生物科研维基百科

分类： 生物信息学

  • Ubuntu下安装R studio及其相关依赖

    一、安装 R 与 R Studio

    快速使用

    # update indices
sudo apt update -qq -y
# install two helper packages we need
sudo apt install --no-install-recommends software-properties-common dirmngr -y
# 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/" -y

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

sudo apt-get install gdebi-core -y
wget https://download2.rstudio.org/server/jammy/amd64/rstudio-server-2024.04.2-764-amd64.deb
sudo gdebi rstudio-server-2024.04.2-764-amd64.deb -n
rm rstudio-server-2024.04.2-764-amd64.deb

sudo chmod -R a+rw /usr/lib/R/library
sudo chmod -R a+rw /usr/share/R/

    以上代码可直接复制使用，以下为代码细节

    安装R

    首先下载CRAN仓库的官方密钥，并将官方仓库添加到系统镜像源。若CRAN发布最新R版本，请参考官方安装文档

    # update indices
sudo apt update -qq -y
# install two helper packages we need
sudo apt install --no-install-recommends software-properties-common dirmngr -y
# 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/" -y

    然后可以直接使用apt安装R

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

    安装R studio

    若Ubuntu发布最新版本，请参考[官方安装文档](RStudio Server – Posit)是否需更换最新安装程序

    #安装某个轻量级dpkg包管理软件，其实这一步可以不用
sudo apt-get install gdebi-core -y
#下载Ubuntu版本的Rstudio的预编译.deb包
wget https://download2.rstudio.org/server/jammy/amd64/rstudio-server-2024.04.2-764-amd64.deb
#安装软件
sudo gdebi rstudio-server-2024.04.2-764-amd64.deb -n
#删除安装包
rm rstudio-server-2024.04.2-764-amd64.deb

    设置权限

    在Ubuntu下R包安装时默认没有某些关键文件夹的权限，需要手动开放

    #添加下面两个目录对所有用户的读写权限
sudo chmod -R a+rw /usr/lib/R/library
sudo chmod -R a+rw /usr/share/R/

    至此安装完成

    二、Linux下依赖安装

    编译链——所有R包源码安装都依赖

    sudo apt install make cmake gcc g++ -y

    生物信息学

    sudo apt install libxml2-dev liblapack-dev libpng-dev zlib1g-dev libcurl4-openssl-dev gfortran -y

    GEOquery依赖：libxml2-dev、liblapack-dev、libpng-dev、libcurl4-openssl-dev、gfortran
    Seurat依赖：zlib1g-dev、libcurl4-openssl-dev、gfortran、libpng-dev

    画图包

    sudo apt install libgmp-dev

    ggstatsplot依赖：libgmp-dev、libmpfr-dev