Merge branch 'release/1.39.0'

.Rbuildignore

@@ -59,3 +59,4 @@ Rplots.pdf$
 ^.ghi
 ^.issues
 ^last.dump*
+^CRAN-SUBMISSION$

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

@@ -18,16 +18,15 @@ jobs:
         config:
           - {os: windows-latest, r: 'devel'    }
           - {os: windows-latest, r: 'release'  }
-          - {os: windows-latest, r: 'oldrel'   }
-          - {os: macOS-14,       r: 'devel'    }
-          - {os: macOS-latest,   r: 'release'  }
-          - {os: macOS-latest,   r: 'oldrel'   }
+#          - {os: macOS-latest,   r: 'devel'    }
+#          - {os: macOS-latest,   r: 'release'  }
+#          - {os: macOS-latest,   r: 'oldrel'   }
           - {os: ubuntu-latest,  r: 'devel'    }
           - {os: ubuntu-latest,  r: 'release'  }
           - {os: ubuntu-latest,  r: 'oldrel'   }
           - {os: ubuntu-latest,  r: 'oldrel-1' }
           - {os: ubuntu-latest,  r: 'oldrel-2' }
-          - {os: ubuntu-latest,  r: '3.5'      }
+          - {os: ubuntu-latest,  r: '3.6'      }
           - {os: ubuntu-latest,  r: 'release'  , language: ko,    label: ko    }
           - {os: ubuntu-latest,  r: 'release'  , language: zh_CN, label: zh_CN }
           - {os: ubuntu-latest,  r: 'release'  , language: zh_TW, label: zh_TW }
@@ -39,31 +38,37 @@ jobs:
       LANGUAGE: ${{ matrix.config.language }}
       ## R CMD check
       _R_CHECK_CRAN_INCOMING_: false
-      _R_CHECK_LENGTH_1_CONDITION_: true
-      _R_CHECK_LENGTH_1_LOGIC2_: true
       _R_CHECK_MATRIX_DATA_: true
       _R_CHECK_SUGGESTS_ONLY_: true
-      _R_CHECK_S3_METHODS_SHOW_POSSIBLE_ISSUES_: true
+      _R_CHECK_THINGS_IN_TEMP_DIR_: true
+      ## R (>= 4.4.0) Note, no trailing underscore (sic!)
+      _R_COMPARE_LANG_OBJECTS: eqonly
 
     steps:
       - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
+      - uses: r-lib/actions/setup-tinytex@v2
+
+      - name: Install system dependencies (Linux)
+        if: runner.os == 'Linux'
+        run: sudo apt-get install -y tidy
+
       - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
           http-user-agent: ${{ matrix.config.http-user-agent }}
           use-public-rspm: true
-          
+
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           extra-packages: any::rcmdcheck
           needs: check
 
-      - name: Install package itself (special case)
+      - name: Install itself (to build vignettes)
         run: |
-          install.packages(".", repos = NULL, type = "source")  ## self vignette engine
+          install.packages(".", repos=NULL, type="source")
         shell: Rscript {0}
 
       - name: Session info
@@ -82,7 +87,7 @@ jobs:
       - name: Check
         run: |
           rcmdcheck::rcmdcheck(
-            args = c("--no-manual", "--as-cran"),
+            args = c("--as-cran", if (.Platform$OS.type == "windows") "--no-manual"),
             error_on = "note",
             check_dir = "check"
           )

