Staging

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

@@ -37,14 +37,14 @@ jobs:
 
       - uses: actions/checkout@v4
 
-      - uses: r-lib/actions/setup-r@v2.10.1
-      - uses: r-lib/actions/setup-pandoc@v2.10.1
+      - uses: r-lib/actions/setup-r@v2.11.1
+      - uses: r-lib/actions/setup-pandoc@v2.11.1
 
-      - uses: r-lib/actions/setup-r-dependencies@v2.10.1
+      - uses: r-lib/actions/setup-r-dependencies@v2.11.1
         with:
           extra-packages: any::rcmdcheck, local::.
 
-      - uses: Vampire/setup-wsl@v3
+      - uses: Vampire/setup-wsl@v4
         with:
             distribution: Ubuntu-22.04
             use-cache: 'false'
@@ -71,7 +71,7 @@ jobs:
           sessioninfo::session_info(pkgs, include_base = TRUE)
         shell: Rscript {0}
 
-      - uses: r-lib/actions/check-r-package@v2.10.1
+      - uses: r-lib/actions/check-r-package@v2.11.1
         env:
           _R_CHECK_CRAN_INCOMING_: false
 

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

@@ -55,14 +55,14 @@ jobs:
 
       - uses: actions/checkout@v4
 
-      - uses: r-lib/actions/setup-r@v2.10.1
+      - uses: r-lib/actions/setup-r@v2.11.1
         with:
           r-version: ${{ matrix.config.r }}
           rtools-version: ${{ matrix.config.rtools }}
 
-      - uses: r-lib/actions/setup-pandoc@v2.10.1
+      - uses: r-lib/actions/setup-pandoc@v2.11.1
 
-      - uses: r-lib/actions/setup-r-dependencies@v2.10.1
+      - uses: r-lib/actions/setup-r-dependencies@v2.11.1
         with:
           extra-packages: any::rcmdcheck, local::.
 
@@ -79,7 +79,7 @@ jobs:
           sessioninfo::session_info(pkgs, include_base = TRUE)
         shell: Rscript {0}
 
-      - uses: r-lib/actions/check-r-package@v2.10.1
+      - uses: r-lib/actions/check-r-package@v2.11.1
         env:
           _R_CHECK_CRAN_INCOMING_: false
 

.github/workflows/Test-coverage.yaml

@@ -42,10 +42,10 @@ jobs:
         if: "!startsWith(github.ref, 'refs/tags/') && github.ref != 'refs/heads/master'"
       - uses: actions/checkout@v4
 
-      - uses: r-lib/actions/setup-r@v2.10.1
-      - uses: r-lib/actions/setup-pandoc@v2.10.1
+      - uses: r-lib/actions/setup-r@v2.11.1
+      - uses: r-lib/actions/setup-pandoc@v2.11.1
 
-      - uses: r-lib/actions/setup-r-dependencies@v2.10.1
+      - uses: r-lib/actions/setup-r-dependencies@v2.11.1
         with:
           extra-packages: any::rcmdcheck, local::., any::covr, any::gridExtra
 

.github/workflows/cmdstan-tarball-check.yaml

@@ -40,12 +40,12 @@ jobs:
           sudo apt-get install -y libcurl4-openssl-dev || true
           sudo apt-get install -y openmpi-bin openmpi-common libopenmpi-dev || true
 
-      - uses: r-lib/actions/setup-r@v2.10.1
+      - uses: r-lib/actions/setup-r@v2.11.1
         with:
           r-version: ${{ matrix.config.r }}
           rtools-version: ${{ matrix.config.rtools }}
 
-      - uses: r-lib/actions/setup-pandoc@v2.10.1
+      - uses: r-lib/actions/setup-pandoc@v2.11.1
 
       - name: Query dependencies
         run: |

R/args.R

@@ -715,12 +715,6 @@ validate_cmdstan_args <- function(self) {
   }
   validate_init(self$init, num_inits)
   validate_seed(self$seed, num_procs)
-  if (!is.null(self$opencl_ids)) {
-    if (cmdstan_version() < "2.26") {
-      stop("Runtime selection of OpenCL devices is only supported with CmdStan version 2.26 or newer.", call. = FALSE)
-    }
-    checkmate::assert_vector(self$opencl_ids, len = 2)
-  }
   invisible(TRUE)
 }
 

R/csv.R

@@ -719,7 +719,7 @@ read_csv_metadata <- function(csv_file) {
         dense_inv_metric <- TRUE
       } else if (inv_metric_next) {
         inv_metric_split <- strsplit(gsub("# ", "", line), ",")
-        numeric_inv_metric_split <- rapply(inv_metric_split, as.numeric)
+        numeric_inv_metric_split <- suppressWarnings(rapply(inv_metric_split, as.numeric))
         if (inv_metric_rows == -1 && dense_inv_metric) {
           inv_metric_rows <- length(inv_metric_split[[1]])
           inv_metric_rows_to_read <- inv_metric_rows
@@ -786,6 +786,7 @@ read_csv_metadata <- function(csv_file) {
     }
   }
   if (csv_file_info$method != "diagnose" &&
+      !isTRUE(csv_file_info$algorithm == "fixed_param") &&
       length(csv_file_info$sampler_diagnostics) == 0 &&
       length(csv_file_info$variables) == 0) {
     stop("Supplied CSV file does not contain any variable names or data!", call. = FALSE)

R/fit.R

@@ -108,6 +108,10 @@ CmdStanFit <- R6::R6Class(
 #'   read into R lazily (i.e., as needed), the `$save_object()` method is the
 #'   safest way to guarantee that everything has been read in before saving.
 #'
+#'   See the "Saving fitted model objects" section of the
+#'   [_Getting started with CmdStanR_](https://mc-stan.org/cmdstanr/articles/cmdstanr.html)
+#'   vignette for some suggestions on faster model saving for large models.
+#'
 #' @param file (string) Path where the file should be saved.
 #' @param ... Other arguments to pass to [base::saveRDS()] besides `object` and `file`.
 #'
@@ -1616,6 +1620,9 @@ CmdStanMCMC$set("public", name = "loo", value = loo)
 #' }
 #'
 sampler_diagnostics <- function(inc_warmup = FALSE, format = getOption("cmdstanr_draws_format", "draws_array")) {
+  if (isTRUE(private$metadata_$algorithm == "fixed_param")) {
+    stop("There are no sampler diagnostics when fixed_param = TRUE.", call. = FALSE)
+  }
   if (is.null(private$sampler_diagnostics_) &&
       !length(self$output_files(include_failed = FALSE))) {
     stop("No chains finished successfully. Unable to retrieve the sampler diagnostics.", call. = FALSE)

R/install.R

@@ -203,8 +203,7 @@ install_cmdstan <- function(dir = NULL,
   } else {
     untar_rc <- utils::untar(
       dest_file,
-      exdir = dir_cmdstan,
-      extras = "--strip-components 1"
+      exdir = dir
     )
     if (untar_rc != 0) {
       stop("Problem extracting tarball. Exited with return code: ", untar_rc, call. = FALSE)