Last updated on 2025-09-09 08:49:45 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.0.0 | 14.33 | 183.66 | 197.99 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 1.0.0 | 9.97 | 192.21 | 202.18 | OK | |
| r-devel-linux-x86_64-fedora-clang | 1.0.0 | 443.17 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 1.0.0 | 429.12 | OK | |||
| r-devel-windows-x86_64 | 1.0.0 | 14.00 | 164.00 | 178.00 | ERROR | |
| r-patched-linux-x86_64 | 1.0.0 | 13.99 | 265.82 | 279.81 | OK | |
| r-release-linux-x86_64 | 1.0.0 | 12.44 | 266.48 | 278.92 | OK | |
| r-release-macos-arm64 | 1.0.0 | 110.00 | OK | |||
| r-release-macos-x86_64 | 1.0.0 | 250.00 | OK | |||
| r-release-windows-x86_64 | 1.0.0 | 15.00 | 246.00 | 261.00 | OK | |
| r-oldrel-macos-arm64 | 1.0.0 | 129.00 | OK | |||
| r-oldrel-macos-x86_64 | 1.0.0 | 182.00 | OK | |||
| r-oldrel-windows-x86_64 | 1.0.0 | 19.00 | 338.00 | 357.00 | OK |
Version: 1.0.0
Check: examples
Result: ERROR
Running examples in ‘specr-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### 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
Flavor: r-devel-linux-x86_64-debian-clang
Version: 1.0.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [7s/9s]
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
Flavor: r-devel-linux-x86_64-debian-clang
Version: 1.0.0
Check: re-building of vignette outputs
Result: 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
Flavor: r-devel-linux-x86_64-debian-clang
Version: 1.0.0
Check: examples
Result: 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
Flavor: r-devel-windows-x86_64
Version: 1.0.0
Check: tests
Result: 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
Flavor: r-devel-windows-x86_64
Version: 1.0.0
Check: re-building of vignette outputs
Result: 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
Flavor: r-devel-windows-x86_64