Last updated on 2026-11-09 01:52:24 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.7.0 | 21.91 | 332.31 | 354.22 | OK | |
| r-devel-linux-x86_64-debian-gcc | 0.7.0 | 17.73 | 223.26 | 240.99 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 0.7.0 | 17.00 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 0.7.0 | 17.00 | 219.89 | 236.89 | OK | |
| r-devel-windows-x86_64 | 0.7.0 | 26.00 | 300.00 | 326.00 | OK | |
| r-patched-linux-x86_64 | 0.7.0 | OK | ||||
| r-release-linux-x86_64 | 0.7.0 | 21.58 | 309.73 | 331.31 | OK | |
| r-release-macos-arm64 | 0.7.0 | 8.00 | 109.00 | 117.00 | OK | |
| r-release-macos-x86_64 | 0.7.0 | 19.00 | 396.00 | 415.00 | OK | |
| r-release-windows-x86_64 | 0.7.0 | 24.00 | 290.00 | 314.00 | OK | |
| r-oldrel-macos-arm64 | 0.7.0 | 7.00 | 115.00 | 122.00 | OK | |
| r-oldrel-macos-x86_64 | 0.7.0 | 18.00 | 365.00 | 383.00 | OK | |
| r-oldrel-windows-x86_64 | 0.7.0 | 32.00 | 386.00 | 418.00 | OK |
Version: 0.7.0
Check: examples
Result: ERROR
Running examples in ‘omock-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: mockVocabularySet
> ### Title: Creates an empty mock CDM database populated with various
> ### vocabulary tables set.
> ### Aliases: mockVocabularySet
>
> ### ** Examples
>
> library(omock)
>
> # Create a mock CDM reference and populate it with mock vocabulary tables
> cdm <- mockCdmReference() |> mockVocabularySet(vocabularySet = "GiBleed")
ℹ Reading GiBleed tables.
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: mockVocabularySet ... <Anonymous> -> parquet___arrow___ArrowReaderProperties__Make
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.7.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [123s/166s]
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(omock)
>
> test_check("omock")
! Input tables only contain the observation_period table, hence only the person table will be updated
i Attempting download with timeout = 120 seconds.
i Reading GiBleed tables.
Saving _problems/test-mockCdmReference-13.R
i Creating '/home/hornik/tmp/scratch/Rtmpm4OWIR/DATASETS'.
i Attempting download with timeout = 120 seconds.
i Deleting prior version of GiBleed.
i Attempting download with timeout = 120 seconds.
i Attempting download with timeout = 120 seconds.
i Loading bundled GiBleed tables from package data.
i Adding drug_strength table.
i Creating local <cdm_reference> object.
i Loading bundled GiBleed tables from package data.
i Adding drug_strength table.
i Creating local <cdm_reference> object.
i Adapting cdmVersion from 5.3 to 5.4.
i Loading bundled GiBleed tables from package data.
i Adding drug_strength table.
i Creating local <cdm_reference> object.
i Loading bundled GiBleed tables from package data.
i Adding drug_strength table.
i Creating local <cdm_reference> object.
i Inserting <cdm_reference> into duckdb.
duckdb keeps downloaded extensions and secrets in a temporary directory:
i /home/hornik/tmp/scratch/Rtmpm4OWIR/duckdb
This is removed when the R session ends.
* Extensions are re-downloaded each session.
* Secrets are lost.
i Run duckdb(shared_home = TRUE) (or create ~/.duckdb) to keep them (suitable for most users).
i Run duckdb(shared_home = FALSE) to accept the temporary directory (and silence this message).
i See ?duckdb_storage for details and alternatives.
i Loading bundled GiBleed tables from package data.
i Adding drug_strength table.
i Creating local <cdm_reference> object.
i Inserting <cdm_reference> into duckdb.
duckdb keeps downloaded extensions and secrets in a temporary directory:
i /home/hornik/tmp/scratch/Rtmpm4OWIR/duckdb
This is removed when the R session ends.
* Extensions are re-downloaded each session.
