# R in Ubuntu22.04
###### tags: `Tutorial`, `Ubuntu`, `R`
目錄：
+ [Install R](#R)
+ [Dependency Problem](#depend)
+ [Using R with Jupyter Notebook](#RJupyter)
+ [Using R with VS code](#RVScode)
+ 必要套件：vscode-R, languageserver
+ 輔助套件：[rmarkdown](#rmd), [radian](#radian)
+ (未使用) [R studio](#rstudio)
其他參考：
+ [Ubuntu22.04重灌筆記](https://hackmd.io/@Chieh997/UbuntuCUDAvenv)
---
<a id='R'></a>
## R
### [Install R & Get CRAN Packages](https://cran.rstudio.com)
Run these lines to tell Ubuntu about the R binaries at CRAN.
```bash=0
# update indices
sudo apt update -qq
# install two helper packages we need
sudo apt install --no-install-recommends software-properties-common dirmngr
# add the signing key (by Michael Rutter) for these repos
# To verify key, run gpg --show-keys /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc
# Fingerprint: E298A3A825C0D65DFD57CBB651716619E084DAB9
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
# add the R 4.0 repo from CRAN -- adjust 'focal' to 'groovy' or 'bionic' as needed
sudo add-apt-repository "deb https://cloud.r-project.org/bin/linux/ubuntu $(lsb_release -cs)-cran40/"
```
Then install R and its dependencies.
```bash=+
sudo apt install --no-install-recommends r-base
```
Run this command (as root or by prefixing sudo) to add the current R 4.0 or later ‘c2d4u’ repository:
```bash=+
sudo add-apt-repository ppa:c2d4u.team/c2d4u4.0+
```
to add the key id for this repository, add the repository, and update the index.
+ Open R in terminal
```bash
R
# or
sudo R
```
+ Run R script in terminal
```bash
Rscript {file_name.R}
```
:::info
Q. [TWCC]`install.packages` with error about setting working diectory?
```
Error in setwd(od) : cannot change working directory
Error in setwd(startdir) : cannot change working directory
Execution halted
```
A. This heppended probably due to the old working directory cannot be found, try mannually set your work directory to the path of R library (check with `.libPaths()`), for example,
```
setwd('/usr/local/lib/R/site-library')
```
Also, remember to use `sudo R` when you try to install new packages in TWCC.
:::
<a id='depend'></a>
### Dependancy Problem
#### GDAL for shapefile
空間統計中常使用的shapefile(`.shp`)，欲開啟相關檔案常需搭配特殊套件(e.g. `rgdal`, `RJSONIO`)。
在安裝套件時可能會遇到dependency的問題，主要在於GDAL並未事先安裝在ubuntu上。
+ [GDAL install](https://mothergeo-py.readthedocs.io/en/latest/development/how-to/gdal-ubuntu-pkg.html)
```bash=
# repository preparation
sudo add-apt-repository ppa:ubuntugis/ppa && sudo apt-get update
sudo apt-get update
# gdal install
sudo apt-get install gdal-bin
sudo apt-get install libgdal-dev
# enviroment variables setting
export CPLUS_INCLUDE_PATH=/usr/include/gdal
export C_INCLUDE_PATH=/usr/include/gdal
```
+ other dependency probelm
可能需要額外安裝`proj`或`protobuf`等，具體參考安裝報錯時的指令。
```bash
sudo apt-get install proj-bin libproj-dev
# or
sudo apt-get install libprotobuf-dev protobuf-compiler
```
<a id='RJupyter'></a>
## [Using R with Jupyter Notebook](https://developers.refinitiv.com/en/article-catalog/article/setup-jupyter-notebook-r)
After R installing, install `IRkernel` with the following codes (`sudo` is required when opening R terminal):
```r=0
# Install R kernel for Jupyter Notebook via CRAN
install.packages('IRkernel')
# Making the kernel available to Jupyter
IRkernel::installspec(user = FALSE)
```
Then open Jupyter Notebook, you will see that there's a new option `R` when you try to open some new notebook.
<a id='RVScode'></a>
## 使用 VS Code 搭配 R
+ [在VS Code中使用R的幾個技巧](https://blog.yfei.page/cn/2020/12/vscode-r/)
+ [REditorSupport/vscode-R - GitHub](https://github.com/REditorSupport/vscode-R/wiki/Installation:-Linux)
+ [languageserver - GitHub](https://github.com/REditorSupport/languageserver)
+ [Using R in VS Code](https://schiff.co.nz/blog/r-and-vscode/)
#### VS Code套件：vscode-R
1. 在 VS Code 的 extension marketplace 搜尋`R`或`reditorsupport.r`以安裝套件.
2. 如果無法順利開啟R terminal，在設定介面的`r.rterm.linux`更改R terminal的路徑。
#### R套件：languageserver
`languageserver`是一個針對 Language Server Protocol 的R套件，輔助 VS Code 或其他平台作為 R editor 的自動補全、Highlight等。
1. 確認並安裝R所需環境
```bash=0
sudo apt install --assume-yes --no-install-recommends build-essential libcurl4-openssl-dev libssl-dev libxml2-dev r-base
```
2. 在R terminal中自CRAN安裝`languageserver`
```
install.packages("languageserver")
```
<a id='rmd'></a>
#### Rmarkdown
1. 在R中安裝rmarkdown套件
```
install.packages("rmarkdown")
```
2. 可搭配VS Code套件：
+ Markdown Preview Enhance: 同步顯示編譯後輸出結果(after run chunk)
+ Markdown All in One: 自動補全、縮排/排版、數學顯示等
3. 若要順利knit，需額外安裝pandoc
```bash=
sudo apt-get install pandoc
```
<a id='radian'></a>
#### (非必要) Python套件: Radian
提供R在VS code上的Terminal Syntax Highlight。
但若啟用radian作為VS code上的預設R terminal，會導致視窗無法通過滾輪上下檢視先前輸入的指令(同tmux那樣)，故不建議使用。
1. 以 pip 安裝 radian，並確認其路徑
```bash=0
pip install -U radian
which radian
```
2. 在設定介面的`r.rterm.linux`更改 R terminal 的預設路徑為 Radian。
---
<a id='rsudio'></a>
:::info
因本身使用ubuntu作為server遠端操作，並未使用Rstudio，以下安裝方式並未實際驗證過，僅做為參考。
:::
## [Install RStudio Desktop](https://posit.co/download/rstudio-desktop/)**待校正
+ [在 Linux 系統安裝 R 與 Rstudio](https://jacky810428.pixnet.net/blog/post/150622106-%E5%9C%A8-linux-%E7%B3%BB%E7%B5%B1%E5%AE%89%E8%A3%9D-r-%E8%88%87-rstudio)
Download the installer (e.g. [.deb](https://download1.rstudio.org/electron/jammy/amd64/rstudio-2022.12.0-353-amd64.deb) for Ubuntu 22.04), then follow their instruction.
### [Install RStudio Server](https://posit.co/download/rstudio-server/)**待校正
After installing R, run the following code
```bash=0
sudo apt-get install gdebi-core
wget https://download2.rstudio.org/server/jammy/amd64/rstudio-server-2022.12.0-353-amd64.deb
sudo gdebi rstudio-server-2022.12.0-353-amd64.deb
```
Check your installation is sucess with
```bash+=
systemctl status rstudio-server
# if not activate
systemctl start rstudio-server
```
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