Class compatibility issue between cicero3 (for monocle3) and monocle3. about cicero-release HOT 8 CLOSED

Additionally, when I force install monocle3 again, the block seems to complete but I'm not sure if the other building/installing processes are even running. The screenshot of this is below

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Hello, from your code it looks like somehow Cicero for monocle2 is being loaded. Can you post your sessionInfo()?

After reinstalling the various packages, are you restarting your R session? R does not reload packages that are already loaded even if they have been reinstalled, so if you haven't restarted R you will keep the same packages.

from cicero-release.

Here's my session info as well as the log for input_cds and the error (which is slighly different, but input_cds is still not correct). This is also after I restarted my R session (I just restarted the notebook kernel, if this isn't equivalent please let me know).

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input_cds is correct. The correct class with monocle3 is cell_data_set

from cicero-release.

The error you posted is related to the fact that the UMAP slot is empty. Have you calculated a UMAP?

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Hi, I've gotten past that error. However I now have this error. Upon searching in past examples it seems like this exact issue hasn't been brought up yet. I've also posted screenshots of my input_cds and umap coordinates

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Also, I saw the error here: cole-trapnell-lab/monocle3#291, but I've already included the fix in my code. Here is a screenshot of how I work with the input_cds, also there is a warning about using a standard svd. Is that the reason behind the bug?

from cicero-release.

Hello,
You're running into this error because you're attempting to make a cicero cds with only 80 cells - with a k value of 50, it's not possible to make sufficient aggregated cell groups. Internally such a small matrix gets converted to a different type which throws the error.

While you could get past the error by lower the k value, Cicero is designed to be used for many more cells (maybe 500), so I would not expect robust results with so few cells.

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