=> Building biology/bedtools Started : Wednesday, 18 APR 2018 at 02:01:49 UTC Platform: 5.3-DEVELOPMENT DragonFly v5.3.0.81.g32506c-DEVELOPMENT #29: Tue Apr 10 08:49:52 PDT 2018 marino@pkgbox64.dragonflybsd.org:/usr/obj/usr/src/sys/X86_64_GENERIC x86_64 -------------------------------------------------- -- Environment -------------------------------------------------- UNAME_r=5.0-SYNTH UNAME_m=x86_64 UNAME_p=x86_64 UNAME_v=DragonFly 5.0-SYNTH UNAME_s=DragonFly PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SSL_NO_VERIFY_PEER=1 TERM=dumb PKG_CACHEDIR=/var/cache/pkg8 PKG_DBDIR=/var/db/pkg8 PORTSDIR=/xports LANG=C HOME=/root USER=root -------------------------------------------------- -- Options -------------------------------------------------- -------------------------------------------------- -- CONFIGURE_ENV -------------------------------------------------- MAKE=gmake PYTHON="/usr/local/bin/python2.7" XDG_DATA_HOME=/construction/biology/bedtools XDG_CONFIG_HOME=/construction/biology/bedtools HOME=/construction/biology/bedtools TMPDIR="/tmp" PATH=/construction/biology/bedtools/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCVER=gcc50 -------------------------------------------------- -- CONFIGURE_ARGS -------------------------------------------------- -------------------------------------------------- -- MAKE_ENV -------------------------------------------------- XDG_DATA_HOME=/construction/biology/bedtools XDG_CONFIG_HOME=/construction/biology/bedtools HOME=/construction/biology/bedtools TMPDIR="/tmp" PATH=/construction/biology/bedtools/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin NO_PIE=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES CCVER=gcc50 PREFIX=/usr/local LOCALBASE=/usr/local LIBDIR="/usr/lib" NOPROFILE=1 CC="cc" CFLAGS="-pipe -D__FreeBSD__=9 -O2 -fno-strict-aliasing" CPP="cpp" CPPFLAGS="" LDFLAGS="" LIBS="" CXX="c++" CXXFLAGS=" -pipe -D__FreeBSD__=9 -O2 -fno-strict-aliasing" MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" -------------------------------------------------- -- MAKE_ARGS -------------------------------------------------- DESTDIR=/construction/biology/bedtools/stage -------------------------------------------------- -- PLIST_SUB -------------------------------------------------- PORTDOCS="" PORTEXAMPLES="" PYTHON_INCLUDEDIR=include/python2.7 PYTHON_LIBDIR=lib/python2.7 PYTHON_PLATFORM=dragonfly5 PYTHON_PYOEXTENSION=pyo PYTHON_SITELIBDIR=lib/python2.7/site-packages PYTHON_SUFFIX=27 PYTHON_VER=2.7 PYTHON_VERSION=python2.7 PYTHON2="" PYTHON3="@comment " OSREL=5.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PROFILE="@comment " DOCSDIR="share/doc/bedtools" EXAMPLESDIR="share/examples/bedtools" DATADIR="share/bedtools" WWWDIR="www/bedtools" ETCDIR="etc/bedtools" -------------------------------------------------- -- SUB_LIST -------------------------------------------------- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/bedtools DOCSDIR=/usr/local/share/doc/bedtools EXAMPLESDIR=/usr/local/share/examples/bedtools WWWDIR=/usr/local/www/bedtools ETCDIR=/usr/local/etc/bedtools -------------------------------------------------- -- /etc/make.conf -------------------------------------------------- SYNTHPROFILE=Release-5.0 USE_PACKAGE_DEPENDS_ONLY=yes PACKAGE_BUILDING=yes BATCH=yes PKG_CREATE_VERBOSE=yes PORTSDIR=/xports DISTDIR=/distfiles WRKDIRPREFIX=/construction PORT_DBDIR=/options PACKAGES=/packages MAKE_JOBS_NUMBER_LIMIT=5 LICENSES_ACCEPTED= NONE HAVE_COMPAT_IA32_KERN= CONFIGURE_MAX_CMD_LEN=262144 _SMP_CPUS=8 UID=0 ARCH=x86_64 OPSYS=DragonFly DFLYVERSION=500000 OSVERSION=9999999 OSREL=5.0 _OSRELEASE=5.0-SYNTH -------------------------------------------------------------------------------- -- Phase: check-sanity -------------------------------------------------------------------------------- ===> License GPLv2 accepted by the user -------------------------------------------------------------------------------- -- Phase: pkg-depends -------------------------------------------------------------------------------- ===> bedtools-2.25.0 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.10.5.txz Installing pkg-1.10.5... Extracting pkg-1.10.5: .......... done ===> bedtools-2.25.0 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of bedtools-2.25.0 -------------------------------------------------------------------------------- -- Phase: fetch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: fetch -------------------------------------------------------------------------------- ===> License GPLv2 accepted by the user ===> Fetching all distfiles required by bedtools-2.25.0 for building -------------------------------------------------------------------------------- -- Phase: checksum -------------------------------------------------------------------------------- ===> License GPLv2 accepted by the user ===> Fetching all distfiles required by bedtools-2.25.0 for building => SHA256 Checksum OK for arq5x-bedtools2-v2.25.0_GH0.tar.gz. -------------------------------------------------------------------------------- -- Phase: extract-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: extract -------------------------------------------------------------------------------- ===> License GPLv2 accepted by the user ===> Fetching all distfiles required by bedtools-2.25.0 for building ===> Extracting for bedtools-2.25.0 ===> License GPLv2 accepted by the user ===> Fetching all distfiles required by bedtools-2.25.0 for building => SHA256 Checksum OK for arq5x-bedtools2-v2.25.0_GH0.tar.gz. -------------------------------------------------------------------------------- -- Phase: patch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: patch -------------------------------------------------------------------------------- ===> Patching for bedtools-2.25.0 ===> Applying ports patches for bedtools-2.25.0 -------------------------------------------------------------------------------- -- Phase: build-depends -------------------------------------------------------------------------------- ===> bedtools-2.25.0 depends on executable: gmake - not found ===> Installing existing package /packages/All/gmake-4.2.1_2.txz Installing gmake-4.2.1_2... `-- Installing gettext-runtime-0.19.8.1_1... | `-- Installing indexinfo-0.3.1... | `-- Extracting indexinfo-0.3.1: .... done `-- Extracting gettext-runtime-0.19.8.1_1: .......... done Extracting gmake-4.2.1_2: .......... done ===> bedtools-2.25.0 depends on executable: gmake - found ===> Returning to build of bedtools-2.25.0 ===> bedtools-2.25.0 depends on file: /usr/local/bin/python2.7 - not found ===> Installing existing package /packages/All/python27-2.7.14_1.txz Installing python27-2.7.14_1... `-- Installing expat-2.2.5... `-- Extracting expat-2.2.5: .......... done `-- Installing libffi-3.2.1_2... `-- Extracting libffi-3.2.1_2: .......... done `-- Installing libressl-2.6.4... `-- Extracting libressl-2.6.4: .......... done `-- Installing ncurses-6.0.0s20171223_1... `-- Extracting ncurses-6.0.0s20171223_1: .......... done `-- Installing readline-7.0.3_1... `-- Extracting readline-7.0.3_1: .......... done Extracting python27-2.7.14_1: .......... done Message from python27-2.7.14_1: =========================================================================== Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: bsddb databases/py-bsddb gdbm databases/py-gdbm sqlite3 databases/py-sqlite3 tkinter x11-toolkits/py-tkinter =========================================================================== ===> bedtools-2.25.0 depends on file: /usr/local/bin/python2.7 - found ===> Returning to build of bedtools-2.25.0 -------------------------------------------------------------------------------- -- Phase: lib-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: configure -------------------------------------------------------------------------------- ===> Configuring for bedtools-2.25.0 -------------------------------------------------------------------------------- -- Phase: build -------------------------------------------------------------------------------- ===> Building for bedtools-2.25.0 gmake[2]: Entering directory '/construction/biology/bedtools/bedtools2-2.25.0' Building BEDTools: ========================================================= DETECTED_VERSION = v2.25.0 CURRENT_VERSION = Updating version file. * Creating BamTools API - Building in src/utils/bedFile * compiling bedFile.cpp - Building in src/utils/BinTree * compiling BinTree.cpp - Building in src/utils/version * compiling version.cpp - Building in src/utils/bedGraphFile * compiling bedGraphFile.cpp - Building in src/utils/chromsweep * compiling chromsweep.cpp - Building in src/utils/Contexts * compiling ContextBase.cpp * compiling ContextIntersect.cpp * compiling ContextFisher.cpp * compiling ContextMap.cpp * compiling ContextSample.cpp * compiling ContextSpacing.cpp * compiling ContextMerge.cpp * compiling ContextJaccard.cpp * compiling ContextClosest.cpp * compiling ContextSubtract.cpp * compiling ContextCoverage.cpp * compiling ContextComplement.cpp * compiling ContextGroupBy.cpp - Building in src/utils/FileRecordTools * compiling FileRecordMgr.cpp * compiling FileRecordMergeMgr.cpp - Building in FileReaders * compiling FileReader.cpp * compiling SingleLineDelimTextFileReader.cpp * compiling BamFileReader.cpp * compiling BufferedStreamMgr.cpp * compiling InputStreamMgr.cpp - Building in Records * compiling Record.cpp * compiling EmptyRecord.cpp * compiling Bed3Interval.cpp * compiling Bed4Interval.cpp * compiling BedGraphInterval.cpp * compiling Bed5Interval.cpp * compiling Bed6Interval.cpp * compiling PlusFields.cpp * compiling BedPlusInterval.cpp * compiling Bed12Interval.cpp * compiling BamRecord.cpp * compiling GffRecord.cpp * compiling GffPlusRecord.cpp * compiling VcfRecord.cpp * compiling NoPosPlusRecord.cpp * compiling BlockMgr.cpp * compiling StrandQueue.cpp * compiling RecordMgr.cpp * compiling RecordList.cpp * compiling RecordKeyList.cpp * compiling RecordKeyVector.cpp - Building in src/utils/FileRecordTools/FileReaders gmake[3]: Nothing to be done for 'all'. - Building in src/utils/FileRecordTools/Records gmake[3]: Nothing to be done for 'all'. - Building in src/utils/general * compiling QuickString.cpp * compiling ParseTools.cpp ParseTools.cpp: In function 'int str2chrPos(const char*, size_t)': ParseTools.cpp:31:7: warning: unused variable 'hasExponent' [-Wunused-variable] bool hasExponent = false; ^ * compiling PushBackStreamBuf.cpp * compiling CompressionTools.cpp * compiling Tokenizer.cpp * compiling CommonHelp.cpp - Building in src/utils/gzstream c++ -pipe -D__FreeBSD__=9 -O2 -fno-strict-aliasing -Wall -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -c -o ../../../obj//gzstream.o gzstream.C -I. - Building in src/utils/fileType * compiling fileType.cpp * compiling FileRecordTypeChecker.cpp - Building in src/utils/bedFilePE * compiling bedFilePE.cpp - Building in src/utils/KeyListOps * compiling KeyListOps.cpp * compiling KeyListOpsMethods.cpp - Building in src/utils/NewChromsweep * compiling NewChromsweep.cpp * compiling CloseSweep.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 BamMultiReader_p.cpp * compiling BamRandomAccessController_p.cpp * compiling BamReader_p.cpp * compiling BamWriter_p.cpp * compiling BamIndexFactory_p.cpp * compiling BamStandardIndex_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:958:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if ( numBytesWritten != (sizeof(offsetCount) + linearOffsets.size()*sizeof(uint64_t)) ) ^ * compiling BamToolsIndex_p.cpp * compiling BamDeviceFactory_p.cpp * compiling BamFile_p.cpp * compiling BamFtp_p.cpp * compiling BamHttp_p.cpp src/api/internal/io/BamHttp_p.cpp: In member function 'bool BamTools::Internal::BamHttp::SendRequest(size_t)': src/api/internal/io/BamHttp_p.cpp:396:63: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] return ( WriteToSocket(requestHeader.c_str(), headerSize) == headerSize ); ^ * 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 ILocalIODevice_p.cpp * compiling RollingBuffer_p.cpp * compiling TcpSocketEngine_p.cpp * compiling TcpSocketEngine_unix_p.cpp * compiling TcpSocket_p.cpp * compiling SamFormatParser_p.cpp * compiling SamFormatPrinter_p.cpp * compiling SamHeaderValidator_p.cpp * compiling BamException_p.