------------------------------------------------------------------------------- -- Phase: setup ------------------------------------------------------------------------------- Installing /packages/All/indexinfo-0.3.1.txz Installing /packages/All/gettext-runtime-0.21.txz Installing /packages/All/gmake-4.3_2.txz Installing /packages/All/libffi-3.3_1.txz Installing /packages/All/expat-2.2.8.txz Installing /packages/All/ncurses-6.2.20200831.txz Installing /packages/All/readline-8.0.4.txz Installing /packages/All/openssl-1.1.1g,1.txz Installing /packages/All/python37-3.7.9.txz ===== Message from python37-3.7.9: -- Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: py37-gdbm databases/py-gdbm@py37 py37-sqlite3 databases/py-sqlite3@py37 py37-tkinter x11-toolkits/py-tkinter@py37 SUCCEEDED 00:00:10 ------------------------------------------------------------------------------- -- Phase: check-sanity ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: pkg-depends ------------------------------------------------------------------------------- ===> bedtools-2.29.2 depends on file: /usr/local/sbin/pkg - found SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: fetch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch ------------------------------------------------------------------------------- ===> bedtools-2.29.2 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by bedtools-2.29.2 for building SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: checksum ------------------------------------------------------------------------------- ===> bedtools-2.29.2 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by bedtools-2.29.2 for building => SHA256 Checksum OK for arq5x-bedtools2-v2.29.2_GH0.tar.gz. SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: extract-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract ------------------------------------------------------------------------------- ===> bedtools-2.29.2 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by bedtools-2.29.2 for building ===> Extracting for bedtools-2.29.2 ===> bedtools-2.29.2 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by bedtools-2.29.2 for building => SHA256 Checksum OK for arq5x-bedtools2-v2.29.2_GH0.tar.gz. Extracted Memory Use: 55.16M SUCCEEDED 00:00:02 ------------------------------------------------------------------------------- -- Phase: patch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch ------------------------------------------------------------------------------- ===> Patching for bedtools-2.29.2 ===> Applying ports patches for bedtools-2.29.2 from /xports/biology/bedtools/files SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: build-depends ------------------------------------------------------------------------------- ===> bedtools-2.29.2 depends on package: gmake>=4.3 - found ===> bedtools-2.29.2 depends on file: /usr/local/bin/python3.7 - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: lib-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: configure ------------------------------------------------------------------------------- ===> bedtools-2.29.2 depends on package: gmake>=4.3 - found ===> bedtools-2.29.2 depends on file: /usr/local/bin/python3.7 - found ===> Configuring for bedtools-2.29.2 SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: build ------------------------------------------------------------------------------- ===> Building for bedtools-2.29.2 gmake[2]: Entering directory '/construction/biology/bedtools/bedtools2-2.29.2' cd src/utils/htslib && gmake config.h gmake[3]: Entering directory '/construction/biology/bedtools/bedtools2-2.29.2/src/utils/htslib' * compiling src/annotateBed/annotateMain.cpp * compiling src/annotateBed/annotateBed.cpp * compiling src/bamToBed/bamToBed.cpp * compiling src/bamToFastq/bamToFastqMain.cpp DETECTED_VERSION = v2.29.2 CURRENT_VERSION = Updating version file. * compiling src/bedtools.cpp Building BEDTools: * compiling src/bamToFastq/bamToFastq.cpp ========================================================= * compiling src/bedToBam/bedToBam.cpp CXXFLAGS is [-g -Wall -O2 -std=c++11 -pipe -D__FreeBSD__=9 -O2 -fno-strict-aliasing ] * compiling src/bedToIgv/bedToIgv.cpp * compiling src/bedpeToBam/bedpeToBam.cpp echo '/* Default config.h generated by Makefile */' > config.h echo '#define HAVE_LIBBZ2 1' >> config.h echo '#define HAVE_LIBLZMA 1' >> config.h echo '#ifndef __APPLE__' >> config.h echo '#define HAVE_LZMA_H 1' >> config.h echo '#endif' >> config.h echo '#define HAVE_FSEEKO 1' >> config.h echo '#define HAVE_DRAND48 1' >> config.h gmake[3]: Leaving directory '/construction/biology/bedtools/bedtools2-2.29.2/src/utils/htslib' * compiling src/bed12ToBed6/bed12ToBed6.cpp src/bedToBam/bedToBam.cpp: In function 'int bedtobam_main(int, char**)': src/bedToBam/bedToBam.cpp:60:10: warning: variable 'haveMapQual' set but not used [-Wunused-but-set-variable] bool haveMapQual = false; ^~~~~~~~~~~ src/annotateBed/annotateMain.cpp: In function 'int annotate_main(int, char**)': src/annotateBed/annotateMain.cpp:39:10: warning: variable 'haveTitles' set but not used [-Wunused-but-set-variable] bool haveTitles = false; ^~~~~~~~~~ src/bamToFastq/bamToFastqMain.cpp: In function 'int bamtofastq_main(int, char**)': src/bamToFastq/bamToFastqMain.cpp:38:10: warning: variable 'haveFastq2' set but not used [-Wunused-but-set-variable] bool haveFastq2 = false; ^~~~~~~~~~ src/bamToBed/bamToBed.cpp: In function 'int bamtobed_main(int, char**)': src/bamToBed/bamToBed.cpp:88:10: warning: variable 'useAlignmentScore' set but not used [-Wunused-but-set-variable] bool useAlignmentScore = false; ^~~~~~~~~~~~~~~~~ * compiling src/closestFile/closestHelp.cpp src/bedpeToBam/bedpeToBam.cpp: In function 'int bedpetobam_main(int, char**)': src/bedpeToBam/bedpeToBam.cpp:61:10: warning: variable 'haveMapQual' set but not used [-Wunused-but-set-variable] bool haveMapQual = false; ^~~~~~~~~~~ * compiling src/closestFile/closestFile.cpp In file included from src/utils/BamTools/include/api/BamReader.h:1, from src/bamToBed/bamToBed.cpp:12: src/utils/BamTools/include/SamHeader.hpp: In function 'int htslib_future::sam_hdr_rebuild(bam_hdr_t*)': src/utils/BamTools/include/SamHeader.hpp:32:16: warning: ignoring return value of 'int sam_hdr_write(samFile*, const bam_hdr_t*)', declared with attribute warn_unused_result [-Wunused-result] sam_hdr_write(fp, hdr); ~~~~~~~~~~~~~^~~~~~~~~ In file included from src/utils/BamTools/include/api/BamReader.h:1, from src/bamToFastq/bamToFastq.h:15, from src/bamToFastq/bamToFastq.cpp:15: src/utils/BamTools/include/SamHeader.hpp: In function 'int htslib_future::sam_hdr_rebuild(bam_hdr_t*)': src/utils/BamTools/include/SamHeader.hpp:32:16: warning: ignoring return value of 'int sam_hdr_write(samFile*, const bam_hdr_t*)', declared with attribute warn_unused_result [-Wunused-result] sam_hdr_write(fp, hdr); ~~~~~~~~~~~~~^~~~~~~~~ * compiling src/clusterBed/clusterMain.cpp * compiling src/clusterBed/clusterBed.cpp * compiling src/complementFile/complementHelp.cpp * compiling src/complementFile/complementFile.cpp src/clusterBed/clusterMain.cpp: In function 'int cluster_main(int, char**)': src/clusterBed/clusterMain.cpp:38:10: warning: variable 'haveMaxDistance' set but not used [-Wunused-but-set-variable] bool haveMaxDistance = false; ^~~~~~~~~~~~~~~ * compiling src/coverageFile/coverageHelp.cpp * compiling src/coverageFile/coverageFile.cpp * compiling src/expand/expand.cpp * compiling src/fastaFromBed/fastaFromBedMain.cpp * compiling src/fastaFromBed/fastaFromBed.cpp * compiling src/flankBed/flankBedMain.cpp * compiling src/flankBed/flankBed.cpp * compiling src/genomeCoverageBed/genomeCoverageMain.cpp * compiling src/genomeCoverageBed/genomeCoverageBed.cpp * compiling src/getOverlap/getOverlap.cpp * compiling src/groupBy/groupByHelp.cpp * compiling src/groupBy/groupBy.cpp * compiling src/intersectFile/intersectHelp.cpp src/getOverlap/getOverlap.cpp: In function 'int getoverlap_main(int, char**)': src/getOverlap/getOverlap.cpp:44:10: warning: variable 'haveColumns' set but not used [-Wunused-but-set-variable] bool haveColumns = false; ^~~~~~~~~~~ * compiling src/intersectFile/intersectFile.cpp In file included from