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Merged
simonpcouch merged 3 commits into from
Mar 26, 2024
Merged

log a backtrace for tuning issues #879

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f55422c
log a backtrace for tuning issues
simonpcouch Mar 23, 2024
ec6ca1a
update expectation for `notes` names
simonpcouch Mar 23, 2024
6c0ebea
Update NEWS.md
simonpcouch Mar 26, 2024
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5 changes: 5 additions & 0 deletions NEWS.md
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Original file line number Diff line number Diff line change
@@ -1,5 +1,10 @@
# tune (development version)

* The package will now log a backtrace for errors and warnings that
occur during tuning. When a tuning process encounters issues, see the new
`trace` column in `collect_notes(.Last.tune.result)` output to find
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simonpcouch marked this conversation as resolved.
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precisely where the error occurred (#873).

# tune 1.2.0

## New Features
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5 changes: 4 additions & 1 deletion R/grid_code_paths.R
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Expand Up @@ -354,7 +354,10 @@ tune_grid_loop_iter <- function(split,
out_all_outcome_names <- list()
out_notes <-
tibble::new_tibble(list(
location = character(0), type = character(0), note = character(0)
location = character(0),
type = character(0),
note = character(0),
trace = list()
))

model_params <- vctrs::vec_slice(params, params$source == "model_spec")
Expand Down
23 changes: 21 additions & 2 deletions R/handlers.R
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Expand Up @@ -3,10 +3,29 @@
catcher <- function(expr) {
signals <- list()
add_cond <- function(cnd) {
signals <<- append(signals, list(cnd))
signals <<- append(signals, list(rlang::cnd_entrace(cnd)))
rlang::cnd_muffle(cnd)
}

res <- try(withCallingHandlers(warning = add_cond, expr), silent = TRUE)
res <-
rlang::try_fetch(
expr,
warning = add_cond,
error = function(e) {
structure(
catch_message(e),
class = "try-error",
# if a simple error, add a traceback.
# otherwise, pass the condition right along.
condition = rlang::`%||%`(rlang::cnd_entrace(e), e)
)
}
)

list(res = res, signals = signals)
}

# A simplified version of the error handler supplied in `try()` source
catch_message <- function(e) {
paste0("Error in ", deparse(conditionCall(e)), ": ", conditionMessage(e), "\n")
}
11 changes: 7 additions & 4 deletions R/logging.R
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Expand Up @@ -307,8 +307,10 @@ log_problems <- function(notes, control, split, loc, res, bad_only = FALSE) {
wrn_msg <- unique(wrn_msg)
wrn_msg <- paste(wrn_msg, collapse = ", ")

wrn_traces <- purrr::map(wrn, `$`, "trace")

wrn_msg <- tibble::new_tibble(
list(location = loc, type = "warning", note = wrn_msg),
list(location = loc, type = "warning", note = wrn_msg, trace = list(wrn_traces[[1]])),
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@simonpcouch simonpcouch Mar 23, 2024

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Note that traces are a tibble subclass.

Each row in the output of this function is a given place in evaluating a resample fold, e.g. Fold1 preprocessor 1/1, model 1/1 (predictions).

It's possible to have more than one warning appear in a given model fit or prediction or metric calculation, so we collapse messages (see above) into one string in that case. For traces, we could just pass all of list(wrn_traces), but that would mean that, to be type-stable, we'd have to list(list(err_cnd$trace)) for errors.

Said another way, right now, to extract the second logged trace, you could write collect_notes()$trace[[2]]. If we supplied all of the warning traces in this line and changed the format for errors to be type-stable, you'd have to write collect_notes()$trace[[2]][[1]]. This [[-fu feels contrary to the point of the collect_*() functions.

This approach banks on the fact that it's likely not useful to have a backtrace for each warning that occurs in a single call to e.g. predict.xgb(); the first is sufficient to help you drop into the right environment to track down an issue.

