=> Building biology/bamtools Started : Thursday, 30 AUG 2018 at 13:00:20 UTC Platform: 5.3-DEVELOPMENT DragonFly 5.3-DEVELOPMENT #140: Wed Aug 29 22:06:30 PDT 2018 root@test.backplane.com:/usr/obj/usr/src/sys/X86_64_GENERIC x86_64 -------------------------------------------------- -- Environment -------------------------------------------------- UNAME_r=5.3-SYNTH UNAME_m=x86_64 UNAME_p=x86_64 UNAME_v=DragonFly 5.3-SYNTH UNAME_s=DragonFly PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SSL_NO_VERIFY_PEER=1 TERM=dumb PKG_CACHEDIR=/var/cache/pkg8 PKG_DBDIR=/var/db/pkg8 PORTSDIR=/xports LANG=C HOME=/root USER=root -------------------------------------------------- -- Options -------------------------------------------------- -------------------------------------------------- -- CONFIGURE_ENV -------------------------------------------------- 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=gcc50 -------------------------------------------------- -- CONFIGURE_ARGS -------------------------------------------------- -------------------------------------------------- -- 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=gcc50 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" -------------------------------------------------- -- MAKE_ARGS -------------------------------------------------- DESTDIR=/construction/biology/bamtools/stage -------------------------------------------------- -- PLIST_SUB -------------------------------------------------- PORTDOCS="" PORTEXAMPLES="" CMAKE_BUILD_TYPE="release" OSREL=5.3 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" -------------------------------------------------- -- 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 -------------------------------------------------- -- /etc/make.conf -------------------------------------------------- SYNTHPROFILE=LiveSystem USE_PACKAGE_DEPENDS_ONLY=yes PACKAGE_BUILDING=yes BATCH=yes PKG_CREATE_VERBOSE=yes PORTSDIR=/xports DISTDIR=/distfiles WRKDIRPREFIX=/construction PORT_DBDIR=/options PACKAGES=/packages MAKE_JOBS_NUMBER_LIMIT=12 _ALTCCVERSION_921dbbb2=none _OBJC_ALTCCVERSION_921dbbb2=none _SMP_CPUS=32 UID=0 ARCH=x86_64 OPSYS=DragonFly DFLYVERSION=500316 OSVERSION=9999999 OSREL=5.3 _OSRELEASE=5.3-SYNTH PYTHONBASE=/usr/local _PKG_CHECKED=1 -------------------------------------------------------------------------------- -- Phase: check-sanity -------------------------------------------------------------------------------- ===> License MIT accepted by the user -------------------------------------------------------------------------------- -- Phase: pkg-depends -------------------------------------------------------------------------------- ===> bamtools-2.5.1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.10.5_1.txz Installing pkg-1.10.5_1... Extracting pkg-1.10.5_1: .......... done ===> bamtools-2.5.1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of bamtools-2.5.1 -------------------------------------------------------------------------------- -- Phase: fetch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: fetch -------------------------------------------------------------------------------- ===> License MIT accepted by the user ===> Fetching all distfiles required by bamtools-2.5.1 for building -------------------------------------------------------------------------------- -- Phase: checksum -------------------------------------------------------------------------------- ===> License MIT accepted by the user ===> Fetching all distfiles required by bamtools-2.5.1 for building => SHA256 Checksum OK for pezmaster31-bamtools-v2.5.1_GH0.tar.gz. -------------------------------------------------------------------------------- -- Phase: extract-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: extract -------------------------------------------------------------------------------- ===> License MIT accepted by the user ===> Fetching all distfiles required by bamtools-2.5.1 for building ===> Extracting for bamtools-2.5.1 => SHA256 Checksum OK for pezmaster31-bamtools-v2.5.1_GH0.tar.gz. -------------------------------------------------------------------------------- -- Phase: patch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: patch -------------------------------------------------------------------------------- ===> Patching for bamtools-2.5.1 ===> Applying ports patches for bamtools-2.5.1 -------------------------------------------------------------------------------- -- Phase: build-depends -------------------------------------------------------------------------------- ===> bamtools-2.5.1 depends on file: /usr/local/bin/cmake - not found ===> Installing existing package /packages/All/cmake-3.11.4_1.txz Installing cmake-3.11.4_1... `-- Installing curl-7.60.0... | `-- Installing ca_root_nss-3.38... | `-- Extracting ca_root_nss-3.38: ........ done | `-- Installing krb5-1.16.1_5... | | `-- Installing gettext-runtime-0.19.8.1_1... | | `-- Installing indexinfo-0.3.1... | | `-- Extracting indexinfo-0.3.1: .... done | | `-- Extracting gettext-runtime-0.19.8.1_1: .......... done | | `-- Installing libressl-2.7.4... | | `-- Extracting libressl-2.7.4: .......... done | | `-- Installing pkgconf-1.4.2,1... | | `-- Extracting pkgconf-1.4.2,1: .......... done | | `-- Installing readline-7.0.3_1... | | `-- Installing ncurses-6.0.0s20171223_1... | | `-- Extracting ncurses-6.0.0s20171223_1: .......... done | | `-- Extracting readline-7.0.3_1: .......... done | `-- Extracting krb5-1.16.1_5: .......... done | `-- Installing libnghttp2-1.32.0... | `-- Extracting libnghttp2-1.32.0: .......... done `-- Extracting curl-7.60.0: .......... done `-- Installing expat-2.2.5... `-- Extracting expat-2.2.5: .......... done `-- Installing jsoncpp-1.8.1_3... `-- Extracting jsoncpp-1.8.1_3: .......... done `-- Installing libarchive-3.3.2,1... | `-- Installing liblz4-1.8.2,1... | `-- Extracting liblz4-1.8.2,1: .......... done | `-- Installing lzo2-2.10_1... | `-- Extracting lzo2-2.10_1: .......... done `-- Extracting libarchive-3.3.2,1: .......... done `-- Installing libuv-1.21.0... `-- Extracting libuv-1.21.0: .......... done `-- Installing rhash-1.3.5... `-- Extracting rhash-1.3.5: .......... done Extracting cmake-3.11.4_1: .......... done Message from ca_root_nss-3.38: ********************************* WARNING ********************************* 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. *********************************** NOTE ********************************** 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 *************************************************************************** ===> bamtools-2.5.1 depends on file: /usr/local/bin/cmake - found ===> Returning to build of bamtools-2.5.1 -------------------------------------------------------------------------------- -- Phase: lib-depends -------------------------------------------------------------------------------- ===> bamtools-2.5.1 depends on shared library: libjsoncpp.so - found (/usr/local/lib/libjsoncpp.so) -------------------------------------------------------------------------------- -- Phase: configure -------------------------------------------------------------------------------- ===> Configuring for bamtools-2.5.1 ===> Performing out-of-source build /bin/mkdir -p /construction/biology/bamtools/.build -- The CXX compiler identification is GNU 5.4.1 -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- 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. -- Found PkgConfig: /usr/local/bin/pkg-config (found version "1.4.2") -- Checking for one of the modules 'jsoncpp>=1' Found system JsonCpp, not using bundled version -- Found ZLIB: /usr/lib/libz.so (found version "1.2.8") -- 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 -------------------------------------------------------------------------------- -- Phase: build -------------------------------------------------------------------------------- ===> Building for bamtools-2.5.1 /usr/local/bin/cmake -H/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/BamTools.dir/all --- --- src/api/CMakeFiles/APIHeaders.dir/all --- --- src/api/CMakeFiles/AlgorithmsHeaders.dir/all --- --- src/api/CMakeFiles/BamTools.dir/all --- /usr/bin/make -f src/api/CMakeFiles/BamTools.dir/build.make src/api/CMakeFiles/BamTools.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 --- /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/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/CMakeFiles/SharedHeaders.dir/all --- --- src/CMakeFiles/SharedHeaders.dir/depend --- --- src/api/CMakeFiles/BamTools.dir/all --- --- src/api/CMakeFiles/BamTools.dir/depend --- --- src/api/CMakeFiles/APIHeaders.dir/all --- --- src/api/CMakeFiles/APIHeaders.dir/depend --- --- src/CMakeFiles/SharedHeaders.dir/all --- 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/BamTools.dir/all --- 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/api/CMakeFiles/APIHeaders.dir/all --- 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/CMakeFiles/SharedHeaders.dir/all --- Scanning dependencies of target SharedHeaders /usr/bin/make -f src/CMakeFiles/SharedHeaders.dir/build.make src/CMakeFiles/SharedHeaders.dir/build --- src/api/CMakeFiles/APIHeaders.dir/all --- Scanning dependencies of target APIHeaders /usr/bin/make -f src/api/CMakeFiles/APIHeaders.dir/build.make src/api/CMakeFiles/APIHeaders.dir/build --- 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/BamTools.dir/all --- Scanning dependencies of target BamTools /usr/bin/make -f src/api/CMakeFiles/BamTools.dir/build.make src/api/CMakeFiles/BamTools.dir/build --- src/CMakeFiles/SharedHeaders.dir/all --- --- SharedHeaders --- 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/AlgorithmsHeaders.dir/all --- Scanning dependencies of target 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/BamAlgorithms.h /construction/biology/bamtools/.build/src/api/include/api/BamAlgorithms.h --- src/api/CMakeFiles/AlgorithmsHeaders.dir/all --- /usr/bin/make -f src/api/CMakeFiles/AlgorithmsHeaders.dir/build.make src/api/CMakeFiles/AlgorithmsHeaders.dir/build --- AlgorithmsHeaders --- 