Test and fix issues with 2.35 RC

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

@@ -37,10 +37,10 @@ jobs:
 
       - uses: actions/checkout@v4
 
-      - uses: r-lib/actions/setup-r@v2.8.7
-      - uses: r-lib/actions/setup-pandoc@v2.8.7
+      - uses: r-lib/actions/setup-r@v2.9.0
+      - uses: r-lib/actions/setup-pandoc@v2.9.0
 
-      - uses: r-lib/actions/setup-r-dependencies@v2.8.7
+      - uses: r-lib/actions/setup-r-dependencies@v2.9.0
         with:
           extra-packages: any::rcmdcheck, local::.
 
@@ -71,7 +71,7 @@ jobs:
           sessioninfo::session_info(pkgs, include_base = TRUE)
         shell: Rscript {0}
 
-      - uses: r-lib/actions/check-r-package@v2.8.7
+      - uses: r-lib/actions/check-r-package@v2.9.0
         env:
           _R_CHECK_CRAN_INCOMING_: false
 

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

@@ -25,7 +25,7 @@ jobs:
         config:
           - {os: macOS-latest, r: 'devel', rtools: ''}
           - {os: macOS-latest, r: 'release', rtools: ''}
-          #- {os: windows-latest, r: 'devel', rtools: '44'}
+          - {os: windows-latest, r: 'devel', rtools: '44'}
           - {os: windows-latest, r: 'release', rtools: '44'}
           - {os: windows-latest, r: 'oldrel', rtools: '43'}
           - {os: ubuntu-latest, r: 'devel', rtools: ''}
@@ -49,14 +49,14 @@ jobs:
 
       - uses: actions/checkout@v4
 
-      - uses: r-lib/actions/setup-r@v2.8.7
+      - uses: r-lib/actions/setup-r@v2.9.0
         with:
           r-version: ${{ matrix.config.r }}
           rtools-version: ${{ matrix.config.rtools }}
 
-      - uses: r-lib/actions/setup-pandoc@v2.8.7
+      - uses: r-lib/actions/setup-pandoc@v2.9.0
 
-      - uses: r-lib/actions/setup-r-dependencies@v2.8.7
+      - uses: r-lib/actions/setup-r-dependencies@v2.9.0
         with:
           extra-packages: any::rcmdcheck, local::.
 
@@ -73,7 +73,7 @@ jobs:
           sessioninfo::session_info(pkgs, include_base = TRUE)
         shell: Rscript {0}
 
-      - uses: r-lib/actions/check-r-package@v2.8.7
+      - uses: r-lib/actions/check-r-package@v2.9.0
         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@v2.8.7
-      - uses: r-lib/actions/setup-pandoc@v2.8.7
+      - uses: r-lib/actions/setup-r@v2.9.0
+      - uses: r-lib/actions/setup-pandoc@v2.9.0
 
-      - uses: r-lib/actions/setup-r-dependencies@v2.8.7
+      - uses: r-lib/actions/setup-r-dependencies@v2.9.0
         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@v2.8.7
+      - uses: r-lib/actions/setup-r@v2.9.0
         with:
           r-version: ${{ matrix.config.r }}
           rtools-version: ${{ matrix.config.rtools }}
 
-      - uses: r-lib/actions/setup-pandoc@v2.8.7
+      - uses: r-lib/actions/setup-pandoc@v2.9.0
 
       - name: Query dependencies
         run: |

R/csv.R

@@ -840,6 +840,14 @@ read_csv_metadata <- function(csv_file) {
     csv_file_info$fitted_params <- wsl_safe_path(csv_file_info$fitted_params,
                                                   revert = TRUE)
   }
+  csv_file_info <- lapply(csv_file_info, function(item) {
+    if (is.character(item) && length(item) == 1) {
+      if (item %in% c("true", "false")) {
+        item <- as.integer(as.logical(item))
+      }
+    }
+    item
+  })
   csv_file_info
 }
 

R/utils.R

@@ -727,7 +727,7 @@ get_cmdstan_flags <- function(flag_name) {
   paste(flags, collapse = " ")
 }
 
-rcpp_source_stan <- function(code, env, verbose = FALSE) {
+rcpp_source_stan <- function(code, env, verbose = FALSE, ...) {
   cxxflags <- get_cmdstan_flags("CXXFLAGS")
   cmdstanr_includes <- system.file("include", package = "cmdstanr", mustWork = TRUE)
   cmdstanr_includes <- paste0(" -I\"", cmdstanr_includes,"\"")
@@ -746,7 +746,7 @@ rcpp_source_stan <- function(code, env, verbose = FALSE) {
         PKG_CXXFLAGS = paste0(cxxflags, cmdstanr_includes, collapse = " "),
         PKG_LIBS = libs
       ),
-      Rcpp::sourceCpp(code = code, env = env, verbose = verbose)
+      Rcpp::sourceCpp(code = code, env = env, verbose = verbose, ...)
     )
   )
   invisible(NULL)
@@ -887,8 +887,12 @@ prep_fun_cpp <- function(fun_start, fun_end, model_lines) {
   }
   fun_body <- gsub("// [[stan::function]]", "// [[Rcpp::export]]\n", fun_body, fixed = TRUE)
   fun_body <- gsub("std::ostream\\*\\s*pstream__\\s*=\\s*nullptr", "", fun_body)
-  fun_body <- gsub("boost::ecuyer1988&\\s*base_rng__", "SEXP base_rng_ptr", fun_body)
-  fun_body <- gsub("base_rng__,", "*(Rcpp::XPtr<boost::ecuyer1988>(base_rng_ptr).get()),", fun_body, fixed = TRUE)
+  if (cmdstan_version() < "2.35.0") {
+    fun_body <- gsub("boost::ecuyer1988&\\s*base_rng__", "SEXP base_rng_ptr", fun_body)
+  } else {
+    fun_body <- gsub("stan::rng_t&\\s*base_rng__", "SEXP base_rng_ptr", fun_body)
+  }
+  fun_body <- gsub("base_rng__,", "*(Rcpp::XPtr<stan::rng_t>(base_rng_ptr).get()),", fun_body, fixed = TRUE)
   fun_body <- gsub("pstream__", "&Rcpp::Rcout", fun_body, fixed = TRUE)
   fun_body <- paste(fun_body, collapse = "\n")
   gsub(pattern = ",\\s*)", replacement = ")", fun_body)
@@ -921,6 +925,7 @@ compile_functions <- function(env, verbose = FALSE, global = FALSE) {
     env$hpp_code[1:(funs[1] - 1)],
     "#include <rcpp_tuple_interop.hpp>",
     "#include <rcpp_eigen_interop.hpp>",
+    "#include <stan_rng.hpp>",
     stan_funs),
   collapse = "\n")
   if (global) {
@@ -935,7 +940,7 @@ compile_functions <- function(env, verbose = FALSE, global = FALSE) {
   if (length(rng_funs) > 0) {
     rng_cpp <- system.file("include", "base_rng.cpp", package = "cmdstanr", mustWork = TRUE)
     rcpp_source_stan(paste0(readLines(rng_cpp), collapse="\n"), env, verbose)
-    env$rng_ptr <- env$base_rng(seed=0)
+    env$rng_ptr <- env$base_rng(seed=1)
   }
 
   # For all RNG functions, pass the initialised Boost RNG by default

inst/include/base_rng.cpp

@@ -1,8 +1,8 @@
 #include <Rcpp.h>
-#include <boost/random/additive_combine.hpp>
+#include <stan_rng.hpp>
 
 // [[Rcpp::export]]
-SEXP base_rng(boost::uint32_t seed = 0) {
-  Rcpp::XPtr<boost::ecuyer1988> rng_ptr(new boost::ecuyer1988(seed));
+SEXP base_rng(boost::uint32_t seed = 1) {
+  Rcpp::XPtr<stan::rng_t> rng_ptr(new stan::rng_t(seed));
   return rng_ptr;
 }

inst/include/model_methods.cpp

@@ -3,13 +3,13 @@
 #include <stan/model/model_base.hpp>
 #include <stan/model/log_prob_grad.hpp>
 #include <stan/model/log_prob_propto.hpp>
-#include <boost/random/additive_combine.hpp>
 #ifdef CMDSTAN_JSON
 #include <cmdstan/io/json/json_data.hpp>
 #else
 #include <stan/io/json/json_data.hpp>
 #include <stan/io/empty_var_context.hpp>
 #endif
+#include <stan_rng.hpp>
 
 std::shared_ptr<stan::io::var_context> var_context(std::string file_path) {
   if (file_path == "") {
@@ -36,7 +36,7 @@ Rcpp::List model_ptr(std::string data_path, boost::uint32_t seed) {
   Rcpp::XPtr<stan::model::model_base> ptr(
     &new_model(*var_context(data_path), seed, &Rcpp::Rcout)
   );
-  Rcpp::XPtr<boost::ecuyer1988> base_rng(new boost::ecuyer1988(seed));
+  Rcpp::XPtr<stan::rng_t> base_rng(new stan::rng_t(seed));
   return Rcpp::List::create(
     Rcpp::Named("model_ptr") = ptr,
     Rcpp::Named("base_rng") = base_rng
@@ -144,7 +144,7 @@ std::vector<double> constrain_variables(SEXP ext_model_ptr, SEXP base_rng,
                                     bool return_trans_pars,
                                     bool return_gen_quants) {
   Rcpp::XPtr<stan::model::model_base> ptr(ext_model_ptr);
-  Rcpp::XPtr<boost::ecuyer1988> rng(base_rng);
+  Rcpp::XPtr<stan::rng_t> rng(base_rng);
   std::vector<int> params_i;
   std::vector<double> vars;
 

inst/include/rcpp_tuple_interop.hpp

@@ -1,3 +1,6 @@
+#ifndef CMDSTANR_RCPP_TUPLE_INTEROP_HPP
+#define CMDSTANR_RCPP_TUPLE_INTEROP_HPP
+
 #include <stan/math/prim/functor/apply.hpp>
 #include <Rcpp.h>
 
@@ -38,3 +41,5 @@ namespace Rcpp {
     }, x);
   }
 }
+
+#endif

inst/include/stan_rng.hpp

@@ -0,0 +1,17 @@
+#ifndef CMDSTANR_STAN_RNG_HPP
+#define CMDSTANR_STAN_RNG_HPP
+
+#include <boost/random/additive_combine.hpp>
+#include <stan/version.hpp>
+
+// A consistent rng_t is defined from 2.35 onwards
+// so add a fallback for older versions
+#if STAN_MAJOR == 2 && STAN_MINOR >= 35
+#include <stan/services/util/create_rng.hpp>
+#else
+namespace stan {
+  using rng_t = boost::ecuyer1988;
+}
+#endif
+
+#endif

tests/testthat/test-model-compile.R

@@ -3,7 +3,7 @@ context("model-compile")
 set_cmdstan_path()
 stan_program <- cmdstan_example_file()
 mod <- cmdstan_model(stan_file = stan_program, compile = FALSE)
-
+cmdstan_make_local(cpp_options = list("PRECOMPILED_HEADERS"="false"))
 
 test_that("object initialized correctly", {
   expect_equal(mod$stan_file(), stan_program)
@@ -130,6 +130,9 @@ test_that("name in STANCFLAGS is set correctly", {
 test_that("switching threads on and off works without rebuild", {
   main_path_o <- file.path(cmdstan_path(), "src", "cmdstan", "main.o")
   main_path_threads_o <- file.path(cmdstan_path(), "src", "cmdstan", "main_threads.o")
+  backup <- cmdstan_make_local()
+  no_threads <- grep("STAN_THREADS", backup, invert = TRUE, value = TRUE)
+  cmdstan_make_local(cpp_options = list(no_threads), append = FALSE)
   if (file.exists(main_path_threads_o)) {
     file.remove(main_path_threads_o)
   }
@@ -155,6 +158,7 @@ test_that("switching threads on and off works without rebuild", {
   expect_equal(before_mtime, after_mtime)
 
   expect_warning(mod$compile(threads = TRUE, dry_run = TRUE), "deprecated")
+  cmdstan_make_local(cpp_options = backup, append = FALSE)
 })
 
 test_that("multiple cpp_options work", {
@@ -483,19 +487,19 @@ test_that("include_paths_stanc3_args() works", {
 
 test_that("cpp_options work with settings in make/local", {
   backup <- cmdstan_make_local()
+  no_threads <- grep("STAN_THREADS", backup, invert = TRUE, value = TRUE)
+  cmdstan_make_local(cpp_options = list(no_threads), append = FALSE)
 
   if (length(mod$exe_file()) > 0 && file.exists(mod$exe_file())) {
     file.remove(mod$exe_file())
   }
 
-  cmdstan_make_local(cpp_options = list(), append = TRUE)
   rebuild_cmdstan()
   mod <- cmdstan_model(stan_file = stan_program)
   expect_null(mod$cpp_options()$STAN_THREADS)
 
   file.remove(mod$exe_file())
 
-  cmdstan_make_local(cpp_options = backup, append = FALSE)
   cmdstan_make_local(cpp_options = list(stan_threads = TRUE), append = TRUE)
 
   file <- file.path(cmdstan_path(), "examples", "bernoulli", "bernoulli.stan")

tests/testthat/test-model-expose-functions.R

@@ -351,12 +351,13 @@ test_that("rng functions can be exposed", {
 
   expect_equal(
     fit$functions$wrap_normal_rng(5,10),
-    -4.5298764235381225873
+    # Stan RNG changed in 2.35
+    ifelse(cmdstan_version() < "2.35.0",-4.529876423, 0.02974925)
   )
 
   expect_equal(
     fit$functions$wrap_normal_rng(5,10),
-    8.1295902610102039887
+    ifelse(cmdstan_version() < "2.35.0", 8.12959026, 10.3881349)
   )
 })
 

tests/testthat/test-profiling.R

@@ -12,7 +12,9 @@ test_that("profiling works if profiling data is present", {
   profiles <- fit$profiles()
   expect_equal(length(profiles), 4)
   expect_equal(dim(profiles[[1]]), c(3,9))
-  expect_equal(profiles[[1]][,"name"], c("glm", "priors", "udf"))
+  for (name in profiles[[1]][,"name"]) {
+    expect_true(name %in% c("udf", "priors", "glm"))
+  }
 
   file.remove(fit$profile_files())
   expect_error(
@@ -24,7 +26,9 @@ test_that("profiling works if profiling data is present", {
   profiles_no_csv <- fit$profiles()
   expect_equal(length(profiles_no_csv), 4)
   expect_equal(dim(profiles_no_csv[[1]]), c(3,9))
-  expect_equal(profiles_no_csv[[1]][,"name"], c("glm", "priors", "udf"))
+  for (name in profiles_no_csv[[1]][,"name"]) {
+    expect_true(name %in% c("udf", "priors", "glm"))
+  }
 })
 
 test_that("profiling errors if no profiling files are present", {