* using log directory 'd:/Rcompile/CRANpkg/local/4.4/butcher.Rcheck'
* using R version 4.4.3 (2025-02-28 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* checking for file 'butcher/DESCRIPTION' ... OK
* this is package 'butcher' version '0.3.6'
* package encoding: UTF-8
* 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 'butcher' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' 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 ... [0s] OK
* checking whether the package can be loaded with stated dependencies ... [0s] OK
* checking whether the package can be unloaded cleanly ... [0s] OK
* checking whether the namespace can be loaded with stated dependencies ... [0s] OK
* checking whether the namespace can be unloaded cleanly ... [0s] OK
* checking loading without being on the library search path ... [0s] 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 ... [6s] OK
* checking Rd files ... [3s] 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... [12s] ERROR
Running examples in 'butcher-Ex.R' failed
The error most likely occurred in:

> ### Name: axe-flexsurvreg
> ### Title: Axing an flexsurvreg.
> ### Aliases: axe-flexsurvreg axe_call.flexsurvreg axe_env.flexsurvreg
> 
> ### ** Examples
> 
> ## Don't show: 
> if (rlang::is_installed("flexsurv")) (if (getRversion() >= "3.4") withAutoprint else force)({ # examplesIf
+ ## End(Don't show)
+ # Load libraries
+ library(parsnip)
+ library(flexsurv)
+ 
+ # Create model and fit
+ flexsurvreg_fit <- surv_reg(mode = "regression", dist = "gengamma") %>%
+   set_engine("flexsurv") %>%
+   fit(Surv(Tstart, Tstop, status) ~ trans, data = bosms3)
+ 
+ out <- butcher(flexsurvreg_fit, verbose = TRUE)
+ 
+ # Another flexsurvreg model object
+ wrapped_flexsurvreg <- function() {
+   some_junk_in_environment <- runif(1e6)
+   fit <- flexsurvreg(Surv(futime, fustat) ~ 1,
+                      data = ovarian, dist = "weibull")
+   return(fit)
+ }
+ 
+ out <- butcher(wrapped_flexsurvreg(), verbose = TRUE)
+ ## Don't show: 
+ }) # examplesIf
> library(parsnip)
> library(flexsurv)
Loading required package: survival
> flexsurvreg_fit <- surv_reg(mode = "regression", dist = "gengamma") %>% 
+     set_engine("flexsurv") %>% fit(Surv(Tstart, Tstop, status) ~ trans, data = bosms3)
Error:
! `surv_reg()` was deprecated in parsnip 1.4.0 and is now defunct.
ℹ Please use `survival_reg()` instead.
Backtrace:
     ▆
  1. ├─(if (getRversion() >= "3.4") withAutoprint else force)(...)
  2. │ └─base::source(...)
  3. │   ├─base::withVisible(eval(ei, envir))
  4. │   └─base::eval(ei, envir)
  5. │     └─base::eval(ei, envir)
  6. ├─... %>% ...
  7. ├─generics::fit(., Surv(Tstart, Tstop, status) ~ trans, data = bosms3)
  8. ├─parsnip::set_engine(., "flexsurv")
  9. └─parsnip::surv_reg(mode = "regression", dist = "gengamma")
 10.   └─lifecycle::deprecate_stop("1.4.0", "surv_reg()", "survival_reg()")
 11.     └─lifecycle:::deprecate_stop0(msg)
 12.       └─rlang::cnd_signal(...)
Execution halted
* checking for unstated dependencies in 'tests' ... OK
* checking tests ... [29s] ERROR
  Running 'testthat.R' [29s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(butcher)
  > 
  > test_check("butcher")
  1 package (dimRed) is needed for this step but is not installed.
  To install run: `install.packages("dimRed")`
  Saving _problems/test-xrf-12.R
  Saving _problems/test-xrf-25.R
  Saving _problems/test-xrf-40.R
  Saving _problems/test-xrf-58.R
  [ FAIL 4 | WARN 0 | SKIP 35 | PASS 196 ]
  
