2020-04-21T05:06:44,515 Created temporary directory: /tmp/pip-ephem-wheel-cache-vtrh842v
2020-04-21T05:06:44,520 Created temporary directory: /tmp/pip-req-tracker-5sb355pg
2020-04-21T05:06:44,520 Initialized build tracking at /tmp/pip-req-tracker-5sb355pg
2020-04-21T05:06:44,521 Created build tracker: /tmp/pip-req-tracker-5sb355pg
2020-04-21T05:06:44,521 Entered build tracker: /tmp/pip-req-tracker-5sb355pg
2020-04-21T05:06:44,523 Created temporary directory: /tmp/pip-wheel-rgd085ks
2020-04-21T05:06:44,528 1 location(s) to search for versions of medspacy-io:
2020-04-21T05:06:44,528 * https://pypi.org/simple/medspacy-io/
2020-04-21T05:06:44,529 Fetching project page and analyzing links: https://pypi.org/simple/medspacy-io/
2020-04-21T05:06:44,530 Getting page https://pypi.org/simple/medspacy-io/
2020-04-21T05:06:44,532 Found index url https://pypi.org/simple
2020-04-21T05:06:44,535 Getting credentials from keyring for https://pypi.org/simple
2020-04-21T05:06:44,536 Getting credentials from keyring for pypi.org
2020-04-21T05:06:44,751   Found link https://files.pythonhosted.org/packages/b2/c2/3606fa97e4eb24c928a94d2baeb5d45c52436a72073e2fa67a70bd2427b0/medspacy-io-0.1.0.dev0.tar.gz#sha256=f94d49aab324ba16fa9784f5701df291cb1fb9cbc075162898be42d1cbbe6170 (from https://pypi.org/simple/medspacy-io/), version: 0.1.0.dev0
2020-04-21T05:06:44,752   Found link https://files.pythonhosted.org/packages/24/a4/f2641846c091919e0da48611ad84342f1f4ff8da6eeb402e0c1c4f74de04/medspacy-io-0.1.0.dev1.tar.gz#sha256=7e2132d48f69ca3ad06ba73cddca34cfc5c23e11aee0d83ba81d253bb38bd618 (from https://pypi.org/simple/medspacy-io/), version: 0.1.0.dev1
2020-04-21T05:06:44,753   Found link https://files.pythonhosted.org/packages/90/8c/151ef0c551088da24c16e20f44113de250cd8e0e11725a75c23bb26d0576/medspacy_io-0.1.0.dev2.tar.gz#sha256=88f7038fc9d743bf05fe4d2c35884555e77c5433ca411d39fc1fe0f3646de36e (from https://pypi.org/simple/medspacy-io/), version: 0.1.0.dev2
2020-04-21T05:06:44,753   Found link https://files.pythonhosted.org/packages/4f/b6/e420dd4fb01c2fa80bfd69e11b7e667717e4b9e2f0a434e1ea3ecb0cd0a6/medspacy_io-0.1.0.dev3.tar.gz#sha256=733f6d91e59e59f7efc244e39111ed87e45e17560658c81bd4dbfb901b41f051 (from https://pypi.org/simple/medspacy-io/), version: 0.1.0.dev3
2020-04-21T05:06:44,754   Found link https://files.pythonhosted.org/packages/fc/03/2f4e43e27609b56e13673c4cd37ffee26b004f2a295c483b4e0c98d1ce07/medspacy_io-0.1.0.dev4.tar.gz#sha256=05bcb5f31f1ad987c2845c792577c46592753707b06f201ff8154f209e963f62 (from https://pypi.org/simple/medspacy-io/), version: 0.1.0.dev4
2020-04-21T05:06:44,755   Found link https://files.pythonhosted.org/packages/e7/50/53cc2c9f6ecbee974e9d1bb4ab5577cdf5924385030d654472dba7f8a567/medspacy_io-0.1.0.dev5.tar.gz#sha256=a69c715fabea7fc5732239876fcd462bb224e021b77180d76f565af57075c9f9 (from https://pypi.org/simple/medspacy-io/), version: 0.1.0.dev5
2020-04-21T05:06:44,755   Found link https://files.pythonhosted.org/packages/6c/9a/0d96dba15bcd43c90c408dafa154859d20f50cad8761876aa35cdf9740d5/medspacy_io-0.1.0.dev6.tar.gz#sha256=2f8cbe19b5a5a0871698b24ecb2cedb26d7a27006bfbefed427f0489b89e9be3 (from https://pypi.org/simple/medspacy-io/), version: 0.1.0.dev6
