Last updated on 2025-12-21 11:49:58 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.4.1 | 6.51 | 122.35 | 128.86 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 0.4.1 | 4.43 | 87.88 | 92.31 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 0.4.1 | 11.00 | 192.76 | 203.76 | ERROR | |
| r-devel-linux-x86_64-fedora-gcc | 0.4.1 | 10.00 | 195.80 | 205.80 | ERROR | |
| r-devel-windows-x86_64 | 0.4.1 | 7.00 | 131.00 | 138.00 | OK | |
| r-patched-linux-x86_64 | 0.4.1 | 4.91 | 123.54 | 128.45 | OK | |
| r-release-linux-x86_64 | 0.4.1 | 5.95 | 122.94 | 128.89 | OK | |
| r-release-macos-arm64 | 0.4.1 | OK | ||||
| r-release-macos-x86_64 | 0.4.1 | 4.00 | 157.00 | 161.00 | OK | |
| r-release-windows-x86_64 | 0.4.1 | 7.00 | 132.00 | 139.00 | OK | |
| r-oldrel-macos-arm64 | 0.4.1 | OK | ||||
| r-oldrel-macos-x86_64 | 0.4.1 | 4.00 | 147.00 | 151.00 | OK | |
| r-oldrel-windows-x86_64 | 0.4.1 | 10.00 | 174.00 | 184.00 | OK |
Version: 0.4.1
Check: examples
Result: ERROR
Running examples in ‘healthdb-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: collapse_episode
> ### Title: Group records no more than n days apart as episodes
> ### Aliases: collapse_episode
>
> ### ** Examples
>
> # make toy data
> df <- make_test_dat() %>%
+ dplyr::select(clnt_id, dates)
>
> head(df)
clnt_id dates
1 1 2015-10-08
2 1 2017-10-23
3 2 2018-11-08
4 3 2015-08-07
5 4 2016-07-21
6 4 2016-11-06
>
> # collapse records no more than 90 days apart
> # end_dt could be absent then it is assumed to be the same as start_dt
> collapse_episode(df, clnt_id, start_dt = dates, gap = 90)
Error in `[.data.table`(data, , `:=`(last_end_dt, lapply(.SD, function(x) data.table::shift(x, :
attempt access index 3/3 in VECTOR_ELT
Calls: collapse_episode -> collapse_episode.data.frame -> [ -> [.data.table
Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc
Version: 0.4.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [64s/83s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> library(testthat)
> library(healthdb)
>
> test_check("healthdb")
Saving _problems/test-collapse_episode-7.R
The following records have start > end:
uid clnt_id dates ans diagx diagx_1 diagx_2 end_date
1 3 1 2020-12-19 any d q 999 2020-12-12
2 1 1 2020-12-28 any t v <NA> 2020-12-21
3 5 5 2019-08-29 any d b 999 2019-08-22
4 2 10 2018-10-27 any x d <NA> 2018-10-20
5 13 12 2016-09-06 noise 999 <NA> 999 2016-08-30
6 24 13 2017-07-07 noise 999 999 <NA> 2017-06-30
7 20 16 2017-09-22 noise 999 <NA> <NA> 2017-09-15
8 7 17 2018-03-24 any p h <NA> 2018-03-17
9 16 18 2015-06-04 noise 999 <NA> 999 2015-05-28
10 12 19 2015-09-08 all z w f 2015-09-01
11 11 21 2018-01-24 all c u d 2018-01-17
12 14 21 2018-08-17 noise 999 <NA> <NA> 2018-08-10
13 6 21 2020-08-16 any b <NA> 999 2020-08-09
14 21 22 2016-08-31 noise 999 <NA> <NA> 2016-08-24
15 9 25 2020-11-30 all b h i 2020-11-23
16 18 30 2018-02-22 noise 999 999 999 2018-02-15
17 8 34 2017-02-12 any x b 999 2017-02-05
18 10 34 2018-10-12 all b g r 2018-10-05
19 19 36 2019-04-30 noise 999 999 <NA> 2019-04-23
20 23 38 2016-05-19 noise 999 999 999 2016-05-12
21 15 45 2016-06-27 noise 999 <NA> 999 2016-06-20
22 25 47 2015-04-19 noise 999 999 999 2015-04-12
23 4 47 2017-08-30 any f v <NA> 2017-08-23
24 17 48 2017-02-04 noise 999 <NA> 999 2017-01-28
25 22 50 2015-02-22 noise 999 <NA> 999 2015-02-15
The following records have missing dates:
uid clnt_id dates ans diagx diagx_1 diagx_2 end_date
1 1 39 2017-09-09 any u d 999 NA
> --------------Inclusion step--------------
i Identify records with condition(s):
* where at least one of the diagx, diagx_1, diagx_2 column(s) in each record
* contains a value exactly matched values in set: letters
i To see the final query generated by 'dbplyr', use dplyr::show_query() on the output.
To extract the SQL string, use dbplyr::remote_query().
This message is displayed once per session.
> --------------Exclusion step--------------
i Identify records with condition(s):
* where at least one of the diagx, diagx_1, diagx_2 column(s) in each record
* contains a value exactly matched values in set: c("a", "b")
i Exclude records in `data` through anti_join with `excl` matching on (by argument): "clnt_id"
> --------------No. rows restriction--------------
i Apply restriction that each client must have at least 2 records with distinct dates. Clients/groups which did not met the condition were excluded.
> --------------Time span restriction--------------
Saving _problems/test-define_case-85.R
Saving _problems/test-define_case-94.R
i Exclude a subset of `data` that satisfies condition: ans == "noise"
Check NAs in the result; SQL handles missing value differently compared to R.
i Exclude a subset of `data` that satisfies condition: ans == "noise"
i Consider being explicit about NA, e.g., condition = var == 'val' | is.na(var)
i Exclude a subset of `data` that satisfies condition: ans == "noise"
Check NAs in the result; SQL handles missing value differently compared to R.
i Consider being explicit about NA, e.g., condition = var == 'val' | is.na(var)
Saving _problems/test-execute_def-12.R
Saving _problems/test-execute_def-35.R
Saving _problems/test-execute_def-66.R
Saving _problems/test-execute_def-102.R
Saving _problems/test-identify_rows_dataframe-3.R
Saving _problems/test-identify_rows_dataframe-11.R
Saving _problems/test-identify_rows_dataframe-18.R
Saving _problems/test-identify_rows_dataframe-26.R
Saving _problems/test-identify_rows_dataframe-34.R
Saving _problems/test-identify_rows_dataframe-43.R
Saving _problems/test-identify_rows_dataframe-49.R
Saving _problems/test-identify_rows_dataframe-62.R
Saving _problems/test-identify_rows_dataframe-68.R
Saving _problems/test-identify_rows_dataframe-75.R
Saving _problems/test-if_dates-41.R
Saving _problems/test-pool_case-45.R
Saving _problems/test-pool_case-64.R
Saving _problems/test-pool_case-83.R
Saving _problems/test-pool_case-134.R
[ FAIL 23 | WARN 2 | SKIP 6 | PASS 189 ]
══ Skipped tests (6) ═══════════════════════════════════════════════════════════
• On CRAN (6): 'test-define_case.R:42:3', 'test-if_dates.R:2:3',
'test-if_dates.R:26:3', 'test-if_dates.R:33:3',
'test-restrict_dates_sql.R:26:3', 'test-restrict_dates_sql.R:101:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-collapse_episode.R:7:3'): basic use works ──────────────────────
Error in ``[.data.table`(data, , `:=`(last_end_dt, lapply(.SD, function(x) data.table::shift(x, n = 1, fill = data.table::first(x)))), by = clnt_id_nm, .SDcols = end_dt_nm)`: attempt access index 8/8 in VECTOR_ELT
Backtrace:
▆
1. ├─healthdb::collapse_episode(...) at test-collapse_episode.R:7:3
2. └─healthdb:::collapse_episode.data.frame(...)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-define_case.R:85:48'): keep first/last works on df ─────────────
Error in ``[.data.table`(dt, , `:=`(incl, data.table::`%chin%`(unlist(.SD), matched_vals) %>% combine_fn(na.rm = TRUE)), by = "rid", .SDcols = vars)`: attempt access index 8/8 in VECTOR_ELT
Backtrace:
▆
1. └─base::sapply(...) at test-define_case.R:85:3
2. └─base::lapply(X = X, FUN = FUN, ...)
3. └─healthdb (local) FUN(X[[i]], ...)
4. └─healthdb::define_case(...) at test-define_case.R:85:48
5. ├─base::eval(incl)
6. │ └─base::eval(incl)
7. ├─healthdb::identify_row(...)
8. └─healthdb:::identify_rows.data.frame(...)
9. ├─...[]
10. └─data.table:::`[.data.table`(...)
── Error ('test-define_case.R:94:3'): passing ... works ────────────────────────
Error in ``[.data.table`(dt, , `:=`(incl, data.table::`%chin%`(unlist(.SD), matched_vals) %>% combine_fn(na.rm = TRUE)), by = "rid", .SDcols = vars)`: attempt access index 7/7 in VECTOR_ELT
Backtrace:
▆
1. └─healthdb::define_case(...) at test-define_case.R:94:3
2. ├─base::eval(incl)
3. │ └─base::eval(incl)
4. ├─healthdb::identify_row(...)
5. └─healthdb:::identify_rows.data.frame(...)
6. ├─...[]
7. └─data.table:::`[.data.table`(...)
── Error ('test-execute_def.R:12:3'): basic use works ──────────────────────────
<dplyr:::mutate_error/rlang_error/error/condition>
Error in `dplyr::mutate(., result = purrr::pmap(list(.data[["fn_call"]], .data[["src_labs"]], .data[["def_lab"]]), function(x, y, z) { if (getOption("healthdb.verbose")) rlang::inform(paste0("\nActions for definition ", z, " using source ", rlang::expr_deparse(with_data_expr[[y]]), ":\n")) eval(x, envir = with_data_env) }, .progress = TRUE), result = purrr::pmap(list(.data[["result"]], .data[["def_lab"]], .data[["src_labs"]]), function(dat, def, src) { dat %>% dplyr::mutate(def = def, src = src, .before = 1) }))`: i In argument: `result = purrr::pmap(...)`.
Caused by error in `purrr::pmap()`:
i In index: 2.
Caused by error in `[.data.table`:
! attempt access index 8/8 in VECTOR_ELT
── Error ('test-execute_def.R:35:3'): mixed binding works ──────────────────────
<dplyr:::mutate_error/rlang_error/error/condition>
Error in `dplyr::mutate(., result = purrr::pmap(list(.data[["fn_call"]], .data[["src_labs"]], .data[["def_lab"]]), function(x, y, z) { if (getOption("healthdb.verbose")) rlang::inform(paste0("\nActions for definition ", z, " using source ", rlang::expr_deparse(with_data_expr[[y]]), ":\n")) eval(x, envir = with_data_env) }, .progress = TRUE), result = purrr::pmap(list(.data[["result"]], .data[["def_lab"]], .data[["src_labs"]]), function(dat, def, src) { dat %>% dplyr::mutate(def = def, src = src, .before = 1) }))`: i In argument: `result = purrr::pmap(...)`.
Caused by error in `purrr::pmap()`:
i In index: 2.
