• using R Under development (unstable) (2026-02-03 r89372)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     clang version 21.1.8     flang version 21.1.8
• running under: Fedora Linux 42 (Workstation Edition)
• using session charset: UTF-8 * current time: 2026-02-03 09:17:10Z
• using option ‘--no-stop-on-test-error’
• checking for file ‘OmopSketch/DESCRIPTION’ ... OK
• this is package ‘OmopSketch’ version ‘1.0.0’
• package encoding: UTF-8
• checking package namespace information ... OK
• checking package dependencies ... OK
• 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 ‘OmopSketch’ can be installed ... [13s/17s] OK See the install log for details.
• checking installed package size ... INFO   installed size is 31.7Mb   sub-directories of 1Mb or more:     doc 29.4Mb     help 2.0Mb
• 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 ... [24s/32s] 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 R/sysdata.rda ... OK
• checking installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [431s/493s] OK   Running ‘testthat.R’ [430s/492s]
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [13m/14m] ERROR Error(s) in re-building vignettes: --- re-building ‘database_characteristics.Rmd’ using rmarkdown --- finished re-building ‘database_characteristics.Rmd’ --- re-building ‘missing_data.Rmd’ using rmarkdown --- finished re-building ‘missing_data.Rmd’ --- re-building ‘summarise_clinical_tables_records.Rmd’ using rmarkdown --- finished re-building ‘summarise_clinical_tables_records.Rmd’ --- re-building ‘summarise_concept_id_counts.Rmd’ using rmarkdown --- finished re-building ‘summarise_concept_id_counts.Rmd’ --- re-building ‘summarise_observation_period.Rmd’ using rmarkdown Quitting from summarise_observation_period.Rmd:160-168 [unnamed-chunk-10] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `if (x$plot_header_text_bold) ...`: ! argument is of length zero --- Backtrace:     ▆  1. └─OmopSketch::plotObservationPeriod(...)  2. └─visOmopResults::barPlot(...)  3. └─visOmopResults:::validateStyle(style = style, obj = "plot", type = type)  4. └─visOmopResults:::formatPlotStyle(x = internalStyle, fontsizeRef = fontsizeRef) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'summarise_observation_period.Rmd' failed with diagnostics: argument is of length zero --- failed re-building ‘summarise_observation_period.Rmd’ --- re-building ‘summarise_person.Rmd’ using rmarkdown --- finished re-building ‘summarise_person.Rmd’ --- re-building ‘summarise_trend.Rmd’ using rmarkdown Quitting from summarise_trend.Rmd:262-277 [unnamed-chunk-15] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `if (x$plot_header_text_bold) ...`: ! argument is of length zero --- Backtrace:     ▆  1. └─OmopSketch::plotTrend(result = result, colour = "sex", facet = "age_group")  2. └─visOmopResults::scatterPlot(...)  3. └─visOmopResults:::validateStyle(style = style, obj = "plot", type = type)  4. └─visOmopResults:::formatPlotStyle(x = internalStyle, fontsizeRef = fontsizeRef) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'summarise_trend.Rmd' failed with diagnostics: argument is of length zero --- failed re-building ‘summarise_trend.Rmd’ SUMMARY: processing the following files failed:   ‘summarise_observation_period.Rmd’ ‘summarise_trend.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: 1 ERROR