CLEANUP: Use Sys.info() for HPC backends, and Sys.getpid() for localhost ones

Author: HenrikBengtsson

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: future.batchtools
-Version: 0.12.2-9938
+Version: 0.12.2-9939
 Depends:
     R (>= 3.2.0),
     parallelly,

R/batchtools_bash.R

@@ -55,6 +55,7 @@ BatchtoolsBashFutureBackend <- function(...,
 #' `r paste(c("\x60\x60\x60bash", readLines("inst/templates/bash.tmpl"), "\x60\x60\x60"), collapse = "\n")`
 #'
 #' @examplesIf interactive()
+#' library(future)
 #' # Limit runtime to 30 seconds per future
 #' plan(batchtools_bash, resources = list(runtime = 30))
 #'

R/batchtools_custom.R

@@ -6,7 +6,23 @@
 #'
 #' @return An object of class `BatchtoolsFuture`.
 #'
-#' @example incl/batchtools_custom.R
+#' @examplesIf interactive()
+#' library(future)
+#'
+#' ## Create custom cluster functions (here same as "local")
+#' cf <- batchtools::makeClusterFunctionsInteractive(external = TRUE)
+#' print(cf)
+#' str(cf)
+#'
+#' # Use custom batchtools backend
+#' plan(future.batchtools::batchtools_custom, cluster.functions = cf)
+#' print(plan())
+#'
+#' message("Main process ID: ", Sys.getpid())
+#'
+#' f <- future(Sys.getpid())
+#' pid <- value(f)
+#' message("Worker process ID: ", pid)
 #'
 #' @rdname BatchtoolsFutureBackend
 #' @keywords internal

R/batchtools_local.R

@@ -69,6 +69,7 @@ BatchtoolsLocalFutureBackend <- function(fs.latency = 0.0, ...) {
 #' `plan(future::cluster, workers = I(1))`.
 #'
 #' @examples
+#' library(future)
 #' plan(future.batchtools::batchtools_local)
 #'
 #' message("Main process ID: ", Sys.getpid())

R/batchtools_lsf.R

@@ -35,14 +35,14 @@ BatchtoolsLsfFutureBackend <- function(...) {
 #' `r paste(c("\x60\x60\x60bash", readLines("inst/templates/lsf.tmpl"), "\x60\x60\x60"), collapse = "\n")`
 #'
 #' @examplesIf interactive()
+#' library(future)
+#'
 #' # Limit runtime to 3 minutes and memory to 200 MiB per future
 #' plan(future.batchtools::batchtools_lsf, resources = list(W = "00:03:00", M = "200"))
 #'
-#' message("Main process ID: ", Sys.getpid())
-#'
-#' f <- future(Sys.getpid())
-#' pid <- value(f)
-#' message("Worker process ID: ", pid)
+#' f <- future(Sys.info())
+#' info <- value(f)
+#' print(info)
 #' 
 #' @references
 #' * <https://en.wikipedia.org/wiki/IBM_Spectrum_LSF>

R/batchtools_multicore.R

@@ -88,6 +88,7 @@ BatchtoolsMulticoreFutureBackend <- function(workers = availableCores(constraint
 #' `plan(future::multicore)`.
 #'
 #' @examples
+#' library(future)
 #' plan(future.batchtools::batchtools_multicore, workers = 2)
 #'
 #' message("Main process ID: ", Sys.getpid())

R/batchtools_openlava.R

@@ -35,14 +35,14 @@ BatchtoolsOpenLavaFutureBackend <- function(...) {
 #' `r paste(c("\x60\x60\x60bash", readLines("inst/templates/openlava.tmpl"), "\x60\x60\x60"), collapse = "\n")`
 #'
 #' @examplesIf interactive()
+#' library(future)
+#'
 #' # Limit runtime to 3 minutes and memory to 200 MiB per future
 #' plan(future.batchtools::batchtools_lsf, resources = list(W = "00:03:00", M = "200"))
 #'
-#' message("Main process ID: ", Sys.getpid())
-#'
-#' f <- future(Sys.getpid())
-#' pid <- value(f)
-#' message("Worker process ID: ", pid)
+#' f <- future(Sys.info())
+#' info <- value(f)
+#' print(info)
 #'
 #' @references
 #' * <https://en.wikipedia.org/wiki/OpenLava>

R/batchtools_sge.R

@@ -34,14 +34,14 @@ BatchtoolsSGEFutureBackend <- function(...) {
 #' `r paste(c("\x60\x60\x60bash", readLines("inst/templates/sge.tmpl"), "\x60\x60\x60"), collapse = "\n")`
 #'
 #' @examplesIf interactive()
+#' library(future)
+#'
 #' # Limit runtime to 3 minutes and memory to 200 MiB per future
 #' plan(future.batchtools::batchtools_sge, resources = list(h_rt = "00:03:00", mem_free = "200M"))
 #'
-#' message("Main process ID: ", Sys.getpid())
-#'
-#' f <- future(Sys.getpid())
-#' pid <- value(f)
-#' message("Worker process ID: ", pid)
+#' f <- future(Sys.info())
+#' info <- value(f)
+#' print(info)
 #' 
 #' @references
 #' * <https://en.wikipedia.org/wiki/Oracle_Grid_Engine>

R/batchtools_slurm.R

@@ -35,14 +35,14 @@ BatchtoolsSlurmFutureBackend <- function(...) {
 #' `r paste(c("\x60\x60\x60bash", readLines("inst/templates/slurm.tmpl"), "\x60\x60\x60"), collapse = "\n")`
 #'
 #' @examplesIf interactive()
+#' library(future)
+#'
 #' # Limit runtime to 3 minutes and memory to 200 MiB per future
 #' plan(future.batchtools::batchtools_slurm, resources = list(time = "00:03:00", mem = "200M"))
 #'
-#' message("Main process ID: ", Sys.getpid())
-#'
-#' f <- future(Sys.getpid())
-#' pid <- value(f)
-#' message("Worker process ID: ", pid)
+#' f <- future(Sys.info())
+#' info <- value(f)
+#' print(info)
 #'
 #' @references
 #' * <https://en.wikipedia.org/wiki/Slurm_Workload_Manager>

R/batchtools_torque.R

@@ -34,14 +34,14 @@ BatchtoolsTorqueFutureBackend <- function(...) {
 #' `r paste(c("\x60\x60\x60bash", readLines("inst/templates/torque.tmpl"), "\x60\x60\x60"), collapse = "\n")`
 #'
 #' @examplesIf interactive()
+#' library(future)
+#'
 #' # Limit runtime to 3 minutes and memory to 200 MiB per future
 #' plan(future.batchtools::batchtools_torque, resources = list(walltime = "00:03:00", mem = "200mb"))
 #'
-#' message("Main process ID: ", Sys.getpid())
-#'
-#' f <- future(Sys.getpid())
-#' pid <- value(f)
-#' message("Worker process ID: ", pid)
+#' f <- future(Sys.info())
+#' info <- value(f)
+#' print(info)
 #' 
 #' @references
 #' * <https://en.wikipedia.org/wiki/TORQUE>