* using log directory 'd:/Rcompile/CRANpkg/local/4.6/specr.Rcheck'
* using R Under development (unstable) (2025-09-03 r88788 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* checking for file 'specr/DESCRIPTION' ... OK
* this is package 'specr' version '1.0.0'
* 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 'specr' 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 ... [3s] OK
* checking whether the package can be loaded with stated dependencies ... [3s] OK
* checking whether the package can be unloaded cleanly ... [3s] OK
* checking whether the namespace can be loaded with stated dependencies ... [3s] OK
* checking whether the namespace can be unloaded cleanly ... [3s] OK
* checking loading without being on the library search path ... [3s] 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 ... [8s] 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... [0s] OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... [5s] ERROR
Running examples in 'specr-Ex.R' failed
The error most likely occurred in:

> ### Name: icc_specs
> ### Title: Compute intraclass correlation coefficient
> ### Aliases: icc_specs
> 
> ### ** Examples
> 
> # Step 1: Run spec curve analysis
> results <- run_specs(df = example_data,
+                      y = c("y1", "y2"),
+                      x = c("x1", "x2"),
+                      model = c("lm"))
Warning: `run_specs()` was deprecated in specr 1.0.0.
ℹ Please use `specr()` instead.
Warning: `setup_specs()` was deprecated in specr 1.0.0.
ℹ Please use `setup()` instead.
ℹ The deprecated feature was likely used in the specr package.
  Please report the issue at <https://github.com/masurp/specr/issues>.
Error in `dplyr::mutate()`:
ℹ In argument: `fit = map(.data$res, broom::glance)`.
Caused by error in `map()`:
ℹ In index: 1.
Caused by error in `ll()`:
! could not find function "ll"
Backtrace:
     ▆
  1. ├─specr::run_specs(...)
  2. │ ├─... %>% dplyr::mutate(subsets = "all")
  3. │ └─specr:::run_spec(specs, df, conf.level = conf.level, keep.results = keep.results)
  4. │   └─... %>% tidyr::unnest(.data$fit, names_sep = "_")
  5. ├─dplyr::mutate(., subsets = "all")
  6. ├─tidyr::unnest(., .data$fit, names_sep = "_")
  7. ├─tidyr::unnest(., .data$coefs)
  8. ├─dplyr::mutate(...)
  9. ├─dplyr:::mutate.data.frame(...)
 10. │ └─dplyr:::mutate_cols(.data, dplyr_quosures(...), by)
 11. │   ├─base::withCallingHandlers(...)
 12. │   └─dplyr:::mutate_col(dots[[i]], data, mask, new_columns)
 13. │     └─mask$eval_all_mutate(quo)
 14. │       └─dplyr (local) eval()
 15. ├─purrr::map(.data$res, broom::glance)
 16. │ └─purrr:::map_("list", .x, .f, ..., .progress = .progress)
 17. │   ├─purrr:::with_indexed_errors(...)
 18. │   │ └─base::withCallingHandlers(...)
 19. │   ├─purrr:::call_with_cleanup(...)
 20. │   ├─generics (local) .f(.x[[i]], ...)
 21. │   └─broom:::glance.lm(.x[[i]], ...)
 22. │     ├─base::with(...)
 23. │     └─base::with.default(...)
 24. │       └─base::eval(substitute(expr), data, enclos = parent.frame())
 25. │         └─base::eval(substitute(expr), data, enclos = parent.frame())
 26. │           └─tibble::tibble(...)
 27. │             └─tibble:::tibble_quos(xs, .rows, .name_repair)
 28. │               └─rlang::eval_tidy(xs[[j]], mask)
 29. ├─stats::AIC(x)
 30. ├─stats:::AIC.default(x)
 31. └─base::.handleSimpleError(...)
 32.   └─purrr (local) h(simpleError(msg, call))
 33.     └─cli::cli_abort(...)
 34.       └─rlang::abort(...)
Execution halted
* checking for unstated dependencies in 'tests' ... OK
* checking tests ... [5s] ERROR
  Running 'testthat.R' [5s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(specr)
  
  Attaching package: 'specr'
  
  The following object is masked from 'package:testthat':
  
