shQuote(log.file)

tdhock · tdhock · commit 62ae838da98c · 2019-12-09T14:55:44.000-07:00
diff --git a/.gitignore b/.gitignore
@@ -1,3 +1,4 @@
+.Rhistory
 *~
 .DS_Store
 /inst/doc
diff --git a/inst/conf/slurm.R b/inst/conf/slurm.R
@@ -1,3 +1,4 @@
+## this is used in tests/testthat/test_slurm.R
 cluster.functions = makeClusterFunctionsSlurm(system.file(
   file.path("templates", "slurm-simple.tmpl"),
   package="batchtools",
diff --git a/inst/conf/slurm.conf b/inst/conf/slurm.conf
@@ -1,3 +1,5 @@
+# this file is used in tests/testthat/test_slurm.R
+
 # slurm.conf file generated by configurator easy.html.
 # Put this file on all nodes of your cluster.
 # See the slurm.conf man page for more information.
diff --git a/inst/templates/slurm-dortmund.tmpl b/inst/templates/slurm-dortmund.tmpl
@@ -14,7 +14,7 @@ if (backend == "mpi") {
 }
 
 # relative paths are not handled well by Slurm
-log.file = fs::path_expand(log.file)
+log.file = shQuote(fs::path_expand(log.file))
 -%>
 
 #SBATCH --job-name=<%= job.name %>
diff --git a/inst/templates/slurm-lido3.tmpl b/inst/templates/slurm-lido3.tmpl
@@ -16,6 +16,9 @@
 
 <%
 
+# relative paths are not handled well by Slurm
+log.file = shQuote(fs::path_expand(log.file))
+
 # queue
 walltime = asInt(resources$walltime, lower = 60L, upper = 31L * 24L * 60L * 60L)
 memory = asInt(resources$memory, lower = 100L, upper = 1024L * 1024L)
diff --git a/inst/templates/slurm-simple.tmpl b/inst/templates/slurm-simple.tmpl
@@ -19,7 +19,7 @@
 
 <%
 # relative paths are not handled well by Slurm
-log.file = fs::path_expand(log.file)
+log.file = shQuote(fs::path_expand(log.file))
 -%>
 
 

Original file line number	Diff line number	Diff line change
`@@ -1,3 +1,4 @@`
	`1`	`+.Rhistory`
`1`	`2`	`*~`
`2`	`3`	`.DS_Store`
`3`	`4`	`/inst/doc`
Original file line number	Diff line number	Diff line change
`@@ -1,3 +1,4 @@`
	`1`	`+## this is used in tests/testthat/test_slurm.R`
`1`	`2`	`cluster.functions = makeClusterFunctionsSlurm(system.file(`
`2`	`3`	`file.path("templates", "slurm-simple.tmpl"),`
`3`	`4`	`package="batchtools",`
Original file line number	Diff line number	Diff line change
`@@ -1,3 +1,5 @@`
	`1`	`+# this file is used in tests/testthat/test_slurm.R`
	`2`	`+`
`1`	`3`	`# slurm.conf file generated by configurator easy.html.`
`2`	`4`	`# Put this file on all nodes of your cluster.`
`3`	`5`	`# See the slurm.conf man page for more information.`
Original file line number	Diff line number	Diff line change
`@@ -14,7 +14,7 @@ if (backend == "mpi") {`
`14`	`14`	`}`
`15`	`15`
`16`	`16`	`# relative paths are not handled well by Slurm`
`17`		`-log.file = fs::path_expand(log.file)`
	`17`	`+log.file = shQuote(fs::path_expand(log.file))`
`18`	`18`	`-%>`
`19`	`19`
`20`	`20`	`#SBATCH --job-name=<%= job.name %>`