Bedtools 2.18.0 build error

bedtools-build-error.log

Script started on Sun 15 Dec 2013 10:11:17 PM EST
]0;bchapman@hsph01:~/bio/cloudbiolinux]0;hsph01: ~/bio/cloudbiolinuxhsph01:~/bio/cloudbiolinux $ export CC=${CC:-`which gcc`} && export CXX=${CXX:-`which g++`} && brew install --verbose  
--inherit --fresh bedtools
==> Downloading https://github.com/arq5x/bedtools2/archive/v2.18.0.tar.gz
Already downloaded: /n/home05/bchapman/.cache/Homebrew/bedtools-2.18.0.tar.gz
tar xf /n/home05/bchapman/.cache/Homebrew/bedtools-2.18.0.tar.gz
==> make
Building BEDTools:
=========================================================
DETECTED_VERSION = v2.18.0
CURRENT_VERSION  = 
Updating version file.
 * Creating BamTools API
- Building in src/utils/BlockedIntervals
- Building in src/utils/bedFile
- Building in src/utils/fileType
- Building in src/utils/bedFilePE
- Building in src/utils/bedGraphFile
- Building in src/utils/BinTree
- Building in src/expand
- Building in src/bedToBam
- Building in src/nekSandbox1
- Building in src/mapBed
- Building in src/sortBed
- Building in src/bed12ToBed6
- Building in src/genomeCoverageBed
- Building in src/linksBed
- Building in src/jaccard
- Building in src/utils/Fasta
- Building in src/utils/BamTools
- Building in src/reldist
- Building in src/coverageBed
- Building in src/utils/chromsweep
- Building in src/bedpeToBam
- Building in src/multiBamCov
- Building in src/unionBedGraphs
- Building in src/nucBed
- Building in src/utils/gzstream
- Building in src/utils/version
- Building in src/maskFastaFromBed
- Building in src/tagBam
- Building in src/mergeBed
- Building in src/windowBed
- Building in src/utils/general
- Building in src/fastaFromBed
- Building in src/utils/sequenceUtilities
- Building in src/sampleFile
- Building in src/clusterBed
- Building in src/bedToIgv
- Building in src/intersectFile
- Building in src/complementBed
- Building in src/utils/tabFile
- Building in src/utils/GenomeFile
- Building in src/annotateBed
- Building in src/pairToPair
- Building in src/windowMaker
- Building in src/utils/Contexts
- Building in src/utils/NewChromsweep
- Building in src/multiIntersectBed
- Building in src/randomBed
- Building in src/bamToFastq
- Building in src/flankBed
- Building in src/slopBed
- Building in src/getOverlap
- Building in src/utils/VectorOps
- Building in src/bamToBed
- Building in src/utils/BamTools-Ancillary
- Building in src/utils/FileRecordTools
- Building in src/shuffleBed
- Building in src/groupBy
- Building in src/subtractBed
- Building in src/pairToBed
- Building in src/regressTest
- Building in src/closestBed
g++ -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -c -o ../../../obj//gzstream.o gzstream.C -I.
