Last updated on 2024-06-01 07:50:14 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.2.0 | 10.96 | 432.07 | 443.03 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 0.2.0 | 7.77 | 305.59 | 313.36 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 0.2.0 | 311.12 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 0.2.0 | 301.51 | ERROR | |||
| r-devel-windows-x86_64 | 0.2.0 | 11.00 | 240.00 | 251.00 | ERROR | |
| r-patched-linux-x86_64 | 0.2.0 | 10.69 | 413.69 | 424.38 | ERROR | |
| r-release-linux-x86_64 | 0.2.0 | 10.70 | 414.79 | 425.49 | ERROR | |
| r-release-macos-arm64 | 0.2.0 | 142.00 | NOTE | |||
| r-release-macos-x86_64 | 0.2.0 | 267.00 | NOTE | |||
| r-release-windows-x86_64 | 0.2.0 | 12.00 | 238.00 | 250.00 | ERROR | |
| r-oldrel-macos-arm64 | 0.2.0 | 155.00 | NOTE | |||
| r-oldrel-macos-x86_64 | 0.2.0 | 231.00 | NOTE | |||
| r-oldrel-windows-x86_64 | 0.2.0 | 14.00 | 330.00 | 344.00 | ERROR |
Version: 0.2.0
Check: for code/documentation mismatches
Result: WARN
Codoc mismatches from Rd file 'mockCohortCharacteristics.Rd':
mockCohortCharacteristics
Code: function(con = NULL, writeSchema = NULL, numberIndividuals =
10, ..., seed = NULL)
Docs: function(connectionDetails = list(con =
DBI::dbConnect(duckdb::duckdb(), ":memory:"),
write_schema = "main", mock_prefix = NULL),
drug_exposure = NULL, drug_strength = NULL,
observation_period = NULL, condition_occurrence =
NULL, visit_occurrence = NULL, concept_ancestor =
NULL, person = NULL, death = NULL, cohort1 = NULL,
cohort2 = NULL, drug_concept_id_size = 5,
ancestor_concept_id_size = 5,
condition_concept_id_size = 5, visit_concept_id_size =
5, visit_occurrence_id_size = 5,
ingredient_concept_id_size = 1, drug_exposure_size =
10, patient_size = 1, min_drug_exposure_start_date =
"2000-01-01", max_drug_exposure_start_date =
"2020-01-01", earliest_date_of_birth = NULL,
latest_date_of_birth = NULL,
earliest_observation_start_date = NULL,
latest_observation_start_date = NULL,
min_days_to_observation_end = NULL,
max_days_to_observation_end = NULL,
earliest_condition_start_date = NULL,
latest_condition_start_date = NULL,
min_days_to_condition_end = NULL,
max_days_to_condition_end = NULL,
earliest_visit_start_date = NULL,
latest_visit_start_date = NULL, min_days_to_visit_end
= NULL, max_days_to_visit_end = NULL, seed = 1, ...)
Argument names in code not in docs:
con writeSchema numberIndividuals
Argument names in docs not in code:
connectionDetails drug_exposure drug_strength observation_period
condition_occurrence visit_occurrence concept_ancestor person death
cohort1 cohort2 drug_concept_id_size ancestor_concept_id_size
condition_concept_id_size visit_concept_id_size
visit_occurrence_id_size ingredient_concept_id_size
drug_exposure_size patient_size min_drug_exposure_start_date
max_drug_exposure_start_date earliest_date_of_birth
latest_date_of_birth earliest_observation_start_date
latest_observation_start_date min_days_to_observation_end
max_days_to_observation_end earliest_condition_start_date
latest_condition_start_date min_days_to_condition_end
max_days_to_condition_end earliest_visit_start_date
latest_visit_start_date min_days_to_visit_end max_days_to_visit_end
Mismatches in argument names (first 3):
Position: 1 Code: con Docs: connectionDetails
Position: 2 Code: writeSchema Docs: drug_exposure
Position: 3 Code: numberIndividuals Docs: drug_strength
Mismatches in argument default values:
Name: 'seed' Code: NULL Docs: 1
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-windows-x86_64
Version: 0.2.0
Check: tests
Result: ERROR
Running ‘spelling.R’ [0s/0s]
Running ‘testthat.R’ [167s/126s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(CohortCharacteristics)
>
> test_check("CohortCharacteristics")
Starting 2 test processes
[ FAIL 3 | WARN 0 | SKIP 11 | PASS 82 ]
══ Skipped tests (11) ══════════════════════════════════════════════════════════
• On CRAN (10): 'test-plotCharacteristics.R:2:3',
'test-plotLargeScaleCharacteristics.R:3:3', 'test-plotSummarised.R:2:3',
'test-plotSummarised.R:91:3', 'test-plotSummarised.R:197:3',
'test-plotSummarised.R:299:3',
'test-summariseLargeScaleCharacteristics.R:2:3',
'test-tableSummarised.R:2:3', 'test-tableSummarised.R:123:3',
'test-summariseCharacteristics.R:1122:3'
• empty test (1): 'test-tableSummarised.R:262:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-summariseCharacteristics.R:53:3'): test summariseCharacteristics ──
Error in `mockCohortCharacteristics(connectionDetails, dus_cohort = dus_cohort,
person = person, comorbidities = comorbidities, medication = medication,
observation_period = observation_period, cohort1 = emptyCohort,
cohort2 = emptyCohort)`: ! `con` must be a DBI connection
Backtrace:
▆
1. └─PatientProfiles (local) mockCohortCharacteristics(...) at test-summariseCharacteristics.R:53:3
2. └─cli::cli_abort(c(`!` = "`con` must be a DBI connection"))
3. └─rlang::abort(...)
── Error ('test-summariseCharacteristics.R:378:3'): test empty cohort ──────────
Error in `mockCohortCharacteristics(connectionDetails = connectionDetails)`: tables must be a list; it can not contain NA; it can not be NULL; it has to be named; elements must have class: data.frame.
Backtrace:
▆
1. └─PatientProfiles (local) mockCohortCharacteristics(connectionDetails = connectionDetails) at test-summariseCharacteristics.R:378:3
2. └─PatientProfiles:::assertList(tables, named = TRUE, class = "data.frame")
3. └─cli::cli_abort(errorMessage, call = call)
4. └─rlang::abort(...)
