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Get example cBioPortal study setup to use for tests and examples

Open karissawhiting opened this issue 2 years ago • 0 comments

Previously examples used roxygen2's @examplesIf like:

@examplesIf !httr::http_error("www.cbioportal.org/api")

However, when cBioPortal 5.0 came out, some of the underlying data used as example data sets were changed ("fusions" became "structural variants"), and this threw errors, causing CRAN problems. I think it's correct that an error is thrown if a user tries to grab data with the wrong profile/data set name so I didn't want to downgrade these errors to a messages in order to pass CRAN, but the data used for examples needs to be stable.

For now, I switched examples to use dontrun{}, and all tests now use:

  skip_on_cran()
  skip_if(httr::http_error("www.cbioportal.org/api"))

But ideally I would like to go back to using conditional if httr::http_error("www.cbioportal.org/api") only for a set of examples/tests that use a stable test study in cBioPortal. I need to talk to cBioPortal to see if they can set one up for me that won't change.

karissawhiting avatar Aug 24 '22 15:08 karissawhiting