- using R version 4.5.1 (2025-06-13 ucrt)
- using platform: x86_64-w64-mingw32
- R was compiled by
gcc.exe (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
- running under: Windows Server 2022 x64 (build 20348)
- using session charset: UTF-8
- checking for file 'neotoma2/DESCRIPTION' ... OK
- this is package 'neotoma2' version '1.0.6'
- 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 hidden files and directories ... OK
- checking for portable file names ... OK
- checking whether package 'neotoma2' 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 ... [2s] OK
- checking whether the package can be loaded with stated dependencies ... [2s] OK
- checking whether the package can be unloaded cleanly ... [2s] OK
- checking whether the namespace can be loaded with stated dependencies ... [2s] OK
- checking whether the namespace can be unloaded cleanly ... [2s] OK
- checking loading without being on the library search path ... [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 ... [10s] OK
- checking Rd files ... [3s] OK
- checking Rd metadata ... 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 ... [4s] ERROR
Running examples in 'neotoma2-Ex.R' failed
The error most likely occurred in:
> ### Name: cite_data,sites-method
> ### Title: Obtain data citations from multiple records.
> ### Aliases: cite_data,sites-method
>
> ### ** Examples
>
> {
+ ds <- get_datasets(1)
+ cite_data(ds)
+ }
Error in `map()`:
ℹ In index: 1.
Caused by error in `map()`:
ℹ In index: 1.
Caused by error in `x$agerange[[1]]`:
! subscript out of bounds
Backtrace:
▆
1. ├─neotoma2::get_datasets(1)
2. ├─neotoma2:::get_datasets.numeric(1)
3. │ └─neotoma2:::parse_dataset(result)
4. │ └─purrr::map(...)
5. │ └─purrr:::map_("list", .x, .f, ..., .progress = .progress)
6. │ ├─purrr:::with_indexed_errors(...)
7. │ │ └─base::withCallingHandlers(...)
8. │ ├─purrr:::call_with_cleanup(...)
9. │ └─neotoma2 (local) .f(.x[[i]], ...)
10. │ └─purrr::map(x$site$datasets, build_dataset)
11. │ └─purrr:::map_("list", .x, .f, ..., .progress = .progress)
12. │ ├─purrr:::with_indexed_errors(...)
13. │ │ └─base::withCallingHandlers(...)
14. │ ├─purrr:::call_with_cleanup(...)
15. │ └─neotoma2 (local) .f(.x[[i]], ...)
16. │ ├─methods::new(...)
17. │ │ ├─methods::initialize(value, ...)
18. │ │ └─methods::initialize(value, ...)
19. │ ├─neotoma2:::use_na(testNull(x$agerange[[1]]$ageold, NA), "int")
20. │ └─neotoma2:::testNull(x$agerange[[1]]$ageold, NA)
21. └─purrr (local) `<fn>`(`<sbscOOBE>`)
22. └─cli::cli_abort(...)
23. └─rlang::abort(...)
Execution halted
- checking for unstated dependencies in 'tests' ... OK
- checking tests ... [11s] OK
Running 'testthat.R' [11s]
- checking for unstated dependencies in vignettes ... OK
- checking package vignettes ... OK
- checking re-building of vignette outputs ... [8s] ERROR
Error(s) in re-building vignettes:
--- re-building 'neotoma2-package.Rmd' using rmarkdown
Quitting from neotoma2-package.Rmd:228-232 [getdatasetsbyid]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
NULL
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'neotoma2-package.Rmd' failed with diagnostics:
ℹ In index: 1.
Caused by error in `map()`:
ℹ In index: 1.
Caused by error in `x$agerange[[1]]`:
! subscript out of bounds
--- failed re-building 'neotoma2-package.Rmd'
SUMMARY: processing the following file failed:
'neotoma2-package.Rmd'
Error: Vignette re-building failed.
Execution halted
- checking PDF version of manual ... [27s] OK
- checking HTML version of manual ... [37s] OK
- DONE
Status: 2 ERRORs