- using R Under development (unstable) (2024-03-24 r86185)
- using platform: x86_64-pc-linux-gnu
- R was compiled by
Debian clang version 18.1.0 (rc4-1)
Debian flang-new version 18.1.0 (rc4-1)
- running under: Debian GNU/Linux trixie/sid
- using session charset: UTF-8
- checking for file ‘PatientProfiles/DESCRIPTION’ ... OK
- checking extension type ... Package
- this is package ‘PatientProfiles’ version ‘0.6.2’
- package encoding: UTF-8
- 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 ‘PatientProfiles’ 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/2s] OK
- checking whether the namespace can be unloaded cleanly ... [1s/1s] OK
- checking loading without being on the library search path ... [1s/1s] 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 ... [22s/28s] OK
- checking Rd files ... [1s/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 R/sysdata.rda ... OK
- checking installed files from ‘inst/doc’ ... OK
- checking files in ‘vignettes’ ... OK
- checking examples ... [2s/2s] OK
- checking for unstated dependencies in ‘tests’ ... OK
- checking tests ... [731s/512s] ERROR
Running ‘spelling.R’ [0s/1s]
Running ‘testthat.R’ [731s/511s]
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/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(PatientProfiles)
>
> test_check("PatientProfiles")
Starting 2 test processes
[ FAIL 65 | WARN 21 | SKIP 1 | PASS 200 ]
══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• empty test (1): 'test-summariseResult.R:209:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-addAttributes.R:5:3'): addAttributes, functionality ────────────
Error in `CDMConnector::datediff()`: No known SQL translation
Backtrace:
▆
1. ├─cdm$cohort1 %>% addDemographics() at test-addAttributes.R:5:3
2. ├─PatientProfiles::addDemographics(.)
3. │ └─x %>% dplyr::compute()
4. ├─dplyr::compute(.)
5. ├─omopgenerics:::compute.cdm_table(.)
6. │ ├─dplyr::compute(...)
7. │ └─CDMConnector:::compute.db_cdm(...)
8. │ └─CDMConnector:::.computeQuery(...)
9. │ └─dbplyr::sql_render(x)
10. │ ├─dbplyr::sql_render(...)
11. │ └─dbplyr:::sql_render.tbl_lazy(...)
12. │ ├─dbplyr::sql_render(...)
13. │ └─dbplyr:::sql_render.lazy_query(...)
14. │ ├─dbplyr::sql_build(query, con = con, sql_options = sql_options)
15. │ └─dbplyr:::sql_build.lazy_select_query(query, con = con, sql_options = sql_options)
16. │ ├─dbplyr::sql_build(op$x, con, sql_options = sql_options)
17. │ └─dbplyr:::sql_build.lazy_select_query(op$x, con, sql_options = sql_options)
18. │ └─dbplyr:::get_select_sql(...)
19. │ └─dbplyr:::translate_select_sql(con, select)
20. │ └─dbplyr::translate_sql_(...)
21. │ └─base::lapply(...)
22. │ └─dbplyr (local) FUN(X[[i]], ...)
23. │ ├─dbplyr::escape(eval_tidy(x, mask), con = con)
24. │ └─rlang::eval_tidy(x, mask)
25. └─CDMConnector::datediff
26. └─cli::cli_abort(...)
27. └─rlang::abort(...)
── Error ('test-addCohortIntersect.R:8:3'): output format - one outcome cohort ──
Error in `CDMConnector::datediff()`: No known SQL translation
Backtrace:
▆
1. ├─cdm$cohort1 %>% ... at test-addCohortIntersect.R:8:3
2. ├─PatientProfiles::addCohortIntersectDays(...)
3. │ └─x %>% ...
4. ├─PatientProfiles::addIntersect(...)
5. │ └─... %>% ...
6. ├─dplyr::mutate(., censor_date = .data[[censorDate %||% "censor_date"]])
7. ├─dplyr::mutate(...)
8. ├─PatientProfiles::addFutureObservation(...)
9. │ └─x %>% ...
10. ├─PatientProfiles::addDemographics(...)
11. │ └─x %>% dplyr::compute()
12. ├─dplyr::compute(.)
13. ├─omopgenerics:::compute.cdm_table(.)
14. │ ├─dplyr::compute(...)
15. │ └─CDMConnector:::compute.db_cdm(...)
16. │ └─CDMConnector:::.computeQuery(...)
17. │ └─dbplyr::sql_render(x)
18. │ ├─dbplyr::sql_render(...)
19. │ └─dbplyr:::sql_render.tbl_lazy(...)
20. │ ├─dbplyr::sql_render(...)
21. │ └─dbplyr:::sql_render.lazy_query(...)
22. │ ├─dbplyr::sql_build(query, con = con, sql_options = sql_options)
23. │ └─dbplyr:::sql_build.lazy_select_query(query, con = con, sql_options = sql_options)
24. │ └─dbplyr:::get_select_sql(...)
25. │ └─dbplyr:::translate_select_sql(con, select)
26. │ └─dbplyr::translate_sql_(...)
27. │ └─base::lapply(...)
28. │ └─dbplyr (local) FUN(X[[i]], ...)
29. │ ├─dbplyr::escape(eval_tidy(x, mask), con = con)
30. │ └─rlang::eval_tidy(x, mask)
31. └─CDMConnector::datediff
32. └─cli::cli_abort(...)
33. └─rlang::abort(...)
── Error ('test-addCohortIntersect.R:107:3'): first vs last event - cohort table ──
Error in `CDMConnector::datediff()`: No known SQL translation
Backtrace:
▆
1. ├─cdm$cohort1 %>% ... at test-addCohortIntersect.R:107:3
2. ├─PatientProfiles::addCohortIntersectDays(...)
3. │ └─x %>% ...
4. ├─PatientProfiles::addIntersect(...)
5. │ └─... %>% ...
6. ├─dplyr::mutate(., censor_date = .data[[censorDate %||% "censor_date"]])
7. ├─dplyr::mutate(...)
8. ├─PatientProfiles::addFutureObservation(...)
9. │ └─x %>% ...
10. ├─PatientProfiles::addDemographics(...)
11. │ └─x %>% dplyr::compute()
12. ├─dplyr::compute(.)
13. ├─omopgenerics:::compute.cdm_table(.)
14. │ ├─dplyr::compute(...)
15. │ └─CDMConnector:::compute.db_cdm(...)
16. │ └─CDMConnector:::.computeQuery(...)
17. │ └─dbplyr::sql_render(x)
18. │ ├─dbplyr::sql_render(...)
19. │ └─dbplyr:::sql_render.tbl_lazy(...)
20. │ ├─dbplyr::sql_render(...)
21. │ └─dbplyr:::sql_render.lazy_query(...)
22. │ ├─dbplyr::sql_build(query, con = con, sql_options = sql_options)
23. │ └─dbplyr:::sql_build.lazy_select_query(query, con = con, sql_options = sql_options)
24. │ └─dbplyr:::get_select_sql(...)
25. │ └─dbplyr:::translate_select_sql(con, select)
26. │ └─dbplyr::translate_sql_(...)
27. │ └─base::lapply(...)
28. │ └─dbplyr (local) FUN(X[[i]], ...)
29. │ ├─dbplyr::escape(eval_tidy(x, mask), con = con)
30. │ └─rlang::eval_tidy(x, mask)
31. └─CDMConnector::datediff
32. └─cli::cli_abort(...)
33. └─rlang::abort(...)
── Error ('test-addCohortIntersect.R:227:3'): multiple cohort entries per person ──
Error in `CDMConnector::datediff()`: No known SQL translation
Backtrace:
▆
1. ├─cdm$cohort1 %>% ... at test-addCohortIntersect.R:227:3
2. ├─PatientProfiles::addCohortIntersectDays(...)
3. │ └─x %>% ...
4. ├─PatientProfiles::addIntersect(...)
5. │ └─... %>% ...
6. ├─dplyr::mutate(., censor_date = .data[[censorDate %||% "censor_date"]])
7. ├─dplyr::mutate(...)
8. ├─PatientProfiles::addFutureObservation(...)
9. │ └─x %>% ...
10. ├─PatientProfiles::addDemographics(...)
11. │ └─x %>% dplyr::compute()
12. ├─dplyr::compute(.)
13. ├─omopgenerics:::compute.cdm_table(.)
14. │ ├─dplyr::compute(...)
15. │ └─CDMConnector:::compute.db_cdm(...)
16. │ └─CDMConnector:::.computeQuery(...)
17. │ └─dbplyr::sql_render(x)
18. │ ├─dbplyr::sql_render(...)
19. │ └─dbplyr:::sql_render.tbl_lazy(...)
20. │ ├─dbplyr::sql_render(...)
21. │ └─dbplyr:::sql_render.lazy_query(...)
22. │ ├─dbplyr::sql_build(query, con = con, sql_options = sql_options)
23. │ └─dbplyr:::sql_build.lazy_select_query(query, con = con, sql_options = sql_options)
24. │ └─dbplyr:::get_select_sql(...)
25. │ └─dbplyr:::translate_select_sql(con, select)
26. │ └─dbplyr::translate_sql_(...)
27. │ └─base::lapply(...)
28. │ └─dbplyr (local) FUN(X[[i]], ...)
29. │ ├─dbplyr::escape(eval_tidy(x, mask), con = con)
30. │ └─rlang::eval_tidy(x, mask)
31. └─CDMConnector::datediff
32. └─cli::cli_abort(...)
33. └─rlang::abort(...)
── Error ('test-addCohortIntersect.R:287:3'): output names ─────────────────────
Error in `CDMConnector::datediff()`: No known SQL translation
Backtrace:
▆
1. ├─cdm$cohort1 %>% ... at test-addCohortIntersect.R:287:3
2. ├─PatientProfiles::addCohortIntersectDays(...)
3. │ └─x %>% ...
4. ├─PatientProfiles::addIntersect(...)
5. │ └─... %>% ...
6. ├─dplyr::mutate(., censor_date = .data[[censorDate %||% "censor_date"]])
7. ├─dplyr::mutate(...)
8. ├─PatientProfiles::addFutureObservation(...)
9. │ └─x %>% ...
10. ├─PatientProfiles::addDemographics(...)
11. │ └─x %>% dplyr::compute()
12. ├─dplyr::compute(.)
13. ├─omopgenerics:::compute.cdm_table(.)
14. │ ├─dplyr::compute(...)
15. │ └─CDMConnector:::compute.db_cdm(...)
16. │ └─CDMConnector:::.computeQuery(...)
17. │ └─dbplyr::sql_render(x)
18. │ ├─dbplyr::sql_render(...)
19. │ └─dbplyr:::sql_render.tbl_lazy(...)
20. │ ├─dbplyr::sql_render(...)
21. │ └─dbplyr:::sql_render.lazy_query(...)
22. │ ├─dbplyr::sql_build(query, con = con, sql_options = sql_options)
23. │ └─dbplyr:::sql_build.lazy_select_query(query, con = con, sql_options = sql_options)
24. │ └─dbplyr:::get_select_sql(...)
25. │ └─dbplyr:::translate_select_sql(con, select)
26. │ └─dbplyr::translate_sql_(...)
27. │ └─base::lapply(...)
28. │ └─dbplyr (local) FUN(X[[i]], ...)
29. │ ├─dbplyr::escape(eval_tidy(x, mask), con = con)
30. │ └─rlang::eval_tidy(x, mask)
31. └─CDMConnector::datediff
32. └─cli::cli_abort(...)
33. └─rlang::abort(...)
── Error ('test-addCohortIntersect.R:458:3'): working examples ─────────────────
Error in `CDMConnector::datediff()`: No known SQL translation
Backtrace:
▆
1. ├─... %>% dplyr::arrange(subject_id, cohort_start_date) at test-addCohortIntersect.R:458:3
2. ├─dplyr::arrange(., subject_id, cohort_start_date)
3. ├─dplyr::collect(.)
4. ├─PatientProfiles::addCohortIntersectCount(., targetCohortTable = "cohort2")
5. │ └─x %>% ...
6. ├─PatientProfiles::addIntersect(...)
7. │ └─... %>% ...
8. ├─dplyr::mutate(., censor_date = .data[[censorDate %||% "censor_date"]])
9. ├─dplyr::mutate(...)
10. ├─PatientProfiles::addFutureObservation(...)
11. │ └─x %>% ...
12. ├─PatientProfiles::addDemographics(...)
13. │ └─x %>% dplyr::compute()
14. ├─dplyr::compute(.)
15. ├─omopgenerics:::compute.cdm_table(.)
16. │ ├─dplyr::compute(...)
17. │ └─CDMConnector:::compute.db_cdm(...)
18. │ └─CDMConnector:::.computeQuery(...)
19. │ └─dbplyr::sql_render(x)
20. │ ├─dbplyr::sql_render(...)
21. │ └─dbplyr:::sql_render.tbl_lazy(...)
22. │ ├─dbplyr::sql_render(...)
23. │ └─dbplyr:::sql_render.lazy_query(...)
24. │ ├─dbplyr::sql_build(query, con = con, sql_options = sql_options)
25. │ └─dbplyr:::sql_build.lazy_select_query(query, con = con, sql_options = sql_options)
26. │ └─dbplyr:::get_select_sql(...)
27. │ └─dbplyr:::translate_select_sql(con, select)
28. │ └─dbplyr::translate_sql_(...)
29. │ └─base::lapply(...)
30. │ └─dbplyr (local) FUN(X[[i]], ...)
31. │ ├─dbplyr::escape(eval_tidy(x, mask), con = con)
32. │ └─rlang::eval_tidy(x, mask)
33. └─CDMConnector::datediff
34. └─cli::cli_abort(...)
35. └─rlang::abort(...)
── Error ('test-addCohortIntersect.R:564:3'): working examples ─────────────────
Error in `CDMConnector::datediff()`: No known SQL translation
Backtrace:
▆
1. ├─... %>% dplyr::arrange(subject_id, cohort_start_date) at test-addCohortIntersect.R:564:3
2. ├─dplyr::arrange(., subject_id, cohort_start_date)
3. ├─dplyr::collect(.)
4. ├─PatientProfiles::addCohortIntersectFlag(., targetCohortTable = "cohort2")
5. │ └─x %>% ...
6. ├─PatientProfiles::addIntersect(...)
7. │ └─... %>% ...
8. ├─dplyr::mutate(., censor_date = .data[[censorDate %||% "censor_date"]])
9. ├─dplyr::mutate(...)
10. ├─PatientProfiles::addFutureObservation(...)
11. │ └─x %>% ...
12. ├─PatientProfiles::addDemographics(...)
13. │ └─x %>% dplyr::compute()
14. ├─dplyr::compute(.)
15. ├─omopgenerics:::compute.cdm_table(.)
16. │ ├─dplyr::compute(...)
17. │ └─CDMConnector:::compute.db_cdm(...)
18. │ └─CDMConnector:::.computeQuery(...)
19. │ └─dbplyr::sql_render(x)
20. │ ├─dbplyr::sql_render(...)
21. │ └─dbplyr:::sql_render.tbl_lazy(...)
22. │ ├─dbplyr::sql_render(...)
23. │ └─dbplyr:::sql_render.lazy_query(...)
24. │ ├─dbplyr::sql_build(query, con = con, sql_options = sql_options)
25. │ └─dbplyr:::sql_build.lazy_select_query(query, con = con, sql_options = sql_options)
26. │ └─dbplyr:::get_select_sql(...)
