Last updated on 2024-10-06 12:49:31 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.1.0 | 6.36 | 534.21 | 540.57 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 0.1.0 | 4.65 | 365.85 | 370.50 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 0.1.0 | 919.20 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 0.1.0 | 878.62 | ERROR | |||
| r-devel-windows-x86_64 | 0.1.0 | 8.00 | 379.00 | 387.00 | ERROR | |
| r-patched-linux-x86_64 | 0.1.0 | 6.61 | 501.24 | 507.85 | ERROR | |
| r-release-linux-x86_64 | 0.1.0 | 6.40 | 498.64 | 505.04 | 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 | 10.00 | 390.00 | 400.00 | 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 | 489.00 | 499.00 | ERROR |
Version: 0.1.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [204s/108s]
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 = 83781 bytes
Input file size = 83979 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 83759
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 = 81618
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 = 81618
Output IDAT size = 81618 bytes (2163 bytes decrease)
Output file size = 81696 bytes (2283 bytes = 2.72% 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 = 74387 bytes
Input file size = 74573 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 73809
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 = 71969
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 = 71969
Output IDAT size = 71969 bytes (2418 bytes decrease)
Output file size = 72047 bytes (2526 bytes = 3.39% 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 = 197677 bytes
Input file size = 198043 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 163297
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 = 163297
Output IDAT size = 163297 bytes (34380 bytes decrease)
Output file size = 163375 bytes (34668 bytes = 17.51% 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 = 181653 bytes
Input file size = 181995 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 = 175839
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 = 175839
Output IDAT size = 175839 bytes (5814 bytes decrease)
Output file size = 175917 bytes (6078 bytes = 3.34% 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 = 67438 bytes
Input file size = 67612 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 (7874 bytes decrease)
Output file size = 59642 bytes (7970 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-debian-clang
Version: 0.1.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [138s/97s]
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 = 89244 bytes
Input file size = 89442 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 = 87169
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 = 87169
Output IDAT size = 87169 bytes (2075 bytes decrease)
Output file size = 87247 bytes (2195 bytes = 2.45% 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 = 79848 bytes
Input file size = 80034 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 = 78233
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 = 78233
Output IDAT size = 78233 bytes (1615 bytes decrease)
Output file size = 78311 bytes (1723 bytes = 2.15% 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 = 226702 bytes
Input file size = 227104 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 192656
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 = 192656
Output IDAT size = 192656 bytes (34046 bytes decrease)
Output file size = 192734 bytes (34370 bytes = 15.13% 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 = 211451 bytes
Input file size = 211829 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 = 205535
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 = 205535
Output IDAT size = 205535 bytes (5916 bytes decrease)
Output file size = 205613 bytes (6216 bytes = 2.93% 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 = 67437 bytes
Input file size = 67611 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 (7868 bytes decrease)
Output file size = 59647 bytes (7964 bytes = 11.78% 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’ [343s/187s]
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 = 85584 bytes
Input file size = 85782 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 = 83490
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 = 83490
Output IDAT size = 83490 bytes (2094 bytes decrease)
Output file size = 83568 bytes (2214 bytes = 2.58% 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 = 80141 bytes
Input file size = 80327 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 = 77902
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 = 77902
Output IDAT size = 77902 bytes (2239 bytes decrease)
Output file size = 77980 bytes (2347 bytes = 2.92% 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 = 245786 bytes
Input file size = 246224 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 204711
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 = 204711
Output IDAT size = 204711 bytes (41075 bytes decrease)
Output file size = 204789 bytes (41435 bytes = 16.83% 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 = 216937 bytes
Input file size = 217327 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 = 211381
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 = 211381
Output IDAT size = 211381 bytes (5556 bytes decrease)
Output file size = 211459 bytes (5868 bytes = 2.70% 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 = 67421 bytes
Input file size = 67595 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 59570
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 = 59570
Output IDAT size = 59570 bytes (7851 bytes decrease)
Output file size = 59648 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
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.1.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [351s/181s]
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 = 77108 bytes
Input file size = 77294 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 75676
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 = 74674
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 = 74674
Output IDAT size = 74674 bytes (2434 bytes decrease)
Output file size = 74752 bytes (2542 bytes = 3.29% 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 = 71393 bytes
Input file size = 71567 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 68361
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 = 68361
Output IDAT size = 68361 bytes (3032 bytes decrease)
Output file size = 68439 bytes (3128 bytes = 4.37% 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 = 195531 bytes
Input file size = 195885 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 159425
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 = 159425
Output IDAT size = 159425 bytes (36106 bytes decrease)
Output file size = 159503 bytes (36382 bytes = 18.57% 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 = 184970 bytes
Input file size = 185312 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 = 179569
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 = 179569
Output IDAT size = 179569 bytes (5401 bytes decrease)
Output file size = 179647 bytes (5665 bytes = 3.06% 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 = 67421 bytes
Input file size = 67595 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 59570
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 = 59570
Output IDAT size = 59570 bytes (7851 bytes decrease)
Output file size = 59648 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
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 0.1.0
Check: tests
Result: ERROR
Running 'testthat.R' [81s]
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
Flavors: r-devel-windows-x86_64, r-release-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’ [192s/104s]
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 = 78139 bytes
Input file size = 78325 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 77633
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 = 76124
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 = 76124
Output IDAT size = 76124 bytes (2015 bytes decrease)
Output file size = 76202 bytes (2123 bytes = 2.71% 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 = 77055 bytes
Input file size = 77241 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 76949
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 = 74677
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 = 74677
Output IDAT size = 74677 bytes (2378 bytes decrease)
Output file size = 74755 bytes (2486 bytes = 3.22% 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 = 215879 bytes
Input file size = 216269 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 180086
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 = 180086
Output IDAT size = 180086 bytes (35793 bytes decrease)
Output file size = 180164 bytes (36105 bytes = 16.69% 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 = 200461 bytes
Input file size = 200827 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 = 194955
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 = 194955
Output IDAT size = 194955 bytes (5506 bytes decrease)
Output file size = 195033 bytes (5794 bytes = 2.89% 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 = 67413 bytes
Input file size = 67587 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 (7844 bytes decrease)
Output file size = 59647 bytes (7940 bytes = 11.75% 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/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-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 = 77087 bytes
Input file size = 77273 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 76938
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 = 74758
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 = 74758
Output IDAT size = 74758 bytes (2329 bytes decrease)
Output file size = 74836 bytes (2437 bytes = 3.15% 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 = 64113 bytes
Input file size = 64275 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 63525
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 = 61843
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 = 61843
Output IDAT size = 61843 bytes (2270 bytes decrease)
Output file size = 61921 bytes (2354 bytes = 3.66% 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 = 160249 bytes
Input file size = 160555 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 131245
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 = 131245
Output IDAT size = 131245 bytes (29004 bytes decrease)
Output file size = 131323 bytes (29232 bytes = 18.21% 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 = 158879 bytes
Input file size = 159185 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 = 153752
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 = 153752
Output IDAT size = 153752 bytes (5127 bytes decrease)
Output file size = 153830 bytes (5355 bytes = 3.36% 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 = 59570
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 = 59570
Output IDAT size = 59570 bytes (7854 bytes decrease)
Output file size = 59648 bytes (7950 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' [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-oldrel-windows-x86_64