makeClusterFunctionsSlurm2(): Inject runOSCommand() that defaults to runOSCommand(..., stderr = FALSE)

Author: HenrikBengtsson

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: future.batchtools
-Version: 0.20.0-9011
+Version: 0.20.0-9012
 Depends:
     R (>= 3.2.0),
     parallelly,

NAMESPACE

@@ -86,7 +86,6 @@ importFrom(batchtools,makeClusterFunctionsTORQUE)
 importFrom(batchtools,makeRegistry)
 importFrom(batchtools,makeSubmitJobResult)
 importFrom(batchtools,removeRegistry)
-importFrom(batchtools,runOSCommand)
 importFrom(batchtools,saveRegistry)
 importFrom(batchtools,setJobNames)
 importFrom(batchtools,submitJobs)

R/makeClusterFutureSlurm2.R

@@ -1,6 +1,6 @@
 # Patch Slurm cluster functions listJobsQueued() and listJobsRunning()
 # to use `sacct` instead of `squeue`
-#' @importFrom batchtools assertRegistry runOSCommand
+#' @importFrom batchtools assertRegistry
 #' @importFrom utils tail
 patchClusterFunctionsSlurm2 <- function(cf) {
   OSError <- import_from("OSError", package = "batchtools")
@@ -12,6 +12,17 @@ patchClusterFunctionsSlurm2 <- function(cf) {
   nodename <- env[["nodename"]]
   org_listJobsQueued <- env[["listJobsQueued"]]
 
+  ## Inject runOSCommand() that defaults to runOSCommand(..., stderr = FALSE)
+  env[["runOSCommand"]] <- function(..., stderr = FALSE) {
+    debug <- isTRUE(getOption("future.batchtools.debug"))
+    if (debug) {
+      mdebugf_push("runOSCommand(..., stderr = FALSE) ...")
+      mprint(list(args = list(..., stderr = stderr)))
+      on.exit(mdebugf_pop())
+    }
+    runOSCommand(..., stderr = stderr)
+  }
+
   ## Allow for a 15-minute offset in time between host and Slurm's sacct server
   isJobQueued <- function(reg, batch_id, since = NULL, offset = 15*60) {
     stopifnot(length(batch_id) == 1L, !is.na(batch_id), nzchar(batch_id))
@@ -38,6 +49,12 @@ patchClusterFunctionsSlurm2 <- function(cf) {
   } ## isJobQueued()
 
   cf$listJobsQueued <- function(reg) {
+    debug <- isTRUE(getOption("future.batchtools.debug"))
+    if (debug) {
+      mdebugf_push("[makeClusterFunctionsSlurm2()]$listJobsQueued() ...")
+      on.exit(mdebugf_pop())
+    }
+    
     batch_id <- getOption("future.batchtools.batch_id", NULL)
 
     ## Queued jobs according to 'squeue'

R/runOSCommand.R

@@ -1,6 +1,7 @@
 #' @importFrom checkmate assertCharacter assertString %??%
 #' @importFrom stringi stri_replace_all_fixed stri_flatten
 runOSCommand = function(sys.cmd, sys.args = character(0L), stdin = "", stdout = TRUE, stderr = TRUE, nodename = "localhost") {
+  isLocalHost <- import_from("isLocalHost", package = "batchtools")
   assertCharacter(sys.cmd, any.missing = FALSE, len = 1L)
   assertCharacter(sys.args, any.missing = FALSE)
   assertString(nodename, min.chars = 1L)
@@ -31,7 +32,3 @@ runOSCommand = function(sys.cmd, sys.args = character(0L), stdin = "", stdout =
 
   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")
-}