2020-04-21T03:26:04,467 Created temporary directory: /tmp/pip-ephem-wheel-cache-mlor90ya
2020-04-21T03:26:04,471 Created temporary directory: /tmp/pip-req-tracker-jbe6_fw9
2020-04-21T03:26:04,472 Initialized build tracking at /tmp/pip-req-tracker-jbe6_fw9
2020-04-21T03:26:04,472 Created build tracker: /tmp/pip-req-tracker-jbe6_fw9
2020-04-21T03:26:04,473 Entered build tracker: /tmp/pip-req-tracker-jbe6_fw9
2020-04-21T03:26:04,474 Created temporary directory: /tmp/pip-wheel-9g_5c92n
2020-04-21T03:26:04,480 1 location(s) to search for versions of medspacy-io:
2020-04-21T03:26:04,480 * https://pypi.org/simple/medspacy-io/
2020-04-21T03:26:04,480 Fetching project page and analyzing links: https://pypi.org/simple/medspacy-io/
2020-04-21T03:26:04,481 Getting page https://pypi.org/simple/medspacy-io/
2020-04-21T03:26:04,483 Found index url https://pypi.org/simple
2020-04-21T03:26:04,487 Getting credentials from keyring for https://pypi.org/simple
2020-04-21T03:26:04,487 Getting credentials from keyring for pypi.org
2020-04-21T03:26:04,691   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
2020-04-21T03:26:04,698 Given no hashes to check 1 links for project 'medspacy-io': discarding no candidates
2020-04-21T03:26:04,699 Using version 0.1.0.dev0 (newest of versions: 0.1.0.dev0)
2020-04-21T03:26:04,705 Collecting medspacy-io==0.1.0.dev0
2020-04-21T03:26:04,708   Created temporary directory: /tmp/pip-unpack-es5j4oa0
2020-04-21T03:26:04,711   Getting credentials from keyring for files.pythonhosted.org
2020-04-21T03:26:04,837   Downloading medspacy-io-0.1.0.dev0.tar.gz (3.8 kB)
2020-04-21T03:26:04,958   Added medspacy-io==0.1.0.dev0 from https://files.pythonhosted.org/packages/b2/c2/3606fa97e4eb24c928a94d2baeb5d45c52436a72073e2fa67a70bd2427b0/medspacy-io-0.1.0.dev0.tar.gz#sha256=f94d49aab324ba16fa9784f5701df291cb1fb9cbc075162898be42d1cbbe6170 to build tracker '/tmp/pip-req-tracker-jbe6_fw9'
2020-04-21T03:26:04,961     Running setup.py (path:/tmp/pip-wheel-9g_5c92n/medspacy-io/setup.py) egg_info for package medspacy-io
2020-04-21T03:26:04,963     Running command python setup.py egg_info
2020-04-21T03:28:27,635       ERROR: Command errored out with exit status 1:
2020-04-21T03:28:27,637        command: /usr/bin/python3 /usr/local/lib/python3.7/dist-packages/pip install --ignore-installed --no-user --prefix /tmp/pip-build-env-01dcgfns/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
2020-04-21T03:28:27,637            cwd: None
2020-04-21T03:28:27,638       Complete output (74 lines):
2020-04-21T03:28:27,638       Collecting setuptools
2020-04-21T03:28:27,639         Using cached setuptools-46.1.3-py3-none-any.whl (582 kB)
2020-04-21T03:28:27,639       Collecting wheel
2020-04-21T03:28:27,639         Using cached wheel-0.34.2-py2.py3-none-any.whl (26 kB)
2020-04-21T03:28:27,640       Collecting cython>=0.25
2020-04-21T03:28:27,640         Using cached Cython-0.29.16-py2.py3-none-any.whl (970 kB)
2020-04-21T03:28:27,640       Collecting cymem<2.1.0,>=2.0.2
2020-04-21T03:28:27,641         Using cached cymem-2.0.3.tar.gz (51 kB)
2020-04-21T03:28:27,641       Collecting preshed<3.1.0,>=3.0.2
2020-04-21T03:28:27,641         Using cached preshed-3.0.2.tar.gz (167 kB)
