Check results for 'PatientProfiles'

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 ‘PatientProfiles/DESCRIPTION’ ... OK
checking extension type ... Package
this is package ‘PatientProfiles’ version ‘1.4.4’
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 ‘PatientProfiles’ can be installed ... [6s/24s] OK See the install log for details.
checking installed package size ... OK
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/3s] OK
checking whether the package can be loaded with stated dependencies ... [1s/2s] OK
checking whether the package can be unloaded cleanly ... [1s/2s] OK
checking whether the namespace can be loaded with stated dependencies ... [1s/4s] OK
checking whether the namespace can be unloaded cleanly ... [1s/4s] OK
checking loading without being on the library search path ... [1s/4s] 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 ... [7s/27s] OK
checking Rd files ... [1s/2s] OK
checking Rd metadata ... 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 ... [1s/4s] OK
checking for unstated dependencies in ‘tests’ ... OK
checking tests ... [5m/10m] OK Running ‘spelling.R’ [0s/1s] Running ‘testthat.R’ [5m/10m]
checking for unstated dependencies in vignettes ... OK
checking package vignettes ... OK
checking re-building of vignette outputs ... [117s/176s] ERROR Error(s) in re-building vignettes: --- re-building ‘cohort-intersect.Rmd’ using rmarkdown --- finished re-building ‘cohort-intersect.Rmd’ --- re-building ‘concept-intersect.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 concept-intersect.Rmd:35-52 [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 'concept-intersect.Rmd' failed with diagnostics: there is no package called 'arrow' --- failed re-building ‘concept-intersect.Rmd’ --- re-building ‘demographics.rmd’ using rmarkdown --- finished re-building ‘demographics.rmd’ --- re-building ‘summarise.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.Rmd:78-130 [unnamed-chunk-3] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <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.Rmd' failed with diagnostics: there is no package called 'arrow' --- failed re-building ‘summarise.Rmd’ --- re-building ‘table-intersect.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 table-intersect.Rmd:34-57 [unnamed-chunk-3] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <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 'table-intersect.Rmd' failed with diagnostics: there is no package called 'arrow' --- failed re-building ‘table-intersect.Rmd’ SUMMARY: processing the following files failed: ‘concept-intersect.Rmd’ ‘summarise.Rmd’ ‘table-intersect.Rmd’ Error: Vignette re-building failed. Execution halted
checking PDF version of manual ... [8s/10s] OK
DONE Status: 1 ERROR
using check arguments '--no-clean-on-error '