  * compiling jaccard.cpp
  * compiling nekSandboxMain.cpp
  * compiling jaccardMain.cpp
  * compiling bedGraphFile.cpp
  * compiling bedFile.cpp
  * compiling expand.cpp
  * compiling flankBed.cpp
  * compiling tabFile.cpp
  * compiling sortMain.cpp
  * compiling flankBedMain.cpp
  * compiling BlockedIntervals.cpp
  * compiling bedFilePE.cpp
  * compiling BinTree.cpp
  * compiling GenomeFile.cpp
  * compiling BamAncillary.cpp
  * compiling sequenceUtils.cpp
  * compiling linksMain.cpp
 * compiling BamAlignment.cpp
compiling RegressTest.cpp
  * compiling bedToBam.cpp
  * compiling tagBamMain.cpp
  * compiling unionBedGraphsMain.cpp
  * compiling mergeMain.cpp
  * compiling NewChromsweep.cpp
  * compiling BamAncillary.cpp
  * compiling sampleMain.cpp
  * compiling fileType.cpp
  * compiling annotateMain.cpp
  * compiling fastaFromBedMain.cpp
  * compiling coverageMain.cpp
  * compiling shuffleBedMain.cpp
  * compiling complementMain.cpp
  * compiling nucBedMain.cpp
  * compiling genomeCoverageMain.cpp
  * compiling reldistMain.cpp
- Building in FileReaders
  * compiling windowMain.cpp
  * compiling intersectMain.cpp
  * compiling randomBedMain.cpp
  * compiling chromsweep.cpp
  * compiling Context.cpp
  * compiling mapMain.cpp
  * compiling slopBedMain.cpp
  * compiling Fasta.cpp
  * compiling getOverlap.cpp
  * compiling VectorOps.cpp
  * compiling QuickString.cpp
  * compiling version.cpp
  * compiling bed12ToBed6.cpp
  * compiling subtractMain.cpp
  * compiling maskFastaFromBedMain.cpp
  * compiling bamToFastqMain.cpp
  * compiling pairToPairMain.cpp
  * compiling windowMakerMain.cpp
  * compiling clusterMain.cpp
  * compiling groupBy.cpp
  * compiling bedToIgv.cpp
  * compiling bedpeToBam.cpp
  * compiling multiBamCovMain.cpp
  * compiling pairToBedMain.cpp
  * compiling multiIntersectBedMain.cpp
  * compiling bamToBed.cpp
  * compiling closestMain.cpp
  * compiling FileReader.cpp
  * compiling SingleLineDelimTransferBuffer.cpp
  * compiling SingleLineDelimTextFileReader.cpp
GenomeFile.cpp: In member function ‘void GenomeFile::loadGenomeFileIntoMap()’:
GenomeFile.cpp:60:26: warning: variable ‘c2’ set but not used [-Wunused-but-set-variable]
bamToFastqMain.cpp: In function ‘int bamtofastq_main(int, char**)’:
bamToFastqMain.cpp:38:10: warning: variable ‘haveFastq2’ set but not used [-Wunused-but-set-variable]
Fasta.cpp: In member function ‘void FastaIndexEntry::clear()’:
Fasta.cpp:28:14: warning: converting to non-pointer type ‘int’ from NULL [-Wconversion-null]
Fasta.cpp:31:17: warning: converting to non-pointer type ‘int’ from NULL [-Wconversion-null]
Fasta.cpp:32:17: warning: converting to non-pointer type ‘int’ from NULL [-Wconversion-null]
  * compiling BamFileReader.cpp
  * compiling ParseTools.cpp
  * compiling FileRecordTypeChecker.cpp
 * compiling BamMultiReader.cpp
  * compiling bamToFastq.cpp
  * compiling PushBackStreamBuf.cpp
  * compiling NewGenomeFile.cpp
  * compiling randomBed.cpp
bamToBed.cpp: In function ‘int bamtobed_main(int, char**)’:
bamToBed.cpp:88:10: warning: variable ‘useAlignmentScore’ set but not used [-Wunused-but-set-variable]