* Secrets are lost.
i Run duckdb(shared_home = TRUE) (or create ~/.duckdb) to keep them (suitable for most users).
i Run duckdb(shared_home = FALSE) to accept the temporary directory (and silence this message).
i See ?duckdb_storage for details and alternatives.
i Loading bundled GiBleed tables from package data.
i Adding drug_strength table.
i Creating local <cdm_reference> object.
i Adapting cdmVersion from 5.3 to 5.4.
i Attempting download with timeout = 120 seconds.
i Reading GiBleed tables.
Saving _problems/test-mockMeasurement-106.R
Joining with `by = join_by(visit_occurrence_id)`
i Reading GiBleed tables.
Saving _problems/test-mockVocabularySet-6.R
Saving _problems/test-mockVocabularySet-7.R
i Reading GiBleed tables.
Saving _problems/test-mockVocabularySet-9.R
Saving _problems/test-mockVocabularySet-11.R
[ FAIL 6 | WARN 0 | SKIP 2 | PASS 231 ]
══ Skipped tests (2) ═══════════════════════════════════════════════════════════
• On CRAN (2): 'test-changeCdmVersion.R:2:3', 'test-mockDatasets.R:81:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-mockCdmReference.R:10:3'): check no error with vocab set in mockVocabulary set ──
Expected `omock::mockCdmReference(cdmName = "liverpool", vocabularySet = "GiBleed")` not to throw any errors.
Actually got a <simpleError> with message:
Cannot call parquet___arrow___ArrowReaderProperties__Make(). See https://arrow.apache.org/docs/r/articles/install.html for help installing Arrow C++ libraries.
── Error ('test-mockMeasurement.R:106:3'): empty measurement concept ───────────
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. └─omock::mockVocabularySet() at test-mockMeasurement.R:106:3
2. └─omock:::readTables(tmpFolder, cv, vocab = T)
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. └─arrow::read_parquet(file = tables[[nm]])
12. ├─ParquetFileReader$create(file, props = props, mmap = mmap, ...)
13. │ └─arrow:::assert_is(props, "ParquetArrowReaderProperties")
14. │ ├─assertthat::assert_that(inherits(object, class), msg = msg)
15. │ │ └─assertthat::see_if(..., env = env, msg = msg)
16. │ │ ├─base::tryCatch(...)
17. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
18. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
19. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
20. │ │ └─base::eval(assertion, env)
21. │ │ └─base::eval(assertion, env)
22. │ └─base::inherits(object, class)
23. └─ParquetArrowReaderProperties$create()
24. └─arrow:::parquet___arrow___ArrowReaderProperties__Make(isTRUE(use_threads))
── Failure ('test-mockVocabularySet.R:6:3'): mockVocabularySet ─────────────────
Expected `cdm <- mockVocabularySet(vocabularySet = dbName)` not to throw any errors.
Actually got a <simpleError> with message:
Cannot call parquet___arrow___ArrowReaderProperties__Make(). See https://arrow.apache.org/docs/r/articles/install.html for help installing Arrow C++ libraries.
── Failure ('test-mockVocabularySet.R:7:3'): mockVocabularySet ─────────────────
Expected `omopgenerics::validateCdmArgument(cdm)` not to throw any errors.
Actually got a <objectNotFoundError> with message:
object 'cdm' not found
── Failure ('test-mockVocabularySet.R:9:3'): mockVocabularySet ─────────────────
Expected `cdm <- mockVocabularySet(vocabularySet = dbName)` not to throw any errors.
Actually got a <simpleError> with message:
Cannot call parquet___arrow___ArrowReaderProperties__Make(). See https://arrow.apache.org/docs/r/articles/install.html for help installing Arrow C++ libraries.
── Error ('test-mockVocabularySet.R:11:3'): mockVocabularySet ──────────────────
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'cdm' not found
Backtrace:
▆
1. ├─testthat::expect_equal(nrow(cdm$person), 0) at test-mockVocabularySet.R:11:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─base::nrow(cdm$person)
[ FAIL 6 | WARN 0 | SKIP 2 | PASS 231 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc