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r-software [2023/07/12 06:39] – aorthr-software [2025/05/12 12:27] (current) – aorth
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 ===== Information ===== ===== Information =====
  
-  * Version: 4.3 (4.3.1)+  * Version: 4.4 (4.4.3)
   * Added: February, 2015   * Added: February, 2015
-  * Updated: July, 2023+  * Updated: May, 2025
   * 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/4.3+<code>$ module load R/4.4
 $ R</code> $ R</code>
  
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 ===== Installation ====== ===== Installation ======
 Notes from the sysadmin during installation. Notes from the sysadmin during installation.
- 
-First, compile the main R application: 
  
 <code>$ cd /tmp <code>$ cd /tmp
-$ wget https://cran.r-project.org/src/base/R-4/R-4.3.1.tar.gz +$ wget https://cran.r-project.org/src/base/R-4/R-4.4.3.tar.xz 
-$ tar xf R-4.3.1.tar.gz +$ tar xf R-4.4.3.tar.xz
-$ cd R-4.3.1+
 $ sudo dnf install tcl-devel tk-devel $ sudo dnf install tcl-devel tk-devel
-$ ./configure --enable-R-shlib --prefix=/export/apps/R/4.3+$ ./configure --enable-R-shlib --prefix=/export/apps/R/4.4
 $ chrt -b 0 make -j4 $ chrt -b 0 make -j4
-$ sudo mv /export/apps/R/4.3 /export/apps/R/4.3.bak +$ sudo mkdir /export/apps/R/4.4 
-$ sudo mkdir /export/apps/R/4.3 +$ sudo chown aorth /export/apps/R/4.4 
-$ sudo chown aorth:aorth /export/apps/R/4.3 +$ make install 
-$ make install</code> +$ sudo chown -R root:root /export/apps/R/4.4</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/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/4.3</code>+
r-software.txt · Last modified: by aorth