Last updated on 2024-10-15 08:50:12 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.1.0 | 6.79 | 534.45 | 541.24 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 0.1.0 | 3.85 | 385.63 | 389.48 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 0.1.0 | 854.47 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 0.1.0 | 558.00 | ERROR | |||
| r-devel-windows-x86_64 | 0.1.0 | 8.00 | 351.00 | 359.00 | ERROR | |
| r-patched-linux-x86_64 | 0.1.0 | 4.92 | 502.18 | 507.10 | ERROR | |
| r-release-linux-x86_64 | 0.1.0 | 6.32 | 496.19 | 502.51 | ERROR | |
| r-release-macos-arm64 | 0.1.0 | 179.00 | OK | |||
| r-release-macos-x86_64 | 0.1.0 | 306.00 | OK | |||
| r-release-windows-x86_64 | 0.1.0 | 8.00 | 358.00 | 366.00 | ERROR | |
| r-oldrel-macos-arm64 | 0.1.0 | 207.00 | OK | |||
| r-oldrel-macos-x86_64 | 0.1.0 | 330.00 | OK | |||
| r-oldrel-windows-x86_64 | 0.1.0 | 10.00 | 488.00 | 498.00 | ERROR |
Version: 0.1.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [204s/109s]
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-devel-linux-x86_64-debian-clang
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-devel-clang/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 = 86164 bytes
Input file size = 86362 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 = 84456
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 = 84456
Output IDAT size = 84456 bytes (1708 bytes decrease)
Output file size = 84534 bytes (1828 bytes = 2.12% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-clang/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 = 74001 bytes
Input file size = 74187 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 72596
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 = 71764
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 = 71764
Output IDAT size = 71764 bytes (2237 bytes decrease)
Output file size = 71842 bytes (2345 bytes = 3.16% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-clang/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 = 195111 bytes
Input file size = 195465 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 163436
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 = 163436
Output IDAT size = 163436 bytes (31675 bytes decrease)
Output file size = 163514 bytes (31951 bytes = 16.35% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-clang/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 = 182534 bytes
Input file size = 182876 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 = 177112
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 = 177112
Output IDAT size = 177112 bytes (5422 bytes decrease)
Output file size = 177190 bytes (5686 bytes = 3.11% 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-devel-clang/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-devel-clang/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-devel-clang/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 = 67432 bytes
Input file size = 67606 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 59573
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 = 59573
Output IDAT size = 59573 bytes (7859 bytes decrease)
Output file size = 59651 bytes (7955 bytes = 11.77% 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-devel-linux-x86_64-debian-clang
Version: 0.1.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [153s/117s]
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-devel-linux-x86_64-debian-gcc
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-devel-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 = 76666 bytes
Input file size = 76852 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 = 74361
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 = 74361
Output IDAT size = 74361 bytes (2305 bytes decrease)
Output file size = 74439 bytes (2413 bytes = 3.14% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-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 = 69988 bytes
Input file size = 70162 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 68927
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 = 67495
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 = 67495
Output IDAT size = 67495 bytes (2493 bytes decrease)
Output file size = 67573 bytes (2589 bytes = 3.69% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-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 = 176048 bytes
Input file size = 176378 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 146276
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 = 146276
Output IDAT size = 146276 bytes (29772 bytes decrease)
Output file size = 146354 bytes (30024 bytes = 17.02% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-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 = 166478 bytes
Input file size = 166796 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 = 161508
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 = 161508
Output IDAT size = 161508 bytes (4970 bytes decrease)
Output file size = 161586 bytes (5210 bytes = 3.12% 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-devel-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-devel-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-devel-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 = 67417 bytes
Input file size = 67591 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 (7850 bytes decrease)
Output file size = 59645 bytes (7946 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-devel-linux-x86_64-debian-gcc
Version: 0.1.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [323s/169s]
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-devel-linux-x86_64-fedora-clang
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: /data/gannet/ripley/R/packages/tests-clang/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 = 76027 bytes
Input file size = 76213 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 = 74245
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 = 74245
Output IDAT size = 74245 bytes (1782 bytes decrease)
Output file size = 74323 bytes (1890 bytes = 2.48% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/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 = 70052 bytes
Input file size = 70226 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 67915
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 = 67915
Output IDAT size = 67915 bytes (2137 bytes decrease)
Output file size = 67993 bytes (2233 bytes = 3.18% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/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 = 195267 bytes
Input file size = 195621 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 157821
