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theislab / single-cell-tutorial

Single cell current best practices tutorial case study for the paper:Luecken and Theis, "Current best practices in single-cell RNA-seq analysis: a tutorial"
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environment installation problem #110

Open Sunyp-IM opened 1 year ago

Sunyp-IM commented 1 year ago

Hello,

I am trying to install the environment by

conda env create -f sc_tutorial_environment.yml

but get the following error:

Pip subprocess error:
  Running command git clone -q https://github.com/flying-sheep/anndata2ri /tmp/pip-req-build-_sxdlckc
  ERROR: Command errored out with exit status 1:
   command: /PHShome/ys738/tutorial/single-cell-tutorial/test/env/bin/python -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-o92j89t3/rpy2_1bf8d8eb188d4e75931a32c7ea456056/setup.py'"'"'; __file__='"'"'/tmp/pip-install-o92j89t3/rpy2_1bf8d8eb188d4e75931a32c7ea456056/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /tmp/pip-pip-egg-info-46eoz0zx
       cwd: /tmp/pip-install-o92j89t3/rpy2_1bf8d8eb188d4e75931a32c7ea456056/
  Complete output (1 lines):
  rpy2 is no longer supporting Python < 3.7.Consider using an older rpy2 release when using an older Python release.
  ----------------------------------------
WARNING: Discarding https://files.pythonhosted.org/packages/a9/11/5f175fc3d2313b53cb3c921db9e8bba58b67d739f5a637146b45f2e0e80c/rpy2-3.5.5.tar.gz#sha256=a252c40e21cf4f23ac6e13bffdcb82b5900b49c3043ed8fd31da5c61fb58d037 (from https://pypi.org/simple/rpy2/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.
  ERROR: Command errored out with exit status 1:
   command: /PHShome/ys738/tutorial/single-cell-tutorial/test/env/bin/python -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-o92j89t3/rpy2_0de3b36ef510453fbd549602b7f057d5/setup.py'"'"'; __file__='"'"'/tmp/pip-install-o92j89t3/rpy2_0de3b36ef510453fbd549602b7f057d5/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /tmp/pip-pip-egg-info-za7i_5lx
       cwd: /tmp/pip-install-o92j89t3/rpy2_0de3b36ef510453fbd549602b7f057d5/
  Complete output (1 lines):
  rpy2 is no longer supporting Python < 3.7.Consider using an older rpy2 release when using an older Python release.
  ----------------------------------------
WARNING: Discarding https://files.pythonhosted.org/packages/40/09/a754484c80f8c58f077b1b9b2249787c689c8dd1559e3eb91cd5b8690dc2/rpy2-3.5.4.tar.gz#sha256=ba0a877b2b96e27d2091383d4652b82aa2271cff4a505243d45da430b712aaf5 (from https://pypi.org/simple/rpy2/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.
  ERROR: Command errored out with exit status 1:
   command: /PHShome/ys738/tutorial/single-cell-tutorial/test/env/bin/python -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-o92j89t3/rpy2_4baddf3e0e7b4f5a8be15c4fcb6ce495/setup.py'"'"'; __file__='"'"'/tmp/pip-install-o92j89t3/rpy2_4baddf3e0e7b4f5a8be15c4fcb6ce495/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /tmp/pip-pip-egg-info-ruvwrq4l
       cwd: /tmp/pip-install-o92j89t3/rpy2_4baddf3e0e7b4f5a8be15c4fcb6ce495/
  Complete output (1 lines):
  rpy2 is no longer supporting Python < 3.7.Consider using an older rpy2 release when using an older Python release.
  ----------------------------------------
WARNING: Discarding https://files.pythonhosted.org/packages/9b/5d/44d001cb386d009e228afbc9327ee07dc9ade108a908dc84a6801c093255/rpy2-3.5.3.tar.gz#sha256=53a092d48b44f46428fb30cb3155664d6d2f7af08ebc4c45df98df4c45a42ccb (from https://pypi.org/simple/rpy2/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.