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 - Building in src/utils/BamTools-Ancillary * compiling BamAncillary.cpp * compiling BamAncillary.cpp - Building in src/utils/BlockedIntervals * compiling BlockedIntervals.cpp - Building in src/utils/Fasta * compiling Fasta.cpp * compiling split.cpp - Building in src/utils/VectorOps * compiling VectorOps.cpp - Building in src/utils/GenomeFile * compiling GenomeFile.cpp GenomeFile.cpp: In member function 'void GenomeFile::loadGenomeFileIntoMap()': GenomeFile.cpp:60:26: warning: variable 'c2' set but not used [-Wunused-but-set-variable] long c2; ^ * compiling NewGenomeFile.cpp - Building in src/utils/RecordOutputMgr * compiling RecordOutputMgr.cpp - Building in src/utils/ToolBase * compiling ToolBase.cpp - Building in src/utils/driver * compiling BedtoolsDriver.cpp - Building in src/annotateBed * compiling annotateMain.cpp annotateMain.cpp: In function 'int annotate_main(int, char**)': annotateMain.cpp:39:10: warning: variable 'haveTitles' set but not used [-Wunused-but-set-variable] bool haveTitles = false; ^ * compiling annotateBed.cpp - Building in src/bamToBed * compiling bamToBed.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] bool useAlignmentScore = false; ^ - Building in src/bamToFastq * compiling bamToFastqMain.cpp bamToFastqMain.cpp: In function 'int bamtofastq_main(int, char**)': bamToFastqMain.cpp:38:10: warning: variable 'haveFastq2' set but not used [-Wunused-but-set-variable] bool haveFastq2 = false; ^ * compiling bamToFastq.cpp - Building in src/bedToBam * compiling bedToBam.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] bool haveMapQual = false; ^ - Building in src/bedpeToBam * compiling bedpeToBam.cpp bedpeToBam.cpp: In function 'int bedpetobam_main(int, char**)': bedpeToBam.cpp:61:10: warning: variable 'haveMapQual' set but not used [-Wunused-but-set-variable] bool haveMapQual = false; ^ - Building in src/bedToIgv * compiling bedToIgv.cpp - Building in src/bed12ToBed6 * compiling bed12ToBed6.cpp - Building in src/closestFile * compiling closestHelp.cpp * compiling closestFile.cpp - Building in src/clusterBed * compiling clusterMain.cpp clusterMain.cpp: In function 'int cluster_main(int, char**)': clusterMain.cpp:38:10: warning: variable 'haveMaxDistance' set but not used [-Wunused-but-set-variable] bool haveMaxDistance = false; ^ * compiling clusterBed.cpp - Building in src/complementFile * compiling complementHelp.cpp * compiling complementFile.cpp - Building in src/coverageFile * compiling coverageHelp.cpp * compiling coverageFile.cpp - Building in src/expand * compiling expand.cpp - Building in src/fastaFromBed * compiling fastaFromBedMain.cpp * compiling fastaFromBed.cpp - Building in src/flankBed * compiling flankBedMain.cpp * compiling flankBed.cpp - Building in src/genomeCoverageBed * compiling genomeCoverageMain.cpp * compiling genomeCoverageBed.cpp - Building in src/getOverlap * compiling getOverlap.cpp getOverlap.cpp: In function 'int getoverlap_main(int, char**)': getOverlap.cpp:44:10: warning: variable 'haveColumns' set but not used [-Wunused-but-set-variable] bool haveColumns = false; ^ - Building in src/groupBy * compiling groupBy.cpp * compiling groupByHelp.cpp - Building in src/intersectFile * compiling intersectHelp.cpp * compiling intersectFile.cpp - Building in src/fisher * compiling fisherHelp.cpp * compiling