Execution Error with any function using seuratextend due to Conda Environment Conflict on Linux

[Mertc-Demir]

Hi,

First of all thank you for this useful package it has plenty of tools I can directly use in my visualizations but when it comes to try trajectory analysis with implemented python tools I've encounter a persistent error which is probably a unique error, but would like to ask your help anyway.

Environment Details:

• OS: Arch Linux
• Conda: Miniconda3
• R Version: 4.4.3
• SeuratExtend Version: Installed from GitHub latest.

Problem Description:
When following the your suggested installation guidelines in the FAQ, the R environment setup is successful. However, executing Palantir.RunDMand any other functions using seuratextend, fails with a persistent symbol lookup error.

Steps to Reproduce:

1. I followed the installation guide from the vignettes/FAQ.md precisely.

2. Created and activated a dedicated R environment:

   conda create -n newenv
   conda activate newenv

3. Installed all R dependencies and I needed (I also tried with exact same dependencies in the guideline the problem likely not related to this one):

   conda install -c conda-forge r-seurat r-hdf5r r-remotes r-ggpubr r-mosaic r-terra r-harmony r-xml r-biocmanager r-spatstat.univar r-tidyverse r-here r-pacman

4. Installed SeuratExtend from within an R session I also needed to install some packages via BiocManager since it failed to install such as GSVA, slingshot:

   remotes::install_github('huayc09/SeuratExtend')

5. Executed the Palantir function in R as per the vignettes:

   dataset_orig <- Palantir.RunDM(dataset_orig, reduction = "RUN.HARMONY")

6. The function correctly identifies that the seuratextend Python environment does not exist and prompts for its creation. After selecting "yes", the environment is created.

7. Immediately upon trying to execute the script, the R session fails with the following error.

The Error

sh: symbol lookup error: sh: undefined symbol: rl_print_keybinding
Error in system2(command = python, args = shQuote(script), stdout = TRUE,  : 
  error in running command '/home/arch_mert/miniconda3/envs/seuratextend/bin/python'

Troubleshooting Attempts:
I tried to fix the problem with gemini, also I do my search manually, it says the rl_print_keybinding error is a classic sign of a library conflict so I tried those.

1. Manual Environment Creation: I manually created the seuratextend environment using the environment-linux.yml file provided in the package. The environment itself built correctly, but calling Palantir.RunDM from the R environment still produced the exact same error.
2. Explicit reticulate Call: Tried to force a stable connection by explicitly telling reticulate which Python environment to use before calling the function:

   reticulate::use_condaenv("seuratextend", required = TRUE)

   This also resulted in the same symbol lookup error. And I relized that py_config() uses .cache/python I wasn't sure if this is problematic but I wanted to make sure so I even did conda clean --all and do everything from scratch but the issue was persistent.

use_condaenv("seuratextend", required = TRUE)
sh: symbol lookup error: sh: undefined symbol: rl_print_keybinding
Error in system2(command = python, args = shQuote(script), stdout = TRUE,  : 
  error in running command '/home/arch_mert/miniconda3/envs/seuratextend/bin/python'

> py_config()
sh: symbol lookup error: sh: undefined symbol: rl_print_keybinding

Error in system2(command = python, args = shQuote(script), stdout = TRUE,  : 
  error in running command '/home/arch_mert/Desktop/Thesis/renv/python/virtualenvs/renv-python-3.10/bin/python'

python:         /home/arch_mert/.cache/R/reticulate/uv/cache/archive-v0/UfDQScGKJf4n6PJdHcf9j/bin/python3
libpython:      /home/arch_mert/.cache/R/reticulate/uv/python/cpython-3.11.13-linux-x86_64-gnu/lib/libpython3.11.so
pythonhome:     /home/arch_mert/.cache/R/reticulate/uv/cache/archive-v0/UfDQScGKJf4n6PJdHcf9j:/home/arch_mert/.cache/R/reticulate/uv/cache/archive-v0/UfDQScGKJf4n6PJdHcf9j
virtualenv:     /home/arch_mert/.cache/R/reticulate/uv/cache/archive-v0/UfDQScGKJf4n6PJdHcf9j/bin/activate_this.py
version:        3.11.13 (main, Jul 11 2025, 22:43:55) [Clang 20.1.4 ]
numpy:          /home/arch_mert/.cache/R/reticulate/uv/cache/archive-v0/UfDQScGKJf4n6PJdHcf9j/lib/python3.11/site-packages/numpy
numpy_version:  2.3.2
NOTE: Python version was forced by py_require() 

I didn't tried but probably unifed enviroment would fix the problem but idk.

Thank you for your work on this very useful package. I hope this is helpful.