When running the Integrating spatial data with scRNA-seq using scanorama tutorial with the provided sample data, the following error occurs.
This may be related to the following warning I also see
<string>:6: VisibleDeprecationWarning: Creating an ndarray from nested sequences exceeding the maximum number of dimensions of 32 is deprecated. If you mean to do this, you must specify 'dtype=object' when creating the ndarray.
How can I overcome this issue?
Here is the output of sc.logging.print_versions()
-----
anndata 0.7.8
scanpy 1.8.2
sinfo 0.3.1
-----
PIL 9.0.1
anndata 0.7.8
annoy NA
backcall 0.2.0
beta_ufunc NA
binom_ufunc NA
cached_property 1.5.2
cffi 1.15.0
colorama 0.4.4
cycler 0.10.0
cython_runtime NA
dateutil 2.8.2
debugpy 1.5.1
decorator 5.1.1
defusedxml 0.7.1
entrypoints 0.4
fbpca NA
h5py 3.6.0
igraph 0.9.9
intervaltree NA
ipykernel 6.9.0
ipython_genutils 0.2.0
ipywidgets 7.6.5
jedi 0.18.1
joblib 1.1.0
jupyter_server 1.13.5
kiwisolver 1.3.2
leidenalg 0.8.8
llvmlite 0.38.0
louvain 0.7.1
matplotlib 3.5.1
matplotlib_inline NA
mpl_toolkits NA
natsort 8.1.0
nbinom_ufunc NA
numba 0.55.1
numexpr 2.8.0
numpy 1.21.5
packaging 21.3
pandas 1.3.5
parso 0.8.3
pexpect 4.8.0
pickleshare 0.7.5
pkg_resources NA
prompt_toolkit 3.0.27
psutil 5.9.0
ptyprocess 0.7.0
pycparser 2.21
pydev_ipython NA
pydevconsole NA
pydevd 2.6.0
pydevd_concurrency_analyser NA
pydevd_file_utils NA
pydevd_plugins NA
pydevd_tracing NA
pygments 2.11.2
pynndescent 0.5.6
pyparsing 3.0.7
pytz 2021.3
scanorama 1.7.1
scanpy 1.8.2
scipy 1.7.3
seaborn 0.11.2
setuptools 59.8.0
sinfo 0.3.1
six 1.16.0
sklearn 1.0.2
sortedcontainers 2.4.0
sphinxcontrib NA
statsmodels 0.13.2
storemagic NA
tables 3.7.0
texttable 1.6.4
threadpoolctl 3.1.0
tornado 6.1
tqdm 4.62.3
traitlets 5.1.1
typing_extensions NA
umap 0.5.2
wcwidth 0.2.5
yaml 6.0
zipp NA
zmq 22.3.0
-----
IPython 7.31.1
jupyter_client 7.1.2
jupyter_core 4.9.1
jupyterlab 3.2.9
notebook 6.4.8
-----
Python 3.7.12 | packaged by conda-forge | (default, Oct 26 2021, 06:08:53) [GCC 9.4.0]
Linux-3.10.0-1062.1.2.el7.x86_64-x86_64-with-debian-10.10
72 logical CPU cores
-----
zappuf
commented
2 years ago
When running the
Integrating spatial data with scRNA-seq using scanoramatutorial with the provided sample data, the following error occurs.This may be related to the following warning I also see
<string>:6: VisibleDeprecationWarning: Creating an ndarray from nested sequences exceeding the maximum number of dimensions of 32 is deprecated. If you mean to do this, you must specify 'dtype=object' when creating the ndarray.How can I overcome this issue?
Here is the output of
sc.logging.print_versions()