R/package.R

In priscian/jjmisc: Various R Functions to Aid Report Creation

#' @importFrom RCurl getURL
has_internet = function(hostname="www.google.com")
{
  try(is.character(RCurl::getURL(hostname))) == TRUE
}


## #' @export
## #' @importFrom BiocInstaller biocLite
bioc_lite <- function(..., local_lib=FALSE)
{
  if (exists("biocLite", envir=.GlobalEnv))
    rm("biocLite", envir=.GlobalEnv)

  if (has_internet()) {
    cat("Downloading 'biocLite()' from source....\n")
    source("https://www.bioconductor.org/biocLite.R")
  } else {
    cat("No Internet connection. Trying to load package \"BiocInstaller\".\n")
    library(BiocInstaller)
  }

  if (!local_lib)
    biocLite(...)
  else {
    #libPath <- Sys.getenv("R_LIBS_USER")
    libPath <- strsplit(Sys.getenv("R_LIBS_USER"), ";", perl=TRUE)[[1]][1]
    biocLite(..., lib=libPath, lib.loc=libPath, instlib=libPath, INSTALL_opts=c("--no-clean-on-error"))
  }
}
## N.B. For "Bioconductor does not yet support R version x.y.z", update base packages like this:
# update.packages(instlib=strsplit(Sys.getenv("R_LIBS_USER"), ";", perl=TRUE)[[1]][1])


#' @export
reload_all <- function(package_name, ..., export_all=FALSE, redocument=FALSE)
{
  require(devtools)

  currentwd <- getwd()
  switchArgs <- list(
    EXPR = package_name,
    "." # Default option.
  )
  switchArgs <- modifyList(switchArgs, getOption("reload_all_package_dirs"))
  packagewd <- do.call(switch, switchArgs)

  devtools::load_all(packagewd, export_all=export_all, ...)
  if (redocument)
    devtools::document(packagewd)

  return (nop())
}
## usage:
# reload_all("climeseries", redocument=TRUE)
# reload_all("jjmisc", redocument=TRUE)