在运行 install.packages() 之前检查已安装的软件包 [重复]

Question

我有一个 R 脚本，它与不同计算机上的多个用户共享。其中一行包含install.packages("xtable") 命令。

问题在于，每次有人运行脚本时，R 显然会花费大量时间重新安装包（实际上确实需要一些时间，因为真实案例有多个包的向量）。

我怎样才能先检查软件包是否已安装，然后只为未安装的软件包运行install.packages()？

Answer 1

试试：require("xtable") 或 "xtable" %in% rownames(installed.packages())

Answer 2

如果你想尽可能简单：

packages <- c("ggplot2", "dplyr", "Hmisc", "lme4", "arm", "lattice", "lavaan")

install.packages(setdiff(packages, rownames(installed.packages())))  

将第一行列出的包替换为运行代码所需的包，瞧！

注意：感谢 Artem 在下面的评论，已编辑以删除条件包装器。

Answer 3

这是我经常用来检查包的功能，否则安装它并再次加载：

pkgTest <- function(x)
  {
    if (!require(x,character.only = TRUE))
    {
      install.packages(x,dep=TRUE)
        if(!require(x,character.only = TRUE)) stop("Package not found")
    }
  }

像pkgTest("xtable") 一样工作。它仅在设置了镜像时才有效，但您可以在 require 调用中输入它。

Answer 4

我建议使用system.file 的更轻量级的解决方案。

is_inst <- function(pkg) {
    nzchar(system.file(package = pkg))
}

is_inst2 <- function(pkg) {
    pkg %in% rownames(installed.packages())
}

library(microbenchmark)
microbenchmark(is_inst("aaa"), is_inst2("aaa"))
## Unit: microseconds
##            expr      min        lq       mean    median       uq       max neval
##  is_inst("aaa")   22.284   24.6335   42.84806   34.6815   47.566   252.568   100
## is_inst2("aaa") 1099.334 1220.5510 1778.57019 1401.5095 1829.973 17653.148   100
microbenchmark(is_inst("ggplot2"), is_inst2("ggplot2"))
## Unit: microseconds
##                expr      min       lq     mean   median       uq      max neval
##  is_inst("ggplot2")  336.845  386.660  459.243  431.710  483.474  867.637   100
## is_inst2("ggplot2") 1144.613 1276.847 1507.355 1410.054 1656.557 2747.508   100

Answer 5

还有 CRAN 包 pacman 具有 p_load 功能来安装一个或多个包（但仅在必要时）然后加载它们。

Answer 6

requiredPackages = c('plyr','ggplot2','ggtern')
for(p in requiredPackages){
  if(!require(p,character.only = TRUE)) install.packages(p)
  library(p,character.only = TRUE)
}

Answer 7

# Function to check whether package is installed
  is.installed <- function(mypkg){
    is.element(mypkg, installed.packages()[,1])
  } 

  # check if package "hydroGOF" is installed
  if (!is.installed("hydroGOF")){
    install.packages("hydroGOF")
  }

Answer 8

我在某个地方找到了一个 packages 脚本，我总是将它放入每个脚本中以加载我的库。它将仅在需要时进行所有库处理（下载、安装和加载）。

# Install function for packages    
packages<-function(x){
  x<-as.character(match.call()[[2]])
  if (!require(x,character.only=TRUE)){
    install.packages(pkgs=x,repos="http://cran.r-project.org")
    require(x,character.only=TRUE)
  }
}
packages(ggplot2)
packages(reshape2)
packages(plyr)
# etc etc

Answer 9

我已经实现了静默安装和加载所需 R 包的功能。希望可能会有所帮助。代码如下：

# Function to Install and Load R Packages
Install_And_Load <- function(Required_Packages)
{
    Remaining_Packages <- Required_Packages[!(Required_Packages %in% installed.packages()[,"Package"])];

    if(length(Remaining_Packages)) 
    {
        install.packages(Remaining_Packages);
    }
    for(package_name in Required_Packages)
    {
        library(package_name,character.only=TRUE,quietly=TRUE);
    }
}

# Specify the list of required packages to be installed and load    
Required_Packages=c("ggplot2", "Rcpp");

# Call the Function
Install_And_Load(Required_Packages);

Answer 10

我使用的解决方案来自 Sacha Epskamp 和曙光的意见。函数如下：

instalaPacotes <- function(pacote) {
  if (!pacote %in% installed.packages()) install.packages(pacote)
}

