在不安裝包的情況下列出 R 包依賴項

Question

有沒有一種簡單的方法來獲取給定包的 R 包依賴項（所有遞歸依賴項）列表，而無需安裝包及其依賴項？ 類似於 portupgrade 或 apt 中的假安裝。

Answer 1

您可以使用available.packages函數的結果。 例如，要查看ggplot2依賴什么：

pack <- available.packages()
pack["ggplot2","Depends"]

這使 ：

[1] "R (>= 2.14), stats, methods"

請注意，根據您想要實現的目標，您可能還需要檢查Imports字段。

Answer 2

另一個簡潔的解決方案是來自庫packrat的內部函數recursivePackageDependencies 。 但是，該軟件包必須安裝在您機器上的某個庫中。 優點是它也適用於自制的非 CRAN 包。 例子：

packrat:::recursivePackageDependencies("ggplot2",lib.loc = .libPaths()[1])

給予：

 [1] "R6"           "RColorBrewer" "Rcpp"         "colorspace"   "dichromat"    "digest"       "gtable"      
 [8] "labeling"     "lazyeval"     "magrittr"     "munsell"      "plyr"         "reshape2"     "rlang"       
 [15] "scales"       "stringi"      "stringr"      "tibble"       "viridisLite" 

Answer 3

我很驚訝沒有人提到tools::package_dependencies() ，這是最簡單的解決方案，並且具有recursive參數（已接受的解決方案不提供）。

查看 CRAN 上前 200 個包的遞歸依賴關系的簡單示例：

library(tidyverse)
avail_pks <- available.packages()
deps <- tools::package_dependencies(packages = avail_pks[1:200, "Package"],
                                    recursive = TRUE)

tibble(Package=names(deps),
       data=map(deps, as_tibble)) %>% 
  unnest(data)
#> # A tibble: 7,125 x 2
#>    Package value         
#>    <chr>   <chr>         
#>  1 A3      xtable        
#>  2 A3      pbapply       
#>  3 A3      parallel      
#>  4 A3      stats         
#>  5 A3      utils         
#>  6 aaSEA   DT            
#>  7 aaSEA   networkD3     
#>  8 aaSEA   shiny         
#>  9 aaSEA   shinydashboard
#> 10 aaSEA   magrittr      
#> # … with 7,115 more rows

^{由reprex 包(v0.3.0) 於 2020 年 12 月 4 日創建}

Answer 4

我沒有安裝 R，我需要找出哪些 R 包依賴於我公司請求使用的 R 包列表。

我編寫了一個 bash 腳本，它遍歷文件中的 R 包列表，並遞歸地發現依賴項。

該腳本使用名為rinput_orig.txt的文件作為輸入（示例如下）。 該腳本將在其工作時創建一個名為rinput.txt的文件。

該腳本將創建以下文件：

• rdepsfound.txt - 列出找到的依賴項，包括依賴於它的 R 包（下面的示例）。
• routput.txt - 列出所有 R 包（來自原始列表和依賴項列表）以及許可證和 CRAN URL（示例如下）。
• r404.txt - 嘗試 curl 時收到 404 的 R 包列表。 如果您的原始列表有任何拼寫錯誤，這會很方便。

bash腳本：

#!/bin/bash

# CLEANUP
rm routput.txt
rm rdepsfound.txt
rm r404.txt

# COPY ORIGINAL INPUT TO WORKING INPUT
cp rinput_orig.txt rinput.txt

IFS=","
while read PACKAGE; do
    echo Processing $PACKAGE...

    PACKAGEURL="http://cran.r-project.org/web/packages/${PACKAGE}/index.html"

    if [ `curl -o /dev/null --silent --head --write-out '%{http_code}\n' ${PACKAGEURL}` != 404 ]; then
        # GET LICENSE INFO OF PACKAGE
        LICENSEINFO=$(curl ${PACKAGEURL} 2>/dev/null | grep -A1 "License:" | grep -v "License:" | gawk 'match($0, /<a href=".*">(.*)<\/a>/, a) {print a[0]}' | sed "s/|/,/g" | sed "s/+/,/g")
        for x in ${LICENSEINFO[*]}
        do
            # SAVE LICENSE
            LICENSE=$(echo ${x} | gawk 'match($0, /<a href=".*">(.*)<\/a>/, a) {print a[1]}')
            break
        done

