- using R Under development (unstable) (2025-02-26 r87830)
- using platform: x86_64-pc-linux-gnu
- R was compiled by
Debian clang version 19.1.7 (1+b1)
Debian flang-new version 19.1.7 (1+b1)
- running under: Debian GNU/Linux trixie/sid
- using session charset: UTF-8
- checking for file ‘formatBibtex/DESCRIPTION’ ... OK
- this is package ‘formatBibtex’ 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 ‘formatBibtex’ can be installed ... OK
See the install log for details.
- checking package directory ... OK
- checking for future file timestamps ... 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 ... [0s/0s] OK
- checking whether the package can be loaded with stated dependencies ... [0s/0s] OK
- checking whether the package can be unloaded cleanly ... [0s/0s] OK
- checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK
- checking whether the namespace can be unloaded cleanly ... [0s/0s] OK
- checking loading without being on the library search path ... [0s/0s] OK
- checking whether startup messages can be suppressed ... [0s/0s] 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 ... [4s/5s] 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 examples ... [0s/1s] ERROR
Running examples in ‘formatBibtex-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: format_bibtex_entry
> ### Title: Format BibTeX Entries in An Opinionated Way
> ### Aliases: format_bibtex_entry format_bibtex_file
>
> ### ** Examples
>
> library(formatBibtex)
>
> ## example BibTeX file that needs formatting
> example_bib <- system.file("examples/example.bib", package = "formatBibtex")
> print(readLines(example_bib), quote = FALSE)
[1] @article{andersen1982cox,
[2] title = {Cox's regression model for counting processes: a large sample study},
[3] author = {Andersen, Per Kragh and Gill, Richard D},
[4] journal = {the annals of statistics},
[5] volume = {10},
[6] number = {4},
[7] pages = {1100-1120},
[8] year = {1982},
[9] publisher = {JSTOR}
[10] }
[11]
[12] @book{chen2012monte,
[13] title={Monte Carlo methods in Bayesian computation},
[14] author={Chen, Ming-Hui and Shao, Qi-Man and Ibrahim, Joseph G},
[15] year={2012},
[16] publisher={Springer Science \\& Business Media}
[17] }
[18]
[19] @article{wu1983convergence,
[20] title={On the convergence properties of the EM algorithm},
[21] author={Wu, C.F. Jeff},
[22] journal={The Annals of statistics},
[23] pages={95--103},
[24] year={1983},
[25] publisher={JSTOR}
[26] }
>
> ## needs the package bibtex
> has_bibtex <- requireNamespace("bibtex", quietly = TRUE)
>
> ## example of format_bibtex_entry()
> if (has_bibtex) {
+ bib <- bibtex::read.bib(example_bib)
+ ## check the default words that need protection by curly braces
+ (default_words <- getOption("formatBibtex.protected_words"))
+ format_bibtex_entry(bib, protected_words = c(default_words, "SMEM"))
+ }
Error in gsub(as.character(pattern), as.character(replacement), x, ignore.case, :
NA in coercion to Rboolean
Calls: format_bibtex_entry ... lapply -> FUN -> format_string -> do.call -> <Anonymous>
Execution halted
- checking PDF version of manual ... [4s/6s] OK
- checking HTML version of manual ... [0s/0s] OK
- checking for non-standard things in the check directory ... OK
- DONE
Status: 1 ERROR