.github/workflows/rhub.yaml

@@ -0,0 +1,95 @@
+# R-hub's generic GitHub Actions workflow file. It's canonical location is at
+# https://github.com/r-hub/actions/blob/v1/workflows/rhub.yaml
+# You can update this file to a newer version using the rhub2 package:
+#
+# rhub::rhub_setup()
+#
+# It is unlikely that you need to modify this file manually.
+
+name: R-hub
+run-name: "${{ github.event.inputs.id }}: ${{ github.event.inputs.name || format('Manually run by {0}', github.triggering_actor) }}"
+
+on:
+  workflow_dispatch:
+    inputs:
+      config:
+        description: 'A comma separated list of R-hub platforms to use.'
+        type: string
+        default: 'linux,windows,macos'
+      name:
+        description: 'Run name. You can leave this empty now.'
+        type: string
+      id:
+        description: 'Unique ID. You can leave this empty now.'
+        type: string
+
+jobs:
+
+  setup:
+    runs-on: ubuntu-latest
+    outputs:
+      containers: ${{ steps.rhub-setup.outputs.containers }}
+      platforms: ${{ steps.rhub-setup.outputs.platforms }}
+
+    steps:
+    # NO NEED TO CHECKOUT HERE
+    - uses: r-hub/actions/setup@v1
+      with:
+        config: ${{ github.event.inputs.config }}
+      id: rhub-setup
+
+  linux-containers:
+    needs: setup
+    if: ${{ needs.setup.outputs.containers != '[]' }}
+    runs-on: ubuntu-latest
+    name: ${{ matrix.config.label }}
+    strategy:
+      fail-fast: false
+      matrix:
+        config: ${{ fromJson(needs.setup.outputs.containers) }}
+    container:
+      image: ${{ matrix.config.container }}
+
+    steps:
+      - uses: r-hub/actions/checkout@v1
+      - uses: r-hub/actions/platform-info@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/setup-deps@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/run-check@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+
+  other-platforms:
+    needs: setup
+    if: ${{ needs.setup.outputs.platforms != '[]' }}
+    runs-on: ${{ matrix.config.os }}
+    name: ${{ matrix.config.label }}
+    strategy:
+      fail-fast: false
+      matrix:
+        config: ${{ fromJson(needs.setup.outputs.platforms) }}
+
+    steps:
+      - uses: r-hub/actions/checkout@v1
+      - uses: r-hub/actions/setup-r@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}
+      - uses: r-hub/actions/platform-info@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/setup-deps@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}
+      - uses: r-hub/actions/run-check@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}

.make/README.md.rsp

@@ -188,14 +188,8 @@ appveyor <- function(text = FALSE) {
 
 covr <- function() {
   bfr <- NULL
-  files <- c("covr.yaml", "R-CMD-check.yaml")
-  for (file in file.path(".github/workflows", files)) {
-    if (file.exists(file)) {
-      bfr <- readLines(file)
-      break
-    }
-  }
-  if (!any(grepl("covr::codecov", bfr, fixed=TRUE))) return()
+  files <- c("test-coverage.yaml", "covr.yaml")
+  if (!any(file_test("-f", file.path(".github/workflows/", files)))) return()
   a("https://app.codecov.io/gh/%s", github_repos(), body=img("https://codecov.io/gh/%s/branch/develop/graph/badge.svg", github_repos(), alt="Coverage Status"))
 }
 %>

CRAN-SUBMISSION

@@ -0,0 +1,3 @@
+Version: 1.39.0
+Date: 2024-11-07 08:30:16 UTC
+SHA: bfc11871dfe0f2c5447d83aadbeaa2600cc57323

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: parallelly
-Version: 1.38.0
+Version: 1.39.0
 Title: Enhancing the 'parallel' Package
 Imports:
     parallel,

NEWS.md

@@ -1,3 +1,26 @@
+# Version 1.39.0 [2024-11-07]
+
+## New Features
+
+ * Environment variables `R_PARALLELLY_RANDOM_PORTS` now supports
+   multiple, comma-separated port specifications, e.g.
+   `"20001:20999"` and `"1068:1099,20001:20999,40530"`.
+
+## Documentation
+
+ * Add example to `help("makeClusterPSOCK")` on how to use
+   `systemd-run` to limit workers' CPU quota and memory allowances.
+
+## Miscellaneous
+
+ * Improved how cgroups v1 and v2 settings are queried.
+
+## Bug Fixes
+
+ * Now `availableCores()` does a better job detecting cgroups v2
+   `cpu.max` CPU restrictions.
+
+
 # Version 1.38.0 [2024-07-27]
 
 ## New Features
@@ -16,7 +39,7 @@
    and `rscript_sh[2]` is for the outer shell quoting of the Rscript
    call.  More precisely, `rscript_sh[1]` is for Rscript arguments
    that need shell quoting (e.g. `Rscript -e "<expr>"`), and
-   `rscript_sh[2]` is for the whole `Rscript ...` call.}
+   `rscript_sh[2]` is for the whole `Rscript ...` call.
 
