Nothing
.onAttach <- function(libname, pkgname) {
packageStartupMessage("##############################################################################
Welcome to pathfindR!
Please cite the article below if you use pathfindR in published reseach:
Ulgen E, Ozisik O, Sezerman OU. 2019. pathfindR: An R Package for Comprehensive
Identification of Enriched Pathways in Omics Data Through Active Subnetworks.
Front. Genet. doi:10.3389/fgene.2019.00858
##############################################################################")
check_java_version()
}
#' Obtain Java Version
#'
#' @return character vector containing the output of 'java -version'
#'
#' @details this function was adapted from the CRAN package \code{sparklyr}
fetch_java_version <- function() {
java_home <- Sys.getenv("JAVA_HOME", unset = NA)
if (!is.na(java_home)) {
java <- file.path(java_home, "bin", "java")
if (identical(.Platform$OS.type, "windows")) {
java <- paste0(java, ".exe")
}
if (!file.exists(java)) {
java <- ""
}
} else {
java <- Sys.which("java")
}
if (java == "") {
stop("Java version not detected. Please download and install Java from ",
dQuote("https://www.java.com/en/"))
}
version <- system2(java, "-version", stderr = TRUE, stdout = TRUE)
if (length(version) < 1) {
stop("Java version not detected. Please download and install Java from ",
dQuote("https://www.java.com/en/"))
}
return(version)
}
#' Check Java Version
#'
#' @param version character vector containing the output of 'java -version'. If
#' NULL, result of \code{\link{fetch_java_version}} is used (default = NULL)
#'
#' @return only parses and checks whether the java version is >= 1.8
#'
#' @details this function was adapted from the CRAN package \code{sparklyr}
check_java_version <- function(version = NULL) {
if (is.null(version)) {
version <- fetch_java_version()
}
# find line with version info
versionLine <- version[grepl("version", version)]
if (length(versionLine) != 1) {
stop("Java version detected but couldn't parse version from ", paste(version,
collapse = " - "))
}
# transform to usable R version string
vers_string <- strsplit(versionLine, "\\s+", perl = TRUE)[[1]]
vers_string <- vers_string[grepl("[0-9]+\\.[0-9]+\\.[0-9]+", vers_string, perl = TRUE)]
if (length(vers_string) != 1) {
vers_string <- strsplit(versionLine, "\\s+", perl = TRUE)[[1]]
vers_string <- vers_string[grepl("[0-9]+", vers_string, perl = TRUE)]
vers_string <- vers_string[!grepl("-", vers_string)]
if (length(vers_string) != 1) {
stop("Java version detected but couldn't parse version from: ", versionLine)
}
}
parsedVersion <- gsub("^\"|\"$", "", vers_string)
parsedVersion <- gsub("_", ".", parsedVersion)
parsedVersion <- gsub("[^0-9.]+", "", parsedVersion)
# ensure Java 1.8 (8) or higher
if (utils::compareVersion(parsedVersion, "1.8") < 0) {
stop("Java version", parsedVersion, " detected but Java >=8 is required.
Please download and install Java from ",
dQuote("https://www.java.com/en/"))
}
}
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