gravatar for Gabriel

2 hours ago by

Paris

Hello, I have a simply singlecellexperiment object, and I have managed to make a shiny app using the iSEE package www.bioconductor.org/packages/release/bioc/html/iSEE.html

I made an app.R file to run the code that returns a shiny app, then I use runApp as you are supposed to do in the end of such a file, I am trying to upload it or deploy it and it's not working

library(BiocManager)
library(rsconnect)
options(repos = BiocManager::repositories())
library(shiny)
library(iSEE)
sce = readRDS("sce.RDS")
app <- iSEE(appTitle="test",sce)
if(interactive()){shiny::runApp(app)}

I get this error:

Error in shiny::runApp(app) :
Can't call runApp() from within runApp(). If your application code contains runApp(), please remove it.

If I put just

iSEE(appTitle="test",sce)

It is able to load and deploy on my shiny apps account and it says "running", however I now get an "out of memory" error on the shinyapps server:

2020-10-08T09:12:21.153674+00:00 shinyapps[2969507]:     aperm, apply, rowsum
2020-10-08T09:12:21.153674+00:00 shinyapps[2969507]: 
2020-10-08T09:12:21.496053+00:00 shinyapps[2969507]: Loading required package: SingleCellExperiment
2020-10-08T09:12:26.698874+00:00 shinyapps[system]: Out of memory!

It's nice that this library works in my R session and local browser, but if I am unable to deploy the GUI app online, it is pretty useless.

I found out that the free version's bundle size is limited to 1GB ( docs.rstudio.com/shinyapps.io/applications.html ), and my app sce object is just around 0.9 GB, I will try to reduce the size and try again.

> format(object.size(sce), units = "GB")

[1] "0.9 Gb"

I reduced the memory size of my sce object to 0.6 GB but the error is still happening. It seems the memory size of "SingleCellExperiment" package is way too large and I suspect it imports some other sce-datasets that are very large, is there any way to route this issue?



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