R包开发

http://blog.fens.me/r-package-faster/

前言

在 开发自己的R包sayHello 一文中，我们看到了如何从底层，按照R语言的标准构建一个R语言的扩展包。但实施过程确实复杂，会让很多的统计学工作者望而却步。如果能有一种比较简单方式，简化开发过程，那该多好啊！

我们是幸运的，Hadley Wickham(ggplot2,plyr的作者)已经帮我们梳理出了一套开发流程。站在巨人的肩膀上，看得更高，走得更远。

目录

1. 开发流程介绍
2. 编写功能代码
3. 调试程序
4. 单元测试
5. 撰写文档
6. 程序打包
7. 程序发布

1. 开发流程介绍

站在巨人的肩膀，开发R包我们有3个武器：devtools, roxygen2, testthat

• devtools：让开发变得简单，各种开发小工具的合集，非常实用。
• roxygen2：通过注释的方式，生成文档，远离Latex的烦恼。
• testthat：单元测试，让R包稳定、健壮，减少升级的痛苦。

标准化的开发流程：

1. 编写功能代码
2. 调试程序
3. 单元测试
4. 撰写文档
5. 程序打包

2. 编写功能代码

1). 安装程序包：devtools, roxygen2, testthat

#依赖库~ sudo apt-get install libcurl4-openssl-dev#请使用root权限启动R~ sudo R> install.packages("devtools")> install.packages("roxygen2")> install.packages("testthat")> library(devtools)> library(roxygen2)> library(testthat)#查看> search() [1] ".GlobalEnv"        "package:testthat"  "package:roxygen2" [4] "package:digest"    "package:stats"     "package:graphics" [7] "package:grDevices" "package:utils"     "package:datasets"[10] "package:methods"   "Autoloads"         "package:base"

构建工程chinaWeather
创建骨架,代替package.skeleton()

> setwd("/home/conan/R")> create("/home/conan/R/chinaWeather")Creating package chinaWeather in /home/conan/RNo DESCRIPTION found. Creating default:Package: chinaWeatherTitle:Description:Version: 0.1Authors@R: # getOptions('devtools.desc.author')Depends: R (>= 3.0.1)License: # getOptions('devtools.desc.license')LazyData: true> setwd("/home/conan/R/chinaWeather")> dir()[1] "DESCRIPTION" "man"         "R"

编辑DESCRIPTION文件

~ vi /home/conan/R/chinaWeather/DESCRIPTIONPackage: chinaWeatherType: PackageTitle: a visualized package for china WeatherDescription: a visualized package for china WeatherAuthor: Dan ZhangMaintainer: Dan ZhangVersion: 0.1Depends: R (>= 3.0.1)License: GPL-2LazyData: trueDate: 2013-08-05

增加函数文件chinaWeather.R

~ vi /home/conan/R/chinaWeather/R/chinaWeather.R#define a filename from current datefilename<-function(date=Sys.time()){  paste(format(date, "%Y%m%d"),".csv",sep="")}

3. 调试程序

加载程序包到R中

> load_all("/home/conan/R/chinaWeather")Loading chinaWeather> filenamefunction(date=Sys.time()){  paste(format(date, "%Y%m%d"),".csv",sep="")}> filename()[1] "20130805.csv"> day<-as.Date("20110701",format="%Y%m%d")> filename(day)[1] "20110701.csv"

4. 单元测试

编写单元测试代码

~ mkdir /home/conan/R/chinaWeather/inst/tests~ vi /home/conan/R/chinaWeather/inst/tests/test.chinaWeather.Rlibrary(testthat)context("filename: current of date")test_that("filename is current of date", {  daystr<-paste(format(Sys.Date(), "%Y%m%d"),".csv",sep="")  expect_that(filename(), equals(daystr))  day<-as.Date("20110701",format="%Y%m%d")  expect_that(filename(day), equals("20110701.csv"))})

运行单元测试

#单个文件的单元测试> source("/home/conan/R/chinaWeather/inst/tests/test.chinaWeather.R")> test_file("/home/conan/R/chinaWeather/inst/tests/test.chinaWeather.R")filename: current of date : ..#对目录下所有文件的单元测试> test_dir("/home/conan/R/chinaWeather/inst/tests/",reporter = "summary")filename: current of date : ..#自动单元测试> src<-"/home/conan/R/chinaWeather/R/"> test<-"/home/conan/R/chinaWeather/inst/tests/"> auto_test(src,test)filename: current of date : ..#对package执行测试> test("/home/conan/R/chinaWeather")Testing chinaWeatherLoading chinaWeatherfilename: current of date : ..

完成单元测试！下面开始撰写文档。

5. 撰写文档

这里撰写文档，使用源代码注释的方式，然后生成latex，再生成doc。比起原始的直接写latex要容易的多。

打开源代码文件：chinaWeather.R

~ vi /home/conan/R/chinaWeather/R/chinaWeather.R#' Define a filename from current date.#'#' @param date input a date type#' @return character a file name#' @keywords filename #' @export#' @examples#' filename()#' filename(as.Date("20110701",format="%Y%m%d"))filename<-function(date=Sys.time()){  paste(format(date, "%Y%m%d"),".csv",sep="")}

生成latex文档

> library(roxygen2)Loading required package: digest> roxygenize("/home/conan/R/chinaWeather")Updating collate directive in  /home/conan/R/chinaWeather/DESCRIPTIONUpdating namespace directivesWriting chinaWeather.RdWriting filename.Rd

