R/fix_mass.R

In muschellij2/massr: Installs MASS

#' @title Fix MASS Functions if installed incorrectly
#'
#' @description Resets correct paths for MASS fucntions
#' @return Logical
fix_mass <- function(){
  files= file.path("lib/", c('mass-fillHoles', "mass-morpho", 
                             "mass-registrations", "mass-skullstripping"))
  files = c(files, file.path("bin/", 
                             c('mass', "mass-chooseTemplates", 
                               "mass-thresholdJacobian", "uninstall-mass")))
  pkgdir = file.path(system.file(package="massr"), "mass")
  files = file.path(pkgdir, files)
  ### Get directory of installing
#   root_temp = dirname(tempdir())
  root_temp = "/"
  install_dir = paste0(root_temp, ".*/inst/mass")
  
  ### change that to the mass dir
  changedir = function(file){
    if (!file.exists(file)){
#       cat(paste0(file, " does not exist!\n"))
      return(FALSE)
    } else {
      suppressWarnings({x = readLines(file)})
      xx = gsub(install_dir, pkgdir, x)
      writeLines(xx, con = file)
      return(TRUE)
    }
  }
  file = file.path(pkgdir, "lib/bash/mass/mass-functions.sh")
  sysname = tolower(Sys.info()[['sysname']])
  if (!file.exists(file)){
    #       cat(paste0(file, " does not exist!\n"))
  } else {
    suppressWarnings({x = readLines(file)})
    if (grepl("inux", sysname)){
      x = gsub("opt=t", "opt=p", x, fixed=TRUE)      
    } else if ( grepl("darwin", sysname) ){
      x = gsub("-${opt} ${LocalTempDir}", "", x, fixed=TRUE)      
#       x = gsub("-${opt} ${LocalTempDir} ", "${LocalTempDir}/", x, fixed=TRUE)
    }
    writeLines(x, con = file)      
  }

  all(sapply(files, changedir))


}