Merge branch 'release/1.38.0'

futureverse · Jul 27, 2024 · b19a140 · b19a140
2 parents 80c1ddb + 403bd14
commit b19a140
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diff --git a/.github/workflows/covr.yaml b/.github/workflows/covr.yaml
@@ -4,10 +4,10 @@ name: covr
 
 jobs:
   covr:
-    if: "! contains(github.event.head_commit.message, '[ci skip]')"
+    if: "! contains(github.event.head_commit.message, '[ci skip]')"    
+
+    timeout-minutes: 45
 
-    timeout-minutes: 10
-
     runs-on: ubuntu-latest
 
     name: covr
@@ -17,48 +17,39 @@ jobs:
 
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
-      RSPM: https://packagemanager.rstudio.com/cran/__linux__/jammy/latest
+      R_KEEP_PKG_SOURCE: yes
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+      ## Test in other locale (optional)
+      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_CRAN_INCOMING_: false
+      _R_CHECK_SUGGESTS_ONLY_: true
+      _R_CHECK_THINGS_IN_TEMP_DIR_: true
+      RCMDCHECK_ERROR_ON: note
+      ## Specific to futures
+      R_FUTURE_RNG_ONMISUSE: error
 
     steps:
       - uses: actions/checkout@v4
 
-      - uses: r-lib/actions/setup-pandoc@v2
-
       - uses: r-lib/actions/setup-r@v2
         with:
-          r-version: release
+          use-public-rspm: true
 
-      - name: Query dependencies
-        run: |
-          install.packages('remotes')
-          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
-          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
-        shell: Rscript {0}
-
-      - name: Cache R packages
-        uses: actions/cache@v3
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          path: ${{ env.R_LIBS_USER }}
-          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
-
-      - name: Install system dependencies
-        env:
-          RHUB_PLATFORM: linux-x86_64-ubuntu-gcc
-        run: |
-          Rscript -e "remotes::install_github('r-hub/sysreqs')"
-          sysreqs=$(Rscript -e "cat(sysreqs::sysreq_commands('DESCRIPTION'))")
-          sudo -s eval "$sysreqs"
+          extra-packages: |
+            any::rcmdcheck
+            any::remotes
+            any::sessioninfo
+            any::covr
+          needs: check
 
       - name: Install dependencies
         run: |
-          install.packages(c("covr", "sessioninfo"))
           remotes::install_deps(dependencies = TRUE)
           install.packages(".", repos=NULL, type="source")
         shell: Rscript {0}
@@ -76,7 +67,7 @@ jobs:
           ##    https://app.codecov.io/gh/<org>/<repo>/settings
           ## 2. Set 'CODECOV_TOKEN' in GitHub Secrets:
           ##    https://github.com/<org>/<repo>/settings/environments/
-          coverage <- covr::package_coverage()
+          coverage <- covr::package_coverage(quiet = FALSE)
           print(coverage)
           covr::codecov(coverage = coverage, token="${{secrets.CODECOV_TOKEN}}")
         shell: Rscript {0}
diff --git a/.github/workflows/revdepcheck-top.yaml b/.github/workflows/revdepcheck-top.yaml
@@ -21,7 +21,6 @@ jobs:
 
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
-      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
@@ -39,37 +38,21 @@ jobs:
       - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
+          use-public-rspm: true
 
-      - name: Query dependencies
-        run: |
-          install.packages('remotes')
-          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
-          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
-        shell: Rscript {0}
-
-      - name: Cache R packages
-        if: runner.os != 'Windows'
-        uses: actions/cache@v3
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          path: ${{ env.R_LIBS_USER }}
-          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
-
-      - name: Install system dependencies (Linux)
-        if: runner.os == 'Linux'
-        env:
-          RHUB_PLATFORM: linux-x86_64-ubuntu-gcc
-        run: |
-          Rscript -e "remotes::install_github('r-hub/sysreqs')"
-          sysreqs=$(Rscript -e "cat(sysreqs::sysreq_commands('DESCRIPTION'))")
-          sudo -s eval "$sysreqs"
+          extra-packages: |
+            any::rcmdcheck
+            any::remotes
+            any::sessioninfo
+            any::covr
+          needs: check
 
