zcang / commot Goto Github PK

I have installed commot[tradeSeq], R3.6.3, and R package tradeSeq.
when running
ct.tl.communication_deg_detection(adata, database_name = 'testDB', pathway_name='true_pathway', summary = 'receiver')
the error comes out.

RRuntimeError: Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object '/opt/R/3.6.3/lib/R/library/methods/libs/methods.so':
libR.so: cannot open shared object file: No such file or directory

I've checked that '/opt/R/3.6.3/lib/R/library/methods/libs/methods.so' exists. I have tried to set directories of R library. And here is the output of%run -m rpy2.situation

rpy2 version:
3.4.2
Python version:
3.8.13 (default, Oct 21 2022, 23:50:54)
[GCC 11.2.0]
Looking for R's HOME:
Environment variable R_HOME: /opt/R/3.6.3/
Calling R RHOME: /opt/R/3.6.3/lib/R
Environment variable R_LIBS_USER: /opt/R/3.6.3/lib/R/library
Warning: The environment variable R_HOME differs from the default R in the PATH.
R's additions to LD_LIBRARY_PATH:
:/opt/R/3.6.3/lib/R/library/methods/libs:/opt/R/3.6.3/lib/R/library/
R version:
In the PATH: R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Loading R library from rpy2: OK
Additional directories to load R packages from:
None
C extension compilation:
include:
['/opt/R/3.6.3/lib/R/include']
libraries:
['R', 'pcre2-8', 'pcre', 'lzma', 'bz2', 'z', 'tirpc', 'rt', 'dl', 'm', 'icuuc', 'icui18n']
library_dirs:
['/usr/local/lib', '/opt/R/3.6.3/lib/R/lib']
extra_compile_args:
[]
extra_link_args:
['-Wl,--export-dynamic', '-fopenmp']

Can you release a version without dependency on rpy2?
It seems rpy2 relies on a very specific combination of Python and R.
I have R 3.6 + Python 3.6, and R 4 + Python 3.10.
But I do not have the Python 3.7 + R 3.6 combination that is required of using tradeseq. I tried using conda, but ended up with a mess, because apparently pip tries to install the most up to date version of pre-requisite packages that either do not compile or are not supported in older Python 3.7.
All of these seem to be related to rpy2.

Can you put up a conda environment? Or release without rpy2?

Hi zcang,

I am interested in this tool, it looks interesting. Could you provide a full tutorial? Thank you very much!

Hi, I notice that for me 4000*600 dataset, the running time of COMMOT is super long (>12 hours in hpc). Is there any approaches I can use to accelerate the training process? Thanks.

Hi there! Thanks a lot for the great work! Congrats!!
I have some questions regarding the length of the arrows in the results of plot_cell_communication function. Does the length indicate the strength of the signal?
I guess V only contains information about the direction, but when I divided V by 2, the arrow length shrinks. However, the parameter angles used in the matplotlib.pyplot.quiver is not specified, which becomes "uv" by default. Then it should be representing some orientations only. I become unsure about whether the scale of matrix V matters.

The function I used is

ct.pl.plot_cell_communication(adata_dis500, database_name='cellchat', pathway_name=pathway,
plot_method='grid', background_legend=True, scale=0.00008, ndsize=ndsize, grid_density=0.4, 
summary='sender', background='summary', clustering='leiden', cmap='summer',
 normalize_v = True, normalize_v_quantile=0.995,)

Would you please give me some advice regarding this? Can we obtain the signaling strength from your method? Thank you very much!

Hello, thanks for putting forward the COMMOT method!

I have a question about the details of the algorithm and I'm not sure if I'd be honoured to have it answered.

In the function cot_combine_sparse(), the final 4-dimensional matrix P is obtained by weighting the results of four solutions, which are P_cot,P_row,P_col,P_blk. The corresbonding four functions are cot_sparse(),cot_row_sparse(),cot_col_sparse(),cot_blk_sparse().

I'm curious as to how these four are logically related, or what each of the four represent. What is the difference between these four functions？Why they have to be split into four functions to be solved？

Looking forward to being addressed, thanks!

Hi,

I am reading the COMMOT paper and I came across a a few questions about the Methods: spatial signalling direction.

1. what is the xi and xj representing? Are they the coordinates for spot i and j?
2. What does N function indicates?
3. V belongs to Rns x d, what is the d here?

Thank you in advance for you time and patience. I am looking forward to your reply.

Best regards,
Ema

Hi, Thank you for such a great tool. I meet error when I run
df_deg, df_yhat = ct.tl.communication_deg_detection(adata_dis500, ... database_name = 'cellchat', pathway_name='SPP1', summary = 'receiver')

Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/public/home/niuxy/Software/miniconda3/envs/commot/lib/python3.8/site-packages/commot/tools/_downstream_analysis.py", line 154, in communication_deg_detection ro.r(string_fitGAM) File "/public/home/niuxy/Software/miniconda3/envs/commot/lib/python3.8/site-packages/rpy2/robjects/__init__.py", line 438, in __call__ res = self.eval(p) File "/public/home/niuxy/Software/miniconda3/envs/commot/lib/python3.8/site-packages/rpy2/robjects/functions.py", line 198, in __call__ return (super(SignatureTranslatedFunction, self) File "/public/home/niuxy/Software/miniconda3/envs/commot/lib/python3.8/site-packages/rpy2/robjects/functions.py", line 126, in __call__ res = conversion.rpy2py(res) File "/public/home/niuxy/Software/miniconda3/envs/commot/lib/python3.8/functools.py", line 874, in wrapper return dispatch(args[0].__class__)(*args, **kw) File "/public/home/niuxy/Software/miniconda3/envs/commot/lib/python3.8/site-packages/anndata2ri/r2py.py", line 28, in rpy2py_s4 return rpy2py_single_cell_experiment(obj) File "/public/home/niuxy/Software/miniconda3/envs/commot/lib/python3.8/site-packages/anndata2ri/r2py.py", line 95, in rpy2py_single_cell_experiment obs = rpy2py_data_frame(col_data) File "/public/home/niuxy/Software/miniconda3/envs/commot/lib/python3.8/site-packages/anndata2ri/r2py.py", line 58, in rpy2py_data_frame columns = {k: rpy2py_vector(v) for k, v in slots["listData"].items()} File "/public/home/niuxy/Software/miniconda3/envs/commot/lib/python3.8/site-packages/anndata2ri/r2py.py", line 58, in <dictcomp> columns = {k: rpy2py_vector(v) for k, v in slots["listData"].items()} File "/public/home/niuxy/Software/miniconda3/envs/commot/lib/python3.8/site-packages/anndata2ri/r2py.py", line 49, in rpy2py_vector return pandas2ri.rpy2py(v) File "/public/home/niuxy/Software/miniconda3/envs/commot/lib/python3.8/functools.py", line 874, in wrapper return dispatch(args[0].__class__)(*args, **kw) File "/public/home/niuxy/Software/miniconda3/envs/commot/lib/python3.8/site-packages/rpy2/robjects/conversion.py", line 200, in _rpy2py raise NotImplementedError( NotImplementedError: Conversion 'rpy2py' not defined for objects of type '<class 'rpy2.robjects.methods.RS4'>'

