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ga4gh / cloud-interop-testing

Interoperable execution of workflows using GA4GH APIs
Apache License 2.0
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testbed_server failes to launch from develop@0da1136 #80

Closed pr80ik closed 5 years ago

pr80ik commented 5 years ago

Steps

  1. create a new virtual environment & activate
  2. checkout latest develop (0da1136)
  3. build pip install -r requirements.txt . && pip install --no-deps -r dev-requirements.txt
  4. run testbed_server

Additional info:

$ python --version
Python 3.6.5

$ python2 --version
Python 2.7.16

$ python3 --version
Python 3.6.5

$ pip --version
pip 19.2.3 from /work/ilmn/git/_other/cloud-interop-testing/venv/lib/python3.6/site-packages/pip (python 3.6)

$ pip3 --version
pip 19.2.3 from /work/ilmn/git/_other/cloud-interop-testing/venv/lib/python3.6/site-packages/pip (python 3.6)

Expected:

Actual:

$ testbed_server
ERROR:connexion.apis.abstract:Failed to add operation for POST /ga4gh/testbed/v1/tests
Traceback (most recent call last):
  File "/projects/cloud-interop-testing/venv/lib/python3.6/site-packages/connexion/apis/abstract.py", line 205, in add_paths
    self.add_operation(path, method)
  File "/projects/cloud-interop-testing/venv/lib/python3.6/site-packages/connexion/apis/abstract.py", line 169, in add_operation
    pass_context_arg_name=self.pass_context_arg_name
  File "/projects/cloud-interop-testing/venv/lib/python3.6/site-packages/connexion/operations/__init__.py", line 8, in make_operation
    return spec.operation_cls.from_spec(spec, *args, **kwargs)
  File "/projects/cloud-interop-testing/venv/lib/python3.6/site-packages/connexion/operations/openapi.py", line 138, in from_spec
    **kwargs
  File "/projects/cloud-interop-testing/venv/lib/python3.6/site-packages/connexion/operations/openapi.py", line 89, in __init__
    pass_context_arg_name=pass_context_arg_name
  File "/projects/cloud-interop-testing/venv/lib/python3.6/site-packages/connexion/operations/abstract.py", line 99, in __init__
    self._resolution = resolver.resolve(self)
  File "/projects/cloud-interop-testing/venv/lib/python3.6/site-packages/connexion/resolver.py", line 40, in resolve
    return Resolution(self.resolve_function_from_operation_id(operation_id), operation_id)
  File "/projects/cloud-interop-testing/venv/lib/python3.6/site-packages/connexion/resolver.py", line 64, in resolve_function_from_operation_id
    raise ResolverError(msg, sys.exc_info())
connexion.exceptions.ResolverError: <ResolverError: Cannot resolve operationId "ga4ghtest.controllers.tests_controller.create_test"! Import error was "No module named 'ga4ghtest.controllers'">

