tidy_bib_file does not find references

[Robinlovelace]

I noticed this issue a while back but thought it may have been a quirk with the particular .Rmd file I was using. However, I've reproduced the error message on many files since.

Please test the reproducible example below and see if you can reproduce the error:

# aim: test tidy_bib 

# install dev version
devtools::install_github("crsh/citr")
#> Skipping install of 'citr' from a github remote, the SHA1 (ecdb245b) has not changed since last install.
#>   Use `force = TRUE` to force installation

# download an Rmd file that contains references
download.file("https://github.com/ITSLeeds/stats19/raw/master/README.Rmd", "test.Rmd")

# download a bibliography
download.file("https://github.com/ITSLeeds/stats19/raw/master/vignettes/references.bib", "references.bib")

# clean the 'messy' bibliography
citr::tidy_bib_file(rmd_file = "test.Rmd", messy_bibliography = "references.bib")
#> Error in citr::tidy_bib_file(rmd_file = "test.Rmd", messy_bibliography = "references.bib"): Found no references in test.Rmd

^{Created on 2019-02-06 by the reprex package (v0.2.1)}

Session info

``` r devtools::session_info() #> ─ Session info ────────────────────────────────────────────────────────── #> setting value #> version R version 3.5.1 (2018-07-02) #> os Debian GNU/Linux 9 (stretch) #> system x86_64, linux-gnu #> ui X11 #> language (EN) #> collate en_US.UTF-8 #> ctype en_US.UTF-8 #> tz Etc/UTC #> date 2019-02-06 #> #> ─ Packages ────────────────────────────────────────────────────────────── #> package * version date lib source #> assertthat 0.2.0 2017-04-11 [1] CRAN (R 3.5.1) #> backports 1.1.2 2017-12-13 [1] CRAN (R 3.5.1) #> base64enc 0.1-3 2015-07-28 [1] CRAN (R 3.5.1) #> callr 3.0.0 2018-08-24 [1] CRAN (R 3.5.1) #> citr 0.3.0 2019-02-06 [1] Github (crsh/citr@ecdb245) #> cli 1.0.1 2018-09-25 [1] CRAN (R 3.5.1) #> crayon 1.3.4 2017-09-16 [1] CRAN (R 3.5.1) #> curl 3.2 2018-03-28 [1] CRAN (R 3.5.1) #> desc 1.2.0 2018-05-01 [1] CRAN (R 3.5.1) #> devtools 2.0.1 2018-10-26 [1] CRAN (R 3.5.1) #> digest 0.6.18 2018-10-10 [1] CRAN (R 3.5.1) #> evaluate 0.12 2018-10-09 [1] CRAN (R 3.5.1) #> fs 1.2.6 2018-08-23 [1] CRAN (R 3.5.1) #> glue 1.3.0 2018-07-17 [1] CRAN (R 3.5.1) #> htmltools 0.3.6 2017-04-28 [1] CRAN (R 3.5.1) #> httpuv 1.4.5 2018-07-19 [1] CRAN (R 3.5.1) #> knitr 1.20 2018-02-20 [1] CRAN (R 3.5.1) #> later 0.7.5 2018-09-18 [1] CRAN (R 3.5.1) #> magrittr 1.5 2014-11-22 [1] CRAN (R 3.5.1) #> memoise 1.1.0 2017-04-21 [1] CRAN (R 3.5.1) #> mime 0.6 2018-10-05 [1] CRAN (R 3.5.1) #> miniUI 0.1.1.1 2018-05-18 [1] CRAN (R 3.5.1) #> pkgbuild 1.0.2 2018-10-16 [1] CRAN (R 3.5.1) #> pkgload 1.0.2 2018-10-29 [1] CRAN (R 3.5.1) #> prettyunits 1.0.2 2015-07-13 [1] CRAN (R 3.5.1) #> processx 3.2.1 2018-12-05 [1] CRAN (R 3.5.1) #> promises 1.0.1 2018-04-13 [1] CRAN (R 3.5.1) #> ps 1.2.1 2018-11-06 [1] CRAN (R 3.5.1) #> R6 2.3.0 2018-10-04 [1] CRAN (R 3.5.1) #> Rcpp 1.0.0 2018-11-07 [1] CRAN (R 3.5.1) #> remotes 2.0.2 2018-10-30 [1] CRAN (R 3.5.1) #> rlang 0.3.0.1 2018-10-25 [1] CRAN (R 