是否有为给定 R 版本下载包和依赖项的新解决方案
Is there a new solution for downloading package and dependencies for a given R version
我看到了2018年here问的问题。我想知道今天是否有更好的答案。
我们的工作计算机被整个 IT 安全部门所困扰，这个部门的存在似乎是为了让它们变得毫无用处。我们被允许 运行 R 3.6.3（4.x 尚未获得批准）。我们无法从公司防火墙后面连接到 CRAN。在过去，这意味着我们将笔记本电脑带回家安装软件包。但现在我们有了一个下载监视器，即使我们使用自己的 wi-fi 也能阻止 CRAN 下载。
我试图通过在个人计算机上下载软件包 .zip 文件，通过 CD 传输它们，然后使用 repos=NULL 安装来解决这个问题。我使用了这个代码
getPackages <- function(packs){
packages <- unlist(
tools::package_dependencies(packs, available.packages(),
which=c("Depends", "Imports"), recursive=TRUE)
)
packages <- union(packs, packages)
packages
}
获取我想要的包的依赖项并使用 download.packages() 下载它们。我试图安装 tidyquant 结果发现有 113 个依赖项。
当然，这会下载所有 113 个软件包的最新版本，其中有几个与 R 3.6.3 不兼容。
我上面提到的解决方案建议找到一个兼容的版本，然后使用
install_version("<package name>",
version = "<version number>",
repos = "http://cran.us.r-project.org")
但这将涉及手动搜索所有 113 个依赖项...另外，我正在寻找一个通用解决方案，我可以与我办公室中现在遇到此问题的其他 10 个人分享。
我希望自 2018 年以来可能会出现更好的解决方案？
更新：
根据以下答案，我尝试了
tmp <- tempfile()
dir.create(tmp)
checkpoint::checkpoint(snapshot_date = "2020-04-01",
r_version = "3.6.3",
checkpoint_location = tmp,
scan_now = FALSE)
packages <- getPackages(c("tidyquant"))
download.packages(packages, destdir="C:\Users\jerem\Downloads\tidyquant", type="win.binary")
我明白了
Running create_checkpoint in the home directory may result
in checkpointing very many packages. Continue? (Y/n) Y
Creating checkpoint directory C:/Users/jerem/AppData/Local/Temp/Rtmpa2YEjU/file1efc6daf58e3/.checkpoint/2020-04-01/lib/x86_64-w64-mingw32/3.6.3
Using checkpoint directory C:/Users/jerem/AppData/Local/Temp/Rtmpa2YEjU/file1efc6daf58e3/.checkpoint/2020-04-01/lib/x86_64-w64-mingw32/3.6.3
Warning messages:
1: In create_checkpoint(snapshot_date, r_version, checkpoint_location, :
Specified R version not the same as current R version
2: In use_checkpoint(snapshot_date, r_version, checkpoint_location, :
Specified R version not the same as current R version
>
> packages <- getPackages(c("tidyquant"))
>
> download.packages(packages, destdir="C:\Users\jerem\Downloads\tidyquant", type="win.binary")
Warning: unable to access index for repository https://mran.microsoft.com/snapshot/2020-04-01/bin/windows/contrib/4.1:
cannot open URL 'https://mran.microsoft.com/snapshot/2020-04-01/bin/windows/contrib/4.1/PACKAGES'
Warning in download.packages(packages, destdir = "C:\Users\jerem\Downloads\tidyquant", :
no package ‘tidyquant’ at the repositories
Warning in download.packages(packages, destdir = "C:\Users\jerem\Downloads\tidyquant", :
no package ‘lubridate’ at the repositories
Warning in download.packages(packages, destdir = "C:\Users\jerem\Downloads\tidyquant", :
no package ‘PerformanceAnalytics’ at the repositories
所有 113 个依赖项都会出现“无包”警告。
我认为这里的关键是
Warning: unable to access index for repository https://mran.microsoft.com/snapshot/2020-04-01/bin/windows/contrib/4.1:
显然 2020 年 4 月不会有 4.1 存储库。我认为它正在尝试，因为机器是 运行ning 4.1。所以看起来我们非常接近....
