Update Hadoop-BAM to version 7.7.0

[heuermh]

Fixes #1158

Currently fails one unit test

$ mvn test
...
- write single bam file back *** FAILED ***
  htsjdk.samtools.SAMFormatException: Does not seem like a BAM file
  at org.seqdoop.hadoop_bam.BAMSplitGuesser.<init>(BAMSplitGuesser.java:88)
  at org.seqdoop.hadoop_bam.BAMInputFormat.addProbabilisticSplits(BAMInputFormat.java:234)
  at org.seqdoop.hadoop_bam.BAMInputFormat.getSplits(BAMInputFormat.java:161)
  at org.seqdoop.hadoop_bam.AnySAMInputFormat.getSplits(AnySAMInputFormat.java:252)
  at org.apache.spark.rdd.NewHadoopRDD.getPartitions(NewHadoopRDD.scala:120)

[AmplabJenkins]

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1480/

Build result: FAILURE

GitHub pull request #1166 of commit 4c5ed07 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 > /home/jenkins/git2/bin/git rev-parse --is-inside-work-tree # timeout=10Fetching changes from the remote Git repository > /home/jenkins/git2/bin/git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > /home/jenkins/git2/bin/git --version # timeout=10 > /home/jenkins/git2/bin/git -c core.askpass=true fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > /home/jenkins/git2/bin/git rev-parse origin/pr/1166/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains 467f21c6fbc1645ca52ae22b3061a2fed4794c05 # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/1166/merge^{commit} # timeout=10Checking out Revision 467f21c6fbc1645ca52ae22b3061a2fed4794c05 (origin/pr/1166/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 467f21c6fbc1645ca52ae22b3061a2fed4794c05First time build. Skipping changelog.Triggering ADAM-prb ? 2.6.0,2.11,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.10,1.5.2,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

[fnothaft]

I think I've got a fix for this. Running some tests, will PR at you if they all pass.

[fnothaft]

Opened the fix as heuermh#4.

[heuermh]

Merged and squashed in rebase.

[fnothaft]

Thanks @heuermh ! I will merge when tests pass.

[AmplabJenkins]

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1483/

Build result: FAILURE

[...truncated 32 lines...]Triggering ADAM-prb ? 2.6.0,2.11,1.3.1,centosTriggering ADAM-prb ? 2.3.0,2.11,1.4.1,centosTriggering ADAM-prb ? 2.6.0,2.11,2.0.0,centosTriggering ADAM-prb ? 2.3.0,2.10,1.4.1,centosTriggering ADAM-prb ? 2.6.0,2.11,1.6.1,centosADAM-prb ? 2.3.0,2.11,1.5.2,centos completed with result FAILUREADAM-prb ? 2.3.0,2.10,1.5.2,centos completed with result FAILUREADAM-prb ? 2.3.0,2.10,2.0.0,centos completed with result FAILUREADAM-prb ? 2.6.0,2.10,1.4.1,centos completed with result FAILUREADAM-prb ? 2.6.0,2.10,1.6.1,centos completed with result FAILUREADAM-prb ? 2.6.0,2.10,2.0.0,centos completed with result FAILUREADAM-prb ? 2.6.0,2.11,1.4.1,centos completed with result FAILUREADAM-prb ? 2.3.0,2.10,1.3.1,centos completed with result FAILUREADAM-prb ? 2.6.0,2.10,1.3.1,centos completed with result FAILUREADAM-prb ? 2.3.0,2.11,1.6.1,centos completed with result FAILUREADAM-prb ? 2.3.0,2.11,1.3.1,centos completed with result FAILUREADAM-prb ? 2.3.0,2.11,2.0.0,centos completed with result FAILUREADAM-prb ? 2.3.0,2.10,1.6.1,centos completed with result FAILUREADAM-prb ? 2.6.0,2.11,1.3.1,centos completed with result FAILUREADAM-prb ? 2.3.0,2.11,1.4.1,centos completed with result FAILUREADAM-prb ? 2.6.0,2.11,2.0.0,centos completed with result FAILUREADAM-prb ? 2.3.0,2.10,1.4.1,centos completed with result FAILUREADAM-prb ? 2.6.0,2.11,1.6.1,centos completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

[heuermh]

Jenkins, retest this please.

[AmplabJenkins]

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1484/

Build result: FAILURE

GitHub pull request #1166 of commit 237dd17 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 > /home/jenkins/git2/bin/git rev-parse --is-inside-work-tree # timeout=10Fetching changes from the remote Git repository > /home/jenkins/git2/bin/git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > /home/jenkins/git2/bin/git --version # timeout=10 > /home/jenkins/git2/bin/git -c core.askpass=true fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > /home/jenkins/git2/bin/git rev-parse origin/pr/1166/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains 48cefe856425fc3a451c06256e318c5e42a720d4 # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/1166/merge^{commit} # timeout=10Checking out Revision 48cefe856425fc3a451c06256e318c5e42a720d4 (origin/pr/1166/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 48cefe856425fc3a451c06256e318c5e42a720d4First time build. Skipping changelog.Triggering ADAM-prb ? 2.6.0,2.11,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.10,1.5.2,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

[AmplabJenkins]

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1485/

Build result: FAILURE

GitHub pull request #1166 of commit 237dd17 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 > /home/jenkins/git2/bin/git rev-parse --is-inside-work-tree # timeout=10Fetching changes from the remote Git repository > /home/jenkins/git2/bin/git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > /home/jenkins/git2/bin/git --version # timeout=10 > /home/jenkins/git2/bin/git -c core.askpass=true fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > /home/jenkins/git2/bin/git rev-parse origin/pr/1166/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains 48cefe856425fc3a451c06256e318c5e42a720d4 # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/1166/merge^{commit} # timeout=10Checking out Revision 48cefe856425fc3a451c06256e318c5e42a720d4 (origin/pr/1166/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 48cefe856425fc3a451c06256e318c5e42a720d4 > /home/jenkins/git2/bin/git rev-list 48cefe856425fc3a451c06256e318c5e42a720d4 # timeout=10Triggering ADAM-prb ? 2.6.0,2.11,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.10,1.5.2,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

[fnothaft]

Jenkins, retest this please.

[fnothaft]

@shaneknapp if you've got a sec, we've been getting more of those nasty "Failed to determine..." errors on this PR, building after a force-push.

[shaneknapp]

honestly, there's not much i can do here except to say that force-pushing
causes problems. :)

On Mon, Sep 12, 2016 at 3:18 PM, Frank Austin Nothaft <
notifications@github.com> wrote:

@shaneknapp https://github.com/shaneknapp if you've got a sec, we've
been getting more of those nasty "Failed to determine..." errors on this
PR, building after a force-push.

—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub
#1166 (comment),
or mute the thread
https://github.com/notifications/unsubscribe-auth/ABiDrMavGZnqS8h5PuK8SueErtU-GV0Wks5qpc_JgaJpZM4J6uAO
.

[shaneknapp]

for more fun^Wbackground: janinko/ghprb#148

[shaneknapp]

so, one option we can try is to set the branch specifier in the job config to use ${ghprbActualCommit} instead of ${sha1}... some report that this works, some report that it doesn't... YMMV.

[AmplabJenkins]

Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1486/
Test PASSed.

[fnothaft]

Merged! Thanks @heuermh!

[heuermh]

Thanks!

[fnothaft]

Thanks for the comment @shaneknapp. I always forget whether this is an issue that there's a fix pending for or not. It looks like on yonder failed build, it had the correct hash for the PR, but tried to check out the wrong hash:

GitHub pull request #1166 of commit 237dd17ad67f264b40639e7c64c0113ffbfd0b3d automatically merged.
[EnvInject] - Loading node environment variables.
Building remotely on amp-jenkins-worker-01 (spark-packaging spark-experimental-docker centos spark-docs spark-release spark-compile) in workspace /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.5.2/label/centos
 > /home/jenkins/git2/bin/git rev-parse --is-inside-work-tree # timeout=10
Fetching changes from the remote Git repository
 > /home/jenkins/git2/bin/git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10
Fetching upstream changes from https://github.com/bigdatagenomics/adam.git
 > /home/jenkins/git2/bin/git --version # timeout=10
 > /home/jenkins/git2/bin/git -c core.askpass=true fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/*:refs/remotes/origin/pr/* # timeout=15
Checking out Revision 741700fe088f45809da18fd394b93e1edb154c24 (origin/pr/1166/merge)
 > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10
 > /home/jenkins/git2/bin/git checkout -f 741700fe088f45809da18fd394b93e1edb154c24
FATAL: Could not checkout 741700fe088f45809da18fd394b93e1edb154c24
hudson.plugins.git.GitException: Could not checkout 741700fe088f45809da18fd394b93e1edb154c24

I'll do it live and switch up the branch specifier, and we'll see what happens.