options("repos"="https://mirrors.ustc.edu.cn/CRAN/")
if(!require("BiocManager")) install.packages("BiocManager",update = F,ask = F)
options(BioC_mirror="https://mirrors.ustc.edu.cn/bioc/")
cran_packages <- c('tidyr',
'tibble',
'dplyr',
'stringr',
'ggplot2',
'ggpubr',
'factoextra',
'FactoMineR',
'WGCNA')
Biocductor_packages <- c('GEOquery',
'hgu133plus2.db',
"KEGG.db",
"limma",
"impute",
"GSEABase",
"GSVA",
"clusterProfiler",
#"genefu",
"org.Hs.eg.db",
"preprocessCore",
"hugene10sttranscriptcluster.db")
for (pkg in cran_packages){
if (! require(pkg,character.only=T) ) {
install.packages(pkg,ask = F,update = F)
require(pkg,character.only=T)
}
}
~~~R
for (pkg in Biocductor_packages){
if (! require(pkg,character.only=T) ) {
BiocManager::install(pkg,ask = F,update = F)
require(pkg,character.only=T)
}
}
#前面的所有提示和报错都先不要管。主要看这里
for (pkg in c(Biocductor_packages,cran_packages)){
require(pkg,character.only=T)
}
哪个报错,就回去安装哪个。如果你没有安装xx包,却提示你xx包不存在,这也正常,是因为复杂的依赖关系,缺啥补啥。
网友评论