        # WRITE PACKAGE AND LICENSE TO OUTPUT FILE
        echo $PACKAGE $LICENSE $PACKAGEURL >> routput.txt

        # GET DEPENDENCIES OF PACKAGE
        DEPS=$(curl ${PACKAGEURL} 2>/dev/null | grep -A1 "Depends:" | grep -v "Depends:" | gawk 'match($0, /<a href=".*">(.*)<\/a>/, a) {print a[0]}')
        for x in ${DEPS[*]}
        do
            FOUNDDEP=$(echo "${x}" | gawk 'match($0, /<a href=".*">(.*)<\/a>/, a) {print a[1]}' | sed "s/<\/span>//g")
            if [ "$FOUNDDEP" != "" ]; then
                echo Found dependency $FOUNDDEP for $PACKAGE...
                grep $FOUNDDEP rinput.txt > /dev/null
                if [ "$?" = "0" ]; then
                    echo $FOUNDDEP already exists in package list...
                else
                    echo Adding $FOUNDDEP to package list...
                    # SAVE FOUND DEPENDENCY BACK TO INPUT LIST
                    echo $FOUNDDEP >> rinput.txt
                    # SAVE FOUND DEPENDENCY TO DEPENDENCY LIST FOR EASY VIEWING OF ALL FOUND DEPENDENCIES
                    echo $FOUNDDEP is a dependency of $PACKAGE >> rdepsfound.txt
                fi
            fi
        done
    else
        echo Skipping $PACKAGE because 404 was received...
        echo $PACKAGE $PACKAGEURL >> r404.txt
    fi

done < rinput.txt
echo -e "\nRESULT:"
sort -u routput.txt

示例 rinput_orig.txt：

shiny
rmarkdown
xtable
RODBC
RJDBC
XLConnect
openxlsx
xlsx
Rcpp

運行腳本時的示例控制台輸出：

Processing shiny...
Processing rmarkdown...
Processing xtable...
Processing RODBC...
Processing RJDBC...
Found dependency DBI for RJDBC...
Adding DBI to package list...
Found dependency rJava for RJDBC...
Adding rJava to package list...
Processing XLConnect...
Found dependency XLConnectJars for XLConnect...
Adding XLConnectJars to package list...
Processing openxlsx...
Processing xlsx...
Found dependency rJava for xlsx...
rJava already exists in package list...
Found dependency xlsxjars for xlsx...
Adding xlsxjars to package list...
Processing Rcpp...
Processing DBI...
Processing rJava...
Processing XLConnectJars...
Processing xlsxjars...
Found dependency rJava for xlsxjars...
rJava already exists in package list...

示例 rdepsfound.txt：

DBI is a dependency of RJDBC
rJava is a dependency of RJDBC
XLConnectJars is a dependency of XLConnect
xlsxjars is a dependency of xlsx

示例 routput.txt：

shiny GPL-3 http://cran.r-project.org/web/packages/shiny/index.html
rmarkdown GPL-3 http://cran.r-project.org/web/packages/rmarkdown/index.html
xtable GPL-2 http://cran.r-project.org/web/packages/xtable/index.html
RODBC GPL-2 http://cran.r-project.org/web/packages/RODBC/index.html
RJDBC GPL-2 http://cran.r-project.org/web/packages/RJDBC/index.html
XLConnect GPL-3 http://cran.r-project.org/web/packages/XLConnect/index.html
openxlsx GPL-3 http://cran.r-project.org/web/packages/openxlsx/index.html
xlsx GPL-3 http://cran.r-project.org/web/packages/xlsx/index.html
Rcpp GPL-2 http://cran.r-project.org/web/packages/Rcpp/index.html
DBI LGPL-2 http://cran.r-project.org/web/packages/DBI/index.html
rJava GPL-2 http://cran.r-project.org/web/packages/rJava/index.html
XLConnectJars GPL-3 http://cran.r-project.org/web/packages/XLConnectJars/index.html
xlsxjars GPL-3 http://cran.r-project.org/web/packages/xlsxjars/index.html

我希望這可以幫助別人！

Answer 5

我針對packrat和tools測試了我自己的解決方案（檢查了本地安裝的包）。
您可以找出方法之間的明顯差異。
tools::package_dependencies看起來為舊 R 版本（直到 4.1.0 和recursive = TRUE ）提供了太多，並且不是有效的解決方案。

R 4.1.0 NEWS
"Function tools::package_dependencies() (in package tools) can now use different dependency types for direct and recursive dependencies."

packrat:::recursivePackageDependencies使用available.packages所以它基於最新的遠程包，而不是本地包。

默認情況下，我的功能是跳過基礎包，如果您也想附加它們，請更改base參數。

在 R 4.1.0 下測試：

get_deps <- function(package, fields = c("Depends", "Imports", "LinkingTo"), base = FALSE) {
  stopifnot((length(package) == 1) && is.character(package))
  stopifnot(all(fields %in% c("Depends", "Imports", "Suggests", "LinkingTo")))
  stopifnot(is.logical(base))
  stopifnot(package %in% rownames(utils::installed.packages(lib.loc = lib.loc)))

  paks_global <- NULL
  
  deps <- function(pak, fileds) {
    pks <- packageDescription(pak)
    res <- NULL
    for (f in fileds) {
      ff <- pks[[f]]
      if (!is.null(ff)) {
        res <- c(
          res,
          vapply(
            strsplit(trimws(strsplit(ff, ",")[[1]]), "[ \n\\(]"),
            function(x) x[1],
            character(1)
          )
        )
      }
    }
    if (is.null(res)) {
      return(NULL)
    }
    for (r in res) {
      if (r != "R" && !r %in% paks_global) {
        paks_global <<- c(r, paks_global)
        deps(r, fields)
      }
    }
  }
  
