I hope others don't have to continue struggling in the software environment.

[user-tq]

# R 4.3.0
           包名    版本            安装位置
1      optparse   1.7.5 /app/BugBase/R_lib/
2      reshape2   1.4.4 /app/BugBase/R_lib/
3          plyr   1.8.8 /app/BugBase/R_lib/
4  RColorBrewer   1.1-3 /app/BugBase/R_lib/
5     gridExtra     2.3 /app/BugBase/R_lib/
6       ggplot2   3.2.1 /app/BugBase/R_lib/
7      beeswarm   0.4.0 /app/BugBase/R_lib/
8          plyr   1.8.8 /app/BugBase/R_lib/
9       RJSONIO 1.3-1.8 /app/BugBase/R_lib/
10       Matrix   1.6-1 /app/BugBase/R_lib/
11     labeling   0.4.2 /app/BugBase/R_lib/
12       digest  0.6.31 /app/BugBase/R_lib/
13         biom  0.3.12 /app/BugBase/R_lib/
14       Matrix   1.6-1 /app/BugBase/R_lib/

[user-tq]

For those who are looking for container installations, I have created an image of the apptainer. To be honest, I'm not good at this and I haven't fixed some R package versions, at least for now it's available.

singularity pull --arch amd64 library://tanqiang/bugbase/bugbase.0.1:latest

You can also make modifications based on my apptainer def file

Bootstrap: docker
From: rocker/r-ver:4.3.0

%files
    # 本地文件复制（可选）
    # 如需添加本地文件可在此处配置

%environment
    export BUGBASE_PATH=/app/BugBase
    export PATH=$PATH:/app/BugBase/bin
    export LC_ALL=C.UTF-8
    export LANG=C.UTF-8

%post
    # 基础系统配置
    apt-get update && apt-get install -y \
        libxml2-dev \
        libssl-dev \
        libcurl4-openssl-dev \
        wget \
        unzip \
        git \
        && rm -rf /var/lib/apt/lists/*

    # 设置工作目录
    mkdir -p /app
    cd /app

    # 克隆仓库
    git clone https://github.com/knights-lab/BugBase.git
    
    Rscript  -e "install.packages('remotes', repos='http://cran.rstudio.com/')"
    Rscript  -e  "install.packages('withr', repos='http://cran.rstudio.com/')"
    Rscript  -e  "install.packages('farver', repos='http://cran.rstudio.com/')"
    Rscript  -e  "remotes::install_version('ggplot2', version='3.2.1', lib='/app/BugBase/R_lib', dependencies=TRUE)"
    Rscript  -e  "library(ggplot2,lib.loc='/app/BugBase/R_lib')"
    Rscript  -e  "remotes::install_version('ggplot2', version='3.2.1', lib='/app/BugBase/R_lib', dependencies=TRUE)"
    #Rscript  -e "remotes::install_version('Matrix', version='1.6_1', lib='/app/BugBase/R_lib', dependencies=TRUE)"
    Rscript -e "install.packages('https://cran.r-project.org/src/contrib/Archive/Matrix/Matrix_1.6-1.tar.gz', \
    repos=NULL, type='source',lib='/app/BugBase/R_lib')"
    Rscript  -e "remotes::install_version('biom', version='0.3.12', lib='/app/BugBase/R_lib', dependencies=TRUE)"

    export BUGBASE_PATH=/app/BugBase
    BugBase/bin/run.bugbase.r -h
    # 修复权限（Singularity不需要单独用户）
    chmod -R 755 /app

%runscript
    exec Rscript "${BUGBASE_PATH}/bin/run.bugbase.r" "$@"