Packrat的use.cache功能如何工作？

Packrat具有use.cache减少包安装时间的功能.

该文档提供以下信息:

use.cache: Install packages into a global cache, which is then shared across projects? The directory to use is read through Sys.getenv("R_PACKRAT_CACHE_DIR"). Not yet implemented for Windows. (logical; defaults to FALSE)

但是,运行install.package()并不会从用户库中获取已安装的软件包.

use.cache工作怎么样？

使用以下命令使用packrat设置缓存:

#Optional to set location of cache:
#Sys.setenv(R_PACKRAT_CACHE_DIR = "/home/willbowditch/R/packratcache")

packrat::set_opts(use.cache=TRUE)

这是写入的packrat.opts,它决定在Rstudio中打开项目时是否使用缓存.

auto.snapshot: TRUE
use.cache: TRUE
print.banner.on.startup: auto
vcs.ignore.lib: TRUE
vcs.ignore.src: FALSE
external.packages:
local.repos:
load.external.packages.on.startup: TRUE
ignored.packages:
quiet.package.installation: TRUE
snapshot.recommended.packages: FALSE
snapshot.fields:
    Imports
    Depends
    LinkingTo

基本库和已安装的库都存储在缓存和符号链接中:

./packrat/lib/x86_64-pc-linux-gnu/3.4.0:
total 2
drwxr-xr-x 2 willbowditch staff  4 Jun 14 16:21 .
drwxr-xr-x 3 willbowditch staff  3 Jun 14 16:20 ..
lrwxrwxrwx 1 willbowditch staff 99 Jun 14 16:21 CheckDigit -> /home/willbowditch/R/packratcache/v2/library/CheckDigit/0ab3083cafb11382646fdda41ddb8b98/CheckDigit
lrwxrwxrwx 1 willbowditch staff 93 Jun 14 16:21 packrat -> /home/willbowditch/R/packratcache/v2/library/packrat/6ad605ba7b4b476d84be6632393f5765/packrat

./packrat/lib-ext:
total 9
drwxr-xr-x 2 willbowditch staff 2 Jun 14 16:20 .
drwxr-xr-x 6 willbowditch staff 9 Jun 14 16:20 ..

./packrat/lib-R:
total 24
drwxr-xr-x 2 willbowditch staff 16 Jun 14 16:20 .
drwxr-xr-x 6 willbowditch staff  9 Jun 14 16:20 ..
lrwxrwxrwx 1 willbowditch staff 29 Jun 14 16:20 base -> /usr/local/lib/R/library/base
lrwxrwxrwx 1 willbowditch staff 33 Jun 14 16:20 compiler -> /usr/local/lib/R/library/compiler
lrwxrwxrwx 1 willbowditch staff 33 Jun 14 16:20 datasets -> /usr/local/lib/R/library/datasets
lrwxrwxrwx 1 willbowditch staff 33 Jun 14 16:20 graphics -> /usr/local/lib/R/library/graphics
lrwxrwxrwx 1 willbowditch staff 34 Jun 14 16:20 grDevices -> /usr/local/lib/R/library/grDevices
lrwxrwxrwx 1 willbowditch staff 29 Jun 14 16:20 grid -> /usr/local/lib/R/library/grid
lrwxrwxrwx 1 willbowditch staff 32 Jun 14 16:20 methods -> /usr/local/lib/R/library/methods
lrwxrwxrwx 1 willbowditch staff 33 Jun 14 16:20 parallel -> /usr/local/lib/R/library/parallel
lrwxrwxrwx 1 willbowditch staff 32 Jun 14 16:20 splines -> /usr/local/lib/R/library/splines
lrwxrwxrwx 1 willbowditch staff 30 Jun 14 16:20 stats -> /usr/local/lib/R/library/stats
lrwxrwxrwx 1 willbowditch staff 31 Jun 14 16:20 stats4 -> /usr/local/lib/R/library/stats4
lrwxrwxrwx 1 willbowditch staff 30 Jun 14 16:20 tcltk -> /usr/local/lib/R/library/tcltk
lrwxrwxrwx 1 willbowditch staff 30 Jun 14 16:20 tools -> /usr/local/lib/R/library/tools
lrwxrwxrwx 1 willbowditch staff 30 Jun 14 16:20 utils -> /usr/local/lib/R/library/utils

如果您尝试安装软件包,它会覆盖符号链接,而不是从缓存中获取软件包,因此不能用于加速软件包的安装.

