Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads. http://genome.cshlp.org/content/early/2017/01/18/gr.214270.116 Note: This was the original repository which will no longer be officially maintained. Please use the new official repository here:
make Setting warning flags -- Configuring done -- Generating done -- Build files have been written to: /Share2/home/yangxr/LabMem/ytwang/Programs/racon/build [ 3%] Building CXX object vendor/edlib/CMakeFiles/edlib_static.dir/edlib/src/edlib.cpp.o Linking CXX static library ../../lib/libedlib_static.a [ 3%] Built target edlib_static Scanning dependencies of target zlibstatic [ 7%] Building C object vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/adler32.o [ 11%] Building C object vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/compress.o [ 14%] Building C object vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/crc32.o [ 18%] Building C object vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/deflate.o [ 22%] Building C object vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/gzclose.o [ 25%] Building C object vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/gzlib.o [ 29%] Building C object vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/gzread.o [ 33%] Building C object vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/gzwrite.o [ 37%] Building C object vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/inflate.o [ 40%] Building C object vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/infback.o [ 44%] Building C object vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/inftrees.o [ 48%] Building C object vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/inffast.o [ 51%] Building C object vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/trees.o [ 55%] Building C object vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/uncompr.o [ 59%] Building C object vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/zutil.o Linking C static library ../../lib/libz.a [ 59%] Built target zlibstatic [ 62%] Building CXX object vendor/thread_pool/CMakeFiles/thread_pool.dir/src/thread_pool.cpp.o In file included from /Share2/home/yangxr/LabMem/ytwang/Programs/racon/vendor/thread_pool/src/thread_pool.cpp:10: /Share2/home/yangxr/LabMem/ytwang/Programs/racon/vendor/thread_pool/include/thread_pool/thread_pool.hpp:16:18: error: future: No such file or directory /Share2/home/yangxr/LabMem/ytwang/Programs/racon/vendor/thread_pool/include/thread_pool/thread_pool.hpp:17:18: error: atomic: No such file or directory In file included from /Share2/home/yangxr/LabMem/ytwang/Programs/racon/vendor/thread_pool/src/thread_pool.cpp:10: /Share2/home/yangxr/LabMem/ytwang/Programs/racon/vendor/thread_pool/include/thread_pool/thread_pool.hpp:68: error: expected type-specifier /Share2/home/yangxr/LabMem/ytwang/Programs/racon/vendor/thread_pool/include/thread_pool/thread_pool.hpp:68: error: expected initializer /Share2/home/yangxr/LabMem/ytwang/Programs/racon/vendor/thread_pool/include/thread_pool/thread_pool.hpp:104: error: ISO C++ forbids declaration of ‘atomic’ with no type /Share2/home/yangxr/LabMem/ytwang/Programs/racon/vendor/thread_pool/include/thread_pool/thread_pool.hpp:104: error: invalid use of ‘::’ /Share2/home/yangxr/LabMem/ytwang/Programs/racon/vendor/thread_pool/include/thread_pool/thread_pool.hpp:104: error: expected ‘;’ before ‘<’ token /Share2/home/yangxr/LabMem/ytwang/Programs/racon/vendor/thread_pool/src/thread_pool.cpp: In member function ‘void thread_pool::Semaphore::wait()’: /Share2/home/yangxr/LabMem/ytwang/Programs/racon/vendor/thread_pool/src/thread_pool.cpp:38: error: expected primary-expression before ‘[’ token /Share2/home/yangxr/LabMem/ytwang/Programs/racon/vendor/thread_pool/src/thread_pool.cpp:38: error: expected primary-expression before ‘]’ token /Share2/home/yangxr/LabMem/ytwang/Programs/racon/vendor/thread_pool/src/thread_pool.cpp: In constructor ‘thread_pool::ThreadPool::ThreadPool(uint32_t)’: /Share2/home/yangxr/LabMem/ytwang/Programs/racon/vendor/thread_pool/src/thread_pool.cpp:47: error: ‘terminate_’ was not declared in this scope /Share2/home/yangxr/LabMem/ytwang/Programs/racon/vendor/thread_pool/src/thread_pool.cpp: In destructor ‘thread_pool::ThreadPool::~ThreadPool()’: /Share2/home/yangxr/LabMem/ytwang/Programs/racon/vendor/thread_pool/src/thread_pool.cpp:56: error: ‘terminate_’ was not declared in this scope /Share2/home/yangxr/LabMem/ytwang/Programs/racon/vendor/thread_pool/src/thread_pool.cpp:60: error: expected initializer before ‘:’ token /Share2/home/yangxr/LabMem/ytwang/Programs/racon/vendor/thread_pool/src/thread_pool.cpp:63: error: expected primary-expression before ‘}’ token /Share2/home/yangxr/LabMem/ytwang/Programs/racon/vendor/thread_pool/src/thread_pool.cpp:63: error: expected ‘;’ before ‘}’ token /Share2/home/yangxr/LabMem/ytwang/Programs/racon/vendor/thread_pool/src/thread_pool.cpp:63: error: expected primary-expression before ‘}’ token /Share2/home/yangxr/LabMem/ytwang/Programs/racon/vendor/thread_pool/src/thread_pool.cpp:63: error: expected ‘)’ before ‘}’ token /Share2/home/yangxr/LabMem/ytwang/Programs/racon/vendor/thread_pool/src/thread_pool.cpp:63: error: expected primary-expression before ‘}’ token /Share2/home/yangxr/LabMem/ytwang/Programs/racon/vendor/thread_pool/src/thread_pool.cpp:63: error: expected ‘;’ before ‘}’ token /Share2/home/yangxr/LabMem/ytwang/Programs/racon/vendor/thread_pool/src/thread_pool.cpp: In static member function ‘static void thread_pool::ThreadPool::worker_thread(thread_pool::ThreadPool*)’: /Share2/home/yangxr/LabMem/ytwang/Programs/racon/vendor/thread_pool/src/thread_pool.cpp:70: error: ‘class thread_pool::ThreadPool’ has no member named ‘terminate_’ /Share2/home/yangxr/LabMem/ytwang/Programs/racon/vendor/thread_pool/src/thread_pool.cpp:81: error: ‘class thread_pool::ThreadPool’ has no member named ‘terminate_’ make[2]: *** [vendor/thread_pool/CMakeFiles/thread_pool.dir/src/thread_pool.cpp.o] Error 1 make[1]: *** [vendor/thread_pool/CMakeFiles/thread_pool.dir/all] Error 2 make: *** [all] Error 2
make Setting warning flags -- Configuring done -- Generating done -- Build files have been written to: /Share2/home/yangxr/LabMem/ytwang/Programs/racon/build [ 3%] Building CXX object vendor/edlib/CMakeFiles/edlib_static.dir/edlib/src/edlib.cpp.o Linking CXX static library ../../lib/libedlib_static.a [ 3%] Built target edlib_static Scanning dependencies of target zlibstatic [ 7%] Building C object vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/adler32.o [ 11%] Building C object vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/compress.o [ 14%] Building C object vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/crc32.o [ 18%] Building C object vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/deflate.o [ 22%] Building C object vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/gzclose.o [ 25%] Building C object vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/gzlib.o [ 29%] Building C object vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/gzread.o [ 33%] Building C object vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/gzwrite.o [ 37%] Building C object vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/inflate.o [ 40%] Building C object vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/infback.o [ 44%] Building C object vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/inftrees.o [ 48%] Building C object vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/inffast.o [ 51%] Building C object vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/trees.o [ 55%] Building C object vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/uncompr.o [ 59%] Building C object vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/zutil.o Linking C static library ../../lib/libz.a [ 59%] Built target zlibstatic [ 62%] Building CXX object vendor/thread_pool/CMakeFiles/thread_pool.dir/src/thread_pool.cpp.o