R/zzz.R

In milescsmith/WGCNA: Weighted Correlation Network Analysis

# first and last lib functions

.onAttach <- function(libname, pkgname) {
  ourVer <- try(gsub("[^0-9_.-]", "", packageVersion("WGCNA"), fixed = FALSE))

  if (inherits(ourVer, "try-error")) ourVer <- ""

  printFlush("==========================================================================\n*")
  printFlush(paste("*  Package WGCNA", ourVer, "loaded.\n*"))

  if (.useNThreads() == 1 && .nProcessorsOnline() > 1) {
    printFlush(spaste(
      "*    Important note: It appears that your system supports multi-threading,\n",
      "*    but it is not enabled within WGCNA in R. \n",
      "*    To allow multi-threading within WGCNA with all available cores, use \n",
      "*\n",
      "*          allowWGCNAThreads()\n",
      "*\n",
      "*    within R. Use disableWGCNAThreads() to disable threading if necessary.\n",
      "*    Alternatively, set the following environment variable on your system:\n",
      "*\n",
      "*          ", .threadAllowVar, "=<number_of_processors>\n",
      "*\n",
      "*    for example \n",
      "*\n",
      "*          ", .threadAllowVar, "=", .nProcessorsOnline(), "\n",
      "*\n",
      "*    To set the environment variable in linux bash shell, type \n",
      "*\n",
      "*           export ", .threadAllowVar, "=", .nProcessorsOnline(),
      "\n*",
      "\n*     before running R. Other operating systems or shells will",
      "\n*     have a similar command to achieve the same aim.\n*"
    ))
  }
  printFlush("==========================================================================\n\n")


  imputeVer <- try(gsub("[^0-9_.-]", "", packageVersion("impute"), fixed = FALSE))

  if (!inherits(imputeVer, "try-error")) {
    if (compareVersion(imputeVer, "1.12") < 0) {
      printFlush(paste(
        "*!*!*!*!*!*!* Caution: installed package 'impute' is too old.\n",
        "Old versions of this package can occasionally crash the code or the entire R session.\n",
        "If you already have the newest version available from CRAN, \n",
        "and you still see this warning, please download the impute package \n",
        "from Bioconductor at \n",
        "http://www.bioconductor.org/packages/release/bioc/html/impute.html . \n",
        "If the above link is dead, search for package 'impute' \n",
        "in the Downloads -> Software section of http://www.bioconductor.org .\n"
      ))
    }
  }
}