── Error ('test-summariseCharacteristics.R:484:3'): test cohort id ─────────────
Error in `mockCohortCharacteristics(connectionDetails, dus_cohort = dus_cohort,
person = person, comorbidities = comorbidities, medication = medication,
observation_period = observation_period, cohort1 = emptyCohort,
cohort2 = emptyCohort)`: ! `con` must be a DBI connection
Backtrace:
▆
1. └─PatientProfiles (local) mockCohortCharacteristics(...) at test-summariseCharacteristics.R:484:3
2. └─cli::cli_abort(c(`!` = "`con` must be a DBI connection"))
3. └─rlang::abort(...)
[ FAIL 3 | WARN 0 | SKIP 11 | PASS 82 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 0.2.0
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘a05_summariseCohortEntries.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 ‘a05_summariseCohortEntries.Rmd’
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
--- re-building ‘a06_summarisePatientCharacteristics.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 78-86 [unnamed-chunk-5] (a06_summarisePatientCharacteristics.Rmd)
Error: processing vignette 'a06_summarisePatientCharacteristics.Rmd' failed with diagnostics:
the condition has length > 1
--- failed re-building ‘a06_summarisePatientCharacteristics.Rmd’
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
--- re-building ‘a07_summariseLargeScaleCharacteristics.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 ‘a07_summariseLargeScaleCharacteristics.Rmd’
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
--- re-building ‘a08_summariseCohortOverlap.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/CohortCharacteristics.Rcheck/vign_test/CohortCharacteristics/vignettes/a08_summariseCohortOverlap_files/figure-html/unnamed-chunk-5-1.png
1344x960 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 37316 bytes
Input file size = 37442 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 33427
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 = 32928
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 = 32928
Output IDAT size = 32928 bytes (4388 bytes decrease)
Output file size = 33006 bytes (4436 bytes = 11.85% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/CohortCharacteristics.Rcheck/vign_test/CohortCharacteristics/vignettes/a08_summariseCohortOverlap_files/figure-html/unnamed-chunk-8-1.png
1344x960 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 66151 bytes
Input file size = 66325 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 53846
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 = 53846
Output IDAT size = 53846 bytes (12305 bytes decrease)
Output file size = 53924 bytes (12401 bytes = 18.70% decrease)
--- finished re-building ‘a08_summariseCohortOverlap.Rmd’
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
--- re-building ‘a09_summariseCohortTiming.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/CohortCharacteristics.Rcheck/vign_test/CohortCharacteristics/vignettes/a09_summariseCohortTiming_files/figure-html/unnamed-chunk-5-1.png
1344x960 pixels, 8 bits/pixel, 255 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 17931 bytes
Input file size = 18810 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 14167
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 = 11762
zc = 9 zm = 8 zs = 1 f = 5 IDAT size = 11690
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 1 f = 5 IDAT size = 11690
Output IDAT size = 11690 bytes (6241 bytes decrease)
Output file size = 11768 bytes (7042 bytes = 37.44% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/CohortCharacteristics.Rcheck/vign_test/CohortCharacteristics/vignettes/a09_summariseCohortTiming_files/figure-html/unnamed-chunk-6-1.png
1344x960 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 46347 bytes
Input file size = 47265 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 41285
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 = 41285
Output IDAT size = 41285 bytes (5062 bytes decrease)
Output file size = 41363 bytes (5902 bytes = 12.49% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/CohortCharacteristics.Rcheck/vign_test/CohortCharacteristics/vignettes/a09_summariseCohortTiming_files/figure-html/unnamed-chunk-7-1.png
1344x960 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 64596 bytes
Input file size = 64758 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 56755
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 = 56755
Output IDAT size = 56755 bytes (7841 bytes decrease)
Output file size = 56833 bytes (7925 bytes = 12.24% decrease)
--- finished re-building ‘a09_summariseCohortTiming.Rmd’
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
SUMMARY: processing the following file failed:
‘a06_summarisePatientCharacteristics.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 0.2.0
Check: tests
Result: ERROR
Running ‘spelling.R’ [0s/1s]
Running ‘testthat.R’ [117s/116s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(CohortCharacteristics)
>
> test_check("CohortCharacteristics")
Starting 2 test processes
[ FAIL 3 | WARN 0 | SKIP 11 | PASS 82 ]
══ Skipped tests (11) ══════════════════════════════════════════════════════════
• On CRAN (10): 'test-plotCharacteristics.R:2:3',
'test-plotLargeScaleCharacteristics.R:3:3', 'test-plotSummarised.R:2:3',
'test-plotSummarised.R:91:3', 'test-plotSummarised.R:197:3',
'test-plotSummarised.R:299:3',
'test-summariseLargeScaleCharacteristics.R:2:3',
'test-tableSummarised.R:2:3', 'test-tableSummarised.R:123:3',
'test-summariseCharacteristics.R:1122:3'
• empty test (1): 'test-tableSummarised.R:262:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-summariseCharacteristics.R:53:3'): test summariseCharacteristics ──
Error in `mockCohortCharacteristics(connectionDetails, dus_cohort = dus_cohort,
person = person, comorbidities = comorbidities, medication = medication,
observation_period = observation_period, cohort1 = emptyCohort,
cohort2 = emptyCohort)`: ! `con` must be a DBI connection
Backtrace:
▆
1. └─PatientProfiles (local) mockCohortCharacteristics(...) at test-summariseCharacteristics.R:53:3
2. └─cli::cli_abort(c(`!` = "`con` must be a DBI connection"))
3. └─rlang::abort(...)
── Error ('test-summariseCharacteristics.R:378:3'): test empty cohort ──────────
Error in `mockCohortCharacteristics(connectionDetails = connectionDetails)`: tables must be a list; it can not contain NA; it can not be NULL; it has to be named; elements must have class: data.frame.
Backtrace:
▆
1. └─PatientProfiles (local) mockCohortCharacteristics(connectionDetails = connectionDetails) at test-summariseCharacteristics.R:378:3
2. └─PatientProfiles:::assertList(tables, named = TRUE, class = "data.frame")
3. └─cli::cli_abort(errorMessage, call = call)
4. └─rlang::abort(...)
── Error ('test-summariseCharacteristics.R:484:3'): test cohort id ─────────────
Error in `mockCohortCharacteristics(connectionDetails, dus_cohort = dus_cohort,
person = person, comorbidities = comorbidities, medication = medication,
observation_period = observation_period, cohort1 = emptyCohort,
cohort2 = emptyCohort)`: ! `con` must be a DBI connection
Backtrace:
▆
1. └─PatientProfiles (local) mockCohortCharacteristics(...) at test-summariseCharacteristics.R:484:3
2. └─cli::cli_abort(c(`!` = "`con` must be a DBI connection"))
3. └─rlang::abort(...)
