When I updated my copy of dplyr, I got a series of warnings about missing files in other packages: rlang, dbplyr, etc.
E.g.: "file link 'quasiquotation' in package 'rlang' does not exist and so has been treated as a topic"
The package can be opened and appears to be working correctly. What do these warnings mean? Should I be concerned about them?
Thanks in advance for any clarification of the above.
Larry Hunsicker
Running R 3.6.3; RStudio 1.2.5033 on Windows 10 up to date.
1 Like
I also use R 3.6.3 on Windows 10 and I don't get any warnings while loading the latest dplyr version, so it is not normal behavior.
Can you try restarting your R session with Ctrl +Shift +F10 and then updating your packages with this command?
update.packages(repos='http://cran.rstudio.com/', ask=FALSE, checkBuilt=TRUE)
mara
March 11, 2020, 12:48pm
3
For a longer discussion of where this issue comes from, see below:
opened 02:44AM - 31 Jan 18 UTC
closed 09:27PM - 12 Aug 19 UTC
feature
markdown
Currently, if you link to a function in another package that has an alias that p… oints to a different Rd/html file, you end up with a missing file link warning when building the package.
For example, if your documentation includes:
```
#' Here is a link to \code{\link[dplyr:transmute]{dplyr::transmute()}}
#' Or the markdown equivalent: [dplry::transmute()]
```
You end up getting the following warning when building the package:
```
...
*** installing help indices
converting help for package 'simpleTest'
finding HTML links ... hello html
Rd warning: C:/user/RPackages/simpleTest/man/hello.Rd:11: missing file link 'transmute'
done
...
```
As was pointed out on [Stack Overflow](https://stackoverflow.com/questions/48430093/how-do-i-resolve-rd-warning-missing-file-link-when-building-packages-in-rstudi/48478698#48478698), you can resolve this by linking to the file, instead of the alias:
```
#' This link works with no warning: \code{\link[dplyr-mutate]{dplyr::transmute()}}
```
However, I don't think you can do this if using the markdown version. It also seems slightly dangerous to link to a RD/html file, which seems more likely to change than a function name; at least it seems possible that a developer might change the Rd file names without thinking of the issues, while function names are at least deprecated first.
So, would it make sense to search the `.libPaths()` using `tools::findHTMLlinks(level = 2)`, while roxygen2 is converting the Roxygen comments to Rd files, and add in the appropriate file link for any functions that uses aliases to point to a different file name?
I'm not sure how much extra overhead this would add, but it would make reading the build messages a little nicer.
1 Like
Thanks, Mara. I assume from the discussion, much of which is beyond me, that there is no problem for me with all these messages. It's a problem with how the packages are assembled. Is this correct?
1 Like
mara
March 11, 2020, 3:58pm
5
An excellent summary! (Much of it's over my head, too
system
April 1, 2020, 3:58pm
6
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