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r-software [2020/05/12 18:20] – aorthr-software [2025/05/12 12:27] (current) – aorth
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 ===== Information ===== ===== Information =====
  
-  * Version: 3.6 (3.6.1)+  * Version: 4.4 (4.4.3)
   * Added: February, 2015   * Added: February, 2015
-  * Updated: October, 2019+  * Updated: May, 2025
   * Link: https://www.r-project.org/   * Link: https://www.r-project.org/
  
 ===== Usage ===== ===== Usage =====
  
-See versions of R that are available:+See which versions are available:
 <code>$ module avail R</code> <code>$ module avail R</code>
  
 Load one version into your environment and run it: Load one version into your environment and run it:
-<code>$ module load R/3.6+<code>$ module load R/4.4
 $ R</code> $ R</code>
  
-Use ''installed.packages()'' to check the list of packages installed in the ILRI environment by default. Here is a good resource on [[https://www.osc.edu/resources/getting_started/howto/howto_install_local_r_packages|installing R packages into user libraries]] if you need other packages.+Use ''installed.packages()'' to check the list of packages installed in the ILRI environment by default. Here is a good resource on [[https://www.osc.edu/resources/available_software/software_list/r#6|installing R packages into user libraries]] if you need other packages.
  
 ===== Installation ====== ===== Installation ======
 Notes from the sysadmin during installation. Notes from the sysadmin during installation.
- 
-First, compile the main R application with GCC 7 from Red Hat's ''devtoolset-7'' software collection: 
  
 <code>$ cd /tmp <code>$ cd /tmp
-$ wget https://cran.r-project.org/src/base/R-3/R-3.6.1.tar.gz +$ wget https://cran.r-project.org/src/base/R-4/R-4.4.3.tar.xz 
-$ tar xf R-3.6.1.tar.gz +$ tar xf R-4.4.3.tar.xz 
-$ cd R-3.6.1 +$ sudo dnf install tcl-devel tk-devel 
-# install packages to enable capabilities in R +$ ./configure --enable-R-shlib --prefix=/export/apps/R/4.4 
-$ sudo yum install libX11-devel libXaw-devel bzip2-devel libcurl-devel xz-devel readline-devel glibc-headers +$ chrt -b 0 make -j4 
-# install a newer compiler from Red Hat software collections +$ sudo mkdir /export/apps/R/4.4 
-$ sudo yum install devtoolset-7-gcc devtoolset-7-gcc-gfortran devtoolset-7-libquadmath-devel devtoolset-7-gcc-c++ +$ sudo chown aorth /export/apps/R/4.4 
-$ scl enable devtoolset-7 bash +$ make install 
-# R packages are written in C99 and GCC 7 uses a newer standard by default, so tell configure script to use C99 explicitly +$ sudo chown -R root:root /export/apps/R/4.4</code>
-$ export CFLAGS='-std=gnu99  -g -O2' +
-$ ./configure --enable-R-shlib --prefix=/export/apps/R/3.6 +
-$ make -j4 +
-$ sudo mkdir -p /export/apps/R/3.6 +
-$ sudo chown aorth:aorth /export/apps/R/3.6 +
-$ make install</code> +
- +
-Then install some common libraries used by our users because some of them are quite complicated, and installing them globally saves tens of thousands of header files and libraries being installed into user libraries anyways: +
- +
-<code>$ export LD_LIBRARY_PATH=/export/apps/gdal/2.4.2/lib +
-$ R +
-> install.packages("BiocManager", repos="https://cran.r-project.org") +
-> install.packages("sf", repo="https://cloud.r-project.org", configure.args=c(sf = "--with-gdal-config=/export/apps/gdal/2.4.2/bin/gdal-config")) +
-> install.packages("poppr", repos="https://cran.r-project.org") +
-> install.packages("vcfR", repos="https://cran.r-project.org")</code>+
r-software.1589307649.txt.gz · Last modified: by aorth