2020-04-21T03:28:27,642       Collecting murmurhash<1.1.0,>=0.28.0
2020-04-21T03:28:27,642         Using cached murmurhash-1.0.2.tar.gz (35 kB)
2020-04-21T03:28:27,643       Collecting thinc==7.4.0
2020-04-21T03:28:27,643         Using cached thinc-7.4.0.tar.gz (1.3 MB)
2020-04-21T03:28:27,643       Collecting blis<0.5.0,>=0.4.0
2020-04-21T03:28:27,644         Using cached blis-0.4.1.tar.gz (1.8 MB)
2020-04-21T03:28:27,644       Collecting wasabi<1.1.0,>=0.0.9
2020-04-21T03:28:27,644         Using cached wasabi-0.6.0-py3-none-any.whl (20 kB)
2020-04-21T03:28:27,645       Collecting srsly<1.1.0,>=0.0.6
2020-04-21T03:28:27,645         Using cached srsly-1.0.2.tar.gz (192 kB)
2020-04-21T03:28:27,646       Collecting catalogue<1.1.0,>=0.0.7
2020-04-21T03:28:27,646         Using cached catalogue-1.0.0-py2.py3-none-any.whl (7.7 kB)
2020-04-21T03:28:27,646       Collecting numpy>=1.7.0
2020-04-21T03:28:27,647         Using cached numpy-1.18.3.zip (5.4 MB)
2020-04-21T03:28:27,647         Installing build dependencies: started
2020-04-21T03:28:27,648         Installing build dependencies: finished with status 'done'
2020-04-21T03:28:27,648         Getting requirements to build wheel: started
2020-04-21T03:28:27,648         Getting requirements to build wheel: finished with status 'done'
2020-04-21T03:28:27,649           Preparing wheel metadata: started
2020-04-21T03:28:27,649           Preparing wheel metadata: finished with status 'error'
2020-04-21T03:28:27,649           ERROR: Command errored out with exit status 1:
2020-04-21T03:28:27,650            command: /usr/bin/python3 /usr/local/lib/python3.7/dist-packages/pip/_vendor/pep517/_in_process.py prepare_metadata_for_build_wheel /tmp/tmpxugs8bzq
2020-04-21T03:28:27,650                cwd: /tmp/pip-install-9rp5b7rf/numpy
2020-04-21T03:28:27,651           Complete output (38 lines):
2020-04-21T03:28:27,651           Processing numpy/random/_bounded_integers.pxd.in
2020-04-21T03:28:27,651           Processing numpy/random/_bit_generator.pyx
2020-04-21T03:28:27,652           Traceback (most recent call last):
2020-04-21T03:28:27,652             File "/tmp/pip-install-9rp5b7rf/numpy/tools/cythonize.py", line 238, in <module>
2020-04-21T03:28:27,652               main()
2020-04-21T03:28:27,653             File "/tmp/pip-install-9rp5b7rf/numpy/tools/cythonize.py", line 234, in main
2020-04-21T03:28:27,653               find_process_files(root_dir)
2020-04-21T03:28:27,653             File "/tmp/pip-install-9rp5b7rf/numpy/tools/cythonize.py", line 225, in find_process_files
2020-04-21T03:28:27,654               process(root_dir, fromfile, tofile, function, hash_db)
2020-04-21T03:28:27,654             File "/tmp/pip-install-9rp5b7rf/numpy/tools/cythonize.py", line 191, in process
2020-04-21T03:28:27,655               processor_function(fromfile, tofile)
2020-04-21T03:28:27,655             File "/tmp/pip-install-9rp5b7rf/numpy/tools/cythonize.py", line 79, in process_pyx
2020-04-21T03:28:27,655               VENDOR, required_version))
2020-04-21T03:28:27,656           RuntimeError: Building NumPy requires Cython >= 0.29.14
2020-04-21T03:28:27,656           Running from numpy source directory.
