Comments (7)
crsh
commented on September 24, 2024
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.
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Robinlovelace
commented on September 24, 2024
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)
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Robinlovelace
commented on September 24, 2024
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.RmdCreated 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!
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crsh
commented on September 24, 2024
Thanks, I'll take a look.
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Robinlovelace
commented on September 24, 2024
Great. I realised the file was changing. Have re-added a reference that is not found - the test should work now. Thanks!
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crsh
commented on September 24, 2024
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. 👍
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Robinlovelace
commented on September 24, 2024
Great fixes. They teach me lots about regex!
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Related Issues (20)
- Referencing from entire zotero library, rather then exported library-user problem HOT 5
- Citr Aborts session when accessing library HOT 9
- RStudio 1.4 to provide Zotero integration HOT 1
- citr crashes connecting to Zotero library HOT 11
- citr currently not available from CRAN HOT 13
- Error in callFun: argument "location" is missing HOT 4
- Allow for different types of citation key formats in tidy_bib_file() HOT 3
- Allow bibtype "Document" to be read by citr HOT 3
- Citr is not allowed to install in R ver. 4.0.2, Please update! HOT 2
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- later: interrupt occurred while executing callback. HOT 1
- Error loading Bibtex for second citation insert, citr crashes after inserting one citation
- Add ability for `tidy_bib_file()` to scan `_bookdown.yml` HOT 1
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- Error in data.frame: arguments imply differing number of rows HOT 2
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