fisher.cpp * compiling kfunc.cpp - Building in src/jaccard * compiling jaccardHelp.cpp * compiling jaccard.cpp - Building in src/linksBed * compiling linksMain.cpp * compiling linksBed.cpp - Building in src/maskFastaFromBed * compiling maskFastaFromBedMain.cpp * compiling maskFastaFromBed.cpp - Building in src/mapFile * compiling mapHelp.cpp * compiling mapFile.cpp - Building in src/mergeFile * compiling mergeHelp.cpp * compiling mergeFile.cpp - Building in src/multiBamCov * compiling multiBamCovMain.cpp multiBamCovMain.cpp: In function 'int multibamcov_main(int, char**)': multiBamCovMain.cpp:38:10: warning: variable 'haveBed' set but not used [-Wunused-but-set-variable] bool haveBed = false; ^ multiBamCovMain.cpp:39:10: warning: variable 'haveBams' set but not used [-Wunused-but-set-variable] bool haveBams = false; ^ multiBamCovMain.cpp:47:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable] bool haveFraction = false; ^ * compiling multiBamCov.cpp - Building in src/multiIntersectBed * compiling multiIntersectBedMain.cpp multiIntersectBedMain.cpp: In function 'int multiintersect_main(int, char**)': multiIntersectBedMain.cpp:45:10: warning: variable 'haveFiles' set but not used [-Wunused-but-set-variable] bool haveFiles = false; ^ multiIntersectBedMain.cpp:47:10: warning: variable 'haveGenome' set but not used [-Wunused-but-set-variable] bool haveGenome = false; ^ multiIntersectBedMain.cpp:48:10: warning: variable 'haveFiller' set but not used [-Wunused-but-set-variable] bool haveFiller = true; ^ * compiling multiIntersectBed.cpp - Building in src/nekSandbox1 * compiling nekSandboxMain.cpp - Building in src/nucBed * compiling nucBedMain.cpp * compiling nucBed.cpp - Building in src/pairToBed * compiling pairToBedMain.cpp pairToBedMain.cpp: In function 'int pairtobed_main(int, char**)': pairToBedMain.cpp:43:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable] bool haveFraction = false; ^ * compiling pairToBed.cpp pairToBed.cpp: In member function 'void BedIntersectPE::FindSpanningOverlaps(const BEDPE&, std::vector&, const string&)': pairToBed.cpp:257:12: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable] CHRPOS spanLength = 0; ^ 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] int spanLength = 0; ^ - Building in src/pairToPair * compiling pairToPairMain.cpp pairToPairMain.cpp: In function 'int pairtopair_main(int, char**)': pairToPairMain.cpp:44:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable] bool haveFraction = false; ^ * compiling pairToPair.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] bool found1 = false; ^ pairToPair.cpp:113:14: warning: variable 'found2' set but not used [-Wunused-but-set-variable] bool found2 = false; ^ - Building in src/randomBed * compiling randomBedMain.cpp * compiling randomBed.cpp - Building in src/regressTest compiling RegressTest.cpp compiling regressTestMain.cpp - Building in src/reldist * compiling reldistMain.cpp * compiling reldist.cpp - Building in src/sampleFile * compiling sampleHelp.cpp * compiling sampleFile.cpp - Building in src/shuffleBed * compiling shuffleBedMain.cpp * compiling shuffleBed.cpp - Building in src/slopBed * compiling slopBedMain.cpp * compiling slopBed.cpp slopBed.cpp: In member function 'void BedSlop::AddSlop(BED&)': slopBed.cpp:86:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if ( ((int)bed.end + (int)_leftSlop) <= chromSize ) ^ slopBed.cpp:100:47: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if ( ((int)bed.end + (int)_rightSlop) <= chromSize ) ^ - Building in src/sortBed * compiling sortMain.cpp * compiling sortBed.cpp - Building in src/spacingFile * compiling spacingHelp.cpp * compiling spacingFile.cpp - Building in src/split * compiling splitBed.cpp splitBed.cpp: In member function 'FILE* BedSplit::saveFileChunk(std::__cxx11::string&, size_t)': splitBed.cpp:151:38: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t {aka long