- using R Under development (unstable) (2026-07-28 r90311 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: 2026-07-29 05:57:03 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
See the install log for details.
- 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 ... [1s] OK
- checking whether the namespace can be unloaded cleanly ... [2s] OK
- checking loading without being on the library search path ... [1s] 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 ... [13s] 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 ... [6s] ERROR
Running 'testthat.R' [6s]
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 ... [19s] OK
- checking HTML version of manual ... [2s] OK
- DONE
Status: 2 ERRORs