27. │ └─dbplyr:::translate_select_sql(con, select)
28. │ └─dbplyr::translate_sql_(...)
29. │ └─base::lapply(...)
30. │ └─dbplyr (local) FUN(X[[i]], ...)
31. │ ├─dbplyr::escape(eval_tidy(x, mask), con = con)
32. │ └─rlang::eval_tidy(x, mask)
33. └─CDMConnector::datediff
34. └─cli::cli_abort(...)
35. └─rlang::abort(...)
── Error ('test-addCohortIntersect.R:651:3'): working examples ─────────────────
Error in `CDMConnector::datediff()`: No known SQL translation
Backtrace:
▆
1. ├─testthat::expect_warning(...) at test-addCohortIntersect.R:651:3
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. ├─... %>% dplyr::arrange(subject_id, cohort_start_date)
8. ├─dplyr::arrange(., subject_id, cohort_start_date)
9. ├─dplyr::collect(.)
10. ├─PatientProfiles::addCohortIntersect(., targetCohortTable = "cohort2")
11. │ └─PatientProfiles:::.addCohortIntersect(...)
12. │ └─x %>% ...
13. ├─PatientProfiles::addIntersect(...)
14. │ └─... %>% ...
15. ├─dplyr::mutate(., censor_date = .data[[censorDate %||% "censor_date"]])
16. ├─dplyr::mutate(...)
17. ├─PatientProfiles::addFutureObservation(...)
18. │ └─x %>% ...
19. ├─PatientProfiles::addDemographics(...)
20. │ └─x %>% dplyr::compute()
21. ├─dplyr::compute(.)
22. ├─omopgenerics:::compute.cdm_table(.)
23. │ ├─dplyr::compute(...)
24. │ └─CDMConnector:::compute.db_cdm(...)
25. │ └─CDMConnector:::.computeQuery(...)
26. │ └─dbplyr::sql_render(x)
27. │ ├─dbplyr::sql_render(...)
28. │ └─dbplyr:::sql_render.tbl_lazy(...)
29. │ ├─dbplyr::sql_render(...)
30. │ └─dbplyr:::sql_render.lazy_query(...)
31. │ ├─dbplyr::sql_build(query, con = con, sql_options = sql_options)
32. │ └─dbplyr:::sql_build.lazy_select_query(query, con = con, sql_options = sql_options)
33. │ └─dbplyr:::get_select_sql(...)
34. │ └─dbplyr:::translate_select_sql(con, select)
35. │ └─dbplyr::translate_sql_(...)
36. │ └─base::lapply(...)
37. │ └─dbplyr (local) FUN(X[[i]], ...)
38. │ ├─dbplyr::escape(eval_tidy(x, mask), con = con)
39. │ └─rlang::eval_tidy(x, mask)
40. └─CDMConnector::datediff
41. └─cli::cli_abort(...)
42. └─rlang::abort(...)
── Error ('test-addCohortIntersect.R:738:3'): censorDate functionality ─────────
Error in `CDMConnector::datediff()`: No known SQL translation
Backtrace:
▆
1. ├─testthat::expect_warning(...) at test-addCohortIntersect.R:738:3
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. ├─... %>% dplyr::arrange(subject_id, cohort_start_date)
8. ├─dplyr::arrange(., subject_id, cohort_start_date)
9. ├─dplyr::collect(.)
10. ├─PatientProfiles::addCohortIntersect(., targetCohortTable = "cohort2")
11. │ └─PatientProfiles:::.addCohortIntersect(...)
12. │ └─x %>% ...
13. ├─PatientProfiles::addIntersect(...)
14. │ └─... %>% ...
15. ├─dplyr::mutate(., censor_date = .data[[censorDate %||% "censor_date"]])
16. ├─dplyr::mutate(...)
17. ├─PatientProfiles::addFutureObservation(...)
18. │ └─x %>% ...
19. ├─PatientProfiles::addDemographics(...)
20. │ └─x %>% dplyr::compute()
21. ├─dplyr::compute(.)
22. ├─omopgenerics:::compute.cdm_table(.)
23. │ ├─dplyr::compute(...)
24. │ └─CDMConnector:::compute.db_cdm(...)
25. │ └─CDMConnector:::.computeQuery(...)
26. │ └─dbplyr::sql_render(x)
27. │ ├─dbplyr::sql_render(...)
28. │ └─dbplyr:::sql_render.tbl_lazy(...)
29. │ ├─dbplyr::sql_render(...)
30. │ └─dbplyr:::sql_render.lazy_query(...)
31. │ ├─dbplyr::sql_build(query, con = con, sql_options = sql_options)
32. │ └─dbplyr:::sql_build.lazy_select_query(query, con = con, sql_options = sql_options)
33. │ └─dbplyr:::get_select_sql(...)
34. │ └─dbplyr:::translate_select_sql(con, select)
35. │ └─dbplyr::translate_sql_(...)
36. │ └─base::lapply(...)
37. │ └─dbplyr (local) FUN(X[[i]], ...)
38. │ ├─dbplyr::escape(eval_tidy(x, mask), con = con)
39. │ └─rlang::eval_tidy(x, mask)
40. └─CDMConnector::datediff
41. └─cli::cli_abort(...)
42. └─rlang::abort(...)
── Error ('test-addCohortIntersect.R:769:3'): casing of empty dates ────────────
Error in `CDMConnector::datediff()`: No known SQL translation
Backtrace:
▆
1. ├─testthat::expect_false(...) at test-addCohortIntersect.R:769:3
2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─... %>% is.numeric()
5. ├─dplyr::pull(., "cohort_2_0_to_inf")
6. ├─utils::head(., 1)
7. ├─PatientProfiles::addCohortIntersectDate(., targetCohortTable = "cohort1")
8. │ └─x %>% ...
9. ├─PatientProfiles::addIntersect(...)
10. │ └─... %>% ...
11. ├─dplyr::mutate(., censor_date = .data[[censorDate %||% "censor_date"]])
12. ├─dplyr::mutate(...)
13. ├─PatientProfiles::addFutureObservation(...)
14. │ └─x %>% ...
15. ├─PatientProfiles::addDemographics(...)
16. │ └─x %>% dplyr::compute()
17. ├─dplyr::compute(.)
18. ├─omopgenerics:::compute.cdm_table(.)
19. │ ├─dplyr::compute(...)
20. │ └─CDMConnector:::compute.db_cdm(...)
21. │ └─CDMConnector:::.computeQuery(...)
22. │ └─dbplyr::sql_render(x)
23. │ ├─dbplyr::sql_render(...)
24. │ └─dbplyr:::sql_render.tbl_lazy(...)
25. │ ├─dbplyr::sql_render(...)
26. │ └─dbplyr:::sql_render.lazy_query(...)
27. │ ├─dbplyr::sql_build(query, con = con, sql_options = sql_options)
28. │ └─dbplyr:::sql_build.lazy_select_query(query, con = con, sql_options = sql_options)
29. │ └─dbplyr:::get_select_sql(...)
30. │ └─dbplyr:::translate_select_sql(con, select)
31. │ └─dbplyr::translate_sql_(...)
32. │ └─base::lapply(...)
33. │ └─dbplyr (local) FUN(X[[i]], ...)
34. │ ├─dbplyr::escape(eval_tidy(x, mask), con = con)
35. │ └─rlang::eval_tidy(x, mask)
36. └─CDMConnector::datediff
37. └─cli::cli_abort(...)
38. └─rlang::abort(...)
── Error ('test-addFutureObservation.R:6:3'): check input length and type for each of the arguments ──
Error in `CDMConnector::datediff()`: No known SQL translation
Backtrace:
▆
1. ├─testthat::expect_warning(addFutureObservation(cdm$cohort1, "cdm")) at test-addFutureObservation.R:6:3
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. ├─PatientProfiles::addFutureObservation(cdm$cohort1, "cdm")
8. │ └─x %>% ...
9. ├─PatientProfiles::addDemographics(...)
10. │ └─x %>% dplyr::compute()
11. ├─dplyr::compute(.)
12. ├─omopgenerics:::compute.cdm_table(.)
13. │ ├─dplyr::compute(...)
14. │ └─CDMConnector:::compute.db_cdm(...)
15. │ └─CDMConnector:::.computeQuery(...)
16. │ └─dbplyr::sql_render(x)
17. │ ├─dbplyr::sql_render(...)
18. │ └─dbplyr:::sql_render.tbl_lazy(...)
19. │ ├─dbplyr::sql_render(...)
20. │ └─dbplyr:::sql_render.lazy_query(...)
21. │ ├─dbplyr::sql_build(query, con = con, sql_options = sql_options)
22. │ └─dbplyr:::sql_build.lazy_select_query(query, con = con, sql_options = sql_options)
23. │ └─dbplyr:::get_select_sql(...)
24. │ └─dbplyr:::translate_select_sql(con, select)
25. │ └─dbplyr::translate_sql_(...)
26. │ └─base::lapply(...)
27. │ └─dbplyr (local) FUN(X[[i]], ...)
28. │ ├─dbplyr::escape(eval_tidy(x, mask), con = con)
29. │ └─rlang::eval_tidy(x, mask)
30. └─CDMConnector::datediff
31. └─cli::cli_abort(...)
32. └─rlang::abort(...)
── Error ('test-addFutureObservation.R:15:3'): check condition_occurrence and cohort1 work ──
Error in `CDMConnector::datediff()`: No known SQL translation
Backtrace:
▆
1. ├─testthat::expect_true(...) at test-addFutureObservation.R:15:3
2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─base::typeof(cdm$cohort1 %>% addFutureObservation() %>% dplyr::collect())
5. ├─cdm$cohort1 %>% addFutureObservation() %>% dplyr::collect()
6. ├─dplyr::collect(.)
7. ├─PatientProfiles::addFutureObservation(.)
8. │ └─x %>% ...
9. ├─PatientProfiles::addDemographics(...)
10. │ └─x %>% dplyr::compute()
11. ├─dplyr::compute(.)
12. ├─omopgenerics:::compute.cdm_table(.)
13. │ ├─dplyr::compute(...)
14. │ └─CDMConnector:::compute.db_cdm(...)
15. │ └─CDMConnector:::.computeQuery(...)
16. │ └─dbplyr::sql_render(x)
17. │ ├─dbplyr::sql_render(...)
18. │ └─dbplyr:::sql_render.tbl_lazy(...)
19. │ ├─dbplyr::sql_render(...)
20. │ └─dbplyr:::sql_render.lazy_query(...)
21. │ ├─dbplyr::sql_build(query, con = con, sql_options = sql_options)
22. │ └─dbplyr:::sql_build.lazy_select_query(query, con = con, sql_options = sql_options)
23. │ └─dbplyr:::get_select_sql(...)
24. │ └─dbplyr:::translate_select_sql(con, select)
25. │ └─dbplyr::translate_sql_(...)
26. │ └─base::lapply(...)
27. │ └─dbplyr (local) FUN(X[[i]], ...)
28. │ ├─dbplyr::escape(eval_tidy(x, mask), con = con)
29. │ └─rlang::eval_tidy(x, mask)
30. └─CDMConnector::datediff
31. └─cli::cli_abort(...)
32. └─rlang::abort(...)
── Error ('test-addFutureObservation.R:64:3'): check working example with cohort1 ──
Error in `CDMConnector::datediff()`: No known SQL translation
Backtrace:
▆
1. ├─cdm$cohort1 %>% addFutureObservation() %>% dplyr::collect() at test-addFutureObservation.R:64:3
2. ├─dplyr::collect(.)
3. ├─PatientProfiles::addFutureObservation(.)
4. │ └─x %>% ...
5. ├─PatientProfiles::addDemographics(...)
6. │ └─x %>% dplyr::compute()
7. ├─dplyr::compute(.)
8. ├─omopgenerics:::compute.cdm_table(.)
9. │ ├─dplyr::compute(...)
10. │ └─CDMConnector:::compute.db_cdm(...)
11. │ └─CDMConnector:::.computeQuery(...)
12. │ └─dbplyr::sql_render(x)
13. │ ├─dbplyr::sql_render(...)
14. │ └─dbplyr:::sql_render.tbl_lazy(...)
15. │ ├─dbplyr::sql_render(...)
16. │ └─dbplyr:::sql_render.lazy_query(...)
17. │ ├─dbplyr::sql_build(query, con = con, sql_options = sql_options)
18. │ └─dbplyr:::sql_build.lazy_select_query(query, con = con, sql_options = sql_options)
19. │ └─dbplyr:::get_select_sql(...)
20. │ └─dbplyr:::translate_select_sql(con, select)
21. │ └─dbplyr::translate_sql_(...)
22. │ └─base::lapply(...)
23. │ └─dbplyr (local) FUN(X[[i]], ...)
24. │ ├─dbplyr::escape(eval_tidy(x, mask), con = con)
25. │ └─rlang::eval_tidy(x, mask)
26. └─CDMConnector::datediff
27. └─cli::cli_abort(...)
28. └─rlang::abort(...)
── Error ('test-addFutureObservation.R:126:3'): check working example with condition_occurrence ──
Error in `dplyr::collect(removeClass(x, "cdm_table"))`: Failed to collect lazy table.
Caused by error:
! rapi_prepare: Failed to prepare query SELECT cohort1.*
FROM main.cohort1
WHERE NOT EXISTS (
SELECT 1 FROM (
SELECT cohort1.*, observation_period_start_date, observation_period_end_date
FROM main.cohort1
LEFT JOIN main.observation_period
ON (cohort1.subject_id = observation_period.person_id)
) RHS
WHERE
(cohort1.cohort_definition_id = RHS.cohort_definition_id) AND
(cohort1.subject_id = RHS.subject_id) AND
(cohort1.cohort_start_date = RHS.cohort_start_date) AND
(cohort1.cohort_end_date = RHS.cohort_end_date) AND
(RHS.cohort_start_date >= RHS.observation_period_start_date AND RHS.cohort_start_date <= RHS.observation_period_end_date AND RHS.cohort_end_date >= RHS.observation_period_start_date AND RHS.cohort_end_date <= RHS.observation_period_end_date)
)
Error: Binder Error: Cannot compare values of type VARCHAR and type DATE - an explicit cast is required
LINE 15: (RHS.cohort_start_date >= RHS.observation_period_start_date AND RHS.cohort_start_date <= RHS.observation_period_end_date AND RHS.cohort_end_date >= RHS.observation_period_start_date AND RHS.cohort_end_date <= RHS.observation_period_end_date)
)...
^
Backtrace:
▆
1. ├─PatientProfiles::mockPatientProfiles(...) at test-addFutureObservation.R:126:3
2. │ └─omopgenerics::newCohortTable(cdm[[cohort]])
3. │ └─omopgenerics:::validateGeneratedCohortSet(cohort, soft = .softValidation)
4. │ └─omopgenerics::checkCohortRequirements(...)
5. │ └─omopgenerics:::checkObservationPeriod(...)
6. │ ├─dplyr::collect(...)
7. │ └─omopgenerics:::collect.cohort_table(...)
8. │ ├─dplyr::collect(x)
9. │ └─omopgenerics:::collect.cdm_table(x)
10. │ ├─dplyr::collect(removeClass(x, "cdm_table"))
11. │ └─dbplyr:::collect.tbl_sql(removeClass(x, "cdm_table"))
12. │ ├─base::withCallingHandlers(...)
13. │ ├─dbplyr::db_collect(...)
14. │ └─dbplyr:::db_collect.DBIConnection(...)