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/projects/cloud-interop-testing/venv/bin/testbed_server", line 10, in <module>
    sys.exit(main())
  File "/projects/cloud-interop-testing/venv/lib/python3.6/site-packages/ga4ghtest/__main__.py", line 16, in main
    app = create_app()
  File "/projects/cloud-interop-testing/venv/lib/python3.6/site-packages/ga4ghtest/__init__.py", line 15, in create_app
    app.add_api('openapi.yaml', arguments={'title': 'Provenance Service'})
  File "/projects/cloud-interop-testing/venv/lib/python3.6/site-packages/connexion/apps/flask_app.py", line 54, in add_api
    api = super(FlaskApp, self).add_api(specification, **kwargs)
  File "/projects/cloud-interop-testing/venv/lib/python3.6/site-packages/connexion/apps/abstract.py", line 155, in add_api
    options=api_options.as_dict())
  File "/projects/cloud-interop-testing/venv/lib/python3.6/site-packages/connexion/apis/abstract.py", line 107, in __init__
    self.add_paths()
  File "/projects/cloud-interop-testing/venv/lib/python3.6/site-packages/connexion/apis/abstract.py", line 212, in add_paths
    self._handle_add_operation_error(path, method, err.exc_info)
  File "/projects/cloud-interop-testing/venv/lib/python3.6/site-packages/connexion/apis/abstract.py", line 226, in _handle_add_operation_error
    six.reraise(*exc_info)
  File "/projects/cloud-interop-testing/venv/lib/python3.6/site-packages/six.py", line 693, in reraise
    raise value
  File "/projects/cloud-interop-testing/venv/lib/python3.6/site-packages/connexion/resolver.py", line 61, in resolve_function_from_operation_id
    return self.function_resolver(operation_id)
  File "/projects/cloud-interop-testing/venv/lib/python3.6/site-packages/connexion/utils.py", line 99, in get_function_from_name
    raise last_import_error
  File "/projects/cloud-interop-testing/venv/lib/python3.6/site-packages/connexion/utils.py", line 87, in get_function_from_name
    module = importlib.import_module(module_name)
  File "/projects/cloud-interop-testing/venv/lib/python3.6/importlib/__init__.py", line 126, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
  File "<frozen importlib._bootstrap>", line 994, in _gcd_import
  File "<frozen importlib._bootstrap>", line 971, in _find_and_load
  File "<frozen importlib._bootstrap>", line 953, in _find_and_load_unlocked
ModuleNotFoundError: No module named 'ga4ghtest.controllers'
pr80ik commented 5 years ago

