Using existing /usr/bin/cmake -- install prefix: /home/yifang/Downloads/bcl2fastq/build -- install exec prefix: . -- install bin dir: ./bin -- install lib dir: ./lib/bcl2fastq-2.17.1.14 -- install libexec dir: ./libexec/bcl2fastq-2.17.1.14 -- install include dir: include/bcl2fastq-2.17.1.14 -- install data dir: share -- install doc dir: doc/bcl2fastq-2.17.1.14 -- install man dir: man -- Could NOT find Boost -- Boost 1.54.0 not found. Boost will be built from the distribution... Building Boost.Build engine with toolset gcc... tools/build/v2/engine/bin.linuxx86_64/b2 Unicode/ICU support for Boost.Regex?... not found. Backing up existing Boost.Build configuration in project-config.jam.1 Generating Boost.Build configuration in project-config.jam... Bootstrapping is done. To build, run: ./b2 To adjust configuration, edit 'project-config.jam'. Further information: - Command line help: ./b2 --help - Getting started guide: http://www.boost.org/more/getting_started/unix-variants.html - Boost.Build documentation: http://www.boost.org/boost-build2/doc/html/index.html Performing configuration checks - zlib : yes (cached) - has_icu builds : yes (cached) Component configuration: - atomic : not building - chrono : building - context : not building - coroutine : not building - date_time : building - exception : not building - filesystem : building - graph : not building - graph_parallel : not building - iostreams : building - locale : not building - log : not building - math : not building - mpi : not building - program_options : building - python : not building - random : not building - regex : building - serialization : building - signals : not building - system : building - test : not building - thread : building - timer : building - wave : not building ...patience... ...patience... ...found 22371 targets... ...updating 5 targets... gcc.compile.c++ bin.v2/libs/thread/build/gcc-4.8/release/link-static/threading-multi/pthread/thread.o In file included from ./boost/bind/bind.hpp:29:0, from ./boost/bind.hpp:22, from ./boost/thread/detail/thread.hpp:29, from ./boost/thread/thread_only.hpp:22, from libs/thread/src/pthread/thread.cpp:11: ./boost/bind/arg.hpp: In constructor ‘boost::arg::arg(const T&)’: ./boost/bind/arg.hpp:37:22: warning: typedef ‘T_must_be_placeholder’ locally defined but not used [-Wunused-local-typedefs] typedef char T_must_be_placeholder[ I == is_placeholder::value? 1: -1 ]; ^ In file included from ./boost/atomic.hpp:12:0, from ./boost/thread/pthread/once_atomic.hpp:20, from ./boost/thread/once.hpp:20, from libs/thread/src/pthread/thread.cpp:17: ./boost/atomic/atomic.hpp: At global scope: ./boost/atomic/atomic.hpp:202:16: error: ‘uintptr_t’ was not declared in this scope typedef atomic atomic_uintptr_t; ^ ./boost/atomic/atomic.hpp:202:25: error: template argument 1 is invalid typedef atomic atomic_uintptr_t; ^ ./boost/atomic/atomic.hpp:202:43: error: invalid type in declaration before ‘;’ token typedef atomic atomic_uintptr_t; ^ In file included from ./boost/system/system_error.hpp:14:0, from ./boost/thread/exceptions.hpp:22, from ./boost/thread/pthread/thread_data.hpp:10, from ./boost/thread/thread_only.hpp:17, from libs/thread/src/pthread/thread.cpp:11: ./boost/system/error_code.hpp:222:36: warning: ‘boost::system::posix_category’ defined but not used [-Wunused-variable] static const error_category & posix_category = generic_category(); ^ ./boost/system/error_code.hpp:223:36: warning: ‘boost::system::errno_ecat’ defined but not used [-Wunused-variable] static const error_category & errno_ecat = generic_category(); ^ ./boost/system/error_code.hpp:224:36: warning: ‘boost::system::native_ecat’ defined but not used [-Wunused-variable] static const error_category & native_ecat = system_category(); ^ "g++" -ftemplate-depth-128 -O3 -finline-functions -Wno-inline -Wall -pedantic -pthread -Wextra -Wno-long-long -Wno-variadic-macros -Wunused-function -pedantic -DBOOST_ALL_NO_LIB=1 -DBOOST_SYSTEM_STATIC_LINK=1 -DBOOST_THREAD_BUILD_LIB=1 -DBOOST_THREAD_DONT_USE_CHRONO -DBOOST_THREAD_POSIX -DNDEBUG -I"." -c -o "bin.v2/libs/thread/build/gcc-4.8/release/link-static/threading-multi/pthread/thread.o" "libs/thread/src/pthread/thread.cpp" ...failed gcc.compile.c++ bin.v2/libs/thread/build/gcc-4.8/release/link-static/threading-multi/pthread/thread.o... gcc.compile.c++ bin.v2/libs/thread/build/gcc-4.8/release/link-static/threading-multi/pthread/once.o In file included from ./boost/bind/bind.hpp:29:0, from ./boost/bind.hpp:22, from ./boost/thread/pthread/once_atomic.hpp:19, from ./boost/thread/once.hpp:20, from libs/thread/src/pthread/./once_atomic.cpp:9, from libs/thread/src/pthread/once.cpp:8: ./boost/bind/arg.hpp: In constructor ‘boost::arg::arg(const T&)’: ./boost/bind/arg.hpp:37:22: warning: typedef ‘T_must_be_placeholder’ locally defined but not used [-Wunused-local-typedefs] typedef char T_must_be_placeholder[ I == is_placeholder::value? 1: -1 ]; ^ In file included from ./boost/atomic.hpp:12:0, from ./boost/thread/pthread/once_atomic.hpp:20, from ./boost/thread/once.hpp:20, from libs/thread/src/pthread/./once_atomic.cpp:9, from libs/thread/src/pthread/once.cpp:8: ./boost/atomic/atomic.hpp: At global scope: ./boost/atomic/atomic.hpp:202:16: error: ‘uintptr_t’ was not declared in this scope typedef atomic atomic_uintptr_t; ^ ./boost/atomic/atomic.hpp:202:25: error: template argument 1 is invalid typedef atomic atomic_uintptr_t; ^ ./boost/atomic/atomic.hpp:202:43: error: invalid type in declaration before ‘;’ token typedef atomic atomic_uintptr_t; ^ "g++" -ftemplate-depth-128 -O3 -finline-functions -Wno-inline -Wall -pedantic -pthread -Wextra -Wno-long-long -Wno-variadic-macros -Wunused-function -pedantic -DBOOST_ALL_NO_LIB=1 -DBOOST_SYSTEM_STATIC_LINK=1 -DBOOST_THREAD_BUILD_LIB=1 -DBOOST_THREAD_DONT_USE_CHRONO -DBOOST_THREAD_POSIX -DNDEBUG -I"." -c -o "bin.v2/libs/thread/build/gcc-4.8/release/link-static/threading-multi/pthread/once.o" "libs/thread/src/pthread/once.cpp" ...failed gcc.compile.c++ bin.v2/libs/thread/build/gcc-4.8/release/link-static/threading-multi/pthread/once.o... ...skipped libboost_thread.a(clean) for lack of pthread/thread.o... ...skipped libboost_thread.a for lack of pthread/thread.o... ...skipped

libboost_thread.a for lack of libboost_thread.a... ...failed updating 2 targets... ...skipped 3 targets... -- Configuring incomplete, errors occurred! See also "/home/yifang/Downloads/bcl2fastq/build/CMakeFiles/CMakeOutput.log". Couldn't configure the project: cmake -H'/home/yifang/Downloads/bcl2fastq/src' -B'/home/yifang/Downloads/bcl2fastq/build' -G'Unix Makefiles' -DBCL2FASTQ_NAME_SHORT:STRING="bcl2fastq" -DBCL2FASTQ_NAME_LONG:STRING="BCL to FASTQ file converter" -DBCL2FASTQ_COPYRIGHT:STRING="Copyright (c) 2007-2015 Illumina, Inc." -DBCL2FASTQ_VERSION_MAJOR:STRING="2" -DBCL2FASTQ_VERSION_MINOR:STRING="17" -DBCL2FASTQ_VERSION_PATCH:STRING="1" -DBCL2FASTQ_VERSION_BUILD:STRING="14" -DBCL2FASTQ_VERSION:STRING="2.17.1.14" -DBCL2FASTQ_SOURCE_DIR:STRING="/home/yifang/Downloads/bcl2fastq/src" -DBCL2FASTQ_PREFIX:PATH="/home/yifang/Downloads/bcl2fastq/build" -DBCL2FASTQ_EXEC_PREFIX:PATH="" -DCMAKE_INSTALL_PREFIX:PATH="/home/yifang/Downloads/bcl2fastq/build" -DBCL2FASTQ_BINDIR:PATH="" -DBCL2FASTQ_LIBDIR:PATH="" -DBCL2FASTQ_LIBEXECDIR:PATH="" -DBCL2FASTQ_INCLUDEDIR:PATH="" -DBCL2FASTQ_DATADIR:PATH="" -DBCL2FASTQ_DOCDIR:PATH="" -DBCL2FASTQ_MANDIR:PATH="" -DCMAKE_BUILD_TYPE:STRING="RelWithDebInfo" -DCMAKE_PARALLEL:STRING="1" Moving CMakeCache.txt to CMakeCache.txt.removed