deep-learning-tools2: error when using python with R-notebook and reticulate

[hannaboe]

I installed the deep-learning-tool with this docker-image: quay.io/nird-toolkit/deep-learning-tools2:20220303-cbd3b76. But when I open a R-notebook, I can't run code that uses python (using the reticulate package).

When I run reticulate::py_discover_config() to check which python version is used I get the following error:

Warning message in system2(conda, c("run", in_env, run_args, shQuote(cmd), args), : “running command ''/opt/conda/bin/conda' run --prefix '/opt/conda' --no-capture-output 'python' -c "import os; print(os.environ['PATH'])"' had status 1” Error in Sys.setenv(PATH = new_path): wrong length for argument Traceback:

1. py_discover_config() 2. python_config(python_version, required_module, python_versions) 3. python_munge_path(python) 4. Sys.setenv(PATH = new_path)

And I get a similar error when I run other code that uses python. For example when trying to train a deep learning model using the R-package keras.

[frafra]

It looks that it is trying to use conda, even if it is not installed, for some reason.

Here is what I tried from the R console:

> library('reticulate')
> reticulate::py_discover_config()

Output:

No non-system installation of Python could be found.
Would you like to download and install Miniconda?
Miniconda is an open source environment management system for Python.
See https://docs.conda.io/en/latest/miniconda.html for more details.

Would you like to install Miniconda? [Y/n]: n
Installation aborted.
python:         /usr/bin/python3
libpython:      [NOT FOUND]
pythonhome:     //usr://usr
version:        3.8.10 (default, Nov 26 2021, 20:14:08)  [GCC 9.3.0]
numpy:          [NOT FOUND]

I then tried to install miniconda using: reticulate::install_miniconda(). It seems to work just fine, and it satisfies all dependencies.

[hannaboe]

Now it doesn't find tensorflow anymore because it looks for it in the r-reticulate environment.

Error: Valid installation of TensorFlow not found. Python environments searched for 'tensorflow' package: /home/hbo042/.local/share/r-miniconda/envs/r-reticulate/bin/python3.8 Python exception encountered: ModuleNotFoundError: No module named 'tensorflow'

Should I try to install tensorflow and all other dependencies within this environment?

This wasn't an issue with the 'old' tensorflow1 deep-learning-tool.

[frafra]

You can avoid to use miniconda and just install numpy, so you avoid having a separate environment.

[hannaboe]

I installed numpy, but that didn't help. I got the same error.
I assumeit is because python is also installed in the r-reticulate environment. It only finds this python installation so it automatically switches to the environment. And tensorflow is not installed in the environment.

[frafra]

Unable to replicate. Feel free to reach me on the phone or just have a meeting.

[frafra]

Fixed by deleting ~/.local/share/r-reticulate, ~/.local/share/r-miniconda.