Question: Hi! I used the package RnBeads in the past to perform some analysis, using the interactive GUI, but now I have problems in loading it. I will post the error lines of code that I get. I am using Rstudio 1.2.5033, R version 4.0.3, Bioconductor 3.12.

> rnb.run.dj()
Loading required package: shiny
Watch shinyjs tutorial videos and read the full documentation:
https://deanattali.com/shinyjs/

Attaching package: ‘shinyjs’

The following object is masked from ‘package:shiny’:

runExample

The following object is masked from ‘package:methylumi’:

show

The following object is masked from ‘package:minfi’:

show

The following object is masked from ‘package:Biostrings’:

show

The following object is masked from ‘package:XVector’:

show

The following object is masked from ‘package:SummarizedExperiment’:

show

The following object is masked from ‘package:GenomicFeatures’:

show

The following object is masked from ‘package:AnnotationDbi’:

show

The following object is masked from ‘package:Biobase’:

show

The following object is masked from ‘package:limma’:

show

The following object is masked from ‘package:GenomicRanges’:

show

The following object is masked from ‘package:GenomeInfoDb’:

show

The following object is masked from ‘package:IRanges’:

show

The following object is masked from ‘package:S4Vectors’:

show

The following object is masked from ‘package:stats4’:

show

The following objects are masked from ‘package:methods’:

removeClass, show

Error in get(name, envir = asNamespace(pkg), inherits = FALSE) :
object '%AND%' not found
Called from: get(name, envir = asNamespace(pkg), inherits = FALSE)
Error during wrapup: unimplemented type (29) in 'eval'

Error: no more error handlers available (recursive errors?); invoking 'abort' restart
Error during wrapup: INTEGER() can only be applied to a 'integer', not a 'unknown type #29'
Error: no more error handlers available (recursive errors?); invoking 'abort' restart

I can't understand especially this line of code, that says:

Error in get(name, envir = asNamespace(pkg), inherits = FALSE) :
object '%AND%' not found

If anyone can help, it would be great!!

Thank you

08.02.21 - edit:
If I click on the error "Show traceback", this is what I see:

Error in get(name, envir = asNamespace(pkg), inherits = FALSE) :
object "%AND%" not found
32.
get(name, envir = asNamespace(pkg), inherits = FALSE)
31.
shiny:::`%AND%`
30.
dots_list(...)
29.
div(class = "form-group directory-input-container", shiny:::`%AND%`(label,
tags$label(label)), div(span(class = "col-xs-9 col-md-11",
style = "padding-left: 0; padding-right: 5px;", div(class = "input-group shiny-input-container",
style = "width:100%;", div(class = "input-group-addon", ...
28.
dots_list(...)
27.
tagList(singleton(tags$head(tags$script(src = "js/directory_input_binding.js"))),
div(class = "form-group directory-input-container", shiny:::`%AND%`(label,
tags$label(label)), div(span(class = "col-xs-9 col-md-11",
style = "padding-left: 0; padding-right: 5px;", div(class = "input-group shiny-input-container", ... at app.R#192
26.
directoryInput("outDir", label = "Select analysis directory",
value = "~")
25.
dots_list(...)
24.
tags$div(title = "Specify parent directory where the analysis reports will be stored.",
directoryInput("outDir", label = "Select analysis directory",
value = "~"))
23.
dots_list(...)
22.
tags$form(class = "well", role = "complementary", ...)
21.
dots_list(...)
20.
div(class = paste0("col-sm-", width), tags$form(class = "well",
role = "complementary", ...))
19.
sidebarPanel(tags$div(title = "Specify parent directory where the analysis reports will be stored.",
directoryInput("outDir", label = "Select analysis directory",
value = "~")), tags$div(title = "Specify the report directory (subdirectory of the analysis directory). Specify a non-existing directory for a new RnBeads analysis or an existing one to inspect the status and/or continue a previously started analysis.",
textInput("reportSubDir", "Choose the name of the report directory", ...
18.
dots_list(...)
17.
div(class = "tab-pane", title = title, `data-value` = value,
`data-icon-class` = iconClass(icon), ...)
16.
tabPanel(tags$div(title = "Specify general parameters, such as report (output) directories, number of cores to use, etc. You can configure new analyses or inspect the status of previous RnBeads runs.",
icon("bar-chart"), "Analysis"), sidebarPanel(tags$div(title = "Specify parent directory where the analysis reports will be stored.",
directoryInput("outDir", label = "Select analysis directory",
value = "~")), tags$div(title = "Specify the report directory (subdirectory of the analysis directory). Specify a non-existing directory for a new RnBeads analysis or an existing one to inspect the status and/or continue a previously started analysis.", ...
15.
navbarPage(windowTitle = "RnBeadsDJ", tags$p(tags$a(href = "https://rnbeads.org",
tags$img(width = 145, height = 50, src = "img/rnbeads_logo.png")),
"DJ"), tabPanel("About", icon = icon("book"), tags$h1("Welcome to the RnBeads Data Juggler"),
tags$p("Here, you can configure and run your RnBeads analyses. You can ..."), ...
14.
dots_list(...)
13.
tagList(useShinyjs(), navbarPage(windowTitle = "RnBeadsDJ", tags$p(tags$a(href = "https://rnbeads.org",
tags$img(width = 145, height = 50, src = "img/rnbeads_logo.png")),
"DJ"), tabPanel("About", icon = icon("book"), tags$h1("Welcome to the RnBeads Data Juggler"),
tags$p("Here, you can configure and run your RnBeads analyses. You can ..."), ...
12.
..stacktraceon..({
library(shiny)
library(shinyjs)
library(RnBeads) ...
11.
eval(exprs, envir)
10.
eval(exprs, envir)
9.
sourceUTF8(fullpath, envir = new.env(parent = sharedEnv))
8.
func(fname, ...)
7.
appObj()
6.
shinyAppDir_appR("app.R", appDir, options = options)
5.
shinyAppDir(x)
4.
as.shiny.appobj.character(appDir)
3.
as.shiny.appobj(appDir)
2.
shiny::runApp(system.file("extdata/RnBeadsDJ", package = "RnBeads"))
1.
rnb.run.dj()

Answer: Sorry for the inconvenince. This should be fixed now in the latest development version (2.9.3) on Bioconductor:
https://bioconductor.org/packages/3.13/bioc/html/RnBeads.html