• using R version 4.4.1 (2024-06-14)
• using platform: x86_64-apple-darwin20
• R was compiled by     Apple clang version 14.0.0 (clang-1400.0.29.202)     GNU Fortran (GCC) 12.2.0
• running under: macOS Ventura 13.3.1
• using session charset: UTF-8
• checking for file ‘CohortCharacteristics/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘CohortCharacteristics’ version ‘1.1.0’
• 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 ‘CohortCharacteristics’ can be installed ... [5s/5s] OK See the install log for details.
• checking installed package size ... NOTE   installed size is 6.4Mb   sub-directories of 1Mb or more:     doc 4.3Mb     help 1.8Mb
• 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 ... [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
• checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK
• checking whether the namespace can be unloaded cleanly ... [1s/1s] OK
• checking loading without being on the library search path ... [1s/1s] 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 ... [5s/5s] OK
• checking Rd files ... [0s/0s] OK
• checking Rd metadata ... OK
• checking Rd cross-references ... OK
• checking for missing documentation entries ... OK
• checking for code/documentation mismatches ... WARNING Codoc mismatches from Rd file 'mockCohortCharacteristics.Rd': mockCohortCharacteristics   Code: function(con = NULL, writeSchema = NULL, numberIndividuals =                  10, ..., seed = NULL)   Docs: function(numberIndividuals = 10, ..., source = "local", con =                  lifecycle::deprecated(), writeSchema =                  lifecycle::deprecated(), seed =                  lifecycle::deprecated())   Argument names in docs not in code:     source   Mismatches in argument names (first 3):     Position: 1 Code: con Docs: numberIndividuals     Position: 2 Code: writeSchema Docs: ...     Position: 3 Code: numberIndividuals Docs: source   Mismatches in argument default values:     Name: 'con' Code: NULL Docs: lifecycle::deprecated()     Name: 'writeSchema' Code: NULL Docs: lifecycle::deprecated()     Name: 'seed' Code: NULL Docs: lifecycle::deprecated()
• checking Rd \usage sections ... OK
• checking Rd contents ... OK
• checking for unstated dependencies in examples ... OK
• checking installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... [14s/14s] OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [357s/221s] OK   Running ‘spelling.R’ [0s/0s]   Running ‘testthat.R’ [356s/220s]
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [18s/21s] ERROR Error(s) in re-building vignettes: --- re-building ‘summarise_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 Quitting from summarise_characteristics.Rmd:24-49 [unnamed-chunk-2] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `loadNamespace()`: ! there is no package called 'arrow' --- Backtrace:      ▆   1. ├─omock::mockCdmFromDataset(datasetName = "GiBleed", source = "duckdb")   2. │ └─omock:::readTables(tmpFolder, cv)   3. │ └─omock:::castColumns(...)   4. │ ├─dplyr::filter(...)   5. │ ├─dplyr:::filter.data.frame(...)   6. │ │ └─dplyr:::dplyr_quosures(...)   7. │ │ └─rlang::quos(..., .ignore_empty = "all")   8. │ └─base::colnames(x)   9. │ └─base::is.data.frame(x)  10. └─base::loadNamespace(x)  11. └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)  12. └─base (local) withOneRestart(expr, restarts[[1L]])  13. └─base (local) doWithOneRestart(return(expr), restart) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'summarise_characteristics.Rmd' failed with diagnostics: there is no package called 'arrow' --- failed re-building ‘summarise_characteristics.Rmd’ --- re-building ‘summarise_cohort_overlap.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_cohort_overlap.Rmd:27-57 [unnamed-chunk-2] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `loadNamespace()`: ! there is no package called 'arrow' --- Backtrace:      ▆   1. ├─omock::mockCdmFromDataset(datasetName = "GiBleed", source = "duckdb")   2. │ └─omock:::readTables(tmpFolder, cv)   3. │ └─omock:::castColumns(...)   4. │ ├─dplyr::filter(...)   5. │ ├─dplyr:::filter.data.frame(...)   6. │ │ └─dplyr:::dplyr_quosures(...)   7. │ │ └─rlang::quos(..., .ignore_empty = "all")   8. │ └─base::colnames(x)   9. │ └─base::is.data.frame(x)  10. └─base::loadNamespace(x)  11. └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)  12. └─base (local) withOneRestart(expr, restarts[[1L]])  13. └─base (local) doWithOneRestart(return(expr), restart) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'summarise_cohort_overlap.Rmd' failed with diagnostics: there is no package called 'arrow' --- failed re-building ‘summarise_cohort_overlap.Rmd’ --- re-building ‘summarise_cohort_timing.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_cohort_timing.Rmd:25-55 [unnamed-chunk-2] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `loadNamespace()`: ! there is no package called 'arrow' --- Backtrace:      ▆   1. ├─omock::mockCdmFromDataset(datasetName = "GiBleed", source = "duckdb")   2. │ └─omock:::readTables(tmpFolder, cv)   3. │ └─omock:::castColumns(...)   4. │ ├─dplyr::filter(...)   5. │ ├─dplyr:::filter.data.frame(...)   6. │ │ └─dplyr:::dplyr_quosures(...)   7. │ │ └─rlang::quos(..., .ignore_empty = "all")   8. │ └─base::colnames(x)   9. │ └─base::is.data.frame(x)  10. └─base::loadNamespace(x)  11. └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)  12. └─base (local) withOneRestart(expr, restarts[[1L]])  13. └─base (local) doWithOneRestart(return(expr), restart) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'summarise_cohort_timing.Rmd' failed with diagnostics: there is no package called 'arrow' --- failed re-building ‘summarise_cohort_timing.Rmd’ --- re-building ‘summarise_large_scale_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 Quitting from summarise_large_scale_characteristics.Rmd:31-48 [unnamed-chunk-2] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `loadNamespace()`: ! there is no package called 'arrow' --- Backtrace:      ▆   1. ├─omock::mockCdmFromDataset(datasetName = "GiBleed", source = "duckdb")   2. │ └─omock:::readTables(tmpFolder, cv)   3. │ └─omock:::castColumns(...)   4. │ ├─dplyr::filter(...)   5. │ ├─dplyr:::filter.data.frame(...)   6. │ │ └─dplyr:::dplyr_quosures(...)   7. │ │ └─rlang::quos(..., .ignore_empty = "all")   8. │ └─base::colnames(x)   9. │ └─base::is.data.frame(x)  10. └─base::loadNamespace(x)  11. └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)  12. └─base (local) withOneRestart(expr, restarts[[1L]])  13. └─base (local) doWithOneRestart(return(expr), restart) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'summarise_large_scale_characteristics.Rmd' failed with diagnostics: there is no package called 'arrow' --- failed re-building ‘summarise_large_scale_characteristics.Rmd’ SUMMARY: processing the following files failed:   ‘summarise_characteristics.Rmd’ ‘summarise_cohort_overlap.Rmd’   ‘summarise_cohort_timing.Rmd’   ‘summarise_large_scale_characteristics.Rmd’ Error: Vignette re-building failed. Execution halted
• checking PDF version of manual ... [6s/6s] OK
• DONE Status: 1 ERROR, 1 WARNING, 1 NOTE
• using check arguments '--no-clean-on-error '