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rsloan-environment

rsloan environment note

詳見 rsloan & memo 只建議用於測試用途 !!!

Oracle VirtualBox

可以從 Oracle VirtualBox 中的喜好設定匯入，若想從實體機瀏覽器測試，可以在設定中額外加一張橋接介面卡。

喜好設定

1

橋接介面卡

2

OS

Ubuntu 14.04.5 LTS trusty

如果想要用 root 可以這麼做(不建議)

sudo passwd root

先裝常用工具

sudo apt-get install vim git -y

在家目錄建立 rws、prj 目錄

mkdir ~/rws
mkdir ~/prj

R

sudo sh -c 'echo "deb http://cran.csie.ntu.edu.tw/bin/linux/ubuntu trusty/" >> /etc/apt/sources.list'
sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9
sudo apt-get update
sudo apt-get install -y r-base libcurl4-openssl-dev libxml2-dev espeak

R Shiny Server

sudo apt-get install -y gdebi-core
wget http://download3.rstudio.org/ubuntu-12.04/x86_64/shiny-server-1.3.0.403-amd64.deb
sudo gdebi shiny-server-1.3.0.403-amd64.deb

瀏覽器

localhost:3838

解決 Shiny Server 套件來源的問題

註解掉 etc/Renviron 檔案上的來源設定

**R_LIBS_USER=${R_LIBS_USER-‘~/R/x86_64-pc-linux-gnu-library/3.3’} **

Reference : http://withr.me/set-up-shiny-server-on-ubuntu-16.04/

編輯 Renviron

sudo vim /usr/lib/R/etc/Renviron

check the default library path in R:

確認 R 的 套件來源

sudo su - -c "R -e \".libPaths()\""

Install the Shiny R package

sudo su - -c "R -e \"install.packages('shiny', repos='http://cran.rstudio.com/')\""

R package install several dependencies or environment

將一些常用的套件所需要的環境用好

sudo apt-get install -y libcurl4-openssl-dev  libssl-dev libxml2-dev libcairo-dev

sudo apt-get install -y default-jdk
export LD_LIBRARY_PATH=/usr/lib/jvm/java-8-openjdk-amd64/jre/lib/amd64/server/
sudo R CMD javareconf

修改套件來源的目錄權限

sudo chmod 777 /usr/local/lib/R/site-library

R Studio Server

https://www.rstudio.com/products/rstudio/download/

sudo apt-get install gdebi-core -y
wget https://download2.rstudio.org/rstudio-server-1.0.136-amd64.deb
sudo gdebi rstudio-server-1.0.136-amd64.deb

P.S : 建議對一下 R Shiny 最新版本

瀏覽器

localhost:8787

RStudio Desktop

https://www.rstudio.com/products/rstudio/download/

看習慣決定要不要裝 RStudio Desktop

use R File Edit

執行 rfile 目錄下的 pbpkgs.R 檔案。 

pbpkgs.R

local({r = getOption("repos")
r["CRAN"] = "https://cloud.r-project.org/"
options(repos=r)})

pkgs = c("devtools", "lattice", "GGally", "lubridate", "stringr", "ggplot2", "scales",
 "reshape2", "data.table", "coefplot", "broom", "RJDBC", "XLConnect", "RJSONIO", "sp", "png", "pixmap", "mapdata", "maptools", "maps", "rgeos", "Rcmdr")

pkgs = pkgs[!( pkgs %in% installed.packages()[,"Package"] )]

# install
if(length(pkgs)){
	install.packages(pkgs)
}

require(devtools)
install_github('rCharts', 'ramnathv')

Edit R Rprofile.site

sudo vim /usr/lib/R/etc/Rprofile.site

可以直接將下面內容直接加入 Rprofile.site 即可

# Haoye edit 
.First = function(){
	# work dir
	# setwd("/home/username/rws")
	setwd("/home/haoye/rws")

	# set a CRAN mirror
	# Automatic redirection to servers worldwide, currently sponsored by Rstudio
	local({r = getOption("repos")
	r["CRAN"] = "https://cloud.r-project.org/"
	options(repos=r)})

	# require package
	pkgs = c("devtools", "lattice", "GGally", "lubridate", "stringr", "ggplot2", "scales", "reshape2", "data.table", "coefplot", "broom")
	for(pkg in pkgs) {
  		library(pkg, character.only = TRUE)
	}
}


.Last = function(){ 

}

LAMP

MariaDB

sudo apt-get install mariadb-server mariadb-client -y

會要你輸入 2 次密碼。

Apache2

sudo apt-get install apache2 -y

PHP

sudo apt-get install php5 libapache2-mod-php5 -y

sudo service apache2 restart

測試 php

sudo vim /var/www/html/info.php

info.php

<?php
phpinfo();
?>

瀏覽器

localhost/info.php

PHP 設定

sudo apt-cache search php5

sudo service apache2 restart

sudo apt-get install php5-mysql php5-curl php5-gd php5-intl php-pear php5-imagick php5-imap php5-mcrypt php5-memcache php5-ming php5-ps php5-pspell php5-recode php5-snmp php5-sqlite php5-tidy php5-xmlrpc php5-xsl

sudo service apache2 restart

sudo apt-get install php5-xcache

sudo service apache2 restart

phpmyadmin

sudo apt-get install phpmyadmin -y

選 apache2、NO

其餘細項設定

sudo ln -s /usr/share/phpmyadmin /var/www/html/phpmyadmin

sudo /etc/init.d/apache2 reload

sudo apt-get install php5-mcrypt -y

sudo php5enmod mcrypt

sudo service apache2 restart

RMySQL 套件

sudo apt-get update

sudo apt-get install r-cran-rmysql -y

直接進入 R 執行

install.packages("RMySQL")

P.S : R Console 的視窗請不要關掉，這樣才能進行後面在 Terminal 上的動作。

觀察安裝後的訊息(後面會用)

/tmp/Rtmp*****R/downloaded_packages

sudo apt-get install libmariadb-client-lgpl-dev -y

ls /tmp/Rtmp*****R/downloaded_packages

whereis mysql

R CMD INSTALL --configure-args='--with-mysql-dir=/usr/lib/mysql' /tmp/Rtmp****R/downloaded_packages/RMySQL_0*****.tar.gz

Mariadb & RMySQL 的測試

進入 Mariadb

mysql -u root -p

建立測試資料

create database rmysql;
grant all on rmysql.* to rmysql@'%' identified by 'rmysql';
grant all on rmysql.* to rmysql@localhost identified by 'rmysql';
use rmysql

CREATE TABLE t_user(
id INT PRIMARY KEY AUTO_INCREMENT,
user varchar(12) NOT NULL UNIQUE
)ENGINE=INNODB DEFAULT CHARSET=utf8;

INSERT INTO t_user(user) values('A1'),('AB'),('fens.me');

SELECT * FROM t_user;

R test RMySQL

匯入 RMySQL 看有沒有成功

library(RMySQL)

conn = dbConnect(MySQL( ), dbname = "rmysql", username = "root", password = "your_passwd")

users = dbGetQuery(conn, "SELECT * FROM t_user")

dbDisconnect(conn)

users

phpmyadmin 錯誤狀況解決

Failed to connect to database: Error: Can't connect to local MySQL server through socket '/tmp/mysql.sock'

ln -s /var/run/mysqld/mysqld.sock /tmp/mysql.sock