search

Santy-8128 / m3vcftools

1 stars 4 forks source link

Failed to build package statgen/libStatGen #1

Open biona001 opened 5 years ago

biona001 commented 5 years ago

After executing cget install -f ./requirements.txt, it prints a long list of items, followed by this error message:

Command failed: ['/usr/local/bin/cmake', '--build', '/Users/biona001/Benjamin_Folder/UCLA/research/m3vcftools/cget/cget/build/tmp-79d5a5d7275748b6a65f1b576e11589f/build', '--config', 'Release', '--', '-j', '16']
Failed to build package statgen/libStatGen

I tried to manually build libStatGen according to instructions from this page, but I encounter the same error.

I have MacOS 10.14.6.

jonathonl commented 5 years ago

Can you attach the full output from cget as a text file?

biona001 commented 5 years ago

@jonathonl The attached file is the error message when I execute cget install -f ./requirements.txt

Again, this is on Mac OS Mojave 10.14.6

error_message.txt

jonathonl commented 5 years ago

You are using a very old version of GCC. Why aren't you using clang, which is the default compiler on MacOS?

biona001 commented 5 years ago

Sorry for the late response.

I am not familiar with GCC or clang, but I tried the command below to switch to clang following this post

export CC=/usr/bin/clang

I still get a similarly long error message with the same error.

jonathonl commented 5 years ago

Does /usr/bin/c++ --version print out anything about about "LLVM" or "clang"? If so, your conda environment is taking priority over the system paths, and you could try running 

export PATH="/usr/bin:${PATH}"

and then rerunning the cget install command.

biona001 commented 5 years ago

Thank you for the help! Yes it works!