2020-04-21T04:25:05,294 Created temporary directory: /tmp/pip-ephem-wheel-cache-ti2fjocf
2020-04-21T04:25:05,300 Created temporary directory: /tmp/pip-req-tracker-50qqa3d9
2020-04-21T04:25:05,301 Initialized build tracking at /tmp/pip-req-tracker-50qqa3d9
2020-04-21T04:25:05,303 Created build tracker: /tmp/pip-req-tracker-50qqa3d9
2020-04-21T04:25:05,303 Entered build tracker: /tmp/pip-req-tracker-50qqa3d9
2020-04-21T04:25:05,305 Created temporary directory: /tmp/pip-wheel-_k5brjf5
2020-04-21T04:25:05,315 1 location(s) to search for versions of medspacy-io:
2020-04-21T04:25:05,315 * https://pypi.org/simple/medspacy-io/
2020-04-21T04:25:05,316 Fetching project page and analyzing links: https://pypi.org/simple/medspacy-io/
2020-04-21T04:25:05,318 Getting page https://pypi.org/simple/medspacy-io/
2020-04-21T04:25:05,320 Found index url https://pypi.org/simple
2020-04-21T04:25:05,324 Getting credentials from keyring for https://pypi.org/simple
2020-04-21T04:25:05,325 Getting credentials from keyring for pypi.org
2020-04-21T04:25:05,535   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
2020-04-21T04:25:05,536   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
2020-04-21T04:25:05,537   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
2020-04-21T04:25:05,537   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
2020-04-21T04:25:05,538   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
2020-04-21T04:25:05,539   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
2020-04-21T04:25:05,548 Given no hashes to check 1 links for project 'medspacy-io': discarding no candidates
2020-04-21T04:25:05,549 Using version 0.1.0.dev2 (newest of versions: 0.1.0.dev2)
2020-04-21T04:25:05,554 Collecting medspacy-io==0.1.0.dev2
2020-04-21T04:25:05,558   Created temporary directory: /tmp/pip-unpack-zduo3b7s
2020-04-21T04:25:05,561   Getting credentials from keyring for files.pythonhosted.org
2020-04-21T04:25:05,658   Downloading medspacy_io-0.1.0.dev2.tar.gz (3.8 kB)
2020-04-21T04:25:05,779   Added medspacy-io==0.1.0.dev2 from https://files.pythonhosted.org/packages/90/8c/151ef0c551088da24c16e20f44113de250cd8e0e11725a75c23bb26d0576/medspacy_io-0.1.0.dev2.tar.gz#sha256=88f7038fc9d743bf05fe4d2c35884555e77c5433ca411d39fc1fe0f3646de36e to build tracker '/tmp/pip-req-tracker-50qqa3d9'
2020-04-21T04:25:05,781     Running setup.py (path:/tmp/pip-wheel-_k5brjf5/medspacy-io/setup.py) egg_info for package medspacy-io
2020-04-21T04:25:05,782     Running command python setup.py egg_info
2020-04-21T04:28:39,184       ERROR: Command errored out with exit status 1:
2020-04-21T04:28:39,185        command: /usr/bin/python3 /usr/local/lib/python3.7/dist-packages/pip install --ignore-installed --no-user --prefix /tmp/pip-build-env-38pg008y/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
2020-04-21T04:28:39,186            cwd: None
2020-04-21T04:28:39,187       Complete output (74 lines):
2020-04-21T04:28:39,187       Collecting setuptools
2020-04-21T04:28:39,188         Using cached setuptools-46.1.3-py3-none-any.whl (582 kB)
2020-04-21T04:28:39,188       Collecting wheel
2020-04-21T04:28:39,189         Using cached wheel-0.34.2-py2.py3-none-any.whl (26 kB)
2020-04-21T04:28:39,189       Collecting cython>=0.25
2020-04-21T04:28:39,190         Using cached Cython-0.29.16-py2.py3-none-any.whl (970 kB)
2020-04-21T04:28:39,190       Collecting cymem<2.1.0,>=2.0.2
