有没有一种简单的方法来获取给定包的 R 包依赖项（所有递归依赖项）列表，而无需安装包及其依赖项？类似于 portupgrade 或 apt 中的虚假安装。
问问题
21994 次
6 回答
41
您可以使用available.packages函数的结果。例如，查看ggplot2依赖于什么：
pack <- available.packages()
pack["ggplot2","Depends"]
这使 ：
[1] "R (>= 2.14), stats, methods"
请注意，根据您想要实现的目标，您可能还需要检查该Imports字段。
于 2013-02-01T11:36:32.053 回答
18
另一个简洁而简单的解决方案是recursivePackageDependencies库中的内部函数packrat。但是，该软件包必须安装在您机器上的某个库中。优点是它也适用于自制的非 CRAN 包。例子：
packrat:::recursivePackageDependencies("ggplot2",lib.loc = .libPaths()[1])
给予：
[1] "R6" "RColorBrewer" "Rcpp" "colorspace" "dichromat" "digest" "gtable"
[8] "labeling" "lazyeval" "magrittr" "munsell" "plyr" "reshape2" "rlang"
[15] "scales" "stringi" "stringr" "tibble" "viridisLite"
于 2018-02-06T14:39:36.143 回答
18
我很惊讶没有人提到tools::package_dependencies()，这是最简单的解决方案，并且有一个recursive论点（公认的解决方案不提供）。
查看 CRAN 上前 200 个包的递归依赖关系的简单示例：
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 包于 2020-12-04 创建(v0.3.0)
于 2020-12-04T21:08:51.103 回答
9
我没有安装 R，我需要找出哪些 R 包依赖于我公司请求使用的 R 包列表。
我编写了一个 bash 脚本，它遍历文件中的 R 包列表，并递归地发现依赖项。
该脚本使用名为rinput_orig.txt的文件作为输入（下面的示例）。该脚本将在其工作时创建一个名为rinput.txt的文件。
该脚本将创建以下文件：
- rdepsfound.txt - 列出找到的依赖项，包括依赖它的 R 包（下面的示例）。
- routput.txt - 列出所有 R 包（来自原始列表和依赖项列表）以及许可证和 CRAN URL（示例如下）。
- r404.txt - 尝试 curl 时收到 404 的 R 包列表。如果您的原始列表有任何拼写错误，这很方便。
bash 脚本：
#!/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
运行脚本时的示例控制台输出：
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
我希望这可以帮助别人！
于 2015-09-03T16:55:45.337 回答
3
我测试了我自己的解决方案（检查了本地安装的包packrat）tools。
您可以发现方法之间的明显差异。
tools::package_dependencies看起来对于旧 R 版本（直到 4.1.0 和）提供了太多，recursive = TRUE并且不是有效的解决方案。
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正在使用available.packages，因此它基于最新的远程包，而不是本地包。
默认情况下，我的功能是跳过基本包，base如果您也想附加它们，请更改 arg。
在 R 4.1.0 下测试：
get_deps <- function(package, fields = c("Depends", "Imports", "LinkingTo"), base = FALSE, lib.loc = NULL) {
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）于 2021-06-25 创建
证明tools在旧 R 版本下的解决方案是错误的。在 R 3.6.3 下测试。
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）于 2021-06-25 创建
于 2021-06-25T07:08:24.590 回答
0
试试这个：tools::package_dependencies(recursive = TRUE)$package_name
例如，这里是 dplyr 的依赖项：
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"
于 2020-12-24T17:18:19.417 回答