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.

from angsd-wrapper.

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.

from angsd-wrapper.