在我以为ClusterProfiler已经安装好的时候，又遇到了一些问题。 后遂记录一下这些问题和解决方法。

报错1：

BiocManager::install(“org.Hs.eg.db”)

Warning messages: 1: In file.copy(savedcopy, lib, recursive = TRUE) : 拷贝C:UsersxyfDocumentsRwin-library4.00LOCKgraphlayoutslibsx64graphlayouts.dll到C:UsersxyfDocumentsRwin-library4.0graphlayoutslibsx64graphlayouts.dll时出了问题：Permission denied 2: In file.copy(savedcopy, lib, recursive = TRUE) : 拷贝C:UsersxyfDocumentsRwin-library4.00LOCKigraphlibsx64igraph.dll到C:UsersxyfDocumentsRwin-library4.0igraphlibsx64igraph.dll时出了问题：Permission denied

在下载这个人类基因注释库的时候报错了。

解决：

我去查了一下，有人说是要到C:UsersxyfDocumentsRwin-library4.0 下，把graphlayouts，igraph 都删掉 参考下面这篇文章： 发现需要把R关掉，才能删，再打开R，再次下载这个包。

发现又报错了：

报错2：

Warning message: package(s) not installed when version(s) same as current; use force = TRUE to re-install: ‘org.Hs.eg.db’

解决：

按照它的提示， 把那句话加到命令里边：

BiocManager::install("org.Hs.eg.db",force =TRUE)
the downloaded binary packages are in
	C:UsersxyfAppDataLocalTempRtmpgVEIZEdownloaded_packages
org.Hs.eg.db
OrgDb object:
| DBSCHEMAVERSION: 2.1
| Db type: OrgDb
| Supporting package: AnnotationDbi
| DBSCHEMA: HUMAN_DB
| ORGANISM: Homo sapiens
| SPECIES: Human
| EGSOURCEDATE: 2020-Sep23
| EGSOURCENAME: Entrez Gene
| EGSOURCEURL: ftp://ftp.ncbi.nlm.nih.gov/gene/DATA
| CENTRALID: EG
| TAXID: 9606
| GOSOURCENAME: Gene Ontology
| GOSOURCEURL: http://current.geneontology.org/ontology/go-basic.obo
| GOSOURCEDATE: 2020-09-10
| GOEGSOURCEDATE: 2020-Sep23
| GOEGSOURCENAME: Entrez Gene
| GOEGSOURCEURL: ftp://ftp.ncbi.nlm.nih.gov/gene/DATA
| KEGGSOURCENAME: KEGG GENOME
| KEGGSOURCEURL: ftp://ftp.genome.jp/pub/kegg/genomes
| KEGGSOURCEDATE: 2011-Mar15
| GPSOURCENAME: UCSC Genome Bioinformatics (Homo sapiens)
| GPSOURCEURL: 
| GPSOURCEDATE: 2020-Aug27
| ENSOURCEDATE: 2020-Aug18
| ENSOURCENAME: Ensembl
| ENSOURCEURL: ftp://ftp.ensembl.org/pub/current_fasta
| UPSOURCENAME: Uniprot
| UPSOURCEURL: http://www.UniProt.org/
| UPSOURCEDATE: Mon Oct  5 00:18:02 2020
Please see: help(select) for usage information
#成功啦

由于在下载注释包的时候，移除了两个包：igraph 和graphlayouts。之后载入clusterprofiler的时候就出问题了。

报错3：

> library(clusterProfiler)
错误: package or namespace load failed for ‘clusterProfiler’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
 不存在叫‘igraph’这个名字的程辑包

library(clusterProfiler) 错误: package or namespace load failed for ‘clusterProfiler’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): 不存在叫‘igraph’这个名字的程辑包

尝试了两种安装方法都没用： biocmanager::install 找不到这个包。 然后：

> install.packages("igragh")
Installing package into ‘C:/Users/xyf/Documents/R/win-library/4.0’
(as ‘lib’ is unspecified)
Warning in install.packages :
  package ‘igragh’ is not available for this version of R
A version of this package for your version of R might be available elsewhere,
see the ideas at
https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages

发现也不行。

解决：

遂上网搜索答案，有人说是因为源，可以换一些镜像源，才能找到那个包。参考下面这篇： 于是：

install.packages(igraph,repos=http://cran.us.r-project.org)
install.packages(graphlayouts,repos=http://cran.us.r-project.org)

这两个在之前删掉的包就又下载好了。 Yes!!!