• using R Under development (unstable) (2025-12-18 r89199)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     Debian clang version 21.1.7 (1)     Debian flang version 21.1.7 (1)
• running under: Debian GNU/Linux forky/sid
• using session charset: UTF-8
• checking for file ‘healthdb/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘healthdb’ version ‘0.4.1’
• package encoding: UTF-8
• checking CRAN incoming feasibility ... [1s/2s] OK
• checking package namespace information ... OK
• checking package dependencies ... OK
• checking if this is a source package ... OK
• checking if there is a namespace ... OK
• checking for executable files ... OK
• checking for hidden files and directories ... OK
• checking for portable file names ... OK
• checking for sufficient/correct file permissions ... OK
• checking serialization versions ... OK
• checking whether package ‘healthdb’ can be installed ... OK See the install log for details.
• checking package directory ... OK
• checking for future file timestamps ... OK
• checking ‘build’ directory ... OK
• checking DESCRIPTION meta-information ... OK
• checking top-level files ... OK
• checking for left-over files ... OK
• checking index information ... OK
• checking package subdirectories ... OK
• checking code files for non-ASCII characters ... OK
• checking R files for syntax errors ... OK
• checking whether the package can be loaded ... [1s/2s] OK
• checking whether the package can be loaded with stated dependencies ... [1s/1s] OK
• checking whether the package can be unloaded cleanly ... [1s/1s] OK
• checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK
• checking whether the namespace can be unloaded cleanly ... [1s/1s] OK
• checking loading without being on the library search path ... [1s/2s] OK
• checking whether startup messages can be suppressed ... [1s/2s] OK
• checking use of S3 registration ... OK
• checking dependencies in R code ... OK
• checking S3 generic/method consistency ... OK
• checking replacement functions ... OK
• checking foreign function calls ... OK
• checking R code for possible problems ... [13s/17s] OK
• checking Rd files ... [0s/1s] OK
• checking Rd metadata ... OK
• checking Rd line widths ... OK
• checking Rd cross-references ... OK
• checking for missing documentation entries ... OK
• checking for code/documentation mismatches ... OK
• checking Rd \usage sections ... OK
• checking Rd contents ... OK
• checking for unstated dependencies in examples ... OK
• checking installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... [2s/3s] 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
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [64s/84s] 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
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [6s/9s] 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
• checking PDF version of manual ... [6s/9s] OK
• checking HTML version of manual ... [2s/3s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 3 ERRORs