* using log directory ‘/srv/hornik/tmp/CRAN_pretest/SeroTrackR.Rcheck’ * using R Under development (unstable) (2025-11-11 r88995) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 19.1.7 (7) Debian flang-new version 19.1.7 (7) * running under: Debian GNU/Linux forky/sid * using session charset: UTF-8 * checking for file ‘SeroTrackR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘SeroTrackR’ version ‘0.5.0’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [3s/4s] NOTE Maintainer: ‘Dionne Argyropoulos ’ New submission Possibly misspelled words in DESCRIPTION: Serological (3:18) Found the following (possibly) invalid URLs: URL: https://dionnecargy.shinyapps.io/PvSeroApp/ From: inst/doc/PvSeroApp_R_Tutorial.html Status: 401 Message: Unauthorized Size of tarball: 59653591 bytes * 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 ‘SeroTrackR’ can be installed ... [8s/8s] 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 ... [2s/2s] OK * checking whether the package can be loaded with stated dependencies ... [2s/2s] OK * checking whether the package can be unloaded cleanly ... [2s/2s] OK * checking whether the namespace can be loaded with stated dependencies ... [2s/2s] OK * checking whether the namespace can be unloaded cleanly ... [2s/2s] OK * checking loading without being on the library search path ... [2s/2s] 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 ... [13s/13s] 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 installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... NONE * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [47s/46s] ERROR Error(s) in re-building vignettes: ... --- re-building ‘Pk_Pv_Pf_Serology_R_Tutorial.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘Pk_Pv_Pf_Serology_R_Tutorial.Rmd’ --- re-building ‘PvSeroApp_R_Tutorial.Rmd’ using rmarkdown Quitting from PvSeroApp_R_Tutorial.Rmd:75-82 [create pdf output] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `loadNamespace()`: ! there is no package called 'kableExtra' --- Backtrace: x 1. +-SeroTrackR::renderQCReport(...) 2. | +-base::suppressWarnings(...) 3. | | \-base::withCallingHandlers(...) 4. | +-rmarkdown::render(...) 5. | | \-knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) 6. | | \-knitr:::process_file(text, output) 7. | | +-xfun:::handle_error(...) 8. | | +-base::withCallingHandlers(...) 9. | | \-knitr:::process_group(group) 10. | | \-knitr:::call_block(x) 11. | | \-knitr:::block_exec(params) 12. | | \-knitr:::eng_r(options) 13. | | +-knitr:::in_input_dir(...) 14. | | | \-knitr:::in_dir(input_dir(), expr) 15. | | \-knitr (local) evaluate(...) 16. | | \-evaluate::evaluate(...) 17. | | +-base::withRestarts(...) 18. | | | \-base (local) withRestartList(expr, restarts) 19. | | | +-base (local) withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) 20. | | | | \-base (local) doWithOneRestart(return(expr), restart) 21. | | | \-base (local) withRestartList(expr, restarts[-nr]) 22. | | | \-base (local) withOneRestart(expr, restarts[[1L]]) 23. | | | \-base (local) doWithOneRestart(return(expr), restart) 24. | | +-evaluate:::with_handlers(...) 25. | | | +-base::eval(call) 26. | | | | \-base::eval(call) 27. | | | \-base::withCallingHandlers(...) 28. | | +-base::withVisible(eval(expr, envir)) 29. | | \-base::eval(expr, envir) 30. | | \-base::eval(expr, envir) 31. | \-... %>% ... 32. \-base::loadNamespace(x) 33. \-base::withRestarts(stop(cond), retry_loadNamespace = function() NULL) 34. \-base (local) withOneRestart(expr, restarts[[1L]]) 35. \-base (local) doWithOneRestart(return(expr), restart) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'PvSeroApp_R_Tutorial.Rmd' failed with diagnostics: there is no package called 'kableExtra' --- failed re-building ‘PvSeroApp_R_Tutorial.Rmd’ SUMMARY: processing the following file failed: ‘PvSeroApp_R_Tutorial.Rmd’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... [5s/5s] WARNING LaTeX errors when creating PDF version. This typically indicates Rd problems. LaTeX errors found: ! LaTeX Error: Unicode character ≤ (U+2264) not set up for use with LaTeX. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ! LaTeX Error: Unicode character ≤ (U+2264) not set up for use with LaTeX. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. * checking PDF version of manual without index ... ERROR * checking HTML version of manual ... [1s/1s] OK * checking for non-standard things in the check directory ... NOTE Found the following files/directories: ‘SeroTrackR-manual.tex’ * checking for detritus in the temp directory ... OK * DONE Status: 2 ERRORs, 1 WARNING, 2 NOTEs