这是我目前的方法来获取包,它们的依赖关系,并按照正确的顺序来获取它们:
# find the dependencies for the packages I want # from https://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 https://stackoverflow.com/a/10841614/1036500 library(tools) write_PACKAGES(local_CRAN)@H_403_4@现在假设我在另一台电脑上安装了R和RStudio(和Rtools或Xcode),没有互联网连接,我插上USB棒,打开RProj文件来设置工作目录,并运行这个脚本:
############################################################# ## 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" )@H_403_4@这工作相当不错,但仍然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,: there is no package called ‘httr’ 3: In library(package,: there is no package called ‘devtools’ 4: In library(package,: there is no package called ‘ggplot2’ 5: In library(package,: there is no package called ‘tidyr’ 6: In library(package,: there is no package called ‘rmarkdown’@H_403_4@似乎编织者必须在rmarkdown之前进行,在tidyr和ggplot2之前重塑2等.
必须有一个更简单和更完整的解决方案来获取源文件列表的问题,需要按照正确顺序放置所有依赖关系.最简单的方法是什么(不使用任何贡献的包)?
这是我目前正在开发的系统,我正在使用源版本的软件包来试图为离线计算机(OSX / Linux / Windows)做任何事情做准备:
> 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@H_403_4@编辑以下Andrie的有用的评论,我已经与miniCRAN一起去,从小插曲中缺少的是如何从本地的repo实际安装包.这是我试过的:
library("miniCRAN") # Specify list of packages to download pkgs <- c('stringr','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,type = "source" )@H_403_4@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)@H_403_4@我在这里缺少什么?
编辑是的,我没有正确使用file:///,它应该是这样的:
install.packages(pkgs,repos = paste0("file:///",local_CRAN),type = "source")@H_403_4@这让我感到震惊,这一切基本上都是按预期的方式工作的.非常感谢.现在我只是想看看:致命错误:curl / curl.h:没有这样的文件或目录,这是阻止RCurl和httr安装.
更多信息:
> Available on CRAN
>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链接到演示文稿,博客文章等
要从本地的miniCRAN存储库安装,您有两个选项.
>首先,你可以使用URI约定文件:///.例如
install.packages("ggplot2",repos="file:///path/to/file/")@H_403_4@>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,您的本地存储库将看起来和感觉完全一样,就像一个CRAN镜像,除了它只包含你想要的包.