GitHub pull request #63 of commit e0df34d43302c55f3f5a944647859cac0754ea8c automatically merged. [EnvInject] - Loading node environment variables. Building remotely on amp-jenkins-worker-02 (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 cde7abe0e90febfe09d835154587f16d824a78a8 # timeout=10 > git rev-parse remotes/origin/pr/63/merge^{commit} # timeout=10 Checking out Revision cde7abe0e90febfe09d835154587f16d824a78a8 (origin/pr/63/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f cde7abe0e90febfe09d835154587f16d824a78a8 First time build. Skipping changelog. [snap-prb] $ /bin/sh -xe /tmp/hudson6053823494909675788.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 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/stdafx.o SNAPLib/stdafx.cpp g++ -O3 -Wno-format -MMD -ISNAPLib -msse -c -o apps/snap/Main.o apps/snap/Main.cpp g++ -O3 -Wno-format -MMD -ISNAPLib -msse -c -o apps/snap/stdafx.o apps/snap/stdafx.cpp g++ -o snap-aligner -O3 -Wno-format -MMD -ISNAPLib -msse -Itests -pthread SNAPLib/AlignerContext.o SNAPLib/AlignerOptions.o SNAPLib/AlignerStats.o SNAPLib/AlignmentResult.o SNAPLib/ApproximateCounter.o SNAPLib/Bam.o SNAPLib/BaseAligner.o SNAPLib/BiasTables.o SNAPLib/BigAlloc.o SNAPLib/BufferedAsync.o SNAPLib/ChimericPairedEndAligner.o SNAPLib/CommandProcessor.o SNAPLib/Compat.o SNAPLib/DataReader.o SNAPLib/DataWriter.o SNAPLib/Error.o SNAPLib/FASTA.o SNAPLib/FASTQ.o SNAPLib/GenericFile.o SNAPLib/GenericFile_Blob.o SNAPLib/GenericFile_HDFS.o SNAPLib/GenericFile_map.o SNAPLib/GenericFile_stdio.o SNAPLib/Genome.o SNAPLib/GenomeIndex.o SNAPLib/GzipDataWriter.o SNAPLib/HashTable.o SNAPLib/Histogram.o SNAPLib/IntersectingPairedEndAligner.o SNAPLib/LandauVishkin.o SNAPLib/MultiInputReadSupplier.o SNAPLib/PairedAligner.o SNAPLib/PairedReadMatcher.o SNAPLib/ParallelTask.o SNAPLib/ProbabilityDistance.o SNAPLib/RangeSplitter.o SNAPLib/Read.o SNAPLib/ReadReader.o SNAPLib/ReadSupplierQueue.o SNAPLib/ReadWriter.o SNAPLib/SAM.o SNAPLib/Seed.o SNAPLib/SeedSequencer.o SNAPLib/SingleAligner.o SNAPLib/SortedDataWriter.o SNAPLib/Tables.o SNAPLib/Util.o SNAPLib/exit.o SNAPLib/mapq.o SNAPLib/stdafx.o apps/snap/Main.o apps/snap/stdafx.o -lrt -lz g++ -O3 -Wno-format -MMD -ISNAPLib -msse -c -o tests/EventTest.o tests/EventTest.cpp g++ -O3 -Wno-format -MMD -ISNAPLib -msse -c -o tests/LandauVishkinTest.o tests/LandauVishkinTest.cpp g++ -O3 -Wno-format -MMD -ISNAPLib -msse -c -o tests/ProbabilityDistanceTest.o tests/ProbabilityDistanceTest.cpp g++ -O3 -Wno-format -MMD -ISNAPLib -msse -c -o tests/TestLib.o tests/TestLib.cpp g++ -O3 -Wno-format -MMD -ISNAPLib -msse -c -o tests/main.o tests/main.cpp g++ -o unit_tests -O3 -Wno-format -MMD -ISNAPLib -msse -Itests -pthread SNAPLib/AlignerContext.o SNAPLib/AlignerOptions.o SNAPLib/AlignerStats.o SNAPLib/AlignmentResult.o SNAPLib/ApproximateCounter.o SNAPLib/Bam.o SNAPLib/BaseAligner.o SNAPLib/BiasTables.o SNAPLib/BigAlloc.o SNAPLib/BufferedAsync.o SNAPLib/ChimericPairedEndAligner.o SNAPLib/CommandProcessor.o SNAPLib/Compat.o SNAPLib/DataReader.o SNAPLib/DataWriter.o SNAPLib/Error.o SNAPLib/FASTA.o SNAPLib/FASTQ.o