当我们的R底层逻辑不清楚的时候，bug就会不经意地来到我们眼前。比如：
library(ggpubr)
Error in value[[3L]](cond) :
Package ‘ggpubr’ version 0.3.0 cannot be unloaded:
Error in unloadNamespace(package) : namespace ‘ggpubr’ is imported by ‘immunarch’ so cannot be unloaded
In addition: Warning message:
package ‘ggpubr’ was built under R version 3.6.3
这时候，我该怎么办呢？就是把上一层的Namespace，给unload掉，再加载。
unloadNamespace(”immunarch“)
library(ggpubr)
library(immunarch)
那么，为什么会报这样的错呢？首先我们要知道什么是命名空间：
《维基百科》中说 “命名空间是对作用域的一种特殊的抽象”，在这里我用一个比方来具体说明一下：
比如张三在公司 A，他的工号是 111，李四在公司 B，他的工号也是 111，因为两个人在不同的公司，他们俩的工号可以相同但是不会引起混乱，这里的公司就表示一个独立的命名空间，如果两个人在一个公司的话，他们的工号就不能相同，否则光看工号也不知道到底是谁
我们在载入一个R包的时候也会把他的命名空间导进来，但是如果再导入一样的，就会冲突了。比如这一天店里里来了两个111 ，都带了对象，我们要说：111的对象麻烦结下账。这下麻烦了。
在R里面如何看当前的命名空间呢？
library(Seurat)
loadedNamespaces()
[1] "gridExtra" "gplots" "graphics" "rsvd" "stringi"
[6] "pbapply" "lattice" "bitops" "vctrs" "Rdpack"
[11] "mgcv" "survival" "spatstat.data" "later" "tidyr"
[16] "tensor" "R.utils" "uwot" "data.table" "rstudioapi"
[21] "base" "npsurv" "deldir" "nlme" "ggplot2"
[26] "SDMTools" "htmlwidgets" "future" "listenv" "ggrepel"
[31] "leiden" "tools" "irlba" "parallel" "magrittr"
[36] "grDevices" "methods" "R.oo" "ape" "Rcpp"
[41] "KernSmooth" "promises" "gdata" "RcppParallel" "httr"
[46] "assertthat" "globals" "lifecycle" "R6" "munsell"
[51] "gtools" "png" "R.methodsS3" "digest" "caTools"
[56] "codetools" "sctransform" "splines" "cowplot" "lmtest"
[61] "colorspace" "pkgconfig" "pillar" "lsei" "ROCR"
[66] "xtable" "utils" "abind" "plyr" "reticulate"
[71] "RANN" "gtable" "zoo" "datasets" "stats"
[76] "tidyselect" "purrr" "reshape2" "ica" "fastmap"
[81] "bibtex" "crosstalk" "goftest" "RcppAnnoy" "viridisLite"
[86] "tibble" "rlang" "cluster" "future.apply" "Seurat"
[91] "zeallot" "glue" "Matrix" "spatstat" "scales"
[96] "backports" "metap" "RColorBrewer" "ggridges" "stringr"
[101] "igraph" "Rtsne" "dplyr" "shiny" "polyclip"
[106] "grid" "spatstat.utils" "gbRd" "httpuv" "htmltools"
[111] "yaml" "lazyeval" "plotly" "tsne" "crayon"
[116] "fitdistrplus" "MASS" "jsonlite" "rpart" "mime"
[121] "compiler"
但是这时候，我再加载
library(Rtsne)
是可以的，为什么？
所以，我们还是看一下这个报错的根源：library的源码，他一定是在某个地方加了判断：
> library
function (package, help, pos = 2, lib.loc = NULL, character.only = FALSE,
logical.return = FALSE, warn.conflicts = TRUE, quietly = FALSE,
verbose = getOption("verbose"))
{
testRversion <- function(pkgInfo, pkgname, pkgpath) {
if (is.null(built <- pkgInfo$Built))
stop(gettextf("package %s has not been installed properly\n",
sQuote(pkgname)), call. = FALSE, domain = NA)
R_version_built_under <- as.numeric_version(built$R)
if (R_version_built_under < "3.0.0")
stop(gettextf("package %s was built before R 3.0.0: please re-install it",
sQuote(pkgname)), call. = FALSE, domain = NA)
current <- getRversion()
if (length(Rdeps <- pkgInfo$Rdepends2)) {
for (dep in Rdeps) if (length(dep) > 1L) {
target <- dep$version
res <- if (is.character(target)) {
do.call(dep$op, list(as.numeric(R.version[["svn rev"]]),
as.numeric(sub("^r", "", dep$version))))
}
