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namespace.R
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namespace.R
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# File src/library/base/R/namespace.R
# Part of the R package, https://www.R-project.org
#
# Copyright (C) 1995-2019 The R Core Team
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# A copy of the GNU General Public License is available at
# https://www.R-project.org/Licenses/
## give the base namespace a table for registered methods
`.__S3MethodsTable__.` <- new.env(hash = TRUE, parent = baseenv())
## NOTA BENE:
## 1) This code should work also when methods is not yet loaded
## 2) We use ':::' instead of '::' inside the code below, for efficiency only
getNamespace <- function(name) {
ns <- .Internal(getRegisteredNamespace(name))
if (! is.null(ns)) ns
else loadNamespace(name)
}
.getNamespace <- function(name) .Internal(getRegisteredNamespace(name))
..getNamespace <- function(name, where) {
ns <- .Internal(getRegisteredNamespace(name))
if (!is.null(ns)) ns
else tryCatch(loadNamespace(name),
error = function(e) {
warning(gettextf("namespace %s is not available and has been replaced\nby .GlobalEnv when processing object %s",
sQuote(name)[1L], sQuote(where)),
domain = NA, call. = FALSE, immediate. = TRUE)
.GlobalEnv
})
}
loadedNamespaces <- function() names(.Internal(getNamespaceRegistry()))
isNamespaceLoaded <- function(name) .Internal(isRegisteredNamespace(name))
getNamespaceName <- function(ns) {
ns <- asNamespace(ns)
if (isBaseNamespace(ns)) "base"
else .getNamespaceInfo(ns, "spec")["name"]
}
getNamespaceVersion <- function(ns) {
ns <- asNamespace(ns)
if (isBaseNamespace(ns))
c(version = paste(R.version$major, R.version$minor, sep = "."))
else .getNamespaceInfo(ns, "spec")["version"]
}
getNamespaceExports <- function(ns) {
ns <- asNamespace(ns)
names(if(isBaseNamespace(ns)) .BaseNamespaceEnv
else .getNamespaceInfo(ns, "exports"))
}
getNamespaceImports <- function(ns) {
ns <- asNamespace(ns)
if (isBaseNamespace(ns)) NULL
else .getNamespaceInfo(ns, "imports")
}
getNamespaceUsers <- function(ns) {
nsname <- getNamespaceName(asNamespace(ns))
users <- character()
for (n in loadedNamespaces()) {
inames <- names(getNamespaceImports(n))
if (match(nsname, inames, 0L))
users <- c(n, users)
}
users
}
getExportedValue <- function(ns, name) {
ns <- asNamespace(ns)
if (isBaseNamespace(ns))
get(name, envir = ns, inherits = FALSE) # incl. error
else {
if (!is.null(oNam <- .getNamespaceInfo(ns, "exports")[[name]])) {
get0(oNam, envir = ns)
} else { ## <pkg> :: <dataset> for lazydata :
ld <- .getNamespaceInfo(ns, "lazydata")
if (!is.null(obj <- ld[[name]]))
obj
else { ## if there's a lazydata object with value NULL:
if(exists(name, envir = ld, inherits = FALSE))
NULL
else
stop(gettextf("'%s' is not an exported object from 'namespace:%s'",
name, getNamespaceName(ns)),
call. = FALSE, domain = NA)
}
}
}
}
`::` <- function(pkg, name) {
pkg <- as.character(substitute(pkg))
name <- as.character(substitute(name))
getExportedValue(pkg, name)
}
## NOTE: Both "::" and ":::" must signal an error for non existing objects
`:::` <- function(pkg, name) {
pkg <- as.character(substitute(pkg))
name <- as.character(substitute(name))
get(name, envir = asNamespace(pkg), inherits = FALSE)
}
attachNamespace <- function(ns, pos = 2L, depends = NULL, exclude, include.only)
{
## only used to run .onAttach
runHook <- function(hookname, env, libname, pkgname) {
if (!is.null(fun <- env[[hookname]])) {
res <- tryCatch(fun(libname, pkgname), error = identity)
if (inherits(res, "error")) {
stop(gettextf("%s failed in %s() for '%s', details:\n call: %s\n error: %s",
hookname, "attachNamespace", nsname,
deparse(conditionCall(res))[1L],
conditionMessage(res)),
call. = FALSE, domain = NA)
}
}
## else if (exists(".First.lib", envir = env, inherits = FALSE) &&
## nsname == Sys.getenv("R_INSTALL_PKG"))
## warning(sprintf("ignoring .First.lib() for package %s",
## sQuote(nsname)), domain = NA, call. = FALSE)
}
runUserHook <- function(pkgname, pkgpath) {
hook <- getHook(packageEvent(pkgname, "attach")) # might be list()