       - name: Install dependencies
         run: |
           remotes::install_deps(dependencies = TRUE)
-          remotes::install_cran("rcmdcheck")
-          install.packages(".", repos=NULL, type="source")  ## needed by parallel workers
-          install.packages("${{ matrix.config.pkg }}", dependencies=TRUE)
+          install.packages(".", repos=NULL, type="source")
         shell: Rscript {0}
 
       - name: Session info
@@ -82,6 +65,7 @@ jobs:
       - name: Check reverse dependency package
         run: |
           pkgname <- "${{ matrix.config.pkg }}"
+          install.packages(pkgname, dependencies = TRUE)
           url <- remotes:::download_version_url(pkgname, version=NULL, repos="https://cloud.r-project.org", type="source")
           tarball <- basename(url)
           utils::download.file(url, destfile = tarball, mode = "wb")

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,20 +1,25 @@
 Package: parallelly
-Version: 1.37.1
+Version: 1.38.0
 Title: Enhancing the 'parallel' Package
 Imports:
     parallel,
     tools,
     utils
-Authors@R: c(person("Henrik", "Bengtsson",
-                    role = c("aut", "cre", "cph"),
-                    email = "[email protected]",
-                    comment = c(ORCID = "0000-0002-7579-5165")))
+Authors@R: c(
+        person("Henrik", "Bengtsson",
+               role = c("aut", "cre", "cph"),
+               email = "[email protected]",
+               comment = c(ORCID = "0000-0002-7579-5165")),
+        person("Mike", "Cheng",
+               role = c("ctb"),
+               email = "[email protected]")
+    )
 Description: Utility functions that enhance the 'parallel' package and support the built-in parallel backends of the 'future' package.  For example, availableCores() gives the number of CPU cores available to your R process as given by the operating system, 'cgroups' and Linux containers, R options, and environment variables, including those set by job schedulers on high-performance compute clusters. If none is set, it will fall back to parallel::detectCores(). Another example is makeClusterPSOCK(), which is backward compatible with parallel::makePSOCKcluster() while doing a better job in setting up remote cluster workers without the need for configuring the firewall to do port-forwarding to your local computer.
 License: LGPL (>= 2.1)
 LazyLoad: TRUE
 ByteCompile: TRUE
 URL: https://parallelly.futureverse.org, https://github.com/HenrikBengtsson/parallelly
 BugReports: https://github.com/HenrikBengtsson/parallelly/issues
 Encoding: UTF-8
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 Roxygen: list(markdown = TRUE)
diff --git a/NAMESPACE b/NAMESPACE
@@ -29,6 +29,8 @@ S3method(print,RichSOCKnode)
 S3method(stopCluster,RichMPIcluster)
 S3method(summary,RichSOCKcluster)
 S3method(summary,RichSOCKnode)
+export(MPI)
+export(PSOCK)
 export(as.cluster)
 export(autoStopCluster)
 export(availableConnections)
@@ -49,7 +51,16 @@ export(killNode)
 export(makeClusterMPI)
 export(makeClusterPSOCK)
 export(makeNodePSOCK)
+export(serializedSize)
 export(supportsMulticore)
+if (getRversion() >= "4.4") S3method(print,sequential_cluster)
+if (getRversion() >= "4.4") S3method(print,sequential_node)
+if (getRversion() >= "4.4") S3method(recvData,sequential_node)
+if (getRversion() >= "4.4") S3method(sendData,sequential_node)
+if (getRversion() >= "4.4") export(SEQ)
+if (getRversion() >= "4.4") export(makeClusterSequential)
+if (getRversion() >= "4.4") importFrom(parallel,recvData)
+if (getRversion() >= "4.4") importFrom(parallel,sendData)
 importFrom(parallel,clusterCall)
 importFrom(parallel,detectCores)
 importFrom(parallel,makeCluster)

