R到3.5因為引入了Bioconductor version: Release (3.8),是一個破天荒地的改變,必須更新!
Ubuntu倒是很穩定,現在其實已經是Ubuntu18了。
deb https://cloud.r-project.org/bin/linux/ubuntu/ xenial-cran35/
sudo apt-get --purge remove r-base
sudo apt-get --purge remove r-base-core
sudo apt-get --purge remove r-base-dev
# sudo apt-get remove -y 'r-cran-*'
# apt-get remove 會刪除軟件包而保留軟件的配置文件
# apt-get purge 會同時清除軟件包和軟件的配置文件
比如我這里:
Removing r-recommended (3.3.3-1xenial0) ...
這個時候,之前的R包其實也需要同樣的被清理
[2] "/usr/local/lib/R/site-library"
[3] "/usr/lib/R/site-library"
[4] "/usr/lib/R/library"
這里,不同Ubuntu系統有點不一樣:
Edit /etc/apt/sources.list and add the line appropriate to your distribution of Ubuntu.
# 18.04
deb https://cloud.r-project.org/bin/linux/ubuntu bionic-cran35/
# 16.04
deb https://cloud.r-project.org/bin/linux/ubuntu xenial-cran35/
# 14.04
deb https://cloud.r-project.org/bin/linux/ubuntu trusty-cran35/
我這里是 Ubuntu16
sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9
sudo apt-get update
sudo apt-get install r-base r-base-core r-base-dev
#
# To update any R libraries installed via APT.
#
sudo apt-get upgrade
當然,還需要安裝一系列R包咯。
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("Sushi", version = "3.8")
BiocManager::install(c('shiny','shinydashboard','stringr','DT','ggplot2'),ask = F,update = F)
BiocManager::install('shinyBS',ask = F,update = F)
BiocManager::install('shinyAce',ask = F,update = F)
BiocManager::install(c('knitr','rmarkdown','rmarkdown','cowplot','dplyr'),ask = F,update = F)
BiocManager::install('RMySQL',ask = F,update = F)
BiocManager::install(c('tm','SnowballC','wordcloud','RColorBrewer'),ask = F,update = F)
BiocManager::install('nik01010/dashboardthemes')
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