- using R Under development (unstable) (2026-08-20 r90438)
- using platform: x86_64-pc-linux-gnu
- R was compiled by
clang version 22.1.8
flang version 22.1.8
- running under: Fedora Linux 44 (Server Edition)
- using session charset: UTF-8
* current time: 2026-08-20 17:23:24 UTC
- using option ‘--no-stop-on-test-error’
- checking for file ‘dsROCrate/DESCRIPTION’ ... OK
- this is package ‘dsROCrate’ version ‘0.2.1’
- 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 ‘dsROCrate’ can be installed ... 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 ... OK
- checking whether the package can be loaded with stated dependencies ... OK
- checking whether the package can be unloaded cleanly ... OK
- checking whether the namespace can be loaded with stated dependencies ... OK
- checking whether the namespace can be unloaded cleanly ... OK
- checking loading without being on the library search path ... OK
- checking whether startup messages can be suppressed ... 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 ... [8s/19s] OK
- checking Rd files ... 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 ... OK
- checking for unstated dependencies in ‘tests’ ... OK
- checking tests ... [6s/11s] OK
Running ‘testthat.R’ [5s/10s]
- checking for unstated dependencies in vignettes ... OK
- checking package vignettes ... OK
- checking re-building of vignette outputs ... [14s/36s] ERROR
Error(s) in re-building vignettes:
--- re-building ‘audit-permissions.Rmd’ using rmarkdown
--- finished re-building ‘audit-permissions.Rmd’
--- re-building ‘deploy-local-datashield-server-with-opal.Rmd’ using rmarkdown
--- finished re-building ‘deploy-local-datashield-server-with-opal.Rmd’
--- re-building ‘getting-started.Rmd’ using rmarkdown
Quitting from getting-started.Rmd:459-468 [unnamed-chunk-26]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `UseMethod()`:
! no applicable method for 'select' applied to an object of class "NULL"
---
Backtrace:
▆
1. ├─dsROCrate::audit(...)
2. └─dsROCrate:::audit.opal(...)
3. ├─dsROCrate:::audit_engine(...)
4. └─dsROCrate:::audit_engine.opal(...)
5. └─purrr::reduce(...)
6. └─purrr:::reduce_impl(.x, .f, ..., .init = .init, .dir = .dir)
7. └─dsROCrate (local) fn(out, elt, ...)
8. ├─dsROCrate::safe_output(...)
9. └─dsROCrate:::safe_output.rocrate(...)
10. ├─dsROCrate::safe_output(...)
11. └─dsROCrate:::safe_output.opal(...)
12. ├─dplyr::select(...)
13. ├─dplyr::mutate(...)
14. ├─dplyr::mutate(...)
15. ├─dplyr::left_join(...)
16. ├─purrr::list_c(...)
17. │ └─vctrs::obj_check_list(x)
18. ├─(function(x) {...
19. │ ├─purrr::map2(...)
20. │ │ └─purrr:::map2_("list", .x, .y, .f, ..., .progress = .progress)
21. │ │ └─purrr:::vctrs_vec_compat(.x, .purrr_user_env)
22. │ ├─base::split(dplyr::select(x, -args), seq_len(nrow(x)))
23. │ └─dplyr::select(x, -args)
24. ├─dplyr::mutate(...)
25. └─dplyr::select(calls_tbl, -symbol)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'getting-started.Rmd' failed with diagnostics:
no applicable method for 'select' applied to an object of class "NULL"
--- failed re-building ‘getting-started.Rmd’
SUMMARY: processing the following file failed:
‘getting-started.Rmd’
Error: Vignette re-building failed.
Execution halted
- checking PDF version of manual ... OK
- checking HTML version of manual ... OK
- checking for non-standard things in the check directory ... OK
- checking for detritus in the temp directory ... OK
- DONE
Status: 1 ERROR