else {
do.call(dep$op, list(current, as.numeric_version(target)))
}
if (!res)
stop(gettextf("This is R %s, package %s needs %s %s",
current, sQuote(pkgname), dep$op, target),
call. = FALSE, domain = NA)
}
}
if (R_version_built_under > current)
warning(gettextf("package %s was built under R version %s",
sQuote(pkgname), as.character(built$R)), call. = FALSE,
domain = NA)
platform <- built$Platform
r_arch <- .Platform$r_arch
if (.Platform$OS.type == "unix") {
if (!nzchar(r_arch) && grepl("\\w", platform) &&
!testPlatformEquivalence(platform, R.version$platform))
stop(gettextf("package %s was built for %s",
sQuote(pkgname), platform), call. = FALSE,
domain = NA)
}
else {
if (nzchar(platform) && !grepl("mingw", platform))
stop(gettextf("package %s was built for %s",
sQuote(pkgname), platform), call. = FALSE,
domain = NA)
}
if (nzchar(r_arch) && file.exists(file.path(pkgpath,
"libs")) && !file.exists(file.path(pkgpath, "libs",
r_arch)))
stop(gettextf("package %s is not installed for 'arch = %s'",
sQuote(pkgname), r_arch), call. = FALSE, domain = NA)
}
checkNoGenerics <- function(env, pkg) {
nenv <- env
ns <- .getNamespace(as.name(pkg))
if (!is.null(ns))
nenv <- asNamespace(ns)
if (exists(".noGenerics", envir = nenv, inherits = FALSE))
TRUE
else {
!any(startsWith(names(env), ".__T"))
}
}
checkConflicts <- function(package, pkgname, pkgpath, nogenerics,
env) {
dont.mind <- c("last.dump", "last.warning", ".Last.value",
".Random.seed", ".Last.lib", ".onDetach", ".packageName",
".noGenerics", ".required", ".no_S3_generics", ".Depends",
".requireCachedGenerics")
sp <- search()
lib.pos <- which(sp == pkgname)
ob <- names(as.environment(lib.pos))
if (!nogenerics) {
these <- ob[startsWith(ob, ".__T__")]
gen <- gsub(".__T__(.*):([^:]+)", "\\1", these)
from <- gsub(".__T__(.*):([^:]+)", "\\2", these)
gen <- gen[from != package]
ob <- ob[!(ob %in% gen)]
}
fst <- TRUE
ipos <- seq_along(sp)[-c(lib.pos, match(c("Autoloads",
"CheckExEnv"), sp, 0L))]
for (i in ipos) {
obj.same <- match(names(as.environment(i)), ob, nomatch = 0L)
if (any(obj.same > 0)) {
same <- ob[obj.same]
same <- same[!(same %in% dont.mind)]
Classobjs <- which(startsWith(same, ".__"))
if (length(Classobjs))
same <- same[-Classobjs]
same.isFn <- function(where) vapply(same, exists,
NA, where = where, mode = "function", inherits = FALSE)
same <- same[same.isFn(i) == same.isFn(lib.pos)]
not.Ident <- function(ch, TRAFO = identity, ...) vapply(ch,
function(.) !identical(TRAFO(get(., i)), TRAFO(get(.,
lib.pos)), ...), NA)
if (length(same))
same <- same[not.Ident(same)]
if (length(same) && identical(sp[i], "package:base"))
same <- same[not.Ident(same, ignore.environment = TRUE)]
if (length(same)) {
if (fst) {
fst <- FALSE
packageStartupMessage(gettextf("\nAttaching package: %s\n",
sQuote(package)), domain = NA)
}
msg <- .maskedMsg(sort(same), pkg = sQuote(sp[i]),
by = i < lib.pos)
packageStartupMessage(msg, domain = NA)
}
}
}
}
if (verbose && quietly)
message("'verbose' and 'quietly' are both true; being verbose then ..")