2020-04-21T04:28:39,191         Using cached cymem-2.0.3.tar.gz (51 kB)
2020-04-21T04:28:39,191       Collecting preshed<3.1.0,>=3.0.2
2020-04-21T04:28:39,192         Using cached preshed-3.0.2.tar.gz (167 kB)
2020-04-21T04:28:39,193       Collecting murmurhash<1.1.0,>=0.28.0
2020-04-21T04:28:39,193         Using cached murmurhash-1.0.2.tar.gz (35 kB)
2020-04-21T04:28:39,194       Collecting thinc==7.4.0
2020-04-21T04:28:39,194         Using cached thinc-7.4.0.tar.gz (1.3 MB)
2020-04-21T04:28:39,195       Collecting blis<0.5.0,>=0.4.0
2020-04-21T04:28:39,195         Using cached blis-0.4.1.tar.gz (1.8 MB)
2020-04-21T04:28:39,196       Collecting wasabi<1.1.0,>=0.0.9
2020-04-21T04:28:39,196         Using cached wasabi-0.6.0-py3-none-any.whl (20 kB)
2020-04-21T04:28:39,197       Collecting srsly<1.1.0,>=0.0.6
2020-04-21T04:28:39,197         Using cached srsly-1.0.2.tar.gz (192 kB)
2020-04-21T04:28:39,198       Collecting catalogue<1.1.0,>=0.0.7
2020-04-21T04:28:39,198         Using cached catalogue-1.0.0-py2.py3-none-any.whl (7.7 kB)
2020-04-21T04:28:39,199       Collecting numpy>=1.7.0
2020-04-21T04:28:39,199         Using cached numpy-1.18.3.zip (5.4 MB)
2020-04-21T04:28:39,200         Installing build dependencies: started
2020-04-21T04:28:39,200         Installing build dependencies: finished with status 'done'
2020-04-21T04:28:39,201         Getting requirements to build wheel: started
2020-04-21T04:28:39,201         Getting requirements to build wheel: finished with status 'done'
2020-04-21T04:28:39,202           Preparing wheel metadata: started
2020-04-21T04:28:39,202           Preparing wheel metadata: finished with status 'error'
2020-04-21T04:28:39,203           ERROR: Command errored out with exit status 1:
2020-04-21T04:28:39,203            command: /usr/bin/python3 /usr/local/lib/python3.7/dist-packages/pip/_vendor/pep517/_in_process.py prepare_metadata_for_build_wheel /tmp/tmpk6_4jszq
2020-04-21T04:28:39,204                cwd: /tmp/pip-install-c46ki3ya/numpy
2020-04-21T04:28:39,204           Complete output (38 lines):
2020-04-21T04:28:39,205           Processing numpy/random/_bounded_integers.pxd.in
2020-04-21T04:28:39,205           Processing numpy/random/_bit_generator.pyx
2020-04-21T04:28:39,206           Traceback (most recent call last):
2020-04-21T04:28:39,206             File "/tmp/pip-install-c46ki3ya/numpy/tools/cythonize.py", line 238, in <module>
2020-04-21T04:28:39,207               main()
2020-04-21T04:28:39,208             File "/tmp/pip-install-c46ki3ya/numpy/tools/cythonize.py", line 234, in main
2020-04-21T04:28:39,208               find_process_files(root_dir)
2020-04-21T04:28:39,209             File "/tmp/pip-install-c46ki3ya/numpy/tools/cythonize.py", line 225, in find_process_files
2020-04-21T04:28:39,209               process(root_dir, fromfile, tofile, function, hash_db)
2020-04-21T04:28:39,210             File "/tmp/pip-install-c46ki3ya/numpy/tools/cythonize.py", line 191, in process
2020-04-21T04:28:39,210               processor_function(fromfile, tofile)
2020-04-21T04:28:39,211             File "/tmp/pip-install-c46ki3ya/numpy/tools/cythonize.py", line 79, in process_pyx
2020-04-21T04:28:39,211               VENDOR, required_version))
2020-04-21T04:28:39,212           RuntimeError: Building NumPy requires Cython >= 0.29.14
2020-04-21T04:28:39,212           Running from numpy source directory.