[ FAIL 3 | WARN 0 | SKIP 11 | PASS 82 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.2.0
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘a05_summariseCohortEntries.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 ‘a05_summariseCohortEntries.Rmd’
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
--- re-building ‘a06_summarisePatientCharacteristics.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 78-86 [unnamed-chunk-5] (a06_summarisePatientCharacteristics.Rmd)
Error: processing vignette 'a06_summarisePatientCharacteristics.Rmd' failed with diagnostics:
the condition has length > 1
--- failed re-building ‘a06_summarisePatientCharacteristics.Rmd’
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
--- re-building ‘a07_summariseLargeScaleCharacteristics.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 ‘a07_summariseLargeScaleCharacteristics.Rmd’
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
--- re-building ‘a08_summariseCohortOverlap.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/CohortCharacteristics.Rcheck/vign_test/CohortCharacteristics/vignettes/a08_summariseCohortOverlap_files/figure-html/unnamed-chunk-5-1.png
1344x960 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 37316 bytes
Input file size = 37442 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 33427
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 = 32928
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 = 32928
Output IDAT size = 32928 bytes (4388 bytes decrease)
Output file size = 33006 bytes (4436 bytes = 11.85% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/CohortCharacteristics.Rcheck/vign_test/CohortCharacteristics/vignettes/a08_summariseCohortOverlap_files/figure-html/unnamed-chunk-8-1.png
1344x960 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 66151 bytes
Input file size = 66325 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 53846
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 = 53846
Output IDAT size = 53846 bytes (12305 bytes decrease)
Output file size = 53924 bytes (12401 bytes = 18.70% decrease)
--- finished re-building ‘a08_summariseCohortOverlap.Rmd’
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
--- re-building ‘a09_summariseCohortTiming.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/CohortCharacteristics.Rcheck/vign_test/CohortCharacteristics/vignettes/a09_summariseCohortTiming_files/figure-html/unnamed-chunk-5-1.png
1344x960 pixels, 8 bits/pixel, 255 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 17931 bytes
Input file size = 18810 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 14167
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 = 11762
zc = 9 zm = 8 zs = 1 f = 5 IDAT size = 11690
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 1 f = 5 IDAT size = 11690
Output IDAT size = 11690 bytes (6241 bytes decrease)
Output file size = 11768 bytes (7042 bytes = 37.44% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/CohortCharacteristics.Rcheck/vign_test/CohortCharacteristics/vignettes/a09_summariseCohortTiming_files/figure-html/unnamed-chunk-6-1.png
1344x960 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 46347 bytes
Input file size = 47265 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 41285
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 = 41285
Output IDAT size = 41285 bytes (5062 bytes decrease)
Output file size = 41363 bytes (5902 bytes = 12.49% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/CohortCharacteristics.Rcheck/vign_test/CohortCharacteristics/vignettes/a09_summariseCohortTiming_files/figure-html/unnamed-chunk-7-1.png
1344x960 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 64596 bytes
Input file size = 64758 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 56755
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 = 56755
Output IDAT size = 56755 bytes (7841 bytes decrease)
Output file size = 56833 bytes (7925 bytes = 12.24% decrease)
--- finished re-building ‘a09_summariseCohortTiming.Rmd’
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
SUMMARY: processing the following file failed:
‘a06_summarisePatientCharacteristics.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.2.0
Check: installed package size
Result: NOTE
installed size is 6.2Mb
sub-directories of 1Mb or more:
doc 5.6Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-windows-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64
Version: 0.2.0
Check: dependencies in R code
Result: NOTE
Namespaces in Imports field not imported from:
‘lifecycle’ ‘lubridate’
All declared Imports should be used.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 0.2.0
Check: tests
Result: ERROR
Running ‘spelling.R’
Running ‘testthat.R’ [115s/68s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(CohortCharacteristics)
>
> test_check("CohortCharacteristics")
Starting 2 test processes
[ FAIL 3 | WARN 0 | SKIP 11 | PASS 82 ]
══ Skipped tests (11) ══════════════════════════════════════════════════════════
• On CRAN (10): 'test-plotCharacteristics.R:2:3',
'test-plotLargeScaleCharacteristics.R:3:3', 'test-plotSummarised.R:2:3',
'test-plotSummarised.R:91:3', 'test-plotSummarised.R:197:3',
'test-plotSummarised.R:299:3',
'test-summariseLargeScaleCharacteristics.R:2:3',
'test-tableSummarised.R:2:3', 'test-tableSummarised.R:123:3',
'test-summariseCharacteristics.R:1122:3'
• empty test (1): 'test-tableSummarised.R:262:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-summariseCharacteristics.R:53:3'): test summariseCharacteristics ──
Error in `mockCohortCharacteristics(connectionDetails, dus_cohort = dus_cohort,
person = person, comorbidities = comorbidities, medication = medication,
observation_period = observation_period, cohort1 = emptyCohort,
cohort2 = emptyCohort)`: ! `con` must be a DBI connection
Backtrace:
▆
1. └─PatientProfiles (local) mockCohortCharacteristics(...) at test-summariseCharacteristics.R:53:3
2. └─cli::cli_abort(c(`!` = "`con` must be a DBI connection"))
3. └─rlang::abort(...)
── Error ('test-summariseCharacteristics.R:378:3'): test empty cohort ──────────
Error in `mockCohortCharacteristics(connectionDetails = connectionDetails)`: tables must be a list; it can not contain NA; it can not be NULL; it has to be named; elements must have class: data.frame.
Backtrace:
▆
1. └─PatientProfiles (local) mockCohortCharacteristics(connectionDetails = connectionDetails) at test-summariseCharacteristics.R:378:3
2. └─PatientProfiles:::assertList(tables, named = TRUE, class = "data.frame")
3. └─cli::cli_abort(errorMessage, call = call)
4. └─rlang::abort(...)
── Error ('test-summariseCharacteristics.R:484:3'): test cohort id ─────────────
Error in `mockCohortCharacteristics(connectionDetails, dus_cohort = dus_cohort,
person = person, comorbidities = comorbidities, medication = medication,
observation_period = observation_period, cohort1 = emptyCohort,
cohort2 = emptyCohort)`: ! `con` must be a DBI connection
Backtrace:
▆
1. └─PatientProfiles (local) mockCohortCharacteristics(...) at test-summariseCharacteristics.R:484:3
2. └─cli::cli_abort(c(`!` = "`con` must be a DBI connection"))
3. └─rlang::abort(...)
