Question: how to debug error in RnBeads Mac mini 10.15.7 R 4.0.3
0
gravatar for saba_nasir111
13 days ago by
saba_nasir1110 wrote:

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!

debug bug rnbeads illuminia R • 106 views
ADD COMMENTlink modified 12 days ago • written 13 days ago by saba_nasir1110

What does

 ?shiny:::`%AND%` 

spit out? Which version of shiny are you using?

ADD REPLYlink modified 12 days ago • written 12 days ago by Friederike6.8k

Shiny version 1.6.0

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

ADD REPLYlink written 10 days ago by saba_nasir1110

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

ADD REPLYlink written 10 days ago by Friederike6.8k
0
gravatar for miky.zo
13 days ago by
miky.zo50
Italy / Busto Arsizio / University of Insubria
miky.zo50 wrote:

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! ;)

ADD COMMENTlink written 13 days ago by miky.zo50
0
gravatar for saba_nasir111
12 days ago by
saba_nasir1110 wrote:

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

ADD COMMENTlink written 12 days ago by saba_nasir1110
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1369 users visited in the last hour
_