标签：readline ott uniq building lin 配置 name 空间 题解
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。
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
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 \n \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/.
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：
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 \name{sayHello} \alias{sayHello} \title{a sayHello function demo} \description{ a sayHello function demo } \usage{ sayHello(name) } \arguments{ \item{name}{a word} } \details{ nothing } \value{ no return } \references{ nothing } \author{ Dan Zhang } \note{ 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 \title, and \name must exist and be unique in Rd files
求助：
Error : sayHello_1.0.tar.gz: Sections \title, and \name 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
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
\name{sayHello} \alias{sayHello} \title{a sayHello function demo} \description{ a sayHello function demo } \usage{ sayHello(name) } \arguments{ \item{name}{a word} } \details{ nothing } \value{ no return } \references{ nothing } \author{ Dan Zhang } \note{ 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！
转载请注明出处：
http://blog.fens.me/r-build-package/
标签：readline ott uniq building lin 配置 name 空间 题解
原文地址：http://www.cnblogs.com/leezx/p/7359108.html
