细胞通讯--Liana安装

###-----liana安装--------####

##------ 1 github官方安装 liana， 失败
# remotes::install_github("saezlab/liana") 


##--------2 手动下载，本地安装，失败
# 手动下载
# https://ghfast.top/ #下载地址
# https://github.com/saezlab/liana/archive/refs/heads/master.zip #输入的网址
# unzip ./liana-master.zip

# 本地安装
install.packages("/public/home/chidm/Downloads/liana-master", repos = NULL, type = "source")
# 注意在Conda 环境中直接用 install.packages() 安装 R 包，影响conda环境，而且不会提醒，导致环境崩溃！！！！
### 影响1：触发编译，安装系统依赖（比如 C++ 头文件）
### 影响2：更新 Conda 环境中的 R 包（有时自动装依赖会冲突）
### 这里会直接影响SingleCellExperiment，导致我的seurat环境崩溃


##-------3. 新建conda环境liana_env，手动安装

conda create -n liana_env r-base=4.2 -y
conda activate liana_env
# 安装 BiocManager
conda install conda-forge::r-biocmanager

# 设置install.packages清华镜像
options(repos = c(CRAN = "https://mirrors.tuna.tsinghua.edu.cn/CRAN/"))
install.packages("remotes")

# 安装 liana 依赖包---BiocManager，失败
# BiocManager::install(c("OmnipathR", "scran", "scater","basilisk", "basilisk.utils")) 

# 安装 liana 依赖包---conda 进行安装，成功
conda install bioconda::bioconductor-omnipathr
conda install bioconda::bioconductor-scran
conda install bioconda::bioconductor-scater
conda install bioconda::bioconductor-basilisk
conda install bioconda::bioconductor-basilisk.utils

library("OmnipathR")
library("scran")
library("scater")
library("basilisk")
library("basilisk.utils")
library(SeuratObject)
library(complexheatmap)

# 再次本地安装liana包
install.packages("/public/home/chidm/Downloads/liana-master", repos = NULL, type = "source")
# ERROR: dependencies ‘SeuratObject’, ‘ComplexHeatmap’ are not available for package ‘liana’

# conda install conda-forge::r-seuratobject
# conda install bioconda::bioconductor-complexheatmap
# conda install -n liana_env -c conda-forge libicu=58
# 加载测试
library(liana)