App deployment fails due to problems in building BiocGenerics

Posit Professional & Hosted Products shinyapps.io
1

Hi !
I am currently unable to deploy (or better say update) a Shiny app on the server.
It seems to be related to generating BiocGenerics! I get an error saying "Error building BiocGenerics (0.48.1)" !

library(BiocManager)
library(rsconnect)
options(
  repos = c(CRAN_mirror = "https://cran.rstudio.com/"),
  BioC_mirror = "https://bioconductor.statistik.tu-dortmund.de/"
)
options(repos = BiocManager::repositories())
deployApp("/Users/oghabian/Documents/projects/UddLab/OBSCN_NEW/shinyApp/", appName = "OBSCN_PSIVIS")

── Preparing for deployment ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
✔ Re-deploying "OBSCN_PSIVIS" using "server: shinyapps.io / username: gacatag"
ℹ Looking up application with id "9532727"...
✔ Found application <https://gacatag.shinyapps.io/OBSCN_PSIVIS/>
ℹ Bundling 14 files: app.R, data/.Rapp.history, data/difAdultSel.rda, data/difListSel.rda, data/difMuscleSel.rda, data/dupInd.rda, data/firstExInd.rda, data/groupSam.rda, data/lastExInd.rda, data/obsInd.rda, data/psidat.rda, data/psimean.rda, data/uniqExGr.rda, and www/IntEREst_medium.jpg
ℹ Capturing R dependencies with renv
✔ Found 43 dependencies
✔ Created 131,011b bundle
ℹ Uploading bundle...
✔ Uploaded bundle with id 8333868
── Deploying to server ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Waiting for task: 1391155842
  building: Processing bundle: 8333868
  building: Building image: 10084880
  building: Building package: BiocGenerics
## Begin Task Log ############################################################################################################################################
## End Task Log ##############################################################################################################################################
Error: Unhandled Exception: child_task=1391155843 child_task_status=failed: Error building image: Error building BiocGenerics (0.48.1). Build exited with non-zero status: 127
In addition: Warning message:
invalid uid value replaced by that for user 'nobody'

Here are the repository info:

BiocManager::repositories()

'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for details.
Replacement repositories:
    BioCsoft: https://bioconductor.statistik.tu-dortmund.de//packages/3.18/bioc
    BioCann: https://bioconductor.statistik.tu-dortmund.de//packages/3.18/data/annotation
    BioCexp: https://bioconductor.statistik.tu-dortmund.de//packages/3.18/data/experiment
    BioCworkflows: https://bioconductor.statistik.tu-dortmund.de//packages/3.18/workflows
    BioCbooks: https://bioconductor.statistik.tu-dortmund.de//packages/3.18/books
                                                                      BioCsoft                                                                        BioCann 
           "https://bioconductor.statistik.tu-dortmund.de//packages/3.18/bioc" "https://bioconductor.statistik.tu-dortmund.de//packages/3.18/data/annotation" 
                                                                       BioCexp                                                                  BioCworkflows 
"https://bioconductor.statistik.tu-dortmund.de//packages/3.18/data/experiment"       "https://bioconductor.statistik.tu-dortmund.de//packages/3.18/workflows" 
                                                                     BioCbooks                                                                    CRAN_mirror 
          "https://bioconductor.statistik.tu-dortmund.de//packages/3.18/books"                                                    "https://cran.rstudio.com/"

Is this related to the server or is the mistake from my side (this used to work up till a couple of weeks ago I think). I can install Bioconductor packages on RStudio on my laptop. My codes are dependent on "GenomicRanges" and "shiny" libraries only. Could you kindly advise me on how to fix the issue?

2

I am also getting these types of errors, depending on the specific dependencies:

Error: Unhandled Exception: child_task=1391503371 child_task_status=failed: Error building image: Error building MASS (7.3-60.0.1). Build exited with non-zero status: 127

Error: Unhandled Exception: child_task=1391502013 child_task_status=failed: Error building image: Error building DBI (1.2.2). Build exited with non-zero status: 127

Tried to install the dev version of rsconnect with remotes::install_github("rstudio/rsconnect") but I still get the same errors.

This is with R version 4.3.3 (2024-02-29) on Ubuntu 22.04.

3

There is a bug report in rsconnect related to this: Error: Unhandled Exception: child_task=1391364942 child_task_status=failed: Error building image: Error building MA · Issue #1048 · rstudio/rsconnect · GitHub

1 Like
4

So as pointed out here: it seems to be the problem with R version on the server and the Bioconductor version that suits it. I locally installed an R v4.1.2 and the related Bioconductor V 3.14 (in parallel to the latest R) . Using these specific versions I succeeded in deploying and updating the app.

Cheers,

Ali