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r-software [2022/05/24 07:52] – aorthr-software [2023/07/12 06:39] (current) – aorth
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 ===== Information ===== ===== Information =====
  
-  * Version: 4.2 (4.2.0)+  * Version: 4.3 (4.3.1)
   * Added: February, 2015   * Added: February, 2015
-  * Updated: May, 2022+  * Updated: July, 2023
   * Link: https://www.r-project.org/   * Link: https://www.r-project.org/
  
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 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/4.3
 $ 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:+First, compile the main R application:
  
 <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-4.3.1.tar.gz 
-$ tar xf R-4.2.0.tar.gz  +$ tar xf R-4.3.1.tar.gz 
-$ cd R-4.2.0 +$ cd R-4.3.1 
-$ ./configure --enable-R-shlib --prefix=/export/apps/R/4.2+$ sudo dnf install tcl-devel tk-devel 
 +$ ./configure --enable-R-shlib --prefix=/export/apps/R/4.3
 $ chrt -b 0 make -j4 $ chrt -b 0 make -j4
-$ sudo mkdir /export/apps/R/4.2 +$ sudo mv /export/apps/R/4.3 /export/apps/R/4.3.bak 
-$ sudo chown aorth:aorth /export/apps/R/4.2+$ sudo mkdir /export/apps/R/4.3 
 +$ sudo chown aorth:aorth /export/apps/R/4.3
 $ make install</code> $ 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: 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/4.2/bin/R+<code>$ /export/apps/R/4.3/bin/R
 # > Sys.setenv(MAKEFLAGS = "-j2") # didn't try # > Sys.setenv(MAKEFLAGS = "-j2") # didn't try
 > options(Ncpus = 4) # This does 4 parallel package installs > options(Ncpus = 4) # This does 4 parallel package installs
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 > install_github("lucidif/HiCeekR", repos=BiocManager::repositories()) > install_github("lucidif/HiCeekR", repos=BiocManager::repositories())
 > q() > q()
-$ sudo chown -R root:root /export/apps/R/4.2</code>+$ sudo chown -R root:root /export/apps/R/4.3</code>
r-software.1653378743.txt.gz · Last modified: 2022/05/24 07:52 by aorth