Hello community,
I'm trying to develop a shinny app that uses RBGL and Graph bioconductor packages among others. The problem that I face is that Shinny is not able to install the package from Bioconductor repository. It outputs: Unhandled Exception: Child Task 873781155 failed: Error parsing manifest: Unable to determine package source for Bioconductor package RBGL: Repository must be specified. There are several posts expressing the same issue. For example here: The solution then was to add:
ioc <- local({
env <- new.env()
on.exit(rm(env))
evalq(source("http://bioconductor.org/biocLite.R", local = TRUE), env)
biocinstallRepos()
})
Unfortunately that doesn't look like an option since, from version of R 4.0 outputs Error: With R version 3.5 or greater, install Bioconductor packages using BiocManager; see https://bioconductor.org/install.
A similar problem is described here. But again it's old enought so the solution does not work any more.
Does anyone know how I could publish the app without getting those errors? Any clue or direction where to look will be more than welcome.
R > 3.6does not use biocLite.R anymore. I think if you installed BiocManager from CRAN and then didBiocManager::repositories()you would get the same result.That would be ok to do in locally. But the problem emerges when uploading it to Shinyapps.io. Somehow does not work there.