2020-04-21T03:28:27,656           setup.py:461: UserWarning: Unrecognized setuptools command, proceeding with generating Cython sources and expanding templates
2020-04-21T03:28:27,657             run_build = parse_setuppy_commands()
2020-04-21T03:28:27,657           Cythonizing sources
2020-04-21T03:28:27,658           Traceback (most recent call last):
2020-04-21T03:28:27,658             File "/usr/local/lib/python3.7/dist-packages/pip/_vendor/pep517/_in_process.py", line 257, in <module>
2020-04-21T03:28:27,658               main()
2020-04-21T03:28:27,659             File "/usr/local/lib/python3.7/dist-packages/pip/_vendor/pep517/_in_process.py", line 240, in main
2020-04-21T03:28:27,659               json_out['return_val'] = hook(**hook_input['kwargs'])
2020-04-21T03:28:27,659             File "/usr/local/lib/python3.7/dist-packages/pip/_vendor/pep517/_in_process.py", line 110, in prepare_metadata_for_build_wheel
2020-04-21T03:28:27,660               return hook(metadata_directory, config_settings)
2020-04-21T03:28:27,660             File "/usr/local/lib/python3.7/dist-packages/setuptools/build_meta.py", line 158, in prepare_metadata_for_build_wheel
2020-04-21T03:28:27,661               self.run_setup()
2020-04-21T03:28:27,661             File "/usr/local/lib/python3.7/dist-packages/setuptools/build_meta.py", line 250, in run_setup
2020-04-21T03:28:27,661               self).run_setup(setup_script=setup_script)
2020-04-21T03:28:27,662             File "/usr/local/lib/python3.7/dist-packages/setuptools/build_meta.py", line 143, in run_setup
2020-04-21T03:28:27,662               exec(compile(code, __file__, 'exec'), locals())
2020-04-21T03:28:27,662             File "setup.py", line 488, in <module>
2020-04-21T03:28:27,663               setup_package()
2020-04-21T03:28:27,663             File "setup.py", line 469, in setup_package
2020-04-21T03:28:27,664               generate_cython()
2020-04-21T03:28:27,664             File "setup.py", line 275, in generate_cython
2020-04-21T03:28:27,664               raise RuntimeError("Running cythonize failed!")
2020-04-21T03:28:27,665           RuntimeError: Running cythonize failed!
2020-04-21T03:28:27,665           ----------------------------------------
2020-04-21T03:28:27,665       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/tmpxugs8bzq Check the logs for full command output.
2020-04-21T03:28:27,666       ----------------------------------------
2020-04-21T03:28:28,428     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-01dcgfns/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.
2020-04-21T03:28:28,771     Traceback (most recent call last):
2020-04-21T03:28:28,771       File "/usr/local/lib/python3.7/dist-packages/setuptools/installer.py", line 128, in fetch_build_egg
2020-04-21T03:28:28,772         subprocess.check_call(cmd)
2020-04-21T03:28:28,772       File "/usr/lib/python3.7/subprocess.py", line 347, in check_call
2020-04-21T03:28:28,773         raise CalledProcessError(retcode, cmd)
2020-04-21T03:28:28,773     subprocess.CalledProcessError: Command '['/usr/bin/python3', '-m', 'pip', '--disable-pip-version-check', 'wheel', '--no-deps', '-w', '/tmp/tmphvuticgf', '--quiet', 'spacy>=2.2.2']' returned non-zero exit status 1.

2020-04-21T03:28:28,774     During handling of the above exception, another exception occurred:

2020-04-21T03:28:28,774     Traceback (most recent call last):
2020-04-21T03:28:28,775       File "<string>", line 1, in <module>
2020-04-21T03:28:28,775       File "/tmp/pip-wheel-9g_5c92n/medspacy-io/setup.py", line 65, in <module>
2020-04-21T03:28:28,775         'tests/data/ehost_test_corpus/saved/doc2.txt.knowtator.xml'])],
2020-04-21T03:28:28,775       File "/usr/local/lib/python3.7/dist-packages/setuptools/__init__.py", line 143, in setup
2020-04-21T03:28:28,776         _install_setup_requires(attrs)
2020-04-21T03:28:28,776       File "/usr/local/lib/python3.7/dist-packages/setuptools/__init__.py", line 138, in _install_setup_requires
2020-04-21T03:28:28,777         dist.fetch_build_eggs(dist.setup_requires)
2020-04-21T03:28:28,777       File "/usr/local/lib/python3.7/dist-packages/setuptools/dist.py", line 698, in fetch_build_eggs
2020-04-21T03:28:28,777         replace_conflicting=True,
2020-04-21T03:28:28,778       File "/usr/local/lib/python3.7/dist-packages/pkg_resources/__init__.py", line 783, in resolve
2020-04-21T03:28:28,778         replace_conflicting=replace_conflicting
2020-04-21T03:28:28,778       File "/usr/local/lib/python3.7/dist-packages/pkg_resources/__init__.py", line 1066, in best_match
2020-04-21T03:28:28,779         return self.obtain(req, installer)
2020-04-21T03:28:28,779       File "/usr/local/lib/python3.7/dist-packages/pkg_resources/__init__.py", line 1078, in obtain
2020-04-21T03:28:28,779         return installer(requirement)
2020-04-21T03:28:28,780       File "/usr/local/lib/python3.7/dist-packages/setuptools/dist.py", line 754, in fetch_build_egg
2020-04-21T03:28:28,780         return fetch_build_egg(self, req)
2020-04-21T03:28:28,781       File "/usr/local/lib/python3.7/dist-packages/setuptools/installer.py", line 130, in fetch_build_egg
2020-04-21T03:28:28,781         raise DistutilsError(str(e))
2020-04-21T03:28:28,781     distutils.errors.DistutilsError: Command '['/usr/bin/python3', '-m', 'pip', '--disable-pip-version-check', 'wheel', '--no-deps', '-w', '/tmp/tmphvuticgf', '--quiet', 'spacy>=2.2.2']' returned non-zero exit status 1.
