R语言5_安装Giotto

环境Ubuntu22/20, R4.1. 已开启科学上网。

第一步，更新服务器环境，进入终端，键入如下命令，

apt-get update
apt install libcurl4-openssl-dev libssl-dev libxml2-dev libcairo2-dev libgtk-3-dev libhdf5-dev libmagick9-dev libcairo2-dev libxt-dev libgsl-dev libgdal-dev
# linux repo 	:: R repo
# ==============================
# libcairo2-dev :: systemfonts
# libgtk 		:: textshaping
# libhdf5-dev 	:: hdf5r
# libmagick9-dev:: magick
# libcairo2-dev libxt-dev :: Cairo
# libgsl-dev	:: RcppGSL
# libgdal-dev	:: gdal; terra

# below all for complete R repo :: magick
apt install libmagick  -dev librsvg2-dev libwebp-dev libpoppler-cpp-dev libtesseract-dev libleptonica-dev tesseract-ocr-eng libfftw3-dev cargo # r-cran-rgdal 

# below all for complete R repo :: car; FactoMineR
apt install liblapack-dev liblapack3 libopenblas-base libopenblas-dev libnlopt-dev

第二步，装CRAN上的包。进入R语言交互环境，键入如下命令，：

# Bayes
install.packages("scales")
install.packages("ggplot2")
install.packages("ggbeeswarm")
install.packages("viridis")
install.packages("pheatmap")
install.packages("Cairo")
install.packages("ggrepel")
install.packages("systemfonts")
install.packages("textshaping")
install.packages("ragg")
install.packages("ggrastr")
install.packages("systemfonts")

# Giotto
install.packages("gmp")
install.packages("ClusterR")
install.packages('devtools')
install.packages('remotes')
install.packages("magick")
install.packages("RcppGSL")
install.packages("FactoMineR")

第三步，装BiocManager上的包。进入R语言交互环境，键入如下命令，

# Bayes
if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")    
BiocManager::install("Rhdf5lib")	# need apt install libhdf5-dev
BiocManager::install("rhdf5filters")
BiocManager::install("GenomeInfoDbData")	# maybe need a VPN since it is big, about 10mB. Less than 5mB can be download without VPN.
BiocManager::install("BayesSpace")

# Giotto
if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("ComplexHeatmap")
Rfast
RcppGSL
RcppZiggurat

第四步，装GIthub上的包。进入R语言交互环境，键入如下命令安装Giotto，（推荐）

library(remotes)
remotes::install_github("RubD/Giotto") 

或者不用C编译器装Giotto，（可选）

# compilation problems (gfortran)?
# this version does not require C compilation
remotes::install_github("RubD/Giotto@cless") 

测试，

library(Giotto)

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