Last updated on 2026-02-17 09:50:09 CET.
| Package | ERROR | NOTE | OK |
|---|---|---|---|
| CohortCharacteristics | 1 | 2 | 11 |
| DrugUtilisation | 14 | ||
| OmopConstructor | 1 | 13 | |
| omopgenerics | 14 | ||
| OmopViewer | 1 | 13 | |
| PatientProfiles | 1 | 13 |
Current CRAN status: ERROR: 1, NOTE: 2, OK: 11
Version: 1.1.1
Check: installed package size
Result: NOTE
installed size is 5.6Mb
sub-directories of 1Mb or more:
doc 3.6Mb
help 1.8Mb
Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64
Version: 1.1.1
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(numberIndividuals = 10, ..., source = "local", con =
lifecycle::deprecated(), writeSchema =
lifecycle::deprecated(), seed =
lifecycle::deprecated())
Argument names in docs not in code:
source
Mismatches in argument names (first 3):
Position: 1 Code: con Docs: numberIndividuals
Position: 2 Code: writeSchema Docs: ...
Position: 3 Code: numberIndividuals Docs: source
Mismatches in argument default values:
Name: 'con' Code: NULL Docs: lifecycle::deprecated()
Name: 'writeSchema' Code: NULL Docs: lifecycle::deprecated()
Name: 'seed' Code: NULL Docs: lifecycle::deprecated()
Flavor: r-oldrel-macos-x86_64
Version: 1.1.1
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘summarise_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 summarise_characteristics.Rmd:24-49 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `loadNamespace()`:
! there is no package called 'arrow'
---
Backtrace:
▆
1. ├─omock::mockCdmFromDataset(datasetName = "GiBleed", source = "duckdb")
2. │ └─omock:::readTables(tmpFolder, cv)
3. │ └─omock:::castColumns(...)
4. │ ├─dplyr::filter(...)
5. │ ├─dplyr:::filter.data.frame(...)
6. │ │ └─dplyr:::filter_impl(...)
7. │ │ └─dplyr:::dplyr_quosures(...)
8. │ │ └─rlang::quos(..., .ignore_empty = "all")
9. │ └─base::colnames(x)
10. │ └─base::is.data.frame(x)
11. └─base::loadNamespace(x)
12. └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
13. └─base (local) withOneRestart(expr, restarts[[1L]])
14. └─base (local) doWithOneRestart(return(expr), restart)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'summarise_characteristics.Rmd' failed with diagnostics:
there is no package called 'arrow'
--- failed re-building ‘summarise_characteristics.Rmd’
--- re-building ‘summarise_cohort_overlap.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 summarise_cohort_overlap.Rmd:27-57 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `loadNamespace()`:
! there is no package called 'arrow'
---
Backtrace:
▆
1. ├─omock::mockCdmFromDataset(datasetName = "GiBleed", source = "duckdb")
2. │ └─omock:::readTables(tmpFolder, cv)
3. │ └─omock:::castColumns(...)
4. │ ├─dplyr::filter(...)
5. │ ├─dplyr:::filter.data.frame(...)
6. │ │ └─dplyr:::filter_impl(...)
7. │ │ └─dplyr:::dplyr_quosures(...)
8. │ │ └─rlang::quos(..., .ignore_empty = "all")
9. │ └─base::colnames(x)
10. │ └─base::is.data.frame(x)
11. └─base::loadNamespace(x)
12. └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
13. └─base (local) withOneRestart(expr, restarts[[1L]])
14. └─base (local) doWithOneRestart(return(expr), restart)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'summarise_cohort_overlap.Rmd' failed with diagnostics:
there is no package called 'arrow'
--- failed re-building ‘summarise_cohort_overlap.Rmd’
--- re-building ‘summarise_cohort_timing.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 summarise_cohort_timing.Rmd:25-55 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `loadNamespace()`:
! there is no package called 'arrow'
---
Backtrace:
▆
1. ├─omock::mockCdmFromDataset(datasetName = "GiBleed", source = "duckdb")
2. │ └─omock:::readTables(tmpFolder, cv)
3. │ └─omock:::castColumns(...)
