先安装MiniConda
再安装 R4.3.1
再安装R包
1. 安装MiniConda
sudo su 切换到管理员root
下载Miniconda
wget https://mirrors.tuna.tsinghua.edu.cn/anaconda/miniconda/Miniconda3-latest-Linux-x86_64.sh
安装Miniconda
bash Miniconda3-latest-Linux-x86_64.sh
回车空格打完两个yes
conda -h
查看conda目前的镜像，命令：
conda config --show
添加镜像源
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/conda-forge/
conda config --add channels http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main/
conda config --add channels http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free/
conda config --add channels https://mirrors.pku.edu.cn/anaconda/pkgs/main/
进入环境变量文件，
vim .bashrc
添加 Miniconda中bin路径
export PATH=/data/username/miniconda3/bin/:$PATH
或者更新一下
source ~/.bashrc
利用conda安装一些软件测试,fastp,fastqc
conda install fastp
conda install fastqc
2.准备安装R
创建一个叫R4.3.1的环境，并安装R。
conda create -n R4.3.1
conda activate R4.3.1
conda install -c conda-forge r-base=4.3.1
控制台显示如下：
(base) root@DESKTOP-727JVLV:/home/ai_qiangyun# conda activate R4.3.1
(R4.3.1) root@DESKTOP-727JVLV:/home/ai_qiangyun# conda isntall -c conda-forge r-base=4.3.1
CommandNotFoundError: No command 'conda isntall'.
Did you mean 'conda install'?
(R4.3.1) root@DESKTOP-727JVLV:/home/ai_qiangyun# conda install -c conda-forge r-base=4.3.1
Collecting package metadata (current_repodata.json): done
Solving environment: unsuccessful initial attempt using frozen solve. Retrying with flexible solve.
Solving environment: unsuccessful attempt using repodata from current_repodata.json, retrying with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: done
## Package Plan ##
environment location: /root/miniconda3/envs/R4.3.1
added / updated specs:
- r-base=4.3.1
The following packages will be downloaded:
package | build
---------------------------|-----------------
_libgcc_mutex-0.1 | conda_forge 3 KB conda-forge
_openmp_mutex-4.5 | 2_gnu 23 KB conda-forge
_r-mutex-1.0.1 | anacondar_1 3 KB conda-forge
binutils_impl_linux-64-2.40| hf600244_0 5.2 MB conda-forge
bwidget-1.9.14 | ha770c72_1 120 KB conda-forge
bzip2-1.0.8 | h7f98852_4 484 KB conda-forge
c-ares-1.19.1 | hd590300_0 111 KB conda-forge
ca-certificates-2023.7.22 | hbcca054_0 146 KB conda-forge
cairo-1.16.0 | hbbf8b49_1016 1.1 MB conda-forge
curl-8.2.0 | hca28451_0 89 KB conda-forge
expat-2.5.0 | hcb278e6_1 134 KB conda-forge
font-ttf-dejavu-sans-mono-2.37| hab24e00_0 388 KB conda-forge
font-ttf-inconsolata-3.000 | h77eed37_0 94 KB conda-forge
font-ttf-source-code-pro-2.038| h77eed37_0 684 KB conda-forge
font-ttf-ubuntu-0.83 | hab24e00_0 1.9 MB conda-forge
fontconfig-2.14.2 | h14ed4e7_0 266 KB conda-forge
fonts-conda-ecosystem-1 | 0 4 KB conda-forge
fonts-conda-forge-1 | 0 4 KB conda-forge
freetype-2.12.1 | hca18f0e_1 611 KB conda-forge
fribidi-1.0.10 | h36c2ea0_0 112 KB conda-forge
gcc_impl_linux-64-13.1.0 | hc4be1a9_0 51.7 MB conda-forge
...................
.
.
.
