Last updated on 2026-11-09 01:52:13 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.1.3 | 5.88 | 907.32 | 913.20 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.1.3 | 4.95 | 292.37 | 297.32 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 1.1.3 | 5.00 | 700.63 | 705.63 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 1.1.3 | 604.87 | OK | |||
| r-devel-windows-x86_64 | 1.1.3 | 10.00 | 573.00 | 583.00 | OK | |
| r-patched-linux-x86_64 | 1.1.3 | OK | ||||
| r-release-linux-x86_64 | 1.1.3 | 6.65 | 869.78 | 876.43 | OK | |
| r-release-macos-arm64 | 1.1.3 | 2.00 | 132.00 | 134.00 | OK | |
| r-release-macos-x86_64 | 1.1.3 | 5.00 | 439.00 | 444.00 | OK | |
| r-release-windows-x86_64 | 1.1.3 | 9.00 | 565.00 | 574.00 | OK | |
| r-oldrel-macos-arm64 | 1.1.3 | 2.00 | 138.00 | 140.00 | OK | |
| r-oldrel-macos-x86_64 | 1.1.3 | 5.00 | 470.00 | 475.00 | OK | |
| r-oldrel-windows-x86_64 | 1.1.3 | 14.00 | 816.00 | 830.00 | OK |
Version: 1.1.3
Check: examples
Result: ERROR
Running examples in ‘CohortCharacteristics-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: availablePlotColumns
> ### Title: Available columns to use in 'facet' and 'colour' arguments in
> ### plot functions.
> ### Aliases: availablePlotColumns
>
> ### ** Examples
>
> {
+ cdm <- mockCohortCharacteristics()
+
+ result <- summariseCharacteristics(cdm$cohort1)
+
+ availablePlotColumns(result)
+
+ }
Error in parquet___arrow___ArrowReaderProperties__Make(isTRUE(use_threads)) :
Cannot call parquet___arrow___ArrowReaderProperties__Make(). See https://arrow.apache.org/docs/r/articles/install.html for help installing Arrow C++ libraries.
Calls: mockCohortCharacteristics
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.1.3
Check: tests
Result: ERROR
Running ‘spelling.R’ [0s/0s]
Running ‘testthat.R’ [77s/43s]
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.
> test-plotCohortAttrition.R: duckdb keeps downloaded extensions and secrets in a temporary directory:
> test-plotCohortAttrition.R: i /home/hornik/tmp/scratch/Rtmpbbr1I8/duckdb
> test-plotCohortAttrition.R: This is removed when the R session ends.
> test-plotCohortAttrition.R: * Extensions are re-downloaded each session.
> test-plotCohortAttrition.R: * Secrets are lost.
> test-plotCohortAttrition.R: i Run duckdb(shared_home = TRUE) (or create ~/.duckdb) to keep them (suitable for most users).
> test-plotCohortAttrition.R: i Run duckdb(shared_home = FALSE) to accept the temporary directory (and silence this message).
> test-plotCohortAttrition.R: i See ?duckdb_storage for details and alternatives.
> test-plotCohortTiming.R: duckdb keeps downloaded extensions and secrets in a temporary directory:
> test-plotCohortTiming.R: i /home/hornik/tmp/scratch/Rtmp67Fbtp/duckdb
> test-plotCohortTiming.R: This is removed when the R session ends.
> test-plotCohortTiming.R: * Extensions are re-downloaded each session.
> test-plotCohortTiming.R: * Secrets are lost.
> test-plotCohortTiming.R: i Run duckdb(shared_home = TRUE) (or create ~/.duckdb) to keep them (suitable for most users).
> test-plotCohortTiming.R: i Run duckdb(shared_home = FALSE) to accept the temporary directory (and silence this message).
> test-plotCohortTiming.R: i See ?duckdb_storage for details and alternatives.
Saving _problems/test-plotCohortAttrition-3.R
> test-plotLargeScaleCharacteristics.R: duckdb keeps downloaded extensions and secrets in a temporary directory:
> test-plotLargeScaleCharacteristics.R: i /home/hornik/tmp/scratch/Rtmpbbr1I8/duckdb
> test-plotLargeScaleCharacteristics.R: This is removed when the R session ends.
> test-plotLargeScaleCharacteristics.R: * Extensions are re-downloaded each session.
> test-plotLargeScaleCharacteristics.R: * Secrets are lost.
> test-plotLargeScaleCharacteristics.R: i Run duckdb(shared_home = TRUE) (or create ~/.duckdb) to keep them (suitable for most users).
> test-plotLargeScaleCharacteristics.R: i Run duckdb(shared_home = FALSE) to accept the temporary directory (and silence this message).
> test-plotLargeScaleCharacteristics.R: i See ?duckdb_storage for details and alternatives.
> test-plotCohortTiming.R: i The following estimates will be calculated:
> test-plotCohortTiming.R: * days_between_cohort_entries: min, q25, median, q75, max, density
> test-plotCohortTiming.R: ! Table is collected to memory as not all requested estimates are supported on the database side.
> test-plotCohortTiming.R: > Start summary of data, at 2026-11-08 13:40:13.651163
> test-plotCohortTiming.R: v Summary finished, at 2026-11-08 13:40:13.998709
> test-plotCohortTiming.R: `result_id` is not present in result.
> test-plotCohortTiming.R: `result_id` is not present in result.
> test-plotCohortTiming.R: `result_id` is not present in result.
> test-plotCohortTiming.R: `result_id` is not present in result.
> test-plotLargeScaleCharacteristics.R: i Summarising large scale characteristics
> test-plotLargeScaleCharacteristics.R: - getting characteristics from table condition_occurrence (1 of 1)
> test-plotLargeScaleCharacteristics.R: - getting characteristics from table condition_occurrence (1 of 1) for time ...
> test-plotCohortTiming.R: i The following estimates will be calculated:
> test-plotCohortTiming.R: * days_between_cohort_entries: min, q25, median, q75, max, density
> test-plotLargeScaleCharacteristics.R: - getting characteristics from table condition_occurrence (1 of 1) for time ...
> test-plotCohortTiming.R: ! Table is collected to memory as not all requested estimates are supported on the database side.
> test-plotCohortTiming.R: > Start summary of data, at 2026-11-08 13:40:18.646205
> test-plotCohortTiming.R: v Summary finished, at 2026-11-08 13:40:18.957533
> test-plotLargeScaleCharacteristics.R: - getting characteristics from table condition_occurrence (1 of 1) for time ...
> test-plotCohortTiming.R: `result_id` is not present in result.
> test-plotCohortTiming.R: `result_id` is not present in result.
> test-plotLargeScaleCharacteristics.R: - getting characteristics from table condition_occurrence (1 of 1) for time ...
> test-plotCohortTiming.R: `result_id` is not present in result.
> test-plotCohortTiming.R: `result_id` is not present in result.
> test-plotLargeScaleCharacteristics.R: - getting characteristics from table condition_occurrence (1 of 1) for time ...
> test-summariseCharacteristics.R: duckdb keeps downloaded extensions and secrets in a temporary directory:
> test-summariseCharacteristics.R: i /home/hornik/tmp/scratch/Rtmp67Fbtp/duckdb
> test-summariseCharacteristics.R: This is removed when the R session ends.
> test-summariseCharacteristics.R: * Extensions are re-downloaded each session.
> test-summariseCharacteristics.R: * Secrets are lost.
> test-summariseCharacteristics.R: i Run duckdb(shared_home = TRUE) (or create ~/.duckdb) to keep them (suitable for most users).
> test-summariseCharacteristics.R: i Run duckdb(shared_home = FALSE) to accept the temporary directory (and silence this message).
> test-summariseCharacteristics.R: i See ?duckdb_storage for details and alternatives.
