R/getConfFile.R

In GladiaTOX: R Package for Processing High Content Screening data

#####################################################################
## This program is distributed in the hope that it will be useful, ##
## but WITHOUT ANY WARRANTY; without even the implied warranty of  ##
## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the    ##
## GNU General Public License for more details.                    ##
#####################################################################

#' @title Get the configuration file
#' @description Get the configuration file location and check that it is
#' writable
#' 
#' @keywords internal
#' 
#' @return Config file
#' 

.getConfFile <- function() {
    conf_file <- Sys.getenv("TCPL_CONF")
    if (conf_file == "") {
        stop(
            "Must add 'TCPL_CONF' environment variable to .Renviron file to ",
            "store configuration settings. See ?gtoxConf for more information."
        )
    } else if (file.exists(conf_file)) {
        if (file.access(conf_file, mode=2) != 0) {
            stop(
                "The file given by 'TCPL_CONF' is not writeable. ",
                "Please check the permissions on the file or update",
                " 'TCPL_CONF' in your .Renviron file."
            )
        }
    } else {
        testfile <- try(cat("", file=conf_file))
        if (is(testfile, "try-error")) {
            stop(
                "Cannot write to the location given by 'TCPL_CONF'. ",
                "Please check the permissions on the file or update ",
                "'TCPL_CONF' in your .Renviron file."
            )
        }
    }
    conf_file
}