Build failed in Jenkins: patient-network #362

PhenoTips Jenkins ci at phenotype.ccm.sickkids.ca
Fri Feb 8 13:51:18 EST 2019


See <https://ci.phenotips.org/job/patient-network/362/display/redirect>

------------------------------------------
Started by upstream project "phenotips-PR" build number 1298
originally caused by:
 GitHub pull request #2819 of commit dd16de23ce4316ebbd577c2affaefeb758b04402, no merge conflicts.
Building in workspace <https://ci.phenotips.org/job/patient-network/ws/>
 > git rev-parse --is-inside-work-tree # timeout=10
Fetching changes from the remote Git repository
 > git config remote.origin.url https://github.com/phenotips/patient-network.git # timeout=10
Fetching upstream changes from https://github.com/phenotips/patient-network.git
 > git --version # timeout=10
Setting http proxy: 20.20.20.10:488
 > git fetch --no-tags --progress https://github.com/phenotips/patient-network.git +refs/heads/*:refs/remotes/origin/* --depth=1
Seen branch in repository origin/INFRA-117
Seen branch in repository origin/PC-186
Seen branch in repository origin/PC-205-match-management-for-users
Seen branch in repository origin/PN-111
Seen branch in repository origin/PN-146
Seen branch in repository origin/PN-181
Seen branch in repository origin/PN-191
Seen branch in repository origin/PN-192
Seen branch in repository origin/PN-195
Seen branch in repository origin/PN-196
Seen branch in repository origin/PN-202
Seen branch in repository origin/PN-203
Seen branch in repository origin/PN-214
Seen branch in repository origin/PN-239
Seen branch in repository origin/PN-242
Seen branch in repository origin/PN-247
Seen branch in repository origin/PN-253
Seen branch in repository origin/PN-256
Seen branch in repository origin/PN-257
Seen branch in repository origin/PN-259
Seen branch in repository origin/PN-261
Seen branch in repository origin/PN-271
Seen branch in repository origin/PN-274
Seen branch in repository origin/PN-277
Seen branch in repository origin/PN-301
Seen branch in repository origin/PN-323
Seen branch in repository origin/PN-323-stable
Seen branch in repository origin/PN-326
Seen branch in repository origin/PN-330
Seen branch in repository origin/PN-335
Seen branch in repository origin/PN-336
Seen branch in repository origin/PN-336-rebased-on-master
Seen branch in repository origin/PN-336-stable
Seen branch in repository origin/PN-337
Seen branch in repository origin/PN-340
Seen branch in repository origin/PN-346
Seen branch in repository origin/PN-346-on-PN-351
Seen branch in repository origin/PN-349
Seen branch in repository origin/PN-350
Seen branch in repository origin/PN-351
Seen branch in repository origin/PN-355
Seen branch in repository origin/PN-357
Seen branch in repository origin/PN-359
Seen branch in repository origin/PN-359-PN-358
Seen branch in repository origin/PN-375
Seen branch in repository origin/PN-376
Seen branch in repository origin/PN-390
Seen branch in repository origin/PN-391
Seen branch in repository origin/PN-393
Seen branch in repository origin/PN-393-stable
Seen branch in repository origin/PN-394
Seen branch in repository origin/PN-396
Seen branch in repository origin/PN-396-stable
Seen branch in repository origin/PN-397
Seen branch in repository origin/PN-397-master
Seen branch in repository origin/PN-404
Seen branch in repository origin/PN-407
Seen branch in repository origin/PN-416
Seen branch in repository origin/PN-417
Seen branch in repository origin/PN-419
Seen branch in repository origin/PN-97
Seen branch in repository origin/RM-122
Seen branch in repository origin/RM-56
Seen branch in repository origin/RM-75
Seen branch in repository origin/bugfix-hasexome
Seen branch in repository origin/code-cleanup
Seen branch in repository origin/dependency-update
Seen branch in repository origin/develop
Seen branch in repository origin/docref-fix
Seen branch in repository origin/email-fix
Seen branch in repository origin/feature-match-filter
Seen branch in repository origin/genes-status
Seen branch in repository origin/master
Seen branch in repository origin/merged
Seen branch in repository origin/notification-bug
Seen branch in repository origin/old-master
Seen branch in repository origin/pn-readme
Seen branch in repository origin/pn-refactor
Seen branch in repository origin/pt-1.4-update
Seen branch in repository origin/pt-1.4-upgrade
Seen branch in repository origin/rebase-on-stable-1.1.x
Seen branch in repository origin/rest-sort-by-score
