------------------------------------------------------------------------------- -- Phase: Environment ------------------------------------------------------------------------------- NO_DEPENDS=1 UNAME_r=6.1 UNAME_m=x86_64 UNAME_p=x86_64 UNAME_v=unknown UNAME_s=DragonFly PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SSL_NO_VERIFY_PEER=1 LANG=C HOME=/root USER=root TERM=dumb SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: showconfig ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: CONFIGURE_ENV ------------------------------------------------------------------------------- XDG_DATA_HOME=/construction/biology/bamtools XDG_CONFIG_HOME=/construction/biology/bamtools HOME=/construction/biology/bamtools TMPDIR="/tmp" PATH=/construction/biology/bamtools/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCVER=gcc80 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: CONFIGURE_ARGS ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: MAKE_ENV ------------------------------------------------------------------------------- XDG_DATA_HOME=/construction/biology/bamtools XDG_CONFIG_HOME=/construction/biology/bamtools HOME=/construction/biology/bamtools TMPDIR="/tmp" PATH=/construction/biology/bamtools/.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=gcc80 PREFIX=/usr/local LOCALBASE=/usr/local NOPROFILE=1 CC="cc" CFLAGS="-pipe -O2 -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" " LIBS="" CXX="c++" CXXFLAGS=" -pipe -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" SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: MAKE_ARGS ------------------------------------------------------------------------------- DESTDIR=/construction/biology/bamtools/stage SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: PLIST_SUB ------------------------------------------------------------------------------- CMAKE_BUILD_TYPE="release" OSREL=6.1 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PROFILE="@comment " DOCSDIR="share/doc/bamtools" EXAMPLESDIR="share/examples/bamtools" DATADIR="share/bamtools" WWWDIR="www/bamtools" ETCDIR="etc/bamtools" SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: SUB_LIST ------------------------------------------------------------------------------- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/bamtools DOCSDIR=/usr/local/share/doc/bamtools EXAMPLESDIR=/usr/local/share/examples/bamtools WWWDIR=/usr/local/www/bamtools ETCDIR=/usr/local/etc/bamtools SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: /etc/make.conf ------------------------------------------------------------------------------- DPORTS_BUILDER=yes DISABLE_LICENSES=yes DEFAULT_VERSIONS=ssl=openssl FORCE_PACKAGE=yes DEVELOPER=yes USE_PACKAGE_DEPENDS_ONLY=yes PORTSDIR=/xports PORT_DBDIR=/options PKG_DBDIR=/var/db/pkg PKG_CACHEDIR=/var/cache/pkg PKG_SUFX=.txz DEVELOPER=1 UID=0 ARCH=x86_64 OPSYS=DragonFly DFLYVERSION=600100 OSVERSION=9999999 OSREL=6.1 _OSRELEASE=6.1-SYNTH DISTDIR=/distfiles WRKDIRPREFIX=/construction BATCH=yes PACKAGE_BUILDING=yes PKG_CREATE_VERBOSE=yes MAKE_JOBS_NUMBER=10 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: setup ------------------------------------------------------------------------------- Installing /packages/All/libnghttp2-1.43.0.txz Installing /packages/All/ca_root_nss-3.63.txz ===== Message from ca_root_nss-3.63: -- FreeBSD does not, and can not warrant that the certification authorities whose certificates are included in this package have in any way been audited for trustworthiness or RFC 3647 compliance. Assessment and verification of trust is the complete responsibility of the system administrator. This package installs symlinks to support root certificates discovery by default for software that uses OpenSSL. This enables SSL Certificate Verification by client software without manual intervention. If you prefer to do this manually, replace the following symlinks with either an empty file or your site-local certificate bundle. * /etc/ssl/cert.pem * /usr/local/etc/ssl/cert.pem * /usr/local/openssl/cert.pem Installing /packages/All/openssl-1.1.1k_1,1.txz Installing /packages/All/curl-7.76.0.txz Installing /packages/All/expat-2.4.1.txz Installing /packages/All/libuv-1.41.0.txz Installing /packages/All/indexinfo-0.3.1.txz Installing /packages/All/gettext-runtime-0.21.txz Installing /packages/All/rhash-1.4.1.txz Installing /packages/All/liblz4-1.9.3,1.txz Installing /packages/All/libarchive-3.5.1,1.txz Installing /packages/All/ncurses-6.2.20210313_1.txz ===== Message from ncurses-6.2.20210313_1: -- { type: install message: < bamtools-2.5.1_2 depends on file: /usr/local/sbin/pkg - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch ------------------------------------------------------------------------------- ===> bamtools-2.5.1_2 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by bamtools-2.5.1_2 for building SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: checksum ------------------------------------------------------------------------------- ===> bamtools-2.5.1_2 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by bamtools-2.5.1_2 for building => SHA256 Checksum OK for pezmaster31-bamtools-v2.5.1_GH0.tar.gz. SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract ------------------------------------------------------------------------------- ===> bamtools-2.5.1_2 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by bamtools-2.5.1_2 for building ===> Extracting for bamtools-2.5.1_2 => SHA256 Checksum OK for pezmaster31-bamtools-v2.5.1_GH0.tar.gz. Extracted Memory Use: 3.03M SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: patch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch ------------------------------------------------------------------------------- ===> Patching for bamtools-2.5.1_2 ===> Applying ports patches for bamtools-2.5.1_2 from /xports/biology/bamtools/files SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: build-depends ------------------------------------------------------------------------------- ===> bamtools-2.5.1_2 depends on file: /usr/local/bin/cmake - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: lib-depends ------------------------------------------------------------------------------- ===> bamtools-2.5.1_2 depends on shared library: libjsoncpp.so - found (/usr/local/lib/libjsoncpp.so) SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: configure ------------------------------------------------------------------------------- ===> bamtools-2.5.1_2 depends on file: /usr/local/bin/cmake - found ===> bamtools-2.5.1_2 depends on shared library: libjsoncpp.so - found (/usr/local/lib/libjsoncpp.so) ===> Configuring for bamtools-2.5.1_2 ===> Performing out-of-source build /bin/mkdir -p /construction/biology/bamtools/.build -- The CXX compiler identification is GNU 8.3.0 -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done CMake Deprecation Warning at CMakeLists.txt:20 (cmake_policy): The OLD behavior for policy CMP0042 will be removed from a future version of CMake. The cmake-policies(7) manual explains that the OLD behaviors of all policies are deprecated and that a policy should be set to OLD only under specific short-term circumstances. Projects should be ported to the NEW behavior and not rely on setting a policy to OLD. -- Could NOT find PkgConfig (missing: PKG_CONFIG_EXECUTABLE) -- Checking for one of the modules 'jsoncpp>=1' Did NOT find system JsonCpp, instead using bundled version -- Found ZLIB: /usr/lib/libz.so (found version "1.2.11") -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_CXX_FLAGS_DEBUG CMAKE_C_COMPILER CMAKE_C_FLAGS CMAKE_C_FLAGS_DEBUG CMAKE_C_FLAGS_RELEASE CMAKE_MODULE_LINKER_FLAGS THREADS_HAVE_PTHREAD_ARG -- Build files have been written to: /construction/biology/bamtools/.build SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: build ------------------------------------------------------------------------------- ===> Building for bamtools-2.5.1_2 /usr/local/bin/cmake -S/construction/biology/bamtools/bamtools-2.5.1 -B/construction/biology/bamtools/.build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/local/bin/cmake -E cmake_progress_start /construction/biology/bamtools/.build/CMakeFiles /construction/biology/bamtools/.build//CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all --- src/CMakeFiles/SharedHeaders.dir/all --- --- src/api/CMakeFiles/APIHeaders.dir/all --- --- src/api/CMakeFiles/BamTools.dir/all --- --- src/api/CMakeFiles/AlgorithmsHeaders.dir/all --- --- src/third_party/jsoncpp/CMakeFiles/jsoncpp.dir/all --- --- src/CMakeFiles/SharedHeaders.dir/all --- /usr/bin/make -f src/CMakeFiles/SharedHeaders.dir/build.make src/CMakeFiles/SharedHeaders.dir/depend --- src/api/CMakeFiles/APIHeaders.dir/all --- /usr/bin/make -f src/api/CMakeFiles/APIHeaders.dir/build.make src/api/CMakeFiles/APIHeaders.dir/depend --- src/api/CMakeFiles/BamTools.dir/all --- /usr/bin/make -f src/api/CMakeFiles/BamTools.dir/build.make src/api/CMakeFiles/BamTools.dir/depend --- src/third_party/jsoncpp/CMakeFiles/jsoncpp.dir/all --- /usr/bin/make -f src/third_party/jsoncpp/CMakeFiles/jsoncpp.dir/build.make src/third_party/jsoncpp/CMakeFiles/jsoncpp.dir/depend --- src/api/CMakeFiles/AlgorithmsHeaders.dir/all --- /usr/bin/make -f src/api/CMakeFiles/AlgorithmsHeaders.dir/build.make src/api/CMakeFiles/AlgorithmsHeaders.dir/depend --- src/CMakeFiles/SharedHeaders.dir/all --- --- src/CMakeFiles/SharedHeaders.dir/depend --- cd /construction/biology/bamtools/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/bamtools/bamtools-2.5.1 /construction/biology/bamtools/bamtools-2.5.1/src /construction/biology/bamtools/.build /construction/biology/bamtools/.build/src /construction/biology/bamtools/.build/src/CMakeFiles/SharedHeaders.dir/DependInfo.cmake --- src/api/CMakeFiles/APIHeaders.dir/all --- --- src/api/CMakeFiles/APIHeaders.dir/depend --- cd /construction/biology/bamtools/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/bamtools/bamtools-2.5.1 /construction/biology/bamtools/bamtools-2.5.1/src/api /construction/biology/bamtools/.build /construction/biology/bamtools/.build/src/api /construction/biology/bamtools/.build/src/api/CMakeFiles/APIHeaders.dir/DependInfo.cmake --- src/api/CMakeFiles/BamTools.dir/all --- --- src/api/CMakeFiles/BamTools.dir/depend --- cd /construction/biology/bamtools/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/bamtools/bamtools-2.5.1 /construction/biology/bamtools/bamtools-2.5.1/src/api /construction/biology/bamtools/.build /construction/biology/bamtools/.build/src/api /construction/biology/bamtools/.build/src/api/CMakeFiles/BamTools.dir/DependInfo.cmake --- src/CMakeFiles/SharedHeaders.dir/all --- Scanning dependencies of target SharedHeaders --- src/api/CMakeFiles/APIHeaders.dir/all --- Scanning dependencies of target APIHeaders --- src/third_party/jsoncpp/CMakeFiles/jsoncpp.dir/all --- --- src/third_party/jsoncpp/CMakeFiles/jsoncpp.dir/depend --- cd /construction/biology/bamtools/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/bamtools/bamtools-2.5.1 /construction/biology/bamtools/bamtools-2.5.1/src/third_party/jsoncpp /construction/biology/bamtools/.build /construction/biology/bamtools/.build/src/third_party/jsoncpp /construction/biology/bamtools/.build/src/third_party/jsoncpp/CMakeFiles/jsoncpp.dir/DependInfo.cmake --- src/CMakeFiles/SharedHeaders.dir/all --- /usr/bin/make -f src/CMakeFiles/SharedHeaders.dir/build.make src/CMakeFiles/SharedHeaders.dir/build --- src/api/CMakeFiles/APIHeaders.dir/all --- /usr/bin/make -f src/api/CMakeFiles/APIHeaders.dir/build.make src/api/CMakeFiles/APIHeaders.dir/build --- src/api/CMakeFiles/AlgorithmsHeaders.dir/all --- --- src/api/CMakeFiles/AlgorithmsHeaders.dir/depend --- cd /construction/biology/bamtools/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/bamtools/bamtools-2.5.1 /construction/biology/bamtools/bamtools-2.5.1/src/api /construction/biology/bamtools/.build /construction/biology/bamtools/.build/src/api /construction/biology/bamtools/.build/src/api/CMakeFiles/AlgorithmsHeaders.dir/DependInfo.cmake --- src/api/CMakeFiles/APIHeaders.dir/all --- --- APIHeaders --- cd /construction/biology/bamtools/.build/src/api && /usr/local/bin/cmake -E copy_if_different /construction/biology/bamtools/bamtools-2.5.1/src/api/api_global.h /construction/biology/bamtools/.build/src/api/include/api/api_global.h --- src/api/CMakeFiles/AlgorithmsHeaders.dir/all --- Scanning dependencies of target AlgorithmsHeaders --- src/third_party/jsoncpp/CMakeFiles/jsoncpp.dir/all --- Scanning dependencies of target jsoncpp --- src/CMakeFiles/SharedHeaders.dir/all --- --- SharedHeaders --- --- src/api/CMakeFiles/APIHeaders.dir/all --- cd /construction/biology/bamtools/.build/src/api && /usr/local/bin/cmake -E copy_if_different /construction/biology/bamtools/bamtools-2.5.1/src/api/BamAlgorithms.h /construction/biology/bamtools/.build/src/api/include/api/BamAlgorithms.h --- src/CMakeFiles/SharedHeaders.dir/all --- cd /construction/biology/bamtools/.build/src && /usr/local/bin/cmake -E copy_if_different /construction/biology/bamtools/bamtools-2.5.1/src/shared/bamtools_global.h /construction/biology/bamtools/.build/src/include/shared/bamtools_global.h --- src/api/CMakeFiles/BamTools.dir/all --- Scanning dependencies of target BamTools --- src/api/CMakeFiles/AlgorithmsHeaders.dir/all --- /usr/bin/make -f src/api/CMakeFiles/AlgorithmsHeaders.dir/build.make src/api/CMakeFiles/AlgorithmsHeaders.dir/build --- src/api/CMakeFiles/APIHeaders.dir/all --- cd /construction/biology/bamtools/.build/src/api && /usr/local/bin/cmake -E copy_if_different /construction/biology/bamtools/bamtools-2.5.1/src/api/BamAlignment.h /construction/biology/bamtools/.build/src/api/include/api/BamAlignment.h --- src/api/CMakeFiles/BamTools.dir/all --- /usr/bin/make -f src/api/CMakeFiles/BamTools.dir/build.make src/api/CMakeFiles/BamTools.dir/build --- src/third_party/jsoncpp/CMakeFiles/jsoncpp.dir/all --- /usr/bin/make -f src/third_party/jsoncpp/CMakeFiles/jsoncpp.dir/build.make src/third_party/jsoncpp/CMakeFiles/jsoncpp.dir/build --- src/third_party/jsoncpp/CMakeFiles/jsoncpp.dir/jsoncpp.cpp.o --- --- src/CMakeFiles/SharedHeaders.dir/all --- [ 0%] Built target SharedHeaders --- src/api/CMakeFiles/AlgorithmsHeaders.dir/all --- --- AlgorithmsHeaders --- --- src/api/CMakeFiles/APIHeaders.dir/all --- cd /construction/biology/bamtools/.build/src/api && /usr/local/bin/cmake -E copy_if_different /construction/biology/bamtools/bamtools-2.5.1/src/api/BamAux.h /construction/biology/bamtools/.build/src/api/include/api/BamAux.h --- src/api/CMakeFiles/AlgorithmsHeaders.dir/all --- cd /construction/biology/bamtools/.build/src/api && /usr/local/bin/cmake -E copy_if_different /construction/biology/bamtools/bamtools-2.5.1/src/api/algorithms/Sort.h /construction/biology/bamtools/.build/src/api/include/api/algorithms/Sort.h --- src/api/CMakeFiles/BamTools.dir/all --- --- src/api/CMakeFiles/BamTools.dir/BamAlignment.cpp.o --- --- src/api/CMakeFiles/BamTools.dir/BamMultiReader.cpp.o --- --- src/api/CMakeFiles/BamTools.dir/BamReader.cpp.o --- --- src/api/CMakeFiles/BamTools.dir/BamWriter.cpp.o --- --- src/api/CMakeFiles/BamTools.dir/SamHeader.cpp.o --- --- src/api/CMakeFiles/BamTools.dir/SamProgram.cpp.o --- --- src/api/CMakeFiles/BamTools.dir/SamProgramChain.cpp.o --- --- src/api/CMakeFiles/APIHeaders.dir/all --- cd /construction/biology/bamtools/.build/src/api && /usr/local/bin/cmake -E copy_if_different /construction/biology/bamtools/bamtools-2.5.1/src/api/BamConstants.h /construction/biology/bamtools/.build/src/api/include/api/BamConstants.h --- src/third_party/jsoncpp/CMakeFiles/jsoncpp.dir/all --- [ 3%] Building CXX object src/third_party/jsoncpp/CMakeFiles/jsoncpp.dir/jsoncpp.cpp.o --- src/api/CMakeFiles/BamTools.dir/all --- --- src/api/CMakeFiles/BamTools.dir/BamWriter.cpp.o --- [ 3%] Building CXX object src/api/CMakeFiles/BamTools.dir/BamWriter.cpp.o --- src/third_party/jsoncpp/CMakeFiles/jsoncpp.dir/all --- cd /construction/biology/bamtools/.build/src/third_party/jsoncpp && /usr/bin/c++ -DBAMTOOLS_JSONCPP_LIBRARY -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/construction/biology/bamtools/bamtools-2.5.1/src -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -Wall -o CMakeFiles/jsoncpp.dir/jsoncpp.cpp.o -c /construction/biology/bamtools/bamtools-2.5.1/src/third_party/jsoncpp/jsoncpp.cpp --- src/api/CMakeFiles/BamTools.dir/all --- cd /construction/biology/bamtools/.build/src/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/construction/biology/bamtools/bamtools-2.5.1/src -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -Wall -o CMakeFiles/BamTools.dir/BamWriter.cpp.o -c /construction/biology/bamtools/bamtools-2.5.1/src/api/BamWriter.cpp --- src/api/CMakeFiles/BamTools.dir/BamMultiReader.cpp.o --- [ 4%] Building CXX object src/api/CMakeFiles/BamTools.dir/BamMultiReader.cpp.o --- src/api/CMakeFiles/APIHeaders.dir/all --- cd /construction/biology/bamtools/.build/src/api && /usr/local/bin/cmake -E copy_if_different /construction/biology/bamtools/bamtools-2.5.1/src/api/BamIndex.h /construction/biology/bamtools/.build/src/api/include/api/BamIndex.h --- src/api/CMakeFiles/BamTools.dir/all --- cd /construction/biology/bamtools/.build/src/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/construction/biology/bamtools/bamtools-2.5.1/src -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -Wall -o CMakeFiles/BamTools.dir/BamMultiReader.cpp.o -c /construction/biology/bamtools/bamtools-2.5.1/src/api/BamMultiReader.cpp --- src/api/CMakeFiles/BamTools.dir/BamReader.cpp.o --- [ 6%] Building CXX object src/api/CMakeFiles/BamTools.dir/BamReader.cpp.o --- src/api/CMakeFiles/BamTools.dir/SamHeader.cpp.o --- [ 7%] Building CXX object src/api/CMakeFiles/BamTools.dir/SamHeader.cpp.o --- src/api/CMakeFiles/BamTools.dir/BamReader.cpp.o --- cd /construction/biology/bamtools/.build/src/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/construction/biology/bamtools/bamtools-2.5.1/src -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -Wall -o CMakeFiles/BamTools.dir/BamReader.cpp.o -c /construction/biology/bamtools/bamtools-2.5.1/src/api/BamReader.cpp --- src/api/CMakeFiles/BamTools.dir/SamHeader.cpp.o --- cd /construction/biology/bamtools/.build/src/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/construction/biology/bamtools/bamtools-2.5.1/src -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -Wall -o CMakeFiles/BamTools.dir/SamHeader.cpp.o -c /construction/biology/bamtools/bamtools-2.5.1/src/api/SamHeader.cpp --- src/api/CMakeFiles/APIHeaders.dir/all --- cd /construction/biology/bamtools/.build/src/api && /usr/local/bin/cmake -E copy_if_different /construction/biology/bamtools/bamtools-2.5.1/src/api/BamMultiReader.h /construction/biology/bamtools/.build/src/api/include/api/BamMultiReader.h --- src/api/CMakeFiles/BamTools.dir/all --- --- src/api/CMakeFiles/BamTools.dir/SamProgram.cpp.o --- [ 9%] Building CXX object src/api/CMakeFiles/BamTools.dir/SamProgram.cpp.o cd /construction/biology/bamtools/.build/src/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/construction/biology/bamtools/bamtools-2.5.1/src -pipe -O2 -fno-strict-aliasing 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/construction/biology/bamtools/.build/src/api/include/api/BamReader.h --- src/api/CMakeFiles/AlgorithmsHeaders.dir/all --- [ 11%] Built target AlgorithmsHeaders --- src/api/CMakeFiles/BamTools.dir/all --- --- src/api/CMakeFiles/BamTools.dir/SamReadGroup.cpp.o --- --- src/api/CMakeFiles/BamTools.dir/BamAlignment.cpp.o --- [ 12%] Building CXX object src/api/CMakeFiles/BamTools.dir/BamAlignment.cpp.o cd /construction/biology/bamtools/.build/src/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/construction/biology/bamtools/bamtools-2.5.1/src -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -Wall -o CMakeFiles/BamTools.dir/BamAlignment.cpp.o -c /construction/biology/bamtools/bamtools-2.5.1/src/api/BamAlignment.cpp --- src/api/CMakeFiles/APIHeaders.dir/all --- cd /construction/biology/bamtools/.build/src/api && /usr/local/bin/cmake -E copy_if_different /construction/biology/bamtools/bamtools-2.5.1/src/api/BamWriter.h /construction/biology/bamtools/.build/src/api/include/api/BamWriter.h cd /construction/biology/bamtools/.build/src/api && /usr/local/bin/cmake -E copy_if_different /construction/biology/bamtools/bamtools-2.5.1/src/api/IBamIODevice.h /construction/biology/bamtools/.build/src/api/include/api/IBamIODevice.h cd /construction/biology/bamtools/.build/src/api && /usr/local/bin/cmake -E copy_if_different /construction/biology/bamtools/bamtools-2.5.1/src/api/SamConstants.h /construction/biology/bamtools/.build/src/api/include/api/SamConstants.h --- src/api/CMakeFiles/BamTools.dir/all --- --- src/api/CMakeFiles/BamTools.dir/SamReadGroup.cpp.o --- [ 14%] Building CXX object src/api/CMakeFiles/BamTools.dir/SamReadGroup.cpp.o cd /construction/biology/bamtools/.build/src/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE 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/construction/biology/bamtools/.build/src/api && /usr/local/bin/cmake -E copy_if_different /construction/biology/bamtools/bamtools-2.5.1/src/api/SamReadGroup.h /construction/biology/bamtools/.build/src/api/include/api/SamReadGroup.h cd /construction/biology/bamtools/.build/src/api && /usr/local/bin/cmake -E copy_if_different /construction/biology/bamtools/bamtools-2.5.1/src/api/SamReadGroupDictionary.h /construction/biology/bamtools/.build/src/api/include/api/SamReadGroupDictionary.h cd /construction/biology/bamtools/.build/src/api && /usr/local/bin/cmake -E copy_if_different /construction/biology/bamtools/bamtools-2.5.1/src/api/SamSequence.h /construction/biology/bamtools/.build/src/api/include/api/SamSequence.h cd /construction/biology/bamtools/.build/src/api && /usr/local/bin/cmake -E copy_if_different /construction/biology/bamtools/bamtools-2.5.1/src/api/SamSequenceDictionary.h /construction/biology/bamtools/.build/src/api/include/api/SamSequenceDictionary.h [ 14%] Built target APIHeaders --- src/api/CMakeFiles/BamTools.dir/all --- --- src/api/CMakeFiles/BamTools.dir/SamReadGroupDictionary.cpp.o --- [ 15%] Building CXX object src/api/CMakeFiles/BamTools.dir/SamReadGroupDictionary.cpp.o cd /construction/biology/bamtools/.build/src/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/construction/biology/bamtools/bamtools-2.5.1/src -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -Wall -o CMakeFiles/BamTools.dir/SamReadGroupDictionary.cpp.o -c /construction/biology/bamtools/bamtools-2.5.1/src/api/SamReadGroupDictionary.cpp --- src/api/CMakeFiles/BamTools.dir/SamSequence.cpp.o --- [ 17%] Building CXX object src/api/CMakeFiles/BamTools.dir/SamSequence.cpp.o cd /construction/biology/bamtools/.build/src/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE 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/construction/biology/bamtools/bamtools-2.5.1/src/api/internal/bam/BamMultiReader_p.cpp --- src/api/CMakeFiles/BamTools.dir/internal/bam/BamRandomAccessController_p.cpp.o --- [ 23%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/bam/BamRandomAccessController_p.cpp.o cd /construction/biology/bamtools/.build/src/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/construction/biology/bamtools/bamtools-2.5.1/src -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -Wall -o CMakeFiles/BamTools.dir/internal/bam/BamRandomAccessController_p.cpp.o -c /construction/biology/bamtools/bamtools-2.5.1/src/api/internal/bam/BamRandomAccessController_p.cpp --- src/api/CMakeFiles/BamTools.dir/internal/bam/BamReader_p.cpp.o --- [ 25%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/bam/BamReader_p.cpp.o cd /construction/biology/bamtools/.build/src/api && /usr/bin/c++ 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src/api/CMakeFiles/BamTools.dir/internal/index/BamIndexFactory_p.cpp.o --- [ 28%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/index/BamIndexFactory_p.cpp.o cd /construction/biology/bamtools/.build/src/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/construction/biology/bamtools/bamtools-2.5.1/src -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -Wall -o CMakeFiles/BamTools.dir/internal/index/BamIndexFactory_p.cpp.o -c /construction/biology/bamtools/bamtools-2.5.1/src/api/internal/index/BamIndexFactory_p.cpp --- src/api/CMakeFiles/BamTools.dir/internal/index/BamStandardIndex_p.cpp.o --- [ 30%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/index/BamStandardIndex_p.cpp.o cd /construction/biology/bamtools/.build/src/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE 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CMakeFiles/BamTools.dir/internal/io/BamFile_p.cpp.o -c /construction/biology/bamtools/bamtools-2.5.1/src/api/internal/io/BamFile_p.cpp --- src/api/CMakeFiles/BamTools.dir/internal/io/BamFtp_p.cpp.o --- [ 36%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/BamFtp_p.cpp.o cd /construction/biology/bamtools/.build/src/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/construction/biology/bamtools/bamtools-2.5.1/src -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -Wall -o CMakeFiles/BamTools.dir/internal/io/BamFtp_p.cpp.o -c /construction/biology/bamtools/bamtools-2.5.1/src/api/internal/io/BamFtp_p.cpp --- src/api/CMakeFiles/BamTools.dir/internal/io/BamHttp_p.cpp.o --- [ 38%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/BamHttp_p.cpp.o cd /construction/biology/bamtools/.build/src/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS 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CMakeFiles/BamTools.dir/internal/io/ByteArray_p.cpp.o -c /construction/biology/bamtools/bamtools-2.5.1/src/api/internal/io/ByteArray_p.cpp --- src/api/CMakeFiles/BamTools.dir/internal/io/HostAddress_p.cpp.o --- [ 44%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/HostAddress_p.cpp.o cd /construction/biology/bamtools/.build/src/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/construction/biology/bamtools/bamtools-2.5.1/src -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -Wall -o