R语言及一些包的安装

若安装失败，可以在安装日志中搜索ANTICONF，ANTICONF下面有提示如何解决失败

  

查看已经安装了哪些包：.packages(all.available = T)

1)dnf install R
2) R
install.packages("getopt")
.packages(all.available = T)
install.packages("BiocManager")
3)
dnf install openssl-devel
4)
BiocManager::install("org.Mm.eg.db")
BiocManager::install("org.Hs.eg.db")
5)
BiocManager::install("clusterProfiler")
packageVersion("rvcheck")
remove.packages("rvcheck")
packageurl <- "https://cran.r-project.org/src/contrib/Archive/rvcheck/rvcheck_0.1.8.tar.gz"
install.packages(packageurl, repos=NULL, type="source")
BiocManager::install("clusterProfiler")

 

1)dnf install R
2)R -e "install.packages('getopt', repos='https://cran.r-project.org/')"
3)R -e "install.packages('BiocManager', repos='https://cran.r-project.org/')"
4)dnf install -y openssl-devel
5)R -e "BiocManager::install('org.Mm.eg.db')"
6)R -e "BiocManager::install('org.Hs.eg.db')"
7)R -e "BiocManager::install('clusterProfiler')"
8)R -e "remove.packages('rvcheck')"

9)R -e "install.packages('https://cran.r-project.org/src/contrib/Archive/rvcheck/rvcheck_0.1.8.tar.gz', repos=NULL, type='source')"

10)R -e "BiocManager::install('clusterProfiler')"

 由于dnf安装的最新版本还是老，所以源码安装

参考资料：https://zhuanlan.zhihu.com/p/419947930   
我在make时报错了：conftest.c:1:10: fatal error: jni.h: No such file or directory，在网上没有合适的解决方案，后来发现上面装的老版本镜像里有jni.h，
于是直接把老版本里的拷贝到了当前镜像的目录里，再make就成功了，后面的步骤也都成功了

docker cp install_r24:/usr/lib/jvm/java-11-openjdk-11.0.15.0.10-1.fc34.x86_64/include ./
docker cp include install_r_source:/usr/lib/jvm/java-11-openjdk-11.0.15.0.10-1.fc34.x86_64/
===== 
dnf install yum-utils
yum-builddep R
mkdir -p /opt/R/
 ./configure --prefix=/opt/R/4.1.1 --enable-memory-profiling --enable-R-shlib --with-blas --with-lapack
make
#加一步拷贝include:
make install
make clean #清理残余
ls /opt/R/4.1.1/
 ln -s /opt/R/4.1.1/bin/R  /usr/local/bin/R
  ln -s /opt/R/4.1.1/bin/Rscript  /usr/local/bin/Rscript

 ==============

# 安装 c("Seurat", "tidyverse", "extrafont", "ggplot2", "data.table")和BiocManager::install("monocle")


dnf install -y libcurl-devel R-rgeos
R -e "install.packages('httr',repos='https://cran.r-project.org/')"  
R -e "install.packages('plotly',repos='https://cran.r-project.org/')"
 R -e "install.packages('SeuratObject',repos='https://cran.r-project.org/')"
 R -e "install.packages('Seurat',repos='https://cran.r-project.org/')" 
 R -e "install.packages('tidyverse',repos='https://cran.r-project.org/')" 
 R -e "install.packages('extrafont',repos='https://cran.r-project.org/')" 
 R -e "install.packages('ggplot2',repos='https://cran.r-project.org/')"
 R -e "install.packages('data.table',repos='https://cran.r-project.org/')"
 R -e "BiocManager::install('monocle')"