Package check result: OK Changes to worse in reverse depends: Package: CohortCharacteristics Check: dependencies in R code New result: WARNING Missing or unexported object: ‘CDMConnector::cdm_from_con’ Package: CohortCharacteristics Check: examples New result: ERROR Running examples in ‘CohortCharacteristics-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: availablePlotColumns > ### Title: Available columns to use in 'facet' and 'colour' arguments in > ### plot functions. > ### Aliases: availablePlotColumns > > ### ** Examples > > { + cdm <- mockCohortCharacteristics() + + result <- summariseCharacteristics(cdm$cohort1) + + availablePlotColumns(result) + + mockDisconnect(cdm) + } Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Execution halted Package: CohortCharacteristics Check: tests New result: ERROR Running ‘spelling.R’ [0s/0s] Running ‘testthat.R’ [108s/58s] 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(CohortCharacteristics) > > test_check("CohortCharacteristics") Starting 2 test processes [ FAIL 12 | WARN 0 | SKIP 17 | PASS 16 ] ══ Skipped tests (17) ══════════════════════════════════════════════════════════ • On CRAN (17): 'test-benchmarkCohortCharacteristics.R:2:3', 'test-plotCharacteristics.R:2:3', 'test-plotCharacteristics.R:136:3', 'test-plotCohortOverlap.R:2:3', 'test-plotCohortTiming.R:2:3', 'test-plotCohortTiming.R:94:3', 'test-summariseCharacteristics.R:1159:3', 'test-summariseCharacteristics.R:1389:3', 'test-summariseCharacteristics.R:1505:3', 'test-summariseCohortCount.R:2:3', 'test-plotLargeScaleCharacteristics.R:3:3', 'test-summariseLargeScaleCharacteristics.R:2:3', 'test-tableCharacteristics.R:2:3', 'test-tableCharacteristics.R:120:3', 'test-tableCohortOverlap.R:2:3', 'test-tableCohortTiming.R:2:3', 'test-tableLargeScaleCharacteristics.R:2:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-plotCohortAttrition.R:2:3'): plot cohort attrition ───────────── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles (local) mockCohortCharacteristics(numberIndividuals = 1000) at test-plotCohortAttrition.R:2:3 ── Error ('test-summariseCharacteristics.R:55:3'): test summariseCharacteristics ── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles (local) mockCohortCharacteristics(...) at test-summariseCharacteristics.R:55:3 ── Error ('test-summariseCharacteristics.R:407:3'): test empty cohort ────────── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles (local) mockCohortCharacteristics(...) at test-summariseCharacteristics.R:407:3 ── Error ('test-summariseCharacteristics.R:517:3'): test cohort id ───────────── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles (local) mockCohortCharacteristics(...) at test-summariseCharacteristics.R:517:3 ── Error ('test-summariseCharacteristics.R:654:3'): arguments tableIntersect ─── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles (local) mockCohortCharacteristics(...) at test-summariseCharacteristics.R:654:3 ── Error ('test-summariseCharacteristics.R:987:3'): arguments cohortIntersect ── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles (local) mockCohortCharacteristics(...) at test-summariseCharacteristics.R:987:3 ── Error ('test-summariseCharacteristics.R:1360:3'): empty input cohort contains name issue #170 ── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles (local) mockCohortCharacteristics(...) at test-summariseCharacteristics.R:1360:3 ── Error ('test-summariseCharacteristics.R:1452:3'): arrange ageGroup ────────── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles (local) mockCohortCharacteristics(...) at test-summariseCharacteristics.R:1452:3 ── Error ('test-summariseCohortAttrition.R:2:3'): check summariseCohortAttrition is deterministic ── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles (local) mockCohortCharacteristics(numberIndividuals = 1000) at test-summariseCohortAttrition.R:2:3 ── Error ('test-summariseCohortOverlap.R:41:3'): summariseCohortOverlap ──────── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles (local) mockCohortCharacteristics(...) at test-summariseCohortOverlap.R:41:3 ── Error ('test-summariseCohortOverlap.R:246:3'): test countBy ───────────────── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles (local) mockCohortCharacteristics(...) at test-summariseCohortOverlap.R:246:3 ── Error ('test-summariseCohortTiming.R:35:3'): summariseCohortTiming ────────── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles (local) mockCohortCharacteristics(...) at test-summariseCohortTiming.R:35:3 [ FAIL 12 | WARN 0 | SKIP 17 | PASS 16 ] Error: Test failures Execution halted Package: CohortSymmetry Check: dependencies in R code New result: WARNING Missing or unexported object: ‘CDMConnector::copy_cdm_to’ Package: CohortSymmetry Check: tests New result: ERROR Running ‘testthat.R’ [16s/16s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview > # * https://testthat.r-lib.org/articles/special-files.html > > library(testthat) > library(CohortSymmetry) > > test_check("CohortSymmetry") [ FAIL 10 | WARN 0 | SKIP 55 | PASS 0 ] ══ Skipped tests (55) ══════════════════════════════════════════════════════════ • On CRAN (55): 'test-attrition.R:2:3', 'test-attrition.R:63:3', 'test-attrition.R:149:3', 'test-attrition.R:310:3', 'test-attrition.R:397:3', 'test-attrition.R:461:3', 'test-attrition.R:592:3', 'test-attrition.R:769:3', 'test-dbs.R:2:3', 'test-dbs.R:50:3', 'test-eunomia.R:2:3', 'test-eunomia.R:65:3', 'test-generateSequenceCohortSet.R:3:3', 'test-generateSequenceCohortSet.R:20:3', 'test-generateSequenceCohortSet.R:58:3', 'test-generateSequenceCohortSet.R:97:3', 'test-generateSequenceCohortSet.R:154:3', 'test-generateSequenceCohortSet.R:206:3', 'test-generateSequenceCohortSet.R:260:3', 'test-generateSequenceCohortSet.R:289:3', 'test-generateSequenceCohortSet.R:331:3', 'test-generateSequenceCohortSet.R:357:3', 'test-generateSequenceCohortSet.R:428:3', 'test-generateSequenceCohortSet.R:516:3', 'test-generateSequenceCohortSet.R:664:3', 'test-generateSequenceCohortSet.R:752:3', 'test-generateSequenceCohortSet.R:765:3', 'test-generateSequenceCohortSet.R:777:3', 'test-generateSequenceCohortSet.R:789:3', 'test-generateSequenceCohortSet.R:801:3', 'test-generateSequenceCohortSet.R:819:3', 'test-generateSequenceCohortSet.R:837:3', 'test-generateSequenceCohortSet.R:849:3', 'test-generateSequenceCohortSet.R:860:3', 'test-generateSequenceCohortSet.R:871:3', 'test-generateSequenceCohortSet.R:895:3', 'test-plotSequenceRatio.R:41:3', 'test-plotSequenceRatio.R:79:3', 'test-plotTemporalSymmetry.R:42:3', 'test-plotTemporalSymmetry.R:85:3', 'test-summariseSequenceRatios.R:203:3', 'test-summariseSequenceRatios.R:415:3', 'test-summariseSequenceRatios.R:522:3', 'test-summariseSequenceRatios.R:604:3', 'test-summariseSequenceRatios.R:763:3', 'test-summariseSequenceRatios.R:801:3', 'test-summariseSequenceRatios.R:839:3', 'test-summariseSequenceRatios.R:877:3', 'test-summariseSequenceRatios.R:960:3', 'test-summariseTemporalSymmetry.R:71:3', 'test-summariseTemporalSymmetry.R:96:3', 'test-tableSequenceRatios.R:46:3', 'test-tableSequenceRatios.R:70:3', 'test-tableTemporalSymmetry.R:46:3', 'test-tableTemporalSymmetry.R:70:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-generateSequenceCohortSet.R:36:3'): one ID against one ID, example 1 ── Error: 'copy_cdm_to' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─CohortSymmetry::mockCohortSymmetry() at test-generateSequenceCohortSet.R:36:3 ── Error ('test-generateSequenceCohortSet.R:78:3'): one ID against one ID, example 3 ── Error: 'copy_cdm_to' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─CohortSymmetry::mockCohortSymmetry() at test-generateSequenceCohortSet.R:78:3 ── Error ('test-plotSequenceRatio.R:18:3'): plot working ─────────────────────── Error: 'copy_cdm_to' is not an exported object from 'namespace:CDMConnector' ── Error ('test-plotTemporalSymmetry.R:18:3'): plot working ──────────────────── Error: 'copy_cdm_to' is not an exported object from 'namespace:CDMConnector' ── Error ('test-summariseSequenceRatios.R:32:3'): summariseSequenceRatios ────── Error: 'copy_cdm_to' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─CohortSymmetry::mockCohortSymmetry(...) at test-summariseSequenceRatios.R:32:3 ── Error ('test-summariseSequenceRatios.R:97:3'): summariseSequenceRatios - testing ratios and CIs, Example 1 ── Error: 'copy_cdm_to' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─CohortSymmetry::mockCohortSymmetry(...) at