15. │ ├─DBI::dbSendQuery(con, sql)
16. │ └─duckdb::dbSendQuery(con, sql)
17. │ └─duckdb (local) .local(conn, statement, ...)
18. │ └─duckdb:::rapi_prepare(conn@conn_ref, statement)
19. └─base::.handleSimpleError(...)
20. └─dbplyr (local) h(simpleError(msg, call))
21. └─cli::cli_abort("Failed to collect lazy table.", parent = cnd)
22. └─rlang::abort(...)
── Error ('test-addFutureObservation.R:198:3'): different name ─────────────────
Error in `dplyr::collect(removeClass(x, "cdm_table"))`: Failed to collect lazy table.
Caused by error:
! rapi_prepare: Failed to prepare query SELECT cohort1.*
FROM main.cohort1
WHERE NOT EXISTS (
SELECT 1 FROM (
SELECT cohort1.*, observation_period_start_date, observation_period_end_date
FROM main.cohort1
LEFT JOIN main.observation_period
ON (cohort1.subject_id = observation_period.person_id)
) RHS
WHERE
(cohort1.cohort_definition_id = RHS.cohort_definition_id) AND
(cohort1.subject_id = RHS.subject_id) AND
(cohort1.cohort_start_date = RHS.cohort_start_date) AND
(cohort1.cohort_end_date = RHS.cohort_end_date) AND
(RHS.cohort_start_date >= RHS.observation_period_start_date AND RHS.cohort_start_date <= RHS.observation_period_end_date AND RHS.cohort_end_date >= RHS.observation_period_start_date AND RHS.cohort_end_date <= RHS.observation_period_end_date)
)
Error: Binder Error: Cannot compare values of type VARCHAR and type DATE - an explicit cast is required
LINE 15: (RHS.cohort_start_date >= RHS.observation_period_start_date AND RHS.cohort_start_date <= RHS.observation_period_end_date AND RHS.cohort_end_date >= RHS.observation_period_start_date AND RHS.cohort_end_date <= RHS.observation_period_end_date)
)...
^
Backtrace:
▆
1. ├─PatientProfiles::mockPatientProfiles(...) at test-addFutureObservation.R:198:3
2. │ └─omopgenerics::newCohortTable(cdm[[cohort]])
3. │ └─omopgenerics:::validateGeneratedCohortSet(cohort, soft = .softValidation)
4. │ └─omopgenerics::checkCohortRequirements(...)
5. │ └─omopgenerics:::checkObservationPeriod(...)
6. │ ├─dplyr::collect(...)
7. │ └─omopgenerics:::collect.cohort_table(...)
8. │ ├─dplyr::collect(x)
9. │ └─omopgenerics:::collect.cdm_table(x)
10. │ ├─dplyr::collect(removeClass(x, "cdm_table"))
11. │ └─dbplyr:::collect.tbl_sql(removeClass(x, "cdm_table"))
12. │ ├─base::withCallingHandlers(...)
13. │ ├─dbplyr::db_collect(...)
14. │ └─dbplyr:::db_collect.DBIConnection(...)
15. │ ├─DBI::dbSendQuery(con, sql)
16. │ └─duckdb::dbSendQuery(con, sql)
17. │ └─duckdb (local) .local(conn, statement, ...)
18. │ └─duckdb:::rapi_prepare(conn@conn_ref, statement)
19. └─base::.handleSimpleError(...)
20. └─dbplyr (local) h(simpleError(msg, call))
21. └─cli::cli_abort("Failed to collect lazy table.", parent = cnd)
22. └─rlang::abort(...)
── Error ('test-addFutureObservation.R:251:3'): priorHistory and future_observation - outside of observation period ──
Error in `dplyr::collect(removeClass(x, "cdm_table"))`: Failed to collect lazy table.
Caused by error:
! rapi_prepare: Failed to prepare query SELECT cohort1.*
FROM main.cohort1
WHERE NOT EXISTS (
SELECT 1 FROM (
SELECT cohort1.*, observation_period_start_date, observation_period_end_date
FROM main.cohort1
LEFT JOIN main.observation_period
ON (cohort1.subject_id = observation_period.person_id)
) RHS
WHERE
(cohort1.cohort_definition_id = RHS.cohort_definition_id) AND
(cohort1.subject_id = RHS.subject_id) AND
(cohort1.cohort_start_date = RHS.cohort_start_date) AND
(cohort1.cohort_end_date = RHS.cohort_end_date) AND
(RHS.cohort_start_date >= RHS.observation_period_start_date AND RHS.cohort_start_date <= RHS.observation_period_end_date AND RHS.cohort_end_date >= RHS.observation_period_start_date AND RHS.cohort_end_date <= RHS.observation_period_end_date)
)
Error: Binder Error: Cannot compare values of type VARCHAR and type DATE - an explicit cast is required
LINE 15: (RHS.cohort_start_date >= RHS.observation_period_start_date AND RHS.cohort_start_date <= RHS.observation_period_end_date AND RHS.cohort_end_date >= RHS.observation_period_start_date AND RHS.cohort_end_date <= RHS.observation_period_end_date)
)...
^
Backtrace:
▆
1. ├─PatientProfiles::mockPatientProfiles(...) at test-addFutureObservation.R:251:3
2. │ └─omopgenerics::newCohortTable(cdm[[cohort]])
3. │ └─omopgenerics:::validateGeneratedCohortSet(cohort, soft = .softValidation)
4. │ └─omopgenerics::checkCohortRequirements(...)
5. │ └─omopgenerics:::checkObservationPeriod(...)
6. │ ├─dplyr::collect(...)
7. │ └─omopgenerics:::collect.cohort_table(...)
8. │ ├─dplyr::collect(x)
9. │ └─omopgenerics:::collect.cdm_table(x)
10. │ ├─dplyr::collect(removeClass(x, "cdm_table"))
11. │ └─dbplyr:::collect.tbl_sql(removeClass(x, "cdm_table"))
12. │ ├─base::withCallingHandlers(...)
13. │ ├─dbplyr::db_collect(...)
14. │ └─dbplyr:::db_collect.DBIConnection(...)
15. │ ├─DBI::dbSendQuery(con, sql)
16. │ └─duckdb::dbSendQuery(con, sql)
17. │ └─duckdb (local) .local(conn, statement, ...)
18. │ └─duckdb:::rapi_prepare(conn@conn_ref, statement)
19. └─base::.handleSimpleError(...)
20. └─dbplyr (local) h(simpleError(msg, call))
21. └─cli::cli_abort("Failed to collect lazy table.", parent = cnd)
22. └─rlang::abort(...)
── Error ('test-addFutureObservation.R:301:3'): multiple observation periods ───
Error in `dplyr::collect(removeClass(x, "cdm_table"))`: Failed to collect lazy table.
Caused by error:
! rapi_prepare: Failed to prepare query SELECT cohort2.*
FROM main.cohort2
WHERE NOT EXISTS (
SELECT 1 FROM (
SELECT cohort2.*, observation_period_start_date, observation_period_end_date
FROM main.cohort2
LEFT JOIN main.observation_period
ON (cohort2.subject_id = observation_period.person_id)
) RHS
WHERE
(cohort2.cohort_definition_id = RHS.cohort_definition_id) AND
(cohort2.subject_id = RHS.subject_id) AND
(cohort2.cohort_start_date = RHS.cohort_start_date) AND
(cohort2.cohort_end_date = RHS.cohort_end_date) AND
(RHS.cohort_start_date >= RHS.observation_period_start_date AND RHS.cohort_start_date <= RHS.observation_period_end_date AND RHS.cohort_end_date >= RHS.observation_period_start_date AND RHS.cohort_end_date <= RHS.observation_period_end_date)
)
Error: Binder Error: Cannot compare values of type VARCHAR and type DATE - an explicit cast is required
LINE 15: (RHS.cohort_start_date >= RHS.observation_period_start_date AND RHS.cohort_start_date <= RHS.observation_period_end_date AND RHS.cohort_end_date >= RHS.observation_period_start_date AND RHS.cohort_end_date <= RHS.observation_period_end_date)
)...
^
Backtrace:
▆
1. ├─PatientProfiles::mockPatientProfiles(...) at test-addFutureObservation.R:301:3
2. │ └─omopgenerics::newCohortTable(cdm[[cohort]])
3. │ └─omopgenerics:::validateGeneratedCohortSet(cohort, soft = .softValidation)
4. │ └─omopgenerics::checkCohortRequirements(...)
5. │ └─omopgenerics:::checkObservationPeriod(...)
6. │ ├─dplyr::collect(...)
7. │ └─omopgenerics:::collect.cohort_table(...)
8. │ ├─dplyr::collect(x)
9. │ └─omopgenerics:::collect.cdm_table(x)
10. │ ├─dplyr::collect(removeClass(x, "cdm_table"))
11. │ └─dbplyr:::collect.tbl_sql(removeClass(x, "cdm_table"))
12. │ ├─base::withCallingHandlers(...)
13. │ ├─dbplyr::db_collect(...)
14. │ └─dbplyr:::db_collect.DBIConnection(...)
15. │ ├─DBI::dbSendQuery(con, sql)
16. │ └─duckdb::dbSendQuery(con, sql)
17. │ └─duckdb (local) .local(conn, statement, ...)
18. │ └─duckdb:::rapi_prepare(conn@conn_ref, statement)
19. └─base::.handleSimpleError(...)
20. └─dbplyr (local) h(simpleError(msg, call))
21. └─cli::cli_abort("Failed to collect lazy table.", parent = cnd)
22. └─rlang::abort(...)
── Error ('test-addInObservation.R:4:3'): addInObservation, input length and type ──
Error in `CDMConnector::datediff()`: No known SQL translation
Backtrace:
▆
1. ├─testthat::expect_warning(addInObservation(cdm$cohort2, "cdm")) at test-addInObservation.R:4:3
2. │ └─testthat:::expect_condition_matching(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─PatientProfiles::addInObservation(cdm$cohort2, "cdm")
8. │ └─... %>% ...
9. ├─dplyr::select(., -"prior_observation", -"future_observation")
10. ├─dplyr::mutate(...)
11. ├─PatientProfiles::addDemographics(...)
12. │ └─x %>% dplyr::compute()
13. ├─dplyr::compute(.)
14. ├─omopgenerics:::compute.cdm_table(.)
15. │ ├─dplyr::compute(...)
16. │ └─CDMConnector:::compute.db_cdm(...)
17. │ └─CDMConnector:::.computeQuery(...)
18. │ └─dbplyr::sql_render(x)
19. │ ├─dbplyr::sql_render(...)
20. │ └─dbplyr:::sql_render.tbl_lazy(...)
21. │ ├─dbplyr::sql_render(...)
22. │ └─dbplyr:::sql_render.lazy_query(...)
23. │ ├─dbplyr::sql_build(query, con = con, sql_options = sql_options)
24. │ └─dbplyr:::sql_build.lazy_select_query(query, con = con, sql_options = sql_options)
25. │ └─dbplyr:::get_select_sql(...)
26. │ └─dbplyr:::translate_select_sql(con, select)
27. │ └─dbplyr::translate_sql_(...)
28. │ └─base::lapply(...)
29. │ └─dbplyr (local) FUN(X[[i]], ...)
30. │ ├─dbplyr::escape(eval_tidy(x, mask), con = con)
31. │ └─rlang::eval_tidy(x, mask)
32. └─CDMConnector::datediff
33. └─cli::cli_abort(...)
34. └─rlang::abort(...)
── Error ('test-addInObservation.R:16:3'): addInObservation, cohort and condition_occurrence ──
Error in `CDMConnector::datediff()`: No known SQL translation
Backtrace:
▆
1. ├─PatientProfiles::addInObservation(cdm$cohort1) at test-addInObservation.R:16:3
2. │ └─... %>% ...
3. ├─dplyr::select(., -"prior_observation", -"future_observation")
4. ├─dplyr::mutate(...)
5. ├─PatientProfiles::addDemographics(...)
6. │ └─x %>% dplyr::compute()
7. ├─dplyr::compute(.)
8. ├─omopgenerics:::compute.cdm_table(.)
9. │ ├─dplyr::compute(...)
10. │ └─CDMConnector:::compute.db_cdm(...)
11. │ └─CDMConnector:::.computeQuery(...)
12. │ └─dbplyr::sql_render(x)
13. │ ├─dbplyr::sql_render(...)
14. │ └─dbplyr:::sql_render.tbl_lazy(...)
15. │ ├─dbplyr::sql_render(...)
16. │ └─dbplyr:::sql_render.lazy_query(...)
17. │ ├─dbplyr::sql_build(query, con = con, sql_options = sql_options)
18. │ └─dbplyr:::sql_build.lazy_select_query(query, con = con, sql_options = sql_options)
19. │ └─dbplyr:::get_select_sql(...)
20. │ └─dbplyr:::translate_select_sql(con, select)
21. │ └─dbplyr::translate_sql_(...)
22. │ └─base::lapply(...)
23. │ └─dbplyr (local) FUN(X[[i]], ...)
24. │ ├─dbplyr::escape(eval_tidy(x, mask), con = con)
25. │ └─rlang::eval_tidy(x, mask)
26. └─CDMConnector::datediff
27. └─cli::cli_abort(...)
28. └─rlang::abort(...)
── Error ('test-addInObservation.R:44:3'): addInObservation, parameters ────────
Error in `CDMConnector::datediff()`: No known SQL translation
Backtrace:
▆
1. ├─PatientProfiles::addInObservation(...) at test-addInObservation.R:44:3
2. │ └─... %>% ...
3. ├─dplyr::select(., -"prior_observation", -"future_observation")
4. ├─dplyr::mutate(...)
5. ├─PatientProfiles::addDemographics(...)
6. │ └─x %>% dplyr::compute()
7. ├─dplyr::compute(.)
8. ├─omopgenerics:::compute.cdm_table(.)
9. │ ├─dplyr::compute(...)
10. │ └─CDMConnector:::compute.db_cdm(...)
11. │ └─CDMConnector:::.computeQuery(...)
12. │ └─dbplyr::sql_render(x)
13. │ ├─dbplyr::sql_render(...)
14. │ └─dbplyr:::sql_render.tbl_lazy(...)
15. │ ├─dbplyr::sql_render(...)
16. │ └─dbplyr:::sql_render.lazy_query(...)
17. │ ├─dbplyr::sql_build(query, con = con, sql_options = sql_options)
18. │ └─dbplyr:::sql_build.lazy_select_query(query, con = con, sql_options = sql_options)
19. │ └─dbplyr:::get_select_sql(...)
20. │ └─dbplyr:::translate_select_sql(con, select)
21. │ └─dbplyr::translate_sql_(...)
22. │ └─base::lapply(...)
23. │ └─dbplyr (local) FUN(X[[i]], ...)
24. │ ├─dbplyr::escape(eval_tidy(x, mask), con = con)
25. │ └─rlang::eval_tidy(x, mask)
26. └─CDMConnector::datediff
27. └─cli::cli_abort(...)
28. └─rlang::abort(...)
── Error ('test-addDemographics.R:15:3'): addDemographics, cohort and condition_occurrence ──
Error in `CDMConnector::datediff()`: No known SQL translation
Backtrace:
▆
1. ├─cdm$cohort1 %>% ... at test-addDemographics.R:15:3
2. ├─PatientProfiles::addDemographics(., ageImposeMonth = TRUE, ageImposeDay = TRUE)
3. │ └─x %>% dplyr::compute()
4. ├─dplyr::compute(.)
