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")
