R shinyapps.io error deploying app: Unable to determine package source for Bioconductor package graph

Question

I am trying to deploy a shinyapp but getting the following error:

> deployApp()
Preparing to deploy application...
Update application currently deployed at
https://komalrathi.shinyapps.io/medulloclassifiershinyapp/? [Y/n] Y
DONE
Uploading bundle for application: 1380990...DONE
Deploying bundle: 2535955 for application: 1380990 ...
Waiting for task: 661489247
  building: Parsing manifest
################################ Begin Task Log ################################ 
################################# End Task Log ################################# 
Error: Unhandled Exception: Child Task 661489248 failed: Error parsing manifest: Unable to determine package source for Bioconductor package graph: Repository must be specified
In addition: Warning messages:
1: invalid uid value replaced by that for user 'nobody' 
2: invalid gid value replaced by that for user 'nobody'

This is my sessionInfo:

> sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.6

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] rsconnect_0.8.15

loaded via a namespace (and not attached):
[1] BiocManager_1.30.9 compiler_3.6.1     tools_3.6.1        curl_4.1           yaml_2.2.0        
[6] jsonlite_1.6       packrat_0.5.0      openssl_1.4.1      askpass_1.1

Here is the minimal app.R code to reproduce the error:

library(shiny)
library(shinydashboard)
library(medulloPackage)

ui <- dashboardPage(
  dashboardHeader(title = "Classifier"),
  dashboardSidebar(
  ),
  dashboardBody(
  )
)

server <- function(input, output) {
}

shinyApp(ui, server)

Before running, you will have to first install medulloPackage using the following:

devtools::install_github("d3b-center/medullo-classifier-package")

The error is coming when I use this package so not sure how to handle it.

Hi, any chance to have a reproducibile example? (ui.R and server.R files?). Seems that the problem is on the bioconductor package (I didn't find it, is there any github version? Have you tried by installing this version with devtools?) — Alessio, Oct 25 '19 at 17:17
@alessio I have updated the question with a minimal example. The error is coming due to a package that I am including in the code. But not sure how to fix it. — Komal Rathi, Oct 25 '19 at 19:22

score 6 · Accepted Answer · answered Oct 25 '19 at 21:08

after a bit of steps I guess the app now loads correctly: take a look at https://abenedetti.shinyapps.io/medullo/

From your code I added a couple of lines:

library(BiocManager)
options(repos = BiocManager::repositories())

Here the full app.R file:

library(shiny)
library(shinydashboard)
library(medulloPackage)

library(BiocManager)
options(repos = BiocManager::repositories())

ui <- dashboardPage(
    dashboardHeader(title = "Classifier"),
    dashboardSidebar(
    ),
    dashboardBody(
    )
)

server <- function(input, output) {
}

shinyApp(ui, server)

I list the steps it took to me, maybe you're already ok with some of them:

Install medullo-classifier-package

I had to manually install these 2 packages:

install.packages("digest")
install.packages("rlang")

Install BioManager with:

if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install()

Also you may take a look at this link for additional details: https://community.rstudio.com/t/failing-to-deploy-shinyapp-depending-on-bioconductor-packages/6970/5

R shinyapps.io error deploying app: Unable to determine package source for Bioconductor package graph

1 Answers1