test) 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/1020/merge^{commit} # timeout=10 > git branch -a --contains af7a4f98ddcb4aa2035464dada0c214580c18ee6 # timeout=10 > git rev-parse remotes/origin/pr/1020/merge^{commit} # timeout=10Checking out Revision af7a4f98ddcb4aa2035464dada0c214580c18ee6 (origin/pr/1020/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f af7a4f98ddcb4aa2035464dada0c214580c18ee6 > git rev-list af7a4f98ddcb4aa2035464dada0c214580c18ee6 # timeout=10Triggering ADAM-prb ? 2.6.0,2.10,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.11,1.5.2,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

@heuermh While there are known issues with Jenkins' git support and force pushes, we don't have the build engineering bandwidth to move this build to another system while still supporting all other builds on Jenkins. I haven't been following this pull request in any detail so I can't comment as to whether the build issues are Jenkins related or not other than the Jenkins picking the wrong git commit, which as mentioned, is a known issue.

One thing that seems to be happening here that I've not previously observed is Jenkins not finding commits even without me force-pushing.
Since https://github.com/bigdatagenomics/adam/pull/1020/commits/fc60199492ebebd9e944295d82d811495b12371d, I've not force-pushed any commits, and at each regularly-pushed commit since, there's been a failed Jenkins run that only picked up the commit on a retest:

https://github.com/bigdatagenomics/adam/pull/1020/commits/2ef52bb9f20975ebd53f43a4c0e68c784a1057b1

1193: "Could not checkout".
1194: retest picked up commit.

https://github.com/bigdatagenomics/adam/pull/1020/commits/92c87a766e9d5e76a376b8675c3a2a2b1f1c726b

1195: "Could not checkout".
1196: retest picked up commit.

https://github.com/bigdatagenomics/adam/pull/1020/commits/34932cdc7044648cb6e54ed84d7a544c0ef5ed3f

1197: started to run, but the test failure observed implies that https://github.com/bigdatagenomics/adam/pull/1020/commits/34932cdc7044648cb6e54ed84d7a544c0ef5ed3f was not included:
Note: To register this class use: kryo.register(org.apache.avro.Schema$LockableArrayList.class);

1198: retest picked up https://github.com/bigdatagenomics/adam/pull/1020/commits/34932cdc7044648cb6e54ed84d7a544c0ef5ed3f and showed a different test failure (which is what 1197 should have done).

Test FAILed.
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https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1199/Build result: FAILUREGitHub pull request #1020 of commit edd2152b8a803fc85b98809a9d8327cfdb181a06 automatically merged.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos spark-test) 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/1020/merge^{commit} # timeout=10 > git branch -a --contains 706ba1ef86c8817f4641f2b71363cf8ebc9c1ed6 # timeout=10 > git rev-parse remotes/origin/pr/1020/merge^{commit} # timeout=10Checking out Revision 706ba1ef86c8817f4641f2b71363cf8ebc9c1ed6 (origin/pr/1020/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 706ba1ef86c8817f4641f2b71363cf8ebc9c1ed6 > git rev-list af7a4f98ddcb4aa2035464dada0c214580c18ee6 # timeout=10Triggering ADAM-prb ? 2.6.0,2.10,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.11,1.5.2,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

Jenkins, retest this please.

Seeing the same thing again: 1199 couldn't find the commit https://github.com/bigdatagenomics/adam/pull/1020/commits/edd2152b8a803fc85b98809a9d8327cfdb181a06 even though it was not force-pushed.
Has this behavior been observed to happen on PRs that have ever involved force-pushed commits?

Test FAILed.
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https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1200/Build result: FAILUREGitHub pull request #1020 of commit edd2152b8a803fc85b98809a9d8327cfdb181a06 automatically merged.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos spark-test) 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/1020/merge^{commit} # timeout=10 > git branch -a --contains 706ba1ef86c8817f4641f2b71363cf8ebc9c1ed6 # timeout=10 > git rev-parse remotes/origin/pr/1020/merge^{commit} # timeout=10Checking out Revision 706ba1ef86c8817f4641f2b71363cf8ebc9c1ed6 (origin/pr/1020/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 706ba1ef86c8817f4641f2b71363cf8ebc9c1ed6 > git rev-list 706ba1ef86c8817f4641f2b71363cf8ebc9c1ed6 # timeout=10Triggering ADAM-prb ? 2.6.0,2.10,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.11,1.5.2,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

Test FAILed.
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https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1201/Build result: FAILUREGitHub pull request #1020 of commit 04d9d2b00e2cc7f3fe4980f816fc225cdb33507d automatically merged.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos spark-test) 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/1020/merge^{commit} # timeout=10 > git branch -a --contains 6b8e2a960140ebb96499ce16f06a3a454bef1907 # timeout=10 > git rev-parse remotes/origin/pr/1020/merge^{commit} # timeout=10Checking out Revision 6b8e2a960140ebb96499ce16f06a3a454bef1907 (origin/pr/1020/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 6b8e2a960140ebb96499ce16f06a3a454bef1907 > git rev-list 706ba1ef86c8817f4641f2b71363cf8ebc9c1ed6 # timeout=10Triggering ADAM-prb ? 2.6.0,2.10,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.11,1.5.2,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

Jenkins, retest this please.

Test FAILed.
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https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1202/Build result: FAILUREGitHub pull request #1020 of commit 04d9d2b00e2cc7f3fe4980f816fc225cdb33507d automatically merged.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos spark-test) 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/1020/merge^{commit} # timeout=10 > git branch -a --contains 6b8e2a960140ebb96499ce16f06a3a454bef1907 # timeout=10 > git rev-parse remotes/origin/pr/1020/merge^{commit} # timeout=10Checking out Revision 6b8e2a960140ebb96499ce16f06a3a454bef1907 (origin/pr/1020/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 6b8e2a960140ebb96499ce16f06a3a454bef1907 > git rev-list 6b8e2a960140ebb96499ce16f06a3a454bef1907 # timeout=10Triggering ADAM-prb ? 2.6.0,2.10,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.11,1.5.2,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

Test FAILed.
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https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1203/Build result: FAILUREGitHub pull request #1020 of commit d404e267ce4a6df62250e4acea79c2ac3b3ebdd4 automatically merged.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos spark-test) 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/1020/merge^{commit} # timeout=10 > git branch -a --contains bf70d27c0fa33f11a3c84176e3124ddc39983fa5 # timeout=10 > git rev-parse remotes/origin/pr/1020/merge^{commit} # timeout=10Checking out Revision bf70d27c0fa33f11a3c84176e3124ddc39983fa5 (origin/pr/1020/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f bf70d27c0fa33f11a3c84176e3124ddc39983fa5 > git rev-list 6b8e2a960140ebb96499ce16f06a3a454bef1907 # timeout=10Triggering ADAM-prb ? 2.6.0,2.10,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.11,1.5.2,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

Jenkins, retest this please.

