search

satijalab / sctransform

R package for modeling single cell UMI expression data using regularized negative binomial regression
GNU General Public License v3.0
206 stars 33 forks source link

Issue when trying to upload shiny app #72

Closed MarcElosua closed 3 years ago

MarcElosua commented 3 years ago

Good morning, First of all, thank you very much for developing such great tools! I am aware that this is not necessarily an sctransform issue but it is worth mentioning.

When I try to upload an ShinyApp to shinyapps.io using Seurat I get the following error: Error: Unhandled Exception: Child Task 807554307 failed: Error parsing manifest: Unable to determine package source for Bioconductor package sctransform: Repository must be specified

I am already declaring options so that bioconductor packages are within the scope of the environment via: options(repos = BiocManager::repositories())

When trying to identify what might be going wrong I run: rsconnect::appDependencies() Where sctransform appears as such: 126 sctransform 0.3.1 Bioconductor

I am aware that sctransform depends on the package multtest and therefore requires biocViews. I assume the problem here is similar to the one detailed here.

Is there a good workaround for this that can ease the deployment of shinyapps?

Again, thank you very much for your work and for your time!

ChristophH commented 3 years ago

Hi Marc,

I actually added the line biocViews: to the package DESCRIPTION file when I added support for the glmGamPoi package. I was hoping to get rid of a CRAN check note, but it didn't make a difference. However, I never removed that line, but it shouldn't be necessary.

Could you try to remove that line in see if that helps? I don't have experience with deploying shiny apps, so can't really give any advice.

MarcElosua commented 3 years ago

Hi @ChristophH, Good to know biocViews is not necessary, I removed the line from the DESCRIPTION file and it worked seamlessly. Here is a link to what I did to resolve it issue solve