How to launch the RnBeads graphical user interface?

Hi guys,

I've to install RnBeads package in R to do quality control of genome-wide methylation analyses.

I found the following commands to install RnBeads package:

#Executing the installation script for all dependencies, as well as the RnBeads package
source("http://rnbeads.org/data/install.R")

#Loading RnBeads in R
library(RnBeads)

#launching the RnBeads graphical user interface in a new browser window
rnb.run.dj()

When I run rnb.run.dj() command, I found this error in Rstudio console:

> rnb.run.dj()
Error in get(name, envir = asNamespace(pkg), inherits = FALSE) : 
  object "%AND%" not found

So, I clicked on "Show Traceback":

 Error in get(name, envir = asNamespace(pkg), inherits = FALSE) : 
  object "%AND%" not found
32.
get(name, envir = asNamespace(pkg), inherits = FALSE) 
31.
shiny:::`%AND%` 
  ...

How could I solve this problem? Has someone else met this kind of problem with RnBeads?

Thank you!

r software error

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written 5.5 years ago by Fede_Santos95 •

Is the shiny package installed? It is good practice to provide your sessionInfo() output. If shiny is installed, and you do not get responses here, consider to post it at support.bioconductor.org as this is the help forum for technical problems with Bioconductor packages.

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written 5.5 years ago by ATpoint

Thank u for your tip!

Unfortunatly, my sessionInfo() has more than 5000 characters, so I'm afraid I can't post all of it.

By the ways, this is a part of my R info session:

    > sessionInfo()
    R version 4.0.4 (2021-02-15)
    Platform: x86_64-w64-mingw32/x64 (64-bit)
    Running under: Windows 10 x64 (build 19042)
attached base packages:
 [1] grid      stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] shinyjs_2.0.0                           shiny_1.6.0                            
 [3] RnBeads_2.8.0                           plyr_1.8.6                             
 [5] methylumi_2.36.0                        minfi_1.36.0                           
 [7] bumphunter_1.32.0                       locfit_1.5-9.4                         
 [9] iterators_1.0.13                        foreach_1.5.1                          
[11] Biostrings_2.58.0                       XVector_0.30.0                         
[13] SummarizedExperiment_1.20.0             MatrixGenerics_1.2.1                   
[15] FDb.InfiniumMethylation.hg19_2.2.0      org.Hs.eg.db_3.12.0                    
[17] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2 GenomicFeatures_1.42.1                 
[19] AnnotationDbi_1.52.0                    reshape2_1.4.4                         
[21] scales_1.1.1                            Biobase_2.50.0                         
[23] illuminaio_0.32.0                       matrixStats_0.58.0                     
[25] limma_3.46.0                            gridExtra_2.3                          
[27] gplots_3.1.1                            ggplot2_3.3.3                          
[29] fields_11.6                             spam_2.6-0                             
[31] dotCall64_1.0-1                         ff_4.0.4                               
[33] bit_4.0.4                               cluster_2.1.0                          
[35] MASS_7.3-53                             GenomicRanges_1.42.0                   
[37] GenomeInfoDb_1.26.2                     IRanges_2.24.1                         
[39] S4Vectors_0.28.1                        BiocGenerics_0.36.0

Shiny package should be installed, and I have always the same problem also after installing it

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written 5.5 years ago by Fede_Santos95 •

Hello Fede_Santos95!

I will close this as it is now actively discussed over at the Bioc forum which is the appropriate forum for technical Bioc questions. Hope you get it running!

https://support.bioconductor.org/p/9135114/

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written 5.5 years ago by ATpoint

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