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1204/Build result: FAILUREGitHub pull request #1020 of commit d404e267ce4a6df62250e4acea79c2ac3b3ebdd4 automatically merged.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos spark-test) 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/1020/merge^{commit} # timeout=10 > git branch -a --contains bf70d27c0fa33f11a3c84176e3124ddc39983fa5 # timeout=10 > git rev-parse remotes/origin/pr/1020/merge^{commit} # timeout=10Checking out Revision bf70d27c0fa33f11a3c84176e3124ddc39983fa5 (origin/pr/1020/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f bf70d27c0fa33f11a3c84176e3124ddc39983fa5 > git rev-list bf70d27c0fa33f11a3c84176e3124ddc39983fa5 # timeout=10Triggering ADAM-prb ? 2.6.0,2.10,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.11,1.5.2,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1205/Build result: FAILUREGitHub pull request #1020 of commit 8ec3eb793afbaa82a15be076b6c917e5dd4a8461 automatically merged.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos spark-test) 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/1020/merge^{commit} # timeout=10 > git branch -a --contains 978da84e81b21363b798ff532ee1751504d76600 # timeout=10 > git rev-parse remotes/origin/pr/1020/merge^{commit} # timeout=10Checking out Revision 978da84e81b21363b798ff532ee1751504d76600 (origin/pr/1020/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 978da84e81b21363b798ff532ee1751504d76600 > git rev-list bf70d27c0fa33f11a3c84176e3124ddc39983fa5 # timeout=10Triggering ADAM-prb ? 2.6.0,2.10,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.11,1.5.2,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

Jenkins, retest this please.

Test FAILed.
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https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1206/Build result: FAILUREGitHub pull request #1020 of commit 8ec3eb793afbaa82a15be076b6c917e5dd4a8461 automatically merged.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos spark-test) 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/1020/merge^{commit} # timeout=10 > git branch -a --contains 978da84e81b21363b798ff532ee1751504d76600 # timeout=10 > git rev-parse remotes/origin/pr/1020/merge^{commit} # timeout=10Checking out Revision 978da84e81b21363b798ff532ee1751504d76600 (origin/pr/1020/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 978da84e81b21363b798ff532ee1751504d76600 > git rev-list 978da84e81b21363b798ff532ee1751504d76600 # timeout=10Triggering ADAM-prb ? 2.6.0,2.10,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.11,1.5.2,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1207/Build result: FAILUREGitHub pull request #1020 of commit 4748c7a0272b180e045f7fd09d4e8ce9fe7fa929 automatically merged.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos spark-test) 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/1020/merge^{commit} # timeout=10 > git branch -a --contains 811b98531a7d43ea500aef82f42139206bde4fa0 # timeout=10 > git rev-parse remotes/origin/pr/1020/merge^{commit} # timeout=10Checking out Revision 811b98531a7d43ea500aef82f42139206bde4fa0 (origin/pr/1020/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 811b98531a7d43ea500aef82f42139206bde4fa0 > git rev-list 978da84e81b21363b798ff532ee1751504d76600 # timeout=10Triggering ADAM-prb ? 2.6.0,2.10,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.11,1.5.2,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

Jenkins, retest this please.

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1208/Build result: FAILUREGitHub pull request #1020 of commit 4748c7a0272b180e045f7fd09d4e8ce9fe7fa929 automatically merged.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos spark-test) 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/1020/merge^{commit} # timeout=10 > git branch -a --contains 811b98531a7d43ea500aef82f42139206bde4fa0 # timeout=10 > git rev-parse remotes/origin/pr/1020/merge^{commit} # timeout=10Checking out Revision 811b98531a7d43ea500aef82f42139206bde4fa0 (origin/pr/1020/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 811b98531a7d43ea500aef82f42139206bde4fa0 > git rev-list 811b98531a7d43ea500aef82f42139206bde4fa0 # timeout=10Triggering ADAM-prb ? 2.6.0,2.10,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.11,1.5.2,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1209/Build result: FAILUREGitHub pull request #1020 of commit 96a1787d8212cf7c01f0706f65866cf22e4db99c automatically merged.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos spark-test) 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/1020/merge^{commit} # timeout=10 > git branch -a --contains a2be2b50056b8f2e775c825d06cc1ce6a1b2eae5 # timeout=10 > git rev-parse remotes/origin/pr/1020/merge^{commit} # timeout=10Checking out Revision a2be2b50056b8f2e775c825d06cc1ce6a1b2eae5 (origin/pr/1020/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f a2be2b50056b8f2e775c825d06cc1ce6a1b2eae5 > git rev-list 811b98531a7d43ea500aef82f42139206bde4fa0 # timeout=10Triggering ADAM-prb ? 2.6.0,2.10,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.11,1.5.2,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

Jenkins, retest this please.

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1210/Build result: FAILUREGitHub pull request #1020 of commit 96a1787d8212cf7c01f0706f65866cf22e4db99c automatically merged.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos spark-test) 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/1020/merge^{commit} # timeout=10 > git branch -a --contains a2be2b50056b8f2e775c825d06cc1ce6a1b2eae5 # timeout=10 > git rev-parse remotes/origin/pr/1020/merge^{commit} # timeout=10Checking out Revision a2be2b50056b8f2e775c825d06cc1ce6a1b2eae5 (origin/pr/1020/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f a2be2b50056b8f2e775c825d06cc1ce6a1b2eae5 > git rev-list a2be2b50056b8f2e775c825d06cc1ce6a1b2eae5 # timeout=10Triggering ADAM-prb ? 2.6.0,2.10,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.11,1.5.2,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

the "could not checkout" errors are caused by github not returning a 200 on
the http connection for the fetch.  i have put much investigation in to
this, and have ruled out anything on our end (meaning it's not excess
network traffic, github rate limiting, etc).
usually a retrigger will get the fetch to actually catch, but i will set up
a local git mirror for the repo on all of the workers.  this was affecting
spark builds really badly, and some databricks folks and i hammered out the
setup and it's worked really well for them.
i'll get the local mirrors set up tomorrow.  it won't take long, or
interrupt builds.
shane
On Wed, Apr 27, 2016 at 2:21 PM, Ryan Williams<EMAIL_ADDRESS>wrote:

One thing that seems to be happening here that I've not previously
observed is Jenkins not finding commits even without me force-pushing.
Since fc60199
https://github.com/bigdatagenomics/adam/pull/1020/commits/fc60199492ebebd9e944295d82d811495b12371d,
I've not force-pushed any commits, and at each regularly-pushed commit
since, there's been a failed Jenkins run that only picked up the commit on
a retest:

2ef52bb
https://github.com/bigdatagenomics/adam/pull/1020/commits/2ef52bb9f20975ebd53f43a4c0e68c784a1057b1

1193
https://amplab.cs.berkeley.edu/jenkins/job/ADAM-prb/1193/HADOOP_VERSION=2.6.0,SCALAVER=2.10,SPARK_VERSION=1.5.2,label=centos/console:
"Could not checkout".
1194
https://amplab.cs.berkeley.edu/jenkins/job/ADAM-prb/1194/HADOOP_VERSION=2.6.0,SCALAVER=2.10,SPARK_VERSION=1.5.2,label=centos/console:
retest picked up commit.

92c87a7
https://github.com/bigdatagenomics/adam/pull/1020/commits/92c87a766e9d5e76a376b8675c3a2a2b1f1c726b

1195
https://amplab.cs.berkeley.edu/jenkins/job/ADAM-prb/1195/HADOOP_VERSION=2.6.0,SCALAVER=2.10,SPARK_VERSION=1.5.2,label=centos/console:
"Could not checkout".
1196
https://amplab.cs.berkeley.edu/jenkins/job/ADAM-prb/1196/HADOOP_VERSION=2.6.0,SCALAVER=2.10,SPARK_VERSION=1.5.2,label=centos/console:
retest picked up commit.

34932cd
https://github.com/bigdatagenomics/adam/pull/1020/commits/34932cdc7044648cb6e54ed84d7a544c0ef5ed3f
  1197
  <https://amplab.cs.berkeley.edu/jenkins/job/ADAM-prb/1197/HADOOP_VERSION=2.6.0,SCALAVER=2.10,SPARK_VERSION=1.5.2,label=centos/console>:
  started to run, but the test failure observed implies that 34932cd
  <https://github.com/bigdatagenomics/adam/pull/1020/commits/34932cdc7044648cb6e54ed84d7a544c0ef5ed3f>
  was not included:

  Note: To register this class use: kryo.register(org.apache.avro.Schema$LockableArrayList.class);

  -

  1198
  <https://amplab.cs.berkeley.edu/jenkins/job/ADAM-prb/1198/HADOOP_VERSION=2.6.0,SCALAVER=2.10,SPARK_VERSION=1.5.2,label=centos/console>:
  retest picked up 34932cd
  <https://github.com/bigdatagenomics/adam/pull/1020/commits/34932cdc7044648cb6e54ed84d7a544c0ef5ed3f>
  and showed a different test failure (which is what 1197 should have done).

—
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Reply to this email directly or view it on GitHub
https://github.com/bigdatagenomics/adam/pull/1020#issuecomment-215233256

Thanks @shaneknapp! Weird that Github is reliably returning not-200 for these fetches for non-force-pushed commits…

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1211/Build result: FAILUREGitHub pull request #1020 of commit 5c6339aa933020f521976ae22c427d351cf2f580 automatically merged.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos spark-test) 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/1020/merge^{commit} # timeout=10 > git branch -a --contains ddd44f87a2322e360015ede2439f13a5aeacc546 # timeout=10 > git rev-parse remotes/origin/pr/1020/merge^{commit} # timeout=10Checking out Revision ddd44f87a2322e360015ede2439f13a5aeacc546 (origin/pr/1020/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f ddd44f87a2322e360015ede2439f13a5aeacc546 > git rev-list a2be2b50056b8f2e775c825d06cc1ce6a1b2eae5 # timeout=10Triggering ADAM-prb ? 2.6.0,2.10,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.11,1.5.2,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

i'll get the local mirrors set up tomorrow.  it won't take long, or
interrupt builds.

Awesome! Thanks @shaneknapp!

Jenkins, retest this please.

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1212/Build result: FAILUREGitHub pull request #1020 of commit 5c6339aa933020f521976ae22c427d351cf2f580 automatically merged.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos spark-test) 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/1020/merge^{commit} # timeout=10 > git branch -a --contains ddd44f87a2322e360015ede2439f13a5aeacc546 # timeout=10 > git rev-parse remotes/origin/pr/1020/merge^{commit} # timeout=10Checking out Revision ddd44f87a2322e360015ede2439f13a5aeacc546 (origin/pr/1020/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f ddd44f87a2322e360015ede2439f13a5aeacc546 > git rev-list ddd44f87a2322e360015ede2439f13a5aeacc546 # timeout=10Triggering ADAM-prb ? 2.6.0,2.10,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.11,1.5.2,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1213/Build result: FAILUREGitHub pull request #1020 of commit af63909fd9f6b248ebd5b8f3d13db3783e4fe2e4 automatically merged.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos spark-test) 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/1020/merge^{commit} # timeout=10 > git branch -a --contains 55580c86dc0c808036ea7241884ba59571a01d54 # timeout=10 > git rev-parse remotes/origin/pr/1020/merge^{commit} # timeout=10Checking out Revision 55580c86dc0c808036ea7241884ba59571a01d54 (origin/pr/1020/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 55580c86dc0c808036ea7241884ba59571a01d54 > git rev-list ddd44f87a2322e360015ede2439f13a5aeacc546 # timeout=10Triggering ADAM-prb ? 2.6.0,2.10,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.11,1.5.2,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

Jenkins, retest this please.