Caused by error in `[.data.table`:
! attempt access index 8/8 in VECTOR_ELT
── Error ('test-execute_def.R:66:3'): binding dfs works ────────────────────────
<dplyr:::mutate_error/rlang_error/error/condition>
Error in `dplyr::mutate(., result = purrr::pmap(list(.data[["fn_call"]], .data[["src_labs"]], .data[["def_lab"]]), function(x, y, z) { if (getOption("healthdb.verbose")) rlang::inform(paste0("\nActions for definition ", z, " using source ", rlang::expr_deparse(with_data_expr[[y]]), ":\n")) eval(x, envir = with_data_env) }, .progress = TRUE), result = purrr::pmap(list(.data[["result"]], .data[["def_lab"]], .data[["src_labs"]]), function(dat, def, src) { dat %>% dplyr::mutate(def = def, src = src, .before = 1) }))`: i In argument: `result = purrr::pmap(...)`.
Caused by error in `purrr::pmap()`:
i In index: 1.
Caused by error in `[.data.table`:
! attempt access index 8/8 in VECTOR_ELT
── Error ('test-execute_def.R:102:3'): multiple def works ──────────────────────
<dplyr:::mutate_error/rlang_error/error/condition>
Error in `dplyr::mutate(., result = purrr::pmap(list(.data[["fn_call"]], .data[["src_labs"]], .data[["def_lab"]]), function(x, y, z) { if (getOption("healthdb.verbose")) rlang::inform(paste0("\nActions for definition ", z, " using source ", rlang::expr_deparse(with_data_expr[[y]]), ":\n")) eval(x, envir = with_data_env) }, .progress = TRUE), result = purrr::pmap(list(.data[["result"]], .data[["def_lab"]], .data[["src_labs"]]), function(dat, def, src) { dat %>% dplyr::mutate(def = def, src = src, .before = 1) }))`: i In argument: `result = purrr::pmap(...)`.
Caused by error in `purrr::pmap()`:
i In index: 1.
Caused by error in `[.data.table`:
! attempt access index 8/8 in VECTOR_ELT
── Error ('test-identify_rows_dataframe.R:3:3'): match by in works ─────────────
Error in ``[.data.table`(dt, , `:=`(incl, data.table::`%chin%`(unlist(.SD), matched_vals) %>% combine_fn(na.rm = TRUE)), by = "rid", .SDcols = vars)`: attempt access index 8/8 in VECTOR_ELT
Backtrace:
▆
1. ├─healthdb:::identify_rows(df, starts_with("diagx"), "in", letters) at test-identify_rows_dataframe.R:3:3
2. └─healthdb:::identify_rows.data.frame(...)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-identify_rows_dataframe.R:11:3'): if_all works ─────────────────
Error in ``[.data.table`(dt, , `:=`(incl, data.table::`%chin%`(unlist(.SD), matched_vals) %>% combine_fn(na.rm = TRUE)), by = "rid", .SDcols = vars)`: attempt access index 8/8 in VECTOR_ELT
Backtrace:
▆
1. ├─healthdb:::identify_rows(...) at test-identify_rows_dataframe.R:11:3
2. └─healthdb:::identify_rows.data.frame(...)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-identify_rows_dataframe.R:18:3'): match by start works ─────────
Error in ``[.data.table`(dt, , `:=`(incl, data.table::`%chin%`(unlist(.SD), matched_vals) %>% combine_fn(na.rm = TRUE)), by = "rid", .SDcols = vars)`: attempt access index 8/8 in VECTOR_ELT
Backtrace:
▆
1. ├─healthdb:::identify_rows(df, starts_with("diagx"), "start", start) at test-identify_rows_dataframe.R:18:3
2. └─healthdb:::identify_rows.data.frame(...)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-identify_rows_dataframe.R:26:3'): match by like works ──────────
Error in ``[.data.table`(dt, , `:=`(incl, data.table::`%chin%`(unlist(.SD), matched_vals) %>% combine_fn(na.rm = TRUE)), by = "rid", .SDcols = vars)`: attempt access index 8/8 in VECTOR_ELT
Backtrace:
▆
1. ├─healthdb:::identify_rows(df, starts_with("diagx"), "like", pattern) at test-identify_rows_dataframe.R:26:3
2. └─healthdb:::identify_rows.data.frame(...)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-identify_rows_dataframe.R:34:3'): match by regex works ─────────
Error in ``[.data.table`(dt, , `:=`(incl, data.table::`%chin%`(unlist(.SD), matched_vals) %>% combine_fn(na.rm = TRUE)), by = "rid", .SDcols = vars)`: attempt access index 8/8 in VECTOR_ELT
Backtrace:
▆
1. ├─healthdb:::identify_rows(df, starts_with("diagx"), "regex", pattern) at test-identify_rows_dataframe.R:34:3
2. └─healthdb:::identify_rows.data.frame(...)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-identify_rows_dataframe.R:43:3'): match by between works ───────
Error in ``[.data.table`(dt, , `:=`(incl, unlist(.SD) %in% matched_vals %>% combine_fn(na.rm = TRUE)), by = "rid", .SDcols = vars)`: attempt access index 8/8 in VECTOR_ELT
Backtrace:
▆
1. ├─healthdb:::identify_rows(df, dates, "between", seq_range) at test-identify_rows_dataframe.R:43:3
2. └─healthdb:::identify_rows.data.frame(df, dates, "between", seq_range)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-identify_rows_dataframe.R:49:3'): type conflict warning works ──
Error in ``[.data.table`(dt, , `:=`(incl, unlist(.SD) %in% matched_vals %>% combine_fn(na.rm = TRUE)), by = "rid", .SDcols = vars)`: attempt access index 8/8 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_warning(...) at test-identify_rows_dataframe.R:49:3
2. │ └─testthat:::expect_condition_matching_(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─healthdb:::identify_rows(df, starts_with("diagx"), "in", 1:10)
8. └─healthdb:::identify_rows.data.frame(...)
9. ├─...[]
10. └─data.table:::`[.data.table`(...)
── Error ('test-identify_rows_dataframe.R:56:3'): summary of numeric vals works ──
Error in ``[.data.table`(dt, , `:=`(incl, unlist(.SD) %in% matched_vals %>% combine_fn(na.rm = TRUE)), by = "rid", .SDcols = vars)`: attempt access index 7/7 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_output(...) at test-identify_rows_dataframe.R:56:3
2. │ └─testthat:::quasi_capture(...)
3. │ ├─testthat (local) .capture(...)
4. │ │ └─testthat::capture_output_lines(code, print, width = width)
5. │ │ └─testthat:::eval_with_output(code, print = print, width = width)
6. │ │ ├─withr::with_output_sink(path, withVisible(code))
7. │ │ │ └─base::force(code)
8. │ │ └─base::withVisible(code)
9. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
10. ├─healthdb:::identify_rows(...)
11. └─healthdb:::identify_rows.data.frame(...)
12. ├─...[]
13. └─data.table:::`[.data.table`(...)
── Error ('test-identify_rows_dataframe.R:62:3'): edge case - character vars works ──
Error in ``[.data.table`(dt, , `:=`(incl, data.table::`%chin%`(unlist(.SD), matched_vals) %>% combine_fn(na.rm = TRUE)), by = "rid", .SDcols = vars)`: attempt access index 8/8 in VECTOR_ELT
Backtrace:
▆
1. ├─healthdb:::identify_rows(df, any_of(var_nm), "in", letters) at test-identify_rows_dataframe.R:62:3
2. └─healthdb:::identify_rows.data.frame(...)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-identify_rows_dataframe.R:68:3'): edge case - unquoted vars works ──
Error in ``[.data.table`(dt, , `:=`(incl, data.table::`%chin%`(unlist(.SD), matched_vals) %>% combine_fn(na.rm = TRUE)), by = "rid", .SDcols = vars)`: attempt access index 8/8 in VECTOR_ELT
Backtrace:
▆
1. ├─healthdb:::identify_rows(...) at test-identify_rows_dataframe.R:68:3
2. └─healthdb:::identify_rows.data.frame(...)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-identify_rows_dataframe.R:75:3'): edge case - vals in an external vector works ──
Error in ``[.data.table`(dt, , `:=`(incl, data.table::`%chin%`(unlist(.SD), matched_vals) %>% combine_fn(na.rm = TRUE)), by = "rid", .SDcols = vars)`: attempt access index 8/8 in VECTOR_ELT
Backtrace:
▆
1. ├─healthdb:::identify_rows(...) at test-identify_rows_dataframe.R:75:3
2. └─healthdb:::identify_rows.data.frame(...)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-if_dates.R:41:3'): straight false due to no gap < within works ──
Error in ``[.data.table`(overlap, , `:=`(N, .N), by = period_id)`: attempt access index 4/4 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_false(if_dates(dates, 2, apart = 7, within = 30)) at test-if_dates.R:41:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─healthdb:::if_dates(dates, 2, apart = 7, within = 30)
5. ├─overlap[, `:=`(N, .N), by = period_id]
6. └─data.table:::`[.data.table`(overlap, , `:=`(N, .N), by = period_id)
── Error ('test-pool_case.R:45:3'): pool mixed works ───────────────────────────
<dplyr:::mutate_error/rlang_error/error/condition>
Error in `dplyr::mutate(., result = purrr::pmap(list(.data[["fn_call"]], .data[["src_labs"]], .data[["def_lab"]]), function(x, y, z) { if (getOption("healthdb.verbose")) rlang::inform(paste0("\nActions for definition ", z, " using source ", rlang::expr_deparse(with_data_expr[[y]]), ":\n")) eval(x, envir = with_data_env) }, .progress = TRUE), result = purrr::pmap(list(.data[["result"]], .data[["def_lab"]], .data[["src_labs"]]), function(dat, def, src) { dat %>% dplyr::mutate(def = def, src = src, .before = 1) }))`: i In argument: `result = purrr::pmap(...)`.
Caused by error in `purrr::pmap()`:
i In index: 1.
Caused by error in `[.data.table`:
! attempt access index 8/8 in VECTOR_ELT
── Error ('test-pool_case.R:64:3'): edge case no date_var works ────────────────
<dplyr:::mutate_error/rlang_error/error/condition>
Error in `dplyr::mutate(., result = purrr::pmap(list(.data[["fn_call"]], .data[["src_labs"]], .data[["def_lab"]]), function(x, y, z) { if (getOption("healthdb.verbose")) rlang::inform(paste0("\nActions for definition ", z, " using source ", rlang::expr_deparse(with_data_expr[[y]]), ":\n")) eval(x, envir = with_data_env) }, .progress = TRUE), result = purrr::pmap(list(.data[["result"]], .data[["def_lab"]], .data[["src_labs"]]), function(dat, def, src) { dat %>% dplyr::mutate(def = def, src = src, .before = 1) }))`: i In argument: `result = purrr::pmap(...)`.
Caused by error in `purrr::pmap()`:
i In index: 1.
Caused by error in `[.data.table`:
! attempt access index 8/8 in VECTOR_ELT
── Error ('test-pool_case.R:83:3'): edge case one date_var works ───────────────
<dplyr:::mutate_error/rlang_error/error/condition>
Error in `dplyr::mutate(., result = purrr::pmap(list(.data[["fn_call"]], .data[["src_labs"]], .data[["def_lab"]]), function(x, y, z) { if (getOption("healthdb.verbose")) rlang::inform(paste0("\nActions for definition ", z, " using source ", rlang::expr_deparse(with_data_expr[[y]]), ":\n")) eval(x, envir = with_data_env) }, .progress = TRUE), result = purrr::pmap(list(.data[["result"]], .data[["def_lab"]], .data[["src_labs"]]), function(dat, def, src) { dat %>% dplyr::mutate(def = def, src = src, .before = 1) }))`: i In argument: `result = purrr::pmap(...)`.
