In Bioconductor/generics: A centralized repository for S4 generic functions

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "README-"
)

Example packages using generics package

select

https://github.com/jimhester/dplyr/tree/generics - https://travis-ci.org/hadley/dplyr/jobs/96281463#L1445-L1540
https://github.com/jimhester/AnnotationDbi/tree/generics - https://gist.github.com/jimhester/8044628a6183c118ce0b
https://github.com/jimhester/GenomicFeatures/tree/generics

Summary of Conflicting Functions

# Get all conflicting functions from two namespaces
conflicts2 <- function(x, y) {
    Filter(Negate(function(x) grepl("\\.__T__", x)),
           intersect(getNamespaceExports(x), getNamespaceExports(y)))
}

# CRAN packages from https://support.rstudio.com/hc/en-us/articles/201057987-Quick-list-of-useful-R-packages
CRAN <- c(
"base",
"stats",
"graphics",
"RMySQL",
"RSQLite",
"XLConnect",
"xlsx",
"foreign",
"readr",
"haven",
"dplyr",
"tidyr",
"stringr",
"lubridate",
"ggplot2",
"ggvis",
"rgl",
"htmlwidgets",
"leaflet",
"dygraphs",
"DT",
"DiagrammeR",
"networkD3",
"googleVis",
"car",
"mgcv",
"lme4",
"nlme",
"randomForest",
"multcomp",
"vcd",
"glmnet",
"survival",
"caret",
"shiny",
"rmarkdown",
"knitr",
"xtable",
"sp",
"maptools",
"maps",
"ggmap",
"zoo",
"xts",
"quantmod",
"Rcpp",
"data.table",
"parallel",
"XML",
"jsonlite",
"httr",
"rvest",
"devtools",
"testthat",
"roxygen2")

# Bioc Packages from top 25 of https://www.bioconductor.org/packages/stats/
Bioc <- c(
"BiocInstaller",
"BiocGenerics",
"IRanges",
"Biobase",
"AnnotationDbi",
"GenomeInfoDb",
"S4Vectors",
"zlibbioc",
"Biostrings",
"limma",
"XVector",
"GenomicRanges",
"BiocParallel",
"annotate",
"Rsamtools",
"genefilter",
"rtracklayer",
"biomaRt",
"graph",
"GenomicAlignments",
"GenomicFeatures",
"preprocessCore",
"affy",
"BSgenome",
"geneplotter")

suppressPackageStartupMessages(invisible(lapply(c(CRAN, Bioc), library, character.only = TRUE, quietly = TRUE)))

all <- expand.grid(CRAN = CRAN, Bioconductor = Bioc, stringsAsFactors = FALSE)

all$conflicts <- Map(conflicts2, all[[1]], all[[2]])

# Filter out all the generics defined in methods

gen_defs <- function(namespace) {
    gens <- getGenerics(where=asNamespace(namespace))

    Map(function(f, package)
        get(f, envir = asNamespace(package), mode = "function"),
        gens@.Data, gens@package)
}

filter_defs <- c(gen_defs("methods"),
                 gen_defs("BiocGenerics"))

in_defs <- function(x, defs) {
    any(as.logical(
        lapply(defs,
            function(xx) {
                identical(xx, x) || .hasSlot(xx, "default") && identical(xx@default@.Data, x)
            })))
}

filter_methods <- function(x, package) {
    if (!length(x)) return(x)
    funs <- lapply(x, get, envir = asNamespace(package), mode = "function")
    in_methods <- vapply(funs, in_defs, logical(1), defs = filter_defs)
    x[!in_methods]
}

all$conflicts <- Map(filter_methods, all$conflicts, all$CRAN)

all$`S3 Generics` <- Map(function(package, funs)
    Filter(function(x) pryr:::is_s3_generic(x, env = asNamespace(package)), funs),
    all$CRAN, all$conflicts)

all$`S4 Generics` <- Map(function(package, funs)
    Filter(function(x) isGeneric(x, where = asNamespace(package)), funs),
    all$CRAN, all$conflicts)

all$normal <- Map(function(conflicts, S3, S4) conflicts[!(conflicts %in% S3 | conflicts %in% S4)],
    all$conflicts, all$`S3 Generics`, all$`S4 Generics`)

res <- all[lengths(all$conflicts) > 0, ]
knitr::kable(res, row.names = FALSE)

Tabulated by function

library(tidyr)
res2 <- unique(unnest(res, conflicts)[c("CRAN", "conflicts")])
res3 <- spread(res2, conflicts, CRAN, fill="")
res4 <- lapply(res3, function(x) x[x != ""])
do.call(`cat`, c(Map(function(nme, pkgs) {
  paste0(" - ", nme, " - ", paste0(pkgs, collapse = ", "))
    }, names(res4), res4, USE.NAMES = FALSE), list(sep = "\n")))