... Hello, I am new to learnr and am running into an issue where my code chunks become non-interactive when I publish my learnr tutorial. (By non-interactive, I mean there is no output or feedback when clicking ‘Run Code’). I believe the problem has to do with my use of a Bioconductor package phyloseq, but I'm not certain.
The exercises in the pre-loaded learnr tutorial (e.g. adjust the code to show only the top 5 rows of mtcars) ARE interactive when I include the following in the set-up code chunk:
library(learnr)
knitr::opts_chunk$set(echo = FALSE)
library(BiocManager)
options(repos = BiocManager::repositories())
library(phyloseq)
However, as soon as I add other packages such as tidyverse to this start-up code, the default exercises become non-interactive in the published version. All that I've altered in the pre-loaded learnr tutorial is this start-up code chunk:
library(learnr)
knitr::opts_chunk$set(echo = FALSE)
library(BiocManager)
options(repos = BiocManager::repositories())
library(phyloseq)
library(tidyverse)
The code chunks work locally when I run the .Rmd; however fail when I publish through the shiny server: https://ajames-shiny-r10.shinyapps.io/trial10/. I've updated R (4.1.0), R Studio (1.4.1106), phyloseq (1.36.0), and Bioconductor (3.14).
Any advice would be hugely appreciated.
Thank you!