SNAPLib/GenericFile.o SNAPLib/GenericFile_Blob.o SNAPLib/GenericFile_HDFS.o SNAPLib/GenericFile_map.o SNAPLib/GenericFile_stdio.o SNAPLib/Genome.o SNAPLib/GenomeIndex.o SNAPLib/GzipDataWriter.o SNAPLib/HashTable.o SNAPLib/Histogram.o SNAPLib/IntersectingPairedEndAligner.o SNAPLib/LandauVishkin.o SNAPLib/MultiInputReadSupplier.o SNAPLib/PairedAligner.o SNAPLib/PairedReadMatcher.o SNAPLib/ParallelTask.o SNAPLib/ProbabilityDistance.o SNAPLib/RangeSplitter.o SNAPLib/Read.o SNAPLib/ReadReader.o SNAPLib/ReadSupplierQueue.o SNAPLib/ReadWriter.o SNAPLib/SAM.o SNAPLib/Seed.o SNAPLib/SeedSequencer.o SNAPLib/SingleAligner.o SNAPLib/SortedDataWriter.o SNAPLib/Tables.o SNAPLib/Util.o SNAPLib/exit.o SNAPLib/mapq.o SNAPLib/stdafx.o tests/EventTest.o tests/LandauVishkinTest.o tests/ProbabilityDistanceTest.o tests/TestLib.o tests/main.o -lrt -lz g++ -O3 -Wno-format -MMD -ISNAPLib -msse -c -o apps/SNAPCommand/SNAPCommand.o apps/SNAPCommand/SNAPCommand.cpp g++ -O3 -Wno-format -MMD -ISNAPLib -msse -c -o apps/SNAPCommand/stdafx.o apps/SNAPCommand/stdafx.cpp echo SNAPCOMMAND_OBJ is apps/SNAPCommand/SNAPCommand.o apps/SNAPCommand/stdafx.o SNAPCOMMAND_OBJ is apps/SNAPCommand/SNAPCommand.o apps/SNAPCommand/stdafx.o echo SNAP_OBJ is apps/snap/Main.o apps/snap/stdafx.o SNAP_OBJ is apps/snap/Main.o apps/snap/stdafx.o g++ -o SNAPCommand -O3 -Wno-format -MMD -ISNAPLib -msse -pthread SNAPLib/AlignerContext.o SNAPLib/AlignerOptions.o SNAPLib/AlignerStats.o SNAPLib/AlignmentResult.o SNAPLib/ApproximateCounter.o SNAPLib/Bam.o SNAPLib/BaseAligner.o SNAPLib/BiasTables.o SNAPLib/BigAlloc.o SNAPLib/BufferedAsync.o SNAPLib/ChimericPairedEndAligner.o SNAPLib/CommandProcessor.o SNAPLib/Compat.o SNAPLib/DataReader.o SNAPLib/DataWriter.o SNAPLib/Error.o SNAPLib/FASTA.o SNAPLib/FASTQ.o SNAPLib/GenericFile.o SNAPLib/GenericFile_Blob.o SNAPLib/GenericFile_HDFS.o SNAPLib/GenericFile_map.o SNAPLib/GenericFile_stdio.o SNAPLib/Genome.o SNAPLib/GenomeIndex.o SNAPLib/GzipDataWriter.o SNAPLib/HashTable.o SNAPLib/Histogram.o SNAPLib/IntersectingPairedEndAligner.o SNAPLib/LandauVishkin.o SNAPLib/MultiInputReadSupplier.o SNAPLib/PairedAligner.o SNAPLib/PairedReadMatcher.o SNAPLib/ParallelTask.o SNAPLib/ProbabilityDistance.o SNAPLib/RangeSplitter.o SNAPLib/Read.o SNAPLib/ReadReader.o SNAPLib/ReadSupplierQueue.o SNAPLib/ReadWriter.o SNAPLib/SAM.o SNAPLib/Seed.o SNAPLib/SeedSequencer.o SNAPLib/SingleAligner.o SNAPLib/SortedDataWriter.o SNAPLib/Tables.o SNAPLib/Util.o SNAPLib/exit.o SNAPLib/mapq.o SNAPLib/stdafx.o apps/SNAPCommand/SNAPCommand.o apps/SNAPCommand/stdafx.o -lrt -lz [snap-prb] $ /bin/sh -xe /tmp/hudson8355147543916834741.sh + ./unit_tests ProbabilityDistanceTest: - basic probabilities: [OK] - indels: [OK] LandauVishkinTest: - equal strings: [OK] - prefixes: [OK] - non-equal strings: [OK] - overly distant strings: [OK] - CIGAR strings: [OK] EventTest: - many waiters: [OK] - single waiters: [OK] 9 / 9 tests passed. Test PASSed. Refer to this link for build results (access rights to CI server needed): https://amplab.cs.berkeley.edu/jenkins//job/snap-prb/19/ Test PASSed. Finished: SUCCESS