Reviewer 2 - Installation instructions - Unable to install dependency

[JonnyTran]

• openOmics version: 0.8.4
• Python version: 3.9
• Operating System: Mac OS X

Description

Running pip install requirements.txt initially received error.

Perhaps an external dependency on this can be specified (required by llvmlite)? The assumption is that the end-user has a working python installation and relevant compilers etc. installed, though this doesn't seem to be specified anywhere?

What I Did

Installing collected packages: MarkupSafe, Werkzeug, numpy, Jinja2, itsdangerous, zope.interface, zope.event, urllib3, threadpoolctl, scipy, retrying, PyYAML, pytz, python-dateutil, pyparsing, ptyprocess, llvmlite, joblib, idna, heapdict, greenlet, Flask, chardet, certifi, brotli, zict, typing-extensions, tornado, toolz, tblib, soupsieve, sortedcontainers, scikit-learn, requests, psutil, plotly, pillow, pexpect, patsy, pandas, packaging, numba, msgpack, locket, gevent, future, flask-compress, decorator, dask, dash-table, dash-renderer, dash-html-components, dash-core-components, colorlog, cloudpickle, xmltodict, xlsxwriter, xlrd, wrapt, wget, suds-jurko, statsmodels, requests-cache, pynndescent, pyerfa, pydot, partd, networkx, lxml, kiwisolver, grequests, fsspec, easydev, docopt, distributed, dash, cython, cycler, cachetools, bokeh, beautifulsoup4, appdirs, validators, umap-learn, typing, sqlalchemy, scikit-allel, rarfile, obonet, matplotlib, large-image, h5py, gunicorn, gtfparse, goatools, filetype, dash-daq, dash-bootstrap-components, bioservices, biopython, astropy, openomics
    Running setup.py install for retrying ... done
    Running setup.py install for llvmlite ... error
    ERROR: Command errored out with exit status 1:
     command: /Users/stephenmoss/.pyenv/versions/3.9.0/bin/python3.9 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/bf/cl_g6mhx7zd9_1mhhvppbzdh0000gn/T/pip-install-sm6pl876/llvmlite_0bff606e31a6496399a22ccfcec04d59/setup.py'"'"'; __file__='"'"'/private/var/folders/bf/cl_g6mhx7zd9_1mhhvppbzdh0000gn/T/pip-install-sm6pl876/llvmlite_0bff606e31a6496399a22ccfcec04d59/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /private/var/folders/bf/cl_g6mhx7zd9_1mhhvppbzdh0000gn/T/pip-record-rgduko9u/install-record.txt --single-version-externally-managed --compile --install-headers /Users/stephenmoss/.pyenv/versions/3.9.0/include/python3.9/llvmlite
         cwd: /private/var/folders/bf/cl_g6mhx7zd9_1mhhvppbzdh0000gn/T/pip-install-sm6pl876/llvmlite_0bff606e31a6496399a22ccfcec04d59/
    Complete output (29 lines):
    running install
    running build
    got version from file /private/var/folders/bf/cl_g6mhx7zd9_1mhhvppbzdh0000gn/T/pip-install-sm6pl876/llvmlite_0bff606e31a6496399a22ccfcec04d59/llvmlite/_version.py {'version': '0.34.0', 'full': 'c5889c9e98c6b19d5d85ebdd982d64a03931f8e2'}
    running build_ext
    /Users/stephenmoss/.pyenv/versions/3.9.0/bin/python3.9 /private/var/folders/bf/cl_g6mhx7zd9_1mhhvppbzdh0000gn/T/pip-install-sm6pl876/llvmlite_0bff606e31a6496399a22ccfcec04d59/ffi/build.py
    LLVM version... Traceback (most recent call last):
      File "/private/var/folders/bf/cl_g6mhx7zd9_1mhhvppbzdh0000gn/T/pip-install-sm6pl876/llvmlite_0bff606e31a6496399a22ccfcec04d59/ffi/build.py", line 105, in main_posix
        out = subprocess.check_output([llvm_config, '--version'])
      File "/Users/stephenmoss/.pyenv/versions/3.9.0/lib/python3.9/subprocess.py", line 420, in check_output
        return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
      File "/Users/stephenmoss/.pyenv/versions/3.9.0/lib/python3.9/subprocess.py", line 501, in run
        with Popen(*popenargs, **kwargs) as process:
      File "/Users/stephenmoss/.pyenv/versions/3.9.0/lib/python3.9/subprocess.py", line 947, in __init__
        self._execute_child(args, executable, preexec_fn, close_fds,
      File "/Users/stephenmoss/.pyenv/versions/3.9.0/lib/python3.9/subprocess.py", line 1819, in _execute_child
        raise child_exception_type(errno_num, err_msg, err_filename)
    FileNotFoundError: [Errno 2] No such file or directory: 'llvm-config'

    During handling of the above exception, another exception occurred:

    Traceback (most recent call last):
      File "/private/var/folders/bf/cl_g6mhx7zd9_1mhhvppbzdh0000gn/T/pip-install-sm6pl876/llvmlite_0bff606e31a6496399a22ccfcec04d59/ffi/build.py", line 191, in <module>
        main()
      File "/private/var/folders/bf/cl_g6mhx7zd9_1mhhvppbzdh0000gn/T/pip-install-sm6pl876/llvmlite_0bff606e31a6496399a22ccfcec04d59/ffi/build.py", line 185, in main
        main_posix('osx', '.dylib')
      File "/private/var/folders/bf/cl_g6mhx7zd9_1mhhvppbzdh0000gn/T/pip-install-sm6pl876/llvmlite_0bff606e31a6496399a22ccfcec04d59/ffi/build.py", line 107, in main_posix
        raise RuntimeError("%s failed executing, please point LLVM_CONFIG "
    RuntimeError: llvm-config failed executing, please point LLVM_CONFIG to the path for llvm-config
    error: command '/Users/stephenmoss/.pyenv/versions/3.9.0/bin/python3.9' failed with exit code 1
    ----------------------------------------
ERROR: Command errored out with exit status 1: /Users/stephenmoss/.pyenv/versions/3.9.0/bin/python3.9 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/bf/cl_g6mhx7zd9_1mhhvppbzdh0000gn/T/pip-install-sm6pl876/llvmlite_0bff606e31a6496399a22ccfcec04d59/setup.py'"'"'; __file__='"'"'/private/var/folders/bf/cl_g6mhx7zd9_1mhhvppbzdh0000gn/T/pip-install-sm6pl876/llvmlite_0bff606e31a6496399a22ccfcec04d59/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /private/var/folders/bf/cl_g6mhx7zd9_1mhhvppbzdh0000gn/T/pip-record-rgduko9u/install-record.txt --single-version-externally-managed --compile --install-headers /Users/stephenmoss/.pyenv/versions/3.9.0/include/python3.9/llvmlite Check the logs for full command output.

I needed to run the following to fix the issue:

brew install llvm@9
LLVM_CONFIG=/usr/local/opt/llvm@9/bin/llvm-config pip install openomics
I tried with brew install llvm (version 11.0.1 and it failed with RuntimeError: Building llvmlite requires LLVM 10.0.x or 9.0.x, got '11.0.1'. Be sure to set LLVM_CONFIG to the right executable path.

[JonnyTran]

Issue has been resolved under Mac OS + Python 3.9 and Python 3.8 when running pip install openomics.

[gawbul]

All works fine for me now 👍