getOverlap.cpp: In function ‘int getoverlap_main(int, char**)’:
getOverlap.cpp:44:10: warning: variable ‘haveColumns’ set but not used [-Wunused-but-set-variable]
  * compiling sortBed.cpp
  * compiling clusterBed.cpp
bedToBam.cpp: In function ‘int bedtobam_main(int, char**)’:
bedToBam.cpp:60:10: warning: variable ‘haveMapQual’ set but not used [-Wunused-but-set-variable]
groupBy.cpp: In function ‘int groupby_main(int, char**)’:
groupBy.cpp:82:10: warning: variable ‘haveOps’ set but not used [-Wunused-but-set-variable]
clusterMain.cpp: In function ‘int cluster_main(int, char**)’:
clusterMain.cpp:38:10: warning: variable ‘haveMaxDistance’ set but not used [-Wunused-but-set-variable]
annotateMain.cpp: In function ‘int annotate_main(int, char**)’:
annotateMain.cpp:39:10: warning: variable ‘haveTitles’ set but not used [-Wunused-but-set-variable]
tagBamMain.cpp: In function ‘int tagbam_main(int, char**)’:
tagBamMain.cpp:38:10: warning: variable ‘haveFraction’ set but not used [-Wunused-but-set-variable]
mergeMain.cpp: In function ‘int merge_main(int, char**)’:
mergeMain.cpp:40:10: warning: variable ‘haveMaxDistance’ set but not used [-Wunused-but-set-variable]
unionBedGraphsMain.cpp: In function ‘int unionbedgraphs_main(int, char**)’:
unionBedGraphsMain.cpp:46:10: warning: variable ‘haveFiles’ set but not used [-Wunused-but-set-variable]
unionBedGraphsMain.cpp:48:10: warning: variable ‘haveGenome’ set but not used [-Wunused-but-set-variable]
unionBedGraphsMain.cpp:49:10: warning: variable ‘haveFiller’ set but not used [-Wunused-but-set-variable]
pairToPairMain.cpp: In function ‘int pairtopair_main(int, char**)’:
pairToPairMain.cpp:44:10: warning: variable ‘haveFraction’ set but not used [-Wunused-but-set-variable]
multiBamCovMain.cpp: In function ‘int multibamcov_main(int, char**)’:
multiBamCovMain.cpp:38:10: warning: variable ‘haveBed’ set but not used [-Wunused-but-set-variable]
multiBamCovMain.cpp:39:10: warning: variable ‘haveBams’ set but not used [-Wunused-but-set-variable]
multiBamCovMain.cpp:47:10: warning: variable ‘haveFraction’ set but not used [-Wunused-but-set-variable]
pairToBedMain.cpp: In function ‘int pairtobed_main(int, char**)’:
pairToBedMain.cpp:43:10: warning: variable ‘haveFraction’ set but not used [-Wunused-but-set-variable]
multiIntersectBedMain.cpp: In function ‘int multiintersect_main(int, char**)’:
multiIntersectBedMain.cpp:45:10: warning: variable ‘haveFiles’ set but not used [-Wunused-but-set-variable]
multiIntersectBedMain.cpp:47:10: warning: variable ‘haveGenome’ set but not used [-Wunused-but-set-variable]
multiIntersectBedMain.cpp:48:10: warning: variable ‘haveFiller’ set but not used [-Wunused-but-set-variable]
bedpeToBam.cpp: In function ‘int bedpetobam_main(int, char**)’:
bedpeToBam.cpp:61:10: warning: variable ‘haveMapQual’ set but not used [-Wunused-but-set-variable]
  * compiling SampleFile.cpp
mapMain.cpp: In function ‘int map_main(int, char**)’:
mapMain.cpp:44:10: warning: variable ‘haveColumn’ set but not used [-Wunused-but-set-variable]
