Install Rstudio Server introduction

本文由简悦 SimpRead 转码，原文地址 claudiu.psychlab.eu

Tutorials from Claudiu’s blog

Install R (`r-base`)

1. Install helper software `software-properties-common` and `dirmngr`

software-properties-common for managing the repositories that you install software from.
dirmngr for managing and downloading certificate revocation lists and for downloading the certificates themselves.

sudo apt update -qq
sudo apt install --no-install-recommends software-properties-common dirmngr

2. Set repository

R (r-base) can be installed by simply running apt install, but the version of R in the default repository is usually not up-to-date. So we are going to tell apt install to obtain the latest version from a CRAN repository.

To do this we can make an entry in /etc/apt/sources.list file by running sudo nano /etc/apt/sources.list and pasting in deb https://<my.favorite.cran.mirror>/bin/linux/ubuntu <code-name-adjective>-cran40/ (where __ may be `https://cloud.r-project.org` and _``_ is the Ubuntu release code name adjective). After, we only need to add the key so that `apt` can perform signature checking of the Release File for the added repository to verify its authenticity. The CRAN repository for Ubuntu is signed with the key of “Michael Rutter [marutter@gmail.com](mailto:marutter@gmail.com){.email}”.

Fortunately, all of this can be done by running the following:

wget -qO- https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc | sudo tee -a /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc

sudo add-apt-repository "deb https://cloud.r-project.org/bin/linux/ubuntu $(lsb_release -cs)-cran40/"

We use lsb_release -cs to access which Ubuntu flavor the machine is running. For this example, I am running Impish Indri (21.10, amd64 only), so I could have typed impish instead of $(lsb_release -cs).

3. Install `r-base`

Install R and its dependencies by running:

sudo apt install --no-install-recommends r-base

Up until this point, everything we done is the step-by-step installation provided by official CRAN Brief Instructions (it is a good idea to also check the full README).

Now we just run R inside the terminal by just calling R.

Install R packages

1. Install `r-base-dev`

R packages can be installed the install.packages() function in R, but it depends on r-base-dev package to compile source code for some R packages.

sudo apt install r-base-dev

2. Install system dependencies

Some R packages have system dependencies. Here we will install the system dependencies for the tidyverse collection of packages.

sudo apt install libcurl4-openssl-dev libssl-dev libxml2-dev

Now we can install tidyverse from within R by running install.packages("tidyverse").

3. Handling the is not writable error

This error is very old and still persistent (see here and here).

Installing package into ‘/usr/local/lib/R/site-library’
(as ‘lib’ is unspecified)
Warning in install.packages :
  'lib = "/usr/local/lib/R/site-library"' is not writable

There are multiple ways around it (see here for adding user to group, here for installing as root, here for using per-project libraries) and although it may create problems with multi-user multi-project workflows, we will just use a personal library (advised here).

Just accept when R asks if you would like to create a personal library.

Install RStudio

1. Install `gdebi-core`

To install both RStudio and RStudio Server we will need gdebi-core to install them from .deb archive files.

sudo apt update

dpkg -l | grep gdebi

sudo apt -y install gdebi-core

2. Install RStudio

RStudio IDE official download page is here.

The installation is as straight forward as:

wget https://download1.rstudio.org/desktop/bionic/amd64/rstudio-2022.02.3-492-amd64.deb
sudo gdebi rstudio-2022.02.3-492-amd64.deb

But I like to manually download the .deb files in ./Download folder and install from there:

cd ./Download
sudo gdebi $(ls | grep rstudio-2022)

Install RStudio Server

RStudio Server provides a browser based interface to R running on a remote Linux server.

It is important to note from the very begining that RStudio Server by default does not allows system users (such as root) to authenticate, so we need a normal user account with sudo privilege on the server.

As mentioned above, to install both RStudio and RStudio Server we will need gdebi-core to install them from .deb archive files. Check that you have it installed.

sudo apt update

dpkg -l | grep gdebi

RStudio Server official download page is here.

The installation is simple (see official CRAN guide):

wget https://download2.rstudio.org/server/bionic/amd64/rstudio-server-2022.02.3-492-amd64.deb
sudo gdebi rstudio-server-2022.02.3-492-amd64.deb

By default RStudio Server runs on port 8787 and accepts connections from all remote clients. After installation you should therefore be able to navigate a web browser to the following address to access the server: http://<server-ip>:8787.

In the browser it will look like this:

A couple of notes related to user authentication (from RStudio Getting Starded guide):

RStudio Server will not permit logins by system users (those with user ids lower than 100).
User credentials are encrypted using RSA as they travel over the network.
You can manage users with standard Linux user administration tools like useradd, userdel, etc.
Each user needs to be created with a home directory.

RStudio Server Commands

See info on:

Also, here we are using the free RStudio Server, but the docs on Rstudio Workbench (formally known as RStudio Server Pro - the paid product offered by RStudio) on Administration provide good information for both.

Stopping and Starting

sudo rstudio-server stop
sudo rstudio-server start
sudo rstudio-server restart

sudo rstudio-server status 

sudo rstudio-server reload 

Managing Active Sessions

sudo rstudio-server active-sessions 

sudo rstudio-server suspend-session <pid> 
sudo rstudio-server force-suspend-session <pid> 
sudo rstudio-server force-suspend-all  

sudo rstudio-server kill-session <pid>  
sudo rstudio-server kill-all   

Taking the Server Offline

sudo rstudio-server offline
sudo rstudio-server online

Special tip: Rstudio Server webapp

If you prefer the RStudio Desktop look to the in-browser one when working on RStudio Server, you can create a webapp launcher for it (see here and here).

Disclaimer: I am not sure why you would like to do this, if you are working remotely on the server and if you are not just use RStudio Desktop.

Steps:

Login to the rstudio server from the browser (:8787).
On the menu bar, go to File (or Tools in some cases) -> Create application shortcut. A dialogue box will appear for the shortcut.
Add it to your desktop by selecting and run it as if you’re running Rstudio Desktop.

Rstudio Server 的安装和使用（附常见问题） - 简书

在本地使用 Rstudio 有很多的限制，不能够长时间跑程序，而服务器上能够满足 R 的很多条件，通过在服务器端安装 Rstudio 能够和本地一样使用 Rstudio。服务器的 Rstudio Server 通过浏览器输入 IP 地址完成。

注意：我这里使用的是 centos 7，需要服务器的 root 权限。

1. Rstudio Server 的安装

1.1 Rstudio Server

wget https://download2.rstudio.org/rstudio-server-rhel-1.1.456-x86_64.rpm
sudo yum install rstudio-server-rhel-1.1.456-x86_64.rpm

1.2 创建配置文件

sudo vi /etc/rstudio/rserver.conf
sudo vi /etc/rstudio/rsession.conf   

###在两个配置文件中添加以下语句
rsession-which-r=/usr/bin/R  ##系统的R程序所在位置，如果个人目录下有利用anaconda安装R，可能会报错。
www-port=8787 ### 通过ip的8787端口连接

1.3 在防火墙配置文件中添加 8787 端口

sudo vi /etc/sysconfig/iptables

###在文件中添加以下语句：
iptables -A INPUT -p tcp -m state --state NEW -m tcp --dport 8787 -j ACCEPT

### 重启防火墙
sudo service iptables restart
sudo netstat -anp ###查看开放的端口信息

1.4 检查 Rstudio-server 是否能够运行并启动服务

#检查配置是否完整
sudo rstudio-server verify-installation

#启动服务
sudo rstudio-server start
#查看状态，当出现active是，配置完成
sudo rstudio-server status
#[root@ lib64]#  rstudio-server status
#● rstudio-server.service - RStudio Server
#  Loaded: loaded (/etc/systemd/system/rstudio-server.service; enabled; vendor preset: disabled)
# Active: active (running) since Tue 2020-07-21 10:22:57 CST; 4s ago

1.5 打开本地的浏览器，输入 IP：端口号，会出现输入用户名和密码的提示。这里的用户名和密码就是每个用户自己的用户名和密码。

成功的网页截图

2. 常见的问题及解决的方法

需要根据上面的步骤，打开 rstudio 的服务以及对应的网络端口。

2.1 RStudio Server 安装完成后，浏览器无法打开 ip:8787 登录页，显示无法访问。

这是因为没有正确的配置网络端口，根据 1.3 修改相关的配置

无法打开网页

2.2 Rstudio server “Unable to connect to service”。在输入用户名和密码后，rstudio 没有能够加载出来，并包以上出错。

通过 rstudio-server verify-installation 检查 Rstudio 相关的服务，并排除故障。

2.3 Rstudio 服务重启的问题。

rstudio-server 有三个命令可以管理 rstudio 的服务

rstudio-server status: 查看 rstudio 的服务情况，看是否报错rstudio-server start/restart: 启动（start）或者重启（restart）服务。rstudio-server stop: 结束服务。

rstudio-server 在重启的过程中，经常会遇到端口占用的问题，报错 Address already in use。这个错误是因为原有的进程占用已经设置好的端口，解决的方法是关闭所有占用该端口的进程。解决方案可以参考 https://blog.csdn.net/qq_43561095/article/details/109535143 这个网址。

报错端口占用. png

2.3.1 查看端口占用情况，这里我们是默认的 8787 端口

lsof -i tcp:8787

image.png

2.3.2 结束对应的进程。这里关闭所有 LISTEN 相关的进程

kill -9 45551  54567 58358 92824

至此，问题解决。

3 参考网址 3.1 https://www.jianshu.com/p/44169741bd22 3.2 https://www.bioinfo-scrounger.com/archives/435/ 3.3 https://community.rstudio.com/t/rstudio-server-unable-to-connect-to-service/40600

Linux 使用 iptables 配置防火墙提示：unrecognized service_iptables: unrecognized service_很简单_的博客 - CSDN 博客

Ubuntu 默认安装是没有开启任何防火墙的。

当使用 service iptables status 时发现提示 iptables:unrecoginzed service。意思是无法识别的服务。

以下方法来自 http://blog.csdn.net/lywzgzl/article/details/39938689，但是测试发现，此方法已经无法在 Ubuntu 中使用

在 ubuntu 中由于不存在 / etc/init.d/iptales 文件，所以无法使用 service 等命令来启动 iptables，需要用 modprobe 命令。

#启动iptables
modprobe ip_tables
#关闭iptables（关闭命令要比启动复杂）
iptables -F
iptables -X
iptables -Z
iptables -P INPUT ACCEPT
iptables -P OUTPUT ACCEPT
iptables -P FORWARD ACCEPT
modprobe -r ip_tables
#依次执行以上命令即可关闭iptables，否则在执行modproble -r ip_tables时将会提示
#FATAL: Module ip_tables is in use.

注：通过以上方法，最终无法解决，通过研究发现，以上的命令已经是旧版，在新版中iptables本身不是一个服务。

而如果要继续使用 iptables 配置，可以通过来自 http://www.cnblogs.com/general0878/p/5757377.html 的方法去实现：

1、查看系统是否安装防火墙
sudo whereis iptables

# 出现如上提示表示已经安装iptables，如果没有安装，可以通过以下命令安装
sudo apt-get install iptables

2、查看防火墙的配置信息
sudo iptables -L

3、新建规则文件
#先新建目录，本身无此目录
mkdir /etc/iptables
vi /etc/iptables/rules.v4

# 两条合起来的命令可以简化成以下写法
mkdir /etc/iptables & vi /etc/iptables/rules.v4

添加以下内容（备注：80 是指 web 服务器端口，3306 是指 MySQL 数据库链接端口，22 是指 SSH 远程管理端口）

*filter
:INPUT DROP [0:0]
:FORWARD ACCEPT [0:0]
:OUTPUT ACCEPT [0:0]
:syn-flood - [0:0]
-A INPUT -i lo -j ACCEPT
-A INPUT -m state --state RELATED,ESTABLISHED -j ACCEPT
-A INPUT -p tcp -m state --state NEW -m tcp --dport 22 -j ACCEPT
-A INPUT -p tcp -m state --state NEW -m tcp --dport 80 -j ACCEPT
-A INPUT -p tcp -m state --state NEW -m tcp --dport 3306 -j ACCEPT
-A INPUT -p icmp -m limit --limit 100/sec --limit-burst 100 -j ACCEPT
-A INPUT -p icmp -m limit --limit 1/s --limit-burst 10 -j ACCEPT
-A INPUT -p tcp -m tcp --tcp-flags FIN,SYN,RST,ACK SYN -j syn-flood
-A INPUT -j REJECT --reject-with icmp-host-prohibited
-A syn-flood -p tcp -m limit --limit 3/sec --limit-burst 6 -j RETURN
-A syn-flood -j REJECT --reject-with icmp-port-unreachable
COMMIT

4、使防火墙生效
iptables-restore < /etc/iptables/rules.v4

5、创建文件，添加以下内容，使防火墙开机启动
vi /etc/network/if-pre-up.d/iptables

#!/bin/bash
iptables-restore < /etc/iptables/rules.v4


6、添加执行权限
chmod +x /etc/network/if-pre-up.d/iptables

7、查看规则是否生效
iptables -L -n

`通过以上方法可以在Ubuntu上正常通过，并且可以清晰的知道其依赖关系。`

再或者如果要折腾 iptables 的用法，可以参考以下收集的文章进行配置： https://serverfault.com/questions/129086/how-to-start-stop-iptables-on-ubuntu https://help.ubuntu.com/community/IptablesHowTo

经过研究发现，在 Ubuntu/Debian 系统上有一个防火墙的简化版，叫做 UFW，原理还是 iptables，但是由于 iptables 需要操作的表和关系很多，所以使用 UFW 来简化这些操作。

Install Rstudio Server introduction

君子欲讷于言而敏于行。

Tutorials from Claudiu’s blog

Install R (`r-base`)

1. Install helper software `software-properties-common` and `dirmngr`

2. Set repository

3. Install `r-base`

Install R packages

1. Install `r-base-dev`

2. Install system dependencies

3. Handling the is not writable error

Install RStudio

1. Install `gdebi-core`

2. Install RStudio

Install RStudio Server

Stopping and Starting

Managing Active Sessions

Taking the Server Offline

Special tip: Rstudio Server webapp

Rstudio Server 的安装和使用（附常见问题） - 简书

1. Rstudio Server 的安装

2. 常见的问题及解决的方法

Linux 使用 iptables 配置防火墙提示：unrecognized service_iptables: unrecognized service_很简单_的博客 - CSDN 博客

Catalog

FEATURED TAGS

FRIENDS

Tutorials from Claudiu’s blog

Install R (r-base)

1. Install helper software software-properties-common and dirmngr

2. Set repository

3. Install r-base

Install R packages

1. Install r-base-dev

2. Install system dependencies

3. Handling the is not writable error

Install RStudio

1. Install gdebi-core

2. Install RStudio

Install RStudio Server

Stopping and Starting

Managing Active Sessions

Taking the Server Offline

Special tip: Rstudio Server webapp

Rstudio Server 的安装和使用（附常见问题） - 简书

1. Rstudio Server 的安装

2. 常见的问题及解决的方法

Linux 使用 iptables 配置防火墙提示：unrecognized service_iptables: unrecognized service_很简单_的博客 - CSDN 博客

Catalog

FEATURED TAGS

FRIENDS

Install R (`r-base`)

1. Install helper software `software-properties-common` and `dirmngr`

3. Install `r-base`

1. Install `r-base-dev`

1. Install `gdebi-core`