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1214/Build result: FAILUREGitHub pull request #1020 of commit af63909fd9f6b248ebd5b8f3d13db3783e4fe2e4 automatically merged.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos spark-test) 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/1020/merge^{commit} # timeout=10 > git branch -a --contains 55580c86dc0c808036ea7241884ba59571a01d54 # timeout=10 > git rev-parse remotes/origin/pr/1020/merge^{commit} # timeout=10Checking out Revision 55580c86dc0c808036ea7241884ba59571a01d54 (origin/pr/1020/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 55580c86dc0c808036ea7241884ba59571a01d54 > git rev-list 55580c86dc0c808036ea7241884ba59571a01d54 # timeout=10Triggering ADAM-prb ? 2.6.0,2.10,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.11,1.5.2,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

yeah, it is weird.  and not reproduceable on the command line (trust me, i
tried).  it's also random enough that it's almost impossible to catch when
it happens, and there's enough traffic that tcpdum/wireshark would be
really hard to set up.  it's most likely something horribly broken in the
interactions between the pull request builder plugin and/or the jenkins git
plugins.
this was my tire fire for a number of months.  :)
On Wed, Apr 27, 2016 at 5:12 PM, Ryan Williams<EMAIL_ADDRESS>wrote:

Thanks @shaneknapp https://github.com/shaneknapp! Weird that Github is
reliably returning not-200 for these fetches for non-force-pushed commits…
—
You are receiving this because you were mentioned.
Reply to this email directly or view it on GitHub
https://github.com/bigdatagenomics/adam/pull/1020#issuecomment-215270063

Gotcha! I seem to be reproducing it pretty reliably here, lmk if you want to try to catch it the next time around, which surely is about to happen given the commit I just pushed…

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1215/Build result: FAILUREGitHub pull request #1020 of commit 7a31a34a8ad9094ecb3304868433f87cf53b3c8d automatically merged.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos spark-test) 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/1020/merge^{commit} # timeout=10 > git branch -a --contains a1e795cdc853a760c783d88f99ad047f91650c02 # timeout=10 > git rev-parse remotes/origin/pr/1020/merge^{commit} # timeout=10Checking out Revision a1e795cdc853a760c783d88f99ad047f91650c02 (origin/pr/1020/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f a1e795cdc853a760c783d88f99ad047f91650c02 > git rev-list 55580c86dc0c808036ea7241884ba59571a01d54 # timeout=10Triggering ADAM-prb ? 2.6.0,2.10,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.11,1.5.2,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

Jenkins, retest this please.

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1216/Build result: FAILUREGitHub pull request #1020 of commit 7a31a34a8ad9094ecb3304868433f87cf53b3c8d automatically merged.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos spark-test) 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/1020/merge^{commit} # timeout=10 > git branch -a --contains a1e795cdc853a760c783d88f99ad047f91650c02 # timeout=10 > git rev-parse remotes/origin/pr/1020/merge^{commit} # timeout=10Checking out Revision a1e795cdc853a760c783d88f99ad047f91650c02 (origin/pr/1020/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f a1e795cdc853a760c783d88f99ad047f91650c02 > git rev-list a1e795cdc853a760c783d88f99ad047f91650c02 # timeout=10Triggering ADAM-prb ? 2.6.0,2.10,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.11,1.5.2,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1217/Build result: FAILUREGitHub pull request #1020 of commit afc90d7639749f3308d8e68392fc21cd0588dadd automatically merged.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos spark-test) 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/1020/merge^{commit} # timeout=10 > git branch -a --contains 06535d600e5829028e4dc12843d3f49eef091c22 # timeout=10 > git rev-parse remotes/origin/pr/1020/merge^{commit} # timeout=10Checking out Revision 06535d600e5829028e4dc12843d3f49eef091c22 (origin/pr/1020/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 06535d600e5829028e4dc12843d3f49eef091c22 > git rev-list a1e795cdc853a760c783d88f99ad047f91650c02 # timeout=10Triggering ADAM-prb ? 2.6.0,2.10,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.11,1.5.2,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

Jenkins, retest this please.

Test PASSed.
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Test PASSed.

Yahtzee!

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1219/Build result: FAILUREGitHub pull request #1020 of commit 1d0ace90f5f943704908550136e69c44ba357450 automatically merged.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos spark-test) 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/1020/merge^{commit} # timeout=10 > git branch -a --contains 3f7fe5ee093b88fc2ec4a8d33b44b49e46ebe2b2 # timeout=10 > git rev-parse remotes/origin/pr/1020/merge^{commit} # timeout=10Checking out Revision 3f7fe5ee093b88fc2ec4a8d33b44b49e46ebe2b2 (origin/pr/1020/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 3f7fe5ee093b88fc2ec4a8d33b44b49e46ebe2b2 > git rev-list 06535d600e5829028e4dc12843d3f49eef091c22 # timeout=10Triggering ADAM-prb ? 2.6.0,2.10,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.11,1.5.2,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

Jenkins, retest this please.

Test PASSed.
Refer to this link for build results (access rights to CI server needed):
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Test PASSed.

(Squashed commits)

Thanks @ryan-williams for the stellar change and for the patience with @AmplabJenkins! I've just merged this.


Renames work on struct field shorthands

When renaming either a local or a struct field, struct field shorthands are now renamed correctly.
Happy to refactor this if it doesn't fit the design of the code. Thanks for adding the suggestion of where to start on the issue.
I wasn't sure if I should also look at the behavior of renaming when placing the cursor at the field shorthand; the following describes the behavior with this patch:
#[test]
fn test_rename_field_shorthand_for_unspecified() {
    // when renaming a shorthand, should we have a way to specify
    // between renaming the field and the local?
    //
    // If not is this the correct default?
    test_rename(
        r#"
struct Foo {
    i: i32,
}
 impl Foo {
    fn new(i: i32) -> Self {
        Self { i<|> }
    }
}
"#,
        "j",
        r#"
struct Foo {
    i: i32,
}
 impl Foo {
    fn new(j: i32) -> Self {
        Self { i: j }
    }
}
"#,
    );
}

Resolves #3431

bors r+
Thanks for fixing this @m-n! This particular bug has been annoying me for quite some time :)


Requiring CSS files from node_modules fails with SyntaxError: Unexpected token

Steps to reproduce in an empty folder
npm install browserify-css
npm install leaflet
echo 'require("leaflet/dist/leaflet.css")' > index.js
browserify index.js -t browserify-css -o bundle.js

/tmp/leaflet-css/node_modules/leaflet/dist/leaflet.css:3
.leaflet-map-pane,
^
ParseError: Unexpected token

Copying the CSS file to the root works
cp node_modules/leaflet/dist/leaflet.css leaflet.css
echo 'require("./leaflet.css")' > index.js
browserify index.js -t browserify-css -o bundle.js

Is there anything we can do about it? Or does browserify treat these files differently and they don't even reach the transform?

You can try the following instead of directly requiring it from node_modules:
echo '@import url("node_modules/leaflet/dist/leaflet.css");' > index.css
echo "require('./index.css');" > index.js
browserify index.js -t browserify-css -o bundle.js

Note that the -t option will only transform module on top-level files.
In your case, you can use browserify index.js -g browserify-css -o bundle.js to transform module in the node_modules directory.

Thanks, with the -g option its working.
My actual setup uses package.json for defining tranforms like
"browserify": {
    "transform": [
      "browserify-css"
    ]
},

as far as I can tell there is not way to define global transforms or set global to true using the package.json, right?