[ FAIL 3 | WARN 0 | SKIP 11 | PASS 82 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.2.0
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘a05_summariseCohortEntries.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 ‘a05_summariseCohortEntries.Rmd’
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
--- re-building ‘a06_summarisePatientCharacteristics.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 78-86 [unnamed-chunk-5] (a06_summarisePatientCharacteristics.Rmd)
Error: processing vignette 'a06_summarisePatientCharacteristics.Rmd' failed with diagnostics:
the condition has length > 1
--- failed re-building ‘a06_summarisePatientCharacteristics.Rmd’
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
--- re-building ‘a07_summariseLargeScaleCharacteristics.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 ‘a07_summariseLargeScaleCharacteristics.Rmd’
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
--- re-building ‘a08_summariseCohortOverlap.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/CohortCharacteristics.Rcheck/vign_test/CohortCharacteristics/vignettes/a08_summariseCohortOverlap_files/figure-html/unnamed-chunk-5-1.png
1344x960 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 37316 bytes
Input file size = 37442 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 33427
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 = 32928
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 = 32928
Output IDAT size = 32928 bytes (4388 bytes decrease)
Output file size = 33006 bytes (4436 bytes = 11.85% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/CohortCharacteristics.Rcheck/vign_test/CohortCharacteristics/vignettes/a08_summariseCohortOverlap_files/figure-html/unnamed-chunk-8-1.png
1344x960 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 66151 bytes
Input file size = 66325 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 53846
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 = 53846
Output IDAT size = 53846 bytes (12305 bytes decrease)
Output file size = 53924 bytes (12401 bytes = 18.70% decrease)
--- finished re-building ‘a08_summariseCohortOverlap.Rmd’
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
--- re-building ‘a09_summariseCohortTiming.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/CohortCharacteristics.Rcheck/vign_test/CohortCharacteristics/vignettes/a09_summariseCohortTiming_files/figure-html/unnamed-chunk-5-1.png
1344x960 pixels, 8 bits/pixel, 255 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 17931 bytes
Input file size = 18810 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 14167
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 = 11762
zc = 9 zm = 8 zs = 1 f = 5 IDAT size = 11690
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 1 f = 5 IDAT size = 11690
Output IDAT size = 11690 bytes (6241 bytes decrease)
Output file size = 11768 bytes (7042 bytes = 37.44% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/CohortCharacteristics.Rcheck/vign_test/CohortCharacteristics/vignettes/a09_summariseCohortTiming_files/figure-html/unnamed-chunk-6-1.png
1344x960 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 46351 bytes
Input file size = 47269 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 41285
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 = 41285
Output IDAT size = 41285 bytes (5066 bytes decrease)
Output file size = 41363 bytes (5906 bytes = 12.49% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/CohortCharacteristics.Rcheck/vign_test/CohortCharacteristics/vignettes/a09_summariseCohortTiming_files/figure-html/unnamed-chunk-7-1.png
1344x960 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 64596 bytes
Input file size = 64758 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 56755
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 = 56755
Output IDAT size = 56755 bytes (7841 bytes decrease)
Output file size = 56833 bytes (7925 bytes = 12.24% decrease)
--- finished re-building ‘a09_summariseCohortTiming.Rmd’
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
SUMMARY: processing the following file failed:
‘a06_summarisePatientCharacteristics.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.2.0
Check: tests
Result: ERROR
Running ‘spelling.R’
Running ‘testthat.R’ [111s/66s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(CohortCharacteristics)
>
> test_check("CohortCharacteristics")
Starting 2 test processes
[ FAIL 3 | WARN 0 | SKIP 11 | PASS 82 ]
══ Skipped tests (11) ══════════════════════════════════════════════════════════
• On CRAN (10): 'test-plotCharacteristics.R:2:3',
'test-plotLargeScaleCharacteristics.R:3:3', 'test-plotSummarised.R:2:3',
'test-plotSummarised.R:91:3', 'test-plotSummarised.R:197:3',
'test-plotSummarised.R:299:3',
'test-summariseLargeScaleCharacteristics.R:2:3',
'test-tableSummarised.R:2:3', 'test-tableSummarised.R:123:3',
'test-summariseCharacteristics.R:1122:3'
• empty test (1): 'test-tableSummarised.R:262:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-summariseCharacteristics.R:53:3'): test summariseCharacteristics ──
Error in `mockCohortCharacteristics(connectionDetails, dus_cohort = dus_cohort,
person = person, comorbidities = comorbidities, medication = medication,
observation_period = observation_period, cohort1 = emptyCohort,
cohort2 = emptyCohort)`: ! `con` must be a DBI connection
Backtrace:
▆
1. └─PatientProfiles (local) mockCohortCharacteristics(...) at test-summariseCharacteristics.R:53:3
2. └─cli::cli_abort(c(`!` = "`con` must be a DBI connection"))
3. └─rlang::abort(...)
── Error ('test-summariseCharacteristics.R:378:3'): test empty cohort ──────────
Error in `mockCohortCharacteristics(connectionDetails = connectionDetails)`: tables must be a list; it can not contain NA; it can not be NULL; it has to be named; elements must have class: data.frame.
Backtrace:
▆
1. └─PatientProfiles (local) mockCohortCharacteristics(connectionDetails = connectionDetails) at test-summariseCharacteristics.R:378:3
2. └─PatientProfiles:::assertList(tables, named = TRUE, class = "data.frame")
3. └─cli::cli_abort(errorMessage, call = call)
4. └─rlang::abort(...)
── Error ('test-summariseCharacteristics.R:484:3'): test cohort id ─────────────
Error in `mockCohortCharacteristics(connectionDetails, dus_cohort = dus_cohort,
person = person, comorbidities = comorbidities, medication = medication,
observation_period = observation_period, cohort1 = emptyCohort,
cohort2 = emptyCohort)`: ! `con` must be a DBI connection
Backtrace:
▆
1. └─PatientProfiles (local) mockCohortCharacteristics(...) at test-summariseCharacteristics.R:484:3
2. └─cli::cli_abort(c(`!` = "`con` must be a DBI connection"))
3. └─rlang::abort(...)
