- using R Under development (unstable) (2025-09-10 r88807)
- using platform: x86_64-pc-linux-gnu
- R was compiled by
clang version 21.1.0
flang version 21.1.0
- running under: Fedora Linux 42 (Workstation Edition)
- using session charset: UTF-8
- using option ‘--no-stop-on-test-error’
- checking for file ‘NBDCtools/DESCRIPTION’ ... OK
- this is package ‘NBDCtools’ version ‘1.0.1’
- 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 ‘NBDCtools’ can be installed ... [11s/47s] WARNING
Found the following significant warnings:
Warning: ✖ The `NBDCtoolsData` package cannot be found. Please install it using:
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 ... [17s/44s] 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 contents of ‘data’ directory ... OK
- checking data for non-ASCII characters ... OK
- checking LazyData ... OK
- checking data for ASCII and uncompressed saves ... OK
- checking installed files from ‘inst/doc’ ... OK
- checking files in ‘vignettes’ ... OK
- checking examples ... ERROR
Running examples in ‘NBDCtools-Ex.R’ failed
The error most likely occurred in:
> ### Name: filter_empty_cols
> ### Title: Filter empty columns
> ### Aliases: filter_empty_cols
>
> ### ** Examples
>
> data <- tibble::tibble(
+ participant_id = c("sub-001", "sub-002", "sub-003"),
+ session_id = c("ses-001", "ses-001", "ses-002"),
+ var1 = c(NA, NA, NA),
+ var2 = c(NA, NA, 2),
+ var3 = c(NA, NA, 3)
+ )
> filter_empty_cols(data)
Error in `check_pkgs()`:
! NBDCtoolsData package is not installed
✖ `NBDCtoolsData`
ℹ Please install the missing packages with:
remotes::install_github(c("nbdc-datahub/NBDCtoolsData"))
Backtrace:
▆
1. └─NBDCtools::filter_empty_cols(data)
2. ├─chk::chk_character(id_cols)
3. │ └─chk::vld_character(x)
4. ├─generics::union(get_id_cols_abcd(), get_id_cols_hbcd())
5. └─NBDCtools::get_id_cols_abcd()
6. └─NBDCtools::get_id_cols(study = "abcd", ...)
7. ├─base::unique(...)
8. ├─base::unlist(...)
9. ├─stringr::str_split(...)
10. │ └─stringr:::check_lengths(string, pattern)
11. │ └─vctrs::vec_size_common(...)
12. ├─dplyr::pull(get_dd(study, release), identifier_columns)
13. └─NBDCtools::get_dd(study, release)
14. └─NBDCtools::get_metadata(study, release, vars, tables, type = "dd")
15. └─NBDCtools:::check_data_pkg_installed()
16. └─NBDCtools:::check_pkgs(...)
17. └─cli::cli_abort(c(abort_msg, x = missing_info, i = install_info))
18. └─rlang::abort(...)
Execution halted
- checking for unstated dependencies in vignettes ... OK
- checking package vignettes ... OK
- checking re-building of vignette outputs ... [26s/63s] OK
- checking PDF version of manual ... [8s/18s] 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, 1 WARNING