if (!missing(package)) {
if (is.null(lib.loc))
lib.loc <- .libPaths()
lib.loc <- lib.loc[dir.exists(lib.loc)]
if (!character.only)
package <- as.character(substitute(package))
if (length(package) != 1L)
stop("'package' must be of length 1")
if (is.na(package) || (package == ""))
stop("invalid package name")
pkgname <- paste0("package:", package)
newpackage <- is.na(match(pkgname, search()))
if (newpackage) {
pkgpath <- find.package(package, lib.loc, quiet = TRUE,
verbose = verbose)
if (length(pkgpath) == 0L) {
txt <- if (length(lib.loc))
gettextf("there is no package called %s", sQuote(package))
else gettext("no library trees found in 'lib.loc'")
if (logical.return) {
warning(txt, domain = NA)
return(FALSE)
}
else stop(txt, domain = NA)
}
which.lib.loc <- normalizePath(dirname(pkgpath),
"/", TRUE)
pfile <- system.file("Meta", "package.rds", package = package,
lib.loc = which.lib.loc)
if (!nzchar(pfile))
stop(gettextf("%s is not a valid installed package",
sQuote(package)), domain = NA)
pkgInfo <- readRDS(pfile)
testRversion(pkgInfo, package, pkgpath)
if (is.character(pos)) {
npos <- match(pos, search())
if (is.na(npos)) {
warning(gettextf("%s not found on search path, using pos = 2",
sQuote(pos)), domain = NA)
pos <- 2
}
else pos <- npos
}
.getRequiredPackages2(pkgInfo, quietly = quietly)
deps <- unique(names(pkgInfo$Depends))
if (packageHasNamespace(package, which.lib.loc)) {
if (isNamespaceLoaded(package)) {
newversion <- as.numeric_version(pkgInfo$DESCRIPTION["Version"])
oldversion <- as.numeric_version(getNamespaceVersion(package))
if (newversion != oldversion) {
tryCatch(unloadNamespace(package), error = function(e) {
P <- if (!is.null(cc <- conditionCall(e)))
paste("Error in", deparse(cc)[1L], ": ")
else "Error : "
stop(gettextf("Package %s version %s cannot be unloaded:\n %s",
sQuote(package), oldversion, paste0(P,
conditionMessage(e), "\n")), domain = NA)
})
}
}
tt <- tryCatch({
attr(package, "LibPath") <- which.lib.loc
ns <- loadNamespace(package, lib.loc)
env <- attachNamespace(ns, pos = pos, deps)
}, error = function(e) {
P <- if (!is.null(cc <- conditionCall(e)))
paste(" in", deparse(cc)[1L])
else ""
msg <- gettextf("package or namespace load failed for %s%s:\n %s",
sQuote(package), P, conditionMessage(e))
if (logical.return)
message(paste("Error:", msg), domain = NA)
else stop(msg, call. = FALSE, domain = NA)
})
if (logical.return && is.null(tt))
return(FALSE)
attr(package, "LibPath") <- NULL
{
on.exit(detach(pos = pos))
nogenerics <- !.isMethodsDispatchOn() || checkNoGenerics(env,
package)
if (warn.conflicts && !exists(".conflicts.OK",
envir = env, inherits = FALSE))
checkConflicts(package, pkgname, pkgpath,
nogenerics, ns)
on.exit()
if (logical.return)
return(TRUE)
else return(invisible(.packages()))
}
}
else stop(gettextf("package %s does not have a namespace and should be re-installed",
sQuote(package)), domain = NA)
}
if (verbose && !newpackage)
warning(gettextf("package %s already present in search()",
sQuote(package)), domain = NA)
}
else if (!missing(help)) {
if (!character.only)
help <- as.character(substitute(help))
pkgName <- help[1L]
pkgPath <- find.package(pkgName, lib.loc, verbose = verbose)
docFiles <- c(file.path(pkgPath, "Meta", "package.rds"),