[ FAIL 3 | WARN 0 | SKIP 11 | PASS 82 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 0.2.0
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘a05_summariseCohortEntries.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 ‘a05_summariseCohortEntries.Rmd’
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
--- re-building ‘a06_summarisePatientCharacteristics.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 78-86 [unnamed-chunk-5] (a06_summarisePatientCharacteristics.Rmd)
Error: processing vignette 'a06_summarisePatientCharacteristics.Rmd' failed with diagnostics:
the condition has length > 1
--- failed re-building ‘a06_summarisePatientCharacteristics.Rmd’
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
--- re-building ‘a07_summariseLargeScaleCharacteristics.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 ‘a07_summariseLargeScaleCharacteristics.Rmd’
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
--- re-building ‘a08_summariseCohortOverlap.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/CohortCharacteristics.Rcheck/vign_test/CohortCharacteristics/vignettes/a08_summariseCohortOverlap_files/figure-html/unnamed-chunk-5-1.png
1344x960 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 37316 bytes
Input file size = 37442 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 33427
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 = 32928
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 = 32928
Output IDAT size = 32928 bytes (4388 bytes decrease)
Output file size = 33006 bytes (4436 bytes = 11.85% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/CohortCharacteristics.Rcheck/vign_test/CohortCharacteristics/vignettes/a08_summariseCohortOverlap_files/figure-html/unnamed-chunk-8-1.png
1344x960 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 66151 bytes
Input file size = 66325 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 53846
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 = 53846
Output IDAT size = 53846 bytes (12305 bytes decrease)
Output file size = 53924 bytes (12401 bytes = 18.70% decrease)
--- finished re-building ‘a08_summariseCohortOverlap.Rmd’
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
--- re-building ‘a09_summariseCohortTiming.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/CohortCharacteristics.Rcheck/vign_test/CohortCharacteristics/vignettes/a09_summariseCohortTiming_files/figure-html/unnamed-chunk-5-1.png
1344x960 pixels, 8 bits/pixel, 255 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 17931 bytes
Input file size = 18810 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 14167
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 = 11762
zc = 9 zm = 8 zs = 1 f = 5 IDAT size = 11690
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 1 f = 5 IDAT size = 11690
Output IDAT size = 11690 bytes (6241 bytes decrease)
Output file size = 11768 bytes (7042 bytes = 37.44% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/CohortCharacteristics.Rcheck/vign_test/CohortCharacteristics/vignettes/a09_summariseCohortTiming_files/figure-html/unnamed-chunk-6-1.png
1344x960 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 46351 bytes
Input file size = 47269 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 41285
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 = 41285
Output IDAT size = 41285 bytes (5066 bytes decrease)
Output file size = 41363 bytes (5906 bytes = 12.49% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/CohortCharacteristics.Rcheck/vign_test/CohortCharacteristics/vignettes/a09_summariseCohortTiming_files/figure-html/unnamed-chunk-7-1.png
1344x960 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 64596 bytes
Input file size = 64758 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 56755
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 = 56755
Output IDAT size = 56755 bytes (7841 bytes decrease)
Output file size = 56833 bytes (7925 bytes = 12.24% decrease)
--- finished re-building ‘a09_summariseCohortTiming.Rmd’
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
SUMMARY: processing the following file failed:
‘a06_summarisePatientCharacteristics.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 0.2.0
Check: tests
Result: ERROR
Running 'spelling.R' [0s]
Running 'testthat.R' [58s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(CohortCharacteristics)
>
> test_check("CohortCharacteristics")
Starting 2 test processes
[ FAIL 3 | WARN 0 | SKIP 11 | PASS 82 ]
══ Skipped tests (11) ══════════════════════════════════════════════════════════
• On CRAN (10): 'test-plotCharacteristics.R:2:3',
'test-plotLargeScaleCharacteristics.R:3:3', 'test-plotSummarised.R:2:3',
'test-plotSummarised.R:91:3', 'test-plotSummarised.R:197:3',
'test-plotSummarised.R:299:3',
'test-summariseLargeScaleCharacteristics.R:2:3',
'test-tableSummarised.R:2:3', 'test-tableSummarised.R:123:3',
'test-summariseCharacteristics.R:1122:3'
• empty test (1): 'test-tableSummarised.R:262:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-summariseCharacteristics.R:53:3'): test summariseCharacteristics ──
Error in `mockCohortCharacteristics(connectionDetails, dus_cohort = dus_cohort,
person = person, comorbidities = comorbidities, medication = medication,
observation_period = observation_period, cohort1 = emptyCohort,
cohort2 = emptyCohort)`: ! `con` must be a DBI connection
Backtrace:
▆
1. └─PatientProfiles (local) mockCohortCharacteristics(...) at test-summariseCharacteristics.R:53:3
2. └─cli::cli_abort(c(`!` = "`con` must be a DBI connection"))
3. └─rlang::abort(...)
── Error ('test-summariseCharacteristics.R:378:3'): test empty cohort ──────────
Error in `mockCohortCharacteristics(connectionDetails = connectionDetails)`: tables must be a list; it can not contain NA; it can not be NULL; it has to be named; elements must have class: data.frame.
Backtrace:
▆
1. └─PatientProfiles (local) mockCohortCharacteristics(connectionDetails = connectionDetails) at test-summariseCharacteristics.R:378:3
2. └─PatientProfiles:::assertList(tables, named = TRUE, class = "data.frame")
3. └─cli::cli_abort(errorMessage, call = call)
4. └─rlang::abort(...)
── Error ('test-summariseCharacteristics.R:484:3'): test cohort id ─────────────
Error in `mockCohortCharacteristics(connectionDetails, dus_cohort = dus_cohort,
person = person, comorbidities = comorbidities, medication = medication,
observation_period = observation_period, cohort1 = emptyCohort,
cohort2 = emptyCohort)`: ! `con` must be a DBI connection
Backtrace:
▆
1. └─PatientProfiles (local) mockCohortCharacteristics(...) at test-summariseCharacteristics.R:484:3
2. └─cli::cli_abort(c(`!` = "`con` must be a DBI connection"))
3. └─rlang::abort(...)