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 = 157821
Output IDAT size = 157821 bytes (37446 bytes decrease)
Output file size = 157899 bytes (37722 bytes = 19.28% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/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 = 177467 bytes
Input file size = 177797 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 = 172524
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 = 172524
Output IDAT size = 172524 bytes (4943 bytes decrease)
Output file size = 172602 bytes (5195 bytes = 2.92% 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: /data/gannet/ripley/R/packages/tests-clang/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: /data/gannet/ripley/R/packages/tests-clang/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: /data/gannet/ripley/R/packages/tests-clang/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 = 67437 bytes
Input file size = 67611 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 59565
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 = 59565
Output IDAT size = 59565 bytes (7872 bytes decrease)
Output file size = 59643 bytes (7968 bytes = 11.79% 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-devel-linux-x86_64-fedora-clang
Version: 0.1.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [237s/121s]
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-devel-linux-x86_64-fedora-gcc
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: /data/gannet/ripley/R/packages/tests-devel/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 = 78879 bytes
Input file size = 79065 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 78667
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 = 76454
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 = 76454
Output IDAT size = 76454 bytes (2425 bytes decrease)
Output file size = 76532 bytes (2533 bytes = 3.20% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/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 = 72212 bytes
Input file size = 72386 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 70815
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 = 69544
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 = 69544
Output IDAT size = 69544 bytes (2668 bytes decrease)
Output file size = 69622 bytes (2764 bytes = 3.82% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/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 = 186554 bytes
Input file size = 186896 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 155227
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 = 155227
Output IDAT size = 155227 bytes (31327 bytes decrease)
Output file size = 155305 bytes (31591 bytes = 16.90% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/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 = 173546 bytes
Input file size = 173876 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 = 168428
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 = 168428
Output IDAT size = 168428 bytes (5118 bytes decrease)
Output file size = 168506 bytes (5370 bytes = 3.09% 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: /data/gannet/ripley/R/packages/tests-devel/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: /data/gannet/ripley/R/packages/tests-devel/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: /data/gannet/ripley/R/packages/tests-devel/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 = 67413 bytes
Input file size = 67587 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 59564
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 = 59564
Output IDAT size = 59564 bytes (7849 bytes decrease)
Output file size = 59642 bytes (7945 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-devel-linux-x86_64-fedora-gcc
Version: 0.1.0
Check: tests
Result: ERROR
Running 'testthat.R' [79s]
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-devel-windows-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
--- 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
--- 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
Flavors: r-devel-windows-x86_64, r-release-windows-x86_64, r-oldrel-windows-x86_64
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
Version: 0.1.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [189s/100s]
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-release-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-release-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 = 78231 bytes
Input file size = 78417 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 = 76512
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 = 76512
Output IDAT size = 76512 bytes (1719 bytes decrease)
Output file size = 76590 bytes (1827 bytes = 2.33% decrease)
** Processing: /home/hornik/tmp/R.check/r-release-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 = 68583 bytes
Input file size = 68757 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 66564
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 = 66410
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 = 66410
Output IDAT size = 66410 bytes (2173 bytes decrease)
Output file size = 66488 bytes (2269 bytes = 3.30% decrease)
** Processing: /home/hornik/tmp/R.check/r-release-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 = 173449 bytes
Input file size = 173779 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 141338
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 = 141338
Output IDAT size = 141338 bytes (32111 bytes decrease)
Output file size = 141416 bytes (32363 bytes = 18.62% decrease)
** Processing: /home/hornik/tmp/R.check/r-release-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 = 172750 bytes
Input file size = 173080 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 = 167512
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 = 167512
Output IDAT size = 167512 bytes (5238 bytes decrease)
Output file size = 167590 bytes (5490 bytes = 3.17% 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-release-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-release-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-release-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 = 67424 bytes
Input file size = 67598 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 (7855 bytes decrease)
Output file size = 59647 bytes (7951 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-release-linux-x86_64
Version: 0.1.0
Check: tests
Result: ERROR
Running 'testthat.R' [80s]
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-release-windows-x86_64
Version: 0.1.0
Check: tests
Result: ERROR
Running 'testthat.R' [115s]
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-oldrel-windows-x86_64