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

Last updated on 2025-04-12 20:52:18 CEST.

Package	ERROR	OK
healthdb	1	13

Package healthdb

Current CRAN status: ERROR: 1, OK: 13

Version: 0.4.1
Check: tests
Result: ERROR Running ‘testthat.R’ [65s/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") 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-------------- 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) 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 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: 1:10 [ FAIL 1 | WARN 2 | SKIP 6 | PASS 225 ] ══ 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-restrict_dates_sql.R:19:3'): apart only works ────────────────── Error in `c_character(...)`: Character input expected Backtrace: ▆ 1. ├─... %>% dplyr::collect() at test-restrict_dates_sql.R:19:3 2. ├─dplyr::collect(.) 3. ├─dbplyr:::collect.tbl_sql(.) 4. │ └─dbplyr::db_sql_render(x$src$con, x, cte = cte) 5. │ ├─dbplyr::db_sql_render(con, sql, ..., sql_options = sql_options) 6. │ └─dbplyr:::db_sql_render.DBIConnection(con, sql, ..., sql_options = sql_options) 7. │ ├─dbplyr::sql_render(sql, con = con, ..., sql_options = sql_options) 8. │ └─dbplyr:::sql_render.tbl_lazy(sql, con = con, ..., sql_options = sql_options) 9. │ ├─dbplyr::sql_render(...) 10. │ └─dbplyr:::sql_render.lazy_query(...) 11. │ ├─dbplyr::sql_build(query, con = con, sql_options = sql_options) 12. │ └─dbplyr:::sql_build.lazy_select_query(query, con = con, sql_options = sql_options) 13. │ ├─dbplyr::sql_build(op$x, con, sql_options = sql_options) 14. │ └─dbplyr:::sql_build.lazy_select_query(op$x, con, sql_options = sql_options) 15. │ ├─dbplyr::sql_build(op$x, con, sql_options = sql_options) 16. │ └─dbplyr:::sql_build.lazy_select_query(op$x, con, sql_options = sql_options) 17. │ ├─dbplyr::sql_build(op$x, con, sql_options = sql_options) 18. │ └─dbplyr:::sql_build.lazy_select_query(op$x, con, sql_options = sql_options) 19. │ ├─dbplyr::sql_build(op$x, con, sql_options = sql_options) 20. │ └─dbplyr:::sql_build.lazy_select_query(op$x, con, sql_options = sql_options) 21. │ └─dbplyr:::get_select_sql(...) 22. │ └─dbplyr:::translate_select_sql(con, select) 23. │ └─dbplyr::translate_sql_(...) 24. │ └─base::lapply(...) 25. │ └─dbplyr (local) FUN(X[[i]], ...) 26. │ ├─dbplyr::escape(eval_tidy(x, mask), con = con) 27. │ └─rlang::eval_tidy(x, mask) 28. └─dplyr::between(...) 29. └─dbplyr::sql_expr(!!x %BETWEEN% !!left %AND% !!right) 30. └─dbplyr::sql(x) 31. └─dbplyr:::c_character(...) 32. └─cli::cli_abort("Character input expected") 33. └─rlang::abort(...) [ FAIL 1 | WARN 2 | SKIP 6 | PASS 225 ] Error: Test failures Execution halted Flavor: r-patched-linux-x86_64