  ══ Skipped tests (35) ══════════════════════════════════════════════════════════
  • On CRAN (34): 'test-c5.R:2:3', 'test-earth.R:2:3', 'test-earth.R:31:3',
    'test-elnet.R:2:3', 'test-flexsurvreg.R:2:3', 'test-flexsurvreg.R:15:3',
    'test-flexsurvreg.R:43:3', 'test-gausspr.R:2:3', 'test-glmnet.R:2:3',
    'test-kknn.R:2:3', 'test-klaR.R:2:3', 'test-klaR.R:17:3', 'test-ksvm.R:2:3',
    'test-mda.R:2:3', 'test-mda.R:23:3', 'test-mda.R:95:3',
    'test-mixOmics.R:2:3', 'test-mixOmics.R:21:3', 'test-mixOmics.R:38:3',
    'test-multnet.R:2:3', 'test-nnet.R:2:3', 'test-randomForest.R:2:3',
    'test-rpart.R:2:3', 'test-rpart.R:18:3', 'test-sclass.R:2:3',
    'test-survreg.R:2:3', 'test-survreg.penal.R:2:3', 'test-train.R:2:3',
    'test-train.R:42:3', 'test-train.recipe.R:9:3', 'test-ui.R:1:1',
    'test-weigh.R:1:1', 'test-xgb.R:6:3', 'test-xgb.R:34:3'
  • {mixOmics} is not installed (1): 'test-recipe.R:419:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-xrf.R:12:3'): xrf + axe_call() works ─────────────────────────
  Expected `x$xgb$call` to equal `rlang::expr(dummy_call())`.
  Differences:
  `actual` is NULL
  `expected` is a call
  
  ── Error ('test-xrf.R:25:3'): xrf + axe_env() works ────────────────────────────
  Error in `x$callbacks <- purrr::map(x$callbacks, function(x) as.function(c(formals(x), body(x)), env = rlang::base_env()))`: ALTLIST classes must provide a Set_elt method [class: XGBAltrepPointerClass, pkg: xgboost]
  Backtrace:
      ▆
   1. ├─butcher::axe_env(res) at test-xrf.R:25:3
   2. └─butcher:::axe_env.xrf(res)
   3.   ├─butcher::axe_env(res$xgb, ...)
   4.   └─butcher:::axe_env.xgb.Booster(res$xgb, ...)
  ── Error ('test-xrf.R:40:3'): xrf + butcher() works ────────────────────────────
  Error in `x$callbacks <- purrr::map(x$callbacks, function(x) as.function(c(formals(x), body(x)), env = rlang::base_env()))`: ALTLIST classes must provide a Set_elt method [class: XGBAltrepPointerClass, pkg: xgboost]
  Backtrace:
      ▆
   1. └─butcher::butcher(res) at test-xrf.R:40:3
   2.   ├─butcher::axe_env(x, verbose = FALSE, ...)
   3.   └─butcher:::axe_env.xrf(x, verbose = FALSE, ...)
   4.     ├─butcher::axe_env(res$xgb, ...)
   5.     └─butcher:::axe_env.xgb.Booster(res$xgb, ...)
  ── Error ('test-xrf.R:58:3'): xrf + predict() works ────────────────────────────
  Error in `x$callbacks <- purrr::map(x$callbacks, function(x) as.function(c(formals(x), body(x)), env = rlang::base_env()))`: ALTLIST classes must provide a Set_elt method [class: XGBAltrepPointerClass, pkg: xgboost]
  Backtrace:
      ▆
   1. └─butcher::butcher(res) at test-xrf.R:58:3
   2.   ├─butcher::axe_env(x, verbose = FALSE, ...)
   3.   └─butcher:::axe_env.xrf(x, verbose = FALSE, ...)
   4.     ├─butcher::axe_env(res$xgb, ...)
   5.     └─butcher:::axe_env.xgb.Booster(res$xgb, ...)
  
  [ FAIL 4 | WARN 0 | SKIP 35 | PASS 196 ]
  Error:
  ! Test failures.
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [11s] OK
* checking PDF version of manual ... [21s] OK
* checking HTML version of manual ... [11s] OK
* DONE
Status: 2 ERRORs