grimbough / biomaRt

R package providing query functionality to BioMart instances like Ensembl
https://bioconductor.org/packages/biomaRt/
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Argument "host" is missing, with no default using `useEnsembl` #72

Open ferygood opened 1 year ago

ferygood commented 1 year ago

Dear biomaRt maintainer,

I have written a function called orthologScale() and it uses biomaRt::useEnsembl(). When I run unit test, I face an error telling me I need to specify argument "host". Please see the detail below:

══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-orthologScale.R:18'): orthologScale returns orthology information and scaling factor ──
  Error in `grepl(x = host, pattern = "http[s]?://ensembl", fixed = FALSE)`: argument "host" is missing, with no default
  Backtrace:
      ▆
   1. └─TEKRABber::orthologScale(...) at test-orthologScale.R:18:4
   2.   └─biomaRt::useEnsembl("ensembl", dataset = geneRef, version = "105")
   3.     └─base::grepl(x = host, pattern = "http[s]?://ensembl", fixed = FALSE)
   4.       └─base::is.factor(x)

However, I have noticed that users only need to specify the host argument if different from www.ensembl.org. page 21 manual page

Therefore, I am confused. Could you give me some suggestions? The version of biomaRt I am using is v2.52.0 and v2.53.0.

Thank you for your time. Looking forward to hearing from you.