file.path(pkgPath, "INDEX"))
if (file.exists(vignetteIndexRDS <- file.path(pkgPath,
"Meta", "vignette.rds")))
docFiles <- c(docFiles, vignetteIndexRDS)
pkgInfo <- vector("list", 3L)
readDocFile <- function(f) {
if (basename(f) %in% "package.rds") {
txt <- readRDS(f)$DESCRIPTION
if ("Encoding" %in% names(txt)) {
to <- if (Sys.getlocale("LC_CTYPE") == "C")
"ASCII//TRANSLIT"
else ""
tmp <- try(iconv(txt, from = txt["Encoding"],
to = to))
if (!inherits(tmp, "try-error"))
txt <- tmp
else warning("'DESCRIPTION' has an 'Encoding' field and re-encoding is not possible",
call. = FALSE)
}
nm <- paste0(names(txt), ":")
formatDL(nm, txt, indent = max(nchar(nm, "w")) +
3L)
}
else if (basename(f) %in% "vignette.rds") {
txt <- readRDS(f)
if (is.data.frame(txt) && nrow(txt))
cbind(basename(gsub("\\.[[:alpha:]]+$", "",
txt$File)), paste(txt$Title, paste0(rep.int("(source",
NROW(txt)), ifelse(nzchar(txt$PDF), ", pdf",
""), ")")))
else NULL
}
else readLines(f)
}
for (i in which(file.exists(docFiles))) pkgInfo[[i]] <- readDocFile(docFiles[i])
y <- list(name = pkgName, path = pkgPath, info = pkgInfo)
class(y) <- "packageInfo"
return(y)
}
else {
if (is.null(lib.loc))
lib.loc <- .libPaths()
db <- matrix(character(), nrow = 0L, ncol = 3L)
nopkgs <- character()
for (lib in lib.loc) {
a <- .packages(all.available = TRUE, lib.loc = lib)
for (i in sort(a)) {
file <- system.file("Meta", "package.rds", package = i,
lib.loc = lib)
title <- if (nzchar(file)) {
txt <- readRDS(file)
if (is.list(txt))
txt <- txt$DESCRIPTION
if ("Encoding" %in% names(txt)) {
to <- if (Sys.getlocale("LC_CTYPE") == "C")
"ASCII//TRANSLIT"
else ""
tmp <- try(iconv(txt, txt["Encoding"], to,
"?"))
if (!inherits(tmp, "try-error"))
txt <- tmp
else warning("'DESCRIPTION' has an 'Encoding' field and re-encoding is not possible",
call. = FALSE)
}
txt["Title"]
}
else NA
if (is.na(title))
title <- " ** No title available ** "
db <- rbind(db, cbind(i, lib, title))
}
if (length(a) == 0L)
nopkgs <- c(nopkgs, lib)
}
dimnames(db) <- list(NULL, c("Package", "LibPath", "Title"))
if (length(nopkgs) && !missing(lib.loc)) {
pkglist <- paste(sQuote(nopkgs), collapse = ", ")
msg <- sprintf(ngettext(length(nopkgs), "library %s contains no packages",
"libraries %s contain no packages"), pkglist)
warning(msg, domain = NA)
}
y <- list(header = NULL, results = db, footer = NULL)
class(y) <- "libraryIQR"
return(y)
}
if (logical.return)
TRUE
else invisible(.packages())
}
<bytecode: 0x08267d50>
<environment: namespace:base>
果不其然：
if (packageHasNamespace(package, which.lib.loc)) {
if (isNamespaceLoaded(package)) {
newversion <- as.numeric_version(pkgInfo$DESCRIPTION["Version"])
oldversion <- as.numeric_version(getNamespaceVersion(package))
if (newversion != oldversion) {
tryCatch(unloadNamespace(package), error = function(e) {
P <- if (!is.null(cc <- conditionCall(e)))
paste("Error in", deparse(cc)[1L], ": ")
else "Error : "
stop(gettextf("Package %s version %s cannot be unloaded:\n %s",
sQuote(package), oldversion, paste0(P,
conditionMessage(e), "\n")), domain = NA)
})
}
遇到这种情况往往是从两个不同的地方导入包导致的。
https://github.com/RevolutionAnalytics/checkpoint/issues/155
https://stackoverflow.com/questions/37031457/problems-trying-to-install-package-in-r
https://zhuanlan.zhihu.com/p/42399724