test-summariseSequenceRatios.R:97:3 ── Error ('test-summariseSequenceRatios.R:164:3'): summariseSequenceRatios - testing ratios and CIs, Example 2 ── Error: 'copy_cdm_to' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─CohortSymmetry::mockCohortSymmetry(...) at test-summariseSequenceRatios.R:164:3 ── Error ('test-summariseTemporalSymmetry.R:2:3'): test summariseTemporalSymmetry ── Error: 'copy_cdm_to' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─CohortSymmetry::mockCohortSymmetry() at test-summariseTemporalSymmetry.R:2:3 ── Error ('test-tableSequenceRatios.R:4:3'): tableSequenceRatios - gt output ─── Error: 'copy_cdm_to' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─CohortSymmetry::mockCohortSymmetry() at test-tableSequenceRatios.R:4:3 ── Error ('test-tableTemporalSymmetry.R:4:3'): tableTemporalSymmetry - gt output ── Error: 'copy_cdm_to' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─CohortSymmetry::mockCohortSymmetry() at test-tableTemporalSymmetry.R:4:3 [ FAIL 10 | WARN 0 | SKIP 55 | PASS 0 ] Error: Test failures Execution halted Package: IncidencePrevalence Check: re-building of vignette outputs New result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘a01_Introduction_to_IncidencePrevalence.Rmd’ using rmarkdown ** Processing: /home/hornik/tmp/CRAN_recheck/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a01_Introduction_to_IncidencePrevalence_files/figure-html/unnamed-chunk-10-1.png 672x480 pixels, 3x8 bits/pixel, RGB Input IDAT size = 30607 bytes Input file size = 30721 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 25704 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 25704 Output IDAT size = 25704 bytes (4903 bytes decrease) Output file size = 25782 bytes (4939 bytes = 16.08% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a01_Introduction_to_IncidencePrevalence_files/figure-html/unnamed-chunk-12-1.png 672x480 pixels, 3x8 bits/pixel, RGB Input IDAT size = 27054 bytes Input file size = 27168 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 22632 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 22632 Output IDAT size = 22632 bytes (4422 bytes decrease) Output file size = 22710 bytes (4458 bytes = 16.41% decrease) --- finished re-building ‘a01_Introduction_to_IncidencePrevalence.Rmd’ --- re-building ‘a02_Creating_denominator_populations.Rmd’ using rmarkdown ** Processing: /home/hornik/tmp/CRAN_recheck/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a02_Creating_denominator_populations_files/figure-html/unnamed-chunk-9-1.png 672x480 pixels, 8 bits/pixel, 236 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 6463 bytes Input file size = 7261 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 5226 zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 5190 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 5190 Output IDAT size = 5190 bytes (1273 bytes decrease) Output file size = 5268 bytes (1993 bytes = 27.45% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a02_Creating_denominator_populations_files/figure-html/unnamed-chunk-10-1.png 672x480 pixels, 8 bits/pixel, 255 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 6802 bytes Input file size = 7657 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 5541 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 5541 Output IDAT size = 5541 bytes (1261 bytes decrease) Output file size = 5619 bytes (2038 bytes = 26.62% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a02_Creating_denominator_populations_files/figure-html/unnamed-chunk-11-1.png 672x480 pixels, 8 bits/pixel, 254 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 6892 bytes Input file size = 7744 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 5599 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 5599 Output IDAT size = 5599 bytes (1293 bytes decrease) Output file size = 5677 bytes (2067 bytes = 26.69% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a02_Creating_denominator_populations_files/figure-html/unnamed-chunk-13-1.png 672x480 pixels, 8 bits/pixel, 255 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 7218 bytes Input file size = 8073 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 5890 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 5890 Output IDAT size = 5890 bytes (1328 bytes decrease) Output file size = 5968 bytes (2105 bytes = 26.07% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a02_Creating_denominator_populations_files/figure-html/unnamed-chunk-14-1.png 672x480 pixels, 8 bits/pixel, 255 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 6563 bytes Input file size = 7418 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 5333 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 5333 Output IDAT size = 5333 bytes (1230 bytes decrease) Output file size = 5411 bytes (2007 bytes = 27.06% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a02_Creating_denominator_populations_files/figure-html/unnamed-chunk-17-1.png 672x480 pixels, 3x8 bits/pixel, RGB Input IDAT size = 35692 bytes Input file size = 35818 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 27947 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 27947 Output IDAT size = 27947 bytes (7745 bytes decrease) Output file size = 28025 bytes (7793 bytes = 21.76% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a02_Creating_denominator_populations_files/figure-html/unnamed-chunk-18-1.png 672x768 pixels, 3x8 bits/pixel, RGB Input IDAT size = 47934 bytes Input file size = 48072 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 37761 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 37761 Output IDAT size = 37761 bytes (10173 bytes decrease) Output file size = 37839 bytes (10233 bytes = 21.29% decrease) Quitting from lines 310-343 [unnamed-chunk-19] (a02_Creating_denominator_populations.Rmd) Error: processing vignette 'a02_Creating_denominator_populations.Rmd' failed with diagnostics: could not find function "cohortSet" --- failed re-building ‘a02_Creating_denominator_populations.Rmd’ --- re-building ‘a03_Creating_target_denominator_populations.Rmd’ using rmarkdown ** Processing: /home/hornik/tmp/CRAN_recheck/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a03_Creating_target_denominator_populations_files/figure-html/unnamed-chunk-4-1.png 288x288 pixels, 8 bits/pixel, 244 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 3203 bytes Input file size = 4025 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 2769 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 2769 Output IDAT size = 2769 bytes (434 bytes decrease) Output file size = 2847 bytes (1178 bytes = 29.27% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a03_Creating_target_denominator_populations_files/figure-html/unnamed-chunk-6-1.png 288x288 pixels, 8 bits/pixel, 239 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 3471 bytes Input file size = 4278 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 3027 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 3027 Output IDAT size = 3027 bytes (444 bytes decrease) Output file size = 3105 bytes (1173 bytes = 27.42% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a03_Creating_target_denominator_populations_files/figure-html/unnamed-chunk-7-1.png 288x288 pixels, 8 bits/pixel, 246 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 3037 bytes Input file size = 3865 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 2562 zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 2555 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 2555 Output IDAT size = 2555 bytes (482 bytes decrease) Output file size = 2633 bytes (1232 bytes = 31.88% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a03_Creating_target_denominator_populations_files/figure-html/unnamed-chunk-8-1.png 288x288 pixels, 8 bits/pixel, 241 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 2905 bytes Input file size = 3718 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 2522 zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 2508 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 2508 Output IDAT size = 2508 bytes (397 bytes decrease) Output file size = 2586 bytes (1132 bytes = 30.45% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a03_Creating_target_denominator_populations_files/figure-html/unnamed-chunk-9-1.png 288x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 9424 bytes Input