Installation issue

[sidrahmaryam-cyber]

Hello, I updated my R and RStudio to latest version, and now when I am trying to install multinichenetr, I am getting this error.

Downloading GitHub repo saeyslab/multinichenetr@HEAD Error in utils::download.file(url, path, method = method, quiet = quiet, : download from 'https://api.github.com/repos/saeyslab/multinichenetr/tarball/HEAD' failed

Can you please let me know the possible issue with this. Thanks

[sidrahmaryam-cyber]

I could somehow work this one out, by trying again and again. However, While running multinichnet, I am getting this error.

plot_oi = make_sample_lr_prod_activity_plots_Omnipath(

• multinichenet_output$prioritization_tables,
• prioritized_tbl_oi_M_50 %>% inner_join(lr_network_all)
• ) Joining with by = join_by(ligand, receptor) Error in UseMethod("mutate") : no applicable method for 'mutate' applied to an object of class "NULL"

Can you please help in this case.

[browaeysrobin]

Hello, I updated my R and RStudio to latest version, and now when I am trying to install multinichenetr, I am getting this error.

Downloading GitHub repo saeyslab/multinichenetr@HEAD Error in utils::download.file(url, path, method = method, quiet = quiet, : download from 'https://api.github.com/repos/saeyslab/multinichenetr/tarball/HEAD' failed

Can you please let me know the possible issue with this. Thanks

Hello, I updated my R and RStudio to latest version, and now when I am trying to install multinichenetr, I am getting this error.

Downloading GitHub repo saeyslab/multinichenetr@HEAD Error in utils::download.file(url, path, method = method, quiet = quiet, : download from 'https://api.github.com/repos/saeyslab/multinichenetr/tarball/HEAD' failed

Can you please let me know the possible issue with this. Thanks

Hi @sidrahmaryam-cyber

The error message during installation pointed to general connection issues (your internet access or general issues connecting to github) and was not MultiNicheNet specific. Therefore it worked after trying a couple of times.

[browaeysrobin]

I could somehow work this one out, by trying again and again. However, While running multinichnet, I am getting this error.

plot_oi = make_sample_lr_prod_activity_plots_Omnipath(

• multinichenet_output$prioritization_tables,
• prioritized_tbl_oi_M_50 %>% inner_join(lr_network_all)
• ) Joining with by = join_by(ligand, receptor) Error in UseMethod("mutate") : no applicable method for 'mutate' applied to an object of class "NULL"

Can you please help in this case.

Can you check whether

1) multinichenet_output$prioritization_tables is not empty 2) prioritized_tbl_oi_M_50 is not empty 3) lr_network_all s not empty 4) prioritized_tbl_oi_M_50 %>% inner_join(lr_network_all)

Normally none of these elements should be empty, but I guess they are in your case here (I will assume this error occurs on your data, not on the vignette data). Possible reasons: problems reading in the lr_network, wrong definition of condition_oi, or senders_oi/receivers_oi, leading to an empty prioritized_tbl_oi_M_50. By looking into these, you should be able to identify where things went wrong.

[browaeysrobin]

Because the main issue you reported is not a MultiNicheNet issue, I will close this issue. Feel free to open a new issue with your other problem. This helps other users find back relevant issues better.