I was able to install numpy and all other python dependencies except matplotlib. Please let me know what is going on.
reticulate::py_install("matplotlib") Collecting package metadata (current_repodata.json): ...working... done Solving environment: ...working... done
All requested packages already installed. reticulate::py_config() python: /opt/anaconda3/bin/python libpython: /opt/anaconda3/lib/libpython3.7m.dylib pythonhome: /opt/anaconda3:/opt/anaconda3 version: 3.7.6 (default, Jan 8 2020, 13:42:34) [Clang 4.0.1 (tags/RELEASE_401/final)] numpy: /opt/anaconda3/lib/python3.7/site-packages/numpy numpy_version: 1.21.6 magic: /opt/anaconda3/lib/python3.7/site-packages/magic
NOTE: Python version was forced by use_python function
reticulate::py_discover_config() python: /opt/anaconda3/bin/python libpython: /opt/anaconda3/lib/libpython3.7m.dylib pythonhome: /opt/anaconda3:/opt/anaconda3 version: 3.7.6 (default, Jan 8 2020, 13:42:34) [Clang 4.0.1 (tags/RELEASE_401/final)] numpy: /opt/anaconda3/lib/python3.7/site-packages/numpy numpy_version: 1.21.6
phate.tree <- phate(tree.data.small$data) Error in py_module_import(module, convert = convert) : ModuleNotFoundError: No module named 'matplotlib.pyplot' Error in py_module_import(module, convert = convert) : ModuleNotFoundError: No module named 'matplotlib.pyplot'
Could you show the output of
reticulate::py_discover_config(required_module="phate")?reticulate::py_discover_config(required_module = "phate") when I run on R
python: /opt/anaconda3/bin/python libpython: /opt/anaconda3/lib/libpython3.7m.dylib pythonhome: /opt/anaconda3:/opt/anaconda3 version: 3.7.6 (default, Jan 8 2020, 13:42:34) [Clang 4.0.1 (tags/RELEASE_401/final)] numpy: /opt/anaconda3/lib/python3.7/site-packages/numpy numpy_version: 1.21.6 phate: /Users/abhaykanodia/.local/lib/python3.7/site-packages/phate-1.0.7-py3.7.egg/phate
NOTE: Python version was forced by use_python function
Output of reticulate::py_discover_config(required_module = "phate"): When I run on Terminal
Error in python_config_impl(python) :
Error 137 occurred running /Users/abhaykanodia/.virtualenvs/r-reticulate/bin/python:
In addition: Warning message:
In system2(command = python, args = shQuote(script), stdout = TRUE, :
running command ''/Users/abhaykanodia/.virtualenvs/r-reticulate/bin/python' '/Library/Frameworks/R.framework/Versions/4.1/Resources/library/reticulate/config/config.py' 2>/dev/null' had status 137
Even though I installed matplotlib when I import phate it says "ModuleNotFoundError: No module named 'matplotlib.pyplot' "
(base) MacBook-Pro:Python abhaykanodia$ python -m pip install matplotlib
Requirement already satisfied: matplotlib in /opt/anaconda3/lib/python3.7/site-packages (3.1.3)
Requirement already satisfied: python-dateutil>=2.1 in /opt/anaconda3/lib/python3.7/site-packages (from matplotlib) (2.8.2)
Requirement already satisfied: cycler>=0.10 in /opt/anaconda3/lib/python3.7/site-packages (from matplotlib) (0.11.0)
Requirement already satisfied: kiwisolver>=1.0.1 in /opt/anaconda3/lib/python3.7/site-packages (from matplotlib) (1.4.2)
Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /opt/anaconda3/lib/python3.7/site-packages (from matplotlib) (3.0.8)
Requirement already satisfied: numpy>=1.11 in /opt/anaconda3/lib/python3.7/site-packages (from matplotlib) (1.21.6)
Requirement already satisfied: typing-extensions in /opt/anaconda3/lib/python3.7/site-packages (from kiwisolver>=1.0.1->matplotlib) (4.2.0)
Requirement already satisfied: six>=1.5 in /opt/anaconda3/lib/python3.7/site-packages (from python-dateutil>=2.1->matplotlib) (1.16.0)
(base) MacBook-Pro:Python abhaykanodia$ Python
Python 3.7.6 (default, Jan 8 2020, 13:42:34)
[Clang 4.0.1 (tags/RELEASE_401/final)] :: Anaconda, Inc. on darwin
Type "help", "copyright", "credits" or "license" for more information.