file size = 9514 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7321 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7321 Output IDAT size = 7321 bytes (2103 bytes decrease) Output file size = 7399 bytes (2115 bytes = 22.23% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a03_Creating_target_denominator_populations_files/figure-html/unnamed-chunk-10-1.png 288x288 pixels, 8 bits/pixel, 241 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 2905 bytes Input file size = 3718 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 2522 zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 2508 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 2508 Output IDAT size = 2508 bytes (397 bytes decrease) Output file size = 2586 bytes (1132 bytes = 30.45% decrease) --- finished re-building ‘a03_Creating_target_denominator_populations.Rmd’ --- re-building ‘a04_Calculating_prevalence.Rmd’ using rmarkdown ** Processing: /home/hornik/tmp/CRAN_recheck/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a04_Calculating_prevalence_files/figure-html/unnamed-chunk-6-1.png 672x480 pixels, 8 bits/pixel, 252 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 8017 bytes Input file size = 8863 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 6653 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 6653 Output IDAT size = 6653 bytes (1364 bytes decrease) Output file size = 6731 bytes (2132 bytes = 24.06% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a04_Calculating_prevalence_files/figure-html/unnamed-chunk-7-1.png 672x480 pixels, 8 bits/pixel, 255 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 12214 bytes Input file size = 13081 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 10834 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 10834 Output IDAT size = 10834 bytes (1380 bytes decrease) Output file size = 10912 bytes (2169 bytes = 16.58% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a04_Calculating_prevalence_files/figure-html/unnamed-chunk-8-1.png 672x480 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 20129 bytes Input file size = 21011 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 18673 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 18673 Output IDAT size = 18673 bytes (1456 bytes decrease) Output file size = 18751 bytes (2260 bytes = 10.76% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a04_Calculating_prevalence_files/figure-html/unnamed-chunk-9-1.png 672x480 pixels, 8 bits/pixel, 249 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 9524 bytes Input file size = 10373 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 8197 zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 8187 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 8187 Output IDAT size = 8187 bytes (1337 bytes decrease) Output file size = 8265 bytes (2108 bytes = 20.32% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a04_Calculating_prevalence_files/figure-html/unnamed-chunk-10-1.png 672x480 pixels, 8 bits/pixel, 250 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 8506 bytes Input file size = 9358 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7117 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7117 Output IDAT size = 7117 bytes (1389 bytes decrease) Output file size = 7195 bytes (2163 bytes = 23.11% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a04_Calculating_prevalence_files/figure-html/unnamed-chunk-11-1.png 672x480 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 20622 bytes Input file size = 21504 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 19177 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 19177 Output IDAT size = 19177 bytes (1445 bytes decrease) Output file size = 19255 bytes (2249 bytes = 10.46% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a04_Calculating_prevalence_files/figure-html/unnamed-chunk-12-1.png 672x480 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 20622 bytes Input file size = 21504 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 19177 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 19177 Output IDAT size = 19177 bytes (1445 bytes decrease) Output file size = 19255 bytes (2249 bytes = 10.46% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a04_Calculating_prevalence_files/figure-html/unnamed-chunk-13-1.png 672x480 pixels, 3x8 bits/pixel, RGB Input IDAT size = 36323 bytes Input file size = 36449 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 29112 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 29112 Output IDAT size = 29112 bytes (7211 bytes decrease) Output file size = 29190 bytes (7259 bytes = 19.92% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a04_Calculating_prevalence_files/figure-html/unnamed-chunk-14-1.png 672x480 pixels, 3x8 bits/pixel, RGB Input IDAT size = 19183 bytes Input file size = 19285 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 16497 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 16497 Output IDAT size = 16497 bytes (2686 bytes decrease) Output file size = 16575 bytes (2710 bytes = 14.05% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a04_Calculating_prevalence_files/figure-html/unnamed-chunk-15-1.png 672x480 pixels, 3x8 bits/pixel, RGB Input IDAT size = 35761 bytes Input file size = 35887 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 29396 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 29396 Output IDAT size = 29396 bytes (6365 bytes decrease) Output file size = 29474 bytes (6413 bytes = 17.87% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a04_Calculating_prevalence_files/figure-html/unnamed-chunk-16-1.png 672x480 pixels, 3x8 bits/pixel, RGB Input IDAT size = 61569 bytes Input file size = 61731 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 46989 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 46989 Output IDAT size = 46989 bytes (14580 bytes decrease) Output file size = 47067 bytes (14664 bytes = 23.75% decrease) --- finished re-building ‘a04_Calculating_prevalence.Rmd’ --- re-building ‘a05_Calculating_incidence.Rmd’ using rmarkdown ** Processing: /home/hornik/tmp/CRAN_recheck/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a05_Calculating_incidence_files/figure-html/unnamed-chunk-7-1.png 672x480 pixels, 8 bits/pixel, 254 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 9347 bytes Input file size = 10211 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7912 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7912 Output IDAT size = 7912 bytes (1435 bytes decrease) Output file size = 7990 bytes (2221 bytes = 21.75% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a05_Calculating_incidence_files/figure-html/unnamed-chunk-8-1.png 672x480 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 15831 bytes Input file size = 16701 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 14582 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 14582 Output IDAT size = 14582 bytes (1249 bytes decrease) Output file size = 14660 bytes (2041 bytes = 12.22% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a05_Calculating_incidence_files/figure-html/unnamed-chunk-9-1.png 672x480 pixels, 8 bits/pixel, 253 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 9250 bytes Input file size = 10111 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7790 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7790 Output IDAT size = 7790 bytes (1460 bytes decrease) Output file size = 7868 bytes (2243 bytes = 22.18% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a05_Calculating_incidence_files/figure-html/unnamed-chunk-10-1.png 672x480 pixels, 8 bits/pixel, 252 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 9344 bytes Input file size = 10202 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7912 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7912 Output IDAT size = 7912 bytes (1432 bytes decrease) Output file size = 7990 bytes (2212 bytes = 21.68% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a05_Calculating_incidence_files/figure-html/unnamed-chunk-11-1.png 672x480 pixels, 8 bits/pixel, 252 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 9255 bytes Input file size = 10113 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7799 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7799 Output IDAT size = 7799 bytes (1456 bytes decrease) Output file size = 7877 bytes (2236 bytes = 