Merge branch 'release/0.12.1'

Author: BHGC Website GHA Workflow Runner

.github/workflows/R-CMD-check.yaml

@@ -22,15 +22,15 @@ jobs:
           - {os: macOS-latest,   r: 'devel'    }
           - {os: macOS-latest,   r: 'release'  }
           - {os: macOS-latest,   r: 'oldrel'   }
-          - {os: ubuntu-20.04,   r: 'devel'    }
-          - {os: ubuntu-20.04,   r: 'release'  }
-          - {os: ubuntu-20.04,   r: 'oldrel'   }
-          - {os: ubuntu-20.04,   r: 'oldrel-1' }
-          - {os: ubuntu-20.04,   r: 'oldrel-2' }
-          - {os: ubuntu-20.04,   r: '3.4'      }
-          - {os: ubuntu-20.04,   r: 'release'  , language: ko,    label: ko    }
-          - {os: ubuntu-20.04,   r: 'release'  , language: zh_CN, label: zh_CN }
-          - {os: ubuntu-20.04,   r: 'release'  , language: zh_TW, label: zh_TW }
+          - {os: ubuntu-22.04,   r: 'devel'    }
+          - {os: ubuntu-22.04,   r: 'release'  }
+          - {os: ubuntu-22.04,   r: 'oldrel'   }
+          - {os: ubuntu-22.04,   r: 'oldrel-1' }
+          - {os: ubuntu-22.04,   r: 'oldrel-2' }
+          - {os: ubuntu-22.04,   r: '3.6'      }
+          - {os: ubuntu-22.04,   r: 'release'  , language: ko,    label: ko    }
+          - {os: ubuntu-22.04,   r: 'release'  , language: zh_CN, label: zh_CN }
+          - {os: ubuntu-22.04,   r: 'release'  , language: zh_TW, label: zh_TW }
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       R_KEEP_PKG_SOURCE: yes
@@ -47,7 +47,7 @@ jobs:
       LANGUAGE: ${{ matrix.config.language }}
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 

.github/workflows/covr.yaml

@@ -8,7 +8,7 @@ jobs:
 
     timeout-minutes: 20
 
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
 
     name: covr
 
@@ -17,7 +17,7 @@ jobs:
 
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
-      RSPM: https://packagemanager.rstudio.com/cran/__linux__/focal/latest
+      RSPM: https://packagemanager.rstudio.com/cran/__linux__/jammy/latest
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
       ## R CMD check
       _R_CHECK_LENGTH_1_CONDITION_: true

.github/workflows/future_tests.yaml

@@ -8,20 +8,22 @@ jobs:
 
     timeout-minutes: 30
 
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
 
     name: future.plan=${{ matrix.future.plan }}
 
     strategy:
       fail-fast: false
       matrix:
         future:
-          - { plan: 'future.batchtools::batchtools_local' }
+          - { plan: 'future.batchtools::batchtools_local'       }
+          - { plan: 'future.batchtools::batchtools_multicore'   }
+          - { plan: 'future.batchtools::batchtools_bash'        }
           - { plan: 'future.batchtools::batchtools_interactive' }
 
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
-      RSPM: https://packagemanager.rstudio.com/cran/__linux__/focal/latest
+      RSPM: https://packagemanager.rstudio.com/cran/__linux__/jammy/latest
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
       ## R CMD check
       _R_CHECK_LENGTH_1_CONDITION_: true
@@ -32,7 +34,7 @@ jobs:
       R_FUTURE_RNG_ONMISUSE: error
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 

.make/Makefile

@@ -356,12 +356,12 @@ test_files: $(R_OUTDIR)/tests/*.R
 
 test: $(R_OUTDIR)/tests/%.R
 	$(CD) $(R_OUTDIR)/tests;\
-	$(R_SCRIPT) -e "for (f in list.files(pattern='[.]R$$')) { print(f); source(f, chdir=TRUE, echo=TRUE) }"
+	$(R_SCRIPT) -e "for (f in list.files(pattern='[.]R$$')) { print(f); source(f, echo=TRUE) }"
 
 test_full: $(R_OUTDIR)/tests/%.R
 	$(CD) $(R_OUTDIR)/tests;\
 	export _R_CHECK_FULL_=TRUE;\
-	$(R_SCRIPT) -e "for (f in list.files(pattern='[.]R$$')) { print(f); source(f, chdir=TRUE, echo=TRUE) }"
+	$(R_SCRIPT) -e "for (f in list.files(pattern='[.]R$$')) { print(f); source(f, echo=TRUE) }"
 
