R语言的启动选项
R --vanilla
vanilla 选项为跳过加载配置文件，跳过保存的会话按钮（vanilla意为单纯的）
1. windows下R配置
config
1.1 限制最大内存
在R或Rstudio的快捷方式里，【右键】->【属性】配置如下：
目标默认为："D:\Program Files\RStudio\bin\rstudio.exe"
修改为："D:\Program Files\RStudio\bin\rstudio.exe" --max-mem-size=4000M
1.2 修改启动后的默认路径
方法1： 起始位置默认为：D:\Program Files\RStudio
修改为："E:\r\r learning"
方法2：修改D:\Program Files\R\R-3.4.2\etc\Rprofile.site 中的最后一段为
if (interactive())
setwd("E://r//r learning//")
cat(c("Current directory is ", getwd()))
意思是每次启动R交互节目后自动执行上面的代码
1.3 设置网络连接的代理
目标修改为："D:\Program Files\RStudio\bin\rstudio.exe" --vanilla http_proxy=http://proxyname.edu.cn/8080/ http_proxy_user=username:password
1.4设置R安装包的镜像仓库
方法1： 直接在R交互模式中运行代码（r["CRANextra"]：因为CRAN上有极少数的包没有Windows版本，但牛津大学的Ripley大人好心提供了Windows的二进制编译版本，所以那些包可以从他那边安装。）
local({r <- getOption("repos")
r["CRAN"] <- "https://mirrors.ustc.edu.cn/CRAN/"
r["CRANextra"] <- "http://www.stats.ox.ac.uk/pub/RWin"
options(repos=r)})
或者：
options(repos = c(CRAN = "https://mirrors.ustc.edu.cn/CRAN/",
CRANextra = "http://www.stats.ox.ac.uk/pub/RWin"))
如下所示：
> local({r = getOption("repos"); r["CRAN"] = "https://mirrors.ustc.edu.cn/CRAN/";
+ options(repos=r)})
> install.packages("ggplot2")
trying URL 'http://cran.ms.unimelb.edu.au/bin/windows/contrib/3.4/ggplot2_2.2.1.zip'
Content type 'application/zip' length 2783370 bytes (2.7 MB)
downloaded 2.7 MB
package ‘ggplot2’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\x2yline\AppData\Local\Temp\RtmpiWeBYP\downloaded_packages
# 安装包过程：下载zip压缩包后自动安装
# 可以手动下载安装包进行手动安装
> list.files("C:\\Users\\x2yline\\AppData\\Local\\Temp\\RtmpiWeBYP\\downloaded_packages")
[1] "ggplot2_2.2.1.zip"
方法2： 在交互模式下设置手动选择镜像模式
> setRepositories(graphics=FALSE)
--- Please select repositories for use in this session ---
1: + CRAN
2: BioC software
3: BioC annotation
4: BioC experiment
5: BioC extra
6: + CRAN (extras)
7: Omegahat
8: R-Forge
9: rforge.net
Enter one or more numbers separated by spaces, or an empty line to cancel
1: 1
> install.packages("ggplot2")
--- Please select a CRAN mirror for use in this session ---
Secure CRAN mirrors
1: 0-Cloud [https] 2: Algeria [https]
3: Australia (Canberra) [https] 4: Australia (Melbourne 1) [https]
5: Australia (Melbourne 2) [https] 6: Australia (Perth) [https]
7: Austria [https] 8: Belgium (Ghent) [https]
9: Brazil (PR) [https] 10: Brazil (RJ) [https]
11: Brazil (SP 1) [https] 12: Brazil (SP 2) [https]
13: Bulgaria [https] 14: Chile 1 [https]
15: Chile 2 [https] 16: China (Guangzhou) [https]
17: China (Lanzhou) [https] 18: Colombia (Cali) [https]
19: Czech Republic [https] 20: Denmark [https]
21: Ecuador (Cuenca) [https] 22: Estonia [https]
23: France (Lyon 1) [https] 24: France (Lyon 2) [https]
25: France (Marseille) [https] 26: France (Montpellier) [https]
27: France (Paris 2) [https] 28: Germany (Gttingen) [https]
29: Germany (Münster) [https] 30: Greece [https]
31: Iceland [https] 32: Indonesia (Jakarta) [https]
33: Ireland [https] 34: Italy (Padua) [https]
35: Japan (Tokyo) [https] 36: Malaysia [https]
37: Mexico (Mexico City) [https] 38: Norway [https]
39: Philippines [https] 40: Serbia [https]
41: Spain (A Corua) [https] 42: Spain (Madrid) [https]
43: Sweden [https] 44: Switzerland [https]
45: Turkey (Denizli) [https] 46: Turkey (Mersin) [https]
47: UK (Bristol) [https] 48: UK (Cambridge) [https]
49: UK (London 1) [https] 50: USA (CA 1) [https]
51: USA (IA) [https] 52: USA (KS) [https]
53: USA (MI 1) [https] 54: USA (OR) [https]
55: USA (TN) [https] 56: USA (TX 1) [https]
57: Vietnam [https] 58: (other mirrors)
Selection: 16
trying URL 'https://mirrors.eliteu.cn/CRAN/bin/windows/contrib/3.4/ggplot2_2.2.1.zip'
Content type 'application/zip' length 2782968 bytes (2.7 MB)
downloaded 2.7 MB
package ‘ggplot2’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\x2yline\AppData\Local\Temp\RtmpYr3CZG\downloaded_packages
方法3： 修改文件D:\Program Files\R\R-3.4.2\etc\Rprofile.site 配置文件（打开R以后自动执行该文件里的所有命令）
原文件为：
# Things you might want to change
# options(papersize="a4")
# options(editor="notepad")
# options(pager="internal")
# set the default help type
# options(help_type="text")
options(help_type="html")