4. │ ├─dplyr::filter(...)
5. │ ├─dplyr:::filter.data.frame(...)
6. │ │ └─dplyr:::filter_impl(...)
7. │ │ └─dplyr:::dplyr_quosures(...)
8. │ │ └─rlang::quos(..., .ignore_empty = "all")
9. │ └─base::colnames(x)
10. │ └─base::is.data.frame(x)
11. └─base::loadNamespace(x)
12. └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
13. └─base (local) withOneRestart(expr, restarts[[1L]])
14. └─base (local) doWithOneRestart(return(expr), restart)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'summarise_cohort_timing.Rmd' failed with diagnostics:
there is no package called 'arrow'
--- failed re-building ‘summarise_cohort_timing.Rmd’
--- re-building ‘summarise_large_scale_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 summarise_large_scale_characteristics.Rmd:31-48 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `loadNamespace()`:
! there is no package called 'arrow'
---
Backtrace:
▆
1. ├─omock::mockCdmFromDataset(datasetName = "GiBleed", source = "duckdb")
2. │ └─omock:::readTables(tmpFolder, cv)
3. │ └─omock:::castColumns(...)
4. │ ├─dplyr::filter(...)
5. │ ├─dplyr:::filter.data.frame(...)
6. │ │ └─dplyr:::filter_impl(...)
7. │ │ └─dplyr:::dplyr_quosures(...)
8. │ │ └─rlang::quos(..., .ignore_empty = "all")
9. │ └─base::colnames(x)
10. │ └─base::is.data.frame(x)
11. └─base::loadNamespace(x)
12. └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
13. └─base (local) withOneRestart(expr, restarts[[1L]])
14. └─base (local) doWithOneRestart(return(expr), restart)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'summarise_large_scale_characteristics.Rmd' failed with diagnostics:
there is no package called 'arrow'
--- failed re-building ‘summarise_large_scale_characteristics.Rmd’
SUMMARY: processing the following files failed:
‘summarise_characteristics.Rmd’ ‘summarise_cohort_overlap.Rmd’
‘summarise_cohort_timing.Rmd’
‘summarise_large_scale_characteristics.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-oldrel-macos-x86_64
Current CRAN status: OK: 14
Current CRAN status: ERROR: 1, OK: 13
Version: 0.2.0
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘buildObservationPeriod.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 buildObservationPeriod.Rmd:161-171 [unnamed-chunk-1]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `loadNamespace()`:
! there is no package called 'arrow'
---
Backtrace:
▆
1. ├─omock::mockCdmFromDataset(datasetName = "GiBleed", source = "duckdb")
2. │ └─omock:::readTables(tmpFolder, cv)
3. │ └─omock:::castColumns(...)
4. │ ├─dplyr::filter(...)
5. │ ├─dplyr:::filter.data.frame(...)
6. │ │ └─dplyr:::filter_impl(...)
7. │ │ └─dplyr:::dplyr_quosures(...)
8. │ │ └─rlang::quos(..., .ignore_empty = "all")
9. │ └─base::colnames(x)
10. │ └─base::is.data.frame(x)
11. └─base::loadNamespace(x)
12. └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
13. └─base (local) withOneRestart(expr, restarts[[1L]])
14. └─base (local) doWithOneRestart(return(expr), restart)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'buildObservationPeriod.Rmd' failed with diagnostics:
there is no package called 'arrow'
--- failed re-building ‘buildObservationPeriod.Rmd’
SUMMARY: processing the following file failed:
‘buildObservationPeriod.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-oldrel-macos-x86_64
Current CRAN status: OK: 14
Current CRAN status: ERROR: 1, OK: 13
Version: 0.7.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [26s/19s]
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(OmopViewer)
>
> test_check("OmopViewer")
Starting 2 test processes.
> test-background.R: i Processing data
> test-appStatic.R: i Processing data
> test-background.R: ! No panels identified, generated shiny will be empty.