You can check out FAQ first at https://github.com/cheton/browserify-css#1-how-do-i-include-css-files-located-inside-the-node_modules-folder
Let's say if you want to require bootstrap.css within your project, you can use CSS @import rule as below:
vendor.css:
/* Load CSS files from your node_modules folder */
@import "node_modules/bootstrap/dist/bootstrap.css";

app.js:
require('./vendor.css');

However, in your case, you include an external module "angular-dialog-service" which requires css files in its index.js, unless you can manually add the following entry to its package.json file with a custom Gulp task:
{
  "browserify": {
    "transform": ["browserify-css"]
  }
}

or { global: true } is the only solution to transform CSS files within external modules.

I second that this should be front page and BOLD,  I just wasted a day until I found this issue.  This isn't obvious AT ALL...

Could someone help submit a PR to update README.md with respect to this issue? I would really appreciate it. Thanks.

I also figured out that you can use it with gulp, the api isn't documented well either
.transform({global: true}, require("browserify-css"))

To add to the comment of @cheton, here's what I had to put to my browserify/babelify call to get this to work:
node_modules/.bin/browserify -g browserify-css \
-t [ babelify \
 --presets [ stage-0 es2015 react ] \
 --plugins [ transform-react-jsx transform-es2015-modules-umd ] ] \
path/to/my/app.jsx -o path/to/my/app.js


Adts 28

@jamiewilbraham I have done a quick look through this PR and no major issues from my perspective. A few suggestions though. Can take another look once you've done a smoke test and fixes have been made!


Return more than 10 aggregations

In order that we can return comprehensive data when responding to requests for aggregations we should be able to return greater than 10.
This means when using language aggregations we have no english works. That's probably wrong.

@jtweed @jennpb  Looking through the data we might need to think about how we do this.
Here's some numbers with some common queries:

Field
With no query
Botany
Paintings
Skeleton

Languages
173
33
30
16

Genres
3042
180
200
135

Subjects
261694
4314
3161
438

Languages: I can see the interface as it stands being able to handle this information
Genres: This seems to get a little harder, 100-200 genres on any UI is tricky.
Subjects: I can't really see how any of these numbers would scale.
What @jamieparkinson and I have spoke about is finding a way to return all of them (although we will definitely be hit with a 10000 bucket size limit) - allowing us to work out what to do next.
Another choice would be to allow us to text search the subjects themselves and attach subjects to the query - the only thing is this doesn't give you the information up front about what subjects there are. Arguably 4314 subjects up front doesn't give an idea of it either.
Languages and workTypes however seem to work well.

This is exactly why I suggested #3975, answering your question there. It's not feasible to desirable to return all for certain aggregations, but it is for others.

Assuming thought that frequency is the most important thing - surfacing outliers feels really important especially for researchers looking for such a thing.
Another use case where this would be useful would is people who aren't using our interface, or analysing data with a machine.
Maybe at first we supply all to allow for testing and also have an aggregationsSort parameter, which could be useful in a few instances (and easy to implement)?
When working with the performance on this we might need to see if pagination is something we do, but by releasing this we allow for the client to chose what they want without offering infinite flexibility.

Resolved by https://github.com/wellcometrust/catalogue/pull/233 (for now)


open_edges: consider when initializing checking against bounding box first

When open_edges is initialized, the scanline checks intersection against all Edges in graph. It might be faster on graphs with many obstacle polygons to check if the scanline crosses the bounding box of each polygon first. For the boxes it does not cross, all edges in that polygon can be ignored.

Using line_profiler to profile visible_vertices(), about 10% of running time is spent on initializing open_edges, so any improvements won't have a dramatic effect, but still worth exploring. (interesting note: 58% of time is spent on insort and bisect).


version number incompatible with PEP 440

When I do a fresh build with buildout, I get warning about the version. The warning is not critical, just cosmetic.
the warning is generated by setuptools-10.2. Build is done here in docker.
 RUN cd pyethereum && curl https://bootstrap.pypa.io/bootstrap-buildout.py | python
 ---> Running in b35db5de9573
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100  6501  100  6501    0     0  18631      0 --:--:-- --:--:-- --:--:-- 18681
Downloading https://pypi.python.org/packages/source/s/setuptools/setuptools-10.2.zip
Extracting in /tmp/tmpQnH4ue
Now working in /tmp/tmpQnH4ue/setuptools-10.2
Building a Setuptools egg in /tmp/tmpJynlZV
/tmp/tmpJynlZV/setuptools-10.2-py2.7.egg
Creating directory '/pyethereum/bin'.
Creating directory '/pyethereum/parts'.
Creating directory '/pyethereum/eggs'.
Creating directory '/pyethereum/develop-eggs'.
Generated script '/pyethereum/bin/buildout'.
 ---> 6f14d09512a9
Removing intermediate container b35db5de9573
Step 3 : RUN cd pyethereum && bin/buildout
 ---> Running in ca7d93e6deed
Develop: '/pyethereum/.'
/pyethereum/eggs/setuptools-10.2-py2.7.egg/setuptools/dist.py:293: UserWarning: The version specified ('23c7d1e') is an invalid version, this may not work as expected with newer versions of setuptools, pip, and PyPI. Please see PEP 440 for more details.

TL;DR: version ('23c7d1e') is not a valid python version, according to https://www.python.org/dev/peps/pep-0440/

I see the version string has changed, but it is still not compatible.
/pyethereum/eggs/setuptools-12.0.5-py2.7.egg/pkg_resources/__init__.py:2510: PEP440Warning: 'pyethereum (0.7.51-40-g8d7d3be)' is being parsed as a legacy, non PEP 440, version. You may find odd behavior and sort order. In particular it will be sorted as less than 0.0. It is recommend to migrate to PEP 440 compatible versions.

depends on: https://github.com/warner/python-versioneer/pull/45


License?

Hi there, I'm really digging Huetone. I wanted to make a fork, but I saw that there is no license. Do you plan on adding one or is it closed to forks/modifications?

Added MIT licence. I'm not a specialist, but it should have no restrictions now :)


Remove weird button highlights

The "play again" button is highlighted. We should avoid this. I think it might be the tab highlight thing. We could just disable that across the app.

are you lookign at this in a11y-fix branch? if so, yes, when Win component loaded, focus is set to that button. focus-visible should take care of that tho.

I noticed the same highlight on the toggle when playing.


fix: handle redirect domains & refs

Fix for https://github.com/leancodepl/patrol/pull/1817

Hi @Ehesp, thanks again for looking into it 🙏🏻
When do you plan to merge this PR?