src/utils/BamTools/include/api/BamReader.h:1, from src/utils/GenomeFile/NewGenomeFile.h:20, from src/genomeCoverageBed/genomeCoverageBed.h:13, from src/genomeCoverageBed/genomeCoverageBed.cpp:13: src/utils/BamTools/include/SamHeader.hpp: In function 'int htslib_future::sam_hdr_rebuild(bam_hdr_t*)': src/utils/BamTools/include/SamHeader.hpp:32:16: warning: ignoring return value of 'int sam_hdr_write(samFile*, const bam_hdr_t*)', declared with attribute warn_unused_result [-Wunused-result] sam_hdr_write(fp, hdr); ~~~~~~~~~~~~~^~~~~~~~~ * compiling src/fisher/fisherHelp.cpp * compiling src/fisher/fisher.cpp * compiling src/fisher/kfunc.cpp * compiling src/jaccard/jaccardHelp.cpp * compiling src/jaccard/jaccard.cpp * compiling src/linksBed/linksMain.cpp * compiling src/linksBed/linksBed.cpp * compiling src/maskFastaFromBed/maskFastaFromBedMain.cpp * compiling src/maskFastaFromBed/maskFastaFromBed.cpp * compiling src/mapFile/mapHelp.cpp * compiling src/mapFile/mapFile.cpp * compiling src/mergeFile/mergeHelp.cpp * compiling src/mergeFile/mergeFile.cpp * compiling src/multiBamCov/multiBamCovMain.cpp * compiling src/multiBamCov/multiBamCov.cpp * compiling src/multiIntersectBed/multiIntersectBedMain.cpp * compiling src/multiIntersectBed/multiIntersectBed.cpp * compiling src/nucBed/nucBedMain.cpp * compiling src/nucBed/nucBed.cpp * compiling src/pairToBed/pairToBedMain.cpp * compiling src/pairToBed/pairToBed.cpp * compiling src/pairToPair/pairToPairMain.cpp In file included from src/utils/BamTools/include/BamReader.hpp:4, from src/utils/BamTools/include/api/BamMultiReader.h:4, from src/multiBamCov/multiBamCov.h:16, from src/multiBamCov/multiBamCov.cpp:13: src/utils/BamTools/include/SamHeader.hpp: In function 'int htslib_future::sam_hdr_rebuild(bam_hdr_t*)': src/utils/BamTools/include/SamHeader.hpp:32:16: warning: ignoring return value of 'int sam_hdr_write(samFile*, const bam_hdr_t*)', declared with attribute warn_unused_result [-Wunused-result] sam_hdr_write(fp, hdr); ~~~~~~~~~~~~~^~~~~~~~~ src/multiIntersectBed/multiIntersectBedMain.cpp: In function 'int multiintersect_main(int, char**)': src/multiIntersectBed/multiIntersectBedMain.cpp:45:10: warning: variable 'haveFiles' set but not used [-Wunused-but-set-variable] bool haveFiles = false; ^~~~~~~~~ src/multiIntersectBed/multiIntersectBedMain.cpp:47:10: warning: variable 'haveGenome' set but not used [-Wunused-but-set-variable] bool haveGenome = false; ^~~~~~~~~~ src/multiIntersectBed/multiIntersectBedMain.cpp:48:10: warning: variable 'haveFiller' set but not used [-Wunused-but-set-variable] bool haveFiller = true; ^~~~~~~~~~ * compiling src/pairToPair/pairToPair.cpp src/multiBamCov/multiBamCovMain.cpp: In function 'int multibamcov_main(int, char**)': src/multiBamCov/multiBamCovMain.cpp:38:10: warning: variable 'haveBed' set but not used [-Wunused-but-set-variable] bool haveBed = false; ^~~~~~~ src/multiBamCov/multiBamCovMain.cpp:39:10: warning: variable 'haveBams' set but not used [-Wunused-but-set-variable] bool haveBams = false; ^~~~~~~~ src/multiBamCov/multiBamCovMain.cpp:47:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable] bool haveFraction = false; ^~~~~~~~~~~~ src/pairToPair/pairToPairMain.cpp: In function 'int pairtopair_main(int, char**)': src/pairToPair/pairToPairMain.cpp:44:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable] bool haveFraction = false; ^~~~~~~~~~~~ src/pairToBed/pairToBedMain.cpp: In function 'int pairtobed_main(int, char**)': src/pairToBed/pairToBedMain.cpp:43:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable] bool haveFraction = false; ^~~~~~~~~~~~ * compiling src/randomBed/randomBedMain.cpp * compiling src/randomBed/randomBed.cpp src/pairToBed/pairToBed.cpp: In member function 'void BedIntersectPE::FindSpanningOverlaps(const BEDPE&, std::vector&, const string&)': src/pairToBed/pairToBed.cpp:257:12: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable] CHRPOS spanLength = 0; ^~~~~~~~~~ src/pairToBed/pairToBed.cpp: In member function 'bool BedIntersectPE::FindOneOrMoreSpanningOverlaps(const BEDPE&, const string&)': src/pairToBed/pairToBed.cpp:310:12: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable] CHRPOS