Built-in templates: Assert that 'Rscript' is available and give an informative error message with hints, if not

Author: HenrikBengtsson

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: future.batchtools
-Version: 0.20.0-9017
+Version: 0.20.0-9018
 Depends:
     R (>= 3.2.0),
     parallelly,

NEWS.md

@@ -17,6 +17,11 @@
    from stdout, which prevents auxillary INFO messages from `sbatch`
    to corrupt the output to be parsed.
 
+ * The built-in job script templates assert that `Rscript` is found,
+   and if not, they give an informative error message suggesting to
+   declare environment modules, via the `resources` argument, that
+   should be loaded by the job script.
+
 ## Bug Fixes
 
   `batchtools_slurm()` would produce "Future of class

inst/templates/lsf.tmpl

@@ -78,6 +78,12 @@ fi
 echo "Session information:"
 echo "- timestamp: $(date +"%Y-%m-%d %H:%M:%S%z")"
 echo "- hostname: $(hostname)"
+
+if command -v Rscript &> /dev/null; then
+    >&2 echo "ERROR: 'Rscript' could not be found. Maybe you need to specify which environment modules to load in the 'resources' argument, e.g. 'plan(future.batchtools::batchtools_lsf, resources = list(modules = c(\"r\")))'. The search PATH for 'Rscript' was ${PATH}"
+    exit 1
+fi
+
 echo "- Rscript path: $(which Rscript)"
 echo "- Rscript version: $(Rscript --version)"
 echo "- Rscript library paths: $(Rscript -e "cat(shQuote(.libPaths()), sep = ' ')")"

inst/templates/openlava.tmpl

@@ -78,6 +78,12 @@ fi
 echo "Session information:"
 echo "- timestamp: $(date +"%Y-%m-%d %H:%M:%S%z")"
 echo "- hostname: $(hostname)"
+
+if command -v Rscript &> /dev/null; then
+    >&2 echo "ERROR: 'Rscript' could not be found. Maybe you need to specify which environment modules to load in the 'resources' argument, e.g. 'plan(future.batchtools::batchtools_openlava, resources = list(modules = c(\"r\")))'. The search PATH for 'Rscript' was ${PATH}"
+    exit 1
+fi
+
 echo "- Rscript path: $(which Rscript)"
 echo "- Rscript version: $(Rscript --version)"
 echo "- Rscript library paths: $(Rscript -e "cat(shQuote(.libPaths()), sep = ' ')")"

inst/templates/sge.tmpl

@@ -87,6 +87,12 @@ fi
 echo "Session information:"
 echo "- timestamp: $(date +"%Y-%m-%d %H:%M:%S%z")"
 echo "- hostname: $(hostname)"
+
+if command -v Rscript &> /dev/null; then
+    >&2 echo "ERROR: 'Rscript' could not be found. Maybe you need to specify which environment modules to load in the 'resources' argument, e.g. 'plan(future.batchtools::batchtools_sge, resources = list(modules = c(\"r\")))'. The search PATH for 'Rscript' was ${PATH}"
+    exit 1
+fi
+
 echo "- Rscript path: $(which Rscript)"
 echo "- Rscript version: $(Rscript --version)"
 echo "- Rscript library paths: $(Rscript -e "cat(shQuote(.libPaths()), sep = ' ')")"

inst/templates/slurm.tmpl

@@ -77,6 +77,12 @@ fi
 echo "Session information:"
 echo "- timestamp: $(date +"%Y-%m-%d %H:%M:%S%z")"
 echo "- hostname: $(hostname)"
+
+if command -v Rscript &> /dev/null; then
+    >&2 echo "ERROR: 'Rscript' could not be found. Maybe you need to specify which environment modules to load in the 'resources' argument, e.g. 'plan(future.batchtools::batchtools_slurm, resources = list(modules = c(\"r\")))'. The search PATH for 'Rscript' was ${PATH}"
+    exit 1
+fi
+
 echo "- Rscript path: $(which Rscript)"
 echo "- Rscript version: $(Rscript --version)"
 echo "- Rscript library paths: $(Rscript -e "cat(shQuote(.libPaths()), sep = ' ')")"

inst/templates/torque.tmpl

@@ -81,6 +81,12 @@ fi
 echo "Session information:"
 echo "- timestamp: $(date +"%Y-%m-%d %H:%M:%S%z")"
 echo "- hostname: $(hostname)"
+
+if command -v Rscript &> /dev/null; then
+    >&2 echo "ERROR: 'Rscript' could not be found. Maybe you need to specify which environment modules to load in the 'resources' argument, e.g. 'plan(future.batchtools::batchtools_torque, resources = list(modules = c(\"r\")))'. The search PATH for 'Rscript' was ${PATH}"
+    exit 1
+fi
+
 echo "- Rscript path: $(which Rscript)"
 echo "- Rscript version: $(Rscript --version)"
 echo "- Rscript library paths: $(Rscript -e "cat(shQuote(.libPaths()), sep = ' ')")"