unsigned int}' [-Wformat=] sprintf(tmp,"%05d",(file_index+1)); ^ * compiling splitBedMain.cpp - Building in src/subtractFile * compiling subtractHelp.cpp * compiling subtractFile.cpp - Building in src/tagBam * compiling tagBamMain.cpp * compiling tagBam.cpp - Building in src/unionBedGraphs * compiling unionBedGraphsMain.cpp unionBedGraphsMain.cpp: In function 'int unionbedgraphs_main(int, char**)': unionBedGraphsMain.cpp:46:10: warning: variable 'haveFiles' set but not used [-Wunused-but-set-variable] bool haveFiles = false; ^ unionBedGraphsMain.cpp:48:10: warning: variable 'haveGenome' set but not used [-Wunused-but-set-variable] bool haveGenome = false; ^ unionBedGraphsMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-Wunused-but-set-variable] bool haveFiller = true; ^ * compiling unionBedGraphs.cpp - Building in src/windowBed * compiling windowMain.cpp * compiling windowBed.cpp - Building in src/windowMaker * compiling windowMakerMain.cpp * compiling windowMaker.cpp - Building main bedtools binary. done. - Creating executables for old CLI. done. gmake[2]: Leaving directory '/construction/biology/bedtools/bedtools2-2.25.0' -------------------------------------------------------------------------------- -- Phase: run-depends -------------------------------------------------------------------------------- ===> bedtools-2.25.0 depends on file: /usr/local/bin/python2.7 - found -------------------------------------------------------------------------------- -- Phase: stage -------------------------------------------------------------------------------- ===> Staging for bedtools-2.25.0 ===> Generating temporary packing list gmake[2]: Entering directory '/construction/biology/bedtools/bedtools2-2.25.0' Building BEDTools: ========================================================= DETECTED_VERSION = v2.25.0 CURRENT_VERSION = v2.25.0 * Creating BamTools API - Building in src/utils/bedFile gmake[3]: '../../../obj//bedFile.o' is up to date. - Building in src/utils/BinTree gmake[3]: '../../../obj//BinTree.o' is up to date. - Building in src/utils/version gmake[3]: Nothing to be done for 'all'. - Building in src/utils/bedGraphFile gmake[3]: '../../../obj//bedGraphFile.o' is up to date. - Building in src/utils/chromsweep gmake[3]: '../../../obj//chromsweep.o' is up to date. - Building in src/utils/Contexts gmake[3]: Nothing to be done for 'all'. - Building in src/utils/FileRecordTools - Building in FileReaders gmake[4]: Nothing to be done for 'all'. - Building in Records gmake[4]: Nothing to be done for 'all'. - Building in src/utils/FileRecordTools/FileReaders gmake[3]: Nothing to be done for 'all'. - Building in src/utils/FileRecordTools/Records gmake[3]: Nothing to be done for 'all'. - Building in src/utils/general gmake[3]: Nothing to be done for 'all'. - Building in src/utils/gzstream gmake[3]: '../../../obj//gzstream.o' is up to date. - Building in src/utils/fileType gmake[3]: Nothing to be done for 'all'. - Building in src/utils/bedFilePE gmake[3]: '../../../obj//bedFilePE.o' is up to date. - Building in src/utils/KeyListOps gmake[3]: Nothing to be done for 'all'. - Building in src/utils/NewChromsweep gmake[3]: Nothing to be done for 'all'. - Building in src/utils/sequenceUtilities gmake[3]: '../../../obj//sequenceUtils.o' is up to date. - Building in src/utils/tabFile gmake[3]: '../../../obj//tabFile.o' is up to date. - Building in src/utils/BamTools gmake[3]: Nothing to be done for 'all'. - Building in src/utils/BamTools-Ancillary gmake[3]: Nothing to be done for 'all'. - Building in src/utils/BlockedIntervals gmake[3]: Nothing to be done for 'all'. - Building in src/utils/Fasta gmake[3]: Nothing to be done for 'all'. - Building in src/utils/VectorOps gmake[3]: '../../../obj//VectorOps.o' is up to date. - Building in src/utils/GenomeFile gmake[3]: '../../../obj//NewGenomeFile.o' is up to date. - Building in src/utils/RecordOutputMgr gmake[3]: '../../../obj//RecordOutputMgr.o' is up to date. - Building in src/utils/ToolBase gmake[3]: '../../../obj//ToolBase.o' is up to date. - Building in src/utils/driver gmake[3]: Nothing to be done for 'all'. - Building in src/annotateBed gmake[3]: Nothing to be done for 'all'. - Building in src/bamToBed gmake[3]: Nothing to be done for 'all'. - Building in src/bamToFastq gmake[3]: Nothing to be done for 'all'. - Building in src/bedToBam gmake[3]: Nothing to be done for 'all'. - Building in src/bedpeToBam gmake[3]: Nothing to be done for 'all'. - Building in src/bedToIgv gmake[3]: Nothing to be done for 'all'. - Building in src/bed12ToBed6 gmake[3]: Nothing to be done for 'all'. - Building in src/closestFile gmake[3]: Nothing to be done for 'all'. - Building in src/clusterBed gmake[3]: Nothing to be done for 'all'. - Building in src/complementFile gmake[3]: Nothing to be done for 'all'. - Building in src/coverageFile gmake[3]: Nothing to be done for 'all'. - Building in src/expand gmake[3]: Nothing to be done for 'all'. - Building in src/fastaFromBed gmake[3]: Nothing to be done for 'all'. - Building in src/flankBed gmake[3]: Nothing to be done for 'all'. - Building in src/genomeCoverageBed gmake[3]: Nothing to be done for 'all'. - Building in src/getOverlap gmake[3]: Nothing to be done for 'all'. - Building in src/groupBy gmake[3]: Nothing to be done for 'all'. - Building in src/intersectFile gmake[3]: Nothing to be done for 'all'. - Building in src/fisher gmake[3]: Nothing to be done for 'all'. - Building in src/jaccard gmake[3]: Nothing to be done for 'all'. - Building in src/linksBed gmake[3]: Nothing to be done for 'all'. - Building in src/maskFastaFromBed gmake[3]: Nothing to be done for 'all'. - Building in src/mapFile gmake[3]: Nothing to be done for 'all'. - Building in src/mergeFile gmake[3]: Nothing to be done for 'all'. - Building in src/multiBamCov gmake[3]: Nothing to be done for 'all'. - Building in src/multiIntersectBed gmake[3]: Nothing to be done for 'all'. - Building in src/nekSandbox1 gmake[3]: Nothing to be done for 'all'. - Building in src/nucBed gmake[3]: Nothing to be done for 'all'. - Building in src/pairToBed gmake[3]: Nothing to be done for 'all'. - Building in src/pairToPair gmake[3]: Nothing to be done for 'all'. - Building in src/randomBed gmake[3]: Nothing to be done for 'all'. - Building in src/regressTest compiling RegressTest.cpp compiling regressTestMain.cpp - Building in src/reldist gmake[3]: Nothing to be done for 'all'. - Building in src/sampleFile gmake[3]: Nothing to be done for 'all'. - Building in src/shuffleBed gmake[3]: Nothing to be done for 'all'. - Building in src/slopBed gmake[3]: Nothing to be done for 'all'. - Building in src/sortBed gmake[3]: Nothing to be done for 'all'. - Building in src/spacingFile gmake[3]: Nothing to be done for 'all'. - Building in src/split gmake[3]: Nothing to be done for 'all'. - Building in src/subtractFile gmake[3]: Nothing to be done for 'all'. - Building in src/tagBam gmake[3]: Nothing to be done for 'all'. - Building in src/unionBedGraphs gmake[3]: Nothing to be done for 'all'. - Building in src/windowBed gmake[3]: Nothing to be done for 'all'. - Building in src/windowMaker gmake[3]: Nothing to be done for 'all'. - Building main bedtools binary. done. - Creating executables for old CLI. 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/bedtools2-2.25.0' ====> Compressing man pages (compress-man) -------------------------------------------------------------------------------- -- Phase: package -------------------------------------------------------------------------------- ===> Building package for bedtools-2.25.0 file sizes/checksums [40]: . done packing files [40]: . done packing directories [0]: . done -------------------------------------------------- -- Termination -------------------------------------------------- Finished: Wednesday, 18 APR 2018 at 02:09:48 UTC Duration: 00:07:59