开发自己的R包(转)

R不必说，数据统计分析可视化的必备语言，R包开发的门槛比较低，所以现在随便一篇文章都会发表一个自己的R包，这样有好处（各种需求早有人帮你解决了）也有坏处（R包太多，混乱，新手上手较难）。作为生信工程师，日常就是查看别人写的R包，分析数据，然后借鉴、修改，根据自己的需求开发新的R包。

参考：

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

R包开发

如何系统地学习 R 语言的各种 packages？

Developing Packages with RStudio

To do：开发一个R包，部署到GitHub上（发paper的标准流程）

前言
R是一个世界范围开发者共同协作的产物，至2013年2月共计近5000个包可在互联网上自由下载。现在作为R的使用者，有朝一日也可以成为R的开发者，把我们自己的知识做成R包分享给世界。

今天我们简单介绍如何开发自己R包。

目录

1. 系统环境
2. vi中制作R包
3. RStudio中制作R包

1. 系统环境

操作系统：Linux Ubuntu 12.04.2 LTS 64bit
R语言版本：R 3.0.1

~ uname -a
Linux conan-deskop 3.5.0-23-generic #35~precise1-Ubuntu SMP Fri Jan 25 17:13:26 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux

~ cat /etc/issue
Ubuntu 12.04.2 LTS 
 l

~ R --version
R version 3.0.1 (2013-05-16) -- "Good Sport"
Copyright (C) 2013 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under the terms of the
GNU General Public License versions 2 or 3.
For more information about these matters see
http://www.gnu.org/licenses/.

2. vi中制作R包

创建目录：/home/conan/R/demo

~ mkdir /home/conan/R/demo
~ cd /home/conan/R/demo

新建R脚本sayHello.R

~ vi sayHello.R
sayHello<-function(name){
    print(paste("Hello",name))
}

自定义一个sayHello的函数，将作为自定义包的第一个函数。

启动R程序

~ R

#清空变量设置工作目录
rm(list=ls())
setwd("/home/conan/R/demo")

#通过sayHello的脚本生成开发包的骨架
package.skeleton(name="sayHello",code_files="/home/conan/R/demo/sayHello.R")
Creating directories ...
Creating DESCRIPTION ...
Creating NAMESPACE ...
Creating Read-and-delete-me ...
Copying code files ...
Making help files ...
Done.
Further steps are described in './sayHello/Read-and-delete-me'.

#退出R的客户端
q()

在当前目录生成sayHello目录

~ ls -l
drwxrwxr-x 4 conan conan 4096  8月  1 15:07 sayHello
-rw-rw-r-- 1 conan conan   59  8月  1 15:04 sayHello.R

~ ls -l sayHello
-rw-rw-r-- 1 conan conan  281  8月  1 15:07 DESCRIPTION
drwxrwxr-x 2 conan conan 4096  8月  1 15:07 man
-rw-rw-r-- 1 conan conan   31  8月  1 15:07 NAMESPACE
drwxrwxr-x 2 conan conan 4096  8月  1 15:07 R
-rw-rw-r-- 1 conan conan  420  8月  1 15:07 Read-and-delete-me

~ ls -l sayHello/man
-rw-rw-r-- 1 conan conan 1043  8月  1 15:07 sayHello-package.Rd
-rw-rw-r-- 1 conan conan 1278  8月  1 15:07 sayHello.Rd

~ ls -l sayHello/R
-rw-rw-r-- 1 conan conan 59  8月  1 15:07 sayHello.R

文件及目录解释：

• DESCRIPTION文件: 包描述文件
• NAMESPACE文件: 包的命名空间文件
• Read-and-delete-me文件: 说明文件，可以删除
• man目录: 存放函数的说明文件的目录
• R目录：存放源文件的目录
• man/sayHello.Rd: sayHello函数的说明文件，latex语法，用来生成PDF文档
• man/sayHello-package.Rd: sayHello包的说明文件，可以删除

编辑DESCRIPTION文件：

~ vi sayHello/DESCRIPTION
Package: sayHello
Type: Package
Title: R package demo for sayHello
LazyLoad: yes
Author: Dan Zhang
Maintainer: Dan Zhang
Description: This package provides a package demo
License: GPL
Version: 1.0
Date: 2013-07-31
Depends: R (>= 3.0.1)
</BSSPIRIT@GMAIL.COM>

编辑NAMESPACE文件：

~ vi sayHello/NAMESPACE
exportPattern("^[[:alpha:]]+")

编辑sayHello.Rd文件：

~ vi sayHello/man/sayHello.Rd

ame{sayHello}
alias{sayHello}
	itle{a sayHello function demo}
description{
a sayHello function demo
}
usage{
sayHello(name)
}
arguments{
  item{name}{a word}
}
details{
nothing
}
value{
no return
}

eferences{
nothing
}
author{
Dan Zhang
}

ote{
nothing
}
seealso{
nothing
}
examples{
sayHello("world")
}
keyword{ sayHello }

删除文件：

~ rm sayHello/Read-and-delete-me
~ rm sayHello/man/sayHello-package.Rd

打包sayHello

~ R CMD build sayHello
* checking for file ‘sayHello/DESCRIPTION’ ... OK
* preparing ‘sayHello’:
* checking DESCRIPTION meta-information ... OK
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
* building ‘sayHello_1.0.tar.gz’

~ ls -l
drwxrwxr-x 4 conan conan 4096  8月  1 15:22 sayHello
-rw-r--r-- 1 conan conan  663  8月  1 15:24 sayHello_1.0.tar.gz
-rw-rw-r-- 1 conan conan   59  8月  1 15:04 sayHello.R

