Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

UMAP fails with later version of irlba package #701

Open
rfriedman22 opened this issue Feb 9, 2024 · 1 comment
Open

UMAP fails with later version of irlba package #701

rfriedman22 opened this issue Feb 9, 2024 · 1 comment
Labels
bug Something isn't working

Comments

@rfriedman22
Copy link
Collaborator

I upgraded from R/4.3.1 to R/4.3.2 and also upgraded my packages. When I did, I got the following error from UMAP:
Error in irlba::irlba function 'as_cholmod_sparse' not provided by package 'Matrix'

This is a documented problem in the irlba package. The solution is to reinstall irlba from source. It’s also an open issue for Seurat. It appears to have happened when Matrix changed to 1.6-2.

I think we should require a maximum version of irlba in the DESCRIPTION or change the way that this dependency gets installed.
@rfriedman22 rfriedman22 added the bug Something isn't working label Feb 9, 2024
@fjh1997
Copy link

fjh1997 commented Feb 27, 2024

may this solution help you ?

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
bug Something isn't working
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
2 participants
@rfriedman22 @fjh1997