  ERROR: Command errored out with exit status 1:
   command: /PHShome/ys738/tutorial/single-cell-tutorial/test/env/bin/python -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-o92j89t3/rpy2_5e14da6ada314beb8b0debfce30760ed/setup.py'"'"'; __file__='"'"'/tmp/pip-install-o92j89t3/rpy2_5e14da6ada314beb8b0debfce30760ed/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /tmp/pip-pip-egg-info-7z8170o7
       cwd: /tmp/pip-install-o92j89t3/rpy2_5e14da6ada314beb8b0debfce30760ed/
  Complete output (1 lines):
  rpy2 is no longer supporting Python < 3.7.Consider using an older rpy2 release when using an older Python release.
  ----------------------------------------
WARNING: Discarding https://files.pythonhosted.org/packages/ee/2f/392c6fd5fad3cd6f2eda24855e6b53d0b61246da105a77b55acd66c3bddd/rpy2-3.5.2.tar.gz#sha256=45ee00fdbad0b481c39369fb315651ddf854cf4ad56d24b7dcb3c74e135bd10e (from https://pypi.org/simple/rpy2/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.
  ERROR: Command errored out with exit status 1:
   command: /PHShome/ys738/tutorial/single-cell-tutorial/test/env/bin/python -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-o92j89t3/rpy2_eccbf35ec2224834a4bef7354fc7f001/setup.py'"'"'; __file__='"'"'/tmp/pip-install-o92j89t3/rpy2_eccbf35ec2224834a4bef7354fc7f001/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /tmp/pip-pip-egg-info-dtd_7sou
       cwd: /tmp/pip-install-o92j89t3/rpy2_eccbf35ec2224834a4bef7354fc7f001/
  Complete output (1 lines):
  rpy2 is no longer supporting Python < 3.7.Consider using an older rpy2 release when using an older Python release.
  ----------------------------------------
WARNING: Discarding https://files.pythonhosted.org/packages/82/3b/7258fa09eff9bb64ea09a8a8220a1f845561f0b8af76306924fbe58a2009/rpy2-3.5.1.tar.gz#sha256=d35717489bd0754b556202a6b990ebc6f3a1c18c9c23b3a862a46a91fc265805 (from https://pypi.org/simple/rpy2/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.
  ERROR: Command errored out with exit status 1:
   command: /PHShome/ys738/tutorial/single-cell-tutorial/test/env/bin/python -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-o92j89t3/rpy2_9a14ebcf66f5471e8bc439ba2dc729d1/setup.py'"'"'; __file__='"'"'/tmp/pip-install-o92j89t3/rpy2_9a14ebcf66f5471e8bc439ba2dc729d1/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /tmp/pip-pip-egg-info-apcl_bp6
       cwd: /tmp/pip-install-o92j89t3/rpy2_9a14ebcf66f5471e8bc439ba2dc729d1/
  Complete output (1 lines):
  rpy2 is no longer supporting Python < 3.7.Consider using an older rpy2 release when using an older Python release.
  ----------------------------------------
WARNING: Discarding https://files.pythonhosted.org/packages/a8/e5/e532f7189d852dfefb4f9fe4baa0ac53f180538ac8acec8d30c4be5887c1/rpy2-3.5.0.tar.gz#sha256=4d8a20253320ae3e402ec20d56640772bdc27731bd14f7d0475a95d86e7cd1c7 (from https://pypi.org/simple/rpy2/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.
  ERROR: Command errored out with exit status 1:
   command: /PHShome/ys738/tutorial/single-cell-tutorial/test/env/bin/python -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-o92j89t3/scanpy_3fd33314094b4ee88ccdf68c7f622a7a/setup.py'"'"'; __file__='"'"'/tmp/pip-install-o92j89t3/scanpy_3fd33314094b4ee88ccdf68c7f622a7a/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /tmp/pip-pip-egg-info-dogw0wzm
       cwd: /tmp/pip-install-o92j89t3/scanpy_3fd33314094b4ee88ccdf68c7f622a7a/
  Complete output (1 lines):
  error in scanpy setup command: "values of 'package_data' dict" must be a list of strings (got '*.txt')
  ----------------------------------------
