Tropicos tests (prefix tp_) don't pass check - will try to fix this

[sckott]

on testthat::check() I get:

* checking tests ...
  Running 'test-all.R' [5s/69s]
 ERROR
Running the tests in 'tests/test-all.R' failed.
Last 13 lines of output:
  itis_taxrank : http://www.itis.gov/ITISWebService/services/ITISService/getTaxonomicRankNameFromTSN?tsn=202385
  ..
  iucn_summary : ..
  phylomatic_tree : http://www.itis.gov/ITISWebService/services/ITISService/getFullHierarchyFromTSN?tsn=36616
  http://www.itis.gov/ITISWebService/services/ITISService/getFullHierarchyFromTSN?tsn=19322
  http://www.itis.gov/ITISWebService/services/ITISService/getFullHierarchyFromTSN?tsn=183327
  ...
  tp_acceptednames : 4
  tp_namedistributions : 5
  tp_namereferences : Error in getOption("tropicoskey", stop("need an API key for Tropicos")) : 
    need an API key for Tropicos
  Calls: test_package ... eval -> eval -> tp_namereferences -> paste -> getOption
  Execution halted
Error: Command failed (1)

[eduardszoecs]

Yep, having the same trouble with the Sweave-file (since CRAN has no API-key and no custumisable Rprofile.site and/or R CMD CHECK doesnot take care of the Rprofile).

I've came around in the vignette with:

<<>>=
options(pmkey = '<insertyourcodehere>')
@
<<echo=FALSE, results=hide>>=
options(pmkey = 'xxx')    # xxx stands for my personal key
@

<<>>=
plants <- c("Myrcia lingua", "Myrcia bella", "Ocotea pulchella")
plantminer(plants)
@

So I'm showing the user a code (to fill with his own key) but internal I'm using my personal key.

So to explicitely define the key in options.
Do you have a API-key which can be used for this? I am not happy with the solution to use my personal key here...
If options() doesn't work with Cran supply the key as argument

[sckott]

If okay with you, I moved all tropicos functions out of taxize. In addition, I removed all the tests as even after removing tropicos tests I was still getting a lot of errors that didn't make sense. We can still run tests basically, just by running examples. Using testthat you can do run_examples('path_to_package', run=F), where the run=F will uncomment the \dontrun lines and run all the examples. I just ran them all and no errors on my end at least. Pushing changes soon

[sckott]

Closing this and opening new issue to fix tropicos functions