[R-pkg-devel] Functions erroneously identified as S3 methods

[Uwe Ligges]

On 03.07.2017 12:53, John Reid wrote:
> Hi,
> 
> I have some functions in my package that are getting confused for S3
> methods. I named them `filter.genes` and `filter.cells` which in
> hindsight looks like a mistake as `filter` is a S3 method.

S3 generic, actually.


> When I submit my package I receive a WARNING:
> 
> * checking S3 generic/method consistency ... WARNING filter: function(x,
> filter, method, sides, circular, init) filter.cells: function(dl,
> .filter, number, cells) filter: function(x, filter, method, sides,
> circular, init) filter.genes: function(dl, .filter, number, genes) See
> section ‘Generic functions and methods’ in the ‘Writing R Extensions’
> manual. Found the following apparent S3 methods exported but not
> registered: filter.cells filter.genes See section ‘Registering S3
> methods’ in the ‘Writing R Extensions’ manual.
> 
> I have deprecated the functions and replaced them with versions named
> with underscores but do not want to remove them until a later release.
> However I received a `pre-test archived` email from the CRAN team:

Resubmit and once you get the auto-rejection reply to the CRAN team 
explaining it by what you wrote here.

Best,
Uwe Ligges


> 
> package DeLorean_1.2.5.tar.gz does not pass the incoming checks automatically, please see the pre-test at:
> <https://win-builder.r-project.org/incoming_pretest/170703_114446_DeLorean_125/00check.log>
> Status: 1 WARNING, 1 NOTE
>    
> Current CRAN status: WARN: 11, OK: 1
> See:<https://CRAN.R-project.org/web/checks/check_results_DeLorean.html>
>    
> Please fix all problems and resubmit a fixed version via the webform.
> If you are not sure how to fix the problems shown, please ask for help on the R-package-devel mailing list:
> <https://stat.ethz.ch/mailman/listinfo/r-package-devel>
> If you are fairly certain the rejection is a false positive, please reply-all to this message and explain.
>    
> More details are given in the directory:
> <https://win-builder.r-project.org/incoming_pretest/170703_114446_DeLorean_125>
> The files will be removed after roughly 7 days.
> 
> 
> How should I proceed?
> 
> FWIW here is the Roxygen documenation for one of the functions:
> 
> #' Filter genes
> #'
> #' @param dl de.lorean object
> #' @param .filter Function that gakes a list of genes as input and returns
> #'     a vector of TRUE/FALSE
> #' @param number Number to sample if filter function or genes not supplied.
> #' @param genes The genes to keep.
> #' @examples
> #' \dontrun{
> #' genes <- c('NANOG', 'DAZ1', 'SOX4', 'PRDM14')
> #' filter.genes(dl, .filter = function(x) x %in% genes)
> #' filter.genes(dl, number = 4)
> #' filter.genes(dl, genes = genes)
> #' }
> #'
> #' @export filter.genes
> #'
> 
> Thanks,
>