查看生成的latex文件

~ cat /home/conan/R/chinaWeather/man/filename.Rd\name{filename}\alias{filename}\title{Define a filename from current date.}\usage{  filename(date = Sys.time())}\arguments{  \item{date}{input a date type}}\value{  character a file name}\description{  Define a filename from current date.}\examples{filename()filename(as.Date("20110701",format="\%Y\%m\%d"))}\keyword{filename}

6. 程序打包

详细的打包解释，请参考：开发自己的R包sayHello

对上面程序过程，更简化操作可以用如下3条命令

> load_all("/home/conan/R/chinaWeather")> test("/home/conan/R/chinaWeather")> document("/home/conan/R/chinaWeather")

程序检查

> check("/home/conan/R/chinaWeather")Updating chinaWeather documentationLoading chinaWeather'/usr/lib/R/bin/R' --vanilla CMD build '/home/conan/R/chinaWeather'  \  --no-manual --no-resave-data* checking for file '/home/conan/R/chinaWeather/DESCRIPTION' ... OK* preparing 'chinaWeather':* checking DESCRIPTION meta-information ... OK* checking for LF line-endings in source and make files* checking for empty or unneeded directories* building 'chinaWeather_0.1.tar.gz''/usr/lib/R/bin/R' --vanilla CMD check  \  '/tmp/RtmpM5NdJp/chinaWeather_0.1.tar.gz' --timings* using log directory '/tmp/RtmpM5NdJp/chinaWeather.Rcheck'* using R version 3.0.1 (2013-05-16)* using platform: x86_64-pc-linux-gnu (64-bit)* using session charset: ASCII* checking for file 'chinaWeather/DESCRIPTION' ... OK* checking extension type ... Package* this is package 'chinaWeather' version '0.1'* checking package namespace information ... OK* checking package dependencies ... OK* checking if this is a source package ... OK* checking if there is a namespace ... OK* checking for executable files ... OK* checking for hidden files and directories ... OK* checking for portable file names ... OK* checking for sufficient/correct file permissions ... OK* checking whether package 'chinaWeather' can be installed ... OK* checking installed package size ... OK* checking package directory ... OK* checking DESCRIPTION meta-information ... OK* checking top-level files ... OK* checking for left-over files ... OK* checking index information ... OK* checking package subdirectories ... OK* checking R files for non-ASCII characters ... OK* checking R files for syntax errors ... OK* checking whether the package can be loaded ... OK* checking whether the package can be loaded with stated dependencies ... OK* checking whether the package can be unloaded cleanly ... OK* checking whether the namespace can be loaded with stated dependencies ... OK* checking whether the namespace can be unloaded cleanly ... OK* checking loading without being on the library search path ... OK* checking for unstated dependencies in R code ... OK* checking S3 generic/method consistency ... OK* checking replacement functions ... OK* checking foreign function calls ... OK* checking R code for possible problems ... OK* checking Rd files ... OK* checking Rd metadata ... OK* checking Rd cross-references ... OK* checking for missing documentation entries ... OK* checking for code/documentation mismatches ... OK* checking Rd \usage sections ... OK* checking Rd contents ... OK* checking for unstated dependencies in examples ... OK* checking examples ... OK* checking PDF version of manual ... OKChecking chinaWeather with devtoolsChecking for any extra files in built .tar.gz file... OK

查检通过.
注：请安装

sudo apt-get install texlive-full

7. 程序发布

我们把写的程序发布到github上面，然后通过devtools，我可以方便的把程序从github下载安装。

在github创建一个新的资源库：chinaWeather

https://github.com/bsspirit/chinaWeather

提交本地代码到github

~ cd /home/conan/R/chinaWeather~ git init~ git add .~ git commit -m 'init commit'~ git remote add origin https://github.com/bsspirit/chinaWeather~ git push -u origin masterTo https://github.com/bsspirit/chinaWeather * [new branch]      master -> masterBranch master set up to track remote branch master from origin.

通过devtools下载，并安装代码。
现在我的chinaWeather包，已经在github上面发布了，如果其他的同学想使用可以下面命令安装。

> library(devtools)> install_github("chinaWeather","bsspirit")Installing github repo(s) chinaWeather/master from bsspiritDownloading chinaWeather.zip from https://github.com/bsspirit/chinaWeather/archive/master.zipInstalling package from /tmp/RtmpSaXYcA/chinaWeather.zipInstalling chinaWeather'/usr/lib/R/bin/R' --vanilla CMD INSTALL  \  '/tmp/RtmpSaXYcA/chinaWeather-master'  \  --library='/home/conan/R/x86_64-pc-linux-gnu-library/3.0'  \  --with-keep.source --install-tests* installing *source* package 'chinaWeather' ...** R** inst** preparing package for lazy loading** help*** installing help indices** building package indices** testing if installed package can be loaded* DONE (chinaWeather)#测试包> library(chinaWeather)> filename()[1] "20130805.csv"#查看文档> ?filenamefilename             package:chinaWeather              R DocumentationDefine a filename from current date.Description:     Define a filename from current date.Usage:       filename(date = Sys.time())Arguments:    date: input a date typeValue:     character a file nameExamples:     filename()     filename(as.Date("20110701",format="%Y%m%d"))

我们完成了，开发R包的全部流程。依赖于devtools, roxygen2, testthat三个包，真是事半功倍，比起完全手动操作提高效率了很多！！