2020-04-21T03:28:28,894 Cleaning up...
2020-04-21T03:28:28,895   Removing source in /tmp/pip-wheel-9g_5c92n/medspacy-io
2020-04-21T03:28:28,931 Removed medspacy-io==0.1.0.dev0 from https://files.pythonhosted.org/packages/b2/c2/3606fa97e4eb24c928a94d2baeb5d45c52436a72073e2fa67a70bd2427b0/medspacy-io-0.1.0.dev0.tar.gz#sha256=f94d49aab324ba16fa9784f5701df291cb1fb9cbc075162898be42d1cbbe6170 from build tracker '/tmp/pip-req-tracker-jbe6_fw9'
2020-04-21T03:28:28,932 Removed build tracker: '/tmp/pip-req-tracker-jbe6_fw9'
2020-04-21T03:28:28,936 ERROR: Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.
2020-04-21T03:28:28,937 Exception information:
2020-04-21T03:28:28,937 Traceback (most recent call last):
2020-04-21T03:28:28,937   File "/usr/local/lib/python3.7/dist-packages/pip/_internal/cli/base_command.py", line 186, in _main
2020-04-21T03:28:28,937     status = self.run(options, args)
2020-04-21T03:28:28,937   File "/usr/local/lib/python3.7/dist-packages/pip/_internal/commands/wheel.py", line 161, in run
2020-04-21T03:28:28,937     resolver.resolve(requirement_set)
2020-04-21T03:28:28,937   File "/usr/local/lib/python3.7/dist-packages/pip/_internal/legacy_resolve.py", line 177, in resolve
2020-04-21T03:28:28,937     discovered_reqs.extend(self._resolve_one(requirement_set, req))
2020-04-21T03:28:28,937   File "/usr/local/lib/python3.7/dist-packages/pip/_internal/legacy_resolve.py", line 333, in _resolve_one
2020-04-21T03:28:28,937     abstract_dist = self._get_abstract_dist_for(req_to_install)
2020-04-21T03:28:28,937   File "/usr/local/lib/python3.7/dist-packages/pip/_internal/legacy_resolve.py", line 282, in _get_abstract_dist_for
2020-04-21T03:28:28,937     abstract_dist = self.preparer.prepare_linked_requirement(req)
2020-04-21T03:28:28,937   File "/usr/local/lib/python3.7/dist-packages/pip/_internal/operations/prepare.py", line 516, in prepare_linked_requirement
2020-04-21T03:28:28,937     req, self.req_tracker, self.finder, self.build_isolation,
2020-04-21T03:28:28,937   File "/usr/local/lib/python3.7/dist-packages/pip/_internal/operations/prepare.py", line 95, in _get_prepared_distribution
2020-04-21T03:28:28,937     abstract_dist.prepare_distribution_metadata(finder, build_isolation)
2020-04-21T03:28:28,937   File "/usr/local/lib/python3.7/dist-packages/pip/_internal/distributions/sdist.py", line 40, in prepare_distribution_metadata
2020-04-21T03:28:28,937     self.req.prepare_metadata()
2020-04-21T03:28:28,937   File "/usr/local/lib/python3.7/dist-packages/pip/_internal/req/req_install.py", line 564, in prepare_metadata
2020-04-21T03:28:28,937     self.metadata_directory = self._generate_metadata()
2020-04-21T03:28:28,937   File "/usr/local/lib/python3.7/dist-packages/pip/_internal/req/req_install.py", line 544, in _generate_metadata
2020-04-21T03:28:28,937     details=self.name or "from {}".format(self.link)
2020-04-21T03:28:28,937   File "/usr/local/lib/python3.7/dist-packages/pip/_internal/operations/build/metadata_legacy.py", line 118, in generate_metadata
2020-04-21T03:28:28,937     command_desc='python setup.py egg_info',
2020-04-21T03:28:28,937   File "/usr/local/lib/python3.7/dist-packages/pip/_internal/utils/subprocess.py", line 242, in call_subprocess
2020-04-21T03:28:28,937     raise InstallationError(exc_msg)
2020-04-21T03:28:28,937 pip._internal.exceptions.InstallationError: Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.