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Teichlab / cellphonedb

MIT License
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error during installation #183

Closed williamsdrake closed 3 years ago

williamsdrake commented 4 years ago

Hi cellphonedb developers,

I am trying to install the cellphonedb package following the readme instructions. My code thus far is: 

python3 -m venv cpdb-venv
source vpdb-venv/bin/activate
pip install cellphonedb

The error:

Running setup.py install for pandas ... error
    ERROR: Command errored out with exit status 1:
     command: /Users/Helen/cpdb-venv/bin/python3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/r6/48jdjc_16zq0hrssr5msbphc0000gn/T/pip-install-9akibw19/pandas/setup.py'"'"'; __file__='"'"'/private/var/folders/r6/48jdjc_16zq0hrssr5msbphc0000gn/T/pip-install-9akibw19/pandas/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /private/var/folders/r6/48jdjc_16zq0hrssr5msbphc0000gn/T/pip-record-64aeb8p5/install-record.txt --single-version-externally-managed --compile --install-headers /Users/Helen/cpdb-venv/include/site/python3.8/pandas
         cwd: /private/var/folders/r6/48jdjc_16zq0hrssr5msbphc0000gn/T/pip-install-9akibw19/pandas/
    Complete output (703 lines):
    running install
    running build
    running build_py
    creating build
    creating build/lib.macosx-10.9-x86_64-3.8
    creating build/lib.macosx-10.9-x86_64-3.8/pandas
    copying pandas/conftest.py -> build/lib.macosx-10.9-x86_64-3.8/pandas
    copying pandas/_version.py -> build/lib.macosx-10.9-x86_64-3.8/pandas
    copying pandas/lib.py -> build/lib.macosx-10.9-x86_64-3.8/pandas
    copying pandas/tslib.py -> build/lib.macosx-10.9-x86_64-3.8/pandas
    copying pandas/__init__.py -> build/lib.macosx-10.9-x86_64-3.8/pandas
    copying pandas/parser.py -> build/lib.macosx-10.9-x86_64-3.8/pandas
    copying pandas/testing.py -> build/lib.macosx-10.9-x86_64-3.8/pandas
    copying pandas/json.py -> build/lib.macosx-10.9-x86_64-3.8/pandas
    creating build/lib.macosx-10.9-x86_64-3.8/pandas/tools
    copying pandas/tools/merge.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tools
    copying pandas/tools/plotting.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tools
    copying pandas/tools/__init__.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tools
    creating build/lib.macosx-10.9-x86_64-3.8/pandas/compat
    copying pandas/compat/chainmap_impl.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/compat
    copying pandas/compat/__init__.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/compat
    copying pandas/compat/chainmap.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/compat
    copying pandas/compat/pickle_compat.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/compat
    creating build/lib.macosx-10.9-x86_64-3.8/pandas/types
    copying pandas/types/concat.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/types
    copying pandas/types/__init__.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/types
    copying pandas/types/common.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/types
    creating build/lib.macosx-10.9-x86_64-3.8/pandas/core
    copying pandas/core/accessor.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/core
    copying pandas/core/categorical.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/core
    copying pandas/core/nanops.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/core
    copying pandas/core/missing.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/core
    copying pandas/core/internals.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/core
    copying pandas/core/algorithms.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/core
    copying pandas/core/config.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/core
    copying pandas/core/resample.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/core
    copying pandas/core/window.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/core
    copying pandas/core/index.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/core
    copying pandas/core/config_init.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/core
    copying pandas/core/generic.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/core
    copying pandas/core/series.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/core
    copying pandas/core/sorting.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/core
    copying pandas/core/__init__.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/core
    copying pandas/core/datetools.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/core
    copying pandas/core/api.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/core
    copying pandas/core/ops.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/core
    copying pandas/core/common.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/core
    copying pandas/core/frame.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/core
    copying pandas/core/indexing.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/core
    copying pandas/core/panel.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/core
    copying pandas/core/base.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/core
    copying pandas/core/strings.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/core
    copying pandas/core/apply.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/core
    creating build/lib.macosx-10.9-x86_64-3.8/pandas/formats
    copying pandas/formats/style.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/formats
    copying pandas/formats/__init__.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/formats
    creating build/lib.macosx-10.9-x86_64-3.8/pandas/util
    copying pandas/util/_depr_module.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/util
    copying pandas/util/_test_decorators.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/util
    copying pandas/util/_validators.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/util
    copying pandas/util/_print_versions.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/util
    copying pandas/util/__init__.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/util
    copying pandas/util/_decorators.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/util
