包列表的离线安装：按顺序获取依赖项
Offline installation of a list of packages: getting dependencies in order
我有一堆软件包的源文件及其依赖项，我想将它们安装在无法访问互联网的计算机上。我想使用 USB 记忆棒将所有这些安装在其他计算机上，但是某些软件包安装失败，因为依赖项没有在软件包之前安装。如何在需要它们的包之前按顺序安装依赖项？
这是我当前获取包及其依赖项并按正确顺序获取它们的方法：
# find the dependencies for the packages I want
# from
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
library(tools)
write_PACKAGES(local_CRAN)
现在假设我在另一台计算机上全新安装了 R 和 RStudio（和 Rtools 或 Xcode）并且没有互联网连接，我插入 USB 记忆棒，打开 RProj 文件以设置工作目录，以及 运行 这个脚本：
#############################################################
## 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" )
这工作得相当好，但仍有一些软件包无法安装：
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 必须在 rmarkdown 之前，reshape2 必须在 tidyr 和 ggplot2 之前，等等
必须有一个更简单、更完整的解决方案来解决以非常特定的顺序获取源文件列表的问题，需要将所有依赖项按正确的顺序放置。最简单的方法是什么（不使用任何贡献的包）？
这是我目前正在使用的系统，我正在使用软件包的源版本，试图为离线计算机 (OSX/Linux/Windows) 做任何准备：
> 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
EDIT 在 Andrie 的有用评论之后，我尝试了 miniCRAN，小插图中缺少的一点是如何从本地仓库实际安装软件包。这是我试过的：
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" )
结果是：
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)
我在这里错过了什么？
EDIT 是的，我没有正确使用 file:///，应该是这样的：
install.packages(pkgs,
repos = paste0("file:///", local_CRAN),
type = "source")
这让我很感动，现在基本上都按预期工作了。非常感谢。现在我只需要查看：fatal error: curl/curl.h: No such file or directory，它会阻止 RCurl 和 httr 安装。
软件包 miniCRAN 可以帮助解决这个问题。您告诉 miniCRAN 您想要安装的软件包列表，然后它会计算出依赖关系，下载这些软件包并在您的本地计算机上创建一个行为类似于 CRAN 的存储库，即它尊重 install.packages() 等.
更多信息：
阅读vignette
我们正在积极开发miniCRAN。跟踪进度并在 github miniCRAN repository
请参阅 project wiki 以获取指向演示文稿、博客文章等的链接
要从本地 miniCRAN 存储库安装，您有两个选择。
首先，您可以使用 URI 约定 file:///。例如
install.packages("ggplot2", repos="file:///path/to/file/")
或者，您可以将目标配置为 HTTP 服务器，并通过 URL 使您的存储库可用。在这种情况下，您的本地存储库看起来和感觉起来就像一个 CRAN 镜像，除了它只包含您想要的包。
我有一堆软件包的源文件及其依赖项，我想将它们安装在无法访问互联网的计算机上。我想使用 USB 记忆棒将所有这些安装在其他计算机上，但是某些软件包安装失败，因为依赖项没有在软件包之前安装。如何在需要它们的包之前按顺序安装依赖项？
这是我当前获取包及其依赖项并按正确顺序获取它们的方法：
# find the dependencies for the packages I want
# from
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
library(tools)
write_PACKAGES(local_CRAN)
现在假设我在另一台计算机上全新安装了 R 和 RStudio（和 Rtools 或 Xcode）并且没有互联网连接，我插入 USB 记忆棒，打开 RProj 文件以设置工作目录，以及 运行 这个脚本：
#############################################################
## 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" )
这工作得相当好，但仍有一些软件包无法安装：
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 必须在 rmarkdown 之前，reshape2 必须在 tidyr 和 ggplot2 之前，等等
必须有一个更简单、更完整的解决方案来解决以非常特定的顺序获取源文件列表的问题，需要将所有依赖项按正确的顺序放置。最简单的方法是什么（不使用任何贡献的包）？
这是我目前正在使用的系统，我正在使用软件包的源版本，试图为离线计算机 (OSX/Linux/Windows) 做任何准备：
> 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
EDIT 在 Andrie 的有用评论之后，我尝试了 miniCRAN，小插图中缺少的一点是如何从本地仓库实际安装软件包。这是我试过的：
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" )
结果是：
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)
我在这里错过了什么？
EDIT 是的，我没有正确使用 file:///，应该是这样的：
install.packages(pkgs,
repos = paste0("file:///", local_CRAN),
type = "source")
这让我很感动，现在基本上都按预期工作了。非常感谢。现在我只需要查看：fatal error: curl/curl.h: No such file or directory，它会阻止 RCurl 和 httr 安装。
软件包 miniCRAN 可以帮助解决这个问题。您告诉 miniCRAN 您想要安装的软件包列表，然后它会计算出依赖关系，下载这些软件包并在您的本地计算机上创建一个行为类似于 CRAN 的存储库，即它尊重 install.packages() 等.
更多信息：
阅读vignette
我们正在积极开发
miniCRAN。跟踪进度并在 github miniCRAN repository 找到最新的开发版本
请参阅 project wiki 以获取指向演示文稿、博客文章等的链接
要从本地 miniCRAN 存储库安装，您有两个选择。
首先，您可以使用 URI 约定
file:///。例如install.packages("ggplot2", repos="file:///path/to/file/")或者，您可以将目标配置为 HTTP 服务器，并通过 URL 使您的存储库可用。在这种情况下，您的本地存储库看起来和感觉起来就像一个 CRAN 镜像，除了它只包含您想要的包。