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@hfrick hfrick Mar 26, 2024

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I'd go with clarity over completeness here and only use the first trace as suggested. If we later realize that this does not get us to a useful debugging point often enough, we can still extend it.

nrow = 1
)

Expand All @@ -322,15 +324,16 @@ log_problems <- function(notes, control, split, loc, res, bad_only = FALSE) {
}
}
if (inherits(res$res, "try-error")) {
err_cnd <- attr(res$res, "condition")
if (should_catalog) {
err_msg <- conditionMessage(attr(res$res, "condition"))
err_msg <- conditionMessage(err_cnd)
} else {
err_msg <- as.character(attr(res$res, "condition"))
err_msg <- as.character(err_cnd)
err_msg <- gsub("\n$", "", err_msg)
}

err_msg <- tibble::new_tibble(
list(location = loc, type = "error", note = err_msg),
list(location = loc, type = "error", note = err_msg, trace = list(err_cnd$trace)),
nrow = 1
)

Expand Down
7 changes: 6 additions & 1 deletion R/tune_bayes.R
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Expand Up @@ -374,7 +374,12 @@ tune_bayes_workflow <- function(object,
for (i in seq_len(iter) + score_card$overall_iter) {
.notes <-
tibble::new_tibble(
list(location = character(0), type = character(0), note = character(0)),
list(
location = character(0),
type = character(0),
note = character(0),
trace = list()
),
nrow = 0
)

Expand Down
60 changes: 30 additions & 30 deletions tests/testthat/_snaps/bayes.md
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Expand Up @@ -148,16 +148,16 @@
# A tibble: 30 x 5
splits id .metrics .notes .iter
<list> <chr> <list> <list> <int>
1 <split [28/4]> Fold01 <tibble [4 x 5]> <tibble [0 x 3]> 0
2 <split [28/4]> Fold02 <tibble [4 x 5]> <tibble [0 x 3]> 0
3 <split [29/3]> Fold03 <tibble [4 x 5]> <tibble [0 x 3]> 0
4 <split [29/3]> Fold04 <tibble [4 x 5]> <tibble [0 x 3]> 0
5 <split [29/3]> Fold05 <tibble [4 x 5]> <tibble [0 x 3]> 0
6 <split [29/3]> Fold06 <tibble [4 x 5]> <tibble [0 x 3]> 0
7 <split [29/3]> Fold07 <tibble [4 x 5]> <tibble [0 x 3]> 0
8 <split [29/3]> Fold08 <tibble [4 x 5]> <tibble [0 x 3]> 0
9 <split [29/3]> Fold09 <tibble [4 x 5]> <tibble [0 x 3]> 0
10 <split [29/3]> Fold10 <tibble [4 x 5]> <tibble [0 x 3]> 0
1 <split [28/4]> Fold01 <tibble [4 x 5]> <tibble [0 x 4]> 0
2 <split [28/4]> Fold02 <tibble [4 x 5]> <tibble [0 x 4]> 0
3 <split [29/3]> Fold03 <tibble [4 x 5]> <tibble [0 x 4]> 0
4 <split [29/3]> Fold04 <tibble [4 x 5]> <tibble [0 x 4]> 0
5 <split [29/3]> Fold05 <tibble [4 x 5]> <tibble [0 x 4]> 0
6 <split [29/3]> Fold06 <tibble [4 x 5]> <tibble [0 x 4]> 0
7 <split [29/3]> Fold07 <tibble [4 x 5]> <tibble [0 x 4]> 0
8 <split [29/3]> Fold08 <tibble [4 x 5]> <tibble [0 x 4]> 0
9 <split [29/3]> Fold09 <tibble [4 x 5]> <tibble [0 x 4]> 0
10 <split [29/3]> Fold10 <tibble [4 x 5]> <tibble [0 x 4]> 0
# i 20 more rows

