FailedConsole Output

GitHub pull request #63 of commit 237186c8b5af0cff8220c79a41a03eebeec1c3ac automatically merged.
[EnvInject] - Loading node environment variables.
Building remotely on amp-jenkins-worker-07 (centos spark-test) in workspace /home/jenkins/workspace/snap-prb
Wiping out workspace first.
Cloning the remote Git repository
Cloning repository https://github.com/amplab/snap.git
 > git init /home/jenkins/workspace/snap-prb # timeout=10
Fetching upstream changes from https://github.com/amplab/snap.git
 > git --version # timeout=10
 > git fetch --tags --progress https://github.com/amplab/snap.git +refs/heads/*:refs/remotes/origin/*
 > git config remote.origin.url https://github.com/amplab/snap.git # timeout=10
 > git config --add remote.origin.fetch +refs/heads/*:refs/remotes/origin/* # timeout=10
 > git config remote.origin.url https://github.com/amplab/snap.git # timeout=10
Fetching upstream changes from https://github.com/amplab/snap.git
 > git fetch --tags --progress https://github.com/amplab/snap.git +refs/pull/*:refs/remotes/origin/pr/*
 > git rev-parse origin/pr/63/merge^{commit} # timeout=10
 > git branch -a --contains 260ea33d7b33d8ce55e2b907b197be2440a36d85 # timeout=10
 > git rev-parse remotes/origin/pr/63/merge^{commit} # timeout=10
Checking out Revision 260ea33d7b33d8ce55e2b907b197be2440a36d85 (origin/pr/63/merge)
 > git config core.sparsecheckout # timeout=10
 > git checkout -f 260ea33d7b33d8ce55e2b907b197be2440a36d85
First time build. Skipping changelog.
[snap-prb] $ /bin/sh -xe /tmp/hudson5204508223292264970.sh
+ make
g++ -O3 -Wno-format -MMD -ISNAPLib -msse   -c -o SNAPLib/AlignerContext.o SNAPLib/AlignerContext.cpp
g++ -O3 -Wno-format -MMD -ISNAPLib -msse   -c -o SNAPLib/AlignerOptions.o SNAPLib/AlignerOptions.cpp
g++ -O3 -Wno-format -MMD -ISNAPLib -msse   -c -o SNAPLib/AlignerStats.o SNAPLib/AlignerStats.cpp
g++ -O3 -Wno-format -MMD -ISNAPLib -msse   -c -o SNAPLib/AlignmentResult.o SNAPLib/AlignmentResult.cpp
g++ -O3 -Wno-format -MMD -ISNAPLib -msse   -c -o SNAPLib/ApproximateCounter.o SNAPLib/ApproximateCounter.cpp
g++ -O3 -Wno-format -MMD -ISNAPLib -msse   -c -o SNAPLib/Bam.o SNAPLib/Bam.cpp
g++ -O3 -Wno-format -MMD -ISNAPLib -msse   -c -o SNAPLib/BaseAligner.o SNAPLib/BaseAligner.cpp
g++ -O3 -Wno-format -MMD -ISNAPLib -msse   -c -o SNAPLib/BiasTables.o SNAPLib/BiasTables.cpp
g++ -O3 -Wno-format -MMD -ISNAPLib -msse   -c -o SNAPLib/BigAlloc.o SNAPLib/BigAlloc.cpp
g++ -O3 -Wno-format -MMD -ISNAPLib -msse   -c -o SNAPLib/BufferedAsync.o SNAPLib/BufferedAsync.cpp
g++ -O3 -Wno-format -MMD -ISNAPLib -msse   -c -o SNAPLib/ChimericPairedEndAligner.o SNAPLib/ChimericPairedEndAligner.cpp
g++ -O3 -Wno-format -MMD -ISNAPLib -msse   -c -o SNAPLib/CommandProcessor.o SNAPLib/CommandProcessor.cpp
g++ -O3 -Wno-format -MMD -ISNAPLib -msse   -c -o SNAPLib/Compat.o SNAPLib/Compat.cpp
g++ -O3 -Wno-format -MMD -ISNAPLib -msse   -c -o SNAPLib/DataReader.o SNAPLib/DataReader.cpp
g++ -O3 -Wno-format -MMD -ISNAPLib -msse   -c -o SNAPLib/DataWriter.o SNAPLib/DataWriter.cpp
g++ -O3 -Wno-format -MMD -ISNAPLib -msse   -c -o SNAPLib/Error.o SNAPLib/Error.cpp
g++ -O3 -Wno-format -MMD -ISNAPLib -msse   -c -o SNAPLib/FASTA.o SNAPLib/FASTA.cpp
g++ -O3 -Wno-format -MMD -ISNAPLib -msse   -c -o SNAPLib/FASTQ.o SNAPLib/FASTQ.cpp
g++ -O3 -Wno-format -MMD -ISNAPLib -msse   -c -o SNAPLib/GenericFile.o SNAPLib/GenericFile.cpp
g++ -O3 -Wno-format -MMD -ISNAPLib -msse   -c -o SNAPLib/GenericFile_Blob.o SNAPLib/GenericFile_Blob.cpp
g++ -O3 -Wno-format -MMD -ISNAPLib -msse   -c -o SNAPLib/GenericFile_HDFS.o SNAPLib/GenericFile_HDFS.cpp