      setup
  
  > 
  > test_check("specr")
  [ FAIL 5 | WARN 0 | SKIP 0 | PASS 16 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-generics.R:9:1'): (code run outside of `test_that()`) ──────────
  <dplyr:::mutate_error/rlang_error/error/condition>
  Error in `dplyr::mutate(., out = pmap(., function(...) {
      l = list(...)
      group_i <- which(sapply(l, is.factor))
      s <- rep(TRUE, nrow(data))
      for (i in group_i) {
          column <- names(l)[i]
          value <- l[[i]]
          if (is.na(value)) 
              next
          s <- s & data[[column]] == value
      }
      do.call(what = l$model_function, args = list(formula = l$formula, 
          data = data[s, ]))
  }))`: ℹ In argument: `out = pmap(...)`.
  Caused by error in `pmap()`:
  ℹ In index: 1.
  Caused by error in `ll()`:
  ! could not find function "ll"
  ── Error ('test-specr.R:12:3'): function returns an object of class 'specr.object' ──
  <dplyr:::mutate_error/rlang_error/error/condition>
  Error in `dplyr::mutate(., out = pmap(., function(...) {
      l = list(...)
      group_i <- which(sapply(l, is.factor))
      s <- rep(TRUE, nrow(data))
      for (i in group_i) {
          column <- names(l)[i]
          value <- l[[i]]
          if (is.na(value)) 
              next
          s <- s & data[[column]] == value
      }
      do.call(what = l$model_function, args = list(formula = l$formula, 
          data = data[s, ]))
  }))`: ℹ In argument: `out = pmap(...)`.
  Caused by error in `pmap()`:
  ℹ In index: 1.
  Caused by error in `ll()`:
  ! could not find function "ll"
  ── Error ('test-specr.R:29:3'): function returns an object of class 'tibble' when no specr.setup is provided ──
  <dplyr:::mutate_error/rlang_error/error/condition>
  Error in `dplyr::mutate(., out = pmap(., function(...) {
      l = list(...)
      group_i <- which(sapply(l, is.factor))
      s <- rep(TRUE, nrow(data))
      for (i in group_i) {
          column <- names(l)[i]
          value <- l[[i]]
          if (is.na(value)) 
              next
          s <- s & data[[column]] == value
      }
      do.call(what = l$model_function, args = list(formula = l$formula, 
          data = data[s, ]))
  }))`: ℹ In argument: `out = pmap(...)`.
  Caused by error in `pmap()`:
  ℹ In index: 1.
  Caused by error in `ll()`:
  ! could not find function "ll"
  ── Error ('test-specr.R:38:3'): Specs and results have the same number of rows ──
  <dplyr:::mutate_error/rlang_error/error/condition>
  Error in `dplyr::mutate(., out = pmap(., function(...) {
      l = list(...)
      group_i <- which(sapply(l, is.factor))
      s <- rep(TRUE, nrow(data))
      for (i in group_i) {
          column <- names(l)[i]
          value <- l[[i]]
          if (is.na(value)) 
              next
          s <- s & data[[column]] == value
      }
      do.call(what = l$model_function, args = list(formula = l$formula, 
          data = data[s, ]))
  }))`: ℹ In argument: `out = pmap(...)`.
  Caused by error in `pmap()`:
  ℹ In index: 1.
  Caused by error in `ll()`:
  ! could not find function "ll"
  ── Error ('test-specr.R:44:3'): Results include confidence intervals ───────────
  <dplyr:::mutate_error/rlang_error/error/condition>
  Error in `dplyr::mutate(., out = pmap(., function(...) {
      l = list(...)
      group_i <- which(sapply(l, is.factor))
      s <- rep(TRUE, nrow(data))
      for (i in group_i) {
          column <- names(l)[i]
          value <- l[[i]]
          if (is.na(value)) 
              next
          s <- s & data[[column]] == value
      }
      do.call(what = l$model_function, args = list(formula = l$formula, 
          data = data[s, ]))
  }))`: ℹ In argument: `out = pmap(...)`.
  Caused by error in `pmap()`:
  ℹ In index: 1.
  Caused by error in `ll()`:
  ! could not find function "ll"
  
  [ FAIL 5 | WARN 0 | SKIP 0 | PASS 16 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [54s] ERROR
Error(s) in re-building vignettes:
--- re-building 'custom-plot.rmd' using rmarkdown

Quitting from custom-plot.rmd:43-46 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
NULL
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'custom-plot.rmd' failed with diagnostics:
ℹ In argument: `out = pmap(...)`.
Caused by error in `pmap()`:
ℹ In index: 1.
Caused by error in `ll()`:
! could not find function "ll"
--- failed re-building 'custom-plot.rmd'

--- re-building 'different-specifications.Rmd' using rmarkdown

Quitting from different-specifications.Rmd:26-39 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
NULL
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'different-specifications.Rmd' failed with diagnostics:
ℹ In argument: `out = pmap(...)`.
Caused by error in `pmap()`:
ℹ In index: 1.
Caused by error in `ll()`:
! could not find function "ll"
--- failed re-building 'different-specifications.Rmd'

--- re-building 'getting-started.rmd' using rmarkdown

Quitting from getting-started.rmd:82-88 [unnamed-chunk-6]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
NULL
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'getting-started.rmd' failed with diagnostics:
ℹ In argument: `out = pmap(...)`.
Caused by error in `pmap()`:
ℹ In index: 1.
Caused by error in `ll()`:
! could not find function "ll"
--- failed re-building 'getting-started.rmd'

--- re-building 'invest-spec.Rmd' using rmarkdown

Quitting from invest-spec.Rmd:32-51 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
NULL
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'invest-spec.Rmd' failed with diagnostics:
ℹ In argument: `out = pmap(...)`.
Caused by error in `pmap()`:
ℹ In index: 1.
Caused by error in `ll()`:
! could not find function "ll"
--- failed re-building 'invest-spec.Rmd'

--- re-building 'measurement-models.Rmd' using rmarkdown
--- finished re-building 'measurement-models.Rmd'

--- re-building 'multilevel-models.Rmd' using rmarkdown
--- finished re-building 'multilevel-models.Rmd'

--- re-building 'parallel-bayesian-models.Rmd' using rmarkdown
--- finished re-building 'parallel-bayesian-models.Rmd'

--- re-building 'parallelization.Rmd' using rmarkdown
--- finished re-building 'parallelization.Rmd'

SUMMARY: processing the following files failed:
  'custom-plot.rmd' 'different-specifications.Rmd'
  'getting-started.rmd' 'invest-spec.Rmd'

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... [21s] OK
* checking HTML version of manual ... [4s] OK
* DONE
Status: 3 ERRORs