它静默工作，如果包“pacote”已经安装，则不回显，否则安装它。不要忘记在引号之间写下包的名称！

Answer 11

Or a massively overticked example from drknexus/repsych on github, glibrary。几乎可以肯定有更有效和更好的方法可以做到这一点，但我很久以前就对其进行了编程，它基本上可以工作。

• 即使未选择存储库也可以使用默认云选项（如果可用）。如果您使用的是旧版本的 R，它将回滚并根据国家/地区代码选择镜像。
• 它会尝试加载库（使用上述某些方法可以提高此步骤的效率）
  • 如果失败，它会尝试安装它
  • 如果安装失败，它将通知您哪些软件包安装失败
• 没错，包，多个包可以连同它们的依赖项一起加载/安装（至少通常情况下，这里可能存在错误）。

例如：glibrary(xtable,sos,data.table) 但我不认为如果你打电话给glibrary("xtable","sos","data.table") 会吓坏。欢迎推/拉/叉。

函数代码：

#' Try to load a library, if that fails, install it, then load it.
#'
#' glibrary short for (get)library.
#' The primary aim of this function is to make loading packages more transparent.  Given that we know we want to load a given package, actually fetching it is a formality.  glibrary skims past this formality to install the requested package.
#'
#' @export
#' @param ... comma seperated package names
#' @param lib.loc See \code{\link{require}}
#' @param quietly See \code{\link{require}}
#' @param warn.conflicts See \code{\link{require}}
#' @param pickmirror If TRUE, glibrary allows the user to select the mirror, otherwise it auto-selects on the basis of the country code
#' @param countrycode This option is ignored and the first mirror with the substring "Cloud", e.g. the RStudio cloud, is selected.  If no mirrors with that substring are identified, glibrary compares this value to results from getCRANmirrors() to select a mirror in the specified country.
#' @return logical; TRUE if glibrary was a success, an error if a package failed to load
#' @note keep.source was an arguement to require that was deprecated in R 2.15
#' @note This warning \code{Warning in install.packages: InternetOpenUrl failed: 'The operation timed out'} indicates that the randomly selected repository is not available.  Check your internet connection.  If your internet connection is fine, set pickmirror=TRUE and manually select an operational mirror.
#' @examples
#' #glibrary(lattice,MASS) #not run to prevent needless dependency
glibrary <- function(..., lib.loc = NULL, quietly = FALSE, warn.conflicts = TRUE, pickmirror = FALSE, countrycode = "us") {
  warningHandle <- function(w) {
    if (grepl("there is no package called",w$message,fixed=TRUE)) {
      return(FALSE) #not-loadable
    } else {
      return(TRUE) #loadable
    }
  }

  character.only <- TRUE  #this value is locked to TRUE so that the function passes the character value to require and not the variable name thislib
  librarynames <- unlist(lapply(as.list(substitute(.(...)))[-1],as.character))
  #if package already loaded, remove it from librarynames before processing further
  si.res <- sessionInfo()
  cur.loaded <- c(si.res$basePkgs,names(si.res$otherPkgs)) #removed names(si.res$loadedOnly) because those are loaded, but not attached, so glibrary does need to handle them.
  librarynames <- librarynames[librarynames %!in% cur.loaded]
  success <- vector("logical", length(librarynames))
  if (length(success)==0) {return(invisible(TRUE))} #everything already loaded, end.

  alreadyInstalled <- installed.packages()[,"Package"]
  needToInstall <- !librarynames %in% alreadyInstalled

  if (any(needToInstall)) {
    if (pickmirror) {chooseCRANmirror()}
    if (getOption("repos")[["CRAN"]] == "@CRAN@") {
      #Select the first "Cloud" if available
      m <- getCRANmirrors(all = FALSE, local.only = FALSE)
      URL <- m[grepl("Cloud",m$Name),"URL"][1] #get the first repos with "cloud" in the name
      if (is.na(URL)) { #if we did not find the cloud,
        #Fall back and use the previous method
        message("\nIn repsych:glibrary:  Now randomly selecting a CRAN mirror. You may reselect your CRAN mirror with chooseCRANmirror().\n")
        #if there is no repository set pick a random one by country code
        getCRANmirrors.res <- getCRANmirrors()
        foundone <- FALSE  #have we found a CRAN mirror yet?
        #is it a valid country code?
        if (!countrycode %in% getCRANmirrors.res$CountryCode) {
          stop("In repsych::glibrary:  Invalid countrycode argument")
        }
        ticker <- 0
        while (!foundone) {
          ticker <- ticker + 1
          URL <- getCRANmirrors.res$URL[sample(grep(countrycode, getCRANmirrors.res$CountryCode), 1)]
          host.list <- strsplit(URL, "/")
          host.clean <- unlist(lapply(host.list, FUN = function(x) {return(x[3])}))
          #make sure we can actually access the package list
          if (nrow(available.packages(contrib.url(URL)))!=0) {foundone <- TRUE}        
          if (ticker > 5) {stop("In repsych::glibrary:  Unable to access valid repository.  Is the internet connection working?")}
        } #end while
      } #end else
      repos <- getOption("repos")
      repos["CRAN"] <- gsub("/$", "", URL[1L])
      options(repos = repos)
    } #done setting CRAN mirror
    #installing packages
    installResults <- sapply(librarynames[needToInstall],install.packages)
    #checking for successful install
    needToInstall <- !librarynames %in% installed.packages()[,"Package"]
    if (any(needToInstall)) {
      stop(paste("In repsych::glibrary: Could not download and/or install: ",paste(librarynames[needToInstall],collapse=", "),"... glibrary stopped.",sep=""))
    } # done reporting any failure to install
  } #done if any needed to install

