Date: Sun, 14 Apr 2019 11:56:28 GMT From: pkg-fallout@FreeBSD.org To: pkg-fallout@FreeBSD.org Subject: [package - head-powerpc64-default][biology/bedtools] Failed for bedtools-2.27.1_2 in build Message-ID: <201904141156.x3EBuSCa021965@pylon.nyi.freebsd.org>
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You are receiving this mail as a port that you maintain is failing to build on the FreeBSD package build server. Please investigate the failure and submit a PR to fix build. Maintainer: jwb@FreeBSD.org Last committer: jbeich@FreeBSD.org Ident: $FreeBSD: head/biology/bedtools/Makefile 494554 2019-03-04 06:55:08Z jbeich $ Log URL: http://pylon.nyi.freebsd.org/data/head-powerpc64-default/p498785_s346161/logs/bedtools-2.27.1_2.log Build URL: http://pylon.nyi.freebsd.org/build.html?mastername=head-powerpc64-default&build=p498785_s346161 Log: =>> Building biology/bedtools build started at Sun Apr 14 11:38:12 UTC 2019 port directory: /usr/ports/biology/bedtools package name: bedtools-2.27.1_2 building for: FreeBSD head-powerpc64-default-job-07 13.0-CURRENT FreeBSD 13.0-CURRENT 1300018 powerpc maintained by: jwb@FreeBSD.org Makefile ident: $FreeBSD: head/biology/bedtools/Makefile 494554 2019-03-04 06:55:08Z jbeich $ Poudriere version: 3.2.8-3-g02cc9753 Host OSVERSION: 1300012 Jail OSVERSION: 1300018 Job Id: 07 !!! Jail is newer than host. (Jail: 1300018, Host: 1300012) !!! !!! This is not supported. !!! !!! Host kernel must be same or newer than jail. !!! !!! Expect build failures. !!! ---Begin Environment--- SHELL=/bin/csh OSVERSION=1300018 UNAME_v=FreeBSD 13.0-CURRENT 1300018 UNAME_r=13.0-CURRENT BLOCKSIZE=K MAIL=/var/mail/root STATUS=1 HOME=/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin LOCALBASE=/usr/local USER=root LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.2.8-3-g02cc9753 MASTERMNT=/usr/local/poudriere/data/.m/head-powerpc64-default/ref POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= PWD=/usr/local/poudriere/data/.m/head-powerpc64-default/ref/.p/pool P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=head-powerpc64-default SCRIPTPREFIX=/usr/local/share/poudriere OLDPWD=/usr/local/poudriere/data/.m/head-powerpc64-default/ref/.p SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR= DEPENDS_ARGS= MAKE_ARGS= ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ---End OPTIONS List--- --MAINTAINER-- jwb@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- MAKE=gmake PYTHON="/usr/local/bin/python3.6" XDG_DATA_HOME=/wrkdirs/usr/ports/biology/bedtools/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/bedtools/work HOME=/wrkdirs/usr/ports/biology/bedtools/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/bedtools/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh --End CONFIGURE_ENV-- --MAKE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/bedtools/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/bedtools/work HOME=/wrkdirs/usr/ports/biology/bedtools/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/bedtools/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin NO_PIE=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES ADDR2LINE="/usr/local/bin/addr2line" AR="/usr/local/bin/ar" AS="/usr/local/bin/as" CPPFILT="/usr/local/bin/c++filt" GPROF="/usr/local/bin/gprof" LD="/usr/local/bin/ld" NM="/usr/local/bin/nm" OBJCOPY="/usr/local/bin/objcopy" OBJDUMP="/usr/local/bin/objdump" RANLIB="/usr/local/bin/ranlib" READELF="/usr/local/bin/readelf" SIZE="/usr/local/bin/size" STRINGS="/usr/local/bin/strings" PREFIX=/usr/local LOCALBASE=/usr/local CC="gcc8" CFLAGS="-O2 -pipe -Wl,-rpath=/usr/local/lib/gcc8 -fno-strict-aliasing " CPP="cpp8" CPPFLAGS="" LDFLAGS=" -Wl,-rpath=/usr/local/lib/gcc8 -L/usr/local/lib/gcc8 " LIBS="" CXX="g++8" CXXFLAGS="- O2 -pipe -Wl,-rpath=/usr/local/lib/gcc8 -Wl,-rpath=/usr/local/lib/gcc8 " 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" --End MAKE_ENV-- --PLIST_SUB-- PYTHON_INCLUDEDIR=include/python3.6m PYTHON_LIBDIR=lib/python3.6 PYTHON_PLATFORM=freebsd13 PYTHON_PYOEXTENSION=opt-1.pyc PYTHON_SITELIBDIR=lib/python3.6/site-packages PYTHON_SUFFIX=36 PYTHON_VER=3.6 PYTHON_VERSION=python3.6 PYTHON2="@comment " PYTHON3="" OSREL=13.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/bedtools" EXAMPLESDIR="share/examples/bedtools" DATADIR="share/bedtools" WWWDIR="www/bedtools" ETCDIR="etc/bedtools" --End PLIST_SUB-- --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 --End SUB_LIST-- ---Begin make.conf--- USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes #### /usr/local/etc/poudriere.d/make.conf #### # XXX: We really need this but cannot use it while 'make checksum' does not # try the next mirror on checksum failure. It currently retries the same # failed mirror and then fails rather then trying another. It *does* # try the next if the size is mismatched though. #MASTER_SITE_FREEBSD=yes # Build ALLOW_MAKE_JOBS_PACKAGES with 2 jobs MAKE_JOBS_NUMBER=2 # stable/10 includes src.conf too late but make.conf is in sys.mk .if ${.CURDIR:M/poudriere/jails/10*/usr/src/usr.bin/xlint*} # Disable build of llib now that head no longer has lint(1) LINT= true .endif #### /usr/ports/Mk/Scripts/ports_env.sh #### _CCVERSION_921dbbb2=cc (GCC) 4.2.1 20070831 patched [FreeBSD] Copyright (C) 2007 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. _ALTCCVERSION_921dbbb2=none _CXXINTERNAL_acaad9ca=Using built-in specs. Target: powerpc64-undermydesk-freebsd Configured with: FreeBSD/powerpc64 system compiler Thread model: posix gcc version 4.2.1 20070831 patched [FreeBSD] "/usr/bin/ld" "--eh-frame-hdr" "-Qy" "-melf64ppc_fbsd" "--enable-new-dtags" "-dynamic-linker" "/libexec/ld-elf.so.1" "/usr/lib/crt1.o" "/usr/lib/crti.o" "/usr/lib/crtbegin.o" "-L/usr/lib" "-L/usr/lib" "/dev/null" "-lstdc++" "-lm" "-lgcc_s" "-lgcc" "-lc" "-lgcc_s" "-lgcc" "/usr/lib/crtsavres.o" "/usr/lib/crtend.o" "/usr/lib/crtn.o" CC_OUTPUT_921dbbb2_58173849=yes CC_OUTPUT_921dbbb2_9bdba57c=yes CC_OUTPUT_921dbbb2_6a4fe7f5=cc1: error: unrecognized command line option "-std=c11" CC_OUTPUT_921dbbb2_6bcac02b=yes CC_OUTPUT_921dbbb2_67d20829=yes CC_OUTPUT_921dbbb2_bfa62e83=cc1: error: unrecognized command line option "-std=gnu11" CC_OUTPUT_921dbbb2_f0b4d593=yes CC_OUTPUT_921dbbb2_308abb44=cc1plus: error: unrecognized command line option "-std=c++0x" CC_OUTPUT_921dbbb2_f00456e5=cc1plus: error: unrecognized command line option "-std=c++11" CC_OUTPUT_921dbbb2_65ad290d=cc1plus: error: unrecognized command line option "-std=c++14" CC_OUTPUT_921dbbb2_f2776b26=cc1plus: error: unrecognized command line option "-std=c++17" CC_OUTPUT_921dbbb2_b2657cc3=yes CC_OUTPUT_921dbbb2_380987f7=cc1plus: error: unrecognized command line option "-std=gnu++11" CC_OUTPUT_921dbbb2_160933ec=cc1plus: error: unrecognized command line option "-std=gnu++14" CC_OUTPUT_921dbbb2_fb62803b=cc1plus: error: unrecognized command line option "-std=gnu++17" _OBJC_CCVERSION_921dbbb2=cc (GCC) 4.2.1 20070831 patched [FreeBSD] Copyright (C) 2007 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. _OBJC_ALTCCVERSION_921dbbb2=none ARCH=powerpc64 OPSYS=FreeBSD _OSRELEASE=13.0-CURRENT OSREL=13.0 OSVERSION=1300018 PYTHONBASE=/usr/local CONFIGURE_MAX_CMD_LEN=262144 HAVE_PORTS_ENV=1 #### Misc Poudriere #### GID=0 UID=0 DISABLE_MAKE_JOBS=poudriere ---End make.conf--- --Resource limits-- cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 33554432 stack size (kbytes, -s) 524288 core file size (512-blocks, -c) unlimited max memory size (kbytes, -m) unlimited locked memory (kbytes, -l) unlimited max user processes (-u) 89999 open files (-n) 1024 virtual mem size (kbytes, -v) unlimited swap limit (kbytes, -w) unlimited socket buffer size (bytes, -b) unlimited pseudo-terminals (-p) unlimited kqueues (-k) unlimited umtx shared locks (-o) unlimited --End resource limits-- =======================<phase: check-sanity >============================ ===> License GPLv2 accepted by the user =========================================================================== =======================<phase: pkg-depends >============================ ===> bedtools-2.27.1_2 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.10.5_5.txz [head-powerpc64-default-job-07] Installing pkg-1.10.5_5... [head-powerpc64-default-job-07] Extracting pkg-1.10.5_5: .......... done ===> bedtools-2.27.1_2 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of bedtools-2.27.1_2 =========================================================================== =======================<phase: fetch-depends >============================ =========================================================================== =======================<phase: fetch >============================ ===> License GPLv2 accepted by the user ===> Fetching all distfiles required by bedtools-2.27.1_2 for building =========================================================================== =======================<phase: checksum >============================ ===> License GPLv2 accepted by the user ===> Fetching all distfiles required by bedtools-2.27.1_2 for building => SHA256 Checksum OK for arq5x-bedtools2-v2.27.1_GH0.tar.gz. =========================================================================== =======================<phase: extract-depends>============================ =========================================================================== =======================<phase: extract >============================ ===> License GPLv2 accepted by the user ===> Fetching all distfiles required by bedtools-2.27.1_2 for building ===> Extracting for bedtools-2.27.1_2 => SHA256 Checksum OK for arq5x-bedtools2-v2.27.1_GH0.tar.gz. =========================================================================== =======================<phase: patch-depends >============================ =========================================================================== =======================<phase: patch >============================ ===> Patching for bedtools-2.27.1_2 ===> Applying FreeBSD patches for bedtools-2.27.1_2 =========================================================================== =======================<phase: build-depends >============================ ===> bedtools-2.27.1_2 depends on executable: gmake - not found ===> Installing existing package /packages/All/gmake-4.2.1_3.txz [head-powerpc64-default-job-07] Installing