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/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 --- --- 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/BamTools.dir/SamReadGroup.cpp.o --- --- src/api/CMakeFiles/BamTools.dir/SamReadGroupDictionary.cpp.o --- --- src/api/CMakeFiles/BamTools.dir/BamAlignment.cpp.o --- [ 1%] 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/BamTools.dir/BamWriter.cpp.o --- [ 3%] Building CXX object src/api/CMakeFiles/BamTools.dir/BamWriter.cpp.o --- src/CMakeFiles/SharedHeaders.dir/all --- [ 6%] Built target 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/BamAux.h /construction/biology/bamtools/.build/src/api/include/api/BamAux.h --- src/api/CMakeFiles/AlgorithmsHeaders.dir/all --- [ 11%] Built target 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/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 --- src/api/CMakeFiles/BamTools.dir/all --- --- src/api/CMakeFiles/BamTools.dir/SamHeader.cpp.o --- [ 4%] Building CXX object 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/BamTools.dir/SamSequence.cpp.o --- --- src/api/CMakeFiles/BamTools.dir/SamSequenceDictionary.cpp.o --- --- src/api/CMakeFiles/BamTools.dir/BamReader.cpp.o --- [ 11%] Building CXX object 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/BamWriter.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/BamWriter.cpp.o -c /construction/biology/bamtools/bamtools-2.5.1/src/api/BamWriter.cpp --- src/api/CMakeFiles/BamTools.dir/SamProgram.cpp.o --- [ 8%] 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 -pipe -O2 -fno-strict-aliasing -fPIC -Wall -o CMakeFiles/BamTools.dir/SamProgram.cpp.o -c /construction/biology/bamtools/bamtools-2.5.1/src/api/SamProgram.cpp --- src/api/CMakeFiles/BamTools.dir/SamProgramChain.cpp.o --- [ 6%] Building CXX object src/api/CMakeFiles/BamTools.dir/SamProgramChain.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/SamProgramChain.cpp.o -c /construction/biology/bamtools/bamtools-2.5.1/src/api/SamProgramChain.cpp --- src/api/CMakeFiles/BamTools.dir/SamReadGroup.cpp.o --- [ 13%] 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 -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/SamReadGroup.cpp.o -c /construction/biology/bamtools/bamtools-2.5.1/src/api/SamReadGroup.cpp --- src/api/CMakeFiles/BamTools.dir/SamReadGroupDictionary.cpp.o --- [ 9%] 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 --- [ 14%] 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 -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/SamSequence.cpp.o -c /construction/biology/bamtools/bamtools-2.5.1/src/api/SamSequence.cpp --- src/api/CMakeFiles/BamTools.dir/SamSequenceDictionary.cpp.o --- [ 16%] Building CXX object src/api/CMakeFiles/BamTools.dir/SamSequenceDictionary.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/SamSequenceDictionary.cpp.o -c /construction/biology/bamtools/bamtools-2.5.1/src/api/SamSequenceDictionary.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/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 [ 16%] Built target APIHeaders --- src/api/CMakeFiles/BamTools.dir/all --- --- src/api/CMakeFiles/BamTools.dir/internal/bam/BamHeader_p.cpp.o --- [ 18%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/bam/BamHeader_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/BamHeader_p.cpp.o -c /construction/biology/bamtools/bamtools-2.5.1/src/api/internal/bam/BamHeader_p.cpp --- src/api/CMakeFiles/BamTools.dir/BamMultiReader.cpp.o --- [ 19%] Building CXX object src/api/CMakeFiles/BamTools.dir/BamMultiReader.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/BamMultiReader.cpp.o -c /construction/biology/bamtools/bamtools-2.5.1/src/api/BamMultiReader.cpp --- src/api/CMakeFiles/BamTools.dir/internal/bam/BamMultiReader_p.cpp.o --- --- src/api/CMakeFiles/BamTools.dir/internal/bam/BamRandomAccessController_p.cpp.o --- --- src/api/CMakeFiles/BamTools.dir/internal/bam/BamMultiReader_p.cpp.o --- [ 21%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/bam/BamMultiReader_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/BamMultiReader_p.cpp.o -c /construction/biology/bamtools/bamtools-2.5.1/src/api/internal/bam/BamMultiReader_p.cpp --- src/api/CMakeFiles/BamTools.dir/internal/bam/BamReader_p.cpp.o --- --- src/api/CMakeFiles/BamTools.dir/internal/bam/BamRandomAccessController_p.cpp.o --- [ 22%] 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 --- [ 24%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/bam/BamReader_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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src/api/CMakeFiles/BamTools.dir/internal/io/BgzfStream_p.cpp.o --- [ 40%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/BgzfStream_p.cpp.o --- src/api/CMakeFiles/BamTools.dir/internal/io/ByteArray_p.cpp.o --- [ 42%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/ByteArray_p.cpp.o --- src/api/CMakeFiles/BamTools.dir/internal/io/BgzfStream_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/BgzfStream_p.cpp.o -c /construction/biology/bamtools/bamtools-2.5.1/src/api/internal/io/BgzfStream_p.cpp --- src/api/CMakeFiles/BamTools.dir/internal/io/ByteArray_p.cpp.o --- cd /construction/biology/bamtools/.build/src/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY 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/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 --- [ 54%] 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 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src/api/CMakeFiles/BamTools.dir/internal/sam/SamFormatPrinter_p.cpp.o --- --- src/api/CMakeFiles/BamTools.dir/internal/sam/SamHeaderValidator_p.cpp.o --- --- src/api/CMakeFiles/BamTools.dir/internal/sam/SamFormatPrinter_p.cpp.o --- [ 59%] 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 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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 --- [ 67%] Building CXX object src/utils/CMakeFiles/BamTools-utils.dir/bamtools_utilities.cpp.o --- src/utils/CMakeFiles/BamTools-utils.dir/bamtools_fasta.cpp.o --- [ 68%] Building CXX object src/utils/CMakeFiles/BamTools-utils.dir/bamtools_fasta.cpp.o --- 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_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 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CMakeFiles/BamTools-utils.dir/bamtools_pileup_engine.cpp.o CMakeFiles/BamTools-utils.dir/bamtools_utilities.cpp.o /usr/bin/ranlib libbamtools-utils.a [ 73%] 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_sort.cpp.o --- --- src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_split.cpp.o --- --- src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_index.cpp.o --- [ 75%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_index.cpp.o --- 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-I/usr/local/include/jsoncpp -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -Wall -o CMakeFiles/bamtools_cmd.dir/bamtools_merge.cpp.o -c /construction/biology/bamtools/bamtools-2.5.1/src/toolkit/bamtools_merge.cpp --- src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_random.cpp.o --- [ 85%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_random.cpp.o --- 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/usr/local/include/jsoncpp -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -Wall -o 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-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/usr/local/include/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_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/usr/local/include/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 --- [ 91%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_convert.cpp.o --- 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/usr/local/include/jsoncpp -pipe -O2 -fno-strict-aliasing -pipe -O2 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&& /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/usr/local/include/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_resolve.cpp.o --- [ 93%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_resolve.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 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-I/usr/local/include/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/usr/local/include/jsoncpp -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -Wall -o CMakeFiles/bamtools_cmd.dir/bamtools.cpp.o -c 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CMakeFiles/bamtools_cmd.dir/bamtools_stats.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools.cpp.o -o bamtools -Wl,-rpath,/construction/biology/bamtools/.build/src/api ../utils/libbamtools-utils.a -L/usr/local/lib -ljsoncpp ../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 -------------------------------------------------------------------------------- -- Phase: run-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: stage -------------------------------------------------------------------------------- ===> Staging for bamtools-2.5.1 ===> Generating temporary packing list /usr/local/bin/cmake -H/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/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 [ 65%] Built target BamTools /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 [ 65%] Built target APIHeaders /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 [ 65%] Built target AlgorithmsHeaders /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 [ 73%] 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 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/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) -------------------------------------------------------------------------------- -- Phase: package -------------------------------------------------------------------------------- ===> Building package for bamtools-2.5.1 file sizes/checksums [27]: . done packing files [27]: . done packing directories [0]: . done -------------------------------------------------- -- Termination -------------------------------------------------- Finished: Thursday, 30 AUG 2018 at 13:01:06 UTC Duration: 00:00:46