 
 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

DESCRIPTION

@@ -1,11 +1,11 @@
 Package: future.batchtools
-Version: 0.12.0
+Version: 0.12.1
 Depends:
     R (>= 3.2.0),
     parallelly,
     future (>= 1.31.0)
 Imports:
-    batchtools (>= 0.9.13),
+    batchtools (>= 0.9.16),
     utils
 Suggests:
     globals,
@@ -16,8 +16,10 @@ Suggests:
 VignetteBuilder:
     R.rsp
 Title: A Future API for Parallel and Distributed Processing using 'batchtools'
-Authors@R: c(person("Henrik", "Bengtsson", role=c("aut", "cre", "cph"),
-                                          email = "[email protected]"))
+Authors@R: c(person("Henrik", "Bengtsson",
+                    role = c("aut", "cre", "cph"),
+                    email = "[email protected]",
+                    comment = c(ORCID = "0000-0002-7579-5165")))
 Description: Implementation of the Future API on top of the 'batchtools' package.
     This allows you to process futures, as defined by the 'future' package,
     in parallel out of the box, not only on your local machine or ad-hoc

NEWS.md

@@ -1,3 +1,11 @@
+# Version 0.12.1 [2023-12-19]
+
+## Bug Fixes
+
+ * `plan(batchtools_multicore)` did not support `workers` argument
+   being a function.
+
+
 # Version 0.12.0 [2023-02-24]
 
 ## New Features
@@ -76,8 +84,8 @@
    Because of this, we temporarily set `fs.latency = 1.0` (second)
    timeout for trying to find the log file.  This makes a big
    difference in case the template used a `--output=<path>` location
-   other than `--output=<%= log.file %>`l in such cases the log file
-   would not be found, requiring a timeout.
+   other than `--output=<%= log.file %>`. In such cases, the log file
+   would not be found, requiring a full timeout to complete.
 
 ## Bug Fixes
 

R/BatchtoolsFuture-class.R

@@ -294,6 +294,7 @@ loggedError <- function(...) UseMethod("loggedError")
 
 
 #' @importFrom batchtools getErrorMessages
+#' @rdname loggedOutput
 #' @export
 loggedError.BatchtoolsFuture <- function(future, ...) {
   stat <- status(future)

R/batchtools_multicore.R

@@ -33,7 +33,11 @@ batchtools_multicore <- function(expr, envir = parent.frame(),
                             registry = list(), ...) {
   if (substitute) expr <- substitute(expr)
 
-  if (is.null(workers)) workers <- availableCores(constraints = "multicore")
+  if (is.null(workers)) {
+    workers <- availableCores(constraints = "multicore")
+  } else if (is.function(workers)) {
+    workers <- workers()
+  }
   stop_if_not(length(workers) == 1L, is.numeric(workers),
             is.finite(workers), workers >= 1L)
 

R/nbrOfWorkers.R

@@ -18,6 +18,7 @@ nbrOfWorkers.batchtools <- function(evaluator) {
   expr <- formals(evaluator)$workers
   workers <- eval(expr, enclos = baseenv())
   if (!is.null(workers)) {
+    if (is.function(workers)) workers <- workers()
     stop_if_not(length(workers) >= 1)
     if (is.numeric(workers)) return(prod(workers))
     if (is.character(workers)) return(length(workers))
@@ -57,6 +58,7 @@ nbrOfWorkers.batchtools_multicore <- function(evaluator) {
   ## 1. Infer from 'workers' argument
   expr <- formals(evaluator)$workers
   workers <- eval(expr, enclos = baseenv())
+  if (is.function(workers)) workers <- workers()
   stop_if_not(length(workers) == 1L, is.numeric(workers), !is.na(workers), is.finite(workers), workers >= 1)
   workers
 }

R/waitForWorker.R

@@ -44,7 +44,8 @@ waitForWorker.BatchtoolsFuture <- function(future,
          await = NULL,
          timeout = getOption("future.wait.timeout", 30 * 24 * 60 * 60),
          delta = getOption("future.wait.interval", 0.2),
-         alpha = getOption("future.wait.alpha", 1.01)) {
+         alpha = getOption("future.wait.alpha", 1.01),
+         ...) {
   debug <- getOption("future.debug", FALSE)
 
   stop_if_not(is.null(await) || is.function(await))