脫機安裝包列表：按順序獲取依賴關系

Question

我有一堆軟件包及其依賴項的源文件，我想安裝在沒有Internet訪問權限的計算機上。 我想使用USB記憶棒在其他計算機上安裝所有這些，但是某些軟件包的安裝失敗，因為在軟件包之前沒有安裝依賴項。 如何在需要它們的軟件包之前按順序安裝依賴項？

這是我當前獲取包及其依賴項的方法，並以正確的順序獲取它們：

# find the dependencies for the packages I want
# from http://stackoverflow.com/a/15650828/1036500
getPackages <- function(packs){
  packages <- unlist(
    tools::package_dependencies(packs, available.packages(),
                                which=c("Depends", "Imports"), recursive=TRUE)
  )
  packages <- union(packages, packs)
  packages
}

# packages I want 
my_packages <- c('stringr', 'devtools', 'ggplot2', 'dplyr', 'tidyr', 'rmarkdown', 'knitr', 'reshape2', 'gdata')

# get names of dependencies and try to get them in the right order, this seems ridiculous... 
my_packages_and_dependencies <- getPackages(my_packages)
dependencies_only <- setdiff(my_packages_and_dependencies, my_packages)
deps_of_deps <- getPackages(dependencies_only)
deps_of_deps_of_deps <- getPackages(deps_of_deps)
my_packages_and_dependencies <- unique(c(deps_of_deps_of_deps, deps_of_deps, dependencies_only, my_packages))

# where to keep the source?
local_CRAN <- paste0(getwd(), "/local_CRAN")

# get them from CRAN, source files
download.packages(pkgs = my_packages_and_dependencies, destdir = local_CRAN, type = "source")
# note that 'tools', 'methods', 'utils, 'stats', etc. art not on CRAN, but are part of base

# from http://stackoverflow.com/a/10841614/1036500
library(tools)
write_PACKAGES(local_CRAN)

現在假設我在另一台安裝了R和RStudio（以及Rtools或Xcode）並且沒有互聯網連接的計算機上，我插入USB記憶棒，打開RProj文件來設置工作目錄，然后運行這個腳本：

#############################################################

## Install from source (Windows/OSX/Linux)

# What do I want to install?
my_packages_and_dependencies <- c("methods", "tools", "bitops", "stats", "colorspace", "graphics", 
                                  "tcltk", "Rcpp", "digest", "jsonlite", "mime", "RCurl", "R6", 
                                  "stringr", "brew", "grid", "RColorBrewer", "dichromat", "munsell", 
                                  "plyr", "labeling", "grDevices", "utils", "httr", "memoise", 
                                  "whisker", "evaluate", "rstudioapi", "roxygen2", "gtable", "scales", 
                                  "proto", "MASS", "assertthat", "magrittr", "lazyeval", "DBI", 
                                  "stringi", "yaml", "htmltools", "caTools", "formatR", "highr", 
                                  "markdown", "gtools", "devtools", "ggplot2", "dplyr", "tidyr", 
                                  "rmarkdown", "knitr", "reshape2", "gdata")

# where are the source files? 
local_CRAN <- paste0(getwd(), "/local_CRAN")

# scan all packages and get files names of wanted source pckgs
# I've got other things in this dir also
wanted_package_source_filenames <- list.files(local_CRAN, pattern = "tar.gz", full.names = TRUE)

# put them in order to make sure deps go first, room for improvement here...
trims <- c(local_CRAN, "/",  "tar.gz")
x1 <- gsub(paste(trims, collapse = "|"), "", wanted_package_source_filenames)
x2 <- sapply( strsplit(x1, "_"), "[[", 1)
idx <- match(my_packages_and_dependencies, x2)
wanted_package_source_filenames <- na.omit(wanted_package_source_filenames[idx])

install.packages(wanted_package_source_filenames, 
                 repos = NULL, 
                 dependencies = TRUE, 
                 contrib.url = local_CRAN, # I thought this would take care of getting dependencies automatically...
                 type  = "source" )

這工作得相當好，但仍然有些軟件包無法安裝：

sapply(my_packages_and_dependencies, require, character.only = TRUE) 

 methods        tools       bitops        stats 
        TRUE         TRUE         TRUE         TRUE 
  colorspace     graphics        tcltk         Rcpp 
        TRUE         TRUE         TRUE         TRUE 
      digest     jsonlite         mime        RCurl 
        TRUE         TRUE         TRUE        FALSE 
          R6      stringr         brew         grid 
        TRUE         TRUE         TRUE         TRUE 
RColorBrewer    dichromat      munsell         plyr 
        TRUE         TRUE         TRUE         TRUE 
    labeling    grDevices        utils         httr 
        TRUE         TRUE         TRUE        FALSE 
     memoise      whisker     evaluate   rstudioapi 
        TRUE         TRUE         TRUE         TRUE 
    roxygen2       gtable       scales        proto 
        TRUE         TRUE         TRUE         TRUE 
        MASS   assertthat     magrittr     lazyeval 
        TRUE         TRUE         TRUE         TRUE 
         DBI      stringi         yaml    htmltools 
        TRUE         TRUE         TRUE         TRUE 
     caTools      formatR        highr     markdown 
        TRUE         TRUE         TRUE         TRUE 
      gtools     devtools      ggplot2        dplyr 
        TRUE        FALSE        FALSE         TRUE 
       tidyr    rmarkdown        knitr     reshape2 
       FALSE        FALSE         TRUE         TRUE 
       gdata 
        TRUE 
Warning messages:
1: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘RCurl’
2: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘httr’
3: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘devtools’
4: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘ggplot2’
5: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘tidyr’
6: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘rmarkdown’

似乎knitr必須在rmarkdown之前，在tidyr和ggplot2等之前重塑2等。

對於以非常特定的順序獲取源文件列表的問題，必須有一個更簡單，更完整的解決方案，需要以正確的順序放置所有依賴項。 最簡單的方法是什么（不使用任何貢獻包）？

這是我目前正在處理的系統，我正在使用軟件包的源版本，試圖為離線計算機（OSX / Linux / Windows）做任何准備：

> sessionInfo()
R version 3.1.2 (2014-10-31)
Platform: x86_64-w64-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=English_United States.1252 
[2] LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

attached base packages:
 [1] tcltk     grid      tools     stats     graphics 
 [6] grDevices utils     datasets  methods   base     

other attached packages:
 [1] gdata_2.13.3       reshape2_1.4.1    
 [3] knitr_1.9          dplyr_0.4.1       
 [5] gtools_3.4.1       markdown_0.7.4    
 [7] highr_0.4          formatR_1.0       
 [9] caTools_1.17.1     htmltools_0.2.6   
[11] yaml_2.1.13        stringi_0.4-1     
[13] DBI_0.3.1          lazyeval_0.1.10   
[15] magrittr_1.5       assertthat_0.1    
[17] proto_0.3-10       scales_0.2.4      
[19] gtable_0.1.2       roxygen2_4.1.0    
[21] rstudioapi_0.2     evaluate_0.5.5    
[23] whisker_0.3-2      memoise_0.2.1     
[25] labeling_0.3       plyr_1.8.1        
[27] munsell_0.4.2      dichromat_2.0-0   
[29] RColorBrewer_1.1-2 brew_1.0-6        
[31] stringr_0.6.2      R6_2.0.1          
[33] mime_0.2           jsonlite_0.9.14   
[35] digest_0.6.8       Rcpp_0.11.4       
[37] colorspace_1.2-5   bitops_1.0-6      
[39] MASS_7.3-35       

loaded via a namespace (and not attached):
[1] parallel_3.1.2

編輯跟隨Andrie的有用評論，我已經開始使用miniCRAN，小插圖中缺少的是如何從本地倉庫實際安裝軟件包。 這就是我嘗試過的：

library("miniCRAN")

# Specify list of packages to download
pkgs <- c('stringr', 'devtools', 'ggplot2', 'dplyr', 'tidyr', 'rmarkdown', 'knitr', 'reshape2', 'gdata')

# Make list of package URLs
revolution <- c(CRAN="http://cran.revolutionanalytics.com")
pkgList <- pkgDep(pkgs, repos=revolution, type="source" )
pkgList

# Set location to store source files 
local_CRAN <- paste0(getwd(), "/local_CRAN")

# Make repo for source
makeRepo(pkgList, path = local_CRAN, repos = revolution, type = "source")

# install...
install.packages(pkgs, 
                 repos = local_CRAN, # do I really need "file:///"?
                 dependencies = TRUE, 
                 contrib.url = local_CRAN,
                 type  = "source" )

結果是：

Installing packages into ‘C:/emacs/R/win-library/3.1’
(as ‘lib’ is unspecified)
Warning in install.packages :
  unable to access index for repository C:/Users/.../local_CRAN/src/contrib
Warning in install.packages :
  packages ‘stringr’, ‘devtools’, ‘ggplot2’, ‘dplyr’, ‘tidyr’, ‘rmarkdown’, ‘knitr’, ‘reshape2’, ‘gdata’ are not available (for R version 3.1.2)

我在這里錯過了什么？

編輯是的，我錯過了正確使用file:/// ，它應該是這樣的：

install.packages(pkgs, 
                 repos = paste0("file:///", local_CRAN),
                 type = "source")

這讓我感覺很快，現在基本上都按預期工作了。 非常感謝。 現在我只是要查看： fatal error: curl/curl.h: No such file or directory ，它阻止了RCurl和httr的安裝。

Answer 1

miniCRAN包可以幫助解決這個問題。 你告訴miniCRAN你想要安裝的軟件包列表，然后計算出依賴關系，下載這些軟件包並在你的本地機器上創建一個類似於CRAN的存儲庫，即它尊重install.packages()等。

更多信息：

• 可在CRAN上使用

• 閱讀小插圖

• 我們正在積極開發miniCRAN 。 跟蹤進度並在github miniCRAN存儲庫中找到最新的開發版本

• 有關演示文稿，博客文章等的鏈接，請參閱項目Wiki

要從本地miniCRAN存儲庫安裝，您有兩個選擇。

1. 首先，您可以使用URI約定file:/// 。 例如

    install.packages("ggplot2", repos="file:///path/to/file/") 

2. 或者，您可以將目標配置為HTTP服務器，並通過URL使您的存儲庫可用。 在這種情況下，您的本地存儲庫外觀和感覺就像一個CRAN鏡像，除了它只包含您想要的包。