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.
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: 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, -- John Reid <http://johnreid.github.io> MRC Biostatistics Unit Cambridge, UK Twitter: @__Reidy__ <https://twitter.com/__Reidy__> [[alternative HTML version deleted]] ______________________________________________ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