---
Expand Down Expand Up @@ -199,16 +199,16 @@
# A tibble: 30 x 5
splits id .metrics .notes .iter
<list> <chr> <list> <list> <int>
1 <split [28/4]> Fold01 <tibble [4 x 5]> <tibble [0 x 3]> 0
2 <split [28/4]> Fold02 <tibble [4 x 5]> <tibble [0 x 3]> 0
3 <split [29/3]> Fold03 <tibble [4 x 5]> <tibble [0 x 3]> 0
4 <split [29/3]> Fold04 <tibble [4 x 5]> <tibble [0 x 3]> 0
5 <split [29/3]> Fold05 <tibble [4 x 5]> <tibble [0 x 3]> 0
6 <split [29/3]> Fold06 <tibble [4 x 5]> <tibble [0 x 3]> 0
7 <split [29/3]> Fold07 <tibble [4 x 5]> <tibble [0 x 3]> 0
8 <split [29/3]> Fold08 <tibble [4 x 5]> <tibble [0 x 3]> 0
9 <split [29/3]> Fold09 <tibble [4 x 5]> <tibble [0 x 3]> 0
10 <split [29/3]> Fold10 <tibble [4 x 5]> <tibble [0 x 3]> 0
1 <split [28/4]> Fold01 <tibble [4 x 5]> <tibble [0 x 4]> 0
2 <split [28/4]> Fold02 <tibble [4 x 5]> <tibble [0 x 4]> 0
3 <split [29/3]> Fold03 <tibble [4 x 5]> <tibble [0 x 4]> 0
4 <split [29/3]> Fold04 <tibble [4 x 5]> <tibble [0 x 4]> 0
5 <split [29/3]> Fold05 <tibble [4 x 5]> <tibble [0 x 4]> 0
6 <split [29/3]> Fold06 <tibble [4 x 5]> <tibble [0 x 4]> 0
7 <split [29/3]> Fold07 <tibble [4 x 5]> <tibble [0 x 4]> 0
8 <split [29/3]> Fold08 <tibble [4 x 5]> <tibble [0 x 4]> 0
9 <split [29/3]> Fold09 <tibble [4 x 5]> <tibble [0 x 4]> 0
10 <split [29/3]> Fold10 <tibble [4 x 5]> <tibble [0 x 4]> 0
# i 20 more rows

---
Expand Down Expand Up @@ -374,16 +374,16 @@
# A tibble: 30 x 5
splits id .metrics .notes .iter
<list> <chr> <list> <list> <int>
1 <split [28/4]> Fold01 <tibble [4 x 5]> <tibble [0 x 3]> 0
2 <split [28/4]> Fold02 <tibble [4 x 5]> <tibble [0 x 3]> 0
3 <split [29/3]> Fold03 <tibble [4 x 5]> <tibble [0 x 3]> 0
4 <split [29/3]> Fold04 <tibble [4 x 5]> <tibble [0 x 3]> 0
5 <split [29/3]> Fold05 <tibble [4 x 5]> <tibble [0 x 3]> 0
6 <split [29/3]> Fold06 <tibble [4 x 5]> <tibble [0 x 3]> 0
7 <split [29/3]> Fold07 <tibble [4 x 5]> <tibble [0 x 3]> 0
8 <split [29/3]> Fold08 <tibble [4 x 5]> <tibble [0 x 3]> 0
9 <split [29/3]> Fold09 <tibble [4 x 5]> <tibble [0 x 3]> 0
10 <split [29/3]> Fold10 <tibble [4 x 5]> <tibble [0 x 3]> 0
1 <split [28/4]> Fold01 <tibble [4 x 5]> <tibble [0 x 4]> 0
2 <split [28/4]> Fold02 <tibble [4 x 5]> <tibble [0 x 4]> 0
3 <split [29/3]> Fold03 <tibble [4 x 5]> <tibble [0 x 4]> 0
4 <split [29/3]> Fold04 <tibble [4 x 5]> <tibble [0 x 4]> 0
5 <split [29/3]> Fold05 <tibble [4 x 5]> <tibble [0 x 4]> 0
6 <split [29/3]> Fold06 <tibble [4 x 5]> <tibble [0 x 4]> 0
7 <split [29/3]> Fold07 <tibble [4 x 5]> <tibble [0 x 4]> 0
8 <split [29/3]> Fold08 <tibble [4 x 5]> <tibble [0 x 4]> 0
9 <split [29/3]> Fold09 <tibble [4 x 5]> <tibble [0 x 4]> 0
10 <split [29/3]> Fold10 <tibble [4 x 5]> <tibble [0 x 4]> 0
# i 20 more rows