gmake-4.2.1_3... [head-powerpc64-default-job-07] `-- Installing gettext-runtime-0.19.8.1_2... <snip> bedToBam.cpp:(.text+0x1648): undefined reference to `BamTools::BamAlignment::SetIsReverseStrand(bool)' /usr/local/bin/ld: obj/bedToBam.o: in function `ProcessBed(BedFile*, GenomeFile*, bool, int, bool)': bedToBam.cpp:(.text+0x2984): undefined reference to `BamTools::BamWriter::BamWriter()' /usr/local/bin/ld: bedToBam.cpp:(.text+0x2a38): undefined reference to `BamTools::BamWriter::SetCompressionMode(BamTools::BamWriter::CompressionMode const&)' /usr/local/bin/ld: bedToBam.cpp:(.text+0x2a70): undefined reference to `BamTools::BamWriter::Open(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::vector<BamTools::RefData, std::allocator<BamTools::RefData> > const&)' /usr/local/bin/ld: bedToBam.cpp:(.text+0x2b98): undefined reference to `BamTools::BamWriter::Close()' /usr/local/bin/ld: bedToBam.cpp:(.text+0x2d24): undefined reference to `BamTools::BamAlignment::BamAlignment()' /usr/local/bin/ld: bedToBam.cpp:(.text+0x2d60): undefined reference to `BamTools::BamWriter::SaveAlignment(BamTools::BamAlignment const&)' /usr/local/bin/ld: bedToBam.cpp:(.text+0x2d6c): undefined reference to `BamTools::BamAlignment::~BamAlignment()' /usr/local/bin/ld: bedToBam.cpp:(.text+0x2f24): undefined reference to `BamTools::BamAlignment::~BamAlignment()' /usr/local/bin/ld: obj/bedpeToBam.o: in function `ConvertBedPEToBam(BEDPE const&, BamTools::BamAlignment&, BamTools::BamAlignment&, std::map<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, std::less<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const, int> > >&, int, int)': bedpeToBam.cpp:(.text+0x11f8): undefined reference to `BamTools::BamAlignment::SetIsFirstMate(bool)' /usr/local/bin/ld: bedpeToBam.cpp:(.text+0x1208): undefined reference to `BamTools::BamAlignment::SetIsSecondMate(bool)' /usr/local/bin/ld: bedpeToBam.cpp:(.text+0x1218): undefined reference to `BamTools::BamAlignment::SetIsPaired(bool)' /usr/local/bin/ld: bedpeToBam.cpp:(.text+0x1228): undefined reference to `BamTools::BamAlignment::SetIsPaired(bool)' /usr/local/bin/ld: bedpeToBam.cpp:(.text+0x1590): undefined reference to `BamTools::BamAlignment::SetIsReverseStrand(bool)' /usr/local/bin/ld: bedpeToBam.cpp:(.text+0x15a0): undefined reference to `BamTools::BamAlignment::SetIsMateReverseStrand(bool)' /usr/local/bin/ld: bedpeToBam.cpp:(.text+0x15d0): undefined reference to `BamTools::BamAlignment::SetIsReverseStrand(bool)' /usr/local/bin/ld: bedpeToBam.cpp:(.text+0x15e0): undefined reference to `BamTools::BamAlignment::SetIsMateReverseStrand(bool)' /usr/local/bin/ld: bedpeToBam.cpp:(.text+0x1688): undefined reference to `BamTools::BamAlignment::SetIsProperPair(bool)' /usr/local/bin/ld: bedpeToBam.cpp:(.text+0x1698): undefined reference to `BamTools::BamAlignment::SetIsProperPair(bool)' /usr/local/bin/ld: obj/bedpeToBam.o: in function `ProcessBedPE(BedFilePE*, GenomeFile*, int, bool)': bedpeToBam.cpp:(.text+0x2df0): undefined reference to `BamTools::BamWriter::BamWriter()' /usr/local/bin/ld: bedpeToBam.cpp:(.text+0x2ea4): undefined reference to `BamTools::BamWriter::SetCompressionMode(BamTools::BamWriter::CompressionMode const&)' /usr/local/bin/ld: bedpeToBam.cpp:(.text+0x2edc): undefined reference to `BamTools::BamWriter::Open(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::vector<BamTools::RefData, std::allocator<BamTools::RefData> > const&)' /usr/local/bin/ld: bedpeToBam.cpp:(.text+0x30d4): undefined reference to `BamTools::BamWriter::Close()' /usr/local/bin/ld: bedpeToBam.cpp:(.text+0x3384): undefined reference to `BamTools::BamAlignment::BamAlignment()' /usr/local/bin/ld: bedpeToBam.cpp:(.text+0x3390): undefined reference to `BamTools::BamAlignment::BamAlignment()' /usr/local/bin/ld: bedpeToBam.cpp:(.text+0x33d0): undefined reference to `BamTools::BamWriter::SaveAlignment(BamTools::BamAlignment const&)' /usr/local/bin/ld: bedpeToBam.cpp:(.text+0x33e0): undefined reference to `BamTools::BamWriter::SaveAlignment(BamTools::BamAlignment const&)' /usr/local/bin/ld: bedpeToBam.cpp:(.text+0x35b4): undefined reference to `BamTools::BamAlignment::~BamAlignment()' /usr/local/bin/ld: bedpeToBam.cpp:(.text+0x35c0): undefined reference to `BamTools::BamAlignment::~BamAlignment()' /usr/local/bin/ld: bedpeToBam.cpp:(.text+0x3744): undefined reference to `BamTools::BamAlignment::~BamAlignment()' /usr/local/bin/ld: bedpeToBam.cpp:(.text+0x3750): undefined reference to `BamTools::BamAlignment::~BamAlignment()' /usr/local/bin/ld: obj/genomeCoverageBed.o: in function `BedGenomeCoverage::CoverageBam(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)': genomeCoverageBed.cpp:(.text+0x3068): undefined reference to `BamTools::BamReader::BamReader()' /usr/local/bin/ld: genomeCoverageBed.cpp:(.text+0x3078): undefined reference to `BamTools::BamReader::Open(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)' /usr/local/bin/ld: genomeCoverageBed.cpp:(.text+0x3090): undefined reference to `BamTools::BamReader::GetHeaderText[abi:cxx11]() const' /usr/local/bin/ld: genomeCoverageBed.cpp:(.text+0x309c): undefined reference to `BamTools::BamReader::GetReferenceData() const' /usr/local/bin/ld: genomeCoverageBed.cpp:(.text+0x31ac): undefined reference to `BamTools::BamAlignment::BamAlignment()' /usr/local/bin/ld: genomeCoverageBed.cpp:(.text+0x3208): undefined reference to `BamTools::BamReader::GetNextAlignment(BamTools::BamAlignment&)' /usr/local/bin/ld: genomeCoverageBed.cpp:(.text+0x321c): undefined reference to `BamTools::BamAlignment::IsMapped() const' /usr/local/bin/ld: genomeCoverageBed.cpp:(.text+0x3230): undefined reference to `BamTools::BamAlignment::IsReverseStrand() const' /usr/local/bin/ld: genomeCoverageBed.cpp:(.text+0x32b0): undefined reference to `BamTools::BamAlignment::GetEndPosition(bool, bool) const' /usr/local/bin/ld: genomeCoverageBed.cpp:(.text+0x3308): undefined reference to `BamTools::BamAlignment::IsReverseStrand() const' /usr/local/bin/ld: genomeCoverageBed.cpp:(.text+0x3354): undefined reference to `BamTools::BamAlignment::IsReverseStrand() const' /usr/local/bin/ld: genomeCoverageBed.cpp:(.text+0x33a4): undefined reference to `BamTools::BamAlignment::IsPaired() const' /usr/local/bin/ld: genomeCoverageBed.cpp:(.text+0x33b8): undefined reference to `BamTools::BamAlignment::IsMateMapped() const' /usr/local/bin/ld: genomeCoverageBed.cpp:(.text+0x33cc): undefined reference to `BamTools::BamAlignment::IsSecondMate() const' /usr/local/bin/ld: genomeCoverageBed.cpp:(.text+0x33e0): undefined reference to `BamTools::BamAlignment::IsReverseStrand() const' /usr/local/bin/ld: genomeCoverageBed.cpp:(.text+0x3434): undefined reference to `BamTools::BamAlignment::IsPaired() const' /usr/local/bin/ld: genomeCoverageBed.cpp:(.text+0x3460): undefined reference to `BamTools::BamAlignment::IsMateReverseStrand() const' /usr/local/bin/ld: genomeCoverageBed.cpp:(.text+0x3474): undefined reference to `BamTools::BamAlignment::IsFirstMate() const' /usr/local/bin/ld: genomeCoverageBed.cpp:(.text+0x3488): undefined reference to `BamTools::BamAlignment::IsReverseStrand() const' /usr/local/bin/ld: genomeCoverageBed.cpp:(.text+0x349c): undefined reference to `BamTools::BamAlignment::IsFirstMate() const' /usr/local/bin/ld: genomeCoverageBed.cpp:(.text+0x34b0): undefined reference to `BamTools::BamAlignment::IsMateReverseStrand() const' /usr/local/bin/ld: genomeCoverageBed.cpp:(.text+0x3694): undefined reference to `BamTools::BamAlignment::IsReverseStrand() const' /usr/local/bin/ld: genomeCoverageBed.cpp:(.text+0x36d4): undefined reference to `BamTools::BamAlignment::IsProperPair() const' /usr/local/bin/ld: genomeCoverageBed.cpp:(.text+0x36e8): undefined reference to `BamTools::BamAlignment::IsMateMapped() const' /usr/local/bin/ld: genomeCoverageBed.cpp:(.text+0x3714): undefined reference to `BamTools::BamAlignment::IsReverseStrand() const' /usr/local/bin/ld: genomeCoverageBed.cpp:(.text+0x3774): undefined reference to `BamTools::BamReader::Close()' /usr/local/bin/ld: genomeCoverageBed.cpp:(.text+0x37b4): undefined reference to `BamTools::BamAlignment::~BamAlignment()' /usr/local/bin/ld: genomeCoverageBed.cpp:(.text+0x3838): undefined reference to `BamTools::BamReader::~BamReader()' /usr/local/bin/ld: genomeCoverageBed.cpp:(.text+0x39a4): undefined reference to `BamTools::BamReader::~BamReader()' /usr/local/bin/ld: genomeCoverageBed.cpp:(.text+0x39e4): undefined reference to `BamTools::BamAlignment::~BamAlignment()' /usr/local/bin/ld: obj/multiBamCov.o: in function `MultiCovBam::CollectCoverage()': multiBamCov.cpp:(.text+0xbe0): undefined reference to `BamTools::BamMultiReader::BamMultiReader()' /usr/local/bin/ld: multiBamCov.cpp:(.text+0xbf0): undefined reference to `BamTools::BamMultiReader::Open(std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&)' /usr/local/bin/ld: multiBamCov.cpp:(.text+0xc14): undefined reference to `BamTools::BamMultiReader::LocateIndexes(BamTools::BamIndex::IndexType const&)' /usr/local/bin/ld: multiBamCov.cpp:(.text+0xc20): undefined reference to `BamTools::BamMultiReader::HasIndexes() const' /usr/local/bin/ld: multiBamCov.cpp:(.text+0xdf0): undefined reference to `BamTools::BamMultiReader::~BamMultiReader()' /usr/local/bin/ld: multiBamCov.cpp:(.text+0xec4): undefined reference to `BamTools::BamMultiReader::GetReferenceID(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const' /usr/local/bin/ld: multiBamCov.cpp:(.text+0xef4): undefined reference to `BamTools::BamMultiReader::SetRegion(BamTools::BamRegion const&)' /usr/local/bin/ld: multiBamCov.cpp:(.text+0x10ac): undefined reference to `BamTools::BamAlignment::BamAlignment()' /usr/local/bin/ld: multiBamCov.cpp:(.text+0x10f8): undefined reference to `BamTools::BamMultiReader::GetNextAlignment(BamTools::BamAlignment&)' /usr/local/bin/ld: multiBamCov.cpp:(.text+0x1120): undefined reference to `BamTools::BamAlignment::IsReverseStrand() const' /usr/local/bin/ld: multiBamCov.cpp:(.text+0x1164): undefined reference to `BamTools::BamAlignment::IsDuplicate() const' /usr/local/bin/ld: multiBamCov.cpp:(.text+0x1174): undefined reference to `BamTools::BamAlignment::IsFailedQC() const' /usr/local/bin/ld: multiBamCov.cpp:(.text+0x1208): undefined reference to `BamTools::BamAlignment::GetEndPosition(bool, bool) const' /usr/local/bin/ld: multiBamCov.cpp:(.text+0x14a4): undefined reference to `BamTools::BamAlignment::IsProperPair() const' /usr/local/bin/ld: multiBamCov.cpp:(.text+0x14bc): undefined reference to `BamTools::BamAlignment::~BamAlignment()' /usr/local/bin/ld: multiBamCov.cpp:(.text+0x1b9c): undefined reference to `BamTools::BamMultiReader::GetErrorString[abi:cxx11]() const' /usr/local/bin/ld: multiBamCov.cpp:(.text+0x1c38): undefined reference to `BamTools::BamMultiReader::GetErrorString[abi:cxx11]() const' /usr/local/bin/ld: multiBamCov.cpp:(.text+0x1c78): undefined reference to `BamTools::BamMultiReader::Close()' /usr/local/bin/ld: multiBamCov.cpp:(.text+0x1cc8): undefined reference to `BamTools::BamMultiReader::~BamMultiReader()' /usr/local/bin/ld: multiBamCov.cpp:(.text+0x1dec): undefined reference to `BamTools::BamAlignment::~BamAlignment()' /usr/local/bin/ld: obj/pairToBed.o: in function `IsCorrectMappingForBEDPE(BamTools::BamAlignment const&)': pairToBed.cpp:(.text+0x28): undefined reference to `BamTools::BamAlignment::IsFirstMate() const' /usr/local/bin/ld: pairToBed.cpp:(.text+0xa8): undefined reference to `BamTools::BamAlignment::IsFirstMate() const' /usr/local/bin/ld: obj/pairToBed.o: in function `BedIntersectPE::IntersectBamPE(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)': pairToBed.cpp:(.text+0x49b8): undefined reference to `BamTools::BamReader::BamReader()' /usr/local/bin/ld: pairToBed.cpp:(.text+0x49c4): undefined reference to `BamTools::BamWriter::BamWriter()' /usr/local/bin/ld: pairToBed.cpp:(.text+0x49d4): undefined reference to `BamTools::BamReader::Open(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)' /usr/local/bin/ld: pairToBed.cpp:(.text+0x49f0): undefined reference to `BamTools::BamReader::GetHeaderText[abi:cxx11]() const' /usr/local/bin/ld: pairToBed.cpp:(.text+0x49fc): undefined reference to `BamTools::BamReader::GetReferenceData() const' /usr/local/bin/ld: pairToBed.cpp:(.text+0x4b18): undefined reference to `BamTools::BamWriter::SetCompressionMode(BamTools::BamWriter::CompressionMode const&)' /usr/local/bin/ld: pairToBed.cpp:(.text+0x4b60): undefined reference to `BamTools::BamWriter::Open(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::vector<BamTools::RefData, std::allocator<BamTools::RefData> > const&)' /usr/local/bin/ld: pairToBed.cpp:(.text+0x4c04): undefined reference to `BamTools::BamAlignment::BamAlignment()' /usr/local/bin/ld: pairToBed.cpp:(.text+0x4c14): undefined reference to `BamTools::BamAlignment::BamAlignment()' /usr/local/bin/ld: pairToBed.cpp:(.text+0x4c78): undefined reference to `BamTools::BamReader::GetNextAlignment(BamTools::BamAlignment&)' /usr/local/bin/ld: pairToBed.cpp:(.text+0x4c90): undefined reference to `BamTools::BamReader::GetNextAlignment(BamTools::BamAlignment&)' /usr/local/bin/ld: pairToBed.cpp:(.text+0x4cd4): undefined reference to `BamTools::BamAlignment::IsPaired() const' /usr/local/bin/ld: pairToBed.cpp:(.text+0x4e5c): undefined reference to `BamTools::BamReader::GetNextAlignment(BamTools::BamAlignment&)' /usr/local/bin/ld: pairToBed.cpp:(.text+0x4f18): undefined reference to `BamTools::BamAlignment::IsPaired() const' /usr/local/bin/ld: pairToBed.cpp:(.text+0x4f2c): undefined reference to `BamTools::BamAlignment::IsPaired() const' /usr/local/bin/ld: pairToBed.cpp:(.text+0x4f64): undefined reference to `BamTools::BamReader::Close()' /usr/local/bin/ld: pairToBed.cpp:(.text+0x4f80): undefined reference to `BamTools::BamAlignment::~BamAlignment()' /usr/local/bin/ld: pairToBed.cpp:(.text+0x4f8c): undefined reference to `BamTools::BamAlignment::~BamAlignment()' /usr/local/bin/ld: pairToBed.cpp:(.text+0x5038): undefined reference to `BamTools::BamWriter::~BamWriter()' /usr/local/bin/ld: pairToBed.cpp:(.text+0x5044): undefined reference to `BamTools::BamReader::~BamReader()' /usr/local/bin/ld: pairToBed.cpp:(.text+0x50b4): undefined reference to `BamTools::BamWriter::Close()' /usr/local/bin/ld: pairToBed.cpp:(.text+0x51ac): undefined reference to `BamTools::BamWriter::~BamWriter()' /usr/local/bin/ld: pairToBed.cpp:(.text+0x51ec): undefined reference to `BamTools::BamReader::~BamReader()' /usr/local/bin/ld: pairToBed.cpp:(.text+0x52c8): undefined reference to `BamTools::BamAlignment::~BamAlignment()' /usr/local/bin/ld: pairToBed.cpp:(.text+0x5308): undefined reference to `BamTools::BamAlignment::~BamAlignment()' /usr/local/bin/ld: obj/pairToBed.o: in function `BedIntersectPE::ConvertBamToBedPE(BamTools::BamAlignment const&, BamTools::BamAlignment const&, std::vector<BamTools::RefData, std::allocator<BamTools::RefData> > const&, BEDPE&)': pairToBed.cpp:(.text._ZN14BedIntersectPE17ConvertBamToBedPEERKN8BamTools12BamAlignmentES3_RKSt6vectorINS0_7RefDataESaIS5_EER5BEDPE[_ZN14BedIntersectPE17ConvertBamToBedPEERKN8BamTools12BamAlignmentES3_RKSt6vectorINS0_7RefDataESaIS5_EER5BEDPE]+0xe0): undefined reference to `BamTools::BamAlignment::IsMapped() const' /usr/local/bin/ld: pairToBed.cpp:(.text._ZN14BedIntersectPE17ConvertBamToBedPEERKN8BamTools12BamAlignmentES3_RKSt6vectorINS0_7RefDataESaIS5_EER5BEDPE[_ZN14BedIntersectPE17ConvertBamToBedPEERKN8BamTools12BamAlignmentES3_RKSt6vectorINS0_7RefDataESaIS5_EER5BEDPE]+0x14c): undefined