[ FAIL 3 | WARN 0 | SKIP 11 | PASS 82 ]
Error: Test failures
Execution halted
Flavors: r-devel-windows-x86_64, r-release-windows-x86_64
Version: 0.2.0
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building 'a05_summariseCohortEntries.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 'a05_summariseCohortEntries.Rmd'
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
--- re-building 'a06_summarisePatientCharacteristics.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 78-86 [unnamed-chunk-5] (a06_summarisePatientCharacteristics.Rmd)
Error: processing vignette 'a06_summarisePatientCharacteristics.Rmd' failed with diagnostics:
the condition has length > 1
--- failed re-building 'a06_summarisePatientCharacteristics.Rmd'
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
--- re-building 'a07_summariseLargeScaleCharacteristics.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 'a07_summariseLargeScaleCharacteristics.Rmd'
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
--- re-building 'a08_summariseCohortOverlap.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 'a08_summariseCohortOverlap.Rmd'
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
--- re-building 'a09_summariseCohortTiming.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 'a09_summariseCohortTiming.Rmd'
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
SUMMARY: processing the following file failed:
'a06_summarisePatientCharacteristics.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: 0.2.0
Check: tests
Result: ERROR
Running ‘spelling.R’ [0s/1s]
Running ‘testthat.R’ [161s/124s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(CohortCharacteristics)
>
> test_check("CohortCharacteristics")
Starting 2 test processes
[ FAIL 3 | WARN 0 | SKIP 11 | PASS 82 ]
══ Skipped tests (11) ══════════════════════════════════════════════════════════
• On CRAN (10): 'test-plotCharacteristics.R:2:3',
'test-plotLargeScaleCharacteristics.R:3:3', 'test-plotSummarised.R:2:3',
'test-plotSummarised.R:91:3', 'test-plotSummarised.R:197:3',
'test-plotSummarised.R:299:3',
'test-summariseLargeScaleCharacteristics.R:2:3',
'test-tableSummarised.R:2:3', 'test-tableSummarised.R:123:3',
'test-summariseCharacteristics.R:1122:3'
• empty test (1): 'test-tableSummarised.R:262:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-summariseCharacteristics.R:53:3'): test summariseCharacteristics ──
Error in `mockCohortCharacteristics(connectionDetails, dus_cohort = dus_cohort,
person = person, comorbidities = comorbidities, medication = medication,
observation_period = observation_period, cohort1 = emptyCohort,
cohort2 = emptyCohort)`: ! `con` must be a DBI connection
Backtrace:
▆
1. └─PatientProfiles (local) mockCohortCharacteristics(...) at test-summariseCharacteristics.R:53:3
2. └─cli::cli_abort(c(`!` = "`con` must be a DBI connection"))
3. └─rlang::abort(...)
── Error ('test-summariseCharacteristics.R:378:3'): test empty cohort ──────────
Error in `mockCohortCharacteristics(connectionDetails = connectionDetails)`: tables must be a list; it can not contain NA; it can not be NULL; it has to be named; elements must have class: data.frame.
Backtrace:
▆
1. └─PatientProfiles (local) mockCohortCharacteristics(connectionDetails = connectionDetails) at test-summariseCharacteristics.R:378:3
2. └─PatientProfiles:::assertList(tables, named = TRUE, class = "data.frame")
3. └─cli::cli_abort(errorMessage, call = call)
4. └─rlang::abort(...)
── Error ('test-summariseCharacteristics.R:484:3'): test cohort id ─────────────
Error in `mockCohortCharacteristics(connectionDetails, dus_cohort = dus_cohort,
person = person, comorbidities = comorbidities, medication = medication,
observation_period = observation_period, cohort1 = emptyCohort,
cohort2 = emptyCohort)`: ! `con` must be a DBI connection
Backtrace:
▆
1. └─PatientProfiles (local) mockCohortCharacteristics(...) at test-summariseCharacteristics.R:484:3
2. └─cli::cli_abort(c(`!` = "`con` must be a DBI connection"))
3. └─rlang::abort(...)
[ FAIL 3 | WARN 0 | SKIP 11 | PASS 82 ]
Error: Test failures
Execution halted
Flavor: r-patched-linux-x86_64
Version: 0.2.0
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘a05_summariseCohortEntries.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 ‘a05_summariseCohortEntries.Rmd’
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
--- re-building ‘a06_summarisePatientCharacteristics.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 78-86 [unnamed-chunk-5] (a06_summarisePatientCharacteristics.Rmd)
Error: processing vignette 'a06_summarisePatientCharacteristics.Rmd' failed with diagnostics:
the condition has length > 1
--- failed re-building ‘a06_summarisePatientCharacteristics.Rmd’
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
--- re-building ‘a07_summariseLargeScaleCharacteristics.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 ‘a07_summariseLargeScaleCharacteristics.Rmd’
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
--- re-building ‘a08_summariseCohortOverlap.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/CohortCharacteristics.Rcheck/vign_test/CohortCharacteristics/vignettes/a08_summariseCohortOverlap_files/figure-html/unnamed-chunk-5-1.png
1344x960 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 37316 bytes
Input file size = 37442 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 33427
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 = 32928
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 = 32928
Output IDAT size = 32928 bytes (4388 bytes decrease)
Output file size = 33006 bytes (4436 bytes = 11.85% decrease)
** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/CohortCharacteristics.Rcheck/vign_test/CohortCharacteristics/vignettes/a08_summariseCohortOverlap_files/figure-html/unnamed-chunk-8-1.png
1344x960 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 66151 bytes
Input file size = 66325 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 53846
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 = 53846
Output IDAT size = 53846 bytes (12305 bytes decrease)
Output file size = 53924 bytes (12401 bytes = 18.70% decrease)
--- finished re-building ‘a08_summariseCohortOverlap.Rmd’
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
--- re-building ‘a09_summariseCohortTiming.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/CohortCharacteristics.Rcheck/vign_test/CohortCharacteristics/vignettes/a09_summariseCohortTiming_files/figure-html/unnamed-chunk-5-1.png
1344x960 pixels, 8 bits/pixel, 255 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 17931 bytes
Input file size = 18810 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 14167
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 = 11762