> test-plotLargeScaleCharacteristics.R: - getting characteristics from table condition_occurrence (1 of 1) for time ...
> test-summariseCharacteristics.R: duckdb keeps downloaded extensions and secrets in a temporary directory:
> test-summariseCharacteristics.R: i /home/hornik/tmp/scratch/Rtmp67Fbtp/duckdb
> test-summariseCharacteristics.R: This is removed when the R session ends.
> test-summariseCharacteristics.R: * Extensions are re-downloaded each session.
> test-summariseCharacteristics.R: * Secrets are lost.
> test-summariseCharacteristics.R: i Run duckdb(shared_home = TRUE) (or create ~/.duckdb) to keep them (suitable for most users).
> test-summariseCharacteristics.R: i Run duckdb(shared_home = FALSE) to accept the temporary directory (and silence this message).
> test-summariseCharacteristics.R: i See ?duckdb_storage for details and alternatives.
> test-summariseCharacteristics.R: duckdb keeps downloaded extensions and secrets in a temporary directory:
> test-summariseCharacteristics.R: i /home/hornik/tmp/scratch/Rtmp67Fbtp/duckdb
> test-summariseCharacteristics.R: This is removed when the R session ends.
> test-summariseCharacteristics.R: * Extensions are re-downloaded each session.
> test-summariseCharacteristics.R: * Secrets are lost.
> test-summariseCharacteristics.R: i Run duckdb(shared_home = TRUE) (or create ~/.duckdb) to keep them (suitable for most users).
> test-summariseCharacteristics.R: i Run duckdb(shared_home = FALSE) to accept the temporary directory (and silence this message).
> test-summariseCharacteristics.R: i See ?duckdb_storage for details and alternatives.
> test-plotLargeScaleCharacteristics.R: - getting characteristics from table condition_occurrence (1 of 1) for time ...
> test-summariseCharacteristics.R: duckdb keeps downloaded extensions and secrets in a temporary directory:
> test-summariseCharacteristics.R: i /home/hornik/tmp/scratch/Rtmp67Fbtp/duckdb
> test-summariseCharacteristics.R: This is removed when the R session ends.
> test-summariseCharacteristics.R: * Extensions are re-downloaded each session.
> test-summariseCharacteristics.R: * Secrets are lost.
> test-summariseCharacteristics.R: i Run duckdb(shared_home = TRUE) (or create ~/.duckdb) to keep them (suitable for most users).
> test-summariseCharacteristics.R: i Run duckdb(shared_home = FALSE) to accept the temporary directory (and silence this message).
> test-summariseCharacteristics.R: i See ?duckdb_storage for details and alternatives.
> test-plotLargeScaleCharacteristics.R: Formatting result
> test-summariseCharacteristics.R: duckdb keeps downloaded extensions and secrets in a temporary directory:
> test-summariseCharacteristics.R: i /home/hornik/tmp/scratch/Rtmp67Fbtp/duckdb
> test-summariseCharacteristics.R: This is removed when the R session ends.
> test-summariseCharacteristics.R: * Extensions are re-downloaded each session.
> test-summariseCharacteristics.R: * Secrets are lost.
> test-summariseCharacteristics.R: i Run duckdb(shared_home = TRUE) (or create ~/.duckdb) to keep them (suitable for most users).
> test-summariseCharacteristics.R: i Run duckdb(shared_home = FALSE) to accept the temporary directory (and silence this message).
> test-summariseCharacteristics.R: i See ?duckdb_storage for details and alternatives.
> test-summariseCharacteristics.R: duckdb keeps downloaded extensions and secrets in a temporary directory:
> test-summariseCharacteristics.R: i /home/hornik/tmp/scratch/Rtmp67Fbtp/duckdb
> test-summariseCharacteristics.R: This is removed when the R session ends.
> test-summariseCharacteristics.R: * Extensions are re-downloaded each session.
> test-summariseCharacteristics.R: * Secrets are lost.
> test-summariseCharacteristics.R: i Run duckdb(shared_home = TRUE) (or create ~/.duckdb) to keep them (suitable for most users).
> test-summariseCharacteristics.R: i Run duckdb(shared_home = FALSE) to accept the temporary directory (and silence this message).
> test-summariseCharacteristics.R: i See ?duckdb_storage for details and alternatives.
> test-summariseCharacteristics.R: duckdb keeps downloaded extensions and secrets in a temporary directory:
> test-summariseCharacteristics.R: i /home/hornik/tmp/scratch/Rtmp67Fbtp/duckdb
> test-summariseCharacteristics.R: This is removed when the R session ends.
> test-summariseCharacteristics.R: * Extensions are re-downloaded each session.
> test-summariseCharacteristics.R: * Secrets are lost.
> test-summariseCharacteristics.R: i Run duckdb(shared_home = TRUE) (or create ~/.duckdb) to keep them (suitable for most users).
> test-summariseCharacteristics.R: i Run duckdb(shared_home = FALSE) to accept the temporary directory (and silence this message).
> test-summariseCharacteristics.R: i See ?duckdb_storage for details and alternatives.
> test-summariseCharacteristics.R: duckdb keeps downloaded extensions and secrets in a temporary directory:
> test-summariseCharacteristics.R: i /home/hornik/tmp/scratch/Rtmp67Fbtp/duckdb
> test-summariseCharacteristics.R: This is removed when the R session ends.
> test-summariseCharacteristics.R: * Extensions are re-downloaded each session.
> test-summariseCharacteristics.R: * Secrets are lost.
> test-summariseCharacteristics.R: i Run duckdb(shared_home = TRUE) (or create ~/.duckdb) to keep them (suitable for most users).
> test-summariseCharacteristics.R: i Run duckdb(shared_home = FALSE) to accept the temporary directory (and silence this message).
> test-summariseCharacteristics.R: i See ?duckdb_storage for details and alternatives.
Saving _problems/test-summariseCharacteristics-62.R
Saving _problems/test-summariseCharacteristics-424.R
Saving _problems/test-summariseCharacteristics-541.R
Saving _problems/test-summariseCharacteristics-681.R
Saving _problems/test-summariseCharacteristics-1014.R
Saving _problems/test-summariseCharacteristics-1397.R
Saving _problems/test-summariseCharacteristics-1492.R
Saving _problems/test-summariseCharacteristics-1644.R
> test-summariseCohortAttrition.R: duckdb keeps downloaded extensions and secrets in a temporary directory:
> test-summariseCohortAttrition.R: i /home/hornik/tmp/scratch/Rtmp67Fbtp/duckdb
> test-summariseCohortAttrition.R: This is removed when the R session ends.
> test-summariseCohortAttrition.R: * Extensions are re-downloaded each session.
> test-summariseCohortAttrition.R: * Secrets are lost.
> test-summariseCohortAttrition.R: i Run duckdb(shared_home = TRUE) (or create ~/.duckdb) to keep them (suitable for most users).
> test-summariseCohortAttrition.R: i Run duckdb(shared_home = FALSE) to accept the temporary directory (and silence this message).
> test-summariseCohortAttrition.R: i See ?duckdb_storage for details and alternatives.
Saving _problems/test-summariseCohortAttrition-3.R
> test-summariseCohortCodelist.R: duckdb keeps downloaded extensions and secrets in a temporary directory:
> test-summariseCohortCodelist.R: i /home/hornik/tmp/scratch/Rtmp67Fbtp/duckdb
> test-summariseCohortCodelist.R: This is removed when the R session ends.
> test-summariseCohortCodelist.R: * Extensions are re-downloaded each session.
> test-summariseCohortCodelist.R: * Secrets are lost.
> test-summariseCohortCodelist.R: i Run duckdb(shared_home = TRUE) (or create ~/.duckdb) to keep them (suitable for most users).
> test-summariseCohortCodelist.R: i Run duckdb(shared_home = FALSE) to accept the temporary directory (and silence this message).