Caused by error in `purrr::pmap()`:
i In index: 1.
Caused by error in `[.data.table`:
! attempt access index 8/8 in VECTOR_ELT
── Error ('test-pool_case.R:134:3'): pool multiple def works ───────────────────
<dplyr:::mutate_error/rlang_error/error/condition>
Error in `dplyr::mutate(., result = purrr::pmap(list(.data[["fn_call"]], .data[["src_labs"]], .data[["def_lab"]]), function(x, y, z) { if (getOption("healthdb.verbose")) rlang::inform(paste0("\nActions for definition ", z, " using source ", rlang::expr_deparse(with_data_expr[[y]]), ":\n")) eval(x, envir = with_data_env) }, .progress = TRUE), result = purrr::pmap(list(.data[["result"]], .data[["def_lab"]], .data[["src_labs"]]), function(dat, def, src) { dat %>% dplyr::mutate(def = def, src = src, .before = 1) }))`: i In argument: `result = purrr::pmap(...)`.
Caused by error in `purrr::pmap()`:
i In index: 1.
Caused by error in `[.data.table`:
! attempt access index 8/8 in VECTOR_ELT
[ FAIL 23 | WARN 2 | SKIP 6 | PASS 189 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 0.4.1
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘healthdb.Rmd’ using rmarkdown
Quitting from healthdb.Rmd:251-258 [unnamed-chunk-14]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
NULL
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'healthdb.Rmd' failed with diagnostics:
ℹ In argument: `result = purrr::pmap(...)`.
Caused by error in `purrr::pmap()`:
ℹ In index: 2.
Caused by error in `[.data.table`:
! attempt access index 7/7 in VECTOR_ELT
--- failed re-building ‘healthdb.Rmd’
SUMMARY: processing the following file failed:
‘healthdb.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc
Version: 0.4.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [46s/63s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> library(testthat)
> library(healthdb)
>
> test_check("healthdb")
Saving _problems/test-collapse_episode-7.R
The following records have start > end:
uid clnt_id dates ans diagx diagx_1 diagx_2 end_date
1 3 1 2020-12-19 any d q 999 2020-12-12
2 1 1 2020-12-28 any t v <NA> 2020-12-21
3 5 5 2019-08-29 any d b 999 2019-08-22
4 2 10 2018-10-27 any x d <NA> 2018-10-20
5 13 12 2016-09-06 noise 999 <NA> 999 2016-08-30
6 24 13 2017-07-07 noise 999 999 <NA> 2017-06-30
7 20 16 2017-09-22 noise 999 <NA> <NA> 2017-09-15
8 7 17 2018-03-24 any p h <NA> 2018-03-17
9 16 18 2015-06-04 noise 999 <NA> 999 2015-05-28
10 12 19 2015-09-08 all z w f 2015-09-01
11 11 21 2018-01-24 all c u d 2018-01-17
12 14 21 2018-08-17 noise 999 <NA> <NA> 2018-08-10
13 6 21 2020-08-16 any b <NA> 999 2020-08-09
14 21 22 2016-08-31 noise 999 <NA> <NA> 2016-08-24
15 9 25 2020-11-30 all b h i 2020-11-23
16 18 30 2018-02-22 noise 999 999 999 2018-02-15
17 8 34 2017-02-12 any x b 999 2017-02-05
18 10 34 2018-10-12 all b g r 2018-10-05
19 19 36 2019-04-30 noise 999 999 <NA> 2019-04-23
20 23 38 2016-05-19 noise 999 999 999 2016-05-12
21 15 45 2016-06-27 noise 999 <NA> 999 2016-06-20
22 25 47 2015-04-19 noise 999 999 999 2015-04-12
23 4 47 2017-08-30 any f v <NA> 2017-08-23
24 17 48 2017-02-04 noise 999 <NA> 999 2017-01-28
25 22 50 2015-02-22 noise 999 <NA> 999 2015-02-15
The following records have missing dates:
uid clnt_id dates ans diagx diagx_1 diagx_2 end_date
1 1 39 2017-09-09 any u d 999 NA
> --------------Inclusion step--------------
i Identify records with condition(s):
* where at least one of the diagx, diagx_1, diagx_2 column(s) in each record
* contains a value exactly matched values in set: letters
i To see the final query generated by 'dbplyr', use dplyr::show_query() on the output.
To extract the SQL string, use dbplyr::remote_query().
This message is displayed once per session.
> --------------Exclusion step--------------
i Identify records with condition(s):
* where at least one of the diagx, diagx_1, diagx_2 column(s) in each record
* contains a value exactly matched values in set: c("a", "b")
i Exclude records in `data` through anti_join with `excl` matching on (by argument): "clnt_id"
> --------------No. rows restriction--------------
i Apply restriction that each client must have at least 2 records with distinct dates. Clients/groups which did not met the condition were excluded.
> --------------Time span restriction--------------
Saving _problems/test-define_case-85.R
Saving _problems/test-define_case-94.R
i Exclude a subset of `data` that satisfies condition: ans == "noise"
Check NAs in the result; SQL handles missing value differently compared to R.
i Exclude a subset of `data` that satisfies condition: ans == "noise"
i Consider being explicit about NA, e.g., condition = var == 'val' | is.na(var)
i Exclude a subset of `data` that satisfies condition: ans == "noise"
Check NAs in the result; SQL handles missing value differently compared to R.
i Consider being explicit about NA, e.g., condition = var == 'val' | is.na(var)
Saving _problems/test-execute_def-12.R
Saving _problems/test-execute_def-35.R
Saving _problems/test-execute_def-66.R
Saving _problems/test-execute_def-102.R
Saving _problems/test-identify_rows_dataframe-3.R
Saving _problems/test-identify_rows_dataframe-11.R
Saving _problems/test-identify_rows_dataframe-18.R
Saving _problems/test-identify_rows_dataframe-26.R
Saving _problems/test-identify_rows_dataframe-34.R
Saving _problems/test-identify_rows_dataframe-43.R
Saving _problems/test-identify_rows_dataframe-49.R
Saving _problems/test-identify_rows_dataframe-62.R
Saving _problems/test-identify_rows_dataframe-68.R
Saving _problems/test-identify_rows_dataframe-75.R
Saving _problems/test-if_dates-41.R
Saving _problems/test-pool_case-45.R
Saving _problems/test-pool_case-64.R
Saving _problems/test-pool_case-83.R
Saving _problems/test-pool_case-134.R
[ FAIL 23 | WARN 2 | SKIP 6 | PASS 189 ]
══ Skipped tests (6) ═══════════════════════════════════════════════════════════
• On CRAN (6): 'test-define_case.R:42:3', 'test-if_dates.R:2:3',
'test-if_dates.R:26:3', 'test-if_dates.R:33:3',
'test-restrict_dates_sql.R:26:3', 'test-restrict_dates_sql.R:101:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-collapse_episode.R:7:3'): basic use works ──────────────────────
Error in ``[.data.table`(data, , `:=`(last_end_dt, lapply(.SD, function(x) data.table::shift(x, n = 1, fill = data.table::first(x)))), by = clnt_id_nm, .SDcols = end_dt_nm)`: attempt access index 8/8 in VECTOR_ELT
Backtrace:
▆
1. ├─healthdb::collapse_episode(...) at test-collapse_episode.R:7:3
2. └─healthdb:::collapse_episode.data.frame(...)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-define_case.R:85:48'): keep first/last works on df ─────────────
Error in ``[.data.table`(dt, , `:=`(incl, data.table::`%chin%`(unlist(.SD), matched_vals) %>% combine_fn(na.rm = TRUE)), by = "rid", .SDcols = vars)`: attempt access index 8/8 in VECTOR_ELT
Backtrace:
▆
1. └─base::sapply(...) at test-define_case.R:85:3
2. └─base::lapply(X = X, FUN = FUN, ...)
3. └─healthdb (local) FUN(X[[i]], ...)
4. └─healthdb::define_case(...) at test-define_case.R:85:48
5. ├─base::eval(incl)
6. │ └─base::eval(incl)
7. ├─healthdb::identify_row(...)
8. └─healthdb:::identify_rows.data.frame(...)
9. ├─...[]
10. └─data.table:::`[.data.table`(...)
── Error ('test-define_case.R:94:3'): passing ... works ────────────────────────
Error in ``[.data.table`(dt, , `:=`(incl, data.table::`%chin%`(unlist(.SD), matched_vals) %>% combine_fn(na.rm = TRUE)), by = "rid", .SDcols = vars)`: attempt access index 7/7 in VECTOR_ELT
Backtrace:
▆
1. └─healthdb::define_case(...) at test-define_case.R:94:3
2. ├─base::eval(incl)
3. │ └─base::eval(incl)
4. ├─healthdb::identify_row(...)
5. └─healthdb:::identify_rows.data.frame(...)
6. ├─...[]
7. └─data.table:::`[.data.table`(...)
── Error ('test-execute_def.R:12:3'): basic use works ──────────────────────────
<dplyr:::mutate_error/rlang_error/error/condition>
Error in `dplyr::mutate(., result = purrr::pmap(list(.data[["fn_call"]], .data[["src_labs"]], .data[["def_lab"]]), function(x, y, z) { if (getOption("healthdb.verbose")) rlang::inform(paste0("\nActions for definition ", z, " using source ", rlang::expr_deparse(with_data_expr[[y]]), ":\n")) eval(x, envir = with_data_env) }, .progress = TRUE), result = purrr::pmap(list(.data[["result"]], .data[["def_lab"]], .data[["src_labs"]]), function(dat, def, src) { dat %>% dplyr::mutate(def = def, src = src, .before = 1) }))`: i In argument: `result = purrr::pmap(...)`.
Caused by error in `purrr::pmap()`:
i In index: 2.
Caused by error in `[.data.table`:
! attempt access index 8/8 in VECTOR_ELT
── Error ('test-execute_def.R:35:3'): mixed binding works ──────────────────────
<dplyr:::mutate_error/rlang_error/error/condition>
Error in `dplyr::mutate(., result = purrr::pmap(list(.data[["fn_call"]], .data[["src_labs"]], .data[["def_lab"]]), function(x, y, z) { if (getOption("healthdb.verbose")) rlang::inform(paste0("\nActions for definition ", z, " using source ", rlang::expr_deparse(with_data_expr[[y]]), ":\n")) eval(x, envir = with_data_env) }, .progress = TRUE), result = purrr::pmap(list(.data[["result"]], .data[["def_lab"]], .data[["src_labs"]]), function(dat, def, src) { dat %>% dplyr::mutate(def = def, src = src, .before = 1) }))`: i In argument: `result = purrr::pmap(...)`.
Caused by error in `purrr::pmap()`:
i In index: 2.
Caused by error in `[.data.table`:
! attempt access index 8/8 in VECTOR_ELT
── Error ('test-execute_def.R:66:3'): binding dfs works ────────────────────────
<dplyr:::mutate_error/rlang_error/error/condition>
Error in `dplyr::mutate(., result = purrr::pmap(list(.data[["fn_call"]], .data[["src_labs"]], .data[["def_lab"]]), function(x, y, z) { if (getOption("healthdb.verbose")) rlang::inform(paste0("\nActions for definition ", z, " using source ", rlang::expr_deparse(with_data_expr[[y]]), ":\n")) eval(x, envir = with_data_env) }, .progress = TRUE), result = purrr::pmap(list(.data[["result"]], .data[["def_lab"]], .data[["src_labs"]]), function(dat, def, src) { dat %>% dplyr::mutate(def = def, src = src, .before = 1) }))`: i In argument: `result = purrr::pmap(...)`.
