any.duplicated() is not found, even if part of the package. about codeandroll2 HOT 5 CLOSED

same with sort.decreasing()

from codeandroll2.

These functions appear to be hidden for some reason

CodeAndRoll2:::sort.decreasing() and CodeAndRoll2:::any.duplicated() works

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• Namespace is weird

# Generated by roxygen2: do not edit by hand

S3method(any,duplicated)
S3method(any,duplicated.rownames.ls.of.df)
S3method(as.character,wNames)
S3method(as.list,df.by.col)
S3method(as.list,df.by.row)
S3method(as.logical,wNames)
S3method(as.numeric,wNames)
S3method(na.omit,mat)
S3method(na.omit,strip)
S3method(range,list)
S3method(reorder,list)
S3method(sort,decreasing)
S3method(sort,mat)
export(MaxN)
export(TPM_normalize)
export(arr.of.lists.2.df)
export(array.fromNames)
export(as.factor.numeric)

• why are some functions listed as S3method and some as export in R?

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So its a problem triggered by Roxygen3

https://stackoverflow.com/questions/18512528/how-to-export-s3-method-so-it-is-available-in-namespace

Just for those late to the party, in the newer versions of roxygen (=> 3.0), the @export tag will work automatically how to deal with methods.

From the Generating Rd files vignette:

S3 generics are regular functions, so document them as such. S3 classes have no formal definition, so document the constructor function. It is your choice whether or not to document S3 methods. You don’t need to document methods for simple generics like print(). If your method is more complicated, you should document it so people know what the parameters do. In base R, you can find documentation for more complex methods like predict.lm(), predict.glm(), and anova.glm().

Older versions of roxygen required explicit @method generic class tags for all S3 methods. From 3.0.0 this is no longer needed as and roxygen2 will figure it out automatically. If you are upgrading, make sure to remove these old tags. Automatic method detection will only fail if the generic and class are ambiguous. For example is all.equal.data.frame() the equal.data.frame method for all, or the data.frame method for all.equal?. If this happens, you can disambiguate with (e.g.) @method all.equal data.frame.

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I am not fully understanding why this is happening now, but an explicit #' @export sort.decreasing solves the problem

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