GitHub pull request #106 of commit ad6f14fd004942b8275f19cb636d373508c542fe 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/106/merge^{commit} # timeout=10 > git branch -a -v --no-abbrev --contains bf4af0eb7a5892e7115d864be69085c7acd53434 # timeout=10 Checking out Revision bf4af0eb7a5892e7115d864be69085c7acd53434 (origin/pr/106/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f bf4af0eb7a5892e7115d864be69085c7acd53434 First time build. Skipping changelog. [snap-prb] $ /bin/sh -xe /tmp/hudson6921987840753452725.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/AlignmentAdjuster.o SNAPLib/AlignmentAdjuster.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 g++ -O3 -Wno-format -MMD -ISNAPLib -msse -c -o SNAPLib/GzipDataWriter.o SNAPLib/GzipDataWriter.cpp g++ -O3 -Wno-format -MMD -ISNAPLib -msse -c -o SNAPLib/HashTable.o SNAPLib/HashTable.cpp g++ -O3 -Wno-format -MMD -ISNAPLib -msse -c -o SNAPLib/Histogram.o SNAPLib/Histogram.cpp g++ -O3 -Wno-format -MMD -ISNAPLib -msse -c -o SNAPLib/IntersectingPairedEndAligner.o SNAPLib/IntersectingPairedEndAligner.cpp g++ -O3 -Wno-format -MMD -ISNAPLib -msse -c -o SNAPLib/LandauVishkin.o SNAPLib/LandauVishkin.cpp g++ -O3 -Wno-format -MMD -ISNAPLib -msse -c -o SNAPLib/MultiInputReadSupplier.o SNAPLib/MultiInputReadSupplier.cpp g++ -O3 -Wno-format -MMD -ISNAPLib -msse -c -o SNAPLib/PairedAligner.o SNAPLib/PairedAligner.cpp g++ -O3 -Wno-format -MMD -ISNAPLib -msse -c -o SNAPLib/PairedReadMatcher.o SNAPLib/PairedReadMatcher.cpp g++ -O3 -Wno-format -MMD -ISNAPLib -msse -c -o SNAPLib/ParallelTask.o SNAPLib/ParallelTask.cpp g++ -O3 -Wno-format -MMD -ISNAPLib -msse -c -o SNAPLib/ProbabilityDistance.o SNAPLib/ProbabilityDistance.cpp g++ -O3 -Wno-format -MMD -ISNAPLib -msse -c -o SNAPLib/RangeSplitter.o SNAPLib/RangeSplitter.cpp g++ -O3 -Wno-format -MMD -ISNAPLib -msse -c -o SNAPLib/Read.o SNAPLib/Read.cpp g++ -O3 -Wno-format -MMD -ISNAPLib -msse -c -o SNAPLib/ReadReader.o SNAPLib/ReadReader.cpp g++ -O3 -Wno-format -MMD -ISNAPLib -msse -c -o SNAPLib/ReadSupplierQueue.o SNAPLib/ReadSupplierQueue.cpp g++ -O3 -Wno-format -MMD -ISNAPLib -msse -c -o SNAPLib/ReadWriter.o SNAPLib/ReadWriter.cpp g++ -O3 -Wno-format -MMD -ISNAPLib -msse -c -o SNAPLib/SAM.o SNAPLib/SAM.cpp g++ -O3 -Wno-format -MMD -ISNAPLib -msse -c -o SNAPLib/Seed.o SNAPLib/Seed.cpp g++ -O3 -Wno-format -MMD -ISNAPLib -msse -c -o SNAPLib/SeedSequencer.o SNAPLib/SeedSequencer.cpp g++ -O3 -Wno-format -MMD -ISNAPLib -msse -c -o SNAPLib/SingleAligner.o SNAPLib/SingleAligner.cpp g++ -O3 -Wno-format -MMD -ISNAPLib -msse -c -o SNAPLib/SortedDataWriter.o SNAPLib/SortedDataWriter.cpp g++ -O3 -Wno-format -MMD -ISNAPLib -msse -c -o SNAPLib/Tables.o SNAPLib/Tables.cpp g++ -O3 -Wno-format -MMD -ISNAPLib -msse -c -o SNAPLib/Util.o SNAPLib/Util.cpp g++ -O3 -Wno-format -MMD -ISNAPLib -msse -c -o SNAPLib/exit.o SNAPLib/exit.cpp g++ -O3 -Wno-format -MMD -ISNAPLib -msse -c -o SNAPLib/mapq.o SNAPLib/mapq.cpp g++ -O3 -Wno-format -MMD -ISNAPLib -msse -c -o SNAPLib/pool.o SNAPLib/pool.cpp SNAPLib/pool.cpp: In constructor 'Pool::Pool(unsigned int)': SNAPLib/pool.cpp:42: error: '_ASSERT' was not declared in this scope SNAPLib/pool.cpp: In destructor 'Pool::~Pool()': SNAPLib/pool.cpp:67: error: '_ASSERT' was not declared in this scope SNAPLib/pool.cpp:78: error: '_ASSERT' was not declared in this scope SNAPLib/pool.cpp:80: warning: deleting 'void*' is undefined SNAPLib/pool.cpp: In member function 'void Pool::allocateMoreObjects()': SNAPLib/pool.cpp:92: error: '_ASSERT' was not declared in this scope SNAPLib/pool.cpp: In member function 'void Pool::preAllocate(unsigned int)': SNAPLib/pool.cpp:140: error: '_ASSERT' was not declared in this scope SNAPLib/pool.cpp: In member function 'PoolEntry* Pool::getEntry()': SNAPLib/pool.cpp:156: error: '_ASSERT' was not declared in this scope SNAPLib/pool.cpp: In member function 'void Pool::releaseEntry(PoolEntry*)': SNAPLib/pool.cpp:193: error: '_ASSERT' was not declared in this scope SNAPLib/pool.cpp: In member function 'void* Pool::allocate()': SNAPLib/pool.cpp:204: error: '_ASSERT' was not declared in this scope SNAPLib/pool.cpp:217: error: 'PVOID' was not declared in this scope SNAPLib/pool.cpp: In member function 'void Pool::free(void*)': SNAPLib/pool.cpp:232: error: '_ASSERT' was not declared in this scope make: *** [SNAPLib/pool.o] Error 1 Build step 'Execute shell' marked build as failure Sending e-mails to: fnothaft@berkeley.edu Setting commit status on GitHub for https://github.com/amplab/snap/commit/bf4af0eb7a5892e7115d864be69085c7acd53434 Test FAILed. Refer to this link for build results (access rights to CI server needed): https://amplab.cs.berkeley.edu/jenkins//job/snap-prb/43/ Test FAILed. Finished: FAILURE