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 [2022/05/24 07:52] – aorthr-software [2026/03/12 06:38] (current) – aorth
Line 4: Line 4:
 ===== Information ===== ===== Information =====
  
-  * Version: 4.2 (4.2.0)+  * Version: 4.5 (4.5.2)
   * Added: February, 2015   * Added: February, 2015
-  * Updated: May, 2022+  * Updated: March, 2026
   * Link: https://www.r-project.org/   * Link: https://www.r-project.org/
  
Line 15: Line 15:
  
 Load one version into your environment and run it: Load one version into your environment and run it:
-<code>$ module load R/4.2+<code>$ module load R/4.5
 $ 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-4.2.0.tar.gz +$ wget https://cran.r-project.org/src/base/R-4/R-4.5.2.tar.xz 
-$ tar xf R-4.2.0.tar.gz  +$ tar xf R-4.5.2.tar.xz 
-$ cd R-4.2.0 +$ cd R-4.5.2 
-$ ./configure --enable-R-shlib --prefix=/export/apps/R/4.2 +$ sudo dnf install tcl-devel tk-devel 
-$ chrt -b 0 make -j4 +$ ./configure --enable-R-shlib --prefix=/export/apps/R/4.5 
-$ sudo mkdir /export/apps/R/4.2 +$ nice make -j4 
-$ sudo chown aorth:aorth /export/apps/R/4.2 +$ sudo mkdir /export/apps/R/4.5 
-$ make install</code> +$ sudo chown aorth /export/apps/R/4.5 
- +$ make install 
-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: +$ sudo chown -R root:root /export/apps/R/4.5</code>
- +
-<code>$ /export/apps/R/4.2/bin/R +
-# > Sys.setenv(MAKEFLAGS = "-j2") # didn't try +
-> options(Ncpus = 4) # This does 4 parallel package installs +
-> install.packages('sf', repo='https://cloud.r-project.org') +
-> 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") +
-> install.packages("devtools", repos="https://cran.r-project.org") +
-> library(devtools) +
-> install_github("HenrikBengtsson/TopDom") +
-> install_github("lucidif/HiCeekR", repos=BiocManager::repositories()) +
-> q() +
-$ sudo chown -R root:root /export/apps/R/4.2</code>+
r-software.1653378743.txt.gz · Last modified: by aorth