seurat软件安装随笔R包的通用安装方法

最新推荐文章于 2025-05-10 10:27:43 发布

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最新推荐文章于 2025-05-10 10:27:43 发布

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文章标签：随笔

本文链接：https://blog.youkuaiyun.com/qq_41493990/article/details/81335005

本文档详细记录了在R环境中安装seurat软件及其依赖包的过程，包括遇到的gcc版本不匹配和libpng16.so缺失的问题。通过模块加载解决gcc版本问题，配置环境变量解决libpng问题。然而，在安装clusterExperiment等包时，遇到了依赖xml2包的错误，由于缺少libicui18n.so.58文件，导致多个包安装失败。尝试yum安装libxml2和libxslt，但biocLite安装xm12未成功，需要进一步寻找解决办法。

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https://personal.broadinstitute.org/rahuls/seurat/InstallSeurat.html

R安装命令1
source(“https://bioconductor.org/biocLite.R“)
biocLite(“Seurat”)

R安装命令2
library(devtools)
install_github(“epurdom？？？/包名”)

R 安装命令3
install.packages(“包名”)

R 安装命令4 批量安装
install.packages(c(“包名”, “包名”, “Hmisc”, “reshape”, “gplots”

seurat解决方法
尝试bioclite安装提示错误gcc版本不对
module load gcc/5.4.0

在/etc/profile.d/

还提示缺少libpng16.so
安装libpng 教程 https://blog.youkuaiyun.com/pkokocl/article/details/78756422
在bioclite安装成功。
module环境变量配置
cd /share/app/Modules/3.2.10/modulefiles/R //进入module下R版本管理目录

vim 3.4.3
添加规则使得在使用R3.4.3时候会加载libpng16的库。
prepend-path PATH /share/app/otherapp/libpng/bin
prepend-path LD_LIBRARY_PATH /share/app/otherapp/libpng/lib

目前需要安装的软件
clusterExperiment 群实验?

source(“https://bioconductor.org/biocLite.R“)
biocLite(“clusterExperiment”)
报错提示

Error : /tmp/RtmpxyZ1bo/R.INSTALL3330647f2c9c/xml2/man/read_xml.Rd:47: unable to load shared object ‘/home/support/R/x86_64-pc-linux-gnu-library/3.4/xml2/libs/xml2.so’:
libicui18n.so.58: cannot open shared object file: No such file or directory
ERROR: installing Rd objects failed for package ‘xml2’
* removing ‘/home/support/R/x86_64-pc-linux-gnu-library/3.4/xml2’
ERROR: dependency ‘xml2’ is not available for package ‘solrium’
* removing ‘/home/support/R/x86_64-pc-linux-gnu-library/3.4/solrium’
ERROR: dependency ‘xml2’ is not available for package ‘bold’
* removing ‘/home/support/R/x86_64-pc-linux-gnu-library/3.4/bold’
ERROR: dependency ‘xml2’ is not available for package ‘natserv’
* removing ‘/home/support/R/x86_64-pc-linux-gnu-library/3.4/natserv’
ERROR: dependency ‘xml2’ is not available for package ‘wikitaxa’
* removing ‘/home/support/R/x86_64-pc-linux-gnu-library/3.4/wikitaxa’
ERROR: dependency ‘solrium’ is not available for package ‘ritis’
* removing ‘/home/support/R/x86_64-pc-linux-gnu-library/3.4/ritis’
ERROR: dependencies ‘xml2’, ‘bold’, ‘ritis’, ‘natserv’, ‘wikitaxa’ are not available for package ‘taxize’
* removing ‘/home/support/R/x86_64-pc-linux-gnu-library/3.4/taxize’
ERROR: dependency ‘taxize’ is not available for package ‘RNeXML’
* removing ‘/home/support/R/x86_64-pc-linux-gnu-library/3.4/RNeXML’
ERROR: dependency ‘RNeXML’ is not available for package ‘phylobase’
* removing ‘/home/support/R/x86_64-pc-linux-gnu-library/3.4/phylobase’
ERROR: dependency ‘phylobase’ is not available for package ‘clusterExperiment’
* removing ‘/home/support/R/x86_64-pc-linux-gnu-library/3.4/clusterExperiment’