如果有帮助
> sessionInfo()
R version 4.1.2 (2021-11-01)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 22000)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C LC_TIME=English_United States.1252
system code page: 65001
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] compiler_4.1.2 tools_4.1.2 checkpoint_1.0.2
我不确定它是否完全满足您的需求，但 checkpoint 包在这里似乎很合适。它允许您从指定日期拍摄的 CRAN 快照下载源包，回到 2014-09-17。 R 4.0.0 是在 2020-04-24 左右发布的，因此来自 2020-04-01 的快照应该适合您的目的。
这是一个可重现的例子：
tmp1 <- tempfile()
dir.create(tmp1)
cwd <- setwd(tmp1)
getOption("repos")
## CRAN
## "https://cloud.r-project.org/"
available.packages()[c("lattice", "Matrix", "nlme"), c("Version", "Repository")]
## Version Repository
## lattice "0.20-45" "https://cloud.r-project.org/src/contrib"
## Matrix "1.4-0" "https://cloud.r-project.org/src/contrib"
## nlme "3.1-155" "https://cloud.r-project.org/src/contrib"
download.packages("Matrix", ".", type = "source")
## trying URL 'https://cloud.r-project.org/src/contrib/Matrix_1.4-0.tar.gz'
## Content type 'application/x-gzip' length 2849865 bytes (2.7 MB)
## ==================================================
## downloaded 2.7 MB
##
## [,1] [,2]
## [1,] "Matrix" "./Matrix_1.4-0.tar.gz"
tmp2 <- tempfile()
dir.create(tmp2)
checkpoint::checkpoint(snapshot_date = "2020-04-01",
r_version = "3.6.3",
checkpoint_location = tmp2,
scan_now = FALSE)
## Creating checkpoint directory /var/folders/n7/v9s56rmd5hn17d3f1qj13l7m0000gn/T//RtmpbrT5Br/filee2045e35c290/.checkpoint/2020-04-01/lib/aarch64-apple-darwin20/3.6.3
## Using checkpoint directory /private/var/folders/n7/v9s56rmd5hn17d3f1qj13l7m0000gn/T/RtmpbrT5Br/filee2045e35c290/.checkpoint/2020-04-01/lib/aarch64-apple-darwin20/3.6.3
## Warning messages:
## 1: In create_checkpoint(snapshot_date, r_version, checkpoint_location, :
## Specified R version not the same as current R version
## 2: In use_checkpoint(snapshot_date, r_version, checkpoint_location, :
## Specified R version not the same as current R version
getOption("repos")
## CRAN
## "https://mran.microsoft.com/snapshot/2020-04-01"
available.packages()[c("lattice", "Matrix", "nlme"), c("Version", "Repository")]
## Version Repository
## lattice "0.20-40" "https://mran.microsoft.com/snapshot/2020-04-01/src/contrib"
## Matrix "1.2-18" "https://mran.microsoft.com/snapshot/2020-04-01/src/contrib"
## nlme "3.1-145" "https://mran.microsoft.com/snapshot/2020-04-01/src/contrib"
download.packages("Matrix", ".", type = "source")
## trying URL 'https://mran.microsoft.com/snapshot/2020-04-01/src/contrib/Matrix_1.2-18.tar.gz'
## Content type 'application/octet-stream' length 1871705 bytes (1.8 MB)
## ==================================================
## downloaded 1.8 MB
##
## [,1] [,2]
## [1,] "Matrix" "./Matrix_1.2-18.tar.gz"
setwd(cwd)
unlink(c(tmp1, tmp2), recursive = TRUE)
如果您实际上不是 运行 R 3.6.3，则会出现有关版本不匹配的警告。如果你只是下载源码包，可以忽略它们，实际上是为了在另一台机器上安装它们 运行 3.6.3.