  deps(package, fields)
  
  setdiff(unique(paks_global), c(
     package,
     "R",
     if (!base) {
       c(
         "stats",
         "graphics",
         "grDevices",
         "utils",
         "datasets",
         "methods",
         "base", 
         "tools"
       )
     } else {
       NULL
     }
   ))
}

own = get_deps("shiny", fields = c("Depends", "Imports"))

packrat = packrat:::recursivePackageDependencies("shiny", lib.loc = .libPaths(), fields = c("Depends", "Imports"))

tools = tools::package_dependencies("shiny", which =  c("Depends", "Imports"), recursive = TRUE)[[1]]

setdiff(own, packrat)
#> character(0)
setdiff(packrat, own)
#> character(0)
setdiff(own, tools)
#> character(0)
setdiff(tools, own)
#> [1] "methods"   "utils"     "grDevices" "tools"     "stats"     "graphics"
setdiff(packrat, tools)
#> character(0)
setdiff(tools, packrat)
#> [1] "methods"   "utils"     "grDevices" "tools"     "stats"     "graphics"

own
#>  [1] "lifecycle"   "ellipsis"    "cachem"      "jquerylib"   "rappdirs"   
#>  [6] "fs"          "sass"        "bslib"       "glue"        "commonmark" 
#> [11] "withr"       "fastmap"     "crayon"      "sourcetools" "base64enc"  
#> [16] "htmltools"   "digest"      "xtable"      "jsonlite"    "mime"       
#> [21] "magrittr"    "rlang"       "later"       "promises"    "R6"         
#> [26] "Rcpp"        "httpuv"
packrat
#>  [1] "R6"          "Rcpp"        "base64enc"   "bslib"       "cachem"     
#>  [6] "commonmark"  "crayon"      "digest"      "ellipsis"    "fastmap"    
#> [11] "fs"          "glue"        "htmltools"   "httpuv"      "jquerylib"  
#> [16] "jsonlite"    "later"       "lifecycle"   "magrittr"    "mime"       
#> [21] "promises"    "rappdirs"    "rlang"       "sass"        "sourcetools"
#> [26] "withr"       "xtable"
tools
#>  [1] "methods"     "utils"       "grDevices"   "httpuv"      "mime"       
#>  [6] "jsonlite"    "xtable"      "digest"      "htmltools"   "R6"         
#> [11] "sourcetools" "later"       "promises"    "tools"       "crayon"     
#> [16] "rlang"       "fastmap"     "withr"       "commonmark"  "glue"       
#> [21] "bslib"       "cachem"      "ellipsis"    "lifecycle"   "sass"       
#> [26] "jquerylib"   "magrittr"    "base64enc"   "Rcpp"        "stats"      
#> [31] "graphics"    "fs"          "rappdirs"

microbenchmark::microbenchmark(get_deps("shiny", fields = c("Depends", "Imports")),
                               packrat:::recursivePackageDependencies("shiny", lib.loc = .libPaths(), fields = c("Depends", "Imports")),
                               tools = tools::package_dependencies("shiny", which =  c("Depends", "Imports"), recursive = TRUE)[[1]],
                               times = 5
)
#> Warning in microbenchmark::microbenchmark(get_deps("shiny", fields =
#> c("Depends", : less accurate nanosecond times to avoid potential integer
#> overflows
#> Unit: milliseconds
#>                                                                                                           expr
#>                                                            get_deps("shiny", fields = c("Depends", "Imports"))
#>  packrat:::recursivePackageDependencies("shiny", lib.loc = .libPaths(),      fields = c("Depends", "Imports"))
#>                                                                                                          tools
#>         min         lq       mean     median         uq        max neval
#>    5.316552   5.607365   6.054568   5.674359   6.633308   7.041258     5
#>   18.767340  19.387588  21.739127  21.581457  23.526169  25.433079     5
#>  411.589734 449.179354 458.526354 465.431262 468.440211 497.991207     5

^{由reprex 包(v0.3.0) 於 2021 年 6 月 25 日創建}

證明舊 R 版本下的tools解決方案是錯誤的。 在 R 3.6.3 下測試。

paks <- tools::package_dependencies("shiny", which =  c("Depends", "Imports"), recursive = TRUE)[[1]]
"lifecycle" %in% paks
#> [1] TRUE
any(c(paks, "shiny") %in% tools::dependsOnPkgs("lifecycle"))
#> [1] FALSE

^{由reprex 包(v0.3.0) 於 2021 年 6 月 25 日創建}

Answer 6

試試這個： tools::package_dependencies(recursive = TRUE)$package_name

例如 - 這是 dplyr 的依賴項：

tools::package_dependencies(recursive = TRUE)$dplyr
 [1] "ellipsis"   "generics"   "glue"       "lifecycle"  "magrittr"   "methods"   
 [7] "R6"         "rlang"      "tibble"     "tidyselect" "utils"      "vctrs"     
[13] "cli"        "crayon"     "fansi"      "pillar"     "pkgconfig"  "purrr"     
[19] "digest"     "assertthat" "grDevices"  "utf8"       "tools"