Differences

This shows you the differences between two versions of the page.

--- r-software [2017/04/24 09:22] – aorth
+++ r-software [2019/10/27 13:45] – aorth
@@ Line 4: / Line 4: @@
 ===== Information =====
-  * Latest version: 3.3.3
+  * Version: 3.6 (3.6.1)
   * Added: February, 2015
-  * Updated: April, 2017
+  * Updated: October, 2019
-  * Link: http://www.r-project.org/
+  * 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>
-===== Installation ======
+Load one version into your environment and run it:
-Notes from the sysadmin during installation (also covers the installation of zlib, bzip2, xz, pcre, and curl, as they are needed by R since ~3.3.x):
+<code>$ module load R/3.6
+$ R</code>
-<code>$ cd /tmp
+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]].
-$ wget http://zlib.net/zlib-1.2.11.tar.xz
-$ tar xf zlib-1.2.11.tar.xz
-$ cd zlib-1.2.11
-$ ./configure --prefix=/export/apps/zlib/1.2.11
-$ make
-$ make check
-$ sudo mkdir -p /export/apps/zlib/1.2.11
-$ sudo chown aorth /export/apps/zlib/1.2.11
-$ make install
-$ sudo chown -R root:root /export/apps/zlib/1.2.11
-$ cd /tmp
+===== Installation ======
-$ wget http://www.bzip.org/1.0.6/bzip2-1.0.6.tar.gz
+Notes from the sysadmin during installation.
-$ tar xf bzip2-1.0.6.tar.gz
-$ cd bzip2-1.0.6
-$ make -f Makefile-libbz2_so
-$ sudo mkdir -p /export/apps/bzip2/1.0.6
-$ sudo chown aorth /export/apps/bzip2/1.0.6
-$ make install PREFIX=/export/apps/bzip2/1.0.6
-$ sudo chown -R root:root /export/apps/bzip2/1.0.6
-$ cd /tmp
+First, compile the main R application with GCC 7 from Red Hat's ''devtoolset-7'' software collection:
-$ wget https://tukaani.org/xz/xz-5.2.3.tar.xz
-$ tar xf xz-5.2.3.tar.xz
-$ cd xz-5.2.3
-$ ./configure --prefix=/export/apps/xz/5.2.3
-$ make
-$ make check
-$ sudo mkdir -p /export/apps/xz/5.2.3
-$ sudo chown aorth /export/apps/xz/5.2.3
-$ make install
-$ sudo chown -R root:root /export/apps/xz/5.2.3
-$ cd /tmp
+<code>$ cd /tmp
-$ wget http://downloads.sourceforge.net/pcre/pcre-8.40.tar.bz2
+$ wget https://cran.r-project.org/src/base/R-3/R-3.6.1.tar.gz
-$ tar xf pcre-8.40.tar.bz2
+$ tar xf R-3.6.1.tar.gz
-$ cd pcre-8.40
+$ cd R-3.6.1
-$ ./configure --prefix=/export/apps/pcre/8.40 --enable-unicode-properties --enable-pcre16 --enable-pcre32 --enable-pcregrep-libz --enable-pcregrep-libbz2 --enable-pcretest-libreadline
+# install packages to enable capabilities in R
-$ make
+$ sudo yum install libX11-devel libXaw-devel bzip2-devel libcurl-devel xz-devel readline-devel
-$ make check
+# install a newer compiler from Red Hat software collections
-$ sudo mkdir -p /export/apps/pcre/8.40
+$ sudo yum install devtoolset-7-gcc devtoolset-7-gcc-gfortran devtoolset-7-libquadmath-devel devtoolset-7-gcc-c++
-$ sudo chown aorth /export/apps/pcre/8.40
+$ scl enable devtoolset-7 bash
-$ make install
+# R packages are written in C99 and GCC 7 uses a newer standard by default, so tell configure script to use C99 explicitly
-$ sudo chown -R root:root /export/apps/pcre/8.40
+$ export CFLAGS='-std=gnu99  -g -O2'
+$ ./configure --enable-R-shlib --prefix=/export/apps/R/3.6
+$ make -j4
+$ sudo mkdir -p /export/apps/R/3.6
+$ sudo chown aorth:aorth /export/apps/R/3.6
+$ make install</code>
-$ cd /tmp
+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):
-$ tar xf curl-7.54.0.tar.gz
-$ cd curl-7.54.0
-$ ./configure --enable-ipv6 --prefix=/export/apps/curl/7.54.0
-$ make
-$ make check
-$ sudo mkdir -p /export/apps/curl/7.54.0
-$ sudo chown aorth /export/apps/curl/7.54.0
-$ make install
-$ sudo chown -R root:root /export/apps/curl/7.54.0
-$ export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/export/apps/zlib/1.2.11/lib:/export/apps/bzip2/1.0.6/lib:/export/apps/xz/5.2.3/lib:/export/apps/pcre/8.40/lib:/export/apps/curl/7.54.0/lib LDFLAGS="$LDFLAGS -L/export/apps/zlib/1.2.11/lib -L/export/apps/bzip2/1.0.6/lib -L/export/apps/xz/5.2.3/lib -L/export/apps/pcre/8.40/lib -L/export/apps/curl/7.54.0/lib" CFLAGS="$CFLAGS -I/export/apps/zlib/1.2.11/include -I/export/apps/bzip2/1.0.6/include -I/export/apps/xz/5.2.3/include -I/export/apps/pcre/8.40/include -I/export/apps/curl/7.54.0/include"
-$ wget https://cran.r-project.org/src/base/R-3/R-3.3.3.tar.gz
-$ tar xf R-3.3.3.tar.gz
-$ cd R-3.3.3
-$ ./configure --enable-R-shlib --prefix=/export/apps/R/3.3.3
-$ make -j4
-$ make install
-$ sudo mkdir -p /export/apps/R/3.3.3
-$ sudo chown aorth /export/apps/R/3.3.3
-$ sudo chown -R root:root /export/apps/R/3.3.3
-$ exit</code>