Deploying Shiny app on shinyapps.io fails due to fgsea Bioconductor package

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1

Hi everyone,

I'm trying to deploy my Shiny app using renv on shinyapps.io, but the deployment fails with an error related to the fgsea package. My setup:

  • RStudio local environment: Windows
  • renv is used with renv.lock
  • IOBR and other packages are installed
  • fgsea is listed in renv.lock (via DOSE/IOBR dependency)

During deployment, I get: Error building fgsea (1.30.0). Build exited with non-zero status: 1

I have tried:

options(renv.bioconductor.validate = FALSE)
options(repos = BiocManager::repositories())

but it still fails.

Questions:

Why does fgsea fail to build on shinyapps.io even though it works locally?

Can fgsea be safely removed from the lock file to allow deployment?

Are there best practices for handling Bioconductor packages with compiled code when deploying Shiny apps?

Thanks in advance for any guidance!

2

Maybe possible to say from the rest of the error message, if you have access to it?

4

0e73f52f9430d7f817739f67e696e6e
0e73f52f9430d7f817739f67e696e6e1299×462 72.7 KB

Thank you very much!

5

That's not an error, it is a warning. Can you please copy-paste the complete error message?

6

Thanks，the error message is too long，so that screenshot is the main error. Just in '-std=c++14' there.

7

There is no error here. warning: means that this is a warning and not an error.

An error message from a compiler typically starts with error:. Look for that.