Rails class method returns nil value inside crutch

I am using crutch to optimize elasticsearch indexing and having issue with crutch.
crutch is like
crutch :scheme_for_loans do |collection|
    Loan.scheme_mapping_for_milaap_group_by_loan(collection.map(&:id))
end

here collection and collection.map(&:id) are getting proper value , but
Loan.scheme_mapping_for_milaap_group_by_loan(collection.map(&:id))

returns nil. Although same statement returns proper value in rails console
Above method is like , if that helps
def self.scheme_mapping_for_milaap_group_by_loan(loan_ids)
    loan_and_scheme_mapping = {}
    Scheme.running.source_scope_for(Scheme.source_scopes[:source_scope_milaap], nil).each do |s|
      next if !s.applicable_for?(Scheme::SCHEME_SCOPE_LOAN)
      loan_ids_applicable_for_match = s.projects.flat_map(&:loans).map(&:id).uniq
      loan_ids.each do |loan_id|
        loan_and_scheme_mapping[loan_id] = s if loan_ids_applicable_for_match.include?(loan_id)
      end
    end
    loan_and_scheme_mapping
 end

Wait, if collection.map(&:id) returns result correctly and Loan.scheme_mapping_for_milaap_group_by_loan(collection.map(&:id)) doesn't then problem is in Loan.scheme_mapping_for_milaap_group_by_loan. It probably doesn't work correct in the crutch scope, so you have to debug it and take a look what's changed there

I tried to debug it by putting puts statements inside Loan.scheme_mapping_for_milaap_group_by_loan method . But looks like it's not even entering inside that method and directly returns nil as those puts statements never gets printed

What will be printed if:
crutch :scheme_for_loans do |collection|
  p Loan.scheme_mapping_for_milaap_group_by_loan(p(collection.map(&:id)))
end

It doesn't print anything . Because it's nil . verified by
crutch :scheme_for_loans do |collection|
     p (Loan.scheme_mapping_for_milaap_group_by_loan(collection.map(&:id))).class
end

which prints NilClass

you forgot to print p(collection.map(&:id))

Well, there is not issue with collection.map(&:id) . It returns proper array of ids.
[5, 9294, 9295, 9297......, 10213]
and If take that array and in console
Loan.scheme_mapping_for_milaap_group_by_loan(array_of_loan_ids)

It gives me a proper hash.  The same statement inside crutch returns nil with same array of ids .
I can confirm that inside crutch this function is not being called .

Wait, if p (Loan.scheme_mapping_for_milaap_group_by_loan(collection.map(&:id))).class returns NilClass, then function have been called definitely, but returned nil and something with the function then

No, otherwise puts statements inside Loan.scheme_mapping_for_milaap_group_by_loan(array_of_loan_ids) would have been printed.
I tried using another function which is just a scope of active record class
crutch :scheme_for_loans do |collection|
        puts "111111111111111"
        puts Loan.not_fully_funded
        puts "2222222222222"
end

the output I get here is
111111111111111

2222222222222

In console If I do
Loan.not_fully_funded.count => returns 123

Maybe you have a tricky code that redefines this function somehow, have no idea frankly. It definitely look like the function was called, but return nil

I think this is a bug . Even if I put
crutch :scheme_for_loans do |collection|
        puts "111111111111111"
        puts Loan.count
        puts "2222222222222"
end

It returns
111111111111111

2222222222222

Now Loan.count,  is Active record method , and I'm sure that we have not overridden this method anywhere .

Interestingly same crutch code works fine in another Index

Looks like I found a pattern for this issue :
class LoansIndex < BaseIndex
  if ActiveRecord::Base.connection.table_exists?('loans') && Loan.count > 0

    define_type Loan.visible.not_fully_funded.limit(2) do
      crutch :test do |collection|
        puts "stories_count: #{MilaapStory.count}"
        puts "loans_count: #{Loan.count}"
        puts "projects_count: #{Project.count}"
    end
end

prints
stories_count: 99
loans_count:
projects_count: 1016

and
class ProjectsIndex < BaseIndex
  if ActiveRecord::Base.connection.table_exists?('projects') && Project.count > 0
    define_type Project.all do
      crutch :test do |collection|
        puts "stories_count: #{MilaapStory.count}"
        puts "loans_count: #{Loan.count}"
        puts "projects_count: #{Project.count}"
    end
end

prints
stories_count: 99
loans_count: 9777
projects_count:

Does it mean that we can't use the method from the class for which index is created ?

That is because ProjectsIndex::Project exists and you are inside of it, ::Project.count would work there


add AggregationTree

#172

Create a new AggregationMerkleSumTree data structure to merkle_sum_tree module
Add test to generate MstInclusionProof starting from AggregationMerkleSumTree

@alxkzmn great point! gonna apply the changes


Replace the usage of wait-for-it.sh in the tendermint image with docker health checks

the docker healthchecks already appear to be present


Postman collection uses deprecated format

Hi, it seems support for importing v1 collections was dropped in Postman v8, so you probably want to update the SCIM collection you host under https://aka.ms/ProvisioningPostman to v2.
Document Details
⚠ Do not edit this section. It is required for docs.microsoft.com ➟ GitHub issue linking.

ID: b633a23e-8b4e-5f76-687b-d9c32ca482dc
Version Independent ID: ed365cbe-971b-6010-21fe-e9ce987eac6c
Content: Build a SCIM endpoint for user provisioning to apps from Azure Active Directory
Content Source: articles/active-directory/app-provisioning/use-scim-to-build-users-and-groups-endpoints.md
Service: active-directory
Sub-service: app-provisioning
GitHub Login: @kenwith
Microsoft Alias: kenwith

@AxelBehrens , Thanks for reaching out. We will investigate and update the thread accordingly.


[DRAFT] ProcessID, Signal, SignalSet, TaskInfo, ResourceUsageInfo

Just a draft of low-level strongly typed wrappers for getting the current PID, querying usage information of a processes, and wrappers for signals and signal sets.

I think shipping this requires that we finish fleshing out posix_spawn functionality, otherwise we wouldn't have a good vetting of some of the design here.


Remove Azure based IPAM from self-managed k8s

Signed-off-by: Vlad Ungureanu<EMAIL_ADDRESS>While reading the docs I realized that by mistake we added the AKS install guide to the self-manged k8s section.
Update self-managed k8s docs to exclude Azure IPAM link (based on AKS).

test-me-please

Coverage increased (+0.04%) to 37.045% when pulling 0801c04c36901cc7ce08f5559027417cf467d9a5 on vladu/fix-docs-azure into 308d67fb19ac264935e950130c09d0535762f452 on master.


