linux环境本地安装IOBR

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####-------1. IOBR有一系列安装包------####
## 1.1 利用library检查包是否已安装（in-house)
# 获取所有未安装的包，并将它们输出为 c() 的格式：
depens <- c('tibble', 'survival', 'survminer', 'limma', 'DESeq2', 'devtools',
            'limSolve', 'GSVA', 'e1071', 'preprocessCore', 'tidyHeatmap',
            'caret', 'glmnet', 'ppcor', 'timeROC', 'pracma', 'factoextra',
            'FactoMineR', 'WGCNA', 'patchwork', 'ggplot2', 'biomaRt',
            'ggpubr', 'ComplexHeatmap')

# 查找未安装的包
missing_pkgs <- depens[!sapply(depens, requireNamespace, quietly = TRUE)]

# 输出未安装的包为字符格式
if (length(missing_pkgs) > 0) {
  cat("未安装的包为:\n")
  cat("c(\"", paste(missing_pkgs, collapse = "\", \""), "\")\n", sep = "")
} else {
  cat("所有包都已安装。\n")
}
# 未安装的package包括：
depens_my <- c("limSolve", "GSVA", "preprocessCore", "tidyHeatmap", 
               "glmnet", "ppcor", "timeROC", "pracma", "WGCNA")

## 1.2 安装依赖包
# conda install conda-forge::r-limsolve #ok
# conda install bioconda::bioconductor-gsva # ok
# conda install bioconda::bioconductor-preprocesscore # ok
# install.packages("tidyHeatmap") # conda不行，使用install.packages
# install.packages("glmnet") #conda不行，使用install.packages
# conda install conda-forge::r-ppcor # oK
# conda install conda-forge::r-timeroc # ok 
# conda install conda-forge::r-pracma # ok
# conda install bioconda::r-wgcna # ok

# 1.3 批量library确认依赖包已安装好
for (pkg in depens_my) {
  if (!requireNamespace(pkg, quietly = TRUE)) {
    message(sprintf("未安装包: %s", pkg))
  } else {
    library(pkg, character.only = TRUE)
    message(sprintf("已加载包: %s", pkg))
  }
}

####-------2.IOBR包的安装------####
#官方推荐，但基本会因网络问题导致安装失败
if (!requireNamespace("IOBR", quietly = TRUE))
  devtools::install_github("IOBR/IOBR") 

# 此处我们采用本地安装的方式
# step1: https://github.com/IOBR/IOBR下载右上角的code全部文件-->IOBR-master.zip
# step2: unzip /public/home/usrs/Downloads/IOBR-master.zip
# step3: install.packages("/public/home/usrs/Downloads/IOBR-master/", repos = NULL, type = "source") 
    # 不从cran下载，而从source文件安装，运行后就安装ok了
Windows本地安装可以参考该教程：https://www.bilibili.com/video/BV1DvnZeoEsY/?vd_source=9f1fdf0f7a9028b3ed2b2aeb08b648b2
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