Differences

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--- r-software [2015/02/19 07:01] – created aorth
+++ r-software [2019/10/27 14:02] – aorth
@@ Line 4: / Line 4: @@
 ===== Information =====
-  * Version: 3.1.2
+  * Version: 3.6 (3.6.1)
   * Added: February, 2015
-  * Link: http://www.r-project.org/
+  * Updated: October, 2019
+  * Link: https://www.r-project.org/
 ===== Usage =====
-=== See versions of R which are available ===
+See versions of R that 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/3.6
+$ 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.
 ===== 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
-$ 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-3/R-3.6.1.tar.gz
-$ tar xf R-3.1.2.tar.gz
+$ tar xf R-3.6.1.tar.gz
-$ cd R-3.1.2
+$ cd R-3.6.1
-$ scl enable devtoolset-2 bash
+# install packages to enable capabilities in R
-$ CC=clang ./configure --enable-R-shlib --prefix=/export/apps/R/3.1.2
+$ sudo yum install libX11-devel libXaw-devel bzip2-devel libcurl-devel xz-devel readline-devel
+# install a newer compiler from Red Hat software collections
+$ sudo yum install devtoolset-7-gcc devtoolset-7-gcc-gfortran devtoolset-7-libquadmath-devel devtoolset-7-gcc-c++
+$ scl enable devtoolset-7 bash
+# R packages are written in C99 and GCC 7 uses a newer standard by default, so tell configure script to use C99 explicitly
+$ export CFLAGS='-std=gnu99  -g -O2'
+$ ./configure --enable-R-shlib --prefix=/export/apps/R/3.6
 $ make -j4
-$ sudo mkdir -p /export/apps/R/3.1.2
+$ sudo mkdir -p /export/apps/R/3.6
-$ sudo chown aorth:aorth /export/apps/R/3.1.2
+$ sudo chown aorth:aorth /export/apps/R/3.6
-$ sudo chown root:root /export/apps/R/3.1.2</code>
+$ make install</code>
+Then install some common libraries used by our users (to save space, overhead from tens of thousands of header and library files, and users's time):