The docker build command also fails as follows


$ docker build -t ga4ghtest .
Sending build context to Docker daemon  1.933MB
Step 1/9 : FROM python:3-alpine
 ---> 39fb80313465
Step 2/9 : RUN mkdir -p /usr/src/app
 ---> Using cache
 ---> 7eb13da5335d
Step 3/9 : WORKDIR /usr/src/app
 ---> Using cache
 ---> 4124ba8d331f
Step 4/9 : COPY requirements.txt /usr/src/app/
 ---> Using cache
 ---> 73f001b429b4
Step 5/9 : RUN pip3 install --no-cache-dir -r requirements.txt
 ---> Running in fd8fda6f1cf0
Collecting connexion==2.0.2 (from -r requirements.txt (line 1))
  Downloading https://files.pythonhosted.org/packages/78/46/7a53cd1771e098d7d6b707a5667d93c8ce6028fe0a4544739eebe9b91303/connexion-2.0.2-py2.py3-none-any.whl (1.0MB)
Collecting flask_cors>=3.0.0 (from -r requirements.txt (line 2))
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Requirement already satisfied: setuptools>=21.0.0 in /usr/local/lib/python3.7/site-packages (from -r requirements.txt (line 4)) (41.2.0)
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Collecting imagesize (from sphinx==1.7.5->toil[wdl]->-r requirements.txt (line 14))
  Downloading https://files.pythonhosted.org/packages/fc/b6/aef66b4c52a6ad6ac18cf6ebc5731ed06d8c9ae4d3b2d9951f261150be67/imagesize-1.1.0-py2.py3-none-any.whl
Collecting sphinxcontrib-websupport (from sphinx==1.7.5->toil[wdl]->-r requirements.txt (line 14))
  Downloading https://files.pythonhosted.org/packages/2a/59/d64bda9b7480a84a3569be4dde267c0f6675b255ba63b4c8e84469940457/sphinxcontrib_websupport-1.1.2-py2.py3-none-any.whl
Collecting Pygments>=2.0 (from sphinx==1.7.5->toil[wdl]->-r requirements.txt (line 14))
  Downloading https://files.pythonhosted.org/packages/5c/73/1dfa428150e3ccb0fa3e68db406e5be48698f2a979ccbcec795f28f44048/Pygments-2.4.2-py2.py3-none-any.whl (883kB)
Collecting packaging (from sphinx==1.7.5->toil[wdl]->-r requirements.txt (line 14))
  Downloading https://files.pythonhosted.org/packages/cf/94/9672c2d4b126e74c4496c6b3c58a8b51d6419267be9e70660ba23374c875/packaging-19.2-py2.py3-none-any.whl
Collecting docutils>=0.11 (from sphinx==1.7.5->toil[wdl]->-r requirements.txt (line 14))
  Downloading https://files.pythonhosted.org/packages/22/cd/a6aa959dca619918ccb55023b4cb151949c64d4d5d55b3f4ffd7eee0c6e8/docutils-0.15.2-py3-none-any.whl (547kB)
Collecting snowballstemmer>=1.1 (from sphinx==1.7.5->toil[wdl]->-r requirements.txt (line 14))
  Downloading https://files.pythonhosted.org/packages/51/16/86a280d59b3bb439e7103ea1a275a191e3d2df8a3543cda0708f7cb4333c/snowballstemmer-1.9.1.tar.gz (82kB)
Collecting babel!=2.0,>=1.3 (from sphinx==1.7.5->toil[wdl]->-r requirements.txt (line 14))
  Downloading https://files.pythonhosted.org/packages/2c/60/f2af68eb046c5de5b1fe6dd4743bf42c074f7141fe7b2737d3061533b093/Babel-2.7.0-py2.py3-none-any.whl (8.4MB)
Building wheels for collected packages: healthcheck, subprocess32, future, toil, strict-rfc3339, PyYAML, inflection, simplejson, msgpack-python, CacheControl, rdflib-jsonld, dill, psutil, addict, MarkupSafe, ruamel.yaml.clib, snowballstemmer
  Building wheel for healthcheck (setup.py): started
  Building wheel for healthcheck (setup.py): finished with status 'done'
  Created wheel for healthcheck: filename=healthcheck-1.3.3-cp37-none-any.whl size=4338 sha256=d4789ac2c796eaf7b58ce6340abbe7d716107e8df3318338a01239a46b45f9be
  Stored in directory: /tmp/pip-ephem-wheel-cache-m447vrwc/wheels/77/92/d6/78b7fa71216256aa09989d8a4dd82f3b0b23ad98b627439b9f
  Building wheel for subprocess32 (setup.py): started
  Building wheel for subprocess32 (setup.py): finished with status 'done'
  Created wheel for subprocess32: filename=subprocess32-3.5.4-cp37-none-any.whl size=6490 sha256=28cb149dbcdef67cf4f65237330239b16cf9656bfabdbe50ec3ffd01aead3b54
