[traits.build workflow] austraits$sources, bug in viewing individual references

[ehwenk]

This correctly gives a list of all references, formatted:

austraits$sources

This correctly gives a list of all dataset_ids:

View(austraits$sources)

However, if you try and explore individual dataset_ids, you get a never-ending nesting of all dataset_ids, but never the actual bibtex information. For instance, try

View(austraits$sources$Falster_2003)

or

austraits$sources$Falster_2003

[GaryTruong]

It is really strange that there seems to be an endless list created for the sources. I tried to work out why it was doing this and I suspect it has something to do with lapply and how it interacts with convert_list_to_bib. I removed the lapply and it seemed to have fixed the endless listing for some studies but then errors out for other studies when I remake austraits.

Alternatively if you want to see the bib info for a specific study you can use [ ] rather than $ to see the reference info.
e.g.

austraits$sources["Falster_2003"]

[ehwenk]

I know there are work-arounds for viewing the information. Daniel asked that I post the issue, since it is a "bug", but also not a high priority one, since it doesn't actually lead to any downstream problems. (Why neither of us found it until I was checking every component of every table one day.)

[dfalster]

I think culprit is RefManger::as.BibEntry. The same problem happens when you use the example from the package:

bib <- c(bibtype = "article", key = "mclean2014", title = "My New Article",
  author = "Mathew W. McLean", journaltitle = "The Journal", date = "2014-01")
y <- as.BibEntry(bib)
View(y)

@GaryTruong Perhaps check issues to see if this one has already been mentioned? https://github.com/ropensci/RefManageR

I wonder what alternative exist? I went with RefManageR as the standard bibtex was throwing some issues. But we could consider going back to bibtex

[GaryTruong]

Yeah you are right, the bug does appear to be from as.BibEntry. I've had a look at the issues page including closed issues and there doesnt seem to be any mention of this bug there.

[GaryTruong]

On further inspection and going down bit of a rabbit hole it looks like the source of the bug stems from RefManageR::BibEntry which builds on utils::bibentry. Both of them generate the same problem

RefManageR::BibEntry(bibtype = "article", key = "mclean2014", title = "My New Article",
         journal = "The Journal", year = 2014, author = "Mathew W. McLean") %>% View

utils::bibentry(bibtype = "article", key = "mclean2014", title = "My New Article",
         journal = "The Journal", year = 2014, author = "Mathew W. McLean") %>% View

We could try bibtex. Do you remember what issues were caused when bibtex was used previously?

[dfalster]

It was a while ago so I'm a bit hazy. But I think I was finding it hard to create a bib entry from a list with bibtex, as only option is to read.bib, which requires file input. Hence RefManager seemed like a good solution.