WARNING: Discarding https://files.pythonhosted.org/packages/75/13/76f3fa526a5e39ee26752c6e78fca509821c57699999e68086094a6ff9cb/scanpy-1.3.6.tar.gz#sha256=ebc7cd0a9726a4a9088a8d0eafb8eb59802f8acb85bc28a2bdf8dbf0144f87c8 (from https://pypi.org/simple/scanpy/) (requires-python:>=3.5). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.
  ERROR: Command errored out with exit status 1:
   command: /PHShome/ys738/tutorial/single-cell-tutorial/test/env/bin/python -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-o92j89t3/scanpy_1a06cb60eacf41da9f18ddbbef3593b9/setup.py'"'"'; __file__='"'"'/tmp/pip-install-o92j89t3/scanpy_1a06cb60eacf41da9f18ddbbef3593b9/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /tmp/pip-pip-egg-info-7yuxe4rl
       cwd: /tmp/pip-install-o92j89t3/scanpy_1a06cb60eacf41da9f18ddbbef3593b9/
  Complete output (1 lines):
  error in scanpy setup command: "values of 'package_data' dict" must be a list of strings (got '*.txt')
  ----------------------------------------
WARNING: Discarding https://files.pythonhosted.org/packages/f6/1a/83abbd428fbd060b041aa5ccf884a3cbba3c7e21342f5c76107386cc6025/scanpy-1.3.5.tar.gz#sha256=22ec896d232c1586fab8bd5a989c0a1251b840f87a67e466a0d784b3b10d0782 (from https://pypi.org/simple/scanpy/) (requires-python:>=3.5). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.
  ERROR: Command errored out with exit status 1:
   command: /PHShome/ys738/tutorial/single-cell-tutorial/test/env/bin/python -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-o92j89t3/scanpy_1fb24f41c22e4c0ab63a7d6a11b5b63c/setup.py'"'"'; __file__='"'"'/tmp/pip-install-o92j89t3/scanpy_1fb24f41c22e4c0ab63a7d6a11b5b63c/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /tmp/pip-pip-egg-info-imxrfwme
       cwd: /tmp/pip-install-o92j89t3/scanpy_1fb24f41c22e4c0ab63a7d6a11b5b63c/
  Complete output (1 lines):
  error in scanpy setup command: "values of 'package_data' dict" must be a list of strings (got '*.txt')
  ----------------------------------------
WARNING: Discarding https://files.pythonhosted.org/packages/47/a2/3edd61806453cccad8828fc74b0d9377cf419abc14b737ed57187e446460/scanpy-1.3.4.tar.gz#sha256=fd1be48c00919ce72e67635a8d31e039d618865bc1456d72abf42570bcd760d6 (from https://pypi.org/simple/scanpy/) (requires-python:>=3.5). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.
  ERROR: Command errored out with exit status 1:
   command: /PHShome/ys738/tutorial/single-cell-tutorial/test/env/bin/python -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-o92j89t3/scanpy_4aff80b97095477b963148ff34c0e2ea/setup.py'"'"'; __file__='"'"'/tmp/pip-install-o92j89t3/scanpy_4aff80b97095477b963148ff34c0e2ea/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /tmp/pip-pip-egg-info-3x6f6xm0
       cwd: /tmp/pip-install-o92j89t3/scanpy_4aff80b97095477b963148ff34c0e2ea/
  Complete output (1 lines):
  error in scanpy setup command: "values of 'package_data' dict" must be a list of strings (got '*.txt')
  ----------------------------------------
WARNING: Discarding https://files.pythonhosted.org/packages/c0/f6/b247ffd1c4f776c4b5b3ee32ffc990a0aee09cf6197002ad3e31a8e0fbad/scanpy-1.3.2.tar.gz#sha256=0dd11ebb2098636fadbc7d3d355e206ffedcdd1d70c3fc85ac9cb95e0e398a5e (from https://pypi.org/simple/scanpy/) (requires-python:>=3.5). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.
  ERROR: Command errored out with exit status 1:
   command: /PHShome/ys738/tutorial/single-cell-tutorial/test/env/bin/python -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-o92j89t3/scanpy_f8269e7304db43c8a3c2bdff41aed4ac/setup.py'"'"'; __file__='"'"'/tmp/pip-install-o92j89t3/scanpy_f8269e7304db43c8a3c2bdff41aed4ac/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /tmp/pip-pip-egg-info-l49aybw0
