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r-software [2018/11/04 16:06] aorthr-software [2023/07/12 06:39] (current) aorth
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 ===== Information ===== ===== Information =====
  
-  * Version: 3.5.1+  * Version: 4.(4.3.1)
   * Added: February, 2015   * Added: February, 2015
-  * Updated: July, 2018+  * Updated: July, 2023
   * 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/3.5.1+<code>$ module load R/4.3
 $ R</code> $ R</code>
  
-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]].+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.
  
-<code>$ wget http://cran.mirror.ac.za/src/base/R-3/R-3.5.1.tar.gz +First, compile the main R application: 
-$ tar xf R-3.5.1.tar.gz + 
-$ cd R-3.5.1 +<code>$ cd /tmp 
-$ sudo yum install gcc-gfortran gcc-c++ libX11-devel libXaw-devel bzip2-devel libcurl-devel xz-devel readline-devel +$ wget https://cran.r-project.org/src/base/R-4/R-4.3.1.tar.gz 
-$ ./configure --enable-R-shlib --prefix=/export/apps/R/3.5.1 +$ tar xf R-4.3.1.tar.gz 
-$ make -j4 +$ cd R-4.3.1 
-$ sudo mkdir -p /export/apps/R/3.5.1 +$ sudo dnf install tcl-devel tk-devel 
-$ sudo chown aorth:aorth /export/apps/R/3.5.1 +$ ./configure --enable-R-shlib --prefix=/export/apps/R/4.
-$ make install +chrt -b 0 make -j4 
-$ sudo chown -R root:root /export/apps/R/3.5.1</code>+$ sudo mv /export/apps/R/4./export/apps/R/4.3.bak 
 +$ sudo mkdir /export/apps/R/4.3 
 +$ sudo chown aorth:aorth /export/apps/R/4.3 
 +$ 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/4.3/bin/
 +# > 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/4.3</code>
r-software.1541347601.txt.gz · Last modified: 2018/11/04 16:06 by aorth