BEDTools-Version-2.14.3 grimmer$ make all
[ -d obj ] || mkdir -p obj
[ -d bin ] || mkdir -p bin
Building BEDTools:
=========================================================
- Building in src/utils/lineFileUtilities
  * compiling lineFileUtilities.cpp

- Building in src/utils/bedFile
  * compiling bedFile.cpp

- Building in src/utils/bedGraphFile
  * compiling bedGraphFile.cpp

- Building in src/utils/chromsweep
  * compiling chromsweep.cpp

- Building in src/utils/gzstream
g++ -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -c -o ../../../obj//gzstream.o gzstream.C -I.

- Building in src/utils/fileType
  * compiling fileType.cpp

- Building in src/utils/bedFilePE
  * compiling bedFilePE.cpp

- Building in src/utils/sequenceUtilities
  * compiling sequenceUtils.cpp

- Building in src/utils/tabFile
  * compiling tabFile.cpp

- Building in src/utils/BamTools
  * compiling BamAlignment.cpp
  * compiling BamMultiReader.cpp
  * compiling BamReader.cpp
  * compiling BamWriter.cpp
  * compiling SamHeader.cpp
  * compiling SamProgram.cpp
  * compiling SamProgramChain.cpp
  * compiling SamReadGroup.cpp
  * compiling SamReadGroupDictionary.cpp
  * compiling SamSequence.cpp
  * compiling SamSequenceDictionary.cpp
  * compiling BamHeader_p.cpp
  * compiling BamIndexFactory_p.cpp
  * compiling BamMultiReader_p.cpp
  * compiling BamRandomAccessController_p.cpp
  * compiling BamReader_p.cpp
  * compiling BamStandardIndex_p.cpp
  * compiling BamToolsIndex_p.cpp
  * compiling BamWriter_p.cpp
  * compiling BgzfStream_p.cpp
  * compiling SamFormatParser_p.cpp
  * compiling SamFormatPrinter_p.cpp
  * compiling SamHeaderValidator_p.cpp
[ -d lib ] || mkdir -p lib
[ -d include ] || mkdir -p include
[ -d include/api ] || mkdir -p include/api
[ -d include/shared ] || mkdir -p include/shared
  * linking 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/BamHeader_p.o src/api/internal/BamIndexFactory_p.o src/api/internal/BamMultiReader_p.o src/api/internal/BamRandomAccessController_p.o src/api/internal/BamReader_p.o src/api/internal/BamStandardIndex_p.o src/api/internal/BamToolsIndex_p.o src/api/internal/BamWriter_p.o src/api/internal/BgzfStream_p.o src/api/internal/SamFormatParser_p.o src/api/internal/SamFormatPrinter_p.o src/api/internal/SamHeaderValidator_p.o

- Building in src/utils/BamTools-Ancillary
  * compiling BamAncillary.cpp

- Building in src/utils/Fasta
  * compiling Fasta.cpp
  * compiling split.cpp

- Building in src/utils/genomeFile
  * compiling genomeFile.cpp

- Building in src/annotateBed
  * compiling annotateMain.cpp
  * compiling annotateBed.cpp
  * linking annotateBed

- Building in src/bamToBed
  * compiling bamToBed.cpp
  * linking bamToBed
ld: in ../utils//BamTools/lib//libbamtools.a, archive has no table of contents for architecture x86_64
collect2: ld returned 1 exit status
make[1]: *** [bamToBed] Error 1

- Building in src/bedToBam
  * compiling bedToBam.cpp
  * linking bedToBam
ld: in ../utils//BamTools/lib//libbamtools.a, archive has no table of contents for architecture x86_64
collect2: ld returned 1 exit status
make[1]: *** [bedToBam] Error 1

- Building in src/bedToIgv
  * compiling bedToIgv.cpp
  * linking bedToIgv

- Building in src/bed12ToBed6
  * compiling bed12ToBed6.cpp
  * linking bed12ToBed6

- Building in src/closestBed
  * compiling closestMain.cpp
  * compiling closestBed.cpp
closestBed.cpp: In member function ‘void BedClosest::FindWindowOverlaps(BED&, std::vector<BED, std::allocator<BED> >&)’:
closestBed.cpp:118: warning: comparison between signed and unsigned integer expressions
closestBed.cpp:126: warning: comparison between signed and unsigned integer expressions
closestBed.cpp:141: warning: comparison between signed and unsigned integer expressions
closestBed.cpp:148: warning: comparison between signed and unsigned integer expressions
  * linking closestBed

