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PacificBiosciences / FALCON-integrate

Mostly deprecated. See https://github.com/PacificBiosciences/FALCON_unzip/wiki/Binaries
https://github.com/PacificBiosciences/FALCON/wiki/Manual
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An gcc error when install FALCON-integrate following userguide #163

Closed wangzhennan14 closed 6 years ago

wangzhennan14 commented 6 years ago

Hi,

When I install FALCON-integrate, there was a gcc error as follow:

Error: execution of an external program failed: 'gcc   -o /Storage/data002/wangzn/software/FALCON-integrate/nim-falcon/src/fc_rr_hctg_track2.exe  /Storage/data002/wangzn/software/FALCON-integrate/nim-falcon/src/nimcache/fc_rr_hctg_track2.o /Storage/data002/wangzn/software/FALCON-integrate/nim-falcon/src/nimcache/stdlib_system.o /Storage/data002/wangzn/software/FALCON-integrate/nim-falcon/src/nimcache/stdlib_sharedlist.o /Storage/data002/wangzn/software/FALCON-integrate/nim-falcon/src/nimcache/stdlib_locks.o /Storage/data002/wangzn/software/FALCON-integrate/nim-falcon/src/nimcache/rr_hctg_track.o /Storage/data002/wangzn/software/FALCON-integrate/nim-falcon/src/nimcache/msgpack4nim_msgpack4nim.o /Storage/data002/wangzn/software/FALCON-integrate/nim-falcon/src/nimcache/stdlib_streams.o /Storage/data002/wangzn/software/FALCON-integrate/nim-falcon/src/nimcache/stdlib_endians.o /Storage/data002/wangzn/software/FALCON-integrate/nim-falcon/src/nimcache/stdlib_strutils.o /Storage/data002/wangzn/software/FALCON-integrate/nim-falcon/src/nimcache/stdlib_sequtils.o /Storage/data002/wangzn/software/FALCON-integrate/nim-falcon/src/nimcache/stdlib_algorithm.o /Storage/data002/wangzn/software/FALCON-integrate/nim-falcon/src/nimcache/stdlib_math.o /Storage/data002/wangzn/software/FALCON-integrate/nim-falcon/src/nimcache/stdlib_hashes.o /Storage/data002/wangzn/software/FALCON-integrate/nim-falcon/src/nimcache/stdlib_parseutils.o /Storage/data002/wangzn/software/FALCON-integrate/nim-falcon/src/nimcache/stdlib_tables.o /Storage/data002/wangzn/software/FALCON-integrate/nim-falcon/src/nimcache/stdlib_intsets.o /Storage/data002/wangzn/software/FALCON-integrate/nim-falcon/src/nimcache/stdlib_lists.o /Storage/data002/wangzn/software/FALCON-integrate/nim-falcon/src/nimcache/stdlib_queues.o /Storage/data002/wangzn/software/FALCON-integrate/nim-falcon/src/nimcache/stdlib_sets.o /Storage/data002/wangzn/software/FALCON-integrate/nim-falcon/src/nimcache/stdlib_strtabs.o /Storage/data002/wangzn/software/FALCON-integrate/nim-falcon/src/nimcache/stdlib_os.o /Storage/data002/wangzn/software/FALCON-integrate/nim-falcon/src/nimcache/stdlib_times.o /Storage/data002/wangzn/software/FALCON-integrate/nim-falcon/src/nimcache/stdlib_posix.o /Storage/data002/wangzn/software/FALCON-integrate/nim-falcon/src/nimcache/stdlib_ospaths.o /Storage/data002/wangzn/software/FALCON-integrate/nim-falcon/src/nimcache/stdlib_critbits.o /Storage/data002/wangzn/software/FALCON-integrate/nim-falcon/src/nimcache/stdlib_macros.o /Storage/data002/wangzn/software/FALCON-integrate/nim-falcon/src/nimcache/binaryheap_binaryheap.o /Storage/data002/wangzn/software/FALCON-integrate/nim-falcon/src/nimcache/sys.o /Storage/data002/wangzn/software/FALCON-integrate/nim-falcon/src/nimcache/functional.o /Storage/data002/wangzn/software/FALCON-integrate/nim-falcon/src/nimcache/stdlib_cpuinfo.o /Storage/data002/wangzn/software/FALCON-integrate/nim-falcon/src/nimcache/stdlib_linux.o /Storage/data002/wangzn/software/FALCON-integrate/nim-falcon/src/nimcache/stdlib_threadpool.o /Storage/data002/wangzn/software/FALCON-integrate/nim-falcon/src/nimcache/stdlib_cpuload.o /Storage/data002/wangzn/software/FALCON-integrate/nim-falcon/src/nimcache/stdlib_osproc.o /Storage/data002/wangzn/software/FALCON-integrate/nim-falcon/src/nimcache/stdlib_parsecsv.o /Storage/data002/wangzn/software/FALCON-integrate/nim-falcon/src/nimcache/stdlib_lexbase.o /Storage/data002/wangzn/software/FALCON-integrate/nim-falcon/src/nimcache/cligen_cligen.o /Storage/data002/wangzn/software/FALCON-integrate/nim-falcon/src/nimcache/cligen_parseopt3.o /Storage/data002/wangzn/software/FALCON-integrate/nim-falcon/src/nimcache/cligen_argcvt.o /Storage/data002/wangzn/software/FALCON-integrate/nim-falcon/src/nimcache/stdlib_terminal.o /Storage/data002/wangzn/software/FALCON-integrate/nim-falcon/src/nimcache/stdlib_termios.o  -pthread -lm -lrt   -ldl'
make[3]: *** [fc_rr_hctg_track2.exe] Error 1
make[3]: Leaving directory `/Storage/data002/wangzn/software/FALCON-integrate/nim-falcon/src'
make[2]: *** [install-nim-falcon] Error 2

What is the matter? And how to solve it? Please give me some advice to solve this probles! Thank you very much! Wang

pb-cdunn commented 6 years ago

You seem to have a mis-configured gcc. Hopefully you were able to resolve this.