5. ├─omopgenerics:::compute.cdm_table(.)
6. │ ├─dplyr::compute(...)
7. │ └─CDMConnector:::compute.db_cdm(...)
8. │ └─CDMConnector:::.computeQuery(...)
9. │ └─dbplyr::sql_render(x)
10. │ ├─dbplyr::sql_render(...)
11. │ └─dbplyr:::sql_render.tbl_lazy(...)
12. │ ├─dbplyr::sql_render(...)
13. │ └─dbplyr:::sql_render.lazy_query(...)
14. │ ├─dbplyr::sql_build(query, con = con, sql_options = sql_options)
15. │ └─dbplyr:::sql_build.lazy_select_query(query, con = con, sql_options = sql_options)
16. │ ├─dbplyr::sql_build(op$x, con, sql_options = sql_options)
17. │ └─dbplyr:::sql_build.lazy_select_query(op$x, con, sql_options = sql_options)
18. │ └─dbplyr:::get_select_sql(...)
19. │ └─dbplyr:::translate_select_sql(con, select)
20. │ └─dbplyr::translate_sql_(...)
21. │ └─base::lapply(...)
22. │ └─dbplyr (local) FUN(X[[i]], ...)
23. │ ├─dbplyr::escape(eval_tidy(x, mask), con = con)
24. │ └─rlang::eval_tidy(x, mask)
25. └─CDMConnector::datediff
26. └─cli::cli_abort(...)
27. └─rlang::abort(...)
── Error ('test-addDemographics.R:97:3'): addDemographics, parameters ──────────
Error in `CDMConnector::datediff()`: No known SQL translation
Backtrace:
▆
1. ├─cdm$cohort1 %>% ... at test-addDemographics.R:97:3
2. ├─PatientProfiles::addDemographics(...)
3. │ └─x %>% dplyr::compute()
4. ├─dplyr::compute(.)
5. ├─omopgenerics:::compute.cdm_table(.)
6. │ ├─dplyr::compute(...)
7. │ └─CDMConnector:::compute.db_cdm(...)
8. │ └─CDMConnector:::.computeQuery(...)
9. │ └─dbplyr::sql_render(x)
10. │ ├─dbplyr::sql_render(...)
11. │ └─dbplyr:::sql_render.tbl_lazy(...)
12. │ ├─dbplyr::sql_render(...)
13. │ └─dbplyr:::sql_render.lazy_query(...)
14. │ ├─dbplyr::sql_build(query, con = con, sql_options = sql_options)
15. │ └─dbplyr:::sql_build.lazy_select_query(query, con = con, sql_options = sql_options)
16. │ ├─dbplyr::sql_build(op$x, con, sql_options = sql_options)
17. │ └─dbplyr:::sql_build.lazy_select_query(op$x, con, sql_options = sql_options)
18. │ └─dbplyr:::get_select_sql(...)
19. │ └─dbplyr:::translate_select_sql(con, select)
20. │ └─dbplyr::translate_sql_(...)
21. │ └─base::lapply(...)
22. │ └─dbplyr (local) FUN(X[[i]], ...)
23. │ ├─dbplyr::escape(eval_tidy(x, mask), con = con)
24. │ └─rlang::eval_tidy(x, mask)
25. └─CDMConnector::datediff
26. └─cli::cli_abort(...)
27. └─rlang::abort(...)
── Error ('test-addDemographics.R:183:3'): partial demographics - cohorts ──────
Error in `CDMConnector::datediff()`: No known SQL translation
Backtrace:
▆
1. ├─cdm$cohort1 %>% ... at test-addDemographics.R:183:3
2. ├─PatientProfiles::addDemographics(...)
3. │ └─x %>% dplyr::compute()
4. ├─dplyr::compute(.)
5. ├─omopgenerics:::compute.cdm_table(.)
6. │ ├─dplyr::compute(...)
7. │ └─CDMConnector:::compute.db_cdm(...)
8. │ └─CDMConnector:::.computeQuery(...)
9. │ └─dbplyr::sql_render(x)
10. │ ├─dbplyr::sql_render(...)
11. │ └─dbplyr:::sql_render.tbl_lazy(...)
12. │ ├─dbplyr::sql_render(...)
13. │ └─dbplyr:::sql_render.lazy_query(...)
14. │ ├─dbplyr::sql_build(query, con = con, sql_options = sql_options)
15. │ └─dbplyr:::sql_build.lazy_select_query(query, con = con, sql_options = sql_options)
16. │ └─dbplyr:::get_select_sql(...)
17. │ └─dbplyr:::translate_select_sql(con, select)
18. │ └─dbplyr::translate_sql_(...)
19. │ └─base::lapply(...)
20. │ └─dbplyr (local) FUN(X[[i]], ...)
21. │ ├─dbplyr::escape(eval_tidy(x, mask), con = con)
22. │ └─rlang::eval_tidy(x, mask)
23. └─CDMConnector::datediff
24. └─cli::cli_abort(...)
25. └─rlang::abort(...)
── Error ('test-addDemographics.R:247:3'): partial demographics - omop tables ──
Error in `CDMConnector::datediff()`: No known SQL translation
Backtrace:
▆
1. ├─cdm$condition_occurrence %>% ... at test-addDemographics.R:247:3
2. ├─PatientProfiles::addDemographics(...)
3. │ └─x %>% dplyr::compute()
4. ├─dplyr::compute(.)
5. ├─omopgenerics:::compute.cdm_table(.)
6. │ ├─dplyr::compute(...)
7. │ └─CDMConnector:::compute.db_cdm(...)
8. │ └─CDMConnector:::.computeQuery(...)
9. │ └─dbplyr::sql_render(x)
10. │ ├─dbplyr::sql_render(...)
11. │ └─dbplyr:::sql_render.tbl_lazy(...)
12. │ ├─dbplyr::sql_render(...)
13. │ └─dbplyr:::sql_render.lazy_query(...)
14. │ ├─dbplyr::sql_build(query, con = con, sql_options = sql_options)
15. │ └─dbplyr:::sql_build.lazy_select_query(query, con = con, sql_options = sql_options)
16. │ └─dbplyr:::get_select_sql(...)
17. │ └─dbplyr:::translate_select_sql(con, select)
18. │ └─dbplyr::translate_sql_(...)
19. │ └─base::lapply(...)
20. │ └─dbplyr (local) FUN(X[[i]], ...)
21. │ ├─dbplyr::escape(eval_tidy(x, mask), con = con)
22. │ └─rlang::eval_tidy(x, mask)
23. └─CDMConnector::datediff
24. └─cli::cli_abort(...)
25. └─rlang::abort(...)
── Error ('test-addDemographics.R:316:3'): priorObservation and future_observation - outside of observation period ──
Error in `CDMConnector::datediff()`: No known SQL translation
Backtrace:
▆
1. ├─cdm$condition_occurrence %>% ... at test-addDemographics.R:316:3
2. ├─PatientProfiles::addDemographics(...)
3. │ └─x %>% dplyr::compute()
4. ├─dplyr::compute(.)
5. ├─omopgenerics:::compute.cdm_table(.)
6. │ ├─dplyr::compute(...)
7. │ └─CDMConnector:::compute.db_cdm(...)
8. │ └─CDMConnector:::.computeQuery(...)
9. │ └─dbplyr::sql_render(x)
10. │ ├─dbplyr::sql_render(...)
11. │ └─dbplyr:::sql_render.tbl_lazy(...)
12. │ ├─dbplyr::sql_render(...)
13. │ └─dbplyr:::sql_render.lazy_query(...)
14. │ ├─dbplyr::sql_build(query, con = con, sql_options = sql_options)
15. │ └─dbplyr:::sql_build.lazy_select_query(query, con = con, sql_options = sql_options)
16. │ └─dbplyr:::get_select_sql(...)
17. │ └─dbplyr:::translate_select_sql(con, select)
18. │ └─dbplyr::translate_sql_(...)
19. │ └─base::lapply(...)
20. │ └─dbplyr (local) FUN(X[[i]], ...)
21. │ ├─dbplyr::escape(eval_tidy(x, mask), con = con)
22. │ └─rlang::eval_tidy(x, mask)
23. └─CDMConnector::datediff
24. └─cli::cli_abort(...)
25. └─rlang::abort(...)
── Error ('test-addDemographics.R:373:3'): priorObservation - multiple observation periods ──
Error in `CDMConnector::datediff()`: No known SQL translation
Backtrace:
▆
1. ├─cdm$cohort1 %>% ... at test-addDemographics.R:373:3
2. ├─PatientProfiles::addDemographics(...)
3. │ └─x %>% dplyr::compute()
4. ├─dplyr::compute(.)
5. ├─omopgenerics:::compute.cdm_table(.)
6. │ ├─dplyr::compute(...)
7. │ └─CDMConnector:::compute.db_cdm(...)
8. │ └─CDMConnector:::.computeQuery(...)
9. │ └─dbplyr::sql_render(x)
10. │ ├─dbplyr::sql_render(...)
11. │ └─dbplyr:::sql_render.tbl_lazy(...)
12. │ ├─dbplyr::sql_render(...)
13. │ └─dbplyr:::sql_render.lazy_query(...)
14. │ ├─dbplyr::sql_build(query, con = con, sql_options = sql_options)
15. │ └─dbplyr:::sql_build.lazy_select_query(query, con = con, sql_options = sql_options)
16. │ └─dbplyr:::get_select_sql(...)
17. │ └─dbplyr:::translate_select_sql(con, select)
18. │ └─dbplyr::translate_sql_(...)
19. │ └─base::lapply(...)
20. │ └─dbplyr (local) FUN(X[[i]], ...)
21. │ ├─dbplyr::escape(eval_tidy(x, mask), con = con)
22. │ └─rlang::eval_tidy(x, mask)
23. └─CDMConnector::datediff
24. └─cli::cli_abort(...)
25. └─rlang::abort(...)
── Error ('test-addDemographics.R:451:3'): check that no extra rows are added ──
Error in `CDMConnector::datediff()`: No known SQL translation
Backtrace:
▆
1. ├─cdm$cohort1 %>% ... at test-addDemographics.R:451:3
2. ├─PatientProfiles::addDemographics(...)
3. │ └─x %>% dplyr::compute()
4. ├─dplyr::compute(.)
5. ├─omopgenerics:::compute.cdm_table(.)
6. │ ├─dplyr::compute(...)
7. │ └─CDMConnector:::compute.db_cdm(...)
8. │ └─CDMConnector:::.computeQuery(...)
9. │ └─dbplyr::sql_render(x)
10. │ ├─dbplyr::sql_render(...)
11. │ └─dbplyr:::sql_render.tbl_lazy(...)
12. │ ├─dbplyr::sql_render(...)
13. │ └─dbplyr:::sql_render.lazy_query(...)
14. │ ├─dbplyr::sql_build(query, con = con, sql_options = sql_options)
15. │ └─dbplyr:::sql_build.lazy_select_query(query, con = con, sql_options = sql_options)
16. │ └─dbplyr:::get_select_sql(...)
17. │ └─dbplyr:::translate_select_sql(con, select)
18. │ └─dbplyr::translate_sql_(...)
19. │ └─base::lapply(...)
20. │ └─dbplyr (local) FUN(X[[i]], ...)
21. │ ├─dbplyr::escape(eval_tidy(x, mask), con = con)
22. │ └─rlang::eval_tidy(x, mask)
23. └─CDMConnector::datediff
24. └─cli::cli_abort(...)
25. └─rlang::abort(...)
── Error ('test-addDemographics.R:538:3'): age at cohort end, no missing, check age computation ──
Error in `CDMConnector::datediff()`: No known SQL translation
Backtrace:
▆
1. ├─... %>% dplyr::collect() at test-addDemographics.R:538:3
2. ├─dplyr::collect(.)
3. ├─PatientProfiles::addDemographics(...)
4. │ └─x %>% dplyr::compute()
5. ├─dplyr::compute(.)
6. ├─omopgenerics:::compute.cdm_table(.)
7. │ ├─dplyr::compute(...)
8. │ └─CDMConnector:::compute.db_cdm(...)
9. │ └─CDMConnector:::.computeQuery(...)
10. │ └─dbplyr::sql_render(x)
11. │ ├─dbplyr::sql_render(...)
12. │ └─dbplyr:::sql_render.tbl_lazy(...)
13. │ ├─dbplyr::sql_render(...)
14. │ └─dbplyr:::sql_render.lazy_query(...)
15. │ ├─dbplyr::sql_build(query, con = con, sql_options = sql_options)
16. │ └─dbplyr:::sql_build.lazy_select_query(query, con = 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:::get_select_sql(...)
20. │ └─dbplyr:::translate_select_sql(con, select)
21. │ └─dbplyr::translate_sql_(...)
22. │ └─base::lapply(...)
23. │ └─dbplyr (local) FUN(X[[i]], ...)
24. │ ├─dbplyr::escape(eval_tidy(x, mask), con = con)
25. │ └─rlang::eval_tidy(x, mask)
26. └─CDMConnector::datediff
27. └─cli::cli_abort(...)
28. └─rlang::abort(...)
── Error ('test-addDemographics.R:1077:3'): test if column exist, overwrite ────
Error in `CDMConnector::datediff()`: No known SQL translation
Backtrace:
▆
1. ├─testthat::expect_warning(...) at test-addDemographics.R:1077:3
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. ├─cdm$cohort1 %>% addDemographics() %>% dplyr::collect()
8. ├─dplyr::collect(.)
9. ├─PatientProfiles::addDemographics(.)
10. │ └─x %>% dplyr::compute()
11. ├─dplyr::compute(.)
12. ├─omopgenerics:::compute.cdm_table(.)
13. │ ├─dplyr::compute(...)
14. │ └─CDMConnector:::compute.db_cdm(...)
15. │ └─CDMConnector:::.computeQuery(...)
16. │ └─dbplyr::sql_render(x)
17. │ ├─dbplyr::sql_render(...)
18. │ └─dbplyr:::sql_render.tbl_lazy(...)
19. │ ├─dbplyr::sql_render(...)
20. │ └─dbplyr:::sql_render.lazy_query(...)
21. │ ├─dbplyr::sql_build(query, con = con, sql_options = sql_options)
22. │ └─dbplyr:::sql_build.lazy_select_query(query, con = con, sql_options = sql_options)
23. │ ├─dbplyr::sql_build(op$x, con, sql_options = sql_options)
24. │ └─dbplyr:::sql_build.lazy_select_query(op$x, con, sql_options = sql_options)
25. │ └─dbplyr:::get_select_sql(...)
26. │ └─dbplyr:::translate_select_sql(con, select)
27. │ └─dbplyr::translate_sql_(...)
28. │ └─base::lapply(...)
29. │ └─dbplyr (local) FUN(X[[i]], ...)
30. │ ├─dbplyr::escape(eval_tidy(x, mask), con = con)
31. │ └─rlang::eval_tidy(x, mask)
32. └─CDMConnector::datediff
33. └─cli::cli_abort(...)
34. └─rlang::abort(...)
── Error ('test-addDemographics.R:1232:3'): overwriting obs period variables ───
Error in `CDMConnector::datediff()`: No known SQL translation
Backtrace:
▆
1. ├─testthat::expect_warning(cdm$cohort1 <- cdm$cohort1 %>% PatientProfiles::addDemographics()) at test-addDemographics.R:1232:3
2. │ └─testthat:::expect_condition_matching(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─cdm$cohort1 %>% PatientProfiles::addDemographics()
8. ├─PatientProfiles::addDemographics(.)
9. │ └─x %>% dplyr::compute()
10. ├─dplyr::compute(.)
11. ├─omopgenerics:::compute.cdm_table(.)
12. │ ├─dplyr::compute(...)
13. │ └─CDMConnector:::compute.db_cdm(...)
14. │ └─CDMConnector:::.computeQuery(...)
15. │ └─dbplyr::sql_render(x)
16. │ ├─dbplyr::sql_render(...)
17. │ └─dbplyr:::sql_render.tbl_lazy(...)
18. │ ├─dbplyr::sql_render(...)
19. │ └─dbplyr:::sql_render.lazy_query(...)
20. │ ├─dbplyr::sql_build(query, con = con, sql_options = sql_options)
21. │ └─dbplyr:::sql_build.lazy_select_query(query, con = con, sql_options = sql_options)
22. │ ├─dbplyr::sql_build(op$x, con, sql_options = sql_options)
23. │ └─dbplyr:::sql_build.lazy_select_query(op$x, con, sql_options = sql_options)
24. │ └─dbplyr:::get_select_sql(...)
25. │ └─dbplyr:::translate_select_sql(con, select)
26. │ └─dbplyr::translate_sql_(...)
27. │ └─base::lapply(...)
28. │ └─dbplyr (local) FUN(X[[i]], ...)
29. │ ├─dbplyr::escape(eval_tidy(x, mask), con = con)
30. │ └─rlang::eval_tidy(x, mask)
31. └─CDMConnector::datediff
32. └─cli::cli_abort(...)
33. └─rlang::abort(...)
── Error ('test-addIntersect.R:55:3'): working examples ────────────────────────
Error in `CDMConnector::datediff()`: No known SQL translation
Backtrace:
▆
1. ├─cdm$cohort1 %>% ... at test-addIntersect.R:55:3
2. ├─PatientProfiles::addIntersect(...)
3. │ └─... %>% ...
4. ├─dplyr::mutate(., censor_date = .data[[censorDate %||% "censor_date"]])
5. ├─dplyr::mutate(...)
6. ├─PatientProfiles::addFutureObservation(...)
7. │ └─x %>% ...
8. ├─PatientProfiles::addDemographics(...)
9. │ └─x %>% dplyr::compute()
10. ├─dplyr::compute(.)
11. ├─omopgenerics:::compute.cdm_table(.)
12. │ ├─dplyr::compute(...)
13. │ └─CDMConnector:::compute.db_cdm(...)
14. │ └─CDMConnector:::.computeQuery(...)
15. │ └─dbplyr::sql_render(x)
16. │ ├─dbplyr::sql_render(...)
17. │ └─dbplyr:::sql_render.tbl_lazy(...)
18. │ ├─dbplyr::sql_render(...)
19. │ └─dbplyr:::sql_render.lazy_query(...)
20. │ ├─dbplyr::sql_build(query, con = con, sql_options = sql_options)
21. │ └─dbplyr:::sql_build.lazy_select_query(query, con = con, sql_options = sql_options)
22. │ └─dbplyr:::get_select_sql(...)
23. │ └─dbplyr:::translate_select_sql(con, select)
24. │ └─dbplyr::translate_sql_(...)
25. │ └─base::lapply(...)
26. │ └─dbplyr (local) FUN(X[[i]], ...)
27. │ ├─dbplyr::escape(eval_tidy(x, mask), con = con)
28. │ └─rlang::eval_tidy(x, mask)
29. └─CDMConnector::datediff
30. └─cli::cli_abort(...)
31. └─rlang::abort(...)
── Error ('test-addIntersect.R:251:3'): working examples with cohort_end_date ──
Error in `CDMConnector::datediff()`: No known SQL translation
Backtrace:
▆
1. ├─dplyr::arrange(...) at test-addIntersect.R:251:3
2. ├─... %>% dplyr::collect()
3. ├─dplyr::collect(.)
4. ├─PatientProfiles::addIntersect(...)
5. │ └─... %>% ...
6. ├─dplyr::mutate(., censor_date = .data[[censorDate %||% "censor_date"]])
7. ├─dplyr::mutate(...)
8. ├─PatientProfiles::addFutureObservation(...)
9. │ └─x %>% ...
10. ├─PatientProfiles::addDemographics(...)
11. │ └─x %>% dplyr::compute()
12. ├─dplyr::compute(.)
13. ├─omopgenerics:::compute.cdm_table(.)
14. │ ├─dplyr::compute(...)
15. │ └─CDMConnector:::compute.db_cdm(...)
16. │ └─CDMConnector:::.computeQuery(...)
17. │ └─dbplyr::sql_render(x)
18. │ ├─dbplyr::sql_render(...)
19. │ └─dbplyr:::sql_render.tbl_lazy(...)
20. │ ├─dbplyr::sql_render(...)
21. │ └─dbplyr:::sql_render.lazy_query(...)
22. │ ├─dbplyr::sql_build(query, con = con, sql_options = sql_options)
23. │ └─dbplyr:::sql_build.lazy_select_query(query, con = con, sql_options = sql_options)
24. │ └─dbplyr:::get_select_sql(...)
25. │ └─dbplyr:::translate_select_sql(con, select)
26. │ └─dbplyr::translate_sql_(...)
27. │ └─base::lapply(...)
28. │ └─dbplyr (local) FUN(X[[i]], ...)
29. │ ├─dbplyr::escape(eval_tidy(x, mask), con = con)
30. │ └─rlang::eval_tidy(x, mask)
31. └─CDMConnector::datediff
32. └─cli::cli_abort(...)
33. └─rlang::abort(...)
── Error ('test-addIntersect.R:323:3'): working examples with extra column ─────
Error in `CDMConnector::datediff()`: No known SQL translation
Backtrace:
▆
1. ├─dplyr::arrange(...) at test-addIntersect.R:323:3
2. ├─... %>% dplyr::collect()
3. ├─dplyr::collect(.)
4. ├─PatientProfiles::addIntersect(...)
5. │ └─... %>% ...
6. ├─dplyr::mutate(., censor_date = .data[[censorDate %||% "censor_date"]])
7. ├─dplyr::mutate(...)
8. ├─PatientProfiles::addFutureObservation(...)
9. │ └─x %>% ...
10. ├─PatientProfiles::addDemographics(...)
11. │ └─x %>% dplyr::compute()
12. ├─dplyr::compute(.)
13. ├─omopgenerics:::compute.cdm_table(.)
14. │ ├─dplyr::compute(...)
15. │ └─CDMConnector:::compute.db_cdm(...)
16. │ └─CDMConnector:::.computeQuery(...)
17. │ └─dbplyr::sql_render(x)
18. │ ├─dbplyr::sql_render(...)
19. │ └─dbplyr:::sql_render.tbl_lazy(...)
20. │ ├─dbplyr::sql_render(...)
21. │ └─dbplyr:::sql_render.lazy_query(...)
22. │ ├─dbplyr::sql_build(query, con = con, sql_options = sql_options)
23. │ └─dbplyr:::sql_build.lazy_select_query(query, con = con, sql_options = sql_options)
24. │ └─dbplyr:::get_select_sql(...)
25. │ └─dbplyr:::translate_select_sql(con, select)
26. │ └─dbplyr::translate_sql_(...)
27. │ └─base::lapply(...)
28. │ └─dbplyr (local) FUN(X[[i]], ...)
29. │ ├─dbplyr::escape(eval_tidy(x, mask), con = con)
30. │ └─rlang::eval_tidy(x, mask)
31. └─CDMConnector::datediff
32. └─cli::cli_abort(...)
33. └─rlang::abort(...)
── Error ('test-addIntersect.R:451:3'): working examples with multiple cohort Ids ──
Error in `CDMConnector::datediff()`: No known SQL translation
Backtrace:
▆
1. ├─dplyr::arrange(...) at test-addIntersect.R:451:3
2. ├─... %>% dplyr::collect()
3. ├─dplyr::collect(.)
4. ├─PatientProfiles::addIntersect(...)
5. │ └─... %>% ...
6. ├─dplyr::mutate(., censor_date = .data[[censorDate %||% "censor_date"]])
7. ├─dplyr::mutate(...)
8. ├─PatientProfiles::addFutureObservation(...)
9. │ └─x %>% ...
10. ├─PatientProfiles::addDemographics(...)
11. │ └─x %>% dplyr::compute()
12. ├─dplyr::compute(.)
13. ├─omopgenerics:::compute.cdm_table(.)
14. │ ├─dplyr::compute(...)
15. │ └─CDMConnector:::compute.db_cdm(...)
16. │ └─CDMConnector:::.computeQuery(...)
17. │ └─dbplyr::sql_render(x)
18. │ ├─dbplyr::sql_render(...)
19. │ └─dbplyr:::sql_render.tbl_lazy(...)
20. │ ├─dbplyr::sql_render(...)
21. │ └─dbplyr:::sql_render.lazy_query(...)
22. │ ├─dbplyr::sql_build(query, con = con, sql_options = sql_options)
23. │ └─dbplyr:::sql_build.lazy_select_query(query, con = con, sql_options = sql_options)
24. │ └─dbplyr:::get_select_sql(...)
25. │ └─dbplyr:::translate_select_sql(con, select)
26. │ └─dbplyr::translate_sql_(...)
27. │ └─base::lapply(...)
28. │ └─dbplyr (local) FUN(X[[i]], ...)
29. │ ├─dbplyr::escape(eval_tidy(x, mask), con = con)
30. │ └─rlang::eval_tidy(x, mask)
31. └─CDMConnector::datediff
32. └─cli::cli_abort(...)
33. └─rlang::abort(...)
── Error ('test-addIntersect.R:547:3'): working examples calculating as incidence target cohort ──
Error in `CDMConnector::datediff()`: No known SQL translation
Backtrace:
▆
1. ├─dplyr::arrange(...) at test-addIntersect.R:547:3
2. ├─... %>% dplyr::collect()
3. ├─dplyr::collect(.)
4. ├─PatientProfiles::addIntersect(...)
5. │ └─... %>% ...
6. ├─dplyr::mutate(., censor_date = .data[[censorDate %||% "censor_date"]])
7. ├─dplyr::mutate(...)
8. ├─PatientProfiles::addFutureObservation(...)
9. │ └─x %>% ...
10. ├─PatientProfiles::addDemographics(...)
11. │ └─x %>% dplyr::compute()
12. ├─dplyr::compute(.)
13. ├─omopgenerics:::compute.cdm_table(.)
14. │ ├─dplyr::compute(...)
15. │ └─CDMConnector:::compute.db_cdm(...)
16. │ └─CDMConnector:::.computeQuery(...)
17. │ └─dbplyr::sql_render(x)
18. │ ├─dbplyr::sql_render(...)
19. │ └─dbplyr:::sql_render.tbl_lazy(...)
20. │ ├─dbplyr::sql_render(...)
21. │ └─dbplyr:::sql_render.lazy_query(...)
22. │ ├─dbplyr::sql_build(query, con = con, sql_options = sql_options)
23. │ └─dbplyr:::sql_build.lazy_select_query(query, con = con, sql_options = sql_options)
24. │ └─dbplyr:::get_select_sql(...)
25. │ └─dbplyr:::translate_select_sql(con, select)
26. │ └─dbplyr::translate_sql_(...)
27. │ └─base::lapply(...)
28. │ └─dbplyr (local) FUN(X[[i]], ...)
29. │ ├─dbplyr::escape(eval_tidy(x, mask), con = con)
30. │ └─rlang::eval_tidy(x, mask)
31. └─CDMConnector::datediff
32. └─cli::cli_abort(...)
33. └─rlang::abort(...)
── Error ('test-addIntersect.R:621:3'): working examples with more than one window ──
Error in `CDMConnector::datediff()`: No known SQL translation
Backtrace:
▆
1. ├─dplyr::arrange(...) at test-addIntersect.R:621:3
2. ├─... %>% dplyr::collect()
3. ├─dplyr::collect(.)
4. ├─PatientProfiles::addIntersect(...)
5. │ └─omopgenerics::cdmReference(x)
6. │ └─omopgenerics:::assertClass(table, "cdm_table")
7. │ ├─base::paste0(...)
8. │ └─base::paste0(base::class(x), collapse = ", ")
9. ├─PatientProfiles::addIntersect(., tableName = "cohort2", value = "date")
10. │ └─... %>% ...
11. ├─dplyr::mutate(., censor_date = .data[[censorDate %||% "censor_date"]])
12. ├─dplyr::mutate(...)
13. ├─PatientProfiles::addFutureObservation(...)
14. │ └─x %>% ...
15. ├─PatientProfiles::addDemographics(...)
16. │ └─x %>% dplyr::compute()
17. ├─dplyr::compute(.)
18. ├─omopgenerics:::compute.cdm_table(.)
19. │ ├─dplyr::compute(...)
20. │ └─CDMConnector:::compute.db_cdm(...)
21. │ └─CDMConnector:::.computeQuery(...)
22. │ └─dbplyr::sql_render(x)
23. │ ├─dbplyr::sql_render(...)
24. │ └─dbplyr:::sql_render.tbl_lazy(...)
25. │ ├─dbplyr::sql_render(...)
26. │ └─dbplyr:::sql_render.lazy_query(...)
27. │ ├─dbplyr::sql_build(query, con = con, sql_options = sql_options)
28. │ └─dbplyr:::sql_build.lazy_select_query(query, con = con, sql_options = sql_options)
29. │ └─dbplyr:::get_select_sql(...)
30. │ └─dbplyr:::translate_select_sql(con, select)
31. │ └─dbplyr::translate_sql_(...)
32. │ └─base::lapply(...)
33. │ └─dbplyr (local) FUN(X[[i]], ...)
34. │ ├─dbplyr::escape(eval_tidy(x, mask), con = con)
35. │ └─rlang::eval_tidy(x, mask)
36. └─CDMConnector::datediff
37. └─cli::cli_abort(...)
38. └─rlang::abort(...)
── Error ('test-addIntersect.R:711:3'): working examples with tables, not cohorts ──
Error in `CDMConnector::datediff()`: No known SQL translation
Backtrace:
▆
1. ├─... %>% dplyr::collect() at test-addIntersect.R:711:3
2. ├─dplyr::collect(.)
3. ├─PatientProfiles::addIntersect(...)
4. │ └─... %>% ...
5. ├─dplyr::mutate(., censor_date = .data[[censorDate %||% "censor_date"]])
6. ├─dplyr::mutate(...)
7. ├─PatientProfiles::addFutureObservation(...)
8. │ └─x %>% ...
9. ├─PatientProfiles::addDemographics(...)
10. │ └─x %>% dplyr::compute()
11. ├─dplyr::compute(.)
12. ├─omopgenerics:::compute.cdm_table(.)
13. │ ├─dplyr::compute(...)
14. │ └─CDMConnector:::compute.db_cdm(...)
15. │ └─CDMConnector:::.computeQuery(...)
16. │ └─dbplyr::sql_render(x)
17. │ ├─dbplyr::sql_render(...)
18. │ └─dbplyr:::sql_render.tbl_lazy(...)
19. │ ├─dbplyr::sql_render(...)
20. │ └─dbplyr:::sql_render.lazy_query(...)
21. │ ├─dbplyr::sql_build(query, con = con, sql_options = sql_options)
22. │ └─dbplyr:::sql_build.lazy_select_query(query, con = con, sql_options = sql_options)
23. │ └─dbplyr:::get_select_sql(...)
