centos操作系统安装R包单细胞拟时序分析CytoTRACE2

探序基因肿瘤研究院  整理

作者操作系统为centos stream8，R版本为4.3.3

devtools::install_github("digitalcytometry/cytotrace2", subdir = "cytotrace2_r")

中途出现错误：

* installing *source* package ‘RcppGSL’ ...
** 成功将‘RcppGSL’程序包解包并MD5和检查
** using staged installation
checking for gsl-config... no
configure: error: gsl-config not found, is GSL installed?
ERROR: configuration failed for package ‘RcppGSL’
* removing ‘/usr/local/lib64/R/library/RcppGSL’
* installing *source* package ‘ncdf4’ ...
** 成功将‘ncdf4’程序包解包并MD5和检查
** using staged installation
configure.ac: starting
checking for nc-config... no
-----------------------------------------------------------------------------------
Error, nc-config not found or not executable.  This is a script that comes with the
netcdf library, version 4.1-beta2 or later, and must be present for configuration
to succeed.
 
If you installed the netcdf library (and nc-config) in a standard location, nc-config
should be found automatically.  Otherwise, you can specify the full path and name of
the nc-config script by passing the --with-nc-config=/full/path/nc-config argument
flag to the configure script.  For example:
 
./configure --with-nc-config=/sw/dist/netcdf4/bin/nc-config
 
Special note for R users:
-------------------------
To pass the configure flag to R, use something like this:
 
R CMD INSTALL --configure-args="--with-nc-config=/home/joe/bin/nc-config" ncdf4
 
where you should replace /home/joe/bin etc. with the location where you have
installed the nc-config script that came with the netcdf 4 distribution.
-----------------------------------------------------------------------------------
ERROR: configuration failed for package ‘ncdf4’
* removing ‘/usr/local/lib64/R/library/ncdf4’
ERROR: dependency ‘RcppGSL’ is not available for package ‘RcppZiggurat’
* removing ‘/usr/local/lib64/R/library/RcppZiggurat’
ERROR: dependency ‘ncdf4’ is not available for package ‘HiClimR’
* removing ‘/usr/local/lib64/R/library/HiClimR’
ERROR: dependency ‘RcppZiggurat’ is not available for package ‘Rfast’
* removing ‘/usr/local/lib64/R/library/Rfast’

于是先安装hdf5:

下载地址：https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.10/hdf5-1.10.5/src/hdf5-1.10.5.tar.gz

解压缩后，./configure--prefix=/usr/local/hdf5,make,make install

配置环境变量：

export HDF5_DIR=/usr/local/hdf5
export LD_LIBRARY_PATH=/usr/local/hdf5/lib:$LD_LIBRARY_PATH
export LIBRARY_PATH=/usr/local/hdf5/lib:$LIBRARY_PATH
export C_INCLUDE_PATH=/usr/local/hdf5/include:$C_INCLUDE_PATH
export CPLUS_INCLUDE_PATH=/usr/local/hdf5/include:$CPLUS_INCLUDE_PATH
export PATH=/usr/local/hdf5/bin:$PATH

再安装netCDF，下载地址：netCDF Downloads

./configure, make, make install

安装gsl：

yum install gsl, yum install gsl-devel

安装R包：RcppGSL：

install.packages("RcppGSL")

安装R包ncdf4：

install.packages("ncdf4")

接着：install.packages("RcppZiggurat"),install.packages("HiClimR"),install.packages("Rfast")

最后：

devtools::install_github("digitalcytometry/cytotrace2", subdir = "cytotrace2_r")

参考：

单细胞拟时序分析之CytoTRACE2：解决找不到分化起点的烦恼 - 企业动态 - 丁香通