mapMain.cpp:45:10: warning: variable ‘haveOperation’ set but not used [-Wunused-but-set-variable]
  * compiling unionBedGraphs.cpp
  * compiling intersectFile.cpp
  * compiling linksBed.cpp
  * compiling maskFastaFromBed.cpp
  * compiling complementBed.cpp
  * compiling coverageBed.cpp
  * compiling fastaFromBed.cpp
  * compiling slopBed.cpp
  * compiling subtractBed.cpp
  * compiling nucBed.cpp
  * compiling windowBed.cpp
  * compiling split.cpp
 * compiling BamReader.cpp
 * compiling BamWriter.cpp
  * compiling tagBam.cpp
  * compiling mapBed.cpp
  * compiling reldist.cpp
  * compiling closestBed.cpp
 * compiling SamHeader.cpp
  * compiling windowMaker.cpp
 * compiling SamProgram.cpp
- Building in Records
  * compiling multiBamCov.cpp
  * compiling CompressionTools.cpp
  * compiling multiIntersectBed.cpp
  * compiling annotateBed.cpp
  * compiling pairToPair.cpp
  * compiling mergeBed.cpp
 * compiling SamProgramChain.cpp
 * compiling SamReadGroup.cpp
  * compiling shuffleBed.cpp
 * compiling SamReadGroupDictionary.cpp
  * compiling pairToBed.cpp
  * compiling BufferedStreamMgr.cpp
  * compiling genomeCoverageBed.cpp
  * compiling InputStreamMgr.cpp
 * compiling BamHeader_p.cpp
 * compiling SamSequenceDictionary.cpp
 * compiling BamMultiReader_p.cpp
 * compiling SamSequence.cpp
  * compiling Bed3Interval.cpp
 * compiling BamReader_p.cpp
 * compiling BamRandomAccessController_p.cpp
 * compiling BamWriter_p.cpp
  * compiling RecordMgr.cpp
  * compiling Bed4Interval.cpp
  * compiling Record.cpp
  * compiling BedGraphInterval.cpp
 * compiling BamIndexFactory_p.cpp
  * compiling Bed5Interval.cpp
  * compiling Bed6Interval.cpp
  * compiling Bed12Interval.cpp
  * compiling BamRecord.cpp
compiling regressTestMain.cpp
  * compiling BedPlusInterval.cpp
 * compiling BamStandardIndex_p.cpp
 * compiling BamToolsIndex_p.cpp
  * compiling VcfRecord.cpp
 * compiling BamDeviceFactory_p.cpp
 * compiling BamFile_p.cpp
 * compiling BamFtp_p.cpp
  * compiling GffRecord.cpp
 * compiling BamHttp_p.cpp
  * compiling RecordKeyList.cpp
  * compiling BlockMgr.cpp
 * compiling BamPipe_p.cpp
 * compiling BgzfStream_p.cpp
 * compiling ByteArray_p.cpp
 * compiling HostAddress_p.cpp
 * compiling HostInfo_p.cpp
 * compiling HttpHeader_p.cpp
 * compiling RollingBuffer_p.cpp
 * compiling TcpSocketEngine_p.cpp
 * compiling ILocalIODevice_p.cpp
 * compiling TcpSocket_p.cpp
 * compiling SamFormatParser_p.cpp
 * compiling TcpSocketEngine_unix_p.cpp
pairToPair.cpp: In member function ‘void PairToPair::FindOverlaps(const BEDPE&)’:
pairToPair.cpp:112:14: warning: variable ‘found1’ set but not used [-Wunused-but-set-variable]
pairToPair.cpp:113:14: warning: variable ‘found2’ set but not used [-Wunused-but-set-variable]
 * compiling SamFormatPrinter_p.cpp
 * compiling SamHeaderValidator_p.cpp
InputStreamMgr.cpp: In member function ‘void InputStreamMgr::readZipChunk()’:
InputStreamMgr.cpp:283:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
pairToBed.cpp: In member function ‘void BedIntersectPE::FindSpanningOverlaps(const BEDPE&, std::vector<BED>&, const string&)’:
