seurat软件安装 随笔R包的通用安装方法
相关文档
http://satijalab.org/seurat/devinstall.html
http://satijalab.org/seurat/install.html
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.csdn.net/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’
关键词
libicui18n.so.58 没有
xm12 没有
yum install libxml2 libxslt
biocLite(“xm12”)失败，并不能用biocLite安装
尝试查找相关xm12资料