* using log directory 'd:/RCompile/CRANincoming/R-devel/IncidencePrevalence.Rcheck' * using R Under development (unstable) (2024-03-16 r86144 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * checking for file 'IncidencePrevalence/DESCRIPTION' ... OK * this is package 'IncidencePrevalence' version '0.7.2' * package encoding: UTF-8 * checking CRAN incoming feasibility ... [12s] NOTE Maintainer: 'Edward Burn ' Number of updates in past 6 months: 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 hidden files and directories ... OK * checking for portable file names ... OK * checking whether package 'IncidencePrevalence' can be installed ... OK * checking installed package size ... OK * 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 ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... 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 ... [12s] OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd line widths ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking installed files from 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... [99s] ERROR Running 'testthat.R' [99s] Running the tests in 'tests/testthat.R' failed. Complete output: > library(testthat) > library(IncidencePrevalence) > > test_check("IncidencePrevalence") Starting 2 test processes [ FAIL 20 | WARN 0 | SKIP 71 | PASS 126 ] ══ Skipped tests (71) ══════════════════════════════════════════════════════════ • On CRAN (71): 'test-benchmarkIncidencePrevalence.R:2:3', 'test-estimatePrevalence.R:153:3', 'test-estimatePrevalence.R:210:3', 'test-estimatePrevalence.R:316:3', 'test-estimatePrevalence.R:446:3', 'test-estimatePrevalence.R:523:3', 'test-estimatePrevalence.R:642:3', 'test-estimatePrevalence.R:688:3', 'test-estimatePrevalence.R:743:3', 'test-estimatePrevalence.R:792:3', 'test-estimatePrevalence.R:816:3', 'test-estimatePrevalence.R:841:3', 'test-estimatePrevalence.R:959:3', 'test-estimatePrevalence.R:991:3', 'test-estimatePrevalence.R:1024:3', 'test-estimatePrevalence.R:1101:3', 'test-estimatePrevalence.R:1158:3', 'test-estimatePrevalence.R:1223:3', 'test-estimatePrevalence.R:1293:3', 'test-estimateIncidence.R:164:3', 'test-estimateIncidence.R:259:3', 'test-estimateIncidence.R:330:3', 'test-estimateIncidence.R:417:3', 'test-estimateIncidence.R:509:3', 'test-estimateIncidence.R:591:3', 'test-estimateIncidence.R:745:3', 'test-estimateIncidence.R:850:3', 'test-estimateIncidence.R:995:3', 'test-estimateIncidence.R:1056:3', 'test-estimateIncidence.R:1111:3', 'test-estimateIncidence.R:1194:3', 'test-estimateIncidence.R:1294:3', 'test-estimateIncidence.R:1400:3', 'test-estimateIncidence.R:1477:3', 'test-estimateIncidence.R:1582:3', 'test-estimateIncidence.R:1688:3', 'test-estimateIncidence.R:1794:3', 'test-estimateIncidence.R:1850:3', 'test-estimateIncidence.R:2031:3', 'test-estimateIncidence.R:2279:3', 'test-estimateIncidence.R:2357:3', 'test-estimateIncidence.R:2743:3', 'test-estimateIncidence.R:2774:3', 'test-estimateIncidence.R:2821:3', 'test-estimateIncidence.R:2877:3', 'test-estimateIncidence.R:2936:3', 'test-estimateIncidence.R:2991:3', 'test-mockIncidencePrevalenceRef.R:38:3', 'test-mockIncidencePrevalenceRef.R:71:3', 'test-mockIncidencePrevalenceRef.R:99:3', 'test-mockIncidencePrevalenceRef.R:150:3', 'test-mockIncidencePrevalenceRef.R:248:3', 'test-generateDenominatorCohortSet.R:138:3', 'test-generateDenominatorCohortSet.R:185:3', 'test-generateDenominatorCohortSet.R:289:3', 'test-generateDenominatorCohortSet.R:325:3', 'test-generateDenominatorCohortSet.R:582:3', 'test-generateDenominatorCohortSet.R:629:3', 'test-generateDenominatorCohortSet.R:708:3', 'test-generateDenominatorCohortSet.R:800:3', 'test-generateDenominatorCohortSet.R:843:3', 'test-generateDenominatorCohortSet.R:895:3', 'test-generateDenominatorCohortSet.R:979:3', 'test-generateDenominatorCohortSet.R:1102:3', 'test-generateDenominatorCohortSet.R:1166:3', 'test-generateDenominatorCohortSet.R:1219:3', 'test-generateDenominatorCohortSet.R:1277:3', 'test-generateDenominatorCohortSet.R:1353:3', 'test-generateDenominatorCohortSet.R:1474:3', 'test-generateDenominatorCohortSet.R:1573:3', 'test-generateDenominatorCohortSet.R:1624:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-benchmarkIncidencePrevalence.R:58:3'): check tables cleaned up ── Error in `CDMConnector::dateadd()`: No known SQL translation Backtrace: ▆ 1. ├─IncidencePrevalence::benchmarkIncidencePrevalence(cdm) at test-benchmarkIncidencePrevalence.R:58:3 2. │ └─IncidencePrevalence::generateDenominatorCohortSet(...) 3. │ └─IncidencePrevalence:::fetchDenominatorCohortSet(...) 4. │ └─IncidencePrevalence:::fetchSingleTargetDenominatorCohortSet(...) 5. │ └─IncidencePrevalence:::getDenominatorCohorts(...) 