R语言设置用户库

1. 注意不要用校园网
2. 注意要到官网上下载，Ubuntu上下载的版本比较古老

① 设置用户库路径（一次性）

# 以 R 4.5.x 为例（用 Rscript -e 'R.version$major; R.version$minor' 确认版本）
mkdir -p ~/R/4.5

# 让 R 每次启动都用你的用户库
printf 'R_LIBS_USER="~/R/4.5"\n' >> ~/.Renviron
cat >> ~/.Rprofile <<'EOF'
userlib <- Sys.getenv("R_LIBS_USER")
if (nzchar(userlib) && dir.exists(userlib)) .libPaths(c(userlib, .libPaths()))
EOF

# 验证路径生效
Rscript -e 'writeLines(.libPaths())'
Rscript -e 'writeLines(Sys.getenv("R_LIBS_USER"))'

② 安装依赖（全部装到你的用户库）

• ggtree / treeio所需要的图形依赖

sudo apt update
sudo apt install -y build-essential libcurl4-openssl-dev libssl-dev libxml2-dev \
                    libgit2-dev libfontconfig1-dev libfreetype6-dev libharfbuzz-dev \
                    libfribidi-dev libpng-dev libtiff5-dev libjpeg-dev

③R中安装

## 0) 用户库优先
dir.create(Sys.getenv("R_LIBS_USER"), showWarnings = FALSE, recursive = TRUE)
.libPaths(c(Sys.getenv("R_LIBS_USER"), .libPaths()))

## 1) 下载设置：官方仓库（或改成中科大均可）
options(download.file.method = "libcurl")
options(timeout = max(600, getOption("timeout")))
options(repos = c(CRAN = "https://cloud.r-project.org"))
options(BioC_mirror = NULL)

## 若要中科大，请改为：
options(repos = c(CRAN = "https://mirrors.ustc.edu.cn/CRAN/"))
# options(BioC_mirror = "https://mirrors.ustc.edu.cn/bioc/")

## 2) 先把 CRAN 侧关键依赖更新到用户库
install.packages(
  c("cli","fansi","glue","rlang","vctrs","lifecycle","tidyselect","scales",
    "systemfonts","textshaping","gdtools","ragg","pkgconfig","Rcpp","pillar","pheatmap", "reshape2","viridis"),
  lib = Sys.getenv("R_LIBS_USER")
)

install.packages(
  c("readr","dplyr","tidyr","tibble","jsonlite","magick","ggVennDiagram","ggvenn"),
  lib = Sys.getenv("R_LIBS_USER")
)

## 3) 先装 Bioc 侧依赖，再装 ggtree
if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")
BiocManager::install(c("yulab.utils","tidytree","treeio","ggtree","AnnotationDbi","GO.db","DESeq2","tximport","apeglm","ggtreeExtra","deeptime","tidyverse","clusterProfiler"),
                     ask = FALSE, update = TRUE, lib = Sys.getenv("R_LIBS_USER"))
                     

if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")
BiocManager::install(c("DESeq2","tximport","apeglm"),
                     ask = FALSE, update = TRUE, lib = Sys.getenv("R_LIBS_USER"))
                     
if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")
BiocManager::install(c("deeptime"),
                     ask = FALSE, update = TRUE, lib = Sys.getenv("R_LIBS_USER"))

## 4) 验证加载
suppressPackageStartupMessages({
  library(ggtree)
  library(treeio)
})
packageVersion("ggtree")

• 安装genespace

if (!requireNamespace("devtools", quietly = TRUE)) install.packages("devtools")
if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")

BiocManager::install(c("Biostrings", "rtracklayer"))

devtools::install_github("jtlovell/GENESPACE")