您可以查看软件包 README 和 ?checkpoint 了解更多详情。
更新
如果您尝试下载 binary 包（.zip for Windows，.tgz for macOS）而不是 source 包 (.tar.gz)，那么 checkpoint 会给你带来麻烦。默认情况下，download.packages 和朋友使用 contrib.url(repos, type) 构造一个 URL 来搜索软件包二进制文件。
contrib.url("https://mran.microsoft.com/snapshot/2020-04-01/src/contrib", "win.binary")
## [1] "https://mran.microsoft.com/snapshot/2020-04-01/bin/windows/contrib/4.1"
contrib.url("https://mran.microsoft.com/snapshot/2020-04-01/src/contrib", "mac.binary")
## [1] "https://mran.microsoft.com/snapshot/2020-04-01/bin/macosx/contrib/4.1"
但是 URL 两处都没有。那是（部分）因为 contrib.url 附加了您当前 运行 的 R 版本，这在您的快照日期可能不存在。因此：
download.packages("Matrix", ".", type = "win.binary")
## Warning: unable to access index for repository https://mran.microsoft.com/snapshot/2020-04-01/bin/windows/contrib/4.1:
## cannot open URL 'https://mran.microsoft.com/snapshot/2020-04-01/bin/windows/contrib/4.1/PACKAGES'
## Warning in download.packages("Matrix", ".", type = "win.binary") :
## no package 'Matrix' at the repositories
## [,1] [,2]
download.packages("Matrix", ".", type = "mac.binary")
## Warning: unable to access index for repository https://mran.microsoft.com/snapshot/2020-04-01/bin/macosx/contrib/4.1:
## cannot open URL 'https://mran.microsoft.com/snapshot/2020-04-01/bin/macosx/contrib/4.1/PACKAGES'
## Warning in download.packages("Matrix", ".", type = "mac.binary") :
## no package 'Matrix' at the repositories
## [,1] [,2]
您实际需要的URL是：
## Windows
"https://cran.microsoft.com/snapshot/2020-04-01/bin/windows/contrib/3.6"
## macOS, OS X, whatever
"https://cran.microsoft.com/snapshot/2020-04-01/bin/macosx/el-capitan/contrib/3.6"
在这种情况下，最好的方法可能是完全避免 checkpoint，直接将有效的 URL 传递给 available.packages 和 download.packages:
pkg <- "tidyquant"
contriburl <- "https://cran.microsoft.com/snapshot/2020-04-01/bin/windows/contrib/3.6"
db <- available.packages(contriburl)
deps <- tools::package_dependencies(pkg, db, recursive = TRUE)[[pkg]]
download.packages(c(pkg, deps), ".", contriburl = contriburl, type = "win.binary")
我看到了2018年here问的问题。我想知道今天是否有更好的答案。
我们的工作计算机被整个 IT 安全部门所困扰，这个部门的存在似乎是为了让它们变得毫无用处。我们被允许 运行 R 3.6.3（4.x 尚未获得批准）。我们无法从公司防火墙后面连接到 CRAN。在过去，这意味着我们将笔记本电脑带回家安装软件包。但现在我们有了一个下载监视器，即使我们使用自己的 wi-fi 也能阻止 CRAN 下载。
我试图通过在个人计算机上下载软件包 .zip 文件，通过 CD 传输它们，然后使用 repos=NULL 安装来解决这个问题。我使用了这个代码
getPackages <- function(packs){
packages <- unlist(
tools::package_dependencies(packs, available.packages(),
which=c("Depends", "Imports"), recursive=TRUE)
)
packages <- union(packs, packages)
packages
}
获取我想要的包的依赖项并使用 download.packages() 下载它们。我试图安装 tidyquant 结果发现有 113 个依赖项。
当然，这会下载所有 113 个软件包的最新版本，其中有几个与 R 3.6.3 不兼容。
我上面提到的解决方案建议找到一个兼容的版本，然后使用
install_version("<package name>",
version = "<version number>",
repos = "http://cran.us.r-project.org")
但这将涉及手动搜索所有 113 个依赖项...另外，我正在寻找一个通用解决方案，我可以与我办公室中现在遇到此问题的其他 10 个人分享。
我希望自 2018 年以来可能会出现更好的解决方案？
更新： 根据以下答案，我尝试了
tmp <- tempfile()
dir.create(tmp)
checkpoint::checkpoint(snapshot_date = "2020-04-01",
r_version = "3.6.3",
checkpoint_location = tmp,
scan_now = FALSE)
packages <- getPackages(c("tidyquant"))
download.packages(packages, destdir="C:\Users\jerem\Downloads\tidyquant", type="win.binary")
我明白了
Running create_checkpoint in the home directory may result
in checkpointing very many packages. Continue? (Y/n) Y
