当前位置：首页 > news >正文

加载R包unloadNamespace时，我该怎么办

news 来源：原创 2024/5/8 5:40:32

加载R包unloadNamespace时，我该怎么办
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] :
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)

在这里插入图片描述

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 $properly\n", sQuote(pkgname)), call. = FALSE, domain = NA) R_version_built_under <- as.numeric_version(built$ 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 $KaTeX parse error: Expected '}', got 'EOF' at end of input: \dots target <- dep$ 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 $KaTeX parse error: Expected 'EOF', got '}' at position 64: \dots }̲ \dots$ 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 $R)), c a l l . = F A L S E, d o m a i n = N A) p l a t f o r m < - b u i l t$ Platform
r_arch <- .Platform $r_arch if (.Platform$ OS.type == “unix”) {
if (!nzchar(r_arch) && grepl("\w", platform) &&
!testPlatformEquivalence(platform, R.version $KaTeX parse error: Expected 'EOF', got '}' at position 176: \dots = NA) }̲ else {\dots$ Depends))
if (packageHasNamespace(package, which.lib.loc)) {
if (isNamespaceLoaded(package)) {
newversion <- as.numeric_version(pkgInfo $KaTeX parse error: Undefined control sequence: \n at position 601: …onMessage(e), "\̲n̲")), domain = N…$ 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:]]+ $", " ", t x t$ File)), paste(txt $T i t l e, p a s t e 0 (r e p . i n t (" (s o u r c e ", N R O W (t x t)), i f e l s e (n z c h a r (t x t$ 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

作者：周运来就是我
链接：https://www.jianshu.com/p/c0f3
Error in unloadNamespace(c(“dplyr”, “recipes”)) :
名字空间‘dplyr’是由‘recipes’, ‘plotly’, ‘dbplyr’, ‘tidyr’, ‘broom’引进的，因此无法将之卸下
In addition: Warning message:
In ns == loadedNamespaces() :
longer object length is not a multiple of shorter object length

library(nichenetr)
Error: package or namespace load failed for ‘nichenetr’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
载入了名字空间‘glue’ 1.4.2，但需要的是>= 1.5.0
library(glue)
Error in value[3L] :
Package ‘glue’ version 1.4.2 cannot be unloaded:
Error in unloadNamespace(package) : 名字空间‘glue’是由‘dplyr’, ‘dbplyr’, ‘tidyr’, ‘ggplot2’, ‘usethis’, ‘broom’, ‘tidyselect’引进的，因此无法将之卸下
In addition: Warning message:
程辑包‘glue’是用R版本4.1.3 来建造的
unloadNamespace(“glue”)
Error in unloadNamespace(“glue”) :
名字空间‘glue’是由‘dplyr’, ‘dbplyr’, ‘tidyr’, ‘ggplot2’, ‘usethis’, ‘broom’, ‘tidyselect’引进的，因此无法将之卸下