> test-appStatic.R: ! No panels identified, generated shiny will be empty.
> test-background.R: i Creating `shiny` from provided data
> test-appStatic.R: i Creating `shiny` from provided data
> test-appStatic.R: v Shiny created in: /Volumes/Temp/tmp/Rtmp3VoEmB/shiny
> test-background.R: v Shiny created in: /Volumes/Temp/tmp/Rtmp1WPzcZ/shiny
> test-background.R: i Processing data
> test-appStatic.R: i Processing data
> test-background.R: ! No panels identified, generated shiny will be empty.
> test-appStatic.R: ! No panels identified, generated shiny will be empty.
> test-background.R: i Creating `shiny` from provided data
> test-appStatic.R: i Creating `shiny` from provided data
> test-background.R: v Shiny created in: /Volumes/Temp/tmp/Rtmp1WPzcZ/shiny
> test-appStatic.R: v Shiny created in: /Volumes/Temp/tmp/Rtmp3VoEmB/shiny
> test-background.R: i Processing data
> test-background.R: ! No panels identified, generated shiny will be empty.
> test-background.R: i Creating `shiny` from provided data
> test-appStatic.R: i Processing data
> test-appStatic.R: ! No panels identified, generated shiny will be empty.
> test-appStatic.R: i Creating `shiny` from provided data
> test-background.R: v Shiny created in: /Volumes/Temp/tmp/Rtmp1WPzcZ/shiny
> test-appStatic.R: v Shiny created in: /Volumes/Temp/tmp/Rtmp3VoEmB/shiny
> test-appStatic.R: i Processing data
> test-appStatic.R: ! No panels identified, generated shiny will be empty.
> test-appStatic.R: i Creating `shiny` from provided data
> test-appStatic.R: v Shiny created in: /Volumes/Temp/tmp/Rtmp3VoEmB/shiny
> test-appStatic.R: i Processing data
> test-appStatic.R: ! No panels identified, generated shiny will be empty.
> test-appStatic.R: i Creating `shiny` from provided data
> test-appStatic.R: v Shiny created in: /Volumes/Temp/tmp/Rtmp3VoEmB/shiny
> test-appStatic.R: i Processing data
> test-appStatic.R: ! No panels identified, generated shiny will be empty.
> test-appStatic.R: i Creating `shiny` from provided data
> test-summary.R: `result_type`, `package_name`, and `package_version` added to settings.
> test-appStatic.R: v Shiny created in: /Volumes/Temp/tmp/Rtmp3VoEmB/shiny
> test-appStatic.R: `package_name` and `package_version` added to settings.
> test-summary.R: `package_name` and `package_version` added to settings.
> test-appStatic.R: i Processing data
> test-appStatic.R: v Data processed: 1 panel idenfied: `custom_result`.
> test-appStatic.R: i Creating `shiny` from provided data
> test-appStatic.R: v Shiny created in: /Volumes/Temp/tmp/Rtmp3VoEmB/shiny
Saving _problems/test-appStatic-41.R
Saving _problems/test-appStatic-42.R
[ FAIL 2 | WARN 0 | SKIP 6 | PASS 83 ]
══ Skipped tests (6) ═══════════════════════════════════════════════════════════
• On CRAN (5): 'test-packagesSupported.R:2:3', 'test-appStatic.R:1:1',
'test-appStatic.R:46:1', 'test-appStatic.R:60:1', 'test-appStatic.R:80:3'
• manual test (1): 'test-functions.R:3:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-appStatic.R:41:3'): logo ─────────────────────────────────────
Expected `copyLogos(logo = logo, directory = tdir)` to be identical to "logo.png".
Differences:
`actual` is NULL
`expected` is a character vector ('logo.png')
── Failure ('test-appStatic.R:42:3'): logo ─────────────────────────────────────
Expected `"www/logo.png" %in% list.files(tdir, recursive = TRUE)` to be TRUE.