Do you have any suggestions?

Added scipy==1.10.1 , as triu is deprecated since SciPy 1.11 and has been removed in SciPy 1.13 .

https://stackoverflow.com/questions/78279136/importerror-cannot-import-name-triu-from-scipy-linalg-gensim

Hello,

I am writing to you because I am currently using your module, but I have been finding this issue specially in this line, which has not let me go further in the analysis I am conducting.

>>> df_cellchat = ct.pp.ligand_receptor_database(species='mouse', signaling_type='Secreted Signaling', database='CellChat')
Traceback (most recent call last):
  File "<string>", line 1, in <module>
AttributeError: module 'commot' has no attribute 'pp'

I have checked everything and I don't seem to find the reason of the problem. I am currently working on Python 3.8.10, and I have installed the last version of COMMOT through GitHub.

When I import the module I get this warning, which I don't know If it has something to do.

>>> import commot as ct
/commot/lib/python3.8/site-packages/anndata/_core/anndata.py:1840: UserWarning: Variable names are not unique. To make them unique, call `.var_names_make_unique`.
  utils.warn_names_duplicates("var")
/commot/lib/python3.8/site-packages/anndata/_core/anndata.py:1840: UserWarning: Variable names are not unique. To make them unique, call `.var_names_make_unique`.

It would mean a lot if you could help me,
Thanks for everything.

Marc

Hi all!

I'd like to use COMMOT in my already processed Seurat data. To this aim, I transformed the Seurat object into AnnData as specified here: https://mojaveazure.github.io/seurat-disk/articles/convert-anndata.html. However, this transformed object has some compatibility problems in Python: Spatial not detected, genes specified differently and not detected...

Is it possible to use COMMOT in my Seurat object to avoid these issues?

Thank you in advance!
Best.

What is a nice job!
There is something wrong. I have installed the right version anndata2ri==1.0.6. However, when importing anndata2ri, I am getting a TypeError. How can I troubleshoot this issue? (I check Requires of anndata2ri: get_version-Version: 3.5.4. May I know which version of get_version you are using?

---> 15 import anndata2ri
16 anndata2ri.activate()

File ~/.conda/envs/commot3/lib/python3.8/site-packages/anndata2ri/init.py:26
22 from get_version import get_version
25 author = "Philipp Angerer"
---> 26 version = get_version(file)
29 def within_flit():
30 for frame in traceback.extract_stack():

File ~/.conda/envs/commot3/lib/python3.8/site-packages/get_version/init.py:273, in get_version(package, dist_name, vcs)
271 for method in methods:
272 try:
--> 273 version = method(parent)
274 except NoVersionFound as e:
275 errors.append(e)

File ~/.conda/envs/commot3/lib/python3.8/site-packages/get_version/init.py:118, in get_version_from_vcs(parent, vcs)
116 parent = parent.resolve()
117 try:
...
--> 151 vcs_e = _detect_vcs()
152 except RuntimeError:
153 return None

TypeError: _detect_vcs() missing 2 required positional arguments: 'expected_vcs' and 'path'

Hi, thanks a lot for the great work!
I am currently using the ct.pl.plot_cluster_communication_network and ct.pl.plot_cluster_communication_network. But it generates two files, containing legend and the actual plot separately. It is a little hard to summarize the results together with it comes to multiple data samples. Would you give me some help regarding this situation? Thank you very much!

Hi, Dr Cang,

COMMOT is an excellent tool for analyzing CCC in ST data.

I can run COMMOT on the sample data from your tutorial. However, I downloaded breast cancer visium data (i.e., filtered_feature_bc_matrix.h5) from
https://www.10xgenomics.com/resources/datasets/human-breast-cancer-block-a-section-1-1-standard-1-1-0, and analyzed it and got the following error.

adata = sc.read_visium("./test/",count_file='filtered_feature_bc_matrix.h5')
adata.var_names_make_unique()

sc.pp.normalize_total(adata, inplace=True)
sc.pp.log1p(adata)

LR=np.array([['Tgfb1', 'Tgfbr1_Tgfbr2', 'Tgfb_pathway'],
['Tgfb2', 'Tgfbr1_Tgfbr2', 'Tgfb_pathway'],
['Tgfb3', 'Tgfbr1_Tgfbr2', 'Tgfb_pathway'],
['Fgf1', 'Fgfr1', 'FGF_pathway'],
['Fgf1', 'Fgfr2', 'FGF_pathway']],dtype=str)
df_ligrec = pd.DataFrame(data=LR)

ct.tl.spatial_communication(adata, database_name='user_database', df_ligrec=df_ligrec, dis_thr=500, heteromeric=True, pathway_sum=True)