> test-summariseCohortCodelist.R: i See ?duckdb_storage for details and alternatives.
> test-plotLargeScaleCharacteristics.R: v Summarising large scale characteristics
> test-summariseCohortOverlap.R: duckdb keeps downloaded extensions and secrets in a temporary directory:
> test-summariseCohortOverlap.R: i /home/hornik/tmp/scratch/Rtmpbbr1I8/duckdb
> test-summariseCohortOverlap.R: This is removed when the R session ends.
> test-summariseCohortOverlap.R: * Extensions are re-downloaded each session.
> test-summariseCohortOverlap.R: * Secrets are lost.
> test-summariseCohortOverlap.R: i Run duckdb(shared_home = TRUE) (or create ~/.duckdb) to keep them (suitable for most users).
> test-summariseCohortOverlap.R: i Run duckdb(shared_home = FALSE) to accept the temporary directory (and silence this message).
> test-summariseCohortOverlap.R: i See ?duckdb_storage for details and alternatives.
Saving _problems/test-summariseCohortCodelist-4.R
> test-summariseCohortTiming.R: duckdb keeps downloaded extensions and secrets in a temporary directory:
> test-summariseCohortTiming.R: i /home/hornik/tmp/scratch/Rtmp67Fbtp/duckdb
> test-summariseCohortTiming.R: This is removed when the R session ends.
> test-summariseCohortTiming.R: * Extensions are re-downloaded each session.
> test-summariseCohortTiming.R: * Secrets are lost.
> test-summariseCohortTiming.R: i Run duckdb(shared_home = TRUE) (or create ~/.duckdb) to keep them (suitable for most users).
> test-summariseCohortTiming.R: i Run duckdb(shared_home = FALSE) to accept the temporary directory (and silence this message).
> test-summariseCohortTiming.R: i See ?duckdb_storage for details and alternatives.
> test-summariseCohortOverlap.R: duckdb keeps downloaded extensions and secrets in a temporary directory:
> test-summariseCohortOverlap.R: i /home/hornik/tmp/scratch/Rtmpbbr1I8/duckdb
> test-summariseCohortOverlap.R: This is removed when the R session ends.
> test-summariseCohortOverlap.R: * Extensions are re-downloaded each session.
> test-summariseCohortOverlap.R: * Secrets are lost.
> test-summariseCohortOverlap.R: i Run duckdb(shared_home = TRUE) (or create ~/.duckdb) to keep them (suitable for most users).
> test-summariseCohortOverlap.R: i Run duckdb(shared_home = FALSE) to accept the temporary directory (and silence this message).
> test-summariseCohortOverlap.R: i See ?duckdb_storage for details and alternatives.
> test-summariseCohortTiming.R: duckdb keeps downloaded extensions and secrets in a temporary directory:
> test-summariseCohortTiming.R: i /home/hornik/tmp/scratch/Rtmp67Fbtp/duckdb
> test-summariseCohortTiming.R: This is removed when the R session ends.
> test-summariseCohortTiming.R: * Extensions are re-downloaded each session.
> test-summariseCohortTiming.R: * Secrets are lost.
> test-summariseCohortTiming.R: i Run duckdb(shared_home = TRUE) (or create ~/.duckdb) to keep them (suitable for most users).
> test-summariseCohortTiming.R: i Run duckdb(shared_home = FALSE) to accept the temporary directory (and silence this message).
> test-summariseCohortTiming.R: i See ?duckdb_storage for details and alternatives.
> test-summariseCohortOverlap.R: duckdb keeps downloaded extensions and secrets in a temporary directory:
> test-summariseCohortOverlap.R: i /home/hornik/tmp/scratch/Rtmpbbr1I8/duckdb
> test-summariseCohortOverlap.R: This is removed when the R session ends.
> test-summariseCohortOverlap.R: * Extensions are re-downloaded each session.
> test-summariseCohortOverlap.R: * Secrets are lost.
> test-summariseCohortOverlap.R: i Run duckdb(shared_home = TRUE) (or create ~/.duckdb) to keep them (suitable for most users).
> test-summariseCohortOverlap.R: i Run duckdb(shared_home = FALSE) to accept the temporary directory (and silence this message).
> test-summariseCohortOverlap.R: i See ?duckdb_storage for details and alternatives.
> test-summariseCohortTiming.R: i The following estimates will be calculated:
> test-summariseCohortTiming.R: * days_between_cohort_entries: min, q25, median, q75, max
> test-summariseCohortTiming.R: ! Table is collected to memory as not all requested estimates are supported on the database side.
> test-summariseCohortTiming.R: > Start summary of data, at 2026-11-08 13:40:38.504753
> test-summariseCohortTiming.R: v Summary finished, at 2026-11-08 13:40:39.212067
Saving _problems/test-summariseCohortTiming-38.R
> test-utilities.R: `group` is not present in settings.
> test-utilities.R: `group` is not present in settings.
> test-utilities.R: `group` is not present in settings.
> test-summariseCohortOverlap.R: duckdb keeps downloaded extensions and secrets in a temporary directory:
> test-summariseCohortOverlap.R: i /home/hornik/tmp/scratch/Rtmpbbr1I8/duckdb
> test-summariseCohortOverlap.R: This is removed when the R session ends.
> test-summariseCohortOverlap.R: * Extensions are re-downloaded each session.
> test-summariseCohortOverlap.R: * Secrets are lost.
> test-summariseCohortOverlap.R: i Run duckdb(shared_home = TRUE) (or create ~/.duckdb) to keep them (suitable for most users).
> test-summariseCohortOverlap.R: i Run duckdb(shared_home = FALSE) to accept the temporary directory (and silence this message).
> test-summariseCohortOverlap.R: i See ?duckdb_storage for details and alternatives.
Saving _problems/test-summariseCohortOverlap-44.R
Saving _problems/test-summariseCohortOverlap-254.R
[ FAIL 14 | WARN 0 | SKIP 24 | PASS 11 ]
══ Skipped tests (24) ══════════════════════════════════════════════════════════
• On CRAN (22): 'test-benchmarkCohortCharacteristics.R:2:3',
'test-plotCharacteristics.R:2:3', 'test-plotCharacteristics.R:176:3',
'test-plotCohortCount.R:2:3', 'test-plotCohortOverlap.R:2:3',
'test-plotCohortTiming.R:2:3', 'test-plotCohortTiming.R:100:3',
'test-summariseCharacteristics.R:1180:3',
'test-summariseCharacteristics.R:1425:3',
'test-summariseCharacteristics.R:1552:3',
'test-plotLargeScaleCharacteristics.R:3:3',
'test-summariseCohortCount.R:2:3',
'test-summariseLargeScaleCharacteristics.R:2:3', 'test-table.R:2:3',
'test-tableCharacteristics.R:2:3', 'test-tableCharacteristics.R:124:3',
'test-tableCohortAttrition.R:2:3', 'test-tableCohortCount.R:2:3',
'test-tableCohortOverlap.R:2:3', 'test-tableCohortTiming.R:2:3',
'test-tableLargeScaleCharacteristics.R:2:3',
'test-tableLargeScaleCharacteristics.R:80:3'
• empty test (2): 'test-plotLargeScaleCharacteristics.R:140:1',
'test-summariseCohortTiming.R:114:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-plotCohortAttrition.R:2:3'): plot cohort attrition ─────────────
Error in `parquet___arrow___ArrowReaderProperties__Make(isTRUE(use_threads))`: Cannot call parquet___arrow___ArrowReaderProperties__Make(). See https://arrow.apache.org/docs/r/articles/install.html for help installing Arrow C++ libraries.