  Stored in directory: /tmp/pip-ephem-wheel-cache-m447vrwc/wheels/68/39/1a/5e402bdfdf004af1786c8b853fd92f8c4a04f22aad179654d1
  Building wheel for future (setup.py): started
  Building wheel for future (setup.py): finished with status 'done'
  Created wheel for future: filename=future-0.17.1-cp37-none-any.whl size=488730 sha256=9f249081f3d491e2bd558453accb27400db4ba162ff9e426cfc9af44b242435d
  Stored in directory: /tmp/pip-ephem-wheel-cache-m447vrwc/wheels/0c/61/d2/d6b7317325828fbb39ee6ad559dbe4664d0896da4721bf379e
  Building wheel for toil (setup.py): started
  Building wheel for toil (setup.py): finished with status 'done'
  Created wheel for toil: filename=toil-3.20.0-cp37-none-any.whl size=432652 sha256=950ea3a72f5f6368810ff429abbb5ae53322d3536112d856ea0254fe024aed86
  Stored in directory: /tmp/pip-ephem-wheel-cache-m447vrwc/wheels/ee/bb/a6/90fe39d300690bfeceb239790ea6891aae2e8a6952519ea2dd
  Building wheel for strict-rfc3339 (setup.py): started
  Building wheel for strict-rfc3339 (setup.py): finished with status 'done'
  Created wheel for strict-rfc3339: filename=strict_rfc3339-0.7-cp37-none-any.whl size=18120 sha256=dfd636a89e7ceed1849ed4ced1c60970ee6fb26b41fdf9c1335deb0dad4d9d03
  Stored in directory: /tmp/pip-ephem-wheel-cache-m447vrwc/wheels/bb/af/c9/b6e9fb5f9b2470e4ed2a7241c9ab3a8cdd3bc8555ae02ca2e6
  Building wheel for PyYAML (setup.py): started
  Building wheel for PyYAML (setup.py): finished with status 'done'
  Created wheel for PyYAML: filename=PyYAML-5.1.2-cp37-cp37m-linux_x86_64.whl size=44103 sha256=33ab973a291dc69dd33f5e6b366200712afaaea3b39cd4c760b1ae56059e7808
  Stored in directory: /tmp/pip-ephem-wheel-cache-m447vrwc/wheels/d9/45/dd/65f0b38450c47cf7e5312883deb97d065e030c5cca0a365030
  Building wheel for inflection (setup.py): started
  Building wheel for inflection (setup.py): finished with status 'done'
  Created wheel for inflection: filename=inflection-0.3.1-cp37-none-any.whl size=6075 sha256=1e7ff14f61de1af8d68a2a9130f4add08cdb9aab2328bbfb3878f0f3dad19867
  Stored in directory: /tmp/pip-ephem-wheel-cache-m447vrwc/wheels/9f/5a/d3/6fc3bf6516d2a3eb7e18f9f28b472110b59325f3f258fe9211
  Building wheel for simplejson (setup.py): started
  Building wheel for simplejson (setup.py): finished with status 'done'
  Created wheel for simplejson: filename=simplejson-3.16.0-cp37-none-any.whl size=55274 sha256=fbac2b87282a5fb834401a4f9ad3475edfbb7e0483bee75a278dc6b3f05bea17
  Stored in directory: /tmp/pip-ephem-wheel-cache-m447vrwc/wheels/5d/1a/1e/0350bb3df3e74215cd91325344cc86c2c691f5306eb4d22c77
  Building wheel for msgpack-python (setup.py): started
  Building wheel for msgpack-python (setup.py): finished with status 'done'
  Created wheel for msgpack-python: filename=msgpack_python-0.5.6-cp37-cp37m-linux_x86_64.whl size=10405 sha256=0155f6010e6e7c0d07b5579d3e6da2653176f8eaac8dea16913f3832be3ab69d
  Stored in directory: /tmp/pip-ephem-wheel-cache-m447vrwc/wheels/d5/de/86/7fa56fda12511be47ea0808f3502bc879df4e63ab168ec0406
  Building wheel for CacheControl (setup.py): started
  Building wheel for CacheControl (setup.py): finished with status 'done'
  Created wheel for CacheControl: filename=CacheControl-0.11.7-cp37-none-any.whl size=18087 sha256=728b95a5bb9d6d4e56cee64da4e5bf89fec55a8ca80a6b954b8d4666be4275e9
  Stored in directory: /tmp/pip-ephem-wheel-cache-m447vrwc/wheels/66/46/36/bc94397c815ad29e5c41ffa5b870d666b1f2ab68b54135c007
  Building wheel for rdflib-jsonld (setup.py): started
  Building wheel for rdflib-jsonld (setup.py): finished with status 'done'
  Created wheel for rdflib-jsonld: filename=rdflib_jsonld-0.4.0-cp37-none-any.whl size=14076 sha256=754bcae7bbad70c17e058d35dd0f9d13635ca89b6edc63376555f332180dc486