    copying pandas/util/_doctools.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/util
    copying pandas/util/testing.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/util
    copying pandas/util/_tester.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/util
    copying pandas/util/decorators.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/util
    creating build/lib.macosx-10.9-x86_64-3.8/pandas/io
    copying pandas/io/feather_format.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/io
    copying pandas/io/parquet.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/io
    copying pandas/io/pytables.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/io
    copying pandas/io/html.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/io
    copying pandas/io/__init__.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/io
    copying pandas/io/clipboards.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/io
    copying pandas/io/parsers.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/io
    copying pandas/io/excel.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/io
    copying pandas/io/api.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/io
    copying pandas/io/common.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/io
    copying pandas/io/date_converters.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/io
    copying pandas/io/pickle.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/io
    copying pandas/io/sql.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/io
    copying pandas/io/s3.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/io
    copying pandas/io/packers.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/io
    copying pandas/io/stata.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/io
    copying pandas/io/gbq.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/io
    creating build/lib.macosx-10.9-x86_64-3.8/pandas/tseries
    copying pandas/tseries/plotting.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tseries
    copying pandas/tseries/converter.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tseries
    copying pandas/tseries/__init__.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tseries
    copying pandas/tseries/api.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tseries
    copying pandas/tseries/offsets.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tseries
    copying pandas/tseries/frequencies.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tseries
    copying pandas/tseries/holiday.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tseries
    creating build/lib.macosx-10.9-x86_64-3.8/pandas/tests
    copying pandas/tests/test_expressions.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests
    copying pandas/tests/test_register_accessor.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests
    copying pandas/tests/test_common.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests
    copying pandas/tests/test_downstream.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests
    copying pandas/tests/test_errors.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests
    copying pandas/tests/test_sorting.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests
    copying pandas/tests/test_join.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests
    copying pandas/tests/test_panel.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests
    copying pandas/tests/__init__.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests
    copying pandas/tests/test_lib.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests
    copying pandas/tests/test_resample.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests
    copying pandas/tests/test_nanops.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests
    copying pandas/tests/test_take.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests
    copying pandas/tests/test_algos.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests
    copying pandas/tests/test_multilevel.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests
    copying pandas/tests/test_compat.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests
    copying pandas/tests/test_config.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests
    copying pandas/tests/test_window.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests
    copying pandas/tests/test_strings.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests
    copying pandas/tests/test_base.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests
    creating build/lib.macosx-10.9-x86_64-3.8/pandas/computation
    copying pandas/computation/expressions.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/computation
    copying pandas/computation/__init__.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/computation
    creating build/lib.macosx-10.9-x86_64-3.8/pandas/_libs
    copying pandas/_libs/__init__.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/_libs
    creating build/lib.macosx-10.9-x86_64-3.8/pandas/plotting
    copying pandas/plotting/_converter.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/plotting
    copying pandas/plotting/_tools.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/plotting
    copying pandas/plotting/_style.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/plotting
    copying pandas/plotting/__init__.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/plotting
    copying pandas/plotting/_core.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/plotting
    copying pandas/plotting/_timeseries.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/plotting
    copying pandas/plotting/_compat.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/plotting
    copying pandas/plotting/_misc.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/plotting
    creating build/lib.macosx-10.9-x86_64-3.8/pandas/api
    copying pandas/api/__init__.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/api
    creating build/lib.macosx-10.9-x86_64-3.8/pandas/errors
    copying pandas/errors/__init__.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/errors
    creating build/lib.macosx-10.9-x86_64-3.8/pandas/compat/numpy
    copying pandas/compat/numpy/__init__.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/compat/numpy
