search

ropensci / taxize

A taxonomic toolbelt for R
https://docs.ropensci.org/taxize
Other
265 stars 59 forks source link

Tropicos tests (prefix `tp_`) don't pass check - will try to fix this #45

Closed sckott closed 11 years ago

sckott commented 11 years ago

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 commented 11 years ago

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 commented 11 years ago

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 commented 11 years ago

Closing this and opening new issue to fix tropicos functions