Caused by error in `purrr::pmap()`:
i In index: 1.
Caused by error in `[.data.table`:
! attempt access index 8/8 in VECTOR_ELT
── Error ('test-execute_def.R:102:3'): multiple def works ──────────────────────
<dplyr:::mutate_error/rlang_error/error/condition>
Error in `dplyr::mutate(., result = purrr::pmap(list(.data[["fn_call"]], .data[["src_labs"]], .data[["def_lab"]]), function(x, y, z) { if (getOption("healthdb.verbose")) rlang::inform(paste0("\nActions for definition ", z, " using source ", rlang::expr_deparse(with_data_expr[[y]]), ":\n")) eval(x, envir = with_data_env) }, .progress = TRUE), result = purrr::pmap(list(.data[["result"]], .data[["def_lab"]], .data[["src_labs"]]), function(dat, def, src) { dat %>% dplyr::mutate(def = def, src = src, .before = 1) }))`: i In argument: `result = purrr::pmap(...)`.
Caused by error in `purrr::pmap()`:
i In index: 1.
Caused by error in `[.data.table`:
! attempt access index 8/8 in VECTOR_ELT
── Error ('test-identify_rows_dataframe.R:3:3'): match by in works ─────────────
Error in ``[.data.table`(dt, , `:=`(incl, data.table::`%chin%`(unlist(.SD), matched_vals) %>% combine_fn(na.rm = TRUE)), by = "rid", .SDcols = vars)`: attempt access index 8/8 in VECTOR_ELT
Backtrace:
▆
1. ├─healthdb:::identify_rows(df, starts_with("diagx"), "in", letters) at test-identify_rows_dataframe.R:3:3
2. └─healthdb:::identify_rows.data.frame(...)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-identify_rows_dataframe.R:11:3'): if_all works ─────────────────
Error in ``[.data.table`(dt, , `:=`(incl, data.table::`%chin%`(unlist(.SD), matched_vals) %>% combine_fn(na.rm = TRUE)), by = "rid", .SDcols = vars)`: attempt access index 8/8 in VECTOR_ELT
Backtrace:
▆
1. ├─healthdb:::identify_rows(...) at test-identify_rows_dataframe.R:11:3
2. └─healthdb:::identify_rows.data.frame(...)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-identify_rows_dataframe.R:18:3'): match by start works ─────────
Error in ``[.data.table`(dt, , `:=`(incl, data.table::`%chin%`(unlist(.SD), matched_vals) %>% combine_fn(na.rm = TRUE)), by = "rid", .SDcols = vars)`: attempt access index 8/8 in VECTOR_ELT
Backtrace:
▆
1. ├─healthdb:::identify_rows(df, starts_with("diagx"), "start", start) at test-identify_rows_dataframe.R:18:3
2. └─healthdb:::identify_rows.data.frame(...)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-identify_rows_dataframe.R:26:3'): match by like works ──────────
Error in ``[.data.table`(dt, , `:=`(incl, data.table::`%chin%`(unlist(.SD), matched_vals) %>% combine_fn(na.rm = TRUE)), by = "rid", .SDcols = vars)`: attempt access index 8/8 in VECTOR_ELT
Backtrace:
▆
1. ├─healthdb:::identify_rows(df, starts_with("diagx"), "like", pattern) at test-identify_rows_dataframe.R:26:3
2. └─healthdb:::identify_rows.data.frame(...)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-identify_rows_dataframe.R:34:3'): match by regex works ─────────
Error in ``[.data.table`(dt, , `:=`(incl, data.table::`%chin%`(unlist(.SD), matched_vals) %>% combine_fn(na.rm = TRUE)), by = "rid", .SDcols = vars)`: attempt access index 8/8 in VECTOR_ELT
Backtrace:
▆
1. ├─healthdb:::identify_rows(df, starts_with("diagx"), "regex", pattern) at test-identify_rows_dataframe.R:34:3
2. └─healthdb:::identify_rows.data.frame(...)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-identify_rows_dataframe.R:43:3'): match by between works ───────
Error in ``[.data.table`(dt, , `:=`(incl, unlist(.SD) %in% matched_vals %>% combine_fn(na.rm = TRUE)), by = "rid", .SDcols = vars)`: attempt access index 8/8 in VECTOR_ELT
Backtrace:
▆
1. ├─healthdb:::identify_rows(df, dates, "between", seq_range) at test-identify_rows_dataframe.R:43:3
2. └─healthdb:::identify_rows.data.frame(df, dates, "between", seq_range)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-identify_rows_dataframe.R:49:3'): type conflict warning works ──
Error in ``[.data.table`(dt, , `:=`(incl, unlist(.SD) %in% matched_vals %>% combine_fn(na.rm = TRUE)), by = "rid", .SDcols = vars)`: attempt access index 8/8 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_warning(...) at test-identify_rows_dataframe.R:49:3
2. │ └─testthat:::expect_condition_matching_(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─healthdb:::identify_rows(df, starts_with("diagx"), "in", 1:10)
8. └─healthdb:::identify_rows.data.frame(...)
9. ├─...[]
10. └─data.table:::`[.data.table`(...)
── Error ('test-identify_rows_dataframe.R:56:3'): summary of numeric vals works ──
Error in ``[.data.table`(dt, , `:=`(incl, unlist(.SD) %in% matched_vals %>% combine_fn(na.rm = TRUE)), by = "rid", .SDcols = vars)`: attempt access index 7/7 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_output(...) at test-identify_rows_dataframe.R:56:3
2. │ └─testthat:::quasi_capture(...)
3. │ ├─testthat (local) .capture(...)
4. │ │ └─testthat::capture_output_lines(code, print, width = width)
5. │ │ └─testthat:::eval_with_output(code, print = print, width = width)
6. │ │ ├─withr::with_output_sink(path, withVisible(code))
7. │ │ │ └─base::force(code)
8. │ │ └─base::withVisible(code)
9. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
10. ├─healthdb:::identify_rows(...)
11. └─healthdb:::identify_rows.data.frame(...)
12. ├─...[]
13. └─data.table:::`[.data.table`(...)
── Error ('test-identify_rows_dataframe.R:62:3'): edge case - character vars works ──
Error in ``[.data.table`(dt, , `:=`(incl, data.table::`%chin%`(unlist(.SD), matched_vals) %>% combine_fn(na.rm = TRUE)), by = "rid", .SDcols = vars)`: attempt access index 8/8 in VECTOR_ELT
Backtrace:
▆
1. ├─healthdb:::identify_rows(df, any_of(var_nm), "in", letters) at test-identify_rows_dataframe.R:62:3
2. └─healthdb:::identify_rows.data.frame(...)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-identify_rows_dataframe.R:68:3'): edge case - unquoted vars works ──
Error in ``[.data.table`(dt, , `:=`(incl, data.table::`%chin%`(unlist(.SD), matched_vals) %>% combine_fn(na.rm = TRUE)), by = "rid", .SDcols = vars)`: attempt access index 8/8 in VECTOR_ELT
Backtrace:
▆
1. ├─healthdb:::identify_rows(...) at test-identify_rows_dataframe.R:68:3
2. └─healthdb:::identify_rows.data.frame(...)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-identify_rows_dataframe.R:75:3'): edge case - vals in an external vector works ──
Error in ``[.data.table`(dt, , `:=`(incl, data.table::`%chin%`(unlist(.SD), matched_vals) %>% combine_fn(na.rm = TRUE)), by = "rid", .SDcols = vars)`: attempt access index 8/8 in VECTOR_ELT
Backtrace:
▆
1. ├─healthdb:::identify_rows(...) at test-identify_rows_dataframe.R:75:3
2. └─healthdb:::identify_rows.data.frame(...)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-if_dates.R:41:3'): straight false due to no gap < within works ──
Error in ``[.data.table`(overlap, , `:=`(N, .N), by = period_id)`: attempt access index 4/4 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_false(if_dates(dates, 2, apart = 7, within = 30)) at test-if_dates.R:41:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─healthdb:::if_dates(dates, 2, apart = 7, within = 30)
5. ├─overlap[, `:=`(N, .N), by = period_id]
6. └─data.table:::`[.data.table`(overlap, , `:=`(N, .N), by = period_id)
── Error ('test-pool_case.R:45:3'): pool mixed works ───────────────────────────
<dplyr:::mutate_error/rlang_error/error/condition>
Error in `dplyr::mutate(., result = purrr::pmap(list(.data[["fn_call"]], .data[["src_labs"]], .data[["def_lab"]]), function(x, y, z) { if (getOption("healthdb.verbose")) rlang::inform(paste0("\nActions for definition ", z, " using source ", rlang::expr_deparse(with_data_expr[[y]]), ":\n")) eval(x, envir = with_data_env) }, .progress = TRUE), result = purrr::pmap(list(.data[["result"]], .data[["def_lab"]], .data[["src_labs"]]), function(dat, def, src) { dat %>% dplyr::mutate(def = def, src = src, .before = 1) }))`: i In argument: `result = purrr::pmap(...)`.
Caused by error in `purrr::pmap()`:
i In index: 1.
Caused by error in `[.data.table`:
! attempt access index 8/8 in VECTOR_ELT
── Error ('test-pool_case.R:64:3'): edge case no date_var works ────────────────
<dplyr:::mutate_error/rlang_error/error/condition>
Error in `dplyr::mutate(., result = purrr::pmap(list(.data[["fn_call"]], .data[["src_labs"]], .data[["def_lab"]]), function(x, y, z) { if (getOption("healthdb.verbose")) rlang::inform(paste0("\nActions for definition ", z, " using source ", rlang::expr_deparse(with_data_expr[[y]]), ":\n")) eval(x, envir = with_data_env) }, .progress = TRUE), result = purrr::pmap(list(.data[["result"]], .data[["def_lab"]], .data[["src_labs"]]), function(dat, def, src) { dat %>% dplyr::mutate(def = def, src = src, .before = 1) }))`: i In argument: `result = purrr::pmap(...)`.
Caused by error in `purrr::pmap()`:
i In index: 1.
Caused by error in `[.data.table`:
! attempt access index 8/8 in VECTOR_ELT
── Error ('test-pool_case.R:83:3'): edge case one date_var works ───────────────
<dplyr:::mutate_error/rlang_error/error/condition>
Error in `dplyr::mutate(., result = purrr::pmap(list(.data[["fn_call"]], .data[["src_labs"]], .data[["def_lab"]]), function(x, y, z) { if (getOption("healthdb.verbose")) rlang::inform(paste0("\nActions for definition ", z, " using source ", rlang::expr_deparse(with_data_expr[[y]]), ":\n")) eval(x, envir = with_data_env) }, .progress = TRUE), result = purrr::pmap(list(.data[["result"]], .data[["def_lab"]], .data[["src_labs"]]), function(dat, def, src) { dat %>% dplyr::mutate(def = def, src = src, .before = 1) }))`: i In argument: `result = purrr::pmap(...)`.
Caused by error in `purrr::pmap()`:
i In index: 1.
Caused by error in `[.data.table`:
! attempt access index 8/8 in VECTOR_ELT
── Error ('test-pool_case.R:134:3'): pool multiple def works ───────────────────
<dplyr:::mutate_error/rlang_error/error/condition>
Error in `dplyr::mutate(., result = purrr::pmap(list(.data[["fn_call"]], .data[["src_labs"]], .data[["def_lab"]]), function(x, y, z) { if (getOption("healthdb.verbose")) rlang::inform(paste0("\nActions for definition ", z, " using source ", rlang::expr_deparse(with_data_expr[[y]]), ":\n")) eval(x, envir = with_data_env) }, .progress = TRUE), result = purrr::pmap(list(.data[["result"]], .data[["def_lab"]], .data[["src_labs"]]), function(dat, def, src) { dat %>% dplyr::mutate(def = def, src = src, .before = 1) }))`: i In argument: `result = purrr::pmap(...)`.
