Cannot push application to shinyapps.io: bioc_xgit error

[nmclark2]

I am having an issue where I am trying to re-deploy a previously published application. I have a strange error that I cannot find any documentation on that is preventing me from deploying. Below are the contents of the deployment log file.

I am running R 4.4.2

ℹ Capturing R dependencies
✔ Found 156 dependencies
✔ Created 29,635,520b bundle
ℹ Uploading bundle...
✔ Uploaded bundle with id 10762008
── Deploying to server ─────────────────────────────────────────────────────────
Waiting for task: 1579163069
  building: Parsing manifest
## Begin Task Log ##############################################################
## End Task Log ################################################################
Error: Unhandled Exception: child_task=1579163070 child_task_status=failed: Error parsing manifest: Unknown repository for package source: bioc_xgit
Execution halted

[mbaynton]

Hi @nmclark2,

It looks like your local R installation has at least one R package that's been installed using bioc_xgit or install_bioc(), which let you install pre-release development versions of packages from Bioconductor. Shinyapps.io gets a list of all the packages your source code needs and tries to install them itself, but it doesn't know how to do that for pre-release Bioconductor packages, so that's why you get this failure.

Do you recall installing a package this way? If so, would you be able to install the last official release of that package instead, and then try deploying your application again?

Thanks
Mike

[nmclark2]

Hi Mike,

Thanks for the insight. I really don't remember doing this, but I have so many packages installed that I could see this happening.

Is there any way for me to easily determine if any of my packages fit this criterion? Otherwise, I could try updating all of the source packages that come from Bioconductor.

[mbaynton]

Is there any way for me to easily determine if any of my packages fit this criterion?

One way would be to run rsconnect::writeManifest() in your project. This will cause a manifest.json file to be produced listing the details of all the packages that shinyapps.io sees. If you open that file and search for bioc_xgit you should be able to see which package(s) are being sourced this way.

[nmclark2]

That's great, thank you! I will try this out and report back if this resolves the issue.

[nmclark2]

It was my Biobase installation that was using bioc_xgit, even though it was fully up to date. Very strange. I force reinstalled the package and that seemed to fix the issue. I'm able to push my application now. Thanks again!