Package: OmopConstructor Check: re-building of vignette outputs New result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘buildObservationPeriod.Rmd’ using rmarkdown trying URL 'https://example-data.ohdsi.dev/GiBleed.zip' Content type 'application/zip' length 6754786 bytes (6.4 MB) ================================================== downloaded 6.4 MB Quitting from buildObservationPeriod.Rmd:371-377 [unnamed-chunk-11] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `if (x$plot_header_text_bold) ...`: ! argument is of length zero --- Backtrace: ▆ 1. └─OmopSketch::plotObservationPeriod(...) 2. └─visOmopResults::scatterPlot(...) 3. └─visOmopResults:::validateStyle(style = style, obj = "plot", type = type) 4. └─visOmopResults:::formatPlotStyle(x = internalStyle, fontsizeRef = fontsizeRef) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'buildObservationPeriod.Rmd' failed with diagnostics: argument is of length zero --- failed re-building ‘buildObservationPeriod.Rmd’ SUMMARY: processing the following file failed: ‘buildObservationPeriod.Rmd’ Error: Vignette re-building failed. Execution halted Package: OmopSketch Check: re-building of vignette outputs New result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘database_characteristics.Rmd’ using rmarkdown trying URL 'https://example-data.ohdsi.dev/GiBleed.zip' Content type 'application/zip' length 6754786 bytes (6.4 MB) ================================================== downloaded 6.4 MB --- finished re-building ‘database_characteristics.Rmd’ --- re-building ‘missing_data.Rmd’ using rmarkdown trying URL 'https://example-data.ohdsi.dev/GiBleed.zip' Content type 'application/zip' length 6754786 bytes (6.4 MB) ================================================== downloaded 6.4 MB --- finished re-building ‘missing_data.Rmd’ --- re-building ‘summarise_clinical_tables_records.Rmd’ using rmarkdown trying URL 'https://example-data.ohdsi.dev/GiBleed.zip' Content type 'application/zip' length 6754786 bytes (6.4 MB) ================================================== downloaded 6.4 MB --- finished re-building ‘summarise_clinical_tables_records.Rmd’ --- re-building ‘summarise_concept_id_counts.Rmd’ using rmarkdown trying URL 'https://example-data.ohdsi.dev/GiBleed.zip' Content type 'application/zip' length 6754786 bytes (6.4 MB) ================================================== downloaded 6.4 MB --- finished re-building ‘summarise_concept_id_counts.Rmd’ --- re-building ‘summarise_observation_period.Rmd’ using rmarkdown trying URL 'https://example-data.ohdsi.dev/GiBleed.zip' Content type 'application/zip' length 6754786 bytes (6.4 MB) ================================================== downloaded 6.4 MB Quitting from summarise_observation_period.Rmd:160-168 [unnamed-chunk-10] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 trying URL 'https://example-data.ohdsi.dev/GiBleed.zip' Content type 'application/zip' length 6754786 bytes (6.4 MB) ================================================== downloaded 6.4 MB --- finished re-building ‘summarise_person.Rmd’ --- re-building ‘summarise_trend.Rmd’ using rmarkdown trying URL 'https://example-data.ohdsi.dev/GiBleed.zip' Content type 'application/zip' length 6754786 bytes (6.4 MB) ================================================== downloaded 6.4 MB Quitting from summarise_trend.Rmd:262-277 [unnamed-chunk-15] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 Package: PhenotypeR [Old version: 0.3.0, New version: 0.3.1] Check: re-building of vignette outputs New result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘CodelistDiagnostics.Rmd’ using rmarkdown trying URL 'https://cdmconnectordata.blob.core.windows.net/cdmconnector-example-data/synpuf-1k_5.3.zip' Content type 'application/zip' length 593048982 bytes (565.6 MB) ================================================== downloaded 565.6 MB Quitting from CodelistDiagnostics.Rmd:87-89 [unnamed-chunk-5] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `safeFontFamily()`: ! The package "systemfonts" is required. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'CodelistDiagnostics.Rmd' failed with diagnostics: The package "systemfonts" is required. --- failed re-building ‘CodelistDiagnostics.Rmd’ --- re-building ‘CohortDiagnostics.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘CohortDiagnostics.Rmd’ --- re-building ‘DatabaseDiagnostics.Rmd’ using rmarkdown trying URL 'https://cdmconnectordata.blob.core.windows.net/cdmconnector-example-data/synpuf-1k_5.3.zip' Content type 'application/zip' length 593048982 bytes (565.6 MB) ================================================== downloaded 565.6 MB [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘DatabaseDiagnostics.Rmd’ --- re-building ‘PhenotypeDiagnostics.Rmd’ using rmarkdown trying URL 'https://cdmconnectordata.blob.core.windows.net/cdmconnector-example-data/synpuf-1k_5.3.zip' Content type 'application/zip' length 593048982 bytes (565.6 MB) ================================================== downloaded 565.6 MB [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘PhenotypeDiagnostics.Rmd’ --- re-building ‘PhenotypeExpectations.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘PhenotypeExpectations.Rmd’ --- re-building ‘PopulationDiagnostics.Rmd’ using rmarkdown trying URL 'https://cdmconnectordata.blob.core.windows.net/cdmconnector-example-data/synpuf-1k_5.3.zip' Content type 'application/zip' length 593048982 bytes (565.6 MB) ================================================== downloaded 565.6 MB Quitting from PopulationDiagnostics.Rmd:70-78 [unnamed-chunk-4] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `safeFontFamily()`: ! The package "systemfonts" is required. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'PopulationDiagnostics.Rmd' failed with diagnostics: The package "systemfonts" is required. --- failed re-building ‘PopulationDiagnostics.Rmd’ --- re-building ‘ShinyDiagnostics.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘ShinyDiagnostics.Rmd’ SUMMARY: processing the following files failed: ‘CodelistDiagnostics.Rmd’ ‘PopulationDiagnostics.Rmd’ Error: Vignette re-building failed. Execution halted