Caused by error in `purrr::pmap()`:
i In index: 1.
Caused by error in `[.data.table`:
! attempt access index 8/8 in VECTOR_ELT
[ FAIL 23 | WARN 2 | SKIP 6 | PASS 189 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.4.1
Check: examples
Result: ERROR
Running examples in ‘healthdb-Ex.R’ failed
The error most likely occurred in:
> ### Name: collapse_episode
> ### Title: Group records no more than n days apart as episodes
> ### Aliases: collapse_episode
>
> ### ** Examples
>
> # make toy data
> df <- make_test_dat() %>%
+ dplyr::select(clnt_id, dates)
>
> head(df)
clnt_id dates
1 1 2015-10-08
2 1 2017-10-23
3 2 2018-11-08
4 3 2015-08-07
5 4 2016-07-21
6 4 2016-11-06
>
> # collapse records no more than 90 days apart
> # end_dt could be absent then it is assumed to be the same as start_dt
> collapse_episode(df, clnt_id, start_dt = dates, gap = 90)
Error in `[.data.table`(data, , `:=`(last_end_dt, lapply(.SD, function(x) data.table::shift(x, :
attempt access index 3/3 in VECTOR_ELT
Calls: collapse_episode -> collapse_episode.data.frame -> [ -> [.data.table
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 0.4.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [103s/181s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> library(testthat)
> library(healthdb)
>
> test_check("healthdb")
Saving _problems/test-collapse_episode-7.R
The following records have start > end:
uid clnt_id dates ans diagx diagx_1 diagx_2 end_date
1 3 1 2020-12-19 any d q 999 2020-12-12
2 1 1 2020-12-28 any t v <NA> 2020-12-21
3 5 5 2019-08-29 any d b 999 2019-08-22
4 2 10 2018-10-27 any x d <NA> 2018-10-20
5 13 12 2016-09-06 noise 999 <NA> 999 2016-08-30
6 24 13 2017-07-07 noise 999 999 <NA> 2017-06-30
7 20 16 2017-09-22 noise 999 <NA> <NA> 2017-09-15
8 7 17 2018-03-24 any p h <NA> 2018-03-17
9 16 18 2015-06-04 noise 999 <NA> 999 2015-05-28
10 12 19 2015-09-08 all z w f 2015-09-01
11 11 21 2018-01-24 all c u d 2018-01-17
12 14 21 2018-08-17 noise 999 <NA> <NA> 2018-08-10
13 6 21 2020-08-16 any b <NA> 999 2020-08-09
14 21 22 2016-08-31 noise 999 <NA> <NA> 2016-08-24
15 9 25 2020-11-30 all b h i 2020-11-23
16 18 30 2018-02-22 noise 999 999 999 2018-02-15
17 8 34 2017-02-12 any x b 999 2017-02-05
18 10 34 2018-10-12 all b g r 2018-10-05
19 19 36 2019-04-30 noise 999 999 <NA> 2019-04-23
20 23 38 2016-05-19 noise 999 999 999 2016-05-12
21 15 45 2016-06-27 noise 999 <NA> 999 2016-06-20
22 25 47 2015-04-19 noise 999 999 999 2015-04-12
23 4 47 2017-08-30 any f v <NA> 2017-08-23
24 17 48 2017-02-04 noise 999 <NA> 999 2017-01-28
25 22 50 2015-02-22 noise 999 <NA> 999 2015-02-15
The following records have missing dates:
uid clnt_id dates ans diagx diagx_1 diagx_2 end_date
1 1 39 2017-09-09 any u d 999 NA
> --------------Inclusion step--------------
i Identify records with condition(s):
* where at least one of the diagx, diagx_1, diagx_2 column(s) in each record
* contains a value exactly matched values in set: letters
i To see the final query generated by 'dbplyr', use dplyr::show_query() on the output.
To extract the SQL string, use dbplyr::remote_query().
This message is displayed once per session.
> --------------Exclusion step--------------
i Identify records with condition(s):
* where at least one of the diagx, diagx_1, diagx_2 column(s) in each record
* contains a value exactly matched values in set: c("a", "b")
i Exclude records in `data` through anti_join with `excl` matching on (by argument): "clnt_id"
> --------------No. rows restriction--------------
i Apply restriction that each client must have at least 2 records with distinct dates. Clients/groups which did not met the condition were excluded.
> --------------Time span restriction--------------
Saving _problems/test-define_case-85.R
Saving _problems/test-define_case-94.R
i Exclude a subset of `data` that satisfies condition: ans == "noise"
Check NAs in the result; SQL handles missing value differently compared to R.
i Exclude a subset of `data` that satisfies condition: ans == "noise"
i Consider being explicit about NA, e.g., condition = var == 'val' | is.na(var)
i Exclude a subset of `data` that satisfies condition: ans == "noise"
Check NAs in the result; SQL handles missing value differently compared to R.
i Consider being explicit about NA, e.g., condition = var == 'val' | is.na(var)
Saving _problems/test-execute_def-12.R
===============>--------------- 50% | ETA: 1s
Saving _problems/test-execute_def-35.R
===============>--------------- 50% | ETA: 2s
Saving _problems/test-execute_def-66.R
Saving _problems/test-execute_def-102.R
Saving _problems/test-identify_rows_dataframe-3.R
Saving _problems/test-identify_rows_dataframe-11.R
Saving _problems/test-identify_rows_dataframe-18.R
Saving _problems/test-identify_rows_dataframe-26.R
Saving _problems/test-identify_rows_dataframe-34.R
Saving _problems/test-identify_rows_dataframe-43.R
Saving _problems/test-identify_rows_dataframe-49.R
Saving _problems/test-identify_rows_dataframe-62.R
Saving _problems/test-identify_rows_dataframe-68.R
Saving _problems/test-identify_rows_dataframe-75.R
Saving _problems/test-if_dates-41.R
Saving _problems/test-pool_case-45.R
Saving _problems/test-pool_case-64.R
Saving _problems/test-pool_case-83.R
Saving _problems/test-pool_case-134.R
[ FAIL 23 | WARN 2 | SKIP 6 | PASS 189 ]
══ Skipped tests (6) ═══════════════════════════════════════════════════════════
• On CRAN (6): 'test-define_case.R:42:3', 'test-if_dates.R:2:3',
'test-if_dates.R:26:3', 'test-if_dates.R:33:3',
'test-restrict_dates_sql.R:26:3', 'test-restrict_dates_sql.R:101:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-collapse_episode.R:7:3'): basic use works ──────────────────────
Error in ``[.data.table`(data, , `:=`(last_end_dt, lapply(.SD, function(x) data.table::shift(x, n = 1, fill = data.table::first(x)))), by = clnt_id_nm, .SDcols = end_dt_nm)`: attempt access index 8/8 in VECTOR_ELT
Backtrace:
▆
1. ├─healthdb::collapse_episode(...) at test-collapse_episode.R:7:3
2. └─healthdb:::collapse_episode.data.frame(...)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-define_case.R:85:48'): keep first/last works on df ─────────────
Error in ``[.data.table`(dt, , `:=`(incl, data.table::`%chin%`(unlist(.SD), matched_vals) %>% combine_fn(na.rm = TRUE)), by = "rid", .SDcols = vars)`: attempt access index 8/8 in VECTOR_ELT
Backtrace:
▆
1. └─base::sapply(...) at test-define_case.R:85:3
2. └─base::lapply(X = X, FUN = FUN, ...)
3. └─healthdb (local) FUN(X[[i]], ...)
4. └─healthdb::define_case(...) at test-define_case.R:85:48
5. ├─base::eval(incl)
6. │ └─base::eval(incl)
7. ├─healthdb::identify_row(...)
8. └─healthdb:::identify_rows.data.frame(...)
9. ├─...[]
10. └─data.table:::`[.data.table`(...)
── Error ('test-define_case.R:94:3'): passing ... works ────────────────────────
Error in ``[.data.table`(dt, , `:=`(incl, data.table::`%chin%`(unlist(.SD), matched_vals) %>% combine_fn(na.rm = TRUE)), by = "rid", .SDcols = vars)`: attempt access index 7/7 in VECTOR_ELT
Backtrace:
▆
1. └─healthdb::define_case(...) at test-define_case.R:94:3
2. ├─base::eval(incl)
3. │ └─base::eval(incl)
4. ├─healthdb::identify_row(...)
5. └─healthdb:::identify_rows.data.frame(...)
6. ├─...[]
7. └─data.table:::`[.data.table`(...)
── Error ('test-execute_def.R:12:3'): basic use works ──────────────────────────
<dplyr:::mutate_error/rlang_error/error/condition>
Error in `dplyr::mutate(., result = purrr::pmap(list(.data[["fn_call"]], .data[["src_labs"]], .data[["def_lab"]]), function(x, y, z) { if (getOption("healthdb.verbose")) rlang::inform(paste0("\nActions for definition ", z, " using source ", rlang::expr_deparse(with_data_expr[[y]]), ":\n")) eval(x, envir = with_data_env) }, .progress = TRUE), result = purrr::pmap(list(.data[["result"]], .data[["def_lab"]], .data[["src_labs"]]), function(dat, def, src) { dat %>% dplyr::mutate(def = def, src = src, .before = 1) }))`: i In argument: `result = purrr::pmap(...)`.
Caused by error in `purrr::pmap()`:
i In index: 2.
Caused by error in `[.data.table`:
! attempt access index 8/8 in VECTOR_ELT
── Error ('test-execute_def.R:35:3'): mixed binding works ──────────────────────
<dplyr:::mutate_error/rlang_error/error/condition>
Error in `dplyr::mutate(., result = purrr::pmap(list(.data[["fn_call"]], .data[["src_labs"]], .data[["def_lab"]]), function(x, y, z) { if (getOption("healthdb.verbose")) rlang::inform(paste0("\nActions for definition ", z, " using source ", rlang::expr_deparse(with_data_expr[[y]]), ":\n")) eval(x, envir = with_data_env) }, .progress = TRUE), result = purrr::pmap(list(.data[["result"]], .data[["def_lab"]], .data[["src_labs"]]), function(dat, def, src) { dat %>% dplyr::mutate(def = def, src = src, .before = 1) }))`: i In argument: `result = purrr::pmap(...)`.
Caused by error in `purrr::pmap()`:
i In index: 2.
Caused by error in `[.data.table`:
! attempt access index 8/8 in VECTOR_ELT
── Error ('test-execute_def.R:66:3'): binding dfs works ────────────────────────
<dplyr:::mutate_error/rlang_error/error/condition>
Error in `dplyr::mutate(., result = purrr::pmap(list(.data[["fn_call"]], .data[["src_labs"]], .data[["def_lab"]]), function(x, y, z) { if (getOption("healthdb.verbose")) rlang::inform(paste0("\nActions for definition ", z, " using source ", rlang::expr_deparse(with_data_expr[[y]]), ":\n")) eval(x, envir = with_data_env) }, .progress = TRUE), result = purrr::pmap(list(.data[["result"]], .data[["def_lab"]], .data[["src_labs"]]), function(dat, def, src) { dat %>% dplyr::mutate(def = def, src = src, .before = 1) }))`: i In argument: `result = purrr::pmap(...)`.