24. │ └─dbplyr:::translate_select_sql(con, select)
25. │ └─dbplyr::translate_sql_(...)
26. │ └─base::lapply(...)
27. │ └─dbplyr (local) FUN(X[[i]], ...)
28. │ ├─dbplyr::escape(eval_tidy(x, mask), con = con)
29. │ └─rlang::eval_tidy(x, mask)
30. └─CDMConnector::datediff
31. └─cli::cli_abort(...)
32. └─rlang::abort(...)
── Error ('test-addIntersect.R:921:3'): test if column exist, overwrite ────────
Error in `CDMConnector::datediff()`: No known SQL translation
Backtrace:
▆
1. ├─testthat::expect_warning(...) at test-addIntersect.R:921:3
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. ├─... %>% dplyr::collect()
8. ├─dplyr::collect(.)
9. ├─PatientProfiles::addIntersect(...)
10. │ └─... %>% ...
11. ├─dplyr::mutate(., censor_date = .data[[censorDate %||% "censor_date"]])
12. ├─dplyr::mutate(...)
13. ├─PatientProfiles::addFutureObservation(...)
14. │ └─x %>% ...
15. ├─PatientProfiles::addDemographics(...)
16. │ └─x %>% dplyr::compute()
17. ├─dplyr::compute(.)
18. ├─omopgenerics:::compute.cdm_table(.)
19. │ ├─dplyr::compute(...)
20. │ └─CDMConnector:::compute.db_cdm(...)
21. │ └─CDMConnector:::.computeQuery(...)
22. │ └─dbplyr::sql_render(x)
23. │ ├─dbplyr::sql_render(...)
24. │ └─dbplyr:::sql_render.tbl_lazy(...)
25. │ ├─dbplyr::sql_render(...)
26. │ └─dbplyr:::sql_render.lazy_query(...)
27. │ ├─dbplyr::sql_build(query, con = con, sql_options = sql_options)
28. │ └─dbplyr:::sql_build.lazy_select_query(query, con = con, sql_options = sql_options)
29. │ └─dbplyr:::get_select_sql(...)
30. │ └─dbplyr:::translate_select_sql(con, select)
31. │ └─dbplyr::translate_sql_(...)
32. │ └─base::lapply(...)
33. │ └─dbplyr (local) FUN(X[[i]], ...)
34. │ ├─dbplyr::escape(eval_tidy(x, mask), con = con)
35. │ └─rlang::eval_tidy(x, mask)
36. └─CDMConnector::datediff
37. └─cli::cli_abort(...)
38. └─rlang::abort(...)
── Error ('test-addIntersect.R:1011:3'): overlapTable is empty, check return columns ──
Error in `CDMConnector::datediff()`: No known SQL translation
Backtrace:
▆
1. ├─dplyr::arrange(...) at test-addIntersect.R:1011:3
2. ├─... %>% dplyr::collect()
3. ├─dplyr::collect(.)
4. ├─PatientProfiles::addIntersect(...)
5. │ └─... %>% ...
6. ├─dplyr::mutate(., censor_date = .data[[censorDate %||% "censor_date"]])
7. ├─dplyr::mutate(...)
8. ├─PatientProfiles::addFutureObservation(...)
9. │ └─x %>% ...
10. ├─PatientProfiles::addDemographics(...)
11. │ └─x %>% dplyr::compute()
12. ├─dplyr::compute(.)
13. ├─omopgenerics:::compute.cdm_table(.)
14. │ ├─dplyr::compute(...)
15. │ └─CDMConnector:::compute.db_cdm(...)
16. │ └─CDMConnector:::.computeQuery(...)
17. │ └─dbplyr::sql_render(x)
18. │ ├─dbplyr::sql_render(...)
19. │ └─dbplyr:::sql_render.tbl_lazy(...)
20. │ ├─dbplyr::sql_render(...)
21. │ └─dbplyr:::sql_render.lazy_query(...)
22. │ ├─dbplyr::sql_build(query, con = con, sql_options = sql_options)
23. │ └─dbplyr:::sql_build.lazy_select_query(query, con = con, sql_options = sql_options)
24. │ └─dbplyr:::get_select_sql(...)
25. │ └─dbplyr:::translate_select_sql(con, select)
26. │ └─dbplyr::translate_sql_(...)
27. │ └─base::lapply(...)
28. │ └─dbplyr (local) FUN(X[[i]], ...)
29. │ ├─dbplyr::escape(eval_tidy(x, mask), con = con)
30. │ └─rlang::eval_tidy(x, mask)
31. └─CDMConnector::datediff
32. └─cli::cli_abort(...)
33. └─rlang::abort(...)
── Error ('test-addIntersect.R:1096:3'): overlap is empty or not, multiple ids, check return columns ──
Error in `CDMConnector::datediff()`: No known SQL translation
Backtrace:
▆
1. ├─dplyr::arrange(...) at test-addIntersect.R:1096:3
2. ├─... %>% dplyr::collect()
3. ├─dplyr::collect(.)
4. ├─PatientProfiles::addCohortIntersectCount(., targetCohortTable = "cohort2")
5. │ └─x %>% ...
6. ├─PatientProfiles::addIntersect(...)
7. │ └─... %>% ...
8. ├─dplyr::mutate(., censor_date = .data[[censorDate %||% "censor_date"]])
9. ├─dplyr::mutate(...)
10. ├─PatientProfiles::addFutureObservation(...)
11. │ └─x %>% ...
12. ├─PatientProfiles::addDemographics(...)
13. │ └─x %>% dplyr::compute()
14. ├─dplyr::compute(.)
15. ├─omopgenerics:::compute.cdm_table(.)
16. │ ├─dplyr::compute(...)
17. │ └─CDMConnector:::compute.db_cdm(...)
18. │ └─CDMConnector:::.computeQuery(...)
19. │ └─dbplyr::sql_render(x)
20. │ ├─dbplyr::sql_render(...)
21. │ └─dbplyr:::sql_render.tbl_lazy(...)
22. │ ├─dbplyr::sql_render(...)
23. │ └─dbplyr:::sql_render.lazy_query(...)
24. │ ├─dbplyr::sql_build(query, con = con, sql_options = sql_options)
25. │ └─dbplyr:::sql_build.lazy_select_query(query, con = con, sql_options = sql_options)
26. │ └─dbplyr:::get_select_sql(...)
27. │ └─dbplyr:::translate_select_sql(con, select)
28. │ └─dbplyr::translate_sql_(...)
29. │ └─base::lapply(...)
30. │ └─dbplyr (local) FUN(X[[i]], ...)
31. │ ├─dbplyr::escape(eval_tidy(x, mask), con = con)
32. │ └─rlang::eval_tidy(x, mask)
33. └─CDMConnector::datediff
34. └─cli::cli_abort(...)
35. └─rlang::abort(...)
── Error ('test-addIntersect.R:1209:3'): non snake columns not repeated in output ──
Error in `CDMConnector::datediff()`: No known SQL translation
Backtrace:
▆
1. ├─cdm$cohort2 %>% addCohortIntersectFlag(targetCohortTable = "cohort1") at test-addIntersect.R:1209:3
2. ├─PatientProfiles::addCohortIntersectFlag(., targetCohortTable = "cohort1")
3. │ └─x %>% ...
4. ├─PatientProfiles::addIntersect(...)
5. │ └─... %>% ...
6. ├─dplyr::mutate(., censor_date = .data[[censorDate %||% "censor_date"]])
7. ├─dplyr::mutate(...)
8. ├─PatientProfiles::addFutureObservation(...)
9. │ └─x %>% ...
10. ├─PatientProfiles::addDemographics(...)
11. │ └─x %>% dplyr::compute()
12. ├─dplyr::compute(.)
13. ├─omopgenerics:::compute.cdm_table(.)
14. │ ├─dplyr::compute(...)
15. │ └─CDMConnector:::compute.db_cdm(...)
16. │ └─CDMConnector:::.computeQuery(...)
17. │ └─dbplyr::sql_render(x)
18. │ ├─dbplyr::sql_render(...)
19. │ └─dbplyr:::sql_render.tbl_lazy(...)
20. │ ├─dbplyr::sql_render(...)
21. │ └─dbplyr:::sql_render.lazy_query(...)
22. │ ├─dbplyr::sql_build(query, con = con, sql_options = sql_options)
23. │ └─dbplyr:::sql_build.lazy_select_query(query, con = con, sql_options = sql_options)
24. │ └─dbplyr:::get_select_sql(...)
25. │ └─dbplyr:::translate_select_sql(con, select)
26. │ └─dbplyr::translate_sql_(...)
27. │ └─base::lapply(...)
28. │ └─dbplyr (local) FUN(X[[i]], ...)
29. │ ├─dbplyr::escape(eval_tidy(x, mask), con = con)
30. │ └─rlang::eval_tidy(x, mask)
31. └─CDMConnector::datediff
32. └─cli::cli_abort(...)
33. └─rlang::abort(...)
── Error ('test-addIntersect.R:1225:3'): no NA when overwrite column ───────────
Error in `CDMConnector::datediff()`: No known SQL translation
Backtrace:
▆
1. ├─cdm$cohort1 %>% ... at test-addIntersect.R:1225:3
2. ├─PatientProfiles::addCohortIntersectFlag(...)
3. │ └─x %>% ...
4. ├─PatientProfiles::addIntersect(...)
5. │ └─... %>% ...
6. ├─dplyr::mutate(., censor_date = .data[[censorDate %||% "censor_date"]])
7. ├─dplyr::mutate(...)
8. ├─PatientProfiles::addFutureObservation(...)
9. │ └─x %>% ...
10. ├─PatientProfiles::addDemographics(...)
11. │ └─x %>% dplyr::compute()
12. ├─dplyr::compute(.)
13. ├─omopgenerics:::compute.cdm_table(.)
14. │ ├─dplyr::compute(...)
15. │ └─CDMConnector:::compute.db_cdm(...)
16. │ └─CDMConnector:::.computeQuery(...)
17. │ └─dbplyr::sql_render(x)
18. │ ├─dbplyr::sql_render(...)
19. │ └─dbplyr:::sql_render.tbl_lazy(...)
20. │ ├─dbplyr::sql_render(...)
21. │ └─dbplyr:::sql_render.lazy_query(...)
22. │ ├─dbplyr::sql_build(query, con = con, sql_options = sql_options)
23. │ └─dbplyr:::sql_build.lazy_select_query(query, con = con, sql_options = sql_options)
24. │ └─dbplyr:::get_select_sql(...)
25. │ └─dbplyr:::translate_select_sql(con, select)
26. │ └─dbplyr::translate_sql_(...)
27. │ └─base::lapply(...)
28. │ └─dbplyr (local) FUN(X[[i]], ...)
29. │ ├─dbplyr::escape(eval_tidy(x, mask), con = con)
30. │ └─rlang::eval_tidy(x, mask)
31. └─CDMConnector::datediff
32. └─cli::cli_abort(...)
33. └─rlang::abort(...)
── Error ('test-addPriorObservation.R:6:3'): check input length and type for each of the arguments ──
Error in `CDMConnector::datediff()`: No known SQL translation
Backtrace:
▆
1. ├─testthat::expect_warning(addPriorObservation(cdm$cohort1, "cdm")) at test-addPriorObservation.R:6:3
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. ├─PatientProfiles::addPriorObservation(cdm$cohort1, "cdm")
8. │ └─x %>% ...
9. ├─PatientProfiles::addDemographics(...)
10. │ └─x %>% dplyr::compute()
11. ├─dplyr::compute(.)
12. ├─omopgenerics:::compute.cdm_table(.)
13. │ ├─dplyr::compute(...)
14. │ └─CDMConnector:::compute.db_cdm(...)
15. │ └─CDMConnector:::.computeQuery(...)
16. │ └─dbplyr::sql_render(x)
17. │ ├─dbplyr::sql_render(...)
18. │ └─dbplyr:::sql_render.tbl_lazy(...)
19. │ ├─dbplyr::sql_render(...)
20. │ └─dbplyr:::sql_render.lazy_query(...)
21. │ ├─dbplyr::sql_build(query, con = con, sql_options = sql_options)
22. │ └─dbplyr:::sql_build.lazy_select_query(query, con = con, sql_options = sql_options)
23. │ └─dbplyr:::get_select_sql(...)
24. │ └─dbplyr:::translate_select_sql(con, select)
25. │ └─dbplyr::translate_sql_(...)
26. │ └─base::lapply(...)
27. │ └─dbplyr (local) FUN(X[[i]], ...)
28. │ ├─dbplyr::escape(eval_tidy(x, mask), con = con)
29. │ └─rlang::eval_tidy(x, mask)
30. └─CDMConnector::datediff
31. └─cli::cli_abort(...)
32. └─rlang::abort(...)
── Error ('test-addPriorObservation.R:15:3'): check condition_occurrence and cohort1 work ──
Error in `CDMConnector::datediff()`: No known SQL translation
Backtrace:
▆
1. ├─testthat::expect_true(...) at test-addPriorObservation.R:15:3
2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─base::typeof(cdm$cohort1 %>% addPriorObservation() %>% dplyr::collect())
5. ├─cdm$cohort1 %>% addPriorObservation() %>% dplyr::collect()
6. ├─dplyr::collect(.)
7. ├─PatientProfiles::addPriorObservation(.)
8. │ └─x %>% ...
9. ├─PatientProfiles::addDemographics(...)
10. │ └─x %>% dplyr::compute()
11. ├─dplyr::compute(.)
12. ├─omopgenerics:::compute.cdm_table(.)
13. │ ├─dplyr::compute(...)
14. │ └─CDMConnector:::compute.db_cdm(...)
15. │ └─CDMConnector:::.computeQuery(...)
16. │ └─dbplyr::sql_render(x)
17. │ ├─dbplyr::sql_render(...)
18. │ └─dbplyr:::sql_render.tbl_lazy(...)
19. │ ├─dbplyr::sql_render(...)
20. │ └─dbplyr:::sql_render.lazy_query(...)
21. │ ├─dbplyr::sql_build(query, con = con, sql_options = sql_options)
22. │ └─dbplyr:::sql_build.lazy_select_query(query, con = con, sql_options = sql_options)
23. │ └─dbplyr:::get_select_sql(...)
24. │ └─dbplyr:::translate_select_sql(con, select)
25. │ └─dbplyr::translate_sql_(...)
26. │ └─base::lapply(...)
27. │ └─dbplyr (local) FUN(X[[i]], ...)
28. │ ├─dbplyr::escape(eval_tidy(x, mask), con = con)
29. │ └─rlang::eval_tidy(x, mask)
30. └─CDMConnector::datediff
31. └─cli::cli_abort(...)
32. └─rlang::abort(...)
── Error ('test-addPriorObservation.R:62:3'): check working example with cohort1 ──
Error in `CDMConnector::datediff()`: No known SQL translation
Backtrace:
▆
1. ├─cdm$cohort1 %>% addPriorObservation() %>% dplyr::collect() at test-addPriorObservation.R:62:3
2. ├─dplyr::collect(.)
3. ├─PatientProfiles::addPriorObservation(.)
4. │ └─x %>% ...
5. ├─PatientProfiles::addDemographics(...)
6. │ └─x %>% dplyr::compute()
7. ├─dplyr::compute(.)
8. ├─omopgenerics:::compute.cdm_table(.)
9. │ ├─dplyr::compute(...)
10. │ └─CDMConnector:::compute.db_cdm(...)
