devtools::test passes but devtools::check fails

[jennahamlin]

Hello -

I am attempting to add in some unit tests for an R shiny application using the following code.

#make testing genetic matrix; unfortunately it took all of these steps
#to get a file like what I load in - this feels like too many - but works
testing_genetic <- matrix(c(1, "-", 0.2, 0.5, 0.1, 0, "-", 0.3, 0.9, 0.8, 0.2,
                            0.2, "-", 0.5, "-", 0.7), nrow = 4,
                          dimnames = list(c("A", "B", "C", "D"),
                                          c("A", "B", "C", "D")))
testing_genetic <- as.data.frame(testing_genetic)
testing_genetic <- droplevels(testing_genetic)
testing_genetic <- data.frame(lapply(testing_genetic, as.character),
                              stringsAsFactors = FALSE)
testing_genetic <- tibble::rownames_to_column(testing_genetic, var = ".")

# rename this column to make a matrix with both
testing_genetic[1, 1] <- "A"
testing_genetic[2, 1] <- "B"
testing_genetic[3, 1] <- "C"
testing_genetic[4, 1] <- "D"

#make example tree
testing_tree <- ape::rtree(4)	
new_tiplabels <- c("A", "B", "C", "D")
testing_tree$tip.label <- new_tiplabels

#convert tree to tibble
testing_tree <- tibble::as_tibble(testing_tree)

#confirm tree is tibble 
str(testing_tree)
tibble [7 x 4] (S3: tbl_tree/tbl_df/tbl/data.frame)
 $ parent       : int [1:7] 7 7 6 5 5 5 6
 $ node         : int [1:7] 1 2 3 4 5 6 7
 $ branch.length: num [1:7] 0.15237 0.73568 0.00114 0.3912 NA ...
 $ label        : chr [1:7] "A" "B" "C" "D" ...

#change header to label in order to use dplyr::full_join
testing_genetic <- dplyr::rename(testing_genetic, label = 1)

test_that("data types correct before combining tree", {
  expect_is(testing_tree, "tbl_tree")
})

 test_that("confirm tree and genetic distance can be combined", {
   expect_silent(dplyr::full_join(testing_tree, testing_genetic, by = "label"))
 })

when running devtools::check this is the error -
cannot coerce class '"phylo"' to a data.frame
Backtrace:

1. tibble::as_tibble(testing_tree)
2. tibble:::as_tibble.default(testing_tree)
3. base::as.data.frame.default(value, stringsAsFactors = FALSE)

Any thoughts or suggestions for how to overcome this error would be greatly appreciated!

[maelle]

@jennahamlin!

Generally for such problems (tests passing in a context and not in another) I like to refer to a GitHub thread collecting such cases, where one can often see something relevant. However, I also had a look at your package out of curiosity.

The problem was that the order of packages loading was different in the two contexts. When running tests with devtools::test(), as_tibble() was the function you wanted which is the one from tidytree. When running tests with devtools::check(), as_tibble() was the as_tibble() from tibble. The fix is to add the namespace before the function i.e. write tidytree::as_tibble(), and also to import tidytree in DESCRIPTION (it was already an indirect dependency of your package). I made a PR to your package.

I found this more or less by chance by looking a bit at how one would convert an object of class phylo to a data.frame, and looking at tidytree docs.

As side-notes,

• in your original test file there's the context() command, that isn't recommended anymore.
• Also note that testthat::expect_is() is getting superseded in testthat 3.0.0 (not on CRAN yet). To learn more about testthat changes, and if you have one hour free, watch the webinar.

[jennahamlin]

Thank you for the pull request to fix the issue (tidytree::as_tibble; instead of tibble::as_tibble).