Open Callithrix-omics opened 4 years ago
I looked at the script file startShiny.R and the problem was that lines
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
bioInstall <- function() {
#source("http://bioconductor.org/biocLite.R")
#}
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
#library(BiocInstaller)
if("genomeIntervals" %in% rownames(installed.packages()) == FALSE) {
#biocLite("genomeIntervals")
BiocManager::install("genomeIntervals")
}
library(genomeIntervals)
} and it seems to work.
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.
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’:
Attaching package: ‘ape’
The following object is masked from ‘package:Hmisc’:
Attaching package: ‘DT’
The following objects are masked from ‘package:shiny’:
Fehler: With R version 3.5 or greater, install Bioconductor packages using BiocManager; see https://bioconductor.org/install Ausführung angehalten