CRAN Package Check Results for Maintainer ‘Kevin Hu <kevin.hu at bccdc.ca>’

Last updated on 2025-12-28 05:50:30 CET.

Package	ERROR	OK
healthdb	1	12

Package healthdb

Current CRAN status: ERROR: 1, OK: 12

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 Flavor: r-devel-windows-x86_64

Version: 0.4.1
Check: tests
Result: ERROR Running 'testthat.R' [48s] 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-windows-x86_64

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] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/dplyr:::mutate_error> Error in `dplyr::mutate()`: 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 --- Backtrace: ▆ 1. ├─sud_def %>% ... 2. ├─healthdb::execute_def(., with_data = list(claim = claim_db, hosp = hosp_df)) 3. │ └─def %>% ... 4. ├─dplyr::mutate(...) 5. ├─dplyr:::mutate.data.frame(...) 6. │ └─dplyr:::mutate_cols(.data, dplyr_quosures(...), by) 7. │ ├─base::withCallingHandlers(...) 8. │ └─dplyr:::mutate_col(dots[[i]], data, mask, new_columns) 9. │ └─mask$eval_all_mutate(quo) 10. │ └─dplyr (local) eval() 11. └─purrr::pmap(...) 12. └─purrr:::pmap_("list", .l, .f, ..., .progress = .progress) 13. ├─purrr:::with_indexed_errors(...) 14. │ └─base::withCallingHandlers(...) 15. ├─purrr:::call_with_cleanup(...) 16. └─healthdb (local) .f(.l[[1L]][[i]], .l[[2L]][[i]], .l[[3L]][[i]], ...) 17. └─base::eval(x, envir = with_data_env) 18. └─base::eval(x, envir = with_data_env) 19. └─healthdb::define_case(...) 20. ├─base::eval(incl) 21. │ └─base::eval(incl) 22. ├─healthdb::identify_row(...) 23. └─healthdb:::identify_rows.data.frame(...) 24. ├─...[] 25. └─data.table:::`[.data.table`(...) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 Flavor: r-devel-windows-x86_64