Fix built-in templates

Author: HenrikBengtsson

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: future.batchtools
-Version: 0.12.2-9928
+Version: 0.12.2-9929
 Depends:
     R (>= 3.2.0),
     parallelly,

inst/templates/lsf.tmpl

@@ -16,7 +16,7 @@
   opts <- unlist(resources, use.names = TRUE)
   opts <- sprintf("-%s=%s", names(opts), opts)
   cat(sprintf("#BSUB %s\n", opts))
-<% } %>
+} %>
 
 echo "Batchtools job name: '<%= job.name %>'"
 

inst/templates/openlava.tmpl

@@ -16,7 +16,7 @@
   opts <- unlist(resources, use.names = TRUE)
   opts <- sprintf("-%s=%s", names(opts), opts)
   cat(sprintf("#BSUB %s\n", opts))
-<% } %>
+} %>
 
 echo "Batchtools job name: '<%= job.name %>'"
 

inst/templates/sge.tmpl

@@ -24,7 +24,7 @@
 #$ -V
 
 ## Resources needed:
-<% if (exists("resources", mode = "list") && length(resources) > 0) {
+<% if (length(resources) > 0) {
   ## As-is resource specifications, e.g.
   ## sge_options <- c("-pe smp 2", "-R yes")
   ## plan(batchtools_sge, resources = list(asis = sge_options))

inst/templates/slurm.tmpl

@@ -5,7 +5,10 @@
 # Author: Henrik Bengtsson 
 ######################################################################
 
-<% Slurm defaults
+
+#SBATCH --job-name=<%= job.name %>
+#SBATCH --output=<%= log.file %>
+<%
 defaults <- list(
   nodes = 1,         # single-host processing
   time = "00:05:00", # 5-min runtime
@@ -14,13 +17,9 @@ defaults <- list(
 resources <- c(resources, defaults[setdiff(names(defaults), names(resources))])
 opts <- unlist(resources, use.names = TRUE)
 opts <- sprintf("--%s=%s", names(opts), opts)
-opts <- paste(opts, collapse = " ") %>
+cat(sprintf("#SBATCH %s\n", opts))
 %>
 
-#SBATCH --job-name=<%= job.name %>
-#SBATCH --output=<%= log.file %>
-#SBATCH <%= opts %>
-
 echo "Batchtools job name: '<%= job.name %>'"
 
 echo "Session information:"

inst/templates/torque.tmpl

@@ -21,9 +21,8 @@
 <% if (length(resources) > 0) {
   opts <- unlist(resources, use.names = TRUE)
   opts <- sprintf("%s=%s", names(opts), opts)
-  opts <- paste(opts, collapse = ",") %>
-#PBS -l <%= opts %>
-<% } %>
+  cat(sprintf("#PBS -l %s\n", opts))
+} %>
 
 echo "Batchtools job name: '<%= job.name %>'"