-
Notifications
You must be signed in to change notification settings - Fork 309
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Stores original position and original cigar during realignment. #417
Conversation
Can one of the admins verify this patch? |
Jenkins, add to whitelist. |
Test FAILed. Build result: FAILUREGitHub pull request #417 of commit ae38a31 automatically merged.[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-slave-01 (centos) 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/417/merge^{commit} # timeout=10Checking out Revision 4f3e5b7 (detached) > git config core.sparsecheckout # timeout=10 > git checkout -f 4f3e5b7 > git rev-list fa32bbf # timeout=10First time build. Skipping changelog.Triggering ADAM-prb » 2.2.0,centosTriggering ADAM-prb » 1.0.4,centosTriggering ADAM-prb » 2.3.0,centosADAM-prb » 2.2.0,centos completed with result FAILUREADAM-prb » 1.0.4,centos completed with result FAILUREADAM-prb » 2.3.0,centos completed with result FAILURETest FAILed. |
Jenkins, retest this please. |
Test FAILed. Build result: FAILUREGitHub pull request #417 of commit ae38a31 automatically merged.[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-slave-01 (centos) 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/417/merge^{commit} # timeout=10Checking out Revision 7406d00 (detached) > git config core.sparsecheckout # timeout=10 > git checkout -f 7406d00 > git rev-list db0f900 # timeout=10Triggering ADAM-prb » 2.3.0,centosTriggering ADAM-prb » 2.2.0,centosTriggering ADAM-prb » 1.0.4,centosADAM-prb » 2.3.0,centos completed with result FAILUREADAM-prb » 2.2.0,centos completed with result FAILUREADAM-prb » 1.0.4,centos completed with result FAILURETest FAILed. |
ae38a31
to
77ea367
Compare
Test FAILed. Build result: FAILUREGitHub pull request #417 of commit 77ea367 automatically merged.[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-slave-01 (centos) 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/417/merge^{commit} # timeout=10Checking out Revision 01b4a29 (detached) > git config core.sparsecheckout # timeout=10 > git checkout -f 01b4a29 > git rev-list db0f900 # timeout=10Triggering ADAM-prb » 1.0.4,centosTriggering ADAM-prb » 2.3.0,centosTriggering ADAM-prb » 2.2.0,centosADAM-prb » 1.0.4,centos completed with result FAILUREADAM-prb » 2.3.0,centos completed with result FAILUREADAM-prb » 2.2.0,centos completed with result FAILURETest FAILed. |
Can one of the admins verify this patch? |
Jenkins, add to whitelist. |
Test FAILed. Build result: FAILUREGitHub pull request #417 of commit 77ea367.[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-slave-01 (centos) 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 77ea367^{commit} # timeout=10Checking out Revision 77ea367 (detached) > git config core.sparsecheckout # timeout=10 > git checkout -f 77ea367 > git rev-list db0f900 # timeout=10Triggering ADAM-prb » 1.0.4,centosTriggering ADAM-prb » 2.3.0,centosTriggering ADAM-prb » 2.2.0,centosADAM-prb » 1.0.4,centos completed with result FAILUREADAM-prb » 2.3.0,centos completed with result FAILUREADAM-prb » 2.2.0,centos completed with result FAILURETest FAILed. |
77ea367
to
f3ef0c8
Compare
Test FAILed. Build result: FAILUREGitHub pull request #417 of commit f3ef0c8 automatically merged.[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-slave-01 (centos) 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/417/merge^{commit} # timeout=10Checking out Revision 2592f2c (detached) > git config core.sparsecheckout # timeout=10 > git checkout -f 2592f2c > git rev-list a9008c4 # timeout=10Triggering ADAM-prb » 2.2.0,centosTriggering ADAM-prb » 1.0.4,centosTriggering ADAM-prb » 2.3.0,centosADAM-prb » 2.2.0,centos completed with result FAILUREADAM-prb » 1.0.4,centos completed with result FAILUREADAM-prb » 2.3.0,centos completed with result FAILURETest FAILed. |
f3ef0c8
to
f0bc0f0
Compare
Test FAILed. Build result: FAILUREGitHub pull request #417 of commit f0bc0f0 automatically merged.[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-slave-01 (centos) 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/417/merge^{commit} # timeout=10Checking out Revision 7dc5bba (detached) > git config core.sparsecheckout # timeout=10 > git checkout -f 7dc5bba > git rev-list c12c117 # timeout=10Triggering ADAM-prb » 2.2.0,centosTriggering ADAM-prb » 1.0.4,centosTriggering ADAM-prb » 2.3.0,centosADAM-prb » 2.2.0,centos completed with result FAILUREADAM-prb » 1.0.4,centos completed with result FAILUREADAM-prb » 2.3.0,centos completed with result FAILURETest FAILed. |
4186c74
to
c3c848c
Compare
Test FAILed. Build result: FAILUREGitHub pull request #417 of commit 4186c74 automatically merged.[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-slave-01 (centos) 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/417/merge^{commit} # timeout=10Checking out Revision 905bb58d27ebdf9a7b4cebedee15265f3ddbfbba (detached) > git config core.sparsecheckout # timeout=10 > git checkout -f 905bb58d27ebdf9a7b4cebedee15265f3ddbfbba > git rev-list 7dc5bba # timeout=10Triggering ADAM-prb » 2.2.0,centosTriggering ADAM-prb » 1.0.4,centosTriggering ADAM-prb » 2.3.0,centosADAM-prb » 2.2.0,centos completed with result FAILUREADAM-prb » 1.0.4,centos completed with result SUCCESSADAM-prb » 2.3.0,centos completed with result FAILURETest FAILed. |
Test PASSed. |
@@ -135,7 +135,7 @@ | |||
<configuration> | |||
<rules> | |||
<requireMavenVersion> | |||
<version>[3.1.1,)</version> | |||
<version>[3.0.4,)</version> |
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
Was this intentional? Some users have reported issues building with Maven 3.0.x.
