探序基因肿瘤研究院 整理
作者系统为centos
R中运行：
devtools::install_github('cole-trapnell-lab/monocle3')
遇到问题：
── R CMD build ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
✔ checking for file ‘/tmp/Rtmprjj0OV/remotes1512fe2099eb60/cole-trapnell-lab-monocle3-98402ed/DESCRIPTION’ ...
─ preparing ‘monocle3’:
✔ checking DESCRIPTION meta-information ...
─ cleaning src
─ checking for LF line-endings in source and make files and shell scripts
─ checking for empty or unneeded directories
Omitted ‘LazyData’ from DESCRIPTION
─ building ‘monocle3_1.3.7.tar.gz’
ERROR: dependencies ‘batchelor’, ‘sf’, ‘spdep’ are not available for package ‘monocle3’
* removing ‘/usr/local/lib64/R/library/monocle3’
Warning messages:
1: In i.p(...) : 安装程序包‘sf’时退出狀態的值不是0
2: In i.p(...) : 安装程序包‘spdep’时退出狀態的值不是0
3: In i.p(...) :
安装程序包‘/tmp/Rtmprjj0OV/file1512fe11aa1370/monocle3_1.3.7.tar.gz’时退出狀態的值不是0
BiocManager::install("batchelor")
BiocManager::install("sf")
** using staged installation
configure: CC: gcc
configure: CXX: g++ -std=gnu++17
checking for gdal-config... no
no
configure: error: gdal-config not found or not executable.
ERROR: configuration failed for package ‘sf’
* removing ‘/usr/local/lib64/R/library/sf’
安装顺序：SQLITE3, proj，gdal
参考：https://www.cnblogs.com/echohye/p/17844185.html
安装proj-8.1.0遇到问题：
checking for SQLITE3... configure: error: Package requirements (sqlite3 >= 3.11) were not met:
Package 'sqlite3', required by 'virtual:world', not found
Consider adjusting the PKG_CONFIG_PATH environment variable if you
installed software in a non-standard prefix.
Alternatively, you may set the environment variables SQLITE3_CFLAGS
and SQLITE3_LIBS to avoid the need to call pkg-config.
See the pkg-config man page for more details.
解决方法：
在环境变量文件bashrc中添加：
export SQLITE3_CFLAGS=/usr/local/include
export SQLITE3_LIBS=/usr/local/lib
source ~/.bashrc
注意自己重新安装的sqlite3在/usr/local/lib，但是/usr/lib64有系统之前安装的，此时会出现编译错误：
...
./.libs/libproj.so: undefined reference to `sqlite3_initialize'
./.libs/libproj.so: undefined reference to `sqlite3_bind_int'
注意在系统有sqlite3库时，应该yum install sqlite3-devel就行，并注意不要把自己编译的sqlite3安装到usr/local中，如有，要把lib,bin,include,share的都要移除。
安装R包添加参数的方法：
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 --with-proj-share=/usr/local/share/proj")
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 --with-proj-share=/usr/local/share --with-sqlite3-lib=/usr/lib64")
其他报错：
configure: error: geos-config not found or not executable.
解决：yum install geos-devel
参考：
https://gdal.org/development/building_from_source.html
http://download.osgeo.org/gdal/
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