22.11% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a05_Calculating_incidence_files/figure-html/unnamed-chunk-12-1.png 672x480 pixels, 3x8 bits/pixel, RGB Input IDAT size = 31000 bytes Input file size = 31114 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 24937 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 24937 Output IDAT size = 24937 bytes (6063 bytes decrease) Output file size = 25015 bytes (6099 bytes = 19.60% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a05_Calculating_incidence_files/figure-html/unnamed-chunk-13-1.png 672x480 pixels, 3x8 bits/pixel, RGB Input IDAT size = 21806 bytes Input file size = 21908 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 18643 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 18643 Output IDAT size = 18643 bytes (3163 bytes decrease) Output file size = 18721 bytes (3187 bytes = 14.55% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a05_Calculating_incidence_files/figure-html/unnamed-chunk-14-1.png 672x480 pixels, 3x8 bits/pixel, RGB Input IDAT size = 35022 bytes Input file size = 35148 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 28425 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 28425 Output IDAT size = 28425 bytes (6597 bytes decrease) Output file size = 28503 bytes (6645 bytes = 18.91% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a05_Calculating_incidence_files/figure-html/unnamed-chunk-14-2.png 672x480 pixels, 3x8 bits/pixel, RGB Input IDAT size = 70303 bytes Input file size = 70477 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 53814 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 53814 Output IDAT size = 53814 bytes (16489 bytes decrease) Output file size = 53892 bytes (16585 bytes = 23.53% decrease) --- finished re-building ‘a05_Calculating_incidence.Rmd’ --- re-building ‘a06_benchmark.Rmd’ using rmarkdown --- finished re-building ‘a06_benchmark.Rmd’ SUMMARY: processing the following file failed: ‘a02_Creating_denominator_populations.Rmd’ Error: Vignette re-building failed. Execution halted Package: OmopSketch Check: re-building of vignette outputs New result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘A-summarise_clinical_tables_records.Rmd’ using rmarkdown ** Processing: /home/hornik/tmp/CRAN_recheck/OmopSketch.Rcheck/vign_test/OmopSketch/vignettes/A-summarise_clinical_tables_records_files/figure-html/unnamed-chunk-9-1.png 1344x960 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 51104 bytes Input file size = 52034 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 44102 zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 43704 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 43704 Output IDAT size = 43704 bytes (7400 bytes decrease) Output file size = 43782 bytes (8252 bytes = 15.86% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/OmopSketch.Rcheck/vign_test/OmopSketch/vignettes/A-summarise_clinical_tables_records_files/figure-html/unnamed-chunk-10-1.png 1344x960 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 72522 bytes Input file size = 73476 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 66292 zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 65648 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 IDAT size = 64521 zc = 9 zm = 8 zs = 1 f = 5 IDAT size = 63903 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 1 f = 5 IDAT size = 63903 Output IDAT size = 63903 bytes (8619 bytes decrease) Output file size = 63981 bytes (9495 bytes = 12.92% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/OmopSketch.Rcheck/vign_test/OmopSketch/vignettes/A-summarise_clinical_tables_records_files/figure-html/unnamed-chunk-11-1.png 1344x960 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 61595 bytes Input file size = 62537 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 55336 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 55336 Output IDAT size = 55336 bytes (6259 bytes decrease) Output file size = 55414 bytes (7123 bytes = 11.39% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/OmopSketch.Rcheck/vign_test/OmopSketch/vignettes/A-summarise_clinical_tables_records_files/figure-html/unnamed-chunk-13-1.png 1344x960 pixels, 3x8 bits/pixel, RGB Input IDAT size = 248215 bytes Input file size = 248653 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 203945 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 203945 Output IDAT size = 203945 bytes (44270 bytes decrease) Output file size = 204023 bytes (44630 bytes = 17.95% decrease) --- finished re-building ‘A-summarise_clinical_tables_records.Rmd’ --- re-building ‘B-summarise_concept_set_counts.Rmd’ using rmarkdown Quitting from lines 17-26 [unnamed-chunk-1] (B-summarise_concept_set_counts.Rmd) Error: processing vignette 'B-summarise_concept_set_counts.Rmd' failed with diagnostics: could not find function "eunomia_is_available" --- failed re-building ‘B-summarise_concept_set_counts.Rmd’ --- re-building ‘C-summarise_observation_period.Rmd’ using rmarkdown ** Processing: /home/hornik/tmp/CRAN_recheck/OmopSketch.Rcheck/vign_test/OmopSketch/vignettes/C-summarise_observation_period_files/figure-html/unnamed-chunk-7-1.png 1344x960 pixels, 8 bits/pixel, 255 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 15522 bytes Input file size = 16389 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 11819 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 IDAT size = 10600 zc = 9 zm = 8 zs = 1 f = 5 IDAT size = 10555 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 1 f = 5 IDAT size = 10555 Output IDAT size = 10555 bytes (4967 bytes decrease) Output file size = 10633 bytes (5756 bytes = 35.12% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/OmopSketch.Rcheck/vign_test/OmopSketch/vignettes/C-summarise_observation_period_files/figure-html/unnamed-chunk-8-1.png 1344x960 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 20076 bytes Input file size = 20958 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 15025 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 IDAT size = 12438 zc = 9 zm = 8 zs = 1 f = 5 IDAT size = 12382 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 1 f = 5 IDAT size = 12382 Output IDAT size = 12382 bytes (7694 bytes decrease) Output file size = 12460 bytes (8498 bytes = 40.55% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/OmopSketch.Rcheck/vign_test/OmopSketch/vignettes/C-summarise_observation_period_files/figure-html/unnamed-chunk-8-2.png 1344x960 pixels, 3x8 bits/pixel, RGB Input IDAT size = 40460 bytes Input file size = 40586 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 IDAT size = 36557 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 5 IDAT size = 36557 Output IDAT size = 36557 bytes (3903 bytes decrease) Output file size = 36635 bytes (3951 bytes = 9.73% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/OmopSketch.Rcheck/vign_test/OmopSketch/vignettes/C-summarise_observation_period_files/figure-html/unnamed-chunk-13-1.png 1344x960 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 42576 bytes Input file size = 43494 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 37744 zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 37463 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 37463 Output IDAT size = 37463 bytes (5113 bytes decrease) Output file size = 37541 bytes (5953 bytes = 13.69% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/OmopSketch.Rcheck/vign_test/OmopSketch/vignettes/C-summarise_observation_period_files/figure-html/unnamed-chunk-14-1.png 1344x960 pixels, 3x8 bits/pixel, RGB Input IDAT size = 169883 bytes Input file size = 170201 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 135709 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 135709 Output IDAT size = 135709 bytes (34174 bytes decrease) Output file size = 135787 bytes (34414 bytes = 20.22% decrease) --- finished re-building ‘C-summarise_observation_period.Rmd’ SUMMARY: processing the following file failed: ‘B-summarise_concept_set_counts.Rmd’ Error: Vignette re-building failed. Execution halted Package: PatientProfiles Check: dependencies in R code New result: WARNING Missing or unexported object: ‘CDMConnector::cdm_from_con’ Package: PatientProfiles Check: re-building of vignette outputs New result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘cohort-intersect.Rmd’ using rmarkdown Quitting from lines 23-38 [unnamed-chunk-1] (cohort-intersect.Rmd) Error: processing