       cwd: /tmp/pip-install-o92j89t3/scanpy_f8269e7304db43c8a3c2bdff41aed4ac/
  Complete output (2 lines):
  error in scanpy setup command: "values of 'package_data' dict" must be a list of strings (got '*.txt')
  ['anndata>=0.6.10', 'matplotlib>=2.2', 'pandas>=0.21', 'scipy', 'seaborn', 'h5py', 'tables', 'scikit-learn>=0.19.1', 'statsmodels', 'networkx', 'natsort', 'joblib', 'numba']
  ----------------------------------------
WARNING: Discarding https://files.pythonhosted.org/packages/78/cf/b2cc01e9c33613d738c1cdeb5af7d250cf965bda187aa258e45ed25a6a15/scanpy-1.3.1.tar.gz#sha256=cbf81b67933c5a8358012ca58a71a5b08fe41a2123c3ecd02d27660c1864eb83 (from https://pypi.org/simple/scanpy/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.
  ERROR: Command errored out with exit status 1:
   command: /PHShome/ys738/tutorial/single-cell-tutorial/test/env/bin/python -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-o92j89t3/scanpy_dab42db58f034dacbf4343922b1eee3e/setup.py'"'"'; __file__='"'"'/tmp/pip-install-o92j89t3/scanpy_dab42db58f034dacbf4343922b1eee3e/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /tmp/pip-pip-egg-info-f74u8w54
       cwd: /tmp/pip-install-o92j89t3/scanpy_dab42db58f034dacbf4343922b1eee3e/
  Complete output (1 lines):
  error in scanpy setup command: 'install_requires' must be a string or list of strings containing valid project/version requirement specifiers; Parse error at "'[doc]'": Expected W:(abcd...)
  ----------------------------------------
WARNING: Discarding https://files.pythonhosted.org/packages/36/70/367316a52e6ab4529ab6489f34cfbea89ea8d6dc6ad95bae01e3f54dfa4d/scanpy-1.3.tar.gz#sha256=c12517cb7c373f0f562b3276057e890744edd015486a4448e502a5f264ff1193 (from https://pypi.org/simple/scanpy/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.
  ERROR: Command errored out with exit status 1:
   command: /PHShome/ys738/tutorial/single-cell-tutorial/test/env/bin/python -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-o92j89t3/scanpy_441a9cdefe6b4366881b69bcac6dc49e/setup.py'"'"'; __file__='"'"'/tmp/pip-install-o92j89t3/scanpy_441a9cdefe6b4366881b69bcac6dc49e/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /tmp/pip-pip-egg-info-jcdxvh3p
       cwd: /tmp/pip-install-o92j89t3/scanpy_441a9cdefe6b4366881b69bcac6dc49e/
  Complete output (1 lines):
  error in scanpy setup command: "values of 'package_data' dict" must be a list of strings (got '*.txt')
  ----------------------------------------
WARNING: Discarding https://files.pythonhosted.org/packages/b3/43/76f4f30dce3d6599ba61a09eeedd4e456c4699d4eb0e11fa70b85e909b48/scanpy-1.2.1.tar.gz#sha256=fa11a3d922b95dea007a6fee53cef320816c7ff538c30a45b4483ef267bbbe5f (from https://pypi.org/simple/scanpy/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.
  ERROR: Command errored out with exit status 1:
   command: /PHShome/ys738/tutorial/single-cell-tutorial/test/env/bin/python -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-o92j89t3/scanpy_4a8e3a157fc5431b8280396df160a9c5/setup.py'"'"'; __file__='"'"'/tmp/pip-install-o92j89t3/scanpy_4a8e3a157fc5431b8280396df160a9c5/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /tmp/pip-pip-egg-info-cdt3h3s0
       cwd: /tmp/pip-install-o92j89t3/scanpy_4a8e3a157fc5431b8280396df160a9c5/
  Complete output (1 lines):
  error in scanpy setup command: "values of 'package_data' dict" must be a list of strings (got '*.txt')
  ----------------------------------------
