安装R包-infercnv和LAPACK系统库

探序基因肿瘤研究院 整理

本作者系统为centos

1. 安装JAGS

下载JAGS-4.3.0.tar.gz,

./configure

出现报错：

checking if sgemm_ is being linked in already... no

checking for ATL_xerbla in -latlas... no

checking for sgemm_ in -lblas... no

checking for sgemm_ in -lmkl... no

checking for sgemm_ in -framework vecLib... no

checking for sgemm_ in -lcxml... no

checking for sgemm_ in -ldxml... no

checking for sgemm_ in -lscs... no

checking for sgemm_ in -lcomplib.sgimath... no

checking for sgemm_ in -lblas... (cached) no

checking for sgemm_ in -lblas... (cached) no

configure: error: "You need to install the LAPACK library"

于是下载：https://www.netlib.org/lapack

安装lapack，BLAS库等方法参照：https://blog.csdn.net/weixin_41277663/article/details/131379753

将libxxx.a文件等都复制到自己的文件夹下。把这个目录配置到环境变量中，./configure仍就configure: error: "You need to install the LAPACK library"，./configure --with-blas=/xxx --with-lapack=/xxx 指定了目录，仍旧报错。将librefblas.a修改成：libblas.a才可以。

如果遇到报错：relocation R_X86_64_32 against `.rodata' can not be used when making a shared object，那么要以./configure --with-blas=/xxx --with-lapack=/xxx这种形式指定LAPACK库地址，编译时会增加-fPIC参数。

或者简单的解决方案：

在系统/usr/lib64目录中，发现：libblas.so.3.8.0，liblapack.so.3.8.0等。于是增加一个软连接，ln -s libblas.so.3.8.0 libblas.a，ln -s liblapack.so.3.8.0 liblapack.a

再./configure --with-blas=/usr/lib64 --with-lapack=/usr/lib64，make，make install，成功

2. 安装R包，rjags

Sys.setenv(LD_LIBRARY_PATH="/usr/local/lib64/JAGS/modules-4/")

Sys.setenv(LD_RUN_PATH="/usr/local/lib64/JAGS/modules-4/")

Sys.setenv(PKG_CONFIG_PATH="/usr/local/lib64/pkgconfig")install.packages("rjags",configure.args="--enable-rpath")

参考：简书-CentOS7和Rstudio server安装LAPACK library、JAGS、rjags 和 inferCNV

rjags包的源代码：

https://cran.ms.unimelb.edu.au/web/packages/rjags/index.html

3. 安装R包infercnv

if(!require("BiocManager",quietly=TRUE))

    install.packages("BiocManager")

BiocManager::install("infercnv")