CMakeFiles/BamTools.dir/internal/io/HostAddress_p.cpp.o -c /construction/biology/bamtools/bamtools-2.5.1/src/api/internal/io/HostAddress_p.cpp --- src/api/CMakeFiles/BamTools.dir/internal/io/HostInfo_p.cpp.o --- [ 46%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/HostInfo_p.cpp.o cd /construction/biology/bamtools/.build/src/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/construction/biology/bamtools/bamtools-2.5.1/src -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -Wall -o CMakeFiles/BamTools.dir/internal/io/HostInfo_p.cpp.o -c /construction/biology/bamtools/bamtools-2.5.1/src/api/internal/io/HostInfo_p.cpp --- src/api/CMakeFiles/BamTools.dir/internal/io/HostAddress_p.cpp.o --- /construction/biology/bamtools/bamtools-2.5.1/src/api/internal/io/HostAddress_p.cpp: In member function 'void BamTools::Internal::HostAddress::Clear()': /construction/biology/bamtools/bamtools-2.5.1/src/api/internal/io/HostAddress_p.cpp:273:49: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'struct BamTools::Internal::IPv6Address'; use assignment or value-initialization instead [-Wclass-memaccess] memset(&m_ip6Address, 0, sizeof(IPv6Address)); ^ In file included from /construction/biology/bamtools/bamtools-2.5.1/src/api/internal/io/HostAddress_p.cpp:10: /construction/biology/bamtools/bamtools-2.5.1/src/api/internal/io/HostAddress_p.h:31:8: note: 'struct BamTools::Internal::IPv6Address' declared here struct IPv6Address ^~~~~~~~~~~ --- src/api/CMakeFiles/BamTools.dir/internal/io/HttpHeader_p.cpp.o --- [ 47%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/HttpHeader_p.cpp.o cd /construction/biology/bamtools/.build/src/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/construction/biology/bamtools/bamtools-2.5.1/src -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -Wall -o CMakeFiles/BamTools.dir/internal/io/HttpHeader_p.cpp.o -c /construction/biology/bamtools/bamtools-2.5.1/src/api/internal/io/HttpHeader_p.cpp --- src/api/CMakeFiles/BamTools.dir/internal/io/ILocalIODevice_p.cpp.o --- [ 49%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/ILocalIODevice_p.cpp.o cd /construction/biology/bamtools/.build/src/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/construction/biology/bamtools/bamtools-2.5.1/src -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -Wall -o CMakeFiles/BamTools.dir/internal/io/ILocalIODevice_p.cpp.o -c /construction/biology/bamtools/bamtools-2.5.1/src/api/internal/io/ILocalIODevice_p.cpp --- src/api/CMakeFiles/BamTools.dir/internal/io/RollingBuffer_p.cpp.o --- [ 50%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/RollingBuffer_p.cpp.o cd /construction/biology/bamtools/.build/src/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/construction/biology/bamtools/bamtools-2.5.1/src -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -Wall -o CMakeFiles/BamTools.dir/internal/io/RollingBuffer_p.cpp.o -c /construction/biology/bamtools/bamtools-2.5.1/src/api/internal/io/RollingBuffer_p.cpp --- src/api/CMakeFiles/BamTools.dir/internal/io/TcpSocket_p.cpp.o --- [ 52%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/TcpSocket_p.cpp.o cd /construction/biology/bamtools/.build/src/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/construction/biology/bamtools/bamtools-2.5.1/src -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -Wall -o CMakeFiles/BamTools.dir/internal/io/TcpSocket_p.cpp.o -c /construction/biology/bamtools/bamtools-2.5.1/src/api/internal/io/TcpSocket_p.cpp --- src/api/CMakeFiles/BamTools.dir/internal/io/TcpSocketEngine_p.cpp.o --- [ 53%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/TcpSocketEngine_p.cpp.o cd /construction/biology/bamtools/.build/src/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/construction/biology/bamtools/bamtools-2.5.1/src -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -Wall -o CMakeFiles/BamTools.dir/internal/io/TcpSocketEngine_p.cpp.o -c /construction/biology/bamtools/bamtools-2.5.1/src/api/internal/io/TcpSocketEngine_p.cpp --- src/api/CMakeFiles/BamTools.dir/internal/io/TcpSocketEngine_unix_p.cpp.o --- [ 55%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/TcpSocketEngine_unix_p.cpp.o cd /construction/biology/bamtools/.build/src/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/construction/biology/bamtools/bamtools-2.5.1/src -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -Wall -o CMakeFiles/BamTools.dir/internal/io/TcpSocketEngine_unix_p.cpp.o -c /construction/biology/bamtools/bamtools-2.5.1/src/api/internal/io/TcpSocketEngine_unix_p.cpp --- src/api/CMakeFiles/BamTools.dir/internal/sam/SamFormatParser_p.cpp.o --- [ 57%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/sam/SamFormatParser_p.cpp.o cd /construction/biology/bamtools/.build/src/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/construction/biology/bamtools/bamtools-2.5.1/src -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -Wall -o CMakeFiles/BamTools.dir/internal/sam/SamFormatParser_p.cpp.o -c /construction/biology/bamtools/bamtools-2.5.1/src/api/internal/sam/SamFormatParser_p.cpp --- src/api/CMakeFiles/BamTools.dir/internal/sam/SamFormatPrinter_p.cpp.o --- [ 58%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/sam/SamFormatPrinter_p.cpp.o cd /construction/biology/bamtools/.build/src/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/construction/biology/bamtools/bamtools-2.5.1/src -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -Wall -o CMakeFiles/BamTools.dir/internal/sam/SamFormatPrinter_p.cpp.o -c /construction/biology/bamtools/bamtools-2.5.1/src/api/internal/sam/SamFormatPrinter_p.cpp --- src/api/CMakeFiles/BamTools.dir/internal/sam/SamHeaderValidator_p.cpp.o --- [ 60%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/sam/SamHeaderValidator_p.cpp.o cd /construction/biology/bamtools/.build/src/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/construction/biology/bamtools/bamtools-2.5.1/src -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -Wall -o CMakeFiles/BamTools.dir/internal/sam/SamHeaderValidator_p.cpp.o -c /construction/biology/bamtools/bamtools-2.5.1/src/api/internal/sam/SamHeaderValidator_p.cpp --- src/api/CMakeFiles/BamTools.dir/internal/utils/BamException_p.cpp.o --- [ 61%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/utils/BamException_p.cpp.o cd /construction/biology/bamtools/.build/src/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/construction/biology/bamtools/bamtools-2.5.1/src -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -Wall -o CMakeFiles/BamTools.dir/internal/utils/BamException_p.cpp.o -c /construction/biology/bamtools/bamtools-2.5.1/src/api/internal/utils/BamException_p.cpp --- src/api/libbamtools.so.2.5.1 --- [ 63%] Linking CXX shared library libbamtools.so cd /construction/biology/bamtools/.build/src/api && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/BamTools.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -shared -Wl,-soname,libbamtools.so.2.5.1 -o libbamtools.so.2.5.1 CMakeFiles/BamTools.dir/BamAlignment.cpp.o CMakeFiles/BamTools.dir/BamMultiReader.cpp.o CMakeFiles/BamTools.dir/BamReader.cpp.o CMakeFiles/BamTools.dir/BamWriter.cpp.o CMakeFiles/BamTools.dir/SamHeader.cpp.o CMakeFiles/BamTools.dir/SamProgram.cpp.o CMakeFiles/BamTools.dir/SamProgramChain.cpp.o CMakeFiles/BamTools.dir/SamReadGroup.cpp.o CMakeFiles/BamTools.dir/SamReadGroupDictionary.cpp.o CMakeFiles/BamTools.dir/SamSequence.cpp.o CMakeFiles/BamTools.dir/SamSequenceDictionary.cpp.o CMakeFiles/BamTools.dir/internal/bam/BamHeader_p.cpp.o CMakeFiles/BamTools.dir/internal/bam/BamMultiReader_p.cpp.o CMakeFiles/BamTools.dir/internal/bam/BamRandomAccessController_p.cpp.o CMakeFiles/BamTools.dir/internal/bam/BamReader_p.cpp.o CMakeFiles/BamTools.dir/internal/bam/BamWriter_p.cpp.o CMakeFiles/BamTools.dir/internal/index/BamIndexFactory_p.cpp.o CMakeFiles/BamTools.dir/internal/index/BamStandardIndex_p.cpp.o CMakeFiles/BamTools.dir/internal/index/BamToolsIndex_p.cpp.o CMakeFiles/BamTools.dir/internal/io/BamDeviceFactory_p.cpp.o CMakeFiles/BamTools.dir/internal/io/BamFile_p.cpp.o CMakeFiles/BamTools.dir/internal/io/BamFtp_p.cpp.o CMakeFiles/BamTools.dir/internal/io/BamHttp_p.cpp.o CMakeFiles/BamTools.dir/internal/io/BamPipe_p.cpp.o CMakeFiles/BamTools.dir/internal/io/BgzfStream_p.cpp.o CMakeFiles/BamTools.dir/internal/io/ByteArray_p.cpp.o CMakeFiles/BamTools.dir/internal/io/HostAddress_p.cpp.o CMakeFiles/BamTools.dir/internal/io/HostInfo_p.cpp.o CMakeFiles/BamTools.dir/internal/io/HttpHeader_p.cpp.o CMakeFiles/BamTools.dir/internal/io/ILocalIODevice_p.cpp.o CMakeFiles/BamTools.dir/internal/io/RollingBuffer_p.cpp.o CMakeFiles/BamTools.dir/internal/io/TcpSocket_p.cpp.o CMakeFiles/BamTools.dir/internal/io/TcpSocketEngine_p.cpp.o