conda env installation error, Palantir error

[33Dr]

Dear all,

I can successfully create my conda environment 'seuratextend' but when I want to run the first Palantir command "mye_small <- Palantir.RunDM(mye_small)" in R studo, then I get following error warning:

Error in py_run_string_impl(code, local, convert) :
ImportError: /home/############/miniconda3/envs/seuratextend/lib/python3.10/site-packages/PIL/_imaging.cpython-310-x86_64-linux-gnu.so: undefined symbol: opj_encoder_set_extra_options

And I cannot import palantir via reticulate::py_run_string("import palantir"). Then the same error warning like above occurs.

Could you please help me. Thank in advance

[huayc09]

I haven't received similar reports before. This looks like a compatibility issue between OpenJPEG and Pillow. However, since both libraries are configured within the conda environment, theoretically this problem shouldn't occur...

Which Linux version are you using? Did you create the environment using create_condaenv_seuratextend(), or did you set it up manually? After creating the environment, did you restart your R session (closing RStudio and reopening it)?