2020-04-21T05:06:44,756   Found link https://files.pythonhosted.org/packages/f6/cd/94865fd844d1ce4c76eb871d20deda80312a8b43d943940d5f1517f42c31/medspacy_io-0.1.0.dev7.tar.gz#sha256=1c56736b9bba810c697f675e69e255f3596864801779c110f6d66dcacde077c1 (from https://pypi.org/simple/medspacy-io/), version: 0.1.0.dev7
2020-04-21T05:06:44,757   Found link https://files.pythonhosted.org/packages/d7/ea/0a29aa44880c43f0bc98b0a15e1fab129e9c2135a77f3fd830b16f131d6c/medspacy_io-0.1.0.dev8.tar.gz#sha256=9159e40c57f9cefdb18523dfbf13b2ff9952000db6b5b7a29f49da29c848b108 (from https://pypi.org/simple/medspacy-io/), version: 0.1.0.dev8
2020-04-21T05:06:44,757   Found link https://files.pythonhosted.org/packages/d9/29/1853ec45d00e6258363235b31bedab847f95ba97ba56e861cedddd96543c/medspacy_io-0.1.0.dev9.tar.gz#sha256=96d04a97c43f4b290bff2248a3cf041decca65f3fb0e2609c941efc8928a5e71 (from https://pypi.org/simple/medspacy-io/), version: 0.1.0.dev9
2020-04-21T05:06:44,758   Found link https://files.pythonhosted.org/packages/8d/f5/cf503163b909bccfb8ffdf3349dec4ca5a1be5837a477052e409cb1b4176/medspacy_io-0.1.0.dev10.tar.gz#sha256=4f290c287b6491486c9ac8e5fe191ec3859a952912a61291699a5eb4c0593d7d (from https://pypi.org/simple/medspacy-io/), version: 0.1.0.dev10
2020-04-21T05:06:44,769 Given no hashes to check 1 links for project 'medspacy-io': discarding no candidates
2020-04-21T05:06:44,770 Using version 0.1.0.dev8 (newest of versions: 0.1.0.dev8)
2020-04-21T05:06:44,775 Collecting medspacy-io==0.1.0.dev8
2020-04-21T05:06:44,779   Created temporary directory: /tmp/pip-unpack-4wu6fr5a
2020-04-21T05:06:44,781   Getting credentials from keyring for files.pythonhosted.org
2020-04-21T05:06:44,878   Downloading medspacy_io-0.1.0.dev8.tar.gz (13 kB)
2020-04-21T05:06:45,042   Added medspacy-io==0.1.0.dev8 from https://files.pythonhosted.org/packages/d7/ea/0a29aa44880c43f0bc98b0a15e1fab129e9c2135a77f3fd830b16f131d6c/medspacy_io-0.1.0.dev8.tar.gz#sha256=9159e40c57f9cefdb18523dfbf13b2ff9952000db6b5b7a29f49da29c848b108 to build tracker '/tmp/pip-req-tracker-5sb355pg'
2020-04-21T05:06:45,045     Running setup.py (path:/tmp/pip-wheel-rgd085ks/medspacy-io/setup.py) egg_info for package medspacy-io
2020-04-21T05:06:45,047     Running command python setup.py egg_info
2020-04-21T05:09:38,173       ERROR: Command errored out with exit status 1:
2020-04-21T05:09:38,174        command: /usr/bin/python3 /usr/local/lib/python3.7/dist-packages/pip install --ignore-installed --no-user --prefix /tmp/pip-build-env-axx7b0eb/overlay --no-warn-script-location --no-binary :none: --only-binary :none: -i https://pypi.org/simple -- setuptools wheel 'cython>=0.25' 'cymem>=2.0.2,<2.1.0' 'preshed>=3.0.2,<3.1.0' 'murmurhash>=0.28.0,<1.1.0' thinc==7.4.0
2020-04-21T05:09:38,175            cwd: None
2020-04-21T05:09:38,175       Complete output (74 lines):
2020-04-21T05:09:38,175       Collecting setuptools
2020-04-21T05:09:38,175         Using cached setuptools-46.1.3-py3-none-any.whl (582 kB)
2020-04-21T05:09:38,176       Collecting wheel
2020-04-21T05:09:38,176         Using cached wheel-0.34.2-py2.py3-none-any.whl (26 kB)
2020-04-21T05:09:38,176       Collecting cython>=0.25
2020-04-21T05:09:38,177         Using cached Cython-0.29.16-py2.py3-none-any.whl (970 kB)
2020-04-21T05:09:38,177       Collecting cymem<2.1.0,>=2.0.2
2020-04-21T05:09:38,178         Using cached cymem-2.0.3.tar.gz (51 kB)
