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nanoporetech / pomoxis

Analysis components from Oxford Nanopore Research
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Install on mac OSX #17

Closed strnadja closed 6 years ago

strnadja commented 6 years ago

Encountering the following error when trying to build on OSX:

[ 20%] Building CXX object vendor/spoa/CMakeFiles/spoa.dir/src/alignment_engine.cpp.o /Users/[...]/pomoxis/submodules/racon/vendor/spoa/src/alignment_engine.cpp:26:9: error: use of undeclared identifier 'exit' exit(1); ^ /Users/[...]/pomoxis/submodules/racon/vendor/spoa/src/alignment_engine.cpp:32:9: error: use of undeclared identifier 'exit' exit(1); ^ 2 errors generated. make[3]: [vendor/spoa/CMakeFiles/spoa.dir/src/alignment_engine.cpp.o] Error 1 make[2]: [vendor/spoa/CMakeFiles/spoa.dir/all] Error 2 make[1]: [all] Error 2 make: [bincache/racon] Error 2

I ought to have all of the dependencies (as listed for Ubuntu) installed. Any ideas appreciated!

Jessica

cjw85 commented 6 years ago

Hi Jessica

Can you confirm the version of OSX you are using? We updated recently the version of racon which we use, and likely have tested only on High Sierra (specifically 10.13.3).

I'm just running through this now, and can't reproduce your error. I've attached the relevant part output from make install for you to compare.

racon_build.log

cjw85 commented 6 years ago

OK, I can see the error. There has been a fix to this in the racon (https://github.com/rvaser/spoa/commit/2f14820766a7508cd8bd799bb13699c61a5f3b8e) I will update the version of racon we specify.

This should now be fixed. The simplest thing for you to do is reclone the pomoxis repository from scratch and run make install. Please report back.

strnadja commented 6 years ago

Looks like that fixed the issue! I'm running El Capitan. Builds with warnings, but no errors.

Thanks!