Caused by error in `purrr::pmap()`:
i In index: 1.
Caused by error in `[.data.table`:
! attempt access index 8/8 in VECTOR_ELT
── Error ('test-execute_def.R:102:3'): multiple def works ──────────────────────
<dplyr:::mutate_error/rlang_error/error/condition>
Error in `dplyr::mutate(., result = purrr::pmap(list(.data[["fn_call"]], .data[["src_labs"]], .data[["def_lab"]]), function(x, y, z) { if (getOption("healthdb.verbose")) rlang::inform(paste0("\nActions for definition ", z, " using source ", rlang::expr_deparse(with_data_expr[[y]]), ":\n")) eval(x, envir = with_data_env) }, .progress = TRUE), result = purrr::pmap(list(.data[["result"]], .data[["def_lab"]], .data[["src_labs"]]), function(dat, def, src) { dat %>% dplyr::mutate(def = def, src = src, .before = 1) }))`: i In argument: `result = purrr::pmap(...)`.
Caused by error in `purrr::pmap()`:
i In index: 1.
Caused by error in `[.data.table`:
! attempt access index 8/8 in VECTOR_ELT
── Error ('test-identify_rows_dataframe.R:3:3'): match by in works ─────────────
Error in ``[.data.table`(dt, , `:=`(incl, data.table::`%chin%`(unlist(.SD), matched_vals) %>% combine_fn(na.rm = TRUE)), by = "rid", .SDcols = vars)`: attempt access index 8/8 in VECTOR_ELT
Backtrace:
▆
1. ├─healthdb:::identify_rows(df, starts_with("diagx"), "in", letters) at test-identify_rows_dataframe.R:3:3
2. └─healthdb:::identify_rows.data.frame(...)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-identify_rows_dataframe.R:11:3'): if_all works ─────────────────
Error in ``[.data.table`(dt, , `:=`(incl, data.table::`%chin%`(unlist(.SD), matched_vals) %>% combine_fn(na.rm = TRUE)), by = "rid", .SDcols = vars)`: attempt access index 8/8 in VECTOR_ELT
Backtrace:
▆
1. ├─healthdb:::identify_rows(...) at test-identify_rows_dataframe.R:11:3
2. └─healthdb:::identify_rows.data.frame(...)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-identify_rows_dataframe.R:18:3'): match by start works ─────────
Error in ``[.data.table`(dt, , `:=`(incl, data.table::`%chin%`(unlist(.SD), matched_vals) %>% combine_fn(na.rm = TRUE)), by = "rid", .SDcols = vars)`: attempt access index 8/8 in VECTOR_ELT
Backtrace:
▆
1. ├─healthdb:::identify_rows(df, starts_with("diagx"), "start", start) at test-identify_rows_dataframe.R:18:3
2. └─healthdb:::identify_rows.data.frame(...)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-identify_rows_dataframe.R:26:3'): match by like works ──────────
Error in ``[.data.table`(dt, , `:=`(incl, data.table::`%chin%`(unlist(.SD), matched_vals) %>% combine_fn(na.rm = TRUE)), by = "rid", .SDcols = vars)`: attempt access index 8/8 in VECTOR_ELT
Backtrace:
▆
1. ├─healthdb:::identify_rows(df, starts_with("diagx"), "like", pattern) at test-identify_rows_dataframe.R:26:3
2. └─healthdb:::identify_rows.data.frame(...)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-identify_rows_dataframe.R:34:3'): match by regex works ─────────
Error in ``[.data.table`(dt, , `:=`(incl, data.table::`%chin%`(unlist(.SD), matched_vals) %>% combine_fn(na.rm = TRUE)), by = "rid", .SDcols = vars)`: attempt access index 8/8 in VECTOR_ELT
Backtrace:
▆
1. ├─healthdb:::identify_rows(df, starts_with("diagx"), "regex", pattern) at test-identify_rows_dataframe.R:34:3
2. └─healthdb:::identify_rows.data.frame(...)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-identify_rows_dataframe.R:43:3'): match by between works ───────
Error in ``[.data.table`(dt, , `:=`(incl, unlist(.SD) %in% matched_vals %>% combine_fn(na.rm = TRUE)), by = "rid", .SDcols = vars)`: attempt access index 8/8 in VECTOR_ELT
Backtrace:
▆
1. ├─healthdb:::identify_rows(df, dates, "between", seq_range) at test-identify_rows_dataframe.R:43:3
2. └─healthdb:::identify_rows.data.frame(df, dates, "between", seq_range)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-identify_rows_dataframe.R:49:3'): type conflict warning works ──
Error in ``[.data.table`(dt, , `:=`(incl, unlist(.SD) %in% matched_vals %>% combine_fn(na.rm = TRUE)), by = "rid", .SDcols = vars)`: attempt access index 8/8 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_warning(...) at test-identify_rows_dataframe.R:49:3
2. │ └─testthat:::expect_condition_matching_(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─healthdb:::identify_rows(df, starts_with("diagx"), "in", 1:10)
8. └─healthdb:::identify_rows.data.frame(...)
9. ├─...[]
10. └─data.table:::`[.data.table`(...)
── Error ('test-identify_rows_dataframe.R:56:3'): summary of numeric vals works ──
Error in ``[.data.table`(dt, , `:=`(incl, unlist(.SD) %in% matched_vals %>% combine_fn(na.rm = TRUE)), by = "rid", .SDcols = vars)`: attempt access index 7/7 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_output(...) at test-identify_rows_dataframe.R:56:3
2. │ └─testthat:::quasi_capture(...)
3. │ ├─testthat (local) .capture(...)
4. │ │ └─testthat::capture_output_lines(code, print, width = width)
5. │ │ └─testthat:::eval_with_output(code, print = print, width = width)
6. │ │ ├─withr::with_output_sink(path, withVisible(code))
7. │ │ │ └─base::force(code)
8. │ │ └─base::withVisible(code)
9. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
10. ├─healthdb:::identify_rows(...)
11. └─healthdb:::identify_rows.data.frame(...)
12. ├─...[]
13. └─data.table:::`[.data.table`(...)
── Error ('test-identify_rows_dataframe.R:62:3'): edge case - character vars works ──
Error in ``[.data.table`(dt, , `:=`(incl, data.table::`%chin%`(unlist(.SD), matched_vals) %>% combine_fn(na.rm = TRUE)), by = "rid", .SDcols = vars)`: attempt access index 8/8 in VECTOR_ELT
Backtrace:
▆
1. ├─healthdb:::identify_rows(df, any_of(var_nm), "in", letters) at test-identify_rows_dataframe.R:62:3
2. └─healthdb:::identify_rows.data.frame(...)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-identify_rows_dataframe.R:68:3'): edge case - unquoted vars works ──
Error in ``[.data.table`(dt, , `:=`(incl, data.table::`%chin%`(unlist(.SD), matched_vals) %>% combine_fn(na.rm = TRUE)), by = "rid", .SDcols = vars)`: attempt access index 8/8 in VECTOR_ELT
Backtrace:
▆
1. ├─healthdb:::identify_rows(...) at test-identify_rows_dataframe.R:68:3
2. └─healthdb:::identify_rows.data.frame(...)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-identify_rows_dataframe.R:75:3'): edge case - vals in an external vector works ──
Error in ``[.data.table`(dt, , `:=`(incl, data.table::`%chin%`(unlist(.SD), matched_vals) %>% combine_fn(na.rm = TRUE)), by = "rid", .SDcols = vars)`: attempt access index 8/8 in VECTOR_ELT
Backtrace:
▆
1. ├─healthdb:::identify_rows(...) at test-identify_rows_dataframe.R:75:3
2. └─healthdb:::identify_rows.data.frame(...)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-if_dates.R:41:3'): straight false due to no gap < within works ──
Error in ``[.data.table`(overlap, , `:=`(N, .N), by = period_id)`: attempt access index 4/4 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_false(if_dates(dates, 2, apart = 7, within = 30)) at test-if_dates.R:41:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─healthdb:::if_dates(dates, 2, apart = 7, within = 30)
5. ├─overlap[, `:=`(N, .N), by = period_id]
6. └─data.table:::`[.data.table`(overlap, , `:=`(N, .N), by = period_id)
── Error ('test-pool_case.R:45:3'): pool mixed works ───────────────────────────
<dplyr:::mutate_error/rlang_error/error/condition>
Error in `dplyr::mutate(., result = purrr::pmap(list(.data[["fn_call"]], .data[["src_labs"]], .data[["def_lab"]]), function(x, y, z) { if (getOption("healthdb.verbose")) rlang::inform(paste0("\nActions for definition ", z, " using source ", rlang::expr_deparse(with_data_expr[[y]]), ":\n")) eval(x, envir = with_data_env) }, .progress = TRUE), result = purrr::pmap(list(.data[["result"]], .data[["def_lab"]], .data[["src_labs"]]), function(dat, def, src) { dat %>% dplyr::mutate(def = def, src = src, .before = 1) }))`: i In argument: `result = purrr::pmap(...)`.
Caused by error in `purrr::pmap()`:
i In index: 1.
Caused by error in `[.data.table`:
! attempt access index 8/8 in VECTOR_ELT
── Error ('test-pool_case.R:64:3'): edge case no date_var works ────────────────
<dplyr:::mutate_error/rlang_error/error/condition>
Error in `dplyr::mutate(., result = purrr::pmap(list(.data[["fn_call"]], .data[["src_labs"]], .data[["def_lab"]]), function(x, y, z) { if (getOption("healthdb.verbose")) rlang::inform(paste0("\nActions for definition ", z, " using source ", rlang::expr_deparse(with_data_expr[[y]]), ":\n")) eval(x, envir = with_data_env) }, .progress = TRUE), result = purrr::pmap(list(.data[["result"]], .data[["def_lab"]], .data[["src_labs"]]), function(dat, def, src) { dat %>% dplyr::mutate(def = def, src = src, .before = 1) }))`: i In argument: `result = purrr::pmap(...)`.
Caused by error in `purrr::pmap()`:
i In index: 1.
Caused by error in `[.data.table`:
! attempt access index 8/8 in VECTOR_ELT
── Error ('test-pool_case.R:83:3'): edge case one date_var works ───────────────
<dplyr:::mutate_error/rlang_error/error/condition>
Error in `dplyr::mutate(., result = purrr::pmap(list(.data[["fn_call"]], .data[["src_labs"]], .data[["def_lab"]]), function(x, y, z) { if (getOption("healthdb.verbose")) rlang::inform(paste0("\nActions for definition ", z, " using source ", rlang::expr_deparse(with_data_expr[[y]]), ":\n")) eval(x, envir = with_data_env) }, .progress = TRUE), result = purrr::pmap(list(.data[["result"]], .data[["def_lab"]], .data[["src_labs"]]), function(dat, def, src) { dat %>% dplyr::mutate(def = def, src = src, .before = 1) }))`: i In argument: `result = purrr::pmap(...)`.
Caused by error in `purrr::pmap()`:
i In index: 1.
Caused by error in `[.data.table`:
! attempt access index 8/8 in VECTOR_ELT
── Error ('test-pool_case.R:134:3'): pool multiple def works ───────────────────
<dplyr:::mutate_error/rlang_error/error/condition>
Error in `dplyr::mutate(., result = purrr::pmap(list(.data[["fn_call"]], .data[["src_labs"]], .data[["def_lab"]]), function(x, y, z) { if (getOption("healthdb.verbose")) rlang::inform(paste0("\nActions for definition ", z, " using source ", rlang::expr_deparse(with_data_expr[[y]]), ":\n")) eval(x, envir = with_data_env) }, .progress = TRUE), result = purrr::pmap(list(.data[["result"]], .data[["def_lab"]], .data[["src_labs"]]), function(dat, def, src) { dat %>% dplyr::mutate(def = def, src = src, .before = 1) }))`: i In argument: `result = purrr::pmap(...)`.
