• using R Under development (unstable) (2026-09-17 r90557)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     clang version 23.1.1     flang version 23.1.1
• running under: Fedora Linux 44 (Server Edition)
• using session charset: UTF-8 * current time: 2026-09-17 15:29:22 UTC
• using option ‘--no-stop-on-test-error’
• checking for file ‘omock/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘omock’ version ‘0.7.0’
• package encoding: UTF-8
• checking package namespace information ... OK
• checking package dependencies ... INFO Package suggested but not available for checking: 'duckdb'
• checking if this is a source package ... OK
• checking if there is a namespace ... OK
• checking for executable files ... OK
• checking for hidden files and directories ... OK
• checking for portable file names ... OK
• checking for sufficient/correct file permissions ... OK
• checking whether package ‘omock’ can be installed ... [18s/24s] OK See the install log for details.
• checking installed package size ... OK
• checking package directory ... OK
• checking ‘build’ directory ... OK
• checking DESCRIPTION meta-information ... OK
• checking top-level files ... OK
• checking for left-over files ... OK
• checking index information ... OK
• checking package subdirectories ... OK
• checking code files for non-ASCII characters ... OK
• checking R files for syntax errors ... OK
• checking whether the package can be loaded ... OK
• checking whether the package can be loaded with stated dependencies ... OK
• checking whether the package can be unloaded cleanly ... OK
• checking whether the namespace can be loaded with stated dependencies ... OK
• checking whether the namespace can be unloaded cleanly ... OK
• checking loading without being on the library search path ... OK
• checking use of S3 registration ... OK
• checking dependencies in R code ... OK
• checking S3 generic/method consistency ... OK
• checking replacement functions ... OK
• checking foreign function calls ... OK
• checking R code for possible problems ... [10s/12s] OK
• checking Rd files ... OK
• checking Rd metadata ... OK
• checking Rd line widths ... OK
• checking Rd cross-references ... OK
• checking for missing documentation entries ... OK
• checking for code/documentation mismatches ... OK
• checking Rd \usage sections ... OK
• checking Rd contents ... OK
• checking for unstated dependencies in examples ... OK
• checking contents of ‘data’ directory ... OK
• checking data for non-ASCII characters ... OK
• checking LazyData ... OK
• checking data for ASCII and uncompressed saves ... OK
• checking R/sysdata.rda ... OK
• checking installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... [12s/14s] OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [111s/120s] ERROR   Running ‘testthat.R’ [111s/120s] 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.   i Creating '/tmp/RtmpqQBxHG/working_dir/RtmpJQpHdc/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.   Saving _problems/test-mockDatasets-50.R   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.   Saving _problems/test-mockDatasets-52.R   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.   Joining with `by = join_by(visit_occurrence_id)`   i Reading GiBleed tables.   i Reading GiBleed tables.   [ FAIL 2 | WARN 0 | SKIP 2 | PASS 236 ]      ══ Skipped tests (2) ═══════════════════════════════════════════════════════════   • On CRAN (2): 'test-changeCdmVersion.R:2:3', 'test-mockDatasets.R:81:3'      ══ Failed tests ════════════════════════════════════════════════════════════════   ── Failure ('test-mockDatasets.R:50:3'): mock datasets cdm creation ────────────   Expected `cdm <- mockCdmFromDataset(datasetName = dbName, source = "duckdb")` not to throw any errors.   Actually got a <rlib_error_package_not_found> with message:     The package "duckdb" is required.   ── Failure ('test-mockDatasets.R:52:3'): mock datasets cdm creation ────────────   Expected `cdm <- mockCdmFromDataset(datasetName = dbName, source = "duckdb")` not to throw any errors.   Actually got a <rlib_error_package_not_found> with message:     The package "duckdb" is required.      [ FAIL 2 | WARN 0 | SKIP 2 | PASS 236 ]   Error:   ! Test failures.   Execution halted
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [28s/28s] ERROR Error(s) in re-building vignettes: --- re-building ‘mock_from_tables.Rmd’ using rmarkdown [WARNING] Deprecated: --mathjax. Use --math-method=mathjax[:URL] instead. --- finished re-building ‘mock_from_tables.Rmd’ --- re-building ‘subset_concepts.Rmd’ using rmarkdown [WARNING] Deprecated: --mathjax. Use --math-method=mathjax[:URL] instead. --- finished re-building ‘subset_concepts.Rmd’ --- re-building ‘synthetic_clinical_tables.Rmd’ using rmarkdown [WARNING] Deprecated: --mathjax. Use --math-method=mathjax[:URL] instead. --- finished re-building ‘synthetic_clinical_tables.Rmd’ --- re-building ‘synthetic_cohorts.Rmd’ using rmarkdown [WARNING] Deprecated: --mathjax. Use --math-method=mathjax[:URL] instead. --- finished re-building ‘synthetic_cohorts.Rmd’ --- re-building ‘synthetic_datasets.Rmd’ using rmarkdown Quitting from synthetic_datasets.Rmd:127-130 [unnamed-chunk-11] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlib_error_package_not_found> Error in `mockCdmFromDataset()`: ! The package "duckdb" is required. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'synthetic_datasets.Rmd' failed with diagnostics: The package "duckdb" is required. --- failed re-building ‘synthetic_datasets.Rmd’ --- re-building ‘synthetic_vocabulary.Rmd’ using rmarkdown [WARNING] Deprecated: --mathjax. Use --math-method=mathjax[:URL] instead. --- finished re-building ‘synthetic_vocabulary.Rmd’ SUMMARY: processing the following file failed:   ‘synthetic_datasets.Rmd’ Error: Vignette re-building failed. Execution halted
• checking PDF version of manual ... OK
• checking HTML version of manual ... OK
• checking for non-standard things in the check directory ... OK
• checking for detritus in the temp directory ... OK
• DONE

Status: 2 ERRORs