ILRI Research Computing

User Tools

Site Tools

You are here: start » r-software
r-software

Differences

This shows you the differences between two versions of the page.

Link to this comparison view

Both sides previous revisionPrevious revision
Next revision		Previous revision
r-software [2020/12/13 08:01] – aorthr-software [2025/05/12 12:27] (current) – aorth
Line 4: Line 4:
 ===== Information ===== ===== Information =====
  
-  * Version: 4.0 (4.0.3)+  * Version: 4.4 (4.4.3)
   * Added: February, 2015   * Added: February, 2015
-  * Updated: December, 2020+  * 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/4.0+<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-4/R-4.0.3.tar.gz +$ wget https://cran.r-project.org/src/base/R-4/R-4.4.3.tar.xz 
-$ cd R-4.0.3 +$ tar xf R-4.4.3.tar.xz 
-# install packages to enable capabilities in R +$ sudo dnf install tcl-devel tk-devel 
-$ sudo yum install libX11-devel libXaw-devel bzip2-devel libcurl-devel xz-devel readline-devel glibc-headers pcre2-devel.x86_64 +$ ./configure --enable-R-shlib --prefix=/export/apps/R/4.4 
-# install a newer compiler from Red Hat software collections +$ chrt -b 0 make -j4 
-$ sudo yum install devtoolset-7-gcc devtoolset-7-gcc-gfortran devtoolset-7-libquadmath-devel devtoolset-7-gcc-c++ +$ sudo mkdir /export/apps/R/4.4 
-$ scl enable devtoolset-7 bash +$ sudo chown aorth /export/apps/R/4.4 
-# R packages are written in C99 and GCC 7 uses a newer standard by default, so tell configure script to use C99 explicitly +$ make install 
-$ export CFLAGS='-std=gnu99 -g -O2' +$ sudo chown -R root:root /export/apps/R/4.4</code>
-$ ./configure --enable-R-shlib --prefix=/export/apps/R/4.0 +
-$ make -j4 +
-$ sudo mkdir -p /export/apps/R/4.0 +
-$ sudo chown aorth:aorth /export/apps/R/4.0 +
-$ 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/apps/R/4.0/bin/R +
-> 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("hierfstat", repos="https://cran.r-project.org") +
-> install.packages("adegenet", repos="https://cran.r-project.org") +
-> install.packages("BiocManager", repos="https://cran.r-project.org") +
-> install.packages("poppr", repos="https://cran.r-project.org") +
-> install.packages("vcfR", repos="https://cran.r-project.org") +
-> q() +
-$ sudo chown -R root:root /export/apps/R/4.0</code>+
r-software.1607846494.txt.gz · Last modified: by aorth