首先按照官网上的代码进行安装

devtools::install_github('cole-trapnell-lab/leidenbase')
devtools::install_github('cole-trapnell-lab/monocle3')

在最后一步安装运行以上两行代码时出现了问题：

checking udunits2.h usability... no
checking udunits2.h presence... no
checking for udunits2.h... no
checking udunits2/udunits2.h usability... no
checking udunits2/udunits2.h presence... no
checking for udunits2/udunits2.h... no
checking for ut_read_xml in -ludunits2... no
configure: error: in `/tmp/RtmphiMa1k/R.INSTALL23ef48d1156/units':
configure: error: 

使用yum在CentOS7上运行：

sudo yum install udunits2-devel

仍然报错：

没有可用软件包 udunits2-devel。

yum没有找到对应依赖包，更新epel第三方软件库，运行命令：

yum install -y epel-release

然后再在terminal和R中分别执行以下两行代码就可以了：

sudo yum install udunits2-devel
install.packages(units)

继续安装monocle3，又报错：

* installing *source* package ‘sf’ ...
** package ‘sf’ successfully unpacked and MD5 sums checked
** using staged installation
configure: CC: gcc -std=gnu99
configure: CXX: g++ -std=gnu++11
checking for gdal-config... no
no
configure: error: gdal-config not found or not executable.
ERROR: configuration failed for package ‘sf’
* removing ‘/local/txm/R/x86_64-pc-linux-gnu-library/4.0/sf’
Warning in install.packages :
  installation of package ‘sf’ had non-zero exit status

提示sf包安装失败，原因是gdal没有安装，在terminal里面执行

sudo yum install gdal gdal-devel 

发现yum最高只能安装1.11.4的gdal，于是尝试手动安装，参考以下博客：https://www.jianshu.com/p/3173513d16a5
geos，proj等包的安装都比较顺利，唯独gdal要么是装不上，要么是装上之后sf还是无法安装，折腾这玩意儿花了劳资3天的时间，参考了无数博客，最后成功的代码如下：

# 在terminal里安装gdal2.4.4
tar -zxvf gdal-2.4.4.tar.gz
cd gdal-2.4.4
./configure --with-gdal-ver=T --prefix=/usr/local --with-geos=/usr/local/bin     # 将软件安装在/usr/local
make
sudo make install
ldconfig
/usr/local/bin/gdalinfo --version     # GDAL 2.4.4, released 2020/01/08 表明安装成功

# 设置环境变量PKG_CONFIG_PATH
vi ~/.bash_profile       
# 在末尾添加下面两行：
PKG_CONFIG_PATH=/usr/lib/pkgconfig:/usr/local/lib/pkgconfig
export PKG_CONFIG_PATH
# 最后重启bash，让环境变量生效：
source ～/.bash_profile

最后，在R中安装sf包和monocle3

install.packages("sf", configure.args = "--with-gdal-config=/usr/local/bin/gdal-config --with-proj-include=/usr/local/include/ --with-proj-lib=/usr/local/lib/")
library(devtools)
devtools::install_github('cole-trapnell-lab/monocle3')

泪目了家人们

完结撒花，泪目

参考

https://stackoverflow.com/questions/50362201/udunits2-r-install-udunits2-h-not-found
https://blog.csdn.net/qq_46480020/article/details/111940512
https://www.omicsclass.com/article/1349
https://github.com/r-spatial/sf/issues/1158