Pass through names array for AW homepage theme-section-list-deck-block.

Requires https://github.com/parameter1/base-cms/pull/386 and a dependency upgrade.

 Subsection for AW Podcasts


[Interface to MLJ] Implement a single class to handle all MLJ models

If the investigation conducted as part of issue #175 is successful, implement a single class to handle all MLJ models.

Dropped as part of the CSE2000 Software Project after a discussion with @pat-alt prioritizing tasks.

closing because we still have #69


Adds recommended torii adapter as a blueprint

In the current documentation, there is boilerplate code to pull in the default Emberfire Torii adapter.
While I agree that this module should not be in the default blueprint, I think that it would be much better to have a separate blueprint available to install the suggested adapter rather than requesting copy-pasta.

I signed it!

Ignore this at present, I was editing the WRONG files... I will fix and rebase.

Thanks for this :balloon:
Let's make the generator firebase-torii-adapter instead of emberfire-torii to be consistent with the firebase-adapter generator.

@tstirrat This commit should fix the errors before, and is a fresh commit. Just waiting on tests to pass!

Sorry I was on vacation for a week. thanks for this!


Default Actions: Put method?

// src/resource.js line 102
Resource.actions = {
        get: {method: 'get'},
        save: {method: 'post'},
        query: {method: 'get'},
        remove: {method: 'delete'},
        delete: {method: 'delete'}
    };

Thanks for releasing vue-resource library. It's more convenient to call RESTful APIs. But, why default actions don'ts have update: {method: 'put'} method? (I add it by myself now)
Thanks.

#23 PR :+1:

@Fauxide Thanks. I saw 3a58c41 has been add. This issue can close. Thanks :-)


warp_image function runs very slow

Hi ! Thanks for your code , It seems that warp_image in flowlib.py run very slow. I wonder if exits other methods to speed it up

Because that's numpy code, only for visualization, not training. You can check this line

Thanks for your reply, I see. I am not understand the wrap process, can you give me some link for study? In pytorch forum, I find people use grid_sample function to implement image warp , what is difference between your code and that function?

@lxtGH Would you please share the link of grid_sample implementation for flow warping! Thanks a lot!

@JiamingSuen Check this: http://pytorch.org/docs/0.3.1/nn.html#grid-sample

@lxtGH I did not write the code, I just re-arrange it into easy-to-use package. Seems that when this code was released, pytorch has no grid_sample module yet.

@Yuliang-Zou Thanks for the reference!
In fact, I'm having trouble writing a flow warping function with grid_sample. Since grid_sample is originally used for STN, I didn't find a straightforward way to generate grid with flow that outputted by the network. Actually I only to make sure what proposed in this thread is correct. It would be nice if you can provide some information. Thanks!

@JiamingSuen My understanding (not necessarily correct):

You compute the flow
You can know the correspondence from (x,y) in Im1 to (x',y') in Im2
Normalize the coordinates (x',y') to [-1, 1], you get grid
x should be Im2, if you are doing inverse warp

Hi, Thanks for your reply
I ask the same question in this issue
but I think the last line of the code should be the input x, is my understanding correct?
@Yuliang-Zou @JiamingSuen


Check if material instance points to valid texture in terrain textures

Looked into this; keys from diagnoser.getCache().textures do include textures found from atlas files. Although, I'm not sure there's a way to differentiate between whether it was an atlas texture, and if it came from terrain_texture.json rather than item_texture.json. Any ideas on what I should do?

Would it help if you used this data?
https://github.com/Blockception/BC-Minecraft-Bedrock-Vanilla-Data/blob/main/src/Lib/Vanilla/ResourcePack/sounds_files.ts

That's just hardcoded vanilla sound paths, the material instance can point to a custom texture.

All found texture atlasses end up atleast in diagnoser.getCache().resourcespack.textures.
Do no vanilla atlast is defined yet 🤔 , probably need to add those to the vanilla collection, and then create a function in the diagnosed to see if its an existing ID or not

It should

Alr. I'll look into this when I get the chance and resolve this and #165


./install.sh => ERROR: Failed to Setup IP tables: Unable to enable SKIP DNAT rule:

If you are reporting a problem, please make sure the following information are provided:
1)Version of docker engine and docker-compose.
Docker:

Client:
Version:      17.09.0-ce
API version:  1.32
Go version:   go1.8.3
Git commit:   afdb6d4
Built:        Tue Sep 26 22:41:23 2017
OS/Arch:      linux/amd64
Server:
Version:      17.09.0-ce
API version:  1.32 (minimum version 1.12)
Go version:   go1.8.3
Git commit:   afdb6d4
Built:        Tue Sep 26 22:42:49 2017
OS/Arch:      linux/amd64
Experimental: false

docker-compose:

docker-compose version 1.17.1, build 6d101fb
docker-py version: 2.5.1
CPython version: 2.7.13
OpenSSL version: OpenSSL 1.0.1t  3 May 2016

2)Config files of harbor, you can get them by packaging "harbor.cfg" and files in the same directory, including subdirectory.

see attached, I just updated hostname and db_password.

3)Log files, you can get them by package the /var/log/harbor/ .

no log of harbor at /var/log/harbor/ yet.

After update the harbor.cfg file, and run ./install.sh, I get the following error.
The environment is centos 7 on Aliyun Cloud.
Thank you.
Adun

[Step 4]: starting Harbor ...
Creating network "harbor_harbor" with the default driver
ERROR: Failed to Setup IP tables: Unable to enable SKIP DNAT rule:  (iptables failed: iptables --wait -t nat -I DOCKER -i br-a97ac2fc79ca -j RETURN: iptables: No chain/target/match by that name.
(exit status 1))

Attach harbor.cfg in a zip.
harbor.zip

The error happened when docker creates the network.
Could you check: https://github.com/moby/moby/issues/16816

Thanks a lot.
The issue is resolved by restart docker daemon.
systemctl restart docker

restarting docker service solved it for me.


change addressing mode notation

immediate  #aa -> aa
zeropage aa -> (aa)
absolute aaaa -> (aaaa)
indirect (aaaa) -> [aaaa]

done.


Switched to non-blocking cache as default cache

are we satisfied with the testing for non-blocking? all the CUDA tests pass with non-blocking?

I ran regression, it passes. I can build an F1 image and try there too.
Dustin Richmond (He/Him)
University of California, PhD (2018)
www.dustinrichmond.com

On Nov 26, 2019, at 11:03 AM, mrutt92<EMAIL_ADDRESS>wrote:
are we satisfied with the testing for non-blocking? all the CUDA tests pass with non-blocking?
—
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thomassquared's San Francisco restaurant list

Added restaurants that I like, used emoji sparringly.  Gifs would be nice.
@githubteacher how'd I do?