vignette 'cohort-intersect.Rmd' failed with diagnostics: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' --- failed re-building ‘cohort-intersect.Rmd’ --- re-building ‘concept-intersect.Rmd’ using rmarkdown Quitting from lines 36-40 [unnamed-chunk-2] (concept-intersect.Rmd) Error: processing vignette 'concept-intersect.Rmd' failed with diagnostics: could not find function "eunomia_is_available" --- failed re-building ‘concept-intersect.Rmd’ --- re-building ‘demographics.rmd’ using rmarkdown Quitting from lines 20-28 [unnamed-chunk-1] (demographics.rmd) Error: processing vignette 'demographics.rmd' failed with diagnostics: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' --- failed re-building ‘demographics.rmd’ --- re-building ‘summarise.Rmd’ using rmarkdown trying URL 'https://example-data.ohdsi.dev/GiBleed.zip' Content type 'application/zip' length 6754786 bytes (6.4 MB) ================================================== downloaded 6.4 MB Quitting from lines 85-138 [unnamed-chunk-4] (summarise.Rmd) Error: processing vignette 'summarise.Rmd' failed with diagnostics: error in evaluating the argument 'dbObj' in selecting a method for function 'dbIsValid': could not find function "eunomia_dir" --- failed re-building ‘summarise.Rmd’ --- re-building ‘table-intersect.Rmd’ using rmarkdown Quitting from lines 35-39 [unnamed-chunk-3] (table-intersect.Rmd) Error: processing vignette 'table-intersect.Rmd' failed with diagnostics: could not find function "eunomia_is_available" --- failed re-building ‘table-intersect.Rmd’ SUMMARY: processing the following files failed: ‘cohort-intersect.Rmd’ ‘concept-intersect.Rmd’ ‘demographics.rmd’ ‘summarise.Rmd’ ‘table-intersect.Rmd’ Error: Vignette re-building failed. Execution halted Package: PatientProfiles Check: tests New result: ERROR Running ‘spelling.R’ [0s/0s] Running ‘testthat.R’ [53s/32s] 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 21 | WARN 0 | SKIP 104 | PASS 27 ] ══ Skipped tests (104) ═════════════════════════════════════════════════════════ • On CRAN (104): 'test-addAttributes.R:2:3', 'test-addCategories.R:2:3', 'test-addCategories.R:69:3', 'test-addCategories.R:106:3', 'test-addCategories.R:155:3', 'test-addConceptIntersect.R:2:3', 'test-addConceptIntersect.R:97:3', 'test-addConceptIntersect.R:138:3', 'test-addConceptIntersect.R:168:3', 'test-addConceptIntersect.R:199:3', 'test-addDeath.R:104:3', 'test-addDeath.R:149:3', 'test-addDeath.R:247:3', 'test-addDeath.R:290:3', 'test-addCohortIntersect.R:277:3', 'test-addCohortIntersect.R:353:3', 'test-addCohortIntersect.R:398:3', 'test-addCohortIntersect.R:509:3', 'test-addCohortIntersect.R:600:3', 'test-addCohortIntersect.R:660:3', 'test-addCohortIntersect.R:734:3', 'test-addCohortIntersect.R:752:3', 'test-addCohortIntersect.R:838:3', 'test-addFutureObservation.R:2:3', 'test-addFutureObservation.R:13:3', 'test-addFutureObservation.R:27:3', 'test-addFutureObservation.R:87:3', 'test-addFutureObservation.R:147:3', 'test-addFutureObservation.R:209:3', 'test-addFutureObservation.R:253:3', 'test-addInObservation.R:2:3', 'test-addInObservation.R:16:3', 'test-addInObservation.R:47:3', 'test-addInObservation.R:170:3', 'test-addIntersect.R:2:3', 'test-addIntersect.R:37:3', 'test-addIntersect.R:226:3', 'test-addIntersect.R:277:3', 'test-addIntersect.R:398:3', 'test-addIntersect.R:502:3', 'test-addIntersect.R:558:3', 'test-addIntersect.R:626:3', 'test-addIntersect.R:775:3', 'test-addIntersect.R:856:3', 'test-addIntersect.R:870:3', 'test-addIntersect.R:940:3', 'test-addIntersect.R:1027:3', 'test-addIntersect.R:1208:3', 'test-addIntersect.R:1219:3', 'test-addObservationPeriodId.R:2:3', 'test-addPriorObservation.R:2:3', 'test-addPriorObservation.R:13:3', 'test-addPriorObservation.R:27:3', 'test-addPriorObservation.R:73:3', 'test-addPriorObservation.R:118:3', 'test-addPriorObservation.R:180:3', 'test-addSex.R:2:3', 'test-addSex.R:13:3', 'test-addSex.R:25:3', 'test-addSex.R:66:3', 'test-addTableIntersect.R:28:3', 'test-addTableIntersect.R:209:3', 'test-addTableIntersect.R:316:3', 'test-addTableIntersect.R:451:3', 'test-addTableIntersect.R:581:3', 'test-checks.R:2:3', 'test-checks.R:106:3', 'test-checks.R:157:3', 'test-checks.R:177:3', 'test-checks.R:189:3', 'test-checks.R:237:3', 'test-checks.R:264:3', 'test-format.R:2:3', 'test-format.R:89:3', 'test-format.R:100:3', 'test-format.R:110:3', 'test-format.R:139:3', 'test-mockPatientProfiles.R:2:3', 'test-name.R:2:3', 'test-addDemographics.R:2:3', 'test-addDemographics.R:24:3', 'test-addDemographics.R:352:3', 'test-addDemographics.R:419:3', 'test-addDemographics.R:685:3', 'test-addDemographics.R:834:3', 'test-addDemographics.R:852:3', 'test-addDemographics.R:964:3', 'test-addDemographics.R:1043:3', 'test-addDemographics.R:1155:3', 'test-addDemographics.R:1220:3', 'test-addDemographics.R:1246:3', 'test-addDemographics.R:1273:3', 'test-addDemographics.R:1289:3', 'test-addDemographics.R:1300:3', 'test-addDemographics.R:1318:3', 'test-addDemographics.R:1346:3', 'test-utilities.R:2:3', 'test-summariseResult.R:205:3', 'test-summariseResult.R:251:3', 'test-summariseResult.R:308:3', 'test-summariseResult.R:352:3', 'test-summariseResult.R:373:3', 'test-summariseResult.R:448:3', 'test-summariseResult.R:534:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-addConceptIntersect.R:243:3'): records out of observation ────── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(con = connection(), writeSchema = writeSchema()) at test-addConceptIntersect.R:243:3 ── Error ('test-addDeath.R:2:3'): addDeathDate ───────────────────────────────── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-addDeath.R:2:3 ── Error ('test-addCohortIntersect.R:6:3'): output format - one outcome cohort ── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-addCohortIntersect.R:6:3 ── Error ('test-addCohortIntersect.R:97:3'): first vs last event - cohort table ── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-addCohortIntersect.R:97:3 ── Error ('test-addCohortIntersect.R:212:3'): multiple cohort entries per person ── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-addCohortIntersect.R:212:3 ── Error ('test-addInObservation.R:60:3'): addInObservation, window ──────────── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-addInObservation.R:60:3 ── Error ('test-addObservationPeriodId.R:193:3'): check when there is the same record in multiple cohorts ── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-addObservationPeriodId.R:193:3 ── Error ('test-addTableIntersect.R:2:3'): basic structures ──────────────────── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(con = connection(), writeSchema = writeSchema()) at test-addTableIntersect.R:2:3 ── Error ('test-addTableIntersect.R:162:3'): addTableIntersectCount example ──── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-addTableIntersect.R:162:3 ── Error ('test-class.R:19:3'): test class consistency across cohort operations ── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-class.R:19:3 ── Error ('test-addDemographics.R:45:3'): addDemographics, cohort and condition_occurrence ── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-addDemographics.R:45:3 ── Error ('test-addDemographics.R:84:3'): addDemographics, parameters ────────── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-addDemographics.R:84:3 ── Error ('test-addDemographics.R:149:3'): partial demographics - cohorts ────── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-addDemographics.R:149:3 ── Error ('test-addDemographics.R:252:3'): partial demographics - omop tables ── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-addDemographics.R:252:3 ── Error ('test-addDemographics.R:324:3'): priorObservation and future_observation - outside of observation period ── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-addDemographics.R:324:3 ── Error ('test-addDemographics.R:540:3'): age at cohort end, no missing, check age computation ── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-addDemographics.R:540:3 ── Error ('test-addDemographics.R:602:3'): age at cohort entry, missing year/month/day of birth ── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-addDemographics.R:602:3 ── Error ('test-addDemographics.R:655:3'): multiple cohortIds, check age at cohort end ── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-addDemographics.R:655:3 ── Error ('test-addDemographics.R:1365:3'): test query functions ─────────────── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(con = connection(), writeSchema = writeSchema()) at test-addDemographics.R:1365:3 ── Error ('test-summariseResult.R:87:3'): groups and strata ──────────────────── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-summariseResult.R:87:3 ── Error ('test-summariseResult.R:166:3'): table in db or local ──────────────── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─PatientProfiles::mockPatientProfiles(...) at test-summariseResult.R:166:3 [ FAIL 21 | WARN 0 | SKIP 104 | PASS 27 ] Error: Test failures Execution halted Package: PhenotypeR Check: re-building of vignette outputs New result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘a01_DatabaseDiagnostics.Rmd’ using rmarkdown Quitting from lines 19-29 [unnamed-chunk-2] (a01_DatabaseDiagnostics.Rmd) Error: processing vignette 'a01_DatabaseDiagnostics.Rmd' failed with diagnostics: could not find function "eunomia_is_available" --- failed re-building ‘a01_DatabaseDiagnostics.Rmd’ --- re-building ‘a02_CodelistDiagnostics.Rmd’ using rmarkdown Quitting from lines 12-22 [unnamed-chunk-1] (a02_CodelistDiagnostics.Rmd) Error: processing vignette 'a02_CodelistDiagnostics.Rmd' failed with diagnostics: could not find function "eunomia_is_available" --- failed re-building ‘a02_CodelistDiagnostics.Rmd’ --- re-building ‘a03_CohortDiagnostics.Rmd’ using rmarkdown Quitting from lines 18-28 [unnamed-chunk-2] (a03_CohortDiagnostics.Rmd) Error: processing vignette 'a03_CohortDiagnostics.Rmd' failed with diagnostics: could not find function "eunomia_is_available" --- failed re-building ‘a03_CohortDiagnostics.Rmd’ --- re-building ‘a04_MatchedDiagnostics.Rmd’ using rmarkdown Quitting from lines 18-28 [unnamed-chunk-2] (a04_MatchedDiagnostics.Rmd) Error: processing vignette 'a04_MatchedDiagnostics.Rmd' failed with diagnostics: could not find function "eunomia_is_available" --- failed re-building ‘a04_MatchedDiagnostics.Rmd’ --- re-building ‘a05_PopulationDiagnostics.Rmd’ using rmarkdown Quitting from lines 11-21 [unnamed-chunk-1] (a05_PopulationDiagnostics.Rmd) Error: processing vignette 'a05_PopulationDiagnostics.Rmd' failed with diagnostics: could not find function "eunomia_is_available" --- failed re-building ‘a05_PopulationDiagnostics.Rmd’ SUMMARY: processing the following files failed: ‘a01_DatabaseDiagnostics.Rmd’ ‘a02_CodelistDiagnostics.Rmd’ ‘a03_CohortDiagnostics.Rmd’ ‘a04_MatchedDiagnostics.Rmd’ ‘a05_PopulationDiagnostics.Rmd’ Error: Vignette re-building failed. Execution halted Package: TestGenerator Check: whether package can be installed New result: ERROR Installation failed. Package: TreatmentPatterns Check: tests New result: ERROR Running ‘testthat.R’ [40s/27s] 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(TreatmentPatterns) > > test_check("TreatmentPatterns") Starting 2 test processes [ FAIL 49 | WARN 0 | SKIP 27 | PASS 89 ] ══ Skipped tests (27) ══════════════════════════════════════════════════════════ • Eunomia [2.0.0] bug (8): 'test-CDMInterfaceDBC.R:6:3', 'test-CDMInterfaceDBC.R:24:3', 'test-CDMInterfaceDBC.R:53:3', 'test-CDMInterfaceDBC.R:80:3', 'test-CDMInterfaceDBC.R:117:3', 'test-computePathways.R:8:3', 'test-computePathways.R:53:3', 'test-multipleCohortTables.R:68:3' • On CRAN (12): 'test-CDMInterface.R:7:3', 'test-export.R:314:3', 'test-export.R:381:3', 'test-export.R:428:3', 'test-export.R:470:3', 'test-export.R:514:3', 'test-export.R:589:3', 'test-export.R:657:3', 'test-export.R:685:3', 'test-pathwaysLogical.R:225:3', 'test-pathwaysMultipleTargetsLogical.R:19:3', 'test-pathwaysMultipleTargetsLogical.R:216:3' • On Linux (7): 'test-computePathways.R:720:3', 'test-executeTreatmentPatterns.R:10:3', 'test-export.R:30:3', 'test-export.R:99:3', 'test-export.R:149:3', 'test-export.R:193:3', 'test-export.R:237:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-CDMInterfaceCDMC.R:8:3'): (code run outside of `test_that()`) ── Error in `eunomia_dir()`: could not find function "eunomia_dir" Backtrace: ▆ 1. ├─DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir()) at test-CDMInterfaceCDMC.R:8:3 2. └─DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir()) 3. └─duckdb (local) .local(drv, ...) 4. └─duckdb:::path_normalize(dbdir) ── Error ('test-computePathways.R:32:3'): computePathways CDMConnector ───────── Error: 'eunomia_dir' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─TreatmentPatterns:::generateCohortTableCDMC() at test-computePathways.R:32:3 2. ├─DBI::dbConnect(duckdb::duckdb(), dbdir = CDMConnector::eunomia_dir()) at tests/testthat/helper-generateCohortTableCDMC.R:5:5 3. └─DBI::dbConnect(duckdb::duckdb(), dbdir = CDMConnector::eunomia_dir()) 4. └─duckdb (local) .local(drv, ...) 5. └─duckdb:::path_normalize(dbdir) ── Error ('test-computePathways.R:78:3'): includeTreatments ──────────────────── Error: 'eunomia_dir' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─TreatmentPatterns:::generateCohortTableCDMC() at test-computePathways.R:78:3 2. ├─DBI::dbConnect(duckdb::duckdb(), dbdir = CDMConnector::eunomia_dir()) at tests/testthat/helper-generateCohortTableCDMC.R:5:5 3. └─DBI::dbConnect(duckdb::duckdb(), dbdir = CDMConnector::eunomia_dir()) 4. └─duckdb (local) .local(drv, ...) 5. └─duckdb:::path_normalize(dbdir) ── Error ('test-computePathways.R:122:3'): indexDateOffset ───────────────────── Error: 'eunomia_dir' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─TreatmentPatterns:::generateCohortTableCDMC() at test-computePathways.R:122:3 2. ├─DBI::dbConnect(duckdb::duckdb(), dbdir = CDMConnector::eunomia_dir()) at tests/testthat/helper-generateCohortTableCDMC.R:5:5 3. └─DBI::dbConnect(duckdb::duckdb(), dbdir = CDMConnector::eunomia_dir()) 4. └─duckdb (local) .local(drv, ...) 5. └─duckdb:::path_normalize(dbdir) ── Error ('test-computePathways.R:177:3'): minEraDuration ────────────────────── Error: 'eunomia_dir' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─TreatmentPatterns:::generateCohortTableCDMC() at test-computePathways.R:177:3 2. ├─DBI::dbConnect(duckdb::duckdb(), dbdir = CDMConnector::eunomia_dir()) at tests/testthat/helper-generateCohortTableCDMC.R:5:5 3. └─DBI::dbConnect(duckdb::duckdb(), dbdir = CDMConnector::eunomia_dir()) 4. └─duckdb (local) .local(drv, ...) 5. └─duckdb:::path_normalize(dbdir) ── Error ('test-computePathways.R:192:3'): splitEventCohorts ─────────────────── Error: 'eunomia_dir' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─TreatmentPatterns:::generateCohortTableCDMC() at test-computePathways.R:192:3 2. ├─DBI::dbConnect(duckdb::duckdb(), dbdir = CDMConnector::eunomia_dir()) at tests/testthat/helper-generateCohortTableCDMC.R:5:5 3. └─DBI::dbConnect(duckdb::duckdb(), dbdir = CDMConnector::eunomia_dir()) 4. └─duckdb (local) .local(drv, ...) 5. └─duckdb:::path_normalize(dbdir) ── Error ('test-computePathways.R:230:3'): splitTime ─────────────────────────── Error: 'eunomia_dir' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─TreatmentPatterns:::generateCohortTableCDMC() at test-computePathways.R:230:3 2. ├─DBI::dbConnect(duckdb::duckdb(), dbdir = CDMConnector::eunomia_dir()) at tests/testthat/helper-generateCohortTableCDMC.R:5:5 3. └─DBI::dbConnect(duckdb::duckdb(), dbdir = CDMConnector::eunomia_dir()) 4. └─duckdb (local) .local(drv, ...) 5. └─duckdb:::path_normalize(dbdir) ── Error ('test-computePathways.R:245:3'): eraCollapseSize ───────────────────── Error: 'eunomia_dir' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─TreatmentPatterns:::generateCohortTableCDMC() at test-computePathways.R:245:3 2. ├─DBI::dbConnect(duckdb::duckdb(), dbdir = CDMConnector::eunomia_dir()) at tests/testthat/helper-generateCohortTableCDMC.R:5:5 3. └─DBI::dbConnect(duckdb::duckdb(), dbdir = CDMConnector::eunomia_dir()) 4. └─duckdb (local) .local(drv, ...) 5. └─duckdb:::path_normalize(dbdir) ── Error ('test-computePathways.R:277:3'): combinationWindow ─────────────────── Error: 'eunomia_dir' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─TreatmentPatterns:::generateCohortTableCDMC() at test-computePathways.R:277:3 2. ├─DBI::dbConnect(duckdb::duckdb(), dbdir = CDMConnector::eunomia_dir()) at tests/testthat/helper-generateCohortTableCDMC.R:5:5 3. └─DBI::dbConnect(duckdb::duckdb(), dbdir = CDMConnector::eunomia_dir()) 4. └─duckdb (local) .local(drv, ...) 