zc = 9 zm = 8 zs = 1 f = 5 IDAT size = 11690
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 1 f = 5 IDAT size = 11690
Output IDAT size = 11690 bytes (6241 bytes decrease)
Output file size = 11768 bytes (7042 bytes = 37.44% decrease)
** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/CohortCharacteristics.Rcheck/vign_test/CohortCharacteristics/vignettes/a09_summariseCohortTiming_files/figure-html/unnamed-chunk-6-1.png
1344x960 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 46347 bytes
Input file size = 47265 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 41285
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 = 41285
Output IDAT size = 41285 bytes (5062 bytes decrease)
Output file size = 41363 bytes (5902 bytes = 12.49% decrease)
** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/CohortCharacteristics.Rcheck/vign_test/CohortCharacteristics/vignettes/a09_summariseCohortTiming_files/figure-html/unnamed-chunk-7-1.png
1344x960 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 64596 bytes
Input file size = 64758 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 56755
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 = 56755
Output IDAT size = 56755 bytes (7841 bytes decrease)
Output file size = 56833 bytes (7925 bytes = 12.24% decrease)
--- finished re-building ‘a09_summariseCohortTiming.Rmd’
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
SUMMARY: processing the following file failed:
‘a06_summarisePatientCharacteristics.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-patched-linux-x86_64
Version: 0.2.0
Check: tests
Result: ERROR
Running ‘spelling.R’ [0s/1s]
Running ‘testthat.R’ [162s/143s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(CohortCharacteristics)
>
> test_check("CohortCharacteristics")
Starting 2 test processes
[ FAIL 3 | WARN 0 | SKIP 11 | PASS 82 ]
══ Skipped tests (11) ══════════════════════════════════════════════════════════
• On CRAN (10): 'test-plotCharacteristics.R:2:3',
'test-plotLargeScaleCharacteristics.R:3:3', 'test-plotSummarised.R:2:3',
'test-plotSummarised.R:91:3', 'test-plotSummarised.R:197:3',
'test-plotSummarised.R:299:3',
'test-summariseLargeScaleCharacteristics.R:2:3',
'test-tableSummarised.R:2:3', 'test-tableSummarised.R:123:3',
'test-summariseCharacteristics.R:1122:3'
• empty test (1): 'test-tableSummarised.R:262:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-summariseCharacteristics.R:53:3'): test summariseCharacteristics ──
Error in `mockCohortCharacteristics(connectionDetails, dus_cohort = dus_cohort,
person = person, comorbidities = comorbidities, medication = medication,
observation_period = observation_period, cohort1 = emptyCohort,
cohort2 = emptyCohort)`: ! `con` must be a DBI connection
Backtrace:
▆
1. └─PatientProfiles (local) mockCohortCharacteristics(...) at test-summariseCharacteristics.R:53:3
2. └─cli::cli_abort(c(`!` = "`con` must be a DBI connection"))
3. └─rlang::abort(...)
── Error ('test-summariseCharacteristics.R:378:3'): test empty cohort ──────────
Error in `mockCohortCharacteristics(connectionDetails = connectionDetails)`: tables must be a list; it can not contain NA; it can not be NULL; it has to be named; elements must have class: data.frame.
Backtrace:
▆
1. └─PatientProfiles (local) mockCohortCharacteristics(connectionDetails = connectionDetails) at test-summariseCharacteristics.R:378:3
2. └─PatientProfiles:::assertList(tables, named = TRUE, class = "data.frame")
3. └─cli::cli_abort(errorMessage, call = call)
4. └─rlang::abort(...)
── Error ('test-summariseCharacteristics.R:484:3'): test cohort id ─────────────
Error in `mockCohortCharacteristics(connectionDetails, dus_cohort = dus_cohort,
person = person, comorbidities = comorbidities, medication = medication,
observation_period = observation_period, cohort1 = emptyCohort,
cohort2 = emptyCohort)`: ! `con` must be a DBI connection
Backtrace:
▆
1. └─PatientProfiles (local) mockCohortCharacteristics(...) at test-summariseCharacteristics.R:484:3
2. └─cli::cli_abort(c(`!` = "`con` must be a DBI connection"))
3. └─rlang::abort(...)
[ FAIL 3 | WARN 0 | SKIP 11 | PASS 82 ]
Error: Test failures
Execution halted
Flavor: r-release-linux-x86_64
Version: 0.2.0
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘a05_summariseCohortEntries.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 ‘a05_summariseCohortEntries.Rmd’
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
--- re-building ‘a06_summarisePatientCharacteristics.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 78-86 [unnamed-chunk-5] (a06_summarisePatientCharacteristics.Rmd)
Error: processing vignette 'a06_summarisePatientCharacteristics.Rmd' failed with diagnostics:
the condition has length > 1
--- failed re-building ‘a06_summarisePatientCharacteristics.Rmd’
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
--- re-building ‘a07_summariseLargeScaleCharacteristics.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 ‘a07_summariseLargeScaleCharacteristics.Rmd’
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
--- re-building ‘a08_summariseCohortOverlap.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/CohortCharacteristics.Rcheck/vign_test/CohortCharacteristics/vignettes/a08_summariseCohortOverlap_files/figure-html/unnamed-chunk-5-1.png
1344x960 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 37316 bytes
Input file size = 37442 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 33427
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 = 32928
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 = 32928
Output IDAT size = 32928 bytes (4388 bytes decrease)
Output file size = 33006 bytes (4436 bytes = 11.85% decrease)
** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/CohortCharacteristics.Rcheck/vign_test/CohortCharacteristics/vignettes/a08_summariseCohortOverlap_files/figure-html/unnamed-chunk-8-1.png
1344x960 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 66151 bytes
Input file size = 66325 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 53846
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 = 53846
Output IDAT size = 53846 bytes (12305 bytes decrease)
Output file size = 53924 bytes (12401 bytes = 18.70% decrease)
--- finished re-building ‘a08_summariseCohortOverlap.Rmd’
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
--- re-building ‘a09_summariseCohortTiming.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/CohortCharacteristics.Rcheck/vign_test/CohortCharacteristics/vignettes/a09_summariseCohortTiming_files/figure-html/unnamed-chunk-5-1.png
1344x960 pixels, 8 bits/pixel, 255 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 17931 bytes
Input file size = 18810 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 14167
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 = 11762
