• using R Under development (unstable) (2025-10-31 r88977)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc-15 (Debian 15.2.0-7) 15.2.0     GNU Fortran (Debian 15.2.0-7) 15.2.0
• running under: Debian GNU/Linux forky/sid
• using session charset: UTF-8
• checking for file ‘OmopSketch/DESCRIPTION’ ... OK
• this is package ‘OmopSketch’ version ‘0.5.1’
• package encoding: UTF-8
• checking CRAN incoming feasibility ... [1s/2s] OK
• checking package namespace information ... OK
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• checking for hidden files and directories ... OK
• checking for portable file names ... OK
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• checking whether package ‘OmopSketch’ can be installed ... OK See the install log for details.
• checking package directory ... OK
• checking for future file timestamps ... 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 ... [1s/1s] OK
• checking whether the package can be loaded with stated dependencies ... [1s/1s] OK
• checking whether the package can be unloaded cleanly ... [1s/1s] OK
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• checking use of S3 registration ... OK
• checking dependencies in R code ... OK
• checking S3 generic/method consistency ... OK
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• checking foreign function calls ... OK
• checking R code for possible problems ... [9s/12s] OK
• checking Rd files ... [0s/0s] OK
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• 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 ... [1s/1s] OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [8s/7s] OK   Running ‘testthat.R’ [7s/7s]
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [120s/158s] 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 ... [5s/7s] OK
• checking HTML version of manual ... [1s/1s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 1 ERROR