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--- r-software [2015/02/19 07:01] – created aorth
+++ r-software [2023/07/11 07:22] – aorth
@@ Line 4: / Line 4: @@
 ===== Information =====
-  * Version: 3.1.2
+  * Version: 4.3 (4.3.0)
   * Added: February, 2015
-  * Link: http://www.r-project.org/
+  * Updated: May, 2023
+  * Link: https://www.r-project.org/
 ===== Usage =====
-=== See versions of R which 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:
+<code>$ module load R/4.3
+$ 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/available_software/software_list/r#6|installing R packages into user libraries]] if you need other packages.
 ===== Installation ======
-Notes from the sysadmin during installation:
+Notes from the sysadmin during installation.
+First, compile the main R application:
 <code>$ cd /tmp
-$ wget http://cran.uni-muenster.de/src/base/R-3/R-3.1.2.tar.gz
+$ wget https://cran.r-project.org/src/base/R-4/R-4.3.0.tar.gz
-$ tar xf R-3.1.2.tar.gz
+$ tar xf R-4.3.0.tar.gz
-$ cd R-3.1.2
+$ cd R-4.3.0
-$ scl enable devtoolset-2 bash
+$ ./configure --enable-R-shlib --prefix=/export/apps/R/4.3
-$ CC=clang ./configure --enable-R-shlib --prefix=/export/apps/R/3.1.2
+$ chrt -b 0 make -j4
-$ make -j4
+$ sudo mkdir /export/apps/R/4.3
-$ sudo mkdir -p /export/apps/R/3.1.2
+$ sudo chown aorth:aorth /export/apps/R/4.3
-$ sudo chown aorth:aorth /export/apps/R/3.1.2
+$ make install</code>
-$ sudo chown root:root /export/apps/R/3.1.2</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>