Traceback (most recent call last):
File "", line 1, in
File "/home/rub2/miniconda3/envs/commot_env/lib/python3.9/site-packages/commot/tools/_spatial_communication.py", line 418, in spatial_communication
model = CellCommunication(adata,
File "/home/rub2/miniconda3/envs/commot_env/lib/python3.9/site-packages/commot/tools/_spatial_communication.py", line 71, in init
tmp_recs = list(set(df_ligrec.iloc[:,1]))
File "/home/rub2/miniconda3/envs/commot_env/lib/python3.9/site-packages/pandas/core/indexing.py", line 925, in getitem
return self._getitem_tuple(key)
File "/home/rub2/miniconda3/envs/commot_env/lib/python3.9/site-packages/pandas/core/indexing.py", line 1506, in _getitem_tuple
self._has_valid_tuple(tup)
File "/home/rub2/miniconda3/envs/commot_env/lib/python3.9/site-packages/pandas/core/indexing.py", line 754, in _has_valid_tuple
self._validate_key(k, i)
File "/home/rub2/miniconda3/envs/commot_env/lib/python3.9/site-packages/pandas/core/indexing.py", line 1409, in _validate_key
self._validate_integer(key, axis)
File "/home/rub2/miniconda3/envs/commot_env/lib/python3.9/site-packages/pandas/core/indexing.py", line 1500, in _validate_integer
raise IndexError("single positional indexer is out-of-bounds")
IndexError: single positional indexer is out-of-bounds

Thanks.

Best,
Beibei

Hi,

Thank you for the great work. I wonder if we could improv the result of plot_cell_communication.

The problem for the currently output of plot_cell_communication is that it is a global image with white margins (see figure 1 below as an example). If the method is able to crop and zoom in just likesc.pl.spatial (see figure 2 below as an example), the usability of plot_cell_communication will be significantly improved.

Very interesting tool !!!

I have 10x visium ST (multiple samples) and have used cell2location to obtain cell abundance per spots using single cell data.
Next, I am interested in exploring the possibilities of utilizing cell level information along with spatial data for analyzing cell-cell communication. It would be great if you can guide how to use cell labels as an input in COMMOT method ?

I would appreciate all the suggestions!!

Hi developer:
I successful install commot in my new conda environment,but i can't import it.
Here is my code:

import commot as ct
Traceback (most recent call last):
File "", line 1, in
File "/sibcb1/chenluonanlab6/daihao/anaconda3/envs/commot/lib/python3.9/site-packages/commot/init.py", line 5, in
from . import preprocessing as pp
File "/sibcb1/chenluonanlab6/daihao/anaconda3/envs/commot/lib/python3.9/site-packages/commot/preprocessing/init.py", line 1, in
from ._infer_spatial import infer_spatial_information
File "/sibcb1/chenluonanlab6/daihao/anaconda3/envs/commot/lib/python3.9/site-packages/commot/preprocessing/_infer_spatial.py", line 4, in
import scanpy as sc
File "/sibcb1/chenluonanlab6/daihao/anaconda3/envs/commot/lib/python3.9/site-packages/scanpy/init.py", line 16, in
from . import plotting as pl
File "/sibcb1/chenluonanlab6/daihao/anaconda3/envs/commot/lib/python3.9/site-packages/scanpy/plotting/init.py", line 1, in
from ._anndata import (
File "/sibcb1/chenluonanlab6/daihao/anaconda3/envs/commot/lib/python3.9/site-packages/scanpy/plotting/_anndata.py", line 28, in
from . import _utils
File "/sibcb1/chenluonanlab6/daihao/anaconda3/envs/commot/lib/python3.9/site-packages/scanpy/plotting/_utils.py", line 35, in
class _AxesSubplot(Axes, axes.SubplotBase, ABC):
TypeError: metaclass conflict: the metaclass of a derived class must be a (non-strict) subclass of the metaclasses of all its bases

Thanks for your attention!

Thank you for this wonderful tool!

I obtained cell-type-level CCC scores and their associated p-values for multiple samples through the following commands:

pathway = "ACTIVIN"
ct.tl.cluster_communication(adata, database_name = 'cellchat', pathway_name = pathway, clustering = 'cell_type', n_permutations = 100)
ccc_scores = adata.uns['commot_cluster-cell_type-cellchat-' + pathway]["communication_matrix"]
ccc_pvals = adata_disthr.uns['commot_cluster-cell_type-cellchat-' + pathway]["communication_pvalue"]

I found that even though prior data processing/normalization/analysis is uniform across samples, the CCC scores for the same (pathway, cell type 1, cell type 2) combo have quite distinct value distributions across different samples. CCC scores that are similarly significant (p-value = 0) can be very different in terms of magnitude across samples, making subsequent analysis and visualization difficult.

Therefore, I have the following questions:

Is it meaningful to compare the magnitude of CCC scores for the same cell type combination across samples?

• If not, what will be a good way to compare the COMMOT results across different samples?
• If so,
  • What is the possible range of communication_matrix?
  • Is communication_matrix normalized? Would you advise performing normalization/scaling to the scores before comparison? Should the scaling be on a sample level, on a (sample, pathway) level, or on a (sample, cell type 1, cell type 2) level?

Any advice will be much appreciated. Thanks again for your help!

Hello, thank you for your nice work for quantifying spatial signaling.
I got an error when calculating customized pathway using ct.tl.spatial_communication.
I followed the steps in your uploaded code in the breast slide.

Then :


I think I generated the right form, since some pathways were successfully calculated,but more pathways got the error' single positional indexer is out-of-bounds' .
Looking forward to your kind help, thank you!

Hi,

I just have one quick question about the output of tl.cluster_communication_spatial_permutation(). It provided both the communication score matrix and the communication p-value matrix. Since I found they were not symmetric matrices, I would like to check the meaning of the column name and row name: which one represents the sender clusters (of course, another should be the receiver)? I did not find the explanation in the tutorial, not sure if I missed something.

Thanks in advance!