Backtrace:
▆
1. ├─CohortCharacteristics:::copyCdm(mockCohortCharacteristics(numberIndividuals = 1000)) at test-plotCohortAttrition.R:2:3
2. │ ├─omopgenerics::insertCdmTo(cdm = cdm, to = to) at ./setup.R:52:5
3. │ └─CDMConnector:::insertCdmTo.db_cdm(cdm = cdm, to = to)
4. │ └─omopgenerics::assertClass(cdm, "cdm_reference")
5. │ ├─omopgenerics:::checkEmpty(...)
6. │ ├─omopgenerics:::checkClass(...)
7. │ ├─omopgenerics:::checkLength(...)
8. │ ├─omopgenerics:::checkNull(createCheckObject(x), null)
9. │ └─omopgenerics:::createCheckObject(x)
10. └─PatientProfiles (local) mockCohortCharacteristics(numberIndividuals = 1000)
11. ├─base::suppressWarnings(...)
12. │ └─base::withCallingHandlers(...)
13. ├─base::suppressMessages(...)
14. │ └─base::withCallingHandlers(...)
15. └─omock::mockCdmReference(cdmName = "PP_MOCK", vocabularySet = "GiBleed")
16. └─omock::mockVocabularySet(...)
17. └─omock:::readTables(tmpFolder, cv, vocab = T)
18. ├─omock:::castColumns(...)
19. │ ├─dplyr::filter(...)
20. │ ├─dplyr:::filter.data.frame(...)
21. │ │ └─dplyr:::filter_impl(...)
22. │ │ └─dplyr:::dplyr_quosures(...)
23. │ │ └─rlang::quos(..., .ignore_empty = "all")
24. │ └─base::colnames(x)
25. │ └─base::is.data.frame(x)
26. └─arrow::read_parquet(file = tables[[nm]])
27. ├─ParquetFileReader$create(file, props = props, mmap = mmap, ...)
28. │ └─arrow:::assert_is(props, "ParquetArrowReaderProperties")
29. │ ├─assertthat::assert_that(inherits(object, class), msg = msg)
30. │ │ └─assertthat::see_if(..., env = env, msg = msg)
31. │ │ ├─base::tryCatch(...)
32. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
33. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
34. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
35. │ │ └─base::eval(assertion, env)
36. │ │ └─base::eval(assertion, env)
37. │ └─base::inherits(object, class)
38. └─ParquetArrowReaderProperties$create()
39. └─arrow:::parquet___arrow___ArrowReaderProperties__Make(isTRUE(use_threads))
── Error ('test-summariseCharacteristics.R:55:3'): test summariseCharacteristics ──
Error in `parquet___arrow___ArrowReaderProperties__Make(isTRUE(use_threads))`: Cannot call parquet___arrow___ArrowReaderProperties__Make(). See https://arrow.apache.org/docs/r/articles/install.html for help installing Arrow C++ libraries.
Backtrace:
▆
1. ├─CohortCharacteristics:::copyCdm(...) at test-summariseCharacteristics.R:55:3
2. │ ├─omopgenerics::insertCdmTo(cdm = cdm, to = to) at ./setup.R:52:5
3. │ └─CDMConnector:::insertCdmTo.db_cdm(cdm = cdm, to = to)
4. │ └─omopgenerics::assertClass(cdm, "cdm_reference")
5. │ ├─omopgenerics:::checkEmpty(...)
6. │ ├─omopgenerics:::checkClass(...)
7. │ ├─omopgenerics:::checkLength(...)
8. │ ├─omopgenerics:::checkNull(createCheckObject(x), null)
9. │ └─omopgenerics:::createCheckObject(x)
10. └─PatientProfiles (local) mockCohortCharacteristics(...)
11. ├─base::suppressWarnings(...)
12. │ └─base::withCallingHandlers(...)
13. ├─base::suppressMessages(...)
14. │ └─base::withCallingHandlers(...)
15. └─omock::mockCdmReference(cdmName = "PP_MOCK", vocabularySet = "GiBleed")
16. └─omock::mockVocabularySet(...)
17. └─omock:::readTables(tmpFolder, cv, vocab = T)
18. ├─omock:::castColumns(...)
19. │ ├─dplyr::filter(...)
20. │ ├─dplyr:::filter.data.frame(...)
21. │ │ └─dplyr:::filter_impl(...)
22. │ │ └─dplyr:::dplyr_quosures(...)
23. │ │ └─rlang::quos(..., .ignore_empty = "all")
24. │ └─base::colnames(x)
25. │ └─base::is.data.frame(x)
26. └─arrow::read_parquet(file = tables[[nm]])
27. ├─ParquetFileReader$create(file, props = props, mmap = mmap, ...)
28. │ └─arrow:::assert_is(props, "ParquetArrowReaderProperties")
29. │ ├─assertthat::assert_that(inherits(object, class), msg = msg)
30. │ │ └─assertthat::see_if(..., env = env, msg = msg)
31. │ │ ├─base::tryCatch(...)
32. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
33. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
34. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
35. │ │ └─base::eval(assertion, env)
36. │ │ └─base::eval(assertion, env)
37. │ └─base::inherits(object, class)
38. └─ParquetArrowReaderProperties$create()
39. └─arrow:::parquet___arrow___ArrowReaderProperties__Make(isTRUE(use_threads))
── Error ('test-summariseCharacteristics.R:423:3'): test empty cohort ──────────
Error in `parquet___arrow___ArrowReaderProperties__Make(isTRUE(use_threads))`: Cannot call parquet___arrow___ArrowReaderProperties__Make(). See https://arrow.apache.org/docs/r/articles/install.html for help installing Arrow C++ libraries.
Backtrace:
▆
1. ├─CohortCharacteristics:::copyCdm(mockCohortCharacteristics(numberIndividuals = 100)) at test-summariseCharacteristics.R:423:3
2. │ ├─omopgenerics::insertCdmTo(cdm = cdm, to = to) at ./setup.R:52:5
3. │ └─CDMConnector:::insertCdmTo.db_cdm(cdm = cdm, to = to)
4. │ └─omopgenerics::assertClass(cdm, "cdm_reference")
5. │ ├─omopgenerics:::checkEmpty(...)
6. │ ├─omopgenerics:::checkClass(...)
7. │ ├─omopgenerics:::checkLength(...)
8. │ ├─omopgenerics:::checkNull(createCheckObject(x), null)
9. │ └─omopgenerics:::createCheckObject(x)
10. └─PatientProfiles (local) mockCohortCharacteristics(numberIndividuals = 100)
11. ├─base::suppressWarnings(...)
12. │ └─base::withCallingHandlers(...)
13. ├─base::suppressMessages(...)
14. │ └─base::withCallingHandlers(...)
15. └─omock::mockCdmReference(cdmName = "PP_MOCK", vocabularySet = "GiBleed")
16. └─omock::mockVocabularySet(...)
17. └─omock:::readTables(tmpFolder, cv, vocab = T)
18. ├─omock:::castColumns(...)
19. │ ├─dplyr::filter(...)
20. │ ├─dplyr:::filter.data.frame(...)
21. │ │ └─dplyr:::filter_impl(...)
22. │ │ └─dplyr:::dplyr_quosures(...)
23. │ │ └─rlang::quos(..., .ignore_empty = "all")
24. │ └─base::colnames(x)
25. │ └─base::is.data.frame(x)
26. └─arrow::read_parquet(file = tables[[nm]])
27. ├─ParquetFileReader$create(file, props = props, mmap = mmap, ...)
28. │ └─arrow:::assert_is(props, "ParquetArrowReaderProperties")
29. │ ├─assertthat::assert_that(inherits(object, class), msg = msg)
30. │ │ └─assertthat::see_if(..., env = env, msg = msg)
31. │ │ ├─base::tryCatch(...)
32. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
33. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
34. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
35. │ │ └─base::eval(assertion, env)
36. │ │ └─base::eval(assertion, env)
37. │ └─base::inherits(object, class)
38. └─ParquetArrowReaderProperties$create()
39. └─arrow:::parquet___arrow___ArrowReaderProperties__Make(isTRUE(use_threads))
── Error ('test-summariseCharacteristics.R:534:3'): test cohort id ─────────────
Error in `parquet___arrow___ArrowReaderProperties__Make(isTRUE(use_threads))`: Cannot call parquet___arrow___ArrowReaderProperties__Make(). See https://arrow.apache.org/docs/r/articles/install.html for help installing Arrow C++ libraries.
Backtrace:
▆
1. ├─CohortCharacteristics:::copyCdm(...) at test-summariseCharacteristics.R:534:3
2. │ ├─omopgenerics::insertCdmTo(cdm = cdm, to = to) at ./setup.R:52:5
3. │ └─CDMConnector:::insertCdmTo.db_cdm(cdm = cdm, to = to)
4. │ └─omopgenerics::assertClass(cdm, "cdm_reference")
5. │ ├─omopgenerics:::checkEmpty(...)
6. │ ├─omopgenerics:::checkClass(...)
7. │ ├─omopgenerics:::checkLength(...)
8. │ ├─omopgenerics:::checkNull(createCheckObject(x), null)
9. │ └─omopgenerics:::createCheckObject(x)
10. └─PatientProfiles (local) mockCohortCharacteristics(...)
11. ├─base::suppressWarnings(...)
12. │ └─base::withCallingHandlers(...)
13. ├─base::suppressMessages(...)
14. │ └─base::withCallingHandlers(...)
15. └─omock::mockCdmReference(cdmName = "PP_MOCK", vocabularySet = "GiBleed")
16. └─omock::mockVocabularySet(...)
17. └─omock:::readTables(tmpFolder, cv, vocab = T)
18. ├─omock:::castColumns(...)
19. │ ├─dplyr::filter(...)
20. │ ├─dplyr:::filter.data.frame(...)
21. │ │ └─dplyr:::filter_impl(...)
22. │ │ └─dplyr:::dplyr_quosures(...)
23. │ │ └─rlang::quos(..., .ignore_empty = "all")
24. │ └─base::colnames(x)
25. │ └─base::is.data.frame(x)
26. └─arrow::read_parquet(file = tables[[nm]])
27. ├─ParquetFileReader$create(file, props = props, mmap = mmap, ...)
28. │ └─arrow:::assert_is(props, "ParquetArrowReaderProperties")
29. │ ├─assertthat::assert_that(inherits(object, class), msg = msg)
30. │ │ └─assertthat::see_if(..., env = env, msg = msg)
31. │ │ ├─base::tryCatch(...)
32. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
33. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
34. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
35. │ │ └─base::eval(assertion, env)
36. │ │ └─base::eval(assertion, env)
37. │ └─base::inherits(object, class)
38. └─ParquetArrowReaderProperties$create()
39. └─arrow:::parquet___arrow___ArrowReaderProperties__Make(isTRUE(use_threads))
── Error ('test-summariseCharacteristics.R:675:3'): arguments tableIntersect ───
Error in `parquet___arrow___ArrowReaderProperties__Make(isTRUE(use_threads))`: Cannot call parquet___arrow___ArrowReaderProperties__Make(). See https://arrow.apache.org/docs/r/articles/install.html for help installing Arrow C++ libraries.
Backtrace:
▆
1. ├─CohortCharacteristics:::copyCdm(...) at test-summariseCharacteristics.R:675:3
2. │ ├─omopgenerics::insertCdmTo(cdm = cdm, to = to) at ./setup.R:52:5
3. │ └─CDMConnector:::insertCdmTo.db_cdm(cdm = cdm, to = to)
4. │ └─omopgenerics::assertClass(cdm, "cdm_reference")
5. │ ├─omopgenerics:::checkEmpty(...)
6. │ ├─omopgenerics:::checkClass(...)
7. │ ├─omopgenerics:::checkLength(...)
8. │ ├─omopgenerics:::checkNull(createCheckObject(x), null)
9. │ └─omopgenerics:::createCheckObject(x)
10. └─PatientProfiles (local) mockCohortCharacteristics(...)
11. ├─base::suppressWarnings(...)
12. │ └─base::withCallingHandlers(...)
13. ├─base::suppressMessages(...)
14. │ └─base::withCallingHandlers(...)
15. └─omock::mockCdmReference(cdmName = "PP_MOCK", vocabularySet = "GiBleed")
16. └─omock::mockVocabularySet(...)
17. └─omock:::readTables(tmpFolder, cv, vocab = T)
18. ├─omock:::castColumns(...)
19. │ ├─dplyr::filter(...)
20. │ ├─dplyr:::filter.data.frame(...)
21. │ │ └─dplyr:::filter_impl(...)
22. │ │ └─dplyr:::dplyr_quosures(...)
23. │ │ └─rlang::quos(..., .ignore_empty = "all")
24. │ └─base::colnames(x)
25. │ └─base::is.data.frame(x)
26. └─arrow::read_parquet(file = tables[[nm]])
27. ├─ParquetFileReader$create(file, props = props, mmap = mmap, ...)
28. │ └─arrow:::assert_is(props, "ParquetArrowReaderProperties")
29. │ ├─assertthat::assert_that(inherits(object, class), msg = msg)
30. │ │ └─assertthat::see_if(..., env = env, msg = msg)
31. │ │ ├─base::tryCatch(...)
32. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
33. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
34. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
35. │ │ └─base::eval(assertion, env)
36. │ │ └─base::eval(assertion, env)
37. │ └─base::inherits(object, class)
38. └─ParquetArrowReaderProperties$create()
39. └─arrow:::parquet___arrow___ArrowReaderProperties__Make(isTRUE(use_threads))
── Error ('test-summariseCharacteristics.R:1008:3'): arguments cohortIntersect ──
Error in `parquet___arrow___ArrowReaderProperties__Make(isTRUE(use_threads))`: Cannot call parquet___arrow___ArrowReaderProperties__Make(). See https://arrow.apache.org/docs/r/articles/install.html for help installing Arrow C++ libraries.
Backtrace:
▆
1. ├─CohortCharacteristics:::copyCdm(...) at test-summariseCharacteristics.R:1008:3
2. │ ├─omopgenerics::insertCdmTo(cdm = cdm, to = to) at ./setup.R:52:5
3. │ └─CDMConnector:::insertCdmTo.db_cdm(cdm = cdm, to = to)
4. │ └─omopgenerics::assertClass(cdm, "cdm_reference")
5. │ ├─omopgenerics:::checkEmpty(...)
6. │ ├─omopgenerics:::checkClass(...)
7. │ ├─omopgenerics:::checkLength(...)
8. │ ├─omopgenerics:::checkNull(createCheckObject(x), null)
9. │ └─omopgenerics:::createCheckObject(x)
10. └─PatientProfiles (local) mockCohortCharacteristics(...)
11. ├─base::suppressWarnings(...)
12. │ └─base::withCallingHandlers(...)
13. ├─base::suppressMessages(...)
14. │ └─base::withCallingHandlers(...)
15. └─omock::mockCdmReference(cdmName = "PP_MOCK", vocabularySet = "GiBleed")
16. └─omock::mockVocabularySet(...)
17. └─omock:::readTables(tmpFolder, cv, vocab = T)
18. ├─omock:::castColumns(...)
19. │ ├─dplyr::filter(...)
20. │ ├─dplyr:::filter.data.frame(...)
21. │ │ └─dplyr:::filter_impl(...)
22. │ │ └─dplyr:::dplyr_quosures(...)
