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

Example packages using generics package

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)

| CRAN | Bioconductor |:-------------|:---------- | base | BiocGenerics | stats | BiocGenerics | dplyr | BiocGenerics | lubridate | BiocGenerics | randomForest | BiocGenerics | parallel | BiocGenerics | base | IRanges | stats | IRanges | RMySQL | IRanges | RSQLite | IRanges | XLConnect | IRanges | dplyr | IRanges | tidyr | IRanges | lubridate | IRanges | nlme | IRanges | vcd | IRanges | sp | IRanges | quantmod | IRanges | data.table | IRanges | testthat | IRanges | dplyr | Biobase | randomForest | Biobase | httr | Biobase | base | AnnotationDbi | RMySQL | AnnotationDbi | RSQLite | AnnotationDbi | XLConnect | AnnotationDbi | dplyr | AnnotationDbi | rmarkdown | AnnotationDbi | sp | AnnotationDbi | quantmod | AnnotationDbi | base | GenomeInfoDb | RMySQL | GenomeInfoDb | RSQLite | GenomeInfoDb | XLConnect | GenomeInfoDb | dplyr | GenomeInfoDb | lubridate | GenomeInfoDb | sp | GenomeInfoDb | quantmod | GenomeInfoDb | base | S4Vectors | stats | S4Vectors | RMySQL | S4Vectors | RSQLite | S4Vectors | XLConnect | S4Vectors | dplyr | S4Vectors | lubridate | S4Vectors | rmarkdown | S4Vectors | sp | S4Vectors | quantmod | S4Vectors | testthat | S4Vectors | base | Biostrings | RMySQL | Biostrings | RSQLite | Biostrings | XLConnect | Biostrings | dplyr | Biostrings | lubridate | Biostrings | nlme | Biostrings | sp | Biostrings | quantmod | Biostrings | testthat | Biostrings | base | XVector | dplyr | XVector | testthat | XVector | base | GenomicRanges | dplyr | GenomicRanges | lubridate | GenomicRanges | vcd | GenomicRanges | sp | GenomicRanges | data.table | GenomicRanges | testthat | GenomicRanges | base | Rsamtools | zoo | Rsamtools | base | genefilter | graphics | genefilter | car | genefilter | sp | genefilter | base | rtracklayer | stats | rtracklayer | RMySQL | rtracklayer | RSQLite | rtracklayer | XLConnect | rtracklayer | sp | rtracklayer | quantmod | rtracklayer | dplyr | biomaRt | base | graph | graphics | graph | dplyr | graph | stringr | graph | lubridate | graph | sp | graph | XML | graph | dplyr | GenomicAlignments | xts | GenomicAlignments | data.table | GenomicAlignments | dplyr | GenomicFeatures | base | affy | graphics | affy | lubridate | affy | base | BSgenome | conflicts | S3 Generics | S4 Generics | normal | --------|:------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------|:------------------------------------|:-------------------------------------------------------------------------------------------------------------------------------------------------------------------| | setdiff, match, is.unsorted, table, evalq, union, intersect | | | setdiff, match, is.unsorted, table, evalq, union, intersect | | mad, xtabs, IQR | | | mad, xtabs, IQR | | intersect, setdiff, union, combine | intersect, setdiff, union | | combine | | intersect, union, setdiff | | intersect, union, setdiff | | | combine | | | combine | | clusterExport, parSapplyLB, clusterApplyLB, parSapply, parApply, clusterMap, clusterApply, clusterEvalQ, clusterCall, parCapply, parRapply, parLapplyLB, parLapply | | | clusterExport, parSapplyLB, clusterApplyLB, parSapply, parApply, clusterMap, clusterApply, clusterEvalQ, clusterCall, parCapply, parRapply, parLapplyLB, parLapply | | t, setdiff, gsub, mean, toupper, merge, chartr, summary, with, match, tolower, diff, by, split\<-, nchar, rev, is.unsorted, sub, table, as.matrix, as.table, which, %in%, within, transform, union, which.min, which.max, drop, intersect | t, mean, merge, summary, with, diff, by, split\<-, rev, as.matrix, as.table, within, transform | | setdiff, gsub, toupper, chartr, match, tolower, nchar, is.unsorted, sub, table, which, %in%, union, which.min, which.max, drop, intersect | | smoothEnds, mad, runmed, window\<-, cor, cov, quantile, median, update, sd, var, IQR | window\<-, quantile, median, update | | smoothEnds, mad, runmed, cor, cov, sd, var, IQR | | summary | | summary | | | summary | | summary | | | summary | | summary | | | slice, collapse, intersect, setdiff, union, desc | collapse, intersect, setdiff, union | | slice, desc | | expand | | | expand | | %within%, intersect, union, setdiff | | %within%, intersect, union, setdiff | | | collapse | collapse | | | | tile | tile | | | | summary, %over%, merge | | summary, merge | %over% | | summary | | summary | | | shift | | | shift | | compare | compare | | | | combine | | | combine | | combine | | | combine | | content | | | content | | summary, ls, sample, eapply, exists | summary | | ls, sample, eapply, exists | | summary | | summary | | | summary | | summary | | | summary | | summary | | | select | | | select | | metadata | | | metadata | | summary | | summary | | | summary | | summary | | | merge, summary, intersect | merge, summary | | intersect | | summary | | summary | | | summary | | summary | | | summary | | summary | | | intersect | intersect | | | | intersect | | intersect | | | summary, merge | | summary, merge | | | summary | | summary | | | t, setdiff, merge, substring, substr, split, expand.grid, summary, droplevels, with, match, by, ifelse, as.matrix, levels, as.table, %in%, within, transform, as.factor, union, intersect | t, merge, split, summary, droplevels, with, by, as.matrix, levels, as.table, within, transform | | setdiff, substring, substr, expand.grid, match, ifelse, %in%, as.factor, union, intersect | | na.exclude, na.omit, complete.cases, window, aggregate, cor, cov, sd, var, xtabs | na.exclude, na.omit, window, aggregate | | complete.cases, cor, cov, sd, var, xtabs | | summary | | summary | | | summary | | summary | | | summary | | summary | | | intersect, setdiff, union, rename | intersect, setdiff, union | | rename | | intersect, union, setdiff | | intersect, union, setdiff | | | metadata | | | metadata | | summary, split, merge | | summary, split, merge | | | summary | | summary | | | compare | compare | | | | setdiff, chartr, substring, substr, summary, match, nchar, is.unsorted, as.matrix, %in%, toString, union, setequal, intersect | summary, as.matrix, toString | | setdiff, chartr, substring, substr, match, nchar, is.unsorted, %in%, union, setequal, intersect | | summary | | summary | | | summary | | summary | | | summary | | summary | | | collapse, intersect, setdiff, setequal, union | collapse, intersect, setdiff, setequal, union | | | | intersect, union, setdiff | | intersect, union, setdiff | | | collapse | collapse | | | | summary | | summary | | | summary | | summary | | | compare | compare | | | | match, rev, is.unsorted, toString | rev, toString | | match, is.unsorted | | slice | | | slice | | compare | compare | | | | setdiff, merge, split, match, is.unsorted, as.factor, union, intersect | merge, split | | setdiff, match, is.unsorted, as.factor, union, intersect | | intersect, setdiff, union | intersect, setdiff, union | | | | intersect, union, setdiff | | intersect, union, setdiff | | | tile | tile | | | | split, merge | | split, merge | | | shift | | | shift | | compare | compare | | | | isOpen, isIncomplete | | | isOpen, isIncomplete | | index | index | | | | anyNA | anyNA | anyNA | | | plot | plot | | | | Anova | Anova | | | | plot | | plot | | | split, summary, close | split, summary, close | | | | offset | | | offset | | summary | | summary | | | summary | | summary | | | summary | | summary | | | summary, split | | summary, split | | | summary | | summary | | | select | | | select | | union | | | union | | plot | plot | | | | union | union | | | | boundary | | | boundary | | union | | union | | | plot | | plot | | | addNode | addNode | | | | first, last | | | first, last | | last, first | last, first | | | | last | | | last | | select | | | select | | open, close | open, close | | | | hist, barplot | hist, barplot | | | | pm | | | pm | | nchar | | | nchar |

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")))