R安装包 | Giftbear Notes

R version: 4.2.1

Seurat

install.packages("Seurat")

rgeos包依赖geos-config:

下载geos: http://download.osgeo.org/geos/geos-3.9.3.tar.bz2

安装geos:

tar jxf geos-3.9.3.tar.bz2
cd geos-3.9.3
./configure --prefix=/opt/software/geos
make
make install
vim ~/.bashrc
export PATH=$PATH:/opt/software/geos/bin
source ~/.bashrc
cp /opt/software/geos/lib/libgeos_c.so.1.14.3 /opt/software/R/lib64/R/lib/libgeos_c.so.1

SingleR

BiocManager::install("SingleR")

BiocManager版本3.16安装SingleR要求C++17:
1. 下载C++11编译的SingleR包: http://bioconductor.org/packages/3.15/bioc/html/SingleR.html
2. 安装SingleR: install.packages("SingleR_1.10.0.tar.gz", repos = NULL)

hdf5r

install.packages("hdf5r")

依赖hdf5:

下载hdf5: https://portal.hdfgroup.org/display/support/HDF5+1.14.1#files

安装hdf5:

tar xzf hdf5-1.14.1-2.tar.gz
cd hdf5-1.14.1-2
./configure --prefix=/opt/software/hdf5
make
make install
vim ~/.bashrc
export PATH=$PATH:/opt/software/hdf5/bin
source ~/.bashrc
# 找不到共享库的问题
vim /etc/ld.so.conf
/opt/software/hdf5/lib
ldconfig

infercnv

BiocManager::install("infercnv")

rjags包依赖jags:

下载jags: https://sourceforge.net/projects/mcmc-jags/files/JAGS/4.x/Source/
安装lapack: yum install lapack lapack-devel

安装jags:

tar xzf JAGS-4.3.2.tar.gz
cd JAGS-4.3.2
./configure --prefix=/opt/software/jags
make
make install
vim ~/.bashrc
export PATH=$PATH:/opt/software/jags/bin
source ~/.bashrc
# 找不到/opt/software/jags/lib64/JAGS/modules-4/basemod.so
cp -R lib lib64

RcppParallel包安装出错: 下载低版本的包安装: install.packages("RcppParallel_4.4.3.tar.gz", repos = NULL)

SPATA2

yum install fftw-devel
yum install proj-devel proj-epsg proj-nad
yum install udunits2-devel
yum install ImageMagick-c++-devel

install.packages("devtools")
if (!base::requireNamespace("BiocManager", quietly = TRUE)){
    install.packages("BiocManager")
}
BiocManager::install(c('BiocGenerics', 'DelayedArray', 'DelayedMatrixStats',
                       'limma', 'S4Vectors', 'SingleCellExperiment',
                       'SummarizedExperiment', 'batchelor', 'Matrix.utils', 'EBImage'))
devtools::install_github(repo = "kueckelj/confuns")
devtools::install_github(repo = "theMILOlab/SPATAData")
devtools::install_github(repo = "theMILOlab/SPATA2")
devtools::install_github('cole-trapnell-lab/monocle3')

*安装参考资料: https://themilolab.github.io/SPATA2/articles/spata-v2-installation.html

依赖gdal-config:

下载gdal: https://gdal.org/download.html

安装gdal:

tar xzf gdal-2.4.4.tar.gz
cd gdal-2.4.4
./configure --prefix=/opt/software/gdal
make
make install
vim ~/.bashrc
export PATH=$PATH:/opt/software/gdal/bin
source ~/.bashrc
ln -s /opt/software/gdal/lib/libgdal.so.20.5.4 /usr/local/lib64/libgdal.so.20

gdal 3.5.0版本依赖proj6:
1. 下载: https://proj.org/en/9.2/download.html
2. proj6依赖sqlite3: 下载sqlite3 (https://sqlite.org/download.html)
3. 安装: ./configure --prefix=/home/software/gdal --with-proj=/home/software/proj6
  a. 编译出现undefined reference to sqlite3_column_origin_name和undefined reference to sqlite3_column_table_name:
  vim sqlite3.c
  添加 #define SQLITE_ENABLE_COLUMN_METADATA 1
  重新编译sqlite3

Monocle3

BiocManager::install(c('BiocGenerics', 'DelayedArray', 'DelayedMatrixStats',
                       'limma', 'lme4', 'S4Vectors', 'SingleCellExperiment',
                       'SummarizedExperiment', 'batchelor', 'HDF5Array',
                       'terra', 'ggrastr'))
install.packages("devtools")
devtools::install_github('cole-trapnell-lab/monocle3')

安装依赖包terra出现proj_api.h not found in standard or given locations:
将proj的include和lib中的文件复制到/usr/local/include和lib下

R安装包问题及解决方案总结

缺乏依赖: 报错信息中会给出类似找不到某个依赖 -> 根据缺少的东西通过yum/apt安装或下载包编译安装
找不到库: 报错信息中会给出相关库找不到的信息 -> 主要是提供寻找库的路径 (一般将编译好的包的bin和lib目录都添加到环境变量)
- GLIBC版本的问题: 查看版本: strings /lib64/libc.so.6 |grep GLIBC_; 下载地址: https://ftp.gnu.org/gnu/glibc/
编译过程中的代码错误: 一般是版本问题 -> 更换低版本安装

添加动态库.so文件到环境变量

当前用户当前终端: export LD_LIBRARY_PATH= (删除变量: unset LD_LIBRARY_PATH)

当前用户环境变量:

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vim ~/.bashrc
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:
source ~/.bashrc

所有用户环境变量:

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vim /etc/profile
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:
source /etc/profile

复制so文件到lib目录: sudo cp .so /usr/lib

ldconfig寻找路径:

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vim /etc/ld.so.conf
/opt/software/hdf5/lib
sudo ldconfig