    copying pandas/compat/numpy/function.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/compat/numpy
    creating build/lib.macosx-10.9-x86_64-3.8/pandas/core/reshape
    copying pandas/core/reshape/tile.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/core/reshape
    copying pandas/core/reshape/merge.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/core/reshape
    copying pandas/core/reshape/concat.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/core/reshape
    copying pandas/core/reshape/util.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/core/reshape
    copying pandas/core/reshape/reshape.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/core/reshape
    copying pandas/core/reshape/__init__.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/core/reshape
    copying pandas/core/reshape/api.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/core/reshape
    copying pandas/core/reshape/melt.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/core/reshape
    copying pandas/core/reshape/pivot.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/core/reshape
    creating build/lib.macosx-10.9-x86_64-3.8/pandas/core/tools
    copying pandas/core/tools/timedeltas.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/core/tools
    copying pandas/core/tools/datetimes.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/core/tools
    copying pandas/core/tools/__init__.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/core/tools
    copying pandas/core/tools/numeric.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/core/tools
    creating build/lib.macosx-10.9-x86_64-3.8/pandas/core/util
    copying pandas/core/util/__init__.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/core/util
    copying pandas/core/util/hashing.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/core/util
    creating build/lib.macosx-10.9-x86_64-3.8/pandas/core/dtypes
    copying pandas/core/dtypes/cast.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/core/dtypes
    copying pandas/core/dtypes/missing.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/core/dtypes
    copying pandas/core/dtypes/concat.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/core/dtypes
    copying pandas/core/dtypes/generic.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/core/dtypes
    copying pandas/core/dtypes/__init__.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/core/dtypes
    copying pandas/core/dtypes/dtypes.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/core/dtypes
    copying pandas/core/dtypes/api.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/core/dtypes
    copying pandas/core/dtypes/common.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/core/dtypes
    copying pandas/core/dtypes/inference.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/core/dtypes
    copying pandas/core/dtypes/base.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/core/dtypes
    creating build/lib.macosx-10.9-x86_64-3.8/pandas/core/groupby
    copying pandas/core/groupby/__init__.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/core/groupby
    copying pandas/core/groupby/groupby.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/core/groupby
    creating build/lib.macosx-10.9-x86_64-3.8/pandas/core/computation
    copying pandas/core/computation/check.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/core/computation
    copying pandas/core/computation/align.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/core/computation
    copying pandas/core/computation/pytables.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/core/computation
    copying pandas/core/computation/engines.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/core/computation
    copying pandas/core/computation/expressions.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/core/computation
    copying pandas/core/computation/__init__.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/core/computation
    copying pandas/core/computation/api.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/core/computation
    copying pandas/core/computation/ops.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/core/computation
    copying pandas/core/computation/common.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/core/computation
    copying pandas/core/computation/eval.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/core/computation
    copying pandas/core/computation/scope.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/core/computation
    copying pandas/core/computation/expr.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/core/computation
    creating build/lib.macosx-10.9-x86_64-3.8/pandas/core/arrays
    copying pandas/core/arrays/categorical.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/core/arrays
    copying pandas/core/arrays/__init__.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/core/arrays
    copying pandas/core/arrays/base.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/core/arrays
    creating build/lib.macosx-10.9-x86_64-3.8/pandas/core/sparse
    copying pandas/core/sparse/scipy_sparse.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/core/sparse
    copying pandas/core/sparse/series.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/core/sparse
    copying pandas/core/sparse/__init__.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/core/sparse
    copying pandas/core/sparse/api.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/core/sparse
    copying pandas/core/sparse/frame.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/core/sparse
    copying pandas/core/sparse/array.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/core/sparse
    creating build/lib.macosx-10.9-x86_64-3.8/pandas/core/indexes
    copying pandas/core/indexes/accessors.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/core/indexes
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    creating build/lib.macosx-10.9-x86_64-3.8/pandas/tests/categorical
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    copying pandas/tests/categorical/test_api.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/categorical
    copying pandas/tests/categorical/test_dtypes.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/categorical