In file included from /Share2/home/yangxr/LabMem/ytwang/Programs/racon/vendor/thread_pool/src/thread_pool.cpp:10: /Share2/home/yangxr/LabMem/ytwang/Programs/racon/vendor/thread_pool/include/thread_pool/thread_pool.hpp:16:18: error: future: No such file or directory /Share2/home/yangxr/LabMem/ytwang/Programs/racon/vendor/thread_pool/include/thread_pool/thread_pool.hpp:17:18: error: atomic: No such file or directory In file included from /Share2/home/yangxr/LabMem/ytwang/Programs/racon/vendor/thread_pool/src/thread_pool.cpp:10: /Share2/home/yangxr/LabMem/ytwang/Programs/racon/vendor/thread_pool/include/thread_pool/thread_pool.hpp:68: error: expected type-specifier /Share2/home/yangxr/LabMem/ytwang/Programs/racon/vendor/thread_pool/include/thread_pool/thread_pool.hpp:68: error: expected initializer /Share2/home/yangxr/LabMem/ytwang/Programs/racon/vendor/thread_pool/include/thread_pool/thread_pool.hpp:104: error: ISO C++ forbids declaration of ‘atomic’ with no type /Share2/home/yangxr/LabMem/ytwang/Programs/racon/vendor/thread_pool/include/thread_pool/thread_pool.hpp:104: error: invalid use of ‘::’ /Share2/home/yangxr/LabMem/ytwang/Programs/racon/vendor/thread_pool/include/thread_pool/thread_pool.hpp:104: error: expected ‘;’ before ‘<’ token /Share2/home/yangxr/LabMem/ytwang/Programs/racon/vendor/thread_pool/src/thread_pool.cpp: In member function ‘void thread_pool::Semaphore::wait()’: /Share2/home/yangxr/LabMem/ytwang/Programs/racon/vendor/thread_pool/src/thread_pool.cpp:38: error: expected primary-expression before ‘[’ token /Share2/home/yangxr/LabMem/ytwang/Programs/racon/vendor/thread_pool/src/thread_pool.cpp:38: error: expected primary-expression before ‘]’ token /Share2/home/yangxr/LabMem/ytwang/Programs/racon/vendor/thread_pool/src/thread_pool.cpp: In constructor ‘thread_pool::ThreadPool::ThreadPool(uint32_t)’: /Share2/home/yangxr/LabMem/ytwang/Programs/racon/vendor/thread_pool/src/thread_pool.cpp:47: error: ‘terminate_’ was not declared in this scope /Share2/home/yangxr/LabMem/ytwang/Programs/racon/vendor/thread_pool/src/thread_pool.cpp: In destructor ‘thread_pool::ThreadPool::~ThreadPool()’: /Share2/home/yangxr/LabMem/ytwang/Programs/racon/vendor/thread_pool/src/thread_pool.cpp:56: error: ‘terminate_’ was not declared in this scope /Share2/home/yangxr/LabMem/ytwang/Programs/racon/vendor/thread_pool/src/thread_pool.cpp:60: error: expected initializer before ‘:’ token /Share2/home/yangxr/LabMem/ytwang/Programs/racon/vendor/thread_pool/src/thread_pool.cpp:63: error: expected primary-expression before ‘}’ token /Share2/home/yangxr/LabMem/ytwang/Programs/racon/vendor/thread_pool/src/thread_pool.cpp:63: error: expected ‘;’ before ‘}’ token /Share2/home/yangxr/LabMem/ytwang/Programs/racon/vendor/thread_pool/src/thread_pool.cpp:63: error: expected primary-expression before ‘}’ token /Share2/home/yangxr/LabMem/ytwang/Programs/racon/vendor/thread_pool/src/thread_pool.cpp:63: error: expected ‘)’ before ‘}’ token /Share2/home/yangxr/LabMem/ytwang/Programs/racon/vendor/thread_pool/src/thread_pool.cpp:63: error: expected primary-expression before ‘}’ token /Share2/home/yangxr/LabMem/ytwang/Programs/racon/vendor/thread_pool/src/thread_pool.cpp:63: error: expected ‘;’ before ‘}’ token /Share2/home/yangxr/LabMem/ytwang/Programs/racon/vendor/thread_pool/src/thread_pool.cpp: In static member function ‘static void thread_pool::ThreadPool::worker_thread(thread_pool::ThreadPool*)’: /Share2/home/yangxr/LabMem/ytwang/Programs/racon/vendor/thread_pool/src/thread_pool.cpp:70: error: ‘class thread_pool::ThreadPool’ has no member named ‘terminate_’ /Share2/home/yangxr/LabMem/ytwang/Programs/racon/vendor/thread_pool/src/thread_pool.cpp:81: error: ‘class thread_pool::ThreadPool’ has no member named ‘terminate_’ make[2]: *** [vendor/thread_pool/CMakeFiles/thread_pool.dir/src/thread_pool.cpp.o] Error 1 make[1]: *** [vendor/thread_pool/CMakeFiles/thread_pool.dir/all] Error 2 make: *** [all] Error 2