* using log directory ‘/home/hornik/tmp/CRAN_special_noSuggests/OmopSketch.Rcheck’
* using R Under development (unstable) (2024-11-11 r87319)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc-14 (Debian 14.2.0-1) 14.2.0
    GNU Fortran (Debian 14.2.0-1) 14.2.0
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* checking for file ‘OmopSketch/DESCRIPTION’ ... OK
* this is package ‘OmopSketch’ version ‘0.1.2’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [6s/7s] OK
* 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 serialization versions ... OK
* checking whether package ‘OmopSketch’ can be installed ... [3s/3s] OK
* 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 ... [0s/0s] OK
* checking whether the package can be unloaded cleanly ... [0s/0s] OK
* checking whether the namespace can be loaded with stated dependencies ... [0s/0s] 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 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 ... [5s/6s] OK
* checking Rd files ... [0s/0s] 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 ... [1s/1s] ERROR
Running examples in ‘OmopSketch-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: mockOmopSketch
> ### Title: Creates a mock database to test OmopSketch package.
> ### Aliases: mockOmopSketch
> 
> ### ** Examples
> 
> mockOmopSketch(numberIndividuals = 100)
Error in mockOmopSketch(numberIndividuals = 100) : 
  The package "duckdb" is required.
Calls: mockOmopSketch -> <Anonymous>
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [5s/3s] OK
  Running ‘testthat.R’ [5s/3s]
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [4s/4s] ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘A-summarise_clinical_tables_records.Rmd’ using rmarkdown

Quitting from lines 36-41 [unnamed-chunk-2] (A-summarise_clinical_tables_records.Rmd)
Error: processing vignette 'A-summarise_clinical_tables_records.Rmd' failed with diagnostics:
The package "duckdb" is required.
--- failed re-building ‘A-summarise_clinical_tables_records.Rmd’

--- re-building ‘B-summarise_concept_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


Quitting from lines 37-51 [unnamed-chunk-2] (B-summarise_concept_counts.Rmd)
Error: processing vignette 'B-summarise_concept_counts.Rmd' failed with diagnostics:
there is no package called 'duckdb'
--- failed re-building ‘B-summarise_concept_counts.Rmd’

--- re-building ‘C-summarise_pop_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 lines 37-50 [unnamed-chunk-2] (C-summarise_pop_characteristics.Rmd)
Error: processing vignette 'C-summarise_pop_characteristics.Rmd' failed with diagnostics:
there is no package called 'duckdb'
--- failed re-building ‘C-summarise_pop_characteristics.Rmd’

SUMMARY: processing the following files failed:
  ‘A-summarise_clinical_tables_records.Rmd’
  ‘B-summarise_concept_counts.Rmd’
  ‘C-summarise_pop_characteristics.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... [3s/3s] OK
* checking HTML version of manual ... [0s/0s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 2 ERRORs