>install.packages('CheckDigit')
Installing package into ‘/home/willbowditch/packrattest/packrat/lib/x86_64-pc-linux-gnu/3.4.0’
(as ‘lib’ is unspecified)
trying URL 'https://mran.microsoft.com/snapshot/2017-06-07/src/contrib/CheckDigit_0.1-1.tar.gz'
Content type 'application/octet-stream' length 3777 bytes
==================================================
downloaded 3777 bytes

* installing *source* package ‘CheckDigit’ ...
** package ‘CheckDigit’ successfully unpacked and MD5 sums checked
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (CheckDigit)

The downloaded source packages are in
    ‘/tmp/RtmpxAU8pv/downloaded_packages’

但它确实加速了你正在处理的packrat项目的启动,如果包是require或library在当前目录中调用.在这种情况下,packrat::init()或者packrat::restore() 从缓存中恢复包,但前提是包已经在启用缓存的Packrat项目中使用过.

> packrat::init()
Initializing packrat project in directory:
- "~/six"
Fetching sources for BH (1.62.0-1) ... OK (CRAN current)
Fetching sources for DBI (0.6-1) ... OK (CRAN current)
Fetching sources for R6 (2.2.0) ... OK (CRAN current)
Fetching sources for Rcpp (0.12.10) ... OK (CRAN current)
Fetching sources for assertthat (0.2.0) ... OK (CRAN current)
Fetching sources for dplyr (0.5.0) ... OK (CRAN current)
Fetching sources for lazyeval (0.2.0) ... OK (CRAN current)
Fetching sources for magrittr (1.5) ... OK (CRAN current)
Fetching sources for packrat (0.4.8-1) ... OK (CRAN current)
Fetching sources for stringi (1.1.5) ... OK (CRAN current)
Fetching sources for tibble (1.3.0) ... OK (CRAN current)
Fetching sources for tidyr (0.6.2) ... OK (CRAN current)
Fetching sources for whisker (0.3-2) ... OK (CRAN current)
Snapshot written to '/home/willbowditch/six/packrat/packrat.lock'
Installing BH (1.62.0-1) ... 
    OK (symlinked cache)
Installing DBI (0.6-1) ... 
    OK (symlinked cache)
Installing R6 (2.2.0) ... 
    OK (symlinked cache)
Installing Rcpp (0.12.10) ... 
    OK (symlinked cache)
Installing assertthat (0.2.0) ... 
    OK (symlinked cache)
Installing lazyeval (0.2.0) ... 
    OK (symlinked cache)
Installing magrittr (1.5) ... 
    OK (symlinked cache)
Installing packrat (0.4.8-1) ... 
    OK (symlinked cache)
Installing stringi (1.1.5) ... 
    OK (symlinked cache)
Installing whisker (0.3-2) ... 
    OK (symlinked cache)
Installing tibble (1.3.0) ... 
    OK (symlinked cache)
Installing dplyr (0.5.0) ... 
    OK (symlinked cache)
Installing tidyr (0.6.2) ... 
    OK (symlinked cache)
Initialization complete!

换句话说,包似乎不是从全局库转到缓存,但它们可以从其他packrat库转到缓存.

据我所知,你不能使用尚未安装在packrat中的软件包来缩短加载时间和缓存选项.tidyverse从源代码安装大型软件包(例如,在Linux系统上)时,这可能是一个问题.

有几种解决方法:

解决方法1:对您的库进行符号链接

一个简单的解决方法是将用户包库符号链接到空的packrat目录.通过此方法安装时间只需几秒钟,只要packrat::clean()在开发结束时运行,它似乎不会干扰创建快照的过程.

脚步

新项目>使用packrat

source('https://raw.githubusercontent.com/willbowditch/ratpack/master/R/ratpack.R')
symlink_packages()
#Develop as normal then run 
packrat::clean()
packrat::snapshot(ignore.stale=TRUE) 

解决方法2:external.packages

Packrat确实为packrat::set_opts(external.packages=c('pkgname'))命令提供了大型软件包的解决方法,但是以这种方式安装的软件包不包含在packrat/src文件夹中.

实际上,该选项将包目录符号链接到packrat/lib-extdiretory.

我采用与symlinking选项相同的方式自动执行此操作 - 获取其主目录中的所有用户包并将它们添加到external.packages选项中.

脚步

新项目>使用packrat

source('https://raw.githubusercontent.com/willbowditch/ratpack/master/R/ratpack.R')
   import_user_packages()
   #All installed packages will now be accessable within the packrat session

在开发结束时重置

   packrat::set_opts(external.packages=NULL)
   packrat::snapshot()
   packrat::restore() #This step will install the packages if they're not in the cache

最简单的选择

在这些选项之间的某处可能是最有意义的 - 用户将他们的大型但常用的包列表进行符号链接(即packrat::set_opts(external.packages=c('tidyverse', 'data.table'))),然后在项目的基础上逐项安装较小的包.