* using log directory 'd:/Rcompile/CRANpkg/local/4.7/stan4bart.Rcheck'
* using R Under development (unstable) (2026-08-10 r90389 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.3.0
    GNU Fortran (GCC) 14.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* current time: 2026-08-12 01:26:18 UTC
* checking for file 'stan4bart/DESCRIPTION' ... OK
* this is package 'stan4bart' version '0.0-12'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'stan4bart' can be installed ... OK
* used C compiler: 'gcc.exe (GCC) 14.3.0'
* used C++ compiler: 'g++.exe (GCC) 14.3.0'
* checking C++ specification ... INFO
  specified C++17
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [2s] OK
* checking whether the package can be loaded with stated dependencies ... [2s] OK
* checking whether the package can be unloaded cleanly ... [2s] OK
* checking whether the namespace can be loaded with stated dependencies ... [2s] OK
* checking whether the namespace can be unloaded cleanly ... [2s] OK
* checking loading without being on the library search path ... [2s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [14s] OK
* checking Rd files ... [1s] OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compiled code ... OK
* checking examples ... [3s] ERROR
Running examples in 'stan4bart-Ex.R' failed
The error most likely occurred in:

> ### Name: stan4bart
> ### Title: Semiparametric Models Using Stan and BART
> ### Aliases: stan4bart
> 
> ### ** Examples
> 
> # simulate data (extension of Friedman MARS paper)
> # x consists of 10 variables, only first 5 matter
> # x_4 is linear
> f <- function(x)
+   10 * sin(pi * x[,1] * x[,2]) + 20 * (x[,3] - 0.5)^2 +
+       10 * x[,4] + 5 * x[,5]
> 
> set.seed(99)
> sigma <- 1.0
> 
> n <- 100
> n.g.1 <- 5L
> n.g.2 <- 8L
> 
> # sample observation level covariates and calculate marginal mean
> x <- matrix(runif(n * 10), n, 10)
> mu.bart  <- f(x) - 10 * x[,4]
> mu.fixef <- 10 * x[,4]
> 
> # varying intercepts and slopes for first grouping factor
> g.1 <- sample(n.g.1, n, replace = TRUE)
> Sigma.b.1 <- matrix(c(1.5^2, .2, .2, 1^2), 2)
> b.1 <- matrix(rnorm(2 * n.g.1), n.g.1) %*% chol(Sigma.b.1)
> 
> # varying intercepts for second grouping factor
> g.2 <- sample(n.g.2, n, replace = TRUE)
> Sigma.b.2 <- as.matrix(1.2)
> b.2 <- rnorm(n.g.2, 0, sqrt(Sigma.b.2))
> 
> mu.ranef <- b.1[g.1,1] + x[,4] * b.1[g.1,2] + b.2[g.2]
> 
> y <- mu.bart + mu.fixef + mu.ranef + rnorm(n, 0, sigma)
> 
> df <- data.frame(y, x, g.1, g.2)
> 
> fit <- stan4bart(
+     formula = y ~
+         X4 +                         # linear component ("fixef")
+         (1 + X4 | g.1) + (1 | g.2) + # multilevel ("ranef")
+         bart(. - g.1 - g.2 - X4),    # use bart for other variables
+     verbose = -1, # suppress ALL output
+     # low numbers for illustration
+     data = df,
+     chains = 1, iter = 10, bart_args = list(n.trees = 5))
Error in parse(text = deparse(RNGkind)[-1L]) : 
  <text>:1:22: unexpected ')'
1:     binom.kind = NULL)
                         ^
Calls: stan4bart ... validObject -> anyStrings -> isTRUE -> validityMethod -> parse
Execution halted
* checking for unstated dependencies in 'tests' ... OK
* checking tests ... [7s] ERROR
  Running 'testthat.R' [7s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > Sys.unsetenv("R_TESTS")
  > if (require(testthat, quietly = TRUE)) {
  +   require(stan4bart)
  +   test_check("stan4bart")
  + } else {
  +   cat("package 'testthat' not available; cannot run unit tests\n")
  + }
  Loading required package: stan4bart
  Loading required package: dbarts
  Saving _problems/test-01-continuous-19.R
  Saving _problems/test-02-binary-18.R
  Saving _problems/test-02-binary-89.R
  Saving _problems/test-03-na_action-29.R
  Saving _problems/test-03-na_action-51.R
  Saving _problems/test-04-factor_levels-25.R
  Saving _problems/test-05-rng-17.R
  Saving _problems/test-05-rng-35.R
  Saving _problems/test-06-no_ranef-19.R
  Saving _problems/test-06-no_ranef-26.R
  Saving _problems/test-07-extractedTrees-19.R
  [ FAIL 16 | WARN 0 | SKIP 2 | PASS 32 ]
  
  ══ Skipped tests (2) ═══════════════════════════════════════════════════════════
  • On CRAN (2): 'test-02-binary.R:33:3', 'test-02-binary.R:128:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-01-continuous.R:16:1'): (code run outside of `test_that()`) ────
  Error in `parse(text = deparse(RNGkind)[-1L])`: <text>:1:22: unexpected ')'
  1:     binom.kind = NULL)
                           ^
  Backtrace:
       ▆
    1. └─stan4bart::stan4bart(...) at test-01-continuous.R:16:1
    2.   └─stan4bart:::stan4bart_fit(...)
    3.     ├─base::eval(control_call)
    4.     │ └─base::eval(control_call)
    5.     └─dbarts::dbartsControl(...)
    6.       └─methods::new(...)
    7.         ├─methods::initialize(value, ...)
    8.         └─dbarts (local) initialize(value, ...)
    9.           ├─methods::callNextMethod()
   10.           └─methods (local) .nextMethod(.Object = .Object, ... = ...)
   11.             └─methods::validObject(.Object)
   12.               ├─methods (local) anyStrings(validityMethod(object))
   13.               │ └─base::isTRUE(x)
   14.               └─dbarts (local) validityMethod(object)
   15.                 └─base::parse(text = deparse(RNGkind)[-1L])
  ── Error ('test-02-binary.R:15:3'): extract matches fitted in causal setting model ──
  Error in `parse(text = deparse(RNGkind)[-1L])`: <text>:1:22: unexpected ')'
  1:     binom.kind = NULL)
                           ^
  Backtrace:
       ▆
    1. └─stan4bart::stan4bart(...) at test-02-binary.R:15:3
    2.   └─stan4bart:::stan4bart_fit(...)
    3.     ├─base::eval(control_call)
    4.     │ └─base::eval(control_call)
    5.     └─dbarts::dbartsControl(...)
    6.       └─methods::new(...)
    7.         ├─methods::initialize(value, ...)
    8.         └─dbarts (local) initialize(value, ...)
    9.           ├─methods::callNextMethod()
   10.           └─methods (local) .nextMethod(.Object = .Object, ... = ...)
   11.             └─methods::validObject(.Object)
   12.               ├─methods (local) anyStrings(validityMethod(object))
   13.               │ └─base::isTRUE(x)
   14.               └─dbarts (local) validityMethod(object)
   15.                 └─base::parse(text = deparse(RNGkind)[-1L])
  ── Error ('test-02-binary.R:85:3'): predict matches supplied data ──────────────
  Error in `parse(text = deparse(RNGkind)[-1L])`: <text>:1:22: unexpected ')'
  1:     binom.kind = NULL)
                           ^
  Backtrace:
       ▆
    1. └─stan4bart::stan4bart(...) at test-02-binary.R:85:3
    2.   └─stan4bart:::stan4bart_fit(...)
    3.     ├─base::eval(control_call)
    4.     │ └─base::eval(control_call)
    5.     └─dbarts::dbartsControl(...)
    6.       └─methods::new(...)
    7.         ├─methods::initialize(value, ...)
    8.         └─dbarts (local) initialize(value, ...)
    9.           ├─methods::callNextMethod()
   10.           └─methods (local) .nextMethod(.Object = .Object, ... = ...)
   11.             └─methods::validObject(.Object)
   12.               ├─methods (local) anyStrings(validityMethod(object))
   13.               │ └─base::isTRUE(x)
   14.               └─dbarts (local) validityMethod(object)
   15.                 └─base::parse(text = deparse(RNGkind)[-1L])
  ── Error ('test-03-na_action.R:24:3'): na.action = na.omit works correctly ─────
  Error in `parse(text = deparse(RNGkind)[-1L])`: <text>:1:22: unexpected ')'
  1:     binom.kind = NULL)
                           ^
  Backtrace:
       ▆
    1. └─stan4bart::stan4bart(...) at test-03-na_action.R:24:3
    2.   └─stan4bart:::stan4bart_fit(...)
    3.     ├─base::eval(control_call)
    4.     │ └─base::eval(control_call)
    5.     └─dbarts::dbartsControl(...)
    6.       └─methods::new(...)
    7.         ├─methods::initialize(value, ...)
    8.         └─dbarts (local) initialize(value, ...)
    9.           ├─methods::callNextMethod()
   10.           └─methods (local) .nextMethod(.Object = .Object, ... = ...)
   11.             └─methods::validObject(.Object)
   12.               ├─methods (local) anyStrings(validityMethod(object))
   13.               │ └─base::isTRUE(x)
   14.               └─dbarts (local) validityMethod(object)
   15.                 └─base::parse(text = deparse(RNGkind)[-1L])
  ── Error ('test-03-na_action.R:46:3'): na.action = na.exclude works correctly ──
  Error in `parse(text = deparse(RNGkind)[-1L])`: <text>:1:22: unexpected ')'
  1:     binom.kind = NULL)
                           ^
  Backtrace:
       ▆
    1. └─stan4bart::stan4bart(...) at test-03-na_action.R:46:3
    2.   └─stan4bart:::stan4bart_fit(...)
    3.     ├─base::eval(control_call)
    4.     │ └─base::eval(control_call)
    5.     └─dbarts::dbartsControl(...)
    6.       └─methods::new(...)
    7.         ├─methods::initialize(value, ...)
    8.         └─dbarts (local) initialize(value, ...)
    9.           ├─methods::callNextMethod()
   10.           └─methods (local) .nextMethod(.Object = .Object, ... = ...)
   11.             └─methods::validObject(.Object)
   12.               ├─methods (local) anyStrings(validityMethod(object))
   13.               │ └─base::isTRUE(x)
   14.               └─dbarts (local) validityMethod(object)
   15.                 └─base::parse(text = deparse(RNGkind)[-1L])
  ── Error ('test-04-factor_levels.R:21:3'): model fits with empty factor levels ──
  Error in `parse(text = deparse(RNGkind)[-1L])`: <text>:1:22: unexpected ')'
  1:     binom.kind = NULL)
                           ^
  Backtrace:
       ▆
    1. └─stan4bart::stan4bart(...) at test-04-factor_levels.R:21:3
    2.   └─stan4bart:::stan4bart_fit(...)
    3.     ├─base::eval(control_call)
    4.     │ └─base::eval(control_call)
    5.     └─dbarts::dbartsControl(...)
    6.       └─methods::new(...)
    7.         ├─methods::initialize(value, ...)
    8.         └─dbarts (local) initialize(value, ...)
    9.           ├─methods::callNextMethod()
   10.           └─methods (local) .nextMethod(.Object = .Object, ... = ...)
   11.             └─methods::validObject(.Object)
   12.               ├─methods (local) anyStrings(validityMethod(object))
   13.               │ └─base::isTRUE(x)
   14.               └─dbarts (local) validityMethod(object)
   15.                 └─base::parse(text = deparse(RNGkind)[-1L])
  ── Error ('test-05-rng.R:13:3'): stan4bart with global seed and one thread is reproducible ──
  Error in `parse(text = deparse(RNGkind)[-1L])`: <text>:1:22: unexpected ')'
  1:     binom.kind = NULL)
                           ^
  Backtrace:
       ▆
    1. └─stan4bart::stan4bart(...) at test-05-rng.R:13:3
    2.   └─stan4bart:::stan4bart_fit(...)
    3.     ├─base::eval(control_call)
    4.     │ └─base::eval(control_call)
    5.     └─dbarts::dbartsControl(...)
    6.       └─methods::new(...)
    7.         ├─methods::initialize(value, ...)
    8.         └─dbarts (local) initialize(value, ...)
    9.           ├─methods::callNextMethod()
   10.           └─methods (local) .nextMethod(.Object = .Object, ... = ...)
   11.             └─methods::validObject(.Object)
   12.               ├─methods (local) anyStrings(validityMethod(object))
   13.               │ └─base::isTRUE(x)
   14.               └─dbarts (local) validityMethod(object)
   15.                 └─base::parse(text = deparse(RNGkind)[-1L])
  ── Error ('test-05-rng.R:30:3'): stan4bart with fixed seed is reproducible ─────
  Error in `parse(text = deparse(RNGkind)[-1L])`: <text>:1:22: unexpected ')'
  1:     binom.kind = NULL)
                           ^
  Backtrace:
       ▆
    1. └─stan4bart::stan4bart(...) at test-05-rng.R:30:3
    2.   └─stan4bart:::stan4bart_fit(...)
    3.     ├─base::eval(control_call)
    4.     │ └─base::eval(control_call)
    5.     └─dbarts::dbartsControl(...)
    6.       └─methods::new(...)
    7.         ├─methods::initialize(value, ...)
    8.         └─dbarts (local) initialize(value, ...)
    9.           ├─methods::callNextMethod()
   10.           └─methods (local) .nextMethod(.Object = .Object, ... = ...)
   11.             └─methods::validObject(.Object)
   12.               ├─methods (local) anyStrings(validityMethod(object))
   13.               │ └─base::isTRUE(x)
   14.               └─dbarts (local) validityMethod(object)
   15.                 └─base::parse(text = deparse(RNGkind)[-1L])
  ── Error ('test-06-no_ranef.R:17:3'): fit issues warning if overparameterized ──
  Error in `parse(text = deparse(RNGkind)[-1L])`: <text>:1:22: unexpected ')'
  1:     binom.kind = NULL)
                           ^
  Backtrace:
       ▆
    1. ├─testthat::expect_warning(...) at test-06-no_ranef.R:17:3
    2. │ └─testthat:::quasi_capture(...)
    3. │   ├─testthat (local) .capture(...)
    4. │   │ └─base::withCallingHandlers(...)
    5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    6. └─stan4bart::stan4bart(...)
    7.   └─stan4bart:::stan4bart_fit(...)
    8.     ├─base::eval(control_call)
    9.     │ └─base::eval(control_call)
   10.     └─dbarts::dbartsControl(...)
   11.       └─methods::new(...)
   12.         ├─methods::initialize(value, ...)
   13.         └─dbarts (local) initialize(value, ...)
   14.           ├─methods::callNextMethod()
   15.           └─methods (local) .nextMethod(.Object = .Object, ... = ...)
   16.             └─methods::validObject(.Object)
   17.               ├─methods (local) anyStrings(validityMethod(object))
   18.               │ └─base::isTRUE(x)
   19.               └─dbarts (local) validityMethod(object)
   20.                 └─base::parse(text = deparse(RNGkind)[-1L])
  ── Error ('test-06-no_ranef.R:23:1'): (code run outside of `test_that()`) ──────
  Error in `parse(text = deparse(RNGkind)[-1L])`: <text>:1:22: unexpected ')'
  1:     binom.kind = NULL)
                           ^
  Backtrace:
       ▆
    1. └─stan4bart::stan4bart(...) at test-06-no_ranef.R:23:1
    2.   └─stan4bart:::stan4bart_fit(...)
    3.     ├─base::eval(control_call)
    4.     │ └─base::eval(control_call)
    5.     └─dbarts::dbartsControl(...)
    6.       └─methods::new(...)
    7.         ├─methods::initialize(value, ...)
    8.         └─dbarts (local) initialize(value, ...)
    9.           ├─methods::callNextMethod()
   10.           └─methods (local) .nextMethod(.Object = .Object, ... = ...)
   11.             └─methods::validObject(.Object)
   12.               ├─methods (local) anyStrings(validityMethod(object))
   13.               │ └─base::isTRUE(x)
   14.               └─dbarts (local) validityMethod(object)
   15.                 └─base::parse(text = deparse(RNGkind)[-1L])
  ── Error ('test-07-extractedTrees.R:14:3'): stan4bart extracts trees correctly ──
  Error in `parse(text = deparse(RNGkind)[-1L])`: <text>:1:22: unexpected ')'
  1:     binom.kind = NULL)
                           ^
  Backtrace:
       ▆
    1. └─stan4bart::stan4bart(...) at test-07-extractedTrees.R:14:3
    2.   └─stan4bart:::stan4bart_fit(...)
    3.     ├─base::eval(control_call)
    4.     │ └─base::eval(control_call)
    5.     └─dbarts::dbartsControl(...)
    6.       └─methods::new(...)
    7.         ├─methods::initialize(value, ...)
    8.         └─dbarts (local) initialize(value, ...)
    9.           ├─methods::callNextMethod()
   10.           └─methods (local) .nextMethod(.Object = .Object, ... = ...)
   11.             └─methods::validObject(.Object)
   12.               ├─methods (local) anyStrings(validityMethod(object))
   13.               │ └─base::isTRUE(x)
   14.               └─dbarts (local) validityMethod(object)
   15.                 └─base::parse(text = deparse(RNGkind)[-1L])
  ── Error ('test-09-bartArgs.R:18:3'): bart args are set correctly ──────────────
  Error in `parse(text = deparse(RNGkind)[-1L])`: <text>:1:22: unexpected ')'
  1:     binom.kind = NULL)
                           ^
  Backtrace:
       ▆
    1. └─stan4bart::stan4bart(...) at test-09-bartArgs.R:18:3
    2.   └─stan4bart:::stan4bart_fit(...)
    3.     ├─base::eval(control_call)
    4.     │ └─base::eval(control_call)
    5.     └─dbarts::dbartsControl(...)
    6.       └─methods::new(...)
    7.         ├─methods::initialize(value, ...)
    8.         └─dbarts (local) initialize(value, ...)
    9.           ├─methods::callNextMethod()
   10.           └─methods (local) .nextMethod(.Object = .Object, ... = ...)
   11.             └─methods::validObject(.Object)
   12.               ├─methods (local) anyStrings(validityMethod(object))
   13.               │ └─base::isTRUE(x)
   14.               └─dbarts (local) validityMethod(object)
   15.                 └─base::parse(text = deparse(RNGkind)[-1L])
  ── Error ('test-10-treatment.R:13:3'): works with logical treatment ────────────
  Error in `parse(text = deparse(RNGkind)[-1L])`: <text>:1:22: unexpected ')'
  1:     binom.kind = NULL)
                           ^
  Backtrace:
       ▆
    1. └─stan4bart::stan4bart(...) at test-10-treatment.R:13:3
    2.   └─stan4bart:::stan4bart_fit(...)
    3.     ├─base::eval(control_call)
    4.     │ └─base::eval(control_call)
    5.     └─dbarts::dbartsControl(...)
    6.       └─methods::new(...)
    7.         ├─methods::initialize(value, ...)
    8.         └─dbarts (local) initialize(value, ...)
    9.           ├─methods::callNextMethod()
   10.           └─methods (local) .nextMethod(.Object = .Object, ... = ...)
   11.             └─methods::validObject(.Object)
   12.               ├─methods (local) anyStrings(validityMethod(object))
   13.               │ └─base::isTRUE(x)
   14.               └─dbarts (local) validityMethod(object)
   15.                 └─base::parse(text = deparse(RNGkind)[-1L])
  ── Error ('test-11-callback.R:44:3'): callback is passed sample correctly ──────
  Error in `parse(text = deparse(RNGkind)[-1L])`: <text>:1:22: unexpected ')'
  1:     binom.kind = NULL)
                           ^
  Backtrace:
       ▆
    1. └─stan4bart::stan4bart(...) at test-11-callback.R:44:3
    2.   └─stan4bart:::stan4bart_fit(...)
    3.     ├─base::eval(control_call)
    4.     │ └─base::eval(control_call)
    5.     └─dbarts::dbartsControl(...)
    6.       └─methods::new(...)
    7.         ├─methods::initialize(value, ...)
    8.         └─dbarts (local) initialize(value, ...)
    9.           ├─methods::callNextMethod()
   10.           └─methods (local) .nextMethod(.Object = .Object, ... = ...)
   11.             └─methods::validObject(.Object)
   12.               ├─methods (local) anyStrings(validityMethod(object))
   13.               │ └─base::isTRUE(x)
   14.               └─dbarts (local) validityMethod(object)
   15.                 └─base::parse(text = deparse(RNGkind)[-1L])
  ── Error ('test-11-callback.R:104:3'): callback works with multiple threads ────
  Error in `parse(text = deparse(RNGkind)[-1L])`: <text>:1:22: unexpected ')'
  1:     binom.kind = NULL)
                           ^
  Backtrace:
       ▆
    1. └─stan4bart::stan4bart(...) at test-11-callback.R:104:3
    2.   └─stan4bart:::stan4bart_fit(...)
    3.     ├─base::eval(control_call)
    4.     │ └─base::eval(control_call)
    5.     └─dbarts::dbartsControl(...)
    6.       └─methods::new(...)
    7.         ├─methods::initialize(value, ...)
    8.         └─dbarts (local) initialize(value, ...)
    9.           ├─methods::callNextMethod()
   10.           └─methods (local) .nextMethod(.Object = .Object, ... = ...)
   11.             └─methods::validObject(.Object)
   12.               ├─methods (local) anyStrings(validityMethod(object))
   13.               │ └─base::isTRUE(x)
   14.               └─dbarts (local) validityMethod(object)
   15.                 └─base::parse(text = deparse(RNGkind)[-1L])
  ── Error ('test-11-callback.R:159:3'): callback works with multiple dimmed results ──
  Error in `parse(text = deparse(RNGkind)[-1L])`: <text>:1:22: unexpected ')'
  1:     binom.kind = NULL)
                           ^
  Backtrace:
       ▆
    1. └─stan4bart::stan4bart(...) at test-11-callback.R:159:3
    2.   └─stan4bart:::stan4bart_fit(...)
    3.     ├─base::eval(control_call)
    4.     │ └─base::eval(control_call)
    5.     └─dbarts::dbartsControl(...)
    6.       └─methods::new(...)
    7.         ├─methods::initialize(value, ...)
    8.         └─dbarts (local) initialize(value, ...)
    9.           ├─methods::callNextMethod()
   10.           └─methods (local) .nextMethod(.Object = .Object, ... = ...)
   11.             └─methods::validObject(.Object)
   12.               ├─methods (local) anyStrings(validityMethod(object))
   13.               │ └─base::isTRUE(x)
   14.               └─dbarts (local) validityMethod(object)
   15.                 └─base::parse(text = deparse(RNGkind)[-1L])
  
  [ FAIL 16 | WARN 0 | SKIP 2 | PASS 32 ]
* checking PDF version of manual ... [23s] OK
* checking HTML version of manual ... [2s] OK
* DONE
Status: 2 ERRORs