# set a site library
# .Library.site <- file.path(chartr("\\", "/", R.home()), "site-library")
# set a CRAN mirror
# local({r <- getOption("repos")
# r["CRAN"] <- "http://my.local.cran"
# options(repos=r)})
# Give a fortune cookie, but only to interactive sessions
# (This would need the fortunes package to be installed.)
# if (interactive())
# fortunes::fortune()
修改后为：
# Things you might want to change
options(papersize="a4")
options(editor="D:\\Program Files\\Sublime Text 3\\sublime_text.exe")
# options(pager="internal")
# set the default help type
# options(help_type="text")
options(help_type="html")
# set a site library
# .Library.site <- file.path(chartr("\\", "/", R.home()), "site-library")
# set a CRAN mirror
# local({r <- getOption("repos")
# r["CRAN"] <- "http://my.local.cran"
# options(repos=r)})
local({r <- getOption("repos")
r["CRAN"] <- "https://mirrors.ustc.edu.cn/CRAN/"
r["CRANextra"] <- "http://www.stats.ox.ac.uk/pub/RWin" # leicheng
options(repos=r)})
# set a bioconductor mirror --leicheng
options(BioC_mirror="http://mirrors.ustc.edu.cn/bioc/")
# blogdown setting ---leicheng
options(servr.daemon = TRUE, blogdown.author = "x2yline")
# Give a fortune cookie, but only to interactive sessions
# (This would need the fortunes package to be installed.)
# if (interactive())
# fortunes::fortune()
if (interactive())
## 指定R包路径
.libPaths( c("D:/R_lib", .libPaths()) )
# setwd("E:/r/r learning/")
{
cat(c("Current directory is ", getwd(), "\n"))
if (file.exists("~/.Rprofile"))
{
base::sys.source("~/.Rprofile", envir = environment())
}
Sys.setenv(R_GSCMD = "D:/green soft/programming/gs922w64.exe")
require(showtext, quietly = TRUE)
showtext_auto()
cwd <- getwd()
setwd(as.character(font_paths()))
font_add("msyh", regular="msyh.ttc", bold="msyhbd.ttc")
font_add("simhei", regular="simhei.ttf")
setwd(cwd)
add_fonts <- function(font_strings)
{
cwd <- getwd()
setwd(as.character(font_paths()))
fonts_file <- list.files()
fonts_file <- fonts_file[which(grepl(font_strings, fonts_file, ignore.case = TRUE))]
for (i in fonts_file) {
font_name <- strsplit(i, "[.]")[[1]][1]
font_name <- sub("-", " ", font_name)
print(font_name)
font_add(font_name, regular=i)
if (grepl("regular$", font_name, ignore.case=TRUE)){
font_add(strsplit(font_name, " ")[[1]][1], regular=i)
cat("\n",font_name, ":regular\n\n")
}
setwd(cwd)
}
}
}
1.5 R包的路径设置
下载完编译完成的包zip文件后，R会把zip文件自动安装在包的存放路径中，查看当前R包的路径：
.libPaths()
修改R包的路径
方法1：（可在R的交互界面或配置文件D:\Program Files\R\R-3.4.2\etc\Rprofile.site 中修改：
.libPath("my R packags Path")
方法2：
在快捷方式属性里的target后面加上语句（与前面的语句用空格隔开）
R_LIBS_USER="my R packags Path"
2. 32位与64位的R语言软件
如果电脑是32位的，就只能使用32位的R软件，如果是64位的电脑，并且内存超过4G就可以使用64位的R软件以允许R占用超过4G的内存
32位：
> sessionInfo()
R version 3.4.2 (2017-09-28)
Platform: i386-w64-mingw32/i386 (32-bit)
Running under: Windows 10 x64 (build 16288)
Matrix products: default
locale:
[1] LC_COLLATE=Chinese (Simplified)_China.936
[2] LC_CTYPE=Chinese (Simplified)_China.936
[3] LC_MONETARY=Chinese (Simplified)_China.936
[4] LC_NUMERIC=C
[5] LC_TIME=Chinese (Simplified)_China.936
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] compiler_3.4.2
64位：
> sessionInfo()
R version 3.4.2 (2017-09-28)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 16288)
Matrix products: default
locale:
[1] LC_COLLATE=Chinese (Simplified)_China.936
[2] LC_CTYPE=Chinese (Simplified)_China.936
[3] LC_MONETARY=Chinese (Simplified)_China.936
[4] LC_NUMERIC=C
[5] LC_TIME=Chinese (Simplified)_China.936
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] compiler_3.4.2
Rstudio默认设置使用64位的R，可以通过【Tools】->【Global Options】进行设置R version：
r_version
2. R的更新
在Rgui中输入
install.packages("installr")
installr::updateR(cran_mirror="https://mirrors.ustc.edu.cn/CRAN/")
接下来安装提示操作就行了
可能会有持续补充。。。
参考：
[1] 谢益辉 肖楠等 R语言忍者秘籍
[2] Gondro C. Primer to analysis of genomic data using R[M]. Springer International Publishing, 2015.
[3] Matloff N. The art of R programming: A tour of statistical software design[M]. No Starch Press, 2011.