6. │ └─studyPopDb %>% ... 7. ├─dplyr::compute(., name = paste0(intermediateTable, "_i_4"), temporary = FALSE) 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::sql_build(op$x, con, sql_options = sql_options) 20. │ └─dbplyr:::sql_build.lazy_select_query(op$x, con, sql_options = sql_options) 21. │ └─dbplyr:::get_select_sql(...) 22. │ └─dbplyr:::translate_select_sql(con, select) 23. │ └─dbplyr::translate_sql_(...) 24. │ └─base::lapply(...) 25. │ └─dbplyr (local) FUN(X[[i]], ...) 26. │ ├─dbplyr::escape(eval_tidy(x, mask), con = con) 27. │ └─rlang::eval_tidy(x, mask) 28. └─CDMConnector::dateadd 29. └─cli::cli_abort(...) 30. └─rlang::abort(...) ── Error ('test-bindEstimates.R:15:3'): check with mock db ───────────────────── Error in `CDMConnector::dateadd()`: No known SQL translation Backtrace: ▆ 1. ├─IncidencePrevalence::generateDenominatorCohortSet(...) at test-bindEstimates.R:15:3 2. │ └─IncidencePrevalence:::fetchDenominatorCohortSet(...) 3. │ └─IncidencePrevalence:::fetchSingleTargetDenominatorCohortSet(...) 4. │ └─IncidencePrevalence:::getDenominatorCohorts(...) 5. │ └─studyPopDb %>% ... 6. ├─dplyr::compute(., name = paste0(intermediateTable, "_i_4"), temporary = FALSE) 7. ├─omopgenerics:::compute.cdm_table(...) 8. │ ├─dplyr::compute(...) 9. │ └─CDMConnector:::compute.db_cdm(...) 10. │ └─CDMConnector:::.computeQuery(...) 11. │ └─dbplyr::sql_render(x) 12. │ ├─dbplyr::sql_render(...) 13. │ └─dbplyr:::sql_render.tbl_lazy(...) 14. │ ├─dbplyr::sql_render(...) 15. │ └─dbplyr:::sql_render.lazy_query(...) 16. │ ├─dbplyr::sql_build(query, con = con, sql_options = sql_options) 17. │ └─dbplyr:::sql_build.lazy_select_query(query, con = con, sql_options = sql_options) 18. │ ├─dbplyr::sql_build(op$x, con, sql_options = sql_options) 19. │ └─dbplyr:::sql_build.lazy_select_query(op$x, con, sql_options = sql_options) 20. │ └─dbplyr:::get_select_sql(...) 21. │ └─dbplyr:::translate_select_sql(con, select) 22. │ └─dbplyr::translate_sql_(...) 23. │ └─base::lapply(...) 24. │ └─dbplyr (local) FUN(X[[i]], ...) 25. │ ├─dbplyr::escape(eval_tidy(x, mask), con = con) 26. │ └─rlang::eval_tidy(x, mask) 27. └─CDMConnector::dateadd 28. └─cli::cli_abort(...) 29. └─rlang::abort(...) ── Error ('test-estimatePrevalence.R:3:3'): mock db: check output format ─────── Error in `CDMConnector::dateadd()`: No known SQL translation Backtrace: ▆ 1. ├─mockIncidencePrevalenceRef() %>% ... at test-estimatePrevalence.R:3:3 2. ├─IncidencePrevalence::generateDenominatorCohortSet(., name = "denominator") 3. │ └─IncidencePrevalence:::fetchDenominatorCohortSet(...) 4. │ └─IncidencePrevalence:::fetchSingleTargetDenominatorCohortSet(...) 5. │ └─IncidencePrevalence:::getDenominatorCohorts(...) 6. │ └─studyPopDb %>% ... 7. ├─dplyr::compute(., name = paste0(intermediateTable, "_i_4"), temporary = FALSE) 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::sql_build(op$x, con, sql_options = sql_options) 20. │ └─dbplyr:::sql_build.lazy_select_query(op$x, con, sql_options = sql_options) 21. │ └─dbplyr:::get_select_sql(...) 22. │ └─dbplyr:::translate_select_sql(con, select) 23. │ └─dbplyr::translate_sql_(...) 24. │ └─base::lapply(...) 25. │ └─dbplyr (local) FUN(X[[i]], ...) 26. │ ├─dbplyr::escape(eval_tidy(x, mask), con = con) 27. │ └─rlang::eval_tidy(x, mask) 28. └─CDMConnector::dateadd 29. └─cli::cli_abort(...) 30. └─rlang::abort(...) ── Error ('test-estimatePrevalence.R:138:3'): mock db: checks on working example ── Error in `CDMConnector::dateadd()`: No known SQL translation Backtrace: ▆ 1. ├─IncidencePrevalence::generateDenominatorCohortSet(...) at test-estimatePrevalence.R:138:3 2. │ └─IncidencePrevalence:::fetchDenominatorCohortSet(...) 3. │ └─IncidencePrevalence:::fetchSingleTargetDenominatorCohortSet(...) 4. │ └─IncidencePrevalence:::getDenominatorCohorts(...) 5. │ └─studyPopDb %>% ... 6. ├─dplyr::compute(., name = paste0(intermediateTable, "_i_4"), temporary = FALSE) 7. ├─omopgenerics:::compute.cdm_table(...) 8. │ ├─dplyr::compute(...) 9. │ └─CDMConnector:::compute.db_cdm(...) 10. │ └─CDMConnector:::.computeQuery(...) 11. │ └─dbplyr::sql_render(x) 12. │ ├─dbplyr::sql_render(...) 13. │ └─dbplyr:::sql_render.tbl_lazy(...) 14. │ ├─dbplyr::sql_render(...) 15. │ └─dbplyr:::sql_render.lazy_query(...) 16. │ ├─dbplyr::sql_build(query, con = con, sql_options = sql_options) 17. │ └─dbplyr:::sql_build.lazy_select_query(query, con = con, sql_options = sql_options) 18. │ ├─dbplyr::sql_build(op$x, con, sql_options = sql_options) 19. │ └─dbplyr:::sql_build.lazy_select_query(op$x, con, sql_options = sql_options) 20. │ └─dbplyr:::get_select_sql(...) 21. │ └─dbplyr:::translate_select_sql(con, select) 22. │ └─dbplyr::translate_sql_(...) 23. │ └─base::lapply(...) 