Seen branch in repository origin/save-found-macthes-for-patient
Seen branch in repository origin/stable-1.1.10
Seen branch in repository origin/stable-1.1.10-rc-2
Seen branch in repository origin/stable-1.1.10-rc-3
Seen branch in repository origin/stable-1.1.10-rc-4
Seen branch in repository origin/stable-1.1.13
Seen branch in repository origin/stable-1.1.6
Seen branch in repository origin/stable-1.1.7
Seen branch in repository origin/stable-1.1.x
Seen branch in repository origin/stable-1.1.x-on-PT-1.4
Seen branch in repository origin/stable-merged-test
Seen branch in repository origin/stable-merged-test-clone
Seen branch in repository origin/translation-bugfix
Seen branch in repository origin/upgrading
Seen branch in repository origin/zero-sided-matching
Seen 97 remote branches
 > git show-ref --tags -d # timeout=10
FATAL: Walk failure.
org.eclipse.jgit.errors.MissingObjectException: Missing commit edf0e66ce05c6364f4f64699b632cc6d4d5f4fa6
	at org.eclipse.jgit.internal.storage.file.WindowCursor.open(WindowCursor.java:159)
	at org.eclipse.jgit.revwalk.RevWalk.getCachedBytes(RevWalk.java:903)
	at org.eclipse.jgit.revwalk.RevCommit.parseHeaders(RevCommit.java:155)
	at org.eclipse.jgit.revwalk.PendingGenerator.next(PendingGenerator.java:147)
	at org.eclipse.jgit.revwalk.StartGenerator.next(StartGenerator.java:184)
	at org.eclipse.jgit.revwalk.RevWalk.next(RevWalk.java:435)
	at org.eclipse.jgit.revwalk.RevWalk.iterator(RevWalk.java:1322)
Caused: org.eclipse.jgit.errors.RevWalkException: Walk failure.
	at org.eclipse.jgit.revwalk.RevWalk.iterator(RevWalk.java:1324)
	at hudson.plugins.git.util.GitUtils$1.invoke(GitUtils.java:200)
	at hudson.plugins.git.util.GitUtils$1.invoke(GitUtils.java:164)
	at org.jenkinsci.plugins.gitclient.AbstractGitAPIImpl.withRepository(AbstractGitAPIImpl.java:29)
	at org.jenkinsci.plugins.gitclient.CliGitAPIImpl.withRepository(CliGitAPIImpl.java:72)
	at hudson.plugins.git.util.GitUtils.filterTipBranches(GitUtils.java:164)
	at hudson.plugins.git.util.DefaultBuildChooser.getAdvancedCandidateRevisions(DefaultBuildChooser.java:250)
	at hudson.plugins.git.util.DefaultBuildChooser.getCandidateRevisions(DefaultBuildChooser.java:54)
	at hudson.plugins.git.GitSCM.determineRevisionToBuild(GitSCM.java:1080)
	at hudson.plugins.git.GitSCM.checkout(GitSCM.java:1187)
	at hudson.scm.SCM.checkout(SCM.java:504)
	at hudson.model.AbstractProject.checkout(AbstractProject.java:1208)
	at hudson.model.AbstractBuild$AbstractBuildExecution.defaultCheckout(AbstractBuild.java:574)
	at jenkins.scm.SCMCheckoutStrategy.checkout(SCMCheckoutStrategy.java:86)
	at hudson.model.AbstractBuild$AbstractBuildExecution.run(AbstractBuild.java:499)
	at hudson.model.Run.execute(Run.java:1810)
	at hudson.maven.MavenModuleSetBuild.run(MavenModuleSetBuild.java:543)
	at hudson.model.ResourceController.execute(ResourceController.java:97)
	at hudson.model.Executor.run(Executor.java:429)
ERROR: Build step failed with exception
java.io.IOException: Cannot retrieve Git metadata for the build
	at org.jenkinsci.plugins.github.util.BuildDataHelper.getCommitSHA1(BuildDataHelper.java:87)
	at org.jenkinsci.plugins.github.status.sources.BuildDataRevisionShaSource.get(BuildDataRevisionShaSource.java:32)
	at org.jenkinsci.plugins.github.status.GitHubCommitStatusSetter.perform(GitHubCommitStatusSetter.java:135)
Caused: org.jenkinsci.plugins.github.common.CombineErrorHandler$ErrorHandlingException
	at org.jenkinsci.plugins.github.common.CombineErrorHandler.handle(CombineErrorHandler.java:74)
	at org.jenkinsci.plugins.github.status.GitHubCommitStatusSetter.perform(GitHubCommitStatusSetter.java:164)
	at hudson.tasks.BuildStepCompatibilityLayer.perform(BuildStepCompatibilityLayer.java:81)
	at hudson.tasks.BuildStepMonitor$1.perform(BuildStepMonitor.java:20)
	at hudson.model.AbstractBuild$AbstractBuildExecution.perform(AbstractBuild.java:744)
	at hudson.model.AbstractBuild$AbstractBuildExecution.performAllBuildSteps(AbstractBuild.java:690)
	at hudson.maven.MavenModuleSetBuild$MavenModuleSetBuildExecution.post2(MavenModuleSetBuild.java:1073)
	at hudson.model.AbstractBuild$AbstractBuildExecution.post(AbstractBuild.java:635)
	at hudson.model.Run.execute(Run.java:1835)
	at hudson.maven.MavenModuleSetBuild.run(MavenModuleSetBuild.java:543)
	at hudson.model.ResourceController.execute(ResourceController.java:97)
	at hudson.model.Executor.run(Executor.java:429)
Build step 'Set GitHub commit status (universal)' marked build as failure


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