search

RamsinghLab / arkas

This is the kallisto package
0 stars 0 forks source link

R CMD Checks reduced to 7 warnings (this PR solved 2 warnings) #35

Closed arcolombo closed 8 years ago

arcolombo commented 8 years ago

there are some issues with the generics and this solved one of the documentation generics of features.

arcolombo commented 8 years ago

I am commit heavy, and probably need to get in the habit of only pushing good commits. not just saving my work.... sort of not a good practice i admit.....

arcolombo commented 8 years ago

I have this down to 6 warnings. I solved 3.

Note: I deleted the demo directory, instead users have plenty of vignettes, and the demo was merely moved to inst/doc folder (NS.rmd). I turned the example.Rmd into a vignette. the demos had warnings returned because of strict documentation guidelines.. .... so I removed, and consolidated.

also the akas::as() function does work on my end but the identical(kexp,SE) is returning false. I also put this into the crossModels.Rmd vignette to test this as true.... but for some reason identical is not returning true.

Also, I was able to remove a warning by adding a generic for 'features', in the same manner that covariates was created (generic, setMethod, setReplacementMethod)... R CMD Check returned that the features was undocumented when there was not a setGeneric for features. so I created one, and removed a warning.

There are 6 warnings left. see attached.
check.txt

arcolombo commented 8 years ago

I will not merge until I can figure out what is going on with the arkas::as() ... FYI.

arcolombo commented 8 years ago

after recent push, there is now 5 warnings and 6 notes. one of them is resolved. updatedCheck-5.txt

arcolombo commented 8 years ago

closing this. I found a great resource for documenting S4 OOP classes, and constructors and will consult the text regrading proper inheritance, and proper documentation. this I am sure I can solve. OOP basics.