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syspremed / exploBATCH

A package for discovering and correcting for batch effect using an approach in Nyamundanda et al (2017).
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old version of bioconductor #8

Open layal-khayal opened 2 years ago

layal-khayal commented 2 years ago

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

Can you please fix it ?

ekopylova commented 2 years ago

@layal-khayal a fix around this for me (without touching the code) was to install any missing packages manually (from toinstall see below) so that the call to source biocLite.R isn't made:

From expBATCH.R:

  installed<-installed.packages()[,1] 
  required<-c("mvtnorm","mclust","sva","stats","ggplot2","RColorBrewer",
              "rARPACK","RcppArmadillo","RcppEigen","Rcpp","parallel",
              "foreach","doParallel","doMC","compiler","devtools")
  toinstall<-required[!(required %in% installed)]
  if(length(toinstall) != 0){
    source("https://bioconductor.org/biocLite.R")
    biocLite(toinstall)
  }