pairToBed.cpp:257:12: warning: variable ‘spanLength’ set but not used [-Wunused-but-set-variable]
pairToBed.cpp: In member function ‘bool BedIntersectPE::FindOneOrMoreSpanningOverlaps(const BEDPE&, const string&)’:
pairToBed.cpp:310:9: warning: variable ‘spanLength’ set but not used [-Wunused-but-set-variable]
 * compiling BamException_p.cpp
src/api/internal/index/BamStandardIndex_p.cpp: In member function ‘void BamTools::Internal::BamStandardIndex::WriteLinearOffsets(const int&, BamTools::Internal::BaiLinearOffsetVector&)’:
src/api/internal/index/BamStandardIndex_p.cpp:958:89: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
src/api/internal/io/BamHttp_p.cpp: In member function ‘bool BamTools::Internal::BamHttp::SendRequest(size_t)’:
src/api/internal/io/BamHttp_p.cpp:396:66: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
src/api/internal/io/TcpSocket_p.cpp: In member function ‘std::string BamTools::Internal::TcpSocket::ReadLine(int64_t)’:
src/api/internal/io/TcpSocket_p.cpp:336:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  * compiling FileRecordMgr.cpp
 * linking lib/libbamtools.a
ar cr lib/libbamtools.a src/api/BamAlignment.o src/api/BamMultiReader.o src/api/BamReader.o src/api/BamWriter.o src/api/SamHeader.o src/api/SamProgram.o src/api/SamProgramChain.o src/api/SamReadGroup.o src/api/SamReadGroupDictionary.o src/api/SamSequence.o src/api/SamSequenceDictionary.o src/api/internal/bam/BamHeader_p.o src/api/internal/bam/BamMultiReader_p.o src/api/internal/bam/BamRandomAccessController_p.o src/api/internal/bam/BamReader_p.o src/api/internal/bam/BamWriter_p.o src/api/internal/index/BamIndexFactory_p.o src/api/internal/index/BamStandardIndex_p.o src/api/internal/index/BamToolsIndex_p.o src/api/internal/io/BamDeviceFactory_p.o src/api/internal/io/BamFile_p.o src/api/internal/io/BamFtp_p.o src/api/internal/io/BamHttp_p.o src/api/internal/io/BamPipe_p.o src/api/internal/io/BgzfStream_p.o src/api/internal/io/ByteArray_p.o src/api/internal/io/HostAddress_p.o src/api/internal/io/HostInfo_p.o src/api/internal/io/HttpHeader_p.o src/api/internal/io/ILocalIODevice_p.o src/api/internal/io/RollingBuffer_p.o src/api/internal/io/TcpSocketEngine_p.o src/api/internal/io/TcpSocketEngine_unix_p.o src/api/internal/io/TcpSocket_p.o src/api/internal/sam/SamFormatParser_p.o src/api/internal/sam/SamFormatPrinter_p.o src/api/internal/sam/SamHeaderValidator_p.o src/api/internal/utils/BamException_p.o
ranlib lib/libbamtools.a
  * compiling RecordOutputMgr.cpp
- Building main bedtools binary.
obj/InputStreamMgr.o: In function `InputStreamMgr::detectBamOrBgzip(int&, int)':
InputStreamMgr.cpp:(.text+0x534): undefined reference to `BamTools::BamReader::OpenStream(std::istream*)'
InputStreamMgr.cpp:(.text+0x6c8): undefined reference to `BamTools::Internal::BgzfStream::OpenStream(std::istream*, BamTools::IBamIODevice::OpenMode)'
collect2: error: ld returned 1 exit status
make: *** [all] Error 1
==> Formula
Tap: homebrew/science
Path: /n/hsphS10/hsphfs1/chb/local/Library/Taps/homebrew-science/bedtools.rb
==> Configuration
HOMEBREW_VERSION: 0.9.5
HEAD: 0c737b1ef9fb9cfb0b715949ac8eed14d6ab1801
HOMEBREW_PREFIX: /n/hsphS10/hsphfs1/chb/local
CPU: 64-core 64-bit dunno
OS X: 0-x86_64
X11: N/A
==> ENV
CC: /usr/bin/gcc
CXX: /usr/bin/g++
OBJC: /usr/bin/gcc
OBJCXX: /usr/bin/g++
CFLAGS: -Os -w -pipe -march=core2 -msse4
CXXFLAGS: -Os -w -pipe -march=core2 -msse4
CPPFLAGS: -isystem/n/hsphS10/hsphfs1/chb/local/include
LDFLAGS: -L/n/hsphS10/hsphfs1/chb/local/lib -Wl,-headerpad_max_install_names
MAKEFLAGS: -j64
CMAKE_PREFIX_PATH: /n/hsphS10/hsphfs1/chb/local
PKG_CONFIG_LIBDIR: /n/hsphS10/hsphfs1/chb/local/lib/pkgconfig:/usr/lib/pkgconfig
ACLOCAL_PATH: /n/hsphS10/hsphfs1/chb/local/share/aclocal
PATH: /n/hsphS10/hsphfs1/chb/local/anaconda/bin:/n/hsphS10/hsphfs1/chb/local/bin:/usr/local/bin:/lsf/7.0/linux2.6-glibc2.3-x86_64/etc:/lsf/7.0/linux2.6-glibc2.3-x86_64/bin:/n/hsphS10/hsphfs1/chb/local/anaconda/bin:/n/hsphS10/hsphfs1/chb/local/bin:/usr/local/bin:/n/sw/gsl-1.15_gcc-4.7.2/bin:/n/sw/firefox-3.6.12:/n/sw/emboss/bin:/n/sw/jdk1.7.0_05/bin:/n/sw/mercurial-2.2.3_python-2.7_no-autoload-python/bin:/n/sw/aspera/bin:/n/sw/git-1.8.3/bin:/n/sw/cmake-2.8.8/bin:/n/sw/R-3.0.1_gcc-4.7.2/bin:/n/sw/jre1.7.0_13/bin:/n/sw/gcc-4.7.2/bin:/n/sw/intel_cluster_studio-2013/mkl/bin/intel64:/n/sw/ncbi-blast-2.2.23+/bin:/n/sw/dropbox/bin:/n/hsphS10/hsphfs1/chb/local/anaconda/bin:/n/hsphS10/hsphfs1/chb/local/bin:/usr/local/bin:/usr/local/openssh-6.3p1/sbin:/usr/local/openssh-6.3p1/bin:/usr/lib64/qt-3.3/bin:/usr/kerberos/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/openssh-6.3p1/bin:/sbin/:/usr/sbin:/bin:/usr/bin:/usr/local/bin:/usr/X11R6/bin:/var/lib/gems/1.8/bin:/n/sw/rc/bin/:/n/home05/bchapman/bin:/sbin/:/usr/sbin:/bin:/usr/bin:/usr/local/bin:/usr/X11R6/bin:/var/lib/gems/1.8/bin:/n/sw/rc/bin/:/sbin/:/usr/sbin:/bin:/usr/bin:/usr/local/bin:/usr/X11R6/bin:/var/lib/gems/1.8/bin:/n/sw/rc/bin/:/n/hsphS10/hsphfs1/chb/local/Library/Contributions/cmd

Error: bedtools did not build
Logs:
     /n/home05/bchapman/Library/Logs/Homebrew/bedtools/01.make

/usr/lib/ruby/1.8/open-uri.rb:277:in `open_http': 404 Not Found (OpenURI::HTTPError)
	from /usr/lib/ruby/1.8/open-uri.rb:616:in `buffer_open'
	from /usr/lib/ruby/1.8/open-uri.rb:164:in `open_loop'
	from /usr/lib/ruby/1.8/open-uri.rb:162:in `catch'
	from /usr/lib/ruby/1.8/open-uri.rb:162:in `open_loop'
	from /usr/lib/ruby/1.8/open-uri.rb:132:in `open_uri'
	from /usr/lib/ruby/1.8/open-uri.rb:518:in `open'
	from /usr/lib/ruby/1.8/open-uri.rb:26:in `open'
	from /n/hsphS10/hsphfs1/chb/local/Library/Homebrew/utils.rb:265:in `open'
	from /n/hsphS10/hsphfs1/chb/local/Library/Homebrew/utils.rb:282:in `each_issue_matching'
	from /n/hsphS10/hsphfs1/chb/local/Library/Homebrew/utils.rb:294:in `issues_for_formula'
	from /n/hsphS10/hsphfs1/chb/local/Library/Homebrew/exceptions.rb:178:in `issues'
	from /n/hsphS10/hsphfs1/chb/local/Library/Homebrew/exceptions.rb:212:in `dump'
	from /n/hsphS10/hsphfs1/chb/local/Library/brew.rb:118
]0;bchapman@hsph01:~/bio/cloudbiolinux]0;hsph01: ~/bio/cloudbiolinuxhsph01:~/bio/cloudbiolinux $ exit
exit

Script done on Sun 15 Dec 2013 10:11:51 PM EST