* using log directory ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/formatBibtex.Rcheck’ * 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 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-debian-clang/formatBibtex-00install.html' 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