2020-04-21T05:09:38,178       Collecting preshed<3.1.0,>=3.0.2
2020-04-21T05:09:38,178         Using cached preshed-3.0.2.tar.gz (167 kB)
2020-04-21T05:09:38,179       Collecting murmurhash<1.1.0,>=0.28.0
2020-04-21T05:09:38,179         Using cached murmurhash-1.0.2.tar.gz (35 kB)
2020-04-21T05:09:38,180       Collecting thinc==7.4.0
2020-04-21T05:09:38,180         Using cached thinc-7.4.0.tar.gz (1.3 MB)
2020-04-21T05:09:38,180       Collecting blis<0.5.0,>=0.4.0
2020-04-21T05:09:38,181         Using cached blis-0.4.1.tar.gz (1.8 MB)
2020-04-21T05:09:38,181       Collecting wasabi<1.1.0,>=0.0.9
2020-04-21T05:09:38,182         Using cached wasabi-0.6.0-py3-none-any.whl (20 kB)
2020-04-21T05:09:38,182       Collecting srsly<1.1.0,>=0.0.6
2020-04-21T05:09:38,183         Using cached srsly-1.0.2.tar.gz (192 kB)
2020-04-21T05:09:38,183       Collecting catalogue<1.1.0,>=0.0.7
2020-04-21T05:09:38,184         Using cached catalogue-1.0.0-py2.py3-none-any.whl (7.7 kB)
2020-04-21T05:09:38,184       Collecting numpy>=1.7.0
2020-04-21T05:09:38,185         Using cached numpy-1.18.3.zip (5.4 MB)
2020-04-21T05:09:38,185         Installing build dependencies: started
2020-04-21T05:09:38,185         Installing build dependencies: finished with status 'done'
2020-04-21T05:09:38,186         Getting requirements to build wheel: started
2020-04-21T05:09:38,186         Getting requirements to build wheel: finished with status 'done'
2020-04-21T05:09:38,187           Preparing wheel metadata: started
2020-04-21T05:09:38,187           Preparing wheel metadata: finished with status 'error'
2020-04-21T05:09:38,188           ERROR: Command errored out with exit status 1:
2020-04-21T05:09:38,188            command: /usr/bin/python3 /usr/local/lib/python3.7/dist-packages/pip/_vendor/pep517/_in_process.py prepare_metadata_for_build_wheel /tmp/tmpz8li7qow
2020-04-21T05:09:38,189                cwd: /tmp/pip-install-_b45nnvs/numpy
2020-04-21T05:09:38,189           Complete output (38 lines):
2020-04-21T05:09:38,190           Processing numpy/random/_bounded_integers.pxd.in
2020-04-21T05:09:38,190           Processing numpy/random/_bit_generator.pyx
2020-04-21T05:09:38,190           Traceback (most recent call last):
2020-04-21T05:09:38,191             File "/tmp/pip-install-_b45nnvs/numpy/tools/cythonize.py", line 238, in <module>
2020-04-21T05:09:38,191               main()
2020-04-21T05:09:38,192             File "/tmp/pip-install-_b45nnvs/numpy/tools/cythonize.py", line 234, in main
2020-04-21T05:09:38,192               find_process_files(root_dir)
2020-04-21T05:09:38,193             File "/tmp/pip-install-_b45nnvs/numpy/tools/cythonize.py", line 225, in find_process_files
2020-04-21T05:09:38,193               process(root_dir, fromfile, tofile, function, hash_db)
2020-04-21T05:09:38,193             File "/tmp/pip-install-_b45nnvs/numpy/tools/cythonize.py", line 191, in process
2020-04-21T05:09:38,194               processor_function(fromfile, tofile)
2020-04-21T05:09:38,194             File "/tmp/pip-install-_b45nnvs/numpy/tools/cythonize.py", line 79, in process_pyx
2020-04-21T05:09:38,195               VENDOR, required_version))
2020-04-21T05:09:38,195           RuntimeError: Building NumPy requires Cython >= 0.29.14
2020-04-21T05:09:38,196           Running from numpy source directory.
