GO,KEGG分析报错

起因
1.做GO富集分析的的时候出现：【Error in h(simpleError(msg, call)) : 在为'pairwise_termsim'函数选择方法时评估'x'参数出了错: simplify only applied to output from gsegO and enrichGO...】
换成"亚卡达力biu"的GO富集分析代码后能用，故搁置。

2.使用光叔的“clusterProfiler包”给做KEGG富集分析的时候，提示没有基因富集到匹配的通路：于是较上劲了

期间出现了 DOSE包版本不对，not available in this R version。。。一堆问题

后来将R升级了版本，才得以解决

下为一些代码记录斗争史

if(!requireNamespace("BiocManager",quietly = T))
  install.packages("BiocManager")
if(!requireNamespace("devtools",quietly = T))
  BiocManager::install("devtools")
if(!requireNamespace("igraph",quietly = T))
  BiocManager::install("igraph",force = TRUE)
if (!require("BiocManager", quietly = TRUE))
  install.packages("BiocManager")

BiocManager::install("HDO.db")
library(DOSE)
devtools::install_github('YuLab-SMU/DOSE')
installed_packages <- installed.packages()
installed_packages["DOSE", "Version"]

library(igraph)
if (!require("BiocManager", quietly = TRUE))
  install.packages("BiocManager")

BiocManager::install("GOSemSim")
install.packages("HDO.db")

if (!require("GOSemSim", quietly = TRUE))
  
  install.packages("GOSemSim")

BiocManager::install("clusterProfiler")

devtools::install_github("YuLab-SMU/DOSE")

devtools::install_github("YuLab-SMU/clusterProfiler")
library(clusterProfiler)

detach("package_name", unload = TRUE)
installed.packages()[,1]
getwd()
detach(igraph)
library(clusterProfiler)
install.packages("E:/R/R-4.1.3/library/clusterProfiler_4.8.3.tar.gz", repos = NULL, type = "source")
install.packages("E:/R/R-4.1.3/library/DOSE_3.26.1.tar.gz", repos = NULL, type = "source")
install.packages("E:/R/R-4.1.3/library/HDO.db_0.99.1.tar.gz", repos = NULL, type = "source")


install.packages('installr')
library(installr)
updateR()