R/dot-checkPackNetConst.R

In stefpeschel/NetCoMi: Network Construction and Comparison for Microbiome Data

# Check whether packages needed for the current netConstruct() run 
# are available.

.checkPackNetConst <- function(measure, zeroMethod, normMethod, 
                               sparsMethod, adjust) {
  
  needpack <- character()
  
  if (measure == "ccrepe") {
    needpack <- c(needpack, "ccrepe")
  } else if (measure == "propr") {
    needpack <- c(needpack, "propr")
  } else if (measure %in% c("kld", "jeffrey", "jsd")) {
    needpack <- c(needpack, "LaplacesDemon")
  }
  
  if (zeroMethod %in% c("multRepl", "alrEM", "bayesMult")) {
    needpack <- c(needpack, "zCompositions")
  }
  
  if (normMethod == "CSS") {
    needpack <- c(needpack, "metagenomeSeq")
  } else if (normMethod == "VST") {
    needpack <- c(needpack, "DESeq2")
  } 
  
  if (sparsMethod %in% c("t-test", "bootstrap") && adjust == "adaptBH") {
    needpack <- c(needpack, "limma")
    
  } else if (sparsMethod == "knn") {
    needpack <- c(needpack, "cccd")
  }
  
  instpack <- needpack[!needpack %in% utils::installed.packages()[,"Package"]]
  
  if (length(instpack) != 0) {
    
    if (length(instpack) > 1) {
      message("Installing missing packages: ", 
              paste0(instpack[1:(length(instpack)-1)], ", ", 
                     instpack[length(instpack)]))
    } else {
      message("Installing missing package: ", instpack)
    }
    
    if (!requireNamespace("BiocManager", quietly = TRUE)) {
      utils::install.packages("BiocManager")
    }
    
    BiocManager::install(pkgs = instpack, dependencies = TRUE)
    
    message("Done.")
    
    message("Check whether installed package(s) can be loaded ...")
    
    for (pack in instpack) {
      requireNamespace(pack)
    }
    
    message("Done.")
  }
  
}