linux学习100篇13:安装clusterProfiler

安装clusterProfiler

> options()$repos 
                         CRAN 
"https://cloud.r-project.org" 
> options()$BioC_mirror
NULL
> #options(BioC_mirror="https://mirrors.ustc.edu.cn/bioc/")
> options(BioC_mirror="http://mirrors.tuna.tsinghua.edu.cn/bioconductor/")
> options("repos" = c(CRAN="https://mirrors.tuna.tsinghua.edu.cn/CRAN/"))
> options()$repos 
                                        CRAN 
"https://mirrors.tuna.tsinghua.edu.cn/CRAN/" 
> options()$BioC_mirror
[1] "http://mirrors.tuna.tsinghua.edu.cn/bioconductor/"
> BiocManager::install("clusterProfiler")
'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories'
for details

replacement repositories:
    CRAN: https://mirrors.tuna.tsinghua.edu.cn/CRAN/

Bioconductor version 3.13 (BiocManager 1.30.15), R 4.1.0 (2021-05-18)
Installation paths not writeable, unable to update packages
  path: /usr/lib/R/library
  packages:
    spatial
Warning message:
package(s) not installed when version(s) same as current; use `force = TRUE` to
  re-install: 'clusterProfiler' 
> #BiocManager::install("clusterProfiler")
> # BiocManager::install("org.Mm.eg.db")
> # BiocManager::install("org.Hs.eg.db")
> library("clusterProfiler")

clusterProfiler v4.0.0  For help: https://guangchuangyu.github.io/software/clusterProfiler

If you use clusterProfiler in published research, please cite:
Guangchuang Yu, Li-Gen Wang, Yanyan Han, Qing-Yu He. clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS: A Journal of Integrative Biology. 2012, 16(5):284-287.

Attaching package: ‘clusterProfiler’

The following object is masked from ‘package:stats’:

    filter

>