11. │ └─CDMConnector:::.computeQuery(...)
12. │ └─dbplyr::sql_render(x)
13. │ ├─dbplyr::sql_render(...)
14. │ └─dbplyr:::sql_render.tbl_lazy(...)
15. │ ├─dbplyr::sql_render(...)
16. │ └─dbplyr:::sql_render.lazy_query(...)
17. │ ├─dbplyr::sql_build(query, con = con, sql_options = sql_options)
18. │ └─dbplyr:::sql_build.lazy_select_query(query, con = con, sql_options = sql_options)
19. │ └─dbplyr:::get_select_sql(...)
20. │ └─dbplyr:::translate_select_sql(con, select)
21. │ └─dbplyr::translate_sql_(...)
22. │ └─base::lapply(...)
23. │ └─dbplyr (local) FUN(X[[i]], ...)
24. │ ├─dbplyr::escape(eval_tidy(x, mask), con = con)
25. │ └─rlang::eval_tidy(x, mask)
26. └─CDMConnector::datediff
27. └─cli::cli_abort(...)
28. └─rlang::abort(...)
── Error ('test-addPriorObservation.R:106:3'): check working example with condition_occurrence ──
Error in `dplyr::collect(removeClass(x, "cdm_table"))`: Failed to collect lazy table.
Caused by error:
! rapi_prepare: Failed to prepare query SELECT cohort1.*
FROM main.cohort1
WHERE NOT EXISTS (
SELECT 1 FROM (
SELECT cohort1.*, observation_period_start_date, observation_period_end_date
FROM main.cohort1
LEFT JOIN main.observation_period
ON (cohort1.subject_id = observation_period.person_id)
) RHS
WHERE
(cohort1.cohort_definition_id = RHS.cohort_definition_id) AND
(cohort1.subject_id = RHS.subject_id) AND
(cohort1.cohort_start_date = RHS.cohort_start_date) AND
(cohort1.cohort_end_date = RHS.cohort_end_date) AND
(RHS.cohort_start_date >= RHS.observation_period_start_date AND RHS.cohort_start_date <= RHS.observation_period_end_date AND RHS.cohort_end_date >= RHS.observation_period_start_date AND RHS.cohort_end_date <= RHS.observation_period_end_date)
)
Error: Binder Error: Cannot compare values of type VARCHAR and type DATE - an explicit cast is required
LINE 15: (RHS.cohort_start_date >= RHS.observation_period_start_date AND RHS.cohort_start_date <= RHS.observation_period_end_date AND RHS.cohort_end_date >= RHS.observation_period_start_date AND RHS.cohort_end_date <= RHS.observation_period_end_date)
)...
^
Backtrace:
▆
1. ├─PatientProfiles::mockPatientProfiles(...) at test-addPriorObservation.R:106:3
2. │ └─omopgenerics::newCohortTable(cdm[[cohort]])
3. │ └─omopgenerics:::validateGeneratedCohortSet(cohort, soft = .softValidation)
4. │ └─omopgenerics::checkCohortRequirements(...)
5. │ └─omopgenerics:::checkObservationPeriod(...)
6. │ ├─dplyr::collect(...)
7. │ └─omopgenerics:::collect.cohort_table(...)
8. │ ├─dplyr::collect(x)
9. │ └─omopgenerics:::collect.cdm_table(x)
10. │ ├─dplyr::collect(removeClass(x, "cdm_table"))
11. │ └─dbplyr:::collect.tbl_sql(removeClass(x, "cdm_table"))
12. │ ├─base::withCallingHandlers(...)
13. │ ├─dbplyr::db_collect(...)
14. │ └─dbplyr:::db_collect.DBIConnection(...)
15. │ ├─DBI::dbSendQuery(con, sql)
16. │ └─duckdb::dbSendQuery(con, sql)
17. │ └─duckdb (local) .local(conn, statement, ...)
18. │ └─duckdb:::rapi_prepare(conn@conn_ref, statement)
19. └─base::.handleSimpleError(...)
20. └─dbplyr (local) h(simpleError(msg, call))
21. └─cli::cli_abort("Failed to collect lazy table.", parent = cnd)
22. └─rlang::abort(...)
── Error ('test-addPriorObservation.R:158:3'): different name ──────────────────
Error in `dplyr::collect(removeClass(x, "cdm_table"))`: Failed to collect lazy table.
Caused by error:
! rapi_prepare: Failed to prepare query SELECT cohort1.*
FROM main.cohort1
WHERE NOT EXISTS (
SELECT 1 FROM (
SELECT cohort1.*, observation_period_start_date, observation_period_end_date
FROM main.cohort1
LEFT JOIN main.observation_period
ON (cohort1.subject_id = observation_period.person_id)
) RHS
WHERE
(cohort1.cohort_definition_id = RHS.cohort_definition_id) AND
(cohort1.subject_id = RHS.subject_id) AND
(cohort1.cohort_start_date = RHS.cohort_start_date) AND
(cohort1.cohort_end_date = RHS.cohort_end_date) AND
(RHS.cohort_start_date >= RHS.observation_period_start_date AND RHS.cohort_start_date <= RHS.observation_period_end_date AND RHS.cohort_end_date >= RHS.observation_period_start_date AND RHS.cohort_end_date <= RHS.observation_period_end_date)
)
Error: Binder Error: Cannot compare values of type VARCHAR and type DATE - an explicit cast is required
LINE 15: (RHS.cohort_start_date >= RHS.observation_period_start_date AND RHS.cohort_start_date <= RHS.observation_period_end_date AND RHS.cohort_end_date >= RHS.observation_period_start_date AND RHS.cohort_end_date <= RHS.observation_period_end_date)
)...
^
Backtrace:
▆
1. ├─PatientProfiles::mockPatientProfiles(...) at test-addPriorObservation.R:158:3
2. │ └─omopgenerics::newCohortTable(cdm[[cohort]])
3. │ └─omopgenerics:::validateGeneratedCohortSet(cohort, soft = .softValidation)
4. │ └─omopgenerics::checkCohortRequirements(...)
5. │ └─omopgenerics:::checkObservationPeriod(...)
6. │ ├─dplyr::collect(...)
7. │ └─omopgenerics:::collect.cohort_table(...)
8. │ ├─dplyr::collect(x)
9. │ └─omopgenerics:::collect.cdm_table(x)
10. │ ├─dplyr::collect(removeClass(x, "cdm_table"))
11. │ └─dbplyr:::collect.tbl_sql(removeClass(x, "cdm_table"))
12. │ ├─base::withCallingHandlers(...)
13. │ ├─dbplyr::db_collect(...)
14. │ └─dbplyr:::db_collect.DBIConnection(...)
15. │ ├─DBI::dbSendQuery(con, sql)
16. │ └─duckdb::dbSendQuery(con, sql)
17. │ └─duckdb (local) .local(conn, statement, ...)
18. │ └─duckdb:::rapi_prepare(conn@conn_ref, statement)
19. └─base::.handleSimpleError(...)
20. └─dbplyr (local) h(simpleError(msg, call))
21. └─cli::cli_abort("Failed to collect lazy table.", parent = cnd)
22. └─rlang::abort(...)
── Error ('test-addPriorObservation.R:209:3'): multiple observation periods ────
Error in `dplyr::collect(removeClass(x, "cdm_table"))`: Failed to collect lazy table.
Caused by error:
! rapi_prepare: Failed to prepare query SELECT cohort2.*
FROM main.cohort2
WHERE NOT EXISTS (
SELECT 1 FROM (
SELECT cohort2.*, observation_period_start_date, observation_period_end_date
FROM main.cohort2
LEFT JOIN main.observation_period
ON (cohort2.subject_id = observation_period.person_id)
) RHS
WHERE
(cohort2.cohort_definition_id = RHS.cohort_definition_id) AND
(cohort2.subject_id = RHS.subject_id) AND
(cohort2.cohort_start_date = RHS.cohort_start_date) AND
(cohort2.cohort_end_date = RHS.cohort_end_date) AND
(RHS.cohort_start_date >= RHS.observation_period_start_date AND RHS.cohort_start_date <= RHS.observation_period_end_date AND RHS.cohort_end_date >= RHS.observation_period_start_date AND RHS.cohort_end_date <= RHS.observation_period_end_date)
)
Error: Binder Error: Cannot compare values of type VARCHAR and type DATE - an explicit cast is required
LINE 15: (RHS.cohort_start_date >= RHS.observation_period_start_date AND RHS.cohort_start_date <= RHS.observation_period_end_date AND RHS.cohort_end_date >= RHS.observation_period_start_date AND RHS.cohort_end_date <= RHS.observation_period_end_date)
)...
^
Backtrace:
▆
1. ├─PatientProfiles::mockPatientProfiles(...) at test-addPriorObservation.R:209:3
2. │ └─omopgenerics::newCohortTable(cdm[[cohort]])
3. │ └─omopgenerics:::validateGeneratedCohortSet(cohort, soft = .softValidation)
4. │ └─omopgenerics::checkCohortRequirements(...)
5. │ └─omopgenerics:::checkObservationPeriod(...)
6. │ ├─dplyr::collect(...)
7. │ └─omopgenerics:::collect.cohort_table(...)
8. │ ├─dplyr::collect(x)
9. │ └─omopgenerics:::collect.cdm_table(x)
10. │ ├─dplyr::collect(removeClass(x, "cdm_table"))
11. │ └─dbplyr:::collect.tbl_sql(removeClass(x, "cdm_table"))
12. │ ├─base::withCallingHandlers(...)
13. │ ├─dbplyr::db_collect(...)
14. │ └─dbplyr:::db_collect.DBIConnection(...)
15. │ ├─DBI::dbSendQuery(con, sql)
16. │ └─duckdb::dbSendQuery(con, sql)
17. │ └─duckdb (local) .local(conn, statement, ...)
18. │ └─duckdb:::rapi_prepare(conn@conn_ref, statement)
19. └─base::.handleSimpleError(...)
20. └─dbplyr (local) h(simpleError(msg, call))
21. └─cli::cli_abort("Failed to collect lazy table.", parent = cnd)
22. └─rlang::abort(...)
── Error ('test-class.R:57:5'): test class consistency across cohort operations ──
Error in `CDMConnector::datediff()`: No known SQL translation
Backtrace:
▆
1. ├─PatientProfiles (local) op(cdm$cohort1) at test-class.R:57:5
2. │ └─... %>% ...
3. ├─dplyr::select(., -"prior_observation", -"future_observation")
4. ├─dplyr::mutate(...)
5. ├─PatientProfiles::addDemographics(...)
6. │ └─x %>% dplyr::compute()
7. ├─dplyr::compute(.)
8. ├─omopgenerics:::compute.cdm_table(.)
9. │ ├─dplyr::compute(...)
10. │ └─CDMConnector:::compute.db_cdm(...)
11. │ └─CDMConnector:::.computeQuery(...)
12. │ └─dbplyr::sql_render(x)
13. │ ├─dbplyr::sql_render(...)
14. │ └─dbplyr:::sql_render.tbl_lazy(...)
15. │ ├─dbplyr::sql_render(...)
16. │ └─dbplyr:::sql_render.lazy_query(...)
17. │ ├─dbplyr::sql_build(query, con = con, sql_options = sql_options)
18. │ └─dbplyr:::sql_build.lazy_select_query(query, con = con, sql_options = sql_options)
19. │ └─dbplyr:::get_select_sql(...)
20. │ └─dbplyr:::translate_select_sql(con, select)
21. │ └─dbplyr::translate_sql_(...)
22. │ └─base::lapply(...)
23. │ └─dbplyr (local) FUN(X[[i]], ...)
24. │ ├─dbplyr::escape(eval_tidy(x, mask), con = con)
25. │ └─rlang::eval_tidy(x, mask)
26. └─CDMConnector::datediff
27. └─cli::cli_abort(...)
28. └─rlang::abort(...)
── Error ('test-checks.R:93:3'): test checkNewName renames duplicate column names in addInObservation ──
Error in `CDMConnector::datediff()`: No known SQL translation
Backtrace:
▆
1. ├─testthat::expect_warning(x <- addInObservation(cdm$cohort1, name = "flag")) at test-checks.R:93:3
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. ├─PatientProfiles::addInObservation(cdm$cohort1, name = "flag")
8. │ └─... %>% ...
9. ├─dplyr::select(., -"prior_observation", -"future_observation")
10. ├─dplyr::mutate(...)
11. ├─PatientProfiles::addDemographics(...)
12. │ └─x %>% dplyr::compute()
13. ├─dplyr::compute(.)
14. ├─omopgenerics:::compute.cdm_table(.)
15. │ ├─dplyr::compute(...)
16. │ └─CDMConnector:::compute.db_cdm(...)
17. │ └─CDMConnector:::.computeQuery(...)
18. │ └─dbplyr::sql_render(x)
19. │ ├─dbplyr::sql_render(...)
20. │ └─dbplyr:::sql_render.tbl_lazy(...)
21. │ ├─dbplyr::sql_render(...)
22. │ └─dbplyr:::sql_render.lazy_query(...)
23. │ ├─dbplyr::sql_build(query, con = con, sql_options = sql_options)
24. │ └─dbplyr:::sql_build.lazy_select_query(query, con = con, sql_options = sql_options)
25. │ └─dbplyr:::get_select_sql(...)
26. │ └─dbplyr:::translate_select_sql(con, select)
27. │ └─dbplyr::translate_sql_(...)
28. │ └─base::lapply(...)
29. │ └─dbplyr (local) FUN(X[[i]], ...)
30. │ ├─dbplyr::escape(eval_tidy(x, mask), con = con)
31. │ └─rlang::eval_tidy(x, mask)
32. └─CDMConnector::datediff
33. └─cli::cli_abort(...)
34. └─rlang::abort(...)
── Error ('test-checks.R:150:3'): test checkWindow in addIntersect ────────────
Error in `CDMConnector::datediff()`: No known SQL translation
Backtrace:
▆
1. ├─testthat::expect_warning(...) at test-checks.R:150:3
2. │ └─testthat:::expect_condition_matching(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─cdm$cohort1 %>% ...
8. ├─PatientProfiles::addIntersect(...)
9. │ └─... %>% ...
10. ├─dplyr::mutate(., censor_date = .data[[censorDate %||% "censor_date"]])
11. ├─dplyr::mutate(...)
12. ├─PatientProfiles::addFutureObservation(...)
13. │ └─x %>% ...
14. ├─PatientProfiles::addDemographics(...)
15. │ └─x %>% dplyr::compute()
16. ├─dplyr::compute(.)
17. ├─omopgenerics:::compute.cdm_table(.)
18. │ ├─dplyr::compute(...)
19. │ └─CDMConnector:::compute.db_cdm(...)
20. │ └─CDMConnector:::.computeQuery(...)
21. │ └─dbplyr::sql_render(x)
22. │ ├─dbplyr::sql_render(...)
23. │ └─dbplyr:::sql_render.tbl_lazy(...)
24. │ ├─dbplyr::sql_render(...)
25. │ └─dbplyr:::sql_render.lazy_query(...)
26. │ ├─dbplyr::sql_build(query, con = con, sql_options = sql_options)
27. │ └─dbplyr:::sql_build.lazy_select_query(query, con = con, sql_options = sql_options)
28. │ └─dbplyr:::get_select_sql(...)
29. │ └─dbplyr:::translate_select_sql(con, select)
30. │ └─dbplyr::translate_sql_(...)
31. │ └─base::lapply(...)
