• using R Under development (unstable) (2025-11-12 r89009)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     clang version 21.1.5     flang version 21.1.5
• running under: Fedora Linux 42 (Workstation Edition)
• using session charset: UTF-8
• using option ‘--no-stop-on-test-error’
• checking for file ‘OmopSketch/DESCRIPTION’ ... OK
• this is package ‘OmopSketch’ version ‘0.5.1’
• 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/47s] OK See the install log for details.
• checking installed package size ... INFO   installed size is 18.1Mb   sub-directories of 1Mb or more:     doc 17.1Mb
• 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 ... [22s/82s] 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 ... [19s/39s] OK   Running ‘testthat.R’ [18s/38s]
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [5m/18m] ERROR Error(s) in re-building vignettes: --- re-building ‘database_characteristics.Rmd’ using rmarkdown Quitting from database_characteristics.Rmd:32-39 [unnamed-chunk-2] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ NULL ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'database_characteristics.Rmd' failed with diagnostics: ✖ `datasetName` a choice between: GiBleed, empty_cdm, synpuf-1k_5.3,   synpuf-1k_5.4, synthea-allergies-10k, synthea-anemia-10k,   synthea-breast_cancer-10k, synthea-contraceptives-10k, synthea-covid19-10k,   synthea-covid19-200k, synthea-dermatitis-10k, synthea-heart-10k,   synthea-hiv-10k, synthea-lung_cancer-10k, synthea-medications-10k,   synthea-metabolic_syndrome-10k, synthea-opioid_addiction-10k,   synthea-rheumatoid_arthritis-10k, …, synthea-veterans-10k, and   synthea-weight_loss-10k. ! `datasetName` must be a choice between: GiBleed, empty_cdm, synpuf-1k_5.3,   synpuf-1k_5.4, synthea-allergies-10k, synthea-anemia-10k,   synthea-breast_cancer-10k, synthea-contraceptives-10k, synthea-covid19-10k,   synthea-covid19-200k, synthea-dermatitis-10k, synthea-heart-10k,   synthea-hiv-10k, synthea-lung_cancer-10k, synthea-medications-10k,   synthea-metabolic_syndrome-10k, synthea-opioid_addiction-10k,   synthea-rheumatoid_arthritis-10k, …, synthea-veterans-10k, and   synthea-weight_loss-10k; with length = 1; it can not contain NA; it can not   be NULL. --- failed re-building ‘database_characteristics.Rmd’ --- re-building ‘missing_data.Rmd’ using rmarkdown trying URL 'https://cdmconnectordata.blob.core.windows.net/cdmconnector-example-data/GiBleed_5.3.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 Quitting from summarise_clinical_tables_records.Rmd:35-41 [unnamed-chunk-2] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ NULL ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'summarise_clinical_tables_records.Rmd' failed with diagnostics: ✖ `datasetName` a choice between: GiBleed, empty_cdm, synpuf-1k_5.3,   synpuf-1k_5.4, synthea-allergies-10k, synthea-anemia-10k,   synthea-breast_cancer-10k, synthea-contraceptives-10k, synthea-covid19-10k,   synthea-covid19-200k, synthea-dermatitis-10k, synthea-heart-10k,   synthea-hiv-10k, synthea-lung_cancer-10k, synthea-medications-10k,   synthea-metabolic_syndrome-10k, synthea-opioid_addiction-10k,   synthea-rheumatoid_arthritis-10k, …, synthea-veterans-10k, and   synthea-weight_loss-10k. ! `datasetName` must be a choice between: GiBleed, empty_cdm, synpuf-1k_5.3,   synpuf-1k_5.4, synthea-allergies-10k, synthea-anemia-10k,   synthea-breast_cancer-10k, synthea-contraceptives-10k, synthea-covid19-10k,   synthea-covid19-200k, synthea-dermatitis-10k, synthea-heart-10k,   