如何用R
后面我们就首先激活环境
conda activate R4.3.1
然后R脚本命令行模式输入一个R就行。退出就输入q()就可以啦~
进入环境
source activate R4.2.2
conda activate R4.2.2
R命令行模式中安装R包,例如，安装ggplot2
(R4.3.1) root@DESKTOP-727JVLV:/home/ai_qiangyun# R
R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-conda-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> ^[[200~install.packages("ggplot2")~
Error: unexpected input in "
> install.packages("ggplot2")
--- Please select a CRAN mirror for use in this session ---
also installing the dependencies ‘lattice’, ‘colorspace’, ‘utf8’, ‘nlme’, ‘Matrix’, ‘farver’, ‘labeling’, ‘munsell’, ‘R6’, ‘RColorBrewer’, ‘viridisLite’, ‘fansi’, ‘magrittr’, ‘pillar’, ‘pkgconfig’, ‘cli’, ‘glue’, ‘gtable’, ‘isoband’, ‘lifecycle’, ‘MASS’, ‘mgcv’, ‘rlang’, ‘scales’, ‘tibble’, ‘vctrs’, ‘withr’
trying URL 'https://mirrors.e-ducation.cn/CRAN/src/contrib/lattice_0.21-8.tar.gz'
Content type 'application/x-gzip' length 589330 bytes (575 KB)
==================================================
downloaded 575 KB
trying URL 'https://mirrors.e-ducation.cn/CRAN/src/contrib/colorspace_2.1-0.tar.gz'
Content type 'application/x-gzip' length 2116339 bytes (2.0 MB)
==================================================
downloaded 2.0 MB
R包安装方法及安装记录
（1）对于一般的R包
install.packages("package name")
（2）对于Bioconductor的包（使用BiocManager安装）
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("package name")
注意：有时候可根据回显添加force = TRUE
安装实例
install.packages("stringi")
install.packages("ggplot2")
install.packages("pls")
install.packages("ggthemes")
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("clusterProfiler")
devtools::install_github("strengejacke/sjmisc")
devtools::install_github("kassambara/ggpubr")
devtools::install_github("cran/nloptr@1.2.2.3")
devtools::install_github("jokergoo/ComplexHeatmap")
devtools::install_github("https://github.com/cran/RbioRXN.git")
查看已经安装了的包
installed.packages()
> installed.packages()
Package LibPath
base "base" "/root/miniconda3/envs/R4.3.1/lib/R/library"
cli "cli" "/root/miniconda3/envs/R4.3.1/lib/R/library"
colorspace "colorspace" "/root/miniconda3/envs/R4.3.1/lib/R/library"
compiler "compiler" "/root/miniconda3/envs/R4.3.1/lib/R/library"
datasets "datasets" "/root/miniconda3/envs/R4.3.1/lib/R/library"
fansi "fansi" "/root/miniconda3/envs/R4.3.1/lib/R/library"
farver "farver" "/root/miniconda3/envs/R4.3.1/lib/R/library"
glue "glue" "/root/miniconda3/envs/R4.3.1/lib/R/library"
graphics "graphics" "/root/miniconda3/envs/R4.3.1/lib/R/library"
grDevices "grDevices" "/root/miniconda3/envs/R4.3.1/lib/R/library"
grid "grid" "/root/miniconda3/envs/R4.3.1/lib/R/library"
gtable "gtable" "/root/miniconda3/envs/R4.3.1/lib/R/library"
isoband "isoband" "/root/miniconda3/envs/R4.3.1/lib/R/library"
labeling "labeling" "/root/miniconda3/envs/R4.3.1/lib/R/library"
lattice "lattice" "/root/miniconda3/envs/R4.3.1/lib/R/library"
lifecycle "lifecycle" "/root/miniconda3/envs/R4.3.1/lib/R/library"
magrittr "magrittr" "/root/miniconda3/envs/R4.3.1/lib/R/library"
MASS "MASS" "/root/miniconda3/envs/R4.3.1/lib/R/library"
Matrix "Matrix" "/root/miniconda3/envs/R4.3.1/lib/R/library"
methods "methods" "/root/miniconda3/envs/R4.3.1/lib/R/library"
mgcv "mgcv" "/root/miniconda3/envs/R4.3.1/lib/R/library"