5. └─duckdb:::path_normalize(dbdir) ── Error ('test-computePathways.R:294:3'): minPostCombinationDuration: 30 ────── Error in `eunomia_dir()`: could not find function "eunomia_dir" Backtrace: ▆ 1. ├─DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir()) at test-computePathways.R:294:3 2. └─DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir()) 3. └─duckdb (local) .local(drv, ...) 4. └─duckdb:::path_normalize(dbdir) ── Error ('test-computePathways.R:403:3'): filterTreatments ──────────────────── Error: 'eunomia_dir' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─TreatmentPatterns:::generateCohortTableCDMC() at test-computePathways.R:403:3 2. ├─DBI::dbConnect(duckdb::duckdb(), dbdir = CDMConnector::eunomia_dir()) at tests/testthat/helper-generateCohortTableCDMC.R:5:5 3. └─DBI::dbConnect(duckdb::duckdb(), dbdir = CDMConnector::eunomia_dir()) 4. └─duckdb (local) .local(drv, ...) 5. └─duckdb:::path_normalize(dbdir) ── Error ('test-computePathways.R:555:3'): FRFS combination ──────────────────── Error in `eunomia_dir()`: could not find function "eunomia_dir" Backtrace: ▆ 1. ├─DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir()) at test-computePathways.R:555:3 2. └─DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir()) 3. └─duckdb (local) .local(drv, ...) 4. └─duckdb:::path_normalize(dbdir) ── Error ('test-computePathways.R:608:3'): LRFS combination ──────────────────── Error in `eunomia_dir()`: could not find function "eunomia_dir" Backtrace: ▆ 1. ├─DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir()) at test-computePathways.R:608:3 2. └─DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir()) 3. └─duckdb (local) .local(drv, ...) 4. └─duckdb:::path_normalize(dbdir) ── Error ('test-computePathways.R:662:3'): No target records ─────────────────── Error: 'eunomia_dir' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. ├─base::suppressWarnings(generateCohortTableCDMC()) at test-computePathways.R:662:3 2. │ └─base::withCallingHandlers(...) 3. └─TreatmentPatterns:::generateCohortTableCDMC() 4. ├─DBI::dbConnect(duckdb::duckdb(), dbdir = CDMConnector::eunomia_dir()) at tests/testthat/helper-generateCohortTableCDMC.R:5:5 5. └─DBI::dbConnect(duckdb::duckdb(), dbdir = CDMConnector::eunomia_dir()) 6. └─duckdb (local) .local(drv, ...) 7. └─duckdb:::path_normalize(dbdir) ── Error ('test-computePathways.R:682:3'): Empty cohort table ────────────────── Error: 'eunomia_dir' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. ├─base::suppressWarnings(generateCohortTableCDMC()) at test-computePathways.R:682:3 2. │ └─base::withCallingHandlers(...) 3. └─TreatmentPatterns:::generateCohortTableCDMC() 4. ├─DBI::dbConnect(duckdb::duckdb(), dbdir = CDMConnector::eunomia_dir()) at tests/testthat/helper-generateCohortTableCDMC.R:5:5 5. └─DBI::dbConnect(duckdb::duckdb(), dbdir = CDMConnector::eunomia_dir()) 6. └─duckdb (local) .local(drv, ...) 7. └─duckdb:::path_normalize(dbdir) ── Error ('test-computePathways.R:704:3'): No target defined ─────────────────── Error: 'eunomia_dir' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. ├─base::suppressWarnings(generateCohortTableCDMC()) at test-computePathways.R:704:3 2. │ └─base::withCallingHandlers(...) 3. └─TreatmentPatterns:::generateCohortTableCDMC() 4. ├─DBI::dbConnect(duckdb::duckdb(), dbdir = CDMConnector::eunomia_dir()) at tests/testthat/helper-generateCohortTableCDMC.R:5:5 5. └─DBI::dbConnect(duckdb::duckdb(), dbdir = CDMConnector::eunomia_dir()) 6. └─duckdb (local) .local(drv, ...) 7. └─duckdb:::path_normalize(dbdir) ── Error ('test-executeTreatmentPatterns.R:28:3'): CDMConnector ──────────────── Error: 'eunomia_dir' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. └─TreatmentPatterns:::generateCohortTableCDMC() at test-executeTreatmentPatterns.R:28:3 2. ├─DBI::dbConnect(duckdb::duckdb(), dbdir = CDMConnector::eunomia_dir()) at tests/testthat/helper-generateCohortTableCDMC.R:5:5 3. └─DBI::dbConnect(duckdb::duckdb(), dbdir = CDMConnector::eunomia_dir()) 4. └─duckdb (local) .local(drv, ...) 5. └─duckdb:::path_normalize(dbdir) ── Error ('test-multipleCohortTables.R:7:3'): multiple cohort_tables ─────────── Error in `eunomia_dir()`: could not find function "eunomia_dir" Backtrace: ▆ 1. ├─DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir()) at test-multipleCohortTables.R:7:3 2. └─DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir()) 3. └─duckdb (local) .local(drv, ...) 4. └─duckdb:::path_normalize(dbdir) ── Error ('test-pathwaysLogical.R:7:3'): A ───────────────────────────────────── Error in `eunomia_dir()`: could not find function "eunomia_dir" Backtrace: ▆ 1. ├─DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir()) at test-pathwaysLogical.R:7:3 2. └─DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir()) 3. └─duckdb (local) .local(drv, ...) 4. └─duckdb:::path_normalize(dbdir) ── Error ('test-pathwaysLogical.R:49:3'): A-B ────────────────────────────────── Error in `eunomia_dir()`: could not find function "eunomia_dir" Backtrace: ▆ 1. ├─DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir()) at test-pathwaysLogical.R:49:3 2. └─DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir()) 3. └─duckdb (local) .local(drv, ...) 4. └─duckdb:::path_normalize(dbdir) ── Error ('test-pathwaysLogical.R:93:3'): A-B-C ──────────────────────────────── Error in `eunomia_dir()`: could not find function "eunomia_dir" Backtrace: ▆ 1. ├─DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir()) at test-pathwaysLogical.R:93:3 2. └─DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir()) 3. └─duckdb (local) .local(drv, ...) 4. └─duckdb:::path_normalize(dbdir) ── Error ('test-pathwaysLogical.R:137:3'): A-B+C ─────────────────────────────── Error in `eunomia_dir()`: could not find function "eunomia_dir" Backtrace: ▆ 1. ├─DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir()) at test-pathwaysLogical.R:137:3 2. └─DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir()) 3. └─duckdb (local) .local(drv, ...) 4. └─duckdb:::path_normalize(dbdir) ── Error ('test-pathwaysLogical.R:181:3'): A+B-C ─────────────────────────────── Error in `eunomia_dir()`: could not find function "eunomia_dir" Backtrace: ▆ 1. ├─DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir()) at test-pathwaysLogical.R:181:3 2. └─DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir()) 3. └─duckdb (local) .local(drv, ...) 4. └─duckdb:::path_normalize(dbdir) ── Error ('test-pathwaysLogical.R:269:3'): A-B-A-B ───────────────────────────── Error in `eunomia_dir()`: could not find function "eunomia_dir" Backtrace: ▆ 1. ├─DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir()) at test-pathwaysLogical.R:269:3 2. └─DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir()) 3. └─duckdb (local) .local(drv, ...) 4. └─duckdb:::path_normalize(dbdir) ── Error ('test-pathwaysLogical.R:314:3'): A-B-A ─────────────────────────────── Error in `eunomia_dir()`: could not find function "eunomia_dir" Backtrace: ▆ 1. ├─DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir()) at test-pathwaysLogical.R:314:3 2. └─DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir()) 3. └─duckdb (local) .local(drv, ...) 4. └─duckdb:::path_normalize(dbdir) ── Error ('test-pathwaysLogical.R:358:3'): A-B-B, collapse to A-B ────────────── Error in `eunomia_dir()`: could not find function "eunomia_dir" Backtrace: ▆ 1. ├─DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir()) at test-pathwaysLogical.R:358:3 2. └─DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir()) 3. └─duckdb (local) .local(drv, ...) 4. └─duckdb:::path_normalize(dbdir) ── Error ('test-pathwaysLogical.R:402:3'): A-B-B ─────────────────────────────── Error in `eunomia_dir()`: could not find function "eunomia_dir" Backtrace: ▆ 1. ├─DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir()) at test-pathwaysLogical.R:402:3 2. └─DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir()) 3. └─duckdb (local) .local(drv, ...) 4. └─duckdb:::path_normalize(dbdir) ── Error ('test-pathwaysLogical.R:446:3'): A+B-A ─────────────────────────────── Error in `eunomia_dir()`: could not find function "eunomia_dir" Backtrace: ▆ 1. ├─DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir()) at test-pathwaysLogical.R:446:3 2. └─DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir()) 3. └─duckdb (local) .local(drv, ...) 4. └─duckdb:::path_normalize(dbdir) ── Error ('test-pathwaysLogical.R:490:3'): A-A-B ─────────────────────────────── Error in `eunomia_dir()`: could not find function "eunomia_dir" Backtrace: ▆ 1. ├─DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir()) at test-pathwaysLogical.R:490:3 2. └─DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir()) 3. └─duckdb (local) .local(drv, ...) 