Dear Developer,

I made several attempts to install commit using jupyter and spyder. However, it kept giving me an error message.

xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun error: command '/usr/bin/clang' failed with exit code 1 [end of output]

note: This error originates from a subprocess, and is likely not a problem with pip. ERROR: Failed building wheel for rvlib Running setup.py clean for rvlib Failed to build rvlib Installing collected packages: python-louvain, Levenshtein, rvlib, requests-futures, rasterio, quantecon, python-Levenshtein, python-igraph, pygsp, pot, pandas, leidenalg, inequality, fiona, deprecation, aws-requests-auth, rasterstats, pynndescent, mapclassify, libpysal, karateclub, geopandas, anndata, umap-learn, tobler, spreg, pointpats, momepy, esda, access, spvcm, spglm, spaghetti, scanpy, quilt3, giddy, spopt, splot, spint, segregation, mgwr, pysal, commot Running setup.py install for rvlib ... error error: subprocess-exited-with-error

× Running setup.py install for rvlib did not run successfully. │ exit code: 1 ╰─> [32 lines of output] running install /Users/ayuhutamisyarif/opt/anaconda3/lib/python3.9/site-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools. warnings.warn( running build running build_py creating build creating build/lib.macosx-10.9-x86_64-cpython-39 creating build/lib.macosx-10.9-x86_64-cpython-39/rvlib copying rvlib/univariate.py -> build/lib.macosx-10.9-x86_64-cpython-39/rvlib copying rvlib/version.py -> build/lib.macosx-10.9-x86_64-cpython-39/rvlib copying rvlib/__init__.py -> build/lib.macosx-10.9-x86_64-cpython-39/rvlib copying rvlib/specials.py -> build/lib.macosx-10.9-x86_64-cpython-39/rvlib running egg_info writing rvlib.egg-info/PKG-INFO writing dependency_links to rvlib.egg-info/dependency_links.txt writing requirements to rvlib.egg-info/requires.txt writing top-level names to rvlib.egg-info/top_level.txt reading manifest file 'rvlib.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' adding license file 'LICENSE.txt' writing manifest file 'rvlib.egg-info/SOURCES.txt' copying rvlib/metadata.yaml -> build/lib.macosx-10.9-x86_64-cpython-39/rvlib running build_ext generating cffi module 'build/temp.macosx-10.9-x86_64-cpython-39/rvlib._rmath_ffi.c' creating build/temp.macosx-10.9-x86_64-cpython-39 building 'rvlib._rmath_ffi' extension creating build/temp.macosx-10.9-x86_64-cpython-39/build creating build/temp.macosx-10.9-x86_64-cpython-39/build/temp.macosx-10.9-x86_64-cpython-39 creating build/temp.macosx-10.9-x86_64-cpython-39/src clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /Users/ayuhutamisyarif/opt/anaconda3/include -arch x86_64 -I/Users/ayuhutamisyarif/opt/anaconda3/include -fPIC -O2 -isystem /Users/ayuhutamisyarif/opt/anaconda3/include -arch x86_64 -Isrc -Iinclude -I/Users/ayuhutamisyarif/opt/anaconda3/include/python3.9 -c build/temp.macosx-10.9-x86_64-cpython-39/rvlib._rmath_ffi.c -o build/temp.macosx-10.9-x86_64-cpython-39/build/temp.macosx-10.9-x86_64-cpython-39/rvlib._rmath_ffi.o -DMATHLIB_STANDALONE -std=c99 xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun error: command '/usr/bin/clang' failed with exit code 1 [end of output]

note: This error originates from a subprocess, and is likely not a problem with pip. error: legacy-install-failure

× Encountered error while trying to install package. ╰─> rvlib

note: This is an issue with the package mentioned above, not pip. hint: See above for output from the failure.

I am very new to python and have no idea about this error. Any advice would be so much appreciated

Best,
Ayu

Please refer to igraph instead of python-igraph in the following three locations:

https://github.com/search?q=repo%3Azcang%2FCOMMOT%20python-igraph&type=code

The reasoning is given in igraph/python-igraph#699

Hi, zcang,

I have another question.

When I want to use 'ct.pl.plot_cell_communication' to plot 'sender' and 'receiver' on the same figure , I set 'ax' and got the following error:
__

I see that in function('plot_cell_signaling') , you use the fig, but after I set ax, fig cannot be input from('ct.pl.plot_cell_communication')

Or is there any other way that I can put these two pictures on the same picture？

Thank you very much!

Thank you for your outstanding contribution in the field of cell-cell communication for spatial transcriptome analysis.

As a Python novice, I have been attempting to apply ct.tl.spatial_communication to my own dataset, and have encountered two questions:

What is the recommended approach for running this function in parallel?
Could you explain the rationale behind restricting the distance threshold to 200μm?

Hello,

This is more of a question than an issue. Thank you for the package, and I appreciate if you have the opportunity to clarify this.

How does commot calculates distance in visium data? Is it read from the spaceranger json file? I tried looking into the anndata object, but couldn't find the spatial scale stored. I suppose it could be estimated from the spots positions, knowing they should be 100 microns apart. Is this how it is done? If it is stored in the anndata, how could I access it to crosscheck with the json file?

Thank you!

Hi,

I have a problem to install commot. It is a problem related to rvlib. I am using Windows 10. This is the error I got:

`Building wheels for collected packages: rvlib
Building wheel for rvlib (setup.py) ... error
error: subprocess-exited-with-error

× python setup.py bdist_wheel did not run successfully.
│ exit code: 1
╰─> [103 lines of output]
running bdist_wheel
running build
running build_py
creating build
creating build\lib.win-amd64-cpython-310
creating build\lib.win-amd64-cpython-310\rvlib
copying rvlib\specials.py -> build\lib.win-amd64-cpython-310\rvlib
copying rvlib\univariate.py -> build\lib.win-amd64-cpython-310\rvlib
copying rvlib\version.py -> build\lib.win-amd64-cpython-310\rvlib
copying rvlib_init_.py -> build\lib.win-amd64-cpython-310\rvlib
running egg_info
writing rvlib.egg-info\PKG-INFO
writing dependency_links to rvlib.egg-info\dependency_links.txt
writing requirements to rvlib.egg-info\requires.txt
writing top-level names to rvlib.egg-info\top_level.txt
reading manifest file 'rvlib.egg-info\SOURCES.txt'
reading manifest template 'MANIFEST.in'
adding license file 'LICENSE.txt'
writing manifest file 'rvlib.egg-info\SOURCES.txt'
copying rvlib\metadata.yaml -> build\lib.win-amd64-cpython-310\rvlib
running build_ext
generating cffi module 'build\temp.win-amd64-cpython-310\Release\rvlib._rmath_ffi.c'
creating build\temp.win-amd64-cpython-310
creating build\temp.win-amd64-cpython-310\Release
building 'rvlib._rmath_ffi' extension
creating build\temp.win-amd64-cpython-310\Release\build
creating build\temp.win-amd64-cpython-310\Release\build\temp.win-amd64-cpython-310
creating build\temp.win-amd64-cpython-310\Release\build\temp.win-amd64-cpython-310\Release
creating build\temp.win-amd64-cpython-310\Release\src
"C:\Program Files\Microsoft Visual Studio\2022\Professional\VC\Tools\MSVC\14.35.32215\bin\HostX86\x64\cl.exe" /c /nologo /O2 /W3 /GL /DNDEBUG /MD -Isrc -Iinclude -IC:\Users\adjedi\Anaconda3\envs\commot-env\include -IC:\Users\adjedi\Anaconda3\envs\commot-env\Include "-IC:\Program Files\Microsoft Visual Studio\2022\Professional\VC\Tools\MSVC\14.35.32215\include" "-IC:\Program Files\Microsoft Visual Studio\2022\Professional\VC\Auxiliary\VS\include" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\um" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\shared" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\winrt" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\cppwinrt" "-IC:\Program Files (x86)\Windows Kits\NETFXSDK\4.8\include\um" /Tcbuild\temp.win-amd64-cpython-310\Release\rvlib._rmath_ffi.c /Fobuild\temp.win-amd64-cpython-310\Release\build\temp.win-amd64-cpython-310\Release\rvlib._rmath_ffi.obj -DMATHLIB_STANDALONE -std=c99
cl : Command line warning D9002 : ignoring unknown option '-std=c99'
rvlib._rmath_ffi.c
include\Rconfig.h(16): warning C4005: 'HAVE_HYPOT': macro redefinition
C:\Users\adjedi\Anaconda3\envs\commot-env\include\pyconfig.h(61): note: see previous definition of 'HAVE_HYPOT'
"C:\Program Files\Microsoft Visual Studio\2022\Professional\VC\Tools\MSVC\14.35.32215\bin\HostX86\x64\cl.exe" /c /nologo /O2 /W3 /GL /DNDEBUG /MD -Isrc -Iinclude -IC:\Users\adjedi\Anaconda3\envs\commot-env\include -IC:\Users\adjedi\Anaconda3\envs\commot-env\Include "-IC:\Program Files\Microsoft Visual Studio\2022\Professional\VC\Tools\MSVC\14.35.32215\include" "-IC:\Program Files\Microsoft Visual Studio\2022\Professional\VC\Auxiliary\VS\include" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\um" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\shared" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\winrt" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\cppwinrt" "-IC:\Program Files (x86)\Windows Kits\NETFXSDK\4.8\include\um" /Tcsrc\bd0.c /Fobuild\temp.win-amd64-cpython-310\Release\src\bd0.obj -DMATHLIB_STANDALONE -std=c99
cl : Command line warning D9002 : ignoring unknown option '-std=c99'
bd0.c
C:\Program Files\Microsoft Visual Studio\2022\Professional\VC\Tools\MSVC\14.35.32215\include\stdarg.h(13): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files\Microsoft Visual Studio\2022\Professional\VC\Tools\MSVC\14.35.32215\include\stdarg.h(14): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files\Microsoft Visual Studio\2022\Professional\VC\Tools\MSVC\14.35.32215\include\stdarg.h(29): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\corecrt_stdio_config.h(12): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\corecrt_stdio_config.h(13): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\corecrt_stdio_config.h(131): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\corecrt_wstdio.h(15): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\corecrt_wstdio.h(16): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\corecrt_wstdio.h(1130): warning C4996: '_vsnwprintf_l': This function or variable may be unsafe. Consider using _vsnwprintf_s_l instead. To disable deprecation, use _CRT_SECURE_NO_WARNINGS. See online help for details.
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\corecrt_wstdio.h(1640): warning C4996: '_vsnwprintf_l': This function or variable may be unsafe. Consider using _vsnwprintf_s_l instead. To disable deprecation, use _CRT_SECURE_NO_WARNINGS. See online help for details.
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\corecrt_wstdio.h(1662): warning C4996: '_vsnwprintf_l': This function or variable may be unsafe. Consider using _vsnwprintf_s_l instead. To disable deprecation, use _CRT_SECURE_NO_WARNINGS. See online help for details.
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\corecrt_wstdio.h(1797): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\corecrt_wstdio.h(1798): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\corecrt_wstdio.h(1854): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\corecrt_wstdio.h(2094): warning C4996: '_vsnwscanf_l': This function or variable may be unsafe. Consider using _vsnwscanf_s_l instead. To disable deprecation, use _CRT_SECURE_NO_WARNINGS. See online help for details.
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\corecrt_wstdio.h(2116): warning C4996: '_vsnwscanf_l': This function or variable may be unsafe. Consider using _vsnwscanf_s_l instead. To disable deprecation, use _CRT_SECURE_NO_WARNINGS. See online help for details.
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\corecrt_wstdio.h(2171): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdio.h(15): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdio.h(16): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdio.h(1412): warning C4996: '_vsnprintf_l': This function or variable may be unsafe. Consider using _vsnprintf_s_l instead. To disable deprecation, use _CRT_SECURE_NO_WARNINGS. See online help for details.
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdio.h(1459): warning C4996: '_vsnprintf_l': This function or variable may be unsafe. Consider using _vsnprintf_s_l instead. To disable deprecation, use _CRT_SECURE_NO_WARNINGS. See online help for details.
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdio.h(1474): warning C4996: '_vsnprintf_l': This function or variable may be unsafe. Consider using _vsnprintf_s_l instead. To disable deprecation, use _CRT_SECURE_NO_WARNINGS. See online help for details.
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdio.h(1755): warning C4996: '_vsprintf_l': This function or variable may be unsafe. Consider using _vsprintf_s_l instead. To disable deprecation, use _CRT_SECURE_NO_WARNINGS. See online help for details.
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdio.h(1776): warning C4996: '_vsprintf_l': This function or variable may be unsafe. Consider using _vsprintf_s_l instead. To disable deprecation, use _CRT_SECURE_NO_WARNINGS. See online help for details.
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdio.h(1899): warning C4996: '_vsnprintf_l': This function or variable may be unsafe. Consider using _vsnprintf_s_l instead. To disable deprecation, use _CRT_SECURE_NO_WARNINGS. See online help for details.
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdio.h(2192): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdio.h(2193): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdio.h(2216): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdio.h(2300): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdio.h(2301): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdio.h(2398): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdio.h(2447): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\corecrt_malloc.h(13): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\corecrt_malloc.h(14): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\corecrt_malloc.h(234): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\corecrt_search.h(16): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\corecrt_search.h(17): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\corecrt_search.h(218): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\corecrt_wstdlib.h(13): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\corecrt_wstdlib.h(14): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\corecrt_wstdlib.h(481): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files\Microsoft Visual Studio\2022\Professional\VC\Tools\MSVC\14.35.32215\include\limits.h(13): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files\Microsoft Visual Studio\2022\Professional\VC\Tools\MSVC\14.35.32215\include\limits.h(14): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files\Microsoft Visual Studio\2022\Professional\VC\Tools\MSVC\14.35.32215\include\limits.h(78): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdlib.h(18): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdlib.h(19): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdlib.h(308): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdlib.h(309): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdlib.h(343): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdlib.h(1217): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdlib.h(1218): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdlib.h(1231): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdlib.h(1289): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdlib.h(1290): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdlib.h(1292): warning C4141: 'deprecated': used more than once
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdlib.h(1300): warning C4141: 'deprecated': used more than once
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdlib.h(1308): warning C4141: 'deprecated': used more than once
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdlib.h(1315): warning C4141: 'deprecated': used more than once
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdlib.h(1322): warning C4141: 'deprecated': used more than once
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdlib.h(1337): warning C4141: 'deprecated': used more than once
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdlib.h(1351): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdlib.h(1361): warning C4068: unknown pragma 'Rf_warning'
src\bd0.c(42): warning C4068: unknown pragma 'Rf_warning'
src\bd0.c(42): warning C4068: unknown pragma 'Rf_warning'
src\bd0.c(42): error C2124: divide or mod by zero
error: command 'C:\Program Files\Microsoft Visual Studio\2022\Professional\VC\Tools\MSVC\14.35.32215\bin\HostX86\x64\cl.exe' failed with exit code 2
[end of output]