3.5.1) #> rmarkdown 1.10 2018-06-11 [1] CRAN (R 3.5.1) #> rprojroot 1.3-2 2018-01-03 [1] CRAN (R 3.5.1) #> sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 3.5.1) #> shiny 1.2.0 2018-11-02 [1] CRAN (R 3.5.1) #> stringi 1.2.4 2018-07-20 [1] CRAN (R 3.5.1) #> stringr 1.3.1 2018-05-10 [1] CRAN (R 3.5.1) #> testthat 2.0.1 2018-10-13 [1] CRAN (R 3.5.1) #> usethis 1.4.0 2018-08-14 [1] CRAN (R 3.5.1) #> withr 2.1.2 2018-03-15 [1] CRAN (R 3.5.1) #> xtable 1.8-3 2018-08-29 [1] CRAN (R 3.5.1) #> yaml 2.2.0 2018-07-25 [1] CRAN (R 3.5.1) #> #> [1] /usr/local/lib/R/site-library #> [2] /usr/local/lib/R/library ```

[crsh]

Thanks for the excellent reproducible example. This should now be fixed. Let me know if you find other examples where it doesn't work as expected.

[Robinlovelace]

Confirmed: it now works again. Great work!

devtools::install_github("crsh/citr")
#> Skipping install of 'citr' from a github remote, the SHA1 (aab8006e) has not changed since last install.
#>   Use `force = TRUE` to force installation
download.file("https://github.com/ITSLeeds/stats19/raw/master/README.Rmd", "test.Rmd")
download.file("https://github.com/ITSLeeds/stats19/raw/master/vignettes/references.bib", "references.bib")
citr::tidy_bib_file(rmd_file = "test.Rmd", messy_bibliography = "references.bib")
#> Warning in do_read_bib(file, encoding = .Encoding, srcfile): encoding
#> 'native.enc' will be ignored
#> Removing 4 unneeded bibliography entries.
#> Writing 2 Bibtex entries ... OK
#> Results written to file 'references.bib'

^{Created on 2019-02-06 by the reprex package (v0.2.1)}

[Robinlovelace]

Heads-up @crsh, sorry, but I've just found another edge case. Please try this:

devtools::install_github("crsh/citr")
#> Skipping install of 'citr' from a github remote, the SHA1 (aab8006e) has not changed since last install.
#>   Use `force = TRUE` to force installation
download.file("https://github.com/ITSLeeds/TDS/blob/master/slides/2-software.Rmd", "test.Rmd")
download.file("https://github.com/ITSLeeds/stats19/raw/master/vignettes/references.bib", "references.bib")
citr::tidy_bib_file(rmd_file = "test.Rmd", messy_bibliography = "references.bib")
#> Error in citr::tidy_bib_file(rmd_file = "test.Rmd", messy_bibliography = "references.bib"): Found no references in test.Rmd

^{Created on 2019-02-06 by the reprex package (v0.2.1)}

Note: if I move the reference from line 105 to line 30, for example, it no longer claims there are no references in there. Please try to reproduce and let me know. Thanks!

[crsh]

Thanks, I'll take a look.

[Robinlovelace]

Great. I realised the file was changing. Have re-added a reference that is not found - the test should work now. Thanks!

[crsh]

This was due to overly aggressive sanitizing of the R Markdown file. I had not come across this issue because I hadn't tried it on xaringan slides. It should work now, but I get an error that reference was not found in the look-up bibliography. Thanks again for the excellent reports. They made debugging a breeze. 👍

[Robinlovelace]

Great fixes. They teach me lots about regex!