- using R Under development (unstable) (2025-12-05 r89103)
- using platform: x86_64-pc-linux-gnu
- R was compiled by
clang version 21.1.6
flang version 21.1.6
- running under: Fedora Linux 42 (Workstation Edition)
- using session charset: UTF-8
- using option ‘--no-stop-on-test-error’
- 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 executable files ... OK
- checking for hidden files and directories ... OK
- checking for portable file names ... OK
- checking for sufficient/correct file permissions ... OK
- checking whether package ‘butcher’ can be installed ... [6s/15s] OK
See the install log for details.
- 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 ... OK
- checking whether the package can be loaded with stated dependencies ... OK
- checking whether the package can be unloaded cleanly ... OK
- checking whether the namespace can be loaded with stated dependencies ... OK
- checking whether the namespace can be unloaded cleanly ... OK
- checking loading without being on the library search path ... 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 ... [12s/35s] OK
- checking Rd files ... OK
- checking Rd metadata ... OK
- checking Rd line widths ... 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/39s] 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 ... [36s/98s] ERROR
Running ‘testthat.R’ [36s/96s]
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 ... [14s/40s] OK
- checking PDF version of manual ... [12s/28s] OK
- checking HTML version of manual ... [8s/18s] OK
- checking for non-standard things in the check directory ... OK
- checking for detritus in the temp directory ... OK
- DONE
Status: 2 ERRORs