- Building in src/complementBed
  * compiling complementMain.cpp
  * compiling complementBed.cpp
  * linking complementBed

- Building in src/coverageBed
  * compiling coverageMain.cpp
  * compiling coverageBed.cpp
  * linking coverageBed
ld: in ../utils//BamTools/lib//libbamtools.a, archive has no table of contents for architecture x86_64
collect2: ld returned 1 exit status
make[1]: *** [coverageBed] Error 1

- Building in src/fastaFromBed
  * compiling fastaFromBedMain.cpp
  * compiling fastaFromBed.cpp
  * linking fastaFromBed

- Building in src/flankBed
  * compiling flankBedMain.cpp
  * compiling flankBed.cpp
  * linking flankBed

- Building in src/genomeCoverageBed
  * compiling genomeCoverageMain.cpp
  * compiling genomeCoverageBed.cpp
  * linking genomeCoverageBed
ld: in ../utils//BamTools/lib//libbamtools.a, archive has no table of contents for architecture x86_64
collect2: ld returned 1 exit status
make[1]: *** [genomeCoverageBed] Error 1

- Building in src/intersectBed
  * compiling intersectMain.cpp
  * compiling intersectBed.cpp
  * linking intersectBed
ld: in ../utils//BamTools/lib//libbamtools.a, archive has no table of contents for architecture x86_64
collect2: ld returned 1 exit status
make[1]: *** [intersectBed] Error 1

- Building in src/linksBed
  * compiling linksMain.cpp
  * compiling linksBed.cpp
  * linking linksBed

- Building in src/maskFastaFromBed
  * compiling maskFastaFromBedMain.cpp
  * compiling maskFastaFromBed.cpp
  * linking maskFastaFromBed

- Building in src/mergeBed
  * compiling mergeMain.cpp
  * compiling mergeBed.cpp
  * linking mergeBed

- Building in src/multiBamCov
  * compiling multiBamCovMain.cpp
  * compiling multiBamCov.cpp
  * linking multiBamCov
ld: in ../utils//BamTools/lib//libbamtools.a, archive has no table of contents for architecture x86_64
collect2: ld returned 1 exit status
make[1]: *** [multiBamCov] Error 1

- Building in src/multiIntersectBed
  * compiling multiIntersectBed.cpp
  * compiling multiIntersectBedMain.cpp
  * linking multiIntersectBed

- Building in src/nucBed
  * compiling nucBedMain.cpp
  * compiling nucBed.cpp
  * linking nucBed

- Building in src/overlap
  * compiling overlap.cpp
  * linking overlap

- Building in src/pairToBed
  * compiling pairToBedMain.cpp
  * compiling pairToBed.cpp
  * linking pairToBed
ld: in ../utils//BamTools/lib//libbamtools.a, archive has no table of contents for architecture x86_64
collect2: ld returned 1 exit status
make[1]: *** [pairToBed] Error 1

- Building in src/pairToPair
  * compiling pairToPairMain.cpp
  * compiling pairToPair.cpp
  * linking pairToPair

- Building in src/shuffleBed
  * compiling shuffleBedMain.cpp
  * compiling shuffleBed.cpp
  * linking shuffleBed

- Building in src/slopBed
  * compiling slopBedMain.cpp
  * compiling slopBed.cpp
  * linking slopBed

- Building in src/sortBed
  * compiling sortMain.cpp
  * compiling sortBed.cpp
  * linking sortBed

- Building in src/subtractBed
  * compiling subtractMain.cpp
  * compiling subtractBed.cpp
  * linking subtractBed

- Building in src/tagBam
  * compiling tagBamMain.cpp
  * compiling tagBam.cpp
  * linking tagBam
ld: in ../utils//BamTools/lib//libbamtools.a, archive has no table of contents for architecture x86_64
collect2: ld returned 1 exit status
make[1]: *** [tagBam] Error 1

- Building in src/unionBedGraphs
  * compiling unionBedGraphs.cpp
  * compiling unionBedGraphsMain.cpp
  * linking unionBedGraphs

- Building in src/windowBed
  * compiling windowMain.cpp
  * compiling windowBed.cpp
  * linking windowBed
ld: in ../utils//BamTools/lib//libbamtools.a, archive has no table of contents for architecture x86_64
collect2: ld returned 1 exit status
make[1]: *** [windowBed] Error 1