for(fun in hook) try(fun(pkgname, pkgpath))
}
ns <- asNamespace(ns, base.OK = FALSE)
nsname <- getNamespaceName(ns)
nspath <- .getNamespaceInfo(ns, "path")
attname <- paste0("package:", nsname)
if (attname %in% search())
stop("namespace is already attached")
env <- attach(NULL, pos = pos, name = attname)
## we do not want to run e.g. .onDetach here
on.exit(.Internal(detach(pos)))
attr(env, "path") <- nspath
exports <- getNamespaceExports(ns)
importIntoEnv(env, exports, ns, exports)
## always exists, might be empty
dimpenv <- .getNamespaceInfo(ns, "lazydata")
dnames <- names(dimpenv)
.Internal(importIntoEnv(env, dnames, dimpenv, dnames))
if(length(depends) > 0L) env$.Depends <- depends
Sys.setenv("_R_NS_LOAD_" = nsname)
on.exit(Sys.unsetenv("_R_NS_LOAD_"), add = TRUE)
runHook(".onAttach", ns, dirname(nspath), nsname)
## adjust variables for 'exclude', 'include.only' arguments
if (! missing(exclude) && length(exclude) > 0)
rm(list = exclude, envir = env)
if (! missing(include.only)) {
vars <- ls(env, all.names = TRUE)
nf <- setdiff(include.only, vars)
if (length(nf) > 0) {
nf <- strwrap(paste(nf, collapse = ", "),
indent = 4L, exdent = 4L)
stop(gettextf("not found in namespace %s: \n\n%s\n",
sQuote(nsname), nf),
call. = FALSE, domain = NA)
}
rm(list = setdiff(vars, include.only), envir = env)
}
lockEnvironment(env, TRUE)
runUserHook(nsname, nspath)
on.exit()
Sys.unsetenv("_R_NS_LOAD_")
invisible(env)
}
## *inside* another function, useful to check for cycles
dynGet <- function(x, ifnotfound = stop(gettextf("%s not found",
sQuote(x)), domain = NA),
minframe = 1L, inherits = FALSE)
{
n <- sys.nframe()
myObj <- structure(list(.b = as.raw(7)), foo = 47L)# "very improbable" object
while (n > minframe) {
n <- n - 1L
env <- sys.frame(n)
r <- get0(x, envir = env, inherits=inherits, ifnotfound = myObj)
if(!identical(r, myObj))
return(r)
}
ifnotfound
}
loadNamespace <- function (package, lib.loc = NULL,
keep.source = getOption("keep.source.pkgs"),
partial = FALSE, versionCheck = NULL,
keep.parse.data = getOption("keep.parse.data.pkgs"))
{
libpath <- attr(package, "LibPath")
package <- as.character(package)[[1L]]
loading <- dynGet("__NameSpacesLoading__", NULL)
if (match(package, loading, 0L))
stop("cyclic namespace dependency detected when loading ",
sQuote(package), ", already loading ",
paste(sQuote(loading), collapse = ", "),
domain = NA)
"__NameSpacesLoading__" <- c(package, loading)
ns <- .Internal(getRegisteredNamespace(package))
if (! is.null(ns)) {
if(!is.null(zop <- versionCheck[["op"]]) &&
!is.null(zversion <- versionCheck[["version"]])) {
current <- getNamespaceVersion(ns)
if(!do.call(zop, list(as.numeric_version(current), zversion)))
stop(gettextf("namespace %s %s is already loaded, but %s %s is required",
sQuote(package), current, zop, zversion),
domain = NA)
}
ns
} else {
## only used here for .onLoad
runHook <- function(hookname, env, libname, pkgname) {
if (!is.null(fun <- env[[hookname]])) {
res <- tryCatch(fun(libname, pkgname), error = identity)
if (inherits(res, "error")) {
stop(gettextf("%s failed in %s() for '%s', details:\n call: %s\n error: %s",
hookname, "loadNamespace", pkgname,
deparse(conditionCall(res))[1L],
conditionMessage(res)),
call. = FALSE, domain = NA)
}
}
}
runUserHook <- function(pkgname, pkgpath) {
hooks <- getHook(packageEvent(pkgname, "onLoad")) # might be list()
for(fun in hooks) try(fun(pkgname, pkgpath))
}
makeNamespace <- function(name, version = NULL, lib = NULL) {
impenv <- new.env(parent = .BaseNamespaceEnv, hash = TRUE)
attr(impenv, "name") <- paste0("imports:", name)
env <- new.env(parent = impenv, hash = TRUE)
name <- as.character(as.name(name))
version <- as.character(version)
info <- new.env(hash = TRUE, parent = baseenv())
env$.__NAMESPACE__. <- info
info$spec <- c(name = name, version = version)
setNamespaceInfo(env, "exports", new.env(hash = TRUE, parent = baseenv()))
dimpenv <- new.env(parent = baseenv(), hash = TRUE)
attr(dimpenv, "name") <- paste0("lazydata:", name)
setNamespaceInfo(env, "lazydata", dimpenv)
setNamespaceInfo(env, "imports", list("base" = TRUE))
## this should be an absolute path
setNamespaceInfo(env, "path",