    creating build/lib.macosx-10.9-x86_64-3.8/pandas/tests/groupby
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    copying pandas/tests/io/formats/test_format.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/io/formats
    copying pandas/tests/io/formats/test_to_csv.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/io/formats
    creating build/lib.macosx-10.9-x86_64-3.8/pandas/tests/io/parser
    copying pandas/tests/io/parser/parse_dates.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/io/parser
    copying pandas/tests/io/parser/na_values.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/io/parser
    copying pandas/tests/io/parser/comment.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/io/parser
    copying pandas/tests/io/parser/skiprows.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/io/parser
    copying pandas/tests/io/parser/header.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/io/parser
    copying pandas/tests/io/parser/dialect.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/io/parser
    copying pandas/tests/io/parser/test_parsers.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/io/parser
    copying pandas/tests/io/parser/compression.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/io/parser
    copying pandas/tests/io/parser/python_parser_only.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/io/parser
    copying pandas/tests/io/parser/index_col.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/io/parser
    copying pandas/tests/io/parser/__init__.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/io/parser
    copying pandas/tests/io/parser/dtypes.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/io/parser
    copying pandas/tests/io/parser/test_read_fwf.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/io/parser
    copying pandas/tests/io/parser/c_parser_only.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/io/parser
    copying pandas/tests/io/parser/test_unsupported.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/io/parser
    copying pandas/tests/io/parser/test_textreader.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/io/parser
    copying pandas/tests/io/parser/usecols.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/io/parser
    copying pandas/tests/io/parser/test_network.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/io/parser
    copying pandas/tests/io/parser/quoting.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/io/parser
    copying pandas/tests/io/parser/common.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/io/parser
    copying pandas/tests/io/parser/mangle_dupes.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/io/parser
    copying pandas/tests/io/parser/multithread.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/io/parser
    copying pandas/tests/io/parser/converters.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/io/parser
    creating build/lib.macosx-10.9-x86_64-3.8/pandas/tests/io/json
    copying pandas/tests/io/json/test_compression.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/io/json
    copying pandas/tests/io/json/test_json_table_schema.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/io/json
    copying pandas/tests/io/json/__init__.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/io/json
    copying pandas/tests/io/json/test_readlines.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/io/json
    copying pandas/tests/io/json/test_ujson.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/io/json
    copying pandas/tests/io/json/test_pandas.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/io/json
    copying pandas/tests/io/json/test_normalize.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/io/json
    creating build/lib.macosx-10.9-x86_64-3.8/pandas/tests/io/sas
    copying pandas/tests/io/sas/test_sas7bdat.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/io/sas
    copying pandas/tests/io/sas/test_sas.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/io/sas
    copying pandas/tests/io/sas/__init__.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/io/sas
    copying pandas/tests/io/sas/test_xport.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/io/sas
    creating build/lib.macosx-10.9-x86_64-3.8/pandas/tests/tseries/offsets
    copying pandas/tests/tseries/offsets/conftest.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/tseries/offsets
    copying pandas/tests/tseries/offsets/test_fiscal.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/tseries/offsets
    copying pandas/tests/tseries/offsets/__init__.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/tseries/offsets
    copying pandas/tests/tseries/offsets/test_yqm_offsets.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/tseries/offsets
    copying pandas/tests/tseries/offsets/common.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/tseries/offsets
    copying pandas/tests/tseries/offsets/test_ticks.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/tseries/offsets
    copying pandas/tests/tseries/offsets/test_offsets.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/tseries/offsets
    creating build/lib.macosx-10.9-x86_64-3.8/pandas/tests/groupby/aggregate
    copying pandas/tests/groupby/aggregate/__init__.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/groupby/aggregate
    copying pandas/tests/groupby/aggregate/test_cython.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/groupby/aggregate
    copying pandas/tests/groupby/aggregate/test_aggregate.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/groupby/aggregate
    copying pandas/tests/groupby/aggregate/test_other.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/groupby/aggregate
    creating build/lib.macosx-10.9-x86_64-3.8/pandas/tests/sparse/series
    copying pandas/tests/sparse/series/__init__.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/sparse/series
    copying pandas/tests/sparse/series/test_indexing.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/sparse/series
    copying pandas/tests/sparse/series/test_series.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/sparse/series
    creating build/lib.macosx-10.9-x86_64-3.8/pandas/tests/sparse/frame
    copying pandas/tests/sparse/frame/test_frame.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/sparse/frame
