pip install fails

[seb-buch]

On linux (Ubuntu 18.04 LTS) with conda 4.8 and cython 0.29.4 pip install fatslim fails with the following exception:

~$ pip install --upgrade --force-reinstall fatslim WARNING: pip is being invoked by an old script wrapper. This will fail in a future version of pip. Please see https://github.com/pypa/pip/issues/5599 for advice on fixing the underlying issue. To avoid this problem you can invoke Python with '-m pip' instead of running pip directly. Collecting fatslim Using cached fatslim-0.2.1.tar.gz (21.2 MB) ERROR: Command errored out with exit status 1: command: /softwares/Anaconda/3.7/bin/python -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-th_7os27/fatslim/setup.py'"'"'; file='"'"'/tmp/pip-install-th_7os27/fatslim/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(file);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' egg_info --egg-base /tmp/pip-install-th_7os27/fatslim/pip-egg-info cwd: /tmp/pip-install-th_7os27/fatslim/ Complete output (58 lines): /softwares/Anaconda/3.7/lib/python3.7/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /tmp/pip-install-th_7os27/fatslim/fatslimlib/core_analysis.pxd tree = Parsing.p_module(s, pxd, full_module_name) Traceback (most recent call last): File "", line 1, in File "/tmp/pip-install-th_7os27/fatslim/setup.py", line 274, in core_analysis]), [ REMOVED Cython Internals ] File "/softwares/Anaconda/3.7/lib/python3.7/site-packages/Cython/Compiler/PyrexTypes.py", line 2486, in from_py_call_code assert not error_condition, '%s: %s' % (error_pos, error_condition) AssertionError: (<StringSourceDescriptor:(tree fragment)>, 12, 263): PyErr_Occurred() INFO: Cython will be used. INFO: Checking for OpenMP support... INFO: OpenMP is present and will be used! Compiling fatslimlib/core_base.pyx because it depends on /softwares/Anaconda/3.7/lib/python3.7/site-packages/Cython/Includes/libc/string.pxd. Compiling fatslimlib/core_datareading.pyx because it depends on /softwares/Anaconda/3.7/lib/python3.7/site-packages/Cython/Includes/libc/string.pxd. Compiling fatslimlib/core_geometry.pyx because it depends on /softwares/Anaconda/3.7/lib/python3.7/site-packages/Cython/Includes/libc/string.pxd. Compiling fatslimlib/core_ns.pyx because it depends on /softwares/Anaconda/3.7/lib/python3.7/site-packages/Cython/Includes/libc/string.pxd. Compiling fatslimlib/core_analysis.pyx because it depends on /softwares/Anaconda/3.7/lib/python3.7/site-packages/Cython/Includes/libc/string.pxd. [1/5] Cythonizing fatslimlib/core_analysis.pyx

ERROR: Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.