Unable to upload an App in shinyapps.io with bioconductor packages
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@xavier-andoni-24818
Last seen 7 weeks ago

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.

shinny graph RBGL • 156 views
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R > 3.6 does not use biocLite.R anymore. I think if you installed BiocManager from CRAN and then did BiocManager::repositories() you would get the same result.

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That would be ok to do in locally. But the problem emerges when uploading it to Shinyapps.io. Somehow does not work there.

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@marcel-ramos-7325
Last seen 5 hours ago
United States

Hi Xavier-Andoni, It appears that you are using R 4.0 which is good because the shiny configurations do not usually support R-devel.

You could try setting the repos option within your session before pushing:

library(BiocManager)
options(repos = BiocManager::repositories())

as mentioned by this user : https://community.rstudio.com/t/error-building-bioconductor-package-within-shiny-app/12607/2

Best, Marcel

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