24. │ └─dbplyr (local) FUN(X[[i]], ...) 25. │ ├─dbplyr::escape(eval_tidy(x, mask), con = con) 26. │ └─rlang::eval_tidy(x, mask) 27. └─CDMConnector::dateadd 28. └─cli::cli_abort(...) 29. └─rlang::abort(...) ── Error ('test-estimatePrevalence.R:1269:3'): mock db: if missing cohort attributes ── Error in `CDMConnector::dateadd()`: No known SQL translation Backtrace: ▆ 1. ├─IncidencePrevalence::generateDenominatorCohortSet(...) at test-estimatePrevalence.R:1269:3 2. │ └─IncidencePrevalence:::fetchDenominatorCohortSet(...) 3. │ └─IncidencePrevalence:::fetchSingleTargetDenominatorCohortSet(...) 4. │ └─IncidencePrevalence:::getDenominatorCohorts(...) 5. │ └─studyPopDb %>% ... 6. ├─dplyr::compute(., name = paste0(intermediateTable, "_i_4"), temporary = FALSE) 7. ├─omopgenerics:::compute.cdm_table(...) 8. │ ├─dplyr::compute(...) 9. │ └─CDMConnector:::compute.db_cdm(...) 10. │ └─CDMConnector:::.computeQuery(...) 11. │ └─dbplyr::sql_render(x) 12. │ ├─dbplyr::sql_render(...) 13. │ └─dbplyr:::sql_render.tbl_lazy(...) 14. │ ├─dbplyr::sql_render(...) 15. │ └─dbplyr:::sql_render.lazy_query(...) 16. │ ├─dbplyr::sql_build(query, con = con, sql_options = sql_options) 17. │ └─dbplyr:::sql_build.lazy_select_query(query, con = con, sql_options = sql_options) 18. │ ├─dbplyr::sql_build(op$x, con, sql_options = sql_options) 19. │ └─dbplyr:::sql_build.lazy_select_query(op$x, con, sql_options = sql_options) 20. │ └─dbplyr:::get_select_sql(...) 21. │ └─dbplyr:::translate_select_sql(con, select) 22. │ └─dbplyr::translate_sql_(...) 23. │ └─base::lapply(...) 24. │ └─dbplyr (local) FUN(X[[i]], ...) 25. │ ├─dbplyr::escape(eval_tidy(x, mask), con = con) 26. │ └─rlang::eval_tidy(x, mask) 27. └─CDMConnector::dateadd 28. └─cli::cli_abort(...) 29. └─rlang::abort(...) ── Error ('test-estimatePrevalence.R:1315:3'): mock db: prevalence using strata vars ── Error in `CDMConnector::dateadd()`: No known SQL translation Backtrace: ▆ 1. ├─IncidencePrevalence::generateDenominatorCohortSet(...) at test-estimatePrevalence.R:1315:3 2. │ └─IncidencePrevalence:::fetchDenominatorCohortSet(...) 3. │ └─IncidencePrevalence:::fetchSingleTargetDenominatorCohortSet(...) 4. │ └─IncidencePrevalence:::getDenominatorCohorts(...) 5. │ └─studyPopDb %>% ... 6. ├─dplyr::compute(., name = paste0(intermediateTable, "_i_4"), temporary = FALSE) 7. ├─omopgenerics:::compute.cdm_table(...) 8. │ ├─dplyr::compute(...) 9. │ └─CDMConnector:::compute.db_cdm(...) 10. │ └─CDMConnector:::.computeQuery(...) 11. │ └─dbplyr::sql_render(x) 12. │ ├─dbplyr::sql_render(...) 13. │ └─dbplyr:::sql_render.tbl_lazy(...) 14. │ ├─dbplyr::sql_render(...) 15. │ └─dbplyr:::sql_render.lazy_query(...) 16. │ ├─dbplyr::sql_build(query, con = con, sql_options = sql_options) 17. │ └─dbplyr:::sql_build.lazy_select_query(query, con = con, sql_options = sql_options) 18. │ ├─dbplyr::sql_build(op$x, con, sql_options = sql_options) 19. │ └─dbplyr:::sql_build.lazy_select_query(op$x, con, sql_options = sql_options) 20. │ └─dbplyr:::get_select_sql(...) 21. │ └─dbplyr:::translate_select_sql(con, select) 22. │ └─dbplyr::translate_sql_(...) 23. │ └─base::lapply(...) 24. │ └─dbplyr (local) FUN(X[[i]], ...) 25. │ ├─dbplyr::escape(eval_tidy(x, mask), con = con) 26. │ └─rlang::eval_tidy(x, mask) 27. └─CDMConnector::dateadd 28. └─cli::cli_abort(...) 29. └─rlang::abort(...) ── Error ('test-exportIncidencePrevalenceResults.R:3:3'): writing results ────── Error in `CDMConnector::dateadd()`: No known SQL translation Backtrace: ▆ 1. ├─IncidencePrevalence::generateDenominatorCohortSet(...) at test-exportIncidencePrevalenceResults.R:3:3 2. │ └─IncidencePrevalence:::fetchDenominatorCohortSet(...) 3. │ └─IncidencePrevalence:::fetchSingleTargetDenominatorCohortSet(...) 4. │ └─IncidencePrevalence:::getDenominatorCohorts(...) 5. │ └─studyPopDb %>% ... 6. ├─dplyr::compute(., name = paste0(intermediateTable, "_i_4"), temporary = FALSE) 7. ├─omopgenerics:::compute.cdm_table(...) 8. │ ├─dplyr::compute(...) 9. │ └─CDMConnector:::compute.db_cdm(...) 10. │ └─CDMConnector:::.computeQuery(...) 11. │ └─dbplyr::sql_render(x) 12. │ ├─dbplyr::sql_render(...) 13. │ └─dbplyr:::sql_render.tbl_lazy(...) 14. │ ├─dbplyr::sql_render(...) 15. │ └─dbplyr:::sql_render.lazy_query(...) 16. │ ├─dbplyr::sql_build(query, con = con, sql_options = sql_options) 17. │ └─dbplyr:::sql_build.lazy_select_query(query, con = con, sql_options = sql_options) 18. │ ├─dbplyr::sql_build(op$x, con, sql_options = sql_options) 19. │ └─dbplyr:::sql_build.lazy_select_query(op$x, con, sql_options = sql_options) 20. │ └─dbplyr:::get_select_sql(...) 21. │ └─dbplyr:::translate_select_sql(con, select) 22. │ └─dbplyr::translate_sql_(...) 23. │ └─base::lapply(...) 24. │ └─dbplyr (local) FUN(X[[i]], ...) 