zc = 9 zm = 8 zs = 1 f = 5 IDAT size = 11690
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 1 f = 5 IDAT size = 11690
Output IDAT size = 11690 bytes (6241 bytes decrease)
Output file size = 11768 bytes (7042 bytes = 37.44% decrease)
** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/CohortCharacteristics.Rcheck/vign_test/CohortCharacteristics/vignettes/a09_summariseCohortTiming_files/figure-html/unnamed-chunk-6-1.png
1344x960 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 46347 bytes
Input file size = 47265 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 41285
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 = 41285
Output IDAT size = 41285 bytes (5062 bytes decrease)
Output file size = 41363 bytes (5902 bytes = 12.49% decrease)
** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/CohortCharacteristics.Rcheck/vign_test/CohortCharacteristics/vignettes/a09_summariseCohortTiming_files/figure-html/unnamed-chunk-7-1.png
1344x960 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 64596 bytes
Input file size = 64758 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 56755
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 = 56755
Output IDAT size = 56755 bytes (7841 bytes decrease)
Output file size = 56833 bytes (7925 bytes = 12.24% decrease)
--- finished re-building ‘a09_summariseCohortTiming.Rmd’
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
SUMMARY: processing the following file failed:
‘a06_summarisePatientCharacteristics.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-release-linux-x86_64
Version: 0.2.0
Check: for code/documentation mismatches
Result: WARN
Codoc mismatches from documentation object 'mockCohortCharacteristics':
mockCohortCharacteristics
Code: function(con = NULL, writeSchema = NULL, numberIndividuals =
10, ..., seed = NULL)
Docs: function(connectionDetails = list(con =
DBI::dbConnect(duckdb::duckdb(), ":memory:"),
write_schema = "main", mock_prefix = NULL),
drug_exposure = NULL, drug_strength = NULL,
observation_period = NULL, condition_occurrence =
NULL, visit_occurrence = NULL, concept_ancestor =
NULL, person = NULL, death = NULL, cohort1 = NULL,
cohort2 = NULL, drug_concept_id_size = 5,
ancestor_concept_id_size = 5,
condition_concept_id_size = 5, visit_concept_id_size =
5, visit_occurrence_id_size = 5,
ingredient_concept_id_size = 1, drug_exposure_size =
10, patient_size = 1, min_drug_exposure_start_date =
"2000-01-01", max_drug_exposure_start_date =
"2020-01-01", earliest_date_of_birth = NULL,
latest_date_of_birth = NULL,
earliest_observation_start_date = NULL,
latest_observation_start_date = NULL,
min_days_to_observation_end = NULL,
max_days_to_observation_end = NULL,
earliest_condition_start_date = NULL,
latest_condition_start_date = NULL,
min_days_to_condition_end = NULL,
max_days_to_condition_end = NULL,
earliest_visit_start_date = NULL,
latest_visit_start_date = NULL, min_days_to_visit_end
= NULL, max_days_to_visit_end = NULL, seed = 1, ...)
Argument names in code not in docs:
con writeSchema numberIndividuals
Argument names in docs not in code:
connectionDetails drug_exposure drug_strength observation_period
condition_occurrence visit_occurrence concept_ancestor person death
cohort1 cohort2 drug_concept_id_size ancestor_concept_id_size
condition_concept_id_size visit_concept_id_size
visit_occurrence_id_size ingredient_concept_id_size
drug_exposure_size patient_size min_drug_exposure_start_date
max_drug_exposure_start_date earliest_date_of_birth
latest_date_of_birth earliest_observation_start_date
latest_observation_start_date min_days_to_observation_end
max_days_to_observation_end earliest_condition_start_date
latest_condition_start_date min_days_to_condition_end
max_days_to_condition_end earliest_visit_start_date
latest_visit_start_date min_days_to_visit_end max_days_to_visit_end
Mismatches in argument names (first 3):
Position: 1 Code: con Docs: connectionDetails
Position: 2 Code: writeSchema Docs: drug_exposure
Position: 3 Code: numberIndividuals Docs: drug_strength
Mismatches in argument default values:
Name: 'seed' Code: NULL Docs: 1
Flavor: r-oldrel-windows-x86_64
Version: 0.2.0
Check: tests
Result: ERROR
Running 'spelling.R' [0s]
Running 'testthat.R' [85s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(CohortCharacteristics)
>
> test_check("CohortCharacteristics")
Starting 2 test processes
[ FAIL 3 | WARN 0 | SKIP 11 | PASS 82 ]
══ Skipped tests (11) ══════════════════════════════════════════════════════════
• On CRAN (10): 'test-plotCharacteristics.R:2:3',
'test-plotLargeScaleCharacteristics.R:3:3', 'test-plotSummarised.R:2:3',
'test-plotSummarised.R:91:3', 'test-plotSummarised.R:197:3',
'test-plotSummarised.R:299:3',
'test-summariseLargeScaleCharacteristics.R:2:3',
'test-tableSummarised.R:2:3', 'test-tableSummarised.R:123:3',
'test-summariseCharacteristics.R:1122:3'
• empty test (1): 'test-tableSummarised.R:262:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-summariseCharacteristics.R:53:3'): test summariseCharacteristics ──
Error in `mockCohortCharacteristics(connectionDetails, dus_cohort = dus_cohort,
person = person, comorbidities = comorbidities, medication = medication,
observation_period = observation_period, cohort1 = emptyCohort,
cohort2 = emptyCohort)`: ! `con` must be a DBI connection
Backtrace:
▆
1. └─PatientProfiles (local) mockCohortCharacteristics(...) at test-summariseCharacteristics.R:53:3
2. └─cli::cli_abort(c(`!` = "`con` must be a DBI connection"))
3. └─rlang::abort(...)
── Error ('test-summariseCharacteristics.R:378:3'): test empty cohort ──────────
Error in `mockCohortCharacteristics(connectionDetails = connectionDetails)`: tables must be a list; it can not contain NA; it can not be NULL; it has to be named; elements must have class: data.frame.
Backtrace:
▆
1. └─PatientProfiles (local) mockCohortCharacteristics(connectionDetails = connectionDetails) at test-summariseCharacteristics.R:378:3
2. └─PatientProfiles:::assertList(tables, named = TRUE, class = "data.frame")
3. └─cli::cli_abort(errorMessage, call = call)
4. └─rlang::abort(...)
── Error ('test-summariseCharacteristics.R:484:3'): test cohort id ─────────────
Error in `mockCohortCharacteristics(connectionDetails, dus_cohort = dus_cohort,
person = person, comorbidities = comorbidities, medication = medication,
observation_period = observation_period, cohort1 = emptyCohort,
cohort2 = emptyCohort)`: ! `con` must be a DBI connection
Backtrace:
▆
1. └─PatientProfiles (local) mockCohortCharacteristics(...) at test-summariseCharacteristics.R:484:3
2. └─cli::cli_abort(c(`!` = "`con` must be a DBI connection"))
3. └─rlang::abort(...)
[ FAIL 3 | WARN 0 | SKIP 11 | PASS 82 ]
Error: Test failures
Execution halted
Flavor: r-oldrel-windows-x86_64