Make sure to call specific BatchtoolsNNNFuture constructors

Author: HenrikBengtsson

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: future.batchtools
-Version: 0.10.0-9028
+Version: 0.10.0-9029
 Depends:
     R (>= 3.2.0),
     parallelly,

R/BatchtoolsMultiprocessFuture-class.R

@@ -39,7 +39,7 @@ BatchtoolsTemplateFuture <- function(expr = NULL, substitute = TRUE, envir = par
 BatchtoolsLsfFuture <- function(expr = NULL, substitute = TRUE, envir = parent.frame(), ...) {
   if (substitute) expr <- substitute(expr)
 
-  future <- BatchtoolsMultiprocessFuture(expr = expr, substitute = FALSE, envir = envir, ...)
+  future <- BatchtoolsTemplateFuture(expr = expr, substitute = FALSE, envir = envir, ...)
   future <- structure(future, class = c("BatchtoolsLsfFuture", class(future)))
 
   future
@@ -51,7 +51,7 @@ BatchtoolsLsfFuture <- function(expr = NULL, substitute = TRUE, envir = parent.f
 BatchtoolsOpenLavaFuture <- function(expr = NULL, substitute = TRUE, envir = parent.frame(), ...) {
   if (substitute) expr <- substitute(expr)
 
-  future <- BatchtoolsMultiprocessFuture(expr = expr, substitute = FALSE, envir = envir, ...)
+  future <- BatchtoolsTemplateFuture(expr = expr, substitute = FALSE, envir = envir, ...)
   future <- structure(future, class = c("BatchtoolsOpenLavaFuture", class(future)))
 
   future
@@ -63,7 +63,7 @@ BatchtoolsOpenLavaFuture <- function(expr = NULL, substitute = TRUE, envir = par
 BatchtoolsSGEFuture <- function(expr = NULL, substitute = TRUE, envir = parent.frame(), ...) {
   if (substitute) expr <- substitute(expr)
 
-  future <- BatchtoolsMultiprocessFuture(expr = expr, substitute = FALSE, envir = envir, ...)
+  future <- BatchtoolsTemplateFuture(expr = expr, substitute = FALSE, envir = envir, ...)
   future <- structure(future, class = c("BatchtoolsSGEFuture", class(future)))
 
   future
@@ -75,7 +75,7 @@ BatchtoolsSGEFuture <- function(expr = NULL, substitute = TRUE, envir = parent.f
 BatchtoolsSlurmFuture <- function(expr = NULL, substitute = TRUE, envir = parent.frame(), ...) {
   if (substitute) expr <- substitute(expr)
 
-  future <- BatchtoolsMultiprocessFuture(expr = expr, substitute = FALSE, envir = envir, ...)
+  future <- BatchtoolsTemplateFuture(expr = expr, substitute = FALSE, envir = envir, ...)
   future <- structure(future, class = c("BatchtoolsSlurmFuture", class(future)))
 
   future
@@ -87,7 +87,7 @@ BatchtoolsSlurmFuture <- function(expr = NULL, substitute = TRUE, envir = parent
 BatchtoolsTorqueFuture <- function(expr = NULL, substitute = TRUE, envir = parent.frame(), ...) {
   if (substitute) expr <- substitute(expr)
 
-  future <- BatchtoolsMultiprocessFuture(expr = expr, substitute = FALSE, envir = envir, ...)
+  future <- BatchtoolsTemplateFuture(expr = expr, substitute = FALSE, envir = envir, ...)
   future <- structure(future, class = c("BatchtoolsTorqueFuture", class(future)))
 
   future

R/batchtools_template.R

@@ -183,6 +183,14 @@ batchtools_by_template <- function(expr, envir = parent.frame(),
     torque   = makeClusterFunctionsTORQUE
   )
 
+  constructor <- switch(type,
+    lsf      = BatchtoolsLsfFuture,
+    openlava = BatchtoolsOpenLavaFuture,
+    sge      = BatchtoolsSGEFuture,
+    slurm    = BatchtoolsSlurmFuture,
+    torque   = BatchtoolsTorqueFuture
+  )
+
   make_cfs_formals <- formals(make_cfs)
 
   ## Get the default template?
@@ -204,7 +212,7 @@ batchtools_by_template <- function(expr, envir = parent.frame(),
   if (length(keep) > 0) dotdotdot <- dotdotdot[-keep]
 
   args <- list(
-    expr = expr, envir = envir, substitute = FALSE,
+    expr = expr, substitute = FALSE, envir = envir,
     globals = globals,
     label = label,
     cluster.functions = cluster.functions,
@@ -213,7 +221,7 @@ batchtools_by_template <- function(expr, envir = parent.frame(),
     workers = workers
   )
   if (length(dotdotdot) > 0) args <- c(args, dotdotdot)
-  future <- do.call(BatchtoolsTemplateFuture, args = args)
+  future <- do.call(constructor, args = args)
 
   if (!future$lazy) future <- run(future)
 

inst/templates/slurm.tmpl

@@ -5,17 +5,16 @@
 # Author: Henrik Bengtsson 
 ######################################################################
 
-#SBATCH --job-name=<%= if (exists("job.name", mode = "character")) job.name else job.hash %>
-#SBATCH --output=<%= log.file %>-%j.out
-#SBATCH --mail-type=END,FAIL
+#SBATCH --job-name=<%= job.name %>
+#SBATCH --output=<%= log.file %>
 #SBATCH --nodes=1
 #SBATCH --time=00:05:00
 
 ## Resources needed:
 <% if (length(resources) > 0) {
   opts <- unlist(resources, use.names = TRUE)
   opts <- sprintf("--%s=%s", names(opts), opts)
-  opts <- paste(opts, collapse = ",") %>
+  opts <- paste(opts, collapse = " ") %>
 #SBATCH <%= opts %>
 <% } %>