normalizePath(file.path(lib, name), "/", TRUE))
setNamespaceInfo(env, "dynlibs", NULL)
## <FIXME delayed S3 method registration>
setNamespaceInfo(env, "S3methods", matrix(NA_character_, 0L, 4L))
## </FIXME delayed S3 method registration>
env$.__S3MethodsTable__. <-
new.env(hash = TRUE, parent = baseenv())
.Internal(registerNamespace(name, env))
env
}
sealNamespace <- function(ns) {
namespaceIsSealed <- function(ns)
environmentIsLocked(ns)
ns <- asNamespace(ns, base.OK = FALSE)
if (namespaceIsSealed(ns))
stop(gettextf("namespace %s is already sealed in 'loadNamespace'",
sQuote(getNamespaceName(ns))),
call. = FALSE, domain = NA)
lockEnvironment(ns, TRUE)
lockEnvironment(parent.env(ns), TRUE)
}
addNamespaceDynLibs <- function(ns, newlibs) {
dynlibs <- .getNamespaceInfo(ns, "dynlibs")
setNamespaceInfo(ns, "dynlibs", c(dynlibs, newlibs))
}
bindTranslations <- function(pkgname, pkgpath)
{
## standard packages are treated differently
std <- c("compiler", "foreign", "grDevices", "graphics", "grid",
"methods", "parallel", "splines", "stats", "stats4",
"tcltk", "tools", "utils")
popath <- if (pkgname %in% std) .popath else file.path(pkgpath, "po")
if(!file.exists(popath)) return()
bindtextdomain(pkgname, popath)
bindtextdomain(paste0("R-", pkgname), popath)
}
assignNativeRoutines <- function(dll, lib, env, nativeRoutines) {
if(length(nativeRoutines) == 0L) return(character())
varnames <- character()
symnames <- character()
if(nativeRoutines$useRegistration) {
## Use the registration information to register ALL the symbols
fixes <- nativeRoutines$registrationFixes
routines <- getDLLRegisteredRoutines.DLLInfo(dll, addNames = FALSE)
lapply(routines,
function(type) {
lapply(type,
function(sym) {
varName <- paste0(fixes[1L], sym$name, fixes[2L])
if(exists(varName, envir = env, inherits = FALSE))
warning(gettextf(
"failed to assign RegisteredNativeSymbol for %s to %s since %s is already defined in the %s namespace",
sym$name, varName, varName, sQuote(package)),
domain = NA, call. = FALSE)
else {
env[[varName]] <- sym
varnames <<- c(varnames,
varName)
symnames <<- c(symnames,
sym$name)
}
})
})
}
symNames <- nativeRoutines$symbolNames
if(length(symNames)) {
symbols <- getNativeSymbolInfo(symNames, dll, unlist = FALSE,
withRegistrationInfo = TRUE)
lapply(seq_along(symNames),
function(i) {
## could vectorize this outside of the loop
## and assign to different variable to
## maintain the original names.
varName <- names(symNames)[i]
origVarName <- symNames[i]
if(exists(varName, envir = env, inherits = FALSE))
if(origVarName != varName)
warning(gettextf(
"failed to assign NativeSymbolInfo for %s to %s since %s is already defined in the %s namespace",
origVarName, varName, varName, sQuote(package)),
domain = NA, call. = FALSE)
else
warning(gettextf(
"failed to assign NativeSymbolInfo for %s since %s is already defined in the %s namespace",
origVarName, varName, sQuote(package)),
domain = NA, call. = FALSE)
else {
assign(varName, symbols[[origVarName]],
envir = env)
varnames <<- c(varnames, varName)
symnames <<- c(symnames, origVarName)
}
})
}
names(symnames) <- varnames
symnames
} ## end{assignNativeRoutines}
## find package, allowing a calling handler to retry if not found.
## could move the retry functionality into find.package.
fp.lib.loc <- c(libpath, lib.loc)
pkgpath <- find.package(package, fp.lib.loc, quiet = TRUE)
if (length(pkgpath) == 0L) {
cond <- packageNotFoundError(package, fp.lib.loc, sys.call())
withRestarts(stop(cond), retry_loadNamespace = function() NULL)
pkgpath <- find.package(package, fp.lib.loc, quiet = TRUE)
if (length(pkgpath) == 0L)
stop(cond)
}
bindTranslations(package, pkgpath)
package.lib <- dirname(pkgpath)
package <- basename(pkgpath) # need the versioned name
if (! packageHasNamespace(package, package.lib)) {
hasNoNamespaceError <-
function (package, package.lib, call = NULL) {
class <- c("hasNoNamespaceError", "error", "condition")
msg <- gettextf("package %s does not have a namespace",
sQuote(package))
structure(list(message = msg, package = package,
package.lib = package.lib, call = call),
class = class)
}
stop(hasNoNamespaceError(package, package.lib))
}
## create namespace; arrange to unregister on error
## Can we rely on the existence of R-ng 'nsInfo.rds' and
## 'package.rds'?
## No, not during builds of standard packages
## stats4 depends on methods, but exports do not matter
## whilst it is being built
iniStdPkgs <- c("methods", "stats", "stats4", "tools", "utils")
nsInfoFilePath <- file.path(pkgpath, "Meta", "nsInfo.rds")
nsInfo <- if(file.exists(nsInfoFilePath)) readRDS(nsInfoFilePath)
else parseNamespaceFile(package, package.lib, mustExist = FALSE)
pkgInfoFP <- file.path(pkgpath, "Meta", "package.rds")
if(file.exists(pkgInfoFP)) {
pkgInfo <- readRDS(pkgInfoFP)
version <- pkgInfo$DESCRIPTION["Version"]
vI <- pkgInfo$Imports
if(is.null(built <- pkgInfo$Built))
stop(gettextf("package %s has not been installed properly\n",
sQuote(package)), # == basename(pkgpath)
call. = FALSE, domain = NA)
R_version_built_under <- as.numeric_version(built$R)
if(R_version_built_under < "4.0.0")
stop(gettextf("package %s was installed before R 4.0.0: please re-install it",
sQuote(package)),
call. = FALSE, domain = NA)
## we need to ensure that S4 dispatch is on now if the package
## will require it, or the exports will be incomplete.
dependsMethods <- "methods" %in% names(pkgInfo$Depends)
if(dependsMethods) loadNamespace("methods")
if(!is.null(zop <- versionCheck[["op"]]) &&
!is.null(zversion <- versionCheck[["version"]]) &&
!do.call(zop, list(as.numeric_version(version), zversion)))
stop(gettextf("namespace %s %s is being loaded, but %s %s is required",
sQuote(package), version, zop, zversion),
domain = NA)
} else {
if(!any(package == iniStdPkgs))
warning(gettextf("package %s has no 'package.rds' in Meta/",
sQuote(package)),
domain = NA)
vI <- NULL
}
## moved from library() in R 3.4.0
checkLicense <- function(pkg, pkgInfo, pkgPath)
{
L <- tools:::analyze_license(pkgInfo$DESCRIPTION["License"])
if(!L$is_empty && !L$is_verified) {
site_file <-
path.expand(file.path(R.home("etc"), "licensed.site"))
if(file.exists(site_file) &&
pkg %in% readLines(site_file)) return()
personal_file <- path.expand("~/.R/licensed")
if(file.exists(personal_file)) {
agreed <- readLines(personal_file)
if(pkg %in% agreed) return()
} else agreed <- character()
if(!interactive())
stop(gettextf(
"package %s has a license that you need to accept in an interactive session",
sQuote(pkg)), domain = NA)
lfiles <- file.path(pkgpath, c("LICENSE", "LICENCE"))
lfiles <- lfiles[file.exists(lfiles)]
if(length(lfiles)) {
message(gettextf(
"package %s has a license that you need to accept after viewing",
sQuote(pkg)), domain = NA)
readline("press RETURN to view license")
encoding <- pkgInfo$DESCRIPTION["Encoding"]
if(is.na(encoding)) encoding <- ""
## difR and EVER have a Windows' 'smart quote' LICEN[CS]E file
if(encoding == "latin1") encoding <- "cp1252"
file.show(lfiles[1L], encoding = encoding)
} else {
message(gettextf(paste("package %s has a license that you need to accept:",
"according to the DESCRIPTION file it is",
"%s", sep="\n"),
sQuote(pkg),
pkgInfo$DESCRIPTION["License"]), domain = NA)
}
choice <- utils::menu(c("accept", "decline"),
title = paste("License for", sQuote(pkg)))
if(choice != 1)
stop(gettextf("license for package %s not accepted",
sQuote(package)), domain = NA, call. = FALSE)
dir.create(dirname(personal_file), showWarnings=FALSE)
writeLines(c(agreed, pkg), personal_file)
}
}
## avoid any bootstrapping issues by these exemptions
if(!package %in% c("datasets", "grDevices", "graphics", # <- ??
iniStdPkgs) &&
isTRUE(getOption("checkPackageLicense", FALSE)))
checkLicense(package, pkgInfo, pkgpath)
## Check that the internals version used to build this package
## matches the version of current R. Failure in this test
## should only occur if the R version is an unreleased devel
## version or the package was build with an unrelease devel
## version. Other mismatches should be caught earlier by the
## version checks.
## Meta will not exist when first building tools,
## so pkgInfo was not created above.
if(dir.exists(file.path(pkgpath, "Meta"))) {
ffile <- file.path(pkgpath, "Meta", "features.rds")
features <- if (file.exists(ffile)) readRDS(ffile) else NULL
needsComp <- as.character(pkgInfo$DESCRIPTION["NeedsCompilation"])
if (identical(needsComp, "yes") ||
file.exists(file.path(pkgpath, "libs"))) {
internalsID <- features$internalsID
if (is.null(internalsID))
## the initial internalsID for packages installed
## prior to introducing features.rds in the meta data
internalsID <- "0310d4b8-ccb1-4bb8-ba94-d36a55f60262"
if (internalsID != .Internal(internalsID()))
stop(gettextf("package %s was installed by an R version with different internals; it needs to be reinstalled for use with this R version",
sQuote(package)), call. = FALSE, domain = NA)
}
}
ns <- makeNamespace(package, version = version, lib = package.lib)
on.exit(.Internal(unregisterNamespace(package)))
## process imports
for (i in nsInfo$imports) {
if (is.character(i))
namespaceImport(ns,
loadNamespace(i, c(lib.loc, .libPaths()),
versionCheck = vI[[i]]),
from = package)
else if (!is.null(i$except))
namespaceImport(ns,
loadNamespace(j <- i[[1L]],
c(lib.loc, .libPaths()),
versionCheck = vI[[j]]),
from = package,
except = i$except)
else
namespaceImportFrom(ns,
loadNamespace(j <- i[[1L]],
c(lib.loc, .libPaths()),
versionCheck = vI[[j]]),
i[[2L]], from = package)
}
for(imp in nsInfo$importClasses)
namespaceImportClasses(ns, loadNamespace(j <- imp[[1L]],
c(lib.loc, .libPaths()),
versionCheck = vI[[j]]),
imp[[2L]], from = package)
for(imp in nsInfo$importMethods)
namespaceImportMethods(ns, loadNamespace(j <- imp[[1L]],
c(lib.loc, .libPaths()),
versionCheck = vI[[j]]),
imp[[2L]], from = package)
## store info for loading namespace for loadingNamespaceInfo to read
"__LoadingNamespaceInfo__" <- list(libname = package.lib,
pkgname = package)
env <- asNamespace(ns)
## save the package name in the environment
env$.packageName <- package
## load the code
codename <- strsplit(package, "_", fixed = TRUE)[[1L]][1L]
codeFile <- file.path(pkgpath, "R", codename)
if (file.exists(codeFile)) {
# The code file has been converted to the native encoding
save.enc <- options(encoding = "native.enc")
res <- try(sys.source(codeFile, env, keep.source = keep.source,
keep.parse.data = keep.parse.data))
options(save.enc)
if(inherits(res, "try-error"))
stop(gettextf("unable to load R code in package %s",
sQuote(package)), call. = FALSE, domain = NA)
}
# a package without R code currently is required to have a namespace
# else warning(gettextf("package %s contains no R code",
# sQuote(package)), call. = FALSE, domain = NA)
## partial loading stops at this point
## -- used in preparing for lazy-loading
if (partial) return(ns)
## lazy-load any sysdata
dbbase <- file.path(pkgpath, "R", "sysdata")
if (file.exists(paste0(dbbase, ".rdb"))) lazyLoad(dbbase, env)
## load any lazydata into a separate environment
dbbase <- file.path(pkgpath, "data", "Rdata")
if(file.exists(paste0(dbbase, ".rdb")))
lazyLoad(dbbase, .getNamespaceInfo(env, "lazydata"))
## register any S3 methods
registerS3methods(nsInfo$S3methods, package, env)
## load any dynamic libraries
dlls <- list()
dynLibs <- nsInfo$dynlibs
nativeRoutines <- list()
for (i in seq_along(dynLibs)) {
lib <- dynLibs[i]
dlls[[lib]] <- library.dynam(lib, package, package.lib)
routines <- assignNativeRoutines(dlls[[lib]], lib, env,
nsInfo$nativeRoutines[[lib]])
nativeRoutines[[lib]] <- routines
## If the DLL has a name as in useDynLib(alias = foo),
## then assign DLL reference to alias. Check if
## names() is NULL to handle case that the nsInfo.rds
## file was created before the names were added to the
## dynlibs vector.
if(!is.null(names(nsInfo$dynlibs))
&& nzchar(names(nsInfo$dynlibs)[i]))
env[[names(nsInfo$dynlibs)[i]]] <- dlls[[lib]]
setNamespaceInfo(env, "DLLs", dlls)
}
addNamespaceDynLibs(env, nsInfo$dynlibs)
setNamespaceInfo(env, "nativeRoutines", nativeRoutines)
## used in e.g. utils::assignInNamespace
Sys.setenv("_R_NS_LOAD_" = package)
on.exit(Sys.unsetenv("_R_NS_LOAD_"), add = TRUE)
## run the load hook
runHook(".onLoad", env, package.lib, package)
## process exports, seal, and clear on.exit action
exports <- nsInfo$exports
for (p in nsInfo$exportPatterns)
exports <- c(ls(env, pattern = p, all.names = TRUE), exports)
##
if(.isMethodsDispatchOn() && methods:::.hasS4MetaData(ns) &&
!identical(package, "methods") ) {
## cache generics, classes in this namespace (but not methods itself,
## which pre-cached at install time
methods::cacheMetaData(ns, TRUE, ns)
## This also ran .doLoadActions
## load actions may have added objects matching patterns
for (p in nsInfo$exportPatterns) {
expp <- ls(ns, pattern = p, all.names = TRUE)
newEx <- !(expp %in% exports)
if(any(newEx))
exports <- c(expp[newEx], exports)
}
## process class definition objects
expClasses <- nsInfo$exportClasses
##we take any pattern, but check to see if the matches are classes
pClasses <- character()
aClasses <- methods::getClasses(ns)
classPatterns <- nsInfo$exportClassPatterns
## defaults to exportPatterns
if(!length(classPatterns))
classPatterns <- nsInfo$exportPatterns
pClasses <- unique(unlist(lapply(classPatterns, grep, aClasses,
value=TRUE)))
if( length(pClasses) ) {
good <- vapply(pClasses, methods::isClass, NA, where = ns)
if( !any(good) && length(nsInfo$exportClassPatterns))
warning(gettextf(
"'exportClassPattern' specified in 'NAMESPACE' but no matching classes in package %s",
sQuote(package)),
call. = FALSE, domain = NA)
expClasses <- c(expClasses, pClasses[good])
}
if(length(expClasses)) {
missingClasses <-
!vapply(expClasses, methods::isClass, NA, where = ns)
if(any(missingClasses))
stop(gettextf("in package %s classes %s were specified for export but not defined",
sQuote(package),
paste(expClasses[missingClasses],
collapse = ", ")),
domain = NA)
expClasses <- paste0(methods::classMetaName(""), expClasses)
}
## process methods metadata explicitly exported or
## implied by exporting the generic function.
allGenerics <- unique(c(methods:::.getGenerics(ns),
methods:::.getGenerics(parent.env(ns))))
expMethods <- nsInfo$exportMethods
## check for generic functions corresponding to exported methods
addGenerics <- expMethods[is.na(match(expMethods, exports))]
if(length(addGenerics)) {
nowhere <- vapply(addGenerics, function(what) !exists(what, mode = "function", envir = ns),
NA, USE.NAMES=FALSE)
if(any(nowhere)) {
warning(gettextf("no function found corresponding to methods exports from %s for: %s",
sQuote(package),
paste(sQuote(sort(unique(addGenerics[nowhere]))), collapse = ", ")),
domain = NA, call. = FALSE)
addGenerics <- addGenerics[!nowhere]
}
if(length(addGenerics)) {
## skip primitives
addGenerics <- addGenerics[vapply(addGenerics, function(what)
!is.primitive(get(what, mode = "function", envir = ns)), NA)]
## the rest must be generic functions, implicit or local
## or have been cached via a DEPENDS package
ok <- vapply(addGenerics, methods:::.findsGeneric, 1L, ns)
if(!all(ok)) {
bad <- sort(unique(addGenerics[!ok]))
msg <-
ngettext(length(bad),
"Function found when exporting methods from the namespace %s which is not S4 generic: %s",
"Functions found when exporting methods from the namespace %s which are not S4 generic: %s")
stop(sprintf(msg, sQuote(package),
paste(sQuote(bad), collapse = ", ")),
domain = NA, call. = FALSE)
}
else if(any(ok > 1L)) #from the cache, don't add
addGenerics <- addGenerics[ok < 2L]
}
### <note> Uncomment following to report any local generic functions
### that should have been exported explicitly. But would be reported
### whenever the package is loaded, which is not when it is relevant.
### </note>
## local <- sapply(addGenerics, function(what) identical(as.character(get(what, envir = ns)@package), package))
## if(any(local))
## message(gettextf("export(%s) from package %s generated by exportMethods()",
## paste(addGenerics[local], collapse = ", ")),
## domain = NA)
exports <- c(exports, addGenerics)
}
expTables <- character()
if(length(allGenerics)) {
expMethods <-
unique(c(expMethods,
exports[!is.na(match(exports, allGenerics))]))
missingMethods <- !(expMethods %in% allGenerics)
if(any(missingMethods))
stop(gettextf("in %s methods for export not found: %s",
sQuote(package),
paste(expMethods[missingMethods],
collapse = ", ")),
domain = NA)
tPrefix <- methods:::.TableMetaPrefix()
allMethodTables <-
unique(c(methods:::.getGenerics(ns, tPrefix),
methods:::.getGenerics(parent.env(ns), tPrefix)))
needMethods <-
(exports %in% allGenerics) & !(exports %in% expMethods)
if(any(needMethods))
expMethods <- c(expMethods, exports[needMethods])
## Primitives must have their methods exported as long
## as a global table is used in the C code to dispatch them:
## The following keeps the exported files consistent with
## the internal table.
pm <- allGenerics[!(allGenerics %in% expMethods)]
if(length(pm)) {
prim <- vapply(pm, function(pmi) {
f <- methods::getFunction(pmi, FALSE,
FALSE, ns)
is.primitive(f)
}, logical(1L))
expMethods <- c(expMethods, pm[prim])
}
for(i in seq_along(expMethods)) {
mi <- expMethods[[i]]
if(!(mi %in% exports) &&
exists(mi, envir = ns, mode = "function",
inherits = FALSE))
exports <- c(exports, mi)
pattern <- paste0(tPrefix, mi, ":")
ii <- grep(pattern, allMethodTables, fixed = TRUE)
if(length(ii)) {
if(length(ii) > 1L) {
warning(gettextf("multiple methods tables found for %s",
sQuote(mi)), call. = FALSE, domain = NA)
ii <- ii[1L]
}
expTables[[i]] <- allMethodTables[ii]
}
else { ## but not possible?
warning(gettextf("failed to find metadata object for %s",
sQuote(mi)), call. = FALSE, domain = NA)
}
}
}
else if(length(expMethods))
stop(gettextf("in package %s methods %s were specified for export but not defined",
sQuote(package),
paste(expMethods, collapse = ", ")),
domain = NA)
exports <- unique(c(exports, expClasses, expTables))
}
## certain things should never be exported.
if (length(exports)) {
stoplist <- c(".__NAMESPACE__.", ".__S3MethodsTable__.",
".packageName", ".First.lib", ".onLoad",
".onAttach", ".conflicts.OK", ".noGenerics")
exports <- exports[! exports %in% stoplist]
}
namespaceExport(ns, exports)
sealNamespace(ns)
runUserHook(package, pkgpath)
on.exit()
Sys.unsetenv("_R_NS_LOAD_")
ns
}
}
## A version which returns TRUE/FALSE
requireNamespace <- function (package, ..., quietly = FALSE)
{
package <- as.character(package)[[1L]] # like loadNamespace
ns <- .Internal(getRegisteredNamespace(package))
res <- TRUE
if (is.null(ns)) {
if(!quietly)
packageStartupMessage(gettextf("Loading required namespace: %s",
package), domain = NA)
value <- tryCatch(loadNamespace(package, ...), error = function(e) e)
if (inherits(value, "error")) {
if (!quietly) {
msg <- conditionMessage(value)
cat("Failed with error: ",
sQuote(msg), "\n", file = stderr(), sep = "")
.Internal(printDeferredWarnings())
}
res <- FALSE
}
}
invisible(res)
}
loadingNamespaceInfo <- function() {
dynGet("__LoadingNamespaceInfo__", stop("not loading a namespace"))
}
topenv <- function(envir = parent.frame(),
matchThisEnv = getOption("topLevelEnvironment")) {
.Internal(topenv(envir, matchThisEnv))
}
unloadNamespace <- function(ns)
{
## check, so we do not load & unload:
if ((is.character(ns) && any(ns == loadedNamespaces())) ||
(is.environment(ns) && any(getNamespaceName(ns) == loadedNamespaces()))) {
## only used to run .onUnload
runHook <- function(hookname, env, ...) {
if (!is.null(fun <- env[[hookname]])) {
res <- tryCatch(fun(...), error=identity)
if (inherits(res, "error")) {
warning(gettextf("%s failed in %s() for '%s', details:\n call: %s\n error: %s",
hookname, "unloadNamespace", nsname,
deparse(conditionCall(res))[1L],
conditionMessage(res)),
call. = FALSE, domain = NA)
}
}
}
ns <- asNamespace(ns, base.OK = FALSE)
nsname <- getNamespaceName(ns)
pos <- match(paste0("package:", nsname), search())
if (! is.na(pos)) detach(pos = pos)
users <- getNamespaceUsers(ns)
if (length(users))
stop(gettextf("namespace %s is imported by %s so cannot be unloaded",
sQuote(getNamespaceName(ns)),
paste(sQuote(users), collapse = ", ")),
domain = NA)
nspath <- .getNamespaceInfo(ns, "path")
hook <- getHook(packageEvent(nsname, "onUnload")) # might be list()
for(fun in rev(hook)) try(fun(nsname, nspath))
runHook(".onUnload", ns, nspath)
.Internal(unregisterNamespace(nsname))
if(.isMethodsDispatchOn() && methods:::.hasS4MetaData(ns))
methods::cacheMetaData(ns, FALSE, ns)
.Internal(lazyLoadDBflush(paste0(nspath, "/R/", nsname, ".rdb")))
}
invisible()
}
isNamespace <- function(ns) .Internal(isNamespaceEnv(ns))
isBaseNamespace <- function(ns) identical(ns, .BaseNamespaceEnv)
getNamespaceInfo <- function(ns, which) {
ns <- asNamespace(ns, base.OK = FALSE)
get(which, envir = ns[[".__NAMESPACE__."]])
}
.getNamespaceInfo <- function(ns, which) {
ns[[".__NAMESPACE__."]][[which]]
}
setNamespaceInfo <- function(ns, which, val) {
ns <- asNamespace(ns, base.OK = FALSE)
info <- ns[[".__NAMESPACE__."]]
info[[which]] <- val
}
asNamespace <- function(ns, base.OK = TRUE) {
if (is.character(ns) || is.name(ns))
ns <- getNamespace(ns)
if (! isNamespace(ns))
stop("not a namespace")
else if (! base.OK && isBaseNamespace(ns))
stop("operation not allowed on base namespace")
else ns
}
namespaceImport <- function(self, ..., from = NULL, except = character(0L))
for (ns in list(...))
namespaceImportFrom(self, asNamespace(ns), from = from,
except = except)
namespaceImportFrom <- function(self, ns, vars, generics, packages,
from = "non-package environment",
except = character(0L))
{
addImports <- function(ns, from, what) {
imp <- structure(list(what), names = getNamespaceName(from))
imports <- getNamespaceImports(ns)
setNamespaceInfo(ns, "imports", c(imports, imp))
}
namespaceIsSealed <- function(ns)
environmentIsLocked(ns)
makeImportExportNames <- function(spec) {
old <- as.character(spec)
new <- names(spec)
if (is.null(new)) new <- old
else {
change <- !nzchar(new)
new[change] <- old[change]
}
names(old) <- new
old
}
whichMethodMetaNames <- function(impvars) {
if(!.isMethodsDispatchOn())
return(numeric())
seq_along(impvars)[startsWith(impvars, ".__T__")]
}
genericPackage <- function(f) {
if(methods::is(f, "genericFunction")) f@package
else if(is.primitive(f)) "base"
else "<unknown>"
}
if (is.character(self))
self <- getNamespace(self)
ns <- asNamespace(ns)
nsname <- getNamespaceName(ns)
impvars <- if (missing(vars)) {
## certain things should never be imported:
## but most of these are never exported (exception: .Last.lib)
stoplist <- c(".__NAMESPACE__.", ".__S3MethodsTable__.",
".packageName", ".First.lib", ".Last.lib",
".onLoad", ".onAttach", ".onDetach",
".conflicts.OK", ".noGenerics")
vars <- getNamespaceExports(ns)
vars <- vars[! vars %in% stoplist]
} else vars
impvars <- impvars[! impvars %in% except]
impvars <- makeImportExportNames(impvars)
impnames <- names(impvars)
if (anyDuplicated(impnames)) {
stop(gettextf("duplicate import names %s",
paste(sQuote(impnames[duplicated(impnames)]),
collapse = ", ")), domain = NA)
}
if (isNamespace(self)) {
if(isBaseNamespace(self)) {
impenv <- self
msg <- gettext("replacing local value with import %s when loading %s")
register <- FALSE
}
else {
if (namespaceIsSealed(self))
stop("cannot import into a sealed namespace")
impenv <- parent.env(self)
msg <- gettext("replacing previous import by %s when loading %s")
register <- TRUE
}
}
else if (is.environment(self)) {
impenv <- self
msg <- gettext("replacing local value with import %s when loading %s")
register <- FALSE
}
else stop("invalid import target")
which <- whichMethodMetaNames(impvars)
if(length(which)) {
## If methods are already in impenv, merge and don't import
delete <- integer()
for(i in which) {
methodsTable <- .mergeImportMethods(impenv, ns, impvars[[i]])
if(is.null(methodsTable))
{} ## first encounter, just import it
else { ##
delete <- c(delete, i)
if(!missing(generics)) {
genName <- generics[[i]]
## if(i > length(generics) || !nzchar(genName))
## {warning("got invalid index for importing ",mlname); next}
fdef <- methods::getGeneric(genName,