Linux安装R和Python | Giftbear Notes

R 4.2.1安装

R下载地址: https://mirrors.ustc.edu.cn/CRAN/

安装依赖:

yum install libcurl-devel
yum install readline-devel
yum install libXt-devel
yum install bzip2-deve
yum install xz-devel.x86_64
yum install pcre-devel
yum install libpng-devel
yum install libtiff-devel
yum install libjpeg-turbo-devel
yum install pango-devel   

# Ubuntu X11 dependencies
sudo apt-get install libx11-dev
sudo apt-get install xorg-dev

编译安装:

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./configure --prefix=/opt/software/R --enable-R-shlib=yes --with-pcre1 --with-libpng --with-x
make
make install

R安装包:

安装CRAN下载的包: install.packages("BiocManager")
*下载地址(可以下载某个版本的包): https://cran.r-project.org/src/contrib/Archive/

安装生信相关的包:

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if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("SingleR")

*下载某个Bioconductor版本包的地址: http://bioconductor.org/about/release-announcements/

安装下载的包(当安装的包需要更高的gcc版本时可以下载低版本的包):
install.packages("/opt/KEGG.db_1.0.tar.gz",repos=NULL)

安装指定地址的包:

1 2	url <- "https://cran.r-project.org/src/contrib/Archive/rvcheck/rvcheck_0.1.8.tar.gz" install.packages(url, repos = NULL, type = "source")

通过devtools安装:

install.packages("devtools")
library(devtools)
install_version("edgeR", version = "3.14.0")
devtools::install_github("davidaknowles/leafcutter/leafcutter")

通过remotes安装:

1 2	install.packages("remotes") remotes::install_github("LTLA/celldex")

包的管理:

# 查看已安装的包
installed.packages()
# 查看包的版本
packageVersion("spatstat.core")
# 删除包
remove.packages("SingleR")

Python 3.9.14安装

Python下载地址: https://www.python.org/downloads/

安装依赖:

yum install libffi-devel
yum install tcl-devel
yum install tk-devel
yum install sqlite-devel
yum install gdbm-devel

编译安装:

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./configure --prefix=/opt/software/python
make
make install

Python安装包:
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python3 -m pip install numpy
python3 -m pip install pandas==2.0.1
pip install numpy.whl
*下载python包地址(当下载速度慢或高版本编译出错时选择):
https://pypi.tuna.tsinghua.edu.cn/simple/
https://www.lfd.uci.edu/~gohlke/pythonlibs/