  Stored in directory: /tmp/pip-ephem-wheel-cache-m447vrwc/wheels/9f/31/d2/ac7f9fea93b5440274e5c67336e35f1c0f9d38e49c71e35b6d
  Building wheel for dill (setup.py): started
  Building wheel for dill (setup.py): finished with status 'done'
  Created wheel for dill: filename=dill-0.2.7.1-cp37-none-any.whl size=54543 sha256=e47b4c1e577fadc38ec340c8cddfdab0e404ad5db319d83a6d397b5686ef51fa
  Stored in directory: /tmp/pip-ephem-wheel-cache-m447vrwc/wheels/99/c4/ed/1b64d2d5809e60d5a3685530432f6159d6a9959739facb61f2
  Building wheel for psutil (setup.py): started
  Building wheel for psutil (setup.py): finished with status 'error'
  ERROR: Command errored out with exit status 1:
   command: /usr/local/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-i6i4535d/psutil/setup.py'"'"'; __file__='"'"'/tmp/pip-install-i6i4535d/psutil/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-v98wqrgi --python-tag cp37
       cwd: /tmp/pip-install-i6i4535d/psutil/
  Complete output (22 lines):
  running bdist_wheel
  running build
  running build_py
  creating build
  creating build/lib.linux-x86_64-3.7
  creating build/lib.linux-x86_64-3.7/psutil
  copying psutil/_pswindows.py -> build/lib.linux-x86_64-3.7/psutil
  copying psutil/__init__.py -> build/lib.linux-x86_64-3.7/psutil
  copying psutil/_pslinux.py -> build/lib.linux-x86_64-3.7/psutil
  copying psutil/_psposix.py -> build/lib.linux-x86_64-3.7/psutil
  copying psutil/_common.py -> build/lib.linux-x86_64-3.7/psutil
  copying psutil/_pssunos.py -> build/lib.linux-x86_64-3.7/psutil
  copying psutil/_psosx.py -> build/lib.linux-x86_64-3.7/psutil
  copying psutil/_compat.py -> build/lib.linux-x86_64-3.7/psutil
  copying psutil/_psbsd.py -> build/lib.linux-x86_64-3.7/psutil
  running build_ext
  building 'psutil._psutil_linux' extension
  creating build/temp.linux-x86_64-3.7
  creating build/temp.linux-x86_64-3.7/psutil
  gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -DTHREAD_STACK_SIZE=0x100000 -fPIC -DPSUTIL_VERSION=301 -I/usr/local/include/python3.7m -c psutil/_psutil_linux.c -o build/temp.linux-x86_64-3.7/psutil/_psutil_linux.o
  unable to execute 'gcc': No such file or directory
  error: command 'gcc' failed with exit status 1
  ----------------------------------------
  ERROR: Failed building wheel for psutil
  Running setup.py clean for psutil
  Building wheel for addict (setup.py): started
  Building wheel for addict (setup.py): finished with status 'done'
  Created wheel for addict: filename=addict-2.2.0-cp37-none-any.whl size=2782 sha256=9fae1070541f68ba53b1beabfc071b03af3d9fcbe90c0b9ab07cefdd532e1ac6
  Stored in directory: /tmp/pip-ephem-wheel-cache-m447vrwc/wheels/1c/35/37/7a99ee58a72dc257689fb4f99c8018c9513555055e3fb87123
  Building wheel for MarkupSafe (setup.py): started
  Building wheel for MarkupSafe (setup.py): finished with status 'done'
  Created wheel for MarkupSafe: filename=MarkupSafe-1.1.1-cp37-none-any.whl size=12629 sha256=b324f2085d8b64cec3287eb4611324fc807a6c0ef2ca20b3acdb3b02b8a29ce4
  Stored in directory: /tmp/pip-ephem-wheel-cache-m447vrwc/wheels/f2/aa/04/0edf07a1b8a5f5f1aed7580fffb69ce8972edc16a505916a77
  Building wheel for ruamel.yaml.clib (setup.py): started
  Building wheel for ruamel.yaml.clib (setup.py): finished with status 'done'
  Created wheel for ruamel.yaml.clib: filename=ruamel.yaml.clib-0.1.2-cp37-none-any.whl size=2898 sha256=928def96778dc5dfc53ca294165af65c341127c10de52d04cb068c608fdc561e
  Stored in directory: /tmp/pip-ephem-wheel-cache-m447vrwc/wheels/28/88/2a/70c4579e647724d98a52b856110558d37e66054af6de5f1795
  Building wheel for snowballstemmer (setup.py): started