4. └─duckdb:::path_normalize(dbdir) ── Error ('test-pathwaysLogical.R:534:3'): A-A-B, collapse to A-B ────────────── Error in `eunomia_dir()`: could not find function "eunomia_dir" Backtrace: ▆ 1. ├─DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir()) at test-pathwaysLogical.R:534:3 2. └─DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir()) 3. └─duckdb (local) .local(drv, ...) 4. └─duckdb:::path_normalize(dbdir) ── Error ('test-pathwaysLogical.R:578:3'): A+B-A+B, collapse to A+B ──────────── Error in `eunomia_dir()`: could not find function "eunomia_dir" Backtrace: ▆ 1. ├─DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir()) at test-pathwaysLogical.R:578:3 2. └─DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir()) 3. └─duckdb (local) .local(drv, ...) 4. └─duckdb:::path_normalize(dbdir) ── Error ('test-pathwaysLogical.R:623:3'): A+B-A+B ───────────────────────────── Error in `eunomia_dir()`: could not find function "eunomia_dir" Backtrace: ▆ 1. ├─DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir()) at test-pathwaysLogical.R:623:3 2. └─DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir()) 3. └─duckdb (local) .local(drv, ...) 4. └─duckdb:::path_normalize(dbdir) ── Error ('test-pathwaysLogical.R:668:3'): A-A+B-B ───────────────────────────── Error in `eunomia_dir()`: could not find function "eunomia_dir" Backtrace: ▆ 1. ├─DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir()) at test-pathwaysLogical.R:668:3 2. └─DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir()) 3. └─duckdb (local) .local(drv, ...) 4. └─duckdb:::path_normalize(dbdir) ── Error ('test-pathwaysLogical.R:711:3'): A-A-C-A+B+C-C ─────────────────────── Error in `eunomia_dir()`: could not find function "eunomia_dir" Backtrace: ▆ 1. ├─DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir()) at test-pathwaysLogical.R:711:3 2. └─DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir()) 3. └─duckdb (local) .local(drv, ...) 4. └─duckdb:::path_normalize(dbdir) ── Error ('test-pathwaysLogical.R:755:3'): A-A+B+C-A+C-C ─────────────────────── Error in `eunomia_dir()`: could not find function "eunomia_dir" Backtrace: ▆ 1. ├─DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir()) at test-pathwaysLogical.R:755:3 2. └─DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir()) 3. └─duckdb (local) .local(drv, ...) 4. └─duckdb:::path_normalize(dbdir) ── Error ('test-pathwaysLogical.R:799:3'): A-A+C-C-B+C-C ─────────────────────── Error in `eunomia_dir()`: could not find function "eunomia_dir" Backtrace: ▆ 1. ├─DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir()) at test-pathwaysLogical.R:799:3 2. └─DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir()) 3. └─duckdb (local) .local(drv, ...) 4. └─duckdb:::path_normalize(dbdir) ── Error ('test-pathwaysLogical.R:844:3'): start event == start target ───────── Error in `eunomia_dir()`: could not find function "eunomia_dir" Backtrace: ▆ 1. ├─DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir()) at test-pathwaysLogical.R:844:3 2. └─DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir()) 3. └─duckdb (local) .local(drv, ...) 4. └─duckdb:::path_normalize(dbdir) ── Error ('test-pathwaysLogical.R:886:3'): end event == end target ───────────── Error in `eunomia_dir()`: could not find function "eunomia_dir" Backtrace: ▆ 1. ├─DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir()) at test-pathwaysLogical.R:886:3 2. └─DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir()) 3. └─duckdb (local) .local(drv, ...) 4. └─duckdb:::path_normalize(dbdir) ── Error ('test-pathwaysLogical.R:928:3'): start-end event == start-end target ── Error in `eunomia_dir()`: could not find function "eunomia_dir" Backtrace: ▆ 1. ├─DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir()) at test-pathwaysLogical.R:928:3 2. └─DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir()) 3. └─duckdb (local) .local(drv, ...) 4. └─duckdb:::path_normalize(dbdir) ── Error ('test-pathwaysLogical.R:970:3'): start event < start target ────────── Error in `eunomia_dir()`: could not find function "eunomia_dir" Backtrace: ▆ 1. ├─DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir()) at test-pathwaysLogical.R:970:3 2. └─DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir()) 3. └─duckdb (local) .local(drv, ...) 4. └─duckdb:::path_normalize(dbdir) ── Error ('test-pathwaysLogical.R:1012:3'): start event < start target, periodPrior = -60 ── Error in `eunomia_dir()`: could not find function "eunomia_dir" Backtrace: ▆ 1. ├─DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir()) at test-pathwaysLogical.R:1012:3 2. └─DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir()) 3. └─duckdb (local) .local(drv, ...) 4. └─duckdb:::path_normalize(dbdir) ── Error ('test-pathwaysLogical.R:1054:3'): start event > end target ─────────── Error in `eunomia_dir()`: could not find function "eunomia_dir" Backtrace: ▆ 1. ├─DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir()) at test-pathwaysLogical.R:1054:3 2. └─DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir()) 3. └─duckdb (local) .local(drv, ...) 4. └─duckdb:::path_normalize(dbdir) ── Error ('test-pathwaysLogical.R:1097:3'): collapse A-B-B-B to A-A+B-B ──────── Error in `eunomia_dir()`: could not find function "eunomia_dir" Backtrace: ▆ 1. ├─DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir()) at test-pathwaysLogical.R:1097:3 2. └─DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir()) 3. └─duckdb (local) .local(drv, ...) 4. └─duckdb:::path_normalize(dbdir) ── Error ('test-pathwaysLogical.R:1143:3'): collapse A-B-B-B to A-B ──────────── Error in `eunomia_dir()`: could not find function "eunomia_dir" Backtrace: ▆ 1. ├─DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir()) at test-pathwaysLogical.R:1143:3 2. └─DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir()) 3. └─duckdb (local) .local(drv, ...) 4. └─duckdb:::path_normalize(dbdir) ── Error ('test-pathwaysLogical.R:1187:3'): collapse A-A-B-B to A-B ──────────── Error in `eunomia_dir()`: could not find function "eunomia_dir" Backtrace: ▆ 1. ├─DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir()) at test-pathwaysLogical.R:1187:3 2. └─DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir()) 3. └─duckdb (local) .local(drv, ...) 4. └─duckdb:::path_normalize(dbdir) ── Error ('test-pathwaysLogical.R:1231:3'): collapse A-A-B-B to A-B 2 ────────── Error in `eunomia_dir()`: could not find function "eunomia_dir" Backtrace: ▆ 1. ├─DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir()) at test-pathwaysLogical.R:1231:3 2. └─DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir()) 3. └─duckdb (local) .local(drv, ...) 4. └─duckdb:::path_normalize(dbdir) ── Error ('test-pathwaysLogical.R:1275:3'): collapse A-A-B-B to A+B 2 ────────── Error in `eunomia_dir()`: could not find function "eunomia_dir" Backtrace: ▆ 1. ├─DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir()) at test-pathwaysLogical.R:1275:3 2. └─DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir()) 3. └─duckdb (local) .local(drv, ...) 4. └─duckdb:::path_normalize(dbdir) ── Error ('test-pathwaysMultipleTargetsLogical.R:311:3'): Events outside target ── Error in `eunomia_dir()`: could not find function "eunomia_dir" Backtrace: ▆ 1. ├─DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir()) at test-pathwaysMultipleTargetsLogical.R:311:3 2. └─DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir()) 3. └─duckdb (local) .local(drv, ...) 4. └─duckdb:::path_normalize(dbdir) ── Error ('test-TreatmentPatternsResults.R:3:3'): Method: new(data.frame) ────── Error: 'eunomia_dir' is not an exported object from 'namespace:CDMConnector' Backtrace: ▆ 1. ├─base::suppressWarnings(generateCohortTableCDMC()) at test-TreatmentPatternsResults.R:3:3 2. │ └─base::withCallingHandlers(...) 3. └─TreatmentPatterns:::generateCohortTableCDMC() 4. ├─DBI::dbConnect(duckdb::duckdb(), dbdir = CDMConnector::eunomia_dir()) at tests/testthat/helper-generateCohortTableCDMC.R:5:5 5. └─DBI::dbConnect(duckdb::duckdb(), dbdir = CDMConnector::eunomia_dir()) 6. └─duckdb (local) .local(drv, ...) 7. └─duckdb:::path_normalize(dbdir) [ FAIL 49 | WARN 0 | SKIP 27 | PASS 89 ] Error: Test failures Execution halted