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() 


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