issue running shiny graphing

[Callithrix-omics]

after I install angsd-wrapper and try to run shiny I get the following error. Any suggestions?

MBP-de-Joanna:angsd-wrapper joannamalukiewicz$ angsd-wrapper shiny graphing angsd-wrapper running from /Applications/angsd-wrapper

Loading required package: survival Loading required package: Formula Loading required package: ggplot2

Attaching package: ‘Hmisc’

The following objects are masked from ‘package:base’:

format.pval, units

Attaching package: ‘ape’

The following object is masked from ‘package:Hmisc’:

zoom

Attaching package: ‘DT’

The following objects are masked from ‘package:shiny’:

dataTableOutput, renderDataTable

Fehler: With R version 3.5 or greater, install Bioconductor packages using BiocManager; see https://bioconductor.org/install Ausführung angehalten

[Callithrix-omics]

I looked at the script file startShiny.R and the problem was that lines

Install packages from BioConductor

bioInstall <- function() { if("biocLite" %in% rownames(installed.packages()) == FALSE) { source("http://bioconductor.org/biocLite.R") } library(BiocInstaller) if("genomeIntervals" %in% rownames(installed.packages()) == FALSE) { biocLite("genomeIntervals") } library(genomeIntervals)

are depricated if you are running Bioconductor with R 3.5 or greater and biocLite need to but changed to the BiocManager as indicated in the error I posted above. I changed the line to the following

Install packages from BioConductor

bioInstall <- function() {

if("biocLite" %in% rownames(installed.packages()) == FALSE) {

    #source("http://bioconductor.org/biocLite.R")
#}
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")

BiocManager::install("BiocInstaller")

#library(BiocInstaller)
if("genomeIntervals" %in% rownames(installed.packages()) == FALSE) {
    #biocLite("genomeIntervals")
    BiocManager::install("genomeIntervals")
}
library(genomeIntervals)

} and it seems to work.

[shamanpi]

Hi @Callithrix-omics, thanks for posting your solution. We're currently working on updating the container files to deal with the R versioning, and should have a fixed version out soon.