r-arguments

.github/workflows/check.yaml

@@ -38,7 +38,7 @@ jobs:
 
       - name: Add r-universe to repos
         run: |
-          cat("\noptions(repos=c(paws='https://paws-r.r-universe.dev',CRAN ='https://cloud.r-project.org'))\n", file = "~/.Rprofile", append = TRUE)
+          cat("\noptions(repos=c(paws='https://paws-r.r-universe.dev',wlandau='https://wlandau.r-universe.dev',CRAN ='https://cloud.r-project.org'))\n", file = "~/.Rprofile", append = TRUE)
         shell: Rscript {0}
 
       - uses: r-lib/actions/setup-r-dependencies@v2

.github/workflows/cover.yaml

@@ -28,7 +28,7 @@ jobs:
 
       - name: Add r-universe to repos
         run: |
-          cat("\noptions(repos=c(paws='https://paws-r.r-universe.dev',CRAN ='https://cloud.r-project.org'))\n", file = "~/.Rprofile", append = TRUE)
+          cat("\noptions(repos=c(paws='https://paws-r.r-universe.dev',wlandau='https://wlandau.r-universe.dev',CRAN ='https://cloud.r-project.org'))\n", file = "~/.Rprofile", append = TRUE)
         shell: Rscript {0}
 
       - uses: r-lib/actions/setup-r-dependencies@v2

.github/workflows/lint.yaml

@@ -21,7 +21,7 @@ jobs:
 
       - name: Add r-universe to repos
         run: |
-          cat("\noptions(repos=c(paws='https://paws-r.r-universe.dev',CRAN ='https://cloud.r-project.org'))\n", file = "~/.Rprofile", append = TRUE)
+          cat("\noptions(repos=c(paws='https://paws-r.r-universe.dev',wlandau='https://wlandau.r-universe.dev',CRAN ='https://cloud.r-project.org'))\n", file = "~/.Rprofile", append = TRUE)
         shell: Rscript {0}
 
       - uses: r-lib/actions/setup-r-dependencies@v2

.github/workflows/pkgdown.yaml

@@ -35,7 +35,7 @@ jobs:
 
       - name: Add r-universe to repos
         run: |
-          cat("\noptions(repos=c(paws='https://paws-r.r-universe.dev',CRAN ='https://cloud.r-project.org'))\n", file = "~/.Rprofile", append = TRUE)
+          cat("\noptions(repos=c(paws='https://paws-r.r-universe.dev',wlandau='https://wlandau.r-universe.dev',CRAN ='https://cloud.r-project.org'))\n", file = "~/.Rprofile", append = TRUE)
         shell: Rscript {0}
 
       - uses: r-lib/actions/setup-r-dependencies@v2

DESCRIPTION

@@ -13,7 +13,7 @@ Description: In computationally demanding analysis projects,
   'clustermq' by Schubert (2019) <doi:10.1093/bioinformatics/btz284>),
   and 'batchtools' by Lang, Bischl, and Surmann (2017).
   <doi:10.21105/joss.00135>.
-Version: 0.0.6.9003
+Version: 0.0.6.9004
 License: MIT + file LICENSE
 URL: https://wlandau.github.io/crew.aws.batch/,
   https://github.com/wlandau/crew.aws.batch
@@ -34,7 +34,7 @@ Depends:
   R (>= 4.0.0)
 Imports:
   cli (>= 3.1.0),
-  crew (>= 0.9.5),
+  crew (>= 0.9.5.9003),
   paws.common (>= 0.7.0),
   paws.compute,
   paws.management,

NEWS.md

@@ -1,8 +1,9 @@
-# crew.aws.batch 0.0.6.9003 (development)
+# crew.aws.batch 0.0.6.9004 (development)
 
 * Send both cancellation and termination requests to end jobs.
 * Fix launcher bug/typo where parameters were supplied to container overrides.
 * Add a new `all` argument to `terminate()` in the AWS Batch monitor.
+* Add `r_arguments` to accept command line arguments to R.
 