  * Add `makeClusterSequential()` available for R (>= 4.4.0).
 
@@ -192,11 +215,11 @@
    such as `system2("Rscript --version")`.  If not, an informative
    error message is produced.
 
- * On Unix, `availableCores()` queries also control groups v2
-   (cgroups2) field `cpu.max` for a possible CPU quota allocation. If
-   a CPU quota is set, then the number of CPUs is rounded to the
-   nearest integer, unless its less that 0.5, in case it's rounded up
-   to a single CPU. An example, where cgroups CPU quotas can be set to
+ * On Unix, `availableCores()` queries also control groups v2 (cgroups
+   v2) field `cpu.max` for a possible CPU quota allocation. If a CPU
+   quota is set, then the number of CPUs is rounded to the nearest
+   integer, unless its less that 0.5, in case it's rounded up to a
+   single CPU. An example, where cgroups CPU quotas can be set to
    limit the total CPU load, is with Linux containers, e.g. `docker
    run --cpus=3.5 ...`.
 

R/availableCores.R

@@ -47,10 +47,10 @@
 #'    Query \code{\link[parallel]{detectCores}(logical = logical)}.
 #'
 #'  \item `"cgroups.cpuset"` -
-#'    On Unix, query control group (cgroup) value \code{cpuset.set}.
+#'    On Unix, query control group (cgroup v1) value \code{cpuset.set}.
 #'
 #'  \item `"cgroups.cpuquota"` -
-#'    On Unix, query control group (cgroup) value
+#'    On Unix, query control group (cgroup v1) value
 #'    \code{cpu.cfs_quota_us} / \code{cpu.cfs_period_us}.
 #'
 #'  \item `"cgroups2.cpu.max"` -
@@ -369,18 +369,18 @@ availableCores <- function(constraints = NULL, methods = getOption2("parallelly.
       ## Number of cores available according to parallel::detectCores()
       n <- detectCores(logical = logical)
     } else if (method == "cgroups.cpuset") {
-      ## Number of cores according to Unix Cgroups CPU set
-      n <- length(getCGroupsCpuSet())
+      ## Number of cores according to Unix cgroups v1 CPU set
+      n <- length(getCGroups1CpuSet())
       if (n == 0L) n <- NA_integer_
     } else if (method == "cgroups.cpuquota") {
-      ## Number of cores according to Unix Cgroups CPU quota
-      n <- getCGroupsCpuQuota()
+      ## Number of cores according to Unix cgroups v1 CPU quota
+      n <- getCGroups1CpuQuota()
       if (!is.na(n)) {
         n <- as.integer(floor(n + 0.5))
 	if (n == 0L) n <- 1L  ## If CPU quota < 0.5, round up to one CPU
       }
     } else if (method == "cgroups2.cpu.max") {
-      ## Number of cores according to Unix Cgroups v2 CPU max quota
+      ## Number of cores according to Unix cgroups v2 CPU max quota
       n <- getCGroups2CpuMax()
       if (!is.na(n)) {
         n <- as.integer(floor(n + 0.5))
@@ -551,7 +551,7 @@ getNproc <- function(ignore = c("OMP_NUM_THREADS", "OMP_THREAD_LIMIT")) {
 #' running on the same machine.  This also a problem on systems where R
 #' gets allotted a specific number of CPU cores, which is the case on
 #' high-performance compute (HPC) clusters, but also on other shared systems
-#' that limits user processes via Linux Control Groups (CGroups).
+#' that limits user processes via Linux Control Groups (cgroups).
 #' For example, a free account on Posit Cloud is limited to a single
 #' CPU core. Parallelizing with 32 workers when only having access to
 #' a single core, will result in 3200% overuse and 32 concurrent R