synthea-hiv-10k, synthea-lung_cancer-10k, synthea-medications-10k,   synthea-metabolic_syndrome-10k, synthea-opioid_addiction-10k,   synthea-rheumatoid_arthritis-10k, …, synthea-veterans-10k, and   synthea-weight_loss-10k; with length = 1; it can not contain NA; it can not   be NULL. --- failed re-building ‘summarise_clinical_tables_records.Rmd’ --- re-building ‘summarise_concept_id_counts.Rmd’ using rmarkdown Quitting from summarise_concept_id_counts.Rmd:32-41 [unnamed-chunk-2] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ NULL ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'summarise_concept_id_counts.Rmd' failed with diagnostics: ✖ `datasetName` a choice between: GiBleed, empty_cdm, synpuf-1k_5.3,   synpuf-1k_5.4, synthea-allergies-10k, synthea-anemia-10k,   synthea-breast_cancer-10k, synthea-contraceptives-10k, synthea-covid19-10k,   synthea-covid19-200k, synthea-dermatitis-10k, synthea-heart-10k,   synthea-hiv-10k, synthea-lung_cancer-10k, synthea-medications-10k,   synthea-metabolic_syndrome-10k, synthea-opioid_addiction-10k,   synthea-rheumatoid_arthritis-10k, …, synthea-veterans-10k, and   synthea-weight_loss-10k. ! `datasetName` must be a choice between: GiBleed, empty_cdm, synpuf-1k_5.3,   synpuf-1k_5.4, synthea-allergies-10k, synthea-anemia-10k,   synthea-breast_cancer-10k, synthea-contraceptives-10k, synthea-covid19-10k,   synthea-covid19-200k, synthea-dermatitis-10k, synthea-heart-10k,   synthea-hiv-10k, synthea-lung_cancer-10k, synthea-medications-10k,   synthea-metabolic_syndrome-10k, synthea-opioid_addiction-10k,   synthea-rheumatoid_arthritis-10k, …, synthea-veterans-10k, and   synthea-weight_loss-10k; with length = 1; it can not contain NA; it can not   be NULL. --- failed re-building ‘summarise_concept_id_counts.Rmd’ --- re-building ‘summarise_observation_period.Rmd’ using rmarkdown Quitting from summarise_observation_period.Rmd:34-40 [unnamed-chunk-2] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ NULL ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'summarise_observation_period.Rmd' failed with diagnostics: ✖ `datasetName` a choice between: GiBleed, empty_cdm, synpuf-1k_5.3,   synpuf-1k_5.4, synthea-allergies-10k, synthea-anemia-10k,   synthea-breast_cancer-10k, synthea-contraceptives-10k, synthea-covid19-10k,   synthea-covid19-200k, synthea-dermatitis-10k, synthea-heart-10k,   synthea-hiv-10k, synthea-lung_cancer-10k, synthea-medications-10k,   synthea-metabolic_syndrome-10k, synthea-opioid_addiction-10k,   synthea-rheumatoid_arthritis-10k, …, synthea-veterans-10k, and   synthea-weight_loss-10k. ! `datasetName` must be a choice between: GiBleed, empty_cdm, synpuf-1k_5.3,   synpuf-1k_5.4, synthea-allergies-10k, synthea-anemia-10k,   synthea-breast_cancer-10k, synthea-contraceptives-10k, synthea-covid19-10k,   synthea-covid19-200k, synthea-dermatitis-10k, synthea-heart-10k,   synthea-hiv-10k, synthea-lung_cancer-10k, synthea-medications-10k,   synthea-metabolic_syndrome-10k, synthea-opioid_addiction-10k,   synthea-rheumatoid_arthritis-10k, …, synthea-veterans-10k, and   synthea-weight_loss-10k; with length = 1; it can not contain NA; it can not   be NULL. --- failed re-building ‘summarise_observation_period.Rmd’ SUMMARY: processing the following files failed:   ‘database_characteristics.Rmd’   ‘summarise_clinical_tables_records.Rmd’   ‘summarise_concept_id_counts.Rmd’ ‘summarise_observation_period.Rmd’ Error: Vignette re-building failed. Execution halted
• checking PDF version of manual ... [8s/10s] 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