32. │ └─dbplyr (local) FUN(X[[i]], ...)
33. │ ├─dbplyr::escape(eval_tidy(x, mask), con = con)
34. │ └─rlang::eval_tidy(x, mask)
35. └─CDMConnector::datediff
36. └─cli::cli_abort(...)
37. └─rlang::abort(...)
── Error ('test-checks.R:249:3'): checkNameStyle ───────────────────────────────
Error in `CDMConnector::datediff()`: No known SQL translation
Backtrace:
▆
1. ├─testthat::expect_true(...) at test-checks.R:249:3
2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─c("count_all", "flag_all") %in% ...
5. ├─base::colnames(...)
6. │ └─base::is.data.frame(x)
7. ├─cdm$cohort1 %>% ...
8. ├─PatientProfiles::addIntersect(...)
9. │ └─... %>% ...
10. ├─dplyr::mutate(., censor_date = .data[[censorDate %||% "censor_date"]])
11. ├─dplyr::mutate(...)
12. ├─PatientProfiles::addFutureObservation(...)
13. │ └─x %>% ...
14. ├─PatientProfiles::addDemographics(...)
15. │ └─x %>% dplyr::compute()
16. ├─dplyr::compute(.)
17. ├─omopgenerics:::compute.cdm_table(.)
18. │ ├─dplyr::compute(...)
19. │ └─CDMConnector:::compute.db_cdm(...)
20. │ └─CDMConnector:::.computeQuery(...)
21. │ └─dbplyr::sql_render(x)
22. │ ├─dbplyr::sql_render(...)
23. │ └─dbplyr:::sql_render.tbl_lazy(...)
24. │ ├─dbplyr::sql_render(...)
25. │ └─dbplyr:::sql_render.lazy_query(...)
26. │ ├─dbplyr::sql_build(query, con = con, sql_options = sql_options)
27. │ └─dbplyr:::sql_build.lazy_select_query(query, con = con, sql_options = sql_options)
28. │ └─dbplyr:::get_select_sql(...)
29. │ └─dbplyr:::translate_select_sql(con, select)
30. │ └─dbplyr::translate_sql_(...)
31. │ └─base::lapply(...)
32. │ └─dbplyr (local) FUN(X[[i]], ...)
33. │ ├─dbplyr::escape(eval_tidy(x, mask), con = con)
34. │ └─rlang::eval_tidy(x, mask)
35. └─CDMConnector::datediff
36. └─cli::cli_abort(...)
37. └─rlang::abort(...)
── Error ('test-summariseCharacteristics.R:51:3'): test summariseCharacteristics ──
Error in `dplyr::collect(removeClass(x, "cdm_table"))`: Failed to collect lazy table.
Caused by error:
! rapi_prepare: Failed to prepare query SELECT cohort1.*
FROM main.cohort1
WHERE NOT EXISTS (
SELECT 1 FROM (
SELECT cohort1.*, observation_period_start_date, observation_period_end_date
FROM main.cohort1
LEFT JOIN main.observation_period
ON (cohort1.subject_id = observation_period.person_id)
) RHS
WHERE
(cohort1.cohort_definition_id = RHS.cohort_definition_id) AND
(cohort1.subject_id = RHS.subject_id) AND
(cohort1.cohort_start_date = RHS.cohort_start_date) AND
(cohort1.cohort_end_date = RHS.cohort_end_date) AND
(RHS.cohort_start_date >= RHS.observation_period_start_date AND RHS.cohort_start_date <= RHS.observation_period_end_date AND RHS.cohort_end_date >= RHS.observation_period_start_date AND RHS.cohort_end_date <= RHS.observation_period_end_date)
)
Error: Binder Error: Cannot compare values of type VARCHAR and type DATE - an explicit cast is required
LINE 15: (RHS.cohort_start_date >= RHS.observation_period_start_date AND RHS.cohort_start_date <= RHS.observation_period_end_date AND RHS.cohort_end_date >= RHS.observation_period_start_date AND RHS.cohort_end_date <= RHS.observation_period_end_date)
)...
^
Backtrace:
▆
1. ├─PatientProfiles::mockPatientProfiles(...) at test-summariseCharacteristics.R:51:3
2. │ └─omopgenerics::newCohortTable(cdm[[cohort]])
3. │ └─omopgenerics:::validateGeneratedCohortSet(cohort, soft = .softValidation)
4. │ └─omopgenerics::checkCohortRequirements(...)
5. │ └─omopgenerics:::checkObservationPeriod(...)
6. │ ├─dplyr::collect(...)
7. │ └─omopgenerics:::collect.cohort_table(...)
8. │ ├─dplyr::collect(x)
9. │ └─omopgenerics:::collect.cdm_table(x)
10. │ ├─dplyr::collect(removeClass(x, "cdm_table"))
11. │ └─dbplyr:::collect.tbl_sql(removeClass(x, "cdm_table"))
12. │ ├─base::withCallingHandlers(...)
13. │ ├─dbplyr::db_collect(...)
14. │ └─dbplyr:::db_collect.DBIConnection(...)
15. │ ├─DBI::dbSendQuery(con, sql)
16. │ └─duckdb::dbSendQuery(con, sql)
17. │ └─duckdb (local) .local(conn, statement, ...)
18. │ └─duckdb:::rapi_prepare(conn@conn_ref, statement)
19. └─base::.handleSimpleError(...)
20. └─dbplyr (local) h(simpleError(msg, call))
21. └─cli::cli_abort("Failed to collect lazy table.", parent = cnd)
22. └─rlang::abort(...)
── Failure ('test-summariseCharacteristics.R:288:3'): test empty cohort ────────
Expected ``%>%`(...)` to run without any errors.
i Actually got a <rlang_error> with text:
No known SQL translation
── Failure ('test-summariseCharacteristics.R:298:3'): test empty cohort ────────
Expected `... <- NULL` to run without any errors.
i Actually got a <rlang_error> with text:
No known SQL translation
── Failure ('test-summariseCharacteristics.R:305:3'): test empty cohort ────────
Expected `... <- NULL` to run without any errors.
i Actually got a <rlang_error> with text:
No known SQL translation
── Failure ('test-summariseLargeScaleCharacteristics.R:87:3'): basic functionality summarise large scale characteristics ──
Expected `... <- NULL` to run without any errors.
i Actually got a <rlang_error> with text:
No known SQL translation
── Error ('test-summariseLargeScaleCharacteristics.R:94:3'): basic functionality summarise large scale characteristics ──
Error in `eval(code, test_env)`: object 'result' not found
Backtrace:
▆
1. └─visOmopResults::splitAdditional(result) at test-summariseLargeScaleCharacteristics.R:94:3
2. └─visOmopResults::splitNameLevel(...)
3. └─visOmopResults:::assertTibble(result, columns = c(name, level))
4. └─visOmopResults:::assertNull(x, null, errorMessage, call)
── Failure ('test-summariseLargeScaleCharacteristics.R:288:3'): basic functionality add large scale characteristics ──
Expected `... <- NULL` to run without any errors.
i Actually got a <rlang_error> with text:
No known SQL translation
── Error ('test-summariseLargeScaleCharacteristics.R:300:3'): basic functionality add large scale characteristics ──
Error in `eval(code, test_env)`: object 'result' not found
Backtrace:
▆
1. ├─testthat::expect_false(any(grepl("0_to_0", colnames(result)))) at test-summariseLargeScaleCharacteristics.R:300:3
2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─base::grepl("0_to_0", colnames(result))
5. │ └─base::is.factor(x)
6. └─base::colnames(result)
7. └─base::is.data.frame(x)
── Error ('test-summariseResult.R:68:3'): groups and strata ────────────────────
Error in `CDMConnector::datediff()`: No known SQL translation
Backtrace:
▆
1. ├─... %>% summariseResult(strata = list("sex")) at test-summariseResult.R:68:3
2. ├─PatientProfiles::summariseResult(., strata = list("sex"))
3. │ └─PatientProfiles:::checkTable(table)
4. │ └─"tbl" %in% class(table)
5. ├─dplyr::collect(.)
6. ├─PatientProfiles::addDemographics(...)
7. │ └─x %>% dplyr::compute()
8. ├─dplyr::compute(.)
9. ├─omopgenerics:::compute.cdm_table(.)
10. │ ├─dplyr::compute(...)
11. │ └─CDMConnector:::compute.db_cdm(...)
12. │ └─CDMConnector:::.computeQuery(...)
13. │ └─dbplyr::sql_render(x)
14. │ ├─dbplyr::sql_render(...)
15. │ └─dbplyr:::sql_render.tbl_lazy(...)
16. │ ├─dbplyr::sql_render(...)
17. │ └─dbplyr:::sql_render.lazy_query(...)
18. │ ├─dbplyr::sql_build(query, con = con, sql_options = sql_options)
19. │ └─dbplyr:::sql_build.lazy_select_query(query, con = con, sql_options = sql_options)
20. │ ├─dbplyr::sql_build(op$x, con, sql_options = sql_options)
21. │ └─dbplyr:::sql_build.lazy_select_query(op$x, con, sql_options = sql_options)
22. │ └─dbplyr:::get_select_sql(...)
23. │ └─dbplyr:::translate_select_sql(con, select)
24. │ └─dbplyr::translate_sql_(...)
25. │ └─base::lapply(...)
26. │ └─dbplyr (local) FUN(X[[i]], ...)
27. │ ├─dbplyr::escape(eval_tidy(x, mask), con = con)
28. │ └─rlang::eval_tidy(x, mask)
29. └─CDMConnector::datediff
30. └─cli::cli_abort(...)
31. └─rlang::abort(...)
── Failure ('test-summariseResult.R:147:3'): table in db or local ──────────────
Expected ``%>%`(...)` to run without any errors.
i Actually got a <rlang_error> with text:
No known SQL translation
── Failure ('test-summariseResult.R:155:3'): table in db or local ──────────────
Expected ``%>%`(...)` to run without any errors.
i Actually got a <rlang_error> with text:
No known SQL translation
── Error ('test-summariseResult.R:169:3'): with and with overall groups and strata ──
Error in `CDMConnector::datediff()`: No known SQL translation
Backtrace:
▆
1. ├─... %>% dplyr::collect() at test-summariseResult.R:169:3
2. ├─dplyr::collect(.)
3. ├─PatientProfiles::addDemographics(...)
4. │ └─x %>% dplyr::compute()
5. ├─dplyr::compute(.)
6. ├─omopgenerics:::compute.cdm_table(.)
7. │ ├─dplyr::compute(...)
8. │ └─CDMConnector:::compute.db_cdm(...)
9. │ └─CDMConnector:::.computeQuery(...)
10. │ └─dbplyr::sql_render(x)
11. │ ├─dbplyr::sql_render(...)
12. │ └─dbplyr:::sql_render.tbl_lazy(...)
13. │ ├─dbplyr::sql_render(...)
14. │ └─dbplyr:::sql_render.lazy_query(...)
15. │ ├─dbplyr::sql_build(query, con = con, sql_options = sql_options)
16. │ └─dbplyr:::sql_build.lazy_select_query(query, con = con, sql_options = sql_options)
17. │ ├─dbplyr::sql_build(op$x, con, sql_options = sql_options)
18. │ └─dbplyr:::sql_build.lazy_select_query(op$x, con, sql_options = sql_options)
19. │ └─dbplyr:::get_select_sql(...)
20. │ └─dbplyr:::translate_select_sql(con, select)
21. │ └─dbplyr::translate_sql_(...)
22. │ └─base::lapply(...)
23. │ └─dbplyr (local) FUN(X[[i]], ...)
24. │ ├─dbplyr::escape(eval_tidy(x, mask), con = con)
25. │ └─rlang::eval_tidy(x, mask)
26. └─CDMConnector::datediff
27. └─cli::cli_abort(...)
28. └─rlang::abort(...)
── Error ('test-summariseResult.R:316:3'): test summary table naming ───────────
Error in `CDMConnector::datediff()`: No known SQL translation
Backtrace:
▆
1. ├─... %>% summariseResult() at test-summariseResult.R:316:3
2. ├─PatientProfiles::summariseResult(.)
3. │ └─PatientProfiles:::checkTable(table)
4. │ └─"tbl" %in% class(table)
5. ├─dplyr::mutate(., age_age = age, age_age_age = age, age_age_age_age = age)
6. ├─PatientProfiles::addDemographics(.)
7. │ └─x %>% dplyr::compute()
8. ├─dplyr::compute(.)
9. ├─omopgenerics:::compute.cdm_table(.)
10. │ ├─dplyr::compute(...)
11. │ └─CDMConnector:::compute.db_cdm(...)
12. │ └─CDMConnector:::.computeQuery(...)
13. │ └─dbplyr::sql_render(x)
14. │ ├─dbplyr::sql_render(...)
15. │ └─dbplyr:::sql_render.tbl_lazy(...)
16. │ ├─dbplyr::sql_render(...)
17. │ └─dbplyr:::sql_render.lazy_query(...)
18. │ ├─dbplyr::sql_build(query, con = con, sql_options = sql_options)
19. │ └─dbplyr:::sql_build.lazy_select_query(query, con = con, sql_options = sql_options)
20. │ ├─dbplyr::sql_build(op$x, con, sql_options = sql_options)
21. │ └─dbplyr:::sql_build.lazy_select_query(op$x, con, sql_options = sql_options)
22. │ └─dbplyr:::get_select_sql(...)
23. │ └─dbplyr:::translate_select_sql(con, select)
24. │ └─dbplyr::translate_sql_(...)
25. │ └─base::lapply(...)
26. │ └─dbplyr (local) FUN(X[[i]], ...)
27. │ ├─dbplyr::escape(eval_tidy(x, mask), con = con)
28. │ └─rlang::eval_tidy(x, mask)
29. └─CDMConnector::datediff
30. └─cli::cli_abort(...)
31. └─rlang::abort(...)
[ FAIL 65 | WARN 21 | SKIP 1 | PASS 200 ]
Error: Test failures
Execution halted
- checking for unstated dependencies in vignettes ... OK
- checking package vignettes ... OK
- checking re-building of vignette outputs ... [25s/33s] ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘addCohortIntersections.Rmd’ using rmarkdown
Quitting from lines 71-81 [unnamed-chunk-4] (addCohortIntersections.Rmd)
Error: processing vignette 'addCohortIntersections.Rmd' failed with diagnostics:
No known SQL translation
--- failed re-building ‘addCohortIntersections.Rmd’
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
Warning: Database is garbage-collected, use dbDisconnect(con, shutdown=TRUE) or duckdb::duckdb_shutdown(drv) to avoid this.
--- re-building ‘addPatientCharacteristics.rmd’ using rmarkdown
Quitting from lines 144-157 [unnamed-chunk-5] (addPatientCharacteristics.rmd)
Error: processing vignette 'addPatientCharacteristics.rmd' failed with diagnostics:
No known SQL translation
--- failed re-building ‘addPatientCharacteristics.rmd’
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
Warning: Database is garbage-collected, use dbDisconnect(con, shutdown=TRUE) or duckdb::duckdb_shutdown(drv) to avoid this.
SUMMARY: processing the following files failed:
‘addCohortIntersections.Rmd’ ‘addPatientCharacteristics.rmd’
Error: Vignette re-building failed.
Execution halted
- checking PDF version of manual ... [7s/9s] OK
- checking HTML version of manual ... [2s/3s] OK
- checking for non-standard things in the check directory ... OK
- DONE
Status: 2 ERRORs