使用devtools安装monocle3

1. 源码编译R

环境：
module purge
module load compiler/gcc/7.3.1

源码编译R
./configure --with-pcre1 --prefix=/path/to/install-R
make
make install

vim env-R.sh
export PATH=/path/to/install-R/bin: $PATH
export LD_LIBRARY_PATH=/path/to/install-R/lib: $LD_LIBRARY_PATH
source env-R.sh

2. 安装devtools

在刚刚安装R的环境下
再module load compiler/cmake/3.23.1
（安装devtools下载的包需要高版本的cmake）

启动R，R

install.packages(“devtools”)

会下载下来很多包，然后依次安装这些包，有的包R下载一次不下来，如果是网络中断而出现的报错，重复这个命令。重复多次，有的包R还是下载不下来，复制网址wget到集群上指定 路径安装会比较方便。
例如stringi这个包，R下载不下来，后还报ICUDM的错，就可以install的时候指定包的位置和ICUDM的位置：

install.packages(“/work/home/xiaxx/packages/monocle3/stringi_1.7.8.tar.gz”,repo=NULL,type=“source”,configure.vars=“ICUDT_DIR=/work/home/xiaxx/packages/monocle3”)

3. 安装monocle3需要的依赖

devtools::install_github(‘cole-trapnell-lab/monocle3’)

（115个，好多依赖，好吓人）
静静等待，多次重复，最后还剩4个包没装好

依次查看每个包编不过的原因

（1）units报错解决办法 — 安装udunits-2.2.20

找不到libudunits2.so，百度搜下这个包
wget https://download-ib01.fedoraproject.org/pub/epel/7/SRPMS/Packages/u/udunits2-2.2.20-2.el7.src.rpm
集群的普通用户使用
rpm2cpio xxx.rpm |cpio -idvm后
是一个tar.gz安装包，解压进入目录

./configure --prefix=/work/home/xiaxx/packages/monocle3/udunits-2.2.20
make
make install

安装好后指定环境：
export UDUNITS2_INCLUDE=/work/home/xiaxx/packages/monocle3/udunits-2.2.20/include
export UDUNITS2_LIBS=/work/home/xiaxx/packages/monocle3/udunits-2.2.20/lib
export LD_LIBRARY_PATH=/work/home/xiaxx/packages/monocle3/udunits-2.2.20/lib: $LD_LIBRARY_PATH
export PATH=/work/home/xiaxx/packages/monocle3/udunits-2.2.20/bin: $PATH

（2）terra报错解决办法 ---- gdal3.4.0及其依赖（proj-6.3.0）及其依赖的依赖（sqlite3.40.0）的编译、和geos3.9.3编译

版本很重要，不然后续编译sf会报错

编译terra发现缺少gdal环境和geos环境，而编译gdal需要proj，编译proj需要sqlite3。

a. 先编译sqlite3

在sqlite3.c里加上这一行
#define SQLITE_ENABLE_COLUMN_METADATA 1

否则在后续编译gdal的时候会出现这个报错：

libgdal.so: undefined reference to ‘sqlite3_column_origin_name’
libgdal.so: undefined reference to ‘sqlite3_column_table_name’

./configure --prefix=/work/home/xiaxx/packages/monocle3/sqlite-version-3.40.0 --disable-tcl
make
make install

设置环境变量
export INCLUDE=/work/home/xiaxx/packages/monocle3/sqlite-version-3.40.0/bin: $INCLUDE
export LD_LIBRARY_PATH=/work/home/xiaxx/packages/monocle3/sqlite-version-3.40.0/lib: $LD_LIBRARY_PATH
export PATH=/work/home/ac947yas04/package/sqlite-version-3.40.0/bin: $PATH
export PKG_CONFIG_PATH=/work/home/xiaxx/packages/monocle3/sqlite-version-3.40.0/lib/pkgconfig: $PKG_CONFIG_PATH

b.再编译proj

./configure --prefix=/work/home/xiaxx/packages/monocle3/proj-6.3.0/build
make
make install
设置环境变量：
export INCLUDE=/work/home/xiaxx/packages/monocle3/proj-6.3.0/build/include: $INCLUDE
export LD_LIBRARY_PATH=/work/home/xiaxx/packages/monocle3/proj-6.3.0/build/lib: $LD_LIBRARY_PATH
export PATH=/work/home/xiaxx/packages/monocle3/proj-6.3.0/build/bin: $PATH
export PKG_CONFIG_PATH=/work/home/xiaxx/packages/monocle3/proj-6.3.0/build/lib/pkgconfig: $PKG_CONFIG_PATH

c.再编译gdal

./configure --prefix=/work/home/xiaxx/packages/monocle3/gdal-3.4.0/build --with-proj=/work/home/xiaxx/packages/monocle3/proj-6.3.0/build （指定下proj路径，只设置环境变量识别不到）
make
make install
设置环境变量：
export INCLUDE=/work/home/xiaxx/packages/monocle3/gdal-3.4.0/buid/include: $INCLUDE
export LD_LIBRARY_PATH=/work/home/xiaxx/packages/monocle3/gdal-3.4.0/buid/lib: $LD_LIBRARY_PATH
export PATH=/work/home/xiaxx/packages/monocle3/gdal-3.4.0/buid/bin: $PATH
export PKG_CONFIG_PATH=/work/home/xiaxx/packages/monocle3/gdal-3.4.0/buid/lib/pkgconfig: $PKG_CONFIG_PATH

d.编译geos

./configure --prefix=/work/home/xiaxx/packages/monocle3/geos-3.9.3/build
make
make install
设置环境变量：
export INCLUDE=/work/home/xiaxx/packages/monocle3/geeos-3.9.3/build/include: $INCLUDE
export LD_LIBRARY_PATH=/work/home/xiaxx/packages/monocle3/geos-3.9.3/build/lib: $LD_LIBRARY_PATH
export PATH=/work/home/xiaxx/packages/monocle3/geos-3.9.3/build/bin: $PATH
export PKG_CONFIG_PATH=/work/home/xiaxx/packages/monocle3/geos-3.9.3/build/lib/pkgconfig: $PKG_CONFIG_PATH

（3）sf – 也是缺少gdal库和geos库

（4）spdep – 依赖于sf

4. 解决缺库问题后继续安装monocles3

启动R，R
devtools::install_github(‘cole-trapnell-lab/monocle3’)

至此，安装完成