  #message("In repsych::glibrary:  Attempting to load requested packages...\n")
  #success <- tryCatch(
  success <- sapply(librarynames,require, lib.loc = lib.loc, quietly = FALSE, warn.conflicts = warn.conflicts, character.only = TRUE)
  #, warning=warningHandle) #end tryCatch
  if(length(success) != length(librarynames)) {stop("A package failed to return a success in glibrary.")}


  if (all(success)) {
    #message("In repsych::glibrary:  Success!")
    return(invisible(TRUE))
  } else {
    stop(paste("\nIn repsych::glibrary, unable to load: ", paste(librarynames[!success]), 
               collapse = " "))
  }
  stop("A problem occured in glibrary") #shouldn't get this far down, all returns should be made.
}
NULL

Answer 12

试试这个怎么样？

#will install the pROC library if you don't have it
if(!is.element('pROC', installed.packages()[,1]))
  {install.packages('pROC')
}else {print("pROC library already installed")}

Answer 13

为什么不直接从脚本中删除该行？如果最终用户没有根据需要安装 xtable 的聪明才智，那么您将遇到更大的问题 :-( 。 也就是说，请查看installed.packages()

编辑：该死，忍者一分钟！

编辑：一般建议：加载包 sos ，您会发现很容易得到很多“是否有执行 XXXXX 的函数”问题的答案。

Answer 14

应该这样做。如果您需要检查多个向量，可以将required.packages 设为向量。

required.packages <- "data.table"
new.packages <- required.packages[!(required.packages %in% installed.packages()[,"Package"])]
if(length(new.packages)) install.packages(new.packages)

Answer 15

阅读了每个人的回复，我在这里和那里得到了一些提示并创建了我的。但实际上与大多数人非常相似。

## These codes are used for installing packages
# function for installing needed packages
installpkg <- function(x){
    if(x %in% rownames(installed.packages())==FALSE) {
        if(x %in% rownames(available.packages())==FALSE) {
            paste(x,"is not a valid package - please check again...")
        } else {
            install.packages(x)           
        }

    } else {
        paste(x,"package already installed...")
    }
}

# install necessary packages
required_packages  <- c("sqldf","car")
lapply(required_packages,installpkg)

Answer 16

查看了我的旧功能，使用上面的提示对其进行了更新，这就是我得到的。

# VERSION 1.0
assign("installP", function(pckgs){
    ins <- function(pckg, mc){
        add <- paste(c(" ", rep("-", mc+1-nchar(pckg)), " "), collapse = "");
        if( !require(pckg,character.only=TRUE) ){
            reps <- c("http://lib.stat.cmu.edu/R/CRAN","http://cran.uk.R-project.org");
            for (r in reps) try(utils::install.packages(pckg, repos=r), silent=TRUE);
            if(!require(pckg,character.only = TRUE)){   cat("Package: ",pckg,add,"not found.\n",sep="");
            }else{                                      cat("Package: ",pckg,add,"installed.\n",sep="");}
        }else{                                          cat("Package: ",pckg,add,"is loaded.\n",sep=""); } }
    invisible(suppressMessages(suppressWarnings(lapply(pckgs,ins, mc=max(nchar(pckgs)))))); cat("\n"); 
}, envir=as.environment("dg_base"))

installP(c("base","a","TFX"))
Package: base ------------------- is loaded.
Package: a ---------------------- not found.
Package: TFX -------------------- installed.