g++ -O3 -Wno-format -MMD -ISNAPLib -msse   -c -o SNAPLib/GenericFile_map.o SNAPLib/GenericFile_map.cpp
g++ -O3 -Wno-format -MMD -ISNAPLib -msse   -c -o SNAPLib/GenericFile_stdio.o SNAPLib/GenericFile_stdio.cpp
g++ -O3 -Wno-format -MMD -ISNAPLib -msse   -c -o SNAPLib/Genome.o SNAPLib/Genome.cpp
g++ -O3 -Wno-format -MMD -ISNAPLib -msse   -c -o SNAPLib/GenomeIndex.o SNAPLib/GenomeIndex.cpp
SNAPLib/GenomeIndex.cpp: In static member function 'static bool GenomeIndex::BuildIndexToDirectory(const Genome*, int, double, bool, const char*, unsigned int, unsigned int, bool, unsigned int, bool, const char*, unsigned int, bool, GenomeIndex*)':
SNAPLib/GenomeIndex.cpp:733: error: jump to label 'lifted_skip_overflow'
SNAPLib/GenomeIndex.cpp:544: error:   from here
SNAPLib/GenomeIndex.cpp:602: error:   crosses initialization of '_uint64 duplicateSeedsProcessed'
SNAPLib/GenomeIndex.cpp:601: error:   crosses initialization of '_uint64 overflowTableIndex'
SNAPLib/GenomeIndex.cpp:600: error:   crosses initialization of 'size_t totalBytesWritten'
SNAPLib/GenomeIndex.cpp:594: error:   crosses initialization of 'FILE* tablesFile'
SNAPLib/GenomeIndex.cpp:581: error:   crosses initialization of 'unsigned int* histogram'
SNAPLib/GenomeIndex.cpp:580: error:   crosses initialization of '_uint64 largestSeed'
SNAPLib/GenomeIndex.cpp:579: error:   crosses initialization of '_uint64 sumOfTooBigForHistogram'
SNAPLib/GenomeIndex.cpp:578: error:   crosses initialization of '_uint64 countOfTooBigForHistogram'
SNAPLib/GenomeIndex.cpp:577: error:   crosses initialization of 'const unsigned int maxHistogramEntry'
SNAPLib/GenomeIndex.cpp:575: error:   crosses initialization of '_int64 lastPrintTime'
SNAPLib/GenomeIndex.cpp:574: error:   crosses initialization of '_uint64 nBackpointersProcessed'
make: *** [SNAPLib/GenomeIndex.o] Error 1
Build step 'Execute shell' marked build as failure
ERROR: Failed to set Jenkins Identity header on email.
java.lang.NullPointerException
	at org.jenkinsci.main.modules.instance_identity.InstanceIdentity.get(InstanceIdentity.java:126)
	at jenkins.plugins.mailer.tasks.MimeMessageBuilder.setJenkinsInstanceIdent(MimeMessageBuilder.java:188)
	at jenkins.plugins.mailer.tasks.MimeMessageBuilder.buildMimeMessage(MimeMessageBuilder.java:166)
	at hudson.tasks.MailSender.createEmptyMail(MailSender.java:391)
	at hudson.tasks.MailSender.createFailureMail(MailSender.java:260)
	at hudson.tasks.MailSender.createMail(MailSender.java:178)
	at hudson.tasks.MailSender.run(MailSender.java:107)
	at hudson.tasks.Mailer.perform(Mailer.java:141)
	at hudson.tasks.BuildStepCompatibilityLayer.perform(BuildStepCompatibilityLayer.java:78)
	at hudson.tasks.BuildStepMonitor$1.perform(BuildStepMonitor.java:20)
	at hudson.model.AbstractBuild$AbstractBuildExecution.perform(AbstractBuild.java:782)
	at hudson.model.AbstractBuild$AbstractBuildExecution.performAllBuildSteps(AbstractBuild.java:723)
	at hudson.model.Build$BuildExecution.post2(Build.java:185)
	at hudson.model.AbstractBuild$AbstractBuildExecution.post(AbstractBuild.java:668)
	at hudson.model.Run.execute(Run.java:1763)
	at hudson.model.FreeStyleBuild.run(FreeStyleBuild.java:43)
	at hudson.model.ResourceController.execute(ResourceController.java:98)
	at hudson.model.Executor.run(Executor.java:410)
Sending e-mails to: fnothaft@berkeley.edu
Test FAILed.
Refer to this link for build results (access rights to CI server needed): 
https://amplab.cs.berkeley.edu/jenkins//job/snap-prb/16/
Test FAILed.
Finished: FAILURE