25. │ ├─dbplyr::escape(eval_tidy(x, mask), con = con) 26. │ └─rlang::eval_tidy(x, mask) 27. └─CDMConnector::dateadd 28. └─cli::cli_abort(...) 29. └─rlang::abort(...) ── Error ('test-exportIncidencePrevalenceResults.R:26:3'): writing results- expected errors ── Error in `CDMConnector::dateadd()`: No known SQL translation Backtrace: ▆ 1. ├─IncidencePrevalence::generateDenominatorCohortSet(...) at test-exportIncidencePrevalenceResults.R:26:3 2. │ └─IncidencePrevalence:::fetchDenominatorCohortSet(...) 3. │ └─IncidencePrevalence:::fetchSingleTargetDenominatorCohortSet(...) 4. │ └─IncidencePrevalence:::getDenominatorCohorts(...) 5. │ └─studyPopDb %>% ... 6. ├─dplyr::compute(., name = paste0(intermediateTable, "_i_4"), temporary = FALSE) 7. ├─omopgenerics:::compute.cdm_table(...) 8. │ ├─dplyr::compute(...) 9. │ └─CDMConnector:::compute.db_cdm(...) 10. │ └─CDMConnector:::.computeQuery(...) 11. │ └─dbplyr::sql_render(x) 12. │ ├─dbplyr::sql_render(...) 13. │ └─dbplyr:::sql_render.tbl_lazy(...) 14. │ ├─dbplyr::sql_render(...) 15. │ └─dbplyr:::sql_render.lazy_query(...) 16. │ ├─dbplyr::sql_build(query, con = con, sql_options = sql_options) 17. │ └─dbplyr:::sql_build.lazy_select_query(query, con = con, sql_options = sql_options) 18. │ ├─dbplyr::sql_build(op$x, con, sql_options = sql_options) 19. │ └─dbplyr:::sql_build.lazy_select_query(op$x, con, sql_options = sql_options) 20. │ └─dbplyr:::get_select_sql(...) 21. │ └─dbplyr:::translate_select_sql(con, select) 22. │ └─dbplyr::translate_sql_(...) 23. │ └─base::lapply(...) 24. │ └─dbplyr (local) FUN(X[[i]], ...) 25. │ ├─dbplyr::escape(eval_tidy(x, mask), con = con) 26. │ └─rlang::eval_tidy(x, mask) 27. └─CDMConnector::dateadd 28. └─cli::cli_abort(...) 29. └─rlang::abort(...) ── Error ('test-estimateIncidence.R:5:3'): mock db: check output format ──────── Error in `CDMConnector::dateadd()`: No known SQL translation Backtrace: ▆ 1. ├─IncidencePrevalence::generateDenominatorCohortSet(...) at test-estimateIncidence.R:5:3 2. │ └─IncidencePrevalence:::fetchDenominatorCohortSet(...) 3. │ └─IncidencePrevalence:::fetchSingleTargetDenominatorCohortSet(...) 4. │ └─IncidencePrevalence:::getDenominatorCohorts(...) 5. │ └─studyPopDb %>% ... 6. ├─dplyr::compute(., name = paste0(intermediateTable, "_i_4"), temporary = FALSE) 7. ├─omopgenerics:::compute.cdm_table(...) 8. │ ├─dplyr::compute(...) 9. │ └─CDMConnector:::compute.db_cdm(...) 10. │ └─CDMConnector:::.computeQuery(...) 11. │ └─dbplyr::sql_render(x) 12. │ ├─dbplyr::sql_render(...) 13. │ └─dbplyr:::sql_render.tbl_lazy(...) 14. │ ├─dbplyr::sql_render(...) 15. │ └─dbplyr:::sql_render.lazy_query(...) 16. │ ├─dbplyr::sql_build(query, con = con, sql_options = sql_options) 17. │ └─dbplyr:::sql_build.lazy_select_query(query, con = con, sql_options = sql_options) 18. │ ├─dbplyr::sql_build(op$x, con, sql_options = sql_options) 19. │ └─dbplyr:::sql_build.lazy_select_query(op$x, con, sql_options = sql_options) 20. │ └─dbplyr:::get_select_sql(...) 21. │ └─dbplyr:::translate_select_sql(con, select) 22. │ └─dbplyr::translate_sql_(...) 23. │ └─base::lapply(...) 24. │ └─dbplyr (local) FUN(X[[i]], ...) 25. │ ├─dbplyr::escape(eval_tidy(x, mask), con = con) 26. │ └─rlang::eval_tidy(x, mask) 27. └─CDMConnector::dateadd 28. └─cli::cli_abort(...) 29. └─rlang::abort(...) ── Error ('test-estimateIncidence.R:135:3'): mock db: checks on working example ── Error in `CDMConnector::dateadd()`: No known SQL translation Backtrace: ▆ 1. ├─IncidencePrevalence::generateDenominatorCohortSet(...) at test-estimateIncidence.R:135:3 2. │ └─IncidencePrevalence:::fetchDenominatorCohortSet(...) 3. │ └─IncidencePrevalence:::fetchSingleTargetDenominatorCohortSet(...) 4. │ └─IncidencePrevalence:::getDenominatorCohorts(...) 5. │ └─studyPopDb %>% ... 6. ├─dplyr::compute(., name = paste0(intermediateTable, "_i_4"), temporary = FALSE) 7. ├─omopgenerics:::compute.cdm_table(...) 8. │ ├─dplyr::compute(...) 9. │ └─CDMConnector:::compute.db_cdm(...) 10. │ └─CDMConnector:::.computeQuery(...) 11. │ └─dbplyr::sql_render(x) 12. │ ├─dbplyr::sql_render(...) 13. │ └─dbplyr:::sql_render.tbl_lazy(...) 14. │ ├─dbplyr::sql_render(...) 15. │ └─dbplyr:::sql_render.lazy_query(...) 16. │ ├─dbplyr::sql_build(query, con = con, sql_options = sql_options) 17. │ └─dbplyr:::sql_build.lazy_select_query(query, con = con, sql_options = sql_options) 18. │ ├─dbplyr::sql_build(op$x, con, sql_options = sql_options) 19. │ └─dbplyr:::sql_build.lazy_select_query(op$x, con, sql_options = sql_options) 20. │ └─dbplyr:::get_select_sql(...) 21. │ └─dbplyr:::translate_select_sql(con, select) 22. │ └─dbplyr::translate_sql_(...) 23. │ └─base::lapply(...) 24. │ └─dbplyr (local) FUN(X[[i]], ...) 