23. │ │ └─rlang::quos(..., .ignore_empty = "all")
24. │ └─base::colnames(x)
25. │ └─base::is.data.frame(x)
26. └─arrow::read_parquet(file = tables[[nm]])
27. ├─ParquetFileReader$create(file, props = props, mmap = mmap, ...)
28. │ └─arrow:::assert_is(props, "ParquetArrowReaderProperties")
29. │ ├─assertthat::assert_that(inherits(object, class), msg = msg)
30. │ │ └─assertthat::see_if(..., env = env, msg = msg)
31. │ │ ├─base::tryCatch(...)
32. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
33. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
34. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
35. │ │ └─base::eval(assertion, env)
36. │ │ └─base::eval(assertion, env)
37. │ └─base::inherits(object, class)
38. └─ParquetArrowReaderProperties$create()
39. └─arrow:::parquet___arrow___ArrowReaderProperties__Make(isTRUE(use_threads))
── Error ('test-summariseCharacteristics.R:1396:3'): empty input cohort contains name issue #170 ──
Error in `parquet___arrow___ArrowReaderProperties__Make(isTRUE(use_threads))`: Cannot call parquet___arrow___ArrowReaderProperties__Make(). See https://arrow.apache.org/docs/r/articles/install.html for help installing Arrow C++ libraries.
Backtrace:
▆
1. ├─CohortCharacteristics:::copyCdm(mockCohortCharacteristics(numberIndividuals = 10)) at test-summariseCharacteristics.R:1396:3
2. │ ├─omopgenerics::insertCdmTo(cdm = cdm, to = to) at ./setup.R:52:5
3. │ └─CDMConnector:::insertCdmTo.db_cdm(cdm = cdm, to = to)
4. │ └─omopgenerics::assertClass(cdm, "cdm_reference")
5. │ ├─omopgenerics:::checkEmpty(...)
6. │ ├─omopgenerics:::checkClass(...)
7. │ ├─omopgenerics:::checkLength(...)
8. │ ├─omopgenerics:::checkNull(createCheckObject(x), null)
9. │ └─omopgenerics:::createCheckObject(x)
10. └─PatientProfiles (local) mockCohortCharacteristics(numberIndividuals = 10)
11. ├─base::suppressWarnings(...)
12. │ └─base::withCallingHandlers(...)
13. ├─base::suppressMessages(...)
14. │ └─base::withCallingHandlers(...)
15. └─omock::mockCdmReference(cdmName = "PP_MOCK", vocabularySet = "GiBleed")
16. └─omock::mockVocabularySet(...)
17. └─omock:::readTables(tmpFolder, cv, vocab = T)
18. ├─omock:::castColumns(...)
19. │ ├─dplyr::filter(...)
20. │ ├─dplyr:::filter.data.frame(...)
21. │ │ └─dplyr:::filter_impl(...)
22. │ │ └─dplyr:::dplyr_quosures(...)
23. │ │ └─rlang::quos(..., .ignore_empty = "all")
24. │ └─base::colnames(x)
25. │ └─base::is.data.frame(x)
26. └─arrow::read_parquet(file = tables[[nm]])
27. ├─ParquetFileReader$create(file, props = props, mmap = mmap, ...)
28. │ └─arrow:::assert_is(props, "ParquetArrowReaderProperties")
29. │ ├─assertthat::assert_that(inherits(object, class), msg = msg)
30. │ │ └─assertthat::see_if(..., env = env, msg = msg)
31. │ │ ├─base::tryCatch(...)
32. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
33. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
34. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
35. │ │ └─base::eval(assertion, env)
36. │ │ └─base::eval(assertion, env)
37. │ └─base::inherits(object, class)
38. └─ParquetArrowReaderProperties$create()
39. └─arrow:::parquet___arrow___ArrowReaderProperties__Make(isTRUE(use_threads))
── Error ('test-summariseCharacteristics.R:1487:3'): arrange ageGroup ──────────
Error in `parquet___arrow___ArrowReaderProperties__Make(isTRUE(use_threads))`: Cannot call parquet___arrow___ArrowReaderProperties__Make(). See https://arrow.apache.org/docs/r/articles/install.html for help installing Arrow C++ libraries.
Backtrace:
▆
1. ├─CohortCharacteristics:::copyCdm(...) at test-summariseCharacteristics.R:1487:3
2. │ ├─omopgenerics::insertCdmTo(cdm = cdm, to = to) at ./setup.R:52:5
3. │ └─CDMConnector:::insertCdmTo.db_cdm(cdm = cdm, to = to)
4. │ └─omopgenerics::assertClass(cdm, "cdm_reference")
5. │ ├─omopgenerics:::checkEmpty(...)
6. │ ├─omopgenerics:::checkClass(...)
7. │ ├─omopgenerics:::checkLength(...)
8. │ ├─omopgenerics:::checkNull(createCheckObject(x), null)
9. │ └─omopgenerics:::createCheckObject(x)
10. └─PatientProfiles (local) mockCohortCharacteristics(...)
11. ├─base::suppressWarnings(...)
12. │ └─base::withCallingHandlers(...)
13. ├─base::suppressMessages(...)
14. │ └─base::withCallingHandlers(...)
15. └─omock::mockCdmReference(cdmName = "PP_MOCK", vocabularySet = "GiBleed")
16. └─omock::mockVocabularySet(...)
17. └─omock:::readTables(tmpFolder, cv, vocab = T)
18. ├─omock:::castColumns(...)
19. │ ├─dplyr::filter(...)
20. │ ├─dplyr:::filter.data.frame(...)
21. │ │ └─dplyr:::filter_impl(...)
22. │ │ └─dplyr:::dplyr_quosures(...)
23. │ │ └─rlang::quos(..., .ignore_empty = "all")
24. │ └─base::colnames(x)
25. │ └─base::is.data.frame(x)
26. └─arrow::read_parquet(file = tables[[nm]])
27. ├─ParquetFileReader$create(file, props = props, mmap = mmap, ...)
28. │ └─arrow:::assert_is(props, "ParquetArrowReaderProperties")
29. │ ├─assertthat::assert_that(inherits(object, class), msg = msg)
30. │ │ └─assertthat::see_if(..., env = env, msg = msg)
31. │ │ ├─base::tryCatch(...)
32. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
33. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
34. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
35. │ │ └─base::eval(assertion, env)
36. │ │ └─base::eval(assertion, env)
37. │ └─base::inherits(object, class)
38. └─ParquetArrowReaderProperties$create()
39. └─arrow:::parquet___arrow___ArrowReaderProperties__Make(isTRUE(use_threads))
── Error ('test-summariseCharacteristics.R:1638:3'): weights in summariseCharacteristics ──
Error in `parquet___arrow___ArrowReaderProperties__Make(isTRUE(use_threads))`: Cannot call parquet___arrow___ArrowReaderProperties__Make(). See https://arrow.apache.org/docs/r/articles/install.html for help installing Arrow C++ libraries.
Backtrace:
▆
1. ├─CohortCharacteristics:::copyCdm(...) at test-summariseCharacteristics.R:1638:3
2. │ ├─omopgenerics::insertCdmTo(cdm = cdm, to = to) at ./setup.R:52:5
3. │ └─CDMConnector:::insertCdmTo.db_cdm(cdm = cdm, to = to)
4. │ └─omopgenerics::assertClass(cdm, "cdm_reference")
5. │ ├─omopgenerics:::checkEmpty(...)
6. │ ├─omopgenerics:::checkClass(...)
7. │ ├─omopgenerics:::checkLength(...)
8. │ ├─omopgenerics:::checkNull(createCheckObject(x), null)
9. │ └─omopgenerics:::createCheckObject(x)
10. └─PatientProfiles (local) mockCohortCharacteristics(...)
11. ├─base::suppressWarnings(...)
12. │ └─base::withCallingHandlers(...)
13. ├─base::suppressMessages(...)
14. │ └─base::withCallingHandlers(...)
