Centos7_miniconda_devtools安装_R语言入门之R包的安装

因为有同时反馈安装R包很慢或卡住。同事提供了一个安装R包的命令给我测试，在安装过程中复现报错信息，把下载慢或卡信的链接中的域名在防火墙中调整出口。

devtools::install_github("GreenleafLab/ArchR", ref="master", repos = BiocManager::repositories())

下载安装miniconda

wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
chmod +x Miniconda3-latest-Linux-x86_64.sh #给下载下来的安装文件添加执行权限
sudo bash Miniconda3-latest-Linux-x86_64.sh

一路Enter----yes—yes直到安装完成
进入conda环境

source ~/.bashrc
conda

国内换源

#全部清华园，备用conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/MindSpore
conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/Paddle
conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/auto
conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/biobakery
conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda
conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/c4aarch64
conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/caffe2
conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/deepmodeling
conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/dglteam
conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/fastai
conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/fermi
conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/idaholab
conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/intel
conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/matsci
conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/menpo/
conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/mordred-descriptor
conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/msys2
conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/numba
conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/ohmeta
conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/omnia
conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/peterjc123
conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/plotly
conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/psi4
conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/pytorch
conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/pytorch-lts
conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/pytorch-test
conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/pytorch3d
conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/pyviz
conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/qiime2
conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/rapidsai
conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/rdkit
conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/simpleitk
conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/stackless
conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/ursky

安装下R语言运行环境，安装R4.0.0(开始时安装R4.3.1提示不支持某个插件，具体不记得了)

conda search R

创建R4.0环境

conda create -n r4.0

进入R4.0环境

conda activate r4.0

安装R4.0

conda install R=4.0 -y

进入R程序

安装devtools

install.packages("devtools")

安装R包报错：

1) grab failed: window not viewable.

Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
[tcl] grab failed: window not viewable.

一般发生在远程linux系统中安装R包，是因为R调用窗口失败，解决方法是

chooseCRANmirror(graphics=FALSE)

输入16回车，再运行一次安装命令。

install.packages("devtools")

可能还会有下面出错信息

1: In install.packages("devtools", dependencies = TRUE) :安装程序包‘systemfonts’时退出狀態的值不是0
2: In install.packages("devtools", dependencies = TRUE) :安装程序包‘textshaping’时退出狀態的值不是0
3: In install.packages("devtools", dependencies = TRUE) :安装程序包‘ragg’时退出狀態的值不是0
4: In install.packages("devtools", dependencies = TRUE) :安装程序包‘pkgdown’时退出狀態的值不是0
5: In install.packages("devtools", dependencies = TRUE) :安装程序包‘devtools’时退出狀態的值不是0

解决办法：

1.install.packages('fontconfig')根据报错提示安装

yum install fontconfig-devel

2.install.packages('textshaping')根据报错提示安装

yum install -y harfbuzz-devel fribidi-devel

3.install.packages('ragg')根据报错提示安装

yum install -y freetype-devel libpng-devel libtiff-devel libjpeg-devel

4.处理完1.2.3再安装下面包已经不再提示错误了。
install.packages('pkgdown')

处理完再试试安装devtools.

在R中使用devtools安装R包

devtools::install_github("GreenleafLab/ArchR", ref="master", repos = BiocManager::repositories())

例如生信分析常用到的Bioconductor，可使用BiocManager::install()来进行安装，例如安装DESeq2包

if (!require("BiocManager", quietly = TRUE))install.packages("BiocManager")BiocManager::install("DESeq2")

又报出错。

ERROR: dependencies ‘SummarizedExperiment’, ‘rhdf5’, ‘motifmatchr’, ‘chromVAR’, ‘uwot’, ‘Rsamtools’, ‘Biostrings’, ‘ComplexHeatmap’, ‘GenomicRanges’ are not available for package ‘ArchR’
* removing ‘/root/miniconda3/envs/r4.0/lib/R/library/ArchR’

参考文章：Miniconda3环境配置，换国内源_miniconda换源-CSDN博客

参考文章：没有人比我更懂R包安装 - 知乎