2020-04-21T04:28:39,213           setup.py:461: UserWarning: Unrecognized setuptools command, proceeding with generating Cython sources and expanding templates
2020-04-21T04:28:39,213             run_build = parse_setuppy_commands()
2020-04-21T04:28:39,214           Cythonizing sources
2020-04-21T04:28:39,214           Traceback (most recent call last):
2020-04-21T04:28:39,215             File "/usr/local/lib/python3.7/dist-packages/pip/_vendor/pep517/_in_process.py", line 257, in <module>
2020-04-21T04:28:39,215               main()
2020-04-21T04:28:39,216             File "/usr/local/lib/python3.7/dist-packages/pip/_vendor/pep517/_in_process.py", line 240, in main
2020-04-21T04:28:39,216               json_out['return_val'] = hook(**hook_input['kwargs'])
2020-04-21T04:28:39,217             File "/usr/local/lib/python3.7/dist-packages/pip/_vendor/pep517/_in_process.py", line 110, in prepare_metadata_for_build_wheel
2020-04-21T04:28:39,217               return hook(metadata_directory, config_settings)
2020-04-21T04:28:39,218             File "/usr/local/lib/python3.7/dist-packages/setuptools/build_meta.py", line 158, in prepare_metadata_for_build_wheel
2020-04-21T04:28:39,218               self.run_setup()
2020-04-21T04:28:39,219             File "/usr/local/lib/python3.7/dist-packages/setuptools/build_meta.py", line 250, in run_setup
2020-04-21T04:28:39,219               self).run_setup(setup_script=setup_script)
2020-04-21T04:28:39,220             File "/usr/local/lib/python3.7/dist-packages/setuptools/build_meta.py", line 143, in run_setup
2020-04-21T04:28:39,220               exec(compile(code, __file__, 'exec'), locals())
2020-04-21T04:28:39,221             File "setup.py", line 488, in <module>
2020-04-21T04:28:39,221               setup_package()
2020-04-21T04:28:39,222             File "setup.py", line 469, in setup_package
2020-04-21T04:28:39,222               generate_cython()
2020-04-21T04:28:39,223             File "setup.py", line 275, in generate_cython
2020-04-21T04:28:39,223               raise RuntimeError("Running cythonize failed!")
2020-04-21T04:28:39,223           RuntimeError: Running cythonize failed!
2020-04-21T04:28:39,224           ----------------------------------------
2020-04-21T04:28:39,224       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/tmpk6_4jszq Check the logs for full command output.
2020-04-21T04:28:39,225       ----------------------------------------
2020-04-21T04:28:39,935     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-38pg008y/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.
2020-04-21T04:28:40,245     Traceback (most recent call last):
2020-04-21T04:28:40,245       File "/usr/local/lib/python3.7/dist-packages/setuptools/installer.py", line 128, in fetch_build_egg
2020-04-21T04:28:40,246         subprocess.check_call(cmd)
2020-04-21T04:28:40,246       File "/usr/lib/python3.7/subprocess.py", line 347, in check_call
2020-04-21T04:28:40,247         raise CalledProcessError(retcode, cmd)
2020-04-21T04:28:40,247     subprocess.CalledProcessError: Command '['/usr/bin/python3', '-m', 'pip', '--disable-pip-version-check', 'wheel', '--no-deps', '-w', '/tmp/tmpx68z1cy_', '--quiet', 'spacy>=2.2.2']' returned non-zero exit status 1.

2020-04-21T04:28:40,248     During handling of the above exception, another exception occurred:

2020-04-21T04:28:40,249     Traceback (most recent call last):
2020-04-21T04:28:40,249       File "<string>", line 1, in <module>
2020-04-21T04:28:40,249       File "/tmp/pip-wheel-_k5brjf5/medspacy-io/setup.py", line 64, in <module>
2020-04-21T04:28:40,250         'tests/data/ehost_test_corpus/saved/doc2.txt.knowtator.xml'])],
2020-04-21T04:28:40,250       File "/usr/local/lib/python3.7/dist-packages/setuptools/__init__.py", line 143, in setup
2020-04-21T04:28:40,250         _install_setup_requires(attrs)
2020-04-21T04:28:40,251       File "/usr/local/lib/python3.7/dist-packages/setuptools/__init__.py", line 138, in _install_setup_requires
2020-04-21T04:28:40,251         dist.fetch_build_eggs(dist.setup_requires)
2020-04-21T04:28:40,252       File "/usr/local/lib/python3.7/dist-packages/setuptools/dist.py", line 698, in fetch_build_eggs
2020-04-21T04:28:40,252         replace_conflicting=True,
2020-04-21T04:28:40,252       File "/usr/local/lib/python3.7/dist-packages/pkg_resources/__init__.py", line 783, in resolve
2020-04-21T04:28:40,253         replace_conflicting=replace_conflicting
2020-04-21T04:28:40,253       File "/usr/local/lib/python3.7/dist-packages/pkg_resources/__init__.py", line 1066, in best_match
2020-04-21T04:28:40,253         return self.obtain(req, installer)
2020-04-21T04:28:40,254       File "/usr/local/lib/python3.7/dist-packages/pkg_resources/__init__.py", line 1078, in obtain
2020-04-21T04:28:40,254         return installer(requirement)
2020-04-21T04:28:40,254       File "/usr/local/lib/python3.7/dist-packages/setuptools/dist.py", line 754, in fetch_build_egg
2020-04-21T04:28:40,255         return fetch_build_egg(self, req)
2020-04-21T04:28:40,255       File "/usr/local/lib/python3.7/dist-packages/setuptools/installer.py", line 130, in fetch_build_egg
2020-04-21T04:28:40,255         raise DistutilsError(str(e))
2020-04-21T04:28:40,256     distutils.errors.DistutilsError: Command '['/usr/bin/python3', '-m', 'pip', '--disable-pip-version-check', 'wheel', '--no-deps', '-w', '/tmp/tmpx68z1cy_', '--quiet', 'spacy>=2.2.2']' returned non-zero exit status 1.