15. └─omock::mockCdmReference(cdmName = "PP_MOCK", vocabularySet = "GiBleed")
16. └─omock::mockVocabularySet(...)
17. └─omock:::readTables(tmpFolder, cv, vocab = T)
18. ├─omock:::castColumns(...)
19. │ ├─dplyr::filter(...)
20. │ ├─dplyr:::filter.data.frame(...)
21. │ │ └─dplyr:::filter_impl(...)
22. │ │ └─dplyr:::dplyr_quosures(...)
23. │ │ └─rlang::quos(..., .ignore_empty = "all")
24. │ └─base::colnames(x)
25. │ └─base::is.data.frame(x)
26. └─arrow::read_parquet(file = tables[[nm]])
27. ├─ParquetFileReader$create(file, props = props, mmap = mmap, ...)
28. │ └─arrow:::assert_is(props, "ParquetArrowReaderProperties")
29. │ ├─assertthat::assert_that(inherits(object, class), msg = msg)
30. │ │ └─assertthat::see_if(..., env = env, msg = msg)
31. │ │ ├─base::tryCatch(...)
32. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
33. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
34. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
35. │ │ └─base::eval(assertion, env)
36. │ │ └─base::eval(assertion, env)
37. │ └─base::inherits(object, class)
38. └─ParquetArrowReaderProperties$create()
39. └─arrow:::parquet___arrow___ArrowReaderProperties__Make(isTRUE(use_threads))
── Error ('test-summariseCohortAttrition.R:2:3'): check summariseCohortAttrition is deterministic ──
Error in `parquet___arrow___ArrowReaderProperties__Make(isTRUE(use_threads))`: Cannot call parquet___arrow___ArrowReaderProperties__Make(). See https://arrow.apache.org/docs/r/articles/install.html for help installing Arrow C++ libraries.
Backtrace:
▆
1. ├─CohortCharacteristics:::copyCdm(mockCohortCharacteristics(numberIndividuals = 1000)) at test-summariseCohortAttrition.R:2:3
2. │ ├─omopgenerics::insertCdmTo(cdm = cdm, to = to) at ./setup.R:52:5
3. │ └─CDMConnector:::insertCdmTo.db_cdm(cdm = cdm, to = to)
4. │ └─omopgenerics::assertClass(cdm, "cdm_reference")
5. │ ├─omopgenerics:::checkEmpty(...)
6. │ ├─omopgenerics:::checkClass(...)
7. │ ├─omopgenerics:::checkLength(...)
8. │ ├─omopgenerics:::checkNull(createCheckObject(x), null)
9. │ └─omopgenerics:::createCheckObject(x)
10. └─PatientProfiles (local) mockCohortCharacteristics(numberIndividuals = 1000)
11. ├─base::suppressWarnings(...)
12. │ └─base::withCallingHandlers(...)
13. ├─base::suppressMessages(...)
14. │ └─base::withCallingHandlers(...)
15. └─omock::mockCdmReference(cdmName = "PP_MOCK", vocabularySet = "GiBleed")
16. └─omock::mockVocabularySet(...)
17. └─omock:::readTables(tmpFolder, cv, vocab = T)
18. ├─omock:::castColumns(...)
19. │ ├─dplyr::filter(...)
20. │ ├─dplyr:::filter.data.frame(...)
21. │ │ └─dplyr:::filter_impl(...)
22. │ │ └─dplyr:::dplyr_quosures(...)
23. │ │ └─rlang::quos(..., .ignore_empty = "all")
24. │ └─base::colnames(x)
25. │ └─base::is.data.frame(x)
26. └─arrow::read_parquet(file = tables[[nm]])
27. ├─ParquetFileReader$create(file, props = props, mmap = mmap, ...)
28. │ └─arrow:::assert_is(props, "ParquetArrowReaderProperties")
29. │ ├─assertthat::assert_that(inherits(object, class), msg = msg)
30. │ │ └─assertthat::see_if(..., env = env, msg = msg)
31. │ │ ├─base::tryCatch(...)
32. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
33. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
34. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
35. │ │ └─base::eval(assertion, env)
36. │ │ └─base::eval(assertion, env)
37. │ └─base::inherits(object, class)
38. └─ParquetArrowReaderProperties$create()
39. └─arrow:::parquet___arrow___ArrowReaderProperties__Make(isTRUE(use_threads))
── Error ('test-summariseCohortCodelist.R:3:3'): test summarise cohortCodelist attribute ──
Error in `parquet___arrow___ArrowReaderProperties__Make(isTRUE(use_threads))`: Cannot call parquet___arrow___ArrowReaderProperties__Make(). See https://arrow.apache.org/docs/r/articles/install.html for help installing Arrow C++ libraries.
Backtrace:
▆
1. ├─CohortCharacteristics:::copyCdm(mockCohortCharacteristics()) at test-summariseCohortCodelist.R:3:3
2. │ ├─omopgenerics::insertCdmTo(cdm = cdm, to = to) at ./setup.R:52:5
3. │ └─CDMConnector:::insertCdmTo.db_cdm(cdm = cdm, to = to)
4. │ └─omopgenerics::assertClass(cdm, "cdm_reference")
5. │ ├─omopgenerics:::checkEmpty(...)
6. │ ├─omopgenerics:::checkClass(...)
7. │ ├─omopgenerics:::checkLength(...)
8. │ ├─omopgenerics:::checkNull(createCheckObject(x), null)
9. │ └─omopgenerics:::createCheckObject(x)
10. └─PatientProfiles (local) mockCohortCharacteristics()
11. ├─base::suppressWarnings(...)
12. │ └─base::withCallingHandlers(...)
13. ├─base::suppressMessages(...)
14. │ └─base::withCallingHandlers(...)
15. └─omock::mockCdmReference(cdmName = "PP_MOCK", vocabularySet = "GiBleed")
16. └─omock::mockVocabularySet(...)
17. └─omock:::readTables(tmpFolder, cv, vocab = T)
18. ├─omock:::castColumns(...)
19. │ ├─dplyr::filter(...)
20. │ ├─dplyr:::filter.data.frame(...)
21. │ │ └─dplyr:::filter_impl(...)
22. │ │ └─dplyr:::dplyr_quosures(...)
23. │ │ └─rlang::quos(..., .ignore_empty = "all")
24. │ └─base::colnames(x)
25. │ └─base::is.data.frame(x)
26. └─arrow::read_parquet(file = tables[[nm]])
27. ├─ParquetFileReader$create(file, props = props, mmap = mmap, ...)
28. │ └─arrow:::assert_is(props, "ParquetArrowReaderProperties")
29. │ ├─assertthat::assert_that(inherits(object, class), msg = msg)
30. │ │ └─assertthat::see_if(..., env = env, msg = msg)
31. │ │ ├─base::tryCatch(...)
32. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
33. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
34. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
35. │ │ └─base::eval(assertion, env)
36. │ │ └─base::eval(assertion, env)
37. │ └─base::inherits(object, class)
38. └─ParquetArrowReaderProperties$create()
39. └─arrow:::parquet___arrow___ArrowReaderProperties__Make(isTRUE(use_threads))
── Error ('test-summariseCohortTiming.R:35:3'): summariseCohortTiming ──────────
Error in `parquet___arrow___ArrowReaderProperties__Make(isTRUE(use_threads))`: Cannot call parquet___arrow___ArrowReaderProperties__Make(). See https://arrow.apache.org/docs/r/articles/install.html for help installing Arrow C++ libraries.
Backtrace:
▆
1. ├─CohortCharacteristics:::copyCdm(...) at test-summariseCohortTiming.R:35:3
2. │ ├─omopgenerics::insertCdmTo(cdm = cdm, to = to) at ./setup.R:52:5
3. │ └─CDMConnector:::insertCdmTo.db_cdm(cdm = cdm, to = to)
4. │ └─omopgenerics::assertClass(cdm, "cdm_reference")
5. │ ├─omopgenerics:::checkEmpty(...)
6. │ ├─omopgenerics:::checkClass(...)
7. │ ├─omopgenerics:::checkLength(...)
8. │ ├─omopgenerics:::checkNull(createCheckObject(x), null)
9. │ └─omopgenerics:::createCheckObject(x)
10. └─PatientProfiles (local) mockCohortCharacteristics(...)
11. ├─base::suppressWarnings(...)
12. │ └─base::withCallingHandlers(...)
13. ├─base::suppressMessages(...)
14. │ └─base::withCallingHandlers(...)
15. └─omock::mockCdmReference(cdmName = "PP_MOCK", vocabularySet = "GiBleed")
16. └─omock::mockVocabularySet(...)
17. └─omock:::readTables(tmpFolder, cv, vocab = T)
18. ├─omock:::castColumns(...)
19. │ ├─dplyr::filter(...)
20. │ ├─dplyr:::filter.data.frame(...)
21. │ │ └─dplyr:::filter_impl(...)
22. │ │ └─dplyr:::dplyr_quosures(...)
23. │ │ └─rlang::quos(..., .ignore_empty = "all")
24. │ └─base::colnames(x)
25. │ └─base::is.data.frame(x)
26. └─arrow::read_parquet(file = tables[[nm]])
27. ├─ParquetFileReader$create(file, props = props, mmap = mmap, ...)
28. │ └─arrow:::assert_is(props, "ParquetArrowReaderProperties")
29. │ ├─assertthat::assert_that(inherits(object, class), msg = msg)
30. │ │ └─assertthat::see_if(..., env = env, msg = msg)
31. │ │ ├─base::tryCatch(...)
32. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
33. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
34. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
35. │ │ └─base::eval(assertion, env)
36. │ │ └─base::eval(assertion, env)
37. │ └─base::inherits(object, class)
38. └─ParquetArrowReaderProperties$create()
39. └─arrow:::parquet___arrow___ArrowReaderProperties__Make(isTRUE(use_threads))
── Error ('test-summariseCohortOverlap.R:41:3'): summariseCohortOverlap ────────
Error in `parquet___arrow___ArrowReaderProperties__Make(isTRUE(use_threads))`: Cannot call parquet___arrow___ArrowReaderProperties__Make(). See https://arrow.apache.org/docs/r/articles/install.html for help installing Arrow C++ libraries.
Backtrace:
▆
1. ├─CohortCharacteristics:::copyCdm(...) at test-summariseCohortOverlap.R:41:3
2. │ ├─omopgenerics::insertCdmTo(cdm = cdm, to = to) at ./setup.R:52:5
3. │ └─CDMConnector:::insertCdmTo.db_cdm(cdm = cdm, to = to)
4. │ └─omopgenerics::assertClass(cdm, "cdm_reference")
5. │ ├─omopgenerics:::checkEmpty(...)
6. │ ├─omopgenerics:::checkClass(...)
7. │ ├─omopgenerics:::checkLength(...)
8. │ ├─omopgenerics:::checkNull(createCheckObject(x), null)
9. │ └─omopgenerics:::createCheckObject(x)
10. └─PatientProfiles (local) mockCohortCharacteristics(...)
11. ├─base::suppressWarnings(...)
12. │ └─base::withCallingHandlers(...)
13. ├─base::suppressMessages(...)
14. │ └─base::withCallingHandlers(...)
15. └─omock::mockCdmReference(cdmName = "PP_MOCK", vocabularySet = "GiBleed")
16. └─omock::mockVocabularySet(...)
17. └─omock:::readTables(tmpFolder, cv, vocab = T)
18. ├─omock:::castColumns(...)
19. │ ├─dplyr::filter(...)
20. │ ├─dplyr:::filter.data.frame(...)
21. │ │ └─dplyr:::filter_impl(...)
22. │ │ └─dplyr:::dplyr_quosures(...)
23. │ │ └─rlang::quos(..., .ignore_empty = "all")
24. │ └─base::colnames(x)
25. │ └─base::is.data.frame(x)
26. └─arrow::read_parquet(file = tables[[nm]])
27. ├─ParquetFileReader$create(file, props = props, mmap = mmap, ...)
28. │ └─arrow:::assert_is(props, "ParquetArrowReaderProperties")
29. │ ├─assertthat::assert_that(inherits(object, class), msg = msg)
30. │ │ └─assertthat::see_if(..., env = env, msg = msg)
31. │ │ ├─base::tryCatch(...)
32. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
33. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
34. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
35. │ │ └─base::eval(assertion, env)
36. │ │ └─base::eval(assertion, env)
37. │ └─base::inherits(object, class)
38. └─ParquetArrowReaderProperties$create()
39. └─arrow:::parquet___arrow___ArrowReaderProperties__Make(isTRUE(use_threads))
── Error ('test-summariseCohortOverlap.R:251:3'): test countBy ─────────────────
Error in `parquet___arrow___ArrowReaderProperties__Make(isTRUE(use_threads))`: Cannot call parquet___arrow___ArrowReaderProperties__Make(). See https://arrow.apache.org/docs/r/articles/install.html for help installing Arrow C++ libraries.
Backtrace:
▆
1. ├─CohortCharacteristics:::copyCdm(...) at test-summariseCohortOverlap.R:251:3
2. │ ├─omopgenerics::insertCdmTo(cdm = cdm, to = to) at ./setup.R:52:5
3. │ └─CDMConnector:::insertCdmTo.db_cdm(cdm = cdm, to = to)
4. │ └─omopgenerics::assertClass(cdm, "cdm_reference")
5. │ ├─omopgenerics:::checkEmpty(...)
6. │ ├─omopgenerics:::checkClass(...)
7. │ ├─omopgenerics:::checkLength(...)
8. │ ├─omopgenerics:::checkNull(createCheckObject(x), null)
9. │ └─omopgenerics:::createCheckObject(x)
10. └─PatientProfiles (local) mockCohortCharacteristics(...)
11. ├─base::suppressWarnings(...)
12. │ └─base::withCallingHandlers(...)
13. ├─base::suppressMessages(...)
14. │ └─base::withCallingHandlers(...)
15. └─omock::mockCdmReference(cdmName = "PP_MOCK", vocabularySet = "GiBleed")
16. └─omock::mockVocabularySet(...)
17. └─omock:::readTables(tmpFolder, cv, vocab = T)
18. ├─omock:::castColumns(...)
19. │ ├─dplyr::filter(...)
20. │ ├─dplyr:::filter.data.frame(...)
21. │ │ └─dplyr:::filter_impl(...)
22. │ │ └─dplyr:::dplyr_quosures(...)
23. │ │ └─rlang::quos(..., .ignore_empty = "all")
24. │ └─base::colnames(x)
25. │ └─base::is.data.frame(x)
26. └─arrow::read_parquet(file = tables[[nm]])
27. ├─ParquetFileReader$create(file, props = props, mmap = mmap, ...)
28. │ └─arrow:::assert_is(props, "ParquetArrowReaderProperties")
29. │ ├─assertthat::assert_that(inherits(object, class), msg = msg)
30. │ │ └─assertthat::see_if(..., env = env, msg = msg)
31. │ │ ├─base::tryCatch(...)
32. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
33. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
34. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
35. │ │ └─base::eval(assertion, env)
36. │ │ └─base::eval(assertion, env)
37. │ └─base::inherits(object, class)
38. └─ParquetArrowReaderProperties$create()
39. └─arrow:::parquet___arrow___ArrowReaderProperties__Make(isTRUE(use_threads))
[ FAIL 14 | WARN 0 | SKIP 24 | PASS 11 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc