Merge branch 'master' into pr/1138

Author: jgabry

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

@@ -59,7 +59,7 @@ jobs:
 
       - name: Install cmdstan
         run: |
-          cmdstanr::check_cmdstan_toolchain(fix = TRUE)
+          cmdstanr::check_cmdstan_toolchain()
           cmdstanr::install_cmdstan(cores = 2, wsl = TRUE, overwrite = TRUE)
         shell: Rscript {0}
 

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

@@ -35,8 +35,11 @@ jobs:
         config:
           - {os: macOS-latest, r: 'devel', opencl: true}
           - {os: macOS-latest, r: 'release', opencl: true}
+          - {os: macos-26, r: 'release', opencl: false}
+          - {os: macos-15-intel, r: 'release', opencl: false}
           - {os: windows-latest, r: 'devel' }
           - {os: windows-latest, r: 'release'}
+          - {os: windows-2022, r: '4.1'}
           - {os: windows-latest, r: 'oldrel'}
           - {os: ubuntu-latest, r: 'devel', opencl: true}
           - {os: ubuntu-latest, r: 'release', opencl: true}
@@ -74,6 +77,28 @@ jobs:
           cache: "always"
           extra-packages: any::rcmdcheck, local::.
 
+      - name: Debug Windows toolchain resolution
+        if: ${{ runner.os == 'Windows' }}
+        run: |
+          rtools_home <- cmdstanr:::rtools4x_home_path()
+          candidates <- cmdstanr:::rtools4x_toolchain_candidates()
+          selected <- cmdstanr:::rtools4x_toolchain_path()
+          cat("R version: ", as.character(getRversion()), "\n", sep = "")
+          cat("Rtools home: ", rtools_home, "\n", sep = "")
+          cat("Toolchain candidates:\n")
+          if (length(candidates) == 0) {
+            cat("  - <none>\n")
+          } else {
+            cat(paste0("  - ", candidates), sep = "\n")
+            cat("\n")
+          }
+          cat("Selected toolchain: ", selected, "\n", sep = "")
+          selected_ok <- cmdstanr:::is_rtools4x_toolchain_usable(selected)
+          if (!selected_ok) {
+            stop("Resolved Windows toolchain path is not usable.")
+          }
+        shell: Rscript {0}
+
       - name: Install POCL on Ubuntu Runners
         if: ${{ matrix.config.os == 'ubuntu-latest' }}
         run: |
@@ -91,7 +116,7 @@ jobs:
 
       - name: Install cmdstan
         run: |
-          cmdstanr::check_cmdstan_toolchain(fix = TRUE)
+          cmdstanr::check_cmdstan_toolchain()
           tarball_url <- Sys.getenv("CMDSTAN_TEST_TARBALL_URL")
           if (nzchar(tarball_url)) {
             cmdstanr::install_cmdstan(

.github/workflows/Test-coverage.yaml

@@ -55,7 +55,7 @@ jobs:
 
       - name: Install cmdstan
         run: |
-          cmdstanr::check_cmdstan_toolchain(fix = TRUE)
+          cmdstanr::check_cmdstan_toolchain()
           cmdstanr::install_cmdstan(cores = 2)
         shell: Rscript {0}
 
@@ -87,7 +87,7 @@ jobs:
           covr::to_cobertura(cov)
         shell: Rscript {0}
 
-      - uses: codecov/codecov-action@v5
+      - uses: codecov/codecov-action@v6
         with:
           # Fail if error if not on PR, or if on PR and token is given
           fail_ci_if_error: ${{ github.event_name != 'pull_request' || secrets.CODECOV_TOKEN }}

DESCRIPTION

@@ -3,11 +3,11 @@ Title: R Interface to 'CmdStan'
 Version: 0.9.0.9000
 Date: 2025-03-30
 Authors@R:
-    c(person(given = "Jonah", family = "Gabry", role = "aut",
+    c(person(given = "Jonah", family = "Gabry", role = c("aut", "cre"),
              email = "jgabry@gmail.com"),
       person(given = "Rok", family = "Češnovar", role = "aut",
              email = "rok.cesnovar@fri.uni-lj.si"),
-      person(given = "Andrew", family = "Johnson", role = c("aut", "cre"),
+      person(given = "Andrew", family = "Johnson", role = "aut",
              email = "andrew.johnson@arjohnsonau.com",
              comment = c(ORCID = "0000-0001-7000-8065")),
       person(given = "Steve", family = "Bronder", role = "aut"),
@@ -16,10 +16,12 @@ Authors@R:
       person(given = "Mikhail", family = "Popov", role = "ctb"),
       person(given = "Mike", family = "Lawrence", role = "ctb"),
       person(given = c("William", "Michael"), family = "Landau", role = "ctb",
-           email = "will.landau@gmail.com", comment = c(ORCID = "0000-0003-1878-3253")),
+             email = "will.landau@gmail.com", comment = c(ORCID = "0000-0003-1878-3253")),
       person(given = "Jacob", family = "Socolar", role = "ctb"),
       person(given = "Martin", family = "Modrák", role = "ctb"),
-      person(given = "Ven", family = "Popov", role = "ctb")
+      person(given = "Ven", family = "Popov", role = "ctb"),
+      person("Visruth", "Srimath Kandali", role = "ctb"),
+      person("Aki", "Vehtari", role = "ctb")
       )
 Description: A lightweight interface to 'Stan' <https://mc-stan.org>.
     The 'CmdStanR' interface is an alternative to 'RStan' that calls the command
@@ -36,12 +38,12 @@ RoxygenNote: 7.3.3
 Roxygen: list(markdown = TRUE, r6 = FALSE)
 SystemRequirements: CmdStan (https://mc-stan.org/users/interfaces/cmdstan)
 Depends:
-    R (>= 3.5.0)
+    R (>= 4.0.0)
 Imports:
     checkmate,
     data.table,
-    jsonlite (>= 1.2.0),
-    posterior (>= 1.4.1),
+    jsonlite (>= 1.8.7),
+    posterior (>= 1.5.0),
     processx (>= 3.5.0),
     R6 (>= 2.4.0),
     withr (>= 2.5.0),
@@ -56,6 +58,7 @@ Suggests:
     progressr,
     qs2,
     rmarkdown,
-    testthat (>= 2.1.0),
+    testthat (>= 3.3.0),
     Rcpp
 VignetteBuilder: knitr
+Config/testthat/edition: 3

NAMESPACE

@@ -37,6 +37,7 @@ export(draws_to_csv)
 export(eng_cmdstan)
 export(install_cmdstan)
 export(print_example_program)
+export(print_stan_file)
 export(read_cmdstan_csv)
 export(rebuild_cmdstan)
 export(register_default_progress_handler)

NEWS.md

@@ -1,6 +1,22 @@
 # cmdstanr (development version)
 
-* Removed deprecated items (replacements in parentheses):
+* Informative error when exposing functions using names that are reserved 
+keywords (@VisruthSK, #1154)
+* `save_cmdstan_config` and `save_metric` default to `FALSE` but can be 
+set to `TRUE` for an entire R session via new global options. (#1159)
+* `cmdstan_model()` no longer fails when `MAKEFLAGS` enables directory-printing 
+output while reading `STANCFLAGS` from `make`. (#1163)
+
+* CmdStanModel objects created using `compile_model_methods = TRUE` that are
+then saved and reloaded no longer error in model fitting methods. Model methods
+are recompiled lazily if needed. (#1158)
+  
+* CmdStan versions older than 2.35.0 are no longer supported. (#1144)
+* Minimum R version increased to 4.0.0. (#1144)
+* Removed legacy Windows toolchain paths for older CmdStan releases. (#1144)
+* `CMDSTANR_USE_MSYS_TOOLCHAIN` is now deprecated and ignored (with a warning). (#1144)
+
+* Removed deprecated items (replacements in parentheses). (#1061)
   - `read_sample_csv()` (`read_cmdstan_csv()`)
   - `write_stan_tempfile()` (`write_stan_file()`)
   - `jacobian_adjustment` argument to `fit$log_prob()` and similar methods (`jacobian` argument)