Hello to all.
I am in the process of writing a package and have 4 warnings. 2 warnings have to deal with S3 set generic/method consistency and setReplacement methods. the other 2 are Rd \usage warnings.
this post is about the 2 warnings about the generics and replacement methods:
* checking S3 generic/method consistency ... WARNING
Loading required package: rtracklayer
Loading required package: knitr
Loading required package: stringdist
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
* checking replacement functions ... WARNING
Loading required package: rtracklayer
Loading required package: knitr
Loading required package: stringdist
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
The S3 consistency warning does not return a violating function, so I'm not sure what to investigate.
I've commented out my Class and methods .R scripts, and re-built and re-checked and get the same error. I've commented out *all* of the generics and methods used by my package and re-checked and get the same warning.
this implies that the S3 inconsistency is not actually due to my generics. What could be a cause of this inconsistency?
The structure that my package inherits is the SummarizedExperiment class and we've aliased the accessors from this package.
so in short, is the library start up warnings the culprit ? or some thing else?
Sincerely,
P.S. I did cross-post here
Any tips on possible triggers for these warnings can guide me into finding the root cause.
The manual refers to method arguments matching exactly the generics. But when I delete all my generics, setMethods, and replacementMethods I get the same WARNING, so how do I make sense of that?
Anthony R. Colombo