 # crew.aws.batch 0.0.6
 

R/crew_controller_aws_batch.R

@@ -43,6 +43,7 @@ crew_controller_aws_batch <- function(
   garbage_collection = FALSE,
   launch_max = 5L,
   processes = NULL,
+  r_arguments = NULL,
   aws_batch_config = list(),
   aws_batch_credentials = list(),
   aws_batch_endpoint = NULL,
@@ -88,6 +89,7 @@ crew_controller_aws_batch <- function(
     launch_max = launch_max,
     tls = tls,
     processes = processes,
+    r_arguments = r_arguments,
     aws_batch_config = aws_batch_config,
     aws_batch_credentials = aws_batch_credentials,
     aws_batch_endpoint = aws_batch_endpoint,

R/crew_launcher_aws_batch.R

@@ -83,15 +83,15 @@
 #'   For more details, visit
 #'   <https://www.paws-r-sdk.com/docs/batch_submit_job/> and the
 #'   "AWS arguments" sections of this help file.
-#' @param aws_batch_propagate_tags `NULL` or a nonempty list.
+#' @param aws_batch_propagate_tags `NULL` or a logical of length 1.
 #'   For more details, visit
 #'   <https://www.paws-r-sdk.com/docs/batch_submit_job/> and the
 #'   "AWS arguments" sections of this help file.
 #' @param aws_batch_timeout `NULL` or a nonempty named list.
 #'   For more details, visit
 #'   <https://www.paws-r-sdk.com/docs/batch_submit_job/> and the
 #'   "AWS arguments" sections of this help file.
-#' @param aws_batch_tags `NULL` or a nonempty list.
+#' @param aws_batch_tags `NULL` or a nonempty named list.
 #'   For more details, visit
 #'   <https://www.paws-r-sdk.com/docs/batch_submit_job/> and the
 #'   "AWS arguments" sections of this help file.
@@ -115,6 +115,7 @@ crew_launcher_aws_batch <- function(
   launch_max = 5L,
   tls = crew::crew_tls(mode = "automatic"),
   processes = NULL,
+  r_arguments = NULL,
   aws_batch_config = list(),
   aws_batch_credentials = list(),
   aws_batch_endpoint = NULL,
@@ -149,6 +150,7 @@ crew_launcher_aws_batch <- function(
     launch_max = launch_max,
     tls = tls,
     processes = processes,
+    r_arguments = r_arguments,
     aws_batch_config = aws_batch_config,
     aws_batch_credentials = aws_batch_credentials,
     aws_batch_endpoint = aws_batch_endpoint,
@@ -316,6 +318,7 @@ crew_class_launcher_aws_batch <- R6::R6Class(
     #' @param launch_max See [crew_launcher_aws_batch()].
     #' @param tls See [crew_launcher_aws_batch()].
     #' @param processes See [crew_launcher_aws_batch()].
+    #' @param r_arguments See [crew_launcher_aws_batch()].
     #' @param aws_batch_config See [crew_launcher_aws_batch()].
     #' @param aws_batch_credentials See [crew_launcher_aws_batch()].
     #' @param aws_batch_endpoint See [crew_launcher_aws_batch()].
@@ -350,6 +353,7 @@ crew_class_launcher_aws_batch <- R6::R6Class(
       launch_max = NULL,
       tls = NULL,
       processes = NULL,
+      r_arguments = NULL,
       aws_batch_config = NULL,
       aws_batch_credentials = NULL,
       aws_batch_endpoint = NULL,
@@ -382,7 +386,8 @@ crew_class_launcher_aws_batch <- R6::R6Class(
         garbage_collection = garbage_collection,
         launch_max = launch_max,
         tls = tls,
-        processes = processes
+        processes = processes,
+        r_arguments = r_arguments
       )
       private$.aws_batch_config <- aws_batch_config
       private$.aws_batch_credentials <- aws_batch_credentials