Comments (3)
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
from taxize.
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
from taxize.
Closing this and opening new issue to fix tropicos functions
from taxize.
Related Issues (20)
- bug: NA returned by get_uid when using division_filter HOT 3
- Update to bold::bold_tax_id() HOT 1
- get_tsn() function failing to retreive data HOT 4
- R taxize gnr_resolve function Internal Server Error (HTTP 500) for specific name
- Bad Gateway (HTTP 502) in get_iucn HOT 6
- HTTP 503 gnr_resolve function HOT 6
- HTTP 400 Error when using Taxize HOT 1
- taxize had controversy outputs
- Is there a function in taxize for getting all genera in a family? HOT 2
- Error 204 halts entire process rather than skipping taxon HOT 2
- `gnr_resolve` not matching the same name multiple times OR matches erroneously
- get_tsn() Error with tibble >= 3.0 HOT 1
- taxize::synonyms return error "The `x` argument of `as_tibble()` can't be missing as of tibble 3.0.0." HOT 7
- continue ncbi_downstream() for loop even when one taxon generates error?
- R CMD Check cannot run via GitHub Actions because of untagged version HOT 7
- classification() unable to find NCBI accession number known to exist in database HOT 2
- Running classification() in R markdown doesn't show options when multiple UIDs are found
- Error in retrieving GBIF backbone taxon ID using `get_gbifid()` HOT 1
- error class2tree output HOT 1
- Error in { : task 1 failed - "Bad Gateway (HTTP 502)" (TROPICOS)
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from taxize.