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quadbio / Pando

Multiome GRN inference.
https://quadbio.github.io/Pando/
MIT License
106 stars 21 forks source link

Installation failure due to Matrix.utils dependency #16

Closed vkartha closed 1 year ago

vkartha commented 1 year ago

Hi there - I am looking forward to trying out this tool, but wasn't able to get it fully installed due to the Matrix.utils dependency, which now appears to officially be off CRAN (https://cran.r-project.org/web/packages/Matrix.utils/index.html). Running R 4.1.2, not sure if anyone else has come across this. It was just taken off 9 days ago it appears, so I am unable to install this dependency, and don't know to what extent Pando utilizes it

casblaauw commented 1 year ago

I've ran into the same issue. Installing Matrix.utils from Github (remotes::install_github('cvarrichio/Matrix.utils')) worked as a temporary fix, but it'd be great if the dependency could be replaced. From what I saw, its only use in Pando is Matrix.utils::aggregate.Matrix() in utils.R/aggregate_matrix(), so hopefully this should be feasible.

vkartha commented 1 year ago

Gotcha, thanks, missed the github option when searching earlier. I guess I was also concerned to see that package removed from CRAN on account of persistent bugs, but hopefully this should work OK for now given the specific usage you pointed out.

joschif commented 1 year ago

Heyhey, I removed the Matrix.utils dependency in the newest version since the package is also not maintained anymore. Building on 4.0-4.2 should work again.

joschif commented 1 year ago

I'm closing this since I believe it should be resolved, but feel free to reopen if the problem persists