25. │ ├─dbplyr::escape(eval_tidy(x, mask), con = con) 26. │ └─rlang::eval_tidy(x, mask) 27. └─CDMConnector::dateadd 28. └─cli::cli_abort(...) 29. └─rlang::abort(...) ── Error ('test-estimateIncidence.R:3038:3'): mock db: if missing cohort attributes ── Error in `CDMConnector::dateadd()`: No known SQL translation Backtrace: ▆ 1. ├─IncidencePrevalence::generateDenominatorCohortSet(...) at test-estimateIncidence.R:3038:3 2. │ └─IncidencePrevalence:::fetchDenominatorCohortSet(...) 3. │ └─IncidencePrevalence:::fetchSingleTargetDenominatorCohortSet(...) 4. │ └─IncidencePrevalence:::getDenominatorCohorts(...) 5. │ └─studyPopDb %>% ... 6. ├─dplyr::compute(., name = paste0(intermediateTable, "_i_4"), temporary = FALSE) 7. ├─omopgenerics:::compute.cdm_table(...) 8. │ ├─dplyr::compute(...) 9. │ └─CDMConnector:::compute.db_cdm(...) 10. │ └─CDMConnector:::.computeQuery(...) 11. │ └─dbplyr::sql_render(x) 12. │ ├─dbplyr::sql_render(...) 13. │ └─dbplyr:::sql_render.tbl_lazy(...) 14. │ ├─dbplyr::sql_render(...) 15. │ └─dbplyr:::sql_render.lazy_query(...) 16. │ ├─dbplyr::sql_build(query, con = con, sql_options = sql_options) 17. │ └─dbplyr:::sql_build.lazy_select_query(query, con = con, sql_options = sql_options) 18. │ ├─dbplyr::sql_build(op$x, con, sql_options = sql_options) 19. │ └─dbplyr:::sql_build.lazy_select_query(op$x, con, sql_options = sql_options) 20. │ └─dbplyr:::get_select_sql(...) 21. │ └─dbplyr:::translate_select_sql(con, select) 22. │ └─dbplyr::translate_sql_(...) 23. │ └─base::lapply(...) 24. │ └─dbplyr (local) FUN(X[[i]], ...) 25. │ ├─dbplyr::escape(eval_tidy(x, mask), con = con) 26. │ └─rlang::eval_tidy(x, mask) 27. └─CDMConnector::dateadd 28. └─cli::cli_abort(...) 29. └─rlang::abort(...) ── Error ('test-estimateIncidence.R:3053:3'): mock db: empty outcome cohort ──── Error in `CDMConnector::dateadd()`: No known SQL translation Backtrace: ▆ 1. ├─IncidencePrevalence::generateDenominatorCohortSet(...) at test-estimateIncidence.R:3053:3 2. │ └─IncidencePrevalence:::fetchDenominatorCohortSet(...) 3. │ └─IncidencePrevalence:::fetchSingleTargetDenominatorCohortSet(...) 4. │ └─IncidencePrevalence:::getDenominatorCohorts(...) 5. │ └─studyPopDb %>% ... 6. ├─dplyr::compute(., name = paste0(intermediateTable, "_i_4"), temporary = FALSE) 7. ├─omopgenerics:::compute.cdm_table(...) 8. │ ├─dplyr::compute(...) 9. │ └─CDMConnector:::compute.db_cdm(...) 10. │ └─CDMConnector:::.computeQuery(...) 11. │ └─dbplyr::sql_render(x) 12. │ ├─dbplyr::sql_render(...) 13. │ └─dbplyr:::sql_render.tbl_lazy(...) 14. │ ├─dbplyr::sql_render(...) 15. │ └─dbplyr:::sql_render.lazy_query(...) 16. │ ├─dbplyr::sql_build(query, con = con, sql_options = sql_options) 17. │ └─dbplyr:::sql_build.lazy_select_query(query, con = con, sql_options = sql_options) 18. │ ├─dbplyr::sql_build(op$x, con, sql_options = sql_options) 19. │ └─dbplyr:::sql_build.lazy_select_query(op$x, con, sql_options = sql_options) 20. │ └─dbplyr:::get_select_sql(...) 21. │ └─dbplyr:::translate_select_sql(con, select) 22. │ └─dbplyr::translate_sql_(...) 23. │ └─base::lapply(...) 24. │ └─dbplyr (local) FUN(X[[i]], ...) 25. │ ├─dbplyr::escape(eval_tidy(x, mask), con = con) 26. │ └─rlang::eval_tidy(x, mask) 27. └─CDMConnector::dateadd 28. └─cli::cli_abort(...) 29. └─rlang::abort(...) ── Error ('test-estimateIncidence.R:3078:3'): mock db: incidence using strata vars ── Error in `CDMConnector::dateadd()`: No known SQL translation Backtrace: ▆ 1. ├─IncidencePrevalence::generateDenominatorCohortSet(...) at test-estimateIncidence.R:3078:3 2. │ └─IncidencePrevalence:::fetchDenominatorCohortSet(...) 3. │ └─IncidencePrevalence:::fetchSingleTargetDenominatorCohortSet(...) 4. │ └─IncidencePrevalence:::getDenominatorCohorts(...) 5. │ └─studyPopDb %>% ... 6. ├─dplyr::compute(., name = paste0(intermediateTable, "_i_4"), temporary = FALSE) 7. ├─omopgenerics:::compute.cdm_table(...) 8. │ ├─dplyr::compute(...) 9. │ └─CDMConnector:::compute.db_cdm(...) 10. │ └─CDMConnector:::.computeQuery(...) 11. │ └─dbplyr::sql_render(x) 12. │ ├─dbplyr::sql_render(...) 13. │ └─dbplyr:::sql_render.tbl_lazy(...) 14. │ ├─dbplyr::sql_render(...) 15. │ └─dbplyr:::sql_render.lazy_query(...) 16. │ ├─dbplyr::sql_build(query, con = con, sql_options = sql_options) 17. │ └─dbplyr:::sql_build.lazy_select_query(query, con = con, sql_options = sql_options) 18. │ ├─dbplyr::sql_build(op$x, con, sql_options = sql_options) 19. │ └─dbplyr:::sql_build.lazy_select_query(op$x, con, sql_options = sql_options) 20. │ └─dbplyr:::get_select_sql(...) 21. │ └─dbplyr:::translate_select_sql(con, select) 22. │ └─dbplyr::translate_sql_(...) 23. │ └─base::lapply(...) 24. │ └─dbplyr (local) FUN(X[[i]], ...) 