how to debug error in RnBeads Mac mini 10.15.7 R 4.0.3
2
0
Entering edit mode
7 months ago

In was running a methylation analysis and this error occurred. How can I debug?

rnb.run.dj()
 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()

When I tried to rerun with debug, this is what I got back :

> rnb.run.dj()
Error in get(name, envir = asNamespace(pkg), inherits = FALSE) : 
  object '%AND%' not found
Called from: get(name, envir = asNamespace(pkg), inherits = FALSE)
Browse[1]>

traceback: eval(substitute(browser(skipCalls = pos), list(pos - (length9sys.frames())- tagList(singleton(tags$head(tags$script(src = "js/directory_input_binding.js"))), at app.R:192 directoryInput('outDir", label = "Select analysis directory", at app.R:192

Thanks in advance!

R Rnbeads debug bug illuminia • 323 views
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0
Entering edit mode

What does

 ?shiny:::`%AND%` 

spit out? Which version of shiny are you using?

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0
Entering edit mode

Shiny version 1.6.0

?shiny:::%AND% No documentation for ‘%AND%’ in specified packages and libraries: you could try ‘??%AND%’

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0
Entering edit mode

It's pretty clear that shiny:::`%AND%` is the issue; since you seem to have the most recent version of shiny, perhaps that internal function was dropped. I'd recommend to get back in touch with the RnBeads developers and ask them which shiny version they've tested it on

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0
Entering edit mode
7 months ago
miky.zo ▴ 60

Hi! I had the same problem, I wrote to rnbeads developers and they suggested to install the latest development version on bioconductor https://bioconductor.org/packages/3.13/bioc/html/RnBeads.html

For me it worked! Hope this will be working also for you! ;)

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0
Entering edit mode
7 months ago

Unfortunately reinstalling did not work and the RnBeads team is unaware how toresolve the error as it is there first time encountering it.

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