2020-04-21T04:28:40,367 Cleaning up...
2020-04-21T04:28:40,368   Removing source in /tmp/pip-wheel-_k5brjf5/medspacy-io
2020-04-21T04:28:40,405 Removed medspacy-io==0.1.0.dev2 from https://files.pythonhosted.org/packages/90/8c/151ef0c551088da24c16e20f44113de250cd8e0e11725a75c23bb26d0576/medspacy_io-0.1.0.dev2.tar.gz#sha256=88f7038fc9d743bf05fe4d2c35884555e77c5433ca411d39fc1fe0f3646de36e from build tracker '/tmp/pip-req-tracker-50qqa3d9'
2020-04-21T04:28:40,406 Removed build tracker: '/tmp/pip-req-tracker-50qqa3d9'
2020-04-21T04:28:40,410 ERROR: Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.
2020-04-21T04:28:40,410 Exception information:
2020-04-21T04:28:40,410 Traceback (most recent call last):
2020-04-21T04:28:40,410   File "/usr/local/lib/python3.7/dist-packages/pip/_internal/cli/base_command.py", line 186, in _main
2020-04-21T04:28:40,410     status = self.run(options, args)
2020-04-21T04:28:40,410   File "/usr/local/lib/python3.7/dist-packages/pip/_internal/commands/wheel.py", line 161, in run
2020-04-21T04:28:40,410     resolver.resolve(requirement_set)
2020-04-21T04:28:40,410   File "/usr/local/lib/python3.7/dist-packages/pip/_internal/legacy_resolve.py", line 177, in resolve
2020-04-21T04:28:40,410     discovered_reqs.extend(self._resolve_one(requirement_set, req))
2020-04-21T04:28:40,410   File "/usr/local/lib/python3.7/dist-packages/pip/_internal/legacy_resolve.py", line 333, in _resolve_one
2020-04-21T04:28:40,410     abstract_dist = self._get_abstract_dist_for(req_to_install)
2020-04-21T04:28:40,410   File "/usr/local/lib/python3.7/dist-packages/pip/_internal/legacy_resolve.py", line 282, in _get_abstract_dist_for
2020-04-21T04:28:40,410     abstract_dist = self.preparer.prepare_linked_requirement(req)
2020-04-21T04:28:40,410   File "/usr/local/lib/python3.7/dist-packages/pip/_internal/operations/prepare.py", line 516, in prepare_linked_requirement
2020-04-21T04:28:40,410     req, self.req_tracker, self.finder, self.build_isolation,
2020-04-21T04:28:40,410   File "/usr/local/lib/python3.7/dist-packages/pip/_internal/operations/prepare.py", line 95, in _get_prepared_distribution
2020-04-21T04:28:40,410     abstract_dist.prepare_distribution_metadata(finder, build_isolation)
2020-04-21T04:28:40,410   File "/usr/local/lib/python3.7/dist-packages/pip/_internal/distributions/sdist.py", line 40, in prepare_distribution_metadata
2020-04-21T04:28:40,410     self.req.prepare_metadata()
2020-04-21T04:28:40,410   File "/usr/local/lib/python3.7/dist-packages/pip/_internal/req/req_install.py", line 564, in prepare_metadata
2020-04-21T04:28:40,410     self.metadata_directory = self._generate_metadata()
2020-04-21T04:28:40,410   File "/usr/local/lib/python3.7/dist-packages/pip/_internal/req/req_install.py", line 544, in _generate_metadata
2020-04-21T04:28:40,410     details=self.name or "from {}".format(self.link)
2020-04-21T04:28:40,410   File "/usr/local/lib/python3.7/dist-packages/pip/_internal/operations/build/metadata_legacy.py", line 118, in generate_metadata
2020-04-21T04:28:40,410     command_desc='python setup.py egg_info',
2020-04-21T04:28:40,410   File "/usr/local/lib/python3.7/dist-packages/pip/_internal/utils/subprocess.py", line 242, in call_subprocess
2020-04-21T04:28:40,410     raise InstallationError(exc_msg)
2020-04-21T04:28:40,410 pip._internal.exceptions.InstallationError: Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.