25. │ ├─dbplyr::escape(eval_tidy(x, mask), con = con) 26. │ └─rlang::eval_tidy(x, mask) 27. └─CDMConnector::dateadd 28. └─cli::cli_abort(...) 29. └─rlang::abort(...) ── Error ('test-generateDenominatorCohortSet.R:4:3'): mock db: check output format ── Error in `CDMConnector::dateadd()`: No known SQL translation Backtrace: ▆ 1. ├─IncidencePrevalence::generateDenominatorCohortSet(...) at test-generateDenominatorCohortSet.R:4:3 2. │ └─IncidencePrevalence:::fetchDenominatorCohortSet(...) 3. │ └─IncidencePrevalence:::fetchSingleTargetDenominatorCohortSet(...) 4. │ └─IncidencePrevalence:::getDenominatorCohorts(...) 5. │ └─studyPopDb %>% ... 6. ├─dplyr::compute(., name = paste0(intermediateTable, "_i_4"), temporary = FALSE) 7. ├─omopgenerics:::compute.cdm_table(...) 8. │ ├─dplyr::compute(...) 9. │ └─CDMConnector:::compute.db_cdm(...) 10. │ └─CDMConnector:::.computeQuery(...) 11. │ └─dbplyr::sql_render(x) 12. │ ├─dbplyr::sql_render(...) 13. │ └─dbplyr:::sql_render.tbl_lazy(...) 14. │ ├─dbplyr::sql_render(...) 15. │ └─dbplyr:::sql_render.lazy_query(...) 16. │ ├─dbplyr::sql_build(query, con = con, sql_options = sql_options) 17. │ └─dbplyr:::sql_build.lazy_select_query(query, con = con, sql_options = sql_options) 18. │ ├─dbplyr::sql_build(op$x, con, sql_options = sql_options) 19. │ └─dbplyr:::sql_build.lazy_select_query(op$x, con, sql_options = sql_options) 20. │ └─dbplyr:::get_select_sql(...) 21. │ └─dbplyr:::translate_select_sql(con, select) 22. │ └─dbplyr::translate_sql_(...) 23. │ └─base::lapply(...) 24. │ └─dbplyr (local) FUN(X[[i]], ...) 25. │ ├─dbplyr::escape(eval_tidy(x, mask), con = con) 26. │ └─rlang::eval_tidy(x, mask) 27. └─CDMConnector::dateadd 28. └─cli::cli_abort(...) 29. └─rlang::abort(...) ── Error ('test-generateDenominatorCohortSet.R:75:3'): mock db: checks on working example ── Error in `CDMConnector::dateadd()`: No known SQL translation Backtrace: ▆ 1. ├─IncidencePrevalence::generateDenominatorCohortSet(...) at test-generateDenominatorCohortSet.R:75:3 2. │ └─IncidencePrevalence:::fetchDenominatorCohortSet(...) 3. │ └─IncidencePrevalence:::fetchSingleTargetDenominatorCohortSet(...) 4. │ └─IncidencePrevalence:::getDenominatorCohorts(...) 5. │ └─studyPopDb %>% ... 6. ├─dplyr::compute(., name = paste0(intermediateTable, "_i_4"), temporary = FALSE) 7. ├─omopgenerics:::compute.cdm_table(...) 8. │ ├─dplyr::compute(...) 9. │ └─CDMConnector:::compute.db_cdm(...) 10. │ └─CDMConnector:::.computeQuery(...) 11. │ └─dbplyr::sql_render(x) 12. │ ├─dbplyr::sql_render(...) 13. │ └─dbplyr:::sql_render.tbl_lazy(...) 14. │ ├─dbplyr::sql_render(...) 15. │ └─dbplyr:::sql_render.lazy_query(...) 16. │ ├─dbplyr::sql_build(query, con = con, sql_options = sql_options) 17. │ └─dbplyr:::sql_build.lazy_select_query(query, con = con, sql_options = sql_options) 18. │ ├─dbplyr::sql_build(op$x, con, sql_options = sql_options) 19. │ └─dbplyr:::sql_build.lazy_select_query(op$x, con, sql_options = sql_options) 20. │ └─dbplyr:::get_select_sql(...) 21. │ └─dbplyr:::translate_select_sql(con, select) 22. │ └─dbplyr::translate_sql_(...) 23. │ └─base::lapply(...) 24. │ └─dbplyr (local) FUN(X[[i]], ...) 25. │ ├─dbplyr::escape(eval_tidy(x, mask), con = con) 26. │ └─rlang::eval_tidy(x, mask) 27. └─CDMConnector::dateadd 28. └─cli::cli_abort(...) 29. └─rlang::abort(...) ── Error ('test-plotting.R:3:3'): basic incidence plot ───────────────────────── Error in `CDMConnector::dateadd()`: No known SQL translation Backtrace: ▆ 1. ├─IncidencePrevalence::generateDenominatorCohortSet(...) at test-plotting.R:3:3 2. │ └─IncidencePrevalence:::fetchDenominatorCohortSet(...) 3. │ └─IncidencePrevalence:::fetchSingleTargetDenominatorCohortSet(...) 4. │ └─IncidencePrevalence:::getDenominatorCohorts(...) 5. │ └─studyPopDb %>% ... 6. ├─dplyr::compute(., name = paste0(intermediateTable, "_i_4"), temporary = FALSE) 7. ├─omopgenerics:::compute.cdm_table(...) 8. │ ├─dplyr::compute(...) 9. │ └─CDMConnector:::compute.db_cdm(...) 10. │ └─CDMConnector:::.computeQuery(...) 11. │ └─dbplyr::sql_render(x) 12. │ ├─dbplyr::sql_render(...) 13. │ └─dbplyr:::sql_render.tbl_lazy(...) 14. │ ├─dbplyr::sql_render(...) 15. │ └─dbplyr:::sql_render.lazy_query(...) 16. │ ├─dbplyr::sql_build(query, con = con, sql_options = sql_options) 17. │ └─dbplyr:::sql_build.lazy_select_query(query, con = con, sql_options = sql_options) 18. │ ├─dbplyr::sql_build(op$x, con, sql_options = sql_options) 19. │ └─dbplyr:::sql_build.lazy_select_query(op$x, con, sql_options = sql_options) 20. │ └─dbplyr:::get_select_sql(...) 21. │ └─dbplyr:::translate_select_sql(con, select) 22. │ └─dbplyr::translate_sql_(...) 23. │ └─base::lapply(...) 24. │ └─dbplyr (local) FUN(X[[i]], ...) 25. │ ├─dbplyr::escape(eval_tidy(x, mask), con = con) 26. │ └─rlang::eval_tidy(x, mask) 27. └─CDMConnector::dateadd 28. └─cli::cli_abort(...) 