reference to `BamTools::BamAlignment::GetEndPosition(bool, bool) const' /usr/local/bin/ld: pairToBed.cpp:(.text._ZN14BedIntersectPE17ConvertBamToBedPEERKN8BamTools12BamAlignmentES3_RKSt6vectorINS0_7RefDataESaIS5_EER5BEDPE[_ZN14BedIntersectPE17ConvertBamToBedPEERKN8BamTools12BamAlignmentES3_RKSt6vectorINS0_7RefDataESaIS5_EER5BEDPE]+0x17c): undefined reference to `BamTools::BamAlignment::IsReverseStrand() const' /usr/local/bin/ld: pairToBed.cpp:(.text._ZN14BedIntersectPE17ConvertBamToBedPEERKN8BamTools12BamAlignmentES3_RKSt6vectorINS0_7RefDataESaIS5_EER5BEDPE[_ZN14BedIntersectPE17ConvertBamToBedPEERKN8BamTools12BamAlignmentES3_RKSt6vectorINS0_7RefDataESaIS5_EER5BEDPE]+0x19c): undefined reference to `BamTools::BamAlignment::IsMapped() const' /usr/local/bin/ld: pairToBed.cpp:(.text._ZN14BedIntersectPE17ConvertBamToBedPEERKN8BamTools12BamAlignmentES3_RKSt6vectorINS0_7RefDataESaIS5_EER5BEDPE[_ZN14BedIntersectPE17ConvertBamToBedPEERKN8BamTools12BamAlignmentES3_RKSt6vectorINS0_7RefDataESaIS5_EER5BEDPE]+0x208): undefined reference to `BamTools::BamAlignment::GetEndPosition(bool, bool) const' /usr/local/bin/ld: pairToBed.cpp:(.text._ZN14BedIntersectPE17ConvertBamToBedPEERKN8BamTools12BamAlignmentES3_RKSt6vectorINS0_7RefDataESaIS5_EER5BEDPE[_ZN14BedIntersectPE17ConvertBamToBedPEERKN8BamTools12BamAlignmentES3_RKSt6vectorINS0_7RefDataESaIS5_EER5BEDPE]+0x238): undefined reference to `BamTools::BamAlignment::IsReverseStrand() const' /usr/local/bin/ld: pairToBed.cpp:(.text._ZN14BedIntersectPE17ConvertBamToBedPEERKN8BamTools12BamAlignmentES3_RKSt6vectorINS0_7RefDataESaIS5_EER5BEDPE[_ZN14BedIntersectPE17ConvertBamToBedPEERKN8BamTools12BamAlignmentES3_RKSt6vectorINS0_7RefDataESaIS5_EER5BEDPE]+0x2f4): undefined reference to `BamTools::BamAlignment::IsMapped() const' /usr/local/bin/ld: pairToBed.cpp:(.text._ZN14BedIntersectPE17ConvertBamToBedPEERKN8BamTools12BamAlignmentES3_RKSt6vectorINS0_7RefDataESaIS5_EER5BEDPE[_ZN14BedIntersectPE17ConvertBamToBedPEERKN8BamTools12BamAlignmentES3_RKSt6vectorINS0_7RefDataESaIS5_EER5BEDPE]+0x3e4): undefined reference to `BamTools::BamAlignment::IsMapped() const' /usr/local/bin/ld: pairToBed.cpp:(.text._ZN14BedIntersectPE17ConvertBamToBedPEERKN8BamTools12BamAlignmentES3_RKSt6vectorINS0_7RefDataESaIS5_EER5BEDPE[_ZN14BedIntersectPE17ConvertBamToBedPEERKN8BamTools12BamAlignmentES3_RKSt6vectorINS0_7RefDataESaIS5_EER5BEDPE]+0x3f8): undefined reference to `BamTools::BamAlignment::IsMapped() const' /usr/local/bin/ld: pairToBed.cpp:(.text._ZN14BedIntersectPE17ConvertBamToBedPEERKN8BamTools12BamAlignmentES3_RKSt6vectorINS0_7RefDataESaIS5_EER5BEDPE[_ZN14BedIntersectPE17ConvertBamToBedPEERKN8BamTools12BamAlignmentES3_RKSt6vectorINS0_7RefDataESaIS5_EER5BEDPE]+0x40c): undefined reference to `BamTools::BamAlignment::IsMapped() const' /usr/local/bin/ld: pairToBed.cpp:(.text._ZN14BedIntersectPE17ConvertBamToBedPEERKN8BamTools12BamAlignmentES3_RKSt6vectorINS0_7RefDataESaIS5_EER5BEDPE[_ZN14BedIntersectPE17ConvertBamToBedPEERKN8BamTools12BamAlignmentES3_RKSt6vectorINS0_7RefDataESaIS5_EER5BEDPE]+0x7b8): undefined reference to `BamTools::BamAlignment::FindTag(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, char*&, unsigned int const&, unsigned int&) const' /usr/local/bin/ld: pairToBed.cpp:(.text._ZN14BedIntersectPE17ConvertBamToBedPEERKN8BamTools12BamAlignmentES3_RKSt6vectorINS0_7RefDataESaIS5_EER5BEDPE[_ZN14BedIntersectPE17ConvertBamToBedPEERKN8BamTools12BamAlignmentES3_RKSt6vectorINS0_7RefDataESaIS5_EER5BEDPE]+0x834): undefined reference to `BamTools::BamAlignment::IsMapped() const' /usr/local/bin/ld: pairToBed.cpp:(.text._ZN14BedIntersectPE17ConvertBamToBedPEERKN8BamTools12BamAlignmentES3_RKSt6vectorINS0_7RefDataESaIS5_EER5BEDPE[_ZN14BedIntersectPE17ConvertBamToBedPEERKN8BamTools12BamAlignmentES3_RKSt6vectorINS0_7RefDataESaIS5_EER5BEDPE]+0xd74): undefined reference to `BamTools::BamAlignment::IsMapped() const' /usr/local/bin/ld: pairToBed.cpp:(.text._ZN14BedIntersectPE17ConvertBamToBedPEERKN8BamTools12BamAlignmentES3_RKSt6vectorINS0_7RefDataESaIS5_EER5BEDPE[_ZN14BedIntersectPE17ConvertBamToBedPEERKN8BamTools12BamAlignmentES3_RKSt6vectorINS0_7RefDataESaIS5_EER5BEDPE]+0x10e4): undefined reference to `BamTools::BamAlignment::FindTag(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, char*&, unsigned int const&, unsigned int&) const' /usr/local/bin/ld: obj/pairToBed.o: in function `BedIntersectPE::ProcessBamBlock(BamTools::BamAlignment const&, BamTools::BamAlignment const&, std::vector<BamTools::RefData, std::allocator<BamTools::RefData> > const&, BamTools::BamWriter&)': pairToBed.cpp:(.text._ZN14BedIntersectPE15ProcessBamBlockERKN8BamTools12BamAlignmentES3_RKSt6vectorINS0_7RefDataESaIS5_EERNS0_9BamWriterE[_ZN14BedIntersectPE15ProcessBamBlockERKN8BamTools12BamAlignmentES3_RKSt6vectorINS0_7RefDataESaIS5_EERNS0_9BamWriterE]+0x8d0): undefined reference to `BamTools::BamAlignment::IsMapped() const' /usr/local/bin/ld: pairToBed.cpp:(.text._ZN14BedIntersectPE15ProcessBamBlockERKN8BamTools12BamAlignmentES3_RKSt6vectorINS0_7RefDataESaIS5_EERNS0_9BamWriterE[_ZN14BedIntersectPE15ProcessBamBlockERKN8BamTools12BamAlignmentES3_RKSt6vectorINS0_7RefDataESaIS5_EERNS0_9BamWriterE]+0x8e4): undefined