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')"