👍


Suggested fix for issue 21

Thanks! I fixed an issue with token parsing (at least in Firefox the token broke...). But it seems to work still.


commonSpells::mapValuesSet  should be renamed values

Currently, we must write:
  val santas     = recipient_for_santa.keys()
  val recipients = recipient_for_santa.mapValuesSet()

This poorly expresses the symmetry between the two operators. Instead we should have
  val santas     = recipient_for_santa.keys()
  val recipients = recipient_for_santa.values()

Fixed in https://github.com/informalsystems/quint/pull/1320


Improve SyntaxNodeComparer

It currently uses recursion + reflection and could probably be a lot more efficient.
I wrote a quick generated version that got rid of the reflection, but it ran into stack overflows. I should redo that without recursion.

Ditching recursion and reflection cut the time this takes to run roughly in half.


✨ Raw result for Maintained check

Add support for raw results for Maintained check
No breaking changes
Add support for raw results for Maintained check

protobuf error cc @naveensrinivasan @azeemsgoogle


Adding ~ expansion to paths

The options that point to paths do not include user home directory expansion or ~ and ~user. We should add it.

Fixed in version 3.10.2


[hotfix][sqlclient][docs] Improved sql client docs

What is the purpose of the change

SQL Client document improvements

Brief change log

Updated doc.

Verifying this change
This change is a trivial rework / code cleanup without any test coverage.
Does this pull request potentially affect one of the following parts:

Dependencies (does it add or upgrade a dependency): no
The public API, i.e., is any changed class annotated with @Public(Evolving): no
The serializers: no
The runtime per-record code paths (performance sensitive): no
Anything that affects deployment or recovery: JobManager (and its components), Checkpointing, Kubernetes/Yarn, ZooKeeper: no
The S3 file system connector: no

Documentation

Does this pull request introduce a new feature? no
If yes, how is the feature documented? (not applicable

@SteNicholas, @fapaul  - Can you please review this PR ?  Thanks

Thanks @knaufk for your review and time.


  But I can't figure out why they didn't happen before this PR.  Any guesses?

On android, libc::copy_file_range doesn't exist.  But why didn't that cause problems before?
Same thing on musl.
On QEMU, undefined reference to copy_file_range'`  at link time.  But again, what changed?

Even before this PR, copy_file_range should've been enabled for all of those targets.

Oh, I see.  The old version used libc::syscall(libc::SYS_copy_file_range, ...).  Now I'm trying to call libc::copy_file_range(...).  Silly Linux.  I wonder if it actually worked before?


WWF-1029 - report datadog logs

@yeelali14 the data you extracted is amazing, we need to make sure we can extract it as arg in DD


SSL Cert Update?

From Braintree:

We will be updating our root SSL provider for API traffic to align with security standards starting April 1, 2020 in sandbox and May 1, 2020 in production. To avoid interruption to your processing, please update your SDK version to the appropriate minimum versions specified on this page.

Does this mean the CA cert file in this repo needs to be updated?

Possibly. I'll check an official repo to compare certs. Thanks for the notice!

tl;dr No update is needed, you're safe.
The minimum version that they reference for Ruby is 2.57, which uses the same cert bundle that we are (that's where this one came from). There is a newer certificate bundle available from 2.81, but it isn't compatible without other changes.

👍 Thank you for taking a look!


Fixes issue #58.

Fixes issue #58
Adds the possibility to manually close wallet opened by RPC. See src/main/js/wallet/MoneroWalletRpc.js at line 270.

Closing this since the issue is not verified / reproduced and may only affect Windows systems.
Please update us if the issue is confirmed.


reduce number of contentful calls

reduce number of contentful calls
candidates

notifications
urlAlias
projects and programmes
resources (tricky as it is also used for previews)

Secondly they should be passed through varnish

We still get extra bills as times, but I'm not convinced that it is still the website doing the majority of those calls.
@timrobertson100 If we want to reduce number of calls it might be an idea to track nr of calls  from indexing and backup?

Thanks- the costs are fine at the moment but I'm tracking the billing. If this changes we can reopen and consider less frequent crawling.


Add libs_url to searchengine api

Resolves #44.

Sorry for the force-push. I've replaced strip() with removesuffix(), then realized it's from python 3.9 while the container uses 3.8, and I've reverted the change.

LGTM, thnkas!


updating to 118542.html

github is an amazing platform for developers.

Please don't edit others' cards, create a new card.


Tokens arrays of tagged template literals not linked to the tagged template

From MDN:

For any particular tagged template literal expression, the tag function will always be called with the exact same literal array, no matter how many times the literal is evaluated.

Input:
function tag(tokens) {
  return tokens;
}

function runTag() {
  return tag`a${123}b${456}c`;
}

const tokens = runTag();

export default function compare() {
  return runTag() === tokens;
}

In the source code, compare() returns true. But in output it returns false because Livepack does not understand the link between tokens and the template literal in runTag().
Output:
const Object$0 = Object,
  ObjectFreeze = Object$0.freeze;
export default (
  (tokens, tag, runTag$0) => (
    runTag$0 = function runTag() {
      return tag`a${123}b${456}c`;
    },
    function compare() {
      return runTag$0() === tokens;
    }
  )
)(
  ObjectFreeze(
    Object$0.defineProperties(
      ["a", "b", "c"],
      { raw: { value: ObjectFreeze(["a", "b", "c"]) } }
    )
  ),
  function tag(tokens) {
    return tokens;
  }
);

This would be annoying to solve.
Instrumentation would need to replace the tag function with a wrapper which records:

the tokens array
the raw property of the tokens array
the function which the tagged template is in

If the tokens array/raw tokens array and the function are both included in output, it'd need to rewrite the runTag function as:
const tokens = (t => t)`a${0}b${0}c`;
function runTag() {
  // Was: tag`a${123}b${456}c`
  return tag(tokens, 123, 456);
}

NB: The tokens array is lexically bound to the tagged template.
const tag = tokens => tokens;
const makeRunTag = () => () => tag`a${1}b${2}c`;
const tokens1 = makeRunTag()();
const tokens2 = makeRunTag()();

console.log(tokens1 === tokens2); // true


[EG] Next pylint

/azp run python - eventgrid - test-weekly

API change check
API changes are not detected in this pull request.

/azp run python - eventgrid - tests-weekly

/azp run python - eventgrid - tests-weekly