evo,millanek

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How to use libc++?

Hi,
My gcc version is 5.3.0.
But when I type "make", errors happened.

g++: error: unrecognized command line option '-stdlib=libc++'
make: *** [Build/evo] Error 1

So please tell me what I need before use this software. Thank you!

make fails in process_vcf_linkGeneNames.cpp

Hi Milan,

When I try to make your code ...

make

... I get the following error:

[...]
g++ -std=c++11   -c -o process_vcf_linkGeneNames.o process_vcf_linkGeneNames.cpp
process_vcf_linkGeneNames.cpp: In function ‘int linkGNMain(int, char**)’:
process_vcf_linkGeneNames.cpp:271:17: error: ‘print_vector_stream’ was not declared in this scope
                 print_vector_stream(ensGene, std::cerr);
                 ^~~~~~~~~~~~~~~~~~~
process_vcf_linkGeneNames.cpp:271:17: note: suggested alternative: ‘print_vector’
                 print_vector_stream(ensGene, std::cerr);
                 ^~~~~~~~~~~~~~~~~~~
                 print_vector
make: *** [<builtin>: process_vcf_linkGeneNames.o] Error 1

I reproduced the bug in this GCC Travis log and this clang Travis log.

I hope you can fix this 👍

If you want (and that would be awesome), you can add the Travis CI checking by accepting this Pull request.

Note there is also a warning:

g++ -c -std=c++11 process_vcf_coding_sequences.cpp -o Build/process_vcf_coding_sequences.o 
In file included from process_vcf_coding_sequences.cpp:9:
process_vcf_coding_sequences.h: In function ‘double getExpectedNumberOfNonsynonymousSites(const string&)’:
process_vcf_coding_sequences.h:348:1: warning: control reaches end of non-void function [-Wreturn-type]
 }
 ^

The reason you did not return is obvious, but I hope you will fix that warning as well, else all your users will take the time to verify the warning is indeed harmless.

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