RnBeads error running rnb.run.dj()
1
1
Entering edit mode
7 months ago
miky.zo ▴ 60

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()
rnbeads methylation bioinformatics ngs help • 606 views
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Start a new R session or unload all the packages and retry.

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I already tried but I still get the error. I even tried to remove packages and reinstalled them, same problem

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7 months ago
fmueller ▴ 30

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

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Now it works!! Thank you very much! 😁

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Entering edit mode

Hi, I had your identical problem, but I still cannot solve with new RnBeads release... as I explained on bioconductor forum at this link: https://support.bioconductor.org/p/9135114/

Could u help me?

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