Caused by error in `purrr::pmap()`:
i In index: 1.
Caused by error in `[.data.table`:
! attempt access index 8/8 in VECTOR_ELT
[ FAIL 23 | WARN 2 | SKIP 6 | PASS 189 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.4.1
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘healthdb.Rmd’ using rmarkdown
Quitting from healthdb.Rmd:251-258 [unnamed-chunk-14]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
NULL
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'healthdb.Rmd' failed with diagnostics:
ℹ In argument: `result = purrr::pmap(...)`.
Caused by error in `purrr::pmap()`:
ℹ In index: 2.
Caused by error in `[.data.table`:
! attempt access index 7/7 in VECTOR_ELT
--- failed re-building ‘healthdb.Rmd’
SUMMARY: processing the following file failed:
‘healthdb.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 0.4.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [98s/161s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> library(testthat)
> library(healthdb)
>
> test_check("healthdb")
Saving _problems/test-collapse_episode-7.R
The following records have start > end:
uid clnt_id dates ans diagx diagx_1 diagx_2 end_date
1 3 1 2020-12-19 any d q 999 2020-12-12
2 1 1 2020-12-28 any t v <NA> 2020-12-21
3 5 5 2019-08-29 any d b 999 2019-08-22
4 2 10 2018-10-27 any x d <NA> 2018-10-20
5 13 12 2016-09-06 noise 999 <NA> 999 2016-08-30
6 24 13 2017-07-07 noise 999 999 <NA> 2017-06-30
7 20 16 2017-09-22 noise 999 <NA> <NA> 2017-09-15
8 7 17 2018-03-24 any p h <NA> 2018-03-17
9 16 18 2015-06-04 noise 999 <NA> 999 2015-05-28
10 12 19 2015-09-08 all z w f 2015-09-01
11 11 21 2018-01-24 all c u d 2018-01-17
12 14 21 2018-08-17 noise 999 <NA> <NA> 2018-08-10
13 6 21 2020-08-16 any b <NA> 999 2020-08-09
14 21 22 2016-08-31 noise 999 <NA> <NA> 2016-08-24
15 9 25 2020-11-30 all b h i 2020-11-23
16 18 30 2018-02-22 noise 999 999 999 2018-02-15
17 8 34 2017-02-12 any x b 999 2017-02-05
18 10 34 2018-10-12 all b g r 2018-10-05
19 19 36 2019-04-30 noise 999 999 <NA> 2019-04-23
20 23 38 2016-05-19 noise 999 999 999 2016-05-12
21 15 45 2016-06-27 noise 999 <NA> 999 2016-06-20
22 25 47 2015-04-19 noise 999 999 999 2015-04-12
23 4 47 2017-08-30 any f v <NA> 2017-08-23
24 17 48 2017-02-04 noise 999 <NA> 999 2017-01-28
25 22 50 2015-02-22 noise 999 <NA> 999 2015-02-15
The following records have missing dates:
uid clnt_id dates ans diagx diagx_1 diagx_2 end_date
1 1 39 2017-09-09 any u d 999 NA
> --------------Inclusion step--------------
i Identify records with condition(s):
* where at least one of the diagx, diagx_1, diagx_2 column(s) in each record
* contains a value exactly matched values in set: letters
i To see the final query generated by 'dbplyr', use dplyr::show_query() on the output.
To extract the SQL string, use dbplyr::remote_query().
This message is displayed once per session.
> --------------Exclusion step--------------
i Identify records with condition(s):
* where at least one of the diagx, diagx_1, diagx_2 column(s) in each record
* contains a value exactly matched values in set: c("a", "b")
i Exclude records in `data` through anti_join with `excl` matching on (by argument): "clnt_id"
> --------------No. rows restriction--------------
i Apply restriction that each client must have at least 2 records with distinct dates. Clients/groups which did not met the condition were excluded.
> --------------Time span restriction--------------
Saving _problems/test-define_case-85.R
Saving _problems/test-define_case-94.R
i Exclude a subset of `data` that satisfies condition: ans == "noise"
Check NAs in the result; SQL handles missing value differently compared to R.
i Exclude a subset of `data` that satisfies condition: ans == "noise"
i Consider being explicit about NA, e.g., condition = var == 'val' | is.na(var)
i Exclude a subset of `data` that satisfies condition: ans == "noise"
Check NAs in the result; SQL handles missing value differently compared to R.
i Consider being explicit about NA, e.g., condition = var == 'val' | is.na(var)
Saving _problems/test-execute_def-12.R
===============>--------------- 50% | ETA: 2s
Saving _problems/test-execute_def-35.R
Saving _problems/test-execute_def-66.R
Saving _problems/test-execute_def-102.R
Saving _problems/test-identify_rows_dataframe-3.R
Saving _problems/test-identify_rows_dataframe-11.R
Saving _problems/test-identify_rows_dataframe-18.R
Saving _problems/test-identify_rows_dataframe-26.R
Saving _problems/test-identify_rows_dataframe-34.R
Saving _problems/test-identify_rows_dataframe-43.R
Saving _problems/test-identify_rows_dataframe-49.R
Saving _problems/test-identify_rows_dataframe-62.R
Saving _problems/test-identify_rows_dataframe-68.R
Saving _problems/test-identify_rows_dataframe-75.R
Saving _problems/test-if_dates-41.R
Saving _problems/test-pool_case-45.R
Saving _problems/test-pool_case-64.R
Saving _problems/test-pool_case-83.R
Saving _problems/test-pool_case-134.R
[ FAIL 23 | WARN 2 | SKIP 6 | PASS 189 ]
══ Skipped tests (6) ═══════════════════════════════════════════════════════════
• On CRAN (6): 'test-define_case.R:42:3', 'test-if_dates.R:2:3',
'test-if_dates.R:26:3', 'test-if_dates.R:33:3',
'test-restrict_dates_sql.R:26:3', 'test-restrict_dates_sql.R:101:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-collapse_episode.R:7:3'): basic use works ──────────────────────
Error in ``[.data.table`(data, , `:=`(last_end_dt, lapply(.SD, function(x) data.table::shift(x, n = 1, fill = data.table::first(x)))), by = clnt_id_nm, .SDcols = end_dt_nm)`: attempt access index 8/8 in VECTOR_ELT
Backtrace:
▆
1. ├─healthdb::collapse_episode(...) at test-collapse_episode.R:7:3
2. └─healthdb:::collapse_episode.data.frame(...)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-define_case.R:85:48'): keep first/last works on df ─────────────
Error in ``[.data.table`(dt, , `:=`(incl, data.table::`%chin%`(unlist(.SD), matched_vals) %>% combine_fn(na.rm = TRUE)), by = "rid", .SDcols = vars)`: attempt access index 8/8 in VECTOR_ELT
Backtrace:
▆
1. └─base::sapply(...) at test-define_case.R:85:3
2. └─base::lapply(X = X, FUN = FUN, ...)
3. └─healthdb (local) FUN(X[[i]], ...)
4. └─healthdb::define_case(...) at test-define_case.R:85:48
5. ├─base::eval(incl)
6. │ └─base::eval(incl)
7. ├─healthdb::identify_row(...)
8. └─healthdb:::identify_rows.data.frame(...)
9. ├─...[]
10. └─data.table:::`[.data.table`(...)
── Error ('test-define_case.R:94:3'): passing ... works ────────────────────────
Error in ``[.data.table`(dt, , `:=`(incl, data.table::`%chin%`(unlist(.SD), matched_vals) %>% combine_fn(na.rm = TRUE)), by = "rid", .SDcols = vars)`: attempt access index 7/7 in VECTOR_ELT
Backtrace:
▆
1. └─healthdb::define_case(...) at test-define_case.R:94:3
2. ├─base::eval(incl)
3. │ └─base::eval(incl)
4. ├─healthdb::identify_row(...)
5. └─healthdb:::identify_rows.data.frame(...)
6. ├─...[]
7. └─data.table:::`[.data.table`(...)
── Error ('test-execute_def.R:12:3'): basic use works ──────────────────────────
<dplyr:::mutate_error/rlang_error/error/condition>
Error in `dplyr::mutate(., result = purrr::pmap(list(.data[["fn_call"]], .data[["src_labs"]], .data[["def_lab"]]), function(x, y, z) { if (getOption("healthdb.verbose")) rlang::inform(paste0("\nActions for definition ", z, " using source ", rlang::expr_deparse(with_data_expr[[y]]), ":\n")) eval(x, envir = with_data_env) }, .progress = TRUE), result = purrr::pmap(list(.data[["result"]], .data[["def_lab"]], .data[["src_labs"]]), function(dat, def, src) { dat %>% dplyr::mutate(def = def, src = src, .before = 1) }))`: i In argument: `result = purrr::pmap(...)`.
Caused by error in `purrr::pmap()`:
i In index: 2.
Caused by error in `[.data.table`:
! attempt access index 8/8 in VECTOR_ELT
── Error ('test-execute_def.R:35:3'): mixed binding works ──────────────────────
<dplyr:::mutate_error/rlang_error/error/condition>
Error in `dplyr::mutate(., result = purrr::pmap(list(.data[["fn_call"]], .data[["src_labs"]], .data[["def_lab"]]), function(x, y, z) { if (getOption("healthdb.verbose")) rlang::inform(paste0("\nActions for definition ", z, " using source ", rlang::expr_deparse(with_data_expr[[y]]), ":\n")) eval(x, envir = with_data_env) }, .progress = TRUE), result = purrr::pmap(list(.data[["result"]], .data[["def_lab"]], .data[["src_labs"]]), function(dat, def, src) { dat %>% dplyr::mutate(def = def, src = src, .before = 1) }))`: i In argument: `result = purrr::pmap(...)`.
Caused by error in `purrr::pmap()`:
i In index: 2.
Caused by error in `[.data.table`:
! attempt access index 8/8 in VECTOR_ELT
── Error ('test-execute_def.R:66:3'): binding dfs works ────────────────────────
<dplyr:::mutate_error/rlang_error/error/condition>
Error in `dplyr::mutate(., result = purrr::pmap(list(.data[["fn_call"]], .data[["src_labs"]], .data[["def_lab"]]), function(x, y, z) { if (getOption("healthdb.verbose")) rlang::inform(paste0("\nActions for definition ", z, " using source ", rlang::expr_deparse(with_data_expr[[y]]), ":\n")) eval(x, envir = with_data_env) }, .progress = TRUE), result = purrr::pmap(list(.data[["result"]], .data[["def_lab"]], .data[["src_labs"]]), function(dat, def, src) { dat %>% dplyr::mutate(def = def, src = src, .before = 1) }))`: i In argument: `result = purrr::pmap(...)`.
Caused by error in `purrr::pmap()`:
i In index: 1.
Caused by error in `[.data.table`:
! attempt access index 8/8 in VECTOR_ELT
── Error ('test-execute_def.R:102:3'): multiple def works ──────────────────────
<dplyr:::mutate_error/rlang_error/error/condition>
Error in `dplyr::mutate(., result = purrr::pmap(list(.data[["fn_call"]], .data[["src_labs"]], .data[["def_lab"]]), function(x, y, z) { if (getOption("healthdb.verbose")) rlang::inform(paste0("\nActions for definition ", z, " using source ", rlang::expr_deparse(with_data_expr[[y]]), ":\n")) eval(x, envir = with_data_env) }, .progress = TRUE), result = purrr::pmap(list(.data[["result"]], .data[["def_lab"]], .data[["src_labs"]]), function(dat, def, src) { dat %>% dplyr::mutate(def = def, src = src, .before = 1) }))`: i In argument: `result = purrr::pmap(...)`.
Caused by error in `purrr::pmap()`:
i In index: 1.
Caused by error in `[.data.table`:
! attempt access index 8/8 in VECTOR_ELT
── Error ('test-identify_rows_dataframe.R:3:3'): match by in works ─────────────
Error in ``[.data.table`(dt, , `:=`(incl, data.table::`%chin%`(unlist(.SD), matched_vals) %>% combine_fn(na.rm = TRUE)), by = "rid", .SDcols = vars)`: attempt access index 8/8 in VECTOR_ELT
Backtrace:
▆
1. ├─healthdb:::identify_rows(df, starts_with("diagx"), "in", letters) at test-identify_rows_dataframe.R:3:3
2. └─healthdb:::identify_rows.data.frame(...)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-identify_rows_dataframe.R:11:3'): if_all works ─────────────────
Error in ``[.data.table`(dt, , `:=`(incl, data.table::`%chin%`(unlist(.SD), matched_vals) %>% combine_fn(na.rm = TRUE)), by = "rid", .SDcols = vars)`: attempt access index 8/8 in VECTOR_ELT
Backtrace:
▆
1. ├─healthdb:::identify_rows(...) at test-identify_rows_dataframe.R:11:3
2. └─healthdb:::identify_rows.data.frame(...)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-identify_rows_dataframe.R:18:3'): match by start works ─────────
Error in ``[.data.table`(dt, , `:=`(incl, data.table::`%chin%`(unlist(.SD), matched_vals) %>% combine_fn(na.rm = TRUE)), by = "rid", .SDcols = vars)`: attempt access index 8/8 in VECTOR_ELT
Backtrace:
▆
1. ├─healthdb:::identify_rows(df, starts_with("diagx"), "start", start) at test-identify_rows_dataframe.R:18:3
2. └─healthdb:::identify_rows.data.frame(...)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-identify_rows_dataframe.R:26:3'): match by like works ──────────
Error in ``[.data.table`(dt, , `:=`(incl, data.table::`%chin%`(unlist(.SD), matched_vals) %>% combine_fn(na.rm = TRUE)), by = "rid", .SDcols = vars)`: attempt access index 8/8 in VECTOR_ELT
Backtrace:
▆
1. ├─healthdb:::identify_rows(df, starts_with("diagx"), "like", pattern) at test-identify_rows_dataframe.R:26:3
2. └─healthdb:::identify_rows.data.frame(...)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-identify_rows_dataframe.R:34:3'): match by regex works ─────────
Error in ``[.data.table`(dt, , `:=`(incl, data.table::`%chin%`(unlist(.SD), matched_vals) %>% combine_fn(na.rm = TRUE)), by = "rid", .SDcols = vars)`: attempt access index 8/8 in VECTOR_ELT
Backtrace:
▆
1. ├─healthdb:::identify_rows(df, starts_with("diagx"), "regex", pattern) at test-identify_rows_dataframe.R:34:3
2. └─healthdb:::identify_rows.data.frame(...)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-identify_rows_dataframe.R:43:3'): match by between works ───────
Error in ``[.data.table`(dt, , `:=`(incl, unlist(.SD) %in% matched_vals %>% combine_fn(na.rm = TRUE)), by = "rid", .SDcols = vars)`: attempt access index 8/8 in VECTOR_ELT
Backtrace:
▆
1. ├─healthdb:::identify_rows(df, dates, "between", seq_range) at test-identify_rows_dataframe.R:43:3
2. └─healthdb:::identify_rows.data.frame(df, dates, "between", seq_range)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-identify_rows_dataframe.R:49:3'): type conflict warning works ──
Error in ``[.data.table`(dt, , `:=`(incl, unlist(.SD) %in% matched_vals %>% combine_fn(na.rm = TRUE)), by = "rid", .SDcols = vars)`: attempt access index 8/8 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_warning(...) at test-identify_rows_dataframe.R:49:3
2. │ └─testthat:::expect_condition_matching_(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─healthdb:::identify_rows(df, starts_with("diagx"), "in", 1:10)
8. └─healthdb:::identify_rows.data.frame(...)
9. ├─...[]
10. └─data.table:::`[.data.table`(...)
── Error ('test-identify_rows_dataframe.R:56:3'): summary of numeric vals works ──
Error in ``[.data.table`(dt, , `:=`(incl, unlist(.SD) %in% matched_vals %>% combine_fn(na.rm = TRUE)), by = "rid", .SDcols = vars)`: attempt access index 7/7 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_output(...) at test-identify_rows_dataframe.R:56:3
2. │ └─testthat:::quasi_capture(...)
3. │ ├─testthat (local) .capture(...)
4. │ │ └─testthat::capture_output_lines(code, print, width = width)
5. │ │ └─testthat:::eval_with_output(code, print = print, width = width)
6. │ │ ├─withr::with_output_sink(path, withVisible(code))
7. │ │ │ └─base::force(code)
8. │ │ └─base::withVisible(code)
9. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
10. ├─healthdb:::identify_rows(...)
11. └─healthdb:::identify_rows.data.frame(...)
12. ├─...[]
13. └─data.table:::`[.data.table`(...)
── Error ('test-identify_rows_dataframe.R:62:3'): edge case - character vars works ──
Error in ``[.data.table`(dt, , `:=`(incl, data.table::`%chin%`(unlist(.SD), matched_vals) %>% combine_fn(na.rm = TRUE)), by = "rid", .SDcols = vars)`: attempt access index 8/8 in VECTOR_ELT
Backtrace:
▆
1. ├─healthdb:::identify_rows(df, any_of(var_nm), "in", letters) at test-identify_rows_dataframe.R:62:3
2. └─healthdb:::identify_rows.data.frame(...)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-identify_rows_dataframe.R:68:3'): edge case - unquoted vars works ──
Error in ``[.data.table`(dt, , `:=`(incl, data.table::`%chin%`(unlist(.SD), matched_vals) %>% combine_fn(na.rm = TRUE)), by = "rid", .SDcols = vars)`: attempt access index 8/8 in VECTOR_ELT
Backtrace:
▆
1. ├─healthdb:::identify_rows(...) at test-identify_rows_dataframe.R:68:3
2. └─healthdb:::identify_rows.data.frame(...)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-identify_rows_dataframe.R:75:3'): edge case - vals in an external vector works ──
Error in ``[.data.table`(dt, , `:=`(incl, data.table::`%chin%`(unlist(.SD), matched_vals) %>% combine_fn(na.rm = TRUE)), by = "rid", .SDcols = vars)`: attempt access index 8/8 in VECTOR_ELT
Backtrace:
▆
1. ├─healthdb:::identify_rows(...) at test-identify_rows_dataframe.R:75:3
2. └─healthdb:::identify_rows.data.frame(...)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-if_dates.R:41:3'): straight false due to no gap < within works ──
Error in ``[.data.table`(overlap, , `:=`(N, .N), by = period_id)`: attempt access index 4/4 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_false(if_dates(dates, 2, apart = 7, within = 30)) at test-if_dates.R:41:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─healthdb:::if_dates(dates, 2, apart = 7, within = 30)
5. ├─overlap[, `:=`(N, .N), by = period_id]
6. └─data.table:::`[.data.table`(overlap, , `:=`(N, .N), by = period_id)
── Error ('test-pool_case.R:45:3'): pool mixed works ───────────────────────────
<dplyr:::mutate_error/rlang_error/error/condition>
Error in `dplyr::mutate(., result = purrr::pmap(list(.data[["fn_call"]], .data[["src_labs"]], .data[["def_lab"]]), function(x, y, z) { if (getOption("healthdb.verbose")) rlang::inform(paste0("\nActions for definition ", z, " using source ", rlang::expr_deparse(with_data_expr[[y]]), ":\n")) eval(x, envir = with_data_env) }, .progress = TRUE), result = purrr::pmap(list(.data[["result"]], .data[["def_lab"]], .data[["src_labs"]]), function(dat, def, src) { dat %>% dplyr::mutate(def = def, src = src, .before = 1) }))`: i In argument: `result = purrr::pmap(...)`.
Caused by error in `purrr::pmap()`:
i In index: 1.
Caused by error in `[.data.table`:
! attempt access index 8/8 in VECTOR_ELT
── Error ('test-pool_case.R:64:3'): edge case no date_var works ────────────────
<dplyr:::mutate_error/rlang_error/error/condition>
Error in `dplyr::mutate(., result = purrr::pmap(list(.data[["fn_call"]], .data[["src_labs"]], .data[["def_lab"]]), function(x, y, z) { if (getOption("healthdb.verbose")) rlang::inform(paste0("\nActions for definition ", z, " using source ", rlang::expr_deparse(with_data_expr[[y]]), ":\n")) eval(x, envir = with_data_env) }, .progress = TRUE), result = purrr::pmap(list(.data[["result"]], .data[["def_lab"]], .data[["src_labs"]]), function(dat, def, src) { dat %>% dplyr::mutate(def = def, src = src, .before = 1) }))`: i In argument: `result = purrr::pmap(...)`.
Caused by error in `purrr::pmap()`:
i In index: 1.
Caused by error in `[.data.table`:
! attempt access index 8/8 in VECTOR_ELT
── Error ('test-pool_case.R:83:3'): edge case one date_var works ───────────────
<dplyr:::mutate_error/rlang_error/error/condition>
Error in `dplyr::mutate(., result = purrr::pmap(list(.data[["fn_call"]], .data[["src_labs"]], .data[["def_lab"]]), function(x, y, z) { if (getOption("healthdb.verbose")) rlang::inform(paste0("\nActions for definition ", z, " using source ", rlang::expr_deparse(with_data_expr[[y]]), ":\n")) eval(x, envir = with_data_env) }, .progress = TRUE), result = purrr::pmap(list(.data[["result"]], .data[["def_lab"]], .data[["src_labs"]]), function(dat, def, src) { dat %>% dplyr::mutate(def = def, src = src, .before = 1) }))`: i In argument: `result = purrr::pmap(...)`.
Caused by error in `purrr::pmap()`:
i In index: 1.
Caused by error in `[.data.table`:
! attempt access index 8/8 in VECTOR_ELT
── Error ('test-pool_case.R:134:3'): pool multiple def works ───────────────────
<dplyr:::mutate_error/rlang_error/error/condition>
Error in `dplyr::mutate(., result = purrr::pmap(list(.data[["fn_call"]], .data[["src_labs"]], .data[["def_lab"]]), function(x, y, z) { if (getOption("healthdb.verbose")) rlang::inform(paste0("\nActions for definition ", z, " using source ", rlang::expr_deparse(with_data_expr[[y]]), ":\n")) eval(x, envir = with_data_env) }, .progress = TRUE), result = purrr::pmap(list(.data[["result"]], .data[["def_lab"]], .data[["src_labs"]]), function(dat, def, src) { dat %>% dplyr::mutate(def = def, src = src, .before = 1) }))`: i In argument: `result = purrr::pmap(...)`.
Caused by error in `purrr::pmap()`:
i In index: 1.
Caused by error in `[.data.table`:
! attempt access index 8/8 in VECTOR_ELT
[ FAIL 23 | WARN 2 | SKIP 6 | PASS 189 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc