test failures on Ubuntu

[maelle]

👋 @kmartinet! Through https://ropensci.r-universe.dev/builds I noticed test failures on Ubuntu that you get through GitHub Actions too:

Error: Running examples in ‘ssarp-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: create_sar
> ### Title: Create a species-area relationship (SAR) plot
> ### Aliases: create_sar create_SAR
> 
> ### ** Examples
> 
> # The GBIF key for the Anolis genus is 8782549
> # Read in example dataset filtered from:
> #  dat <- rgbif::occ_search(taxonKey = 8782549,
> #                           hasCoordinate = TRUE,
> #                           limit = 10000)
> dat <- read.csv(system.file("extdata",
+                             "ssarp_Example_Dat.csv",
+                             package = "ssarp"))
Warning in file(file, "rt") :
  file("") only supports open = "w+" and open = "w+b": using the former
Error in read.table(file = file, header = header, sep = sep, quote = quote,  : 
  no lines available in input
Calls: read.csv -> read.table

Does that ring any bell?

[maelle]

Note that I work on an Ubuntu machine and would be happy to investigate if needed.

[kmartinet]

Hi @maelle ! Yes, this was an issue that we were unsure how to solve during the review process. Here is @ jhollist's post in the ssarp review that discusses an open issue and PRs related to this problem. R-CMD-check is failing because the Ubuntu distributions cannot find the extdata folder where the example data is stored. I believe this issue has something to do with how R packages are installed on Ubuntu machines?

I attempted to use the testthat /testdata folder to avoid extdata, but it didn't solve the problem (here's the commit for that attempt). I also edited test-coverage.yaml to run tests from source, but it continued to fail (here's the line of code I tried).

I would very much appreciate your insight on this issue! I was thinking that I could wrap each instance of using files from extdata in a statement that will skip it if the OS believes the file does not exist, but that doesn't feel like a real solution.

[maelle]

Oooh it seems it's a case-sensitivity issue, I will open a PR!