CMakeFiles/BamTools.dir/internal/io/TcpSocketEngine_unix_p.cpp.o CMakeFiles/BamTools.dir/internal/sam/SamFormatParser_p.cpp.o CMakeFiles/BamTools.dir/internal/sam/SamFormatPrinter_p.cpp.o CMakeFiles/BamTools.dir/internal/sam/SamHeaderValidator_p.cpp.o CMakeFiles/BamTools.dir/internal/utils/BamException_p.cpp.o -lz cd /construction/biology/bamtools/.build/src/api && /usr/local/bin/cmake -E cmake_symlink_library libbamtools.so.2.5.1 libbamtools.so.2.5.1 libbamtools.so [ 65%] Built target BamTools --- src/utils/CMakeFiles/BamTools-utils.dir/all --- /usr/bin/make -f src/utils/CMakeFiles/BamTools-utils.dir/build.make src/utils/CMakeFiles/BamTools-utils.dir/depend --- src/utils/CMakeFiles/BamTools-utils.dir/depend --- cd /construction/biology/bamtools/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/bamtools/bamtools-2.5.1 /construction/biology/bamtools/bamtools-2.5.1/src/utils /construction/biology/bamtools/.build /construction/biology/bamtools/.build/src/utils /construction/biology/bamtools/.build/src/utils/CMakeFiles/BamTools-utils.dir/DependInfo.cmake Scanning dependencies of target BamTools-utils /usr/bin/make -f src/utils/CMakeFiles/BamTools-utils.dir/build.make src/utils/CMakeFiles/BamTools-utils.dir/build --- src/utils/CMakeFiles/BamTools-utils.dir/bamtools_fasta.cpp.o --- --- src/utils/CMakeFiles/BamTools-utils.dir/bamtools_options.cpp.o --- --- src/utils/CMakeFiles/BamTools-utils.dir/bamtools_pileup_engine.cpp.o --- --- src/utils/CMakeFiles/BamTools-utils.dir/bamtools_utilities.cpp.o --- [ 68%] Building CXX object src/utils/CMakeFiles/BamTools-utils.dir/bamtools_utilities.cpp.o cd /construction/biology/bamtools/.build/src/utils && /usr/bin/c++ -DBAMTOOLS_UTILS_LIBRARY -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/construction/biology/bamtools/bamtools-2.5.1/src -I/construction/biology/bamtools/bamtools-2.5.1/src/api -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -Wall -o CMakeFiles/BamTools-utils.dir/bamtools_utilities.cpp.o -c /construction/biology/bamtools/bamtools-2.5.1/src/utils/bamtools_utilities.cpp --- src/utils/CMakeFiles/BamTools-utils.dir/bamtools_options.cpp.o --- [ 68%] Building CXX object src/utils/CMakeFiles/BamTools-utils.dir/bamtools_options.cpp.o cd /construction/biology/bamtools/.build/src/utils && /usr/bin/c++ -DBAMTOOLS_UTILS_LIBRARY -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/construction/biology/bamtools/bamtools-2.5.1/src -I/construction/biology/bamtools/bamtools-2.5.1/src/api -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -Wall -o CMakeFiles/BamTools-utils.dir/bamtools_options.cpp.o -c /construction/biology/bamtools/bamtools-2.5.1/src/utils/bamtools_options.cpp --- src/utils/CMakeFiles/BamTools-utils.dir/bamtools_fasta.cpp.o --- [ 69%] Building CXX object src/utils/CMakeFiles/BamTools-utils.dir/bamtools_fasta.cpp.o cd /construction/biology/bamtools/.build/src/utils && /usr/bin/c++ -DBAMTOOLS_UTILS_LIBRARY -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/construction/biology/bamtools/bamtools-2.5.1/src -I/construction/biology/bamtools/bamtools-2.5.1/src/api -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -Wall -o CMakeFiles/BamTools-utils.dir/bamtools_fasta.cpp.o -c /construction/biology/bamtools/bamtools-2.5.1/src/utils/bamtools_fasta.cpp --- src/utils/CMakeFiles/BamTools-utils.dir/bamtools_pileup_engine.cpp.o --- [ 71%] Building CXX object src/utils/CMakeFiles/BamTools-utils.dir/bamtools_pileup_engine.cpp.o cd /construction/biology/bamtools/.build/src/utils && /usr/bin/c++ -DBAMTOOLS_UTILS_LIBRARY -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/construction/biology/bamtools/bamtools-2.5.1/src -I/construction/biology/bamtools/bamtools-2.5.1/src/api -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -Wall -o CMakeFiles/BamTools-utils.dir/bamtools_pileup_engine.cpp.o -c /construction/biology/bamtools/bamtools-2.5.1/src/utils/bamtools_pileup_engine.cpp --- src/third_party/jsoncpp/CMakeFiles/jsoncpp.dir/all --- --- src/third_party/jsoncpp/libjsoncpp.a --- [ 73%] Linking CXX static library libjsoncpp.a cd /construction/biology/bamtools/.build/src/third_party/jsoncpp && /usr/local/bin/cmake -P CMakeFiles/jsoncpp.dir/cmake_clean_target.cmake cd /construction/biology/bamtools/.build/src/third_party/jsoncpp && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/jsoncpp.dir/link.txt --verbose=1 /usr/bin/ar qc libjsoncpp.a CMakeFiles/jsoncpp.dir/jsoncpp.cpp.o /usr/bin/ranlib libjsoncpp.a [ 73%] Built target jsoncpp --- src/utils/CMakeFiles/BamTools-utils.dir/all --- --- src/utils/libbamtools-utils.a --- [ 74%] Linking CXX static library libbamtools-utils.a cd /construction/biology/bamtools/.build/src/utils && /usr/local/bin/cmake -P CMakeFiles/BamTools-utils.dir/cmake_clean_target.cmake cd /construction/biology/bamtools/.build/src/utils && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/BamTools-utils.dir/link.txt --verbose=1 /usr/bin/ar qc libbamtools-utils.a CMakeFiles/BamTools-utils.dir/bamtools_fasta.cpp.o CMakeFiles/BamTools-utils.dir/bamtools_options.cpp.o CMakeFiles/BamTools-utils.dir/bamtools_pileup_engine.cpp.o CMakeFiles/BamTools-utils.dir/bamtools_utilities.cpp.o /usr/bin/ranlib libbamtools-utils.a [ 74%] Built target BamTools-utils --- src/toolkit/CMakeFiles/bamtools_cmd.dir/all --- /usr/bin/make -f src/toolkit/CMakeFiles/bamtools_cmd.dir/build.make src/toolkit/CMakeFiles/bamtools_cmd.dir/depend --- src/toolkit/CMakeFiles/bamtools_cmd.dir/depend --- cd /construction/biology/bamtools/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/bamtools/bamtools-2.5.1 /construction/biology/bamtools/bamtools-2.5.1/src/toolkit /construction/biology/bamtools/.build /construction/biology/bamtools/.build/src/toolkit /construction/biology/bamtools/.build/src/toolkit/CMakeFiles/bamtools_cmd.dir/DependInfo.cmake Scanning dependencies of target bamtools_cmd /usr/bin/make -f src/toolkit/CMakeFiles/bamtools_cmd.dir/build.make src/toolkit/CMakeFiles/bamtools_cmd.dir/build --- src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_convert.cpp.o --- --- src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_count.cpp.o --- --- src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_coverage.cpp.o --- --- src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_filter.cpp.o --- --- src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_header.cpp.o --- --- src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_index.cpp.o --- --- src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_merge.cpp.o --- --- src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_random.cpp.o --- --- src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_resolve.cpp.o --- --- src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_revert.cpp.o --- --- src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_convert.cpp.o --- [ 80%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_convert.cpp.o --- src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_filter.cpp.o --- [ 80%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_filter.cpp.o --- src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_random.cpp.o --- [ 80%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_random.cpp.o --- src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_revert.cpp.o --- [ 80%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_revert.cpp.o --- src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_count.cpp.o --- [ 82%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_count.cpp.o --- src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_revert.cpp.o --- cd /construction/biology/bamtools/.build/src/toolkit && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/construction/biology/bamtools/bamtools-2.5.1/src -I/construction/biology/bamtools/bamtools-2.5.1/src/api -I/construction/biology/bamtools/bamtools-2.5.1/src/utils -I/construction/biology/bamtools/bamtools-2.5.1/src/third_party -I/construction/biology/bamtools/.build/src/toolkit -I/construction/biology/bamtools/bamtools-2.5.1/src/third_party/jsoncpp -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -Wall -o CMakeFiles/bamtools_cmd.dir/bamtools_revert.cpp.o -c /construction/biology/bamtools/bamtools-2.5.1/src/toolkit/bamtools_revert.cpp --- src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_convert.cpp.o --- cd /construction/biology/bamtools/.build/src/toolkit && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/construction/biology/bamtools/bamtools-2.5.1/src -I/construction/biology/bamtools/bamtools-2.5.1/src/api -I/construction/biology/bamtools/bamtools-2.5.1/src/utils -I/construction/biology/bamtools/bamtools-2.5.1/src/third_party -I/construction/biology/bamtools/.build/src/toolkit -I/construction/biology/bamtools/bamtools-2.5.1/src/third_party/jsoncpp -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -Wall -o CMakeFiles/bamtools_cmd.dir/bamtools_convert.cpp.o -c /construction/biology/bamtools/bamtools-2.5.1/src/toolkit/bamtools_convert.cpp --- src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_random.cpp.o --- cd /construction/biology/bamtools/.build/src/toolkit && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/construction/biology/bamtools/bamtools-2.5.1/src -I/construction/biology/bamtools/bamtools-2.5.1/src/api -I/construction/biology/bamtools/bamtools-2.5.1/src/utils -I/construction/biology/bamtools/bamtools-2.5.1/src/third_party -I/construction/biology/bamtools/.build/src/toolkit -I/construction/biology/bamtools/bamtools-2.5.1/src/third_party/jsoncpp -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -Wall -o CMakeFiles/bamtools_cmd.dir/bamtools_random.cpp.o -c /construction/biology/bamtools/bamtools-2.5.1/src/toolkit/bamtools_random.cpp --- src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_filter.cpp.o --- cd /construction/biology/bamtools/.build/src/toolkit && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/construction/biology/bamtools/bamtools-2.5.1/src -I/construction/biology/bamtools/bamtools-2.5.1/src/api -I/construction/biology/bamtools/bamtools-2.5.1/src/utils -I/construction/biology/bamtools/bamtools-2.5.1/src/third_party -I/construction/biology/bamtools/.build/src/toolkit -I/construction/biology/bamtools/bamtools-2.5.1/src/third_party/jsoncpp -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -Wall -o CMakeFiles/bamtools_cmd.dir/bamtools_filter.cpp.o -c /construction/biology/bamtools/bamtools-2.5.1/src/toolkit/bamtools_filter.cpp --- src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_count.cpp.o --- cd /construction/biology/bamtools/.build/src/toolkit && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/construction/biology/bamtools/bamtools-2.5.1/src -I/construction/biology/bamtools/bamtools-2.5.1/src/api -I/construction/biology/bamtools/bamtools-2.5.1/src/utils -I/construction/biology/bamtools/bamtools-2.5.1/src/third_party -I/construction/biology/bamtools/.build/src/toolkit -I/construction/biology/bamtools/bamtools-2.5.1/src/third_party/jsoncpp -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -Wall -o CMakeFiles/bamtools_cmd.dir/bamtools_count.cpp.o -c /construction/biology/bamtools/bamtools-2.5.1/src/toolkit/bamtools_count.cpp --- src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_header.cpp.o --- [ 84%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_header.cpp.o cd /construction/biology/bamtools/.build/src/toolkit && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/construction/biology/bamtools/bamtools-2.5.1/src -I/construction/biology/bamtools/bamtools-2.5.1/src/api -I/construction/biology/bamtools/bamtools-2.5.1/src/utils -I/construction/biology/bamtools/bamtools-2.5.1/src/third_party -I/construction/biology/bamtools/.build/src/toolkit -I/construction/biology/bamtools/bamtools-2.5.1/src/third_party/jsoncpp -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -Wall -o CMakeFiles/bamtools_cmd.dir/bamtools_header.cpp.o -c /construction/biology/bamtools/bamtools-2.5.1/src/toolkit/bamtools_header.cpp --- src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_merge.cpp.o --- [ 85%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_merge.cpp.o cd /construction/biology/bamtools/.build/src/toolkit && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/construction/biology/bamtools/bamtools-2.5.1/src -I/construction/biology/bamtools/bamtools-2.5.1/src/api -I/construction/biology/bamtools/bamtools-2.5.1/src/utils -I/construction/biology/bamtools/bamtools-2.5.1/src/third_party -I/construction/biology/bamtools/.build/src/toolkit -I/construction/biology/bamtools/bamtools-2.5.1/src/third_party/jsoncpp -pipe -O2 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--- [ 90%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_coverage.cpp.o cd /construction/biology/bamtools/.build/src/toolkit && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/construction/biology/bamtools/bamtools-2.5.1/src -I/construction/biology/bamtools/bamtools-2.5.1/src/api -I/construction/biology/bamtools/bamtools-2.5.1/src/utils -I/construction/biology/bamtools/bamtools-2.5.1/src/third_party -I/construction/biology/bamtools/.build/src/toolkit -I/construction/biology/bamtools/bamtools-2.5.1/src/third_party/jsoncpp -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -Wall -o CMakeFiles/bamtools_cmd.dir/bamtools_coverage.cpp.o -c /construction/biology/bamtools/bamtools-2.5.1/src/toolkit/bamtools_coverage.cpp --- src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_sort.cpp.o --- [ 92%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_sort.cpp.o cd /construction/biology/bamtools/.build/src/toolkit && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/construction/biology/bamtools/bamtools-2.5.1/src -I/construction/biology/bamtools/bamtools-2.5.1/src/api -I/construction/biology/bamtools/bamtools-2.5.1/src/utils -I/construction/biology/bamtools/bamtools-2.5.1/src/third_party -I/construction/biology/bamtools/.build/src/toolkit -I/construction/biology/bamtools/bamtools-2.5.1/src/third_party/jsoncpp -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -Wall -o CMakeFiles/bamtools_cmd.dir/bamtools_sort.cpp.o -c /construction/biology/bamtools/bamtools-2.5.1/src/toolkit/bamtools_sort.cpp --- src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_split.cpp.o --- [ 93%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_split.cpp.o cd /construction/biology/bamtools/.build/src/toolkit && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/construction/biology/bamtools/bamtools-2.5.1/src -I/construction/biology/bamtools/bamtools-2.5.1/src/api -I/construction/biology/bamtools/bamtools-2.5.1/src/utils -I/construction/biology/bamtools/bamtools-2.5.1/src/third_party -I/construction/biology/bamtools/.build/src/toolkit -I/construction/biology/bamtools/bamtools-2.5.1/src/third_party/jsoncpp -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -Wall -o CMakeFiles/bamtools_cmd.dir/bamtools_split.cpp.o -c /construction/biology/bamtools/bamtools-2.5.1/src/toolkit/bamtools_split.cpp --- src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_stats.cpp.o --- [ 95%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_stats.cpp.o cd /construction/biology/bamtools/.build/src/toolkit && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/construction/biology/bamtools/bamtools-2.5.1/src -I/construction/biology/bamtools/bamtools-2.5.1/src/api -I/construction/biology/bamtools/bamtools-2.5.1/src/utils -I/construction/biology/bamtools/bamtools-2.5.1/src/third_party -I/construction/biology/bamtools/.build/src/toolkit -I/construction/biology/bamtools/bamtools-2.5.1/src/third_party/jsoncpp -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -Wall -o CMakeFiles/bamtools_cmd.dir/bamtools_stats.cpp.o -c /construction/biology/bamtools/bamtools-2.5.1/src/toolkit/bamtools_stats.cpp --- src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools.cpp.o --- [ 96%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools.cpp.o cd /construction/biology/bamtools/.build/src/toolkit && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/construction/biology/bamtools/bamtools-2.5.1/src -I/construction/biology/bamtools/bamtools-2.5.1/src/api -I/construction/biology/bamtools/bamtools-2.5.1/src/utils -I/construction/biology/bamtools/bamtools-2.5.1/src/third_party -I/construction/biology/bamtools/.build/src/toolkit -I/construction/biology/bamtools/bamtools-2.5.1/src/third_party/jsoncpp -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -Wall -o CMakeFiles/bamtools_cmd.dir/bamtools.cpp.o -c /construction/biology/bamtools/bamtools-2.5.1/src/toolkit/bamtools.cpp --- src/toolkit/bamtools --- [ 98%] Linking CXX executable bamtools cd /construction/biology/bamtools/.build/src/toolkit && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/bamtools_cmd.dir/link.txt --verbose=1 /usr/bin/c++ -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing CMakeFiles/bamtools_cmd.dir/bamtools_convert.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools_count.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools_coverage.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools_filter.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools_header.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools_index.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools_merge.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools_random.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools_resolve.