29. └─rlang::abort(...) ── Error ('test-plotting.R:36:3'): basic prevalence plot ─────────────────────── Error in `CDMConnector::dateadd()`: No known SQL translation Backtrace: ▆ 1. ├─IncidencePrevalence::generateDenominatorCohortSet(...) at test-plotting.R:36:3 2. │ └─IncidencePrevalence:::fetchDenominatorCohortSet(...) 3. │ └─IncidencePrevalence:::fetchSingleTargetDenominatorCohortSet(...) 4. │ └─IncidencePrevalence:::getDenominatorCohorts(...) 5. │ └─studyPopDb %>% ... 6. ├─dplyr::compute(., name = paste0(intermediateTable, "_i_4"), temporary = FALSE) 7. ├─omopgenerics:::compute.cdm_table(...) 8. │ ├─dplyr::compute(...) 9. │ └─CDMConnector:::compute.db_cdm(...) 10. │ └─CDMConnector:::.computeQuery(...) 11. │ └─dbplyr::sql_render(x) 12. │ ├─dbplyr::sql_render(...) 13. │ └─dbplyr:::sql_render.tbl_lazy(...) 14. │ ├─dbplyr::sql_render(...) 15. │ └─dbplyr:::sql_render.lazy_query(...) 16. │ ├─dbplyr::sql_build(query, con = con, sql_options = sql_options) 17. │ └─dbplyr:::sql_build.lazy_select_query(query, con = con, sql_options = sql_options) 18. │ ├─dbplyr::sql_build(op$x, con, sql_options = sql_options) 19. │ └─dbplyr:::sql_build.lazy_select_query(op$x, con, sql_options = sql_options) 20. │ └─dbplyr:::get_select_sql(...) 21. │ └─dbplyr:::translate_select_sql(con, select) 22. │ └─dbplyr::translate_sql_(...) 23. │ └─base::lapply(...) 24. │ └─dbplyr (local) FUN(X[[i]], ...) 25. │ ├─dbplyr::escape(eval_tidy(x, mask), con = con) 26. │ └─rlang::eval_tidy(x, mask) 27. └─CDMConnector::dateadd 28. └─cli::cli_abort(...) 29. └─rlang::abort(...) ── Error ('test-plotting.R:73:3'): plot facets ───────────────────────────────── Error in `CDMConnector::dateadd()`: No known SQL translation Backtrace: ▆ 1. ├─IncidencePrevalence::generateDenominatorCohortSet(...) at test-plotting.R:73:3 2. │ └─IncidencePrevalence:::fetchDenominatorCohortSet(...) 3. │ └─IncidencePrevalence:::fetchSingleTargetDenominatorCohortSet(...) 4. │ └─IncidencePrevalence:::getDenominatorCohorts(...) 5. │ └─studyPopDb %>% ... 6. ├─dplyr::compute(., name = paste0(intermediateTable, "_i_4"), temporary = FALSE) 7. ├─omopgenerics:::compute.cdm_table(...) 8. │ ├─dplyr::compute(...) 9. │ └─CDMConnector:::compute.db_cdm(...) 10. │ └─CDMConnector:::.computeQuery(...) 11. │ └─dbplyr::sql_render(x) 12. │ ├─dbplyr::sql_render(...) 13. │ └─dbplyr:::sql_render.tbl_lazy(...) 14. │ ├─dbplyr::sql_render(...) 15. │ └─dbplyr:::sql_render.lazy_query(...) 16. │ ├─dbplyr::sql_build(query, con = con, sql_options = sql_options) 17. │ └─dbplyr:::sql_build.lazy_select_query(query, con = con, sql_options = sql_options) 18. │ ├─dbplyr::sql_build(op$x, con, sql_options = sql_options) 19. │ └─dbplyr:::sql_build.lazy_select_query(op$x, con, sql_options = sql_options) 20. │ └─dbplyr:::get_select_sql(...) 21. │ └─dbplyr:::translate_select_sql(con, select) 22. │ └─dbplyr::translate_sql_(...) 23. │ └─base::lapply(...) 24. │ └─dbplyr (local) FUN(X[[i]], ...) 25. │ ├─dbplyr::escape(eval_tidy(x, mask), con = con) 26. │ └─rlang::eval_tidy(x, mask) 27. └─CDMConnector::dateadd 28. └─cli::cli_abort(...) 29. └─rlang::abort(...) ── Error ('test-plotting.R:118:3'): plot colour ──────────────────────────────── Error in `CDMConnector::dateadd()`: No known SQL translation Backtrace: ▆ 1. ├─IncidencePrevalence::generateDenominatorCohortSet(...) at test-plotting.R:118:3 2. │ └─IncidencePrevalence:::fetchDenominatorCohortSet(...) 3. │ └─IncidencePrevalence:::fetchSingleTargetDenominatorCohortSet(...) 4. │ └─IncidencePrevalence:::getDenominatorCohorts(...) 5. │ └─studyPopDb %>% ... 6. ├─dplyr::compute(., name = paste0(intermediateTable, "_i_4"), temporary = FALSE) 7. ├─omopgenerics:::compute.cdm_table(...) 8. │ ├─dplyr::compute(...) 9. │ └─CDMConnector:::compute.db_cdm(...) 10. │ └─CDMConnector:::.computeQuery(...) 11. │ └─dbplyr::sql_render(x) 12. │ ├─dbplyr::sql_render(...) 13. │ └─dbplyr:::sql_render.tbl_lazy(...) 14. │ ├─dbplyr::sql_render(...) 15. │ └─dbplyr:::sql_render.lazy_query(...) 16. │ ├─dbplyr::sql_build(query, con = con, sql_options = sql_options) 17. │ └─dbplyr:::sql_build.lazy_select_query(query, con = con, sql_options = sql_options) 18. │ ├─dbplyr::sql_build(op$x, con, sql_options = sql_options) 19. │ └─dbplyr:::sql_build.lazy_select_query(op$x, con, sql_options = sql_options) 20. │ └─dbplyr:::get_select_sql(...) 21. │ └─dbplyr:::translate_select_sql(con, select) 22. │ └─dbplyr::translate_sql_(...) 23. │ └─base::lapply(...) 24. │ └─dbplyr (local) FUN(X[[i]], ...) 25. │ ├─dbplyr::escape(eval_tidy(x, mask), con = con) 26. │ └─rlang::eval_tidy(x, mask) 27. └─CDMConnector::dateadd 28. └─cli::cli_abort(...) 