WARNING: Discarding https://files.pythonhosted.org/packages/8e/0a/5124937fa23ec0311ad10e9eda00731cf2152755f5b78c4751f371050ee2/scanpy-1.2.0.tar.gz#sha256=5065bf203ecb67176373a94b5b0914bc8a6da990e7f6b67b0f08be3de9dd2f03 (from https://pypi.org/simple/scanpy/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.
  ERROR: Command errored out with exit status 1:
   command: /PHShome/ys738/tutorial/single-cell-tutorial/test/env/bin/python -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-o92j89t3/scanpy_0c1d497596cc424ab3b349ae6bacff9f/setup.py'"'"'; __file__='"'"'/tmp/pip-install-o92j89t3/scanpy_0c1d497596cc424ab3b349ae6bacff9f/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /tmp/pip-pip-egg-info-qmezagzm
       cwd: /tmp/pip-install-o92j89t3/scanpy_0c1d497596cc424ab3b349ae6bacff9f/
  Complete output (1 lines):
  error in scanpy setup command: "values of 'package_data' dict" must be a list of strings (got '*.txt')
  ----------------------------------------
WARNING: Discarding https://files.pythonhosted.org/packages/81/02/5df31ff33b28b9b438d70f0d82a9452acc6aa67e8652e6d9169920e4574d/scanpy-1.1.tar.gz#sha256=4be902d350ccc34b57447081e26091a74cd254ff4ba11b4c8c228f38d645e727 (from https://pypi.org/simple/scanpy/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.
  ERROR: Command errored out with exit status 1:
   command: /PHShome/ys738/tutorial/single-cell-tutorial/test/env/bin/python -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-o92j89t3/scanpy_7a0d42446100419b8ef978066f4f32d3/setup.py'"'"'; __file__='"'"'/tmp/pip-install-o92j89t3/scanpy_7a0d42446100419b8ef978066f4f32d3/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /tmp/pip-pip-egg-info-kobc5xlh
       cwd: /tmp/pip-install-o92j89t3/scanpy_7a0d42446100419b8ef978066f4f32d3/
  Complete output (1 lines):
  error in scanpy setup command: "values of 'package_data' dict" must be a list of strings (got '*.txt')
  ----------------------------------------
WARNING: Discarding https://files.pythonhosted.org/packages/f6/12/d1c24809472c8d0c75d9d21de6fea83600dfde47fdf8d505d7340d6cd3c8/scanpy-1.0.4.tar.gz#sha256=ca2424d265e4118dfd71719fd18738e1396d8090987c613b99a8633cf4775cd2 (from https://pypi.org/simple/scanpy/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.
  ERROR: Command errored out with exit status 1:
   command: /PHShome/ys738/tutorial/single-cell-tutorial/test/env/bin/python -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-o92j89t3/scanpy_c8919e6b3dab4d8ab374bd91e06699d4/setup.py'"'"'; __file__='"'"'/tmp/pip-install-o92j89t3/scanpy_c8919e6b3dab4d8ab374bd91e06699d4/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /tmp/pip-pip-egg-info-y5ej_ol2
       cwd: /tmp/pip-install-o92j89t3/scanpy_c8919e6b3dab4d8ab374bd91e06699d4/
  Complete output (1 lines):
  error in scanpy setup command: "values of 'package_data' dict" must be a list of strings (got '*.txt')
  ----------------------------------------
WARNING: Discarding https://files.pythonhosted.org/packages/45/15/09af7e433871b94ec26086cd1b2de71eb376d006698701d1c52d3c8acb0a/scanpy-1.0.3.post1.tar.gz#sha256=d83f7da9bc838a69182e612ea9e9003751247c317433788d842cb29e434257e6 (from https://pypi.org/simple/scanpy/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.
ERROR: Package 'anndata2ri' requires a different Python: 3.6.15 not in '>=3.7'

failed

CondaEnvException: Pip failed

The error seems to be related to python version. Could you tell me how to solve this problem?

Thank you

Sunyp-IM commented 1 year ago

I changed to last line "- git+https://github.com/flying-sheep/anndata2ri" to "- anndata2ri<=1.0.6" and the error is gone.