note: This error originates from a subprocess, and is likely not a problem with pip.
ERROR: Failed building wheel for rvlib
Running setup.py clean for rvlib
Failed to build rvlib
Installing collected packages: rvlib, requests-futures, quantecon, python-Levenshtein, pygsp, pot, pandas, miniful, matplotlib, inequality, cligj, click-plugins, botocore, aws-requests-auth, statsmodels, seaborn, s3transfer, rasterio, pynndescent, mapclassify, libpysal, fst-pso, fiona, anndata, umap-learn, spreg, rasterstats, pyfume, pointpats, geopandas, esda, boto3, tobler, spvcm, spglm, spaghetti, scanpy, quilt3, momepy, giddy, FuzzyTM, access, spopt, splot, spint, segregation, mgwr, gensim, pysal, karateclub, commot
Running setup.py install for rvlib ... error
error: subprocess-exited-with-error

× Running setup.py install for rvlib did not run successfully.
│ exit code: 1
╰─> [105 lines of output]
running install
C:\Users\adjedi\Anaconda3\envs\commot-env\lib\site-packages\setuptools\command\install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools.
warnings.warn(
running build
running build_py
creating build
creating build\lib.win-amd64-cpython-310
creating build\lib.win-amd64-cpython-310\rvlib
copying rvlib\specials.py -> build\lib.win-amd64-cpython-310\rvlib
copying rvlib\univariate.py -> build\lib.win-amd64-cpython-310\rvlib
copying rvlib\version.py -> build\lib.win-amd64-cpython-310\rvlib
copying rvlib_init_.py -> build\lib.win-amd64-cpython-310\rvlib
running egg_info
writing rvlib.egg-info\PKG-INFO
writing dependency_links to rvlib.egg-info\dependency_links.txt
writing requirements to rvlib.egg-info\requires.txt
writing top-level names to rvlib.egg-info\top_level.txt
reading manifest file 'rvlib.egg-info\SOURCES.txt'
reading manifest template 'MANIFEST.in'
adding license file 'LICENSE.txt'
writing manifest file 'rvlib.egg-info\SOURCES.txt'
copying rvlib\metadata.yaml -> build\lib.win-amd64-cpython-310\rvlib
running build_ext
generating cffi module 'build\temp.win-amd64-cpython-310\Release\rvlib._rmath_ffi.c'
creating build\temp.win-amd64-cpython-310
creating build\temp.win-amd64-cpython-310\Release
building 'rvlib._rmath_ffi' extension
creating build\temp.win-amd64-cpython-310\Release\build
creating build\temp.win-amd64-cpython-310\Release\build\temp.win-amd64-cpython-310
creating build\temp.win-amd64-cpython-310\Release\build\temp.win-amd64-cpython-310\Release
creating build\temp.win-amd64-cpython-310\Release\src
"C:\Program Files\Microsoft Visual Studio\2022\Professional\VC\Tools\MSVC\14.35.32215\bin\HostX86\x64\cl.exe" /c /nologo /O2 /W3 /GL /DNDEBUG /MD -Isrc -Iinclude -IC:\Users\adjedi\Anaconda3\envs\commot-env\include -IC:\Users\adjedi\Anaconda3\envs\commot-env\Include "-IC:\Program Files\Microsoft Visual Studio\2022\Professional\VC\Tools\MSVC\14.35.32215\include" "-IC:\Program Files\Microsoft Visual Studio\2022\Professional\VC\Auxiliary\VS\include" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\um" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\shared" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\winrt" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\cppwinrt" "-IC:\Program Files (x86)\Windows Kits\NETFXSDK\4.8\include\um" /Tcbuild\temp.win-amd64-cpython-310\Release\rvlib._rmath_ffi.c /Fobuild\temp.win-amd64-cpython-310\Release\build\temp.win-amd64-cpython-310\Release\rvlib._rmath_ffi.obj -DMATHLIB_STANDALONE -std=c99
cl : Command line warning D9002 : ignoring unknown option '-std=c99'
rvlib._rmath_ffi.c
include\Rconfig.h(16): warning C4005: 'HAVE_HYPOT': macro redefinition
C:\Users\adjedi\Anaconda3\envs\commot-env\include\pyconfig.h(61): note: see previous definition of 'HAVE_HYPOT'
"C:\Program Files\Microsoft Visual Studio\2022\Professional\VC\Tools\MSVC\14.35.32215\bin\HostX86\x64\cl.exe" /c /nologo /O2 /W3 /GL /DNDEBUG /MD -Isrc -Iinclude -IC:\Users\adjedi\Anaconda3\envs\commot-env\include -IC:\Users\adjedi\Anaconda3\envs\commot-env\Include "-IC:\Program Files\Microsoft Visual Studio\2022\Professional\VC\Tools\MSVC\14.35.32215\include" "-IC:\Program Files\Microsoft Visual Studio\2022\Professional\VC\Auxiliary\VS\include" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\um" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\shared" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\winrt" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\cppwinrt" "-IC:\Program Files (x86)\Windows Kits\NETFXSDK\4.8\include\um" /Tcsrc\bd0.c /Fobuild\temp.win-amd64-cpython-310\Release\src\bd0.obj -DMATHLIB_STANDALONE -std=c99
cl : Command line warning D9002 : ignoring unknown option '-std=c99'
bd0.c
C:\Program Files\Microsoft Visual Studio\2022\Professional\VC\Tools\MSVC\14.35.32215\include\stdarg.h(13): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files\Microsoft Visual Studio\2022\Professional\VC\Tools\MSVC\14.35.32215\include\stdarg.h(14): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files\Microsoft Visual Studio\2022\Professional\VC\Tools\MSVC\14.35.32215\include\stdarg.h(29): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\corecrt_stdio_config.h(12): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\corecrt_stdio_config.h(13): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\corecrt_stdio_config.h(131): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\corecrt_wstdio.h(15): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\corecrt_wstdio.h(16): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\corecrt_wstdio.h(1130): warning C4996: '_vsnwprintf_l': This function or variable may be unsafe. Consider using _vsnwprintf_s_l instead. To disable deprecation, use _CRT_SECURE_NO_WARNINGS. See online help for details.
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\corecrt_wstdio.h(1640): warning C4996: '_vsnwprintf_l': This function or variable may be unsafe. Consider using _vsnwprintf_s_l instead. To disable deprecation, use _CRT_SECURE_NO_WARNINGS. See online help for details.
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\corecrt_wstdio.h(1662): warning C4996: '_vsnwprintf_l': This function or variable may be unsafe. Consider using _vsnwprintf_s_l instead. To disable deprecation, use _CRT_SECURE_NO_WARNINGS. See online help for details.