29. └─rlang::abort(...) ── Error ('test-plotting.R:167:3'): plot options ─────────────────────────────── Error in `CDMConnector::dateadd()`: No known SQL translation Backtrace: ▆ 1. ├─IncidencePrevalence::generateDenominatorCohortSet(...) at test-plotting.R:167:3 2. │ └─IncidencePrevalence:::fetchDenominatorCohortSet(...) 3. │ └─IncidencePrevalence:::fetchSingleTargetDenominatorCohortSet(...) 4. │ └─IncidencePrevalence:::getDenominatorCohorts(...) 5. │ └─studyPopDb %>% ... 6. ├─dplyr::compute(., name = paste0(intermediateTable, "_i_4"), temporary = FALSE) 7. ├─omopgenerics:::compute.cdm_table(...) 8. │ ├─dplyr::compute(...) 9. │ └─CDMConnector:::compute.db_cdm(...) 10. │ └─CDMConnector:::.computeQuery(...) 11. │ └─dbplyr::sql_render(x) 12. │ ├─dbplyr::sql_render(...) 13. │ └─dbplyr:::sql_render.tbl_lazy(...) 14. │ ├─dbplyr::sql_render(...) 15. │ └─dbplyr:::sql_render.lazy_query(...) 16. │ ├─dbplyr::sql_build(query, con = con, sql_options = sql_options) 17. │ └─dbplyr:::sql_build.lazy_select_query(query, con = con, sql_options = sql_options) 18. │ ├─dbplyr::sql_build(op$x, con, sql_options = sql_options) 19. │ └─dbplyr:::sql_build.lazy_select_query(op$x, con, sql_options = sql_options) 20. │ └─dbplyr:::get_select_sql(...) 21. │ └─dbplyr:::translate_select_sql(con, select) 22. │ └─dbplyr::translate_sql_(...) 23. │ └─base::lapply(...) 24. │ └─dbplyr (local) FUN(X[[i]], ...) 25. │ ├─dbplyr::escape(eval_tidy(x, mask), con = con) 26. │ └─rlang::eval_tidy(x, mask) 27. └─CDMConnector::dateadd 28. └─cli::cli_abort(...) 29. └─rlang::abort(...) [ FAIL 20 | WARN 0 | SKIP 71 | PASS 126 ] Error: Test failures Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [54s] ERROR Error(s) in re-building vignettes: --- re-building 'a01_Introduction_to_IncidencePrevalence.Rmd' using rmarkdown Quitting from lines 73-81 [unnamed-chunk-6] (a01_Introduction_to_IncidencePrevalence.Rmd) Error: processing vignette 'a01_Introduction_to_IncidencePrevalence.Rmd' failed with diagnostics: No known SQL translation --- failed re-building 'a01_Introduction_to_IncidencePrevalence.Rmd' --- re-building 'a02_Creating_denominator_populations.Rmd' using rmarkdown Quitting from lines 98-110 [unnamed-chunk-8] (a02_Creating_denominator_populations.Rmd) Error: processing vignette 'a02_Creating_denominator_populations.Rmd' failed with diagnostics: No known SQL translation --- failed re-building 'a02_Creating_denominator_populations.Rmd' --- re-building 'a03_Creating_target_denominator_populations.Rmd' using rmarkdown Warning: Connection is garbage-collected, use dbDisconnect() to avoid this. Warning: Connection is garbage-collected, use dbDisconnect() to avoid this. Quitting from lines 91-96 [unnamed-chunk-3] (a03_Creating_target_denominator_populations.Rmd) Error: processing vignette 'a03_Creating_target_denominator_populations.Rmd' failed with diagnostics: No known SQL translation --- failed re-building 'a03_Creating_target_denominator_populations.Rmd' --- re-building 'a04_Calculating_prevalence.Rmd' using rmarkdown Quitting from lines 53-72 [setup] (a04_Calculating_prevalence.Rmd) Error: processing vignette 'a04_Calculating_prevalence.Rmd' failed with diagnostics: No known SQL translation --- failed re-building 'a04_Calculating_prevalence.Rmd' --- re-building 'a05_Calculating_incidence.Rmd' using rmarkdown 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. Warning: Database is garbage-collected, use dbDisconnect(con, shutdown=TRUE) or duckdb::duckdb_shutdown(drv) to avoid this. Quitting from lines 79-98 [setup] (a05_Calculating_incidence.Rmd) Error: processing vignette 'a05_Calculating_incidence.Rmd' failed with diagnostics: No known SQL translation --- failed re-building 'a05_Calculating_incidence.Rmd' --- re-building 'a06_Plotting_options.Rmd' using rmarkdown Quitting from lines 37-54 [setup] (a06_Plotting_options.Rmd) Error: processing vignette 'a06_Plotting_options.Rmd' failed with diagnostics: No known SQL translation --- failed re-building 'a06_Plotting_options.Rmd' SUMMARY: processing the following files failed: 'a01_Introduction_to_IncidencePrevalence.Rmd' 'a02_Creating_denominator_populations.Rmd' 'a03_Creating_target_denominator_populations.Rmd' 'a04_Calculating_prevalence.Rmd' 'a05_Calculating_incidence.Rmd' 'a06_Plotting_options.Rmd' Error: Vignette re-building failed. Execution halted 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. 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. 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. Warning: Database is garbage-collected, use dbDisconnect(con, shutdown=TRUE) or duckdb::duckdb_shutdown(drv) to avoid this. * checking PDF version of manual ... [21s] OK * checking HTML version of manual ... OK * DONE Status: 2 ERRORs, 1 NOTE