• using R version 4.4.2 Patched (2025-01-16 r87584)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc-14 (Debian 14.2.0-12) 14.2.0     GNU Fortran (Debian 14.2.0-12) 14.2.0
• running under: Debian GNU/Linux trixie/sid
• using session charset: UTF-8
• checking for file ‘PhenotypeR/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘PhenotypeR’ version ‘0.1.0’
• 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 ‘PhenotypeR’ 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
• checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK
• checking whether the namespace can be unloaded cleanly ... [1s/2s] 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 ... [6s/9s] OK
• checking Rd files ... [0s/1s] 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 installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... [1s/2s] OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [9m/11m] OK   Running ‘testthat.R’ [9m/11m]
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [83s/141s] ERROR Error(s) in re-building vignettes:   ... --- re-building ‘a01_DatabaseDiagnostics.Rmd’ using rmarkdown --- finished re-building ‘a01_DatabaseDiagnostics.Rmd’ --- re-building ‘a02_CodelistDiagnostics.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 61-63 [unnamed-chunk-3] (a02_CodelistDiagnostics.Rmd) Error: processing vignette 'a02_CodelistDiagnostics.Rmd' failed with diagnostics: unused argument (settingsColumns = settingsColumns) --- failed re-building ‘a02_CodelistDiagnostics.Rmd’ --- re-building ‘a03_CohortDiagnostics.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 ** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/PhenotypeR.Rcheck/vign_test/PhenotypeR/vignettes/a03_CohortDiagnostics_files/figure-html/unnamed-chunk-5-1.png 672x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 25275 bytes Input file size = 25389 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 19669   zc = 9 zm = 8 zs = 1 f = 0   zc = 1 zm = 8 zs = 2 f = 0   zc = 9 zm = 8 zs = 3 f = 0   zc = 9 zm = 8 zs = 0 f = 5   zc = 9 zm = 8 zs = 1 f = 5   zc = 1 zm = 8 zs = 2 f = 5   zc = 9 zm = 8 zs = 3 f = 5                                 Selecting parameters:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 19669 Output IDAT size = 19669 bytes (5606 bytes decrease) Output file size = 19747 bytes (5642 bytes = 22.22% decrease) --- finished re-building ‘a03_CohortDiagnostics.Rmd’ --- re-building ‘a04_MatchedDiagnostics.Rmd’ using rmarkdown --- finished re-building ‘a04_MatchedDiagnostics.Rmd’ --- re-building ‘a05_PopulationDiagnostics.Rmd’ using rmarkdown [WARNING] This document format requires a nonempty <title> element.   Defaulting to 'a05_PopulationDiagnostics.knit' as the title.   To specify a title, use 'title' in metadata or --metadata title="...". --- finished re-building ‘a05_PopulationDiagnostics.Rmd’ SUMMARY: processing the following file failed:   ‘a02_CodelistDiagnostics.Rmd’ Error: Vignette re-building failed. Execution halted
• checking PDF version of manual ... [4s/7s] OK
• checking HTML version of manual ... [0s/1s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 1 ERROR