Aside from relaxing the Maven version requirement, this code looks ready to merge to me. |
Should I change it to 3.1.1? What is the preferred Maven version? |
Yes. 3.1.1 please. -Matt
|
c3c848c
to
e20ec43
Compare
Unfortunately, changing the version from 3.0.4 to 3.1.1 causes the build to fail: niranjan93@crick:~/adam$ mvn test |
Test PASSed. |
I believe that someone fixed this. I just checked and the Maven version for -Matt On Sat, Nov 1, 2014 at 2:39 PM, UCB AMPLab notifications@github.com wrote:
|
@@ -305,7 +305,7 @@ | |||
<dependency> | |||
<groupId>org.bdgenomics.bdg-formats</groupId> | |||
<artifactId>bdg-formats</artifactId> | |||
<version>0.3.1</version> | |||
<version>0.3.2</version> |
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
Is the bump to bdg-formats intentional?
I'm not actually sure why it's 0.3.2. Should I change it to 0.3.1? |
Yes, please. Once you change it to 0.3.1, I'll be happy to merge this code. -Matt On Sat, Nov 1, 2014 at 3:31 PM, niranjan93 notifications@github.com wrote:
|
e20ec43
to
ccc640b
Compare
Test FAILed. Build result: FAILUREGitHub pull request #417 of commit ccc640b automatically merged.[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-slave-01 (centos) 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/417/merge^{commit} # timeout=10Checking out Revision 5a3a8ea90533d65453d705fda97b9408ec65e730 (detached) > git config core.sparsecheckout # timeout=10 > git checkout -f 5a3a8ea90533d65453d705fda97b9408ec65e730 > git rev-list c648a6f2090c2b8df001dfef497bea6c70f02df4 # timeout=10Triggering ADAM-prb » 2.2.0,centosTriggering ADAM-prb » 1.0.4,centosTriggering ADAM-prb » 2.3.0,centosADAM-prb » 2.2.0,centos completed with result FAILUREADAM-prb » 1.0.4,centos completed with result FAILUREADAM-prb » 2.3.0,centos completed with result FAILURETest FAILed. |
@massie the bdg-formats dependency needs to be 0.3.2; we added the originalCigar and originalPosition fields in 0.3.2. |
…ment. Addresses issue bigdatagenomics#348 in the adam project.
ccc640b
to
fef9713
Compare
Test FAILed. Build result: FAILUREGitHub pull request #417 of commit fef9713 automatically merged.[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-slave-01 (centos) 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/417/merge^{commit} # timeout=10Checking out Revision a7a2569f68f2981425bb14e2fffc1bdbd8024b8c (detached) > git config core.sparsecheckout # timeout=10 > git checkout -f a7a2569f68f2981425bb14e2fffc1bdbd8024b8c > git rev-list 5a3a8ea90533d65453d705fda97b9408ec65e730 # timeout=10Triggering ADAM-prb » 2.2.0,centosTriggering ADAM-prb » 1.0.4,centosTriggering ADAM-prb » 2.3.0,centosADAM-prb » 2.2.0,centos completed with result FAILUREADAM-prb » 1.0.4,centos completed with result FAILUREADAM-prb » 2.3.0,centos completed with result FAILURETest FAILed. |
I changed 0.3.1 back to 0.3.2, but the build still fails. I made sure that I didn't change anything else. I also did another rebase before pushing, but Git notified me that everything is up to date. niranjan93@crick: On branch NK_schema_tagsnothing to commit (working directory clean) |
I have no idea why the font became so big. I had just pasted the command line output from crick. Sorry. |
Jenkins, retest this please. |
There is no need to be sorry. Hopefully the tests will pass now. |
Big fonts are back in vogue; it's like hair in the 80's. ;) |
Test PASSed. |
Stores original position and original cigar during realignment.
I see it passes now. Thanks Matt! Thanks Frank! |
Thanks, @niranjan93 ! |
Stores original position and original cigar during realignment.
Addresses issue #348 in the adam project.