2020-04-21T05:09:38,196           setup.py:461: UserWarning: Unrecognized setuptools command, proceeding with generating Cython sources and expanding templates
2020-04-21T05:09:38,197             run_build = parse_setuppy_commands()
2020-04-21T05:09:38,197           Cythonizing sources
2020-04-21T05:09:38,198           Traceback (most recent call last):
2020-04-21T05:09:38,198             File "/usr/local/lib/python3.7/dist-packages/pip/_vendor/pep517/_in_process.py", line 257, in <module>
2020-04-21T05:09:38,198               main()
2020-04-21T05:09:38,199             File "/usr/local/lib/python3.7/dist-packages/pip/_vendor/pep517/_in_process.py", line 240, in main
2020-04-21T05:09:38,199               json_out['return_val'] = hook(**hook_input['kwargs'])
2020-04-21T05:09:38,200             File "/usr/local/lib/python3.7/dist-packages/pip/_vendor/pep517/_in_process.py", line 110, in prepare_metadata_for_build_wheel
2020-04-21T05:09:38,200               return hook(metadata_directory, config_settings)
2020-04-21T05:09:38,201             File "/usr/local/lib/python3.7/dist-packages/setuptools/build_meta.py", line 158, in prepare_metadata_for_build_wheel
2020-04-21T05:09:38,201               self.run_setup()
2020-04-21T05:09:38,202             File "/usr/local/lib/python3.7/dist-packages/setuptools/build_meta.py", line 250, in run_setup
2020-04-21T05:09:38,202               self).run_setup(setup_script=setup_script)
2020-04-21T05:09:38,202             File "/usr/local/lib/python3.7/dist-packages/setuptools/build_meta.py", line 143, in run_setup
2020-04-21T05:09:38,203               exec(compile(code, __file__, 'exec'), locals())
2020-04-21T05:09:38,203             File "setup.py", line 488, in <module>
2020-04-21T05:09:38,204               setup_package()
2020-04-21T05:09:38,204             File "setup.py", line 469, in setup_package
2020-04-21T05:09:38,205               generate_cython()
2020-04-21T05:09:38,205             File "setup.py", line 275, in generate_cython
2020-04-21T05:09:38,205               raise RuntimeError("Running cythonize failed!")
2020-04-21T05:09:38,206           RuntimeError: Running cythonize failed!
2020-04-21T05:09:38,206           ----------------------------------------
2020-04-21T05:09:38,207       ERROR: Command errored out with exit status 1: /usr/bin/python3 /usr/local/lib/python3.7/dist-packages/pip/_vendor/pep517/_in_process.py prepare_metadata_for_build_wheel /tmp/tmpz8li7qow Check the logs for full command output.
