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)

CRAN	Bioconductor	conflicts	S3 Generics	S4 Generics	normal
base	BiocGenerics	setdiff, match, is.unsorted, table, evalq, union, intersect			setdiff, match, is.unsorted, table, evalq, union, intersect
stats	BiocGenerics	mad, xtabs, IQR			mad, xtabs, IQR
dplyr	BiocGenerics	intersect, setdiff, union, combine	intersect, setdiff, union		combine
lubridate	BiocGenerics	intersect, union, setdiff		intersect, union, setdiff
randomForest	BiocGenerics	combine			combine
parallel	BiocGenerics	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
base	IRanges	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
stats	IRanges	smoothEnds, mad, runmed, window<-, cor, cov, quantile, median, update, sd, var, IQR	window<-, quantile, median, update		smoothEnds, mad, runmed, cor, cov, sd, var, IQR
RMySQL	IRanges	summary		summary
RSQLite	IRanges	summary		summary
XLConnect	IRanges	summary		summary
dplyr	IRanges	slice, collapse, intersect, setdiff, union, desc	collapse, intersect, setdiff, union		slice, desc
tidyr	IRanges	expand			expand
lubridate	IRanges	%within%, intersect, union, setdiff		%within%, intersect, union, setdiff
nlme	IRanges	collapse	collapse
vcd	IRanges	tile	tile
sp	IRanges	summary, %over%, merge		summary, merge	%over%
quantmod	IRanges	summary		summary
data.table	IRanges	shift			shift
testthat	IRanges	compare	compare
dplyr	Biobase	combine			combine
randomForest	Biobase	combine			combine
httr	Biobase	content			content
base	AnnotationDbi	summary, ls, sample, eapply, exists	summary		ls, sample, eapply, exists
RMySQL	AnnotationDbi	summary		summary
RSQLite	AnnotationDbi	summary		summary
XLConnect	AnnotationDbi	summary		summary
dplyr	AnnotationDbi	select			select
rmarkdown	AnnotationDbi	metadata			metadata
sp	AnnotationDbi	summary		summary
quantmod	AnnotationDbi	summary		summary
base	GenomeInfoDb	merge, summary, intersect	merge, summary		intersect
RMySQL	GenomeInfoDb	summary		summary
RSQLite	GenomeInfoDb	summary		summary
XLConnect	GenomeInfoDb	summary		summary
dplyr	GenomeInfoDb	intersect	intersect
lubridate	GenomeInfoDb	intersect		intersect
sp	GenomeInfoDb	summary, merge		summary, merge
quantmod	GenomeInfoDb	summary		summary
base	S4Vectors	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
stats	S4Vectors	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
RMySQL	S4Vectors	summary		summary
RSQLite	S4Vectors	summary		summary
XLConnect	S4Vectors	summary		summary
dplyr	S4Vectors	intersect, setdiff, union, rename	intersect, setdiff, union		rename
lubridate	S4Vectors	intersect, union, setdiff		intersect, union, setdiff
rmarkdown	S4Vectors	metadata			metadata
sp	S4Vectors	summary, split, merge		summary, split, merge
quantmod	S4Vectors	summary		summary
testthat	S4Vectors	compare	compare
base	Biostrings	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
RMySQL	Biostrings	summary		summary
RSQLite	Biostrings	summary		summary
XLConnect	Biostrings	summary		summary
dplyr	Biostrings	collapse, intersect, setdiff, setequal, union	collapse, intersect, setdiff, setequal, union
lubridate	Biostrings	intersect, union, setdiff		intersect, union, setdiff
nlme	Biostrings	collapse	collapse
sp	Biostrings	summary		summary
quantmod	Biostrings	summary		summary
testthat	Biostrings	compare	compare
base	XVector	match, rev, is.unsorted, toString	rev, toString		match, is.unsorted
dplyr	XVector	slice			slice
testthat	XVector	compare	compare
base	GenomicRanges	setdiff, merge, split, match, is.unsorted, as.factor, union, intersect	merge, split		setdiff, match, is.unsorted, as.factor, union, intersect
dplyr	GenomicRanges	intersect, setdiff, union	intersect, setdiff, union
lubridate	GenomicRanges	intersect, union, setdiff		intersect, union, setdiff
vcd	GenomicRanges	tile	tile
sp	GenomicRanges	split, merge		split, merge
data.table	GenomicRanges	shift			shift
testthat	GenomicRanges	compare	compare
base	Rsamtools	isOpen, isIncomplete			isOpen, isIncomplete
zoo	Rsamtools	index	index
base	genefilter	anyNA	anyNA	anyNA
graphics	genefilter	plot	plot
car	genefilter	Anova	Anova
sp	genefilter	plot		plot
base	rtracklayer	split, summary, close	split, summary, close
stats	rtracklayer	offset			offset
RMySQL	rtracklayer	summary		summary
RSQLite	rtracklayer	summary		summary
XLConnect	rtracklayer	summary		summary
sp	rtracklayer	summary, split		summary, split
quantmod	rtracklayer	summary		summary
dplyr	biomaRt	select			select
base	graph	union			union
graphics	graph	plot	plot
dplyr	graph	union	union
stringr	graph	boundary			boundary
lubridate	graph	union		union
sp	graph	plot		plot
XML	graph	addNode	addNode
dplyr	GenomicAlignments	first, last			first, last
xts	GenomicAlignments	last, first	last, first
data.table	GenomicAlignments	last			last
dplyr	GenomicFeatures	select			select
base	affy	open, close	open, close
graphics	affy	hist, barplot	hist, barplot
lubridate	affy	pm			pm
base	BSgenome	nchar			nchar

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")))

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