reference to `BamTools::BamAlignment::IsMapped() const' /usr/local/bin/ld: pairToBed.cpp:(.text._ZN14BedIntersectPE15ProcessBamBlockERKN8BamTools12BamAlignmentES3_RKSt6vectorINS0_7RefDataESaIS5_EERNS0_9BamWriterE[_ZN14BedIntersectPE15ProcessBamBlockERKN8BamTools12BamAlignmentES3_RKSt6vectorINS0_7RefDataESaIS5_EERNS0_9BamWriterE]+0x9e8): undefined reference to `BamTools::BamWriter::SaveAlignment(BamTools::BamAlignment const&)' /usr/local/bin/ld: pairToBed.cpp:(.text._ZN14BedIntersectPE15ProcessBamBlockERKN8BamTools12BamAlignmentES3_RKSt6vectorINS0_7RefDataESaIS5_EERNS0_9BamWriterE[_ZN14BedIntersectPE15ProcessBamBlockERKN8BamTools12BamAlignmentES3_RKSt6vectorINS0_7RefDataESaIS5_EERNS0_9BamWriterE]+0x9f8): undefined reference to `BamTools::BamWriter::SaveAlignment(BamTools::BamAlignment const&)' /usr/local/bin/ld: pairToBed.cpp:(.text._ZN14BedIntersectPE15ProcessBamBlockERKN8BamTools12BamAlignmentES3_RKSt6vectorINS0_7RefDataESaIS5_EERNS0_9BamWriterE[_ZN14BedIntersectPE15ProcessBamBlockERKN8BamTools12BamAlignmentES3_RKSt6vectorINS0_7RefDataESaIS5_EERNS0_9BamWriterE]+0xa40): undefined reference to `BamTools::BamAlignment::IsMapped() const' /usr/local/bin/ld: pairToBed.cpp:(.text._ZN14BedIntersectPE15ProcessBamBlockERKN8BamTools12BamAlignmentES3_RKSt6vectorINS0_7RefDataESaIS5_EERNS0_9BamWriterE[_ZN14BedIntersectPE15ProcessBamBlockERKN8BamTools12BamAlignmentES3_RKSt6vectorINS0_7RefDataESaIS5_EERNS0_9BamWriterE]+0xa64): undefined reference to `BamTools::BamWriter::SaveAlignment(BamTools::BamAlignment const&)' /usr/local/bin/ld: pairToBed.cpp:(.text._ZN14BedIntersectPE15ProcessBamBlockERKN8BamTools12BamAlignmentES3_RKSt6vectorINS0_7RefDataESaIS5_EERNS0_9BamWriterE[_ZN14BedIntersectPE15ProcessBamBlockERKN8BamTools12BamAlignmentES3_RKSt6vectorINS0_7RefDataESaIS5_EERNS0_9BamWriterE]+0xa74): undefined reference to `BamTools::BamWriter::SaveAlignment(BamTools::BamAlignment const&)' /usr/local/bin/ld: pairToBed.cpp:(.text._ZN14BedIntersectPE15ProcessBamBlockERKN8BamTools12BamAlignmentES3_RKSt6vectorINS0_7RefDataESaIS5_EERNS0_9BamWriterE[_ZN14BedIntersectPE15ProcessBamBlockERKN8BamTools12BamAlignmentES3_RKSt6vectorINS0_7RefDataESaIS5_EERNS0_9BamWriterE]+0xa84): undefined reference to `BamTools::BamAlignment::IsMapped() const' /usr/local/bin/ld: pairToBed.cpp:(.text._ZN14BedIntersectPE15ProcessBamBlockERKN8BamTools12BamAlignmentES3_RKSt6vectorINS0_7RefDataESaIS5_EERNS0_9BamWriterE[_ZN14BedIntersectPE15ProcessBamBlockERKN8BamTools12BamAlignmentES3_RKSt6vectorINS0_7RefDataESaIS5_EERNS0_9BamWriterE]+0xb74): undefined reference to `BamTools::BamWriter::SaveAlignment(BamTools::BamAlignment const&)' /usr/local/bin/ld: pairToBed.cpp:(.text._ZN14BedIntersectPE15ProcessBamBlockERKN8BamTools12BamAlignmentES3_RKSt6vectorINS0_7RefDataESaIS5_EERNS0_9BamWriterE[_ZN14BedIntersectPE15ProcessBamBlockERKN8BamTools12BamAlignmentES3_RKSt6vectorINS0_7RefDataESaIS5_EERNS0_9BamWriterE]+0xb84): undefined reference to `BamTools::BamWriter::SaveAlignment(BamTools::BamAlignment const&)' /usr/local/bin/ld: pairToBed.cpp:(.text._ZN14BedIntersectPE15ProcessBamBlockERKN8BamTools12BamAlignmentES3_RKSt6vectorINS0_7RefDataESaIS5_EERNS0_9BamWriterE[_ZN14BedIntersectPE15ProcessBamBlockERKN8BamTools12BamAlignmentES3_RKSt6vectorINS0_7RefDataESaIS5_EERNS0_9BamWriterE]+0xb98): undefined reference to `BamTools::BamWriter::SaveAlignment(BamTools::BamAlignment const&)' /usr/local/bin/ld: pairToBed.cpp:(.text._ZN14BedIntersectPE15ProcessBamBlockERKN8BamTools12BamAlignmentES3_RKSt6vectorINS0_7RefDataESaIS5_EERNS0_9BamWriterE[_ZN14BedIntersectPE15ProcessBamBlockERKN8BamTools12BamAlignmentES3_RKSt6vectorINS0_7RefDataESaIS5_EERNS0_9BamWriterE]+0xba8): undefined reference to `BamTools::BamWriter::SaveAlignment(BamTools::BamAlignment const&)' /usr/local/bin/ld: obj/tagBam.o: in function `TagBam::Tag()': tagBam.cpp:(.text+0x730): undefined reference to `BamTools::BamReader::BamReader()' /usr/local/bin/ld: tagBam.cpp:(.text+0x73c): undefined reference to `BamTools::BamWriter::BamWriter()' /usr/local/bin/ld: tagBam.cpp:(.text+0x74c): undefined reference to `BamTools::BamReader::Open(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)' /usr/local/bin/ld: tagBam.cpp:(.text+0x76c): undefined reference to `BamTools::BamReader::GetHeaderText[abi:cxx11]() const' /usr/local/bin/ld: tagBam.cpp:(.text+0x778): undefined reference to `BamTools::BamReader::GetReferenceData() const' /usr/local/bin/ld: tagBam.cpp:(.text+0x874): undefined reference to `BamTools::BamWriter::SetCompressionMode(BamTools::BamWriter::CompressionMode const&)' /usr/local/bin/ld: tagBam.cpp:(.text+0x8b4): undefined reference to `BamTools::BamWriter::Open(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::vector<BamTools::RefData, std::allocator<BamTools::RefData> > const&)' /usr/local/bin/ld: tagBam.cpp:(.text+0x8d8): undefined reference to `BamTools::BamAlignment::BamAlignment()' /usr/local/bin/ld: tagBam.cpp:(.text+0x968): undefined reference to `BamTools::BamReader::GetNextAlignment(BamTools::BamAlignment&)' /usr/local/bin/ld: tagBam.cpp:(.text+0x97c): undefined reference to `BamTools::BamAlignment::IsMapped() const' /usr/local/bin/ld: tagBam.cpp:(.text+0xab4): undefined reference to `BamTools::BamAlignment::GetEndPosition(bool, bool) const' /usr/local/bin/ld: tagBam.cpp:(.text+0xae4): undefined reference to `BamTools::BamAlignment::IsReverseStrand() const' /usr/local/bin/ld: tagBam.cpp:(.text+0x11a4): undefined reference to `BamTools::BamAlignment::IsValidSize(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const' /usr/local/bin/ld: tagBam.cpp:(.text+0x1364): undefined reference to `BamTools::BamWriter::SaveAlignment(BamTools::BamAlignment const&)' /usr/local/bin/ld: tagBam.cpp:(.text+0x1a0c): undefined reference to `BamTools::BamAlignment::FindTag(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, char*&, unsigned int const&, unsigned int&) const' /usr/local/bin/ld: tagBam.cpp:(.text+0x1ba4): undefined reference to `BamTools::BamAlignment::BuildCharData()' /usr/local/bin/ld: tagBam.cpp:(.text+0x1bb4): undefined reference to `BamTools::BamReader::Close()' /usr/local/bin/ld: tagBam.cpp:(.text+0x1bc0): undefined reference to `BamTools::BamWriter::Close()' /usr/local/bin/ld: tagBam.cpp:(.text+0x1ce4): undefined reference to `BamTools::BamAlignment::~BamAlignment()' /usr/local/bin/ld: tagBam.cpp:(.text+0x1d58): undefined reference to `BamTools::BamWriter::~BamWriter()' /usr/local/bin/ld: tagBam.cpp:(.text+0x1d64): undefined reference to `BamTools::BamReader::~BamReader()' /usr/local/bin/ld: tagBam.cpp:(.text+0x1f8c): undefined reference to `BamTools::BamAlignment::~BamAlignment()' /usr/local/bin/ld: tagBam.cpp:(.text+0x2008): undefined reference to `BamTools::BamWriter::~BamWriter()' /usr/local/bin/ld: tagBam.cpp:(.text+0x2048): undefined reference to `BamTools::BamReader::~BamReader()' /usr/local/bin/ld: obj/windowBed.o: in function `BedWindow::WindowIntersectBam(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)': windowBed.cpp:(.text+0x1b6c): undefined reference to `BamTools::BamReader::BamReader()' /usr/local/bin/ld: windowBed.cpp:(.text+0x1b78): undefined reference to `BamTools::BamWriter::BamWriter()' /usr/local/bin/ld: windowBed.cpp:(.text+0x1b88): undefined reference to `BamTools::BamReader::Open(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)' /usr/local/bin/ld: windowBed.cpp:(.text+0x1ba4): undefined reference to `BamTools::BamReader::GetHeaderText[abi:cxx11]() const' /usr/local/bin/ld: windowBed.cpp:(.text+0x1bb0): undefined reference to `BamTools::BamReader::GetReferenceData() const' /usr/local/bin/ld: windowBed.cpp:(.text+0x1cc4): undefined reference to `BamTools::BamWriter::SetCompressionMode(BamTools::BamWriter::CompressionMode const&)' /usr/local/bin/ld: windowBed.cpp:(.text+0x1d04): undefined reference to `BamTools::BamWriter::Open(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::vector<BamTools::RefData, std::allocator<BamTools::RefData> > const&)' /usr/local/bin/ld: windowBed.cpp:(.text+0x1d5c): undefined reference to `BamTools::BamAlignment::BamAlignment()' /usr/local/bin/ld: windowBed.cpp:(.text+0x1df8): undefined reference to `BamTools::BamReader::GetNextAlignment(BamTools::BamAlignment&)' /usr/local/bin/ld: windowBed.cpp:(.text+0x1e0c): undefined reference to `BamTools::BamAlignment::IsMapped() const' /usr/local/bin/ld: windowBed.cpp:(.text+0x1e30): undefined reference to `BamTools::BamWriter::SaveAlignment(BamTools::BamAlignment const&)' /usr/local/bin/ld: windowBed.cpp:(.text+0x1f48): undefined reference to `BamTools::BamAlignment::GetEndPosition(bool, bool) const' /usr/local/bin/ld: windowBed.cpp:(.text+0x1f68): undefined reference to `BamTools::BamAlignment::IsFirstMate() const' /usr/local/bin/ld: windowBed.cpp:(.text+0x1fa8): undefined reference to `BamTools::BamAlignment::IsSecondMate() const' /usr/local/bin/ld: windowBed.cpp:(.text+0x22ac): undefined reference to `BamTools::BamAlignment::IsReverseStrand() const' /usr/local/bin/ld: windowBed.cpp:(.text+0x2560): undefined reference to `BamTools::BamWriter::SaveAlignment(BamTools::BamAlignment const&)' /usr/local/bin/ld: windowBed.cpp:(.text+0x2594): undefined reference to `BamTools::BamReader::Close()' /usr/local/bin/ld: windowBed.cpp:(.text+0x25ac): undefined reference to `BamTools::BamAlignment::~BamAlignment()' /usr/local/bin/ld: windowBed.cpp:(.text+0x2738): undefined reference to `BamTools::BamWriter::~BamWriter()' /usr/local/bin/ld: windowBed.cpp:(.text+0x2744): undefined reference to `BamTools::BamReader::~BamReader()' /usr/local/bin/ld: windowBed.cpp:(.text+0x27c4): undefined reference to `BamTools::BamWriter::Close()' /usr/local/bin/ld: windowBed.cpp:(.text+0x2938): undefined reference to `BamTools::BamReader::~BamReader()' /usr/local/bin/ld: windowBed.cpp:(.text+0x297c): undefined reference to `BamTools::BamAlignment::~BamAlignment()' /usr/local/bin/ld: windowBed.cpp:(.text+0x2a00): undefined reference to `BamTools::BamWriter::~BamWriter()' collect2: error: ld returned 1 exit status gmake[1]: *** [Makefile:147: all] Error 1 gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/bedtools/work/bedtools2-2.27.1' *** Error code 1 Stop. make: stopped in /usr/ports/biology/bedtools
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