2020-04-21T05:09:38,207       ----------------------------------------
2020-04-21T05:09:38,954     ERROR: Command errored out with exit status 1: /usr/bin/python3 /usr/local/lib/python3.7/dist-packages/pip install --ignore-installed --no-user --prefix /tmp/pip-build-env-axx7b0eb/overlay --no-warn-script-location --no-binary :none: --only-binary :none: -i https://pypi.org/simple -- setuptools wheel 'cython>=0.25' 'cymem>=2.0.2,<2.1.0' 'preshed>=3.0.2,<3.1.0' 'murmurhash>=0.28.0,<1.1.0' thinc==7.4.0 Check the logs for full command output.
2020-04-21T05:09:39,269     Traceback (most recent call last):
2020-04-21T05:09:39,270       File "/usr/local/lib/python3.7/dist-packages/setuptools/installer.py", line 128, in fetch_build_egg
2020-04-21T05:09:39,270         subprocess.check_call(cmd)
2020-04-21T05:09:39,271       File "/usr/lib/python3.7/subprocess.py", line 347, in check_call
2020-04-21T05:09:39,271         raise CalledProcessError(retcode, cmd)
2020-04-21T05:09:39,271     subprocess.CalledProcessError: Command '['/usr/bin/python3', '-m', 'pip', '--disable-pip-version-check', 'wheel', '--no-deps', '-w', '/tmp/tmpllp5tzs8', '--quiet', 'spacy>=2.2.2']' returned non-zero exit status 1.

2020-04-21T05:09:39,272     During handling of the above exception, another exception occurred:

2020-04-21T05:09:39,273     Traceback (most recent call last):
2020-04-21T05:09:39,273       File "<string>", line 1, in <module>
2020-04-21T05:09:39,273       File "/tmp/pip-wheel-rgd085ks/medspacy-io/setup.py", line 65, in <module>
2020-04-21T05:09:39,274         'tests/data/ehost_test_corpus/saved/doc2.txt.knowtator.xml'])],
2020-04-21T05:09:39,274       File "/usr/local/lib/python3.7/dist-packages/setuptools/__init__.py", line 143, in setup
2020-04-21T05:09:39,274         _install_setup_requires(attrs)
2020-04-21T05:09:39,275       File "/usr/local/lib/python3.7/dist-packages/setuptools/__init__.py", line 138, in _install_setup_requires
2020-04-21T05:09:39,275         dist.fetch_build_eggs(dist.setup_requires)
2020-04-21T05:09:39,275       File "/usr/local/lib/python3.7/dist-packages/setuptools/dist.py", line 698, in fetch_build_eggs
2020-04-21T05:09:39,276         replace_conflicting=True,
2020-04-21T05:09:39,276       File "/usr/local/lib/python3.7/dist-packages/pkg_resources/__init__.py", line 783, in resolve
2020-04-21T05:09:39,277         replace_conflicting=replace_conflicting
2020-04-21T05:09:39,277       File "/usr/local/lib/python3.7/dist-packages/pkg_resources/__init__.py", line 1066, in best_match
2020-04-21T05:09:39,277         return self.obtain(req, installer)
2020-04-21T05:09:39,278       File "/usr/local/lib/python3.7/dist-packages/pkg_resources/__init__.py", line 1078, in obtain
2020-04-21T05:09:39,278         return installer(requirement)
2020-04-21T05:09:39,278       File "/usr/local/lib/python3.7/dist-packages/setuptools/dist.py", line 754, in fetch_build_egg
2020-04-21T05:09:39,279         return fetch_build_egg(self, req)
2020-04-21T05:09:39,279       File "/usr/local/lib/python3.7/dist-packages/setuptools/installer.py", line 130, in fetch_build_egg
2020-04-21T05:09:39,279         raise DistutilsError(str(e))
2020-04-21T05:09:39,280     distutils.errors.DistutilsError: Command '['/usr/bin/python3', '-m', 'pip', '--disable-pip-version-check', 'wheel', '--no-deps', '-w', '/tmp/tmpllp5tzs8', '--quiet', 'spacy>=2.2.2']' returned non-zero exit status 1.
2020-04-21T05:09:39,391 Cleaning up...