    copying pandas/tests/sparse/frame/test_to_from_scipy.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/sparse/frame
    copying pandas/tests/sparse/frame/__init__.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/sparse/frame
    copying pandas/tests/sparse/frame/test_analytics.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/sparse/frame
    copying pandas/tests/sparse/frame/test_apply.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/sparse/frame
    copying pandas/tests/sparse/frame/test_indexing.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/sparse/frame
    copying pandas/tests/sparse/frame/test_to_csv.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/sparse/frame
    creating build/lib.macosx-10.9-x86_64-3.8/pandas/tests/indexing/interval
    copying pandas/tests/indexing/interval/__init__.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/indexing/interval
    copying pandas/tests/indexing/interval/test_interval.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/indexing/interval
    copying pandas/tests/indexing/interval/test_interval_new.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/indexing/interval
    creating build/lib.macosx-10.9-x86_64-3.8/pandas/tests/scalar/interval
    copying pandas/tests/scalar/interval/__init__.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/scalar/interval
    copying pandas/tests/scalar/interval/test_interval.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/scalar/interval
    creating build/lib.macosx-10.9-x86_64-3.8/pandas/tests/scalar/timedelta
    copying pandas/tests/scalar/timedelta/__init__.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/scalar/timedelta
    copying pandas/tests/scalar/timedelta/test_timedelta.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/scalar/timedelta
    copying pandas/tests/scalar/timedelta/test_formats.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/scalar/timedelta
    copying pandas/tests/scalar/timedelta/test_construction.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/scalar/timedelta
    copying pandas/tests/scalar/timedelta/test_arithmetic.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/scalar/timedelta
    creating build/lib.macosx-10.9-x86_64-3.8/pandas/tests/scalar/period
    copying pandas/tests/scalar/period/test_period.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/scalar/period
    copying pandas/tests/scalar/period/__init__.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/scalar/period
    copying pandas/tests/scalar/period/test_asfreq.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/scalar/period
    creating build/lib.macosx-10.9-x86_64-3.8/pandas/tests/scalar/timestamp
    copying pandas/tests/scalar/timestamp/test_timezones.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/scalar/timestamp
    copying pandas/tests/scalar/timestamp/test_timestamp.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/scalar/timestamp
    copying pandas/tests/scalar/timestamp/__init__.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/scalar/timestamp
    copying pandas/tests/scalar/timestamp/test_comparisons.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/scalar/timestamp
    copying pandas/tests/scalar/timestamp/test_rendering.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/scalar/timestamp
    copying pandas/tests/scalar/timestamp/test_unary_ops.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/scalar/timestamp
    copying pandas/tests/scalar/timestamp/test_arithmetic.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/scalar/timestamp
    creating build/lib.macosx-10.9-x86_64-3.8/pandas/tests/indexes/interval
    copying pandas/tests/indexes/interval/__init__.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/indexes/interval
    copying pandas/tests/indexes/interval/test_interval_range.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/indexes/interval
    copying pandas/tests/indexes/interval/test_interval.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/indexes/interval
    copying pandas/tests/indexes/interval/test_astype.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/indexes/interval
    copying pandas/tests/indexes/interval/test_construction.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/indexes/interval
    copying pandas/tests/indexes/interval/test_interval_new.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/indexes/interval
    copying pandas/tests/indexes/interval/test_interval_tree.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/indexes/interval
    creating build/lib.macosx-10.9-x86_64-3.8/pandas/tests/indexes/period
    copying pandas/tests/indexes/period/test_period.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/indexes/period
    copying pandas/tests/indexes/period/__init__.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/indexes/period
    copying pandas/tests/indexes/period/test_scalar_compat.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/indexes/period
    copying pandas/tests/indexes/period/test_indexing.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/indexes/period
    copying pandas/tests/indexes/period/test_astype.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/indexes/period
    copying pandas/tests/indexes/period/test_formats.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/indexes/period
    copying pandas/tests/indexes/period/test_setops.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/indexes/period
    copying pandas/tests/indexes/period/test_construction.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/indexes/period
    copying pandas/tests/indexes/period/test_partial_slicing.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/indexes/period
    copying pandas/tests/indexes/period/test_ops.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/indexes/period
    copying pandas/tests/indexes/period/test_arithmetic.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/indexes/period
    copying pandas/tests/indexes/period/test_tools.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/indexes/period
    copying pandas/tests/indexes/period/test_asfreq.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/indexes/period
    copying pandas/tests/indexes/period/test_period_range.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/indexes/period
