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uci-cbcl / EXTREME

An online EM implementation of the MEME model for fast motif discovery in large ChIP-Seq and DNase-Seq Footprinting data
GNU General Public License v2.0
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"duplicate symbols for architecture x86_64" when compiling on mac os x (10.11.6) #4

Closed themantalope closed 8 years ago

themantalope commented 8 years ago

Hi,

When trying to run python setup.py build on mac os x v10.11.6, I'm getting several duplicate symbols errors:

gcc -bundle -undefined dynamic_lookup -Wl,-F. -arch x86_64 build/temp.macosx-10.11-intel-2.7/memewrapper.o build/temp.macosx-10.11-intel-2.7/llr.o build/temp.macosx-10.11-intel-2.7/likelihood.o -o build/lib.macosx-10.11-intel-2.7/meme.so
duplicate symbol _exp_table in:
    build/temp.macosx-10.11-intel-2.7/memewrapper.o
    build/temp.macosx-10.11-intel-2.7/llr.o
duplicate symbol _log_table in:
    build/temp.macosx-10.11-intel-2.7/memewrapper.o
    build/temp.macosx-10.11-intel-2.7/llr.o
duplicate symbol _NO_STATUS in:
    build/temp.macosx-10.11-intel-2.7/memewrapper.o
    build/temp.macosx-10.11-intel-2.7/llr.o
duplicate symbol _exp_table in:
    build/temp.macosx-10.11-intel-2.7/memewrapper.o
    build/temp.macosx-10.11-intel-2.7/likelihood.o
duplicate symbol _log_table in:
    build/temp.macosx-10.11-intel-2.7/memewrapper.o
    build/temp.macosx-10.11-intel-2.7/likelihood.o
duplicate symbol _NO_STATUS in:
    build/temp.macosx-10.11-intel-2.7/memewrapper.o
    build/temp.macosx-10.11-intel-2.7/likelihood.o
ld: 6 duplicate symbols for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
error: command 'gcc' failed with exit status 1

any idea what could be causing this? are there environment settings or and configuration that needs to be added to setup.py?

daquang commented 8 years ago

Have you tried running EXTREME without compiling the Cython code? Do you absolutely need E-values? In my experience, the E-values can usually be trusted with a grain of salt. I only included the E-value calculations because researchers tend to be shallow and judge you by the size of your E-values, regardless of whether that number was validly calculated.

themantalope commented 8 years ago

Alright, I'll run it without the e-values for now, I may take a look again later.