Creating checkpoint directory C:/Users/jerem/AppData/Local/Temp/Rtmpa2YEjU/file1efc6daf58e3/.checkpoint/2020-04-01/lib/x86_64-w64-mingw32/3.6.3
Using checkpoint directory C:/Users/jerem/AppData/Local/Temp/Rtmpa2YEjU/file1efc6daf58e3/.checkpoint/2020-04-01/lib/x86_64-w64-mingw32/3.6.3
Warning messages:
1: In create_checkpoint(snapshot_date, r_version, checkpoint_location, :
Specified R version not the same as current R version
2: In use_checkpoint(snapshot_date, r_version, checkpoint_location, :
Specified R version not the same as current R version
>
> packages <- getPackages(c("tidyquant"))
>
> download.packages(packages, destdir="C:\Users\jerem\Downloads\tidyquant", type="win.binary")
Warning: unable to access index for repository https://mran.microsoft.com/snapshot/2020-04-01/bin/windows/contrib/4.1:
cannot open URL 'https://mran.microsoft.com/snapshot/2020-04-01/bin/windows/contrib/4.1/PACKAGES'
Warning in download.packages(packages, destdir = "C:\Users\jerem\Downloads\tidyquant", :
no package ‘tidyquant’ at the repositories
Warning in download.packages(packages, destdir = "C:\Users\jerem\Downloads\tidyquant", :
no package ‘lubridate’ at the repositories
Warning in download.packages(packages, destdir = "C:\Users\jerem\Downloads\tidyquant", :
no package ‘PerformanceAnalytics’ at the repositories
所有 113 个依赖项都会出现“无包”警告。
我认为这里的关键是
Warning: unable to access index for repository https://mran.microsoft.com/snapshot/2020-04-01/bin/windows/contrib/4.1:
显然 2020 年 4 月不会有 4.1 存储库。我认为它正在尝试，因为机器是 运行ning 4.1。所以看起来我们非常接近....
如果有帮助
> sessionInfo()
R version 4.1.2 (2021-11-01)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 22000)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C LC_TIME=English_United States.1252
system code page: 65001
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] compiler_4.1.2 tools_4.1.2 checkpoint_1.0.2
我不确定它是否完全满足您的需求，但 checkpoint 包在这里似乎很合适。它允许您从指定日期拍摄的 CRAN 快照下载源包，回到 2014-09-17。 R 4.0.0 是在 2020-04-24 左右发布的，因此来自 2020-04-01 的快照应该适合您的目的。
这是一个可重现的例子：
tmp1 <- tempfile()
dir.create(tmp1)
cwd <- setwd(tmp1)
getOption("repos")
## CRAN
## "https://cloud.r-project.org/"
available.packages()[c("lattice", "Matrix", "nlme"), c("Version", "Repository")]
## Version Repository
## lattice "0.20-45" "https://cloud.r-project.org/src/contrib"
## Matrix "1.4-0" "https://cloud.r-project.org/src/contrib"
## nlme "3.1-155" "https://cloud.r-project.org/src/contrib"
download.packages("Matrix", ".", type = "source")
## trying URL 'https://cloud.r-project.org/src/contrib/Matrix_1.4-0.tar.gz'
## Content type 'application/x-gzip' length 2849865 bytes (2.7 MB)
## ==================================================
## downloaded 2.7 MB
##
## [,1] [,2]
## [1,] "Matrix" "./Matrix_1.4-0.tar.gz"
tmp2 <- tempfile()
dir.create(tmp2)
checkpoint::checkpoint(snapshot_date = "2020-04-01",
r_version = "3.6.3",
checkpoint_location = tmp2,
scan_now = FALSE)