munsell "munsell" "/root/miniconda3/envs/R4.3.1/lib/R/library"
nlme "nlme" "/root/miniconda3/envs/R4.3.1/lib/R/library"
parallel "parallel" "/root/miniconda3/envs/R4.3.1/lib/R/library"
pkgconfig "pkgconfig" "/root/miniconda3/envs/R4.3.1/lib/R/library"
R6 "R6" "/root/miniconda3/envs/R4.3.1/lib/R/library"
RColorBrewer "RColorBrewer" "/root/miniconda3/envs/R4.3.1/lib/R/library"
rlang "rlang" "/root/miniconda3/envs/R4.3.1/lib/R/library"
scales "scales" "/root/miniconda3/envs/R4.3.1/lib/R/library"
splines "splines" "/root/miniconda3/envs/R4.3.1/lib/R/library"
stats "stats" "/root/miniconda3/envs/R4.3.1/lib/R/library"
stats4 "stats4" "/root/miniconda3/envs/R4.3.1/lib/R/library"
tcltk "tcltk" "/root/miniconda3/envs/R4.3.1/lib/R/library"
tools "tools" "/root/miniconda3/envs/R4.3.1/lib/R/library"
utf8 "utf8" "/root/miniconda3/envs/R4.3.1/lib/R/library"
utils "utils" "/root/miniconda3/envs/R4.3.1/lib/R/library"
vctrs "vctrs" "/root/miniconda3/envs/R4.3.1/lib/R/library"
viridisLite "viridisLite" "/root/miniconda3/envs/R4.3.1/lib/R/library"
withr "withr" "/root/miniconda3/envs/R4.3.1/lib/R/library"
Version Priority
base "4.3.1" "base"
cli "3.6.1" NA
colorspace "2.1-0" NA
compiler "4.3.1" "base"
datasets "4.3.1" "base"
fansi "1.0.4" NA
farver "2.1.1" NA
....
它会给出来，所有已安装的R包的详细信息，包括包名，路径，版本，优先级，建议等
提取已安装的包名：
as.data.frame(installed.packages())$Package
查看已加载的R包
这里的小括号不可以省略
(.packages())
可以看到，默认加载了7个基础包。
安装BIOManager遇到问题 ， 节点选择需要弹窗，但是无法弹出，加一行命令
chooseCRANmirror(graphics=FALSE)
运行结果如下：
> install.packages("BiocManager")
--- Please select a CRAN mirror for use in this session ---
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") :
[tcl] grab failed: window not viewable.
>
>
>
> chooseCRANmirror(graphics=FALSE)
Secure CRAN mirrors
1: 0-Cloud [https]
2: Australia (Canberra) [https]
3: Australia (Melbourne 1) [https]
4: Australia (Melbourne 2) [https]
5: Australia (Perth) [https]
6: Austria [https]
7: Belgium (Brussels) [https]
8: Brazil (PR) [https]
9: Brazil (SP 1) [https]
10: Brazil (SP 2) [https]
11: Bulgaria [https]
12: Canada (MB) [https]
13: Canada (ON) [https]
14: Chile (Santiago) [https]
15: China (Beijing 2) [https]
16: China (Beijing 3) [https]
17: China (Hefei) [https]
18: China (Hong Kong) [https]
19: China (Guangzhou) [https]
20: China (Jinan) [https]
21: China (Lanzhou) [https]
安装成功后就可以用BiocManager安装R包了
> library(BiocManager)
Bioconductor version 3.17 (BiocManager 1.30.21.1), R 4.3.1 (2023-06-16)
> BiocManager::install("limma")
'getOption("repos")' replaces Bioconductor standard repositories, see
'help("repositories", package = "BiocManager")' for details.
Replacement repositories:
CRAN: https://mirrors.e-ducation.cn/CRAN
Bioconductor version 3.17 (BiocManager 1.30.21.1), R 4.3.1 (2023-06-16)
Installing package(s) 'BiocVersion', 'limma'
trying URL 'https://bioconductor.org/packages/3.17/bioc/src/contrib/BiocVersion_3.17.1.tar.gz'
Content type 'application/x-gzip' length 971 bytes
==================================================
downloaded 971 bytes
参考：
Miniconda官网
Miniconda安装及使用--小白上路
清华开源Anaconda库
liunx如何把命令添加到环境变量，方便调用
Liunx系统安装R
R包安装方法及安装记录
R语言中如何查看已安装的R包
R语言 - Linux安装R语言扩展包相关命令（Windows雷同）
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