Matrix 1.6-2 breaking irlba

[frac2738]

I got an error while running addDoubletScores: <simpleError in irlba::irlba(mat, nDimensions, nDimensions): function 'as_cholmod_sparse' not provided by package 'Matrix'>

It seems that changes in Matrix 1.6-2. are breaking irlba, and ArchR as a consequence.

Not a bug of arcR, but it should be noted that there might be an issue with Matrix 1.6-2 and irlba

[rcorces]

Hi @frac2738! Thanks for using ArchR! Please make sure that your post belongs in the Issues section. Only bugs and error reports belong in the Issues section. Usage questions and feature requests should be posted in the Discussions section, not in Issues.
It is worth noting that there are very few actual bugs in ArchR. If you are getting an error, it is probably something specific to your dataset, usage, or computational environment, all of which are extremely challenging to troubleshoot. As such, we require reproducible examples (preferably using the tutorial dataset) from users who want assistance. If you cannot reproduce your error, we will not be able to help. Before going through the work of making a reproducible example, search the previous Issues, Discussions, function definitions, or the ArchR manual and you will likely find the answers you are looking for. If your post does not contain a reproducible example, it is unlikely to receive a response.
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[Sky970415]

I think there is a conflict when Seurat update their packages. Most of ArchR function are using Seurat function but ArchR does not make update with it.

[zijunmeng]

install Matrix version = 1.6_1.1.

[james-cranley]

i have the same issue. will try to downgrade to Matrix version = 1.6_1.1

[james-cranley]

With my ArchR conda environment active I ran: conda install -c conda-forge r-matrix=1.6_1.1

This seems to have fixed it.