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tbepler / protein-sequence-embedding-iclr2019

Source code for "Learning protein sequence embeddings using information from structure" - ICLR 2019
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Build error #10

Closed partrita closed 4 years ago

partrita commented 4 years ago 
$ python setup.py build_ext --inplace
running build_ext
building 'src.metrics' extension
gcc -pthread -B /home/banya/miniconda3/envs/protein/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/banya/miniconda3/envs/protein/lib/python3.7/site-packages/numpy/core/include -I/home/banya/miniconda3/envs/protein/include/python3.7m -c src/metrics.c -o build/temp.linux-x86_64-3.7/src/metrics.o
In file included from /usr/lib64/gcc/x86_64-solus-linux/9/include-fixed/syslimits.h:7,
                 from /usr/lib64/gcc/x86_64-solus-linux/9/include-fixed/limits.h:34,
                 from /home/banya/miniconda3/envs/protein/include/python3.7m/Python.h:11,
                 from src/metrics.c:17:
/usr/lib64/gcc/x86_64-solus-linux/9/include-fixed/limits.h:194:15: fatal error: limits.h: No such file or directory
  194 | #include_next <limits.h>  /* recurse down to the real one */
      |               ^~~~~~~~~~
compilation terminated.
error: command 'gcc' failed with exit status 1

I hope that docker image will help me a lot.

tbepler commented 4 years ago

It sounds like you need to install gcc in your conda environment.

conda install gcc

before running setup.py should do the trick.

tbepler commented 4 years ago

Closing this issue. If the above didn't resolve the issue feel free to reopen.