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, 3x8 bits/pixel, RGB Input IDAT size = 91730 bytes Input file size = 91940 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 = 90202 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 = 90202 Output IDAT size = 90202 bytes (1528 bytes decrease) Output file size = 90280 bytes (1660 bytes = 1.81% 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, 3x8 bits/pixel, RGB Input IDAT size = 67687 bytes Input file size = 67861 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 65435 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 = 65435 Output IDAT size = 65435 bytes (2252 bytes decrease) Output file size = 65513 bytes (2348 bytes = 3.46% 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, 3x8 bits/pixel, RGB Input IDAT size = 214928 bytes Input file size = 215318 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 175072 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 = 175072 Output IDAT size = 175072 bytes (39856 bytes decrease) Output file size = 175150 bytes (40168 bytes = 18.66% 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 = 192600 bytes Input file size = 192954 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 = 187349 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 = 187349 Output IDAT size = 187349 bytes (5251 bytes decrease) Output file size = 187427 bytes (5527 bytes = 2.86% decrease) --- finished re-building ‘A-summarise_clinical_tables_records.Rmd’ --- re-building ‘B-summarise_concept_counts.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 ** Processing: /home/hornik/tmp/CRAN_recheck/OmopSketch.Rcheck/vign_test/OmopSketch/vignettes/B-summarise_concept_counts_files/figure-html/unnamed-chunk-8-1.png 1344x960 pixels, 3x8 bits/pixel, RGB Input IDAT size = 34134 bytes Input file size = 34260 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 31877 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 = 31028 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 = 31028 Output IDAT size = 31028 bytes (3106 bytes decrease) Output file size = 31106 bytes (3154 bytes = 9.21% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/OmopSketch.Rcheck/vign_test/OmopSketch/vignettes/B-summarise_concept_counts_files/figure-html/unnamed-chunk-9-1.png 1344x960 pixels, 3x8 bits/pixel, RGB Input IDAT size = 34134 bytes Input file size = 34260 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 31877 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 = 31028 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 = 31028 Output IDAT size = 31028 bytes (3106 bytes decrease) Output file size = 31106 bytes (3154 bytes = 9.21% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/OmopSketch.Rcheck/vign_test/OmopSketch/vignettes/B-summarise_concept_counts_files/figure-html/unnamed-chunk-10-1.png 1344x960 pixels, 3x8 bits/pixel, RGB Input IDAT size = 67418 bytes Input file size = 67592 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 59567 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 = 59567 Output IDAT size = 59567 bytes (7851 bytes decrease) Output file size = 59645 bytes (7947 bytes = 11.76% decrease) --- finished re-building ‘B-summarise_concept_counts.Rmd’ Warning: Connection is garbage-collected, use dbDisconnect() to avoid this. --- re-building ‘C-summarise_pop_characteristics.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 57-60 [unnamed-chunk-3] (C-summarise_pop_characteristics.Rmd) Error: processing vignette 'C-summarise_pop_characteristics.Rmd' failed with diagnostics: `variable_name` must not contain NA. --- failed re-building ‘C-summarise_pop_characteristics.Rmd’ Warning: Connection is garbage-collected, use dbDisconnect() to avoid this. SUMMARY: processing the following file failed: ‘C-summarise_pop_characteristics.Rmd’ Error: Vignette re-building failed. Execution halted Package: OmopSketch Check: tests New result: ERROR Running ‘testthat.R’ [104s/54s] 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(OmopSketch) > > test_check("OmopSketch") Starting 2 test processes [ FAIL 4 | WARN 0 | SKIP 20 | PASS 82 ] ══ Skipped tests (20) ══════════════════════════════════════════════════════════ • On CRAN (20): 'test-mockOmopSketch.R:2:3', 'test-plotInObservation.R:2:3', 'test-summariseClinicalRecords.R:2:3', 'test-summariseClinicalRecords.R:81:3', 'test-summariseClinicalRecords.R:213:3', 'test-summariseInObservation.R:2:3', 'test-summariseInObservation.R:96:3', 'test-summariseInObservation.R:148:3', 'test-summariseInObservation.R:184:3', 'test-summariseConceptCounts.R:2:3', 'test-summariseConceptCounts.R:428:3', 'test-summariseOmopSnapshot.R:2:3', 'test-summariseOmopSnapshot.R:10:3', 'test-summarisePopulationCharacteristics.R:2:3', 'test-summarisePopulationCharacteristics.R:149:3', 'test-summarisePopulationCharacteristics.R:165:3', 'test-summariseRecordCount.R:2:3', 'test-summariseRecordCount.R:92:3', 'test-summariseRecordCount.R:112:3', 'test-summariseRecordCount.R:189:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-summarisePopulationCharacteristics.R:125:3'): summarisePopulationCharacteristics() works ── Expected `... <- NULL` to run without any errors. i Actually got a with text: `variable_name` must not contain NA. ── Error ('test-summarisePopulationCharacteristics.R:130:3'): summarisePopulationCharacteristics() works ── Error in `eval(code, test_env)`: object 'summarisedPopulation' not found Backtrace: ▆ 1. ├─testthat::expect_true(inherits(summarisedPopulation, "summarised_result")) at test-summarisePopulationCharacteristics.R:130:3 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object") 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. └─base::inherits(summarisedPopulation, "summarised_result") ── Failure ('test-summarisePopulationCharacteristics.R:183:3'): summarisePopulationCharacteristics() works with mockOmopSKetch ── Expected `summarisedPopulation <- summarisePopulationCharacteristics(cdm = cdm)` to run without any errors. i Actually got a with text: `variable_name` must not contain NA. ── Error ('test-summarisePopulationCharacteristics.R:186:3'): summarisePopulationCharacteristics() works with mockOmopSKetch ── Error in `eval(code, test_env)`: object 'summarisedPopulation' not found Backtrace: ▆ 1. ├─testthat::expect_true(inherits(summarisedPopulation, "summarised_result")) at test-summarisePopulationCharacteristics.R:186:3 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object") 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. └─base::inherits(summarisedPopulation, "summarised_result") [ FAIL 4 | WARN 0 | SKIP 20 | PASS 82 ] Error: Test failures Execution halted