Differences:
`actual`: FALSE
`expected`: TRUE
[ FAIL 2 | WARN 0 | SKIP 6 | PASS 83 ]
Error:
! Test failures.
Execution halted
Flavor: r-oldrel-macos-x86_64
Current CRAN status: ERROR: 1, OK: 13
Version: 1.4.5
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘cohort-intersect.Rmd’ using rmarkdown
--- finished re-building ‘cohort-intersect.Rmd’
--- re-building ‘concept-intersect.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 concept-intersect.Rmd:35-52 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `loadNamespace()`:
! there is no package called 'arrow'
---
Backtrace:
▆
1. ├─omock::mockCdmFromDataset(datasetName = "GiBleed", source = "duckdb")
2. │ └─omock:::readTables(tmpFolder, cv)
3. │ └─omock:::castColumns(...)
4. │ ├─dplyr::filter(...)
5. │ ├─dplyr:::filter.data.frame(...)
6. │ │ └─dplyr:::filter_impl(...)
7. │ │ └─dplyr:::dplyr_quosures(...)
8. │ │ └─rlang::quos(..., .ignore_empty = "all")
9. │ └─base::colnames(x)
10. │ └─base::is.data.frame(x)
11. └─base::loadNamespace(x)
12. └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
13. └─base (local) withOneRestart(expr, restarts[[1L]])
14. └─base (local) doWithOneRestart(return(expr), restart)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'concept-intersect.Rmd' failed with diagnostics:
there is no package called 'arrow'
--- failed re-building ‘concept-intersect.Rmd’
--- re-building ‘demographics.rmd’ using rmarkdown
--- finished re-building ‘demographics.rmd’
--- re-building ‘summarise.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 summarise.Rmd:78-130 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `loadNamespace()`:
! there is no package called 'arrow'
---
Backtrace:
▆
1. ├─omock::mockCdmFromDataset(datasetName = "GiBleed", source = "duckdb")
2. │ └─omock:::readTables(tmpFolder, cv)
3. │ └─omock:::castColumns(...)
4. │ ├─dplyr::filter(...)
5. │ ├─dplyr:::filter.data.frame(...)
6. │ │ └─dplyr:::filter_impl(...)
7. │ │ └─dplyr:::dplyr_quosures(...)
8. │ │ └─rlang::quos(..., .ignore_empty = "all")
9. │ └─base::colnames(x)
10. │ └─base::is.data.frame(x)
11. └─base::loadNamespace(x)
12. └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
13. └─base (local) withOneRestart(expr, restarts[[1L]])
14. └─base (local) doWithOneRestart(return(expr), restart)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'summarise.Rmd' failed with diagnostics:
there is no package called 'arrow'
--- failed re-building ‘summarise.Rmd’
--- re-building ‘table-intersect.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 table-intersect.Rmd:34-57 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `loadNamespace()`:
! there is no package called 'arrow'
---
Backtrace:
▆
1. ├─omock::mockCdmFromDataset(datasetName = "GiBleed", source = "duckdb")
2. │ └─omock:::readTables(tmpFolder, cv)
3. │ └─omock:::castColumns(...)
4. │ ├─dplyr::filter(...)
5. │ ├─dplyr:::filter.data.frame(...)
6. │ │ └─dplyr:::filter_impl(...)
7. │ │ └─dplyr:::dplyr_quosures(...)
8. │ │ └─rlang::quos(..., .ignore_empty = "all")
9. │ └─base::colnames(x)
10. │ └─base::is.data.frame(x)
11. └─base::loadNamespace(x)
12. └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
13. └─base (local) withOneRestart(expr, restarts[[1L]])
14. └─base (local) doWithOneRestart(return(expr), restart)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'table-intersect.Rmd' failed with diagnostics:
there is no package called 'arrow'
--- failed re-building ‘table-intersect.Rmd’
SUMMARY: processing the following files failed:
‘concept-intersect.Rmd’ ‘summarise.Rmd’ ‘table-intersect.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-oldrel-macos-x86_64