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