could not find function ".getValidity"

dktanwar commented 4 years ago

Working directory

/mnt/IM/projects/software/ssc

File to be used

/mnt/IM/projects/software/ssc/ssc.Rmd

Problem

Line 72 in the Rmd file

> o <- getOverlapValidity(o)
Error in .getValidity(sources[w, , drop = FALSE], rules) :
  could not find function ".getValidity"

dktanwar commented 4 years ago

Hi @plger

Upon checking all code, I couldn't find this function: .getValidity

dktanwar commented 4 years ago

Further digging into this, https://www.rdocumentation.org/packages/methods/versions/3.6.2/topics/validObject

To me it seems like it shoud be getValidy instead .getValidity

https://github.com/mansuylab/shortRNA/blob/f6854faef0b013300a126d6caf2c4f1cfd393232/R/assignment.R#L560

Although I tried this but I get an error:

> sources[w, ] <- getValidity(sources[w, , drop = FALSE], rules)

Error in getValidity(sources[w, , drop = FALSE], rules) : 
  unused argument (rules)

And, when I tried without rules, error:

> sources[w, ] <- getValidity(sources[w, , drop = FALSE])

Error in getValidity(sources[w, , drop = FALSE]) : 
  trying to get slot "validity" from an object (class "data.table") that is not an S4 object

plger commented 4 years ago

Hi, it has nothing to do with validObject, and should be getOverlapValidity (I renamed the function and forgot to change the nested call).

shortRNAhub / shortRNA