ValueError: a must be scalar or 1 dimensional, use .ravel to flatten

I have encountered ERROE: “ValueError: a must be scalar or 1 dimensional, use .ravel to flatten” cellphonedb 3.0 Here the error ‘’’ [ ][APP][14/02/22-18:50:05][WARNING] Latest local available version is v2.0.0, using it [ ][APP][14/02/22-18:50:05][WARNING] User selected downloaded database v2.0.0 is available, using it [ ][CORE][14/02/22-18:50:05][INFO] Initializing SqlAlchemy CellPhoneDB Core [ ][CORE][14/02/22-18:50:05][INFO] Using custom database at /public1/home/scfa1516/.cpdb/releases/v2.0.0/cellphone.db [ ][APP][14/02/22-18:50:05][INFO] Launching Method cpdb_statistical_analysis_local_method_launcher [ ][APP][14/02/22-18:50:05][INFO] Launching Method _set_paths [ ][APP][14/02/22-18:50:05][INFO] Launching Method _load_meta_counts [ ][APP][14/02/22-18:58:03][INFO] Launching Method _check_counts_data [ ][CORE][14/02/22-18:58:03][INFO] Launching Method cpdb_statistical_analysis_launcher [ ][CORE][14/02/22-18:58:03][INFO] Launching Method _counts_validations [ ][CORE][14/02/22-18:58:04][INFO] Launching Method get_interactions_genes_complex [ ][CORE][14/02/22-18:58:05][INFO] [Cluster Statistical Analysis] Threshold:0.1 Iterations:1000 Debug-seed:-1 Threads:40 Precision:3 [ ][APP][14/02/22-18:58:07][ERROR] Unexpected error Traceback (most recent call last): File “/public1/home/scfa1516/miniconda3/envs/cpdb/lib/python3.8/site-packages/cellphonedb/src/api_endpoints/terminal_api/method_terminal_api_endpoints/method_terminal_commands.py”, line 131, in statistical_analysis LocalMethodLauncher(cpdb_app.create_app(verbose, database)).
File “/public1/home/scfa1516/miniconda3/envs/cpdb/lib/python3.8/site-packages/cellphonedb/src/local_launchers/local_method_launcher.py”, line 62, in cpdb_statistical_analysis_local_method_launcher self.cellphonedb_app.method.cpdb_statistical_analysis_launcher( File “/public1/home/scfa1516/miniconda3/envs/cpdb/lib/python3.8/site-packages/cellphonedb/src/core/methods/method_launcher.py”, line 95, in cpdb_statistical_analysis_launcher cpdb_statistical_analysis_method.call(meta, File “/public1/home/scfa1516/miniconda3/envs/cpdb/lib/python3.8/site-packages/cellphonedb/src/core/methods/cpdb_statistical_analysis_method.py”, line 27, in call cpdb_statistical_analysis_complex_method.call(meta.copy(), File “/public1/home/scfa1516/miniconda3/envs/cpdb/lib/python3.8/site-packages/cellphonedb/src/core/methods/cpdb_statistical_analysis_complex_method.py”, line 61, in call clusters = cpdb_statistical_analysis_helper.build_clusters(meta, counts_filtered, complex_composition_filtered, skip_percent=False) File “/public1/home/scfa1516/miniconda3/envs/cpdb/lib/python3.8/site-packages/cellphonedb/src/core/methods/cpdb_statistical_analysis_helper.py”, line 141, in build_clusters npg.aggregate(meta[CELL_TYPE].cat.codes, counts.values, func=‘mean’, axis=1), File “/public1/home/scfa1516/miniconda3/envs/cpdb/lib/python3.8/site-packages/numpy_groupies/aggregate_numpy.py”, line 249, in aggregate return _aggregate_base(group_idx, a, size=size, fill_value=fill_value, File “/public1/home/scfa1516/miniconda3/envs/cpdb/lib/python3.8/site-packages/numpy_groupies/aggregate_numpy.py”, line 219, in _aggregate_base group_idx, a, flat_size, ndim_idx, size = input_validation(group_idx, a, File “/public1/home/scfa1516/miniconda3/envs/cpdb/lib/python3.8/site-packages/numpy_groupies/utils.py”, line 341, in input_validation raise ValueError(“a must be scalar or 1 dimensional, use .ravel to” ValueError: a must be scalar or 1 dimensional, use .ravel to flatten ‘’’ Here the input files

package list Package Version

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aniso8601 9.0.1 anndata 0.7.8 annoy 1.17.0 attrs 21.4.0 backports.zoneinfo 0.2.1 bbknn 1.5.1 boto3 1.20.47 botocore 1.23.47 CellPhoneDB 3.0.0 certifi 2021.10.8 cffi 1.15.0 charset-normalizer 2.0.11 click 7.1.1 conda-pack 0.6.0 cycler 0.11.0 Cython 0.29.27 fbpca 1.0 Flask 1.1.4 Flask-RESTful 0.3.9 Flask-Testing 0.8.1 fonttools 4.28.2 geosketch 0.3 h5py 2.10.0 idna 3.3 igraph 0.9.9 iniconfig 1.1.1 itsdangerous 1.1.0 Jinja2 2.11.2 jmespath 0.10.0 joblib 1.1.0 kiwisolver 1.3.2 leidenalg 0.8.8 llvmlite 0.37.0 MarkupSafe 2.0.1 matplotlib 3.5.0 natsort 8.0.0 networkx 2.6.3 nose 1.3.7 numba 0.54.1 numexpr 2.7.3 numpy 1.18.0 numpy-groupies 0.9.1 packaging 21.3 pandas 1.1.4 patsy 0.5.2 pika 1.2.0 Pillow 8.4.0 pip 21.2.4 pluggy 1.0.0 py 1.11.0 pycparser 2.21 pynndescent 0.5.5 pyparsing 3.0.6 pytest 6.2.5 pytest-runner 5.3.1 python-dateutil 2.8.2 python-igraph 0.9.9 pytz 2021.3 pytz-deprecation-shim 0.1.0.post0 PyYAML 5.4.1 request2 0.2 requests 2.27.1 rpy2 3.4.1 s3transfer 0.5.1 scanpy 1.8.2 scikit-learn 0.22 scipy 1.7.2 seaborn 0.11.2 setuptools 58.0.4 setuptools-scm 6.3.2 sinfo 0.3.4 six 1.16.0 SQLAlchemy 1.3.9 statsmodels 0.13.1 stdlib-list 0.8.0 tables 3.6.1 texttable 1.6.4 threadpoolctl 3.0.0 toml 0.10.2 tomli 1.2.2 tqdm 4.62.3 tzdata 2021.5 tzlocal 4.1 umap-learn 0.5.2 urllib3 1.26.8 Werkzeug 1.0.1 wheel 0.37.0 xlrd 1.2.0

[defendant602]

I reinstalled cellphoneDB v3.0 using conda environment and it solved my problem. Thanks !

[FanZhang9]

indeed, problem in my installation, it’s solved,Thanks