Last updated on 2024-10-19 03:49:27 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.1.1 | 6.13 | 582.24 | 588.37 | OK | |
| r-devel-linux-x86_64-debian-gcc | 0.1.1 | 3.85 | 421.38 | 425.23 | OK | |
| r-devel-linux-x86_64-fedora-clang | 0.1.1 | 939.85 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 0.1.1 | 893.86 | OK | |||
| r-devel-windows-x86_64 | 0.1.1 | 9.00 | 403.00 | 412.00 | OK | |
| r-patched-linux-x86_64 | 0.1.0 | ERROR | ||||
| r-release-linux-x86_64 | 0.1.1 | 6.36 | 543.77 | 550.13 | OK | |
| r-release-macos-arm64 | 0.1.1 | 189.00 | OK | |||
| r-release-macos-x86_64 | 0.1.1 | 313.00 | OK | |||
| r-release-windows-x86_64 | 0.1.1 | 10.00 | 395.00 | 405.00 | OK | |
| r-oldrel-macos-arm64 | 0.1.1 | 209.00 | OK | |||
| r-oldrel-macos-x86_64 | 0.1.1 | 334.00 | OK | |||
| r-oldrel-windows-x86_64 | 0.1.1 | 10.00 | 439.00 | 449.00 | OK |
Version: 0.1.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [187s/101s]
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 <rlang_error> 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 <rlang_error> 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
Flavor: r-patched-linux-x86_64
Version: 0.1.0
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘A-summarise_clinical_tables_records.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/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 = 67222 bytes
Input file size = 67396 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 66103
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 = 64758
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 = 64758
Output IDAT size = 64758 bytes (2464 bytes decrease)
Output file size = 64836 bytes (2560 bytes = 3.80% decrease)
** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/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 = 70635 bytes
Input file size = 70809 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 67543
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 = 67543
Output IDAT size = 67543 bytes (3092 bytes decrease)
Output file size = 67621 bytes (3188 bytes = 4.50% decrease)
** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/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 = 194925 bytes
Input file size = 195279 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 155943
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 = 155943
Output IDAT size = 155943 bytes (38982 bytes decrease)
Output file size = 156021 bytes (39258 bytes = 20.10% decrease)
** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/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 = 177163 bytes
Input file size = 177493 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 = 171751
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 = 171751
Output IDAT size = 171751 bytes (5412 bytes decrease)
Output file size = 171829 bytes (5664 bytes = 3.19% 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/R.check/r-patched-gcc/Work/PKGS/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/R.check/r-patched-gcc/Work/PKGS/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/R.check/r-patched-gcc/Work/PKGS/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 = 67422 bytes
Input file size = 67596 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 59569
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 = 59569
Output IDAT size = 59569 bytes (7853 bytes decrease)
Output file size = 59647 bytes (7949 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
Flavor: r-patched-linux-x86_64