## Creating checkpoint directory /var/folders/n7/v9s56rmd5hn17d3f1qj13l7m0000gn/T//RtmpbrT5Br/filee2045e35c290/.checkpoint/2020-04-01/lib/aarch64-apple-darwin20/3.6.3
## Using checkpoint directory /private/var/folders/n7/v9s56rmd5hn17d3f1qj13l7m0000gn/T/RtmpbrT5Br/filee2045e35c290/.checkpoint/2020-04-01/lib/aarch64-apple-darwin20/3.6.3
## Warning messages:
## 1: In create_checkpoint(snapshot_date, r_version, checkpoint_location, :
## Specified R version not the same as current R version
## 2: In use_checkpoint(snapshot_date, r_version, checkpoint_location, :
## Specified R version not the same as current R version
getOption("repos")
## CRAN
## "https://mran.microsoft.com/snapshot/2020-04-01"
available.packages()[c("lattice", "Matrix", "nlme"), c("Version", "Repository")]
## Version Repository
## lattice "0.20-40" "https://mran.microsoft.com/snapshot/2020-04-01/src/contrib"
## Matrix "1.2-18" "https://mran.microsoft.com/snapshot/2020-04-01/src/contrib"
## nlme "3.1-145" "https://mran.microsoft.com/snapshot/2020-04-01/src/contrib"
download.packages("Matrix", ".", type = "source")
## trying URL 'https://mran.microsoft.com/snapshot/2020-04-01/src/contrib/Matrix_1.2-18.tar.gz'
## Content type 'application/octet-stream' length 1871705 bytes (1.8 MB)
## ==================================================
## downloaded 1.8 MB
##
## [,1] [,2]
## [1,] "Matrix" "./Matrix_1.2-18.tar.gz"
setwd(cwd)
unlink(c(tmp1, tmp2), recursive = TRUE)
如果您实际上不是 运行 R 3.6.3，则会出现有关版本不匹配的警告。如果你只是下载源码包，可以忽略它们，实际上是为了在另一台机器上安装它们 运行 3.6.3.
您可以查看软件包 README 和 ?checkpoint 了解更多详情。
更新
如果您尝试下载 binary 包（.zip for Windows，.tgz for macOS）而不是 source 包 (.tar.gz)，那么 checkpoint 会给你带来麻烦。默认情况下，download.packages 和朋友使用 contrib.url(repos, type) 构造一个 URL 来搜索软件包二进制文件。
contrib.url("https://mran.microsoft.com/snapshot/2020-04-01/src/contrib", "win.binary")
## [1] "https://mran.microsoft.com/snapshot/2020-04-01/bin/windows/contrib/4.1"
contrib.url("https://mran.microsoft.com/snapshot/2020-04-01/src/contrib", "mac.binary")
## [1] "https://mran.microsoft.com/snapshot/2020-04-01/bin/macosx/contrib/4.1"
但是 URL 两处都没有。那是（部分）因为 contrib.url 附加了您当前 运行 的 R 版本，这在您的快照日期可能不存在。因此：
download.packages("Matrix", ".", type = "win.binary")
## Warning: unable to access index for repository https://mran.microsoft.com/snapshot/2020-04-01/bin/windows/contrib/4.1:
## cannot open URL 'https://mran.microsoft.com/snapshot/2020-04-01/bin/windows/contrib/4.1/PACKAGES'
## Warning in download.packages("Matrix", ".", type = "win.binary") :
## no package 'Matrix' at the repositories
## [,1] [,2]
download.packages("Matrix", ".", type = "mac.binary")
## Warning: unable to access index for repository https://mran.microsoft.com/snapshot/2020-04-01/bin/macosx/contrib/4.1:
## cannot open URL 'https://mran.microsoft.com/snapshot/2020-04-01/bin/macosx/contrib/4.1/PACKAGES'
## Warning in download.packages("Matrix", ".", type = "mac.binary") :
## no package 'Matrix' at the repositories
## [,1] [,2]
您实际需要的URL是：
## Windows
"https://cran.microsoft.com/snapshot/2020-04-01/bin/windows/contrib/3.6"
## macOS, OS X, whatever
"https://cran.microsoft.com/snapshot/2020-04-01/bin/macosx/el-capitan/contrib/3.6"
在这种情况下，最好的方法可能是完全避免 checkpoint，直接将有效的 URL 传递给 available.packages 和 download.packages:
pkg <- "tidyquant"
contriburl <- "https://cran.microsoft.com/snapshot/2020-04-01/bin/windows/contrib/3.6"
db <- available.packages(contriburl)
deps <- tools::package_dependencies(pkg, db, recursive = TRUE)[[pkg]]
download.packages(c(pkg, deps), ".", contriburl = contriburl, type = "win.binary")