Python Key Troubleshooting [81-100]
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81. AnnDataReadError: Above error raised while reading key ‘/layers’ of type <class ‘h5py._hl.group.Group’> from /.
⑴ (package) Issue: Issue occurs when running scanpy.read_h5ad
⑵ (package) Solution: Upgrade anndata version from 0.7.8 to 0.9.2 (ref)
82. KeyError: ‘y’
⑴ ( ** grammar** ) Issue: Issue occurs when executing sc.pl.violin(adata, keys=celltype, groupby='annotation')
⑵ ( ** grammar** ) Cause: adata.obs[celltype] contains NaN values
83. Korean fonts not visible on the plot, displaying as ‘ㅁㅁㅁ’
⑴ ( ** grammar** ) Solution
① Method 1. Search for available fonts on the system, set a Korean-supported font as default
② Method 2. Available fonts can also be found using the following code
③ Method 3. Download the .ttf font file and set the path of this font file as the default font
84. ModuleNotFoundError: No module named ‘jax.experimental.global_device_array’
⑴ (package) Cause: GlobalDeviceArray was deprecated in JAX version 0.4.1 and removed in JAX version 0.4.7
85. OSError: cannot write mode I;16 as JPEG
⑴ (grammar) Issue: Error occurs when executing Image.open("input_image.tif").save('output_image.jpg', 'JPEG')
⑵ (grammar) Solution: Image.open("input_image.tif").save('output_image.png', 'PNG') works (ref)
86. AttributeError: module ‘PIL.Image’ has no attribute ‘ANTIALIAS’
⑴ (grammar) Issue: img = img.resize((256, 256), Image.ANTIALIAS)
⑵ (grammar) Solution: img = img.resize((256, 256), Image.LANCZOS)
87. FileExistsError: [Errno 17] JVM DLL not found: Define/path/or/set/JAVA_HOME/variable/properly
⑴ (package) Solution
sudo apt update
sudo apt install default-jdk
readlink -f $(which java)
export JAVA_HOME=/usr/lib/jvm/java-11-openjdk-amd64
export PATH=$JAVA_HOME/bin:$PATH
88. ModuleNotFoundError: No module named ‘faiss’
⑴ (package) Solution: pip install faiss-cpu and pip install faiss-gpu
89. ModuleNotFoundError: No module named ‘PIL’
⑴ (package) Solution: pip install Pillow
90. AttributeError: ‘Series’ object has no attribute ‘iteritems’
⑴ (package) Solution: Change the Pandas package version to below 2.0.0. (ref)
91. SyntaxError: Missing parentheses in call to ‘print’. Did you mean print(‘Macros:’)? [end of output] note: This error originates from a subprocess, and is likely not a problem with pip. error: metadata-generation-failed × Encountered error while generating package metadata. ╰─> See above for output. note: This is an issue with the package mentioned above, not pip.
⑴ (package) Issue: pip install multiprocessing
⑵ (package) Solution: The multiprocessing package is used in Python 2.x, so trying to install the multiprocessing package in Python 3.x will result in an error.
92. IndentationError: unindent does not match any outer indentation level
⑴ (grammar) Solution 1: Use spaces consistently (ref)
⑵ (grammar) Solution 2: Errors often occur in newly added parts of the code. In such cases, copying a part of the existing code with the same indentation level and pasting it into the newly added code can resolve the issue.
93. OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata. Segmentation fault (core dumped)
⑴ (system) Solution: Use the command export OPENBLAS_NUM_THREADS=4 to limit the number of OpenBLAS threads system-wide.
94. AttributeError: module ‘pulp’ has no attribute ‘list_solvers’. Did you mean: ‘listSolvers’?
⑴ (package) Solution: pip install pulp==2.7
95. Preparing metadata (setup.py) … error error: subprocess-exited-with-error … error in pysam setup command: use_2to3 is invalid … note: This error originates from a subprocess, and is likely not a problem with pip. error: metadata-generation-failed
⑴ (package) Issue: An error occurs when running pip install lapels.
⑵ (package) Solution: Downgrade the Python environment to version 3.5 or lower.
96. easy_install: command not found
⑴ (package) Solution: easy_install no longer exists, it was replaced by pip install. (ref)
97. ‘str’ object has no attribute ‘decode’
⑴ (grammar) Solution: Simply drop the .decode('utf-8') part (ref)
98. ImportError: Unable to find a usable engine; tried using: ‘pyarrow’, ‘fastparquet’.
⑴ (package) Solution: pip install pyarrow
99. AttributeError: module ‘numpy’ has no attribute ‘float’?
⑴ (package) Solution: Lower the numpy version. Downgrading numpy to version 1.20 on Python 3.7 resolves the issue.
100. RuntimeError: Numpy is not available
⑴ (package) Solution: Lower the version of numpy below 2 (e.g., numpy==1.24).
Written: 2024.06.07 15:03
Revised: 2024.09.06 18:53