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/Users/abhaykanodia/PHATE/Python/phate/__init__.py", line 3, in <module>
File "/Users/abhaykanodia/PHATE/Python/phate/phate.py", line 17, in <module>
ModuleNotFoundError: No module named 'matplotlib.pyplot'
I think the main issue here is that you did not install phate in your python path, because your python version is in an anaconda environment and your phate version is in the user path. You need to homogenize your environments
Thanks a lot for your help!
I was able to resolve the issue but now the issue is with magic now. I would be very grateful if I could resolve this issue.
I ran these commands and the output was as follows:
In R:
In Terminal
pip3 install magic-impute
Requirement already satisfied: magic-impute in ./opt/anaconda3/lib/python3.9/site-packages (3.0.0)
Requirement already satisfied: scipy>=1.1.0 in ./opt/anaconda3/lib/python3.9/site-packages (from magic-impute) (1.7.1)
Requirement already satisfied: scikit-learn>=0.19.1 in ./opt/anaconda3/lib/python3.9/site-packages (from magic-impute) (0.24.2)
Requirement already satisfied: graphtools>=1.4.0 in ./opt/anaconda3/lib/python3.9/site-packages (from magic-impute) (1.5.2)
Requirement already satisfied: tasklogger>=1.0.0 in ./opt/anaconda3/lib/python3.9/site-packages (from magic-impute) (1.1.2)
Requirement already satisfied: matplotlib in ./opt/anaconda3/lib/python3.9/site-packages (from magic-impute) (3.4.3)
Requirement already satisfied: future in ./opt/anaconda3/lib/python3.9/site-packages (from magic-impute) (0.18.2)
Requirement already satisfied: numpy>=1.14.0 in ./opt/anaconda3/lib/python3.9/site-packages (from magic-impute) (1.20.3)
Requirement already satisfied: pandas>=0.25 in ./opt/anaconda3/lib/python3.9/site-packages (from magic-impute) (1.3.4)
Requirement already satisfied: scprep>=1.0 in ./opt/anaconda3/lib/python3.9/site-packages (from magic-impute) (1.1.0)
Requirement already satisfied: pygsp>=0.5.1 in ./opt/anaconda3/lib/python3.9/site-packages (from graphtools>=1.4.0->magic-impute) (0.5.1)
Requirement already satisfied: Deprecated in ./opt/anaconda3/lib/python3.9/site-packages (from graphtools>=1.4.0->magic-impute) (1.2.13)
Requirement already satisfied: python-dateutil>=2.7.3 in ./opt/anaconda3/lib/python3.9/site-packages (from pandas>=0.25->magic-impute) (2.8.2)
Requirement already satisfied: pytz>=2017.3 in ./opt/anaconda3/lib/python3.9/site-packages (from pandas>=0.25->magic-impute) (2021.3)
Requirement already satisfied: six>=1.5 in ./opt/anaconda3/lib/python3.9/site-packages (from python-dateutil>=2.7.3->pandas>=0.25->magic-impute) (1.16.0)
Requirement already satisfied: joblib>=0.11 in ./opt/anaconda3/lib/python3.9/site-packages (from scikit-learn>=0.19.1->magic-impute) (1.1.0)
Requirement already satisfied: threadpoolctl>=2.0.0 in ./opt/anaconda3/lib/python3.9/site-packages (from scikit-learn>=0.19.1->magic-impute) (2.2.0)
Requirement already satisfied: packaging in ./opt/anaconda3/lib/python3.9/site-packages (from scprep>=1.0->magic-impute) (21.0)
Requirement already satisfied: decorator>=4.3.0 in ./opt/anaconda3/lib/python3.9/site-packages (from scprep>=1.0->magic-impute) (5.1.0)
Requirement already satisfied: wrapt<2,>=1.10 in ./opt/anaconda3/lib/python3.9/site-packages (from Deprecated->graphtools>=1.4.0->magic-impute) (1.12.1)
Requirement already satisfied: kiwisolver>=1.0.1 in ./opt/anaconda3/lib/python3.9/site-packages (from matplotlib->magic-impute) (1.3.1)
Requirement already satisfied: cycler>=0.10 in ./opt/anaconda3/lib/python3.9/site-packages (from matplotlib->magic-impute) (0.10.0)
Requirement already satisfied: pillow>=6.2.0 in ./opt/anaconda3/lib/python3.9/site-packages (from matplotlib->magic-impute) (8.4.0)
Requirement already satisfied: pyparsing>=2.2.1 in ./opt/anaconda3/lib/python3.9/site-packages (from matplotlib->magic-impute) (3.0.4)
Thank you!