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools_revert.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools_sort.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools_split.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools_stats.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools.cpp.o -o bamtools -Wl,-z,origin,-rpath,/construction/biology/bamtools/.build/src/api ../utils/libbamtools-utils.a ../third_party/jsoncpp/libjsoncpp.a ../api/libbamtools.so.2.5.1 [100%] Built target bamtools_cmd /usr/local/bin/cmake -E cmake_progress_start /construction/biology/bamtools/.build/CMakeFiles 0 SUCCEEDED 00:01:09 ------------------------------------------------------------------------------- -- Phase: run-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: stage ------------------------------------------------------------------------------- ===> Staging for bamtools-2.5.1_2 ===> Generating temporary packing list /usr/local/bin/cmake -S/construction/biology/bamtools/bamtools-2.5.1 -B/construction/biology/bamtools/.build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/local/bin/cmake -E cmake_progress_start /construction/biology/bamtools/.build/CMakeFiles /construction/biology/bamtools/.build//CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all /usr/bin/make -f src/CMakeFiles/SharedHeaders.dir/build.make src/CMakeFiles/SharedHeaders.dir/depend cd /construction/biology/bamtools/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/bamtools/bamtools-2.5.1 /construction/biology/bamtools/bamtools-2.5.1/src /construction/biology/bamtools/.build /construction/biology/bamtools/.build/src /construction/biology/bamtools/.build/src/CMakeFiles/SharedHeaders.dir/DependInfo.cmake /usr/bin/make -f src/CMakeFiles/SharedHeaders.dir/build.make src/CMakeFiles/SharedHeaders.dir/build cd /construction/biology/bamtools/.build/src && /usr/local/bin/cmake -E copy_if_different /construction/biology/bamtools/bamtools-2.5.1/src/shared/bamtools_global.h /construction/biology/bamtools/.build/src/include/shared/bamtools_global.h [ 0%] Built target SharedHeaders /usr/bin/make -f src/api/CMakeFiles/APIHeaders.dir/build.make src/api/CMakeFiles/APIHeaders.dir/depend cd /construction/biology/bamtools/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/bamtools/bamtools-2.5.1 /construction/biology/bamtools/bamtools-2.5.1/src/api /construction/biology/bamtools/.build /construction/biology/bamtools/.build/src/api /construction/biology/bamtools/.build/src/api/CMakeFiles/APIHeaders.dir/DependInfo.cmake /usr/bin/make -f src/api/CMakeFiles/APIHeaders.dir/build.make src/api/CMakeFiles/APIHeaders.dir/build cd /construction/biology/bamtools/.build/src/api && /usr/local/bin/cmake -E copy_if_different /construction/biology/bamtools/bamtools-2.5.1/src/api/api_global.h /construction/biology/bamtools/.build/src/api/include/api/api_global.h cd /construction/biology/bamtools/.build/src/api && /usr/local/bin/cmake -E copy_if_different /construction/biology/bamtools/bamtools-2.5.1/src/api/BamAlgorithms.h /construction/biology/bamtools/.build/src/api/include/api/BamAlgorithms.h cd /construction/biology/bamtools/.build/src/api && /usr/local/bin/cmake -E copy_if_different /construction/biology/bamtools/bamtools-2.5.1/src/api/BamAlignment.h /construction/biology/bamtools/.build/src/api/include/api/BamAlignment.h cd /construction/biology/bamtools/.build/src/api && /usr/local/bin/cmake -E copy_if_different /construction/biology/bamtools/bamtools-2.5.1/src/api/BamAux.h /construction/biology/bamtools/.build/src/api/include/api/BamAux.h cd /construction/biology/bamtools/.build/src/api && /usr/local/bin/cmake -E copy_if_different /construction/biology/bamtools/bamtools-2.5.1/src/api/BamConstants.h /construction/biology/bamtools/.build/src/api/include/api/BamConstants.h cd /construction/biology/bamtools/.build/src/api && /usr/local/bin/cmake -E copy_if_different /construction/biology/bamtools/bamtools-2.5.1/src/api/BamIndex.h /construction/biology/bamtools/.build/src/api/include/api/BamIndex.h cd /construction/biology/bamtools/.build/src/api && /usr/local/bin/cmake -E copy_if_different /construction/biology/bamtools/bamtools-2.5.1/src/api/BamMultiReader.h /construction/biology/bamtools/.build/src/api/include/api/BamMultiReader.h cd /construction/biology/bamtools/.build/src/api && /usr/local/bin/cmake -E copy_if_different /construction/biology/bamtools/bamtools-2.5.1/src/api/BamReader.h /construction/biology/bamtools/.build/src/api/include/api/BamReader.h cd /construction/biology/bamtools/.build/src/api && /usr/local/bin/cmake -E copy_if_different /construction/biology/bamtools/bamtools-2.5.1/src/api/BamWriter.h /construction/biology/bamtools/.build/src/api/include/api/BamWriter.h cd /construction/biology/bamtools/.build/src/api && /usr/local/bin/cmake -E copy_if_different /construction/biology/bamtools/bamtools-2.5.1/src/api/IBamIODevice.h /construction/biology/bamtools/.build/src/api/include/api/IBamIODevice.h cd /construction/biology/bamtools/.build/src/api && /usr/local/bin/cmake -E copy_if_different /construction/biology/bamtools/bamtools-2.5.1/src/api/SamConstants.h /construction/biology/bamtools/.build/src/api/include/api/SamConstants.h cd /construction/biology/bamtools/.build/src/api && /usr/local/bin/cmake -E copy_if_different /construction/biology/bamtools/bamtools-2.5.1/src/api/SamHeader.h /construction/biology/bamtools/.build/src/api/include/api/SamHeader.h cd /construction/biology/bamtools/.build/src/api && /usr/local/bin/cmake -E copy_if_different /construction/biology/bamtools/bamtools-2.5.1/src/api/SamProgram.h /construction/biology/bamtools/.build/src/api/include/api/SamProgram.h cd /construction/biology/bamtools/.build/src/api && /usr/local/bin/cmake -E copy_if_different /construction/biology/bamtools/bamtools-2.5.1/src/api/SamProgramChain.h /construction/biology/bamtools/.build/src/api/include/api/SamProgramChain.h cd /construction/biology/bamtools/.build/src/api && /usr/local/bin/cmake -E copy_if_different /construction/biology/bamtools/bamtools-2.5.1/src/api/SamReadGroup.h /construction/biology/bamtools/.build/src/api/include/api/SamReadGroup.h cd /construction/biology/bamtools/.build/src/api && /usr/local/bin/cmake -E copy_if_different /construction/biology/bamtools/bamtools-2.5.1/src/api/SamReadGroupDictionary.h /construction/biology/bamtools/.build/src/api/include/api/SamReadGroupDictionary.h cd /construction/biology/bamtools/.build/src/api && /usr/local/bin/cmake -E copy_if_different /construction/biology/bamtools/bamtools-2.5.1/src/api/SamSequence.h /construction/biology/bamtools/.build/src/api/include/api/SamSequence.h cd /construction/biology/bamtools/.build/src/api && /usr/local/bin/cmake -E copy_if_different /construction/biology/bamtools/bamtools-2.5.1/src/api/SamSequenceDictionary.h /construction/biology/bamtools/.build/src/api/include/api/SamSequenceDictionary.h [ 0%] Built target APIHeaders /usr/bin/make -f src/api/CMakeFiles/BamTools.dir/build.make src/api/CMakeFiles/BamTools.dir/depend cd /construction/biology/bamtools/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/bamtools/bamtools-2.5.1 /construction/biology/bamtools/bamtools-2.5.1/src/api /construction/biology/bamtools/.build /construction/biology/bamtools/.build/src/api /construction/biology/bamtools/.build/src/api/CMakeFiles/BamTools.dir/DependInfo.cmake /usr/bin/make -f src/api/CMakeFiles/BamTools.dir/build.make src/api/CMakeFiles/BamTools.dir/build [ 63%] Built target BamTools /usr/bin/make -f src/api/CMakeFiles/AlgorithmsHeaders.dir/build.make src/api/CMakeFiles/AlgorithmsHeaders.dir/depend cd /construction/biology/bamtools/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/bamtools/bamtools-2.5.1 /construction/biology/bamtools/bamtools-2.5.1/src/api /construction/biology/bamtools/.build /construction/biology/bamtools/.build/src/api /construction/biology/bamtools/.build/src/api/CMakeFiles/AlgorithmsHeaders.dir/DependInfo.cmake /usr/bin/make -f src/api/CMakeFiles/AlgorithmsHeaders.dir/build.make src/api/CMakeFiles/AlgorithmsHeaders.dir/build cd /construction/biology/bamtools/.build/src/api && /usr/local/bin/cmake -E copy_if_different /construction/biology/bamtools/bamtools-2.5.1/src/api/algorithms/Sort.h /construction/biology/bamtools/.build/src/api/include/api/algorithms/Sort.h [ 63%] Built target AlgorithmsHeaders /usr/bin/make -f src/third_party/jsoncpp/CMakeFiles/jsoncpp.dir/build.make src/third_party/jsoncpp/CMakeFiles/jsoncpp.dir/depend cd /construction/biology/bamtools/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/bamtools/bamtools-2.5.1 /construction/biology/bamtools/bamtools-2.5.1/src/third_party/jsoncpp /construction/biology/bamtools/.build /construction/biology/bamtools/.build/src/third_party/jsoncpp /construction/biology/bamtools/.build/src/third_party/jsoncpp/CMakeFiles/jsoncpp.dir/DependInfo.cmake /usr/bin/make -f src/third_party/jsoncpp/CMakeFiles/jsoncpp.dir/build.make src/third_party/jsoncpp/CMakeFiles/jsoncpp.dir/build [ 66%] Built target jsoncpp /usr/bin/make -f src/utils/CMakeFiles/BamTools-utils.dir/build.make src/utils/CMakeFiles/BamTools-utils.dir/depend cd /construction/biology/bamtools/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/bamtools/bamtools-2.5.1 /construction/biology/bamtools/bamtools-2.5.1/src/utils /construction/biology/bamtools/.build /construction/biology/bamtools/.build/src/utils /construction/biology/bamtools/.build/src/utils/CMakeFiles/BamTools-utils.dir/DependInfo.cmake /usr/bin/make -f src/utils/CMakeFiles/BamTools-utils.dir/build.make src/utils/CMakeFiles/BamTools-utils.dir/build [ 74%] Built target BamTools-utils /usr/bin/make -f src/toolkit/CMakeFiles/bamtools_cmd.dir/build.make src/toolkit/CMakeFiles/bamtools_cmd.dir/depend cd /construction/biology/bamtools/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/bamtools/bamtools-2.5.1 /construction/biology/bamtools/bamtools-2.5.1/src/toolkit /construction/biology/bamtools/.build /construction/biology/bamtools/.build/src/toolkit /construction/biology/bamtools/.build/src/toolkit/CMakeFiles/bamtools_cmd.dir/DependInfo.cmake /usr/bin/make -f src/toolkit/CMakeFiles/bamtools_cmd.dir/build.make src/toolkit/CMakeFiles/bamtools_cmd.dir/build [100%] Built target bamtools_cmd /usr/local/bin/cmake -E cmake_progress_start /construction/biology/bamtools/.build/CMakeFiles 0 /usr/bin/make -f CMakeFiles/Makefile2 preinstall /usr/bin/make -f src/api/CMakeFiles/BamTools.dir/build.make src/api/CMakeFiles/BamTools.dir/preinstall Linking CXX shared library CMakeFiles/CMakeRelink.dir/libbamtools.so cd /construction/biology/bamtools/.build/src/api && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/BamTools.dir/relink.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -shared -Wl,-soname,libbamtools.so.2.5.1 -o CMakeFiles/CMakeRelink.dir/libbamtools.so.2.5.1 CMakeFiles/BamTools.dir/BamAlignment.cpp.o CMakeFiles/BamTools.dir/BamMultiReader.cpp.o CMakeFiles/BamTools.dir/BamReader.cpp.o CMakeFiles/BamTools.dir/BamWriter.cpp.o CMakeFiles/BamTools.dir/SamHeader.cpp.o CMakeFiles/BamTools.dir/SamProgram.cpp.o CMakeFiles/BamTools.dir/SamProgramChain.cpp.o CMakeFiles/BamTools.dir/SamReadGroup.cpp.o CMakeFiles/BamTools.dir/SamReadGroupDictionary.cpp.o CMakeFiles/BamTools.dir/SamSequence.cpp.o CMakeFiles/BamTools.dir/SamSequenceDictionary.cpp.o CMakeFiles/BamTools.dir/internal/bam/BamHeader_p.cpp.o CMakeFiles/BamTools.dir/internal/bam/BamMultiReader_p.cpp.o CMakeFiles/BamTools.dir/internal/bam/BamRandomAccessController_p.cpp.o CMakeFiles/BamTools.dir/internal/bam/BamReader_p.cpp.o CMakeFiles/BamTools.dir/internal/bam/BamWriter_p.cpp.o CMakeFiles/BamTools.dir/internal/index/BamIndexFactory_p.cpp.o CMakeFiles/BamTools.dir/internal/index/BamStandardIndex_p.cpp.o CMakeFiles/BamTools.dir/internal/index/BamToolsIndex_p.cpp.o CMakeFiles/BamTools.dir/internal/io/BamDeviceFactory_p.cpp.o CMakeFiles/BamTools.dir/internal/io/BamFile_p.cpp.o CMakeFiles/BamTools.dir/internal/io/BamFtp_p.cpp.o CMakeFiles/BamTools.dir/internal/io/BamHttp_p.cpp.o CMakeFiles/BamTools.dir/internal/io/BamPipe_p.cpp.o CMakeFiles/BamTools.dir/internal/io/BgzfStream_p.cpp.o CMakeFiles/BamTools.dir/internal/io/ByteArray_p.cpp.o CMakeFiles/BamTools.dir/internal/io/HostAddress_p.cpp.o CMakeFiles/BamTools.dir/internal/io/HostInfo_p.cpp.o CMakeFiles/BamTools.dir/internal/io/HttpHeader_p.cpp.o CMakeFiles/BamTools.dir/internal/io/ILocalIODevice_p.cpp.o CMakeFiles/BamTools.dir/internal/io/RollingBuffer_p.cpp.o CMakeFiles/BamTools.dir/internal/io/TcpSocket_p.cpp.o CMakeFiles/BamTools.dir/internal/io/TcpSocketEngine_p.cpp.o CMakeFiles/BamTools.dir/internal/io/TcpSocketEngine_unix_p.cpp.o CMakeFiles/BamTools.dir/internal/sam/SamFormatParser_p.cpp.o CMakeFiles/BamTools.dir/internal/sam/SamFormatPrinter_p.cpp.o CMakeFiles/BamTools.dir/internal/sam/SamHeaderValidator_p.cpp.o CMakeFiles/BamTools.dir/internal/utils/BamException_p.cpp.o -lz cd /construction/biology/bamtools/.build/src/api && /usr/local/bin/cmake -E cmake_symlink_library CMakeFiles/CMakeRelink.dir/libbamtools.so.2.5.1 CMakeFiles/CMakeRelink.dir/libbamtools.so.2.5.1 CMakeFiles/CMakeRelink.dir/libbamtools.so /usr/bin/make -f src/toolkit/CMakeFiles/bamtools_cmd.dir/build.make src/toolkit/CMakeFiles/bamtools_cmd.dir/preinstall Linking CXX executable CMakeFiles/CMakeRelink.dir/bamtools cd /construction/biology/bamtools/.build/src/toolkit && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/bamtools_cmd.dir/relink.txt --verbose=1 /usr/bin/c++ -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing CMakeFiles/bamtools_cmd.dir/bamtools_convert.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools_count.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools_coverage.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools_filter.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools_header.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools_index.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools_merge.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools_random.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools_resolve.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools_revert.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools_sort.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools_split.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools_stats.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools.cpp.o -o CMakeFiles/CMakeRelink.dir/bamtools ../utils/libbamtools-utils.a ../third_party/jsoncpp/libjsoncpp.a ../api/libbamtools.so.2.5.1 Installing the project stripped... /usr/local/bin/cmake -DCMAKE_INSTALL_DO_STRIP=1 -P cmake_install.cmake -- Install configuration: "Release" -- Installing: /construction/biology/bamtools/stage/usr/local/include/bamtools/shared/bamtools_global.h -- Installing: /construction/biology/bamtools/stage/usr/local/lib/pkgconfig/bamtools-1.pc -- Installing: /construction/biology/bamtools/stage/usr/local/lib/libbamtools.so.2.5.1 -- Installing: /construction/biology/bamtools/stage/usr/local/lib/libbamtools.so -- Installing: /construction/biology/bamtools/stage/usr/local/include/bamtools/api/api_global.h -- Installing: /construction/biology/bamtools/stage/usr/local/include/bamtools/api/BamAlgorithms.h -- Installing: /construction/biology/bamtools/stage/usr/local/include/bamtools/api/BamAlignment.h -- Installing: /construction/biology/bamtools/stage/usr/local/include/bamtools/api/BamAux.h -- Installing: /construction/biology/bamtools/stage/usr/local/include/bamtools/api/BamConstants.h -- Installing: /construction/biology/bamtools/stage/usr/local/include/bamtools/api/BamIndex.h -- Installing: /construction/biology/bamtools/stage/usr/local/include/bamtools/api/BamMultiReader.h -- Installing: /construction/biology/bamtools/stage/usr/local/include/bamtools/api/BamReader.h -- Installing: /construction/biology/bamtools/stage/usr/local/include/bamtools/api/BamWriter.h -- Installing: /construction/biology/bamtools/stage/usr/local/include/bamtools/api/IBamIODevice.h -- Installing: /construction/biology/bamtools/stage/usr/local/include/bamtools/api/SamConstants.h -- Installing: /construction/biology/bamtools/stage/usr/local/include/bamtools/api/SamHeader.h -- Installing: /construction/biology/bamtools/stage/usr/local/include/bamtools/api/SamProgram.h -- Installing: /construction/biology/bamtools/stage/usr/local/include/bamtools/api/SamProgramChain.h -- Installing: /construction/biology/bamtools/stage/usr/local/include/bamtools/api/SamReadGroup.h -- Installing: /construction/biology/bamtools/stage/usr/local/include/bamtools/api/SamReadGroupDictionary.h -- Installing: /construction/biology/bamtools/stage/usr/local/include/bamtools/api/SamSequence.h -- Installing: /construction/biology/bamtools/stage/usr/local/include/bamtools/api/SamSequenceDictionary.h -- Installing: /construction/biology/bamtools/stage/usr/local/include/bamtools/api/algorithms/Sort.h -- Installing: /construction/biology/bamtools/stage/usr/local/bin/bamtools ====> 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 SUCCEEDED 00:00:02 ------------------------------------------------------------------------------- -- 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 bamtools-2.5.1_2 file sizes/checksums [24]: 0% file sizes/checksums [24]: 100% packing files [24]: 0% packing files [24]: 100% packing directories [0]: 0% packing directories [0]: 100% SUCCEEDED 00:00:03 TOTAL TIME 00:01:30