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GreenleafLab / ArchR

ArchR : Analysis of Regulatory Chromatin in R (www.ArchRProject.com)
MIT License
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Matrix 1.6-2 breaking irlba #2050

Open frac2738 opened 10 months ago

frac2738 commented 10 months ago

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 commented 10 months ago

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.
In addition to a reproducible example, you must do the following things before we help you, unless your original post already contained this information: 1. If you've encountered an error, have you already searched previous Issues to make sure that this hasn't already been solved? 2. Did you post your log file? If not, add it now. 3.__ Remove any screenshots that contain text and instead copy and paste the text using markdown's codeblock syntax (three consecutive backticks). You can do this by editing your original post.

Sky970415 commented 9 months ago

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 commented 8 months ago

install Matrix version = 1.6_1.1.

james-cranley commented 8 months ago

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

james-cranley commented 8 months ago

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.

alekseybelikov commented 1 month ago

Solved matrix errors by downgrading to version 1.6-5 and then installing irlba from source

install.packages("https://cran.r-project.org/src/contrib/Archive/Matrix/Matrix_1.6-5.tar.gz", repos = NULL, type = "source")

install.packages("irlba", type = "source")
rshikha95 commented 1 month ago

Hi Alekseybelikov

Thank you so much for the solution! I struggled with this error and was trying removing/re-installing one or the other version of Matrix package. Now for me this solution has worked as well.