本地安装sayHello

~ R CMD INSTALL sayHello_1.0.tar.gz
* installing to library ‘/home/conan/R/x86_64-pc-linux-gnu-library/3.0’
* installing *source* package ‘sayHello’ ...
** R
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (sayHello)

~ ls /home/conan/R/x86_64-pc-linux-gnu-library/3.0
bitops  digest  manipulate  rstudio  sayHello  XML

sayHello包，已经在当前账号下进行安装

使用sayHello函数

~ R

library(sayHello)
sayHello("Conan")
[1] "Hello Conan"

#查看sayHello文档
?sayHello

sayHello               package:sayHello                R Documentation

a sayHello function demo

Description:
     a sayHello function demo
Usage:
     sayHello(name)
Arguments:
    name: a word
Details:
     nothing
Value:
     no return
Note:
     nothing
Author(s):
     Dan Zhang
References:
     nothing

我们包已经成功制作完成！并在本地进行安装和使用！！

检查R包
如果要提交R包和CRAN，必须要执行check检查。如果有任何的error和warning都将不被通过。

退出R的客户端,回到命令行

先安装latex的依赖包(500mb+)

~ sudo apt-get install texlive
~ sudo apt-get install texlive-xetex
~ sudo apt-get install texlive-latex-base
~ sudo apt-get install texlive-fonts-extra 
~ sudo apt-get install texlive-latex-recommended
~ sudo apt-get install texlive-fonts-recommended

执行check

~ R CMD check sayHello_1.0.tar.gz

* using log directory ‘/home/conan/R/demo/sayHello.Rcheck’
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘sayHello/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘sayHello’ version ‘1.0’
* 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 ‘sayHello’ 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 ... WARNING
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
* checking PDF version of manual without hyperrefs or index ... OK

WARNING: There was 1 warning.
See
  ‘/home/conan/R/demo/sayHello.Rcheck/00check.log’
for details.

发现有一个警告，checking PDF version of manual ... WARNING。是latex生成pdf错误。

查检警告的debug日志

~ R CMD Rd2pdf sayHello_1.0.tar.gz
Converting Rd files to LaTeX ...
  sayHello_1.0.tar.gz
Warning in readLines(f) :
  incomplete final line found on 'sayHello_1.0.tar.gz'
Warning in parse_Rd("sayHello_1.0.tar.gz", encoding = "unknown", fragment = FALSE,  :
  sayHello_1.0.tar.gz:16: unexpected '}'
Warning: sayHello_1.0.tar.gz:1: All text must be in a section
Warning: sayHello_1.0.tar.gz:2: All text must be in a section
Warning: sayHello_1.0.tar.gz:3: All text must be in a section
Warning: sayHello_1.0.tar.gz:4: All text must be in a section
Warning: sayHello_1.0.tar.gz:5: All text must be in a section
Warning: sayHello_1.0.tar.gz:6: All text must be in a section
Warning: sayHello_1.0.tar.gz:7: All text must be in a section
Warning: sayHello_1.0.tar.gz:8: All text must be in a section
Warning: sayHello_1.0.tar.gz:9: All text must be in a section
Warning: sayHello_1.0.tar.gz:10: All text must be in a section
Warning: sayHello_1.0.tar.gz:11: All text must be in a section
Warning: sayHello_1.0.tar.gz:12: All text must be in a section
Warning: sayHello_1.0.tar.gz:15: All text must be in a section
Error : sayHello_1.0.tar.gz: Sections 	itle, and 
ame must exist and be unique in Rd files

求助：
Error : sayHello_1.0.tar.gz: Sections itle, and ame must exist and be unique in Rd files
这个问题我检查了好多次始终没有解决。请求帮助！！

问题解决：安装完整包

sudo apt-get install texlive-full

上传R包
当解决了上面的WARN就可以上传了。。。(待续)

卸载R包

remove.packages("sayHello")
Removing package from ‘/home/conan/R/x86_64-pc-linux-gnu-library/3.0’

~ ls /home/conan/R/x86_64-pc-linux-gnu-library/3.0
bitops  digest  manipulate  rstudio  XML

3. RStudio中制作R包

RStudio Server的安装及配置，请参考：多人在线协作R开发RStudio Server

RStudio已经为我们准备了一个有界面的环境，方便我们制作R包。

1. 创建一个工程sayHello
2. 编辑DESCRIPTION
3. 创建sayHello.R的脚本
4. 编辑sayHello.Rd的文档

1). 创建一个工程sayHello
2). 编辑rstudio/sayHello/DESCRIPTION

Package: sayHello
Type: Package
Title: R package demo for sayHell
LazyLoad: yes
Author: Dan Zhang
Maintainer: Dan Zhang
Description: This package provides a package demo
License: GPL
Version: 1.0
Date: 2013-07-31
Depends: R (>= 3.0.1)
</BSSPIRIT@GMAIL.COM>

3). 编辑rstudio/sayHello/R/sayHello.R的脚本

sayHello<-function(name){
  print(paste("Hi",name))
}

4). 编辑rstudio/sayHello/man/sayHello.Rd的文档

ame{sayHello}
alias{sayHello}
	itle{a sayHello function demo}
description{
a sayHello function demo
}
usage{
sayHello(name)
}
arguments{
  item{name}{a word}
}
details{
nothing
}
value{
no return
}

eferences{
nothing
}
author{
Dan Zhang
}

ote{
nothing
}
seealso{
nothing
}
examples{
sayHello("world")
}
keyword{ sayHello }

5). 执行build和reload
6). 执行check
在RStudio中可以更方便的进行R的开包，打包，检查等的过程。RStudio就是R的神器！

虽然还没有发布自己的R包，不过很快了！！有此想法已经多时了！！每一天加油！