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\corecrt_wstdio.h(1797): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\corecrt_wstdio.h(1798): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\corecrt_wstdio.h(1854): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\corecrt_wstdio.h(2094): warning C4996: '_vsnwscanf_l': This function or variable may be unsafe. Consider using _vsnwscanf_s_l instead. To disable deprecation, use _CRT_SECURE_NO_WARNINGS. See online help for details.
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\corecrt_wstdio.h(2116): warning C4996: '_vsnwscanf_l': This function or variable may be unsafe. Consider using _vsnwscanf_s_l instead. To disable deprecation, use _CRT_SECURE_NO_WARNINGS. See online help for details.
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\corecrt_wstdio.h(2171): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdio.h(15): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdio.h(16): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdio.h(1412): warning C4996: '_vsnprintf_l': This function or variable may be unsafe. Consider using _vsnprintf_s_l instead. To disable deprecation, use _CRT_SECURE_NO_WARNINGS. See online help for details.
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdio.h(1459): warning C4996: '_vsnprintf_l': This function or variable may be unsafe. Consider using _vsnprintf_s_l instead. To disable deprecation, use _CRT_SECURE_NO_WARNINGS. See online help for details.
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdio.h(1474): warning C4996: '_vsnprintf_l': This function or variable may be unsafe. Consider using _vsnprintf_s_l instead. To disable deprecation, use _CRT_SECURE_NO_WARNINGS. See online help for details.
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdio.h(1755): warning C4996: '_vsprintf_l': This function or variable may be unsafe. Consider using _vsprintf_s_l instead. To disable deprecation, use _CRT_SECURE_NO_WARNINGS. See online help for details.
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdio.h(1776): warning C4996: '_vsprintf_l': This function or variable may be unsafe. Consider using _vsprintf_s_l instead. To disable deprecation, use _CRT_SECURE_NO_WARNINGS. See online help for details.
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdio.h(1899): warning C4996: '_vsnprintf_l': This function or variable may be unsafe. Consider using _vsnprintf_s_l instead. To disable deprecation, use _CRT_SECURE_NO_WARNINGS. See online help for details.
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdio.h(2192): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdio.h(2193): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdio.h(2216): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdio.h(2300): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdio.h(2301): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdio.h(2398): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdio.h(2447): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\corecrt_malloc.h(13): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\corecrt_malloc.h(14): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\corecrt_malloc.h(234): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\corecrt_search.h(16): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\corecrt_search.h(17): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\corecrt_search.h(218): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\corecrt_wstdlib.h(13): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\corecrt_wstdlib.h(14): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\corecrt_wstdlib.h(481): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files\Microsoft Visual Studio\2022\Professional\VC\Tools\MSVC\14.35.32215\include\limits.h(13): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files\Microsoft Visual Studio\2022\Professional\VC\Tools\MSVC\14.35.32215\include\limits.h(14): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files\Microsoft Visual Studio\2022\Professional\VC\Tools\MSVC\14.35.32215\include\limits.h(78): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdlib.h(18): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdlib.h(19): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdlib.h(308): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdlib.h(309): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdlib.h(343): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdlib.h(1217): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdlib.h(1218): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdlib.h(1231): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdlib.h(1289): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdlib.h(1290): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdlib.h(1292): warning C4141: 'deprecated': used more than once
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdlib.h(1300): warning C4141: 'deprecated': used more than once
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdlib.h(1308): warning C4141: 'deprecated': used more than once
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdlib.h(1315): warning C4141: 'deprecated': used more than once
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdlib.h(1322): warning C4141: 'deprecated': used more than once
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdlib.h(1337): warning C4141: 'deprecated': used more than once
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdlib.h(1351): warning C4068: unknown pragma 'Rf_warning'
C:\Program Files (x86)\Windows Kits\10\include\10.0.22621.0\ucrt\stdlib.h(1361): warning C4068: unknown pragma 'Rf_warning'
src\bd0.c(42): warning C4068: unknown pragma 'Rf_warning'
src\bd0.c(42): warning C4068: unknown pragma 'Rf_warning'
src\bd0.c(42): error C2124: divide or mod by zero
error: command 'C:\Program Files\Microsoft Visual Studio\2022\Professional\VC\Tools\MSVC\14.35.32215\bin\HostX86\x64\cl.exe' failed with exit code 2
[end of output]