    creating build/lib.macosx-10.9-x86_64-3.8/pandas/tests/indexes/datetimes
    copying pandas/tests/indexes/datetimes/test_misc.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/indexes/datetimes
    copying pandas/tests/indexes/datetimes/test_missing.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/indexes/datetimes
    copying pandas/tests/indexes/datetimes/test_date_range.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/indexes/datetimes
    copying pandas/tests/indexes/datetimes/test_timezones.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/indexes/datetimes
    copying pandas/tests/indexes/datetimes/__init__.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/indexes/datetimes
    copying pandas/tests/indexes/datetimes/test_datetimelike.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/indexes/datetimes
    copying pandas/tests/indexes/datetimes/test_scalar_compat.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/indexes/datetimes
    copying pandas/tests/indexes/datetimes/test_indexing.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/indexes/datetimes
    copying pandas/tests/indexes/datetimes/test_astype.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/indexes/datetimes
    copying pandas/tests/indexes/datetimes/test_formats.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/indexes/datetimes
    copying pandas/tests/indexes/datetimes/test_setops.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/indexes/datetimes
    copying pandas/tests/indexes/datetimes/test_datetime.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/indexes/datetimes
    copying pandas/tests/indexes/datetimes/test_construction.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/indexes/datetimes
    copying pandas/tests/indexes/datetimes/test_partial_slicing.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/indexes/datetimes
    copying pandas/tests/indexes/datetimes/test_ops.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/indexes/datetimes
    copying pandas/tests/indexes/datetimes/test_arithmetic.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/indexes/datetimes
    copying pandas/tests/indexes/datetimes/test_tools.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/indexes/datetimes
    creating build/lib.macosx-10.9-x86_64-3.8/pandas/tests/indexes/timedeltas
    copying pandas/tests/indexes/timedeltas/__init__.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/indexes/timedeltas
    copying pandas/tests/indexes/timedeltas/test_timedelta.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/indexes/timedeltas
    copying pandas/tests/indexes/timedeltas/test_scalar_compat.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/indexes/timedeltas
    copying pandas/tests/indexes/timedeltas/test_indexing.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/indexes/timedeltas
    copying pandas/tests/indexes/timedeltas/test_astype.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/indexes/timedeltas
    copying pandas/tests/indexes/timedeltas/test_formats.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/indexes/timedeltas
    copying pandas/tests/indexes/timedeltas/test_setops.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/indexes/timedeltas
    copying pandas/tests/indexes/timedeltas/test_construction.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/indexes/timedeltas
    copying pandas/tests/indexes/timedeltas/test_partial_slicing.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/indexes/timedeltas
    copying pandas/tests/indexes/timedeltas/test_ops.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/indexes/timedeltas
    copying pandas/tests/indexes/timedeltas/test_arithmetic.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/indexes/timedeltas
    copying pandas/tests/indexes/timedeltas/test_timedelta_range.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/indexes/timedeltas
    copying pandas/tests/indexes/timedeltas/test_tools.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/tests/indexes/timedeltas
    creating build/lib.macosx-10.9-x86_64-3.8/pandas/_libs/tslibs
    copying pandas/_libs/tslibs/__init__.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/_libs/tslibs
    creating build/lib.macosx-10.9-x86_64-3.8/pandas/api/types
    copying pandas/api/types/__init__.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/api/types
    creating build/lib.macosx-10.9-x86_64-3.8/pandas/api/extensions
    copying pandas/api/extensions/__init__.py -> build/lib.macosx-10.9-x86_64-3.8/pandas/api/extensions
    creating build/lib.macosx-10.9-x86_64-3.8/pandas/io/formats/templates
    copying pandas/io/formats/templates/html.tpl -> build/lib.macosx-10.9-x86_64-3.8/pandas/io/formats/templates
    UPDATING build/lib.macosx-10.9-x86_64-3.8/pandas/_version.py
    set build/lib.macosx-10.9-x86_64-3.8/pandas/_version.py to '0.23.4'
    running build_ext
    building 'pandas._libs.algos' extension
    creating build/temp.macosx-10.9-x86_64-3.8
    creating build/temp.macosx-10.9-x86_64-3.8/pandas
    creating build/temp.macosx-10.9-x86_64-3.8/pandas/_libs
    gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -arch x86_64 -g -Ipandas/_libs/src/klib -Ipandas/_libs/src -I/Users/Helen/cpdb-venv/lib/python3.8/site-packages/numpy/core/include -I/Users/Helen/cpdb-venv/include -I/Library/Frameworks/Python.framework/Versions/3.8/include/python3.8 -c pandas/_libs/algos.c -o build/temp.macosx-10.9-x86_64-3.8/pandas/_libs/algos.o -Wno-unused-function
    xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
    error: command 'gcc' failed with exit status 1
    ----------------------------------------
ERROR: Command errored out with exit status 1: /Users/Helen/cpdb-venv/bin/python3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/r6/48jdjc_16zq0hrssr5msbphc0000gn/T/pip-install-9akibw19/pandas/setup.py'"'"'; __file__='"'"'/private/var/folders/r6/48jdjc_16zq0hrssr5msbphc0000gn/T/pip-install-9akibw19/pandas/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /private/var/folders/r6/48jdjc_16zq0hrssr5msbphc0000gn/T/pip-record-64aeb8p5/install-record.txt --single-version-externally-managed --compile --install-headers /Users/Helen/cpdb-venv/include/site/python3.8/pandas Check the logs for full command output.

