netClustering(cell chat, type = "functional") Error

[nandini0910]

Hi @sqjin! I recently reinstalled CellChat v1.6.1. When I run either
cellchat <- netClustering(cellchat, type = "functional") or cellchat <- netClustering(cellchat, type = "structural")
I get the following error.
Error: Strategy 'multiprocess' is defunct in future (>= 1.32.0) [2023-03-06]. Instead, explicitly specify either 'multisession' (recommended) or 'multicore'.

My temporary solution was changing the 'multiprocess' to 'multisession' using
trace(netClustering, edit=TRUE)

How can this be fixed permanently?

[sqjin]

@nandini0910 Can you try plan(multisession, workers = 4)

[nandini0910]

@sqjin The code works but the results seem different with each change. Is that supposed to happen?

Results before the update:
identify_signaling_groups_based_on_their_functional_similarity_before_update.pdf
identify_signaling_groups_based_on_their_structural_similarity_before_update.pdf
identify_signaling_groups_based_on_their_structural_similarity_zoomed_out_before_update.pdf

Results after the update with changing to 'multiprocess' to 'multisession'
identify_signaling_groups_based_on_their_functional_similarity.pdf
identify_signaling_groups_based_on_their_structural_similarity_zoomed_out.pdf
identify_signaling_groups_based_on_their_structural_similarity.pdf

Results after the update with changing to plan(multisession, workers = 4)
identify_signaling_groups_based_on_their_functional_similarity.pdf
identify_signaling_groups_based_on_their_structural_similarity_zoomed_out.pdf
identify_signaling_groups_based_on_their_structural_similarity.pdf

[wdg118]

@sqjin this does not work. After running plan("multisession", workers = 4) I get the error message:

And then when I run cellchat <- netClustering(cellchat, type = "functional") again I still get the same original error message as @nandini0910

Error: Strategy 'multiprocess' is defunct in future (>= 1.32.0) [2023-03-06]. Instead, explicitly specify either 'multisession' (recommended) or 'multicore'

[ksbb1853223]

@sqjin this does not work. After running plan("multisession", workers = 4) I get the error message:

And then when I run cellchat <- netClustering(cellchat, type = "functional") again I still get the same original error message as @nandini0910

Error: Strategy 'multiprocess' is defunct in future (>= 1.32.0) [2023-03-06]. Instead, explicitly specify either 'multisession' (recommended) or 'multicore'

I encountered the same problem. Solved it by downgrading the future package to 1.28.0.

[sqjin]

@nandini0910 Roughly, Results before the update: is similar to the Results after the update with changing to plan(multisession, workers = 4). Isn't it?

[karabicicim]

I am experiencing inconsistency issues when running my code as I get different results with each run. Is this a normal occurrence, and if not, how can I address it?
cellchat_trimean <- computeNetSimilarity(cellchat_trimean, type = "functional")
cellchat_trimean <- netEmbedding(cellchat_trimean, type = "functional")
cellchat_trimean <- netClustering(cellchat_trimean, type = "functional", do.parallel = TRUE)
netVisual_embedding(cellchat_trimean, type = "functional", label.size = 3.5)