  Building wheel for snowballstemmer (setup.py): finished with status 'done'
  Created wheel for snowballstemmer: filename=snowballstemmer-1.9.1-cp37-none-any.whl size=101576 sha256=b09260e8e96f25410bdbe6a1e6ba0d3175fb2792a1c6201423d79f94cbd027c3
  Stored in directory: /tmp/pip-ephem-wheel-cache-m447vrwc/wheels/ae/9b/66/6b8f275ec6dfa2138a56faaf2b4314ca44a4746286560d5578
Successfully built healthcheck subprocess32 future toil strict-rfc3339 PyYAML inflection simplejson msgpack-python CacheControl rdflib-jsonld dill addict MarkupSafe ruamel.yaml.clib snowballstemmer
Failed to build psutil
Installing collected packages: jsonschema, PyYAML, six, Werkzeug, click, MarkupSafe, Jinja2, itsdangerous, flask, inflection, openapi-spec-validator, clickclick, idna, chardet, urllib3, certifi, requests, connexion, flask-cors, swagger-ui-bundle, python-dateutil, healthcheck, subprocess32, future, monotonic, jsonref, pytz, simplejson, swagger-spec-validator, msgpack-python, bravado-core, typing-extensions, bravado, CacheControl, ruamel.yaml.clib, ruamel.yaml, lockfile, mistune, pyparsing, isodate, rdflib, rdflib-jsonld, schema-salad, dill, docker-pycreds, websocket-client, docker, psutil, addict, alabaster, imagesize, sphinxcontrib-websupport, Pygments, packaging, docutils, snowballstemmer, babel, sphinx, pathlib2, toil, rfc3987, webcolors, strict-rfc3339
  Running setup.py install for psutil: started
    Running setup.py install for psutil: finished with status 'error'
    ERROR: Command errored out with exit status 1:
     command: /usr/local/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-i6i4535d/psutil/setup.py'"'"'; __file__='"'"'/tmp/pip-install-i6i4535d/psutil/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-67ree8og/install-record.txt --single-version-externally-managed --compile
         cwd: /tmp/pip-install-i6i4535d/psutil/
    Complete output (22 lines):
    running install
    running build
    running build_py
    creating build
    creating build/lib.linux-x86_64-3.7
    creating build/lib.linux-x86_64-3.7/psutil
    copying psutil/_pswindows.py -> build/lib.linux-x86_64-3.7/psutil
    copying psutil/__init__.py -> build/lib.linux-x86_64-3.7/psutil
    copying psutil/_pslinux.py -> build/lib.linux-x86_64-3.7/psutil
    copying psutil/_psposix.py -> build/lib.linux-x86_64-3.7/psutil
    copying psutil/_common.py -> build/lib.linux-x86_64-3.7/psutil
    copying psutil/_pssunos.py -> build/lib.linux-x86_64-3.7/psutil
    copying psutil/_psosx.py -> build/lib.linux-x86_64-3.7/psutil
    copying psutil/_compat.py -> build/lib.linux-x86_64-3.7/psutil
    copying psutil/_psbsd.py -> build/lib.linux-x86_64-3.7/psutil
    running build_ext
    building 'psutil._psutil_linux' extension
    creating build/temp.linux-x86_64-3.7
    creating build/temp.linux-x86_64-3.7/psutil
    gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -DTHREAD_STACK_SIZE=0x100000 -fPIC -DPSUTIL_VERSION=301 -I/usr/local/include/python3.7m -c psutil/_psutil_linux.c -o build/temp.linux-x86_64-3.7/psutil/_psutil_linux.o
    unable to execute 'gcc': No such file or directory
    error: command 'gcc' failed with exit status 1
    ----------------------------------------
ERROR: Command errored out with exit status 1: /usr/local/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-i6i4535d/psutil/setup.py'"'"'; __file__='"'"'/tmp/pip-install-i6i4535d/psutil/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-67ree8og/install-record.txt --single-version-externally-managed --compile Check the logs for full command output.
The command '/bin/sh -c pip3 install --no-cache-dir -r requirements.txt' returned a non-zero code: 1
pr80ik commented 5 years ago

works with d0af956