2020-04-21T05:09:39,392   Removing source in /tmp/pip-wheel-rgd085ks/medspacy-io
2020-04-21T05:09:39,443 Removed medspacy-io==0.1.0.dev8 from https://files.pythonhosted.org/packages/d7/ea/0a29aa44880c43f0bc98b0a15e1fab129e9c2135a77f3fd830b16f131d6c/medspacy_io-0.1.0.dev8.tar.gz#sha256=9159e40c57f9cefdb18523dfbf13b2ff9952000db6b5b7a29f49da29c848b108 from build tracker '/tmp/pip-req-tracker-5sb355pg'
2020-04-21T05:09:39,444 Removed build tracker: '/tmp/pip-req-tracker-5sb355pg'
2020-04-21T05:09:39,448 ERROR: Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.
2020-04-21T05:09:39,449 Exception information:
2020-04-21T05:09:39,449 Traceback (most recent call last):
2020-04-21T05:09:39,449   File "/usr/local/lib/python3.7/dist-packages/pip/_internal/cli/base_command.py", line 186, in _main
2020-04-21T05:09:39,449     status = self.run(options, args)
2020-04-21T05:09:39,449   File "/usr/local/lib/python3.7/dist-packages/pip/_internal/commands/wheel.py", line 161, in run
2020-04-21T05:09:39,449     resolver.resolve(requirement_set)
2020-04-21T05:09:39,449   File "/usr/local/lib/python3.7/dist-packages/pip/_internal/legacy_resolve.py", line 177, in resolve
2020-04-21T05:09:39,449     discovered_reqs.extend(self._resolve_one(requirement_set, req))
2020-04-21T05:09:39,449   File "/usr/local/lib/python3.7/dist-packages/pip/_internal/legacy_resolve.py", line 333, in _resolve_one
2020-04-21T05:09:39,449     abstract_dist = self._get_abstract_dist_for(req_to_install)
2020-04-21T05:09:39,449   File "/usr/local/lib/python3.7/dist-packages/pip/_internal/legacy_resolve.py", line 282, in _get_abstract_dist_for
2020-04-21T05:09:39,449     abstract_dist = self.preparer.prepare_linked_requirement(req)
2020-04-21T05:09:39,449   File "/usr/local/lib/python3.7/dist-packages/pip/_internal/operations/prepare.py", line 516, in prepare_linked_requirement
2020-04-21T05:09:39,449     req, self.req_tracker, self.finder, self.build_isolation,
2020-04-21T05:09:39,449   File "/usr/local/lib/python3.7/dist-packages/pip/_internal/operations/prepare.py", line 95, in _get_prepared_distribution
2020-04-21T05:09:39,449     abstract_dist.prepare_distribution_metadata(finder, build_isolation)
2020-04-21T05:09:39,449   File "/usr/local/lib/python3.7/dist-packages/pip/_internal/distributions/sdist.py", line 40, in prepare_distribution_metadata
2020-04-21T05:09:39,449     self.req.prepare_metadata()
2020-04-21T05:09:39,449   File "/usr/local/lib/python3.7/dist-packages/pip/_internal/req/req_install.py", line 564, in prepare_metadata
2020-04-21T05:09:39,449     self.metadata_directory = self._generate_metadata()
2020-04-21T05:09:39,449   File "/usr/local/lib/python3.7/dist-packages/pip/_internal/req/req_install.py", line 544, in _generate_metadata
2020-04-21T05:09:39,449     details=self.name or "from {}".format(self.link)
2020-04-21T05:09:39,449   File "/usr/local/lib/python3.7/dist-packages/pip/_internal/operations/build/metadata_legacy.py", line 118, in generate_metadata
2020-04-21T05:09:39,449     command_desc='python setup.py egg_info',
2020-04-21T05:09:39,449   File "/usr/local/lib/python3.7/dist-packages/pip/_internal/utils/subprocess.py", line 242, in call_subprocess
2020-04-21T05:09:39,449     raise InstallationError(exc_msg)
2020-04-21T05:09:39,449 pip._internal.exceptions.InstallationError: Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.