Add documentation for a missing parameter; fix reference to 'parse_fi…

…le_or_name' in example

R/job_loop.R

@@ -25,9 +25,8 @@
 #'     cores = 2
 #' )
 #'
-job_loop <- function(
-        loops, name, create_shell = FALSE, partition = "shared", memory = "10G",
-        cores = 1L, tc = 20, email = "ALL", logdir = "logs") {
+job_loop <- function(loops, name, create_shell = FALSE, partition = "shared", memory = "10G",
+    cores = 1L, tc = 20, email = "ALL", logdir = "logs") {
     ## Check that the loops are correctly defined
     if (!is.list(loops)) {
         stop("'loops' should be a named list.", call. = FALSE)

R/job_single.R

@@ -56,11 +56,10 @@
 #' ## An array job
 #' job_single("jhpce_job_array", task_num = 20, create_logdir = FALSE)
 #'
-job_single <- function(
-        name, create_shell = FALSE, partition = "shared", memory = "10G",
-        cores = 1L, email = "ALL", logdir = "logs", task_num = NULL, tc = 20,
-        command = 'Rscript -e "options(width = 120); sessioninfo::session_info()"',
-        create_logdir = TRUE) {
+job_single <- function(name, create_shell = FALSE, partition = "shared", memory = "10G",
+    cores = 1L, email = "ALL", logdir = "logs", task_num = NULL, tc = 20,
+    command = 'Rscript -e "options(width = 120); sessioninfo::session_info()"',
+    create_logdir = TRUE) {
     #   Grab the path to the shell script, and the shell script's name,
     #   respectively
     sh_file <- parse_file_or_name(name, should_exist = FALSE, r_ok = FALSE)

R/utils.R

@@ -167,6 +167,7 @@ parse_slurm_time <- function(tim) {
 #' (relative or absolute) to the shell or R script to create
 #' @param should_exist A \code{logical(1)} vector. If TRUE, the specified script
 #' must already exist; if FALSE, it must not exist
+#' @param r_ok A \code{logical(1)} vector. If TRUE, \code{name} may end in '.R'
 #'
 #' @return A \code{character(1)} giving the absolute or relative path to the
 #' shell script
@@ -185,7 +186,7 @@ parse_slurm_time <- function(tim) {
 #'     "my_script"
 #' )
 #' returned_scripts <- sapply(
-#'     acceptable_names, parse_file_or_name,
+#'     acceptable_names, slurmjobs:::parse_file_or_name,
 #'     should_exist = FALSE
 #' )
 #' print(returned_scripts)