# tune model only - failure in recipe is caught elegantly
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20 changes: 10 additions & 10 deletions tests/testthat/_snaps/censored-reg.md
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Expand Up @@ -30,16 +30,16 @@
# A tibble: 10 x 4
splits id .metrics .notes
<list> <chr> <list> <list>
1 <split [164/20]> Fold01 <tibble [1 x 4]> <tibble [0 x 3]>
2 <split [165/19]> Fold02 <tibble [1 x 4]> <tibble [0 x 3]>
3 <split [165/19]> Fold03 <tibble [1 x 4]> <tibble [0 x 3]>
4 <split [166/18]> Fold04 <tibble [1 x 4]> <tibble [0 x 3]>
5 <split [166/18]> Fold05 <tibble [1 x 4]> <tibble [0 x 3]>
6 <split [166/18]> Fold06 <tibble [1 x 4]> <tibble [0 x 3]>
7 <split [166/18]> Fold07 <tibble [1 x 4]> <tibble [0 x 3]>
8 <split [166/18]> Fold08 <tibble [1 x 4]> <tibble [0 x 3]>
9 <split [166/18]> Fold09 <tibble [1 x 4]> <tibble [0 x 3]>
10 <split [166/18]> Fold10 <tibble [1 x 4]> <tibble [0 x 3]>
1 <split [164/20]> Fold01 <tibble [1 x 4]> <tibble [0 x 4]>
2 <split [165/19]> Fold02 <tibble [1 x 4]> <tibble [0 x 4]>
3 <split [165/19]> Fold03 <tibble [1 x 4]> <tibble [0 x 4]>
4 <split [166/18]> Fold04 <tibble [1 x 4]> <tibble [0 x 4]>
5 <split [166/18]> Fold05 <tibble [1 x 4]> <tibble [0 x 4]>
6 <split [166/18]> Fold06 <tibble [1 x 4]> <tibble [0 x 4]>
7 <split [166/18]> Fold07 <tibble [1 x 4]> <tibble [0 x 4]>
8 <split [166/18]> Fold08 <tibble [1 x 4]> <tibble [0 x 4]>
9 <split [166/18]> Fold09 <tibble [1 x 4]> <tibble [0 x 4]>
10 <split [166/18]> Fold10 <tibble [1 x 4]> <tibble [0 x 4]>

---

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46 changes: 23 additions & 23 deletions tests/testthat/_snaps/extract.md
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Expand Up @@ -49,9 +49,9 @@
# A tibble: 3 x 5
splits id .metrics .notes .extracts
<list> <chr> <list> <list> <list>
1 <split [32/13]> Bootstrap1 <tibble [2 x 4]> <tibble [1 x 3]> <tibble [1 x 2]>
2 <split [32/17]> Bootstrap2 <tibble [2 x 4]> <tibble [1 x 3]> <tibble [1 x 2]>
3 <split [32/11]> Bootstrap3 <tibble [2 x 4]> <tibble [1 x 3]> <tibble [1 x 2]>
1 <split [32/13]> Bootstrap1 <tibble [2 x 4]> <tibble [1 x 4]> <tibble [1 x 2]>
2 <split [32/17]> Bootstrap2 <tibble [2 x 4]> <tibble [1 x 4]> <tibble [1 x 2]>
3 <split [32/11]> Bootstrap3 <tibble [2 x 4]> <tibble [1 x 4]> <tibble [1 x 2]>

There were issues with some computations:

Expand All @@ -69,9 +69,9 @@
# A tibble: 3 x 5
splits id .metrics .notes .extracts
<list> <chr> <list> <list> <list>
1 <split [32/13]> Bootstrap1 <tibble [2 x 4]> <tibble [1 x 3]> <tibble [1 x 2]>
2 <split [32/17]> Bootstrap2 <tibble [2 x 4]> <tibble [1 x 3]> <tibble [1 x 2]>
3 <split [32/11]> Bootstrap3 <tibble [2 x 4]> <tibble [1 x 3]> <tibble [1 x 2]>
1 <split [32/13]> Bootstrap1 <tibble [2 x 4]> <tibble [1 x 4]> <tibble [1 x 2]>
2 <split [32/17]> Bootstrap2 <tibble [2 x 4]> <tibble [1 x 4]> <tibble [1 x 2]>
3 <split [32/11]> Bootstrap3 <tibble [2 x 4]> <tibble [1 x 4]> <tibble [1 x 2]>

There were issues with some computations:

Expand All @@ -89,9 +89,9 @@
# A tibble: 3 x 5
splits id .metrics .notes .extracts
<list> <chr> <list> <list> <list>
1 <split [32/13]> Bootstrap1 <tibble [2 x 4]> <tibble [2 x 3]> <tibble [1 x 2]>
2 <split [32/17]> Bootstrap2 <tibble [2 x 4]> <tibble [2 x 3]> <tibble [1 x 2]>
3 <split [32/11]> Bootstrap3 <tibble [2 x 4]> <tibble [2 x 3]> <tibble [1 x 2]>
1 <split [32/13]> Bootstrap1 <tibble [2 x 4]> <tibble [2 x 4]> <tibble [1 x 2]>
2 <split [32/17]> Bootstrap2 <tibble [2 x 4]> <tibble [2 x 4]> <tibble [1 x 2]>
3 <split [32/11]> Bootstrap3 <tibble [2 x 4]> <tibble [2 x 4]> <tibble [1 x 2]>

There were issues with some computations:

Expand All @@ -110,9 +110,9 @@
# A tibble: 3 x 5
splits id .metrics .notes .extracts
<list> <chr> <list> <list> <list>
1 <split [32/13]> Bootstrap1 <tibble [2 x 4]> <tibble [1 x 3]> <tibble [1 x 2]>
2 <split [32/17]> Bootstrap2 <tibble [2 x 4]> <tibble [0 x 3]> <tibble [1 x 2]>
3 <split [32/11]> Bootstrap3 <tibble [2 x 4]> <tibble [0 x 3]> <tibble [1 x 2]>
1 <split [32/13]> Bootstrap1 <tibble [2 x 4]> <tibble [1 x 4]> <tibble [1 x 2]>
2 <split [32/17]> Bootstrap2 <tibble [2 x 4]> <tibble [0 x 4]> <tibble [1 x 2]>
3 <split [32/11]> Bootstrap3 <tibble [2 x 4]> <tibble [0 x 4]> <tibble [1 x 2]>

There were issues with some computations:

Expand All @@ -125,17 +125,17 @@
Code
res_extract_warning$.notes[[1]]
Output
# A tibble: 1 x 3
location type note
<chr> <chr> <chr>
1 preprocessor 1/1, model 1/1 (extracts) warning AHHH
# A tibble: 1 x 4
location type note trace
<chr> <chr> <chr> <list>
1 preprocessor 1/1, model 1/1 (extracts) warning AHHH <rlng_trc [46 x 5]>

---

Code
res_extract_error$.extracts[[1]]$.extracts[[1]]
Output
[1] "Error in extractor(object) : AHHH\n"
[1] "Error in extractor(object): AHHH\n"
attr(,"class")
[1] "try-error"
attr(,"condition")
Expand All @@ -146,17 +146,17 @@
Code
res_extract_error$.notes[[1]]
Output
# A tibble: 1 x 3
location type note
<chr> <chr> <chr>
1 preprocessor 1/1, model 1/1 (extracts) error Error in extractor(object): AHHH
# A tibble: 1 x 4
location type note trace
<chr> <chr> <chr> <list>
1 preprocessor 1/1, model 1/1 (extracts) error Error in extractor(ob~ <rlng_trc>

---

Code
res_extract_both$.extracts[[1]]$.extracts[[1]]
Output
[1] "Error in extractor(object) : AHHH\n"
[1] "Error in extractor(object): AHHH\n"
attr(,"class")
[1] "try-error"
attr(,"condition")
Expand All @@ -167,7 +167,7 @@
Code
res_extract_error_once$.extracts[[1]]$.extracts[[1]]
Output
[1] "Error in extractor(object) : oh no\n"
[1] "Error in extractor(object): oh no\n"
attr(,"class")
[1] "try-error"
attr(,"condition")
Expand Down
20 changes: 10 additions & 10 deletions tests/testthat/_snaps/grid.md
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Expand Up @@ -66,14 +66,14 @@
# A tibble: 10 x 4
splits id .metrics .notes
<list> <chr> <list> <list>
1 <split [28/4]> Fold01 <tibble [4 x 5]> <tibble [0 x 3]>
2 <split [28/4]> Fold02 <tibble [4 x 5]> <tibble [0 x 3]>
3 <split [29/3]> Fold03 <tibble [4 x 5]> <tibble [0 x 3]>
4 <split [29/3]> Fold04 <tibble [4 x 5]> <tibble [0 x 3]>
5 <split [29/3]> Fold05 <tibble [4 x 5]> <tibble [0 x 3]>
6 <split [29/3]> Fold06 <tibble [4 x 5]> <tibble [0 x 3]>
7 <split [29/3]> Fold07 <tibble [4 x 5]> <tibble [0 x 3]>
8 <split [29/3]> Fold08 <tibble [4 x 5]> <tibble [0 x 3]>
9 <split [29/3]> Fold09 <tibble [4 x 5]> <tibble [0 x 3]>
10 <split [29/3]> Fold10 <tibble [4 x 5]> <tibble [0 x 3]>
1 <split [28/4]> Fold01 <tibble [4 x 5]> <tibble [0 x 4]>
2 <split [28/4]> Fold02 <tibble [4 x 5]> <tibble [0 x 4]>
3 <split [29/3]> Fold03 <tibble [4 x 5]> <tibble [0 x 4]>
4 <split [29/3]> Fold04 <tibble [4 x 5]> <tibble [0 x 4]>
5 <split [29/3]> Fold05 <tibble [4 x 5]> <tibble [0 x 4]>
6 <split [29/3]> Fold06 <tibble [4 x 5]> <tibble [0 x 4]>
7 <split [29/3]> Fold07 <tibble [4 x 5]> <tibble [0 x 4]>
8 <split [29/3]> Fold08 <tibble [4 x 5]> <tibble [0 x 4]>
9 <split [29/3]> Fold09 <tibble [4 x 5]> <tibble [0 x 4]>
10 <split [29/3]> Fold10 <tibble [4 x 5]> <tibble [0 x 4]>

2 changes: 1 addition & 1 deletion tests/testthat/_snaps/last-fit.md
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Expand Up @@ -28,7 +28,7 @@
# A tibble: 1 x 6
splits id .metrics .notes .predictions .workflow
<list> <chr> <list> <list> <list> <list>
1 <split [24/8]> train/test split <tibble [2 x 4]> <tibble [0 x 3]> <tibble [8 x 4]> <workflow>
1 <split [24/8]> train/test split <tibble [2 x 4]> <tibble [0 x 4]> <tibble [8 x 4]> <workflow>

# argument order gives errors for recipe/formula

Expand Down
8 changes: 4 additions & 4 deletions tests/testthat/_snaps/logging.md
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Expand Up @@ -71,16 +71,16 @@
# log issues

Code
expect_equal(tune:::log_problems(note_1, ctrl_f, rs, "toledo", res_1, bad_only = FALSE),
dplyr::bind_rows(note_1, note_2))
problems_1 <- tune:::log_problems(note_1, ctrl_f, rs, "toledo", res_1,
bad_only = FALSE)
Message
x Fold01: toledo: Error in log("a"): non-numeric argument to mathematical function

---

Code
expect_equal(tune:::log_problems(note_1, ctrl_f, rs, "toledo", res_3, bad_only = FALSE),
dplyr::bind_rows(note_1, note_3))
problems_2 <- tune:::log_problems(note_1, ctrl_f, rs, "toledo", res_3,
bad_only = FALSE)
Message
! Fold01: toledo: NaNs produced

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8 changes: 4 additions & 4 deletions tests/testthat/_snaps/resample.md
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Expand Up @@ -92,8 +92,8 @@
# A tibble: 2 x 4
splits id .metrics .notes
<list> <chr> <list> <list>
1 <split [16/16]> Fold1 <tibble [2 x 4]> <tibble [0 x 3]>
2 <split [16/16]> Fold2 <tibble [2 x 4]> <tibble [0 x 3]>
1 <split [16/16]> Fold1 <tibble [2 x 4]> <tibble [0 x 4]>
2 <split [16/16]> Fold2 <tibble [2 x 4]> <tibble [0 x 4]>

# argument order gives errors for recipe/formula

Expand Down Expand Up @@ -126,8 +126,8 @@
# A tibble: 2 x 4
splits id .metrics .notes
<list> <chr> <list> <list>
1 <split [16/16]> Fold1 <tibble [2 x 4]> <tibble [0 x 3]>
2 <split [16/16]> Fold2 <tibble [2 x 4]> <tibble [0 x 3]>
1 <split [16/16]> Fold1 <tibble [2 x 4]> <tibble [0 x 4]>
2 <split [16/16]> Fold2 <tibble [2 x 4]> <tibble [0 x 4]>

# `fit_resamples()` when objects need tuning

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