Installing the R Language

Procedure

1. Use PuTTY to log in to the server as the root user.
2. Go to the /path/to/CNVFILTER directory.

   cd /path/to/CNVFILTER

3. Download the R language source package.

   wget https://cran.r-project.org/src/base/R-4/R-4.2.0.tar.gz

4. Decompress the source package.

   tar xvf R-4.2.0.tar.gz

5. Go to the directory generated after the decompression.

   cd R-4.2.0

6. Perform the compilation and installation.

   yum install libXt-devel libX11-devel readline-devel
   ./configure --prefix=/path/to/CNVFILTER/R_install
   make
   make install

7. Load the environment variables.

   export PATH=/path/to/CNVFILTER/R_install/bin:$PATH
   export LB_LIBRARY_PATH=/path/to/CNVFILTER/R_install/lib/R/lib:$ LB_LIBRARY_PATH

8. (Optional) If the network speed is slow, run the following command to add an image source of the R language.
   1. Create an ~/.Rprofile file.

      vi ~/.Rprofile

   2. Press i to enter the insert mode and add the following content:

      options("repos"= c(CRAN="http://mirrors.tuna.tsinghua.edu.cn/CRAN/"))
      options(BioC_mirror="http://mirrors.tuna.tsinghua.edu.cn/bioconductor/")

   3. Press Esc, type :wq!, and press Enter to save the file and exit.