run.R script fails in air-gapped environments due to the use of BiocManager
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michaelmayer2 commented
We need to configure run.R script in such a way that BiocManager does not reach out to bioconductor.org for the online check but use the internal Package Manager URL.
For more information, see
https://cran.r-project.org/web/packages/BiocManager/vignettes/BiocManager.html#offline-use
https://packagemanager.posit.co/client/#/repos/bioconductor/setup