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,41 @@
+# Version 1.38.0 [2024-07-27]
+
+## New Features
+
+ * Now argument `rshcmd` of `makeNodePSOCK()` can be a function. It
+   must accept at least two arguments named `rshopts` and
+   `worker`. The `rshopts` argument is a character vector of length
+   zero or more. The `worker` argument is a string hostname. The
+   function must return a single string.
+
+ * Now `makeNodePSOCK()` accepts `rscript_sh = "none"`, which skips
+   quoting the Rscript call.
+
+ * Now `makeNodePSOCK()` accepts `rscript_sh` of length one or two.
+   If `length(rscript_sh) == 2`, then `rscript_sh[1]` is for the inner
+   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.}
+
+ * Add `makeClusterSequential()` available for R (>= 4.4.0).
+
+ * Starting with R 4.5.0 (currently R-devel), one can use
+   `parallel::makeCluster(n, type = parallelly::PSOCK)` as an
+   alternative to `parallelly::makeClusterPSOCK(n)`.  Similarly, `type
+   = parallelly::MPI` creates a cluster using
+   `parallelly::makeClusterMPI()`, and `type = parallelly::SEQ`
+   creates a cluster using `parallelly::makeClusterSequential()`.
+
+ * Add `serializedSize()` for calculating the size of an object by
+   counting the number of bytes required to serialize it.
+
+## Bug Fixes
+
+ * Environment variable `R_PARALLELLY_MAXWORKERS_LOCALHOST` was
+   interpreted as integers rather than doubles.
+
+
 # Version 1.37.1 [2024-02-29]
 
 ## Bug Fixes

diff --git a/R/availableConnections.R b/R/availableConnections.R
@@ -19,7 +19,11 @@
 #' to a greater number via command-line option `--max-connections=N`, e.g.
 #'
 #' ```r
-#' $ R --max-connection=512
+#' $ Rscript -e "parallelly::availableConnections()"
+#' [1] 128
+#'
+#' $ Rscript --max-connections=512 -e "parallelly::availableConnections()"
+#' [1] 512
 #' ```
 #'
 #' For R (< 4.4.0), the limit can only be changed by rebuilding \R from

diff --git a/R/availableCores.R b/R/availableCores.R
@@ -603,7 +603,7 @@ checkNumberOfLocalWorkers <- function(workers) {
   if (length(ignore) > 0) {
     methods <- eval(formals(availableCores)$methods)
     methods <- setdiff(methods, ignore)
-        ncores <- availableCores(methods = methods)
+    ncores <- availableCores(methods = methods)
   } else {
     ncores <- availableCores()
   }

diff --git a/R/makeClusterMPI.R b/R/makeClusterMPI.R
@@ -21,6 +21,15 @@
 #' @return An object of class `c("RichMPIcluster", "MPIcluster", "cluster")` consisting
 #' of a list of `"MPInode"` workers.
 #'
+#' @section Alternative usage:
+#'
+#' In R (>= 4.4.0), an alternatively to using
+#' `cl <- parallelly::makeClusterMPI(workers)` is:
+#'
+#' ```
+#' cl <- parallel::makeCluster(workers, type = parallelly::MPI)
+#' ```
+#'
 #' @examples
 #' \donttest{\dontrun{
 #' if (requireNamespace("Rmpi") && requireNamespace("snow")) {
@@ -38,6 +47,7 @@
 #' @seealso
 #' [makeClusterPSOCK()] and [parallel::makeCluster()].
 #'
+#' @aliases MPI
 #' @importFrom parallel makeCluster
 #' @export
 makeClusterMPI <- function(workers, ..., autoStop = FALSE, verbose = getOption2("parallelly.debug", FALSE)) {