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cortes-ciriano-lab / SComatic

A tool for detecting somatic variants in single cell data
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Warning for R package installation #14

Closed gangcai closed 1 year ago

gangcai commented 1 year ago

$ Rscript r_requirements_install.R

Warning message: package ‘VGAM’ is not available (for R version 3.6.1)

Francesc-Muyas commented 1 year ago

Dear user, Could you please try to do this in R? 

package_url <- "https://cran.r-project.org/src/contrib/Archive/VGAM/VGAM_1.1-7.tar.gz"
install.packages(package_url, repos=NULL, type="source")

In any case, R (and this package) is only used in the BetaBinEstimation.py script, so unless you need this step for re-calculating the Beta-binomial parameters, you can go ahead with your analysis.

Cheers, Fran

gangcai commented 1 year ago

Thanks for the reply. Above solution works for R 3.6.1. Since current VGAM requires R >=4.0.0, maybe it's better to recommend installation of this version of R at the very beginning.

vladimirkovacevic commented 11 months ago

I'm still getting the same error which is being solved but the suggestion given here. You may consider updating r_requiremens file accordingly. Thanks!