Mac OS 10.13.6 Python v. 3.8

I would love to try using this for my single cell datasets, so any guidance is appreciated. Thank you

lesleycheung commented 4 years ago

Same error. Please help. Thanks. 

Running setup.py install for pandas ... error
ERROR: Command errored out with exit status 1:
 command: /Users/Singlecell/cpdb-venv/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/02/5cyzq_0j6lv64hrcz5m_blr008nlvy/T/pip-install-a2e0xvkl/pandas/setup.py'"'"'; __file__='"'"'/private/var/folders/02/5cyzq_0j6lv64hrcz5m_blr008nlvy/T/pip-install-a2e0xvkl/pandas/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /private/var/folders/02/5cyzq_0j6lv64hrcz5m_blr008nlvy/T/pip-record-rk9bcfb4/install-record.txt --single-version-externally-managed --compile --install-headers /Users/Singlecell/cpdb-venv/include/site/python3.8/pandas
     cwd: /private/var/folders/02/5cyzq_0j6lv64hrcz5m_blr008nlvy/T/pip-install-a2e0xvkl/pandas/
Complete output (3402 lines):
Weimin-LinA commented 4 years ago

I successfully installed the cellphoneDB package a few months ago and it can run smoothly, but now I use the same steps to reinstall it but I get an error. I don’t know if this is caused by a software upgrade.

czlcaltech commented 4 years ago

I also faced with the same error. And don't know the solutions to it. Tested both in Linux and MacOS platform.

mzhibo commented 4 years ago

Same error, I am installing it in Linux. Does anyone know how to fix it? ERROR: Command errored out with exit status 1: /home/mzhibo/anaconda3/envs/CellPhoneDB/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-c3im6d06/pandas/setup.py'"'"'; __file__='"'"'/tmp/pip-install-c3im6d06/pandas/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-v8g6uejn/install-record.txt --single-version-externally-managed --compile --install-headers /home/mzhibo/anaconda3/envs/CellPhoneDB/include/python3.8/pandas Check the logs for full command output.

mzhibo commented 4 years ago

Mine was fixed after using python 3.6

Sumithrasank commented 3 years ago

I get the same error using python3.8

rlittman16 commented 3 years ago

Using python3.6 also worked for me

MingwuDuan commented 3 years ago

Using python3.6 also worked for me

me too.

prete commented 3 years ago

This error shows up when using python 3.8 (you can check your python version using python -V) and, for the time being, CellphoneDB only seems to work only with python version from 3.5.0 to 3.7.9.

Your options for now are: