CRAN Package Check Results for Package stan4bart

Last updated on 2026-07-29 10:56:30 CEST.

Check Details

Version: 0.0-12
Check: package dependencies
Result: ERROR Package required but not available: ‘dbarts’ See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual. Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-release-macos-x86_64

Version: 0.0-12
Check: examples
Result: 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 Flavor: r-devel-windows-x86_64

Version: 0.0-12
Check: tests
Result: 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 ] Flavor: r-devel-windows-x86_64