* using log directory ‘/data/localhost/ripley/R/packages/tests-clang-trunk/omock.Rcheck’ * using R Under development (unstable) (2026-09-03 r90476) * using platform: x86_64-pc-linux-gnu * R was compiled by clang version 23.1.0 flang version 23.1.0 * running under: Fedora Linux 44 (Server Edition) * using session charset: UTF-8 * current time: 2026-09-03 08:03:34 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 ... [17s/20s] OK * 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/16s] 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 ... [11s/14s] OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ [106s/117s] [106s/117s] ERROR 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/Rtmp2qbXEn/working_dir/RtmpzyO7Ms/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 object. i Loading bundled GiBleed tables from package data. i Adding drug_strength table. i Creating local 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 object. i Loading bundled GiBleed tables from package data. i Adding drug_strength table. i Creating local object. i Inserting into duckdb. Saving _problems/test-mockDatasets-50.R i Loading bundled GiBleed tables from package data. i Adding drug_strength table. i Creating local object. i Inserting into duckdb. Saving _problems/test-mockDatasets-52.R i Loading bundled GiBleed tables from package data. i Adding drug_strength table. i Creating local 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 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 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/48s] ERROR Error(s) in re-building vignettes: --- re-building ‘mock_from_tables.Rmd’ using rmarkdown --- finished re-building ‘mock_from_tables.Rmd’ --- re-building ‘subset_concepts.Rmd’ using rmarkdown --- finished re-building ‘subset_concepts.Rmd’ --- re-building ‘synthetic_clinical_tables.Rmd’ using rmarkdown --- finished re-building ‘synthetic_clinical_tables.Rmd’ --- re-building ‘synthetic_cohorts.Rmd’ using rmarkdown --- finished re-building ‘synthetic_cohorts.Rmd’ --- re-building ‘synthetic_datasets.Rmd’ using rmarkdown Quitting from synthetic_datasets.Rmd:127-130 [unnamed-chunk-11] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 --- 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 See ‘/data/localhost/ripley/R/packages/tests-clang-trunk/omock.Rcheck/00check.log’ for details. Command exited with non-zero status 1 Time 4:25.82, 195.34 + 9.70