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drieslab / Giotto

Spatial omics analysis toolbox
https://drieslab.github.io/Giotto_website/
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Error: 'miniconda_path' is not an exported object from 'namespace:reticulate' #91

Closed yanwengong closed 3 years ago

yanwengong commented 3 years ago

Hi.

I created a Conda env called giotto where I install all the required python package through conda install (note I have anaconda3 instead of miniconda ).

python_path <- "/Users/your_username/anaconda3/envs/giotto/bin/python" instrs = createGiottoInstructions(show_plot = TRUE, save_plot = TRUE, save_dir = results_folder, python_path = python_path)

I got the error of "Error: 'miniconda_path' is not an exported object from 'namespace:reticulate'"

Then, I tried to use the following code to install the python packages automatically: python_path = NULL if(is.null(python_path)) { installGiottoEnvironment(force_miniconda = TRUE) }

Got the same error " Error: 'miniconda_path' is not an exported object from 'namespace:reticulate' "

Do you know what's happening?

RubD commented 3 years ago

Hi,

Can you try to install the Giotto environment like installGiottoEnvironment(force_miniconda = TRUE) from a fresh R session? So without loading any other library (besided Giotto) or running a prior analysis. This should normally work.

If that works I can further try to figure out why you can not provide your own python path. That should normally work. Which reticulate version are you using?

yanwengong commented 3 years ago

Hi. I tried installGiottoEnvironment(force_miniconda = TRUE) from a fresh R session, but still get " Error: 'miniconda_path' is not an exported object from 'namespace:reticulate'"

packageVersion("reticulate") [1] ‘1.13’

RubD commented 3 years ago

Ok, thanks for the feedback. I think it's related to the version of reticulate you're using. If you upgrade to the newest version it should work. I think anything > 1.15 should actually work. If this solves the issue, then I'll also update this in Giotto.

yanwengong commented 3 years ago

Hi. I updated reticulate to ‘1.18’ and it worked. Thanks for the suggestion!