Include batchtools::runOSCommand() - to be patched

Author: HenrikBengtsson

DESCRIPTION

@@ -1,12 +1,14 @@
 Package: future.batchtools
-Version: 0.20.0-9010
+Version: 0.20.0-9011
 Depends:
     R (>= 3.2.0),
     parallelly,
     future (>= 1.58.0)
 Imports:
     batchtools (>= 0.9.17),
-    utils
+    utils,
+    checkmate,
+    stringi
 Suggests:
     globals,
     future.apply,

NAMESPACE

@@ -91,6 +91,9 @@ importFrom(batchtools,saveRegistry)
 importFrom(batchtools,setJobNames)
 importFrom(batchtools,submitJobs)
 importFrom(batchtools,waitForJobs)
+importFrom(checkmate,"%??%")
+importFrom(checkmate,assertCharacter)
+importFrom(checkmate,assertString)
 importFrom(future,FutureBackend)
 importFrom(future,FutureError)
 importFrom(future,FutureInterruptError)
@@ -110,6 +113,8 @@ importFrom(future,tweak)
 importFrom(parallelly,availableCores)
 importFrom(parallelly,availableWorkers)
 importFrom(parallelly,supportsMulticore)
+importFrom(stringi,stri_flatten)
+importFrom(stringi,stri_replace_all_fixed)
 importFrom(tools,pskill)
 importFrom(utils,capture.output)
 importFrom(utils,file_test)

R/runOSCommand.R

@@ -0,0 +1,37 @@
+#' @importFrom checkmate assertCharacter assertString %??%
+#' @importFrom stringi stri_replace_all_fixed stri_flatten
+runOSCommand = function(sys.cmd, sys.args = character(0L), stdin = "", nodename = "localhost") {
+  assertCharacter(sys.cmd, any.missing = FALSE, len = 1L)
+  assertCharacter(sys.args, any.missing = FALSE)
+  assertString(nodename, min.chars = 1L)
+
+  if (!isLocalHost(nodename)) {
+    command = sprintf("%s %s", sys.cmd, stri_flatten(sys.args, " "))
+    if (getRversion() < "4.0.0") {
+      command = shQuote(command)
+    }
+    command = stri_replace_all_fixed(command, "\\$", "$")
+    sys.args = c("-q", nodename, command)
+    sys.cmd = "ssh"
+  }
+
+  "!DEBUG [runOSCommand]: cmd: `sys.cmd` `stri_flatten(sys.args, ' ')`"
+
+  if (nzchar(Sys.which(sys.cmd))) {
+    res = suppressWarnings(system2(command = sys.cmd, args = sys.args, stdin = stdin, stdout = TRUE, stderr = TRUE, wait = TRUE))
+    output = as.character(res)
+    exit.code = attr(res, "status") %??% 0L
+  } else {
+    output = "command not found"
+    exit.code = 127L
+  }
+
+  "!DEBUG [runOSCommand]: OS result (stdin '`stdin`', exit code `exit.code`):"
+  "!DEBUG [runOSCommand]: `paste0(output, sep = '\n')`"
+
+  return(list(sys.cmd = sys.cmd, sys.args = sys.args, exit.code = exit.code, output = output))
+}
+
+isLocalHost = function(nodename) {
+  is.null(nodename) || nodename %chin% c("localhost", "127.0.0.1", "::1")
+}