note: This error originates from a subprocess, and is likely not a problem with pip.
error: legacy-install-failure

× Encountered error while trying to install package.
╰─> rvlib

note: This is an issue with the package mentioned above, not pip.
hint: See above for output from the failure.`

Do you have any ideas to solve it ?

Thanks a lot,

Best

Hi Zixuan. Could you provide the codes for simulating the data? Or where should I find them?

Hi, when I want to use 'ct.pl.plot_cell_communication' to plot CCC, I got the following error:

Maybe you can help me solve it？

Hi COMMOT developers,
Thanks for providing such an awesome tool for us. I am now using COMMOT on my Visium data and having some questions about the distance threshold:

1. The default unit in adata.obsm['spatial'] is pixel but not μm, so the value you used in the tutorial is 200 pixel, but not 200μm, am I right?
2. I noted that you used 1000 μm for Visium data in the NM paper. How did you tranform the pixel to μm? What scale factor should be used?
3. Is there any general guidance on selecting this threshold? Or some recommended value?

Thanks in advance.

Yang

hi, thanks for the tool! I have a question for you.
when I run 'ct.tl.communication_deg_detection' :
'df_deg, df_yhat = ct.tl.communication_deg_detection(adata,
database_name = 'cellchat', pathway_name='GRN', summary = 'receiver')'
some errors occurred: (i have no idea about this, looking forward to your reply!)
Traceback (most recent call last):
File "/dellfsqd2/ST_LBI/USER/zhaowandong/projects/wochong/05.test/ccc/A8_deg.py", line 18, in
df_deg, df_yhat = ct.tl.communication_deg_detection(adata,
File "/dellfsqd2/ST_LBI/USER/zhaowandong/Tools/anaconda3/envs/py3.8/lib/python3.8/site-packages/commot/tools/_downstream_analysis.py", line 168, in communication_deg_detection
ro.r(string_cluster)
File "/dellfsqd2/ST_LBI/USER/zhaowandong/Tools/anaconda3/envs/py3.8/lib/python3.8/site-packages/rpy2/robjects/init.py", line 501, in call
res, visible = rinterface.evalr_expr_with_visible( # type: ignore
File "/dellfsqd2/ST_LBI/USER/zhaowandong/Tools/anaconda3/envs/py3.8/lib/python3.8/site-packages/rpy2/rinterface.py", line 183, in evalr_expr_with_visible
raise embedded.RRuntimeError(_rinterface._geterrmessage())
rpy2.rinterface_lib.embedded.RRuntimeError: Error in .clusterExpressionPatterns(models = models, nPoints = nPoints, :
Not all gene IDs are present in the models object.

Hello

I followed tutorial https://github.com/zcang/COMMOT/blob/main/docs/notebooks/visium-mouse_brain.ipynb on one of the 10x visium based ST test data in our lab.

But in output, it looks like there might be an issue with the orientation of images.

ct.pl.plot_cell_communication(adata_dis500, database_name='cellchat', pathway_name='COMPLEMENT', plot_method='grid', background_legend=True,
scale=0.00003, ndsize=10, grid_density=0.5, summary='sender', background='image', clustering='leiden', cmap='Alphabet',
normalize_v = True, normalize_v_quantile=0.995)

Please let me know how can I fix this issue .

I would appreciate all the suggestion!!!

Hi ,
When I use 'ct.tl.spatial_communication', I noticed that your description of ‘dis_thr’ in the tutorial is 'The threshold of spatial distance of signaling.', but I don't understand what the units of this number are, is it the number of cells? Or um?
And how do I set an appropriate distance for my organization? According to the max area?