lmcinnes / lmcinnes/umap

UMAP compatibility issue

Open
#835 0 comments 0 reactions 0 assignees View on GitHub

Nobody has claimed this yet.

Dominant language
Python
Stars
8.3k
Forks
871
Avg merge
1d 13h
Merged PRs (30d)
5

Description

Hi everyone, I'm or RStudio trying to use umap and umap-learn to find out immune clusters but since the last umap package update a keep seing this error:

`flowDF_scaled.umap <- umap(flowDF_scaled, method = "umap-learn", verbose = TRUE)
[2022-02-02 10:45:30] calling umap-learn (v0.5.2)
[2022-02-02 10:45:30] setting arguments: 14
Error in py_call_impl(callable, dots$args, dots$keywords) :
TypeError: ufunc 'bitwise_and' not supported for the input types, and the inputs could not be safely coerced to any supported types according to the casting rule ''safe''

Detailed traceback:
File "C:\Users\AppData\Local\R-MINI~ 1\envs\R-RETI~ 1\lib\site-packages\umap\umap_.py", line 2772, in fit_transform
self.fit(X, y)
File "C:\Users\AppData\Local\R-MINI~ 1\envs\R-RETI~ 1\lib\site-packages\umap\umap_.py", line 2563, in fit
raise_disconnected_warning(
File "C:\Users\AppData\Local\R-MINI~ 1\envs\R-RETI~ 1\lib\site-packages\umap\umap_.py", line 117, in raise_disconnected_warning
if verbose & (vertices_disconnected == 0) & (edges_removed > 0):
In addition: Warning message:
In detect.umap.learn(config) :
Detected umap-learn 0.5.2 but last supported version is 0.4;
setting arguments to match version 0.4.
To override this behavior, set config$umap_learn_args manually.`

Can anyone help me?

RStudio 2021.09.2+382 "Ghost Orchid" Release (fc9e217980ee9320126e33cdf334d4f4e105dc4f, 2022-01-04)
R version 4.1.2 (2021-11-01) -- "Bird Hippie"
UMAP version 0.2.7
Reticulate version 1.24
UMAP-Learn version 0.5.2

Contributor guide

Open the contributing guide

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start with the reported traceback in umap/umap_.py, especially fit_transform and raise_disconnected_warning. Reproduce the failure with umap-learn 0.5.2 through the R package and compare it with the package's version-detection warning; done means the compatibility behavior is verified and the reported error no longer occurs.

Written by the indexing model from the issue text.

Assessment

Tech stack
python, r
Domain
machine-learning
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
25/100

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.