spanLength = 0; ^~~~~~~~~~ src/pairToPair/pairToPair.cpp: In member function 'void PairToPair::FindOverlaps(const BEDPE&)': src/pairToPair/pairToPair.cpp:112:14: warning: variable 'found1' set but not used [-Wunused-but-set-variable] bool found1 = false; ^~~~~~ src/pairToPair/pairToPair.cpp:113:14: warning: variable 'found2' set but not used [-Wunused-but-set-variable] bool found2 = false; ^~~~~~ * compiling src/regressTest/regressTestMain.cpp * compiling src/regressTest/RegressTest.cpp In file included from src/utils/BamTools/include/api/BamReader.h:1, from src/pairToBed/pairToBed.h:15, from src/pairToBed/pairToBed.cpp:13: src/utils/BamTools/include/SamHeader.hpp: In function 'int htslib_future::sam_hdr_rebuild(bam_hdr_t*)': src/utils/BamTools/include/SamHeader.hpp:32:16: warning: ignoring return value of 'int sam_hdr_write(samFile*, const bam_hdr_t*)', declared with attribute warn_unused_result [-Wunused-result] sam_hdr_write(fp, hdr); ~~~~~~~~~~~~~^~~~~~~~~ * compiling src/reldist/reldistMain.cpp * compiling src/reldist/reldist.cpp * compiling src/sampleFile/sampleHelp.cpp * compiling src/sampleFile/sampleFile.cpp * compiling src/shiftBed/shiftBedMain.cpp src/reldist/reldist.cpp: In member function 'void RelativeDistance::CalculateRelativeDistance()': src/reldist/reldist.cpp:129:25: warning: comparison of integer expressions of different signedness: 'CHRPOS' {aka 'long int'} and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] if (low_idx != chrom_mids->size() - 1) ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ * compiling src/shiftBed/shiftBed.cpp * compiling src/shuffleBed/shuffleBedMain.cpp * compiling src/shuffleBed/shuffleBed.cpp * compiling src/slopBed/slopBedMain.cpp * compiling src/slopBed/slopBed.cpp * compiling src/sortBed/sortMain.cpp * compiling src/sortBed/sortBed.cpp * compiling src/spacingFile/spacingHelp.cpp * compiling src/spacingFile/spacingFile.cpp * compiling src/split/splitBedMain.cpp * compiling src/split/splitBed.cpp * compiling src/subtractFile/subtractHelp.cpp * compiling src/subtractFile/subtractFile.cpp * compiling src/summaryFile/summaryHelp.cpp * compiling src/summaryFile/summaryFile.cpp * compiling src/tagBam/tagBamMain.cpp * compiling src/tagBam/tagBam.cpp * compiling src/unionBedGraphs/unionBedGraphsMain.cpp * compiling src/unionBedGraphs/unionBedGraphs.cpp * compiling src/windowBed/windowMain.cpp * compiling src/windowBed/windowBed.cpp * compiling src/windowMaker/windowMakerMain.cpp In file included from src/utils/BamTools/include/api/BamReader.h:1, from src/tagBam/tagBam.h:17, from src/tagBam/tagBam.cpp:13: src/utils/BamTools/include/SamHeader.hpp: In function 'int htslib_future::sam_hdr_rebuild(bam_hdr_t*)': src/utils/BamTools/include/SamHeader.hpp:32:16: warning: ignoring return value of 'int sam_hdr_write(samFile*, const bam_hdr_t*)', declared with attribute warn_unused_result [-Wunused-result] sam_hdr_write(fp, hdr); ~~~~~~~~~~~~~^~~~~~~~~ src/unionBedGraphs/unionBedGraphsMain.cpp: In function 'int unionbedgraphs_main(int, char**)': src/unionBedGraphs/unionBedGraphsMain.cpp:46:10: warning: variable 'haveFiles' set but not used [-Wunused-but-set-variable] bool haveFiles = false; ^~~~~~~~~ src/unionBedGraphs/unionBedGraphsMain.cpp:48:10: warning: variable 'haveGenome' set but not used [-Wunused-but-set-variable] bool haveGenome = false; ^~~~~~~~~~ src/unionBedGraphs/unionBedGraphsMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-Wunused-but-set-variable] bool haveFiller = true; ^~~~~~~~~~ In file included from src/utils/BamTools/include/api/BamReader.h:1, from src/windowBed/windowBed.h:15, from src/windowBed/windowBed.cpp:13: src/utils/BamTools/include/SamHeader.hpp: In function 'int htslib_future::sam_hdr_rebuild(bam_hdr_t*)': src/utils/BamTools/include/SamHeader.hpp:32:16: warning: ignoring return value of 'int sam_hdr_write(samFile*, const bam_hdr_t*)', declared with attribute warn_unused_result [-Wunused-result] sam_hdr_write(fp, hdr); ~~~~~~~~~~~~~^~~~~~~~~ * compiling src/windowMaker/windowMaker.cpp * compiling src/utils/FileRecordTools/FileRecordMgr.cpp * compiling src/utils/FileRecordTools/FileRecordMergeMgr.cpp * compiling src/utils/FileRecordTools/FileReaders/FileReader.cpp * compiling src/utils/FileRecordTools/FileReaders/SingleLineDelimTextFileReader.cpp * compiling src/utils/FileRecordTools/FileReaders/BamFileReader.cpp * compiling src/utils/FileRecordTools/FileReaders/BufferedStreamMgr.cpp * compiling src/utils/FileRecordTools/FileReaders/InputStreamMgr.cpp * compiling src/utils/FileRecordTools/Records/Record.cpp * compiling src/utils/FileRecordTools/Records/EmptyRecord.cpp * compiling src/utils/FileRecordTools/Records/Bed3Interval.cpp * compiling src/utils/FileRecordTools/Records/Bed4Interval.cpp src/utils/FileRecordTools/FileReaders/BufferedStreamMgr.cpp: In member function 'bool BufferedStreamMgr::readFileChunk()': src/utils/FileRecordTools/FileReaders/BufferedStreamMgr.cpp:147:23: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] if (_mainBufCurrLen < _useBufSize) { ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ * compiling src/utils/FileRecordTools/Records/BedGraphInterval.cpp * compiling src/utils/FileRecordTools/Records/Bed5Interval.cpp * compiling src/utils/FileRecordTools/Records/Bed6Interval.cpp * compiling src/utils/FileRecordTools/Records/PlusFields.cpp * compiling src/utils/FileRecordTools/Records/GffRecord.cpp In file included from src/utils/BamTools/include/api/BamReader.h:1, from src/utils/FileRecordTools/FileReaders/InputStreamMgr.h:14, from src/utils/FileRecordTools/FileReaders/InputStreamMgr.cpp:8: src/utils/BamTools/include/SamHeader.hpp: In function 'int htslib_future::sam_hdr_rebuild(bam_hdr_t*)': src/utils/BamTools/include/SamHeader.hpp:32:16: warning: ignoring return value of 'int sam_hdr_write(samFile*, const bam_hdr_t*)', declared with attribute warn_unused_result [-Wunused-result] sam_hdr_write(fp, hdr); ~~~~~~~~~~~~~^~~~~~~~~ * compiling src/utils/FileRecordTools/Records/GffPlusRecord.cpp * compiling src/utils/FileRecordTools/Records/NoPosPlusRecord.cpp * compiling src/utils/FileRecordTools/Records/BedPlusInterval.cpp * compiling src/utils/FileRecordTools/Records/Bed12Interval.cpp * compiling src/utils/FileRecordTools/Records/BamRecord.cpp * compiling src/utils/FileRecordTools/Records/VcfRecord.cpp * compiling src/utils/FileRecordTools/Records/BlockMgr.cpp * compiling src/utils/FileRecordTools/Records/StrandQueue.cpp * compiling src/utils/FileRecordTools/Records/RecordMgr.cpp * compiling src/utils/FileRecordTools/Records/RecordList.cpp * compiling src/utils/FileRecordTools/Records/RecordKeyList.cpp * compiling src/utils/FileRecordTools/Records/RecordKeyVector.cpp * compiling src/utils/bedFile/bedFile.cpp src/utils/FileRecordTools/Records/BlockMgr.cpp: In member function 'int BlockMgr::getNonRedundantOverlap()': src/utils/FileRecordTools/Records/BlockMgr.cpp:194:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i = 1; i < _overlapStarts.size(); ++i) ~~^~~~~~~~~~~~~~~~~~~~~~~ * compiling src/utils/BinTree/BinTree.cpp * compiling src/utils/version/version.cpp * compiling src/utils/bedGraphFile/bedGraphFile.cpp * compiling src/utils/chromsweep/chromsweep.cpp * compiling src/utils/Contexts/ContextBase.cpp * compiling src/utils/Contexts/ContextIntersect.cpp * compiling src/utils/Contexts/ContextFisher.cpp * compiling src/utils/Contexts/ContextMap.cpp * compiling src/utils/Contexts/ContextSample.cpp * compiling src/utils/Contexts/ContextSpacing.cpp * compiling src/utils/Contexts/ContextMerge.cpp * compiling src/utils/Contexts/ContextJaccard.cpp * compiling src/utils/Contexts/ContextClosest.cpp * compiling src/utils/Contexts/ContextSubtract.cpp * compiling src/utils/Contexts/ContextCoverage.cpp * compiling src/utils/Contexts/ContextComplement.cpp * compiling src/utils/Contexts/ContextGroupBy.cpp * compiling src/utils/Contexts/ContextSummary.cpp * compiling src/utils/general/ParseTools.cpp * compiling src/utils/general/PushBackStreamBuf.cpp * compiling src/utils/general/CompressionTools.cpp * compiling src/utils/general/Tokenizer.cpp * compiling src/utils/general/CommonHelp.cpp * compiling src/utils/general/ErrorMsg.cpp c++ -g -Wall -O2 -std=c++11 -pipe -D__FreeBSD__=9 -O2 -fno-strict-aliasing -Isrc/utils/gzstream -c -o obj/gzstream.o src/utils/gzstream/gzstream.C * compiling src/utils/fileType/fileType.cpp * compiling src/utils/fileType/FileRecordTypeChecker.cpp * compiling src/utils/bedFilePE/bedFilePE.cpp * compiling src/utils/KeyListOps/KeyListOps.cpp * compiling src/utils/KeyListOps/KeyListOpsMethods.cpp * compiling src/utils/NewChromsweep/NewChromsweep.cpp * compiling src/utils/NewChromsweep/CloseSweep.cpp * compiling src/utils/sequenceUtilities/sequenceUtils.cpp src/utils/fileType/FileRecordTypeChecker.cpp: In member function 'bool FileRecordTypeChecker::isTextDelimtedFormat(const char*, size_t)': src/utils/fileType/FileRecordTypeChecker.cpp:366:19: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] for (int j=0; j < len; j++) { ~~^~~~~ * compiling src/utils/tabFile/tabFile.cpp * compiling src/utils/BamTools-Ancillary/BamAncillary.cpp * compiling src/utils/BlockedIntervals/BlockedIntervals.cpp * compiling src/utils/Fasta/Fasta.cpp * compiling src/utils/Fasta/split.cpp * compiling src/utils/VectorOps/VectorOps.cpp * compiling src/utils/GenomeFile/NewGenomeFile.cpp * compiling src/utils/GenomeFile/GenomeFile.cpp * compiling src/utils/RecordOutputMgr/RecordOutputMgr.cpp * compiling src/utils/ToolBase/ToolBase.cpp * compiling src/utils/driver/BedtoolsDriver.cpp cd src/utils/htslib && gmake lib-static gmake[3]: Entering directory '/construction/biology/bedtools/bedtools2-2.29.2/src/utils/htslib' cc -pipe -D__FreeBSD__=9 -O2 -fno-strict-aliasing -I. -c -o kfunc.o kfunc.c - Creating executables for old CLI. src/utils/GenomeFile/GenomeFile.cpp: In member function 'void GenomeFile::loadGenomeFileIntoMap()': src/utils/GenomeFile/GenomeFile.cpp:60:26: warning: variable 'c2' set but not used [-Wunused-but-set-variable] long c2; ^~ done. cc -pipe -D__FreeBSD__=9 -O2 -fno-strict-aliasing -I. -c -o knetfile.o knetfile.c cc -pipe -D__FreeBSD__=9 -O2 -fno-strict-aliasing -I. -c -o kstring.o kstring.c cc -pipe -D__FreeBSD__=9 -O2 -fno-strict-aliasing -I. -c -o bcf_sr_sort.o bcf_sr_sort.c cc -pipe -D__FreeBSD__=9 -O2 -fno-strict-aliasing -I. -c -o bgzf.o bgzf.c cc -pipe -D__FreeBSD__=9 -O2 -fno-strict-aliasing -I. -c -o errmod.o errmod.c cc -pipe -D__FreeBSD__=9 -O2 -fno-strict-aliasing -I. -c -o faidx.o faidx.c cc -pipe -D__FreeBSD__=9 -O2 -fno-strict-aliasing -I. -c -o hfile.o hfile.c src/utils/RecordOutputMgr/RecordOutputMgr.cpp: In member function 'void RecordOutputMgr::printClosest(RecordKeyVector&, const std::vector*)': src/utils/RecordOutputMgr/RecordOutputMgr.cpp:170:42: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] if (context->getNumClosestHitsWanted() > keyList.size()) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ src/utils/RecordOutputMgr/RecordOutputMgr.cpp: In member function 'void RecordOutputMgr::reportOverlapSummary(RecordKeyVector&)': src/utils/RecordOutputMgr/RecordOutputMgr.cpp:455:24: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] for (size_t i = 1; i < _context->getNumInputFiles(); i++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cc -pipe -D__FreeBSD__=9 -O2 -fno-strict-aliasing -I. -c -o hfile_net.o hfile_net.c echo '#define HTS_VERSION "1.9"' > version.h cc -pipe -D__FreeBSD__=9 -O2 -fno-strict-aliasing -I. -c -o hts_os.o hts_os.c cc -pipe -D__FreeBSD__=9 -O2 -fno-strict-aliasing -I. -c -o md5.o md5.c cc -pipe -D__FreeBSD__=9 -O2 -fno-strict-aliasing -I. -c -o multipart.o multipart.c cc -pipe -D__FreeBSD__=9 -O2 -fno-strict-aliasing -I. -c -o probaln.o probaln.c cc -pipe -D__FreeBSD__=9 -O2 -fno-strict-aliasing -I. -c -o realn.o realn.c cc -pipe -D__FreeBSD__=9 -O2 -fno-strict-aliasing -I. -c -o regidx.o regidx.c cc -pipe -D__FreeBSD__=9 -O2 -fno-strict-aliasing -I. -c -o sam.o sam.c cc -pipe -D__FreeBSD__=9 -O2 -fno-strict-aliasing -I. -c -o synced_bcf_reader.o synced_bcf_reader.c cc -pipe -D__FreeBSD__=9 -O2 -fno-strict-aliasing -I. -c -o vcf_sweep.o vcf_sweep.c cc -pipe -D__FreeBSD__=9 -O2 -fno-strict-aliasing -I. -c -o tbx.o tbx.c cc -pipe -D__FreeBSD__=9 -O2 -fno-strict-aliasing -I. -c -o textutils.o textutils.c cc -pipe -D__FreeBSD__=9 -O2 -fno-strict-aliasing -I. -c -o thread_pool.o thread_pool.c cc -pipe -D__FreeBSD__=9 -O2 -fno-strict-aliasing -I. -c -o vcf.o vcf.c cc -pipe -D__FreeBSD__=9 -O2 -fno-strict-aliasing -I. -c -o vcfutils.o vcfutils.c cc -pipe -D__FreeBSD__=9 -O2 -fno-strict-aliasing -I. -c -o cram/cram_codecs.o cram/cram_codecs.c cc -pipe -D__FreeBSD__=9 -O2 -fno-strict-aliasing -I. -c -o cram/cram_decode.o cram/cram_decode.c cc -pipe -D__FreeBSD__=9 -O2 -fno-strict-aliasing -I. -c -o cram/cram_encode.o cram/cram_encode.c cc -pipe -D__FreeBSD__=9 -O2 -fno-strict-aliasing -I. -c -o cram/cram_external.o cram/cram_external.c cc -pipe -D__FreeBSD__=9 -O2 -fno-strict-aliasing -I. -c -o cram/cram_index.o cram/cram_index.c cc -pipe -D__FreeBSD__=9 -O2 -fno-strict-aliasing -I. -c -o cram/cram_io.o cram/cram_io.c cc -pipe -D__FreeBSD__=9 -O2 -fno-strict-aliasing -I. -c -o cram/cram_samtools.o cram/cram_samtools.c cc -pipe -D__FreeBSD__=9 -O2 -fno-strict-aliasing -I. -c -o cram/cram_stats.o cram/cram_stats.c cc -pipe -D__FreeBSD__=9 -O2 -fno-strict-aliasing -I. -c -o cram/files.o cram/files.c cc -pipe -D__FreeBSD__=9 -O2 -fno-strict-aliasing -I. -c -o cram/mFILE.o cram/mFILE.c cc -pipe -D__FreeBSD__=9 -O2 -fno-strict-aliasing -I. -c -o cram/open_trace_file.o cram/open_trace_file.c cc -pipe -D__FreeBSD__=9 -O2 -fno-strict-aliasing -I. -c -o cram/pooled_alloc.o cram/pooled_alloc.c cc -pipe -D__FreeBSD__=9 -O2 -fno-strict-aliasing -I. -c -o cram/rANS_static.o cram/rANS_static.c cc -pipe -D__FreeBSD__=9 -O2 -fno-strict-aliasing -I. -c -o cram/sam_header.o cram/sam_header.c cc -pipe -D__FreeBSD__=9 -O2 -fno-strict-aliasing -I. -c -o cram/string_alloc.o cram/string_alloc.c cc -pipe -D__FreeBSD__=9 -O2 -fno-strict-aliasing -I. -c -o hts.o hts.c ar -rc libhts.a kfunc.o knetfile.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o hfile.o hfile_net.o hts.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/files.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/sam_header.o cram/string_alloc.o ranlib libhts.a gmake[3]: Leaving directory '/construction/biology/bedtools/bedtools2-2.29.2/src/utils/htslib' - Building main bedtools binary. done. gmake[2]: Leaving directory '/construction/biology/bedtools/bedtools2-2.29.2' SUCCEEDED 00:01:26 ------------------------------------------------------------------------------- -- Phase: run-depends ------------------------------------------------------------------------------- ===> bedtools-2.29.2 depends on file: /usr/local/bin/python3.7 - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: stage ------------------------------------------------------------------------------- ===> Staging for bedtools-2.29.2 ===> bedtools-2.29.2 depends on file: /usr/local/bin/python3.7 - found ===> Generating temporary packing list gmake[2]: Entering directory '/construction/biology/bedtools/bedtools2-2.29.2' Building BEDTools: ========================================================= CXXFLAGS is [-g -Wall -O2 -std=c++11 -pipe -D__FreeBSD__=9 -O2 -fno-strict-aliasing ] DETECTED_VERSION = v2.29.2 CURRENT_VERSION = v2.29.2 * compiling src/bedToBam/bedToBam.cpp src/bedToBam/bedToBam.cpp: In function 'int bedtobam_main(int, char**)': src/bedToBam/bedToBam.cpp:60:10: warning: variable 'haveMapQual' set but not used [-Wunused-but-set-variable] bool haveMapQual = false; ^~~~~~~~~~~ * compiling src/coverageFile/coverageFile.cpp * compiling src/expand/expand.cpp * compiling src/fastaFromBed/fastaFromBedMain.cpp * compiling src/fastaFromBed/fastaFromBed.cpp * compiling src/genomeCoverageBed/genomeCoverageMain.cpp * compiling src/groupBy/groupByHelp.cpp * compiling src/jaccard/jaccardHelp.cpp * compiling src/linksBed/linksBed.cpp * compiling src/mapFile/mapFile.cpp * compiling src/pairToBed/pairToBedMain.cpp src/pairToBed/pairToBedMain.cpp: In function 'int pairtobed_main(int, char**)': src/pairToBed/pairToBedMain.cpp:43:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable] bool haveFraction = false; ^~~~~~~~~~~~ * compiling src/randomBed/randomBed.cpp * compiling src/shuffleBed/shuffleBedMain.cpp * compiling src/slopBed/slopBedMain.cpp * compiling src/slopBed/slopBed.cpp * compiling src/subtractFile/subtractFile.cpp * compiling src/summaryFile/summaryFile.cpp * compiling src/tagBam/tagBam.cpp In file included from src/utils/BamTools/include/api/BamReader.h:1, from src/tagBam/tagBam.h:17, from src/tagBam/tagBam.cpp:13: src/utils/BamTools/include/SamHeader.hpp: In function 'int htslib_future::sam_hdr_rebuild(bam_hdr_t*)': src/utils/BamTools/include/SamHeader.hpp:32:16: warning: ignoring return value of 'int sam_hdr_write(samFile*, const bam_hdr_t*)', declared with attribute warn_unused_result [-Wunused-result] sam_hdr_write(fp, hdr); ~~~~~~~~~~~~~^~~~~~~~~ * compiling src/windowMaker/windowMaker.cpp * compiling src/utils/FileRecordTools/FileRecordMgr.cpp * compiling src/utils/FileRecordTools/Records/Bed4Interval.cpp * compiling src/utils/FileRecordTools/Records/BedPlusInterval.cpp * compiling src/utils/FileRecordTools/Records/BamRecord.cpp * compiling src/utils/Contexts/ContextSample.cpp * compiling src/utils/Contexts/ContextCoverage.cpp * compiling src/utils/general/PushBackStreamBuf.cpp * compiling src/utils/general/CommonHelp.cpp * compiling src/utils/fileType/fileType.cpp * compiling src/utils/KeyListOps/KeyListOpsMethods.cpp * compiling src/utils/NewChromsweep/NewChromsweep.cpp * compiling src/utils/sequenceUtilities/sequenceUtils.cpp * compiling src/utils/Fasta/Fasta.cpp * compiling src/utils/Fasta/split.cpp * compiling src/utils/GenomeFile/GenomeFile.cpp src/utils/GenomeFile/GenomeFile.cpp: In member function 'void GenomeFile::loadGenomeFileIntoMap()': src/utils/GenomeFile/GenomeFile.cpp:60:26: warning: variable 'c2' set but not used [-Wunused-but-set-variable] long c2; ^~ * compiling src/utils/RecordOutputMgr/RecordOutputMgr.cpp src/utils/RecordOutputMgr/RecordOutputMgr.cpp: In member function 'void RecordOutputMgr::printClosest(RecordKeyVector&, const std::vector*)': src/utils/RecordOutputMgr/RecordOutputMgr.cpp:170:42: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] if (context->getNumClosestHitsWanted() > keyList.size()) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ src/utils/RecordOutputMgr/RecordOutputMgr.cpp: In member function 'void RecordOutputMgr::reportOverlapSummary(RecordKeyVector&)': src/utils/RecordOutputMgr/RecordOutputMgr.cpp:455:24: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] for (size_t i = 1; i < _context->getNumInputFiles(); i++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - Building main bedtools binary. done. mkdir -p /construction/biology/bedtools/stage/usr/local/bin for file in bin/* ; do \ cp -f $file /construction/biology/bedtools/stage/usr/local/bin; \ done gmake[2]: Leaving directory '/construction/biology/bedtools/bedtools2-2.29.2' /usr/bin/strip /construction/biology/bedtools/stage/usr/local/bin/bedtools ====> Compressing man pages (compress-man) ====> Running Q/A tests (stage-qa) Warning: You have disabled the licenses framework with DISABLE_LICENSES, unable to run checks Warning: Possible REINPLACE_CMD issues: - - REINPLACE_CMD ran, but did not modify file contents: docs/Makefile - - REINPLACE_CMD ran, but did not modify file contents: tutorial/Makefile - - REINPLACE_CMD ran, but did not modify file contents: src/nekSandbox1/Makefile - - REINPLACE_CMD ran, but did not modify file contents: src/utils/htslib/Makefile SUCCEEDED 00:01:58 ------------------------------------------------------------------------------- -- Phase: check-plist ------------------------------------------------------------------------------- ====> Checking for pkg-plist issues (check-plist) ===> Parsing plist ===> Checking for items in STAGEDIR missing from pkg-plist ===> Checking for items in pkg-plist which are not in STAGEDIR ===> No pkg-plist issues found (check-plist) SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: package ------------------------------------------------------------------------------- ===> Building package for bedtools-2.29.2 file sizes/checksums [38]: 0% file sizes/checksums [38]: 100% packing files [38]: 0% packing files [38]: 100% packing directories [0]: 0% packing directories [0]: 100% SUCCEEDED 00:00:04 TOTAL TIME 00:03:43