Micromamba env created from yaml: /bin/micromamba env: No such file or directory

[ktmeaton]

Error

Very exciting to see micromamba supported, thank you so much! I'm getting this error when I try to use reticulate=1.30 in an environment created from a YAML file with micromamba=1.49. It appears as if reticulate can't find the python binary, and is trying to use the 'conda' binary instead.

Error in normalizePath(conda, winslash = "/", mustWork = TRUE) :
  path[1]="/home/username/.local/bin/micromamba env": No such file or directory
Calls: <Anonymous> ... python_munge_path -> get_python_conda_info -> normalizePath
Execution halted

Environment from CLI (Works)

Creating the environment plainly from the CLI works for me with no errors.

micromamba create -y -n reticulate-from-cli r-base=4.2.1 r-reticulate=1.30
micromamba run -n reticulate-from-cli Rscript -e 'reticulate::use_condaenv("reticulate-from-cli")'

Environment from YAML (Error)

However creating from an environment.yaml file causes errors.

name: reticulate-from-yaml
channels:
  - conda-forge
  - defaults
dependencies:
  - conda-forge::r-base=4.2.1
  - conda-forge::r-reticulate=1.30

micromamba env create  -y -f environment.yaml -n reticulate-from-yaml
micromamba run -n reticulate-from-yaml Rscript -e 'reticulate::use_condaenv("reticulate-from-yaml")'

Error in normalizePath(conda, winslash = "/", mustWork = TRUE) :
  path[1]="/home/username/.local/bin/micromamba env": No such file or directory
Calls: <Anonymous> ... python_munge_path -> get_python_conda_info -> normalizePath
Execution halted

These two environments are otherwise identical with no differences, and both have python3.11 installed.

micromamba -n reticulate-from-cli list > reticulate-from-cli.txt
micromamba -n reticulate-from-yaml list > reticulate-from-yaml.txt

diff reticulate-from-cli.txt reticulate-from-yaml.txt

conda vs mamba vs micromamba

This seems to be restricted to micromamba=1.49 as mamba=1.49 has no errors.

mamba env create -f environment.yaml -n reticulate-from-yaml-mamba
mamba run -n reticulate-from-yaml-mamba Rscript -e 'reticulate::use_condaenv("reticulate-from-yaml-mamba")'

I'm mystified about this error, any feedback would be greatly appreciated!

[zia1138]

@ktmeaton Curious if you use commit ae96550 and use devtools::install('reticulate') to install from source and then run:
use_condaenv("~/path_to_env", "~/pathto_micromamba/micromamba")
Does it work then? It's not an ideal fix since it uses globals, but it does help isolate the issue.
Thanks!

[kmartinez834]

I ran into a similar problem when trying to use Micromamba.

SOLUTION:

options(reticulate.conda_binary = "/pathto_micromamba/micromamba")
use_condaenv(condaenv = "/path_to_env/micromamba_env")

---

More info:
I'm running RStudio 4.4.2 hosted through my institution's Debian server. Micromamba 2.0.2-0 is loaded as a module, and I have a micromamba environment in my home directory.

I got the following error using the most recent release reticulate_1.41.0:

use_condaenv(condaenv = "/path_to_env/micromamba_env", conda = "/pathto_micromamba/micromamba")
Error: Unable to find conda binary. Is Anaconda installed?

For some reason, the conda argument isn't working. But setting the conda_binary option works (see solution).